Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009650.1 Corchorus capsularis cultivar CVL-1 contig09671, 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: 20097
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:892 original size:332 final size:332
Alignment explanation
Indices: 1--3371 Score: 4384
Period size: 331 Copynumber: 10.2 Consensus size: 332
* *
1 AAATTGACCCGTAAGAGTTTTCCTCAATTTTTAGCCACAATACTCATAACTAATATATTATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
* *
66 TGTCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAA-
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* *
128 TTCTAATTAAATCGAAACAATATTCAGATGCTCGTAGAAATAAATCCTTAAATGCAATGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
* *
193 TGATTTTGTTAGATGAATATAG-TGAATTCAAGGAGTC-TGGCACCCAAAATCACGCAAAATTGA
196 TGATTTGGTTAGATGAATATAGAT-AATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGA
* * *
256 GTCGGGGCCCCGGAACCCGTTTTTAGCCAATAACTGTGATGATTAGTACACGATTTCGGCTAAAA
260 GTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
321 TTTAGCAA
325 TTTAGCAA
* *
329 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTGATAACGAATATATTATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
* * *
394 TGTCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGAAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* * * * *
458 TTCTAATTAAATAGAAACAAGATTTAAATGCTCGTAGAAATAAATCTTTAAATCCAACGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
*
523 TGATTTTGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
196 TGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
* *
588 TCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAAT
261 TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
653 TTAGCAA
326 TTAGCAA
* ** *
660 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGTCACAATACTCATAAGGATTATATTATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
725 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* *
790 TTCTAATTAAATCAAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
*
855 TGATTTGGTTAGATGAATATAG-TGAATTCAAGGAGTCTTGGCACAAAAAATCACGCAAAATTGA
196 TGATTTGGTTAGATGAATATAGAT-AATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGA
*
919 GTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTTATGGTTAGTACACGATTTC-GC-AAAA
260 GTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
982 CTTTAGCAA
325 -TTTAGCAA
* * * * *
991 AAATTGACCCGTAAGAGTTTTCCTAAATTTTTAGCCACAATAGTCATAACTAATATATTATTGAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
*
1056 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* * *
1121 TTCTAATTAAATCGAAACAAGTTTCACATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATA
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
* * * *
1186 TGATTTGGTTTGATAAATATAGATAATTCAAGGAATCTTGGCACCAAAAATCACGTAAAATTGAG
196 TGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
* *
1251 TCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
261 TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
*
1316 TTGGCAA
326 TTAGCAA
* * *
1323 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCAACAATACTCATAACGAATATATTATTCGA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
* * *
1388 TGTCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGAAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* *
1452 TTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
* *
1517 TGATTTTGTTAGATGAATATAG-TGAATTCAAGGAGTCTTGGCACCCAAAATCACGCAAAATTGA
196 TGATTTGGTTAGATGAATATAGAT-AATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGA
** *
1581 GTCGGGGCCCCGGAACAAGTTTTTAGCCAAAAACTGTGATGATTAGT-CAACGATTTCGGCTAAA
260 GTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTAC-ACGATTTCGGCTAAA
1645 A--T-----
324 ATTTAGCAA
**
1647 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAGGAATATATTATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
*
1712 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTCCCTATTTTTTCGGAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* *
1777 TTCTAATTAAATCAAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
* *
1842 TGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGACACCAAAAATCACGCAAAATTGTG
196 TGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
* * *
1907 TCGGGCCCCCGGAATGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGAGTTAGTACACGAT
261 TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAC--TG-T-G--A-T----G-GTTAGTACACGAT
1972 TTCGGCTAAAA-TTATGCAA
314 TTCGGCTAAAATTTA-GCAA
* * * *
1991 AAAATGACCCGATAA-ATTTTCCCTCAATTTTAAGCCACAATACTCATATA-AAATATATAATTC
1 AAATTGACCCG-TAAGATTTTTCCTCAATTTTTAGCCACAATACTCATA-ACAAATATATTATTC
* * * * * *
2054 -ATCTCCAAAAATATTGACGGGCTTTTCATGCTTTTAATATCATTTTT--T-TTATTTTCCGAAT
64 AAT-GCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATT-TTTTCGGAAT
2115 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAAGTAAATCCTTAAATCCAATGT
127 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAA-TAAATCCTTAAATCCAATGT
* * * * * *
2179 -GATAGAGATTTGATTAGATTAATATAGATATTTCAAGGAGTCTTCGCACCAAAAATCATGCAAA
191 GGAT-GTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAA
* * * * * *
2243 ATTTAATCAGGGGCCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAATACACAATTTCGG
255 ATTGAGTC-GGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGG
2308 CTAAAATTTTA-CAA
319 CTAAAA-TTTAGCAA
* ** * * * *
2322 AATTTGA-CCGATATTATTTTATTCTCAATTTTTAGCCACAATACACATAAAAAATATATAATT-
1 AAATTGACCCG-TAAGATTTT-TCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTC
* ** * * **
2385 TACCCCAAAAAGT-TTGAAGGGCTTTTCATGCTTCAAATATCGTTTTTCCT-TTATTTTCTAAAT
64 AATGCCAAAAA-TATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATT-TTTTCGGAAT
* * * *
2448 TAATTTATAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTT-AATCCAATGTG
127 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTG
* * * * * * * ***
2512 GAAGAGATTTGGTTAGATGAATATAAATATTTCAAGGATTTTTGGCACCAAAAACCATTTAAAAT
192 GATGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAAT
* * *
2577 TGAGTCGGGGTCCCAGAACGCGTTTTTACCCAAAAAACTGTGATGGTATTAGTACACGATTTCGG
257 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCC-AAAAACTGTGATGG--TTAGTACACGATTTCGG
**
2642 CTAAAATTTTTCAA
319 CTAAAATTTAGCAA
** * * * *
2656 AAATTGACCCGTAAGATTTTTCCTCTTTTTTTAGACGCAATACTCATAAGAAATATATAATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
* * *
2721 CGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTCGGAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
* * * *
2786 TTCTAATTAAATCGAAACAAGATTTAGATGCTTGTA-AAAGTAAATCCTTAAATCCAATGAGTAT
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAA-TAAATCCTTAAATCCAATGTGGAT
* *
2850 GTGATTTGGTTAGATGAATACATATACA-TCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTG
195 GTGATTTGGTTAGATGAATATAGATA-ATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTG
* * * * *
2914 TGTCGGGGCCCCGGAAAGCATTTTTAGCCAAAAAAATGTGATGGTTAGTACATGATTTCGGCTAA
259 AGTCGGGGCCCCGGAACGCGTTTTTAGCC-AAAAACTGTGATGGTTAGTACACGATTTCGGCTAA
2979 AA-TTATGCAAAA
323 AATTTA-GC--AA
* * * * *
2991 AAATT-ACCC-AATAGATTTTTCCTTAATTTTAAGCCACAATACTTATAGA-AAATATATAATTC
1 AAATTGACCCGTA-AGATTTTTCCTCAATTTTTAGCCACAATACTCATA-ACAAATATATTATTC
* * * * * *
3053 AACGCCAAAAAGATT--ATGGCGTTTTCATGCTTCTAATATCATTTTTCCTTTATTTTTC-GAAT
64 AATGCCAAAAATATTGAAGGGC-TTTTCACGCTTCTAATATCGTTTTTCCTAT-TTTTTCGGAAT
* *
3115 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTT
127 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATG-T
* * ** * * *
3180 GCAT-AGATTTAATTAGATG-ATATAGATATTTCAAGGAGTCTTGGCACCAAAAACCATGCAAAA
191 GGATGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAA
* * * * * * ** *
3243 TTGAATCAGGGGTCTCGAAACGCATTTTTAGCCAAAAACTGTGATGATTAGTACATAATTTCAGC
256 TTGAGTC-GGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGC
* *
3308 TAAAATTTCGTAA
320 TAAAATTTAGCAA
* * * *
3321 AATTTGACCCATAAGATTGTTTTCTCAATTTTTAACCACAATACTCATAAC
1 AAATTGACCCGTAAGATT-TTTCCTCAATTTTTAGCCACAATACTCATAAC
3372 GGTTTAGCCA
Statistics
Matches: 2702, Mismatches: 262, Indels: 154
0.87 0.08 0.05
Matches are distributed among these distances:
324 70 0.03
325 201 0.07
326 1 0.00
327 2 0.00
328 110 0.04
329 14 0.01
330 111 0.04
331 798 0.30
332 533 0.20
333 255 0.09
334 205 0.08
335 114 0.04
336 2 0.00
337 22 0.01
338 2 0.00
339 1 0.00
340 1 0.00
341 10 0.00
342 126 0.05
343 30 0.01
344 90 0.03
345 4 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAACAAATATATTATTCAA
TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
TGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTAGCAA
Found at i:2784 original size:667 final size:662
Alignment explanation
Indices: 1--3370 Score: 4318
Period size: 667 Copynumber: 5.1 Consensus size: 662
* * **
1 AAATTGACCCGTAAGAGTTTTCCTCAATTTTTAGCCACAATACTCATAACTAATATATTATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGACACAATACTCATAAGAAATATATTATTCAA
* * *
66 TGTCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCCGAATTAA-
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGGAATTAAT
* *
128 TTCTAATTAAATCGAAACAATATTCAGATGCTCGTAGAAATAAATCCTTAAATGCAATGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
*
193 TGATTTTGTTAGATGAATATAGTGAATTCAAGGAGTC-TGGCACCCAAAATCACGCAAAATTGAG
196 TGA-TTTGTTAGATGAATATAGTGAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
* * * *
257 TCGGGGCCCCGGAACCCGTTTTTAGCCAATAACTGTGATGATTAGTACACGATTTCGGCTAAAAT
260 TCGGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
* **
322 TTAGCAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTGATAACGAATATAT
325 TTA-CAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATAT
* * * *
387 TATTCAATGTCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGAA
389 TATTCAATGCCAAAAATTTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGA
* * * * *
452 ATTAATTTCTAATTAAATAGAAACAAGATTTAAATGCTCGTAGAAATAAATCTTTAAATCCAACG
454 ATTAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCCAATG
* *
517 TGGATGTGATTTTGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAA
519 TGGAAGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAA
*
582 ATTGAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGATGG-TTAGTACACGATTTCGA
584 ATTGAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGATGGATTAGTACACGATTTCGG
*
646 CTAAAATTTAGCAA
649 CTAAAATTTGGCAA
* * *
660 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGTCACAATACTCATAAGGATTATATTATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGACACAATACTCATAAGAAATATATTATTCAA
*
725 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGGAATTAAT
* *
790 TTCTAATTAAATCAAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
*
855 TGATTTGGTTAGATGAATATAGTGAATTCAAGGAGTCTTGGCACAAAAAATCACGCAAAATTGAG
196 TGATTT-GTTAGATGAATATAGTGAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAG
* *
920 TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTTATGGTTAGTACACGATTTC-GC-AAAAC
260 TCGGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA-
* * * **
983 TTTAGCAAAAATTGACCCGTAAGAGTTTTCCTAAATTTTTAGCCACAATAGTCATAACTAATATA
324 TTTA-CAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATA
* *
1048 TTATTGAATGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCC
388 TTATTCAATGCCAAAAAT-TTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCG
*
1113 GAATTAATTTCTAATTAAATCGAAACAAGTTTCACATGCTCGTAGAAATAAATCCTTAAATCCAA
452 GAATTAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCCAA
* * * *
1178 TGTGGATA-TGATTTGGTTTGATAAATATAGATAATTCAAGGAATCTTGGCACCAAAAATCACGT
517 TGTGGA-AGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGC
*
1242 AAAATTGAGTCGAGGCCCC-GAAACGCGTTTTTAGCCAAAAACTGTGATGG-TTAGTACACGATT
581 AAAATTGAGTCGGGGCCCCAG-AACGCGTTTTTAGCCAAAAACTGTGATGGATTAGTACACGATT
1305 TCGGCTAAAATTTGGCAA
645 TCGGCTAAAATTTGGCAA
1323 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAG-CAACAATACTCATAACG-AATATATTATTC
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGAC-ACAATACTCATAA-GAAATATATTATTC
* * *
1386 GATGTCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGAAATTA
64 AATGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGGAATTA
* *
1450 ATTTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGA
129 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGA
*
1515 TGTGATTTTGTTAGATGAATATAGTGAATTCAAGGAGTCTTGGCACCCAAAATCACGCAAAATTG
194 TGTGA-TTTGTTAGATGAATATAGTGAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTG
* *
1580 AGTCGGGGCCCCGGAAC-AAGTTTTTAGCCAAAAACTGTGATGATTAGT-CAACGATTTCGGCTA
258 AGTCGGGGCCCCGGAACGCA-TTTTTAGCCAAAAACTGTGATGGTTAGTAC-ACGATTTCGGCTA
**
1643 AAA--T----AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAGGAATA
321 AAATTTACAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATA
*
1702 TATTATTCAATGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTCCCTATTTTTT
386 TATTATTCAATGCCAAAAAT-TTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTT
*
1767 CGGAATTAATTTCTAATTAAATCAAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCC
450 CGGAATTAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCC
* *
1832 AATGTGGATGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGACACCAAAAATCACG
515 AATGTGGAAGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACG
* * * * *
1897 CAAAATTGTGTCGGGCCCCCGGAATGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGAGTT
580 CAAAATTGAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGA----T-G-----GA-TT
1962 AGTACACGATTTCGGCTAAAATTAT-GCAA
634 AGTACACGATTTCGGCTAAAATT-TGGCAA
* * * * *
1991 AAAATGACCCGATAA-ATTTTCCCTCAATTTTAAGCCACAATACTCATATA-AAATATATAATTC
1 AAATTGACCCG-TAAGATTTTTCCTCAATTTTTAGACACAATACTCATA-AGAAATATATTATTC
* * * * *
2054 -ATCTCCAAAAATATTGACGGGCTTTTCATGCTTTTAATATCATTTTT--T-TTATTTTCCGAAT
64 AAT-GCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATT-TTTTCGGAAT
2115 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAAGTAAATCCTTAAATCCAATGT
127 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAA-TAAATCCTTAAATCCAATGT
* * * * *
2179 -GATAGAGATTTGATTAGATTAATATAGAT-ATTTCAAGGAGTCTTCGCACCAAAAATCATGCAA
191 GGAT-GTGATTTG-TTAGATGAATATAG-TGAATTCAAGGAGTCTTGGCACCAAAAATCACGCAA
* * * * *
2242 AATTTAATCAGGGGCCTCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAATACACAATTTCG
253 AATTGAGTC-GGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCG
* ** * *
2307 GCTAAAATTTTACAAAATTTGA-CCGATATTATTTTATTCTCAATTTTTAGCCACAATACACATA
317 GCTAAAA-TTTACAAAAATTGACCCG-TAAGATTTT-TCCTCAATTTTTAGCCACAATACTCATA
* * ** * *
2371 AAAAATATATAATT-TACCCCAAAAAGTTTGAAGGGCTTTTCATGCTTCAAATATCGTTTTTCCT
379 AAAAATATATTATTCAATGCCAAAAA-TTTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCT
** * * * * *
2435 -TTATTTTCTAAATTAATTTATAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCC
443 ATT-TTTTCGGAATTAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAGAAATAAATCC
* * * * *
2499 TT-AATCCAATGTGGAAGAGATTTGGTTAGATGAATATAAATATTTCAAGGATTTTTGGCACCAA
507 TTAAATCCAATGTGGAAGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAA
* *** * *
2563 AAACCATTTAAAATTGAGTCGGGGTCCCAGAACGCGTTTTTACCCAAAAAACTGTGATGGTATTA
572 AAATCACGCAAAATTGAGTCGGGGCCCCAGAACGCGTTTTTAGCC-AAAAACTGTGATGG-ATTA
**
2628 GTACACGATTTCGGCTAAAATTTTTCAA
635 GTACACGATTTCGGCTAAAATTTGGCAA
** * *
2656 AAATTGACCCGTAAGATTTTTCCTCTTTTTTTAGACGCAATACTCATAAGAAATATATAATTCAA
1 AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGACACAATACTCATAAGAAATATATTATTCAA
* *
2721 CGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTCGGAATTAAT
66 TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGGAATTAAT
* * * *
2786 TTCTAATTAAATCGAAACAAGATTTAGATGCTTGTA-AAAGTAAATCCTTAAATCCAATGAGTAT
131 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAA-TAAATCCTTAAATCCAATGTGGAT
2850 GTGATTTGGTTAGATGAATACATA-T-ACA-TCAAGGAGTCTTGGCACCAAAAATCACGCAAAAT
195 GTGATTT-GTTAGATGAAT--ATAGTGA-ATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAAT
* * * *
2912 TGTGTCGGGGCCCCGGAAAGCATTTTTAGCCAAAAAAATGTGATGGTTAGTACATGATTTCGGCT
256 TGAGTCGGGGCCCCGGAACGCATTTTTAGCC-AAAAACTGTGATGGTTAGTACACGATTTCGGCT
* * * * * *
2977 AAAATTATGCAAAAAAATT-ACCC-AATAGATTTTTCCTTAATTTTAAGCCACAATACTTATAGA
320 AAAATT-T--ACAAAAATTGACCCGTA-AGATTTTTCCTCAATTTTTAGCCACAATACTCATAAA
* * * * * * *
3040 AAATATATAATTCAACGCCAAAAAGATT--ATGGCGTTTTCATGCTTCTAATATCATTTTTCCTT
381 AAATATATTATTCAATGCCAAAAA-TTTGAAGGGC-TTTTCACGCTTCTAATATCGTTTTTCCTA
* * *
3103 TATTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
444 T-TTTTTCGGAATTAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAGAAATAAATCCT
* * ** *
3167 TAAATCCAATGTTGCA-TAGATTTAATTAGATG-ATATAGATATTTCAAGGAGTCTTGGCACCAA
508 TAAATCCAATGTGGAAGT-GATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAA
* * * * * *
3230 AAACCATGCAAAATTGAATCAGGGGTCTC-GAAACGCATTTTTAGCCAAAAACTGTGAT-GATTA
572 AAATCACGCAAAATTGAGTC-GGGGCCCCAG-AACGCGTTTTTAGCCAAAAACTGTGATGGATTA
** * * *
3293 GTACATAATTTCAGCTAAAATTTCGTAA
635 GTACACGATTTCGGCTAAAATTTGGCAA
* * *
3321 AATTTGACCCATAAGATTGTTTTCTCAATTTTTA-ACCACAATACTCATAA
1 AAATTGACCCGTAAGATT-TTTCCTCAATTTTTAGA-CACAATACTCATAA
3371 CGGTTTAGCC
Statistics
Matches: 2402, Mismatches: 223, Indels: 165
0.86 0.08 0.06
Matches are distributed among these distances:
656 274 0.11
657 1 0.00
659 68 0.03
660 40 0.02
661 23 0.01
662 396 0.16
663 384 0.16
664 10 0.00
665 162 0.07
666 70 0.03
667 453 0.19
668 212 0.09
669 53 0.02
670 1 0.00
671 2 0.00
674 94 0.04
675 121 0.05
676 38 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (662 bp):
AAATTGACCCGTAAGATTTTTCCTCAATTTTTAGACACAATACTCATAAGAAATATATTATTCAA
TGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTCGGAATTAAT
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAGAAATAAATCCTTAAATCCAATGTGGATG
TGATTTGTTAGATGAATATAGTGAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAATTGAGT
CGGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATT
TACAAAAATTGACCCGTAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATTA
TTCAATGCCAAAAATTTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCGGAAT
TAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAGAAATAAATCCTTAAATCCAATGTG
GAAGTGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCACCAAAAATCACGCAAAAT
TGAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGATGGATTAGTACACGATTTCGGCT
AAAATTTGGCAA
Found at i:3377 original size:23 final size:23
Alignment explanation
Indices: 3351--3398 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
3341 TTTCTCAATT
3351 TTTAACCACAATACTCATAACGG
1 TTTAACCACAATACTCATAACGG
*
3374 TTTAGCCACAATACTCATAACGG
1 TTTAACCACAATACTCATAACGG
3397 TT
1 TT
3399 AGTCTAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (23 bp):
TTTAACCACAATACTCATAACGG
Found at i:4156 original size:30 final size:30
Alignment explanation
Indices: 4120--4182 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
4110 TGATTTCAGA
4120 TTAACAGTGTCATTTGGATTAAGAAAATAT
1 TTAACAGTGTCATTTGGATTAAGAAAATAT
4150 TTAACAGTGTCATTTGGATTAAGAAAATAT
1 TTAACAGTGTCATTTGGATTAAGAAAATAT
4180 TTA
1 TTA
4183 TGAATTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (30 bp):
TTAACAGTGTCATTTGGATTAAGAAAATAT
Found at i:5083 original size:16 final size:16
Alignment explanation
Indices: 5062--5109 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 16
5052 AGCTCCATGA
5062 GAAGACAGAGGATTAT
1 GAAGACAGAGGATTAT
5078 GAAGACACGGAGTTTGATTAT
1 GAAGACA--GAG---GATTAT
5099 GAAGACAGAGG
1 GAAGACAGAGG
5110 CCTCCGCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 8 0.30
18 3 0.11
19 3 0.11
21 13 0.48
ACGTcount: A:0.40, C:0.08, G:0.33, T:0.19
Consensus pattern (16 bp):
GAAGACAGAGGATTAT
Found at i:5143 original size:90 final size:90
Alignment explanation
Indices: 4968--5336 Score: 638
Period size: 90 Copynumber: 4.1 Consensus size: 90
4958 CACAAAGGTA
* * * *
4968 CACGAGAAGAGAGGAGGATTATAAAGACACGGAATTTGATTATGAAGAC--AGGCCTCAGCAGTG
1 CACGAGAAGACA-GAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTG
5031 AGGCGAGGCCAGGAGCCACGAAGCTC
65 AGGCGAGGCCAGGAGCCACGAAGCTC
*
5057 CATGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTGA
1 CACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTGA
5122 GGCGAGGCCAGGAGCCACGAAGCTC
66 GGCGAGGCCAGGAGCCACGAAGCTC
*
5147 CACGAGAAGAC--AGGATTATGAAGACACGGAGTTCGATTATGAAGACAGAGGCCTCCGCAGTGA
1 CACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTGA
*
5210 GGCGAGGCCAGGAGCCACAAAGCTC
66 GGCGAGGCCAGGAGCCACGAAGCTC
5235 CACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTGA
1 CACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTGA
5300 GGCGAGGCCAGGAGCCACGAAGCTC
66 GGCGAGGCCAGGAGCCACGAAGCTC
5325 CACGAGAAGACA
1 CACGAGAAGACA
5337 CACACGATGG
Statistics
Matches: 266, Mismatches: 10, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
88 120 0.45
89 10 0.04
90 136 0.51
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.13
Consensus pattern (90 bp):
CACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCCTCCGCAGTGA
GGCGAGGCCAGGAGCCACGAAGCTC
Found at i:5261 original size:16 final size:16
Alignment explanation
Indices: 5240--5287 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 16
5230 AGCTCCACGA
5240 GAAGACAGAGGATTAT
1 GAAGACAGAGGATTAT
5256 GAAGACACGGAGTTTGATTAT
1 GAAGACA--GAG---GATTAT
5277 GAAGACAGAGG
1 GAAGACAGAGG
5288 CCTCCGCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 8 0.30
18 3 0.11
19 3 0.11
21 13 0.48
ACGTcount: A:0.40, C:0.08, G:0.33, T:0.19
Consensus pattern (16 bp):
GAAGACAGAGGATTAT
Found at i:5279 original size:178 final size:176
Alignment explanation
Indices: 4982--5336 Score: 638
Period size: 178 Copynumber: 2.0 Consensus size: 176
4972 AGAAGAGAGG
*
4982 AGGATTATAAAGACACGGAATTTGATTATGAAGACAGGCCTCAGCAGTGAGGCGAGGCCAGGAGC
1 AGGATTATAAAGACACGGAATTCGATTATGAAGACAGGCCTCAGCAGTGAGGCGAGGCCAGGAGC
* *
5047 CACGAAGCTCCATGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCC
66 CACAAAGCTCCACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCC
5112 TCCGCAGTGAGGCGAGGCCAGGAGCCACGAAGCTCCACGAGAAGAC
131 TCCGCAGTGAGGCGAGGCCAGGAGCCACGAAGCTCCACGAGAAGAC
* * *
5158 AGGATTATGAAGACACGGAGTTCGATTATGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGGA
1 AGGATTATAAAGACACGGAATTCGATTATGAAGAC--AGGCCTCAGCAGTGAGGCGAGGCCAGGA
5223 GCCACAAAGCTCCACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGG
64 GCCACAAAGCTCCACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGG
5288 CCTCCGCAGTGAGGCGAGGCCAGGAGCCACGAAGCTCCACGAGAAGAC
129 CCTCCGCAGTGAGGCGAGGCCAGGAGCCACGAAGCTCCACGAGAAGAC
5336 A
1 A
5337 CACACGATGG
Statistics
Matches: 171, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
176 32 0.19
178 139 0.81
ACGTcount: A:0.33, C:0.21, G:0.32, T:0.14
Consensus pattern (176 bp):
AGGATTATAAAGACACGGAATTCGATTATGAAGACAGGCCTCAGCAGTGAGGCGAGGCCAGGAGC
CACAAAGCTCCACGAGAAGACAGAGGATTATGAAGACACGGAGTTTGATTATGAAGACAGAGGCC
TCCGCAGTGAGGCGAGGCCAGGAGCCACGAAGCTCCACGAGAAGAC
Found at i:11818 original size:14 final size:14
Alignment explanation
Indices: 11799--11826 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11789 CAAACCTTTA
11799 AAACGTAACAATTT
1 AAACGTAACAATTT
11813 AAACGTAACAATTT
1 AAACGTAACAATTT
11827 GGGTCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
AAACGTAACAATTT
Found at i:11982 original size:31 final size:31
Alignment explanation
Indices: 11946--12024 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
11936 ATTTTCAGCC
* * *
11946 ACCAATTTGAGTCTAAACCTTTTAAAAGTTG
1 ACCAATTTGAGCCTAAACCTTTCAAAAGGTG
* *
11977 TCCAATTTGAACCTAAACCTTTCAAAAGGTG
1 ACCAATTTGAGCCTAAACCTTTCAAAAGGTG
12008 ACCAATTTGAGCCTAAA
1 ACCAATTTGAGCCTAAA
12025 AACATAAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (31 bp):
ACCAATTTGAGCCTAAACCTTTCAAAAGGTG
Found at i:18231 original size:145 final size:145
Alignment explanation
Indices: 17968--18259 Score: 584
Period size: 145 Copynumber: 2.0 Consensus size: 145
17958 ATGTGAATGT
17968 TGAAACTAGCAAGTTCAAGTAGTGTACATATATACTATTTGAATTTGATCAAACTATGTCTATTA
1 TGAAACTAGCAAGTTCAAGTAGTGTACATATATACTATTTGAATTTGATCAAACTATGTCTATTA
18033 TTCCATGTTAAATCTATTTTAAAATGATGATTGATGATAGTATATAAGTATTATATAAGTACTAC
66 TTCCATGTTAAATCTATTTTAAAATGATGATTGATGATAGTATATAAGTATTATATAAGTACTAC
18098 TATCAGCAAAACTCA
131 TATCAGCAAAACTCA
18113 TGAAACTAGCAAGTTCAAGTAGTGTACATATATACTATTTGAATTTGATCAAACTATGTCTATTA
1 TGAAACTAGCAAGTTCAAGTAGTGTACATATATACTATTTGAATTTGATCAAACTATGTCTATTA
18178 TTCCATGTTAAATCTATTTTAAAATGATGATTGATGATAGTATATAAGTATTATATAAGTACTAC
66 TTCCATGTTAAATCTATTTTAAAATGATGATTGATGATAGTATATAAGTATTATATAAGTACTAC
18243 TATCAGCAAAACTCA
131 TATCAGCAAAACTCA
18258 TG
1 TG
18260 GTGATCCATC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (145 bp):
TGAAACTAGCAAGTTCAAGTAGTGTACATATATACTATTTGAATTTGATCAAACTATGTCTATTA
TTCCATGTTAAATCTATTTTAAAATGATGATTGATGATAGTATATAAGTATTATATAAGTACTAC
TATCAGCAAAACTCA
Found at i:19967 original size:31 final size:31
Alignment explanation
Indices: 19926--20090 Score: 148
Period size: 31 Copynumber: 5.5 Consensus size: 31
19916 TTTGGTTAAT
*
19926 TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * * **
19957 TGTTCAAATAAGGGTCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
19986 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* **
20017 TGCTCAAATAAGGGCCCAATC-TTTG--AATT
1 TGCTCAAATAAGGGCCTAA-CGTTTGCCAAAA
20046 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
20077 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
20091 TCTGTCT
Statistics
Matches: 105, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.03
29 39 0.37
30 7 0.07
31 53 0.50
32 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:20013 original size:60 final size:60
Alignment explanation
Indices: 19930--20094 Score: 276
Period size: 60 Copynumber: 2.8 Consensus size: 60
19920 GTTAATTGCT
* * *
19930 CAAATAAGGGTCTAACGTTTGCCAAAATGTTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGC
* **
19990 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGC
20050 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTG
20095 TCT
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGC
Found at i:20070 original size:29 final size:30
Alignment explanation
Indices: 19930--20071 Score: 105
Period size: 29 Copynumber: 4.7 Consensus size: 30
19920 GTTAATTGCT
* ** **
19930 CAAATAAGGGTCTAACGTTTGCCAAAATGTT
1 CAAATAAGGGCCTAACGTTTG-CAATTTGGC
* * *
19961 CAAATAAGGGTCTGATC-TTT-TAATTTGGC
1 CAAATAAGGGCCT-AACGTTTGCAATTTGGC
**
19990 CAAATAAGGGCCTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGCCTAACGTTTG-CAATTTGGC
*
20020 TCAAATAAGGGCCCAATC-TTTG-AATTTGGC
1 -CAAATAAGGGCCTAA-CGTTTGCAATTTGGC
20050 CAAATAAGGGCCTAACGTTTGC
1 CAAATAAGGGCCTAACGTTTGC
20072 CAAAATGCTC
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.03
29 40 0.46
30 4 0.05
31 37 0.43
32 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (30 bp):
CAAATAAGGGCCTAACGTTTGCAATTTGGC
Done.