Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 128 of 193
Found at i:40453224 original size:24 final size:24
Alignment explanation
Indices: 40453197--40453246 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40453187 TCATATAAGT
40453197 ATGTTTAACATGCAAATCACATAC
1 ATGTTTAACATGCAAATCACATAC
40453221 ATGTTTAACATGCAAATCACATAC
1 ATGTTTAACATGCAAATCACATAC
40453245 AT
1 AT
40453247 ACTCAAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (24 bp):
ATGTTTAACATGCAAATCACATAC
Found at i:40453311 original size:23 final size:23
Alignment explanation
Indices: 40453285--40453337 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
40453275 TTTTCATACG
*
40453285 AATATCACATATGCCATATAACA
1 AATAACACATATGCCATATAACA
40453308 AATAACACATATGCCATATAACA
1 AATAACACATATGCCATATAACA
40453331 AATAACA
1 AATAACA
40453338 TAAGAATGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.23
Consensus pattern (23 bp):
AATAACACATATGCCATATAACA
Found at i:40457670 original size:26 final size:27
Alignment explanation
Indices: 40457633--40457692 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
40457623 AAGAAAATAA
*
40457633 AAATTAATAATAATATTTAAATCAAT-
1 AAATTAACAATAATATTTAAATCAATC
40457659 AAATTAACAATAATATTTAAATCAATC
1 AAATTAACAATAATATTTAAATCAATC
40457686 AAATTAA
1 AAATTAA
40457693 ATGAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATTAACAATAATATTTAAATCAATC
Found at i:40466303 original size:21 final size:21
Alignment explanation
Indices: 40466279--40466320 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40466269 TTATTAAACT
* *
40466279 TTTCGAAATATGTATTTTTAA
1 TTTCGAAACATATATTTTTAA
40466300 TTTCGAAACATATATTTTTAA
1 TTTCGAAACATATATTTTTAA
40466321 AACTGTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTCGAAACATATATTTTTAA
Found at i:40467892 original size:60 final size:60
Alignment explanation
Indices: 40467709--40467881 Score: 244
Period size: 60 Copynumber: 2.9 Consensus size: 60
40467699 TTAATATAAT
40467709 ATTTGGTACCTGAACTTGACACTTTTTTT--TAGTTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGACA-TTTTTTTCCTAGTTT-GTACCTAAACTTTTTTTGGACCCA
* * *
40467769 AATTGGTACCTGAACTTGACA-CTTTTTCCTAGTCTAGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTCCTAGT-TTGTACCTAAACTTTTTTTGGACCCA
* * *
40467829 ATTTGGTACCTGATCTTGACATTTTTTTCCTAATTTGTACCTAATCTTTTTTT
1 ATTTGGTACCTGAACTTGACATTTTTTTCCTAGTTTGTACCTAAACTTTTTTT
40467882 AGATTCAATT
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
58 5 0.05
60 84 0.84
61 11 0.11
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTTCCTAGTTTGTACCTAAACTTTTTTTGGACCCA
Found at i:40468144 original size:31 final size:29
Alignment explanation
Indices: 40468058--40468144 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 29
40468048 GGACCCCAAA
*
40468058 AAGTTTAAGTACCAACTTAAAAAAAGTGTC
1 AAGTTT-AGTACCAAATTAAAAAAAGTGTC
* *
40468088 AAGTTTAGATACCAAATTAGGAAAAATTGTC
1 AAGTTTAG-TACCAAATTA-AAAAAAGTGTC
40468119 AAGTTTGAGTACCAAATTGAAAAAAA
1 AAGTTT-AGTACCAAATT-AAAAAAA
40468145 AAATGTTTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
29 2 0.04
30 15 0.31
31 29 0.59
32 3 0.06
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGTTTAGTACCAAATTAAAAAAAGTGTC
Found at i:40468606 original size:29 final size:30
Alignment explanation
Indices: 40468515--40468592 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
40468505 TTAAAATTTT
* *
40468515 AAAAATA-AAAAATTAACTTTATATAAAT-
1 AAAAATACAAAGATTAAATTTATATAAATA
*
40468543 TAAAATACAAAGATTAAATTTATATAAATA
1 AAAAATACAAAGATTAAATTTATATAAATA
40468573 AAAAA-ACAAAGATTAAATTT
1 AAAAATACAAAGATTAAATTT
40468593 CAAAAATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 6 0.14
29 34 0.77
30 4 0.09
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATACAAAGATTAAATTTATATAAATA
Found at i:40470233 original size:34 final size:34
Alignment explanation
Indices: 40470194--40470269 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
40470184 AGTAAATAAC
*
40470194 ATTTGGGTAAGGTAAAAAGTAAAAAATAAAAAAT
1 ATTTGGGTAAGATAAAAAGTAAAAAATAAAAAAT
* * *
40470228 ATTTGGGTAAGATATAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAAGTAAAAAATAAAAAAT
40470262 ATTTGGGT
1 ATTTGGGT
40470270 TTAGTTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAAGTAAAAAATAAAAAAT
Found at i:40470904 original size:59 final size:59
Alignment explanation
Indices: 40470841--40470953 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
40470831 CTAAATTTAA
* * *
40470841 CATTTTTTCTTAATTTAGTACCTAAACTTTTGTT-GACCCAATTTAGTACCTAAACTTGG
1 CATTTTTGCCTAATTTAATACCTAAACTTTT-TTAGACCCAATTTAGTACCTAAACTTGG
* * ** *
40470900 CATTTTTGCCTAATTTAATGCCTAAGCTTTTTTAGATTCAATTTGGTACCTAAA
1 CATTTTTGCCTAATTTAATACCTAAACTTTTTTAGACCCAATTTAGTACCTAAA
40470954 TTTATAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
58 2 0.04
59 43 0.96
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (59 bp):
CATTTTTGCCTAATTTAATACCTAAACTTTTTTAGACCCAATTTAGTACCTAAACTTGG
Found at i:40476797 original size:30 final size:30
Alignment explanation
Indices: 40476761--40476817 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40476751 TCCACACAAA
40476761 AAAAAAAAAAAGATT-AGGTACCAAATTAGG
1 AAAAAAAAAAAG-TTCAGGTACCAAATTAGG
**
40476791 AAAAAAATCAAGTTCAGGTACCAAATT
1 AAAAAAAAAAAGTTCAGGTACCAAATT
40476818 GGACCTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (30 bp):
AAAAAAAAAAAGTTCAGGTACCAAATTAGG
Found at i:40476894 original size:31 final size:30
Alignment explanation
Indices: 40476828--40477022 Score: 164
Period size: 30 Copynumber: 6.5 Consensus size: 30
40476818 GGACCTTAAA
* * *
40476828 AAGTTTAACTACCAACTTAAAAAAAATGTC
1 AAGTTTAAATACCAAATTAGAAAAAATGTC
* * *
40476858 GAGTTTAAATATCAAATTAGGAAAAAGTGTC
1 AAGTTTAAATACCAAATTA-GAAAAAATGTC
* * * *
40476889 AAGTTTGAGTACCAACTTAAAAAAAATGTC
1 AAGTTTAAATACCAAATTAGAAAAAATGTC
* *
40476919 GAGTTTAAATACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAATACCAAATT-AGAAAAAATGTC
* * *
40476950 AAGTTTGAGTACCAAATTGGACAAAAAAT-T-
1 AAGTTTAAATACCAAATT--AGAAAAAATGTC
* *
40476980 --GTTTAAGTACCAAATTAGAAAAAATTTC
1 AAGTTTAAATACCAAATTAGAAAAAATGTC
*
40477008 AAGTTTAGATACCAA
1 AAGTTTAAATACCAA
40477023 TTGTTATATT
Statistics
Matches: 129, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
26 8 0.06
27 1 0.01
28 15 0.12
30 49 0.38
31 49 0.38
32 7 0.05
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (30 bp):
AAGTTTAAATACCAAATTAGAAAAAATGTC
Found at i:40476902 original size:61 final size:61
Alignment explanation
Indices: 40476828--40477022 Score: 240
Period size: 61 Copynumber: 3.2 Consensus size: 61
40476818 GGACCTTAAA
* * * *
40476828 AAGTTTAACTACCAACTTAAAAAAAATGTCGAGTTTAAATATCAAATTAGGAAAAAGTGTC
1 AAGTTTGAGTACCAACTTAAAAAAAATGTCGAGTTTAAATACCAAATTAAGAAAAAGTGTC
40476889 AAGTTTGAGTACCAACTTAAAAAAAATGTCGAGTTTAAATACCAAATTAAGAAAAAGTGTC
1 AAGTTTGAGTACCAACTTAAAAAAAATGTCGAGTTTAAATACCAAATTAAGAAAAAGTGTC
* * * * *
40476950 AAGTTTGAGTACCAAATTGGACAAAAAAT-T---GTTTAAGTACCAAATT-AGAAAAAATTTC
1 AAGTTTGAGTACCAACTT--AAAAAAAATGTCGAGTTTAAATACCAAATTAAGAAAAAGTGTC
40477008 AAGTTT-AGATACCAA
1 AAGTTTGAG-TACCAA
40477023 TTGTTATATT
Statistics
Matches: 122, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
57 2 0.02
58 22 0.18
59 15 0.12
61 74 0.61
62 1 0.01
63 8 0.07
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (61 bp):
AAGTTTGAGTACCAACTTAAAAAAAATGTCGAGTTTAAATACCAAATTAAGAAAAAGTGTC
Found at i:40477354 original size:19 final size:19
Alignment explanation
Indices: 40477330--40477367 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40477320 AATTTGAACG
40477330 AGTTAAAATTTAGTGTCTT
1 AGTTAAAATTTAGTGTCTT
40477349 AGTTAAAATTTAGTGTCTT
1 AGTTAAAATTTAGTGTCTT
40477368 GAATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (19 bp):
AGTTAAAATTTAGTGTCTT
Found at i:40478341 original size:18 final size:19
Alignment explanation
Indices: 40478318--40478353 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40478308 TTAACTTTCA
*
40478318 TCAAATC-AACCCTAAAAC
1 TCAAATCTAACACTAAAAC
40478336 TCAAATCTAACACTAAAA
1 TCAAATCTAACACTAAAA
40478354 AGATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (19 bp):
TCAAATCTAACACTAAAAC
Found at i:40482044 original size:31 final size:33
Alignment explanation
Indices: 40482009--40482078 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 33
40481999 ATAAACCAAT
40482009 TTTAATCTCT-TTAAAAATTGTAAAATTAT-AG
1 TTTAATCTCTATTAAAAATTGTAAAATTATAAG
* * *
40482040 TTTAAT-TCTATTACAGATTGTAAAATTTTAAG
1 TTTAATCTCTATTAAAAATTGTAAAATTATAAG
40482072 TTTAATC
1 TTTAATC
40482079 GATTCTATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.09
31 22 0.67
32 8 0.24
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (33 bp):
TTTAATCTCTATTAAAAATTGTAAAATTATAAG
Found at i:40485222 original size:15 final size:16
Alignment explanation
Indices: 40485194--40485225 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40485184 AAACCATTGA
40485194 ATCAAATCATATAATG
1 ATCAAATCATATAATG
40485210 ATCAAAT-ATATAATG
1 ATCAAATCATATAATG
40485225 A
1 A
40485226 GGAAGATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (16 bp):
ATCAAATCATATAATG
Found at i:40491343 original size:3 final size:3
Alignment explanation
Indices: 40491335--40491359 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40491325 ATTATTCAAA
40491335 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
40491360 TGTGATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40492022 original size:17 final size:15
Alignment explanation
Indices: 40491989--40492054 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
40491979 ACACATTACA
40491989 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
40492004 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCT-T-CTTC
*
40492021 TTTATTT-CTT-TAT-
1 TTTCTTTCCTTCT-TC
40492034 TTT-TTTCC-TC-TC
1 TTTCTTTCCTTCTTC
40492046 TTTCTTTCC
1 TTTCTTTCC
40492055 CCTTTTTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
11 1 0.02
12 7 0.16
13 10 0.23
14 1 0.02
15 11 0.26
16 3 0.07
17 10 0.23
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:40494095 original size:21 final size:21
Alignment explanation
Indices: 40494071--40494111 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40494061 GGAAATGAAA
*
40494071 AATACAAAAAAATTTAAAATT
1 AATACAAAAAAACTTAAAATT
**
40494092 AATATGAAAAAACTTAAAAT
1 AATACAAAAAAACTTAAAAT
40494112 CGATAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AATACAAAAAAACTTAAAATT
Found at i:40498519 original size:29 final size:31
Alignment explanation
Indices: 40498451--40498520 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
40498441 TTTTTAAAAA
* * *
40498451 TTTTAAATTAATAAAAATATTTCATTTTACC
1 TTTTAAAATAATAAAAATATTTAATTTAACC
* *
40498482 TTCTAAAAATAAT-AAAAT-TTTAATTTAATC
1 TT-TTAAAATAATAAAAATATTTAATTTAACC
40498512 TTTTAAAAT
1 TTTTAAAAT
40498521 TTTTACTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 6 0.19
30 11 0.34
31 7 0.22
32 8 0.25
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTTAAAATAATAAAAATATTTAATTTAACC
Found at i:40499729 original size:43 final size:43
Alignment explanation
Indices: 40499676--40499847 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
40499666 ATGCCGCTAT
* *
40499676 AGAAAATGGTCTTTAGCGGCGCTTTTCCCGCAAACGCCACTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
** * * ** * *
40499719 AGAACATGGTCTTTAGAAGCGATTTT-CCATAAACTTCGCAAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
* * * *
40499761 AGATCATGTTCTTTAGCGGCGCTTTCCCCACAAACGCTACTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
* * *
40499804 AAAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
40499847 A
1 A
40499848 ATTAACAGAA
Statistics
Matches: 100, Mismatches: 28, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
42 30 0.30
43 70 0.70
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
Found at i:40501701 original size:23 final size:23
Alignment explanation
Indices: 40501675--40501771 Score: 101
Period size: 23 Copynumber: 4.2 Consensus size: 23
40501665 ACACTAGCGC
*
40501675 GCTCTCCGTTTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTTCGTGT
*
40501698 GCTCTCTGTTT-GCACGTT--TCGT
1 GCTCTCCGTTTAGCAC-TTCGT-GT
40501720 GCTCTCCGTTATTAGCACTTCGTGT
1 GCTCTCCG-T-TTAGCACTTCGTGT
* *
40501745 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCCGTTTAGCACTTCGTGT
40501768 GCTC
1 GCTC
40501772 AGTACTTTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
21 1 0.02
22 13 0.21
23 31 0.49
24 4 0.06
25 13 0.21
26 1 0.02
ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTCTCCGTTTAGCACTTCGTGT
Found at i:40501807 original size:39 final size:39
Alignment explanation
Indices: 40501736--40501810 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
40501726 CGTTATTAGC
* *
40501736 ACTTCGTGTGCTCTCTGATTAGCACTTCGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAACACTTCGTGTGCTCAGT
* *
40501775 ACTTTGTGTACTCTCTGTTTAACACTGT-GTGTGCTC
1 ACTTCGTGTACTCTCTGATTAACACT-TCGTGTGCTC
40501811 TCTGTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 30 0.97
40 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.41
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAACACTTCGTGTGCTCAGT
Found at i:40502798 original size:21 final size:21
Alignment explanation
Indices: 40502765--40502820 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
40502755 TTGTTGCCTA
* * * *
40502765 TGCTTCCTTCGCTTCTCTCGT
1 TGCTGCCTCCGCTTCCCTCGC
*
40502786 TGCTGCCTCCGCTTCCCTTGC
1 TGCTGCCTCCGCTTCCCTCGC
*
40502807 TGTTGCCTCCGCTT
1 TGCTGCCTCCGCTT
40502821 TAAGTTGTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.41, G:0.18, T:0.41
Consensus pattern (21 bp):
TGCTGCCTCCGCTTCCCTCGC
Found at i:40505384 original size:41 final size:40
Alignment explanation
Indices: 40505289--40505595 Score: 269
Period size: 41 Copynumber: 7.5 Consensus size: 40
40505279 TTAAAACACT
* *
40505289 GCTAATGCTCTGACCTTCAGCGTGCTT-TCCCAAAAACGCC
1 GCTAATGCTCTGACCTTTAGCGCGCTTCT-CCAAAAACGCC
* * *
40505329 GTTAATGCTGTGACCTTTAGCGTCACTTCTCCAAAAACGCC
1 GCTAATGCTCTGACCTTTAGCG-CGCTTCTCCAAAAACGCC
* * * * *
40505370 GCTAATTCTTTGACCTTCAACGGCGCTT-TCCCAAAAACACC
1 GCTAATGCTCTGACCTTTAGC-GCGCTTCT-CCAAAAACGCC
* * *
40505411 GTTAATGCTCTGACTTTTAGCGCCGCTTCTCCAAAAAAGCC
1 GCTAATGCTCTGACCTTTAGCG-CGCTTCTCCAAAAACGCC
**
40505452 GCTAATGCTCTGACCTTTAGCAGCGCTTCTCCAAAAACATC
1 GCTAATGCTCTGACCTTTAGC-GCGCTTCTCCAAAAACGCC
* * * * * ***
40505493 GCTAGTGCTTTGACTTTTAGCGACGCTAC-CAAAAAAAATC
1 GCTAATGCTCTGACCTTTAGCG-CGCTTCTCCAAAAACGCC
* * * *
40505533 ACTAATGCTCTAAACTTTAGCGACGCTTCTCCAAAAATGCC
1 GCTAATGCTCTGACCTTTAGCG-CGCTTCTCCAAAAACGCC
*
40505574 GTTAATGCTCTGACCTTTAGCG
1 GCTAATGCTCTGACCTTTAGCG
40505596 GCATTTTTTC
Statistics
Matches: 212, Mismatches: 46, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
40 53 0.25
41 155 0.73
42 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (40 bp):
GCTAATGCTCTGACCTTTAGCGCGCTTCTCCAAAAACGCC
Found at i:40505417 original size:82 final size:81
Alignment explanation
Indices: 40505289--40505595 Score: 296
Period size: 82 Copynumber: 3.8 Consensus size: 81
40505279 TTAAAACACT
* * * * *
40505289 GCTAATGCTCTGACCTTCAGCGTGCTTTCCCAAAAACGCCGTTAATGCTGTGACCTTTAGCGTCA
1 GCTAATGCTCTGACCTTCAGCGCGCTTTCCCAAAAACACCGTTAATGCTCTGACTTTTAGCGCCA
*
40505354 CTTCTCCAAAAACGCC
66 CTTCTCCAAAAAAGCC
* * *
40505370 GCTAATTCTTTGACCTTCAACGGCGCTTTCCCAAAAACACCGTTAATGCTCTGACTTTTAGCGCC
1 GCTAATGCTCTGACCTTCAGC-GCGCTTTCCCAAAAACACCGTTAATGCTCTGACTTTTAGCGCC
*
40505435 GCTTCTCCAAAAAAGCC
65 ACTTCTCCAAAAAAGCC
* * * * * *
40505452 GCTAATGCTCTGACCTTTAGCAGCGC-TTCTCCAAAAACATCGCTAGTGCTTTGACTTTTAGCGA
1 GCTAATGCTCTGACCTTCAGC-GCGCTTTC-CCAAAAACACCGTTAATGCTCTGACTTTTAGCGC
* * * **
40505516 CGCTAC-CAAAAAAAATC
64 CACTTCTCCAAAAAAGCC
* * * * ** *
40505533 ACTAATGCTCTAAACTTTAGCGACGC-TTCTCCAAAAATGCCGTTAATGCTCTGACCTTTAGCG
1 GCTAATGCTCTGACCTTCAGCG-CGCTTTC-CCAAAAACACCGTTAATGCTCTGACTTTTAGCG
40505596 GCATTTTTTC
Statistics
Matches: 189, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 80 0.42
82 108 0.57
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (81 bp):
GCTAATGCTCTGACCTTCAGCGCGCTTTCCCAAAAACACCGTTAATGCTCTGACTTTTAGCGCCA
CTTCTCCAAAAAAGCC
Found at i:40505561 original size:81 final size:82
Alignment explanation
Indices: 40505392--40505595 Score: 225
Period size: 81 Copynumber: 2.5 Consensus size: 82
40505382 ACCTTCAACG
* * * * * *
40505392 GCGCTT-TCCCAAAAACACCGTTAATGCTCTGACTTTTAGCGCCGCTTCTCCAAAAAAGCCGCTA
1 GCGCTTCT-CCAAAAACACCGCTAATGCTCTGACTTTTAGCGACGCTACTCAAAAAAAACCACTA
* *
40505456 ATGCTCTGACCTTTAGCA
65 ATGCTCTAAACTTTAGCA
* * * *
40505474 GCGCTTCTCCAAAAACATCGCTAGTGCTTTGACTTTTAGCGACGCTAC-CAAAAAAAATCACTAA
1 GCGCTTCTCCAAAAACACCGCTAATGCTCTGACTTTTAGCGACGCTACTCAAAAAAAACCACTAA
40505538 TGCTCTAAACTTTAGC-
66 TGCTCTAAACTTTAGCA
** * *
40505554 GACGCTTCTCCAAAAATGCCGTTAATGCTCTGACCTTTAGCG
1 G-CGCTTCTCCAAAAACACCGCTAATGCTCTGACTTTTAGCG
40505596 GCATTTTTTC
Statistics
Matches: 101, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 59 0.58
82 40 0.40
83 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (82 bp):
GCGCTTCTCCAAAAACACCGCTAATGCTCTGACTTTTAGCGACGCTACTCAAAAAAAACCACTAA
TGCTCTAAACTTTAGCA
Found at i:40510524 original size:6 final size:6
Alignment explanation
Indices: 40510515--40510549 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
40510505 ATGTATACGT
40510515 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
40510550 TACCTTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:40521055 original size:43 final size:43
Alignment explanation
Indices: 40520957--40521265 Score: 319
Period size: 43 Copynumber: 7.3 Consensus size: 43
40520947 TTATAAGAAA
* **
40520957 AAACGCCACTAAAGAACATGGTCTTTAGCGGCGC-TTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
* * * *
40520999 AAAGGCCGCCTAAAGACCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCG-CTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
* * **
40521043 AAACGCCGCTAAA-AA-AT-GTCTTTAGCGACGC-CTAGCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
* * *
40521082 AAACGCCGCGAAAGAACATGGT-TTTCAGCGGCGCTTTTTCAAT
1 AAACGCCGCTAAAGAACATGGTCTTT-AGCGGCGCTTTTTCCAC
* * *
40521125 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTGTCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
* **
40521168 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGC-TTAGCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
* * * *
40521210 AAACGCCGCTATA-AATAGTGTTCTTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCTAAAGAACA-TGGTCTTTAGCGGCGCTTTTTCCAC
40521253 AAACGCCGCTAAA
1 AAACGCCGCTAAA
40521266 ATTAACAGAT
Statistics
Matches: 218, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
39 16 0.07
40 14 0.06
41 10 0.05
42 46 0.21
43 117 0.54
44 15 0.07
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
Found at i:40521257 original size:128 final size:125
Alignment explanation
Indices: 40520957--40521265 Score: 356
Period size: 125 Copynumber: 2.4 Consensus size: 125
40520947 TTATAAGAAA
* * * ** * * *
40520957 AAACGCCACTAAAGAACATGG-TCTTTAGCGGCGCTTCCCCACAAAGGCCGCCTAAAGACCATGT
1 AAACGCCGCGAAAGAACATGGTTCTTTAGCGGCGTTTTTCCACAAACGCCG-CTAAAGAACATGG
* * *
40521021 TCTTTAGCGGCGCTTTTTCAACAAACGCCGCTAAAAAATGTCTTTAGCGACGCCTAGCCAC
65 TCTTTAGCAGCGCTTTGTCAACAAACGCCGCTAAAAAATGTCTTTAACGACGCCTAGCCAC
* * *
40521082 AAACGCCGCGAAAGAACATGGTT-TTCAGCGGCGCTTTTTCAATAAACGCCGCTAAAGAACATGG
1 AAACGCCGCGAAAGAACATGGTTCTTTAGCGGCG-TTTTTCCACAAACGCCGCTAAAGAACATGG
* *
40521146 TCTTTAGCAGCGCTTTGTCAACAAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTAGCCAC
65 TCTTTAGCAGCGCTTTGTCAACAAACGCCGCTAAA-AA-AT-GTCTTTAACGACGCCTAGCCAC
* * *
40521210 AAACGCCGCTATA-AATA-GTGTTCTTTAGCGGCGTTTTTTCCACAAACGCCGCTAAA
1 AAACGCCGCGAAAGAACATG-GTTCTTTAGCGGCG-TTTTTCCACAAACGCCGCTAAA
40521266 ATTAACAGAT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
125 72 0.47
126 15 0.10
127 8 0.05
128 59 0.38
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (125 bp):
AAACGCCGCGAAAGAACATGGTTCTTTAGCGGCGTTTTTCCACAAACGCCGCTAAAGAACATGGT
CTTTAGCAGCGCTTTGTCAACAAACGCCGCTAAAAAATGTCTTTAACGACGCCTAGCCAC
Found at i:40529818 original size:335 final size:335
Alignment explanation
Indices: 40529206--40530098 Score: 1630
Period size: 335 Copynumber: 2.7 Consensus size: 335
40529196 TTTGGAGTAT
* * *
40529206 AAACTTTCTTTCATTGTTAATCGTCTTCAAATTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
1 AAACTTTCTTTCATCGTTAATCATCTTCAAACTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
*
40529271 AAAACGTCCCAATTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTGGTCTA
66 AAAACGTCCCAATTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTAGTCTA
* * *
40529336 GTTGTCGGTTTGAGCATTAGATTCTAACTTGAATATGATGTGTATCATGTTTAAAACATGTCGGT
131 GTTGTCGGTTTGAGCATTAAATTCTAACTTGAATATGATGTGTATCATGTTTAAAACACGTCGAT
** *
40529401 CAAATTGTAAACACGCCTATGCCTAATATATTGACAACATGAATATCACATATTGAAAGAACATA
196 CAAATTGTAAACACTTCTATGCCTAATGTATTGACAACATGAATATCACATATTGAAAGAACATA
*
40529466 CAGAATTGTTGAAATCTAGGAAGGTTATTTATGCCTAAGTTGACAACTAGGTTGGTTGAAAGACT
261 CAGAATTGTTAAAATCTAGGAAGGTTATTTATGCCTAAGTTGACAACTAGGTTGGTTGAAAGACT
40529531 AGTTTCATAA
326 AGTTTCATAA
40529541 AAACTTTCTTTCATCGTTAATCATCTTCAAACTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
1 AAACTTTCTTTCATCGTTAATCATCTTCAAACTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
*
40529606 AAAACGTCCCACTTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTAGTCTA
66 AAAACGTCCCAATTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTAGTCTA
40529671 GTTGTCGGTTTGAGCATTAAATTCTAACTTGAATATGATGTGTATCATGTTTAAAACACGTCGAT
131 GTTGTCGGTTTGAGCATTAAATTCTAACTTGAATATGATGTGTATCATGTTTAAAACACGTCGAT
40529736 CAAATTGTAAACACTTCTATGCCTAATGTATTGACAACATGAATATCACATATTGAAAGAACATA
196 CAAATTGTAAACACTTCTATGCCTAATGTATTGACAACATGAATATCACATATTGAAAGAACATA
40529801 CAGAATTGTTAAAATCTAGGAAGGTTATTTATGCCTAAGTTGACAACTAGGTTGGTTGAAAGACT
261 CAGAATTGTTAAAATCTAGGAAGGTTATTTATGCCTAAGTTGACAACTAGGTTGGTTGAAAGACT
40529866 AGTTTCATAA
326 AGTTTCATAA
40529876 AAACTTTCTTTCATCGTTAATCATCTTCAAACTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
1 AAACTTTCTTTCATCGTTAATCATCTTCAAACTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
40529941 AAAACGTCCCAATTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTAGTCTA
66 AAAACGTCCCAATTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTAGTCTA
*
40530006 GTTGTCGGTTTGAGCATTAAATTCTAACTTGAATATGATGTGTATCATGTTTAAAACACGTGGAT
131 GTTGTCGGTTTGAGCATTAAATTCTAACTTGAATATGATGTGTATCATGTTTAAAACACGTCGAT
*
40530071 C--ATTGTAAACA-TGTCTATGCTTAATGTA
196 CAAATTGTAAACACT-TCTATGCCTAATGTA
40530099 ATCATCCTAG
Statistics
Matches: 542, Mismatches: 15, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
332 1 0.00
333 24 0.04
335 517 0.95
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (335 bp):
AAACTTTCTTTCATCGTTAATCATCTTCAAACTATGGTCTAATTTTAGATTGGTCCCAAAACTTT
AAAACGTCCCAATTGAGTCATTAAAGTATTAGTATTTTTATTACTTTAGTCCTTCTATTAGTCTA
GTTGTCGGTTTGAGCATTAAATTCTAACTTGAATATGATGTGTATCATGTTTAAAACACGTCGAT
CAAATTGTAAACACTTCTATGCCTAATGTATTGACAACATGAATATCACATATTGAAAGAACATA
CAGAATTGTTAAAATCTAGGAAGGTTATTTATGCCTAAGTTGACAACTAGGTTGGTTGAAAGACT
AGTTTCATAA
Found at i:40539067 original size:21 final size:21
Alignment explanation
Indices: 40539041--40539093 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
40539031 AAAAATATAT
*
40539041 AAATATATAAAT-ATTTTCAAA
1 AAATATATAAATAAATTT-AAA
40539062 AAATATA-ATAATAAATTTAAA
1 AAATATATA-AATAAATTTAAA
*
40539083 AAATGTATAAA
1 AAATATATAAA
40539094 ATTACATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATATATAAATAAATTTAAA
Found at i:40539115 original size:52 final size:51
Alignment explanation
Indices: 40539031--40539161 Score: 174
Period size: 52 Copynumber: 2.5 Consensus size: 51
40539021 AGAAATATAT
* *
40539031 AAAAATATAT-AAATATATAAATATTTTCAAAAAATATAATAATAAATTTA
1 AAAAATATATAAAATAAATAAATATTTTCAAAAAATATAATAATAAAATTA
* * *
40539081 AAAAATGTATAAAATTACATAAATATTTTTAAAAAATATAATAATAAAATTA
1 AAAAATATATAAAA-TAAATAAATATTTTCAAAAAATATAATAATAAAATTA
*
40539133 AAAATATATATAAAAATAAAAAAATATTT
1 AAAA-ATATAT-AAAATAAATAAATATTT
40539162 ATGTATTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
50 9 0.13
51 3 0.04
52 38 0.54
53 16 0.23
54 4 0.06
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (51 bp):
AAAAATATATAAAATAAATAAATATTTTCAAAAAATATAATAATAAAATTA
Found at i:40539147 original size:18 final size:19
Alignment explanation
Indices: 40539112--40539159 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
40539102 AATATTTTTA
*
40539112 AAAAATATAATAATAAAATT
1 AAAAATAT-ATAATAAAAAT
40539132 AAAAATATAT-ATAAAAAT
1 AAAAATATATAATAAAAAT
*
40539150 AAAAAAATAT
1 AAAAATATAT
40539160 TTATGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 16 0.62
19 2 0.08
20 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATATATAATAAAAAT
Found at i:40539159 original size:20 final size:20
Alignment explanation
Indices: 40539110--40539155 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40539100 TAAATATTTT
40539110 TAAAAAATATAATAATAAAA
1 TAAAAAATATAATAATAAAA
*
40539130 TTAAAAATAT-AT-ATAAAAA
1 TAAAAAATATAATAAT-AAAA
40539149 TAAAAAA
1 TAAAAAA
40539156 ATATTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAAATATAATAATAAAA
Found at i:40539587 original size:20 final size:20
Alignment explanation
Indices: 40539534--40539607 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
40539524 TTTGGTGCTG
40539534 TTTTTTTACTGTTTTGATTGT
1 TTTTTTTACTGTTTT-ATTGT
40539555 TGTTTTTTA-T-TTTT-TTGT
1 T-TTTTTTACTGTTTTATTGT
*** *
40539573 TTTTTTTACTGTTTTGGCGC
1 TTTTTTTACTGTTTTATTGT
40539593 TTTTTTTACTGTTTT
1 TTTTTTTACTGTTTT
40539608 GGTTGTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 7 0.15
18 6 0.13
19 4 0.09
20 20 0.43
21 2 0.04
22 7 0.15
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.73
Consensus pattern (20 bp):
TTTTTTTACTGTTTTATTGT
Found at i:40539619 original size:20 final size:19
Alignment explanation
Indices: 40539521--40539619 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 19
40539511 ATTATATTGT
40539521 TGTTTTGGTGCTGTTTTTTTAC
1 TGTTTTGGT--TG-TTTTTTAC
40539543 TGTTTTGATTGTTGTTTTTTA-
1 TGTTTTG---GTTGTTTTTTAC
* *
40539564 TTTTTTTGTT-TTTTTTAC
1 TGTTTTGGTTGTTTTTTAC
*
40539582 TGTTTTGG-CGCTTTTTTTAC
1 TGTTTTGGTTG--TTTTTTAC
40539602 TGTTTTGGTTGTTATTTT
1 TGTTTTGGTTGTT-TTTT
40539620 TGTTGTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
17 7 0.11
18 9 0.15
19 2 0.03
20 20 0.32
21 6 0.10
22 14 0.23
23 2 0.03
25 2 0.03
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.70
Consensus pattern (19 bp):
TGTTTTGGTTGTTTTTTAC
Found at i:40539629 original size:31 final size:31
Alignment explanation
Indices: 40539595--40539652 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
40539585 TTTGGCGCTT
* *
40539595 TTTTTACTGTT-TTGGTTGTTATTTTTGTTG
1 TTTTTAATGTTGTTGGCTGTTATTTTTGTTG
*
40539625 TTTTTAATGTTGTTTGCTGTTATTTTTG
1 TTTTTAATGTTGTTGGCTGTTATTTTTG
40539653 CTGCTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.09, C:0.03, G:0.19, T:0.69
Consensus pattern (31 bp):
TTTTTAATGTTGTTGGCTGTTATTTTTGTTG
Found at i:40539696 original size:21 final size:21
Alignment explanation
Indices: 40539632--40539696 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 21
40539622 TTGTTTTTAA
*
40539632 TGTTGTTT-GCTGTTATTTTT
1 TGTTGTTTGGATGTTATTTTT
* * *
40539652 GCTGCTGTTTTGGTTATTA-TTTT
1 --TGTTG-TTTGGATGTTATTTTT
40539675 TGTTGTTTGGATGTTATTTTT
1 TGTTGTTTGGATGTTATTTTT
40539696 T
1 T
40539697 TATGCGTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 4 0.12
23 7 0.21
24 5 0.15
ACGTcount: A:0.08, C:0.05, G:0.22, T:0.66
Consensus pattern (21 bp):
TGTTGTTTGGATGTTATTTTT
Found at i:40540545 original size:24 final size:24
Alignment explanation
Indices: 40540517--40540579 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
40540507 AGAAATAATC
40540517 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
40540541 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
40540565 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
40540580 TATTAGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:40542494 original size:24 final size:24
Alignment explanation
Indices: 40542465--40542515 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
40542455 AGAAATAATC
40542465 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
40542489 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
40542513 TTT
1 TTT
40542516 GAGTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:40542524 original size:24 final size:24
Alignment explanation
Indices: 40542465--40542527 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
40542455 AGAAATAATC
*
40542465 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTG
* *
40542489 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTG
* *
40542513 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
40542528 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTATTTG
Found at i:40544848 original size:24 final size:25
Alignment explanation
Indices: 40544816--40544876 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
40544806 TAATAAAACC
*
40544816 TTAAATTTATTACTTAATTA-AAATT
1 TTAATTTTATTACTT-ATTATAAATT
* * *
40544841 TT-ATTTTAATACTTTTTATACATT
1 TTAATTTTATTACTTATTATAAATT
40544865 TTAATTTTATTA
1 TTAATTTTATTA
40544877 TAATATTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.10
24 16 0.55
25 10 0.34
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTTTATTACTTATTATAAATT
Found at i:40545913 original size:2 final size:2
Alignment explanation
Indices: 40545906--40545934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40545896 TTTAACAATA
40545906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40545935 AACGTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40547358 original size:20 final size:19
Alignment explanation
Indices: 40547333--40547375 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
40547323 AATCGAACCG
40547333 ATTTTTAATATATATT-TTTA
1 ATTTTTAA-ATAT-TTATTTA
40547353 ATTTTTTAAATATTTATTTA
1 A-TTTTTAAATATTTATTTA
40547373 ATT
1 ATT
40547376 AAATTGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTAAATATTTATTTA
Found at i:40547989 original size:14 final size:12
Alignment explanation
Indices: 40547961--40548008 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
40547951 TGAGATATGC
*
40547961 TTTTAAAAAGTA
1 TTTTGAAAAGTA
40547973 TTTTGGAAAAGTGA
1 TTTT-GAAAAGT-A
40547987 TTTTGAAAAGTA
1 TTTTGAAAAGTA
40547999 CTTTTGAAAA
1 -TTTTGAAAA
40548009 ACTTGGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 5 0.16
13 22 0.69
14 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (12 bp):
TTTTGAAAAGTA
Found at i:40549057 original size:20 final size:22
Alignment explanation
Indices: 40549028--40549079 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
40549018 AAAAATTATT
*
40549028 AAAATTTTATATAATAA-TAAAA
1 AAAATTATATA-AATAATTAAAA
40549050 AAAATTAT-TAAATAATTAAAA
1 AAAATTATATAAATAATTAAAA
40549071 AAAATTATA
1 AAAATTATA
40549080 GATAATATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTATATAAATAATTAAAA
Found at i:40549072 original size:23 final size:22
Alignment explanation
Indices: 40549028--40549086 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
40549018 AAAAATTATT
*
40549028 AAAATTTTATATAATAATAAAA
1 AAAATTTTAAATAATAATAAAA
40549050 AAAATTATTAAATAAT--TAAAA
1 AAAATT-TTAAATAATAATAAAA
* *
40549071 AAAATTATAGATAATA
1 AAAATTTTAAATAATA
40549087 TGATAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 7 0.22
21 11 0.34
22 6 0.19
23 8 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATTTTAAATAATAATAAAA
Found at i:40556872 original size:19 final size:19
Alignment explanation
Indices: 40556850--40556889 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40556840 AATTTGGGTA
40556850 TAATCTGAAAAAAAAAAAT
1 TAATCTGAAAAAAAAAAAT
* **
40556869 TAATTTGACCAAAAAAAAT
1 TAATCTGAAAAAAAAAAAT
40556888 TA
1 TA
40556890 TATTTACCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATCTGAAAAAAAAAAAT
Found at i:40564835 original size:23 final size:22
Alignment explanation
Indices: 40564808--40564851 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
40564798 GTATTATCGC
*
40564808 TCTAAAATGTAAATTATATATTT
1 TCTAAAAGGTAAATTA-ATATTT
*
40564831 TCTAAAAGGTCAATTAATATT
1 TCTAAAAGGTAAATTAATATT
40564852 AGTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (22 bp):
TCTAAAAGGTAAATTAATATTT
Found at i:40568847 original size:281 final size:281
Alignment explanation
Indices: 40568337--40568891 Score: 776
Period size: 281 Copynumber: 2.0 Consensus size: 281
40568327 ACATCCAGCT
*
40568337 TTACTAGTTTGTAAAGAAAATACATGAAAAAACCAGTACATTGATCTTATTAGACAATATACAAT
1 TTACTAGTTTGTAAAGAAAATACATGAAAAAACCAGTACATTGATCTTACTAGACAATATACAAT
* * * * * * **
40568402 TTTAGGGCCAACAATTCCATTAATCTTACAGTTTAATAACAAAAATGGTTTTATATGATTAACAT
66 TTTAGAGCCAACAATTCCATTAATCTTACACTTCAACAAAAAAAATGGTTATATACAATTAACAT
* * * *
40568467 CTACGAAGCTTATTGATGCGATCTAACCTTTCCACTTGAAAGACACCAAGTTAAAACTCGATTAA
131 CTACAAAGCTTATTGATGCAATCTAACCTTTCCACTTGAAAGACACCAAGTTAAAACTCAACTAA
* * *
40568532 ATTTGATGACATAACATCAATGATTATTGATTCCAGTCCTCAAATGA-ACAAATCTATTTCATAA
196 ATTTGATAACACAACATCAATGATTATGGATTCCAGTCCTCAAATGATA-AAATCTATTTCATAA
* *
40568596 AAGAGTTTAATCAAAATGCAAC
260 AACAGTGTAATCAAAATGCAAC
* * * * **
40568618 TTACTAGTTTGTAAAGAACATGCATGACAAAACCAGTATATTGATC-TACTAGAC-ATCATGTAA
1 TTACTAGTTTGTAAAGAAAATACATGAAAAAACCAGTACATTGATCTTACTAGACAAT-ATACAA
40568681 TTTTAGAGCCAACAATTCCATTAATCTTACACTTCAACAAAAAAAATGGTTATATACAATTAACA
65 TTTTAGAGCCAACAATTCCATTAATCTTACACTTCAACAAAAAAAATGGTTATATACAATTAACA
* *
40568746 TCTACAAAGCTTATTGATGCAATCTAACCTTTTTCACTT-AGAAGACACCGAGTTAAAACTCAAC
130 TCTACAAAGCTTATTGATGCAATCTAACC-TTTCCACTTGA-AAGACACCAAGTTAAAACTCAAC
* * * *
40568810 TAAATTTGATAATACAATATCAATGGTTATGGATTCCAGTCCTCAAATGATAAAATCTATTTTAT
193 TAAATTTGATAACACAACATCAATGATTATGGATTCCAGTCCTCAAATGATAAAATCTATTTCAT
40568875 AAAACAGTGTAATCAAA
258 AAAACAGTGTAATCAAA
40568892 CTGAATTCAA
Statistics
Matches: 240, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
279 2 0.01
280 96 0.40
281 141 0.59
282 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (281 bp):
TTACTAGTTTGTAAAGAAAATACATGAAAAAACCAGTACATTGATCTTACTAGACAATATACAAT
TTTAGAGCCAACAATTCCATTAATCTTACACTTCAACAAAAAAAATGGTTATATACAATTAACAT
CTACAAAGCTTATTGATGCAATCTAACCTTTCCACTTGAAAGACACCAAGTTAAAACTCAACTAA
ATTTGATAACACAACATCAATGATTATGGATTCCAGTCCTCAAATGATAAAATCTATTTCATAAA
ACAGTGTAATCAAAATGCAAC
Found at i:40572022 original size:27 final size:27
Alignment explanation
Indices: 40571992--40572050 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
40571982 AATCTAAGGC
*
40571992 TAAATAGATTAAATATG-TAGATTTTTT
1 TAAATAGATTAAATAAGTTAG-TTTTTT
* *
40572019 TAAATTGGTTAAATAAGTTAGTTTTTT
1 TAAATAGATTAAATAAGTTAGTTTTTT
*
40572046 AAAAT
1 TAAAT
40572051 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (27 bp):
TAAATAGATTAAATAAGTTAGTTTTTT
Found at i:40572051 original size:27 final size:27
Alignment explanation
Indices: 40572000--40572051 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40571990 GCTAAATAGA
* *
40572000 TTAAATATGTAGATTTTTTTAAATTGG
1 TTAAATAAGTAGATTTTTTAAAATTGG
40572027 TTAAATAAGTTAG-TTTTTTAAAATT
1 TTAAATAAG-TAGATTTTTTAAAATT
40572052 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (27 bp):
TTAAATAAGTAGATTTTTTAAAATTGG
Found at i:40578236 original size:33 final size:33
Alignment explanation
Indices: 40578199--40578271 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
40578189 AGGATTATAC
*
40578199 TAATATAAGTTATCTTTCATTAAAAAATAAGGT
1 TAATATAAGTTATATTTCATTAAAAAATAAGGT
40578232 TAATATAAGTTATATTTCATTAAAAAATAAGGT
1 TAATATAAGTTATATTTCATTAAAAAATAAGGT
*
40578265 CAATATA
1 TAATATA
40578272 CTATCTAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (33 bp):
TAATATAAGTTATATTTCATTAAAAAATAAGGT
Found at i:40578500 original size:24 final size:24
Alignment explanation
Indices: 40578451--40578500 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
40578441 GCCTTCCATG
* *
40578451 TTCAATTTGGTATTCAATTTTTTT
1 TTCAATTTGGTATTCAAGTTTGTT
*
40578475 TTCAATTTGGTACTT-GAGTTTGTT
1 TTCAATTTGGTA-TTCAAGTTTGTT
40578499 TT
1 TT
40578501 GGTCCCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.18, C:0.08, G:0.14, T:0.60
Consensus pattern (24 bp):
TTCAATTTGGTATTCAAGTTTGTT
Found at i:40582972 original size:102 final size:102
Alignment explanation
Indices: 40582796--40582999 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
40582786 GGTGAACATC
40582796 CTAGCTATCAAGCCAACACAGAGGGTTCAAAGTATCATAAACTTTGATCATAGCACCAAAAAGAA
1 CTAGCTATCAAGCCAACACAGAGGGTTCAAAGTATCATAAACTTTGATCATAGCACCAAAAAGAA
40582861 AACTGACCTTAAAATGCGGAGGAAAACATTCTTTTAA
66 AACTGACCTTAAAATGCGGAGGAAAACATTCTTTTAA
40582898 CTAGCTATCAAGCCAACACAGAGGGTTCAAAGTATCATAAACTTTGATCATAGCACCAAAAAGAA
1 CTAGCTATCAAGCCAACACAGAGGGTTCAAAGTATCATAAACTTTGATCATAGCACCAAAAAGAA
40582963 AACTGACCTTAAAATGCGGAGGAAAACATTCTTTTAA
66 AACTGACCTTAAAATGCGGAGGAAAACATTCTTTTAA
40583000 TTTAACCCTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (102 bp):
CTAGCTATCAAGCCAACACAGAGGGTTCAAAGTATCATAAACTTTGATCATAGCACCAAAAAGAA
AACTGACCTTAAAATGCGGAGGAAAACATTCTTTTAA
Found at i:40588272 original size:9 final size:9
Alignment explanation
Indices: 40588248--40588282 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
40588238 CAGTGTTGGT
40588248 TTTATTTTA
1 TTTATTTTA
40588257 TTTTATTTTA
1 -TTTATTTTA
*
40588267 TTTATTTTG
1 TTTATTTTA
40588276 TTTATTT
1 TTTATTT
40588283 AAAGCGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:40592168 original size:31 final size:31
Alignment explanation
Indices: 40592133--40592193 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
40592123 AACAACTCAA
40592133 TGACTTAAATAAAAACTTTCAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
* **
40592164 TGACTTAAATAGAAACTTTTGAATAGTTCA
1 TGACTTAAATAAAAACTTTCAAATAGTTCA
40592194 ATGAGCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAG
Found at i:40596464 original size:12 final size:12
Alignment explanation
Indices: 40596447--40596502 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
40596437 ACATTCAAAT
40596447 AACCAAAATAAC
1 AACCAAAATAAC
*
40596459 AACCAAAATAGC
1 AACCAAAATAAC
* *
40596471 AGCAAAAATAAC
1 AACCAAAATAAC
* *
40596483 AACAAAAACAAC
1 AACCAAAATAAC
40596495 AACACAAA
1 AAC-CAAA
40596503 TAATAGCATC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
12 33 0.92
13 3 0.08
ACGTcount: A:0.68, C:0.23, G:0.04, T:0.05
Consensus pattern (12 bp):
AACCAAAATAAC
Found at i:40596503 original size:24 final size:24
Alignment explanation
Indices: 40596451--40596505 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
40596441 TCAAATAACC
* * * *
40596451 AAAATAACAACCAAAATAGCAGCA
1 AAAATAACAACAAAAACAACAACA
40596475 AAAATAACAACAAAAACAACAACA
1 AAAATAACAACAAAAACAACAACA
*
40596499 CAAATAA
1 AAAATAA
40596506 TAGCATCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (24 bp):
AAAATAACAACAAAAACAACAACA
Found at i:40596529 original size:44 final size:44
Alignment explanation
Indices: 40596480--40596570 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 44
40596470 CAGCAAAAAT
*
40596480 AACAACAA-A-AACAACAACACAAATAATAGCATC-AAAACAGTAAA
1 AACAACAACACAA-AACAACA-AAA-AATAGCAACTAAAACAGTAAA
40596524 AACAACAACACTAAAACAACAAAAAATAGCAACTAAAACAGTAAA
1 AACAACAACAC-AAAACAACAAAAAATAGCAACTAAAACAGTAAA
40596569 AA
1 AA
40596571 AAAATAGCAC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
44 16 0.38
45 17 0.40
46 7 0.17
47 2 0.05
ACGTcount: A:0.67, C:0.20, G:0.04, T:0.09
Consensus pattern (44 bp):
AACAACAACACAAAACAACAAAAAATAGCAACTAAAACAGTAAA
Found at i:40596539 original size:23 final size:23
Alignment explanation
Indices: 40596513--40596572 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
40596503 TAATAGCATC
40596513 AAAACAGTAAAAACAACAAC-ACT
1 AAAACAGTAAAAA-AACAACAACT
* *
40596536 AAAACA--ACAAAAAATAGCAACT
1 AAAACAGTA-AAAAAACAACAACT
40596558 AAAACAGTAAAAAAA
1 AAAACAGTAAAAAAA
40596573 AATAGCACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 5 0.16
22 13 0.42
23 12 0.39
24 1 0.03
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (23 bp):
AAAACAGTAAAAAAACAACAACT
Found at i:40596558 original size:22 final size:21
Alignment explanation
Indices: 40596532--40596591 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 21
40596522 AAAACAACAA
40596532 CACTAAAACAACAAAAAATAG
1 CACTAAAACAACAAAAAATAG
*
40596553 CAACTAAAACAGTAAAAAAAAATAG
1 C-ACTAAAAC---AACAAAAAATAG
*
40596578 CACCAAAACAACAA
1 CACTAAAACAACAA
40596592 TATAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 5 0.16
22 8 0.25
24 7 0.22
25 12 0.38
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.08
Consensus pattern (21 bp):
CACTAAAACAACAAAAAATAG
Found at i:40596571 original size:24 final size:23
Alignment explanation
Indices: 40596504--40596587 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
40596494 CAACACAAAT
*
40596504 AATAGCA-TCAAAACAGTAAAAAC
1 AATAGCACT-AAAACAGTAAAAAA
* * *
40596527 AACAACACTAAAACA--ACAAAA
1 AATAGCACTAAAACAGTAAAAAA
40596548 AATAGCAACTAAAACAGTAAAAAAA
1 AATAGC-ACTAAAACAGT-AAAAAA
*
40596573 AATAGCACCAAAACA
1 AATAGCACTAAAACA
40596588 ACAATATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
21 8 0.17
22 9 0.19
23 11 0.23
24 9 0.19
25 11 0.23
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (23 bp):
AATAGCACTAAAACAGTAAAAAA
Found at i:40596586 original size:46 final size:45
Alignment explanation
Indices: 40596492--40596597 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 45
40596482 CAACAAAAAC
* * *
40596492 AACAACACAAATAATAGCATCAAAACAGTAAAAACAACAACACTAA
1 AACAACA-AAATAATAGCAACAAAACAGTAAAAACAAAAACACCAA
40596538 AACAACAAAA-AATAGCAACTAAAACAGTAAAAA-AAAATAGCACCAA
1 AACAACAAAATAATAGCAAC-AAAACAGTAAAAACAAAA-A-CACCAA
*
40596584 AACAACAATATAAT
1 AACAACAAAATAAT
40596598 TTTTTTATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 11 0.21
45 17 0.33
46 21 0.40
47 3 0.06
ACGTcount: A:0.65, C:0.19, G:0.05, T:0.11
Consensus pattern (45 bp):
AACAACAAAATAATAGCAACAAAACAGTAAAAACAAAAACACCAA
Found at i:40600053 original size:21 final size:20
Alignment explanation
Indices: 40599994--40600061 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
40599984 GAAATATTAT
40599994 TAAATAATTGAAAAAAAACC
1 TAAATAATTGAAAAAAAACC
* * **
40600014 ATGAATGATATG-ATGAAAACAC
1 -TAAATAAT-TGAAAAAAAAC-C
40600036 TAAATAATTGAAAAAAAATCC
1 TAAATAATTGAAAAAAAA-CC
40600057 TAAAT
1 TAAAT
40600062 GTGGGAAGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 2 0.06
21 29 0.83
22 4 0.11
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (20 bp):
TAAATAATTGAAAAAAAACC
Found at i:40603597 original size:12 final size:12
Alignment explanation
Indices: 40603577--40603627 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
40603567 AAACCAAGAA
*
40603577 GCTGTTGTTGCT
1 GCTGCTGTTGCT
*
40603589 GCTGCTGTTGTT
1 GCTGCTGTTGCT
*
40603601 GTTGCTGTTGCT
1 GCTGCTGTTGCT
* *
40603613 GTTGCTGTTGTT
1 GCTGCTGTTGCT
40603625 GCT
1 GCT
40603628 CTTGTTCTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.16, G:0.33, T:0.51
Consensus pattern (12 bp):
GCTGCTGTTGCT
Found at i:40603603 original size:6 final size:6
Alignment explanation
Indices: 40603582--40603622 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
40603572 AAGAAGCTGT
* *
40603582 TGTTGC TGCTGC TGTTGT TGTTGC TGTTGC TGTTGC TGTTG
1 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTG
40603623 TTGCTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.15, G:0.34, T:0.51
Consensus pattern (6 bp):
TGTTGC
Found at i:40603624 original size:15 final size:15
Alignment explanation
Indices: 40603577--40603627 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
40603567 AAACCAAGAA
*
40603577 GCTGTTGTTGCTGCT
1 GCTGTTGTTGCTGTT
40603592 GCTGTTG-T--TGTT
1 GCTGTTGTTGCTGTT
40603604 GC---TGTTGCTGTT
1 GCTGTTGTTGCTGTT
40603616 GCTGTTGTTGCT
1 GCTGTTGTTGCT
40603628 CTTGTTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
9 2 0.07
10 1 0.03
12 11 0.38
14 1 0.03
15 14 0.48
ACGTcount: A:0.00, C:0.16, G:0.33, T:0.51
Consensus pattern (15 bp):
GCTGTTGTTGCTGTT
Found at i:40605583 original size:17 final size:17
Alignment explanation
Indices: 40605561--40605596 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40605551 TTGTCCATTC
*
40605561 TATTTTTGATTTTAATT
1 TATTTTTAATTTTAATT
*
40605578 TATTTTTAATTTTTATT
1 TATTTTTAATTTTAATT
40605595 TA
1 TA
40605597 AAAAGTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTTAATTTTAATT
Found at i:40608251 original size:17 final size:17
Alignment explanation
Indices: 40608229--40608261 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40608219 TCTAATTGAA
*
40608229 AAAAAATATTACTAAAT
1 AAAAAATATTAATAAAT
40608246 AAAAAATATTAATAAA
1 AAAAAATATTAATAAA
40608262 AAACCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATATTAATAAAT
Found at i:40609619 original size:15 final size:15
Alignment explanation
Indices: 40609596--40609636 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
40609586 TGATAAATTA
40609596 AAAAATTAAGTGCTG
1 AAAAATTAAGTGCTG
* *
40609611 AAAAGTTAAGTGTTG
1 AAAAATTAAGTGCTG
*
40609626 AAAAAATAAGT
1 AAAAATTAAGT
40609637 ATTGAAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (15 bp):
AAAAATTAAGTGCTG
Found at i:40610237 original size:20 final size:22
Alignment explanation
Indices: 40610198--40610237 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
40610188 TTAGGAGACA
*
40610198 ACTAATAAAACATTACATTATC
1 ACTAATAAAACATTAAATTATC
40610220 ACTAAT-AAA-ATTAAATTA
1 ACTAATAAAACATTAAATTA
40610238 ATTAAGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
ACTAATAAAACATTAAATTATC
Found at i:40612062 original size:13 final size:14
Alignment explanation
Indices: 40612046--40612074 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40612036 ACTAAATTTG
40612046 TTGATT-AAATGAT
1 TTGATTGAAATGAT
40612059 TTGATTGAAATGAT
1 TTGATTGAAATGAT
40612073 TT
1 TT
40612075 TTTAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TTGATTGAAATGAT
Found at i:40614108 original size:29 final size:28
Alignment explanation
Indices: 40614076--40614135 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
40614066 AAAATCAAAT
* *
40614076 CAAATAAAAATTTTATATATAAAATTACA
1 CAAATAAAAA-TTCAAATATAAAATTACA
* *
40614105 CAAAATCAAAATTCAAATATAATATTACA
1 C-AAATAAAAATTCAAATATAAAATTACA
40614134 CA
1 CA
40614136 TTAGATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.04
29 17 0.65
30 8 0.31
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (28 bp):
CAAATAAAAATTCAAATATAAAATTACA
Found at i:40627235 original size:60 final size:59
Alignment explanation
Indices: 40627163--40627620 Score: 356
Period size: 60 Copynumber: 7.6 Consensus size: 59
40627153 CGAGAATTTG
*
40627163 AAAAAATTAAATTTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTATCTGATA
1 AAAAAATCAAA-TTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTATCTGATA
* * * * *
40627223 AAAAAATCAAATTTTTGGGTGTTGGCCCTGCAATGG-TCGACACCCCCTTTTTTGTCAGATA
1 AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCT-GACA-CCCC-TATTTATCTGATA
* * **
40627284 AAAAATTC-AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCTGTATTTATCTGATAA
1 AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTATCTGAT-A
* * * * * *
40627343 AAAAAATCAAATTTTTGGGTGATGGCCATGCAATGGCCGACGCCCCCT-TTTCTCAGA-A
1 AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCTGAC-ACCCCTATTTATCTGATA
** * *
40627401 AAAAGTTCAAATTTTTTTGGTGTTGGCTATGCAAT-GATCGACACCCCTATTTATCTGATAAA
1 AAAAAATCAAA-TTTTTTGGTGTTGGCCATGCAATGGCT-GACACCCCTATTTATCTGAT--A
* * * ** ** * * **
40627463 AAAAAATCAAATTTTTGGGTGTTGGTCATGCAATGACCAACA-CTTTTTTTTTCAAATA
1 AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTATCTGATA
* * * * *
40627521 AAAAAATTTCTAAATTTTTTAGTGTTGGACATGCAATGG-TCGACACCCCCTTTTTATTTGGT-
1 AAAAAA--TC-AAATTTTTTGGTGTTGGCCATGCAATGGCT-GACA-CCCCTATTTATCTGATA
* * * *
40627583 AAAAAATTAATTTTTTTTGGTGTTGTCCATGTAATGGC
1 AAAAAATCAA-ATTTTTTGGTGTTGGCCATGCAATGGC
40627621 CAACACCAAC
Statistics
Matches: 309, Mismatches: 67, Indels: 43
0.74 0.16 0.10
Matches are distributed among these distances:
58 33 0.11
59 69 0.22
60 113 0.37
61 70 0.23
62 16 0.05
63 8 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (59 bp):
AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTATCTGATA
Found at i:40627376 original size:120 final size:122
Alignment explanation
Indices: 40627163--40627588 Score: 505
Period size: 119 Copynumber: 3.5 Consensus size: 122
40627153 CGAGAATTTG
*
40627163 AAAAAATT-AAATTTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTATCTGAT-AAAA
1 AAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTATTTATCTGATAAAAA
* * *
40627226 AAATCAAATTTTTGGGTGTTGGCCCTGCAATGGTCGACACCCCCTTTTTTGTCAGAT
66 AAATCAAATTTTTGGGTGTTGGCCATGCAATGGACGACACCCCCTTTTTTCTCAGAT
**
40627283 AAAAAATTC-AA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACCTGTATTTATCTGATAAAAA
1 AAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTATTTATCTGATAAAAA
* * *
40627346 AAATCAAATTTTTGGGTGATGGCCATGCAATGGCCGACGCCCCC--TTTTCTCAGA-
66 AAATCAAATTTTTGGGTGTTGGCCATGCAATGGACGACACCCCCTTTTTTCTCAGAT
* * **
40627400 AAAAAGTTCAAATTTTTTTGGTGTTGGCTATGCAATGATCGACACCCCTATTTATCTGATAAAAA
1 AAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTATTTATCTGAT-AAAA
* * * * * *
40627465 AAAATCAAATTTTTGGGTGTTGGTCATGCAAT-GAC--CAACACTTTTTTTTTCAAAT
65 AAAATCAAATTTTTGGGTGTTGGCCATGCAATGGACGACACCCCCTTTTTTCTCAGAT
* * * * * *
40627520 AAAAAAATTTCTAAA-TTTTTTAGTGTTGGACATGCAATGGTCGACACCCCCTTTTTATTTGGTA
1 -AAAAAA-TTC-AAATTTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTATTTATCTGATA
40627584 AAAAA
62 AAAAA
40627589 TTAATTTTTT
Statistics
Matches: 263, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
117 11 0.04
118 11 0.04
119 96 0.37
120 88 0.33
121 5 0.02
122 36 0.14
123 16 0.06
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (122 bp):
AAAAAATTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTATTTATCTGATAAAAA
AAATCAAATTTTTGGGTGTTGGCCATGCAATGGACGACACCCCCTTTTTTCTCAGAT
Found at i:40629027 original size:12 final size:12
Alignment explanation
Indices: 40629012--40629041 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40629002 GCTCGTTTGA
40629012 GGGCTCATCATT
1 GGGCTCATCATT
*
40629024 GGGCTCATCCTT
1 GGGCTCATCATT
40629036 GGGCTC
1 GGGCTC
40629042 GAAATCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.30, G:0.30, T:0.30
Consensus pattern (12 bp):
GGGCTCATCATT
Found at i:40629782 original size:15 final size:16
Alignment explanation
Indices: 40629746--40629785 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
40629736 GCCATCTGAA
*
40629746 AAATTAAAAAATAATT
1 AAATAAAAAAATAATT
40629762 AGAATAAAAAAATAATT
1 A-AATAAAAAAATAATT
40629779 -AATAAAA
1 AAATAAAA
40629786 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 1 0.05
17 14 0.64
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AAATAAAAAAATAATT
Found at i:40630722 original size:22 final size:23
Alignment explanation
Indices: 40630697--40630745 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
40630687 GGTGAGCTGA
*
40630697 AATTTC-GGTTTTGCTGAGATGG
1 AATTTCTGGTTTAGCTGAGATGG
* *
40630719 AA-TTCTGGTTTAGGTGAGTTGG
1 AATTTCTGGTTTAGCTGAGATGG
40630741 AATTT
1 AATTT
40630746 GGGTGGTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.14
22 17 0.77
23 2 0.09
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (23 bp):
AATTTCTGGTTTAGCTGAGATGG
Found at i:40631024 original size:84 final size:84
Alignment explanation
Indices: 40630927--40631626 Score: 1134
Period size: 84 Copynumber: 8.3 Consensus size: 84
40630917 ATTATTTGAT
* * *
40630927 TATAATAATAATTTTTGATTTAAATATTTAAATTTAGTAAATAATTTATTGTCAAATCAACATAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
40630992 TATTTGATAAAAATTGTAA
66 TATTTGATAAAAATTGTAA
*
40631011 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATACAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
*
40631076 TATTTGATAAAAATTTTAA
66 TATTTGATAAAAATTGTAA
* *
40631095 TATAATAATAGTTTTTTGTATTTAAATATTTAAAATTAGTAAATAATATATTGTCAAATCAACAC
1 TATAATAATA-ATTTTTG-ATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACAC
*
40631160 ATTATTTGATAAAAATTTTAA
64 ATTATTTGATAAAAATTGTAA
* *
40631181 TATAATAATAATTTTTGCTTTAAATATTTAAAATTAGTAAATAATATATTGTCAAATCAACACAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
*
40631246 TATTTGATAAAAATTTTAA
66 TATTTGATAAAAATTGTAA
* * *
40631265 TATAATAATAATTTTTAATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAGTCAATACAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
*
40631330 TATTTGATAAAAATTTTAA
66 TATTTGATAAAAATTGTAA
*
40631349 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACATAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
40631414 TATTTGATAAAAATTGTAA
66 TATTTGATAAAAATTGTAA
* * *
40631433 TATAATAATAATTTTT-ATTTAAATATTTAAAATTAGAAAATAATGTATTCTCAAATTAACACAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
40631497 TATTTGATAAAAATTGTAA
66 TATTTGATAAAAATTGTAA
* * * * *
40631516 TATAATAAT-ATTTTTTATTTAAATATTTAAATTTAATAAATAATGTGTTGTCAAATCAATACAT
1 TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
40631580 TATTTGATAAAAATTGTAA
66 TATTTGATAAAAATTGTAA
40631599 TATAATAATAATTTTTTGTATTTAAATA
1 TATAATAATAA-TTTTTG-ATTTAAATA
40631627 ATGTTAAATT
Statistics
Matches: 578, Mismatches: 32, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
82 6 0.01
83 141 0.24
84 330 0.57
85 17 0.03
86 84 0.15
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (84 bp):
TATAATAATAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACAT
TATTTGATAAAAATTGTAA
Found at i:40631317 original size:254 final size:253
Alignment explanation
Indices: 40630838--40631626 Score: 1207
Period size: 254 Copynumber: 3.2 Consensus size: 253
40630828 TAAATTTAAA
* * * *
40630838 ATTTGATAAAAATTTTAATATAATAATA-ATTTT-T-TTTAAAAATTTAAAATTAATAAATAATG
1 ATTTGATAAAAATTTTAATATAATAATATTTTTTGTATTTAAATATTTAAAATTAGTAAATAATA
* *
40630900 TATTATCAAATC-A-ACA-TA-TT-AT-----TTG-ATTATAATAATAATTTTTGATTTAAATAT
66 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATAT
* * *
40630954 TTAAATTTAGTAAATAATTTATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAA
131 TTAAAATTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
*
40631019 TAATTTTTGATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATACATT
196 TAATTTTTAATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATACATT
40631077 ATTTGATAAAAATTTTAATATAATAATAGTTTTTTGTATTTAAATATTTAAAATTAGTAAATAAT
1 ATTTGATAAAAATTTTAATATAATAATA-TTTTTTGTATTTAAATATTTAAAATTAGTAAATAAT
* *
40631142 ATATTGTCAAATCAACACATTATTTGATAAAAATTTTAATATAATAATAATTTTTGCTTTAAATA
65 ATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATA
*
40631207 TTTAAAATTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTTTAATATAATA
130 TTTAAAATTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATA
*
40631272 ATAATTTTTAATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAGTCAATACATT
195 ATAATTTTTAATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATACATT
* *
40631331 ATTTGATAAAAATTTTAATATAATAATAATTTTTG-ATTTAAATATTTAAAATTAGTAAATAATG
1 ATTTGATAAAAATTTTAATATAATAATATTTTTTGTATTTAAATATTTAAAATTAGTAAATAATA
*
40631395 TATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTT-ATTTAAATAT
66 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATAT
* * * *
40631459 TTAAAATTAGAAAATAATGTATTCTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAA
131 TTAAAATTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
* * * *
40631524 T-ATTTTTTATTTAAATATTTAAATTTAATAAATAATGTGTTGTCAAATCAATACATT
196 TAATTTTTAATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATACATT
*
40631581 ATTTGATAAAAATTGTAATATAATAATAATTTTTTGTATTTAAATA
1 ATTTGATAAAAATTTTAATATAATAAT-ATTTTTTGTATTTAAATA
40631627 ATGTTAAATT
Statistics
Matches: 502, Mismatches: 31, Indels: 21
0.91 0.06 0.04
Matches are distributed among these distances:
239 28 0.06
241 4 0.01
242 1 0.00
243 36 0.07
244 1 0.00
245 3 0.01
246 2 0.00
247 2 0.00
248 2 0.00
250 77 0.15
251 77 0.15
252 89 0.18
253 8 0.02
254 172 0.34
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (253 bp):
ATTTGATAAAAATTTTAATATAATAATATTTTTTGTATTTAAATATTTAAAATTAGTAAATAATA
TATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATAT
TTAAAATTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
TAATTTTTAATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAATACATT
Found at i:40631459 original size:45 final size:45
Alignment explanation
Indices: 40631410--40631542 Score: 106
Period size: 45 Copynumber: 3.1 Consensus size: 45
40631400 TCAAATCAAC
40631410 ATATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTT-A
1 ATATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAA
* * ** *
40631454 A-A-TA-TT--T-AAAATTAG-AAAATAAT-GT-ATTCTCAAATTAA
1 ATATTATTTGATAAAAATT-GTAATATAATAATAATT-TTTATTTAA
* *
40631492 CACATTATTTGATAAAAATTGTAATATAATAATATTTTTTATTTAA
1 -ATATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAA
40631538 ATATT
1 ATATT
40631543 TAAATTTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 25
0.63 0.12 0.25
Matches are distributed among these distances:
36 3 0.05
37 5 0.08
38 14 0.22
39 3 0.05
40 1 0.02
41 4 0.06
42 4 0.06
43 1 0.02
44 3 0.05
45 17 0.27
46 7 0.11
47 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (45 bp):
ATATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAA
Found at i:40631466 original size:38 final size:38
Alignment explanation
Indices: 40631423--40631559 Score: 88
Period size: 38 Copynumber: 3.5 Consensus size: 38
40631413 TTATTTGATA
40631423 AAAATTGTAATATAATAATAATTTTTATTTAAATATTT
1 AAAATTGTAATATAATAATAATTTTTATTTAAATATTT
* * ** *
40631461 AAAATTAG-AAAATAAT-GT-ATTCTCAAATTAACACATTATTTGAT
1 AAAATT-GTAATATAATAATAATT-T-TTATTTA-A-A-TA-TT--T
*
40631505 AAAAATTGTAATATAATAATATTTTTTATTTAAATATTT
1 -AAAATTGTAATATAATAATAATTTTTATTTAAATATTT
40631544 -AAATT-TAATA-AATAAT
1 AAAATTGTAATATAATAAT
40631560 GTGTTGTCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 29
0.65 0.10 0.25
Matches are distributed among these distances:
35 6 0.08
36 8 0.11
37 7 0.09
38 17 0.23
39 3 0.04
40 1 0.01
41 4 0.05
42 4 0.05
43 1 0.01
44 3 0.04
45 17 0.23
46 2 0.03
47 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAATTGTAATATAATAATAATTTTTATTTAAATATTT
Found at i:40634609 original size:2 final size:2
Alignment explanation
Indices: 40634602--40634626 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40634592 TGATGATTAT
40634602 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40634627 CTGGTACTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40635914 original size:59 final size:59
Alignment explanation
Indices: 40635477--40636052 Score: 525
Period size: 62 Copynumber: 9.6 Consensus size: 59
40635467 AGGAGAAGTT
* * ** * ** *
40635477 GGTGTCGGCCATTACATGACCAATACAAAAAAAAATT-AATTTTTTACCAAATAAAAAGGG
1 GGTGTCGGCCATTGCATGGCC-A-ACACCAAAAAATTAAATTTTTTATCTGACAAAAAGGG
* * * * *
40635537 GATGTCGGCTATTGCATGGCCAACACAAAAAAAATTCGAATTTTTTATCTAACAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACAC-CAAAAAATT-AAATTTTTTATCTGACAAAAAGGG
* * * * * * * *
40635598 GATGTCGACTATAGAATGGCCAACACAAAAAAAATTTAAATTTTTTTAATATGA-AAAAATGG
1 GGTGTCGGCCATTGCATGGCCAACAC-CAAAAAA-TTAAA-TTTTTT-ATCTGACAAAAAGGG
* *
40635660 GGTGTCAGCCATTGCATGGCCAACACCAAAAAAATTTAAAAATTTTTTATCTG-CAAAGAGGG
1 GGTGTCGGCCATTGCATGGCCAACACC-AAAAAA-TT--AAATTTTTTATCTGACAAAAAGGG
* *
40635722 GATGTCGGCCATTGCATGGCCAACACCAAAAAAATTTAAATTTTTTTTATTTGA-AAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACACC-AAAAAA-TTAAA--TTTTTTATCTGACAAAAAGGG
** * ** * * *
40635784 GGTGTCGGCCATTGCATGATCAACACCCAAAAATTTGATTTTTTATCAGATAAATA-GG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTAAATTTTTTATCTGACAAAAAGGG
* * *
40635842 GGTGTCAGCCATTGCATGGCCAATACCAAAAAATTAAATTTTTTATTTGACAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTAAATTTTTTATCTGACAAAAAGGG
* * * * * *
40635901 GGTGTCGGCCATTGCATGGCCAACATCCAAAAATTTGATTTTTTTATCAGATAAATA-GG
1 GGTGTCGGCCATTGCATGGCCAACA-CCAAAAAATTAAATTTTTTATCTGACAAAAAGGG
* *
40635960 GGTGTCGGCTATTGCATGGCCAACACCAAAAAATTGAATTTTTTATCTGACAAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTAAATTTTTTATCTGAC-AAAAAGGG
* * *
40636020 GGTGTCGGCCGTTACATGGCGAACACCAAAAAA
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAA
40636053 ATTTGATTTT
Statistics
Matches: 430, Mismatches: 68, Indels: 36
0.81 0.13 0.07
Matches are distributed among these distances:
58 82 0.19
59 69 0.16
60 78 0.18
61 58 0.13
62 130 0.30
63 10 0.02
64 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTAAATTTTTTATCTGACAAAAAGGG
Found at i:40636789 original size:18 final size:19
Alignment explanation
Indices: 40636748--40636789 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
40636738 TGTTTAGCAT
* *
40636748 TTTTTTTTGTTCAAAAGTG
1 TTTTTTATGTTCAAAAGTA
*
40636767 CTTTTTATGTT-AAAAGTA
1 TTTTTTATGTTCAAAAGTA
40636785 TTTTT
1 TTTTT
40636790 GAAAAGCATT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTTTATGTTCAAAAGTA
Found at i:40638961 original size:25 final size:23
Alignment explanation
Indices: 40638933--40638992 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
40638923 CGGGTGCATG
*
40638933 AATATTTTATATTTGAAATTTATTT
1 AATATTTT-TATTTGAAATTTA-TA
* *
40638958 AATATAATTTATTTGATATTTATA
1 AATAT-TTTTATTTGAAATTTATA
40638982 AATATTTTTAT
1 AATATTTTTAT
40638993 AAGCATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 5 0.17
24 6 0.20
25 17 0.57
26 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
AATATTTTTATTTGAAATTTATA
Found at i:40662307 original size:15 final size:15
Alignment explanation
Indices: 40662287--40662326 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
40662277 CTCTATAACA
40662287 TCATCATCATCTTCG
1 TCATCATCATCTTCG
* *
40662302 TCATCATTATCTTCT
1 TCATCATCATCTTCG
*
40662317 TCACCATCAT
1 TCATCATCAT
40662327 TGTTATCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.03, T:0.42
Consensus pattern (15 bp):
TCATCATCATCTTCG
Found at i:40664227 original size:15 final size:15
Alignment explanation
Indices: 40664207--40664243 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
40664197 CTGGATCATA
40664207 TTCATCATCATCCTC
1 TTCATCATCATCCTC
* *
40664222 TTCATCTTCCTCCTC
1 TTCATCATCATCCTC
40664237 TTCATCA
1 TTCATCA
40664244 GACTCCGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCATCATCATCCTC
Found at i:40669282 original size:218 final size:218
Alignment explanation
Indices: 40668888--40669281 Score: 646
Period size: 217 Copynumber: 1.8 Consensus size: 218
40668878 TGAAATGAAC
*
40668888 ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAATTCTAGAGGGGA
1 ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAACTCTAGAGGGGA
* * *
40668953 AAAAGCCTAGAAAAAGATTAACTACAGCTTTGACAGAACTGATTTCACCCATCTCTACAGACCAA
66 AAAAGCCCAGAAAAAGATTAACTACAGCTTTGACAGAACTGATTTCACACACCTCTACAGACCAA
* ** *
40669018 GAGGCACTTTGCACTCATCATGGTCTAGTGTGCATTATAGAAAAAAATCTTACAGCTTCATCCCC
131 GAGGCACTTTGCACTCATCACGGTCTAGCATGAATTATAGAAAAAAATCTTACAGCTTCATCCCC
40669083 ATCCAAAATTTTGCAAAATAAAT
196 ATCCAAAATTTTGCAAAATAAAT
* *
40669106 ATTCCAACCTAATTGCAGCACCTTGGCAAATGTCACTTAATTGGAGCTTCAAACTCTAGA-GGGA
1 ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAACTCTAGAGGGGA
* *
40669170 AAAAGCCCGGAAAAAGATTAACTACAGCTTTGACAGAACTGATTTCACACACCTCTACAGATCAA
66 AAAAGCCCAGAAAAAGATTAACTACAGCTTTGACAGAACTGATTTCACACACCTCTACAGACCAA
* **
40669235 GAGGCACTTTGCATTCATTGCGGTCTAGCATGAATTATAGAAAAAAA
131 GAGGCACTTTGCACTCATCACGGTCTAGCATGAATTATAGAAAAAAA
40669282 AAAACTTGAA
Statistics
Matches: 161, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
217 104 0.65
218 57 0.35
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.25
Consensus pattern (218 bp):
ATTCCAACCTAATTGCAACACCCTGGCAAATGTCACTTAATTGGAGCTTCAAACTCTAGAGGGGA
AAAAGCCCAGAAAAAGATTAACTACAGCTTTGACAGAACTGATTTCACACACCTCTACAGACCAA
GAGGCACTTTGCACTCATCACGGTCTAGCATGAATTATAGAAAAAAATCTTACAGCTTCATCCCC
ATCCAAAATTTTGCAAAATAAAT
Found at i:40674180 original size:30 final size:30
Alignment explanation
Indices: 40674146--40674220 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
40674136 CATTTAACAC
40674146 AACAGTCACTCAACTT-T-GAAAATGTGACAA
1 AACAGTCACT-AACTTATCGAAAA-GTGACAA
40674176 AACAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAAC-TTATCGAAAAGTGACAA
*
40674207 AATAGTCACTAACT
1 AACAGTCACTAACT
40674221 CAACACCCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 3 0.07
30 13 0.32
31 20 0.49
32 5 0.12
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (30 bp):
AACAGTCACTAACTTATCGAAAAGTGACAA
Found at i:40674301 original size:3 final size:3
Alignment explanation
Indices: 40674295--40674327 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
40674285 AAGATGAAGA
*
40674295 AGG AGG AGG AGG AGG AGG AGG AGG AGG AAG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
40674328 TTCGGGTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:40676276 original size:29 final size:27
Alignment explanation
Indices: 40676127--40676275 Score: 88
Period size: 29 Copynumber: 5.2 Consensus size: 27
40676117 TGCAAAATAA
* * **
40676127 TAAAAGTTAGAAAAAAATTTAGGTCTTT
1 TAAAAGTTA-AAAAAAATTTTGGACCCT
* *
40676155 TAAAAGTTGGGAAAAAAA-TTTGAGGCCCT
1 TAAAAGTT--AAAAAAAATTTTG-GACCCT
* *
40676184 TAAAAACTAAAAAAAATATTTTGGGACCCT
1 T-AAAAGTTAAAAAAA-ATTTT-GGACCCT
*
40676214 TAAAAGTTGACAAAAAAAATTTT-GA-CAT
1 TAAAAGTT---AAAAAAAATTTTGGACCCT
40676242 GTAAAAGTTAAAAAAAATTTTGGACCTCT
1 -TAAAAGTTAAAAAAAATTTTGGACC-CT
40676271 TAAAA
1 TAAAA
40676276 ATAAAAATAA
Statistics
Matches: 94, Mismatches: 13, Indels: 28
0.70 0.10 0.21
Matches are distributed among these distances:
26 12 0.13
27 2 0.02
28 25 0.27
29 28 0.30
30 14 0.15
31 6 0.06
32 7 0.07
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (27 bp):
TAAAAGTTAAAAAAAATTTTGGACCCT
Found at i:40687221 original size:31 final size:31
Alignment explanation
Indices: 40687183--40687245 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
40687173 CGGCAAATTC
40687183 ATTGTAATTTGACTTTAAAATCATAAAAAAG
1 ATTGTAATTTGACTTTAAAATCATAAAAAAG
40687214 ATTGTAATTTGACTTTAAAATCATAAAAAAG
1 ATTGTAATTTGACTTTAAAATCATAAAAAAG
40687245 A
1 A
40687246 AGAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (31 bp):
ATTGTAATTTGACTTTAAAATCATAAAAAAG
Found at i:40700689 original size:18 final size:18
Alignment explanation
Indices: 40700668--40700703 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40700658 TATTTTGAAA
40700668 TTATTTGTCAAAAACTAT
1 TTATTTGTCAAAAACTAT
40700686 TTATTTGTCAAAAACTAT
1 TTATTTGTCAAAAACTAT
40700704 CTTAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
TTATTTGTCAAAAACTAT
Found at i:40700721 original size:15 final size:16
Alignment explanation
Indices: 40700701--40700732 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40700691 TGTCAAAAAC
40700701 TATCTTAAA-AGTTAT
1 TATCTTAAATAGTTAT
40700716 TATCTTAAATAGTTAT
1 TATCTTAAATAGTTAT
40700732 T
1 T
40700733 TACGAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TATCTTAAATAGTTAT
Found at i:40703926 original size:156 final size:153
Alignment explanation
Indices: 40703615--40703897 Score: 383
Period size: 156 Copynumber: 1.8 Consensus size: 153
40703605 GGTTAAAGCA
* * *
40703615 GAAGGTTGAGGAGGTTGTATGCTTGCAGTTACAGTCGAGGAGGCAAATAAGCTTGAAAATACACC
1 GAAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
* **
40703680 ACTCCTGCTGCTATTGCTAGCACCACTGCTAACCAGGCTCATGCTACCGCTACAACTTCCATTGA
66 ACTCCTGCTGCTA-T-CTA-CACCACTGCTAACCAAGCTCACACTACCGCTACAACTTCCATTGA
* *
40703745 AGCCAGCAGATGGTGGAGCTGGTGCT
128 AGCCAGCAGATGGCGGAGCCGGTGCT
*
40703771 GAAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACTCC
1 GAAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
* * * * * *
40703836 GCTGCTGCTGCTA-C-A-ACCACTGCTAATCAAGCTGACACTACTGCTACAACTTCCATTTAAGC
66 ACTCCTGCTGCTATCTACACCACTGCTAACCAAGCTCACACTACCGCTACAACTTCCATTGAAGC
40703898 TAGCCGGAGA
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
150 40 0.35
152 1 0.01
153 1 0.01
156 72 0.63
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (153 bp):
GAAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
ACTCCTGCTGCTATCTACACCACTGCTAACCAAGCTCACACTACCGCTACAACTTCCATTGAAGC
CAGCAGATGGCGGAGCCGGTGCT
Found at i:40708143 original size:25 final size:24
Alignment explanation
Indices: 40708102--40708149 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
40708092 TAACATTTAA
*
40708102 AATATTAAAAATCA-TTTTAAAAC
1 AATATTAAAAATAATTTTTAAAAC
40708125 AATATATAAAAACTAATTTTTAAAA
1 AATAT-TAAAAA-TAATTTTTAAAA
40708150 TATTGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 6 0.29
25 2 0.10
26 8 0.38
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
AATATTAAAAATAATTTTTAAAAC
Found at i:40712288 original size:73 final size:76
Alignment explanation
Indices: 40712165--40712374 Score: 264
Period size: 79 Copynumber: 2.7 Consensus size: 76
40712155 CTCTTGACAA
* * *
40712165 ATGCATGCATGCATATACACACACGTGCACTAAAGATCGATAAAAATTGACCATTGG-GCA-C-A
1 ATGCATGCATACATATATACACAC--GCACTAAAGATCGATAAAAATTGACCATTGGAACAGCAA
40712227 CACACATAAATAC
64 CACACATAAATAC
* *
40712240 ATGCATGCATACATATATATACACGCACTAAAGATCGATAAAAGTTGACCATTGGACACAGCAAC
1 ATGCATGCATACATATATACACACGCACTAAAGATCGATAAAAATTGACCATTGGA-ACAGCAAC
*
40712305 ACACATAAATGC
65 ACACATAAATAC
* * * *
40712317 ATGCATACATATATATATACCCACACGCGCTGAAGATCGATAAAAATTGACCATTGGA
1 ATGCATGCATACATATATA--CACACGCACTAAAGATCGATAAAAATTGACCATTGGA
40712375 CCTCATTTGG
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
73 30 0.26
75 23 0.20
76 1 0.01
77 30 0.26
79 33 0.28
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.21
Consensus pattern (76 bp):
ATGCATGCATACATATATACACACGCACTAAAGATCGATAAAAATTGACCATTGGAACAGCAACA
CACATAAATAC
Found at i:40720019 original size:39 final size:39
Alignment explanation
Indices: 40719944--40720019 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
40719934 ATTTGACCAA
* *
40719944 AACATCTTATAATTTAGAAACCAATCTAATATTTAAGTG
1 AACATCTTATAATTTAGAAACCAATCTAAAAATTAAGTG
* ** *
40719983 AACATCTTGTAATTTAGGGACCAATTTAAAAATTAAG
1 AACATCTTATAATTTAGAAACCAATCTAAAAATTAAG
40720020 CGGTAGTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (39 bp):
AACATCTTATAATTTAGAAACCAATCTAAAAATTAAGTG
Found at i:40724658 original size:2 final size:2
Alignment explanation
Indices: 40724651--40724715 Score: 57
Period size: 2 Copynumber: 34.0 Consensus size: 2
40724641 TCTTTATCCA
* *
40724651 AT AT AT AT AT AT AT AT AT AT AT A- AA AGT AT AT AT AA AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
40724692 AT GT A- AT A- AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40724716 GAATGTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
1 4 0.08
2 46 0.90
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:40732509 original size:23 final size:23
Alignment explanation
Indices: 40732457--40732510 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
40732447 CTCACCGAGA
*
40732457 AATTA-TTTTATGAATTCTTTTC
1 AATTATTTTTATGAATTCTTCTC
* **
40732479 ACTATATTTTTATGGTTTCTTCTC
1 AAT-TATTTTTATGAATTCTTCTC
40732503 AATTATTT
1 AATTATTT
40732511 AATGATAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (23 bp):
AATTATTTTTATGAATTCTTCTC
Found at i:40736079 original size:6 final size:6
Alignment explanation
Indices: 40736068--40736106 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
40736058 CCAGCCGCCA
40736068 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCT
40736107 CCCCCACCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTTCC
Found at i:40738281 original size:31 final size:28
Alignment explanation
Indices: 40738245--40738320 Score: 71
Period size: 31 Copynumber: 2.6 Consensus size: 28
40738235 ACTTAGGCCT
*
40738245 CTCAAAAGTTTTTGAAATTCTTATTAAAAC
1 CTCAAAA-TTTTTGAAATT-TTAATAAAAC
** *
40738275 CTTCAAAAATTTTAAAAATTTTAATCAAAC
1 C-TC-AAAATTTTTGAAATTTTAATAAAAC
*
40738305 CTCATAATTTTTGAAA
1 CTCAAAATTTTTGAAA
40738321 AATCTCATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
28 10 0.27
29 2 0.05
30 10 0.27
31 11 0.30
32 4 0.11
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (28 bp):
CTCAAAATTTTTGAAATTTTAATAAAAC
Found at i:40738321 original size:29 final size:31
Alignment explanation
Indices: 40738246--40738321 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
40738236 CTTAGGCCTC
*
40738246 TCAAAAGTTTTTG-AAATTCTTATTAAAACCT
1 TCAAAA-TTTTTGAAAATTCTTAATAAAACCT
* * *
40738277 TCAAAAATTTTAAAAATT-TTAATCAAACC-
1 TCAAAATTTTTGAAAATTCTTAATAAAACCT
*
40738306 TCATAATTTTTGAAAA
1 TCAAAATTTTTGAAAA
40738322 ATCTCATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 13 0.35
30 13 0.35
31 11 0.30
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (31 bp):
TCAAAATTTTTGAAAATTCTTAATAAAACCT
Found at i:40745486 original size:2 final size:2
Alignment explanation
Indices: 40745479--40745510 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40745469 AGATTCTTCG
40745479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40745511 GTGCCTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40752603 original size:16 final size:16
Alignment explanation
Indices: 40752582--40752616 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40752572 ATAAAAATAT
*
40752582 TAAAAAATCTGAAAAA
1 TAAAAAAACTGAAAAA
*
40752598 TAAAAAAACTTAAAAA
1 TAAAAAAACTGAAAAA
40752614 TAA
1 TAA
40752617 TTTTACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (16 bp):
TAAAAAAACTGAAAAA
Found at i:40752711 original size:6 final size:7
Alignment explanation
Indices: 40752689--40752721 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
40752679 TTTTTCATGA
40752689 TTTATTTT
1 TTTA-TTT
40752697 TTTATTT
1 TTTATTT
40752704 TTTATTT
1 TTTATTT
40752711 TTTATTT
1 TTTATTT
40752718 TTTA
1 TTTA
40752722 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:40753026 original size:16 final size:17
Alignment explanation
Indices: 40752993--40753026 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40752983 ATTATATAAT
40752993 ATTTAAATATATAGTTTA
1 ATTTAAATATATA-TTTA
40753011 ATTTAAATATAT-TTTA
1 ATTTAAATATATATTTA
40753027 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATATATTTA
Found at i:40754647 original size:15 final size:15
Alignment explanation
Indices: 40754586--40754636 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
40754576 CGAAAAAAAA
40754586 GAGAAAAAGAAAGAAAG
1 GAGAAAAAG-AAG-AAG
*
40754603 GA-AGAAAGAAGAAG
1 GAGAAAAAGAAGAAG
* *
40754617 GAGAAGAAGGAGAAG
1 GAGAAAAAGAAGAAG
40754632 GAGAA
1 GAGAA
40754637 GGAGAAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.17
15 17 0.59
16 5 0.17
17 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
GAGAAAAAGAAGAAG
Found at i:40754810 original size:18 final size:18
Alignment explanation
Indices: 40754787--40754821 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40754777 GGAAGAAAGG
40754787 TAAGTTT-GATTAATTTTT
1 TAAGTTTAG-TTAATTTTT
40754805 TAAGTTTAGTTAATTTT
1 TAAGTTTAGTTAATTTT
40754822 AAATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
TAAGTTTAGTTAATTTTT
Found at i:40755015 original size:21 final size:20
Alignment explanation
Indices: 40754989--40755031 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
40754979 TAATTTACTT
40754989 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAG-TAG
*
40755010 TAATTTTATTTTGTTAGTAG
1 TAATTTAATTTTGTTAGTAG
40755030 TA
1 TA
40755032 GTAAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (20 bp):
TAATTTAATTTTGTTAGTAG
Found at i:40757278 original size:30 final size:30
Alignment explanation
Indices: 40757235--40757594 Score: 368
Period size: 30 Copynumber: 11.9 Consensus size: 30
40757225 CTCAAGAGGT
* *
40757235 CCCC-AAACTTTTCTAAAATTAAATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * *
40757264 CCCCTAAACCTTTCTAAAATCACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* *
40757294 -CTCTCAAACTTTTCCAAAATTATATTTTAA
1 CCCCT-AAACTTTTCCAAAATTACATTTTAA
* *
40757324 CTCTTAAACTTTTCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * *
40757354 CCCCAAAAACTTTTCTAAAATTATATTTTAA
1 CCCC-TAAACTTTTCCAAAATTACATTTTAA
* * *
40757385 CCTCTAAAGTTTTCCAAAATTACATTTTTAC
1 CCCCTAAACTTTTCCAAAATTACA-TTTTAA
* *
40757416 CCCCTAAACTTTTCTAAAATTACATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * *
40757446 CCCTTAAACTTTTCCAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* *
40757476 CCTCTAAACTTTTTCCAAAATTACACTTTAA
1 CCCCTAAAC-TTTTCCAAAATTACATTTTAA
* *
40757507 TCCCC-AAACTTTTCCAAAATCATATTTTAA
1 -CCCCTAAACTTTTCCAAAATTACATTTTAA
* * *
40757537 CCCCCAAACTTTTCTAAAATCACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
** *
40757567 CATAC-AAACTTTTCCAAAATCACATTTT
1 C-CCCTAAACTTTTCCAAAATTACATTTT
40757595 GACCTCCGAG
Statistics
Matches: 275, Mismatches: 47, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
29 11 0.04
30 185 0.67
31 76 0.28
32 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.39
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:40757384 original size:61 final size:60
Alignment explanation
Indices: 40757235--40757594 Score: 381
Period size: 61 Copynumber: 6.0 Consensus size: 60
40757225 CTCAAGAGGT
* * * * *
40757235 CCCC-AAACTTTTCTAAAATTAAATTTTAACCCCTAAACCTTTCTAAAATCACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAACTCTTAAACTTTTCCAAAATCACATTTTAA
* * * *
40757294 -CTCTCAAACTTTTCCAAAATTATATTTTAACTCTTAAACTTTTCCAAAATTACATTTTAA
1 CCCCT-AAACTTTTCTAAAATTACATTTTAACTCTTAAACTTTTCCAAAATCACATTTTAA
* * * * *
40757354 CCCCAAAAACTTTTCTAAAATTATATTTTAAC-CTCTAAAGTTTTCCAAAATTACATTTTTAC
1 CCCC-TAAACTTTTCTAAAATTACATTTTAACTCT-TAAACTTTTCCAAAATCACA-TTTTAA
* * *
40757416 CCCCTAAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCATATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAACTCTTAAACTTTTCCAAAATCACATTTTAA
* * * ** *
40757476 CCTCTAAACTTTTTCCAAAATTACACTTTAA-TCCCCAAACTTTTCCAAAATCATATTTTAA
1 CCCCTAAAC-TTTTCTAAAATTACATTTTAACT-CTTAAACTTTTCCAAAATCACATTTTAA
* *
40757537 CCCCCAAACTTTTCTAAAATCACATTTTAACATAC--AAACTTTTCCAAAATCACATTTT
1 CCCCTAAACTTTTCTAAAATTACATTTTAAC-T-CTTAAACTTTTCCAAAATCACATTTT
40757595 GACCTCCGAG
Statistics
Matches: 256, Mismatches: 34, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.01
60 103 0.40
61 138 0.54
62 13 0.05
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.39
Consensus pattern (60 bp):
CCCCTAAACTTTTCTAAAATTACATTTTAACTCTTAAACTTTTCCAAAATCACATTTTAA
Found at i:40757402 original size:91 final size:90
Alignment explanation
Indices: 40757239--40757594 Score: 430
Period size: 91 Copynumber: 3.9 Consensus size: 90
40757229 AGAGGTCCCC
* * *
40757239 AAACTTTTCTAAAATTAAATTTTAACCCCTAAACCTTTCTAAAATCACATTTTAA-CTCTCAAAC
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTTTAACCTCT-AAAC
* *
40757303 TTTTCCAAAATTATATTTTAACTCTT
65 TTTTCCAAAATTACATTTTAACTCCT
* * * *
40757329 AAACTTTTCCAAAATTACATTTTAACCCCAAAAACTTTTCTAAAATTATATTTTAACCTCTAAAG
1 AAACTTTTCCAAAATTACATTTTAACCCC-TAAACTTTTCTAAAATCACATTTTAACCTCTAAAC
* *
40757394 TTTTCCAAAATTACATTTTTACCCCCT
65 TTTTCCAAAATTACA-TTTTAACTCCT
* * * * *
40757421 AAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCATATTTTAACCTCTAAACT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTTTAACCTCTAAAC-
* *
40757486 TTTTCCAAAATTACACTTTAA-TCCCC
65 TTTTCCAAAATTACATTTTAACT-CCT
* * * *
40757512 AAACTTTTCCAAAATCATATTTTAACCCCCAAACTTTTCTAAAATCACATTTTAACATAC-AAAC
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTTTAACCT-CTAAAC
*
40757576 TTTTCCAAAATCACATTTT
65 TTTTCCAAAATTACATTTT
40757595 GACCTCCGAG
Statistics
Matches: 227, Mismatches: 33, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
90 44 0.19
91 129 0.57
92 54 0.24
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (90 bp):
AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTTTAACCTCTAAACT
TTTCCAAAATTACATTTTAACTCCT
Found at i:40762741 original size:16 final size:14
Alignment explanation
Indices: 40762714--40762769 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
40762704 GATTTTACCC
40762714 AAAAAAGAAAAATGAGG
1 AAAAAAG-AAAA--AGG
*
40762731 AAAAAAGAAAAAAAGA
1 AAAAAAG--AAAAAGG
40762747 AAAAAAGAAAAAGG
1 AAAAAAGAAAAAGG
40762761 AAAAAAGAA
1 AAAAAAGAA
40762770 GAAAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 15 0.42
16 9 0.25
17 7 0.19
18 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAGG
Found at i:40762742 original size:8 final size:8
Alignment explanation
Indices: 40762714--40762777 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
40762704 GATTTTACCC
40762714 AAAAAAGA
1 AAAAAAGA
* *
40762722 AAAATGAGG
1 AAAA-AAGA
40762731 AAAAAAGA
1 AAAAAAGA
40762739 AAAAAAGA
1 AAAAAAGA
40762747 AAAAAAG-
1 AAAAAAGA
*
40762754 -AAAAAGG
1 AAAAAAGA
40762761 AAAAAAGA
1 AAAAAAGA
40762769 AGAAAAAGA
1 A-AAAAAGA
40762778 GAGGTCGAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
6 6 0.13
8 28 0.60
9 13 0.28
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:40762752 original size:33 final size:31
Alignment explanation
Indices: 40762714--40762777 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 31
40762704 GATTTTACCC
40762714 AAAAAAGAAAAATGAGGAAAAAAGAA-AAAAAGA
1 AAAAAAG-AAAA--AGGAAAAAAGAAGAAAAAGA
40762747 AAAAAAGAAAAAGGAAAAAAGAAGAAAAAGA
1 AAAAAAGAAAAAGGAAAAAAGAAGAAAAAGA
40762778 GAGGTCGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 12 0.40
31 7 0.23
32 4 0.13
33 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (31 bp):
AAAAAAGAAAAAGGAAAAAAGAAGAAAAAGA
Found at i:40762771 original size:17 final size:16
Alignment explanation
Indices: 40762714--40762776 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 16
40762704 GATTTTACCC
*
40762714 AAAAAAGAAAAATGAGG
1 AAAAAAGAAAAA-AAGG
40762731 AAAAAAGAAAAAAA-G
1 AAAAAAGAAAAAAAGG
*
40762746 AAAAAA-AGAAAAAGG
1 AAAAAAGAAAAAAAGG
40762761 AAAAAAGAAGAAAAAG
1 AAAAAAGAA-AAAAAG
40762777 AGAGGTCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.15
15 14 0.35
16 2 0.05
17 18 0.45
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGG
Done.