Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020889.1 Corchorus olitorius cultivar O-4 contig20922, 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: 11025
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:1415 original size:332 final size:333
Alignment explanation
Indices: 504--2616 Score: 2688
Period size: 332 Copynumber: 6.3 Consensus size: 333
494 AGTCTTCGCT
* * * *
504 GGGCCCCGTAACGCGTTTTTTAGGCGAAAACTATGATGGTTAGCACACA-ATTTCGGTCAAGATT
1 GGGCCCCGGAACGCG-TTTTTAGCCGAAAACTGTGATAGTTAGCACA-AGATTTCGGTCAAGATT
* * *
568 TTGCAAAAATTGACTCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCAAAAATATATATAT
64 TTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAAT--TC-----T-CATA-A-
* ** * * *
633 ATATATATATATAAATCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTC
119 A-A-A-ATATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTC
* * * * *
698 ATATGCTTTTCTGAATTAATTTCCAATTAAATCGAATCCGGATTCTGATGCTAGTAAAAACAATT
181 ATATGCTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAAT
* * * *
763 TTTTAAATCTTATGGGGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCC
246 CTTTAAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCC
*
828 AAAAATCACACAAAACTGAG-CC
311 AAAAATCACACAAAACTGAGTCA
* * * *
850 GGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTAATAGTTAAACACACGATTTCGGTCAAGATT
1 GGG-CCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTT-AGCACAAGATTTCGGTCAAGATT
* * * * *
915 TTGCAAAAATTGACTCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCTTTAAAAATATATA
64 TTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTCTCATAAAAAATATATA
* * * * *
980 AATCATCACCAAAAATATTGAAGGGTTTTTCACGCTTCGAATCTCGTTTTTCCTATGTTTTTCTG
129 AATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCG
* *
1045 AATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCATAA
194 AATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTAT
* *
1110 GTGGATGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTTTTGGCGCCAAAAATCACACAA
259 GTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAA
1175 AACTGAGTC-
324 AACTGAGTCA
**
1184 GGGCCTTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGATTTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGATTTT
* *
1249 GCAAAAATTGACCCGAATGATTTTTCCTCAATCTTTGGAAAAAATTCTCATAAAAAATATATAAA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTCTCATAAAAAATATATAAA
* ** * *
1314 TCATCGCCAAAAAGATTGAAGGGTTTTTCGTGTTTCGAATATCGTTTCTCATATGCTTTTCCGAA
131 TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGAA
* * * *
1379 TTAATTTCCAATTAAATCGACACTAGATTTTGATGCTCGTAAAAA-AGAAACTTTAAATCTTATG
196 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACA-AATCTTTAAATCTTATG
* * * * *
1443 TGGCTGAGATTTGGGTAGAAGAATATAGATATTCCAAGGAGTCTTGACGCAAAAAATCATACAAA
260 TGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAA
* **
1508 ACTTAGTTG
325 ACTGAGTCA
* * * * *
1517 GGGCCCCGGAACGCGTTTTTTGCCGAAAACTGTGATTGTTAGCACACGATTACGATCAAGATTTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGATTTT
* * * *
1582 GCGAAAATTGTCCCGAATGATTTTTCCTAAATTTTTGGCCAAAATAT-TCATAAAAATATATATA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAAT-TCTCAT-AAAA-A-ATATA
* * *
1646 TAAATCATCACCAACAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGTTTTTC
127 TAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTC
*
1711 CGAATTAATTTCCAATTAAATTGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTT
192 CGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTT
* * ** * * *
1776 ATGTGGTTGAGATTTGGGTAGATGAAGATAGATATTCCTAGGAGTCTTCGTGCCAAAAATCATAC
257 ATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACAC
*
1841 AAAACTGAG-CT
322 AAAACTGAGTCA
* * * * * **
1852 GGGCCCCGTAACGTGTTTTTAGCCGATAACTATGATGGTTAGCACACA-ATTTCAATCAAGATTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACA-AGATTTCGGTCAAGATTT
* * * * *
1916 GGCAAAAATAGACCCGAATGATTTTTCTTCAATTTTTGGCCAAAATACTCA-AAAAAATATATAA
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTCTCATAAAAAATATATAA
* ** * * * * *
1980 ATCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTAATATGCTTTTCTGA
130 ATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGA
*
2045 ATTAATTT-CAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAATTCTTTAAATCTTATG
195 ATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATG
* * *
2109 GGGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAATCACACAAA
260 TGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAA
*
2174 ACTGAGCCA
325 ACTGAGTCA
* * * * *
2183 GGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAACACACGATTTCAGTCAAGATTTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGATTTT
*
2248 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTGTCATAAAAAATATATAAA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTCTCATAAAAAATATATAAA
* * * *
2313 TCATCGCCAAAAAGATTGAAGGGTTTTTCACG-TTACGAATATCATTTCTCCTATGCTTTTCCGA
131 TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTT-CGAATATCGTTTTTCATATGCTTTTCCGA
* *
2377 ATTAATTTCCAATTAAATCGAAACTAGATTTTGATGCTCGTAAAAA-AAA-CTTTAAATCTTATG
195 ATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATG
* * * * *
2440 TGGTTGAGATTTGGGTAGATGAATATAGATATTCCAAA-GAGACTTTGCGCAAAAAATCATACAA
260 TGGCTGAGATTTGGGTAGATGAATATAGATATT-CAAAGGAGTCTTGGCGCCAAAAATCACACAA
* *
2504 AACTTAGTCG
324 AACTGAGTCA
* * * *
2514 GGGCCCCGGAATGTGTTTTTAGCCGAAAACTGTGATTA-TTAGCACATGATTACGGTCAAGATTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGA-TAGTTAGCACAAGATTTCGGTCAAGATTT
* * *
2578 TGCGAAAATTGTCCCGAATGATTTTTCCTAAATTTTTGG
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGG
2617 CCAACTACTT
Statistics
Matches: 1549, Mismatches: 198, Indels: 55
0.86 0.11 0.03
Matches are distributed among these distances:
330 115 0.07
331 334 0.22
332 336 0.22
333 175 0.11
334 196 0.13
335 100 0.06
336 186 0.12
337 2 0.00
338 1 0.00
339 1 0.00
340 1 0.00
345 1 0.00
346 24 0.02
347 77 0.05
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (333 bp):
GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGATTTT
GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTCTCATAAAAAATATATAAA
TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGAA
TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGT
GGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAA
CTGAGTCA
Found at i:1645 original size:666 final size:664
Alignment explanation
Indices: 504--2616 Score: 2947
Period size: 666 Copynumber: 3.2 Consensus size: 664
494 AGTCTTCGCT
* * *
504 GGGCCCCGTAACGCGTTTTTTAGGCGAAAACTATGATGGTTAGCACACAATTTCGGTCAAGATTT
1 GGGCCCCGGAACGCG-TTTTTAGCCGAAAACTATGATAGTTAGCACACAATTTCGGTCAAGATTT
* * * *
569 TGCAAAAATTGACTCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCAAAAATATATATATA
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGG--AAAAAATTC-----T-CATA-A-A
634 TATATATATATAAATCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTCA
120 -A-A-ATATATAAATCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTCA
* * *
699 TATGCTTTTCTGAATTAATTTCCAATTAAATCGAATCCGGATTCTGATGCTAGTAAAAACAATTT
182 TATGCTTTTCTGAATTAATTTCCAATTAAATCGAA-CTGGATTCTGATGCTCGTAAAAACAATTC
764 TTTAAATCTTATGGGGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCA
246 TTTAAATCTTATGGGGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCA
*
829 AAAATCACACAAAACTGAGCCGGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTAATAGTTAAA
311 AAAATCACACAAAACTGAGCCGGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTT-AA
* *
894 CACACGATTTCGGTCAAGATTTTGCAAAAATTGACTCGAATGATTTTTCCTCAATTTTTGGCCAA
375 CACACGATTTCGATCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAA
* * * * *
959 AATACTCTTTAAAAATATATAAATCATCACCAAAAATATTGAAGGGTTTTTCACGCTTCGAATCT
440 AATATTCATAAAAAATATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATAT
*
1024 CGTTTTTCCTATGTTTTTCTGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAA
505 CGTTTTTCCTATGTTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAA
* * *
1089 AAACAAATCTTTAAATCATAAGTGGATGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTT
570 AAACAAATCTTTAAATCTTATGTGGTTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTT
*
1154 TTGGCGCCAAAAATCACACAAAACTGAGTC-
635 TT-GCGCCAAAAATCATACAAAACTGAGTCG
** *
1184 GGGCCTTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACA-AGATTTCGGTCAAGATTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTATGATAGTTAGCACACA-ATTTCGGTCAAGATTT
*
1248 TGCAAAAATTGACCCGAATGATTTTTCCTCAATCTTTGGAAAAAATTCTCATAAAAAATATATAA
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGAAAAAATTCTCATAAAAAATATATAA
* ** * ** * * *
1313 ATCATCGCCAAAAAGATTGAAGGGTTTTTCGTGTTTCGAATATCGTTTCTCATATGCTTTTCCGA
130 ATCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTCATATGCTTTTCTGA
* * **
1378 ATTAATTTCCAATTAAATCGACACTAGATTTTGATGCTCGTAAAAA-AGAAACTTTAAATCTTAT
195 ATTAATTTCCAATTAAATCGA-ACTGGATTCTGATGCTCGTAAAAACA-ATTCTTTAAATCTTAT
* * * ** * * *
1442 GTGGCTGAGATTTGGGTAGAAGAATATAGATATTCCAAGGAGTCTTGACGCAAAAAATCATACAA
258 GGGGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAATCACACAA
* ** * * * * * *
1507 AACTTAGTTGGGGCCCCGGAACGCGTTTTTTGCCGAAAACTGTGATTGTTAGCACACGATTACGA
323 AACTGAGCCGGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAACACACGATTTCGA
* * *
1572 TCAAGATTTTGCGAAAATTGTCCCGAATGATTTTTCCTAAATTTTTGGCCAAAATATTCATAAAA
388 TCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATATTCAT-AAA
*
1637 ATATATATATAAATCATCACCAACAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCT
452 A-A-ATATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCT
*
1702 ATGTTTTTCCGAATTAATTTCCAATTAAATTGAAACTGGATTCTGATGCTCGTAAAAACAAATCT
515 ATGTTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCT
* ** * *
1767 TTAAATCTTATGTGGTTGAGATTTGGGTAGATGAAGATAGATATTCCTAGGAGTCTTCGTGCCAA
580 TTAAATCTTATGTGGTTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGT-TTTGCGCCAA
*
1832 AAATCATACAAAACTGAG-CT
644 AAATCATACAAAACTGAGTCG
* * * * ** *
1852 GGGCCCCGTAACGTGTTTTTAGCCGATAACTATGATGGTTAGCACACAATTTCAATCAAGATTTG
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTATGATAGTTAGCACACAATTTCGGTCAAGATTTT
* * ** *
1917 GCAAAAATAGACCCGAATGATTTTTCTTCAATTTTTGGCCAAAATACTCA-AAAAAATATATAAA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGAAAAAATTCTCATAAAAAATATATAAA
*
1981 TCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTAATATGCTTTTCTGAA
131 TCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTCATATGCTTTTCTGAA
2046 TTAATTT-CAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAATTCTTTAAATCTTATGG
196 TTAATTTCCAATTAAATCG-AACTGGATTCTGATGCTCGTAAAAACAATTCTTTAAATCTTATGG
2110 GGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAATCACACAAAA
260 GGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAATCACACAAAA
*
2175 CTGAGCCAGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAACACACGATTTC-AGT
325 CTGAGCCGGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAACACACGATTTCGA-T
*
2239 CAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAAT-TGTCATAAAA
389 CAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATAT-TCATAAAA
* * *
2303 AATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACG-TTACGAATATCATTTCTCCTAT
453 AATATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTT-CGAATATCGTTTTTCCTAT
* * *
2367 GCTTTTCCGAATTAATTTCCAATTAAATCGAAACTAGATTTTGATGCTCGTAAAAA-AAA-CTTT
517 GTTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTT
* *
2430 AAATCTTATGTGGTTGAGATTTGGGTAGATGAATATAGATATTCCAAA-GAGACTTTGCGCAAAA
582 AAATCTTATGTGGTTGAGATTTGGGTAGATGAATATAGATATT-CAAAGGAG-TTTTGCGCCAAA
*
2494 AATCATACAAAACTTAGTCG
645 AATCATACAAAACTGAGTCG
* * * ** *
2514 GGGCCCCGGAATGTGTTTTTAGCCGAAAACTGTGATTA-TTAGCACATGATTACGGTCAAGATTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTATGA-TAGTTAGCACACAATTTCGGTCAAGATTT
* * *
2578 TGCGAAAATTGTCCCGAATGATTTTTCCTAAATTTTTGG
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGG
2617 CCAACTACTT
Statistics
Matches: 1263, Mismatches: 152, Indels: 54
0.86 0.10 0.04
Matches are distributed among these distances:
661 73 0.06
662 93 0.07
663 109 0.09
664 1 0.00
665 74 0.06
666 431 0.34
667 82 0.06
668 290 0.23
669 4 0.00
670 1 0.00
671 3 0.00
672 1 0.00
677 7 0.01
678 1 0.00
679 81 0.06
680 12 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (664 bp):
GGGCCCCGGAACGCGTTTTTAGCCGAAAACTATGATAGTTAGCACACAATTTCGGTCAAGATTTT
GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGAAAAAATTCTCATAAAAAATATATAAA
TCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTCATATGCTTTTCTGAA
TTAATTTCCAATTAAATCGAACTGGATTCTGATGCTCGTAAAAACAATTCTTTAAATCTTATGGG
GCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAATCACACAAAAC
TGAGCCGGGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAACACACGATTTCGATCA
AGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATATTCATAAAAAAT
ATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGTTT
TTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAAT
CTTATGTGGTTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTTTTGCGCCAAAAATCAT
ACAAAACTGAGTCG
Found at i:2438 original size:331 final size:332
Alignment explanation
Indices: 504--2620 Score: 2740
Period size: 331 Copynumber: 6.3 Consensus size: 332
494 AGTCTTCGCT
* * * * *
504 GGGCCCCGTAACGCGTTTTTTAGGCGAAAACTATGATGGTTAGCACACAATTTCGGTCAAGATTT
1 GGGCCCCGGAACGCG-TTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCGGTCAAGATTT
* *
569 TGCAAAAATTGACTCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCAAAAATATATATATA
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAAT--TC-----T-CATA-A-A
* ** * * *
634 TATATATATATAAATCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTCA
120 -A-A-ATATATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCA
* * * * **
699 TATGCTTTTCTGAATTAATTTCCAATTAAATCGAATCCGGATTCTGATGCTAGTAAAAACAATTT
182 TATGCTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAA-AC
* * *
764 TTTAAATCTTATGGGGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCA
246 TTTAAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCA
*
829 AAAATCACACAAAACTGAGCCG
311 AAAATCACACAAAACTGAGTCG
* * * *
851 GGACCCTGGAACGCGTTTTTAGCCGAAAACTGTAATAGTTAAACACACGATTTCGGTCAAGATTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTT-AGCACACGATTTCGGTCAAGATTT
* * * *
916 TGCAAAAATTGACTCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCTTTAAAAATATATAA
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAAATATATAA
* * * * *
981 ATCATCACCAAAAATATTGAAGGGTTTTTCACGCTTCGAATCTCGTTTTTCCTATGTTTTTCTGA
130 ATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGA
* *
1046 ATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCATAAG
195 ATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAA-CTTTAAATCTTATG
* *
1111 TGGATGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTTTTGGCGCCAAAAATCACACAAA
259 TGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAA
1176 ACTGAGTC-
324 ACTGAGTCG
** *
1184 GGGCCTTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGATTTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCGGTCAAGATTTT
* **
1249 GCAAAAATTGACCCGAATGATTTTTCCTCAATCTTTGGAAAAAATTCTCATAAAAAATATATAAA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAAATATATAAA
* ** * *
1314 TCATCGCCAAAAAGATTGAAGGGTTTTTCGTGTTTCGAATATCGTTTCTCATATGCTTTTCCGAA
131 TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGAA
* * * *
1379 TTAATTTCCAATTAAATCGACACTAGATTTTGATGCTCGTAAAAAAGAAACTTTAAATCTTATGT
196 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGT-AAAAACAAACTTTAAATCTTATGT
* * * * *
1444 GGCTGAGATTTGGGTAGAAGAATATAGATATTCCAAGGAGTCTTGACGCAAAAAATCATACAAAA
260 GGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAA
* *
1509 CTTAGTTG
325 CTGAGTCG
* * * *
1517 GGGCCCCGGAACGCGTTTTTTGCCGAAAACTGTGATTGTTAGCACACGATTACGATCAAGATTTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCGGTCAAGATTTT
* * *
1582 GCGAAAATTGTCCCGAATGATTTTTCCTAAATTTTTGGCCAAAATAT-TCATAAAAATATATATA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAAT-TCTCAT-AAAA-A-ATATA
* * *
1646 TAAATCATCACCAACAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGTTTTTC
127 TAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTC
*
1711 CGAATTAATTTCCAATTAAATTGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTT
192 CGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAA-CTTTAAATCTT
* * ** * * *
1776 ATGTGGTTGAGATTTGGGTAGATGAAGATAGATATTCCTAGGAGTCTTCGTGCCAAAAATCATAC
256 ATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACAC
*
1841 AAAACTGAG-CT
321 AAAACTGAGTCG
* * * * * * ** *
1852 GGGCCCCGTAACGTGTTTTTAGCCGATAACTATGATGGTTAGCACACAATTTCAATCAAGATTTG
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCGGTCAAGATTTT
* * *
1917 GCAAAAATAGACCCGAATGATTTTTCTTCAATTTTTGGCCAAAATACTCA-AAAAAATATATAAA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAAATATATAAA
* ** * * * * *
1981 TCATCTCCAAAAACTTTGAAGGATTTTTTATGCTTCGAATATCGTTTTTAATATGCTTTTCTGAA
131 TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGAA
* *
2046 TTAATTT-CAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAATTCTTTAAATCTTATGG
196 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAA-ACTTTAAATCTTATGT
* *
2110 GGCTGAGATTTGGGCAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAATCACACAAAA
260 GGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAA
* *
2175 CTGAGCCA
325 CTGAGTCG
* * * *
2183 GGACCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAACACACGATTTCAGTCAAGATTTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCGGTCAAGATTTT
* *
2248 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGACAAAATTGTCATAAAAAATATATAAA
66 GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAAATATATAAA
* * * *
2313 TCATCGCCAAAAAGATTGAAGGGTTTTTCACG-TTACGAATATCATTTCTCCTATGCTTTTCCGA
131 TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTT-CGAATATCGTTTTTCATATGCTTTTCCGA
* *
2377 ATTAATTTCCAATTAAATCGAAACTAGATTTTGATGCTCGTAAAAA-AAACTTTAAATCTTATGT
195 ATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAACTTTAAATCTTATGT
* * * * *
2441 GGTTGAGATTTGGGTAGATGAATATAGATATTCCAAA-GAGACTTTGCGCAAAAAATCATACAAA
260 GGCTGAGATTTGGGTAGATGAATATAGATATT-CAAAGGAGTCTTGGCGCCAAAAATCACACAAA
*
2505 ACTTAGTCG
324 ACTGAGTCG
* * * *
2514 GGGCCCCGGAATGTGTTTTTAGCCGAAAACTGTGATTA-TTAGCACATGATTACGGTCAAGATTT
1 GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGA-TAGTTAGCACACGATTTCGGTCAAGATTT
* * *
2578 TGCGAAAATTGTCCCGAATGATTTTTCCTAAATTTTTGGCCAA
65 TGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAA
2621 CTACTTCTAT
Statistics
Matches: 1551, Mismatches: 202, Indels: 50
0.86 0.11 0.03
Matches are distributed among these distances:
330 114 0.07
331 337 0.22
332 329 0.21
333 185 0.12
334 193 0.12
335 108 0.07
336 179 0.12
337 1 0.00
338 1 0.00
339 1 0.00
340 1 0.00
345 1 0.00
346 21 0.01
347 80 0.05
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (332 bp):
GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCGGTCAAGATTTT
GCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATTCTCATAAAAAATATATAAA
TCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCATATGCTTTTCCGAA
TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAACTTTAAATCTTATGTG
GCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAAC
TGAGTCG
Found at i:3285 original size:15 final size:15
Alignment explanation
Indices: 3265--3293 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3255 AAAGAAATAT
3265 AAAATATAAGTTTTA
1 AAAATATAAGTTTTA
3280 AAAATATAAGTTTT
1 AAAATATAAGTTTT
3294 TTTTTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
AAAATATAAGTTTTA
Found at i:10834 original size:333 final size:333
Alignment explanation
Indices: 10207--10997 Score: 1110
Period size: 333 Copynumber: 2.4 Consensus size: 333
10197 GGCGATGATC
* * * *
10207 TTTTATGAGTGTTTTGGCCAAAAATTGAGGAAAAATCATTCGGGTCAATTTTTGTAAAATCTTGA
1 TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTG-
* * *
10272 CCGAAATCGTGTG-TGATTTTTGCAAAACCACAGTTTTCGGCTAAAAACGCGTTCCGGGG-ATCC
65 CCGAAATCGTGTGCT-A--ATT-----ATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCATCC
* * * * * * * *
10335 AACTCAGTTTTGTGTGATTTTTGGCGCCAAAACTCCTTTGAATATCTATATTCATCTACCCAAAT
122 AACTCAATTTTGTATGAGTTTCGGCACCAAAACTCCTTGGAATAACTAGATTCATCTACCCAAAT
* * *
10400 CTCAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATTCGGTTTCGATTTAATTGG
187 CTCAGCCACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGG
* *
10465 AAATTAATTCGGAAAAGTATAGAAAAAACGATATTCGAAGCTTAAAAAACCCTT-AATTCTTTTT
252 AAATTAATTCGGAAAAGCATAGAAAAAACAATATTCGAAGCTTAAAAAACCCTTCAA-TCTTTTT
10529 GGCGATGATTTATATACT
316 GGCGATGATTTATATACT
10547 TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTAG
1 TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTT-G
**
10612 CCGAAATCGTGTGCTAATTATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCA-CCAGTTCAAT
65 CCGAAATCGTGTGCTAATTATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCATCCAACTCAAT
*
10676 TTTGTATGAGTTTCGGCACCAAGACTCCTTGGAATAACTAGATTCATCTACCCAAATCTCAGCCA
130 TTTGTATGAGTTTCGGCACCAAAACTCCTTGGAATAACTAGATTCATCTACCCAAATCTCAGCCA
* *
10741 CATAAGATTTATAGATTTGTTTTTATGAGCATC-GAAATCCAGTTTCGATTTAATAT-GAAATTA
195 CATAAGATTTAAAGATTTGTTTTTACGAGCATCAG-AATCCAGTTTCGATTTAAT-TGGAAATTA
* * *
10804 ATTCGGAAAAGCGTAGGAAAAACAATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATG
258 ATTCGGAAAAGCATAGAAAAAACAATATTCGAAGCTTAAAAAACCCTTCAATCTTTTTGGCGATG
10869 ATTTATATACT
323 ATTTATATACT
*
10880 TTTTATTAGTATTTTGGCCAAAATTTAAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTGG
1 TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTT-G
* * *
10945 CCGAAATCGTTTGCGTTA-CATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGC
65 CCGAAATCGTGTGC-TAATTATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGC
10998 CCGACTCAGT
Statistics
Matches: 411, Mismatches: 33, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
332 1 0.00
333 327 0.80
334 6 0.01
338 2 0.00
340 73 0.18
341 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (333 bp):
TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTGC
CGAAATCGTGTGCTAATTATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCATCCAACTCAATT
TTGTATGAGTTTCGGCACCAAAACTCCTTGGAATAACTAGATTCATCTACCCAAATCTCAGCCAC
ATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAAATTAATT
CGGAAAAGCATAGAAAAAACAATATTCGAAGCTTAAAAAACCCTTCAATCTTTTTGGCGATGATT
TATATACT
Done.