Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 152 of 208
Found at i:49384074 original size:20 final size:20
Alignment explanation
Indices: 49384046--49384085 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
49384036 TTCGGCAATG
49384046 TATAACCATACACAAATCAA
1 TATAACCATACACAAATCAA
* * *
49384066 TATATCCATATACAATTCAA
1 TATAACCATACACAAATCAA
49384086 CTTCGACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
TATAACCATACACAAATCAA
Found at i:49388372 original size:28 final size:31
Alignment explanation
Indices: 49388303--49388365 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 31
49388293 TATATTTGTA
*
49388303 ATAGACTATTTTAATCATTTTTTATAATTTTT
1 ATAG-CTATTTTAATCATTTTTTATAATTTAT
49388335 ATAGCT-TTTTAAT-A-TTTTTATAATTTAT
1 ATAGCTATTTTAATCATTTTTTATAATTTAT
49388363 ATA
1 ATA
49388366 TTATTTTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 16 0.53
29 1 0.03
30 7 0.23
31 2 0.07
32 4 0.13
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (31 bp):
ATAGCTATTTTAATCATTTTTTATAATTTAT
Found at i:49388446 original size:21 final size:21
Alignment explanation
Indices: 49388422--49388483 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
49388412 TTTTTTAAAT
49388422 TTTTTTATTATTTTTAATAAC
1 TTTTTTATTATTTTTAATAAC
* *
49388443 TTTTATATT-TTTTT-ACAAC
1 TTTTTTATTATTTTTAATAAC
*
49388462 TTTTAATAATTATTTTATAATA
1 TTTT--TTATTATTTT-TAATA
49388484 TTCTAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 5 0.16
21 11 0.35
22 4 0.13
23 1 0.03
24 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTATTATTTTTAATAAC
Found at i:49388465 original size:29 final size:29
Alignment explanation
Indices: 49388414--49388470 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
49388404 TTATCTTCTT
** *
49388414 TTTTAAATTTTTTTATTATTTTTAATAAC
1 TTTTAAATTTTTTTACAACTTTTAATAAC
*
49388443 TTTTATATTTTTTTACAACTTTTAATAA
1 TTTTAAATTTTTTTACAACTTTTAATAA
49388471 TTATTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTAAATTTTTTTACAACTTTTAATAAC
Found at i:49391710 original size:3 final size:3
Alignment explanation
Indices: 49391702--49391730 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
49391692 CTTTAAGTAA
49391702 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
49391731 AAGGTTATGA
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:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49392161 original size:4 final size:4
Alignment explanation
Indices: 49392154--49392184 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
49392144 TAAAAAAAAA
49392154 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
49392185 AGAAGAAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:49392191 original size:8 final size:9
Alignment explanation
Indices: 49392149--49392188 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
49392139 AATGTTAAAA
*
49392149 AAAAAAAAG
1 AAAAGAAAG
49392158 -AAAGAAAG
1 AAAAGAAAG
49392166 -AAAGAAAG
1 AAAAGAAAG
49392174 -AAAGAAAG
1 AAAAGAAAG
49392182 AAAAGAA
1 AAAAGAA
49392189 GAAGCTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:49392852 original size:29 final size:31
Alignment explanation
Indices: 49392788--49392853 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
49392778 GCTAAAATTA
*
49392788 AATTTTAAATTTTAATAGTTAATATTTTTAT
1 AATTTTAAATATTAATAGTTAATATTTTTAT
49392819 AATTTTAAAGTATTAA-A-TTAA-ATTTTTAT
1 AATTTTAAA-TATTAATAGTTAATATTTTTAT
*
49392848 TATTTT
1 AATTTT
49392854 TAAGAGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 10 0.31
32 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
AATTTTAAATATTAATAGTTAATATTTTTAT
Found at i:49393193 original size:18 final size:18
Alignment explanation
Indices: 49393163--49393198 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
49393153 AATGTACAGG
49393163 TGACAGTTGTGAATATAA
1 TGACAGTTGTGAATATAA
49393181 TGACAAGTT-TGAATATAA
1 TGAC-AGTTGTGAATATAA
49393199 AAAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (18 bp):
TGACAGTTGTGAATATAA
Found at i:49393275 original size:27 final size:25
Alignment explanation
Indices: 49393244--49393299 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
49393234 TTAAAATTAC
* *
49393244 ATATGAATTTTGATTTAATGTGCAATT
1 ATATGAACTTTAATTT-A-GTGCAATT
*
49393271 ATATGAACTTTAATTTAGTGTAATT
1 ATATGAACTTTAATTTAGTGCAATT
49393296 ATAT
1 ATAT
49393300 ACATGAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
26 1 0.04
27 14 0.54
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (25 bp):
ATATGAACTTTAATTTAGTGCAATT
Found at i:49393315 original size:30 final size:30
Alignment explanation
Indices: 49393276--49393347 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
49393266 CAATTATATG
*
49393276 AACTTTAATTTAGTGT-AATTATATACATGA
1 AACTTTAATTTAGT-TCAAATATATACATGA
* * *
49393306 AACTCTAATTGTGGTTCAAATATATACTTGA
1 AACTTTAATT-TAGTTCAAATATATACATGA
49393337 AACTTTAATTT
1 AACTTTAATTT
49393348 TAATTTAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (30 bp):
AACTTTAATTTAGTTCAAATATATACATGA
Found at i:49393708 original size:19 final size:20
Alignment explanation
Indices: 49393659--49393698 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
49393649 ATTTATATAA
49393659 ATTCACTAAAAATTAAAATT
1 ATTCACTAAAAATTAAAATT
49393679 ATTCACTAAAAATTAAAATT
1 ATTCACTAAAAATTAAAATT
49393699 TTCTTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTCACTAAAAATTAAAATT
Found at i:49405373 original size:40 final size:40
Alignment explanation
Indices: 49405329--49405499 Score: 258
Period size: 40 Copynumber: 4.3 Consensus size: 40
49405319 GCTCCTCGTT
* * *
49405329 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
49405369 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
49405409 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
49405449 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
49405487 CAAATGCCTTCGG
1 CAAATGCCTTCGG
49405500 ATCTTCGTCC
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
38 20 0.16
39 14 0.11
40 88 0.71
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:49405513 original size:78 final size:81
Alignment explanation
Indices: 49405329--49405548 Score: 258
Period size: 80 Copynumber: 2.8 Consensus size: 81
49405319 GCTCCTCGTT
* * * * * *
49405329 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCA
*
49405393 GATTTAGTAACTCGCA
66 GAATTAGTAACTCGCA
49405409 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCA
1 CAAATGCCTTCGGGACTTAACCCGGATATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCA
49405472 GAATTAGT-ACTCGCA
66 GAATTAGTAACTCGCA
*** * *
49405487 CAAATGCCTTC-GGATCTTCGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATATTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
49405548 C
64 C
49405549 GGACAGCATT
Statistics
Matches: 123, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
77 12 0.10
78 41 0.33
79 21 0.17
80 49 0.40
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAACCCGGATATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCA
GAATTAGTAACTCGCA
Found at i:49405947 original size:13 final size:13
Alignment explanation
Indices: 49405929--49405953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49405919 AGGATGAGCA
49405929 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
49405942 TTTTTTTTCTTT
1 TTTTTTTTCTTT
49405954 CTAGTTTCGG
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:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:49412701 original size:80 final size:80
Alignment explanation
Indices: 49412597--49412820 Score: 278
Period size: 79 Copynumber: 2.8 Consensus size: 80
49412587 GCTCCTCGTT
* *
49412597 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
49412662 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* * *
49412677 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
*
49412740 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * *
49412756 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
49412818 GGA
64 GGA
49412821 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
78 13 0.10
79 55 0.44
80 54 0.44
81 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:49412758 original size:39 final size:40
Alignment explanation
Indices: 49412597--49412820 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
49412587 GCTCCTCGTT
* * *
49412597 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
49412637 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
49412677 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
49412717 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
49412756 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
49412797 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
49412821 CAGCATTCAA
Statistics
Matches: 164, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.29
40 105 0.64
41 9 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:49415022 original size:13 final size:13
Alignment explanation
Indices: 49415004--49415033 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49414994 GAGTACGTAT
49415004 AAAACATAACTTG
1 AAAACATAACTTG
49415017 AAAACATAACTTG
1 AAAACATAACTTG
49415030 AAAA
1 AAAA
49415034 TAGAGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AAAACATAACTTG
Found at i:49416510 original size:44 final size:44
Alignment explanation
Indices: 49416447--49416535 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
49416437 GATGCTTGCT
49416447 TGGTAACTATTATTATATATAAACTCTGAAAAAGGTAAATAACA
1 TGGTAACTATTATTATATATAAACTCTGAAAAAGGTAAATAACA
*
49416491 TGGTAACTATTATTATATATAAACTCTGACAAAGGTAAATAACA
1 TGGTAACTATTATTATATATAAACTCTGAAAAAGGTAAATAACA
49416535 T
1 T
49416536 TTCCAACTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (44 bp):
TGGTAACTATTATTATATATAAACTCTGAAAAAGGTAAATAACA
Found at i:49426099 original size:23 final size:22
Alignment explanation
Indices: 49426072--49426119 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
49426062 ATTTATTTAA
*
49426072 TTATTT-TTTAGGTCATTAGGAAT
1 TTATTTCTTTA-GTAATTAGG-AT
49426095 TTATTTCTTTAGTAATTAGGAT
1 TTATTTCTTTAGTAATTAGGAT
49426117 TTA
1 TTA
49426120 ATCTTTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (22 bp):
TTATTTCTTTAGTAATTAGGAT
Found at i:49428868 original size:13 final size:13
Alignment explanation
Indices: 49428831--49428881 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
49428821 CAAAAGCTCG
49428831 TAAAAACATAGTTT
1 TAAAAACATA-TTT
*
49428845 ATAAAATCATATTT
1 -TAAAAACATATTT
49428859 TAAAAACATATATT
1 TAAAAACATAT-TT
49428873 T-AAAACATA
1 TAAAAACATA
49428882 AGCTCACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 18 0.55
14 6 0.18
15 9 0.27
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (13 bp):
TAAAAACATATTT
Found at i:49428924 original size:13 final size:13
Alignment explanation
Indices: 49428906--49428932 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49428896 CACGTATAAT
49428906 ACATAACTTGAAA
1 ACATAACTTGAAA
49428919 ACATAACTTGAAA
1 ACATAACTTGAAA
49428932 A
1 A
49428933 TAAAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ACATAACTTGAAA
Found at i:49432470 original size:20 final size:20
Alignment explanation
Indices: 49432421--49432471 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
49432411 ATTTGCATTT
*
49432421 CGGTGCCTCTGTATACACTT
1 CGGTGCCTCTGTATACACTA
* *
49432441 CAGTGTCTCTGT-TCACACTA
1 CGGTGCCTCTGTAT-ACACTA
49432461 CGGTGCCTCTG
1 CGGTGCCTCTG
49432472 ATTGCACAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (20 bp):
CGGTGCCTCTGTATACACTA
Found at i:49437373 original size:15 final size:16
Alignment explanation
Indices: 49437355--49437388 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49437345 AACTTTTAAA
*
49437355 TAATT-TTTTTGTATT
1 TAATTCTTTTAGTATT
49437370 TAATTCTTTTAGTATT
1 TAATTCTTTTAGTATT
49437386 TAA
1 TAA
49437389 GAATCAAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (16 bp):
TAATTCTTTTAGTATT
Found at i:49441662 original size:34 final size:34
Alignment explanation
Indices: 49441619--49441687 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
49441609 AAAGATCGGT
49441619 AGATTTGATAATTCAATCCCAAATTCTAATTCCA
1 AGATTTGATAATTCAATCCCAAATTCTAATTCCA
49441653 AGATTTGATAATTCAATCCCAAATTCTAATTCCA
1 AGATTTGATAATTCAATCCCAAATTCTAATTCCA
49441687 A
1 A
49441688 CTCCGACGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (34 bp):
AGATTTGATAATTCAATCCCAAATTCTAATTCCA
Found at i:49442596 original size:6 final size:6
Alignment explanation
Indices: 49442585--49442624 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
49442575 TGGCGTGATA
49442585 CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCCC
49442625 TTTCTCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:49448969 original size:20 final size:19
Alignment explanation
Indices: 49448923--49448970 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
49448913 ATAAAAATAA
*
49448923 ATGAGTTTAATGGTGGAAG
1 ATGAATTTAATGGTGGAAG
* *
49448942 AGTAAATTTAATGGTGGACTG
1 A-TGAATTTAATGGTGGA-AG
49448963 ATGAATTT
1 ATGAATTT
49448971 GATCAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.35
Consensus pattern (19 bp):
ATGAATTTAATGGTGGAAG
Found at i:49452381 original size:39 final size:41
Alignment explanation
Indices: 49452322--49452411 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
49452312 AAAAATTATA
* * * *
49452322 TTTAATATAATAAAATATTTATTATATTT-A-TTTGTGTTT
1 TTTAATATAAGAAAACATTTATTATATTTAAGGTAGTGTTT
49452361 TTTAATATAAGAAAACATTTATTATATTTAAGGTAGTGTTT
1 TTTAATATAAGAAAACATTTATTATATTTAAGGTAGTGTTT
49452402 TTTAATATAA
1 TTTAATATAA
49452412 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 27 0.60
40 1 0.02
41 17 0.38
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (41 bp):
TTTAATATAAGAAAACATTTATTATATTTAAGGTAGTGTTT
Found at i:49460044 original size:21 final size:21
Alignment explanation
Indices: 49460020--49460061 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
49460010 TTTGCCTAAG
*
49460020 ATATGAATTGGATTGAATTGA
1 ATATGAATTGGATTAAATTGA
*
49460041 ATATGAATTGTATTAAATTGA
1 ATATGAATTGGATTAAATTGA
49460062 GCTAAATTTA
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:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
ATATGAATTGGATTAAATTGA
Found at i:49460237 original size:21 final size:20
Alignment explanation
Indices: 49460195--49460253 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
49460185 TTGTGTATAT
*
49460195 TTATATATTTGAATTGAATG
1 TTATATATATGAATTGAATG
* * *
49460215 TTGTATATGTGAATTATAATG
1 TTATATATATGAATT-GAATG
49460236 TTATATATATGAAATTGA
1 TTATATATATG-AATTGA
49460254 TCACATATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 13 0.42
21 14 0.45
22 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.47
Consensus pattern (20 bp):
TTATATATATGAATTGAATG
Found at i:49460914 original size:18 final size:17
Alignment explanation
Indices: 49460888--49460922 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49460878 AAAGATGAAA
49460888 TAATAAAATATGAAAAAT
1 TAATAAAATAT-AAAAAT
*
49460906 TAATTAAATATAAAAAT
1 TAATAAAATATAAAAAT
49460923 ATTATCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAATAAAATATAAAAAT
Found at i:49461972 original size:25 final size:24
Alignment explanation
Indices: 49461939--49462026 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
49461929 TAAGCGTCCC
*
49461939 GATATAAGGCTCTCCAGAGCTTTCT
1 GATA-AAGGCTCTCCAGAGCTTCCT
* *
49461964 GATTAAAGGCTCTTTCATGAGCTTCCA
1 GA-TAAAGGCTC-TCCA-GAGCTTCCT
* *
49461991 GACTAATGGCTCTCTAGAGCTTCCT
1 GA-TAAAGGCTCTCCAGAGCTTCCT
*
49462016 GATAATGGCTC
1 GATAAAGGCTC
49462027 GCTTGAACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
24 9 0.17
25 19 0.37
26 7 0.13
27 17 0.33
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (24 bp):
GATAAAGGCTCTCCAGAGCTTCCT
Found at i:49462025 original size:24 final size:24
Alignment explanation
Indices: 49461942--49462061 Score: 86
Period size: 24 Copynumber: 4.9 Consensus size: 24
49461932 GCGTCCCGAT
* *
49461942 ATAA-GGCTCTCCAGAGCTTTCTG
1 ATAATGGCTCTCTAGAGCTTCCTG
* * *
49461965 ATTAAAGGCTCTTTCATGAGCTTCCAG
1 A-TAATGGCTCTCT-A-GAGCTTCCTG
49461992 ACTAATGGCTCTCTAGAGCTTCCTG
1 A-TAATGGCTCTCTAGAGCTTCCTG
* * *
49462017 ATAATGGCTCGCTTGAACTTCCCT-
1 ATAATGGCTCTCTAGAGCTT-CCTG
49462041 AT-ATGGCTCT-TATGAGCTTCC
1 ATAATGGCTCTCTA-GAGCTTCC
49462062 CGTTATACAG
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
22 3 0.04
23 13 0.17
24 21 0.27
25 19 0.25
26 2 0.03
27 19 0.25
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (24 bp):
ATAATGGCTCTCTAGAGCTTCCTG
Found at i:49462142 original size:27 final size:25
Alignment explanation
Indices: 49462007--49462146 Score: 110
Period size: 25 Copynumber: 5.7 Consensus size: 25
49461997 TGGCTCTCTA
* * **
49462007 GAGCTTCCTGATA-ATGGCTCGCTT
1 GAGCTTCCCGTTATATGGCTCGAAT
* **
49462031 GAACTTCCC--TATATGGCTCTTAT
1 GAGCTTCCCGTTATATGGCTCGAAT
** *
49462054 GAGCTTCCCGTTATACAGCTTGAAT
1 GAGCTTCCCGTTATATGGCTCGAAT
*
49462079 GAGCTTCCTGTTATATGGCTC-ACAT
1 GAGCTTCCCGTTATATGGCTCGA-AT
*
49462104 GAGCTTCCCGTTATATGGCTCGAGAGA
1 GAGCTTCCCGTTATATGGCTCGA-A-T
49462131 GAGCTTCCCGTT-TATG
1 GAGCTTCCCGTTATATG
49462147 TGCTTTTATG
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
22 2 0.02
23 16 0.17
24 8 0.09
25 48 0.52
26 6 0.07
27 12 0.13
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGAAT
Found at i:49463076 original size:13 final size:13
Alignment explanation
Indices: 49463058--49463096 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
49463048 ATTTCGTCCA
49463058 CACAGGCGTGTGT
1 CACAGGCGTGTGT
*
49463071 CACAGGTGTGTGT
1 CACAGGCGTGTGT
* *
49463084 CTCAGCCGTGTGT
1 CACAGGCGTGTGT
49463097 GTCCTAGCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.36, T:0.28
Consensus pattern (13 bp):
CACAGGCGTGTGT
Found at i:49465058 original size:12 final size:12
Alignment explanation
Indices: 49465029--49465063 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
49465019 GAATTAGTCC
*
49465029 TATTATTATTAT
1 TATTACTATTAT
49465041 TATTACTATTAT
1 TATTACTATTAT
49465053 TATTACCTATT
1 TATTA-CTATT
49465064 TATTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTACTATTAT
Found at i:49478371 original size:21 final size:23
Alignment explanation
Indices: 49478326--49478372 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
49478316 TCACCTGCAA
* *
49478326 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
49478349 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
49478370 TAA
1 TAA
49478373 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:49485063 original size:29 final size:30
Alignment explanation
Indices: 49485013--49485070 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
49485003 ATGAGTGATA
49485013 AAAAAGAGAGAGTGATTCAAAA-GAAAAAG
1 AAAAAGAGAGAGTGATTCAAAATGAAAAAG
*
49485042 AAAAAGAGATGAGTGA-TGAAAATGAAAAA
1 AAAAAGAGA-GAGTGATTCAAAATGAAAAA
49485071 AAGAGTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.62, C:0.02, G:0.24, T:0.12
Consensus pattern (30 bp):
AAAAAGAGAGAGTGATTCAAAATGAAAAAG
Found at i:49493733 original size:760 final size:756
Alignment explanation
Indices: 49492600--49493983 Score: 2261
Period size: 760 Copynumber: 1.8 Consensus size: 756
49492590 GTGAACCAGC
* * *
49492600 TCGGGTTAATCAAGTCATTTCACGTAGATGCCTGATCACCGATGAGAAGTTTTGTTTTGATGTCT
1 TCGGGTTAATCAAGTCATTTCACGTAGATGCCTGATCACCGACGAGAAGTTTCGTTTTGATGTCG
** *
49492665 TATGAAAATTGAGATTGGGAGATGCATAAGCGGAAGCAGGCAATTTGAGTTCAAAAGATGGCTTG
66 TATGAAAATTGAGATTGGGAGATGCATAAGCAAAAGCAGGCAATTTGAGTTCAAAAGATGGCTTA
*
49492730 GATTGATGTTTTTTTATAGACTCGATTTAATAAAGAAATAATTTATAAATTGATAGATAAAATGG
131 GATTGATGTTTTTTTATAGACTAGATTTAATAAAGAAATAATTTATAAATTGATAGATAAAATGG
* *
49492795 AAGGGAAGTTGAACTCAAGCTTCAAGAATGTTTTAATACTAAAAAGTATTGCCCCGAGTCTTATA
196 AAGAGAAGTTGAACTCAAGCTTCAAGAATGTTTCAATACTAAAAAGTATTGCCCCGAGTCTTATA
* *
49492860 TTGCTCAAGGTGAATTTAGATGAAGGATAGAAGCAGACCTTGACCTGTTGCCTACATGGAGGTAA
261 TTGCTCAAGGTGAATTTAGATGAAGGATAGAAGCAGACCTTGACCCGTTACCTACATGGAGGTAA
* * * * *
49492925 GAACCAGAGGTATAATAATATGGTTGAATGCCATACGGGTTCGGTGATAAGTTCAATGGAGTTTG
326 GAACCAAAGGTATAATAATATGGTTGAACGCCACACGAGTTCGGTGATAAGTTCAATGGAGTTCG
* * *
49492990 GACTGATGCCACTAGCAAGCTAGATAAGTCGCTTCGAGTCTCGAACGAAAGAAGAGAAGAGGTAA
391 GACTGACGCCACTAGCAAGCTAGATAAATCGCTTCGAGACTCGAACGAAAGAAGAGAAGAGGTAA
* *
49493055 CCTCAGAAGAACAAAAGTTCTATTAAGTTTAATTGATCAAATTCTATCACCTTTTACAATAAACA
456 CCTCAGAAGAACAAAAGTTCTATTAAGTTTAATTGATCAAATTCTATAACCTTTTACAATAAAAA
49493120 AGTAAACTATTTATAGGCAAAGACTAAGCTAGCCGAATAGCCACATACATCATTAGGAATTAAGC
521 AGTAAACTATTTATAGGCAAAGACTAAGCTAGCCGAATAGCCACATACATCATTAGGAATTAAGC
* *
49493185 AAAGGAATTCATCTAATGGTCTTGCTAAATTTGGCTGAATGTGAGCTCCAATGGTCAGCTTCTAG
586 AAAGGAATTCATCTAATGGTCTAGCTAAATTCGGCTGAATGTGAGCTCCAATGGTCAGCTTCTAG
49493250 ATGCATAAATGAATCTTGGACAACTTGGATGGTGCATGGATGAGCAAGGTTCGCCCAATGAGTAT
651 ATGCATAAATGAATCTTGGACAACTTGGATGGTGCATGGATGAGCAAGGTTCGCCCAATGAGTAT
49493315 AAATGAGCTCATTAAGATGCAAATTTTTGGTGCGATCTGGT
716 AAATGAGCTCATTAAGATGCAAATTTTTGGTGCGATCTGGT
* * * **
49493356 TCGGGTTAATCGAGTCGTTTCACGTAGTTGTCC-GATCGTCGACGAGAAGTCTTCGTTTTGATGT
1 TCGGGTTAATCAAGTCATTTCACGTAGATG-CCTGATCACCGACGAGAAGT-TTCGTTTTGATGT
* * * *
49493420 CGTATGAAAATTGAG-TTATGGAGATGTATAAGCAAAAGCAGGCAATTTGGGTTTAAAAGATGGC
64 CGTATGAAAATTGAGATT-GGGAGATGCATAAGCAAAAGCAGGCAATTTGAGTTCAAAAGATGGC
* *
49493484 TTAGATTGATGTTTTTTTTATACG-TTAGGTTTAAATAAAGAAATAATTTATAAATTGATAGATA
128 TTAGATTGATG-TTTTTTTATA-GACTAGATTT-AATAAAGAAATAATTTATAAATTGATAGATA
* *
49493548 AAATGGAATAGAAGTTGAACTCAAGCTTCAAGAATGTTTCAATACTAAAAAAGTATTGCCCCTAG
190 AAATGGAAGAGAAGTTGAACTCAAGCTTCAAGAATGTTTCAATACT-AAAAAGTATTGCCCCGAG
* * * *
49493613 TCTTATATTGCTTAAGGTGAATTTTGATGAAGGATAGAAGCGGACCTTGACCCGTTACCTATATG
254 TCTTATATTGCTCAAGGTGAATTTAGATGAAGGATAGAAGCAGACCTTGACCCGTTACCTACATG
* *
49493678 GAGGTAAGAACCAAAGGTATAATAATATGGTTGAACGCCACACTAGTTTGGTGATAAGTTCAATG
319 GAGGTAAGAACCAAAGGTATAATAATATGGTTGAACGCCACACGAGTTCGGTGATAAGTTCAATG
* *
49493743 GAGTTCGGATTGACGCCACTAGCAAGCTAGATAAATCGCTTCGAGACTCGAACGAAAGAAGAGAG
384 GAGTTCGGACTGACGCCACTAGCAAGCTAGATAAATCGCTTCGAGACTCGAACGAAAGAAGAGAA
49493808 GAGGTAACCTCAGAAGAACAAAAGTTCTATTAAGTTTAATTGATCAAATTCTATAACCTTTTACA
449 GAGGTAACCTCAGAAGAACAAAAGTTCTATTAAGTTTAATTGATCAAATTCTATAACCTTTTACA
* *
49493873 ATAAAAAAGTAATCTATTTATAGGCAAAGACTAAGCTAGCCGAATAGCCACATACATCCTTAGGA
514 ATAAAAAAGTAAACTATTTATAGGCAAAGACTAAGCTAGCCGAATAGCCACATACATCATTAGGA
*
49493938 ATTAAGCAAATGAATTCATCTAATGGTCTAGCTAAATTCGGCTGAA
579 ATTAAGCAAAGGAATTCATCTAATGGTCTAGCTAAATTCGGCTGAA
49493984 CATGGACAGC
Statistics
Matches: 574, Mismatches: 47, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
756 43 0.07
757 78 0.14
758 15 0.03
759 75 0.13
760 363 0.63
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (756 bp):
TCGGGTTAATCAAGTCATTTCACGTAGATGCCTGATCACCGACGAGAAGTTTCGTTTTGATGTCG
TATGAAAATTGAGATTGGGAGATGCATAAGCAAAAGCAGGCAATTTGAGTTCAAAAGATGGCTTA
GATTGATGTTTTTTTATAGACTAGATTTAATAAAGAAATAATTTATAAATTGATAGATAAAATGG
AAGAGAAGTTGAACTCAAGCTTCAAGAATGTTTCAATACTAAAAAGTATTGCCCCGAGTCTTATA
TTGCTCAAGGTGAATTTAGATGAAGGATAGAAGCAGACCTTGACCCGTTACCTACATGGAGGTAA
GAACCAAAGGTATAATAATATGGTTGAACGCCACACGAGTTCGGTGATAAGTTCAATGGAGTTCG
GACTGACGCCACTAGCAAGCTAGATAAATCGCTTCGAGACTCGAACGAAAGAAGAGAAGAGGTAA
CCTCAGAAGAACAAAAGTTCTATTAAGTTTAATTGATCAAATTCTATAACCTTTTACAATAAAAA
AGTAAACTATTTATAGGCAAAGACTAAGCTAGCCGAATAGCCACATACATCATTAGGAATTAAGC
AAAGGAATTCATCTAATGGTCTAGCTAAATTCGGCTGAATGTGAGCTCCAATGGTCAGCTTCTAG
ATGCATAAATGAATCTTGGACAACTTGGATGGTGCATGGATGAGCAAGGTTCGCCCAATGAGTAT
AAATGAGCTCATTAAGATGCAAATTTTTGGTGCGATCTGGT
Found at i:49495311 original size:20 final size:20
Alignment explanation
Indices: 49495282--49495324 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
49495272 ATTCACTGAT
49495282 TTAAAATAAGACAC-AATTAA
1 TTAAAATAAGAC-CTAATTAA
*
49495302 TTAAATTAAGACCTAATTAA
1 TTAAAATAAGACCTAATTAA
49495322 TTA
1 TTA
49495325 GGTTAGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (20 bp):
TTAAAATAAGACCTAATTAA
Found at i:49495632 original size:803 final size:803
Alignment explanation
Indices: 49494088--49495687 Score: 2686
Period size: 803 Copynumber: 2.0 Consensus size: 803
49494078 TTAAGATGCA
** *
49494088 ACTTTTGCTGAAAAGTGACCAGCAATTAAAAGAAAATTGGACAGCCATTTGAAGTGTGAATGCTC
1 ACTTTTGCTGAAAAGTGACCAGCAATTAAAAGAAAATTGGACAGCCAAATGAAGTGTGAAAGCTC
* * * *
49494153 TGCTTTGAAGAGTCCTTGAGTGGGAATACCATGAACTGAACAGCTAAAATGAGTCCAGCAATGTG
66 AGCTTTGAAGAGTCCTTGAGTGGGAACACCATGAACCGAACAGCCAAAATGAGTCCAGCAATGTG
* *
49494218 AAAGAAATAAATGGCAGCTTTGGAGTAGGAAACATCATCTCCTTTGGCCGAAGAGTCACATAGGA
131 AAAGAAATAAATAGCAGCTTTGAAGTAGGAAACATCATCTCCTTTGGCCGAAGAGTCACATAGGA
*
49494283 AACTTCAATAATCAGCACACCATTTTAATTGCATTCCATGCATGTATTGCCAAATACATTGAATC
196 AACTTCAAAAATCAGCACACCATTTTAATTGCATTCCATGCATGTATTGCCAAATACATTGAATC
*
49494348 CAACGTGCATGCATCTTTTAAATGCACTCCCACATTCGGCCAACCTACAAAAGGAGCAAATGAAC
261 CAACGTGCATGCATCTTTTAAATGCAATCCCACATTCGGCCAACCTACAAAAGGAGCAAATGAAC
* *
49494413 TTAAATTAATTTGTATTCAGCTGAAACATAATTAAAACATAATCTGGACAATTTAAATTCACATA
326 TTAAATTAATTTATATTCAGCTGAAACATAATTAAAACACAATCTGGACAATTTAAATTCACATA
* *
49494478 TTTAAAACAAGACACAATTAATTAAATTAAGACCTAATTAATTCGATTAGGACAATACACATTAA
391 TTTAAAACAAGACACAATTAATTAAATTAAGACCTAATTAATTAGATTAGGACAAGACACATTAA
*
49494543 AACATGCTATAAAACATATTTATAAGCTGTAGAAATTAAGATGACTTAAAAACATGTAAGAAACA
456 AACATGCTATAAAACATATTTATAAGCTATAGAAATTAAGATGACTTAAAAACATGTAAGAAACA
49494608 CAATTAACATGCATAATTAAATTCGTCCAGATTTAAGACCAATTAAACAATAAAAATTAATTGAG
521 CAATTAACATGCATAATTAAATTCGTCCAGATTTAAGACCAATTAAACAATAAAAATTAATTGAG
* **
49494673 TTGTATATAACTAAATTAACTAACTCAAATAATTATTTCAGCAACTATATTATCACATAAATGGA
586 CTGTATATAACTAAATTAACTAACTCAAATAATTATTTCAAAAACTATATTATCACATAAATGGA
*** *
49494738 ATTAAGCTAGATTTGAGCTAATTTGTGCTATTGGAGCTGGAAACGAGCTAAACGGAGCTCAATGA
651 ATTAAGCTAGATTTGAGCTAATTCAAGCTATTGGAGCTGGAAACGAGCTAAACGGAGCTCAACGA
49494803 AATGGAATTGAACTAATTCAGCTCGCATGGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAG
716 AATGGAATTGAACTAATTCAGCTCGCATGGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAG
*
49494868 TGTGTCCGGGGCGTGGTTGTATC
781 TGTGCCCGGGGCGTGGTTGTATC
* *
49494891 ACTTTTGCTGAAAAGTGACCAGCAATTAAAAGGAAATT-GAGTAGCCAAATGAAGTGTGAAAGCT
1 ACTTTTGCTGAAAAGTGACCAGCAATTAAAAGAAAATTGGA-CAGCCAAATGAAGTGTGAAAGCT
* *
49494955 CAGCTTTGAAGAGT-TTTGAAGTGTGAACACCATGAACCGAACAGCCAAAATGTA-TCCAGCAAT
65 CAGCTTTGAAGAGTCCTTG-AGTGGGAACACCATGAACCGAACAGCCAAAATG-AGTCCAGCAAT
* * * * * *
49495018 GTGAAAGAATTCATTAGCAGCTTTGAAGTAGGAAACATCATCTCCTTTGGCCGGATAGTCACTTA
128 GTGAAAGAAATAAATAGCAGCTTTGAAGTAGGAAACATCATCTCCTTTGGCCGAAGAGTCACATA
*
49495083 GGAAACTTCAAAAATCAGCACATCATTTTAATTGCATTCCATGCATGTATTGCCAAATACATTGA
193 GGAAACTTCAAAAATCAGCACACCATTTTAATTGCATTCCATGCATGTATTGCCAAATACATTGA
*
49495148 ATCCAATGTGCATGCATCTTTTAAATGCAATCCCACATTCGGCCAACCTACAAAAGGAGCAAATG
258 ATCCAACGTGCATGCATCTTTTAAATGCAATCCCACATTCGGCCAACCTACAAAAGGAGCAAATG
*
49495213 AACTTACATTAATTTATATTCAGCTGAAACATAATTAAAACACAATCTGGACAATTTAAATTCAC
323 AACTTAAATTAATTTATATTCAGCTGAAACATAATTAAAACACAATCTGGACAATTTAAATTCAC
* * *
49495278 -TGATTTAAAATAAGACACAATTAATTAAATTAAGACCTAATTAATTAGGTTAGGACAAGACAGA
388 AT-ATTTAAAACAAGACACAATTAATTAAATTAAGACCTAATTAATTAGATTAGGACAAGACACA
* *
49495342 TTAAAACATGCTATAAAACATATTTATAAGCTATAGGAATTAAGATGACTTAAAAATATGTAAGA
452 TTAAAACATGCTATAAAACATATTTATAAGCTATAGAAATTAAGATGACTTAAAAACATGTAAGA
*
49495407 AACACAATTAACATGCATAATTAAATTCGTCCAGATTTAAGACCAATTAAACAATGAAAATTAAT
517 AACACAATTAACATGCATAATTAAATTCGTCCAGATTTAAGACCAATTAAACAATAAAAATTAAT
**
49495472 TGAGCTGTATATAACTAAATTAACTAACTCAAATAATTATTTCAAAAACTATATTATCGTATAAA
582 TGAGCTGTATATAACTAAATTAACTAACTCAAATAATTATTTCAAAAACTATATTATCACATAAA
* * * * *
49495537 TGGAATTAAGCTAGATTTGAGCTGATTCAAGCTCTTGGAGTTGGAAACGAGCTACATGGAGCTCA
647 TGGAATTAAGCTAGATTTGAGCTAATTCAAGCTATTGGAGCTGGAAACGAGCTAAACGGAGCTCA
49495602 ACGAAATGGAATTGAACTAATTCAGCTCGCATGGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCA
712 ACGAAATGGAATTGAACTAATTCAGCTCGCATGGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCA
49495667 AAAGTGTGCCCGGGGCGTGGT
777 AAAGTGTGCCCGGGGCGTGGT
49495688 CGGATCAAGA
Statistics
Matches: 743, Mismatches: 50, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
802 6 0.01
803 736 0.99
804 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (803 bp):
ACTTTTGCTGAAAAGTGACCAGCAATTAAAAGAAAATTGGACAGCCAAATGAAGTGTGAAAGCTC
AGCTTTGAAGAGTCCTTGAGTGGGAACACCATGAACCGAACAGCCAAAATGAGTCCAGCAATGTG
AAAGAAATAAATAGCAGCTTTGAAGTAGGAAACATCATCTCCTTTGGCCGAAGAGTCACATAGGA
AACTTCAAAAATCAGCACACCATTTTAATTGCATTCCATGCATGTATTGCCAAATACATTGAATC
CAACGTGCATGCATCTTTTAAATGCAATCCCACATTCGGCCAACCTACAAAAGGAGCAAATGAAC
TTAAATTAATTTATATTCAGCTGAAACATAATTAAAACACAATCTGGACAATTTAAATTCACATA
TTTAAAACAAGACACAATTAATTAAATTAAGACCTAATTAATTAGATTAGGACAAGACACATTAA
AACATGCTATAAAACATATTTATAAGCTATAGAAATTAAGATGACTTAAAAACATGTAAGAAACA
CAATTAACATGCATAATTAAATTCGTCCAGATTTAAGACCAATTAAACAATAAAAATTAATTGAG
CTGTATATAACTAAATTAACTAACTCAAATAATTATTTCAAAAACTATATTATCACATAAATGGA
ATTAAGCTAGATTTGAGCTAATTCAAGCTATTGGAGCTGGAAACGAGCTAAACGGAGCTCAACGA
AATGGAATTGAACTAATTCAGCTCGCATGGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAG
TGTGCCCGGGGCGTGGTTGTATC
Found at i:49496128 original size:64 final size:64
Alignment explanation
Indices: 49496026--49496153 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
49496016 AAATCAAGAT
*
49496026 TCACTTTCTTCCTTTCAAGAAAATTAAGAAACCAAATCTTGGTCCAATTTTGCTGTTTTGAGCG
1 TCACTTTCTTCCTTTCAAGAAAATCAAGAAACCAAATCTTGGTCCAATTTTGCTGTTTTGAGCG
** * *
49496090 TCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGTCCAATTTTGCTGTTTTGAGCG
1 TCACTTTCTTCCTTTCAAGAAAATCAAGAAACCAAATCTTGGTCCAATTTTGCTGTTTTGAGCG
49496154 ATTTCAAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (64 bp):
TCACTTTCTTCCTTTCAAGAAAATCAAGAAACCAAATCTTGGTCCAATTTTGCTGTTTTGAGCG
Found at i:49514842 original size:12 final size:12
Alignment explanation
Indices: 49514827--49514860 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
49514817 AAGGATGACA
49514827 GAAAAAGAAATT
1 GAAAAAGAAATT
49514839 GAAAAAGAAATT
1 GAAAAAGAAATT
49514851 GAAAAAGAAA
1 GAAAAAGAAA
49514861 AAGAGAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:49514847 original size:18 final size:18
Alignment explanation
Indices: 49514839--49514876 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
49514829 AAAAGAAATT
49514839 GAAAAAGA-AATTGAAAAA
1 GAAAAAGAGAA-TGAAAAA
49514857 GAAAAAGAGAATGAAAAA
1 GAAAAAGAGAATGAAAAA
49514875 GA
1 GA
49514877 GCAAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (18 bp):
GAAAAAGAGAATGAAAAA
Found at i:49514954 original size:31 final size:31
Alignment explanation
Indices: 49514893--49514955 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
49514883 AGAGATTGAG
* *
49514893 AGTGAAAAAGGAATGTGAAACAGACAAGAAA
1 AGTGAAAAAGAAATGTGAAAAAGACAAGAAA
49514924 AGTGAAAAAGAAAT-TGAAGAAAGA-AGAGAAA
1 AGTGAAAAAGAAATGTGAA-AAAGACA-AGAAA
49514955 A
1 A
49514956 TGAGTTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.62, C:0.03, G:0.25, T:0.10
Consensus pattern (31 bp):
AGTGAAAAAGAAATGTGAAAAAGACAAGAAA
Found at i:49519706 original size:95 final size:95
Alignment explanation
Indices: 49519508--49519697 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
49519498 AATGCATGGT
49519508 ATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGACGATTACGTTTA
1 ATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGACGATTACGTTTA
49519573 CCATTTGATTTATTACTCGTGATTTATTCA
66 CCATTTGATTTATTACTCGTGATTTATTCA
49519603 ATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGACGATTACGTTTA
1 ATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGACGATTACGTTTA
49519668 CCATTTGATTTATTACTCGTGATTTATTCA
66 CCATTTGATTTATTACTCGTGATTTATTCA
49519698 TGGTTTGTGG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (95 bp):
ATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGACGATTACGTTTA
CCATTTGATTTATTACTCGTGATTTATTCA
Found at i:49520253 original size:33 final size:34
Alignment explanation
Indices: 49520216--49520287 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
49520206 GAGTTAGTTT
49520216 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
49520249 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
49520283 ATTAA
1 ATTAA
49520288 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:49520955 original size:64 final size:64
Alignment explanation
Indices: 49520853--49520980 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
49520843 AAATCAAGAT
*
49520853 TCACTTTCTTGTTTTCAAGAAAATCAAGAAACCGAATCTTGGTCCAATTTTACTGTTTTGAGCG
1 TCACTTTCTTGTTTTCAAGAAAATCAAGAAACCAAATCTTGGTCCAATTTTACTGTTTTGAGCG
* *
49520917 TCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGTCCAATTTTGCTGTTTTGAGCG
1 TCACTTTCTTGTTTTCAAGAAAATCAAGAAACCAAATCTTGGTCCAATTTTACTGTTTTGAGCG
49520981 ATTTCAAGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (64 bp):
TCACTTTCTTGTTTTCAAGAAAATCAAGAAACCAAATCTTGGTCCAATTTTACTGTTTTGAGCG
Found at i:49530662 original size:20 final size:20
Alignment explanation
Indices: 49530628--49530671 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
49530618 GTCTTAACCG
49530628 AATTAATTAGTTCTTAG-TTT
1 AATTAATTAGTTCTT-GTTTT
49530648 AATTAATT-GTGTCTTGTTTT
1 AATTAATTAGT-TCTTGTTTT
49530668 AATT
1 AATT
49530672 TAAGATGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (20 bp):
AATTAATTAGTTCTTGTTTT
Found at i:49534525 original size:23 final size:23
Alignment explanation
Indices: 49534464--49534525 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
49534454 TTGAACCATA
* ***
49534464 ACCATTTTGTACCAAATTGTATT
1 ACCATTTTGTAACAAATCACATT
*
49534487 ACCATTTCG-AATCAAATCACATT
1 ACCATTTTGTAA-CAAATCACATT
49534510 ACCATTTTGTAACAAA
1 ACCATTTTGTAACAAA
49534526 CCCAAAACCG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (23 bp):
ACCATTTTGTAACAAATCACATT
Found at i:49539240 original size:23 final size:23
Alignment explanation
Indices: 49539214--49539275 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
49539204 TTGAACCATA
* *
49539214 ACCATTTTGTACCAAAT-AGTATT
1 ACCATTTCGTACCAAATCA-CATT
*
49539237 ACCATTTCGAACCAAATCACATT
1 ACCATTTCGTACCAAATCACATT
*
49539260 ACCATTTCGTAACAAA
1 ACCATTTCGTACCAAA
49539276 CCCAAAACCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (23 bp):
ACCATTTCGTACCAAATCACATT
Found at i:49541008 original size:13 final size:13
Alignment explanation
Indices: 49540985--49541021 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
49540975 CCAAAGATTG
49540985 TTAAA-ACAACTT
1 TTAAAGACAACTT
49540997 TTAAAGACAACTT
1 TTAAAGACAACTT
*
49541010 TTAAAGAAAACT
1 TTAAAGACAACT
49541022 CAAGATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (13 bp):
TTAAAGACAACTT
Found at i:49554483 original size:20 final size:21
Alignment explanation
Indices: 49554449--49554507 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
49554439 AGGTGGAATT
* **
49554449 GAGCTC-AAGTGAGCTGATTG
1 GAGCTCGAATTGAGCTGAAGG
49554469 GAG-TCGAATTGAGCT-AAGG
1 GAGCTCGAATTGAGCTGAAGG
*
49554488 GAGCTGGAATTGAGCTGAAG
1 GAGCTCGAATTGAGCTGAAG
49554508 TCAGATTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 7 0.22
20 22 0.69
21 3 0.09
ACGTcount: A:0.29, C:0.12, G:0.37, T:0.22
Consensus pattern (21 bp):
GAGCTCGAATTGAGCTGAAGG
Found at i:49556047 original size:29 final size:30
Alignment explanation
Indices: 49555997--49556054 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
49555987 TAAGTGATAA
49555997 AAAAAGATAGAACGATGCAAAA-GAAAAAG
1 AAAAAGATAGAACGATGCAAAATGAAAAAG
**
49556026 AAAAAGATACGAGTGATG-AAAATGAAAAA
1 AAAAAGATA-GAACGATGCAAAATGAAAAA
49556055 AAGAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (30 bp):
AAAAAGATAGAACGATGCAAAATGAAAAAG
Found at i:49560884 original size:12 final size:12
Alignment explanation
Indices: 49560867--49560902 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
49560857 TAAATTCAAA
49560867 TTTTTTTAAACT
1 TTTTTTTAAACT
*
49560879 TTTTTTTAAAAT
1 TTTTTTTAAACT
*
49560891 TTTTTTGAAACT
1 TTTTTTTAAACT
49560903 ACGATTACGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (12 bp):
TTTTTTTAAACT
Found at i:49570353 original size:20 final size:20
Alignment explanation
Indices: 49570330--49570370 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
49570320 AAAACTAGAA
49570330 ACAATTAATTAAGTTAAGAC
1 ACAATTAATTAAGTTAAGAC
**
49570350 ACAATTAATTCGGTTAAGAC
1 ACAATTAATTAAGTTAAGAC
49570370 A
1 A
49570371 AGACATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
ACAATTAATTAAGTTAAGAC
Found at i:49587851 original size:12 final size:12
Alignment explanation
Indices: 49587834--49587860 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
49587824 ATTCCGAAGT
49587834 ATATATATATAC
1 ATATATATATAC
49587846 ATATATATATAC
1 ATATATATATAC
49587858 ATA
1 ATA
49587861 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:49588419 original size:27 final size:28
Alignment explanation
Indices: 49588307--49588432 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
49588297 CATGAGATTG
* * * *
49588307 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
* *
49588336 ACACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
49588364 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
49588392 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
49588419 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
49588433 GACTTAATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.27
28 48 0.55
29 16 0.18
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:49588421 original size:55 final size:57
Alignment explanation
Indices: 49588307--49588432 Score: 175
Period size: 55 Copynumber: 2.2 Consensus size: 57
49588297 CATGAGATTG
* *
49588307 GCACTAAGTGTGCGGGTTTAAATTGTACAACACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACAACACTAAGTGTGCAAGTTTGATTATATA
* * * *
49588364 GCACTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACAACACTAAGTGTGCAAGTTTGATTATATA
*
49588419 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
49588433 GACTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 24 0.39
56 20 0.32
57 18 0.29
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTATACAACACTAAGTGTGCAAGTTTGATTATATA
Found at i:49588443 original size:27 final size:27
Alignment explanation
Indices: 49588337--49588445 Score: 130
Period size: 28 Copynumber: 4.0 Consensus size: 27
49588327 AATTGTACAA
* *
49588337 CACTAAGTGTGCAAGTTTGATTATATAG
1 CACTAAGTGTGCGA-CTTGATTATATAG
*
49588365 CACTAAGTGTGCGAGTTTGATTATATAG
1 CACTAAGTGTGCGA-CTTGATTATATAG
*
49588393 CACTAAGTGTGCGAGTTGATTATATAG
1 CACTAAGTGTGCGACTTGATTATATAG
* *
49588420 CACTGAGTGTGCGGACTT-AATATATA
1 CACTAAGTGTGC-GACTTGATTATATA
49588446 CTTTTGAATC
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
27 30 0.40
28 45 0.60
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (27 bp):
CACTAAGTGTGCGACTTGATTATATAG
Found at i:49590590 original size:41 final size:41
Alignment explanation
Indices: 49590545--49590662 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 41
49590535 AAAACGCCGC
* * *
49590545 AAAAGGTTAGAGCTATAGTGGCGTTTTTTCATAAACACTGT
1 AAAAGGTTAGAGCTATAGCGACATTTTTTCATAAACACTGT
***
49590586 AAAAGGTTAGAGCTATAGCGACATTTTTTCATAAACACCAC
1 AAAAGGTTAGAGCTATAGCGACATTTTTTCATAAACACTGT
* * * *
49590627 AAACGATTGGAGCTATAGCGGCATTTTTATCATAAA
1 AAAAGGTTAGAGCTATAGCGACATTTTT-TCATAAA
49590663 TGTTGCAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 59 0.89
42 7 0.11
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (41 bp):
AAAAGGTTAGAGCTATAGCGACATTTTTTCATAAACACTGT
Found at i:49591660 original size:19 final size:19
Alignment explanation
Indices: 49591636--49591675 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
49591626 TCAAATTTGA
49591636 GGCCATCCATCCATTGGGT
1 GGCCATCCATCCATTGGGT
49591655 GGCCATCCATCCATTGGGT
1 GGCCATCCATCCATTGGGT
49591674 GG
1 GG
49591676 TATAGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (19 bp):
GGCCATCCATCCATTGGGT
Found at i:49592185 original size:21 final size:21
Alignment explanation
Indices: 49592159--49592203 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
49592149 ATGAAAACAT
*
49592159 TATAAGTAAACCATGTTATTA
1 TATAAGTAAACCAGGTTATTA
49592180 TATAAGTAAACCAGGTTATTA
1 TATAAGTAAACCAGGTTATTA
49592201 TAT
1 TAT
49592204 CTTTGTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
TATAAGTAAACCAGGTTATTA
Found at i:49593563 original size:66 final size:65
Alignment explanation
Indices: 49593461--49593598 Score: 145
Period size: 66 Copynumber: 2.1 Consensus size: 65
49593451 ACAAATTGCT
** * * *
49593461 CAACTTAAAGCGGAGGAAGCATTGGGAGAAGCAGAGGCTCAA-AGAAAATATGATGAACTCTAGC
1 CAACTTAAAGCGGAGGAAGCAGCGGGAGAAGCAGAGG--CAACAAAAAATATGACGAACTCCAGC
49593525 TA
64 TA
* * * *
49593527 CAACTTAAAGCGGAGGCAGTAGCGAGG-GAAGTAGAGGCAAGCAAAAAATATGACGAACTCCAGT
1 CAACTTAAAGCGGAGGAAGCAGCG-GGAGAAGCAGAGGCAA-CAAAAAATATGACGAACTCCAGC
49593591 TA
64 TA
49593593 CAACTT
1 CAACTT
49593599 CAGAATATGA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
64 3 0.05
66 55 0.92
67 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.16
Consensus pattern (65 bp):
CAACTTAAAGCGGAGGAAGCAGCGGGAGAAGCAGAGGCAACAAAAAATATGACGAACTCCAGCTA
Found at i:49593988 original size:15 final size:15
Alignment explanation
Indices: 49593970--49594000 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49593960 CACTAAAAGC
49593970 GCCTCTAAAGGTCAT
1 GCCTCTAAAGGTCAT
*
49593985 GCCTCTAAGGGTCAT
1 GCCTCTAAAGGTCAT
49594000 G
1 G
49594001 TTCTTTAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (15 bp):
GCCTCTAAAGGTCAT
Found at i:49594057 original size:43 final size:43
Alignment explanation
Indices: 49593989--49594132 Score: 157
Period size: 43 Copynumber: 3.4 Consensus size: 43
49593979 GGTCATGCCT
* * *
49593989 CTAAGGGTCATGTTCTTTAGAGGCGTTTGTGGGAAAAGCGCCA
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCA
*
49594032 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCA
** ** ** * *
49594075 CTAAAAATTTTGTTCTTTAGCGGTATTT-T-ATGAGAAGCGCCT
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGA-GAAAAGCGCCA
49594117 CTAAAGGTCATGTTCT
1 CTAAAGGTCATGTTCT
49594133 ATAGTGATGT
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 22 0.26
43 61 0.73
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCA
Found at i:49594474 original size:22 final size:22
Alignment explanation
Indices: 49594441--49594496 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
49594431 TTTTATTTAT
*
49594441 TAAAATATATTTTTAAAAATT-
1 TAAAGTATATTTTTAAAAATTC
* *
49594462 TGAAAGTATATTTTTATATATTC
1 T-AAAGTATATTTTTAAAAATTC
49594485 TAAAGTATATTT
1 TAAAGTATATTT
49594497 GTTAGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TAAAGTATATTTTTAAAAATTC
Found at i:49595463 original size:29 final size:28
Alignment explanation
Indices: 49595422--49595477 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
49595412 GAATTTGACA
* * * *
49595422 TTTTTTCTTAATTTAGTATCTAAACTTT
1 TTTTTTCTCAATTCAATACCTAAACTTT
49595450 TTTTTTGCTCAATTCAATACCTAAACTT
1 TTTTTT-CTCAATTCAATACCTAAACTT
49595478 GACACTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTTTTCTCAATTCAATACCTAAACTTT
Found at i:49595509 original size:60 final size:60
Alignment explanation
Indices: 49595416--49595576 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 60
49595406 GTACTTGAAT
* *
49595416 TTGACATTTTTTCTTAATTT-AGTA-TCTAAACTTTTTTTTTGCTCAATTCAATACCTAAAC
1 TTGACATTTTTTCTTAATTTGA-TACT-TAAACTTTTTTTTAGCCCAATTCAATACCTAAAC
* * *** *
49595476 TTGACACTTTTTCTTAATTTGATACTTAAACTTTTTTTGAGCCCAATTTGGTACCTGAAC
1 TTGACATTTTTTCTTAATTTGATACTTAAACTTTTTTTTAGCCCAATTCAATACCTAAAC
* * * *
49595536 TTGACATTTTTTCCTAATTTGGTACTTGAGCTTTTTTTTAG
1 TTGACATTTTTTCTTAATTTGATACTTAAACTTTTTTTTAG
49595577 GTTCAATTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
60 83 0.98
61 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50
Consensus pattern (60 bp):
TTGACATTTTTTCTTAATTTGATACTTAAACTTTTTTTTAGCCCAATTCAATACCTAAAC
Found at i:49605115 original size:29 final size:29
Alignment explanation
Indices: 49605073--49605131 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
49605063 ACAATTGACC
*
49605073 ATTGTCTAATACCACCATTTAAACTGCAT
1 ATTGTCTAATACCACCATTTAAACCGCAT
49605102 ATTGTCTAATACCACCATTTAAACCGCAT
1 ATTGTCTAATACCACCATTTAAACCGCAT
49605131 A
1 A
49605132 CATGCTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
ATTGTCTAATACCACCATTTAAACCGCAT
Found at i:49612643 original size:23 final size:23
Alignment explanation
Indices: 49612617--49612668 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
49612607 GGTGGAGAGC
* * *
49612617 TTATTGGCACTTTGGTGTGATTT
1 TTATTGGAACTTTGATGTGATTG
*
49612640 TTATTAGAACTTTGATGTGATTG
1 TTATTGGAACTTTGATGTGATTG
49612663 TTATTG
1 TTATTG
49612669 TCATTTCGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (23 bp):
TTATTGGAACTTTGATGTGATTG
Found at i:49612886 original size:21 final size:19
Alignment explanation
Indices: 49612862--49612913 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
49612852 TTGAGTATGT
*
49612862 TAATTGATATTGAATATTGAA
1 TAATTCATATTG-AT-TTGAA
*
49612883 TAATTCATGTTGATTTGAA
1 TAATTCATATTGATTTGAA
49612902 TAATTTCATATT
1 TAA-TTCATATT
49612914 AATGTTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 9 0.33
21 10 0.37
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (19 bp):
TAATTCATATTGATTTGAA
Found at i:49616397 original size:45 final size:43
Alignment explanation
Indices: 49616310--49616492 Score: 180
Period size: 45 Copynumber: 4.2 Consensus size: 43
49616300 AATAATAACA
* * *
49616310 GATACACGGTGG-ATCAGCACATAGCACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACATAGAACCA-CCTTATAATCAAT
* * *
49616353 GATACTCGGTGAAATTAGCACATAGTAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACATAG-AACCACCTT-ATAATCAAT
* *
49616398 -AGTACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACATAG-AACCACC-TTATAATCAAT
49616443 GATACCCGGTGGAATCAGCAC----AACCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACATAGAACCACC-TTATAATCAAT
*
49616483 GGTACCCGGT
1 GATACCCGGT
49616493 ACACGTAGTA
Statistics
Matches: 121, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
40 28 0.23
43 10 0.08
44 16 0.13
45 64 0.53
46 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
GATACCCGGTGGAATCAGCACATAGAACCACCTTATAATCAAT
Found at i:49619004 original size:16 final size:15
Alignment explanation
Indices: 49618975--49619003 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49618965 GGGTATAGTA
49618975 AAATATTTTAAAAAT
1 AAATATTTTAAAAAT
49618990 AAATATTTTAAAAA
1 AAATATTTTAAAAA
49619004 AAGAAACACA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTTTAAAAAT
Found at i:49630244 original size:19 final size:19
Alignment explanation
Indices: 49630222--49630259 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49630212 TCAATCATTC
49630222 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
49630241 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
49630260 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:49632122 original size:13 final size:13
Alignment explanation
Indices: 49632103--49632166 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
49632093 TAAACCAATA
*
49632103 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
49632116 TTCTT-AAAAGCAC
1 TT-TTCAAAAGCAC
* *
49632129 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
49632142 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
49632155 TTTTCAAAAGCA
1 TTTTCAAAAGCA
49632167 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
12 2 0.04
13 41 0.91
14 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:49633067 original size:44 final size:43
Alignment explanation
Indices: 49632989--49633116 Score: 120
Period size: 42 Copynumber: 3.0 Consensus size: 43
49632979 ATGGCAGTAC
* * *
49632989 ATGATTTCGTATAGGACCATGTCT-GGG-ATGTTGGCATCGATTT
1 ATGATTTCGTGTAAGACCATGTCTAGGGCA--TTGGCATCGATAT
49633032 GA-GATTTACGTGTAAGACCATGTCTAGGGCATTGGCATCG-TAT
1 -ATGATTT-CGTGTAAGACCATGTCTAGGGCATTGGCATCGATAT
* * * * *
49633075 ATGATTTTGTGTAAGACCCTATCTAGGACAGTGGCATCGATA
1 ATGATTTCGTGTAAGACCATGTCTAGGGCATTGGCATCGATA
49633117 GTTGATCACA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
42 28 0.39
43 14 0.20
44 25 0.35
45 3 0.04
46 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
ATGATTTCGTGTAAGACCATGTCTAGGGCATTGGCATCGATAT
Found at i:49639901 original size:10 final size:11
Alignment explanation
Indices: 49639869--49639901 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
49639859 TCAGAAAAGA
49639869 TATATGAAAATT
1 TATAT-AAAATT
49639881 TATATAAAATT
1 TATATAAAATT
49639892 TATA-AAAATT
1 TATATAAAATT
49639902 AAAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.29
11 10 0.48
12 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TATATAAAATT
Found at i:49640241 original size:20 final size:20
Alignment explanation
Indices: 49640200--49640243 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
49640190 TTTTTGACAA
*
49640200 TTTTTTGTATTTTATCTTTT
1 TTTTTTGTATTTTATCTATT
* *
49640220 TTTTTTGTGTTTTATGTATT
1 TTTTTTGTATTTTATCTATT
49640240 TTTT
1 TTTT
49640244 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (20 bp):
TTTTTTGTATTTTATCTATT
Found at i:49640579 original size:15 final size:16
Alignment explanation
Indices: 49640555--49640593 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
49640545 TGAATTTAAT
49640555 TTATTTTAAA-AA-TA
1 TTATTTTAAATAACTA
49640569 TTATATTTAAATAACTA
1 TTAT-TTTAAATAACTA
49640586 TTATTTTA
1 TTATTTTA
49640594 TTTTTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 6 0.27
17 6 0.27
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTTTAAATAACTA
Found at i:49642031 original size:79 final size:79
Alignment explanation
Indices: 49641900--49642057 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
49641890 AAGACAATCC
*
49641900 AGTACTTGATTGGATCGGGAATGGTAAGACTAACATACTTGCCATACAGTTTAGGAGATTGATTG
1 AGTACTTGATTGGATCGGGAATGGTAAGAATAACATACTTGCCATACAGTTTAGGAGATTGATTG
*
49641965 AGTGATTGACATTT
66 AGTGATCGACATTT
49641979 AGTACTTGATTGGATCGGGAATGGTAAGAATAACATACTTGCCATACAGTTTAGGAGATTGATTG
1 AGTACTTGATTGGATCGGGAATGGTAAGAATAACATACTTGCCATACAGTTTAGGAGATTGATTG
49642044 AGTGATCGACATTT
66 AGTGATCGACATTT
49642058 CATTACTCTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (79 bp):
AGTACTTGATTGGATCGGGAATGGTAAGAATAACATACTTGCCATACAGTTTAGGAGATTGATTG
AGTGATCGACATTT
Found at i:49644509 original size:42 final size:42
Alignment explanation
Indices: 49644429--49644550 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
49644419 TAGTACATAG
*
49644429 CAAAACAATCGATTGGAAAGT-AAAACAATCAATTGAAACAA
1 CAAAACAATCGATTGTAAAGTGAAAACAATCAATTGAAACAA
*
49644470 CAAAACAATCGATTGTAAAGTGAAAACAATCAATTGAAACAG
1 CAAAACAATCGATTGTAAAGTGAAAACAATCAATTGAAACAA
*
49644512 CAAAACAATCGATTGTAAAGTGAAAACAATCGATTGAAA
1 CAAAACAATCGATTGTAAAGTGAAAACAATCAATTGAAA
49644551 AGAATCATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 20 0.26
42 57 0.74
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (42 bp):
CAAAACAATCGATTGTAAAGTGAAAACAATCAATTGAAACAA
Found at i:49644537 original size:21 final size:21
Alignment explanation
Indices: 49644429--49644552 Score: 137
Period size: 21 Copynumber: 6.0 Consensus size: 21
49644419 TAGTACATAG
*
49644429 CAAAACAATCGATTGGAAAGT
1 CAAAACAATCGATTGAAAAGT
* *
49644450 -AAAACAATCAATTGAAACA-A
1 CAAAACAATCGATTGAAA-AGT
*
49644470 CAAAACAATCGATTGTAAAGT
1 CAAAACAATCGATTGAAAAGT
* *
49644491 GAAAACAATCAATTGAAACAG-
1 CAAAACAATCGATTGAAA-AGT
*
49644512 CAAAACAATCGATTGTAAAGT
1 CAAAACAATCGATTGAAAAGT
*
49644533 GAAAACAATCGATTGAAAAG
1 CAAAACAATCGATTGAAAAG
49644553 AATCATTTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
20 18 0.21
21 64 0.76
22 2 0.02
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.19
Consensus pattern (21 bp):
CAAAACAATCGATTGAAAAGT
Found at i:49649568 original size:21 final size:20
Alignment explanation
Indices: 49649529--49649577 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
49649519 GAAATAATTG
* *
49649529 ATTGAAAAACATAACAATCA
1 ATTGAAAAACAAAAAAATCA
*
49649549 ATTGAAACAACAAAAAAATCG
1 ATTGAAA-AACAAAAAAATCA
49649570 ATTGAAAA
1 ATTGAAAA
49649578 GAATCATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.61, C:0.12, G:0.08, T:0.18
Consensus pattern (20 bp):
ATTGAAAAACAAAAAAATCA
Found at i:49652707 original size:25 final size:25
Alignment explanation
Indices: 49652663--49652736 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
49652653 AGGGATTATC
* *
49652663 GATTCTTAGCTCGTATGAGCTTACT
1 GATTCATAGCTCGTATGAGCATACT
*
49652688 GA-TCTATAGCTCGTAAGAGCATACT
1 GATTC-ATAGCTCGTATGAGCATACT
49652713 GATTCATAGCTCGTATGAGCATAC
1 GATTCATAGCTCGTATGAGCATAC
49652737 ATGTACAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.05
25 39 0.91
26 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (25 bp):
GATTCATAGCTCGTATGAGCATACT
Found at i:49652924 original size:30 final size:28
Alignment explanation
Indices: 49652890--49652945 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
49652880 GAAATACATG
49652890 GAAATGAT-ATTACATGATATATTGAAACGT
1 GAAATGATGA-TACATG-TATA-TGAAACGT
*
49652920 GAAATGGTGATACATGTATATGAAAC
1 GAAATGATGATACATGTATATGAAAC
49652946 TTGCTTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 4 0.17
30 13 0.54
31 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (28 bp):
GAAATGATGATACATGTATATGAAACGT
Found at i:49657204 original size:49 final size:49
Alignment explanation
Indices: 49657130--49657264 Score: 216
Period size: 49 Copynumber: 2.8 Consensus size: 49
49657120 GATAATAACA
* *
49657130 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCCTGCAC
1 TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGATGTTTCCTGCAC
*
49657179 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGATGTTTCCTGCAC
1 TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGATGTTTCCTGCAC
* * *
49657228 TGCCAAAGCCATATCCCAGATATAGTTTTACATGGGA
1 TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGA
49657265 GTTCTCATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 79 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (49 bp):
TGCCAAAGCCATATCCTAGATATGGTCTTACATGGGATGTTTCCTGCAC
Found at i:49657396 original size:56 final size:49
Alignment explanation
Indices: 49657129--49657417 Score: 156
Period size: 49 Copynumber: 5.7 Consensus size: 49
49657119 TGATAATAAC
* ** *
49657129 ATGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTT--CCTGCA
1 ATGCC-AAGCCATGTCCCAGACATGGTCTTACATGGGACCTTTAATCT-CA
* * * * ** *
49657178 CTGCCAATGCCATATCCTAGATATGGTCTTACATGGGATGTTT--CCTGCA
1 ATGCCAA-GCCATGTCCCAGACATGGTCTTACATGGGACCTTTAATCT-CA
* * * * * * * * *
49657227 CTGCCAAAGCCATATCCCAGATATAGTTTTACATGGGA-GTTCTCATATCG
1 ATGCC-AAGCCATGTCCCAGACATGGTCTTACATGGGACCTT-TAATCTCA
* ** *
49657277 GTGCCCAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCA
1 ATG-CCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTTTAATCTCA
* *
49657327 ATGCCAACACCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAA
1 ATGCCAA-GCCATGTCCCAGACATGGTCTTACATGGGACCT-T--TAATCTC-A
* *
49657381 TGATGCCAATGCCATGTCCCATACATGGTTTTACATG
1 --ATGCCAA-GCCATGTCCCAGACATGGTCTTACATG
49657418 AGATCTCATT
Statistics
Matches: 196, Mismatches: 30, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
48 5 0.03
49 80 0.41
50 68 0.35
51 6 0.03
53 6 0.03
54 1 0.01
56 30 0.15
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTTTAATCTCA
Found at i:49657731 original size:23 final size:23
Alignment explanation
Indices: 49657699--49657743 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
49657689 CCGATTTGCT
*
49657699 CCCTCCGTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTG
*
49657722 CCCTCTGTTTATTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCT
49657744 TTTCTGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.31, G:0.07, T:0.60
Consensus pattern (23 bp):
CCCTCCGTTTATTTTCTTTTCTG
Found at i:49657762 original size:61 final size:61
Alignment explanation
Indices: 49657685--49657847 Score: 227
Period size: 66 Copynumber: 2.6 Consensus size: 61
49657675 CCTTCTAGCC
*
49657685 TCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
1 TCTGTCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
* * *
49657746 TCTGTCGATTTTCTCCCTTCGTTTCTTTTCTTTTCTTTTCTGTCCTCTGTTTATTTTCTTTTCTT
1 TCTGTCGATTTGCTCCC-TC----CGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTT
49657811 T
61 T
**
49657812 TCTGTCGATTTGCTCCCTTTGTTTCTTTTCTTTTCT
1 TCTGTCGATTTGCTCCCTCCGTTTCTTTTCTTTTCT
49657848 TTTCTGCCGA
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
61 30 0.34
62 2 0.02
65 1 0.01
66 56 0.63
ACGTcount: A:0.03, C:0.26, G:0.09, T:0.61
Consensus pattern (61 bp):
TCTGTCGATTTGCTCCCTCCGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
Found at i:49657775 original size:38 final size:37
Alignment explanation
Indices: 49657715--49657860 Score: 148
Period size: 38 Copynumber: 4.1 Consensus size: 37
49657705 GTTTCTTTTC
49657715 TTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGTCGA
1 TTTTCT-CCCTC-GTTTATTTTCTTTTCTTTTCTGTCGA
*
49657754 TTTTCTCCCTTCGTTTCTTTTCTTTTCTTTTCTGTC--
1 TTTTCTCCC-TCGTTTATTTTCTTTTCTTTTCTGTCGA
49657790 ----CT--CT-GTTTATTTTCTTTTCTTTTCTGTCGA
1 TTTTCTCCCTCGTTTATTTTCTTTTCTTTTCTGTCGA
* * * *
49657820 TTTGCTCCCTTTGTTTCTTTTCTTTTCTTTTCTGCCGA
1 TTTTCTCCC-TCGTTTATTTTCTTTTCTTTTCTGTCGA
49657858 TTT
1 TTT
49657861 GCCAGTTTCT
Statistics
Matches: 92, Mismatches: 4, Indels: 23
0.77 0.03 0.19
Matches are distributed among these distances:
28 23 0.25
29 1 0.01
30 1 0.01
32 2 0.02
34 2 0.02
36 1 0.01
37 1 0.01
38 53 0.58
39 8 0.09
ACGTcount: A:0.03, C:0.24, G:0.09, T:0.64
Consensus pattern (37 bp):
TTTTCTCCCTCGTTTATTTTCTTTTCTTTTCTGTCGA
Found at i:49657777 original size:5 final size:5
Alignment explanation
Indices: 49657767--49657814 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
49657757 TCTCCCTTCG
* *
49657767 TTTCT TTTCT TTTCT TTTCT GTCCTCT GTTTAT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT -T-TTCT -TTTCT TTTCT TTTCT TTTCT
49657815 GTCGATTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 29 0.78
6 3 0.08
7 5 0.14
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTCT
Found at i:49657801 original size:66 final size:66
Alignment explanation
Indices: 49657706--49657855 Score: 273
Period size: 66 Copynumber: 2.3 Consensus size: 66
49657696 GCTCCCTCCG
*
49657706 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTTCTCCCTTCGTTTC
1 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTGCTCCCTTCGTTTC
49657771 T
66 T
* *
49657772 TTTCTTTTCTTTTCTGTCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTGCTCCCTTTGTTTC
1 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTGCTCCCTTCGTTTC
49657837 T
66 T
49657838 TTTCTTTTCTTTTCTGCC
1 TTTCTTTTCTTTTCTGCC
49657856 GATTTGCCAG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 80 1.00
ACGTcount: A:0.03, C:0.25, G:0.08, T:0.65
Consensus pattern (66 bp):
TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTGCTCCCTTCGTTTC
T
Found at i:49657869 original size:33 final size:35
Alignment explanation
Indices: 49657794--49657870 Score: 86
Period size: 38 Copynumber: 2.2 Consensus size: 35
49657784 TCTGTCCTCT
* * *
49657794 GTTTATTTTCTTTTCTTTTCTGTCGATTTGCTCCCTTT
1 GTTTCTTTTCTTTTCTTTTCTGCCGATTTG--CCC-TA
49657832 GTTTCTTTTCTTTTCTTTTCTGCCGATTTG-CC-A
1 GTTTCTTTTCTTTTCTTTTCTGCCGATTTGCCCTA
49657865 GTTTCT
1 GTTTCT
49657871 GCTGATTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.17
35 2 0.06
38 28 0.78
ACGTcount: A:0.05, C:0.22, G:0.12, T:0.61
Consensus pattern (35 bp):
GTTTCTTTTCTTTTCTTTTCTGCCGATTTGCCCTA
Found at i:49657880 original size:66 final size:66
Alignment explanation
Indices: 49657706--49657881 Score: 167
Period size: 66 Copynumber: 2.7 Consensus size: 66
49657696 GCTCCCTCCG
* ** * ** * *
49657706 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTTCTCCCTTCGTTTC
1 TTTCTTTTCTTTTCTGTCCTCTGTCCAGTTTCTGCTCATTTCTGTCGATTTGCTCCCTTCGTTTC
49657771 T
66 T
** * ** * *
49657772 TTTCTTTTCTTTTCTGTCCTCTGTTTATTTTCTTTTCTTTTCTGTCGATTTGCTCCCTTTGTTTC
1 TTTCTTTTCTTTTCTGTCCTCTGTCCAGTTTCTGCTCATTTCTGTCGATTTGCTCCCTTCGTTTC
49657837 T
66 T
* *
49657838 TTTCTTTTCTTTTCTG-CCGATTTG-CCAGTTTCTGCTGATTTCTG
1 TTTCTTTTCTTTTCTGTCC--TCTGTCCAGTTTCTGCTCATTTCTG
49657882 AGTTATTGCA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
65 2 0.02
66 92 0.95
67 3 0.03
ACGTcount: A:0.04, C:0.24, G:0.10, T:0.62
Consensus pattern (66 bp):
TTTCTTTTCTTTTCTGTCCTCTGTCCAGTTTCTGCTCATTTCTGTCGATTTGCTCCCTTCGTTTC
T
Found at i:49658271 original size:42 final size:39
Alignment explanation
Indices: 49658204--49658318 Score: 128
Period size: 42 Copynumber: 2.9 Consensus size: 39
49658194 AATTTTTGGA
*
49658204 TTAGGCTTAAGAATTGATGATTGTTGTTTGTTGATAAGG
1 TTAGGCTTAAGAATTGATGACTGTTGTTTGTTGATAAGG
* * *
49658243 TGCCTTGGCTTAAGAATTGATGACTGTTGTCTGTTG-T-TGG
1 T---TAGGCTTAAGAATTGATGACTGTTGTTTGTTGATAAGG
*
49658283 TTAGGCTTAAGAAATGCAT-ACTGTTGTTTGTTGATA
1 TTAGGCTTAAGAATTG-ATGACTGTTGTTTGTTGATA
49658319 GTATTGTTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
37 26 0.41
38 3 0.05
39 1 0.02
40 3 0.05
41 1 0.02
42 29 0.46
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.43
Consensus pattern (39 bp):
TTAGGCTTAAGAATTGATGACTGTTGTTTGTTGATAAGG
Found at i:49660702 original size:47 final size:48
Alignment explanation
Indices: 49660651--49660783 Score: 152
Period size: 47 Copynumber: 2.8 Consensus size: 48
49660641 ATTAAATTAA
*
49660651 ATTTAATATTAATTATTTTAAATTGTATAAATTCATATAAGA-AATTT
1 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGATAATTT
*
49660698 ATTTAA-ATT-ATATATTATTAAATTATACAAATTCATATAAGATAATTT
1 ATTTAATATTAAT-TATT-TTAAATTATATAAATTCATATAAGATAATTT
* *
49660746 A-TTAGT-TATAATTATTTTAAATTTTATTAAA-TCATATA
1 ATTTAATAT-TAATTATTTTAAATTATA-TAAATTCATATA
49660784 TTTTAATTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
45 2 0.03
46 7 0.09
47 49 0.66
48 14 0.19
49 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (48 bp):
ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGATAATTT
Found at i:49660747 original size:24 final size:24
Alignment explanation
Indices: 49660679--49660747 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
49660669 TAAATTGTAT
**
49660679 AAATTCATATAAGA-AATTTATTT
1 AAATTCATATAAGATAATTTATAC
** *
49660702 AAATT-ATATATTATTAAATTATAC
1 AAATTCATATAAGA-TAATTTATAC
49660726 AAATTCATATAAGATAATTTAT
1 AAATTCATATAAGATAATTTAT
49660748 TAGTTATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
22 6 0.17
23 5 0.14
24 18 0.51
25 6 0.17
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (24 bp):
AAATTCATATAAGATAATTTATAC
Found at i:49660800 original size:16 final size:17
Alignment explanation
Indices: 49660766--49660806 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
49660756 ATTATTTTAA
49660766 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAA-CATAT
49660783 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAACATAT
49660799 A-TTTAATT
1 ATTTTAATT
49660807 TTAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 5 0.22
18 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAATTAAACATAT
Found at i:49660877 original size:66 final size:65
Alignment explanation
Indices: 49660807--49661118 Score: 176
Period size: 61 Copynumber: 5.1 Consensus size: 65
49660797 ATATTTAATT
49660807 TTAATTATTTAAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
1 TTAATTATTTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
49660872 A
65 A
* * * * **
49660873 TTAATTA-TTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TTAAT
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
49660926 A
65 A
* * *
49660927 ATAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAA
1 TTAATTAT-TTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAA
49660991 TA
64 TA
* * * * * * * * **
49660993 TTGATTA-TTAAGAATT-TTATTA-A--ATTATATATTTTAATTAT-AATATATTTA-ATAATTA
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATT-TGAGTAAATTCATATAAGAA
*
49661051 TG
64 TA
*
49661053 TT-A--ATTT---A-TA-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
*
49661110 TTGATTATT
1 TTAATTATT
49661119 AAGAATTTTA
Statistics
Matches: 181, Mismatches: 37, Indels: 62
0.65 0.13 0.22
Matches are distributed among these distances:
53 5 0.03
54 15 0.08
55 7 0.04
56 27 0.15
57 12 0.07
58 4 0.02
59 11 0.06
60 19 0.10
61 30 0.17
62 2 0.01
63 4 0.02
64 11 0.06
65 11 0.06
66 23 0.13
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
Found at i:49660889 original size:120 final size:120
Alignment explanation
Indices: 49660765--49661174 Score: 702
Period size: 120 Copynumber: 3.4 Consensus size: 120
49660755 AATTATTTTA
* * * *
49660765 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATTTTAATTAT-TTAAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTT-AATTTATATTT
* *
49660829 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
49660885 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTAATTTATATTTT
49660950 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
49661005 AATTTTATTAAATTATATATTTTAATTATAATATATTT-A--ATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTAATTTATATTTT
49661067 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
49661122 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTT
49661175 TAAATATGAT
Statistics
Matches: 277, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
117 115 0.42
118 1 0.00
119 1 0.00
120 158 0.57
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:49660925 original size:15 final size:15
Alignment explanation
Indices: 49660890--49660941 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
49660880 TTAAGAATTT
*
49660890 TATTAAATTAT-ATA
1 TATTTAATTATAATA
49660904 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
49660918 TATTTAATAATAAT-
1 TATTTAATTATAATA
49660932 TATGTTAATT
1 TAT-TTAATT
49660942 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:49661151 original size:18 final size:18
Alignment explanation
Indices: 49661123--49661171 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
49661113 ATTATTAAGA
49661123 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
49661140 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
49661156 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
49661172 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:49661157 original size:16 final size:16
Alignment explanation
Indices: 49661123--49661177 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
49661113 ATTATTAAGA
49661123 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
49661140 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
49661156 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
49661170 ATGTTTAA
1 AT-TTTAA
49661178 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:49661386 original size:44 final size:45
Alignment explanation
Indices: 49661321--49661411 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
49661311 ACCTCTATTC
* * *
49661321 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
49661365 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
49661410 CA
1 CA
49661412 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:49661426 original size:17 final size:16
Alignment explanation
Indices: 49661392--49661444 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
49661382 GATTAGCTAT
49661392 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49661408 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
49661425 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49661441 TACA
1 TACA
49661445 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:49665964 original size:21 final size:21
Alignment explanation
Indices: 49665938--49665991 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
49665928 ACCCTTAAAT
*
49665938 GCATCCACAACA-AAGTTAGAG
1 GCATCCACAACAGAA-TCAGAG
* *
49665959 GCATCCACACCAGAATCAGAT
1 GCATCCACAACAGAATCAGAG
49665980 GCATCCACAACA
1 GCATCCACAACA
49665992 CTCTTCAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.41, C:0.31, G:0.15, T:0.13
Consensus pattern (21 bp):
GCATCCACAACAGAATCAGAG
Found at i:49672716 original size:14 final size:14
Alignment explanation
Indices: 49672697--49672725 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49672687 GGTGTTCTAG
49672697 AATGAATGAACAGA
1 AATGAATGAACAGA
49672711 AATGAATGAACAGA
1 AATGAATGAACAGA
49672725 A
1 A
49672726 CGACCATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AATGAATGAACAGA
Found at i:49679814 original size:26 final size:26
Alignment explanation
Indices: 49679784--49679835 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
49679774 AAAATTAATG
*
49679784 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATAGAATGTT
49679810 CTAATTAAACTGAAATATAGAATGTT
1 CTAATTAAACTGAAATATAGAATGTT
49679836 TTCTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (26 bp):
CTAATTAAACTGAAATATAGAATGTT
Found at i:49681634 original size:12 final size:12
Alignment explanation
Indices: 49681617--49681642 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49681607 CAAAACAGGA
49681617 TTTTAGCGGCGT
1 TTTTAGCGGCGT
49681629 TTTTAGCGGCGT
1 TTTTAGCGGCGT
49681641 TT
1 TT
49681643 GGACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:49681796 original size:41 final size:41
Alignment explanation
Indices: 49681739--49682020 Score: 350
Period size: 41 Copynumber: 6.9 Consensus size: 41
49681729 GATTTTTTGG
* * * * *
49681739 GGGCATTTAGTGGCGTTTTTTAAAAAGCGCCGCAAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
49681780 GGGCCTTTAGCAGCGTTTTTTAAAAACCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
49681821 GGGCCTTTAGCGGCGGTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
49681862 GAGCCTTTAGCGGCATTTTTGAATAAGAGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
49681903 GGGCCTTTAGCAGCGTTTTTGAAAAAGCACTGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
49681944 GGGCTTTTAGCGGCGTTGTTGAAAAAGCGCAGCTAATACTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
49681985 -GACCTTTAGCGGCGTTTTTGGAAAAGCGCTGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
49682021 AATAATAAAA
Statistics
Matches: 208, Mismatches: 33, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 0.15
41 177 0.85
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:49686939 original size:13 final size:13
Alignment explanation
Indices: 49686921--49686950 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49686911 ACTTCCTAGG
49686921 TAATGCTATTCTT
1 TAATGCTATTCTT
49686934 TAATGCTATTCTT
1 TAATGCTATTCTT
49686947 TAAT
1 TAAT
49686951 CTTAACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (13 bp):
TAATGCTATTCTT
Found at i:49687987 original size:26 final size:26
Alignment explanation
Indices: 49687957--49688008 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
49687947 AAAATTAATG
49687957 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49687983 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49688009 TTCTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:49689161 original size:43 final size:43
Alignment explanation
Indices: 49689112--49689234 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 43
49689102 AAAGGTTATA
* *
49689112 TTTTTAGCGGCGCTTGTGGAAAAAGCGTCGCTAAAGGTCATGG
1 TTTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
* ** * *
49689155 TTTTTAGCGACTTTTGTGGGAAAAGCGCCGCTAAATATCATGG
1 TTTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
* * * * * * *
49689198 TCTATAGCGGTGTTTTTGGGTAAAAGCGCCACTAAAG
1 TTTTTAGCGGCGCTTGT-GGAAAAAGCGCCGCTAAAG
49689235 TTAGCAAGGC
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
43 47 0.75
44 16 0.25
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (43 bp):
TTTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
Found at i:49689659 original size:26 final size:26
Alignment explanation
Indices: 49689629--49689680 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
49689619 AAAATTAATG
49689629 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49689655 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49689681 TTCTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:49690834 original size:43 final size:43
Alignment explanation
Indices: 49690785--49690907 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 43
49690775 AAAGGTTATA
* *
49690785 TTTTTAGCGGCGCTTGTGGAAAAAGCGTCGCTAAAGGTCATGG
1 TTTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
* ** * *
49690828 TTTTTAGCGACTTTTGTGGGAAAAGCGCCGCTAAATATCATGG
1 TTTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
* * * * * * *
49690871 TCTATAGCGGTGTTTTTGGGTAAAAGCGCCACTAAAG
1 TTTTTAGCGGCGCTTGT-GGAAAAAGCGCCGCTAAAG
49690908 TTAGCAAGGC
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
43 47 0.75
44 16 0.25
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (43 bp):
TTTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
Found at i:49691331 original size:26 final size:26
Alignment explanation
Indices: 49691301--49691352 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
49691291 AAAATTAATG
49691301 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49691327 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49691353 TTCTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:49692507 original size:43 final size:43
Alignment explanation
Indices: 49692458--49692544 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
49692448 AAAGGTTATA
* * *
49692458 TTTTTAGCGGCGCTTGTGGAAAAAGCGTCGCTAAAGGTCATGG
1 TTTTTAGCGACGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
** * *
49692501 TTTTTAGCGACTTTTGTGGGAAAAGCGCCGCTAAATATCATGG
1 TTTTTAGCGACGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
49692544 T
1 T
49692545 CTATAGTGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (43 bp):
TTTTTAGCGACGCTTGTGGAAAAAGCGCCGCTAAAGATCATGG
Found at i:49693005 original size:26 final size:26
Alignment explanation
Indices: 49692975--49693026 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
49692965 AAAATTAATG
49692975 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49693001 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
49693027 TTCTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:49695368 original size:28 final size:27
Alignment explanation
Indices: 49695224--49695376 Score: 101
Period size: 28 Copynumber: 5.8 Consensus size: 27
49695214 TCAAAATATA
* * *
49695224 ATTATAATTTTTAT-TATTTATTTATT
1 ATTATAATTTATATATATGTAATTATT
*
49695250 ATTTAATAATTT-T-TATAGGTAATTAATGT
1 A-TT-ATAATTTATATATATGTAATT-AT-T
*
49695279 TTTCATAATTTATATAT-T-T--TTATT
1 ATT-ATAATTTATATATATGTAATTATT
*
49695303 AAT-TAATTT-TA-ATAATGTAATTATT
1 ATTATAATTTATATAT-ATGTAATTATT
*
49695328 ATTATTATTTATATATATGTAATTATTT
1 ATTATAATTTATATATATGTAATTA-TT
*
49695356 TTTATAATTTATATATATGTA
1 ATTATAATTTATATATATGTA
49695377 TAGATTTATT
Statistics
Matches: 99, Mismatches: 12, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 7 0.07
23 1 0.01
24 2 0.02
25 9 0.09
26 9 0.09
27 20 0.20
28 42 0.42
29 2 0.02
30 3 0.03
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (27 bp):
ATTATAATTTATATATATGTAATTATT
Done.