Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001290.1 Hibiscus syriacus cultivar Beakdansim tig00002526_pilon, 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: 84363
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7180 original size:20 final size:20
Alignment explanation
Indices: 7155--7192 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7145 TTTTGGTGCA
7155 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
*
7175 GAGGGAATCGATTCCCCC
1 GAGGGAATCGATACCCCC
7193 TTTGAAGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:7224 original size:21 final size:21
Alignment explanation
Indices: 7198--7237 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7188 CCCCCTTTGA
*
7198 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
7219 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
7238 CTGGGGTTAT
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:7243 original size:20 final size:20
Alignment explanation
Indices: 7157--7243 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
7147 TTGGTGCAGA
*
7157 GGGAATCGATA-CCCCCATG
1 GGGAATCGATACCCCCCCTG
* **
7176 AGGGAATCGATTCCCCCTTTGAAG
1 -GGGAATCGATACCCCCCCT---G
* * *
7200 GGGAACCGATTCCCCCCACAG
1 GGGAATCGATACCCCCC-CTG
7221 GGGAATCGATACCCCCCCTG
1 GGGAATCGATACCCCCCCTG
7241 GGG
1 GGG
7244 TTATGGTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
20 15 0.29
21 21 0.40
23 15 0.29
24 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (20 bp):
GGGAATCGATACCCCCCCTG
Found at i:8423 original size:20 final size:20
Alignment explanation
Indices: 8398--8435 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8388 TTTTGGTGCA
8398 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
*
8418 GAGGGAATCGATTCCCCC
1 GAGGGAATCGATACCCCC
8436 TTTGAAGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:8467 original size:21 final size:21
Alignment explanation
Indices: 8441--8480 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8431 CCCCCTTTGA
*
8441 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
8462 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
8481 TGGGGTTATG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:12000 original size:63 final size:64
Alignment explanation
Indices: 11831--12001 Score: 197
Period size: 63 Copynumber: 2.7 Consensus size: 64
11821 ACAGTTTTTT
* * * *
11831 TTTTGA-AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC
1 TTTTGAGAAAAATCCTTGAGTTTGTTTCTTTGGAAACAAA-ATTTGTATCTCTTGAGACAATTTC
* * * * * *
11895 TTTTGAGAAAAAAACCATTGAGATTGTTCCATT-GAAAC-AAATTT-TATCTCTTGAGATAGTTT
1 TTTTGAG-AAAAATCC-TTGAGTTTGTTTCTTTGGAAACAAAATTTGTATCTCTTGAGACAATTT
11957 C
64 C
11958 TTTTGAGAAAAATCCTTGAGTTTGTTTCTTTGGAAACAAAATTT
1 TTTTGAGAAAAATCCTTGAGTTTGTTTCTTTGGAAACAAAATTT
12002 ACCATCTTTA
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
61 13 0.15
62 12 0.14
63 29 0.33
64 9 0.10
65 2 0.02
66 11 0.12
67 12 0.14
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (64 bp):
TTTTGAGAAAAATCCTTGAGTTTGTTTCTTTGGAAACAAAATTTGTATCTCTTGAGACAATTTC
Found at i:12469 original size:132 final size:131
Alignment explanation
Indices: 12228--12742 Score: 514
Period size: 132 Copynumber: 3.9 Consensus size: 131
12218 TGAAACCATT
* * * * **
12228 ACCCCTAGATAATCAGTCGTCCTCATCACGTAGGAATCATGTTATCATCCCTAAAGATGGCTTGC
1 ACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGATGGCCTAT
* * *
12293 CATCCTCATCATGTAGGAA-TCGTGTCATCGCCCCGACCATACCTCATCATCACATAGGAGCCGT
66 CATCCTCATCACGTAGGAACT-GTGTCATC-CCCCGACCAGACCTCCTCATCACATAGGAGCCGT
12357 GTC
129 GTC
* * * * * *
12360 ACCCCCATATAACCAACCGTCCAT-ATCACGTAGGAACCGTGTTATCATCCCTAAAAATAGCCTA
1 ACCCCTAGATAACCAGCCGTCC-TCATCACGTAGGAACCATGTTATCATCCCTAAAGATGGCCTA
* * *
12424 TCATCTTCATCACGTAGGAACTGTGTCATCCCCCTGACCAGACCTCCTCATCACGTAGGAGCTGT
65 TCATCCTCATCACGTAGGAACTGTGTCATCCCCC-GACCAGACCTCCTCATCACATAGGAGCCGT
12489 GTC
129 GTC
* ** * *
12492 ACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACTGTGTTATCATTCCTAAAGATGGTCTAT
1 ACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGATGGCCTAT
* * ** * * * * * *
12557 CATCCTCATCACATAGAAACCATGTTATCCCCCGACCAGATCTCCTTATCACTTAAGAGTCGTGT
66 CATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATCACATAGGAGCCGTGT
12622 C
131 C
* * * * *
12623 ACCCCTAGATAACTAGTCGTCCTCATCGCGTAGGAACCATGTTATTACCCTTCTTAAAGATGGCC
1 ACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCC--C-TAAAGATGGCC
* * * * ** * * *
12688 GGAAC-TCTTCATCACGTATGAGTTGTGTCATCCACCGACCAGATCTTCTCATCAC
63 -TATCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATCAC
12743 GTATCAGCCC
Statistics
Matches: 312, Mismatches: 63, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
131 73 0.23
132 186 0.60
133 3 0.01
134 48 0.15
135 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (131 bp):
ACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGATGGCCTAT
CATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATCACATAGGAGCCGTGT
C
Found at i:12521 original size:43 final size:41
Alignment explanation
Indices: 12425--12533 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 41
12415 AATAGCCTAT
*
12425 CATCTTCATCACGTAGGAACTGTGTCATCCCCCTGACCAGAC
1 CATCCTCATCACGTAGGAACTGTGTCA-CCCCCTGACCAGAC
*
12467 C-TCCTCATCACGTAGGAGCTGTGTCA-CCCCTAGATAACCAG-C
1 CATCCTCATCACGTAGGAACTGTGTCACCCCCT-G---ACCAGAC
12509 CATCCTCATCACGTAGGAACTGTGT
1 CATCCTCATCACGTAGGAACTGTGT
12534 TATCATTCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 5 0.08
40 1 0.02
41 23 0.39
42 3 0.05
43 27 0.46
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (41 bp):
CATCCTCATCACGTAGGAACTGTGTCACCCCCTGACCAGAC
Found at i:12746 original size:40 final size:41
Alignment explanation
Indices: 12696--12798 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
12686 CCGGAACTCT
* *
12696 TCATCACGTATGAGTTGTGTCATCCA-CCGACCAGATCTTC
1 TCATCACGTATGAGTCGTGTCATCCACCCGACCAGATCTAC
* * * * *
12736 TCATCACGTATCAGCCCTATCATTCACCCGACCAGATCTAC
1 TCATCACGTATGAGTCGTGTCATCCACCCGACCAGATCTAC
* *
12777 TCATCATGTAGGAGTCGTGTCA
1 TCATCACGTATGAGTCGTGTCA
12799 CCCATAAACG
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
40 20 0.41
41 29 0.59
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (41 bp):
TCATCACGTATGAGTCGTGTCATCCACCCGACCAGATCTAC
Found at i:14570 original size:35 final size:34
Alignment explanation
Indices: 14505--14572 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
14495 CCATATTTCT
14505 GGTTATTTTATTTTAGTCCTTAATATTATTTAGG
1 GGTTATTTTATTTTAGTCCTTAATATTATTTAGG
14539 GGTTATTTTCATTTATAGTACC-T-ATATTATTTAG
1 GGTTATTTT-ATTT-TAGT-CCTTAATATTATTTAG
14573 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 9 0.29
35 15 0.48
36 5 0.16
37 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.54
Consensus pattern (34 bp):
GGTTATTTTATTTTAGTCCTTAATATTATTTAGG
Found at i:14656 original size:30 final size:30
Alignment explanation
Indices: 14614--14822 Score: 199
Period size: 30 Copynumber: 7.0 Consensus size: 30
14604 TTTGTGTTTA
*
14614 AGTCCCTTAAGTTTCTATTTTTTCTATTTT
1 AGTCCCTTAAATTTCTATTTTTTCTATTTT
* * * **
14644 AATCCCTCAAGTTTCTATTTTTGGTATTTT
1 AGTCCCTTAAATTTCTATTTTTTCTATTTT
* * *
14674 AGTCCTTTAAATATC-AGTTTTTCTATTTT
1 AGTCCCTTAAATTTCTATTTTTTCTATTTT
* * *
14703 AGTCCCATAAGTTTCTATTTTTGT-GATTTT
1 AGTCCCTTAAATTTCTATTTTT-TCTATTTT
* *
14733 AGTCCCTTAAATTTCTATTTTTACTTTTTT
1 AGTCCCTTAAATTTCTATTTTTTCTATTTT
* *
14763 AGTCCTTTAAATTTCTATTTATGT-TATTTT
1 AGTCCCTTAAATTTCTATTT-TTTCTATTTT
* * * *
14793 AATCTCTTAAATTTATGTTTTTTCTATTTT
1 AGTCCCTTAAATTTCTATTTTTTCTATTTT
14823 GGTTCTTTTA
Statistics
Matches: 141, Mismatches: 33, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
29 24 0.17
30 115 0.82
31 2 0.01
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (30 bp):
AGTCCCTTAAATTTCTATTTTTTCTATTTT
Found at i:17224 original size:3 final size:3
Alignment explanation
Indices: 17218--17245 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17208 TCATCCAAGT
17218 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
17246 AACCCAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:25783 original size:53 final size:53
Alignment explanation
Indices: 25724--25861 Score: 143
Period size: 53 Copynumber: 2.6 Consensus size: 53
25714 TAAAATATAA
* * * * * * *
25724 AAATTAACACATATTTACAATGGTGTAAGTATGTACATCTCTCAATATTTTA-
1 AAATTAACACATACTTACAACGATGAAAGTATATACAACTCTCAATATATTAG
* *
25776 ACAATTAACACATACTTACACCGATGAAAGTATATACAACTCTTAATATATTAG
1 A-AATTAACACATACTTACAACGATGAAAGTATATACAACTCTCAATATATTAG
** * *
25830 AAATTAACACCCACTTACACCAATGAAAGTAT
1 AAATTAACACATACTTACAACGATGAAAGTAT
25862 TTTTATATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 1 0.01
53 70 0.97
54 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (53 bp):
AAATTAACACATACTTACAACGATGAAAGTATATACAACTCTCAATATATTAG
Found at i:25872 original size:2 final size:2
Alignment explanation
Indices: 25865--25906 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
25855 AAAGTATTTT
* * *
25865 TA TA TA TA TT TT TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25907 AAATTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25876 original size:12 final size:12
Alignment explanation
Indices: 25859--25897 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25849 CCAATGAAAG
25859 TATTTTTATATA
1 TATTTTTATATA
*
25871 TATTTTTAAATA
1 TATTTTTATATA
* *
25883 TATATATATATA
1 TATTTTTATATA
25895 TAT
1 TAT
25898 ATATATATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTTATATA
Found at i:40956 original size:135 final size:129
Alignment explanation
Indices: 40669--40977 Score: 336
Period size: 135 Copynumber: 2.3 Consensus size: 129
40659 TCAACATCAG
* ** * * * * *
40669 CTGACCAGATCTCCTCATCACGTAGGAGCAACGTCAACATTAGATAACCAGTCGTCCTCATTACG
1 CTGACCAGATATCCTCATCACGTAGGAGC-GTGTCACCCTTAGATAACCAGCCATCCTCATCACG
* *
40734 TAGGAACTATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGTAGGAGCAGTGTCATCCC
65 TAGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
* *
40799 CTGACTAGATATCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGCCATCCTCATCGCG
1 CTGACCAGATATCCTCATCACGTAGGAG-CGTGTCACCCTTAGATAACCAGCCATCCTCATCACG
* *
40864 TAGGAACCGA-GTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGCATGAGTC-GTG
65 TAGGAA-CGATGTTATCA--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGCAGGAG-CAGTG
40927 TCAT-CC
123 TCATCCC
* * * *
40933 TTCGACCAGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGA
1 CT-GACCAGATATCCTCATCACGTA-GGAGCGTGTCACCCTTAGA
40978 CGACCCGAAC
Statistics
Matches: 150, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
130 66 0.44
131 3 0.02
132 1 0.01
133 1 0.01
134 7 0.05
135 69 0.46
136 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (129 bp):
CTGACCAGATATCCTCATCACGTAGGAGCGTGTCACCCTTAGATAACCAGCCATCCTCATCACGT
AGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
Found at i:40995 original size:43 final size:40
Alignment explanation
Indices: 40900--41003 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
40890 AAGATGGCCA
* ** *
40900 AGAACTCTTCATCACGCATGAGTCGTGTCATCCTTCGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
** *
40940 AGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTT---CGACC
*
40983 CGAACTCTTCATCACGTATGA
1 AGAACTCTTCATCACGTATGA
41004 GCAGTGTCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 28 0.56
43 22 0.44
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
Found at i:41198 original size:10 final size:10
Alignment explanation
Indices: 41178--41212 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
41168 ATTTATTTTT
41178 TTATT-ATTA
1 TTATTAATTA
41187 TTATTAATTA
1 TTATTAATTA
*
41197 TTATTAACTA
1 TTATTAATTA
41207 TTATTA
1 TTATTA
41213 TTAATTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATTAATTA
Found at i:41198 original size:13 final size:13
Alignment explanation
Indices: 41178--41218 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
41168 ATTTATTTTT
41178 TTATTATTATT-A
1 TTATTATTATTAA
41190 TTAATTATTATTAA
1 TT-ATTATTATTAA
*
41204 CTATTATTATTAA
1 TTATTATTATTAA
41217 TT
1 TT
41219 TTACATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:46611 original size:26 final size:26
Alignment explanation
Indices: 46575--46624 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
46565 AACAAAGGTT
* *
46575 CTTTACATTTTGTTTTTATTTTTTAG
1 CTTTACATTTTATTATTATTTTTTAG
46601 CTTTACATTTTATTATTATTTTTT
1 CTTTACATTTTATTATTATTTTTT
46625 TCGTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (26 bp):
CTTTACATTTTATTATTATTTTTTAG
Found at i:47839 original size:34 final size:34
Alignment explanation
Indices: 47792--47859 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
47782 TCCATTAAAA
*
47792 ATATTGGATTATTTTCTATTTCTCTTTAGAATTT
1 ATATTGGAATATTTTCTATTTCTCTTTAGAATTT
*
47826 ATATTGTAATATTTTCTATTTCTCTTTAGAATTT
1 ATATTGGAATATTTTCTATTTCTCTTTAGAATTT
47860 CCTGTTACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (34 bp):
ATATTGGAATATTTTCTATTTCTCTTTAGAATTT
Found at i:48668 original size:20 final size:20
Alignment explanation
Indices: 48643--48694 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
48633 TCACGAAATA
48643 TAAGATTATCAGTGAGAATG
1 TAAGATTATCAGTGAGAATG
* * *
48663 TAAGATTACCGGTGGGAATG
1 TAAGATTATCAGTGAGAATG
48683 TAAGATTATCAG
1 TAAGATTATCAG
48695 GGAATAGGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.29
Consensus pattern (20 bp):
TAAGATTATCAGTGAGAATG
Found at i:49887 original size:21 final size:21
Alignment explanation
Indices: 49863--49960 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
49853 TATCGCAAAT
* *
49863 TCGCATTGCAATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
49884 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
49905 TCGTGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
49925 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
49946 TCGCATTGCGATAGT
1 TCGCGTTGCGATAGT
49961 CTACAGTTGT
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.23
21 47 0.77
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:49979 original size:22 final size:22
Alignment explanation
Indices: 49951--50062 Score: 81
Period size: 22 Copynumber: 5.3 Consensus size: 22
49941 GAAAATCGCA
49951 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
* * * **
49973 TTGCGAT-TTTTCCAAAT-TCG
1 TTGCGATAGTCTACAGTTGTCG
* ** *
49993 TTTCGATTTTCTA-AATT--CG
1 TTGCGATAGTCTACAGTTGTCG
** *
50012 TTGCGATAGTCTACAGCAGTTG
1 TTGCGATAGTCTACAGTTGTCG
50034 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
50056 TTGCGAT
1 TTGCGAT
50063 TTTCCAAATT
Statistics
Matches: 67, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 12 0.18
20 13 0.19
21 8 0.12
22 34 0.51
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:49999 original size:20 final size:20
Alignment explanation
Indices: 49970--50018 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
49960 TCTACAGTTG
49970 TCGTTGCGATTTTTCCAAAT
1 TCGTTGCGATTTTTCCAAAT
* *
49990 TCGTTTCGA-TTTTCTAAAT
1 TCGTTGCGATTTTTCCAAAT
50009 TCGTTGCGAT
1 TCGTTGCGAT
50019 AGTCTACAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (20 bp):
TCGTTGCGATTTTTCCAAAT
Found at i:50024 original size:19 final size:19
Alignment explanation
Indices: 49928--50046 Score: 53
Period size: 19 Copynumber: 5.8 Consensus size: 19
49918 TTTCATTTCG
*
49928 CGTTGCGATAGT-TGAAAAT
1 CGTTGCGATAGTCT-AAATT
*
49947 CGCATTGCGATAGTCTACAGTTGT
1 CG--TTGCGATAGTCTA-A-AT-T
** *
49971 CGTTGCGATTTTTCCAAATT
1 CGTTGCGA-TAGTCTAAATT
* **
49991 CGTTTCGATTTTCTAAATT
1 CGTTGCGATAGTCTAAATT
50010 CGTTGCGATAGTCTACAGCAGTT
1 CGTTGCGATAGTCTA-A--A-TT
50033 -GTTGCGATAGTCTA
1 CGTTGCGATAGTCTA
50047 CAGTTGTCGT
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
19 24 0.31
20 9 0.12
21 12 0.15
22 24 0.31
23 6 0.08
24 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCTAAATT
Found at i:50169 original size:6 final size:6
Alignment explanation
Indices: 50158--50250 Score: 179
Period size: 6 Copynumber: 15.7 Consensus size: 6
50148 AGACACATAT
50158 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
50206 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
50251 CGAGACGGAC
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.06
6 82 0.94
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:50893 original size:22 final size:22
Alignment explanation
Indices: 50865--50917 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
50855 AATTTGGAAA
50865 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
50887 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
50909 ATCGCAACG
1 ATCGCAACG
50918 CGAAACAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:50955 original size:21 final size:21
Alignment explanation
Indices: 50929--50982 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
50919 GAAACAGAAA
50929 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
50950 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
50971 ATCGCAACGCGA
1 ATCGCAACGCGA
50983 AATGCAACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:50990 original size:21 final size:21
Alignment explanation
Indices: 50906--50990 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
50896 ACAACTGTAG
50906 ACTATCGCAACGCGAAA--CA
1 ACTATCGCAACGCGAAATTCA
** **
50925 GAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATTCA
**
50947 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATTCA
*
50968 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATTCA
50989 AC
1 AC
50991 GTAAATTTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
20 13 0.24
21 39 0.72
22 2 0.04
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATTCA
Found at i:55063 original size:21 final size:20
Alignment explanation
Indices: 55021--55068 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
55011 CAAATATATG
**
55021 AATCGCATTGCGATTTTCTA
1 AATCGCATTGCGAAATTCTA
*
55041 AATTCGCATTGCGAAATTGTA
1 AA-TCGCATTGCGAAATTCTA
55062 AATCGCA
1 AATCGCA
55069 ACACATAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (20 bp):
AATCGCATTGCGAAATTCTA
Found at i:55254 original size:22 final size:22
Alignment explanation
Indices: 55229--55271 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55219 GGCGACATCC
*
55229 GTCCCTATCTCCGACGAAATCT
1 GTCCCCATCTCCGACGAAATCT
55251 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
55272 CGTATATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCT
Found at i:55712 original size:20 final size:20
Alignment explanation
Indices: 55667--55712 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
55657 ACGCGACTTT
* *
55667 AGTTTCGCGTTGCGATTTTC
1 AGTTTCGCGTTGCGAATTTA
*
55687 ATTTTCGCGTTGCGAATTTA
1 AGTTTCGCGTTGCGAATTTA
55707 AGTTTC
1 AGTTTC
55713 AGAAACTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
AGTTTCGCGTTGCGAATTTA
Found at i:57536 original size:63 final size:62
Alignment explanation
Indices: 57428--57547 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 62
57418 AGGTCGGTAC
* *
57428 TTTACGTGAAGACAATGGTACGCTACGTGATGAGGTACGGTCTTTACATGGTGAGGTGGATGT
1 TTTACGCGAAGACAATGGTACGCTACGTGATGAGGTAC-GTCTTTACATGATGAGGTGGATGT
* * * * *
57491 TTTACGCGATGACAATGGTGCGCTATGTGGTGAGGTATC-TACTTTACGTGATGAGGT
1 TTTACGCGAAGACAATGGTACGCTACGTGATGAGGTA-CGT-CTTTACATGATGAGGT
57548 AGTCGCTCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
62 1 0.02
63 46 0.96
64 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.33, T:0.32
Consensus pattern (62 bp):
TTTACGCGAAGACAATGGTACGCTACGTGATGAGGTACGTCTTTACATGATGAGGTGGATGT
Found at i:57872 original size:21 final size:21
Alignment explanation
Indices: 57844--57962 Score: 134
Period size: 21 Copynumber: 5.7 Consensus size: 21
57834 AATGCACCTG
*
57844 TCATCGTTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
57865 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
*
57886 TCATCGTTCAATAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
57907 -CTACCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTC
**
57928 TCATCGTTCAAGAGATCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
57949 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
57963 CCCGATTCAC
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.02
21 79 0.95
22 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:57891 original size:42 final size:42
Alignment explanation
Indices: 57844--57962 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
57834 AATGCACCTG
* * *
57844 TCATCGTTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCCTA
*
57886 TCATCGTTCAATAGGCCCCTCCTACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCCTA
** *
57928 TCATCGTTCAAGAGATCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAG
57963 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCCTA
Found at i:59371 original size:64 final size:64
Alignment explanation
Indices: 59261--59418 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
59251 TTAATTGAAT
59261 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTG
* * *
59326 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTG
59390 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
59419 GTTTATTCAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTG
Found at i:59577 original size:20 final size:20
Alignment explanation
Indices: 59520--59570 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
59510 TCGTTGTGAT
**
59520 AGTCAAATTCGCAACG-TTA
1 AGTCAAATTCGCAACGCGAA
59539 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
59559 AGTCAAATTCGC
1 AGTCAAATTCGC
59571 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAA
Found at i:59601 original size:14 final size:15
Alignment explanation
Indices: 59566--59601 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
59556 GAAAGTCAAA
59566 TTCGCG-TTGCGATT
1 TTCGCGTTTGCGATT
59580 TTCG-GTTTGCGA-T
1 TTCGCGTTTGCGATT
59593 TTCGCGTTT
1 TTCGCGTTT
59602 CAAATTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.06, C:0.19, G:0.28, T:0.47
Consensus pattern (15 bp):
TTCGCGTTTGCGATT
Found at i:59663 original size:20 final size:20
Alignment explanation
Indices: 59638--59681 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
59628 AACGCGATAA
*
59638 TCGCGTTGCGAATTTGACTT
1 TCGCGTTACGAATTTGACTT
*
59658 TCGCGTTATGAATTTGACTT
1 TCGCGTTACGAATTTGACTT
59678 TCGC
1 TCGC
59682 AACAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTACGAATTTGACTT
Found at i:59950 original size:18 final size:18
Alignment explanation
Indices: 59927--59962 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
59917 AAGCCGGTTG
59927 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
59945 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
59963 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:63287 original size:41 final size:40
Alignment explanation
Indices: 63242--63335 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 40
63232 GAAATTTAGT
** *
63242 GTTGCGAATTTGAC-TTCTTTGTTGCGATTTTCTAAATTCGC
1 GTTGCGAATTTGACATTC-GCGTTGCGATTTAC-AAATTCGC
63283 GTTGCG-ATTT-ACAAATTCGCGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGAC--ATTCGCGTTGCGATTTACAAATTCGC
63323 GTTGCGAATTTGA
1 GTTGCGAATTTGA
63336 AAAATGGGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
39 2 0.04
40 18 0.40
41 21 0.47
42 4 0.09
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACATTCGCGTTGCGATTTACAAATTCGC
Found at i:63300 original size:20 final size:20
Alignment explanation
Indices: 63262--63329 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
63252 TGACTTCTTT
*
63262 GTTGCGATTTTCTAAATTCGC
1 GTTGCGATTTAC-AAATTCGC
63283 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
63303 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
63323 GTTGCGA
1 GTTGCGA
63330 ATTTGAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 35 0.76
21 11 0.24
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:66415 original size:30 final size:29
Alignment explanation
Indices: 66344--66418 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
66334 AAAAATCGAA
* * *
66344 TTAAACGGGATGAGGAAAAATCGTTTATG
1 TTAAACGGGACGGGGAAAAACCGTTTATG
66373 TTAAACGGGACGGGGAAAAACCGTTTATG
1 TTAAACGGGACGGGGAAAAACCGTTTATG
66402 TTAAACGGGGACGGGGA
1 TTAAAC-GGGACGGGGA
66419 CAGATTTGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 32 0.76
30 10 0.24
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (29 bp):
TTAAACGGGACGGGGAAAAACCGTTTATG
Found at i:68406 original size:2 final size:2
Alignment explanation
Indices: 68399--68431 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68389 TTCGCATTTT
68399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68432 TAGTCTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68843 original size:24 final size:25
Alignment explanation
Indices: 68816--68862 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
68806 TAAATGATAG
68816 AAATTA-AA-ATAATTATTAAAATAA
1 AAATTAGAATATAATT-TTAAAATAA
*
68840 AAATTAGAATCTAATTTTAAAAT
1 AAATTAGAATATAATTTTAAAAT
68863 TATATCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 9 0.45
26 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATTAGAATATAATTTTAAAATAA
Done.