Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009913.1 Corchorus capsularis cultivar CVL-1 contig09934, 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: 36860
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1504 original size:6 final size:6
Alignment explanation
Indices: 1495--1521 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1485 AAAACAAAGC
1495 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
1522 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:1536 original size:13 final size:13
Alignment explanation
Indices: 1518--1552 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1508 AATCTAAATC
*
1518 TAAAGCAGATTAA
1 TAAAGCAAATTAA
1531 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
1544 TAAAACAAA
1 TAAAGCAAA
1553 CAATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:7573 original size:436 final size:436
Alignment explanation
Indices: 6630--7861 Score: 1724
Period size: 436 Copynumber: 2.8 Consensus size: 436
6620 TCATGTCCTT
** ** * * * * *
6630 ATGAAAGAAATAGATCATGCAATAACCTTTCAACCGACACTTGAACAACATCAATCAGACAAATG
1 ATGAAAGTCATAGATCACACAAAAACCTTTTAACCAACACTTGAACAACCTCAATCGGAC-AAT-
* * * * * * *
6695 GATCGGACCGGAAATTACACAATAATAAATAGACCGGCAACCGAAACCACAAAATTTCAGAAGCA
64 --T-GGACCGAAAATTATATAATATTAGATAGACTGGCAATCGAAACCACAAAATTTCAGAAGCA
* * * * * * * * *
6760 TTTTTTAGAATCAAAAAATTAAAATTGGCTTCTGAGTTCTTCATGAAAGTTGTACATCATTAAAT
126 TTTTTTAGAATCAAAACATTAAAATTGGTTTTTGAGTCCTTCGTGGAAGTCGTAGATCATGAAAT
* * * *
6825 TATCTTTTAATAGACACTTGAATCACTTTAATCGGA-AAATATAACAAAAAATTCAAAAATAAAA
191 TATCTTTTAATAGACACTTGAATCACCTTAATCGGACAAATGTAAAAAAAAATACAAAAATAAAA
*
6889 ACCAACGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTAT
256 GCCAACGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTAT
*
6954 GACGATCATTTGATAAATGATCCAGCAAAAAAAAATTTGTTTATGGAGACCAAACATAAAAATTA
321 GACGATCATTTGATAAATAATCCAGC--AAAAAAATTTGTTTATGGAGACCAAACATAAAAATTA
* * *
7019 CCTCTTGAATCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAAGACTTTA
384 CCTCTTGAATCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGACCTCA
* * *
7072 ATGAAACTCGTAGATCACACAATAAA-CTTTTAACGAACACTTGAACAACCTCAATCGGACAATT
1 ATGAAAGTCATAGATCACACAA-AAACCTTTTAACCAACACTTGAACAACCTCAATCGGACAATT
* * * *
7136 GGACCGAAAATTATATAATATTAGATAAACTGGCAATCGAGACCACAAAATTTAAGAAACA-TTT
65 GGACCGAAAATTATATAATATTAGATAGACTGGCAATCGAAACCACAAAATTTCAGAAGCATTTT
*
7200 TTAGAATCAAAACATTAAAATTGGTTTTTGAGTCCTTCGTGGAAGTCGTGGATCATGAAATTATC
130 TTAGAATCAAAACATTAAAATTGGTTTTTGAGTCCTTCGTGGAAGTCGTAGATCATGAAATTATC
*
7265 TTTTAATAGACACTTGAATCACCTTAATCGGACAAATGTAAGAAAAAAATACAAAAATAAAAGTC
195 TTTTAATAGACACTTGAATCACCTTAATCGGACAAATGTAA-AAAAAAATACAAAAATAAAAGCC
*
7330 AACGCGTTAAATCGTCCAACCCATAATTGTAAATGATTAAATAGAATAAAGCATAAAAGTATGAC
259 AACGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATGAC
* *
7395 GATCATTTGATAAATAATCCAGCAAACAAATTTGTTTATGGAGACCAAACATAAAAATTACCTTT
324 GATCATTTGATAAATAATCCAGCAAAAAAATTTGTTTATGGAGACCAAACATAAAAATTACCTCT
*
7460 TGAATCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGCCCTCA
389 TGAATCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGACCTCA
*
7508 ATGAAAGTCATAGATCACACAAAAACCTTTTAACCAACACTTAAACAACCTCAATCGGACAATTG
1 ATGAAAGTCATAGATCACACAAAAACCTTTTAACCAACACTTGAACAACCTCAATCGGACAATTG
*
7573 GACCGAAAATTATATAATATTAGATAGACTGGCAATCGAAACCACAAAATTTCAGAAGTATTTTT
66 GACCGAAAATTATATAATATTAGATAGACTGGCAATCGAAACCACAAAATTTCAGAAGCATTTTT
* * *
7638 TAGAATCAAAACATTAAAATTGATTTTTGAGTCCATCGTGGAAGTCGTAGATCATGAAATTACCT
131 TAGAATCAAAACATTAAAATTGGTTTTTGAGTCCTTCGTGGAAGTCGTAGATCATGAAATTATCT
* * * * *
7703 TTCAATAGACACTTGAATCACCTTGATCGGAC-AA-GCAAAACAAAACATAGAAGAACT-AAAGC
196 TTTAATAGACACTTGAATCACCTTAATCGGACAAATGTAAAA-AAAA-ATACAA-AAATAAAAGC
* * * *
7765 CGAA-ACGTTCAGTCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTA-G
258 C-AACGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATG
*
7828 TAGGATCATTTGATAAATAATCCAGCAAAAAAAT
322 -ACGATCATTTGATAAATAATCCAGCAAAAAAAT
7862 GATTTGTTTA
Statistics
Matches: 707, Mismatches: 73, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
434 2 0.00
435 11 0.02
436 381 0.54
437 157 0.22
438 106 0.15
441 3 0.00
442 45 0.06
443 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (436 bp):
ATGAAAGTCATAGATCACACAAAAACCTTTTAACCAACACTTGAACAACCTCAATCGGACAATTG
GACCGAAAATTATATAATATTAGATAGACTGGCAATCGAAACCACAAAATTTCAGAAGCATTTTT
TAGAATCAAAACATTAAAATTGGTTTTTGAGTCCTTCGTGGAAGTCGTAGATCATGAAATTATCT
TTTAATAGACACTTGAATCACCTTAATCGGACAAATGTAAAAAAAAATACAAAAATAAAAGCCAA
CGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGAATAAAGCATAAAAGTATGACGA
TCATTTGATAAATAATCCAGCAAAAAAATTTGTTTATGGAGACCAAACATAAAAATTACCTCTTG
AATCCTCCACGAAACTCATTAATCAAATTCAACTTTCAAGACCTCA
Found at i:10605 original size:22 final size:22
Alignment explanation
Indices: 10573--10694 Score: 95
Period size: 22 Copynumber: 5.5 Consensus size: 22
10563 TCTAGTTATT
*
10573 ATTTTGATAACCTATGTATGAA
1 ATTTTGATAACCTATATATGAA
*
10595 ATTTTGTTAACCTCA-ATATGAA
1 ATTTTGATAACCT-ATATATGAA
* * *
10617 ATTTTGATACCCTTTTTATGAA
1 ATTTTGATAACCTATATATGAA
* *
10639 ATTTTGATAA-CTACACTATTAA
1 ATTTTGATAACCTATA-TATGAA
* * * * *
10661 GTTTTAATAATCTGTCTATGAA
1 ATTTTGATAACCTATATATGAA
*
10683 ATTTTGGTAACC
1 ATTTTGATAACC
10695 ATGCCCTGAA
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
21 2 0.03
22 70 0.93
23 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (22 bp):
ATTTTGATAACCTATATATGAA
Found at i:11357 original size:99 final size:99
Alignment explanation
Indices: 11137--11337 Score: 270
Period size: 99 Copynumber: 2.1 Consensus size: 99
11127 ATGAGTTACA
*
11137 ACTTACAATTGGAT-CTTTAATCCTTTTTATACTTTCAATAATACCTCACCGTTATATATACATT
1 ACTTA-AATTGGATACTTTAATTCTTTTTATACTTTCAATAATACCTCACCGTTATATATACATT
11201 ACATTCAAATTCAAATAATAATTCCAATTAAAGTG
65 ACATTCAAATTCAAATAATAATTCCAATTAAAGTG
* * *
11236 AGTTACAATTGGGTA-TTTAATTCTTTTTAT-CATTTCAATAACT-CCTCACTGTTATATATACA
1 ACTTA-AATTGGATACTTTAATTCTTTTTATAC-TTTCAATAA-TACCTCACCGTTATATATACA
* *
11298 -TACATT-ACATTCAAATAATAATTCCAATTAAAGTT
63 TTACATTCAAATTCAAATAATAATTCCAATTAAAGTG
11333 ACTTA
1 ACTTA
11338 GTTGGCATAT
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
97 31 0.34
98 7 0.08
99 53 0.58
100 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (99 bp):
ACTTAAATTGGATACTTTAATTCTTTTTATACTTTCAATAATACCTCACCGTTATATATACATTA
CATTCAAATTCAAATAATAATTCCAATTAAAGTG
Found at i:13186 original size:22 final size:22
Alignment explanation
Indices: 13155--13222 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
13145 AATTAAGTGT
*
13155 CCTCTTTATGAAATTTTGTTAATC
1 CCTC-TTATGAAATTTTGATAA-C
*
13179 TCC-C-TATGAAATATTGATAAC
1 -CCTCTTATGAAATTTTGATAAC
*
13200 CCTCTTATGAAATTTTGAAAAC
1 CCTCTTATGAAATTTTGATAAC
13222 C
1 C
13223 AAACTATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 30 0.81
24 1 0.03
25 2 0.05
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (22 bp):
CCTCTTATGAAATTTTGATAAC
Found at i:13326 original size:29 final size:29
Alignment explanation
Indices: 13250--13354 Score: 79
Period size: 31 Copynumber: 3.5 Consensus size: 29
13240 GCCCTAATAT
* *
13250 CCAAATTGGGTCTAAACCTTTCCAAATTTA
1 CCAAATTGGGCCTAAACCTTT-CAAATTGA
* * *
13280 CTCAATTTGAGCATAAACCTTT-AAATATGA
1 C-CAAATTGGGCCTAAACCTTTCAAAT-TGA
* *
13310 CCAAATTGGGCCTAAACGTTAGCAAATTG-
1 CCAAATTGGGCCTAAACCTT-TCAAATTGA
13339 CACAAATTTGGGCCTA
1 C-CAAA-TTGGGCCTA
13355 TTTTGGACGG
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
29 20 0.34
30 10 0.17
31 29 0.49
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (29 bp):
CCAAATTGGGCCTAAACCTTTCAAATTGA
Found at i:13721 original size:22 final size:22
Alignment explanation
Indices: 13672--13747 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
13662 AAAATACCAC
* * *
13672 TATGAAAATTTGGTAATGATATT
1 TATGAAAATTTGATAAT-CTCTT
13695 T-TGAAAATTTGATAATCTCTT
1 TATGAAAATTTGATAATCTCTT
* * *
13716 TATGAAATTTTGATAACCTCTC
1 TATGAAAATTTGATAATCTCTT
13738 TAT-AAAATTT
1 TATGAAAATTT
13748 TGTTGACCCC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 10 0.22
22 34 0.76
23 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (22 bp):
TATGAAAATTTGATAATCTCTT
Found at i:13877 original size:25 final size:23
Alignment explanation
Indices: 13823--13886 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
13813 GATAACAACA
* *
13823 CTATGAAATTTCGATAATCTTCT
1 CTATGAAATTTTGATAATATTCT
13846 -TAT-AAATTTTGATAATATGATCT
1 CTATGAAATTTTGATAATAT--TCT
*
13869 CTATGAAATTCTGATAAT
1 CTATGAAATTTTGATAAT
13887 CACTATATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.38
22 3 0.09
23 3 0.09
24 3 0.09
25 12 0.35
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (23 bp):
CTATGAAATTTTGATAATATTCT
Found at i:14011 original size:20 final size:20
Alignment explanation
Indices: 13961--14011 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
13951 TAACCTTCGT
*
13961 ATGAAAATTTGATAACCACA
1 ATGAAATTTTGATAACCACA
*
13981 ATAAAAAATTTTGATAACCACA
1 AT--GAAATTTTGATAACCACA
*
14003 CTGAAATTT
1 ATGAAATTT
14012 CAATAACCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.32
22 17 0.68
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (20 bp):
ATGAAATTTTGATAACCACA
Found at i:14100 original size:22 final size:21
Alignment explanation
Indices: 14047--14129 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
14037 TAAGCCGATT
* * *
14047 CTATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAATCTC
*
14068 GCTATGGAATTTTGATAATCTC
1 -CTATGAAATTTTGATAATCTC
* * *
14090 CTCATGAAATTATAATAATCATA
1 CT-ATGAAATTTTGATAATC-TC
*
14113 TTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
14130 CCACGAAGAG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
21 2 0.04
22 44 0.92
23 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
CTATGAAATTTTGATAATCTC
Found at i:15428 original size:15 final size:16
Alignment explanation
Indices: 15408--15440 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
15398 ATAAAATATT
*
15408 TTATTTCAT-AAATTA
1 TTATTTAATCAAATTA
15423 TTATTTAATCAAATTA
1 TTATTTAATCAAATTA
15439 TT
1 TT
15441 TCGGATTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAATCAAATTA
Found at i:22670 original size:11 final size:11
Alignment explanation
Indices: 22627--22664 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22617 TTTCTGTATA
*
22627 AAATAAATTAT
1 AAATTAATTAT
22638 CAAA-TAATTAT
1 -AAATTAATTAT
22649 AAATTAATTAT
1 AAATTAATTAT
22660 AAATT
1 AAATT
22665 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:23884 original size:2 final size:2
Alignment explanation
Indices: 23877--23902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23867 TTTAGTAACA
23877 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
23903 GCCCCCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29195 original size:45 final size:45
Alignment explanation
Indices: 29128--29214 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
29118 TAGAGTAGTG
* *
29128 GAATTACTAAAAGATCCCTACCCCGAATTAGTGATAAGCTGGGTA
1 GAATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGGGTA
* *
29173 GAATTACTAAAAGATCCATACCCCGGATTAATGATGAGCTGG
1 GAATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGG
29215 AGAAGTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (45 bp):
GAATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGGGTA
Found at i:29559 original size:166 final size:167
Alignment explanation
Indices: 29268--29598 Score: 454
Period size: 166 Copynumber: 2.0 Consensus size: 167
29258 AATGTCTTAA
* * * * *
29268 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGGATTGCTTATGGAGCTAGAGAAC
* ** * *
29333 TTATTTTTTTCGTCTTTTCCTACTTAGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
66 TAACATTTTTCGTCTTTACCTACTTAGCAGATTACTTAAATGTCATAACTTTTGATTCTTGAGGG
*
29398 GATTAAATAAGTAATA-TTTTTGGTCATTTCTCAATGG
131 GATTAAATAAGTAA-ACTTTGTGGTCATTTCTCAATGG
* *
29435 ACTTGAATAGAGTAGTGGAATTAATAAATGATCTCC-ATCAAGGATTG-TTGAT-GAGCTAGAGA
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATC-CCTACCAAGGATTGCTT-ATGGAGCTAGAGA
* * *
29497 ACTAACATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCATAATTTTTTATTCTTGAG
64 ACTAACATTTTTCGTCTTTACCTACTTAGCAGATTACTTAAATGTCATAACTTTTGATTCTTGAG
*
29562 GGGATTAAATAATTAAACTTTGTGGTCATTTCTCAAT
129 GGGATTAAATAAGTAAACTTTGTGGTCATTTCTCAAT
29599 TGACAAATGA
Statistics
Matches: 144, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
165 1 0.01
166 101 0.70
167 40 0.28
168 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGGATTGCTTATGGAGCTAGAGAAC
TAACATTTTTCGTCTTTACCTACTTAGCAGATTACTTAAATGTCATAACTTTTGATTCTTGAGGG
GATTAAATAAGTAAACTTTGTGGTCATTTCTCAATGG
Found at i:31441 original size:45 final size:45
Alignment explanation
Indices: 31392--31477 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
31382 ACTTCTCCAA
*
31392 CTCATCATTAATCCGAGGTAGGGATTTTTTAGTAATTCCACCCAG
1 CTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCACCCAG
*
31437 CTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCAC
31478 TACTCTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
CTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCACCCAG
Found at i:35426 original size:21 final size:21
Alignment explanation
Indices: 35401--35443 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
35391 ATATTGTCTT
35401 TCAATTCATTTTTTAACTAAA
1 TCAATTCATTTTTTAACTAAA
35422 TCAATTCATTTTTTAACTAAA
1 TCAATTCATTTTTTAACTAAA
35443 T
1 T
35444 TATTGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
TCAATTCATTTTTTAACTAAA
Found at i:35593 original size:36 final size:36
Alignment explanation
Indices: 35553--35657 Score: 85
Period size: 36 Copynumber: 3.1 Consensus size: 36
35543 ATCACTACTT
35553 ATTGTTGATTTAAATTATACTCTATTTGATTTAGGA
1 ATTGTTGATTTAAATTATACTCTATTTGATTTAGGA
* ** * ** *
35589 ATTGTGGCCTTAATTTGGACTTTA-TT--TTT-GG-
1 ATTGTTGATTTAAATTATACTCTATTTGATTTAGGA
* * *
35620 GTTGTTGATTTAAATTATAGTCCATTTGATTTAGGA
1 ATTGTTGATTTAAATTATACTCTATTTGATTTAGGA
35656 AT
1 AT
35658 AATCACACTA
Statistics
Matches: 46, Mismatches: 18, Indels: 10
0.62 0.24 0.14
Matches are distributed among these distances:
31 14 0.30
32 4 0.09
33 3 0.07
34 3 0.07
35 4 0.09
36 18 0.39
ACGTcount: A:0.26, C:0.07, G:0.18, T:0.50
Consensus pattern (36 bp):
ATTGTTGATTTAAATTATACTCTATTTGATTTAGGA
Done.