Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 114 of 196
Found at i:34616834 original size:20 final size:20
Alignment explanation
Indices: 34616771--34616835 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
34616761 AGTTTTTCCC
* * * *
34616771 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
34616791 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
34616810 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
34616831 AGCTC
1 AGCTC
34616836 GTTTGAACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:34619687 original size:16 final size:16
Alignment explanation
Indices: 34619666--34619696 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34619656 CTATACATGC
*
34619666 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
34619682 AAAATACAAAAGACA
1 AAAATACAAAAGACA
34619697 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:34622494 original size:10 final size:9
Alignment explanation
Indices: 34622472--34622502 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
34622462 ATATAAATCC
34622472 AAAAAATAA
1 AAAAAATAA
34622481 AAAAAATAA
1 AAAAAATAA
34622490 TAAAAAATAA
1 -AAAAAATAA
34622500 AAA
1 AAA
34622503 TAGGGCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:34622731 original size:13 final size:14
Alignment explanation
Indices: 34622706--34622734 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34622696 TTTAAATAAC
34622706 AATAAAGTAAAATA
1 AATAAAGTAAAATA
34622720 AATAAA-TAAAATA
1 AATAAAGTAAAATA
34622733 AA
1 AA
34622735 AACACTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAGTAAAATA
Found at i:34623148 original size:20 final size:21
Alignment explanation
Indices: 34623125--34623176 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
34623115 AAATGCAATA
34623125 ATTAAATTAAAA-ACAAAAA-T
1 ATTAAATTAAAATA-AAAAATT
34623145 ATTAAAATTAAAATAAAAAATT
1 ATT-AAATTAAAATAAAAAATT
*
34623167 GTTAAATTAA
1 ATTAAATTAA
34623177 TAGAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 21 0.75
22 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
ATTAAATTAAAATAAAAAATT
Found at i:34630793 original size:18 final size:18
Alignment explanation
Indices: 34630770--34630821 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
34630760 ATTTTATATG
*
34630770 AAAATCCCAGAATGATTT
1 AAAATCCCAGAAGGATTT
34630788 AAAATCCCAGAAGGATTT
1 AAAATCCCAGAAGGATTT
*
34630806 AAAATCCCTGAAGGAT
1 AAAATCCCAGAAGGAT
34630822 ATAGAGCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAATCCCAGAAGGATTT
Found at i:34636047 original size:40 final size:40
Alignment explanation
Indices: 34635770--34636033 Score: 340
Period size: 40 Copynumber: 6.7 Consensus size: 40
34635760 TTGAATGATG
* * * * *
34635770 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
34635810 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
34635850 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT-AA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34635888 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
34635928 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
34635968 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
34636009 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
34636034 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
38 10 0.05
39 46 0.23
40 135 0.67
41 10 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34643820 original size:40 final size:40
Alignment explanation
Indices: 34643736--34643960 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
34643726 TTGAATGATG
* * * *
34643736 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
34643776 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34643816 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34643855 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34643895 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
34643936 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
34643961 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34643982 original size:119 final size:119
Alignment explanation
Indices: 34643736--34643983 Score: 281
Period size: 119 Copynumber: 2.1 Consensus size: 119
34643726 TTGAATGATG
* *
34643736 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
34643801 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
34643855 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
34643918 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
34643975 TCC-GGTTAA
1 TCCGGGTTAA
34643984 ATTCCGAAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 75 0.69
120 31 0.28
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:34662937 original size:11 final size:11
Alignment explanation
Indices: 34662921--34663060 Score: 71
Period size: 11 Copynumber: 13.9 Consensus size: 11
34662911 TAAAAATATT
34662921 TATTTTAAAAA
1 TATTTTAAAAA
34662932 TATTTT--AAA
1 TATTTTAAAAA
34662941 -A--TTAAAAA
1 TATTTTAAAAA
* *
34662949 -A-ATTAAAAG
1 TATTTTAAAAA
34662958 TATTTTAAAAA
1 TATTTTAAAAA
34662969 TATTTT--AAA
1 TATTTTAAAAA
34662978 -A-TTTAAAAA
1 TATTTTAAAAA
*
34662987 -ATTTAAAAAAA
1 TATTT-TAAAAA
*
34662998 TTATTTTAAAAG
1 -TATTTTAAAAA
34663010 TATTTT--AAA
1 TATTTTAAAAA
34663019 -A-TTTAAAAA
1 TATTTTAAAAA
*
34663028 -ATTTAAAAAAA
1 TATTT-TAAAAA
*
34663039 TTATTTTAAAAG
1 -TATTTTAAAAA
34663051 TATTTTAAAA
1 TATTTTAAAA
34663061 TTTTAAAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.02
7 6 0.06
8 7 0.07
9 22 0.22
10 5 0.05
11 44 0.43
12 8 0.08
13 8 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:34663015 original size:41 final size:41
Alignment explanation
Indices: 34662888--34663071 Score: 232
Period size: 41 Copynumber: 4.5 Consensus size: 41
34662878 ACCAAAAATT
* * *
34662888 TATTTTAAAAATTAAAACAAAAATAAAAATATTTATTTTAAAAA
1 TATTTT-AAAATTTAAA-AAAATTAAAAA-AATTATTTTAAAAA
*
34662932 TATTTTAAAA-TTAAAAAAATT---AAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
* *
34662969 TATTTTAAAATTTAAAAAATTTAAAAAAATTATTTTAAAAG
1 TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
* *
34663010 TATTTTAAAATTTAAAAAATTTAAAAAAATTATTTTAAAAG
1 TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
34663051 TATTTTAAAATTTTAAAAAAA
1 TATTTTAAAA-TTTAAAAAAA
34663072 ATTATTGTAT
Statistics
Matches: 127, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
37 22 0.17
38 12 0.09
41 70 0.55
42 13 0.10
43 4 0.03
44 6 0.05
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (41 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
Found at i:34663040 original size:10 final size:9
Alignment explanation
Indices: 34662924--34663037 Score: 56
Period size: 9 Copynumber: 12.0 Consensus size: 9
34662914 AAATATTTAT
34662924 TTTAAAAATA
1 TTTAAAAA-A
*
34662934 TTT-TAAAA
1 TTTAAAAAA
34662942 -TTAAAAAA
1 TTTAAAAAA
* *
34662950 ATTAAAAGTAT
1 TTTAAAA--AA
34662961 TTTAAAAATA
1 TTTAAAAA-A
*
34662971 TTT-TAAAA
1 TTTAAAAAA
34662979 TTTAAAAAA
1 TTTAAAAAA
34662988 TTTAAAAAAATTA
1 TTT--AAAAA--A
*
34663001 TTTTAAAAGTA
1 -TTTAAAA-AA
*
34663012 TTT-TAAAA
1 TTTAAAAAA
34663020 TTTAAAAAA
1 TTTAAAAAA
34663029 TTTAAAAAA
1 TTTAAAAAA
34663038 ATTATTTTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.03
8 13 0.16
9 35 0.44
10 9 0.11
11 13 0.16
12 4 0.05
13 1 0.01
14 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:34668934 original size:18 final size:18
Alignment explanation
Indices: 34668911--34668951 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34668901 ATGTGTATCA
*
34668911 ATAAATA-ATTTAAAAATT
1 ATAAATATA-TTAAAAAAT
34668929 ATAAATATATTAAAAAAT
1 ATAAATATATTAAAAAAT
34668947 ATAAA
1 ATAAA
34668952 ATACTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATATATTAAAAAAT
Found at i:34686854 original size:16 final size:16
Alignment explanation
Indices: 34686833--34686864 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34686823 GAGAAAAGGA
34686833 ACCTTAAGAAATTAGC
1 ACCTTAAGAAATTAGC
34686849 ACCTTAAGAAATTAGC
1 ACCTTAAGAAATTAGC
34686865 CTCGCGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
ACCTTAAGAAATTAGC
Found at i:34691828 original size:21 final size:21
Alignment explanation
Indices: 34691788--34691829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34691778 AATTCCTAAG
**
34691788 ATATGAATTGCATTGTATTGA
1 ATATGAATTGCATTAAATTGA
*
34691809 ATATGAATTGTATTAAATTGA
1 ATATGAATTGCATTAAATTGA
34691830 TGTTAAATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (21 bp):
ATATGAATTGCATTAAATTGA
Found at i:34692383 original size:25 final size:26
Alignment explanation
Indices: 34692276--34692378 Score: 106
Period size: 26 Copynumber: 4.0 Consensus size: 26
34692266 ACAGCTCTTA
*
34692276 TGAGCGTCTCGA-TATATGGCTCTTCG
1 TGAGCTTCTCGATTA-ATGGCTCTTCG
* * * *
34692302 TGAGTTTCTCGATTAAAGGTTCTTTG
1 TGAGCTTCTCGATTAATGGCTCTTCG
34692328 TGAGCTTC-CTGATTAATGGCTC-TC-
1 TGAGCTTCTC-GATTAATGGCTCTTCG
34692352 TGGAGCTTCTCGATTAATGGCTCTTCG
1 T-GAGCTTCTCGATTAATGGCTCTTCG
34692379 AAGCTACCCG
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
24 1 0.02
25 21 0.34
26 38 0.61
27 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (26 bp):
TGAGCTTCTCGATTAATGGCTCTTCG
Found at i:34697493 original size:16 final size:16
Alignment explanation
Indices: 34697459--34697508 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
34697449 ATGACATCAG
34697459 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
34697475 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
34697491 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
34697507 TC
1 TC
34697509 CTGAGTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.18
16 19 0.68
17 4 0.14
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:34697749 original size:40 final size:41
Alignment explanation
Indices: 34697700--34697803 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
34697690 ACCAATTTGG
* * *
34697700 CACCTAGTGTCTCATCGGATAATTC-GAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGGATAAATCTGAAGCAGTAAATTGA
**
34697740 CACCCAGTGTCTCATCAAATAAATCTGAAGCAGTAAATTGA
1 CACCCAGTGTCTCATCGGATAAATCTGAAGCAGTAAATTGA
*
34697781 CACCCAGTGTCTCATCGGTTAAA
1 CACCCAGTGTCTCATCGGATAAA
34697804 CAGAAGTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 21 0.38
41 34 0.62
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGGATAAATCTGAAGCAGTAAATTGA
Found at i:34698723 original size:4 final size:4
Alignment explanation
Indices: 34698714--34698790 Score: 72
Period size: 4 Copynumber: 19.0 Consensus size: 4
34698704 TTGCTTTCTC
34698714 CTTT CTTT CTTT CTTT -TTT -TTT CTTTT CTTT CTTTT CTTT CTTT CCTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT C-TTT CTTT CTTT -CTTT
*
34698763 C-TT -TTT CATTTT GTTT CTTT CTTT CTTT
1 CTTT CTTT C--TTT CTTT CTTT CTTT CTTT
34698791 ATTCGTTTAC
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
3 10 0.16
4 38 0.60
5 12 0.19
6 3 0.05
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (4 bp):
CTTT
Found at i:34698745 original size:9 final size:9
Alignment explanation
Indices: 34698714--34698790 Score: 79
Period size: 9 Copynumber: 8.4 Consensus size: 9
34698704 TTGCTTTCTC
34698714 CTTTC-TTT
1 CTTTCTTTT
34698722 CTTTCTTTTT
1 CTTTC-TTTT
*
34698732 TTTTCTTTT
1 CTTTCTTTT
34698741 CTTTCTTTT
1 CTTTCTTTT
*
34698750 CTTTCTTTC
1 CTTTCTTTT
34698759 CTTTCTTTTT
1 CTTTC-TTTT
34698769 CATTT-TGTTT
1 C-TTTCT-TTT
34698779 CTTTC-TTT
1 CTTTCTTTT
34698787 CTTT
1 CTTT
34698791 ATTCGTTTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
8 12 0.20
9 29 0.49
10 15 0.25
11 3 0.05
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:34704171 original size:19 final size:19
Alignment explanation
Indices: 34704143--34704184 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
34704133 TAATGGACTT
34704143 TATAGGATAA-TTTATTGG
1 TATAGGATAATTTTATTGG
34704161 TATAGGGATAATTTTTATTGG
1 TATA-GGATAA-TTTTATTGG
34704182 TAT
1 TAT
34704185 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
21 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (19 bp):
TATAGGATAATTTTATTGG
Found at i:34704574 original size:5 final size:5
Alignment explanation
Indices: 34704564--34704589 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34704554 CTACATTGTA
34704564 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
34704590 AAGTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:34706741 original size:49 final size:49
Alignment explanation
Indices: 34706684--34706787 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
34706674 TCATGCGTTA
* * * *
34706684 TAATTTTATACAGTGTTGA-GTTTGTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTT-TGATTCATGATATTAAACTCAATTT
*
34706733 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
34706782 TAATTT
1 TAATTT
34706788 GTTTTTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 46 0.94
50 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:34708232 original size:110 final size:117
Alignment explanation
Indices: 34708113--34708378 Score: 336
Period size: 122 Copynumber: 2.3 Consensus size: 117
34708103 AATAAAGTAG
*
34708113 ATTA-TAAATTATAATTTAATAATAATTA-GTTAAATTATATTTTATATTATTATATATTATGA-
1 ATTATTAAATTATAATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGAT
*
34708175 TT-TTAGTAAATTCATA-TAAGAATA-A-GA-ATTTTATTAAATTATATATT
66 TTATTAGTAAATTCATATTAAGAATATATAACATTTTATTAAATTATATATT
* *
34708222 ATTATTAAATTAT-ATTTAATAATAATTATTTTAAATTATATTTTATAGTGTTATATATTATGAT
1 ATTATTAAATTATAATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGA-
34708286 TTTATTAGTAAATTCATATTTAAGAATATTTATTAATCATTTTATTAAATTATATATT
65 TTTATTAGTAAATTCATA-TTAAGAATA--TA-TAA-CATTTTATTAAATTATATATT
* * * *
34708344 TTTATTAAATTAT-ATTTTAGAACAATTATGTTAAA
1 ATTATTAAATTATAATTTAATAATAATTATGTTAAA
34708379 ATATGATTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
109 19 0.14
110 39 0.29
112 2 0.01
113 14 0.10
115 8 0.06
118 1 0.01
120 1 0.01
122 50 0.37
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (117 bp):
ATTATTAAATTATAATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGAT
TTATTAGTAAATTCATATTAAGAATATATAACATTTTATTAAATTATATATT
Found at i:34708255 original size:26 final size:28
Alignment explanation
Indices: 34708201--34708264 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
34708191 TAAGAATAAG
* * *
34708201 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
34708229 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
34708255 AATTATATTT
1 AATTATATTT
34708265 TATAGTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:34708550 original size:39 final size:41
Alignment explanation
Indices: 34708505--34708610 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 41
34708495 TTTCCTTATG
*
34708505 CTATTACACCTTTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACACCTTTATTCCATTCAACCAAACAAAAGAATTAC
* *
34708545 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTAC-AC-CT-TT--ATTCCATTCAACCAAACAAAAGAATTAC
* *
34708590 CTATTACGCCTCTATTCCATT
1 CTATTACACCTTTATTCCATT
34708611 ACACCTCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
39 5 0.09
40 2 0.04
41 9 0.17
42 2 0.04
43 1 0.02
44 24 0.45
45 5 0.09
46 5 0.09
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACACCTTTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:34708585 original size:44 final size:46
Alignment explanation
Indices: 34708522--34708613 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
34708512 ACCTTTATTC
*
34708522 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
34708566 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
34708612 CA
1 CA
34708614 CCTCTATTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.42
45 4 0.09
46 22 0.49
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:34708617 original size:16 final size:16
Alignment explanation
Indices: 34708592--34708629 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
34708582 AGAATTACCT
*
34708592 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
34708608 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
34708624 ATTACA
1 ATTACA
34708630 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:34709612 original size:9 final size:9
Alignment explanation
Indices: 34709598--34709628 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34709588 GTTAAACGAA
34709598 TCGAGTTAT
1 TCGAGTTAT
*
34709607 TCGAGTTAA
1 TCGAGTTAT
34709616 TCGAGTTAT
1 TCGAGTTAT
34709625 TCGA
1 TCGA
34709629 ATCAACTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:34713090 original size:29 final size:29
Alignment explanation
Indices: 34713044--34713099 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
34713034 TGTGACTTGT
*
34713044 TTTAATAGTACAAGGACTAAATTGATTCA
1 TTTAATAGTACAAAGACTAAATTGATTCA
* * *
34713073 TTTAGTAGTAGAAAGACTAATTTGATT
1 TTTAATAGTACAAAGACTAAATTGATT
34713100 AGGTCCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (29 bp):
TTTAATAGTACAAAGACTAAATTGATTCA
Found at i:34716439 original size:16 final size:16
Alignment explanation
Indices: 34716418--34716452 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
34716408 CTTGTTTTAT
*
34716418 TATTATAATAATATAA
1 TATTATAAAAATATAA
34716434 TATTATAAAAATATAA
1 TATTATAAAAATATAA
34716450 TAT
1 TAT
34716453 AACAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTATAAAAATATAA
Found at i:34723555 original size:21 final size:21
Alignment explanation
Indices: 34723522--34723561 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34723512 TTTGATTTTT
* *
34723522 TTCATGATGAAAATGCTGAAA
1 TTCAAGATCAAAATGCTGAAA
34723543 TTCAAGATCAAAATGCTGA
1 TTCAAGATCAAAATGCTGA
34723562 TGTGGCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
TTCAAGATCAAAATGCTGAAA
Found at i:34733445 original size:30 final size:29
Alignment explanation
Indices: 34733409--34733474 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
34733399 GCCCAAATAT
34733409 TATGTTATAAAACAT-ATTATATTAATTATA
1 TATGTTATAAAA-ATAATTATATTAATT-TA
* *
34733439 TATGTTA-AATAATAATTATATTTATTTA
1 TATGTTATAAAAATAATTATATTAATTTA
34733467 TAT-TTATA
1 TATGTTATA
34733475 TTAAATCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 8 0.25
29 14 0.44
30 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (29 bp):
TATGTTATAAAAATAATTATATTAATTTA
Found at i:34737683 original size:20 final size:20
Alignment explanation
Indices: 34737654--34737691 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34737644 TCCAAAAGAA
*
34737654 ATATAAATATAAACTTATAT
1 ATATAAATATAAAATTATAT
*
34737674 ATATATATATAAAATTAT
1 ATATAAATATAAAATTAT
34737692 TGGTTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAAATATAAAATTATAT
Found at i:34746213 original size:9 final size:9
Alignment explanation
Indices: 34746177--34746219 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
34746167 AACAAAAAGG
34746177 AAGAAAAGAA
1 AAGAAAA-AA
*
34746187 AACAAAAAA
1 AAGAAAAAA
*
34746196 ATAGCAAAAA
1 A-AGAAAAAA
34746206 AAGAAAAAA
1 AAGAAAAAA
34746215 AAGAA
1 AAGAA
34746220 TAGAAAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:34746216 original size:23 final size:23
Alignment explanation
Indices: 34746180--34746226 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
34746170 AAAAAGGAAG
34746180 AAAAGAAAACAAAAAAATAGCAAA
1 AAAAGAAAACAAAAAAATAG-AAA
*
34746204 AAAAGAAAA-AAAAGAATAGAAA
1 AAAAGAAAACAAAAAAATAGAAA
34746226 A
1 A
34746227 GAGGATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAGAAAACAAAAAAATAGAAA
Found at i:34746226 original size:20 final size:20
Alignment explanation
Indices: 34746162--34746226 Score: 53
Period size: 23 Copynumber: 3.1 Consensus size: 20
34746152 CGCAGCACAC
* *
34746162 AAAAGAACAAAAAGGA-AG-
1 AAAAGAAAAAAAAGAATAGA
*
34746180 AAAAGAAAACAAAAAAATAGCAAA
1 AAAAGAAAA-AAAAGAATAG---A
34746204 AAAAGAAAAAAAAGAATAGA
1 AAAAGAAAAAAAAGAATAGA
34746224 AAA
1 AAA
34746227 GAGGATGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 8 0.22
19 5 0.14
20 6 0.16
23 9 0.24
24 9 0.24
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAATAGA
Found at i:34747359 original size:19 final size:20
Alignment explanation
Indices: 34747331--34747370 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
34747321 TTCTAAATTA
*
34747331 TTATCCACATGA-TTTAAAT
1 TTATCAACATGATTTTAAAT
*
34747350 TTATCAACATTATTTTAAAT
1 TTATCAACATGATTTTAAAT
34747370 T
1 T
34747371 CTTTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATCAACATGATTTTAAAT
Found at i:34747468 original size:25 final size:24
Alignment explanation
Indices: 34747428--34747477 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
34747418 CATTATTTTT
*
34747428 AATATATATATATGTG-TTTATAA
1 AATATATATATATGTGCCTTATAA
*
34747451 AATATATTATAATTTGTGCCTTATAA
1 AATATA-TAT-ATATGTGCCTTATAA
34747477 A
1 A
34747478 TTTTTATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 6 0.27
26 7 0.32
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
AATATATATATATGTGCCTTATAA
Found at i:34747686 original size:26 final size:27
Alignment explanation
Indices: 34747656--34747706 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
34747646 TAGAATTTGT
34747656 TTGTTATTC-ATCAT-TTGCTTTGTATA
1 TTGTTATTCAATCATATTG-TTTGTATA
34747682 TTGTTATTCAATCATATTGTTTGTA
1 TTGTTATTCAATCATATTGTTTGTA
34747707 GGAATTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.39
27 11 0.48
28 3 0.13
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (27 bp):
TTGTTATTCAATCATATTGTTTGTATA
Found at i:34751104 original size:19 final size:18
Alignment explanation
Indices: 34751080--34751125 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
34751070 ACGCTCTTTT
*
34751080 TGCATTCATTTCATGCATA
1 TGCATTCATGTCAT-CATA
34751099 TGCATTGCATGTCATCATA
1 TGCATT-CATGTCATCATA
34751118 TGCATTCA
1 TGCATTCA
34751126 AGATTACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.64
20 7 0.28
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (18 bp):
TGCATTCATGTCATCATA
Found at i:34753650 original size:35 final size:35
Alignment explanation
Indices: 34753611--34753680 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
34753601 GCTCCATATA
*
34753611 TATAAATTTAACAACCGCATATCACC-ATGTACATT
1 TATAAATTCAACAACCGCATAT-ACCAATGTACATT
*
34753646 TATAAATTCAATAACCGCATATACCTAATGTACAT
1 TATAAATTCAACAACCGCATATACC-AATGTACAT
34753681 ATGCCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.10
35 20 0.65
36 8 0.26
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (35 bp):
TATAAATTCAACAACCGCATATACCAATGTACATT
Found at i:34753958 original size:41 final size:41
Alignment explanation
Indices: 34753902--34754004 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
34753892 TGATTCGATA
* * * *
34753902 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
* ** *
34753943 CACCGGCATTAAGCCTGCTAGACGTAAAGTTTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
34753984 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
34754005 GCATATAGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
Found at i:34754019 original size:41 final size:41
Alignment explanation
Indices: 34753902--34754019 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
34753892 TGATTCGATA
* * * * *
34753902 CACCGGCTTTTAGCCTGCTAGACCTATAGTCC-GAAATGTTT
1 CACCGGCATTAAGCCTGCTAGACATATAG-CCTGAATTATTT
* * **
34753943 CACCGGCATTAAGCCTGCTAGACGTAAAGTTTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACATATAGCCTGAATTATTT
*
34753984 CACCGGCATTAAGCCTGCTAGGCATATAGCCTGAAT
1 CACCGGCATTAAGCCTGCTAGACATATAGCCTGAAT
34754020 AACTGAGATG
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGCCTGAATTATTT
Found at i:34754297 original size:14 final size:15
Alignment explanation
Indices: 34754278--34754307 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
34754268 TCTAACCTCT
34754278 TATATATATTT-ATA
1 TATATATATTTCATA
34754292 TATATATATTTCATA
1 TATATATATTTCATA
34754307 T
1 T
34754308 CTTTTCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATATTTCATA
Found at i:34754655 original size:21 final size:21
Alignment explanation
Indices: 34754629--34754672 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
34754619 TAAAATCAAC
*
34754629 TTCAGCTTGTAGAACATAAAA
1 TTCAGCTTATAGAACATAAAA
34754650 TTCAGCTTATAGAACATAAAA
1 TTCAGCTTATAGAACATAAAA
34754671 TT
1 TT
34754673 TGCTATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCAGCTTATAGAACATAAAA
Found at i:34758900 original size:35 final size:35
Alignment explanation
Indices: 34758861--34758930 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
34758851 GCTCCATATA
*
34758861 TATAAATTTAACAACCGCATATCACC-ATGTACATT
1 TATAAATTCAACAACCGCATAT-ACCAATGTACATT
*
34758896 TATAAATTCAATAACCGCATATACCTAATGTACAT
1 TATAAATTCAACAACCGCATATACC-AATGTACAT
34758931 ATGCCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.10
35 20 0.65
36 8 0.26
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (35 bp):
TATAAATTCAACAACCGCATATACCAATGTACATT
Found at i:34759208 original size:41 final size:41
Alignment explanation
Indices: 34759152--34759254 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
34759142 TGATTCGATA
* * * *
34759152 CACCGGCTTTTAGCCTGCTAGACCTATAGTCTGAAATGTTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCTGAAATATTT
* *
34759193 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCTGAAATATTT
*
34759234 CACCGGCATTAAGCCTTCTAG
1 CACCGGCATTAAGCCTGCTAG
34759255 GCACATAGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCTGAAATATTT
Found at i:34759268 original size:41 final size:41
Alignment explanation
Indices: 34759152--34759269 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
34759142 TGATTCGATA
* * * * * *
34759152 CACCGGCTTTTAGCCTGCTAGAC-CTATAGTCTGAAATGTTT
1 CACCGGCATTAAGCCTGCTAGACAC-AAAGCCTGAATTATTT
** *
34759193 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATTT
* * *
34759234 CACCGGCATTAAGCCTTCTAGGCACATAGCCTGAAT
1 CACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
34759270 AACTGAGATG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATTT
Found at i:34759544 original size:12 final size:12
Alignment explanation
Indices: 34759527--34759557 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
34759517 TTCTAACCTC
34759527 TTATATATATAT
1 TTATATATATAT
34759539 TTATATATATAT
1 TTATATATATAT
34759551 TTCATAT
1 TT-ATAT
34759558 CTTTTCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATATATAT
Found at i:34759905 original size:21 final size:21
Alignment explanation
Indices: 34759879--34759922 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
34759869 TAAAATCAAC
* *
34759879 TTCAGCTTGTAGAACATAAAA
1 TTCAGCTTATAAAACATAAAA
34759900 TTCAGCTTATAAAACATAAAA
1 TTCAGCTTATAAAACATAAAA
34759921 TT
1 TT
34759923 TGCTATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (21 bp):
TTCAGCTTATAAAACATAAAA
Found at i:34767869 original size:44 final size:43
Alignment explanation
Indices: 34767806--34767929 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 43
34767796 ATCGCATCAA
34767806 ATTGAAACTAGAAATCTTATCTCTCTGAGATTACAGCGGAGCAG
1 ATTGAAACTAG-AATCTTATCTCTCTGAGATTACAGCGGAGCAG
* * * *
34767850 ATTGAAGCTAGTAATCTTATCTCGCGGAGATTACAGTGGAGCAG
1 ATTGAAACTAG-AATCTTATCTCTCTGAGATTACAGCGGAGCAG
*
34767894 ATT-AAAATAAAGAATCTTATCTCTCTGA-AGTTACAG
1 ATTGAAACT--AGAATCTTATCTCTCTGAGA-TTACAG
34767930 TAGAGTTGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 4 0.06
44 62 0.91
45 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (43 bp):
ATTGAAACTAGAATCTTATCTCTCTGAGATTACAGCGGAGCAG
Found at i:34768016 original size:46 final size:46
Alignment explanation
Indices: 34767949--34768051 Score: 197
Period size: 46 Copynumber: 2.2 Consensus size: 46
34767939 TCGCATCAGG
*
34767949 TCTTATCTCCCTGAGATTACAGTTGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
34767995 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
34768041 TCTTATCTCCC
1 TCTTATCTCCC
34768052 AAGCGGTGCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
Found at i:34770046 original size:21 final size:22
Alignment explanation
Indices: 34770020--34770069 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
34770010 CACGTTCTTC
*
34770020 TAAATTATTATCCACATGA-TT
1 TAAATTATTATCAACATGATTT
*
34770041 TAAA-T-TTATCAACATTATTT
1 TAAATTATTATCAACATGATTT
34770061 TAAATTATT
1 TAAATTATT
34770070 TTTACTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
21 5 0.21
22 2 0.08
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAATTATTATCAACATGATTT
Found at i:34770396 original size:27 final size:26
Alignment explanation
Indices: 34770348--34770398 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
34770338 TAGAATTTGT
*
34770348 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTATTCATCAATTGCTTTGTATA
34770374 TTGTTATTCAATCACATTG-TTTGTA
1 TTGTTATTC-ATCA-ATTGCTTTGTA
34770399 AGAATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (26 bp):
TTGTTATTCATCAATTGCTTTGTATA
Found at i:34775548 original size:40 final size:42
Alignment explanation
Indices: 34775502--34775592 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 42
34775492 CCGATGTGAT
34775502 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTG
1 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCC-----G
34775549 ATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 --GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
34775593 ATGTGATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
44 1 0.02
49 41 0.98
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (42 bp):
GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
Found at i:34776363 original size:47 final size:47
Alignment explanation
Indices: 34775479--34776334 Score: 1399
Period size: 47 Copynumber: 18.1 Consensus size: 47
34775469 GAAATGATAG
* * *
34775479 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTG--TATATGTGTGA
* * * *
34775528 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTG--TATATGTGTGA
* * *
34775577 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
34775624 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
34775671 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
34775718 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
34775765 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
34775812 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
34775859 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
34775906 TAGGGCCTAATAGCCGAGGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
34775953 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
34776000 T-AGGCCTAATAGCCGAGGTGATGAATGTGAAAGTATATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
34776046 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
34776093 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
34776140 TATGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
34776187 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
34776234 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* * *
34776281 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
34776328 CAAGGCC
1 TAAGGCC
34776335 GAGTGGCCAA
Statistics
Matches: 775, Mismatches: 31, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 0.06
47 647 0.83
49 84 0.11
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:34776553 original size:37 final size:37
Alignment explanation
Indices: 34776497--34776575 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
34776487 CCGAGCTCTA
* * *
34776497 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
34776534 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
34776571 AAGAC
1 AAGAC
34776576 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:34785778 original size:51 final size:51
Alignment explanation
Indices: 34785702--34785865 Score: 283
Period size: 51 Copynumber: 3.2 Consensus size: 51
34785692 CTAATCAATG
34785702 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
* *
34785753 ACAAGTGATTAGTGGTTGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
* * *
34785804 ACAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
34785855 ACAAGTGATAA
1 ACAAGTGATAA
34785866 ATGTGATCCG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 105 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
Found at i:34786776 original size:155 final size:156
Alignment explanation
Indices: 34786493--34786805 Score: 576
Period size: 155 Copynumber: 2.0 Consensus size: 156
34786483 CTATTCCGGT
34786493 GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
1 GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
*
34786558 TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAATCCTGATAATGCTCTGTAACCCT
66 TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAACCCTGATAATGCTCTGTAACCCT
34786623 GTTTTGGTAACAGATACGGGTTAGGG
131 GTTTTGGTAACAGATACGGGTTAGGG
34786649 GTTGGATACAGG-TAAGGGGTGTTACAATATATGA-TTTTTATAAGTTTTATTATGAATATTGAT
1 GTTGGATAC-GGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGAT
*
34786712 ATGTAATGAAACATTTGAAATTTCTATCTGATTGATCTGTAAACCCTGATAATGCTCTGTAACCC
65 ATGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAACCCTGATAATGCTCTGTAACCC
*
34786777 TGTTTTGGTAACATATACGGGTTAGGG
130 TGTTTTGGTAACAGATACGGGTTAGGG
34786804 GT
1 GT
34786806 GTTACAGGGA
Statistics
Matches: 153, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
155 120 0.78
156 31 0.20
157 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (156 bp):
GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAACCCTGATAATGCTCTGTAACCCT
GTTTTGGTAACAGATACGGGTTAGGG
Found at i:34787793 original size:40 final size:40
Alignment explanation
Indices: 34787704--34787967 Score: 368
Period size: 40 Copynumber: 6.6 Consensus size: 40
34787694 GTCGAGGTAT
* * * * *
34787704 AAACAGGGGCACGAAAGTGCATTCA-GAGTACCGAATTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* *
34787743 AAACAGGGGCACATATGTGCAATCAGGGGTATCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* * ** *
34787783 AAACAGGGGCACGTATGTACAATAAGGGGTATTGATGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
*
34787823 AAACAGGGGCACGTATATGCAATCAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* *
34787863 AAACAGGGGCATGTATGTGCAATTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* *
34787903 AAACAAGGGCACGTATGTGCAATCAGGGGTACCGGAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
34787943 AAACAGGGGCACGTATGTGCAATCA
1 AAACAGGGGCACGTATGTGCAATCA
34787968 TACAATAATT
Statistics
Matches: 198, Mismatches: 26, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
39 21 0.11
40 177 0.89
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (40 bp):
AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
Found at i:34789234 original size:25 final size:25
Alignment explanation
Indices: 34789200--34789252 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
34789190 AAATAATTTC
34789200 TAAAATTAAATATAACAATTAATAA
1 TAAAATTAAATATAACAATTAATAA
* *
34789225 TAAATTTAAATATAATAATTAATAA
1 TAAAATTAAATATAACAATTAATAA
34789250 TAA
1 TAA
34789253 GTTTTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAATTAAATATAACAATTAATAA
Found at i:34789248 original size:12 final size:12
Alignment explanation
Indices: 34789200--34789246 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
34789190 AAATAATTTC
34789200 TAAAATTAAATA
1 TAAAATTAAATA
34789212 TAACAATT-AATAA
1 TAA-AATTAAAT-A
*
34789225 TAAATTTAAATA
1 TAAAATTAAATA
34789237 TAATAATTAA
1 TAA-AATTAA
34789247 TAATAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 13 0.45
13 16 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATTAAATA
Found at i:34794521 original size:23 final size:23
Alignment explanation
Indices: 34794478--34794520 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
34794468 TAAATAATTT
34794478 AAAATTTCATAAAAATCAAAATC
1 AAAATTTCATAAAAATCAAAATC
34794501 AAAATTT-A-AAAAATTCAAAA
1 AAAATTTCATAAAAA-TCAAAA
34794521 AAACAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAATTTCATAAAAATCAAAATC
Found at i:34800090 original size:18 final size:19
Alignment explanation
Indices: 34800067--34800111 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
34800057 TTCAAAAAAA
34800067 TTAAAATAATTT-T-AAATT
1 TTAAAAT-ATTTATAAAATT
34800085 TTAAAATATTTATAAAAATT
1 TTAAAATATTTAT-AAAATT
34800105 TTAAAAT
1 TTAAAAT
34800112 TTATATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
20 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATATTTATAAAATT
Found at i:34800136 original size:9 final size:9
Alignment explanation
Indices: 34800080--34800142 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
34800070 AAATAATTTT
34800080 AAATTTTAA
1 AAATTTTAA
34800089 AATATTTATAA
1 AA-ATTT-TAA
34800100 AAATTTT-A
1 AAATTTTAA
34800108 AAA-TTT--
1 AAATTTTAA
*
34800114 ATATTTTAAA
1 AAATTTT-AA
34800124 AAATTTTAA
1 AAATTTTAA
*
34800133 AAATTGTAA
1 AAATTTTAA
34800142 A
1 A
34800143 TAATATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
6 2 0.04
7 6 0.13
8 4 0.09
9 14 0.31
10 14 0.31
11 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
AAATTTTAA
Found at i:34800150 original size:33 final size:34
Alignment explanation
Indices: 34800082--34800151 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
34800072 ATAATTTTAA
* * *
34800082 ATTTTAAAATATTTATAAAAATTTTAAAATTTAT
1 ATTTTAAAAAATTTATAAAAATTGTAAAATATAT
34800116 ATTTTAAAAAATTT-TAAAAATTGTAAATAATATAT
1 ATTTTAAAAAATTTATAAAAATTGT-AA-AATATAT
34800151 A
1 A
34800152 AAAAAAGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 9 0.29
34 15 0.48
35 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
ATTTTAAAAAATTTATAAAAATTGTAAAATATAT
Found at i:34801072 original size:31 final size:31
Alignment explanation
Indices: 34801035--34801098 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
34801025 TTGCAAAATG
* *
34801035 GTCACTGAACTATTCAAAAG-TTTTCATTTAA
1 GTCACTGAACTATACAAAAGCTCTT-ATTTAA
*
34801066 GTCACTGAATTATACAAAAGCTCTTATTTAA
1 GTCACTGAACTATACAAAAGCTCTTATTTAA
34801097 GT
1 GT
34801099 AGTTGGGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (31 bp):
GTCACTGAACTATACAAAAGCTCTTATTTAA
Found at i:34803662 original size:13 final size:15
Alignment explanation
Indices: 34803636--34803667 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
34803626 ATGTAATTTT
34803636 TTTTCTTTATTTTCC
1 TTTTCTTTATTTTCC
34803651 TTTTC-TTA-TTTCC
1 TTTTCTTTATTTTCC
34803664 TTTT
1 TTTT
34803668 GTTTTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTATTTTCC
Found at i:34803900 original size:5 final size:5
Alignment explanation
Indices: 34803890--34803915 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34803880 TGAGCATTCG
34803890 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
34803916 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:34804713 original size:30 final size:31
Alignment explanation
Indices: 34804674--34804733 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
34804664 GGAGGTGGAT
*
34804674 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
34804705 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
34804734 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:34805204 original size:30 final size:29
Alignment explanation
Indices: 34805170--34805242 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
34805160 TTAACAGCTC
*
34805170 AGTGACTAAAATGTTACAACACTT-AACGTA
1 AGTGACTAAAATGTT--AACACTTAAACATA
*
34805200 AGTGACTAAAACG-TAACACTTCAAACATA
1 AGTGACTAAAATGTTAACACTT-AAACATA
34805229 AGTGACTAAAATGT
1 AGTGACTAAAATGT
34805243 AACCTGAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 7 0.19
29 18 0.49
30 12 0.32
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTTAACACTTAAACATA
Found at i:34808145 original size:4 final size:4
Alignment explanation
Indices: 34808136--34808168 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
34808126 AATTAAAACT
34808136 CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA C
34808169 CTTGGGAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:34810208 original size:181 final size:180
Alignment explanation
Indices: 34809953--34810300 Score: 486
Period size: 181 Copynumber: 1.9 Consensus size: 180
34809943 AAAAAATTCA
* * *
34809953 AATTTGAATATTCGAATCAATCGATTCAAACTCAAATTCGATCTCATCCAATTTGATCATTAAAA
1 AATTTGAATATTCGAATCAATCAATTCAAACTCAAATTCGACCCCATCCAATTTGATCATTAAAA
** * * *
34810018 AACTCAAACCACCTGACCTTAAA-TCCAAATTGAATTAAATTTGGATTAACTTGGACATAAAGTG
66 AACTCAAACCACCCAACCCTAAACT-CAAATTGAATTAAATTT-GAATAACTTGAACATAAAGTG
*
34810082 AGTAAAACTTGAACTGATTCGAACTTC-TTAATGACCCAATTTGGAAATATCCG
129 AGTAAAACCTGAACTGATTCGAAC--CATTAATGACCCAATTTGGAAATATCCG
* * *
34810135 AATTTGAATATTCGAATCGATCAATTCAAACTCCAATTC-ACCCCATCCTATTTGATCATTAAAA
1 AATTTGAATATTCGAATCAATCAATTCAAACTCAAATTCGACCCCATCCAATTTGATCATTAAAA
* * * * *
34810199 ATCTCAAACCACCCAACCCTAAACTCAAATTGAATTGAATTTGAATAACTTGAACGTGAAGTGAT
66 AACTCAAACCACCCAACCCTAAACTCAAATTGAATTAAATTTGAATAACTTGAACATAAAGTGAG
34810264 TAAAACCTGAACTGATTCGAACCATTAATGACCCAAT
131 TAAAACCTGAACTGATTCGAACCATTAATGACCCAAT
34810301 CCAAAAAAAC
Statistics
Matches: 147, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
178 1 0.01
179 13 0.09
180 39 0.27
181 57 0.39
182 37 0.25
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.30
Consensus pattern (180 bp):
AATTTGAATATTCGAATCAATCAATTCAAACTCAAATTCGACCCCATCCAATTTGATCATTAAAA
AACTCAAACCACCCAACCCTAAACTCAAATTGAATTAAATTTGAATAACTTGAACATAAAGTGAG
TAAAACCTGAACTGATTCGAACCATTAATGACCCAATTTGGAAATATCCG
Found at i:34815499 original size:3 final size:3
Alignment explanation
Indices: 34815493--34815520 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34815483 CAAAAAAATT
34815493 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34815521 AGGAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:34816817 original size:41 final size:41
Alignment explanation
Indices: 34816760--34816955 Score: 236
Period size: 41 Copynumber: 4.8 Consensus size: 41
34816750 GAGTTTTTGG
* *
34816760 GGTCTTTAGCGACATTTTCTGAA-AAGCGTCGCTAATGCTCA
1 GGTCTTTAGCGGCATTTT-TGAATAAGCGCCGCTAATGCTCA
*
34816801 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATTCTCA
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
* * *
34816842 GGTCTTTAGCAGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
* * *
34816883 GGTCTTTAGCGGCGTTTTTTAATAAGCGCTGCTAATGCTC-
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
* **
34816923 -GTACCTTTAGCGGCGTTTTTGAGGAAGCGCCGC
1 GGT--CTTTAGCGGCATTTTTGAATAAGCGCCGC
34816956 AAAAACATTT
Statistics
Matches: 139, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.01
40 4 0.03
41 133 0.96
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (41 bp):
GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
Found at i:34817549 original size:20 final size:21
Alignment explanation
Indices: 34817515--34817553 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34817505 TAAATAATAT
34817515 TTAGGGGTTAGGGATTTAGTG
1 TTAGGGGTTAGGGATTTAGTG
*
34817536 TTAGGGTTTA-GGATTTAG
1 TTAGGGGTTAGGGATTTAG
34817554 ATTAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (21 bp):
TTAGGGGTTAGGGATTTAGTG
Found at i:34817571 original size:80 final size:76
Alignment explanation
Indices: 34817451--34817601 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 76
34817441 GGATTCGGTG
*
34817451 TTAGGTTAGAGTTTAGGGTTTAGACTAATTAATATATTTTAAATTATATAACATTAAATAATATT
1 TTAGGTTAGAGTTTAGGATTTAGACTAATTAATATATTTT-AATT-TAT-ACATTAAATAATATT
34817516 TAGGGGTTAGGGAT
63 TAGGGGTTAGGGAT
* * * * * * *
34817530 TTAGTGTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTA
1 TTAG-GTTAGAGTTTAGGATTTAGACTAATTAATATATTTTAATTTATACATTAAATAATATTTA
34817595 GGGGTTA
65 GGGGTTA
34817602 TGGGGTTAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 22 0.35
78 3 0.05
79 8 0.13
80 30 0.48
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (76 bp):
TTAGGTTAGAGTTTAGGATTTAGACTAATTAATATATTTTAATTTATACATTAAATAATATTTAG
GGGTTAGGGAT
Found at i:34817721 original size:89 final size:89
Alignment explanation
Indices: 34817535--34817785 Score: 439
Period size: 89 Copynumber: 2.8 Consensus size: 89
34817525 GGGATTTAGT
*
34817535 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
*
34817600 TATGGGGTTAGTGATTTGGGGTCGA
66 TA-GGGGTTAGTGATTCGGGGTCGA
*
34817625 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATATTTAGGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
*
34817690 TAGGGGTTAGTGATTCGGGGTTGA
66 TAGGGGTTAGTGATTCGGGGTCGA
*
34817714 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGTT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
*
34817779 TAAGGGT
66 TAGGGGT
34817786 AGGGGTTTAG
Statistics
Matches: 154, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 89 0.58
90 65 0.42
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (89 bp):
GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
TAGGGGTTAGTGATTCGGGGTCGA
Found at i:34817822 original size:28 final size:28
Alignment explanation
Indices: 34817769--34817839 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
34817759 ATTAAATAAT
*
34817769 GTTTAGGGTTTAAGGGTAGGGGTTT-AG
1 GTTTAGGGTTTAAGGGTAGGGATTTAAG
* *
34817796 AGTTTAGGG-TTAAGAGTTAGTGATTTAAG
1 -GTTTAGGGTTTAAG-GGTAGGGATTTAAG
* *
34817825 GTTTAGAGATTAAGG
1 GTTTAGGGTTTAAGG
34817840 TTTAAGCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 5 0.14
28 24 0.67
29 7 0.19
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (28 bp):
GTTTAGGGTTTAAGGGTAGGGATTTAAG
Found at i:34818567 original size:23 final size:22
Alignment explanation
Indices: 34818520--34818574 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
34818510 TAATTTTATC
34818520 AAAAACTTT--TAAATATTACT
1 AAAAACTTTAATAAATATTACT
* *
34818540 TAAAACTTTAATAATTATTTACT
1 AAAAACTTTAATAAATA-TTACT
*
34818563 AAAAATTTTAAT
1 AAAAACTTTAAT
34818575 GAAAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
22 5 0.18
23 15 0.54
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAACTTTAATAAATATTACT
Found at i:34824099 original size:35 final size:35
Alignment explanation
Indices: 34824059--34824127 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
34824049 TTCAATTTTC
34824059 GAAAGTGATAATTTATCAGTCAATAGATACATTTA
1 GAAAGTGATAATTTATCAGTCAATAGATACATTTA
* *
34824094 GAAAGTGATAATTTATCATTCAATGGATACATTT
1 GAAAGTGATAATTTATCAGTCAATAGATACATTT
34824128 TCATGGGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (35 bp):
GAAAGTGATAATTTATCAGTCAATAGATACATTTA
Found at i:34838962 original size:33 final size:33
Alignment explanation
Indices: 34838925--34839017 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
34838915 TATCTCGGCG
* *
34838925 GACTTACTCTTTTTCGTGTTTACTGTCCCGATA
1 GACTTACTCTGTTTCGTGTTTACTATCCCGATA
* *
34838958 GACTTACTCTGTTTCGTGTTTGCTATCCCGATG
1 GACTTACTCTGTTTCGTGTTTACTATCCCGATA
*
34838991 GACTTACTCTG-TTCTGTGTTTATTATC
1 GACTTACTCTGTTTC-GTGTTTACTATC
34839018 TTGGTAGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 3 0.06
33 50 0.94
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
GACTTACTCTGTTTCGTGTTTACTATCCCGATA
Found at i:34842446 original size:25 final size:25
Alignment explanation
Indices: 34842408--34842460 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
34842398 TTTGAAAAAA
** *
34842408 ATTAATTTTGATAAAGTAAA-ATTAT
1 ATTAATTTAAATAAA-TAAATATGAT
34842433 ATTAATTTAAATAAATAAATATGAT
1 ATTAATTTAAATAAATAAATATGAT
34842458 ATT
1 ATT
34842461 TTTAGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (25 bp):
ATTAATTTAAATAAATAAATATGAT
Found at i:34843734 original size:33 final size:29
Alignment explanation
Indices: 34843689--34843749 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
34843679 TCAGCTTACC
*
34843689 GTTACACCGTTAACGGCTCAGTGACTAAAAT
1 GTTACACCGTTAAC-G-TAAGTGACTAAAAT
34843720 GTTACAACACGTTAACGTAAGTGACTAAAA
1 GTTAC-AC-CGTTAACGTAAGTGACTAAAA
34843750 CATAACACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 17 0.63
32 3 0.11
33 7 0.26
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (29 bp):
GTTACACCGTTAACGTAAGTGACTAAAAT
Found at i:34847838 original size:40 final size:38
Alignment explanation
Indices: 34847749--34847839 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 38
34847739 ATAAGTTCTT
* *
34847749 AATTTCATAAAATTTTATAACCTATATTTTAATTTATA
1 AATTTTATAAAATTTTATAACATATATTTTAATTTATA
* *
34847787 AATATTGTATAAAATTTTATGACAT-TTTTTTAATTCTTATA
1 AAT-TT-TATAAAATTTTATAACATATATTTTAA-T-TTATA
34847828 ACATTTTATAAA
1 A-ATTTTATAAA
34847840 TATATTTGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
38 3 0.07
39 9 0.20
40 22 0.50
41 8 0.18
42 2 0.05
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (38 bp):
AATTTTATAAAATTTTATAACATATATTTTAATTTATA
Found at i:34849546 original size:15 final size:15
Alignment explanation
Indices: 34849526--34849555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34849516 GGGATATGTT
34849526 GAAGCAGCAGCTTGG
1 GAAGCAGCAGCTTGG
*
34849541 GAAGCAGCGGCTTGG
1 GAAGCAGCAGCTTGG
34849556 ATTTCCTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.43, T:0.13
Consensus pattern (15 bp):
GAAGCAGCAGCTTGG
Found at i:34851440 original size:31 final size:32
Alignment explanation
Indices: 34851405--34851473 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
34851395 TTAAGAGCCA
* *
34851405 AATGACTT-AAATAAAAATTTTCGAATAATTC
1 AATGACTTGAAATAAAAACTTTCAAATAATTC
* * *
34851436 AATGA-TTGAAATGAAAACTTTCAAATAGTTT
1 AATGACTTGAAATAAAAACTTTCAAATAATTC
34851467 AATGACT
1 AATGACT
34851474 ATTTTGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.06
31 28 0.90
32 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (32 bp):
AATGACTTGAAATAAAAACTTTCAAATAATTC
Found at i:34855793 original size:45 final size:45
Alignment explanation
Indices: 34855744--34855858 Score: 137
Period size: 44 Copynumber: 2.6 Consensus size: 45
34855734 ACCAGTATGG
*** * *
34855744 GAAGACAAGATCTGCTTATT-TTTTATCTACTTCATGCCAGTACAT
1 GAAGACAAGATCTGCTT-TTCTCCGATCTACTTCACGCCAATACAT
* *
34855789 GAAGACAAGATCTG-TTTTCTCCGGTCTACTTCACGTCAATACAT
1 GAAGACAAGATCTGCTTTTCTCCGATCTACTTCACGCCAATACAT
34855833 GAAGACAAGATCTGCTTTT-TCCGATC
1 GAAGACAAGATCTGCTTTTCTCCGATC
34855859 GATTCCACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
43 2 0.03
44 40 0.67
45 18 0.30
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (45 bp):
GAAGACAAGATCTGCTTTTCTCCGATCTACTTCACGCCAATACAT
Found at i:34856193 original size:45 final size:45
Alignment explanation
Indices: 34856098--34856241 Score: 132
Period size: 45 Copynumber: 3.2 Consensus size: 45
34856088 GTACATGAAA
* * * *
34856098 ACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAG
1 ACAAGATCTGCTTTCTTCGATCTGCTCCACCACCAGTACGGGAAG
* *
34856143 GCAAGATCTGCTTTCTTCGATCTGCTCCACCACCTA-TACGGGGAG
1 ACAAGATCTGCTTTCTTCGATCTGCTCCACCACC-AGTACGGGAAG
* * * * * **
34856188 ACAAGATCTGGTATCTAT-GATCTACTTCA-CGCCAGTACATGAAG
1 ACAAGATCTGCTTTCT-TCGATCTGCTCCACCACCAGTACGGGAAG
34856232 ACAAGATCTG
1 ACAAGATCTG
34856242 TTATCTTTCA
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
43 1 0.01
44 19 0.23
45 59 0.73
46 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (45 bp):
ACAAGATCTGCTTTCTTCGATCTGCTCCACCACCAGTACGGGAAG
Found at i:34875929 original size:24 final size:25
Alignment explanation
Indices: 34875880--34875935 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
34875870 CCTATCTCAT
* * * *
34875880 TATATATATTTTTATAATTTTTATA
1 TATATATAATATTATAATTGTGATA
34875905 T-TATATAATATTATAATTGTGATA
1 TATATATAATATTATAATTGTGATA
34875929 TATATAT
1 TATATAT
34875936 GAGATGATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATATAATATTATAATTGTGATA
Found at i:34877242 original size:23 final size:23
Alignment explanation
Indices: 34877212--34877287 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
34877202 AGTGTTACTA
34877212 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
34877235 ATCAGTGGTAGCTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
* *
34877258 ATCAGTGGTAGCTTCGACTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
34877281 ATCAGTG
1 ATCAGTG
34877288 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.02
23 47 0.96
24 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:34882026 original size:38 final size:38
Alignment explanation
Indices: 34881763--34882026 Score: 334
Period size: 38 Copynumber: 7.0 Consensus size: 38
34881753 TAATACACTG
* * * **
34881763 GCAC-AAGCCTGCTAAGCACAGAGCCCGAATAACACTT
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACCA
* *
34881800 GCACAAAGCCTGCTAGGCACATAGCCCGAATAACACCG
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACCA
*
34881838 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACTA
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACCA
* *
34881876 GCACAAAGCTTGCTAGGCATATAGCCCGAATATCACCA
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACCA
* * *
34881914 GCACAAAGCCTGCTAGGCA-AGTAGCCCGGATATCATCG
1 GCACAAAGCCTGCTAGGCACA-TAGCCCGAATATCACCA
* ** *
34881952 GCACAAAACCTATTAGGCACTTAGCCCGAATATCACCA
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACCA
* *
34881990 ACACAAAGCCTGCTAGGCACATATCCCGAATATCACC
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACC
34882027 GCATTTCTAT
Statistics
Matches: 197, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
37 5 0.03
38 192 0.97
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.16
Consensus pattern (38 bp):
GCACAAAGCCTGCTAGGCACATAGCCCGAATATCACCA
Found at i:34884033 original size:15 final size:15
Alignment explanation
Indices: 34884013--34884042 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34884003 AGTGATAACA
34884013 TACAAATATTTTATT
1 TACAAATATTTTATT
34884028 TACAAATATTTTATT
1 TACAAATATTTTATT
34884043 GAGATTAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TACAAATATTTTATT
Found at i:34890715 original size:24 final size:25
Alignment explanation
Indices: 34890688--34890756 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
34890678 TGCTCATACG
*
34890688 AGCTGTA-AACGGGAAGCTCTTCCA
1 AGCTGTATAACGGGAAGCTCGTCCA
* * *
34890712 AGCTGAATAACGGGAAACTCGTGCA
1 AGCTGTATAACGGGAAGCTCGTCCA
* *
34890737 AGTTGTATAATGGGAAGCTC
1 AGCTGTATAACGGGAAGCTC
34890757 ATGCGAGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
AGCTGTATAACGGGAAGCTCGTCCA
Found at i:34893943 original size:30 final size:30
Alignment explanation
Indices: 34893902--34894042 Score: 139
Period size: 30 Copynumber: 4.7 Consensus size: 30
34893892 TAACCTCTGT
34893902 ACTTTTC-AAAATTTACATTTTGA-CCCTAA
1 ACTTTTCTAAAA-TTACATTTTGACCCCTAA
*
34893931 ACTTTTCTAAAATTTACATTTTGACCCCAAA
1 ACTTTTCTAAAA-TTACATTTTGACCCCTAA
* * *
34893962 AC-TTTCTAAAATTACATTTCGACCCTTAG
1 ACTTTTCTAAAATTACATTTTGACCCCTAA
* *
34893991 AC-TTTCTCAAAATTGCACTTTGACCCCTAA
1 ACTTTTCT-AAAATTACATTTTGACCCCTAA
* *
34894021 ACTCTT-AAGAAATTACATTTTG
1 ACTTTTCTA-AAATTACATTTTG
34894043 GCCCATATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
29 29 0.31
30 55 0.59
31 9 0.10
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (30 bp):
ACTTTTCTAAAATTACATTTTGACCCCTAA
Found at i:34893966 original size:60 final size:59
Alignment explanation
Indices: 34893902--34894042 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
34893892 TAACCTCTGT
*
34893902 ACTTTTCAAAATTTACATTTTGACCC-TAAACTTT-TCTAAAATTTACATTTTGACCCCAAA
1 ACTTTTCAAAA-TTACATTTTGACCCTTAAACTTTCTC-AAAA-TTACACTTTGACCCCAAA
* * * *
34893962 AC-TTTCTAAAATTACATTTCGACCCTTAGACTTTCTCAAAATTGCACTTTGACCCCTAA
1 ACTTTTC-AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACACTTTGACCCCAAA
* *
34894021 ACTCTTAAGAAATTACATTTTG
1 ACTTTTCA-AAATTACATTTTG
34894043 GCCCATATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
59 35 0.51
60 31 0.46
61 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (59 bp):
ACTTTTCAAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACACTTTGACCCCAAA
Found at i:34894013 original size:59 final size:58
Alignment explanation
Indices: 34893905--34894070 Score: 151
Period size: 59 Copynumber: 2.8 Consensus size: 58
34893895 CCTCTGTACT
* *
34893905 TTTCAAAATTTACATTTTGACCCTAAACTTTTCTAAAATTTACATTTTGACCCCAAAAC
1 TTTCAAAA-TTACATTTCGACCCTAAACTTTTCTAAAATTTACACTTTGACCCCAAAAC
* * *
34893964 TTTCTAAAATTACATTTCGACCCTTAGAC-TTTCTCAAAA-TTGCACTTTGACCCCTAAAC
1 TTTC-AAAATTACATTTCGACCC-TAAACTTTTCT-AAAATTTACACTTTGACCCCAAAAC
* * * * *
34894023 TCTTAAGAAATTACATTTTGGCCC-ATATTTTTGCTAAAA-TTACACTTT
1 T-TTCA-AAATTACATTTCGACCCTAAACTTTT-CTAAAATTTACACTTT
34894071 TTCCCCAGAA
Statistics
Matches: 89, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
58 2 0.02
59 56 0.63
60 31 0.35
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (58 bp):
TTTCAAAATTACATTTCGACCCTAAACTTTTCTAAAATTTACACTTTGACCCCAAAAC
Found at i:34894651 original size:5 final size:6
Alignment explanation
Indices: 34894592--34894671 Score: 70
Period size: 6 Copynumber: 12.3 Consensus size: 6
34894582 CGGCCCGAAG
* * * *
34894592 AAGAAGA AAGAAGA AAGAAAA AAGAAG AAGAAA AAGGGAG AAGAAA AGGAGAA
1 AAGAA-A AAGAA-A AAG-AAA AAGAAA AAGAAA AA-GAAA AAGAAA AAGA-AA
34894645 AAGAAA AAGAAA AAGAAAA AAGAAA AA
1 AAGAAA AAGAAA AAG-AAA AAGAAA AA
34894672 CAATTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
6 30 0.49
7 29 0.48
8 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:34894652 original size:38 final size:37
Alignment explanation
Indices: 34894593--34894664 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
34894583 GGCCCGAAGA
*
34894593 AGAAGAAAGAAGAAAGAAAAAAGAAGAAGAAAAAGGG
1 AGAAGAAAGAAGAAAGAAAAAAGAAAAAGAAAAAGGG
*
34894630 AGAAGAAAAGGAGAAA-AGAAAAAGAAAAAGAAAAA
1 AGAAG-AAAGAAGAAAGA-AAAAAGAAAAAGAAAAA
34894665 AGAAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 6 0.19
38 25 0.81
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (37 bp):
AGAAGAAAGAAGAAAGAAAAAAGAAAAAGAAAAAGGG
Found at i:34894654 original size:19 final size:19
Alignment explanation
Indices: 34894592--34894671 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
34894582 CGGCCCGAAG
*
34894592 AAGAAGAAAGAAGAAAGAAAA
1 AAGAA-AAAGAAAAAAG-AAA
* * * *
34894613 AAGAAGAAGAAAAAGGGAG
1 AAGAAAAAGAAAAAAGAAA
* *
34894632 AAGAAAAGGAGAAAAGAAA
1 AAGAAAAAGAAAAAAGAAA
34894651 AAGAAAAAGAAAAAAGAAA
1 AAGAAAAAGAAAAAAGAAA
34894670 AA
1 AA
34894672 CAATTTAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
19 33 0.72
20 8 0.17
21 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
AAGAAAAAGAAAAAAGAAA
Found at i:34894669 original size:7 final size:7
Alignment explanation
Indices: 34894592--34894671 Score: 58
Period size: 7 Copynumber: 11.1 Consensus size: 7
34894582 CGGCCCGAAG
*
34894592 AAGAAGA
1 AAGAAAA
*
34894599 AAGAAGA
1 AAGAAAA
34894606 AAGAAAA
1 AAGAAAA
*
34894613 AAG-AAG
1 AAGAAAA
34894619 AAGAAAA
1 AAGAAAA
34894626 AGGGAGAAGAA
1 A---AGAA-AA
*
34894637 AAGGAGAA
1 AA-GAAAA
34894645 AAG-AAA
1 AAGAAAA
34894651 AAG-AAA
1 AAGAAAA
34894657 AAGAAAA
1 AAGAAAA
34894664 AAGAAAA
1 AAGAAAA
34894671 A
1 A
34894672 CAATTTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
6 16 0.26
7 31 0.51
8 5 0.08
9 2 0.03
10 4 0.07
11 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:34894669 original size:13 final size:13
Alignment explanation
Indices: 34894592--34894671 Score: 74
Period size: 13 Copynumber: 6.2 Consensus size: 13
34894582 CGGCCCGAAG
*
34894592 AAGAAGAAAGAAGA
1 AAGAAAAAAGAA-A
*
34894606 AAGAAAAAAGAAG
1 AAGAAAAAAGAAA
* * *
34894619 AAGAAAAAGGGAG
1 AAGAAAAAAGAAA
*
34894632 AAG-AAAAGGAGAA
1 AAGAAAAAAGA-AA
34894645 AAG-AAAAAGAAA
1 AAGAAAAAAGAAA
34894657 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
34894670 AA
1 AA
34894672 CAATTTAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.19
13 35 0.61
14 11 0.19
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:34895080 original size:15 final size:16
Alignment explanation
Indices: 34895062--34895091 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34895052 TAATTTAGTT
34895062 TTATTT-ATTTAAATA
1 TTATTTCATTTAAATA
34895077 TTATTTCATTTAAAT
1 TTATTTCATTTAAAT
34895092 TTAATTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTCATTTAAATA
Found at i:34895603 original size:17 final size:17
Alignment explanation
Indices: 34895583--34895632 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
34895573 AAAAAAATTA
*
34895583 TGTTTTCAAAACTTTCG
1 TGTTTTCAAAATTTTCG
*
34895600 TGTTTTCAAAATTTTTG
1 TGTTTTCAAAATTTTCG
34895617 TGTTTTCAAAATTTTC
1 TGTTTTCAAAATTTTC
34895633 ATGTGTTCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (17 bp):
TGTTTTCAAAATTTTCG
Found at i:34895683 original size:20 final size:20
Alignment explanation
Indices: 34895642--34895712 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
34895632 CATGTGTTCG
* *
34895642 TGTTTTCAAAAAAAATTCTCA
1 TGTTTTAAAAAAAAAAT-TCA
***
34895663 TGTTTTTTTAAAAAAATTCA
1 TGTTTTAAAAAAAAAATTCA
34895683 TG-TTTAAAAAAAAAATTCA
1 TGTTTTAAAAAAAAAATTCA
34895702 TGTTTTCAAAA
1 TGTTTT-AAAA
34895713 TTTTCTTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 16 0.39
20 8 0.20
21 17 0.41
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (20 bp):
TGTTTTAAAAAAAAAATTCA
Found at i:34895712 original size:19 final size:19
Alignment explanation
Indices: 34895642--34895712 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
34895632 CATGTGTTCG
34895642 TGTTTTCAAAAAAAATTCTCA
1 TGTTTTCAAAAAAAA-T-TCA
**
34895663 TGTTTTTTTAAAAAAATTCA
1 TG-TTTTCAAAAAAAATTCA
**
34895683 TGTTTAAAAAAAAAATTCA
1 TGTTTTCAAAAAAAATTCA
34895702 TGTTTTCAAAA
1 TGTTTTCAAAA
34895713 TTTTCTTGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 23 0.55
20 5 0.12
21 3 0.07
22 11 0.26
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (19 bp):
TGTTTTCAAAAAAAATTCA
Found at i:34895785 original size:21 final size:21
Alignment explanation
Indices: 34895761--34895803 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34895751 TCATCTATCG
* *
34895761 AAAATTTCCGTGTTTTCAAAA
1 AAAATTTCCGCGTTTCCAAAA
*
34895782 AAAATTTCTGCGTTTCCAAAA
1 AAAATTTCCGCGTTTCCAAAA
34895803 A
1 A
34895804 TTCAAGTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (21 bp):
AAAATTTCCGCGTTTCCAAAA
Found at i:34895838 original size:18 final size:17
Alignment explanation
Indices: 34895817--34895911 Score: 66
Period size: 18 Copynumber: 5.4 Consensus size: 17
34895807 AAGTGATTTA
34895817 AAAAATCGTCGTGTTTTC
1 AAAAATC-TCGTGTTTTC
**
34895835 AAAAA-CTCCAGTTTTC
1 AAAAATCTCGTGTTTTC
* * *
34895851 AAAATTTTCATGTTTTTC
1 AAAAATCTCGTG-TTTTC
*
34895869 AAAAAATTCTCGTGTTTTA
1 -AAAAA-TCTCGTGTTTTC
* *
34895888 AAAAATTTTCGTGTTCTC
1 AAAAA-TCTCGTGTTTTC
34895906 AAAAAT
1 AAAAAT
34895912 AAAAAATGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
16 12 0.20
17 5 0.08
18 30 0.50
19 8 0.13
20 5 0.08
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (17 bp):
AAAAATCTCGTGTTTTC
Found at i:34895876 original size:20 final size:19
Alignment explanation
Indices: 34895851--34895902 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
34895841 TCCAGTTTTC
*
34895851 AAAATTTTCATGTTTTTCAA
1 AAAATTTTCGTGTTTTT-AA
*
34895871 AAAATTCTCGTG-TTTTAA
1 AAAATTTTCGTGTTTTTAA
34895889 AAAATTTTCGTGTT
1 AAAATTTTCGTGTT
34895903 CTCAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.46
19 5 0.18
20 10 0.36
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
AAAATTTTCGTGTTTTTAA
Found at i:34901287 original size:11 final size:11
Alignment explanation
Indices: 34901272--34901315 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
34901262 AAAAGAGAGA
34901272 AAAAAAGACAAC
1 AAAAAA-ACAAC
34901284 AAAAAAACAAC
1 AAAAAAACAAC
**
34901295 AAAAAAGGAAC
1 AAAAAAACAAC
34901306 AAAAAAACAA
1 AAAAAAACAA
34901316 AGCAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.80, C:0.14, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:34901298 original size:22 final size:22
Alignment explanation
Indices: 34901272--34901342 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
34901262 AAAAGAGAGA
34901272 AAAAAAGACAACAAAAAAACAAC
1 AAAAAAG-CAACAAAAAAACAAC
*
34901295 AAAAAAGGAACAAAAAAACAAAGC
1 AAAAAAGCAACAAAAAAAC-AA-C
*
34901319 AAAAAAG-AA-AAAACAAAAAAC
1 AAAAAAGCAACAAAA-AAACAAC
34901340 AAA
1 AAA
34901343 GAAAAGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.09
22 17 0.40
23 14 0.33
24 8 0.19
ACGTcount: A:0.80, C:0.13, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAAAAGCAACAAAAAAACAAC
Found at i:34901298 original size:23 final size:23
Alignment explanation
Indices: 34901272--34901358 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
34901262 AAAAGAGAGA
*
34901272 AAAAAAGACAACAAAAAAACAAC
1 AAAAAAGAAAACAAAAAAACAAC
*
34901295 AAAAAAG-GAACAAAAAAACAAAGC
1 AAAAAAGAAAACAAAAAAAC-AA-C
*
34901319 AAAAAAGAAAAAACAAAAAACAA-
1 AAAAAAGAAAACA-AAAAAACAAC
* *
34901342 AGAAAAGAAAAGAAAAA
1 AAAAAAGAAAACAAAAA
34901359 TCAAGATGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
22 15 0.27
23 20 0.36
24 8 0.15
25 5 0.09
26 7 0.13
ACGTcount: A:0.80, C:0.10, G:0.09, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAACAAAAAAACAAC
Found at i:34901323 original size:14 final size:14
Alignment explanation
Indices: 34901285--34901358 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
34901275 AAAGACAACA
34901285 AAAAAACAACAAAA-
1 AAAAAACAA-AAAAG
**
34901299 AAGGAACAAAAAA-
1 AAAAAACAAAAAAG
* *
34901312 ACAAAGCAAAAAAG
1 AAAAAACAAAAAAG
*
34901326 AAAAAACAAAAAAC
1 AAAAAACAAAAAAG
*
34901340 AAAGAAA-AGAAAAG
1 AAA-AAACAAAAAAG
34901354 AAAAA
1 AAAAA
34901359 TCAAGATGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 15 0.32
14 29 0.62
15 3 0.06
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAAAG
Found at i:34901329 original size:19 final size:18
Alignment explanation
Indices: 34901307--34901347 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
34901297 AAAAGGAACA
34901307 AAAAAACAAAGCAAA-AAAG
1 AAAAAACAAA--AAACAAAG
34901326 AAAAAACAAAAAACAAAG
1 AAAAAACAAAAAACAAAG
34901344 AAAA
1 AAAA
34901348 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 10 0.48
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAACAAAG
Found at i:34901357 original size:26 final size:26
Alignment explanation
Indices: 34901307--34901358 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
34901297 AAAAGGAACA
34901307 AAAAAACAAAGCAAAAAAGAAAAAAC
1 AAAAAACAAAGCAAAAAAGAAAAAAC
*
34901333 AAAAAACAAAGAAAAGAAAAGAAAAA
1 AAAAAACAAAG-CAA-AAAAGAAAAA
34901359 TCAAGATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
27 2 0.09
28 10 0.43
ACGTcount: A:0.83, C:0.08, G:0.10, T:0.00
Consensus pattern (26 bp):
AAAAAACAAAGCAAAAAAGAAAAAAC
Found at i:34901358 original size:22 final size:22
Alignment explanation
Indices: 34901274--34901358 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
34901264 AAGAGAGAAA
* *
34901274 AAAAGACAACAAAAAAACAACAA
1 AAAAGAAAACAAAAAAACAA-AG
*
34901297 AAAAG-GAACAAAAAAACAAAG
1 AAAAGAAAACAAAAAAACAAAG
*
34901318 CAAAAAAGAAAAAACAAAAAACAAAG
1 ---AAAAGAAAACA-AAAAAACAAAG
*
34901344 AAAAGAAAAGAAAAA
1 AAAAGAAAACAAAAA
34901359 TCAAGATGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
22 17 0.33
23 15 0.29
24 5 0.10
25 3 0.06
26 11 0.21
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAGAAAACAAAAAAACAAAG
Found at i:34902349 original size:76 final size:76
Alignment explanation
Indices: 34902240--34903674 Score: 1823
Period size: 76 Copynumber: 18.6 Consensus size: 76
34902230 TGTTTTTTTT
* * *
34902240 TTTTTC-AAATATCAACTCATAATACAGATGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-T
34902304 TTTAAATTTCTG
65 TTTAAATTTCTG
*
34902316 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-T
34902380 TTTAAATTT-TCG
65 TTTAAATTTCT-G
*
34902392 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-T
*
34902456 TTTAAATTTTTG
65 TTTAAATTTCTG
* *
34902468 TTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT-TT
1 TTTTTC--AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATT
*
34902532 TTTTTTAATTTCTG
63 TTTTTAAATTTCTG
**
34902546 TTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGTTGAGGTATT
1 --TTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA-T
34902611 TTTTTTAAATTTCTG
62 TTTTTTAAATTTCTG
* *
34902626 CTTTTTTCAAAAAATCAACTCATAATACAAAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT
*
34902691 TTTTAATTTAATTTCTAT
64 TTTT-A---AATTTCT-G
* *
34902709 TTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTATTTT
1 TTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTT
34902774 TTT-AATTTCTG
65 TTTAAATTTCTG
* *
34902785 TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTATTTT
1 -TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTT
34902850 TTT-AATTTCTG
65 TTTAAATTTCTG
*
34902861 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
*
34902926 TTTAATTTCTG
66 TTAAATTTCTG
* * *
34902937 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACACTGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA-TT
*
34903002 TTTTTTAATTTCTG
63 TTTTTAAATTTCTG
* * * * *
34903016 --CTTCAAAAAATCAACTCATAATACAGAAGTGAATTGAGCCTCAGGTCACGCTGAGGTATTTTT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
*
34903079 TTTAATTTCTG
66 TTAAATTTCTG
* *
34903090 TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA-TT
34903155 TTTTTAAATTTCTG
63 TTTTTAAATTTCTG
*
34903169 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
1 --TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT
*
34903234 CTTTTAAATTTCCG
64 -TTTTAAATTTCTG
*
34903248 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-T
*
34903312 TTTAAATTTCCG
65 TTTAAATTTCTG
* *
34903324 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGTTATTTCT
1 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-T
*
34903388 TTTAAATTTTTG
65 TTTAAATTTCTG
* * * * ** *
34903400 TTTTTC-AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTGGACCATGCCGAGGTATTTC
1 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-
*
34903464 TTTTAAATTTTTG
64 TTTTAAATTTCTG
*
34903477 TTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA--TT
1 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTT
*
34903539 TTTCAA-TTCATG
65 TTTAAATTTC-TG
* ** * *
34903551 TTTTTC-AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTA--
1 TTTTTCAAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGGGTCAC--GCCGAGGTATT
** *
34903613 -TTTTCGATTTTTG
63 TTTTTAAATTTCTG
* * * *
34903626 TTTTTC-GAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC
34903675 GCACACCGAG
Statistics
Matches: 1258, Mismatches: 67, Indels: 69
0.90 0.05 0.05
Matches are distributed among these distances:
73 2 0.00
74 70 0.06
75 169 0.13
76 405 0.32
77 120 0.10
78 166 0.13
79 195 0.16
80 59 0.05
81 6 0.00
82 66 0.05
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (76 bp):
TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
TTAAATTTCTG
Found at i:34902971 original size:153 final size:150
Alignment explanation
Indices: 34902240--34903674 Score: 1800
Period size: 153 Copynumber: 9.3 Consensus size: 150
34902230 TGTTTTTTTT
* * *
34902240 TTTTTCAAATATCAACTCATAATACAGATGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-TT
* *
34902305 TTAAATTTCTGTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCC
65 TTAAATTTCTGTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCT
34902369 GAGGTATTTCTTTTAAATTT-TCG
130 GAGGTATTT-TTTT-AATTTCT-G
*
34902392 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-TT
* *
34902457 TTAAATTTTTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
65 TTAAATTTCTGTTTTTC--AAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCAC
*
34902522 GCTGAGGTTTTTTTTTAATTTCTG
127 GCTGAGGTATTTTTTTAATTTCTG
**
34902546 TTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGTTGAGGTATT
1 --TTTTTC--AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA-T
*
34902611 TTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAAAGGTGAGTTGAGCCTCGGGT
61 TTTTTTAAATTTCTG--TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
34902676 CACGCTGAGGTATTTTTTTAATTTAATTTCTAT
124 CACGCTGAGGTA---TTTT--TTTAATTTCT-G
* *
34902709 TTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTATTTT
1 TTTTTC--AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTT
*
34902774 TTT-AATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCACG
64 TTTAAATTTCTG-TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACG
34902838 CTGAGGTATTTTTTTAATTTCTG
128 CTGAGGTATTTTTTTAATTTCTG
*
34902861 TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
* * *
34902926 TTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACA
65 TTAAATTTCTG--TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACG
34902991 CTGAGGTATTTTTTTTTAATTTCTG
128 CTGAGGTA--TTTTTTTAATTTCTG
* * * * *
34903016 --CTTCAAAAAATCAACTCATAATACAGAAGTGAATTGAGCCTCAGGTCACGCTGAGGTATTTTT
1 TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
* *
34903079 TTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCAGGTCACG
65 TTAAATTTCTG--TTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACG
34903144 CTGAGGTATTTTTTTTAAATTTCTG
128 CTGAGGTA-TTTTTTT-AATTTCTG
*
34903169 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT
* *
34903234 CTTTTAAATTTCCGTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAT
63 -TTTTAAATTTCTGTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC
* *
34903298 GCCGAGGTATTTCTTTTAAATTTCCG
127 GCTGAGGTATTT-TTTT-AATTTCTG
* *
34903324 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGTTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-TT
* * * * * ** *
34903389 TTAAATTTTTGTTTTTC-AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTGGACCATGC
65 TTAAATTTCTGTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGC
* *
34903453 CGAGGTATTTCTTTTAAATTTTTG
129 TGAGGTATTT-TTTT-AATTTCTG
*
34903477 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTA--TTT
1 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
* * ** *
34903540 TTCAA-TTCATGTTTTTC-AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACA
65 TTAAATTTC-TGTTTTTCAAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGGGTCAC-
** *
34903603 TG-TCGAGGTA--TTTTCGATTTTTG
127 -GCT-GAGGTATTTTTTTAATTTCTG
* * * *
34903626 TTTTTCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC
34903675 GCACACCGAG
Statistics
Matches: 1172, Mismatches: 75, Indels: 75
0.89 0.06 0.06
Matches are distributed among these distances:
149 51 0.04
150 5 0.00
151 112 0.10
152 192 0.16
153 286 0.24
154 41 0.03
155 104 0.09
156 46 0.04
157 87 0.07
158 151 0.13
159 11 0.01
160 17 0.01
161 59 0.05
162 10 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (150 bp):
TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTT
TAAATTTCTGTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTG
AGGTATTTTTTTAATTTCTG
Found at i:34903930 original size:30 final size:30
Alignment explanation
Indices: 34903897--34904025 Score: 131
Period size: 30 Copynumber: 4.3 Consensus size: 30
34903887 TTTTCAAATT
34903897 TTACATTTTGACCCC-AAACTTTTCTAAAA
1 TTACATTTTGACCCCAAAACTTTTCTAAAA
34903926 TTTACATTTTGACCCCAAAAC-TTTCTAAAA
1 -TTACATTTTGACCCCAAAACTTTTCTAAAA
* ** *
34903956 TTACATTTCGACCCTTAGAC-TTTCTCAAAA
1 TTACATTTTGACCCCAAAACTTTTCT-AAAA
* * * *
34903986 TTACACTTTGACCCCTAAACTCTT-AAGAAA
1 TTACATTTTGACCCCAAAACTTTTCTA-AAA
34904016 TTACATTTTG
1 TTACATTTTG
34904026 GCCCATATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
29 22 0.26
30 56 0.67
31 6 0.07
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.37
Consensus pattern (30 bp):
TTACATTTTGACCCCAAAACTTTTCTAAAA
Done.