Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003092.1 Hibiscus syriacus cultivar Beakdansim tig00006451_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: 71851
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:280 original size:19 final size:19
Alignment explanation
Indices: 234--280 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
224 TTTATAATAT
*
234 TTATTTTATTTATTAAATC
1 TTATTTTAATTATTAAATC
*
253 TTA-TTTAATTACTTTAA-C
1 TTATTTTAATTA-TTAAATC
271 TTATTTTAAT
1 TTATTTTAAT
281 CATGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTTAATTATTAAATC
Found at i:520 original size:19 final size:19
Alignment explanation
Indices: 484--521 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
474 ATATTTCTAA
*
484 ATAAATAAATATTTTATTT
1 ATAAATAAATATTATATTT
503 ATAAATATAA-ATTATATTT
1 ATAAATA-AATATTATATTT
522 TTTTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATAAATATTATATTT
Found at i:1041 original size:19 final size:21
Alignment explanation
Indices: 1019--1066 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1009 TATATATATT
1019 TATTATTTCA-TAAT-ATTTA
1 TATTATTTCATTAATGATTTA
*
1038 TATTATTTTATTAATGATTTA
1 TATTATTTCATTAATGATTTA
*
1059 TTTTATTT
1 TATTATTT
1067 TTTTAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 4 0.16
21 12 0.48
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTTCATTAATGATTTA
Found at i:11697 original size:10 final size:10
Alignment explanation
Indices: 11682--11717 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
11672 ATGCTTGAAG
*
11682 AAAAAAATGAA
1 AAAAAAAAG-A
11693 AAAAAAAAGA
1 AAAAAAAAGA
11703 AAAAAAAAGA
1 AAAAAAAAGA
11713 AAAAA
1 AAAAA
11718 GAAAAAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:11697 original size:12 final size:11
Alignment explanation
Indices: 11682--11722 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
11672 ATGCTTGAAG
*
11682 AAAAAAATGAA
1 AAAAAAAAGAA
11693 AAAAAAAAG-A
1 AAAAAAAAGAA
11703 AAAAAAAAGAA
1 AAAAAAAAGAA
11714 AAAAGAAAA
1 AAAA-AAAA
11723 AAGGGGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.37
11 13 0.48
12 4 0.15
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:11705 original size:7 final size:7
Alignment explanation
Indices: 11684--11725 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
11674 GCTTGAAGAA
*
11684 AAAAATG
1 AAAAAAG
11691 AAAAAA-
1 AAAAAAG
*
11697 AAAAGAAA
1 AAAA-AAG
11705 AAAAAAG
1 AAAAAAG
11712 AAAAAAG
1 AAAAAAG
11719 AAAAAAG
1 AAAAAAG
11726 GGGGTCAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:11715 original size:17 final size:16
Alignment explanation
Indices: 11691--11724 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
11681 GAAAAAAATG
11691 AAAAAAAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
11707 AAAAGAAAAAAGAAAAA
1 AAAA-AAAAAAGAAAAA
11724 A
1 A
11725 GGGGGTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAA
Found at i:12123 original size:19 final size:17
Alignment explanation
Indices: 12077--12125 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
12067 TATTTTCTTT
12077 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
* *
12093 AGATTAAATTTATTTTCG
1 AAATTCAATTTATTTT-G
12111 AAAATTCAATTTATT
1 -AAATTCAATTTATT
12126 CTTTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 1 0.04
19 12 0.46
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:12619 original size:114 final size:114
Alignment explanation
Indices: 12419--12755 Score: 584
Period size: 114 Copynumber: 3.0 Consensus size: 114
12409 TACCACGTTA
*
12419 TCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
12484 TTTGGTATGAACCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
*
12533 TCATAGTAGAAATAAGAAGAACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
12598 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
* *
12647 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * * *
12712 TTCGGTAGGAACCACAAAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
12756 CTGCATGATC
Statistics
Matches: 212, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 212 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
Found at i:13574 original size:115 final size:110
Alignment explanation
Indices: 13311--13729 Score: 425
Period size: 116 Copynumber: 3.7 Consensus size: 110
13301 TTCCAGTTCG
* *
13311 AGTTCATAATTAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCT-AAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
13376 AACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAA
64 AACCTTTTG-CTAAATCCATCACTTGATGGATCAACATTTCCAGAGAA
* *
13423 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
1 -AGTTCATAATGAGAAGAA--C-TCATCT-AAGAAG-AAGAAGAAGTTCATAATGAGAAGAACTT
* *
13488 GTTCAACCTTTTGCTAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
60 GTTCAACCTTTTGCTAAATCCATCACTTGATGGATCAACATTTCCAGAGAA
* *
13539 AGTTCATAATGAGAAGAACTCATCT--GAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAA
1 AGTTCATAATGAGAAGAACTCATCTAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * * *
13602 CCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGCATCAACCTTTCCAGAGAA
66 CCTTTTGC-TAAATCCATCAC---------TTGA-T-GGATCAACATTTCCAGAGAA
* *
13659 AGTTCATAATGAGAAGAACTCATCT--GAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCA
1 AGTTCATAATGAGAAGAACTCATCTAAGAAG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
13722 ACCTTTTG
65 ACCTTTTG
13730 AATGACTCTA
Statistics
Matches: 267, Mismatches: 21, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
108 38 0.14
109 14 0.05
112 6 0.02
113 18 0.07
115 47 0.18
116 55 0.21
118 3 0.01
119 1 0.00
120 46 0.17
121 39 0.15
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (110 bp):
AGTTCATAATGAGAAGAACTCATCTAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCTAAATCCATCACTTGATGGATCAACATTTCCAGAGAA
Found at i:13741 original size:121 final size:121
Alignment explanation
Indices: 13528--13815 Score: 417
Period size: 121 Copynumber: 2.4 Consensus size: 121
13518 TGGATCAGCT
13528 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGTTCACAATGAGAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCACAATGAGAAGA
* * * * * *
13592 GCTTGTTCAACCTTTTGCATAATTCTATCACAGAAAGAGATA-GATTAGCATCAACC
66 GCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATATG-TCAACATCAACC
*
13648 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCACAATGAGAAGA
* * *
13713 GCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATATGTCAACATCATCC
66 GCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATATGTCAACATCAACC
*
13769 ---CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAG
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAG
13816 AATTTATTCA
Statistics
Matches: 154, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
118 9 0.06
119 36 0.23
120 40 0.26
121 68 0.44
122 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (121 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCACAATGAGAAGA
GCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATATGTCAACATCAACC
Found at i:13966 original size:3 final size:3
Alignment explanation
Indices: 13960--14020 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
13950 TTCCATTTTC
*
13960 TAT TAT TAT T-T ATAT TAT TAT T-T ATAT TAT TAT TAT T-T TAT TTT
1 TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* *
14004 TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
14021 CAAACGGGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13977 original size:12 final size:12
Alignment explanation
Indices: 13960--14006 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
13950 TTCCATTTTC
13960 TATTATTATTTA
1 TATTATTATTTA
13972 TATTATTATTTA
1 TATTATTATTTA
13984 TATTATTA-TTA
1 TATTATTATTTA
*
13995 TTTTATT-TTTA
1 TATTATTATTTA
14006 T
1 T
14007 TAAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 13 0.39
12 20 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:14014 original size:20 final size:21
Alignment explanation
Indices: 13972--14020 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
13962 TTATTATTTA
**
13972 TATTATTATTTATATTATTAT
1 TATTATTATTTATATTAAAAT
*
13993 TATT-TTATTTTTATTAAAAT
1 TATTATTATTTATATTAAAAT
14013 TATTATTA
1 TATTATTA
14021 CAAACGGGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTATTATTTATATTAAAAT
Found at i:15658 original size:20 final size:19
Alignment explanation
Indices: 15633--15674 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
15623 CTATTTTATA
15633 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
15653 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
15672 AAT
1 AAT
15675 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:19161 original size:89 final size:89
Alignment explanation
Indices: 19010--19190 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
19000 TAAAATAAGA
19010 GTATTTGAAATAAATTTTGAATACTTCAAAATGTTGCGTTTCATTAGGTGGTAGCACAACCAACA
1 GTATTTGAAATAAATTTTGAATACTTCAAAATGTTGCGTTTCATTAGGTGGTAGCACAACCAACA
19075 AGGCTCAATAAATGTATCTTAGAT
66 AGGCTCAATAAATGTATCTTAGAT
19099 GTATTTGAAATAAATTTTGAATACTTCAAAATGTTGCGTTTCATTAGGTGGTAGCACAACCAACA
1 GTATTTGAAATAAATTTTGAATACTTCAAAATGTTGCGTTTCATTAGGTGGTAGCACAACCAACA
19164 AGGCTCAATAAATGTATCTTAGAT
66 AGGCTCAATAAATGTATCTTAGAT
19188 GTA
1 GTA
19191 GTGTACTAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (89 bp):
GTATTTGAAATAAATTTTGAATACTTCAAAATGTTGCGTTTCATTAGGTGGTAGCACAACCAACA
AGGCTCAATAAATGTATCTTAGAT
Found at i:19660 original size:4 final size:4
Alignment explanation
Indices: 19651--19676 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19641 TGATCTTGGT
19651 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
19677 CTGCGTACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:20212 original size:17 final size:17
Alignment explanation
Indices: 20190--20224 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20180 GATAGTTAAA
*
20190 AGAATGACAATTGATTC
1 AGAATGACAAATGATTC
20207 AGAATGACAAATGATTC
1 AGAATGACAAATGATTC
20224 A
1 A
20225 CCTAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (17 bp):
AGAATGACAAATGATTC
Found at i:21333 original size:15 final size:16
Alignment explanation
Indices: 21297--21330 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21287 ATCAACATAT
21297 ATAA-TTTTTATATAA
1 ATAATTTTTTATATAA
*
21312 ATAATTTTTTATTTAA
1 ATAATTTTTTATATAA
21328 ATA
1 ATA
21331 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAATTTTTTATATAA
Found at i:21496 original size:20 final size:20
Alignment explanation
Indices: 21467--21521 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
21457 TAATGTAACA
21467 TTCC-CTGGTAATCTTTTAT
1 TTCCACTGGTAATCTTTTAT
21486 TTCCACTGGTAATCTTTTAT
1 TTCCACTGGTAATCTTTTAT
* *
21506 TCCCACTGATAATCTT
1 TTCCACTGGTAATCTT
21522 ACATTTCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.47
Consensus pattern (20 bp):
TTCCACTGGTAATCTTTTAT
Found at i:36325 original size:13 final size:13
Alignment explanation
Indices: 36307--36352 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
36297 TATAAAGACT
36307 AAAATAAAAAATA
1 AAAATAAAAAATA
*
36320 AAAATAAAACAAAA
1 AAAATAAAA-AATA
* *
36334 AAAATTAACAATA
1 AAAATAAAAAATA
36347 AAAATA
1 AAAATA
36353 CTGAATGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:40950 original size:21 final size:22
Alignment explanation
Indices: 40909--40954 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40899 CTTTTACCCT
*
40909 CATTCACAGTGATGTTTGGGGC
1 CATTCACAATGATGTTTGGGGC
*
40931 CATTTACAATGATG-TTGGGGC
1 CATTCACAATGATGTTTGGGGC
40952 CAT
1 CAT
40955 CCACTATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (22 bp):
CATTCACAATGATGTTTGGGGC
Found at i:44922 original size:16 final size:17
Alignment explanation
Indices: 44896--44934 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
44886 TAATCAAATG
44896 TATAA-ATTTTT-TATT
1 TATAATATTTTTATATT
44911 TATAATATTTTTATATT
1 TATAATATTTTTATATT
44928 T-TAATAT
1 TATAATAT
44935 ATACCTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATAATATTTTTATATT
Found at i:45713 original size:23 final size:23
Alignment explanation
Indices: 45663--45713 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
45653 TTTGTGGTAT
* *
45663 ATTTTTCTTTGTCTTTGAGGCAT
1 ATTTTTCTATGTCTTTGAGGCAC
*
45686 GTTTTTCTATGTCTTT-ATGGCAC
1 ATTTTTCTATGTCTTTGA-GGCAC
45709 ATTTT
1 ATTTT
45714 ATCATTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (23 bp):
ATTTTTCTATGTCTTTGAGGCAC
Found at i:46864 original size:21 final size:21
Alignment explanation
Indices: 46835--46887 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
46825 ATTCTGACTA
46835 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
46856 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
46877 TCGCAATGCGA
1 TCGCATTGCGA
46888 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:46902 original size:20 final size:20
Alignment explanation
Indices: 46877--46970 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
46867 TTTTCCTAAT
46877 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
46897 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
46918 TTGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
46938 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
46958 TCGCAATGCGAAT
1 TCGCAATGCGAAT
46971 CTATAAATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:47896 original size:24 final size:24
Alignment explanation
Indices: 47845--47898 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
47835 GTATTCGAAA
*
47845 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCAGGAC
* *
47869 TTTGATCTTGGTCAATACTAGGAT
1 TTTGATCTTGGTCAATACCAGGAC
47893 TTTGAT
1 TTTGAT
47899 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGGAC
Found at i:50346 original size:20 final size:20
Alignment explanation
Indices: 50321--50403 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
50311 CAACGCAGAA
50321 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
50341 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
50361 ATCACAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
50381 ATCGCAACGCAGAAATGACT
1 ATCGCAACGCGGAAATGACT
50401 ATC
1 ATC
50404 ACAATGAGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 52 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:50380 original size:40 final size:40
Alignment explanation
Indices: 50325--50407 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
50315 GCAGAAATCG
*
50325 CAACGCGAATATGACTATCGCAACACGGAAATGACTATCA
1 CAACGCGAATATGACTATCGCAACACAGAAATGACTATCA
*
50365 CAACGCGGAAT-TGACTATCGCAACGCAGAAATGACTATCA
1 CAACGC-GAATATGACTATCGCAACACAGAAATGACTATCA
50405 CAA
1 CAA
50408 TGAGAGAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (40 bp):
CAACGCGAATATGACTATCGCAACACAGAAATGACTATCA
Found at i:50456 original size:19 final size:18
Alignment explanation
Indices: 50432--50513 Score: 73
Period size: 19 Copynumber: 4.6 Consensus size: 18
50422 CGAGAGAATA
50432 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATG-AAATC
*
50451 GCAATGCGAAATGAAAAGC
1 GCAATGCGAAATG-AAATC
*
50470 GCAA--CG-AGTG-AATC
1 GCAATGCGAAATGAAATC
*
50484 GCAATGCGAAAATGAAATA
1 GCAATGCG-AAATGAAATC
*
50503 GCAACGCGAAA
1 GCAATGCGAAA
50514 CTAATTTCGC
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 7 0.13
16 5 0.10
17 2 0.04
18 6 0.12
19 32 0.62
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.12
Consensus pattern (18 bp):
GCAATGCGAAATGAAATC
Found at i:50584 original size:33 final size:34
Alignment explanation
Indices: 50523--50618 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
50513 ACTAATTTCG
50523 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
50557 CGTTGCGATTTTCATTTT-GCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* ** * *
50590 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
50619 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:52156 original size:42 final size:42
Alignment explanation
Indices: 52092--52202 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
52082 CTAGAATGTT
* * * * *
52092 GGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT-G
1 GGGA-GGA-CTCTTGAACGATGACAGGGGACTCCTGAACGATAG
** *
52135 GGAGAGGACTCTTGAGGGATGATAGGGGACTCCTGAACGATAG
1 GG-GAGGACTCTTGAACGATGACAGGGGACTCCTGAACGATAG
*
52178 GGGAGGCCTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
52203 TGAGTCGGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
42 44 0.81
43 8 0.15
44 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.19
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGACTCCTGAACGATAG
Found at i:52728 original size:34 final size:34
Alignment explanation
Indices: 52681--52834 Score: 157
Period size: 34 Copynumber: 4.4 Consensus size: 34
52671 TGAAACTTAA
*
52681 AATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
** * * *
52715 AATCGCAATGCG-AAATGAAAATCGCAACAACAA
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
* *
52748 AATCGCAACGCGAAAATGACTATCGCAATGCGAAAATG
1 AATCGCAATGCGAAAATGACTATCGCAA--CG-AGA-G
**
52786 ACTATCGCAATGCGAATTTGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAAAATGACTATCGCAACGAGAG
52822 AATCGCAATGCGA
1 AATCGCAATGCGA
52835 TTTTCATTTC
Statistics
Matches: 97, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
33 27 0.28
34 36 0.37
36 3 0.03
37 4 0.04
38 3 0.03
40 24 0.25
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.16
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGACTATCGCAACGAGAG
Found at i:52774 original size:20 final size:20
Alignment explanation
Indices: 52749--52817 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
52739 CAACAACAAA
52749 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
52769 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
52789 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
52809 ATCGCAACG
1 ATCGCAACG
52818 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:52887 original size:20 final size:20
Alignment explanation
Indices: 52862--53065 Score: 312
Period size: 20 Copynumber: 10.5 Consensus size: 20
52852 AATTCTTTCG
**
52862 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
52882 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
52902 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
52922 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
52942 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
52962 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
52982 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
52996 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
53016 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
53036 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
53056 TTGCGATAGT
1 TTGCGATAGT
53066 AAACTATTCT
Statistics
Matches: 171, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
14 7 0.04
16 6 0.04
18 6 0.04
20 152 0.89
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:54975 original size:20 final size:20
Alignment explanation
Indices: 54950--55039 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
54940 GCAAAACTTT
54950 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
54970 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
54990 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
55010 CTATCGCAACGC-AAAATGA
1 AAATCGCAACACGAAAATGA
55029 AAATCGCAACA
1 AAATCGCAACA
55040 ACAGAATTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:55436 original size:22 final size:21
Alignment explanation
Indices: 55375--55436 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 21
55365 TGACCGTGAA
* *
55375 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTC-GAGATGGGGAC
*
55397 TGATATCGTC--G-TGGGGAC
1 TGATTTCGTCGAGATGGGGAC
55415 TGATTTCGTCAGAGATGGGGAC
1 TGATTTCGTC-GAGATGGGGAC
55437 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
21 1 0.03
22 15 0.47
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (21 bp):
TGATTTCGTCGAGATGGGGAC
Found at i:55639 original size:20 final size:20
Alignment explanation
Indices: 55612--55664 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
55602 GCGCTATGTA
55612 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
55632 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
55652 AATCGCATTGCGA
1 AATCGCATTGCGA
55665 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:55678 original size:21 final size:21
Alignment explanation
Indices: 55652--55748 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
55642 CGATTTACGT
* *
55652 AATCGCATTGCGAATTAGGAA
1 AATCGCAATGCGAATTAGGGA
* *
55673 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCGAATTAGGGA
* *
55694 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCGAATTAGGGA
* *
55715 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCGAATTAGGGA
55736 AATCGCAATGCGA
1 AATCGCAATGCGA
55749 TAGTCAGAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (21 bp):
AATCGCAATGCGAATTAGGGA
Found at i:55707 original size:42 final size:42
Alignment explanation
Indices: 55652--55748 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
55642 CGATTTACGT
*
55652 AATCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGA
1 AATCGCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGA
* * *
55694 AATCGCAACGCGAATTTGGGAAATCGCAACGCGAATTTGGGA
1 AATCGCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGA
55736 AATCGCAATGCGA
1 AATCGCAATGCGA
55749 TAGTCAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (42 bp):
AATCGCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGA
Found at i:61649 original size:58 final size:59
Alignment explanation
Indices: 61538--61651 Score: 169
Period size: 58 Copynumber: 1.9 Consensus size: 59
61528 AATAAGGGTA
* **
61538 TAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTGAGGACTAATTTGGAATGAGATAT
1 TAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTGAGGACTAATTTAAAATGAGATAT
*
61597 TAGTTTGAGGATGAAATTATAATATT-AAAAGTTT-AGAGACTAATTTAAAATGAGA
1 TAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTGAG-GACTAATTTAAAATGAGA
61652 GTCATAGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 2 0.04
58 24 0.48
59 24 0.48
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (59 bp):
TAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTGAGGACTAATTTAAAATGAGATAT
Found at i:61660 original size:59 final size:59
Alignment explanation
Indices: 61520--61661 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 59
61510 ATTTAAAACT
* * *
61520 TAATTTAGAATAAGGGTATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTGAGGAC
1 TAATTTAGAATGAGAGTATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTGAGGAC
* *
61579 TAATTTGGAATGAGA-TATTAGTTTGAGGATGAAATTATAATATT-AAAAGTTT-AGAGAC
1 TAATTTAGAATGAGAGTA-TAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTGAG-GAC
*
61637 TAATTTAAAATGAGAGTCATAGTTT
1 TAATTTAGAATGAGAGT-ATAGTTT
61662 AGAGACATAC
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.03
58 26 0.36
59 43 0.60
60 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (59 bp):
TAATTTAGAATGAGAGTATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTGAGGAC
Found at i:65229 original size:6 final size:6
Alignment explanation
Indices: 65220--65251 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
65210 TAATTAATTT
65220 ATATAA ATATAA ATATAA ATATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT
65252 CGAAAGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:67877 original size:29 final size:29
Alignment explanation
Indices: 67835--67916 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
67825 AAACTAAATT
67835 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
67864 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
67893 GATGTTATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
67917 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Done.