Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 172 of 182
Found at i:52467100 original size:22 final size:22
Alignment explanation
Indices: 52467075--52467120 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
52467065 TTAGCCTTTC
*
52467075 CATTTTTA-CTTTTTCATTTTTT
1 CATTTTCATCTTTTT-ATTTTTT
52467097 CATTTTCATCTTTTTATTTTTT
1 CATTTTCATCTTTTTATTTTTT
52467119 CA
1 CA
52467121 CATCACTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (22 bp):
CATTTTCATCTTTTTATTTTTT
Found at i:52467300 original size:22 final size:22
Alignment explanation
Indices: 52467275--52467320 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
52467265 TTAGCCTTTC
*
52467275 CATTTTTA-CTTTTTCATTTTTT
1 CATTTTCATCTTTTT-ATTTTTT
52467297 CATTTTCATCTTTTTATTTTTT
1 CATTTTCATCTTTTTATTTTTT
52467319 CA
1 CA
52467321 CATCACTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (22 bp):
CATTTTCATCTTTTTATTTTTT
Found at i:52467336 original size:200 final size:199
Alignment explanation
Indices: 52466993--52467379 Score: 765
Period size: 200 Copynumber: 1.9 Consensus size: 199
52466983 TTTGATCAAC
52466993 ATTTGAGCCGCCATTTTTGGGTTTTCAACTCAAATCCCCTTTGGTCTAAGGCGCCCTTTGCGAGT
1 ATTTGAGCCGCCATTTTTGGGTTTTCAACTCAAATCCCCTTTGGTCTAAGGCGCCCTTTGCGAGT
52467058 TTTCACCTTAGCCTTTCCATTTTTACTTTTTCATTTTTTCATTTTCATCTTTTTATTTTTTCACA
66 TTTCACCTTAGCCTTTCCATTTTTACTTTTTCATTTTTTCATTTTCATCTTTTTATTTTTTCACA
52467123 TCACTTCTTTTTCTTTTTCTTTTTTTTTTTGGGATTCAAACTGCCCTTTGCGGGTTNTATTCTGA
131 TCACTTCTTTTTCTTTTTCTTTTTTTTTTTGGGATTCAAACTGCCCTTTGCGGGTT-TATTCTGA
52467188 CCAAA
195 CCAAA
52467193 ATTTGAGCCGCCATTTTTGGGTTTTCAACTCAAATCCCCTTTGGTCTAAGGCGCCCTTTGCGAGT
1 ATTTGAGCCGCCATTTTTGGGTTTTCAACTCAAATCCCCTTTGGTCTAAGGCGCCCTTTGCGAGT
52467258 TTTCACCTTAGCCTTTCCATTTTTACTTTTTCATTTTTTCATTTTCATCTTTTTATTTTTTCACA
66 TTTCACCTTAGCCTTTCCATTTTTACTTTTTCATTTTTTCATTTTCATCTTTTTATTTTTTCACA
52467323 TCACTTCTTTTTCTTTTTCTTTTTTTTTTTGGGATTCAAACTGCCCTTTGCGGGTTT
131 TCACTTCTTTTTCTTTTTCTTTTTTTTTTTGGGATTCAAACTGCCCTTTGCGGGTTT
52467380 TTACCTTGGC
Statistics
Matches: 187, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
199 1 0.01
200 186 0.99
ACGTcount: A:0.15, C:0.22, G:0.12, T:0.50
Consensus pattern (199 bp):
ATTTGAGCCGCCATTTTTGGGTTTTCAACTCAAATCCCCTTTGGTCTAAGGCGCCCTTTGCGAGT
TTTCACCTTAGCCTTTCCATTTTTACTTTTTCATTTTTTCATTTTCATCTTTTTATTTTTTCACA
TCACTTCTTTTTCTTTTTCTTTTTTTTTTTGGGATTCAAACTGCCCTTTGCGGGTTTATTCTGAC
CAAA
Found at i:52472722 original size:53 final size:53
Alignment explanation
Indices: 52472663--52472814 Score: 207
Period size: 53 Copynumber: 2.9 Consensus size: 53
52472653 TACTAAAAAA
* *
52472663 AATTAAATGATTTTGTTTAAGACCGACAACATTGTGTCTTACAAATAATACAT
1 AATTAAATGATTTTGTTTAAGACCGACAACATTGTATCTTACAAATAAAACAT
* * * *
52472716 AATTAAATGATTTTATTTAAGACTGACATCATTTTATCTTACAAATAAAACAT
1 AATTAAATGATTTTGTTTAAGACCGACAACATTGTATCTTACAAATAAAACAT
* * *
52472769 AATTAAA-CAGTTTTGTTCAAGACCAACAACATTGTATCTTACAAAT
1 AATTAAATGA-TTTTGTTTAAGACCGACAACATTGTATCTTACAAAT
52472815 TGAAAAATAC
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 84 0.99
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (53 bp):
AATTAAATGATTTTGTTTAAGACCGACAACATTGTATCTTACAAATAAAACAT
Found at i:52474445 original size:26 final size:26
Alignment explanation
Indices: 52474406--52474463 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
52474396 AATTTTTAAA
52474406 TAAAT-AATTAATAGAATCA-ATTGGT
1 TAAATCAATTAATAGAATCAGA-TGGT
*
52474431 TAAATCAATTCATAGAATCAGATGGT
1 TAAATCAATTAATAGAATCAGATGGT
*
52474457 CAAATCA
1 TAAATCA
52474464 GTCACTGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 23 0.79
27 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (26 bp):
TAAATCAATTAATAGAATCAGATGGT
Found at i:52476087 original size:22 final size:23
Alignment explanation
Indices: 52476056--52476098 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
52476046 TGAAAATTTA
52476056 AAATAATGAAAT-TAAATAAAACT
1 AAATAATGAAATATAAA-AAAACT
52476079 AAAT-ATGAAATATAAAAAAA
1 AAATAATGAAATATAAAAAAA
52476099 TGCTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATAATGAAATATAAAAAAACT
Found at i:52476252 original size:8 final size:8
Alignment explanation
Indices: 52476241--52476288 Score: 73
Period size: 8 Copynumber: 6.1 Consensus size: 8
52476231 GCTTTTTCCT
52476241 TTTTTTTC
1 TTTTTTTC
52476249 TTTTTTTC
1 TTTTTTTC
52476257 -TTTTTTC
1 TTTTTTTC
52476264 -TTTTTTC
1 TTTTTTTC
52476271 TTTTTTTTC
1 -TTTTTTTC
52476280 TTTTTTTC
1 TTTTTTTC
52476288 T
1 T
52476289 GCTGGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.37
8 17 0.45
9 7 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:52476285 original size:7 final size:7
Alignment explanation
Indices: 52476242--52476276 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
52476232 CTTTTTCCTT
52476242 TTTTTTC
1 TTTTTTC
52476249 TTTTTTTC
1 -TTTTTTC
52476257 TTTTTTC
1 TTTTTTC
52476264 TTTTTTC
1 TTTTTTC
52476271 TTTTTT
1 TTTTTT
52476277 TTCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:52476589 original size:3 final size:3
Alignment explanation
Indices: 52476576--52476615 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
52476566 TATTTCTTTT
52476576 TTC TT- TTC TTC TTC TTC TTCC TTC TTC TTC TT- TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TT
52476616 TCGGAAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:52476601 original size:13 final size:12
Alignment explanation
Indices: 52476576--52476615 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
52476566 TATTTCTTTT
52476576 TTCTT-TTCTTC
1 TTCTTCTTCTTC
52476587 TTCTTCTTCCTTC
1 TTCTTCTT-CTTC
52476600 TTCTTCTT-TTC
1 TTCTTCTTCTTC
52476611 TTCTT
1 TTCTT
52476616 TCGGAAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 13 0.48
12 2 0.07
13 12 0.44
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTCTTCTTC
Found at i:52477047 original size:29 final size:29
Alignment explanation
Indices: 52476969--52477084 Score: 115
Period size: 29 Copynumber: 4.0 Consensus size: 29
52476959 GCCAAAATAT
* * *
52476969 AATTTTAAGAAAATTTAAGGGTCAAAATGT
1 AATTTTAA-AAAGTTTAGGGGTCAAAATGC
* * * * ***
52476999 AATTTCAAAGAGCTTAGGGGTTATGGTGC
1 AATTTTAAAAAGTTTAGGGGTCAAAATGC
*
52477028 AATTTTAAAAAGTTTTGGGGTCAAAATGC
1 AATTTTAAAAAGTTTAGGGGTCAAAATGC
*
52477057 AATTTTAAAAAGTTTAGGGGTCTAAATG
1 AATTTTAAAAAGTTTAGGGGTCAAAATG
52477085 AAAAAAATTA
Statistics
Matches: 66, Mismatches: 20, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
29 59 0.89
30 7 0.11
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (29 bp):
AATTTTAAAAAGTTTAGGGGTCAAAATGC
Found at i:52477411 original size:22 final size:23
Alignment explanation
Indices: 52477380--52477422 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
52477370 TGAAAATTTA
52477380 AAATAATGAAAT-TAAATAAAACT
1 AAATAATGAAATATAAA-AAAACT
52477403 AAAT-ATGAAATATAAAAAAA
1 AAATAATGAAATATAAAAAAA
52477423 TGCTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATAATGAAATATAAAAAAACT
Found at i:52477578 original size:11 final size:11
Alignment explanation
Indices: 52477564--52477598 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
52477554 GGCTTTTTCC
52477564 TTTTTT-TTCT
1 TTTTTTCTTCT
52477574 TTTTTTCTTCT
1 TTTTTTCTTCT
52477585 TTTTTTCTT-T
1 TTTTTTCTTCT
52477595 TTTT
1 TTTT
52477599 CTGCTGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 11 0.46
11 13 0.54
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:52477893 original size:13 final size:13
Alignment explanation
Indices: 52477875--52477899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52477865 TATTTCTTTT
52477875 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
52477888 CTTCTTCTTCTT
1 CTTCTTCTTCTT
52477900 TTTTTCTTTT
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
CTTCTTCTTCTTC
Found at i:52478040 original size:18 final size:20
Alignment explanation
Indices: 52478017--52478056 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
52478007 TCTTTTGCTG
52478017 TTGAAAC-TCTCTT-TTTTT
1 TTGAAACTTCTCTTCTTTTT
*
52478035 TTGAAACTTTTCTTCTTTTT
1 TTGAAACTTCTCTTCTTTTT
52478055 TT
1 TT
52478057 ATTCGTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.65
Consensus pattern (20 bp):
TTGAAACTTCTCTTCTTTTT
Found at i:52478268 original size:29 final size:28
Alignment explanation
Indices: 52478245--52478307 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 28
52478235 GGGGTTATGG
52478245 TGCAATTTTAAAAAGTTTCAGGGTCAAAA
1 TGCAATTTTAAAAAGTTT-AGGGTCAAAA
52478274 TGCAATTTTAAAAAGTTTAGGGGTCAAAA
1 TGCAATTTTAAAAAGTTTA-GGGTCAAAA
52478303 TGCAA
1 TGCAA
52478308 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (28 bp):
TGCAATTTTAAAAAGTTTAGGGTCAAAA
Found at i:52478307 original size:58 final size:59
Alignment explanation
Indices: 52478189--52478307 Score: 141
Period size: 58 Copynumber: 2.0 Consensus size: 59
52478179 GCCAAAATAT
* * ***
52478189 AATTTTAAGAAAATTTAAGGGTCAAAATGCAATTTCAAAGAGCTCAGGGGTTATGGTGC
1 AATTTTAAGAAAATTTAAGGGTCAAAATGCAATTTCAAAAAGCTCAGGGGTCAAAATGC
* * * * *
52478248 AATTTTAA-AAAGTTTCAGGGTCAAAATGCAATTTTAAAAAGTTTAGGGGTCAAAATGC
1 AATTTTAAGAAAATTTAAGGGTCAAAATGCAATTTCAAAAAGCTCAGGGGTCAAAATGC
52478306 AA
1 AA
52478308 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 42 0.84
59 8 0.16
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.29
Consensus pattern (59 bp):
AATTTTAAGAAAATTTAAGGGTCAAAATGCAATTTCAAAAAGCTCAGGGGTCAAAATGC
Found at i:52478626 original size:78 final size:78
Alignment explanation
Indices: 52478488--52479553 Score: 877
Period size: 77 Copynumber: 13.8 Consensus size: 78
52478478 AGAAATCGAG
* *
52478488 AATAGCTCGGCATGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTGAAAAAC
1 AATACCTCGGCATG-GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
52478553 AG-AATTTGAAAA-A
65 AGAAATTT-AAAAGA
* * *
52478566 AATACCTCGGCATGCGACCCGAGGCACAACTCACCCCTCGCAGTATGAGTTGATTTTTGAAAAAC
1 AATACCTCGGCATG-GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
*
52478631 A-AGAA-TT-GAA-A
65 AGA-AATTTAAAAGA
* * * *
52478642 AATACATCGGCGT-GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
52478706 GAAATTTAAAAGA
66 GAAATTTAAAAGA
* * * * *
52478719 AATACGTCAGCATGG-TCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
52478783 GAAATTTAAAAGA
66 GAAATTTAAAAGA
** *
52478796 AATACCTCGGCATGG-TTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
52478860 GAAATTTAAAAGA
66 GAAATTTAAAAGA
**
52478873 AATACCTCGGCATGG-TTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG---AA
*
52478937 AAACATAAATTTAAAAGA
61 AAACAGAAATTTAAAAGA
* * *
52478955 AATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAA
1 AATACCTCGGCATG-GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG--AAA
*
52479020 AATAGAAATTT-AAA-A
62 AACAGAAATTTAAAAGA
* * * * *
52479035 AATACCTCAGCGT-GACCCGAGGCTCAACTAACCTCTCGTATTATGAGTTGATTTTTGAAAAAAA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG---AAAA
*
52479099 ATAGAAA-TT--AA-A
63 ACAGAAATTTAAAAGA
* * ** * ** * **
52479111 AATACCTCAGCGT-GACTTGAGGCTCAACTCACCTTTCATATTATGAGTTGATTTTAAAAAAAGA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TGAAAA-A
52479175 CAGAAA-TT--AA-A
64 CAGAAATTTAAAAGA
* * * * * ***
52479186 AATACCTCAGCGT-GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAAAGA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TTGAAAA-A
52479250 CAGAAA-TT--AA-A
64 CAGAAATTTAAAAGA
* * * * *
52479261 AATACCTCAGCGT-GACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTTTAAA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTT-GA
52479325 AAAGACAGAAA-TT--AA-A
60 AAA-ACAGAAATTTAAAAGA
* * * * * *
52479341 AATACCTCAGCGT-GACCCGAGACTCAACTCACCTCTCGTATTATGACTTGA--TTT-AAAAA-A
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
* ** *
52479401 AAAGATAGAAATTAAA
66 GAA-ATTTAAA--AGA
* * * * *
52479417 AATACCTCAGCGT-GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAAA
52479481 CAGAAA-TT--AA-A
64 CAGAAATTTAAAAGA
* * * * *
52479492 AATACCTCAGCGT-GACCCGAGGCTCAACTCACCTCTCGTATTATAAGTTGATTTTTGAAAAA
1 AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
52479554 AAGCAGAAAT
Statistics
Matches: 884, Mismatches: 67, Indels: 79
0.86 0.07 0.08
Matches are distributed among these distances:
69 3 0.00
70 2 0.00
71 4 0.00
73 9 0.01
74 52 0.06
75 191 0.22
76 119 0.13
77 200 0.23
78 115 0.13
79 7 0.01
80 84 0.10
81 9 0.01
82 48 0.05
83 8 0.01
84 33 0.04
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (78 bp):
AATACCTCGGCATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
GAAATTTAAAAGA
Found at i:52478844 original size:154 final size:149
Alignment explanation
Indices: 52478507--52479572 Score: 1006
Period size: 151 Copynumber: 6.9 Consensus size: 149
52478497 GCATGCGACC
*
52478507 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTGAAAAACAG-AATTTGAAAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT-AAAAAAATAC
* * * *
52478571 CTCGGCATGCGACCCGAGGCACAACTCACCCCTCGCAGTATGAGTTGATTTTTGAAAAACA-AGA
65 CTCAGCATG-G-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGA-A
* *
52478635 ATTGAAAAATACATCGGCGTGACT
127 ATT-AAAAATACCTCAGCGTGACT
*
52478659 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAA-AAATAC
* * * *
52478724 GTCAGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACAGAAATT
65 CTCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-T
* * **
52478789 TAAAAGAAATACCTCGGCATGGTT
129 T--AA-AAATACCTCAGCGTGACT
*
52478813 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAA-AAATAC
* ** *
52478878 CTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAACAT
65 CTCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG---AAAAACAG
*
52478943 AAATTTAAAAGAAATACCTCAGCGTGTGACC
125 AAA-TT--AA-AAATACCTCAGC--GTGACT
* *
52478974 CGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAAAATAGAAATTT-AAAAAAT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG--AAAAACAGAAATTTAAAAAAAT
* * * * * *
52479038 ACCTCAGCGTGACCCGAGGCTCAACTAACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAATAG
63 ACCTCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG---AAAAACAG
52479103 AAATTAAAAATACCTCAGCGTGACT
125 AAATTAAAAATACCTCAGCGTGACT
* * ** * **
52479128 TGAGGCTCAACTCACCTTTCATATTATGAGTTGATTTTAAAAAAAGACAGAAA-TT--AAAAATA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TGAAAA-ACAGAAATTTAAAAAAATA
* * * * * ***
52479190 CCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAAAGACAGAA
64 CCTCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TTGAAAA-ACAGAA
*
52479255 ATTAAAAATACCTCAGCGTGACC
127 ATTAAAAATACCTCAGCGTGACT
* * *
52479278 CGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTTTAAAAAAGACAGAAA-TT--AA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTT-GAAAA-ACAGAAATTTAAAA
* * * * * * ***
52479340 AAATACCTCAGCGTGACCCGAGACTCAACTCACCTCTCGTATTATGACTTGATTTAAAAAAAAAG
59 AAATACCTCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT--TTGAAAA-
*
52479405 ATAGAAATTAAAAATACCTCAGCGTGAC-
121 ACAGAAATTAAAAATACCTCAGCGTGACT
* *
52479433 CTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAACAGAAA-TT--AAAAAT
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAAACAGAAATTTAAAAAAAT
* * * * *
52479495 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATAAGTTGATTTTTGAAAAAAAGCAG
63 ACCTCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAAA-CAG
52479560 AAATTGAAAAATA
125 AAATT-AAAAATA
52479573 TTTCTTGAAA
Statistics
Matches: 806, Mismatches: 74, Indels: 68
0.85 0.08 0.07
Matches are distributed among these distances:
149 4 0.00
150 59 0.07
151 179 0.22
152 71 0.09
153 30 0.04
154 152 0.19
155 74 0.09
156 86 0.11
157 2 0.00
159 31 0.04
160 18 0.02
161 35 0.04
162 49 0.06
163 3 0.00
164 13 0.02
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAAAATACC
TCAGCATGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
AAAATACCTCAGCGTGACT
Found at i:52479207 original size:75 final size:75
Alignment explanation
Indices: 52478503--52479572 Score: 977
Period size: 75 Copynumber: 13.9 Consensus size: 75
52478493 CTCGGCATGC
* * * * *
52478503 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT--GAAAAACAGAATTTGAAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATT-TTAAAAAAAACAGAAATT--AAAA
* *
52478566 AATACCTCGGCATGC
63 AATACCTCAGC--GT
* * * * * ** *
52478581 GACCCGAGGCACAACTCACCCCTCGCAGTATGAGTTGATTTT-TGAAAAACA-AGAATTGAAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAACAGA-AATTAAAAAA
* *
52478644 TACATCGGCGT
65 TACCTCAGCGT
* * ** *
52478655 GA-CTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TGAAAAATAGAAATTTAAAAG
1 GACCT-GAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAACAGAAA-TT-AAA-
* *
52478718 AAATACGTCAGCAT
62 AAATACCTCAGCGT
* * * * **
52478732 GGTCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-CGAAAAACAGAAATTTAAAAG
1 -GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAACAGAAA-TT-AAA-
* *
52478795 AAATACCTCGGCAT
62 AAATACCTCAGCGT
** * * **
52478809 G-GTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-CGAAAAACAGAAATTTAAAAG
1 GACCT-GAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAACAGAAA-TT-AAA-
* *
52478872 AAATACCTCGGCAT
62 AAATACCTCAGCGT
** * * *
52478886 G-GTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAACATAAATTTA
1 GACCT-GAGGCTCAACTCACCTCTCGTATTATGAGTTGA---TTTT-AAAAAAAACAGAAA-TT-
52478950 AAAGAAATACCTCAGCGTGT
59 AAA-AAATACCTCAGC--GT
* * * * * *
52478970 GACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAAAATAGAAATTTAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGA--TTTTAAAAAAAACAGAAA-TTAAAA
52479035 AATACCTCAGCGT
63 AATACCTCAGCGT
* * *
52479048 GACCCGAGGCTCAACTAACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAATAGAAATT-AAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT-AAAAAAAACAGAAATTAAAAA
52479112 ATACCTCAGCGT
64 ATACCTCAGCGT
* * *
52479124 GACTTGAGGCTCAACTCACCTTTCATATTATGAGTTGATTTTAAAAAAAGACAGAAATT-AAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAA-ACAGAAATTAAAAAA
52479188 TACCTCAGCGT
65 TACCTCAGCGT
*
52479199 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAAAGACAGAAATT-AAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAA-ACAGAAATTAAAAAA
52479263 TACCTCAGCGT
65 TACCTCAGCGT
* *
52479274 GACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTTTAAAAAAGACAGAAATT-
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGA------TTTTAAAAAAAACAGAAATTA
52479338 AAAAATACCTCAGCGT
60 AAAAATACCTCAGCGT
* * * * *
52479354 GACCCGAGACTCAACTCACCTCTCGTATTATGACTTGATTTAAAAAAAAAGATAGAAATT-AAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTT-TAAAAAAA-ACAGAAATTAAAAA
52479418 ATACCTCAGCGT
64 ATACCTCAGCGT
*
52479430 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAACAGAAATT-AAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTTAAAAAAAACAGAAATTAAAAAA
52479494 TACCTCAGCGT
65 TACCTCAGCGT
* * * *
52479505 GACCCGAGGCTCAACTCACCTCTCGTATTATAAGTTGATTTTTGAAAAAAAGCAGAAATTGAAAA
1 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT-AAAAAAAACAGAAATTAAAAA
52479570 ATA
64 ATA
52479573 TTTCTTGAAA
Statistics
Matches: 890, Mismatches: 70, Indels: 65
0.87 0.07 0.06
Matches are distributed among these distances:
73 1 0.00
74 57 0.06
75 210 0.24
76 144 0.16
77 207 0.23
78 98 0.11
79 1 0.00
80 77 0.09
81 12 0.01
82 43 0.05
83 6 0.01
84 34 0.04
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (75 bp):
GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAACAGAAATTAAAAAAT
ACCTCAGCGT
Found at i:52479462 original size:231 final size:227
Alignment explanation
Indices: 52478503--52479572 Score: 1094
Period size: 231 Copynumber: 4.6 Consensus size: 227
52478493 CTCGGCATGC
*
52478503 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTG--AAAAACAGAATTTGAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TTGAAAAAAACAGAAATT--AAAA
* * * * * * * *
52478566 AATACCTCGGCATGCGACCCGAGGCACAACTCACCCCTCGCAGTATGAGTTGATTTTTGAAAAAC
62 AATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAA
* * *
52478631 A-AG-AATTGAAAAATACATCGGCGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
125 ACAGAAATTAAAAAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*** * *
52478694 TT-TTGAAAA-ATAGAAATTTAAAAGAAATACGTCAGCAT
190 TTAAAAAAAAGATAGAAA-TT-AAAGAAATACCTCAGCGT
** * ***
52478732 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGAAAAAAACAGAAA-TT-AAA-AA
* * *** * * **
52478797 ATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTCGAAAAACA
63 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAACA
* * **
52478860 GAAATTTAAAAGAAATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
128 GAAA-TT-AAA-AAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* *
52478925 TTTTTTGAAAAAAAACATA-AATTTAAAAGAAATACCTCAGCGTGT
189 ---TTT-AAAAAAAAGATAGAAATT-AAAGAAATACCTCAGC--GT
* *
52478970 GACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAAAATAGAAATTTAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTGAAAAAAACAGAAA-TTAAAA
* *
52479035 AATACCTCAGCGTGACCCGAGGCTCAACTAACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAA
62 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTT-TAAAAAAA
* * * ** *
52479100 TAGAAATT-AAAAATACCTCAGCGTGACTTGAGGCTCAACTCACCTTTCATATTATGAGTTGATT
126 CAGAAATTAAAAAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
52479164 TTAAAAAAAGACAGAAATT-AA-AAATACCTCAGCGT
191 TAAAAAAAAGATAGAAATTAAAGAAATACCTCAGCGT
* * * *
52479199 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAAAGACAGAAATT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-GAAAAAA-ACAGAAATTAAAAAA
52479263 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTTTAAAAAA
64 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA----TTTTTTAAAAAA
* * * * *
52479328 GACAGAAATT-AAAAATACCTCAGCGTGACCCGAGACTCAACTCACCTCTCGTATTATGACTTGA
125 -ACAGAAATTAAAAAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
52479392 TTTAAAAAAAAAGATAGAAATT-AA-AAATACCTCAGCGT
189 TTT-AAAAAAAAGATAGAAATTAAAGAAATACCTCAGCGT
* * *
52479430 GACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAACAGAAATT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTGAAAAAAACAGAAATTAAAAAA
* *
52479494 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATAAGTTGATTTTTGAAAAAAAGCA
64 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAA-CA
*
52479559 GAAATTGAAAAATA
128 GAAATTAAAAAATA
52479573 TTTCTTGAAA
Statistics
Matches: 723, Mismatches: 81, Indels: 75
0.82 0.09 0.09
Matches are distributed among these distances:
226 64 0.09
227 31 0.04
228 48 0.07
229 93 0.13
230 80 0.11
231 192 0.27
232 8 0.01
233 12 0.02
234 7 0.01
235 3 0.00
236 18 0.02
237 6 0.01
238 81 0.11
239 46 0.06
240 3 0.00
241 21 0.03
242 10 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (227 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGAAAAAAACAGAAATTAAAAAATA
CCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAACAGAA
ATTAAAAAATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAAA
AAAAGATAGAAATTAAAGAAATACCTCAGCGT
Found at i:52483122 original size:543 final size:543
Alignment explanation
Indices: 52482095--52483180 Score: 2172
Period size: 543 Copynumber: 2.0 Consensus size: 543
52482085 AATGATCTCC
52482095 TTCCGGCGACACTAAGACTGCTCCGATCCCATGCCCCAATGCATTCGATGCACCATCAAAACTCA
1 TTCCGGCGACACTAAGACTGCTCCGATCCCATGCCCCAATGCATTCGATGCACCATCAAAACTCA
52482160 TCTTCCATGATTTCTCTTTTGATGACTCACCCTCTTTTTTTGAAATGCACATCAAGTCTTCATCT
66 TCTTCCATGATTTCTCTTTTGATGACTCACCCTCTTTTTTTGAAATGCACATCAAGTCTTCATCT
52482225 GGGAAATCAAATCTCAAAGGCTCGTATTCTTCCACTGTTCGACTTGCCAAGAAGTCAGCTATCGC
131 GGGAAATCAAATCTCAAAGGCTCGTATTCTTCCACTGTTCGACTTGCCAAGAAGTCAGCTATCGC
52482290 GCTTCCCTTTATCAATTTTTGGCTCACATACACGATATCATACTCAGTCAGTAAGATCTGCCATC
196 GCTTCCCTTTATCAATTTTTGGCTCACATACACGATATCATACTCAGTCAGTAAGATCTGCCATC
52482355 GTGCCATTCTTCTTGAGAGTGCAGGTGACTCCATCATGTACTTTATTGGATCCAATTTTGAAAGT
261 GTGCCATTCTTCTTGAGAGTGCAGGTGACTCCATCATGTACTTTATTGGATCCAATTTTGAAAGT
52482420 AACCATGTCGTATGATACAACATGTATTGTCTGAGCCTTCGAACCATCCAAATCAATGCGCAACA
326 AACCATGTCGTATGATACAACATGTATTGTCTGAGCCTTCGAACCATCCAAATCAATGCGCAACA
52482485 AAACTTCTCAATTGAAGGGTACTTTGCCTCATATTCTGTGAACTTTTTGCTGAGGTAGTAAATCG
391 AAACTTCTCAATTGAAGGGTACTTTGCCTCATATTCTGTGAACTTTTTGCTGAGGTAGTAAATCG
52482550 CCTTTTCTCTTTTCCCGACTCATCATGTTGTCCCAGTACGCAACCCATTGAGTTCTCAAACACGG
456 CCTTTTCTCTTTTCCCGACTCATCATGTTGTCCCAGTACGCAACCCATTGAGTTCTCAAACACGG
52482615 TCAGGTACAATATCAAGGGTTTT
521 TCAGGTACAATATCAAGGGTTTT
52482638 TTCCGGCGACACTAAGACTGCTCCGATCCCATGCCCCAATGCATTCGATGCACCATCAAAACTCA
1 TTCCGGCGACACTAAGACTGCTCCGATCCCATGCCCCAATGCATTCGATGCACCATCAAAACTCA
52482703 TCTTCCATGATTTCTCTTTTGATGACTCACCCTCTTTTTTTGAAATGCACATCAAGTCTTCATCT
66 TCTTCCATGATTTCTCTTTTGATGACTCACCCTCTTTTTTTGAAATGCACATCAAGTCTTCATCT
52482768 GGGAAATCAAATCTCAAAGGCTCGTATTCTTCCACTGTTCGACTTGCCAAGAAGTCAGCTATCGC
131 GGGAAATCAAATCTCAAAGGCTCGTATTCTTCCACTGTTCGACTTGCCAAGAAGTCAGCTATCGC
52482833 GCTTCCCTTTATCAATTTTTGGCTCACATACACGATATCATACTCAGTCAGTAAGATCTGCCATC
196 GCTTCCCTTTATCAATTTTTGGCTCACATACACGATATCATACTCAGTCAGTAAGATCTGCCATC
52482898 GTGCCATTCTTCTTGAGAGTGCAGGTGACTCCATCATGTACTTTATTGGATCCAATTTTGAAAGT
261 GTGCCATTCTTCTTGAGAGTGCAGGTGACTCCATCATGTACTTTATTGGATCCAATTTTGAAAGT
52482963 AACCATGTCGTATGATACAACATGTATTGTCTGAGCCTTCGAACCATCCAAATCAATGCGCAACA
326 AACCATGTCGTATGATACAACATGTATTGTCTGAGCCTTCGAACCATCCAAATCAATGCGCAACA
52483028 AAACTTCTCAATTGAAGGGTACTTTGCCTCATATTCTGTGAACTTTTTGCTGAGGTAGTAAATCG
391 AAACTTCTCAATTGAAGGGTACTTTGCCTCATATTCTGTGAACTTTTTGCTGAGGTAGTAAATCG
52483093 CCTTTTCTCTTTTCCCGACTCATCATGTTGTCCCAGTACGCAACCCATTGAGTTCTCAAACACGG
456 CCTTTTCTCTTTTCCCGACTCATCATGTTGTCCCAGTACGCAACCCATTGAGTTCTCAAACACGG
52483158 TCAGGTACAATATCAAGGGTTTT
521 TCAGGTACAATATCAAGGGTTTT
52483181 CAGGGGTTGG
Statistics
Matches: 543, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
543 543 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (543 bp):
TTCCGGCGACACTAAGACTGCTCCGATCCCATGCCCCAATGCATTCGATGCACCATCAAAACTCA
TCTTCCATGATTTCTCTTTTGATGACTCACCCTCTTTTTTTGAAATGCACATCAAGTCTTCATCT
GGGAAATCAAATCTCAAAGGCTCGTATTCTTCCACTGTTCGACTTGCCAAGAAGTCAGCTATCGC
GCTTCCCTTTATCAATTTTTGGCTCACATACACGATATCATACTCAGTCAGTAAGATCTGCCATC
GTGCCATTCTTCTTGAGAGTGCAGGTGACTCCATCATGTACTTTATTGGATCCAATTTTGAAAGT
AACCATGTCGTATGATACAACATGTATTGTCTGAGCCTTCGAACCATCCAAATCAATGCGCAACA
AAACTTCTCAATTGAAGGGTACTTTGCCTCATATTCTGTGAACTTTTTGCTGAGGTAGTAAATCG
CCTTTTCTCTTTTCCCGACTCATCATGTTGTCCCAGTACGCAACCCATTGAGTTCTCAAACACGG
TCAGGTACAATATCAAGGGTTTT
Found at i:52487536 original size:297 final size:297
Alignment explanation
Indices: 52486997--52489376 Score: 4733
Period size: 297 Copynumber: 8.0 Consensus size: 297
52486987 GTGCTGATTT
* *
52486997 AAATGTTCTTGACAAAAGAGGATACGCTAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52487062 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52487127 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52487192 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52487257 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52487294 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52487359 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52487424 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52487489 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52487554 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52487591 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52487656 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52487721 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52487786 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52487851 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52487888 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52487953 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52488018 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52488083 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52488148 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52488185 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52488250 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52488315 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52488380 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52488445 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52488482 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52488547 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52488612 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52488677 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52488742 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52488779 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52488844 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
52488909 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52488974 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52489039 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52489076 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
1 AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
52489141 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
66 TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
*
52489206 AAATCGTATCGACCCTTATGGTGCATTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
131 AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
52489271 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
196 CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
52489336 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
261 ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
52489373 AAAT
1 AAAT
52489377 GCAGCATTAA
Statistics
Matches: 2080, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
297 2080 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (297 bp):
AAATATTCTTGACAAAAGAGGATACGCCAACGGCTCCCATTCTAATTCCCGGTCTGAAGCTATCG
TGATTCTTCTTTCTCGATCTTTTTGAAATTGTTTTCTTCTTTGATGTATATCTAGCTTGAACCCC
AAATCGTATCGACCCTTATGGTGCGTTGGTTTCAAAGCTCTAACCATCCCTTGTTGATATTTTCC
CAAGCCTTTCCTCGCTCGAGCTTTTTTTCCCACAGTCTGCTTAATTCCCATCTTGGTATTTCTCG
ACACTTTGGGAATGGGGATCTTATTCCCTTCAGCAAC
Found at i:52496515 original size:7 final size:7
Alignment explanation
Indices: 52496512--52496552 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
52496502 GCTTTTTCCT
52496512 TTTTTTC
1 TTTTTTC
52496519 TTTTTTC
1 TTTTTTC
52496526 TTTTTTTC
1 -TTTTTTC
*
52496534 TTCTTT-
1 TTTTTTC
52496540 TTTTTTC
1 TTTTTTC
52496547 TTTTTT
1 TTTTTT
52496553 TCTGCTGGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 5 0.17
7 18 0.60
8 7 0.23
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:52496521 original size:8 final size:8
Alignment explanation
Indices: 52496504--52496555 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
52496494 CGACTCGGGC
*
52496504 TTTTTCCT
1 TTTTTTCT
52496512 TTTTTTC-
1 TTTTTTCT
52496519 TTTTTTCT
1 TTTTTTCT
52496527 TTTTTTC-
1 TTTTTTCT
*
52496534 -TTCTT-T
1 TTTTTTCT
52496540 TTTTTTCT
1 TTTTTTCT
52496548 TTTTTTCT
1 TTTTTTCT
52496556 GCTGGGCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
6 4 0.11
7 11 0.30
8 22 0.59
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTCT
Found at i:52496521 original size:15 final size:14
Alignment explanation
Indices: 52496503--52496551 Score: 64
Period size: 13 Copynumber: 3.4 Consensus size: 14
52496493 ACGACTCGGG
52496503 CTTTTTCCTTTTTTT
1 CTTTTT-CTTTTTTT
52496518 CTTTTTTCTTTTTTT
1 C-TTTTTCTTTTTTT
*
52496533 CTTCTT-TTTTTTT
1 CTTTTTCTTTTTTT
52496546 CTTTTT
1 CTTTTT
52496552 TTCTGCTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.39
14 4 0.13
15 10 0.32
16 5 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
CTTTTTCTTTTTTT
Found at i:52496524 original size:10 final size:10
Alignment explanation
Indices: 52496519--52496553 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
52496509 CCTTTTTTTC
52496519 TTTTTTCTTT
1 TTTTTTCTTT
52496529 TTTTCTTCTTT
1 TTTT-TTCTTT
52496540 TTTTTTCTTT
1 TTTTTTCTTT
52496550 TTTT
1 TTTT
52496554 CTGCTGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:52498337 original size:61 final size:58
Alignment explanation
Indices: 52498214--52498346 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 58
52498204 ATCACTTTAA
* * * **
52498214 TATTAAATTAATATAATACTTATCAAGATAAATATCATATTAAATCTAGTATTACATG
1 TATTAAATTAATATAATACTTATCAAGATAAATATCAAATTAAATCTAATATTAAAAC
* * * *
52498272 TATTAAATTAATATAATATTTATCTATAAGATAAATATTAAATTTAATTTAATATTAAAAC
1 TATTAAATTAATATAATACTTATC---AAGATAAATATCAAATTAAATCTAATATTAAAAC
*
52498333 TATTAAAATAATAT
1 TATTAAATTAATAT
52498347 TATTTTTAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 23 0.37
61 39 0.63
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (58 bp):
TATTAAATTAATATAATACTTATCAAGATAAATATCAAATTAAATCTAATATTAAAAC
Found at i:52498547 original size:42 final size:42
Alignment explanation
Indices: 52498488--52498571 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
52498478 CCGTAGTGCC
52498488 CAGTGGTGCAGTCGCGACACCCTCACGACACCCGAATTCGGT
1 CAGTGGTGCAGTCGCGACACCCTCACGACACCCGAATTCGGT
52498530 CAGTGGTGCAGTCGCGACACCCTCACGACACCCGAATTCGGT
1 CAGTGGTGCAGTCGCGACACCCTCACGACACCCGAATTCGGT
52498572 TTGGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.17
Consensus pattern (42 bp):
CAGTGGTGCAGTCGCGACACCCTCACGACACCCGAATTCGGT
Found at i:52499684 original size:16 final size:16
Alignment explanation
Indices: 52499663--52499701 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
52499653 TTGGATCCAG
52499663 TCCAATGTATCATTCT
1 TCCAATGTATCATTCT
52499679 TCCAATGTATCATTCT
1 TCCAATGTATCATTCT
52499695 TCCAATG
1 TCCAATG
52499702 AATACTTCTA
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:0.26, C:0.26, G:0.08, T:0.41
Consensus pattern (16 bp):
TCCAATGTATCATTCT
Found at i:52499882 original size:9 final size:9
Alignment explanation
Indices: 52499865--52499901 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52499855 TGAGTTTTCG
52499865 AATTCGAAT
1 AATTCGAAT
*
52499874 AACTCGAAT
1 AATTCGAAT
52499883 AATTCGAAT
1 AATTCGAAT
52499892 AATTCGAAT
1 AATTCGAAT
52499901 A
1 A
52499902 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52500308 original size:17 final size:17
Alignment explanation
Indices: 52500282--52500314 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52500272 ACTTTCACTC
52500282 AAACTTTTA-TTCCCCA
1 AAACTTTTATTTCCCCA
52500298 AAACTTTTTATTTCCCC
1 AAAC-TTTTATTTCCCC
52500315 CCTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (17 bp):
AAACTTTTATTTCCCCA
Found at i:52503807 original size:67 final size:67
Alignment explanation
Indices: 52503724--52503859 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
52503714 TGTGATGTTC
*
52503724 TTTAAGGGTTAATGTAGGATTTTGTGTTTTGATTGAATATTCTTTTTGGTTTCTATGTGCTGTTT
1 TTTAAGGGTTAATGTAGGATTCTGTGTTTTGATTGAATATTCTTTTTGGTTTCTATGTGCTGTTT
52503789 TT
66 TT
*
52503791 TTTAAGGGTTAATGTAGGATTCTGTGTTTTGATTGAATTTTCTTTTTGGTTTCTATGTGCTGTTT
1 TTTAAGGGTTAATGTAGGATTCTGTGTTTTGATTGAATATTCTTTTTGGTTTCTATGTGCTGTTT
52503856 TT
66 TT
52503858 TT
1 TT
52503860 ATTTTTATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.15, C:0.05, G:0.22, T:0.57
Consensus pattern (67 bp):
TTTAAGGGTTAATGTAGGATTCTGTGTTTTGATTGAATATTCTTTTTGGTTTCTATGTGCTGTTT
TT
Found at i:52519715 original size:22 final size:22
Alignment explanation
Indices: 52519673--52519728 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
52519663 TTGTTTTAAG
* *
52519673 AGTTTTGAACATTATTCAATAA
1 AGTTTTAAAAATTATTCAATAA
52519695 AGTTTTAAAAATT-TTCTAATAA
1 AGTTTTAAAAATTATTC-AATAA
*
52519717 ATATTTTAAAAA
1 A-GTTTTAAAAA
52519729 ACTAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 17 0.59
23 9 0.31
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (22 bp):
AGTTTTAAAAATTATTCAATAA
Found at i:52521386 original size:3 final size:3
Alignment explanation
Indices: 52521378--52521421 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
52521368 GGTTAAATAA
52521378 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
52521422 CAATTTTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:52528084 original size:62 final size:62
Alignment explanation
Indices: 52528013--52528130 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
52528003 AAAAATAACC
*
52528013 AAATTAGAGTATAAGTACACATAGTGAAATGACAAACAGCAGAATTTGACATATATTAAACT
1 AAATTAGAGTATAAGGACACATAGTGAAATGACAAACAGCAGAATTTGACATATATTAAACT
*
52528075 AAATTAGAGTATAAGGACACATAGTGCAATGACAAACAGCAGAATTTGACATATAT
1 AAATTAGAGTATAAGGACACATAGTGAAATGACAAACAGCAGAATTTGACATATAT
52528131 AAATAATACT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (62 bp):
AAATTAGAGTATAAGGACACATAGTGAAATGACAAACAGCAGAATTTGACATATATTAAACT
Found at i:52531685 original size:16 final size:16
Alignment explanation
Indices: 52531664--52531712 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
52531654 ATATCTAATC
52531664 ATATAATAAATTATTA
1 ATATAATAAATTATTA
52531680 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
52531693 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
52531710 ATA
1 ATA
52531713 AATTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
13 11 0.44
16 10 0.40
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:52531699 original size:13 final size:13
Alignment explanation
Indices: 52531689--52531721 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
52531679 AATATAATTT
52531689 ATTATTTTAATAA
1 ATTATTTTAATAA
52531702 ATTA-TTTAATAA
1 ATTATTTTAATAA
52531714 ATTATTTT
1 ATTATTTT
52531722 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATTTTAATAA
Found at i:52531764 original size:16 final size:17
Alignment explanation
Indices: 52531728--52531764 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
52531718 TTTTTATTTT
*
52531728 TAATAATAAATTTTAAA
1 TAATAATAAATTCTAAA
52531745 -AATAAT-AATTCTAAA
1 TAATAATAAATTCTAAA
52531760 TAATA
1 TAATA
52531765 TTTTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTCTAAA
Found at i:52534060 original size:33 final size:32
Alignment explanation
Indices: 52534018--52534095 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 32
52534008 ATGCCAATCG
*
52534018 TATACATATCATCCCATTATTGTAGTGTCATCA
1 TATACATATCATCCCATT-CTGTAGTGTCATCA
52534051 TATACATATCAT--C--TCTGTAGTGTCATCA
1 TATACATATCATCCCATTCTGTAGTGTCATCA
52534079 TATACATATCATCCCAT
1 TATACATATCATCCCAT
52534096 CATAAAAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 25 0.62
29 1 0.03
30 1 0.03
31 1 0.03
33 12 0.30
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (32 bp):
TATACATATCATCCCATTCTGTAGTGTCATCA
Found at i:52539429 original size:19 final size:19
Alignment explanation
Indices: 52539405--52539443 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52539395 AAGGGTAAGC
52539405 TTTTAAAGCCTAGTGTGGG
1 TTTTAAAGCCTAGTGTGGG
52539424 TTTTAAAGCCTAGTGTGGG
1 TTTTAAAGCCTAGTGTGGG
52539443 T
1 T
52539444 CTTATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (19 bp):
TTTTAAAGCCTAGTGTGGG
Found at i:52539692 original size:45 final size:45
Alignment explanation
Indices: 52539642--52539731 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
52539632 ACAACTACCG
* * *
52539642 ATATTCACAGACAAGTTGCCATGTAGGTTGTGGACGAAGTCACCA
1 ATATTCACAGACAAGCTGCCATGTAGGTTGTAGACGAAGCCACCA
* *
52539687 ATATTCACAGACAAGCTGTCATGTAGGTTGTAGATGAAGCCACCA
1 ATATTCACAGACAAGCTGCCATGTAGGTTGTAGACGAAGCCACCA
52539732 TGTATGTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
ATATTCACAGACAAGCTGCCATGTAGGTTGTAGACGAAGCCACCA
Found at i:52543888 original size:20 final size:20
Alignment explanation
Indices: 52543863--52543930 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
52543853 ATAAGATATG
*
52543863 TGTTTATATGGATGAATTAT
1 TGTTTATATGGATGAATTAA
* **
52543883 TGTTTATACGGATGAACCAA
1 TGTTTATATGGATGAATTAA
* *
52543903 TGGTTATATGAATGAATTACA
1 TGTTTATATGGATGAATTA-A
52543924 -GTTTATA
1 TGTTTATA
52543931 CGAATAGAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 36 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (20 bp):
TGTTTATATGGATGAATTAA
Found at i:52544865 original size:13 final size:13
Alignment explanation
Indices: 52544847--52544871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52544837 ATATGTTTGG
52544847 ATATGAAATTGAT
1 ATATGAAATTGAT
52544860 ATATGAAATTGA
1 ATATGAAATTGA
52544872 CATTGAATTT
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:52547396 original size:21 final size:21
Alignment explanation
Indices: 52547370--52547429 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
52547360 GACACATAAA
*
52547370 TGCCTGAAACGACACACTAGG
1 TGCCTGAAACGACACACGAGG
*
52547391 TGCCTGATACGACACACGAGG
1 TGCCTGAAACGACACACGAGG
52547412 TGCCTGAAATGCGACACA
1 TGCCTGAAA--CGACACA
52547430 TAAAGTGCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 27 0.79
23 7 0.21
ACGTcount: A:0.32, C:0.28, G:0.25, T:0.15
Consensus pattern (21 bp):
TGCCTGAAACGACACACGAGG
Found at i:52547437 original size:23 final size:23
Alignment explanation
Indices: 52547356--52547464 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 23
52547346 CCTGATCAGT
52547356 ATACGACACATAAA-TGCCTG-A
1 ATACGACACATAAAGTGCCTGAA
*
52547377 A-ACGACACACT-AGGTGCCTG--
1 ATACGACACA-TAAAGTGCCTGAA
** *
52547397 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
* *
52547420 ATGCGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAA
* *
52547443 ATACAACACATATAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
52547465 TCGGCAAAGC
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
20 10 0.14
21 25 0.35
23 37 0.51
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:52548167 original size:11 final size:11
Alignment explanation
Indices: 52548151--52548175 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52548141 TTAAATTTTC
52548151 CTATTCAATTT
1 CTATTCAATTT
52548162 CTATTCAATTT
1 CTATTCAATTT
52548173 CTA
1 CTA
52548176 CCGTAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.52
Consensus pattern (11 bp):
CTATTCAATTT
Found at i:52549207 original size:11 final size:11
Alignment explanation
Indices: 52549191--52549224 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
52549181 AAAACCCTAG
*
52549191 TTTTTCCTTTC
1 TTTTTCTTTTC
52549202 TTTTTCTTTTC
1 TTTTTCTTTTC
52549213 TTCTTTCTTTTC
1 TT-TTTCTTTTC
52549225 CCCTGTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:52549340 original size:14 final size:14
Alignment explanation
Indices: 52549303--52549336 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
52549293 ATATATTAGT
52549303 TAATAATAATAATGA
1 TAATAAT-ATAATGA
52549318 TAATAATATAAT-A
1 TAATAATATAATGA
52549331 TAATAA
1 TAATAA
52549337 ATATCTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 5 0.26
15 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATATAATGA
Found at i:52550393 original size:25 final size:25
Alignment explanation
Indices: 52550337--52550398 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
52550327 AGCCCTATCA
*
52550337 AGCTTTCCGTTATATGGTTCATGAG
1 AGCTTCCCGTTATATGGTTCATGAG
* *
52550362 AGTTTCCCGTTATATGGTT-ATTGCG
1 AGCTTCCCGTTATATGGTTCA-TGAG
*
52550387 CGCTTCCCGTTA
1 AGCTTCCCGTTA
52550399 ATAGCTCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGTTCATGAG
Found at i:52550511 original size:26 final size:26
Alignment explanation
Indices: 52550462--52550539 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
52550452 ACCGCAACTC
* *
52550462 TTATGAGCGTCCCGA-TATATGGCT-T
1 TTATGAGCTTCCCGATTA-AAGGCTCT
52550487 TTCATGAGCTTCCCGATTAAAGGCTCT
1 TT-ATGAGCTTCCCGATTAAAGGCTCT
* * * *
52550514 TTGTGAGCTTTCTGATTAAAAGCTCT
1 TTATGAGCTTCCCGATTAAAGGCTCT
52550540 CCGGAGCTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.05
26 37 0.84
27 5 0.11
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (26 bp):
TTATGAGCTTCCCGATTAAAGGCTCT
Found at i:52559531 original size:26 final size:25
Alignment explanation
Indices: 52559473--52559539 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
52559463 CACCTTAGCT
*
52559473 TTTATGAGCTTCCCGATTATGGCTC
1 TTTATGAGCTTCCCGATAATGGCTC
** * *
52559498 TTCGTGAGCTTCCTGGTAATTGGCTC
1 TTTATGAGCTTCCCGATAA-TGGCTC
52559524 TTTATGAGCTTCCCGA
1 TTTATGAGCTTCCCGA
52559540 CATTGCTTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (25 bp):
TTTATGAGCTTCCCGATAATGGCTC
Found at i:52561134 original size:31 final size:31
Alignment explanation
Indices: 52561096--52561212 Score: 155
Period size: 31 Copynumber: 3.7 Consensus size: 31
52561086 GCATATGTTT
52561096 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
52561127 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
52561158 TATACATTGACGAATTTGATTCGTATATGGATA
1 TATACATTGCCGAATTTGATTTGTATAT--AGA
*
52561191 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
52561213 AGCATTATAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
31 55 0.74
32 7 0.09
33 12 0.16
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:52561401 original size:43 final size:43
Alignment explanation
Indices: 52561331--52561434 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
52561321 TCGTGGTGTA
* *
52561331 ATTTCGTGTAAGACCAAAGCTGCGCTATTGACATCGATTTGAG
1 ATTTCGTGTAAGACCATAGCTGCGCTATTGACATCGATATGAG
* * *
52561374 ATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATATGAG
1 ATTTCGTGTAAGACCATAGCTGCGCTATTGACATCGATATGAG
*
52561417 ATTTCCATGTAAGACCAT
1 ATTT-CGTGTAAGACCAT
52561435 GTCTGGGACA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 42 0.79
44 11 0.21
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (43 bp):
ATTTCGTGTAAGACCATAGCTGCGCTATTGACATCGATATGAG
Found at i:52562871 original size:25 final size:25
Alignment explanation
Indices: 52562839--52562897 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
52562829 TCTTGTGATG
52562839 TGAGTTGTGTTTGCATGATACATGA
1 TGAGTTGTGTTTGCATGATACATGA
*
52562864 TGGGTTGTGTTTGCATGATACATGA
1 TGAGTTGTGTTTGCATGATACATGA
52562889 TGAGTTGTG
1 TGAGTTGTG
52562898 GGACCCTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.20, C:0.07, G:0.32, T:0.41
Consensus pattern (25 bp):
TGAGTTGTGTTTGCATGATACATGA
Found at i:52565103 original size:43 final size:43
Alignment explanation
Indices: 52564995--52565147 Score: 182
Period size: 43 Copynumber: 3.6 Consensus size: 43
52564985 ATCACATACA
* * *
52564995 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCTCATATCG
* * ** *
52565037 ATGCCACTGTTTCAGACAGGGTCTTACATGTAATCTCATATCG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCTCATATCG
* * * *
52565080 ATGCCAATATCCCGGACATGGTCTTCCACGTAATCTTATATCG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCTCATATCG
*
52565123 ATGCCAATGTCCCAGACATGGTCTT
1 ATGCCAATATCCCAGACATGGTCTT
52565148 GCACAAAACC
Statistics
Matches: 91, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 5 0.05
43 86 0.95
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACATGTAATCTCATATCG
Found at i:52568182 original size:17 final size:17
Alignment explanation
Indices: 52568162--52568194 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52568152 TTTTACATAA
52568162 TTTCTCT-TTTTATTTTT
1 TTTCTCTATTTT-TTTTT
52568179 TTTCTCTATTTTTTTT
1 TTTCTCTATTTTTTTT
52568195 CTTGTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTCTATTTTTTTTT
Found at i:52568190 original size:13 final size:13
Alignment explanation
Indices: 52568172--52568196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52568162 TTTCTCTTTT
52568172 TATTTTTTTTCTC
1 TATTTTTTTTCTC
52568185 TATTTTTTTTCT
1 TATTTTTTTTCT
52568197 TGTTCCTTTA
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTTTCTC
Found at i:52571469 original size:3 final size:3
Alignment explanation
Indices: 52571463--52571508 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
52571453 GAGTACAGAA
* * * *
52571463 GAT GAT GAA GAT GGT GAT TAT GAA GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
52571509 TTGCAGAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:52578142 original size:28 final size:27
Alignment explanation
Indices: 52578066--52578143 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 27
52578056 AATTATTCAC
* *
52578066 ATGCTTTATCAAATAAATCCACCCAATC
1 ATGC-TTATCAAATAAATCTACCCAATA
** *
52578094 ATGCTT-T-GGATCAATCTACCCAATA
1 ATGCTTATCAAATAAATCTACCCAATA
52578119 ATGCTTCATCAAATAAATCTACCCA
1 ATGCTT-ATCAAATAAATCTACCCA
52578144 CATGCTTTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
25 19 0.49
26 1 0.03
27 3 0.08
28 16 0.41
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.29
Consensus pattern (27 bp):
ATGCTTATCAAATAAATCTACCCAATA
Found at i:52582527 original size:21 final size:21
Alignment explanation
Indices: 52582501--52582555 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
52582491 AAAGCGGTGA
*
52582501 CGGTGAGATTAGTTACTGCAG
1 CGGTGAGATTAGATACTGCAG
* *
52582522 CGGTGAGATTGGATACTGTAG
1 CGGTGAGATTAGATACTGCAG
* *
52582543 CGGTAAAATTAGA
1 CGGTGAGATTAGA
52582556 AACAATGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGCAG
Found at i:52585227 original size:70 final size:69
Alignment explanation
Indices: 52585110--52585316 Score: 308
Period size: 70 Copynumber: 3.0 Consensus size: 69
52585100 ATGACTTCTT
* *
52585110 ATCTTTCCATTGGCACAATTAGATTCTAGATTTTGTAGCTATGAACAAAATGGAATCCGTTTCTT
1 ATCTTTCCATT-GCACAATTAGATTCTAGATTTTGTAGCTATCAACAAAATGGAATCCATTTCTT
52585175 TGTTC
65 TGTTC
*
52585180 ATCTTTCCATTGACACAATTAGATTCTAGATTTTGTAGCTATCAACAAAATGGAATCCTTTTCTT
1 ATCTTTCCATTG-CACAATTAGATTCTAGATTTTGTAGCTATCAACAAAATGGAATCCATTTCTT
*
52585245 TGTTT
65 TGTTC
* * *
52585250 ATCTTTCCATTGCTGCAATTAGATTCTAG-TTTTGTAGCTATTAACAAAAATGGAAGCCATTTCT
1 ATCTTTCCATTGC-ACAATTAGATTCTAGATTTTGTAGCTATCAAC-AAAATGGAATCCATTTCT
52585314 TTG
64 TTG
52585317 AACCAGTTTA
Statistics
Matches: 127, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
69 17 0.13
70 110 0.87
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (69 bp):
ATCTTTCCATTGCACAATTAGATTCTAGATTTTGTAGCTATCAACAAAATGGAATCCATTTCTTT
GTTC
Found at i:52599208 original size:20 final size:22
Alignment explanation
Indices: 52599185--52599232 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
52599175 AAAAAGATCT
*
52599185 TTTTTTGC-CTTTAAATTTG-A
1 TTTTTTGCGCTTTAAAATTGAA
*
52599205 TTTTTT-CGGTTTAAAATTGAA
1 TTTTTTGCGCTTTAAAATTGAA
52599226 TTTTTTG
1 TTTTTTG
52599233 AAACATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTTTGCGCTTTAAAATTGAA
Found at i:52599935 original size:20 final size:22
Alignment explanation
Indices: 52599912--52599959 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
52599902 AAAAAGATCT
*
52599912 TTTTTTGC-CTTTAAATTTG-A
1 TTTTTTGCGCTTTAAAATTGAA
*
52599932 TTTTTT-CGGTTTAAAATTGAA
1 TTTTTTGCGCTTTAAAATTGAA
52599953 TTTTTTG
1 TTTTTTG
52599960 AAACATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTTTGCGCTTTAAAATTGAA
Found at i:52607033 original size:18 final size:18
Alignment explanation
Indices: 52606998--52607033 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52606988 GCATAAATGT
* *
52606998 TATGACTAATTGTTAAAA
1 TATGACTAACTGTCAAAA
52607016 TATGACTAACTGTCAAAA
1 TATGACTAACTGTCAAAA
52607034 AGAAGTCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TATGACTAACTGTCAAAA
Found at i:52611541 original size:28 final size:28
Alignment explanation
Indices: 52611473--52611572 Score: 112
Period size: 28 Copynumber: 3.4 Consensus size: 28
52611463 AATTTTAAAA
52611473 TTTAAAATTTACATTTTGACC-CCTAACTTTT
1 TTTAAAA-TTACATTTTGACCTCC-AA--TTT
*
52611504 TTTAAAATTATATTTTGACCTCCAATTT
1 TTTAAAATTACATTTTGACCTCCAATTT
**
52611532 TTTAAAATTACATTTTGACCTTAAATTT
1 TTTAAAATTACATTTTGACCTCCAATTT
*
52611560 TCCTAAAATTACA
1 T-TTAAAATTACA
52611573 ATTCAACCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 29 0.47
29 10 0.16
30 14 0.23
31 9 0.15
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTAAAATTACATTTTGACCTCCAATTT
Found at i:52611970 original size:5 final size:5
Alignment explanation
Indices: 52611960--52612010 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
52611950 AGGGGCTTTC
* * *
52611960 GAAAA GAAAA GAAAAAA GAAAA GAGAA GAGAA G-AGA GAAAA GAAAA GAAAA
1 GAAAA GAAAA G--AAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
52612011 AAGAAAGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 2 0.05
5 32 0.82
7 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:52611978 original size:12 final size:12
Alignment explanation
Indices: 52611961--52612016 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
52611951 GGGGCTTTCG
52611961 AAAAGAAAAGAA
1 AAAAGAAAAGAA
*
52611973 AAAAGAAAAGAG
1 AAAAGAAAAGAA
* * *
52611985 AAGAGAAGAGAG
1 AAAAGAAAAGAA
52611997 AAAAGAAAAGAA
1 AAAAGAAAAGAA
52612009 AAAAGAAA
1 AAAAGAAA
52612017 GAGAGAAGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:52612156 original size:13 final size:13
Alignment explanation
Indices: 52612138--52612165 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52612128 CCCGAATAAG
52612138 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
52612151 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
52612164 AA
1 AA
52612166 TAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:52612706 original size:15 final size:15
Alignment explanation
Indices: 52612686--52612736 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
52612676 GCCCAACAGT
52612686 AGAAAAAAAAAGGGA
1 AGAAAAAAAAAGGGA
*
52612701 AGAAAAAAATA-GGA
1 AGAAAAAAAAAGGGA
*
52612715 A-AAAGAAAAAAGAGA
1 AGAAA-AAAAAAGGGA
*
52612730 AGGAAAA
1 AGAAAAA
52612737 GGCCCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 9 0.31
15 15 0.52
16 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (15 bp):
AGAAAAAAAAAGGGA
Found at i:52612908 original size:16 final size:16
Alignment explanation
Indices: 52612851--52612900 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
52612841 TTTTTTACAT
52612851 TTTTTAATTTTAGA-AA
1 TTTTTAA-TTTAGATAA
* *
52612867 TATTTCATTT--ATAA
1 TTTTTAATTTAGATAA
52612881 TTTTTAATTTAGATAA
1 TTTTTAATTTAGATAA
52612897 TTTT
1 TTTT
52612901 AATATTAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 1 0.04
14 10 0.37
15 3 0.11
16 13 0.48
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTTAATTTAGATAA
Found at i:52615383 original size:24 final size:24
Alignment explanation
Indices: 52615356--52615404 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
52615346 TCAAAAATTC
52615356 TTGCGTTTTAAAATAAAATGGTTA
1 TTGCGTTTTAAAATAAAATGGTTA
*
52615380 TTGCGTTTTAAAATAAAATGTTTA
1 TTGCGTTTTAAAATAAAATGGTTA
52615404 T
1 T
52615405 CTTTTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (24 bp):
TTGCGTTTTAAAATAAAATGGTTA
Found at i:52615813 original size:3 final size:3
Alignment explanation
Indices: 52615805--52615844 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
52615795 TTTGTTTTAA
52615805 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52615845 AATCAAGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:52618240 original size:30 final size:31
Alignment explanation
Indices: 52618199--52618268 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
52618189 ACAATTTGAC
* *
52618199 ACATG-AACTTTGAT-TTAGTGT-AATTATAT
1 ACATGAAACTTTGATCATAGT-TCAAATATAT
*
52618228 ACATTAAACTTTGATCATAGTTCAAATATAT
1 ACATGAAACTTTGATCATAGTTCAAATATAT
52618259 ACATGAAACT
1 ACATGAAACT
52618269 CTAATTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 10 0.29
31 20 0.59
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (31 bp):
ACATGAAACTTTGATCATAGTTCAAATATAT
Found at i:52619160 original size:15 final size:16
Alignment explanation
Indices: 52619134--52619168 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52619124 AACACAATTA
52619134 AAAAACACTTCAAAAC
1 AAAAACACTTCAAAAC
*
52619150 AAAAACA-TTCAAATC
1 AAAAACACTTCAAAAC
52619165 AAAA
1 AAAA
52619169 GAAACATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAACACTTCAAAAC
Found at i:52620165 original size:15 final size:16
Alignment explanation
Indices: 52620140--52620169 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52620130 ATGTGAATAA
52620140 TATTATTTAAAATTTT
1 TATTATTTAAAATTTT
52620156 TATT-TTTAAAATTT
1 TATTATTTAAAATTT
52620170 ACTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATTTAAAATTTT
Found at i:52620200 original size:18 final size:18
Alignment explanation
Indices: 52620162--52620197 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52620152 TTTTTATTTT
*
52620162 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
52620180 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
52620198 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:52620310 original size:12 final size:12
Alignment explanation
Indices: 52620295--52620319 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52620285 AATATTAAAA
52620295 ATATAATATTTT
1 ATATAATATTTT
52620307 ATATAATATTTT
1 ATATAATATTTT
52620319 A
1 A
52620320 AATATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATAATATTTT
Found at i:52624008 original size:22 final size:22
Alignment explanation
Indices: 52623982--52624026 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
52623972 TTTCTGGGTC
*
52623982 TCCCACTCTTTTACGTTAATGT
1 TCCCACTCTTTTACGTCAATGT
52624004 TCCCACTCTTTTACGTCAATGT
1 TCCCACTCTTTTACGTCAATGT
52624026 T
1 T
52624027 TTCTCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (22 bp):
TCCCACTCTTTTACGTCAATGT
Found at i:52628122 original size:18 final size:18
Alignment explanation
Indices: 52628088--52628145 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
52628078 TAATGTTTAT
*
52628088 TTATATATTAT-TATAAA
1 TTATATAATATATATAAA
52628105 TTATATAATATATATAAA
1 TTATATAATATATATAAA
* *
52628123 TAAAATAATATATTATAACA
1 TTATATAATATA-TATAA-A
52628143 TTA
1 TTA
52628146 ACAGAAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.29
18 16 0.47
19 5 0.15
20 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATATAATATATATAAA
Found at i:52629811 original size:11 final size:11
Alignment explanation
Indices: 52629797--52629844 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
52629787 ATATCCGAAC
52629797 AATAATAACAA
1 AATAATAACAA
*
52629808 AATAATAGCAA
1 AATAATAACAA
* *
52629819 CATAATAATAA
1 AATAATAACAA
**
52629830 AATGGTAACAA
1 AATAATAACAA
52629841 AATA
1 AATA
52629845 GGGAGAAAAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATAACAA
Found at i:52635467 original size:44 final size:43
Alignment explanation
Indices: 52635365--52635485 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 43
52635355 CCTTTATTTT
* * * * *
52635365 AATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTC
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
* *
52635408 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATTACTGGCCTC
52635452 AATCTGCTCCACTGTAACCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGAT
52635486 CTGACATTCT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 28 0.42
44 39 0.58
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
AATCTGCTCCACTGTAACTCAGGGAGATAAGATTACTGGCCTC
Found at i:52644793 original size:63 final size:63
Alignment explanation
Indices: 52644694--52644822 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 63
52644684 AGCTAGTAGA
52644694 CTCTTTCCCAAGACGACTTCTCGAGCCCGAGTATCCTGAAATTTCTTTTCCCATTGATTAACT
1 CTCTTTCCCAAGACGACTTCTCGAGCCCGAGTATCCTGAAATTTCTTTTCCCATTGATTAACT
* *
52644757 CTCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCTGAAATTTCTTTTCCCATTGATTAGCT
1 CTCTTTCCCAAGACGACTTCTCGAGCCCGAGTATCCTGAAATTTCTTTTCCCATTGATTAACT
52644820 CTC
1 CTC
52644823 GTCTTTTCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.35
Consensus pattern (63 bp):
CTCTTTCCCAAGACGACTTCTCGAGCCCGAGTATCCTGAAATTTCTTTTCCCATTGATTAACT
Found at i:52650737 original size:23 final size:21
Alignment explanation
Indices: 52650695--52650737 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
52650685 GAATAATAGT
*
52650695 AATACAAATAACAAATACAAC
1 AATACAAATAACAAAGACAAC
*
52650716 AATACGAATATAACAACGACAA
1 AATAC-AA-ATAACAAAGACAA
52650738 TGCATATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.63, C:0.19, G:0.05, T:0.14
Consensus pattern (21 bp):
AATACAAATAACAAAGACAAC
Found at i:52650865 original size:20 final size:19
Alignment explanation
Indices: 52650828--52650867 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
52650818 AATTATATGC
*
52650828 ACAAATCAATATACATAAA
1 ACAAATCAATATAAATAAA
*
52650847 ACAAATGAACTATAAATAAA
1 ACAAATCAA-TATAAATAAA
52650867 A
1 A
52650868 TGAAAGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (19 bp):
ACAAATCAATATAAATAAA
Found at i:52652134 original size:17 final size:16
Alignment explanation
Indices: 52652114--52652148 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
52652104 GCTGAAAATT
52652114 TTTAATTTGTGGGCTTG
1 TTTAATTT-TGGGCTTG
*
52652131 TTTAGTTTTGGGCTTG
1 TTTAATTTTGGGCTTG
52652147 TT
1 TT
52652149 GGGTTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.09, C:0.06, G:0.29, T:0.57
Consensus pattern (16 bp):
TTTAATTTTGGGCTTG
Found at i:52654239 original size:28 final size:25
Alignment explanation
Indices: 52654208--52654262 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
52654198 AATAATTCTA
52654208 TTTTAAATCAATAAAATTAACACAACTT
1 TTTTAAA--AATAAAATTAACACAA-TT
*
52654236 TTTTAAAAATAAAATTAGCACAATT
1 TTTTAAAAATAAAATTAACACAATT
52654261 TT
1 TT
52654263 GTTTATTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
28 7 0.27
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (25 bp):
TTTTAAAAATAAAATTAACACAATT
Found at i:52654424 original size:28 final size:28
Alignment explanation
Indices: 52654355--52654424 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
52654345 TTGTACTTAC
*
52654355 TTGGTACTTAAAATTCTTTTTGACCTAA
1 TTGGTACTTAAACTTCTTTTTGACCTAA
* ** *
52654383 TTTGTAC-CCAACTTTTTTTTGACCTAA
1 TTGGTACTTAAACTTCTTTTTGACCTAA
*
52654410 TTGGTACTTGAACTT
1 TTGGTACTTAAACTT
52654425 GAATCGTGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.47
Consensus pattern (28 bp):
TTGGTACTTAAACTTCTTTTTGACCTAA
Found at i:52666972 original size:15 final size:15
Alignment explanation
Indices: 52666948--52666979 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52666938 TATATATGCA
*
52666948 AAATATAAAAGACAT
1 AAATACAAAAGACAT
52666963 AAATACAAAAGACAT
1 AAATACAAAAGACAT
52666978 AA
1 AA
52666980 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:52672408 original size:25 final size:25
Alignment explanation
Indices: 52672374--52672432 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
52672364 AACTTTAGCA
52672374 TGCTCTCTGATTATTAGCACATCAG
1 TGCTCTCTGATTATTAGCACATCAG
* * *
52672399 TGCTCTCTGATTTTTAGCACGTTAG
1 TGCTCTCTGATTATTAGCACATCAG
52672424 TGCTCTCTG
1 TGCTCTCTG
52672433 TTTAGCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.41
Consensus pattern (25 bp):
TGCTCTCTGATTATTAGCACATCAG
Found at i:52672439 original size:22 final size:22
Alignment explanation
Indices: 52672387--52672478 Score: 96
Period size: 22 Copynumber: 4.0 Consensus size: 22
52672377 TCTCTGATTA
*
52672387 TTAGCACATCAGTGCTCTCTGATTT
1 TTAGCACATTAGTGCTCTCTG---T
*
52672412 TTAGCACGTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
*
52672434 TTAGCA-ATTCTGTGCTCTCTGT
1 TTAGCACATT-AGTGCTCTCTGT
* *
52672456 TTAGCACTTTAGTGCTATCTGT
1 TTAGCACATTAGTGCTCTCTGT
52672478 T
1 T
52672479 CATTAGTGCA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.03
22 35 0.60
23 2 0.03
25 19 0.33
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.43
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:52678295 original size:15 final size:15
Alignment explanation
Indices: 52678275--52678311 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
52678265 TACAAGAGGA
52678275 AATCAATGGCACCAT
1 AATCAATGGCACCAT
52678290 AATCAATGGCACCAT
1 AATCAATGGCACCAT
*
52678305 AAACAAT
1 AATCAAT
52678312 TGTTTATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (15 bp):
AATCAATGGCACCAT
Found at i:52685401 original size:6 final size:6
Alignment explanation
Indices: 52685367--52685411 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
52685357 CACAACACCT
* **
52685367 TAACAG TAATCAG TAACGG TAGTAG TAACAG TAACAG TAACAG TA
1 TAACAG TAA-CAG TAACAG TAACAG TAACAG TAACAG TAACAG TA
52685412 TTCAACAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.22
Consensus pattern (6 bp):
TAACAG
Found at i:52685748 original size:21 final size:20
Alignment explanation
Indices: 52685724--52685781 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
52685714 ATGAAGTACA
52685724 CATAACAATATTCAGTAACTT
1 CATAACAATATTCAGTAAC-T
52685745 CATAATTC-A-ATTCAGT-ACT
1 CATAA--CAATATTCAGTAACT
*
52685764 CAAAAACAATATTCAGTA
1 C-ATAACAATATTCAGTA
52685782 TTCCATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 12 0.40
21 12 0.40
22 1 0.03
23 1 0.03
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
CATAACAATATTCAGTAACT
Found at i:52685789 original size:40 final size:40
Alignment explanation
Indices: 52685727--52685805 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
52685717 AAGTACACAT
52685727 AACAATATTCAGTAACTTCATAATTCAATTCAGTACTCAAA
1 AACAATATTCAGTAACTTCATAATTCAATTCAGTA-TCAAA
52685768 AACAATATTCAGT-A-TTCCATAATTCAATTCAGTATCAA
1 AACAATATTCAGTAACTT-CATAATTCAATTCAGTATCAA
52685806 TCTCAATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
39 6 0.16
40 18 0.49
41 13 0.35
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (40 bp):
AACAATATTCAGTAACTTCATAATTCAATTCAGTATCAAA
Found at i:52687625 original size:16 final size:16
Alignment explanation
Indices: 52687604--52687637 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52687594 CATTTCACTA
*
52687604 TTCTATCTTTTGTATT
1 TTCTATCTTTTATATT
52687620 TTCTATCTTTTATATT
1 TTCTATCTTTTATATT
52687636 TT
1 TT
52687638 GCATGAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71
Consensus pattern (16 bp):
TTCTATCTTTTATATT
Found at i:52699814 original size:21 final size:21
Alignment explanation
Indices: 52699788--52699834 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
52699778 TGGAGGAAGT
*
52699788 GTTTTCAAACAGTATTACTGC
1 GTTTTCAAACAGCATTACTGC
*
52699809 GTTTTCAGACAGCATTACTGC
1 GTTTTCAAACAGCATTACTGC
*
52699830 ATTTT
1 GTTTT
52699835 TGGTGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (21 bp):
GTTTTCAAACAGCATTACTGC
Found at i:52702460 original size:13 final size:13
Alignment explanation
Indices: 52702444--52702478 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
52702434 TAGCTTCTCT
*
52702444 TTTTCAGAAGTGC
1 TTTTCAAAAGTGC
52702457 TTTTCAAAAGTGC
1 TTTTCAAAAGTGC
*
52702470 TTTTGAAAA
1 TTTTCAAAA
52702479 CCCAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAGTGC
Found at i:52706701 original size:15 final size:15
Alignment explanation
Indices: 52706681--52706710 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52706671 AGCTACTGAT
52706681 TTTTTAGTATTTAAA
1 TTTTTAGTATTTAAA
52706696 TTTTTAGTATTTAAA
1 TTTTTAGTATTTAAA
52706711 CACTGAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTTTTAGTATTTAAA
Found at i:52709166 original size:25 final size:25
Alignment explanation
Indices: 52709138--52709233 Score: 90
Period size: 25 Copynumber: 3.8 Consensus size: 25
52709128 AGCGTCCCGA
52709138 TATTTGGCTCTCACGAGCTTCCTAT
1 TATTTGGCTCTCACGAGCTTCCTAT
* *
52709163 TATTTGGCCCTTACGAGCTTCCTGA-
1 TATTTGGCTCTCACGAGCTTCCT-AT
* * *
52709188 TAATTGGCTCTCATGAGCTTCTCGAT
1 TATTTGGCTCTCACGAGCTTC-CTAT
*
52709214 TA-ATGGCTCTC-CGAAGCTTC
1 TATTTGGCTCTCACG-AGCTTC
52709234 TCGATATTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
24 1 0.02
25 53 0.91
26 4 0.07
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (25 bp):
TATTTGGCTCTCACGAGCTTCCTAT
Found at i:52709370 original size:25 final size:25
Alignment explanation
Indices: 52709315--52709392 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
52709305 TCTCGATAAC
* *
52709315 TGGCTCGCAAGAGCTTCCTGTTATA
1 TGGCTCACAAGAGCTTCCTGTTACA
** *
52709340 CAGCTCACATGAGCTTCCTGTTACA
1 TGGCTCACAAGAGCTTCCTGTTACA
* *
52709365 TGGCTCGA-AAGAGTTTCCTAATTACA
1 TGGCTC-ACAAGAGCTTCCT-GTTACA
52709391 TG
1 TG
52709393 CTCGTATGAG
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
25 33 0.80
26 8 0.20
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (25 bp):
TGGCTCACAAGAGCTTCCTGTTACA
Found at i:52710100 original size:40 final size:39
Alignment explanation
Indices: 52710056--52710134 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
52710046 GGTCGTGTAG
52710056 GTCACACAGCCTAGGCCGATTTGGGCATGTAGGCCAACA
1 GTCACACAGCCTAGGCCGATTTGGGCATGTAGGCCAACA
52710095 NGTCACACAGCCTAGGCCGATTTGGGCATGTAGGCCAACA
1 -GTCACACAGCCTAGGCCGATTTGGGCATGTAGGCCAACA
52710135 TGGGCATCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (39 bp):
GTCACACAGCCTAGGCCGATTTGGGCATGTAGGCCAACA
Found at i:52721409 original size:32 final size:32
Alignment explanation
Indices: 52721368--52721439 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
52721358 AGTATGTGGC
* *
52721368 CATGTGGGTCACAC-AGCCTA-GGCCGATTTGGG
1 CATGTGGGTCACACGAG-C-AGGGCCAATATGGG
52721400 CATGTGGGTCACACGAGCAGGGCCAATATGGG
1 CATGTGGGTCACACGAGCAGGGCCAATATGGG
52721432 CATGTGGG
1 CATGTGGG
52721440 CCCACACGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 1 0.03
32 33 0.92
33 2 0.06
ACGTcount: A:0.21, C:0.22, G:0.38, T:0.19
Consensus pattern (32 bp):
CATGTGGGTCACACGAGCAGGGCCAATATGGG
Found at i:52721705 original size:17 final size:18
Alignment explanation
Indices: 52721673--52721707 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52721663 AGCATGCGGG
52721673 ACATGTTAATTCTGTTAT
1 ACATGTTAATTCTGTTAT
*
52721691 ACATGTTTA-TCTGTTAT
1 ACATGTTAATTCTGTTAT
52721708 CTGTATCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
ACATGTTAATTCTGTTAT
Found at i:52721815 original size:25 final size:26
Alignment explanation
Indices: 52721781--52721831 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
52721771 GCCGATATAT
*
52721781 TGGCAGCTT-GCTATAAACTATTCTG
1 TGGCAGCTTGGCTACAAACTATTCTG
52721806 TGGCAGCTTGGCTACAAACTATTCTG
1 TGGCAGCTTGGCTACAAACTATTCTG
52721832 ATAAGTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (26 bp):
TGGCAGCTTGGCTACAAACTATTCTG
Found at i:52727371 original size:28 final size:28
Alignment explanation
Indices: 52727321--52727407 Score: 130
Period size: 26 Copynumber: 3.2 Consensus size: 28
52727311 AAAATTTACT
52727321 AAAATATTAT--CTTTTTTTTATTTA-C
1 AAAATATTATAACTTTTTTTTATTTATC
52727346 TAAAATATTATAACTTTTTTTTATTTATC
1 -AAAATATTATAACTTTTTTTTATTTATC
52727375 AAAATATTATAA--TTTTTTTATTTATC
1 AAAATATTATAACTTTTTTTTATTTATC
52727401 AAAATAT
1 AAAATAT
52727408 ACAAAAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
26 31 0.53
28 26 0.45
29 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (28 bp):
AAAATATTATAACTTTTTTTTATTTATC
Found at i:52727884 original size:26 final size:27
Alignment explanation
Indices: 52727850--52727902 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
52727840 ATAACTCTAT
52727850 TTTAATTAA-GTTTTAAATTAAAATAG
1 TTTAATTAATGTTTTAAATTAAAATAG
* *
52727876 TTTACTTAATTTTTTAAATTAAAATAG
1 TTTAATTAATGTTTTAAATTAAAATAG
52727903 AGTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (27 bp):
TTTAATTAATGTTTTAAATTAAAATAG
Found at i:52727911 original size:27 final size:27
Alignment explanation
Indices: 52727860--52727911 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
52727850 TTTAATTAAG
*
52727860 TTTTAAATTAAAATAGTTTACTTAATT
1 TTTTAAATTAAAATAGGTTACTTAATT
52727887 TTTTAAATTAAAATAGAGTTA-TTAA
1 TTTTAAATTAAAATAG-GTTACTTAA
52727912 ATGAGAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (27 bp):
TTTTAAATTAAAATAGGTTACTTAATT
Found at i:52727952 original size:18 final size:19
Alignment explanation
Indices: 52727889--52727947 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
52727879 ACTTAATTTT
52727889 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
52727908 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
52727926 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
52727945 TTA
1 TTA
52727948 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:52728547 original size:27 final size:27
Alignment explanation
Indices: 52728509--52728560 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
52728499 CATTCTAGTC
52728509 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
52728536 CTTTGGCACCATTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
52728561 GTGATTGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:52728568 original size:27 final size:27
Alignment explanation
Indices: 52728511--52728569 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
52728501 TTCTAGTCCT
*
52728511 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* *
52728538 TTGGCACCATTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
52728565 TTGGC
1 TTGGC
52728570 CTGATCAGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:52728652 original size:28 final size:28
Alignment explanation
Indices: 52728621--52728690 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
52728611 TTGTTTTGGT
**
52728621 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGGGATA
52728649 ATATTTTGGTAAATAAAAAAAAGGGATA
1 ATATTTTGGTAAATAAAAAAAAGGGATA
*
52728677 ATATTTTGATAAAT
1 ATATTTTGGTAAAT
52728691 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGGGATA
Found at i:52730752 original size:24 final size:24
Alignment explanation
Indices: 52730724--52730771 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52730714 TAAATAACTA
52730724 TTATAAGATCTTTAGAATAATATT
1 TTATAAGATCTTTAGAATAATATT
52730748 TTATAAGATCTTTAGAATAATATT
1 TTATAAGATCTTTAGAATAATATT
52730772 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
TTATAAGATCTTTAGAATAATATT
Found at i:52730959 original size:26 final size:26
Alignment explanation
Indices: 52730923--52730978 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
52730913 AAAAATAACT
52730923 AAAATATTATAACTTTTTTATTTACC
1 AAAATATTATAACTTTTTTATTTACC
*
52730949 AAAATATTATAATTTTTTTATTTACC
1 AAAATATTATAACTTTTTTATTTACC
52730975 AAAA
1 AAAA
52730979 ACAAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATATTATAACTTTTTTATTTACC
Found at i:52731132 original size:4 final size:4
Alignment explanation
Indices: 52731123--52731244 Score: 94
Period size: 4 Copynumber: 30.0 Consensus size: 4
52731113 GAAGGAGAGG
*
52731123 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GGAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA
*
52731170 GGAAA G-GA GAAGA GAAA -AAA GAAA GAAA G-AA GAAGA GGAAA GGAGAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA -GA-AA
* *
52731217 GAAA -AAA GAAA AAAA AAAA GGAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA -GAAA GAAA
52731245 AGGAAAGGAG
Statistics
Matches: 100, Mismatches: 6, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
3 15 0.15
4 57 0.57
5 23 0.23
6 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:52731224 original size:13 final size:13
Alignment explanation
Indices: 52731188--52731264 Score: 50
Period size: 13 Copynumber: 5.7 Consensus size: 13
52731178 GAAGAGAAAA
*
52731188 AAGAAAGAAAGAAG
1 AAGAAA-AAAGGAG
**
52731202 AAGAGGAAAGGAG
1 AAGAAAAAAGGAG
*
52731215 AAGAAAAAA-GAA
1 AAGAAAAAAGGAG
*
52731227 AAAAAAAAAGGA-
1 AAGAAAAAAGGAG
52731239 AAGAAAAGGAAAGGAG
1 AAG-AAA--AAAGGAG
52731255 AAGAGAAAAA
1 AAGA-AAAAA
52731265 AAAAGAAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
12 12 0.24
13 18 0.37
14 7 0.14
15 7 0.14
16 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGGAG
Found at i:52731239 original size:76 final size:73
Alignment explanation
Indices: 52731137--52731304 Score: 234
Period size: 76 Copynumber: 2.2 Consensus size: 73
52731127 GAAAGAAAGA
* *
52731137 AAGAAAGAAAGAAAGAAAAAGAAGGAAAGGAAAGGAAAGGAGAAGAGAAAAAAGAAAGAAAGAAG
1 AAGAAA-AAAGAAA-AAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA-AAAG-AAGAAG
52731202 AAGAGGAAAGG-A-G
62 -AG-GG-AAGGAAGG
52731215 AAGAAAAAAGAAAAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGAAGAGGG
1 AAGAAAAAAGAAAAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGAAGAGGG
52731280 AAGGAAGG
66 AAGGAAGG
52731288 AA-AAAAAAGAAAAAAAA
1 AAGAAAAAAGAAAAAAAA
52731305 GGTAATTTTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
71 4 0.05
72 18 0.21
73 5 0.06
74 6 0.07
75 4 0.05
76 36 0.42
77 7 0.08
78 6 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (73 bp):
AAGAAAAAAGAAAAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGAAGAGGG
AAGGAAGG
Found at i:52731256 original size:71 final size:73
Alignment explanation
Indices: 52731131--52731304 Score: 207
Period size: 71 Copynumber: 2.4 Consensus size: 73
52731121 GGGAAAGAAA
* * * *
52731131 GAAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGGAAAGGAAAGGAGAAGAGAA-A-AAAGAAA
1 GAAAGGAAGGAAGAAA-AAAGAAAAA-AA-AAAAGGAAAGAAAAGGAGAAGAGAAGAGAAA-AAA
52731194 GAAAGAAGAAGAG
62 -AAAGAAGAAGAG
52731207 GAAAGG-A-GAAGAAAAAAGAAAAAAAAAAAGGAAAGAAAAGGA-AAGGAGAAGAGAAAAAAAAA
1 GAAAGGAAGGAAGAAAAAAGAAAAAAAAAAAGGAAAGAAAAGGAGAA-GAGAAGAGAAAAAAAAA
52731269 GAAGAAGAG
65 GAAGAAGAG
*
52731278 GGAAGGAAGGAA-AAAAAAGAAAAAAAA
1 GAAAGGAAGGAAGAAAAAAGAAAAAAAA
52731305 GGTAATTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
70 2 0.02
71 37 0.42
72 22 0.25
73 15 0.17
74 6 0.07
75 1 0.01
76 5 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (73 bp):
GAAAGGAAGGAAGAAAAAAGAAAAAAAAAAAGGAAAGAAAAGGAGAAGAGAAGAGAAAAAAAAAG
AAGAAGAG
Found at i:52734706 original size:11 final size:11
Alignment explanation
Indices: 52734690--52734716 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52734680 TTTATAACTT
52734690 AATTTGGATAC
1 AATTTGGATAC
52734701 AATTTGGATAC
1 AATTTGGATAC
52734712 AATTT
1 AATTT
52734717 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:52738166 original size:27 final size:27
Alignment explanation
Indices: 52738067--52738169 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 27
52738057 AACACGAGTA
*
52738067 GTGCCGCCAATCAGT-ATGGCACCATTG
1 GTGCCGCCAATCA-TCTTGGCACCATTG
** * *
52738094 GTGCCGCCAATC-TCCTTTACACCGTCG
1 GTGCCGCCAATCAT-CTTGGCACCATTG
* * *
52738121 GTGCTGCCAAT-AACTTTGGCACCTTTG
1 GTGCCGCCAATCATC-TTGGCACCATTG
52738148 GTGCCGCCAATCATCTTGGCAC
1 GTGCCGCCAATCATCTTGGCAC
52738170 GACTAGGGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 54 0.93
28 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.26
Consensus pattern (27 bp):
GTGCCGCCAATCATCTTGGCACCATTG
Done.