Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012741.1 Corchorus olitorius cultivar O-4 contig12774, 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: 16385
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2798 original size:7 final size:7
Alignment explanation
Indices: 2786--2811 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2776 CCACTCTAAG
2786 GCCATCC
1 GCCATCC
2793 GCCATCC
1 GCCATCC
2800 GCCATCC
1 GCCATCC
2807 GCCAT
1 GCCAT
2812 ATCTTCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.15, T:0.15
Consensus pattern (7 bp):
GCCATCC
Found at i:6169 original size:16 final size:16
Alignment explanation
Indices: 6148--6178 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6138 TCTTTGTCAG
6148 AGAGAAAATTCAAGAC
1 AGAGAAAATTCAAGAC
6164 AGAGAAAATTCAAGA
1 AGAGAAAATTCAAGA
6179 TGGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.19, T:0.13
Consensus pattern (16 bp):
AGAGAAAATTCAAGAC
Found at i:6567 original size:20 final size:20
Alignment explanation
Indices: 6539--6594 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
6529 TTTAATTGGT
*
6539 GTAGATGAAGATGTGCTCTG
1 GTAGGTGAAGATGTGCTCTG
*
6559 GTAGGTGAAAAAATGTGCTCTG
1 GTAGGTG--AAGATGTGCTCTG
*
6581 GTAGGTGTAGATGT
1 GTAGGTGAAGATGT
6595 TGGTCCCGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.30
Consensus pattern (20 bp):
GTAGGTGAAGATGTGCTCTG
Found at i:9424 original size:333 final size:332
Alignment explanation
Indices: 8699--10572 Score: 2029
Period size: 333 Copynumber: 5.6 Consensus size: 332
8689 TTAATACGAC
* * * * * *
8699 AAAAAATAGGGAAAACGATATTAGAAGCGTTAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATA
1 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTCAATTATA
* * *** *
8764 TATTATTTATGATTATTGTGGCAAAAAATTGATGAAAAAAAATCCGGGTCAATTTTTGCAAAATT
66 TA-TATTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATT
* * * * * *
8829 TTAGCCGAAATCGTGCACAATCCATCACGGTGTATGACTAAAAACGCGTTCCGGGGCCCCGGCTC
130 TTAGCCGAAATCGTGTACTATCCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCCCAGCTC
* * * *
8894 AGTTTTGCATGATTTTTGGCGCCAA-AATTCATTGAAATATCTATATTCATCTATGATCTAACCA
195 AGTTTAGCATGATTTTTGGCGCCAAGAA-TCCTTAAAATAT-T-TA-T-ATC--TCATCTAACCA
*
8958 AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAAT
253 AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATCATGTTTCGATTTAAT
9023 AAGAAATTAATTCATA
318 AAGAAATTAATTC-TA
* * *
9039 AAAAAATAGAAAAAACAATATTCGAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTCAATTATA
1 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTCAATTATA
* * * * * * *
9104 TACATTTACTGAGTAATGTGGCTAAAAATTGAGGAAAAATCTTTCGGATCATTTTTTGTAAAAGT
66 TATATTTA-TGAGTATTGTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATT
* * * **
9169 TTAGTCGAAATCGTGTACTATCCATCACGATTTTTGCCTAAAACCGCGTTCCGGGGTTCCAGCTC
130 TTAGCCGAAATCGTGTACTATCCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCCCAGCTC
9234 AGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATTTATATCT-ATCTAACCAAATCTCA
195 AGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATTTATATCTCATCTAACCAAATCTCA
* ** * * * *
9298 GCTACATTGGATTTAAATATTTGTTTTTTACGAGTATCAGAATCTTGTTTCGATTTTATTAGAAA
260 GCCACATTGGATTTAAGGATTTG-TTTTTACGAGCATCAGAATCATGTTTCGATTTAATAAGAAA
9363 TTAATTCTA
324 TTAATTCTA
* * *
9372 AAAAAATATGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATA
1 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTCAATTATA
* * ** * * *
9437 TATTTTTTATGAGTATTGTGGGAAAAAGATTGATAAAAAAAT-TTT-GGGTTAATTTTGGCATAA
66 TA-TATTTATGAGTATTGTGGCAAAAA-ATTGA-GGAAAAATCTTTCGGGTCAATTTTTGCAAAA
* * * * ** *
9500 TTTTAGCCGAAATCGTATACAATCCATCACGGTTTATGACTAAAAACGCGTTCTAGGGCCCCGGC
128 TTTTAGCCGAAATCGTGTACTATCCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCCCAGC
* * * *
9565 TCAGTTTTGCATGATTTTTGGCGCCAAGATTCATTGAAATATTTATAT-TCATCTAACCAAATCT
193 TCAGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATTTATATCTCATCTAACCAAATCT
* ** * *
9629 CAGCCATATTGGATTTAAGGATTAATTTTTACGAGCATCTGAATCATGTTTAGATTTAATAAGAA
258 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATCATGTTTCGATTTAATAAGAA
9694 ATTAATTCGTAA
323 ATTAATTC-T-A
* * * * *
9706 AAAAAAAAGGAAAAACGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGAGTTCTATTATA
1 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTCAATTATA
* * *
9771 TACT-TTTATTGAGTAATGTGGCTAAAAATTGAGGAAAAAATCTTTCGGGTCAATTTTTGTAAAA
66 TA-TATTTA-TGAGTATTGTGGCAAAAAATTGAGG-AAAAATCTTTCGGGTCAATTTTTGCAAAA
* * * * *
9835 TTTTAGCCGAAATTGTATACTATCCATCACGATTTTTGGCTAAAAATGCGTTCCGGGGCCCCAGA
128 TTTTAGCCGAAATCGTGTACTATCCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCCCAGC
* * *
9900 TCAGTTTAGCATGATTTTTGGCGTCAAGAATCCTTAAAATATCTATATC-CATATAACCAAATCT
193 TCAGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATTTATATCTCATCTAACCAAATCT
** * * * *
9964 CAGATACATTGGATTTAAGGATTTGTTTTTACGAGTATCAGAATCTTGTTTCGATTTTATTAGAA
258 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATCATGTTTCGATTTAATAAGAA
*
10029 ATTAATTCGA
323 ATTAATTCTA
* * **
10039 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTTGATTATA
1 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTCAATTATA
* * * *
10104 TAT-TTTGTGAATGTTGTGG--AAAAATTGAGGAAAAAACTTTCGGGTCAA-TTTTGCAAAATTT
66 TATATTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTT
* ** * ** * ** *
10165 TAGCCGAAATCGTGTACTATCCATCACGATTTTCGGTTAAAAACGCATTTTGGGACAGCGGCTCA
131 TAGCCGAAATCGTGTACTATCCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCCCAGCTCA
* ** * * *
10230 GATTT-TCATGATTTTTGGCGCTGAGATTGCTTGAAATATATATCTATAT-TCATCTAATCAAAT
196 G-TTTAGCATGATTTTTGGCGCCAAGAATCCTT-AAA-ATAT-T-TATATCTCATCTAACCAAAT
* *
10293 TTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTA-AATCAT-TTTCTGATTTAATC
256 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC-AGAATCATGTTTC-GATTTAATA
10356 AGAAATTAATT-TGGA
319 AGAAATTAATTCT--A
* * * * * * *
10371 AAAAAATTAGGAAAAACGATATTGGAAGCGTGAAAAACCTTTTCAATTTTTTTGGCATTGAATTA
1 AAAAAA-TAGGAAAAACAATATTAGAAGCGTGAAAAGCC-CTTCAATCTTTTTGGCGTTCAATTA
* * * * * * * * *
10436 TTTAT-TTTCATGAGTACTGTGGCCAAAAATTCAAGAAACATTTTTCGGGTCAGTTTTTTGTAAA
64 TATATATTT-ATGAGTATTGTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCA-ATTTTTGCAAA
* * * * * * * *
10500 ATTTTAGCCAAAATTGTGTACTAACAATCTCGGTTTTT-AGCTAAAAACGCGTTCCGAGTCCCCA
127 ATTTTAGCCGAAATCGTGTACTATCCATCACGATTTTTGA-CTAAAAACGCGTTCCGGGGCCCCA
10564 GCTCAGTTT
191 GCTCAGTTT
10573 TGTTAGGATT
Statistics
Matches: 1283, Mismatches: 219, Indels: 66
0.82 0.14 0.04
Matches are distributed among these distances:
327 86 0.07
328 23 0.02
329 15 0.01
330 4 0.00
331 85 0.07
332 55 0.04
333 361 0.28
334 162 0.13
335 202 0.16
336 3 0.00
337 24 0.02
338 5 0.00
339 66 0.05
340 190 0.15
341 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (332 bp):
AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTCAATTATA
TATATTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTT
TAGCCGAAATCGTGTACTATCCATCACGATTTTTGACTAAAAACGCGTTCCGGGGCCCCAGCTCA
GTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATTTATATCTCATCTAACCAAATCTCAG
CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATCATGTTTCGATTTAATAAGAAATT
AATTCTA
Found at i:10081 original size:667 final size:666
Alignment explanation
Indices: 8686--10572 Score: 2510
Period size: 666 Copynumber: 2.8 Consensus size: 666
8676 TTCCTGGTAA
* * * * * * *
8686 AAATTAATACGACAAAAAATAGGGAAAACGATATTAGAAGCGTTAAAAGTCCTCCAATCTTTTTG
1 AAATTAATTCGA-AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTG
* * * * * *
8751 GCGTTAAATTATATATTATTTATGATTATTGTGGCAAAAAATTGATGAAAAAAAATCCGGGTCAA
65 GCGTTGAATTATATATTTTTTATGAATATTGTGGGAAAAAATTGAT-AAAAAAATTTCGGGTCAA
* * *
8816 TTTTTGCAAAATTTTAGCCGAAATCGTGCACAATCCATCACGGTGTATGACTAAAAACGCGTTCC
129 -TTTTGCAAAATTTTAGCCGAAATCGTGTACAATCCATCACGGTTTATGACTAAAAACGCGTTCT
* * *
8881 GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAATTCATTGAAATATCTATATTCATCT
193 AGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGATTCATTGAAATA--TATA-T-ATAT
*
8946 ATGATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATG
254 -TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATG
* * * * *
9011 TTTCGATTTAATAAGAAATTAATTCAT-AAAAAAATAGAAAAAACAATATTCGAAGCGTGAAAAG
318 TTTAGATTTAATAAGAAATTAATTCGTAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAG
* *
9075 CCCTTCAATCTTTTTGGTGTTCAATTATATACATTTACTGAGTAATGTGGCTAAAAATTGAGGAA
383 CCCTTCAATCTTTTTGGAGTTCAATTATATACTTTTA-TGAGTAATGTGGCTAAAAATTGAGGAA
* * * *
9140 AAATCTTTCGGATCATTTTTTGTAAAAGTTTAGTCGAAATCGTGTACTATCCATCACGATTTTTG
447 AAATCTTTCGGGTCATTTTTTGTAAAATTTTAGCCGAAATTGTGTACTATCCATCACGATTTTTG
* * **
9205 CCTAAAACCGCGTTCCGGGGTTCCAGCTCAGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAA
512 GCTAAAAACGCGTTCCGGGGCCCCAGCTCAGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAA
* * * * *
9270 ATATTTATATCTATCTAACCAAATCTCAGCTACATTGGATTTAAATATTTGTTTTTTACGAGTAT
577 ATATCTATATCCATATAACCAAATCTCAGATACATTGGATTTAAAGATTTGTTTTTTACGAGTAT
9335 CAGAATCTTGTTTCGATTTTATTAG
642 CAGAATCTTGTTTCGATTTTATTAG
* *
9360 AAATTAATTCTAAAAAAATATGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGG
1 AAATTAATTCGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGG
* * *
9425 CGTTGAATTATATATTTTTTATGAGTATTGTGGGAAAAAGATTGATAAAAAAATTTTGGGTTAAT
66 CGTTGAATTATATATTTTTTATGAATATTGTGGGAAAAA-ATTGATAAAAAAATTTCGGGTCAAT
* *
9490 TTTGGCATAATTTTAGCCGAAATCGTATACAATCCATCACGGTTTATGACTAAAAACGCGTTCTA
130 TTT-GCAAAATTTTAGCCGAAATCGTGTACAATCCATCACGGTTTATGACTAAAAACGCGTTCTA
9555 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGATTCATTGAAATAT-T-TATATTCATC
194 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGATTCATTGAAATATATATATATTCATC
* **
9618 TAACCAAATCTCAGCCATATTGGATTTAAGGATTAATTTTTACGAGCATCTGAATCATGTTTAGA
259 TAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTAGA
* *
9683 TTTAATAAGAAATTAATTCGTAAAAAAAAAAGGAAAAACGATATTAGAAGCGTGGAAAGCCCTTC
324 TTTAATAAGAAATTAATTCGTAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTC
*
9748 AATCTTTTTGGAGTTCTATTATATACTTTTATTGAGTAATGTGGCTAAAAATTGAGGAAAAAATC
389 AATCTTTTTGGAGTTCAATTATATACTTTTA-TGAGTAATGTGGCTAAAAATTGAGG-AAAAATC
* *
9813 TTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATTGTATACTATCCATCACGATTTTTGGCTAA
452 TTTCGGGTCATTTTTTGTAAAATTTTAGCCGAAATTGTGTACTATCCATCACGATTTTTGGCTAA
* * *
9878 AAATGCGTTCCGGGGCCCCAGATCAGTTTAGCATGATTTTTGGCGTCAAGAATCCTTAAAATATC
517 AAACGCGTTCCGGGGCCCCAGCTCAGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATC
*
9943 TATATCCATATAACCAAATCTCAGATACATTGGATTTAAGGATTTG-TTTTTACGAGTATCAGAA
582 TATATCCATATAACCAAATCTCAGATACATTGGATTTAAAGATTTGTTTTTTACGAGTATCAGAA
10007 TCTTGTTTCGATTTTATTAG
647 TCTTGTTTCGATTTTATTAG
*
10027 AAATTAATTCGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGG
1 AAATTAATTCGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGG
* * * *
10092 CGTTTG-ATTATATA--TTTTGTGAATGTTGT-GG-AAAAATTGAGGAAAAAACTTTCGGGTCAA
66 CG-TTGAATTATATATTTTTTATGAATATTGTGGGAAAAAATTGA-TAAAAAAATTTCGGGTCAA
* * ** *
10152 TTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCACGATTT-TCGGTTAAAAACGCATT-T
129 TTTTGCAAAATTTTAGCCGAAATCGTGTACAATCCATCACGGTTTAT-GACTAAAAACGCGTTCT
* ** **
10215 TGGGACAGCGGCTCAGATTTT-CATGATTTTTGGCGCTGAGATTGC-TTGAAATATATATCTATA
193 AGGG-CCCCGGCTCAG-TTTTGCATGATTTTTGGCGCCAAGATT-CATTGAAATATATA--TATA
* * *
10278 TTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCAT-
253 TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATG
* * * * * *
10342 TTTCTGATTTAATCAGAAATTAATTTGGAAAAAAATTAGGAAAAACGATATTGGAAGCGTGAAAA
318 TTT-AGATTTAATAAGAAATTAATTCGTAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * * * * *
10407 ACCTTTTCAATTTTTTTGGCA-TTGAATTATTTA-TTTTCATGAGTACTGTGGCCAAAAATTCAA
382 GCC-CTTCAATCTTTTTGG-AGTTCAATTATATACTTTT-ATGAGTAATGTGGCTAAAAATTGAG
* * * * * * *
10470 GAAACATTTTTCGGGTCAGTTTTTTGTAAAATTTTAGCCAAAATTGTGTACTAACAATCTCGGTT
444 GAAAAATCTTTCGGGTCA-TTTTTTGTAAAATTTTAGCCGAAATTGTGTACTATCCATCACGATT
* * *
10535 TTTAGCTAAAAACGCGTTCCGAGTCCCCAGCTCAGTTT
508 TTTGGCTAAAAACGCGTTCCGGGGCCCCAGCTCAGTTT
10573 TGTTAGGATT
Statistics
Matches: 1075, Mismatches: 119, Indels: 46
0.87 0.10 0.04
Matches are distributed among these distances:
661 5 0.00
662 92 0.09
663 29 0.03
664 2 0.00
665 30 0.03
666 299 0.28
667 227 0.21
668 169 0.16
670 1 0.00
671 1 0.00
672 4 0.00
673 200 0.19
674 16 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (666 bp):
AAATTAATTCGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGG
CGTTGAATTATATATTTTTTATGAATATTGTGGGAAAAAATTGATAAAAAAATTTCGGGTCAATT
TTGCAAAATTTTAGCCGAAATCGTGTACAATCCATCACGGTTTATGACTAAAAACGCGTTCTAGG
GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGATTCATTGAAATATATATATATTCATCTA
ACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTAGATT
TAATAAGAAATTAATTCGTAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAA
TCTTTTTGGAGTTCAATTATATACTTTTATGAGTAATGTGGCTAAAAATTGAGGAAAAATCTTTC
GGGTCATTTTTTGTAAAATTTTAGCCGAAATTGTGTACTATCCATCACGATTTTTGGCTAAAAAC
GCGTTCCGGGGCCCCAGCTCAGTTTAGCATGATTTTTGGCGCCAAGAATCCTTAAAATATCTATA
TCCATATAACCAAATCTCAGATACATTGGATTTAAAGATTTGTTTTTTACGAGTATCAGAATCTT
GTTTCGATTTTATTAG
Found at i:10741 original size:2 final size:2
Alignment explanation
Indices: 10736--10763 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10726 GTGTCAGATT
10736 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10764 TAAGATAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:14611 original size:24 final size:24
Alignment explanation
Indices: 14560--14612 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
14550 GGTGGTGGAT
* * *
14560 TTTCTTGATGAGAAAATTTGTAAT
1 TTTCTCGATGAGAAAATTTGAAAA
14584 TTTCTCGATGAG-AAATATTGAAAA
1 TTTCTCGATGAGAAAAT-TTGAAAA
14608 TTTCT
1 TTTCT
14613 TGTTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTCTCGATGAGAAAATTTGAAAA
Found at i:14841 original size:29 final size:30
Alignment explanation
Indices: 14814--14873 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
14804 TTACGTTTTG
14814 TCCCTTAAACT-TCAATTTTGGACATTTTAC
1 TCCC-TAAACTCTCAATTTTGGACATTTTAC
* *
14844 TTCCTAAACTCTCAATTTTGGACGTTTTAC
1 TCCCTAAACTCTCAATTTTGGACATTTTAC
14874 CCCGTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.43
Consensus pattern (30 bp):
TCCCTAAACTCTCAATTTTGGACATTTTAC
Found at i:15024 original size:32 final size:32
Alignment explanation
Indices: 14910--15025 Score: 126
Period size: 32 Copynumber: 3.6 Consensus size: 32
14900 ACCGTCATGC
* * *
14910 CGATGATGTGGCATTACCAAGTTAGACCAAAT
1 CGATGATGTGGCATTGCCACGTCAGACCAAAT
* * * *
14942 TGATGATGTGGCATTGCCACGTCGGACCGAAC
1 CGATGATGTGGCATTGCCACGTCAGACCAAAT
* * *
14974 CAATGATGTGGCATTGCCATGTCATACCAAAT
1 CGATGATGTGGCATTGCCACGTCAGACCAAAT
15006 CGATGATGTGGC-TATGCCAC
1 CGATGATGTGGCAT-TGCCAC
15026 ATCAACGACA
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
31 1 0.01
32 66 0.99
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (32 bp):
CGATGATGTGGCATTGCCACGTCAGACCAAAT
Done.