Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016004.1 Corchorus olitorius cultivar O-4 contig16037, 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: 33203
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1928 original size:133 final size:133
Alignment explanation
Indices: 1767--2182 Score: 602
Period size: 133 Copynumber: 3.1 Consensus size: 133
1757 ACTGAAGTGC
* * * *
1767 GAAAATGATGAAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAATATAAAATAGAGCTTATA
1 GAAAAAGACGAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATAGAGCTTATA
* * *
1831 TGCAAGAAGACAAAAACGACCCTTCGACCGAAAGGGTATTTTTAGAAGTAGAAAATACTAAACTG
65 TGCAAGAAGACAAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTT
1896 AAAT
130 AAAT
* * * *
1900 GAAAAAGACGAAAATGACCCTTCGACCGATAGGGTATTCTTGAAAATAGATAATAGAGCTTATAT
1 GAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATAGAGCTTATAT
*
1965 GCAAGAAGACAAAAACGACCCTTCGACTGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTA
66 GCAAGAAGACAAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTA
2030 AAT
131 AAT
* * * *
2033 GCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACCAAACTTAA
1 GAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATA--GAGCTTAT
* ** *
2098 ATGCAA-CAGATGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACT
64 ATGCAAGAAGACAAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACT
2162 TAAAT
129 TAAAT
*
2167 GCAAAAGACGAAAATG
1 GAAAAAGACGAAAATG
2183 GGGCTCTATC
Statistics
Matches: 255, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
132 3 0.01
133 167 0.65
134 74 0.29
135 11 0.04
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (133 bp):
GAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATAGAGCTTATAT
GCAAGAAGACAAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTA
AAT
Found at i:1934 original size:67 final size:67
Alignment explanation
Indices: 1776--2182 Score: 536
Period size: 67 Copynumber: 6.1 Consensus size: 67
1766 CGAAAATGAT
* * * * *
1776 GAAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAATATAAAATA--GAGCTTATATGCAAGA
1 GAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAA-A
1838 AGAC
64 AGAC
* * * * * *
1842 AAAAACGACCCTTCGACCGAAAGGGTATTTTTAGAAGTAGAAAATACTAAACTGAAATGAAAAAG
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
1907 AC
66 AC
* * * * * * *
1909 GAAAATGACCCTTCGACCGATAGGGTATTCTTGAAAATAGATAATA--GAGCTTATATGCAAGAA
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAA-AA
1972 GAC
65 GAC
* * *
1975 AAAAACGACCCTTCGACTGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
2040 AC
66 AC
* *
2042 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACCAAACTTAAATGCAACAG
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
*
2107 AT
66 AC
2109 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
1 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
2174 AC
66 AC
2176 GAAAATG
1 GAAAATG
2183 GGGCTCTATC
Statistics
Matches: 292, Mismatches: 43, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
65 12 0.04
66 80 0.27
67 180 0.62
68 20 0.07
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (67 bp):
GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAG
AC
Found at i:2068 original size:200 final size:200
Alignment explanation
Indices: 1777--2154 Score: 546
Period size: 200 Copynumber: 1.9 Consensus size: 200
1767 GAAAATGATG
* * * *
1777 AAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATATAAAATAGAGCTTATATGCAAGAAGAC
1 AAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATAGAAAATAAAACTTAAATGCAAGAAGAC
* *
1842 AAAAACGACCCTTCGACCGAAAGGGTATTTTTAGAAGTAGAAAATACTAAACTGAAATGAAAAAG
66 AAAAACGACCCTTCGACCGAAAGGGTATTTTTAGAAATAGAAAATACCAAACTGAAATGAAAAAG
* *
1907 ACGAAAATGACCCTTCGACCGATAGGGTATTCTTGAAAATAGATAATAGAGCTTATATGCAAGAA
131 ACGAAAATGACCCTTCGACCGAAAGGGTATTCTTGAAAATAGAAAATAGAGCTTATATGCAAGAA
1972 GACAA
196 GACAA
*
1977 AAAC-GACCC-TTCGACTGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAA-AA
1 AAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAATAGAAAATA--AAACTTAAATGCAAGAA
* * * * *
2039 GACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACCAAACTTAAATGCAA
63 GACAAAAACGACCCTTCGACCGAAAGGGTATTTTTAGAAATAGAAAATACCAAACTGAAATGAAA
* * * *
2104 CAGATGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATA
128 AAGACGAAAATGACCCTTCGACCGAAAGGGTATTCTTGAAAATAGAAAATA
2155 CTAAACTTAA
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
198 3 0.02
199 34 0.22
200 109 0.69
201 11 0.07
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (200 bp):
AAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATAGAAAATAAAACTTAAATGCAAGAAGAC
AAAAACGACCCTTCGACCGAAAGGGTATTTTTAGAAATAGAAAATACCAAACTGAAATGAAAAAG
ACGAAAATGACCCTTCGACCGAAAGGGTATTCTTGAAAATAGAAAATAGAGCTTATATGCAAGAA
GACAA
Found at i:3510 original size:16 final size:16
Alignment explanation
Indices: 3489--3522 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3479 GTAGCTTCCA
3489 AAAGATGGGATATACT
1 AAAGATGGGATATACT
3505 AAAGATGGGATATACT
1 AAAGATGGGATATACT
3521 AA
1 AA
3523 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (16 bp):
AAAGATGGGATATACT
Found at i:3631 original size:28 final size:28
Alignment explanation
Indices: 3599--3702 Score: 147
Period size: 28 Copynumber: 3.7 Consensus size: 28
3589 TGTGAACTTA
* *
3599 AAAATTACCAAAATGCCCCTCAACGTGC
1 AAAATGACCAAAATGCCCCTGAACGTGC
*
3627 AAAATGACCAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGAACGTGC
* *
3655 AAAATGACCAAAATGCCCCCTGAATGT-A
1 AAAATGACCAAAATG-CCCCTGAACGTGC
3683 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
3703 AGATGACCTA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.07
28 55 0.80
29 9 0.13
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAACGTGC
Found at i:4448 original size:69 final size:69
Alignment explanation
Indices: 4364--4728 Score: 572
Period size: 69 Copynumber: 5.3 Consensus size: 69
4354 CTCATTAAAC
* * * * * *
4364 TTGGCTTATGGAAAAGCCTCTGCT-G-TATGGATGGAACCAATGTTTAAACTGACTCGCATGGAA
1 TTGGCTTGTGGAAAAGCCTATG-TGGCT-TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAA
4427 ACGAGT
64 ACGAGT
* * * * *
4433 TTGACTTATGGAAAAGTCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
4498 GAGT
66 GAGT
*
4502 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACCGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
4567 GAGT
66 GAGT
*
4571 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACCGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
4636 GAGT
66 GAGT
*
4640 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
4705 GAGT
66 GAGT
4709 TTGGCTTGTGGAAAAGCCTA
1 TTGGCTTGTGGAAAAGCCTA
4729 AACATTCGGA
Statistics
Matches: 277, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
68 1 0.00
69 275 0.99
70 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:5396 original size:50 final size:50
Alignment explanation
Indices: 5342--5541 Score: 310
Period size: 50 Copynumber: 4.0 Consensus size: 50
5332 CTTAAATGCC
* ** *
5342 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATCCAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * *
5392 CTTTGAAAACCGAATTTTGATCTTGAACTTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
*
5442 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* *
5492 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
5542 TTGTAAATCT
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 138 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:5557 original size:15 final size:16
Alignment explanation
Indices: 5537--5570 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5527 TGGAATGCAA
*
5537 TCTTATTGT-AAATCT
1 TCTTATTGTGAAAACT
5552 TCTTATTGTGAAAACT
1 TCTTATTGTGAAAACT
5568 TCT
1 TCT
5571 CCTGAGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (16 bp):
TCTTATTGTGAAAACT
Found at i:5871 original size:14 final size:15
Alignment explanation
Indices: 5844--5872 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5834 CTTCTCTTTT
5844 TTTTTTTATCATTCA
1 TTTTTTTATCATTCA
5859 TTTTTTTAT-ATTCA
1 TTTTTTTATCATTCA
5873 CTTGAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTTATCATTCA
Found at i:6619 original size:8 final size:8
Alignment explanation
Indices: 6608--6636 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6598 TTTTCTGTTT
6608 TTTTTTCA
1 TTTTTTCA
6616 TTTTTTCA
1 TTTTTTCA
6624 -TTTTTCA
1 TTTTTTCA
6631 TTTTTT
1 TTTTTT
6637 TTTGGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:6628 original size:27 final size:25
Alignment explanation
Indices: 6590--6639 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
6580 TTCCAAGTGC
*
6590 TTTTTCCATTTTCTGTTTTTTTTTCA
1 TTTTTCCATTTTC-ATTTTTTTTTCA
*
6616 TTTTTTCATTTTTCATTTTTTTTT
1 TTTTTCCA-TTTTCATTTTTTTTT
6640 GGATTATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTTTCCATTTTCATTTTTTTTTCA
Found at i:8720 original size:21 final size:22
Alignment explanation
Indices: 8685--8726 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
8675 CTAAGGTTTA
* *
8685 ATGGGATGCATGAATGAATGCC
1 ATGGCATGCATGAATAAATGCC
8707 ATGGCATG-ATGAATAAATGC
1 ATGGCATGCATGAATAAATGC
8727 ATGAGGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (22 bp):
ATGGCATGCATGAATAAATGCC
Found at i:15579 original size:28 final size:28
Alignment explanation
Indices: 15546--15622 Score: 113
Period size: 27 Copynumber: 2.8 Consensus size: 28
15536 AATGTGAACT
15546 TCAAAATGACCAAAATGCCCCTTAACATG
1 TCAAAATGACCAAAATGCCCCTTAA-ATG
*
15575 -CAAAATGACCAAAATGCCCC-TGAATG
1 TCAAAATGACCAAAATGCCCCTTAAATG
*
15601 TAAAAATGACCAAAATGCCCCT
1 TCAAAATGACCAAAATGCCCCT
15623 AGATGACCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 3 0.07
27 21 0.48
28 20 0.45
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (28 bp):
TCAAAATGACCAAAATGCCCCTTAAATG
Found at i:18751 original size:19 final size:18
Alignment explanation
Indices: 18718--18753 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18708 TTGAGATAAT
18718 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
18736 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
18754 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:21871 original size:15 final size:14
Alignment explanation
Indices: 21851--21880 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
21841 TCAAAAAGCC
21851 CACTAGAGTTCGTTT
1 CACTAGAGTTC-TTT
21866 CACTAGAGTTCTTT
1 CACTAGAGTTCTTT
21880 C
1 C
21881 TCATAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (14 bp):
CACTAGAGTTCTTT
Found at i:24573 original size:87 final size:87
Alignment explanation
Indices: 24417--24581 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 87
24407 TGAATGTGAT
* * * ** *
24417 CTTCCTAATGGAGTTATGGGTGGTTATGGTGCAAAATCTTTGGAAAATATTATGGTAGAGGGTAG
1 CTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGGAAAATATTATGGTAGAGGATAG
24482 TTTGAATTCAAATTTTTATGTC
66 TTTGAATTCAAATTTTTATGTC
* * * *
24504 CTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGGAAACTGA-TGTGGTGGTGGATA
1 CTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGGAAAAT-ATTATGGTAGAGGATA
*
24568 TTTTGAATTCAAAT
65 GTTTGAATTCAAAT
24582 CGGAGTGGTC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
87 65 0.98
88 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (87 bp):
CTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGGAAAATATTATGGTAGAGGATAG
TTTGAATTCAAATTTTTATGTC
Found at i:24770 original size:12 final size:12
Alignment explanation
Indices: 24753--24782 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24743 TTGAGCTTTG
24753 GAGGATATTGAA
1 GAGGATATTGAA
*
24765 GAGGATATTGAG
1 GAGGATATTGAA
24777 GAGGAT
1 GAGGAT
24783 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (12 bp):
GAGGATATTGAA
Found at i:25767 original size:22 final size:22
Alignment explanation
Indices: 25722--25767 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
25712 ATTTTTTATG
* * *
25722 ACCTTCTTATGAAATTTTGGTA
1 ACCTTCCTATAAAATTTTAGTA
*
25744 ACCTTCCTATAAAATTTTATTA
1 ACCTTCCTATAAAATTTTAGTA
25766 AC
1 AC
25768 GATATATGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (22 bp):
ACCTTCCTATAAAATTTTAGTA
Found at i:26067 original size:23 final size:23
Alignment explanation
Indices: 26041--26116 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
26031 CCTCATTATG
**
26041 AAATTTTGATAAACCTTTCTATA
1 AAATTTTGATAAACCTCCCTATA
26064 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
* *
26087 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAACCTCCCTATA
26109 AAATTTTG
1 AAATTTTG
26117 GTATGATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 18 0.37
23 31 0.63
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:26103 original size:22 final size:22
Alignment explanation
Indices: 25816--26116 Score: 182
Period size: 22 Copynumber: 13.5 Consensus size: 22
25806 TTAACCTTCT
* * *
25816 TATGAAACTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
25838 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCAC
* *
25860 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
25882 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
25905 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* ** * *
25926 ATATGATACATTGATAACCACAT
1 -TATGAAATTTTGATAACCTCAC
* *
25949 TATGAAAATTTGAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
25970 ATAT-AAATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * * *
25993 TCTGAAATATTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * * *
26015 TATGAAATTGTAACAACCTCAT
1 TATGAAATTTTGATAACCTCAC
**
26037 TATGAAATTTTGATAAACCTTTC
1 TATGAAATTTTGAT-AACCTCAC
* *
26060 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
*
26083 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
26104 TTATGAAATTTTG
1 -TATGAAATTTTG
26117 GTATGATTTT
Statistics
Matches: 214, Mismatches: 52, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
21 8 0.04
22 143 0.67
23 63 0.29
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:26150 original size:22 final size:22
Alignment explanation
Indices: 26125--26283 Score: 141
Period size: 22 Copynumber: 7.3 Consensus size: 22
26115 TGGTATGATT
*
26125 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCACTATGAAA
* * *
26147 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
26169 TTTTGATCTA-CACACTATGAAA
1 TTTTGAT-AACCTCACTATGAAA
*
26191 TTTTGATAACCCTC-TTATGAAA
1 TTTTGATAA-CCTCACTATGAAA
* *
26213 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-CACTATGAAA
26235 TTTTGATAACCTTCA-TATGAAA
1 TTTTGATAACC-TCACTATGAAA
* *
26257 TTTTGATATCCTC-C-CTGAAA
1 TTTTGATAACCTCACTATGAAA
26277 TTTTGAT
1 TTTTGAT
26284 TATTCCATAA
Statistics
Matches: 111, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
20 14 0.13
21 5 0.05
22 84 0.76
23 7 0.06
24 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:26254 original size:66 final size:66
Alignment explanation
Indices: 26125--26269 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
26115 TGGTATGATT
* * ** *
26125 TTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACACACTATGAA
1 TTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTATGAAATTTTGATCAACACACTATGAA
26190 A
66 A
*
26191 TTTTGATAACCCTC-TTATGAAATTTTG-AAAACTAAACTATGAAATTTTGAT-AAC-CTTCATA
1 TTTTGATAA-CCTCATTATGAAATTTTGTAAAACT-AACTATGAAATTTTGATCAACAC-AC-TA
26252 TGAAA
62 TGAAA
*
26257 TTTTGATATCCTC
1 TTTTGATAACCTC
26270 CCTGAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
64 1 0.01
65 11 0.16
66 52 0.76
67 4 0.06
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (66 bp):
TTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTATGAAATTTTGATCAACACACTATGAA
A
Found at i:26682 original size:22 final size:22
Alignment explanation
Indices: 26362--26759 Score: 173
Period size: 22 Copynumber: 17.9 Consensus size: 22
26352 CCAGAAATAC
* *
26362 CACTATGAAATTTTGGTAATCA
1 CACTATGAAATTTTGATAACCA
* * * *
26384 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** *
26406 CTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** * * * *
26428 TTCTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAACCA
** *
26450 CTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* **
26472 CACTTTGAAATTTTGATAAGAA
1 CACTATGAAATTTTGATAACCA
*
26494 AACTATGAAATTTTGATAATCCGA
1 CACTATGAAATTTTGATAA-CC-A
* * *
26518 TCTCTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAACCA
* *
26541 CTCTATGAGA-TTTGATAACC-
1 CACTATGAAATTTTGATAACCA
** * * * *
26561 TTCTATCAAATTTTGGTACTCCT
1 CACTATGAAATTTTGATA-ACCA
* *
26584 CA-TGAAATTGAGACTTTT-ATAACCTT
1 CACT---A-TGA-AATTTTGATAACC-A
* *
26610 CA-TATAAAATTTTGATAACAA
1 CACTATGAAATTTTGATAACCA
** *
26631 CACTAAAAAATTTTAATAACCA
1 CACTATGAAATTTTGATAACCA
*
26653 CAATATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
* * * * *
26675 CCCCATGATATATT-ACTAACCT
1 CACTATGAAATTTTGA-TAACCA
*
26697 C-CTTATGAAATTTTGTTAACCA
1 CAC-TATGAAATTTTGATAACCA
*
26719 CACTATGAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCA
* *
26741 CGCTATGACATTTTGATAA
1 CACTATGAAATTTTGATAA
26760 TTTCCTTAAT
Statistics
Matches: 281, Mismatches: 75, Indels: 40
0.71 0.19 0.10
Matches are distributed among these distances:
20 7 0.02
21 25 0.09
22 210 0.75
23 5 0.02
24 2 0.01
25 19 0.07
26 8 0.03
27 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:26739 original size:44 final size:43
Alignment explanation
Indices: 26389--26995 Score: 214
Period size: 44 Copynumber: 13.9 Consensus size: 43
26379 AATCACATTT
* * ** *
26389 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTTTC-TA
1 TGAAATTTTGATAACCACACTATGAAATTTT-ATAACC-TCCATA
* * * * ** *
26433 TAAAATTTTGTTGACCCCTTTATGAAATTTTGATAACCT-CACTT
1 TGAAATTTTGATAACCACACTATGAAATTTT-ATAACCTCCA-TA
** *
26477 TGAAATTTTGATAAGAAAACTATGAAATTTTGATAATCCGATCTC-TA
1 TGAAATTTTGATAACCACACTATGAAATTTT-ATAA-CC--TC-CATA
* * * * * *
26524 TGAAATTTCGATAATCACTCTATGAGATTTGATAACCTTC-TA
1 TGAAATTTTGATAACCACACTATGAAATTTTATAACCTCCATA
* * * * * *
26566 TCAAATTTTGGTACTCCTCA-TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAATTTTGATA-ACCACACT---A-TGA-AATTTTATAACCTCCATA
* * ** * *
26614 TAAAATTTTGATAACAACACTAAAAAATTTTAATAACCACAATA
1 TGAAATTTTGATAACCACACTATGAAATTTT-ATAACCTCCATA
* * * * *
26658 TGAAATTTTGATAACCACCCCATGATATATTACTAACCTCCTTA
1 TGAAATTTTGATAACCACACTATGAAATTTTA-TAACCTCCATA
*
26702 TGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTCGC-TA
1 TGAAATTTTGATAACCACACTATGAAATT-TTATAACCTC-CATA
* *** *
26746 TGACATTTTGATAATTTC-CT-T---A----ATAACCTTTC-TA
1 TGAAATTTTGATAACCACACTATGAAATTTTATAACC-TCCATA
* * * *
26780 TAAAATTGTGATAACCACACTATAAAATTTCAGTAACCTTCC-TA
1 TGAAATTTTGATAACCACACTATGAAATTTTA-TAACC-TCCATA
* * * *
26824 AGAAATTTTAATAACCTA-ATCCTATGAAATTTTGGTAACC-ACATTA
1 TGAAATTTTGATAACC-ACA--CTATGAAATTTT-ATAACCTCCA-TA
** * *
26870 TGAAATTTTGATAACTTTC-CCATGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAAC-CACACTATGAAATTTT-ATAACCTCCATA
* *
26914 TGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCC-TCA
1 TGAAATTTTGATAACCACACTATGAAATTTT-ATAACCTCCAT-A
* * *
26958 TGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 TGAAATTTTGATAACCA-CACTATGAAATTTT-ATAACC
26996 ACACAGAGAC
Statistics
Matches: 420, Mismatches: 101, Indels: 84
0.69 0.17 0.14
Matches are distributed among these distances:
34 21 0.05
35 3 0.01
36 1 0.00
39 2 0.00
42 16 0.04
43 15 0.04
44 255 0.61
45 14 0.03
46 37 0.09
47 41 0.10
48 14 0.03
49 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (43 bp):
TGAAATTTTGATAACCACACTATGAAATTTTATAACCTCCATA
Found at i:26829 original size:22 final size:23
Alignment explanation
Indices: 26804--26855 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
26794 CCACACTATA
*
26804 AAATTTCAGTAACCT-TCCTAAG
1 AAATTTCAATAACCTATCCTAAG
* *
26826 AAATTTTAATAACCTAATCCTATG
1 AAATTTCAATAACCT-ATCCTAAG
26850 AAATTT
1 AAATTT
26856 TGGTAACCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.52
24 12 0.48
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (23 bp):
AAATTTCAATAACCTATCCTAAG
Found at i:26874 original size:22 final size:22
Alignment explanation
Indices: 26846--26998 Score: 125
Period size: 22 Copynumber: 7.0 Consensus size: 22
26836 AACCTAATCC
*
26846 TATGAAATTTTGGTAACCACAT
1 TATGAAATTTTGATAACCACAT
** *
26868 TATGAAATTTTGATAACTTTC-C
1 TATGAAATTTTGATAAC-CACAT
*
26890 CATGAAATTTTGATAACTTC-CA-
1 TATGAAATTTTGATAAC--CACAT
* *
26912 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCACAT
* * *
26934 TATGGAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCACAT
* * *
26956 CATGAAATTATAATAACCATC-T
1 TATGAAATTTTGATAACCA-CAT
26978 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
26999 CAGAGACAAG
Statistics
Matches: 103, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 96 0.93
23 3 0.03
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:26943 original size:66 final size:66
Alignment explanation
Indices: 26782--26999 Score: 219
Period size: 66 Copynumber: 3.3 Consensus size: 66
26772 CCTTTCTATA
* * * * * *
26782 AAATTGTGATAACCACACTAT-AAAATTTCAGTAACCTTCCT-AAGAAATTTTAATAACCTAATC
1 AAATTTTGGTAACCACACTATGAAATTTTGA-TAACC-TCCTCATGAAATTATAATAACC--ATC
*
26845 CTATG
62 ATATG
* * * * *
26850 AAATTTTGGTAACCACATTATGAAATTTTGATAACTTTCC-CATGAAATTTTGATAA-CTTCCAT
1 AAATTTTGGTAACCACACTATGAAATTTTGATAAC-CTCCTCATGAAATTATAATAACCAT-CAT
26913 ATG
64 ATG
* *
26916 AAATTTTGGTAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTAT
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATCATAT
26981 G
66 G
*
26982 AAATTTTGATAACCACAC
1 AAATTTTGGTAACCACAC
27000 AGAGACAAGA
Statistics
Matches: 126, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
65 4 0.03
66 74 0.59
67 3 0.02
68 38 0.30
69 7 0.06
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
AAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATCATAT
G
Found at i:27468 original size:13 final size:13
Alignment explanation
Indices: 27432--27470 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
27422 TCTAAATTGA
27432 AATTTT-ATAATT
1 AATTTTAATAATT
27444 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
27459 AATTTTAATAAT
1 AATTTTAATAAT
27471 GCCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Done.