Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015322.1 Corchorus capsularis cultivar CVL-1 contig15343, 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: 14832
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2462 original size:233 final size:233
Alignment explanation
Indices: 2055--2522 Score: 936
Period size: 233 Copynumber: 2.0 Consensus size: 233
2045 TCATATCTAC
2055 CCTTGGCCTCGAACTTGATCTTCCACGATCCACCATCAGAGCACCATTCTCTTCATCTTTCTTTT
1 CCTTGGCCTCGAACTTGATCTTCCACGATCCACCATCAGAGCACCATTCTCTTCATCTTTCTTTT
2120 CAGTTTCTTTCAATATATCATACTCATAAATTGCAGAAGTTACATCTTGCAAGCTCAGGGTGTTC
66 CAGTTTCTTTCAATATATCATACTCATAAATTGCAGAAGTTACATCTTGCAAGCTCAGGGTGTTC
2185 CTACCAGCCATCAAAGCTCTAGTCACATGATCATACCTATCGGTAAGAGAATTAATCAACAAAAC
131 CTACCAGCCATCAAAGCTCTAGTCACATGATCATACCTATCGGTAAGAGAATTAATCAACAAAAC
2250 TGCTTTATCAATCTCTTTCATGACTTCATCCACACTTG
196 TGCTTTATCAATCTCTTTCATGACTTCATCCACACTTG
2288 CCTTGGCCTCGAACTTGATCTTCCACGATCCACCATCAGAGCACCATTCTCTTCATCTTTCTTTT
1 CCTTGGCCTCGAACTTGATCTTCCACGATCCACCATCAGAGCACCATTCTCTTCATCTTTCTTTT
2353 CAGTTTCTTTCAATATATCATACTCATAAATTGCAGAAGTTACATCTTGCAAGCTCAGGGTGTTC
66 CAGTTTCTTTCAATATATCATACTCATAAATTGCAGAAGTTACATCTTGCAAGCTCAGGGTGTTC
2418 CTACCAGCCATCAAAGCTCTAGTCACATGATCATACCTATCGGTAAGAGAATTAATCAACAAAAC
131 CTACCAGCCATCAAAGCTCTAGTCACATGATCATACCTATCGGTAAGAGAATTAATCAACAAAAC
2483 TGCTTTATCAATCTCTTTCATGACTTCATCCACACTTG
196 TGCTTTATCAATCTCTTTCATGACTTCATCCACACTTG
2521 CC
1 CC
2523 AGCTGAGTAA
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 235 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (233 bp):
CCTTGGCCTCGAACTTGATCTTCCACGATCCACCATCAGAGCACCATTCTCTTCATCTTTCTTTT
CAGTTTCTTTCAATATATCATACTCATAAATTGCAGAAGTTACATCTTGCAAGCTCAGGGTGTTC
CTACCAGCCATCAAAGCTCTAGTCACATGATCATACCTATCGGTAAGAGAATTAATCAACAAAAC
TGCTTTATCAATCTCTTTCATGACTTCATCCACACTTG
Found at i:5187 original size:16 final size:16
Alignment explanation
Indices: 5166--5199 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5156 GTAACTATAA
5166 ATACCAATCATTTCAG
1 ATACCAATCATTTCAG
5182 ATACCAATCATTTCAG
1 ATACCAATCATTTCAG
5198 AT
1 AT
5200 TTCATATTCA
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:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (16 bp):
ATACCAATCATTTCAG
Found at i:6792 original size:12 final size:12
Alignment explanation
Indices: 6774--6806 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6764 ATGTCCAGCA
6774 AATTGTAATCTGC
1 AATTGTAAT-TGC
6787 -ATTGTAATTGC
1 AATTGTAATTGC
6798 AATTGTAAT
1 AATTGTAAT
6807 ACATAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (12 bp):
AATTGTAATTGC
Found at i:7410 original size:14 final size:14
Alignment explanation
Indices: 7393--7781 Score: 116
Period size: 14 Copynumber: 27.3 Consensus size: 14
7383 CATTTGGGAT
7393 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
7407 TTGAAGCATTGAAATA
1 TTGAAGAATTG-AA-A
*
7423 TTG-A-AATTAAAACA
1 TTGAAGAATT-GAA-A
* *
7437 TTGAAGGATTGAAT
1 TTGAAGAATTGAAA
* *
7451 TTGCAGAGTTGAAA
1 TTGAAGAATTGAAA
7465 TTGAAG-ATTGCAACA
1 TTGAAGAATTG-AA-A
* *
7480 TTGAAGGATTGAAT
1 TTGAAGAATTGAAA
7494 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
* *
7508 TTGACGCATTGAAA
1 TTGAAGAATTGAAA
*
7522 GTG-A-AATTGAAACA
1 TTGAAGAATTG-AA-A
** *
7536 TCAAAGAATTGCAA
1 TTGAAGAATTGAAA
* *
7550 TTGAAGAAATAAAA
1 TTGAAGAATTGAAA
* *
7564 TTGAGGCATTGAAA
1 TTGAAGAATTGAAA
7578 -T-----ATTGAAACA
1 TTGAAGAATTG-AA-A
7588 TTGAAGAATTGAAGCA
1 TTGAAGAATTGAA--A
* *
7604 TGGAA-AA-TAAAA
1 TTGAAGAATTGAAA
* * *
7616 TATCAAAGAATCGCAA
1 T-T-GAAGAATTGAAA
** *
7632 TTGAAGTCTTGACA
1 TTGAAGAATTGAAA
*
7646 TTGAAGCATTGACATA
1 TTGAAGAATTGA-A-A
7662 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
7676 TTGAA-ACATTGAAATA
1 TTGAAGA-ATTG-AA-A
7692 TTG-A-AATTGAAGGA
1 TTGAAGAATTGAA--A
*
7706 TTGAAGGATTGAAA
1 TTGAAGAATTGAAA
*
7720 -TGAAGTATTGAAGAA
1 TTGAAGAATTG-A-AA
*
7735 TTG-A-AA-GGAACA
1 TTGAAGAATTGAA-A
7747 TTGAAGAATTTGAAGCA
1 TTGAAGAA-TTGAA--A
*
7764 TTGAAGATTTGAAA
1 TTGAAGAATTGAAA
7778 TTGA
1 TTGA
7782 GGCATTGAAT
Statistics
Matches: 275, Mismatches: 58, Indels: 84
0.66 0.14 0.20
Matches are distributed among these distances:
8 4 0.01
9 2 0.01
10 1 0.00
11 2 0.01
12 11 0.04
13 20 0.07
14 132 0.48
15 33 0.12
16 61 0.22
17 9 0.03
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:7417 original size:8 final size:7
Alignment explanation
Indices: 7393--7532 Score: 53
Period size: 8 Copynumber: 19.7 Consensus size: 7
7383 CATTTGGGAT
7393 TTGAAGAA
1 TTGAAG-A
7401 TTGAA-A
1 TTGAAGA
7407 TTGAAGCA
1 TTGAAG-A
*
7415 TTGAAATA
1 TTG-AAGA
7423 TTGAA-A
1 TTGAAGA
* *
7429 TTAAAACA
1 TT-GAAGA
7437 TTGAAGGA
1 TTGAA-GA
*
7445 TTGAA-T
1 TTGAAGA
*
7451 TTGCAGA
1 TTGAAGA
7458 GTTGAA-A
1 -TTGAAGA
7465 TTGAAGA
1 TTGAAGA
*
7472 TTGCAACA
1 TTG-AAGA
7480 TTGAAGGA
1 TTGAA-GA
*
7488 TTGAA-T
1 TTGAAGA
7494 TTGAAGAA
1 TTGAAG-A
7502 TTGAA-A
1 TTGAAGA
*
7508 TTGACGCA
1 TTGAAG-A
7516 TTGAA-A
1 TTGAAGA
*
7522 GTGAA-A
1 TTGAAGA
7528 TTGAA
1 TTGAA
7533 ACATCAAAGA
Statistics
Matches: 101, Mismatches: 16, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
6 38 0.38
7 13 0.13
8 48 0.48
9 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (7 bp):
TTGAAGA
Found at i:7418 original size:22 final size:22
Alignment explanation
Indices: 7393--7506 Score: 85
Period size: 22 Copynumber: 5.2 Consensus size: 22
7383 CATTTGGGAT
7393 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
7415 TTGAA-ATATTGAAATTAAAACA
1 TTGAAGA-ATTGAAATTGAAGCA
* * *
7437 TTGAAGGATTGAATTTGCAG-A
1 TTGAAGAATTGAAATTGAAGCA
7458 GTTG-A-AATTGAAGATTGCAA-CA
1 -TTGAAGAATTGAA-ATTG-AAGCA
* * *
7480 TTGAAGGATTGAATTTGAAGAA
1 TTGAAGAATTGAAATTGAAGCA
7502 TTGAA
1 TTGAA
7507 ATTGACGCAT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
20 6 0.09
21 11 0.16
22 47 0.67
23 6 0.09
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGCA
Found at i:7526 original size:28 final size:28
Alignment explanation
Indices: 7393--7790 Score: 118
Period size: 30 Copynumber: 14.0 Consensus size: 28
7383 CATTTGGGAT
* *
7393 TTGAAGAATTGAAATTGAAGCATTGAAATA
1 TTGAAGCATTGAAATTGAAGAATTG-AA-A
* * *
7423 TTGAA--ATTAAAACATTGAAGGATTGAAT
1 TTGAAGCATT-GAA-ATTGAAGAATTGAAA
*
7451 TTGCAG-AGTTGAAATTGAAG-ATTGCAACA
1 TTGAAGCA-TTGAAATTGAAGAATTG-AA-A
* *
7480 TTGAAGGATTGAATTTGAAGAATTGAAA
1 TTGAAGCATTGAAATTGAAGAATTGAAA
* *
7508 TTGACGCATTGAAAGTG-A-AATTGAAACA
1 TTGAAGCATTGAAATTGAAGAATTG-AA-A
** * * * *
7536 TCAAAGAATTGCAATTGAAGAAATAAAA
1 TTGAAGCATTGAAATTGAAGAATTGAAA
*
7564 TTGAGGCATTGAAATATTGAA-ACATTGAAGAA
1 TTGAAGCATTG-AA-ATTGAAGA-ATTG-A-AA
* * *
7596 TTGAAGCATGGAAAAT-AA-AATATCAAA
1 TTGAAGCATTGAAATTGAAGAAT-TGAAA
* * ** *
7623 --G-A--ATCGCAATTGAAGTCTTGACA
1 TTGAAGCATTGAAATTGAAGAATTGAAA
7646 TTGAAGCATTGACATATTGAAGAATTGAAA
1 TTGAAGCATTGA-A-ATTGAAGAATTGAAA
*
7676 TTGAAACATTGAAATATTG-A-AATTGAAGGA
1 TTGAAGCATTG-AA-ATTGAAGAATTGAA--A
* *
7706 TTGAAGGATTGAAA-TGAAGTATTGAAGAA
1 TTGAAGCATTGAAATTGAAGAATTG-A-AA
*
7735 TTGAA--A-GGAACATTGAAGAATTTGAAGCA
1 TTGAAGCATTGAA-ATTGAAGAA-TTGAA--A
* *
7764 TTGAAG-ATTTGAAATTGAGGCATTGAA
1 TTGAAGCA-TTGAAATTGAAGAATTGAA
7791 TAATTGATGA
Statistics
Matches: 274, Mismatches: 52, Indels: 84
0.67 0.13 0.20
Matches are distributed among these distances:
22 6 0.02
23 5 0.02
24 2 0.01
25 2 0.01
26 9 0.03
27 14 0.05
28 72 0.26
29 57 0.21
30 81 0.30
31 12 0.04
32 14 0.05
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (28 bp):
TTGAAGCATTGAAATTGAAGAATTGAAA
Found at i:7655 original size:8 final size:8
Alignment explanation
Indices: 7644--7790 Score: 55
Period size: 8 Copynumber: 18.9 Consensus size: 8
7634 GAAGTCTTGA
7644 CATTGAAG
1 CATTGAAG
7652 CATTGACA-
1 CATTGA-AG
*
7660 TATTGAAG
1 CATTGAAG
*
7668 AATTGAA-
1 CATTGAAG
*
7675 -ATTGAAA
1 CATTGAAG
*
7682 CATTGAAA
1 CATTGAAG
*
7690 TATTGAA-
1 CATTGAAG
7697 -ATTGAAG
1 CATTGAAG
*
7704 GATTGAAG
1 CATTGAAG
*
7712 GATTGAA-
1 CATTGAAG
7719 -A-TGAAG
1 CATTGAAG
*
7725 TATTGAAG
1 CATTGAAG
*
7733 AATTGAAAGG
1 CATTG-AA-G
7743 AACATTGAAG
1 --CATTGAAG
*
7753 AATTTGAAG
1 CA-TTGAAG
7762 CATTGAAG
1 CATTGAAG
7770 -ATTTGAA-
1 CA-TTGAAG
*
7777 -ATTGAGG
1 CATTGAAG
7784 CATTGAA
1 CATTGAA
7791 TAATTGATGA
Statistics
Matches: 113, Mismatches: 9, Indels: 34
0.72 0.06 0.22
Matches are distributed among these distances:
5 4 0.04
6 17 0.15
7 4 0.04
8 70 0.62
9 10 0.09
10 2 0.02
11 2 0.02
12 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.29
Consensus pattern (8 bp):
CATTGAAG
Found at i:7666 original size:16 final size:15
Alignment explanation
Indices: 7645--7731 Score: 67
Period size: 16 Copynumber: 5.9 Consensus size: 15
7635 AAGTCTTGAC
7645 ATTGAAGCATTGACAT
1 ATTGAAGCATTGA-AT
*
7661 ATTGAAGAATTGAA-
1 ATTGAAGCATTGAAT
*
7675 ATTGAAACATTGAAAT
1 ATTGAAGCATTG-AAT
*
7691 ATTGAA--ATTGAAGG
1 ATTGAAGCATTGAA-T
*
7705 ATTGAAGGATTGAA-
1 ATTGAAGCATTGAAT
*
7719 A-TGAAGTATTGAA
1 ATTGAAGCATTGAA
7732 GAATTGAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
13 13 0.21
14 21 0.34
15 3 0.05
16 24 0.39
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (15 bp):
ATTGAAGCATTGAAT
Found at i:7678 original size:22 final size:21
Alignment explanation
Indices: 7661--7756 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 21
7651 GCATTGACAT
7661 ATTGAAGAATTGAAATTGAAAC
1 ATTGAAGAATTGAAATTG-AAC
*
7683 ATTGAA-ATATTGAAATTGAAGG
1 ATTGAAGA-ATTGAAATTGAA-C
* *
7705 ATTGAAGGATTGAAA-TGAAGT
1 ATTGAAGAATTGAAATTGAA-C
*
7726 ATTGAAGAATTGAAA-GGAAC
1 ATTGAAGAATTGAAATTGAAC
7746 ATTGAAGAATT
1 ATTGAAGAATT
7757 TGAAGCATTG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.17
21 25 0.38
22 29 0.45
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (21 bp):
ATTGAAGAATTGAAATTGAAC
Found at i:7775 original size:16 final size:16
Alignment explanation
Indices: 7646--7776 Score: 66
Period size: 16 Copynumber: 8.3 Consensus size: 16
7636 AGTCTTGACA
*
7646 TTGAAGCATTG-ACAT
1 TTGAAGCATTGAAGAT
*
7661 ATTGAAGAATTGAA-A-
1 -TTGAAGCATTGAAGAT
*
7676 TTGAAACATTGAA-AT
1 TTGAAGCATTGAAGAT
7691 ATTGAA--ATTGAAGGA-
1 -TTGAAGCATTGAA-GAT
*
7706 TTGAAGGATTGAA-A-
1 TTGAAGCATTGAAGAT
* *
7720 -TGAAGTATTGAAGAA
1 TTGAAGCATTGAAGAT
7735 TTGAAAGGAACATTGAAGAAT
1 TTG-AA-G--CATTGAAG-AT
7756 TTGAAGCATTGAAGAT
1 TTGAAGCATTGAAGAT
7772 TTGAA
1 TTGAA
7777 ATTGAGGCAT
Statistics
Matches: 94, Mismatches: 6, Indels: 30
0.72 0.05 0.23
Matches are distributed among these distances:
13 11 0.12
14 25 0.27
16 32 0.34
17 11 0.12
18 1 0.01
19 1 0.01
20 9 0.10
21 4 0.04
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (16 bp):
TTGAAGCATTGAAGAT
Found at i:7797 original size:22 final size:22
Alignment explanation
Indices: 7756--7797 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7746 ATTGAAGAAT
*
7756 TTGAAGCATTGAAGATTTGAAA
1 TTGAAGCATTGAAGAATTGAAA
* *
7778 TTGAGGCATTGAATAATTGA
1 TTGAAGCATTGAAGAATTGA
7798 TGAATGGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (22 bp):
TTGAAGCATTGAAGAATTGAAA
Found at i:7869 original size:24 final size:23
Alignment explanation
Indices: 7830--7917 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 23
7820 GGATCATTGA
*
7830 AGTAATTTGAAAAATTGAAGCAAT
1 AGTAA-TTGAAGAATTGAAGCAAT
*
7854 GAGTAATTGAAGAATTTAAGCAAT
1 -AGTAATTGAAGAATTGAAGCAAT
* * *
7878 AAGTGATCGAAGAATTGAAGAAAT
1 -AGTAATTGAAGAATTGAAGCAAT
*
7902 A--AATTGAAGTATTGAA
1 AGTAATTGAAGAATTGAA
7918 TAATTAAAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 12 0.23
23 1 0.02
24 35 0.66
25 5 0.09
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.27
Consensus pattern (23 bp):
AGTAATTGAAGAATTGAAGCAAT
Found at i:7959 original size:16 final size:16
Alignment explanation
Indices: 7940--7979 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
7930 CGAAGAGATA
*
7940 AATTGAATCATTGAAG
1 AATTGAAGCATTGAAG
*
7956 AATTGAAGCATTGAAT
1 AATTGAAGCATTGAAG
7972 AATTGAAG
1 AATTGAAG
7980 AAAGAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (16 bp):
AATTGAAGCATTGAAG
Found at i:9018 original size:8 final size:8
Alignment explanation
Indices: 9005--9048 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
8995 CTCTTTTCCA
9005 TTCATTTT
1 TTCATTTT
9013 TTCATTTT
1 TTCATTTT
9021 TTCATTTT
1 TTCATTTT
*
9029 TTTA-TTT
1 TTCATTTT
9036 TTCATTTT
1 TTCATTTT
9044 TTCAT
1 TTCAT
9049 CATCATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (8 bp):
TTCATTTT
Found at i:9036 original size:15 final size:16
Alignment explanation
Indices: 9005--9048 Score: 72
Period size: 15 Copynumber: 2.8 Consensus size: 16
8995 CTCTTTTCCA
9005 TTCATTTTTTCATTTT
1 TTCATTTTTTCATTTT
*
9021 TTCATTTTTTTA-TTT
1 TTCATTTTTTCATTTT
9036 TTCATTTTTTCAT
1 TTCATTTTTTCAT
9049 CATCATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCATTTTTTCATTTT
Found at i:9414 original size:16 final size:15
Alignment explanation
Indices: 9393--9430 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9383 ACTTTCGATT
9393 TTGATTTTGATTTTGA
1 TTGATTTT-ATTTTGA
*
9409 TTGATTTTATTTTTA
1 TTGATTTTATTTTGA
9424 TT-ATTTT
1 TTGATTTT
9431 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (15 bp):
TTGATTTTATTTTGA
Found at i:9436 original size:21 final size:21
Alignment explanation
Indices: 9412--9453 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9402 ATTTTGATTG
9412 ATTTTATTT-TTATTATTTTTT
1 ATTTT-TTTATTATTATTTTTT
9433 ATTTTTTTATTATTATTTTTT
1 ATTTTTTTATTATTATTTTTT
9454 TTACCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (21 bp):
ATTTTTTTATTATTATTTTTT
Found at i:9441 original size:18 final size:18
Alignment explanation
Indices: 9413--9455 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9403 TTTTGATTGA
*
9413 TTTTATTTTTATTATT-T
1 TTTTTTTTTTATTATTAT
9430 TTTATTTTTTTATTATTAT
1 TTT-TTTTTTTATTATTAT
9449 TTTTTTT
1 TTTTTTT
9456 ACCTTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 16 0.70
19 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTATTATTAT
Found at i:9453 original size:15 final size:14
Alignment explanation
Indices: 9412--9456 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
9402 ATTTTGATTG
*
9412 ATTTTATTTTTATT
1 ATTTTATTTTTTTT
*
9426 ATTTTTTATTTTTTT
1 ATTTTAT-TTTTTTT
9441 ATTATTATTTTTTTT
1 ATT-TTATTTTTTTT
9456 A
1 A
9457 CCTTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 6 0.23
15 17 0.65
16 3 0.12
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
ATTTTATTTTTTTT
Found at i:9751 original size:3 final size:3
Alignment explanation
Indices: 9743--9790 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
9733 GTTTTCAAAA
*
9743 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9791 TTGAAAACCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9876 original size:13 final size:14
Alignment explanation
Indices: 9858--9894 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
9848 CATGACTCTC
9858 TTTTTGAAAAA-CA
1 TTTTTGAAAAAGCA
9871 TTTTTGAAAAAGCA
1 TTTTTGAAAAAGCA
9885 TTTTTGAAAA
1 TTTTTGAAAA
9895 CCATGACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (14 bp):
TTTTTGAAAAAGCA
Found at i:9906 original size:48 final size:50
Alignment explanation
Indices: 9789--9906 Score: 206
Period size: 49 Copynumber: 2.4 Consensus size: 50
9779 ATTATCATTA
9789 TTTTGAAAACCATGACTCTC-TTTTGAAAAACATTTTTTGAAGAAAACAT
1 TTTTGAAAACCATGACTCTCTTTTTGAAAAACATTTTTTGAAGAAAACAT
*
9838 TTTTGAAAACCATGACTCTCTTTTTGAAAAACA-TTTTTGAA-AAAGCAT
1 TTTTGAAAACCATGACTCTCTTTTTGAAAAACATTTTTTGAAGAAAACAT
9886 TTTTGAAAACCATGACTCTCT
1 TTTTGAAAACCATGACTCTCT
9907 AATATTCCAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
48 27 0.40
49 28 0.42
50 12 0.18
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (50 bp):
TTTTGAAAACCATGACTCTCTTTTTGAAAAACATTTTTTGAAGAAAACAT
Done.