Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, whole genome shotgun sequence
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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 8 of 22
Found at i:3071753 original size:8 final size:8
Alignment explanation
Indices: 3071707--3071753 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
3071697 GTAATTATAA
3071707 TTTTTATT
1 TTTTTATT
*
3071715 TTATTA-T
1 TTTTTATT
*
3071722 TTTTTA-A
1 TTTTTATT
*
3071729 TTCTTATT
1 TTTTTATT
3071737 TTTTTATT
1 TTTTTATT
3071745 TTTTTATT
1 TTTTTATT
3071753 T
1 T
3071754 ATATATTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 11 0.34
8 21 0.66
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTATT
Found at i:3073056 original size:31 final size:32
Alignment explanation
Indices: 3073013--3073079 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
3073003 TAATATTCTA
*
3073013 TTTTATTATTATATTTAATTAAGTTCAT-TAAT
1 TTTTATTATTATA-TTAAATAAGTTCATATAAT
*
3073045 TTTTATT-TTATATTAAATAAGTTCTTATAAT
1 TTTTATTATTATATTAAATAAGTTCATATAAT
3073076 TTTT
1 TTTT
3073080 TTGAAGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 12 0.38
31 13 0.41
32 7 0.22
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (32 bp):
TTTTATTATTATATTAAATAAGTTCATATAAT
Found at i:3073068 original size:30 final size:31
Alignment explanation
Indices: 3073013--3073106 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 31
3073003 TAATATTCTA
*
3073013 TTTTATTATTATATTTAATTAAGTTCAT-TAAT
1 TTTTATT-TTATA-TTAAATAAGTTCATATAAT
*
3073045 TTTTATTTTATATTAAATAAGTTCTTATAAT
1 TTTTATTTTATATTAAATAAGTTCATATAAT
** * **
3073076 TTTT-TTGAAGATTAAATAAGTTTTTATAAT
1 TTTTATTTTATATTAAATAAGTTCATATAAT
3073106 T
1 T
3073107 AACAGTTGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 35 0.64
31 13 0.24
32 7 0.13
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.57
Consensus pattern (31 bp):
TTTTATTTTATATTAAATAAGTTCATATAAT
Found at i:3073378 original size:28 final size:28
Alignment explanation
Indices: 3073325--3073385 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
3073315 TTATTTATTT
* *
3073325 TAAAATTTATTTAACTTAAAATAAAATA
1 TAAAATTTATTGAACTTAAAATAAAAAA
* *
3073353 TAAAATTTAATTGAATTTAATA-AAAAAA
1 TAAAATTT-ATTGAACTTAAAATAAAAAA
3073381 TAAAA
1 TAAAA
3073386 AACTTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (28 bp):
TAAAATTTATTGAACTTAAAATAAAAAA
Found at i:3073386 original size:29 final size:28
Alignment explanation
Indices: 3073325--3073392 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 28
3073315 TTATTTATTT
* *
3073325 TAAAATTTATTTAACTTAAAATAAAATA
1 TAAAATTTATTGAACTTAAAAAAAAATA
*
3073353 TAAAATTTAATTGAATTTAATAAAAAAATA
1 TAAAATTT-ATTGAACTTAA-AAAAAAATA
* *
3073383 AAAAACTTAT
1 TAAAATTTAT
3073393 AAAATTTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 8 0.24
29 11 0.33
30 14 0.42
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (28 bp):
TAAAATTTATTGAACTTAAAAAAAAATA
Found at i:3074197 original size:5 final size:5
Alignment explanation
Indices: 3074187--3074218 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
3074177 CTGGGGCAGG
*
3074187 GGAGA GGAGA GGAGA GGAGA GGAGA GGCGA GG
1 GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GG
3074219 GGTTGGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.62, T:0.00
Consensus pattern (5 bp):
GGAGA
Found at i:3106469 original size:21 final size:22
Alignment explanation
Indices: 3106429--3106486 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
3106419 TTGTGAATAA
* * * *
3106429 ATATATTTAAAAGTTGAAAATT
1 ATATATTTATAATTTTAAAAAT
3106451 A-ATATTTATAATTTTAAAAAT
1 ATATATTTATAATTTTAAAAAT
*
3106472 ATTTATTT-TAATTTT
1 ATATATTTATAATTTT
3106487 TTAAACTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
ATATATTTATAATTTTAAAAAT
Found at i:3108873 original size:4 final size:4
Alignment explanation
Indices: 3108864--3108893 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
3108854 ACATTTGTAA
3108864 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
3108894 ATTATGCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:3111550 original size:279 final size:279
Alignment explanation
Indices: 3111037--3111791 Score: 882
Period size: 279 Copynumber: 2.7 Consensus size: 279
3111027 CTTATAGAAT
* * * * * * * ** *
3111037 ACGACAAATTCAATTATAAGGAAATACGTGTAAATTAATGAATTCGTTAGAACTTATAAATGATC
1 ACGACAAATTCAATTATAACGAAACAC-AGTAAGTTGATAAACTCGACAGAATTTATAAATGATC
* * * *
3111102 ATAAATATATTGATAAAATTGAAAGTGAAAA-GATAG-ATTCAAAATTACATATTGATTC-ATAA
65 ATAAATATATTGATAAATTTAAAAGTGAAAAGGA-AGAATT-AAGATTACATATTGATTCGA-AT
* * * *
3111164 CTTATTAATGATTTACAACAAATTTAAAGAAAATTAATGGTTTACGACAAATTCAAAAATGATTG
127 CTCATCAATGATTTACAACAAATTCAAAGAAAATTAATGATTTACGACAAATTCAAAAATGATTG
*
3111229 AAGTATAAAAGATATGACGAGCAACTAATAATCATGTAAAAGCACACAAGTAAATG-GTCGTATA
192 AAGTATAAAAGATATGACGAGCAACTAATAATCA-GTAAAAGCACACAAGTAAATGACT-GTATA
*
3111293 CAAATCAATGATTT-TTTACATAAC
255 CAAATCAATGATTTGTTTACAAAAC
** * *
3111317 GTGACAAATTCAATTATAACGAAACATGCA-TACGTTGATAAACTCGACAGAATTTATAATTGAT
1 ACGACAAATTCAATTATAACGAAACA--CAGTAAGTTGATAAACTCGACAGAATTTATAAATGAT
* *
3111381 CATAAATATATTG-TAAATTTAAAAGTGAAAAGGAAGAATTAAGATAACGTATTGATTCGAATCT
64 CATAAATATATTGATAAATTTAAAAGTGAAAAGGAAGAATTAAGATTACATATTGATTCGAATCT
* *
3111445 CATCAATGATTTACGACAAATTCAAAGACAATTAATGATTTACGACAAATTCAAAAATGATTGAA
129 CATCAATGATTTACAACAAATTCAAAGAAAATTAATGATTTACGACAAATTCAAAAATGATTGAA
** * * * * *
3111510 GTATAAAAGATATGACGATTAACTAATAATTGCA-TAAAAGCATATATGTAGATGACTGTATATA
194 GTATAAAAGATATGACGAGCAACTAATAA-T-CAGTAAAAGCACACAAGTAAATGACTGTATACA
*
3111574 AATCAATGATTTGTTTACAAAAT
257 AATCAATGATTTGTTTACAAAAC
* **
3111597 ACGACAAATTCAATTATAACGAAACACATGTAAGTTTATAAACTCGTTAGAATTTATCACAA--A
1 ACGACAAATTCAATTATAACGAAACACA-GTAAGTTGATAAACTCGACAGAATTTAT-A-AATGA
* * * *
3111660 TCATAACTATATTGATAAATTTAAAAGTGAAAAGGAATAATTAAGATTACATATTGATTTGTATC
63 TCATAAATATATTGATAAATTTAAAAGTGAAAAGGAAGAATTAAGATTACATATTGATTCGAATC
* * * * * *
3111725 TCATCAATAATTTACAACAAATACAAATAAAATTAATAATTTACGACAAATTTAAAGATGATTGA
128 TCATCAATGATTTACAACAAATTCAAAGAAAATTAATGATTTACGACAAATTCAAAAATGATTGA
3111790 AG
193 AG
3111792 CGTATATGAT
Statistics
Matches: 404, Mismatches: 57, Indels: 27
0.83 0.12 0.06
Matches are distributed among these distances:
278 2 0.00
279 156 0.39
280 137 0.34
281 107 0.26
282 2 0.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (279 bp):
ACGACAAATTCAATTATAACGAAACACAGTAAGTTGATAAACTCGACAGAATTTATAAATGATCA
TAAATATATTGATAAATTTAAAAGTGAAAAGGAAGAATTAAGATTACATATTGATTCGAATCTCA
TCAATGATTTACAACAAATTCAAAGAAAATTAATGATTTACGACAAATTCAAAAATGATTGAAGT
ATAAAAGATATGACGAGCAACTAATAATCAGTAAAAGCACACAAGTAAATGACTGTATACAAATC
AATGATTTGTTTACAAAAC
Found at i:3119318 original size:16 final size:16
Alignment explanation
Indices: 3119288--3119319 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3119278 ATACCAAGTG
3119288 ATTATTTCTTAAAAAT
1 ATTATTTCTTAAAAAT
3119304 ATTACTTTCTTAAAAA
1 ATTA-TTTCTTAAAAA
3119320 GGTGATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATTTCTTAAAAAT
Found at i:3125025 original size:4 final size:4
Alignment explanation
Indices: 3125016--3125063 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
3125006 TTTACATTTG
*
3125016 CATA CATA CATA CAAA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3125064 TATATATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:3129397 original size:21 final size:23
Alignment explanation
Indices: 3129367--3129415 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3129357 TTTCTTATTT
* *
3129367 TTTTTATAAA-AATATAATAATA
1 TTTTTATAAATAATAAAAAAATA
3129389 TTTTT-TAAATTAATAAAAAAATA
1 TTTTTATAAA-TAATAAAAAAATA
3129412 TTTT
1 TTTT
3129416 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTTATAAATAATAAAAAAATA
Found at i:3129970 original size:6 final size:6
Alignment explanation
Indices: 3129959--3129983 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3129949 CATGAAGCTT
3129959 CGGTGG CGGTGG CGGTGG CGGTGG C
1 CGGTGG CGGTGG CGGTGG CGGTGG C
3129984 CATGCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.64, T:0.16
Consensus pattern (6 bp):
CGGTGG
Found at i:3131335 original size:31 final size:30
Alignment explanation
Indices: 3131299--3131380 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
3131289 TGAAGAGATG
* *
3131299 AAATTATAAAATTTTTAAAAAATTAAGGGTA
1 AAATTATAAAATTTTTAAAAAAATAA-GGAA
*
3131330 AAATTAT-AAATATTTAAAATAAAATAAGGAA
1 AAATTATAAAAT-TTTTAAA-AAAATAAGGAA
3131361 AAATT-TATAAATTTTTAAAA
1 AAATTATA-AAATTTTTAAAA
3131381 CTTTGGAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
30 6 0.14
31 27 0.63
32 10 0.23
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATTATAAAATTTTTAAAAAAATAAGGAA
Found at i:3132704 original size:20 final size:20
Alignment explanation
Indices: 3132681--3132719 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3132671 CAGCTACGAG
* *
3132681 GAAGACAGAGAATTCCCAGA
1 GAAGACAGAAAACTCCCAGA
3132701 GAAGACAGAAAACTCCCAG
1 GAAGACAGAAAACTCCCAG
3132720 CAAGACAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (20 bp):
GAAGACAGAAAACTCCCAGA
Found at i:3132726 original size:19 final size:20
Alignment explanation
Indices: 3132682--3132727 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3132672 AGCTACGAGG
* * *
3132682 AAGACAGAGAATTCCCAGAG
1 AAGACAGAAAACTCCCAGAC
3132702 AAGACAGAAAACTCCCAG-C
1 AAGACAGAAAACTCCCAGAC
3132721 AAGACAG
1 AAGACAG
3132728 CAGCAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.24, G:0.22, T:0.07
Consensus pattern (20 bp):
AAGACAGAAAACTCCCAGAC
Found at i:3138107 original size:15 final size:15
Alignment explanation
Indices: 3138087--3138117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3138077 AGTTTAGAGG
*
3138087 GAAAAGAAGAGAAAA
1 GAAAAGAACAGAAAA
3138102 GAAAAGAACAGAAAA
1 GAAAAGAACAGAAAA
3138117 G
1 G
3138118 CAATGGCAGT
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:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (15 bp):
GAAAAGAACAGAAAA
Found at i:3146543 original size:38 final size:37
Alignment explanation
Indices: 3146501--3146575 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
3146491 ATATATGTAA
*
3146501 ATCAATATCAT-ATTACTTAAAATAACAAATAACATTTT
1 ATCAA-ATCATAATTACTTAAAATAA-AAATAAAATTTT
* * *
3146539 ATCAAATGATAATTAGTTGAAATAAAAATAAAATTTT
1 ATCAAATCATAATTACTTAAAATAAAAATAAAATTTT
3146576 GACCTAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 15 0.47
38 17 0.53
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (37 bp):
ATCAAATCATAATTACTTAAAATAAAAATAAAATTTT
Found at i:3150531 original size:14 final size:14
Alignment explanation
Indices: 3150491--3150539 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
3150481 AAAATCAAAG
3150491 TAATTTAATT-TTT
1 TAATTTAATTATTT
3150504 TAATTTTAAAAATTATTT
1 TAA-TTT---AATTATTT
3150522 TAATTTAATTATTT
1 TAATTTAATTATTT
3150536 TAAT
1 TAAT
3150540 AATATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 3 0.10
14 15 0.48
17 7 0.23
18 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAATTTAATTATTT
Found at i:3156237 original size:10 final size:10
Alignment explanation
Indices: 3156211--3156240 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3156201 AGGTAGAGAA
*
3156211 AGAGAGAGAG
1 AGAGAGGGAG
3156221 AGAGAGGGAG
1 AGAGAGGGAG
3156231 AGAGAGGGAG
1 AGAGAGGGAG
3156241 TACCTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (10 bp):
AGAGAGGGAG
Found at i:3157466 original size:2 final size:2
Alignment explanation
Indices: 3157459--3157486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3157449 TTCTACTGAG
3157459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3157487 GGAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3159800 original size:22 final size:24
Alignment explanation
Indices: 3159758--3159803 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
3159748 ATTTATATTT
*
3159758 TTTTATTTTATTTGAAAATTTTAA
1 TTTTAATTTATTTGAAAATTTTAA
3159782 TTTTAATTT-TTT-AAAATTTTAA
1 TTTTAATTTATTTGAAAATTTTAA
3159804 AATTTTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 3 0.14
24 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAATTTATTTGAAAATTTTAA
Found at i:3163402 original size:23 final size:21
Alignment explanation
Indices: 3163383--3163424 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3163373 AAATTCTTCA
3163383 AACTGATTACCATCGTTTCTT
1 AACTGATTACCATCGTTTCTT
*
3163404 AACTGATTATCATC--TTCTT
1 AACTGATTACCATCGTTTCTT
3163423 AA
1 AA
3163425 TTGAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (21 bp):
AACTGATTACCATCGTTTCTT
Found at i:3167676 original size:13 final size:13
Alignment explanation
Indices: 3167654--3167703 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
3167644 GTGCAAGGAG
*
3167654 AGAAAAAAAAAAA
1 AGAAAGAAAAAAA
*
3167667 AGAAAGAAAAAGA
1 AGAAAGAAAAAAA
*
3167680 AGAAGGAAAAAAA
1 AGAAAGAAAAAAA
3167693 AGAAGAGAAAA
1 AGAA-AGAAAA
3167704 TGGAGTTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
13 26 0.84
14 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAAAA
Found at i:3167692 original size:16 final size:15
Alignment explanation
Indices: 3167654--3167703 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
3167644 GTGCAAGGAG
3167654 AGAAAAAAAA-AA-A
1 AGAAAAAAAAGAAGA
3167667 AGAAAGAAAAAGAAGA
1 AGAAA-AAAAAGAAGA
3167683 AGGAAAAAAAAGAAG-
1 A-GAAAAAAAAGAAGA
3167698 AGAAAA
1 AGAAAA
3167704 TGGAGTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 5 0.15
14 10 0.30
15 3 0.09
16 11 0.33
17 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAGAAGA
Found at i:3170081 original size:22 final size:22
Alignment explanation
Indices: 3169956--3170124 Score: 101
Period size: 22 Copynumber: 7.4 Consensus size: 22
3169946 AAATTATAAA
*
3169956 AATAAATTATTAACATTTTAAT
1 AATAAATTATTAATATTTTAAT
3169978 AATAAATTATTAATA-TTTAGAT
1 AATAAATTATTAATATTTTA-AT
* * * ** *
3170000 TATTAATTATTAAAAACATTATT
1 AATAAATTATT-AATATTTTAAT
* * * *
3170023 ATTAAATTACTAATA--ATAAA
1 AATAAATTATTAATATTTTAAT
*
3170043 AATAAATTTATTTATATTTTAAT
1 AATAAA-TTATTAATATTTTAAT
*
3170066 CATAAATTATTAATATGTTAGGTAAAT
1 AATAAATTATTAATAT-TT---T-AAT
*
3170093 TATAAAATTATTAATATTTTAAT
1 AAT-AAATTATTAATATTTTAAT
*
3170116 TATAAATTA
1 AATAAATTA
3170125 ATAAAACTTT
Statistics
Matches: 113, Mismatches: 22, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
20 7 0.06
21 11 0.10
22 43 0.38
23 27 0.24
24 4 0.04
26 1 0.01
27 7 0.06
28 13 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AATAAATTATTAATATTTTAAT
Found at i:3170143 original size:50 final size:50
Alignment explanation
Indices: 3170044--3170149 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
3170034 AATAATAAAA
* * * * *
3170044 ATAAATTTATTTATATTTTAATCATAAATTATTAATATGTTAGGTAAATT
1 ATAAAATTATTAATATTTTAATCATAAATTAATAAAATGTTAAGTAAATT
*
3170094 ATAAAATTATTAATATTTTAATTATAAATTAATAAAACT-TTAAAG-AAATT
1 ATAAAATTATTAATATTTTAATCATAAATTAATAAAA-TGTT-AAGTAAATT
3170144 ATAAAA
1 ATAAAA
3170150 AAATCAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 45 0.94
51 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (50 bp):
ATAAAATTATTAATATTTTAATCATAAATTAATAAAATGTTAAGTAAATT
Found at i:3175644 original size:2 final size:2
Alignment explanation
Indices: 3175635--3175675 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3175625 TAAAAAAGTC
*
3175635 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3175676 TAGGAATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3178552 original size:13 final size:14
Alignment explanation
Indices: 3178524--3178552 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3178514 GTCATCATTA
3178524 TTTTATAAAGTATC
1 TTTTATAAAGTATC
3178538 TTTTATAAA-TATC
1 TTTTATAAAGTATC
3178551 TT
1 TT
3178553 CATGGCATAT
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:0.07, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTTATAAAGTATC
Found at i:3178912 original size:12 final size:11
Alignment explanation
Indices: 3178888--3178944 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
3178878 CTTCCCCTTC
*
3178888 CCCCCTCTCCT
1 CCCCTTCTCCT
3178899 CCCCTTCTCTCT
1 CCCCTTCTC-CT
3178911 CCCCTTCTCCT
1 CCCCTTCTCCT
*
3178922 --CCTTTTCCT
1 CCCCTTCTCCT
*
3178931 CTCCTT-TCCT
1 CCCCTTCTCCT
3178941 CCCC
1 CCCC
3178945 CCCTCGCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 8 0.20
10 7 0.17
11 14 0.35
12 11 0.28
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (11 bp):
CCCCTTCTCCT
Found at i:3180995 original size:16 final size:16
Alignment explanation
Indices: 3180974--3181013 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3180964 AAACCACTCA
3180974 ATACATACATACATAT
1 ATACATACATACATAT
*
3180990 ATACATACATACTTAT
1 ATACATACATACATAT
*
3181006 ATATATAC
1 ATACATAC
3181014 TTGAAAGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATACATACATAT
Found at i:3183269 original size:2 final size:2
Alignment explanation
Indices: 3183262--3183294 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3183252 CCATACATAC
3183262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3183295 GAAGAGCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3199211 original size:138 final size:138
Alignment explanation
Indices: 3198963--3199230 Score: 367
Period size: 138 Copynumber: 1.9 Consensus size: 138
3198953 AAGGCTTACT
* * * ** * *
3198963 CAATCTTGTGTGCATATGAGACTACTTTCTTTTCTAGCTTTCAACAAATTCATAATGATTTTGCT
1 CAATCTTGTGTGCATACGAGACCACTTTATTTTCTAGCTTTCAACAAACCCATAATGAATTTACT
* ** *
3199028 TATAGAAAACACTAACATCTTTTGTACTTAAGCAATGTGGGATAGAAATCTTATAAGATATCACT
66 TATAGAAAACACTAACATCTTTAGTACTTAAGCAAAATGGGATAGAAACCTTATAAGATATCACT
3199093 GCTTGGCC
131 GCTTGGCC
* * *
3199101 CAATCTTGTG-GACGTACGAGACCACTTTATTTTCTAGCTTTCAATAAGCCCATAATGAATTTAC
1 CAATCTTGTGTG-CATACGAGACCACTTTATTTTCTAGCTTTCAACAAACCCATAATGAATTTAC
* * *
3199165 TTATATAAAACACTAACATCTTTAGTACTTAGGCAAAATGGGATAGAAACCTTATGAGATATCAC
65 TTATAGAAAACACTAACATCTTTAGTACTTAAGCAAAATGGGATAGAAACCTTATAAGATATCAC
3199230 T
130 T
3199231 ACATTTCTAA
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
137 1 0.01
138 111 0.99
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (138 bp):
CAATCTTGTGTGCATACGAGACCACTTTATTTTCTAGCTTTCAACAAACCCATAATGAATTTACT
TATAGAAAACACTAACATCTTTAGTACTTAAGCAAAATGGGATAGAAACCTTATAAGATATCACT
GCTTGGCC
Found at i:3199588 original size:16 final size:17
Alignment explanation
Indices: 3199567--3199605 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3199557 TGGATTTAGA
3199567 ATAAATTTAAAAG-ATT
1 ATAAATTTAAAAGAATT
3199583 ATAAA-TTAAAAGAATT
1 ATAAATTTAAAAGAATT
3199599 A-AAATTT
1 ATAAATTT
3199606 TTAATTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
ATAAATTTAAAAGAATT
Found at i:3199593 original size:15 final size:16
Alignment explanation
Indices: 3199567--3199604 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3199557 TGGATTTAGA
3199567 ATAAATTTAAAAG-ATT
1 ATAAA-TTAAAAGAATT
3199583 ATAAATTAAAAGAATT
1 ATAAATTAAAAGAATT
3199599 A-AAATT
1 ATAAATT
3199605 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
ATAAATTAAAAGAATT
Found at i:3204673 original size:2 final size:2
Alignment explanation
Indices: 3204666--3204691 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3204656 TTGAATAATG
3204666 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3204692 CTTTTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3225266 original size:3 final size:3
Alignment explanation
Indices: 3225258--3225291 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3225248 AGAAAACATA
* *
3225258 TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3225292 TTTGAAGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3227727 original size:22 final size:22
Alignment explanation
Indices: 3227663--3227730 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
3227653 GCATAACTAG
* * *
3227663 TTTTTAACTATTATGTTACTAA
1 TTTTTAAATATTACGTTACTGA
3227685 TTTTTAAATATTACGTTACTGA
1 TTTTTAAATATTACGTTACTGA
*
3227707 TTTTTAGATATTAC-TTGACTGA
1 TTTTTAAATATTACGTT-ACTGA
3227729 TT
1 TT
3227731 AATATGACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (22 bp):
TTTTTAAATATTACGTTACTGA
Found at i:3227770 original size:22 final size:23
Alignment explanation
Indices: 3227739--3227799 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
3227729 TTAATATGAC
* *
3227739 ATTGTATGACTAGTTGAT-AAGT
1 ATTGCATGACTAGTTAATAAAGT
*
3227761 ATTGCGTGACTAGTTAATAAAGT
1 ATTGCATGACTAGTTAATAAAGT
*
3227784 ATTGCATGACTCGTTA
1 ATTGCATGACTAGTTA
3227800 GTTAGGCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (23 bp):
ATTGCATGACTAGTTAATAAAGT
Found at i:3227857 original size:22 final size:22
Alignment explanation
Indices: 3227828--3227891 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
3227818 TATGCATTGT
*
3227828 CTAAAAATCAATTACGTAATAC
1 CTAAAAATCAATCACGTAATAC
*
3227850 TTAAAAATCAATCACGTAATAC
1 CTAAAAATCAATCACGTAATAC
**
3227872 CTAAAAATCAAAGACGTAAT
1 CTAAAAATCAATCACGTAAT
3227892 GATTAAGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (22 bp):
CTAAAAATCAATCACGTAATAC
Found at i:3230920 original size:27 final size:28
Alignment explanation
Indices: 3230852--3231131 Score: 117
Period size: 28 Copynumber: 10.2 Consensus size: 28
3230842 TAATAACTTT
* * * *
3230852 TTCATCATGATGTGTAACAATTAAATTT
1 TTCAACATGACGTGTAACAACTAAATTC
**
3230880 TTCAACATTTCGTGTAACAACTAAA-TC
1 TTCAACATGACGTGTAACAACTAAATTC
* * * * *
3230907 TTCAATATGACGTGTTGA-AATTACATTT
1 TTCAACATGACGTG-TAACAACTAAATTC
**
3230935 TTCAACATGACACGTAACAACTAAATT-
1 TTCAACATGACGTGTAACAACTAAATTC
* * * * * * * * *
3230962 TTTAACATAACATTTACCTATTACATTT
1 TTCAACATGACGTGTAACAACTAAATTC
* ** *
3230990 TTCAAAATGATATATAACAACTAAATT-
1 TTCAACATGACGTGTAACAACTAAATTC
* * *
3231017 TTCAACATGACATGTAAAAACTATA-TC
1 TTCAACATGACGTGTAACAACTAAATTC
* * * * *
3231044 TTTAACATAACGTTTAATAACTAAATTT
1 TTCAACATGACGTGTAACAACTAAATTC
* * * * *
3231072 TTCAATATCACGTATAAC-ACTTACATTT
1 TTCAACATGACGTGTAACAAC-TAAATTC
*
3231100 TTCAACAT-AGCATGTAACAACTAAATT-
1 TTCAACATGA-CGTGTAACAACTAAATTC
3231127 TTCAA
1 TTCAA
3231132 TATGGAGTAT
Statistics
Matches: 185, Mismatches: 58, Indels: 19
0.71 0.22 0.07
Matches are distributed among these distances:
26 1 0.01
27 85 0.46
28 97 0.52
29 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (28 bp):
TTCAACATGACGTGTAACAACTAAATTC
Found at i:3231039 original size:82 final size:83
Alignment explanation
Indices: 3230927--3231128 Score: 223
Period size: 82 Copynumber: 2.4 Consensus size: 83
3230917 CGTGTTGAAA
* * * * *
3230927 TTACATTTTTCAACATGACACGTAACAACTAAATTTTTAACATAACATTTACCT-ATTACATTTT
1 TTACAATTTTCAACATGACATGTAACAACTAAATTTTTAACATAACATTTA-ATAACTAAATTTT
* *
3230991 TCAAAATGATATATAACAAC
65 TCAAAATCACATATAAC-AC
* * * *
3231011 -TA-AATTTTCAACATGACATGTAAAAACTATATCTTTAACATAACGTTTAATAACTAAATTTTT
1 TTACAATTTTCAACATGACATGTAACAACTAAATTTTTAACATAACATTTAATAACTAAATTTTT
* *
3231074 CAATATCACGTATAACAC
66 CAAAATCACATATAACAC
*
3231092 TTACATTTTTCAACAT-AGCATGTAACAACTAAATTTT
1 TTACAATTTTCAACATGA-CATGTAACAACTAAATTTT
3231129 CAATATGGAG
Statistics
Matches: 97, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
81 3 0.03
82 65 0.67
83 29 0.30
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (83 bp):
TTACAATTTTCAACATGACATGTAACAACTAAATTTTTAACATAACATTTAATAACTAAATTTTT
CAAAATCACATATAACAC
Found at i:3231144 original size:55 final size:53
Alignment explanation
Indices: 3230866--3231184 Score: 166
Period size: 55 Copynumber: 5.8 Consensus size: 53
3230856 TCATGATGTG
* * * * * *
3230866 TAACAATTAAATTTTTCAACATTTCGTGTAACAACTAAATCTTCAATATGACGTGT
1 TAAC-ATTACATTTTTCAACA-TGCATGTAACAACTAAATTTTCAATATCACGT-A
* * * * * *
3230922 TGAA-ATTACATTTTTCAACATGACACGTAACAACTAAATTTTTAACATAACATT
1 T-AACATTACATTTTTCAACATG-CATGTAACAACTAAATTTTCAATATCACGTA
* * * * * *
3230976 TACCTATTACATTTTTCAAAATGATATATAACAACTAAATTTTCAACATGACATGTA
1 TAAC-ATTACATTTTTCAACATG-CATGTAACAACTAAATTTTCAATAT--CACGTA
* * * * * * * *
3231033 -AAAACTATATCTTT-AACATAACGTTTAATAACTAAATTTTTCAATATCACGTA
1 TAACATTACATTTTTCAACAT-GCATGTAACAACTAAA-TTTTCAATATCACGTA
*
3231086 TAACACTTACATTTTTCAACATAGCATGTAACAACTAAATTTTCAATATGGA-GTA
1 TAACA-TTACATTTTTCAACAT-GCATGTAACAACTAAATTTTCAATAT-CACGTA
* ** *
3231141 TAACA--AAATTTTAGAACATGGCATGTAAC-ACTACATTTTTCAAT
1 TAACATTACATTTTTCAACAT-GCATGTAACAACTA-AATTTTCAAT
3231185 GTGGTGTTAA
Statistics
Matches: 204, Mismatches: 46, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
51 4 0.02
52 29 0.14
53 6 0.03
54 21 0.10
55 119 0.58
56 21 0.10
57 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (53 bp):
TAACATTACATTTTTCAACATGCATGTAACAACTAAATTTTCAATATCACGTA
Found at i:3231168 original size:52 final size:51
Alignment explanation
Indices: 3231103--3231203 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 51
3231093 TACATTTTTC
3231103 AACATAGCATGTAACAACTA-AATTTTCAATATGGAGTATAACAAAATTTTAG
1 AACATAGCATGTAAC-ACTACAATTTTCAATATGGAGT-TAACAAAATTTTAG
* * * * *
3231155 AACATGGCATGTAACACTACATTTTTCAATGTGGTGTTAACAACATTTT
1 AACATAGCATGTAACACTACAATTTTCAATATGGAGTTAACAAAATTTT
3231204 TTTCATAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 15 0.35
52 28 0.65
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (51 bp):
AACATAGCATGTAACACTACAATTTTCAATATGGAGTTAACAAAATTTTAG
Found at i:3234022 original size:17 final size:17
Alignment explanation
Indices: 3234000--3234032 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3233990 CAATATACTT
3234000 CAAC-TTATTGCACATTA
1 CAACTTTATT-CACATTA
3234017 CAACTTTATTCACATT
1 CAACTTTATTCACATT
3234033 TATAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (17 bp):
CAACTTTATTCACATTA
Found at i:3236624 original size:12 final size:12
Alignment explanation
Indices: 3236607--3236638 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3236597 ATCATTCGAT
3236607 CTCTTTCTTTCC
1 CTCTTTCTTTCC
3236619 CTCTTTCTTTCC
1 CTCTTTCTTTCC
*
3236631 TTCTTTCT
1 CTCTTTCT
3236639 CCCAGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
CTCTTTCTTTCC
Found at i:3241563 original size:2 final size:2
Alignment explanation
Indices: 3241556--3241580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3241546 TTATGTGCTT
3241556 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3241581 TGCTTGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3256084 original size:25 final size:25
Alignment explanation
Indices: 3256062--3256109 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3256052 ATTTATTTAT
3256062 ATTTTTT-AAAAATTTTATAATTTC
1 ATTTTTTCAAAAATTTTATAATTTC
* *
3256086 ATTTTTTCAATAATTTTTTAATTT
1 ATTTTTTCAAAAATTTTATAATTT
3256110 TTATACCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTTTCAAAAATTTTATAATTTC
Found at i:3256164 original size:63 final size:63
Alignment explanation
Indices: 3256037--3256231 Score: 158
Period size: 63 Copynumber: 3.1 Consensus size: 63
3256027 CCTCCAACAA
* * * * *
3256037 TTTTTAAATTTTATAATTTATTTATATTTTTTAAAAATTTTATAATTTCATTTTTTCAATAAT
1 TTTTTAAATTTTATAACTTATTTATACTTTTTAAAAATTTTATAATTTCATCTTTACAAAAAT
* * * * * *
3256100 TTTTTAATTTTTATACCTTGTTTCTACTTTTTAAAAATTTTATAATTTCGTCTTTAGAAAAAT
1 TTTTTAAATTTTATAACTTATTTATACTTTTTAAAAATTTTATAATTTCATCTTTACAAAAAT
*** * * * * * * ** * *
3256163 TTAAAAAAAATTT-TACCATATTTTTATTTTTTAAAATTTTTATAATTTTTTCTTTATAATAAT
1 TT-TTTAAATTTTATAACTTATTTATACTTTTTAAAAATTTTATAATTTCATCTTTACAAAAAT
3256226 TTTTTA
1 TTTTTA
3256232 TTTAATAAAA
Statistics
Matches: 103, Mismatches: 28, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
62 1 0.01
63 97 0.94
64 5 0.05
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.59
Consensus pattern (63 bp):
TTTTTAAATTTTATAACTTATTTATACTTTTTAAAAATTTTATAATTTCATCTTTACAAAAAT
Found at i:3257036 original size:14 final size:14
Alignment explanation
Indices: 3257004--3257054 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3256994 TAATTTTTAA
* * *
3257004 ATTTTATTTATATG
1 ATTTTATATAAATT
3257018 ATTTTATATAAAATT
1 ATTTTATAT-AAATT
*
3257033 -TTTTATCTAAATT
1 ATTTTATATAAATT
3257046 ATTTTATAT
1 ATTTTATAT
3257055 TATTATCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 5 0.17
14 22 0.73
15 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
ATTTTATATAAATT
Found at i:3257093 original size:20 final size:18
Alignment explanation
Indices: 3257065--3257114 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3257055 TATTATCAAA
*
3257065 TATTAAATTTTTAACATAAT
1 TATTTAATTTTTAA-AT-AT
*
3257085 TATTTAATTTATAAATAT
1 TATTTAATTTTTAAATAT
*
3257103 TTTTTAATTTTT
1 TATTTAATTTTT
3257115 TATCTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 12 0.46
19 2 0.08
20 12 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTAATTTTTAAATAT
Found at i:3261574 original size:14 final size:13
Alignment explanation
Indices: 3261521--3261574 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
3261511 AGTATGTTAA
*
3261521 TATATTTTTTAATT
1 TATA-TTTTTAAAT
*
3261535 TATATTTTTAAAG
1 TATATTTTTAAAT
3261548 TA-A-TTTT-AAT
1 TATATTTTTAAAT
3261558 TATAGTTTTTAAAT
1 TATA-TTTTTAAAT
3261572 TAT
1 TAT
3261575 TAAAGATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 4 0.12
11 5 0.15
12 1 0.03
13 13 0.39
14 10 0.30
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (13 bp):
TATATTTTTAAAT
Found at i:3264414 original size:14 final size:14
Alignment explanation
Indices: 3264395--3264432 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3264385 ATCAAAAAAT
3264395 AATTTTTT-TGTGAA
1 AATTTTTTATGT-AA
3264409 AATTTTTTATGTAA
1 AATTTTTTATGTAA
*
3264423 AATATTTTAT
1 AATTTTTTAT
3264433 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (14 bp):
AATTTTTTATGTAA
Found at i:3264430 original size:15 final size:16
Alignment explanation
Indices: 3264390--3264430 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3264380 TCGTAATCAA
*
3264390 AAAATAATTTTTTTGTG
1 AAAAT-ATTTTTATGTG
3264407 AAAAT-TTTTTATGT-
1 AAAATATTTTTATGTG
3264421 AAAATATTTT
1 AAAATATTTT
3264431 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.23
15 12 0.55
17 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (16 bp):
AAAATATTTTTATGTG
Found at i:3264793 original size:23 final size:24
Alignment explanation
Indices: 3264763--3264813 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3264753 AATCGTTAAA
*
3264763 TAATAATTATT-G-AAATATTTTTT
1 TAATAATTATTAGTAAA-ATTTATT
3264786 TAATAATTATTAGTAAAATTTATT
1 TAATAATTATTAGTAAAATTTATT
3264810 TAAT
1 TAAT
3264814 TTATAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 11 0.44
24 11 0.44
25 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATAATTATTAGTAAAATTTATT
Found at i:3264797 original size:26 final size:24
Alignment explanation
Indices: 3264761--3264813 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3264751 GTAATCGTTA
* *
3264761 AATAATAATTATTGAAATATTTTTTT
1 AATAATAATTAGT-AAA-ATTTATTT
*
3264787 AATAATTATTAGTAAAATTTATTT
1 AATAATAATTAGTAAAATTTATTT
3264811 AAT
1 AAT
3264814 TTATAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.42
25 3 0.12
26 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
AATAATAATTAGTAAAATTTATTT
Found at i:3264899 original size:16 final size:15
Alignment explanation
Indices: 3264878--3264929 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
3264868 TAATTTTAAT
3264878 AATATTGAATAATTTA
1 AATATT-AATAATTTA
*
3264894 AATATTAATATTTTA
1 AATATTAATAATTTA
* *
3264909 AAT-TAAAAAATTTA
1 AATATTAATAATTTA
3264923 AA-ATTAA
1 AATATTAA
3264930 ATATTAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 13 0.43
15 11 0.37
16 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
AATATTAATAATTTA
Found at i:3264908 original size:15 final size:16
Alignment explanation
Indices: 3264878--3264911 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3264868 TAATTTTAAT
3264878 AATATTGAATAATTTA
1 AATATTGAATAATTTA
*
3264894 AATATT-AATATTTTA
1 AATATTGAATAATTTA
3264909 AAT
1 AAT
3264912 TAAAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATTGAATAATTTA
Found at i:3270564 original size:5 final size:5
Alignment explanation
Indices: 3270519--3270563 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
3270509 TTTCGTGGTA
*
3270519 TTTTC TTTTC TTTTC TTTTC TTTTC TTTGC TTTTTC TTTTGC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT-C TTT
3270564 GGTGTTGCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 28 0.78
6 8 0.22
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:3270976 original size:86 final size:89
Alignment explanation
Indices: 3270872--3271060 Score: 242
Period size: 90 Copynumber: 2.1 Consensus size: 89
3270862 CATGTTAAGA
* * *
3270872 TAATTAT-TAAAAATATTTAGTAATTAAAATTATAATAC-AATGCTA-TATCTAATTAGTTAAAG
1 TAATTATATAAAAATATTTAGCAATTAAAATTATAATACAAATACTATTATCTAACTAGTTAAAG
* *
3270934 TTACACTACAATATTGTTAATTAG
66 TTACACTACAATACTATTAATTAG
* * *
3270958 TAATTATATAAAAA-ATTTAGCAATTATAATTATGATACAATAATACTATTATCTAGCTAGTTAA
1 TAATTATATAAAAATATTTAGCAATTAAAATTATAATAC-A-AATACTATTATCTAACTAGTTAA
* *
3271022 AGTTATACTATAATACTATTAATTAG
64 AGTTACACTACAATACTATTAATTAG
3271048 TAATTATATAAAA
1 TAATTATATAAAA
3271061 TATCTAATAA
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
86 28 0.32
87 6 0.07
89 6 0.07
90 48 0.55
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (89 bp):
TAATTATATAAAAATATTTAGCAATTAAAATTATAATACAAATACTATTATCTAACTAGTTAAAG
TTACACTACAATACTATTAATTAG
Found at i:3271098 original size:90 final size:90
Alignment explanation
Indices: 3270925--3271098 Score: 213
Period size: 90 Copynumber: 1.9 Consensus size: 90
3270915 TATATCTAAT
* * * * * **
3270925 TAGTTAAAGTTACACTACAATATTGTTAATTAGTAATTATATAAAAAATTTAGCAATTATAATTA
1 TAGTTAAAGTTACACTACAATACTATTAATTAGTAATTATATAAAAAATCTAACAATTAGAAGCA
*
3270990 TGATACAATAATACTATTATCTAGC
66 TAATACAATAATACTATTATCTAGC
* * * *
3271015 TAGTTAAAGTTATACTATAATACTATTAATTAGTAATTATATAAAATATCTAATAATTAGAAGCA
1 TAGTTAAAGTTACACTACAATACTATTAATTAGTAATTATATAAAAAATCTAACAATTAGAAGCA
* * *
3271080 TAATATAATATTATTATTA
66 TAATACAATAATACTATTA
3271099 CTGTTAGTTA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (90 bp):
TAGTTAAAGTTACACTACAATACTATTAATTAGTAATTATATAAAAAATCTAACAATTAGAAGCA
TAATACAATAATACTATTATCTAGC
Found at i:3272562 original size:33 final size:33
Alignment explanation
Indices: 3272517--3272596 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
3272507 TTAGTATGTC
**
3272517 ACATTATCATCAATAACAATATGTCAATATATT
1 ACATTATCATCAATAACAATACATCAATATATT
* *
3272550 ACATTATTATCAATAATAATACATCAATATATT
1 ACATTATCATCAATAACAATACATCAATATATT
*
3272583 ATATTATCATCAAT
1 ACATTATCATCAAT
3272597 TATGATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (33 bp):
ACATTATCATCAATAACAATACATCAATATATT
Found at i:3272710 original size:31 final size:31
Alignment explanation
Indices: 3272675--3272734 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3272665 AATAATTAGT
*
3272675 TATAAAAACTTATTTAATTCAAAATAAAAAA
1 TATAAAAACTTATTTAATACAAAATAAAAAA
** *
3272706 TATAAAAGTTTATTTGATACAAAATAAAA
1 TATAAAAACTTATTTAATACAAAATAAAA
3272735 TATAAGGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (31 bp):
TATAAAAACTTATTTAATACAAAATAAAAAA
Found at i:3272751 original size:29 final size:28
Alignment explanation
Indices: 3272702--3272758 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
3272692 TTCAAAATAA
3272702 AAAATATAAAAGTTTATTTGATACAAAAT
1 AAAATATAAAAGTTTATTTGATA-AAAAT
**
3272731 AAAATATAAGGGTTTGA-TTGATAAAAAT
1 AAAATATAAAAGTTT-ATTTGATAAAAAT
3272759 TTATTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 19 0.76
30 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (28 bp):
AAAATATAAAAGTTTATTTGATAAAAAT
Found at i:3276589 original size:2 final size:2
Alignment explanation
Indices: 3276582--3276609 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3276572 TAGCTCAGTA
3276582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3276610 TATTGGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3281696 original size:18 final size:21
Alignment explanation
Indices: 3281660--3281697 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
3281650 CATCCAGGTC
3281660 TGTCTCTCTCTTCTCTCCCCT
1 TGTCTCTCTCTTCTCTCCCCT
3281681 TGTC-CTCT-TTCT-TCCCC
1 TGTCTCTCTCTTCTCTCCCC
3281698 ACCCTACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 4 0.24
21 4 0.24
ACGTcount: A:0.00, C:0.47, G:0.05, T:0.47
Consensus pattern (21 bp):
TGTCTCTCTCTTCTCTCCCCT
Found at i:3286798 original size:2 final size:2
Alignment explanation
Indices: 3286791--3286831 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3286781 GTAAACACAA
3286791 AG AG AG AG AG AG AG -G AG AG AG AG AG AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3286831 A
1 A
3286832 ATACCCAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3286810 original size:13 final size:13
Alignment explanation
Indices: 3286792--3286830 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
3286782 TAAACACAAA
3286792 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
3286805 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
3286818 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
3286831 AATACCCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Found at i:3291931 original size:15 final size:15
Alignment explanation
Indices: 3291882--3291932 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3291872 AATTATCAAG
3291882 TAAAAATTATTAAATAA
1 TAAAAA-TATTAAA-AA
* * *
3291899 AAAAAAT-TTAGAAT
1 TAAAAATATTAAAAA
3291913 TAAAAATATTAAAAA
1 TAAAAATATTAAAAA
3291928 TAAAA
1 TAAAA
3291933 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 7 0.26
15 14 0.52
16 1 0.04
17 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TAAAAATATTAAAAA
Found at i:3295119 original size:32 final size:32
Alignment explanation
Indices: 3295083--3295151 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
3295073 AAAATTAAAA
* *
3295083 AATTATAAAAAAT-TAAAATTTATTAAGTATAT
1 AATTATAAAAAATAAAAAAATTATTAAGTAT-T
*
3295115 AATTA-AAAAAATAAAAAAATTATTAATTATT
1 AATTATAAAAAATAAAAAAATTATTAAGTATT
3295146 AATTAT
1 AATTAT
3295152 TTTTTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
AATTATAAAAAATAAAAAAATTATTAAGTATT
Found at i:3297628 original size:6 final size:6
Alignment explanation
Indices: 3297617--3297664 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
3297607 ACCACATGCC
*
3297617 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT -GAC-T ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3297663 AT
1 AT
3297665 GTAATATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 1 0.03
5 4 0.11
6 33 0.87
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:3298899 original size:118 final size:118
Alignment explanation
Indices: 3298768--3299021 Score: 289
Period size: 118 Copynumber: 2.2 Consensus size: 118
3298758 TCATCCCCAC
* ** * * * *
3298768 CACATATGTCTAGCACCAAACCTTGTTAGCTAAGCT-TAAGCATGTGTCTTGCT-TCAACATACA
1 CACACATGTCTAGCACCAAACCTTCCTAGCT-AGCTCCAAGCATGTGTCTTACTCT-AACACAAA
* * * * * * **
3298831 TGTGCAGCA-CTATAACTCTTGCTAGATAGGGATAACGAGCATGTGTCTCATTGAG
64 TGTCCACCATC-ATAACCCTTGCTAGATAGAGATAACAAGCAAGTGTCTCATCAAG
* * *
3298886 CGCACATGTCTAGCACCAAACCTTCCTAGCTAGGTCCAAGCATGTGTCTTACTCTAGCACAAATG
1 CACACATGTCTAGCACCAAACCTTCCTAGCTAGCTCCAAGCATGTGTCTTACTCTAACACAAATG
*
3298951 TCCACCATCATAGCCCTTGCTAGATAGAGATAACAAGCAAGTGTCTCATCAAG
66 TCCACCATCATAACCCTTGCTAGATAGAGATAACAAGCAAGTGTCTCATCAAG
3299004 CACACATGTCTAGCACCA
1 CACACATGTCTAGCACCA
3299022 TGGCTTCTGT
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
117 3 0.03
118 108 0.96
119 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (118 bp):
CACACATGTCTAGCACCAAACCTTCCTAGCTAGCTCCAAGCATGTGTCTTACTCTAACACAAATG
TCCACCATCATAACCCTTGCTAGATAGAGATAACAAGCAAGTGTCTCATCAAG
Found at i:3304317 original size:13 final size:13
Alignment explanation
Indices: 3304299--3304324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3304289 TGAAGGTATG
3304299 TTGAATATATTAA
1 TTGAATATATTAA
3304312 TTGAATATATTAA
1 TTGAATATATTAA
3304325 ATAAGCAGAC
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:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TTGAATATATTAA
Found at i:3307139 original size:27 final size:27
Alignment explanation
Indices: 3307101--3307170 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
3307091 TTTCTCATGC
3307101 TTGCTGCCATTGGCAGTGCCTTGGTGG
1 TTGCTGCCATTGGCAGTGCCTTGGTGG
3307128 TTGCTGCCATTGGCAGTGCCTTGGTGG
1 TTGCTGCCATTGGCAGTGCCTTGGTGG
*
3307155 TTGCTGCCAATGGCAG
1 TTGCTGCCATTGGCAG
3307171 CGTTCTTGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.10, C:0.23, G:0.36, T:0.31
Consensus pattern (27 bp):
TTGCTGCCATTGGCAGTGCCTTGGTGG
Found at i:3307402 original size:2 final size:2
Alignment explanation
Indices: 3307395--3307439 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3307385 CTTTTATGTG
* *
3307395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3307437 TA T
1 TA T
3307440 TACTATTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3308391 original size:6 final size:6
Alignment explanation
Indices: 3308374--3308416 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
3308364 TTTTACACAC
* * * *
3308374 ACATAC ACATAT ACATAT ATATAT ACATAT ATATAT ATATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
3308417 TATACCCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (6 bp):
ACATAT
Found at i:3308393 original size:2 final size:2
Alignment explanation
Indices: 3308382--3308420 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3308372 ACACATACAC
* *
3308382 AT AT AC AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3308421 CCCAAAGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3308397 original size:12 final size:12
Alignment explanation
Indices: 3308382--3308420 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
3308372 ACACATACAC
3308382 ATATACATATAT
1 ATATACATATAT
3308394 ATATACATATAT
1 ATATACATATAT
*
3308406 ATATATATATAT
1 ATATACATATAT
3308418 ATA
1 ATA
3308421 CCCAAAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATACATATAT
Found at i:3310263 original size:31 final size:31
Alignment explanation
Indices: 3310222--3310282 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3310212 ATTTTTAATA
* * * * *
3310222 TCATATATTTTGTTTTTATTTTTTACTATAC
1 TCATAGATTTTATTTTCATTTCTTAATATAC
3310253 TCATAGATTTTATTTTCATTTCTTAATATA
1 TCATAGATTTTATTTTCATTTCTTAATATA
3310283 ATTTTCTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.61
Consensus pattern (31 bp):
TCATAGATTTTATTTTCATTTCTTAATATAC
Found at i:3317636 original size:22 final size:22
Alignment explanation
Indices: 3317577--3317639 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 22
3317567 TCACTTAATT
* *
3317577 AAATGGATTTCTTCATTGAGTA
1 AAATGGATTTTTTCTTTGAGTA
* *
3317599 AAGTGAATTTTTTTTCTTTGAGTA
1 AAATGGA--TTTTTTCTTTGAGTA
3317623 AAATGGATTTTTTCTTT
1 AAATGGATTTTTTCTTT
3317640 CAAAGAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 15 0.45
24 18 0.55
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (22 bp):
AAATGGATTTTTTCTTTGAGTA
Found at i:3323791 original size:16 final size:16
Alignment explanation
Indices: 3323770--3323807 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3323760 TTTTTTGTTT
3323770 ATGGGTTCACTTCATC
1 ATGGGTTCACTTCATC
3323786 ATGGGTTCACTTCATC
1 ATGGGTTCACTTCATC
3323802 ATGGGT
1 ATGGGT
3323808 GAGGTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (16 bp):
ATGGGTTCACTTCATC
Found at i:3324357 original size:32 final size:32
Alignment explanation
Indices: 3324319--3324379 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3324309 AATATGTAAG
*
3324319 TCAAAAATAATTTTTTTC-AAATATTATTCAAA
1 TCAAAAATAA-TTTTTTCGAAATAATATTCAAA
3324351 TCAAAAATAATTTTTTCGAAATAATATTC
1 TCAAAAATAATTTTTTCGAAATAATATTC
3324380 GGAATGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (32 bp):
TCAAAAATAATTTTTTCGAAATAATATTCAAA
Found at i:3324564 original size:43 final size:43
Alignment explanation
Indices: 3324507--3324596 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
3324497 GCTATGCTGG
*
3324507 TTTTGAGGATATCTTAGAAATATTGATGAAAGAAATTAAATGC
1 TTTTGAGGATATCTTAGAAATATGGATGAAAGAAATTAAATGC
* *
3324550 TTTTGAGGATATCTTAGAATTATGGATGAAAGAAATTAAATGT
1 TTTTGAGGATATCTTAGAAATATGGATGAAAGAAATTAAATGC
3324593 TTTT
1 TTTT
3324597 TGAATTTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (43 bp):
TTTTGAGGATATCTTAGAAATATGGATGAAAGAAATTAAATGC
Found at i:3329423 original size:15 final size:15
Alignment explanation
Indices: 3329400--3329438 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3329390 TGCAGTTCAG
*
3329400 CTTTCTTTTTCTCTT
1 CTTTTTTTTTCTCTT
*
3329415 CTTTTTTTTTTTCTT
1 CTTTTTTTTTCTCTT
3329430 CTTCTTTTT
1 CTT-TTTTT
3329439 CATTTCTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTTTTCTCTT
Found at i:3329432 original size:18 final size:17
Alignment explanation
Indices: 3329405--3329438 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3329395 TTCAGCTTTC
3329405 TTTTTCTCTTCTTTTTT
1 TTTTTCTCTTCTTTTTT
3329422 TTTTTCTTCTTCTTTTT
1 TTTTTC-TCTTCTTTTT
3329439 CATTTCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTCTTCTTTTTT
Found at i:3331129 original size:16 final size:17
Alignment explanation
Indices: 3331098--3331130 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3331088 TAAACAACAC
*
3331098 AATATGATAAATAATTT
1 AATATGATAAAAAATTT
3331115 AATAT-ATAAAAAATTT
1 AATATGATAAAAAATTT
3331131 CAACTCATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATGATAAAAAATTT
Found at i:3332221 original size:7 final size:7
Alignment explanation
Indices: 3332211--3332249 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
3332201 GACTCCAGGG
3332211 TTCATGC
1 TTCATGC
*
3332218 TTCATGT
1 TTCATGC
3332225 TTCATGC
1 TTCATGC
*
3332232 TTCAGGC
1 TTCATGC
3332239 TTCATGC
1 TTCATGC
3332246 TTCA
1 TTCA
3332250 ATAGGAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (7 bp):
TTCATGC
Found at i:3332230 original size:14 final size:14
Alignment explanation
Indices: 3332206--3332249 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3332196 CTCTTGACTC
*
3332206 CAGGGTTCATGCTT
1 CAGGCTTCATGCTT
* *
3332220 CATGTTTCATGCTT
1 CAGGCTTCATGCTT
3332234 CAGGCTTCATGCTT
1 CAGGCTTCATGCTT
3332248 CA
1 CA
3332250 ATAGGAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (14 bp):
CAGGCTTCATGCTT
Found at i:3333584 original size:16 final size:18
Alignment explanation
Indices: 3333563--3333595 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3333553 TCCAAGTCAA
3333563 ATAAAA-TA-AGAAAAAC
1 ATAAAAGTAGAGAAAAAC
3333579 ATAAAAGTAGAGAAAAA
1 ATAAAAGTAGAGAAAAA
3333596 AACTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (18 bp):
ATAAAAGTAGAGAAAAAC
Found at i:3334159 original size:25 final size:26
Alignment explanation
Indices: 3334112--3334160 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
3334102 ATGAGTGACA
*
3334112 CTTTCTCTTCACTTATGCTATCATGT
1 CTTTCTCTTCACCTATGCTATCATGT
3334138 CTTTCT-TTCACCT-TGCTCATCAT
1 CTTTCTCTTCACCTATGCT-ATCAT
3334161 ATTATGCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.14, C:0.31, G:0.06, T:0.49
Consensus pattern (26 bp):
CTTTCTCTTCACCTATGCTATCATGT
Found at i:3340578 original size:18 final size:18
Alignment explanation
Indices: 3340545--3340579 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3340535 TTAGAAGTAT
* *
3340545 TTTATTAATTATAAATAA
1 TTTATTAATAAAAAATAA
3340563 TTTATTAATAAAAAATA
1 TTTATTAATAAAAAATA
3340580 TATACAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTATTAATAAAAAATAA
Found at i:3345221 original size:31 final size:32
Alignment explanation
Indices: 3345184--3345271 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
3345174 AACAGTACTC
* *
3345184 ATTACTTGA-AAGTGTCTTCAACAGAGTACTTT
1 ATTACTTCATAAGTGTCTTCAACACAG-ACTTT
**
3345216 A-TACTTCATTGGTGTCTTCAACACAGACTTT
1 ATTACTTCATAAGTGTCTTCAACACAGACTTT
**
3345247 ATTACTTCATTGGTGTCTTCAACAC
1 ATTACTTCATAAGTGTCTTCAACAC
3345272 TTTCAATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 12 0.24
32 38 0.76
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (32 bp):
ATTACTTCATAAGTGTCTTCAACACAGACTTT
Found at i:3345236 original size:32 final size:32
Alignment explanation
Indices: 3345195--3345271 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
3345185 TTACTTGAAA
*
3345195 GTGTCTTCAACAGAGTACTTTA-TACTTCATTG
1 GTGTCTTCAACACAG-ACTTTATTACTTCATTG
3345227 GTGTCTTCAACACAGACTTTATTACTTCATTG
1 GTGTCTTCAACACAGACTTTATTACTTCATTG
3345259 GTGTCTTCAACAC
1 GTGTCTTCAACAC
3345272 TTTCAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 6 0.14
32 37 0.86
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (32 bp):
GTGTCTTCAACACAGACTTTATTACTTCATTG
Found at i:3350082 original size:26 final size:24
Alignment explanation
Indices: 3350035--3350089 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
3350025 ATATTTTTAA
3350035 TATTTACATATATAAATAAAATATGT
1 TATTTACATATATAAATAAAAT-T-T
* ** *
3350061 TATTTACTTATATATTTTAAATTT
1 TATTTACATATATAAATAAAATTT
3350085 TATTT
1 TATTT
3350090 GAATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
26 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
TATTTACATATATAAATAAAATTT
Found at i:3363222 original size:16 final size:17
Alignment explanation
Indices: 3363183--3363222 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3363173 AAGGTTGCAG
3363183 TCAAGC-TGAGCCAAGC
1 TCAAGCTTGAGCCAAGC
*
3363199 TGAA-CTTGAG-CAAGC
1 TCAAGCTTGAGCCAAGC
3363214 TCAAGCTTG
1 TCAAGCTTG
3363223 TGTCAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (17 bp):
TCAAGCTTGAGCCAAGC
Found at i:3364656 original size:14 final size:14
Alignment explanation
Indices: 3364637--3364671 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3364627 TTTGTTGTTC
* *
3364637 TTTTTTTTTTTTAA
1 TTTTTTTCTTTCAA
3364651 TTTTTTTCTTTCAA
1 TTTTTTTCTTTCAA
3364665 TTTTTTT
1 TTTTTTT
3364672 GAAAACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTTTCAA
Found at i:3369027 original size:2 final size:2
Alignment explanation
Indices: 3369020--3369048 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3369010 TTGTTGGTTT
3369020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3369049 GGGTGAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3372289 original size:2 final size:2
Alignment explanation
Indices: 3372282--3372308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3372272 TATTTTGTAC
3372282 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3372309 TTGCTACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3378060 original size:12 final size:12
Alignment explanation
Indices: 3378043--3378068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3378033 ATTTCCTCTC
3378043 TGTTCAATTGTT
1 TGTTCAATTGTT
3378055 TGTTCAATTGTT
1 TGTTCAATTGTT
3378067 TG
1 TG
3378069 GGTTGAGGGG
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:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (12 bp):
TGTTCAATTGTT
Found at i:3394838 original size:81 final size:82
Alignment explanation
Indices: 3394753--3395050 Score: 279
Period size: 81 Copynumber: 3.7 Consensus size: 82
3394743 AAAGCTGTGG
* *
3394753 AAACTGAAGTCAAATATTCAGAAGCAAAGCCTCCA-TCATTAGAAATTACTCCAACAAACAAAGA
1 AAACTGAAGTCAAAGATTCTGAAGCAAAGCCTCCAGTCATTAGAAATTACTCCAACAAACAAAGA
*
3394817 TAGCGAAGAAGCCACAA
66 TAGTGAAGAAGCCACAA
* * * * * * **
3394834 AAACTGAAATCAAGGATTCTGAAGCAAAG-CTGCAGTCATTAGAAGTTGCACCAACGGACAAAGA
1 AAACTGAAGTCAAAGATTCTGAAGCAAAGCCTCCAGTCATTAGAAATTACTCCAACAAACAAAGA
***
3394898 TAGTGAAGAAGCTTTAA
66 TAGTGAAGAAGCCACAA
* * * * * *
3394915 AAATTGAAGTCAAGGATGCTGAAGGAAAGCCT-CAGTCATCAGAAGATT-CTACAACAAACAAAG
1 AAACTGAAGTCAAAGATTCTGAAGCAAAGCCTCCAGTCATTAGAA-ATTACTCCAACAAACAAAG
*
3394978 ATAGTGAAGAAGCTGCAGAA
65 ATAGTGAAGAAGC--CACAA
* * * *
3394998 AGAA-T--AGTTAATGATTCTGAAGCAAGGCCTCCA-TCATTAGAAGTTACTCCAAC
1 A-AACTGAAGTCAAAGATTCTGAAGCAAAGCCTCCAGTCATTAGAAATTACTCCAAC
3395051 TAGCAAGGTT
Statistics
Matches: 174, Mismatches: 35, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
80 6 0.03
81 156 0.90
82 6 0.03
83 4 0.02
84 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (82 bp):
AAACTGAAGTCAAAGATTCTGAAGCAAAGCCTCCAGTCATTAGAAATTACTCCAACAAACAAAGA
TAGTGAAGAAGCCACAA
Found at i:3396731 original size:21 final size:21
Alignment explanation
Indices: 3396706--3396750 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3396696 ATAATAAAAA
3396706 TAAAAAT-TTATTT-AATATTT
1 TAAAAATATT-TTTAAATATTT
*
3396726 TAAAAATATTTTTAAATTTTT
1 TAAAAATATTTTTAAATATTT
3396747 TAAA
1 TAAA
3396751 TATTATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAAATATTTTTAAATATTT
Found at i:3396746 original size:20 final size:20
Alignment explanation
Indices: 3396706--3396745 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3396696 ATAATAAAAA
3396706 TAAAAATTTATTTAATATTT
1 TAAAAATTTATTTAATATTT
3396726 TAAAAATATT-TTTAA-ATTT
1 TAAAAAT-TTATTTAATATTT
3396745 T
1 T
3396746 TTAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAAATTTATTTAATATTT
Found at i:3406137 original size:112 final size:112
Alignment explanation
Indices: 3405961--3406227 Score: 288
Period size: 112 Copynumber: 2.4 Consensus size: 112
3405951 TTGTTGTTTC
* * * * * **
3405961 GTTGTTGCATTGATTTGTCAATGTTACATCCCACA-TTTTTGCGTTGGTTTTTCTCTTTGGATTA
1 GTTGTTCCATTGAGTTATCAATGTTACAACCCACATTTTTTGCGTTGGTATTTCTCTTTACATTA
** ** *
3406025 AAGCTCAA-GCTAGGAGATGTTTTGTCTTCTGGGGTTTTG-TTATTTT
66 AAGCT-AATGAGAGGAGAAATTTTGTCATCTGGGGTTTTGTTTATTTT
* * *
3406071 GTTGTATCCTTTGAGTTATCAATGTTACAACCAACATTTTTTGTGTTGGTATTTCTCTTTACATT
1 GTTGT-TCCATTGAGTTATCAATGTTACAACCCACATTTTTTGCGTTGGTATTTCTCTTTACATT
*
3406136 AAAGCTAATGAGAGGAGAAATTTTGTCATCTGGGTTTTTGTTACTTATTTT
65 AAAGCTAATGAGAGGAGAAATTTTGTCATCTGGGGTTTTG-T--TTATTTT
* * * *
3406187 GTTGTTTCATTGATTTAGCAGTGTTACAACCCACATTTTTT
1 GTTGTTCCATTGAGTTATCAATGTTACAACCCACATTTTTT
3406228 TTTTGTTTCA
Statistics
Matches: 128, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
110 5 0.04
111 26 0.20
112 55 0.43
115 30 0.23
116 12 0.09
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (112 bp):
GTTGTTCCATTGAGTTATCAATGTTACAACCCACATTTTTTGCGTTGGTATTTCTCTTTACATTA
AAGCTAATGAGAGGAGAAATTTTGTCATCTGGGGTTTTGTTTATTTT
Found at i:3420416 original size:18 final size:19
Alignment explanation
Indices: 3420381--3420417 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3420371 GTTTATTAAT
3420381 TTTTAAAATAAATATTTTA
1 TTTTAAAATAAATATTTTA
*
3420400 TTTTAAAA-AATTATTTTA
1 TTTTAAAATAAATATTTTA
3420418 CATTGTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAAATAAATATTTTA
Found at i:3421088 original size:12 final size:12
Alignment explanation
Indices: 3421062--3421095 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3421052 TAAACGTAAC
*
3421062 ATTTTA-AAGCA
1 ATTTTATAATCA
3421073 ATTTTATAATCA
1 ATTTTATAATCA
3421085 ATTTTATAATC
1 ATTTTATAATC
3421096 TTATTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (12 bp):
ATTTTATAATCA
Found at i:3422149 original size:20 final size:20
Alignment explanation
Indices: 3422104--3422152 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3422094 TAATAAAAGG
* *
3422104 TATTTTTATTTTTTATCACT
1 TATTTTTATTTTTTATAAAT
*
3422124 TTTTTTTATTATTTTA-AAAT
1 TATTTTTATT-TTTTATAAAT
3422144 TATTTTTAT
1 TATTTTTAT
3422153 CAACTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTTATTTTTTATAAAT
Found at i:3460142 original size:44 final size:41
Alignment explanation
Indices: 3460078--3460159 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
3460068 TTTTTGACAA
*
3460078 AATCATTTTCTAGTAACCTTTCTACTATTGGAGAGAACTATGAC
1 AATCATTTTCTAGTAACCTTTC--C-ATAGGAGAGAACTATGAC
**
3460122 AATCATTTTCTAGTCTCCTTTCCATAGGAGAGAACTAT
1 AATCATTTTCTAGTAACCTTTCCATAGGAGAGAACTAT
3460160 TGTGTGAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 14 0.40
42 1 0.03
44 20 0.57
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (41 bp):
AATCATTTTCTAGTAACCTTTCCATAGGAGAGAACTATGAC
Found at i:3462507 original size:2 final size:2
Alignment explanation
Indices: 3462500--3462525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3462490 GTTTTGTAGG
3462500 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3462526 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3474791 original size:29 final size:29
Alignment explanation
Indices: 3474744--3474800 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3474734 TATTAAAAAA
**
3474744 TATTTAAATAAGTTATTATTTTTTTATTG
1 TATTTAAATAAGTTATTATAGTTTTATTG
*
3474773 TATTTAATTAAGATT-TTATAGTTTTATT
1 TATTTAAATAAG-TTATTATAGTTTTATT
3474801 ATAAGTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (29 bp):
TATTTAAATAAGTTATTATAGTTTTATTG
Found at i:3476981 original size:22 final size:24
Alignment explanation
Indices: 3476929--3476992 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
3476919 AATATAAAGT
* *
3476929 AAATTAAATAAAAAAATTTATATCA
1 AAATTATATAAATAAATTTATA-CA
3476954 AAATTATATAAATAAATTT-TA-A
1 AAATTATATAAATAAATTTATACA
3476976 AAATTAT-TCAAATAAAT
1 AAATTATAT-AAATAAAT
3476993 CAACCTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 16 0.44
24 2 0.06
25 17 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATTATATAAATAAATTTATACA
Found at i:3481045 original size:13 final size:12
Alignment explanation
Indices: 3481023--3481052 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
3481013 AGAATTATAG
3481023 TATTTATATTAA
1 TATTTATATTAA
3481035 TATTATATATTAA
1 TATT-TATATTAA
3481048 TATTT
1 TATTT
3481053 TGAAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTATATTAA
Found at i:3488967 original size:3 final size:3
Alignment explanation
Indices: 3488959--3488995 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3488949 TTTGCATGCT
3488959 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3488996 ACAATGTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3498776 original size:21 final size:21
Alignment explanation
Indices: 3498737--3498777 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3498727 AAATTATTAA
*
3498737 ATTAAAAAAATAATTATAATT
1 ATTAAAAAAATAATAATAATT
3498758 ATTAAAAAAATCAA-AATAAT
1 ATTAAAAAAAT-AATAATAAT
3498778 AAAAGAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAAAAAAATAATAATAATT
Found at i:3502173 original size:117 final size:117
Alignment explanation
Indices: 3501980--3502214 Score: 398
Period size: 117 Copynumber: 2.0 Consensus size: 117
3501970 AATTCCAGTT
*
3501980 GAGAATTATTAGTAAGAGGAGCAGATTGAGAGAGGTTGCACTCCTCAAGAAATTCAAAATGTGCT
1 GAGAATTATTAGTAAGAGAAGCAGATTGAGAGAGGTTGCACTCCTCAAGAAATTCAAAATGTGCT
*
3502045 TGTCACCGATTTAGCAAATTCACTTAAATAATTATCAAAAGAAGAACTTGGA
66 TGTCACCGATTTAGCAAATTCACTGAAATAATTATCAAAAGAAGAACTTGGA
* * *
3502097 GAGAATTATTAGTAAGAGAAGCAGATTGAGAGAGGTTGCAGTCCTCAAGATATTCAAATTGTGCT
1 GAGAATTATTAGTAAGAGAAGCAGATTGAGAGAGGTTGCACTCCTCAAGAAATTCAAAATGTGCT
** *
3502162 TGTCATTGATTTAGCAAATTCACTGACATAATTATCAAAAGAAGAACTTGGA
66 TGTCACCGATTTAGCAAATTCACTGAAATAATTATCAAAAGAAGAACTTGGA
3502214 G
1 G
3502215 CTAATAACTC
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 110 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (117 bp):
GAGAATTATTAGTAAGAGAAGCAGATTGAGAGAGGTTGCACTCCTCAAGAAATTCAAAATGTGCT
TGTCACCGATTTAGCAAATTCACTGAAATAATTATCAAAAGAAGAACTTGGA
Found at i:3513254 original size:5 final size:5
Alignment explanation
Indices: 3513244--3513269 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3513234 AAAATCGAGC
3513244 TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG T
3513270 ATACTTCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:3521937 original size:21 final size:21
Alignment explanation
Indices: 3521913--3521975 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
3521903 TTACCAGTGA
* *
3521913 TTCTCCCAGGTTTAACATTGG
1 TTCTCCCAGGTTTAACACTAG
*
3521934 TTCTCCCAGGTTTAATACTAG
1 TTCTCCCAGGTTTAACACTAG
*
3521955 TTCTCCCAGGTTTAATACTAG
1 TTCTCCCAGGTTTAACACTAG
3521976 CTTCAAGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (21 bp):
TTCTCCCAGGTTTAACACTAG
Found at i:3526027 original size:15 final size:15
Alignment explanation
Indices: 3526004--3526040 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3525994 TTTTTTGTTG
*
3526004 TATTCTAAATAATGA
1 TATTATAAATAATGA
3526019 TATTATAAATAATGA
1 TATTATAAATAATGA
3526034 TATTATA
1 TATTATA
3526041 TTAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (15 bp):
TATTATAAATAATGA
Found at i:3536585 original size:75 final size:75
Alignment explanation
Indices: 3536447--3536587 Score: 194
Period size: 75 Copynumber: 1.9 Consensus size: 75
3536437 TAGTCATATG
* * ** * * * *
3536447 TCAATTATATCATGTGAACATAATATTGTTGTGATAAGTTAATTTGGTACATGAACAGATAAAAT
1 TCAATTATATCATATGAACATAATATTATCATGATAAATTAATGTGGTACATAAAAAGATAAAAT
3536512 TAACCATGTC
66 TAACCATGTC
3536522 TCAATTATATCATATGAACATAATATTATCATGATAAATTAATGTGGTACATAAATAAG-TAAAA
1 TCAATTATATCATATGAACATAATATTATCATGATAAATTAATGTGGTACATAAA-AAGATAAAA
3536586 TT
65 TT
3536588 CAAAAAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 55 0.96
76 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (75 bp):
TCAATTATATCATATGAACATAATATTATCATGATAAATTAATGTGGTACATAAAAAGATAAAAT
TAACCATGTC
Found at i:3537635 original size:28 final size:28
Alignment explanation
Indices: 3537604--3537667 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
3537594 AAGAGTTTGA
*
3537604 TTAAATATAATAAAAAATATAAATTTTT
1 TTAAATATAATAAAAAATATAAAATTTT
* ** * *
3537632 TTAAATGTTTTAAATAATTTAAAATTTT
1 TTAAATATAATAAAAAATATAAAATTTT
3537660 TTAAATAT
1 TTAAATAT
3537668 TATGTTTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TTAAATATAATAAAAAATATAAAATTTT
Found at i:3540821 original size:2 final size:2
Alignment explanation
Indices: 3540814--3540843 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3540804 TCTTATTTAA
3540814 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3540844 AAAGGCTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.