Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012346.1 Corchorus olitorius cultivar O-4 contig12379, 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: 17690
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:4721 original size:676 final size:671
Alignment explanation
Indices: 3428--5455 Score: 3281
Period size: 676 Copynumber: 3.0 Consensus size: 671
3418 GGGAGTGCTG
* *
3428 CAAGAGCTTGATATATAGTTTAAATATACAATTGATGGAGTGACCAACTGTATTGGAATATTTTA
1 CAAGAGCTTGATCTATGGTTTAAATATACAATTGATGGAGTGACCAACTGTATTGGAATATTTTA
** *
3493 AAGCATTTACGGTTCCAAAGAAACCATTGGAACCTAACCAGCTTTCATGGACTAGGCTATTGCTA
66 AAGCATTTACGGTTCCAAAGAAACCATTGGAATATAACCAGCTTTCATGGACTGGGCTATTGCTA
* * * *
3558 CAATATACAGTTATTGGTTACCTCAAGTTAAAAATGCAAGATTCCTCTGCAGTTCATGGTCAAAA
131 CAAAATACAGTTATTGGTCACCTCAAGTTTAAAATGCAGGATTCCTCTGCAGTTCATGGTCAAAA
*
3623 AGCAAATAGTTGTTCAATGCATGTAAAGTTTTGGTAACATCCTTGCTTCTTTTCAGTTGAGGGTT
196 AGCAAATAGTTGTTCAATGCATGTAAAGTTTTGGTAACATCCCTGCTTCTTTTCAGTTGAGGGTT
3688 GGGTATAGATTAAGATGCTTGAACAATAGGCGTTAGACTGGCTGCTCTCTAATAAAGAAAACCAA
261 GGGTATAGATTAAGATGCTTGAACAATA-GCGTTAGACT-GCTGCTCTCTAATAAAGAAAACCAA
*
3753 TTGCTCCTTTACAGTAT-TAAGTGCTATCAAGTTCCACCTATAGGATTCCATGGGAGGACATGAT
324 TTGC-CCTTTACAGTATCT-AGTGCTATCAAGTTCCAGCTATAGGATTCCATGGGAGGACATGAT
* *
3817 GAAAGAGTGTTAAGCAGGCCATTATGGAAGGAGAGACAATGCAAGGGTCGAAATTAAAGTTGCAC
387 GAAAGAGTGTTAAGCAGGCCATTATGGAAGGAGAGACAATGCAAGGGTCGAAATTTAAGTTGCGC
* * *
3882 AAGCATAATATCTGAATTGGCATGGCCCAACTCCATTATCGATAATCTTTCTCTTGTAAAAGAGC
452 ATGCACAATATCTGAATTGGCATGGCCCAACTCCATTATCGATATTCTTTCTCTTGTAAAAGAGC
* ** *
3947 AAACTCTGGTCTTTGGTTAACAAATGCAAAATTCAAGATGTAGGTACGGTGCAATAGATGTAGAG
517 AAACTCTGGTCTTTGGTTGACTGATGCAAACTTCAAGATGTAGGTACGGTGCAATAGATGTAGAG
* * * *
4012 GCTTCGACGGAGAGCAATAGGCTATCGGTTGTGACACTGATAGATTGGAATCTGCAGTGAGGGAT
582 GCTCCGAC-GAGAGCAACAGACTATC-GTTGTGACACTGATAGATTGGAATCTGCAGTGGGGGAT
**
4077 CACGTGTACTGTGTTGAAGGCATGCGG
645 CACGTGTACTGTGTTGAAGGCATGCAA
* *
4104 TAAGAGCTTGATCTATGGTTTAAATATACGATTGATGGAGTGACCAACTGTA-TGGAATATTTTA
1 CAAGAGCTTGATCTATGGTTTAAATATACAATTGATGGAGTGACCAACTGTATTGGAATATTTTA
* ** *
4168 AAGCATTTACAGTTCCAAAGAAATTATTGGAATTTAACCAGCTTTCATGGACTGGGCTATTGCTA
66 AAGCATTTACGGTTCCAAAGAAACCATTGGAATATAACCAGCTTTCATGGACTGGGCTATTGCTA
* *
4233 CAAAATATAGTTATTGGTCACCTCAAGTTTAAAATGCAGGATTCCTTTGCAGTTCATGGTCAAAA
131 CAAAATACAGTTATTGGTCACCTCAAGTTTAAAATGCAGGATTCCTCTGCAGTTCATGGTCAAAA
* *
4298 AGAAAATAGTTGTTCAATGCATGTAAAGCTTTGGTAACATCCCTGCTTCTTTTCAGTTGAGGGTT
196 AGCAAATAGTTGTTCAATGCATGTAAAGTTTTGGTAACATCCCTGCTTCTTTTCAGTTGAGGGTT
*
4363 GGGTATAGATTAAGATGCTTGAACAATAGACGTTAGACTAGCTACTCTCTAATAAAGAAAAACCA
261 GGGTATAGATTAAGATGCTTGAACAATAG-CGTTAGACT-GCTGCTCTCTAATAAAG-AAAACCA
*
4428 ATTTCCCTTTTACAGTATCTAGTGCTATCAAGTTCCAGCTATAGGATTCCATGGGAGGACATGAT
323 ATTGCCC-TTTACAGTATCTAGTGCTATCAAGTTCCAGCTATAGGATTCCATGGGAGGACATGAT
* *
4493 GAAAGAGTGTTAATCAGGTCATTATGGAAGGAGAGACAATGCAAGGGTCGAAATTTAAGTTGCGC
387 GAAAGAGTGTTAAGCAGGCCATTATGGAAGGAGAGACAATGCAAGGGTCGAAATTTAAGTTGCGC
*
4558 ATGCACAATATTTGAATTGGCATGGCCCAACTCCATTATCGATATTCTTTCTCTTGTAAAAGAGC
452 ATGCACAATATCTGAATTGGCATGGCCCAACTCCATTATCGATATTCTTTCTCTTGTAAAAGAGC
* *
4623 AAACTCTGGTCTTTGGTTGACTGAGGCAAACTTCAAGATGTAGGTATGGTGCAATAGATGTAGAG
517 AAACTCTGGTCTTTGGTTGACTGATGCAAACTTCAAGATGTAGGTACGGTGCAATAGATGTAGAG
*
4688 GCTCCGACGAAGAGCAACAAACTATCTGTTGTGACACTGATAGATTGGAATCTGCAGTGGGGGAT
582 GCTCCGACG-AGAGCAACAGACTATC-GTTGTGACACTGATAGATTGGAATCTGCAGTGGGGGAT
*
4753 CACGTGTATTGTGTTGAAGGCATGCAA
645 CACGTGTACTGTGTTGAAGGCATGCAA
* *
4780 CAAGAGCTTGATCTATGGTTTAAATATACAATTGATGGAGTGACCAACTCTATTAGAATATTTTA
1 CAAGAGCTTGATCTATGGTTTAAATATACAATTGATGGAGTGACCAACTGTATTGGAATATTTTA
* *
4845 AAGCATTTATGGTTCCAAAGAAACCATTGAAATATAACCAGCTTTCATGGACTGGGCTATTGCTA
66 AAGCATTTACGGTTCCAAAGAAACCATTGGAATATAACCAGCTTTCATGGACTGGGCTATTGCTA
*
4910 CAAAATACAGTTATTGGTCACCTCAAG-TTAAAAGTGCAGGATTCCTCTGCAATTCATGGTCAAA
131 CAAAATACAGTTATTGGTCACCTCAAGTTTAAAA-TGCAGGATTCCTCTGCAGTTCATGGTCAAA
4974 AAGCAAATAGTTGTTCAATGCATGTAAAGTTTTGGTAACATCCCTGCTTCTTTTCAGTTGAGGGT
195 AAGCAAATAGTTGTTCAATGCATGTAAAGTTTTGGTAACATCCCTGCTTCTTTTCAGTTGAGGGT
* * * *
5039 TGGGTATAGATTAAGATGCTTGAATAATATGTGTTAGACTGATTGCTCTTTAATAAAGAAAACCA
260 TGGGTATAGATTAAGATGCTTGAACAATA-GCGTTAGACTG-CTGCTCTCTAATAAAGAAAACCA
*
5104 ATTGCCCCTTTACAGGT-GCTAGTGCTATCAAGTTCCAGCTATAGGATTCCATGGGAGGACATGA
323 ATTG-CCCTTTACA-GTATCTAGTGCTATCAAGTTCCAGCTATAGGATTCCATGGGAGGACATGA
* * *
5168 TGAAAGAATGTTAAGCAGGCCATTATGGAAGGAGAGACAATGCAAGGGTTGAAATTTAAGTTGTG
386 TGAAAGAGTGTTAAGCAGGCCATTATGGAAGGAGAGACAATGCAAGGGTCGAAATTTAAGTTGCG
* * *
5233 CATGCACAATATCTGAATTGGCATGGCCCAACTCCATTATCGATATTATTTCTCTTGTAAGAGAT
451 CATGCACAATATCTGAATTGGCATGGCCCAACTCCATTATCGATATTCTTTCTCTTGTAAAAGAG
* *
5298 CAAACTTTTGTCTTTGGTTGACTGATGCAAACTTCAAGATGTAGGTACGGTGCAATAGATGTAGA
516 CAAACTCTGGTCTTTGGTTGACTGATGCAAACTTCAAGATGTAGGTACGGTGCAATAGATGTAGA
5363 GGCTCCGACTGAGAGCAACAGACTATCGATTGTGACACTGATAGATTGGAATCTGCAGTGGGGGA
581 GGCTCCGAC-GAGAGCAACAGACTATCG-TTGTGACACTGATAGATTGGAATCTGCAGTGGGGGA
*
5428 TCACGTGTACTATGTTGAAGGCATGCAA
644 TCACGTGTACTGTGTTGAAGGCATGCAA
5456 ACATCTTGAA
Statistics
Matches: 1255, Mismatches: 84, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
674 1 0.00
675 249 0.20
676 761 0.61
677 243 0.19
678 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (671 bp):
CAAGAGCTTGATCTATGGTTTAAATATACAATTGATGGAGTGACCAACTGTATTGGAATATTTTA
AAGCATTTACGGTTCCAAAGAAACCATTGGAATATAACCAGCTTTCATGGACTGGGCTATTGCTA
CAAAATACAGTTATTGGTCACCTCAAGTTTAAAATGCAGGATTCCTCTGCAGTTCATGGTCAAAA
AGCAAATAGTTGTTCAATGCATGTAAAGTTTTGGTAACATCCCTGCTTCTTTTCAGTTGAGGGTT
GGGTATAGATTAAGATGCTTGAACAATAGCGTTAGACTGCTGCTCTCTAATAAAGAAAACCAATT
GCCCTTTACAGTATCTAGTGCTATCAAGTTCCAGCTATAGGATTCCATGGGAGGACATGATGAAA
GAGTGTTAAGCAGGCCATTATGGAAGGAGAGACAATGCAAGGGTCGAAATTTAAGTTGCGCATGC
ACAATATCTGAATTGGCATGGCCCAACTCCATTATCGATATTCTTTCTCTTGTAAAAGAGCAAAC
TCTGGTCTTTGGTTGACTGATGCAAACTTCAAGATGTAGGTACGGTGCAATAGATGTAGAGGCTC
CGACGAGAGCAACAGACTATCGTTGTGACACTGATAGATTGGAATCTGCAGTGGGGGATCACGTG
TACTGTGTTGAAGGCATGCAA
Found at i:13409 original size:13 final size:13
Alignment explanation
Indices: 13391--13455 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 13
13381 AATGATTATT
13391 TTTTCAAAAATGA
1 TTTTCAAAAATGA
13404 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
*
13418 TTTTCAAGAAATAA
1 TTTTCAA-AAATGA
13432 TTTTCAAAAATGA
1 TTTTCAAAAATGA
13445 GTTTTCAAAAA
1 -TTTTCAAAAA
13456 GGTTTTGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
13 13 0.28
14 31 0.67
15 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:14126 original size:24 final size:22
Alignment explanation
Indices: 14088--14146 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 22
14078 ATGGTGAAGC
14088 AAAA-AAAAAAAAAAGCAAAGA
1 AAAAGAAAAAAAAAAGCAAAGA
14109 AAAAGAAAAAAGAGAAAGCAAAGA
1 AAAAGAAAAAA-A-AAAGCAAAGA
14133 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
14147 GAAACATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.11
22 8 0.23
23 2 0.06
24 21 0.60
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAAAGCAAAGA
Found at i:15144 original size:37 final size:37
Alignment explanation
Indices: 15081--15558 Score: 435
Period size: 37 Copynumber: 12.9 Consensus size: 37
15071 CAAAACCTCA
* * *
15081 AAATCCTTGTTCAAGATTCCTGTTTAGGTGTCTTATC
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* *
15118 AAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTTATT
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* *
15155 AAATCCTTATTTTAGGTCCCTGTTTAGGTGTCTTATC
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* *
15192 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATC
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* * * *
15229 GAAAT-CTGGTTCAAGATCCCTGTTTAGGTGTCTCATC
1 -AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* * * * *
15266 AAAAT-CTTGTTCAAGATTCATGTTTAGGT-TCTTATT
1 -AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* * * *
15302 AAATCTTTATTTAAGGTCCCTATTTAGATGTCTTATC
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* *
15339 AAAAT-CTTGTTTAAGATCCCTGTTTAGGTTTCTTATC
1 -AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* * * *
15376 AAATCCTTATTTAAGGTGCCTGTTTAGGTTTCTTGTC
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
** * * * *
15413 AAAATTTTTTGTTTAAGATCCTTGTTCAGGTTTCTTATC
1 -AAA-TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* * * *
15452 AAATCCTTATTTAAGGTCCCCGTTTAGGTGTCTCATTA
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTA-TC
* ** * * * *
15490 AAAT-CTTGTTCAAAATTCTTGTTTAGGTTTCTTATT
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
* * *
15526 AAATCCTTATTTAAGGTACCTATTTAGGTGTCT
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCT
15559 CTTCAAAATC
Statistics
Matches: 356, Mismatches: 76, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
35 4 0.01
36 30 0.08
37 277 0.78
38 19 0.05
39 26 0.07
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (37 bp):
AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTTATC
Found at i:15205 original size:74 final size:74
Alignment explanation
Indices: 15081--15568 Score: 518
Period size: 74 Copynumber: 6.6 Consensus size: 74
15071 CAAAACCTCA
* * * * * *
15081 AAATCCTTGTTCAAGATTCCTGTTTAGGTGTCTTATC-AAATCCTTGTTTAAGGTCCCTATTTAG
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAAT-CTTGTTTAAGATCCCTGTTTAG
*
15145 GTGTCTTATT
65 GTTTCTTATT
* * *
15155 AAATCCTTATTTTAGGTCCCTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAG
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAAT-CTTGTTTAAGATCCCTGTTTAG
* * *
15219 GTGTCTCATCG
65 GTTTCTTAT-T
** * * * * * *
15230 AAAT-CTGGTTCAAGATCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCATGTTTAGG
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCTTGTTTAAGATCCCTGTTTAGG
15294 -TTCTTATT
66 TTTCTTATT
* * *
15302 AAATCTTTATTTAAGGTCCCTATTTAGATGTCTTATCAAAATCTTGTTTAAGATCCCTGTTTAGG
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCTTGTTTAAGATCCCTGTTTAGG
*
15367 TTTCTTATC
66 TTTCTTATT
* * * * * *
15376 AAATCCTTATTTAAGGTGCCTGTTTAGGTTTCTTGTCAAAATTTTTTGTTTAAGATCCTTGTTCA
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAA--TCTTGTTTAAGATCCCTGTTTA
*
15441 GGTTTCTTATC
64 GGTTTCTTATT
* * * * * * *
15452 AAATCCTTATTTAAGGTCCCCGTTTAGGTGTCTCATTAAAATCTTGTTCAAAATTCTTGTTTAGG
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCTTGTTTAAGATCCCTGTTTAGG
15517 TTTCTTATT
66 TTTCTTATT
* *
15526 AAATCCTTATTTAAGGTACCTATTTAGGTGTCTCT-TCAAAATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCT-TATCAAAATC
15569 CCAGCTTAGG
Statistics
Matches: 346, Mismatches: 61, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
72 4 0.01
73 54 0.16
74 215 0.62
75 8 0.02
76 65 0.19
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (74 bp):
AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCTTGTTTAAGATCCCTGTTTAGG
TTTCTTATT
Found at i:16104 original size:54 final size:54
Alignment explanation
Indices: 15664--16086 Score: 618
Period size: 54 Copynumber: 7.8 Consensus size: 54
15654 GTCTCTGTAG
* * *
15664 TAAGTTGATCTTAAGTTGATCTAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
1 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
*
15718 TAAGTTGATCTTAAGATGACCCTGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
1 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
15772 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
1 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
* *
15826 TAAGTTAATCTTAA-ATTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
1 TAAGTTGATCTTAAGA-TGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
*
15880 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTTAGAGATC
1 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
* *
15934 TAAGTTGATCTTAAGATGGCCCAGTGTGGTCTTTCATAGAAGCTTTT-AGAGGTC
1 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAGATC
* * * * *
15988 TAAGTTGATCTTCAA-ATTACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATC
1 TAAGTTGATCTT-AAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
* * * * * *
16042 TAAGTTGATTTTAAGTTGATCCAGTGTGGTCATTCAAATAAGTTT
1 TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTT
16087 ACGATGATCA
Statistics
Matches: 335, Mismatches: 28, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
53 7 0.02
54 321 0.96
55 7 0.02
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (54 bp):
TAAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATC
Found at i:16232 original size:33 final size:33
Alignment explanation
Indices: 16190--16267 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
16180 ATTAATTAAG
* * * *
16190 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
16223 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
16256 AAGTTCAAAATC
1 AAGTTCAAAATC
16268 CACAGTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:16399 original size:7 final size:7
Alignment explanation
Indices: 16389--16450 Score: 124
Period size: 7 Copynumber: 8.9 Consensus size: 7
16379 AATTCAAAAT
16389 TCAGAAC
1 TCAGAAC
16396 TCAGAAC
1 TCAGAAC
16403 TCAGAAC
1 TCAGAAC
16410 TCAGAAC
1 TCAGAAC
16417 TCAGAAC
1 TCAGAAC
16424 TCAGAAC
1 TCAGAAC
16431 TCAGAAC
1 TCAGAAC
16438 TCAGAAC
1 TCAGAAC
16445 TCAGAA
1 TCAGAA
16451 TCCACAATCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.15
Consensus pattern (7 bp):
TCAGAAC
Found at i:16459 original size:7 final size:7
Alignment explanation
Indices: 16449--16661 Score: 237
Period size: 7 Copynumber: 30.3 Consensus size: 7
16439 CAGAACTCAG
*
16449 AATCCAC
1 AATCCAA
16456 AATCCAAA
1 AATCC-AA
*
16464 AATCCAG
1 AATCCAA
*
16471 AATCCAG
1 AATCCAA
*
16478 AATCCAG
1 AATCCAA
*
16485 AATCCAG
1 AATCCAA
*
16492 AATCCAG
1 AATCCAA
*
16499 AATCCAG
1 AATCCAA
*
16506 AATCCAG
1 AATCCAA
*
16513 AATCCAG
1 AATCCAA
16520 AATCCAA
1 AATCCAA
*
16527 AATCCAG
1 AATCCAA
16534 AATCCAA
1 AATCCAA
16541 AATCCAA
1 AATCCAA
16548 AATCCAA
1 AATCCAA
16555 AATCCAA
1 AATCCAA
16562 AATCCAA
1 AATCCAA
16569 AATCCAA
1 AATCCAA
16576 AATCCAA
1 AATCCAA
*
16583 AATTCAA
1 AATCCAA
16590 AATCCAA
1 AATCCAA
*
16597 AATTCAA
1 AATCCAA
*
16604 AATTCAA
1 AATCCAA
*
16611 AATTCAA
1 AATCCAA
*
16618 AATTCAA
1 AATCCAA
*
16625 AATTCAA
1 AATCCAA
*
16632 AATTCAA
1 AATCCAA
*
16639 AATTCAA
1 AATCCAA
*
16646 AATTCAA
1 AATCCAA
*
16653 AATTCAA
1 AATCCAA
16660 AA
1 AA
16662 CCTGCATTTC
Statistics
Matches: 197, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
7 191 0.97
8 6 0.03
ACGTcount: A:0.53, C:0.24, G:0.04, T:0.19
Consensus pattern (7 bp):
AATCCAA
Done.