Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020227.1 Corchorus olitorius cultivar O-4 contig20260, 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: 19054
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:1899 original size:131 final size:131
Alignment explanation
Indices: 1651--1887 Score: 413
Period size: 131 Copynumber: 1.8 Consensus size: 131
1641 AGGAATCTCC
*
1651 TCAAATGAAGAGATTTTTAACGTTTCTGGTCTCTGCTTTGGTATTTATGATTTTGTTCATTGAAT
1 TCAAATGAAGAGATTTTTAACGTTTCTGGTCTCTGCTTTGCTATTTATGATTTTGTTCATTGAAT
* *
1716 TTTGTAAGTCCATTGTTTTTGAGAATTGCAAAGGACCAACCAAGAAAATAGTTCATGAATTATAT
66 TTTATAAGTCCATTGTTTCTGAGAATTGCAAAGGACCAACCAAGAAAATAGTTCATGAATTATAT
1781 A
131 A
* * *
1782 TCAAATGAAGAGATTTTTGACGTTTCTGGTCTGTGCTTTGCTATTTATGATTTTGTTCATTGACT
1 TCAAATGAAGAGATTTTTAACGTTTCTGGTCTCTGCTTTGCTATTTATGATTTTGTTCATTGAAT
1847 TTTATAAGTCCATTG-TTCTGAGAATTGCAAAGGACCAACCA
66 TTTATAAGTCCATTGTTTCTGAGAATTGCAAAGGACCAACCA
1888 TGTATCCTAG
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
130 25 0.25
131 75 0.75
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (131 bp):
TCAAATGAAGAGATTTTTAACGTTTCTGGTCTCTGCTTTGCTATTTATGATTTTGTTCATTGAAT
TTTATAAGTCCATTGTTTCTGAGAATTGCAAAGGACCAACCAAGAAAATAGTTCATGAATTATAT
A
Found at i:6977 original size:13 final size:13
Alignment explanation
Indices: 6959--6988 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6949 AACCGTTAAT
6959 ATCAAAATCATAA
1 ATCAAAATCATAA
*
6972 ATCAAAGTCATAA
1 ATCAAAATCATAA
6985 ATCA
1 ATCA
6989 GAGTAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (13 bp):
ATCAAAATCATAA
Found at i:8046 original size:26 final size:25
Alignment explanation
Indices: 8005--8066 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
7995 TCCTATTTTC
8005 TTCTTCTTGTTTTTTTCCTT-CCTTCCT
1 TTCTTCTT-TTTTTTTCCTTGCC-T-CT
8032 TTC-TCTTTTTCTTTTCCTTGCCTCT
1 TTCTTCTTTTT-TTTTCCTTGCCTCT
8057 TTCTTCTTTT
1 TTCTTCTTTT
8067 CTTCATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 8 0.25
26 19 0.59
27 5 0.16
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (25 bp):
TTCTTCTTTTTTTTTCCTTGCCTCT
Found at i:8280 original size:34 final size:34
Alignment explanation
Indices: 8240--8342 Score: 94
Period size: 34 Copynumber: 3.2 Consensus size: 34
8230 GCGCTGGGCT
8240 GCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTG
1 GCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTG
* *** *
8274 GCCCAAC-GCCAG----GCCCAAG-CGCTGGGCT-
1 GCCCAACAGCCCGCTCTGCCTGGGCCGC-GCGCTG
*
8302 GCCCAACAGCCCGCTCTGCTTGGGCCGCGCGCTG
1 GCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTG
8336 GCCCAAC
1 GCCCAAC
8343 GCCAGGCCTG
Statistics
Matches: 50, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
28 10 0.20
29 12 0.24
33 11 0.22
34 17 0.34
ACGTcount: A:0.13, C:0.46, G:0.31, T:0.11
Consensus pattern (34 bp):
GCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTG
Found at i:8292 original size:62 final size:62
Alignment explanation
Indices: 8218--8350 Score: 257
Period size: 62 Copynumber: 2.1 Consensus size: 62
8208 ATGGGCCACG
8218 CGCCAGGCCCAAGCGCTGGGCTGCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTGGCCCAA
1 CGCCAGGCCCAAGCGCTGGGCTGCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTGGCCCAA
*
8280 CGCCAGGCCCAAGCGCTGGGCTGCCCAACAGCCCGCTCTGCTTGGGCCGCGCGCTGGCCCAA
1 CGCCAGGCCCAAGCGCTGGGCTGCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTGGCCCAA
8342 CGCCAGGCC
1 CGCCAGGCC
8351 TGCTTATGCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.13, C:0.45, G:0.32, T:0.10
Consensus pattern (62 bp):
CGCCAGGCCCAAGCGCTGGGCTGCCCAACAGCCCGCTCTGCCTGGGCCGCGCGCTGGCCCAA
Found at i:9785 original size:22 final size:22
Alignment explanation
Indices: 9758--9804 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
9748 AAAAATTTAT
* *
9758 GAGGAGAGATAGTGAGTGGGAG
1 GAGGAGAGAGAGTAAGTGGGAG
*
9780 GAGGAGAGAGATTAAGTGGGAG
1 GAGGAGAGAGAGTAAGTGGGAG
9802 GAG
1 GAG
9805 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.53, T:0.13
Consensus pattern (22 bp):
GAGGAGAGAGAGTAAGTGGGAG
Found at i:11582 original size:22 final size:22
Alignment explanation
Indices: 11557--12154 Score: 217
Period size: 22 Copynumber: 27.3 Consensus size: 22
11547 ATTACGCTAT
*
11557 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
11579 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
11601 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * * **
11623 TTTCGA-GATCTTTTTAT-AAA
1 TTTTGATAACCTTCCTATGAAA
** *
11643 TTTTTTTTAACCTTCTTATGAAA
1 -TTTTGATAACCTTCCTATGAAA
* * * *
11666 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
**
11688 TTTT-A-AAGATCTCACTATGAAA
1 TTTTGATAACCT-TC-CTATGAAA
*
11710 TTTTGATAA-CTTCCACAATGAAA
1 TTTTGATAACCTT-C-CTATGAAA
*
11733 TTTTGATAA-CTGAT-CTATGAGA
1 TTTTGATAACCT--TCCTATGAAA
* * *
11755 TGTTGATAA-CTTACATATG-AT
1 TTTTGATAACCTT-CCTATGAAA
* *
11776 TTATTGATAACC-ACATTATGAAA
1 TT-TTGATAACCTTC-CTATGAAA
* * *
11799 ATTT-AAAAACTTCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* ** *
11820 TTGTT-AGTAATCACCCTCTGAAA
1 TT-TTGA-TAACCTTCCTATGAAA
* *
11843 TTTTGATAATC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * * *
11865 TTGTAATAACC-TCGTTATTAAA
1 TTTTGATAACCTTC-CTATGAAA
*
11887 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
11910 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
11933 TTTTGATAACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* *
11955 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
**
11971 TTTTGATAACCTCTCCCTATGATTT
1 TTTTGATAACCT-T-CCTATGA-AA
*
11996 TTTTGATAACC-TCATTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * *
12018 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * *
12040 TTTTGATCTA-CATACTATGAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
12062 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* **
12084 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
*
12106 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
12128 TTTTGATATCC-TCC-CTGAAA
1 TTTTGATAACCTTCCTATGAAA
12148 TTTTGAT
1 TTTTGAT
12155 TACTCCATAA
Statistics
Matches: 429, Mismatches: 105, Indels: 86
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
20 18 0.04
21 27 0.06
22 258 0.60
23 95 0.22
24 5 0.01
25 12 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:11910 original size:23 final size:23
Alignment explanation
Indices: 11884--11963 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
11874 CCTCGTTATT
11884 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
11907 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
11930 AAATTTTGAT-AACC-TCCTTATG
1 AAATTTTGATAAACCTTCC-TATA
*
11952 AAATCTTGATAA
1 AAATTTTGATAA
11964 CTACAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.31
23 33 0.65
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCCTATA
Found at i:12355 original size:44 final size:44
Alignment explanation
Indices: 12235--12426 Score: 148
Period size: 44 Copynumber: 4.4 Consensus size: 44
12225 AGAAATACCA
* * * *
12235 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * *
12279 TTATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
* * *
12323 CTATGAAATTTTGATATTCACATTATGTAATTTTGATAA--CTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* *
12365 ACT-TGAAATTTTGATAA-CA-ACTCTATGAAATTTTGATAA-TCTT
1 -CTATGAAATTTTGATAATCACA-T-TATGAAATTTTGATAACCCCT
12408 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
12427 CGATCTTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 30 0.25
43 20 0.17
44 63 0.53
45 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:12426 original size:21 final size:21
Alignment explanation
Indices: 12260--12424 Score: 113
Period size: 22 Copynumber: 7.7 Consensus size: 21
12250 AATCACATTT
* * *
12260 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACTTC-CTA
*
12282 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACTTC-CTA
* * * **
12304 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACTTC-CTA
12326 TGAAATTTTGAT-A-TTCACATTA
1 TGAAATTTTGATAACTTC-C--TA
* *
12348 TGTAATTTTGATAACTTACT-
1 TGAAATTTTGATAACTTCCTA
**
12368 TGAAATTTTGATAACAACTCTA
1 TGAAATTTTGATAACTTC-CTA
12390 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAA-CTTCCTA
12412 T-AAATTTTGATAA
1 TGAAATTTTGATAA
12425 TCCGATCTTT
Statistics
Matches: 117, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
20 16 0.14
21 16 0.14
22 79 0.68
23 4 0.03
24 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (21 bp):
TGAAATTTTGATAACTTCCTA
Found at i:12537 original size:22 final size:21
Alignment explanation
Indices: 12508--12622 Score: 69
Period size: 22 Copynumber: 5.4 Consensus size: 21
12498 AAATTGAGAC
*
12508 TTTTATAACCTTCATATGAAA
1 TTTTATAACCTCCATATGAAA
12529 TTTTGATAACCTCCCA-ATGAAA
1 TTTT-ATAACCT-CCATATGAAA
* * *
12551 TATTAGTAACCTCCTTATAAAA
1 TTTTA-TAACCTCCATATGAAA
*
12573 TTTTGTTAA---CCATATGAAA
1 TTTT-ATAACCTCCATATGAAA
* *
12592 TTCATATAACCTCGC-TATGACA
1 TT-TTATAACCTC-CATATGAAA
12614 TTTTGATAA
1 TTTT-ATAA
12623 TCTCTTTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
19 13 0.18
20 1 0.01
21 8 0.11
22 46 0.65
23 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTTATAACCTCCATATGAAA
Found at i:12714 original size:22 final size:22
Alignment explanation
Indices: 12627--12839 Score: 141
Period size: 22 Copynumber: 9.6 Consensus size: 22
12617 TGATAATCTC
12627 TTTGATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
** * *
12649 TTCAATAACCTTC-CTAAGAAAT
1 TTTGATAACC-ACACTATGAAAT
* *
12671 TTTAATAA-CATGATCCTATGAAAT
1 TTTGATAACCA-CA--CTATGAAAT
*
12695 TTTGGTAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
*
12717 TTTGATAACCTTC-CTATGAAAT
1 TTTGATAACC-ACACTATGAAAT
***
12739 TTTGATAACTTTTA-TATGAAAT
1 TTTGATAAC-CACACTATGAAAT
* * *
12761 TTTGGTAACCATACTATGAAAA
1 TTTGATAACCACACTATGAAAT
* *
12783 TTTGATAACCTC-CTCATAAAAT
1 TTTGATAACCACACT-ATGAAAT
* * *
12805 TATAATAACCATC-TTATGAAAT
1 TTTGATAACCA-CACTATGAAAT
12827 TTTGATAACCACA
1 TTTGATAACCACA
12840 TAGAGACAGG
Statistics
Matches: 147, Mismatches: 31, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
21 6 0.04
22 120 0.82
23 4 0.03
24 15 0.10
25 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAT
Found at i:12757 original size:44 final size:45
Alignment explanation
Indices: 12627--12835 Score: 162
Period size: 44 Copynumber: 4.7 Consensus size: 45
12617 TGATAATCTC
** * * *
12627 TTTGATAACCA-CACTATGAAATTTCAATAAC-CTTCCTAAGAAAT
1 TTTGATAACCATC-CTATGAAATTTTGATAACTCCTCATATGAAAT
* * * *
12671 TTTAATAACATGATCCTATGAAATTTTGGTAA--CCACACTATGAAAT
1 TTTGATAAC--CATCCTATGAAATTTTGATAACTCCTCA-TATGAAAT
* * *
12717 TTTGATAACCTTCCTATGAAATTTTGATAACT-TTTATATGAAAT
1 TTTGATAACCATCCTATGAAATTTTGATAACTCCTCATATGAAAT
* * *
12761 TTTGGTAACCATACTATGAAAATTTGATAACCTCCTCATA--AAAT
1 TTTGATAACCATCCTATGAAATTTTGATAA-CTCCTCATATGAAAT
* * *
12805 TATAATAACCATCTTATGAAATTTTGATAAC
1 TTTGATAACCATCCTATGAAATTTTGATAAC
12836 CACATAGAGA
Statistics
Matches: 129, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
43 1 0.01
44 88 0.68
45 5 0.04
46 34 0.26
47 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (45 bp):
TTTGATAACCATCCTATGAAATTTTGATAACTCCTCATATGAAAT
Found at i:12787 original size:66 final size:65
Alignment explanation
Indices: 12627--12839 Score: 232
Period size: 66 Copynumber: 3.2 Consensus size: 65
12617 TGATAATCTC
* * **
12627 TTTGATAACCACACTATG-AAATTTCAATAACCTTCCTAAGAAATTTTAATAACATGATCCTATG
1 TTTGATAACCACACTATGAAAATTT-GATAACCTTCCTATGAAATTTTAATAAC-T--TTTTATG
12691 AAAT
62 AAAT
* * *
12695 TTTGGTAACCACACTATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACTTTTATATGAAA
1 TTTGATAACCACACTATGAAAATTTGATAACCTTCCTATGAAATTTTAATAACTTTT-TATGAAA
12760 T
65 T
* * * * * *
12761 TTTGGTAACCATACTATGAAAATTTGATAACC-TCCTCATAAAATTATAATAACCATCTTATGAA
1 TTTGATAACCACACTATGAAAATTTGATAACCTTCCT-ATGAAATTTTAATAA-CTTTTTATGAA
12825 AT
64 AT
12827 TTTGATAACCACA
1 TTTGATAACCACA
12840 TAGAGACAGG
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
65 5 0.04
66 69 0.55
67 4 0.03
68 42 0.34
69 5 0.04
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (65 bp):
TTTGATAACCACACTATGAAAATTTGATAACCTTCCTATGAAATTTTAATAACTTTTTATGAAAT
Found at i:13913 original size:26 final size:26
Alignment explanation
Indices: 13877--13935 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
13867 AAAGGAGGAT
*
13877 TTCACAAGAGCAGTTTTGGAAGAAAA
1 TTCACAAGAGCAATTTTGGAAGAAAA
13903 TTCACAAGAGCAATTTTGGAAGAAAA
1 TTCACAAGAGCAATTTTGGAAGAAAA
13929 TTCACAA
1 TTCACAA
13936 CTTTTGATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.24
Consensus pattern (26 bp):
TTCACAAGAGCAATTTTGGAAGAAAA
Found at i:17098 original size:42 final size:43
Alignment explanation
Indices: 17051--17133 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
17041 CGTATTTGAC
*
17051 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
17093 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA
17134 CACGTTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:17146 original size:20 final size:21
Alignment explanation
Indices: 17121--17163 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
17111 TAATCGTGTC
*
17121 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
17141 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
17162 AA
1 AA
17164 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:17641 original size:12 final size:12
Alignment explanation
Indices: 17624--17654 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17614 TACCCTATGT
17624 AAACACGACACG
1 AAACACGACACG
17636 AAACACGACACG
1 AAACACGACACG
*
17648 GAACACG
1 AAACACG
17655 GATTGCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:18078 original size:29 final size:30
Alignment explanation
Indices: 18006--18085 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 30
17996 GCTAAATACC
*
18006 CAAAATAATCCCTTATGTTTTGCTTTTGGAA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGAA
*
18037 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGAA
*
18066 CAAATTAATCCCTTATGTTT
1 CAAAATAATCCCTTATGTTT
18086 CAAAAATGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 25 0.54
31 21 0.46
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGAA
Found at i:18244 original size:31 final size:31
Alignment explanation
Indices: 18209--18306 Score: 151
Period size: 31 Copynumber: 3.1 Consensus size: 31
18199 AAGGGACTGA
18209 TTTGTCCCAAAAGAAAAACATAAGGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGAATTTT
* *
18240 TTTGTCCCAAAAGAAAAACATAAGGGATTTG
1 TTTGTCCCAAAAGAAAAACATAAGGAATTTT
*
18271 TTTGTCCCAAAAAGAAAAATATAAGAGAATTTT
1 TTTGTCCC-AAAAGAAAAACATAAG-GAATTTT
18304 TTT
1 TTT
18307 AGTATTTAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 37 0.62
32 15 0.25
33 8 0.13
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGAATTTT
Done.