Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016310.1 Corchorus olitorius cultivar O-4 contig16343, 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: 87813
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:934 original size:9 final size:9
Alignment explanation
Indices: 905--939 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
895 CCAAATTACA
905 TATGGAAAT
1 TATGGAAAT
*
914 TAAGGAAAT
1 TATGGAAAT
923 TATGGAAAT
1 TATGGAAAT
932 TAT-GAAAT
1 TATGGAAAT
940 CAAATGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.21
9 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (9 bp):
TATGGAAAT
Found at i:2289 original size:49 final size:47
Alignment explanation
Indices: 2224--2357 Score: 157
Period size: 49 Copynumber: 2.8 Consensus size: 47
2214 AATCTTTTAC
*
2224 TTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTATT
1 TTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACTTTTAAT
* *
2271 TTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAAT
1 TTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACTTTTAAT
* *
2320 TTT-CATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
2358 TTGGCACGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
47 15 0.20
48 20 0.26
49 40 0.53
50 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACTTTTAAT
Found at i:6461 original size:41 final size:41
Alignment explanation
Indices: 6404--6486 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
6394 GGTCAAGCCC
*
6404 ATTAGGATTGATATTGGAGAGATAATGGTTCTAAAACACCA
1 ATTAGGATTGATATTGGAGAGATAATGGTTATAAAACACCA
6445 ATTAGGATTGATATTGGAGAGATAATGGTTATAAAACACCA
1 ATTAGGATTGATATTGGAGAGATAATGGTTATAAAACACCA
6486 A
1 A
6487 GGAAATCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (41 bp):
ATTAGGATTGATATTGGAGAGATAATGGTTATAAAACACCA
Found at i:6934 original size:22 final size:22
Alignment explanation
Indices: 6883--6934 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
6873 CTGAGAAAAT
*
6883 CTTGATTTTCCTTTGATTTCCC
1 CTTGATTTTCCTTCGATTTCCC
* * **
6905 CATCATTTTCCTTCGATTTTTC
1 CTTGATTTTCCTTCGATTTCCC
6927 CTTGATTT
1 CTTGATTT
6935 CCATTCTTTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.08, T:0.56
Consensus pattern (22 bp):
CTTGATTTTCCTTCGATTTCCC
Found at i:12000 original size:22 final size:21
Alignment explanation
Indices: 11971--12011 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
11961 TATTTGACAC
11971 TTTCTTGACCC-CTATGGTTAG
1 TTTCTTGACCCACTA-GGTTAG
11992 TTTCATTGACCCACTAGGTT
1 TTTC-TTGACCCACTAGGTT
12012 GCATGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
TTTCTTGACCCACTAGGTTAG
Found at i:15474 original size:24 final size:24
Alignment explanation
Indices: 15442--15492 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
15432 GTCCTTAATT
15442 GAAAGAGATGCAAAAGTTGCAAAC
1 GAAAGAGATGCAAAAGTTGCAAAC
15466 GAAAGAGATGCAAAAGTTGCAAAC
1 GAAAGAGATGCAAAAGTTGCAAAC
15490 GAA
1 GAA
15493 GTCAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.25, T:0.12
Consensus pattern (24 bp):
GAAAGAGATGCAAAAGTTGCAAAC
Found at i:20210 original size:24 final size:27
Alignment explanation
Indices: 20183--20233 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
20173 ATGATGAAAA
*
20183 AGAG-AAA-AAGCGCGGAGCTT-TTTT
1 AGAGAAAATAAGCACGGAGCTTGTTTT
20207 AGAGAAAATAAGCACGGAGCTTGTTTT
1 AGAGAAAATAAGCACGGAGCTTGTTTT
20234 TTGCGCGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 3 0.13
26 12 0.52
27 4 0.17
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (27 bp):
AGAGAAAATAAGCACGGAGCTTGTTTT
Found at i:22638 original size:21 final size:21
Alignment explanation
Indices: 22614--22657 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
22604 TTATCATTCA
*
22614 AATAAATTGTTTAATGCATCT
1 AATAAATTGTTCAATGCATCT
*
22635 AATAAATTGTTCAATGTATCT
1 AATAAATTGTTCAATGCATCT
22656 AA
1 AA
22658 GTAGTCGCAT
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:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (21 bp):
AATAAATTGTTCAATGCATCT
Found at i:22927 original size:31 final size:31
Alignment explanation
Indices: 22892--23061 Score: 214
Period size: 31 Copynumber: 5.5 Consensus size: 31
22882 GGTGTCCGAC
* *
22892 GTGGCATGCCACGTGTACCAAAAAGCGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
22923 GTGGCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
* * * *
22954 GTGGCACACCACTTGTACCGAAAAGCGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
22985 ATGGCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
** ** *
23016 GTATCACGCCGTGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
* *
23047 GTGGCATGTCACGTG
1 GTGGCACGCCACGTG
23062 CACAAAAGGA
Statistics
Matches: 116, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 116 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACCAAAAAGTGACAT
Found at i:36707 original size:80 final size:82
Alignment explanation
Indices: 36502--36742 Score: 389
Period size: 82 Copynumber: 3.0 Consensus size: 82
36492 CAATCTCCAT
* *
36502 TGGCTACACTGTTCAATTGATTTCAGCTAATGAACACTGACGGCTTCTTGCTCAAATTAGTTTGA
1 TGGCTGCACTGTTCAATTGATTTCAGCTAATGAACATTGACGGCTTCTTGCTCAAATTAGTTTGA
*
36567 GC-TCGTATGTCTTGTTG
66 -CATCGTATGTCTTGCTG
* * *
36584 TGGCTGCACTGTTCAATTGATTTCTGCTGATGAACATTGACGGCTTCTTGTTCAAATTAGTTTGA
1 TGGCTGCACTGTTCAATTGATTTCAGCTAATGAACATTGACGGCTTCTTGCTCAAATTAGTTTGA
36649 CATCGT-TGTCTTGCTG
66 CATCGTATGTCTTGCTG
36665 TGGCTGCACTG-TCAATTGATTTCAGCTAATGAACATTGACGGCTTCTTGCTCAAATTAGTTTGA
1 TGGCTGCACTGTTCAATTGATTTCAGCTAATGAACATTGACGGCTTCTTGCTCAAATTAGTTTGA
*
36729 TATCGTATGTCTTG
66 CATCGTATGTCTTG
36743 TTGCTCAAAT
Statistics
Matches: 147, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
80 55 0.37
81 28 0.19
82 64 0.44
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (82 bp):
TGGCTGCACTGTTCAATTGATTTCAGCTAATGAACATTGACGGCTTCTTGCTCAAATTAGTTTGA
CATCGTATGTCTTGCTG
Found at i:37108 original size:3 final size:3
Alignment explanation
Indices: 37102--37142 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
37092 GAATATATAT
37102 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
37143 GTTTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39538 original size:401 final size:401
Alignment explanation
Indices: 38789--39595 Score: 1560
Period size: 401 Copynumber: 2.0 Consensus size: 401
38779 TTAGGGGCTA
*
38789 AATTATATATTTTTTCACTTGAGGGACCAATTTGCTACTTTCGCACCACTTCAGAACCAATTAAT
1 AATTATATATTTTTTAACTTGAGGGACCAATTTGCTACTTTCGCACCACTTCAGAACCAATTAAT
*
38854 TGCCTAAATAAGTCATCGCATGATCAGCTTTGACATAAATAAAATTCAGATATTATTTATCTCAT
66 TGCCTAAACAAGTCATCGCATGATCAGCTTTGACATAAATAAAATTCAGATATTATTTATCTCAT
38919 GATCAGCTTTGACATAAATGAAATTCAGAATCCATGACTGCAGGGTGCAAAATATATATCCAAGG
131 GATCAGCTTTGACATAAATGAAATTCAGAATCCATGACTGCAGGGTGCAAAATATATATCCAAGG
38984 TAAGCAATCCCCTTTCAAAGAATTATAAAATGACCAACTAGATACAACATAAAGAAGAAGAATTA
196 TAAGCAATCCCCTTTCAAAGAATTATAAAATGACCAACTAGATACAACATAAAGAAGAAGAATTA
39049 ACGTCTGCCAAAAAAAAAGAAGAAGAATTAACATAGAAACCCCATTAGGCCATTAAAAAAAAAGA
261 ACGTCTGCCAAAAAAAAAGAAGAAGAATTAACATAGAAACCCCATTAGGCCATTAAAAAAAAAGA
*
39114 AAAAGAAATCGGGCCCCTTTAAAACTTGGGAGAGGATTCTTCCACTACTTAAAAAGGAGAATAGG
326 AAAAGAAATCGGGCCCCTTTAAAACTTGAGAGAGGATTCTTCCACTACTTAAAAAGGAGAATAGG
39179 ATTTAGTAATT
391 ATTTAGTAATT
*
39190 AATTATATATTTTTTAACTTGAGGGACCAATTTGCTACTTTCGCACCACTTCAGGACCAATTAAT
1 AATTATATATTTTTTAACTTGAGGGACCAATTTGCTACTTTCGCACCACTTCAGAACCAATTAAT
39255 TGCCTAAACAAGTCATCGCATGATCAGCTTTGACATAAATAAAATTCAGATATTATTTATCTCAT
66 TGCCTAAACAAGTCATCGCATGATCAGCTTTGACATAAATAAAATTCAGATATTATTTATCTCAT
39320 GATCAGCTTTGACATAAATGAAATTCAGAATCCATGACTGCAGGGTGCAAAATATATATCCAAGG
131 GATCAGCTTTGACATAAATGAAATTCAGAATCCATGACTGCAGGGTGCAAAATATATATCCAAGG
39385 TAAGCAATCCCCTTTCAAAGAATTATAAAATGACCAACTAGATACAACATAAAGAAGAAGAATTA
196 TAAGCAATCCCCTTTCAAAGAATTATAAAATGACCAACTAGATACAACATAAAGAAGAAGAATTA
*
39450 ACGTCTGCCAAAAAAAAAGAAGAAGAATTAACATAGTAACCCCATTAGGCCATTAAAAAAAAAGA
261 ACGTCTGCCAAAAAAAAAGAAGAAGAATTAACATAGAAACCCCATTAGGCCATTAAAAAAAAAGA
*
39515 AAAAGAAATCGGGCCCGTTTAAAACTTGAGAGAGGATTCTTCCACTACTTAAAAAGGAGAATAGG
326 AAAAGAAATCGGGCCCCTTTAAAACTTGAGAGAGGATTCTTCCACTACTTAAAAAGGAGAATAGG
39580 ATTTAGTAATT
391 ATTTAGTAATT
39591 AATTA
1 AATTA
39596 ATCAATTTAT
Statistics
Matches: 400, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
401 400 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (401 bp):
AATTATATATTTTTTAACTTGAGGGACCAATTTGCTACTTTCGCACCACTTCAGAACCAATTAAT
TGCCTAAACAAGTCATCGCATGATCAGCTTTGACATAAATAAAATTCAGATATTATTTATCTCAT
GATCAGCTTTGACATAAATGAAATTCAGAATCCATGACTGCAGGGTGCAAAATATATATCCAAGG
TAAGCAATCCCCTTTCAAAGAATTATAAAATGACCAACTAGATACAACATAAAGAAGAAGAATTA
ACGTCTGCCAAAAAAAAAGAAGAAGAATTAACATAGAAACCCCATTAGGCCATTAAAAAAAAAGA
AAAAGAAATCGGGCCCCTTTAAAACTTGAGAGAGGATTCTTCCACTACTTAAAAAGGAGAATAGG
ATTTAGTAATT
Found at i:40815 original size:11 final size:11
Alignment explanation
Indices: 40785--40815 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40775 TTGTTTGTTC
*
40785 TTTCCTTTTCT
1 TTTCTTTTTCT
40796 TTTCTTTTTCT
1 TTTCTTTTTCT
40807 TTTCTTTTT
1 TTTCTTTTT
40816 TTCCTACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:41305 original size:52 final size:51
Alignment explanation
Indices: 41223--41328 Score: 194
Period size: 52 Copynumber: 2.1 Consensus size: 51
41213 CATGCTTTAA
*
41223 TATTTTCCAAAGTCATGACTTAATGTGGATAAAGTATTCATTAGATCAGTC
1 TATTTTCCAAAGTCACGACTTAATGTGGATAAAGTATTCATTAGATCAGTC
41274 TATTGTTCCAAAGTCACGACTTAATGTGGATAAAGTATTCATTAGATCAGTC
1 TATT-TTCCAAAGTCACGACTTAATGTGGATAAAGTATTCATTAGATCAGTC
41326 TAT
1 TAT
41329 ATATATAATG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 4 0.08
52 49 0.92
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (51 bp):
TATTTTCCAAAGTCACGACTTAATGTGGATAAAGTATTCATTAGATCAGTC
Found at i:41966 original size:2 final size:2
Alignment explanation
Indices: 41955--41986 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41945 TGCAATTCAA
41955 AT AT -T 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 A
41987 CACATCGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42450 original size:22 final size:22
Alignment explanation
Indices: 42422--42463 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42412 GACAAACTTG
*
42422 TAACCCGAATGATCCGAGAAGT
1 TAACCCGAATGATCCAAGAAGT
*
42444 TAACCCGGATGATCCAAGAA
1 TAACCCGAATGATCCAAGAA
42464 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (22 bp):
TAACCCGAATGATCCAAGAAGT
Found at i:43152 original size:16 final size:15
Alignment explanation
Indices: 43112--43154 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
43102 CAGACTCGAG
43112 ACCCGAATGACCTGA
1 ACCCGAATGACCTGA
*
43127 ACCC-AGATGAGCTGAA
1 ACCCGA-ATGACCTG-A
43143 ACCCGAATGACC
1 ACCCGAATGACC
43155 CAAGAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 1 0.04
15 11 0.48
16 10 0.43
17 1 0.04
ACGTcount: A:0.35, C:0.33, G:0.21, T:0.12
Consensus pattern (15 bp):
ACCCGAATGACCTGA
Found at i:43697 original size:101 final size:103
Alignment explanation
Indices: 43580--43782 Score: 313
Period size: 105 Copynumber: 2.0 Consensus size: 103
43570 TATCTAAGTT
*
43580 TTTTAATAAAATTAGTAAAAAGATAAAAATAAAATAG-GTATAA-GATATTAGATTTAATTAAAT
1 TTTTAATAAAATTAGTAAAAAGATAAAAATAAAATAGAGTATAAGGATATTAGATTTAATCAAAT
*
43643 AAAAATAGAGTTTTTTGTTGAGTAAAACTATAAAAATA
66 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATA
* * *
43681 TTTTAATTAAAA-TAGTAAAATGGTAAAAATAAAATAGTACTTATAAGGATATTAGATTTAATCA
1 TTTTAA-TAAAATTAGTAAAAAGATAAAAATAAAATAG-A-GTATAAGGATATTAGATTTAATCA
43745 AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
63 AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
43783 TTTAAGCAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
101 29 0.32
102 5 0.05
104 5 0.05
105 53 0.58
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (103 bp):
TTTTAATAAAATTAGTAAAAAGATAAAAATAAAATAGAGTATAAGGATATTAGATTTAATCAAAT
AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATA
Found at i:47008 original size:124 final size:124
Alignment explanation
Indices: 46788--47035 Score: 478
Period size: 124 Copynumber: 2.0 Consensus size: 124
46778 CATCTCGGTT
* *
46788 TGTTGGTTTCCTCTACCTCTGCCACGGGTGGCCATTGTTGTTTCCACGCATGAACTTAAAGGCTA
1 TGTTGGTTTCCTCTACCTCTGCCACGGGTGGCCATTGTTGCTTCCACGCAGGAACTTAAAGGCTA
46853 CTGATACCAATTAACGTAGCGGAAGGATAGAAAAGGATTCACTCACAAGAAATAGGCTA
66 CTGATACCAATTAACGTAGCGGAAGGATAGAAAAGGATTCACTCACAAGAAATAGGCTA
46912 TGTTGGTTTCCTCTACCTCTGCCACGGGTGGCCATTGTTGCTTCCACGCAGGAACTTAAAGGCTA
1 TGTTGGTTTCCTCTACCTCTGCCACGGGTGGCCATTGTTGCTTCCACGCAGGAACTTAAAGGCTA
46977 CTGATACCAATTAACGTAGCGGAAGGATAGAAAAGGATTCACTCACAAGAAATAGGCTA
66 CTGATACCAATTAACGTAGCGGAAGGATAGAAAAGGATTCACTCACAAGAAATAGGCTA
47036 GATTATGTTA
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (124 bp):
TGTTGGTTTCCTCTACCTCTGCCACGGGTGGCCATTGTTGCTTCCACGCAGGAACTTAAAGGCTA
CTGATACCAATTAACGTAGCGGAAGGATAGAAAAGGATTCACTCACAAGAAATAGGCTA
Found at i:48977 original size:46 final size:47
Alignment explanation
Indices: 48924--49018 Score: 158
Period size: 46 Copynumber: 2.0 Consensus size: 47
48914 CATTGTTTAA
*
48924 ACTTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTA-ATAT
1 ACTTTTATAGTTTTACTCAAAT-AAAACTCTATTTTTTATTTATATAT
48970 ACTTTTATAGTTTTACTCAAATAAAACTCTATTTTTTATTTATATAT
1 ACTTTTATAGTTTTACTCAAATAAAACTCTATTTTTTATTTATATAT
49017 AC
1 AC
49019 CTATTTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
45 9 0.20
46 31 0.67
47 6 0.13
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.51
Consensus pattern (47 bp):
ACTTTTATAGTTTTACTCAAATAAAACTCTATTTTTTATTTATATAT
Found at i:49853 original size:25 final size:24
Alignment explanation
Indices: 49802--49858 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
49792 GTCAGTCTTG
*
49802 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
49825 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
49850 AATTTATTT
1 AATTTATTT
49859 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:77383 original size:61 final size:61
Alignment explanation
Indices: 77209--77370 Score: 288
Period size: 61 Copynumber: 2.6 Consensus size: 61
77199 TTTAAGTTTT
* * *
77209 GAATTCAAAGTGTTATGAATAGAAAAAATAGGTATTACTAGAGATTTCCTTTGTTAAATCCC
1 GAATTC-AAGTGTTGTGAATAGAAAAAATAGGTATTATTAGAGATTTCTTTTGTTAAATCCC
77271 GAATTCAAGTGTTGTGAATAGAAAAAATAGGTATTATTAGAGATTTCTTTTGTTAAATCCC
1 GAATTCAAGTGTTGTGAATAGAAAAAATAGGTATTATTAGAGATTTCTTTTGTTAAATCCC
77332 GAATTCAAGTGTTGTGAATAGAAAAAATAGGTATTATTA
1 GAATTCAAGTGTTGTGAATAGAAAAAATAGGTATTATTA
77371 CAGCTCGATT
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 91 0.94
62 6 0.06
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (61 bp):
GAATTCAAGTGTTGTGAATAGAAAAAATAGGTATTATTAGAGATTTCTTTTGTTAAATCCC
Found at i:82177 original size:15 final size:16
Alignment explanation
Indices: 82149--82178 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
82139 TCATTTGATC
82149 TGATCAAGAAACAAAG
1 TGATCAAGAAACAAAG
82165 TGATCAA-AAACAAA
1 TGATCAAGAAACAAA
82179 TTTTAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (16 bp):
TGATCAAGAAACAAAG
Found at i:83465 original size:39 final size:40
Alignment explanation
Indices: 83409--83489 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
83399 TTTAATTCCT
83409 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
83449 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
83488 AT
1 AT
83490 TCTTATGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:83983 original size:17 final size:17
Alignment explanation
Indices: 83961--83994 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
83951 TACAACTTTG
83961 TTAGTAATCTTAGACTT
1 TTAGTAATCTTAGACTT
83978 TTAGTAATCTTAGACTT
1 TTAGTAATCTTAGACTT
83995 AAAAATTAAA
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:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGTAATCTTAGACTT
Found at i:85369 original size:13 final size:13
Alignment explanation
Indices: 85336--85388 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
85326 GCACCCAAAA
*
85336 CATTTAT-TAAAA
1 CATTTATATAAAG
85348 CATTT-TATAAAG
1 CATTTATATAAAG
85360 CATTTATATAAAG
1 CATTTATATAAAG
*
85373 CAGTTATA-AAA-
1 CATTTATATAAAG
85384 CATTT
1 CATTT
85389 CCTCAATGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:85601 original size:19 final size:19
Alignment explanation
Indices: 85561--85601 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
85551 AGATCATAGT
* *
85561 AAAACCAAGATAATCAATC
1 AAAACCAAGATAATAAACC
*
85580 AAAACCGAGATAATAAACC
1 AAAACCAAGATAATAAACC
85599 AAA
1 AAA
85602 TCAATCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAACCAAGATAATAAACC
Found at i:86611 original size:15 final size:14
Alignment explanation
Indices: 86593--86646 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
86583 AATTTTCTTA
86593 TTTTCCTATTTCCCTTT
1 TTTTCCT-TTTCCC--T
*
86610 TTTTTCTTTT-CCT
1 TTTTCCTTTTCCCT
*
86623 TTTCCCTTTTCCCT
1 TTTTCCTTTTCCCT
86637 TTTTCCTTTT
1 TTTTCCTTTT
86647 TCTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 9 0.28
14 12 0.38
15 2 0.06
16 3 0.09
17 6 0.19
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCCTTTTCCCT
Found at i:86647 original size:7 final size:7
Alignment explanation
Indices: 86593--86652 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
86583 AATTTTCTTA
86593 TTTTCCT
1 TTTTCCT
*
86600 ATTTCCCT
1 -TTTTCCT
**
86608 TTTTTTT
1 TTTTCCT
86615 CTTTTCCT
1 -TTTTCCT
*
86623 TTTCCCT
1 TTTTCCT
*
86630 TTTCCCT
1 TTTTCCT
86637 TTTTCCT
1 TTTTCCT
86644 TTTT-CT
1 TTTTCCT
86650 TTT
1 TTT
86653 CTTTTCTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 5 0.12
7 27 0.63
8 11 0.26
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCCT
Found at i:86647 original size:15 final size:15
Alignment explanation
Indices: 86593--86648 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
86583 AATTTTCTTA
*
86593 TTTTCCTATTTCCCT
1 TTTTCCTTTTTCCCT
* *
86608 TTTT-TTTCTTTTCC-
1 TTTTCCTT-TTTCCCT
*
86622 TTTTCCCTTTTCCCT
1 TTTTCCTTTTTCCCT
86637 TTTTCCTTTTTC
1 TTTTCCTTTTTC
86649 TTTTCTTTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTCCTTTTTCCCT
Found at i:86654 original size:5 final size:5
Alignment explanation
Indices: 86644--86668 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
86634 CCTTTTTCCT
86644 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
86669 CCTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:86807 original size:3 final size:3
Alignment explanation
Indices: 86796--86833 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
86786 CTCTTTTTTT
86796 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
86834 CGGTGGCCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.