Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009170.1 Corchorus capsularis cultivar CVL-1 contig09191, 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: 66958
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:9473 original size:7 final size:7
Alignment explanation
Indices: 9461--9487 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
9451 TTTCCTTATC
9461 TTCTTCT
1 TTCTTCT
9468 TTCTTCT
1 TTCTTCT
9475 TTCTTCT
1 TTCTTCT
9482 TTCTTC
1 TTCTTC
9488 CCCATCGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TTCTTCT
Found at i:11995 original size:49 final size:49
Alignment explanation
Indices: 11879--12001 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 49
11869 GAGAGATCTA
* * * *
11879 TCACATGTGAACGGGGTAGTTTGTTCGATTAGCCGCACTGAGGAGAGCTG
1 TCACATGTGAACGGGG-AGTTTGTTAGATTAGCCGCACGGAGGAAAACTG
* *
11929 TCACATGTGAAGGGGGAGTTTGTTAGATTAGTCGCA-GGAGGGAAAACTG
1 TCACATGTGAACGGGGAGTTTGTTAGATTAGCCGCACGGA-GGAAAACTG
*
11978 TTA-ATGTGAACGAGGGAGTTTGTT
1 TCACATGTGAACG-GGGAGTTTGTT
12002 GGAATTTACA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
48 10 0.16
49 38 0.60
50 15 0.24
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (49 bp):
TCACATGTGAACGGGGAGTTTGTTAGATTAGCCGCACGGAGGAAAACTG
Found at i:13317 original size:19 final size:18
Alignment explanation
Indices: 13289--13330 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
13279 AATTAATTGT
13289 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
13307 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
13326 CTTAA
1 TTTAA
13331 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:13718 original size:31 final size:31
Alignment explanation
Indices: 13683--13744 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
13673 GATCCACTAT
13683 GACAGATATGGCATTTTCATTGTAAATAGCA
1 GACAGATATGGCATTTTCATTGTAAATAGCA
13714 GACAGATATGGCATTTTCATTGTAAATAGCA
1 GACAGATATGGCATTTTCATTGTAAATAGCA
13745 TAAGGCAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (31 bp):
GACAGATATGGCATTTTCATTGTAAATAGCA
Found at i:16312 original size:31 final size:31
Alignment explanation
Indices: 16277--16384 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 31
16267 CTTTATCAAT
* *
16277 TGGATTCAATTGACCAAATCTTGTGAATATA
1 TGGATTAAATTGACCAAATCTTGTGAATACA
* *
16308 TGGATTAAATTGACCCAATCTTGTGAGTACA
1 TGGATTAAATTGACCAAATCTTGTGAATACA
* * * *
16339 TGGACTAAATTGATCAAATCTTGAGAGTACA
1 TGGATTAAATTGACCAAATCTTGTGAATACA
* *
16370 TGAAATAAATTGACC
1 TGGATTAAATTGACC
16385 CTCTGGCAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (31 bp):
TGGATTAAATTGACCAAATCTTGTGAATACA
Found at i:18950 original size:20 final size:20
Alignment explanation
Indices: 18913--18952 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18903 TGTGGGACTG
* * *
18913 TTTGGTATTGTTTTGTAATT
1 TTTGGGATTATTTAGTAATT
18933 TTTGGGATTATTTAGTAATT
1 TTTGGGATTATTTAGTAATT
18953 GTTAAGTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (20 bp):
TTTGGGATTATTTAGTAATT
Found at i:21556 original size:1 final size:1
Alignment explanation
Indices: 21550--21586 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
21540 TGTTAATATC
21550 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21587 GCCACACATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27508 original size:23 final size:23
Alignment explanation
Indices: 27481--27529 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
27471 AATCCCTGCT
* * *
27481 AAAAGCAAATAGAAAGGAAAAAA
1 AAAAGCAAAAAAAAAAGAAAAAA
27504 AAAAGCAAAAAAAAAAGAAAAAA
1 AAAAGCAAAAAAAAAAGAAAAAA
27527 AAA
1 AAA
27530 GGAAGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (23 bp):
AAAAGCAAAAAAAAAAGAAAAAA
Found at i:27513 original size:12 final size:11
Alignment explanation
Indices: 27497--27529 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
27487 AAATAGAAAG
27497 GAAAAAAAAAA
1 GAAAAAAAAAA
27508 GCAAAAAAAAAA
1 G-AAAAAAAAAA
27520 GAAAAAAAAA
1 GAAAAAAAAA
27530 GGAAGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:27537 original size:14 final size:12
Alignment explanation
Indices: 27493--27529 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
27483 AAGCAAATAG
*
27493 AAAGGAAAAAAA
1 AAAGAAAAAAAA
*
27505 AAAGCAAAAAAA
1 AAAGAAAAAAAA
27517 AAAGAAAAAAAA
1 AAAGAAAAAAAA
27529 A
1 A
27530 GGAAGAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:32074 original size:28 final size:28
Alignment explanation
Indices: 32042--32097 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
32032 GAACCAACTA
32042 TTGATTAAATCATTTAAACATGAAATGG
1 TTGATTAAATCATTTAAACATGAAATGG
32070 TTGATTAAATCATTTAAACATGAAATGG
1 TTGATTAAATCATTTAAACATGAAATGG
32098 CTAATCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (28 bp):
TTGATTAAATCATTTAAACATGAAATGG
Found at i:32113 original size:28 final size:28
Alignment explanation
Indices: 32045--32123 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
32035 CCAACTATTG
* * *
32045 ATTAAATCATTTAAACATGAAATGGTTG
1 ATTAAAACATTTAAACATGAAATGGCTA
*
32073 ATTAAATCATTTAAACATGAAATGGCTA
1 ATTAAAACATTTAAACATGAAATGGCTA
* *
32101 ATCTAAAAC-TTTAGACATCAAAT
1 AT-TAAAACATTTAAACATGAAAT
32124 AATAGTATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 40 0.89
29 5 0.11
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (28 bp):
ATTAAAACATTTAAACATGAAATGGCTA
Found at i:36943 original size:29 final size:29
Alignment explanation
Indices: 36901--36962 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
36891 TGATTAATGA
* *
36901 GAATGGTTCATCTTCCTATAGATGTTATG
1 GAATGATTCATCTTCATATAGATGTTATG
36930 GAATGATTCATCTTCATATAGATGTTATG
1 GAATGATTCATCTTCATATAGATGTTATG
36959 GAAT
1 GAAT
36963 TGTTTATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (29 bp):
GAATGATTCATCTTCATATAGATGTTATG
Found at i:36971 original size:29 final size:29
Alignment explanation
Indices: 36901--36973 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
36891 TGATTAATGA
* *
36901 GAATGGTTCATCTTCCTATAGATGTTATG
1 GAATTGTTCATCTTCATATAGATGTTATG
36930 GAA-TGATTCATCTTCATATAGATGTTATG
1 GAATTG-TTCATCTTCATATAGATGTTATG
*
36959 GAATTGTTTATCTTC
1 GAATTGTTCATCTTC
36974 TTACATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 1 0.03
29 36 0.92
30 2 0.05
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (29 bp):
GAATTGTTCATCTTCATATAGATGTTATG
Found at i:38565 original size:25 final size:25
Alignment explanation
Indices: 38511--38572 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 25
38501 GAAAAATGAA
* *
38511 TTCCCTATGTCCTATATGTTTTATC
1 TTCCTTATGTTCTATATGTTTTATC
38536 TTCCTTATGTTCTATATGTTTTATC
1 TTCCTTATGTTCTATATGTTTTATC
38561 TTCCTATATGTT
1 TTCCT-TATGTT
38573 TTATCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 28 0.82
26 6 0.18
ACGTcount: A:0.16, C:0.19, G:0.08, T:0.56
Consensus pattern (25 bp):
TTCCTTATGTTCTATATGTTTTATC
Found at i:38569 original size:17 final size:17
Alignment explanation
Indices: 38547--38580 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
38537 TCCTTATGTT
38547 CTATATGTTTTATCTTC
1 CTATATGTTTTATCTTC
38564 CTATATGTTTTATCTTC
1 CTATATGTTTTATCTTC
38581 TTTTGAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (17 bp):
CTATATGTTTTATCTTC
Found at i:39512 original size:31 final size:30
Alignment explanation
Indices: 39477--39578 Score: 141
Period size: 31 Copynumber: 3.3 Consensus size: 30
39467 TTCGGGCGGG
*
39477 TTCGGGTTCGGGTACATCGGGTTCAGGTATT
1 TTCGGGTTCGGGTA-ATCGGGTTCGGGTATT
*
39508 TTCGGGTTCGGGTAATTTCAGGTTCGGGTATT
1 TTCGGGTTCGGGTAA--TCGGGTTCGGGTATT
*
39540 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTA-ATCGGGTTCGGGTATT
39571 TTCGGGTT
1 TTCGGGTT
39579 TGGGATCGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
30 1 0.02
31 36 0.56
32 27 0.42
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40
Consensus pattern (30 bp):
TTCGGGTTCGGGTAATCGGGTTCGGGTATT
Found at i:39514 original size:16 final size:16
Alignment explanation
Indices: 39477--39578 Score: 145
Period size: 16 Copynumber: 6.5 Consensus size: 16
39467 TTCGGGCGGG
*
39477 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
* *
39492 ATCGGGTTCAGGTATT
1 TTCGGGTTCGGGTATT
*
39508 TTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTATT
*
39524 TTCAGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
39540 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
39555 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
39571 TTCGGGTT
1 TTCGGGTT
39579 TGGGATCGGA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
15 27 0.36
16 49 0.64
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:39600 original size:23 final size:23
Alignment explanation
Indices: 39571--39628 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
39561 TTCGGGTATT
* * *
39571 TTCGGGTTTGGGATCGGATCTGG
1 TTCGGGTTCGGGACCGGATCGGG
* *
39594 TTCGGGTTCGGGCCCGGGTCGGG
1 TTCGGGTTCGGGACCGGATCGGG
39617 TTCGGGTTCGGG
1 TTCGGGTTCGGG
39629 TTCACTTTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.03, C:0.19, G:0.48, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGGACCGGATCGGG
Found at i:39603 original size:6 final size:6
Alignment explanation
Indices: 39592--39631 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
39582 GATCGGATCT
**
39592 GGTTCG GGTTCG GGCCCG GG-TCG GGTTCG GGTTCG GGTTC
1 GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTTC
39632 ACTTTCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.28
Consensus pattern (6 bp):
GGTTCG
Found at i:40738 original size:16 final size:16
Alignment explanation
Indices: 40717--40748 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40707 GGGTCGGGTT
40717 CGGGTTCGGATTCGGG
1 CGGGTTCGGATTCGGG
*
40733 CGGGTTCGGGTTCGGG
1 CGGGTTCGGATTCGGG
40749 TTCGGGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.53, T:0.25
Consensus pattern (16 bp):
CGGGTTCGGATTCGGG
Found at i:40739 original size:22 final size:23
Alignment explanation
Indices: 40699--40771 Score: 98
Period size: 22 Copynumber: 3.3 Consensus size: 23
40689 TATTTTGATC
40699 TCGGGTTCGGGTCGGGTTCGGGT
1 TCGGGTTCGGGTCGGGTTCGGGT
*
40722 TCGGATTCGGG-CGGGTTCGGGT
1 TCGGGTTCGGGTCGGGTTCGGGT
*
40744 TCGGGTTCGGGT--TGTCTCGGGT
1 TCGGGTTCGGGTCGGGT-TCGGGT
40766 TCGGGT
1 TCGGGT
40772 ATTTTCGGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.04
22 33 0.73
23 10 0.22
ACGTcount: A:0.01, C:0.18, G:0.49, T:0.32
Consensus pattern (23 bp):
TCGGGTTCGGGTCGGGTTCGGGT
Found at i:40763 original size:16 final size:16
Alignment explanation
Indices: 40744--40786 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
40734 GGGTTCGGGT
40744 TCGGGTTCGGGT-TGTC
1 TCGGGTTCGGGTAT-TC
*
40760 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTC
40776 TCGGGTTCGGG
1 TCGGGTTCGGG
40787 CGGGTTTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.02, C:0.16, G:0.44, T:0.37
Consensus pattern (16 bp):
TCGGGTTCGGGTATTC
Found at i:40764 original size:28 final size:28
Alignment explanation
Indices: 40705--40771 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
40695 GATCTCGGGT
*
40705 TCGGG-TCGGGTTCGGGTTCGGATTCGG
1 TCGGGTTCGGGTTCGGGTTCGGATTCGC
* *
40732 GCGGGTTCGGGTTCGGGTTCGGGTT-GTC
1 TCGGGTTCGGGTTCGGGTTCGGATTCG-C
40760 TCGGGTTCGGGT
1 TCGGGTTCGGGT
40772 ATTTTCGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.01, C:0.18, G:0.49, T:0.31
Consensus pattern (28 bp):
TCGGGTTCGGGTTCGGGTTCGGATTCGC
Found at i:40786 original size:6 final size:6
Alignment explanation
Indices: 40699--40756 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
40689 TATTTTGATC
*
40699 TCGGGT TCGGG- TCGGGT TCGGGT TCGGAT TCGGG- -CGGGT TCGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
40744 TCGGGT TCGGGT T
1 TCGGGT TCGGGT T
40757 GTCTCGGGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 38 0.81
ACGTcount: A:0.02, C:0.17, G:0.50, T:0.31
Consensus pattern (6 bp):
TCGGGT
Found at i:42754 original size:15 final size:15
Alignment explanation
Indices: 42733--42799 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
42723 AGGTTGCTCT
*
42733 AGAAGAGCTCACTCC
1 AGAAGAGATCACTCC
*
42748 TGAAGAGATCACTCC
1 AGAAGAGATCACTCC
*
42763 AGAAGAG-TCCACTCT
1 AGAAGAGAT-CACTCC
* * *
42778 TGTAGAGATTACTCC
1 AGAAGAGATCACTCC
42793 AGAAGAG
1 AGAAGAG
42800 TCCATAGACA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 1 0.03
15 38 0.95
16 1 0.03
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (15 bp):
AGAAGAGATCACTCC
Found at i:42769 original size:30 final size:30
Alignment explanation
Indices: 42733--42803 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
42723 AGGTTGCTCT
42733 AGAAGAG-CTCACTCCTGAAGAGATCACTCC
1 AGAAGAGTC-CACTCCTGAAGAGATCACTCC
* * *
42763 AGAAGAGTCCACTCTTGTAGAGATTACTCC
1 AGAAGAGTCCACTCCTGAAGAGATCACTCC
42793 AGAAGAGTCCA
1 AGAAGAGTCCA
42804 TAGACATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (30 bp):
AGAAGAGTCCACTCCTGAAGAGATCACTCC
Found at i:44861 original size:34 final size:32
Alignment explanation
Indices: 44822--44891 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 32
44812 GTCCATAAAT
44822 ATGTTATTAATGAGAATGGTTCATCTTCCTATAG
1 ATGTTATT-ATG-GAATGGTTCATCTTCCTATAG
44856 ATG---TTATGGAATGGTTCATCTTCCTATAG
1 ATGTTATTATGGAATGGTTCATCTTCCTATAG
44885 ATGTTAT
1 ATGTTAT
44892 GGAATTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
29 24 0.73
30 3 0.09
31 2 0.06
32 1 0.03
34 3 0.09
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (32 bp):
ATGTTATTATGGAATGGTTCATCTTCCTATAG
Found at i:44877 original size:29 final size:29
Alignment explanation
Indices: 44835--44907 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
44825 TTATTAATGA
44835 GAATGGTTCATCTTCCTATAGATGTTATG
1 GAATGGTTCATCTTCCTATAGATGTTATG
44864 GAATGGTTCATCTTCCTATAGATGTTATG
1 GAATGGTTCATCTTCCTATAGATGTTATG
* *
44893 GAATTGTTTATCTTC
1 GAATGGTTCATCTTC
44908 TTACATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (29 bp):
GAATGGTTCATCTTCCTATAGATGTTATG
Found at i:48432 original size:17 final size:17
Alignment explanation
Indices: 48410--48446 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
48400 CATCTATTTG
48410 ATGCTAAATATCTATCA
1 ATGCTAAATATCTATCA
48427 ATGCTAAATATCTATCA
1 ATGCTAAATATCTATCA
48444 ATG
1 ATG
48447 GTGTCAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (17 bp):
ATGCTAAATATCTATCA
Found at i:51119 original size:29 final size:29
Alignment explanation
Indices: 51077--51135 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
51067 ACTTTTATCA
51077 CGATTTTATCACTTTGTCAGTCTTAGGTC
1 CGATTTTATCACTTTGTCAGTCTTAGGTC
*
51106 CGATTTTATCACTTTGTTAGTCTTAGGTC
1 CGATTTTATCACTTTGTCAGTCTTAGGTC
51135 C
1 C
51136 TAAGATCCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (29 bp):
CGATTTTATCACTTTGTCAGTCTTAGGTC
Found at i:52456 original size:46 final size:45
Alignment explanation
Indices: 52403--52495 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 45
52393 ACCTGTCAAG
52403 ACGGCGTCCTATAATGAT-GGGTAAAACAAAGTGAAAAGAAATATTA
1 ACGGCGTCCTATAATGATGGGGTAAAACAAA--GAAAAGAAATATTA
* * *
52449 ACGGCGTCCTATACTGATGGGGTAAAACCAAGAGAAGAAATATTA
1 ACGGCGTCCTATAATGATGGGGTAAAACAAAGAAAAGAAATATTA
52494 AC
1 AC
52496 CTTTTGAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 15 0.35
46 17 0.40
47 11 0.26
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (45 bp):
ACGGCGTCCTATAATGATGGGGTAAAACAAAGAAAAGAAATATTA
Found at i:52711 original size:26 final size:27
Alignment explanation
Indices: 52682--52732 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
52672 CTATATACTC
52682 CCTC-TGTTCCTTTTTAATTGTCCCAA
1 CCTCTTGTTCCTTTTTAATTGTCCCAA
*
52708 CCTCTTGTTGCTTTTTAATTGTCCC
1 CCTCTTGTTCCTTTTTAATTGTCCC
52733 TCTCTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.12, C:0.29, G:0.10, T:0.49
Consensus pattern (27 bp):
CCTCTTGTTCCTTTTTAATTGTCCCAA
Found at i:58041 original size:2 final size:2
Alignment explanation
Indices: 58034--58118 Score: 86
Period size: 2 Copynumber: 44.0 Consensus size: 2
58024 TGATAAATAA
* * *
58034 AG AG AG AG AG AG AG GG AG AG AG -G AG AG AT AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
58075 AG GG AG AG AG AG AG AG AG AG -G AG GG AG GG AG GG AG AG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
58115 AG AG
1 AG AG
58119 TTAGTTAATT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
1 3 0.05
2 63 0.95
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.01
Consensus pattern (2 bp):
AG
Found at i:58077 original size:29 final size:29
Alignment explanation
Indices: 58034--58118 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 29
58024 TGATAAATAA
* *
58034 AGAGAGAGAGAGAGGGAGAGAGGAGAGAT
1 AGAGAGAGAGGGAGGGAGAGAGGAGAGAG
58063 AGAGAGAGAGGGAGGGAGAGA-GAGAGAG
1 AGAGAGAGAGGGAGGGAGAGAGGAGAGAG
* *
58091 AGAGGAGGGAGGGAGGGAGAGAGAAGAG
1 AGA-GAGAGAGGGAGGGAGAGAGGAGAG
58119 TTAGTTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 9 0.18
29 37 0.74
30 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.01
Consensus pattern (29 bp):
AGAGAGAGAGGGAGGGAGAGAGGAGAGAG
Done.