Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013989.1 Corchorus capsularis cultivar CVL-1 contig14010, 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: 74797
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3290 original size:38 final size:38
Alignment explanation
Indices: 3247--3322 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3237 TATTTGAATT
3247 TTAATTAGATTTCACCGAGTTTGTTTGTTGGGGATGGG
1 TTAATTAGATTTCACCGAGTTTGTTTGTTGGGGATGGG
3285 TTAATTAGATTTCACCGAGTTTGTTTGTTGGGGATGGG
1 TTAATTAGATTTCACCGAGTTTGTTTGTTGGGGATGGG
3323 GTTTGTTGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.08, G:0.32, T:0.42
Consensus pattern (38 bp):
TTAATTAGATTTCACCGAGTTTGTTTGTTGGGGATGGG
Found at i:5604 original size:2 final size:2
Alignment explanation
Indices: 5597--5633 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5587 TCTGTCCCTG
**
5597 TA TA TA TA TA CG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5634 TAGCATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15380 original size:20 final size:20
Alignment explanation
Indices: 15355--15393 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
15345 ATGTCTTTTC
15355 ATATAATTACAATCATAAAA
1 ATATAATTACAATCATAAAA
15375 ATATAATTACAATCATAAA
1 ATATAATTACAATCATAAA
15394 GCATATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATAATTACAATCATAAAA
Found at i:16015 original size:29 final size:25
Alignment explanation
Indices: 15967--16035 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 25
15957 ATTTAATTTT
15967 GATATTTTCTTTGTAACCAAAACAAAAAA
1 GATATTTTCTTTG-AACC--AA-AAAAAA
*
15996 GATATTTTCTTTGACTCCAAAAAAAA
1 GATATTTTCTTTGA-ACCAAAAAAAA
16022 GATATTTTCTTTGA
1 GATATTTTCTTTGA
16036 TTGTAAACGT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 20 0.53
27 2 0.05
28 1 0.03
29 15 0.39
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (25 bp):
GATATTTTCTTTGAACCAAAAAAAA
Found at i:18812 original size:3 final size:3
Alignment explanation
Indices: 18806--18838 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
18796 AATGAGAAGA
*
18806 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18839 TGTTTACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28009 original size:7 final size:7
Alignment explanation
Indices: 27994--28032 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
27984 ATAGATAAAG
27994 TATATAA
1 TATATAA
*
28001 TAGAT-A
1 TATATAA
28007 -ATATAA
1 TATATAA
28013 TATATAA
1 TATATAA
28020 TATATAA
1 TATATAA
28027 TATATA
1 TATATA
28033 GAGAGAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 3 0.11
6 2 0.07
7 23 0.82
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:28018 original size:19 final size:19
Alignment explanation
Indices: 27994--28030 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27984 ATAGATAAAG
27994 TATATAATAGATAATATAA
1 TATATAATAGATAATATAA
*
28013 TATATAATATATAATATA
1 TATATAATAGATAATATA
28031 TAGAGAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TATATAATAGATAATATAA
Found at i:28880 original size:74 final size:76
Alignment explanation
Indices: 28786--28926 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 76
28776 TTTTGCGATT
* * *
28786 CATTTCGAATGGGTTTAAGAAGAAAGTTTTGGTG-TTCA-ATCCATTATAAATGGGCTTGTATGG
1 CATTTCAAATGGGTTTAAGAAGAAAATTTTGGTGTTTAAGATCCATTATAAATGGGCTTGTATGG
28849 TTGTGTAATAA
66 TTGTGTAATAA
*
28860 CATTTCAAATGGGTTTAAGAAGAAAATTTTGGTGTTTAATGATCCATTATAGATGGGCTTGTATG
1 CATTTCAAATGGGTTTAAGAAGAAAATTTTGGTGTTTAA-GATCCATTATAAATGGGCTTGTATG
28925 GT
65 GT
28927 CTTGCTTCAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
74 32 0.53
75 3 0.05
77 25 0.42
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.38
Consensus pattern (76 bp):
CATTTCAAATGGGTTTAAGAAGAAAATTTTGGTGTTTAAGATCCATTATAAATGGGCTTGTATGG
TTGTGTAATAA
Found at i:31371 original size:13 final size:13
Alignment explanation
Indices: 31353--31382 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31343 AGAAATTTTC
31353 CTGTCTCAACCTG
1 CTGTCTCAACCTG
31366 CTGTCTCAACCTG
1 CTGTCTCAACCTG
31379 CTGT
1 CTGT
31383 TAGTGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.37, G:0.17, T:0.33
Consensus pattern (13 bp):
CTGTCTCAACCTG
Found at i:34196 original size:33 final size:33
Alignment explanation
Indices: 34140--34233 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 33
34130 CTCTTACAAA
*
34140 CAATGAAGTT-ACGAGCCTTCATCATGCCATTT
1 CAATGAAGTTCACGAGCCTTCATCACGCCATTT
* ***
34172 CAATGAAGTTCACGGGCCTTCATCACGTTGTTT
1 CAATGAAGTTCACGAGCCTTCATCACGCCATTT
34205 CAATGAAGTTCACGAGCCTTCATCACGCC
1 CAATGAAGTTCACGAGCCTTCATCACGCC
34234 TTAACAAGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 10 0.19
33 43 0.81
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (33 bp):
CAATGAAGTTCACGAGCCTTCATCACGCCATTT
Found at i:40066 original size:55 final size:54
Alignment explanation
Indices: 40000--40111 Score: 170
Period size: 55 Copynumber: 2.1 Consensus size: 54
39990 ACGGTACGTC
40000 TTTATCATTGTTAATCTTCATTTTTGCTGTTTTAGTATACTTTATGATTTGAATA
1 TTTATCATTGTTAATCTTCATTTTTGCTGTTTTAGTAT-CTTTATGATTTGAATA
** * * *
40055 TTTATCATTGTTAATCTTCATTTTTTTTGTTTTAGTCTTTTTATGATTTTAATA
1 TTTATCATTGTTAATCTTCATTTTTGCTGTTTTAGTATCTTTATGATTTGAATA
40109 TTT
1 TTT
40112 CTTTATATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
54 17 0.33
55 35 0.67
ACGTcount: A:0.21, C:0.08, G:0.09, T:0.62
Consensus pattern (54 bp):
TTTATCATTGTTAATCTTCATTTTTGCTGTTTTAGTATCTTTATGATTTGAATA
Found at i:46704 original size:17 final size:17
Alignment explanation
Indices: 46682--46733 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
46672 ATTCTCCCCT
46682 TGTGGTACCAGGTAGCA
1 TGTGGTACCAGGTAGCA
* *
46699 TGTGGTACTAAGTAGCA
1 TGTGGTACCAGGTAGCA
* * *
46716 TGAGGTATCAGATAGCA
1 TGTGGTACCAGGTAGCA
46733 T
1 T
46734 CTGCTGTATC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (17 bp):
TGTGGTACCAGGTAGCA
Found at i:47440 original size:150 final size:153
Alignment explanation
Indices: 47151--47442 Score: 398
Period size: 150 Copynumber: 1.9 Consensus size: 153
47141 TGCCAAGGGA
* * * *
47151 CTTAGATTCTCTCCACAAGACTATGGAAAAAATTCCAAGTAAAACAGAACTCCCCTTGATGGTGA
1 CTTAGATTATCTCCAAAAGACTATGGAAAAAATTCCAAGTAAAACAGAACTCCCCTTCATAGTGA
* * *
47216 ACTTGGTTTCTCTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCC
66 A--T-GTTGCACTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCC
47281 AATGAAGCTGATTTTCCACCAGTAGG
128 AATGAAGCTGATTTTCCACCAGTAGG
* *
47307 CTTAGATTATCTCCATAAAG-CTATGGAAAAATTTCTAAGTAAAACAGAACT-CCCTATCATAGT
1 CTTAGATTATCTCCA-AAAGACTATGGAAAAAATTCCAAGTAAAACAGAACTCCCCT-TCATAGT
*
47370 GAA-GTTGCAC-CCC-AAATTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCCA
64 GAATGTTGCACTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCCA
47432 ATTG-AGCTGAT
129 A-TGAAGCTGAT
47443 ACTTTGCCAG
Statistics
Matches: 123, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
150 55 0.45
151 5 0.04
152 5 0.04
155 4 0.03
156 51 0.41
157 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (153 bp):
CTTAGATTATCTCCAAAAGACTATGGAAAAAATTCCAAGTAAAACAGAACTCCCCTTCATAGTGA
ATGTTGCACTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCCAAT
GAAGCTGATTTTCCACCAGTAGG
Found at i:47461 original size:150 final size:151
Alignment explanation
Indices: 47071--47462 Score: 431
Period size: 156 Copynumber: 2.6 Consensus size: 151
47061 CTGGACTTCA
* * * * ** *
47071 CACCTCAAACTGTCTTTAAATGAAAAACTTGCATAAGTTTTTCA-CCTTAAGTCTGATTGAACTG
1 CACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCC-TAAGTCCAATTGAGCTG
* * *
47135 AAACTTTGCCAAGG-GACTTAGATTCTCTCCACAAGACTATGGAAAAAATTCCAAGTAAAACAGA
65 ATACTTTGCC-AGGAGACTTAGATTATCTCCAAAAGACTATGGAAAAAATTCCAAGTAAAACAGA
* * *
47199 ACTCCCCTTGATGGTGAACTTGGTTT
129 ACTCCCCTTCATAGTGAA--T-GTTG
*
47225 CTCTCCCTAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCCAA-TGAAGC
1 CAC-CCC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCCAATTG-AGC
* * * * *
47289 TGAT--TTTCCACCAGTAGGCTTAGATTATCTCCATAAAG-CTATGGAAAAATTTCTAAGTAAAA
63 TGATACTTT--GCCAGGAGACTTAGATTATCTCCA-AAAGACTATGGAAAAAATTCCAAGTAAAA
47351 CAGAACT-CCCTATCATAGTGAA-GTTG
125 CAGAACTCCCCT-TCATAGTGAATGTTG
* *
47377 CACCCCAAATTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCCAATTGAGCTGA
1 CACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCCAATTGAGCTGA
47442 TACTTTGCCAGGAGACTTAGA
66 TACTTTGCCAGGAGACTTAGA
47463 CTATGGAAAA
Statistics
Matches: 201, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
150 67 0.33
151 5 0.02
152 8 0.04
154 5 0.02
155 10 0.05
156 101 0.50
157 5 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (151 bp):
CACCCCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCCAATTGAGCTGA
TACTTTGCCAGGAGACTTAGATTATCTCCAAAAGACTATGGAAAAAATTCCAAGTAAAACAGAAC
TCCCCTTCATAGTGAATGTTG
Found at i:47579 original size:142 final size:136
Alignment explanation
Indices: 47327--47593 Score: 331
Period size: 142 Copynumber: 1.9 Consensus size: 136
47317 CTCCATAAAG
* *
47327 CTATGGAAAAATTTCTAAGTAAAACAGAACTCCCTATCATAGTGAAGTTGCACCCCAAATTGTCC
1 CTATGGAAAAAATTCTAAGTAAAACAGAACTCCCTATCATAGTGAAGTTGCACCCCAAACTGTCC
* * * *
47392 TTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCCAATTGAGCTGATACTTTGCCAGGAGA
66 TTAACTAAAAAACTAGCATAAGTTTTTCATACTAAGTCCAATTGAGATGAAACTTAGCCAGGAGA
47457 CTTAGA
131 CTTAGA
* *
47463 CTATGGAAAAAATTCTAAGTAAAACCA-AACTCCCTATCATTGGTGAAGTGGTTTCTCACCCCAA
1 CTATGGAAAAAATTCTAAGTAAAA-CAGAACTCCCTATCA-TAGTGAA---G-TT-GCACCCCAA
* ** **
47527 ACTGTCCTTAACTAAAAAACTTGCAT-AGATTTTTCATTTTAAGTCCGTTTGAGATGAAACTTAG
59 ACTGTCCTTAACTAAAAAACTAGCATAAG-TTTTTCATACTAAGTCCAATTGAGATGAAACTTAG
47591 CCA
123 CCA
47594 ATATGGTCCA
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
136 35 0.32
137 8 0.07
140 1 0.01
141 4 0.04
142 62 0.56
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (136 bp):
CTATGGAAAAAATTCTAAGTAAAACAGAACTCCCTATCATAGTGAAGTTGCACCCCAAACTGTCC
TTAACTAAAAAACTAGCATAAGTTTTTCATACTAAGTCCAATTGAGATGAAACTTAGCCAGGAGA
CTTAGA
Found at i:50516 original size:55 final size:56
Alignment explanation
Indices: 50456--50569 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 56
50446 CGTGGTACAT
50456 TTTATCATTGTTAAACTTCAA-TTTTGC-TGTTTTAGTACTTTTTATGATTTGAATA
1 TTTATCATTGTTAAACTTCAATTTTTGCTTGTTTTAGTA-TTTTTATGATTTGAATA
* * *
50511 TTTATCATTGTTAATCTTCAATTTTTTCTTGTTTTAGTATTTTTATGATTTTAATA
1 TTTATCATTGTTAAACTTCAATTTTTGCTTGTTTTAGTATTTTTATGATTTGAATA
50567 TTT
1 TTT
50570 CCTTTTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
55 20 0.37
56 24 0.44
57 10 0.19
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.60
Consensus pattern (56 bp):
TTTATCATTGTTAAACTTCAATTTTTGCTTGTTTTAGTATTTTTATGATTTGAATA
Found at i:51408 original size:18 final size:19
Alignment explanation
Indices: 51385--51422 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
51375 ATCTGTTGGA
* *
51385 TTTAG-TCAGTTTTTTGAG
1 TTTAGTTCAGCTTTCTGAG
51403 TTTAGTTCAGCTTTCTGAG
1 TTTAGTTCAGCTTTCTGAG
51422 T
1 T
51423 CAATTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.53
Consensus pattern (19 bp):
TTTAGTTCAGCTTTCTGAG
Found at i:55063 original size:56 final size:56
Alignment explanation
Indices: 54977--55089 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
54967 GGTCCCGGTG
*
54977 CCTTATCCCCCTCGCAATCTTTAATGGCTTCCCAAACTTCTTCCTCATTAATCACT
1 CCTTATCCCCCTCACAATCTTTAATGGCTTCCCAAACTTCTTCCTCATTAATCACT
55033 CCTTATCCCCCTCACAATCTTTAATGGCTTCCCAAACTTCTTCCTCATTAATCACT
1 CCTTATCCCCCTCACAATCTTTAATGGCTTCCCAAACTTCTTCCTCATTAATCACT
55089 C
1 C
55090 TTTCAAGCCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.22, C:0.38, G:0.04, T:0.35
Consensus pattern (56 bp):
CCTTATCCCCCTCACAATCTTTAATGGCTTCCCAAACTTCTTCCTCATTAATCACT
Found at i:55378 original size:18 final size:18
Alignment explanation
Indices: 55355--55415 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
55345 AACTTGATGA
55355 TAATTTAAGAGTTTGATT
1 TAATTTAAGAGTTTGATT
** ** *
55373 TAATTTTTGAACTTGATGA
1 TAATTTAAGAGTTTGAT-T
* *
55392 TAATTTGAGAGTTTAATT
1 TAATTTAAGAGTTTGATT
55410 TAATTT
1 TAATTT
55416 GATTCAAGAG
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
18 19 0.61
19 12 0.39
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.51
Consensus pattern (18 bp):
TAATTTAAGAGTTTGATT
Found at i:55384 original size:37 final size:37
Alignment explanation
Indices: 55342--55415 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
55332 TGATTTGATC
*
55342 TTGAACTTGATGATAATTTAAGAGTTTGATTTAATTT
1 TTGAACTTGATGATAATTTAAGAGTTTAATTTAATTT
*
55379 TTGAACTTGATGATAATTTGAGAGTTTAATTTAATTT
1 TTGAACTTGATGATAATTTAAGAGTTTAATTTAATTT
55416 GATTCAAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (37 bp):
TTGAACTTGATGATAATTTAAGAGTTTAATTTAATTT
Found at i:55397 original size:19 final size:19
Alignment explanation
Indices: 55342--55397 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
55332 TGATTTGATC
55342 TTGAACTTGATGATAATTT
1 TTGAACTTGATGATAATTT
** ** *
55361 AAGAGTTTGAT-TTAATTT
1 TTGAACTTGATGATAATTT
55379 TTGAACTTGATGATAATTT
1 TTGAACTTGATGATAATTT
55398 GAGAGTTTAA
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGAACTTGATGATAATTT
Found at i:57914 original size:3 final size:3
Alignment explanation
Indices: 57906--57942 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
57896 AACAATATAC
57906 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
57943 TAGGAGAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:59008 original size:22 final size:22
Alignment explanation
Indices: 58980--59022 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
58970 TGGATTCTTG
58980 CCCCAACCAAACGCCCAGGTTA
1 CCCCAACCAAACGCCCAGGTTA
59002 CCCCAACCAAACGCCCAGGTT
1 CCCCAACCAAACGCCCAGGTT
59023 TTGGAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.47, G:0.14, T:0.09
Consensus pattern (22 bp):
CCCCAACCAAACGCCCAGGTTA
Found at i:65008 original size:16 final size:16
Alignment explanation
Indices: 64987--65017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64977 TTGAAAAATA
64987 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
65003 TTACTAAATTTTTAT
1 TTACTAAATATTTAT
65018 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:67219 original size:3 final size:3
Alignment explanation
Indices: 67211--67242 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
67201 TATAACCAAA
67211 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
67243 AGAAAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Done.