Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008022.1 Corchorus capsularis cultivar CVL-1 contig08043, 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: 79080
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8334 original size:16 final size:16
Alignment explanation
Indices: 8313--8429 Score: 164
Period size: 16 Copynumber: 7.4 Consensus size: 16
8303 TTATCTGGAT
*
8313 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
*
8329 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
8345 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTC
8361 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
8377 TCAGGTCATTCGGGTT
1 TCGGGTCATTCGGGTC
8393 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
*
8409 TCGGGTC-TACGGGTC
1 TCGGGTCATTCGGGTC
8424 TCGGGT
1 TCGGGT
8430 TGGGCGGTTC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
15 13 0.14
16 78 0.86
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:8897 original size:21 final size:21
Alignment explanation
Indices: 8872--8919 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
8862 TAGTCAATTT
8872 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
8893 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
8914 ATAATA
1 ATAATA
8920 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:9057 original size:9 final size:8
Alignment explanation
Indices: 9042--9138 Score: 62
Period size: 9 Copynumber: 12.0 Consensus size: 8
9032 TATTCGGGTT
9042 TCGGGTCA
1 TCGGGTCA
9050 TACGGGTC-
1 T-CGGGTCA
9058 TCGGGTCA
1 TCGGGTCA
*
9066 TTCGGGT-T
1 -TCGGGTCA
*
9074 TCGGTTCA
1 TCGGGTCA
*
9082 TCTGGGTTA
1 TC-GGGTCA
9091 -CGGGTCA
1 TCGGGTCA
9098 TTCGGGTC-
1 -TCGGGTCA
9106 TCGGGTCA
1 TCGGGTCA
9114 TCTGGGT--
1 TC-GGGTCA
9121 TGCGGGTCA
1 T-CGGGTCA
9130 TTCGGGTCA
1 -TCGGGTCA
9139 CAGGTTCGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 25
0.69 0.06 0.25
Matches are distributed among these distances:
7 28 0.40
8 8 0.11
9 33 0.47
10 1 0.01
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.32
Consensus pattern (8 bp):
TCGGGTCA
Found at i:9061 original size:16 final size:16
Alignment explanation
Indices: 9023--9137 Score: 112
Period size: 16 Copynumber: 7.2 Consensus size: 16
9013 TCGGGTTAAT
* *
9023 GTCTCGAGTTATTCGG
1 GTCTCGGGTCATTCGG
* *
9039 GTTTCGGGTCATACGG
1 GTCTCGGGTCATTCGG
9055 GTCTCGGGTCATTCGG
1 GTCTCGGGTCATTCGG
* *
9071 GTTTCGGTTCA-TCTGG
1 GTCTCGGGTCATTC-GG
9087 GT-TACGGGTCATTCGG
1 GTCT-CGGGTCATTCGG
9103 GTCTCGGGTCA-TCTGG
1 GTCTCGGGTCATTC-GG
9119 GT-TGCGGGTCATTCGG
1 GTCT-CGGGTCATTCGG
9135 GTC
1 GTC
9138 ACAGGTTCGT
Statistics
Matches: 82, Mismatches: 9, Indels: 15
0.77 0.08 0.14
Matches are distributed among these distances:
15 6 0.07
16 71 0.87
17 5 0.06
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.34
Consensus pattern (16 bp):
GTCTCGGGTCATTCGG
Found at i:9069 original size:32 final size:32
Alignment explanation
Indices: 9033--9136 Score: 149
Period size: 32 Copynumber: 3.2 Consensus size: 32
9023 GTCTCGAGTT
9033 ATTCGGGTTTCGGGTCATAC-GGGTCT-CGGGTC
1 ATTCGGGTTTCGGGTCAT-CTGGGT-TACGGGTC
*
9065 ATTCGGGTTTCGGTTCATCTGGGTTACGGGTC
1 ATTCGGGTTTCGGGTCATCTGGGTTACGGGTC
* *
9097 ATTCGGGTCTCGGGTCATCTGGGTTGCGGGTC
1 ATTCGGGTTTCGGGTCATCTGGGTTACGGGTC
9129 ATTCGGGT
1 ATTCGGGT
9137 CACAGGTTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
31 2 0.03
32 64 0.97
ACGTcount: A:0.09, C:0.20, G:0.38, T:0.34
Consensus pattern (32 bp):
ATTCGGGTTTCGGGTCATCTGGGTTACGGGTC
Found at i:9121 original size:48 final size:48
Alignment explanation
Indices: 9037--9130 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
9027 CGAGTTATTC
* * *
9037 GGGTTTCGGGTCATACGGGTCTCGGGTCATTCGGGTTTCGGTTCATCT
1 GGGTTACGGGTCATACGGGTCTCGGGTCATTCGGGTTGCGGGTCATCT
*
9085 GGGTTACGGGTCATTCGGGTCTCGGGTCA-TCTGGGTTGCGGGTCAT
1 GGGTTACGGGTCATACGGGTCTCGGGTCATTC-GGGTTGCGGGTCAT
9131 TCGGGTCACA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.09, C:0.20, G:0.38, T:0.33
Consensus pattern (48 bp):
GGGTTACGGGTCATACGGGTCTCGGGTCATTCGGGTTGCGGGTCATCT
Found at i:9151 original size:48 final size:48
Alignment explanation
Indices: 9043--9160 Score: 118
Period size: 48 Copynumber: 2.5 Consensus size: 48
9033 ATTCGGGTTT
* * *
9043 CGGGTCA-TACGGGTCTCGGGTCATTCGGGTTTCGGTTCATCTGGGTTA
1 CGGGTCAGT-CGGGTCTCGGGTCATTCGGGTTGCGGGTCATCTGGGTCA
*
9091 CGGGTCATTCGGGTCTCGGGTCA-TCTGGGTTGCGGGTCAT-TCGGGTCA
1 CGGGTCAGTCGGGTCTCGGGTCATTC-GGGTTGCGGGTCATCT-GGGTCA
* *
9139 CAGGTTC-GTCGGGTCTTGGGTC
1 C-GGGTCAGTCGGGTCTCGGGTC
9161 GGGCGAGTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 3 0.05
48 52 0.87
49 5 0.08
ACGTcount: A:0.08, C:0.22, G:0.38, T:0.31
Consensus pattern (48 bp):
CGGGTCAGTCGGGTCTCGGGTCATTCGGGTTGCGGGTCATCTGGGTCA
Found at i:9626 original size:22 final size:22
Alignment explanation
Indices: 9589--9653 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
9579 TACTTTATTA
*
9589 GTTATAATAAACTAATAATCTAC
1 GTTATTAT-AACTAATAATCTAC
* *
9612 GTTATTATAACTAAT-ATATAT
1 GTTATTATAACTAATAATCTAC
*
9633 GATAATTA-AACTAATAATCTA
1 G-TTATTATAACTAATAATCTA
9654 ACTTTAATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.34
22 16 0.46
23 7 0.20
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (22 bp):
GTTATTATAACTAATAATCTAC
Found at i:10034 original size:54 final size:54
Alignment explanation
Indices: 9965--10084 Score: 197
Period size: 54 Copynumber: 2.2 Consensus size: 54
9955 CAGTAAAGAG
*
9965 CAAA-AATTAAACATTCTCATTTAGTTTTTTGATTAATATTAAATGAAAAAATT
1 CAAATAATTAAACATTCTCATTTACTTTTTTGATTAATATTAAATGAAAAAATT
* *
10018 CAAATAATTAATCATTCTCATTTACTTTTTTGATTAATATTAAATGAAAAAGTT
1 CAAATAATTAAACATTCTCATTTACTTTTTTGATTAATATTAAATGAAAAAATT
*
10072 CAAATTATTAAAC
1 CAAATAATTAAAC
10085 TTTTACCAGC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 4 0.07
54 57 0.93
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (54 bp):
CAAATAATTAAACATTCTCATTTACTTTTTTGATTAATATTAAATGAAAAAATT
Found at i:12847 original size:15 final size:15
Alignment explanation
Indices: 12827--12861 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
12817 GCGAAGAGTT
12827 AATGGTGCAGGAATC
1 AATGGTGCAGGAATC
12842 AATGGTGCAGGAATC
1 AATGGTGCAGGAATC
12857 AATGG
1 AATGG
12862 GTCAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.20
Consensus pattern (15 bp):
AATGGTGCAGGAATC
Found at i:14593 original size:13 final size:11
Alignment explanation
Indices: 14570--14605 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
14560 TAATACATGT
14570 TATGTTATATA
1 TATGTTATATA
14581 TATGTTATATA
1 TATGTTATATA
14592 TATGTTATATA
1 TATGTTATATA
14603 TAT
1 TAT
14606 CTATACCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATGTTATATA
Found at i:15642 original size:15 final size:15
Alignment explanation
Indices: 15622--15653 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
15612 CCGAACTCGA
15622 GAACCCGCCCAACCC
1 GAACCCGCCCAACCC
15637 GAACCCGCCCAACCC
1 GAACCCGCCCAACCC
15652 GA
1 GA
15654 TTTGACTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.56, G:0.16, T:0.00
Consensus pattern (15 bp):
GAACCCGCCCAACCC
Found at i:15717 original size:16 final size:16
Alignment explanation
Indices: 15692--15818 Score: 127
Period size: 16 Copynumber: 7.9 Consensus size: 16
15682 AACCCGCCCG
*
15692 ACCCGAATGACCCGCA
1 ACCCGAATGACCCGAA
*
15708 ACCC-AGATGACCCGAG
1 ACCCGA-ATGACCCGAA
* * *
15724 ATCCGAATGACTCGTA
1 ACCCGAATGACCCGAA
15740 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
15756 ACCCGAATGACCC-ATA
1 ACCCGAATGACCCGA-A
15772 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
*
15788 ACCCGTATGACCCGAA
1 ACCCGAATGACCCGAA
*
15804 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
15819 GAAGTTAACC
Statistics
Matches: 91, Mismatches: 12, Indels: 16
0.76 0.10 0.13
Matches are distributed among these distances:
15 4 0.04
16 84 0.92
17 3 0.03
ACGTcount: A:0.35, C:0.37, G:0.18, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:15730 original size:32 final size:32
Alignment explanation
Indices: 15692--15807 Score: 169
Period size: 32 Copynumber: 3.6 Consensus size: 32
15682 AACCCGCCCG
* *
15692 ACCCGAATGACCCGCAACCCAGATGACCCGAG
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
* *
15724 ATCCGAATGACTCGTAACCCAGATGACCCGAA
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
*
15756 ACCCGAATGACCCATAACCCAGATGACCCGAA
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
* *
15788 ACCCGTATGACCCGAAACCC
1 ACCCGAATGACCCGTAACCC
15808 GAATAACCCG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.34, C:0.38, G:0.18, T:0.10
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCCAGATGACCCGAA
Found at i:17220 original size:42 final size:42
Alignment explanation
Indices: 17150--17231 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
17140 TGTTGACACA
* *
17150 TACCCCACCGGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACCGGATAATCAATTATATATTTAATATTCAAAACC
* *
17192 TACCTCACCTGATAATCAATTATATATTTAATATTCAAAA
1 TACCCCACCGGATAATCAATTATATATTTAATATTCAAAA
17232 TTAATATCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (42 bp):
TACCCCACCGGATAATCAATTATATATTTAATATTCAAAACC
Found at i:17490 original size:16 final size:16
Alignment explanation
Indices: 17471--17590 Score: 161
Period size: 16 Copynumber: 7.6 Consensus size: 16
17461 AGAATCGGTA
17471 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
17487 GACCCGAGACCCAAAT
1 GACCCGAAACCCGAAT
* * *
17503 AATCCGAAACCCGTAT
1 GACCCGAAACCCGAAT
*
17519 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
17535 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
17551 AACCCG-AACCCAAAT
1 GACCCGAAACCCGAAT
17566 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
17582 GACCCGAAA
1 GACCCGAAA
17591 AAAAACTGAC
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
15 13 0.15
16 74 0.85
ACGTcount: A:0.38, C:0.37, G:0.17, T:0.07
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:18331 original size:2 final size:2
Alignment explanation
Indices: 18320--18356 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18310 CTACAGTTCC
18320 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18357 CCATCATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19758 original size:2 final size:2
Alignment explanation
Indices: 19751--19784 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19741 CAAATTTTAT
*
19751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19785 GTTCTGTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23290 original size:44 final size:44
Alignment explanation
Indices: 23235--23355 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 44
23225 AGAGTTTGAA
* *
23235 TTGATTCAAGGGTCTTGGTAACTTGGTCTTGAATTGTTGATAAT
1 TTGATTCAAGGGTCTTGGTGACTTGGTCTTGAATTGATGATAAT
* *
23279 TTGACTCAAGGGT-TCTGGCGACTTGGTCTTGAATTGATGATAAT
1 TTGATTCAAGGGTCT-TGGTGACTTGGTCTTGAATTGATGATAAT
* *
23323 TTGATTCAAGTGTCTTGGTGACTTGATCTTGAA
1 TTGATTCAAGGGTCTTGGTGACTTGGTCTTGAA
23356 AGAACAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.01
44 65 0.97
45 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.40
Consensus pattern (44 bp):
TTGATTCAAGGGTCTTGGTGACTTGGTCTTGAATTGATGATAAT
Found at i:34303 original size:11 final size:11
Alignment explanation
Indices: 34281--34317 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
34271 ACTTGAATGT
34281 TTGAAG-TCAA
1 TTGAAGATCAA
34291 TTGAAGATCAA
1 TTGAAGATCAA
*
34302 TTGGAGATC-A
1 TTGAAGATCAA
34312 TTGAAG
1 TTGAAG
34318 TCGATAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 12 0.50
11 12 0.50
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (11 bp):
TTGAAGATCAA
Found at i:37146 original size:13 final size:13
Alignment explanation
Indices: 37128--37153 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37118 ATGTTGGTGG
37128 GTTTTCTTTAATT
1 GTTTTCTTTAATT
37141 GTTTTCTTTAATT
1 GTTTTCTTTAATT
37154 TTCTTGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
GTTTTCTTTAATT
Found at i:42938 original size:24 final size:24
Alignment explanation
Indices: 42911--42962 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42901 CGCTGTCAGC
* * *
42911 ATAACGGCGTCTAAACGCCGTCAT
1 ATAAAGGCATCTAAACACCGTCAT
* *
42935 ATAAAGGCATTTAGACACCGTCAT
1 ATAAAGGCATCTAAACACCGTCAT
42959 ATAA
1 ATAA
42963 TTCTTCCGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (24 bp):
ATAAAGGCATCTAAACACCGTCAT
Found at i:43183 original size:24 final size:24
Alignment explanation
Indices: 43156--43241 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
43146 ACAATATTGT
*
43156 GGCATCCAGACGCCCCTATTTGGC
1 GGCATCCAGACGCCACTATTTGGC
* * * *
43180 GGCATCTAGATGGCACTATTGGGC
1 GGCATCCAGACGCCACTATTTGGC
* *
43204 GGCGTCCAGACGCCACTAATTGGC
1 GGCATCCAGACGCCACTATTTGGC
* *
43228 GGCGTCTAGACGCC
1 GGCATCCAGACGCC
43242 GCTACATGCA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (24 bp):
GGCATCCAGACGCCACTATTTGGC
Found at i:43325 original size:32 final size:31
Alignment explanation
Indices: 43289--43357 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
43279 AATCAGTTAA
*
43289 ATATAGCGGCGTTTTGTTCTTTAGACGCCGCT
1 ATATAG-GGCGCTTTGTTCTTTAGACGCCGCT
*
43321 ATATAAGGGCGCTTTGTTTTTTAGACGCCGCT
1 ATAT-AGGGCGCTTTGTTCTTTAGACGCCGCT
43353 ATATA
1 ATATA
43358 AGGGTATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 1 0.03
32 31 0.91
33 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
ATATAGGGCGCTTTGTTCTTTAGACGCCGCT
Found at i:43358 original size:32 final size:32
Alignment explanation
Indices: 43296--43361 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
43286 TAAATATAGC
*
43296 GGCGTTTTGTTCTTTAGACGCCGCTATATAAG
1 GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
*
43328 GGCGCTTTGTTTTTTAGACGCCGCTATATAAG
1 GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
43360 GG
1 GG
43362 TATACCCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (32 bp):
GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
Found at i:45847 original size:24 final size:24
Alignment explanation
Indices: 45815--45869 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
45805 ACATCCTCTC
45815 CATTTGCAGCCTC-AATGGGTTCGT
1 CATTTGCAGCCTCAAATGGG-TCGT
45839 CATTTGCAGCCTCAAATGGGTCGT
1 CATTTGCAGCCTCAAATGGGTCGT
45863 CATTTGC
1 CATTTGC
45870 TACTAAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (24 bp):
CATTTGCAGCCTCAAATGGGTCGT
Found at i:47090 original size:216 final size:215
Alignment explanation
Indices: 46717--47149 Score: 821
Period size: 216 Copynumber: 2.0 Consensus size: 215
46707 TAGCAGAAAA
*
46717 TTACTTATTCAGATAAACAGAAACTTAGATGCCGTGCAATACAGTCCCCATGTTGACTTAGCTGC
1 TTACTTATTCAGATAAACAGAAACTTAGATGCCATGCAATACAGTCCCCATGTTGACTTAGCTGC
46782 ATGTCTCCATAGACATGGGAGAAACACATTAGCAAAACCTTACCATGTCATGAACACAAAACCTC
66 ATGTCTCCATAGACATGGGAGAAACACATTAGCAAAACCTTACCATGTCATGAACACAAAACCTC
46847 AAATTTAGTAACCGTAACACAAAATCATAAATCCATTCAGTAAACTTAAGTTTAAGATACCACAT
131 AAATTTAGTAACCGTAACACAAAATCATAAATCCATTCAGTAAACTTAAGTTTAAGATACCACAT
*
46912 AAATACATCTGTGAACAAGT
196 AAATACATCTATGAACAAGT
*
46932 TTACTTATTCAGATAAACAGAAACTTAGATGCCATGCAATACAGTCCCCATGTTTTACTTAGCTG
1 TTACTTATTCAGATAAACAGAAACTTAGATGCCATGCAATACAGTCCCCATG-TTGACTTAGCTG
46997 CATGTCTCCATAGACATGGGAGAAACACATTAGCAAAACCTTACCATGTCATGAACACAAAACCT
65 CATGTCTCCATAGACATGGGAGAAACACATTAGCAAAACCTTACCATGTCATGAACACAAAACCT
*
47062 CAAATTTAGTAATCGTAACACAAAATCATAAATCCATTCAGTAAACTTAAGTTTAAGATACCACA
130 CAAATTTAGTAACCGTAACACAAAATCATAAATCCATTCAGTAAACTTAAGTTTAAGATACCACA
47127 TAAATACATCTATGAACAAGT
195 TAAATACATCTATGAACAAGT
47148 TT
1 TT
47150 CTTGATTAGA
Statistics
Matches: 213, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
215 51 0.24
216 162 0.76
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (215 bp):
TTACTTATTCAGATAAACAGAAACTTAGATGCCATGCAATACAGTCCCCATGTTGACTTAGCTGC
ATGTCTCCATAGACATGGGAGAAACACATTAGCAAAACCTTACCATGTCATGAACACAAAACCTC
AAATTTAGTAACCGTAACACAAAATCATAAATCCATTCAGTAAACTTAAGTTTAAGATACCACAT
AAATACATCTATGAACAAGT
Found at i:47672 original size:28 final size:28
Alignment explanation
Indices: 47617--47708 Score: 136
Period size: 28 Copynumber: 3.4 Consensus size: 28
47607 ACTTACTCTT
*
47617 GAGGAGAA-GG-GC-GCAAATCGAAGGA
1 GAGGAGAAGGGCGCTGCGAATCGAAGGA
*
47642 GAGGAGAAGGGCGCTGCGAATCGATGGA
1 GAGGAGAAGGGCGCTGCGAATCGAAGGA
*
47670 GAGGTGAAGGGCGCTGCGAATCGAAGGA
1 GAGGAGAAGGGCGCTGCGAATCGAAGGA
47698 GAGGAGAAGGG
1 GAGGAGAAGGG
47709 AGAACACTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
25 8 0.14
26 2 0.03
27 2 0.03
28 47 0.80
ACGTcount: A:0.33, C:0.12, G:0.48, T:0.08
Consensus pattern (28 bp):
GAGGAGAAGGGCGCTGCGAATCGAAGGA
Found at i:54046 original size:21 final size:21
Alignment explanation
Indices: 54001--54040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53991 ACAGCTCACC
* *
54001 TGGGTGATCAGACAATCTACA
1 TGGGTGATCAGACAAGCCACA
54022 TGGGTGATCAGACAAGCCA
1 TGGGTGATCAGACAAGCCA
54041 TGTGGGCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (21 bp):
TGGGTGATCAGACAAGCCACA
Found at i:55049 original size:22 final size:24
Alignment explanation
Indices: 55007--55051 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
54997 CTAACAAACT
55007 ACAAAATTAACTAAGAAAGCAATCA
1 ACAAAATTAACT-AGAAAGCAATCA
55032 ACAAAATTAA-T-GAAAGCAAT
1 ACAAAATTAACTAGAAAGCAAT
55052 TAATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.18
Consensus pattern (24 bp):
ACAAAATTAACTAGAAAGCAATCA
Found at i:67069 original size:155 final size:155
Alignment explanation
Indices: 66875--67179 Score: 610
Period size: 155 Copynumber: 2.0 Consensus size: 155
66865 CTTGTAAGGA
66875 ATTTTTACTACTAATCTTTGTTCTTTGTGTAGGTACAATGGGAGATAGACAAGAAGAGCACAAAT
1 ATTTTTACTACTAATCTTTGTTCTTTGTGTAGGTACAATGGGAGATAGACAAGAAGAGCACAAAT
66940 TGAGAAGAAAACACACTACTACATGAAGGTTGCTAACAAGGGGCGCAAAGAGATCATCTTTGATC
66 TGAGAAGAAAACACACTACTACATGAAGGTTGCTAACAAGGGGCGCAAAGAGATCATCTTTGATC
67005 CTGGAGAATGGGTTTGGTTGAGATC
131 CTGGAGAATGGGTTTGGTTGAGATC
67030 ATTTTTACTACTAATCTTTGTTCTTTGTGTAGGTACAATGGGAGATAGACAAGAAGAGCACAAAT
1 ATTTTTACTACTAATCTTTGTTCTTTGTGTAGGTACAATGGGAGATAGACAAGAAGAGCACAAAT
67095 TGAGAAGAAAACACACTACTACATGAAGGTTGCTAACAAGGGGCGCAAAGAGATCATCTTTGATC
66 TGAGAAGAAAACACACTACTACATGAAGGTTGCTAACAAGGGGCGCAAAGAGATCATCTTTGATC
67160 CTGGAGAATGGGTTTGGTTG
131 CTGGAGAATGGGTTTGGTTG
67180 CATCTAAGGA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 150 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (155 bp):
ATTTTTACTACTAATCTTTGTTCTTTGTGTAGGTACAATGGGAGATAGACAAGAAGAGCACAAAT
TGAGAAGAAAACACACTACTACATGAAGGTTGCTAACAAGGGGCGCAAAGAGATCATCTTTGATC
CTGGAGAATGGGTTTGGTTGAGATC
Found at i:77865 original size:10 final size:10
Alignment explanation
Indices: 77846--77875 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
77836 TAACTCCAAT
77846 TATGGACTTA
1 TATGGACTTA
*
77856 TATTGACTTA
1 TATGGACTTA
77866 TATGGACTTA
1 TATGGACTTA
77876 ATATAATCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (10 bp):
TATGGACTTA
Done.