Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020853.1 Corchorus olitorius cultivar O-4 contig20886, 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: 30581
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:1436 original size:659 final size:658
Alignment explanation
Indices: 115--3988 Score: 5528
Period size: 659 Copynumber: 5.9 Consensus size: 658
105 TCAGTCTTTC
* * * *
115 GACTCTTTGAAATATCTCTATTCATTGAACCAAATCTCAGCCACATTGCATATAAGGATTGTTTT
1 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGA----TTT
* * * * * *
180 TTTTTTAAGATCATCTGAATCTCTTTTCGAATTAATTAGAAATTATTTTGGAAATATATGGAAAA
62 TTTTTTACGATCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAA-AAATGGAAAA
* *
245 AAACGATATTAGAAGCGTGAAAATCCCGTTAATAATTTTGGCGTTGAATTATATA-TTTTTCCGA
126 AAACGATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTA
* * * * * *
309 GTACGGTGGAAAAAATTTCA-TAAAAAATTTTTCGAGTCACTTTTTAGCCAAAATCGTGTACAAA
191 GTACTGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTACTAA
* * * * *
373 CCATCACGTTTTTTTGGCTAAAAACGCGTTTCGGGACTCCGGCTCAGTTTTGCATGATTTTTGGC
256 CCATCACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
* * * * *
438 AGAAAGCCTCCTTGAAATATCTCTATTCATCGAAGCAAATATCAGCCGCTTTGGATTTAACGATT
321 AAAAAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATT
* *
503 TGTTTTTACGAGGCATCTGAATTTTGTTTTGATTTAATTAGAAATAAATTCAGAAAAAAAGGAAA
386 TGTTTTTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAA
*
568 AAAGATTTAAGAAGCGTGAAAAGCCCTACAATTTTTTTTTTGCATTGAATTATATATTTTTTATG
451 AAAGATTTAAGAAGCGTGAAAAGCCTTACAA--TTTTTTTTGCATTGAATTATATATTTTTTATG
*
633 AGTCTTGTGGCAAAAAATTGTGGAAAAACATTTCTTGTCAATTTTTTGCAAAATTTTAGCCGAAA
514 AGTCTTGTGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAA
* * *
698 TCGTGTACCATCCCATCACGGTTCTTGGCTAAAAACGCGTTCCGGAGTCCTGGCTCAGTATTGCA
579 TCGTGTACCAT-CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCA
763 TGATTTTTTGCGTAAA
643 TGATTTTTTGCGTAAA
*
779 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTTTATATAAGGA-TTTTTT
1 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGATTTTTTT
**
843 TTACTCTCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGG-AAAAATGGAAAAAAAAC
66 TTACGATCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAATGG-AAAAAAAC
907 TG-TATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGTA
130 -GATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGTA
* * * *
971 CTGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTTTTAGCTGAAATCGTGTACGTTA-G
194 CTGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTAC-TAACC
* * * *
1035 ATCACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCAGTTCACTTTTTCATGATTTTTGGCAA
258 ATCACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC-A
* *
1100 AAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTT
322 AAAAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATTT
*
1165 -TTTTTACGAGACATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAACGGAAA
387 GTTTTTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA-GGAAA
*
1229 AAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATCGAATTATATATTTTTTATGAG
451 AAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATTGAATTATATATTTTTTATGAG
*
1294 TCTTGTGGCAAAAAATTGTGGAAAAACATTTCGTTTCAATTTTTTGCAAAATTTTAGCCGAAATC
516 TCTTGTGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAATC
* *
1359 GTGTACCATCTCATCACGGTTCTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAGTATTGCATG
581 GTGTACCATC-CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCATG
1424 ATTTTTTGCGTAAA
645 ATTTTTTGCGTAAA
* *
1438 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGGCACATTTTATATAAGGATTTTTTT
1 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGA-TTTTTT
** *
1503 TTTACTCTCATCTGAATCTCGTTTAGATTTAATAAGAAATTAATTTGG-AAAAATGGAAAAAAAT
65 TTTACGATCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAATGGAAAAAAA-
* *
1567 TG-TATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTACTA
129 CGATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGTA
* * * * * * * *
1631 CTGTGGCAAAAAGTTT-TGGAAAAAATTTTTTGGGTCATTTTTTAGCTGAAATAGTGTACTAACT
194 CTGTGGCAAAAA-TTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTACTAACC
* * *
1695 ATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCCGGCTCAGTTTTGGATGATTTTTGGCAA
258 ATCACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC--
* * * * *
1760 AAAAAACCTCCTTGAAATATCTCAATTCATCGAACCAAATCTCAGCCACTTTGGATTCAAGAATT
321 AAAAAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATT
* *
1825 TGTTTTTTCGAGACATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAA
386 TGTTTTTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAA
1890 AAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATT-AATTTATATATTTTTTATGA
451 AAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATTGAA-TTATATATTTTTTATGA
* ** * *
1954 GTCTGGCAGCAAAAAATGGTGGAAAAACATTTCATGTCAATTTTTTGCAAAATTTTAGCCGAAAT
515 GTCTTGTGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAAT
* * * * * * * *
2019 CGTATACAATCCATCACGGTTTTTGGTTAAAAATGCGTTCCGGAGCCCCGACTCAATTTTTCATG
580 CGTGTACCATCCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCATG
* *
2084 ATTTTTGGCGCAAA
645 ATTTTTTGCGTAAA
* * * * *
2098 GACTCTTTGAAATATGTATATTCATCAAAGCAAATCTCAGCCACATTGTATACAAGGATTTTTTT
1 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGATTTTTTT
* * * * *
2163 TTACGATCAAT-TAAATCTCGTTTCGATTGAATTAGAAATTCATTTGGAAAAAATGG-AAAAACC
66 TTACGATC-ATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAATGGAAAAAAAC
2226 GATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATA-TTTTTCCTAGTAC
130 GATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGTAC
* * * *
2290 TGTGGCAAAAATTTTAGGAAAAATTTTTTCGGGTCACTTCTTAGCCGAAATCGTGTACTAACGAT
195 TGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTACTAACCAT
* *
2355 CACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGTC-TGATTTTTGGCAGA
260 CACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTG-CATGATTTTTGGCAAA
* * * *
2419 AAGCCTCATTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACTTTGGATTTTAGGATATGT
324 AAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATTTGT
* *
2484 TTTTACGAGGCATCTCAATTTTGTTTCGATTTAATTAGAAATAAATTCGG----CAA--AAAAAA
389 TTTTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAAA
* * * *
2543 GATTTAAGAAGCGTGGAAAGCCTCACAATTTTTTTTTGTATTGAATAATATATTTTTTATGAGTC
454 GATTTAAGAAGCGTGAAAAGCCTTACAA-TTTTTTTTGCATTGAATTATATATTTTTTATGAGTC
* * *
2608 TTGTGTCAAAAAATTGAGGAAAAAGATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAATCGT
518 TTGTGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAATCGT
2673 GTACCATCCCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCATGAT
583 GTACCAT-CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCATGAT
2738 TTTTTGCGTAAA
647 TTTTTGCGTAAA
* * * * *
2750 GACTCTTTGACACATCTATATTCATCGAAGCAAATCACAGCCACATTTTATTTAAGGATTTTTTT
1 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGATTTTTTT
** *
2815 TTACTCTCATCTGAATCTCGTTTAGATTTAATAAGAAATTAATTTGAGAAAAAATGGGAAAAAAA
66 TTACGATCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTG-GAAAAAAT-GG-AAAAAA
* * ** *
2880 ACAATATTAGAAGCGTAAAAATCCCGTTAATATTTTTAACGTTGAAGTATATATTTTTTCCTAGT
128 ACGATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGT
* * *
2945 ACTGTGGCAAAAATTTTAGGAAAAAATATTTCGGGTCACTTCTTAGCCGAAATCGTGTACTAACA
193 ACTGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTACT-A-A
* * *
3010 CCATCACTGTTTTTGGGCAAAAAACGCGTTTC-GGGTCCCGGCTCAGTTTTGCCTGATTTTTGGC
256 CCATCACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
* * *
3074 AGAAAGCGTCCTTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACTTTGGATTTAAGGATT
321 AAAAAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATT
* *
3139 TGTTTTTACGAGGCATTTGAGTTTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAAAGG-AA
386 TGTTTTTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAA
*
3201 AAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATT-AGGTTATATATTTTTTATGA
451 AAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATTGA-ATTATATATTTTTTATGA
* * * * *
3265 GTC-TGCCGTCAAAAAATGGTGGAAAAACATTTCGTGTCAAATATTTGCAAAATTTTAGCCGAAA
515 GTCTTG-TGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAA
* * * * *
3329 TCGTGTACAATCCAACACGGTTTTTGGTTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCAT
579 TCGTGTACCATCCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCAT
* * *
3394 GATTTTTGGGGCAAA
644 GATTTTTTGCGTAAA
*
3409 GACTCTTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGTATATAAGGA-TTTTTT
1 GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGATTTTTTT
* *
3473 TTACGATCAAT-TGAATCTCGTTTCGATTTAATTAGATATTAATTTGGAAAAAATGG-AAAAAAC
66 TTACGATC-ATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAATGGAAAAAAAC
* * * *
3536 GATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCATTGACTTATATATTTTTTCCGAGAAC
130 GATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGTAC
*
3601 TGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTTACTTCTTAGCCGAAATCGTGTACTAACCAT
195 TGTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTACTAACCAT
* * *
3666 CACGGTTTTTGGGCTAAAATCGCGTTTCGGGGCCCCGGCTCAGTTTTGCCTGATTTTTGGCAGAA
260 CACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCA-AA
* *
3731 AA-CCTCCTTGAAATATCTCTATTCATTGAATCAAATCTCAGCCATTTTGGATTTAAGGATTTGT
324 AAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATTTGT
* * * * *
3795 TTTTTCGAGGCATCTGAATTTTGTTTTGATTTAATTAGAAAAAAATTCGAAAAAAAAAGAAAAAA
389 TTTTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAAA
* * *
3860 GATTTAAGAAGCGTGAAAAGCCTTACTA-TTTTTTTGTATTGAATTATATA-TTTGTATGAGTCT
454 GATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATTGAATTATATATTTTTTATGAGTCT
* ** * * * *
3923 TGTGGGAAAAAATTAAGGAAAAACATTTCGTTTCAATGTTTTACAAAATTTTAGTCGAAATCGTG
519 TGTGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTG
3988 T
584 T
3989 GGTAAAAGTA
Statistics
Matches: 2901, Mismatches: 262, Indels: 104
0.89 0.08 0.03
Matches are distributed among these distances:
650 32 0.01
651 95 0.03
652 188 0.06
653 145 0.05
654 186 0.06
655 26 0.01
656 192 0.07
657 87 0.03
658 365 0.13
659 552 0.19
660 538 0.19
661 385 0.13
662 57 0.02
664 53 0.02
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (658 bp):
GACTCTTTGAAATATCTATATTCATCGAACCAAATCACAGCCACATTGTATATAAGGATTTTTTT
TTACGATCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAATGGAAAAAAACG
ATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGGCGTTGAATTATATATTTTTTCCTAGTACT
GTGGCAAAAATTTCAGGAAAAAATTTTTCGAGTCACTTCTTAGCCGAAATCGTGTACTAACCATC
ACGGTTTTTGGGCAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAAAAA
GCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTT
TTACGAGGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAAAGA
TTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTTGCATTGAATTATATATTTTTTATGAGTCTTG
TGGCAAAAAATTGTGGAAAAACATTTCGTGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTA
CCATCCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATATTGCATGATTTTT
TGCGTAAA
Found at i:4218 original size:12 final size:13
Alignment explanation
Indices: 4201--4231 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4191 TTTTTTGATT
4201 AAAAAATA-TTTA
1 AAAAAATATTTTA
4213 AAAAAATATTTTA
1 AAAAAATATTTTA
4226 AAAAAA
1 AAAAAA
4232 GCCAGGGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAAATATTTTA
Found at i:6734 original size:325 final size:324
Alignment explanation
Indices: 5361--7450 Score: 1532
Period size: 325 Copynumber: 6.4 Consensus size: 324
5351 CTTGGTTCTT
* * * * * *
5361 GGCTAAAAACGCGTTCCGAAGT-CCCGGCTCAGTATTGCATGATTTTTTGCGTAAAGACTCTTTG
1 GGCTAAAAACGCGTTCCGGA-TCCCCGGCTCAATTTTGCATGA-TTTTTGGGCAAAGACTCCTTG
* * * * ** ***
5425 AAATATCTACATTCATCGAACCAAATCACAACCACATTTTATATAAGGATTT-TTTTTAC-TCTC
64 AAATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGGC
* * * * * * * *
5488 ATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAATGGAAAAAACTATATTAGAA
129 ATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA---AAAAGA-T-T-TAAGAA
* * * * * *
5553 GCGTGAAAATCCCGTT--AATATTTTTGGCGTTGAATTGTATATATTTTTTCTTACTGC-TGTGG
188 GCGTGAAAA-GCC-TTACAAT-TTTTTTGCATTGAA-T-TATATATTTTTTATGAGT-CTTGTGG
* * *
5615 CAAAAAATTTCATGAAAAAAATTTTCGGGTC-AC---T-----TTTTAGCCGAAATCGTGTACTA
247 C-AAAAA-TTGAGGAAAAAAA-TTTCGTGTCAACTTTTGCAAATTTTAGCCGAAATCGTGTACTA
*
5671 ACTATCACGGTTTTTG
309 ACCATCACGGTTTTTG
* * *
5687 GGCTAAAAACGCGTTTCGGGA-CCCCGGCTCAGTTTTGCATGATTTTT-GGCAAAAAACCTCCTT
1 GGCTAAAAACGCG-TTCCGGATCCCCGGCTCAATTTTGCATGATTTTTGGGC-AAAGA-CTCCTT
* * * *
5750 GAAATATCTCA-ATTCATAGAAACAAATCTCAGCCACATTGGAT-TCAAGAATTTGTTTTTTCGA
63 GAAATATCT-ATATTCATCGAATCAAATCTCAGCCACATTGGATAT-AAGGATTTGTTTTTACGA
* * *
5813 GACATTTGAATTTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAAAGAATTAAG
126 GGCATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGG---AAAA--AAAAAAGATTTAAG
** * *
5878 AAGCGTGAAAAGTTTTACATCTTTTTTTGCATTAAATTATATATTTTTTATGAGTCTTGTGGCAA
186 AAGCGTGAAAAGCCTTACA-ATTTTTTTGCATTGAATTATATATTTTTTATGAGTCTTGTGGC-A
* * ** * * * * *
5943 AAAATTGATGAATAACTTTTCGTGTCAATTTTTTGCAAATTTTATCCGAAACCGTGTACCGAATC
249 AAAATTGAGGAAAAAAATTTCGTGTCAA-CTTTTGCAAATTTTAGCCGAAATCGTGTA-CTAACC
6008 ATCACGGTTTTT-
312 ATCACGGTTTTTG
* *** * *
6020 GGCTAAAAACGCATTCCGGAAT-TTTGGCTCAATATTGCATGATTTTT-GGCATAAAGACTCTTT
1 GGCTAAAAACGCGTTCCGG-ATCCCCGGCTCAATTTTGCATGATTTTTGGGC--AAAGACTCCTT
* * * * *
6083 CAAATATCTATATTCATCGAACCAAATCTCAACCACATTGTATATAAGGACCTTTTTTTTTTAC-
63 GAAATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGGA---TTTGTTTTTACG
*** * * * * * * **
6147 TCTCATCTGAATCTCGTTTCGATTTAATAAGAAATTAATTTGGAAAAAAAAACCTATATT-AGAA
125 AGGCATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAA-AGAT-TTAAGAA
** * * * ** *
6211 TTGTGAAAATTCCGTT--AATATTTTTGGCGTTGAATTATATAGTTTTTCCT-AATAC-TGTGGC
188 GCGTGAAAA-GCC-TTACAAT-TTTTTTGCATTGAATTATATA-TTTTTTATGAGT-CTTGTGGC
* *
6272 AAAAATTTCAGGAAAAAAATTTTCGGGTC-AC--TT-C-----TTAGCCGAAATCGTGTACTAAC
248 AAAAA-TTGAGGAAAAAAA-TTTCGTGTCAACTTTTGCAAATTTTAGCCGAAATCGTGTACTAAC
*
6328 AATCACGGTTTTTG
311 CATCACGGTTTTTG
* * ** ** * *
6342 GGCCAAAAACGCGTTTCGGGGCCCCAACTCAGTTTTGCATGA-TTTTGGGCAGAATGCCTCCTTG
1 GGCTAAAAACGCGTTCCGGATCCCCGGCTCAATTTTGCATGATTTTTGGGCA-AA-GACTCCTTG
* * * * *
6406 AAATATCTCTATTCATTGAATAAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGGC
64 AAATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGGC
6471 ATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAAAAAGATTTAAGAAGCGTGA
129 ATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAAAGATTTAAGAAGCGTGA
* *
6535 AAAGCCTTACAATTTTTTTGTATTGAATTATATATTTTTTATGAGTCTTGTGGCAAAATATTGAC
194 AAAGCCTTACAATTTTTTTGCATTGAATTATATATTTTTTATGAGTCTTGTGGCAAAA-ATTGAG
*
6600 GAAAAACATTTCGTGTCAACTTTTGCAAAATTTTAGCCGAAATCGTGTAC-AATCCATCACGGTT
258 GAAAAAAATTTCGTGTCAACTTTTGC-AAATTTTAGCCGAAATCGTGTACTAA-CCATCACGGTT
6664 TTT-
321 TTTG
*
6667 GGCTAAAAACGCGTTCCGGATCCCCGGCTCAATTTTGCATGATTTTTGGTGCAAAGACTCTTTGA
1 GGCTAAAAACGCGTTCCGGATCCCCGGCTCAATTTTGCATGATTTTTGG-GCAAAGACTCCTTGA
* * * * *
6732 AATATTTATATTCATCGAA-CTAAATCTCAGCCACATTGTATATAAGGATTTTTTTTTTATGA-T
65 AATATCTATATTCATCGAATC-AAATCTCAGCCACATTGGATATAAGGA-TTTGTTTTTACGAGG
* * * * *
6795 CAATTGAATCTCGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGAAAAAGTATATT-AG
128 CATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAAA---AAAAAG-AT-TTAAG
* * * * ** *
6859 AAGCATGAAAATCCCGTT--AATATTTTTGGCATTGACTTATATATTTTTTCCGAATAC-TGTGG
186 AAGCGTGAAAA-GCC-TTACAAT-TTTTTTGCATTGAATTATATATTTTTTATGAGT-CTTGTGG
* * *
6921 CAAAAATTTTAGGAAAAAAATTTTCGGGTC-AC---T-----TTTTAGTCGAAATCGTGTACTAA
247 CAAAAA-TTGAGGAAAAAAA-TTTCGTGTCAACTTTTGCAAATTTTAGCCGAAATCGTGTACTAA
6977 CCATCACGGTTTTTG
310 CCATCACGGTTTTTG
* * *
6992 GGCTAAAAACGCGTTTCGTGA-CCCCGGCTCAGTTTTGCCTGATTTTT-GGCAGAA-AGCATCCT
1 GGCTAAAAACGCGTTCCG-GATCCCCGGCTCAATTTTGCATGATTTTTGGGCA-AAGA-C-TCCT
* * * * *
7054 TGAAATATCTCTATTCATCGTATCAAATCTCAGTCACTTTGGATTTAAGGATTTGTTTTTACGAG
62 TGAAATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAG
* *
7119 GCATCTGAATTTTTTTTCGATTTAATTAGAAATAAATTCGGAAAAAAGGAAAAAAGATTTAAGAA
127 GCATTTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAA--AAAAAAGATTTAAGAA
* * * * *
7184 GTGTGAAAAGCCTTACAATTTTTTTTTGTATTAAATTATATATTTTTTATGAGTCTTATAGCAAA
188 GCGTGAAAAGCCTTACAA--TTTTTTTGCATTGAATTATATATTTTTTATGAGTCTTGTGGC-AA
* * * * * *
7249 AAATTGAGGAAAAATAGTTCGTGTTAATTTTTTTGCAAAATTTTAGCCGAAATCGTGCA-TCATC
250 AAATTGAGGAAAAAAATTTCGTGTCAA--CTTTTGC-AAATTTTAGCCGAAATCGTGTACT-AAC
*
7313 TTATCACGGTTTTT-
311 -CATCACGGTTTTTG
* * * * * * * *
7327 GGCTAAAAACGCATTCCGGAGT-CCCGACTCAATATTGCATGATTTTTTGCGTAAAAAATCTTTG
1 GGCTAAAAACGCGTTCCGGA-TCCCCGGCTCAATTTTGCATGA-TTTTTGGGCAAAGACTCCTTG
* * * * *
7391 AAATATCTATATTCATCGAACCAAATCTCAGCCATATTGTATATAAGGTTTTTTTTTTAC
64 AAATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTAC
7451 TCTCATCTGA
Statistics
Matches: 1389, Mismatches: 253, Indels: 235
0.74 0.13 0.13
Matches are distributed among these distances:
316 17 0.01
317 46 0.03
318 17 0.01
319 20 0.01
320 36 0.03
321 23 0.02
322 98 0.07
323 34 0.02
324 108 0.08
325 292 0.21
326 133 0.10
327 43 0.03
328 42 0.03
329 1 0.00
330 17 0.01
331 58 0.04
332 45 0.03
333 155 0.11
334 34 0.02
335 139 0.10
336 28 0.02
337 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (324 bp):
GGCTAAAAACGCGTTCCGGATCCCCGGCTCAATTTTGCATGATTTTTGGGCAAAGACTCCTTGAA
ATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGGCAT
TTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAAAGATTTAAGAAGCGTGAAA
AGCCTTACAATTTTTTTGCATTGAATTATATATTTTTTATGAGTCTTGTGGCAAAAATTGAGGAA
AAAAATTTCGTGTCAACTTTTGCAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
Found at i:7007 original size:650 final size:653
Alignment explanation
Indices: 5325--7540 Score: 3106
Period size: 650 Copynumber: 3.4 Consensus size: 653
5315 AATTTTGTAC
** * * *
5325 TTTTA-CC-AAATCGTGTACC-ATCCCATCTTGGTTCTTGGCTAAAAACGCGTTCCGAAGTCCCG
1 TTTTAGCCGAAATCGTGTACCAAT-CCATCACGGTTTTTGGCTAAAAACGCATTCCGGAGTCCCG
* * *
5387 GCTCAGTATTGCATGATTTTTTGCGTAAAGACTCTTTGAAATATCTACATTCATCGAACCAAATC
65 GCTCAATATTGCATGATTTTTGGCGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATC
* *
5452 ACAACCACATTTTATATAAGGA--TTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATAAG
130 TCAACCACATTGTATATAAGGATTTTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATAAG
*
5515 AAATTAATTTGGAAAAAATGGAAAAAACTATATTAGAAGCGTGAAAATCCCGTTAATATTTTTGG
195 AAATTAATTTGGAAAAAATGG-AAAAACTATATTAGAAGCATGAAAATCCCGTTAATATTTTTGG
* * * *
5580 CGTTGAATTGTATATATTTTTTCTTACTGCTGTGGCAAAAAATTTCATGAAAAAAATTTTCGGGT
259 CGTTGAA-T-TATATATTTTTTCCTAATACTGTGGC-AAAAATTTCAGGAAAAAAATTTTCGGGT
*
5645 CACTTTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACC
321 CACTTTTTAGCCGAAATCGTGTACTAACAATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACC
* * *
5710 CCGGCTCAGTTTTGCATGATTTTTGGCAAAAAACCTCCTTGAAATATCTCAATTCATAGAA-ACA
386 CCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATAGAATA-A
* * * * * *
5774 AATCTCAGCCACATTGGATTCAAGAATTTGTTTTTTCGAGACATTTGAATTTTGTTTCAATTTAA
450 AATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGGCATTTGAATTTTGTTTCGATTTAA
* ** *
5839 TTAGAAATAAATTCGGAAAAAAAGGAAAAAAGAATTAAGAAGCGTGAAAAGTTTTACATCTTTTT
515 TTAGAAATAAATTCGG---AAAA-GAAAAAAGATTTAAGAAGCGTGAAAAGCCTTACA-ATTTTT
* * * *
5904 TTGCATTAAATTATATATTTTTTATGAGTCTTGTGGCAAAAAATTGATGAATAACTTTTCGTGTC
575 TTGTATTAAATTATATATTTTTTATGAGTCTTGTGGCAAAAAATTGACGAAAAACATTTCGTGTC
5969 AATTTTTTGC-AAA
640 AATTTTTTGCAAAA
* * * ***
5982 TTTTATCCGAAACCGTGTACCGAAT-CATCACGGTTTTTGGCTAAAAACGCATTCCGGAATTTTG
1 TTTTAGCCGAAATCGTGTACC-AATCCATCACGGTTTTTGGCTAAAAACGCATTCCGGAGTCCCG
* *
6046 GCTCAATATTGCATGATTTTTGGCATAAAGACTCTTTCAAATATCTATATTCATCGAACCAAATC
65 GCTCAATATTGCATGATTTTTGGCGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATC
6111 TCAACCACATTGTATATAAGGACCTTTTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATA
130 TCAACCACATTGTATATAAGGA--TTTTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATA
* *** *
6176 AGAAATTAATTTGG-AAAAA---AAAACCTATATTAGAATTGTGAAAATTCCGTTAATATTTTTG
193 AGAAATTAATTTGGAAAAAATGGAAAAACTATATTAGAAGCATGAAAATCCCGTTAATATTTTTG
*
6237 GCGTTGAATTATATAGTTTTTCCTAATACTGTGGCAAAAATTTCAGGAAAAAAATTTTCGGGTCA
258 GCGTTGAATTATATATTTTTTCCTAATACTGTGGCAAAAATTTCAGGAAAAAAATTTTCGGGTCA
* * *
6302 CTTCTTAGCCGAAATCGTGTACTAACAATCACGGTTTTTGGGCCAAAAACGCGTTTCGGGGCCCC
323 CTTTTTAGCCGAAATCGTGTACTAACAATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCC
** * * *
6367 AACTCAGTTTTGCATGATTTTGGGCAGAATGCCTCCTTGAAATATCTCTATTCATTGAATAAAAT
388 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATAGAATAAAAT
6432 CTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGGCATTTGAATTTTGTTTCGATTTAATTA
453 CTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGGCATTTGAATTTTGTTTCGATTTAATTA
*
6497 GAAATAAATTCGG-AAA-AAAAAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTGTATTG
518 GAAATAAATTCGGAAAAGAAAAAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTGTATTA
* *
6560 AATTATATATTTTTTATGAGTCTTGTGGCAAAATATTGACGAAAAACATTTCGTGTCAA-CTTTT
583 AATTATATATTTTTTATGAGTCTTGTGGCAAAAAATTGACGAAAAACATTTCGTGTCAATTTTTT
6624 GCAAAA
648 GCAAAA
*
6630 TTTTAGCCGAAATCGTGTA-CAATCCATCACGGTTTTTGGCTAAAAACGCGTTCCGGA-TCCCCG
1 TTTTAGCCGAAATCGTGTACCAATCCATCACGGTTTTTGGCTAAAAACGCATTCCGGAGT-CCCG
* * * * *
6693 GCTCAATTTTGCATGATTTTTGGTGCAAAGACTCTTTGAAATATTTATATTCATCGAACTAAATC
65 GCTCAATATTGCATGATTTTTGGCGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATC
* * *
6758 TCAGCCACATTGTATATAAGGATTTTTTTTTTA-TGATCAAT-TGAATCTCGTTTCGATTTAATT
130 TCAACCACATTGTATATAAGGATTTTTTTTTTACT-CTC-ATCTGAATCTCGTTTCGATTTAATA
*
6821 AGAAATTAATTTGGAAAAAAATGGAAAAAGTATATTAGAAGCATGAAAATCCCGTTAATATTTTT
193 AGAAATTAATTTGG-AAAAAATGGAAAAACTATATTAGAAGCATGAAAATCCCGTTAATATTTTT
* * * *
6886 GGCATTGACTTATATATTTTTTCCGAATACTGTGGCAAAAATTTTAGGAAAAAAATTTTCGGGTC
257 GGCGTTGAATTATATATTTTTTCCTAATACTGTGGCAAAAATTTCAGGAAAAAAATTTTCGGGTC
* * *
6951 ACTTTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGTGACCC
322 ACTTTTTAGCCGAAATCGTGTACTAACAATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCC
* * * * *
7016 CGGCTCAGTTTTGCCTGATTTTTGGCAGAAAGCATCCTTGAAATATCTCTATTCATCGTATCAAA
387 CGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATAGAATAAAA
* * *
7081 TCTCAGTCACTTTGGATTTAAGGATTTGTTTTTACGAGGCATCTGAATTTTTTTTCGATTTAATT
452 TCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGGCATTTGAATTTTGTTTCGATTTAATT
*
7146 AGAAATAAATTCGGAAAAAAGGAAAAAAGATTTAAGAAGTGTGAAAAGCCTTACAATTTTTTTTT
517 AGAAATAAATTCGG--AAAA-GAAAAAAGATTTAAGAAGCGTGAAAAGCCTTACAA--TTTTTTT
* * * * * *
7211 GTATTAAATTATATATTTTTTATGAGTCTTATAGCAAAAAATTGAGGAAAAATAGTTCGTGTTAA
577 GTATTAAATTATATATTTTTTATGAGTCTTGTGGCAAAAAATTGACGAAAAACATTTCGTGTCAA
7276 TTTTTTTGCAAAA
642 -TTTTTTGCAAAA
* * *
7289 TTTTAGCCGAAATCGTGCATC-ATCTTATCACGGTTTTTGGCTAAAAACGCATTCCGGAGTCCCG
1 TTTTAGCCGAAATCGTGTACCAATC-CATCACGGTTTTTGGCTAAAAACGCATTCCGGAGTCCCG
* * * *
7353 ACTCAATATTGCATGATTTTTTGCGTAAAAAATCTTTGAAATATCTATATTCATCGAACCAAATC
65 GCTCAATATTGCATGATTTTTGGCGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATC
* * *
7418 TCAGCCATATTGTATATAAGG-TTTTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATAAT
130 TCAACCACATTGTATATAAGGATTTTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATAAG
* * * *
7482 AAATTAATTTGAAAAAAAATAGAAAAAACGATATTAAAAGCATGAAAATCCCGTTAATA
195 AAATTAATTTG-GAAAAAAT-GGAAAAACTATATTAGAAGCATGAAAATCCCGTTAATA
7541 ATTATATATT
Statistics
Matches: 1393, Mismatches: 131, Indels: 67
0.88 0.08 0.04
Matches are distributed among these distances:
644 1 0.00
645 48 0.03
646 6 0.00
647 124 0.09
648 86 0.06
649 30 0.02
650 286 0.21
651 3 0.00
653 3 0.00
655 250 0.18
656 23 0.02
657 70 0.05
658 50 0.04
659 205 0.15
660 147 0.11
661 3 0.00
662 5 0.00
663 53 0.04
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (653 bp):
TTTTAGCCGAAATCGTGTACCAATCCATCACGGTTTTTGGCTAAAAACGCATTCCGGAGTCCCGG
CTCAATATTGCATGATTTTTGGCGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATCT
CAACCACATTGTATATAAGGATTTTTTTTTTACTCTCATCTGAATCTCGTTTCGATTTAATAAGA
AATTAATTTGGAAAAAATGGAAAAACTATATTAGAAGCATGAAAATCCCGTTAATATTTTTGGCG
TTGAATTATATATTTTTTCCTAATACTGTGGCAAAAATTTCAGGAAAAAAATTTTCGGGTCACTT
TTTAGCCGAAATCGTGTACTAACAATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCCGGC
TCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATAGAATAAAATCTC
AGCCACTTTGGATTTAAGGATTTGTTTTTACGAGGCATTTGAATTTTGTTTCGATTTAATTAGAA
ATAAATTCGGAAAAGAAAAAAGATTTAAGAAGCGTGAAAAGCCTTACAATTTTTTTGTATTAAAT
TATATATTTTTTATGAGTCTTGTGGCAAAAAATTGACGAAAAACATTTCGTGTCAATTTTTTGCA
AAA
Found at i:11214 original size:3 final size:3
Alignment explanation
Indices: 11203--11233 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11193 TATTATTTGG
*
11203 ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11234 ATTACACGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:22097 original size:30 final size:30
Alignment explanation
Indices: 22063--22126 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
22053 GCGCATCACA
22063 AATCATATGGAGCAATAGTTTAACCACTAT
1 AATCATATGGAGCAATAGTTTAACCACTAT
22093 AATCATATGGAGCAATAGTTTAACCACTAT
1 AATCATATGGAGCAATAGTTTAACCACTAT
22123 AATC
1 AATC
22127 GTCGGAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (30 bp):
AATCATATGGAGCAATAGTTTAACCACTAT
Found at i:22946 original size:2 final size:2
Alignment explanation
Indices: 22941--22976 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22931 TTATATAATA
22941 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22977 ACTGATGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25797 original size:15 final size:15
Alignment explanation
Indices: 25779--25828 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
25769 ATCAGAGTCT
25779 TCATCTCTTTCAACA
1 TCATCTCTTTCAACA
* *
25794 TCATCTCTTTCCACC
1 TCATCTCTTTCAACA
*
25809 TCATCTCTTTCAACT
1 TCATCTCTTTCAACA
25824 TCATC
1 TCATC
25829 AACATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (15 bp):
TCATCTCTTTCAACA
Done.