Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 171 of 185
Found at i:52152084 original size:44 final size:43
Alignment explanation
Indices: 52151978--52152452 Score: 285
Period size: 44 Copynumber: 10.9 Consensus size: 43
52151968 AATATTAGAG
* *
52151978 ATCTTATCTCCCTG-AGATTACAGTGGAGCAGATCGTA--TCAA
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGCACAA
* * *
52152019 GTCTTATCTCCCTG-AGATTACAGAGGAGCAGATCGGAGCCACAA
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAG-CACAA
* * * * **
52152063 ACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATACAA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAA-GCACAA
* * * * *
52152107 GTCTTATCTCCCT-AAGGTTACAGTGGAGTAGACCGAAGAATTTCAG
1 ATCTTATCTCCCTGAA-GTTACAGTGGAGCAGATCGAAGCA---CAA
* * *
52152153 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAG-CACAA
* * *
52152197 ATCTTATCTTCCTG-AGTTTACAGCGGAGCAGATCGAAG-ACACT
1 ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGCACA-A
* ** **
52152240 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATA-AA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCACAA
* * * * *
52152282 TGATCTTATCTCTCTGAATTTACAGTAGAGTAGATC---GCATCAG
1 --ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCA-CAA
* * * * *
52152325 GTCTTATCTCCCTGATA-TTACAATGGAGCAGACCGAAGGATTTCAG
1 ATCTTATCTCCCTGA-AGTTACAGTGGAGCAGATCGAAGCA---CAA
* * * *
52152371 ATCTTATCTCCCTTAGGTTACAGTGGAACAGATTGAAGC-CAGA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCACA-A
*
52152414 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAG
1 -ATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAG
52152453 ACACTATCCT
Statistics
Matches: 331, Mismatches: 74, Indels: 55
0.72 0.16 0.12
Matches are distributed among these distances:
41 61 0.18
42 5 0.02
43 36 0.11
44 158 0.48
45 2 0.01
46 67 0.20
47 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCACAA
Found at i:52152202 original size:90 final size:84
Alignment explanation
Indices: 52151976--52152447 Score: 303
Period size: 90 Copynumber: 5.4 Consensus size: 84
52151966 TGAATATTAG
* * *
52151976 AGATCTTATCTCCCTG-AGATTACAGTGGAGCAGATCGTATC-AAGTCTTATCTCCCTGAGATTA
1 AGATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTGAAACAAAGTCTTATCTCCCTGAGATTA
*
52152039 CAGAGGAGCAGATCGGAGCCAC
65 CAGAGGAGCAGATCGAAG--AC
* * * * * * *
52152061 AAACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATACAAGTCTTATCTCCCTAAGGTT
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAA-ACA-AAGTCTTATCTCCCTGAGATT
* * *
52152126 ACAGTGGAGTAGACCGAAGAATTTC
64 ACAGAGGAGCAGATCGAAG-A---C
* * * * *
52152151 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTTCCTGAGTTT
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAA-ACA-AAGTCTTATCTCCCTGAGATT
*
52152216 ACAGCGGAGCAGATCGAAGAC
64 ACAGAGGAGCAGATCGAAGAC
* * * * *
52152237 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGA-AT
1 A-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACAAA-G-TCTTATCTCCCTGAGA-
* * *
52152301 TTACAGTA-GAGTAGATCGCA-TC
62 TTACAG-AGGAGCAGATCGAAGAC
* * ** * *
52152323 AGGTCTTATCTCCCTGATA-TTACAATGGAGCAGACCGAAGGATTTCAGA-TCTTATCTCCCTTA
1 AGATCTTATCTCCCTGA-AGTTACAGTGGAGCAGATTGAA--A---CAAAGTCTTATCTCCCTGA
* * * * *
52152386 GGTTACAGTGGAACAGATTGAAGCCAG
60 GATTACAGAGGAGCAGATCGAAG--AC
*
52152413 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGAT
1 AGATCTTATCTCCCTGAAG-TTACAGTGGAGCAGAT
52152448 CGAAGACACT
Statistics
Matches: 294, Mismatches: 68, Indels: 45
0.72 0.17 0.11
Matches are distributed among these distances:
85 61 0.21
86 8 0.03
87 90 0.31
88 35 0.12
89 1 0.00
90 99 0.34
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (84 bp):
AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACAAAGTCTTATCTCCCTGAGATTAC
AGAGGAGCAGATCGAAGAC
Found at i:52152218 original size:134 final size:133
Alignment explanation
Indices: 52152020--52152267 Score: 320
Period size: 134 Copynumber: 1.9 Consensus size: 133
52152010 TCGTATCAAG
*
52152020 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGGAGCCACAAACCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACA
* * * * * * *
52152085 GTGGGGCAGGTTGAATATACAAGTCTTATCTCCCT-AAGGTTACAGTGGAGTAGACCGAAGAATT
66 GCGGAGCAGATCGAAGACACAA-TCCTATCTCCCTGAA-GTTACAGTGGAGTAGACCGAAGAATT
52152149 TCAGA
129 TCAGA
* * * * * *
52152154 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTTCCTG-AGTTTAC
1 TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAG-TTAC
*
52152218 AGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAG
65 AGCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTACAGTGGAG
52152268 CAGATTAAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
133 25 0.26
134 72 0.74
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (133 bp):
TCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACA
GCGGAGCAGATCGAAGACACAATCCTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTC
AGA
Found at i:52152317 original size:87 final size:87
Alignment explanation
Indices: 52151982--52152318 Score: 280
Period size: 87 Copynumber: 3.9 Consensus size: 87
52151972 TTAGAGATCT
*
52151982 TATCTCCCTG-AGATTACAGTGGAGCAGATCG--TAT-CAAGTCTTATCTCCCTGAGA-TTACAG
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGA-ATTTACAG
* * *
52152042 -AGGAGCAGATCGGAGCCACAAACC
64 TA-GAGCAGATCGAAGACACAATCC
* * *
52152066 TTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATACAAGTCTTATCTCCCT-AAGGTTACAG
1 -TATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAA-TTTACAG
* * * *
52152130 TGGAGTAGACCGAAGA-ATTTCAGATCT
64 TAGAGCAGATCGAAGACA---CA-ATCC
* *** * * * * **
52152157 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTTCCTGAGTTTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAATTTACAGTA
*
52152222 GAGCAGATCGAAGACACTATCC
66 GAGCAGATCGAAGACACAATCC
* *
52152244 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATA-AATGATCTTATCTCTCTGAATTTACAG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAA-G-TCTTATCTCCCTGAATTTACAG
*
52152307 TAGAGTAGATCG
64 TAGAGCAGATCG
52152319 CATCAGGTCT
Statistics
Matches: 200, Mismatches: 37, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
85 27 0.14
86 6 0.03
87 65 0.32
88 33 0.17
90 65 0.32
91 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATACAAGTCTTATCTCCCTGAATTTACAGTA
GAGCAGATCGAAGACACAATCC
Found at i:52154330 original size:17 final size:17
Alignment explanation
Indices: 52154308--52154340 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52154298 TATTTAATTC
52154308 TTTTAATAT-ATTATATA
1 TTTTAA-ATCATTATATA
52154325 TTTTAAATCATTATAT
1 TTTTAAATCATTATAT
52154341 GTATAAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAATCATTATATA
Found at i:52161219 original size:30 final size:28
Alignment explanation
Indices: 52161175--52161276 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 28
52161165 GGTCAATCTA
52161175 TAATTTTAAGAAAGTTTAGGGTTTAAAAATG
1 TAATTTTAA-AAAGTTTAGGG-TT-AAAATG
* * * *
52161206 AAATTTTGAAAAGTTGAGGGGTCAAAATG
1 TAATTTTAAAAAGTTTA-GGGTTAAAATG
52161235 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
1 TAATTTTA-AAAAGTTTAG-GGTTAAAATG
52161265 TAATTTTAAAAA
1 TAATTTTAAAAA
52161277 AATAAAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
29 17 0.28
30 33 0.55
31 10 0.17
ACGTcount: A:0.44, C:0.01, G:0.20, T:0.35
Consensus pattern (28 bp):
TAATTTTAAAAAGTTTAGGGTTAAAATG
Found at i:52161264 original size:59 final size:60
Alignment explanation
Indices: 52161141--52161276 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
52161131 TTTAGGTGTC
* * **
52161141 AAATGAAAATTTTG-GAAGTTTAGGGGTCAATCTATAATTTTAAGAAAGTTTAGGGTTTAA
1 AAATG-AAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAGAAAGTTTAGGGTTTAA
*
52161201 AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATGTAATTTT-AGAAAAGTTTAGAGG-TT-A
1 AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAG-AAAGTTTAG-GGTTTAA
* *
52161260 AAATGTAATTTTAAAAA
1 AAATGAAATTTTGAAAA
52161277 AATAAAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 26 0.39
60 38 0.58
61 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.35
Consensus pattern (60 bp):
AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAGAAAGTTTAGGGTTTAA
Found at i:52165009 original size:18 final size:18
Alignment explanation
Indices: 52164982--52165034 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
52164972 TGCATGCATC
* *
52164982 ATGCATGCTCTTTGTTTG
1 ATGCATGCTCCTTGTTTA
* *
52165000 ATGCACGCTCCGTGTTTA
1 ATGCATGCTCCTTGTTTA
52165018 ATGCATGCTCCTTGTTT
1 ATGCATGCTCCTTGTTT
52165035 CTTACAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (18 bp):
ATGCATGCTCCTTGTTTA
Found at i:52169697 original size:16 final size:16
Alignment explanation
Indices: 52169666--52169704 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
52169656 TGTTGTTTAG
*
52169666 TAGAATAACTCATGTT
1 TAGAACAACTCATGTT
* *
52169682 TGGAACAACTCGTGTT
1 TAGAACAACTCATGTT
52169698 TAGAACA
1 TAGAACA
52169705 CTCTTTGTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (16 bp):
TAGAACAACTCATGTT
Found at i:52182436 original size:66 final size:66
Alignment explanation
Indices: 52182330--52182462 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
52182320 GGAAACAAGC
52182330 TATCATGAATGCGAGACCACGGATCCTTTTCTAACATTCTGTTCTTGGTCAAAATATGTAAGCCT
1 TATCATGAATGCGAGACCACGGATCCTTTTCTAACATTCTGTTCTTGGTCAAAATATGTAAGCCT
52182395 T
66 T
52182396 TATCATGAATGCGAGACCACGGATCCTTTTCTAACATTCTGTTCTTGGTCAAAATATGTAAGCCT
1 TATCATGAATGCGAGACCACGGATCCTTTTCTAACATTCTGTTCTTGGTCAAAATATGTAAGCCT
52182461 T
66 T
52182462 T
1 T
52182463 CTCCTTCTCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (66 bp):
TATCATGAATGCGAGACCACGGATCCTTTTCTAACATTCTGTTCTTGGTCAAAATATGTAAGCCT
T
Found at i:52185733 original size:23 final size:23
Alignment explanation
Indices: 52185689--52185733 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52185679 TTTTAAAAAA
* *
52185689 ATATGTTTTTTAATTGATATTTT
1 ATATATTTTTTAATTGAAATTTT
52185712 ATATATTTTTATAATT-AAATTT
1 ATATATTTTT-TAATTGAAATTT
52185734 ACATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATATATTTTTTAATTGAAATTTT
Found at i:52187122 original size:11 final size:11
Alignment explanation
Indices: 52187106--52187160 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
52187096 ATAATTATAC
52187106 AAAATTATTTA
1 AAAATTATTTA
52187117 AAAATTA--TA
1 AAAATTATTTA
52187126 AAAA-TATATT-
1 AAAATTAT-TTA
*
52187136 AACATTATTTA
1 AAAATTATTTA
52187147 AAAATTA-TTA
1 AAAATTATTTA
52187157 AAAA
1 AAAA
52187161 GAATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 12 0.32
11 17 0.46
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATTATTTA
Found at i:52187122 original size:21 final size:21
Alignment explanation
Indices: 52187092--52187135 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52187082 CCGCTGGTTT
*
52187092 TTTAATAATTATACAAAAT-TA
1 TTTAAAAATTATA-AAAATATA
52187113 TTTAAAAATTATAAAAATATA
1 TTTAAAAATTATAAAAATATA
52187134 TT
1 TT
52187136 AACATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAAAATTATAAAAATATA
Found at i:52187334 original size:20 final size:20
Alignment explanation
Indices: 52187309--52187350 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52187299 TATCTATTTG
*
52187309 AATTAT-AAGAAATTGTAAAA
1 AATTATCAAG-AATTATAAAA
52187329 AATTATCAAGAATTATAAAA
1 AATTATCAAGAATTATAAAA
52187349 AA
1 AA
52187351 AAAAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (20 bp):
AATTATCAAGAATTATAAAA
Found at i:52189210 original size:25 final size:24
Alignment explanation
Indices: 52189173--52189224 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
52189163 AATGGAAAAG
*
52189173 AAAAAAGACAAAA-AAAAGAAAGTT
1 AAAAAAGACAAAAGAAAA-AAAATT
*
52189197 AAAAAAGCATAAAAGAAAAAAAATT
1 AAAAAAG-ACAAAAGAAAAAAAATT
52189222 AAA
1 AAA
52189225 TTGCTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.10
Consensus pattern (24 bp):
AAAAAAGACAAAAGAAAAAAAATT
Found at i:52204946 original size:31 final size:29
Alignment explanation
Indices: 52204908--52204981 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
52204898 TCTACAAAAG
*
52204908 TAGTCACTTTTATTTGACTCAA-GTTACATTT
1 TAGTCACTTATATTTGA---AATGTTACATTT
* *
52204939 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATATTTGAAATGTTACATTT
52204968 TAGTCACTTATATT
1 TAGTCACTTATATT
52204982 ATTATTTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 21 0.55
31 15 0.39
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATATTTGAAATGTTACATTT
Found at i:52211230 original size:21 final size:21
Alignment explanation
Indices: 52211204--52211244 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52211194 ATCTGCTCAA
* *
52211204 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
52211225 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
52211245 TTACTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:52214201 original size:15 final size:15
Alignment explanation
Indices: 52214183--52214225 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
52214173 ATAATATTTT
*
52214183 AAATATAAGTGAATA
1 AAATATAAGTGAAAA
*
52214198 AAATATAATCTGAAAA
1 AAATATAA-GTGAAAA
*
52214214 AAATAAAAGTGA
1 AAATATAAGTGA
52214226 CTTTTTGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (15 bp):
AAATATAAGTGAAAA
Found at i:52228580 original size:17 final size:18
Alignment explanation
Indices: 52228544--52228581 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52228534 TTTCTAATTC
*
52228544 AATAAAAATAATTTAGCA
1 AATAAAAATAATTTACCA
*
52228562 AATAAAAGTAA-TTACCA
1 AATAAAAATAATTTACCA
52228579 AAT
1 AAT
52228582 GTTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AATAAAAATAATTTACCA
Found at i:52231627 original size:20 final size:20
Alignment explanation
Indices: 52231602--52231641 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
52231592 TAATTAGTAG
52231602 CTCTCAATTAGGCTTTTATA
1 CTCTCAATTAGGCTTTTATA
52231622 CTCTCAATTAGGCTTTTATA
1 CTCTCAATTAGGCTTTTATA
52231642 TAATCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (20 bp):
CTCTCAATTAGGCTTTTATA
Found at i:52240185 original size:16 final size:16
Alignment explanation
Indices: 52240164--52240205 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52240154 TTATTAAATT
*
52240164 ATATATTTTAATTATA
1 ATATATTTTAATAATA
52240180 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
52240195 AT-TATGTTTAA
1 ATATAT-TTTAA
52240206 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:52240190 original size:15 final size:15
Alignment explanation
Indices: 52240155--52240196 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52240145 TTAAGAATTT
*
52240155 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52240169 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52240183 TATTTAATAATAAT
1 TATTTAATTATAAT
52240197 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52240434 original size:45 final size:44
Alignment explanation
Indices: 52240350--52240440 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
52240340 AGCTCTATCC
*
52240350 CATTCAACCAAACACAAGATTACTATTACGCCACTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCACTATTCCATTA
*** * *
52240394 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCACTATTCCATTA
52240439 CA
1 CA
52240441 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCACTATTCCATTA
Found at i:52240440 original size:16 final size:16
Alignment explanation
Indices: 52240419--52240465 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
52240409 TTGATTTGCT
*
52240419 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
52240435 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* * *
52240451 AATAAACCTTTAATC
1 ATTACACCTCTAATC
52240466 TAATACAGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:52240682 original size:27 final size:28
Alignment explanation
Indices: 52240647--52240717 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 28
52240637 TAATTTTAAA
*
52240647 AATTTAGTGACTAAAT-A-AAAAATTACT
1 AATTAAGTGACTAAATAACAAAAATTA-T
*
52240674 AATTAAGTGATTAAAATAAAACAAAAATTAT
1 AATTAAGTGACT-AAAT--AACAAAAATTAT
52240705 AATTAAGTGACTA
1 AATTAAGTGACTA
52240718 TCTGTGTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 10 0.28
28 4 0.11
30 1 0.03
31 13 0.36
32 8 0.22
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (28 bp):
AATTAAGTGACTAAATAACAAAAATTAT
Found at i:52244443 original size:30 final size:30
Alignment explanation
Indices: 52244389--52244454 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
52244379 AAGTTTTAAA
* *
52244389 TTAATAATAATAAAATTATAATTTAGTCTTT
1 TTAAAAATAATAAAATTATAATTTAAT-TTT
*
52244420 TTAAAAATGATAAAATT-TAATTTAATTTT
1 TTAAAAATAATAAAATTATAATTTAATTTT
52244449 TTAAAA
1 TTAAAA
52244455 TTTACAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 9 0.28
30 8 0.25
31 15 0.47
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATTTT
Found at i:52245323 original size:7 final size:7
Alignment explanation
Indices: 52245311--52245339 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
52245301 ATCTTTCATT
52245311 CATTTCA
1 CATTTCA
52245318 CATTTCA
1 CATTTCA
52245325 CATTTCA
1 CATTTCA
52245332 CATTTCA
1 CATTTCA
52245339 C
1 C
52245340 CTATTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (7 bp):
CATTTCA
Found at i:52257390 original size:25 final size:24
Alignment explanation
Indices: 52257298--52257446 Score: 102
Period size: 24 Copynumber: 6.1 Consensus size: 24
52257288 CCATAAGCAA
* **
52257298 CCCGATAGTGGCTCTCCGGAGCTT
1 CCCGATAATGGCTCTCATGAGCTT
** * * *
52257322 GTCGATATTGGCTCGCATGAGATT
1 CCCGATAATGGCTCTCATGAGCTT
* * *
52257346 CCCGTTTATGGCT-TGTATGAGCTT
1 CCCGATAATGGCTCT-CATGAGCTT
*
52257370 CCTGATAATTGGCTCTCATGAGCTT
1 CCCGATAA-TGGCTCTCATGAGCTT
* * *
52257395 CCCGATTATGGCTCTTATGAGTTT
1 CCCGATAATGGCTCTCATGAGCTT
* * *
52257419 CCCGTTATATGACTCACATGAGCTT
1 CCCGATA-ATGGCTCTCATGAGCTT
52257444 CCC
1 CCC
52257447 ATTATATGAC
Statistics
Matches: 92, Mismatches: 29, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
24 56 0.61
25 35 0.38
26 1 0.01
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (24 bp):
CCCGATAATGGCTCTCATGAGCTT
Found at i:52257439 original size:49 final size:49
Alignment explanation
Indices: 52257324--52257451 Score: 129
Period size: 49 Copynumber: 2.7 Consensus size: 49
52257314 CGGAGCTTGT
* * * *
52257324 CGAT-ATTGGCTCGCATGAGATTCCCGTTTATGGCTTGTATGAGCTTCC
1 CGATAATTGACTCACATGAGCTTCCCGATTATGGCTTGTATGAGCTTCC
* * * *
52257372 TGATAATTGGCTCTCATGAGCTTCCCGATTATGGCTCT-TATGAGTTTCC
1 CGATAATTGACTCACATGAGCTTCCCGATTATGGCT-TGTATGAGCTTCC
*
52257421 CG-TTATATGACTCACATGAGCTTCCC-ATTAT
1 CGATAAT-TGACTCACATGAGCTTCCCGATTAT
52257452 ATGACTCAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 11 0.16
49 56 0.82
50 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (49 bp):
CGATAATTGACTCACATGAGCTTCCCGATTATGGCTTGTATGAGCTTCC
Found at i:52257470 original size:25 final size:25
Alignment explanation
Indices: 52257417--52257470 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
52257407 TCTTATGAGT
* **
52257417 TTCCCGTTATATGACTCACATGAGC
1 TTCCCATTATATGACTCACAAAAGC
* *
52257442 TTCCCATTATATGACTCAGAAAAGG
1 TTCCCATTATATGACTCACAAAAGC
52257467 TTCC
1 TTCC
52257471 TATTTACATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (25 bp):
TTCCCATTATATGACTCACAAAAGC
Found at i:52262699 original size:28 final size:28
Alignment explanation
Indices: 52262668--52262722 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
52262658 ATCAAATGTC
*
52262668 AATTTCGTAATTCAATCATACAAAAGTT
1 AATTTCATAATTCAATCATACAAAAGTT
52262696 AATTTCATAATTCAATCATACAAAAGT
1 AATTTCATAATTCAATCATACAAAAGT
52262723 GAAGTGGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (28 bp):
AATTTCATAATTCAATCATACAAAAGTT
Found at i:52273944 original size:6 final size:6
Alignment explanation
Indices: 52273935--52273967 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
52273925 TTTTAGTTCG
52273935 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
52273968 TGCTACCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:52285648 original size:25 final size:25
Alignment explanation
Indices: 52285565--52285724 Score: 174
Period size: 25 Copynumber: 6.6 Consensus size: 25
52285555 TTATTATGCA
* *
52285565 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACTGATGTG
*
52285590 CT-AT-A-CAGAGAGCACAGATGTG
1 CTAATAATCAGAGAGCACTGATGTG
* * *
52285612 C---TAATC-GAAGAGCATTAACGTG
1 CTAATAATCAG-AGAGCACTGATGTG
52285634 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGATGTG
* *
52285659 CTAATAATTAGAGATCACTGATGTG
1 CTAATAATCAGAGAGCACTGATGTG
52285684 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGATGTG
52285709 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
52285725 GCGCTAAAGT
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 28 0.25
24 2 0.02
25 80 0.70
26 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGATGTG
Found at i:52290305 original size:22 final size:22
Alignment explanation
Indices: 52290275--52290317 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52290265 GTAATGAAAC
52290275 ACTTCCACTCTATGAACATGCG
1 ACTTCCACTCTATGAACATGCG
* *
52290297 ACTTTCACTCTATTAACATGC
1 ACTTCCACTCTATGAACATGC
52290318 CAATGACGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (22 bp):
ACTTCCACTCTATGAACATGCG
Found at i:52292001 original size:45 final size:45
Alignment explanation
Indices: 52291937--52292029 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
52291927 GTCCCTATAC
*
52291937 TTTAATTTGATCAATTTCAATTTATGTACTTTTTGGATTGGTCAA
1 TTTAATTTGATCAATTTCAATTTATGTACTTTTTGAATTGGTCAA
* *
52291982 TTTAATTTGATCAATTTCAATTTATGTATTTTTTGAATTTGTCAA
1 TTTAATTTGATCAATTTCAATTTATGTACTTTTTGAATTGGTCAA
52292027 TTT
1 TTT
52292030 TAGCCCTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.55
Consensus pattern (45 bp):
TTTAATTTGATCAATTTCAATTTATGTACTTTTTGAATTGGTCAA
Found at i:52295733 original size:20 final size:20
Alignment explanation
Indices: 52295708--52295758 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
52295698 AATTTTATAT
*
52295708 AAAATATATTTTATTAAATA
1 AAAATATATTTTAATAAATA
52295728 AAAATA-ATATTTAATAAATA
1 AAAATATAT-TTTAATAAATA
* *
52295748 GAATTATATTT
1 AAAATATATTT
52295759 CTAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATATATTTTAATAAATA
Found at i:52300422 original size:18 final size:18
Alignment explanation
Indices: 52300399--52300436 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
52300389 GCATAATTAA
52300399 ATCATTGTATCTATAGAT
1 ATCATTGTATCTATAGAT
52300417 ATCATTGTATCTATAGAT
1 ATCATTGTATCTATAGAT
52300435 AT
1 AT
52300437 GTGTTCTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (18 bp):
ATCATTGTATCTATAGAT
Found at i:52302688 original size:20 final size:20
Alignment explanation
Indices: 52302622--52302695 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
52302612 AAGATTACAA
*
52302622 AAAAAATTAAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
* *
52302642 CAAAAATTTAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
52302662 -TAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
52302681 AAAAAATTCCAAAAT
1 AAAAAATT-CAAAAT
52302696 TTATATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.09
19 12 0.26
20 24 0.52
21 6 0.13
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:52308014 original size:58 final size:59
Alignment explanation
Indices: 52307952--52308064 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 59
52307942 ATTAATTTAA
* *
52307952 TATTAAATTAATATAATACTTATC-AAGATAAATA-TTAGATTAAATTTAATATCAAATC
1 TATTAAACTAATAAAATACTTATCTAAGATAAATATTTA-ATTAAATTTAATATCAAATC
* *
52308010 TATTAAACTAATAAAATATTTATCTATAAGATAAATATTTAATTTAATTTAATAT
1 TATTAAACTAATAAAATACTTATC--TAAGATAAATATTTAATTAAATTTAATAT
52308065 TAAGATAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 21 0.45
61 23 0.49
62 3 0.06
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (59 bp):
TATTAAACTAATAAAATACTTATCTAAGATAAATATTTAATTAAATTTAATATCAAATC
Found at i:52327280 original size:5 final size:5
Alignment explanation
Indices: 52327270--52327298 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
52327260 ACACCTTGCT
52327270 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
52327299 TTGTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:52329714 original size:42 final size:42
Alignment explanation
Indices: 52329655--52329736 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
52329645 CAAGCAAACA
52329655 CACATAACATGCAAAAGAAAAGACGACCCTTGGACTAAATCG
1 CACATAACATGCAAAAGAAAAGACGACCCTTGGACTAAATCG
*
52329697 CACATAACATGCAAAAGAAAAGACGGCCCTTGGACTAAAT
1 CACATAACATGCAAAAGAAAAGACGACCCTTGGACTAAAT
52329737 TAGGCAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (42 bp):
CACATAACATGCAAAAGAAAAGACGACCCTTGGACTAAATCG
Found at i:52331348 original size:19 final size:17
Alignment explanation
Indices: 52331313--52331348 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
52331303 TAATTTTATA
52331313 TTAAAAATATAAATATT
1 TTAAAAATATAAATATT
52331330 TTAATAAATATATAATATT
1 TTAA-AAATATA-AATATT
52331349 AACAAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAAATATAAATATT
Found at i:52334222 original size:6 final size:6
Alignment explanation
Indices: 52334213--52334240 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52334203 ATGCAATTAC
52334213 AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATA
52334241 CATATTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:52340462 original size:23 final size:23
Alignment explanation
Indices: 52340419--52340462 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52340409 GTTTATTTAT
* *
52340419 TGTTTGTTTATTATTTATGAACA
1 TGTTTGTTTAATATTCATGAACA
*
52340442 TGTTTGTTTAATATTCGTGAA
1 TGTTTGTTTAATATTCATGAA
52340463 TTATGAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (23 bp):
TGTTTGTTTAATATTCATGAACA
Found at i:52343078 original size:13 final size:13
Alignment explanation
Indices: 52343060--52343087 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52343050 ATGTTTTTCC
52343060 CATGAACTATAAA
1 CATGAACTATAAA
52343073 CATGAACTATAAA
1 CATGAACTATAAA
52343086 CA
1 CA
52343088 AAATAATAAG
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:0.54, C:0.18, G:0.07, T:0.21
Consensus pattern (13 bp):
CATGAACTATAAA
Found at i:52350862 original size:17 final size:19
Alignment explanation
Indices: 52350840--52350874 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
52350830 CTAAAATAGT
52350840 AACAAGA-TTA-ACAATAA
1 AACAAGAGTTATACAATAA
52350857 AACAAGAGTTATACAATA
1 AACAAGAGTTATACAATA
52350875 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (19 bp):
AACAAGAGTTATACAATAA
Found at i:52353423 original size:27 final size:28
Alignment explanation
Indices: 52353377--52353432 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
52353367 TTTAAAAGAC
* *
52353377 TTTTAAAATATTTTTTTTTATTTTTTAT
1 TTTTAAAATATTTTTTTTTAATATTTAT
52353405 TTTTAAAATA-TTTTTTTTAATATTTAT
1 TTTTAAAATATTTTTTTTTAATATTTAT
52353432 T
1 T
52353433 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTAAAATATTTTTTTTTAATATTTAT
Found at i:52359549 original size:65 final size:65
Alignment explanation
Indices: 52359475--52359601 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
52359465 ACTTACTTAT
*
52359475 ATAATATAGCGACCTTGGATA-TAGTTTA-TCTTTAATATTACTATTATAACACAACTAGATTAC
1 ATAATATAGCAACCTTGGA-AGTAGTTTACT-TTTAATATTACTATTATAACACAACTAGATTAC
52359538 TA
64 TA
*
52359540 ATAATATAGCAACCTTGGAAGTAGTTTACTTTTAATATTACTATTATAGCACAACTAGATTA
1 ATAATATAGCAACCTTGGAAGTAGTTTACTTTTAATATTACTATTATAACACAACTAGATTA
52359602 ATATTTGAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
64 1 0.02
65 56 0.97
66 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (65 bp):
ATAATATAGCAACCTTGGAAGTAGTTTACTTTTAATATTACTATTATAACACAACTAGATTACTA
Found at i:52365111 original size:21 final size:20
Alignment explanation
Indices: 52365050--52365111 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 20
52365040 CATTTTATTT
52365050 TATTTTTAAACTGTTTTTATAAA
1 TATTTTTAAA-T-TTTTTA-AAA
*
52365073 T-TTTTAAATATTTATTTAAAA
1 TATTTTTAA-ATTT-TTTAAAA
52365094 TATTTTTATAATTTTTTA
1 TATTTTTA-AATTTTTTA
52365112 TTAGGGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 10 0.30
22 20 0.61
23 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTTTAAATTTTTTAAAA
Found at i:52367983 original size:99 final size:99
Alignment explanation
Indices: 52367874--52368135 Score: 258
Period size: 99 Copynumber: 2.6 Consensus size: 99
52367864 GGCAACTCAA
* ** * ** *
52367874 GAGCTTTGGGCAATTCTGGTTTTG-GCA-CTTTGAGCACTTTAGACAATTCTGGTTTTGTTAACT
1 GAGCTTTGGGCAATTCTGG-CTTGAGCACCTCAG-GAACTTTAGACAATTCTGACTTTGGTAACT
* * * *
52367937 CGGGAATTTTTGGTAATTCAGGTTTTGACAATTTAG
64 CGAGAACTTTTGGTAATTCAGGATTTGACAACTTAG
* *
52367973 GAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGGCAATTTTGACTTTGGTAACTCG
1 GAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGACAATTCTGACTTTGGTAACTCG
* ** *
52368038 AGAACTTTTGGTAATTTAGGATTTGGTAACTTGG
66 AGAACTTTTGGTAATTCAGGATTTGACAACTTAG
* * * * * * * * *
52368072 GAGCTTTGGGCAATTTTGGCTTGGGCGCCTTAGGAACTTTGGGCAATTTTGGCTTCGGTAACTC
1 GAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGACAATTCTGACTTTGGTAACTC
52368136 AGGAGCTTTG
Statistics
Matches: 137, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
98 3 0.02
99 131 0.96
100 3 0.02
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (99 bp):
GAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGACAATTCTGACTTTGGTAACTCG
AGAACTTTTGGTAATTCAGGATTTGACAACTTAG
Found at i:52368018 original size:33 final size:32
Alignment explanation
Indices: 52367971--52368192 Score: 151
Period size: 33 Copynumber: 6.8 Consensus size: 32
52367961 TTGACAATTT
* *
52367971 AGGAGCTTTGGGCAATTCTGGCTTGAGCACCTC
1 AGGAACTTTGGGCAATTCTGGCTTG-GCAACTC
* * * *
52368004 AGGAACTTTAGGCAATTTTGACTTTGGTAACTC
1 AGGAACTTTGGGCAATTCTGGC-TTGGCAACTC
* * * * *
52368037 -GAGAACTTTTGGTAATT-TAGGATTTGGTAACTT
1 AG-GAACTTTGGGCAATTCT-GG-CTTGGCAACTC
* * * ** *
52368070 GGGAGCTTTGGGCAATTTTGGCTTGGGCGCCTT
1 AGGAACTTTGGGCAATTCTGGCTT-GGCAACTC
* *
52368103 AGGAACTTTGGGCAATTTTGGCTTCGGTAACTC
1 AGGAACTTTGGGCAATTCTGGCTT-GGCAACTC
* *
52368136 AGGAGCTTTGGGCAATTCTGGCTTGGGCATCTC
1 AGGAACTTTGGGCAATTCTGGCTT-GGCAACTC
* *
52368169 AGGAACTTTAGGCAATTCTAGCTT
1 AGGAACTTTGGGCAATTCTGGCTT
52368193 TGGTAACTTG
Statistics
Matches: 149, Mismatches: 33, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
32 4 0.03
33 140 0.94
34 5 0.03
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (32 bp):
AGGAACTTTGGGCAATTCTGGCTTGGCAACTC
Found at i:52368111 original size:66 final size:66
Alignment explanation
Indices: 52368039--52368202 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 66
52368029 GGTAACTCGA
* * * * * *
52368039 GAACTTTTGGTAATTTAGGATTTGGTAACTTGGGAGCTTTGGGCAATTTTGGCTTGGGCGCCTTA
1 GAACTTTAGGCAATTTAGGCTTTGGTAACTTGGGAGCTTTGGGCAATTCTGGCTTGGGCACCTCA
52368104 G
66 G
* * * ** *
52368105 GAACTTTGGGCAATTTTGGCTTCGGTAACTCAGGAGCTTTGGGCAATTCTGGCTTGGGCATCTCA
1 GAACTTTAGGCAATTTAGGCTTTGGTAACTTGGGAGCTTTGGGCAATTCTGGCTTGGGCACCTCA
52368170 G
66 G
52368171 GAACTTTAGGCAATTCTA-GCTTTGGTAACTTG
1 GAACTTTAGGCAATT-TAGGCTTTGGTAACTTG
52368203 AGAATTTTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 80 0.99
67 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (66 bp):
GAACTTTAGGCAATTTAGGCTTTGGTAACTTGGGAGCTTTGGGCAATTCTGGCTTGGGCACCTCA
G
Found at i:52368183 original size:99 final size:99
Alignment explanation
Indices: 52367971--52368192 Score: 241
Period size: 99 Copynumber: 2.2 Consensus size: 99
52367961 TTGACAATTT
*
52367971 AGGAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGGCAATTTTGACTTTGGTAACT
1 AGGAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGGCAATTTTGACTTCGGTAACT
* * * * *
52368036 CGAGAACTTTTGGTAATTTAGGATTTGGTAACTT
66 CGAGAACTTTGGGCAATTTAGGATTGGGCAACTC
* * * * * * *
52368070 GGGAGCTTTGGGCAATTTTGGCTTGGGCGCCTTAGGAACTTTGGGCAATTTTGGCTTCGGTAACT
1 AGGAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGGCAATTTTGACTTCGGTAACT
* * *
52368135 C-AGGAGCTTTGGGCAATTCT-GGCTTGGGCATCTC
66 CGA-GAACTTTGGGCAATT-TAGGATTGGGCAACTC
* * *
52368169 AGGAACTTTAGGCAATTCTAGCTT
1 AGGAGCTTTGGGCAATTCTGGCTT
52368193 TGGTAACTTG
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
98 1 0.01
99 98 0.98
100 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (99 bp):
AGGAGCTTTGGGCAATTCTGGCTTGAGCACCTCAGGAACTTTAGGCAATTTTGACTTCGGTAACT
CGAGAACTTTGGGCAATTTAGGATTGGGCAACTC
Found at i:52368463 original size:22 final size:21
Alignment explanation
Indices: 52368438--52368482 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
52368428 ACACCAAAAC
*
52368438 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
52368460 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
52368481 AG
1 AG
52368483 CGCCACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:52368713 original size:43 final size:43
Alignment explanation
Indices: 52368552--52368756 Score: 238
Period size: 42 Copynumber: 4.8 Consensus size: 43
52368542 GCGTCGCTAA
* *
52368552 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
52368595 CTTTAGCGGCGC--TTCCCTACAAATGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGAC
* * *
52368637 CTTTAGCGGCAC-TTCCCCACAAACGTCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * * * *
52368679 CTTTAGCGACGCTTTTCCCACAAACGCTGCTAAAGA-TATTGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGAC
*
52368722 CTTTAGCGGCACTTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAA
52368757 AATATATCTT
Statistics
Matches: 139, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.04
42 65 0.47
43 48 0.35
44 21 0.15
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:52368784 original size:16 final size:16
Alignment explanation
Indices: 52368754--52368783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52368744 AAACGCCGCT
52368754 AAAAATATATCTTTTA
1 AAAAATATATCTTTTA
52368770 AAAAATATAT-TTTT
1 AAAAATATATCTTTT
52368784 TTCAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATATATCTTTTA
Found at i:52369095 original size:43 final size:43
Alignment explanation
Indices: 52369029--52369119 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
52369019 ATATATGCAA
* * * *
52369029 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
52369072 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
52369115 -GTAAT
1 GGTAAT
52369120 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:52372995 original size:42 final size:42
Alignment explanation
Indices: 52372920--52373230 Score: 353
Period size: 42 Copynumber: 7.4 Consensus size: 42
52372910 ACGTCACTAA
* * *
52372920 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAATATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
* *
52372964 CTTTAGCGGCGCTTAGAAAAAAAGGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
52373006 CTTTAGCGGCGCTTAGAAAGAAACGCC-CTTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGC-TAAAGATCATGTT
* *
52373048 CTTTAGCGGCGCTTA-TAAAAAACGCTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
52373089 CTTTAGTGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * * * *
52373131 CTTTAGCGACGCTTTGGAAGAAAGCGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* **
52373174 CTATAGCGGCGCTTATTAAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGA-TCA-TGTT
52373216 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
52373231 TTTCACAAAC
Statistics
Matches: 230, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
41 37 0.16
42 148 0.64
43 32 0.14
44 13 0.06
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:52373079 original size:125 final size:125
Alignment explanation
Indices: 52372920--52373230 Score: 412
Period size: 125 Copynumber: 2.4 Consensus size: 125
52372910 ACGTCACTAA
*
52372920 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTAGAAAAA
1 CTTTAGCGGCGCTT--AT-AAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTAGAAAAA
* * * *
52372985 AAGGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAGAAAGAAA-CGCC-CTTAAAGATCATGTT
62 AACGCCGCTAAAGATCATGCTCTTTAGCGACGCTTAGAAAGAAAGCGCCTCTAAAAG-TAATGTT
* * *
52373048 CTTTAGCGGCGCTTATAAAAAACGCTGCTAAAGATCATGTTCTTTAGTGGCGCTTAGGAAAAAAC
1 CTTTAGCGGCGCTTATAAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
* * *
52373113 GCCGCTAAAGATCATGTTCTTTAGCGACGCTTTGGAAGAAAGCGCCTCTAAAAGTAATGTT
65 GCCGCTAAAGATCATGCTCTTTAGCGACGCTTAGAAAGAAAGCGCCTCTAAAAGTAATGTT
*
52373174 CTATAGCGGCGCTTATTAAAAAACGCCGCTAAAAGT-AGTGTTCTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA-TAAAAAACGCCGCTAAAA-TCA-TGTTCTTTAGCGGCGCTTA
52373231 TTTCACAAAC
Statistics
Matches: 163, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
125 81 0.50
126 28 0.17
127 41 0.25
128 13 0.08
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (125 bp):
CTTTAGCGGCGCTTATAAAAAACGCCGCTAAAATCATGTTCTTTAGCGGCGCTTAGAAAAAAACG
CCGCTAAAGATCATGCTCTTTAGCGACGCTTAGAAAGAAAGCGCCTCTAAAAGTAATGTT
Found at i:52373113 original size:83 final size:82
Alignment explanation
Indices: 52372939--52373231 Score: 337
Period size: 83 Copynumber: 3.5 Consensus size: 82
52372929 CGCTTACATA
* * * *
52372939 AAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTAGAAAAAAAGGCCGCTAAAGATCATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-TAAAAAACGCTGCTAAAGATCATG
*
52373004 CTCTTTAGCGGCGCTTAG
65 TTCTTTAGCGGCGCTTAG
52373022 AAAGAAACGCC-CTTAAAGATCATGTTCTTTAGCGGCGCTTATAAAAAACGCTGCTAAAGATCAT
1 AAA-AAACGCCGC-TAAAGATCATGTTCTTTAGCGGCGCTTATAAAAAACGCTGCTAAAGATCAT
*
52373086 GTTCTTTAGTGGCGCTTAGG
64 GTTCTTTAGCGGCGCTTA-G
* *
52373106 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTT-TGGAAGAAAGCGCCT-CTAAA-AGT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAT--AA-AAAACG-CTGCTAAAGA-T
* * *
52373168 AATGTTCTATAGCGGCGCTTATT
61 CATGTTCTTTAGCGGCGCTTA-G
52373191 AAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTAT
1 AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTAT
52373232 TTCACAAACG
Statistics
Matches: 184, Mismatches: 14, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
82 1 0.01
83 73 0.40
84 44 0.24
85 63 0.34
86 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (82 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATAAAAAACGCTGCTAAAGATCATGT
TCTTTAGCGGCGCTTAG
Found at i:52373662 original size:12 final size:12
Alignment explanation
Indices: 52373645--52373684 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
52373635 TTTTGAACCT
*
52373645 CTGCTTCTATTG
1 CTGCTTCTATCG
*
52373657 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
52373669 CTGCTTCTCTCG
1 CTGCTTCTATCG
52373681 CTGC
1 CTGC
52373685 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:52373695 original size:21 final size:21
Alignment explanation
Indices: 52373669--52373737 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
52373659 GCTTCTCTCG
*
52373669 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
52373690 CTGCTTCTCTCGTTGTAGCCG
1 CTGCTTCTCTCGCTGCAGCCT
* *
52373711 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
52373732 CTGCTT
1 CTGCTT
52373738 TAAGTTGCTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.01, C:0.42, G:0.22, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:52375645 original size:18 final size:18
Alignment explanation
Indices: 52375622--52375662 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
52375612 AAGGTAAATA
52375622 AAATTA-ATAAAATTATAT
1 AAATTATAT-AAATTATAT
52375640 AAATTATATAAATTATAT
1 AAATTATATAAATTATAT
52375658 AAATT
1 AAATT
52375663 TAAGGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTATATAAATTATAT
Found at i:52375675 original size:43 final size:43
Alignment explanation
Indices: 52375627--52375825 Score: 168
Period size: 43 Copynumber: 5.0 Consensus size: 43
52375617 AAATAAAATT
52375627 AATAAAATTATATAAATTATATAAATTATATAAATTTAAGGTA
1 AATAAAATTATATAAATTATATAAATTATATAAATTTAAGGTA
*** *
52375670 AAT-AAA--AT-T-AA-TATCGGAA-TAT-T-AATTCAAGGTA
1 AATAAAATTATATAAATTATATAAATTATATAAATTTAAGGTA
52375704 AATAAAATTA-ATAAAATTATATAAATTATATAAATTTAAGGTA
1 AATAAAATTATAT-AAATTATATAAATTATATAAATTTAAGGTA
*** *
52375747 AAT-AAA--AT-T-AA-TATCGGAA-TAT-T-AATTCAAGGTA
1 AATAAAATTATATAAATTATATAAATTATATAAATTTAAGGTA
52375781 AATAAAATTA-ATAAAATTATATAAATTATATAAATTTAAGGTA
1 AATAAAATTATAT-AAATTATATAAATTATATAAATTTAAGGTA
52375824 AA
1 AA
52375826 ATTTAAGGTA
Statistics
Matches: 119, Mismatches: 16, Indels: 42
0.67 0.09 0.24
Matches are distributed among these distances:
34 26 0.22
35 8 0.07
36 6 0.05
37 14 0.12
38 4 0.03
39 5 0.04
40 14 0.12
41 6 0.05
42 8 0.07
43 28 0.24
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (43 bp):
AATAAAATTATATAAATTATATAAATTATATAAATTTAAGGTA
Found at i:52375678 original size:34 final size:35
Alignment explanation
Indices: 52375640--52375807 Score: 118
Period size: 34 Copynumber: 4.7 Consensus size: 35
52375630 AAAATTATAT
52375640 AAATTATAT-AAATTATATAAATTTAAGGTAAATA
1 AAATTATATGAAATTATATAAATTTAAGGTAAATA
* *
52375674 AAATTAATATCGGAA-TAT-T-AATTCAAGGTAAATA
1 AAATT-ATAT-GAAATTATATAAATTTAAGGTAAATA
*
52375708 AAATTAATAAAATTATATAAATTATATAAATTTAAGGTAAATA
1 AAA-T--T---A-TAT-GAAATTATATAAATTTAAGGTAAATA
* *
52375751 AAATTAATATCGGAA-TAT-T-AATTCAAGGTAAATA
1 AAATT-ATAT-GAAATTATATAAATTTAAGGTAAATA
*
52375785 AAATTA-ATAAAATTATATAAATT
1 AAATTATATGAAATTATATAAATT
52375808 ATATAAATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
31 2 0.02
32 5 0.05
33 2 0.02
34 45 0.42
35 7 0.07
36 6 0.06
37 8 0.07
38 2 0.02
39 2 0.02
40 6 0.06
41 3 0.03
42 2 0.02
43 17 0.16
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (35 bp):
AAATTATATGAAATTATATAAATTTAAGGTAAATA
Found at i:52375754 original size:77 final size:77
Alignment explanation
Indices: 52375627--52375825 Score: 382
Period size: 77 Copynumber: 2.6 Consensus size: 77
52375617 AAATAAAATT
52375627 AATAAAATT-ATATAAATTATATAAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATA
1 AATAAAATTAATA-AAATTATATAAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATA
52375691 TTAATTCAAGGTA
65 TTAATTCAAGGTA
52375704 AATAAAATTAATAAAATTATATAAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATAT
1 AATAAAATTAATAAAATTATATAAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATAT
52375769 TAATTCAAGGTA
66 TAATTCAAGGTA
52375781 AATAAAATTAATAAAATTATATAAATTATATAAATTTAAGGTAAA
1 AATAAAATTAATAAAATTATATAAATTATATAAATTTAAGGTAAA
52375826 ATTTAAGGTA
Statistics
Matches: 121, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
77 118 0.98
78 3 0.02
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (77 bp):
AATAAAATTAATAAAATTATATAAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATAT
TAATTCAAGGTA
Found at i:52375829 original size:12 final size:12
Alignment explanation
Indices: 52375812--52375837 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52375802 TAAATTATAT
52375812 AAATTTAAGGTA
1 AAATTTAAGGTA
52375824 AAATTTAAGGTA
1 AAATTTAAGGTA
52375836 AA
1 AA
52375838 TAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AAATTTAAGGTA
Found at i:52377366 original size:34 final size:34
Alignment explanation
Indices: 52377328--52377405 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
52377318 TTCTTCCAGC
*
52377328 ATGCAAAATCTAAATGCAAAATCATTTTTTACGG
1 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
52377362 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
1 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
*
52377396 ATGGAAAATC
1 ATGCAAAATC
52377406 ATTTTTTACG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (34 bp):
ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
Found at i:52377405 original size:21 final size:21
Alignment explanation
Indices: 52377379--52377418 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52377369 ATCTAAATGC
52377379 AAAATCAATTTTTACGGATGG
1 AAAATCAATTTTTACGGATGG
*
52377400 AAAATCATTTTTTACGGAT
1 AAAATCAATTTTTACGGAT
52377419 ACATAGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
AAAATCAATTTTTACGGATGG
Found at i:52378668 original size:263 final size:261
Alignment explanation
Indices: 52377951--52378692 Score: 1209
Period size: 261 Copynumber: 2.8 Consensus size: 261
52377941 ATTTTTGCGT
52377951 CCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAAACAATATTTGTGGCGCTTTTA
1 CCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAAACAATATTTGTGGCGCTTTTA
*
52378016 AAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTATAGTTAAAGGAAATTTGTG
66 AAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACAGTTAAAGGAAATTTGTG
*
52378081 GCGTTTCTTCGTGAAACGCCGGTAATATATCACCTTTTGCGGCGATTTTCAAATGCGCCACTAAT
131 GCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTTGCGGCGATTTTCAAATGCGCCACTAAT
* * *
52378146 ATCAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGTGGCGCTTTAGCTAAAGC
196 AACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTGTTGCGGCGCTTTAGCTAAAGC
52378211 G
261 G
52378212 CCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAAACAATATTTGTGGCGCTTTTA
1 CCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAAACAATATTTGTGGCGCTTTTA
*
52378277 AAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACAGTTAAAGGAAATTTCTG
66 AAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACAGTTAAAGGAAATTTGTG
* *
52378342 GCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTTGCGGCGATTTTCAACTGCACCACTAAT
131 GCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTTGCGGCGATTTTCAAATGCGCCACTAAT
52378407 AACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTGTTGCGGCGCTTTAGCTAAAGC
196 AACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTGTTGCGGCGCTTTAGCTAAAGC
52378472 G
261 G
* ** * *
52378473 CCACTAATAAAAATAGGAAACGACGTCGTTTCCTCAGCTCGTGATTTGCGA-ATTTGTGGCGTTT
1 CCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGT-A--AACAATATTTGTGGCGCTT
* * * *
52378537 TTATAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAAGGCAATTT
63 TTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACAGTTAAAGGAAATTT
* * *
52378602 GTGGCGTTTCTTCGTAAAACGCAGGTAATATATCA-CTTTTAGCGGCGTTTTTTAAATGCGCCAC
128 GTGGCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTT-GCGGCGATTTTCAAATGCGCCAC
* * **
52378666 TAAAAGAAAACAACAAAACGGCACCGT
192 TAATA-ACAAGGACAAAACGGCACCGT
52378693 CTTTGTCACA
Statistics
Matches: 449, Mismatches: 27, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
261 294 0.65
262 6 0.01
263 129 0.29
264 20 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (261 bp):
CCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAAACAATATTTGTGGCGCTTTTA
AAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACAGTTAAAGGAAATTTGTG
GCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTTGCGGCGATTTTCAAATGCGCCACTAAT
AACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTGTTGCGGCGCTTTAGCTAAAGC
G
Found at i:52378744 original size:115 final size:116
Alignment explanation
Indices: 52378530--52378769 Score: 385
Period size: 115 Copynumber: 2.1 Consensus size: 116
52378520 GCGAATTTGT
52378530 GGCG-TTTTTATAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAA
1 GGCGTTTTTTATAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAA
* * ** *
52378594 GGCAATTTGTGGCGTTTCTTCGTAAAACGCAGGTAATATATCACTTTTAGC
66 GGAAATTTGCGGCGTTTCTTCACAAAACGCAGGTAATATATCACCTTTAGC
52378645 GGCGTTTTTTA-AATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAA
1 GGCGTTTTTTATAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAA
* * * *
52378709 GGAAATTTGCGGCGTTTCTTTACAAAATGCCGGTAATATATGACCTTTAGC
66 GGAAATTTGCGGCGTTTCTTCACAAAACGCAGGTAATATATCACCTTTAGC
52378760 GGCGTTTTTT
1 GGCGTTTTTT
52378770 CTGAAGCGCC
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 109 0.95
116 6 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (116 bp):
GGCGTTTTTTATAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAA
GGAAATTTGCGGCGTTTCTTCACAAAACGCAGGTAATATATCACCTTTAGC
Found at i:52379253 original size:21 final size:20
Alignment explanation
Indices: 52379229--52379296 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
52379219 TCTTAAATCT
*
52379229 TAAACCCCAAACCTAAAACAC
1 TAAACCCTAAACCTAAAAC-C
* *
52379250 TAAACTCTAAACTCT-AAACTG
1 TAAACCCTAAAC-CTAAAAC-C
52379271 TAAACCCTAAACC-ATAAACC
1 TAAACCCTAAACCTA-AAACC
52379291 TAAACC
1 TAAACC
52379297 ATATTTTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 7 0.18
21 29 0.76
22 2 0.05
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (20 bp):
TAAACCCTAAACCTAAAACC
Found at i:52379254 original size:7 final size:7
Alignment explanation
Indices: 52379244--52379295 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
52379234 CCCAAACCTA
*
52379244 AAACACT
1 AAACTCT
52379251 AAACTCT
1 AAACTCT
52379258 AAACTCT
1 AAACTCT
*
52379265 AAACTGT
1 AAACTCT
*
52379272 AAACCCT
1 AAACTCT
52379279 AAAC-CAT
1 AAACTC-T
52379286 AAAC-CT
1 AAACTCT
52379292 AAAC
1 AAAC
52379296 CATATTTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.15
7 34 0.85
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACTCT
Found at i:52379648 original size:9 final size:8
Alignment explanation
Indices: 52379632--52379673 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
52379622 CCCTAACCGT
52379632 AACCCCTA
1 AACCCCTA
52379640 AATCCCCTA
1 AA-CCCCTA
52379649 AATCCCCT-
1 AA-CCCCTA
52379657 AACCCCT-
1 AACCCCTA
52379664 AACCCCTA
1 AACCCCTA
52379672 AA
1 AA
52379674 GCATGACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 12 0.38
8 6 0.19
9 14 0.44
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.17
Consensus pattern (8 bp):
AACCCCTA
Found at i:52379664 original size:7 final size:7
Alignment explanation
Indices: 52379622--52379672 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
52379612 TGCGTTGAAA
52379622 CCCTAA-
1 CCCTAAC
*
52379628 CCGTAAC
1 CCCTAAC
52379635 CCCTAAATC
1 CCCT-AA-C
52379644 CCCTAAATC
1 CCCT-AA-C
52379653 CCCTAAC
1 CCCTAAC
52379660 CCCTAAC
1 CCCTAAC
52379667 CCCTAA
1 CCCTAA
52379673 AGCATGACAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 5 0.12
7 17 0.43
8 4 0.10
9 14 0.35
ACGTcount: A:0.31, C:0.49, G:0.02, T:0.18
Consensus pattern (7 bp):
CCCTAAC
Found at i:52380274 original size:113 final size:114
Alignment explanation
Indices: 52380132--52380350 Score: 266
Period size: 113 Copynumber: 1.9 Consensus size: 114
52380122 CAACCCCAAC
* ** *
52380132 CATTAGCGGCGCTTCACTAAAAACGCCGCTAAGGCCTCAAAAGATAT-GAAAACGGTGCCG-TTG
1 CATTAGCGGCGCTTCACTAAAAACGCCGCTAAGGCCACAAAAGAT-TGGAAAACGGCACAGTTTG
*
52380195 GACATATGTTTTTT-GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCATGAA
65 G-CATAGGTTTTTTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCATGAA
* * ** * *
52380245 CATTAGCGGCGCTATC-GTAAAAGCGCCGCTAATTCCACGAAAGCTTGGAAAACGGCACAGTTTG
1 CATTAGCGGCGCT-TCACTAAAAACGCCGCTAAGGCCACAAAAGATTGGAAAACGGCACAGTTTG
* *
52380309 GCTTAGGTTTTTTAGCGGCGCTTTTCCAAAAACGCCGCTAAA
65 GCATAGGTTTTTTAGCGGCGCTTCTCCAAAAACGCCGCTAAA
52380351 TCCCAAAATC
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
112 1 0.01
113 55 0.62
114 33 0.37
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (114 bp):
CATTAGCGGCGCTTCACTAAAAACGCCGCTAAGGCCACAAAAGATTGGAAAACGGCACAGTTTGG
CATAGGTTTTTTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCATGAA
Found at i:52380310 original size:188 final size:187
Alignment explanation
Indices: 52379944--52380310 Score: 408
Period size: 188 Copynumber: 2.0 Consensus size: 187
52379934 AACCCCTGAG
* * * *
52379944 CATTAGCGGCGCTTCCCAAAAAACGCCGCTAAATCCCCAAAAAGCTCCAAAAACGGCACCGTTCG
1 CATTAGCGGCGCTTCACAAAAAACGCCGCTAAAGCCCCAAAAAGATACAAAAACGGCACCGTTCG
* *
52380009 GCTTAGTTTTCTTGCGGCGCTTCTCCAAAAACGCCGCTAAAGGAAGCATTAGCGGCGCTTCATTT
66 GCATAGTTTTCTTGCGGCGCTTCTCCAAAAACGCCGCTAAAGGAAGCATTAGCGGCGCTTCA-GT
** *
52380074 GAAAACGCCGCTAAAGCCACTAAAAGTTAAGAAAACGGTGCCGTTTGGCAACCCCAAC
130 GAAAACGCCGCTAAAGCCACTAAAAGTTAAGAAAACGGCACAGTTTGGCAACCCCAAC
* * * ** **
52380132 CATTAGCGGCGCTTCACTAAAAACGCCGCTAAGGCCTC-AAAAGATATGAAAACGGTGCCGTT-G
1 CATTAGCGGCGCTTCACAAAAAACGCCGCTAAAGCCCCAAAAAGATACAAAAACGGCACCGTTCG
52380195 GACATATGTTTT-TTGCGGCGCTTCTCCAAAAACGCCGCTAAAGCCATGAA-CATTAGCGGCGCT
66 G-CATA-GTTTTCTTGCGGCGCTTCTCCAAAAACGCCGCTAAAG----GAAGCATTAGCGGCGCT
** * *
52380258 ATC-GT-AAAAGCGCCGCTAATTCCAC-GAAAGCTT-GGAAAACGGCACAGTTTGGC
125 -TCAGTGAAAA-CGCCGCTAAAGCCACTAAAAG-TTAAGAAAACGGCACAGTTTGGC
52380311 TTAGGTTTTT
Statistics
Matches: 150, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
186 2 0.01
187 52 0.35
188 62 0.41
189 16 0.11
190 13 0.09
191 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (187 bp):
CATTAGCGGCGCTTCACAAAAAACGCCGCTAAAGCCCCAAAAAGATACAAAAACGGCACCGTTCG
GCATAGTTTTCTTGCGGCGCTTCTCCAAAAACGCCGCTAAAGGAAGCATTAGCGGCGCTTCAGTG
AAAACGCCGCTAAAGCCACTAAAAGTTAAGAAAACGGCACAGTTTGGCAACCCCAAC
Found at i:52380401 original size:72 final size:71
Alignment explanation
Indices: 52380246--52380456 Score: 169
Period size: 72 Copynumber: 2.9 Consensus size: 71
52380236 AGCCATGAAC
* * * * * * * *
52380246 ATTAGCGGCGC-TATCGTAAAAGCGCCGCTAATTCCACGAAAGCTTGGAAAACGGCACAGTTTGG
1 ATTAGCGGCGCTTAT--TAAAAACGCCGCTAAATCCCCAAAAACTTAG-AAACGGCACCGTTTGT
***
52380310 CTTAGGTTT
63 CTTAGGAAA
* *
52380319 TTTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAT-CCCAAAATC-TACGGAAACGGCACCGTTTG
1 ATTAGCGGCGCTTATT--AAAAACGCCGCTAAATCCCCAAAAACTTA--GAAACGGCACCGTTTG
52380381 TCTTAGGAAA
62 TCTTAGGAAA
* * **
52380391 ATTAGTGGCGCTTGATTAAAAACGTCGCTAAATCCCCAAAAACTTAGAAACGGCGTCGTTTGTCT
1 ATTAGCGGCGCTT-ATTAAAAACGCCGCTAAATCCCCAAAAACTTAGAAACGGCACCGTTTGTCT
52380456 T
65 T
52380457 TGGTTTTTGC
Statistics
Matches: 111, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
71 2 0.02
72 70 0.63
73 34 0.31
74 5 0.05
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (71 bp):
ATTAGCGGCGCTTATTAAAAACGCCGCTAAATCCCCAAAAACTTAGAAACGGCACCGTTTGTCTT
AGGAAA
Found at i:52380694 original size:40 final size:40
Alignment explanation
Indices: 52380612--52380687 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
52380602 TGAATGCGTA
* * *
52380612 TTTGCGGCGTTTTTATGAAAAACGCCGCTATTGCTTACCT
1 TTTGCGGCGTTTTTATCAAAAACGCCGCTAATGATTACCT
* *
52380652 TTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATT
1 TTTGCGGCGTTTTTATCAAAAACGCCGCTAATGATT
52380688 GACTTTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTGCGGCGTTTTTATCAAAAACGCCGCTAATGATTACCT
Found at i:52381442 original size:7 final size:7
Alignment explanation
Indices: 52381432--52381483 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
52381422 CACTAACTCT
*
52381432 TAACCTC
1 TAACCCC
**
52381439 TAACCTT
1 TAACCCC
52381446 TAACCCC
1 TAACCCC
52381453 TAACCCC
1 TAACCCC
52381460 TAACCCC
1 TAACCCC
* **
52381467 TAGCTAC
1 TAACCCC
52381474 TAACCCC
1 TAACCCC
52381481 TAA
1 TAA
52381484 ATCTTATTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.31, C:0.44, G:0.02, T:0.23
Consensus pattern (7 bp):
TAACCCC
Found at i:52382226 original size:50 final size:50
Alignment explanation
Indices: 52382172--52382274 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
52382162 ATCAAAAGCG
* *
52382172 GGCATTAGCGGCGCTTTTTCAAAAATGCCACTAAAGGCCCAAGCATTAGC
1 GGCATTAGCGGCGCTTATTCAAAAACGCCACTAAAGGCCCAAGCATTAGC
* *
52382222 GGCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTAGC
1 GGCATTAGCGGCGCTTATTCAAAAACGCCACTAAAGGCCCAAGCATTAGC
52382272 GGC
1 GGC
52382275 GCTTCTTCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.19
Consensus pattern (50 bp):
GGCATTAGCGGCGCTTATTCAAAAACGCCACTAAAGGCCCAAGCATTAGC
Found at i:52382351 original size:41 final size:41
Alignment explanation
Indices: 52382223--52382383 Score: 270
Period size: 41 Copynumber: 4.0 Consensus size: 41
52382213 AGCATTAGCG
52382223 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
52382264 GCATTAGCGGCGCTTCTTCACAAA-GCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
*
52382304 GCATTAGCGGCGCTTATTCAAAAACGCCGTTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
52382345 GAATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCC
52382384 CTAAAACTCA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 38 0.34
41 73 0.66
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
Found at i:52382358 original size:81 final size:82
Alignment explanation
Indices: 52382223--52382383 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 82
52382213 AGCATTAGCG
* *
52382223 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCACAAA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAA
52382288 -GCCGCTAAAGGCCCGA
66 CGCCGCTAAAGGCCCGA
* *
52382304 GCATTAGCGGCGCTTATTCAAAAACGCCGTTAAAGGCCCGAGAATTAGCGGCGCTTTTTCAAAAA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAA
52382369 CGCCGCTAAAGGCCC
66 CGCCGCTAAAGGCCC
52382384 CTAAAACTCA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 61 0.81
82 14 0.19
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (82 bp):
GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAA
CGCCGCTAAAGGCCCGA
Found at i:52382566 original size:41 final size:40
Alignment explanation
Indices: 52382439--52382570 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
52382429 ACTTTTTGGA
* ** *
52382439 AAACGCCGGTAATGCTT-ATTTTTAGCGGCGTTTTCCAAC
1 AAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTATC
* * ** * *
52382478 AAGCGCCGCTAATGCTCGACCTTTAGCAGCG-TTTTTATA
1 AAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTATC
*
52382517 AAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTTTATCC
1 AAA-CGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT-C
52382559 AAACGCCGCTAA
1 AAACGCCGCTAA
52382571 AAACGCCGCT
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 20 0.28
40 33 0.46
41 16 0.22
42 3 0.04
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (40 bp):
AAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTATC
Found at i:52382576 original size:12 final size:12
Alignment explanation
Indices: 52382559--52382584 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52382549 TTTTTTATCC
52382559 AAACGCCGCTAA
1 AAACGCCGCTAA
52382571 AAACGCCGCTAA
1 AAACGCCGCTAA
52382583 AA
1 AA
52382585 GCCTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:52385832 original size:15 final size:18
Alignment explanation
Indices: 52385812--52385851 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
52385802 AGGAATTTTA
52385812 GGTAATTC-AG-GCTTT-
1 GGTAATTCAAGAGCTTTG
52385827 GGTAATTCAAGAGCTTTG
1 GGTAATTCAAGAGCTTTG
52385845 GGTAATT
1 GGTAATT
52385852 TTGGCTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 2 0.09
17 5 0.23
18 7 0.32
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.38
Consensus pattern (18 bp):
GGTAATTCAAGAGCTTTG
Found at i:52385849 original size:33 final size:33
Alignment explanation
Indices: 52385802--52386372 Score: 317
Period size: 33 Copynumber: 17.3 Consensus size: 33
52385792 TCAACACCTT
* * *
52385802 AGGAATTTTAGGTAATTCAGGCTTTGGTAATTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* * * ** *
52385835 AAGAGCTTTGGGTAATTTTGGCTTGGGC-ACTTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAAC-TC
* * * * *
52385868 AGGAACTCTAGGCAATTCAGGCATTGGTAACTT
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* * * *
52385901 AGGAACTTTTGGTGATTCATGTTTTGGCAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* * ** * * *
52385934 AGGAGCTTTGGGTAATTTTGACTTGGGCACCTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* *
52385967 AGGAACTTTAGGCAATTCAGGCTTTGGTAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* * * * * *
52386000 AAGAAATTTTGATAATTCGGGTTTTGGCAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* * * *
52386033 AGGAGCTTTAGGCAATTCTGGC-TTGGACACCTC
1 AGGAACTTTAGGTAATTCAGGCTTTGG-CAACTC
* * * *
52386066 ATGAACTTTAGGCAATTCTGGCTTTGGTAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* *
52386099 AAGAACTTTTA-GTAATTCAGGTTTTGGCAACTC
1 AGGAAC-TTTAGGTAATTCAGGCTTTGGCAACTC
** * *
52386132 AGGAGTTTTAGATAATTCTGGCTTT-GCTAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGC-AACTC
* * * * *
52386165 AAGAGCTTTTGGTAATTCAAGTTTTGGCAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* * * * *
52386198 GGGAACTTTGGGTAATTCTA-GCTTGGGCACCTT
1 AGGAACTTTAGGTAATTC-AGGCTTTGGCAACTC
* * ** *
52386231 GGGAAACTTTAGGCAATTCTTGCTTTGGTAACTC
1 AGG-AACTTTAGGTAATTCAGGCTTTGGCAACTC
* * * * * *
52386265 AAGAACTTTTGGTAATTCAGGTTTTAGTAGCTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
** * * *
52386298 AGGAGTTTTAGGTAATTCTGG-TTTGGGCACCTT
1 AGGAACTTTAGGTAATTCAGGCTTT-GGCAACTC
* * ** *
52386331 TGGAACTCTAGGTAATTCTTGCTTTGGTAACTC
1 AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
* *
52386364 TGAAACTTT
1 AGGAACTTT
52386373 GACTTCATCA
Statistics
Matches: 395, Mismatches: 130, Indels: 26
0.72 0.24 0.05
Matches are distributed among these distances:
32 14 0.04
33 342 0.87
34 39 0.10
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (33 bp):
AGGAACTTTAGGTAATTCAGGCTTTGGCAACTC
Found at i:52386133 original size:99 final size:99
Alignment explanation
Indices: 52385807--52386155 Score: 448
Period size: 99 Copynumber: 3.5 Consensus size: 99
52385797 ACCTTAGGAA
* * * * * * *
52385807 TTTTAGGTAATTCAGGCTTTGGTAATTCAAGAGCTTTGGGTAATTTTGGCTTGGGCACTTCAGGA
1 TTTTA-GTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGGGCACCTCAGGA
* * * *
52385872 ACTCTAGGCAATTCAGGCATTGGTAACTTAGGAAC
65 ACTTTAGGCAATTCAGGCTTTGGTAACTCAAGAAC
* * * * * *
52385907 TTTTGGTGATTCATGTTTTGGCAACTCAGGAGCTTTGGGTAATTTTGACTTGGGCACCTCAGGAA
1 TTTTAGTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGGGCACCTCAGGAA
*
52385972 CTTTAGGCAATTCAGGCTTTGGTAACTCAAGAAA
66 CTTTAGGCAATTCAGGCTTTGGTAACTCAAGAAC
* * * *
52386006 TTTT-GATAATTCGGGTTTTGGCAACTCAGGAGCTTTAGGCAATTCTGGCTTGGACACCTCATGA
1 TTTTAG-TAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGGGCACCTCAGGA
*
52386070 ACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAAC
65 ACTTTAGGCAATTCAGGCTTTGGTAACTCAAGAAC
* *
52386105 TTTTAGTAATTCAGGTTTTGGCAACTCAGGAGTTTTAGATAATTCTGGCTT
1 TTTTAGTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTT
52386156 TGCTAACTCA
Statistics
Matches: 218, Mismatches: 29, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
98 1 0.00
99 212 0.97
100 5 0.02
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (99 bp):
TTTTAGTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGGGCACCTCAGGAA
CTTTAGGCAATTCAGGCTTTGGTAACTCAAGAAC
Found at i:52386182 original size:99 final size:97
Alignment explanation
Indices: 52385813--52386215 Score: 410
Period size: 99 Copynumber: 4.1 Consensus size: 97
52385803 GGAATTTTAG
* * * * * * * * *
52385813 GTAATTCAGGCTTTGGTAATTCAAGAGCTTTGGGTAATTTTGGCTTGGGCACTTCAGGAACTCTA
1 GTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTT-GGCACCTCAAGAACTTTA
* * *
52385878 GGCAATTCAGGCATTGGTAACTTAGGAACTTTT
65 GGCAATTCAGGCTTTGGTAACTCAAGAACTTTT
* * * * * *
52385911 GGTGATTCATGTTTTGGCAACTCAGGAGCTTTGGGTAATTTTGACTTGGGCACCTCAGGAACTTT
1 -GTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTT-GGCACCTCAAGAACTTT
*
52385976 AGGCAATTCAGGCTTTGGTAACTCAAGAAATTTT
64 AGGCAATTCAGGCTTTGGTAACTCAAGAACTTTT
* * *
52386010 GATAATTCGGGTTTTGGCAACTCAGGAGCTTTAGGCAATTCTGGCTTGGACACCTCATGAACTTT
1 G-TAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGG-CACCTCAAGAACTTT
*
52386075 AGGCAATTCTGGCTTTGGTAACTCAAGAACTTTT
64 AGGCAATTCAGGCTTTGGTAACTCAAGAACTTTT
* * * * *
52386109 AGTAATTCAGGTTTTGGCAACTCAGGAGTTTTAGATAATTCTGGCTTTGCTAACTCAAGAGCTTT
1 -GTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGGC-ACCTCAAGAACTTT
* * * * * ** *
52386174 TGGTAATTCAAGTTTTGGCAACTCGGGAACTTTGG
64 AGGCAATTCAGGCTTTGGTAACTCAAGAACTTT-T
52386209 GTAATTC
1 GTAATTC
52386216 TAGCTTGGGC
Statistics
Matches: 259, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
98 4 0.02
99 254 0.98
100 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (97 bp):
GTAATTCAGGTTTTGGCAACTCAGGAGCTTTAGGTAATTCTGGCTTGGCACCTCAAGAACTTTAG
GCAATTCAGGCTTTGGTAACTCAAGAACTTTT
Found at i:52386348 original size:166 final size:165
Alignment explanation
Indices: 52385980--52386322 Score: 436
Period size: 166 Copynumber: 2.1 Consensus size: 165
52385970 AACTTTAGGC
* * * * * * ** *
52385980 AATTCAGGCTTTGGTAACTCAAGAAATTTTGATAATTCGGGTTTTGGCAACTCAGGAGCTTTAGG
1 AATTCTGGCTTTGCTAACTCAAGAACTCTAGGTAATTCAAGTTTTGGCAACTCAGGAACTTTAGG
* *
52386045 CAATTCTGGCTTGGACACCTCATGAACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTTTA
66 CAATTCTAGCTTGGACACCTCAGGAACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTTTA
*
52386110 GTAATTCAGGTTTTGGCAACTCAGGAGTTTTAGAT
131 GTAATTCAGGTTTTAGCAACTCAGGAGTTTTAGAT
* * * * *
52386145 AATTCTGGCTTTGCTAACTCAAGAGCTTTTGGTAATTCAAGTTTTGGCAACTCGGGAACTTTGGG
1 AATTCTGGCTTTGCTAACTCAAGAACTCTAGGTAATTCAAGTTTTGGCAACTCAGGAACTTTAGG
* * ** *
52386210 TAATTCTAGCTTGGGCACCTTGGGAAACTTTAGGCAATTCTTGCTTTGGTAACTCAAGAACTTTT
66 CAATTCTAGCTTGGACACCTCAGG-AACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTTT
* * * *
52386275 GGTAATTCAGGTTTTAGTAGCTCAGGAGTTTTAGGT
130 AGTAATTCAGGTTTTAGCAACTCAGGAGTTTTAGAT
52386311 AATTCTGG-TTTG
1 AATTCTGGCTTTG
52386323 GGCACCTTTG
Statistics
Matches: 155, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
165 77 0.50
166 78 0.50
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (165 bp):
AATTCTGGCTTTGCTAACTCAAGAACTCTAGGTAATTCAAGTTTTGGCAACTCAGGAACTTTAGG
CAATTCTAGCTTGGACACCTCAGGAACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTTTA
GTAATTCAGGTTTTAGCAACTCAGGAGTTTTAGAT
Found at i:52386373 original size:166 final size:166
Alignment explanation
Indices: 52385980--52386373 Score: 409
Period size: 166 Copynumber: 2.4 Consensus size: 166
52385970 AACTTTAGGC
* * * * * * ** * * *
52385980 AATTCAGGCTTTGGTAACTCAAGAAATTTTGATAATTCGGGTTTTGGCAACTCAGG-AGCTTTAG
1 AATTCTGGCTTTGCTAACTCAAGAACTCTAGGTAATTCAAGCTTTGGCAACTC-GGAAACTTTGG
* * * ***
52386044 GCAATTCTGGCTTGGACACCTCATG-AACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTT
65 GTAATTCTAGCTTGGGCACCTTGGGAAACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTT
*
52386108 TAGTAATTCAGGTTTTGGCAACTCAGGAGTTTTAGAT
130 TAGTAATTCAGGTTTTAGCAACTCAGGAGTTTTAGAT
* * * * *
52386145 AATTCTGGCTTTGCTAACTCAAGAGCTTTTGGTAATTCAAGTTTTGGCAACTCGGGAACTTTGGG
1 AATTCTGGCTTTGCTAACTCAAGAACTCTAGGTAATTCAAGCTTTGGCAACTCGGAAACTTTGGG
*
52386210 TAATTCTAGCTTGGGCACCTTGGGAAACTTTAGGCAATTCTTGCTTTGGTAACTCAAGAACTTTT
66 TAATTCTAGCTTGGGCACCTTGGGAAACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTTT
* * * *
52386275 GGTAATTCAGGTTTTAGTAGCTCAGGAGTTTTAGGT
131 AGTAATTCAGGTTTTAGCAACTCAGGAGTTTTAGAT
* *** ** * *
52386311 AATTCTGG-TTTGGGC-ACCTTTGGAACTCTAGGTAATTCTTGCTTTGGTAACTCTGAAACTTTG
1 AATTCTGGCTTT--GCTAACTCAAGAACTCTAGGTAATTCAAGCTTTGGCAACTCGGAAACTTTG
52386374 ACTTCATCAG
Statistics
Matches: 191, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
164 2 0.01
165 74 0.39
166 113 0.59
167 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (166 bp):
AATTCTGGCTTTGCTAACTCAAGAACTCTAGGTAATTCAAGCTTTGGCAACTCGGAAACTTTGGG
TAATTCTAGCTTGGGCACCTTGGGAAACTTTAGGCAATTCTGGCTTTGGTAACTCAAGAACTTTT
AGTAATTCAGGTTTTAGCAACTCAGGAGTTTTAGAT
Found at i:52386388 original size:99 final size:100
Alignment explanation
Indices: 52386145--52386363 Score: 287
Period size: 100 Copynumber: 2.2 Consensus size: 100
52386135 AGTTTTAGAT
* * * * * * * * ** *
52386145 AATTCTGGCTTTGCTAACTCAAGAGCTTTTGGTAATTCAAGTTTTGGCAACTCGGGAACTTTGGG
1 AATTCTTGCTTTGGTAACTCAAGAACTTTTGGTAATTCAGGTTTTAGTAGCTCAGGAGTTTTAGG
*
52386210 TAATTCTAGCTTGGGCACCTTGGGAAACTTTAGGC
66 TAATTCTAGCTTGGGCACCTTGGGAAACTCTAGGC
52386245 AATTCTTGCTTTGGTAACTCAAGAACTTTTGGTAATTCAGGTTTTAGTAGCTCAGGAGTTTTAGG
1 AATTCTTGCTTTGGTAACTCAAGAACTTTTGGTAATTCAGGTTTTAGTAGCTCAGGAGTTTTAGG
* * * *
52386310 TAATTCTGGTTTGGGCACCTTTGG-AACTCTAGGT
66 TAATTCTAGCTTGGGCACCTTGGGAAACTCTAGGC
52386344 AATTCTTGCTTTGGTAACTC
1 AATTCTTGCTTTGGTAACTC
52386364 TGAAACTTTG
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
99 28 0.27
100 75 0.73
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.37
Consensus pattern (100 bp):
AATTCTTGCTTTGGTAACTCAAGAACTTTTGGTAATTCAGGTTTTAGTAGCTCAGGAGTTTTAGG
TAATTCTAGCTTGGGCACCTTGGGAAACTCTAGGC
Found at i:52386465 original size:33 final size:33
Alignment explanation
Indices: 52386419--52386530 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 33
52386409 AGCTTTTGGA
* * *
52386419 AATTCTGGCTTTGGAAACTTTGGCACTTTAGGC
1 AATTCAGGTTTTGGAAACTCTGGCACTTTAGGC
* * * *
52386452 AACTCAGGTTTTGGCAACTCCGGAACTTTAGGC
1 AATTCAGGTTTTGGAAACTCTGGCACTTTAGGC
* * *
52386485 AATTCAGGTCTT-GACAACTCTGGCATTTTAGGT
1 AATTCAGGTTTTGGA-AACTCTGGCACTTTAGGC
*
52386518 ATTTCAGGTTTTG
1 AATTCAGGTTTTG
52386531 AGATTTCTGG
Statistics
Matches: 61, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (33 bp):
AATTCAGGTTTTGGAAACTCTGGCACTTTAGGC
Found at i:52387943 original size:170 final size:168
Alignment explanation
Indices: 52387618--52387959 Score: 587
Period size: 170 Copynumber: 2.0 Consensus size: 168
52387608 TAAAAATTCT
* *
52387618 AAAATTTATATATTTTCTAAAAGAATATAATTTTTTTAAAAAAATTCTAAAGAATATATAAAGAA
1 AAAATTTATATATTTTCTAAAAGAATAAAATTCTTTTAAAAAAATTCTAAAGAATATATAAAGAA
52387683 AATTAAAATTTTAAAAATTTTCTAAAACAATAATTTTGGGACCTAAATAAGTTAATTAATTATTC
66 AATTAAAATTTTAAAAATTTTCTAAAACAATAATTTTGGGACCTAAATAAGTTAATTAATTATTC
52387748 AAATGTATTGTATCTTTTCTTTTTCTTATTTTGCTTTG
131 AAATGTATTGTATCTTTTCTTTTTCTTATTTTGCTTTG
* *
52387786 AAAACTTTATATCTTTTTTAAAAGCATATAAAATTCTTTT-AAAAAATTCTAAAGAATATATAAA
1 AAAA-TTTATATATTTTCTAAAAG-A-ATAAAATTCTTTTAAAAAAATTCTAAAGAATATATAAA
* *
52387850 GAAAATTAAAATTTTAAAAATTTTCTAAAATAATAATTTTGGGACCTTAATAAGTTAATTAATTA
63 GAAAATTAAAATTTTAAAAATTTTCTAAAACAATAATTTTGGGACCTAAATAAGTTAATTAATTA
*
52387915 TTCAAATGTATTGTATCTTTTTTTTTTCTTATTTTGCTTTG
128 TTCAAATGTATTGTATCTTTTCTTTTTCTTATTTTGCTTTG
52387956 AAAA
1 AAAA
52387960 ATTTTTCAGA
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
168 4 0.02
169 17 0.10
170 132 0.80
171 11 0.07
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (168 bp):
AAAATTTATATATTTTCTAAAAGAATAAAATTCTTTTAAAAAAATTCTAAAGAATATATAAAGAA
AATTAAAATTTTAAAAATTTTCTAAAACAATAATTTTGGGACCTAAATAAGTTAATTAATTATTC
AAATGTATTGTATCTTTTCTTTTTCTTATTTTGCTTTG
Found at i:52388158 original size:17 final size:19
Alignment explanation
Indices: 52388136--52388218 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
52388126 ATGGAAACAT
52388136 AATCTT-CA-AGGATATGC
1 AATCTTACATAGGATATGC
*
52388153 AATCTTACATATGATATGC
1 AATCTTACATAGGATATGC
* *
52388172 AATCTTAGATATGATTTATGC
1 AATCTTACATAGGA--TATGC
* * *
52388193 AATCTTAGATATGATATAC
1 AATCTTACATAGGATATGC
52388212 AATCTTA
1 AATCTTA
52388219 GAAGATATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.10
18 2 0.03
19 32 0.54
21 19 0.32
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATAGGATATGC
Found at i:52388193 original size:21 final size:19
Alignment explanation
Indices: 52388146--52388220 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
52388136 AATCTTCAAG
*
52388146 GATATGCAATCTTACATAT
1 GATATGCAATCTTAGATAT
52388165 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52388184 GATTTATGCAATCTTAGATAT
1 GA--TATGCAATCTTAGATAT
*
52388205 GATATACAATCTTAGA
1 GATATGCAATCTTAGA
52388221 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 33 0.63
21 19 0.37
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52388491 original size:23 final size:23
Alignment explanation
Indices: 52388447--52388491 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
52388437 TCTTATTTTG
* *
52388447 TTGATTTGTTTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
52388470 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
52388492 CAAATCTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.64
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:52388955 original size:29 final size:27
Alignment explanation
Indices: 52388923--52389001 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
52388913 ATATTTATAT
52388923 ATATATGTTTTTTTTTATAATTCACATAC
1 ATATAT-TTTTTTTTTATAATT-ACATAC
* * *
52388952 ATATATATTTTTCTTAT-ATGTACATAT
1 ATATATTTTTTTTTTATAAT-TACATAC
52388979 ATATATTTTTATATTTTATAATT
1 ATATATTTTT-T-TTTTATAATT
52389002 TTTATCTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 16 0.39
28 11 0.27
29 12 0.29
30 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (27 bp):
ATATATTTTTTTTTTATAATTACATAC
Found at i:52388976 original size:23 final size:22
Alignment explanation
Indices: 52388949--52388992 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
52388939 ATAATTCACA
*
52388949 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
52388972 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
52388993 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:52395855 original size:45 final size:45
Alignment explanation
Indices: 52395797--52396243 Score: 477
Period size: 45 Copynumber: 9.9 Consensus size: 45
52395787 GTGAAAACAG
* * * *
52395797 CAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* ** * *
52395842 CAGATCTTATCTTCTTGTATTGGCAGTAAAGTAGATCAAATATAG
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* * * *
52395887 CAGATCTTGTCTTCTTATATTGGTAGCGAAGTAGATCAAAGATAA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* * *
52395932 CAGATCTTATCTTCTTGTATTGGCAGTGAAGTAGATCAAAGTTAA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* *
52395977 CAGATCTTGA-CTTCCTGTACTGGCAGCGAAGTAGATCAAAGATAG
1 CAGATCTT-ATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* * * * *
52396022 CAGATCTTGTCTTCCTATATTGGTAGCCAAGTAGATCGAAGATAA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* * *
52396067 CAGATCTTGTCTTTCTGTATCGGCAGCGAAGTAGATCAAAGATAA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* * * * * *
52396112 CATATC-TAGGCTTCCTATATTGGTAGTGAAGTAGATCAAAGATCA
1 CAGATCTTA-TCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
* ** * * *
52396157 CGGATCTTGCCTTCCTGTATTGGCAGAGAAGTAGATCGAAA-ACAG
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATC-AAAGATAA
* * *
52396202 TAGATCTTATCTTCCTTTATTGGCAGCGAAGTAGATCGAAGA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGA
52396244 CAGAAGTAAC
Statistics
Matches: 331, Mismatches: 65, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
44 3 0.01
45 323 0.98
46 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (45 bp):
CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAA
Found at i:52396041 original size:135 final size:135
Alignment explanation
Indices: 52395797--52396243 Score: 535
Period size: 135 Copynumber: 3.3 Consensus size: 135
52395787 GTGAAAACAG
* * * * * *
52395797 CAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTT-ATCTTCTTGTA
1 CAGATCTTATCTTCTTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGA-CTTCCTGTA
* * *
52395861 TTGGCAGTAAAGTAGATCAAATATAGCAGATCTTGTCTTCTTATATTGGTAGCGAAGTAGATCAA
65 TTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAA
52395926 AGATAA
130 AGATAA
* * *
52395932 CAGATCTTATCTTCTTGTATTGGCAGTGAAGTAGATCAAAGTTAACAGATCTTGACTTCCTGTAC
1 CAGATCTTATCTTCTTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGACTTCCTGTAT
* * *
52395997 TGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCCAAGTAGATCGAA
66 TGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAA
52396062 GATAA
131 GATAA
* * * * * *
52396067 CAGATCTTGTCTT-TCTGTATCGGCAGCGAAGTAGATCAAAGATAACATATCTAGGCTTCCTATA
1 CAGATCTTATCTTCT-TGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGACTTCCTGTA
* * * * * *
52396131 TTGGTAGTGAAGTAGATCAAAGATCA-CGGATCTTGCCTTCCTGTATTGGCAGAGAAGTAGATCG
65 TTGGCAGTGAAGTAGATCAAAGAT-AGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC-
* *
52396195 AAA-ACAG
128 AAAGATAA
* *
52396202 TAGATCTTATCTTCCTT-TATTGGCAGCGAAGTAGATCGAAGA
1 CAGATCTTATCTT-CTTGTATTGGCAGCGAAGTAGATCAAAGA
52396244 CAGAAGTAAC
Statistics
Matches: 267, Mismatches: 39, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
134 1 0.00
135 260 0.97
136 5 0.02
137 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (135 bp):
CAGATCTTATCTTCTTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGACTTCCTGTAT
TGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAA
GATAA
Found at i:52396405 original size:44 final size:44
Alignment explanation
Indices: 52396346--52396456 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
52396336 CTCCAGTCTC
* *
52396346 ATCTCTCC-GAGGTTGCAGTGGAGCAGATTGAATAAGCCAA-CCTT
1 ATCTC-CCTGAGGTTGCAGTGGAGCAGATTGAAGAAACCAATCC-T
* * *
52396390 ATCTCCCTGAGGTTGCAGTAGAACAGATTGAAGAAACTAATCCT
1 ATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAAACCAATCCT
* * *
52396434 ATCTCCCTAAAGTAGCAGTGGAG
1 ATCTCCCTGAGGTTGCAGTGGAG
52396457 TGGATCAGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 2 0.04
44 51 0.93
45 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (44 bp):
ATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAAACCAATCCT
Found at i:52397052 original size:22 final size:21
Alignment explanation
Indices: 52397010--52397066 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
52397000 ATGCAATCTT
* * *
52397010 AGATATGATATGCAATCTTAG
1 AGATATGATTTGTAATATTAG
52397031 AAGATATGATTTGTAATATTAG
1 -AGATATGATTTGTAATATTAG
* *
52397053 AGATTTAATTTGTA
1 AGATATGATTTGTA
52397067 GATACCCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.40
Consensus pattern (21 bp):
AGATATGATTTGTAATATTAG
Found at i:52399021 original size:13 final size:12
Alignment explanation
Indices: 52398994--52399038 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
52398984 TTCTTTTTGT
52398994 TTGTAAATTTAC
1 TTGTAAATTTAC
52399006 TTGTAAATTGTAC
1 TTGTAAATT-TAC
* * *
52399019 TTGTATATATAT
1 TTGTAAATTTAC
52399031 TTGTAAAT
1 TTGTAAAT
52399039 ATTTATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (12 bp):
TTGTAAATTTAC
Found at i:52400357 original size:13 final size:12
Alignment explanation
Indices: 52400333--52400362 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
52400323 GAAAAGAACA
52400333 AAATATATATAT
1 AAATATATATAT
52400345 AAATATAATATAT
1 AAATAT-ATATAT
52400358 AAATA
1 AAATA
52400363 AACTATGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATATATAT
Found at i:52402095 original size:45 final size:44
Alignment explanation
Indices: 52402037--52402134 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
52402027 AAGACTTGTA
* ** *
52402037 TCTTCGATCTACTTCACCACCAATATGGGAAGATAAGATCTGCTT
1 TCTTCGATCTACTTCA-CACAAATACAGGAAGACAAGATCTGCTT
* * *
52402082 TTTTCGATTTACTTCACACAAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACACAAATACAGGAAGACAAGATCTGCTT
52402126 TCTTCGATC
1 TCTTCGATC
52402135 GATTCCACTG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 30 0.68
45 14 0.32
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (44 bp):
TCTTCGATCTACTTCACACAAATACAGGAAGACAAGATCTGCTT
Found at i:52402411 original size:50 final size:50
Alignment explanation
Indices: 52402259--52403021 Score: 444
Period size: 50 Copynumber: 15.3 Consensus size: 50
52402249 ATCTGAAATT
* * * *
52402259 TTCAAT-TTGTTTAACTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGC
1 TTCAATCTT-TTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* ** *** * *** * * * *
52402309 TTCAATCTGTTCT-ACCGCACCGTCAAGGAAGTAAGATCTGTCGTTGTGGC
1 TTCAATCT-TTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * *
52402359 TTCAATCTTTTTAATTGTAATATCAGGGAAACCAGATTCACCGTCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * * *** * *
52402409 TTCAATCTGTTCT-ACTGCACT-TCTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCT-TTTTAATTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* *
52402459 TTCAATTTTTTTAATTGCAATATCCGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* ** * * * *** * *
52402509 TTCAATCTGTTCCATTGCACT-GCTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTTTTTAATTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
*
52402559 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCATCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* ** * ** * *** * *
52402609 TTCAATCTGTTCCATTGCACTGCCAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * *
52402659 TTTAATTTTTTTAACTGCAATATCAGGGAAACCAGATCCGCTGTCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* **** * * * *** * * *
52402709 TTCAATCTATTCCGCTGCACT-GCTAAGGAAGTAAGATCCGCTGTTGTGGC
1 TTCAATCTTTTTAATTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* *
52402759 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCTGTCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * **** * * *** * *
52402809 TTAAATCTATTCCGCTGCACTA-CTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTTTTTAATTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
52402859 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* **** * * * *** * * *
52402909 TTCAATCTATTCCGCTGCACT-GCTAAGGAAGTAAGATCTGCCGTTGTGGC
1 TTCAATCTTTTTAATTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* **
52402959 TTCAATCTTTTTAATTGCAATATCAGAGAAACCAGATCCGCTATCGTAGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
52403009 TTCAATCTTTTTA
1 TTCAATCTTTTTA
52403022 CTTTTCAACC
Statistics
Matches: 503, Mismatches: 195, Indels: 30
0.69 0.27 0.04
Matches are distributed among these distances:
49 12 0.02
50 478 0.95
51 12 0.02
52 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
Found at i:52402437 original size:100 final size:100
Alignment explanation
Indices: 52402259--52403016 Score: 1133
Period size: 100 Copynumber: 7.6 Consensus size: 100
52402249 ATCTGAAATT
* * * * *
52402259 TTCAAT-TTGTTTAACTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCTA
1 TTCAATCTT-TTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * *
52402323 CCGCACCG-TCAAGGAAGTAAGATCTGTCGTTGTGGC
65 CTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGGC
* * * *
52402359 TTCAATCTTTTTAATTGTAATATCAGGGAAACCAGATTCACCGTCGTAGCTTCAATCTGTTCTAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
52402424 TGCACTTCTAAGGAAGTAAGATCCGCCGTTGTGGC
66 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
* * *
52402459 TTCAATTTTTTTAATTGCAATATCCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAT
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
52402524 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
66 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
* *
52402559 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCAT
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
52402624 TGCACTGCCAAGGAAGTAAGATCCGCCGTTGTGGC
66 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
* * * * * *
52402659 TTTAATTTTTTTAACTGCAATATCAGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTATTCCGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
52402724 TGCACTGCTAAGGAAGTAAGATCCGCTGTTGTGGC
66 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
* * * * *
52402759 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCTGTCGTAGCTTAAATCTATTCCGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
52402824 TGCACTACTAAGGAAGTAAGATCCGCCGTTGTGGC
66 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
* *
52402859 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCGC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
52402924 TGCACTGCTAAGGAAGTAAGATCTGCCGTTGTGGC
66 TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
* **
52402959 TTCAATCTTTTTAATTGCAATATCAGAGAAACCAGATCCGCTATCGTAGCTTCAATCT
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCT
52403017 TTTTACTTTT
Statistics
Matches: 609, Mismatches: 47, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
100 606 1.00
101 3 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (100 bp):
TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
TGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
Found at i:52411105 original size:20 final size:20
Alignment explanation
Indices: 52411080--52411119 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
52411070 TAAAGGTCTT
52411080 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
52411100 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
52411120 ATGAGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:52414947 original size:13 final size:13
Alignment explanation
Indices: 52414929--52414953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52414919 AAAAGAACAA
52414929 AATATATAAATAT
1 AATATATAAATAT
52414942 AATATATAAATA
1 AATATATAAATA
52414954 AACTATGGGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATATAAATAT
Found at i:52415045 original size:25 final size:26
Alignment explanation
Indices: 52414977--52415046 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
52414967 ATATATATGT
* * * *
52414977 GAAAATCTGTATGTATATAATATAAA
1 GAAAATGTATATGTATAAAATAGAAA
*
52415003 GAAAATGTATGAAT-TATAAAATGGAAA
1 GAAAATGTAT--ATGTATAAAATAGAAA
52415030 -AAAATGTATATGTATAA
1 GAAAATGTATATGTATAA
52415047 TAAAACGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
24 2 0.06
25 5 0.14
26 17 0.47
27 10 0.28
28 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.14, T:0.31
Consensus pattern (26 bp):
GAAAATGTATATGTATAAAATAGAAA
Found at i:52416741 original size:4 final size:4
Alignment explanation
Indices: 52416734--52416761 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
52416724 ATATGCATGT
52416734 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
52416762 GTTTATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:52416961 original size:23 final size:22
Alignment explanation
Indices: 52416932--52416975 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
52416922 ATAATTCACA
*
52416932 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
52416955 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
52416976 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:52417155 original size:3 final size:3
Alignment explanation
Indices: 52417147--52417178 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52417137 TTTATTTATC
52417147 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
52417179 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52417183 original size:3 final size:3
Alignment explanation
Indices: 52417177--52417220 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
52417167 ATTATTATTA
52417177 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
52417221 CTTGATCATG
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:52418285 original size:26 final size:25
Alignment explanation
Indices: 52418256--52418312 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
52418246 ATTGAGTTAG
*
52418256 GATTATAAAATATGACTTGTCAAGTC
1 GATTATAAAA-ATGACTTGTCAACTC
***
52418282 GATTGATTTGAATGACTTGTCAACTC
1 GATT-ATAAAAATGACTTGTCAACTC
52418308 GATTA
1 GATTA
52418313 ACTTGAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 22 0.85
27 3 0.12
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (25 bp):
GATTATAAAAATGACTTGTCAACTC
Found at i:52418318 original size:26 final size:26
Alignment explanation
Indices: 52418267--52418319 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
52418257 ATTATAAAAT
* * *
52418267 ATGACTTGTCAAGTCGATTGATTTGA
1 ATGACTTGTCAACTCGATTAACTTGA
52418293 ATGACTTGTCAACTCGATTAACTTGA
1 ATGACTTGTCAACTCGATTAACTTGA
52418319 A
1 A
52418320 ATTTTTCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (26 bp):
ATGACTTGTCAACTCGATTAACTTGA
Found at i:52418930 original size:44 final size:44
Alignment explanation
Indices: 52418867--52418957 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
52418857 GTGGTTTTTT
52418867 TGTAAGTATTATGTGAAAATAGGAAACGGACATAGCATTACACA
1 TGTAAGTATTATGTGAAAATAGGAAACGGACATAGCATTACACA
*
52418911 TGTAAGTATTATGTGAAAATAGGAAACGGACGTAGCATTACACA
1 TGTAAGTATTATGTGAAAATAGGAAACGGACATAGCATTACACA
52418955 TGT
1 TGT
52418958 GATGCGATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (44 bp):
TGTAAGTATTATGTGAAAATAGGAAACGGACATAGCATTACACA
Found at i:52423815 original size:16 final size:18
Alignment explanation
Indices: 52423784--52423816 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52423774 ACGTGGAAAT
52423784 TATATGACTAATACATTA
1 TATATGACTAATACATTA
52423802 TATATGA-TAA-ACATT
1 TATATGACTAATACATT
52423817 GATTTAACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (18 bp):
TATATGACTAATACATTA
Found at i:52424385 original size:33 final size:33
Alignment explanation
Indices: 52424287--52424397 Score: 105
Period size: 33 Copynumber: 3.4 Consensus size: 33
52424277 GGTTGGGTAA
* * * * *
52424287 TTTAGGTATTTCTGGTTTGGGTAACTCAGGAAC
1 TTTAGGCAATTCTGGTTTCGGTAATTCAGGAAT
* * *
52424320 TTTGGGCAATTCTGGTTTCGGCACTTCAGGAAT
1 TTTAGGCAATTCTGGTTTCGGTAATTCAGGAAT
* * *
52424353 TTTAGGCAATTCTGGTTTTGTTAATTCGGGAAT
1 TTTAGGCAATTCTGGTTTCGGTAATTCAGGAAT
* *
52424386 TTTCGGTAATTC
1 TTTAGGCAATTC
52424398 AGGAGCTTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (33 bp):
TTTAGGCAATTCTGGTTTCGGTAATTCAGGAAT
Done.