Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 181 of 204
Found at i:53653539 original size:3 final size:3
Alignment explanation
Indices: 53653531--53653557 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53653521 TATTAACATG
53653531 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
53653558 TAGGGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53657655 original size:27 final size:27
Alignment explanation
Indices: 53657625--53657686 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
53657615 TATAAGCGAA
53657625 TAATATTATCAATAATAACAACAA-TAG
1 TAATATTATCAATAATAACAA-AAGTAG
* * *
53657652 TAATAATATTAATAATAATAAAAGTAG
1 TAATATTATCAATAATAACAAAAGTAG
53657679 TAATATTA
1 TAATATTA
53657687 ATAGTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (27 bp):
TAATATTATCAATAATAACAAAAGTAG
Found at i:53657664 original size:24 final size:24
Alignment explanation
Indices: 53657637--53657689 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53657627 ATATTATCAA
*
53657637 TAATAACAACAATAGTAATAATAT
1 TAATAACAACAAAAGTAATAATAT
* * *
53657661 TAATAATAATAAAAGTAGTAATAT
1 TAATAACAACAAAAGTAATAATAT
53657685 TAATA
1 TAATA
53657690 GTGATAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
TAATAACAACAAAAGTAATAATAT
Found at i:53659092 original size:42 final size:42
Alignment explanation
Indices: 53659040--53659164 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
53659030 ATGATGTACA
* * * *
53659040 GAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAA-T
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACT
* *
53659081 GGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGTTAAACT
1 -GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACT
* *
53659124 GAAGCTCAAAAGAGCTAAACGGAAACTCATTAA-GGTTAAAC
1 GAAGCTCATAAGAGCTAAACGGAAACCCA-TAAGGGTTAAAC
53659165 AAAAACTCAT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
42 67 0.94
43 4 0.06
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAACT
Found at i:53659152 original size:21 final size:21
Alignment explanation
Indices: 53659046--53659210 Score: 82
Period size: 21 Copynumber: 7.9 Consensus size: 21
53659036 TACAGAAGCA
* * *
53659046 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTAAACGGAAACT
* * * * *
53659067 CATAAGGGTTGAATGGAAGCT
1 CATAAGAGCTAAACGGAAACT
* * *
53659088 CATAAGAGCTGAATGGAAACC
1 CATAAGAGCTAAACGGAAACT
* * * *
53659109 CATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACT
*
53659130 CAAAAGAGCTAAACGGAAACT
1 CATAAGAGCTAAACGGAAACT
* **
53659151 CATTAAG-GTTAAACAAAAACT
1 CA-TAAGAGCTAAACGGAAACT
* * * *
53659172 CATATGAG-TTAACAGAAGCT
1 CATAAGAGCTAAACGGAAACT
* *
53659192 CGTGAGAGCTAAACGGAAA
1 CATAAGAGCTAAACGGAAA
53659211 GTAAACACGA
Statistics
Matches: 104, Mismatches: 37, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
20 17 0.16
21 84 0.81
22 3 0.03
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (21 bp):
CATAAGAGCTAAACGGAAACT
Found at i:53663519 original size:41 final size:42
Alignment explanation
Indices: 53663461--53663665 Score: 219
Period size: 41 Copynumber: 5.0 Consensus size: 42
53663451 TATTGGAATG
*
53663461 ATACACCGGC-ATGAAGCCTGCTAGGC-CTAAAGCCT-AATTTG
1 ATACACCGGCAAT-AAGCCTGCTAGGCAC-AAAGCCTGAATTTA
* * * * *
53663502 GTACACCGGC-ATGAAGCCTGCTAGACATAAAGTCTGAA-ATA
1 ATACACCGGCAAT-AAGCCTGCTAGGCACAAAGCCTGAATTTA
53663543 ACT-CACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAA-TTA
1 A-TACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTTA
*
53663584 ATTCACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAA-TTA
1 ATACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTTA
* * * *
53663625 ATTCACCGGCAATAAGCCTACTAGGCACAAGGCTTGAATTT
1 ATACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTT
53663666 CACTGATACA
Statistics
Matches: 144, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 136 0.94
42 7 0.05
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (42 bp):
ATACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTTA
Found at i:53670087 original size:113 final size:113
Alignment explanation
Indices: 53669943--53670268 Score: 413
Period size: 113 Copynumber: 2.9 Consensus size: 113
53669933 AAAATAAGAA
* * * * * * *
53669943 TTAGCGGCATTTTTAGGAAAGTGCCGCAAAAAACCGAAGCTCAACGACACCGTTTTCTTAGTTTT
1 TTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACTAAGCACAACGGCGCCGTTTTCTTAGTTTT
* * *
53670008 CGGGGATTTAGCGACATTTTTTAGAAAGCGCCGCTAATTCTCAGGTCT
66 CGGGGATTTAGCGGCATTTTTTAGAAAGCGCCGCTAATGCTCAGGGCT
* * * * *
53670056 TTAGCGGCGTTTCTAGAAAAGCGCCACAAAAAAACTAAGCACAACGGCGTCGTTTTCTTAGCTTT
1 TTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACTAAGCACAACGGCGCCGTTTTCTTAGTTTT
53670121 CGGGGATTTAGCGGCA-TTTTTAGGAAAGCGCCGCTAATGCTCAGGGCT
66 CGGGGATTTAGCGGCATTTTTTA-GAAAGCGCCGCTAATGCTCAGGGCT
* * * *
53670169 TTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGTGCCGTTTT-TTGAGTT
1 TTAGCGGCGTTTTTAGGAAAGCGCCGC-AAAAAAACTAAGCACAACGGCGCCGTTTTCTT-AGTT
** *
53670233 TTTAGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGC
64 TTCGGGGATTTAGCGGCATTTTTTAGAAAGCGCCGC
53670269 AAAAAAAATA
Statistics
Matches: 182, Mismatches: 27, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
112 6 0.03
113 115 0.63
114 55 0.30
115 6 0.03
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (113 bp):
TTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAAACTAAGCACAACGGCGCCGTTTTCTTAGTTTT
CGGGGATTTAGCGGCATTTTTTAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:53670289 original size:73 final size:73
Alignment explanation
Indices: 53670161--53670341 Score: 247
Period size: 73 Copynumber: 2.5 Consensus size: 73
53670151 CCGCTAATGC
* * ** * *
53670161 TCAGGGCTTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGTGCCGTTTT
1 TCAGGGATTTAGCGGAGTTTTTAAGAAAGCGCCGCAAAAAAAACTAAACCCAACGGCGCCGTTTT
53670226 TTGAGTTT
66 TTGAGTTT
* * * *
53670234 TTAGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAAAA-TAAACCCAAACGGCGCTGTTT
1 TCAGGGATTTAGCGGAGTTTTTAAGAAAGCGCCGCAAAAAAAACTAAACCC-AACGGCGCCGTTT
53670298 TTTGAGTTT
65 TTTGAGTTT
*
53670307 TCGGGGATTTAGCGGAGTTTTTAAGAAAGCGCCGC
1 TCAGGGATTTAGCGGAGTTTTTAAGAAAGCGCCGC
53670342 TAATGCTCAG
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
72 6 0.06
73 89 0.94
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (73 bp):
TCAGGGATTTAGCGGAGTTTTTAAGAAAGCGCCGCAAAAAAAACTAAACCCAACGGCGCCGTTTT
TTGAGTTT
Found at i:53670641 original size:17 final size:16
Alignment explanation
Indices: 53670616--53670663 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
53670606 AGTGTTATGC
53670616 TTTAGGGGTTAGGGGAA
1 TTTAGGGGTTAGGGG-A
* *
53670633 TTTATGGGTTAGAGGA
1 TTTAGGGGTTAGGGGA
*
53670649 TTTAGGGGTCAGGGG
1 TTTAGGGGTTAGGGG
53670664 TTAGTGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.21, C:0.02, G:0.46, T:0.31
Consensus pattern (16 bp):
TTTAGGGGTTAGGGGA
Found at i:53670684 original size:22 final size:23
Alignment explanation
Indices: 53670633--53670684 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
53670623 GTTAGGGGAA
*
53670633 TTTATGGGTTAGAGGATTTAGGG
1 TTTAGGGGTTAGAGGATTTAGGG
* * *
53670656 GTCAGGGGTTAG-TGATTTAGGG
1 TTTAGGGGTTAGAGGATTTAGGG
53670678 TTTAGGG
1 TTTAGGG
53670685 TTTCAACAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.19, C:0.02, G:0.42, T:0.37
Consensus pattern (23 bp):
TTTAGGGGTTAGAGGATTTAGGG
Found at i:53674344 original size:194 final size:193
Alignment explanation
Indices: 53673998--53674443 Score: 570
Period size: 194 Copynumber: 2.3 Consensus size: 193
53673988 GAAATATTGT
* * * ** * * *
53673998 TGTATATTGC-TTCGAGTTTTTCAAAAATTGAAGAGAAATGTCTTTGAAAAACGGGAATACGGGT
1 TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACAT-TTTTAAGAACGGGAATACAGGT
* * ** * * * *
53674062 TTTGTTTAACTGTCTGAATTGCTTCTTGACAAAACCCAGTTTACAACATTTCTGACGTTATAAAA
65 GTTGTTTAACTGTCCGAATTGCTTCTCAACAAAACCCAGTTTACAACATATCCGAAGCTATAAAA
53674127 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
130 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
* * *
53674191 TGTATATTGCTTTTGAGTTTTACAAAAGTCGAAGAGAAACATTTTTAAGAATGGGAATTCAGGTG
1 TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACATTTTTAAGAACGGGAATACAGGTG
* * ** *
53674256 TTGTTTAACTGTCCGAATTTCTTCTCAACAAAACCCCATTTTATGACATATCCGAAGCTATGAAA
66 TTGTTTAACTGTCCGAATTGCTTCTCAACAAAA-CCCAGTTTACAACATATCCGAAGCTATAAAA
* * * *
53674321 TCTTGATTCCTTAATGTTTCTGCTGGATTTGTGTTTATGATTGTTGATATATGCTGTTTGTTGC
130 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
* * * *
53674385 TATATATTGCTTTTGAGTTTTTCAAGAGTCGAAGAAAAACGACTTTTAAGAACGGGAAT
1 TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAAC-ATTTTTAAGAACGGGAAT
53674444 CTGTTTGTCG
Statistics
Matches: 216, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
193 56 0.26
194 144 0.67
195 16 0.07
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (193 bp):
TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACATTTTTAAGAACGGGAATACAGGTG
TTGTTTAACTGTCCGAATTGCTTCTCAACAAAACCCAGTTTACAACATATCCGAAGCTATAAAAT
CTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
Found at i:53676135 original size:43 final size:42
Alignment explanation
Indices: 53676010--53676119 Score: 175
Period size: 43 Copynumber: 2.6 Consensus size: 42
53676000 GAGTGGTGCT
* *
53676010 AAGGTCATGATTTTTAGCGGCGTTTCTGTTAGAAGTGCCGCTA
1 AAGGTCTTG-TTTTTAGCGGCGTTTCTGTTAGAAGCGCCGCTA
*
53676053 AAGGTCTTGTTCTTTAGCGGCGTTTGTGTTAGAAGCGCCGCTA
1 AAGGTCTTGTT-TTTAGCGGCGTTTCTGTTAGAAGCGCCGCTA
53676096 AAGGTCTTGTTTTTAGCGGCGTTT
1 AAGGTCTTGTTTTTAGCGGCGTTT
53676120 ATTTTTAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
42 15 0.24
43 48 0.76
ACGTcount: A:0.17, C:0.16, G:0.29, T:0.37
Consensus pattern (42 bp):
AAGGTCTTGTTTTTAGCGGCGTTTCTGTTAGAAGCGCCGCTA
Found at i:53676220 original size:59 final size:59
Alignment explanation
Indices: 53676156--53676275 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
53676146 TGGCGTTGTC
53676156 AACAGTAGCATTTTTTGCAGCGCTTCTAAAAGCGTCACAAATACTTTTAGCGGCGTTAA
1 AACAGTAGCATTTTTTGCAGCGCTTCTAAAAGCGTCACAAATACTTTTAGCGGCGTTAA
53676215 AACAGTAGCATTTTTTGCAGCGCTTCTAAAAGCGTCACAAATACTTTTAGCGGCGTTAA
1 AACAGTAGCATTTTTTGCAGCGCTTCTAAAAGCGTCACAAATACTTTTAGCGGCGTTAA
53676274 AA
1 AA
53676276 AACGCCGCTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (59 bp):
AACAGTAGCATTTTTTGCAGCGCTTCTAAAAGCGTCACAAATACTTTTAGCGGCGTTAA
Found at i:53676244 original size:29 final size:29
Alignment explanation
Indices: 53676156--53676245 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
53676146 TGGCGTTGTC
53676156 AACAGTAGCATTTTTTGCAGCGCTTCTAA
1 AACAGTAGCATTTTTTGCAGCGCTTCTAA
* *
53676185 AAGC-GTCA-CAAATACTTTT--AGCGGCGT-TAA
1 AA-CAGT-AGC--AT-TTTTTGCAGC-GCTTCTAA
53676215 AACAGTAGCATTTTTTGCAGCGCTTCTAA
1 AACAGTAGCATTTTTTGCAGCGCTTCTAA
53676244 AA
1 AA
53676246 GCGTCACAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 22
0.64 0.06 0.31
Matches are distributed among these distances:
27 4 0.09
28 5 0.11
29 15 0.33
30 13 0.28
31 5 0.11
32 4 0.09
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (29 bp):
AACAGTAGCATTTTTTGCAGCGCTTCTAA
Found at i:53678561 original size:21 final size:21
Alignment explanation
Indices: 53678537--53678596 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
53678527 CGGGTCGTTG
53678537 CAGAAACCCATAGGGGTTGAA
1 CAGAAACCCATAGGGGTTGAA
* * * *
53678558 CAGAAGCTCATAGGAGCTGAA
1 CAGAAACCCATAGGGGTTGAA
* * *
53678579 CGGAAATCCATAAGGGTT
1 CAGAAACCCATAGGGGTT
53678597 AAACTGAAGC
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (21 bp):
CAGAAACCCATAGGGGTTGAA
Found at i:53678606 original size:42 final size:42
Alignment explanation
Indices: 53678539--53678653 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
53678529 GGTCGTTGCA
* * * * *
53678539 GAAACCCATAGGGGTTGAACAGAAGCTCATAGGAGCTGAACG
1 GAAATCCATAAGGGTTAAACAGAAGCTCATAAGAGCTAAACG
* * *
53678581 GAAATCCATAAGGGTTAAACTGAAGCTTAAAAGAGCTAAACG
1 GAAATCCATAAGGGTTAAACAGAAGCTCATAAGAGCTAAACG
*
53678623 GAAATCCATTAA-GGTTAAACAGAAACTCATA
1 GAAATCCA-TAAGGGTTAAACAGAAGCTCATA
53678654 TGAGTTAACA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 57 0.95
43 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.18
Consensus pattern (42 bp):
GAAATCCATAAGGGTTAAACAGAAGCTCATAAGAGCTAAACG
Found at i:53683818 original size:30 final size:30
Alignment explanation
Indices: 53683784--53683846 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
53683774 ACTTAACAAG
*
53683784 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
53683814 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
53683844 CAA
1 CAA
53683847 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:53686011 original size:6 final size:6
Alignment explanation
Indices: 53686000--53686025 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53685990 CTGTGTGTTC
53686000 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
53686026 CTTTGTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:53691090 original size:6 final size:6
Alignment explanation
Indices: 53691079--53691111 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
53691069 ACATTACATC
53691079 TATTTA TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TAT
53691112 AAAATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:53696790 original size:31 final size:31
Alignment explanation
Indices: 53696723--53696792 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
53696713 TTACACGATG
* **
53696723 GTCATTAAACTATTTAAAAATTTTCATTTAA
1 GTCACTAAACTATTTAAAAATTTTCAGCTAA
* * * *
53696754 ATCACTAAATTATTTGAAAATTTTTAGCTAA
1 GTCACTAAACTATTTAAAAATTTTCAGCTAA
53696785 GTCACTAA
1 GTCACTAA
53696793 GATGTTAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATTTAAAAATTTTCAGCTAA
Found at i:53698111 original size:58 final size:58
Alignment explanation
Indices: 53698021--53698137 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
53698011 ATGGAGAAAG
53698021 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
1 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
53698079 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
1 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
53698137 T
1 T
53698138 TCCTCCATAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (58 bp):
TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
Found at i:53702460 original size:15 final size:15
Alignment explanation
Indices: 53702419--53702467 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
53702409 TAATAGTACA
53702419 CAACCAAACACAAACAC
1 CAACCAAAC-CAAAC-C
*
53702436 AAACCAAACCAAACC
1 CAACCAAACCAAACC
* *
53702451 CAACCCAACCCAACC
1 CAACCAAACCAAACC
53702466 CA
1 CA
53702468 GTGACGGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.54
16 5 0.18
17 8 0.29
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (15 bp):
CAACCAAACCAAACC
Found at i:53703145 original size:19 final size:19
Alignment explanation
Indices: 53703121--53703159 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53703111 CGGATAGCTT
53703121 TAACTTTGGAGAGATTTTA
1 TAACTTTGGAGAGATTTTA
*
53703140 TAACTTTGGGGAGATTTTA
1 TAACTTTGGAGAGATTTTA
53703159 T
1 T
53703160 TACCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (19 bp):
TAACTTTGGAGAGATTTTA
Found at i:53711663 original size:24 final size:23
Alignment explanation
Indices: 53711618--53711665 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
53711608 ATTTTTAATT
*
53711618 AATAAAATAATTAAATAAATAAA
1 AATAAAATAATTAAACAAATAAA
* *
53711641 AATAAAAGTAATTGAACATATAAA
1 AATAAAA-TAATTAAACAAATAAA
53711665 A
1 A
53711666 TACAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (23 bp):
AATAAAATAATTAAACAAATAAA
Found at i:53713290 original size:28 final size:28
Alignment explanation
Indices: 53713236--53713292 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
53713226 TAATTTGACA
* * * *
53713236 TTCTTTTTCTAATGTGATACTTGTATTT
1 TTCTTTGTCTAATATGATACCTATATTT
*
53713264 TTCTTTGTCTAATATGGTACCTATATTT
1 TTCTTTGTCTAATATGATACCTATATTT
53713292 T
1 T
53713293 ACAAAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (28 bp):
TTCTTTGTCTAATATGATACCTATATTT
Found at i:53713490 original size:21 final size:22
Alignment explanation
Indices: 53713464--53713508 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53713454 ATTTTGTTTG
53713464 ATAAATT-A-AATGCAAAACTAA
1 ATAAATTCACAAT-CAAAACTAA
53713485 ATAAATTCACAATCAAAACTAA
1 ATAAATTCACAATCAAAACTAA
53713507 AT
1 AT
53713509 TTATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 12 0.55
23 3 0.14
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAATTCACAATCAAAACTAA
Found at i:53723592 original size:8 final size:8
Alignment explanation
Indices: 53723581--53723648 Score: 56
Period size: 8 Copynumber: 9.0 Consensus size: 8
53723571 TGGTAACTCT
53723581 TAAAATTA
1 TAAAATTA
53723589 TAAAATT-
1 TAAAATTA
53723596 T--AATT-
1 TAAAATTA
* *
53723601 TAATATTT
1 TAAAATTA
53723609 TAAAATTA
1 TAAAATTA
*
53723617 TAAAAATA
1 TAAAATTA
53723625 T-AAATTA
1 TAAAATTA
*
53723632 TTAAAATAA
1 -TAAAATTA
53723641 TAAAATTA
1 TAAAATTA
53723649 CATTTTGAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
5 5 0.10
7 9 0.19
8 29 0.60
9 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAAATTA
Found at i:53723643 original size:16 final size:15
Alignment explanation
Indices: 53723611--53723644 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
53723601 TAATATTTTA
53723611 AAATTATAAAAATAT
1 AAATTATAAAAATAT
*
53723626 AAATTATTAAAATAAT
1 AAATTATAAAAAT-AT
53723642 AAA
1 AAA
53723645 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTATAAAAATAT
Found at i:53723661 original size:16 final size:16
Alignment explanation
Indices: 53723642--53723672 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53723632 TTAAAATAAT
53723642 AAAATTACATTTTGAG
1 AAAATTACATTTTGAG
*
53723658 AAAATTATATTTTGA
1 AAAATTACATTTTGA
53723673 CAATATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (16 bp):
AAAATTACATTTTGAG
Found at i:53729262 original size:12 final size:12
Alignment explanation
Indices: 53729242--53729275 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53729232 AATATAATAT
*
53729242 ATATAGATATCG
1 ATATAGATATCC
*
53729254 ATATCGATATCC
1 ATATAGATATCC
53729266 ATATAGATAT
1 ATATAGATAT
53729276 ATGTTATGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (12 bp):
ATATAGATATCC
Found at i:53735587 original size:18 final size:18
Alignment explanation
Indices: 53735543--53735589 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
53735533 TAAAAAATTG
*
53735543 TATTTAATTATAAATATAA
1 TATTTAA-TATAAATAAAA
*
53735562 T-TAATAATATAAATAAAA
1 TAT-TTAATATAAATAAAA
53735580 TATTTAATAT
1 TATTTAATAT
53735590 CGGAAACAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTTAATATAAATAAAA
Found at i:53739228 original size:17 final size:17
Alignment explanation
Indices: 53739206--53739239 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53739196 AAAATATTAT
53739206 TTAAATTAATTTCTCAA
1 TTAAATTAATTTCTCAA
*
53739223 TTAAATTATTTTCTCAA
1 TTAAATTAATTTCTCAA
53739240 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTAATTTCTCAA
Found at i:53744755 original size:29 final size:29
Alignment explanation
Indices: 53744684--53744772 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 29
53744674 ACCAAAAATT
*
53744684 TATTTTAAAAATTAAAACAAAAATTAAAAAAAG
1 TATTTTAAAAATT--AA-AAAAATT-TAAAAAG
53744717 TATTTT-AAAATTAAAAAAATTTAAAAAG
1 TATTTTAAAAATTAAAAAAATTTAAAAAG
**
53744745 TATTTTAAAAATTTTAAAAATTTAAAAA
1 TATTTTAAAAATTAAAAAAATTTAAAAA
53744773 ATTTAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 12 0.23
29 26 0.50
30 2 0.04
32 6 0.12
33 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (29 bp):
TATTTTAAAAATTAAAAAAATTTAAAAAG
Found at i:53744755 original size:40 final size:40
Alignment explanation
Indices: 53744711--53744823 Score: 140
Period size: 40 Copynumber: 2.8 Consensus size: 40
53744701 CAAAAATTAA
53744711 AAAAAGTATTTTAAAATTAAAAAAATTT-AAAAAGTATTTT
1 AAAAA-TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
* *
53744751 AAAAAT-TTTAAAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTT-AAAAAAGTATTTT
* * **
53744791 AGAATTATTTTAAAATTAAAAAAAAATAAAAAA
1 AAAAATATTTTAAAATTAAAAAAATTTAAAAAA
53744824 AATAAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
38 18 0.29
39 1 0.02
40 27 0.44
41 16 0.26
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
Found at i:53744783 original size:10 final size:9
Alignment explanation
Indices: 53744723--53744782 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
53744713 AAAGTATTTT
*
53744723 AAAATTAAA
1 AAAATTTAA
53744732 AAAATTTAA
1 AAAATTTAA
*
53744741 AAAGTATTTTA
1 AAA--ATTTAA
*
53744752 AAAATTTTA
1 AAAATTTAA
53744761 AAAATTTAA
1 AAAATTTAA
53744770 AAAATTTAA
1 AAAATTTAA
53744779 AAAA
1 AAAA
53744783 AGTATTTTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
9 38 0.83
11 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTTAA
Found at i:53744820 original size:10 final size:10
Alignment explanation
Indices: 53744802--53744834 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
53744792 GAATTATTTT
*
53744802 AAAATTAAAA
1 AAAAATAAAA
53744812 AAAAAT-AAA
1 AAAAATAAAA
53744821 AAAAATAAAA
1 AAAAATAAAA
53744831 AAAA
1 AAAA
53744835 TTATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:53744821 original size:9 final size:9
Alignment explanation
Indices: 53744809--53744835 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
53744799 TTTAAAATTA
53744809 AAAAAAAAT
1 AAAAAAAAT
53744818 AAAAAAAAT
1 AAAAAAAAT
53744827 AAAAAAAAT
1 AAAAAAAAT
53744836 TATTATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:53747525 original size:17 final size:17
Alignment explanation
Indices: 53747499--53747541 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
53747489 TTTTTTTTTG
53747499 TTTTTATAAAAAAATAA
1 TTTTTATAAAAAAATAA
*
53747516 TTTTTTTAAAAAAATATA
1 TTTTTATAAAAAAATA-A
*
53747534 TATTTATA
1 TTTTTATA
53747542 CGAGTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTATAAAAAAATAA
Found at i:53748182 original size:47 final size:47
Alignment explanation
Indices: 53748093--53748183 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
53748083 TAGTTTAATA
* *****
53748093 TTTTGTGATTTTTTATTAATGTAAAATTATTTTGTTAGTATTTTGTG
1 TTTTGTGATTTTTTAGTAATGTAAAATTAAAAAATTAGTATTTTGTG
53748140 TTTTGTGATTTTTTAGTAATGTAAAATTAAAAAATATA-TATTTT
1 TTTTGTGATTTTTTAGTAATGTAAAATTAAAAAAT-TAGTATTTT
53748184 TATAGTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 35 0.95
48 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (47 bp):
TTTTGTGATTTTTTAGTAATGTAAAATTAAAAAATTAGTATTTTGTG
Found at i:53748354 original size:101 final size:101
Alignment explanation
Indices: 53748182--53748432 Score: 479
Period size: 101 Copynumber: 2.5 Consensus size: 101
53748172 AATATATATT
*
53748182 TTTATAGTTATTTTTTTAGTAATTTATGATTA-GTT-TATAAATTGTTAGTGTTTAGTTTAGGGT
1 TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGGGT
53748245 TTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAAA
66 TTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAAA
53748281 TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGGGT
1 TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGGGT
53748346 TTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAAA
66 TTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAAA
53748382 TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGT
1 TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGT
53748433 AATTTATTTT
Statistics
Matches: 149, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
99 31 0.21
100 3 0.02
101 115 0.77
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (101 bp):
TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGGGT
TTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAAA
Found at i:53750910 original size:76 final size:76
Alignment explanation
Indices: 53750741--53751023 Score: 412
Period size: 76 Copynumber: 3.8 Consensus size: 76
53750731 ACTTTTTTGC
* * * *
53750741 CATTTTAGTTTTTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACCTTGTATTTATGTAAT
1 CATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT
53750806 GAC-TTTTCA-
66 GACTTTTTCAG
* * *
53750815 CTAATTCAGTAATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTAGGTAA
1 C-ATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAA
53750880 TGACTTTTTCAG
65 TGACTTTTTCAG
53750892 CATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT
1 CATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT
53750957 GACTTTTTC-G
66 GACTTTTTCAG
* * * * *
53750967 TCATTTCAGTTATTAATTTTTGGG-GTTTTTTGTAATTTAAATAATAAACTTTGTATT
1 -CATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATT
53751024 ATTTACGTAA
Statistics
Matches: 190, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
74 1 0.01
75 90 0.47
76 98 0.52
77 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.51
Consensus pattern (76 bp):
CATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT
GACTTTTTCAG
Found at i:53750996 original size:151 final size:151
Alignment explanation
Indices: 53750741--53751023 Score: 426
Period size: 151 Copynumber: 1.9 Consensus size: 151
53750731 ACTTTTTTGC
* *
53750741 CATTTTAGTTTTTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACCTTGTATTTATGTAAT
1 CATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACCTTGTATTTATGTAAT
* * *
53750806 GACTTTTCACTAATTCAGTAATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTA
66 GACTTTTCACTAATTCAGTAATTAATTTTAGGGTGTTTTTTGCAATTTAAATAATAAACTTTGTA
53750871 TTTAGGTAATGACTTTTTCAG
131 TTTAGGTAATGACTTTTTCAG
* *
53750892 CATTTCAGTTATTAATTTTAGGGTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT
1 CATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACCTTGTATTTATGTAAT
* * * * *
53750957 GACTTTTTC-GTCATTTCAGTTATTAATTTTTGGG-GTTTTTTGTAATTTAAATAATAAACTTTG
66 GAC-TTTTCACT-AATTCAGTAATTAATTTTAGGGTGTTTTTTGCAATTTAAATAATAAACTTTG
53751020 TATT
129 TATT
53751024 ATTTACGTAA
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
151 94 0.80
152 24 0.20
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.51
Consensus pattern (151 bp):
CATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACCTTGTATTTATGTAAT
GACTTTTCACTAATTCAGTAATTAATTTTAGGGTGTTTTTTGCAATTTAAATAATAAACTTTGTA
TTTAGGTAATGACTTTTTCAG
Found at i:53754095 original size:19 final size:19
Alignment explanation
Indices: 53754041--53754095 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
53754031 ATTCAGAAGC
* *
53754041 TAACAAAATTAATAAC--C
1 TAACAAAATTACTAACAAA
* **
53754058 TAACAAAATAACTTTCAAA
1 TAACAAAATTACTAACAAA
53754077 TAACAAAATTACTAACAAA
1 TAACAAAATTACTAACAAA
53754096 ACTCTCCATT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 12 0.43
19 16 0.57
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (19 bp):
TAACAAAATTACTAACAAA
Found at i:53754178 original size:18 final size:18
Alignment explanation
Indices: 53754133--53754185 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
53754123 AACTAAAATA
* *
53754133 CCTTATCTT-TTTTTTTT
1 CCTTATCTTCTTTCTTCT
* *
53754150 CCTTTTTTTCTTTCTTCT
1 CCTTATCTTCTTTCTTCT
*
53754168 CCTTATCTTCTTACTTCT
1 CCTTATCTTCTTTCTTCT
53754186 GTTCTGCTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (18 bp):
CCTTATCTTCTTTCTTCT
Found at i:53755498 original size:7 final size:7
Alignment explanation
Indices: 53755488--53755522 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
53755478 TTTGAGATTT
53755488 AAGGTTC
1 AAGGTTC
53755495 AAGGTTC
1 AAGGTTC
53755502 AAGGTTC
1 AAGGTTC
53755509 AAGGATTC
1 AAGG-TTC
*
53755517 GAGGTT
1 AAGGTT
53755523 ACAGGTTACG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (7 bp):
AAGGTTC
Found at i:53755507 original size:14 final size:15
Alignment explanation
Indices: 53755483--53755522 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
53755473 TTAGATTTGA
*
53755483 GATTTAAGGTTCAAG
1 GATTCAAGGTTCAAG
53755498 G-TTCAAGGTTCAAG
1 GATTCAAGGTTCAAG
*
53755512 GATTCGAGGTT
1 GATTCAAGGTT
53755523 ACAGGTTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (15 bp):
GATTCAAGGTTCAAG
Found at i:53758364 original size:20 final size:20
Alignment explanation
Indices: 53758339--53758378 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53758329 CATAAAATGA
*
53758339 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
53758359 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53758379 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53760210 original size:18 final size:19
Alignment explanation
Indices: 53760187--53760233 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
53760177 ACATATATGT
*
53760187 ATAATAATGATGAAAAT-A
1 ATAATAATAATGAAAATAA
53760205 ATAATAATAATGAAAATAA
1 ATAATAATAATGAAAATAA
53760224 ATAAT-ATAAT
1 ATAATAATAAT
53760234 AATAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (19 bp):
ATAATAATAATGAAAATAA
Found at i:53760213 original size:21 final size:21
Alignment explanation
Indices: 53760200--53760244 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
53760190 ATAATGATGA
53760200 AAATAATAATAATAATGAAAAT
1 AAATAAT-ATAATAATGAAAAT
53760222 AAATAATATAATAAT-AAATAT
1 AAATAATATAATAATGAAA-AT
53760243 AA
1 AA
53760245 TAGTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 12 0.55
22 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATAATATAATAATGAAAAT
Found at i:53760237 original size:15 final size:15
Alignment explanation
Indices: 53760202--53760241 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
53760192 AATGATGAAA
53760202 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
*
53760216 -GAA-AATAAATAAT
1 ATAATAATAAATAAT
53760229 ATAATAATAAATA
1 ATAATAATAAATA
53760242 TAATAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 3 0.14
13 8 0.38
14 2 0.10
15 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:53760315 original size:9 final size:8
Alignment explanation
Indices: 53760303--53760384 Score: 51
Period size: 9 Copynumber: 9.5 Consensus size: 8
53760293 ATAAATATGC
53760303 TAATATGAA
1 TAATAT-AA
53760312 TAATGATAA
1 TAAT-ATAA
53760321 TAATACTAA
1 TAATA-TAA
53760330 TAATAATAA
1 TAAT-ATAA
*
53760339 -AATACGAA
1 TAATA-TAA
*
53760347 GAAGTATATA
1 TAA-TATA-A
53760357 TAATATAA
1 TAATATAA
53760365 TAATATTAA
1 TAATA-TAA
*
53760374 -AATACAA
1 TAATATAA
53760381 TAAT
1 TAAT
53760385 TAAAAGTAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
7 3 0.05
8 19 0.32
9 30 0.50
10 8 0.13
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (8 bp):
TAATATAA
Found at i:53762459 original size:42 final size:41
Alignment explanation
Indices: 53762358--53762637 Score: 286
Period size: 40 Copynumber: 6.8 Consensus size: 41
53762348 GTTTTTTTCG
53762358 TCTGCTCCACTGA-TGCTTAGGGAGATAAGAC-TGGATGTGA
1 TCTGCTCCACT-ACTGCTTAGGGAGATAAGACTTGGATGTGA
* * *
53762398 TCTGCTCCACTAATGCTTAGGGAGATAAGATCTGTGGTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGTGA
* * *
53762440 TCTGCTCCGCTACTACTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGTGA
* *
53762480 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGTGA
** * *
53762522 TCCACTCCGCTACTGCTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGTGA
* * * * *
53762562 TCTGCTCCATTATTGCTTAAGGAGATAAGATCTGTGGTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGTGA
*
53762604 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTG
53762638 CAACTTTTGA
Statistics
Matches: 198, Mismatches: 30, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
39 7 0.04
40 84 0.42
41 11 0.06
42 84 0.42
43 12 0.06
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGTGA
Found at i:53762462 original size:82 final size:82
Alignment explanation
Indices: 53762352--53762637 Score: 430
Period size: 82 Copynumber: 3.5 Consensus size: 82
53762342 AGATTGGTTT
* * *
53762352 TTTTCGTCTGCTCCACTGA-TGCTTAGGGAGATAAGACTGGATGTGATCTGCTCCACTAATGCTT
1 TTTT-GTCTGCTCCGCT-ACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTT
53762416 AGGGAGATAAGATCTGTGG
64 AGGGAGATAAGATCTGTGG
* *
53762435 TTTTGTCTGCTCCGCTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
1 TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAG
53762500 GGAGATAAGATCTGTGG
66 GGAGATAAGATCTGTGG
** * * *
53762517 TTTTGTCCACTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCATTATTGCTTAA
1 TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAG
53762582 GGAGATAAGATCTGTGG
66 GGAGATAAGATCTGTGG
* * *
53762599 TTCTGTCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTG
53762638 CAACTTTTGA
Statistics
Matches: 186, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
81 1 0.01
82 181 0.97
83 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (82 bp):
TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTAATGCTTAG
GGAGATAAGATCTGTGG
Found at i:53763053 original size:72 final size:72
Alignment explanation
Indices: 53762816--53763155 Score: 486
Period size: 72 Copynumber: 4.6 Consensus size: 72
53762806 AACATGTGAA
* *
53762816 CTGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
53762880 TCAGCGTGTC
63 TCAGCGTGTC
*
53762890 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTC
*
53762955 AACGTGTC
65 AGCGTGTC
* *
53762963 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
53763028 GCGTGTC
66 GCGTGTC
* *
53763035 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTAACAACAGAAATTGAAATTA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----ATTTTGAA-AACAGAAATTGAAATTA
53763100 CCTCAGCGTGTC
61 CCTCAGCGTGTC
** *
53763112 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
53763156 AGTAGAAATT
Statistics
Matches: 242, Mismatches: 17, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
71 2 0.01
72 72 0.30
73 71 0.29
74 31 0.13
76 6 0.02
77 60 0.25
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (72 bp):
CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTC
Found at i:53763265 original size:73 final size:71
Alignment explanation
Indices: 53763173--53763364 Score: 235
Period size: 69 Copynumber: 2.7 Consensus size: 71
53763163 ATTAAAAGGT
* * * * *
53763173 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGA-AAACAGAAATTAAAAATACCTCAGCGTGC
*
53763238 CCTGAGGC
64 CCCGAGGC
* * * * *
53763246 TCAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCGGCGTGCCC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAATACCTCAGCGTGCCC
53763309 CGAGGC
66 CGAGGC
*
53763315 TCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAGAAATTAAAA
53763365 GGTTCAACCC
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
69 52 0.52
70 6 0.06
71 2 0.02
72 17 0.17
73 23 0.23
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAATACCTCAGCGTGCCC
CGAGGC
Found at i:53763395 original size:53 final size:54
Alignment explanation
Indices: 53763315--53763446 Score: 230
Period size: 54 Copynumber: 2.5 Consensus size: 54
53763305 GCCCCGAGGC
*
53763315 TCAACTCACTTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
* *
53763368 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
53763422 TCAACTCACCTCTCGCAATATGAGT
1 TCAACTCACCTCTCGCAATATGAGT
53763447 CAATTTAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 26 0.35
54 48 0.65
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (54 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
Found at i:53763540 original size:176 final size:176
Alignment explanation
Indices: 53763246--53763622 Score: 754
Period size: 176 Copynumber: 2.1 Consensus size: 176
53763236 GTCCTGAGGC
53763246 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
1 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
53763311 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
66 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
53763376 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
131 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
53763422 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
1 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
53763487 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
66 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
53763552 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
131 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
53763598 TCAACTCACCTCTCGCAATATGAGT
1 TCAACTCACCTCTCGCAATATGAGT
53763623 TGATTTTTTG
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 201 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (176 bp):
TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
Found at i:53763601 original size:54 final size:54
Alignment explanation
Indices: 53763491--53763689 Score: 328
Period size: 54 Copynumber: 3.7 Consensus size: 54
53763481 GCCCCGAGGC
*
53763491 TCAACTCACTTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
* *
53763544 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
* *
53763598 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTAAAAGGT
*
53763653 TCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
53763690 CTTAATTTGA
Statistics
Matches: 136, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
53 26 0.19
54 60 0.44
55 50 0.37
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (54 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
Found at i:53763680 original size:109 final size:107
Alignment explanation
Indices: 53763491--53763689 Score: 335
Period size: 109 Copynumber: 1.8 Consensus size: 107
53763481 GCCCCGAGGC
* *
53763491 TCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCACCTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTC
53763556 TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
66 TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
* *
53763598 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACC
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTGAAAAACAGAAATTAAAAGGCTCAACCCACC
*
53763663 TCTCGTAATATGAGTTGATTTTTGAAA
64 TCTCGCAATATGAGTTGATTTTTGAAA
53763690 CTTAATTTGA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
107 27 0.32
109 58 0.68
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (107 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTC
TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
Found at i:53763810 original size:72 final size:73
Alignment explanation
Indices: 53763695--53764000 Score: 494
Period size: 73 Copynumber: 4.2 Consensus size: 73
53763685 TGAAACTTAA
** * *
53763695 TTTGAAAAGCAGATTTTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
53763760 AGTTGAAT
66 AGTTGAAT
*
53763768 TTTGAAAA-CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
53763832 AGTTGAAT
66 AGTTGAAT
* *
53763840 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
53763905 AGTTGAAT
66 AGTTGAAT
*
53763913 TTTGAAAAGCA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
1 TTTGAAAAGCAGAA-ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
53763977 GAGTTGAATT
65 GAGTTGAA-T
53763987 TTTG-AAA-CAGAAAT
1 TTTGAAAAGCAGAAAT
53764001 AAAAGCATCA
Statistics
Matches: 219, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
72 73 0.33
73 141 0.64
74 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (73 bp):
TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
AGTTGAAT
Found at i:53763874 original size:145 final size:147
Alignment explanation
Indices: 53763695--53763993 Score: 532
Period size: 145 Copynumber: 2.0 Consensus size: 147
53763685 TGAAACTTAA
* **
53763695 TTTGAAAAGCAGATTTTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
1 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
53763760 AGTTGAATTTTGAAAA-CAGAA-ATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
66 AGTTGAATTTTGAAAAGCA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
53763823 CGCAATATGAGTTGAA-T
130 CGCAATATGAGTTGAATT
*
53763840 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
53763905 AGTTGAATTTTGAAAAGCAAAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTC
66 AGTTGAATTTTGAAAAGCAAAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTC
53763970 GCAATATGAGTTGAATT
131 GCAATATGAGTTGAATT
53763987 TTTGAAA
1 TTTGAAA
53763994 CAGAAATAAA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
145 79 0.54
146 60 0.41
147 8 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (147 bp):
TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
AGTTGAATTTTGAAAAGCAAAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTC
GCAATATGAGTTGAATT
Found at i:53766156 original size:1 final size:1
Alignment explanation
Indices: 53766150--53766211 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
53766140 TGGCATTTGA
* * * * * * *
53766150 TTTTTTTTGTTTTTTTTCTTGTCTTTTTTTCTTTTTGTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53766212 CATGACTGTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.06, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:53766184 original size:28 final size:27
Alignment explanation
Indices: 53766153--53766211 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
53766143 CATTTGATTT
53766153 TTTTTGTTTTTTTTCTTGTCTTTTTTTC
1 TTTTTGTTTTTTTT-TTGTCTTTTTTTC
* *
53766181 TTTTTGTTTTTTTTTTTTTTTTTTTTC
1 TTTTTGTTTTTTTTTTGTCTTTTTTTC
53766208 TTTT
1 TTTT
53766212 CATGACTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (27 bp):
TTTTTGTTTTTTTTTTGTCTTTTTTTC
Found at i:53766211 original size:13 final size:13
Alignment explanation
Indices: 53766150--53766211 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
53766140 TGGCATTTGA
*
53766150 TTTTT-TTTGTTT
1 TTTTTCTTTTTTT
* *
53766162 TTTTTCTTGTCTT
1 TTTTTCTTTTTTT
53766175 TTTTTCTTTTTGTT
1 TTTTTCTTTTT-TT
*
53766189 TTTTTTTTTTTTT
1 TTTTTCTTTTTTT
53766202 TTTTTCTTTT
1 TTTTTCTTTT
53766212 CATGACTGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
12 5 0.12
13 24 0.59
14 12 0.29
ACGTcount: A:0.00, C:0.06, G:0.05, T:0.89
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:53770191 original size:1 final size:1
Alignment explanation
Indices: 53770185--53770216 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
53770175 CTTGCTTCCT
53770185 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53770217 TTTGGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:53771716 original size:86 final size:84
Alignment explanation
Indices: 53771452--53771752 Score: 279
Period size: 86 Copynumber: 3.5 Consensus size: 84
53771442 GAAGACAAAG
* * **
53771452 GATCTTGCCTT-CTGCATTGACAGCGAAGCAGATCGAAGACACAA-CCTTGCCTCTTTGTTCGGT
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCTC---CATCGGT
* * * *
53771515 TGTGATAGAGCTGGTTGAAGACAAAA
62 TG-CATGGAGC-AGTTGAAG-CAAGA
* * *
53771541 GATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGC
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCCATCGGTTGC
*
53771605 AGTGGAGCTAGTTAAAG-AAGCA
65 A-TGGAGC-AGTTGAAGCAAG-A
53771627 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
*
53771692 TTGGAGCAGATTGAAGCCAGA
66 -TGGAGCAG-TTGAAGCAAGA
** * * *
53771713 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAAAGA
1 GATCTTGCCTTCCTG-CATTAACAGCGAAGCAGATCAAAGA
53771753 TAGTAATCCT
Statistics
Matches: 180, Mismatches: 23, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
85 7 0.04
86 103 0.57
87 23 0.13
89 13 0.07
90 32 0.18
91 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
TGGAGCAGTTGAAGCAAGA
Found at i:53771934 original size:44 final size:43
Alignment explanation
Indices: 53771878--53771993 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
53771868 GAAGAATTGC
* *
53771878 AGATCTTATCCCCCTGAAGTTACAGTGGAGCAGATTGAAGCCA
1 AGATCTTATCCCCCTGAAGTTACAGTGGAGCAGATCGAAGACA
*
53771921 GAGATCTTATCCCCC-G-AGATTACAGCGGAGCAGATCGAAGACA
1 -AGATCTTATCCCCCTGAAG-TTACAGTGGAGCAGATCGAAGACA
** * *
53771964 CTATCCTATCTCCCTGAAGTTACAGTGGAG
1 AGATCTTATCCCCCTGAAGTTACAGTGGAG
53771994 TGGGTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 12 0.20
43 33 0.54
44 16 0.26
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (43 bp):
AGATCTTATCCCCCTGAAGTTACAGTGGAGCAGATCGAAGACA
Found at i:53773512 original size:3 final size:3
Alignment explanation
Indices: 53773475--53773504 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
53773465 AATCTAGTCC
*
53773475 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53773505 GTTATTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:53775865 original size:21 final size:20
Alignment explanation
Indices: 53775839--53775877 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
53775829 AACTCGAACA
53775839 ATTTCACTCAACTCGAATTTC
1 ATTTCACTCAACTC-AATTTC
*
53775860 ATTTCACTCAGCTCAATT
1 ATTTCACTCAACTCAATT
53775878 CAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTCACTCAACTCAATTTC
Found at i:53790235 original size:3 final size:3
Alignment explanation
Indices: 53790212--53790397 Score: 109
Period size: 3 Copynumber: 62.0 Consensus size: 3
53790202 GAGGGAAGAG
* * *
53790212 TAT TAT TTT TAA TAT TGT TAT TAT TAT TAT ATAT TAT TACT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TA-T TAT TAT
* * * *
53790259 TAT TA- TATT TAT TA- TAT TA- TATT TAT T-T TAT TAC TGT TAC TGT
1 TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * *
53790302 TAT T-T TA- TAT ATATT TAT TAC CAT TAT ATATT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT -TA-T TAT TAT TAT TAT -TA-T TAT TAT TAT TAT TAT
* * * * *
53790349 TAA CA- TAT TGT TAT TTT TAT TAT T-T TAT TAT TAT TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53790395 TAT
1 TAT
53790398 CATGGTACTA
Statistics
Matches: 139, Mismatches: 28, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
2 15 0.11
3 104 0.75
4 18 0.13
5 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:53790258 original size:23 final size:22
Alignment explanation
Indices: 53790224--53790397 Score: 117
Period size: 23 Copynumber: 7.8 Consensus size: 22
53790214 TTATTTTTAA
*
53790224 TATTGTTATTATTATTATATAT
1 TATTATTATTATTATTATATAT
53790246 TATTACTTATTATTATTATAT-T
1 TATTA-TTATTATTATTATATAT
*
53790268 TATTA-TATTA-TATT-TATTT
1 TATTATTATTATTATTATATAT
* * *
53790287 TATTACTGTTACTGTTATTTTATA-
1 TATTA---TTATTATTATTATATAT
**
53790311 TA-TATTTATTACCATTATATATT
1 TATTA-TTATTATTATTATATA-T
* *
53790334 TATTATTATTATTAGTAACATAT
1 TATTATTATTATTA-TTATATAT
* * *
53790357 TGTTATTTTTATTATTTTATTAT
1 TATTATTATTATTATTATA-TAT
*
53790380 TATTATTCTTATTATTAT
1 TATTATTATTATTATTAT
53790398 CATGGTACTA
Statistics
Matches: 117, Mismatches: 22, Indels: 25
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.03
19 10 0.09
20 5 0.04
21 11 0.09
22 12 0.10
23 60 0.51
24 13 0.11
25 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (22 bp):
TATTATTATTATTATTATATAT
Found at i:53790278 original size:14 final size:14
Alignment explanation
Indices: 53790241--53790291 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
53790231 ATTATTATTA
*
53790241 TATATTATTACTTAT
1 TATATTA-TATTTAT
53790256 TATTATTATATTTAT
1 TA-TATTATATTTAT
53790271 TATATTATATTTAT
1 TATATTATATTTAT
*
53790285 TTTATTA
1 TATATTA
53790292 CTGTTACTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 18 0.55
15 10 0.30
16 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATATTATATTTAT
Found at i:53795907 original size:3 final size:3
Alignment explanation
Indices: 53795899--53795929 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53795889 TCTAGGAACC
53795899 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53795930 CAGCAGTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53799464 original size:51 final size:51
Alignment explanation
Indices: 53799401--53799509 Score: 209
Period size: 51 Copynumber: 2.1 Consensus size: 51
53799391 AATCAGCAGT
53799401 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
1 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
53799452 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
1 ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
*
53799503 ATACTAT
1 ATCCTAT
53799510 CTATATCTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (51 bp):
ATCCTATAAAACTCGATAGTATGGTAGAAAAAAAATATGAATCTTTCTACC
Found at i:53810933 original size:31 final size:31
Alignment explanation
Indices: 53810895--53810955 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
53810885 CGTATGCTAG
* *
53810895 GCCATGTGGGTCAAATGGGCCAAATACCCAA
1 GCCATGTGGGTCAAACGGGCCAAACACCCAA
*
53810926 GCCATGTGGGTCACACGGGCCAAACACCCA
1 GCCATGTGGGTCAAACGGGCCAAACACCCA
53810956 GGCCGTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.13
Consensus pattern (31 bp):
GCCATGTGGGTCAAACGGGCCAAACACCCAA
Found at i:53813411 original size:21 final size:22
Alignment explanation
Indices: 53813382--53813422 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
53813372 TAACTATAAT
53813382 GTAAAAACAATGAT-ATAAATA
1 GTAAAAACAATGATGATAAATA
*
53813403 GTAACAACAATGATGATAAA
1 GTAAAAACAATGATGATAAA
53813423 ATATAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (22 bp):
GTAAAAACAATGATGATAAATA
Found at i:53813468 original size:25 final size:23
Alignment explanation
Indices: 53813431--53813483 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
53813421 AAATATAAGA
*
53813431 AATAATAGAATAATGGCAA-TAAT
1 AATAATAGAATAATAG-AATTAAT
53813454 AATAAGTAGTAATAATAGAATTAAT
1 AATAA-TAG-AATAATAGAATTAAT
53813479 AATAA
1 AATAA
53813484 AAATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 16 0.62
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.28
Consensus pattern (23 bp):
AATAATAGAATAATAGAATTAAT
Found at i:53816193 original size:33 final size:34
Alignment explanation
Indices: 53816156--53816225 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
53816146 AAAATAGAAG
* *
53816156 TTTTAGGTTCATTAAAAGTTGGTA-AATATTTTT
1 TTTTAGGTCCATTAAAAGTTGGTAGAAAATTTTT
* *
53816189 TTTTATGTCCCTTAAAAGTTGGTAGAAAATTTTT
1 TTTTAGGTCCATTAAAAGTTGGTAGAAAATTTTT
53816223 TTT
1 TTT
53816226 GAGCCTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 21 0.66
34 11 0.34
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (34 bp):
TTTTAGGTCCATTAAAAGTTGGTAGAAAATTTTT
Found at i:53816236 original size:32 final size:33
Alignment explanation
Indices: 53816167--53816240 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
53816157 TTTAGGTTCA
* *
53816167 TTAAAAGTTGGTAAATATTTTTTTTTATGTCCC
1 TTAAAAGTTGGTAAAAATTTTTTTTGATGTCCC
*
53816200 TTAAAAGTTGGTAGAAAATTTTTTTTGA-G-CCT
1 TTAAAAGTTGGTA-AAAATTTTTTTTGATGTCCC
53816232 TTAAAAGTT
1 TTAAAAGTT
53816241 AGAAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 11 0.30
33 14 0.38
34 12 0.32
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (33 bp):
TTAAAAGTTGGTAAAAATTTTTTTTGATGTCCC
Found at i:53816244 original size:29 final size:29
Alignment explanation
Indices: 53816211--53816335 Score: 98
Period size: 29 Copynumber: 4.3 Consensus size: 29
53816201 TAAAAGTTGG
*
53816211 TAGAAAATTTTTTTTGAGCCTTTAAAAGT
1 TAGAAAAATTTTTTTGAGCCTTTAAAAGT
** * * *
53816240 TAGAAAAAAAATTTTGGGGCCCCTTAAAAGT
1 TAG-AAAAATTTTTTTGAG-CCTTTAAAAGT
53816271 T-GATAACAATTTTTTTGA-CCTTTAAAAGT
1 TAGA-AA-AATTTTTTTGAGCCTTTAAAAGT
* *
53816300 T--AAAAATTTTTTTGGGCCTCTTAAAAAT
1 TAGAAAAATTTTTTTGAGCCT-TTAAAAGT
53816328 TA-AAAAAT
1 TAGAAAAAT
53816336 AATATTTCGA
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
26 10 0.13
27 5 0.07
28 9 0.12
29 21 0.28
30 13 0.17
31 18 0.24
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (29 bp):
TAGAAAAATTTTTTTGAGCCTTTAAAAGT
Found at i:53816332 original size:27 final size:26
Alignment explanation
Indices: 53816278--53816333 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 26
53816268 AGTTGATAAC
*
53816278 AATTTTTTTGACCTTTAAAAGTTAAA
1 AATTTTTTTGACCTTTAAAAATTAAA
*
53816304 AATTTTTTTGGGCCTCTTAAAAATTAAA
1 AATTTTTTT-GACCT-TTAAAAATTAAA
53816332 AA
1 AA
53816334 ATAATATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
27 4 0.15
28 13 0.50
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (26 bp):
AATTTTTTTGACCTTTAAAAATTAAA
Found at i:53816908 original size:31 final size:31
Alignment explanation
Indices: 53816860--53816954 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
53816850 CATTTATATT
* **
53816860 TTATATATTATTATATTAAATTATTTGAATA
1 TTATTTATTATTATATTAAATTATTCAAATA
* *
53816891 -TAGTTTATTTTTATATTAAATTACTCAAATA
1 TTA-TTTATTATTATATTAAATTATTCAAATA
* *
53816922 TTATTTATTATTATATTTAATTATTAAAATA
1 TTATTTATTATTATATTAAATTATTCAAATA
53816953 TT
1 TT
53816955 TTTGTAAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 2 0.04
31 49 0.92
32 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TTATTTATTATTATATTAAATTATTCAAATA
Found at i:53819103 original size:22 final size:24
Alignment explanation
Indices: 53819068--53819112 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
53819058 TTATTAAATA
* *
53819068 TTAAAATAATATAATATAAATATT
1 TTAAAATAATATAAAAAAAATATT
53819092 TTAAAA-AA-ATAAAAAAAATAT
1 TTAAAATAATATAAAAAAAATAT
53819113 GGACGAGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TTAAAATAATATAAAAAAAATATT
Found at i:53819424 original size:15 final size:16
Alignment explanation
Indices: 53819406--53819438 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53819396 TATTTATTAA
*
53819406 ATTTATAAT-TATTTT
1 ATTTAAAATGTATTTT
53819421 ATTTAAAATGTATTTT
1 ATTTAAAATGTATTTT
53819437 AT
1 AT
53819439 GTCACTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTAAAATGTATTTT
Found at i:53821774 original size:7 final size:7
Alignment explanation
Indices: 53821762--53821790 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
53821752 GAGGCAGCCG
53821762 ATTGACA
1 ATTGACA
53821769 ATTGACA
1 ATTGACA
53821776 ATTGACA
1 ATTGACA
53821783 ATTGACA
1 ATTGACA
53821790 A
1 A
53821791 CCCCACCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (7 bp):
ATTGACA
Found at i:53821841 original size:25 final size:27
Alignment explanation
Indices: 53821813--53821876 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
53821803 TAAGAAAGGA
53821813 ACAAGTAA-G-AGTTCCAAGTTGGTTG
1 ACAAGTAAGGAAGTTCCAAGTTGGTTG
53821838 ACAAGTAATAGTGTAAGTTCCAAGTTGGTTG
1 ACAAGT-A-AG-G-AAGTTCCAAGTTGGTTG
53821869 ACAAGTAA
1 ACAAGTAA
53821877 TAGTGTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
25 6 0.18
26 1 0.03
27 1 0.03
29 2 0.06
30 1 0.03
31 22 0.67
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (27 bp):
ACAAGTAAGGAAGTTCCAAGTTGGTTG
Found at i:53821857 original size:31 final size:31
Alignment explanation
Indices: 53821822--53821884 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
53821812 AACAAGTAAG
53821822 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
1 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
53821853 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
1 AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
53821884 A
1 A
53821885 TTACAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (31 bp):
AGTTCCAAGTTGGTTGACAAGTAATAGTGTA
Found at i:53824108 original size:18 final size:19
Alignment explanation
Indices: 53824085--53824131 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
53824075 ACATATATGT
*
53824085 ATAATAATGATGAAAAT-A
1 ATAATAATAATGAAAATAA
53824103 ATAATAATAATGAAAATAA
1 ATAATAATAATGAAAATAA
53824122 ATAAT-ATAAT
1 ATAATAATAAT
53824132 AATAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (19 bp):
ATAATAATAATGAAAATAA
Found at i:53824111 original size:21 final size:21
Alignment explanation
Indices: 53824098--53824142 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
53824088 ATAATGATGA
53824098 AAATAATAATAATAATGAAAAT
1 AAATAAT-ATAATAATGAAAAT
53824120 AAATAATATAATAAT-AAATAT
1 AAATAATATAATAATGAAA-AT
53824141 AA
1 AA
53824143 TAGTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 12 0.55
22 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATAATATAATAATGAAAAT
Found at i:53824135 original size:15 final size:15
Alignment explanation
Indices: 53824100--53824139 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
53824090 AATGATGAAA
53824100 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
*
53824114 -GAA-AATAAATAAT
1 ATAATAATAAATAAT
53824127 ATAATAATAAATA
1 ATAATAATAAATA
53824140 TAATAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 3 0.14
13 8 0.38
14 2 0.10
15 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:53826353 original size:42 final size:41
Alignment explanation
Indices: 53826252--53826531 Score: 286
Period size: 40 Copynumber: 6.8 Consensus size: 41
53826242 GTTTTTTTCG
53826252 TCTGCTCCACTGA-TGCTTAGGGAGATAAGAC-TGGATGTGA
1 TCTGCTCCACT-ACTGCTTAGGGAGATAAGACTTGGATGTGA
* * *
53826292 TCTGCTCCACTGCTGCTTAGGGAGATAAGATCTGTGGTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGTGA
* * *
53826334 TCTGCTCCGCTACTACTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGTGA
* *
53826374 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGTGA
** * *
53826416 TCCACTCCGCTACTGCTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGTGA
* * * * *
53826456 TCTACTCCATTATTGCTTAGGGAGATAAGATCTGTGGTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGTGA
*
53826498 TCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTG
53826532 CAACTTTTGA
Statistics
Matches: 199, Mismatches: 29, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
39 6 0.03
40 86 0.43
41 11 0.06
42 84 0.42
43 12 0.06
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGTGA
Found at i:53826353 original size:82 final size:82
Alignment explanation
Indices: 53826246--53826531 Score: 430
Period size: 82 Copynumber: 3.5 Consensus size: 82
53826236 AGATTGGTTT
* * * *
53826246 TTTTCGTCTGCTCCACTGA-TGCTTAGGGAGATAAGACTGGATGTGATCTGCTCCACTGCTGCTT
1 TTTT-GTCTGCTCCGCT-ACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTT
53826310 AGGGAGATAAGATCTGTGG
64 AGGGAGATAAGATCTGTGG
*
53826329 TTTTGTCTGCTCCGCTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
1 TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
53826394 GGAGATAAGATCTGTGG
66 GGAGATAAGATCTGTGG
** * * *
53826411 TTTTGTCCACTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTACTCCATTATTGCTTAG
1 TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
53826476 GGAGATAAGATCTGTGG
66 GGAGATAAGATCTGTGG
* * *
53826493 TTCTGTCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTG
53826532 CAACTTTTGA
Statistics
Matches: 186, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
81 1 0.01
82 181 0.97
83 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (82 bp):
TTTTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
GGAGATAAGATCTGTGG
Found at i:53826863 original size:73 final size:72
Alignment explanation
Indices: 53826710--53827047 Score: 500
Period size: 72 Copynumber: 4.6 Consensus size: 72
53826700 AACATGTGAA
* *
53826710 CTGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
53826774 TCAGCGTGTC
63 TCAGCGTGTC
*
53826784 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTC
*
53826849 AACGTGTC
65 AGCGTGTC
* *
53826857 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
53826922 GCGTGTC
66 GCGTGTC
* *
53826929 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAA-AACAGAAATTGAAATTACC
53826994 TCAGCGTGTC
63 TCAGCGTGTC
** *
53827004 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
53827048 AGTAGAAATT
Statistics
Matches: 242, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
71 2 0.01
72 72 0.30
73 71 0.29
74 37 0.15
75 60 0.25
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (72 bp):
CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTC
Found at i:53827013 original size:147 final size:145
Alignment explanation
Indices: 53826710--53827047 Score: 502
Period size: 147 Copynumber: 2.3 Consensus size: 145
53826700 AACATGTGAA
* *
53826710 CTGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
53826774 TCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTG
63 TCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTG
53826839 AAAATACCTCAACGTGTC
128 AAAATACCTCAACGTGTC
* *
53826857 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
* *
53826922 GCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAA-CAGAAATTG
66 GCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAA-AAGCAGAAATTG
* *
53826986 AAATTACCTCAGCGTGTC
128 AAAATACCTCAACGTGTC
** *
53827004 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
53827048 AGTAGAAATT
Statistics
Matches: 174, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
145 70 0.40
146 13 0.07
147 89 0.51
148 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (145 bp):
CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAA
ATACCTCAACGTGTC
Found at i:53827157 original size:73 final size:71
Alignment explanation
Indices: 53827065--53827256 Score: 226
Period size: 69 Copynumber: 2.7 Consensus size: 71
53827055 ATTAAAAGGT
* * * * *
53827065 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGA-AAACAGAAATTAAAAATACCTCAGCGTGC
*
53827130 CCTGAGGC
64 CCCGAGGC
* * * * *
53827138 TCAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCGGCGTGCCC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAATACCTCAGCGTGCCC
53827201 CGAGGC
66 CGAGGC
* *
53827207 TCAACTCACTTTTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAGAAATTAAAA
53827257 GGTTCAACCC
Statistics
Matches: 99, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
69 51 0.52
70 6 0.06
71 2 0.02
72 17 0.17
73 23 0.23
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAATACCTCAGCGTGCCC
CGAGGC
Found at i:53827287 original size:53 final size:54
Alignment explanation
Indices: 53827219--53827338 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
53827209 AACTCACTTT
53827219 TCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTAAAAGGTTCAACCCACCTC
1 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGTTCAACCCACCTC
* *
53827272 TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGTTCAACTCACCTC
1 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGTTCAACCCACCTC
53827326 TCGCAATATGAGT
1 TCGCAATATGAGT
53827339 CAATTTAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
53 16 0.25
54 48 0.75
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (54 bp):
TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGTTCAACCCACCTC
Found at i:53827432 original size:176 final size:176
Alignment explanation
Indices: 53827138--53827514 Score: 736
Period size: 176 Copynumber: 2.1 Consensus size: 176
53827128 GTCCTGAGGC
53827138 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
1 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
*
53827203 AGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
66 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
53827268 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
131 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
53827314 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
1 TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
*
53827379 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAATAGAAATTAAAAGGTTCAACCCA
66 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
53827444 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
131 CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
53827490 TCAACTCACCTCTCGCAATATGAGT
1 TCAACTCACCTCTCGCAATATGAGT
53827515 TGATTTTTTG
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 199 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (176 bp):
TCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGTTCAACCCA
CCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
Found at i:53827493 original size:54 final size:54
Alignment explanation
Indices: 53827383--53827581 Score: 319
Period size: 54 Copynumber: 3.7 Consensus size: 54
53827373 GCCCCGAGGC
* *
53827383 TCAACTCACTTCTCGCAATATGAGTTGA-TTTTGAAAAATAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
* *
53827436 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
* *
53827490 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTAAAAGGT
*
53827545 TCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
53827582 CTTAATTTGA
Statistics
Matches: 135, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
53 26 0.19
54 59 0.44
55 50 0.37
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (54 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
Found at i:53827572 original size:109 final size:107
Alignment explanation
Indices: 53827383--53827581 Score: 326
Period size: 109 Copynumber: 1.8 Consensus size: 107
53827373 GCCCCGAGGC
* * *
53827383 TCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAATAGAAATTAAAAGGTTCAACCCACCTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTC
53827448 TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
66 TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
* *
53827490 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACC
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTGAAAAACAGAAATTAAAAGGCTCAACCCACC
*
53827555 TCTCGTAATATGAGTTGATTTTTGAAA
64 TCTCGCAATATGAGTTGATTTTTGAAA
53827582 CTTAATTTGA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 27 0.32
109 57 0.68
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (107 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTC
TCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
Found at i:53827702 original size:72 final size:73
Alignment explanation
Indices: 53827587--53827892 Score: 494
Period size: 73 Copynumber: 4.2 Consensus size: 73
53827577 TGAAACTTAA
** * *
53827587 TTTGAAAAGCAGATTTTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
53827652 AGTTGAAT
66 AGTTGAAT
*
53827660 TTTGAAAA-CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
53827724 AGTTGAAT
66 AGTTGAAT
* *
53827732 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
53827797 AGTTGAAT
66 AGTTGAAT
*
53827805 TTTGAAAAGCA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
1 TTTGAAAAGCAGAA-ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
53827869 GAGTTGAATT
65 GAGTTGAA-T
53827879 TTTG-AAA-CAGAAAT
1 TTTGAAAAGCAGAAAT
53827893 AAAAGCATCA
Statistics
Matches: 219, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
72 73 0.33
73 141 0.64
74 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (73 bp):
TTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
AGTTGAAT
Found at i:53827766 original size:145 final size:147
Alignment explanation
Indices: 53827587--53827885 Score: 532
Period size: 145 Copynumber: 2.0 Consensus size: 147
53827577 TGAAACTTAA
* **
53827587 TTTGAAAAGCAGATTTTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
1 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
53827652 AGTTGAATTTTGAAAA-CAGAA-ATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
66 AGTTGAATTTTGAAAAGCA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
53827715 CGCAATATGAGTTGAA-T
130 CGCAATATGAGTTGAATT
*
53827732 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
53827797 AGTTGAATTTTGAAAAGCAAAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTC
66 AGTTGAATTTTGAAAAGCAAAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTC
53827862 GCAATATGAGTTGAATT
131 GCAATATGAGTTGAATT
53827879 TTTGAAA
1 TTTGAAA
53827886 CAGAAATAAA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
145 79 0.54
146 60 0.41
147 8 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (147 bp):
TTTGAAAAGCAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAAAATG
AGTTGAATTTTGAAAAGCAAAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTC
GCAATATGAGTTGAATT
Found at i:53829555 original size:69 final size:69
Alignment explanation
Indices: 53829421--53829555 Score: 164
Period size: 69 Copynumber: 2.0 Consensus size: 69
53829411 AAACCCCTTT
* * * ** * * *
53829421 GGTCTCAAGGTGCCCTTTGCGGGTTTTCACCTTGACCTCTCCATTTTCTTTTTTTTTTGAATGAA
1 GGTCACAAGGCGCCCTTTGCGGGTTTTCACCTTGACCACTCCATTTTCAGTATTTCTGGAATGAA
53829486 TGAA
66 TGAA
* *
53829490 GGTCACAAGGCGCCCTTTGCGGGTTTTCACCTTGGCCACTCC-TTTTCAAGTATTTCTGGACTGA
1 GGTCACAAGGCGCCCTTTGCGGGTTTTCACCTTGACCACTCCATTTTC-AGTATTTCTGGAATGA
53829554 AT
65 AT
53829556 CCGAATTTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 5 0.09
69 50 0.91
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (69 bp):
GGTCACAAGGCGCCCTTTGCGGGTTTTCACCTTGACCACTCCATTTTCAGTATTTCTGGAATGAA
TGAA
Found at i:53830060 original size:1 final size:1
Alignment explanation
Indices: 53830054--53830116 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
53830044 TGGCATTTGA
* * * * * * * *
53830054 TTTTTTTTTGTTTTTTTTCTTGTCTTTTTTTCTTTTTGTTTTTTTTTTCTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53830117 CATGACTGTC
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:53830069 original size:10 final size:10
Alignment explanation
Indices: 53830054--53830116 Score: 60
Period size: 9 Copynumber: 6.4 Consensus size: 10
53830044 TGGCATTTGA
53830054 TTTTTTTTT-
1 TTTTTTTTTC
*
53830063 GTTTTTTTTC
1 TTTTTTTTTC
53830073 TTGTCTTTTTT-
1 TT-T-TTTTTTC
* *
53830084 TCTTTTTGT-
1 TTTTTTTTTC
53830093 TTTTTTTTTC
1 TTTTTTTTTC
53830103 TTTTTTTTTC
1 TTTTTTTTTC
53830113 TTTT
1 TTTT
53830117 CATGACTGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 20 0.45
10 16 0.36
11 2 0.05
12 6 0.14
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:53830089 original size:27 final size:26
Alignment explanation
Indices: 53830054--53830116 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 26
53830044 TGGCATTTGA
*
53830054 TTTTT-TTTTGTTTTTTTTCTTGTCTT
1 TTTTTCTTTTGTTTTTTTT-TTCTCTT
*
53830080 TTTTTCTTTTTGTTTTTTTTTTCTTTT
1 TTTTTC-TTTTGTTTTTTTTTTCTCTT
53830107 TTTTTCTTTT
1 TTTTTCTTTT
53830117 CATGACTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 9 0.27
27 11 0.33
28 13 0.39
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (26 bp):
TTTTTCTTTTGTTTTTTTTTTCTCTT
Found at i:53834532 original size:12 final size:12
Alignment explanation
Indices: 53834515--53834569 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
53834505 ACATATATGT
53834515 ATAATAATGATGA
1 ATAATAATGAT-A
*
53834528 A-AATAATAATA
1 ATAATAATGATA
*
53834539 ATAATAATGAAA
1 ATAATAATGATA
53834551 ATAAATAAT-ATA
1 AT-AATAATGATA
53834563 ATAATAA
1 ATAATAA
53834570 ATATAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 7 0.19
12 22 0.61
13 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (12 bp):
ATAATAATGATA
Found at i:53834535 original size:3 final size:3
Alignment explanation
Indices: 53834515--53834569 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
53834505 ACATATATGT
*
53834515 ATA ATA ATG ATGA A-A ATA ATA ATA ATA ATA ATGA A-A ATAA ATA AT-
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA
53834560 ATA ATA ATA A
1 ATA ATA ATA A
53834570 ATATAATAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:53834541 original size:21 final size:21
Alignment explanation
Indices: 53834515--53834577 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
53834505 ACATATATGT
*
53834515 ATAATAATGATGAAAATAATA
1 ATAATAATAATGAAAATAATA
53834536 ATAATAATAATGAAAATAAATA
1 ATAATAATAATGAAAAT-AATA
53834558 AT-ATAATAAT-AAATATAATA
1 ATAATAATAATGAAA-ATAATA
53834578 GTAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 7 0.18
21 26 0.67
22 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAATAATAATGAAAATAATA
Found at i:53834742 original size:26 final size:26
Alignment explanation
Indices: 53834682--53834746 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
53834672 TACGAAGAAG
*
53834682 TATATATAATATAATAATAATATTAA
1 TATAAATAATATAATAATAATATTAA
*
53834708 AATACAATAAT-TAA-AAGTAATATTATA
1 TATA-AATAATATAATAA-TAATATTA-A
53834735 TATAAAT-ATATA
1 TATAAATAATATA
53834747 CAATATTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 4 0.12
26 19 0.59
27 9 0.28
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
TATAAATAATATAATAATAATATTAA
Found at i:53837157 original size:20 final size:21
Alignment explanation
Indices: 53837125--53837173 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
53837115 CAATCACAGG
*
53837125 TCTTTTTTT--TTTTCCA-AC
1 TCTTTTTTTAATTTTCAAGAC
*
53837143 TTTTTTTTTAATTTTCAAGAC
1 TCTTTTTTTAATTTTCAAGAC
53837164 TCTTTTTTTA
1 TCTTTTTTTA
53837174 GTTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
20 6 0.24
21 11 0.44
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.67
Consensus pattern (21 bp):
TCTTTTTTTAATTTTCAAGAC
Found at i:53838782 original size:12 final size:12
Alignment explanation
Indices: 53838759--53838795 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
53838749 GTGAGAAAAA
*
53838759 AAATATAAATAT
1 AAATATATATAT
*
53838771 ACATATATATAT
1 AAATATATATAT
53838783 AAATATATATAT
1 AAATATATATAT
53838795 A
1 A
53838796 TAAAATGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATATAT
Found at i:53838790 original size:14 final size:14
Alignment explanation
Indices: 53838773--53838799 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53838763 ATAAATATAC
53838773 ATATATATATAAAT
1 ATATATATATAAAT
53838787 ATATATATATAAA
1 ATATATATATAAA
53838800 ATGAGTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:53838952 original size:3 final size:3
Alignment explanation
Indices: 53838934--53839016 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
53838924 AATGATAGTC
* * * **
53838934 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53838982 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
53839017 TGATTAAACA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53840904 original size:44 final size:45
Alignment explanation
Indices: 53840841--53841129 Score: 134
Period size: 44 Copynumber: 6.6 Consensus size: 45
53840831 GATCTACTCT
* * * *
53840841 ACTGTAACTTCAGAGAGATAAGATCCT-TTAT-TTTAATCCGCTCC
1 ACTGTAATTTCAGGGAGATAAGAT-CTACTATCTTCAATCCGCTCC
* * *
53840885 ACTGTAATTTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCG
1 ACTGTAATTTCAGGGAGATAAGATCTACTATCTTCAATCCGCTCC
* * * ** **
53840929 GCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTACTCC
1 ACTGTAATTTCAGGGAGATAAGATCT-ACTA-TCTTCAATCCGCTCC
** * * * ** *
53840975 ACTGTAACCTCAAGGAGATAAGA-C--CTGA--TGCGATCTACTCT
1 ACTGTAATTTCAGGGAGATAAGATCTACT-ATCTTCAATCCGCTCC
** * * *
53841016 ACTGTAACCTCAGAGAGATAAGATCCTA-AAT-TTTAATCCGCTCC
1 ACTGTAATTTCAGGGAGATAAGAT-CTACTATCTTCAATCCGCTCC
* * * * * *
53841060 ACTGTAACTTCAGAGAGATAGGAT-TACTAGCTTCAATCTGCTCT
1 ACTGTAATTTCAGGGAGATAAGATCTACTATCTTCAATCCGCTCC
* *
53841104 GCTGTAATCTCAGGGAGATAAGATCT
1 ACTGTAATTTCAGGGAGATAAGATCT
53841130 GAAATTCTTC
Statistics
Matches: 187, Mismatches: 43, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
41 31 0.17
42 3 0.02
43 6 0.03
44 111 0.59
45 4 0.02
46 32 0.17
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
ACTGTAATTTCAGGGAGATAAGATCTACTATCTTCAATCCGCTCC
Found at i:53840981 original size:46 final size:46
Alignment explanation
Indices: 53840930--53841144 Score: 155
Period size: 44 Copynumber: 4.9 Consensus size: 46
53840920 ATCTGCTCGG
* *
53840930 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCA
* * * *
53840976 CTGTAACCTCAAGGAGATAAGACCTG--A---TGCGATCTACTCTA
1 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCA
* * **
53841017 CTGTAACCTCAGAGAGATAAGATCCT-AAATT-TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGATCTACTCCA
* * * * * * * **
53841061 CTGTAACTTCAGAGAGATAGGAT-T--ACTAGCTTCAATCTGCTCTG
1 CTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGATCTACTCCA
*
53841105 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCT
1 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCT
53841145 GCTTCGCTGT
Statistics
Matches: 130, Mismatches: 28, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
41 33 0.25
42 3 0.02
43 3 0.02
44 56 0.43
45 2 0.02
46 31 0.24
47 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (46 bp):
CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCA
Found at i:53841122 original size:175 final size:175
Alignment explanation
Indices: 53840824--53841140 Score: 562
Period size: 175 Copynumber: 1.8 Consensus size: 175
53840814 CGGCTTCAAT
* * **
53840824 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
* * *
53840889 TAATTTCAGGGAGATAGGATTACTATCTTCAATCTGCTCGGCTGTAATCTCAGGGAGATAAGATC
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCGGCTGTAATCTCAGGGAGATAAGATC
53840954 TGAAATTCTTCGGTCTACTCCACTGTAACCTCAAGGAGATAAGAC
131 TGAAATTCTTCGGTCTACTCCACTGTAACCTCAAGGAGATAAGAC
53840999 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
*
53841064 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATC
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCGGCTGTAATCTCAGGGAGATAAGATC
53841129 TGAAATTCTTCG
131 TGAAATTCTTCG
53841141 ATCTGCTTCG
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 134 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (175 bp):
CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCGGCTGTAATCTCAGGGAGATAAGATC
TGAAATTCTTCGGTCTACTCCACTGTAACCTCAAGGAGATAAGAC
Found at i:53843819 original size:12 final size:12
Alignment explanation
Indices: 53843783--53843824 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
53843773 AAAAAAAAAA
53843783 CATTATTATTAT
1 CATTATTATTAT
53843795 -ATTATATATTAT
1 CATTAT-TATTAT
*
53843807 CATTATTACTAT
1 CATTATTATTAT
53843819 CATTAT
1 CATTAT
53843825 CTCTATGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
CATTATTATTAT
Found at i:53845088 original size:31 final size:31
Alignment explanation
Indices: 53844995--53845090 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
53844985 GGAAAATTAC
* *
53844995 AAGACTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53845026 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
53845058 AAGAGTAATAGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
53845089 AA
1 AA
53845091 ATTATCTAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:53847166 original size:27 final size:27
Alignment explanation
Indices: 53847128--53847180 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
53847118 AAACTATATT
*
53847128 TTTTTTATTTTTAAAATACACCACATA
1 TTTTTTATTTTTAAAAAACACCACATA
*
53847155 TTTTTTATTTTTAAAAAACACTACAT
1 TTTTTTATTTTTAAAAAACACCACAT
53847181 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTTTATTTTTAAAAAACACCACATA
Found at i:53849618 original size:5 final size:5
Alignment explanation
Indices: 53849610--53849657 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
53849600 CGAACAAATA
* *
53849610 ATTCG ATTCG ATTCG ATTCG ATTTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG A-TTCG AT-TCG ATTCG ATTCG ATTCG AT
53849658 AAAACTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 29 0.78
6 6 0.16
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (5 bp):
ATTCG
Done.