Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 130 of 208
Found at i:39879031 original size:112 final size:112
Alignment explanation
Indices: 39878709--39879052 Score: 508
Period size: 112 Copynumber: 3.1 Consensus size: 112
39878699 ATCGCAATAC
* * * * *
39878709 ATGAATGTATGTATGACCATGAGGTTAAAACCAATGGCAAGATCTAATAGGAATAAATGAATGTA
1 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTAATATGACTGAATGAATGTA
* ** ** * ** *
39878774 TGTAAAACCATGAGGTTAAGACCCATGGCAAGATCCGATATGACTGA
66 TGTAAAACCATGTGGTTAAGACCCATGGCATTATATGAAATGTTTGT
* *
39878821 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGAAAGATCTGATATGACTGAATGAATGTA
1 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTAATATGACTGAATGAATGTA
* *
39878886 TGTAAAACCATGTGGTTAAGACCTATGGAATTATATGAAATGTTTGT
66 TGTAAAACCATGTGGTTAAGACCCATGGCATTATATGAAATGTTTGT
*
39878933 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTTATATGACTGAATGAATGTA
1 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTAATATGACTGAATGAATGTA
*
39878998 TGTAAGACCATGTGGTTAAGACCCATGGCATTATATGAAATGTTTGT
66 TGTAAAACCATGTGGTTAAGACCCATGGCATTATATGAAATGTTTGT
39879045 ATGAATGT
1 ATGAATGT
39879053 TCATGGCGTA
Statistics
Matches: 209, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 209 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (112 bp):
ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTAATATGACTGAATGAATGTA
TGTAAAACCATGTGGTTAAGACCCATGGCATTATATGAAATGTTTGT
Found at i:39879052 original size:56 final size:56
Alignment explanation
Indices: 39878709--39879027 Score: 415
Period size: 56 Copynumber: 5.7 Consensus size: 56
39878699 ATCGCAATAC
* * * * * * *
39878709 ATGAATGTATGTATGACCATGAGGTTAAAACCAATGGCAAGATCTAATAGGAATAA
1 ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCAAGATCTGATATGACTGA
* *
39878765 ATGAATGTATGTAAAACCATGAGGTTAAGACCCATGGCAAGATCCGATATGACTGA
1 ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCAAGATCTGATATGACTGA
* *
39878821 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGAAAGATCTGATATGACTGA
1 ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCAAGATCTGATATGACTGA
* * * * * * ** *
39878877 ATGAATGTATGTAAAACCATGTGGTTAAGACCTATGG-AATTATATGAAATGTTTGT
1 ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCAA-GATCTGATATGACTGA
* *
39878933 ATGAATGTATGTAAGACCATGAGGTTAAAACCCATGGCAAGATCTTATATGACTGA
1 ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCAAGATCTGATATGACTGA
*
39878989 ATGAATGTATGTAAGACCATGTGGTTAAGACCCATGGCA
1 ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCA
39879028 TTATATGAAA
Statistics
Matches: 225, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
55 2 0.01
56 221 0.98
57 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (56 bp):
ATGAATGTATGTAAGACCATGAGGTTAAGACCCATGGCAAGATCTGATATGACTGA
Found at i:39881242 original size:20 final size:20
Alignment explanation
Indices: 39881204--39881256 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
39881194 ATTTTGTTAT
39881204 TCCTTCATAATTTCGGGTACA
1 TCCTTCATAATTTCGGGTA-A
*
39881225 -CCTTCATAATTAT-TGGTAA
1 TCCTTCATAATT-TCGGGTAA
*
39881244 TCCCTCATAATTT
1 TCCTTCATAATTT
39881257 TTAGTGTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (20 bp):
TCCTTCATAATTTCGGGTAA
Found at i:39888296 original size:20 final size:20
Alignment explanation
Indices: 39888267--39888359 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
39888257 TTAGCACTCC
*
39888267 AAAAATTATGAGGTAA-TACA
1 AAAAAATATGAGG-AAGTACA
39888287 AAAAAATATGAGGAAGTACAA
1 AAAAAATATGAGGAAGTAC-A
* * *
39888308 AAAAAATTATTAGAAAGTACC
1 AAAAAA-TATGAGGAAGTACA
* *
39888329 AAAAAGTATGAGGGAA-TATA
1 AAAAAATATGA-GGAAGTACA
*
39888349 AAAAATTATGA
1 AAAAAATATGA
39888360 TGTTTTATTA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.03
20 31 0.53
21 15 0.25
22 11 0.19
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAAAATATGAGGAAGTACA
Found at i:39888311 original size:22 final size:22
Alignment explanation
Indices: 39888286--39888333 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
39888276 GAGGTAATAC
*
39888286 AAAAAAATATGAGGAAGTACAA
1 AAAAAAATATGAGAAAGTACAA
* * *
39888308 AAAAAATTATTAGAAAGTACCA
1 AAAAAAATATGAGAAAGTACAA
39888330 AAAA
1 AAAA
39888334 GTATGAGGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (22 bp):
AAAAAAATATGAGAAAGTACAA
Found at i:39888809 original size:20 final size:20
Alignment explanation
Indices: 39888590--39888810 Score: 72
Period size: 20 Copynumber: 10.8 Consensus size: 20
39888580 AAAAATAGGT
* *
39888590 ATACTAAAAAATATGAGGAA
1 ATACCAAAAATTATGAGGAA
* * * *
39888610 GTAACAAAAATTGTGAGGGA
1 ATACCAAAAATTATGAGGAA
** *
39888630 ATATAAAAAATTATGAGAAA
1 ATACCAAAAATTATGAGGAA
* * **
39888650 ATACAAAAAAATATATAAAAAA
1 ATAC-CAAAAAT-TATGAGGAA
* *
39888672 AGTGCCAAAAA-AATGAGGAA
1 A-TACCAAAAATTATGAGGAA
** *
39888692 CCACCAAAAATTTTGAGGAA
1 ATACCAAAAATTATGAGGAA
* * *
39888712 ATATCAAAAA-AAT-A-TAA
1 ATACCAAAAATTATGAGGAA
* *
39888729 GTACCAAAAAATTTTGAGGAA
1 ATACC-AAAAATTATGAGGAA
* * * *
39888750 GTATCAAAAATTATAAGGGA
1 ATACCAAAAATTATGAGGAA
* **
39888770 ATACAAAAAAAAAACCATGAGGAA
1 ATAC----CAAAAATTATGAGGAA
39888794 ATACCAAAAATTATGAG
1 ATACCAAAAATTATGAG
39888811 ATAATACTAA
Statistics
Matches: 138, Mismatches: 51, Indels: 24
0.65 0.24 0.11
Matches are distributed among these distances:
17 5 0.04
18 6 0.04
19 9 0.07
20 75 0.54
21 13 0.09
22 13 0.09
23 2 0.01
24 15 0.11
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.19
Consensus pattern (20 bp):
ATACCAAAAATTATGAGGAA
Found at i:39889148 original size:20 final size:20
Alignment explanation
Indices: 39889116--39889230 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
39889106 AAGAAAGCAA
*
39889116 CAAAAACTATGAGGAAGTAC
1 CAAAAATTATGAGGAAGTAC
* *
39889136 CAAGATTTATGAGGAAGTAC
1 CAAAAATTATGAGGAAGTAC
* * *
39889156 CAAAACTTATGAGGATGTAT
1 CAAAAATTATGAGGAAGTAC
* *
39889176 CAAAAATTACGAGGAAATAC
1 CAAAAATTATGAGGAAGTAC
* * * **
39889196 CAAAAAATACGAAGAAAAAC
1 CAAAAATTATGAGGAAGTAC
39889216 C-AAAATTATGAGGAA
1 CAAAAATTATGAGGAA
39889231 TTTCCAAAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
19 11 0.14
20 66 0.86
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAAAATTATGAGGAAGTAC
Found at i:39889536 original size:20 final size:21
Alignment explanation
Indices: 39889469--39889537 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
39889459 AATAAGGATT
*
39889469 TACCAAAAATTA-TA-AGAATG
1 TACCAAAAATTATTAGAGAA-C
* *
39889489 TACCAAAATTTATGAG-GAAC
1 TACCAAAAATTATTAGAGAAC
*
39889509 TACAAAAAATTATTAGAGAA-
1 TACCAAAAATTATTAGAGAAC
39889529 TACCAAAAA
1 TACCAAAAA
39889538 ATAGGAAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 32 0.82
21 7 0.18
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (21 bp):
TACCAAAAATTATTAGAGAAC
Found at i:39889929 original size:37 final size:37
Alignment explanation
Indices: 39889883--39890017 Score: 200
Period size: 37 Copynumber: 3.6 Consensus size: 37
39889873 ATTTAACCGA
*
39889883 TTTAAATCACTACATAATTAAAAAAATTACATAAGTC
1 TTTAAATCACTACATAATTAAAAACATTACATAAGTC
*
39889920 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
1 TTTAAATCACTACATAATTAAAAACATTACATAAGTC
*
39889957 TTTAAATCACTATATAATTAAAAACATTACATAAGTC
1 TTTAAATCACTACATAATTAAAAACATTACATAAGTC
* * *
39889994 TTAAAATTAAC-ACATAATTGAAAA
1 TTTAAA-TCACTACATAATTAAAAA
39890018 GTAAGTCTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 86 0.97
38 3 0.03
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (37 bp):
TTTAAATCACTACATAATTAAAAACATTACATAAGTC
Found at i:39889952 original size:17 final size:17
Alignment explanation
Indices: 39889893--39889990 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
39889883 TTTAAATCAC
*
39889893 TACATAATTAAAAAAAT
1 TACATAATTAAAAACAT
** * *
39889910 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
39889930 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* * *
39889947 TACATAAGTCTTTAAATCAC
1 TACATAA---TTAAAAACAT
*
39889967 TATATAATTAAAAACAT
1 TACATAATTAAAAACAT
39889984 TACATAA
1 TACATAA
39889991 GTCTTAAAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 33 0.57
20 25 0.43
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:39889999 original size:20 final size:20
Alignment explanation
Indices: 39889900--39889999 Score: 77
Period size: 20 Copynumber: 5.3 Consensus size: 20
39889890 CACTACATAA
*
39889900 TTAAAAAAATTACATAAGTC
1 TTAAAAACATTACATAAGTC
** * *
39889920 TTTGAATCACTACATAA---
1 TTAAAAACATTACATAAGTC
39889937 TTAAAAACATTACATAAGTC
1 TTAAAAACATTACATAAGTC
* * * *
39889957 TTTAAATCACTATATAA---
1 TTAAAAACATTACATAAGTC
39889974 TTAAAAACATTACATAAGTC
1 TTAAAAACATTACATAAGTC
39889994 TTAAAA
1 TTAAAA
39890000 TTAACACATA
Statistics
Matches: 57, Mismatches: 17, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
17 26 0.46
20 31 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (20 bp):
TTAAAAACATTACATAAGTC
Found at i:39893254 original size:21 final size:21
Alignment explanation
Indices: 39893230--39893269 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39893220 AATGTCCAAG
39893230 TTGAAAAG-TAAAATAAAAAAT
1 TTGAAAAGCT-AAATAAAAAAT
*
39893251 TTGAATAGCTAAATAAAAA
1 TTGAAAAGCTAAATAAAAA
39893270 GTTTCAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (21 bp):
TTGAAAAGCTAAATAAAAAAT
Found at i:39893563 original size:19 final size:19
Alignment explanation
Indices: 39893539--39893655 Score: 72
Period size: 19 Copynumber: 5.5 Consensus size: 19
39893529 TGTTTGTTTT
39893539 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
* * *
39893558 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGG-TT-GGTA-A--AT-GGTA
39893583 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
* * *
39893602 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGG-TT-GGTA-A--AT-GGTA
39893627 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
39893646 ATTGGGTTGG
1 ATTGGGTTGG
39893656 GTAATTGGGT
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
19 26 0.35
20 6 0.08
21 8 0.11
22 4 0.05
23 8 0.11
24 6 0.08
25 16 0.22
ACGTcount: A:0.21, C:0.02, G:0.36, T:0.42
Consensus pattern (19 bp):
ATTGGGTTGGTAAATGGTA
Found at i:39893586 original size:25 final size:25
Alignment explanation
Indices: 39893558--39893634 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
39893548 GTAAATGGTA
39893558 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGGTTTGGGTAGACTTTAGTTT
* * *
39893583 ATTGGG-TT-GGTA-A--AT-GGTA
1 ATTGGGTTTGGGTAGACTTTAGTTT
39893602 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGGTTTGGGTAGACTTTAGTTT
39893627 ATTGGGTT
1 ATTGGGTT
39893635 GGTAAATGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
19 8 0.20
20 3 0.08
21 4 0.10
22 2 0.05
23 4 0.10
24 3 0.08
25 16 0.40
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (25 bp):
ATTGGGTTTGGGTAGACTTTAGTTT
Found at i:39893586 original size:44 final size:44
Alignment explanation
Indices: 39893536--39893658 Score: 239
Period size: 44 Copynumber: 2.8 Consensus size: 44
39893526 AGCTGTTTGT
39893536 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGGTAGACTTTAG
1 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGGTAGACTTTAG
39893580 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGGTAGACTTTAG
1 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGGTAGACTTTAG
39893624 TTTATTGGGTTGGTAAATGGTAATTGGG-TTGGGTA
1 TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGGTA
39893659 ATTGGGTTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
43 7 0.09
44 72 0.91
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (44 bp):
TTTATTGGGTTGGTAAATGGTAATTGGGTTTGGGTAGACTTTAG
Found at i:39893660 original size:13 final size:13
Alignment explanation
Indices: 39893642--39893666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39893632 GTTGGTAAAT
39893642 GGTAATTGGGTTG
1 GGTAATTGGGTTG
39893655 GGTAATTGGGTT
1 GGTAATTGGGTT
39893667 TATTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
GGTAATTGGGTTG
Found at i:39899570 original size:16 final size:17
Alignment explanation
Indices: 39899524--39899572 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
39899514 TCAAGTTTTT
39899524 TATTTTTAATTAATAAA
1 TATTTTTAATTAATAAA
* **
39899541 TATTTTTATTTTAATTCA
1 TATTTTTA-ATTAATAAA
39899559 T-TTTTTAATTAATA
1 TATTTTTAATTAATA
39899573 TCAAATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.19
17 14 0.54
18 7 0.27
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTTAATTAATAAA
Found at i:39900193 original size:60 final size:60
Alignment explanation
Indices: 39900115--39900227 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
39900105 ATTTTTGGTC
* **
39900115 CAATTTGGTACCTAAACTTGATA-T-TTTTTCTTAAGTTGGTATTTAATCTTTTTGGGAGTT
1 CAATTTGGTACCTAAACTT-A-ACTCTTTTTCCTAAGTTGGTACCTAATCTTTTTGGGAGTT
* * *
39900175 CAATTTGGTACTTGAACTTAACTCTTTTTCCTAATTTGGTACCTAATCTTTTT
1 CAATTTGGTACCTAAACTTAACTCTTTTTCCTAAGTTGGTACCTAATCTTTTT
39900228 TTGTTCGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.02
59 2 0.04
60 42 0.93
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (60 bp):
CAATTTGGTACCTAAACTTAACTCTTTTTCCTAAGTTGGTACCTAATCTTTTTGGGAGTT
Found at i:39900670 original size:62 final size:64
Alignment explanation
Indices: 39900603--39900782 Score: 183
Period size: 62 Copynumber: 2.9 Consensus size: 64
39900593 TTGAACCTAA
* * * *
39900603 AAAAAAAAAAGCTTAGGTGCC-AAGTA-GAAAAAAAATTTCAAGTTCAAGTACCAAATTGGGCC
1 AAAAAAAAAAGTTTAGGTACCAAAGTAGGAAAAAAAATGTCAAGTTCAAGTACCAAATTGAGCC
* * * * *
39900665 --CAAAAAAAGTTTAGCTACCAAATTAGGGAAAAAAATGTCAATTTCAAGTACCAAATTGAGCC
1 AAAAAAAAAAGTTTAGGTACCAAAGTAGGAAAAAAAATGTCAAGTTCAAGTACCAAATTGAGCC
* ** * * *
39900727 AAAAAAAAAAGTTTAGGTACTAATTTAGG--AAAAAGTGTCAAGTTCAGGTATCAAAT
1 AAAAAAAAAAGTTTAGGTACCAAAGTAGGAAAAAAAATGTCAAGTTCAAGTACCAAAT
39900783 GTTATATTAA
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
60 15 0.15
61 4 0.04
62 55 0.57
64 23 0.24
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.23
Consensus pattern (64 bp):
AAAAAAAAAAGTTTAGGTACCAAAGTAGGAAAAAAAATGTCAAGTTCAAGTACCAAATTGAGCC
Found at i:39901472 original size:13 final size:13
Alignment explanation
Indices: 39901454--39901478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39901444 TAAAAGAGAT
39901454 ATTAATTAAAAAG
1 ATTAATTAAAAAG
39901467 ATTAATTAAAAA
1 ATTAATTAAAAA
39901479 TATATTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:39910728 original size:20 final size:20
Alignment explanation
Indices: 39910695--39910768 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 20
39910685 ACAAAAAAAA
*
39910695 TTTAAAAAAT-AAAATAATT
1 TTTAAAAATTCAAAATAATT
39910714 TTTAAAAATTCAAAATAATT
1 TTTAAAAATTCAAAATAATT
*
39910734 TTT-AAAATTCAAAA-AAAT
1 TTTAAAAATTCAAAATAATT
*
39910752 TTTAAAATTTCCAAAAT
1 TTTAAAAATT-CAAAAT
39910769 TTATATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.12
19 25 0.52
20 17 0.35
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAATTCAAAATAATT
Found at i:39910759 original size:18 final size:19
Alignment explanation
Indices: 39910686--39910760 Score: 82
Period size: 18 Copynumber: 4.0 Consensus size: 19
39910676 ATCTCTCTCA
* * *
39910686 CAAAAAAAATTTAAAAAAT
1 CAAAATAAATTTTAAAATT
*
39910705 -AAAATAATTTTTAAAAATT
1 CAAAATAAATTTT-AAAATT
*
39910724 CAAAATAATTTTTAAAATT
1 CAAAATAAATTTTAAAATT
39910743 CAAAA-AAATTTTAAAATT
1 CAAAATAAATTTTAAAATT
39910761 TCCAAAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
18 21 0.43
19 16 0.33
20 12 0.24
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
CAAAATAAATTTTAAAATT
Found at i:39910767 original size:19 final size:20
Alignment explanation
Indices: 39910705--39910768 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
39910695 TTTAAAAAAT
39910705 AAAATAATTTTTAAAAATT-C
1 AAAATAATTTTT-AAAATTCC
39910725 AAAATAATTTTTAAAATT-C
1 AAAATAATTTTTAAAATTCC
*
39910744 AAAA-AAATTTTAAAATTTCC
1 AAAATAATTTTTAAAA-TTCC
39910764 AAAAT
1 AAAAT
39910769 TTATATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 10 0.25
19 13 0.32
20 17 0.43
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTCC
Found at i:39912961 original size:50 final size:51
Alignment explanation
Indices: 39912907--39913014 Score: 182
Period size: 50 Copynumber: 2.1 Consensus size: 51
39912897 AAATAGTATG
*
39912907 TTTTTTTAATCGCGTCTATCTGACAGGCGCAAATCAATTTTTTATATT-AA
1 TTTTTTTAATCGCGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAAA
* *
39912957 TTTTTTTAATCGCGCCTATCTGACAGGCGCGAATCAATTTTTTATGTTAAA
1 TTTTTTTAATCGCGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAAA
39913008 TTTTTTT
1 TTTTTTT
39913015 CCTTTAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 45 0.83
51 9 0.17
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (51 bp):
TTTTTTTAATCGCGCCTATCTGACAGGCGCAAATCAATTTTTTATATTAAA
Found at i:39913174 original size:15 final size:15
Alignment explanation
Indices: 39913154--39913193 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
39913144 AAAAAATCAA
*
39913154 ATAAAATTACATTTT
1 ATAAAATTACATTAT
39913169 ATAAAAATTACATTAT
1 AT-AAAATTACATTAT
39913185 ATAAAATTA
1 ATAAAATTA
39913194 TCAATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:39913516 original size:39 final size:39
Alignment explanation
Indices: 39913472--39913638 Score: 241
Period size: 39 Copynumber: 4.3 Consensus size: 39
39913462 GATATCCAAG
* * *
39913472 TTGATATAAAAAAAATTAAATAAGTTAATAGCAACTATA
1 TTGATATAAAAAAAATTAAATGAGTTAACAACAACTATA
*
39913511 TTGATATAAAAAAAATTAAATGAGTTAACAACAACTATG
1 TTGATATAAAAAAAATTAAATGAGTTAACAACAACTATA
* *
39913550 TTGATATAAAAATAAA-TAAATGAGTTAACAGCAACTATG
1 TTGATATAAAAA-AAATTAAATGAGTTAACAACAACTATA
*
39913589 TTGATATAAAAAAAATTAAATGAGTTAACAACAATTATA
1 TTGATATAAAAAAAATTAAATGAGTTAACAACAACTATA
39913628 -TGAT-TAAAAAA
1 TTGATATAAAAAA
39913639 GTCAGTTATG
Statistics
Matches: 118, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
37 7 0.06
38 7 0.06
39 101 0.86
40 3 0.03
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (39 bp):
TTGATATAAAAAAAATTAAATGAGTTAACAACAACTATA
Found at i:39913783 original size:60 final size:60
Alignment explanation
Indices: 39913719--39913837 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
39913709 ATACTAAATT
* * * *
39913719 AAACACAATAATTTATAACTTAATCCTAATTTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
39913779 AAACACAAAAATTTATAACATAATCCTAAATTACTAGCAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
39913838 TAAAAAACAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:39913985 original size:52 final size:52
Alignment explanation
Indices: 39913929--39914038 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 52
39913919 TTATTAAACG
39913929 AAAAAAAATTAATATAAAAAATTGATTCACGCCTGTCAGATAGGCG-GAATTA
1 AAAAAAAATTAATATAAAAAATTGATTCACGCCTGTCAGATAGGCGCG-ATTA
* * *
39913981 AAAAAAATTTAATATAAAAAATTGATTCGCGCCTGTCAGATATGCGCGATTA
1 AAAAAAAATTAATATAAAAAATTGATTCACGCCTGTCAGATAGGCGCGATTA
39914033 AAAAAA
1 AAAAAA
39914039 TACCATTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 53 0.98
53 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (52 bp):
AAAAAAAATTAATATAAAAAATTGATTCACGCCTGTCAGATAGGCGCGATTA
Found at i:39915091 original size:15 final size:15
Alignment explanation
Indices: 39915071--39915128 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
39915061 TAAAACCTTA
39915071 ATAAATAATAAATAT
1 ATAAATAATAAATAT
39915086 ATAAAT-ATACAAT-T
1 ATAAATAATA-AATAT
39915100 GATAAAGGTAATAAA-AT
1 -ATAAA--TAATAAATAT
*
39915117 ATACATAATAAA
1 ATAAATAATAAA
39915129 AATTAAAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
14 11 0.31
15 14 0.39
16 4 0.11
17 4 0.11
18 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (15 bp):
ATAAATAATAAATAT
Found at i:39915416 original size:2 final size:2
Alignment explanation
Indices: 39915409--39915440 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39915399 ATTAATAATA
39915409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39915441 CTCACAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39916478 original size:17 final size:17
Alignment explanation
Indices: 39916453--39916495 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
39916443 GCCACGCGGC
39916453 ATATATAAAATTTAAAA
1 ATATATAAAATTTAAAA
* *
39916470 ATTTATAAAATTTTAAA
1 ATATATAAAATTTAAAA
39916487 ATATATAAA
1 ATATATAAA
39916496 TTAATTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAAAATTTAAAA
Found at i:39916481 original size:9 final size:9
Alignment explanation
Indices: 39916456--39916495 Score: 57
Period size: 8 Copynumber: 4.7 Consensus size: 9
39916446 ACGCGGCATA
39916456 TATAAAATT
1 TATAAAATT
39916465 TA-AAAATT
1 TATAAAATT
39916473 TATAAAATT
1 TATAAAATT
*
39916482 T-TAAAATA
1 TATAAAATT
39916490 TATAAA
1 TATAAA
39916496 TTAATTAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 15 0.54
9 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TATAAAATT
Found at i:39920073 original size:14 final size:14
Alignment explanation
Indices: 39920054--39920083 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39920044 TACTTGTTTC
39920054 AAACATATATTTTA
1 AAACATATATTTTA
*
39920068 AAACATATGTTTTA
1 AAACATATATTTTA
39920082 AA
1 AA
39920084 TAAAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (14 bp):
AAACATATATTTTA
Found at i:39925206 original size:33 final size:33
Alignment explanation
Indices: 39925152--39925215 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
39925142 TAAGTTGAGA
39925152 CCAAAATTAAAATTTATTTTTGAAAAATCATAC
1 CCAAAATTAAAATTTATTTTTGAAAAATCATAC
*
39925185 CCAAAATTTTAAATTTA-TTTTGAAAAATCAT
1 CCAAAA-TTAAAATTTATTTTTGAAAAATCAT
39925216 CAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (33 bp):
CCAAAATTAAAATTTATTTTTGAAAAATCATAC
Found at i:39926106 original size:17 final size:17
Alignment explanation
Indices: 39926084--39926116 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39926074 ACCCAGAAAG
39926084 GAAGAA-AAACAAAAAAT
1 GAAGAAGAAA-AAAAAAT
39926101 GAAGAAGAAAAAAAAA
1 GAAGAAGAAAAAAAAA
39926117 CAATAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (17 bp):
GAAGAAGAAAAAAAAAT
Found at i:39928022 original size:25 final size:25
Alignment explanation
Indices: 39927988--39928038 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
39927978 CAAAATTGGC
39927988 AGAATTATGTAAATTTAATATCAAA
1 AGAATTATGTAAATTTAATATCAAA
39928013 AGAATTATGTAAATTTAATATCAAA
1 AGAATTATGTAAATTTAATATCAAA
39928038 A
1 A
39928039 TAACTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (25 bp):
AGAATTATGTAAATTTAATATCAAA
Found at i:39929764 original size:20 final size:20
Alignment explanation
Indices: 39929739--39929778 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39929729 GACCTATCTT
39929739 TTGCTTCA-TCATTCTTGTTC
1 TTGCTTCAGTCA-TCTTGTTC
*
39929759 TTGCTTGAGTCATCTTGTTC
1 TTGCTTCAGTCATCTTGTTC
39929779 CTTCCTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.53
Consensus pattern (20 bp):
TTGCTTCAGTCATCTTGTTC
Found at i:39933655 original size:23 final size:22
Alignment explanation
Indices: 39933612--39933655 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
39933602 TTTCAAGTCA
39933612 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
39933635 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
39933656 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:39933853 original size:12 final size:13
Alignment explanation
Indices: 39933825--39933905 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 13
39933815 GATACCGGTT
39933825 CACATAGTAGCCTA
1 CACATAGTA-CCTA
39933839 CACATAGTA-CTA
1 CACATAGTACCTA
39933851 CACAT-GTGACC-A
1 CACATAGT-ACCTA
39933863 TCAC-TA-T-CCGATA
1 -CACATAGTACC--TA
*
39933876 CACATAGTAGCCTG
1 CACATAGTA-CCTA
39933890 CACATAGTA-CTA
1 CACATAGTACCTA
39933902 CACA
1 CACA
39933906 CGTGATCGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 24
0.68 0.03 0.30
Matches are distributed among these distances:
10 2 0.04
11 2 0.04
12 21 0.39
13 7 0.13
14 20 0.37
16 2 0.04
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (13 bp):
CACATAGTACCTA
Found at i:39933883 original size:51 final size:51
Alignment explanation
Indices: 39933825--39934016 Score: 221
Period size: 51 Copynumber: 3.8 Consensus size: 51
39933815 GATACCGGTT
* *
39933825 CACATAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT-AGCTATCCGATA
* *
39933876 CACATAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTAT-CTAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAGCTATCCGA-TA
* * * * * * *
39933927 CGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCGATA
*
39933977 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATA
39934017 ACTTTCACTT
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
50 43 0.36
51 73 0.62
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCGATA
Found at i:39934004 original size:101 final size:101
Alignment explanation
Indices: 39933827--39934011 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
39933817 TACCGGTTCA
*
39933827 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACATAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACATAGTAGCCTGCA
39933892 CATAGTACTACACACGTGATCGAAGCTATCTAGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCTAGTACG
* * * * *
39933929 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACATAGTAGCCTGCA
39933993 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
39934012 CCATAACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 1 0.01
101 42 0.55
102 33 0.43
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCTAGTACG
Found at i:39934034 original size:101 final size:101
Alignment explanation
Indices: 39933822--39934045 Score: 274
Period size: 101 Copynumber: 2.2 Consensus size: 101
39933812 AATGATACCG
*
39933822 GTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACATAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACATAGTAGC
* *
39933887 CTGCACATAGTACTACACACGTGATCGAAGCTATCTA
65 CTGCACATAGTACTACACACGTGATCCAAACTATCTA
* * * * * * *
39933924 GTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACATAGTAGC
*
39933988 CTGCACATAGTACTACACACGTGA-CCATAACTTTC-A
65 CTGCACATAGTACTACACACGTGATCCA-AACTATCTA
* *
39934024 CTTTCACATAGTGGCCTACACA
1 -GTTCACATAGTAGCCTACACA
39934046 CAGTCTGTGC
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
100 4 0.04
101 63 0.61
102 36 0.35
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (101 bp):
GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACATAGTAGCC
TGCACATAGTACTACACACGTGATCCAAACTATCTA
Found at i:39935900 original size:14 final size:14
Alignment explanation
Indices: 39935881--39935910 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39935871 ATTGAGCTGG
39935881 AACATTATTATTGA
1 AACATTATTATTGA
39935895 AACATTATTATTGA
1 AACATTATTATTGA
39935909 AA
1 AA
39935911 TTGTTAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (14 bp):
AACATTATTATTGA
Found at i:39938150 original size:39 final size:39
Alignment explanation
Indices: 39938106--39938188 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
39938096 AGGCATATAC
39938106 TAAAATCAAAGAAGAAAGAAGTTAGTAAACGTAAATTAA
1 TAAAATCAAAGAAGAAAGAAGTTAGTAAACGTAAATTAA
39938145 TAAAATCAAAGAAGAAAGAAGTTAGTAAACGTAAATTAA
1 TAAAATCAAAGAAGAAAGAAGTTAGTAAACGTAAATTAA
39938184 TAAAA
1 TAAAA
39938189 ATAGAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.20
Consensus pattern (39 bp):
TAAAATCAAAGAAGAAAGAAGTTAGTAAACGTAAATTAA
Found at i:39940430 original size:16 final size:16
Alignment explanation
Indices: 39940398--39940427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39940388 AACGGTTTAA
39940398 AAAATAATAGTATAAT
1 AAAATAATAGTATAAT
39940414 AAAATAATA-TATAA
1 AAAATAATAGTATAA
39940428 ATAGGTACAT
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:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATAATAGTATAAT
Found at i:39949905 original size:28 final size:28
Alignment explanation
Indices: 39949873--39949926 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
39949863 GCTCCTTTGT
39949873 TACATGTAAAGGACACAAATTCCTTAGC
1 TACATGTAAAGGACACAAATTCCTTAGC
39949901 TACATGTAAAGGACACAAATTCCTTA
1 TACATGTAAAGGACACAAATTCCTTA
39949927 ACTTAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (28 bp):
TACATGTAAAGGACACAAATTCCTTAGC
Found at i:39956822 original size:15 final size:15
Alignment explanation
Indices: 39956802--39956830 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39956792 ATGCCTCACA
39956802 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
39956817 CACCGTGTTATCAA
1 CACCGTGTTATCAA
39956831 ACAACAATAC
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:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:39958666 original size:13 final size:14
Alignment explanation
Indices: 39958648--39958679 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
39958638 TCTAAATCCT
39958648 TTGATTGAA-AATC
1 TTGATTGAAGAATC
39958661 TTGATTGAAGAATC
1 TTGATTGAAGAATC
39958675 TTGAT
1 TTGAT
39958680 AAATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (14 bp):
TTGATTGAAGAATC
Found at i:39967645 original size:104 final size:105
Alignment explanation
Indices: 39967464--39967655 Score: 368
Period size: 104 Copynumber: 1.8 Consensus size: 105
39967454 TCACTCATCT
39967464 CCATAAACAATCTGAGGTGAAGGTGAGGATCCTCAGTTGGAATTCTACTGAATTGGCCCACTGTA
1 CCATAAACAATCTGAGGTGAAGGTGAGGATCCTCAGTTGGAATTCTACTGAATTGGCCCACTGTA
39967529 TGAAGCATCAAGAACATGACTGGGTTCAACTTGAATTGGC
66 TGAAGCATCAAGAACATGACTGGGTTCAACTTGAATTGGC
*
39967569 CCATAAACAATCTGAGGTGAAGGTGA-GATCCTCAGTTGGTATTCTACTGAATTGGCCCACTGTA
1 CCATAAACAATCTGAGGTGAAGGTGAGGATCCTCAGTTGGAATTCTACTGAATTGGCCCACTGTA
39967633 TGAAGCATCAAGAACATGACTGG
66 TGAAGCATCAAGAACATGACTGG
39967656 CTTTAGCTCG
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 60 0.70
105 26 0.30
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (105 bp):
CCATAAACAATCTGAGGTGAAGGTGAGGATCCTCAGTTGGAATTCTACTGAATTGGCCCACTGTA
TGAAGCATCAAGAACATGACTGGGTTCAACTTGAATTGGC
Found at i:39971112 original size:31 final size:31
Alignment explanation
Indices: 39971070--39971131 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39971060 GTATATGGGA
39971070 AAAAAAAATCAAGACTATTAGGGACGATTGG
1 AAAAAAAATCAAGACTATTAGGGACGATTGG
* *
39971101 AAAAAATATCAAGACTATTAGGGACTATTGG
1 AAAAAAAATCAAGACTATTAGGGACGATTGG
39971132 TCGATCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.23
Consensus pattern (31 bp):
AAAAAAAATCAAGACTATTAGGGACGATTGG
Found at i:39974880 original size:24 final size:24
Alignment explanation
Indices: 39974811--39974887 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
39974801 TCCCGCTCAT
**
39974811 TGGTTACTGCAAGAAAAGTTTAAA
1 TGGTTACTGCAAGAAAAGTTTGGA
*
39974835 TGGTTACTGCAAGAAAATTTTGGA
1 TGGTTACTGCAAGAAAAGTTTGGA
39974859 TGGTTACTGCAAGAAAAGTTTGGA
1 TGGTTACTGCAAGAAAAGTTTGGA
39974883 TGGTT
1 TGGTT
39974888 TCGGCACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (24 bp):
TGGTTACTGCAAGAAAAGTTTGGA
Found at i:39981263 original size:22 final size:22
Alignment explanation
Indices: 39981112--39981393 Score: 112
Period size: 22 Copynumber: 12.8 Consensus size: 22
39981102 ACACCACACT
39981112 AGTAGGCACTGAAGTGCAAATC
1 AGTAGGCACTGAAGTGCAAATC
* * *
39981134 AGTGGGCACCT-TAGTGCAAAGC
1 AGTAGGCA-CTGAAGTGCAAATC
* * **
39981156 AATAGGCACCGAAAAGCAAATC
1 AGTAGGCACTGAAGTGCAAATC
* * **
39981178 GGTACGCACCT-AAGTTTAGAAT-
1 AGTAGGCA-CTGAAGTGCA-AATC
**
39981200 AGTAGGCACTGTAA-TGCAAAAA
1 AGTAGGCACTG-AAGTGCAAATC
* ** *
39981222 AGTAGGTACCAAAGTACAAATC
1 AGTAGGCACTGAAGTGCAAATC
* *
39981244 AGTAGGCACTGTAGTGCAAAGC
1 AGTAGGCACTGAAGTGCAAATC
* * *
39981266 AATAGGCACGGAAGTGTAGAAT-
1 AGTAGGCACTGAAGTGCA-AATC
**
39981288 AGTAGGC-CCCATAGTGCAAAGT-
1 AGTAGGCACTGA-AGTGCAAA-TC
* * *
39981310 AATAGGCA-TCGAAGTGCAACTT
1 AGTAGGCACT-GAAGTGCAAATC
* * * *
39981332 AGTAGGCACCGAAATGTAAAGC
1 AGTAGGCACTGAAGTGCAAATC
* **
39981354 AGTATGCACCAAAGTGCAAATC
1 AGTAGGCACTGAAGTGCAAATC
* *
39981376 AGTAGGCACCGAACTGCA
1 AGTAGGCACTGAAGTGCA
39981394 GAACAATATA
Statistics
Matches: 182, Mismatches: 63, Indels: 30
0.66 0.23 0.11
Matches are distributed among these distances:
21 12 0.07
22 159 0.87
23 11 0.06
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (22 bp):
AGTAGGCACTGAAGTGCAAATC
Found at i:39981382 original size:66 final size:65
Alignment explanation
Indices: 39981222--39981401 Score: 150
Period size: 66 Copynumber: 2.7 Consensus size: 65
39981212 AATGCAAAAA
* * * * *
39981222 AGTAGGTACCAAAGTACAAATCAGTAGGCACTGTAGTGCAAAGCAATAGGCACGGAAGTGTAGAA
1 AGTAGGCACCAAAGTGCAAATCAGTAGGCAC-GAAGTGCAAAGCAATAGGCACCGAAATGTAGAA
*
39981287 T
65 C
* * * *** *
39981288 AGTAGGCCCCATAGTGCAAAGT-AATAGGCATCGAAGTGCAACTTAGTAGGCACCGAAATGTA-A
1 AGTAGGCACCAAAGTGCAAA-TCAGTAGGCA-CGAAGTGCAAAGCAATAGGCACCGAAATGTAGA
39981351 AGC
64 A-C
* *
39981354 AGTATGCACCAAAGTGCAAATCAGTAGGCACCGAACTGCAGAA-CAATA
1 AGTAGGCACCAAAGTGCAAATCAGTAGGCA-CGAAGTGCA-AAGCAATA
39981402 TATATGATAA
Statistics
Matches: 87, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
65 3 0.03
66 81 0.93
67 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (65 bp):
AGTAGGCACCAAAGTGCAAATCAGTAGGCACGAAGTGCAAAGCAATAGGCACCGAAATGTAGAAC
Found at i:39982753 original size:30 final size:30
Alignment explanation
Indices: 39982713--39982799 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
39982703 TAAAGTTAAT
*
39982713 TACATAATATAAATAGTAATATACATAACA
1 TACATGATATAAATAGTAATATACATAACA
*
39982743 TACCTGATATAAACT-GTAATATACATAACA
1 TACATGATATAAA-TAGTAATATACATAACA
* * *
39982773 TACATGATATAAACAATAAAATACATA
1 TACATGATATAAATAGTAATATACATA
39982800 CATGATATCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.29
Consensus pattern (30 bp):
TACATGATATAAATAGTAATATACATAACA
Found at i:39982814 original size:38 final size:38
Alignment explanation
Indices: 39982771--39982845 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
39982761 ATATACATAA
* *
39982771 CATACATGATATAAACAATAAAATACAT-ACATGATATC
1 CATACATAATATAAACAACAAAATACATAACAT-ATATC
* *
39982809 CATACATAATATAAAGAACAATATACATAACATATAT
1 CATACATAATATAAACAACAAAATACATAACATATAT
39982846 AAACAGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.27
Consensus pattern (38 bp):
CATACATAATATAAACAACAAAATACATAACATATATC
Found at i:39982891 original size:25 final size:26
Alignment explanation
Indices: 39982863--39982925 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
39982853 AATGTACCTA
* *
39982863 ACATACATAATATCCATAC-TATTAT
1 ACATACATAATATCCATACATAATAG
**
39982888 ACATACATAATAGGCATACATAATAG
1 ACATACATAATATCCATACATAATAG
39982914 ACATAC-TAATAT
1 ACATACATAATAT
39982926 ATCAATTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.30
Consensus pattern (26 bp):
ACATACATAATATCCATACATAATAG
Found at i:39982907 original size:13 final size:13
Alignment explanation
Indices: 39982863--39982924 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
39982853 AATGTACCTA
*
39982863 ACATACATAATAT
1 ACATACATAATAG
* * *
39982876 CCATAC-TATTAT
1 ACATACATAATAG
39982888 ACATACATAATAG
1 ACATACATAATAG
*
39982901 GCATACATAATAG
1 ACATACATAATAG
39982914 ACATAC-TAATA
1 ACATACATAATA
39982925 TATCAATTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
12 15 0.37
13 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (13 bp):
ACATACATAATAG
Found at i:39990140 original size:14 final size:14
Alignment explanation
Indices: 39990121--39990156 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39990111 AAAAATCTGC
*
39990121 AACCCATTAACCCT
1 AACCCAATAACCCT
*
39990135 AACCCAATAACCGT
1 AACCCAATAACCCT
39990149 AACCCAAT
1 AACCCAAT
39990157 TCAAAAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.17
Consensus pattern (14 bp):
AACCCAATAACCCT
Found at i:39991539 original size:13 final size:13
Alignment explanation
Indices: 39991521--39991545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39991511 TAAGATAAAT
39991521 TTGCTTGTGTTTG
1 TTGCTTGTGTTTG
39991534 TTGCTTGTGTTT
1 TTGCTTGTGTTT
39991546 TAGATCCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.28, T:0.64
Consensus pattern (13 bp):
TTGCTTGTGTTTG
Found at i:39992291 original size:19 final size:19
Alignment explanation
Indices: 39992267--39992313 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
39992257 GACTTAAAAT
39992267 TTCAGTTAATTTTGGATAA
1 TTCAGTTAATTTTGGATAA
* *
39992286 TTCAGTTGATTTTGGTTAA
1 TTCAGTTAATTTTGGATAA
*
39992305 TTCGGTTAA
1 TTCAGTTAA
39992314 ATGAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (19 bp):
TTCAGTTAATTTTGGATAA
Found at i:39992712 original size:4 final size:4
Alignment explanation
Indices: 39992703--39992728 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39992693 TAAAAATTGC
39992703 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
39992729 AACAACAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:40003629 original size:12 final size:13
Alignment explanation
Indices: 40003613--40003646 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
40003603 AAATCTAATT
40003613 TTTTTAAAATATA
1 TTTTTAAAATATA
40003626 TTTTTCAAAATAT-
1 TTTTT-AAAATATA
40003639 TTTTTAAA
1 TTTTTAAA
40003647 GGAAACGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 10 0.50
14 7 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:40003629 original size:14 final size:13
Alignment explanation
Indices: 40003610--40003643 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
40003600 TTTAAATCTA
*
40003610 ATTTTTTTAAAAT
1 ATTTTTTCAAAAT
40003623 ATATTTTTCAAAAT
1 AT-TTTTTCAAAAT
40003637 ATTTTTT
1 ATTTTTT
40003644 AAAGGAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTTTCAAAAT
Found at i:40006618 original size:24 final size:24
Alignment explanation
Indices: 40006590--40006641 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40006580 TTAGTAAGTC
* *
40006590 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
40006614 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
40006638 AAAT
1 AAAT
40006642 CTTTTAGAAA
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:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:40010138 original size:18 final size:19
Alignment explanation
Indices: 40010094--40010144 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
40010084 GTTGATTTTA
40010094 AAAAATTAAATTATTAAAAT
1 AAAAA-TAAATTATTAAAAT
**
40010114 -ATTATAAATTA-TAAAAT
1 AAAAATAAATTATTAAAAT
40010131 AAAAATAAA-TATTA
1 AAAAATAAATTATTA
40010145 TAAAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 8 0.32
18 15 0.60
19 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATAAATTATTAAAAT
Found at i:40010162 original size:27 final size:27
Alignment explanation
Indices: 40010110--40010165 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
40010100 TAAATTATTA
*
40010110 AAATATTATAAATTATAAAATAAAAAT
1 AAATATTATAAAATATAAAATAAAAAT
**
40010137 AAATATTATAAAAATATTCAATAAAAAT
1 AAATATTAT-AAAATATAAAATAAAAAT
40010165 A
1 A
40010166 TCATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATATTATAAAATATAAAATAAAAAT
Found at i:40011824 original size:18 final size:17
Alignment explanation
Indices: 40011779--40011824 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
40011769 TACATTTCTC
40011779 TATATATTTTTTAATTTT
1 TATATA-TTTTTAATTTT
40011797 TCATA-ATTTTTAATTTT
1 T-ATATATTTTTAATTTT
*
40011814 TATATACTTTT
1 TATATATTTTT
40011825 GACTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 17 0.68
18 2 0.08
19 3 0.12
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATATTTTTAATTTT
Found at i:40014487 original size:44 final size:46
Alignment explanation
Indices: 40014429--40014570 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 46
40014419 CCTTCAAACA
* * * * *
40014429 TGTTGTGCATCCACAACCAGT-GGCAGATTTTATCTG-TAT-TATTT
1 TGTTGTGTACCCACAACCACTAGGCAGATTCTATCTGCGATGT-TTT
* *
40014473 TGTTGTGTACCCACAGCC-CTAGGCAGATTCTATCTGCGGTGTTTT
1 TGTTGTGTACCCACAACCACTAGGCAGATTCTATCTGCGATGTTTT
* * * * *
40014518 TGTTGTGTACTCACAACCA-TAAGCAAATTCCATCTGCGGTGTTTT
1 TGTTGTGTACCCACAACCACTAGGCAGATTCTATCTGCGATGTTTT
*
40014563 TGCTGTGT
1 TGTTGTGT
40014571 GTCCACAGCC
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 29 0.36
45 50 0.62
46 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (46 bp):
TGTTGTGTACCCACAACCACTAGGCAGATTCTATCTGCGATGTTTT
Found at i:40014553 original size:45 final size:45
Alignment explanation
Indices: 40014470--40014570 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
40014460 ATCTGTATTA
* * * * *
40014470 TTTTGTTGTGTACCCACAGCCCTAGGCAGATTCTATCTGCGGTGT
1 TTTTGTTGTGTACCCACAACCATAAGCAAATTCCATCTGCGGTGT
*
40014515 TTTTGTTGTGTACTCACAACCATAAGCAAATTCCATCTGCGGTGT
1 TTTTGTTGTGTACCCACAACCATAAGCAAATTCCATCTGCGGTGT
*
40014560 TTTTGCTGTGT
1 TTTTGTTGTGT
40014571 GTCCACAGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (45 bp):
TTTTGTTGTGTACCCACAACCATAAGCAAATTCCATCTGCGGTGT
Found at i:40017511 original size:16 final size:16
Alignment explanation
Indices: 40017474--40017513 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40017464 TTGATAAAAT
* *
40017474 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
40017490 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
40017506 TAAAATTA
1 TAAAATTA
40017514 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:40017574 original size:66 final size:69
Alignment explanation
Indices: 40017502--40017647 Score: 208
Period size: 75 Copynumber: 2.1 Consensus size: 69
40017492 AAATTAATTG
*
40017502 TTAGTAAAATTATCAAATTATTAA-T-TATTAATTG-TATTAATTGTTGTAATAAAATCTAACAT
1 TTAGTAAAATTATCAAATTATTAATTATATTAATTGTTATTAATTGTTGTAACAAAATCTAACAT
40017564 TTGA
66 TTGA
40017568 TTAGTAAAATTATCAAATTATTAATTATATTAATTGTTAATTATATTAATTGTTGTAACAAAATC
1 TTAGTAAAATTATCAAATTATTAATTATATTAATTG-----T-TATTAATTGTTGTAACAAAATC
40017633 TAACATTTGA
60 TAACATTTGA
40017643 TTAGT
1 TTAGT
40017648 TTACATTTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
66 24 0.34
67 1 0.01
68 9 0.13
75 36 0.51
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (69 bp):
TTAGTAAAATTATCAAATTATTAATTATATTAATTGTTATTAATTGTTGTAACAAAATCTAACAT
TTGA
Found at i:40017607 original size:16 final size:16
Alignment explanation
Indices: 40017583--40017621 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40017573 AAAATTATCA
*
40017583 AATTATTAATTATATT
1 AATTGTTAATTATATT
40017599 AATTGTTAATTATATT
1 AATTGTTAATTATATT
40017615 AATTGTT
1 AATTGTT
40017622 GTAACAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
AATTGTTAATTATATT
Found at i:40017831 original size:60 final size:60
Alignment explanation
Indices: 40017738--40017879 Score: 275
Period size: 60 Copynumber: 2.4 Consensus size: 60
40017728 CCAATATTAC
40017738 ACCAATGTTATCACTTTCAATTGCTATCCTGTCAATTGTTATGTGCAGAATTTACCAAAT
1 ACCAATGTTATCACTTTCAATTGCTATCCTGTCAATTGTTATGTGCAGAATTTACCAAAT
*
40017798 ACCAATGTTATCACTTTCAATTGCTATCCTGTCAATTGTTATGTGCAGGATTTACCAAAT
1 ACCAATGTTATCACTTTCAATTGCTATCCTGTCAATTGTTATGTGCAGAATTTACCAAAT
40017858 ACCAATGTTATCACTTTCAATT
1 ACCAATGTTATCACTTTCAATT
40017880 TGTATCATGC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (60 bp):
ACCAATGTTATCACTTTCAATTGCTATCCTGTCAATTGTTATGTGCAGAATTTACCAAAT
Found at i:40017946 original size:19 final size:19
Alignment explanation
Indices: 40017919--40017984 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
40017909 TTTGTCGGGG
*
40017919 AAATGAAATTGAAAACTAA
1 AAATAAAATTGAAAACTAA
40017938 AAATAAAATTGAAAACATAA
1 AAATAAAATTGAAAAC-TAA
* *
40017958 AAATAAAATTAAAAACTTA
1 AAATAAAATTGAAAACTAA
*
40017977 AACTAAAA
1 AAATAAAA
40017985 ACTTAAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.68, C:0.06, G:0.05, T:0.21
Consensus pattern (19 bp):
AAATAAAATTGAAAACTAA
Found at i:40018068 original size:20 final size:20
Alignment explanation
Indices: 40018040--40018105 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
40018030 AATGTCGGGG
*
40018040 AAATGAAATTGAAAACATAA
1 AAATAAAATTGAAAACATAA
40018060 AAATAAAATTGAAAAC-TAA
1 AAATAAAATTGAAAACATAA
*
40018079 AACTAAAAACTT--AAACATAA
1 AAAT-AAAA-TTGAAAACATAA
40018099 AAATAAA
1 AAATAAA
40018106 TATATATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 13 0.32
20 25 0.62
21 2 0.05
ACGTcount: A:0.68, C:0.08, G:0.05, T:0.20
Consensus pattern (20 bp):
AAATAAAATTGAAAACATAA
Found at i:40018099 original size:14 final size:13
Alignment explanation
Indices: 40018051--40018105 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
40018041 AATGAAATTG
40018051 AAAACATAAAAA-T
1 AAAAC-TAAAAACT
* *
40018064 AAAATTGAAAACT
1 AAAACTAAAAACT
40018077 AAAACTAAAAACT
1 AAAACTAAAAACT
*
40018090 TAAACATAAAAA-T
1 AAAAC-TAAAAACT
40018103 AAA
1 AAA
40018106 TATATATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 5 0.15
13 23 0.68
14 6 0.18
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (13 bp):
AAAACTAAAAACT
Found at i:40018141 original size:16 final size:16
Alignment explanation
Indices: 40018120--40018154 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40018110 TATATTTTTT
40018120 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
40018136 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
40018152 AAA
1 AAA
40018155 TATATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:40018406 original size:24 final size:24
Alignment explanation
Indices: 40018357--40018413 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
40018347 AATTGACTAC
* *
40018357 ATTTTTTTTTACTTTAATCATTGA
1 ATTTTTTTTTACATTAATCATCGA
*
40018381 ATGTTTTTTTTACATTAGTC-TCGA
1 AT-TTTTTTTTACATTAATCATCGA
40018405 ATTTTTTTT
1 ATTTTTTTT
40018414 AATTTGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.24
24 7 0.24
25 15 0.52
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.63
Consensus pattern (24 bp):
ATTTTTTTTTACATTAATCATCGA
Found at i:40036510 original size:20 final size:20
Alignment explanation
Indices: 40036465--40036510 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
40036455 TGTTTATTTC
40036465 TCTTTTTAGTTGTTTTGTTT
1 TCTTTTTAGTTGTTTTGTTT
*
40036485 TATTTTTA-TT-TTCTTGTATT
1 TCTTTTTAGTTGTT-TTGT-TT
40036505 TCTTTT
1 TCTTTT
40036511 AATTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.76
Consensus pattern (20 bp):
TCTTTTTAGTTGTTTTGTTT
Found at i:40051538 original size:48 final size:48
Alignment explanation
Indices: 40051445--40051540 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
40051435 ATCAGCAATT
* ** *
40051445 ATACATAACATATGACACATACAAAGTCATATTTGCTTCCCCTTTTCA
1 ATACATAACATATAACACATACAAAGTCATATTAACTTACCCTTTTCA
* * ** *
40051493 ATACATAACATATAACATATTCGGAGTCATATTAACTTACTCTTTTCA
1 ATACATAACATATAACACATACAAAGTCATATTAACTTACCCTTTTCA
40051541 TATCCTTCCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.35
Consensus pattern (48 bp):
ATACATAACATATAACACATACAAAGTCATATTAACTTACCCTTTTCA
Found at i:40051869 original size:49 final size:49
Alignment explanation
Indices: 40051787--40051913 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
40051777 TGGCCCACCA
* * * * *
40051787 ACCTGGTTAACAACTAACATGTCTTACCAGTGGCCCATCATACACGCCT
1 ACCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCATCATACACGCCC
* * * *
40051836 ATCTAGTTAGCAACTAATATGCCCTACCAGTGGCCCATCATATACTCCC
1 ACCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCATCATACACGCCC
* * *
40051885 ACCTGGTTAGCAACTAGCATGCCTTACCA
1 ACCTAGTTAGCAACTAACATGCCCTACCA
40051914 ATGGTCAAGC
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.25
Consensus pattern (49 bp):
ACCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCATCATACACGCCC
Found at i:40056751 original size:3 final size:3
Alignment explanation
Indices: 40056743--40056773 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40056733 TGGGTAAACA
*
40056743 CTT CTT CTT CTT CTT CGT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
40056774 CTCAACCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:40058780 original size:101 final size:102
Alignment explanation
Indices: 40058664--40058846 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 102
40058654 AAAGTGATGG
* * * *
40058664 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-CAAGA-A-TGATAGGTCGCATGTGTAG
1 TCACGTGTATAGTACTATATGCAGGCTACTAAGTGTATC-AGATAGTGAT-GGTCACATGTGTAG
40058726 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
64 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
40058765 TCACGTGTATAGTACTATATGCAGGCTACTAAGTGTATCAGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTATAGTACTATATGCAGGCTACTAAGTGTATCAGATAGTGATGGTCACATGTGTAGTA
40058830 CTATGTGCAGGCTACTA
66 CTATGTGCAGGCTACTA
40058847 GGTGAACCGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (102 bp):
TCACGTGTATAGTACTATATGCAGGCTACTAAGTGTATCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:40058809 original size:51 final size:50
Alignment explanation
Indices: 40058664--40058846 Score: 156
Period size: 51 Copynumber: 3.6 Consensus size: 50
40058654 AAAGTGATGG
* * * * * *
40058664 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACAAGA-A-TGATAGG
1 TCACATGTATAGTACTATGTGCAGGCTACTAAGCGTACCAGATAGT-AT-GA
* * * *
40058714 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTATAGTACTATGTGCAGGCTACTAAGCGTACCAGATAG-TAT-GA
* * * * *
40058765 TCACGTGTATAGTACTATATGCAGGCTACTAAGTGTATCAGATAGTGATGG
1 TCACATGTATAGTACTATGTGCAGGCTACTAAGCGTACCAGATAGT-ATGA
*
40058816 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACATGTATAGTACTATGTGCAGGCTACTA
40058847 GGTGAACCGG
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
50 37 0.34
51 69 0.64
52 1 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACATGTATAGTACTATGTGCAGGCTACTAAGCGTACCAGATAGTATGA
Found at i:40059224 original size:24 final size:24
Alignment explanation
Indices: 40059192--40059239 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
40059182 AGTGAATAAG
40059192 ATATGAAATGAAAGATTAATGAGT
1 ATATGAAATGAAAGATTAATGAGT
40059216 ATATGAAATGAAAGATTAATGAGT
1 ATATGAAATGAAAGATTAATGAGT
40059240 CTATTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (24 bp):
ATATGAAATGAAAGATTAATGAGT
Found at i:40060526 original size:15 final size:15
Alignment explanation
Indices: 40060505--40060547 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40060495 TTACATATTC
40060505 GTAAATTGACATTTA
1 GTAAATTGACATTTA
* *
40060520 GTGAATT-ACATATTC
1 GTAAATTGACAT-TTA
40060535 GTAAATTGACATT
1 GTAAATTGACATT
40060548 CAAAGTTCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 4 0.17
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (15 bp):
GTAAATTGACATTTA
Found at i:40060527 original size:30 final size:30
Alignment explanation
Indices: 40060491--40060547 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
40060481 AATGTGTTAA
40060491 TGAATTACATATTCGTAAATTGACATTTAG
1 TGAATTACATATTCGTAAATTGACATTTAG
40060521 TGAATTACATATTCGTAAATTGACATT
1 TGAATTACATATTCGTAAATTGACATT
40060548 CAAAGTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (30 bp):
TGAATTACATATTCGTAAATTGACATTTAG
Found at i:40067634 original size:37 final size:39
Alignment explanation
Indices: 40067545--40067645 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 39
40067535 CAATCGCCCG
*
40067545 TAAGAGCTAATCCACCTGATAACACACCAGTATCACCCG
1 TAAGAGCTAATCCACCTGATAACACACCAGTATCACCCA
* * **
40067584 TAAGATCTAATCCACCTGATAACACACCAG-AT-GCTTA
1 TAAGAGCTAATCCACCTGATAACACACCAGTATCACCCA
40067621 TAAGAGCTAATCCATCC-GATAACAC
1 TAAGAGCTAATCCA-CCTGATAACAC
40067646 GCCAATTGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
37 22 0.40
38 4 0.07
39 29 0.53
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.21
Consensus pattern (39 bp):
TAAGAGCTAATCCACCTGATAACACACCAGTATCACCCA
Found at i:40070778 original size:36 final size:36
Alignment explanation
Indices: 40070731--40070805 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
40070721 CATAATGCTA
*
40070731 AATTATGCATAAAAATGCTTATTTTGCTAATTATTG
1 AATTATGCATAAAAATACTTATTTTGCTAATTATTG
40070767 AATTATGCATAAAAATACTTATTTTGCTAATTATTG
1 AATTATGCATAAAAATACTTATTTTGCTAATTATTG
40070803 AAT
1 AAT
40070806 CTAAATTACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (36 bp):
AATTATGCATAAAAATACTTATTTTGCTAATTATTG
Found at i:40084291 original size:28 final size:28
Alignment explanation
Indices: 40084250--40084327 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
40084240 CGTCCAGATA
* * *
40084250 CATACATA-AGATAGCCATAGAGGCATC
1 CATACAAATAGATAGCCACAAAGGCATC
40084277 CATACAAATAGATAGCCACAAAGGCATC
1 CATACAAATAGATAGCCACAAAGGCATC
* *
40084305 CACATAACATTAGATAGCCACAA
1 CATACAA-A-TAGATAGCCACAA
40084328 GGCTCTCACA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.16
28 22 0.51
29 1 0.02
30 13 0.30
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (28 bp):
CATACAAATAGATAGCCACAAAGGCATC
Found at i:40084342 original size:29 final size:30
Alignment explanation
Indices: 40084253--40084358 Score: 112
Period size: 29 Copynumber: 3.6 Consensus size: 30
40084243 CCAGATACAT
* * * *
40084253 ACATAAGATAGCCATAGAGGCATCCATACA
1 ACATTAGATAGCCACAAAGGCATCCACACA
*
40084283 A-A-TAGATAGCCACAAAGGCATCCACATA
1 ACATTAGATAGCCACAAAGGCATCCACACA
40084311 ACATTAGATAGCCAC-AAGGC-TCTCACACA
1 ACATTAGATAGCCACAAAGGCATC-CACACA
* *
40084340 ACATTAGATATCCATAAAG
1 ACATTAGATAGCCACAAAG
40084359 ATGCCTACAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 24 0.38
29 25 0.39
30 15 0.23
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (30 bp):
ACATTAGATAGCCACAAAGGCATCCACACA
Found at i:40085384 original size:24 final size:23
Alignment explanation
Indices: 40085348--40085393 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
40085338 GTTAATGCTA
*
40085348 TCGAATCGATCAAAGCAGCGCTGC
1 TCGAAACGATCAAA-CAGCGCTGC
* *
40085372 TCGAAACGGTCAAACTGCGCTG
1 TCGAAACGATCAAACAGCGCTG
40085394 TAAGGTTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (23 bp):
TCGAAACGATCAAACAGCGCTGC
Found at i:40085939 original size:324 final size:324
Alignment explanation
Indices: 40085131--40086104 Score: 1723
Period size: 325 Copynumber: 3.0 Consensus size: 324
40085121 CTTAACTCAT
40085131 TTCTTTTTAACTTTGAACATCATAATCACATAGCAGAACCTTGTCATAATTGCTTCAATAAGCTC
1 TTCTTTTTAACTTTGAACATCATAATCACATAGCAGAACCTTGTCATAATTGCTTCAATAAGCTC
*
40085196 AACGTAATTGCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTTC
66 AACGTAACTGCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTTC
* * * **
40085261 AAAGTTGGTCCTCTCATTCCCGGCTCATAATCGGGTGGAGAGATATGGAGATACTGATGAATCTG
131 AAATTTGATCCTCTCATTCTCGGCTCATAATCGGGTGGAGAGATATGGAGATGGTGATGAATCTG
40085326 ATGCAAAGCTGCGTTAATGCTATCGAATCGATCAAAGCAGCGCTGCTCGAAACGGTCAAACTGCG
196 ATGCAAAGCTGCGTTAATGCTATCGAATCGATCAAAGCAGCGCTGCTCGAAACGGTCAAACTGCG
40085391 CTGTAAGGTTCTCGAGTGTAATAGTAGGAGCAGCGGTAAGGTGACTCGGTAGTGGAAAATGAGG
261 CTGTAAGGTTCTCGAGTGTAATAGTAGGAGCAGCGGTAAGGTGACTCGGTAGTGGAAAATGAGG
*
40085455 TTTTTTTTTAACTTTGAACATCATAATCACATAGCAGAACCTTGTCATAATTGCTTCAATAAGCT
1 -TTCTTTTTAACTTTGAACATCATAATCACATAGCAGAACCTTGTCATAATTGCTTCAATAAGCT
*
40085520 CAACGTAACTTCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTT
65 CAACGTAACTGCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTT
*
40085585 CAAATTTGATCCTCTCATTCTCGGCTCATAATCGGGTGGAGAGATACGGAGATGGTGATGAATCT
130 CAAATTTGATCCTCTCATTCTCGGCTCATAATCGGGTGGAGAGATATGGAGATGGTGATGAATCT
* * *
40085650 GATGCAAAGCTGCGTTAATGCTATCGAATCGATCAAAGTAGCGCTGCTCTAAACGGTCAAACTAC
195 GATGCAAAGCTGCGTTAATGCTATCGAATCGATCAAAGCAGCGCTGCTCGAAACGGTCAAACTGC
* * *
40085715 GCTGTAAGGTTCTCGAGTGTAATAGTAGGAGTAGCGATAAGATGACTCGGTAGTGGAAAATGAGG
260 GCTGTAAGGTTCTCGAGTGTAATAGTAGGAGCAGCGGTAAGGTGACTCGGTAGTGGAAAATGAGG
* *
40085780 TTCTTTTTAACTTTGAACATCATAATCACATAGCAAAACCTTGTCATAATTTCTTCAATAAGCTC
1 TTCTTTTTAACTTTGAACATCATAATCACATAGCAGAACCTTGTCATAATTGCTTCAATAAGCTC
40085845 AACGTAACTGCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTTC
66 AACGTAACTGCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTTC
*
40085910 AAATTTGATCCTCTCATTCTCGACTCATAATCGGGTGGAGAGATATGGAGATGGTGATGAATCTG
131 AAATTTGATCCTCTCATTCTCGGCTCATAATCGGGTGGAGAGATATGGAGATGGTGATGAATCTG
* * * *
40085975 ATGCAAAGCTGCGTTAATGCTATCGAATCAATCAAAGGAGCGTTGCTCGAAACGATCAAACTGCG
196 ATGCAAAGCTGCGTTAATGCTATCGAATCGATCAAAGCAGCGCTGCTCGAAACGGTCAAACTGCG
* *
40086040 CTGTAAAGTTCTCGAGTGTAATAGTAGGAGCAGCGGTAAGGTGACTCGGTAGTGAAAAATGAGG
261 CTGTAAGGTTCTCGAGTGTAATAGTAGGAGCAGCGGTAAGGTGACTCGGTAGTGGAAAATGAGG
40086104 T
1 T
40086105 GGGTTTGCAT
Statistics
Matches: 617, Mismatches: 32, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
324 308 0.50
325 309 0.50
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (324 bp):
TTCTTTTTAACTTTGAACATCATAATCACATAGCAGAACCTTGTCATAATTGCTTCAATAAGCTC
AACGTAACTGCTCTTAGGCAGCATCTCATGCAAGGCTACAAATCTTACCTTTCCAAGGGTATTTC
AAATTTGATCCTCTCATTCTCGGCTCATAATCGGGTGGAGAGATATGGAGATGGTGATGAATCTG
ATGCAAAGCTGCGTTAATGCTATCGAATCGATCAAAGCAGCGCTGCTCGAAACGGTCAAACTGCG
CTGTAAGGTTCTCGAGTGTAATAGTAGGAGCAGCGGTAAGGTGACTCGGTAGTGGAAAATGAGG
Found at i:40087025 original size:18 final size:18
Alignment explanation
Indices: 40087002--40087043 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40086992 GTCTAGCAAC
40087002 TGAGGTGGGGACTGAAGA
1 TGAGGTGGGGACTGAAGA
* * *
40087020 TGAGGTTGTGCCTGAAGA
1 TGAGGTGGGGACTGAAGA
40087038 TGAGGT
1 TGAGGT
40087044 TGCGCCTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.45, T:0.24
Consensus pattern (18 bp):
TGAGGTGGGGACTGAAGA
Found at i:40087044 original size:18 final size:18
Alignment explanation
Indices: 40087013--40087051 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
40087003 GAGGTGGGGA
*
40087013 CTGAAGATGAGGTTGTGC
1 CTGAAGATGAGGTTGCGC
40087031 CTGAAGATGAGGTTGCGC
1 CTGAAGATGAGGTTGCGC
40087049 CTG
1 CTG
40087052 GAGTCTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (18 bp):
CTGAAGATGAGGTTGCGC
Found at i:40104248 original size:73 final size:74
Alignment explanation
Indices: 40104112--40104515 Score: 480
Period size: 73 Copynumber: 5.5 Consensus size: 74
40104102 ATAATTAGTG
* * *
40104112 GATATTGCTCGTTTGAGCAACTATTCGATAGAATCAGTAAATATTGCTCGTTTGAGCAC-TTCAG
1 GATATTGCTCGTTTGAGC-ACTTTTAG-TAGAATCAGTAGATATTGCTCGTTTGAGCACTTTCAG
*
40104176 TAGAGTCAATA
64 TAGAATCAATA
* * * * * * * * **
40104187 GACATTGTTCGTTTTAGAACATTTAGTAGGATCAGTAGATATTTCTTG-TTGAGCAGGTTCAGTA
1 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTAGATATTGCTCGTTTGAGCACTTTCAGTA
*
40104251 GAATCATTA
66 GAATCAATA
* *
40104260 GATATTGCTCGTTTGAGCAC-TTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACATTT-AGT
1 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTAGATATTGCTCGTTTGAGCAC-TTTCAGT
* * *
40104323 AGGATTAGTA
65 AGAATCAATA
* * *
40104333 GATAATGCTCG-TTGAGCACTTTTAGTAGAATCAGTAGATATTTCTCGTTTGAGCACTTTCATTA
1 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTAGATATTGCTCGTTTGAGCACTTTCAGTA
*
40104397 GAATCAGTA
66 GAATCAATA
* * *
40104406 GACATTGCTC-ATTGAGCACTTTTAGTAGTATCAGTAGATATTGCTCGTTTGAGCACTTTCAGTA
1 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTAGATATTGCTCGTTTGAGCACTTTCAGTA
40104470 GAAT-AAGTA
66 GAATCAA-TA
40104479 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTA
1 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTA
40104516 TTCCATTTTT
Statistics
Matches: 277, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
72 41 0.15
73 191 0.69
74 31 0.11
75 14 0.05
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (74 bp):
GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTAGATATTGCTCGTTTGAGCACTTTCAGTA
GAATCAATA
Found at i:40104251 original size:36 final size:37
Alignment explanation
Indices: 40104073--40104515 Score: 479
Period size: 36 Copynumber: 12.0 Consensus size: 37
40104063 ATAATCAATG
* * * * * *
40104073 GATAATGCTCGTTTGAGTAAGCATTCAGTATAATTAGTG
1 GATATTGCTCGTTTGAG-CA-CTTTCAGTAGAATCAGTA
40104112 GATATTGCTCGTTTGAGCAACTATTC-GATAGAATCAGTA
1 GATATTGCTCGTTTGAGC-ACT-TTCAG-TAGAATCAGTA
* * *
40104151 AATATTGCTCGTTTGAGCAC-TTCAGTAGAGTCAATA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
* * * * *
40104187 GACATTGTTCGTTTTAGAACATTT-AGTAGGATCAGTA
1 GATATTGCTCGTTTGAGCAC-TTTCAGTAGAATCAGTA
* * ** *
40104224 GATATTTCTTG-TTGAGCAGGTTCAGTAGAATCATTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
40104260 GATATTGCTCGTTTGAGCAC-TTCAGTAGAATCAGTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
* * *
40104296 GACATTGCTCGTTTGAGCACATTT-AGTAGGATTAGTA
1 GATATTGCTCGTTTGAGCAC-TTTCAGTAGAATCAGTA
* *
40104333 GATAATGCTCG-TTGAGCACTTTTAGTAGAATCAGTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
* *
40104369 GATATTTCTCGTTTGAGCACTTTCATTAGAATCAGTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
* * * *
40104406 GACATTGCTC-ATTGAGCACTTTTAGTAGTATCAGTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
*
40104442 GATATTGCTCGTTTGAGCACTTTCAGTAGAATAAGTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
*
40104479 GATATTGCTCGTTTGAGCACTTTTAGTAGAATCAGTA
1 GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
40104516 TTCCATTTTT
Statistics
Matches: 336, Mismatches: 55, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
35 5 0.01
36 145 0.43
37 133 0.40
38 8 0.02
39 45 0.13
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (37 bp):
GATATTGCTCGTTTGAGCACTTTCAGTAGAATCAGTA
Found at i:40104271 original size:109 final size:109
Alignment explanation
Indices: 40104112--40104515 Score: 542
Period size: 109 Copynumber: 3.7 Consensus size: 109
40104102 ATAATTAGTG
*
40104112 GATATTGCTCGTTTGAGCAACTATTC-GATAGAATCAGTAAATATTGCTCGTTTGAGCACTTCAG
1 GATATTGCTCG-TTGAGC-ACT-TTCAG-TAGAATCAGTAGATATTGCTCGTTTGAGCACTTCAG
* * * * *
40104176 TAGAGTCAATAGACATTGTTCGTTTTAGAACATTTAGTAGGATCAGTA
62 TAGAATCAGTAGACATTGCTCGTTTGAGCACATTTAGTAGGATCAGTA
* * ** *
40104224 GATATTTCTTGTTGAGCAGGTTCAGTAGAATCATTAGATATTGCTCGTTTGAGCACTTCAGTAGA
1 GATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCACTTCAGTAGA
*
40104289 ATCAGTAGACATTGCTCGTTTGAGCACATTTAGTAGGATTAGTA
66 ATCAGTAGACATTGCTCGTTTGAGCACATTTAGTAGGATCAGTA
* * * *
40104333 GATAATGCTCGTTGAGCACTTTTAGTAGAATCAGTAGATATTTCTCGTTTGAGCACTTTCATTAG
1 GATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCAC-TTCAGTAG
* * *
40104398 AATCAGTAGACATTGCTC-ATTGAGCACTTTTAGTAGTATCAGTA
65 AATCAGTAGACATTGCTCGTTTGAGCACATTTAGTAGGATCAGTA
* *
40104442 GATATTGCTCGTTTGAGCACTTTCAGTAGAATAAGTAGATATTGCTCGTTTGAGCACTTTTAGTA
1 GATATTGCTCG-TTGAGCACTTTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCAC-TTCAGTA
40104507 GAATCAGTA
64 GAATCAGTA
40104516 TTCCATTTTT
Statistics
Matches: 258, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
109 159 0.62
110 84 0.33
111 6 0.02
112 9 0.03
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (109 bp):
GATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCACTTCAGTAGA
ATCAGTAGACATTGCTCGTTTGAGCACATTTAGTAGGATCAGTA
Found at i:40113151 original size:17 final size:17
Alignment explanation
Indices: 40113120--40113153 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40113110 GGAAAATGTT
* *
40113120 AAATTTGAGTTTTCTAC
1 AAATTTGAATATTCTAC
40113137 AAATTTGAATATTCTAC
1 AAATTTGAATATTCTAC
40113154 TAATAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (17 bp):
AAATTTGAATATTCTAC
Found at i:40113544 original size:15 final size:15
Alignment explanation
Indices: 40113510--40113546 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
40113500 TTTTAAACAA
*
40113510 ATTTTATATGTTTTT
1 ATTTTATATGTTTGT
40113525 A-TTTATATGTTTGT
1 ATTTTATATGTTTGT
40113539 ATTTTATA
1 ATTTTATA
40113547 ATTCTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (15 bp):
ATTTTATATGTTTGT
Found at i:40114278 original size:15 final size:16
Alignment explanation
Indices: 40114239--40114279 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
40114229 TTTTCATTAA
40114239 ATAAA-ATAAAATAAT
1 ATAAACATAAAATAAT
*
40114254 AGAAAC-TAAAA-AAT
1 ATAAACATAAAATAAT
40114268 ATAAACATAAAA
1 ATAAACATAAAA
40114280 CTTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (16 bp):
ATAAACATAAAATAAT
Found at i:40124150 original size:43 final size:43
Alignment explanation
Indices: 40124081--40124268 Score: 216
Period size: 43 Copynumber: 4.4 Consensus size: 43
40124071 GTGCTTCTTC
* * *
40124081 CACAAACGCCGCTATAGATCAGGACCTTTAGTGGCGCTTTTTT
1 CACAAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTTT
*
40124124 TACAAACGCCGCTATAAG-TCAAGACCTTTAGCGGCGCTTTTTT
1 CACAAACGCCGCTA-AAGATCAAGACCTTTAGCGGCGCTTTTTT
* * * **
40124167 CGCAAACGCCGCTAAAGATCAAGACCTTTAGCAGCTCTTTTCC
1 CACAAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTTT
* * * **
40124210 CACAAACGCTGCTAAAGATCAGGACCTTTAGCGACGCTTTTCA
1 CACAAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTTT
* *
40124253 CAAAAACGCCACTAAA
1 CACAAACGCCGCTAAA
40124269 AACATAACAT
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
42 3 0.02
43 118 0.96
44 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
CACAAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTTT
Found at i:40124701 original size:43 final size:43
Alignment explanation
Indices: 40124629--40124719 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
40124619 CACATTGCAA
* * * * *
40124629 GGTAATAAAAAATATAATGCATTTTCTTAATTAAGTAAATCTT
1 GGTAATAAAAAATATAATACATCTACTTAATCAAGGAAATCTT
*
40124672 GGTAATAAAAGATATAATACATCTACTTAATCAAGGAAATCTT
1 GGTAATAAAAAATATAATACATCTACTTAATCAAGGAAATCTT
40124715 -GTAAT
1 GGTAAT
40124720 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 5 0.12
43 37 0.88
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAAATATAATACATCTACTTAATCAAGGAAATCTT
Found at i:40129386 original size:14 final size:14
Alignment explanation
Indices: 40129355--40129403 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
40129345 TCTCAACCCT
* *
40129355 TAAACAATAAACCA
1 TAAACCATAATCCA
* *
40129369 TAAACCGTAATCCC
1 TAAACCATAATCCA
40129383 TAAACCCATAATCCA
1 TAAA-CCATAATCCA
40129398 TAAACC
1 TAAACC
40129404 TTAAAATAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:40130087 original size:18 final size:20
Alignment explanation
Indices: 40130064--40130114 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
40130054 CAAAACATGC
*
40130064 AAAAAACTAAACTG-G-ATA
1 AAAAAACTAAACTGAGAACA
40130082 AAAAAACTAAACTGAGAACA
1 AAAAAACTAAACTGAGAACA
40130102 AAAAATACTAAAC
1 AAAAA-ACTAAAC
40130115 CGGGATGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
20 7 0.24
21 7 0.24
ACGTcount: A:0.65, C:0.14, G:0.08, T:0.14
Consensus pattern (20 bp):
AAAAAACTAAACTGAGAACA
Found at i:40130282 original size:7 final size:7
Alignment explanation
Indices: 40130270--40130447 Score: 65
Period size: 7 Copynumber: 24.9 Consensus size: 7
40130260 ACTAGTTAAT
40130270 CTAAACC
1 CTAAACC
40130277 CTAAACC
1 CTAAACC
*
40130284 ATAAACC
1 CTAAACC
40130291 CTAAAACC
1 CT-AAACC
*
40130299 ATAAACC
1 CTAAACC
* *
40130306 CTTAACA
1 CTAAACC
40130313 C-ATAACC
1 CTA-AACC
40130320 TCTAAACC
1 -CTAAACC
*
40130328 TTAAACC
1 CTAAACC
* *
40130335 C-CAGCC
1 CTAAACC
*
40130341 TTTAAACC
1 -CTAAACC
*
40130349 ATAAACC
1 CTAAACC
* *
40130356 ATAACCC
1 CTAAACC
40130363 CTAAACC
1 CTAAACC
*
40130370 CATAATCC
1 C-TAAACC
*
40130378 ATAAACC
1 CTAAACC
* **
40130385 TTAAAATG
1 CT-AAACC
*
40130393 GT-AACAC
1 CTAAAC-C
40130400 CTAAACC
1 CTAAACC
* *
40130407 TTAAACT
1 CTAAACC
40130414 CTAAACC
1 CTAAACC
* *
40130421 ATATACC
1 CTAAACC
40130428 CTAAACC
1 CTAAACC
**
40130435 AAAAACC
1 CTAAACC
40130442 CTAAAC
1 CTAAAC
40130448 TATAGTGATA
Statistics
Matches: 120, Mismatches: 41, Indels: 20
0.66 0.23 0.11
Matches are distributed among these distances:
6 5 0.04
7 88 0.73
8 26 0.22
9 1 0.01
ACGTcount: A:0.46, C:0.34, G:0.02, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:40130299 original size:15 final size:14
Alignment explanation
Indices: 40130271--40130447 Score: 99
Period size: 14 Copynumber: 11.9 Consensus size: 14
40130261 CTAGTTAATC
40130271 TAAACCCTAAACCA
1 TAAACCCTAAACCA
40130285 TAAACCCTAAAACCA
1 TAAACCCT-AAACCA
*
40130300 TAAACCCTTAACACA
1 TAAACCCTAAAC-CA
*
40130315 T-AACCTCTAAACCT
1 TAAACC-CTAAACCA
40130329 TAAACCCCAGCCTTTAAACCA
1 TAAA---C--CC--TAAACCA
* * *
40130350 TAAACCATAACCCC
1 TAAACCCTAAACCA
*
40130364 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
*
40130379 TAAACCTTAAA--A
1 TAAACCCTAAACCA
* *
40130391 TGGTAACACCTAAACCT
1 T--AAAC-CCTAAACCA
*
40130408 TAAACTCTAAACCA
1 TAAACCCTAAACCA
*
40130422 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
40130436 AAAACCCTAAAC
1 TAAACCCTAAAC
40130448 TATAGTGATA
Statistics
Matches: 124, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
12 2 0.02
14 63 0.51
15 43 0.35
16 1 0.01
17 1 0.01
18 2 0.02
19 1 0.01
20 1 0.01
21 10 0.08
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:40130319 original size:29 final size:29
Alignment explanation
Indices: 40130271--40130447 Score: 91
Period size: 29 Copynumber: 5.9 Consensus size: 29
40130261 CTAGTTAATC
40130271 TAAACCCTAAACCATAAACC-CTAAAACCA
1 TAAACCCTAAACCATAAACCTCT-AAACCA
* *
40130300 TAAACCCTTAACACAT-AACCTCTAAACCT
1 TAAACCCTAAAC-CATAAACCTCTAAACCA
* * *
40130329 TAAACCCCAGCCTTTAAACCATAAACC-ATAACCCC
1 TAAA---C--CC--TAAACCATAAACCTCTAAACCA
*
40130364 TAAACCCATAATCCATAAACCT-TAAA--A
1 TAAACCC-TAAACCATAAACCTCTAAACCA
* *
40130391 TGGTAACACCTAAACCTTAAA-CTCTAAACCA
1 T--AAAC-CCTAAACCATAAACCTCTAAACCA
* *
40130422 TATACCCTAAACCAAAAACC-CTAAAC
1 TAAACCCTAAACCATAAACCTCTAAAC
40130448 TATAGTGATA
Statistics
Matches: 113, Mismatches: 17, Indels: 37
0.68 0.10 0.22
Matches are distributed among these distances:
27 1 0.01
28 19 0.17
29 58 0.51
30 9 0.08
31 2 0.02
32 2 0.02
34 2 0.02
35 12 0.11
36 8 0.07
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (29 bp):
TAAACCCTAAACCATAAACCTCTAAACCA
Found at i:40130389 original size:22 final size:21
Alignment explanation
Indices: 40130342--40130447 Score: 72
Period size: 21 Copynumber: 5.0 Consensus size: 21
40130332 ACCCCAGCCT
*
40130342 TTAAACCATAAACCATAACCC
1 TTAAACCATAAACCATAAACC
* *
40130363 CTAAACCCATAATCCATAAACC
1 TTAAA-CCATAAACCATAAACC
***
40130385 TTAAAATGGTAACACC-TAAACC
1 TT-AAACCATAA-ACCATAAACC
*
40130407 TTAAACTC-TAAACCATATACC
1 TTAAAC-CATAAACCATAAACC
* * *
40130428 CTAAACCAAAAACCCTAAAC
1 TTAAACCATAAACCATAAAC
40130448 TATAGTGATA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
20 4 0.06
21 29 0.45
22 26 0.41
23 5 0.08
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:40130728 original size:41 final size:41
Alignment explanation
Indices: 40130622--40130826 Score: 204
Period size: 41 Copynumber: 5.0 Consensus size: 41
40130612 TAAATTATTT
* * * *
40130622 TAAATCCCTGAGTATTAGCAGCGCTTT-TTAGAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCA-AAAACGCCGC
** * * * *
40130663 TAAA--AATAGAGAATTCGCGGCGCTTTCTCAAAAAAGCCAC
1 TAAAGCCCT-GAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * *
40130703 TAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCTGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
40130744 TAAAGCCCTGAGCATTAGCGGCGCTTTC-CTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTC-AAAAACGCCGC
* * *
40130785 TAAAGCCTTGAGCATTAGCGGCACTTTC-CCAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
40130825 TA
1 TA
40130827 CAGCTGCGCT
Statistics
Matches: 136, Mismatches: 23, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 39 0.29
41 95 0.70
42 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
Found at i:40143529 original size:22 final size:20
Alignment explanation
Indices: 40143497--40143536 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
40143487 TCAAGTTTAA
*
40143497 ATTTTTACTAATTATTTTTT
1 ATTTTTACTAACTATTTTTT
40143517 ATTTTATATCTAACTATTTT
1 ATTTT-TA-CTAACTATTTT
40143537 AATTTATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTACTAACTATTTTTT
Found at i:40147808 original size:38 final size:38
Alignment explanation
Indices: 40147757--40147830 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
40147747 TAAAGATGAC
40147757 GAAATTCAGATTTCTTTAAATTACCTCACAAATCATAT
1 GAAATTCAGATTTCTTTAAATTACCTCACAAATCATAT
40147795 GAAATTCAGATTTCTTTAAATTACCTCACAAATCAT
1 GAAATTCAGATTTCTTTAAATTACCTCACAAATCAT
40147831 GTTTAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.36
Consensus pattern (38 bp):
GAAATTCAGATTTCTTTAAATTACCTCACAAATCATAT
Found at i:40151557 original size:18 final size:20
Alignment explanation
Indices: 40151534--40151576 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
40151524 CATATACATG
40151534 CATACATTTT-A-TAATACA
1 CATACATTTTAATTAATACA
40151552 CATACATTTTAATTAATACA
1 CATACATTTTAATTAATACA
40151572 CATAC
1 CATAC
40151577 TTATACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (20 bp):
CATACATTTTAATTAATACA
Found at i:40159574 original size:17 final size:19
Alignment explanation
Indices: 40159542--40159586 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
40159532 CCAGTTCTAT
*
40159542 TAAATAAATCATT-AAAAA
1 TAAAAAAATCATTAAAAAA
40159560 TAAAAAAAT-ATTAAAAAA
1 TAAAAAAATCATTAAAAAA
40159578 TAAAAAAAT
1 TAAAAAAAT
40159587 TTATGATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAAATCATTAAAAAA
Found at i:40160503 original size:3 final size:3
Alignment explanation
Indices: 40160495--40160523 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40160485 ATTAGTGATA
40160495 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40160524 CCAAATCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40161189 original size:53 final size:55
Alignment explanation
Indices: 40161110--40161273 Score: 188
Period size: 61 Copynumber: 2.9 Consensus size: 55
40161100 GTCTCGAATT
* *
40161110 TTTTTTTTTTTAGTTTTGGGACACTGATGACCGGCACCAACTTTATCA-AATTAA
1 TTTTTTTTTTTGGTTTTGGGACACTGATGGCCGGCACCAACTTTATCAGAATTAA
* * * *
40161164 -TTTTTTTTTGGGTTCTGGGACACTGATGGCTGGCACCAACATCAACTTTATCAGATTTAA
1 TTTTTTTTTTTGGTTTTGGGACACTGATGGCCGG---C-AC--CAACTTTATCAGAATTAA
* *
40161224 TTTTTTTTTTTGGTTTTGGAACACTGATGGCCGGCACCAACTTTAACAGA
1 TTTTTTTTTTTGGTTTTGGGACACTGATGGCCGGCACCAACTTTATCAGA
40161274 TATATATAGG
Statistics
Matches: 91, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
53 28 0.31
55 12 0.13
56 1 0.01
57 4 0.04
58 1 0.01
59 11 0.12
60 5 0.05
61 29 0.32
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (55 bp):
TTTTTTTTTTTGGTTTTGGGACACTGATGGCCGGCACCAACTTTATCAGAATTAA
Found at i:40164269 original size:6 final size:6
Alignment explanation
Indices: 40164258--40164319 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
40164248 ATATATAAAT
* * * * * *
40164258 AATTGA AATTGA AAGTGG TATTG- AATTGA AATTCA ATTTGA AATTAA
1 AATTGA AATTGA AATTGA AATTGA AATTGA AATTGA AATTGA AATTGA
*
40164305 AATTGG AATTGA AAT
1 AATTGA AATTGA AAT
40164320 GAATTTATAT
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (6 bp):
AATTGA
Found at i:40164316 original size:18 final size:18
Alignment explanation
Indices: 40164258--40164319 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
40164248 ATATATAAAT
*
40164258 AATTGAAATTGAAAGTGG
1 AATTGAAATTGAAATTGG
* *
40164276 TATTG-AATTGAAATT-C
1 AATTGAAATTGAAATTGG
*
40164292 AATTTGAAATTAAAATTGG
1 AA-TTGAAATTGAAATTGG
40164311 AATTGAAAT
1 AATTGAAAT
40164320 GAATTTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 20 0.57
19 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (18 bp):
AATTGAAATTGAAATTGG
Found at i:40164535 original size:11 final size:11
Alignment explanation
Indices: 40164502--40164543 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
40164492 TATATTGAAT
40164502 TGAAATTAAAA
1 TGAAATTAAAA
* *
40164513 TTGGACTTAAAA
1 -TGAAATTAAAA
40164525 TGAAATTAAAA
1 TGAAATTAAAA
40164536 TGAAATTA
1 TGAAATTA
40164544 TATTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (11 bp):
TGAAATTAAAA
Found at i:40164576 original size:18 final size:17
Alignment explanation
Indices: 40164530--40164569 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
40164520 TAAAATGAAA
*
40164530 TTAAAATGAAATTATAT
1 TTAAAATGAAAATATAT
40164547 TTAAAATGAAAATATAT
1 TTAAAATGAAAATATAT
40164564 TTAAAA
1 TTAAAA
40164570 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TTAAAATGAAAATATAT
Done.