Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 134 of 196
Found at i:39946825 original size:42 final size:41
Alignment explanation
Indices: 39946735--39946825 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
39946725 GGTTTAGAGT
* *
39946735 TTTTAGGGTTAGGGTTTTGTTAAAATAATTTAAGGTTAGGT
1 TTTTAGGGTTAGGGTTTTGTTAAAATAATTAAAGGTTAGGG
* *
39946776 TTGTTAGGTTTAGGGTTTTGTTAAAATAATTAAAGGTTCTGGG
1 TT-TTAGGGTTAGGGTTTTGTTAAAATAATTAAAGGTT-AGGG
39946819 TTTTAGG
1 TTTTAGG
39946826 AATTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 2 0.05
42 38 0.86
43 4 0.09
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (41 bp):
TTTTAGGGTTAGGGTTTTGTTAAAATAATTAAAGGTTAGGG
Found at i:39947334 original size:126 final size:126
Alignment explanation
Indices: 39947002--39947521 Score: 812
Period size: 126 Copynumber: 4.1 Consensus size: 126
39946992 GATTTTGGTT
*
39947002 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGGAGACGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* *
39947067 ATGCTTCGAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATGGATGCTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
* *
39947128 TTTTTCTACAGTAGTTCCT-AAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAGAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* **
39947192 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACACTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGATGCTC
* * * *
39947253 TTTTTCTACAGTAATTCCTGAAAAAATAATTTTGAGAAGACGTTTCCGAGCAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
*
39947318 ATGTTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGATGCTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGATGCTC
* * *
39947379 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGTTTTTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * *
39947444 ATGCTTCAAGCAGGATGCCCTATCAGCAAAATTATTGAAAAAAGCTCCCACGTGGATGCTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
* *
39947505 TTTTTTTATAGTAGTTC
1 TTTTTCTACAGTAGTTC
39947522 ATGCTTGGCC
Statistics
Matches: 363, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
125 115 0.32
126 248 0.68
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
Found at i:39948382 original size:23 final size:22
Alignment explanation
Indices: 39948349--39948614 Score: 148
Period size: 23 Copynumber: 11.3 Consensus size: 22
39948339 AGAAATTGAG
*
39948349 CAGCATGTATATACCAATTTGGA
1 CAGCAT-TATATACAAATTTGGA
*
39948372 CAGCACTTATACACAAAATTT-GA
1 CAGCA-TTATATAC-AAATTTGGA
*
39948395 CAGCATGTATATACAAAATTGGA
1 CAGCAT-TATATACAAATTTGGA
* *
39948418 CAGCATT-TATCCACCAAAATTGGG
1 CAGCATTATAT--A-CAAATTTGGA
*
39948442 CAGCATATATATATATACCAATTTGGA
1 CAGC----AT-TATATACAAATTTGGA
*
39948469 CAGCACTTATACACAAAATTT-GA
1 CAGCA-TTATATAC-AAATTTGGA
* * *
39948492 CAACATGTATATACAAAATTGAA
1 CAGCAT-TATATACAAATTTGGA
* *
39948515 CAGCATT-TATTCACCAAAATTGGG
1 CAGCATTATA-T-A-CAAATTTGGA
*
39948539 CAGCATATATGTAGC-AATTTGGA
1 CAGCAT-TATATA-CAAATTTGGA
*
39948562 CAGCACTTATACACAAAATTT-GA
1 CAGCA-TTATATAC-AAATTTGGA
*
39948585 CAGCATGTATATACAAAATTGGA
1 CAGCAT-TATATACAAATTTGGA
39948608 CAGCATT
1 CAGCATT
39948615 TATTCACCAA
Statistics
Matches: 191, Mismatches: 25, Indels: 55
0.70 0.09 0.20
Matches are distributed among these distances:
21 5 0.03
22 23 0.12
23 95 0.50
24 47 0.25
25 2 0.01
26 1 0.01
27 11 0.06
28 3 0.02
29 1 0.01
30 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (22 bp):
CAGCATTATATACAAATTTGGA
Found at i:39948445 original size:93 final size:93
Alignment explanation
Indices: 39948319--39948655 Score: 514
Period size: 93 Copynumber: 3.6 Consensus size: 93
39948309 TCTACCCTGT
* * * *
39948319 TTGGACAGC-TCTTATACATCAGAAATTGAGCAGCATGTATATACCAATTTGGACAGCACTTATA
1 TTGGACAGCAT-TTATTCACCA-AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATA
39948383 CACAAAATTTGACAGCATGTATATACAAAA
64 CACAAAATTTGACAGCATGTATATACAAAA
*
39948413 TTGGACAGCATTTATCCACCAAAATTGGGCAGCATATATATATATACCAATTTGGACAGCACTTA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGC----ATATATATACCAATTTGGACAGCACTTA
*
39948478 TACACAAAATTTGACAACATGTATATACAAAA
62 TACACAAAATTTGACAGCATGTATATACAAAA
* * *
39948510 TTGAACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
39948575 CAAAATTTGACAGCATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
* *
39948603 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGAC
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGAC
39948656 CATTAAAGCA
Statistics
Matches: 227, Mismatches: 11, Indels: 11
0.91 0.04 0.04
Matches are distributed among these distances:
93 120 0.53
94 17 0.07
95 1 0.00
97 89 0.39
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (93 bp):
TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
CAAAATTTGACAGCATGTATATACAAAA
Found at i:39949372 original size:28 final size:28
Alignment explanation
Indices: 39949340--39949466 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
39949330 ATTTAATAAG
** * *
39949340 TTCGCACACTTAGTGCTCAATAATCAAA
1 TTCGCACACTTAGTGCTTTACAATTAAA
* * *
39949368 TTCGCACACTTCGTGCTTTGCCATTAAA
1 TTCGCACACTTAGTGCTTTACAATTAAA
*
39949396 CTCGCACACTTAGTGCTTTACAATTAAA
1 TTCGCACACTTAGTGCTTTACAATTAAA
*
39949424 CTCGCACACTTAGTGCTTTACAATTAAA
1 TTCGCACACTTAGTGCTTTACAATTAAA
39949452 TTCGCACACTTAGTG
1 TTCGCACACTTAGTG
39949467 TCGAAAGTCA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 87 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (28 bp):
TTCGCACACTTAGTGCTTTACAATTAAA
Found at i:39951952 original size:36 final size:39
Alignment explanation
Indices: 39951889--39951978 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 39
39951879 GTCTCCAATT
* **
39951889 TCACATTTCAATTC-AGTTTCACTTTTT-CACTTTCAA-
1 TCACAATTCAATTCAAAATTCACTTTTTCCACTTTCAAG
*
39951925 TCACAATTCAATTCAAAATTCAC-TTTTCCATTTTCAAG
1 TCACAATTCAATTCAAAATTCACTTTTTCCACTTTCAAG
*
39951963 TCA-ATATTCATTTCAA
1 TCACA-ATTCAATTCAA
39951979 TTCCACACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 17 0.38
37 15 0.33
38 13 0.29
ACGTcount: A:0.31, C:0.23, G:0.02, T:0.43
Consensus pattern (39 bp):
TCACAATTCAATTCAAAATTCACTTTTTCCACTTTCAAG
Found at i:39953242 original size:19 final size:19
Alignment explanation
Indices: 39953196--39953242 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
39953186 TTTACTTTAT
*
39953196 TTAATAATAATAATAATAA
1 TTAATAATCATAATAATAA
**
39953215 TATAA-AATCATAATAATGG
1 T-TAATAATCATAATAATAA
39953234 TTAATAATC
1 TTAATAATC
39953243 TTAGATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 17 0.74
20 3 0.13
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (19 bp):
TTAATAATCATAATAATAA
Found at i:39958069 original size:30 final size:30
Alignment explanation
Indices: 39958042--39958100 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
39958032 AAAGAGAGCT
39958042 TTGAGAAATTTAAGGAGAAATTTGAGAGTG
1 TTGAGAAATTTAAGGAGAAATTTGAGAGTG
*
39958072 TTGAGAAATTTAGGGAGAAATTTGAGAGT
1 TTGAGAAATTTAAGGAGAAATTTGAGAGT
39958101 TTTTTGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (30 bp):
TTGAGAAATTTAAGGAGAAATTTGAGAGTG
Found at i:39958768 original size:18 final size:19
Alignment explanation
Indices: 39958734--39958784 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
39958724 AACATCGTTT
*
39958734 TTATTTTAATCATTTTAAC
1 TTATTTTAATCAATTTAAC
39958753 TTATTTT-ATCAATTTAA-
1 TTATTTTAATCAATTTAAC
*
39958770 TTAATTTAAT-AATTT
1 TTATTTTAATCAATTT
39958785 CAATTATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 11 0.38
18 11 0.38
19 7 0.24
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTAATCAATTTAAC
Found at i:39960072 original size:10 final size:10
Alignment explanation
Indices: 39960039--39960079 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
39960029 TTTGACGATT
39960039 AAATTATTAA
1 AAATTATTAA
* *
39960049 AATTTTTATAA
1 AAATTAT-TAA
39960060 AAATTATTAA
1 AAATTATTAA
39960070 AAATTATTAA
1 AAATTATTAA
39960080 TTTTATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAATTATTAA
Found at i:39960806 original size:28 final size:29
Alignment explanation
Indices: 39960749--39960811 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
39960739 GTTCAAATAA
*
39960749 CAAATTGGGCACCAAAAAAGTTTAAGTAC
1 CAAATTGGGCACAAAAAAAGTTTAAGTAC
39960778 CAAATTGGGC-CAAAAAAAGTTT-AGATAC
1 CAAATTGGGCACAAAAAAAGTTTAAG-TAC
39960806 CAAATT
1 CAAATT
39960812 ATAAAAAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 2 0.06
28 20 0.62
29 10 0.31
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (29 bp):
CAAATTGGGCACAAAAAAAGTTTAAGTAC
Found at i:39961105 original size:93 final size:93
Alignment explanation
Indices: 39960945--39961134 Score: 219
Period size: 93 Copynumber: 2.0 Consensus size: 93
39960935 CTTAAATCTC
* * * * * *
39960945 AAATAATCCAAGCTTAAAAGTGGTCAAAATCTAAAATGATTTGAACACGTAATGGCTTGACTTGA
1 AAATAATCCAAACTTAAAAGTGATCAAAATCTAAAATAATTTGAACACGCAATGACTTGACTAGA
* *
39961010 AAATCCTGAATCCT-AAACAATAAACCCA
66 AAAACCTAAAT-CTAAAACAATAAACCCA
39961038 AAATAATCCAAACTTTGAAAA-TGATCAAAATCTAAAATAATTT-AA-ATCGCAATGACTTGA-T
1 AAATAATCCAAAC-TT-AAAAGTGATCAAAATCTAAAATAATTTGAACA-CGCAATGACTTGACT
*
39961099 CAGAAAAACCTAAATTTAAAACAATAAACCCA
63 -AGAAAAACCTAAATCTAAAACAATAAACCCA
39961131 AAAT
1 AAAT
39961135 CACCCTAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
92 3 0.04
93 54 0.65
94 22 0.27
95 4 0.05
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (93 bp):
AAATAATCCAAACTTAAAAGTGATCAAAATCTAAAATAATTTGAACACGCAATGACTTGACTAGA
AAAACCTAAATCTAAAACAATAAACCCA
Found at i:39963037 original size:22 final size:21
Alignment explanation
Indices: 39963007--39963064 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
39962997 AAATGGTATC
39963007 TACAAATCAAATCTCTAAGAT
1 TACAAATCAAATCTCTAAGAT
*
39963028 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCAAATC-TCTAAGAT
*
39963051 TACATATCAAATCT
1 TACAAATCAAATCT
39963065 ACGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 17 0.53
23 11 0.34
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (21 bp):
TACAAATCAAATCTCTAAGAT
Found at i:39965821 original size:24 final size:24
Alignment explanation
Indices: 39965789--39965835 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39965779 GTGCTTCCCG
39965789 TTAATTGCTCTTCGAAGCCACCCA
1 TTAATTGCTCTTCGAAGCCACCCA
*
39965813 TTAATTGCTCTTCGAAGCTACCC
1 TTAATTGCTCTTCGAAGCCACCC
39965836 GTTATAGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (24 bp):
TTAATTGCTCTTCGAAGCCACCCA
Found at i:39965846 original size:24 final size:24
Alignment explanation
Indices: 39965789--39965848 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
39965779 GTGCTTCCCG
*
39965789 TTAATTGCTCTTCGAAGCCACCCA
1 TTAATGGCTCTTCGAAGCCACCCA
* * *
39965813 TTAATTGCTCTTCGAAGCTACCCG
1 TTAATGGCTCTTCGAAGCCACCCA
39965837 TT-ATAGGCTCTT
1 TTAAT-GGCTCTT
39965849 TGTGAGCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (24 bp):
TTAATGGCTCTTCGAAGCCACCCA
Found at i:39969913 original size:13 final size:13
Alignment explanation
Indices: 39969895--39969919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39969885 CTGGTTCAGC
39969895 GTCAATTTAGATG
1 GTCAATTTAGATG
39969908 GTCAATTTAGAT
1 GTCAATTTAGAT
39969920 TAGAAAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
GTCAATTTAGATG
Found at i:39973832 original size:22 final size:21
Alignment explanation
Indices: 39973792--39973833 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39973782 AAAATTTTAT
* *
39973792 AAAAATATTAAAGTTTATGAA
1 AAAAATATTAAAATGTATGAA
39973813 AAAAATATTAAACATGTATGA
1 AAAAATATTAAA-ATGTATGA
39973834 TAAATATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAATATTAAAATGTATGAA
Found at i:39979180 original size:58 final size:59
Alignment explanation
Indices: 39979098--39979238 Score: 169
Period size: 58 Copynumber: 2.4 Consensus size: 59
39979088 AACATTTGCC
* * * * * *
39979098 AAGTTCAGGCCCCAATATGAGAACAAGTACCAAGTTCAGGGACTAACTTG-GAAAAAAA
1 AAGTTCAAGCCTCAATGTGAGAACAAGTACCAAGTTAAGGAACTAACTTGACAAAAAAA
* * *
39979156 AAGTTCAAGCCTCAATGTGGGAACAATTATCAAGTTAAGGAACTAACTTGACCAAAAAAA
1 AAGTTCAAGCCTCAATGTGAGAACAAGTACCAAGTTAAGGAACTAACTTGA-CAAAAAAA
39979216 AAGTTC-AGACCTCAATGTGAGAA
1 AAGTTCAAG-CCTCAATGTGAGAA
39979239 TTATTGCTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 42 0.60
59 2 0.03
60 26 0.37
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (59 bp):
AAGTTCAAGCCTCAATGTGAGAACAAGTACCAAGTTAAGGAACTAACTTGACAAAAAAA
Found at i:39979191 original size:31 final size:31
Alignment explanation
Indices: 39979067--39979191 Score: 82
Period size: 31 Copynumber: 4.2 Consensus size: 31
39979057 TTGAACTCTA
* *
39979067 AAGTTCAAGCCTCAATGTGGGAACATTTGCC
1 AAGTTCAAGCCTCAATGTGGGAACAATTACC
* * * * *
39979098 AAGTTCAGGCCCCAATATGAGAACAAGTACC
1 AAGTTCAAGCCTCAATGTGGGAACAATTACC
* * **
39979129 AAGTTCAGGGACT-AACT-T-GGAA-AA--AAA
1 AAGTTCA-AGCCTCAA-TGTGGGAACAATTACC
*
39979156 AAGTTCAAGCCTCAATGTGGGAACAATTATC
1 AAGTTCAAGCCTCAATGTGGGAACAATTACC
39979187 AAGTT
1 AAGTT
39979192 AAGGAACTAA
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
26 4 0.06
27 11 0.16
28 4 0.06
29 4 0.06
30 3 0.04
31 40 0.57
32 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (31 bp):
AAGTTCAAGCCTCAATGTGGGAACAATTACC
Found at i:39984453 original size:18 final size:18
Alignment explanation
Indices: 39984430--39984464 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39984420 ACACCAATAC
*
39984430 CTGCTATCAACTAACTAA
1 CTGCTAACAACTAACTAA
39984448 CTGCTAACAACTAACTA
1 CTGCTAACAACTAACTA
39984465 TAACAGTTAA
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:0.40, C:0.29, G:0.06, T:0.26
Consensus pattern (18 bp):
CTGCTAACAACTAACTAA
Found at i:39988900 original size:6 final size:6
Alignment explanation
Indices: 39988889--39988925 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
39988879 TTGAGTAGGG
39988889 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA G
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA G
39988926 GTCGTACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (6 bp):
GTTTGA
Found at i:39988902 original size:18 final size:18
Alignment explanation
Indices: 39988879--39988920 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39988869 GGTAAGAGGC
*
39988879 TTGAGTAGGGGTTTGAGT
1 TTGAGTAGGAGTTTGAGT
**
39988897 TTGAGTTTGAGTTTGAGT
1 TTGAGTAGGAGTTTGAGT
39988915 TTGAGT
1 TTGAGT
39988921 TTGAGGTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (18 bp):
TTGAGTAGGAGTTTGAGT
Found at i:39989193 original size:18 final size:18
Alignment explanation
Indices: 39989153--39989193 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39989143 AATATGGAAA
*
39989153 GTAATTTTAAAAGATATT
1 GTAATATTAAAAGATATT
* *
39989171 ATAATATTAAAAGATTTT
1 GTAATATTAAAAGATATT
39989189 GTAAT
1 GTAAT
39989194 CGCAAGGGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
GTAATATTAAAAGATATT
Found at i:39990567 original size:17 final size:18
Alignment explanation
Indices: 39990522--39990567 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39990512 AATTATACGT
*
39990522 ATAATAA-TAATATTAAA
1 ATAATAACTAATAATAAA
*
39990539 ATGATAAC-AATAAT-AA
1 ATAATAACTAATAATAAA
39990555 ATAATAACTAATA
1 ATAATAACTAATA
39990568 CTATAATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAATAACTAATAATAAA
Found at i:39991222 original size:18 final size:18
Alignment explanation
Indices: 39991174--39991227 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
39991164 TATTTTCAAT
* *
39991174 AAAAAATAAAATAAT-AA
1 AAAAAAGAAAAAAATAAA
***
39991191 AAAAAAGGCTAAAATAAA
1 AAAAAAGAAAAAAATAAA
39991209 AAAAAAGAAAAAAATAAA
1 AAAAAAGAAAAAAATAAA
39991227 A
1 A
39991228 CGAAACTCAA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAAAGAAAAAAATAAA
Found at i:39992536 original size:132 final size:132
Alignment explanation
Indices: 39992367--39993497 Score: 1815
Period size: 132 Copynumber: 8.6 Consensus size: 132
39992357 CCACTGCCGA
* * * *
39992367 CCAGGG-AGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTACC
1 CCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCC
* *
39992431 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCGCTGC
65 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
39992496 TGC
130 TGC
* *
39992499 CCAGGGAAGTAAAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
39992564 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
**
39992629 AT
131 GC
* *
39992631 CCAGGGAAGTAGAATTACCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
* * *
39992696 TCTTTGATCTGCTCCACTATTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
39992761 GC
131 GC
*
39992763 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
39992828 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
39992893 GC
131 GC
*
39992895 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAATTCTGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
* *
39992960 TCATCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
39993025 GC
131 GC
* *
39993027 CCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCACC
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCC
*
39993091 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCTGCTGC
65 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
39993156 TGC
130 TGC
* *
39993159 CCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAGAAT-T-CAT
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC--
* * **
39993222 CATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCTACTG
64 CATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTG
39993287 CTGC
129 CTGC
*
39993291 CCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
* * * * * *
39993356 TCTTTGATCTGCTTCGCTGTCT-ATGTAGGAAGGCAAGATCTGAAATCTTCAATCTATTCCGCTG
66 TCTTTGATCTGCTCCACT-ACTGCT-TAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTG
*
39993420 CTGT
129 CTGC
* *
39993424 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACATGGAGGTAAAAT-TCACC
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCC
39993488 ATCTTTGATC
65 ATCTTTGATC
39993498 AGCTTCGCTG
Statistics
Matches: 936, Mismatches: 54, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
130 1 0.00
131 1 0.00
132 823 0.88
133 110 0.12
134 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (132 bp):
CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCA
TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
GC
Found at i:39994881 original size:15 final size:15
Alignment explanation
Indices: 39994861--39994899 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
39994851 AGCCTCTCCA
*
39994861 TTTTATTTTTCATTT
1 TTTTATTTTTCATCT
39994876 TTTTA-TTTTCATCT
1 TTTTATTTTTCATCT
*
39994890 TTTCATTTTT
1 TTTTATTTTT
39994900 TTCACATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTCATCT
Found at i:39994909 original size:22 final size:22
Alignment explanation
Indices: 39994867--39994909 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39994857 TCCATTTTAT
**
39994867 TTTTCATTTTTTTATTTTCATC
1 TTTTCATTTTTTTATCATCATC
39994889 TTTTCATTTTTTTCA-CATCAT
1 TTTTCATTTTTTT-ATCATCAT
39994910 TTCTTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCATTTTTTTATCATCATC
Found at i:39994920 original size:6 final size:6
Alignment explanation
Indices: 39994909--39994935 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39994899 TTTCACATCA
39994909 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
39994936 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:39996486 original size:17 final size:18
Alignment explanation
Indices: 39996441--39996486 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39996431 AACTATACGT
*
39996441 ATAATAA-TAATATTAAA
1 ATAATAACTAATAATAAA
*
39996458 ATGATAAC-AATAAT-AA
1 ATAATAACTAATAATAAA
39996474 ATAATAACTAATA
1 ATAATAACTAATA
39996487 CTATAATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAATAACTAATAATAAA
Found at i:40001166 original size:6 final size:6
Alignment explanation
Indices: 40001155--40001235 Score: 108
Period size: 6 Copynumber: 13.5 Consensus size: 6
40001145 GTTGTGGGTC
**
40001155 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGATT
1 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT
** * *
40001203 GAGTTT GGGCTT GAGCCT GAGCCT GAGCCT GAG
1 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAG
40001236 TCGAGCTTGC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.17, C:0.26, G:0.36, T:0.21
Consensus pattern (6 bp):
GAGCCT
Found at i:40014031 original size:50 final size:50
Alignment explanation
Indices: 40013966--40014094 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
40013956 TAAAGTCATA
* ** * *
40013966 TCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* ** *
40014016 TCCCAAACATAGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* *
40014066 TCCCAGACATGGTCTTACATGGGATCTCT
1 TCCCAAACATGGTCTTACATGGGACCTCT
40014095 TTACCCAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:40022607 original size:6 final size:6
Alignment explanation
Indices: 40022596--40022620 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40022586 TACTAAATAA
40022596 TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT T
40022621 AAATTGTGAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:40028903 original size:37 final size:34
Alignment explanation
Indices: 40028864--40028973 Score: 115
Period size: 33 Copynumber: 3.4 Consensus size: 34
40028854 ATAATAAAAT
* *
40028864 ATTAAATTAGATTAAT-T-AATATTTTATATATC
1 ATTATATTAAATTAATCTAAATATTTTATATATC
*
40028896 ATTATATTAAATT-ATCTAAATCTTTTATATATC
1 ATTATATTAAATTAATCTAAATATTTTATATATC
* * * *
40028929 ATTATTTTAAATT-ATTTAAATA--TAATTTATC
1 ATTATATTAAATTAATCTAAATATTTTATATATC
40028960 ATTATATTAAATTA
1 ATTATATTAAATTA
40028974 TTTAAATCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
31 21 0.32
32 12 0.18
33 33 0.50
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.52
Consensus pattern (34 bp):
ATTATATTAAATTAATCTAAATATTTTATATATC
Found at i:40028927 original size:33 final size:33
Alignment explanation
Indices: 40028885--40029023 Score: 141
Period size: 31 Copynumber: 4.4 Consensus size: 33
40028875 TTAATTAATA
*
40028885 TTTTATATATCATTATATTAAATTATCTAAATC
1 TTTTATATATCATTATATTAAATTATTTAAATC
*
40028918 TTTTATATATCATTATTTTAAATTATTTAAA--
1 TTTTATATATCATTATATTAAATTATTTAAATC
* * *
40028949 TATAATTTATCATTATATTAAATTATTTAAATC
1 TTTTATATATCATTATATTAAATTATTTAAATC
* *
40028982 --TTAT-T-T-ATTATATTTAATT-TTTAAAAATA
1 TTTTATATATCATTATATTAAATTATTT--AAATC
40029011 TTTTATATATCAT
1 TTTTATATATCAT
40029024 CAATTTTAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.03
28 12 0.14
29 5 0.06
30 1 0.01
31 34 0.39
32 1 0.01
33 30 0.34
34 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTTATATATCATTATATTAAATTATTTAAATC
Found at i:40028942 original size:10 final size:9
Alignment explanation
Indices: 40028929--40028980 Score: 50
Period size: 9 Copynumber: 5.2 Consensus size: 9
40028919 TTTATATATC
40028929 ATTATTTTAA
1 ATTA-TTTAA
40028939 ATTATTTAA
1 ATTATTTAA
*
40028948 ATATAATTTATC
1 AT-T-ATTTA-A
40028960 ATTATATTAA
1 ATTAT-TTAA
40028970 ATTATTTAA
1 ATTATTTAA
40028979 AT
1 AT
40028981 CTTATTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 13 0.36
10 12 0.33
11 9 0.25
12 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTATTTAA
Found at i:40028963 original size:31 final size:31
Alignment explanation
Indices: 40028864--40028989 Score: 126
Period size: 31 Copynumber: 4.0 Consensus size: 31
40028854 ATAATAAAAT
* * * * *
40028864 ATTAAATTAGATTAATTAATATTTTATATATC
1 ATTATATTAAATTATTTAA-ATATTATTTATC
* * *
40028896 ATTATATTAAATTATCTAAATCTTTTATATATC
1 ATTATATTAAATTATTTAAA--TATTATTTATC
* *
40028929 ATTATTTTAAATTATTTAAATATAATTTATC
1 ATTATATTAAATTATTTAAATATTATTTATC
*
40028960 ATTATATTAAATTATTTAAATCTTATTTAT
1 ATTATATTAAATTATTTAAATATTATTTAT
40028990 TATATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
31 36 0.45
32 15 0.19
33 29 0.36
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTATTTATC
Found at i:40029015 original size:27 final size:27
Alignment explanation
Indices: 40028985--40029043 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
40028975 TTAAATCTTA
*
40028985 TTTATTATAT-TTAATTTTTAAAAATAT
1 TTTATTATATATCAA-TTTTAAAAATAT
40029012 TTTA-TATATCATCAATTTTAAAAATAT
1 TTTATTATAT-ATCAATTTTAAAAATAT
40029039 TTTAT
1 TTTAT
40029044 ATTAATTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.18
27 20 0.71
28 3 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTATATATCAATTTTAAAAATAT
Found at i:40031358 original size:24 final size:23
Alignment explanation
Indices: 40031305--40031359 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
40031295 AAAATATTCT
** *
40031305 TAATTAAATTTATTTTTTAAAAC
1 TAATTAAATTTAAATTTTAAAAA
*
40031328 TAGTTAAATTTAAATTTTAAAATA
1 TAATTAAATTTAAATTTTAAAA-A
40031352 TAATTAAA
1 TAATTAAA
40031360 GTGTGTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATTAAATTTAAATTTTAAAAA
Found at i:40032980 original size:16 final size:16
Alignment explanation
Indices: 40032911--40032978 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
40032901 TTTGGTTCGC
40032911 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40032927 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40032943 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
40032959 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
40032975 TGTA
1 TGTA
40032979 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40033010 original size:45 final size:44
Alignment explanation
Indices: 40032959--40033053 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
40032949 GGATTAGAGG
* * *
40032959 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
40033004 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
40033048 TGTAAT
1 TGTAAT
40033054 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:40033236 original size:18 final size:17
Alignment explanation
Indices: 40033215--40033249 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40033205 TTATTATTTA
*
40033215 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40033233 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40033250 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40033243 original size:28 final size:27
Alignment explanation
Indices: 40033173--40033245 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
40033163 TTTATTATCA
*
40033173 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
40033201 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
40033228 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
40033246 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:40033388 original size:18 final size:17
Alignment explanation
Indices: 40033361--40033395 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40033351 ATTATTATTA
*
40033361 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40033379 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40033396 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40033406 original size:146 final size:149
Alignment explanation
Indices: 40033134--40033407 Score: 500
Period size: 146 Copynumber: 1.9 Consensus size: 149
40033124 ATGATTATTG
*
40033134 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
40033199 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
40033264 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
40033283 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
40033346 ACATAATTATTA-TTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
40033408 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
146 50 0.41
147 44 0.36
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:40033503 original size:18 final size:17
Alignment explanation
Indices: 40033463--40033515 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
40033453 AAATATAAAT
40033463 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
40033477 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
40033492 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
40033510 TAAAAT
1 TAAAAT
40033516 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:40033514 original size:59 final size:58
Alignment explanation
Indices: 40033342--40033635 Score: 158
Period size: 59 Copynumber: 4.9 Consensus size: 58
40033332 TTACTCATAT
* * *
40033342 TTAAACATAATTATTATT-AATATATTTTAATTAAAATATATAATTTAATAAAATT--C
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTAAA
* * * * * *
40033398 TTAATAATTAAT-ATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-GTAAAATATA
1 TTAA-AA-TAATAATTATTAAAT-ATATTT--T--AATTAAAATATATGAT-TTAATAAAAT-TA
40033460 AA
57 AA
* *
40033462 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTAA
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT-AAA
** * * * ** * * * *
40033521 -TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT-ATAAAATATAAT
1 TTAA--AATAATAATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAAT-TAAA
*
40033581 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
40033636 TAAAATAATT
Statistics
Matches: 173, Mismatches: 40, Indels: 48
0.66 0.15 0.18
Matches are distributed among these distances:
56 10 0.06
57 11 0.06
58 8 0.05
59 59 0.34
60 35 0.20
61 25 0.14
62 7 0.04
63 14 0.08
64 4 0.02
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (58 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTAAA
Found at i:40033554 original size:119 final size:120
Alignment explanation
Indices: 40033342--40033635 Score: 486
Period size: 119 Copynumber: 2.5 Consensus size: 120
40033332 TTACTCATAT
*
40033342 TTAAACATAATTATTATT-AATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
40033406 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
40033462 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
40033526 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
40033581 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
40033636 TAAAATAATT
Statistics
Matches: 165, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 119 0.72
120 46 0.28
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:40033573 original size:60 final size:59
Alignment explanation
Indices: 40033389--40033575 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
40033379 ATATAATTTA
*
40033389 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
40033450 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
40033508 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
40033569 ATAAAAT
1 ATAAAAT
40033576 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:40035628 original size:8 final size:8
Alignment explanation
Indices: 40035611--40035642 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
40035601 TTCAATCACC
*
40035611 AAAACCAT
1 AAAACAAT
40035619 AAAACAAT
1 AAAACAAT
40035627 AAAACAAT
1 AAAACAAT
40035635 AAAACAAT
1 AAAACAAT
40035643 CTGTTTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.72, C:0.16, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAACAAT
Found at i:40038406 original size:13 final size:13
Alignment explanation
Indices: 40038388--40038428 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
40038378 TTCAAAACAT
40038388 AAATAAAATTTAA
1 AAATAAAATTTAA
40038401 AAAT--AATTTATA
1 AAATAAAATTTA-A
*
40038413 AAATAAAATATAA
1 AAATAAAATTTAA
40038426 AAA
1 AAA
40038429 ACTATTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 6 0.25
12 5 0.21
13 8 0.33
14 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATTTAA
Found at i:40038615 original size:19 final size:19
Alignment explanation
Indices: 40038570--40038613 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
40038560 ATTATTCTCA
* *
40038570 ATTTTTATATTTTTTATTT
1 ATTTTTATATTTTTAATCT
40038589 ATTTTTATAATTTTTAATCT
1 ATTTTTAT-ATTTTTAATCT
40038609 ATTTT
1 ATTTT
40038614 ATTTTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTATATTTTTAATCT
Found at i:40041288 original size:41 final size:41
Alignment explanation
Indices: 40041175--40041294 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
40041165 GTGATAATCG
* * * * * *
40041175 GGCTTTATGCCTAGCAAGCTTTATGCCGGTGAATTATATCA
1 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTATCATAACA
* * *
40041216 GGCTTTACGCCTAGTAGGCTTAATGTCGGTGTACCATAACA
1 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTATCATAACA
**
40041257 GGCTTTACGCCTAGCAGGCTTCGTGCCGGTGTATCATA
1 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTATCATA
40041295 TTAAGATTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (41 bp):
GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTATCATAACA
Found at i:40044782 original size:42 final size:42
Alignment explanation
Indices: 40044692--40044783 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
40044682 AAGTTTCCAT
* * * *
40044692 TCAACCCTAATGGGTTTCCGTTCAGCTCTGCAAAGCTTCAGT
1 TCAACCCTAATAGGTTTCCGTTCAACTCTACAAAGCTTCAGC
* * * *
40044734 TTAACCCTATTAGGTTTCCGTTCAACTCTTAC-GAGCTTCTGC
1 TCAACCCTAATAGGTTTCCGTTCAACTC-TACAAAGCTTCAGC
40044776 TCAACCCT
1 TCAACCCT
40044784 TATGGATTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (42 bp):
TCAACCCTAATAGGTTTCCGTTCAACTCTACAAAGCTTCAGC
Found at i:40048721 original size:16 final size:16
Alignment explanation
Indices: 40048700--40048731 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40048690 ACACTCCAAA
*
40048700 CCCTTTATTCGTCGCT
1 CCCTTTATCCGTCGCT
40048716 CCCTTTATCCGTCGCT
1 CCCTTTATCCGTCGCT
40048732 AAAATAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.41, G:0.12, T:0.41
Consensus pattern (16 bp):
CCCTTTATCCGTCGCT
Found at i:40049454 original size:255 final size:254
Alignment explanation
Indices: 40049016--40049511 Score: 776
Period size: 255 Copynumber: 1.9 Consensus size: 254
40049006 GCCTGTCTCT
* * * *
40049016 ATGCCCGTGTAACTCTCTGACTTAGGTCACAGACCAAGTAACACACCCGTGTACTAGGCCGTGTG
1 ATGCCCGTGTAACTCTCTAACTTAGGTCACAGACCAAGTAACACACCCATGCACTAGGCCGTATG
* * * * * *
40049081 TTATGAAATTAAGGTGCAAGGGTCACACGGCCAAGTCACACTCCCGTGTGCTAGGCCGTGTGCAA
66 TTATGAAAATAAGGTGCAAGGGTCACACGGCCAAGCCACACGCCCGTGTCCTAGGCCATGTGAAA
*
40049146 AAACCTGAGCATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACAGGACCAGACCACATGCCCA
131 AAACCTGAGCATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCCA
* *
40049211 TGTGCTTGGCCGTGTGTCACACACGGCTGAGACACACGCCCGTGTCCCATTCCGTGTTC
196 TGTGCTTGGCCATGTGTCACACACGGCTGAGACACACACCCGTGTCCCATTCCGTGTTC
* * * * *
40049270 ATGCCCGTGTAACTCTCTAACTTGGGTCACATGGCCAAGTCACACGCCCATGCGCTAGGCCGTAT
1 ATGCCCGTGTAACTCTCTAACTTAGGTCACA-GACCAAGTAACACACCCATGCACTAGGCCGTAT
* *
40049335 GTTATGAAAATAAGGTGCATGGGTCACACGGCCAAGCCACACGCCCGTGTCCTAGTCCATGTGAA
65 GTTATGAAAATAAGGTGCAAGGGTCACACGGCCAAGCCACACGCCCGTGTCCTAGGCCATGTGAA
* *
40049400 AAAACCTGAGCATTTTGTTTCTAAATTTTAAGGATGCAGTGGACACACGACCAGACCACATGCCC
130 AAAACCTGAGCATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCC
*
40049465 ATGTGCTTGGCCATGTGTTACACACGGCTGAGACACACACCCGTGTC
195 ATGTGCTTGGCCATGTGTCACACACGGCTGAGACACACACCCGTGTC
40049512 TCTGCCCGTG
Statistics
Matches: 218, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
254 29 0.13
255 189 0.87
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (254 bp):
ATGCCCGTGTAACTCTCTAACTTAGGTCACAGACCAAGTAACACACCCATGCACTAGGCCGTATG
TTATGAAAATAAGGTGCAAGGGTCACACGGCCAAGCCACACGCCCGTGTCCTAGGCCATGTGAAA
AAACCTGAGCATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCCA
TGTGCTTGGCCATGTGTCACACACGGCTGAGACACACACCCGTGTCCCATTCCGTGTTC
Found at i:40050346 original size:21 final size:21
Alignment explanation
Indices: 40050287--40050431 Score: 57
Period size: 21 Copynumber: 6.9 Consensus size: 21
40050277 AACAGAAGCA
* * * *
40050287 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTTAACGGAAACT
* * *
40050308 CATAAG-GGTTGAATGGAAGCT
1 CATAAGAGCTT-AACGGAAACT
40050329 CATAAGAGCTTAACGGAAAC-
1 CATAAGAGCTTAACGGAAACT
* * *
40050349 CTATAAG-GGTTAAACAGAAGCT
1 C-ATAAGAGCTT-AACGGAAACT
* * *
40050371 CAAAAGAGCTGAACGAAAACT
1 CATAAGAGCTTAACGGAAACT
* **
40050392 CATATGAG-TTAAACAAAAACT
1 CATAAGAGCTT-AACGGAAACT
*
40050413 CGTAAGAG-TTAAACGGAAA
1 CATAAGAGCTT-AACGGAAA
40050432 GTAAACACGA
Statistics
Matches: 91, Mismatches: 26, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
20 7 0.08
21 78 0.86
22 6 0.07
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.18
Consensus pattern (21 bp):
CATAAGAGCTTAACGGAAACT
Found at i:40050348 original size:42 final size:42
Alignment explanation
Indices: 40050277--40050431 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 42
40050267 CTGAAGGCTG
* * * *
40050277 AACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
** * *
40050319 AATGGAAGCTCATAAGAGCTTAACGGAAACCTATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * * * *
40050361 AACAGAAGCTCAAAAGAGCTGAACGAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * *
40050403 AACAAAAACTCGTAAGAGTTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTAAACGGAAA
40050432 GTAAACACGA
Statistics
Matches: 89, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
Found at i:40052269 original size:9 final size:9
Alignment explanation
Indices: 40052255--40052294 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
40052245 GATCAAGTAA
40052255 AATTAAATT
1 AATTAAATT
40052264 AATTAAATT
1 AATTAAATT
* *
40052273 AATCAGATT
1 AATTAAATT
40052282 AATTAAAATT
1 AATT-AAATT
40052292 AAT
1 AAT
40052295 ATGATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:40052797 original size:26 final size:26
Alignment explanation
Indices: 40052737--40052797 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
40052727 AACATTAAAT
*
40052737 TTAATTTAATACTTAATAGTATTTTA
1 TTAATTTAATACTTAATAGTATTATA
*
40052763 TTAATTTAATA-TTAA-AGTGATTATC
1 TTAATTTAATACTTAATAGT-ATTATA
40052788 TTAATATTAA
1 TTAAT-TTAA
40052798 ATTTAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.10
25 13 0.42
26 15 0.48
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (26 bp):
TTAATTTAATACTTAATAGTATTATA
Found at i:40055931 original size:5 final size:5
Alignment explanation
Indices: 40055921--40055946 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40055911 CTAATGGTTG
40055921 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
40055947 TTATATTAAA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:40068191 original size:14 final size:13
Alignment explanation
Indices: 40068153--40068192 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
40068143 AAATAAATTA
40068153 TATATTTGTTAGTTT
1 TATATTT-TTA-TTT
40068168 TATATTTTTATTT
1 TATATTTTTATTT
40068181 TATAGTTTTTAT
1 TATA-TTTTTAT
40068193 AGTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TATATTTTTATTT
Found at i:40072089 original size:12 final size:11
Alignment explanation
Indices: 40072062--40072092 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
40072052 CTAGATTAAT
40072062 TAAAAAATTCA
1 TAAAAAATTCA
40072073 TAAAAAATTCA
1 TAAAAAATTCA
40072084 TAAAAAATT
1 TAAAAAATT
40072093 AGAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAAATTCA
Found at i:40078095 original size:28 final size:29
Alignment explanation
Indices: 40078041--40078110 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
40078031 TTTACTTTTC
* *
40078041 TTTTATATATATATATATTATAGTTTT-TAG
1 TTTTATAT-T-TATATATTACAGTTTTATAA
* *
40078071 TTTTATATTTATATTTTACATTTTTATAA
1 TTTTATATTTATATATTACAGTTTTATAA
40078100 TTTTAT-TTTAT
1 TTTTATATTTAT
40078111 TTAATAAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 18 0.51
29 9 0.26
30 8 0.23
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTTATATTTATATATTACAGTTTTATAA
Found at i:40079257 original size:19 final size:19
Alignment explanation
Indices: 40079217--40079259 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40079207 CCCTTTATTA
* *
40079217 AATTTATTTACTTTATTTT
1 AATTTATATAATTTATTTT
40079236 AATTTATATAATTT-TTTAT
1 AATTTATATAATTTATTT-T
40079255 AATTT
1 AATTT
40079260 TATTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTATATAATTTATTTT
Found at i:40082270 original size:41 final size:41
Alignment explanation
Indices: 40082209--40082322 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
40082199 TTAATTTAAA
* * *
40082209 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACATAGCCTGCTAGGCTTATAACCTGATT
* * *
40082251 CAGATCACCGGTACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACATAGCCTGCTAGGCTTATAACCTGATT
*
40082292 CAGATCACCGGCACATAGCCTGCTAGACTTA
1 CAGATCACCGGCACATAGCCTGCTAGGCTTA
40082323 AAGTCTGAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
41 59 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACATAGCCTGCTAGGCTTATAACCTGATT
Found at i:40084308 original size:22 final size:23
Alignment explanation
Indices: 40084275--40084333 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
40084265 AGAATGATAC
*
40084275 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
40084296 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
40084320 GTGATAAATTTAAA
1 ATGATAAATTTAAA
40084334 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:40085403 original size:15 final size:15
Alignment explanation
Indices: 40085383--40085417 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40085373 GGCCATATGA
*
40085383 TAGTTGGGCTAGGTG
1 TAGTTGGGCTAGGCG
40085398 TAGTTGGGCTAGGCG
1 TAGTTGGGCTAGGCG
40085413 TAGTT
1 TAGTT
40085418 TGGGTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.43, T:0.34
Consensus pattern (15 bp):
TAGTTGGGCTAGGCG
Found at i:40086108 original size:132 final size:130
Alignment explanation
Indices: 40085961--40086392 Score: 567
Period size: 132 Copynumber: 3.3 Consensus size: 130
40085951 TGCTATTTTT
* * * * * *
40085961 AACCTACTCCACTGCTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTCCTACATTG
1 AACCTATTCCACTGCTG-TCAGGGAGATAGGACTGGCGACTTAAATCTGCTTCCCTACTACCTTG
* *
40086026 GGAAGATAATATTCGTCGTCTTTGATATGTTCCACTAATGTTTAGGGAGACATGATCTACAATCT
65 GGAAGATAAGATTC-ACGTCTTTGATATGTTCCACTAATGTTTAGGGAGACATGATCTACAATCT
40086091 TC
129 TC
* *
40086093 AACCTATTCCGCTGCTGTCTAGGGAGATAGGACTGGCGACTTAAATCTGCTTCCCTACTACCGTG
1 AACCTATTCCACTGCTGTC-AGGGAGATAGGACTGGCGACTTAAATCTGCTTCCCTACTACCTTG
* * * * * * *
40086158 AGAAGATAAGATTCACCATTTTTGATTTGTTCTACTACTGTTCAGGGAGACATGATCTACAATCT
65 GGAAGATAAGATTCA-CGTCTTTGATATGTTCCACTAATGTTTAGGGAGACATGATCTACAATCT
40086223 TC
129 TC
* * * * *
40086225 AACCTATTCCACTGTTGTCCAGGAAGATAGGACTGACGACTTAAATTTGCTTCCCTACTACCTTA
1 AACCTATTCCACTGCTGT-CAGGGAGATAGGACTGGCGACTTAAATCTGCTTCCCTACTACCTTG
* * *
40086290 GGAAGATAAGATTCACTGTCTTTGATCTGTTCCGCTATTGTTTAGGGAGACATGATCTACAATCT
65 GGAAGATAAGATTCAC-GTCTTTGATATGTTCCACTAATGTTTAGGGAGACATGATCTACAATCT
40086355 TC
129 TC
*
40086357 AACCTATTCCACTGCTGTTAAGGGAGATAGGACTGG
1 AACCTATTCCACTGCTG-TCAGGGAGATAGGACTGG
40086393 TATCTTCGAT
Statistics
Matches: 259, Mismatches: 36, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
131 3 0.01
132 254 0.98
133 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (130 bp):
AACCTATTCCACTGCTGTCAGGGAGATAGGACTGGCGACTTAAATCTGCTTCCCTACTACCTTGG
GAAGATAAGATTCACGTCTTTGATATGTTCCACTAATGTTTAGGGAGACATGATCTACAATCTTC
Found at i:40086456 original size:88 final size:88
Alignment explanation
Indices: 40086354--40087052 Score: 1013
Period size: 88 Copynumber: 7.9 Consensus size: 88
40086344 ATCTACAATC
* * * * ** *
40086354 TTCAACCTATTCCACTGCTGTTAAGGGAGA-TAGGACTGGTATCTTCGATCTACTTCGCTGCGAA
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGG-CTGGGGTCTTCGATCTACTTCGCTGCCAA
40086418 TACAGGAAGACAAGATCTGCTATT
65 TACAGGAAGACAAGATCTGCTATT
* ** * *
40086442 TTCAACCTACTCCACTGCTGCTCAAGGAGACAAGGCTGGTATATTCGATCTACTTTGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
40086507 ACAGGAAGACAAGATCTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* * * *
40086530 TTCAACCTACTTCACTGTTGCTCAGGGAGACAAGCCTGGGGTCTTCGATCTACTTCGCTGTCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
*
40086595 ACAGGAAGACAAGATCTACTATT
66 ACAGGAAGACAAGATCTGCTATT
* * * * *
40086618 TTTAACCTAATCCACTGCTGCTCAAGGAGACAAAGCTAGGGTCTTCGATCTACTTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
* *
40086683 ACAGAAAGACAAGATCTGTTATT
66 ACAGGAAGACAAGATCTGCTATT
* * * *
40086706 TTTAACCTACTCCACTGGTGCTCAGAGAGACAAGGCTGGGGTCTTCGATCTACTTCACTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
*
40086771 ACAGGAAGACAAGATTTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* ** * *
40086794 TTTAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTTGATCTACTTCGCTACCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
*
40086859 ACAGGAAGACAAGATCTACTATT
66 ACAGGAAGACAAGATCTGCTATT
*
40086882 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTAGGGTCTTCGATCTACTTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
*
40086947 ACAGGAAGACAAAATCTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* **
40086970 TTTAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGGTAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
*
40087035 ACAGGAAGACAATATCTG
66 ACAGGAAGACAAGATCTG
40087053 TTTAGGATTA
Statistics
Matches: 548, Mismatches: 62, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
88 545 0.99
89 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (88 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTACTTCGCTGCCAAT
ACAGGAAGACAAGATCTGCTATT
Found at i:40087086 original size:25 final size:26
Alignment explanation
Indices: 40087058--40087106 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
40087048 ATCTGTTTAG
*
40087058 GATTATGTTATAAATT-TTGTGTTAA
1 GATTAAGTTATAAATTGTTGTGTTAA
40087083 GATTAAGTTATAAATTGTTGTGTT
1 GATTAAGTTATAAATTGTTGTGTT
40087107 TAGTTTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (26 bp):
GATTAAGTTATAAATTGTTGTGTTAA
Found at i:40087499 original size:55 final size:55
Alignment explanation
Indices: 40087416--40087528 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
40087406 TTAAAAAAAA
* *
40087416 TTTTAATCGTGCCTATCTGACAGATGCGAATCAATT-TGTATATTAAAAAATATTT
1 TTTTAATCGCGCCTATCTAACAGATGCGAATCAATTATGTATATT-AAAAATATTT
* * * *
40087471 TTTTAATCGCGGCTATTTAACAGGTGCGAATCAATTATTTATATTAAAAATATTT
1 TTTTAATCGCGCCTATCTAACAGATGCGAATCAATTATGTATATTAAAAATATTT
40087526 TTT
1 TTT
40087529 GTTTAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 44 0.86
56 7 0.14
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (55 bp):
TTTTAATCGCGCCTATCTAACAGATGCGAATCAATTATGTATATTAAAAATATTT
Found at i:40087815 original size:15 final size:16
Alignment explanation
Indices: 40087775--40087813 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40087765 TTAACTCATT
40087775 TAATTTTTATATAATG
1 TAATTTTTATATAATG
40087791 TAATTTTTATATAATG
1 TAATTTTTATATAATG
40087807 TAATTTT
1 TAATTTT
40087814 ATTTGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TAATTTTTATATAATG
Found at i:40091054 original size:27 final size:27
Alignment explanation
Indices: 40090990--40091074 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
40090980 GCTGTGGGCC
* *
40090990 CCACCATTGGCGCCTCTCA-ACATGGCG
1 CCACCATTGGCGCCTCTCAGATA-GGCA
* * * *
40091017 CAACTAGTGGCGCCTCTCAGATAGGCT
1 CCACCATTGGCGCCTCTCAGATAGGCA
*
40091044 CCACCATTGGCGCCTCTGAGATAGGCA
1 CCACCATTGGCGCCTCTCAGATAGGCA
40091071 CCAC
1 CCAC
40091075 TACTCTTGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 45 0.96
28 2 0.04
ACGTcount: A:0.21, C:0.36, G:0.24, T:0.19
Consensus pattern (27 bp):
CCACCATTGGCGCCTCTCAGATAGGCA
Found at i:40092745 original size:31 final size:31
Alignment explanation
Indices: 40092709--40092767 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
40092699 CAATGATTAC
40092709 TGAACTACTCGAAAGTTTTCATTTAAGTCAT
1 TGAACTACTCGAAAGTTTTCATTTAAGTCAT
** *
40092740 TGAACTTTTCGAAAGTTTTTATTTAAGT
1 TGAACTACTCGAAAGTTTTCATTTAAGT
40092768 GGGCTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (31 bp):
TGAACTACTCGAAAGTTTTCATTTAAGTCAT
Found at i:40093971 original size:14 final size:14
Alignment explanation
Indices: 40093950--40093983 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40093940 TGGTATGGGT
40093950 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
40093963 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
40093977 TTATAGG
1 TTATAGG
40093984 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:40094135 original size:22 final size:23
Alignment explanation
Indices: 40094110--40094156 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
40094100 GAGGAAAGTT
40094110 TAAAGAACATAAAAT-AAAAAAA
1 TAAAGAACATAAAATGAAAAAAA
** *
40094132 TAAATTACTTAAAATGAAAAAAA
1 TAAAGAACATAAAATGAAAAAAA
40094155 TA
1 TA
40094157 TGGGGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAAGAACATAAAATGAAAAAAA
Found at i:40103660 original size:3 final size:3
Alignment explanation
Indices: 40103654--40103678 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40103644 CATAATAAAA
40103654 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
40103679 AGAGATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:40110593 original size:31 final size:31
Alignment explanation
Indices: 40110557--40110618 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40110547 AGATAATTTT
40110557 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
40110588 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
40110619 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:40110927 original size:3 final size:3
Alignment explanation
Indices: 40110919--40110944 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40110909 ATCTATCCTT
40110919 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40110945 TAACTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40115883 original size:29 final size:30
Alignment explanation
Indices: 40115851--40115918 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
40115841 TCAAAATTTT
40115851 ATGTATAAAATTACACA-AAATCAAAGTTC
1 ATGTATAAAATTACACATAAATCAAAGTTC
* * * *
40115880 ATGTATGACATTGCACATTAGATCAAAGTTC
1 ATGTATAAAATTACACA-TAAATCAAAGTTC
40115911 ATGTATAA
1 ATGTATAA
40115919 TTTTGATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.44
31 18 0.56
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (30 bp):
ATGTATAAAATTACACATAAATCAAAGTTC
Found at i:40120238 original size:20 final size:20
Alignment explanation
Indices: 40120215--40120259 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
40120205 TTAGATTTAT
40120215 TAAAAATTAG-AAAAAAAATA
1 TAAAAATT-GTAAAAAAAATA
*
40120235 TAAAAATTGTAAAAAAATTA
1 TAAAAATTGTAAAAAAAATA
40120255 TAAAA
1 TAAAA
40120260 TACATCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (20 bp):
TAAAAATTGTAAAAAAAATA
Found at i:40123193 original size:89 final size:87
Alignment explanation
Indices: 40123067--40123268 Score: 225
Period size: 89 Copynumber: 2.3 Consensus size: 87
40123057 AAACTTAAAA
* *
40123067 AAAAAAGAGCAATTAAGTCCCCT-T-TTTTTTCACTCAATT-GAGCACTTAAACTTTTAAAATGC
1 AAAAAA-AGCAATTAAG-CCCCTCTCTTTTTTCACTCAATTGGA-CACCTAAACTTTCAAAATGC
* * * *
40123129 ATC-AAAAAGGCCTTCACACTTCTTC
63 ATCTAAAAA-ACCCTCAAAATTCTTC
* *
40123154 AAAAAAAGCAATTAAGCCCCTGCTCTTTTTTCCACTCAATTGGATACCTGAACTTTCAAAATGCA
1 AAAAAAAGCAATTAAGCCCCT-CTCTTTTTT-CACTCAATTGGACACCTAAACTTTCAAAATGCA
*
40123219 TCTAAAAAACCCTCAAAATTTTTC
64 TCTAAAAAACCCTCAAAATTCTTC
40123243 -AAAAAAGCAATTAAGCCCCTACTCTT
1 AAAAAAAGCAATTAAGCCCCT-CTCTT
40123269 ATTAAAAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
85 5 0.05
86 10 0.10
87 7 0.07
88 31 0.31
89 39 0.39
90 7 0.07
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.30
Consensus pattern (87 bp):
AAAAAAAGCAATTAAGCCCCTCTCTTTTTTCACTCAATTGGACACCTAAACTTTCAAAATGCATC
TAAAAAACCCTCAAAATTCTTC
Found at i:40123298 original size:23 final size:23
Alignment explanation
Indices: 40123267--40123325 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
40123257 GCCCCTACTC
* *
40123267 TTATTAAAAATTAGAAAAATAAA
1 TTATAAAAAATTAAAAAAATAAA
40123290 TTATAAAAAA-TAAAAAAATAAA
1 TTATAAAAAATTAAAAAAATAAA
*
40123312 TTTTAGAAAAATTA
1 TTATA-AAAAATTA
40123326 TTAAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.48
23 14 0.45
24 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
TTATAAAAAATTAAAAAAATAAA
Found at i:40123506 original size:9 final size:9
Alignment explanation
Indices: 40123492--40123741 Score: 56
Period size: 10 Copynumber: 27.1 Consensus size: 9
40123482 TTTTGGTACA
40123492 ATAATTTTT
1 ATAATTTTT
40123501 ATAATTTTTTT
1 ATAA--TTTTT
* *
40123512 ACAAATTTT
1 ATAATTTTT
40123521 AT-ATTTCTT
1 ATAATTT-TT
40123530 -TACATTTTGT
1 ATA-ATTTT-T
40123540 ATAATTTTCT
1 ATAATTTT-T
*
40123550 -TACGA-CTTT
1 ATA--ATTTTT
*
40123559 ATAAAATTTT
1 AT-AATTTTT
*
40123569 ATAA-TTAT
1 ATAATTTTT
40123577 AT-A-TTTT
1 ATAATTTTT
40123584 ATAATTTTT
1 ATAATTTTT
* *
40123593 TTACGTTTTT
1 ATA-ATTTTT
*
40123603 ATAAAATTTT
1 AT-AATTTTT
*
40123613 ACAATTTTT
1 ATAATTTTT
*
40123622 TTATATTTTT
1 ATA-ATTTTT
40123632 -TACGATTTTT
1 ATA--ATTTTT
*
40123642 ATATTTTTTT
1 ATA-ATTTTT
*
40123652 CTAATTTTT
1 ATAATTTTT
*
40123661 ATTAAATTTT
1 A-TAATTTTT
*
40123671 -TAATATTT
1 ATAATTTTT
*
40123679 -TAATATTT
1 ATAATTTTT
* *
40123687 ATTAAATTTA
1 A-TAATTTTT
*
40123697 ATAATATTT
1 ATAATTTTT
**
40123706 ATAGCTTTT
1 ATAATTTTT
*
40123715 ATTGA-TTTT
1 A-TAATTTTT
*
40123724 AT-TTTTTT
1 ATAATTTTT
40123732 ATAATTTTT
1 ATAATTTTT
40123741 A
1 A
40123742 ATAAAAGCAA
Statistics
Matches: 176, Mismatches: 40, Indels: 50
0.66 0.15 0.19
Matches are distributed among these distances:
7 6 0.03
8 31 0.18
9 61 0.35
10 63 0.36
11 15 0.09
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:40123522 original size:20 final size:19
Alignment explanation
Indices: 40123497--40123651 Score: 82
Period size: 20 Copynumber: 7.8 Consensus size: 19
40123487 GTACAATAAT
40123497 TTTTATAATTTTTTTACAAA
1 TTTTATAATTTTTTTAC-AA
* *
40123517 TTTTAT-ATTTCTTTACAT
1 TTTTATAATTTTTTTACAA
* *
40123535 TTTGTATAATTTTCTTACGAC
1 TTT-TATAATTTTTTTAC-AA
* *
40123556 TTTATAAAATTTTATAATTATATA
1 TTT-TATAATTTT-T--TTACA-A
**
40123580 TTTTATAATTTTTTTACGT
1 TTTTATAATTTTTTTACAA
**
40123599 TTTTATAA-AATTTTACAA
1 TTTTATAATTTTTTTACAA
* * *
40123617 TTTTTTTATATTTTTTACGA
1 TTTTATAAT-TTTTTTACAA
40123637 TTTT-TATATTTTTTT
1 TTTTATA-ATTTTTTT
40123652 CTAATTTTTA
Statistics
Matches: 101, Mismatches: 24, Indels: 21
0.69 0.16 0.14
Matches are distributed among these distances:
18 16 0.16
19 27 0.27
20 30 0.30
21 12 0.12
22 1 0.01
23 9 0.09
24 6 0.06
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTTACAA
Found at i:40123630 original size:29 final size:28
Alignment explanation
Indices: 40123579--40123686 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 28
40123569 ATAATTATAT
**
40123579 ATTTTATAATTTTTTTACGTTTTTATAAA
1 ATTTTA-AATTTTTTTATATTTTTATAAA
*
40123608 ATTTTACAATTTTTTTATATTTTT-TACGA
1 ATTTTA-AATTTTTTTATATTTTTATA-AA
* * * *
40123637 TTTTTATATTTTTTTCTAATTTTTATTAA
1 ATTTTAAATTTTTTTAT-ATTTTTATAAA
* * *
40123666 ATTTTTAATATTTTAATATTT
1 ATTTTAAATTTTTTTATATTT
40123687 ATTAAATTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 7
0.73 0.18 0.08
Matches are distributed among these distances:
28 15 0.25
29 45 0.74
30 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTTTAAATTTTTTTATATTTTTATAAA
Found at i:40123658 original size:19 final size:18
Alignment explanation
Indices: 40123609--40123662 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
40123599 TTTTATAAAA
40123609 TTTTACAATTTTTTTATATT
1 TTTTACAA--TTTTTATATT
*
40123629 TTTTACGATTTTTATATT
1 TTTTACAATTTTTATATT
*
40123647 TTTTTCTAATTTTTAT
1 TTTTAC-AATTTTTAT
40123663 TAAATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 15 0.50
19 8 0.27
20 7 0.23
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTACAATTTTTATATT
Found at i:40123672 original size:39 final size:38
Alignment explanation
Indices: 40123580--40123695 Score: 94
Period size: 39 Copynumber: 3.0 Consensus size: 38
40123570 TAATTATATA
**
40123580 TTTTATAATTTTTTTACG-TTTTTATAAAATTTTACAATTT
1 TTTTATAA--TTTTTACGATTTTTAT-ATTTTTTACAATTT
* *
40123620 TTTTATATTTTTTACGATTTTTATATTTTTTTCTAATTT
1 TTTTATAATTTTTACGATTTTTATATTTTTTAC-AATTT
** * *
40123659 TTATTA-AATTTTTAATATTTTAATATTTATTA-AATTT
1 TT-TTATAATTTTTACGATTTTTATATTTTTTACAATTT
40123696 AATAATATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
37 5 0.08
38 14 0.22
39 34 0.54
40 10 0.16
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (38 bp):
TTTTATAATTTTTACGATTTTTATATTTTTTACAATTT
Found at i:40123689 original size:26 final size:27
Alignment explanation
Indices: 40123653--40123705 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
40123643 TATTTTTTTC
* *
40123653 TAATTTTTATTAAATTT-TTAATATTT
1 TAATATTTATTAAATTTAATAATATTT
40123679 TAATATTTATTAAATTTAATAATATTT
1 TAATATTTATTAAATTTAATAATATTT
40123706 ATAGCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TAATATTTATTAAATTTAATAATATTT
Found at i:40123886 original size:85 final size:88
Alignment explanation
Indices: 40123753--40123967 Score: 312
Period size: 85 Copynumber: 2.5 Consensus size: 88
40123743 TAAAAGCAAG
40123753 GGCTTAATTGATTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
1 GGCTTAATTGATTTTTTT-AAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
*
40123818 CAATT-ACGTGTAA-AAAAAGTAGA
65 CAATTGA-GTGCAAGAAAAAGTAGA
* * *
40123841 GGCTTAATTG-TTTTTTT-TAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCT
1 GGCTTAATTGATTTTTTTAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
*
40123904 AATTGAGTGCAAGAAAAAGTAGG
66 AATTGAGTGCAAGAAAAAGTAGA
* *
40123927 GGCTTAATTGCTTTTTTTCAAAAAGTTTGAGGGTTTTTTTG
1 GGCTTAATTGATTTTTTT-AAAAAGTTTGAGGGTCTTTTTG
40123968 CACCCTTAAG
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
85 52 0.45
86 20 0.17
87 14 0.12
88 10 0.09
89 19 0.17
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (88 bp):
GGCTTAATTGATTTTTTTAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
AATTGAGTGCAAGAAAAAGTAGA
Found at i:40124129 original size:24 final size:24
Alignment explanation
Indices: 40124097--40124146 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
40124087 ACAATTGACA
* *
40124097 AGGAAAAGACGCATTGGTGAAAAT
1 AGGAAAAGACGCATCGATGAAAAT
*
40124121 AGGAAAAGACGTATCGATGAAAAT
1 AGGAAAAGACGCATCGATGAAAAT
40124145 AG
1 AG
40124147 TACAAAACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (24 bp):
AGGAAAAGACGCATCGATGAAAAT
Found at i:40131037 original size:47 final size:47
Alignment explanation
Indices: 40130986--40131150 Score: 170
Period size: 47 Copynumber: 3.5 Consensus size: 47
40130976 ACTTGACCGA
* * * * * *
40130986 TGGTTTATCCACAACTTATTTTACTCGGCATTCACCTGTTCGACCGG
1 TGGTTTATCCACAACATATTTTAGTCGACAATCACCTGCTCGACCAG
* * * * *
40131033 TGGTTTGTCCACAACATATCTTAGTCGACAATCATCTGCTCAACTAG
1 TGGTTTATCCACAACATATTTTAGTCGACAATCACCTGCTCGACCAG
* * *
40131080 TGGTTTATCCACAACATATTTTAGTC-ATCAGTCACCTGCTCTACTAG
1 TGGTTTATCCACAACATATTTTAGTCGA-CAATCACCTGCTCGACCAG
* *
40131127 TGGTATATCCACAACGTATTTTAG
1 TGGTTTATCCACAACATATTTTAG
40131151 CAGCTTTTAT
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
46 1 0.01
47 98 0.99
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (47 bp):
TGGTTTATCCACAACATATTTTAGTCGACAATCACCTGCTCGACCAG
Found at i:40132199 original size:2 final size:2
Alignment explanation
Indices: 40132192--40132225 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40132182 TCTAGTAGAG
40132192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40132226 TAGTGAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40133662 original size:24 final size:24
Alignment explanation
Indices: 40133635--40133686 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
40133625 AATCAAAATA
*
40133635 AAATATATTATA-TTAATAAATGCT
1 AAATATATTATACTT-ATAAATACT
40133659 AAATATATTATACTTATAAATACT
1 AAATATATTATACTTATAAATACT
40133683 AAAT
1 AAAT
40133687 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTTATAAATACT
Found at i:40142305 original size:25 final size:26
Alignment explanation
Indices: 40142256--40142312 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
40142246 ACCCTTTAAA
*
40142256 GTATATATTAAAATATGCACATATAT
1 GTATATATAAAAATATGCACATATAT
***
40142282 -TATATATAAAAATATGCGTGTATAT
1 GTATATATAAAAATATGCACATATAT
40142307 GTATAT
1 GTATAT
40142313 CAAATACAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (26 bp):
GTATATATAAAAATATGCACATATAT
Found at i:40144230 original size:43 final size:43
Alignment explanation
Indices: 40144175--40144330 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
40144165 AACTCATACA
* *
40144175 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
*
40144218 ATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AATAAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCAAATATCG
* * * *
40144259 ATGCCAATGTCCCAGACATGGTCTTTCACGT--TCACATAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAAT-A-TCG
*
40144302 ATGCCAACGTCCTAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
40144331 AAAAACACAG
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
40 4 0.04
41 27 0.29
42 10 0.11
43 51 0.55
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
Found at i:40144273 original size:41 final size:42
Alignment explanation
Indices: 40144170--40144289 Score: 136
Period size: 41 Copynumber: 2.9 Consensus size: 42
40144160 TCGGAAACTC
* * * * *
40144170 ATACAATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAT
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACACGTAATAAA
*
40144212 ATATCGATGCCACTGTCCCAGACAGGGTCTTACACG-AATAAA
1 ATA-CGATGCCAATGTCCCAGACAGGGTCTTACACGTAATAAA
* *
40144254 ATACGATGCCAATGTCCCAGACATGGTCTTTCACGT
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACACGT
40144290 TCACATAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
41 29 0.44
42 10 0.15
43 26 0.39
44 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACACGTAATAAA
Found at i:40144325 original size:84 final size:84
Alignment explanation
Indices: 40144170--40144330 Score: 195
Period size: 84 Copynumber: 1.9 Consensus size: 84
40144160 TCGGAAACTC
* *
40144170 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCATATATCGATGCCACTGTCCCAGAC
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCATATATCGATGCCACTGTCCCAGAC
40144235 AGGGTCTTACACGAATAAA
66 AGGGTCTTACACGAATAAA
* * * * *
40144254 ATACGATGCCAATGTCCCAGACATGGTCTTTCACGT--TCACATAAGTCGATGCCAAC-GTCCTA
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCATAT-A-TCGATGCC-ACTGTCCCA
40144316 GAC-GTGGTCTTACAC
63 GACAG-GGTCTTACAC
40144331 AAAAACACAG
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
82 5 0.08
83 2 0.03
84 57 0.86
85 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (84 bp):
ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCATATATCGATGCCACTGTCCCAGAC
AGGGTCTTACACGAATAAA
Found at i:40145503 original size:14 final size:15
Alignment explanation
Indices: 40145484--40145512 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40145474 TCACGAAACT
40145484 TTCACACAT-ATAAA
1 TTCACACATAATAAA
40145498 TTCACACATAATAAA
1 TTCACACATAATAAA
40145513 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:40151707 original size:31 final size:31
Alignment explanation
Indices: 40151669--40151732 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
40151659 ATCACTCAAC
40151669 TTCAAAAAATTTTAAAATAA-TCATTAAACTA
1 TTCAAAAAATTTT-AAATAAGTCATTAAACTA
**
40151700 TTCAAAAAATTTTATTTAAGTCATTAAACTA
1 TTCAAAAAATTTTAAATAAGTCATTAAACTA
40151731 TT
1 TT
40151733 ACATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (31 bp):
TTCAAAAAATTTTAAATAAGTCATTAAACTA
Found at i:40153794 original size:18 final size:17
Alignment explanation
Indices: 40153761--40153799 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
40153751 TTGTATAAAT
40153761 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
40153779 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
40153796 TGTG
1 TGTG
40153800 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:40153931 original size:8 final size:8
Alignment explanation
Indices: 40153918--40153946 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
40153908 CACTAGAGAC
40153918 CAGTGTTA
1 CAGTGTTA
40153926 CAGTGTTA
1 CAGTGTTA
40153934 CAGTGTTA
1 CAGTGTTA
40153942 CAGTG
1 CAGTG
40153947 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:40154124 original size:18 final size:17
Alignment explanation
Indices: 40154091--40154129 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
40154081 TTGTATAAAT
40154091 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
40154109 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
40154126 TGTG
1 TGTG
40154130 GAAGAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:40154261 original size:8 final size:8
Alignment explanation
Indices: 40154248--40154276 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
40154238 CACTAGAGAC
40154248 CAGTGTTA
1 CAGTGTTA
40154256 CAGTGTTA
1 CAGTGTTA
40154264 CAGTGTTA
1 CAGTGTTA
40154272 CAGTG
1 CAGTG
40154277 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:40154298 original size:330 final size:330
Alignment explanation
Indices: 40153697--40154352 Score: 1303
Period size: 330 Copynumber: 2.0 Consensus size: 330
40153687 CGACTAAATT
40153697 ACAAAAATAGTCGTTTTGCATCCGAGGTAAGTTATATGTAAATAATAGTTATATTTGTATAAATT
1 ACAAAAATAGTCGTTTTGCATCCGAGGTAAGTTATATGTAAATAATAGTTATATTTGTATAAATT
*
40153762 GTGAATTATATTTGATATGTGAATTAATATTGAATGTGGAAGGAAAGTTGTTCATGAATTATTCA
66 GTGAATTATATTTGATATGTGAATTAATATTGAATGTGGAAGAAAAGTTGTTCATGAATTATTCA
40153827 AGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCCGGTTGAACTTAGGAATAGAATTG
131 AGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCCGGTTGAACTTAGGAATAGAATTG
40153892 GATACAAGTGACATGTCACTAGAGACCAGTGTTACAGTGTTACAGTGTTACAGTGAGTCCCGGGT
196 GATACAAGTGACATGTCACTAGAGACCAGTGTTACAGTGTTACAGTGTTACAGTGAGTCCCGGGT
40153957 GCTGGGTGATCTAGCATGTGTTGCAGACACCTGACAGCTTGTGTGAGCAGGCCCGTGGACATTTC
261 GCTGGGTGATCTAGCATGTGTTGCAGACACCTGACAGCTTGTGTGAGCAGGCCCGTGGACATTTC
40154022 CGTGG
326 CGTGG
40154027 ACAAAAATAGTCGTTTTGCATCCGAGGTAAGTTATATGTAAATAATAGTTATATTTGTATAAATT
1 ACAAAAATAGTCGTTTTGCATCCGAGGTAAGTTATATGTAAATAATAGTTATATTTGTATAAATT
40154092 GTGAATTATATTTGATATGTGAATTAATATTGAATGTGGAAGAAAAGTTGTTCATGAATTATTCA
66 GTGAATTATATTTGATATGTGAATTAATATTGAATGTGGAAGAAAAGTTGTTCATGAATTATTCA
40154157 AGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCCGGTTGAACTTAGGAATAGAATTG
131 AGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCCGGTTGAACTTAGGAATAGAATTG
40154222 GATACAAGTGACATGTCACTAGAGACCAGTGTTACAGTGTTACAGTGTTACAGTGAGTCCCGGGT
196 GATACAAGTGACATGTCACTAGAGACCAGTGTTACAGTGTTACAGTGTTACAGTGAGTCCCGGGT
40154287 GCTGGGTGATCTAGCATGTGTTGCAGACACCTGACAGCTTGTGTGAGCAGGCCCGTGGACATTTC
261 GCTGGGTGATCTAGCATGTGTTGCAGACACCTGACAGCTTGTGTGAGCAGGCCCGTGGACATTTC
40154352 C
326 C
40154353 AGTGTTATTG
Statistics
Matches: 325, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
330 325 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (330 bp):
ACAAAAATAGTCGTTTTGCATCCGAGGTAAGTTATATGTAAATAATAGTTATATTTGTATAAATT
GTGAATTATATTTGATATGTGAATTAATATTGAATGTGGAAGAAAAGTTGTTCATGAATTATTCA
AGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCCGGTTGAACTTAGGAATAGAATTG
GATACAAGTGACATGTCACTAGAGACCAGTGTTACAGTGTTACAGTGTTACAGTGAGTCCCGGGT
GCTGGGTGATCTAGCATGTGTTGCAGACACCTGACAGCTTGTGTGAGCAGGCCCGTGGACATTTC
CGTGG
Found at i:40154406 original size:22 final size:23
Alignment explanation
Indices: 40154363--40154434 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
40154353 AGTGTTATTG
40154363 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40154386 TTCAGTGGTAGCTT-GGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
40154408 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
40154431 ATCA
1 ATCA
40154435 ATGTGGCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 21 0.46
23 25 0.54
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:40159387 original size:40 final size:40
Alignment explanation
Indices: 40159303--40159485 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
40159293 TTGAATGCTG
* * * *
40159303 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
40159342 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40159383 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATA-CAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40159422 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40159462 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40159486 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40159454 original size:79 final size:81
Alignment explanation
Indices: 40159303--40159482 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
40159293 TTGAATGCTG
* * * *
40159303 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
* *
40159367 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
40159383 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACAAT-TCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACAATATCCGGACTAAGAT-CCGAAGGCA
40159444 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTTTAAAA
40159462 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40159483 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 51 0.58
80 25 0.28
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:40159506 original size:39 final size:39
Alignment explanation
Indices: 40159383--40159532 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 39
40159373 AGTTATTAAT
* ** * *
40159383 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAG--ATACAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTCTA-AAA
** *
40159422 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
40159462 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
40159502 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
40159533 GAGCTATATC
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.03
39 52 0.55
40 37 0.39
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:40159506 original size:79 final size:79
Alignment explanation
Indices: 40159356--40159522 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
40159346 GGACTAAGAT
* * * * **
40159356 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAA
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
* *
40159421 TTCCGGGTTAAGTC
66 TACCGGGCTAAGTC
* * *
40159435 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTACT
1 CCGAAGGCATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACA
*
40159498 ATGACCGGGCTATGTC
65 AT-ACCGGGCTAAGTC
40159514 CCGAAGGCA
1 CCGAAGGCA
40159523 CTTGAACGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 14 0.19
79 60 0.81
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
TACCGGGCTAAGTC
Found at i:40167303 original size:40 final size:40
Alignment explanation
Indices: 40167206--40167389 Score: 169
Period size: 40 Copynumber: 4.6 Consensus size: 40
40167196 TTGAATGCTG
* * * *
40167206 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
40167245 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * * **
40167286 TCTGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACCAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40167326 TCCGGGTTAAGTCTCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40167366 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40167390 GAATGAGTTA
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 106 0.91
41 10 0.09
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40172465 original size:18 final size:17
Alignment explanation
Indices: 40172432--40172470 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
40172422 TTGTATAAAT
40172432 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
40172450 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
40172467 TGTG
1 TGTG
40172471 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:40172733 original size:23 final size:23
Alignment explanation
Indices: 40172707--40172772 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
40172697 GTTATTGATT
40172707 AGTGGTAGCTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATTTC
40172730 AGTGGTAGCTAT-GGCTACATTTC
1 AGTGGTAGCT-TCGGCTACATTTC
40172753 AGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTTCGGCTACAT
40172773 ATCAATGTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.02
23 39 0.95
24 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATTTC
Found at i:40174139 original size:26 final size:27
Alignment explanation
Indices: 40174110--40174163 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
40174100 ATACATATAT
* *
40174110 TATAGGAAACATATGTATA-TATAAAA
1 TATAGAAAACATATATATATTATAAAA
**
40174136 TATAGAAAATGTATATATATTATAAAA
1 TATAGAAAACATATATATATTATAAAA
40174163 T
1 T
40174164 GTATATGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (27 bp):
TATAGAAAACATATATATATTATAAAA
Found at i:40177294 original size:14 final size:14
Alignment explanation
Indices: 40177240--40177296 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
40177230 AATGGTCAAA
40177240 TTATAGTTTTAATCCTT
1 TTATA-TTTTAAT-C-T
40177257 TTATATTTTCAA-CT
1 TTATATTTT-AATCT
* *
40177271 TTAAAATTTAATCT
1 TTATATTTTAATCT
40177285 TTATATTTTAAT
1 TTATATTTTAAT
40177297 TTTTGACAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 20 0.59
15 1 0.03
16 4 0.12
17 7 0.21
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (14 bp):
TTATATTTTAATCT
Found at i:40180127 original size:14 final size:14
Alignment explanation
Indices: 40180104--40180136 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40180094 ATTGTGGATT
*
40180104 TAAA-AATTAATAA
1 TAAATAATTAAAAA
40180117 TAAATAATTAAAAA
1 TAAATAATTAAAAA
40180131 TAAATA
1 TAAATA
40180137 GAACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATAATTAAAAA
Found at i:40180198 original size:20 final size:20
Alignment explanation
Indices: 40180162--40180199 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40180152 CTTAATTAGT
*
40180162 TTATAAAATTTAAAAAAGTA
1 TTATAAAATGTAAAAAAGTA
40180182 TTAT-AAATGTAACAAAAG
1 TTATAAAATGTAA-AAAAG
40180200 GAAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (20 bp):
TTATAAAATGTAAAAAAGTA
Found at i:40180522 original size:15 final size:15
Alignment explanation
Indices: 40180504--40180536 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40180494 AAAAAATGAA
40180504 AAAAGAAAAGAAAAT
1 AAAAGAAAAGAAAAT
*
40180519 AAAAGAAAATAAAAT
1 AAAAGAAAAGAAAAT
40180534 AAA
1 AAA
40180537 TAAAGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAAGAAAAGAAAAT
Found at i:40182190 original size:167 final size:164
Alignment explanation
Indices: 40181440--40182251 Score: 743
Period size: 167 Copynumber: 4.9 Consensus size: 164
40181430 TTCGAAATTG
* * * * * *
40181440 TTGTGTCAAATCTTTTGAATTTTGAATTCTTCGCGTAGTTTAATCTGATCTAAATCTCGGAAGCG
1 TTGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTAAATCTCAGAAGCG
* * *
40181505 TCGTGAG-TTCGTTCGTTTGCTCAGATTTGTATTTCTCAAATTGAATTTATGTTTGTTATAGATT
65 -C-TGAGCTT-GTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATT
**
40181569 GGATTTAGATTTCTCCTTTAAGTGTTGATCTGCTCAGAAAT
127 GGATTTAGA-TTCT--TTTTTGTGTTGATCTGCTCAGAAAT
* * * * * *
40181610 TGATGTGTCAAATCTTTTGAATTCTGAATTATTCGCGTAGTGGT-ATCTTATCTGAATCTCTG-A
1 T--TGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGT-GTCATCTGATCTAAATCTCAGAA
* *
40181673 TC-TTGAG-TTCGTTGGTTTG-T---A-----A-TTCTCGAATTGAATTTATGTTTGTTACAGAT
62 GCGCTGAGCTT-GTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGAT
* *
40181726 TGGATTTAGATTATTTTTTACATGTT-ACTCTGCTCAGAAATT
126 TGGATTTAGATTCTTTTTT--GTGTTGA-TCTGCTCAGAAA-T
* *
40181768 GTTGTGTCAAATCATTTTGAA---T---TATTCGA-GTAGAGTCATCTGATCTAAATCTCGGAA-
1 -TTGTGTCAAAT-ATTTTGAATTTTGAATATTC-ACGTAGTGTCATCTGATCTAAATCTCAGAAG
* *
40181825 -G-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTTTCGAATTGAATTTATGTTTGTTACAGATTG
63 CGCTGAGCTTGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTG
40181888 GATTTAGATTATCTTCTTTTG-GTTGATCTGCTCAGAAAT
128 GATTTAGA-T-TCTT-TTTTGTGTTGATCTGCTCAGAAAT
* * *
40181927 TGTCGTGTCAAATCTTTTGAATTTTGAATTATTCGCGTAGTGTCATCTGATCTAATTCTCAGAAG
1 T-T-GTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTAAATCTCAGAAG
* * * * *
40181992 CGTCGTGAG-TTCCTTGGTTTGCTCGGATTTGTATTTCTCTATTTGAATTTATGTTTGTTACGGA
63 CG-C-TGAGCTT-GTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGA
*
40182056 TTGGATTTAGCTTCTTTTTATGTGTTGATCTGCTCAGAAA-
125 TTGGATTTAGATTCTTTTT-TGTGTTGATCTGCTCAGAAAT
40182096 TTGTGTCAAATATTTTGAATTTTGAACTATTCACGTAGTGTCATCTGATC-AGAATCTCAGAAGC
1 TTGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTA-AATCTCAGAAGC
* * *
40182160 GACTTGAGCTTGTTGGTTGGCTCAGATTTGTATATCTCGAAATGAATTTATGTTTGTTACAGATT
64 G-C-TGAGCTTGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATT
* **
40182225 GGACTT-GGGT-TTTTTTGTGTTGATCTG
127 GGATTTAGATTCTTTTTTGTGTTGATCTG
40182252 GTCAATTCTG
Statistics
Matches: 539, Mismatches: 55, Indels: 102
0.77 0.08 0.15
Matches are distributed among these distances:
150 15 0.03
151 26 0.05
152 1 0.00
154 1 0.00
155 4 0.01
156 1 0.00
157 29 0.05
158 48 0.09
159 12 0.02
160 64 0.12
161 2 0.00
162 4 0.01
163 4 0.01
164 13 0.02
165 5 0.01
166 33 0.06
167 114 0.21
168 22 0.04
169 7 0.01
170 20 0.04
171 62 0.12
172 51 0.09
173 1 0.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (164 bp):
TTGTGTCAAATATTTTGAATTTTGAATATTCACGTAGTGTCATCTGATCTAAATCTCAGAAGCGC
TGAGCTTGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTGGAT
TTAGATTCTTTTTTGTGTTGATCTGCTCAGAAAT
Done.