Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018135.1 Corchorus olitorius cultivar O-4 contig18168, 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: 59846
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1558 original size:322 final size:325
Alignment explanation
Indices: 3--2601 Score: 2392
Period size: 322 Copynumber: 8.0 Consensus size: 325
1 TT
* * * * **
3 TTTCAAGGAGTCTTGGTGCCAAAAACCATGCAAAACTGAGTC-GGGACCCAGTAATACGTTTTTA
1 TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCAGGAACGCGTTTTTA
* * * * * * *
67 GCAAAAAATCGTGATTGTTAGTACACGATTTCAGCTGAAATTTTACAAAAATAGACTCGAAAGAT
65 GCCAAAAACCGTGATGGTTA-T---C-ATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGAT
* *
132 TTTTCCTCAAATTTTTTAGCCAAAATAATCATAGAAATATATAATTCAAC-TATAAAATGATTGA
125 TTTTCCTC-AA-TTTTTAGCCACAATAATCATAGAAATATATAATTCAACATA-AAAAAGATTGA
* * * * * * *
196 TGGGCTTTTCACGCTTTTGATATCGTTTTTTCATTTTTTTCTGAATTAATTTCAAATAAAATTGA
187 AGGGATTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCTGAATTAATTTCTAATAAAATCGA
* * * * * *
261 AATAAGATTCTGATTCTCGTAAAAAGAAATCCTTAAATCCACTGTTGCTGAGATTTGGTTGGATG
251 AACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG
*
326 ACTATAGAT-
316 AATATAGATA
* ** * *
335 TGTTGAAGGAGAATTGGCACCAAAAATCATGCAAAACTGAGCC-GGAGCCCATGAACGCGTTTTT
1 T-TTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGG-GCCCAGGAACGCGTTTTT
* * * * * * *
399 AGCCCAATATCGTAATTGTTAACGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAA
64 AGCCAAAAACCGTGATGGTT-A--T---C-ATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAA
* *
464 GATTATTCAC-CAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAAAATT
122 GATTTTTC-CTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACAT-AAAAAAGATT
* * * *
528 GAA-TGACTTTTCATGCCTCTAATATTGTTTTTCCATTTTTTATCTGAATTAATTTCTAATAAAA
185 GAAGGGA-TTTTCACGCTTCTAATATCGTTTTTCCA-TTTTT-TCTGAATTAATTTCTAATAAAA
* * * **
592 TCGAAATAAGATTCTGATTCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTTTTTA
247 TCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTA
*
657 GATAAATATAGATA
312 GATGAATATAGATA
* * * * * * * *
671 ATTCAAGGAGTCTTGGCGCCAAAAAT-ACTTCGGAAAC-GAGCCGGGGCCTAAGATCGCATTTTT
1 TTTCAAGGAGTCTTGGCGCCAAAAATCA-TGC-AAAACTGAGCCAGGGCCCAGGAACGCGTTTTT
* * * **
734 AG-CAAATAATCGTAATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAATTAATGCG-AAG
64 AGCCAAA-AACCGTGATGGTT-AT---C-ATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAG
* * * *
797 TATTTTTCCTCAATTTTTAGTCACAATTACCATAGAAATATATAATTCAACGTAAAAAAGATTGA
123 -ATTTTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGA
* ** * *
862 AGGG---TT---G--T-T--T-T--TTTTT-C-TTTTCTAAGAAAATTAATTTCTGATAAAATTG
187 AGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTG--AATTAATTTCTAATAAAATCG
* *
911 AAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGAATTGGTTAGAT
250 AAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
*
976 GAATATAGATT
315 GAATATAGATA
* * * * * *
987 TTTCAAGCAGTCTTGCCGCCAAAAATCATGTAAAACTGAGTC-GAGACCCAGGAATGCGTTTTTA
1 TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAG-GGCCCAGGAACGCGTTTTTA
*
1051 GCCAAAAACCGTGATGGTTAGTACAAGATTTCAGCTAAAATTTTACAAAAATTGA-CCGAAAGAT
65 GCCAAAAACCGTGATGGTTA-T-C---ATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGAT
* * * *
1115 TTTTCCTCAAATTTTAGCCACAATTATCATAGAAATATATAATTTAACATCAAAAAGATTGAAGG
125 TTTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGAAGG
*
1180 GCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATAAAATCGAAACA
190 GATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATAAAATCGAAACA
* *
1245 AGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGTTGAGATTTGGTTAGATGAATA
255 AGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATA
1310 TAGATA
320 TAGATA
* * ** * * * * *
1316 TTTGAAGGAGTCTTGACTTCAAAAATCATGCAAAATTGAGCCACGGTCTAGGAACACGTTTTTAG
1 TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCAGGAACGCGTTTTTAG
* ** *
1381 CCAAAAACCGTTATGG-T-T-ATTTCAGCTAAAATTTTATAAAAATCGACCCGAAAGATTTTTCC
66 CCAAAAACCGTGATGGTTATCATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCC
* * *
1443 TCAAATTTTAGCCACAATAATCATAGAAATATATAATTCAACATCAAAAATATTGAAGGGATTTT
131 TCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGAAGGGATTTT
1508 CACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTC
196 CACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTC
* * *
1573 TAATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATTTAGATA
261 TGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * ** * * * * ** *
1638 TTTCAAGGAGTATTGACTTCAAAAATCATTCAAAATTGAGCCTGGGTCCAGGAACATGTTTATAG
1 TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCAGGAACGCGTTTTTAG
* * *
1703 CCAAAAACCGTGATGGTTAGTATTCGATTTCAGCTAAAATTTTGCAAAAATTTATCCGAAATA-T
66 CCAAAAACCGTGATGG-T--TA-TC-ATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATT
* * * * * * * * *
1767 TTTCTTTAATTTTTAGCCACAATTATCGTAGTAACATATAACTCAACGTCAAAAAGATT-AA---
126 TTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGAAGGG
** ****** * * *
1828 ATGGTCA---TT-T--T-TC-TTTTT---TTTAAAAAAAATGAATATCTAATAAAATCGAAAAAA
191 ATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAA
* * *
1882 GATTATGATGCTCGAAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-GCATGACTA
256 GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG-ATGAATA
*
1946 TATAT-
320 TAGATA
* * * * *
1951 TGTTTAAGGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGCC-GGAGCCCATGAACGCATATTT
1 T-TTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGG-GCCCAGGAACGCGTTTTT
* * ** ** *
2015 AGCCCAATATTGTGATTCTTAGTACTCGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA
64 AGCCAAAAACCGTGA-TGGT--TA-TC-ATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGA
* *
2080 TTTTTCATCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTAAAAAAGATTGAA-
124 TTTTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGAAG
* * * * *
2144 TGACTTTTCATGCCTCTAATATTGTTTTTCCATTTTTTATTTGAATTAATTTCTAATAAAATCGA
189 GGA-TTTTCACGCTTCTAATATCGTTTTTCCA-TTTTT-TCTGAATTAATTTCTAATAAAATCGA
* * * *
2209 AATAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGTTTAGATG
251 AACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG
*
2274 AATGTAGATGA
316 AATATAGAT-A
* * * * * *
2285 -TTCAAGGAGTCTTGGCGCAAAAAATCATTCAAAACCGAGCCAGGGCCCAGGATCGCATTTTTTG
1 TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCAGGAACGCGTTTTTAG
* *
2349 CCAAAAACCGTGATGGTTAGTGCACGATTTCAGCTAAAATTTTGTAAAAATT-AGTCCG-AAGTA
66 CCAAAAACCGTGATGGTTA-T---C-ATTTCAGCTAAAATTTTGCAAAAATTGA-CCCGAAAG-A
* * *
2412 TTTTTCCTCAATTTTTAGTCACAATTACCATAGAAATATATAATTCAACATAAAAAAGATTGAAG
124 TTTTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGAAG
*** *
2477 GG----T--CG--T-T--TA---TTTTT-C--TTTTTAAAACATTAA-TTCTAATAAAATTGAAA
189 GGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGA-ATTAATTTCTAATAAAATCGAAA
*
2524 C-AGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATGAA
253 CAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAA
2588 TATAGATA
318 TATAGATA
2596 TTTCAA
1 TTTCAA
2602 AAATCATGCA
Statistics
Matches: 1906, Mismatches: 274, Indels: 194
0.80 0.12 0.08
Matches are distributed among these distances:
311 1 0.00
312 70 0.04
313 22 0.01
314 196 0.10
315 127 0.07
316 173 0.09
317 12 0.01
318 15 0.01
319 5 0.00
320 1 0.00
321 31 0.02
322 278 0.15
323 4 0.00
324 3 0.00
325 6 0.00
326 6 0.00
327 6 0.00
328 5 0.00
329 215 0.11
330 32 0.02
331 15 0.01
332 250 0.13
333 187 0.10
334 46 0.02
335 193 0.10
336 7 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (325 bp):
TTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCAGGAACGCGTTTTTAG
CCAAAAACCGTGATGGTTATCATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCC
TCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACATAAAAAAGATTGAAGGGATTTT
CACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTC
TGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
Found at i:2310 original size:646 final size:634
Alignment explanation
Indices: 2--2601 Score: 2348
Period size: 651 Copynumber: 4.0 Consensus size: 634
1 T
* * * * * ** *
2 TTTTCAAGGAGTCTTGGTGCCAAAAACCATGCAAAACTGAGTCGGGACC-CAGTAATACGTTTTT
1 TTTTCAAGGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGCCGGG-CCTAAG-AACGCATTTTT
* * * * * * * *
66 AGCAAAAAATCGTGATTGTTAGTACACGATTTCAGCTGAAATTTTACAAAAATAGACTCGAAAGA
64 AGC-CAATATAGTGATT-TTAGTACTCGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGA
* *
131 TTTTTCCTCAAATTTTTTAGCCAAAATAATCATAGAAATATATAATTCAAC-TATAAAATGATTG
127 TTTTTCCTC-AA-TTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTA-AAAAAGATTG
* * * * * * * * *
195 ATGGGCTTTTCACGCTTTTGATATCGTTTTTTCATTTTTT-TCTGAATTAATTTCAAATAAAATT
189 A--AGATTTTCATGC-TCTAATATTGTTTTTCCATTTTTTATCTGAATTAATTTCTAATAAAATC
* * * * * * *
259 GAAATAAGATTCTGATTCTCGTAAAAAGAAATCCTTAAATCCACTGTTGCTGAGATTTGGTTGGA
251 GAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGA
* * * ** * *
324 TGACTATAGATTGTTGAAGGAGAATTGGCAC-CAAAAATCATGCAAAACTGAGCCGGAGCCCATG
316 TGAATATAGA-TATTCAAGGAGTCTT-G-ACGCAAAAATCATTCAAAACTGAGCCGG-GCCCAGG
** * * * * * *
388 AACGCGTTTTTAGCCCAATATCGTAATTGTTAACGTACACGATTTCGGCTAAAATTTTGCAAAAA
377 AACATG-TTTTAGCCAAAAACCGTGATGGTT-A-GTACACGATTTCAGCTAAAATTTTGCAAAAA
* * * *
453 TTGA-CTCGAAAGATTATTCAC-CAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACA
439 TTTATC-CGAAATATTTTTC-CTCAATTTTTAGCCACAATTATCATAGAAATATATAATTCAACA
* * * * * ***
516 TAAAAAAAAATTGAATGACTTTTCATGCCTCTAATATTGTTTTTCCATTTTTTATCTGAATTAAT
502 T-CAAAAAGATTGAA-G---------G-GTC--AT-TTATTCTT---TTTTTTA-AAAAATTAA-
* * *
581 TTCTAATAAAATCGAAATAAGATTCTGATTCTCGTAAAAACATATCCTTAAATCCAATGTGGCTG
547 TTCTAATAAAATCGAAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
** *
646 AGATTTTTTTAGATAAATATAGA
612 AGATTTGGTTAGATGAATATAGA
* * *
669 TAATTCAAGGAGTCTTGGCGCCAAAAATACTT-CGGAAAC-GAGCCGGGGCCTAAGATCGCATTT
1 T-TTTCAAGGAGTCTTGGCGCCAAAAAT-CTTGC-AAAACTGAGCC-GGGCCTAAGAACGCATTT
* * * * * * * **
732 TTAGCAAATAATCGTAATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAATTAATGCG-AA
62 TTAGCCAAT-ATAGTGAT-TTTAGTACTCGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAA
* * *
796 GTATTTTTCCTCAATTTTTAGTCACAATTACCATAGAAATATATAATTCAACGTAAAAAAGATTG
125 G-ATTTTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTAAAAAAGATTG
** * **** * *
861 AAG--GGT--TG---T--T-TT-TTTTT-C-TTTTCTAAGAAAATTAATTTCTGATAAAATTGAA
189 AAGATTTTCATGCTCTAATATTGTTTTTCCATTTTTTATCTGAATTAATTTCTAATAAAATCGAA
*
913 ACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGT-GACTGAGAATTGGTTAGATG
254 ACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGA-TGAGATTTGGTTAGATG
* * * * *
977 AATATAGATTTTTCAAGCAGTCTTGCCGCCAAAAATCATGT-AAAACTGAGTCGAGACCCAGGAA
318 AATATAGA-TATTCAAGGAGTCTTGACG-CAAAAATCAT-TCAAAACTGAGCCG-GGCCCAGGAA
* * * *
1041 TGCGT-TTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTTCAGCTAAAATTTTACAAAAATTG
379 --CATGTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTT
* * *
1105 A-CCGAAAGATTTTTCCTCAAATTTTAGCCACAATTATCATAGAAATATATAATTTAACATCAAA
442 ATCCGAAATATTTTTCCTCAATTTTTAGCCACAATTATCATAGAAATATATAATTCAACATCAAA
****
1169 AAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTGAATTAATTTCTAATA
507 AAGATTGAAGGG----TCA---TT-T-AT-TC---TTT---TTTTTAAAAAATTAA-TTCTAATA
* * *
1234 AAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGTTGAGATTTGG
555 AAATCGAAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG
1299 TTAGATGAATATAGA
620 TTAGATGAATATAGA
* * ** * * * * * * *
1314 TATTTGAAGGAGTCTTGACTTCAAAAATCATGCAAAATTGAGCCACGGTCTAGGAACACGTTTTT
1 T-TTTCAAGGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGCC-GGGCCTAAGAACGCATTTTT
* ** * * ** *
1379 AGCCAA-AAACCG-TTATGGT--T--ATTTCAGCTAAAATTTTATAAAAATCGACCCGAAAGATT
64 AGCCAATATAGTGATTTTAGTACTCGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATT
* * * *
1438 TTTCCTCAAATTTTAGCCACAATAATCATAGAAATATATAATTCAACATCAAAAATATTGAAGGG
129 TTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTAAAAAAGATTGAA--G
* *
1503 ATTTTCACGCTTCTAATATCGTTTTTCCA-TTTTT-TCTGAATTAATTTCTAATAAAATCGAAAC
192 ATTTTCATGC-TCTAATATTGTTTTTCCATTTTTTATCTGAATTAATTTCTAATAAAATCGAAAC
* * *
1566 AAGATTCTAATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAAT
256 AAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGAAT
* * * * *
1631 TTAGATATTTCAAGGAGTATTGACTTCAAAAATCATTCAAAATTGAGCCTGGGTCCAGGAACATG
321 ATAGATA-TTCAAGGAGTCTTGAC-GCAAAAATCATTCAAAACTGAGCC-GGGCCCAGGAACATG
**
1696 TTTATAGCCAAAAACCGTGATGGTTAGTATTCGATTTCAGCTAAAATTTTGCAAAAATTTATCCG
383 TTT-TAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTTATCCG
* * * * * * *
1761 AAATA-TTTTCTTTAATTTTTAGCCACAATTATCGTAGTAACATATAACTCAACGTCAAAAAGAT
447 AAATATTTTTCCTCAATTTTTAGCCACAATTATCATAGAAATATATAATTCAACATCAAAAAGAT
* * * *
1825 TAAATGGTCATTT-TTCTTTTTTTTAAAAAAAATGAATATCTAATAAAATCGAAAAAAGATTATG
512 TGAAGGGTCATTTATTCTTTTTTTT--AAAAAATTAAT-TCTAATAAAATCGAAAAAAGATTCTG
* * *
1889 ATGCTCGAAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-GCATGACTATATA
574 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG-ATGAATATAGA
* * * *
1950 TTGTTTAAGGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGCCGGAGCCCATGAACGCATATTT
1 TT-TTCAAGGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGCCGG-GCCTAAGAACGCATTTTT
* *
2015 AGCCCAATATTGTGATTCTTAGTACTCGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA
64 AG-CCAATATAGTGATT-TTAGTACTCGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGA
*
2080 TTTTTCATCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTAAAAAAGATTGAAT
127 TTTTTCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTAAAAAAGATTGAA-
*
2145 GACTTTTCATGCCTCTAATATTGTTTTTCCATTTTTTATTTGAATTAATTTCTAATAAAATCGAA
191 GA-TTTTCATG-CTCTAATATTGTTTTTCCATTTTTTATCTGAATTAATTTCTAATAAAATCGAA
* * *
2210 ATAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGTTTAGATGA
254 ACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGA
* * * *
2275 ATGTAGATGATTCAAGGAGTCTTGGCGCAAAAAATCATTCAAAACCGAGCCAGGGCCCAGGATCG
319 ATATAGAT-ATTCAAGGAGTCTTGACGC-AAAAATCATTCAAAACTGAGCC-GGGCCCAGGA--A
* * *
2340 CAT-TTTTTGCCAAAAACCGTGATGGTTAGTGCACGATTTCAGCTAAAATTTTGTAAAAA-TTAG
379 CATGTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTTA-
* * * *
2403 TCCGAAGTATTTTTCCTCAATTTTTAGTCACAATTACCATAGAAATATATAATTCAACATAAAAA
443 TCCGAAATATTTTTCCTCAATTTTTAGCCACAATTATCATAGAAATATATAATTCAACATCAAAA
* * * *
2468 AGATTGAAGGGTCGTTTATT-TTTCTTTTTAAAACATTAATTCTAATAAAATTG-AAACAGATTC
508 AGATTGAAGGGTCATTTATTCTTT-TTTTTAAAAAATTAATTCTAATAAAATCGAAAAAAGATTC
*
2531 TGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGA
572 TGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
2594 TATTTCAA
1 T-TTTCAA
2602 AAATCATGCA
Statistics
Matches: 1591, Mismatches: 253, Indels: 201
0.78 0.12 0.10
Matches are distributed among these distances:
634 5 0.00
635 4 0.00
636 133 0.08
637 92 0.06
638 6 0.00
639 3 0.00
640 8 0.01
641 6 0.00
642 3 0.00
643 7 0.00
644 193 0.12
645 162 0.10
646 208 0.13
647 82 0.05
648 62 0.04
649 37 0.02
650 14 0.01
651 380 0.24
652 20 0.01
653 3 0.00
654 1 0.00
656 1 0.00
660 1 0.00
662 1 0.00
664 1 0.00
666 44 0.03
667 11 0.01
668 92 0.06
669 11 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (634 bp):
TTTTCAAGGAGTCTTGGCGCCAAAAATCTTGCAAAACTGAGCCGGGCCTAAGAACGCATTTTTAG
CCAATATAGTGATTTTAGTACTCGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTT
TCCTCAATTTTTAGCCACAATAATCATAGAAATATATAATTCAACGTAAAAAAGATTGAAGATTT
TCATGCTCTAATATTGTTTTTCCATTTTTTATCTGAATTAATTTCTAATAAAATCGAAACAAGAT
TCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGAATATAGA
TATTCAAGGAGTCTTGACGCAAAAATCATTCAAAACTGAGCCGGGCCCAGGAACATGTTTTAGCC
AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTTATCCGAAATATTTT
TCCTCAATTTTTAGCCACAATTATCATAGAAATATATAATTCAACATCAAAAAGATTGAAGGGTC
ATTTATTCTTTTTTTTAAAAAATTAATTCTAATAAAATCGAAAAAAGATTCTGATGCTCGTAAAA
ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
Found at i:2715 original size:2 final size:2
Alignment explanation
Indices: 2708--2732 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2698 TACATTGTTT
2708 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2733 TATGATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22232 original size:22 final size:23
Alignment explanation
Indices: 22186--22238 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
22176 TATATCAATA
22186 ATCAATCAGTTTTGTCATGTTAT
1 ATCAATCAGTTTTGTCATGTTAT
*
22209 ATCAATTAGTTTTG-CGA-GTTAT
1 ATCAATCAGTTTTGTC-ATGTTAT
22231 ATCAATCA
1 ATCAATCA
22239 AAACGTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (23 bp):
ATCAATCAGTTTTGTCATGTTAT
Found at i:27087 original size:11 final size:11
Alignment explanation
Indices: 27067--27101 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
27057 TTGACAGCAC
27067 AACAAAAACAA
1 AACAAAAACAA
*
27078 AACGAAAACAA
1 AACAAAAACAA
27089 AACAAAAACAA
1 AACAAAAACAA
27100 AA
1 AA
27102 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:39486 original size:2 final size:2
Alignment explanation
Indices: 39479--39514 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39469 TAATGTTTGC
39479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39515 TTGGTATCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44319 original size:24 final size:24
Alignment explanation
Indices: 44236--44323 Score: 88
Period size: 24 Copynumber: 3.4 Consensus size: 24
44226 GTTGAAGGTT
44236 GTTTGAAGAAAATATGAAGGTTGA-A
1 GTTTGAAG-AAA-ATGAAGGTTGAGA
* *
44261 GGTTGAAGAAAATGAAGTAAAGATTAAGA
1 GTTTGAAGAAAATGAAG----G-TTGAGA
44290 GTTTGAAGAAAATGAAGGTTGAGA
1 GTTTGAAGAAAATGAAGGTTGAGA
44314 GTTTGAAGAA
1 GTTTGAAGAA
44324 GTTGTTAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
23 6 0.11
24 18 0.34
25 8 0.15
27 1 0.02
28 3 0.06
29 17 0.32
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (24 bp):
GTTTGAAGAAAATGAAGGTTGAGA
Done.