Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 125 of 199
Found at i:37984293 original size:100 final size:105
Alignment explanation
Indices: 37984168--37984354 Score: 258
Period size: 100 Copynumber: 1.8 Consensus size: 105
37984158 TTTCCTTTAC
* * * * * *
37984168 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GT-TC-TCATAT-A-GGTGCCAATGCC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCGTAATATAATGATGCCAATGCC
37984228 ATGTCCCAGACATGGTCTTACGGAGGACCACTCATCTCGG
66 ATGTCCCAGACATGGTCTTACGGAGGACCACTCATCTCGG
* *
37984268 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTAATCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCGTAATAT-AATGATGCCAATGC
37984333 CATGTCCCAGACATGGTCTTAC
65 CATGTCCCAGACATGGTCTTAC
37984355 ATAGGATCTC
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 33 0.45
101 1 0.01
102 2 0.03
103 4 0.05
105 1 0.01
106 32 0.44
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (105 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCGTAATATAATGATGCCAATGCC
ATGTCCCAGACATGGTCTTACGGAGGACCACTCATCTCGG
Found at i:37996744 original size:40 final size:39
Alignment explanation
Indices: 37996694--37996959 Score: 264
Period size: 40 Copynumber: 6.7 Consensus size: 39
37996684 TACCGGGTAT
* * *
37996694 AAACAAGGGCATGTATGTGCAATCAGGCGTACCGAAGTAC
1 AAACAGGGGCACGAATGTGCAATCAGG-GTACCGAAGTAC
* *
37996734 AAATAGGGGCACGTATGTGCAATCATGGGTACCGAAGTAC
1 AAACAGGGGCACGAATGTGCAATCA-GGGTACCGAAGTAC
** * * *
37996774 AAACAGGGGCATAAATGTCCAAACAGGGGTACCAAAGTAC
1 AAACAGGGGCACGAATGTGCAATCA-GGGTACCGAAGTAC
* * * *
37996814 AAAAAGGGGTATGAATGTGCAATCAAGGGTACTGAAGTAC
1 AAACAGGGGCACGAATGTGCAATC-AGGGTACCGAAGTAC
* * * *
37996854 AAACAGGGACACGAATGTGCAATTAGGGGTACCAAATTAC
1 AAACAGGGGCACGAATGTGCAATCA-GGGTACCGAAGTAC
*
37996894 AAACAGGGGCAC-ATATGCGCAATCAGTGGTACCGAAGTAC
1 AAACAGGGGCACGA-ATGTGCAATCAG-GGTACCGAAGTAC
* * *
37996934 AAACAAGGGTACGAATGTGTAATCAG
1 AAACAGGGGCACGAATGTGCAATCAG
37996960 ACAATAGTTA
Statistics
Matches: 185, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.02
40 178 0.96
41 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (39 bp):
AAACAGGGGCACGAATGTGCAATCAGGGTACCGAAGTAC
Found at i:37996816 original size:20 final size:20
Alignment explanation
Indices: 37996760--37996902 Score: 81
Period size: 20 Copynumber: 7.2 Consensus size: 20
37996750 GTGCAATCAT
*
37996760 GGGTACCGAAGTACAAACAG
1 GGGTACCAAAGTACAAACAG
* * *
37996780 GGGCA-TAAATGTCCAAACAG
1 GGGTACCAAA-GTACAAACAG
*
37996800 GGGTACCAAAGTACAAAAAG
1 GGGTACCAAAGTACAAACAG
** * * * *
37996820 GGGTATGAATGTGCAATCAA
1 GGGTACCAAAGTACAAACAG
**
37996840 GGGTACTGAAGTACAAACAG
1 GGGTACCAAAGTACAAACAG
** * * * **
37996860 GGACACGAATGTGCAATTAG
1 GGGTACCAAAGTACAAACAG
*
37996880 GGGTACCAAATTACAAACAG
1 GGGTACCAAAGTACAAACAG
37996900 GGG
1 GGG
37996903 CACATATGCG
Statistics
Matches: 83, Mismatches: 38, Indels: 4
0.66 0.30 0.03
Matches are distributed among these distances:
19 2 0.02
20 78 0.94
21 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.15
Consensus pattern (20 bp):
GGGTACCAAAGTACAAACAG
Found at i:37996925 original size:120 final size:121
Alignment explanation
Indices: 37996694--37996958 Score: 322
Period size: 120 Copynumber: 2.2 Consensus size: 121
37996684 TACCGGGTAT
* * * * * *
37996694 AAACAAGGGCATGTATGTGCAATC-AGGCGTACCGAAGTACAAATAGGGGCACGTATGTGCAATC
1 AAACAAGGGTACGAATGTGCAATCAAGGCGTACCGAAGTACAAACAGGGACACGAATGTGCAATC
* * *
37996758 ATGGGTACCGAAGTACAAACAGGGGCATAAATGTCCAAACAGGGGTACCAAAGTAC
66 AGGGGTACCAAAGTACAAACAGGGGCACAAATGTCCAAACAGGGGTACCAAAGTAC
* *
37996814 AAA-AAGGGGTATGAATGTGCAATCAAGG-GTACTGAAGTACAAACAGGGACACGAATGTGCAAT
1 AAACAA-GGGTACGAATGTGCAATCAAGGCGTACCGAAGTACAAACAGGGACACGAATGTGCAAT
* * * * * *
37996877 TAGGGGTACCAAATTACAAACAGGGGCACATATG-CGCAATCAGTGGTACCGAAGTAC
65 CAGGGGTACCAAAGTACAAACAGGGGCACAAATGTC-CAAACAGGGGTACCAAAGTAC
*
37996934 AAACAAGGGTACGAATGTGTAATCA
1 AAACAAGGGTACGAATGTGCAATCA
37996959 GACAATAGTT
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
119 3 0.02
120 116 0.94
121 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (121 bp):
AAACAAGGGTACGAATGTGCAATCAAGGCGTACCGAAGTACAAACAGGGACACGAATGTGCAATC
AGGGGTACCAAAGTACAAACAGGGGCACAAATGTCCAAACAGGGGTACCAAAGTAC
Found at i:38013416 original size:34 final size:34
Alignment explanation
Indices: 38013372--38013439 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
38013362 GCACAGTTGA
* *
38013372 ATAGTCTTGGGACTAAGCCCTTTTCAGTATCAGTG
1 ATAGTCTTGGGACTAAGCCCATCTCAGTA-CAGTG
* *
38013407 ATAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ATAGTCTTGGGACTAAGCCCATCTCAGTACAGTG
38013440 TCAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (34 bp):
ATAGTCTTGGGACTAAGCCCATCTCAGTACAGTG
Found at i:38013979 original size:16 final size:16
Alignment explanation
Indices: 38013958--38013993 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
38013948 GGCCTTGGCC
38013958 ATGTGATCCATTTTTA
1 ATGTGATCCATTTTTA
38013974 ATGTGATCCATTTTTA
1 ATGTGATCCATTTTTA
38013990 ATGT
1 ATGT
38013994 AACCCATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (16 bp):
ATGTGATCCATTTTTA
Found at i:38014000 original size:16 final size:16
Alignment explanation
Indices: 38013965--38014000 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38013955 GCCATGTGAT
* *
38013965 CCATTTTTAATGTGAT
1 CCATTTTTAATGTAAC
38013981 CCATTTTTAATGTAAC
1 CCATTTTTAATGTAAC
38013997 CCAT
1 CCAT
38014001 GCTAGCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (16 bp):
CCATTTTTAATGTAAC
Found at i:38016037 original size:19 final size:19
Alignment explanation
Indices: 38016013--38016050 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
38016003 TATGTCGAAA
38016013 TAACAAACTAGTTAACCTT
1 TAACAAACTAGTTAACCTT
38016032 TAACAAACTAGTTAACCTT
1 TAACAAACTAGTTAACCTT
38016051 AATTGCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (19 bp):
TAACAAACTAGTTAACCTT
Found at i:38021940 original size:15 final size:15
Alignment explanation
Indices: 38021920--38021950 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38021910 AAAACTTAAC
38021920 ATGTAGAGCTATCAG
1 ATGTAGAGCTATCAG
38021935 ATGTAGAGCTATCAG
1 ATGTAGAGCTATCAG
38021950 A
1 A
38021951 CTTACTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGTAGAGCTATCAG
Found at i:38023316 original size:18 final size:18
Alignment explanation
Indices: 38023293--38023330 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38023283 ATTGCGACAA
38023293 TTATTTAATTGAAA-TAAT
1 TTATTT-ATTGAAATTAAT
*
38023311 TTATTTATTTAAATTAAT
1 TTATTTATTGAAATTAAT
38023329 TT
1 TT
38023331 TAAGATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATTTATTGAAATTAAT
Found at i:38032163 original size:14 final size:15
Alignment explanation
Indices: 38032135--38032186 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
38032125 AGAACAGTTT
38032135 AATAATTTTTAATAA
1 AATAATTTTTAATAA
38032150 AATAATTTTT-ATAA
1 AATAATTTTTAATAA
*
38032164 AATGAA-TTTTAATTA
1 AAT-AATTTTTAATAA
*
38032179 AATCATTT
1 AATAATTT
38032187 AATAAGACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
AATAATTTTTAATAA
Found at i:38033439 original size:20 final size:20
Alignment explanation
Indices: 38033414--38033456 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38033404 TTATGTAAAC
* * *
38033414 AAATGTTTTAATTTTTTTTT
1 AAATGTTCTAATGTGTTTTT
38033434 AAATGTTCTAATGTGTTTTT
1 AAATGTTCTAATGTGTTTTT
38033454 AAA
1 AAA
38033457 ATGTGTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (20 bp):
AAATGTTCTAATGTGTTTTT
Found at i:38033458 original size:21 final size:20
Alignment explanation
Indices: 38033414--38033460 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
38033404 TTATGTAAAC
* * *
38033414 AAATGTTTTAATTTTTTTTT
1 AAATGTTCTAATTGTTTTTA
38033434 AAATGTTCTAATGTGTTTTTA
1 AAATGTTCTAAT-TGTTTTTA
38033455 AAATGT
1 AAATGT
38033461 GTTGTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (20 bp):
AAATGTTCTAATTGTTTTTA
Found at i:38033654 original size:29 final size:26
Alignment explanation
Indices: 38033621--38033677 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
38033611 AGAGGTTAAT
38033621 TTATAAATT-TAATGATATTTTAGAATTTC
1 TTATAAATTAT-AT-ATATTTT--AATTTC
38033650 TTATAAATTATATATATTTTAATTTC
1 TTATAAATTATATATATTTTAATTTC
38033676 TT
1 TT
38033678 TATGGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.30
28 7 0.26
29 11 0.41
30 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TTATAAATTATATATATTTTAATTTC
Found at i:38033664 original size:26 final size:29
Alignment explanation
Indices: 38033621--38033677 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 29
38033611 AGAGGTTAAT
38033621 TTATAAATTTAATGATAT-TTTAGAATTTC
1 TTATAAATTTAATGATATATTT-GAATTTC
*
38033650 TTATAAA-TT-AT-ATATATTTTAATTTC
1 TTATAAATTTAATGATATATTTGAATTTC
38033676 TT
1 TT
38033678 TATGGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.46
27 5 0.19
28 2 0.08
29 7 0.27
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (29 bp):
TTATAAATTTAATGATATATTTGAATTTC
Found at i:38034806 original size:93 final size:93
Alignment explanation
Indices: 38034624--38034809 Score: 211
Period size: 93 Copynumber: 2.0 Consensus size: 93
38034614 ACGATAAGAG
* * *
38034624 TATTGGTGGATGAACCATCCGTCTATGCAGATAAAAGTTGCAAATATGTTGTGAATGAACCACTG
1 TATTGGTGGATAAACCATCCATCGATGCAGATAAAAGTTGCAAATATGTTGTGAATGAACCACTG
* **
38034689 ATCGTGCAGATAAACTGATGACTAAAAT
66 ATCGAGCAGATAAACTGACAACTAAAAT
* *
38034717 TATTGGTGGATAAACCATCCAT-GAGTGCAGATAAAAGTTG-ATTAATATGTTGTGGATGAATCA
1 TATTGGTGGATAAACCATCCATCGA-TGCAGATAAAAGTTGCA--AATATGTTGTGAATGAACCA
*
38034780 CT-AGTCGAGTAGAT-AACT-ACCAACTAAAAT
63 CTGA-TCGAGCAGATAAACTGA-CAACTAAAAT
38034810 AAGTTGTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
92 3 0.04
93 48 0.61
94 28 0.35
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (93 bp):
TATTGGTGGATAAACCATCCATCGATGCAGATAAAAGTTGCAAATATGTTGTGAATGAACCACTG
ATCGAGCAGATAAACTGACAACTAAAAT
Found at i:38035560 original size:18 final size:19
Alignment explanation
Indices: 38035537--38035578 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
38035527 AAACCAAAAG
38035537 TAAATCAA-TTTTACATTC
1 TAAATCAATTTTTACATTC
*
38035555 TAAATCAATTTTTGCATTC
1 TAAATCAATTTTTACATTC
38035574 TAAAT
1 TAAAT
38035579 GTTGGAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (19 bp):
TAAATCAATTTTTACATTC
Found at i:38036709 original size:96 final size:97
Alignment explanation
Indices: 38036545--38036738 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 97
38036535 CTTAAATTTT
38036545 GTAAATGGCTTGGAATATAAGTAAATGTTGCTTGACTTAAAAGTTAGTAACATATAATAGCTTGT
1 GTAAATGGCTTGGAATATAAGTAAATGTTGCTTGACTTAAAAGTTAGTAACATATAATAGCTTGT
38036610 AATGATGTTTAAGCTAATGTATCTAAT-GTAA
66 AATGATGTTTAAGCTAATGTATCTAATGGTAA
38036641 GTAAATGGCTTGGAATATAAGTAAATGTTGCTTGACTTAAAAGTTAGTAACATATAATAGCTTGT
1 GTAAATGGCTTGGAATATAAGTAAATGTTGCTTGACTTAAAAGTTAGTAACATATAATAGCTTGT
38036706 AATGATGTTTAAGCTAATGTATCTAATGGTAA
66 AATGATGTTTAAGCTAATGTATCTAATGGTAA
38036738 G
1 G
38036739 GTTAGAGTAA
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 92 0.95
97 5 0.05
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (97 bp):
GTAAATGGCTTGGAATATAAGTAAATGTTGCTTGACTTAAAAGTTAGTAACATATAATAGCTTGT
AATGATGTTTAAGCTAATGTATCTAATGGTAA
Found at i:38040602 original size:23 final size:23
Alignment explanation
Indices: 38040559--38040622 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
38040549 AACAGAAATA
*
38040559 ATTTTT-TAAAAACTTTGAGATTTT
1 ATTTTTATATAAA-TTT-AGATTTT
38040583 ATTTTTATATAAATTTAGATTTT
1 ATTTTTATATAAATTTAGATTTT
* **
38040606 ATCTTTACGTAAATTTA
1 ATTTTTATATAAATTTA
38040623 AATTAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.60
24 9 0.26
25 5 0.14
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (23 bp):
ATTTTTATATAAATTTAGATTTT
Found at i:38041780 original size:18 final size:18
Alignment explanation
Indices: 38041757--38041792 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38041747 ATGATAAAAA
*
38041757 ATAAAAAATTTAAAATTT
1 ATAAAAAAATTAAAATTT
*
38041775 ATAAAAAAATTATAATTT
1 ATAAAAAAATTAAAATTT
38041793 TTACACAAAT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAAAATTAAAATTT
Found at i:38045318 original size:2 final size:2
Alignment explanation
Indices: 38045311--38045347 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38045301 TATAGTAGTA
38045311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38045348 AGTAAACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38045710 original size:23 final size:24
Alignment explanation
Indices: 38045656--38045712 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
38045646 ATAGAAATGT
38045656 ATAAAATAAAATAATAATACCTAA
1 ATAAAATAAAATAATAATACCTAA
* *
38045680 A-AACATAAAATAAT-AT-CTTATA
1 ATAAAATAAAATAATAATACCTA-A
38045702 ATAAAATAAAA
1 ATAAAATAAAA
38045713 GGATCTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.11
22 4 0.14
23 20 0.71
24 1 0.04
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (24 bp):
ATAAAATAAAATAATAATACCTAA
Found at i:38045783 original size:21 final size:21
Alignment explanation
Indices: 38045746--38045797 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
38045736 GGAAAAATAA
38045746 AATAA-AATAAAAAGACTAAT
1 AATAATAATAAAAAGACTAAT
* *
38045766 AATAATAATATAATGACTAAT
1 AATAATAATAAAAAGACTAAT
*
38045787 AAAAATAATAA
1 AATAATAATAA
38045798 CAATAAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (21 bp):
AATAATAATAAAAAGACTAAT
Found at i:38048422 original size:12 final size:13
Alignment explanation
Indices: 38048405--38048434 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
38048395 GGCTCGGAAA
38048405 TGATA-GAAATGT
1 TGATAGGAAATGT
38048417 TGATAGGAAATGT
1 TGATAGGAAATGT
38048430 TGATA
1 TGATA
38048435 ACAGTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (13 bp):
TGATAGGAAATGT
Found at i:38049907 original size:11 final size:11
Alignment explanation
Indices: 38049887--38049923 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
38049877 AGCCCGACCC
38049887 ATATTAAATAT
1 ATATTAAATAT
*
38049898 ATATTTAATAT
1 ATATTAAATAT
*
38049909 ATATAAAATAT
1 ATATTAAATAT
38049920 ATAT
1 ATAT
38049924 ATTTCATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:38049975 original size:25 final size:26
Alignment explanation
Indices: 38049892--38050057 Score: 214
Period size: 25 Copynumber: 6.4 Consensus size: 26
38049882 GACCCATATT
* * *
38049892 AAATATATATTT-AATATATAT-AAA
1 AAATATATATTTGATTAAAAATAAAA
* *
38049916 ATATATATATTTCATTAAAAATAAAAA
1 AAATATATATTTGATTAAAAAT-AAAA
38049943 AATATATATATTTGATTAAAAAT-AAA
1 AA-ATATATATTTGATTAAAAATAAAA
*
38049969 ATATATATATTTGATTAAAAATAAAAA
1 AAATATATATTTGATTAAAAAT-AAAA
*
38049996 AAAAATATATTTGATTAAAAAT-AAA
1 AAATATATATTTGATTAAAAATAAAA
38050021 AAATATATATTTGATTAAAAATAAAA
1 AAATATATATTTGATTAAAAATAAAA
38050047 AAATATATATT
1 AAATATATATT
38050058 AATATATAAT
Statistics
Matches: 125, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
24 11 0.09
25 50 0.40
26 18 0.14
27 27 0.22
28 19 0.15
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATATATATTTGATTAAAAATAAAA
Found at i:38049996 original size:52 final size:51
Alignment explanation
Indices: 38049892--38050057 Score: 244
Period size: 52 Copynumber: 3.2 Consensus size: 51
38049882 GACCCATATT
* * * *
38049892 AAATATATATTT-AATATATATAAAATATATATATTTCATTAAAAATAAAAA
1 AAATATATATTTGATTAAAAATAAAATATATATATTTGATTAAAAAT-AAAA
38049943 AATATATATATTTGATTAAAAATAAAATATATATATTTGATTAAAAATAAAAA
1 AA-ATATATATTTGATTAAAAATAAAATATATATATTTGATTAAAAAT-AAAA
* *
38049996 AAAAATATATTTGATTAAAAATAAAAAATATATATTTGATTAAAAATAAAA
1 AAATATATATTTGATTAAAAATAAAATATATATATTTGATTAAAAATAAAA
38050047 AAATATATATT
1 AAATATATATT
38050058 AATATATAAT
Statistics
Matches: 106, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
51 16 0.15
52 53 0.50
53 37 0.35
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (51 bp):
AAATATATATTTGATTAAAAATAAAATATATATATTTGATTAAAAATAAAA
Found at i:38050172 original size:18 final size:18
Alignment explanation
Indices: 38050151--38050186 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38050141 TATGGCATGT
*
38050151 TATAAAAAAATTAAAAAA
1 TATAAAAAAACTAAAAAA
*
38050169 TATAAAAATACTAAAAAA
1 TATAAAAAAACTAAAAAA
38050187 ATGTTTAGAA
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:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TATAAAAAAACTAAAAAA
Found at i:38050257 original size:31 final size:32
Alignment explanation
Indices: 38050195--38050257 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
38050185 AAATGTTTAG
**
38050195 AATGAACTTGAACAAATGGTTGTCCAGATTCA
1 AATGAACTTGAACAAATCATTGTCCAGATTCA
* *
38050227 AATGAACTTGGAC-AATCATTGTCCATATTCA
1 AATGAACTTGAACAAATCATTGTCCAGATTCA
38050258 TTCTCTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (32 bp):
AATGAACTTGAACAAATCATTGTCCAGATTCA
Found at i:38052629 original size:31 final size:29
Alignment explanation
Indices: 38052586--38052647 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
38052576 TTTTATAAAT
*
38052586 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
38052616 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
38052646 AA
1 AA
38052648 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:38052866 original size:13 final size:13
Alignment explanation
Indices: 38052816--38052866 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
38052806 TTTAAACAAA
* *
38052816 ACTTTTTAAAATC
1 ACTTTTCAAAAAC
* **
38052829 ACTTTTCTACCAC
1 ACTTTTCAAAAAC
38052842 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
38052855 ACTTTTCAAAAA
1 ACTTTTCAAAAA
38052867 AAATGAAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:38057451 original size:21 final size:22
Alignment explanation
Indices: 38057397--38057453 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
38057387 TTAAAAATGT
*
38057397 TTTTTGTATTAATATCTAAATAA
1 TTTTT-TATTAATATCTAAACAA
* *
38057420 TTTTATGTTAA-ATCTAAACAA
1 TTTTTTATTAATATCTAAACAA
38057441 TTTTTTATTAATA
1 TTTTTTATTAATA
38057454 AAAAGCAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 18 0.64
22 6 0.21
23 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTTTATTAATATCTAAACAA
Found at i:38065335 original size:35 final size:34
Alignment explanation
Indices: 38065288--38065370 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 34
38065278 CATGTACACA
*
38065288 GTTTACACGGTGTCGCACC-AAAGGACTTGTATACC
1 GTTTACATGGTGTCGC-CCGAAA-GACTTGTATACC
*
38065323 GTTTACATGGTGTCGCCCTGAAAGACTTGTATATC
1 GTTTACATGGTGTCGCCC-GAAAGACTTGTATACC
38065358 GTTTACATGGTGT
1 GTTTACATGGTGT
38065371 TACCTCGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 2 0.05
35 39 0.89
36 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (34 bp):
GTTTACATGGTGTCGCCCGAAAGACTTGTATACC
Found at i:38065996 original size:15 final size:15
Alignment explanation
Indices: 38065976--38066007 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
38065966 ACGAATATAG
38065976 TAAGATTAAGAAGCT
1 TAAGATTAAGAAGCT
38065991 TAAGATTAAGAAGCT
1 TAAGATTAAGAAGCT
38066006 TA
1 TA
38066008 CTAGTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAAGATTAAGAAGCT
Found at i:38075881 original size:20 final size:20
Alignment explanation
Indices: 38075848--38075886 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38075838 ATTATTTTGG
38075848 AATTTTATACAAAACCATTA
1 AATTTTATACAAAACCATTA
*
38075868 AATTTATATA-AAAATCATT
1 AATTT-TATACAAAACCATT
38075887 GCCATCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTTATACAAAACCATTA
Found at i:38093117 original size:30 final size:30
Alignment explanation
Indices: 38093046--38093117 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
38093036 CTAAGGTTAC
* *
38093046 CTCTCAATCTCACCTAGGCTTATAAATTAT
1 CTCTGAATCTCACCTAGGCATATAAATTAT
* * * *
38093076 GTCTTG-GTCTCACCTCGGCATATAGATTAT
1 CTC-TGAATCTCACCTAGGCATATAAATTAT
38093106 CTCTGAATCTCA
1 CTCTGAATCTCA
38093118 TTATTCAGCA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
29 2 0.06
30 29 0.91
31 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (30 bp):
CTCTGAATCTCACCTAGGCATATAAATTAT
Found at i:38094711 original size:35 final size:36
Alignment explanation
Indices: 38094672--38094773 Score: 113
Period size: 35 Copynumber: 2.9 Consensus size: 36
38094662 TATGGAAGCG
* *
38094672 AGCCTTCCGTAAGCCTTCCTTCATGTG-TGGAAGAA
1 AGCCTTCCGTAAGCCTTCCTCCATATGTTGGAAGAA
* *
38094707 AGCC-TCCATAAGCCTCTCC-CCATATGTTGGAAGCA
1 AGCCTTCCGTAAGCCT-TCCTCCATATGTTGGAAGAA
* *
38094742 AGCCTTCCGTAAGCTTTCCTCTATATG-TGGAA
1 AGCCTTCCGTAAGCCTTCCTCCATATGTTGGAA
38094774 AAAAACACCC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
34 15 0.27
35 26 0.46
36 15 0.27
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (36 bp):
AGCCTTCCGTAAGCCTTCCTCCATATGTTGGAAGAA
Found at i:38094748 original size:70 final size:73
Alignment explanation
Indices: 38094601--38094761 Score: 195
Period size: 70 Copynumber: 2.2 Consensus size: 73
38094591 CAGAGCAAAA
* * * * * * *
38094601 CCTTCCATAACCCTTCCTTATGTGTTGGGAGCAAGACCTTCTATAAGCCACTCCCCCTCTGTATG
1 CCTTCCGTAAGCCTTCCTTATGTGTTGGAAGAAAGACCTTCCATAAGCCACTCCCCATATGTATG
*
38094666 GAAGCGAG
66 GAAGCAAG
*
38094674 CCTTCCGTAAGCCTTCCTTCATGTG-TGGAAGAAAG-CC-TCCATAAGCCTCTCCCCATATGT-T
1 CCTTCCGTAAGCCTTCCTT-ATGTGTTGGAAGAAAGACCTTCCATAAGCCACTCCCCATATGTAT
38094735 GGAAGCAAG
65 GGAAGCAAG
*
38094744 CCTTCCGTAAGCTTTCCT
1 CCTTCCGTAAGCCTTCCT
38094762 CTATATGTGG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
70 26 0.34
71 19 0.25
72 2 0.03
73 25 0.32
74 5 0.06
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.28
Consensus pattern (73 bp):
CCTTCCGTAAGCCTTCCTTATGTGTTGGAAGAAAGACCTTCCATAAGCCACTCCCCATATGTATG
GAAGCAAG
Found at i:38094875 original size:36 final size:36
Alignment explanation
Indices: 38094783--38094875 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
38094773 AAAAAACACC
* *
38094783 CTGTAAGCATTCCCCCATGTACTATGAGCAGGCCTT
1 CTGTAAGCATTCCCCCATGTGCTAAGAGCAGGCCTT
** * **
38094819 CCATAAGCTTTCCCTTATGTGCTAAGAGCAGGCCTT
1 CTGTAAGCATTCCCCCATGTGCTAAGAGCAGGCCTT
*
38094855 CTGTAAGCCTTCCCCCATGTG
1 CTGTAAGCATTCCCCCATGTG
38094876 TGTAAGCAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.29
Consensus pattern (36 bp):
CTGTAAGCATTCCCCCATGTGCTAAGAGCAGGCCTT
Found at i:38094959 original size:107 final size:107
Alignment explanation
Indices: 38094786--38094984 Score: 233
Period size: 107 Copynumber: 1.9 Consensus size: 107
38094776 AAACACCCTG
* * * *
38094786 TAAGCATTCCCCCATGTACTATGAGCAGGCCTTCCATAAGCTTTCCCTTATGTGCTAAGAGCAGG
1 TAAGCATTCCCCCATGTACTAGGAGCAGACCTTCCATAAGCTTTCCCTTATCTACTAAGAGCAGG
* *
38094851 CCTT-CTGTAAGCCTTCCCCCATGTGTGTAAGCAAGCTCCTCT
66 CCTTAC-ATAAGCATTCCCCCATGTGTGTAAGCAAGCTCCTCT
* * * * * *
38094893 TAAGCCTT-CCCCATGTACTAGGAGTAGACCTTTCGTAAGC-TTCCCTTTTATCTACTAGGAGTA
1 TAAGCATTCCCCCATGTACTAGGAGCAGACCTTCCATAAGCTTTCCC--TTATCTACTAAGAGCA
*
38094956 GGCCTTACATAAGTATTCCCCCATGTGTG
64 GGCCTTACATAAGCATTCCCCCATGTGTG
38094985 GAAACAGACC
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
105 5 0.07
106 27 0.36
107 43 0.57
108 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.31
Consensus pattern (107 bp):
TAAGCATTCCCCCATGTACTAGGAGCAGACCTTCCATAAGCTTTCCCTTATCTACTAAGAGCAGG
CCTTACATAAGCATTCCCCCATGTGTGTAAGCAAGCTCCTCT
Found at i:38100572 original size:19 final size:19
Alignment explanation
Indices: 38100548--38100587 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
38100538 TGTTTAAGAA
38100548 AACTAGATTTTAACTAAGT
1 AACTAGATTTTAACTAAGT
38100567 AACTAGATTTTAACTAAGT
1 AACTAGATTTTAACTAAGT
38100586 AA
1 AA
38100588 ATTAACTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (19 bp):
AACTAGATTTTAACTAAGT
Found at i:38102065 original size:10 final size:10
Alignment explanation
Indices: 38102038--38102068 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
38102028 GCAAATCTAT
*
38102038 TGAAAATATA
1 TGAAAATTTA
38102048 TGAAAATTTA
1 TGAAAATTTA
38102058 TGAAAATTTA
1 TGAAAATTTA
38102068 T
1 T
38102069 TATAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (10 bp):
TGAAAATTTA
Found at i:38103703 original size:7 final size:7
Alignment explanation
Indices: 38103691--38103735 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
38103681 GCCATCATCC
38103691 CTCTCAT
1 CTCTCAT
38103698 CTCTCAT
1 CTCTCAT
38103705 CTCTCAT
1 CTCTCAT
38103712 CTCTCAT
1 CTCTCAT
38103719 C-CTC-T
1 CTCTCAT
*
38103724 CTCTCAA
1 CTCTCAT
38103731 CTCTC
1 CTCTC
38103736 TTAGCTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
5 2 0.06
6 6 0.17
7 27 0.77
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (7 bp):
CTCTCAT
Found at i:38103714 original size:19 final size:19
Alignment explanation
Indices: 38103691--38103735 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
38103681 GCCATCATCC
*
38103691 CTCTCATCTCTCATCTCTCAT
1 CTCTCATC-CTC-TCTCTCAA
38103712 CTCTCATCCTCTCTCTCAA
1 CTCTCATCCTCTCTCTCAA
38103731 CTCTC
1 CTCTC
38103736 TTAGCTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 3 0.13
21 8 0.35
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (19 bp):
CTCTCATCCTCTCTCTCAA
Found at i:38110586 original size:20 final size:20
Alignment explanation
Indices: 38110561--38110598 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38110551 GTTTTTCTAG
38110561 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
38110581 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
38110599 TAAAGGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:38114194 original size:16 final size:17
Alignment explanation
Indices: 38114173--38114208 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
38114163 TCCATCATCC
38114173 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
38114189 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
38114206 CTC
1 CTC
38114209 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:38117920 original size:22 final size:22
Alignment explanation
Indices: 38117884--38117926 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38117874 AACTCATAAC
38117884 ACATTTAGAGAATTTTGTATTT
1 ACATTTAGAGAATTTTGTATTT
* * *
38117906 ACATTTTGAGGATTTTTTATT
1 ACATTTAGAGAATTTTGTATT
38117927 CTCTTCGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (22 bp):
ACATTTAGAGAATTTTGTATTT
Found at i:38130458 original size:85 final size:85
Alignment explanation
Indices: 38130361--38130569 Score: 271
Period size: 88 Copynumber: 2.4 Consensus size: 85
38130351 AAAATATTAC
*
38130361 TGAGATAATAACAAAAATTAAATTTTGTTAAAAAATTACTTTCA-AGAGTACTTTTATTCTATC-
1 TGAGATAATAACAAAAATTAAATTTTG-AAAAAAATTA-TTTCATAGAGTACTTTTATTCTATCA
** *
38130424 AATGGTACGTAAAA-AGAACTTT
64 AAAAGTAAGTAAAAGA-AACTTT
* *
38130446 TGAGATAATAACAAAAATTAAGTTTTGCCAAAAAAAATTATTTCATAGATTACTTTTATTCTATC
1 TGAGATAATAACAAAAATTAAATTTTG---AAAAAAATTATTTCATAGAGTACTTTTATTCTATC
*
38130511 AAAAATTAAGTAAAAGAAACTTT
63 AAAAAGTAAGTAAAAGAAACTTT
*
38130534 TGAGATAATAACAAAAATTAAATTTTGCAAAAAATT
1 TGAGATAATAACAAAAATTAAATTTTGAAAAAAATT
38130570 TTCTTCAAAG
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
85 34 0.31
86 5 0.05
87 27 0.25
88 42 0.39
89 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (85 bp):
TGAGATAATAACAAAAATTAAATTTTGAAAAAAATTATTTCATAGAGTACTTTTATTCTATCAAA
AAGTAAGTAAAAGAAACTTT
Found at i:38130527 original size:87 final size:87
Alignment explanation
Indices: 38130361--38130567 Score: 287
Period size: 87 Copynumber: 2.4 Consensus size: 87
38130351 AAAATATTAC
**
38130361 TGAGATAATAACAAAAATTAAATTTTG-TTAAAAAATTACTTTCAAGAGTACTTTTATTCTATCA
1 TGAGATAATAACAAAAATTAAATTTTGCAAAAAAAATTACTTTCAAGAGTACTTTTATTCTATCA
** *
38130425 ATGGTACGTAAAAAG-AACTTT
66 AAAGTAAGTAAAAAGAAACTTT
* *
38130446 TGAGATAATAACAAAAATTAAGTTTTGCCAAAAAAAATTA-TTTCATAGATTACTTTTATTCTAT
1 TGAGATAATAACAAAAATTAAATTTTG-CAAAAAAAATTACTTTCA-AGAGTACTTTTATTCTAT
*
38130510 CAAAAATTAAGT-AAAAGAAACTTT
64 C-AAAAGTAAGTAAAAAGAAACTTT
38130534 TGAGATAATAACAAAAATTAAATTTTGCAAAAAA
1 TGAGATAATAACAAAAATTAAATTTTGCAAAAAA
38130568 TTTTCTTCAA
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
85 26 0.24
86 5 0.05
87 39 0.36
88 38 0.35
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (87 bp):
TGAGATAATAACAAAAATTAAATTTTGCAAAAAAAATTACTTTCAAGAGTACTTTTATTCTATCA
AAAGTAAGTAAAAAGAAACTTT
Found at i:38139820 original size:18 final size:19
Alignment explanation
Indices: 38139794--38139834 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
38139784 CGTTCGTTTC
38139794 CAAAACATTATTCA-TTTA
1 CAAAACATTATTCACTTTA
*
38139812 CAAATCATTATTCACTTTA
1 CAAAACATTATTCACTTTA
38139831 -AAAA
1 CAAAA
38139835 AATTTTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAACATTATTCACTTTA
Found at i:38140391 original size:23 final size:24
Alignment explanation
Indices: 38140347--38140391 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
38140337 AAAATCCTAC
*
38140347 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
38140371 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
38140392 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:38143812 original size:24 final size:24
Alignment explanation
Indices: 38143767--38143828 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
38143757 ACGAGCTTCC
* *
38143767 CCATTAATGGCTCTTTTAAGCTTT
1 CCATTAATGGCTCATATAAGCTTT
* * *
38143791 CCATTTATGGCTCATATGAGCTTC
1 CCATTAATGGCTCATATAAGCTTT
*
38143815 CCAATAATTGGCTC
1 CCATTAA-TGGCTC
38143829 GCAAGAGCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (24 bp):
CCATTAATGGCTCATATAAGCTTT
Found at i:38143903 original size:25 final size:24
Alignment explanation
Indices: 38143825--38143904 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
38143815 CCAATAATTG
* * *
38143825 GCTCGCAAGAGCTTCACGTTATACA
1 GCTCACAAGAGCTTCCCGAT-TACA
* *
38143850 GCTCACATGAGCTT-CCTATTACA
1 GCTCACAAGAGCTTCCCGATTACA
*
38143873 CGGCTCAGAAGAGCTTCCCGATTACA
1 --GCTCACAAGAGCTTCCCGATTACA
38143899 TGCTCA
1 -GCTCA
38143905 TATGGGTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 4 0.09
24 2 0.05
25 29 0.67
26 8 0.19
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (24 bp):
GCTCACAAGAGCTTCCCGATTACA
Found at i:38148626 original size:18 final size:18
Alignment explanation
Indices: 38148586--38148623 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
38148576 GTTAACGAAC
38148586 AAATATATAAATATAAAT
1 AAATATATAAATATAAAT
* *
38148604 AAATATCTATATA-AAAT
1 AAATATATAAATATAAAT
38148621 AAA
1 AAA
38148624 ATAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATATAAATATAAAT
Found at i:38149114 original size:20 final size:20
Alignment explanation
Indices: 38149071--38149119 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
38149061 ATGAGCAATT
* *
38149071 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATA
**
38149091 AAATCAAATTGATTGGAATA
1 AAATCAAATTGATTAAAATA
*
38149111 AAATAAAAT
1 AAATCAAAT
38149120 CAACATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATA
Found at i:38150196 original size:17 final size:17
Alignment explanation
Indices: 38150174--38150208 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38150164 ACATATCCTT
*
38150174 TCAACTTTTATGGCCCA
1 TCAACTTTTATGGACCA
38150191 TCAACTTTTATGGACCA
1 TCAACTTTTATGGACCA
38150208 T
1 T
38150209 ACCCCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (17 bp):
TCAACTTTTATGGACCA
Found at i:38155295 original size:77 final size:80
Alignment explanation
Indices: 38155198--38155376 Score: 204
Period size: 83 Copynumber: 2.2 Consensus size: 80
38155188 CTATTGCACA
* *
38155198 GCAGGATTAAATCCCAAAACAAAATTAT-TTACTTAAATCTT-GTCTGGAAACAAAATC-A-AAA
1 GCAGGAATAAATCCCAAAACAAAATTATCTGA-TTAAATCTTCGTCTGGAAACAAAATCAACAAA
*
38155259 TGAAATATGTTAAACG
65 TAAAATATGTTAAACG
** * * *
38155275 GCAGGAATAAATCCTGAAACAGAATTATCTGATTAAGTCTTCGTTTGGAAACAAAATCAAGATCA
1 GCAGGAATAAATCCCAAAACAAAATTATCTGATTAAATCTTCGTCTGGAAACAAAATC-A-A-CA
* *
38155340 AATAAAATCTGTTAAATG
63 AATAAAATATGTTAAACG
38155358 GCAGGAATAAATCCCAAAA
1 GCAGGAATAAATCCCAAAA
38155377 TAGATTATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
77 32 0.39
78 17 0.20
81 1 0.01
83 33 0.40
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.26
Consensus pattern (80 bp):
GCAGGAATAAATCCCAAAACAAAATTATCTGATTAAATCTTCGTCTGGAAACAAAATCAACAAAT
AAAATATGTTAAACG
Found at i:38155519 original size:88 final size:84
Alignment explanation
Indices: 38155318--38155608 Score: 300
Period size: 88 Copynumber: 3.4 Consensus size: 84
38155308 TAAGTCTTCG
* * ** * ** *
38155318 TTTGGAAACAAAATCAAGATCAAATAAAATCTGTTAAATGGCAGGAATAAATCCCAAAATAGA--
1 TTTGGAAACAAAATAAAAATGGAATAAAATCTATTAAACAGCA-GAATAAATCCCGAAATAGATT
*
38155381 TTATTCAA-TTTAATTCTAA
65 TTATTTAATTTTAATTCTAA
* * *
38155400 TTTGGAAACAAAATTAAAATCGAATAAAATCTATTAAACAGCGAGAATAAATCCCGAAATAAATT
1 TTTGGAAACAAAATAAAAATGGAATAAAATCTATTAAACAGC-AGAATAAATCCCGAAATAGATT
**
38155465 TTATTTAATTTTAATTTCTTG
65 TTATTTAATTTTAA-TTCTAA
* * * * *
38155486 TTTGGCAACAAAATAAAAAAATGGAATAAAATCTGTTGAACAGCAAGAATAAATCCTGAAACAGA
1 TTTGGAAACAAAAT--AAAAATGGAATAAAATCTATTAAACAGC-AGAATAAATCCCGAAATAGA
* *
38155551 TTTTATTTAATTTTAATACTCA
63 TTTTATTTAATTTTAATTCTAA
*
38155573 TTTGGAAACAAAATCAAAAATGAAATAAAATCTATT
1 TTTGGAAACAAAAT-AAAAATGGAATAAAATCTATT
38155609 TGAATGGAGG
Statistics
Matches: 175, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
82 53 0.30
83 1 0.01
84 7 0.04
85 5 0.03
86 36 0.21
87 16 0.09
88 57 0.33
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (84 bp):
TTTGGAAACAAAATAAAAATGGAATAAAATCTATTAAACAGCAGAATAAATCCCGAAATAGATTT
TATTTAATTTTAATTCTAA
Found at i:38155635 original size:87 final size:85
Alignment explanation
Indices: 38155318--38155651 Score: 288
Period size: 88 Copynumber: 3.9 Consensus size: 85
38155308 TAAGTCTTCG
* * * *
38155318 TTTGGAAACAAAATC-AAGATCAAATAAAATCTGTTAAATGGCAGGAATAAATCCCAAAATAGA-
1 TTTGGAAACAAAATCAAAAATGAAATAAAATCTGTTAAATGG-AAGAATAAATCCCAAAACAGAT
38155381 -TTATTCAA-TTTAATTCTAA
65 TTTATTCAATTTTAATTCTAA
* * * * * *
38155400 TTTGGAAACAAAAT-TAAAATCG-AATAAAATCTATTAAACAGCG-AGAATAAATCCCGAAATAA
1 TTTGGAAACAAAATCAAAAAT-GAAATAAAATCTGTTAAA-TG-GAAGAATAAATCCCAAAACAG
* **
38155462 ATTTTATTTAATTTTAATTTCTTG
63 ATTTTATTCAATTTTAA-TTCTAA
* * * * **
38155486 TTTGGCAACAAAATAAAAAAATGGAATAAAATCTGTTGAACA-GCAAGAATAAATCCTGAAACAG
1 TTTGGAAACAAAAT-CAAAAATGAAATAAAATCTGTT-AA-ATGGAAGAATAAATCCCAAAACAG
* * *
38155550 ATTTTATTTAATTTTAATACTCA
63 ATTTTATTCAATTTTAATTCTAA
* * * *
38155573 TTTGGAAACAAAATCAAAAATGAAATAAAATCTATTTGAATGGAGGGAATAAATCCCAAAACAGG
1 TTTGGAAACAAAATCAAAAATGAAATAAAATCT-GTTAAATGGA-AGAATAAATCCCAAAACAGA
38155638 TTTTATTCAATTTT
64 TTTTATTCAATTTT
38155652 TATTTTTATT
Statistics
Matches: 204, Mismatches: 31, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
82 50 0.25
83 1 0.00
84 8 0.04
85 6 0.03
86 37 0.18
87 48 0.24
88 51 0.25
89 2 0.01
90 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (85 bp):
TTTGGAAACAAAATCAAAAATGAAATAAAATCTGTTAAATGGAAGAATAAATCCCAAAACAGATT
TTATTCAATTTTAATTCTAA
Found at i:38155806 original size:20 final size:19
Alignment explanation
Indices: 38155781--38155820 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
38155771 GTCCACGAAC
38155781 AAATATATAAATATAAATAA
1 AAATATATAAATA-AAATAA
* *
38155801 AAATATTTATATAAAATAA
1 AAATATATAAATAAAATAA
38155820 A
1 A
38155821 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATATAAATAAAATAA
Found at i:38157431 original size:2 final size:2
Alignment explanation
Indices: 38157424--38157459 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38157414 GGATTACCTA
38157424 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
38157460 TTTGTTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:38169140 original size:5 final size:5
Alignment explanation
Indices: 38169130--38169154 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38169120 AAAACTTTTA
38169130 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
38169155 AAGCCTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:38171610 original size:9 final size:10
Alignment explanation
Indices: 38171567--38171613 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
38171557 ATAAATTATA
38171567 ATTAAAAATC
1 ATTAAAAATC
38171577 ATTAAAAATC
1 ATTAAAAATC
*
38171587 ATT-AAAATT
1 ATTAAAAATC
*
38171596 ATTAAAAATT
1 ATTAAAAATC
38171606 A-TAAAAAT
1 ATTAAAAAT
38171614 ACCAAAAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (10 bp):
ATTAAAAATC
Found at i:38171612 original size:19 final size:19
Alignment explanation
Indices: 38171569--38171613 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
38171559 AAATTATAAT
38171569 TAAAAATCATTAAAAATCA
1 TAAAAATCATTAAAAATCA
* * *
38171588 TTAAAATTATTAAAAATTA
1 TAAAAATCATTAAAAATCA
38171607 TAAAAAT
1 TAAAAAT
38171614 ACCAAAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATCATTAAAAATCA
Found at i:38186115 original size:15 final size:16
Alignment explanation
Indices: 38186089--38186123 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
38186079 ATTTATAAAT
38186089 TTTAATATTGATAGTA
1 TTTAATATTGATAGTA
38186105 TTTAA-ATTGATAGTA
1 TTTAATATTGATAGTA
38186120 TTTA
1 TTTA
38186124 TAAATTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTAATATTGATAGTA
Found at i:38187017 original size:14 final size:15
Alignment explanation
Indices: 38186987--38187020 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
38186977 CTGTTTAGGG
*
38186987 TTTCATTTCTATCCA
1 TTTCATTGCTATCCA
38187002 TTTCATTGCT-TCCA
1 TTTCATTGCTATCCA
38187016 TTTCA
1 TTTCA
38187021 GTTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTCATTGCTATCCA
Found at i:38187458 original size:2 final size:2
Alignment explanation
Indices: 38187446--38187505 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
38187436 TTTACCTTCT
*
38187446 TA TA CA 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
*
38187488 TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA
38187506 AGTGATGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38188785 original size:17 final size:17
Alignment explanation
Indices: 38188765--38188857 Score: 74
Period size: 17 Copynumber: 5.9 Consensus size: 17
38188755 TTATTTTCTA
38188765 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
38188782 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
38188796 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * *
38188812 TATTAGTATT-AAAATT
1 TATAAGTTTTCTAAATT
* *
38188828 TATTAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
*
38188843 TATAATTTTTCTAAA
1 TATAAGTTTTCTAAA
38188858 AAAGTGTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 10 0.17
14 2 0.03
15 10 0.17
16 15 0.25
17 22 0.37
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:38188793 original size:30 final size:30
Alignment explanation
Indices: 38188758--38188814 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
38188748 TATTGTTTTA
*
38188758 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
*
38188788 TTTTCTAAATAATTTTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
38188815 TAGTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:38188808 original size:13 final size:13
Alignment explanation
Indices: 38188758--38188810 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
38188748 TATTGTTTTA
*
38188758 TTTTCTATATAAG
1 TTTTCTAAATAAG
38188771 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
38188788 TTTTCTAAATAAT
1 TTTTCTAAATAAG
38188801 TTTTCTAAAT
1 TTTTCTAAAT
38188811 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
16 2 0.06
17 11 0.32
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (13 bp):
TTTTCTAAATAAG
Found at i:38188841 original size:15 final size:15
Alignment explanation
Indices: 38188806--38188845 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 15
38188796 ATAATTTTTC
38188806 TAAATTTATTAGTAT
1 TAAATTTATTAGTAT
38188821 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
38188837 TAAATTTAT
1 TAAATTTAT
38188846 AATTTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:38188904 original size:15 final size:15
Alignment explanation
Indices: 38188884--38189006 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 15
38188874 TTATTTGCTT
38188884 ACATAATACATAATA
1 ACATAATACATAATA
38188899 ACATAATACATAACTTA
1 ACATAATACATAA--TA
* * *
38188916 TATATAAGCTTGCATAACTT
1 -ACATAA---TACATAA-TA
* *
38188936 ACATAATAACTTCCATA
1 ACATAAT-ACAT-AATA
* *
38188953 AC-TTATATATAATA
1 ACATAATACATAATA
*
38188967 ACATAAT--A-AATT
1 ACATAATACATAATA
38188979 ACATAATACATAATA
1 ACATAATACATAATA
38188994 ACATAATACATAA
1 ACATAATACATAA
38189007 CTTATATATA
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
12 10 0.12
13 1 0.01
14 6 0.08
15 34 0.43
16 4 0.05
17 7 0.09
18 6 0.08
19 5 0.06
20 1 0.01
21 6 0.08
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.32
Consensus pattern (15 bp):
ACATAATACATAATA
Found at i:38188933 original size:21 final size:20
Alignment explanation
Indices: 38188907--38188964 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
38188897 TAACATAATA
*
38188907 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
*
38188928 CATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
38188949 CATAACTTATATATAA
1 CATAACTTATATATAA
38188965 TAACATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:38188974 original size:8 final size:7
Alignment explanation
Indices: 38188961--38189006 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
38188951 TAACTTATAT
38188961 ATAATAAC
1 ATAAT-AC
38188969 ATAATA-
1 ATAATAC
*
38188975 A-ATTAC
1 ATAATAC
38188981 ATAATAC
1 ATAATAC
38188988 ATAATAAC
1 ATAAT-AC
38188996 ATAATAC
1 ATAATAC
38189003 ATAA
1 ATAA
38189007 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:38189028 original size:21 final size:21
Alignment explanation
Indices: 38189002--38189078 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
38188992 TAACATAATA
* *
38189002 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
38189023 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
** *
38189044 CATAACTTA-ATACACCACTTA
1 CATAACTTACATA-ATAACTTC
*
38189065 AATAACTTACATAA
1 CATAACTTACATAA
38189079 CTTACATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 37 0.79
22 7 0.15
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:38189078 original size:9 final size:9
Alignment explanation
Indices: 38188881--38189500 Score: 204
Period size: 9 Copynumber: 71.6 Consensus size: 9
38188871 TAATTATTTG
38188881 CTTACATAA
1 CTTACATAA
38188890 --TACATAA
1 CTTACATAA
*
38188897 -TAACATAA
1 CTTACATAA
38188905 --TACATAA
1 CTTACATAA
*
38188912 CTTATATATAA
1 C-T-TACATAA
*
38188923 GCTTGCATAA
1 -CTTACATAA
38188933 CTTACATAATAA
1 CTTAC---ATAA
*
38188945 CTTCCATAA
1 CTTACATAA
*
38188954 CTTATAT-A
1 CTTACATAA
38188962 --TA-ATAA
1 CTTACATAA
*
38188968 CATA-ATAA
1 CTTACATAA
*
38188976 ATTACATAA
1 CTTACATAA
38188985 --TACATAA
1 CTTACATAA
*
38188992 -TAACATAA
1 CTTACATAA
38189000 --TACATAA
1 CTTACATAA
*
38189007 CTTATATATAA
1 C-T-TACATAA
*
38189018 GCTTGCATAA
1 -CTTACATAA
38189028 CTTACATAATAA
1 CTTAC---ATAA
*
38189040 CTTCCATAA
1 CTTACATAA
38189049 CTTA-ATACACCA
1 CTTACAT--A--A
*
38189061 CTTAAATAA
1 CTTACATAA
38189070 CTTACATAA
1 CTTACATAA
*
38189079 CTTACATAG
1 CTTACATAA
38189088 CTTACATAA
1 CTTACATAA
*
38189097 C-T-CATTA
1 CTTACATAA
38189104 CTTACATAA
1 CTTACATAA
*
38189113 CATACATAA
1 CTTACATAA
38189122 --TACATAA
1 CTTACATAA
38189129 CTTACATAA
1 CTTACATAA
**
38189138 AATAC--AA
1 CTTACATAA
*
38189145 CTTACATAT
1 CTTACATAA
38189154 CTTACATAA
1 CTTACATAA
38189163 --TACATAA
1 CTTACATAA
*
38189170 CTTATATAA
1 CTTACATAA
38189179 --TACA-ACA
1 CTTACATA-A
*
38189186 CTTACAGAA
1 CTTACATAA
* *
38189195 ATTAAATAA
1 CTTACATAA
*
38189204 CTTGCATAA
1 CTTACATAA
* *
38189213 --AACATAG
1 CTTACATAA
*
38189220 CCTACATAA
1 CTTACATAA
*
38189229 CTTATATAA
1 CTTACATAA
*
38189238 CTTTCATAA
1 CTTACATAA
**
38189247 AATAC--AA
1 CTTACATAA
*
38189254 CTTACATAT
1 CTTACATAA
*
38189263 TTTACATAAAA
1 CTTACAT--AA
38189274 CTTACATAA
1 CTTACATAA
*
38189283 --TACATCA
1 CTTACATAA
38189290 CTTACATAA
1 CTTACATAA
*
38189299 CTTAAATAA
1 CTTACATAA
*
38189308 CTTGCATAA
1 CTTACATAA
38189317 --TACATAGA
1 CTTACATA-A
38189325 C-TACATAA
1 CTTACATAA
**
38189333 CTTA-ATTTTC
1 CTTACA--TAA
38189343 CTTACATAA
1 CTTACATAA
38189352 --TACA-ACA
1 CTTACATA-A
*
38189359 CTTACACAA
1 CTTACATAA
*
38189368 CTTAAATAA
1 CTTACATAA
*
38189377 CTTGCATAA
1 CTTACATAA
*
38189386 --TACATAG
1 CTTACATAA
*
38189393 CCTACATAA
1 CTTACATAA
**
38189402 CTTA-ATTTGC
1 CTTACA--TAA
38189412 CTTACATAA
1 CTTACATAA
**
38189421 --TACAGCA
1 CTTACATAA
38189428 CTTACATAA
1 CTTACATAA
*
38189437 CTTACATAG
1 CTTACATAA
*
38189446 GTTACATAA
1 CTTACATAA
*
38189455 --TACACAA
1 CTTACATAA
*
38189462 CTTAAATAA
1 CTTACATAA
*
38189471 CTTATATAA
1 CTTACATAA
38189480 --TACATAA
1 CTTACATAA
38189487 CTTACATAA
1 CTTACATAA
*
38189496 TTTAC
1 CTTAC
38189501 TTAATACATA
Statistics
Matches: 451, Mismatches: 92, Indels: 136
0.66 0.14 0.20
Matches are distributed among these distances:
5 2 0.00
6 5 0.01
7 101 0.22
8 30 0.07
9 241 0.53
10 23 0.05
11 24 0.05
12 23 0.05
13 2 0.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (9 bp):
CTTACATAA
Found at i:38189109 original size:16 final size:17
Alignment explanation
Indices: 38189069--38189494 Score: 107
Period size: 16 Copynumber: 25.1 Consensus size: 17
38189059 CACTTAAATA
38189069 ACTTACATAACTTACAT
1 ACTTACATAACTTACAT
38189086 AGCTTACATAAC-T-CATT
1 A-CTTACATAACTTACA-T
*
38189103 ACTTACATAACATACAT
1 ACTTACATAACTTACAT
*
38189120 A-ATACATAACTTACAT
1 ACTTACATAACTTACAT
**
38189136 AAAATAC--AACTTACAT
1 -ACTTACATAACTTACAT
38189152 ATCTTACATAA--TACAT
1 A-CTTACATAACTTACAT
* *
38189168 AACTTATATAA--TACAAC
1 -ACTTACATAACTTAC-AT
* * *
38189185 ACTTACAGAAATTAAAT
1 ACTTACATAACTTACAT
* *
38189202 AACTTGCATAA--AACAT
1 -ACTTACATAACTTACAT
* *
38189218 AGCCTACATAACTTATAT
1 A-CTTACATAACTTACAT
* **
38189236 AACTTTCATAAAATACA-
1 -ACTTACATAACTTACAT
**
38189253 ACTTACATATTTTACAT
1 ACTTACATAACTTACAT
38189270 AAAACTTACATAA--TACAT
1 ---ACTTACATAACTTACAT
*
38189288 CACTTACATAACTTAAAT
1 -ACTTACATAACTTACAT
*
38189306 AACTTGCATAA--TACAT
1 -ACTTACATAACTTACAT
38189322 AGAC-TACATAACTTA-ATTTT
1 --ACTTACATAACTTACA---T
* *
38189342 CCTTACATAA--TACAAC
1 ACTTACATAACTTAC-AT
* *
38189358 ACTTACACAACTTAAAT
1 ACTTACATAACTTACAT
*
38189375 AACTTGCATAA--TACAT
1 -ACTTACATAACTTACAT
*
38189391 AGCCTACATAACTTA-ATTT
1 A-CTTACATAACTTACA--T
* *
38189410 GCCTTACATAA--TACAGC
1 -ACTTACATAACTTACA-T
38189427 ACTTACATAACTTACAT
1 ACTTACATAACTTACAT
* *
38189444 AGGTTACATAA--TACACA
1 A-CTTACATAACTTACA-T
* *
38189461 ACTTAAATAACTTATAT
1 ACTTACATAACTTACAT
*
38189478 A-ATACATAACTTACAT
1 ACTTACATAACTTACAT
38189494 A
1 A
38189495 ATTTACTTAA
Statistics
Matches: 299, Mismatches: 61, Indels: 99
0.65 0.13 0.22
Matches are distributed among these distances:
15 3 0.01
16 155 0.52
17 23 0.08
18 90 0.30
19 18 0.06
20 10 0.03
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (17 bp):
ACTTACATAACTTACAT
Found at i:38189162 original size:34 final size:34
Alignment explanation
Indices: 38189115--38189486 Score: 137
Period size: 34 Copynumber: 10.7 Consensus size: 34
38189105 TTACATAACA
38189115 TACATAA--TACATAACTTACATAAAATACAACT
1 TACATAACTTACATAACTTACATAAAATACAACT
* * *
38189147 TACATATCTTACATAATACATAACTTATATAATACAACACT
1 TACATAACTTACAT-A-AC-TTAC--ATAAAATAC-A-ACT
* * * * * * * *
38189188 TACAGAAATTAAATAACTTGCATAAAACATAGCC
1 TACATAACTTACATAACTTACATAAAATACAACT
* *
38189222 TACATAACTTATATAACTTTCATAAAATACAACT
1 TACATAACTTACATAACTTACATAAAATACAACT
**
38189256 TACATATTTTACATAAAACTTACAT--AATACATCACT
1 TACATAACTTACAT--AACTTACATAAAATACA--ACT
* * *
38189292 TACATAACTTAAATAACTTGCATAATACATA-GAC-
1 TACATAACTTACATAACTTACATAA-A-ATACAACT
**
38189326 TACATAACTTA-ATTTTCCTTACAT--AATACAACACT
1 TACATAACTTACA--TAACTTACATAAAATAC-A-ACT
* * * *
38189361 TACACAACTTAAATAACTTGCAT--AATACATAGCC
1 TACATAACTTACATAACTTACATAAAATACA-A-CT
**
38189395 TACATAACTTA-ATTTGCCTTACAT--AATACAGCACT
1 TACATAACTTACA--TAACTTACATAAAATACA--ACT
** * *
38189430 TACATAACTTACATAGGTTACATAATACACAACT
1 TACATAACTTACATAACTTACATAAAATACAACT
* *
38189464 TAAATAACTTATATAA--TACATAA
1 TACATAACTTACATAACTTACATAA
38189487 CTTACATAAT
Statistics
Matches: 254, Mismatches: 55, Indels: 62
0.68 0.15 0.17
Matches are distributed among these distances:
31 3 0.01
32 14 0.06
33 4 0.02
34 116 0.46
35 46 0.18
36 37 0.15
37 4 0.02
38 5 0.02
39 10 0.04
40 2 0.01
41 13 0.05
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (34 bp):
TACATAACTTACATAACTTACATAAAATACAACT
Found at i:38189171 original size:25 final size:26
Alignment explanation
Indices: 38189066--38189336 Score: 126
Period size: 25 Copynumber: 10.7 Consensus size: 26
38189056 CACCACTTAA
*
38189066 ATAACTTACATAACTTACATAGCTTAC
1 ATAACTTACATAACTTACATA-CATAC
*
38189093 ATAAC-T-CATTACTTACATAACATAC
1 ATAACTTACATAACTTACAT-ACATAC
*
38189118 ATAA--TACATAACTTACATAAAATAC
1 ATAACTTACATAACTTACAT-ACATAC
*
38189143 --AACTTACATATCTTACATA-ATAC
1 ATAACTTACATAACTTACATACATAC
*
38189166 ATAACTTATATAA--TACA-ACACTTAC
1 ATAACTTACATAACTTACATACA--TAC
* * * * *
38189191 AGAAATTAAATAACTTGCATA-AAAC
1 ATAACTTACATAACTTACATACATAC
* * * * *
38189216 ATAGCCTACATAACTTATATAACTTTC
1 ATAACTTACATAACTTACAT-ACATAC
** **
38189243 ATAAAATAC--AACTTACATATTTTAC
1 ATAACTTACATAACTTACATA-CATAC
*
38189268 ATAAAACTTACATAA--TACATCACTTAC
1 AT--AACTTACATAACTTACAT-ACATAC
* *
38189295 ATAACTTAAATAACTTGCATA-ATAC
1 ATAACTTACATAACTTACATACATAC
38189320 ATAGAC-TACATAACTTA
1 ATA-ACTTACATAACTTA
38189337 ATTTTCCTTA
Statistics
Matches: 185, Mismatches: 36, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
22 1 0.01
23 11 0.06
24 3 0.02
25 124 0.67
26 6 0.03
27 36 0.19
28 2 0.01
29 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (26 bp):
ATAACTTACATAACTTACATACATAC
Found at i:38189372 original size:69 final size:69
Alignment explanation
Indices: 38189274--38189458 Score: 289
Period size: 69 Copynumber: 2.7 Consensus size: 69
38189264 TTACATAAAA
*
38189274 CTTACATAATACATCACTTACATAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
1 CTTACATAATACAACACTTACATAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
*
38189339 TTTC
66 TTGC
* *
38189343 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATAACTTAAT
1 CTTACATAATACAACACTTACATAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
38189408 TTGC
66 TTGC
* * ** *
38189412 CTTACATAATACAGCACTTACATAACTTACATAGGTTACATAATACA
1 CTTACATAATACAACACTTACATAACTTAAATAACTTGCATAATACA
38189459 CAACTTAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 106 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (69 bp):
CTTACATAATACAACACTTACATAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
TTGC
Found at i:38189458 original size:25 final size:25
Alignment explanation
Indices: 38189430--38189511 Score: 101
Period size: 25 Copynumber: 3.3 Consensus size: 25
38189420 ATACAGCACT
**
38189430 TACATAACTTACATAGGTTACATAA
1 TACATAACTTACATAACTTACATAA
* * *
38189455 TACACAACTTAAATAACTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
38189480 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
38189505 TACATAA
1 TACATAA
38189512 ATATATATCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:38195658 original size:66 final size:65
Alignment explanation
Indices: 38195552--38195721 Score: 198
Period size: 66 Copynumber: 2.6 Consensus size: 65
38195542 AGCAAATTAC
* * * * * * *
38195552 ACAACTTAAAACGGAGGCAGCATCAAGAGAAGCTGAGGTTCGAA-AAAGATGTGAAGAACTCCAG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTC-AACAAAG-TATGAAGAACTCCAA
38195616 CT
64 CT
38195618 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAAC
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAC-AAAGTATGAAGAACTCCAAC
38195683 T
65 T
** * * *
38195684 GTAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
38195722 CTGCAGTGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 2 0.02
66 84 0.93
67 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.14
Consensus pattern (65 bp):
ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAGTATGAAGAACTCCAACT
Found at i:38195718 original size:21 final size:21
Alignment explanation
Indices: 38195692--38195741 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
38195682 CTGTAGCTTA
*
38195692 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
* * *
38195713 AAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
38195734 AAGCAGAG
1 AAGCAGAG
38195742 CAGCGTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:38196149 original size:43 final size:43
Alignment explanation
Indices: 38196075--38196222 Score: 194
Period size: 43 Copynumber: 3.4 Consensus size: 43
38196065 GTGGCGTTTC
* * *
38196075 ATGGTCATTT-GCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATT
1 ATGGTC-TTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTT
* * *
38196118 AGGGTCTTTAGCGGCGTTTGTTTGG-AAAGCGCCGCTAAAGGTC
1 ATGGTCTTTAGCGGCGTTTG-TCGGAAAAGCGCCGCTAAAGGTT
38196161 ATGGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTCT
1 ATGGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGT-T
38196205 -TGGTCTTTAGCGGCGTTT
1 ATGGTCTTTAGCGGCGTTT
38196223 ATTTCTAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
42 6 0.06
43 84 0.90
44 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (43 bp):
ATGGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTT
Found at i:38198224 original size:7 final size:7
Alignment explanation
Indices: 38198179--38198312 Score: 164
Period size: 7 Copynumber: 18.9 Consensus size: 7
38198169 ATGCATGATG
38198179 TGATATA
1 TGATATA
38198186 T-AGTATA
1 TGA-TATA
38198193 TGTATATA
1 TG-ATATA
38198201 TGTATATA
1 TG-ATATA
38198209 TGTATATA
1 TG-ATATA
38198217 TGATATA
1 TGATATA
*
38198224 TAATATA
1 TGATATA
*
38198231 TAATATA
1 TGATATA
38198238 TGATATA
1 TGATATA
38198245 TGATATA
1 TGATATA
*
38198252 TAATATA
1 TGATATA
*
38198259 TAATATA
1 TGATATA
38198266 TGATATA
1 TGATATA
38198273 TGATATA
1 TGATATA
*
38198280 TAATATA
1 TGATATA
*
38198287 TAATATA
1 TGATATA
38198294 TGATATA
1 TGATATA
38198301 TGAT-TA
1 TGATATA
38198307 TGATAT
1 TGATAT
38198313 GTATGTTTGT
Statistics
Matches: 117, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
6 7 0.06
7 87 0.74
8 22 0.19
9 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.45
Consensus pattern (7 bp):
TGATATA
Found at i:38198244 original size:28 final size:28
Alignment explanation
Indices: 38198204--38198312 Score: 193
Period size: 28 Copynumber: 3.9 Consensus size: 28
38198194 GTATATATGT
38198204 ATATATGTATATATGATATATAATATATA
1 ATATATG-ATATATGATATATAATATATA
38198233 ATATATGATATATGATATATAATATATA
1 ATATATGATATATGATATATAATATATA
38198261 ATATATGATATATGATATATAATATATA
1 ATATATGATATATGATATATAATATATA
*
38198289 ATATATGATATATGAT-TATGATAT
1 ATATATGATATATGATATATAATAT
38198313 GTATGTTTGT
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
27 7 0.09
28 65 0.82
29 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
ATATATGATATATGATATATAATATATA
Found at i:38198566 original size:5 final size:5
Alignment explanation
Indices: 38198556--38198624 Score: 59
Period size: 5 Copynumber: 13.8 Consensus size: 5
38198546 GGTGGACATT
* * * * *
38198556 ATATG ATATG ATATG TTATG CTATG AT-TCA ATATA ATATG ATATA ATATG
1 ATATG ATATG ATATG ATATG ATATG ATAT-G ATATG ATATG ATATG ATATG
* *
38198606 ATAAG TTATG ATATG ATAT
1 ATATG ATATG ATATG ATAT
38198625 ATTCTGGTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
4 1 0.02
5 49 0.96
6 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (5 bp):
ATATG
Found at i:38205449 original size:22 final size:20
Alignment explanation
Indices: 38205424--38205471 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
38205414 ATGCATGACG
38205424 TGATATAT-AGTATATGTATGTA
1 TGATATATGA-TATATG-AT-TA
38205446 TGATATATGATATATGATTA
1 TGATATATGATATATGATTA
38205466 TGATAT
1 TGATAT
38205472 GTATGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 14 0.56
23 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (20 bp):
TGATATATGATATATGATTA
Found at i:38205454 original size:7 final size:7
Alignment explanation
Indices: 38205424--38205471 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
38205414 ATGCATGACG
38205424 TGATATA
1 TGATATA
38205431 T-AGTATA
1 TGA-TATA
*
38205438 TGTATGTA
1 TG-ATATA
38205446 TGATATA
1 TGATATA
38205453 TGATATA
1 TGATATA
38205460 TGAT-TA
1 TGATATA
38205466 TGATAT
1 TGATAT
38205472 GTATGTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
6 7 0.20
7 22 0.63
8 5 0.14
9 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (7 bp):
TGATATA
Found at i:38205458 original size:20 final size:22
Alignment explanation
Indices: 38205427--38205471 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 22
38205417 CATGACGTGA
*
38205427 TATATAGTATATGT-ATGTATGA
1 TATATAGTATATATGAT-TATGA
38205449 TATAT-G-ATATATGATTATGA
1 TATATAGTATATATGATTATGA
38205469 TAT
1 TAT
38205472 GTATGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 13 0.62
21 3 0.14
22 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (22 bp):
TATATAGTATATATGATTATGA
Found at i:38205467 original size:13 final size:14
Alignment explanation
Indices: 38205424--38205471 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
38205414 ATGCATGACG
38205424 TGATATAT-AGTATA
1 TGATATATGA-TATA
*
38205438 TGTATGTATGATATA
1 TG-ATATATGATATA
38205453 TGATATATGAT-TA
1 TGATATATGATATA
38205466 TGATAT
1 TGATAT
38205472 GTATGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 8 0.27
14 10 0.33
15 11 0.37
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (14 bp):
TGATATATGATATA
Found at i:38214573 original size:20 final size:20
Alignment explanation
Indices: 38214525--38214573 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
38214515 TTATGTCCCG
*
38214525 GATCGCACTTACGTGCCCCT
1 GATCGCACTTACGTACCCCT
*
38214545 G-TTGCACTT-CGGTACCCCT
1 GATCGCACTTAC-GTACCCCT
38214564 GATCGCACTT
1 GATCGCACTT
38214574 TTGTGCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 8 0.33
ACGTcount: A:0.14, C:0.37, G:0.20, T:0.29
Consensus pattern (20 bp):
GATCGCACTTACGTACCCCT
Found at i:38215531 original size:18 final size:18
Alignment explanation
Indices: 38215508--38215543 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
38215498 GTCAATAAGT
38215508 TACACGAGCATG-GACACA
1 TACACGAGC-TGAGACACA
38215526 TACACGAGCTGAGACACA
1 TACACGAGCTGAGACACA
38215544 ACCGTGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
TACACGAGCTGAGACACA
Found at i:38224388 original size:25 final size:25
Alignment explanation
Indices: 38224354--38224410 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
38224344 TTCTGTACAT
38224354 ATATGCTTACACGAGCTGTAAATCA
1 ATATGCTTACACGAGCTGTAAATCA
* * * *
38224379 GTATGGTTACATGAGCTGTGAATCA
1 ATATGCTTACACGAGCTGTAAATCA
38224404 ATATGCT
1 ATATGCT
38224411 CACCCAAGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (25 bp):
ATATGCTTACACGAGCTGTAAATCA
Found at i:38228736 original size:20 final size:19
Alignment explanation
Indices: 38228690--38228741 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
38228680 AAAAAATCTT
*
38228690 AAAATATTTAACAATTACA
1 AAAATATTTAAAAATTACA
38228709 AAAATATTTAAAAATTACA
1 AAAATATTTAAAAATTACA
38228728 AAAATTATTTAAAA
1 AAAA-TATTTAAAA
38228742 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATTTAAAAATTACA
Found at i:38228771 original size:20 final size:19
Alignment explanation
Indices: 38228690--38228771 Score: 83
Period size: 19 Copynumber: 4.2 Consensus size: 19
38228680 AAAAAATCTT
* *
38228690 AAAATATTTAACAATTACA
1 AAAATATTTAAAAAATACA
*
38228709 AAAATATTTAAAAATTACA
1 AAAATATTTAAAAAATACA
* *
38228728 AAAATTATTTAAAATAAAATA
1 AAAA-TATTTAAAA-AATACA
* *
38228749 AAATTATTTAAAAAATAGA
1 AAAATATTTAAAAAATACA
38228768 AAAA
1 AAAA
38228772 AAAATCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 29 0.55
20 18 0.34
21 6 0.11
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAATATTTAAAAAATACA
Found at i:38228798 original size:10 final size:10
Alignment explanation
Indices: 38228785--38228812 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
38228775 ATCAAAATAT
38228785 TAAAATTTAC
1 TAAAATTTAC
38228795 TAAAATTTAC
1 TAAAATTTAC
38228805 TAAAATTT
1 TAAAATTT
38228813 TTAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TAAAATTTAC
Found at i:38228819 original size:9 final size:9
Alignment explanation
Indices: 38228784--38228855 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 9
38228774 AATCAAAATA
38228784 TTAAAATTT
1 TTAAAATTT
*
38228793 ACTAAAATTT
1 -TTAAAATTT
*
38228803 ACTAAAATTT
1 -TTAAAATTT
*
38228813 TTAAAATATA
1 TTAAAAT-TT
*
38228823 TTAAAAATT
1 TTAAAATTT
* *
38228832 TTAATATTC
1 TTAAAATTT
38228841 TTAAAATTT
1 TTAAAATTT
38228850 TATAAA
1 T-TAAA
38228856 TCATATTTGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
9 21 0.42
10 29 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTT
Found at i:38228819 original size:19 final size:19
Alignment explanation
Indices: 38228689--38228835 Score: 59
Period size: 19 Copynumber: 7.6 Consensus size: 19
38228679 AAAAAAATCT
*
38228689 TAAAATATTTAACAAT-TAC
1 TAAAATTTTTAA-AATATAC
* *
38228708 AAAAATATTTAAAA-ATTAC
1 TAAAATTTTTAAAATA-TAC
* * *
38228727 AAAAATTATTTAAAATAAAA
1 TAAAATT-TTTAAAATATAC
* *
38228747 TAAAATTATTTAAAAAATAGA
1 TAAAATT-TTTAAAATATA-C
* *** *
38228768 AAAAAAAATCAAAATAT--
1 TAAAATTTTTAAAATATAC
* *
38228785 TAAAATTTACTAAAATTTAC
1 TAAAATTT-TTAAAATATAC
*
38228805 TAAAATTTTTAAAATATAT
1 TAAAATTTTTAAAATATAC
*
38228824 TAAAAATTTTAA
1 TAAAATTTTTAA
38228836 TATTCTTAAA
Statistics
Matches: 96, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
17 4 0.04
18 8 0.08
19 39 0.41
20 39 0.41
21 6 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (19 bp):
TAAAATTTTTAAAATATAC
Found at i:38228856 original size:9 final size:8
Alignment explanation
Indices: 38228778--38228856 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 8
38228768 AAAAAAAATC
*
38228778 AAAATATT
1 AAAATTTT
38228786 AAAATTTACT
1 AAAATTT--T
38228796 AAAATTTACT
1 AAAATTT--T
38228806 AAAATTTTT
1 AAAA-TTTT
38228815 AAAATATATT
1 AAAAT-T-TT
38228825 AAAAATTTT
1 -AAAATTTT
*
38228834 AATATTCTT
1 AAAATT-TT
38228843 AAAATTTT
1 AAAATTTT
38228851 ATAAAT
1 A-AAAT
38228857 CATATTTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
8 15 0.25
9 19 0.32
10 18 0.30
11 8 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:38235508 original size:31 final size:29
Alignment explanation
Indices: 38235466--38235544 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
38235456 TATTAAATCT
*
38235466 ATACATAAACTTTTATTTAATGTGCAATGTC
1 ATACATGAACTTTTATTT--TGTGCAATGTC
* * * *
38235497 ATACATGAACTTTGATTTTGTTCGATTTC
1 ATACATGAACTTTTATTTTGTGCAATGTC
*
38235526 ATACATGAAATTTTGATTT
1 ATACATGAACTTTT-ATTT
38235545 GATTAAGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 20 0.50
30 4 0.10
31 16 0.40
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (29 bp):
ATACATGAACTTTTATTTTGTGCAATGTC
Found at i:38237647 original size:33 final size:31
Alignment explanation
Indices: 38237586--38237652 Score: 73
Period size: 33 Copynumber: 2.1 Consensus size: 31
38237576 ATAAAAGATG
* *
38237586 TATAAAATTTTTAAATATTAAAATAATAAAA
1 TATAAAATTTTTAAAAATTAAAAAAATAAAA
*
38237617 TATAAATATTTTTTAAAAAATT-AAAAAATAATA
1 TATAAA-A-TTTTT-AAAAATTAAAAAAATAAAA
38237650 TAT
1 TAT
38237653 GCAGCCAGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 6 0.20
32 1 0.03
33 17 0.57
34 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TATAAAATTTTTAAAAATTAAAAAAATAAAA
Found at i:38238248 original size:20 final size:19
Alignment explanation
Indices: 38238205--38238241 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
38238195 CAAAAAATTG
38238205 TAAAAATTATTTTTAAAAAT
1 TAAAAATTA-TTTTAAAAAT
38238225 TAAAAATTA-TTTAAAAA
1 TAAAAATTATTTTAAAAA
38238242 GTATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAATTATTTTAAAAAT
Found at i:38239999 original size:42 final size:42
Alignment explanation
Indices: 38239892--38240289 Score: 471
Period size: 42 Copynumber: 9.4 Consensus size: 42
38239882 ACGTCGCTAA
* *
38239892 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
*
38239936 CTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAATCATGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATGTT
* * *
38239979 CTATAGTGGCGCTTAGAAAAAAACGCAGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
38240021 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * *
38240063 CTTTAGCGACGCTTAGAGACAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
38240105 ATTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* ** *
38240147 CTTTAGCGGCGCTTTGGAGGAAAACGCCTCTAAAGATCATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGATCATGTT
* ** * *
38240190 CTTTAGCGGCGCTTTGGAGGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* **
38240233 CTATAGCGGCGCTT-GTTTAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGA-TCA-TGTT
38240275 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
38240290 TTTCACAAAC
Statistics
Matches: 315, Mismatches: 33, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.01
42 185 0.59
43 115 0.37
44 13 0.04
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:38244573 original size:9 final size:9
Alignment explanation
Indices: 38244556--38244713 Score: 140
Period size: 9 Copynumber: 17.4 Consensus size: 9
38244546 CTGCCTCATT
*
38244556 TGTAGGTTA
1 TGTAAGTTA
38244565 TGTAAGTTA
1 TGTAAGTTA
* *
38244574 TTTAATTTA
1 TGTAAGTTA
*
38244583 TGCAAGTTTA
1 TGTAAG-TTA
38244593 TGTAAGTTA
1 TGTAAGTTA
*
38244602 TGTAGGTTA
1 TGTAAGTTA
*
38244611 CT-TAATTTA
1 -TGTAAGTTA
38244620 TGTAAGTTA
1 TGTAAGTTA
38244629 TGTAAGTTA
1 TGTAAGTTA
* *
38244638 TTTAATTTA
1 TGTAAGTTA
*
38244647 TGTAGGTTA
1 TGTAAGTTA
38244656 TGTAAGTTA
1 TGTAAGTTA
*
38244665 TGTAACTTA
1 TGTAAGTTA
* *
38244674 TTTAATTTA
1 TGTAAGTTA
38244683 T-TCAAGTTA
1 TGT-AAGTTA
*
38244692 TGTAAGTAA
1 TGTAAGTTA
* *
38244701 TTTAATTTA
1 TGTAAGTTA
38244710 TGTA
1 TGTA
38244714 TAAGCTTGTA
Statistics
Matches: 118, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
8 2 0.02
9 106 0.90
10 10 0.08
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:38249181 original size:114 final size:114
Alignment explanation
Indices: 38248974--38249189 Score: 256
Period size: 114 Copynumber: 1.9 Consensus size: 114
38248964 ATTAAGTTTC
* * *
38248974 TTGCGGCGTTTTAATCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTCCAAATAAGCGCCA
1 TTGCGGCGTCTTAAACAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
* * ** * *
38249039 CTAATGAATCTATACGTGTAGTCGAAACGATGCGTTTTCCTAAGAAATG
66 CTAAAGAAGCTATACGTCAAGACAAAACGATGCGTTTTCCTAAGAAATG
* **
38249088 TTGCGGCG-CTTAAACATAAGCGCCACTAAAAGCTGATATTCAGCGGCGTTTACGGATAAGCGCC
1 TTGCGGCGTCTTAAACAAAAGCGCCACTAAAAGCTGATA-TCAGCGGCGTTTACAAATAAGCGCC
* ** *
38249152 AGTAAAGGCGCTATA-GCTCAAGACAAAACGTTGCGTTT
65 ACTAAAGAAGCTATACG-TCAAGACAAAACGATGCGTTT
38249190 CGGCTTCACA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
113 28 0.33
114 56 0.67
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (114 bp):
TTGCGGCGTCTTAAACAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
CTAAAGAAGCTATACGTCAAGACAAAACGATGCGTTTTCCTAAGAAATG
Found at i:38249563 original size:114 final size:114
Alignment explanation
Indices: 38249311--38249986 Score: 1120
Period size: 114 Copynumber: 5.9 Consensus size: 114
38249301 TAATAATGTG
* * *
38249311 CTTCAGCGGCGTTTTTATAGAAATGCCACCAATTCTACTATACGTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
38249376 TGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
66 TGTTTAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
* * * * *
38249426 CTTCAGCGGCGTTTCTATAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGTTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
* * *
38249491 TGTTTAACATTTTTTGCAGCGCTTACAAACAAACGCTGCTAATGATACA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
*
38249540 CTTCAGCGGCGTTTTTACAGAAACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
* *
38249605 TGTTTAACATTTTTTGCGGCGCTTACAAGCAAACGCTGCTAATGATCCA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
* * *
38249654 CTTCAGCGGCGTTTTTACGGAAACGCCACCAATTCTACTATACCTCAATCCTGTACACTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
*
38249719 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
*
38249768 CTTCAACGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
*
38249833 TGTTTAACATTTTTTGCTGCGCTTACAAACAAACGCCGCTAATGATCCA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
*
38249882 CTTCAGCGGCGTTCTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
* * *
38249947 TATTTAACA-TTTTTGTGGCGCTTACAAACAAATGCCGCTA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTA
38249987 CTGCCATTAT
Statistics
Matches: 525, Mismatches: 36, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
113 28 0.05
114 429 0.82
115 68 0.13
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (114 bp):
CTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
Found at i:38252698 original size:39 final size:37
Alignment explanation
Indices: 38252629--38252705 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 37
38252619 TCACATCGAT
*
38252629 AATTACTTAAAATTTTAAAAATATAGAAAATTATTTA
1 AATTACTTAAAATTTTAAAAATATAGAAAATTAATTA
* *
38252666 AATTATTTAAATATTTTGTAAAATATTA-AAAATTAATTA
1 AATTACTTAAA-ATTTT-AAAAATA-TAGAAAATTAATTA
38252705 A
1 A
38252706 TAGTTCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 10 0.29
38 5 0.15
39 17 0.50
40 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (37 bp):
AATTACTTAAAATTTTAAAAATATAGAAAATTAATTA
Found at i:38260361 original size:17 final size:17
Alignment explanation
Indices: 38260339--38260372 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38260329 CATAGTCCTG
38260339 ATTCAGGCAATCTATAT
1 ATTCAGGCAATCTATAT
* *
38260356 ATTCAGGTAGTCTATAT
1 ATTCAGGCAATCTATAT
38260373 TGAGATAGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (17 bp):
ATTCAGGCAATCTATAT
Found at i:38260929 original size:113 final size:114
Alignment explanation
Indices: 38260638--38261218 Score: 535
Period size: 114 Copynumber: 5.1 Consensus size: 114
38260628 CCTGAAGAAC
* *
38260638 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTAT-TGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
* *
38260702 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGA-AT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTAA-GGTATATTAGATAT
* * * * **
38260751 TCA-TGGCGTTTTTTATAAAAAAACACCGCT-AAAGAATAGT-ATTAGCGGCGTTTAACAAAAAG
1 T-AGTGGCG--TTTT-TAAAAAAACGCCG-TAAAAGAACA-TAATTAGTGGCGTTTATCTGAAAG
* ** * * *
38260813 CGCCGC-AAATATCTTAAGGAAAACGCACCGTTTTGTCTTAAGGTAGATTA-ATAT
60 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TTAAGGTATATTAGATAT
* * *
38260867 TAGTGGCGTTTTTAAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATCTGGAGGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
* *
38260932 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACT-T
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTAA-GGTATATTAGA-TAT
* * * * * *
38260982 T-GTGGCGTTTTCT-ATAAAACGCCGCAAAAGAATAGT-ATTAGCGGTGTTT-TCGTTAAAGCGC
1 TAGTGGCGTTTT-TAAAAAAACGCCGTAAAAGAACA-TAATTAGTGGCGTTTATC-TGAAAGCGC
* ** * * ** * *
38261043 CGC-AAATATCTTAATGAAAACACACCGTTTCATCTTGAGGTAGATTAG-TAT
63 CGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TTAAGGTATATTAGATAT
* * * ** *
38261094 TAGTGGCATTTTTAGAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
*
38261159 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA-AT
66 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTTAAGGTATATTAGATAT
38261208 TAGTGGCGTTT
1 TAGTGGCGTTT
38261219 ACGATAAAAC
Statistics
Matches: 370, Mismatches: 70, Indels: 55
0.75 0.14 0.11
Matches are distributed among these distances:
111 1 0.00
112 6 0.02
113 131 0.35
114 134 0.36
115 11 0.03
116 73 0.20
117 14 0.04
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATCTGAAAGCGCCGC
AAAATACCTTAACCAAAACGCAGCGTTTGGTTTAAGGTATATTAGATAT
Found at i:38261122 original size:227 final size:226
Alignment explanation
Indices: 38260638--38261236 Score: 853
Period size: 227 Copynumber: 2.6 Consensus size: 226
38260628 CCTGAAGAAC
*
38260638 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCGCCGCA
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCGCCGCA
*
38260703 AAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTCA-TGGCGTTTTTTAT
66 AAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATT-AGTGGCGTTTTCTAT
* *
38260767 AAAAAAACACCGCTAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGG
130 ---AAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGG
* **
38260832 AAAACGCACCGTTTTGTCTTAAGGTAGATTAATAT
192 AAAACACACCGTTTCATCTTAAGGTAGATTAATAT
* * *
38260867 TAGTGGCGTTTTTAAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATCTGGAGGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTAT-TGTAAGCGCCGC
* *
38260932 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACTTTGTGGCGTTTTCTAT
65 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTAT
* * ** *
38260997 AAAACGCCGCAAAAGAATAGTATTAGCGGTGTTT-TCGTTAAAGCGCCGCAAATATCTTAATGAA
130 AAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAAC-AAAAAGCGCCGCAAATATCTTAAGGAA
* *
38261061 AACACACCGTTTCATCTTGAGGTAGATTAGTAT
194 AACACACCGTTTCATCTTAAGGTAGATTAATAT
* * * *
38261094 TAGTGGCATTTTTAGAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCGCCGC
** * * *
38261159 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGA-GGTATATTAGAATTAGTGGCGTTTACGA
65 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAATTAGTGGCGTTTTCTA
38261223 TAAAACGCCGCAAA
129 TAAAACGCCGCAAA
38261237 TATCTTAAAG
Statistics
Matches: 333, Mismatches: 32, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
226 1 0.00
227 207 0.62
228 4 0.01
229 50 0.15
230 71 0.21
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (226 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCGCCGCA
AAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTATA
AAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAA
CACACCGTTTCATCTTAAGGTAGATTAATAT
Found at i:38261261 original size:74 final size:75
Alignment explanation
Indices: 38261153--38261292 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 75
38261143 TATTTTTATG
* * * *
38261153 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA-ATTAGTGGCGT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
38261217 TTACGATAAAA
65 TTACGATAAAA
* *
38261228 CGCCGC-AAATATCTTAAAGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
38261292 T
66 T
38261293 TTAAAAAAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 1 0.02
74 51 0.88
75 6 0.10
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
TACGATAAAA
Found at i:38261285 original size:188 final size:188
Alignment explanation
Indices: 38261035--38261421 Score: 621
Period size: 188 Copynumber: 2.1 Consensus size: 188
38261025 GTGTTTTCGT
* * *
38261035 TAAAGCGCCGCAAATATCTTAATGAAAACACACCGTTTCATCTTGAGGTAGATTAGTATTAGTGG
1 TAAAACGCCGCAAATATCTTAAAGAAAACACACCGTTTCATCTTGAGGTAGATTAATATTAGTGG
* * ** *
38261100 CATTTTTAGAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGCAAAATA
66 CATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATA
38261165 CCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGA
131 CCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGA
* **
38261223 TAAAACGCCGCAAATATCTTAAAGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGG
1 TAAAACGCCGCAAATATCTTAAAGAAAACACACCGTTTCATCTTGAGGTAGATTAATATTAGTGG
* *
38261288 CGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATG
66 CATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATA
* * * *
38261353 CCTTAACCAAAATGCAGCGTTTGGTTTTGATGTATATTAGAATTAGTGGCGTTTATGG
131 CCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGA
38261411 TAAAACGCCGC
1 TAAAACGCCGC
38261422 TAAAGAATAG
Statistics
Matches: 182, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
188 182 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (188 bp):
TAAAACGCCGCAAATATCTTAAAGAAAACACACCGTTTCATCTTGAGGTAGATTAATATTAGTGG
CATTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGACGTTTATTTGGAAGCGCCGCAAAATA
CCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGA
Found at i:38261302 original size:74 final size:75
Alignment explanation
Indices: 38261153--38261311 Score: 196
Period size: 74 Copynumber: 2.1 Consensus size: 75
38261143 TATTTTTATG
* * * *
38261153 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
* *
38261218 TACGATAAAA
66 TACAAAAAAA
* *
38261228 CGCCGC-AAATATCTTAAAGAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
1 CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAGA-ATTAGTGGCGT
**
38261291 TTTTAAAAAAA
65 TTACAAAAAAA
*
38261302 CGCCGTAAAA
1 CGCCGCAAAA
38261312 GAACATAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 61 0.86
75 9 0.13
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAAACAAAACGCACCGTTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
TACAAAAAAA
Found at i:38261859 original size:7 final size:7
Alignment explanation
Indices: 38261849--38261929 Score: 78
Period size: 7 Copynumber: 11.9 Consensus size: 7
38261839 GGTTTATGGA
38261849 TTAGGGG
1 TTAGGGG
38261856 TTAGGGG
1 TTAGGGG
*
38261863 TGT-TGGG
1 T-TAGGGG
38261870 TTAGGGG
1 TTAGGGG
38261877 TTAGGGG
1 TTAGGGG
38261884 TTAGGGG
1 TTAGGGG
38261891 TTA--GG
1 TTAGGGG
38261896 TTAGGGG
1 TTAGGGG
**
38261903 TTAGATG
1 TTAGGGG
* *
38261910 TTAAGAG
1 TTAGGGG
*
38261917 TTAGGGT
1 TTAGGGG
38261924 TTAGGG
1 TTAGGG
38261930 TTATAAAATC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 5 0.08
6 1 0.02
7 53 0.88
8 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.49, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:38261899 original size:19 final size:20
Alignment explanation
Indices: 38261875--38261929 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
38261865 TTGGGTTAGG
38261875 GGTTAGGGGTTAGGGGTT-A
1 GGTTAGGGGTTAGGGGTTAA
**
38261894 GGTTAGGGGTTAGATGTTAA
1 GGTTAGGGGTTAGGGGTTAA
*
38261914 GAGTTAGGGTTTAGGG
1 G-GTTAGGGGTTAGGG
38261930 TTATAAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (20 bp):
GGTTAGGGGTTAGGGGTTAA
Found at i:38261912 original size:26 final size:26
Alignment explanation
Indices: 38261868--38261921 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
38261858 AGGGGTGTTG
* * *
38261868 GGTTAGGGGTTAGGGGTTAGGGGTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTA
*
38261894 GGTTAGGGGTTAGATGTTAAGAGTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTA
38261920 GG
1 GG
38261922 GTTTAGGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.31
Consensus pattern (26 bp):
GGTTAGGGGTTAGAGGTTAAGAGTTA
Found at i:38262034 original size:14 final size:14
Alignment explanation
Indices: 38262015--38262058 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
38262005 TAGAGGTCAT
38262015 GGGTTAAGGGTTTA
1 GGGTTAAGGGTTTA
*
38262029 GGGTTAAGGGTTAA
1 GGGTTAAGGGTTTA
* *
38262043 AGGTT-AGGGGTTA
1 GGGTTAAGGGTTTA
38262056 GGG
1 GGG
38262059 GTTAGGGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.30
Consensus pattern (14 bp):
GGGTTAAGGGTTTA
Found at i:38262041 original size:21 final size:21
Alignment explanation
Indices: 38262015--38262089 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
38262005 TAGAGGTCAT
38262015 GGGTTAAGGGTTTAGGGTTAA
1 GGGTTAAGGGTTTAGGGTTAA
* *
38262036 GGGTTAAAGG-TTAGGGGTTAG
1 GGGTTAAGGGTTTA-GGGTTAA
* *
38262057 GGGTT-AGGGATT-GGGTTAT
1 GGGTTAAGGGTTTAGGGTTAA
*
38262076 GGTTTAA-GGTTTAG
1 GGGTTAAGGGTTTAG
38262090 ATTAATTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 14 0.32
20 8 0.18
21 22 0.50
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (21 bp):
GGGTTAAGGGTTTAGGGTTAA
Found at i:38262061 original size:14 final size:13
Alignment explanation
Indices: 38262015--38262074 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
38262005 TAGAGGTCAT
*
38262015 GGGTTAAGGGTTTA
1 GGGTT-AGGGGTTA
*
38262029 GGGTTAAGGGTTAA
1 GGGTTAGGGGTT-A
*
38262043 AGGTTAGGGGTTA
1 GGGTTAGGGGTTA
*
38262056 GGGGTTAGGGATT-
1 -GGGTTAGGGGTTA
38262069 GGGTTA
1 GGGTTA
38262075 TGGTTTAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 6 0.16
13 6 0.16
14 26 0.68
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.32
Consensus pattern (13 bp):
GGGTTAGGGGTTA
Done.