Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015187.1 Corchorus capsularis cultivar CVL-1 contig15208, 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: 33281
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:994 original size:335 final size:335
Alignment explanation
Indices: 1--3567 Score: 3019
Period size: 335 Copynumber: 10.6 Consensus size: 335
* *
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACATGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGA
* * * *
66 TCTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATTTTTCCTCAATTTTTGGCG-AAATCAA
66 TTTCGGCTAAAATTTTG-CAAAAACTGATCCGGAAAATTTTTCCTCAATTTTTGGCGAAAAT-AC
** * * * **
130 TCAGAAAAAAGTATATAATTCAACATAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCAAT
129 TCAGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGTT
* * * * *
195 TTT-CTAATATT-TT--AAAAA-AATTTCCGATTAGATGGAAACGAGATT-TAGATCCTCGTAAA
194 TTTCCTAAT-TTCTTACAAAAATAATTTCTGATTAAATCGAAACAAGATTCT-GATGCTCGT-AA
* * * * * * * *
254 AAAAATATCCTTAAATCAAATGTGACTGAGATTTGGTCAGATTAATAGAGATATTTCACGGATTC
256 AAACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* *
319 CTGGCGCCAAAAATG
321 TTGGCGCCAAAAATC
* * * * *
334 AAGCAAAATTGAGACGGGGACCCCGGAACACG-TTTTATG-CAAAAACCGTGATGGTTAGTACAC
1 ATGCAAAACTGAGCCGGAG-CTCCGGAACACGTTTTTA-GCCAAAAACCGTGATGGTTAGTACA-
* * * * * * *
397 A-ATTTCGACTGAAATTTTGAAAAAAATGA-CAC-GAAAATTATTTTCTCAATTTTTGGCCAGAA
63 AGATTTCGGCTAAAATTTTGCAAAAACTGATC-CGGAAAATT-TTTCCTCAATTTTTGGCGAAAA
* *
459 TACTCA-TAAAAA-TATATAATTCAATGCAACAAAA-CATTGAAGGGCTTCTCAAGCTTCTAATA
126 TACTCAGAAAAAAGTATATAATTCAACGCAA-AAAAGC-TTGAAGGGCTTCTCAAGCTTCTAATA
* * * * * * *
521 TTGTTTTTCTTAATTTATTAC-AAATTAATTTTTTATTAAATCGATACAACG-TTCTGATGCTCG
189 TCGTTTTTCCTAATTTCTTACAAAAATAATTTCTGATTAAATCGAAACAA-GATTCTGATGCTCG
* * * * * * *
584 TAAAAACACATCTTTAAATCCAATTTGGCTAAGACTTGGGTATATGAATATAGATATTTCAAGGA
253 TAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
649 GTCTTGGCGCCAAAAATC
318 GTCTTGGCGCCAAAAATC
* * * *
667 ATGCAAAACTGACCCGGAGCTCCGGAGCACATTTTTAGCCAAAAACCGTGATGGTTAGCACAAGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGA
* * * * * *
732 TTTCGGTTAAAATTTTGTGAAAAACTAATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
66 TTTCGGCTAAAATTTTG-CAAAAACTGATCCGGAAAATTTTTCCTCAATTTTTGGCGAAAATACT
* * * * * *
797 CAGAAAAAAGTATATAATTGAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCATTT
130 CAGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGTTT
* * * * *
862 TTCCT-ATTTCTTA-AAAAATATTTTCTGATTAGATGGAAACGAGATT-TAGATCCTCGTTAAAA
195 TTCCTAATTTCTTACAAAAATAATTTCTGATTAAATCGAAACAAGATTCT-GATGCTCG-TAAAA
* * * * * * * *
924 AAATATCCTTAAATCCAATGTGACTGAGATTTTGTTAGATTAATAGAGATATTTCACGGAATCCT
258 ACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
*
989 GGCGCCAAAAATG
323 GGCGCCAAAAATC
* * *
1002 AAGCAAAATTGAGCC-GAGGACCCCGGAACACG-TTTTATG-CAAAAACCGTGATGGTTAGTACA
1 ATGCAAAACTGAGCCGGA-G-CTCCGGAACACGTTTTTA-GCCAAAAACCGTGATGGTTAGTACA
* * * * * *
1064 CA-ATTTCGACTGAAATTTTGCAAAAATTGA-CCCGAAAATTATTTCCTCAATTTTTGGCCAGAA
63 -AGATTTCGGCTAAAATTTTGCAAAAACTGATCCGGAAAATT-TTTCCTCAATTTTTGGCGAAAA
* * * *
1127 TACTCATAAAATA-TATATAATTCAATGCAAAAAAACATTGAAGGGCTTCTCAAGCTTCTAATAT
126 TACTCAGAAAAAAGTATATAATTCAACGCAAAAAAGC-TTGAAGGGCTTCTCAAGCTTCTAATAT
* * * * * *
1191 TGTTTTTCTTAATTTCTTAC-CAATTAAATTT-TTATTAAATCGAAACAAGGTTCTGATGCTCGT
190 CGTTTTTCCTAATTTCTTACAAAAAT-AATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGT
* * * * * *
1254 AAAAACACATCTTTAAATCCAATTTGGCTAAGACTTGGGTAGATGAATATAGATATTTCAAGGAG
254 AAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
1319 TCTTGGCGCCAAAAATC
319 TCTTGGCGCCAAAAATC
* *
1336 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGA
* * * * *
1401 TTTCGGCTAAAATTTTGTGAAAAACTAATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
66 TTTCGGCTAAAATTTTG-CAAAAACTGATCCGGAAAATTTTTCCTCAATTTTTGGCGAAAATACT
* * * * * * * *
1466 CAGAAAAAAGTATATAATTGAACACAAAAAAGCTTGAAGGCCTTTTTACGCTTCTTATATCATTT
130 CAGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGTTT
* * * * * *
1531 TTCCT-ATTTTTTA-AAAAATTAATTTGTGATTAGATCGAAACGAGATTCAGATCCTCGTAAAAA
195 TTCCTAATTTCTTACAAAAA-TAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAAAAA
* * * * * * *
1594 AATATCCTTCAATCCAATGTGGCTGAGATTTGGTTAGATTAATAAATATATTTCATGGAGTCCTG
259 CATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
* *
1659 GTGCC-AAAATG
324 GCGCCAAAAATC
* * * * * * *
1670 AAGCAAAACTGAGTCGGGGACCCCGGAACACGTTTTTAGGCAAAAAACTGTGAT-G-AAGTACAC
1 ATGCAAAACTGAGCCGGAG-CTCCGGAACACGTTTTTA-GCCAAAAACCGTGATGGTTAGTACA-
** * ** * *
1733 A-ATTTTCTACTAAAATTTTGCAAAAACTGATCC-GAAAATTACTTCCTCAATTTTTTTCCACAA
63 AGA-TTTCGGCTAAAATTTTGCAAAAACTGATCCGGAAAATT-TTTCCTCAATTTTTGGCGAAAA
* **
1796 TACTCACAAAAAA-TATATAATTCAATC-CAAAAAATATTGAA-GGCTTCT-AA-----T-AT-T
126 TACTCAGAAAAAAGTATATAATTCAA-CGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATAT
* * * *
1850 -GTTTTTCTTAATTTCTTACCAAATTAATTTCTGATTAAATCGAAACAAGATTATGATGCTCGTA
190 CGTTTTTCCTAATTTCTTACAAAAATAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTA
* ** *
1914 AAAATCCTCATTTTGGTCAACCAGCCGTGGAGGCCACATCTTTAAATCCAATTTGTTTGAGAGTT
255 AAAA----CA------T-----A----T--------C--C-TTAAATCCAATGTGGCTGAGATTT
* * * * *
1979 GGGTATATGAATATAGATATTTTAAGGAGACTTGGTGCCAAAAATC
290 GGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATC
* * * * *
2025 ATGCAAAACTGAGGCAGAGCGCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTA-AACC
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAA-G
* **** *** *
2089 ATTTCGGCTAAAATTTTGCAAAAACTGA-CCAGAAAAAAAAAATCCTCTGCTTTTGGCAAAAATA
65 ATTTCGGCTAAAATTTTGCAAAAACTGATCC-G-GAAAATTTTTCCTCAATTTTTGGCGAAAATA
* * * *** *
2153 CTCATAAAAAAAG-AAATAATTCAATGCAAAAATTATTGAAGGGCTTCTCAAGGTTCTAATATCG
128 CTCA-GAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCG
* * * * * **
2217 ---TTCTTAATTTCATACCAAATTAATTTCTGATTAAATCGAAACGAGATTCTGATGCTCACAAA
192 TTTTTCCTAATTTCTTACAAAAATAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAAA
* * * *
2279 AACATATCCTTAAATCCAATTTGGCTGAGGTTTTGATAGATGAATATAGATATTTCAAGTG-GTC
257 AACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG-GAGTC
* * *
2343 TTGGTGTCAAAAAAC
321 TTGGCGCCAAAAATC
* **
2358 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCTAAAAACCGTGA----TACGTACGTG
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTA-GTACAAG
* * ** * *
2419 ATTTCGGCTAAAATTTTGGGAAAAACTTATCCGGAAGCTTTTACCTCAATTTCTGGCGAAAATAC
65 ATTTCGGCTAAAATTTT-GCAAAAACTGATCCGGAAAATTTTTCCTCAATTTTTGGCGAAAATAC
* * * * * * * *
2484 TCAGAAAATAGTGTTTAATTCAACACAAAATAGCTTGAAGGCCTTTTCACA-CTTCTTATATCGT
129 TCAGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCA-AGCTTCTAATATCGT
* * * * * * *
2548 TTTTCCT-ATTT-TTAAAAAAAATTAATTTGTGATTATATCTAAATAAGATTCAGATTCTCGTAA
193 TTTTCCTAATTTCTT-ACAAAAA-TAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAA
* * * * * *
2611 AAAAATATCCTTAAATCCAATGTGGTTGATATTTGGTTAGATTAATAAAGATATTTCACGGAGTC
256 AAACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * *
2676 CTGACACCAAAAATG
321 TTGGCGCCAAAAATC
* * * * * * *
2691 AAGCAAAACTAAGCCGGGGACCCCGGAACATGTTTTTATG-CAAAAACCGTGATTGTTAGTACAC
1 ATGCAAAACTGAGCCGGAG-CTCCGGAACACGTTTTTA-GCCAAAAACCGTGATGGTTAGTACAA
* * *
2755 GATTTCAGCTAAAATTTTGCAAAAACTGA-CCCGAAAATTATTTCCTCAATTTTTGGCGATAATA
64 GATTTCGGCTAAAATTTTGCAAAAACTGATCCGGAAAATT-TTTCCTCAATTTTTGGCGAAAATA
* * ** ** *
2819 CTCACAAAAAA-TATATAATTCAATGCAAAAAATATCAAAGGGCTTCTCAAGCTTCTAATATCAT
128 CTCAGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGT
* *
2883 TTTT-CTCAATTTCTTACCAAATTAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAAA
193 TTTTCCT-AATTTCTTACAAAAATAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAAA
* * * * * *
2947 AACACATCTTTAAATCCAATTTGGCTGAGACTTGGCTAGATGAATATAGATATATCAAGGAGTCT
257 AACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
*
3012 TGAG-GCCAAAAACC
322 TG-GCGCCAAAAATC
* * ** *
3026 ATGCAAAATTGAGTCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCACGATGGTTAGTACACGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGA
* ** * * * *
3091 TTTCGGCTAAAATTTTGCAAAAACTGACCCCAAAAAAAATTTTCCTCAACTTTTGTCCAAAATAC
66 TTTCGGCTAAAATTTTGCAAAAACTGA-TCC-GGAAAATTTTTCCTCAATTTTTGGCGAAAATAC
* * *** *
3156 TCATAAAAAAAG-ATATAATTCAATGCAAAAATTATTGAAGGGCTTCTCAAGGTTCTAATATCGT
129 TCA-GAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGT
* * * ** * *
3220 TTTTCTTAATTT-TATACCAAATTAATTTCTGATTAAATCGAATTAAGATTCTGATACTCATAAA
193 TTTTCCTAATTTCT-TACAAAAATAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAAA
* * * * *
3284 AGCATATCCTTAAATCCAATTTGGCTGAGATTTGGGTAGATGAATATAGATATTTTAAGGGGTCT
257 AACATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
*
3349 TGGTGCCAAAAATC
322 TGGCGCCAAAAATC
* * ** *
3363 ATGCAAAACTGAGTCGGAGCTCCGGAACACGGTTTTAGTAAAAAACCGTGATGGTTAGTACACGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGA
* ** ** **** * * *
3428 TTTCGGCTAAAATTTTGTAAAAA-TTTTACCCAAAAAAAACTCCTCTATTTTTGGCTACAATACT
66 TTTCGGCTAAAATTTTGCAAAAACTGAT-CCGGAAAATTTTTCCTCAATTTTTGGCGAAAATACT
* * * ** *
3492 CA-TAAAAA-TATATCATTCAATGCAAAAAATATTGAAGGGCTTCTCAAGCTTCTAATATCGCTT
130 CAGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGTTT
*
3555 TTCTTAATTTCTT
195 TTCCTAATTTCTT
3568 GATGCTCGTA
Statistics
Matches: 2583, Mismatches: 507, Indels: 288
0.76 0.15 0.09
Matches are distributed among these distances:
323 7 0.00
324 46 0.02
325 5 0.00
326 1 0.00
328 1 0.00
329 8 0.00
330 93 0.04
331 59 0.02
332 62 0.02
333 537 0.21
334 479 0.19
335 580 0.22
336 150 0.06
337 285 0.11
338 3 0.00
339 1 0.00
343 1 0.00
344 1 0.00
348 1 0.00
351 1 0.00
353 18 0.01
354 92 0.04
355 44 0.02
356 33 0.01
357 7 0.00
358 2 0.00
359 2 0.00
363 60 0.02
364 2 0.00
365 1 0.00
366 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (335 bp):
ATGCAAAACTGAGCCGGAGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGA
TTTCGGCTAAAATTTTGCAAAAACTGATCCGGAAAATTTTTCCTCAATTTTTGGCGAAAATACTC
AGAAAAAAGTATATAATTCAACGCAAAAAAGCTTGAAGGGCTTCTCAAGCTTCTAATATCGTTTT
TCCTAATTTCTTACAAAAATAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTAAAAACA
TATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC
GCCAAAAATC
Found at i:1379 original size:669 final size:666
Alignment explanation
Indices: 1--3450 Score: 3526
Period size: 669 Copynumber: 5.1 Consensus size: 666
*
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACATGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
* *
66 TCTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATTTTTCCTCAATTTTTGGCG-AAATCAA
66 TTTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAAT-AA
* *
130 TCAGAAAAAAGTATATAATTCAACATAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCAAT
130 TCAGAAAAAAGTATATAATTCAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCATT
* *
195 TTT-CTAATATT-TT-AAAAA-AATTTCCGATTAGATGGAAACGAGATTTAGATCCTCGTAAAAA
195 TTTCCT-AT-TTCTTAAAAAATAATTTCTGATTAGATCGAAACGAGATTTAGATCCTCGT-AAAA
* * * * *
256 AAATATCCTTAAATCAAATGTGACTGAGATTTGGTCAGATTAATAGAGATATTTCACGGATTCCT
257 AAATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAATAGAGATATTTCAAGGAGTCCT
*
321 GGCGCCAAAAATGAAGCAAAATTGAGACGGGGACCCCGGAACACGTTTTATGCAAAAACCGTGAT
322 GGCGCCAAAAATGAAGCAAAATTGAG-CCGGGACCCCGGAACACGTTTTATGCAAAAACCGTGAT
* * * * *
386 GGTTAGTACACAATTTCGACTGAAATTTTGAAAAAAATGACACGAAAATTATTTTCTCAATTTTT
386 GGTTAGTACACAATTTCGACTAAAATTTTGCAAAAACTGACCCGAAAATTATTTCCTCAATTTTT
* *
451 GGCCAGAATACTCAT-AAAAATATATAATTCAATGCAACAAAACATTGAAGGGCTTCTCAAGCTT
451 GGCCAAAATACTCATAAAAAATATATAATTCAATGCAAAAAAACATTGAAGGGCTTCTCAAGCTT
* * * *
515 CTAATATTGTTTTTCTTAATTTATTACAAATTAATTTTTTATTAAATCGATACAACG-TTCTGAT
516 CTAATATTGTTTTTCTTAATTT-TTACCAATTAATTTCTGATTAAATCGAAACAA-GATTCTGAT
* *
579 GCTCGTAAAAACACATCTTTAAATCCAATTTGGCTAAGACTTGGGTATATGAATATAGATATTTC
579 GCTCGTAAAAACACATCTTTAAATCCAATTTGGCTGAGACTTGGGTAGATGAATATAGATATTTC
644 AAGGAGTCTTGGCGCCAAAAATC
644 AAGGAGTCTTGGCGCCAAAAATC
* * * *
667 ATGCAAAACTGACCCGGAGCTCCGGAGCACATTTTTAGCCAAAAACCGTGATGGTTAGCACAAGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
* *
732 TTTCGGTTAAAATTTTGTGAAAAACTAATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
66 TTTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
*
797 CAGAAAAAAGTATATAATTGAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCATTT
131 CAGAAAAAAGTATATAATTCAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCATTT
* *
862 TTCCTATTTCTTAAAAAATATTTTCTGATTAGATGGAAACGAGATTTAGATCCTCGTTAAAAAAA
196 TTCCTATTTCTTAAAAAATAATTTCTGATTAGATCGAAACGAGATTTAGATCCTCG-TAAAAAAA
* * * *
927 TATCCTTAAATCCAATGTGACTGAGATTTTGTTAGATTAATAGAGATATTTCACGGAATCCTGGC
260 TATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAATAGAGATATTTCAAGGAGTCCTGGC
992 GCCAAAAATGAAGCAAAATTGAGCCGAGGACCCCGGAACACGTTTTATGCAAAAACCGTGATGGT
325 GCCAAAAATGAAGCAAAATTGAGCCG-GGACCCCGGAACACGTTTTATGCAAAAACCGTGATGGT
* *
1057 TAGTACACAATTTCGACTGAAATTTTGCAAAAATTGACCCGAAAATTATTTCCTCAATTTTTGGC
389 TAGTACACAATTTCGACTAAAATTTTGCAAAAACTGACCCGAAAATTATTTCCTCAATTTTTGGC
* *
1122 CAGAATACTCATAAAATATATATAATTCAATGCAAAAAAACATTGAAGGGCTTCTCAAGCTTCTA
454 CAAAATACTCATAAAAAATATATAATTCAATGCAAAAAAACATTGAAGGGCTTCTCAAGCTTCTA
* *
1187 ATATTGTTTTTCTTAATTTCTTACCAATTAAATTT-TTATTAAATCGAAACAAGGTTCTGATGCT
519 ATATTGTTTTTCTTAATTT-TTACCAATT-AATTTCTGATTAAATCGAAACAAGATTCTGATGCT
*
1251 CGTAAAAACACATCTTTAAATCCAATTTGGCTAAGACTTGGGTAGATGAATATAGATATTTCAAG
582 CGTAAAAACACATCTTTAAATCCAATTTGGCTGAGACTTGGGTAGATGAATATAGATATTTCAAG
1316 GAGTCTTGGCGCCAAAAATC
647 GAGTCTTGGCGCCAAAAATC
1336 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
*
1401 TTTCGGCTAAAATTTTGTGAAAAACTAATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
66 TTTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
* * *
1466 CAGAAAAAAGTATATAATTGAACACAAAAAAGCTTGAAGGCCTTTTTACGCTTCTTATATCATTT
131 CAGAAAAAAGTATATAATTCAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCATTT
* * *
1531 TTCCTATTTTTTAAAAAATTAATTTGTGATTAGATCGAAACGAGATTCAGATCCTCGTAAAAAAA
196 TTCCTATTTCTTAAAAAA-TAATTTCTGATTAGATCGAAACGAGATTTAGATCCTCGTAAAAAAA
* * * * *
1596 TATCCTTCAATCCAATGTGGCTGAGATTTGGTTAGATTAATAAATATATTTCATGGAGTCCTGGT
260 TATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAATAGAGATATTTCAAGGAGTCCTGGC
* * * *
1661 GCC-AAAATGAAGCAAAACTGAGTCGGGGACCCCGGAACACGTTTTTAGGCAAAAAACTGTGAT-
325 GCCAAAAATGAAGCAAAATTGAG-CCGGGACCCCGGAACACG-TTTTATGC-AAAAACCGTGATG
* * * *
1724 G-AAGTACACAATTTTCTACTAAAATTTTGCAAAAACTGATCCGAAAATTACTTCCTCAATTTTT
387 GTTAGTACACAA-TTTCGACTAAAATTTTGCAAAAACTGACCCGAAAATTATTTCCTCAATTTTT
** * * * *
1788 TTCCACAATACTCACAAAAAATATATAATTCAAT-CCAAAAAATATTGAA--G--------GCTT
451 GGCCAAAATACTCATAAAAAATATATAATTCAATGCAAAAAAACATTGAAGGGCTTCTCAAGCTT
*
1842 CTAATATTGTTTTTCTTAATTTCTTACCAAATTAATTTCTGATTAAATCGAAACAAGATTATGAT
516 CTAATATTGTTTTTCTTAATTT-TTACC-AATTAATTTCTGATTAAATCGAAACAAGATTCTGAT
**
1907 GCTCGTAAAAATCCTCATTTTGGTCAACCAGCCGTGGAGGCCACATCTTTAAATCCAATTTGTTT
579 GCTCG---------T-A--------AA--A-------A---CACATCTTTAAATCCAATTTGGCT
* * * * *
1972 GAGAGTTGGGTATATGAATATAGATATTTTAAGGAGACTTGGTGCCAAAAATC
614 GAGACTTGGGTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATC
* * * * *
2025 ATGCAAAACTGAGGCAGAGCGCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTAAACCA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
* * * **** ** *
2090 TTTCGGCTAAAATTTTG-CAAAAACTGA-CCAGAAAAAAAAAATCCTCTGCTTTT-GGCAAAAAT
66 TTTCGGCTAAAATTTTGTGAAAAACTGATCC-G-GAAGATTTTTCCTC-AATTTTGGGCGAAAAT
* * * ** *** * * * *
2152 ACTCATAAAAAAAG-AAATAATTCAATGCAAAAATTATTGAAGGGCTTCTCAAGGTTCTAATATC
128 AATCA-GAAAAAAGTATATAATTCAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATC
* * * * * * * * **
2216 GTTCTT--AATTTCATACCAAATTAATTTCTGATTAAATCGAAACGAGATTCT-GATGCTCACAA
192 ATTTTTCCTATTTCTTA-AAAAATAATTTCTGATTAGATCGAAACGAGATT-TAGATCCTCGTAA
* * * * * * *
2278 AAACATATCCTTAAATCCAATTTGGCTGAGGTTTTGATAGATGAATATAGATATTTCAAGTG-GT
255 AAAAATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAATAGAGATATTTCAAG-GAGT
* * * ** * * *
2342 CTTGGTGTCAAAAAACATGCAAAACTGAGCC-GGAGCTCCGGAACACGTTTT-TAGCTAAAAACC
319 CCTGGCGCCAAAAATGAAGCAAAATTGAGCCGGGA-CCCCGGAACACGTTTTAT-GC-AAAAACC
*** * * * * ** *
2405 GTGA----TACGTACGTGATTTCGGCTAAAATTTTGGGAAAAACTTATCCGGAAGCTT-TTACCT
381 GTGATGGTTA-GTACACAATTTCGACTAAAATTTT-GCAAAAACTGA-CCCGAAAATTATTTCCT
* * * * * * ** * * *
2465 CAATTTCTGGCGAAAATACTCAGAAAATAGTGTTTAATTCAACACAAAATAGC-TTGAAGGCCTT
443 CAATTTTTGGCCAAAATACTCATAAAA-AATATATAATTCAATGCAAAAAAACATTGAAGGGCTT
* * * * ** * * * *
2529 TTCACA-CTTCTTATATCGTTTTTCCT-ATTTTTAAAAAAAATTAATTTGTGATTATATCTAAAT
507 CTCA-AGCTTCTAATATTGTTTTTCTTAATTTTT---ACCAATTAATTTCTGATTAAATCGAAAC
* * * * * * * * * * *
2592 AAGATTCAGATTCTCGTAAAAAAATATCCTTAAATCCAATGTGGTTGATATTTGGTTAGATTAAT
568 AAGATTCTGATGCTCGTAAAAACACATCTTTAAATCCAATTTGGCTGAGACTTGGGTAGATGAAT
* * * * * *
2657 AAAGATATTTCACGGAGTCCTGACACCAAAAATG
633 ATAGATATTTCAAGGAGTCTTGGCGCCAAAAATC
* * * * ** *
2691 AAGCAAAACTAAGCCGGGGACCCCGGAACATGTTTTTATG-CAAAAACCGTGATTGTTAGTACAC
1 ATGCAAAACTGAGCCGGAG-CTCCGGAACACATTTTTA-GCCAAAAACCGTGATGGTTAGTACAC
* * * * * *
2755 GATTTCAGCTAAAATTTTG-CAAAAACTGA-CCCGAAAATTATTTCCTCAATTTTTGGCGATAAT
64 GATTTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATT-TTTCCTCAATTTTGGGCGAAAAT
* * ** ** ** * * *
2818 ACTCACAAAAAA-TATATAATTCAATGCAAAAAATATCAAAGGGCTTCTCAAGCTTCTAATATCA
128 AATCAGAAAAAAGTATATAATTCAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCA
* * * * * *
2882 TTTTTCTCAATTTCTTACCAAATTAATTTCTGATTAAATCGAAACAAGATTCT-GATGCTCGTAA
193 TTTTTC-CTATTTCTTA-AAAAATAATTTCTGATTAGATCGAAACGAGATT-TAGATCCTCGTAA
* * * * * * * * *
2946 AAACACATCTTTAAATCCAATTTGGCTGAGACTTGGCTAGATGAATATAGATATATCAAGGAGTC
255 AAAAATATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAATAGAGATATTTCAAGGAGTC
* ** * * *
3011 TTGAG-GCCAAAAACCATGCAAAATTGAGTC-GGAGCTCCGGAACACGTTTT-TAGCCAAAAACC
320 CTG-GCGCCAAAAATGAAGCAAAATTGAGCCGGGA-CCCCGGAACACGTTTTAT-G-CAAAAACC
** * * * **
3073 ACGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCCAAAAAAAATTTTCCTC
381 GTGATGGTTAGTACACAATTTCGACTAAAATTTTGCAAAAACTGA-CCCGAAAATTA-TTTCCTC
* * * **
3138 AACTTTTGTCCAAAATACTCATAAAAAAAGATATAATTCAATGC-AAAAATTATTGAAGGGCTTC
444 AATTTTTGGCCAAAATACTCAT-AAAAAATATATAATTCAATGCAAAAAAACATTGAAGGGCTTC
* * **
3202 TCAAGGTTCTAATATCGTTTTTCTTAATTTTATACCAAATTAATTTCTGATTAAATCGAATTAAG
508 TCAAGCTTCTAATATTGTTTTTCTTAATTTT-TACC-AATTAATTTCTGATTAAATCGAAACAAG
* * * * * *
3267 ATTCTGATACTCATAAAAGCATATCCTTAAATCCAATTTGGCTGAGATTTGGGTAGATGAATATA
571 ATTCTGATGCTCGTAAAAACACATCTTTAAATCCAATTTGGCTGAGACTTGGGTAGATGAATATA
* * *
3332 GATATTTTAAGGGGTCTTGGTGCCAAAAATC
636 GATATTTCAAGGAGTCTTGGCGCCAAAAATC
* ** **
3363 ATGCAAAACTGAGTCGGAGCTCCGGAACACGGTTTTAGTAAAAAACCGTGATGGTTAGTACACGA
1 ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
3428 TTTCGGCTAAAATTTTGT-AAAAA
66 TTTCGGCTAAAATTTTGTGAAAAA
3451 TTTTACCCAA
Statistics
Matches: 2370, Mismatches: 313, Indels: 197
0.82 0.11 0.07
Matches are distributed among these distances:
658 37 0.02
659 32 0.01
665 65 0.03
666 275 0.12
667 80 0.03
668 459 0.19
669 551 0.23
670 64 0.03
671 88 0.04
672 182 0.08
673 9 0.00
674 1 0.00
676 1 0.00
677 2 0.00
678 2 0.00
679 1 0.00
684 15 0.01
685 39 0.02
686 43 0.02
687 119 0.05
688 29 0.01
689 207 0.09
690 11 0.00
694 2 0.00
695 4 0.00
696 51 0.02
697 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (666 bp):
ATGCAAAACTGAGCCGGAGCTCCGGAACACATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
TTTCGGCTAAAATTTTGTGAAAAACTGATCCGGAAGATTTTTCCTCAATTTTGGGCGAAAATAAT
CAGAAAAAAGTATATAATTCAACACAAAAAAGCTTGAAGGGCTTTTCACGCTTCTTATATCATTT
TTCCTATTTCTTAAAAAATAATTTCTGATTAGATCGAAACGAGATTTAGATCCTCGTAAAAAAAT
ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAATAGAGATATTTCAAGGAGTCCTGGCG
CCAAAAATGAAGCAAAATTGAGCCGGGACCCCGGAACACGTTTTATGCAAAAACCGTGATGGTTA
GTACACAATTTCGACTAAAATTTTGCAAAAACTGACCCGAAAATTATTTCCTCAATTTTTGGCCA
AAATACTCATAAAAAATATATAATTCAATGCAAAAAAACATTGAAGGGCTTCTCAAGCTTCTAAT
ATTGTTTTTCTTAATTTTTACCAATTAATTTCTGATTAAATCGAAACAAGATTCTGATGCTCGTA
AAAACACATCTTTAAATCCAATTTGGCTGAGACTTGGGTAGATGAATATAGATATTTCAAGGAGT
CTTGGCGCCAAAAATC
Found at i:4385 original size:9 final size:9
Alignment explanation
Indices: 4367--4395 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4357 AATAAAGTAA
4367 ATATAT-AT
1 ATATATAAT
4375 ATATATAAT
1 ATATATAAT
4384 ATATATAAT
1 ATATATAAT
4393 ATA
1 ATA
4396 AGTCAGAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATAAT
Found at i:11881 original size:6 final size:6
Alignment explanation
Indices: 11872--11898 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11862 TCTTACATAC
11872 GGATTT GGATTT GGATTT GGATTT GGA
1 GGATTT GGATTT GGATTT GGATTT GGA
11899 AGCTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (6 bp):
GGATTT
Found at i:12903 original size:22 final size:22
Alignment explanation
Indices: 12873--12915 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12863 CGGGACGGCC
*
12873 TGCCCTGGCTAAGCCGCCCTCA
1 TGCCCTGGCGAAGCCGCCCTCA
*
12895 TGCCGTGGCGAAGCCGCCCTC
1 TGCCCTGGCGAAGCCGCCCTC
12916 TTGGGACGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.44, G:0.28, T:0.16
Consensus pattern (22 bp):
TGCCCTGGCGAAGCCGCCCTCA
Found at i:13920 original size:5 final size:5
Alignment explanation
Indices: 13910--13955 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
13900 TTAATGTCAC
13910 GTATG GTATG GTATG GTATG GTATG GTATG GTATG GTATG GTATG G
1 GTATG GTATG GTATG GTATG GTATG GTATG GTATG GTATG GTATG G
13956 GCATCATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (5 bp):
GTATG
Found at i:15099 original size:2 final size:2
Alignment explanation
Indices: 15081--15160 Score: 81
Period size: 2 Copynumber: 40.5 Consensus size: 2
15071 GCCGGTTTTA
* * * * *
15081 AT AT CT AT AT CT AT AT AT AT AT AT AT GT AC GT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
15122 AT AT AT AT AT AT TT TT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15161 AGAGCTGATG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:15258 original size:2 final size:2
Alignment explanation
Indices: 15251--15280 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15241 AATACATAAG
15251 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15281 GAACGGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17070 original size:2 final size:2
Alignment explanation
Indices: 17063--17089 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17053 TAATCAGAAG
17063 TA 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 TA T
17090 TCTGTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25378 original size:48 final size:48
Alignment explanation
Indices: 25307--25402 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
25297 TAATGTAATT
25307 TAATGAACAAATTTAAAGGAGAAGAAAATTTGTTTTGTGAATCCAGTA
1 TAATGAACAAATTTAAAGGAGAAGAAAATTTGTTTTGTGAATCCAGTA
25355 TAATGAACAAATTTAAAGGAGAAGAAAATTTGTTTTGTGAATCCAGTA
1 TAATGAACAAATTTAAAGGAGAAGAAAATTTGTTTTGTGAATCCAGTA
25403 ATACTTTTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (48 bp):
TAATGAACAAATTTAAAGGAGAAGAAAATTTGTTTTGTGAATCCAGTA
Found at i:26803 original size:5 final size:5
Alignment explanation
Indices: 26793--26819 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
26783 TATGAGGGAT
26793 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
26820 ACTGTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:27235 original size:3 final size:3
Alignment explanation
Indices: 27227--27276 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
27217 TGTTCCTTTA
* *
27227 TAT TAT TAT TAT TAT TTT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27275 TA
1 TA
27277 CTAGACAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28665 original size:2 final size:2
Alignment explanation
Indices: 28647--28685 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
28637 TATGGTTCTT
28647 TA TA T- TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28686 CTACATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30602 original size:3 final size:3
Alignment explanation
Indices: 30596--30668 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
30586 GTTGTTGTTG
*
30596 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30643 TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
30669 CAGACTCTCA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:32916 original size:13 final size:13
Alignment explanation
Indices: 32898--32930 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
32888 TTGGAAAAAG
32898 TGCTTTTGAGAAA
1 TGCTTTTGAGAAA
*
32911 TGCTTTTGAGAAG
1 TGCTTTTGAGAAA
32924 TGCTTTT
1 TGCTTTT
32931 TTAAATTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.45
Consensus pattern (13 bp):
TGCTTTTGAGAAA
Done.