Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 122 of 163
Found at i:39278212 original size:23 final size:21
Alignment explanation
Indices: 39278169--39278212 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
39278159 CTTAGTCTAG
*
39278169 CTTAGTTTTCTCTTTAGTTCT
1 CTTAGTTTTCTCTTCAGTTCT
*
39278190 CTTAGGTTTTCTTCTTCATTTCT
1 CTTA-GTTTTC-TCTTCAGTTCT
39278213 AAGGTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.09, C:0.20, G:0.09, T:0.61
Consensus pattern (21 bp):
CTTAGTTTTCTCTTCAGTTCT
Found at i:39283770 original size:58 final size:56
Alignment explanation
Indices: 39283666--39283848 Score: 305
Period size: 56 Copynumber: 3.2 Consensus size: 56
39283656 TATGTAAAAC
39283666 TATGTAAAATTATTAAGCCCAAAAAATTTTGTTAATGGTTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAATTTTGTTAATGGTTAGTAAAATTATCAAAT
39283722 TATGTAAAATTATTAAGCCCAAAAAAACTTTTGTTAATGGTTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCC-AAAAAA-TTTTGTTAATGGTTAGTAAAATTATCAAAT
* *
39283780 TATGTAAAATTATTAAGCCCCAAAAAA-TGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAG-CCCAAAAAATTTTGTTAATGGTTAGTAAAATTATCAAAT
*
39283836 TAGGTAAAATTAT
1 TATGTAAAATTAT
39283849 GTTATGGTTT
Statistics
Matches: 121, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
56 59 0.49
57 6 0.05
58 53 0.44
59 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAATTTTGTTAATGGTTAGTAAAATTATCAAAT
Found at i:39283867 original size:24 final size:24
Alignment explanation
Indices: 39283840--39283961 Score: 106
Period size: 23 Copynumber: 4.8 Consensus size: 24
39283830 TCAAATTAGG
* *
39283840 TAAAATTATGTTATGGTTTTTACA-
1 TAAAATTAGGTTAGGGTTTTTA-AT
39283864 T-AAATTAGGTTAGGGTTTTTAAT
1 TAAAATTAGGTTAGGGTTTTTAAT
39283887 TAAAATAGGTTAGGGTTTAGGGTTTTTAAT
1 T-AAA-A--TTA-GG-TTAGGGTTTTTAAT
39283917 TAAATTAGTTAGGGTTAGGGTTTTTAAT
1 TAAA--A-TTA-GGTTAGGGTTTTTAAT
39283945 TAAAA-TAGGTTAGGGTT
1 TAAAATTAGGTTAGGGTT
39283962 ATTAGGGTTT
Statistics
Matches: 87, Mismatches: 2, Indels: 19
0.81 0.02 0.18
Matches are distributed among these distances:
22 1 0.01
23 29 0.33
24 3 0.03
25 2 0.02
26 2 0.02
28 21 0.24
29 12 0.14
30 17 0.20
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (24 bp):
TAAAATTAGGTTAGGGTTTTTAAT
Found at i:39283943 original size:28 final size:29
Alignment explanation
Indices: 39283871--39284274 Score: 476
Period size: 29 Copynumber: 13.2 Consensus size: 29
39283861 ACATAAATTA
*
39283871 GGTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
39283900 GGTTTAGGGTTTTTAATTAAATTA-GTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
39283929 GGTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
39283958 GGTTATTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GG---TTAGGG--TTT--TT-AATTAAATTAGGTTAG
39283995 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
*
39284029 GGTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
**
39284058 GGTTAGGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
**
39284086 GGTTAGGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
39284114 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
*
39284148 GGTTAGGGTTTTTAATTAAAAT-GAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAG-GTTAG
39284177 GGTTAGGGTTTTTAATTAAATGAAATTAGGTTAG
1 GGTTAGGGTTTTTAA-T---T-AAATTAGGTTAG
39284211 GGTTAGGGTTTTTAATTAAATTAGG-TAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
39284239 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
39284268 GGTTAGG
1 GGTTAGG
39284275 NNNNNNNNNN
Statistics
Matches: 340, Mismatches: 11, Indels: 48
0.85 0.03 0.12
Matches are distributed among these distances:
28 85 0.25
29 102 0.30
30 29 0.09
32 14 0.04
33 15 0.04
34 75 0.22
35 1 0.00
36 2 0.01
37 17 0.05
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:39284006 original size:34 final size:34
Alignment explanation
Indices: 39283884--39284261 Score: 425
Period size: 34 Copynumber: 12.1 Consensus size: 34
39283874 TAGGGTTTTT
*
39283884 AATTAAAATAGGTTAGGGTTTAGGG--TTT--TT-
1 AATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTA
39283914 AATTAAATTA-GTTAGGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* **
39283947 AAATAGGTTAGGGTTA---TTAGGGTTTTTAATTA
1 AATTAAATTA-GGTTAGGGTTAGGGTTTTTAATTA
39283979 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284013 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284046 -A--AAA-TAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284076 AATT-AA--A--TTA-GGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284104 AATT-AA--A--TTA-GGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284132 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
*
39284165 -A--AAATGA-GTTAGGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
*
39284195 AATGAAATTAGGTTAGGGTTAGGG--TTT--TT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284224 AATTAAATTAGG-TAGGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39284257 AATTA
1 AATTA
39284262 GGTTAGGGTT
Statistics
Matches: 308, Mismatches: 10, Indels: 57
0.82 0.03 0.15
Matches are distributed among these distances:
28 67 0.22
29 70 0.23
30 25 0.08
31 9 0.03
32 34 0.11
33 20 0.06
34 79 0.26
35 4 0.01
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (34 bp):
AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
Found at i:39284059 original size:23 final size:26
Alignment explanation
Indices: 39284029--39284214 Score: 160
Period size: 28 Copynumber: 6.4 Consensus size: 26
39284019 ATTAGGTTAG
39284029 GGTTAGGGTTTTTAATTAA-AATAGGTTA
1 GGTTAGGGTTTTTAATTAATAA-A--TTA
39284057 GGGTTAGGGTTTTTAATTAAATTAAATTA
1 -GGTTAGGGTTTTTAATT-AA-TAAATTA
39284086 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT-AA-TAAATTA
39284114 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATT-AA-T-AA--A--TTA
39284147 GGGTTAGGGTTTTTAATTAA-AATGAGTTA
1 -GGTTAGGGTTTTTAATTAATAA--A-TTA
39284176 GGGTTAGGGTTTTTAATTAAATGAAATTA
1 -GGTTAGGGTTTTTAATT-AAT-AAATTA
39284205 GGTTAGGGTT
1 GGTTAGGGTT
39284215 AGGGTTTTTA
Statistics
Matches: 144, Mismatches: 1, Indels: 25
0.85 0.01 0.15
Matches are distributed among these distances:
28 60 0.42
29 47 0.33
30 9 0.06
31 2 0.01
32 4 0.03
33 5 0.03
34 17 0.12
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (26 bp):
GGTTAGGGTTTTTAATTAATAAATTA
Found at i:39284265 original size:23 final size:26
Alignment explanation
Indices: 39284026--39284274 Score: 119
Period size: 28 Copynumber: 8.4 Consensus size: 26
39284016 TAAATTAGGT
*
39284026 TAGGGTTAGGGTTTTTAATTAAAATAGG
1 TAGGGTTAGGGTTTTTAATT-AAAT-TG
*
39284054 TTAGGGTTAGGGTTTTTAATTAAATTAAAT
1 -TAGGGTTAGGGTTTTTAATTAAATT---G
*
39284084 TA-GGTTAGGGTTTTTAATTAAATTAAAT
1 TAGGGTTAGGGTTTTTAATTAAATT---G
39284112 TA-GGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TAGGGTTAGGG--TTT--TT-AATTAAATT--G
*
39284144 TTAGGGTTAGGGTTTTTAATTAAAATGAG
1 -TAGGGTTAGGGTTTTTAATT-AAAT-TG
39284173 TTAGGGTTAGGGTTTTTAATTAAA-TG
1 -TAGGGTTAGGGTTTTTAATTAAATTG
39284199 AAATTA-GGTTAGGGTTAGGGTTTTTAATTAAATTAGG
1 ----TAGGGTTA------GGGTTTTTAATTAAATT--G
39284236 TAGGGTTAGGGTTTTTAATTAAATTAGG
1 TAGGGTTAGGGTTTTTAATTAAATT--G
39284264 TTAGGGTTAGG
1 -TAGGGTTAGG
39284275 NNNNNNNNNN
Statistics
Matches: 188, Mismatches: 6, Indels: 52
0.76 0.02 0.21
Matches are distributed among these distances:
26 1 0.01
28 68 0.36
29 61 0.32
30 9 0.05
32 6 0.03
33 13 0.07
34 28 0.15
35 1 0.01
37 1 0.01
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (26 bp):
TAGGGTTAGGGTTTTTAATTAAATTG
Found at i:39284359 original size:29 final size:29
Alignment explanation
Indices: 39284317--39284412 Score: 120
Period size: 29 Copynumber: 3.1 Consensus size: 29
39284307 NNNNNNNNNN
39284317 GGGTTAGGGTTTTTAATTAAAATAGGTTA
1 GGGTTAGGGTTTTTAATTAAAATAGGTTA
*
39284346 GGGTTAGGATTTTTAATTAAATTAAATTAGGTTA
1 GGGTTAGGGTTTTTAATT--A--AAA-TAGGTTA
* *
39284380 GGGTTAGGGTTTTTAAATAAATTAGGTTA
1 GGGTTAGGGTTTTTAATTAAAATAGGTTA
39284409 GGGT
1 GGGT
39284413 ATCAAATAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
29 28 0.48
30 2 0.03
31 1 0.02
32 1 0.02
33 3 0.05
34 23 0.40
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
GGGTTAGGGTTTTTAATTAAAATAGGTTA
Found at i:39284377 original size:34 final size:34
Alignment explanation
Indices: 39284331--39284403 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
39284321 TAGGGTTTTT
*
39284331 AATTAAAATAGGTTAGGGTTAGGATTTTTAATTA
1 AATTAAAATAGGTTAGGGTTAGGATTTTTAAATA
* *
39284365 AATTAAATTAGGTTAGGGTTAGGGTTTTTAAATA
1 AATTAAAATAGGTTAGGGTTAGGATTTTTAAATA
39284399 AATTA
1 AATTA
39284404 GGTTAGGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (34 bp):
AATTAAAATAGGTTAGGGTTAGGATTTTTAAATA
Found at i:39284410 original size:34 final size:32
Alignment explanation
Indices: 39284317--39284403 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 32
39284307 NNNNNNNNNN
39284317 GGGTTAGGGTTTTTAATTAAA--A-TAGGTTA
1 GGGTTAGGGTTTTTAATTAAATTATTAGGTTA
*
39284346 GGGTTAGGATTTTTAATTAAATTAAATTAGGTTA
1 GGGTTAGGGTTTTTAATTAAATT--ATTAGGTTA
*
39284380 GGGTTAGGGTTTTTAAATAAATTA
1 GGGTTAGGGTTTTTAATTAAATTA
39284404 GGTTAGGGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 20 0.40
32 1 0.02
33 1 0.02
34 28 0.56
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (32 bp):
GGGTTAGGGTTTTTAATTAAATTATTAGGTTA
Found at i:39286579 original size:25 final size:25
Alignment explanation
Indices: 39286529--39286584 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
39286519 ACTTTATAAC
*
39286529 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
39286554 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
39286577 AAATAATA
1 AAATAATA
39286585 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:39286691 original size:8 final size:9
Alignment explanation
Indices: 39286672--39286727 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
39286662 CCGGTCATTG
39286672 TTAAAAATA
1 TTAAAAATA
39286681 TTAAAAA-A
1 TTAAAAATA
39286689 TTAAAAATTA
1 TTAAAAA-TA
*
39286699 TTTTAAAAAAA
1 --TTAAAAATA
39286710 TATAAAAATA
1 T-TAAAAATA
*
39286720 TTTAAAAT
1 TTAAAAAT
39286728 TATCTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 8 0.21
9 14 0.36
10 9 0.23
11 1 0.03
12 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TTAAAAATA
Found at i:39286706 original size:20 final size:19
Alignment explanation
Indices: 39286673--39286726 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
39286663 CGGTCATTGT
39286673 TAAAAATA-TTAAAAAAT-
1 TAAAAATATTTAAAAAATA
39286690 TAAAAATTATTTTAAAAAAATA
1 TAAAAA-TA-TTT-AAAAAATA
39286712 TAAAAATATTTAAAA
1 TAAAAATATTTAAAA
39286727 TTATCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
19 4 0.12
20 5 0.16
21 9 0.28
22 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATATTTAAAAAATA
Found at i:39286709 original size:21 final size:20
Alignment explanation
Indices: 39286673--39286726 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
39286663 CGGTCATTGT
39286673 TAAAAATA-TT-AAAAAAT-
1 TAAAAATATTTAAAAAAATA
39286690 TAAAAATTATTTTAAAAAAATA
1 TAAAAA-TA-TTTAAAAAAATA
39286712 TAAAAATATTTAAAA
1 TAAAAATATTTAAAA
39286727 TTATCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
20 9 0.28
21 9 0.28
22 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAATATTTAAAAAAATA
Found at i:39286711 original size:31 final size:31
Alignment explanation
Indices: 39286674--39286739 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
39286664 GGTCATTGTT
*
39286674 AAAAATATTAAAAA-ATTAAAAATTATTTTAA
1 AAAAATA-TAAAAATATTAAAAATTATCTTAA
*
39286705 AAAAATATAAAAATATTTAAAATTATCTTAA
1 AAAAATATAAAAATATTAAAAATTATCTTAA
39286736 AAAA
1 AAAA
39286740 TGAAATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAATATAAAAATATTAAAAATTATCTTAA
Found at i:39286761 original size:17 final size:18
Alignment explanation
Indices: 39286735--39286768 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39286725 AATTATCTTA
39286735 AAAAATGAAATTGAATAG
1 AAAAATGAAATTGAATAG
*
39286753 AAAAA-GAAATTTAATA
1 AAAAATGAAATTGAATA
39286769 TGGATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAATGAAATTGAATAG
Found at i:39286808 original size:22 final size:22
Alignment explanation
Indices: 39286783--39286824 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39286773 TTTTAGAGAT
39286783 TTTTGGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
39286805 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
39286825 TTTGAGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:39286832 original size:30 final size:30
Alignment explanation
Indices: 39286796--39286854 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39286786 TGGAAGGAAA
* *
39286796 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
39286826 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
39286855 AATTTTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:39286851 original size:22 final size:22
Alignment explanation
Indices: 39286826--39286871 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
39286816 ATTTGAGAGT
39286826 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
39286848 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
39286870 TT
1 TT
39286872 TAGATAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:39291203 original size:24 final size:24
Alignment explanation
Indices: 39291135--39291209 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
39291125 AAGACCGTCT
* *
39291135 CGTTATTAGCTC-TCATGAGCTTCT
1 CGTTAATAGCTCTTC-TGAGCTTCC
* *
39291159 CGTTATATGGTTCTTGC-GAGCTTCC
1 CGTTA-ATAGCTCTT-CTGAGCTTCC
*
39291184 CGTTAATAGCTCTTCTGAGCATCC
1 CGTTAATAGCTCTTCTGAGCTTCC
39291208 CG
1 CG
39291210 ATTTGGTTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
23 1 0.03
24 21 0.52
25 16 0.40
26 1 0.03
27 1 0.03
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (24 bp):
CGTTAATAGCTCTTCTGAGCTTCC
Found at i:39291301 original size:25 final size:25
Alignment explanation
Indices: 39291273--39291345 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 25
39291263 CTCGATATAT
39291273 GGCTCTTCGGAGCTTCCCAATTAAA
1 GGCTCTTCGGAGCTTCCCAATTAAA
* * * *
39291298 GGCTCTTTCATGAGCTTCTCGATTAAT
1 GGCTC-TTC-GGAGCTTCCCAATTAAA
*
39291325 GGCTCTCCGGAGCTTCCCAAT
1 GGCTCTTCGGAGCTTCCCAAT
39291346 ATTAGCTCGC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 15 0.39
26 5 0.13
27 18 0.47
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.32
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCAATTAAA
Found at i:39293036 original size:14 final size:14
Alignment explanation
Indices: 39293001--39293040 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39292991 TTTAAAAATC
39293001 AGATAAGGGTTTAA
1 AGATAAGGGTTTAA
* *
39293015 AGACAAGGGTTTAG
1 AGATAAGGGTTTAA
*
39293029 AGTTAAGGGTTT
1 AGATAAGGGTTT
39293041 TTAAGGGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.33, T:0.30
Consensus pattern (14 bp):
AGATAAGGGTTTAA
Found at i:39293429 original size:126 final size:126
Alignment explanation
Indices: 39293204--39293494 Score: 474
Period size: 126 Copynumber: 2.3 Consensus size: 126
39293194 TTGTTAAATT
39293204 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
39293269 GTTTCTAAGCAAATAGTGTCAAAAACACTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTAAGCAAAAAGTGTCAAAAACACTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTG
* * *
39293330 AAAGAAGCTCCTATGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
* * * * *
39293395 GTTTTTGAGCAAAAAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTATTG
66 GTTTCTAAGCAAAAAGTGTCAAAAACACTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTG
* *
39293456 AAATAAGCTCCCACATGGACGCACTTTTGCTACAGTAGC
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGC
39293495 GCATGTTTGG
Statistics
Matches: 150, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 150 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTAAGCAAAAAGTGTCAAAAACACTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTG
Found at i:39296320 original size:18 final size:18
Alignment explanation
Indices: 39296293--39296330 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39296283 GAAAAATGAA
* *
39296293 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
39296311 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
39296329 AC
1 AC
39296331 GCACCTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:39298183 original size:11 final size:11
Alignment explanation
Indices: 39298164--39298219 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
39298154 GAAATTTCAA
39298164 AGGAATTTGAG
1 AGGAATTTGAG
39298175 AGGAATTTGAG
1 AGGAATTTGAG
39298186 A-GAATATTG-G
1 AGGAAT-TTGAG
*
39298196 AGAGAAATTGAG
1 AG-GAATTTGAG
*
39298208 A-GAAATTGAG
1 AGGAATTTGAG
39298218 AG
1 AG
39298220 AAAGGATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 16 0.41
11 18 0.46
12 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:39298200 original size:12 final size:10
Alignment explanation
Indices: 39298170--39298222 Score: 70
Period size: 10 Copynumber: 5.0 Consensus size: 10
39298160 TCAAAGGAAT
*
39298170 TTGAGAGGAAT
1 TTGAGA-GAAA
39298181 TTGAGAGAATA
1 TTGAGAGAA-A
39298192 TTGGAGAGAAA
1 TT-GAGAGAAA
39298203 TTGAGAGAAA
1 TTGAGAGAAA
39298213 TTGAGAGAAA
1 TTGAGAGAAA
39298223 GGATTTAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
10 21 0.54
11 11 0.28
12 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:39298209 original size:22 final size:20
Alignment explanation
Indices: 39298170--39298222 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
39298160 TCAAAGGAAT
*
39298170 TTGAGAGGAATTTGAGAGAATA
1 TTGAGA-GAAATTGAGAGAA-A
39298192 TTGGAGAGAAATTGAGAGAAA
1 TT-GAGAGAAATTGAGAGAAA
39298213 TTGAGAGAAA
1 TTGAGAGAAA
39298223 GGATTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.28
21 3 0.10
22 14 0.48
23 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (20 bp):
TTGAGAGAAATTGAGAGAAA
Found at i:39299668 original size:50 final size:50
Alignment explanation
Indices: 39299601--39299700 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
39299591 CAAGGACAAA
* * * *
39299601 TTCAGTAACATTTAACCATTAGGCTAGTAATTTTCTTATTTAACAAATGC
1 TTCACTAACACTTAACCATTAGGCCAGTAACTTTCTTATTTAACAAATGC
39299651 TTCACTAACACTTAACCATTAGGCCAGTAACTTTCTTATTTAACAAATGC
1 TTCACTAACACTTAACCATTAGGCCAGTAACTTTCTTATTTAACAAATGC
39299701 ACAATGATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (50 bp):
TTCACTAACACTTAACCATTAGGCCAGTAACTTTCTTATTTAACAAATGC
Found at i:39300985 original size:15 final size:16
Alignment explanation
Indices: 39300965--39300998 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39300955 AATCTTTTAA
39300965 AAACTATAAAAAT-AT
1 AAACTATAAAAATGAT
*
39300980 AAACTATTAAAATGAT
1 AAACTATAAAAATGAT
39300996 AAA
1 AAA
39300999 ATTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
AAACTATAAAAATGAT
Found at i:39302617 original size:20 final size:21
Alignment explanation
Indices: 39302579--39302618 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39302569 TTTTGTGTTT
*
39302579 TTTTTGTATATTTAAATTTTAA
1 TTTTTATATATTT-AATTTTAA
39302601 TTTTTATATATTT-ATTTT
1 TTTTTATATATTTAATTTT
39302619 CAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTATATATTTAATTTTAA
Found at i:39307326 original size:21 final size:21
Alignment explanation
Indices: 39307302--39307351 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
39307292 GAGGTAGTGG
39307302 CTGTTGCTCCTGCAACAGAAC
1 CTGTTGCTCCTGCAACAGAAC
39307323 CTGTTGCTCCTGCAACAGAAC
1 CTGTTGCTCCTGCAACAGAAC
39307344 CTGTTGCT
1 CTGTTGCT
39307352 GAAGAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGTTGCTCCTGCAACAGAAC
Found at i:39310895 original size:22 final size:22
Alignment explanation
Indices: 39310870--39310914 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
39310860 TACTAGCATA
39310870 ATTTACCCTTACATTTTTAATG
1 ATTTACCCTTACATTTTTAATG
39310892 ATTTACCCTTACATTTTTAATG
1 ATTTACCCTTACATTTTTAATG
39310914 A
1 A
39310915 AGTATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTACCCTTACATTTTTAATG
Found at i:39312252 original size:10 final size:11
Alignment explanation
Indices: 39312234--39312265 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
39312224 TTCAAATATT
39312234 ATAAAAATAAA
1 ATAAAAATAAA
39312245 AT-AAAAT-AA
1 ATAAAAATAAA
39312254 ATAAAAATAAA
1 ATAAAAATAAA
39312265 A
1 A
39312266 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.21
10 10 0.53
11 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:39312445 original size:31 final size:32
Alignment explanation
Indices: 39312392--39312458 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
39312382 AGAATATTAT
*
39312392 TTTGACTCTTTTTCAAAAAGGTTGATGGTCAAA
1 TTTGACTCTTTTT-AAAAAGGTTGAGGGTCAAA
39312425 TTTGACTCTTTTT-AAAAGGTTGAGGGTCAAA
1 TTTGACTCTTTTTAAAAAGGTTGAGGGTCAAA
39312456 TTT
1 TTT
39312459 AACTAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 20 0.61
33 13 0.39
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.42
Consensus pattern (32 bp):
TTTGACTCTTTTTAAAAAGGTTGAGGGTCAAA
Found at i:39314865 original size:40 final size:40
Alignment explanation
Indices: 39314795--39314873 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
39314785 TCGACACCCT
*
39314795 TAAAAAAAGTATCAATACCTTTTACCATGTATAGATACCA
1 TAAAAAAAGTATCAATACCTTTCACCATGTATAGATACCA
* * *
39314835 TAAAGAAAA-TATCATTACCTTTCACTATGTATTGATACC
1 TAAA-AAAAGTATCAATACCTTTCACCATGTATAGATACC
39314874 CTTCTTCCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (40 bp):
TAAAAAAAGTATCAATACCTTTCACCATGTATAGATACCA
Found at i:39317706 original size:19 final size:19
Alignment explanation
Indices: 39317682--39317719 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39317672 ACAAGCTCAA
39317682 AATGAA-AAAAAGAAGAAGC
1 AATGAACAAAAAGAA-AAGC
*
39317701 AATGAACAAACAGAAAAGC
1 AATGAACAAAAAGAAAAGC
39317720 CACAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.11, G:0.18, T:0.05
Consensus pattern (19 bp):
AATGAACAAAAAGAAAAGC
Found at i:39332105 original size:32 final size:32
Alignment explanation
Indices: 39332036--39332107 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
39332026 GTCTCTTATG
* * *
39332036 CAATTTGATCCTTAATTTAGTTTTAATTAATT
1 CAATTTGATCCTCAATTTAATTTCAATTAATT
* *
39332068 TAATTTGAT-CTCGATTTAATTTCAATTACATT
1 CAATTTGATCCTCAATTTAATTTCAATTA-ATT
39332100 CAATTTGA
1 CAATTTGA
39332108 CCATTGCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (32 bp):
CAATTTGATCCTCAATTTAATTTCAATTAATT
Found at i:39335100 original size:24 final size:24
Alignment explanation
Indices: 39335073--39335124 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39335063 TTAGTAAGTC
*
39335073 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39335097 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39335121 AAAT
1 AAAT
39335125 CTTCCAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39336340 original size:24 final size:24
Alignment explanation
Indices: 39336313--39336364 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39336303 TTAGTAAGTC
*
39336313 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39336337 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39336361 AAAT
1 AAAT
39336365 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39337636 original size:49 final size:49
Alignment explanation
Indices: 39337537--39337636 Score: 141
Period size: 49 Copynumber: 2.0 Consensus size: 49
39337527 TTATTTTATT
* * *
39337537 TTAGAATAAGGTTTTTCAACCTTATTACACTTCATCTATTTGATATTGA
1 TTAGAATAAGGTGTTTCAACCTTACTACACTTCATCTATTAGATATTGA
39337586 TTAGAATAAGGTGTTTCAACCTTACTACAC-TCATTCTATTAGA-ATATGA
1 TTAGAATAAGGTGTTTCAACCTTACTACACTTCA-TCTATTAGATAT-TGA
39337635 TT
1 TT
39337637 TTACAAGCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
48 5 0.11
49 41 0.89
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (49 bp):
TTAGAATAAGGTGTTTCAACCTTACTACACTTCATCTATTAGATATTGA
Found at i:39343193 original size:30 final size:30
Alignment explanation
Indices: 39343158--39343222 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 30
39343148 AGATTGCAAA
39343158 AGAGAGGAACAAAATAAAGTTCAGGAAATG
1 AGAGAGGAACAAAATAAAGTTCAGGAAATG
* *
39343188 AGAGA-GTACAGAATAAAGTTCAGGAAATG
1 AGAGAGGAACAAAATAAAGTTCAGGAAATG
39343217 AGAGAG
1 AGAGAG
39343223 TATACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.51, C:0.06, G:0.29, T:0.14
Consensus pattern (30 bp):
AGAGAGGAACAAAATAAAGTTCAGGAAATG
Found at i:39353629 original size:44 final size:43
Alignment explanation
Indices: 39353555--39353713 Score: 130
Period size: 42 Copynumber: 3.7 Consensus size: 43
39353545 ATATGTGTTA
* * *
39353555 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATT
1 TCGTATAAGACCATGTCTGGGAC-ATGGCATCGATATTGAGATT
* * *
39353598 TATGTATAAGACCATGTCTGGGTCATCGGCATC-ATATT-TGATT
1 T-CGTATAAGACCATGTCTGGGACAT-GGCATCGATATTGAGATT
* *
39353641 TCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATT--GATT
1 TCGTATAAGACCATGTCTGGGACA-TGGCATCGATATTGAGATT
* * * *
39353683 ACATGTAAGACCACGTCTGGGACATTGGCAT
1 TCGTATAAGACCATGTCTGGGACA-TGGCAT
39353714 TTTACGAGGT
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
42 55 0.57
43 15 0.16
44 26 0.27
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
TCGTATAAGACCATGTCTGGGACATGGCATCGATATTGAGATT
Found at i:39363503 original size:13 final size:13
Alignment explanation
Indices: 39363485--39363511 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39363475 AACGTTCTCT
39363485 AGTATACTATTTC
1 AGTATACTATTTC
39363498 AGTATACTATTTC
1 AGTATACTATTTC
39363511 A
1 A
39363512 TGTAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
AGTATACTATTTC
Found at i:39367182 original size:31 final size:31
Alignment explanation
Indices: 39367144--39367212 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
39367134 GAGCAACAGC
*
39367144 ATGTTTCACTTGTAGAGATGAAAACTATCCA
1 ATGTTTCACTTGTAGAGATGAAAACGATCCA
* *
39367175 ATGTTTCACTTGTAGAGCTGTAAACGATCCA
1 ATGTTTCACTTGTAGAGATGAAAACGATCCA
*
39367206 ATTTTTC
1 ATGTTTC
39367213 GTTTTTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (31 bp):
ATGTTTCACTTGTAGAGATGAAAACGATCCA
Found at i:39368421 original size:20 final size:20
Alignment explanation
Indices: 39368365--39368431 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
39368355 TTGTACGAGA
* *
39368365 TTGCACATT-GGTGCCACTAT
1 TTGCAC-TTCGGTGCCATTGT
* *
39368385 TTGCATTTCGATGCCATTGT
1 TTGCACTTCGGTGCCATTGT
39368405 TTGCACTTCGGTGCCATTGT
1 TTGCACTTCGGTGCCATTGT
*
39368425 TAGCACT
1 TTGCACT
39368432 AGGTGTCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 2 0.05
20 37 0.95
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCACTTCGGTGCCATTGT
Found at i:39370961 original size:20 final size:21
Alignment explanation
Indices: 39370936--39370981 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
39370926 AAATAGATAT
39370936 GGTTT-TAG-GTTATAAAATTG
1 GGTTTATAGTGTTA-AAAATTG
39370956 GGTTTTATAGTGTTAAAAATTG
1 GG-TTTATAGTGTTAAAAATTG
39370978 GGTT
1 GGTT
39370982 AAATAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.09
21 5 0.22
22 12 0.52
23 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
GGTTTATAGTGTTAAAAATTG
Found at i:39372204 original size:23 final size:22
Alignment explanation
Indices: 39372160--39372205 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
39372150 AAATTTCTAA
*
39372160 ACTTTACTTTTTATTCAGAAAC
1 ACTTTAATTTTTATTCAGAAAC
39372182 ACTTTAATTTGTTATATCA-AAAC
1 ACTTTAATTT-TTAT-TCAGAAAC
39372205 A
1 A
39372206 TATAATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 9 0.43
24 3 0.14
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.43
Consensus pattern (22 bp):
ACTTTAATTTTTATTCAGAAAC
Found at i:39375467 original size:21 final size:21
Alignment explanation
Indices: 39375438--39375488 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
39375428 CACATGGCTG
* * * *
39375438 TGTACCTCAGTCACATGGGCA
1 TGTATCTCAGCCACACGGCCA
*
39375459 TGTGTCTCAGCCACACGGCCA
1 TGTATCTCAGCCACACGGCCA
39375480 TGTATCTCA
1 TGTATCTCA
39375489 CTTACACGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (21 bp):
TGTATCTCAGCCACACGGCCA
Found at i:39385515 original size:35 final size:34
Alignment explanation
Indices: 39385469--39385534 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
39385459 TTATCTAATA
39385469 TTTTAAATATAAATATTTATTTTATTT-TATTTTAT
1 TTTTAAATATAAATA-TT-TTTTATTTATATTTTAT
*
39385504 TTTTATATATAAATATTTTTTATTTATATTT
1 TTTTAAATATAAATATTTTTTATTTATATTT
39385535 GTTCCCTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 8 0.28
34 7 0.24
35 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (34 bp):
TTTTAAATATAAATATTTTTTATTTATATTTTAT
Found at i:39387114 original size:43 final size:42
Alignment explanation
Indices: 39387024--39387160 Score: 120
Period size: 42 Copynumber: 3.2 Consensus size: 42
39387014 AAGCTACACA
* * * *
39387024 AAAGCACATAAGTGCTAAACGGAAACCCGTAAGGGTTAAATG
1 AAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * *
39387066 GAAGCTTATAAGAGCTAAATGAAAACCCAATAAGGGTTAAACT-
1 AAAGCTCATAAGAGCTAAACGAAAACCC-ATAAGGGTTAAA-TG
* *
39387109 AAAGCTCAAAAGAGCTAAAC-AGAAACTCATTAA-GGTTAAACTG
1 AAAGCTCATAAGAGCTAAACGA-AAACCCA-TAAGGGTTAAA-TG
39387152 AAA-CTCATA
1 AAAGCTCATA
39387161 TGAGTTAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
42 38 0.49
43 38 0.49
44 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (42 bp):
AAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
Found at i:39387167 original size:21 final size:21
Alignment explanation
Indices: 39387101--39387168 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
39387091 CCCAATAAGG
* *
39387101 GTTAAACT-AAAGCTCAAAAGA
1 GTTAAACTGAAA-CTCATATGA
* * *
39387122 GCTAAACAGAAACTCAT-TAA
1 GTTAAACTGAAACTCATATGA
39387142 GGTTAAACTGAAACTCATATGA
1 -GTTAAACTGAAACTCATATGA
39387164 GTTAA
1 GTTAA
39387169 TTGAAGCTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.03
21 30 0.83
22 5 0.14
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (21 bp):
GTTAAACTGAAACTCATATGA
Found at i:39394796 original size:44 final size:45
Alignment explanation
Indices: 39394748--39394840 Score: 111
Period size: 46 Copynumber: 2.1 Consensus size: 45
39394738 GTTGAAACAA
**
39394748 AATAGAAGATGTGATAATTA-AT-CATTTA-AAAATAATTATAATTT
1 AATAGAAGATACGATAATTATATACA-TTACAAAAT-ATTATAATTT
*
39394792 AATAGAAGCTACGATAATTATTATACATTACAAAATATTATAATTT
1 AATAGAAGATACGATAATTA-TATACATTACAAAATATTATAATTT
39394838 AAT
1 AAT
39394841 TTACAATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 17 0.40
46 18 0.43
47 7 0.17
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (45 bp):
AATAGAAGATACGATAATTATATACATTACAAAATATTATAATTT
Found at i:39397662 original size:11 final size:11
Alignment explanation
Indices: 39397646--39397675 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
39397636 CTTTGATTTT
39397646 AAAAAAAAAGA
1 AAAAAAAAAGA
39397657 AAAAAAAAAGA
1 AAAAAAAAAGA
39397668 AAAGAAAA
1 AAA-AAAA
39397676 GGAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:39397670 original size:16 final size:15
Alignment explanation
Indices: 39397646--39397675 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39397636 CTTTGATTTT
39397646 AAAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
39397661 AAAAAGAAAAGAAAA
1 AAAAA-AAAAGAAAA
39397676 GGAAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAA
Found at i:39398659 original size:50 final size:50
Alignment explanation
Indices: 39398604--39398973 Score: 215
Period size: 50 Copynumber: 7.4 Consensus size: 50
39398594 CAGTGGAACT
* *
39398604 GATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAAAAAAAAA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAAAAAA
* * *** * * * * ** *
39398654 GATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTGGAACA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TATTGCAATAAAAAA
* * * *
39398704 GATTGAAGCTACGTCGACAGATCTGGTTTCCCTGATATTGCAATTAAAAA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAAAAAA
* * * * *** * * * * ** *
39398754 GATTGAAGCCACAAAGGCGGATATTACTT-CCTTAGCAGTGCAGTGGAACA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TATTGCAATAAAAAA
* * * *
39398804 GATTGAAGCTACGACGACAGATCTGATTTCCCTGATATTGCAATTAAAAA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAAAAAA
* * *** * * * * ** *
39398854 GATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTGGAACA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TATTGCAATAAAAAA
* * *
39398904 GATTGAAGCTACGACGACGGATCTGGTTTCCCTAATATTGCAATTAAAAA
1 GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAAAAAA
* *
39398954 GATTGAAGCCACAACGGCGG
1 GATTGAAGCTACGACGGCGG
39398974 GTCTTACTTT
Statistics
Matches: 224, Mismatches: 90, Indels: 12
0.69 0.28 0.04
Matches are distributed among these distances:
49 12 0.05
50 200 0.89
51 12 0.05
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (50 bp):
GATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAAAAAA
Found at i:39398727 original size:100 final size:100
Alignment explanation
Indices: 39398548--39398990 Score: 733
Period size: 100 Copynumber: 4.4 Consensus size: 100
39398538 GGTTGAAAAG
* * * *
39398548 TAAAAAGATTGAAGCCACAACGGCAGATTTTACTTCCTTAGTAGTGCAGTGGAACTGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
*** *
39398613 TACGACGGTGGATCTGGTTTCCCTGATATTGCAAA
66 TACGACGACAGATCTGGTTTCCCTGATATTGCAAT
*
39398648 AAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
*
39398713 TACGTCGACAGATCTGGTTTCCCTGATATTGCAAT
66 TACGACGACAGATCTGGTTTCCCTGATATTGCAAT
* *
39398748 TAAAAAGATTGAAGCCACAAAGGCGGATATTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
*
39398813 TACGACGACAGATCTGATTTCCCTGATATTGCAAT
66 TACGACGACAGATCTGGTTTCCCTGATATTGCAAT
39398848 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
* *
39398913 TACGACGACGGATCTGGTTTCCCTAATATTGCAAT
66 TACGACGACAGATCTGGTTTCCCTGATATTGCAAT
* *
39398948 TAAAAAGATTGAAGCCACAACGGCGGGTCTTACTTTCTTAGCA
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCA
39398991 TCATAAAGCC
Statistics
Matches: 321, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 321 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (100 bp):
TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
TACGACGACAGATCTGGTTTCCCTGATATTGCAAT
Found at i:39402360 original size:44 final size:45
Alignment explanation
Indices: 39402312--39402404 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
39402302 GTTGAAACAA
*
39402312 AATAGAAGATGTGATAATTA-AT-CATTTA-AAAATAATTATAATTT
1 AATAGAAGATATGATAATTATATACA-TTACAAAAT-ATTATAATTT
*
39402356 AATAGAAGTTATGATAATTATTATACATTACAAAATATTATAATTT
1 AATAGAAGATATGATAATTA-TATACATTACAAAATATTATAATTT
39402402 AAT
1 AAT
39402405 TTACAATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 18 0.42
46 18 0.42
47 7 0.16
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (45 bp):
AATAGAAGATATGATAATTATATACATTACAAAATATTATAATTT
Found at i:39403329 original size:26 final size:26
Alignment explanation
Indices: 39403287--39403336 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
39403277 TTAATTAATG
*
39403287 TAATTAAAAATATAATATTTAAAAAT
1 TAATTAAAAATATAATACTTAAAAAT
*
39403313 TAATTAAATAT-TAAATACTTAAAA
1 TAATTAAAAATAT-AATACTTAAAA
39403337 TCAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATTAAAAATATAATACTTAAAAAT
Found at i:39413542 original size:7 final size:7
Alignment explanation
Indices: 39413530--39413555 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39413520 ACAAATAATC
39413530 AAATATT
1 AAATATT
39413537 AAATATT
1 AAATATT
39413544 AAATATT
1 AAATATT
39413551 AAATA
1 AAATA
39413556 AAAGAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:39427060 original size:14 final size:14
Alignment explanation
Indices: 39427041--39427074 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39427031 GTTTTTAATC
* *
39427041 ATATTAGTATTTTA
1 ATATTAGGACTTTA
39427055 ATATTAGGACTTTA
1 ATATTAGGACTTTA
39427069 ATATTA
1 ATATTA
39427075 ACCTATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (14 bp):
ATATTAGGACTTTA
Found at i:39430746 original size:46 final size:45
Alignment explanation
Indices: 39430640--39430836 Score: 234
Period size: 46 Copynumber: 4.6 Consensus size: 45
39430630 CATATGACCT
* *
39430640 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
39430683 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
39430729 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* ** * *
39430766 CTTATCACTTTGTTTCTTGATCAGATAAGTGTACCTAAAACTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
39430812 CTTATCACTTTATCACTTGATCAGA
1 CTTATCACTTTATCACTTGATCAGA
39430837 AGTACTCAAA
Statistics
Matches: 130, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
37 28 0.22
39 2 0.02
40 2 0.02
41 1 0.01
42 1 0.01
43 10 0.08
44 5 0.04
45 21 0.16
46 60 0.46
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:39430767 original size:37 final size:37
Alignment explanation
Indices: 39430726--39430798 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
39430716 GCTGAAGCTA
39430726 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* **
39430763 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTA
39430799 CCTAAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:39430786 original size:83 final size:83
Alignment explanation
Indices: 39430680--39430836 Score: 251
Period size: 83 Copynumber: 1.9 Consensus size: 83
39430670 AGCTAGGCTA
* * *
39430680 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTACCTAAAACTACCACTTATCACTTTATCAC
39430745 TTGATCAGATAAGTGTAG
66 TTGATCAGATAAGTGTAG
****
39430763 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTACCTAAAACTACCACTTATCACTTTATCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTACCTAAAACTACCACTTATCACTTTATCAC
39430828 TTGATCAGA
66 TTGATCAGA
39430837 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (83 bp):
CCACTTATCACTTTACCACTTGATCAGATAAGTGTACCTAAAACTACCACTTATCACTTTATCAC
TTGATCAGATAAGTGTAG
Found at i:39434355 original size:32 final size:32
Alignment explanation
Indices: 39434313--39434374 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
39434303 AAATATAATT
*
39434313 ATTATCTTTATATGTAAAATATTTCAAATATC
1 ATTATCTTTATATGCAAAATATTTCAAATATC
* * *
39434345 ATTATGTTTATATGCGAAATATTTTAAATA
1 ATTATCTTTATATGCAAAATATTTCAAATA
39434375 CACATACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (32 bp):
ATTATCTTTATATGCAAAATATTTCAAATATC
Found at i:39439696 original size:17 final size:17
Alignment explanation
Indices: 39439666--39439698 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39439656 ATACGAATCT
39439666 AAAACTAAAAAAAAAAC
1 AAAACTAAAAAAAAAAC
39439683 AAAAC-AAAACAAAAAA
1 AAAACTAAAA-AAAAAA
39439699 ATATCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAACTAAAAAAAAAAC
Found at i:39439825 original size:119 final size:117
Alignment explanation
Indices: 39439491--39439825 Score: 335
Period size: 119 Copynumber: 2.9 Consensus size: 117
39439481 TACGAAAGCC
* ** * * *
39439491 TGATATAAGATTCTTCAAAAACATTAATAAAACAAAATAATCAAACCTTAATACAAACTTAAAGC
1 TGATATAAGATACAACAAAAACATTAATAAAACAAAATAATCATACTTTAATACAAACTTAAAAC
* * * *
39439556 TAATAAAACACAACAACAA-AAAATAACATTTC---AAGTAAATACAAAGAAC
66 TAATAAAACACAACAACAACAAAAAAAC-TTTCTTTAAGTAAACACAAAAAAA
* * * *
39439605 TAATATAAGATACCACAAAAACATTAATAAAACAAATTAATCATACCTTTAATACGAA-TCTAAA
1 TGATATAAGATACAACAAAAACATTAATAAAACAAAATAATCATA-CTTTAATACAAACT-TAAA
* * * *
39439669 ACTAAAAAAAAAACAA-AACAAAACAAAAAAA-TATCTTTAA-TACACACAAAAAAAA
64 ACT-AATAAAACACAACAAC--AACAAAAAAACTTTCTTTAAGTAAACAC-AAAAAAA
* * * *
39439724 TGATATAAGATACAACAATAACAGTAATAAAACAAACTAATCATACATTTAATACAAACTTAAAT
1 TGATATAAGATACAACAAAAACATTAATAAAACAAAATAATCATAC-TTTAATACAAACTTAAAA
39439789 CTAATAAAACACAACAACAACAAAAAAATCTTTCTTT
65 CTAATAAAACACAACAACAACAAAAAAA-CTTTCTTT
39439826 TAAATATAAA
Statistics
Matches: 179, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
114 40 0.22
115 19 0.11
116 13 0.07
117 12 0.07
118 22 0.12
119 72 0.40
120 1 0.01
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (117 bp):
TGATATAAGATACAACAAAAACATTAATAAAACAAAATAATCATACTTTAATACAAACTTAAAAC
TAATAAAACACAACAACAACAAAAAAACTTTCTTTAAGTAAACACAAAAAAA
Found at i:39442024 original size:14 final size:14
Alignment explanation
Indices: 39441995--39442033 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
39441985 AATTTACAGC
*
39441995 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
39442009 ATTTACAAATATAT
1 ATATACAAATAAAT
39442023 ATATACAAATA
1 ATATACAAATA
39442034 CAATGTACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:39442649 original size:6 final size:6
Alignment explanation
Indices: 39442640--39442693 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
39442630 GTGTGAATGA
** *
39442640 AATAAT AATAAT AATGTT AATAAT AATAAC AATAAAT AA-AAT AA-AAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AAT-AAT AATAAT AATAAT
39442687 AA-AAT AA
1 AATAAT AA
39442694 GGGTATAGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 15 0.37
6 22 0.54
7 4 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (6 bp):
AATAAT
Found at i:39442654 original size:9 final size:9
Alignment explanation
Indices: 39442640--39442693 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
39442630 GTGTGAATGA
39442640 AATAATAAT
1 AATAATAAT
**
39442649 AATAATGTT
1 AATAATAAT
39442658 AATAATAAT
1 AATAATAAT
*
39442667 AACAATAAAT
1 AATAAT-AAT
39442677 AA-AATAA-
1 AATAATAAT
39442684 AATAA-AAT
1 AATAATAAT
39442692 AA
1 AA
39442694 GGGTATAGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 4 0.11
8 6 0.16
9 22 0.59
10 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
AATAATAAT
Found at i:39444171 original size:23 final size:22
Alignment explanation
Indices: 39444128--39444185 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39444118 AAAGGGTATC
* *
39444128 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39444149 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39444172 TGCATATCATATCT
1 TACAAATCATATCT
39444186 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39444188 original size:19 final size:20
Alignment explanation
Indices: 39444141--39444209 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 20
39444131 AAATTAAATC
* *
39444141 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
39444161 TCTTCTAAGATTGC-ATATCATA
1 ---TCTAAGATTGCAATATCATA
39444183 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
39444204 TCTAAG
1 TCTAAG
39444210 GTCATATCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.26
21 14 0.33
22 7 0.17
23 10 0.24
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:39444215 original size:19 final size:21
Alignment explanation
Indices: 39444175--39444216 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39444165 CTAAGATTGC
*
39444175 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGAGTGCAT
39444196 ATATCATATCTAAG-GT-CAT
1 ATATCATATCTAAGAGTGCAT
39444215 AT
1 AT
39444217 CTAAGATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 1 0.05
21 14 0.70
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGAGTGCAT
Found at i:39445207 original size:88 final size:88
Alignment explanation
Indices: 39445089--39445747 Score: 931
Period size: 88 Copynumber: 7.5 Consensus size: 88
39445079 GCTGGGGGCA
* * * * * *
39445089 TCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCTGCTGCATC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
* *
39445154 CCAGGGACGCAAGGCTGGTGCCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
39445177 TCGATCTGCTTCGCTGTCGGCGCAGAAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
* *
39445242 CCAGCGAGCCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * *
39445265 TCGATCTACTTCGCTGTCAGTGCAGGAAGGTAAGATCTACTATTTTCAGCCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
** *
39445330 CCAATGAGGCAATGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
39445353 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCTGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
39445418 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
39445441 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCTGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
* *
39445506 CCAGGGACGCAAGGCTGGTGCCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
39445529 TCGATCTGCTTTGCTGTCGGTGCAGAAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
*
39445594 CCAGGGAGCCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * *
39445617 TCGATCTACTTCGCTGTCAGTGCAGGAAGGTAAGATCTACTATTTTCAGCCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
** *
39445682 CCAATGAGGCAATGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
39445705 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTAT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTAT
39445748 CTTCGATCTA
Statistics
Matches: 511, Mismatches: 60, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 511 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:39445472 original size:44 final size:44
Alignment explanation
Indices: 39445336--39445474 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
39445326 TAACCCAATG
*
39445336 AGGCAATGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * * ** * * **** *
39445380 AGGCAAGATCTGCTATTTTTAACCTAC-TCTGCTG-CAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTC-GCTGTCGGTGCAGGA
39445424 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
39445468 AGGCAAG
1 AGGCAAG
39445475 ATCTGCTATT
Statistics
Matches: 64, Mismatches: 27, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
43 15 0.23
44 34 0.53
45 15 0.23
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.27
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
Found at i:39445789 original size:44 final size:45
Alignment explanation
Indices: 39445727--39446016 Score: 227
Period size: 44 Copynumber: 6.6 Consensus size: 45
39445717 GCTGTCGGTG
**
39445727 CAGGAAGGTAAGATCTGCTATCTTCGATCTACTTC-ACGCTAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGACGCTAATA
* * * * * *
39445771 CATGAAGAAAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGACGCTAATA
** * *
39445816 TGGGAAGACAAGATCTG-TATCTTCGATCCACTTCCTAC-C-AATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTT-CGACGCTAATA
* * * * *
39445859 TAGGAAGACAGGACCTGCTATCTTCGATCTACTTC-ATGCCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGACGCTAATA
* * * * * * *
39445903 CATGAAGACAAGATATGCTTTCTTCGATCTACTTCGCCACCAGTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGACGCTAATA
** * *
39445948 TGGGAAGATAAGATCTGC-ATCTTCGATCCACTTCGCTAC-C-AATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCG--ACGCTAATA
* *
39445992 TAGGAAGACAGGATCTGCTATCTTC
1 CAGGAAGACAAGATCTGCTATCTTC
39446017 ACTGATCTAC
Statistics
Matches: 194, Mismatches: 43, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
42 1 0.01
43 19 0.10
44 127 0.65
45 46 0.24
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (45 bp):
CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGACGCTAATA
Found at i:39445883 original size:88 final size:86
Alignment explanation
Indices: 39445736--39446016 Score: 273
Period size: 88 Copynumber: 3.2 Consensus size: 86
39445726 GCAGGAAGGT
* * *
39445736 AAGATCTGCTATCTTCGATCTACTT-CACGCTAATACATGAAGAAAAGATCTGCTTTCTTCGATC
1 AAGATCTGCTATCTTCGATCTACTTCCAC-C-AATATAGGAAGAAAAGATCTGCTATCTTCGATC
39445800 TACTTCGCCACTAGTATGGGAAGAC
64 TACTTCGCCACTA-TAT-GGAAGAC
* * * *
39445825 AAGATCTG-TATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCT
1 AAGATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGAAAAGATCTGCTATCTTCGATCT
* *
39445889 ACTTCATGCCAATACAT-GAAGAC
65 ACTTC--GCCACTATATGGAAGAC
* * * * *
39445912 AAGATATGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGC-ATCTTCGATC
1 AAGATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGAAAAGATCTGCTATCTTCGATC
* * *
39445976 CACTTCGCTACCAATATAGGAAGAC
64 TACTTCGCCA-CTATAT-GGAAGAC
*
39446001 AGGATCTGCTATCTTC
1 AAGATCTGCTATCTTC
39446017 ACTGATCTAC
Statistics
Matches: 157, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
86 3 0.02
87 16 0.10
88 77 0.49
89 51 0.32
90 10 0.06
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (86 bp):
AAGATCTGCTATCTTCGATCTACTTCCACCAATATAGGAAGAAAAGATCTGCTATCTTCGATCTA
CTTCGCCACTATATGGAAGAC
Found at i:39445885 original size:132 final size:133
Alignment explanation
Indices: 39445741--39446016 Score: 473
Period size: 132 Copynumber: 2.1 Consensus size: 133
39445731 AAGGTAAGAT
* *
39445741 CTGCTATCTTCGATCTACTTCACGCTAATACATGAAGAAAAGATCTGCTTTCTTCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATATGCTTTCTTCGATCTACTTC
* *
39445806 GCCACTAGTATGGGAAGACAAGATCTGTATCTTCGATCCACTTC-CTACCAATATAGGAAGACAG
66 GCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAG
39445870 GAC
131 GAC
* *
39445873 CTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATATGCTTTCTTCGATCTACTTC
*
39445938 GCCACCAGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAG
66 GCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAG
*
39446003 GAT
131 GAC
39446006 CTGCTATCTTC
1 CTGCTATCTTC
39446017 ACTGATCTAC
Statistics
Matches: 135, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
132 102 0.76
133 33 0.24
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (133 bp):
CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATATGCTTTCTTCGATCTACTTC
GCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAG
GAC
Found at i:39447246 original size:6 final size:6
Alignment explanation
Indices: 39447235--39447263 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
39447225 TTAGCCTCTC
39447235 CTTTTT CTTTTT CTTTTT CTTTTT -TTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
39447264 GAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
CTTTTT
Found at i:39451340 original size:17 final size:17
Alignment explanation
Indices: 39451318--39451361 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
39451308 TAGGAAATAA
39451318 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
39451335 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
39451352 -ATATGTATAT
1 AAAATGTATAT
39451362 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:39451854 original size:23 final size:22
Alignment explanation
Indices: 39451811--39451868 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39451801 AAAGGGTATC
* *
39451811 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39451832 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39451855 TGCATATCATATCT
1 TACAAATCATATCT
39451869 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39451871 original size:19 final size:20
Alignment explanation
Indices: 39451824--39451894 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 20
39451814 AAATTAAATC
* *
39451824 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
39451844 TCTTCTAAGATTGC-ATATCATA
1 ---TCTAAGATTGCAATATCATA
39451866 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
39451887 TCTAAGAT
1 TCTAAGAT
39451895 CATATCTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.25
21 16 0.36
22 7 0.16
23 10 0.23
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:39451914 original size:14 final size:12
Alignment explanation
Indices: 39451881--39451906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39451871 GATTGCATAT
39451881 ATCATATCTAAG
1 ATCATATCTAAG
39451893 ATCATATCTAAG
1 ATCATATCTAAG
39451905 AT
1 AT
39451907 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:39453336 original size:24 final size:25
Alignment explanation
Indices: 39453307--39453356 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
39453297 AATAGCATTA
39453307 TTTTTAT-TTTGGTCACTCTAATTT
1 TTTTTATATTTGGTCACTCTAATTT
39453331 TTTTTATCAATTTGGTCACTCTAATT
1 TTTTTAT--ATTTGGTCACTCTAATT
39453357 AAGATAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.30
27 16 0.70
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTTTATATTTGGTCACTCTAATTT
Found at i:39453743 original size:21 final size:22
Alignment explanation
Indices: 39453719--39453770 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
39453709 GCCCAAATAT
39453719 ATAACCTAACCCTAA-AA-CCC
1 ATAACCTAACCCTAATAAGCCC
* *
39453739 AATAACCCAAGCCTAATAAGCCC
1 -ATAACCTAACCCTAATAAGCCC
39453762 ATAACCTAA
1 ATAACCTAA
39453771 AATTTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 13 0.50
22 10 0.38
23 3 0.12
ACGTcount: A:0.46, C:0.35, G:0.04, T:0.15
Consensus pattern (22 bp):
ATAACCTAACCCTAATAAGCCC
Found at i:39454750 original size:5 final size:5
Alignment explanation
Indices: 39454740--39454768 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39454730 TACCACTTTC
39454740 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
39454769 GGTCCATAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:39454751 original size:23 final size:21
Alignment explanation
Indices: 39454713--39454754 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
39454703 GTCTTGTGTT
39454713 ACTTTTTTTTTCTATTTTACC
1 ACTTTTTTTTTCTATTTTACC
*
39454734 ACTTTCTTTTATTTTATTTTA
1 ACTTT-TTTT-TTCTATTTTA
39454755 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (21 bp):
ACTTTTTTTTTCTATTTTACC
Found at i:39455278 original size:3 final size:3
Alignment explanation
Indices: 39455272--39455373 Score: 204
Period size: 3 Copynumber: 34.0 Consensus size: 3
39455262 TTTTGTGCCC
39455272 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39455320 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39455368 TTA TTA
1 TTA TTA
39455374 ATGTTATAAT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39457429 original size:21 final size:22
Alignment explanation
Indices: 39457398--39457439 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
39457388 GATAGTTCTC
*
39457398 TTCTTGAATTATGCTATTTATG
1 TTCTTGAATTATACTATTTATG
*
39457420 TTCTT-AATTATATTATTTAT
1 TTCTTGAATTATACTATTTAT
39457440 ACTTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (22 bp):
TTCTTGAATTATACTATTTATG
Found at i:39458187 original size:18 final size:18
Alignment explanation
Indices: 39458164--39458210 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
39458154 GTTGCACCGA
*
39458164 GGCTTGCTTTGCCGCCAG
1 GGCTTGCTTTGCCCCCAG
39458182 GGCTTGCTTTGCCCCCAG
1 GGCTTGCTTTGCCCCCAG
39458200 GGCTTGCTTTG
1 GGCTTGCTTTG
39458211 GGGGGGCCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.32, G:0.32, T:0.32
Consensus pattern (18 bp):
GGCTTGCTTTGCCCCCAG
Found at i:39460497 original size:23 final size:24
Alignment explanation
Indices: 39460460--39460505 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
39460450 CTAGTTTTTT
39460460 TAAATTCATTTAAAACTT-GTTTAA
1 TAAATTCATTTAAAA-TTCGTTTAA
39460484 TAAATT-ATTTAAAATTCGTTTA
1 TAAATTCATTTAAAATTCGTTTA
39460506 TTGTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.62
24 6 0.29
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
TAAATTCATTTAAAATTCGTTTAA
Found at i:39461342 original size:21 final size:18
Alignment explanation
Indices: 39461295--39461344 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
39461285 AATAATGCAT
39461295 ATTTTTTTTCTATTTTAA
1 ATTTTTTTTCTATTTTAA
*
39461313 ATTCCTTTTTCTAAATTTTAA
1 ATT-TTTTTTCT--ATTTTAA
39461334 CATTTTTTTTC
1 -ATTTTTTTTC
39461345 GAATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.12
19 7 0.27
21 13 0.50
22 3 0.12
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTTTCTATTTTAA
Found at i:39464574 original size:3 final size:3
Alignment explanation
Indices: 39464559--39464588 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
39464549 TACAGGTAAC
*
39464559 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39464589 TGGTTTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39470335 original size:29 final size:32
Alignment explanation
Indices: 39470284--39470345 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 32
39470274 AGTTTATATA
39470284 TTTATAATTTTTAAAGGAATAAA-T-CAATTT
1 TTTATAATTTTTAAAGGAATAAAGTGCAATTT
* **
39470314 TTTATAA-TTTTAGAGGGGTAAAGTGCAATTT
1 TTTATAATTTTTAAAGGAATAAAGTGCAATTT
39470345 T
1 T
39470346 ACTTTAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.44
30 8 0.30
31 7 0.26
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (32 bp):
TTTATAATTTTTAAAGGAATAAAGTGCAATTT
Found at i:39481454 original size:43 final size:43
Alignment explanation
Indices: 39481407--39481489 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
39481397 GGGAGTATGA
* *
39481407 AAACGTCTTGAAGAAGAAAGGCAGTTGAAGTGACAAGGCGTGG
1 AAACGTCTTGAAGAAGAAAAGCAGATGAAGTGACAAGGCGTGG
39481450 AAACGTCTTGAAGAAGAAAAGCAGATGAAGTGACAAGGCG
1 AAACGTCTTGAAGAAGAAAAGCAGATGAAGTGACAAGGCG
39481490 ATGAACAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.33, T:0.14
Consensus pattern (43 bp):
AAACGTCTTGAAGAAGAAAAGCAGATGAAGTGACAAGGCGTGG
Found at i:39489776 original size:5 final size:5
Alignment explanation
Indices: 39489766--39489842 Score: 54
Period size: 5 Copynumber: 15.6 Consensus size: 5
39489756 AATTAAAATG
* * *
39489766 TATAT TATAT TATAT TA-ACT TA-A- TAAAT AAGTAAT TATGT TATAT
1 TATAT TATAT TATAT TATA-T TATAT TATAT TA-TA-T TATAT TATAT
* *
39489811 TATAA TATAT TATAA T-TAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
39489843 TATATAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
3 2 0.04
4 5 0.09
5 46 0.81
6 2 0.04
7 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:39489848 original size:10 final size:10
Alignment explanation
Indices: 39489806--39489848 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
39489796 GTAATTATGT
39489806 TATATTATAA
1 TATATTATAA
39489816 TATATTATAA
1 TATATTATAA
*
39489826 T-TATTATAT
1 TATATTATAA
*
39489835 TATATTATTA
1 TATATTATAA
39489845 TATA
1 TATA
39489849 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATTATAA
Found at i:39492961 original size:16 final size:17
Alignment explanation
Indices: 39492937--39492971 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39492927 AATATATATA
*
39492937 TGTGTAAATGTGA-AAT
1 TGTGCAAATGTGATAAT
39492953 TGTGCAAATGTGATAAT
1 TGTGCAAATGTGATAAT
39492970 TG
1 TG
39492972 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (17 bp):
TGTGCAAATGTGATAAT
Found at i:39493106 original size:25 final size:25
Alignment explanation
Indices: 39493078--39493127 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39493068 GCGCGTTCTT
* *
39493078 TGATTA-TTAGCACGTTGGTGCTCTC
1 TGATTACTT-GCACGATAGTGCTCTC
39493103 TGATTACTTGCACGATAGTGCTCTC
1 TGATTACTTGCACGATAGTGCTCTC
39493128 CGTTTAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (25 bp):
TGATTACTTGCACGATAGTGCTCTC
Found at i:39493566 original size:22 final size:22
Alignment explanation
Indices: 39493541--39493609 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
39493531 TATTTGATTA
*
39493541 TTAGCACATTAGTGCTATCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
39493563 TTAGCATATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
39493585 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
39493607 TTA
1 TTA
39493610 ATAGTGCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:39494118 original size:5 final size:5
Alignment explanation
Indices: 39494108--39494137 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
39494098 TAAATAAGTA
39494108 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
39494138 TATNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:39496814 original size:18 final size:18
Alignment explanation
Indices: 39496789--39496830 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39496779 AAACTTGAAA
* *
39496789 AATTGAGAGAGCTGAGAG
1 AATTGAGAGAACAGAGAG
*
39496807 AGTTGAGAGAACAGAGAG
1 AATTGAGAGAACAGAGAG
39496825 AATTGA
1 AATTGA
39496831 ATTTGAGTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.36, T:0.17
Consensus pattern (18 bp):
AATTGAGAGAACAGAGAG
Found at i:39503868 original size:16 final size:16
Alignment explanation
Indices: 39503847--39503880 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39503837 AAAAGATTAT
*
39503847 GATCAAATTAGTCTTA
1 GATCAAATCAGTCTTA
39503863 GATCAAATCAGTCTTA
1 GATCAAATCAGTCTTA
39503879 GA
1 GA
39503881 GCTAAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (16 bp):
GATCAAATCAGTCTTA
Found at i:39504019 original size:16 final size:16
Alignment explanation
Indices: 39504000--39504030 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39503990 AGAAAATAAA
*
39504000 TATAATATGTAAATGG
1 TATAATATATAAATGG
39504016 TATAATATATAAATG
1 TATAATATATAAATG
39504031 AATAAATACA
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:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
TATAATATATAAATGG
Found at i:39504667 original size:22 final size:22
Alignment explanation
Indices: 39504629--39504670 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
39504619 TTTATTATTC
39504629 TAAATATTAAAAAATAAAATTA
1 TAAATATTAAAAAATAAAATTA
*
39504651 TAAA-ATTATAAAGATAAAAT
1 TAAATATTA-AAAAATAAAAT
39504671 AACTCAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATATTAAAAAATAAAATTA
Found at i:39510485 original size:16 final size:16
Alignment explanation
Indices: 39510464--39510494 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39510454 TCAAAATTTC
39510464 TATTTAATTTTTATAA
1 TATTTAATTTTTATAA
39510480 TATTTAATTTTTATA
1 TATTTAATTTTTATA
39510495 TTAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTAATTTTTATAA
Found at i:39514139 original size:15 final size:15
Alignment explanation
Indices: 39514119--39514147 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39514109 TTCTTTTATG
39514119 TTCTTCTTTTGTTTC
1 TTCTTCTTTTGTTTC
39514134 TTCTTCTTTTGTTT
1 TTCTTCTTTTGTTT
39514148 TACTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (15 bp):
TTCTTCTTTTGTTTC
Found at i:39515493 original size:42 final size:42
Alignment explanation
Indices: 39515433--39515586 Score: 159
Period size: 42 Copynumber: 3.7 Consensus size: 42
39515423 TCGAAAGTTT
* *
39515433 AACAGAAGCTTATGAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTG
* * * *
39515475 AACGGAAGCTCATAAGAGCTAAACAAAAACCTATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTG
* *
39515517 AACAGAAGCTCAAAAGAGCTGAAC-GAAAACCCA-ATAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACAG-AAACCCATA-AGGGTTG
** * * *
39515559 AATTGAAACTCATATGAGTTAAACAGAA
1 AACAGAAGCTCATAAGAGCTAAACAGAA
39515587 GCTCGTGAGA
Statistics
Matches: 90, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 1 0.01
42 88 0.98
43 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTG
Found at i:39515635 original size:12 final size:12
Alignment explanation
Indices: 39515613--39515639 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39515603 CGGAAAGTAA
39515613 ACACGAAAGTTC
1 ACACGAAAGTTC
39515625 ACACGAAAGTTC
1 ACACGAAAGTTC
39515637 ACA
1 ACA
39515640 ACAAATGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (12 bp):
ACACGAAAGTTC
Found at i:39524040 original size:11 final size:11
Alignment explanation
Indices: 39524012--39524055 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
39524002 TACCAAACAA
39524012 CAACCAAATAG
1 CAACCAAATAG
39524023 -AGACCAAATAG
1 CA-ACCAAATAG
* *
39524034 CACCCAAAAAG
1 CAACCAAATAG
39524045 CAACCAAATAG
1 CAACCAAATAG
39524056 TGAATAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 1 0.04
11 25 0.93
12 1 0.04
ACGTcount: A:0.55, C:0.27, G:0.11, T:0.07
Consensus pattern (11 bp):
CAACCAAATAG
Found at i:39525482 original size:5 final size:5
Alignment explanation
Indices: 39525464--39525493 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
39525454 AAAGGTAAAC
39525464 AAAGA AAA-A AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A
39525494 GCTTTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:39530076 original size:27 final size:27
Alignment explanation
Indices: 39530038--39530090 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
39530028 TTCATCATGG
39530038 TCATAATAGCAGTAACTTAAGAAACCA
1 TCATAATAGCAGTAACTTAAGAAACCA
39530065 TCATAATAGCAGTAACTTAAGAAACC
1 TCATAATAGCAGTAACTTAAGAAACC
39530091 TTGCATTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (27 bp):
TCATAATAGCAGTAACTTAAGAAACCA
Found at i:39538645 original size:24 final size:24
Alignment explanation
Indices: 39538593--39538645 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
39538583 ATTAGTAAGT
*
39538593 CAAATAAACTATACTAATAAATGC
1 CAAATAAACTATACTAATAAATAC
* * *
39538617 TAAATATATTATACTAATAAATAC
1 CAAATAAACTATACTAATAAATAC
39538641 CAAAT
1 CAAAT
39538646 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (24 bp):
CAAATAAACTATACTAATAAATAC
Found at i:39554911 original size:31 final size:31
Alignment explanation
Indices: 39554876--39554939 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
39554866 TTTAGTTTTG
* *
39554876 GTTACTGAATC-ATTTGAAAGTTTTTATTTAA
1 GTTACTGAA-CAATTTAAAAATTTTTATTTAA
39554907 GTTACTGAACAATTTAAAAATTTTTATTTAA
1 GTTACTGAACAATTTAAAAATTTTTATTTAA
39554938 GT
1 GT
39554940 CATTGGCCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (31 bp):
GTTACTGAACAATTTAAAAATTTTTATTTAA
Found at i:39559540 original size:3 final size:3
Alignment explanation
Indices: 39559532--39559587 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
39559522 ATCAGAAGAG
39559532 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39559580 AAT AAT AA
1 AAT AAT AA
39559588 GGGATTTGGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39567600 original size:26 final size:25
Alignment explanation
Indices: 39567541--39567600 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
39567531 AAAAGACTCT
**
39567541 TTTTATTATATTTATAGACATTATG
1 TTTTATTATATTTATAGACATTAAA
* *
39567566 TCTTAATTATATTTATAGATATTAAAA
1 T-TTTATTATATTTATAGACATT-AAA
39567593 TTTTATTA
1 TTTTATTA
39567601 CTTTGTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.04
26 25 0.89
27 2 0.07
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (25 bp):
TTTTATTATATTTATAGACATTAAA
Found at i:39570903 original size:2 final size:2
Alignment explanation
Indices: 39570896--39570950 Score: 56
Period size: 2 Copynumber: 26.5 Consensus size: 2
39570886 GAATAAAAGG
** **
39570896 TC TC TC TC TC GG TGC TC TC TC TC TC GG TGC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC T-C TC TC TC TC TC TC TC
39570940 TC TC TC TC TC T
1 TC TC TC TC TC T
39570951 ATACGCAAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.00, C:0.44, G:0.11, T:0.45
Consensus pattern (2 bp):
TC
Found at i:39570916 original size:15 final size:15
Alignment explanation
Indices: 39570896--39570947 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
39570886 GAATAAAAGG
39570896 TCTCTCTCTCGGTGC
1 TCTCTCTCTCGGTGC
39570911 TCTCTCTCTCGGTGC
1 TCTCTCTCTCGGTGC
39570926 TCTCTCTCTC--T-C
1 TCTCTCTCTCGGTGC
39570938 TCTCTCTCTC
1 TCTCTCTCTC
39570948 TCTATACGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
12 11 0.30
13 1 0.03
15 25 0.68
ACGTcount: A:0.00, C:0.44, G:0.12, T:0.44
Consensus pattern (15 bp):
TCTCTCTCTCGGTGC
Found at i:39579308 original size:21 final size:20
Alignment explanation
Indices: 39579284--39579371 Score: 65
Period size: 22 Copynumber: 4.3 Consensus size: 20
39579274 TTATTAAACA
39579284 TTAATATTTAATTAATTATAT
1 TTAATATTTAATTAATTAT-T
** * *
39579305 TTAATAATGCAATAAATATAAT
1 TTAAT-ATTTAATTAAT-TATT
*
39579327 TTATTATATTAATTAATTATT
1 TTAATAT-TTAATTAATTATT
39579348 TT-ATATTATAATT--TTATT
1 TTAATATT-TAATTAATTATT
39579366 TTAATA
1 TTAATA
39579372 ATANNNNNNN
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
18 7 0.13
19 4 0.08
20 8 0.15
21 12 0.23
22 19 0.37
23 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
TTAATATTTAATTAATTATT
Found at i:39581309 original size:31 final size:30
Alignment explanation
Indices: 39581257--39581333 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
39581247 AATTCTCCTT
**
39581257 ATTTATATTAATT-C-TAAATTCTA-AATATG
1 ATTTATA-TAATTACTTAAATTCTAGAA-ACA
39581286 ATTTATATAATTTACTTAAATTCTAGAAACA
1 ATTTATATAA-TTACTTAAATTCTAGAAACA
39581317 ATTTATATAATTACTTA
1 ATTTATATAATTACTTA
39581334 GCATTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 3 0.07
29 9 0.21
30 8 0.19
31 20 0.48
32 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTTATATAATTACTTAAATTCTAGAAACA
Found at i:39583817 original size:6 final size:6
Alignment explanation
Indices: 39583798--39583836 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
39583788 TCATTTCCCA
39583798 TATGTT TCATGTT TATGTT TATGTT TATGTT TATGTT TA
1 TATGTT T-ATGTT TATGTT TATGTT TATGTT TATGTT TA
39583837 GTTCCGTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (6 bp):
TATGTT
Done.