Volcani
Center / Institute
of Animal Science
ShiftDetector Example Data Set:
Query: examplE1.abi Prediction Length 824 (1 .. 824)
Sbjct: intron5 cattle GATA4 Length 1292 (1 .. 1292)
Score = 531 bits (276), Expect = e-150
Identities = 356/396 (89%)
Strand = Plus / Plus
Query: 3 acgacttattgacaaaatggcaacaactctgccaaggccagtgaagacgggcgggcacac
62
|||||||| |||| |||||||||||||| ||||||||||||||||||||||| |||||||
Sbjct: 324 acgacttagtgactaaatggcaacaactgtgccaaggccagtgaagacgggctggcacac
383
Query: 63 agcatgactgcaacctgaatcagactgtgggcgtgctcgggggcgtggcgaacccatcgc
122
|||||||||||||||||||||||||||||||| ||| |||| |||||||||||||||||
Sbjct: 384 agcatgactgcaacctgaatcagactgtgggctcgctgggggacgtggcgaacccatcgc
443
Query: 123 aggccttgggagagagaacggggcttactgagaaagtctgtctcctcaataaggctcgct
182
|||||||||||| |||||||||||| ||||| ||||||||||||||||| ||| | |||
Sbjct: 444 aggccttgggaggcagaacggggctttctgagcaagtctgtctcctcaatgagggtggct
503
Query: 183 tgatcttggcggcagagatttttcaacaggaggatgaggtcctccctcgcctgtgggagc
242
||||||||||||||| | ||||||||||||||||||||||| ||| |||||||| |||
Sbjct: 504 tgatcttggcggcaggtagatttcaacaggaggatgaggtccttcctggcctgtggaagc
563
Query: 243 tgcaaaacgcagggtgggaggcgtgtgggtgatgaggggtcacagggaggatgctattgt
302
|||| | |||||||||||||| || || |||||| |||||||||| |||||||||||||
Sbjct: 564 tgcagcaggcagggtgggaggcttggggttgatgaagggtcacaggcaggatgctattgt
623
Query: 303 aatgagagcgggctgcaggtcccgcttcacacgtgtccagtgatgggcgagcgggacccc
362
||||||||| |||||||||||| ||||||||||||||||| ||||||| ||||||||||
Sbjct: 624 aatgagagctggctgcaggtccagcttcacacgtgtccagagatgggccagcgggaccct
683
Query: 363 cctctccctctctcagatatgagggcaaccccgctc 398
||| ||| ||| |||||||||| |||||||| ||||
Sbjct: 684 cctgtccttctgtcagatatgatggcaaccctgctc 719
_________________________________________________________________________________________
example2.abi:
Shift of 1 nucleotides was detected (Expect 1.53e-05)View results
Shift starts at base 82 : probability score 2.44e-04
The predicted sequence of the molecule following
the shift is:
>example2.abi Prediction VHL
TGGGAATTAA AGGAGACTGG ACATCGTCAA GTCGCTTTAC GAAGATTTGG
AAGACCCCCC
CAATTTGCAG AAAGACCTGG GGGGGCTGAC AAAGGGGGGC ATGGCAAATC
AACCGATGGG
GGATGGAAGA TGTTTTGTGA AACTTAAACT TGGT
Query: Query= example2.abi Prediction VHL (154 letters)
Sbjct:
>gi|14726189|ref|XM_052341.1| Homo sapiens von Hippel-Lindau
syndrome (VHL), mRNA
Length = 1809
Score = 69.9 bits (35), Expect = 7e-12
Identities = 47/51 (92%)
Strand = Plus / Plus
Query: 4 gaattaaaggagactggacatcgtcaagtcgctttacgaagatttggaaga
54
|||||| ||||||||||||||||||| |||||| ||||||||| |||||||
Sbjct: 732 gaattacaggagactggacatcgtcaggtcgctctacgaagatctggaaga
782
_________________________________________________________________________________________
example3.abi
Shift of 1 nucleotides was detected (Expect 1.53e-05)View results
Shift starts at base 163 : probability score 3.91e-03
The predicted sequence of the molecule following
the shift is:
>example3.abi Prediction MEN1
GCTTGGGNNC NGNCCNGGTG NCNGTGTNGG GNCGGCCCNG AAGCCCCCTG
GGACTGTCGC
TGGCCCAGCC GGGGGGCCTG AAGGTGGCAA CCCGGCCCAG GTGCCAGCCC
GCCCAGCATN
ACCCCCCGCG GGGGGTCCAG TGGTCCNTGG NAAGG
Query: example3.abi Prediction MEN1 (155 letters)
Sbjct:
>gi|14783407|ref|XM_045620.1| Homo sapiens multiple
endocrine neoplasia I (MEN1), mRNA
Length = 2606
Score = 81.8 bits (41), Expect = 2e-15
Identities = 90/107 (84%)
Strand = Plus / Plus
Query: 36 cccngaagccccctgggactgtcgctggcccagccggggggcctgaaggtggcaacccgg
95
||| |||||| |||||||||||||||||| ||||| | || ||||||||||||| | |||
Sbjct: 1507 cccggaagcctcctgggactgtcgctggcacagcccgaggccctgaaggtggcagcacgg
1566
Query: 96 cccaggtgccagcccgcccagcatnaccccccgcggggggtccagtg
142
| ||||||||||| | | |||||| ||| || ||| ||||||||||
Sbjct: 1567 ctcaggtgccagcacccgcagcatcaccaccgccggagggtccagtg
1613
_________________________________________________________________________________________
example4.abi
Shift of 1 nucleotides was detected (Expect 9.54e-07)View results
Shift starts at base 123 : probability score 3.91e-03
The predicted sequence of the molecule following
the shift is:
>examplE4.abi Prediction SHOX
GGCTGCCCAT CCCGTCCCTT GCCGGGTCCG NCCCGGTCGT CGNCGGTGTN
GTCGNCGNCT
TTTTTTGCAN CTNNAAAGAT TCCAGCATCG TCGACCTGGT GCCTAAGGCC
CGTTAGCCCG
GGTAGGCCCT TTTTTCTTGA CCNGNNATGA ATTTTTTNAN CCCCCCGTTN
CTTTGGTCCT
TGGTNAAACT GNTTTNNTNG GGCGTTCTTT TTNATNANTT CAAATTTAAT
NGTTNCTTTT
TGNCNNNTGG TTGTTTTTNN TGATTTANNN NTATCNNNCN ATGGTTAATT
AGTAAATTNN
AANNGTTTTT ATGAAATTNG NNTNAAANCT NCNAANNAAN GTNNNGGTTG
NTTGGGTNNT
TTNAATTNAA AGNAANCNNT CNTTANTNAA CCGTANTTTN ATTTNAATTA
AAATTGCNTT
TGAANTTNGG AATNGGGNNA TNAAAGGGAT TTTNCNNTAA ANTAAAAACT
NCCATTTTTT
GTNNTTTCNN CCNNNNGTAA NNAATTTTTN AGNCTGNNNN NNNCCNNNTT
NNNNGGTTTT
CAGGNNNANC TANTTAANTT TTCNTAANTA ATTGNNNTTT GTCNANNNNA
NTTAAATCTG
TNNANNATTT TTNGNAANTN NNCTTATGNA AANTAATNAT GNANTGAACN
GNNNNTAAAN
NAANCTTTTC ANNNTNNAAA CTTNNTNGTT GNTGTNNNNN GTTNATNNNC
ATGNNGAANT
NGNNNAANTN NCCCCNNATC CNTTNNTNNG TTTANNANCA TGNTTNGTNA
TNNNCNNGTN
NNNNNANNNT NNNCNGTNNT TNNTNNTNAA NNTNNNGNAN NNATNNNNGG
NATTNGTANN
CNNNGGNNCN NGNNCCTTTT TTANNAGNNN GGGNNATGNC ANTGGTNANT
NCTGGGGGGT
TNNGNNNNGA CNTNNNNNNT CNTNNNGNNT NNGG
Query: examplE4.abi Prediction SHOX Length 934 (1
.. 934)
Sbjct: gi 2276452 (U82668 SHOX gene)Length 85132
(1 .. 85132)
Score = 54.5 bits (28), Expect = 2e-06
Identities = 91/130 (70%)
Strand = Plus / Plus
Query: 1 ggctgcccatcccgtcccttgccgggtccgncccggtcgtcgncggtgtngtcgncgncn
60
||||||||||| |||| || |||| ||||| | ||| || || || || | || || |
Sbjct: 56996 ggctgcccatcgcgtcgctggccgagtccgcctcggccgccgccgtggtcgccgccgccg
57055
Query: 61 nnnnnngcanctnnaaagattccagcatcgtcgacctggtgcctaaggcccgttagcccg
120
||| | || |||||||||||| ||||||| || ||||| ||
||| ||
Sbjct: 57056 ccaaaagcaacagcaagaattccagcatcgccgacctgcggctcaaggcgcggaagcacg
57115
Query: 121 ggtaggccct 130
| |||||||
Sbjct: 57116 cggaggccct 57125
_________________________________________________________________________________________
example5.abi
Shift of 3 nucleotides was detected (Expect 9.54e-07)View results
Shift starts at base 211 : probability score 1.53e-05
The predicted sequence of the molecule following
the shift is:
>examplE5.abi Prediction MEN1
CTCCTACTAC AAGGAGGGGC CCCACCACCA CCCCTTCTTC TTCATCATCA
CAGGTTGGAG
CCCAGTAGGT GGTAATCTTC TCCACCACCC ACTTCTTCAA CACCCTCCAT
GGTTTACAGC
ACCCTTTTAA GAACAATAAT CCTTGTGATG TGCGGCAGGT ANTATTNTCC
TCTTTGCAGN
NGGGAAGAAG CAGACNCNAN AGGAGAGATG ATNTGCCGAC ATAACCCACG
GCGTGGCGGG
GGTGGTGGTG AAGCATCATC ACTTGGCTCC ACATCATCAT CCTCCTCCNN
NNNNNNNNNN
NNNNNNNNNN NNTNCTTCTT CCCTTTTTTT CTTCCCCTCC TCTTCTCTTN
TTTCCTTTTC
TCCTCCCTCC CCTTCTTCTC CCTCCTCTTC NCCCCCTTTT TTTCTNNTCN
TCCTCNTTNT
NTTNTTNTCC TNCTNCTCTT NTTTCNNNNC TCTTCTTCTT CTCTNCTCCN
TTNNTTCCNT
CNNTCCCTCT TCTCCTTNNT NCTTCTTTTT TCNTTCTTCT CTNTNCCCTT
CTTCTTCTTC
TTCTCCCCCT CCTCCTCTTC CTCTCCCTCC TTCTTCTTCC TTGTTGNTCN
TTCGTGCTTT
TTTNTTNCTT CTCTNNGCNG CCTGNNGNCG CTTGGTNGTC GCCTCCTGCT
GCTCTCCTCC
GTNGNNTGTT GTTCTCCGCC TTCTTNNCTC NGNTNTCNTC GTCTTCTTCG
TNGCTGNCTT
NTTTCTTCTT CTTGTTGCCG CTNNNNTCGT GNCTCCAGCC TGCTNCTATC
GTTNCTCCCN
TCATCGATGT GGCACCACNA TATGAACNNN CCTTCTNNAC TNTGCGATGC
GNCNNTACAA
TCTACTACNN CGNNCATCCG CCTNTNNTNC TTNTTTCGCA TACTACTATC
CGCTNTTCTC
CTCCATATTN NCCNCCCNTC ATTNANTNNN GGANCNNTCT NATAACATCT
CTTCGTTGTC
GTCGTTCCTC TTCACACCTT TCTNCTCTAT TNTNCACGTN NGANGCNATN
ATTTTCTCNT
CTCCNTCATN NTNCACCATA GNCGATCTTT NTTNTTCTTN CATTAANTCA
CTNNTCNTC
Query: examplE5.abi Prediction MEN1 (1079 letters)
Sbjct:
>gi|1945388|gb|U93237.1|HSU93237 Human menin (MEN1)
gene, complete cds
Length = 9180
Score = 163 bits (82), Expect = 5e-39
Identities = 126/142 (88%)
Strand = Plus / Plus
Query: 45 tcatcacaggttggagcccagtaggtggtaatcttctccaccacccacttcttcaacacc
104
|||||||||||||||||||||||||||| |||||| |||| |||||||||||||| |||
Sbjct: 2724 tcatcacaggttggagcccagtaggtgggaatcttatccatgacccacttcttcaaaacc
2783
Query: 105 ctccatggtttacagcacccttttaagaacaataatccttgtgatgtgcggcaggtanta
164
||||||||||||||| |||||||||||||| ||| |||||||| || |||||||| ||
Sbjct: 2784 ctccatggtttacagaacccttttaagaactgtaagccttgtgaggttcggcaggtgtta
2843
Query: 165 ttntcctctttgcagnngggaa 186
|| |||||||||||| |||||
Sbjct: 2844 ttttcctctttgcagttgggaa 2865
_________________________________________________________________________________________
example6.abi
Shift of 1 nucleotides was detected (Expect 9.54e-07)View results
Shift starts at analyzed base 279 : probability score 9.54e-07
The predicted sequence of the molecule following the shift is:
>example6.abi Prediction SHOX
CCAGCTGCAG CTGGGCCTGG ACCTGGGGNA GGGGACCCGG GGGGGGGGAG GGGCNNGA
Query= example6.abi Prediction SHOX (58 letters)
Sbjct:
gi 2276452 (U82668 SHOX gene)Length 85132
(1 .. 85132)
Score = 46.1 bits (23), Expect = 0.001
Identities = 34/38 (89%)
Strand = Plus / Minus
Query: 45 ccagctgcagctgggcctggacctggggnaggggaccc
38
||||||||||||| ||||||||||| || || ||||||
Sbjct: 56911 ccagctgcagctgagcctggacctgcgggagcggaccc
56874
_________________________________________________________________________________________
example7.abi
Shift of 1 nucleotides was detected (Expect 9.54e-07)View results
Shift starts at analyzed base 116 : probability score 1.53e-05
The predicted sequence of the molecule following the shift is:
>example7.abi Prediction SHOX
TCGGGCTGCC CATCCCGTCC CTGGCCGGGT CCCCCCCGGC CCCCGNCGTT TTCCCCCCCC
CCCCCATTAG CAAAAGCAAG AATTCCAGCA TCCCCGACCT GCGGCCCAAG GCGCGGAAGC
ACGGGGAGGC CCTGGTGCCC TGACCCCCCG TGCAGTTTTC CCCGCCCTCG GACCCCCGTG
CCCCGTGCCC CCTTTCTGCC CCGGGCGTNC CGAC
Query= example7.abi Prediction SHOX (214 letters)
Sbjct:
>gi|14770049|ref|XM_030575.1| Homo sapiens short stature homeobox (SHOX), mRNA
Length = 4561
Score = 87.7 bits (44), Expect = 4e-15
Identities = 56/60 (93%)
Strand = Plus / Plus
Query: 69 agcaaaagcaagaattccagcatccccgacctgcggcccaaggcgcggaagcacggggag 128
||||| |||||||||||||||||| |||||||||||| ||||||||||||||||| ||||
Sbjct: 1499 agcaacagcaagaattccagcatcgccgacctgcggctcaaggcgcggaagcacgcggag 1558
Score = 38.2 bits (19), Expect = 3.0
Identities = 25/27 (92%)
Strand = Plus / Plus
Query: 1 tcgggctgcccatcccgtccctggccg 27
|||||||||||||| |||| |||||||
Sbjct: 1431 tcgggctgcccatcgcgtcgctggccg 1457
Query= >example8.abi Prediction MEN1 (155 letters)
Sbjct:
>gi|17458136|ref|XM_006532.5| Homo sapiens hypothetical gene supported by U93236; Y12338; BC002544;
BC002664; NM_000244 (LOC119824), mRNA
Length = 2711
Score = 81.8 bits (41), Expect = 2e-13
Identities = 90/107 (84%)
Strand = Plus / Plus
Query: 36 cccngaagccccctgggactgtcgctggcccagccggggggcctgaaggtggcaacccgg 95
||| |||||| |||||||||||||||||| ||||| | || ||||||||||||| | |||
Sbjct: 1612 cccggaagcctcctgggactgtcgctggcacagcccgaggccctgaaggtggcagcacgg 1671
Query: 96 cccaggtgccagcccgcccagcatnaccccccgcggggggtccagtg 142
| ||||||||||| | | |||||| ||| || ||| ||||||||||
Sbjct: 1672 ctcaggtgccagcacccgcagcatcaccaccgccggagggtccagtg 1718
Query: Query= example9.abi Prediction VHL (191 letters)
Sbjct:
>gi|15431046|gb|AC069461.2| Homo sapiens chromosome 3 clone RP11-1022P15 map 3p, complete sequence
Length = 193214
Score = 71.9 bits (36), Expect = 2e-10
Identities = 75/88 (85%)
Strand = Plus / Minus
Query: 80 ttgactaggccccggaacaccttgaggcatccccctttcagggtaaaaactgggagggcc 139
|||||||||| ||||| |||| |||||||| | ||||||| ||| | ||||| |||||
Sbjct: 178942 ttgactaggctccggacaacctggaggcatcgctctttcagagtatacactggaagggca 178883
Query: 140 aaaaccaaattcccagtggcagactagg 167
|||||||||| | |||||||||||||||
Sbjct: 178882 aaaaccaaatcctcagtggcagactagg 178855
Query= >example10.abi Prediction MEN1 (248 letters)
Sbjct:
>gi|17458136|ref|XM_006532.5| Homo sapiens hypothetical gene supported by U93236; Y12338; BC002544;
BC002664; NM_000244 (LOC119824), mRNA
Length = 2711
Score = 176 bits (89), Expect = 6e-42
Identities = 145/165 (87%)
Strand = Plus / Plus
Query: 81 tcccgtggcccccctctctctcatcgcccccctctatgcccgcttcaccccccagatccg 140
|||||||||| ||| ||| |||||||| |||||||||||||||||||| ||||||||||
Sbjct: 302 tcccgtggccgacctgtctatcatcgccgccctctatgcccgcttcaccgcccagatccg 361
Query: 141 aggcgccctcgccctctccctctctcctcgagaagggggtgtctccccccgtgagcgggt 200
||||||| ||| ||| ||||||| |||||||||||||||||||||| |||||||| |||
Sbjct: 362 aggcgccgtcgacctgtccctctatcctcgagaagggggtgtctccagccgtgagctggt 421
Query: 201 gaaaaangtctnctatgtcatatagnacagnctcagccgctccta 245
||| || |||| | ||||||||| | |||| ||||||||||||||
Sbjct: 422 gaagaaggtctccgatgtcatatggaacagcctcagccgctccta 466