Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006412.1 Hibiscus syriacus cultivar Beakdansim tig00015462_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: 84157
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3556 original size:30 final size:30
Alignment explanation
Indices: 3499--3566 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
3489 ATGCATAAGT
* **
3499 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
3529 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
3559 ATATGCAT
1 AAATGCAT
3567 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:11710 original size:39 final size:40
Alignment explanation
Indices: 11656--11813 Score: 115
Period size: 39 Copynumber: 3.8 Consensus size: 40
11646 CATCAGCTGG
* * *
11656 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC-G-A
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA-CCCCAGAA
*
11695 CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCAGATAA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCAG--AA
* *
11737 CCAG-TCGTCCTCATCACGTAGGAACCATGTTATCACCCCATAGATAA
1 CCAGATC-TCCTCATCACGTAGGAGCC--G-TGTCACCCC--AG--AA
* * *
11784 CCAGCTGTCCTCATCACGTAGGAACCGTGT
1 CCAGATCTCCTCATCACGTAGGAGCCGTGT
11814 TATCACATCT
Statistics
Matches: 99, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
38 4 0.04
39 29 0.29
41 2 0.02
42 22 0.22
44 3 0.03
45 9 0.09
47 29 0.29
48 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCAGAA
Found at i:11794 original size:47 final size:45
Alignment explanation
Indices: 11724--11819 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 45
11714 AGGAGTCGTG
11724 TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
1 TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
*
11769 TCACCCCATAGATAACCAG-CTGTCCTCATCACGTAGGAACCGTGTTA
1 TCACCCC--AGATAACCAGTC-GTCCTCATCACGTAGGAACCATGTTA
11816 TCAC
1 TCAC
11820 ATCTCCTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 7 0.15
46 1 0.02
47 39 0.83
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (45 bp):
TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
Found at i:11949 original size:43 final size:40
Alignment explanation
Indices: 11838--11954 Score: 103
Period size: 43 Copynumber: 2.9 Consensus size: 40
11828 AAGATGGCCA
*
11838 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCACGACC
* * * * *
11878 AGATA-TCCTCATCATGTAGGATCCGTGTCA-CCCTTAGACGACC
1 AGA-ACTCTTCATCACGTATGAGCAGTGTCATCCC----ACGACC
* *
11921 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
11955 CAACAACCAG
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
39 3 0.05
40 23 0.40
41 1 0.02
42 1 0.02
43 26 0.46
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCACGACC
Found at i:12113 original size:10 final size:10
Alignment explanation
Indices: 12098--12123 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12088 CCGGGTCTTT
12098 TTATTTATTA
1 TTATTTATTA
12108 TTATTTATTA
1 TTATTTATTA
12118 TTATTT
1 TTATTT
12124 TATTTAATTT
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATTTATTA
Found at i:12337 original size:16 final size:16
Alignment explanation
Indices: 12316--12348 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12306 TAATAAATAG
12316 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
12332 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
12348 A
1 A
12349 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:12429 original size:10 final size:10
Alignment explanation
Indices: 12414--12488 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
12404 CATTTAATAA
12414 ATAAACGAAC
1 ATAAACGAAC
12424 ATAAACGAAC
1 ATAAACGAAC
12434 ---AA-GAAC
1 ATAAACGAAC
12440 ATAAACGAAC
1 ATAAACGAAC
** *
12450 ACGAAC-ATAA
1 ATAAACGA-AC
12460 ATGAACACGAAC
1 AT-AA-ACGAAC
12472 ATAAACGAAC
1 ATAAACGAAC
12482 ATAAACG
1 ATAAACG
12489 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
9 3 0.06
10 33 0.65
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:12441 original size:16 final size:16
Alignment explanation
Indices: 12418--12482 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
12408 TAATAAATAA
12418 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
12434 AAGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
12450 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
12466 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
12482 A
1 A
12483 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:13252 original size:14 final size:14
Alignment explanation
Indices: 13235--13290 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
13225 AATGAACATA
13235 AACGAACATAATCG
1 AACGAACATAATCG
13249 AACGAACAT-A---
1 AACGAACATAATCG
* *
13259 AACAAACATAACCG
1 AACGAACATAATCG
13273 AACGAACATAATCG
1 AACGAACATAATCG
13287 AACG
1 AACG
13291 TTCACGAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:13255 original size:24 final size:24
Alignment explanation
Indices: 13215--13289 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
13205 GATTGAGTTA
*
13215 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
13239 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
13263 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
13287 AAC
1 AAC
13290 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:25847 original size:3 final size:3
Alignment explanation
Indices: 25841--25875 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
25831 AATAATAGTA
*
25841 ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
25876 AATCAACAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:32660 original size:3 final size:3
Alignment explanation
Indices: 32652--32696 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
32642 TCTTTAAAAT
32652 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
32697 GAATTGGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:36879 original size:22 final size:23
Alignment explanation
Indices: 36842--36888 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
36832 AACCCTAAAT
36842 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
36865 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
36887 AA
1 AA
36889 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:42858 original size:15 final size:15
Alignment explanation
Indices: 42838--42867 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42828 TACATTTTAG
42838 ATGCAACTGTTTGAA
1 ATGCAACTGTTTGAA
42853 ATGCAACTGTTTGAA
1 ATGCAACTGTTTGAA
42868 GTCGAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
ATGCAACTGTTTGAA
Found at i:44786 original size:16 final size:18
Alignment explanation
Indices: 44755--44787 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44745 AAGCTTGAGA
44755 AAACTTAAAGAGAATTAG
1 AAACTTAAAGAGAATTAG
44773 AAAC-TAAA-AGAATTA
1 AAACTTAAAGAGAATTA
44788 CAAGTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (18 bp):
AAACTTAAAGAGAATTAG
Found at i:45267 original size:20 final size:20
Alignment explanation
Indices: 45254--45291 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
45244 CGATACTGAA
45254 GGAGTAGCATCGATACCAAG
1 GGAGTAGCATCGATACCAAG
*
45274 GGAGTAGCATTGATACCA
1 GGAGTAGCATCGATACCA
45292 TGGGTATCGA
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:0.34, C:0.18, G:0.29, T:0.18
Consensus pattern (20 bp):
GGAGTAGCATCGATACCAAG
Found at i:46018 original size:23 final size:23
Alignment explanation
Indices: 45992--46040 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
45982 CGGTTTTTTA
*
45992 GGACAAATCTACGTGGTCCTTCG
1 GGACAAATCTACGCGGTCCTTCG
**
46015 GGACATTTCTACGCGGTCCTTCG
1 GGACAAATCTACGCGGTCCTTCG
46038 GGA
1 GGA
46041 TAATACTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (23 bp):
GGACAAATCTACGCGGTCCTTCG
Found at i:46058 original size:23 final size:23
Alignment explanation
Indices: 46004--46084 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 23
45994 ACAAATCTAC
* * * *
46004 GTGGTCCTTCGGGACATTTCTAC
1 GTGGCCCTTCGGGACAATACTAT
* * *
46027 GCGGTCCTTCGGGATAATACTAT
1 GTGGCCCTTCGGGACAATACTAT
* * *
46050 GTGGCCCTTTGGGACATTTCTAT
1 GTGGCCCTTCGGGACAATACTAT
*
46073 GTGGCACTTCGG
1 GTGGCCCTTCGG
46085 TGCAATTTCT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.33
Consensus pattern (23 bp):
GTGGCCCTTCGGGACAATACTAT
Found at i:50232 original size:19 final size:19
Alignment explanation
Indices: 50199--50247 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
50189 AGAATGTTTA
**
50199 AAAGTATCGGTACTTATAT
1 AAAGTATCGAAACTTATAT
*
50218 AAAGTATCGAAACTTTTAT
1 AAAGTATCGAAACTTATAT
*
50237 AGGAGTATCGA
1 A-AAGTATCGA
50248 TACTCTTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (19 bp):
AAAGTATCGAAACTTATAT
Found at i:54378 original size:21 final size:21
Alignment explanation
Indices: 54352--54396 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54342 GATTTCTGGG
* *
54352 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
54373 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
54394 CAA
1 CAA
54397 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:58681 original size:21 final size:21
Alignment explanation
Indices: 58655--58699 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
58645 GATTTCTGGG
* *
58655 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
58676 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
58697 CAA
1 CAA
58700 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:60120 original size:22 final size:22
Alignment explanation
Indices: 60094--60136 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
60084 TAATAAATTA
60094 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
60116 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
60137 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:60145 original size:22 final size:22
Alignment explanation
Indices: 60096--60144 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
60086 ATAAATTATT
**
60096 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
60118 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
60141 TAAA
1 TAAA
60145 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:60148 original size:54 final size:54
Alignment explanation
Indices: 60084--60663 Score: 409
Period size: 54 Copynumber: 10.6 Consensus size: 54
60074 ACAACTACAA
60084 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
60138 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * * ** **
60195 TTTTAAAATAAAT-CAATACATACTAATAAAT-TATTTAAAATAAAGAAATCCATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
** * ** * ** ** * *
60249 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATTCATATTT
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATA--C
* * * * * *
60306 TAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAATTCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** * *
60358 TAATAAATTATTTAAAATAAATCAATCCATACAACTCCAATAATAAATCAAACCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * *
60418 TAAAATAAATCAATCTATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
60470 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
60524 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
60578 TAATAAATTATTTAAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTT-AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
60633 TAATAAATTATTTAAAATAAATCAAACCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
60664 CAACTACAAT
Statistics
Matches: 428, Mismatches: 63, Indels: 70
0.76 0.11 0.12
Matches are distributed among these distances:
49 12 0.03
50 26 0.06
52 2 0.00
53 3 0.01
54 232 0.54
55 60 0.14
56 8 0.02
57 17 0.04
58 38 0.09
59 5 0.01
60 4 0.01
61 2 0.00
62 13 0.03
63 6 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:60154 original size:32 final size:32
Alignment explanation
Indices: 60116--60820 Score: 426
Period size: 32 Copynumber: 25.4 Consensus size: 32
60106 CAATCCATAT
60116 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
60148 TTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
60178 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60196 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
60228 TTTAAAATAAA-GAA---AT-C-CAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60250 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60282 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60304 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60336 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
60368 TTTAAAATAAATCAATCCATAC-AACTCCA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
60398 --T--AATAAATCAAACCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60423 -------TAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60448 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60480 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60502 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60534 TTTAAAATAAATC-A---AT-C-AAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60556 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60588 TTTAAAAATAAATCAAT-C---C--AT--A-T-
1 TTT-AAAATAAATCAATCCATACTAATAAATTA
60611 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
60643 TTTAAAATAAATCAAACCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
60673 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60691 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
60723 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60745 TTTAAAATAAATCAATCCATACTAATATATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60777 TTTAAAATAAATCAATCCATACTAGTAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
60809 TTTTAAATAAAT
1 TTTAAAATAAAT
60821 TATTTTAAAA
Statistics
Matches: 540, Mismatches: 28, Indels: 210
0.69 0.04 0.27
Matches are distributed among these distances:
20 2 0.00
22 124 0.23
23 20 0.04
24 10 0.02
25 8 0.01
26 62 0.11
27 6 0.01
28 23 0.04
29 2 0.00
30 9 0.02
31 17 0.03
32 244 0.45
33 13 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:60254 original size:22 final size:22
Alignment explanation
Indices: 60228--60270 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
60218 TAATAAATTA
60228 TTTAAAATAAAGAAATCCATAT
1 TTTAAAATAAAGAAATCCATAT
**
60250 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAAGAAATCCATA
60271 CTAATAAATT
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:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAAGAAATCCATAT
Found at i:60308 original size:22 final size:22
Alignment explanation
Indices: 60282--60324 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
60272 TAATAAATTA
60282 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
60304 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
60325 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:60333 original size:22 final size:22
Alignment explanation
Indices: 60284--60332 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
60274 ATAAATTATT
**
60284 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
60306 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
60329 TAAA
1 TAAA
60333 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:60340 original size:86 final size:86
Alignment explanation
Indices: 60250--60609 Score: 391
Period size: 86 Copynumber: 4.2 Consensus size: 86
60240 AAATCCATAT
* *
60250 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA-TTTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTATTAAAATAA
*
60314 ATCAATTCATACTAATAAATTA
66 ATCAAATCATACTAATAAA-TA
* * * **
60336 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTCCAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTATTAAAATAA
* *
60400 AT-AAATCAAAC-CAT--AT-
66 ATCAAATCATACTAATAAATA
* * * *
60416 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTATTAAAATAA
* * * **
60481 TTAAAAT-A-AATCAATCCATA
66 ATCAAATCATACT-AATAAATA
* * *
60501 TTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCAATA-TTTTAAAATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTATTAAAATA
60565 AATC-AATCCATACTAATAAATTA
65 AATCAAAT-CATACTAATAAA-TA
60588 TTTAAAAATAAATCAATCCATA
1 TTT-AAAATAAATCAATCCATA
60610 TTTTAAAATA
Statistics
Matches: 228, Mismatches: 32, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
80 57 0.25
81 3 0.01
82 7 0.03
84 7 0.03
85 15 0.07
86 114 0.50
87 25 0.11
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (86 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTATTAAAATAA
ATCAAATCATACTAATAAATA
Found at i:60344 original size:14 final size:14
Alignment explanation
Indices: 60327--60379 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
60317 AATTCATACT
60327 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
60341 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
60359 AATAAATTATTTAA
1 AATAAATTATTTAA
60373 AATAAAT
1 AATAAAT
60380 CAATCCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:60531 original size:22 final size:22
Alignment explanation
Indices: 60482--60530 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
60472 ATAAATTATT
**
60482 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
60504 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
60527 TAAA
1 TAAA
60531 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:60585 original size:22 final size:22
Alignment explanation
Indices: 60536--60584 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
60526 ATAAATTATT
**
60536 TAAAATAAATCAATCAATATTT
1 TAAAATAAATCAATCAATATAA
*
60558 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCAATA-TAA
60581 TAAA
1 TAAA
60585 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:60617 original size:22 final size:22
Alignment explanation
Indices: 60586--60631 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
60576 ACTAATAAAT
60586 TATTTAAAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATCCA
*
60608 TATTTTAAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATCCA
60630 TA
1 TA
60632 CTAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
TATTTAAAAATAAATCAATCCA
Found at i:60640 original size:22 final size:22
Alignment explanation
Indices: 60592--60639 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
60582 AAATTATTTA
**
60592 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATAAT
60614 AAAATAAATCAATCCATACTAAT
1 AAAATAAATCAATCCATA-TAAT
60637 AAA
1 AAA
60640 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAAATCAATCCATATAAT
Found at i:60720 original size:22 final size:22
Alignment explanation
Indices: 60645--60719 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
60635 ATAAATTATT
* *
60645 TAAAATAAATCAAACCATACAA
1 TAAAATAAATCAATCCATATAA
**
60667 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
60693 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
60716 TAAA
1 TAAA
60720 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:60743 original size:54 final size:54
Alignment explanation
Indices: 60674--60797 Score: 239
Period size: 54 Copynumber: 2.3 Consensus size: 54
60664 CAACTACAAT
60674 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
60728 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATATATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
60782 AATAAATCAATCCATA
1 AATAAATCAATCCATA
60798 CTAGTAAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:60749 original size:22 final size:22
Alignment explanation
Indices: 60723--60765 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
60713 TAATAAATTA
60723 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
60745 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
60766 CTAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:60833 original size:15 final size:15
Alignment explanation
Indices: 60802--60992 Score: 249
Period size: 15 Copynumber: 12.3 Consensus size: 15
60792 TCCATACTAG
60802 TAAATTATTTT-AAA
1 TAAATTATTTTAAAA
60816 TAAATTATTTTAAAATAAA
1 TAAATTATTTT---A-AAA
* *
60835 TAAATCCATATTTTATAC
1 TAAAT---TATTTTAAAA
*
60853 TAATTTATTTTAAAA
1 TAAATTATTTTAAAA
*
60868 TAAATTATTTTATAA
1 TAAATTATTTTAAAA
60883 TAAATTATTTTAAAA
1 TAAATTATTTTAAAA
*
60898 TAAATTATTTTATAA
1 TAAATTATTTTAAAA
60913 TAAATTATTTTAAAA
1 TAAATTATTTTAAAA
*
60928 TAAATTATTTTATAA
1 TAAATTATTTTAAAA
*
60943 TAAATTATTTTATAA
1 TAAATTATTTTAAAA
60958 TAAATTATTTTAAAA
1 TAAATTATTTTAAAA
60973 TAAATTATTTTAAAA
1 TAAATTATTTTAAAA
60988 TAAAT
1 TAAAT
60993 AACCTTATTA
Statistics
Matches: 157, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
14 11 0.07
15 126 0.80
18 5 0.03
19 9 0.06
22 6 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATTATTTTAAAA
Found at i:60879 original size:30 final size:30
Alignment explanation
Indices: 60802--60992 Score: 276
Period size: 30 Copynumber: 6.2 Consensus size: 30
60792 TCCATACTAG
60802 TAAATTATTTTA-AATAAATTATTTTAAAATAAA
1 TAAATTATTTTATAATAAATTATTTT---A-AAA
* *
60835 TAAATCCATATTTTATACTAATTTATTTTAAAA
1 TAAAT---TATTTTATAATAAATTATTTTAAAA
60868 TAAATTATTTTATAATAAATTATTTTAAAA
1 TAAATTATTTTATAATAAATTATTTTAAAA
60898 TAAATTATTTTATAATAAATTATTTTAAAA
1 TAAATTATTTTATAATAAATTATTTTAAAA
*
60928 TAAATTATTTTATAATAAATTATTTTATAA
1 TAAATTATTTTATAATAAATTATTTTAAAA
*
60958 TAAATTATTTTAAAATAAATTATTTTAAAA
1 TAAATTATTTTATAATAAATTATTTTAAAA
60988 TAAAT
1 TAAAT
60993 AACCTTATTA
Statistics
Matches: 147, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
30 115 0.78
33 13 0.09
34 1 0.01
36 7 0.05
37 11 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAATTATTTTATAATAAATTATTTTAAAA
Found at i:62741 original size:27 final size:27
Alignment explanation
Indices: 62679--62747 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 27
62669 TTTCATTGTT
62679 TTTTATTTTCTCTTCATACTTCAGAAG
1 TTTTATTTTCTCTTCATACTTCAGAAG
*
62706 TTTGATTTTCTCTTCATACTT-ATGATAGG
1 TTTTATTTTCTCTTCATACTTCA-GA-A-G
62735 TTTT-TTTTCTCTT
1 TTTTATTTTCTCTT
62748 TACAAACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 22 0.59
28 10 0.27
29 4 0.11
ACGTcount: A:0.17, C:0.16, G:0.09, T:0.58
Consensus pattern (27 bp):
TTTTATTTTCTCTTCATACTTCAGAAG
Found at i:64530 original size:10 final size:10
Alignment explanation
Indices: 64512--64541 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
64502 GAATAATTTG
*
64512 CTTCTATCGA
1 CTTCCATCGA
64522 CTTCCATCGA
1 CTTCCATCGA
64532 CTTCCATCGA
1 CTTCCATCGA
64542 ACGTAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.37, G:0.10, T:0.33
Consensus pattern (10 bp):
CTTCCATCGA
Found at i:67723 original size:18 final size:17
Alignment explanation
Indices: 67662--67729 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 17
67652 AAGTTGTGTA
67662 ATAATTTTAGAATA-AAT
1 ATAATTTTA-AATATAAT
*
67679 ATATATTTTAATATTTAAAT
1 ATA-ATTTTAA-ATAT-AAT
*
67699 TTAATTTTAAAGTATAAT
1 ATAATTTTAAA-TATAAT
67717 ATAATTTTTAAAT
1 ATAA-TTTTAAAT
67730 TTTGTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
17 4 0.10
18 16 0.39
19 16 0.39
20 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATAATTTTAAATATAAT
Found at i:75652 original size:20 final size:19
Alignment explanation
Indices: 75611--75654 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
75601 TGGTAATTTT
*
75611 AAAATTTATTTTTTTATAA
1 AAAATTTATTTGTTTATAA
75630 AAAATATTATTATGTTTATAA
1 AAAAT-TTATT-TGTTTATAA
75651 AAAA
1 AAAA
75655 ACCTAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 5 0.23
21 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAATTTATTTGTTTATAA
Found at i:81365 original size:14 final size:14
Alignment explanation
Indices: 81346--81375 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
81336 AAACGATAGT
*
81346 TTGAAATACATTTG
1 TTGAAAGACATTTG
81360 TTGAAAGACATTTG
1 TTGAAAGACATTTG
81374 TT
1 TT
81376 TCGTTTTACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (14 bp):
TTGAAAGACATTTG
Found at i:82037 original size:2 final size:2
Alignment explanation
Indices: 82032--82072 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
82022 ATAAACAATT
82032 TA TA TA TA 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 TA TA TA TA T
82073 TTATTTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82934 original size:2 final size:2
Alignment explanation
Indices: 82927--82951 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
82917 CTCAGGGTAA
82927 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
82952 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.