Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014698.1 Corchorus capsularis cultivar CVL-1 contig14719, 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: 31094
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Found at i:65 original size:33 final size:33
Alignment explanation
Indices: 4--87 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
1 GGG
* *
4 CCATGTCGCGTGGCCGGTGATGGCCGGGCATCT
1 CCATATCGCGTGGCCGGTGATGGCCGGGCAACT
* *
37 CCATATCGCATGGCCGGTG-TTGCGCGGGCAACT
1 CCATATCGCGTGGCCGGTGATGGC-CGGGCAACT
70 CCA-AGTCGCGTGGCCGGT
1 CCATA-TCGCGTGGCCGGT
88 CACTCGCGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 4 0.09
33 40 0.91
ACGTcount: A:0.12, C:0.31, G:0.37, T:0.20
Consensus pattern (33 bp):
CCATATCGCGTGGCCGGTGATGGCCGGGCAACT
Found at i:5459 original size:11 final size:10
Alignment explanation
Indices: 5422--5450 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5412 TTCTGGTCGA
5422 AATTTTTTTT
1 AATTTTTTTT
5432 AATTTTTTTT
1 AATTTTTTTT
5442 AATTTTTTT
1 AATTTTTTT
5451 GATATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:13436 original size:49 final size:49
Alignment explanation
Indices: 13374--13599 Score: 208
Period size: 49 Copynumber: 4.6 Consensus size: 49
13364 TCAGGAAGGG
* *
13374 TAAACAACACCTTCCGGTGAGGAAGGGCAAGACATGAATAAGACAAAAT
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAAACAGGAATAAGACAAAAT
**** * * *
13423 TAAACAACACCTTCCGACCTGGAAGGGCAAAATAGGAATATGACAAAGT
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAAACAGGAATAAGACAAAAT
* ** * *
13472 TAAACAATACCTTCCAAATG-GGAAAGGACAAAACGGGAATAAGACAAAAT
1 TAAACAACACCTTCC-GGTGAGG-AAGGGCAAAACAGGAATAAGACAAAAT
* * * *
13522 TAAACAACACCTTCCGGTGAGAAAGGGC-AAACTGGTAATTAGAC--AAC
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAAACAGG-AATAAGACAAAAT
* * *
13569 TAAACAACACCTTCTGGTGTGGTAGGGCAAA
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAA
13600 CTGGGAAAAC
Statistics
Matches: 142, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
47 26 0.18
48 8 0.06
49 70 0.49
50 38 0.27
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.16
Consensus pattern (49 bp):
TAAACAACACCTTCCGGTGAGGAAGGGCAAAACAGGAATAAGACAAAAT
Found at i:13623 original size:41 final size:41
Alignment explanation
Indices: 13566--14091 Score: 521
Period size: 41 Copynumber: 13.0 Consensus size: 41
13556 GTAATTAGAC
* * * *
13566 AACTAAACAACACCTTCTGGTGTGGTAGGGCAAACTGGGAA
1 AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
*
13607 AACTAAATAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
1 AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
* * *
13648 AACTAAACAATACCTTCCGAT-GGGAAGTGCAAAC--CGAA
1 AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
* * ** *
13686 ATGAGTAAACAACACCTTCCGTTGGGGAAGGGTGAA-T-AGAA
1 A--ACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
** * *
13727 ATGTAAACAACACCTTCCGACT-GGGAAGCGCAAACTGGGAT
1 AACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAA
* * * **
13768 AAGTAAACAACACCTTCCGGTGAGGAAGGGCAAAC-CAGAA
1 AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
* * *
13808 TGAGTAAACAACACCTTCCG-TCGGGGAAAGGCAAACTGGG--
1 -AACTAAACAACACCTTCCGAT-GGGGAAGGGCAAACTGGGAA
** * *
13848 ATGTAAACAACACCTTCCGACT-GGGAAGGACAAATTGGG-A
1 AACTAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAA
* *
13888 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAAGTGGG-A
1 AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
13928 AACTTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
1 AAC-TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
* * * *
13970 AACTAAACAACACCTTCCGGTGGAGAAGGGTAAAAC--GAAA
1 AACTAAACAACACCTTCCGATGGGGAAGGG-CAAACTGGGAA
14010 AACTAAACAACACCTTCCGATGGGGAAGGGCAAAAC-GGG-A
1 AACTAAACAACACCTTCCGATGGGGAAGGGC-AAACTGGGAA
*
14050 AACTTAACAACACCTTCCGATGGGGAAGGGCAAACT-GGAA
1 AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
14090 AA
1 AA
14092 TGTGGAAACA
Statistics
Matches: 407, Mismatches: 56, Indels: 45
0.80 0.11 0.09
Matches are distributed among these distances:
38 4 0.01
39 64 0.16
40 140 0.34
41 190 0.47
42 9 0.02
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (41 bp):
AACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA
Found at i:13782 original size:161 final size:157
Alignment explanation
Indices: 13558--14087 Score: 550
Period size: 161 Copynumber: 3.3 Consensus size: 157
13548 GCAAACTGGT
* * *
13558 AATT-AGACAACTAAACAACACCTTCTGGTGTGGTAGGGCAAACTGGGAAAACTAAATAACACCT
1 AATTGAGA-AACTAAACAACACCTTCCGGTG-GGAAGGGCAAACTGGG-AAACTAAACAACACCT
*
13622 TCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAATACCTTCCGATGGGAAGTGCAAACCGAAA
63 TCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCG-TGGGAAG-GCAAACCGAAA
* **
13687 TGAGTAAACAACACCTTCCGTTGGGGAAGGGTG
126 T-AGTAAACAACACCTTCCGATGGGGAAGGGCA
* * * *
13720 AA-T-AGAAATGTAAACAACACCTTCCGACTGGGAAGCGCAAACTGGGATAAGTAAACAACACCT
1 AATTGAGAAA-CTAAACAACACCTTCCG-GTGGGAAGGGCAAACTGGGA-AACTAAACAACACCT
* * ** * * * *
13783 TCCGGTGAGGAAGGGCAAAC-CAGAATGAGTAAACAACACCTTCCGTCGGGGAAAGGCAAACTGG
63 TCCGATGGGGAAGGGCAAACTGGGAA-AACTAAACAACACCTTCCGT--GGG-AAGGCAAACCGA
* *
13847 GAT-GTAAACAACACCTTCCGACT-GGGAAGGACA
124 AATAGTAAACAACACCTTCCGA-TGGGGAAGGGCA
* *
13880 AATTGGGAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAAGTGGGAAACTTAAACAACACCTT
1 AATTGAGAAACTAAACAACACCTTCCGGT-GGGAAGGGCAAACTGGGAAAC-TAAACAACACCTT
* *
13945 CCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGGTGGAGAAGGGTAAAACGAAA
64 CCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCC-GTGG-GAA-GGCAAACCGAAA
* *
14010 AACTAAACAACACCTTCCGATGGGGAAGGGCA
126 TAGTAAACAACACCTTCCGATGGGGAAGGGCA
** * * *
14042 AAACGGGAAACTTAACAACACCTTCCGATGGGGAAGGGCAAACTGG
1 AATTGAGAAACTAAACAACACCTTCCGGT-GGGAAGGGCAAACTGG
14088 AAAATGTGGA
Statistics
Matches: 304, Mismatches: 46, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
160 40 0.13
161 169 0.56
162 92 0.30
163 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (157 bp):
AATTGAGAAACTAAACAACACCTTCCGGTGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCC
GATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGTGGGAAGGCAAACCGAAATAGTA
AACAACACCTTCCGATGGGGAAGGGCA
Found at i:13784 original size:120 final size:118
Alignment explanation
Indices: 13610--14086 Score: 427
Period size: 121 Copynumber: 4.0 Consensus size: 118
13600 CTGGGAAAAC
* * *
13610 TAAATAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAACTAAACAATACCTTCCGATGGGAA
1 TAAACAACACCTTCCGACT-GGGAA-GGCAAACTGGG-AAACTAAACAACACCTTCCGGTGGGAA
* * * **
13674 GTGCAAACC-GAAATGAGTAAACAACACCTTCCGTTGGGGAAGGGTGAA-TAGAAATG
63 GGGCAAACCAG-AATGAGTAAACAACACCTTCCGTCGGGGAAAGGCAAACT-GAAATG
*
13730 TAAACAACACCTTCCGACTGGGAAGCGCAAACTGGGATAAGTAAACAACACCTTCCGGTGAGGAA
1 TAAACAACACCTTCCGACTGGGAAG-GCAAACTGGGA-AACTAAACAACACCTTCCGGTG-GGAA
**
13795 GGGCAAACCAGAATGAGTAAACAACACCTTCCGTCGGGGAAAGGCAAACTGGGATG
63 GGGCAAACCAGAATGAGTAAACAACACCTTCCGTCGGGGAAAGGCAAACTGAAATG
*
13851 TAAACAACACCTTCCGACTGGGAAGGACAAATTGGGAAACTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGACTGGGAAGG-CAAACTGGGAAACTAAACAACACCTTCCGGT-GGGAAG
*** * * **
13916 GGCAAAGTGGGAA--ACTTAAACAACACCTTCCGAT-GGGGAAGGGCAAACTGGGAAAAC
64 GGCAAA-CCAGAATGA-GTAAACAACACCTTCCG-TCGGGGAAAGGCAAACT--GAAATG
* * ** *
13973 TAAACAACACCTTCCG-GTGGAGAAGGGTAAAAC-GAAAAACTAAACAACACCTTCCGATGGGGA
1 TAAACAACACCTTCCGACTGG-GAA-GG-CAAACTGGGAAACTAAACAACACCTTCCGGT-GGGA
** * * *
14036 AGGGCAAAACGGGAA--ACTTAACAACACCTTCCGAT-GGGGAAGGGCAAACTG
62 AGGGC-AAACCAGAATGAGTAAACAACACCTTCCG-TCGGGGAAAGGCAAACTG
14087 GAAAATGTGG
Statistics
Matches: 309, Mismatches: 32, Indels: 33
0.83 0.09 0.09
Matches are distributed among these distances:
119 4 0.01
120 112 0.36
121 124 0.40
122 61 0.20
123 8 0.03
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (118 bp):
TAAACAACACCTTCCGACTGGGAAGGCAAACTGGGAAACTAAACAACACCTTCCGGTGGGAAGGG
CAAACCAGAATGAGTAAACAACACCTTCCGTCGGGGAAAGGCAAACTGAAATG
Found at i:13938 original size:202 final size:196
Alignment explanation
Indices: 13566--14084 Score: 582
Period size: 202 Copynumber: 2.6 Consensus size: 196
13556 GTAATTAGAC
* * * *
13566 AACTAAACAACACCTTCTGGTGTGGTAGGGCAAACTGGGAAAACTAAATAACACCTTCCGATGGG
1 AACTAAACAACACCTTCCGGTG-GGAAGGGCAAAC--CGAAAACTAAACAACACCTTCCGATGGG
* *
13631 GAAGGGCAAACTGGGAAAACTAAACAATACCTTCCGATGGGAAGTGCAAACCGAAATGAGTAAAC
63 GAAGGGCAAACTGGG-AAACTAAACAACACCTTCCGATGGGAAG-GCAAACCGAAA-GACTAAAC
* **
13696 AACACCTTCCGTTGGGGAAGGGTGAATAGAAATGTAAACAACACCTTCCGACT-GGGAAGCGCAA
125 AACACCTTCCGGTGGGGAAGGGCAAATAGAAATGTAAACAACACCTTCCGA-TGGGGAAGCGCAA
*
13760 ACTGGGAT
189 ACTGGGAA
* * *
13768 AAGTAAACAACACCTTCCGGTGAGGAAGGGCAAACCAGAATGAGTAAACAACACCTTCCG-TCGG
1 AACTAAACAACACCTTCCGGTG-GGAAGGGCAAACC-GAA-AACTAAACAACACCTTCCGAT-GG
* ** ** *
13832 GGAAAGGCAAACTGGG-ATGTAAACAACACCTTCCGACTGGGAAGGACAAATTGGGAA-ACTAAA
62 GGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGA-TGGGAAGG-CAAA-CCGAAAGACTAAA
* *
13895 CAACACCTTCCGGTGGGGAAGGGCAAAGTGGGAAACT-TAAACAACACCTTCCGATGGGGAAGGG
124 CAACACCTTCCGGTGGGGAAGGGCAAA-T-AGAAA-TGTAAACAACACCTTCCGATGGGGAAGCG
13959 CAAACTGGGAA
186 CAAACTGGGAA
* *
13970 AACTAAACAACACCTTCCGGTGGAGAAGGGTAAAACGAAAAACTAAACAACACCTTCCGATGGGG
1 AACTAAACAACACCTTCCGGTGG-GAAGGGCAAACCG-AAAACTAAACAACACCTTCCGATGGGG
*
14035 AAGGGCAAAAC-GGGAAACTTAACAACACCTTCCGATGGGGAAGGGCAAAC
64 AAGGGC-AAACTGGGAAACTAAACAACACCTTCCGAT-GGGAA-GGCAAAC
14085 TGGAAAATGT
Statistics
Matches: 268, Mismatches: 32, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
200 47 0.18
201 49 0.18
202 169 0.63
203 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (196 bp):
AACTAAACAACACCTTCCGGTGGGAAGGGCAAACCGAAAACTAAACAACACCTTCCGATGGGGAA
GGGCAAACTGGGAAACTAAACAACACCTTCCGATGGGAAGGCAAACCGAAAGACTAAACAACACC
TTCCGGTGGGGAAGGGCAAATAGAAATGTAAACAACACCTTCCGATGGGGAAGCGCAAACTGGGA
A
Found at i:14862 original size:50 final size:51
Alignment explanation
Indices: 14770--15100 Score: 248
Period size: 50 Copynumber: 6.5 Consensus size: 51
14760 TTCATCATTT
* * * * *
14770 TTTTATTTACAAATTATTTTAAAAAATTCC-TCATTTAATTCAAAGATTTCAT
1 TTTTATTTACAAATTA--ATCAAAAGTTCCATCATTTAGTTCAAAGATTTCAC
* * *
14822 TTTTA-TTACAAATTAATCAGAAGTTCCATCATTTGGTTCAAAGATCTC-C
1 TTTTATTTACAAATTAATCAAAAGTTCCATCATTTAGTTCAAAGATTTCAC
** * *
14871 TTTTATTTACAAATTAATCAAAAGTTTAATTA-CTAGCTT-AAAGATTTCAC
1 TTTTATTTACAAATTAATCAAAAGTTCCATCATTTAG-TTCAAAGATTTCAC
* * * * * * *
14921 CTTTA-TCACCAAATTAATCCAAAGTTTCATCTTTTAGTTCAAAGGTTTCAT
1 TTTTATTTA-CAAATTAATCAAAAGTTCCATCATTTAGTTCAAAGATTTCAC
* * * *
14972 TTTTATTTACAAATCAATCAAACATTTCCAAT-TTTTAGTTCAAAGATCTCA-
1 TTTTATTTACAAATTAATCAAA-AGTTCC-ATCATTTAGTTCAAAGATTTCAC
* * * * * * *
15023 TTTTATTTACAAGTTAATCAAAACTCCCCTCATTTAGCTCAAAAAATCTCA-
1 TTTTATTTACAAATTAATCAAAAGTTCCATCATTTAGTTC-AAAGATTTCAC
*
15074 TTCTTATTTGCAAATTAATCAAAAGTT
1 TT-TTATTTACAAATTAATCAAAAGTT
15101 TAATTTTTAG
Statistics
Matches: 222, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
49 26 0.12
50 78 0.35
51 68 0.31
52 48 0.22
53 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (51 bp):
TTTTATTTACAAATTAATCAAAAGTTCCATCATTTAGTTCAAAGATTTCAC
Found at i:14961 original size:100 final size:100
Alignment explanation
Indices: 14811--15105 Score: 251
Period size: 103 Copynumber: 2.9 Consensus size: 100
14801 CATTTAATTC
** * *
14811 AAAGATTTCATTTTTATTACAAATTAATCAGAAGTTCCATCATTTGGTTCAAAGATCTC-CTTTT
1 AAAGATTTCACCTTTATCACAAATTAATCAGAAGTTCCATCATTTAGTTCAAAGATCTCACTTTT
*
14875 ATTTACAAATTAATCAAAAGTTTAATTACTAGCTT
66 ATTTACAAATCAATCAAAAGTTTAATTACTAGCTT
* * * * *
14910 AAAGATTTCACCTTTATCACCAAATTAATCCA-AAGTTTCATCTTTTAGTTCAAAGGTTTCATTT
1 AAAGATTTCACCTTTATCA-CAAATTAAT-CAGAAGTTCCATCATTTAGTTCAAAGATCTCACTT
**
14974 TTATTTACAAATCAATCAAACA-TTTCCAATTTTTAG-TT
64 TTATTTACAAATCAATCAAA-AGTTT--AATTACTAGCTT
* * * * * * * * * *
15012 CAAAGATCTCA-TTTTATTTACAAGTTAATCAAAACTCCCCTCATTTAGCTCAAAAAATCTCA-T
1 -AAAGATTTCACCTTTA-TCACAAATTAATCAGAAGTTCCATCATTTAGTTC-AAAGATCTCACT
* *
15075 TCTTATTTGCAAATTAATCAAAAGTTTAATT
63 T-TTATTTACAAATCAATCAAAAGTTTAATT
15106 TTTAGTCTAA
Statistics
Matches: 157, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
99 16 0.10
100 32 0.20
101 32 0.20
102 31 0.20
103 46 0.29
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.40
Consensus pattern (100 bp):
AAAGATTTCACCTTTATCACAAATTAATCAGAAGTTCCATCATTTAGTTCAAAGATCTCACTTTT
ATTTACAAATCAATCAAAAGTTTAATTACTAGCTT
Found at i:15027 original size:51 final size:49
Alignment explanation
Indices: 14568--15160 Score: 234
Period size: 50 Copynumber: 11.7 Consensus size: 49
14558 CACTTAAAAG
* * *
14568 TTTTATTT-CAAATTTATCAAAA-GTCAATCTTTTAGCTT-TAA-A-TTCA
1 TTTTATTTACAAATTAATCAAAATTTC-ATCTTTTAG-TTCAAAGATTTCA
* * *
14614 CTTTTA-TTACAAATTGATCAAAAGTTCAACCTTTTAGGTT-ACAA-ATTTCA
1 -TTTTATTTACAAATTAATCAAAATTTC-ATCTTTTA-GTTCA-AAGATTTCA
* * * * * * * *
14664 TTTTTAATCACCAATTATTCAAGAA-TTCATATTTTAACTTAAAAG-TTACA
1 -TTTTATTTACAAATTAATCAA-AATTTCATCTTTT-AGTTCAAAGATTTCA
* * *
14714 TCTTTA-TCACAAATTAATCAAAAATTTCTTCTCTTAGCTT-AAAGATTTCATCA
1 T-TTTATTTACAAATTAATC-AAAATTTCATCTTTTAG-TTCAAAGA-TT--TCA
* * * * * *
14767 TTTTTTTATTTACAAATTATTTTAAAAAATTCCTCATTTAATTCAAAGATTTCA
1 ---TTTTATTTACAAATTA--ATCAAAATTTCATCTTTTAGTTCAAAGATTTCA
* * * * * *
14821 TTTT-TATTACAAATTAATCAGAAGTTCCATCATTTGGTTCAAAGATCTCC
1 TTTTAT-TTACAAATTAATCA-AAATTTCATCTTTTAGTTCAAAGATTTCA
* **
14871 TTTTATTTACAAATTAATCAAAAGTTTAAT-TACTAGCTT-AAAGATTTCA
1 TTTTATTTACAAATTAATCAAAA-TTTCATCTTTTAG-TTCAAAGATTTCA
* * * *
14920 CCTTTA-TCACCAAATTAATCCAAAGTTTCATCTTTTAGTTCAAAGGTTTCA
1 -TTTTATTTA-CAAATTAAT-CAAAATTTCATCTTTTAGTTCAAAGATTTCA
* *
14971 TTTTTATTTACAAATCAATCAAACATTTCCAAT-TTTTAGTTCAAAGATCTCA
1 -TTTTATTTACAAATTAATCAAA-ATTT-C-ATCTTTTAGTTCAAAGATTTCA
* ** * * * * *
15023 TTTTATTTACAAGTTAATCAAAACTCCCCTCATTTAGCTCAAAAAATCTCA
1 TTTTATTTACAAATTAATCAAAA-TTTCATCTTTTAGTTC-AAAGATTTCA
* * ** *
15074 TTCTTATTTGCAAATTAATCAAAAGTTTAAT-TTTTAG-TCTAAAGACATAA
1 TT-TTATTTACAAATTAATCAAAA-TTTCATCTTTTAGTTC-AAAGATTTCA
* *
15124 TTTTCATTTACAAATTTATCAAAATTTTAATCTTTTA
1 TTTT-ATTTACAAATTAATCAAAA-TTTCATCTTTTA
15161 CTTAAATTTA
Statistics
Matches: 416, Mismatches: 85, Indels: 86
0.71 0.14 0.15
Matches are distributed among these distances:
46 2 0.00
47 18 0.04
48 12 0.03
49 42 0.10
50 149 0.36
51 107 0.26
52 43 0.10
53 4 0.01
54 3 0.01
55 4 0.01
56 14 0.03
57 17 0.04
58 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (49 bp):
TTTTATTTACAAATTAATCAAAATTTCATCTTTTAGTTCAAAGATTTCA
Found at i:16798 original size:12 final size:12
Alignment explanation
Indices: 16768--16851 Score: 54
Period size: 12 Copynumber: 7.5 Consensus size: 12
16758 GACCATGACC
* *
16768 GGCCAACGCATG
1 GGCCATCGCACG
*
16780 GGACATCGCACG
1 GGCCATCGCACG
*
16792 GGCCATCGCACA
1 GGCCATCGCACG
*
16804 AGCCATC-CA--
1 GGCCATCGCACG
* *
16813 -GCCA-C-AACC
1 GGCCATCGCACG
16822 GGCCATCGCACG
1 GGCCATCGCACG
*
16834 GGCCATCGCGCG
1 GGCCATCGCACG
16846 GGCCAT
1 GGCCAT
16852 TAGCTATTCC
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
7 2 0.04
8 4 0.07
10 4 0.07
11 3 0.05
12 44 0.77
ACGTcount: A:0.23, C:0.40, G:0.29, T:0.08
Consensus pattern (12 bp):
GGCCATCGCACG
Done.