Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001292.1 Hibiscus syriacus cultivar Beakdansim tig00002528_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: 174166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:115543 original size:19 final size:18
Alignment explanation
Indices: 115507--115555 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
115497 TAGATTTTTA
*
115507 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
115524 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
115543 ATTTTATTGTTTT
1 ATTTTATTGTTTT
115556 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:115623 original size:13 final size:13
Alignment explanation
Indices: 115595--115629 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
115585 TTTTATTATA
115595 TTATTAAATA-TT
1 TTATTAAATATTT
115607 TTATTAAATATTT
1 TTATTAAATATTT
115620 TTA-TAAATAT
1 TTATTAAATAT
115630 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:116383 original size:13 final size:13
Alignment explanation
Indices: 116365--116396 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
116355 CCATGTATAG
116365 TATATATATAAAC
1 TATATATATAAAC
116378 TATATATATAAAC
1 TATATATATAAAC
116391 TATATA
1 TATATA
116397 AAGTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:116385 original size:22 final size:22
Alignment explanation
Indices: 116349--116398 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
116339 AATATGTATG
* *
116349 TATAAACCATGTATAGTATA-TA
1 TATAAACCATATATA-TAAACTA
*
116371 TATAAACTATATATATAAACTA
1 TATAAACCATATATATAAACTA
116393 TATAAA
1 TATAAA
116399 GTAAATTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (22 bp):
TATAAACCATATATATAAACTA
Found at i:116496 original size:14 final size:14
Alignment explanation
Indices: 116471--116541 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
116461 TAGTTTATAG
*
116471 AAACCTTAAACCCT
1 AAACCATAAACCCT
*
116485 AAATCATAAACCCT
1 AAACCATAAACCCT
** **
116499 AATTC-TAAACTTT
1 AAACCATAAACCCT
*
116512 AAACCATAAACACT
1 AAACCATAAACCCT
116526 AAACCATAAACCCT
1 AAACCATAAACCCT
116540 AA
1 AA
116542 TTTAAATAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
13 9 0.20
14 37 0.80
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:116516 original size:41 final size:40
Alignment explanation
Indices: 116471--116547 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
116461 TAGTTTATAG
* * *
116471 AAACCTTAAACCCTAAATCATAAACCCTAATTCTAAACTTT
1 AAACCATAAACACTAAACCATAAACCCTAATT-TAAACTTT
116512 AAACCATAAACACTAAACCATAAACCCTAATTTAAA
1 AAACCATAAACACTAAACCATAAACCCTAATTTAAA
116548 TAGACTAGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 4 0.12
41 29 0.88
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (40 bp):
AAACCATAAACACTAAACCATAAACCCTAATTTAAACTTT
Found at i:116726 original size:14 final size:14
Alignment explanation
Indices: 116707--116753 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
116697 ATTTTGTCTT
116707 TATATAAATTAAAC
1 TATATAAATTAAAC
116721 TATAT-AATT----
1 TATATAAATTAAAC
116730 TATATAAATTAAAC
1 TATATAAATTAAAC
*
116744 TATATTAATT
1 TATATAAATT
116754 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:116732 original size:23 final size:24
Alignment explanation
Indices: 116705--116754 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
116695 TTATTTTGTC
116705 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
116728 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
116752 TTT
1 TTT
116755 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:117041 original size:16 final size:16
Alignment explanation
Indices: 117020--117106 Score: 129
Period size: 16 Copynumber: 5.4 Consensus size: 16
117010 TGGATCATTT
*
117020 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
117036 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
* *
117052 ACAGATCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
* *
117068 ATAAGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
117084 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
117100 ACAGGTC
1 ACAGGTC
117107 GGGTAATACC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:118746 original size:16 final size:15
Alignment explanation
Indices: 118720--118751 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
118710 GTATAGTATA
118720 TATATTTTTTTTTAT
1 TATATTTTTTTTTAT
118735 TATATGTTTTTTTTAT
1 TATAT-TTTTTTTTAT
118751 T
1 T
118752 TAAAGGCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TATATTTTTTTTTAT
Found at i:119633 original size:29 final size:29
Alignment explanation
Indices: 119591--119647 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
119581 AAAAAGAGGT
119591 TTGTATTTGGTAAAGTTTAAATTTCAGTG
1 TTGTATTTGGTAAAGTTTAAATTTCAGTG
* * **
119620 TTGTGTTTTGTAAAGTTTGCATTTCAGT
1 TTGTATTTGGTAAAGTTTAAATTTCAGT
119648 CATTGAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (29 bp):
TTGTATTTGGTAAAGTTTAAATTTCAGTG
Found at i:122509 original size:16 final size:17
Alignment explanation
Indices: 122488--122524 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
122478 TCCTTAAGTC
122488 TTTCATAA-TTTATTTA
1 TTTCATAATTTTATTTA
*
122504 TTTCATAATTTTATTTT
1 TTTCATAATTTTATTTA
122521 TTTC
1 TTTC
122525 TTTCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCATAATTTTATTTA
Found at i:123023 original size:2 final size:2
Alignment explanation
Indices: 123016--123074 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
123006 TGTGTTTGTT
123016 TA TA TA TA TA TA TA TA 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
123058 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
123075 TTTTTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128046 original size:16 final size:16
Alignment explanation
Indices: 128025--128057 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
128015 AAAAATGATC
128025 AAAAAAAT-GATAATCG
1 AAAAAAATCGA-AATCG
128041 AAAAAAATCGAAATCG
1 AAAAAAATCGAAATCG
128057 A
1 A
128058 TTTAGTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAAAAATCGAAATCG
Found at i:139665 original size:31 final size:31
Alignment explanation
Indices: 139629--139688 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
139619 AACTTAAAAG
139629 AGTTTTACAAT-ACTGAAATTTAAATAATTTT
1 AGTTTTACAATGA-TGAAATTTAAATAATTTT
*
139660 AGTTTTATAATGATGAAATTTAAATAATT
1 AGTTTTACAATGATGAAATTTAAATAATT
139689 CATACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATGATGAAATTTAAATAATTTT
Found at i:139737 original size:22 final size:22
Alignment explanation
Indices: 139711--139921 Score: 287
Period size: 22 Copynumber: 9.6 Consensus size: 22
139701 ATAATAAATT
*
139711 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
139733 TTTTAAAATAAATTTCTCCATA
1 TTTTAAAATAAATCAATCCATA
139755 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
139777 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
139799 TTTTAAAATAAATTTTTACATA
1 TTTTAAAATAAATCAATCCATA
*
139821 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* *** *
139843 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
139865 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
139887 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
139909 TTTTAAAATAAAT
1 TTTTAAAATAAAT
139922 TTTAAAATAG
Statistics
Matches: 162, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 162 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:139938 original size:11 final size:12
Alignment explanation
Indices: 139908--139947 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
139898 ATCAATCTAT
139908 ATTTTAAAATAA
1 ATTTTAAAATAA
*
139920 ATTTTAAAATAG
1 ATTTTAAAATAA
139932 A-TTT-AAAT-A
1 ATTTTAAAATAA
139941 ATTTTAA
1 ATTTTAA
139948 TTTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:140322 original size:14 final size:14
Alignment explanation
Indices: 140303--140329 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
140293 ATACAAATTA
140303 TAAAAATAAATTTT
1 TAAAAATAAATTTT
140317 TAAAAATAAATTT
1 TAAAAATAAATTT
140330 ATTTTTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAATAAATTTT
Found at i:150106 original size:43 final size:43
Alignment explanation
Indices: 150022--150106 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
150012 AACGATATAC
* * ** *
150022 CGCAATAGGTGTTGAGGTTTAGCGGCGTTTGTCTTAGAAACGT
1 CGCAATAGGTGTTGAGATTTAACGGCGTTTGTCCCACAAACGT
* *
150065 CGCAATCGGTGTTGAGATTTAACGGCGTTTTTCCCACAAACG
1 CGCAATAGGTGTTGAGATTTAACGGCGTTTGTCCCACAAACG
150107 CCGCTATTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
CGCAATAGGTGTTGAGATTTAACGGCGTTTGTCCCACAAACGT
Found at i:150277 original size:43 final size:43
Alignment explanation
Indices: 150102--150275 Score: 233
Period size: 43 Copynumber: 4.1 Consensus size: 43
150092 TTTTTCCCAC
** * *
150102 AAACGCCGCTATTGACTGTGTATTTAGCGGTGTTTATCTTTGA
1 AAACGCCGCTATTGACTGTGTATTTAGCGGCATTTGTCTTTTA
* * * *
150145 AAACGCCGATATTGACTGTTTATTTGGCGGTATTTGTCTTTTA
1 AAACGCCGCTATTGACTGTGTATTTAGCGGCATTTGTCTTTTA
*
150188 AAACGCCGCTATTGACTGTGTATTTGGCGGCATTTGTCTTTTA
1 AAACGCCGCTATTGACTGTGTATTTAGCGGCATTTGTCTTTTA
* * *
150231 AAACACCGCTATTGACTGTGTATTTAGTGGCATTTGT-TATTA
1 AAACGCCGCTATTGACTGTGTATTTAGCGGCATTTGTCTTTTA
150273 AAA
1 AAA
150276 ACGCTGCAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 7 0.06
43 111 0.94
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (43 bp):
AAACGCCGCTATTGACTGTGTATTTAGCGGCATTTGTCTTTTA
Found at i:153706 original size:41 final size:41
Alignment explanation
Indices: 153639--153900 Score: 183
Period size: 41 Copynumber: 6.4 Consensus size: 41
153629 CGTTTATTGA
* * * *
153639 AAAAACGCCACTATATATGAACTCTATTACGTCGTTTGTAT
1 AAAAACGCCGCTAAAGATGAACTCTATTACGGCGTTTGTAT
*
153680 AAAAACGCCGCTAAAGATGGAA-TCTATTACGGCGTTTTTAT
1 AAAAACGCCGCTAAAGAT-GAACTCTATTACGGCGTTTGTAT
* * * *
153721 CAAAACACCGCTAAAGGT-ATACTCTATTGCGGCGTTTGT-T
1 AAAAACGCCGCTAAAGATGA-ACTCTATTACGGCGTTTGTAT
* * * * *
153761 GAAAAACACCACTATAGATGAACCCTATTGCGGCGTTTGTAT
1 -AAAAACGCCGCTAAAGATGAACTCTATTACGGCGTTTGTAT
* * * * *
153803 AAAAACGCTGCTAAAG-TAGTACTCTGTTATGGCATTTGT-T
1 AAAAACGCCGCTAAAGAT-GAACTCTATTACGGCGTTTGTAT
* * * * * * ** *
153843 GGAAAATGCCACTATAGATTAACCCTATTACATCGTTTGTAC
1 -AAAAACGCCGCTAAAGATGAACTCTATTACGGCGTTTGTAT
*
153885 AAAAACACCGCTAAAG
1 AAAAACGCCGCTAAAG
153901 TTACCATTTT
Statistics
Matches: 167, Mismatches: 44, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
39 1 0.01
40 4 0.02
41 156 0.93
42 6 0.04
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGATGAACTCTATTACGGCGTTTGTAT
Found at i:153766 original size:82 final size:82
Alignment explanation
Indices: 153659--153901 Score: 224
Period size: 82 Copynumber: 3.0 Consensus size: 82
153649 CTATATATGA
* * * * * *
153659 ACTCTATTACGTCGTTTGTATAAAAACGCCGCTAAAGATGGAA-TCTATTACGGCGTTTTTATCA
1 ACTCTATTACGGCGTTTGTATAAAAACACCACTAAAGAT-GAACCCTATTACGGCGTTTGTATAA
153723 AAACACCGCTAAAGGTA-T
65 AAACACCGCTAAA-GTAGT
* * *
153741 ACTCTATTGCGGCGTTTGT-TGAAAAACACCACTATAGATGAACCCTATTGCGGCGTTTGTATAA
1 ACTCTATTACGGCGTTTGTAT-AAAAACACCACTAAAGATGAACCCTATTACGGCGTTTGTATAA
* *
153805 AAACGCTGCTAAAGTAGT
65 AAACACCGCTAAAGTAGT
* * * * ** * * ** *
153823 ACTCTGTTATGGCATTTGT-TGGAAAATGCCACTATAGATTAACCCTATTACATCGTTTGTACAA
1 ACTCTATTACGGCGTTTGTAT-AAAAACACCACTAAAGATGAACCCTATTACGGCGTTTGTATAA
153887 AAACACCGCTAAAGT
65 AAACACCGCTAAAGT
153902 TACCATTTTG
Statistics
Matches: 133, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
81 7 0.05
82 126 0.95
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (82 bp):
ACTCTATTACGGCGTTTGTATAAAAACACCACTAAAGATGAACCCTATTACGGCGTTTGTATAAA
AACACCGCTAAAGTAGT
Found at i:156352 original size:183 final size:183
Alignment explanation
Indices: 156044--156412 Score: 616
Period size: 183 Copynumber: 2.0 Consensus size: 183
156034 AAATTAAATG
*
156044 TTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
*
156109 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATT
* ** * *
156174 GGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTATATATAATATATATAATA
131 GAGTTTTAAATGGTTTGAACTGAGCCCATATGTTATATATAATATATATAAAA
156227 TTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT-
1 TTTTTTAATT-AAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTC
*
156291 ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAA
64 AGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAA
* *
156355 TTGAGTTTTAAATGGTTTGAACTGAGCTCATATGTTATATATAATATATTTAAAA
129 TTGAGTTTTAAATGGTTTGAACTGAGCCCATATGTTATATATAATATATATAAAA
156410 TTT
1 TTT
156413 AAAATTTAAT
Statistics
Matches: 174, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
183 120 0.69
184 9 0.05
185 45 0.26
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (183 bp):
TTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATT
GAGTTTTAAATGGTTTGAACTGAGCCCATATGTTATATATAATATATATAAAA
Found at i:156437 original size:9 final size:9
Alignment explanation
Indices: 156418--156451 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
156408 AATTTAAAAT
156418 TTAATTTCGG
1 TTAA-TTCGG
156428 TTAATTCGG
1 TTAATTCGG
156437 TTAATTCGG
1 TTAATTCGG
156446 TTAATT
1 TTAATT
156452 AACCGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:156543 original size:72 final size:72
Alignment explanation
Indices: 156461--156689 Score: 209
Period size: 72 Copynumber: 3.2 Consensus size: 72
156451 TAACCGAATT
156461 CGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTTAACCGTTAACCGACCGAACTAATT
1 CGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTTAACCGTTAACCGACCGAACTAATT
156526 CGATAAC
66 CGATAAC
* ******* *** * *** *
156533 CGAACCGAATTAACCG--AA-CTAATTCGGTTCGGTCGATTAACCGAATTAATTCG-GTTAATTA
1 CGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTTAACCG--TTAA-CCGACCGAACTA
* **
156594 A-CCGA-ATT
63 ATTCGATAAC
*
156602 CGAACCGAATTAACCGTTAACCGAATTCTAAAAATTTTCTTAACCGTTAACCGACCGAACTAATT
1 CGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTTAACCGTTAACCGACCGAACTAATT
156667 CGATAAC
66 CGATAAC
156674 CGAACCGAATTAACCG
1 CGAACCGAATTAACCG
156690 AACTAATTCG
Statistics
Matches: 110, Mismatches: 38, Indels: 18
0.66 0.23 0.11
Matches are distributed among these distances:
69 33 0.30
70 14 0.13
71 14 0.13
72 49 0.45
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (72 bp):
CGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTTAACCGTTAACCGACCGAACTAATT
CGATAAC
Found at i:156585 original size:22 final size:22
Alignment explanation
Indices: 156560--156601 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
156550 ACTAATTCGG
*
156560 TTCGGTCGATTAACCGAATTAA
1 TTCGGTCAATTAACCGAATTAA
*
156582 TTCGGTTAATTAACCGAATT
1 TTCGGTCAATTAACCGAATT
156602 CGAACCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (22 bp):
TTCGGTCAATTAACCGAATTAA
Found at i:156691 original size:141 final size:141
Alignment explanation
Indices: 156437--156730 Score: 579
Period size: 141 Copynumber: 2.1 Consensus size: 141
156427 GTTAATTCGG
156437 TTAATTCGGTTAATTAACCGAATTCGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTT
1 TTAATTCGGTTAATTAACCGAATTCGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTT
156502 AACCGTTAACCGACCGAACTAATTCGATAACCGAACCGAATTAACCGAACTAATTCGGTTCGGTC
66 AACCGTTAACCGACCGAACTAATTCGATAACCGAACCGAATTAACCGAACTAATTCGGTTCGGTC
156567 GATTAACCGAA
131 GATTAACCGAA
*
156578 TTAATTCGGTTAATTAACCGAATTCGAACCGAATTAACCGTTAACCGAATTCTAAAAATTTTCTT
1 TTAATTCGGTTAATTAACCGAATTCGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTT
156643 AACCGTTAACCGACCGAACTAATTCGATAACCGAACCGAATTAACCGAACTAATTCGGTTCGGTC
66 AACCGTTAACCGACCGAACTAATTCGATAACCGAACCGAATTAACCGAACTAATTCGGTTCGGTC
156708 GATTAACCGAA
131 GATTAACCGAA
156719 TTAATTCGGTTA
1 TTAATTCGGTTA
156731 TTTGAACACC
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 152 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (141 bp):
TTAATTCGGTTAATTAACCGAATTCGAACCGAATTAACCGTTAACCGAATTCTAAAAAATTTCTT
AACCGTTAACCGACCGAACTAATTCGATAACCGAACCGAATTAACCGAACTAATTCGGTTCGGTC
GATTAACCGAA
Found at i:160448 original size:2 final size:2
Alignment explanation
Indices: 160441--160468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
160431 TTGAAATGTA
160441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160469 TCATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171767 original size:17 final size:18
Alignment explanation
Indices: 171745--171778 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
171735 TCAGTCGGTC
171745 CGGTT-CGAACGGTTCAG
1 CGGTTCCGAACGGTTCAG
*
171762 CGGTTCCGACCGGTTCA
1 CGGTTCCGAACGGTTCA
171779 CTAGTAGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (18 bp):
CGGTTCCGAACGGTTCAG
Found at i:171792 original size:24 final size:24
Alignment explanation
Indices: 171760--171811 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
171750 CGAACGGTTC
*
171760 AGCGGTTCCGACCGGTTCACTAGT
1 AGCGATTCCGACCGGTTCACTAGT
171784 AGCGATTCCGACCGGTTCACTAGT
1 AGCGATTCCGACCGGTTCACTAGT
171808 AGCG
1 AGCG
171812 GTTCAACCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.23
Consensus pattern (24 bp):
AGCGATTCCGACCGGTTCACTAGT
Found at i:172071 original size:19 final size:19
Alignment explanation
Indices: 172047--172092 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
172037 AAGTAATGTG
*
172047 AATGAAATAAATGGTTTTT
1 AATGAAATAAATGATTTTT
172066 AATGAAATAAATGATTTTT
1 AATGAAATAAATGATTTTT
172085 AATGAAAT
1 AATGAAAT
172093 GTTATAGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (19 bp):
AATGAAATAAATGATTTTT
Found at i:172671 original size:21 final size:21
Alignment explanation
Indices: 172642--172688 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
172632 ATTCTGACTA
172642 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
172663 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
172684 TCGCA
1 TCGCA
172689 ATTAGAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:172709 original size:20 final size:20
Alignment explanation
Indices: 172684--172731 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
172674 TTTTCCGAAT
*
172684 TCGCAATTAGAATATGTAAA
1 TCGCAATGAGAATATGTAAA
*
172704 TCGCAATGCGAATATGTAAA
1 TCGCAATGAGAATATGTAAA
*
172724 TCACAATG
1 TCGCAATG
172732 CGATTATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (20 bp):
TCGCAATGAGAATATGTAAA
Found at i:172732 original size:20 final size:20
Alignment explanation
Indices: 172693--172739 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
172683 TTCGCAATTA
*
172693 GAATATGTAAATCGCAATGC
1 GAATATGTAAATCACAATGC
172713 GAATATGTAAATCACAATGC
1 GAATATGTAAATCACAATGC
*
172733 GATTATG
1 GAATATG
172740 ACTATCGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
GAATATGTAAATCACAATGC
Found at i:172747 original size:40 final size:40
Alignment explanation
Indices: 172703--172828 Score: 96
Period size: 40 Copynumber: 3.2 Consensus size: 40
172693 GAATATGTAA
* *
172703 ATCGCAATGCGAATATGTA-AATCACAATGCGATTATGACT
1 ATCGCAACGCGAATATG-ACAATCACAACGCGATTATGACT
* * * * *
172743 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATGACAATCACAACGCGATTATGACT
* * * * * *
172783 ATCGCAA--AGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATGACAATCACAACGCGATTATGACT
*
172821 GTCGCAAC
1 ATCGCAAC
172829 ACTGAATTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 36 0.48
39 1 0.01
40 38 0.51
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACAATCACAACGCGATTATGACT
Found at i:172754 original size:20 final size:20
Alignment explanation
Indices: 172731--172828 Score: 155
Period size: 20 Copynumber: 5.0 Consensus size: 20
172721 AAATCACAAT
*
172731 GCGATTATGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
172751 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
172771 GCGATTCTGACTATCGCAA-
1 GCGATTCTGACTATCGCAAC
*
172790 -AGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
172809 GCGATTCTGACTGTCGCAAC
1 GCGATTCTGACTATCGCAAC
172829 ACTGAATTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
18 17 0.24
20 55 0.76
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:172804 original size:38 final size:39
Alignment explanation
Indices: 172731--172829 Score: 155
Period size: 38 Copynumber: 2.5 Consensus size: 39
172721 AAATCACAAT
* *
172731 GCGATTATGACTATCGCAACGCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC-AGATTCTGACTATCGCAAC
172771 GCGATTCTGACTATCGCAA-AGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAACAGATTCTGACTATCGCAAC
*
172809 GCGATTCTGACTGTCGCAACA
1 GCGATTCTGACTATCGCAACA
172830 CTGAATTTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 36 0.65
39 1 0.02
40 18 0.33
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
GCGATTCTGACTATCGCAACAGATTCTGACTATCGCAAC
Found at i:173685 original size:23 final size:22
Alignment explanation
Indices: 173635--173687 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
173625 GGTATTCAAA
173635 ATTTGATCTTGGTCAATACCCG
1 ATTTGATCTTGGTCAATACCCG
*
173657 ACTTTGATCTTGGTCAATACTCGG
1 A-TTTGATCTTGGTCAATAC-CCG
173681 ATTTGAT
1 ATTTGAT
173688 GATGTTTCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 1 0.04
23 24 0.86
24 3 0.11
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (22 bp):
ATTTGATCTTGGTCAATACCCG
Done.