Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010504.1 Corchorus capsularis cultivar CVL-1 contig10525, 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: 28714
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1343 original size:667 final size:662
Alignment explanation
Indices: 1--3310 Score: 4104
Period size: 667 Copynumber: 5.0 Consensus size: 662
* *
1 CGTTTTTAGCGAAAAAATCTATGATGGTTACTACACGATTTCTACTAAAATTTAGCAAAAAAATT
1 CGTTTTTAGCG-AAAAA-CTGTGATGGTTACTACACGATTTCGACTAAAATTTAG-AAAAAAATT
* * *
66 GACCCGAAAAATTTTCCCTCAATTTTT-TCCAAAATACTCATTTAAAATTTATAATTCAAGGCCA
63 GACCCG-AAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCA
* * *
130 AAAAGAAAGAAGGGTTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAATTAATTTCT
127 AAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCT
* *
195 AATTAAATAGAAACTGGTTTCTGATGCTCGAATAAAAAAATCCTTATGTCCAACGTGGCTTAGAT
192 AATTAAATCGAAACTGGTTTCTGATGCTCGAA-AAAAAAATCCTTATGTCCAATGTGGCTTAGAT
* *
260 TTGGCTT-CTGGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAGT-ATGCAAAAAAGAGCT
256 TTGG-TTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAA-TCATGCAAAACAGAGCT
* * *
323 GGGTCCCCGGAACACGTTTTTAGCGAAAAACTATGATGGTTACTACACGATTTCGACTAAAATTT
319 GGGT-CCCGGAACGCATTTTTAGCGAAAAACTATGAT-GATACTACACGATTTCGACTAAAATTT
*
388 AGCAAAAAATTGACACG-AAAAATTTTCCCTCAATTTTT-GCCAAAATACTCATTGAAAATTTAT
382 AGCAAAAAATTGACCCGAAAAAATTTT-CCTCAATTTTTGGCCAAAATACTCATTGAAAATTTAT
* * * * *
451 AATTCAAGGCCAAAAAGAAAGAAGGGCTTTTGACGCTTCTAATTTTGTTTTTCCTATATTTTTCT
446 AATTCAAGGCCAAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCC
* ** **
516 GAATTAATTTCTAATTAAATCGAAACTGATTTCTGATGCTCGAAAAAAAAATATTTATGTCCATT
511 GAATTAATTTCTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAAC
* * *
581 GTGGCTTAGATTTGGCTACTCGAATATAGATATTTCAAAGAGTCTTGACGCCAAAAATCATGCTA
576 GTGGCTTAGATTTGGCTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
*
646 AACAGAGCTGGGTCACCGGAACG
641 AACAGAGCTGGGGC-CCGGAACG
* * * *
669 GGTTTTTAGCGAAAAACTGTGATAGTTACTACACGATTTCGACAAAAATTTTGTAAAAAAATT-A
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAG-AAAAAAATTGA
* ***
733 TCCGTAAAATTTTTCCTCAATTTTTAGAAAAAAAATACTCATTGAAAATTTATAATTCAAGGCCA
65 CCCG-AAAATTTTTCCTCAATTTTT-G-GCCAAAATACTCATTGAAAATTTATAATTCAAGGCCA
* *
798 AAAAGAATGAAGGGCTTGTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATGTCT
127 AAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCT
863 AATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATT
192 AATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATT
* * * * *
928 TGGCTACTCGAATATAGATATTTCAAGGAGTCGTGGCACCAAAAATCATGTAAAACATAGCTGAG
257 TGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCTG-G
** * * * *
993 GTATCGGAATGTATTTTTAGCGAAAAACTGTGATGATGCTACACGATTTCGACTAAAATTTAGCA
321 GTCCCGGAACGCATTTTTAGCGAAAAACTATGATGATACTACACGATTTCGACTAAAATTTAGCA
*
1058 AAAAATTTACCCGAAAAAATTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTC
386 AAAAATTGACCCGAAAAAATTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTC
* *
1123 AAGGCCCAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATG-TTTTCCGGATT
451 AAGGCCAAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAATT
* * * * *
1187 TATTTGTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAGAAATCCTTATGTCCAATGTTGC
516 AATTTCTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAACGTGGC
* * * * **
1252 TTAGATATGGCTACT-GAAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCTTACAAAATT
581 TTAGATTTGGCTACTCG-AATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACA
* *
1316 GAGCCGGGGGCTCCAGAACG
645 GAG-CTGGGGC-CCGGAACG
* * * * *
1336 CGTTTTTAACGAAAAAGTGTGATGGTTACTACACAATTTCGACTAAAAATTTTGTAAAAAATTGA
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACT-AAAATTTAGAAAAAAATTGA
* * *
1401 TCCGAAATGTTTTTCCTCAATATTTT-GCTAAAATACTCATTGAAAATTTATAATTCAAGGCCAA
65 CCCGAAA-ATTTTTCCTCAAT-TTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAA
* * * * *
1465 AAAGATTGAAGGGCTTTTCACGCTTC-AAGTTTCATTTTTCTTAT-CTTTTCTGAATTAATTTCT
128 AAAGAATGAAGGGCTTTTCACGCTTCTAA-TTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCT
* * * *
1528 AATTAAATCGAAACTGGTTTCTGATGCTCG-AAAACAAATCCTTATGTCCAATTTGACTTAGATA
192 AATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATT
* *
1592 TGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGTCGAAAATCATGCAAAACAGAG-TCGG
257 TGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCT-GG
* * * * * *
1656 GGCCCTAGAACGCGTTTCTAGCGAAAAACTATGATAAT-CTACACAATTTCGACTAAAATTTAGC
321 GTCCC-GGAACGCATTTTTAGCGAAAAACTATGATGATACTACACGATTTCGACTAAAATTTAGC
* * * *
1720 AAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTTGCCAAAAAACTCATTGAAAGTTTATAATT
385 AAAAAATTGACCCGAAAAAATTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATT
*
1785 CAAGGCCCAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAAT
450 CAAGGCCAAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAAT
* *
1850 TAATTTCTAATTAAATCGAAACTTGTTTCTGATGCTCGAATAAAAAAATCCTTATGTCCGACGTG
515 TAATTTCTAATTAAATCGAAACTGGTTTCTGATGCTCGAA-AAAAAAATCCTTATGTCCAACGTG
* * * *
1915 GCTTAGATTTGGCTTCTCG-ATATAGATATTTCAAGGAGTCTTGGCGCCAGAAATTATGCAAAAA
579 GCTTAGATTTGGCTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
*
1979 AGAGCTGGGTCCCCGGAACG
644 AGAGCTGGG-GCCCGGAACG
* * * *
1999 CGTTTTTAGCGAAAAACTATGATGGTTACTACACGATTTCTACTAAAATTTAGCAAAAAGTTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGAAAAAAATTGAC
*
2064 CCGAAAAATTTTCCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
66 CCG-AAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
2129 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCTAAT
130 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCTAAT
*
2194 TAAATTGAAACTGGTTTCTGATGCTCGAAAAAAAATATCCTTATGTCCAATGTGGCTTAGATTTG
195 TAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAA-ATCCTTATGTCCAATGTGGCTTAGATTTG
* * * *
2259 ATTACTTGAATATAGATATTTCAAGGTGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGAG-
259 GTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCTGG-GT
* *
2323 CCTCGGAATGCATTTTTAGCGAAAAACTGTGATGATTACTACACGATTTCGACTAAAATTTAGCA
323 CC-CGGAACGCATTTTTAGCGAAAAACTATGATGA-TACTACACGATTTCGACTAAAATTTAGCA
* *
2388 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTCAAAATTTATAATTC
386 AAAAATTGACCCGAAAAAATTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTC
* *
2453 AAGGCCAAAAAGAACGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATT
451 AAGGCCAAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAATT
* *
2518 AATTTCTAATTAAATTGAAACTGGTTTCTGATGCTCGAAAAAAAAATCATTATGTCCAACGTGGC
516 AATTTCTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAACGTGGC
** * *
2583 TTAGATTTGATTTCTTGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAG
581 TTAGATTTGGCTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAG
* * *
2648 AGCCGAGGCCCTGGAACT
646 AGCTGGGGCCC-GGAACG
** * * *
2666 TATTTTTAGCGAAAAACTGTGATGATTACTACACAATTTCGACTAAAA-TTAGCAAAAAATTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGAAAAAAATTGAC
* * * * *
2730 CCGAGAAATTTTTACTCAAATTTTGGCCAAAATACTCA-TAAAAATATATAATTCAATGCCAAAA
66 CCGA-AAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
* * * ** * * * ** * *
2794 A-AGTTAAAGGGCTTTTCGCATTTTTAATATCG-TTTTCCTATCTTTTT-TTAATTAATTTTTAT
130 AGA-ATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCTAA
* * * * *
2856 TTAAATCGAAACTGGTTTCCGATGCTCGAAAAAACTAATCCTTATAAT-CAATGTGGCTGAAATT
194 TTAAATCGAAACTGGTTTCTGATGCTCGAAAAAA-AAATCCTTAT-GTCCAATGTGGCTTAGATT
* * * * * * * * * * *
2920 TGGTTAGTTGTATATTGATATTTCAAGGAGTTTTTGTGTCAAAAATCAT-CTGAAACTGAGTCGG
257 TGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGC-AAAACAGAG-CTG
* * * * * * * * * * *
2984 GGCCCCGGTTA-GCGTTTTTAGCCAAATACTGTAATGGTTAGTACACGATTTCGGCTAAAATTTT
320 GGTCCCGG-AACGCATTTTTAGCGAAAAACTATGAT-GATACTACACGATTTCGACTAAAATTTA
* * * * * * ** *
3048 TCAAAAAACTGACTCAAAAAAATTTTTCCTCAA-TTTTAGCCTACAATACTCA-AAATAAATATA
383 GCAAAAAATTGACCCGAAAAAA-TTTTCCTCAATTTTTGGCC-AAAATACTCATTGA-AAATTTA
* * * ** ** *
3111 TAATTAAATGCAAAAAAGGTTGAAGGATTTTTCACGCTTCT-ATTATCGTTTTTCTTATGTTTTT
445 TAATTCAAGGCCAAAAAGAATGAAGGGCTTTTCACGCTTCTAATT-TCGTTTTTCCTATGTTTTT
* * * * *
3175 TCGAATTAATTTCTAATTAAATTGAAACTGGTTTCTGATTCTCGAAAAAACAAATTCTTATATCC
509 CCGAATTAATTTCTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAA-AAATCCTTATGTCC
* * *** * * * *
3240 AATGTGGCTGAGATTTCATTAGAT-GAATATAGATATTTCAAGGAGTCTCGACG-CAAAACAACA
573 AACGTGGCTTAGATTTGGCTA-CTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAA-ATCA
3303 TGCAAAAC
636 TGCAAAAC
3311 TGAGACGGGG
Statistics
Matches: 2319, Mismatches: 273, Indels: 103
0.86 0.10 0.04
Matches are distributed among these distances:
661 4 0.00
662 107 0.05
663 431 0.19
664 356 0.15
665 328 0.14
666 382 0.16
667 544 0.23
668 163 0.07
669 4 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (662 bp):
CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGAAAAAAATTGAC
CCGAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAAA
GAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCTAATT
AAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATTTGGT
TACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCTGGGTCCC
GGAACGCATTTTTAGCGAAAAACTATGATGATACTACACGATTTCGACTAAAATTTAGCAAAAAA
TTGACCCGAAAAAATTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGC
CAAAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAATTAATTT
CTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAACGTGGCTTAGA
TTTGGCTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCTG
GGGCCCGGAACG
Found at i:1546 original size:334 final size:332
Alignment explanation
Indices: 1--3320 Score: 4163
Period size: 333 Copynumber: 10.0 Consensus size: 332
* *
1 CGTTTTTAGCGAAAAAATCTATGATGGTTACTACACGATTTCTACTAAAATTTAGCAAAAAAATT
1 CGTTTTTAGCG-AAAAA-CTGTGATGGTTACTACACGATTTCGACTAAAATTTAGC-AAAAAATT
* * *
66 GACCCGAAAAATTTTCCCTCAATTTTT-TCCAAAATACTCATTTAAAATTTATAATTCAAGGCCA
63 GACCCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCA
* * *
130 AAAAGAAAGAAGGGTTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAATTAATTTCT
128 AAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCT
* *
195 AATTAAATAGAAACTGGTTTCTGATGCTCGAATAAAAAAATCCTTATGTCCAACGTGGCTTAGAT
193 AATTAAATCGAAACTGGTTTCTGATGCTCGAA-AAAAAAATCCTTATGTCCAATGTGGCTTAGAT
* * *
260 TTGGCTTCTGGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAGT-ATGCAAAAAAGAGCTG
257 TTGGCTACT-GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAA-TCATGCAAAACAGAGCCG
* *
324 GGTCCCCGGAACA
320 GGGCCCCGGAACG
*
337 CGTTTTTAGCGAAAAACTATGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
* *
402 ACGAAAAATTTTCCCTCAATTTTT-GCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
66 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
* * * *
466 AGAAAGAAGGGCTTTTGACGCTTCTAATTTTGTTTTTCCTATATTTTTCTGAATTAATTTCTAAT
131 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAAT
* ** *
531 TAAATCGAAACTGATTTCTGATGCTCGAAAAAAAAATATTTATGTCCATTGTGGCTTAGATTTGG
196 TAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATTTGG
* * * * * *
596 CTACTCGAATATAGATATTTCAAAGAGTCTTGACGCCAAAAATCATGCTAAACAGAGCTGGGTCA
261 CTACT-GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGGCC
661 CCGGAACG
325 CCGGAACG
* * * * *
669 GGTTTTTAGCGAAAAACTGTGATAGTTACTACACGATTTCGACAAAAATTTTGTAAAAAAATT-A
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAG-CAAAAAATTGA
* * ***
733 TCCGTAAAATTTTTCCTCAATTTTTAGAAAAAAAATACTCATTGAAAATTTATAATTCAAGGCCA
65 CCCGAAAAATTTTTCCTCAATTTTT-G-GCCAAAATACTCATTGAAAATTTATAATTCAAGGCCA
* * *
798 AAAAGAATGAAGGGCTTGTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATGTCT
128 AAAAGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCT
863 AATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATT
193 AATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATT
* * * * * *
928 TGGCTACTCGAATATAGATATTTCAAGGAGTCGTGGCACCAAAAATCATGTAAAACATAGCTGAG
258 TGGCTACT-GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGG
*** *
993 GTATCGGAATG
322 GCCCCGGAACG
** * * *
1004 TATTTTTAGCGAAAAACTGTGAT-GATGCTACACGATTTCGACTAAAATTTAGCAAAAAATTTAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
* *
1068 CCGAAAAAATTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCCAAA
66 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
* * * *
1133 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATG-TTTTCCGGATTTATTTGTAAT
131 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAAT
* * *
1197 TAAATCGAAACTGGTTTCTGATGCTCGAAAAAGAAATCCTTATGTCCAATGTTGCTTAGATATGG
196 TAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATTTGG
* * * **
1262 CTACTGAAATATAGATATTTCAAGGACTCTTGGCGCCAAAAATCTTACAAAATTGAGCCGGGGGC
261 CTACTG-AATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCC-GGGGC
* *
1327 TCCAGAACG
324 CCCGGAACG
* * * * *
1336 CGTTTTTAACGAAAAAGTGTGATGGTTACTACACAATTTCGACTAAAAATTTTGTAAAAAATTGA
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACT-AAAATTTAGCAAAAAATTGA
* ** *
1401 TCCGAAATGTTTTTCCTCAATATTTT-GCTAAAATACTCATTGAAAATTTATAATTCAAGGCCAA
65 CCCGAAAAATTTTTCCTCAAT-TTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAA
* * * *
1465 AAAGATTGAAGGGCTTTTCACGCTTC-AAGTTTCATTTTTCTTAT-CTTTTCTGAATTAATTTCT
129 AAAGAATGAAGGGCTTTTCACGCTTCTAA-TTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCT
* * * *
1528 AATTAAATCGAAACTGGTTTCTGATGCTCG-AAAACAAATCCTTATGTCCAATTTGACTTAGATA
193 AATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATT
* * * *
1592 TGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGTCGAAAATCATGCAAAACAGAGTCGGG
258 TGGCTACT-GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGG
**
1657 GCCCTAGAACG
322 GCCCCGGAACG
* * ** *
1668 CGTTTCTAGCGAAAAACTATGAT-AAT-CTACACAATTTCGACTAAAATTTAGCAAAAAATTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
* * * *
1731 CCGAAAAATTTTTCCTCAATTTTTTGCCAAAAAACTCATTGAAAGTTTATAATTCAAGGCCCAAA
66 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
*
1796 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCCGAATTAATTTCTAAT
131 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAAT
* * *
1861 TAAATCGAAACTTGTTTCTGATGCTCGAATAAAAAAATCCTTATGTCCGACGTGGCTTAGATTTG
196 TAAATCGAAACTGGTTTCTGATGCTCGAA-AAAAAAATCCTTATGTCCAATGTGGCTTAGATTTG
* * * * * *
1926 GCTTCTCG-ATATAGATATTTCAAGGAGTCTTGGCGCCAGAAATTATGCAAAAAAGAGCTGGGTC
260 GCTACT-GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGGC
1990 CCCGGAACG
324 CCCGGAACG
* * *
1999 CGTTTTTAGCGAAAAACTATGATGGTTACTACACGATTTCTACTAAAATTTAGCAAAAAGTTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
*
2064 CCGAAAAATTTTCCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
66 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
*
2129 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCTAAT
131 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAAT
*
2194 TAAATTGAAACTGGTTTCTGATGCTCGAAAAAAAATATCCTTATGTCCAATGTGGCTTAGATTTG
196 TAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAA-ATCCTTATGTCCAATGTGGCTTAGATTTG
** * *
2259 ATTACTTGAATATAGATATTTCAAGGTGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGAGC
260 GCTAC-TGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGGC
* *
2324 CTCGGAATG
324 CCCGGAACG
* *
2333 CATTTTTAGCGAAAAACTGTGATGATTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
*
2398 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTCAAAATTTATAATTCAAGGCCAAAA
66 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
* *
2463 AGAACGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCAGAATTAATTTCTAAT
131 AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAAT
* * * *
2528 TAAATTGAAACTGGTTTCTGATGCTCGAAAAAAAAATCATTATGTCCAACGTGGCTTAGATTTGA
196 TAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATTTGG
* * *
2593 TTTCTTGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGAGGCC
261 CTAC-TGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGGCC
* *
2658 CTGGAACT
325 CCGGAACG
** * *
2666 TATTTTTAGCGAAAAACTGTGATGATTACTACACAATTTCGACTAAAA-TTAGCAAAAAATTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
* * * * * *
2730 CCGAGAAATTTTTACTCAAATTTTGGCCAAAATACTCA-TAAAAATATATAATTCAATGCCAAAA
66 CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
* * * ** * * * * * *
2794 A-AGTTAAAGGGCTTTTCGCATTTTTAATATCG-TTTTCCTATCTTTTT-TTAATTAATTTTTAT
131 AGA-ATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAA
* * * * *
2856 TTAAATCGAAACTGGTTTCCGATGCTCGAAAAAACTAATCCTTATAAT-CAATGTGGCTGAAATT
195 TTAAATCGAAACTGGTTTCTGATGCTCGAAAAAA-AAATCCTTAT-GTCCAATGTGGCTTAGATT
* * * * * * * * * * *
2920 TGGTTAGTTGTATATTGATATTTCAAGGAGTTTTTGTGTCAAAAATCAT-CTGAAACTGAGTCGG
258 TGGCTA-CTGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGC-AAAACAGAGCCGG
*
2984 GGCCCCGGTTA-G
321 GGCCCCGG-AACG
* * * * * ** *
2996 CGTTTTTAGCCAAATACTGTAATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAAACTGAC
1 CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
** * * ** * * * *
3061 TCAAAAAAATTTTTCCTCAA-TTTTAGCCTACAATACTCA-AAATAAATATATAATTAAATGCAA
66 -CCGAAAAATTTTTCCTCAATTTTTGGCC-AAAATACTCATTGA-AAATTTATAATTCAAGGCCA
** ** *
3124 AAAAGGTTGAAGGATTTTTCACGCTTCT-ATTATCGTTTTTCTTATGTTTTT-TCGAATTAATTT
128 AAAAGAATGAAGGGCTTTTCACGCTTCTAATT-TCGTTTTTCCTATGTTTTTCT-GAATTAATTT
* * * * *
3187 CTAATTAAATTGAAACTGGTTTCTGATTCTCGAAAAAACAAATTCTTATATCCAATGTGGCTGAG
191 CTAATTAAATCGAAACTGGTTTCTGATGCTCGAAAAAA-AAATCCTTATGTCCAATGTGGCTTAG
*** * * * * * *
3252 ATTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGACG-CAAAACAACATGCAAAACTGAGA
255 ATTTGGCTA-CTGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAA-ATCATGCAAAACAGAGC
3316 CGGGG
318 CGGGG
3321 GGGCCATGAA
Statistics
Matches: 2623, Mismatches: 320, Indels: 83
0.87 0.11 0.03
Matches are distributed among these distances:
328 4 0.00
329 152 0.06
330 195 0.07
331 272 0.10
332 422 0.16
333 670 0.26
334 538 0.21
335 358 0.14
336 12 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (332 bp):
CGTTTTTAGCGAAAAACTGTGATGGTTACTACACGATTTCGACTAAAATTTAGCAAAAAATTGAC
CCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCATTGAAAATTTATAATTCAAGGCCAAAA
AGAATGAAGGGCTTTTCACGCTTCTAATTTCGTTTTTCCTATGTTTTTCTGAATTAATTTCTAAT
TAAATCGAAACTGGTTTCTGATGCTCGAAAAAAAAATCCTTATGTCCAATGTGGCTTAGATTTGG
CTACTGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGCCGGGGCCC
CGGAACG
Found at i:5417 original size:1 final size:1
Alignment explanation
Indices: 5411--5438 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5401 CTATCGTATC
5411 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
5439 GGCGCTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7107 original size:2 final size:2
Alignment explanation
Indices: 7092--7128 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7082 CACATCGTTC
7092 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT 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
7129 ATAGCAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7702 original size:10 final size:10
Alignment explanation
Indices: 7687--7714 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
7677 CTATTTCTCG
7687 TGCCCCATTA
1 TGCCCCATTA
7697 TGCCCCATTA
1 TGCCCCATTA
7707 TGCCCCAT
1 TGCCCCAT
7715 CCACCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.43, G:0.11, T:0.29
Consensus pattern (10 bp):
TGCCCCATTA
Found at i:11770 original size:21 final size:21
Alignment explanation
Indices: 11746--11789 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11736 TAAAAGTGTA
* *
11746 AAAAATGGGGCGGTATTTAGC
1 AAAAATAGGGCAGTATTTAGC
*
11767 AAAACTAGGGCAGTATTTAGC
1 AAAAATAGGGCAGTATTTAGC
11788 AA
1 AA
11790 CCCCCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCAGTATTTAGC
Found at i:12075 original size:30 final size:29
Alignment explanation
Indices: 12006--12085 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
11996 GTAGCGTTTA
12006 GACGTTTTGTCCCCC-GAACTTCAATCTTG
1 GACGTTTTG-CCCCCTGAACTTCAATCTTG
* *
12035 GACATTTTGCCCCCTGAACTTCAATTTTGG
1 GACGTTTTGCCCCCTGAACTTCAATCTT-G
*
12065 GACGTTTTGCCCCCTCAACTT
1 GACGTTTTGCCCCCTGAACTT
12086 AACGGCTCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 5 0.11
29 20 0.44
30 20 0.44
ACGTcount: A:0.17, C:0.31, G:0.16, T:0.35
Consensus pattern (29 bp):
GACGTTTTGCCCCCTGAACTTCAATCTTG
Found at i:12311 original size:29 final size:30
Alignment explanation
Indices: 12265--12337 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
12255 GTTAGGTTGA
12265 GGGGGCAAAACGTCCCAAAATTAAAGTTCG
1 GGGGGCAAAACGTCCCAAAATTAAAGTTCG
* * *
12295 GGGGGCAAAATGT-CCAAGATTGAAGTTCG
1 GGGGGCAAAACGTCCCAAAATTAAAGTTCG
12324 GGGGGCAAAACGTC
1 GGGGGCAAAACGTC
12338 TAAACGCTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (30 bp):
GGGGGCAAAACGTCCCAAAATTAAAGTTCG
Found at i:12718 original size:17 final size:17
Alignment explanation
Indices: 12696--12732 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
12686 ATATCCCCTT
12696 ATTACTAAGGCCCCAAA
1 ATTACTAAGGCCCCAAA
12713 ATTACTAAGGCCCCAAA
1 ATTACTAAGGCCCCAAA
12730 ATT
1 ATT
12733 TAAGACATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.22
Consensus pattern (17 bp):
ATTACTAAGGCCCCAAA
Found at i:23959 original size:2 final size:2
Alignment explanation
Indices: 23952--23977 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23942 TTTGATGGGC
23952 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
23978 CATGTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24635 original size:29 final size:29
Alignment explanation
Indices: 24593--24663 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
24583 TGTTAACCAT
*
24593 CCAATATATATGAACCCAACAAATACGTA
1 CCAATATATATGAACCCAACAAATACGCA
24622 CCAATATATATGAACCCAACAAATACGCA
1 CCAATATATATGAACCCAACAAATACGCA
*
24651 TCAATATATATGA
1 CCAATATATATGA
24664 TGGGATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.23
Consensus pattern (29 bp):
CCAATATATATGAACCCAACAAATACGCA
Found at i:25694 original size:40 final size:40
Alignment explanation
Indices: 25630--25763 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
25620 ATAAACGAGC
25630 AAAACAGAGTATAGTAG--A-AT--TATTGATAAATAGGA
1 AAAACAGAGTATAGTAGATATATAGTATTGATAAATAGGA
25665 AAAACAGAGTATAGTAGATATATAGTATTGATAAATAGGA
1 AAAACAGAGTATAGTAGATATATAGTATTGATAAATAGGA
25705 AAAACAGAGTATAGTAGATATATAGTATTGATAAATAGGA
1 AAAACAGAGTATAGTAGATATATAGTATTGATAAATAGGA
25745 AAAACAGAGTA-AGTAGATA
1 AAAACAGAGTATAGTAGATA
25764 ATACCCTAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
35 17 0.18
37 1 0.01
38 2 0.02
39 8 0.09
40 66 0.70
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.25
Consensus pattern (40 bp):
AAAACAGAGTATAGTAGATATATAGTATTGATAAATAGGA
Found at i:26625 original size:2 final size:2
Alignment explanation
Indices: 26618--26650 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
26608 AGGACGAGGC
26618 TA TA TA 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 TA TA TA T
26651 GTCCAGCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28687 original size:2 final size:2
Alignment explanation
Indices: 28680--28714 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28670 CTCTACTGTG
28680 TA TA TA TA 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 TA TA TA TA T
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.