Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000682.1 Hibiscus syriacus cultivar Beakdansim tig00001330_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: 59056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2659 original size:26 final size:26
Alignment explanation
Indices: 2610--2666 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2600 GTCTCCAACG
*
2610 TTTATGTTCGTTTATGTTTGTGTTCA
1 TTTATGTTCGTTTATGTTTATGTTCA
* *
2636 TTTATGTTCGTGTTCT-TTTATGTTCG
1 TTTATGTTCGT-TTATGTTTATGTTCA
2662 TTTAT
1 TTTAT
2667 TTATTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.63
Consensus pattern (26 bp):
TTTATGTTCGTTTATGTTTATGTTCA
Found at i:2660 original size:16 final size:16
Alignment explanation
Indices: 2614--2670 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
2604 CCAACGTTTA
* *
2614 TGTTCGTTTATGTTTG
1 TGTTCATTTATGTTCG
2630 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
2646 TGTTCTTTTATGTTCG
1 TGTTCATTTATGTTCG
2662 T-TT-ATTTAT
1 TGTTCATTTAT
2671 TAAATGAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.14
15 2 0.05
16 30 0.81
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.63
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:2720 original size:31 final size:31
Alignment explanation
Indices: 2673--2751 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
2663 TTATTTATTA
* *
2673 AATGAAC-AATATGAACAAGTTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
2703 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
2734 AATGAACGAACATGAACA
1 AATGAACGAACATGAACA
2752 CAAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 7 0.15
31 39 0.85
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGCTATATTCCTT
Found at i:4131 original size:14 final size:15
Alignment explanation
Indices: 4112--4140 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4102 AACTATAAGC
4112 AAAGAT-TTAATTTT
1 AAAGATATTAATTTT
4126 AAAGATATTAATTTT
1 AAAGATATTAATTTT
4141 TATTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AAAGATATTAATTTT
Found at i:13723 original size:22 final size:25
Alignment explanation
Indices: 13696--13801 Score: 83
Period size: 19 Copynumber: 4.6 Consensus size: 25
13686 TCTATATTAA
13696 AATTTAAAATTTTATT-ATTAT-TT
1 AATTTAAAATTTTATTAATTATATT
*
13719 -ATTT---ATTTCATTAATTATATT
1 AATTTAAAATTTTATTAATTATATT
*
13740 AACTTTAAAATTTTATT-ATCAT-TT
1 AA-TTTAAAATTTTATTAATTATATT
*
13764 -ATTT---ATTTCATTAATTATATT
1 AATTTAAAATTTTATTAATTATATT
13785 AACTTTAAAATTTTATT
1 AA-TTTAAAATTTTATT
13802 TATGTTTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 25
0.67 0.06 0.27
Matches are distributed among these distances:
19 14 0.22
20 9 0.14
21 4 0.06
22 9 0.14
23 7 0.11
24 2 0.03
25 4 0.06
26 14 0.22
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTTAAAATTTTATTAATTATATT
Found at i:13739 original size:14 final size:15
Alignment explanation
Indices: 13703--13785 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 15
13693 TAAAATTTAA
* *
13703 AATTTTATTATTATT
1 AATTATATTATCATT
*
13718 TATT-TATT-TCATT
1 AATTATATTATCATT
* *
13731 AATTATATTAACTTT
1 AATTATATTATCATT
*
13746 AAAATTTTATTATCATT
1 --AATTATATTATCATT
*
13763 TATT-TATT-TCATT
1 AATTATATTATCATT
13776 AATTATATTA
1 AATTATATTA
13786 ACTTTAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
13 15 0.29
14 16 0.31
15 9 0.17
17 12 0.23
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATATTATCATT
Found at i:13750 original size:45 final size:45
Alignment explanation
Indices: 13688--13801 Score: 201
Period size: 45 Copynumber: 2.5 Consensus size: 45
13678 AGTATGTGTC
* *
13688 TATATTAAAATTTAAAATTTTATTATTATTTATTTATTTCATTAAT
1 TATATT-AACTTTAAAATTTTATTATCATTTATTTATTTCATTAAT
13734 TATATTAACTTTAAAATTTTATTATCATTTATTTATTTCATTAAT
1 TATATTAACTTTAAAATTTTATTATCATTTATTTATTTCATTAAT
13779 TATATTAACTTTAAAATTTTATT
1 TATATTAACTTTAAAATTTTATT
13802 TATGTTTATC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 60 0.91
46 6 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (45 bp):
TATATTAACTTTAAAATTTTATTATCATTTATTTATTTCATTAAT
Found at i:13752 original size:26 final size:26
Alignment explanation
Indices: 13723--13797 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 26
13713 TTATTTATTT
13723 ATTTCATTAATTATATTAACTTTAAA
1 ATTTCATTAATTATATTAACTTTAAA
* *
13749 ATTTTATT-ATCAT-TT-A-TTT---
1 ATTTCATTAATTATATTAACTTTAAA
13768 ATTTCATTAATTATATTAACTTTAAA
1 ATTTCATTAATTATATTAACTTTAAA
13794 ATTT
1 ATTT
13798 TATTTATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 7 0.18
20 4 0.11
21 2 0.05
22 4 0.11
23 4 0.11
24 2 0.05
25 4 0.11
26 11 0.29
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTCATTAATTATATTAACTTTAAA
Found at i:13791 original size:23 final size:23
Alignment explanation
Indices: 13720--13791 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
13710 TTATTATTTA
13720 TTTATTTCATTAATTATATTAAC
1 TTTATTTCATTAATTATATTAAC
* *
13743 TTTAAAATT--TT-ATTATCATTTA-
1 TTT--ATTTCATTAATTAT-ATTAAC
13765 TTTATTTCATTAATTATATTAAC
1 TTTATTTCATTAATTATATTAAC
13788 TTTA
1 TTTA
13792 AAATTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 3 0.08
22 14 0.37
23 18 0.47
25 3 0.08
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATTTCATTAATTATATTAAC
Found at i:13804 original size:23 final size:22
Alignment explanation
Indices: 13732--13801 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
13722 TATTTCATTA
13732 ATTATATTAACTTTAAAATTTT
1 ATTATATTAACTTTAAAATTTT
* *
13754 ATTATCATTTA-TTT--ATTTCATT
1 ATTAT-ATTAACTTTAAAATT--TT
13776 AATTATATTAACTTTAAAATTTT
1 -ATTATATTAACTTTAAAATTTT
13799 ATT
1 ATT
13802 TATGTTTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
20 3 0.08
22 17 0.46
23 14 0.38
25 3 0.08
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATATTAACTTTAAAATTTT
Found at i:13810 original size:45 final size:44
Alignment explanation
Indices: 13688--13815 Score: 193
Period size: 45 Copynumber: 2.8 Consensus size: 44
13678 AGTATGTGTC
*
13688 TATATTAAAATTTAAAATTTTATTATTATTTATTTATTTCATTAAT
1 TATATT-AACTTTAAAATTTTATTA-TATTTATTTATTTCATTAAT
13734 TATATTAACTTTAAAATTTTATTATCATTTATTTATTTCATTAAT
1 TATATTAACTTTAAAATTTTATTAT-ATTTATTTATTTCATTAAT
*
13779 TATATTAACTTTAAAATTTTATTTATGTTTATCTTAT
1 TATATTAACTTTAAAATTTTA-TTATATTTAT-TTAT
13816 ATAAAATATT
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
44 1 0.01
45 62 0.81
46 14 0.18
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (44 bp):
TATATTAACTTTAAAATTTTATTATATTTATTTATTTCATTAAT
Found at i:14280 original size:14 final size:14
Alignment explanation
Indices: 14261--14290 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14251 TTTAGATTTT
*
14261 TTAAAATTACATTA
1 TTAAAAATACATTA
14275 TTAAAAATACATTA
1 TTAAAAATACATTA
14289 TT
1 TT
14291 GATAATTATA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:14385 original size:14 final size:14
Alignment explanation
Indices: 14368--14488 Score: 91
Period size: 14 Copynumber: 8.6 Consensus size: 14
14358 AATTATGTGA
* *
14368 TAGGGTTTATGATT
1 TAGGGTTTAGGGTT
*
14382 TAGGTTTTAGGGTT
1 TAGGGTTTAGGGTT
*
14396 TATGGTTTAGGAG-T
1 TAGGGTTTAGG-GTT
***
14410 TAGGGTTTATACTT
1 TAGGGTTTAGGGTT
* * *
14424 TAGGATTCATGGTT
1 TAGGGTTTAGGGTT
* * *
14438 TAGGATTCATGGTT
1 TAGGGTTTAGGGTT
14452 TAGGGTTTAGGGTT
1 TAGGGTTTAGGGTT
*
14466 TATGGTTTAGGGTT
1 TAGGGTTTAGGGTT
*
14480 TATGGTTTA
1 TAGGGTTTA
14489 ATTTATACAC
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
14 87 0.99
15 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.47
Consensus pattern (14 bp):
TAGGGTTTAGGGTT
Found at i:14392 original size:21 final size:20
Alignment explanation
Indices: 14368--14488 Score: 100
Period size: 21 Copynumber: 5.8 Consensus size: 20
14358 AATTATGTGA
14368 TAGGGTTTATGATTTAGGTTT
1 TAGGGTTTATGATTTAGG-TT
* *
14389 TAGGGTTTATGGTTTAGGAGT
1 TAGGGTTTATGATTTAGG-TT
14410 TAGGGTTTAT-ACTTTAGGATT
1 TAGGGTTTATGA-TTTAGG-TT
* * * *
14431 CATGGTTTAGGATTCATGGTT
1 TAGGGTTTATGATTTA-GGTT
* *
14452 TAGGGTTTAGGGTTTATGGTT
1 TAGGGTTTATGATTTA-GGTT
*
14473 TAGGGTTTATGGTTTA
1 TAGGGTTTATGATTTA
14489 ATTTATACAC
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
21 80 0.96
22 3 0.04
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.47
Consensus pattern (20 bp):
TAGGGTTTATGATTTAGGTT
Found at i:14404 original size:7 final size:7
Alignment explanation
Indices: 14371--14488 Score: 73
Period size: 7 Copynumber: 16.9 Consensus size: 7
14361 TATGTGATAG
14371 GGTTTAT
1 GGTTTAT
*
14378 GATTTA-
1 GGTTTAT
*
14384 GGTTTTAG
1 GG-TTTAT
14392 GGTTTAT
1 GGTTTAT
14399 GGTTTA-
1 GGTTTAT
* *
14405 GGAGTTAG
1 GG-TTTAT
14413 GGTTTAT
1 GGTTTAT
**
14420 ACTTTA-
1 GGTTTAT
*
14426 GGATTCAT
1 GG-TTTAT
14434 GGTTTA-
1 GGTTTAT
*
14440 GGATTCAT
1 GG-TTTAT
*
14448 GGTTTAG
1 GGTTTAT
*
14455 GGTTTAG
1 GGTTTAT
14462 GGTTTAT
1 GGTTTAT
*
14469 GGTTTAG
1 GGTTTAT
14476 GGTTTAT
1 GGTTTAT
14483 GGTTTA
1 GGTTTA
14489 ATTTATACAC
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
6 5 0.06
7 72 0.85
8 8 0.09
ACGTcount: A:0.19, C:0.03, G:0.31, T:0.47
Consensus pattern (7 bp):
GGTTTAT
Found at i:14426 original size:35 final size:35
Alignment explanation
Indices: 14387--14476 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
14377 TGATTTAGGT
*
14387 TTTAGGGTTTATGGTTTAGGAGTT-AGGGTTTATAC
1 TTTAGGGTTTATGGTTTAGGA-TTCAGGGTTTAGAC
* * * **
14422 TTTAGGATTCATGGTTTAGGATTCATGGTTTAGGG
1 TTTAGGGTTTATGGTTTAGGATTCAGGGTTTAGAC
14457 TTTAGGGTTTATGGTTTAGG
1 TTTAGGGTTTATGGTTTAGG
14477 GTTTATGGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 2 0.04
35 44 0.96
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (35 bp):
TTTAGGGTTTATGGTTTAGGATTCAGGGTTTAGAC
Found at i:14807 original size:17 final size:18
Alignment explanation
Indices: 14768--14804 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
14758 AATGTCAAAT
14768 AATTAAAATTACAAGACAC
1 AATTAAAA-TACAAGACAC
14787 AATTAAAA-ACAAG-CAC
1 AATTAAAATACAAGACAC
14803 AA
1 AA
14805 ATTGAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
19 8 0.44
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AATTAAAATACAAGACAC
Found at i:17098 original size:11 final size:11
Alignment explanation
Indices: 17082--17186 Score: 57
Period size: 11 Copynumber: 9.2 Consensus size: 11
17072 AGAGTTTGAC
17082 CTTGAATCGAG
1 CTTGAATCGAG
*
17093 CTTGAACCGAG
1 CTTGAATCGAG
**
17104 CTCAAATTCGAG
1 CTTGAA-TCGAG
* *
17116 TTTGAGTTCGAG
1 CTTGA-ATCGAG
17128 CTTGAATCGAG
1 CTTGAATCGAG
** *
17139 CTCAAAATTGAG
1 CT-TGAATCGAG
*
17151 CTTCAATCGAG
1 CTTGAATCGAG
** *
17162 CTCAAAATTGAG
1 CT-TGAATCGAG
*
17174 CTTCAATCGAG
1 CTTGAATCGAG
17185 CT
1 CT
17187 CGAGTCTCGA
Statistics
Matches: 68, Mismatches: 22, Indels: 8
0.69 0.22 0.08
Matches are distributed among these distances:
11 37 0.54
12 31 0.46
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (11 bp):
CTTGAATCGAG
Found at i:17137 original size:23 final size:23
Alignment explanation
Indices: 17065--17138 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
17055 AGTTTCAAAT
* * *
17065 TCGAGTTAGAGTTTGACCTTGAA
1 TCGAGTTTGAGTTCGAGCTTGAA
* ** **
17088 TCGAGCTTGA-ACCGAGCTCAAA
1 TCGAGTTTGAGTTCGAGCTTGAA
17110 TTCGAGTTTGAGTTCGAGCTTGAA
1 -TCGAGTTTGAGTTCGAGCTTGAA
17134 TCGAG
1 TCGAG
17139 CTCAAAATTG
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
22 6 0.17
23 22 0.61
24 8 0.22
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (23 bp):
TCGAGTTTGAGTTCGAGCTTGAA
Found at i:17151 original size:23 final size:23
Alignment explanation
Indices: 17125--17187 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
17115 GTTTGAGTTC
*
17125 GAGCTTGAATCGAGCTCAAAATT
1 GAGCTTCAATCGAGCTCAAAATT
17148 GAGCTTCAATCGAGCTCAAAATT
1 GAGCTTCAATCGAGCTCAAAATT
17171 GAGCTTCAATCGAGCTC
1 GAGCTTCAATCGAGCTC
17188 GAGTCTCGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (23 bp):
GAGCTTCAATCGAGCTCAAAATT
Found at i:18442 original size:4 final size:4
Alignment explanation
Indices: 18433--18458 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18423 TTAGCATAAA
18433 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
18459 ATAGTATTTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:18804 original size:16 final size:15
Alignment explanation
Indices: 18779--18808 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18769 GAATTTGACC
18779 TAAATAAATTTAAAT
1 TAAATAAATTTAAAT
18794 TAAATTAAATTTAAA
1 TAAA-TAAATTTAAA
18809 GTCAACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATAAATTTAAAT
Found at i:19283 original size:2 final size:2
Alignment explanation
Indices: 19278--19311 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19268 GTATTTTTTA
19278 AT AT AT 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 AT AT AT
19312 CCTGGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21251 original size:22 final size:23
Alignment explanation
Indices: 21226--21269 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21216 GAACATTTAA
21226 TAATGCATT-CGTTTATGTTCGG
1 TAATGCATTCCGTTTATGTTCGG
*
21248 TAATGCATTCCTTTTATGTTCG
1 TAATGCATTCCGTTTATGTTCG
21270 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (23 bp):
TAATGCATTCCGTTTATGTTCGG
Found at i:21377 original size:90 final size:91
Alignment explanation
Indices: 21259--21458 Score: 321
Period size: 90 Copynumber: 2.2 Consensus size: 91
21249 AATGCATTCC
* *
21259 TTTTATGTTCGTTTATTTAATTAAATTTATATTTATCTTCGTTTATTTATATTCTCTTAA-AAAA
1 TTTTATGTTCGTTTGTTTAATTAAATTTATATTTATATTCGTTTATTTATATTCTCTTAAGAAAA
21323 TTTACTTGATTTAAAATAAAGTTACA
66 TTTACTTGATTTAAAATAAAGTTACA
* * * **
21349 TTTTATGTTAGTTTGTTTAATTAAATTTATATTTATATTCGTTTATTTTTATTCTTTTAAGAATT
1 TTTTATGTTCGTTTGTTTAATTAAATTTATATTTATATTCGTTTATTTATATTCTCTTAAGAAAA
*
21414 TTTACTTGATTTAAAATAAAGTTGCA
66 TTTACTTGATTTAAAATAAAGTTACA
21440 TTTTATGTTCGTTTGTTTA
1 TTTTATGTTCGTTTGTTTA
21459 TGTTTGTTTA
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 55 0.55
91 45 0.45
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (91 bp):
TTTTATGTTCGTTTGTTTAATTAAATTTATATTTATATTCGTTTATTTATATTCTCTTAAGAAAA
TTTACTTGATTTAAAATAAAGTTACA
Found at i:21488 original size:20 final size:20
Alignment explanation
Indices: 21449--21488 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21439 ATTTTATGTT
* **
21449 CGTTTGTTTATGTTTGTTTA
1 CGTTCGTTTATGTTCATTTA
21469 CGTTCGTTTATGTTCATTTA
1 CGTTCGTTTATGTTCATTTA
21489 TCATTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (20 bp):
CGTTCGTTTATGTTCATTTA
Found at i:22337 original size:31 final size:30
Alignment explanation
Indices: 22313--22410 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 30
22303 ATTTGAACTA
* *
22313 TAAATCTTAGATCAAATATTAATTTAACACC
1 TAAATCTTAGATAAAATATCAATTTAACA-C
* ** *
22344 TAAATTTTAGATAAAATATCAATTCGACTC
1 TAAATCTTAGATAAAATATCAATTTAACAC
* *
22374 TTGAAT-TTTGAATAAAATATCAATTTAACCAC
1 -TAAATCTTAG-ATAAAATATCAATTTAA-CAC
22406 -AAATC
1 TAAATC
22411 CTATTAAACT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
30 7 0.14
31 42 0.82
32 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAATCTTAGATAAAATATCAATTTAACAC
Found at i:22592 original size:2 final size:2
Alignment explanation
Indices: 22585--22630 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
22575 AAGCTAATTG
22585 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
22627 AT AT
1 AT AT
22631 TGAGCAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24980 original size:24 final size:24
Alignment explanation
Indices: 24946--25052 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
24936 AAACGGAGAT
* *
24946 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
24970 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
24994 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
25018 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
25042 ATCAGAAATCA
1 ATCAGAAATCA
25053 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:25052 original size:48 final size:48
Alignment explanation
Indices: 24946--25054 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
24936 AAACGGAGAT
* * * * *
24946 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
24994 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
25042 ATCAGAAATCAGA
1 ATCAGAAATCAGA
25055 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:26199 original size:18 final size:18
Alignment explanation
Indices: 26178--26213 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26168 CTTCCATCCG
*
26178 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
26196 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
26214 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:27533 original size:7 final size:7
Alignment explanation
Indices: 27521--27552 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
27511 TGGTCAACTC
27521 CGGTCAA
1 CGGTCAA
27528 CGGTCAA
1 CGGTCAA
27535 CGGGTCAA
1 C-GGTCAA
27543 CGGTCAA
1 CGGTCAA
27550 CGG
1 CGG
27553 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:27542 original size:8 final size:8
Alignment explanation
Indices: 27522--27599 Score: 64
Period size: 8 Copynumber: 10.5 Consensus size: 8
27512 GGTCAACTCC
27522 GGTCAAC-
1 GGTCAACG
27529 GGTCAACG
1 GGTCAACG
27537 GGTCAAC-
1 GGTCAACG
27544 GGTCAACG
1 GGTCAACG
27552 GGT---CG
1 GGTCAACG
27557 GGTCAACG
1 GGTCAACG
**
27565 GGTCGGGTCG
1 GGTC--AACG
27575 GGTCAACG
1 GGTCAACG
27583 GGT---CG
1 GGTCAACG
27588 GGTCAACG
1 GGTCAACG
27596 GGTC
1 GGTC
27600 GGTTCGGGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
5 10 0.18
7 14 0.25
8 27 0.47
10 6 0.11
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:27542 original size:15 final size:15
Alignment explanation
Indices: 27522--27568 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
27512 GGTCAACTCC
27522 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
27537 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
27552 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
27565 GGTC
1 GGTC
27569 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:27573 original size:18 final size:18
Alignment explanation
Indices: 27550--27626 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
27540 CAACGGTCAA
27550 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
27568 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
27581 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
27599 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
27617 CGGGTCGGGT
1 CGGGTCGGGT
27627 TGTGACCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 13 0.25
18 38 0.75
ACGTcount: A:0.12, C:0.21, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:27582 original size:31 final size:31
Alignment explanation
Indices: 27544--27622 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
27534 ACGGGTCAAC
27544 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
27575 GGTCAACGGGTCGGGTCAACGGGTCGGTTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
27606 GGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
27623 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:27621 original size:13 final size:13
Alignment explanation
Indices: 27529--27601 Score: 74
Period size: 13 Copynumber: 5.1 Consensus size: 13
27519 TCCGGTCAAC
*
27529 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
27544 GGTCAACGGGTCG
1 GGTCAACGGGTCG
27557 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
27575 GGTCAACGGGTCG
1 GGTCAACGGGTCG
27588 GGTCAACGGGTCG
1 GGTCAACGGGTCG
27601 G
1 G
27602 TTCGGGTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
13 27 0.52
15 12 0.23
18 13 0.25
ACGTcount: A:0.16, C:0.23, G:0.45, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:30344 original size:18 final size:18
Alignment explanation
Indices: 30321--30355 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
30311 ATTAAAAAAC
30321 TCGAAATATGTTAATTAT
1 TCGAAATATGTTAATTAT
30339 TCGAAATATGTTAATTA
1 TCGAAATATGTTAATTA
30356 CAATACTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
TCGAAATATGTTAATTAT
Found at i:33951 original size:14 final size:14
Alignment explanation
Indices: 33932--33958 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33922 AACAGACTAT
33932 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
33946 TCTGTTTTCTACA
1 TCTGTTTTCTACA
33959 AATATACCCA
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:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (14 bp):
TCTGTTTTCTACAG
Found at i:36372 original size:3 final size:3
Alignment explanation
Indices: 36364--36389 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36354 TATGATCACC
36364 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
36390 AGAAAGCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:38830 original size:17 final size:17
Alignment explanation
Indices: 38784--38854 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
38774 ATGTTAAATA
*
38784 AAATAAAA-AAAATATT
1 AAATAAAATAAAATAAT
*
38800 AAA-AAATATTAAATACAT
1 AAATAAA-ATAAAATA-AT
*
38818 AAATGAAA-AAAATAGA-
1 AAATAAAATAAAATA-AT
38834 AAATAAAATAAAATAAT
1 AAATAAAATAAAATAAT
38851 AAAT
1 AAAT
38855 CGAATGGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
15 3 0.07
16 12 0.28
17 21 0.49
18 5 0.12
19 2 0.05
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (17 bp):
AAATAAAATAAAATAAT
Found at i:38837 original size:31 final size:31
Alignment explanation
Indices: 38768--38849 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
38758 TCTAAAAGAG
* *
38768 TAGAAAATGTTAAATAAAATAAAAAAAATAT
1 TAGAAAATATTAAATAAAATAAAAAAAATAA
* *
38799 TAAAAAATATTAAAT-ACATAAATGAAAAA-AA
1 TAGAAAATATTAAATAAAATAAA--AAAAATAA
38830 TAGAAAATA--AAATAAAATAA
1 TAGAAAATATTAAATAAAATAA
38850 TAAATCGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
29 4 0.10
30 11 0.26
31 22 0.52
32 5 0.12
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (31 bp):
TAGAAAATATTAAATAAAATAAAAAAAATAA
Found at i:38848 original size:34 final size:33
Alignment explanation
Indices: 38784--38854 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
38774 ATGTTAAATA
* * *
38784 AAATAAAAAAAATATTAAAAAATATTAAATACAT
1 AAATAAAAAAAATATGAAAAAAAATAAAATA-AT
*
38818 AAATGAAAAAAATA-GAAAATAAAATAAAATAAT
1 AAATAAAAAAAATATGAAAA-AAAATAAAATAAT
38851 AAAT
1 AAAT
38855 CGAATGGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 10 0.31
34 22 0.69
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (33 bp):
AAATAAAAAAAATATGAAAAAAAATAAAATAAT
Found at i:38900 original size:36 final size:38
Alignment explanation
Indices: 38824--38903 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 38
38814 ACATAAATGA
* *
38824 AAAAAATAGAAAATAAAATAAAATAATAAATCGAATGG
1 AAAAAATAGAAAATAAAATAAAATAACAAATCGAAAGG
* *
38862 AAAAAGTA-AAAATAATA-AAAATAAACAAATC-AAAGG
1 AAAAAATAGAAAATAAAATAAAAT-AACAAATCGAAAGG
38898 AAAAAA
1 AAAAAA
38904 ACAAACTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
36 14 0.39
37 15 0.42
38 7 0.19
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (38 bp):
AAAAAATAGAAAATAAAATAAAATAACAAATCGAAAGG
Found at i:39720 original size:8 final size:8
Alignment explanation
Indices: 39707--39733 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
39697 AAATTCCCCG
39707 CCTCTGTT
1 CCTCTGTT
39715 CCTCTGTT
1 CCTCTGTT
39723 CCTCTGTT
1 CCTCTGTT
39731 CCT
1 CCT
39734 TGCATGCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.11, T:0.48
Consensus pattern (8 bp):
CCTCTGTT
Found at i:40968 original size:106 final size:106
Alignment explanation
Indices: 40783--41132 Score: 612
Period size: 106 Copynumber: 3.3 Consensus size: 106
40773 TATTGTTCCA
* *
40783 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGGTTTGGGAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAA
*
40847 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
40889 AGTCCAATATCCTTCGCAGTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAAC
40954 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
40995 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAAC
41060 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
41101 AGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATT
41133 TGACTCTAAA
Statistics
Matches: 235, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
106 235 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:42951 original size:26 final size:25
Alignment explanation
Indices: 42897--42948 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
42887 TTGATGAGAC
*
42897 ATGTGAATGTAAAAAAAGGAAAACTA
1 ATGTGAATGTAAAAAAA-GAAAACAA
*
42923 ATGTGAATGTAAAGAAAA-ATAACAA
1 ATGTGAATGTAAA-AAAAGAAAACAA
42948 A
1 A
42949 ATGCACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 13 0.57
27 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (25 bp):
ATGTGAATGTAAAAAAAGAAAACAA
Found at i:44721 original size:37 final size:36
Alignment explanation
Indices: 44647--44721 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
44637 AATGTTAAAT
** * *
44647 AAAATAAAAAAAATATTAAAAAATATTAAATACATA
1 AAAATAAAAAAAATAGAAAAAAAAATAAAATACATA
44683 AAAATGAAAAAAAATAGAAAATAAAAATAAAATA-ATA
1 AAAAT-AAAAAAAATAGAAAA-AAAAATAAAATACATA
44720 AA
1 AA
44722 TCGAATGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 5 0.15
37 18 0.55
38 10 0.30
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (36 bp):
AAAATAAAAAAAATAGAAAAAAAAATAAAATACATA
Found at i:44722 original size:18 final size:16
Alignment explanation
Indices: 44643--44722 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 16
44633 AGAAAATGTT
44643 AAAT-AAAATAAAAAA
1 AAATAAAAATAAAAAA
* *
44658 AATATTAAAAAATATTAAAT
1 AA-A-T-AAAAATA-AAAAA
* *
44678 ACATAAAAATGAAAAA
1 AAATAAAAATAAAAAA
44694 AAATAGAAAATAAAAATA
1 AAATA-AAAATAAAAA-A
44712 AAATAATAAAT
1 AAATAA-AAAT
44723 CGAATGGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.04
16 8 0.16
17 17 0.35
18 11 0.22
19 7 0.14
20 4 0.08
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAAAAA
Found at i:49533 original size:42 final size:42
Alignment explanation
Indices: 49474--49558 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
49464 CTAGATTGTA
*
49474 TGGACCATCAAAACGTGGTGGCCTGGTGTCTTCTTCTTCTTC
1 TGGACCATCAAAACGTGGTAGCCTGGTGTCTTCTTCTTCTTC
*
49516 TGGACCATCAAAACGTGGTAGCCTTGTGTCTTCTTCTTCTTC
1 TGGACCATCAAAACGTGGTAGCCTGGTGTCTTCTTCTTCTTC
49558 T
1 T
49559 TCTAGCACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (42 bp):
TGGACCATCAAAACGTGGTAGCCTGGTGTCTTCTTCTTCTTC
Found at i:49700 original size:117 final size:116
Alignment explanation
Indices: 49553--50506 Score: 766
Period size: 117 Copynumber: 8.1 Consensus size: 116
49543 GTCTTCTTCT
* * * * *
49553 TCTTCTTCTAGCACTGGCATTAGAAGAACTGAAG-CAAAGCCTTTTTCAAATAGAACCAAACAAG
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCCATTTT-AAAAAGAACCAAACAAG
* * * *
49617 AAACAGAGTTGCCGGTGCAAATTCCTAGTGCTAAAGTATCAAGGCTGGTGTCA
65 AAACAGAGTTGCCAGTGCAAATTCC-AGCGCTCAAGTAACAAGGCTGGTGTCA
* * * * * * *
49670 TTTTCTTCTATCTGTAGCATTATAAAAACTGAAG-CTAAGCCAAATTTAAAAAGAACCACACAAG
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCC-ATTTTAAAAAGAACCAAACAAG
* * * *
49734 AAAAAGGGTTACCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCA
65 AAACAGAGTTGCCAGTGCAAATT-CCAGCGCTCAAGTAACAAGGCTGGTGTCA
** * * * * * *
49787 TCTTCTTCTAGCTCTAGCATTAGAAAAACACAAGCCAAGGCAAGTTTAAAAGGAACCAGACAAGA
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCCATTTTAAAAAGAACCAAACAAGA
* * ** * *
49852 AAAAGAGTTGCCAGTGAAAATTTCCAGAACTCGAGTAACAAGACTGGTGTCA
66 AACAGAGTTGCCAGTGCAAA-TTCCAGCGCTCAAGTAACAAGGCTGGTGTCA
* *
49904 TCTTCTTCTAGCTCCAGC-TCTAGCACTAGCAATACTGAAGTC-AAGCCATCTTCAAAAAGAACC
1 TCTTCTTCTAGCTCTAGCAT-TAG-A--A--AA-ACTGAAGTCAAAGCCAT-TTTAAAAAGAACC
* * * *
49967 AATCATAG-AACAGAGCTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAA-GATCGGTGTCA
58 AAACA-AGAAACAGAGTTGCCAGTGCAAATT-CCAGCGCTCAAGTAACAAGGCT-GGTGTCA
* * * * * * *
50027 TCTTCTTCTAGCTCTAGAACTAGTAAAACAGAAG-CCAAGCCATCTTCAAAAAGAACCAATCAAG
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCCAT-TTTAAAAAGAACCAAACAAG
* * * * * * *
50091 AAAAAGAGCTT-CCAGAGCAAATTTCCAGCGCTCAAGTAAGAAGACTAGCGTTA
65 AAACAGAG-TTGCCAGTGCAAA-TTCCAGCGCTCAAGTAACAAGGCTGGTGTCA
* * * * *
50144 TCTTCTGCTAGCTCAAGCATTAAAAAAACAGAAGTCAAA-CCAAGTTTAAAAAGAACCAAACAAG
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCC-ATTTTAAAAAGAACCAAACAAG
* * * * * * * *
50208 AAACCGAGCTT-CCAGAGAAAATTTGCAACGCTCAAGTAACAAGGTTAGTTTCA
65 AAACAGAG-TTGCCAGTGCAAA-TTCCAGCGCTCAAGTAACAAGGCTGGTGTCA
* * * *
50261 TCTTCTTCTAGCTCTAGCATTAAAAAAACTGAGGTC-AAGCCATCTTCAAAAGGAACCAATA-AA
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCCAT-TTTAAAAAGAACCAA-ACAA
* * * *
50324 GAAACAGAGTTTCCTGTGCAAATTCCCAACGCTCAAGTAACAAGCCTGGTGTCA
64 GAAACAGAGTTGCCAGTGCAAATT-CCAGCGCTCAAGTAACAAGGCTGGTGTCA
* *
50378 TCTTCTTCTAGCTCTAGC-TCTAGCATTATCAATACTGAAGACAAA-TCATATTTAAAAAGAACC
1 TCTTCTTCTAGCTCTAGCAT-TAG-A--A--AA-ACTGAAGTCAAAGCCAT-TTTAAAAAGAACC
* * * * *
50441 AATCAAGAAACAAAGTTGCCAGTGCAAATTCCCAGCGATCAAGAAACAAGGTTGGTGTCA
58 AAACAAGAAACAGAGTTGCCAGTGCAAATT-CCAGCGCTCAAGTAACAAGGCTGGTGTCA
50501 TCTTCT
1 TCTTCT
50507 AGCTCCTGTA
Statistics
Matches: 673, Mismatches: 127, Indels: 68
0.78 0.15 0.08
Matches are distributed among these distances:
116 12 0.02
117 464 0.69
118 24 0.04
120 3 0.00
122 11 0.02
123 155 0.23
124 4 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (116 bp):
TCTTCTTCTAGCTCTAGCATTAGAAAAACTGAAGTCAAAGCCATTTTAAAAAGAACCAAACAAGA
AACAGAGTTGCCAGTGCAAATTCCAGCGCTCAAGTAACAAGGCTGGTGTCA
Found at i:50009 original size:240 final size:237
Alignment explanation
Indices: 49553--50534 Score: 901
Period size: 234 Copynumber: 4.2 Consensus size: 237
49543 GTCTTCTTCT
* * * * * * * *
49553 TCTTCTTCTAGCACTGGCATTAGAAGAACTGAAGCAAAGCCTTTTTCAAATA-GAACCAAACAAG
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACAGAAGCCAAGCCATCTTCAAA-AGGAACCAATCAAG
* * * * * * * *
49617 AAACAGAGTTGCCGGTGCAAA-TTCCTAGTGCTAAAGTATCAAGGCTGGTGTCATTTTCTTCTAT
65 AAAAAGAGTT-CCAGTGCAAATTTCC-AGAGCTCAAGTAACAAGACTGGTGTCATCTTCTTCTAG
** * * * *
49681 CTGTAGCAT-T---ATA-AAAACTGAAG-CTAAGCCAAATTTAAAAAGAACCACA-CAAGAAAAA
128 CTCAAGC-TCTAGCATACAATACTGAAGTC-AAACCATATTTAAAAAGAACCA-ATCAAGAAACA
* * * *
49739 GGGTTACCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCA
190 GAGCTGCCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGTTAGTGTCA
* * ** *
49787 TCTTCTTCTAGCTCTAGCATTAGAAAAACACAAGCCAAGGCAAGTTTAAAAGGAACCAGA-CAAG
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACAGAAGCCAAGCCATCTTCAAAAGGAACCA-ATCAAG
* * *
49851 AAAAAGAGTTGCCAGTGAAAATTTCCAGAACTCGAGTAACAAGACTGGTGTCATCTTCTTCTAGC
65 AAAAAGAGTT-CCAGTGCAAATTTCCAGAGCTCAAGTAACAAGACTGGTGTCATCTTCTTCTAGC
* * * *
49916 TCCAGCTCTAGCACTAGCAATACTGAAGTCAAGCCATCTTCAAAAAGAACCAATCATAG-AACAG
129 TCAAGCTCTAGCA-TA-CAATACTGAAGTCAAACCATATTTAAAAAGAACCAATCA-AGAAACAG
* * **
49980 AGCTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAAGATCGGTGTCA
191 AGCTGCCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGTTAGTGTCA
* * * *
50027 TCTTCTTCTAGCTCTAGAACTAGTAAAACAGAAGCCAAGCCATCTTCAAAAAGAACCAATCAAGA
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACAGAAGCCAAGCCATCTTCAAAAGGAACCAATCAAGA
* * * * * * *
50092 AAAAGAGCTTCCAGAGCAAATTTCCAGCGCTCAAGTAAGAAGACTAGCGTTATCTTCTGCTAGCT
66 AAAAGAG-TTCCAGTGCAAATTTCCAGAGCTCAAGTAACAAGACTGGTGTCATCTTCTTCTAGCT
* * * *
50157 CAAGCAT-TA--A-A-AAAACAGAAGTCAAACCA-AGTTTAAAAAGAACCAAACAAGAAACCGAG
130 CAAGC-TCTAGCATACAATACTGAAGTCAAACCATA-TTTAAAAAGAACCAATCAAGAAACAGAG
* * * ** * *
50216 CTTCCAGAGAAAATTTGCAACGCTCAAGTAACAAGGTTAGTTTCA
193 CTGCCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGTTAGTGTCA
* * * * *
50261 TCTTCTTCTAGCTCTAGCATTAAAAAAACTGAGGTCAAGCCATCTTCAAAAGGAACCAATAAAGA
1 TCTTCTTCTAGCTCTAGCATTAGAAAAACAGAAGCCAAGCCATCTTCAAAAGGAACCAATCAAGA
* * * *
50326 AACAGAGTTTCCTGTGCAAATTCCCA-ACGCTCAAGTAACAAGCCTGGTGTCATCTTCTTCTAGC
66 AAAAGAG-TTCCAGTGCAAATTTCCAGA-GCTCAAGTAACAAGACTGGTGTCATCTTCTTCTAGC
* * * *
50390 TCTAGCTCTAGCATTATCAATACTGAAGACAAATCATATTTAAAAAGAACCAATCAAGAAACAAA
129 TCAAGCTCTAGCA-TA-CAATACTGAAGTCAAACCATATTTAAAAAGAACCAATCAAGAAACAGA
* * * *
50455 GTTGCCAGTGCAAATTCCCAGCGATCAAGAAACAAGGTTGGTGTCA
192 GCTGCCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGTTAGTGTCA
*
50501 ---TCTTCTAGCTCCT-GTATTAGAAAAACAGAAGCCA
1 TCTTCTTCTAGCT-CTAGCATTAGAAAAACAGAAGCCA
50535 CGACATGTTC
Statistics
Matches: 600, Mismatches: 120, Indels: 53
0.78 0.16 0.07
Matches are distributed among these distances:
233 5 0.01
234 288 0.48
235 5 0.01
236 2 0.00
237 27 0.05
238 6 0.01
239 2 0.00
240 258 0.43
241 7 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (237 bp):
TCTTCTTCTAGCTCTAGCATTAGAAAAACAGAAGCCAAGCCATCTTCAAAAGGAACCAATCAAGA
AAAAGAGTTCCAGTGCAAATTTCCAGAGCTCAAGTAACAAGACTGGTGTCATCTTCTTCTAGCTC
AAGCTCTAGCATACAATACTGAAGTCAAACCATATTTAAAAAGAACCAATCAAGAAACAGAGCTG
CCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGTTAGTGTCA
Found at i:50506 original size:357 final size:349
Alignment explanation
Indices: 49553--50506 Score: 977
Period size: 357 Copynumber: 2.7 Consensus size: 349
49543 GTCTTCTTCT
* * * * * *
49553 TCTTCTTCTAGCACTGGCATTAGAAGAACTGAAG-CAAAGCCTTTTTCAAATAGAACCAA-ACAA
1 TCTTCTTCTAGCTCTAGCATTAAAAAAACTGAAGTC-AAGCCATCTTCAAA-AGAACCAATA-AA
* * * * *
49616 GAAACAGAGTTGCCGGTGCAAATTCCTAGTGCTAAAGTATCAAGGCTGGTGTCATTTTCTTCTA-
63 GAAACAGAGTTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAA-GCTGGTGTCATCTTCTTCTAG
* *
49680 -TCT-G-TAGCATTATAAAAACTGAAGCTAAGCCAAATTTAAAAAGAACCACA-CAAGAAAAAGG
127 CTCTAGCTAGCATTAT--AAACTGAAGC-AAGCCATATTTAAAAAGAACCA-ATCAAGAAAAAGA
* *
49741 GTTACCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCATCTTCTTCTAGCTCTAGCA
188 GTT-CCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCATCTTCTGCTAGCTCAAGCA
* ** * * *
49806 TTAGAAAAACACAAGCCAAGGCAAGTTTAAAAGGAACCAGACAAGAAAAAGAGTTGCCAGTGAAA
252 TTAAAAAAACACAAGCCAAACCAAGTTTAAAAAGAACCAAACAAGAAAAAGAGTTGCCAGAGAAA
* *
49871 ATTTCCAGAACTCGAGTAACAAGACTGGTGTCA
317 ATTTCCAGAACTCAAGTAACAAGACTAGTGTCA
* *
49904 TCTTCTTCTAGCTCCAGC-TCTAGCACTAGCAATACTGAAGTCAAGCCATCTTCAAAAAGAACCA
1 TCTTCTTCTAGCTCTAGCAT-TA--A--A--AAAACTGAAGTCAAGCCATCTTC-AAAAGAACCA
* * *
49968 ATCATAG-AACAGAGCTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAAGATCGGTGTCATCTTC
58 AT-AAAGAAACAGAGTTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAAGCT-GGTGTCATCTTC
* * *
50032 TTCTAGCTCTAGAACTAG---TA-AAACAGAAGCCAAGCCATCTTCAAAAAGAACCAATCAAGAA
121 TTCTAGCTCTAG--CTAGCATTATAAACTGAAG-CAAGCCATATTTAAAAAGAACCAATCAAGAA
* * * * * *
50093 AAAGAGCTTCCAGAGCAAATTTCCAGCGCTCAAGTAAGAAGACTAGCGTTATCTTCTGCTAGCTC
183 AAAGAG-TTCCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCATCTTCTGCTAGCTC
* * **
50158 AAGCATTAAAAAAACAGAAGTCAAACCAAGTTTAAAAAGAACCAAACAAGAAACCGAGCTT-CCA
247 AAGCATTAAAAAAACACAAGCCAAACCAAGTTTAAAAAGAACCAAACAAGAAAAAGAG-TTGCCA
* * ** *
50222 GAGAAAATTTGCA-ACGCTCAAGTAACAAGGTTAGTTTCA
311 GAGAAAATTTCCAGA-ACTCAAGTAACAAGACTAGTGTCA
*
50261 TCTTCTTCTAGCTCTAGCATTAAAAAAACTGAGGTCAAGCCATCTTCAAAAGGAACCAATAAAGA
1 TCTTCTTCTAGCTCTAGCATTAAAAAAACTGAAGTCAAGCCATCTTCAAAA-GAACCAATAAAGA
* * **
50326 AACAGAGTTTCCTGTGCAAATTCCCAACGCTCAAGTAACAAGCCTGGTGTCATCTTCTTCTAGCT
65 AACAGAGTTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAAG-CTGGTGTCATCTTCTTCTAGCT
**
50391 CTAGCTCTAGCATTATCAATACTGAAGACAAATCATATTTAAAAAGAACCAATCAAGAAACAA-A
129 CTAG--CTAGCATTAT-AA-ACTGAAG-CAAGCCATATTTAAAAAGAACCAATCAAGAAA-AAGA
* * * *
50455 GTTGCCAGTGCAAATTCCCAGCGATCAAGAAACAAGGTTGGTGTCATCTTCT
188 GTT-CCAGTGCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCATCTTCT
50507 AGCTCCTGTA
Statistics
Matches: 494, Mismatches: 74, Indels: 64
0.78 0.12 0.10
Matches are distributed among these distances:
350 8 0.02
351 111 0.22
352 1 0.00
353 1 0.00
354 2 0.00
355 2 0.00
356 8 0.02
357 337 0.68
358 14 0.03
359 4 0.01
360 3 0.01
363 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (349 bp):
TCTTCTTCTAGCTCTAGCATTAAAAAAACTGAAGTCAAGCCATCTTCAAAAGAACCAATAAAGAA
ACAGAGTTGCCAGTGCAAATTCCCAGTGCTCAAGTAACAAGCTGGTGTCATCTTCTTCTAGCTCT
AGCTAGCATTATAAACTGAAGCAAGCCATATTTAAAAAGAACCAATCAAGAAAAAGAGTTCCAGT
GCAAATTCCCAGCGCTCAAGTAACAAGGCTAGTGTCATCTTCTGCTAGCTCAAGCATTAAAAAAA
CACAAGCCAAACCAAGTTTAAAAAGAACCAAACAAGAAAAAGAGTTGCCAGAGAAAATTTCCAGA
ACTCAAGTAACAAGACTAGTGTCA
Done.