Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016302.1 Corchorus capsularis cultivar CVL-1 contig16323, 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: 53733
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:123 original size:21 final size:21
Alignment explanation
Indices: 99--142 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
89 GCAAAAGTGT
*
99 AAAAATGGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
*
120 AAAACTAGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
141 AA
1 AA
143 CCCCCTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGGTATTTAGC
Found at i:911 original size:63 final size:63
Alignment explanation
Indices: 809--998 Score: 251
Period size: 62 Copynumber: 3.0 Consensus size: 63
799 ATGCTCGACA
* * * * * *
809 AAATTCATTTTTTGT-AATAAAGTTT-TGAAACTGAACCATATAAATAGATGAAATAACTATTG
1 AAATTCATATTTTGTAAATAAAGTTTCGGAATC-GAGCCATATAAATAGATAAAATAACTGTTG
* *
871 AAATTCATATCTTGTAAATAAAGTTTCGGAATCGAGCCATACAAATAGATAAAATAACTGTTG
1 AAATTCATATTTTGTAAATAAAGTTTCGGAATCGAGCCATATAAATAGATAAAATAACTGTTG
* * *
934 -AATTCATATTTTGTAAATCAAGTTTCGGATTCAAGCCATATAAATAGATAAAATAACTGTTG
1 AAATTCATATTTTGTAAATAAAGTTTCGGAATCGAGCCATATAAATAGATAAAATAACTGTTG
996 AAA
1 AAA
999 GAGTATTTTG
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
62 70 0.62
63 38 0.34
64 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (63 bp):
AAATTCATATTTTGTAAATAAAGTTTCGGAATCGAGCCATATAAATAGATAAAATAACTGTTG
Found at i:10539 original size:22 final size:23
Alignment explanation
Indices: 10494--10541 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
10484 ATCAGGTAAT
* *
10494 AAATAAGGTTTTTTTTTTCAAGAA
1 AAATAAGGTTTATTTTAT-AAGAA
10518 AAATAAGGTTTATTTTAT-AGAA
1 AAATAAGGTTTATTTTATAAGAA
10540 AA
1 AA
10542 TTAAATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
24 16 0.73
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (23 bp):
AAATAAGGTTTATTTTATAAGAA
Found at i:12985 original size:30 final size:30
Alignment explanation
Indices: 12938--13009 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
12928 TACTATATAG
12938 TACTTTGTTCA-TTTTTTTTTT-GGCACCAA
1 TACTTTGTTCATTTTTTTTTTTGGGCACC-A
*
12967 TACTTTGTTCATTTTTTTTTTTGGGCATCA
1 TACTTTGTTCATTTTTTTTTTTGGGCACCA
12997 TACTTTGTTCATT
1 TACTTTGTTCATT
13010 GTTTAGTAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 11 0.28
30 24 0.60
31 5 0.12
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.58
Consensus pattern (30 bp):
TACTTTGTTCATTTTTTTTTTTGGGCACCA
Found at i:14301 original size:29 final size:29
Alignment explanation
Indices: 14259--14317 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
14249 GTTTTGTTGT
14259 GGCCTGTGGGAATGATTTCAGCTTAAAAG
1 GGCCTGTGGGAATGATTTCAGCTTAAAAG
*
14288 GGCCTGTGGGAATGATTTCAGTTTAAAAG
1 GGCCTGTGGGAATGATTTCAGCTTAAAAG
14317 G
1 G
14318 TTTTTGTTGT
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:0.27, C:0.12, G:0.32, T:0.29
Consensus pattern (29 bp):
GGCCTGTGGGAATGATTTCAGCTTAAAAG
Found at i:20691 original size:30 final size:30
Alignment explanation
Indices: 20655--20711 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
20645 CTTTTTCTTC
20655 TTTGACAAAACATTAGCAAAGAAAAGAAAA
1 TTTGACAAAACATTAGCAAAGAAAAGAAAA
* *
20685 TTTGACAAAAGATTAGCAAAGACAAGA
1 TTTGACAAAACATTAGCAAAGAAAAGA
20712 GGCATTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (30 bp):
TTTGACAAAACATTAGCAAAGAAAAGAAAA
Found at i:21348 original size:17 final size:17
Alignment explanation
Indices: 21326--21360 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21316 AATGGCATTT
21326 CAAATTTGGGAACAAAA
1 CAAATTTGGGAACAAAA
21343 CAAATTTGGGAACAAAA
1 CAAATTTGGGAACAAAA
21360 C
1 C
21361 TTGAACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (17 bp):
CAAATTTGGGAACAAAA
Found at i:22002 original size:24 final size:24
Alignment explanation
Indices: 21968--22028 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
21958 TTGATTTGCA
*
21968 ACCTCTACTTCATCATCAT-TCAGG
1 ACCTCTTCTTCATCATCATCT-AGG
21992 ACCTCTTCTTCATCATCATCTAGG
1 ACCTCTTCTTCATCATCATCTAGG
*
22016 ACATCTTCTTCAT
1 ACCTCTTCTTCAT
22029 GTTGTGGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.38
Consensus pattern (24 bp):
ACCTCTTCTTCATCATCATCTAGG
Found at i:22694 original size:156 final size:158
Alignment explanation
Indices: 22492--22807 Score: 462
Period size: 156 Copynumber: 2.0 Consensus size: 158
22482 AAAAAGAATT
* *
22492 ATAAAGATTAAAGAACCATAAAACATAGAAGCACGACGATCATCAACAAAAAAGTGAGTTTAAAG
1 ATAAAGACTAAAGAACCATAAAACATAGAAGCACGACGATCATCAACAAAAAAGTAAGTTTAAAG
*
22557 AACAATGA-CTCTATTTCATCATATC-A-A-CGAACTAATC-TAGTATAAGTTTATCTCCTTAGT
66 AACAATGATC-CTATTTCATCATATCAATATC-AACTAATCATAGTATAAATTTATCTCCTTAGT
*
22617 TTCTTAAAAAGAAAAGAAAACTTACATTGGA
129 TTATTAAAAAG-AAAGAAAACTTACATTGGA
* * *
22648 ATAAAGACTAAAGAACCATAAAACATAGAAGCAGGACGATCATCAACAAAAGAGTAAGTTTAATG
1 ATAAAGACTAAAGAACCATAAAACATAGAAGCACGACGATCATCAACAAAAAAGTAAGTTTAAAG
**
22713 AACTTTGATCCTATTTCATCATATCAATTTATCAACTAATCATAGTATAAATTTATCTCCTTAGT
66 AACAATGATCCTATTTCATCATATCAA--TATCAACTAATCATAGTATAAATTTATCTCCTTAGT
*
22778 TTATTAAGAAGAAAGAAAACTTACATTGGA
129 TTATTAAAAAGAAAGAAAACTTACATTGGA
22808 TTTCTGAGCA
Statistics
Matches: 143, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
156 81 0.57
157 2 0.01
160 28 0.20
161 32 0.22
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (158 bp):
ATAAAGACTAAAGAACCATAAAACATAGAAGCACGACGATCATCAACAAAAAAGTAAGTTTAAAG
AACAATGATCCTATTTCATCATATCAATATCAACTAATCATAGTATAAATTTATCTCCTTAGTTT
ATTAAAAAGAAAGAAAACTTACATTGGA
Found at i:23343 original size:2 final size:2
Alignment explanation
Indices: 23336--23393 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
23326 GGACCCTTTT
23336 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
23378 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
23394 TATATATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:23771 original size:111 final size:112
Alignment explanation
Indices: 23565--23784 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 112
23555 TTCTATTATA
* * *
23565 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACATATACCAAACAATA
1 TATTATTAATAATTGTGTTGTTTATTCAATTGAACATATTAAATAAGCACACATACCAAACAATA
* *
23630 CAAAATGCAATGAATTACTGGATTTAAAGAAAAATATAAGCACCTAT
66 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACCTAT
*
23677 TATTATTAATAATTGTGTTGTTTATTCAATTGAACATATTAAA-AAGCACACATACTAAACAATA
1 TATTATTAATAATTGTGTTGTTTATTCAATTGAACATATTAAATAAGCACACATACCAAACAATA
* *
23741 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC
23785 AAAATGACTA
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
111 59 0.59
112 41 0.41
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (112 bp):
TATTATTAATAATTGTGTTGTTTATTCAATTGAACATATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACCTAT
Found at i:28533 original size:16 final size:16
Alignment explanation
Indices: 28512--28552 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
28502 ATAAAGAGAT
28512 TATTATAATATAATTG
1 TATTATAATATAATTG
28528 TATTATAATATAATTG
1 TATTATAATATAATTG
*
28544 TATAATAAT
1 TATTATAAT
28553 TTATTAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TATTATAATATAATTG
Found at i:28707 original size:10 final size:10
Alignment explanation
Indices: 28694--28719 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28684 CATTTCTAAC
28694 AACTTCTTCA
1 AACTTCTTCA
28704 AACTTCTTCA
1 AACTTCTTCA
28714 AACTTC
1 AACTTC
28720 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:28785 original size:26 final size:26
Alignment explanation
Indices: 28756--28823 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
28746 TTCCTTCATT
* *
28756 TTAATCATAAACTAGTTAAATATTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
28782 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
28808 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
28824 AAACTAAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:30518 original size:18 final size:18
Alignment explanation
Indices: 30479--30517 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
30469 ACTCAGACTC
*
30479 AAACTAACTGACTCAAAA
1 AAACTAACTAACTCAAAA
30497 AAACTGAACTAACTCAAAA
1 AAACT-AACTAACTCAAAA
30516 AA
1 AA
30518 CGGACTGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (18 bp):
AAACTAACTAACTCAAAA
Found at i:40726 original size:18 final size:17
Alignment explanation
Indices: 40699--40733 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40689 ATAAATTTTT
40699 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
*
40716 AAAAGAAAAAAAGGAAAG
1 AAAA-AAAAAAAGAAAAG
40734 GTGAGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:46870 original size:18 final size:18
Alignment explanation
Indices: 46847--46884 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
46837 ATATCGCCTG
46847 AGGCGCTCGCCCGATCGA
1 AGGCGCTCGCCCGATCGA
46865 AGGCGCTCGCCCGATCGA
1 AGGCGCTCGCCCGATCGA
46883 AG
1 AG
46885 TGAGGCGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.37, G:0.34, T:0.11
Consensus pattern (18 bp):
AGGCGCTCGCCCGATCGA
Found at i:46893 original size:22 final size:20
Alignment explanation
Indices: 46845--46894 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
46835 TCATATCGCC
46845 TGAGGCGCTCGCCCGATCGA
1 TGAGGCGCTCGCCCGATCGA
46865 --AGGCGCTCGCCCGATCGAA
1 TGAGGCGCTCGCCCGATCG-A
46884 GTGAGGCGCTC
1 -TGAGGCGCTC
46895 ACATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 17 0.65
19 1 0.04
22 8 0.31
ACGTcount: A:0.16, C:0.34, G:0.36, T:0.14
Consensus pattern (20 bp):
TGAGGCGCTCGCCCGATCGA
Found at i:49703 original size:27 final size:27
Alignment explanation
Indices: 49643--49695 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
49633 CTTTGAAAGT
* *
49643 AAAATAAAATATGAAAAAAGTTTATCTC
1 AAAA-AAAATATGAAAAAAGTTCAACTC
49671 AAAAAAAATATGAAAAAAGTTCAAC
1 AAAAAAAATATGAAAAAAGTTCAAC
49696 ATGAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (27 bp):
AAAAAAAATATGAAAAAAGTTCAACTC
Found at i:50841 original size:71 final size:71
Alignment explanation
Indices: 50762--50909 Score: 278
Period size: 71 Copynumber: 2.1 Consensus size: 71
50752 GCAAAAATGA
*
50762 TTAAATCAAGTCATTTTAATAGTTTAGTTCATAACTTCCAAGAATTTAACAGAAAAAGTAAGATT
1 TTAAATCAAGTCATTTTAATAGTTTAGTTCATAACTTACAAGAATTTAACAGAAAAAGTAAGATT
50827 AATTAG
66 AATTAG
*
50833 TTAAATCAAGTCATTTTAATAGTTTAGTTCATAACTTACAAGAATTTGACAGAAAAAGTAAGATT
1 TTAAATCAAGTCATTTTAATAGTTTAGTTCATAACTTACAAGAATTTAACAGAAAAAGTAAGATT
50898 AATTAG
66 AATTAG
50904 TTAAAT
1 TTAAAT
50910 TCAAAATTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (71 bp):
TTAAATCAAGTCATTTTAATAGTTTAGTTCATAACTTACAAGAATTTAACAGAAAAAGTAAGATT
AATTAG
Found at i:51500 original size:30 final size:31
Alignment explanation
Indices: 51464--51521 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
51454 GCTAATTACT
51464 AAATATTCAAATAAGGA-TTAACATTTCTGA
1 AAATATTCAAATAAGGACTTAACATTTCTGA
* * *
51494 AAATATTCAATTTAGGACTTAACTTTTC
1 AAATATTCAAATAAGGACTTAACATTTC
51522 AATTTTCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (31 bp):
AAATATTCAAATAAGGACTTAACATTTCTGA
Found at i:52166 original size:60 final size:59
Alignment explanation
Indices: 52073--52234 Score: 245
Period size: 60 Copynumber: 2.7 Consensus size: 59
52063 GCTAATTGCT
* * * *
52073 CAAATAAGAGCCTAACATTTGCCAAAATGCTCAAAGAAGGG-TCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTT-CGAAAATGCTCAAATAAGGGCTC-GATCTTTTAATTTGGC
52133 CAAATAAGGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTT-TCGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
52193 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTT-TCGAAAATGCTCAAATAAGGGC
52235 CTGGTGTCAG
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
60 92 0.97
61 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTTCGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:52168 original size:31 final size:30
Alignment explanation
Indices: 52133--52236 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
52123 TTAATTTGGC
52133 CAAATAAGGGCCTAACGTTGTCGAAAATGCT
1 CAAATAAGGGCCTAACGTT-TCGAAAATGCT
* * * **
52164 CAAATAAGGGCTCGATC-TTT-TAATTTGGC-
1 CAAATAAGGGC-CTAACGTTTCGAAAAT-GCT
52193 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTT-TCGAAAATGCT
52224 CAAATAAGGGCCT
1 CAAATAAGGGCCT
52237 GGTGTCAGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 16 0.28
30 6 0.11
31 29 0.51
32 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (30 bp):
CAAATAAGGGCCTAACGTTTCGAAAATGCT
Found at i:52203 original size:29 final size:29
Alignment explanation
Indices: 52104--52203 Score: 80
Period size: 29 Copynumber: 3.4 Consensus size: 29
52094 CCAAAATGCT
*
52104 CAAAGAAGGG-TCTGATCTTTTAATTTGGC
1 CAAATAAGGGCTC-GATCTTTTAATTTGGC
* * * **
52133 CAAATAAGGGC-CTAACGTTGTCGAAAAT-GC
1 CAAATAAGGGCTCGATC-TT-T-TAATTTGGC
52163 TCAAATAAGGGCTCGATCTTTTAATTTGGC
1 -CAAATAAGGGCTCGATCTTTTAATTTGGC
52193 CAAATAAGGGC
1 CAAATAAGGGC
52204 CTAACGTTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
28 2 0.04
29 26 0.49
30 6 0.11
31 16 0.30
32 3 0.06
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:52302 original size:31 final size:30
Alignment explanation
Indices: 52267--52371 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
52257 ATGAGACAGA
52267 CCCTTATTTGAGCATTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTGA-AAACGTTAGG
** **
52298 CCCTTATTTG-GCCAAATT-AAAA-GATCGGG
1 CCCTTATTTGAG-CATTTTGAAAACG-TTAGG
52327 CCCTTATTTGAGCATTTTGATAAACGTTAGG
1 CCCTTATTTGAGCATTTTGA-AAACGTTAGG
*
52358 TCCTTATTTGAGCA
1 CCCTTATTTGAGCA
52372 ATTAACCTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 20 0.34
30 4 0.07
31 33 0.56
32 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGAAAACGTTAGG
Found at i:53694 original size:2 final size:2
Alignment explanation
Indices: 53687--53725 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53677 ATATGTTGAC
53687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53726 ATTACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.