Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 118 of 145
Found at i:39106511 original size:51 final size:51
Alignment explanation
Indices: 39106456--39106553 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
39106446 AATTATTTAA
39106456 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAAATT
* * * *
39106507 AAATATGGATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
39106554 GAGGAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.07
51 39 0.93
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:39106551 original size:12 final size:11
Alignment explanation
Indices: 39106515--39106574 Score: 61
Period size: 11 Copynumber: 5.3 Consensus size: 11
39106505 TTAAATATGG
39106515 ATTTGAGAGAA
1 ATTTGAGAGAA
*
39106526 ATTTTGA-AGGA
1 A-TTTGAGAGAA
39106537 ATTTGAGAGCAA
1 ATTTGAGAG-AA
39106549 A-TTGAGAGGAA
1 ATTTGAGA-GAA
39106560 ATTTGAGAGAGA
1 ATTTGAGAGA-A
39106572 ATT
1 ATT
39106575 AGTTTGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 5 0.12
11 18 0.44
12 18 0.44
ACGTcount: A:0.42, C:0.02, G:0.28, T:0.28
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:39106562 original size:23 final size:21
Alignment explanation
Indices: 39106515--39106574 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 21
39106505 TTAAATATGG
39106515 ATTTGAGAGAAATTTTGAAGGA
1 ATTTGAGAGAAA-TTTGAAGGA
39106537 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGA-AGG-A
39106560 ATTTGAGAGAGAATT
1 ATTTGAGAGA-AATT
39106575 AGTTTGTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
23 15 0.45
24 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.28, T:0.28
Consensus pattern (21 bp):
ATTTGAGAGAAATTTGAAGGA
Found at i:39106919 original size:16 final size:16
Alignment explanation
Indices: 39106900--39106930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39106890 CCTAAACTAA
*
39106900 TAAAGTAATAAATTAT
1 TAAACTAATAAATTAT
39106916 TAAACTAATAAATTA
1 TAAACTAATAAATTA
39106931 ACACATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAACTAATAAATTAT
Found at i:39113551 original size:29 final size:29
Alignment explanation
Indices: 39113514--39113569 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
39113504 ATTTATTAGA
**
39113514 GTTAAGTGGGGTGATTTAGGGTTTAAATG
1 GTTAAGTGGAATGATTTAGGGTTTAAATG
* *
39113543 GTTAGGTGGAATGATTTCGGGTTTAAA
1 GTTAAGTGGAATGATTTAGGGTTTAAA
39113570 ATAAATGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.38
Consensus pattern (29 bp):
GTTAAGTGGAATGATTTAGGGTTTAAATG
Found at i:39117465 original size:23 final size:23
Alignment explanation
Indices: 39117414--39117465 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39117404 TTCACACCAA
*
39117414 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACAAC
*
39117437 AATTTGGGCAGCATATAA-ACAAC
1 AATTTGGACAGCATA-AATACAAC
*
39117460 AGTTTG
1 AATTTG
39117466 AGCAACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACAAC
Found at i:39117526 original size:35 final size:34
Alignment explanation
Indices: 39117467--39117541 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 34
39117457 AACAGTTTGA
*
39117467 GCAACATTTTACACCAAAACTGGACAGCATATAT
1 GCAACATTTAACACCAAAACTGGACAGCATATAT
* *
39117501 GCAACATTTAAGCATCAAAATTGGACAGCATATAT
1 GCAACATTTAA-CACCAAAACTGGACAGCATATAT
*
39117536 GTAACA
1 GCAACA
39117542 AATTGGGCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (34 bp):
GCAACATTTAACACCAAAACTGGACAGCATATAT
Found at i:39117577 original size:24 final size:24
Alignment explanation
Indices: 39117505--39117752 Score: 182
Period size: 23 Copynumber: 10.5 Consensus size: 24
39117495 ATATATGCAA
39117505 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGACAG
* * * * *
39117529 CATATATGTAAC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
* *
39117552 CATTTAAACATCAAAATTGGAAAG
1 CATTTAAGCATCAAAATTGGACAG
* * * * *
39117576 CATATATGTAAC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
*
39117599 CATTTAAGCATCAAAATTTGACAG
1 CATTTAAGCATCAAAATTGGACAG
* * * * *
39117623 CATATATGTAAC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
*
39117646 CATTTAAGCATCAAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
* * * * * *
39117670 TATATATGTAAC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
*
39117693 CATTTAAGCATCAAAATTTGACAG
1 CATTTAAGCATCAAAATTGGACAG
* * * * *
39117717 CATATATGTAAC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
39117740 CATTTAAGCATCA
1 CATTTAAGCATCA
39117753 CATACTTACT
Statistics
Matches: 162, Mismatches: 57, Indels: 10
0.71 0.25 0.04
Matches are distributed among these distances:
23 86 0.53
24 76 0.47
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (24 bp):
CATTTAAGCATCAAAATTGGACAG
Found at i:39117578 original size:47 final size:47
Alignment explanation
Indices: 39117505--39117752 Score: 442
Period size: 47 Copynumber: 5.3 Consensus size: 47
39117495 ATATATGCAA
39117505 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
* *
39117552 CATTTAAACATCAAAATTGGAAAGCATATATGTAACAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
*
39117599 CATTTAAGCATCAAAATTTGACAGCATATATGTAACAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
* *
39117646 CATTTAAGCATCAAAATTGGGCAGTATATATGTAACAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
*
39117693 CATTTAAGCATCAAAATTTGACAGCATATATGTAACAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
39117740 CATTTAAGCATCA
1 CATTTAAGCATCA
39117753 CATACTTACT
Statistics
Matches: 190, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 190 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (47 bp):
CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAG
Found at i:39118687 original size:43 final size:43
Alignment explanation
Indices: 39118619--39118746 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 43
39118609 AGCTCGTACA
* **
39118619 ATGCCATCGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCATCGTCCCAGACGTGATCTTACACATAATCACATATCG
*
39118662 ATGCCA-CTGTCCCAGACAG-GATCTTACACATAATCAGATATCG
1 ATGCCATC-GTCCCAGAC-GTGATCTTACACATAATCACATATCG
* * * * *
39118705 ATGCCGA-AGTCTCAGACGTGGTCTTACACAAAAACACATATC
1 ATGCC-ATCGTCCCAGACGTGATCTTACACATAATCACATATC
39118747 AGAATCCTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.03
43 67 0.94
44 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCATCGTCCCAGACGTGATCTTACACATAATCACATATCG
Found at i:39119671 original size:28 final size:28
Alignment explanation
Indices: 39119631--39119687 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
39119621 TATGTTTGTT
39119631 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
39119659 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
39119687 T
1 T
39119688 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:39119906 original size:14 final size:15
Alignment explanation
Indices: 39119887--39119915 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39119877 TCACGAAACT
39119887 TTCACACAT-ATAAA
1 TTCACACATAATAAA
39119901 TTCACACATAATAAA
1 TTCACACATAATAAA
39119916 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:39120036 original size:26 final size:26
Alignment explanation
Indices: 39120006--39120060 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
39119996 TATTACACTA
39120006 TCTGTAGATAATGAGGGTTTCAAACT
1 TCTGTAGATAATGAGGGTTTCAAACT
*
39120032 TCTGTAGATAATGAGGGTTTCAAATT
1 TCTGTAGATAATGAGGGTTTCAAACT
39120058 TCT
1 TCT
39120061 CAATCCCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (26 bp):
TCTGTAGATAATGAGGGTTTCAAACT
Found at i:39121299 original size:18 final size:16
Alignment explanation
Indices: 39121276--39121309 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
39121266 AGTAAAATAT
39121276 AAATTACAAACATAAAAA
1 AAATTA-AAACA-AAAAA
39121294 AAATTAAAACAAAAAA
1 AAATTAAAACAAAAAA
39121310 CTCCAACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATTAAAACAAAAAA
Found at i:39121309 original size:17 final size:18
Alignment explanation
Indices: 39121276--39121309 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39121266 AGTAAAATAT
*
39121276 AAATTACAAACATAAAAA
1 AAATTACAAACAAAAAAA
39121294 AAATTA-AAACAAAAAA
1 AAATTACAAACAAAAAA
39121310 CTCCAACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (18 bp):
AAATTACAAACAAAAAAA
Found at i:39121424 original size:15 final size:14
Alignment explanation
Indices: 39121387--39121437 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
39121377 ATATAATCTT
*
39121387 AAAAATTA-AATAT
1 AAAAATTATAATAA
*
39121400 AAATATTATAAGTAA
1 AAAAATTATAA-TAA
*
39121415 AAAAATTATAATAT
1 AAAAATTATAATAA
*
39121429 AGAAATTAT
1 AAAAATTAT
39121438 TGTTACAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
15 12 0.39
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (14 bp):
AAAAATTATAATAA
Found at i:39122278 original size:2 final size:2
Alignment explanation
Indices: 39122271--39122359 Score: 83
Period size: 2 Copynumber: 43.5 Consensus size: 2
39122261 ATTTCAAACT
*
39122271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA -A GTA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
** * *
39122314 TA NNN T- TCA CA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39122357 TA T
1 TA T
39122360 CGTATAAGTA
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
1 2 0.03
2 69 0.93
3 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:39124273 original size:21 final size:21
Alignment explanation
Indices: 39124247--39124302 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
39124237 AATAGCGGTG
*
39124247 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
39124268 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
39124289 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
39124303 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:39126122 original size:13 final size:13
Alignment explanation
Indices: 39126104--39126153 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
39126094 CAATGACATT
39126104 TATTCAAGCTCAA
1 TATTCAAGCTCAA
*
39126117 TATTCAAG-T-AT
1 TATTCAAGCTCAA
39126128 TATTCAAGCTCAA
1 TATTCAAGCTCAA
39126141 TATTCAAGCTCAA
1 TATTCAAGCTCAA
39126154 GAGGAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 9 0.27
12 2 0.06
13 22 0.67
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (13 bp):
TATTCAAGCTCAA
Found at i:39126131 original size:24 final size:24
Alignment explanation
Indices: 39126103--39126148 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
39126093 TCAATGACAT
39126103 TTATTCAAGCTCAATATTCAAGTA
1 TTATTCAAGCTCAATATTCAAGTA
39126127 TTATTCAAGCTCAATATTCAAG
1 TTATTCAAGCTCAATATTCAAG
39126149 CTCAAGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (24 bp):
TTATTCAAGCTCAATATTCAAGTA
Found at i:39130008 original size:13 final size:13
Alignment explanation
Indices: 39129990--39130039 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
39129980 AATGACATAT
39129990 TATTCAAGCTCAA
1 TATTCAAGCTCAA
*
39130003 TATTCAAG-T-AT
1 TATTCAAGCTCAA
39130014 TATTCAAGCTCAA
1 TATTCAAGCTCAA
39130027 TATTCAAGCTCAA
1 TATTCAAGCTCAA
39130040 GAGGAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 9 0.27
12 2 0.06
13 22 0.67
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (13 bp):
TATTCAAGCTCAA
Found at i:39130019 original size:24 final size:24
Alignment explanation
Indices: 39129987--39130034 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39129977 TTCAATGACA
39129987 TATTATTCAAGCTCAATATTCAAG
1 TATTATTCAAGCTCAATATTCAAG
39130011 TATTATTCAAGCTCAATATTCAAG
1 TATTATTCAAGCTCAATATTCAAG
39130035 CTCAAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (24 bp):
TATTATTCAAGCTCAATATTCAAG
Found at i:39131413 original size:32 final size:34
Alignment explanation
Indices: 39131371--39131443 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 34
39131361 TTTTGTTATG
* *
39131371 TATTTCATTAATTAA-AACAATACATTTT-AATA
1 TATTTTATTAATTAATAACAATACATTTTAAAAA
**
39131403 TATTTTATTAATTAATATGAATACATTTTAAAAA
1 TATTTTATTAATTAATAACAATACATTTTAAAAA
39131437 TATTTTA
1 TATTTTA
39131444 AAATATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 14 0.40
33 11 0.31
34 10 0.29
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (34 bp):
TATTTTATTAATTAATAACAATACATTTTAAAAA
Found at i:39133338 original size:7 final size:7
Alignment explanation
Indices: 39133326--39133354 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39133316 GTCAAGATTT
39133326 CTAACTA
1 CTAACTA
39133333 CTAACTA
1 CTAACTA
39133340 CTAACTA
1 CTAACTA
39133347 CTAACTA
1 CTAACTA
39133354 C
1 C
39133355 CATAGCTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (7 bp):
CTAACTA
Found at i:39137866 original size:14 final size:13
Alignment explanation
Indices: 39137847--39137882 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
39137837 CCCAAAGCAA
39137847 AAAAAAAAAACCAG
1 AAAAAAAAAA-CAG
*
39137861 AAAAAAGAAACAG
1 AAAAAAAAAACAG
39137874 AAAAAAAAA
1 AAAAAAAAA
39137883 TCATAATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAG
Found at i:39137931 original size:19 final size:19
Alignment explanation
Indices: 39137907--39137945 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
39137897 CATTTTCAGT
39137907 AGGCCCAA-CTCAGCAGGCC
1 AGGCCCAAGC-CAGCAGGCC
39137926 AGGCCCAAGCCAGCAGGCC
1 AGGCCCAAGCCAGCAGGCC
39137945 A
1 A
39137946 CCAGCAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.41, G:0.28, T:0.03
Consensus pattern (19 bp):
AGGCCCAAGCCAGCAGGCC
Found at i:39138022 original size:1 final size:1
Alignment explanation
Indices: 39138016--39138087 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
39138006 AGCCCAGCAG
* * * * * * * * * *
39138016 AAAAAAAAGAAAAGAGAAGAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39138081 AAAAAAA
1 AAAAAAA
39138088 GTTTAATTTG
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:39138028 original size:8 final size:8
Alignment explanation
Indices: 39138017--39138088 Score: 94
Period size: 8 Copynumber: 9.0 Consensus size: 8
39138007 GCCCAGCAGA
39138017 AAAAAAAG
1 AAAAAAAG
*
39138025 -AAAAGAG
1 AAAAAAAG
*
39138032 AAGAAAAG
1 AAAAAAAG
39138040 -AAAAAAG
1 AAAAAAAG
39138047 AAAAAAAG
1 AAAAAAAG
39138055 AAAAAAAG
1 AAAAAAAG
39138063 AAAAAAAG
1 AAAAAAAG
39138071 AAAAAAAAAG
1 --AAAAAAAG
39138081 AAAAAAAG
1 AAAAAAAG
39138089 TTTAATTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
7 12 0.21
8 36 0.64
10 8 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:39138040 original size:15 final size:15
Alignment explanation
Indices: 39138017--39138076 Score: 93
Period size: 15 Copynumber: 3.9 Consensus size: 15
39138007 GCCCAGCAGA
*
39138017 AAAAAAAGAAAAGAG
1 AAAAAAAGAAAAAAG
*
39138032 AAGAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
39138047 AAAAAAAGAAAAAAAG
1 AAAAAAAG-AAAAAAG
39138063 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
39138077 AAAGAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
15 26 0.63
16 15 0.37
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:39138052 original size:31 final size:32
Alignment explanation
Indices: 39138014--39138086 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
39138004 TTAGCCCAGC
* *
39138014 AGAAAAAAAAG-AAAAGAGAAGAAAAGAAAAA
1 AGAAAAAAAAGAAAAAAAGAAAAAAAGAAAAA
39138045 AG-AAAAAAAGAAAAAAAGAAAAAAAGAAAAA
1 AGAAAAAAAAGAAAAAAAGAAAAAAAGAAAAA
*
39138076 AAAAGAAAAAA
1 AGAA-AAAAAA
39138087 AGTTTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 8 0.22
31 21 0.58
32 1 0.03
33 6 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (32 bp):
AGAAAAAAAAGAAAAAAAGAAAAAAAGAAAAA
Found at i:39138084 original size:15 final size:14
Alignment explanation
Indices: 39138016--39138087 Score: 76
Period size: 15 Copynumber: 5.1 Consensus size: 14
39138006 AGCCCAGCAG
39138016 AAAAAAAAGAAAAGA
1 AAAAAAAAGAAAA-A
* *
39138031 GAAGAAAAGAAAAA
1 AAAAAAAAGAAAAA
39138045 AGAAAAAAAG-AAAA
1 A-AAAAAAAGAAAAA
* *
39138059 AAAGAAAA-AAAGA
1 AAAAAAAAGAAAAA
39138072 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
39138086 AA
1 AA
39138088 GTTTAATTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
13 16 0.35
14 12 0.26
15 18 0.39
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:39138738 original size:71 final size:69
Alignment explanation
Indices: 39138632--39139126 Score: 263
Period size: 71 Copynumber: 7.0 Consensus size: 69
39138622 AAATCTTTCT
* *** * *
39138632 GTGTTTCAAAAATCTTCGT-TTTTTTTAAATTTCGGTG-TTTCAAAAATTTCCGCGTTTCCAAAA
1 GTGTTTAAAAAAT-TTCGTGTTTTCAAAAATTTCGGTGTTTTCAAAAATTTCCGTGTTTCAAAAA
39138695 ATTCA
65 ATTCA
* * *
39138700 GGTGATTTAAAAAATCTTCGTGTTTTCAAAAACTTCGGTG-TTTC-AAAATTTTCATGTTTTCAA
1 -GTG-TTTAAAAAAT-TTCGTGTTTTCAAAAATTTCGGTGTTTTCAAAAATTTCCGTG-TTTC-A
*
39138763 AAAAATTCCC
61 AAAAATT-CA
* * *
39138773 GTGTTTTAAAAATTTCCGTGTTTTCAAAAATTTTC-GTGTTTTCAAAAACTCCCGTGTTTCAAAA
1 GTGTTTAAAAAATTT-CGTGTTTTCAAAAA-TTTCGGTGTTTTCAAAAATTTCCGTGTTTCAAAA
**
39138837 TTTTCA
64 AATTCA
* *
39138843 -TGTTTTCAAAAAAATTCTCGTGTTTT-AAAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTCAA
1 GTG-TTT--AAAAAATT-TCGTGTTTTCAAAAATTTCGGTGTTTTCAAAAATTTCCGTGTTTC-A
39138906 AAAAATCCTC-
61 AAAAAT--TCA
* * * * * * * *
39138916 GTATATTTAAAACTTCCGTG-TTTCAAAAATTTTC-GTGTTTTAAAAAAAATTCTGATTTTTCAA
1 GTGT-TTAAAAAATTTCGTGTTTTCAAAAA-TTTCGGTGTTTT-CAAAAATTTCCG-TGTTTCAA
39138979 AAAATTTTCGA
62 AAAA--TTC-A
* *
39138990 GCT-TTT-AAAAATTTCG-GTGATTCAAAAATTTTC-GTGTTTTCAAAAATTTTCCCCTGTTTC-
1 G-TGTTTAAAAAATTTCGTGT-TTTCAAAAA-TTTCGGTGTTTTCAAAAA-TTT-CCGTGTTTCA
*
39139050 AAAATTGTC-
61 AAAAAT-TCA
* * * * *
39139059 GTGTTTTCAAAAATTTTCGTGTTTTTAAGAATTTTC-GTG-TTTCTAAAA-TTCTCGTGTTTTAA
1 GTG-TTT-AAAAAATTTCGTGTTTTCAA-AAATTTCGGTGTTTTCAAAAATTTC-CGTGTTTCAA
39139121 AAAATT
62 AAAATT
39139127 TTTCGTGTTC
Statistics
Matches: 334, Mismatches: 51, Indels: 82
0.72 0.11 0.18
Matches are distributed among these distances:
68 2 0.01
69 15 0.04
70 46 0.14
71 108 0.32
72 104 0.31
73 49 0.15
74 9 0.03
75 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (69 bp):
GTGTTTAAAAAATTTCGTGTTTTCAAAAATTTCGGTGTTTTCAAAAATTTCCGTGTTTCAAAAAA
TTCA
Found at i:39138802 original size:89 final size:88
Alignment explanation
Indices: 39138709--39139124 Score: 400
Period size: 89 Copynumber: 4.6 Consensus size: 88
39138699 AGGTGATTTA
* *
39138709 AAAAATCTTCGTGTTTTCAAAAACTTCGGTGTTTCAAAATTTTCATGTTTTCAAAAAAATTCCCG
1 AAAAATTTTCGTGTTTTCAAAAACTTC-GTGTTTCAAAATTTTCGTGTTTTCAAAAAAATTCCCG
39138774 TGTTTTAAAAATTTCCGTGTTTTC
65 TGTTTTAAAAATTTCCGTGTTTTC
* * *
39138798 AAAAATTTTCGTGTTTTCAAAAACTCCCGTGTTTCAAAATTTTCATGTTTTCAAAAAAATTCTCG
1 AAAAATTTTCGTGTTTTCAAAAACT-TCGTGTTTCAAAATTTTCGTGTTTTCAAAAAAATTCCCG
39138863 TGTTTTAAAAATTTCCGTGTTTTC
65 TGTTTTAAAAATTTCCGTGTTTTC
* * * * * *
39138887 AAAAATTTTCGTG-TTTCAAAAAAATCCTCGTATATTTAAAACTTCCGTG-TTTC--AAAAATTT
1 AAAAATTTTCGTGTTTTC--AAAAA-CTTCGTGT-TTCAAAATTTTCGTGTTTTCAAAAAAATTC
* * *
39138948 TCGTGTTTTAAAAAAAATTCTGAT-TTTTC
62 CCGTGTTTT--AAAAATTTCCG-TGTTTTC
* * * **
39138977 AAAAAATTTTCGAGCTTTT-AAAAATTTCGGTGATTCAAAAATTTTCGTGTTTTCAAAAATTTTC
1 -AAAAATTTTCGTG-TTTTCAAAAACTTC-GTGTTTC-AAAATTTTCGTGTTTTCAAAAAAATTC
* *
39139041 CCCTG-TTTCAAAATTGT-CGTGTTTTC
62 CCGTGTTTTAAAAATT-TCCGTGTTTTC
* ** *
39139067 AAAAATTTTCGTGTTTTTAAGAATTTTCGTGTTTCTAAAATTCTCGTGTTTT-AAAAAA
1 AAAAATTTTCGTGTTTTCAA-AAACTTCGTGTTTC-AAAATTTTCGTGTTTTCAAAAAA
39139125 TTTTTCGTGT
Statistics
Matches: 272, Mismatches: 35, Indels: 41
0.78 0.10 0.12
Matches are distributed among these distances:
88 29 0.11
89 137 0.50
90 62 0.23
91 30 0.11
92 3 0.01
93 11 0.04
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (88 bp):
AAAAATTTTCGTGTTTTCAAAAACTTCGTGTTTCAAAATTTTCGTGTTTTCAAAAAAATTCCCGT
GTTTTAAAAATTTCCGTGTTTTC
Found at i:39138909 original size:18 final size:17
Alignment explanation
Indices: 39138620--39139143 Score: 297
Period size: 18 Copynumber: 29.3 Consensus size: 17
39138610 TGTGTAAAAA
39138620 AAAAATCTTTCTGTGTTTC
1 AAAAAT-TTTC-GTGTTTC
* * *
39138639 AAAAATCTTCGTTTTTT
1 AAAAATTTTCGTGTTTC
**
39138656 TTAAA-TTTCGGTGTTTC
1 AAAAATTTTC-GTGTTTC
* *
39138673 AAAAATTTCCGCGTTTCC
1 AAAAATTTTCGTGTTT-C
*** *
39138691 AAAAATTCAGGTGATTTA
1 AAAAATTTTCGTG-TTTC
*
39138709 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
39138727 AAAAA-CTTCGGTGTTTC
1 AAAAATTTTC-GTGTTTC
*
39138744 -AAAATTTTCATGTTTTC
1 AAAAATTTTCGTG-TTTC
** *
39138761 AAAAAAATTCCCGTGTTTT
1 --AAAAATTTTCGTGTTTC
*
39138780 AAAAATTTCCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
39138798 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* **
39138816 AAAAACTCCCGTGTTTC
1 AAAAATTTTCGTGTTTC
*
39138833 -AAAATTTTCATGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
39138850 AAAAAAATTCTCGTGTTTT
1 --AAAAATTTTCGTGTTTC
*
39138869 AAAAATTTCCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
39138887 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
** *
39138904 AAAAAAATCCTCGTATATT-
1 --AAAAATTTTCGTGT-TTC
* * *
39138923 TAAAACTTCCGTGTTTC
1 AAAAATTTTCGTGTTTC
*
39138940 AAAAATTTTCGTGTTTTA
1 AAAAATTTTCGTG-TTTC
** *
39138958 AAAAAAATTCTGATTTTTC
1 AAAAATTTTC-G-TGTTTC
* *
39138977 AAAAAATTTTCGAGCTTTT
1 -AAAAATTTTCGTG-TTTC
*
39138996 AAAAA-TTTCGGTGATTC
1 AAAAATTTTC-GTGTTTC
39139013 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
39139031 AAAAATTTTCCCCTGTTTC
1 AAAAATTTT--CGTGTTTC
*
39139050 -AAAATTGTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
39139067 AAAAATTTTCGTGTTTTT
1 AAAAATTTTCGTG-TTTC
*
39139085 AAGAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
39139102 TAAAATTCTCGTGTTTTA
1 AAAAATTTTCGTG-TTTC
39139120 AAAAATTTTTCGTGTTCTC
1 AAAAA-TTTTCGTGTT-TC
39139139 AAAAA
1 AAAAA
39139144 AAATAATTAT
Statistics
Matches: 384, Mismatches: 86, Indels: 70
0.71 0.16 0.13
Matches are distributed among these distances:
16 22 0.06
17 120 0.31
18 158 0.41
19 51 0.13
20 33 0.09
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:39142162 original size:11 final size:11
Alignment explanation
Indices: 39142135--39142170 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
39142125 AACTAATCCT
39142135 CTCTCATATTTC
1 CTCTCA-ATTTC
*
39142147 TTCTCAATTTC
1 CTCTCAATTTC
39142158 CTCTCAATTTC
1 CTCTCAATTTC
39142169 CT
1 CT
39142171 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:39142393 original size:26 final size:26
Alignment explanation
Indices: 39142364--39142419 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
39142354 CGTTATAATT
* *
39142364 TTTAAATATTATTTA-AGAATTTTTTA
1 TTTAAACATT-TTTAGAGAATTTTTAA
* *
39142390 TTTATACATTTTTAGATAATTTTTAA
1 TTTAAACATTTTTAGAGAATTTTTAA
39142416 TTTA
1 TTTA
39142420 TTATTTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTAAACATTTTTAGAGAATTTTTAA
Found at i:39143851 original size:10 final size:10
Alignment explanation
Indices: 39143836--39143871 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
39143826 TTTTGAATAT
39143836 TTTGATATTA
1 TTTGATATTA
39143846 TTTGATATTA
1 TTTGATATTA
39143856 TTTGATATTA
1 TTTGATATTA
39143866 TTTGAT
1 TTTGAT
39143872 GTAATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (10 bp):
TTTGATATTA
Found at i:39143897 original size:25 final size:25
Alignment explanation
Indices: 39143863--39143910 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
39143853 TTATTTGATA
39143863 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
39143888 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
39143911 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:39151936 original size:74 final size:74
Alignment explanation
Indices: 39151815--39152034 Score: 422
Period size: 74 Copynumber: 3.0 Consensus size: 74
39151805 ACCGTAGTTG
39151815 TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAGCCCCTAAAGATCATTGTAAAGTATAT
1 TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAGCCCCTAAAGATCATTGTAAAGTATAT
39151880 CTCAAATAT
66 CTCAAATAT
39151889 TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAGCCCCTAAAGATCATTGTAAAGTATAT
1 TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAGCCCCTAAAGATCATTGTAAAGTATAT
39151954 CTCAAATAT
66 CTCAAATAT
*
39151963 TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAGCCCCCCAAAGATCATTGTAAAGTATA
1 TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAG-CCCCTAAAGATCATTGTAAAGTATA
39152028 TCTCAAA
65 TCTCAAA
39152035 CATCACCGTA
Statistics
Matches: 144, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
74 113 0.78
75 31 0.22
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (74 bp):
TTGGATCCATGGTCCGTTAATGAGGTTGTGACGTTACAGCCCCTAAAGATCATTGTAAAGTATAT
CTCAAATAT
Found at i:39152368 original size:16 final size:16
Alignment explanation
Indices: 39152347--39152379 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39152337 AAGCTGACTT
39152347 ATCAGTTAAAATCATC
1 ATCAGTTAAAATCATC
39152363 ATCAGTTAAAATCATC
1 ATCAGTTAAAATCATC
39152379 A
1 A
39152380 CCTAAACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (16 bp):
ATCAGTTAAAATCATC
Found at i:39155522 original size:16 final size:14
Alignment explanation
Indices: 39155470--39155523 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 14
39155460 TTTCTTTTTC
39155470 TTTTTTATTATTAT
1 TTTTTTATTATTAT
39155484 TTATTTTGATTATTAT
1 TT-TTTT-ATTATTAT
*
39155500 TTATTTATTATTTAT
1 TTTTTTATTA-TTAT
39155515 ATTTTTTAT
1 -TTTTTTAT
39155524 GCTTTAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.18
15 11 0.32
16 17 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTTATTATTAT
Found at i:39155523 original size:27 final size:25
Alignment explanation
Indices: 39155450--39155523 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
39155440 TAGTCCCCAA
* *
39155450 ATTATATATTT-TTCTTTTTCTTTTTT
1 ATTAT-TATTTATT-TTTTTATTATTT
*
39155476 ATTATTATTTATTTTGATTATTATTT
1 ATTATTATTTATTTT-TTTATTATTT
39155502 ATTTATTATTTATATTTTTTAT
1 A-TTATTATTTAT-TTTTTTAT
39155524 GCTTTAGGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 7 0.17
26 15 0.38
27 15 0.38
28 3 0.08
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (25 bp):
ATTATTATTTATTTTTTTATTATTT
Found at i:39156541 original size:4 final size:4
Alignment explanation
Indices: 39156534--39156576 Score: 61
Period size: 4 Copynumber: 10.5 Consensus size: 4
39156524 CCAAGTAAGT
39156534 AATA AATA AAGT- AATA AATA AAGTA AATA AATA AATA AATA AA
1 AATA AATA AA-TA AATA AATA AA-TA AATA AATA AATA AATA AA
39156577 AATTGGGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 1 0.03
4 30 0.83
5 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:39156562 original size:21 final size:21
Alignment explanation
Indices: 39156536--39156576 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39156526 AAGTAAGTAA
39156536 TAAATAAAGT-AATAAATAAAG
1 TAAATAAA-TAAATAAATAAAG
39156557 TAAATAAATAAATAAATAAA
1 TAAATAAATAAATAAATAAA
39156577 AATTGGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
TAAATAAATAAATAAATAAAG
Found at i:39156572 original size:12 final size:13
Alignment explanation
Indices: 39156530--39156576 Score: 73
Period size: 12 Copynumber: 3.8 Consensus size: 13
39156520 ATATCCAAGT
39156530 AAGT-AATAAATA
1 AAGTAAATAAATA
39156542 AAGT-AATAAATA
1 AAGTAAATAAATA
39156554 AAGTAAATAAATA
1 AAGTAAATAAATA
39156567 AA-TAAATAAA
1 AAGTAAATAAA
39156577 AATTGGGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 24 0.71
13 10 0.29
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (13 bp):
AAGTAAATAAATA
Found at i:39160143 original size:211 final size:211
Alignment explanation
Indices: 39159776--39160200 Score: 726
Period size: 211 Copynumber: 2.0 Consensus size: 211
39159766 AGAAAATAAA
* *
39159776 TCTTATGGGAGGTTCCAGCCTCCAGTTGTCTCGTTCCGCCTTGGGTTCAATCCTCGGCTTTTAGA
1 TCTTATGGGAGGTTCAAGCCTCCAGTTGTCTCGTTCCACCTTGGGTTCAATCCTCGGCTTTTAGA
* * *
39159841 TGATCATTCCCAAACCAAATAAGCCAGTTATAGTGGAGGAGGATGCCTATGACCACCAGCTCCAA
66 TGATCATTCCCAAACCAAATAAGCCAGTTATAGTGGAAGAGGACGCCTACGACCACCAGCTCCAA
* *
39159906 GGATTTAGACTTACGATTTTGTGGAACCTGACTCTAGCCAACAATCGA-TTCTGTGGGATCGTCT
131 GGATTTAGACTTACAATTTAGTGGAACCTGACTCTAGCCAACAATC-ACTTCTGTGGGATCGTCT
* *
39159970 TATGTTAGATTAACGCT
195 TATGTTAGATCAACACT
*
39159987 TCTTATGGGAGGTTCAAGCCTCCGGTTGTCTCGTTCCACCTTGGGTTCAATCCTCGGCTTTTAGA
1 TCTTATGGGAGGTTCAAGCCTCCAGTTGTCTCGTTCCACCTTGGGTTCAATCCTCGGCTTTTAGA
*
39160052 TGATCCTTCCCAAACCAAATAAGCCAGTTATAGTGGAAGAGGACGCCTACGACCACCAGCTCCAA
66 TGATCATTCCCAAACCAAATAAGCCAGTTATAGTGGAAGAGGACGCCTACGACCACCAGCTCCAA
*
39160117 GGATTTAGACTTACAATTTAGTGGAACCTGACTCTTGCCAACAATCACTTCTGTGGGATCGTCTT
131 GGATTTAGACTTACAATTTAGTGGAACCTGACTCTAGCCAACAATCACTTCTGTGGGATCGTCTT
39160182 ATGTTAGATCAACACT
196 ATGTTAGATCAACACT
39160198 TCT
1 TCT
39160201 CAATGGCGAA
Statistics
Matches: 201, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
210 1 0.00
211 200 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (211 bp):
TCTTATGGGAGGTTCAAGCCTCCAGTTGTCTCGTTCCACCTTGGGTTCAATCCTCGGCTTTTAGA
TGATCATTCCCAAACCAAATAAGCCAGTTATAGTGGAAGAGGACGCCTACGACCACCAGCTCCAA
GGATTTAGACTTACAATTTAGTGGAACCTGACTCTAGCCAACAATCACTTCTGTGGGATCGTCTT
ATGTTAGATCAACACT
Found at i:39160698 original size:16 final size:16
Alignment explanation
Indices: 39160677--39160707 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39160667 AATTGAAGAT
39160677 AAATAAAGATAAATAA
1 AAATAAAGATAAATAA
*
39160693 AAATAAAGATCAATA
1 AAATAAAGATAAATA
39160708 TGATATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (16 bp):
AAATAAAGATAAATAA
Found at i:39161525 original size:16 final size:16
Alignment explanation
Indices: 39161504--39161536 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39161494 AAGTTGACTT
39161504 ATCAGTTAAAATCATC
1 ATCAGTTAAAATCATC
39161520 ATCAGTTAAAATCATC
1 ATCAGTTAAAATCATC
39161536 A
1 A
39161537 CCTAAACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (16 bp):
ATCAGTTAAAATCATC
Found at i:39176642 original size:16 final size:16
Alignment explanation
Indices: 39176621--39176654 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39176611 CAGAAAACTA
39176621 AAAGTCTTCCAGTTTC
1 AAAGTCTTCCAGTTTC
*
39176637 AAAGTCTTCTAGTTTC
1 AAAGTCTTCCAGTTTC
39176653 AA
1 AA
39176655 CGTCCAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAGTCTTCCAGTTTC
Found at i:39180359 original size:18 final size:17
Alignment explanation
Indices: 39180336--39180369 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39180326 CCTTAAAAAT
*
39180336 TATAATATTATAAATTAG
1 TATAATAGTA-AAATTAG
39180354 TATAATAGTAAAATTA
1 TATAATAGTAAAATTA
39180370 CATGTCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TATAATAGTAAAATTAG
Found at i:39184989 original size:20 final size:20
Alignment explanation
Indices: 39184952--39184989 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39184942 TTAAACTCCA
* *
39184952 GAAGATAAATACATTTAATT
1 GAAGATAAATAAAGTTAATT
39184972 GAAGATAAATAAAGTTAA
1 GAAGATAAATAAAGTTAA
39184990 ATAAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
GAAGATAAATAAAGTTAATT
Found at i:39185044 original size:15 final size:14
Alignment explanation
Indices: 39185023--39185058 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
39185013 ATAATCCTTA
*
39185023 ATAATTATCTTAAT
1 ATAATTATCCTAAT
39185037 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
39185052 ATAATTA
1 ATAATTA
39185059 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:39190287 original size:12 final size:12
Alignment explanation
Indices: 39190265--39190298 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
39190255 AAGAAAAGAA
39190265 AAAATTAAAAATT
1 AAAATT-AAAATT
39190278 AAAATTAAAATT
1 AAAATTAAAATT
39190290 -AAATTAAAA
1 AAAATTAAAA
39190299 GAATATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 6 0.29
13 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATTAAAATT
Found at i:39190295 original size:5 final size:6
Alignment explanation
Indices: 39190265--39190298 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
39190255 AAGAAAAGAA
39190265 AAAATT AAAAATT AAAATT AAAATT -AAATT AAAA
1 AAAATT -AAAATT AAAATT AAAATT AAAATT AAAA
39190299 GAATATCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:39200932 original size:18 final size:18
Alignment explanation
Indices: 39200909--39200943 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39200899 CCCAGGTTTT
*
39200909 AATATCGATACCAAAATC
1 AATATCGACACCAAAATC
39200927 AATATCGACACCAAAAT
1 AATATCGACACCAAAAT
39200944 TTCTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (18 bp):
AATATCGACACCAAAATC
Found at i:39204212 original size:434 final size:434
Alignment explanation
Indices: 39203404--39204271 Score: 1736
Period size: 434 Copynumber: 2.0 Consensus size: 434
39203394 AAGGTAGAGA
39203404 AGATCGAACACAAATATTTACGTGGAAAACTCCTCCGAAGAGGATAAAAACCACGATAAATAAGG
1 AGATCGAACACAAATATTTACGTGGAAAACTCCTCCGAAGAGGATAAAAACCACGATAAATAAGG
39203469 CTTCGACTTTTCACTAAATGATTAAACAAACGAGAGTACAATATAGACAAAATAAACCTAAATGT
66 CTTCGACTTTTCACTAAATGATTAAACAAACGAGAGTACAATATAGACAAAATAAACCTAAATGT
39203534 ACTAAACATACAAACTCAAACCCTGAAAGCAAAGCCCTAACTCGGGAACAAAATTACTCCATAGT
131 ACTAAACATACAAACTCAAACCCTGAAAGCAAAGCCCTAACTCGGGAACAAAATTACTCCATAGT
39203599 TACCATGAAGCTCTCACCAAAACTCATATGTAACTACATATTGTCACCCTCAAGAAAAGCTCTTG
196 TACCATGAAGCTCTCACCAAAACTCATATGTAACTACATATTGTCACCCTCAAGAAAAGCTCTTG
39203664 TTGATTGGCATGTCAAAATAGGGATACAACGGCCCCTTTAAATAGGTCAAGATTAGAGTTCTAAT
261 TTGATTGGCATGTCAAAATAGGGATACAACGGCCCCTTTAAATAGGTCAAGATTAGAGTTCTAAT
39203729 CATATTAAAATGTCCCTGGAATAATTAGAGCTCAACTAGGAGAAGAAGTCCAACTTGGAGTCTAA
326 CATATTAAAATGTCCCTGGAATAATTAGAGCTCAACTAGGAGAAGAAGTCCAACTTGGAGTCTAA
39203794 GATGCGGCTACATTTAGTGAGATATCGTCATGATGACGCAAGGT
391 GATGCGGCTACATTTAGTGAGATATCGTCATGATGACGCAAGGT
39203838 AGATCGAACACAAATATTTACGTGGAAAACTCCTCCGAAGAGGATAAAAACCACGATAAATAAGG
1 AGATCGAACACAAATATTTACGTGGAAAACTCCTCCGAAGAGGATAAAAACCACGATAAATAAGG
39203903 CTTCGACTTTTCACTAAATGATTAAACAAACGAGAGTACAATATAGACAAAATAAACCTAAATGT
66 CTTCGACTTTTCACTAAATGATTAAACAAACGAGAGTACAATATAGACAAAATAAACCTAAATGT
39203968 ACTAAACATACAAACTCAAACCCTGAAAGCAAAGCCCTAACTCGGGAACAAAATTACTCCATAGT
131 ACTAAACATACAAACTCAAACCCTGAAAGCAAAGCCCTAACTCGGGAACAAAATTACTCCATAGT
39204033 TACCATGAAGCTCTCACCAAAACTCATATGTAACTACATATTGTCACCCTCAAGAAAAGCTCTTG
196 TACCATGAAGCTCTCACCAAAACTCATATGTAACTACATATTGTCACCCTCAAGAAAAGCTCTTG
39204098 TTGATTGGCATGTCAAAATAGGGATACAACGGCCCCTTTAAATAGGTCAAGATTAGAGTTCTAAT
261 TTGATTGGCATGTCAAAATAGGGATACAACGGCCCCTTTAAATAGGTCAAGATTAGAGTTCTAAT
39204163 CATATTAAAATGTCCCTGGAATAATTAGAGCTCAACTAGGAGAAGAAGTCCAACTTGGAGTCTAA
326 CATATTAAAATGTCCCTGGAATAATTAGAGCTCAACTAGGAGAAGAAGTCCAACTTGGAGTCTAA
39204228 GATGCGGCTACATTTAGTGAGATATCGTCATGATGACGCAAGGT
391 GATGCGGCTACATTTAGTGAGATATCGTCATGATGACGCAAGGT
39204272 CACAACTCTC
Statistics
Matches: 434, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
434 434 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (434 bp):
AGATCGAACACAAATATTTACGTGGAAAACTCCTCCGAAGAGGATAAAAACCACGATAAATAAGG
CTTCGACTTTTCACTAAATGATTAAACAAACGAGAGTACAATATAGACAAAATAAACCTAAATGT
ACTAAACATACAAACTCAAACCCTGAAAGCAAAGCCCTAACTCGGGAACAAAATTACTCCATAGT
TACCATGAAGCTCTCACCAAAACTCATATGTAACTACATATTGTCACCCTCAAGAAAAGCTCTTG
TTGATTGGCATGTCAAAATAGGGATACAACGGCCCCTTTAAATAGGTCAAGATTAGAGTTCTAAT
CATATTAAAATGTCCCTGGAATAATTAGAGCTCAACTAGGAGAAGAAGTCCAACTTGGAGTCTAA
GATGCGGCTACATTTAGTGAGATATCGTCATGATGACGCAAGGT
Found at i:39206642 original size:28 final size:28
Alignment explanation
Indices: 39206606--39206702 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
39206596 ACATGGTACA
*
39206606 AATAACAATAAGCACTGAAGTGCAAAAT
1 AATAACAATAAGCACCGAAGTGCAAAAT
* * * *
39206634 AATATCAATAAGCACCGGAGTGTAAATTT
1 AATAACAATAAGCACCGAAGTGCAAA-AT
* * * *
39206663 TACAACAATAAGCACCGAAGTACGAAAT
1 AATAACAATAAGCACCGAAGTGCAAAAT
39206691 AAT-ACAATAAGC
1 AATAACAATAAGC
39206703 GCGCTAATTT
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
27 9 0.17
28 24 0.45
29 20 0.38
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (28 bp):
AATAACAATAAGCACCGAAGTGCAAAAT
Found at i:39209216 original size:23 final size:24
Alignment explanation
Indices: 39209177--39209226 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
39209167 AAATATTTTT
*
39209177 TATTTTTTTTTAATTTTTAAAT-A
1 TATTTTTTTTTAATTTTCAAATGA
*
39209200 TATTTTTTATTT-TTTTTCAAATGA
1 TATTTTTT-TTTAATTTTCAAATGA
39209224 TAT
1 TAT
39209227 GACATCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
TATTTTTTTTTAATTTTCAAATGA
Found at i:39213293 original size:18 final size:18
Alignment explanation
Indices: 39213270--39213304 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39213260 ATATANNNNN
* *
39213270 TTTATAACATTATTAAAA
1 TTTATAAAAATATTAAAA
39213288 TTTATAAAAATATTAAA
1 TTTATAAAAATATTAAA
39213305 TAAATTTTAA
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:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTATAAAAATATTAAAA
Found at i:39213467 original size:17 final size:18
Alignment explanation
Indices: 39213434--39213467 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39213424 CTAGACATTT
39213434 TTTAAAAATTATATAAAG
1 TTTAAAAATTATATAAAG
39213452 TTTAAAAATTAT-TAAA
1 TTTAAAAATTATATAAA
39213468 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTAAAAATTATATAAAG
Found at i:39214626 original size:26 final size:26
Alignment explanation
Indices: 39214574--39214626 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
39214564 TATAAAATTT
* **
39214574 TAATAAATAAAAAATATATTTTTATA
1 TAATAAATAAAAAATATATATGAATA
39214600 TAATAAATCAAAAAATA-ATATGAATA
1 TAATAAAT-AAAAAATATATATGAATA
39214626 T
1 T
39214627 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
TAATAAATAAAAAATATATATGAATA
Found at i:39218170 original size:22 final size:24
Alignment explanation
Indices: 39218136--39218181 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
39218126 TATATTTTTC
*
39218136 TATTTTTCTATTTT-TAAATATTT
1 TATTTTTCAATTTTATAAATATTT
*
39218159 TATTTTT-AATTTTATAAGTATTT
1 TATTTTTCAATTTTATAAATATTT
39218182 AAAGTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTTTTCAATTTTATAAATATTT
Found at i:39218375 original size:23 final size:23
Alignment explanation
Indices: 39218315--39218376 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
39218305 ACTTAACAAT
* *
39218315 ATTTTTATATATTTTCTATTTTTCT
1 ATTTTTAAATA-TTT-TATTTTTCA
39218340 ATTTTTAAATATTTTATTTTT-A
1 ATTTTTAAATATTTTATTTTTCA
*
39218362 ATTTTATAAGTATTT
1 ATTTT-TAAATATTT
39218377 AAAGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 5 0.15
23 15 0.45
24 3 0.09
25 10 0.30
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (23 bp):
ATTTTTAAATATTTTATTTTTCA
Found at i:39218463 original size:195 final size:196
Alignment explanation
Indices: 39218123--39218514 Score: 777
Period size: 195 Copynumber: 2.0 Consensus size: 196
39218113 TGATTTTAGA
39218123 TTATATATTTTTCTATTTTTCTATTTTTAAATATTTTATTTTTAATTTTATAAGTATTTAAAGTT
1 TTATATATTTTTCTATTTTTCTATTTTTAAATATTTTATTTTTAATTTTATAAGTATTTAAAGTT
39218188 TATATATAATTTCTAAAAAAATATTTTTTATTAAAAAGACCATGTGGCATTATGTTATTAACTAA
66 TATATATAATTTCTAAAAAAATATTTTTTATTAAAAAGACCATGTGGCATTATGTTATTAACTAA
39218253 AATAACTTCCATTTTTCCAACGTTTATTACAGATTGGACTAAAAAAATCAGAACTTAACAATATT
131 AATAACTTCCATTTTTCCAACGTTTATTACAGATTGGACTAAAAAAATCAGAACTTAACAATATT
39218318 T
196 T
39218319 TTATATA-TTTTCTATTTTTCTATTTTTAAATATTTTATTTTTAATTTTATAAGTATTTAAAGTT
1 TTATATATTTTTCTATTTTTCTATTTTTAAATATTTTATTTTTAATTTTATAAGTATTTAAAGTT
39218383 TATATATAATTTCTAAAAAAATATTTTTTATTAAAAAGACCATGTGGCATTATGTTATTAACTAA
66 TATATATAATTTCTAAAAAAATATTTTTTATTAAAAAGACCATGTGGCATTATGTTATTAACTAA
39218448 AATAACTTCCATTTTTCCAACGTTTATTACAGATTGGACTAAAAAAATCAGAACTTAACAATATT
131 AATAACTTCCATTTTTCCAACGTTTATTACAGATTGGACTAAAAAAATCAGAACTTAACAATATT
39218513 T
196 T
39218514 T
1 T
39218515 AGGAATGAAA
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 189 0.96
196 7 0.04
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (196 bp):
TTATATATTTTTCTATTTTTCTATTTTTAAATATTTTATTTTTAATTTTATAAGTATTTAAAGTT
TATATATAATTTCTAAAAAAATATTTTTTATTAAAAAGACCATGTGGCATTATGTTATTAACTAA
AATAACTTCCATTTTTCCAACGTTTATTACAGATTGGACTAAAAAAATCAGAACTTAACAATATT
T
Found at i:39219807 original size:76 final size:76
Alignment explanation
Indices: 39219681--39219826 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 76
39219671 TGTAACGACC
* *
39219681 CGATAATCAGGGGTGTCGGAAAGTGCATTCCCGAGATTTCGTTCCCGTAAATCAGACTCGTAAAT
1 CGATAATCAGGGGTATCGGAAAGTGCATTCCCGAGATCTCGTTCCCGTAAATCAGACTCGTAAAT
39219746 ATTTAACAACT
66 ATTTAACAACT
* ** *
39219757 CGATAGTCAGGGGTATCGGAAAGTGCATTCTTGAGA-CTCTGTTCCCGTAAATCGGACTCGTAAA
1 CGATAATCAGGGGTATCGGAAAGTGCATTCCCGAGATCTC-GTTCCCGTAAATCAGACTCGTAAA
39219821 TATTTA
65 TATTTA
39219827 TTAAAAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 2 0.03
76 61 0.97
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (76 bp):
CGATAATCAGGGGTATCGGAAAGTGCATTCCCGAGATCTCGTTCCCGTAAATCAGACTCGTAAAT
ATTTAACAACT
Found at i:39220135 original size:25 final size:26
Alignment explanation
Indices: 39220085--39220144 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
39220075 TATATTATAT
*
39220085 TAAAATAATAATAAACTAATGTATAA
1 TAAAATAATAATAAACTAATGAATAA
*
39220111 TAAAATAA-AAT-AAGTAAATGAATAA
1 TAAAATAATAATAAACT-AATGAATAA
*
39220136 -AAAAAAATA
1 TAAAATAATA
39220145 GAAAGCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 9 0.31
25 12 0.41
26 8 0.28
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (26 bp):
TAAAATAATAATAAACTAATGAATAA
Found at i:39220184 original size:6 final size:6
Alignment explanation
Indices: 39220175--39220205 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39220165 AACTGAAAGG
*
39220175 AAAGAA AAAGAA AAAGAA AAAGAG AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
39220206 GACGCAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:39223672 original size:19 final size:17
Alignment explanation
Indices: 39223639--39223673 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
39223629 CTTTATTTTA
39223639 TTTAAGAATAAATTAAG
1 TTTAAGAATAAATTAAG
39223656 TTTATAGAATGAAATTAA
1 TTTA-AGAAT-AAATTAA
39223674 ATCATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (17 bp):
TTTAAGAATAAATTAAG
Found at i:39226251 original size:58 final size:59
Alignment explanation
Indices: 39226160--39226276 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 59
39226150 AAGCCAGCAG
39226160 AAAAAGATGCAAGCGCTTCTGCATTTGTAAACCATGGTTCGTTCCTTGCTTTAGATGAC
1 AAAAAGATGCAAGCGCTTCTGCATTTGTAAACCATGGTTCGTTCCTTGCTTTAGATGAC
39226219 AAAAAGATGC-AGCGCTTCTGCATTTGTAAACCATGGTTCGTTCCTTGCTTTAGATGAC
1 AAAAAGATGCAAGCGCTTCTGCATTTGTAAACCATGGTTCGTTCCTTGCTTTAGATGAC
39226277 CCAATGGTGT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 48 0.83
59 10 0.17
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (59 bp):
AAAAAGATGCAAGCGCTTCTGCATTTGTAAACCATGGTTCGTTCCTTGCTTTAGATGAC
Found at i:39233098 original size:11 final size:11
Alignment explanation
Indices: 39233064--39233102 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39233054 CAATAACGAT
*
39233064 AAAATAGTAGG
1 AAAATAGTAGC
* *
39233075 AATATAATAGC
1 AAAATAGTAGC
39233086 AAAATAGTAGC
1 AAAATAGTAGC
39233097 AAAATA
1 AAAATA
39233103 ACAATAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.21
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:39236804 original size:30 final size:31
Alignment explanation
Indices: 39236770--39236829 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
39236760 AAACATTTTA
*
39236770 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
39236800 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
39236830 TCCCNNNNNN
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:39249148 original size:1 final size:1
Alignment explanation
Indices: 39249142--39249177 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
39249132 CATGCCTTTC
39249142 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39249178 TGAACATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39249186 original size:72 final size:72
Alignment explanation
Indices: 39249106--39249246 Score: 255
Period size: 72 Copynumber: 2.0 Consensus size: 72
39249096 GAAACTATGC
39249106 TGAACATGCAAAATAATCTACGGGTACATGCCTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 TGAACATGCAAAATAATCTACGGGTACATGCCTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39249171 AAAAAAA
66 AAAAAAA
* * *
39249178 TGAACATGCAAAATAATCTACGGGTACATGCCTTTCAAAAAAAAAAAAAAAAAGAAACAAGAAAA
1 TGAACATGCAAAATAATCTACGGGTACATGCCTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39249243 AAAA
66 AAAA
39249247 TATACAGGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (72 bp):
TGAACATGCAAAATAATCTACGGGTACATGCCTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAA
Found at i:39250886 original size:34 final size:34
Alignment explanation
Indices: 39250843--39250910 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
39250833 GGGCCCCTCC
39250843 ACCTATTACCAAGTGGTATTAGGTTTGATGCTTA
1 ACCTATTACCAAGTGGTATTAGGTTTGATGCTTA
39250877 ACCTATTACCAAGTGGTATTAGGTTTGATGCTTA
1 ACCTATTACCAAGTGGTATTAGGTTTGATGCTTA
39250911 GCAACAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (34 bp):
ACCTATTACCAAGTGGTATTAGGTTTGATGCTTA
Found at i:39261721 original size:2 final size:2
Alignment explanation
Indices: 39261714--39261748 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39261704 TTCCGATTTA
39261714 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
39261749 TTTGCAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:39265480 original size:18 final size:18
Alignment explanation
Indices: 39265459--39265493 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39265449 AATTTCCCAT
39265459 CTTTTCTATGTCTAATTC
1 CTTTTCTATGTCTAATTC
* *
39265477 CTTTTCTTTTTCTAATT
1 CTTTTCTATGTCTAATT
39265494 GGAAATGATT
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:0.14, C:0.20, G:0.03, T:0.63
Consensus pattern (18 bp):
CTTTTCTATGTCTAATTC
Found at i:39288081 original size:27 final size:27
Alignment explanation
Indices: 39288046--39288100 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
39288036 AAACTGTTGG
*
39288046 TTTCATTTTTTCTCTTATTTTCAATTTT
1 TTTCATTTTATCTCTTATTTT-AATTTT
*
39288074 TTTC-TTTTATCTCTTCTTTTAATTTT
1 TTTCATTTTATCTCTTATTTTAATTTT
39288100 T
1 T
39288101 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 14 0.56
28 4 0.16
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTCATTTTATCTCTTATTTTAATTTT
Found at i:39288107 original size:26 final size:26
Alignment explanation
Indices: 39288050--39288108 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
39288040 TGTTGGTTTC
39288050 ATTTTT-TCTCTTATTTTCAATTTTT
1 ATTTTTATCTCTTATTTTCAATTTTT
* *
39288075 TTCTTTTATCTCTTCTTTT-AATTTTT
1 AT-TTTTATCTCTTATTTTCAATTTTT
39288101 AATTTTTA
1 -ATTTTTA
39288109 ATTAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.04
26 16 0.57
27 11 0.39
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (26 bp):
ATTTTTATCTCTTATTTTCAATTTTT
Found at i:39293098 original size:17 final size:17
Alignment explanation
Indices: 39293076--39293108 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39293066 AGTGCCTAAA
39293076 AACTATATTTTTAAGTT
1 AACTATATTTTTAAGTT
*
39293093 AACTATGTTTTTAAGT
1 AACTATATTTTTAAGT
39293109 GTNNNNNNNN
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (17 bp):
AACTATATTTTTAAGTT
Found at i:39293145 original size:2 final size:2
Alignment explanation
Indices: 39293138--39293195 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
39293128 NNNNNNNNNN
39293138 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39293180 TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG
39293196 ATACTAATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:39294312 original size:31 final size:31
Alignment explanation
Indices: 39294277--39294341 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
39294267 CTTTCAGAGC
39294277 TTTCATTCAAATCATTGAACTATTTAAAAAT
1 TTTCATTCAAATCATTGAACTATTTAAAAAT
* ** * * *
39294308 TTTCATTTAGGTTATTGAACTATTTGAAAGT
1 TTTCATTCAAATCATTGAACTATTTAAAAAT
39294339 TTT
1 TTT
39294342 TATTTGAGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTCATTCAAATCATTGAACTATTTAAAAAT
Found at i:39299720 original size:164 final size:165
Alignment explanation
Indices: 39299524--39299858 Score: 645
Period size: 164 Copynumber: 2.0 Consensus size: 165
39299514 GACTCATTTT
39299524 TTAAGTCGGACTTAGCCTAAGCTTAAAAAATGAGCCTAATTTTTTATTTGGCCCTGCCCAAACCC
1 TTAA-TCGGACTTAGCCTAAGCTTAAAAAATGAGCCTAATTTTTTATTTGGCCCTGCCCAAACCC
*
39299589 GACCCGGCTCATGAACAATCTTGTCCCAAATTCAATTAATCTCATAAATATATTTATATTTTTTT
65 GACCCGGCTCATGAACAATCTTGTCCCAAATTCAATTAAACTCATAAATATATTTATATTTTTTT
39299654 ATTTTATTTTGTTTCAAGCTTTGTTTTAATTTTTAA
130 ATTTTATTTTGTTTCAAGCTTTGTTTTAATTTTTAA
39299690 TTAATCGGACTTAGCCT-AGCTTAAAAAATGAGCCTAATTTTTTATTTGGCCCTGCCCAAACCCG
1 TTAATCGGACTTAGCCTAAGCTTAAAAAATGAGCCTAATTTTTTATTTGGCCCTGCCCAAACCCG
39299754 ACCCGGCTCATGAACAATCTTGTCCCAAATTCAATTAAACTCATAAATATATTTATATTTTTTTA
66 ACCCGGCTCATGAACAATCTTGTCCCAAATTCAATTAAACTCATAAATATATTTATATTTTTTTA
39299819 TTTTATTTTGTTTCAAGCTTTGTTTTAATTTTTAA
131 TTTTATTTTGTTTCAAGCTTTGTTTTAATTTTTAA
39299854 TTAAT
1 TTAAT
39299859 AAACATTGTT
Statistics
Matches: 168, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
164 151 0.90
165 13 0.08
166 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (165 bp):
TTAATCGGACTTAGCCTAAGCTTAAAAAATGAGCCTAATTTTTTATTTGGCCCTGCCCAAACCCG
ACCCGGCTCATGAACAATCTTGTCCCAAATTCAATTAAACTCATAAATATATTTATATTTTTTTA
TTTTATTTTGTTTCAAGCTTTGTTTTAATTTTTAA
Found at i:39304175 original size:31 final size:31
Alignment explanation
Indices: 39304140--39304212 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
39304130 TCTTCGAAAG
*
39304140 TTTTCATTTAAGTCACTGAACTATTTAAAAA
1 TTTTCATTTAAGTCACTAAACTATTTAAAAA
* * * * *
39304171 TTTTCATTTAGGTCATTAAACTCTTTGAAAG
1 TTTTCATTTAAGTCACTAAACTATTTAAAAA
*
39304202 TTTTTATTTAA
1 TTTTCATTTAA
39304213 ATTGCTAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTTCATTTAAGTCACTAAACTATTTAAAAA
Found at i:39304243 original size:62 final size:62
Alignment explanation
Indices: 39304127--39304280 Score: 164
Period size: 62 Copynumber: 2.5 Consensus size: 62
39304117 ATGATCACCG
* * * * * *
39304127 AACTCTTCGAAAGTTTTCATTTAAGTCACTGAACTATTTAAAAATTTTCATTTAGGTCATTA
1 AACTCTTTGAAAGTTTTTATTTAAATCACTAAACTATTCAAAAATTATCATTTAGGTCATTA
** * * * * *
39304189 AACTCTTTGAAAGTTTTTATTTAAATTGCTAAATTATTCAAAAGTTATCCTTTAGGTTATTG
1 AACTCTTTGAAAGTTTTTATTTAAATCACTAAACTATTCAAAAATTATCATTTAGGTCATTA
* * *
39304251 AACTATTTAAAAGTTTTTATGTAAATCACT
1 AACTCTTTGAAAGTTTTTATTTAAATCACT
39304281 GAGTTGTTAA
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (62 bp):
AACTCTTTGAAAGTTTTTATTTAAATCACTAAACTATTCAAAAATTATCATTTAGGTCATTA
Found at i:39307657 original size:21 final size:20
Alignment explanation
Indices: 39307633--39307694 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
39307623 GGAAATCTAG
39307633 TTTCCTTGTAAGAAAAGCAAT
1 TTTCCTTG-AAGAAAAGCAAT
*
39307654 TTTCC-TGAAG--TA-C--T
1 TTTCCTTGAAGAAAAGCAAT
39307668 TTTCCTTGCAAGAAAAGCAAT
1 TTTCCTTG-AAGAAAAGCAAT
39307689 TTTCCT
1 TTTCCT
39307695 AAAGCAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
14 6 0.19
15 2 0.06
16 4 0.12
17 1 0.03
18 1 0.03
19 4 0.12
20 2 0.06
21 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTCCTTGAAGAAAAGCAAT
Found at i:39310028 original size:32 final size:32
Alignment explanation
Indices: 39309946--39310031 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 32
39309936 TATTAATTAA
*** *
39309946 CACTTTCTCTGTAATGTTATATTTCTGTGACT
1 CACTTTCTCTGTAATGTTATATTTCAAAGAAT
*
39309978 -ACATTCT-TAGTAA--TTATATTTCAAAGAAT
1 CACTTTCTCT-GTAATGTTATATTTCAAAGAAT
39310007 CACTTTCTCTGTAATGTTATATTTC
1 CACTTTCTCTGTAATGTTATATTTC
39310032 TGTGACTACG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
29 12 0.28
30 11 0.26
31 11 0.26
32 9 0.21
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (32 bp):
CACTTTCTCTGTAATGTTATATTTCAAAGAAT
Found at i:39320044 original size:126 final size:124
Alignment explanation
Indices: 39319818--39320091 Score: 422
Period size: 126 Copynumber: 2.2 Consensus size: 124
39319808 TCTCAATTTC
* * * *
39319818 CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCAAATAGCA
1 CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAACAGCA
*
39319883 TCCTGCTAGAATCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAGAATTATTTCTT
66 TCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTT
*
39319943 CTAGGACCTACTGTAGCAAAAGCGTGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAACAGC
1 C-AGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAACAGC
* **** *
39320008 ATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTT
65 ATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTT
39320068 CAGGACCTACTGTAGCAAAAGCGC
1 CAGGACCTACTGTAGCAAAAGCGC
39320092 ATAAACGTGG
Statistics
Matches: 135, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 22 0.16
125 12 0.09
126 101 0.75
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (124 bp):
CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTATCAAACAGCA
TCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTT
Found at i:39320767 original size:23 final size:24
Alignment explanation
Indices: 39320732--39320779 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
39320722 ATATTATGTT
39320732 AAAAATAATATAAAA-ATATTCAAA
1 AAAAATAATATAAAATA-ATTCAAA
*
39320756 AAAAATTA-ATAAAATAATTCAAA
1 AAAAATAATATAAAATAATTCAAA
39320779 A
1 A
39320780 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATAATATAAAATAATTCAAA
Found at i:39320788 original size:19 final size:18
Alignment explanation
Indices: 39320766--39320817 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 18
39320756 AAAAATTAAT
39320766 AAAATAATTCAAAATTTA
1 AAAATAATTCAAAATTTA
39320784 AAAA-AATTCTAAAAATTTTA
1 AAAATAATTC--AAAA-TTTA
39320804 AAAATAATATCAAA
1 AAAATAAT-TCAAA
39320818 TACTCATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 11 0.38
21 3 0.10
22 2 0.07
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAATTCAAAATTTA
Found at i:39326029 original size:175 final size:172
Alignment explanation
Indices: 39325666--39326030 Score: 405
Period size: 175 Copynumber: 2.1 Consensus size: 172
39325656 TCAAACTAAG
*
39325666 AACTTAAATGATTTA--TTTTTAATACCCCGTTACAATACTTCAAACACTTCTTCAACTTCAATG
1 AACTTAAATGATTTACTTTTTTAATACCCCGTTACAATACTTCAAACACTTCTTCAACTTCAATC
* * * * * * * *
39325729 AAATGCAAAAATAAGCTTTCCAAACGAGGATAATGCACTTCAAAATTCTTGAAATCATATCATCT
66 AAATGCAAAAATAAACATTCCAAACAAGAATAATACACTTCAAAA-TCATCAAATCATATCATCC
39325794 TACATTAATAAGAAATCCATGCCAATCAAGTTAAAACTCAATC
130 TACATTAATAAGAAATCCATGCCAATCAAGTTAAAACTCAATC
* * * * **
39325837 AATTTGAACGGTTTACTTTTTTAATACCTTGTTACAATACTTCAAAAGCACTTCTTCAACTTCAA
1 AACTTAAATGATTTACTTTTTTAATACCCCGTTACAATACTTC-AAA-CACTTCTTCAACTTCAA
** * * * *
39325902 -CAAAGTGCACGAATAAACATTCCGAACAAGAATAATACACTTCAACA-CATCAAATTCATCTCC
64 TCAAA-TGCAAAAATAAACATTCCAAACAAGAATAATACACTTCAAAATCATCAAA-TCATATCA
* * * * * *
39325965 TCCTACATTAGTAAGAATATTCATGTCAATTAAGTTAAGACTTAATC
127 TCCTACATTAATAAGAA-ATCCATGCCAATCAAGTTAAAACTCAATC
39326012 AACTTAAATGATTTACTTT
1 AACTTAAATGATTTACTTT
39326031 CTAATATCCT
Statistics
Matches: 156, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
171 11 0.07
173 29 0.19
174 27 0.17
175 89 0.57
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (172 bp):
AACTTAAATGATTTACTTTTTTAATACCCCGTTACAATACTTCAAACACTTCTTCAACTTCAATC
AAATGCAAAAATAAACATTCCAAACAAGAATAATACACTTCAAAATCATCAAATCATATCATCCT
ACATTAATAAGAAATCCATGCCAATCAAGTTAAAACTCAATC
Found at i:39326181 original size:156 final size:159
Alignment explanation
Indices: 39325904--39326205 Score: 373
Period size: 156 Copynumber: 1.9 Consensus size: 159
39325894 AACTTCAACA
* *
39325904 AAGTGCACGAATAAACATTCCGAACAAGAATAATACACTTCAACACATCAAATTCATCTCCTCCT
1 AAGTGCAAGAATAAACATTCCGAACAAGAATAATACACTTCAACACATCAAATTCAGCTCCTCCT
* * ** * *
39325969 ACATTAGTAAGAATATTCATGTCAATTAAGTTAAGACTTAATCAACTTAAATGATTTACTTTCTA
66 ACATTAGTAAGAACATCCATACCAATCAAGTTAAGAATTAATCAACTTAAATGATTTACTTTCTA
*
39326034 ATATCCTATTACAACAATCAACTTCAGTG
131 ATACCCTATTACAACAATCAACTTCAGTG
** * *
39326063 AAGTGCAAGAATAAATTTTCCGAACAA-AGAT-A-ACACTTCAACATACTCAAA-TGAGC-CCTC
1 AAGTGCAAGAATAAACATTCCGAACAAGA-ATAATACACTTCAACACA-TCAAATTCAGCTCCTC
* * * *
39326123 CTATATTAGTAAGAACGTCCATACCAATCAAGTTAA-AATTAAATTAACTTGAATGATTTACTTT
64 CTACATTAGTAAGAACATCCATACCAATCAAGTTAAGAATT-AATCAACTTAAATGATTTACTTT
*
39326187 TTAATACCCTATTACAACA
128 CTAATACCCTATTACAACA
39326206 CTTCGAATTA
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
155 3 0.02
156 71 0.58
157 15 0.12
158 7 0.06
159 26 0.21
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (159 bp):
AAGTGCAAGAATAAACATTCCGAACAAGAATAATACACTTCAACACATCAAATTCAGCTCCTCCT
ACATTAGTAAGAACATCCATACCAATCAAGTTAAGAATTAATCAACTTAAATGATTTACTTTCTA
ATACCCTATTACAACAATCAACTTCAGTG
Found at i:39335715 original size:30 final size:28
Alignment explanation
Indices: 39335665--39335730 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
39335655 TGTGAAAAAG
* *
39335665 TAAAAAGTGATGGGTCAAAGTGTAAATAT
1 TAAAAAGTGAGGGGTCAAAGTATAAAT-T
* *
39335694 TCAAAAATTGAGGGGTTAAAGTATAAATT
1 T-AAAAAGTGAGGGGTCAAAGTATAAATT
39335723 TAAAAAGT
1 TAAAAAGT
39335731 TAAAAGACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.19
29 3 0.10
30 22 0.71
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (28 bp):
TAAAAAGTGAGGGGTCAAAGTATAAATT
Found at i:39344752 original size:13 final size:13
Alignment explanation
Indices: 39344734--39344810 Score: 127
Period size: 13 Copynumber: 5.9 Consensus size: 13
39344724 AGTTCTTCAT
39344734 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
39344747 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
39344760 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
*
39344773 TGATTTTGAGAAG
1 TGCTTTTGAGAAG
39344786 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
39344799 TGATTTTGAGAA
1 TGCTTTTGAGAA
39344811 ATTTAAGTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:39348041 original size:30 final size:30
Alignment explanation
Indices: 39348006--39348066 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
39347996 AAGGGCAGAA
* *
39348006 CAAAGAATCAGCAGA-AGGCAGAGATGAGGG
1 CAAAGAAGCAGCAGAGA-GCAGAGATAAGGG
39348036 CAAAGAAGCAGCAGAGAGCAGAGATAAGGG
1 CAAAGAAGCAGCAGAGAGCAGAGATAAGGG
39348066 C
1 C
39348067 GTTCGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.36, T:0.05
Consensus pattern (30 bp):
CAAAGAAGCAGCAGAGAGCAGAGATAAGGG
Found at i:39348653 original size:33 final size:33
Alignment explanation
Indices: 39348593--39348663 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
39348583 AAAATTTGTT
* * * *
39348593 TTTTGTTGTTATTTTCTTTTTTCTTTTTTACTG
1 TTTTGTTGTTATTCTCTTTTATCTTTTTCACTA
*
39348626 TTTTGTTGTTGTTCTCTTTTCAT-TTTTTCACTA
1 TTTTGTTGTTATTCTCTTTT-ATCTTTTTCACTA
39348659 TTTTG
1 TTTTG
39348664 CTATTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.07, C:0.11, G:0.10, T:0.72
Consensus pattern (33 bp):
TTTTGTTGTTATTCTCTTTTATCTTTTTCACTA
Found at i:39348672 original size:22 final size:21
Alignment explanation
Indices: 39348647--39348697 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
39348637 TTCTCTTTTC
39348647 ATTTTTTCACTATTTTGCTATT
1 ATTTTTT-ACTATTTTGCTATT
* *
39348669 ATTTTATTACTATTTTGTTTTT
1 ATTTT-TTACTATTTTGCTATT
39348691 ATTTTTT
1 ATTTTTT
39348698 TGGATGCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (21 bp):
ATTTTTTACTATTTTGCTATT
Found at i:39352955 original size:2 final size:2
Alignment explanation
Indices: 39352948--39352977 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39352938 GTTCCTAGAA
39352948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39352978 GTGTGTGTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39356149 original size:23 final size:23
Alignment explanation
Indices: 39356100--39356142 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39356090 TACTTGAATA
*
39356100 TGTATTTGTACTTGAAATTATGT
1 TGTATTCGTACTTGAAATTATGT
39356123 TGTATTCGTACTT-AAATTAT
1 TGTATTCGTACTTGAAATTAT
39356143 ATTTGTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (23 bp):
TGTATTCGTACTTGAAATTATGT
Found at i:39356154 original size:23 final size:23
Alignment explanation
Indices: 39356107--39356155 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
39356097 ATATGTATTT
*
39356107 GTACTTGAAATTATGTTGTATTC
1 GTACTTGAAATTATGTTGTACTC
*
39356130 GTACTT-AAATTATATTTGTACTC
1 GTACTTGAAATTAT-GTTGTACTC
39356153 GTA
1 GTA
39356156 AAAGTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (23 bp):
GTACTTGAAATTATGTTGTACTC
Found at i:39356896 original size:94 final size:94
Alignment explanation
Indices: 39356730--39356969 Score: 252
Period size: 94 Copynumber: 2.6 Consensus size: 94
39356720 AAGCTTGGGC
* * *
39356730 GGTGTATGTTTTATAACTTTGTCAAATTTAGCCAAGTG-CTTTAAGAGGCTAGAAGCAATCATTC
1 GGTGTATGCTTTATAACTTTGTAAAATTTAGCTAAGTGTC-TTAAGAGGCTAGAAGCAATCATTC
* * *
39356794 TATGAAACTTAGTGAGCAATTTCCTTTTAG-
65 TATGAAACTTAGCGAGCAATTT-CGTGTAGA
* * * * * * *
39356824 GGTGTTTGCTTTATAACTTTATAAAATTTAGCTAAGTGTCTTATGAGGTTAGAAGTGATTC-TTT
1 GGTGTATGCTTTATAACTTTGTAAAATTTAGCTAAGTGTCTTAAGAGGCTAGAAG-CAATCATTC
* *
39356888 TATTAAACTTAGCGAGCAATTTCGTGTCGA
65 TATGAAACTTAGCGAGCAATTTCGTGTAGA
* * * * *
39356918 GGTGTCTACTTTAAAACTTTGTAAAATGTAGCTAAGTGTCTTAAAAGGCTAG
1 GGTGTATGCTTTATAACTTTGTAAAATTTAGCTAAGTGTCTTAAGAGGCTAG
39356970 CAACTTTTCT
Statistics
Matches: 120, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
93 4 0.03
94 112 0.93
95 4 0.03
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (94 bp):
GGTGTATGCTTTATAACTTTGTAAAATTTAGCTAAGTGTCTTAAGAGGCTAGAAGCAATCATTCT
ATGAAACTTAGCGAGCAATTTCGTGTAGA
Found at i:39365345 original size:9 final size:9
Alignment explanation
Indices: 39365328--39365364 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39365318 TGAGTTTTCG
39365328 AATTCGAAT
1 AATTCGAAT
*
39365337 AACTCGAAT
1 AATTCGAAT
39365346 AATTCGAAT
1 AATTCGAAT
39365355 AATTCGAAT
1 AATTCGAAT
39365364 A
1 A
39365365 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39365606 original size:19 final size:20
Alignment explanation
Indices: 39365566--39365606 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
39365556 CCAAAACCCT
*
39365566 CAAAATCTTTTATTTTCCCC
1 CAAAATCTTTTATCTTCCCC
39365586 CAAAAT-TTTTA-CTTCCTCC
1 CAAAATCTTTTATCTTCC-CC
39365605 CA
1 CA
39365607 CTTTTCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (20 bp):
CAAAATCTTTTATCTTCCCC
Found at i:39367836 original size:17 final size:18
Alignment explanation
Indices: 39367816--39367867 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
39367806 GAAAAATCCT
*
39367816 AAAAACTAAAAA-AAAAA
1 AAAAACCAAAAAGAAAAA
*
39367833 AAAACCCAAAAAGAAAAA
1 AAAAACCAAAAAGAAAAA
* * *
39367851 AAGAATCGAAAAGAAAA
1 AAAAACCAAAAAGAAAA
39367868 TCAAGGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.79, C:0.10, G:0.08, T:0.04
Consensus pattern (18 bp):
AAAAACCAAAAAGAAAAA
Found at i:39368053 original size:7 final size:7
Alignment explanation
Indices: 39368041--39368078 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
39368031 TTAGTGCAGA
39368041 AATGGGC
1 AATGGGC
39368048 AATGGGC
1 AATGGGC
39368055 AATGGGC
1 AATGGGC
39368062 AATGGGC
1 AATGGGC
39368069 AATGGGC
1 AATGGGC
39368076 AAT
1 AAT
39368079 TCCTAATTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.39, T:0.16
Consensus pattern (7 bp):
AATGGGC
Found at i:39369230 original size:23 final size:23
Alignment explanation
Indices: 39369189--39369232 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39369179 TCATAAAAAA
*
39369189 TTATTATTAATATTGTAATATAT
1 TTATTATTAAAATTGTAATATAT
39369212 TTATTATTAAAATAT-TAATAT
1 TTATTATTAAAAT-TGTAATAT
39369233 TAATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTATTAAAATTGTAATATAT
Found at i:39369233 original size:6 final size:6
Alignment explanation
Indices: 39369222--39369279 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
39369212 TTATTATTAA
*
39369222 AATATT AATATT AATATT AATATT AATATT AATATT -ATAAT AATA-T
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
*
39369268 AATATA AATATT
1 AATATT AATATT
39369280 TTAAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
5 9 0.19
6 38 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:39371319 original size:43 final size:43
Alignment explanation
Indices: 39371251--39371338 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
39371241 TCTCCACTCA
39371251 TCTCAACCCCCACCACCGCCACCTTCCCTCTCACTCCTCACCG
1 TCTCAACCCCCACCACCGCCACCTTCCCTCTCACTCCTCACCG
* * *
39371294 TCTCAACCCCCACCATCGTTC-CCTTCCCTCTCACTCTTCACCG
1 TCTCAACCCCCACCACCG-CCACCTTCCCTCTCACTCCTCACCG
39371337 TC
1 TC
39371339 GATCTCACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.15, C:0.57, G:0.05, T:0.24
Consensus pattern (43 bp):
TCTCAACCCCCACCACCGCCACCTTCCCTCTCACTCCTCACCG
Found at i:39379471 original size:6 final size:6
Alignment explanation
Indices: 39379460--39379495 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
39379450 TTTTTTTATA
*
39379460 AGGGGT AGGGGT AGGGGT AGGGGT AGGGGT AAGGGT
1 AGGGGT AGGGGT AGGGGT AGGGGT AGGGGT AGGGGT
39379496 TTTCCTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.19, C:0.00, G:0.64, T:0.17
Consensus pattern (6 bp):
AGGGGT
Found at i:39384234 original size:21 final size:20
Alignment explanation
Indices: 39384191--39384234 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
39384181 TTATATTCAA
* **
39384191 TAAATAAACAAAAAAATCCT
1 TAAAAAAACAAAAAAATAAT
39384211 TAAAAAAACAAATAAAATAAT
1 TAAAAAAACAAA-AAAATAAT
39384232 TAA
1 TAA
39384235 CCAAAACCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAAAAAACAAAAAAATAAT
Found at i:39384437 original size:2 final size:2
Alignment explanation
Indices: 39384430--39384456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39384420 AAAACAATGA
39384430 TC 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 TC T
39384457 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39391736 original size:20 final size:21
Alignment explanation
Indices: 39391697--39391741 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
39391687 ATATTTTCAA
*
39391697 TTATTTTAATTGTATTTTAT-
1 TTATTTTAATTGTATATTATC
39391717 TTATTTTAA-TGTTATATTATC
1 TTATTTTAATTG-TATATTATC
39391738 TTAT
1 TTAT
39391742 AAAAACTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 16 0.73
21 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATTTTAATTGTATATTATC
Found at i:39404471 original size:39 final size:34
Alignment explanation
Indices: 39404428--39404503 Score: 82
Period size: 37 Copynumber: 2.1 Consensus size: 34
39404418 TAAAATAACG
39404428 GAGCAGAATAAAAAAGAAA-AAAATATATTGAATGGAGAA
1 GAGCA-AA-AAAAAAGAAAGAAAA-ATA--GAA-GGAGAA
*
39404467 GAGCAAAAACAAAGAAAGAAAAATAGAAGGAGAA
1 GAGCAAAAAAAAAGAAAGAAAAATAGAAGGAGAA
39404501 GAG
1 GAG
39404504 AACCTTCCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
34 9 0.26
35 3 0.09
37 12 0.34
38 6 0.17
39 5 0.14
ACGTcount: A:0.63, C:0.04, G:0.24, T:0.09
Consensus pattern (34 bp):
GAGCAAAAAAAAAGAAAGAAAAATAGAAGGAGAA
Found at i:39410551 original size:133 final size:134
Alignment explanation
Indices: 39410303--39410570 Score: 513
Period size: 133 Copynumber: 2.0 Consensus size: 134
39410293 TTATGATATC
39410303 ACTTAAAATAAAAATAAATAACAATTATTTATTTTATGAAAATATGTTTATAAGCATTATATATT
1 ACTTAAAATAAAAATAAATAACAATTATTTATTTTATGAAAATATGTTTATAAGCATTATATATT
39410368 TATATTAACATTTTATTAATAGCAAACATAATTAGTAATAAATTTTTAGGTTAAATTATAAAATG
66 TATATTAACATTTTATTAATAGCAAACATAATTAGTAATAAATTTTTAGGTTAAATTATAAAATG
39410433 AAAT
131 AAAT
39410437 ACTTAAAAT-AAAATAAATAACAATTATTTATTTTATGAAAATATGTTTATAAGCATTATATATT
1 ACTTAAAATAAAAATAAATAACAATTATTTATTTTATGAAAATATGTTTATAAGCATTATATATT
39410501 TATATTAACATTTTATTAATAGCAAA-ACTAATTAGTAATAAATTTTTAGGTTAAATTATAAAAT
66 TATATTAACATTTTATTAATAGCAAACA-TAATTAGTAATAAATTTTTAGGTTAAATTATAAAAT
39410565 GAAAT
130 GAAAT
39410570 A
1 A
39410571 AAATTTTAAA
Statistics
Matches: 133, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
132 1 0.01
133 123 0.92
134 9 0.07
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (134 bp):
ACTTAAAATAAAAATAAATAACAATTATTTATTTTATGAAAATATGTTTATAAGCATTATATATT
TATATTAACATTTTATTAATAGCAAACATAATTAGTAATAAATTTTTAGGTTAAATTATAAAATG
AAAT
Found at i:39411751 original size:94 final size:95
Alignment explanation
Indices: 39411586--39411767 Score: 321
Period size: 94 Copynumber: 1.9 Consensus size: 95
39411576 TTACTTTTTT
*
39411586 TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATT
1 TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATG
*
39411651 ATCTTTATATTAATCTTTAATTTTAGTTTC
66 ACCTTTATATTAATCTTTAATTTTAGTTTC
*
39411681 TTTTTATGATTTGTGAATTTAGGTTTTAG-TTTTTTATTGATTAATGGTTAATGTTTTTATTATG
1 TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATG
*
39411745 ACCTTTATATTAATCTTTGATTT
66 ACCTTTATATTAATCTTTAATTT
39411768 AGAATTGATT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 54 0.65
95 29 0.35
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.60
Consensus pattern (95 bp):
TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATG
ACCTTTATATTAATCTTTAATTTTAGTTTC
Found at i:39413127 original size:94 final size:95
Alignment explanation
Indices: 39412962--39413143 Score: 321
Period size: 94 Copynumber: 1.9 Consensus size: 95
39412952 TTACTTTTTT
*
39412962 TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATT
1 TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATG
*
39413027 ATCTTTATATTAATCTTTAATTTTAGTTTC
66 ACCTTTATATTAATCTTTAATTTTAGTTTC
*
39413057 TTTTTATGATTTGTGAATTTAGGTTTTAG-TTTTTTATTGATTAATGGTTAATGTTTTTATTATG
1 TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATG
*
39413121 ACCTTTATATTAATCTTTGATTT
66 ACCTTTATATTAATCTTTAATTT
39413144 AGAATTGATT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 54 0.65
95 29 0.35
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.60
Consensus pattern (95 bp):
TTTTTATGATTTGTGAATTTAGGTTTTAGTTTTTTTATTGATTAAGGGTTAATGTTTTTATTATG
ACCTTTATATTAATCTTTAATTTTAGTTTC
Found at i:39415074 original size:15 final size:15
Alignment explanation
Indices: 39415056--39415085 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39415046 AATTATTAAT
*
39415056 ATATGATATGATATA
1 ATATGATATAATATA
39415071 ATATGATATAATATA
1 ATATGATATAATATA
39415086 GCGTTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATGATATAATATA
Found at i:39415257 original size:25 final size:26
Alignment explanation
Indices: 39415210--39415258 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
39415200 AATATATTAT
*
39415210 GTATTACTATTATAATATGTGATATA
1 GTATTACTATTAAAATATGTGATATA
39415236 GTATTAC-ATTAAAACTAT-TGATA
1 GTATTACTATTAAAA-TATGTGATA
39415259 CATATATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
GTATTACTATTAAAATATGTGATATA
Found at i:39422130 original size:21 final size:20
Alignment explanation
Indices: 39422106--39422146 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
39422096 AGTAGTTTTT
*
39422106 AATGAAAATTTGGATCAATGA
1 AATGAAAATTTGCAT-AATGA
*
39422127 AATGAAAGTTTGCATAATGA
1 AATGAAAATTTGCATAATGA
39422147 TGTCAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (20 bp):
AATGAAAATTTGCATAATGA
Found at i:39426421 original size:20 final size:22
Alignment explanation
Indices: 39426370--39426424 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
39426360 TAAAATATAC
*
39426370 ATACGTACATATATTTAATGTT
1 ATACATACATATATTTAATGTT
*
39426392 AT--ATATATATATTT-AT-TT
1 ATACATACATATATTTAATGTT
39426410 ATACATACATATATT
1 ATACATACATATATT
39426425 CTTTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 20 0.71
22 2 0.07
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (22 bp):
ATACATACATATATTTAATGTT
Found at i:39428977 original size:12 final size:12
Alignment explanation
Indices: 39428960--39428987 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39428950 GTTCTAATAT
39428960 AATTGAACCAAG
1 AATTGAACCAAG
39428972 AATTGAACCAAG
1 AATTGAACCAAG
39428984 AATT
1 AATT
39428988 AACGTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (12 bp):
AATTGAACCAAG
Done.