Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014474.1 Corchorus olitorius cultivar O-4 contig14507, 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: 57229
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:13608 original size:5 final size:5
Alignment explanation
Indices: 13588--13632 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 5
13578 GAACTTCAAG
13588 TAAAA -AAAA T-AAA TAAAA TAAAA TAAAA T-AAA T-AAA T-AAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
13633 ATTAAAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 20 0.54
5 17 0.46
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:13634 original size:23 final size:23
Alignment explanation
Indices: 13588--13632 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
13578 GAACTTCAAG
13588 TAAAAAAAATAAATAAAATAAAA
1 TAAAAAAAATAAATAAAATAAAA
*
13611 TAAAATAAATAAAT-AAATAAAA
1 TAAAAAAAATAAATAAAATAAAA
13633 ATTAAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (23 bp):
TAAAAAAAATAAATAAAATAAAA
Found at i:19279 original size:17 final size:17
Alignment explanation
Indices: 19254--19287 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19244 AACCCGCCCG
*
19254 AACCCGAACCCGAAAAA
1 AACCAGAACCCGAAAAA
*
19271 AACCAGAACCGGAAAAA
1 AACCAGAACCCGAAAAA
19288 TCTAAAACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.29, G:0.15, T:0.00
Consensus pattern (17 bp):
AACCAGAACCCGAAAAA
Found at i:19540 original size:15 final size:16
Alignment explanation
Indices: 19529--19582 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
19519 CGAACCCGAA
19529 TTAACCTGACCCAAAT
1 TTAACCTGACCCAAAT
* * *
19545 TTGACCCGAACCCGAA-
1 TTAACCTG-ACCCAAAT
*
19561 TCAACCTGACCCAAAT
1 TTAACCTGACCCAAAT
19577 TTAACC
1 TTAACC
19583 AAATTCGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 6 0.21
16 16 0.57
17 6 0.21
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.20
Consensus pattern (16 bp):
TTAACCTGACCCAAAT
Found at i:19554 original size:32 final size:32
Alignment explanation
Indices: 19518--19617 Score: 121
Period size: 32 Copynumber: 3.2 Consensus size: 32
19508 CAGTCCGAAA
*
19518 CCGAACCCGAATTAACCTGACCCAAATTTGAC
1 CCGAACCCGAATCAACCTGACCCAAATTTGAC
*
19550 CCGAACCCGAATCAACCTGACCCAAATTT-AA
1 CCGAACCCGAATCAACCTGACCCAAATTTGAC
* ** * * *
19581 CCAAATTCGAATCAATCTGATCCAAATTTAAC
1 CCGAACCCGAATCAACCTGACCCAAATTTGAC
19613 CCGAA
1 CCGAA
19618 AATGGCCTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 25 0.43
32 33 0.57
ACGTcount: A:0.38, C:0.32, G:0.10, T:0.20
Consensus pattern (32 bp):
CCGAACCCGAATCAACCTGACCCAAATTTGAC
Found at i:19595 original size:31 final size:31
Alignment explanation
Indices: 19516--19613 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
19506 CCCAGTCCGA
* *
19516 AACCGAACCCGAATTAACCTGACCCAAATTT
1 AACCAAACCCGAATCAACCTGACCCAAATTT
* *
19547 GACCCGAACCCGAATCAACCTGACCCAAATTT
1 -AACCAAACCCGAATCAACCTGACCCAAATTT
** * *
19579 AACCAAATTCGAATCAATCTGATCCAAATTT
1 AACCAAACCCGAATCAACCTGACCCAAATTT
19610 AACC
1 AACC
19614 CGAAAATGGC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 29 0.50
32 29 0.50
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.20
Consensus pattern (31 bp):
AACCAAACCCGAATCAACCTGACCCAAATTT
Found at i:21778 original size:22 final size:21
Alignment explanation
Indices: 21726--21779 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
21716 TGCTTCTTGA
21726 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
21747 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
21766 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
21780 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:22801 original size:42 final size:43
Alignment explanation
Indices: 22750--22843 Score: 156
Period size: 45 Copynumber: 2.2 Consensus size: 43
22740 AGTGCCTTAC
22750 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGGTAATTCATCAAAATAAAG
22791 CTAATATTCTACTCCTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGGTAATTCATCAAAATAAAG
22836 CTAATATT
1 CTAATATT
22844 AATTGTTGCT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 39 0.80
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGGTAATTCATCAAAATAAAG
Found at i:25100 original size:23 final size:24
Alignment explanation
Indices: 25056--25100 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25046 TCATGCATCC
* *
25056 TCATGTCAACATTGCATTTTTAAG
1 TCATGGCAACATTACATTTTTAAG
25080 TCATGGCAACA-TACATTTTTA
1 TCATGGCAACATTACATTTTTA
25101 GCATTGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (24 bp):
TCATGGCAACATTACATTTTTAAG
Found at i:27134 original size:61 final size:62
Alignment explanation
Indices: 27041--27167 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 62
27031 TCTATGGGTA
** ** *
27041 AAAATATTGAATTCTAGAATTAGTTTGGTTTCATAATTCAGTTTAATCCTCAATAAGTTGGT
1 AAAATATTGAATTCTAGAATTAGCCTAATTTCATAATTCAGTTTAATCCTCAATAAGTTAGT
* * * ** *
27103 AAAA-ATTGAATTTTAGAATTAGCCTAATTTCATAGTTTAGTTTAATTGTCAATAGGTTAGT
1 AAAATATTGAATTCTAGAATTAGCCTAATTTCATAATTCAGTTTAATCCTCAATAAGTTAGT
27164 AAAA
1 AAAA
27168 GGGAAGAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
61 50 0.93
62 4 0.07
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (62 bp):
AAAATATTGAATTCTAGAATTAGCCTAATTTCATAATTCAGTTTAATCCTCAATAAGTTAGT
Found at i:27698 original size:17 final size:18
Alignment explanation
Indices: 27657--27698 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
27647 TAAAAAGGTT
27657 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
*
27675 TTC-AAAATTCAAAAAAA
1 TTCAAAAATCCAAAAAAA
27692 -TCAAAAA
1 TTCAAAAA
27699 GGATTTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 17 0.77
18 3 0.14
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:27800 original size:52 final size:52
Alignment explanation
Indices: 27709--27864 Score: 231
Period size: 52 Copynumber: 3.0 Consensus size: 52
27699 GGATTTCACT
*
27709 CAGTTTTCAAAGTATTCAATATTAGCTCTTTTTGTAATTGGGAAAGTTCCCAC
1 CAGTTTTCAAAGTATTCAAT-TTAGCTCTTTTTCTAATTGGGAAAGTTCCCAC
* * * * *
27762 CAGTCTTCAGAGTATTCAATCTAGCTCTTTTTCAAATTGGGTAAGTTCCCAC
1 CAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCTAATTGGGAAAGTTCCCAC
* *
27814 CAGTTTTCAAAGTATTCAATTTAGCTTTTTTTTTAATTGGGAAAGTTCCCA
1 CAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCTAATTGGGAAAGTTCCCA
27865 TCAGGTTATA
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 72 0.80
53 18 0.20
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (52 bp):
CAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCTAATTGGGAAAGTTCCCAC
Found at i:29708 original size:2 final size:2
Alignment explanation
Indices: 29703--29749 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
29693 TATAAAAATT
29703 TA TA TA TA TA TA TA TA TA -A TA TA TA -A TA TA -A TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29741 TA T- TA TA TA
1 TA TA TA TA TA
29750 ACTTAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 5 0.12
2 35 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29750 original size:17 final size:17
Alignment explanation
Indices: 29702--29750 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
29692 ATATAAAAAT
29702 TTATATATATATATATATA
1 TTATAT-TATATA-ATATA
* *
29721 ATATATAATATAATATA
1 TTATATTATATAATATA
29738 TTATATTATATAA
1 TTATATTATATAA
29751 CTTAAAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 16 0.62
18 5 0.19
19 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATATTATATAATATA
Found at i:31630 original size:30 final size:30
Alignment explanation
Indices: 31569--31637 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
31559 AATAAAGGGT
* * *
31569 AAAACGATTTCGTGTTTTACAAATAAGGGC
1 AAAACGTTTTCGTGTTTTACAAAAAAAGGC
*
31599 AAAACGTTTTCG-GATTTTTCAAAAAAAGGC
1 AAAACGTTTTCGTG-TTTTACAAAAAAAGGC
31629 AAAACGTTT
1 AAAACGTTT
31638 CGAATGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (30 bp):
AAAACGTTTTCGTGTTTTACAAAAAAAGGC
Found at i:32166 original size:31 final size:29
Alignment explanation
Indices: 32131--32201 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
32121 TTTGACAGCT
*
32131 TGCCCCTAATTGACGCCAAATTGAAACGTTG
1 TGCCCCAAATTGA--CCAAATTGAAACGTTG
* *
32162 TGCCCCAAATAGACCAAATTGAAATGTTG
1 TGCCCCAAATTGACCAAATTGAAACGTTG
32191 TGCCCCAAATT
1 TGCCCCAAATT
32202 AGGCTGAGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 25 0.69
31 11 0.31
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (29 bp):
TGCCCCAAATTGACCAAATTGAAACGTTG
Found at i:40950 original size:45 final size:45
Alignment explanation
Indices: 40886--40972 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
40876 AGCAACAACT
* *
40886 AATATTAGCTTTATTTTGATGAATTATATAGAGATGGAGTAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGAAGGAGTAGTAG
*
40931 AATATTAGCTTTATTTTGATGAATTACCTAGAGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGAAGGAGTAG
40973 AATTTAGGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACATAGAGAAGGAGTAGTAG
Found at i:48223 original size:151 final size:153
Alignment explanation
Indices: 47790--48274 Score: 771
Period size: 152 Copynumber: 3.2 Consensus size: 153
47780 GTTAGACTTT
*
47790 TCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCAGCCGAGTGGGGCAGTCCAACGTAGCACGGA
1 TCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGGCAGTCCAACGTAGCACGGA
* * * * *
47855 AAATAGA-AAAAGGATTCGGGGATCGTCGACTTTGAAAGAGTGAAAGCTTATGGAGACGCCGAGT
66 AAATTGAGAAGAGGAGTCGGGGATCGCCGACTTTGAAAGAGAGAAAGCTTATGGAGACGCCGAGT
* *
47919 TGAGAAGACAAGATCTTGCTGAG
131 TGAGAAGACAGGATCTTGCTGTG
** *
47942 TCCCACTAGGCGTGCCAAAAAGAGATGTTAGTGCGGCCGAGTGGGGCAGTCCAACGTAGCACGGA
1 TCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGGCAGTCCAACGTAGCACGGA
*
48007 AAATTGAGAAG-GGAGTCGGGGATCGCCGACTTTGAAAGAGAGAAAGCTTATGGAGACACCGAGT
66 AAATTGAGAAGAGGAGTCGGGGATCGCCGACTTTGAAAGAGAGAAAGCTTATGGAGACGCCGAGT
*
48071 TGAGAAAACAGGATCTTGCTGTG
131 TGAGAAGACAGGATCTTGCTGTG
* *
48094 TCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAAT-GGGCAGTCCAATGTAGCACGGA
1 TCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGGCAGTCCAACGTAGCACGGA
* *
48158 AAATTGAGAAGAGG-GTCGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACGCCAAGT
66 AAATTGAGAAGAGGAGTCGGGGATCGCCGACTTTGAAAGAGAGAAAGCTTATGGAGACGCCGAGT
*
48222 TGAGAAGACAGGATCTTGCTTTG
131 TGAGAAGACAGGATCTTGCTGTG
*
48245 TCCCACCGGGCGTGCCATAAAGAGATGTTG
1 TCCCACCGGGCGTGCCAAAAAGAGATGTTG
48275 TGCCAAAAAT
Statistics
Matches: 307, Mismatches: 24, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
151 129 0.42
152 176 0.57
153 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.18
Consensus pattern (153 bp):
TCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGGCAGTCCAACGTAGCACGGA
AAATTGAGAAGAGGAGTCGGGGATCGCCGACTTTGAAAGAGAGAAAGCTTATGGAGACGCCGAGT
TGAGAAGACAGGATCTTGCTGTG
Found at i:51018 original size:19 final size:20
Alignment explanation
Indices: 50970--51030 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
50960 ATCGCTGTTC
50970 TAATAATCCT-ATCTGTACAG
1 TAATAAT-CTAATCTGTACAG
50990 TACATAATCTAATCTGTACAG
1 TA-ATAATCTAATCTGTACAG
* *
51011 T-GTAATCTCATCTGTACAG
1 TAATAATCTAATCTGTACAG
51030 T
1 T
51031 TGTCAAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 17 0.46
20 4 0.11
21 16 0.43
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TAATAATCTAATCTGTACAG
Found at i:53687 original size:16 final size:16
Alignment explanation
Indices: 53663--53693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53653 TTGAAATATA
*
53663 TTACTAAATCTTTATT
1 TTACCAAATCTTTATT
53679 TTACCAAATCTTTAT
1 TTACCAAATCTTTAT
53694 AAATTTGTAG
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACCAAATCTTTATT
Found at i:54067 original size:20 final size:20
Alignment explanation
Indices: 54015--54069 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
54005 AATGTTAAGC
* * *
54015 TTTTCAATAACATTTTAAAT
1 TTTTTAATAACCTTATAAAT
* * *
54035 TTATTAGTCACCTTATAAAT
1 TTTTTAATAACCTTATAAAT
54055 TTTTTAATAACCTTA
1 TTTTTAATAACCTTA
54070 AAAGTTAAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTTAATAACCTTATAAAT
Found at i:54199 original size:21 final size:22
Alignment explanation
Indices: 54173--54233 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
54163 CCTTTTTTGG
* *
54173 CCTTATAAAGTTTTTTA-ATCA
1 CCTTATTAAGTTTTTTACATAA
*
54194 CCTTATTAAGTGTTTTTACCTAA
1 CCTTATTAAGT-TTTTTACATAA
54217 CCTTATTAAGTTTTTTA
1 CCTTATTAAGTTTTTTA
54234 GTAATCTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.29
22 12 0.34
23 13 0.37
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.51
Consensus pattern (22 bp):
CCTTATTAAGTTTTTTACATAA
Found at i:54242 original size:21 final size:21
Alignment explanation
Indices: 54173--54243 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
54163 CCTTTTTTGG
* *
54173 CCTTATAAAGTTTTTTAATCA
1 CCTTATTAAGTTTTTTAATAA
*
54194 CCTTATTAAGTGTTTTTACCTAA
1 CCTTATTAAGT-TTTTTA-ATAA
*
54217 CCTTATTAAGTTTTTTAGTAA
1 CCTTATTAAGTTTTTTAATAA
*
54238 TCTTAT
1 CCTTAT
54244 GTGAATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 18 0.42
22 12 0.28
23 13 0.30
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (21 bp):
CCTTATTAAGTTTTTTAATAA
Found at i:54414 original size:39 final size:39
Alignment explanation
Indices: 54339--54415 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
54329 TTAAGAATAA
* *
54339 TTTTAGTAACCTTATAAATATTTTTAATGATAATAAAAC
1 TTTTAGTAACCTTATAAATATTTTCAATGACAATAAAAC
* * *
54378 TTTTTGTAACCTTATTAAA-ATTTTCAGTGACCATAAAA
1 TTTTAGTAACCTTA-TAAATATTTTCAATGACAATAAAA
54416 GTCTTTCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 28 0.88
40 4 0.12
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.43
Consensus pattern (39 bp):
TTTTAGTAACCTTATAAATATTTTCAATGACAATAAAAC
Found at i:54618 original size:86 final size:86
Alignment explanation
Indices: 54527--54695 Score: 329
Period size: 86 Copynumber: 2.0 Consensus size: 86
54517 ATTTTCTTGG
*
54527 TAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATTTATTCAATC
1 TAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATC
54592 ACCTCGTTTAAGATTTTTCCA
66 ACCTCGTTTAAGATTTTTCCA
54613 TAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATC
1 TAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATC
54678 ACCTCGTTTAAGATTTTT
66 ACCTCGTTTAAGATTTTT
54696 AGTGATCTTA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (86 bp):
TAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATC
ACCTCGTTTAAGATTTTTCCA
Found at i:54780 original size:20 final size:21
Alignment explanation
Indices: 54731--54800 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 21
54721 GACTTAACTT
* *
54731 AAGTTTTATTTAGTGACCTTGT-
1 AAGTTTTA--TAGTAACCTTATG
*
54753 AAGATTTATAGTTAA-CTTATG
1 AAGTTTTATAG-TAACCTTATG
54774 AA-TTTTATAGTAACCTTATG
1 AAGTTTTATAGTAACCTTATG
54794 AAGTTTT
1 AAGTTTT
54801 TTCTAGTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 8 0.20
22 7 0.17
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (21 bp):
AAGTTTTATAGTAACCTTATG
Found at i:54825 original size:23 final size:23
Alignment explanation
Indices: 54776--54826 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
54766 AACTTATGAA
* *
54776 TTTTATAGTAACCTTATGAAGTT
1 TTTTATAGTAACCATATGAAGTG
*
54799 TTTTCTAGTAACCATATTG-AGTG
1 TTTTATAGTAACCATA-TGAAGTG
54822 TTTTA
1 TTTTA
54827 GAAATCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (23 bp):
TTTTATAGTAACCATATGAAGTG
Found at i:55182 original size:20 final size:21
Alignment explanation
Indices: 55146--55185 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
55136 TATAATAATC
55146 TTAAACTCTTTTAGTGATTTA
1 TTAAACTCTTTTAGTGATTTA
*
55167 TTAAACT-TTTTTGTGATTT
1 TTAAACTCTTTTAGTGATTT
55186 TTTTTGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (21 bp):
TTAAACTCTTTTAGTGATTTA
Done.