Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014979.1 Corchorus capsularis cultivar CVL-1 contig15000, 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: 23212
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1992 original size:18 final size:18
Alignment explanation
Indices: 1957--1992 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1947 ACAATTATTA
*
1957 ATATAATAAAATATCAAG
1 ATATAATAAAATACCAAG
*
1975 ATATAATAAATTACCAAG
1 ATATAATAAAATACCAAG
1993 TGATCAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (18 bp):
ATATAATAAAATACCAAG
Found at i:4322 original size:15 final size:14
Alignment explanation
Indices: 4302--4363 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 14
4292 TACTTAGTTT
4302 ATTAGTTTATGTTTA
1 ATTAGTTTAT-TTTA
*
4317 ATTAG--TA-TCTA
1 ATTAGTTTATTTTA
4328 ATTAGTTTATTATTA
1 ATTAGTTTATT-TTA
4343 ATTAG--TA-TTTA
1 ATTAGTTTATTTTA
4354 ATTAGTTTAT
1 ATTAGTTTAT
4364 GATTAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
11 16 0.42
12 1 0.03
13 8 0.21
14 1 0.03
15 12 0.32
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTAGTTTATTTTA
Found at i:4331 original size:26 final size:26
Alignment explanation
Indices: 4302--4369 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
4292 TACTTAGTTT
4302 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
4328 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
4354 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
4370 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:4409 original size:24 final size:25
Alignment explanation
Indices: 4378--4438 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
4368 AAAATGAAGG
* *
4378 AAAATGAATTTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
4402 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
4427 GAAATGAAGTTT
1 AAAATGAAGTTT
4439 AGGATTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:6584 original size:45 final size:44
Alignment explanation
Indices: 6504--6599 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 44
6494 AAGACCTCAA
* *
6504 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACTTCCCAATGAAATATTGATAACC-ACAC
* ** *
6549 TATGAGATGTTGATAACTT-CCATATGGTATATTGATAACCACAT
1 TATGAAATGTTGATAACTTCCCA-ATGAAATATTGATAACCACAC
6593 TATGAAA
1 TATGAAA
6600 ATTTAAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 12 0.28
45 31 0.72
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (44 bp):
TATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCACAC
Found at i:6767 original size:45 final size:45
Alignment explanation
Indices: 6687--6772 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
6677 AAGACCTCAA
* *
6687 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCAACAC
* **
6732 TATGAGATGTTGATAACTT-CCATATGGTATATTGATAACCA
1 TATGAAATGTTGATAACTTCCCA-ATGAAATATTGATAACCA
6773 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCAACAC
Found at i:6836 original size:22 final size:21
Alignment explanation
Indices: 6807--6847 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
6797 ATATGAATTG
**
6807 TTATAAATTTTTTTAACCTTC
1 TTATAAATTTAGTTAACCTTC
6828 TTATGAAATTTAGTTAACCT
1 TTAT-AAATTTAGTTAACCT
6848 CGAAATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATAAATTTAGTTAACCTTC
Found at i:6937 original size:181 final size:181
Alignment explanation
Indices: 6444--6988 Score: 1009
Period size: 181 Copynumber: 3.0 Consensus size: 181
6434 AACCTTTTTG
*
6444 TATAATTTTTTTTAACTTTCTTATGAAATTTAGTTAACCTCGAAATTTTGAAGACCTCAATATGA
1 TATAATTTTTTTTAACCTTCTTATGAAATTTAGTTAACCTCGAAATTTTGAAGACCTCAATATGA
6509 AATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACTTCCATAT
66 AATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACTTCCATAT
*
6574 GGTATATTGATAACCACATTATGAAAATTTAAAAACCCTCCATATGAATTGT
131 GGTATATTGATAACCACGTTATGAAAATTTAAAAA-CCTCCATATGAATTGT
*
6626 TATTAATTTTTTTTAACCTTCTTATGAAATTTAGTTAACCTCAAAATTTTGAAGACCTCAATATG
1 TA-TAATTTTTTTTAACCTTCTTATGAAATTTAGTTAACCTCGAAATTTTGAAGACCTCAATATG
6691 AAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACTTCCATA
65 AAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACTTCCATA
6756 TGGTATATTGATAACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGT
130 TGGTATATTGATAACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGT
* *
6808 TATAAATTTTTTTAACCTTCTTATGAAATTTAGTTAACCTCGAAATTTTCAAGACCTCAATATGA
1 TATAATTTTTTTTAACCTTCTTATGAAATTTAGTTAACCTCGAAATTTTGAAGACCTCAATATGA
* *
6873 AATTTTGATAAGTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATAT
66 AATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACTTCCATAT
6938 GGTATATTGATAACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGT
131 GGTATATTGATAACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGT
6989 CAGTAATCAC
Statistics
Matches: 354, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
181 174 0.49
182 20 0.06
183 160 0.45
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (181 bp):
TATAATTTTTTTTAACCTTCTTATGAAATTTAGTTAACCTCGAAATTTTGAAGACCTCAATATGA
AATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACTTCCATAT
GGTATATTGATAACCACGTTATGAAAATTTAAAAACCTCCATATGAATTGT
Found at i:7017 original size:22 final size:22
Alignment explanation
Indices: 6992--7320 Score: 144
Period size: 22 Copynumber: 15.1 Consensus size: 22
6982 GAATTGTCAG
*
6992 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
7014 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
7036 TAACCTCACTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
7058 TAAATCTTC-CTATGAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
7081 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** * *
7104 TAACTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
7125 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
7142 TAACCTCCCTATGATTTTTTTGA
1 TAATCACACTATGA-AATTTTGA
* * * *
7165 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* * *
7187 TAATCTCCCTATGACATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
7209 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
7231 TAACTCTC-TTGTGAAATTTTGA
1 TAA-TCACACTATGAAATTTTGA
* *
7253 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
7275 TAACCTTCAC-ATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
7297 TAACCTTCAC-ATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
7319 TA
1 TA
7321 TCCTCCCTGA
Statistics
Matches: 238, Mismatches: 51, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
16 7 0.03
17 2 0.01
18 1 0.00
19 2 0.01
20 1 0.00
21 6 0.03
22 153 0.64
23 63 0.26
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:7364 original size:19 final size:20
Alignment explanation
Indices: 7264--7358 Score: 102
Period size: 22 Copynumber: 4.6 Consensus size: 20
7254 AACTAAACTA
* *
7264 TGAAATTTTGATAACCTTCACA
1 TGAAATTTTGATATCC-TC-CC
* *
7286 TGAAATTTTGATAACCTTCACA
1 TGAAATTTTGATATCC-TC-CC
7308 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
7328 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
7347 TGAAATTTTGAT
1 TGAAATTTTGAT
7359 TACTCCATAA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 18 0.26
20 12 0.17
21 2 0.03
22 37 0.54
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:7476 original size:128 final size:129
Alignment explanation
Indices: 7331--7594 Score: 494
Period size: 128 Copynumber: 2.1 Consensus size: 129
7321 TCCTCCCTGA
*
7331 ATTTTGATATCCTCCTTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTG
1 ATTTTGATATCCTCCTTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAAATTG
*
7396 ATAACTATACTATGAAA-TTTCATAACCTCCTCAGAAATACCACTATGAAATTTTTGTAATCAC
66 ATAACCATACTATGAAATTTTCATAACCTCCTCAGAAATACCACTATGAAATTTTTGTAATCAC
7459 ATTTTGATATCCTCCTTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAAATTG
1 ATTTTGATATCCTCCTTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAAATTG
*
7524 ATAACCATACTATGAAATTTTGATAACCTCCTCAGAAATACCACTATGAAATTTTTGTAATCAC
66 ATAACCATACTATGAAATTTTCATAACCTCCTCAGAAATACCACTATGAAATTTTTGTAATCAC
7588 ATTTTGA
1 ATTTTGA
7595 AAATTTGATA
Statistics
Matches: 132, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
128 80 0.61
129 52 0.39
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (129 bp):
ATTTTGATATCCTCCTTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAAATTG
ATAACCATACTATGAAATTTTCATAACCTCCTCAGAAATACCACTATGAAATTTTTGTAATCAC
Found at i:7617 original size:22 final size:22
Alignment explanation
Indices: 7592--7715 Score: 83
Period size: 22 Copynumber: 5.6 Consensus size: 22
7582 AATCACATTT
7592 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
7614 TGAAAATTTGGTGACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * *
7636 T-AAAATTTTGTTGACCCCTTTA
1 TGAAAA-TTTGATAACCTCTTTA
* * * *
7658 TG-AAATTCTTATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * * *
7680 TGTAATTTTGATAATCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
7702 TGAAAATTTGATAA
1 TGAAAATTTGATAA
7716 TAATGCTATG
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
21 6 0.07
22 69 0.85
23 6 0.07
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:7618 original size:44 final size:44
Alignment explanation
Indices: 7568--7693 Score: 103
Period size: 44 Copynumber: 2.9 Consensus size: 44
7558 GAAATACCAC
*
7568 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCCCTT
* * * * * * *
7612 TATGAAAATTTGGTGACCTC-TTTAT-AAAATTTTGTTGACCCCTT
1 TATGAAATTTTTGTAATCACATTT-TGAAAA-TTTGATAACCCCTT
* * * * *
7656 TATGAAATTCTTATAATCACATTATGTAATTTTGATAA
1 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAA
7694 TCTCGCTTTG
Statistics
Matches: 58, Mismatches: 20, Indels: 8
0.67 0.23 0.09
Matches are distributed among these distances:
43 7 0.12
44 47 0.81
45 4 0.07
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCCCTT
Found at i:7793 original size:22 final size:22
Alignment explanation
Indices: 7656--7794 Score: 99
Period size: 22 Copynumber: 6.2 Consensus size: 22
7646 TTGACCCCTT
7656 TATGAAATTCTT-ATAATCACAT-
1 TATGAAATT-TTGATAATCAC-TC
* * *
7678 TATGTAATTTTGATAATCTCGC
1 TATGAAATTTTGATAATCACTC
* * *
7700 TTTGAAAATTTGATAAT-AATGC
1 TATGAAATTTTGATAATCACT-C
* *
7722 TATGAAATTTTGACAATC-TTCC
1 TATGAAATTTTGATAATCACT-C
7744 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAAT-C-A-CTC
*
7768 TATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAATCACTC
7790 TATGA
1 TATGA
7795 GATTGGATAA
Statistics
Matches: 91, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
21 14 0.15
22 58 0.64
23 1 0.01
24 5 0.05
25 13 0.14
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACTC
Found at i:7873 original size:22 final size:23
Alignment explanation
Indices: 7844--7898 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
7834 AAATTGAGAC
* *
7844 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
7865 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
7887 TTTTGATAACCT
1 TTTTGATAACCT
7899 CCCCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:7909 original size:22 final size:22
Alignment explanation
Indices: 7859--7909 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
7849 TAACCTTCAT
*
7859 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
7881 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
7903 ATGAAAT
1 ATGAAAT
7910 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:7973 original size:22 final size:22
Alignment explanation
Indices: 7915--7973 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
7905 GAAATATTTA
*
7915 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
7937 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
*
7959 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
7974 TCCCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:8115 original size:22 final size:21
Alignment explanation
Indices: 8009--8146 Score: 78
Period size: 22 Copynumber: 6.2 Consensus size: 21
7999 TTGTGATAAT
* **
8009 TAACCACCTATGAAATTTCAA
1 TAACCTCCTATGAAATTTTGA
* * * *
8030 TAACCGACCTAAGAGATTTTAA
1 TAACC-TCCTATGAAATTTTGA
* *
8052 TAACCTGATCTTATGAAATTTTGG
1 TAACC---TCCTATGAAATTTTGA
* *
8076 TAACCACACTATGTAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
* *
8098 TAACCTCCTCATGAAATTGTAA
1 TAACCTCCT-ATGAAATTTTGA
* *
8120 TAACCATCTTATTAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
8142 TAACC
1 TAACC
8147 ACATAGAGAC
Statistics
Matches: 89, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
21 8 0.09
22 63 0.71
23 3 0.03
24 15 0.17
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:8147 original size:22 final size:22
Alignment explanation
Indices: 8045--8147 Score: 84
Period size: 22 Copynumber: 4.6 Consensus size: 22
8035 GACCTAAGAG
*
8045 ATTTTAATAACCTGATCTTATGAA
1 ATTTTGATAACC--ATCTTATGAA
* * *
8069 ATTTTGGTAACCA-CACTATGTA
1 ATTTTGATAACCATC-TTATGAA
*
8091 ATTTTGATAACC-TCCTCATGAA
1 ATTTTGATAACCAT-CTTATGAA
* * *
8113 ATTGTAATAACCATCTTATTAA
1 ATTTTGATAACCATCTTATGAA
8135 ATTTTGATAACCA
1 ATTTTGATAACCA
8148 CATAGAGACA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
21 1 0.02
22 48 0.79
23 2 0.03
24 10 0.16
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTTTGATAACCATCTTATGAA
Found at i:8344 original size:19 final size:20
Alignment explanation
Indices: 8313--8350 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
8303 TATTGACATT
8313 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
8332 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
8351 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:8544 original size:38 final size:35
Alignment explanation
Indices: 8489--8564 Score: 107
Period size: 38 Copynumber: 2.1 Consensus size: 35
8479 TTAAGACAAA
8489 AAAGACAAAGCAAAATTAAATACAACGATTGGAAAC
1 AAAGACAAAGCAAAATTAAATACAACG-TTGGAAAC
**
8525 AAAGACAAAAGGCAAAATTAAATAGGACGTTGGAAAC
1 AAAGAC-AAA-GCAAAATTAAATACAACGTTGGAAAC
8562 AAA
1 AAA
8565 AAGTCAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 6 0.17
37 14 0.39
38 16 0.44
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.13
Consensus pattern (35 bp):
AAAGACAAAGCAAAATTAAATACAACGTTGGAAAC
Found at i:8708 original size:31 final size:31
Alignment explanation
Indices: 8667--8729 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
8657 CAATTTAGAT
*
8667 ATATGTTTTAAAGAA-AAGGGTACAACTGGAA
1 ATATATTTTAAA-AATAAGGGTACAACTGGAA
*
8698 ATATATTTTAAAAATAAGGGTACAATTGGAA
1 ATATATTTTAAAAATAAGGGTACAACTGGAA
8729 A
1 A
8730 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (31 bp):
ATATATTTTAAAAATAAGGGTACAACTGGAA
Found at i:10789 original size:10 final size:10
Alignment explanation
Indices: 10774--10803 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
10764 ATTCACACAT
10774 GGAGTTAGCC
1 GGAGTTAGCC
10784 GGAGTTAGCC
1 GGAGTTAGCC
*
10794 GAAGTTAGCC
1 GGAGTTAGCC
10804 ATTGACTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (10 bp):
GGAGTTAGCC
Found at i:11620 original size:31 final size:31
Alignment explanation
Indices: 11585--11650 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
11575 AACTTTATGT
*
11585 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
11616 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
11647 TTTC
1 TTTC
11651 TAAATTGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:11990 original size:19 final size:21
Alignment explanation
Indices: 11958--12000 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
11948 TTCTTTACTA
11958 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
11979 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
11998 TTA
1 TTA
12001 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:12216 original size:22 final size:22
Alignment explanation
Indices: 12166--12250 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
12156 TGTCTCTACG
12166 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
12188 TGATTATTATAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* *
12211 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
12232 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
12251 GTGTGGGGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 45 0.92
23 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:12285 original size:22 final size:22
Alignment explanation
Indices: 12165--12305 Score: 77
Period size: 22 Copynumber: 6.3 Consensus size: 22
12155 TTGTCTCTAC
* * *
12165 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATCTCATAGG
* * * * *
12187 ATGATTATTATAATTTCATAAG
1 GTGGTTATTAAAATCTCATAGG
* * *
12209 GAGGTTATCAAAAT-TCCATAGT
1 GTGGTTATTAAAATCT-CATAGG
** *
12231 GTGGTTACCAAAATTTCATAGTG
1 GTGGTTATTAAAATCTCATAG-G
* *
12254 TGGGGTTATTAAAATCTCTTAGG
1 -GTGGTTATTAAAATCTCATAGG
* * *
12277 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATCTCATAGG
12299 GTGGTTA
1 GTGGTTA
12306 ATTATCACAA
Statistics
Matches: 90, Mismatches: 25, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.01
22 71 0.79
23 2 0.02
24 16 0.18
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATCTCATAGG
Found at i:12366 original size:22 final size:22
Alignment explanation
Indices: 12341--12399 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
12331 ATCAAAGAGA
*
12341 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
12363 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
12385 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
12400 TAAATATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:12523 original size:22 final size:23
Alignment explanation
Indices: 12471--12659 Score: 109
Period size: 22 Copynumber: 8.6 Consensus size: 23
12461 TAAGGAGTAC
* *
12471 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
12492 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
12513 CGAAATTTCATAGAGATCGGAATAT
1 CAAAATTTCATAGAGAT--GATTAT
*
12538 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
12559 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
12581 CAAAATTTCA-AAACGA-GGTTAT
1 CAAAATTTCATAGA-GATGATTAT
*
12603 CAAAATTTCATA-ATGA-GGTTAT
1 CAAAATTTCATAGA-GATGATTAT
* *
12625 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
12646 CAAAAATTTCATAG
1 C-AAAATTTCATAG
12660 TGGTATTTCT
Statistics
Matches: 134, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
20 10 0.07
21 24 0.18
22 78 0.58
23 5 0.04
24 5 0.04
25 12 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:12609 original size:44 final size:44
Alignment explanation
Indices: 12552--12661 Score: 141
Period size: 44 Copynumber: 2.5 Consensus size: 44
12542 ATTTATAGAA
**
12552 AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAACG
1 AGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAAAACG
* * * *
12596 AGGTTATCAAAATTTCATAATGAGGTTATCAAATTTTCAAAATG
1 AGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAAAACG
*
12640 TGATTA-CAAAAATTTCATAGTG
1 AGATTATC-AAAATTTCATAGTG
12662 GTATTTCTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 55 0.98
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
AGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAAAACG
Found at i:12770 original size:19 final size:19
Alignment explanation
Indices: 12740--12787 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
12730 TTATGGAGTA
12740 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
* *
12760 ATCAAAATTCAGGGATGAT
1 ATCAAAATTCAAGGAGGAT
12779 ATCAAAATT
1 ATCAAAATT
12788 TCATATGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:12806 original size:22 final size:22
Alignment explanation
Indices: 12778--13340 Score: 223
Period size: 22 Copynumber: 25.7 Consensus size: 22
12768 TCAGGGATGA
12778 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
12800 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
12822 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
12844 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
12865 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
12888 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** *
12910 TATCAAAAAATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
12932 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
12948 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
12970 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
12993 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
13016 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
13038 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
13060 TATCAAAATTTCAGAGTGTACGAT
1 TATCAAAATTTCATA-TG-AAGGT
*
13084 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
13106 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
13128 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
13150 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
13173 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
13195 TATCAAAATTTCTTATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
13217 CT-TCAAAATTCCTTA-GAGAGGT
1 -TATCAAAATTTCATATGA-AGGT
* * *
13239 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
13261 TAAAAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
13282 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
13304 TATTAAAATTTCATAGGAAGAT
1 TATCAAAATTTCATATGAAGGT
13326 TATCAAAATTTCATA
1 TATCAAAATTTCATA
13341 ATGGGATCAT
Statistics
Matches: 407, Mismatches: 95, Indels: 78
0.70 0.16 0.13
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 2 0.00
20 3 0.01
21 28 0.07
22 275 0.68
23 71 0.17
24 14 0.03
25 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:12855 original size:66 final size:66
Alignment explanation
Indices: 12778--13206 Score: 264
Period size: 66 Copynumber: 6.5 Consensus size: 66
12768 TCAGGGATGA
* * * *
12778 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCACAAGAGG
1 TATCAAAATTTCATATGGAGGTTATCAAAATTTCATAG-GTAGATTATCAAAATTTCATAAGAGG
12842 GT
65 GT
* * * * *
12844 TATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA-
1 TATCAAAATTTCATATGGAGGT-TATCAAAATTTCATAGGTAGATTATCAAAATTTCATAA-GAG
12907 GGT
64 GGT
** * **
12910 TATCAAAAAATCATATGGAGGTTATCAAAA-TT--T--GTAG-TTATCAAGATTTCATAAGAAAG
1 TATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGTAGATTATCAAAATTTCATAAGAGGG
12969 T
66 T
* * * * *
12970 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCAT-AGCG
1 TATCAAAATTTCATATGGAGG-TTATCAAAATTTCATAGGTAGA-TTATCAAAATTTCATAAGAG
13034 AGGT
64 -GGT
* *
13038 TATCACAATTTCATAGTGTGA--TTATCAAAATTTCAGAGTGTACGATTA-CTAACAA-TTCATA
1 TATCAAAATTTCATA-TG-GAGGTTATCAAAATTTCATAG-GTA-GATTATC-AA-AATTTCATA
*
13099 TG-GAGGT
60 AGAG-GGT
* * * ** * * * * * * *
13106 TTTTAAATTTTCATAACGTGGTTATCAATATATCATATGG-AGGTTATCAACATCTCAT-AGTGT
1 TATCAAAATTTCATATGGAGGTTATCAAAATTTCATA-GGTAGATTATCAAAATTTCATAAGAG-
13169 TGGT
64 -GGT
*
13173 TATCAAAATTTCAT-TGGGAAGTTATCAAAATTTC
1 TATCAAAATTTCATAT-GGAGGTTATCAAAATTTC
13207 TTATTGAGGT
Statistics
Matches: 277, Mismatches: 57, Indels: 57
0.71 0.15 0.15
Matches are distributed among these distances:
59 2 0.01
60 34 0.12
61 12 0.04
62 2 0.01
63 1 0.00
64 1 0.00
65 10 0.04
66 82 0.30
67 53 0.19
68 71 0.26
69 7 0.03
70 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (66 bp):
TATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGTAGATTATCAAAATTTCATAAGAGGG
T
Found at i:17472 original size:22 final size:22
Alignment explanation
Indices: 17447--17494 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
17437 TTATTGCACC
*
17447 ATTACAAGGTGTTATAGAAAAG
1 ATTACAAGGTGTAATAGAAAAG
*
17469 ATTACAAGGTGTAATAGAAAGG
1 ATTACAAGGTGTAATAGAAAAG
17491 ATTA
1 ATTA
17495 TACATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (22 bp):
ATTACAAGGTGTAATAGAAAAG
Found at i:20140 original size:17 final size:17
Alignment explanation
Indices: 20110--20144 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20100 GGTGAAATGG
*
20110 GTCGGTTGAGTCGGTTT
1 GTCGGGTGAGTCGGTTT
*
20127 GTCGGGTGATTCGGTTT
1 GTCGGGTGAGTCGGTTT
20144 G
1 G
20145 GGAAGTCCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.11, G:0.43, T:0.40
Consensus pattern (17 bp):
GTCGGGTGAGTCGGTTT
Done.