Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010286.1 Corchorus capsularis cultivar CVL-1 contig10307, 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: 52968
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5201 original size:23 final size:25
Alignment explanation
Indices: 5165--5225 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
5155 TATACTATCA
5165 AATTTATATGTAAA-AA-TAAATAT
1 AATTTATATGTAAATAACTAAATAT
* * *
5188 AATTTATCTTTAAATAACTATATAT
1 AATTTATATGTAAATAACTAAATAT
5213 AATTTA-ATG-AAAT
1 AATTTATATGTAAAT
5226 GTATAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 16 0.52
24 3 0.10
25 12 0.39
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (25 bp):
AATTTATATGTAAATAACTAAATAT
Found at i:6619 original size:84 final size:84
Alignment explanation
Indices: 6478--6812 Score: 439
Period size: 87 Copynumber: 4.0 Consensus size: 84
6468 TCCGTCCCTG
** * * *
6478 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGGTGGTGGAAGAGTGGCTTTAGACTTTTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
* *
6543 ACCAGCAGGAGCAGCTTGA
66 AGCAGCAGGAGCAGCTTCA
*
6562 GTCTCAAGGGGAGATGGCTTGGCTACAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCT-
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
6626 --CAGC---AGCAGCTTCA
66 AGCAGCAGGAGCAGCTTCA
* * *
6640 GTCTCAAGGGGAGATGGCTTGACTTCAGATGGTTTCGACGATGGAGGAGTGGCTTTGGACTTCTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
6705 AGCAGCAGTAGCAGCAGCTTCA
66 AGCAGCAG--G-AGCAGCTTCA
* * * * *
6727 TTCTCAAGGGGAGATGGCTTGGCTGCATATTGTTTCGGCGGTGGAGGAGTGGCTTTAGACTTCTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
* *
6792 AGCAACATGAGCAGCTTCA
66 AGCAGCAGGAGCAGCTTCA
6811 GT
1 GT
6813 GATGGCTCCC
Statistics
Matches: 221, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
78 70 0.32
81 8 0.04
84 69 0.31
85 1 0.00
87 73 0.33
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.27
Consensus pattern (84 bp):
GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
AGCAGCAGGAGCAGCTTCA
Found at i:6669 original size:78 final size:78
Alignment explanation
Indices: 6478--6795 Score: 366
Period size: 78 Copynumber: 3.9 Consensus size: 78
6468 TCCGTCCCTG
** * *
6478 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGGTGGTGGAAGAGTGGCTTTAGACTTTTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGAC--TTC
* *
6543 ACCAGCAGGAGCAGCTTGA
64 -TCAGC---AGCAGCTTCA
*
6562 GTCTCAAGGGGAGATGGCTTGGCTACAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
6627 AGCAGCAGCTTCA
66 AGCAGCAGCTTCA
* * *
6640 GTCTCAAGGGGAGATGGCTTGACTTCAGATGGTTTCGACGATGGAGGAGTGGCTTTGGACTTCTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCT-
6705 AGCAGCAGTAGCAGCAGCTTCA
65 -----C---AGCAGCAGCTTCA
* * * * *
6727 TTCTCAAGGGGAGATGGCTTGGCTGCATATTGTTTCGGCGGTGGAGGAGTGGCTTTAGACTTCTC
1 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
6792 AGCA
66 AGCA
6796 ACATGAGCAG
Statistics
Matches: 207, Mismatches: 18, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
78 74 0.36
81 5 0.02
82 3 0.01
84 56 0.27
87 69 0.33
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (78 bp):
GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGACGATGGAGGAGTGGCTTTAGACTTCTC
AGCAGCAGCTTCA
Found at i:6779 original size:165 final size:162
Alignment explanation
Indices: 6478--6795 Score: 465
Period size: 165 Copynumber: 1.9 Consensus size: 162
6468 TCCGTCCCTG
* ** * *
6478 GTCTCAAGGGGAGATGGCTTGGCTGCAGATGGTTTCGGTGGTGGAAGAGTGGCTTTAGACTTTTC
1 GTCTCAAGGGGAGATGGCTTGACTGCAGATGGTTTCGACGATGGAAGAGTGGCTTTAGACTTCTC
*
6543 ACCAGCAGGAGCAGCTTGAGTCTCAAGGGGAGATGGCTTGGCTACAGATGGTTTCGACGATGGAG
66 ACCAGCAGGAGCAGCTTCAGTCTCAAGGGGAGATGGCTTGGCTACAGATGGTTTCGACGATGGAG
6608 GAGTGGCTTTAGACTTCTCAGCAGCAGCTTCA
131 GAGTGGCTTTAGACTTCTCAGCAGCAGCTTCA
* * *
6640 GTCTCAAGGGGAGATGGCTTGACTTCAGATGGTTTCGACGATGGAGGAGTGGCTTTGGACTTCTC
1 GTCTCAAGGGGAGATGGCTTGACTGCAGATGGTTTCGACGATGGAAGAGTGGCTTTAGACTTCTC
* * * * * * *
6705 AGCAGCAGTAGCAGCAGCTTCATTCTCAAGGGGAGATGGCTTGGCTGCATATTGTTTCGGCGGTG
66 ACCAGCAG--G-AGCAGCTTCAGTCTCAAGGGGAGATGGCTTGGCTACAGATGGTTTCGACGATG
6770 GAGGAGTGGCTTTAGACTTCTCAGCA
128 GAGGAGTGGCTTTAGACTTCTCAGCA
6796 ACATGAGCAG
Statistics
Matches: 137, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 64 0.47
164 1 0.01
165 72 0.53
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (162 bp):
GTCTCAAGGGGAGATGGCTTGACTGCAGATGGTTTCGACGATGGAAGAGTGGCTTTAGACTTCTC
ACCAGCAGGAGCAGCTTCAGTCTCAAGGGGAGATGGCTTGGCTACAGATGGTTTCGACGATGGAG
GAGTGGCTTTAGACTTCTCAGCAGCAGCTTCA
Found at i:7326 original size:176 final size:176
Alignment explanation
Indices: 7018--7527 Score: 524
Period size: 176 Copynumber: 2.9 Consensus size: 176
7008 CATGCAAGCC
7018 CTCATGTTTTCCAATTCAATTTGGATCTGAAAGTAAAGATTATTCATCATAAGTCATAACTGGTT
1 CTCATGTTTTCCAATTCAATTTGGATCTGAAAGT-AAGATTATTCA-CATAAGTCATAACTGGTT
* * * ** * *
7083 GAGGAACACATATAAAGGCA-TG--TG-AC-AT-A-AGAAATC-ACTTGTAAATTTTATAACAAG
64 GAAGAACACATACAAAGGTAGTGACTGAACAATCACAG-CTTCTAATTCTAAATTTTATAACAAG
**
7140 TTTTACCTTTGCAAGCTTCTCCAAGATAACATTCTCCACCGCAGGGTCAGCT
128 TTTTACCTTTGCAAGCTTCTCCAAGATGGCATTCTCCACC-C--GGTCAGCT
** *
7192 CTCATGTTTT-TTATCTCAGTTTGGATCTGAAAGT-AGATTATTC-C-TAAGTCATAACTGGTTG
1 CTCATGTTTTCCAAT-TCAATTTGGATCTGAAAGTAAGATTATTCACATAAGTCATAACTGGTTG
7253 AAGAACACATACAAAGGTAGTGACTGAACAATCACAGCTTCTAATTCTAAATTTTATAACAAGTT
65 AAGAACACATACAAAGGTAGTGACTGAACAATCACAGCTTCTAATTCTAAATTTTATAACAAGTT
* *
7318 TTACCTTTGCAAGCTTCTCCAAGATGGCA------GCCCTGTCAGCT
130 TTACCTTTGCAAGCTTCTCCAAGATGGCATTCTCCACCCGGTCAGCT
7359 CTCATGTTTTCCAATTCAATTTGGATCTGAAAGTAAAGATTATTCATCATAAGTCATAACTGGTT
1 CTCATGTTTTCCAATTCAATTTGGATCTGAAAGT-AAGATTATTCA-CATAAGTCATAACTGGTT
* * * * * * ***
7424 G-AGAAACACATACAGAGGTAGTGACAGAAGAAATCACAACTTGTAAATTTTAGAACAACTATAA
64 GAAG-AACACATACAAAGGTAGTGACTGAA-CAATCACAGCTTCT-AATTCTA-AA-TTTTATAA
*
7488 C---CTTTACCTTTGCAAGCTTCTCCAAGATGGCATTCTCCAC
124 CAAGTTTTACCTTTGCAAGCTTCTCCAAGATGGCATTCTCCAC
7528 ATCAGGAGCA
Statistics
Matches: 282, Mismatches: 28, Indels: 47
0.79 0.08 0.13
Matches are distributed among these distances:
167 35 0.12
168 2 0.01
169 43 0.15
170 5 0.02
171 3 0.01
172 51 0.18
173 45 0.16
174 36 0.13
175 5 0.02
176 56 0.20
179 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (176 bp):
CTCATGTTTTCCAATTCAATTTGGATCTGAAAGTAAGATTATTCACATAAGTCATAACTGGTTGA
AGAACACATACAAAGGTAGTGACTGAACAATCACAGCTTCTAATTCTAAATTTTATAACAAGTTT
TACCTTTGCAAGCTTCTCCAAGATGGCATTCTCCACCCGGTCAGCT
Found at i:8044 original size:31 final size:30
Alignment explanation
Indices: 8002--8087 Score: 138
Period size: 29 Copynumber: 2.9 Consensus size: 30
7992 CTGGCTAAAT
*
8002 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAG-AAGC
*
8033 GCTCAAATTGGTCCTAAACCTTTGA-AAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGAAGC
8062 GCTCAATTTGGTCCTAAACCTTTGAG
1 GCTCAATTTGGTCCTAAACCTTTGAG
8088 TGGTCGCTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
29 27 0.53
31 24 0.47
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTGAGAAGC
Found at i:8099 original size:31 final size:30
Alignment explanation
Indices: 8002--8100 Score: 137
Period size: 31 Copynumber: 3.3 Consensus size: 30
7992 CTGGCTAAAT
*
8002 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGAG-GC
* *
8033 GCTCAAATTGGTCCTAAACCTTTGA-AAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGAGGC
*
8062 GCTCAATTTGGTCCTAAACCTTTGAGTGGTC
1 GCTCAATTTGGTCCTAAACCTTTGAGAGG-C
8093 GCTCAATT
1 GCTCAATT
8101 CAGTTCTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
29 26 0.43
30 1 0.02
31 33 0.55
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTGAGAGGC
Found at i:9012 original size:10 final size:10
Alignment explanation
Indices: 8997--9036 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
8987 GTATTCTTTG
8997 ATTATTTTAA
1 ATTATTTTAA
9007 ATTATTTTAA
1 ATTATTTTAA
*
9017 A-TA--GTAA
1 ATTATTTTAA
9024 ATTATTTTAA
1 ATTATTTTAA
9034 ATT
1 ATT
9037 TTTATTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
7 4 0.16
8 2 0.08
9 2 0.08
10 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
ATTATTTTAA
Found at i:14899 original size:31 final size:31
Alignment explanation
Indices: 14862--14931 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
14852 AATAGGACTG
14862 AATTGAGCGAC-CGCTCAAAGGTTTAGGACCA
1 AATTGAGCG-CTCGCTCAAAGGTTTAGGACCA
*
14893 ATTTGAGCGCTCGCTCAAAGGTTTAGGACCA
1 AATTGAGCGCTCGCTCAAAGGTTTAGGACCA
14924 AATTGAGC
1 AATTGAGC
14932 ATTTAGCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (31 bp):
AATTGAGCGCTCGCTCAAAGGTTTAGGACCA
Found at i:16906 original size:1 final size:1
Alignment explanation
Indices: 16900--16943 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
16890 CATCGAATAC
* * *
16900 AAAAAAAAAATAAAAAAAATAAAAATAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16944 TGATATATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (1 bp):
A
Found at i:43520 original size:20 final size:21
Alignment explanation
Indices: 43482--43522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43472 ACGTGATCGG
* *
43482 AAATAATTTAATTTGGTTTGA
1 AAATAAGTTAATGTGGTTTGA
43503 AAATAAGTTAATGT-GTTTGA
1 AAATAAGTTAATGTGGTTTGA
43523 TCTTAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (21 bp):
AAATAAGTTAATGTGGTTTGA
Found at i:44620 original size:2 final size:2
Alignment explanation
Indices: 44613--44643 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44603 AATTAATGTA
44613 AT AT 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 A
44644 CTGGAGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45036 original size:48 final size:48
Alignment explanation
Indices: 44965--45061 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
44955 TTAAATCTAA
*
44965 CTTAAAGTTTATCTCCTCCTTTGCTAATCTTAGATGATATTTCCTCTC
1 CTTAAAGTTTATCTCCTCCTTTGCTAATCTTAGATAATATTTCCTCTC
*
45013 CTTAAAGTTTATCTCCTCCTTTGCTAATCTTAGGTAATATTTCCTCTC
1 CTTAAAGTTTATCTCCTCCTTTGCTAATCTTAGATAATATTTCCTCTC
45061 C
1 C
45062 ACTAGTGGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.45
Consensus pattern (48 bp):
CTTAAAGTTTATCTCCTCCTTTGCTAATCTTAGATAATATTTCCTCTC
Found at i:45536 original size:54 final size:56
Alignment explanation
Indices: 45477--45589 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 56
45467 TGTATGTTGA
45477 TGATTTGATATCC-TT-TTAGTACAATTTTTTCCCTTTTGAATCCGGAGGATGGCT
1 TGATTTGATATCCTTTATTAGTACAATTTTTTCCCTTTTGAATCCGGAGGATGGCT
*
45531 TGATTTGATATCCTTTTAATTAGTACAATTTTTTTCCTTTTGAATCCGGAGGATGGCT
1 TGATTTGATATCC-TTT-ATTAGTACAATTTTTTCCCTTTTGAATCCGGAGGATGGCT
45589 T
1 T
45590 CACTGATGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
54 13 0.24
56 2 0.04
58 39 0.72
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (56 bp):
TGATTTGATATCCTTTATTAGTACAATTTTTTCCCTTTTGAATCCGGAGGATGGCT
Found at i:46099 original size:18 final size:18
Alignment explanation
Indices: 46076--46111 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
46066 GTCTACCTTG
46076 TCCAACTTCGTTAGCTTA
1 TCCAACTTCGTTAGCTTA
46094 TCCAACTTCGTTAGCTTA
1 TCCAACTTCGTTAGCTTA
46112 GTAAAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (18 bp):
TCCAACTTCGTTAGCTTA
Found at i:46956 original size:32 final size:32
Alignment explanation
Indices: 46899--46984 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
46889 GATCTGGTCA
* * * *
46899 AACCCAAACTGAACCCGAACCCGAATAAATCT
1 AACCCAAATTCAACCAGAACCCGAATAAACCT
* * * *
46931 GACCTAAATTCAATCAGAACCCGAATTAACCT
1 AACCCAAATTCAACCAGAACCCGAATAAACCT
*
46963 AACCCAAATTCAACCCGAACCC
1 AACCCAAATTCAACCAGAACCC
46985 AAAAATGATC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.42, C:0.35, G:0.08, T:0.15
Consensus pattern (32 bp):
AACCCAAATTCAACCAGAACCCGAATAAACCT
Found at i:46985 original size:17 final size:16
Alignment explanation
Indices: 46936--47018 Score: 53
Period size: 17 Copynumber: 5.0 Consensus size: 16
46926 AATCTGACCT
*
46936 AAATTCAATCAGAACCC
1 AAATTCAA-CCGAACCC
* *
46953 GAATT-AACCTAACCC
1 AAATTCAACCGAACCC
46968 AAATTCAACCCGAACCC
1 AAATTCAA-CCGAACCC
* * *
46985 AAAAATGATCCGAACCC
1 -AAATTCAACCGAACCC
47002 AAAATT-AATCCGAACCC
1 -AAATTCAA-CCGAACCC
47019 GATGACCTGA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
15 10 0.19
16 5 0.10
17 32 0.62
18 5 0.10
ACGTcount: A:0.45, C:0.33, G:0.07, T:0.16
Consensus pattern (16 bp):
AAATTCAACCGAACCC
Found at i:47639 original size:11 final size:11
Alignment explanation
Indices: 47615--47668 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
47605 TTGACAACGT
47615 AACAAAAACAA
1 AACAAAAACAA
* *
47626 AACGAAAACGA
1 AACAAAAACAA
47637 AACAAAAACAA
1 AACAAAAACAA
47648 AA-AACAAA-AA
1 AACAA-AAACAA
*
47658 AACGAAAACAA
1 AACAAAAACAA
47669 TGCCAAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.78, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:47639 original size:16 final size:15
Alignment explanation
Indices: 47620--47668 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
47610 AACGTAACAA
47620 AAACAAAACGAAAAC
1 AAACAAAACGAAAAC
*
47635 GAAACAAAAACAAAAAAC
1 -AAAC-AAAAC-GAAAAC
47653 AAA-AAAACGAAAAC
1 AAACAAAACGAAAAC
47667 AA
1 AA
47669 TGCCAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 7 0.24
15 5 0.17
16 4 0.14
17 8 0.28
18 5 0.17
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (15 bp):
AAACAAAACGAAAAC
Found at i:48079 original size:19 final size:19
Alignment explanation
Indices: 48055--48094 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
48045 CATAGATTCG
48055 TTGATTTTCTACTTACTAT
1 TTGATTTTCTACTTACTAT
*
48074 TTGATTTTCTACTTATTAT
1 TTGATTTTCTACTTACTAT
48093 TT
1 TT
48095 CAAATCCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (19 bp):
TTGATTTTCTACTTACTAT
Found at i:50514 original size:27 final size:27
Alignment explanation
Indices: 50484--50538 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
50474 ATTAATGACC
50484 AGAGAGTTGACCTTGGTCATCCTAGCA
1 AGAGAGTTGACCTTGGTCATCCTAGCA
50511 AGAGAGTTGACCTTGGTCATCCTAGCA
1 AGAGAGTTGACCTTGGTCATCCTAGCA
50538 A
1 A
50539 TACTTGGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (27 bp):
AGAGAGTTGACCTTGGTCATCCTAGCA
Found at i:51418 original size:20 final size:20
Alignment explanation
Indices: 51393--51430 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
51383 CAAGAATAAA
51393 TAAGGAAATAAGGAAAATCT
1 TAAGGAAATAAGGAAAATCT
51413 TAAGGAAATAAGGAAAAT
1 TAAGGAAATAAGGAAAAT
51431 GATAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (20 bp):
TAAGGAAATAAGGAAAATCT
Done.