Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017876.1 Corchorus olitorius cultivar O-4 contig17909, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43290
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:1295 original size:331 final size:328
Alignment explanation
Indices: 1--2250 Score: 1478
Period size: 331 Copynumber: 6.8 Consensus size: 328
* * *
1 TTAGTACACGATTTCGGCTAAAATTTTGCAACAATTGATCCG-AAAGATTTTGT-CTCAATTTTT
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAG-TTTT-TCCTCAATTTTT
* * * * * * * * * *
64 AGCCATAATACTCAAGAAAAATGTACAATTC-ATACCAAAAAGATTGAAGGGCTTTTCACGCCTC
64 GGACACAATACTC-ATAAAAATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATGCTTC
* * * *
128 TAATATCGTTTTTCA-TATTTGTTTCCGAATTAATTTCTAATAAAATCAAAACAAGATTCC-AAT
128 TAATATCG-ATTTCACTATTTTTTTCTGAATTAATTTCTAATAAAAT-GAAACAAGATTCCGAA-
* * *
191 GCTCGTAAAAACAAAACCTTAAATCCAATGTGGCT-ATG-TTTTAGTTAGGTGAATAAAGATATT
190 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA-GATTTT-GTTAGATGAATATAGATATT
* * * * * * * ** *
254 TCAAGGAGTCTGCGCGCCAAAAGTCATGCAAATA-TGAGACGGGGCCC-GAAACATGATTTTAGC
253 TCAAGGAGTTTGGGTG-AAAAAATCAAGCAAA-ACTGAGCCGGGGCCCTGAAACGCGTTTTTAGC
* *
317 AAAAAACTGTGACGG
316 -AAAAAC-CTGATGG
* * * * * * * *
332 TTAGTACATGATTTCGGCTAAGATTATACAAAAATTGACGCGAAAAATTTTTACTCAATTTTTGG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTGG
* * * * *** * * *
397 -CAAAATACTCGA-GAAAATTTACAATTC-TTGCCAAAAATATTGAAGGGCTTTTCACGCCTT-T
66 ACACAATACTC-ATAAAAATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATG-CTTCT
** * * * * * *
458 AATATCTTTTTTCA-TATTTGTTTCCGAATTAATTTCTAAGAAAATAAAAACTAGATTCCGATGC
129 AATATC-GATTTCACTATTTTTTTCTGAATTAATTTCTAATAAAAT-GAAACAAGATTCCGAAGC
* * * * * * **
522 TCGTCAAAACAAATCCTCAAATCCATTGTGGCTAAGATTTCGTTAGATGAATATGGATATTTGGA
192 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAA
* * * * * * * * * *
587 GGAGTCTGCGCGCCAAAAATCATGCAAAA-TTAACAAGGGGCCC-GGAACACGTTTTTAGGAAAA
257 GGAGTTTGGGTG-AAAAAATCAAGCAAAACTGAGC-CGGGGCCCTGAAACGCGTTTTTA-G----
* * *
650 AAAAAACTATGATAG
315 CAAAAAC-CTGATGG
* * * * **
665 TTAGTACACCATTTC-GCCTAAAA-TTTAC-AAAATGGACCCAAAAAAATTTTCCTCAATTTTTG
1 TTAGTACACGATTTCAG-CTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTG
* * * * * * * * *
727 G-CTAGAATACTCGTAAAAAATATATAACTCAACGCCAAAAAGATCGAAGGGTTTTTCACGCTTC
65 GAC-ACAATACTCAT-AAAAATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATGCTTC
* * * * ***
791 TAATATCGGTTTTC-TTATTTTTTTCTGAATTAATTTCTAATTAAAGTGAAATAAGATTAAAAAT
128 TAATATC-GATTTCACTATTTTTTTCTGAATTAATTTCTAA-TAAAATGAAACAAGATTCCGAA-
* * * * * * * * *
855 GCTCATAAAAACAATTCTTTTAATCAAATATGGCTAAGATTTTGTTAGATTAATATAAATATTTC
190 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTC
* * *
920 AAGGAGTCTGGCCG-GAAAAAATCATA-CAAAACTGAGCTGGGGCCCTGAAACGCGTTTTTAGTA
255 AAGGAGTTTGG--GTGAAAAAATCA-AGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCA
*
983 AAAGTCCTGATGG
317 AAA-ACCTGATGG
* * ** ** * *
996 TTAGTATACGTTTTTGGCTAATCTTTTGCAAAAATTGTCCCGAAAAGTTTTTCCTCAATTCTTGG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTGG
* * *
1061 ACACAATACTCATAAAAGGTATACAATTCGACACCGAAAAGATTGAAGGG-TTTTCGTGCTTCTA
66 ACACAATACTCATAAAA-ATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATGCTTCTA
* * * * * *
1125 ATTTCGATTTCACTGGTTTTTTTCCGTATTTATTTCTAATAAAATGAAAC-CGATTTCCGAAGCT
130 ATATCGATTTCACT-ATTTTTTTCTGAATTAATTTCTAATAAAATGAAACAAGA-TTCCGAAGCT
*** *
1189 CGTAAAAACAAATCCTTAAATCCAATGTAATTGAGATTTGGTTAGATGAATATAGATATTTCAAG
193 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAG
* * * * *
1254 GAGTTTGGGTGACAAAAATCAAGAAAAACTGGGCCGGGGCCCCGAAATGCGTTTTTAGCAAAACC
258 GAGTTTGGGTGA-AAAAATCAAGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCAAAA-A
*
1319 CCTGATTG
321 CCTGATGG
* * * *
1327 TTGGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCG-AAAGATTTTGCCTCGATTTTTA
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAG-TTTTTCCTCAATTTTTG
* * * * *
1391 GCCATAATATTCGAGAAAAATATACGACTC-A-AGCC-AAATAGATTGAAGGGCTTTTCATGCTT
65 GACACAATACTC-ATAAAAATATACAACTCGACA-CCGAAA-AGATTGAAGGGCTTTTCATGCTT
* * * * * * * *
1453 CTAATATAGTTTTTCAC-ATATGTTTCTGAATTAATTTCTAAGAAAATCAAAACAAGATTCTGAT
127 CTAATATCG-ATTTCACTATTTTTTTCTGAATTAATTTCTAATAAAAT-GAAACAAGATTCCGAA
* * * * *
1517 CCTCATAAAAACAAATCCTCAAAT-CAATTGTGGCTAAGATTTCGTTAGATGAATATAGATATTT
190 GCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGCTGAGATTTTGTTAGATGAATATAGATATTT
* * ** * * * * * *
1581 CAAGAACTTTACGCGCCAAAAATTATGCAAAACTGAGAC--GGACCT-AGAACGCATTGTTACCT
254 CAAGGAGTTTGGGTG-AAAAAATCAAGCAAAACTGAGCCGGGGCCCTGA-AACGC---G-----T
* *
1643 TTTTAGCAAAAAACTGTGACGG
309 TTTTAGC-AAAAAC-CTGATGG
* ** * * * * **
1665 TTAGTACACGATTTCGGCTAAAATTTTATAAAAGTGGACTCAAAAAAATTTTCCTCAATTTTTGG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTGG
* * * * * * * *
1730 CCAGAATACTCGTAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTA
66 ACACAATACTCAT-AAAAATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATGCTTCTA
** * * * ** *
1795 ATATC-ATTTTTCTTTTTTCTTTTTCTGAACTAATTTCAAATTAAAGCGAAACAAGA-TCCAAAT
130 ATATCGA--TTTCACTATT-TTTTTCTGAATTAATTTCTAA-TAAAATGAAACAAGATTCCGAA-
* * * *
1858 GCTCGTAAAAACAATTCTTTTAATCCATTGTGGCTGAGATTTTGTTAGACT-AATATAGATATTT
190 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGA-TGAATATAGATATTT
** * * *
1922 CAAGGAGTTTGGGTGGAAAAAATCAAGCAAAACTGAGTTGGGGCACTGGAACGCGTTTTTAGTAA
254 CAAGGAGTTTGGGT-GAAAAAATCAAGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCAA
1987 AAACCGTGATGG
318 AAACC-TGATGG
* * * *
1999 TTAGTACACGTTTTCAGCTAAAATTTTGCAAAAATTGTCACGAAAATTTTTTCCTCAATTTTTGG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTGG
* * * *
2064 ACACAATACTCATAAAAGTATACGATTCGACAACGAAAAGATTGAAGGGCTTTTCATGCTTCTAA
66 ACACAATACTCATAAAAATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATGCTTCTAA
* ** * *
2129 TATCGTTTTTTCT-TATTTTTCCTGAATTAATTTCTAATTAAATCGAAACAA-A-T----A-CTC
131 TATCGATTTCACTAT-TTTTTTCTGAATTAATTTCTAATAAAAT-GAAACAAGATTCCGAAGCTC
* * * * ** * *
2186 ATGAAAACAAATCCTTTAATGCAATGTATCTAAGA-TTTGTTTAGATGAATATAAATATTTCAAG
194 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTG-TTAGATGAATATAGATATTTCAAG
2250 G
258 G
2251 TGTCTGGGCA
Statistics
Matches: 1508, Mismatches: 328, Indels: 173
0.75 0.16 0.09
Matches are distributed among these distances:
323 5 0.00
324 51 0.03
326 1 0.00
328 4 0.00
329 203 0.13
330 71 0.05
331 418 0.28
332 76 0.05
333 173 0.11
334 144 0.10
335 92 0.06
336 16 0.01
337 10 0.01
338 78 0.05
339 39 0.03
340 8 0.01
341 103 0.07
342 7 0.00
343 9 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (328 bp):
TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTTGG
ACACAATACTCATAAAAATATACAACTCGACACCGAAAAGATTGAAGGGCTTTTCATGCTTCTAA
TATCGATTTCACTATTTTTTTCTGAATTAATTTCTAATAAAATGAAACAAGATTCCGAAGCTCGT
AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAG
TTTGGGTGAAAAAATCAAGCAAAACTGAGCCGGGGCCCTGAAACGCGTTTTTAGCAAAAACCTGA
TGG
Found at i:2008 original size:672 final size:659
Alignment explanation
Indices: 1--2255 Score: 1985
Period size: 672 Copynumber: 3.4 Consensus size: 659
* * * *
1 TTAGTACACGATTTCGGCTAAAATTTTGCAACAATTGATCCGAAAGATTTTGTCTCAATTTTTAG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTGCCTCAATTTTTAG
* * * * *
66 CCATAATACTCAAGAAAAATGTACAATTCATA-CCAAAAAGATTGAAGGGCTTTTCACGCCTCTA
66 CCATAATACTCGAGAAAAATATACAACTCACAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTA
* * * *
130 ATATCGTTTTTCATATTTGTTTCCGAATTAATTTCTAATAAAATCAAAACAAGATTCCAATGCTC
131 ATATCGTTTTTCACATATGTTTCTGAATTAATTTCTAATAAAATCAAAACAAGATTCTAATGCTC
* * * * *
195 GTAAAAACAAAACCTTAAATCCAATGTGGCTATGTTTTAGTTAGGTGAATA-AAGATATTTCAAG
196 ATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTT-GTTAGATGAATATAA-ATATTTCAAG
* * * *
259 GAGTCTGCGCGCCAAAAGTCATGCAAATA-TGAGACGGGGCCCGAA-ACATGA-TTTTAGCAAAA
259 GAGTCT-CGCGCCAAAAATCATGCAAA-ACTGAGACGGGACCTGAACGCATGATTTTTAGCAAAA
* * * * *
321 AACTGTGACGGTTAGTACATGATTTCGGCTAAGATTATACAAAAATTGACGCGAAAAATTTTTAC
322 AACTGTGACGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAAATTTTTCC
* * ** *
386 TCAATTTTTGGCAAAATACTCG-AGAAAATTTACAATTCTTGCCAAAAATATTGAAGGGCTTTTC
387 TCAATTTTTGGCAAAATACTCGTAAAAAATATACAATTCACGCCAAAAAGATTGAAGGGCTTTTC
* * * * *
450 ACGCCTT-TAATATCTTTTTTCATATTTGTTTCCGAATTAATTTCTAAGAAAATAAAAACTAGAT
452 ACG-CTTCTAATATCATTTTTCTTATTTTTTTCCGAATTAATTTCTAATAAAA-AGAAAC-AGAT
* * * * *
514 TCCGATGCTCGTCAAAACAAATCCTCAAATCCATTGTGGCTAAGATTTCGTTAGATGAATATGGA
514 TCCAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGTTAGATGAATATAGA
** * * * ** * * * * *
579 TATTTGGAGGAGTCTGCGCGCCAAAAATCATGCAAAATTAACAAGGGGCCCGGAACACGTTTTTA
579 TATTTCAAGGAGTTTGGGTGGAAAAAATCAAGCAAAACTGAGAAGGGGCCCGGAACGCGTTTTTA
*
644 GGAAAAAAAAAACTATGATAG
644 -G----AAAAAACCATGATAG
* * * * *
665 TTAGTACACCATTTC-GCCTAAAA-TTTAC-AAAATGGACCCAAAAAAATTTT-CCTCAATTTTT
1 TTAGTACACGATTTCAG-CTAAAATTTTGCAAAAATTGACCC-GAAAGATTTTGCCTCAATTTTT
* * * * * *
726 GGCTAGAATACTCGTA-AAAAATATATAACTCA-ACGCCAAAAAGATCGAAGGGTTTTTCACGCT
64 AGCCATAATACTCG-AGAAAAATATACAACTCACA-GCCAAAAAGATTGAAGGGCTTTTCACGCT
* ** * * * * * **
789 TCTAATATCGGTTTTCTTATTTTTTTCTGAATTAATTTCTAATTAAAGT-GAAATAAGATTAAAA
127 TCTAATATCGTTTTTCACATATGTTTCTGAATTAATTTCTAA-TAAAATCAAAACAAGATT-CTA
* * * * * *
853 ATGCTCATAAAAACAATTCTTTTAATCAAATATGGCTAAGATTTTGTTAGATTAATATAAATATT
190 ATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTAAGA-TTTGTTAGATGAATATAAATATT
* ** * *
918 TCAAGGAGTCTGGCCGGAAAAAATCATACAAAACTGAG-CTGGGGCCCTGAAACGC--G-TTTTT
254 TCAAGGAGTCTCG-CGCCAAAAATCATGCAAAACTGAGAC--GGGACCTG-AACGCATGATTTTT
* ** * * * * * ** * * *
979 AGTAAAAGTC-CTGATGGTTAGTATACGTTTTTGGCTAATCTTTTGCAAAAATTGTCCCGAAAAG
315 AGCAAAAAACTGTGACGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAAA
* * * ** * *
1043 TTTTTCCTCAATTCTTGGACACAATACTCATAAAAGGTATACAATTCGACACCGAAAAGATTGAA
380 TTTTTCCTCAATTTTTGG-CAAAATACTCGTAAAAAATATACAATTC-ACGCCAAAAAGATTGAA
** * ** ** * * *
1108 GGG-TTTTCGTGCTTCTAATTTCGATTTCACTGGTTTTTTTCCGTATTTATTTCTAATAAAATGA
443 GGGCTTTTCACGCTTCTAATATC-ATTTTTCTTATTTTTTTCCGAATTAATTTCTAATAAAAAGA
* * *** *
1172 AACCGATTTCCGAA-GCTCGTAAAAACAAATCCTTAAATCCAATGTAATTGAGATTTGGTTAGAT
507 AACAGA-TTCC-AATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGTTAGAT
* * ** *
1236 GAATATAGATATTTCAAGGAGTTTGGGT-GACAAAAATCAAGAAAAACTGGGCCGGGGCCCCGAA
570 GAATATAGATATTTCAAGGAGTTTGGGTGGA-AAAAATCAAGCAAAACTGAGAAGGGG-CCCGGA
* * * * *
1300 ATGCGTTTTTAGCAAAACCCCTGATTG
633 ACGCGTTTTTAGAAAAAACCATGATAG
* *
1327 TTGGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTGCCTCGATTTTTAG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTGCCTCAATTTTTAG
* * * *
1392 CCATAATATTCGAGAAAAATATACGACTCA-AGCCAAATAGATTGAAGGGCTTTTCATGCTTCTA
66 CCATAATACTCGAGAAAAATATACAACTCACAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTA
* * * *
1456 ATATAGTTTTTCACATATGTTTCTGAATTAATTTCTAAGAAAATCAAAACAAGATTCTGATCCTC
131 ATATCGTTTTTCACATATGTTTCTGAATTAATTTCTAATAAAATCAAAACAAGATTCTAATGCTC
* *
1521 ATAAAAACAAATCCTCAAAT-CAATTGTGGCTAAGATTTCGTTAGATGAATATAGATATTTCAAG
196 ATAAAAACAAATCCTTAAATCCAA-TGTGGCTAAGATTT-GTTAGATGAATATAAATATTTCAAG
* * * *
1585 AACTTTACGCGCCAAAAATTATGCAAAACTGAGAC-GGACCTAGAACGCATTGTTACCTTTTTAG
259 GAGTCT-CGCGCCAAAAATCATGCAAAACTGAGACGGGACCT-GAACGCA-TG--A--TTTTTAG
* * * * * *
1649 CAAAAAACTGTGACGGTTAGTACACGATTTCGGCTAAAATTTTATAAAAGTGGACTCAAAAAAAT
317 CAAAAAACTGTGACGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAAATT
* * *
1714 TTTCCTCAATTTTTGGCCAGAATACTCGTAAAAAATATATAACTCAACGCCAAAAAGATTGAAGG
382 TTTCCTCAATTTTTGG-CAAAATACTCGTAAAAAATATACAATTC-ACGCCAAAAAGATTGAAGG
* * * * **
1779 GCTTTTCACGCTTCTAATATCATTTTTCTTTTTTCTTTTTCTGAACTAATTTCAAATTAAAGCGA
445 GCTTTTCACGCTTCTAATATCATTTTTC-TTATT-TTTTTCCGAATTAATTTCTAA-TAAAAAGA
* * * *
1844 AACAAGA-TCCAAATGCTCGTAAAAACAATTCTTTTAATCCATTGTGGCTGAGATTTTGTTAGAC
507 AAC-AGATTCC-AATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGTTAGA-
** *
1908 T-AATATAGATATTTCAAGGAGTTTGGGTGGAAAAAATCAAGCAAAACTGAGTTGGGGCACTGGA
569 TGAATATAGATATTTCAAGGAGTTTGGGTGGAAAAAATCAAGCAAAACTGAGAAGGGGC-CCGGA
* * *
1972 ACGCGTTTTTAGTAAAAACCGTGATGG
633 ACGCGTTTTTAGAAAAAACCATGATAG
* * * * *
1999 TTAGTACACGTTTTCAGCTAAAATTTTGCAAAAATTGTCACGAAA-ATTTTTTCCTCAATTTTTG
1 TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGA-TTTTGCCTCAATTTTTA
* * * * * * * * *
2063 GACACAATACTC-ATAAAAGTATACGATTCGACA-ACGAAAAGATTGAAGGGCTTTTCATGCTTC
65 GCCATAATACTCGAGAAAAATATACAACTC-ACAGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
* * * * *
2126 TAATATCGTTTTT-TCTTATTTTTCCTGAATTAATTTCTAATTAAATCGAAACAA-A---T-A--
129 TAATATCGTTTTTCACATATGTTT-CTGAATTAATTTCTAATAAAATCAAAACAAGATTCTAATG
* * * **
2183 CTCATGAAAACAAATCCTTTAATGCAATGTATCTAAGATTTGTTTAGATGAATATAAATATTTCA
193 CTCATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTG-TTAGATGAATATAAATATTTCA
*
2248 AGGTGTCT
257 AGGAGTCT
2256 GGGCATCAAA
Statistics
Matches: 1261, Mismatches: 270, Indels: 119
0.76 0.16 0.07
Matches are distributed among these distances:
660 10 0.01
661 7 0.01
662 151 0.12
663 176 0.14
664 205 0.16
665 94 0.07
666 120 0.10
667 60 0.05
668 13 0.01
669 100 0.08
670 19 0.02
671 45 0.04
672 255 0.20
673 6 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (659 bp):
TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTGCCTCAATTTTTAG
CCATAATACTCGAGAAAAATATACAACTCACAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTA
ATATCGTTTTTCACATATGTTTCTGAATTAATTTCTAATAAAATCAAAACAAGATTCTAATGCTC
ATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGTTAGATGAATATAAATATTTCAAGGA
GTCTCGCGCCAAAAATCATGCAAAACTGAGACGGGACCTGAACGCATGATTTTTAGCAAAAAACT
GTGACGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAAATTTTTCCTCAA
TTTTTGGCAAAATACTCGTAAAAAATATACAATTCACGCCAAAAAGATTGAAGGGCTTTTCACGC
TTCTAATATCATTTTTCTTATTTTTTTCCGAATTAATTTCTAATAAAAAGAAACAGATTCCAATG
CTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGTTAGATGAATATAGATATTTCA
AGGAGTTTGGGTGGAAAAAATCAAGCAAAACTGAGAAGGGGCCCGGAACGCGTTTTTAGAAAAAA
CCATGATAG
Found at i:2437 original size:49 final size:49
Alignment explanation
Indices: 2380--2474 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
2370 GTAAGTCCTG
* *
2380 TCGAGTAAAATATCCAATGATTGGTTTCAAATTTGCCCAAAGTAAAAAA
1 TCGAGTAAAATATCCAAAGATTGGTTTCAAATTCGCCCAAAGTAAAAAA
*
2429 TCGAGTAAAATATCCAAAGATTGGTTTCGAATTCGCCCAAAGTAAA
1 TCGAGTAAAATATCCAAAGATTGGTTTCAAATTCGCCCAAAGTAAA
2475 GAATTGCTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (49 bp):
TCGAGTAAAATATCCAAAGATTGGTTTCAAATTCGCCCAAAGTAAAAAA
Found at i:3896 original size:25 final size:25
Alignment explanation
Indices: 3822--3896 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
3812 AATCCAAATA
3822 AAGTAACTTATAACAGATCAAAAAC
1 AAGTAACTTATAACAGATCAAAAAC
* * * * *
3847 TAAG-AA---GTAAGA-ACCCAAATC
1 -AAGTAACTTATAACAGATCAAAAAC
3868 AAGTAACTTATAACAGATCAAAAAC
1 AAGTAACTTATAACAGATCAAAAAC
3893 AAGT
1 AAGT
3897 TTGAATTGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 11
0.62 0.18 0.20
Matches are distributed among these distances:
20 3 0.09
21 8 0.24
22 4 0.12
24 4 0.12
25 12 0.35
26 3 0.09
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.19
Consensus pattern (25 bp):
AAGTAACTTATAACAGATCAAAAAC
Found at i:10637 original size:27 final size:27
Alignment explanation
Indices: 10607--10662 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
10597 CTTTCTTCCA
10607 TTTAATGTTTGCTAGAAATTTATCTGC
1 TTTAATGTTTGCTAGAAATTTATCTGC
*
10634 TTTAATGTTTGCTAGATATTTATCTGC
1 TTTAATGTTTGCTAGAAATTTATCTGC
10661 TT
1 TT
10663 GGTTTCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (27 bp):
TTTAATGTTTGCTAGAAATTTATCTGC
Found at i:27701 original size:16 final size:16
Alignment explanation
Indices: 27676--27706 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27666 CTAGGAGCCA
27676 AATTTCGATTGCTGCC
1 AATTTCGATTGCTGCC
*
27692 AATTTTGATTGCTGC
1 AATTTCGATTGCTGC
27707 TAGTCTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (16 bp):
AATTTCGATTGCTGCC
Found at i:34952 original size:21 final size:21
Alignment explanation
Indices: 34926--34966 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34916 AAAAAAGTTA
34926 AAGCACTCAACGAAGGAGTAT
1 AAGCACTCAACGAAGGAGTAT
*
34947 AAGCACTCACCGAAGGAGTA
1 AAGCACTCAACGAAGGAGTA
34967 AGAGGAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (21 bp):
AAGCACTCAACGAAGGAGTAT
Found at i:36168 original size:17 final size:17
Alignment explanation
Indices: 36139--36208 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
36129 AGATCAAATA
36139 AATGTTAACTAAATACT
1 AATGTTAACTAAATACT
* *
36156 AATTTTAATTAAATACT
1 AATGTTAACTAAATACT
* *
36173 TATGTTCACTAAATACT
1 AATGTTAACTAAATACT
*
36190 AATGTTAACCAAATACT
1 AATGTTAACTAAATACT
36207 AA
1 AA
36209 CACCAACATT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (17 bp):
AATGTTAACTAAATACT
Found at i:37344 original size:104 final size:104
Alignment explanation
Indices: 37163--37408 Score: 393
Period size: 104 Copynumber: 2.3 Consensus size: 104
37153 TTTTCTAAAC
* * *
37163 AATTCAATTGTTTGATTGAAATCTGTAACTAAGTTTTACTTTAGCAACTCATGATTCATAGCAAC
1 AATTCAATAGTTTGATTAAAATCTCTAACTAAGTTTTACTTTAGCAACTCATGATTCATAGCAAC
*
37228 TTGTAGTTAAAATTATTTTCTAAACATGAATGAACATTT
66 TTGTAGTTAAAATCATTTTCTAAACATGAATGAACATTT
* *
37267 GATTCAATAGTTTGATTAAAATCTCTAACTAAGTTTTAGTTTAGCAACTCATGATTCATAGCAAC
1 AATTCAATAGTTTGATTAAAATCTCTAACTAAGTTTTACTTTAGCAACTCATGATTCATAGCAAC
*
37332 TTGTAGTTAAAATCATTTTGTAAACATGAATGAACATTT
66 TTGTAGTTAAAATCATTTTCTAAACATGAATGAACATTT
* *
37371 AATTCAATAGTTTGATTGATATATCTCCAACTAAGTTT
1 AATTCAATAGTTTGATT-A-AAATCTCTAACTAAGTTT
37409 GAATCCCTTC
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
104 113 0.87
105 1 0.01
106 16 0.12
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (104 bp):
AATTCAATAGTTTGATTAAAATCTCTAACTAAGTTTTACTTTAGCAACTCATGATTCATAGCAAC
TTGTAGTTAAAATCATTTTCTAAACATGAATGAACATTT
Found at i:40953 original size:17 final size:17
Alignment explanation
Indices: 40912--40946 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40902 TGCTTAAAGA
40912 TGGATTTTTATGTGTGG
1 TGGATTTTTATGTGTGG
40929 TGGATTTTTATGTGTGG
1 TGGATTTTTATGTGTGG
40946 T
1 T
40947 TGGTTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.54
Consensus pattern (17 bp):
TGGATTTTTATGTGTGG
Done.