Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 10 of 253
Found at i:2900939 original size:3 final size:3
Alignment explanation
Indices: 2900933--2900973 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2900923 TTTTTCGCTT
2900933 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2900974 TACTATTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2901066 original size:28 final size:27
Alignment explanation
Indices: 2901014--2901066 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
2901004 GGTCTCTCTA
*
2901014 ATATATTTAAATTTTAGATTTATTTGC
1 ATATATTTAAATTTTAGATTCATTTGC
*
2901041 ATATACTTTAATTTTTA-ATATCATTT
1 ATATA-TTTAAATTTTAGAT-TCATTT
2901067 AGTCTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (27 bp):
ATATATTTAAATTTTAGATTCATTTGC
Found at i:2901328 original size:14 final size:15
Alignment explanation
Indices: 2901311--2901389 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 15
2901301 AGGGTTTATT
2901311 GTTTATAG-TTTAAG
1 GTTTATAGTTTTAAG
*
2901325 GTTTTATGGTTTT--G
1 G-TTTATAGTTTTAAG
* *
2901339 GATTTA-GGTTTTATG
1 G-TTTATAGTTTTAAG
* *
2901354 GTTTA-AGATTTAGG
1 GTTTATAGTTTTAAG
2901368 GTTTATAGTTTTAAG
1 GTTTATAGTTTTAAG
*
2901383 TTTTATA
1 GTTTATA
2901390 ATTTAGGATC
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 6 0.12
14 22 0.42
15 21 0.40
16 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (15 bp):
GTTTATAGTTTTAAG
Found at i:2901347 original size:21 final size:21
Alignment explanation
Indices: 2901305--2901380 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
2901295 TGTTTAAGGG
*
2901305 TTTATTGTTTATAG-TTTAAGGT
1 TTTATGGTTT-TAGATTT-AGGT
*
2901327 TTTATGGTTTTGGATTTAGGT
1 TTTATGGTTTTAGATTTAGGT
* *
2901348 TTTATGGTTTAAGATTTAGGG
1 TTTATGGTTTTAGATTTAGGT
*
2901369 TTTATAGTTTTA
1 TTTATGGTTTTA
2901381 AGTTTTATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 34 0.74
22 12 0.26
ACGTcount: A:0.21, C:0.00, G:0.22, T:0.57
Consensus pattern (21 bp):
TTTATGGTTTTAGATTTAGGT
Found at i:2901387 original size:29 final size:29
Alignment explanation
Indices: 2901284--2901396 Score: 70
Period size: 29 Copynumber: 3.8 Consensus size: 29
2901274 GTTTAGGATT
* **
2901284 TAGTATTTAAGTGTTTAAGGGTTTATTGTTTA
1 TAGT-TTTAAGT-TTTAA-GATTTAGGGTTTA
* * * *
2901316 TAG-TTTAAGGTTTTATGGTTTTGGATTTA
1 TAGTTTTAA-GTTTTAAGATTTAGGGTTTA
* * *
2901345 -GGTTTTATGGTTTAAGATTTAGGGTTTA
1 TAGTTTTAAGTTTTAAGATTTAGGGTTTA
2901373 TAGTTTTAAGTTTTATA-ATTTAGG
1 TAGTTTTAAGTTTTA-AGATTTAGG
2901397 ATCTAGTGAT
Statistics
Matches: 62, Mismatches: 15, Indels: 11
0.70 0.17 0.12
Matches are distributed among these distances:
28 16 0.26
29 31 0.50
30 10 0.16
31 2 0.03
32 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.23, T:0.53
Consensus pattern (29 bp):
TAGTTTTAAGTTTTAAGATTTAGGGTTTA
Found at i:2901489 original size:29 final size:29
Alignment explanation
Indices: 2901418--2901493 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
2901408 TATGTTTATA
2901418 GTTTTATGATTTAGGAATCTATATTTAAGG
1 GTTTTATGATTTAGG-ATCTATATTTAAGG
* * *
2901448 GTTTAAGGGTTTAGTG-TCTATAGTTT-AGG
1 GTTTTATGATTTAG-GATCTATA-TTTAAGG
2901477 GTTTTATGATTTAGGAT
1 GTTTTATGATTTAGGAT
2901494 TCAAGGTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.03
29 21 0.57
30 14 0.38
31 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (29 bp):
GTTTTATGATTTAGGATCTATATTTAAGG
Found at i:2901534 original size:21 final size:21
Alignment explanation
Indices: 2901470--2901538 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
2901460 AGTGTCTATA
* *
2901470 GTTTAGGGTTTTATGATTTAGG
1 GTTTAAGG-TTTATAATTTAGG
* *
2901492 ATTCAAGGTTTA-ATATTTAGG
1 GTTTAAGGTTTATA-ATTTAGG
2901513 GTTTAAGGTTTATAATTTAGG
1 GTTTAAGGTTTATAATTTAGG
2901534 GTTTA
1 GTTTA
2901539 TGACTAGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 33 0.85
22 6 0.15
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (21 bp):
GTTTAAGGTTTATAATTTAGG
Found at i:2913429 original size:34 final size:31
Alignment explanation
Indices: 2913387--2913449 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 31
2913377 AAAAATATGG
2913387 TAAAATAAACAATATATAATATATAGTATAATA
1 TAAAATAAACAATATATAATA-ATA-TATAATA
* *
2913420 TAAATATAAATAATATGTAATAATATATAA
1 TAAA-ATAAACAATATATAATAATATATAA
2913450 AAATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 7 0.26
34 15 0.56
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (31 bp):
TAAAATAAACAATATATAATAATATATAATA
Found at i:2913432 original size:10 final size:11
Alignment explanation
Indices: 2913391--2913463 Score: 66
Period size: 10 Copynumber: 6.8 Consensus size: 11
2913381 ATATGGTAAA
*
2913391 ATAAACAATAT
1 ATAAATAATAT
2913402 AT-AATATATAGT
1 ATAAATA-ATA-T
2913414 ATAATATAA-AT
1 ATAA-ATAATAT
2913425 ATAAATAATAT
1 ATAAATAATAT
*
2913436 GT-AATAATAT
1 ATAAATAATAT
2913446 ATAAA-AATAT
1 ATAAATAATAT
2913456 AT-AATAAT
1 ATAAATAAT
2913464 GCGATGGATA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
9 2 0.04
10 26 0.50
11 15 0.29
12 4 0.08
13 2 0.04
14 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:2913435 original size:25 final size:25
Alignment explanation
Indices: 2913397--2913446 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2913387 TAAAATAAAC
2913397 AATATATAATATATAGT-ATAATATA
1 AATATATAATATAT-GTAATAATATA
2913422 AATATA-AATAATATGTAATAATATA
1 AATATATAAT-ATATGTAATAATATA
2913447 TAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AATATATAATATATGTAATAATATA
Found at i:2913454 original size:20 final size:21
Alignment explanation
Indices: 2913397--2913463 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 21
2913387 TAAAATAAAC
2913397 AATATAT-AATATATAGTATAAT
1 AATATATAAATA-ATA-TATAAT
* *
2913419 ATAAATATAAATAATATGTAAT
1 A-ATATATAAATAATATATAAT
2913441 AATATATAAA-AATATATAAT
1 AATATATAAATAATATATAAT
2913461 AAT
1 AAT
2913464 GCGATGGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.31
21 8 0.21
22 7 0.18
23 8 0.21
24 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
AATATATAAATAATATATAAT
Found at i:2915141 original size:73 final size:73
Alignment explanation
Indices: 2915061--2915287 Score: 267
Period size: 83 Copynumber: 3.0 Consensus size: 73
2915051 GTGAACCTGT
* * *
2915061 TTGAGAACATTTGAGGGTTATATCTGGAATGTCCTCGATTTGTTCCTTGTAAACTAAATCATCTT
1 TTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAACTAAATCATCTT
2915126 AGATCTAC
66 AGATCTAC
*
2915134 TTGAGAACATTTGAGAGTCATATCTGCAATGTCCTTGATTTGTTCCTTGTAAGCACAAGGATGCC
1 TTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAA--AC-----T---
* **
2915199 AAACCATCTT-GAGTCTGT
56 AAATCATCTTAGA-TCTAC
* *
2915217 TTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTCTAAATTAAATCATCTT
1 TTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAACTAAATCATCTT
2915282 AGATCT
66 AGATCT
2915288 GCTTCAGTAT
Statistics
Matches: 131, Mismatches: 11, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
73 60 0.46
74 2 0.02
75 2 0.02
76 1 0.01
80 1 0.01
81 1 0.01
82 2 0.02
83 62 0.47
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (73 bp):
TTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAACTAAATCATCTT
AGATCTAC
Found at i:2915425 original size:119 final size:119
Alignment explanation
Indices: 2915272--2915561 Score: 528
Period size: 119 Copynumber: 2.4 Consensus size: 119
2915262 CTTCTAAATT
* * *
2915272 AAATCATCTTAGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAATGTC
1 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAAAGTC
2915337 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
66 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
*
2915391 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTCAGATCTGCTATATTTGAGAAAGTC
1 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAAAGTC
2915456 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
66 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
2915510 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAA-GTCTAGATCTGCTAT
1 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGT-TAGATCTGCTAT
2915562 TTTCAATTTG
Statistics
Matches: 165, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
118 2 0.01
119 163 0.99
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (119 bp):
AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAAAGTC
TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
Found at i:2923398 original size:37 final size:37
Alignment explanation
Indices: 2923348--2923446 Score: 189
Period size: 37 Copynumber: 2.7 Consensus size: 37
2923338 CCCCACACGT
*
2923348 ACGTAGTTATCGGGTCTTACCCGGACATAATCTCCAC
1 ACGTAGTCATCGGGTCTTACCCGGACATAATCTCCAC
2923385 ACGTAGTCATCGGGTCTTACCCGGACATAATCTCCAC
1 ACGTAGTCATCGGGTCTTACCCGGACATAATCTCCAC
2923422 ACGTAGTCATCGGGTCTTACCCGGA
1 ACGTAGTCATCGGGTCTTACCCGGA
2923447 ATATATTTCC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.25
Consensus pattern (37 bp):
ACGTAGTCATCGGGTCTTACCCGGACATAATCTCCAC
Found at i:2923609 original size:48 final size:48
Alignment explanation
Indices: 2923552--2923829 Score: 421
Period size: 48 Copynumber: 5.8 Consensus size: 48
2923542 AATACACACC
2923552 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
* *
2923600 TTTCACATTAGCCATTCGGATTTACCACATATATATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
** * * *
2923648 TTTCATGTTAGCCATTCAGCTTTATCACATATATATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
** *
2923696 TTTCATGTTAACCATTCGGCTTTACCACATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
*
2923744 TTTCATATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
* * * *
2923792 TTTCACACTAGCCATTCAGCTTTACCACACATATATAT
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATAT
2923830 TTATCTTGTA
Statistics
Matches: 212, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 212 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (48 bp):
TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
Found at i:2929663 original size:12 final size:12
Alignment explanation
Indices: 2929646--2929723 Score: 55
Period size: 12 Copynumber: 7.0 Consensus size: 12
2929636 TAAAATAAAC
2929646 AATATATAATAA
1 AATATATAATAA
2929658 AATATATAAT-A
1 AATATATAATAA
* *
2929669 TATCGTATAATATA
1 AAT-ATATAATA-A
2929683 AATATA-AAT--
1 AATATATAATAA
*
2929692 AATATGTAAT--
1 AATATATAATAA
2929702 AATATAT-A-AA
1 AATATATAATAA
2929712 AATATATAATAA
1 AATATATAATAA
2929724 TGCGATGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
9 6 0.12
10 16 0.31
11 4 0.08
12 21 0.40
13 2 0.04
14 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (12 bp):
AATATATAATAA
Found at i:2929693 original size:10 final size:11
Alignment explanation
Indices: 2929640--2929724 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 11
2929630 ATATGGTAAA
*
2929640 ATAAACAATAT
1 ATAAATAATAT
*
2929651 AT-AATAAAAT
1 ATAAATAATAT
*
2929661 ATATAATATATCGT
1 ATA-AATA-AT-AT
2929675 ATAATATAA-AT
1 ATAA-ATAATAT
2929686 ATAAATAATAT
1 ATAAATAATAT
*
2929697 GT-AATAATAT
1 ATAAATAATAT
2929707 ATAAA-AATAT
1 ATAAATAATAT
2929717 AT-AATAAT
1 ATAAATAAT
2929725 GCGATGGATA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
9 2 0.03
10 31 0.53
11 12 0.20
12 4 0.07
13 3 0.05
14 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:2929696 original size:25 final size:24
Alignment explanation
Indices: 2929650--2929707 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
2929640 ATAAACAATA
2929650 TATAATA-AAATATATAATATATCG
1 TATAATATAAATATATAATATAT-G
2929674 TATAATATAAATATA-AATAATATG
1 TATAATATAAATATATAAT-ATATG
2929698 TAATAATATA
1 T-ATAATATA
2929708 TAAAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
TATAATATAAATATATAATATATG
Found at i:2929715 original size:20 final size:21
Alignment explanation
Indices: 2929640--2929724 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 21
2929630 ATATGGTAAA
* *
2929640 ATAAACAATATATAATAAAAT
1 ATAAATAATATATAATAATAT
* *
2929661 ATATAATATATCGTATAATATAAAT
1 ATA-AATA-AT-ATATAATA-ATAT
*
2929686 ATAAATAATATGTAATAATAT
1 ATAAATAATATATAATAATAT
2929707 ATAAA-AATATATAATAAT
1 ATAAATAATATATAATAAT
2929725 GCGATGGATA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.22
21 11 0.20
22 9 0.17
23 4 0.07
24 11 0.20
25 7 0.13
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATAATATATAATAATAT
Found at i:2934119 original size:26 final size:26
Alignment explanation
Indices: 2934090--2934141 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2934080 AACAAAAGCA
2934090 AGTAATCTGGATTAAGTATGAAGCTT
1 AGTAATCTGGATTAAGTATGAAGCTT
2934116 AGTAATCTGGATTAAGTATGAAGCTT
1 AGTAATCTGGATTAAGTATGAAGCTT
2934142 TGTCTAGAAA
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:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
AGTAATCTGGATTAAGTATGAAGCTT
Found at i:2936853 original size:42 final size:41
Alignment explanation
Indices: 2936679--2936850 Score: 258
Period size: 41 Copynumber: 4.2 Consensus size: 41
2936669 CAAAAATGCT
* * *
2936679 GCTAAAA-ACTGAGCAATAGCGGCGCTTTTGGTAAAAAGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
*
2936719 ACTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
2936760 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
* *
2936801 GCTAAAAGTCAGAGCATTAGCAGCG-TTTGTGGTCAAAACGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTT-TGGT-AAAACGCC
2936843 GCTAAAAG
1 GCTAAAAG
2936851 TCATATAACT
Statistics
Matches: 122, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 9 0.07
41 97 0.80
42 16 0.13
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.20
Consensus pattern (41 bp):
GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
Found at i:2936938 original size:14 final size:15
Alignment explanation
Indices: 2936921--2936962 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2936911 AAATCCTAAC
2936921 AAACCCTAAACACT-
1 AAACCCTAAACACTA
** *
2936935 AAACTATAAACCCTA
1 AAACCCTAAACACTA
2936950 AAACCCTAAACAC
1 AAACCCTAAACAC
2936963 CGCAATAGGT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACCCTAAACACTA
Found at i:2937472 original size:24 final size:24
Alignment explanation
Indices: 2937445--2937493 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2937435 CGTATACTTA
*
2937445 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
2937469 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
2937493 T
1 T
2937494 GTTATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:2937828 original size:21 final size:22
Alignment explanation
Indices: 2937782--2937843 Score: 99
Period size: 21 Copynumber: 2.9 Consensus size: 22
2937772 TTTTAAAGTT
* *
2937782 TATGGATTATGGATTATGGGTT
1 TATGGATTATGGTTTATGGGTC
2937804 TATGGATTATGGTTTA-GGGTC
1 TATGGATTATGGTTTATGGGTC
2937825 TATGGATTATGGTTTATGG
1 TATGGATTATGGTTTATGG
2937844 TTTAAGGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.45
Consensus pattern (22 bp):
TATGGATTATGGTTTATGGGTC
Found at i:2937844 original size:7 final size:7
Alignment explanation
Indices: 2937779--2937847 Score: 75
Period size: 7 Copynumber: 9.7 Consensus size: 7
2937769 CTATTTTAAA
2937779 GTTTATG
1 GTTTATG
*
2937786 GATTATG
1 GTTTATG
*
2937793 GATTATGG
1 GTTTAT-G
2937801 GTTTATG
1 GTTTATG
*
2937808 GATTATG
1 GTTTATG
*
2937815 GTTTAGG
1 GTTTATG
*
2937822 GTCTATG
1 GTTTATG
*
2937829 GATTATG
1 GTTTATG
2937836 GTTTATG
1 GTTTATG
2937843 GTTTA
1 GTTTA
2937848 AGGGTTGGGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
7 45 0.88
8 6 0.12
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.48
Consensus pattern (7 bp):
GTTTATG
Found at i:2937859 original size:21 final size:21
Alignment explanation
Indices: 2937835--2937904 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
2937825 TATGGATTAT
2937835 GGTTTATGGTTTAAGGGTTGG
1 GGTTTATGGTTTAAGGGTTGG
*
2937856 GGTTTAAGGTTT-AGGTGTTGG
1 GGTTTATGGTTTAAGG-GTTGG
* * *
2937877 AGG-TTATGGGTTATGGGTTATG
1 -GGTTTATGGTTTAAGGGTT-GG
2937899 GGTTTA
1 GGTTTA
2937905 GGGGTTACGT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.08
21 28 0.72
22 8 0.21
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (21 bp):
GGTTTATGGTTTAAGGGTTGG
Found at i:2937890 original size:7 final size:7
Alignment explanation
Indices: 2937878--2937902 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2937868 AGGTGTTGGA
2937878 GGTTATG
1 GGTTATG
2937885 GGTTATG
1 GGTTATG
2937892 GGTTATG
1 GGTTATG
2937899 GGTT
1 GGTT
2937903 TAGGGGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTATG
Found at i:2937897 original size:14 final size:14
Alignment explanation
Indices: 2937781--2937902 Score: 63
Period size: 14 Copynumber: 8.6 Consensus size: 14
2937771 ATTTTAAAGT
* *
2937781 TTATGGATTATGGA
1 TTATGGGTTATGGG
*
2937795 TTATGGGTTTATGGA
1 TTATGGG-TTATGGG
*
2937810 TTATGGTTTA-GGG
1 TTATGGGTTATGGG
* *
2937823 TCTATGGATTATGGT
1 T-TATGGGTTATGGG
* *
2937838 TTATGGTTTAAGGG
1 TTATGGGTTATGGG
* * *
2937852 TT-GGGGTTTAAGGT
1 TTATGGG-TTATGGG
*
2937866 TTA-GGTGTT-GGAGG
1 TTATGG-GTTATG-GG
2937880 TTATGGGTTATGGG
1 TTATGGGTTATGGG
2937894 TTATGGGTT
1 TTATGGGTT
2937903 TAGGGGTTAC
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
13 6 0.07
14 59 0.69
15 20 0.24
ACGTcount: A:0.18, C:0.01, G:0.37, T:0.44
Consensus pattern (14 bp):
TTATGGGTTATGGG
Found at i:2939970 original size:26 final size:26
Alignment explanation
Indices: 2939947--2940007 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2939937 CATTAAAATC
* **
2939947 AAACTCAGGTATTTAACTGAAAAACA
1 AAACTCAAGTATCAAACTGAAAAACA
*
2939973 AAACTCAAGTATCAAACTGAAAAAAA
1 AAACTCAAGTATCAAACTGAAAAACA
*
2939999 AAATTCAAG
1 AAACTCAAG
2940008 GCACATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.20
Consensus pattern (26 bp):
AAACTCAAGTATCAAACTGAAAAACA
Found at i:2940044 original size:30 final size:30
Alignment explanation
Indices: 2940010--2940076 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
2940000 AATTCAAGGC
2940010 ACATAATTTAAAGATCAAATTTCATAACTT
1 ACATAATTTAAAGATCAAATTTCATAACTT
2940040 ACATAATTTAAAGATCAAATTTCATAACTT
1 ACATAATTTAAAGATCAAATTTCATAACTT
2940070 ACATAAT
1 ACATAAT
2940077 ACATGAGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (30 bp):
ACATAATTTAAAGATCAAATTTCATAACTT
Found at i:2940091 original size:46 final size:46
Alignment explanation
Indices: 2940032--2940164 Score: 230
Period size: 46 Copynumber: 2.9 Consensus size: 46
2940022 GATCAAATTT
*
2940032 CATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAATA
1 CATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAAAA
* * *
2940078 CATGAGTTACATAATTTAAAGATCAAATTTCAAAACTTACATAAAA
1 CATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAAAA
2940124 CATAACTTACATAATTTAAAGATCAAATTTCATAACTTACA
1 CATAACTTACATAATTTAAAGATCAAATTTCATAACTTACA
2940165 GCTTTTACAT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (46 bp):
CATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAAAA
Found at i:2940181 original size:9 final size:9
Alignment explanation
Indices: 2940169--2940221 Score: 69
Period size: 9 Copynumber: 6.3 Consensus size: 9
2940159 CTTACAGCTT
2940169 TTACATAAC
1 TTACATAAC
2940178 TTACATAA-
1 TTACATAAC
*
2940186 -TAAATAAC
1 TTACATAAC
2940194 TTACATAA-
1 TTACATAAC
2940202 -TACATAAC
1 TTACATAAC
2940210 TTACATAAC
1 TTACATAAC
2940219 TTA
1 TTA
2940222 ATTATACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 13 0.34
9 25 0.66
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (9 bp):
TTACATAAC
Found at i:2940194 original size:16 final size:16
Alignment explanation
Indices: 2940173--2940217 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2940163 CAGCTTTTAC
2940173 ATAACTTACATAATAA
1 ATAACTTACATAATAA
*
2940189 ATAACTTACATAATAC
1 ATAACTTACATAATAA
2940205 ATAACTTACATAA
1 ATAACTTACATAA
2940218 CTTAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAACTTACATAATAA
Found at i:2940198 original size:25 final size:25
Alignment explanation
Indices: 2940169--2940247 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
2940159 CTTACAGCTT
2940169 TTACATAACTTACATAATAAATAAC
1 TTACATAACTTACATAATAAATAAC
*
2940194 TTACATAA--TACATAACTTACATAAC
1 TTACATAACTTACATAA--TAAATAAC
* *
2940219 TTA-ATTATACTTATA-AATAAACAAC
1 TTACA-TA-ACTTACATAATAAATAAC
2940244 TTAC
1 TTAC
2940248 CCGTGTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
23 7 0.16
24 1 0.02
25 29 0.67
26 1 0.02
27 2 0.05
28 3 0.07
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (25 bp):
TTACATAACTTACATAATAAATAAC
Found at i:2941953 original size:12 final size:12
Alignment explanation
Indices: 2941936--2941960 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2941926 AAGATCGAGG
2941936 GATGAATCTGAT
1 GATGAATCTGAT
2941948 GATGAATCTGAT
1 GATGAATCTGAT
2941960 G
1 G
2941961 GAGAGGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:2945294 original size:13 final size:14
Alignment explanation
Indices: 2945278--2945306 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2945268 TTCTAAATAT
2945278 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
2945291 TTATAATTGTTTAA
1 TTATAATTGTTTAA
2945305 TT
1 TT
2945307 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:2947019 original size:29 final size:28
Alignment explanation
Indices: 2946986--2947040 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2946976 ATGGTGGATG
* *
2946986 GTAATTCAAAGCTGATTTTTTATTAAGCA
1 GTAATTAAAAGCTGA-ATTTTATTAAGCA
*
2947015 GTAATTAAAAGTTGAATTTTATTAAG
1 GTAATTAAAAGCTGAATTTTATTAAG
2947041 AAAAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (28 bp):
GTAATTAAAAGCTGAATTTTATTAAGCA
Found at i:2964152 original size:64 final size:64
Alignment explanation
Indices: 2964051--2964234 Score: 289
Period size: 64 Copynumber: 2.9 Consensus size: 64
2964041 CATAATCATT
*
2964051 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTGTTTGACATAAACACCA
1 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
* *
2964115 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTTTAATTATTTGACATAAATACCA
1 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
* * * *
2964179 CATCTAGTTAGG-GACATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGACAT
1 CATCTAGTTAGGAG-CACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACAT
2964235 GCACAGATAC
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
63 1 0.01
64 110 0.99
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (64 bp):
CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
Found at i:2964795 original size:44 final size:44
Alignment explanation
Indices: 2964306--2964781 Score: 587
Period size: 44 Copynumber: 10.8 Consensus size: 44
2964296 GCGAATCCTA
* * *
2964306 CAGATTTGGCATCTCTGTATTAGTG-A-AGAGCAGATCAAAGATAA
1 CAGATTTGGCGTCTCTGTATT-G-GCAGAGAGCAGATCGAAGATAG
* * *
2964350 CAAATTTAGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * * *
2964394 CAGATTTAGCGTCTCTATATTGTCAGAGGGCAAATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* ** * *
2964438 CAGATTTGGCATCTCTGTATTGGTGGATAGCAGATCGAAGATAT
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * *
2964482 CAGATTTGGCGTCTTTGTATTGTCAGAGGGCAGATTGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
2964526 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
2964570 CAGATTTGGCGTCTCTGTATTGGCAGAGAACAAATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* ** *
2964614 CAGATTTGGCATCTCTGTATTGGTGGAGAGCAGATCGAAGATAT
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * *
2964658 CAGATTTAGCGTCTCTGTATTGTCAGAGGGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
2964702 TAGATTTAGCGTCTCTGTTTTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
2964746 CAGATTTGGCATCTCTGTATTGGCAAAGAGCAGATC
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATC
2964782 AAAAATAATA
Statistics
Matches: 365, Mismatches: 65, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 363 0.99
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
Found at i:2968701 original size:19 final size:19
Alignment explanation
Indices: 2968677--2968714 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2968667 AATTACTAAG
2968677 TTAGAAAATTTGACATGGA
1 TTAGAAAATTTGACATGGA
2968696 TTAGAAAATTTGACATGGA
1 TTAGAAAATTTGACATGGA
2968715 GAATGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TTAGAAAATTTGACATGGA
Found at i:2978592 original size:64 final size:64
Alignment explanation
Indices: 2978518--2978701 Score: 289
Period size: 64 Copynumber: 2.9 Consensus size: 64
2978508 CATAATCATT
*
2978518 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTGTTTGACATAAACACCA
1 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
* *
2978582 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTTTAATTATTTGACATAAATACCA
1 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
* * * *
2978646 CATCTAGTTAGG-GACATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGACAT
1 CATCTAGTTAGGAG-CACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACAT
2978702 GCACAGATAC
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
63 1 0.01
64 110 0.99
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (64 bp):
CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
Found at i:2979262 original size:44 final size:44
Alignment explanation
Indices: 2978773--2979248 Score: 596
Period size: 44 Copynumber: 10.8 Consensus size: 44
2978763 GCGAATCCTA
* * *
2978773 CAGATTTGGCATCTCTGTATTAGTG-A-AGAGCAGATCAAAGATAA
1 CAGATTTGGCGTCTCTGTATT-G-GCAGAGAGCAGATCGAAGATAG
* *
2978817 CAAATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * * *
2978861 CAGATTTAGCGTCTCTATATTGTCAGAGGGCAAATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* ** * *
2978905 CAGATTTGGCATCTCTGTATTGGTGGATAGCAGATCGAAGATAT
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * *
2978949 CAGATTTGGCGTCTTTGTATTGTCAGAGGGCAGATTGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
2978993 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
2979037 CAGATTTGGCGTCTCTGTATTGGCAAAGAACAAATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* ** * *
2979081 CAGATTTGGCATCTCTGTATTGGTGGAGAGCAAATCGAAGATAT
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * *
2979125 CAGATTTAGCGTCTCTGTATTGTCAGAGGGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
2979169 CAGATTTGGCGTCTCTGTTTTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
2979213 CAGATTTGGCATCTCTGTATTGGCAAAGAGCAGATC
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATC
2979249 AAAAATAATA
Statistics
Matches: 365, Mismatches: 65, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 363 0.99
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
Found at i:2982628 original size:22 final size:22
Alignment explanation
Indices: 2982611--2982653 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2982601 TTTAAAATTC
2982611 AAAAAA-TTAAAGACTAAAAAT
1 AAAAAAGTTAAAGACTAAAAAT
2982632 AAAAAAGTTAAAGTA-TAAAAAT
1 AAAAAAGTTAAAG-ACTAAAAAT
2982654 TGAATGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 13 0.65
23 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAAAAGTTAAAGACTAAAAAT
Found at i:2984059 original size:31 final size:30
Alignment explanation
Indices: 2984023--2984094 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
2984013 GATTAAATCA
*
2984023 AAATTAAAGTTTCAAGTATAGATTTGAACC
1 AAATTAAAGTTTCAAGTATAGAATTGAACC
* * * * *
2984053 ACAATTAGAGTTTCACGTGTATAATTGAATC
1 A-AATTAAAGTTTCAAGTATAGAATTGAACC
2984084 AAATTAAAGTT
1 AAATTAAAGTT
2984095 AATGTATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATAGAATTGAACC
Found at i:2987253 original size:96 final size:96
Alignment explanation
Indices: 2987089--2987308 Score: 296
Period size: 96 Copynumber: 2.3 Consensus size: 96
2987079 TCATCATACG
* * * * * * *
2987089 TAATTATTCATCATAAAAATAGTAAAAAGTAACAGCATCAATAATTCATCAACTATGCCTGTCCC
1 TAATTATTCATCATAAAAATAATAAAAAATAAAAACATCAATAATTCATCAACAATACCTATCCC
* *
2987154 ACTAGCGAAAGTGGTGAAAACTCTTGATAAT
66 ACTAGCAAAAGTGGTGAAAACTCTTCATAAT
* * *
2987185 TAATTATTCATCATAAAAATAATAAAAAATAAAAACTTGAGTAATTCATCAACAATACCTATCCC
1 TAATTATTCATCATAAAAATAATAAAAAATAAAAACATCAATAATTCATCAACAATACCTATCCC
* * *
2987250 ACTAGCAAAAGTGGTGAAGACTTTTCATACT
66 ACTAGCAAAAGTGGTGAAAACTCTTCATAAT
*
2987281 TAATTATCCATCATAAAAATAATAAAAA
1 TAATTATTCATCATAAAAATAATAAAAA
2987309 GGTGACAGCG
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 108 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (96 bp):
TAATTATTCATCATAAAAATAATAAAAAATAAAAACATCAATAATTCATCAACAATACCTATCCC
ACTAGCAAAAGTGGTGAAAACTCTTCATAAT
Found at i:2987799 original size:16 final size:16
Alignment explanation
Indices: 2987778--2987828 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
2987768 TAGAATTCAT
2987778 ATCAATTCTAAAGCAA
1 ATCAATTCTAAAGCAA
* *
2987794 ATCAATT-TATAATTCAT
1 ATCAATTCTA-AA-GCAA
2987811 ATCAATTCTAAAGCAA
1 ATCAATTCTAAAGCAA
2987827 AT
1 AT
2987829 ATTAATAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 13 0.46
17 11 0.39
18 2 0.07
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (16 bp):
ATCAATTCTAAAGCAA
Found at i:2987816 original size:17 final size:17
Alignment explanation
Indices: 2987771--2987822 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2987761 AAAAAAATAG
2987771 AATTCATATCAATTCTA
1 AATTCATATCAATTCTA
* *
2987788 AA-GCAAATCAATT-TA
1 AATTCATATCAATTCTA
2987803 TAATTCATATCAATTCTA
1 -AATTCATATCAATTCTA
2987821 AA
1 AA
2987823 GCAAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTCATATCAATTCTA
Found at i:2989684 original size:15 final size:14
Alignment explanation
Indices: 2989658--2989692 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2989648 GTAATAATGA
2989658 AAATATAACAATAT
1 AAATATAACAATAT
*
2989672 ATATATGAACAATAT
1 AAATAT-AACAATAT
2989687 AAATAT
1 AAATAT
2989693 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATATAACAATAT
Found at i:2990286 original size:25 final size:25
Alignment explanation
Indices: 2990239--2990286 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2990229 AATAAAAATA
* *
2990239 AATAAAATAATAGATATTTTATTCG
1 AATAAAATAATAGATAATATATTCG
* *
2990264 AATAAAATTATATATAATATATT
1 AATAAAATAATAGATAATATATT
2990287 ATCAAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
AATAAAATAATAGATAATATATTCG
Found at i:2996676 original size:23 final size:23
Alignment explanation
Indices: 2996646--2996691 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2996636 TGTTCACTCT
2996646 TTAAATAAAAATGCAAAATCAAG
1 TTAAATAAAAATGCAAAATCAAG
*
2996669 TTAAATAAAAATGTAAAATCAAG
1 TTAAATAAAAATGCAAAATCAAG
2996692 GAATGGCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (23 bp):
TTAAATAAAAATGCAAAATCAAG
Found at i:2999767 original size:41 final size:41
Alignment explanation
Indices: 2999706--2999819 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
2999696 AAAAACACTG
2999706 TTAGTGGTGTTTTA-CTTAAAAACGCCGCTATTCATCAGTTT
1 TTAGTGGTGTTTTAGC-TAAAAACGCCGCTATTCATCAGTTT
* *
2999747 TTAGTGGTGTTTTAGCTAAAAACGCCGCTATTGATTAGTTT
1 TTAGTGGTGTTTTAGCTAAAAACGCCGCTATTCATCAGTTT
* ** *
2999788 TTAGTGGCGTTTGGGCCAAAAACGCCGCTATT
1 TTAGTGGTGTTTTAGCTAAAAACGCCGCTATT
2999820 GTTTAGTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 65 0.98
42 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TTAGTGGTGTTTTAGCTAAAAACGCCGCTATTCATCAGTTT
Found at i:2999820 original size:41 final size:41
Alignment explanation
Indices: 2999723--2999830 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
2999713 TGTTTTACTT
* * * * *
2999723 AAAAACGCCGCTATTCATCAGTTTTTAGTGGTGTTTTAGCT
1 AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGAGCC
*
2999764 AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGGGCC
1 AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGAGCC
*
2999805 AAAAACGCCGCTATTGTTTAGTTTTT
1 AAAAACGCCGCTATTGATTAGTTTTT
2999831 TGCAGCGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGAGCC
Found at i:3009110 original size:15 final size:15
Alignment explanation
Indices: 3009098--3009128 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
3009088 GTATAAATAT
3009098 AAATAGAGAAAATTA
1 AAATAGAGAAAATTA
3009113 AAATAGAGAAATATTA
1 AAATAGAGAAA-ATTA
3009129 TATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
AAATAGAGAAAATTA
Found at i:3037500 original size:9 final size:9
Alignment explanation
Indices: 3037488--3037537 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
3037478 AAATAAAAAT
3037488 AATTTTAAA
1 AATTTTAAA
3037497 AATTTGTAAA
1 AATTT-TAAA
3037507 ACATTATTAAA
1 A-ATT-TTAAA
*
3037518 ATTTTTAAA
1 AATTTTAAA
*
3037527 AATGTTAAA
1 AATTTTAAA
3037536 AA
1 AA
3037538 AATAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 19 0.54
10 7 0.20
11 8 0.23
12 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (9 bp):
AATTTTAAA
Found at i:3037682 original size:13 final size:13
Alignment explanation
Indices: 3037664--3037689 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3037654 GACATCATAG
3037664 ACCATGAATGTAA
1 ACCATGAATGTAA
3037677 ACCATGAATGTAA
1 ACCATGAATGTAA
3037690 CATCCCGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ACCATGAATGTAA
Found at i:3040681 original size:26 final size:26
Alignment explanation
Indices: 3040652--3040704 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3040642 TTTACAGTTT
3040652 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
3040678 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
3040704 T
1 T
3040705 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:3042314 original size:12 final size:12
Alignment explanation
Indices: 3042297--3042327 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3042287 TACTCGGGAA
3042297 GAGGCCGTGGTC
1 GAGGCCGTGGTC
*
3042309 GAGGCCGTGGTT
1 GAGGCCGTGGTC
3042321 GAGGCCG
1 GAGGCCG
3042328 AGGTAGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.52, T:0.16
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:3048695 original size:26 final size:26
Alignment explanation
Indices: 3048666--3048718 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3048656 TTTACAGTTT
3048666 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
3048692 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
3048718 T
1 T
3048719 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:3161196 original size:16 final size:16
Alignment explanation
Indices: 3161175--3161233 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
3161165 TACCACTCTA
*
3161175 ATAACTTATATACTAC
1 ATAACTTATATACTAT
3161191 ATAACTCTATATAACTTAT
1 ATAACT-TATAT-AC-TAT
* *
3161210 ATAACTTAGATAATAT
1 ATAACTTATATACTAT
3161226 ATAACTTA
1 ATAACTTA
3161234 ATAATTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 17 0.46
17 6 0.16
18 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAACTTATATACTAT
Found at i:3161212 original size:9 final size:9
Alignment explanation
Indices: 3161175--3161237 Score: 64
Period size: 9 Copynumber: 7.4 Consensus size: 9
3161165 TACCACTCTA
3161175 ATAACTTAT
1 ATAACTTAT
*
3161184 AT-AC-TAC
1 ATAACTTAT
3161191 ATAACTCTAT
1 ATAACT-TAT
3161201 ATAACTTAT
1 ATAACTTAT
*
3161210 ATAACTTAG
1 ATAACTTAT
3161219 ATAA--TAT
1 ATAACTTAT
3161226 ATAACTTA-
1 ATAACTTAT
3161234 ATAA
1 ATAA
3161238 TTACATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 10 0.22
8 8 0.18
9 19 0.42
10 8 0.18
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAACTTAT
Found at i:3161245 original size:16 final size:16
Alignment explanation
Indices: 3161175--3161250 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
3161165 TACCACTCTA
*
3161175 ATAACTT-ATATACTAC
1 ATAACTTAATA-ATTAC
*
3161191 ATAACTCTATATAACTTAT
1 ATAACT-TA-ATAA-TTAC
*
3161210 ATAACTTAGATAA-TAT
1 ATAACTTA-ATAATTAC
3161226 ATAACTTAATAATTAC
1 ATAACTTAATAATTAC
*
3161242 ATAATTTAA
1 ATAACTTAA
3161251 ATATATATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.08
16 27 0.54
17 1 0.02
18 7 0.14
19 11 0.22
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAACTTAATAATTAC
Found at i:3161245 original size:23 final size:25
Alignment explanation
Indices: 3161175--3161246 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
3161165 TACCACTCTA
3161175 ATAACTTATAT-AC-TACATAACTCTAT
1 ATAACTTATATAACTTACATAA---TAT
*
3161201 ATAACTTATATAACTTAGATAATAT
1 ATAACTTATATAACTTACATAATAT
3161226 ATAACTTA-ATAA-TTACATAAT
1 ATAACTTATATAACTTACATAAT
3161247 TTAAATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.19
24 4 0.10
25 11 0.26
26 11 0.26
27 2 0.05
28 6 0.14
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (25 bp):
ATAACTTATATAACTTACATAATAT
Found at i:3169772 original size:1 final size:1
Alignment explanation
Indices: 3169766--3169800 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
3169756 GATGAGGAGA
*
3169766 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3169801 GGTGTGATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:3178448 original size:43 final size:43
Alignment explanation
Indices: 3178351--3178470 Score: 170
Period size: 43 Copynumber: 2.8 Consensus size: 43
3178341 TTTATTGAAA
*
3178351 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGC-ATTTGTGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGACTTGTGG
* * * * *
3178393 GAGATCGCCGCTAAAGGTCAAGGCTTTTAGTGGCGGCTTGTGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGACTTGTGG
*
3178436 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
3178471 CTTTTTTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 30 0.45
43 37 0.55
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGACTTGTGG
Found at i:3178620 original size:31 final size:29
Alignment explanation
Indices: 3178543--3178621 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
3178533 TTCCTGCATT
* *
3178543 AAAATCCAACCAAATACAACAAATATAATA
1 AAAATACAACCAAAAAC-ACAAATATAATA
* * * *
3178573 TAAATGCAGCCAAAAACACAAATTTAACATA
1 AAAATACAACCAAAAACACAAATAT-A-ATA
3178604 AAAATACAACCAAAAACA
1 AAAATACAACCAAAAACA
3178622 TTAATTCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 7 0.18
30 14 0.36
31 18 0.46
ACGTcount: A:0.62, C:0.20, G:0.03, T:0.15
Consensus pattern (29 bp):
AAAATACAACCAAAAACACAAATATAATA
Found at i:3182622 original size:12 final size:12
Alignment explanation
Indices: 3182607--3182632 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3182597 ATCATCCTCT
3182607 TCATCAGATTCA
1 TCATCAGATTCA
3182619 TCATCAGATTCA
1 TCATCAGATTCA
3182631 TC
1 TC
3182633 CCTCGATATT
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:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:3184511 original size:9 final size:9
Alignment explanation
Indices: 3184497--3184606 Score: 109
Period size: 9 Copynumber: 12.6 Consensus size: 9
3184487 TATTTAAGTA
3184497 TTATGTAAG
1 TTATGTAAG
3184506 TTATGTAAG
1 TTATGTAAG
* *
3184515 TTATAT-AT
1 TTATGTAAG
*
3184523 TTATCTAAG
1 TTATGTAAG
*
3184532 TTATATAAG
1 TTATGTAAG
*
3184541 TTATATAAG
1 TTATGTAAG
*
3184550 TTATGTATG
1 TTATGTAAG
*
3184559 TTATATAAG
1 TTATGTAAG
3184568 TTATGTAAG
1 TTATGTAAG
*
3184577 TTA--TATG
1 TTATGTAAG
*
3184584 TTATATAAG
1 TTATGTAAG
*
3184593 TTATGTAAA
1 TTATGTAAG
3184602 TTATG
1 TTATG
3184607 ATATCAAATA
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 72 0.86
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3184583 original size:25 final size:25
Alignment explanation
Indices: 3184531--3184605 Score: 114
Period size: 25 Copynumber: 2.9 Consensus size: 25
3184521 ATTTATCTAA
*
3184531 GTTATATAAGTTATATAAGTTATGTAT
1 GTTATATAAGTTATGTAAGTTA--TAT
3184558 GTTATATAAGTTATGTAAGTTATAT
1 GTTATATAAGTTATGTAAGTTATAT
*
3184583 GTTATATAAGTTATGTAAATTAT
1 GTTATATAAGTTATGTAAGTTAT
3184606 GATATCAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 25 0.54
27 21 0.46
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (25 bp):
GTTATATAAGTTATGTAAGTTATAT
Found at i:3184731 original size:15 final size:15
Alignment explanation
Indices: 3184711--3184764 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
3184701 AAGTAGCGGG
3184711 ATTAAATAATTTTTA
1 ATTAAATAATTTTTA
*
3184726 ATTAAATAATATTT-
1 ATTAAATAATTTTTA
3184740 A-TAAA-AATTATTTTA
1 ATTAAATAA-T-TTTTA
3184755 ATTAAATAAT
1 ATTAAATAAT
3184765 ATACATGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.06
13 5 0.16
14 4 0.12
15 14 0.44
16 5 0.16
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAAATAATTTTTA
Found at i:3189579 original size:14 final size:14
Alignment explanation
Indices: 3189544--3189586 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3189534 ATAATAATAT
3189544 ACCTTAAACTTT-A
1 ACCTTAAACTTTAA
3189557 ACCTTAAACTTTAA
1 ACCTTAAACTTTAA
* *
3189571 ACCTCAAACTATAA
1 ACCTTAAACTTTAA
3189585 AC
1 AC
3189587 TTACACTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
ACCTTAAACTTTAA
Found at i:3189838 original size:15 final size:15
Alignment explanation
Indices: 3189820--3189851 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3189810 AAATAATAAT
*
3189820 TTATATATATTTATC
1 TTATATACATTTATC
3189835 TTATATACATTTATC
1 TTATATACATTTATC
3189850 TT
1 TT
3189852 CTACATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:3189848 original size:25 final size:24
Alignment explanation
Indices: 3189787--3189832 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3189777 ACCACTTTTC
*
3189787 ATATATATATTTATATATTTTTAAA
1 ATATATA-ATTTATATATATTTAAA
3189812 ATA-ATAATTTATATATATTTA
1 ATATATAATTTATATATATTTA
3189833 TCTTATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 3 0.15
25 3 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATATAATTTATATATATTTAAA
Found at i:3190294 original size:18 final size:18
Alignment explanation
Indices: 3190271--3190315 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
3190261 TTACACCCTA
*
3190271 AATATATATTATAA-TCTT
1 AATATATATTAGAAGT-TT
3190289 AATATATATTAGAAGTTT
1 AATATATATTAGAAGTTT
3190307 AATATATAT
1 AATATATAT
3190316 AACAAGGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
AATATATATTAGAAGTTT
Found at i:3190673 original size:41 final size:41
Alignment explanation
Indices: 3190627--3190898 Score: 409
Period size: 41 Copynumber: 6.6 Consensus size: 41
3190617 TTACTTTTTT
* * *
3190627 GCGGCGTTTTTCCATAAGCGCCGCTAAAACATCGGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
3190668 GCGGCGTTTTTCCAAAAGCCCCGCTAAAACCTCGGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
3190709 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
*
3190750 GCGGCGTTTTTCCAAAAGTGCCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
3190791 GCGTCATTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* * * * *
3190832 GCAGCGTTTTTGCAGAAGCACCACTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
3190873 GCGGCGTTTTTCCAAAAACACCGCTA
1 GCGGCGTTTTTCCAAAAGCGCCGCTA
3190899 TTGTACAGTT
Statistics
Matches: 210, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 210 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (41 bp):
GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
Found at i:3190935 original size:41 final size:41
Alignment explanation
Indices: 3190871--3191003 Score: 162
Period size: 41 Copynumber: 3.3 Consensus size: 41
3190861 CCTCGACCTA
**
3190871 TAGCGGCGTTT-TTCCAAAAACACCGCTATTG-TACAGTTTT
1 TAGCGGCGTTTGGGCCAAAAACACCGCTATTGCT-CAGTTTT
3190911 TAGCGGCGTTTGGGCCAAAAACACCGCTATTGCTCAGTTTT
1 TAGCGGCGTTTGGGCCAAAAACACCGCTATTGCTCAGTTTT
** ** * *
3190952 TAGCGGCGTTTGGATCAAAAATGCTGCTATTGCTCTGTTTT
1 TAGCGGCGTTTGGGCCAAAAACACCGCTATTGCTCAGTTTT
*
3190993 TTGCGGCGTTT
1 TAGCGGCGTTT
3191004 TATTGCAAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 11 0.13
41 70 0.85
42 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TAGCGGCGTTTGGGCCAAAAACACCGCTATTGCTCAGTTTT
Found at i:3204196 original size:22 final size:23
Alignment explanation
Indices: 3204171--3204220 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
3204161 TTTTTATTGT
3204171 TCTTTCTCTTCCATT-TTTTTCC
1 TCTTTCTCTTCCATTCTTTTTCC
**
3204193 TCTTT-TCTTCTTTTCTTTTTCC
1 TCTTTCTCTTCCATTCTTTTTCC
3204215 T-TTTCT
1 TCTTTCT
3204221 TCTCTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (23 bp):
TCTTTCTCTTCCATTCTTTTTCC
Found at i:3204226 original size:22 final size:22
Alignment explanation
Indices: 3204186--3204228 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
3204176 CTCTTCCATT
3204186 TTTTTCCTCTTTTCTTCTTTTC
1 TTTTTCCTCTTTTCTTCTTTTC
3204208 TTTTT-C-CTTTTCTTCTCTTTC
1 TTTTTCCTCTTTTCTTCT-TTTC
3204229 CTTGGGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTCCTCTTTTCTTCTTTTC
Found at i:3206564 original size:13 final size:13
Alignment explanation
Indices: 3206534--3206571 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3206524 TAAGATTGTA
3206534 AAAAAT-ATAAAT
1 AAAAATAATAAAT
*
3206546 AAAAATAATTAAT
1 AAAAATAATAAAT
*
3206559 AAAAATAAAAAAT
1 AAAAATAATAAAT
3206572 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:3206729 original size:11 final size:11
Alignment explanation
Indices: 3206708--3206774 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
3206698 AAATTTTGAA
3206708 TATTGTAAAAAT
1 TATT-TAAAAAT
3206720 TATTTAAAAAT
1 TATTTAAAAAT
3206731 TA-TTAAAAAT
1 TATTTAAAAAT
* **
3206741 GATAAAAAAAT
1 TATTTAAAAAT
* *
3206752 TA-TGAATAAT
1 TATTTAAAAAT
*
3206762 TATTAAAAAAT
1 TATTTAAAAAT
3206773 TA
1 TA
3206775 ATATATATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
10 16 0.36
11 24 0.55
12 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:3206736 original size:10 final size:10
Alignment explanation
Indices: 3206713--3206770 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
3206703 TTGAATATTG
3206713 TAAAAATTATT
1 TAAAAATTA-T
3206724 TAAAAATTAT
1 TAAAAATTAT
*
3206734 TAAAAATGAT
1 TAAAAATTAT
*
3206744 AAAAAAATTAT
1 -TAAAAATTAT
* *
3206755 GAATAATTAT
1 TAAAAATTAT
3206765 TAAAAA
1 TAAAAA
3206771 ATTAATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
10 22 0.56
11 17 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:3206737 original size:21 final size:21
Alignment explanation
Indices: 3206713--3206774 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
3206703 TTGAATATTG
*
3206713 TAAAAATTATTTAAAAATTAT
1 TAAAAATTATTAAAAAATTAT
* *
3206734 TAAAAATGATAAAAAAATTAT
1 TAAAAATTATTAAAAAATTAT
* *
3206755 GAATAATTATTAAAAAATTA
1 TAAAAATTATTAAAAAATTA
3206775 ATATATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAAAATTATTAAAAAATTAT
Found at i:3213416 original size:126 final size:126
Alignment explanation
Indices: 3213191--3213425 Score: 425
Period size: 126 Copynumber: 1.9 Consensus size: 126
3213181 TAGCCTTAAA
* *
3213191 AGGATATTTGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGTACGATTCTTC
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
* *
3213256 GAATTCTTTAAATACCGAACATTTCCTTTATTTTGAAAATTTTTTAGAGTGAACTGGTAAG
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTTAGAGTGAACTGGTAAG
*
3213317 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
3213382 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTT
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTT
3213426 GAAAGAAGAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 104 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (126 bp):
AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTTAGAGTGAACTGGTAAG
Found at i:3213538 original size:13 final size:13
Alignment explanation
Indices: 3213531--3213555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3213521 ATAATAATAG
3213531 TAATTAATAGAAA
1 TAATTAATAGAAA
3213544 TAATTAATAGAA
1 TAATTAATAGAA
3213556 CAACAGTAAT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
TAATTAATAGAAA
Found at i:3213901 original size:15 final size:16
Alignment explanation
Indices: 3213862--3213899 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
3213852 ATATATTTAC
*
3213862 ATAATAAATATATAAT
1 ATAATAAATAAATAAT
3213878 A-AATAAATAAATAAT
1 ATAATAAATAAATAAT
3213893 ATAATAA
1 ATAATAA
3213900 TATGAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAAATAAATAAT
Found at i:3214311 original size:18 final size:18
Alignment explanation
Indices: 3214288--3214360 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
3214278 ATAACAAGTA
*
3214288 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
3214306 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
3214324 ATGGT-TTAGTAGGGT-GTGG
1 -GGGTGAT-GGA-GGTAGTGG
3214343 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
3214361 ATGGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.63
19 10 0.23
20 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.27
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:3214339 original size:29 final size:29
Alignment explanation
Indices: 3214306--3214405 Score: 85
Period size: 37 Copynumber: 3.2 Consensus size: 29
3214296 GAGTTAGTGG
3214306 GGGTGATGGAGGTAGTGGATGGTTTAGTA
1 GGGTGATGGAGGTAGTGGATGGTTTAGTA
3214335 GGGTGTGGGGGTGATGGAGGTAGTGGATGGTTTAGTA
1 --------GGGTGATGGAGGTAGTGGATGGTTTAGTA
* * *
3214372 GGGTGATAGAGTTAGT-GATCGGTTTAGTG
1 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
3214401 GGGTG
1 GGGTG
3214406 TTTAATTTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
28 3 0.05
29 27 0.46
37 29 0.49
ACGTcount: A:0.18, C:0.01, G:0.50, T:0.31
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGATGGTTTAGTA
Found at i:3214352 original size:37 final size:37
Alignment explanation
Indices: 3214302--3214376 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3214292 GATGGAGTTA
3214302 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
3214339 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
3214376 G
1 G
3214377 ATAGAGTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.55, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
Found at i:3214796 original size:85 final size:85
Alignment explanation
Indices: 3214642--3215029 Score: 586
Period size: 85 Copynumber: 4.6 Consensus size: 85
3214632 AACGAAGATA
* *
3214642 AGATCTG-CAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACTC
* **
3214706 TACCACTGCTCGAAGAG-CC
66 CACCACTGCTCGGCGAGCCC
* **
3214725 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTGAGTCTTTAACCTACT
1 A-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACT
*
3214790 CCACCACTGCTCGGTGAGCCC
65 CCACCACTGCTCGGCGAGCCC
* *
3214811 A-AGTCTGTAAACTTTAGCCTGTTACCCTACTGCTTTA-GGGGTTAAGGCGAGTCTTCGACCTAT
1 AGA-TCTGTAAATTTTAGCCTGTTACCCTACTGC-TTAGGGGGTTAAGGCGAGTCTTCGACCTAC
3214874 TCCACCACTGCTCGGCGAGCCC
64 TCCACCACTGCTCGGCGAGCCC
* *
3214896 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTTTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACTC
**
3214961 TGCCACTGCTCGGCGAGCCC
66 CACCACTGCTCGGCGAGCCC
3214981 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
3215030 TGTATCTTTG
Statistics
Matches: 278, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
83 1 0.00
84 10 0.04
85 260 0.94
86 7 0.03
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.29
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACTC
CACCACTGCTCGGCGAGCCC
Found at i:3215100 original size:44 final size:44
Alignment explanation
Indices: 3215051--3215195 Score: 145
Period size: 44 Copynumber: 3.3 Consensus size: 44
3215041 TCTGCTCCAA
3215051 TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
1 TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
* * * * * * *
3215095 GATTGCTTAGGGAGTTAA-AGC-ATGTATCTT-TGATCTGCT-CCAC
1 TATTGCTTAGGGAGATAAGATCTAT-AATCTTCAGCT-TGTTACC-C
* *
3215138 TATTACTTAGGGAGATAAGATCTATAATTTTCAGCTTGTTACCC
1 TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
*
3215182 TATTGCTTAAGGAG
1 TATTGCTTAGGGAG
3215196 TTAAAGCCTG
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
42 6 0.08
43 26 0.34
44 38 0.50
45 6 0.08
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (44 bp):
TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
Found at i:3215112 original size:87 final size:87
Alignment explanation
Indices: 3215000--3215202 Score: 325
Period size: 87 Copynumber: 2.3 Consensus size: 87
3214990 AATTTTAGCC
* * * * *
3215000 TGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTGCTCCAATATTGCTTAGGGAG
1 TGTTACCCTATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCAATATTACTTAGGGAG
3215065 ATAAGATCTATAATCTTCAGCT
66 ATAAGATCTATAATCTTCAGCT
* *
3215087 TGTTACCCGATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTATTACTTAGGGAG
1 TGTTACCCTATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCAATATTACTTAGGGAG
*
3215152 ATAAGATCTATAATTTTCAGCT
66 ATAAGATCTATAATCTTCAGCT
*
3215174 TGTTACCCTATTGCTTAAGGAGTTAAAGC
1 TGTTACCCTATTGCTTAGGGAGTTAAAGC
3215203 CTGCTGAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 106 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (87 bp):
TGTTACCCTATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCAATATTACTTAGGGAG
ATAAGATCTATAATCTTCAGCT
Found at i:3215148 original size:43 final size:43
Alignment explanation
Indices: 3215011--3215151 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 43
3215001 GTTACCCTAC
* * * *
3215011 TGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTGCTCCAATAT
1 TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
* * * * * * *
3215054 TGCTTAGGGAGAT-AAG-ATCTATAATCTTCAGCTTGTTACC-CGAT
1 TGCTTAGGGAGTTAAAGCATGTAT-CT-TTGATC-TGCT-CCACTAT
3215098 TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
1 TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
*
3215141 TACTTAGGGAG
1 TGCTTAGGGAG
3215152 ATAAGATCTA
Statistics
Matches: 72, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
41 4 0.06
42 5 0.07
43 31 0.43
44 21 0.29
45 6 0.08
46 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (43 bp):
TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
Found at i:3222920 original size:21 final size:21
Alignment explanation
Indices: 3222894--3222938 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3222884 ACTGGCTCAT
*
3222894 CATGTTGTTCTATGACTCCAG
1 CATGTTGTTCTAGGACTCCAG
* *
3222915 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTAGGACTCCAG
3222936 CAT
1 CAT
3222939 TTGATCCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTAGGACTCCAG
Found at i:3226686 original size:126 final size:126
Alignment explanation
Indices: 3226457--3226690 Score: 407
Period size: 126 Copynumber: 1.9 Consensus size: 126
3226447 TAAAATGATA
* *
3226457 TTCGAATATTCAAAACAAACAAAGAGAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAGTTC
1 TTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAATTC
3226522 TTTAAATACCAAACATTGCCTTTATTTTAAAAATTTTTGAGAGTGAACTGGTAAGAGGATC
66 TTTAAATACCAAACATTGCCTTTATTTTAAAAATTTTTGAGAGTGAACTGGTAAGAGGATC
* *
3226583 TTCGAATATTCAAGACAAACAAAGAAAGTGAAACCCAGTACGTTAGGGCACGATTCTTCGAATTC
1 TTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAATTC
*
3226648 TTTAAATACCGAACATTGCCTTTATTTTGAAAAA-TTTTGAGAG
66 TTTAAATACCAAACATTGCCTTTATTTT-AAAAATTTTTGAGAG
3226691 AAGATCAATG
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
126 97 0.95
127 5 0.05
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (126 bp):
TTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAATTC
TTTAAATACCAAACATTGCCTTTATTTTAAAAATTTTTGAGAGTGAACTGGTAAGAGGATC
Found at i:3226805 original size:13 final size:13
Alignment explanation
Indices: 3226772--3226822 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
3226762 CTAACCATAT
* *
3226772 ATAAATAATAAAA
1 ATAATTAATAGAA
3226785 ATAA-TAATA-ATA
1 ATAATTAATAGA-A
*
3226797 GTAATTAATAGAA
1 ATAATTAATAGAA
3226810 ATAATTAATAGAA
1 ATAATTAATAGAA
3226823 CAACAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
13 22 0.67
14 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
ATAATTAATAGAA
Found at i:3227150 original size:14 final size:14
Alignment explanation
Indices: 3227131--3227161 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3227121 ATATATTTAC
*
3227131 ATAATAAATATATA
1 ATAATAAATAAATA
3227145 ATAATAAATAAATA
1 ATAATAAATAAATA
3227159 ATA
1 ATA
3227162 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:3227162 original size:19 final size:18
Alignment explanation
Indices: 3227133--3227169 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3227123 ATATTTACAT
3227133 AATAAATATATAATAATA
1 AATAAATATATAATAATA
3227151 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
3227170 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:3227580 original size:18 final size:18
Alignment explanation
Indices: 3227557--3227592 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3227547 ATAACAAGTA
*
3227557 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
3227575 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
3227593 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:3227608 original size:29 final size:29
Alignment explanation
Indices: 3227575--3227637 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
3227565 GAGTTAGTGG
*
3227575 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
1 GGGTGATGGAGGTAGT-GATCGATTTAGTA
* *
3227604 GGGTGATGGAGTTAGTGATCGATTTAGTG
1 GGGTGATGGAGGTAGTGATCGATTTAGTA
3227633 GGGTG
1 GGGTG
3227638 TTTAATTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.19, C:0.02, G:0.48, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGATCGATTTAGTA
Found at i:3228259 original size:19 final size:19
Alignment explanation
Indices: 3228235--3228332 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
3228225 AATCTTTAAG
3228235 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3228254 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
3228273 GATA--CACTCTTAGATAT
1 GATATGCAATCTTAGATAT
3228290 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3228309 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3228330 GAT
1 GAT
3228333 CTTGTAATCT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 16 0.22
19 48 0.66
21 9 0.12
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3228265 original size:36 final size:35
Alignment explanation
Indices: 3228225--3228332 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 35
3228215 ATGGAAATAT
3228225 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
*
3228261 AATC-TT-AGATATGATACACTCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
3228297 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
3228333 CTTGTAATCT
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 27 0.46
37 1 0.02
38 6 0.10
40 10 0.17
41 6 0.10
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:3228745 original size:16 final size:15
Alignment explanation
Indices: 3228717--3228768 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 15
3228707 TCTATGCATG
3228717 TATATAT-ATTATAT
1 TATATATCATTATAT
3228731 TATATATCATGTATAT
1 TATATATCAT-TATAT
3228747 CGTATATCATCTATTATAT
1 --TATAT-ATC-ATTATAT
3228766 TAT
1 TAT
3228769 TTATGTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
16 5 0.16
17 3 0.09
18 5 0.16
19 8 0.25
20 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (15 bp):
TATATATCATTATAT
Found at i:3234089 original size:20 final size:20
Alignment explanation
Indices: 3234065--3234115 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
3234055 AAAAAAAAAG
3234065 AAAAA-AGAAAAGAAAAATA
1 AAAAAGAGAAAAGAAAAATA
* * *
3234084 ATAAAATA-ATAATAAAAATA
1 A-AAAAGAGAAAAGAAAAATA
3234104 AAAAAGAGAAAA
1 AAAAAGAGAAAA
3234116 AAGAAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 6 0.24
20 18 0.72
21 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (20 bp):
AAAAAGAGAAAAGAAAAATA
Found at i:3235068 original size:44 final size:44
Alignment explanation
Indices: 3235016--3235193 Score: 191
Period size: 44 Copynumber: 4.0 Consensus size: 44
3235006 TAAGATTTGG
3235016 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * ** *
3235060 CATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * * * *
3235104 TATCCCTGTATTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
3235148 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
3235192 CA
1 CA
3235194 CTTCTGTGCT
Statistics
Matches: 105, Mismatches: 23, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
42 1 0.01
43 13 0.12
44 75 0.71
45 16 0.15
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:3235311 original size:117 final size:117
Alignment explanation
Indices: 3235100--3235335 Score: 409
Period size: 117 Copynumber: 2.0 Consensus size: 117
3235090 AGATTTCAGC
* * *
3235100 ATGGTATCCCTGTATTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAG
1 ATGGCATCCCTGTATTTATAGGGAACAAGTTGAAGATAACAAATTTGGCATCCCTGTGTTTATAG
*
3235165 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGTAG
66 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
* *
3235217 ATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAACAAATTTGGTATCCCTGTGTTTATAG
1 ATGGCATCCCTGTATTTATAGGGAACAAGTTGAAGATAACAAATTTGGCATCCCTGTGTTTATAG
*
3235282 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCGAAGCAG
66 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
3235334 AT
1 AT
3235336 CGAGGATTTC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (117 bp):
ATGGCATCCCTGTATTTATAGGGAACAAGTTGAAGATAACAAATTTGGCATCCCTGTGTTTATAG
GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
Found at i:3235400 original size:44 final size:44
Alignment explanation
Indices: 3235218--3235449 Score: 186
Period size: 44 Copynumber: 5.3 Consensus size: 44
3235208 GCAAAGTAGA
* *
3235218 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAACAAATT
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAACAGATT
* *
3235262 TGGTATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATT
* * * * * * ** *
3235306 TGACA-CTTCTGTGCTTACAGCGAAGCAGATCGAGGATTTCAG-TA
1 TGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAACAGATT
* *
3235350 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAACAGATT
* * * * * *
3235394 TGGCATCTCTGTATTGT-CAGAGAGCAGATCGAAGATACCAGATT
1 TGGCATCCCTGTGTT-TATAGGGAACAGATCGAAGATAACAGATT
*
3235438 TGGCATCTCTGT
1 TGGCATCCCTGT
3235450 ATTGGAGGAG
Statistics
Matches: 149, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
42 1 0.01
43 12 0.08
44 118 0.79
45 18 0.12
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATT
Found at i:3235442 original size:88 final size:89
Alignment explanation
Indices: 3235248--3235449 Score: 207
Period size: 88 Copynumber: 2.3 Consensus size: 89
3235238 GGAACAAGTT
* *
3235248 GAAGATAACAAATTTGGTATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACT
1 GAAGATAACAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACT
* *
3235313 TCTGTGCTTACAGCGAAGCAGATC
66 TCTGTGATTACAGAGAAGCAGATC
* ** * * * * *
3235337 GAGGATTTCAG-TATGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGCA-
1 GAAGATAACAGATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAACAGATCTGACAC
*
3235399 TCTCTGT-ATTGTCAGAG-AGCAGATC
65 T-TCTGTGATT-ACAGAGAAGCAGATC
* *
3235424 GAAGATACCAGATTTGGCATCTCTGT
1 GAAGATAACAGATTTGGCATCCCTGT
3235450 ATTGGAGGAG
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
87 20 0.22
88 64 0.70
89 7 0.08
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (89 bp):
GAAGATAACAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACT
TCTGTGATTACAGAGAAGCAGATC
Found at i:3235450 original size:44 final size:44
Alignment explanation
Indices: 3235380--3235472 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
3235370 GGAACAAGTT
*
3235380 GAAGATAGCAGATTTGGCATCTCTGTATTGTCA-GAGAGCAGATC
1 GAAGATACCAGATTTGGCATCTCTGTATTG-CAGGAGAGCAGATC
*
3235424 GAAGATACCAGATTTGGCATCTCTGTATTGGAGGAGAGCAGATC
1 GAAGATACCAGATTTGGCATCTCTGTATTGCAGGAGAGCAGATC
3235468 GAAGA
1 GAAGA
3235473 CATAGCTGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (44 bp):
GAAGATACCAGATTTGGCATCTCTGTATTGCAGGAGAGCAGATC
Found at i:3236111 original size:205 final size:205
Alignment explanation
Indices: 3235459--3236168 Score: 1233
Period size: 205 Copynumber: 3.5 Consensus size: 205
3235449 TATTGGAGGA
* * *
3235459 GAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
*
3235524 TTGTCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
*
3235589 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCCTG
131 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
3235654 TGCTTACAAG
196 TGCTTACAAG
* *
3235664 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAACAAATCTATGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
* *
3235729 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAATTCTGGCATCTCCACTTCGACGGAGAGCA-A
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
** *
3235793 CACATAGCAGATCCAAAATTTAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
3235858 TGCTTACAAG
196 TGCTTACAAG
**
3235868 GAGCAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
* *
3235933 TTGGCATCTCTGTATTATCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACGGAGGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
*
3235998 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
3236063 TGCTTACAAG
196 TGCTTACAAG
* *
3236073 GAGCAAATCAAAGACATAGCTAATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
*
3236138 TTGGCATCTCTGTATTGTCAGGGAACAAATC
66 TTGGCATCTCTGTATTGTCAGAGAACAAATC
3236169 GAAGAAGCAG
Statistics
Matches: 474, Mismatches: 30, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
204 192 0.41
205 282 0.59
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (205 bp):
GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
TGCTTACAAG
Found at i:3236323 original size:45 final size:45
Alignment explanation
Indices: 3236248--3236357 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 45
3236238 GTTTGCAATG
* * * *
3236248 AGCAGATTAAAGA-ACCAAATTTAGCGTCTCTGTATTAGACGGGG
1 AGCAGATCAAAGATAACAGATTTAGCGTCTCTGTATTAGACGGGA
* * *
3236292 AGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGCCGGGA
1 AGCAGATCAAAGATAACAGATTTAGCGTCTCTGTATTAGACGGGA
*
3236337 AGCAGATCAAAGATAGCAGAT
1 AGCAGATCAAAGATAACAGAT
3236358 ATCGCCTTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
44 11 0.20
45 45 0.80
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (45 bp):
AGCAGATCAAAGATAACAGATTTAGCGTCTCTGTATTAGACGGGA
Found at i:3236737 original size:19 final size:19
Alignment explanation
Indices: 3236713--3236791 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
3236703 AATCTTTAAG
3236713 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3236732 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3236751 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3236768 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3236789 GAT
1 GAT
3236792 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3236744 original size:36 final size:36
Alignment explanation
Indices: 3236703--3236790 Score: 119
Period size: 36 Copynumber: 2.4 Consensus size: 36
3236693 ATGAAAATAT
3236703 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGACAATCTTAGATATGATATGC
3236739 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG--ACAATCTTAGATATGATATGC
*
3236775 AATCTTGAAGATATGA
1 AATCTTTAAGATATGA
3236791 TCTTGTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 2 0.04
36 29 0.63
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (36 bp):
AATCTTTAAGATATGACAATCTTAGATATGATATGC
Found at i:3238887 original size:23 final size:24
Alignment explanation
Indices: 3238861--3238915 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
3238851 TATTATTAGA
3238861 AATTTTGA-ATGTATTGGAGATT-C
1 AATTTTGACATG-ATTGGAGATTAC
* * *
3238884 AATTATGACATGATTTGTGATTAC
1 AATTTTGACATGATTGGAGATTAC
3238908 AATTTTGA
1 AATTTTGA
3238916 TTCAACAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (24 bp):
AATTTTGACATGATTGGAGATTAC
Found at i:3243894 original size:28 final size:28
Alignment explanation
Indices: 3243858--3243912 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3243848 AAGTACTGAA
*
3243858 AGCGTGTCCAACTAGAAGCGTTTTTTGT
1 AGCGCGTCCAACTAGAAGCGTTTTTTGT
3243886 AGCGCGTCCAACTAGAAGCGTTTTTTG
1 AGCGCGTCCAACTAGAAGCGTTTTTTG
3243913 CTAGGTTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (28 bp):
AGCGCGTCCAACTAGAAGCGTTTTTTGT
Found at i:3247300 original size:16 final size:15
Alignment explanation
Indices: 3247223--3247393 Score: 60
Period size: 16 Copynumber: 11.5 Consensus size: 15
3247213 AATCTAACCC
3247223 TATATA-TA-TTTAT
1 TATATATTATTTTAT
*
3247236 T-TCTATTATTATTAT
1 TATATATTATT-TTAT
* *
3247251 ATATATATAAATTT-T
1 -TATATATTATTTTAT
*
3247266 TATATTGTTATTTGT-T
1 TATA-TATTATTT-TAT
3247282 TATATAGTTATTTTAT
1 TATATA-TTATTTTAT
* *
3247298 TATGTATTATATATAT
1 TATATATTAT-TTTAT
*
3247314 TATTTATTATTTT-T
1 TATATATTATTTTAT
*
3247328 CACTA-ATTATTATTAT
1 TA-TATATTATT-TTAT
* *
3247344 TTTACATTA--TTAT
1 TATATATTATTTTAT
3247357 T-TATATTATTGTTA-
1 TATATATTATT-TTAT
* *
3247371 TAT-TTTTACTTGTAT
1 TATATATTA-TTTTAT
3247386 TATATATT
1 TATATATT
3247394 TATTAATTAT
Statistics
Matches: 117, Mismatches: 20, Indels: 39
0.66 0.11 0.22
Matches are distributed among these distances:
12 9 0.08
13 8 0.07
14 20 0.17
15 32 0.27
16 42 0.36
17 6 0.05
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (15 bp):
TATATATTATTTTAT
Found at i:3247360 original size:20 final size:21
Alignment explanation
Indices: 3247311--3247360 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
3247301 GTATTATATA
*
3247311 TATTATTTATTATTTTTCACT
1 TATTATTTATTATTTTACACT
*
3247332 AATTA-TTATTATTTTACA-T
1 TATTATTTATTATTTTACACT
3247351 TATTATTTAT
1 TATTATTTAT
3247361 ATTATTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTATTTATTATTTTACACT
Found at i:3247397 original size:53 final size:53
Alignment explanation
Indices: 3247225--3247397 Score: 153
Period size: 57 Copynumber: 3.2 Consensus size: 53
3247215 TCTAACCCTA
* * *
3247225 TATATATTTATTTCTATTATTATTATATATATATAAATTTTTATATTGTTATTTGT-T
1 TATATATTTATTT-TATTATTATTAT-T-TATAT-TA-TTTTATATTTTTACTTGTAT
* * *
3247282 TATATAGTTATTTTATTATGTATTATATATATTA-TTTATTATTTTTCAC-T-AAT
1 TATATATTTATTTTATTAT-TATTATTTATATTATTTTA-TATTTTT-ACTTGTAT
*
3247335 TAT-TA-TTATTTTA-CATTATTATTTATATTATTGTTATATTTTTACTTGTAT
1 TATATATTTATTTTATTATTATTATTTATATTATT-TTATATTTTTACTTGTAT
3247386 TATATATTTATT
1 TATATATTTATT
3247398 AATTATTTAT
Statistics
Matches: 97, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
49 15 0.15
50 11 0.11
51 16 0.16
52 8 0.08
53 16 0.16
54 2 0.02
55 5 0.05
56 6 0.06
57 18 0.19
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (53 bp):
TATATATTTATTTTATTATTATTATTTATATTATTTTATATTTTTACTTGTAT
Found at i:3247462 original size:20 final size:18
Alignment explanation
Indices: 3247439--3247502 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
3247429 ATATACTTTC
3247439 ATATTATATATAATTATTTT
1 ATATTATATAT-ATT-TTTT
*
3247459 ATATTATTATGTCATTTTTT
1 ATATTA-TATAT-ATTTTTT
*
3247479 ATACTAT-TATATTTTTT
1 ATATTATATATATTTTTT
*
3247496 ATCTTAT
1 ATATTAT
3247503 TATCATTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 12 0.32
18 2 0.05
19 1 0.03
20 15 0.41
21 7 0.19
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTATATATATTTTTT
Found at i:3247494 original size:17 final size:18
Alignment explanation
Indices: 3247455--3247510 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
3247445 TATATAATTA
*
3247455 TTTTATATTATTATGTCATT
1 TTTTATCTTATTA--TCATT
3247475 TTTTATAC-TATTAT-ATT
1 TTTTAT-CTTATTATCATT
3247492 TTTTATCTTATTATCATT
1 TTTTATCTTATTATCATT
3247510 T
1 T
3247511 AAGTTTTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 15 0.47
18 5 0.16
20 11 0.34
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTATCTTATTATCATT
Found at i:3247809 original size:17 final size:17
Alignment explanation
Indices: 3247752--3247809 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
3247742 TCTAAACCAT
*
3247752 TATATTTTATATTTTTA
1 TATATTATATATTTTTA
*
3247769 TATAATTAT-TATTCTTA
1 TAT-ATTATATATTTTTA
3247786 TA-A--ATATATTTTTA
1 TATATTATATATTTTTA
3247800 TATATTATAT
1 TATATTATAT
3247810 CATTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 2 0.06
17 16 0.48
18 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATATATTTTTA
Found at i:3249818 original size:33 final size:33
Alignment explanation
Indices: 3249776--3249848 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
3249766 TTAAACCTAA
*
3249776 TTTT-AACTAGTTTTAAACATCAAAACCTTCTT
1 TTTTAAACTAGTTTTAAACATCAAAACCCTCTT
*
3249808 TTTTAAACTAGTTTTAAACGTCAAAACCCTCTT
1 TTTTAAACTAGTTTTAAACATCAAAACCCTCTT
3249841 TTTTAAAC
1 TTTTAAAC
3249849 ATAATAACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 4 0.11
33 34 0.89
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (33 bp):
TTTTAAACTAGTTTTAAACATCAAAACCCTCTT
Done.