Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005799.1 Hibiscus syriacus cultivar Beakdansim tig00013599_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: 86951
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4133 original size:30 final size:30
Alignment explanation
Indices: 4097--4159 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
4087 CTCCAACGAA
4097 AACCCTTTGCCCCATCCGAGTTCCCACCAC
1 AACCCTTTGCCCCATCCGAGTTCCCACCAC
4127 AACCCTTTGCCCCATCCGAGTTCCCACCAC
1 AACCCTTTGCCCCATCCGAGTTCCCACCAC
4157 AAC
1 AAC
4160 TTTAATATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.49, G:0.10, T:0.19
Consensus pattern (30 bp):
AACCCTTTGCCCCATCCGAGTTCCCACCAC
Found at i:5646 original size:28 final size:27
Alignment explanation
Indices: 5596--5653 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
5586 CTTATGGATT
*
5596 AAGAATGGACCTAACTAATCAAAAATAA
1 AAGAATGGACCTAAC-AATCAAAAAAAA
5624 AAGAATGGACCTAA-AATTACAAAAAAAA
1 AAGAATGGACCTAACAA-T-CAAAAAAAA
5652 AA
1 AA
5654 AAAACTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 1 0.04
28 24 0.89
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.16
Consensus pattern (27 bp):
AAGAATGGACCTAACAATCAAAAAAAA
Found at i:6151 original size:16 final size:17
Alignment explanation
Indices: 6130--6181 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
6120 TTTTAAATTT
6130 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
6146 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
*
6161 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
6178 AATT
1 AATT
6182 TAATTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:12395 original size:21 final size:21
Alignment explanation
Indices: 12370--12420 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
12360 AGAAATATTT
12370 AAATATTTTTAA-ATTTTAAAA
1 AAATATTTTTAATA-TTTAAAA
**
12391 AAATAGTTTTTTTTATTTAAAA
1 AAATA-TTTTTAATATTTAAAA
12413 AAATATTT
1 AAATATTT
12421 CATAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 17 0.65
23 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATATTTTTAATATTTAAAA
Found at i:12552 original size:2 final size:2
Alignment explanation
Indices: 12545--12573 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12535 CGATTGTAAG
12545 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 T
12574 TATTTTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33912 original size:34 final size:34
Alignment explanation
Indices: 33869--33971 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 34
33859 GCTGAACTCC
*
33869 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
1 GATCATTGAAGGCGAGGCTTACGTTGTTTACATG
*
33903 GATCATTGAAGGAGAGGCTTACGTTGTTTACATG
1 GATCATTGAAGGCGAGGCTTACGTTGTTTACATG
*
33937 GATCATTGAAGGCGAGGATTACGTTGTTTACATG
1 GATCATTGAAGGCGAGGCTTACGTTGTTTACATG
33971 G
1 G
33972 CCCCAATAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (34 bp):
GATCATTGAAGGCGAGGCTTACGTTGTTTACATG
Found at i:37154 original size:46 final size:46
Alignment explanation
Indices: 37101--37192 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
37091 CATACAATTA
*
37101 TCGAATTCTTATTAATGGAGATAAACAAACATAAATCAAAGGATTC
1 TCGAATTCTTATTAATGGAGATAAACAAACAGAAATCAAAGGATTC
* *
37147 TCGAATTCTTATTAATGGAGATAAACAAACAGAAATCGAAGTATTC
1 TCGAATTCTTATTAATGGAGATAAACAAACAGAAATCAAAGGATTC
37193 ATGAACTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (46 bp):
TCGAATTCTTATTAATGGAGATAAACAAACAGAAATCAAAGGATTC
Found at i:39966 original size:34 final size:34
Alignment explanation
Indices: 39923--40025 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 34
39913 GCTGAACTCC
39923 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
1 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
39957 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
1 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
* **
39991 GATCATTGAAGGCGAGGTTTACATTGTTTACATG
1 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
40025 G
1 G
40026 CCCCAATAAC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (34 bp):
GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
Found at i:43336 original size:116 final size:118
Alignment explanation
Indices: 43136--43376 Score: 371
Period size: 116 Copynumber: 2.1 Consensus size: 118
43126 AAAAGAAAAG
43136 AAAAACATGATTAAATTTAATTCAAAATTTGAATGAATAAATAAGAGAAATGAAAAAAGAAGGTC
1 AAAAA-ATGATTAAATTTAATTCAAAATTTGAATGAATAAATAAGAGAAATGAAAAAAGAAGGTC
* * ** *
43201 AGAAACTAAACATTTTATAAAATTATAAAAATTAAGGAGCC-TAATTATAAATAT
65 AAAAACTAAAAAACTTATAAAATTATAAAAATCAA-GAGCCGTAATTATAAATAT
* * *
43255 AAAAAATGATTAAATTTAATTTAAAA-TTGAATGAATTAATAAGAGAAAT-AAAAAAGAGGGTCA
1 AAAAAATGATTAAATTTAATTCAAAATTTGAATGAATAAATAAGAGAAATGAAAAAAGAAGGTCA
43318 AAAACTAAAAAACTTATAAAATTATAAAAATCAAGAGCCGTAATTATAAATAT
66 AAAACTAAAAAACTTATAAAATTATAAAAATCAAGAGCCGTAATTATAAATAT
43371 AAAAAA
1 AAAAAA
43377 ATTGAGGGCC
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
115 5 0.04
116 61 0.54
117 22 0.19
118 20 0.18
119 5 0.04
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (118 bp):
AAAAAATGATTAAATTTAATTCAAAATTTGAATGAATAAATAAGAGAAATGAAAAAAGAAGGTCA
AAAACTAAAAAACTTATAAAATTATAAAAATCAAGAGCCGTAATTATAAATAT
Found at i:46649 original size:34 final size:34
Alignment explanation
Indices: 46606--46674 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
46596 GCTGAACTCC
**
46606 GATCATTGAAGGCGAGGCTTATGTTGTTTACATG
1 GATCATTGAAGGCGAGGCTTACATTGTTTACATG
46640 GATCATTGAAGGCGAGGCTTACATTGTTTACATG
1 GATCATTGAAGGCGAGGCTTACATTGTTTACATG
46674 G
1 G
46675 CCCCAATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (34 bp):
GATCATTGAAGGCGAGGCTTACATTGTTTACATG
Found at i:49142 original size:9 final size:10
Alignment explanation
Indices: 49119--49144 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
49109 AAATATATAT
49119 TTTTTGAGTA
1 TTTTTGAGTA
49129 TTTTTGAGTA
1 TTTTTGAGTA
49139 TTTTTG
1 TTTTTG
49145 GTAGGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.19, T:0.65
Consensus pattern (10 bp):
TTTTTGAGTA
Found at i:51828 original size:17 final size:17
Alignment explanation
Indices: 51806--51838 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51796 AATTAACTAC
51806 AAAAATCATATTAATTA
1 AAAAATCATATTAATTA
51823 AAAAATCATATTAATT
1 AAAAATCATATTAATT
51839 TTTTTCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATCATATTAATTA
Found at i:52734 original size:15 final size:15
Alignment explanation
Indices: 52716--52850 Score: 243
Period size: 15 Copynumber: 9.0 Consensus size: 15
52706 TAAAATAATT
*
52716 TAAAATAATTTATTT
1 TAAAATAATTTATTA
*
52731 TAAAATAATTTATTT
1 TAAAATAATTTATTA
52746 TAAAATAATTTATTA
1 TAAAATAATTTATTA
52761 TAAAATAATTTATTA
1 TAAAATAATTTATTA
52776 TAAAATAATTTATTA
1 TAAAATAATTTATTA
52791 TAAAATAATTTATTA
1 TAAAATAATTTATTA
*
52806 TAAAATAATTTATTT
1 TAAAATAATTTATTA
52821 TAAAATAATTTATTA
1 TAAAATAATTTATTA
52836 TAAAATAATTTATTA
1 TAAAATAATTTATTA
52851 GTATGGATTG
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
15 117 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAAATAATTTATTA
Found at i:52868 original size:22 final size:22
Alignment explanation
Indices: 52852--52894 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52842 AATTTATTAG
*
52852 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
52874 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
52895 TAATTTATTA
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:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:52912 original size:32 final size:32
Alignment explanation
Indices: 52874--53066 Score: 210
Period size: 32 Copynumber: 6.7 Consensus size: 32
52864 TATTTTAAAA
52874 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
52906 TATGAATTGATTTATTTT--A-AA---A-TA-
1 TATGAATTGATTTATTTTAAATAATTTATTAG
52930 TA-G-ATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
*
52960 TATGGATTGATTTATTTT-AA-AA--TA-T-G
1 TATGAATTGATTTATTTTAAATAATTTATTAG
* *
52986 ---G-ATTGGTTTATTTTAAATAATTTTTTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
53014 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
*
53046 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
53067 ATATAGATTG
Statistics
Matches: 136, Mismatches: 5, Indels: 40
0.75 0.03 0.22
Matches are distributed among these distances:
22 25 0.18
23 4 0.03
24 5 0.04
25 4 0.03
26 3 0.02
27 2 0.01
28 4 0.03
29 4 0.03
30 5 0.04
31 4 0.03
32 76 0.56
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TATGAATTGATTTATTTTAAATAATTTATTAG
Found at i:52915 original size:54 final size:54
Alignment explanation
Indices: 52828--53163 Score: 359
Period size: 54 Copynumber: 6.1 Consensus size: 54
52818 TTTTAAAATA
* *
52828 ATTTATTATAAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATT-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTG
52883 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGA-ATTG
* *
52937 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTG
* *
52991 GTTTATTTTAAATAATTTTTTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AA-AA--TA-T-G-A---ATTG
** ** *
53055 ATTTATTTTAAA-ATATAGATT-G-ATTTA-TCATTGTATTTGT---ATA-G-ATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGAATTGATT-TATTT-TAAAATATGAATTG
*
53103 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTG
53157 ATTTATT
1 ATTTATT
53164 ATTGTAGTTG
Statistics
Matches: 237, Mismatches: 20, Indels: 49
0.77 0.07 0.16
Matches are distributed among these distances:
48 21 0.09
49 3 0.01
50 8 0.03
51 4 0.02
52 3 0.01
53 3 0.01
54 143 0.60
55 9 0.04
56 4 0.02
58 3 0.01
59 1 0.00
60 1 0.00
61 4 0.02
62 8 0.03
63 3 0.01
64 19 0.08
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTG
Found at i:52950 original size:108 final size:108
Alignment explanation
Indices: 52828--53163 Score: 398
Period size: 108 Copynumber: 3.1 Consensus size: 108
52818 TTTTAAAATA
*
52828 ATTTATTATAAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTA
1 ATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTA
52893 AATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
65 AATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
* *
52937 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGGTTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAA
* *
53002 ATAATTTTTTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGG
66 ATAATTTATTAGTATGAATTGATTTATTTT-AA-AA--TA-TAG-ATTG
* * * * ***
53051 ATTGA-TTT--AT--TTTA-AAATATAGATTGATTTATCATTGTATTTGTAT-AGATTGATTTAT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT--TT-TA-AAATATGA-ATTGATTTAT
*
53109 TTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
61 TTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
53157 ATTTATT
1 ATTTATT
53164 ATTGTAGTTG
Statistics
Matches: 197, Mismatches: 18, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
106 7 0.04
107 3 0.02
108 101 0.51
109 13 0.07
110 6 0.03
111 6 0.03
112 48 0.24
113 6 0.03
114 7 0.04
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (108 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAA
ATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
Found at i:52985 original size:22 final size:22
Alignment explanation
Indices: 52960--53002 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52950 AATTTATTAG
52960 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
52982 TATGGATTGGTTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
53003 TAATTTTTTA
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:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:53075 original size:22 final size:22
Alignment explanation
Indices: 53050--53114 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 22
53040 TATTAGTATG
53050 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
***
53072 GATTGATTTATCATTGTATTTGTATA
1 GATTGATTTAT--TT-TA-AAATATA
53098 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
53115 TAATTTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
22 11 0.32
23 2 0.06
24 4 0.12
25 2 0.06
26 15 0.44
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:53231 original size:22 final size:22
Alignment explanation
Indices: 53206--53248 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53196 AATTTATTAG
*
53206 TATGAATTGATTTATTTTAAAA
1 TATGAATAGATTTATTTTAAAA
*
53228 TATGGATAGATTTATTTTAAA
1 TATGAATAGATTTATTTTAAA
53249 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (22 bp):
TATGAATAGATTTATTTTAAAA
Found at i:53243 original size:80 final size:80
Alignment explanation
Indices: 52928--53243 Score: 472
Period size: 80 Copynumber: 3.9 Consensus size: 80
52918 TATTTTAAAA
* *
52928 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGGT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
* *
52993 TTATT-TTAAATAATTTTT
66 TTATTATT--GT-A-TTTG
* *
53011 TAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATT
1 TA-TA-G-ATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATT
*
53076 GATTTATCATTGTATTTG
63 GATTTATTATTGTATTTG
53094 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
53159 TTATTATTGTAGTTG
66 TTATTATTGTATTTG
* *
53174 TATAGATTGATATATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATAGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
53239 TTATT
66 TTATT
53244 TTAAATAATT
Statistics
Matches: 218, Mismatches: 11, Indels: 11
0.91 0.05 0.05
Matches are distributed among these distances:
80 139 0.64
81 1 0.00
82 2 0.01
83 7 0.03
84 3 0.01
85 2 0.01
86 62 0.28
87 2 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (80 bp):
TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTATTTG
Found at i:55504 original size:14 final size:14
Alignment explanation
Indices: 55487--55518 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55477 CATTCATTCA
55487 TGTTCGTTTACATT
1 TGTTCGTTTACATT
*
55501 TGTTCGTTTATATT
1 TGTTCGTTTACATT
55515 TGTT
1 TGTT
55519 TATATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.62
Consensus pattern (14 bp):
TGTTCGTTTACATT
Found at i:56608 original size:4 final size:4
Alignment explanation
Indices: 56599--56624 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
56589 CTTAACTCCT
56599 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
56625 CCCTGAAGGG
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:60488 original size:24 final size:24
Alignment explanation
Indices: 60461--60506 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
60451 CGAGCAACAA
*
60461 TTCGAGAAACACCGACATCTTCGG
1 TTCGAGAAACACCGACAGCTTCGG
* *
60485 TTCGGGAAACCCCGACAGCTTC
1 TTCGAGAAACACCGACAGCTTC
60507 AGTCAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (24 bp):
TTCGAGAAACACCGACAGCTTCGG
Found at i:61087 original size:8 final size:8
Alignment explanation
Indices: 61074--61098 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61064 GGTGATCGAA
61074 ATAAAAAT
1 ATAAAAAT
61082 ATAAAAAT
1 ATAAAAAT
61090 ATAAAAAT
1 ATAAAAAT
61098 A
1 A
61099 ACTAAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:61994 original size:23 final size:24
Alignment explanation
Indices: 61956--62000 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
61946 AAACTATTAG
*
61956 TTTTCATATGTTTTAATACTTAAA
1 TTTTCATATGTTTTAAAACTTAAA
*
61980 TTTTCA-ATTTTTTAAAACTTA
1 TTTTCATATGTTTTAAAACTTA
62001 CCGTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTCATATGTTTTAAAACTTAAA
Found at i:73629 original size:25 final size:26
Alignment explanation
Indices: 73601--73656 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
73591 TCATAACAAA
*
73601 AATAATTATATTTAA-TTTAA-TTTAG
1 AATAATGAT-TTTAATTTTAATTTTAG
*
73626 AATAA-GATTTTAATTTTAATTTTAT
1 AATAATGATTTTAATTTTAATTTTAG
73651 AATAAT
1 AATAAT
73657 ATAAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 7 0.27
25 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
AATAATGATTTTAATTTTAATTTTAG
Found at i:73895 original size:20 final size:22
Alignment explanation
Indices: 73872--73913 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
73862 AATTTTAAAA
73872 TAAATC-TA-AAAATAATAATG
1 TAAATCATATAAAATAATAATG
73892 TAAATCAATATAAAATAATAAT
1 TAAATC-ATATAAAATAATAAT
73914 ATACATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATCATATAAAATAATAATG
Found at i:74877 original size:25 final size:23
Alignment explanation
Indices: 74849--74894 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
74839 TGGTATTCAT
*
74849 TTTTAATTTAATTTAAAAATTAATA
1 TTTTAA-TTAAATT-AAAATTAATA
74874 TTTTAATTAAATTAAAATTAA
1 TTTTAATTAAATTAAAATTAA
74895 GATCAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAATTAAATTAAAATTAATA
Found at i:81970 original size:31 final size:31
Alignment explanation
Indices: 81934--82019 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 31
81924 CTTCAAACAA
*
81934 TACAAAATGGTAATTAAATTTATCGAACTGT
1 TACAAAATGGTAATTAAATTTATCGAAATGT
* *
81965 TACAAAATGATTATTAAATTTTATCGAAATGT
1 TACAAAATGGTAATTAAA-TTTATCGAAATGT
*
81997 TACAAAATGGTCATTAAATTTAT
1 TACAAAATGGTAATTAAATTTAT
82020 GAATTTTTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 21 0.43
32 28 0.57
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (31 bp):
TACAAAATGGTAATTAAATTTATCGAAATGT
Found at i:83066 original size:36 final size:36
Alignment explanation
Indices: 83004--83178 Score: 214
Period size: 36 Copynumber: 4.9 Consensus size: 36
82994 TCTGTTCTAG
* * *
83004 TTGAATCGGAAGTG-CAGACGCCTCCTTCCGGTC-GAC
1 TTGAATCGGAAGTGTC-GATGCTTCCTTCCGTTCAG-C
* *
83040 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAGT
1 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
*
83076 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGT
1 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
*
83112 TTGAATCGGAAGTGTCGATGCTTTCTTCCGTTCA-C
1 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
* *
83147 TTTGAATCGGAAGTG-CGACGTTTCCTTCCGTT
1 -TTGAATCGGAAGTGTCGATGCTTCCTTCCGTT
83179 ATTCTTGTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
35 14 0.11
36 109 0.87
37 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (36 bp):
TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCAGC
Found at i:83125 original size:72 final size:71
Alignment explanation
Indices: 83004--83178 Score: 244
Period size: 72 Copynumber: 2.4 Consensus size: 71
82994 TCTGTTCTAG
* *
83004 TTGAATCGGAAGTGCAGACGCCTCCTTCCGGTCGACTTGAATCGAAAGTGTCGATGCTTCCTTCC
1 TTGAATCGGAAGTGC-GACGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTTCC
*
83069 GTTCAGT
65 GTTCACT
* * * *
83076 TTGAATCGGAAGTGTCGATGCTTCCTTCCGTTC-AGTTTGAATCGGAAGTGTCGATGCTTTCTTC
1 TTGAATCGGAAGTG-CGACGCTTCCTTCCGTTCGA-CTTGAATCGAAAGTGTCGATGCTTCCTTC
83140 CGTTCACT
64 CGTTCACT
*
83148 TTGAATCGGAAGTGCGACGTTTCCTTCCGTT
1 TTGAATCGGAAGTGCGACGCTTCCTTCCGTT
83179 ATTCTTGTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 16 0.17
72 75 0.82
73 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (71 bp):
TTGAATCGGAAGTGCGACGCTTCCTTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTTCCG
TTCACT
Found at i:83412 original size:44 final size:44
Alignment explanation
Indices: 83344--83435 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
83334 GTATAGTCTT
*
83344 CACAGCATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
1 CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
83388 CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
1 CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
83432 CACA
1 CACA
83436 GCTTACAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (44 bp):
CACAACATGATTGTAGCACCATGAACTACAGGATCGTTTGTGGA
Found at i:84898 original size:21 final size:21
Alignment explanation
Indices: 84874--84965 Score: 109
Period size: 21 Copynumber: 4.4 Consensus size: 21
84864 TTGAAAATCG
*
84874 CGTTGCGATAGTTTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
84895 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
84916 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
84934 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
84957 CGTTGCGAT
1 CGTTGCGAT
84966 TTTCCATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.03
19 4 0.07
20 9 0.15
21 38 0.64
22 4 0.07
23 2 0.03
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:84948 original size:41 final size:41
Alignment explanation
Indices: 84895--84976 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
84885 TTTACAGTGT
84895 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
84936 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
84977 ATAGTTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:85063 original size:40 final size:40
Alignment explanation
Indices: 84988--85083 Score: 133
Period size: 40 Copynumber: 2.4 Consensus size: 40
84978 TAGTTGAAAA
*
84988 TCGCATGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
1 TCGCATGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
85028 TCGCATG-GATAGTCTACAGTGTCGTTGCGATTTTTCAAAT
1 TCGCATGCGATAGTCTACAGTGTCGTTGCGA-TTTTCCATT
*
85068 TCG-TTGCGATAGTCTA
1 TCGCATGCGATAGTCTA
85084 TAGTAAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 24 0.48
40 26 0.52
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
TCGCATGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:85763 original size:20 final size:20
Alignment explanation
Indices: 85738--85810 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
85728 AGAGAAAATT
85738 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
85758 ATCGCAA--CGACACTGTACACT
1 ATCGCAACGCGA-AATGGA-A-A
*
85779 ATCGCAACGCGAAATGGATA
1 ATCGCAACGCGAAATGGAAA
85799 ATCGCAACGCGA
1 ATCGCAACGCGA
85811 TTTTCACTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.07
19 4 0.10
20 20 0.49
21 7 0.17
22 4 0.10
23 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:85794 original size:41 final size:40
Alignment explanation
Indices: 85737--85876 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 40
85727 TAGAGAAAAT
85737 TATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGTACAC
1 TATCGCAACGCGAAATGGAAAATCGCAACG-CGA-TGTACAC
* * *
85778 TATCGCAACGCGAAATGGATAATCGCAACGCGATTTTCAC
1 TATCGCAACGCGAAATGGAAAATCGCAACGCGATGTACAC
** ** * * *
85818 TATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGGAA-AATCGCAACGCGATGTAC-AC
85860 TATCGCAACGCGAAATG
1 TATCGCAACGCGAAATG
85877 CAGCGCGAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 21 0.25
41 47 0.56
42 16 0.19
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (40 bp):
TATCGCAACGCGAAATGGAAAATCGCAACGCGATGTACAC
Found at i:85842 original size:21 final size:21
Alignment explanation
Indices: 85799--85872 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
85789 GAAATGGATA
85799 ATCGCAACGCGATTTTC-ACT
1 ATCGCAACGCGATTTTCAACT
85819 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
85840 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
85861 ATCGCAACGCGA
1 ATCGCAACGCGA
85873 AATGCAGCGC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:86193 original size:38 final size:38
Alignment explanation
Indices: 86142--86219 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
86132 AAAGGTCGTT
*
86142 ATAAATACTCGAATCAAGATTGGAAAGGAGGATGGATC
1 ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
86180 ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
1 ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
86218 AT
1 AT
86220 GCATAATCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (38 bp):
ATAAATACTCGAATCAAGATGGGAAAGGAGGATGGATC
Found at i:86479 original size:29 final size:29
Alignment explanation
Indices: 86437--86495 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
86427 AGAGGAAATT
86437 CTGTTGTCATGACAATTAGAAGAATGTTA
1 CTGTTGTCATGACAATTAGAAGAATGTTA
86466 CTGTTGTCATGACAATTAGAAGAATGTTA
1 CTGTTGTCATGACAATTAGAAGAATGTTA
86495 C
1 C
86496 ATTAAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (29 bp):
CTGTTGTCATGACAATTAGAAGAATGTTA
Done.