Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 142 of 211
Found at i:42276429 original size:19 final size:17
Alignment explanation
Indices: 42276382--42276432 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
42276372 TATCATTAGC
42276382 TTAAGTTAATTAA-AGA
1 TTAAGTTAATTAATAGA
42276398 TTAAGGTTTAATTAATCATGA
1 TTAA-G-TTAATTAAT-A-GA
42276419 TTAAGTTAATTAAT
1 TTAAGTTAATTAAT
42276433 TAAGCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.13
17 1 0.03
18 8 0.27
19 9 0.30
20 2 0.07
21 6 0.20
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (17 bp):
TTAAGTTAATTAATAGA
Found at i:42277598 original size:38 final size:38
Alignment explanation
Indices: 42277553--42277641 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
42277543 TTCGTACGCT
* *
42277553 AGTATGCACTTTGTGTGCCAGGATACATTTTGTGTGCC
1 AGTATGCACTTTGTGTGCCAGGATACACTTAGTGTGCC
** * * *
42277591 ACG-ATGCACTTCATGTGTCAGGATGCACTTAGTGTGCT
1 A-GTATGCACTTTGTGTGCCAGGATACACTTAGTGTGCC
42277629 AGTATGCACTTTG
1 AGTATGCACTTTG
42277642 CACAGTAGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
37 1 0.03
38 38 0.95
39 1 0.03
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (38 bp):
AGTATGCACTTTGTGTGCCAGGATACACTTAGTGTGCC
Found at i:42277626 original size:19 final size:19
Alignment explanation
Indices: 42277556--42277639 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
42277546 GTACGCTAGT
*
42277556 ATGCACTTTGTGTGCCAGG
1 ATGCACTTAGTGTGCCAGG
* * * *
42277575 ATACATTTTGTGTGCCACG
1 ATGCACTTAGTGTGCCAGG
*
42277594 ATGCACTTCA-TGTGTCAGG
1 ATGCACTT-AGTGTGCCAGG
* *
42277613 ATGCACTTAGTGTGCTAGT
1 ATGCACTTAGTGTGCCAGG
42277632 ATGCACTT
1 ATGCACTT
42277640 TGCACAGTAG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.02
19 51 0.98
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (19 bp):
ATGCACTTAGTGTGCCAGG
Found at i:42280856 original size:45 final size:45
Alignment explanation
Indices: 42280768--42280989 Score: 254
Period size: 45 Copynumber: 5.0 Consensus size: 45
42280758 TCGTTATACA
* * *
42280768 GTGG-ATCAGCACATAAC-ACCACCCTTATAATCAACT-ATATTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAA-TGATACTCG
** **
42280811 GTGGAATCAGCACATAGCAACCACCTTTATTTTCAATGATTTTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACTCG
** * *
42280856 GTGGAGCCAGC-CTATAGCAACCACCATTATAATCAATGGTACTCG
1 GTGGAATCAGCAC-ATAGCAACCACCTTTATAATCAATGATACTCG
* * *
42280901 GTGGAATTAGCACATAGCAACCACCTTTATAATCAATGGTACCCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACTCG
* *
42280946 GTGGAATCAGCATATAGCAACCACCTTTATAATCAATGGTACTC
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACTC
42280990 AGTACACGTA
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
43 4 0.03
44 14 0.09
45 134 0.88
46 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACTCG
Found at i:42286183 original size:31 final size:30
Alignment explanation
Indices: 42286148--42286238 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 30
42286138 GGCGCAACCT
*
42286148 AAAGAAGTGCATTTGTGGCTATCTCTGTTAA
1 AAAGAAG-GCATTTGTGGCTATCTCTATTAA
* *
42286179 AAAGAA-GCCTTTTTGGCTATCTCTATTAA
1 AAAGAAGGCATTTGTGGCTATCTCTATTAA
* * *
42286208 AAGGAA-GCCTTTATGG-TGATCTCTATTAA
1 AAAGAAGGCATTTGTGGCT-ATCTCTATTAA
42286237 AA
1 AA
42286239 GGAAACTTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.02
29 47 0.87
31 6 0.11
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (30 bp):
AAAGAAGGCATTTGTGGCTATCTCTATTAA
Found at i:42286195 original size:29 final size:29
Alignment explanation
Indices: 42286159--42286310 Score: 141
Period size: 29 Copynumber: 5.3 Consensus size: 29
42286149 AAGAAGTGCA
*
42286159 TTTGTGGCTATCTCTGTTAAAAAGAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
* *
42286188 TTTTTGGCTATCTCTATTAAAAGGAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
* * *
42286217 TTTATGG-TGATCTCTATTAAAAGGAA-AC
1 TTTGTGGCT-ATCTCTGTTAAAAGGAAGCC
* * *
42286245 TTGTGTGGCGATCTTTGTTAAAAGGAAGTC
1 TT-TGTGGCTATCTCTGTTAAAAGGAAGCC
** *
42286275 TTTGTGGAAATCTCTG-TCAAAGGACA-CC
1 TTTGTGGCTATCTCTGTTAAAAGGA-AGCC
42286303 TTTGTGGC
1 TTTGTGGC
42286311 GAGACTCTGA
Statistics
Matches: 102, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
28 19 0.19
29 80 0.78
30 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (29 bp):
TTTGTGGCTATCTCTGTTAAAAGGAAGCC
Found at i:42293549 original size:12 final size:12
Alignment explanation
Indices: 42293532--42293559 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42293522 CACTTAAGAA
42293532 TATACTATTAAG
1 TATACTATTAAG
42293544 TATACTATTAAG
1 TATACTATTAAG
42293556 TATA
1 TATA
42293560 TTTAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
TATACTATTAAG
Found at i:42297635 original size:3 final size:3
Alignment explanation
Indices: 42297627--42297667 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42297617 CTATCATTTA
42297627 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
42297668 TTTTCCCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:42303447 original size:22 final size:23
Alignment explanation
Indices: 42303406--42303448 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
42303396 GGAAAGATTT
*
42303406 AATTACAATGAAGAGTAAAAAAG
1 AATTACAATGAAAAGTAAAAAAG
42303429 AATTACAAT-AAAAGTAAAAA
1 AATTACAATGAAAAGTAAAAA
42303449 TATTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.19
Consensus pattern (23 bp):
AATTACAATGAAAAGTAAAAAAG
Found at i:42303684 original size:22 final size:22
Alignment explanation
Indices: 42303624--42303681 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
42303614 AATCTTCAAG
42303624 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
42303643 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
42303665 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
42303682 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:42306672 original size:3 final size:3
Alignment explanation
Indices: 42306664--42306709 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
42306654 TTTTGTACTC
*
42306664 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42306710 GTATACCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42307588 original size:70 final size:70
Alignment explanation
Indices: 42307475--42307608 Score: 214
Period size: 70 Copynumber: 1.9 Consensus size: 70
42307465 TCCTTTCAAA
** *
42307475 CTCAAGTTTTAAACGATCTCGGGAATTAAGAGGAGGTCGTGTCCTAACTTACTGGGCATGATCCT
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
42307540 TTTTT
66 TTTTT
* * *
42307545 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATTGTGTCCTAACTTATTGGGCATGATCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
42307609 CCTTTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (70 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
TTTTT
Found at i:42313283 original size:24 final size:24
Alignment explanation
Indices: 42313256--42313308 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
42313246 CCCAAAGTAT
*
42313256 AGTGGATTGAACCTTAAAGATTAC
1 AGTGGATTAAACCTTAAAGATTAC
*
42313280 AGTGGATTAAACCTTGAAGATTAC
1 AGTGGATTAAACCTTAAAGATTAC
42313304 AGTGG
1 AGTGG
42313309 GGGAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (24 bp):
AGTGGATTAAACCTTAAAGATTAC
Found at i:42313500 original size:62 final size:62
Alignment explanation
Indices: 42313403--42313563 Score: 288
Period size: 62 Copynumber: 2.6 Consensus size: 62
42313393 GAGCCTGAAC
42313403 TTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAGCATTCACACACAT-CTAG
1 TTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAGCATTCACACAC-TGCTAG
* *
42313465 TTAGGAGATTTTGGTTCATTCCGATCATAATATCCTAATCACTAGCATTCACACACTGCTAG
1 TTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAGCATTCACACACTGCTAG
42313527 TTAGGAGATTTTGATTCATTCCGATCATAACATCCTA
1 TTAGGAGATTTTGATTCATTCCGATCATAACATCCTA
42313564 GTCATTAGGC
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
61 1 0.01
62 93 0.99
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (62 bp):
TTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAGCATTCACACACTGCTAG
Found at i:42313827 original size:44 final size:44
Alignment explanation
Indices: 42313688--42314071 Score: 254
Period size: 44 Copynumber: 8.7 Consensus size: 44
42313678 GAAGATGACA
*
42313688 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCAAAT-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AAATC
* * * **
42313733 AAACCTATCTCCCTGAAGTTGCAGTGGAACAGATT--AAAGTTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAAT-C
* * *
42313776 AAGTCTTAT-TCCCCTGAAGTTGTAGTGGGGCAGATTGAATAAATC
1 AA-TCTTATCT-CCCTGAAGTTGCAGTGGAGCAGATTGAAAAAATC
* *
42313821 AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAAAT-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAAATC
* * * *
42313865 AGA-CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAATC
* * ** *
42313909 AAGTCTTATC-CCTCTGAAGTTGCAGTGG-GCCAAACT-AAAGTTATG
1 AA-TCTTATCTCC-CTGAAGTTGCAGTGGAG-CAGATTGAAA-AAATC
* * *
42313954 AATCTTATCTCCCTGAAGCTGCATTGGAGCAGATT-AAAGCCAAT-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA--AAATC
* * * * * ** *
42313998 AACCTTATCTCCCTGGAGTTGCAGCGAAGCAGGTT-AAAGCTACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-AAATC
*
42314042 AATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGC
42314072 GGTGTAACAC
Statistics
Matches: 266, Mismatches: 54, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
41 2 0.01
43 9 0.03
44 179 0.67
45 73 0.27
46 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAATC
Found at i:42313926 original size:133 final size:131
Alignment explanation
Indices: 42313688--42314021 Score: 384
Period size: 133 Copynumber: 2.5 Consensus size: 131
42313678 GAAGATGACA
* * *
42313688 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAATAAACCTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAG-CAAAT-AACTTATCTCCCTGAAGTT
* ** * * * * *
42313753 GCAGTGGAACAGATTAAAGTTACAAGTCTTATTCCCCTGAAGTTGTAGTGGGGCAGATTGAA-TA
64 GCAGTGGAACAGACTAAAGAAACAAGTCTTATTCCCCTGAAGTTGCAGTGGGCCAAACTAAAGT-
42313817 AATC
128 AATC
* * *
42313821 AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAAATAGACTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCAAATA-ACTTATCTCCCTGAAGTTG
** *
42313886 CAGTGGAGTAGACTGAAGAAAGCAAGTCTTA-TCCCTCTGAAGTTGCAGTGGGCCAAACTAAAGT
65 CAGTGGAACAGACTAAAGAAA-CAAGTCTTATTCCC-CTGAAGTTGCAGTGGGCCAAACTAAAGT
* *
42313950 TATG
128 AATC
* * * *
42313954 AATCTTATCTCCCTGAAGCTGCATTGGAGCAGATTAAAGCCAATAACCTTATCTCCCTGGAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCAAATAA-CTTATCTCCCTGAAGTTG
42314019 CAG
65 CAG
42314022 CGAAGCAGGT
Statistics
Matches: 170, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
131 1 0.01
132 42 0.25
133 126 0.74
134 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (131 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCAAATAACTTATCTCCCTGAAGTTGC
AGTGGAACAGACTAAAGAAACAAGTCTTATTCCCCTGAAGTTGCAGTGGGCCAAACTAAAGTAAT
C
Found at i:42315466 original size:40 final size:40
Alignment explanation
Indices: 42315375--42315579 Score: 248
Period size: 38 Copynumber: 5.3 Consensus size: 40
42315365 AGCTCTCGTT
* ** *
42315375 CAAATGCCTTCGGGACATGGCCCGG-TTATAGTAACT-ACA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
42315414 -AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
42315453 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-TCGC-
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
42315491 CAAATTCCTTC-GGACTTAA-CCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
42315529 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
42315568 -AAATGCCTTCGG
1 CAAATGCCTTCGG
42315580 ATCTTAGTCC
Statistics
Matches: 146, Mismatches: 13, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
36 12 0.08
37 12 0.08
38 63 0.43
39 26 0.18
40 33 0.23
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42319905 original size:79 final size:81
Alignment explanation
Indices: 42319804--42319988 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
42319794 GCTACTCGTT
* *
42319804 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
42319867 AGATTTAGTAAC-TCGCA
64 AGATATAGTAACTTAGCA
* ** *
42319884 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCAG
* *
42319948 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
42319964 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42319989 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCAG
ATATAGTAACTTAGCA
Found at i:42319988 original size:40 final size:40
Alignment explanation
Indices: 42319785--42319988 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
42319775 CGGAATTTAA
** *
42319785 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42319825 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42319865 CCAGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42319904 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42319944 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42319984 CCGGA
1 CCGGA
42319989 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42337169 original size:41 final size:41
Alignment explanation
Indices: 42337124--42337239 Score: 205
Period size: 41 Copynumber: 2.8 Consensus size: 41
42337114 TTAATATGAA
42337124 ACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGTTATGGT
1 ACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGTTATGGT
42337165 ACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGTTATGGT
1 ACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGTTATGGT
* * *
42337206 ACATCGGCATTAAGCTTGCTAGGCGTAAAGCCTG
1 ACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTG
42337240 ATGTAATTCA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (41 bp):
ACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGTTATGGT
Found at i:42341965 original size:14 final size:14
Alignment explanation
Indices: 42341946--42341977 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42341936 AGGTCATTTA
42341946 GCCCAACCAAACTG
1 GCCCAACCAAACTG
42341960 GCCCAACCAAACTG
1 GCCCAACCAAACTG
42341974 GCCC
1 GCCC
42341978 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:42347089 original size:14 final size:14
Alignment explanation
Indices: 42347070--42347101 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42347060 AGGTCATTTA
42347070 GCCCAACCAAACTG
1 GCCCAACCAAACTG
42347084 GCCCAACCAAACTG
1 GCCCAACCAAACTG
42347098 GCCC
1 GCCC
42347102 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:42359475 original size:9 final size:9
Alignment explanation
Indices: 42359457--42359493 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42359447 TGTTCATTTG
*
42359457 ACCAAGTTA
1 ACCAAATTA
42359466 ACCAAATTA
1 ACCAAATTA
*
42359475 ACTAAATTA
1 ACCAAATTA
42359484 ACCAAATTA
1 ACCAAATTA
42359493 A
1 A
42359494 AACTACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (9 bp):
ACCAAATTA
Found at i:42366248 original size:18 final size:19
Alignment explanation
Indices: 42366210--42366273 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
42366200 CCAAACTCAC
*
42366210 TTTCTTTTTCAAT-T-TTCT
1 TTTCTTTCTCAATCTCTT-T
42366228 TTTCTTTCTCACAT-TC-TT
1 TTTCTTTCTCA-ATCTCTTT
**
42366246 TTTCGCTCTCAATCTCTTT
1 TTTCTTTCTCAATCTCTTT
42366265 TTTCTTTCT
1 TTTCTTTCT
42366274 TTCGTTCTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 2 0.05
18 22 0.59
19 13 0.35
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTCTTTCTCAATCTCTTT
Found at i:42385539 original size:26 final size:26
Alignment explanation
Indices: 42385510--42385561 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
42385500 TTTCTCATCC
42385510 CAATTTTAACCAAG-TAAAACTTTTGA
1 CAATTTTAACCAAGATAAAA-TTTTGA
* *
42385536 CAATTTTACCCACGATAAAATTTTGA
1 CAATTTTAACCAAGATAAAATTTTGA
42385562 GAAAATTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (26 bp):
CAATTTTAACCAAGATAAAATTTTGA
Found at i:42388531 original size:16 final size:16
Alignment explanation
Indices: 42388512--42388546 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42388502 TCTTCTTTAC
42388512 TTACTCACTTACTTGT
1 TTACTCACTTACTTGT
* *
42388528 TTACTTACTTGCTTGT
1 TTACTCACTTACTTGT
42388544 TTA
1 TTA
42388547 AATAACTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (16 bp):
TTACTCACTTACTTGT
Found at i:42388899 original size:50 final size:50
Alignment explanation
Indices: 42388822--42389091 Score: 373
Period size: 50 Copynumber: 5.4 Consensus size: 50
42388812 TCCCAAATAC
** * * * *
42388822 GGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCTGACAT
1 GGTCTTACATGGGACCTCTTATCTCGGTGCCAATGCCATGTCCCAGACAT
* ** * *
42388872 GATCTTACGGGGGACCTCTCATCTCGGTGCCAATGCCATGCCCCAGACAT
1 GGTCTTACATGGGACCTCTTATCTCGGTGCCAATGCCATGTCCCAGACAT
* * *
42388922 GGTCTTACATGGGACCTCTTATCTCGATGCCAACGCCATGTCCCAGACAC
1 GGTCTTACATGGGACCTCTTATCTCGGTGCCAATGCCATGTCCCAGACAT
*
42388972 GGTCTTACATGGGACCTCTTATCTCGGTGCCAATGCCATATCCCAGACAT
1 GGTCTTACATGGGACCTCTTATCTCGGTGCCAATGCCATGTCCCAGACAT
42389022 GGTCTTACATGGGACCTCTTATCTCGGTGCCAACATG--ATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTTATCTCGGTGCC-A-ATGCCATGTCCCAGACAT
42389072 GGTCTTACATGGGACCTCTT
1 GGTCTTACATGGGACCTCTT
42389092 TACCCAAATG
Statistics
Matches: 196, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
50 192 0.98
51 1 0.01
52 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
GGTCTTACATGGGACCTCTTATCTCGGTGCCAATGCCATGTCCCAGACAT
Found at i:42389462 original size:30 final size:30
Alignment explanation
Indices: 42389428--42389484 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
42389418 CCTCGACTCT
*
42389428 AACTTTGACAAAATTACAATTTTTCCCTTA
1 AACTTTGACAAAATTACAACTTTTCCCTTA
* * *
42389458 AACTTTTACATAATTACACCTTTTCCC
1 AACTTTGACAAAATTACAACTTTTCCC
42389485 CAAAGCTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (30 bp):
AACTTTGACAAAATTACAACTTTTCCCTTA
Found at i:42389547 original size:19 final size:19
Alignment explanation
Indices: 42389523--42389564 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
42389513 TATTCTTATG
*
42389523 TTTTATGACATGCTGAATA
1 TTTTATGACATGCTGAACA
42389542 TTTTATGACATGCTGAACA
1 TTTTATGACATGCTGAACA
42389561 TTTT
1 TTTT
42389565 TCCCTTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (19 bp):
TTTTATGACATGCTGAACA
Found at i:42404353 original size:64 final size:64
Alignment explanation
Indices: 42404252--42404380 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
42404242 TCACAATATG
*
42404252 ATTGAAATAGCTCAATATGTAACTTGAACATTTAAATAGATATTAAAGAAATTATAGTTATCTT
1 ATTGAAATAGCTCAATATGTAACTTGAACATTTAAATAGATATTAAAGAAATTACAGTTATCTT
42404316 ATTGAAATAGCTCAATATGTAACTTGAACATTTAAATAGATATTAAAGAAATTACAGTTATCTT
1 ATTGAAATAGCTCAATATGTAACTTGAACATTTAAATAGATATTAAAGAAATTACAGTTATCTT
42404380 A
1 A
42404381 AAATGTAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (64 bp):
ATTGAAATAGCTCAATATGTAACTTGAACATTTAAATAGATATTAAAGAAATTACAGTTATCTT
Found at i:42406732 original size:19 final size:18
Alignment explanation
Indices: 42406699--42406764 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
42406689 AAAATATAAA
42406699 AAAAATTTAGAAAAAATATT
1 AAAAA-TTA-AAAAAATATT
** *
42406719 AAATTTTAATAAAAATATA
1 AAAAATTAA-AAAAATATT
*
42406738 AAAAATTAAAAAATTATT
1 AAAAATTAAAAAAATATT
42406756 -AAAATTAAA
1 AAAAATTAAA
42406765 TTTTTTATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 9 0.24
18 8 0.21
19 18 0.47
20 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATTAAAAAAATATT
Found at i:42406785 original size:37 final size:36
Alignment explanation
Indices: 42406744--42406827 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
42406734 TATAAAAAAT
* * *
42406744 TAAAAAATTATTAAAAT-TAAATTTTTTATAAAAATCG
1 TAAAAAATTA-AAAAATATAAA-ATTTTATAAAAATCA
42406781 TAAAAAA-TAAAAAATAGTAAAATTTTATAAAAATCA
1 TAAAAAATTAAAAAATA-TAAAATTTTATAAAAATCA
42406817 TAAAAAATTAA
1 TAAAAAATTAA
42406828 TGACCCCTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 5 0.12
36 22 0.54
37 14 0.34
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (36 bp):
TAAAAAATTAAAAAATATAAAATTTTATAAAAATCA
Found at i:42406792 original size:44 final size:42
Alignment explanation
Indices: 42406716--42406804 Score: 117
Period size: 44 Copynumber: 2.1 Consensus size: 42
42406706 TAGAAAAAAT
*
42406716 ATTAAATTTTAATAAAAATATAAAAAATTAAAAAATTATTAAA
1 ATTAAATTTTAATAAAAATATAAAAAATTAAAAAA-TAGTAAA
* *
42406759 ATTAAATTTTTTATAAAAATCGTAAAAAA-TAAAAAATAGTAAA
1 ATTAAA-TTTTAATAAAAAT-ATAAAAAATTAAAAAATAGTAAA
42406802 ATT
1 ATT
42406805 TTATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
43 15 0.37
44 19 0.46
45 7 0.17
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (42 bp):
ATTAAATTTTAATAAAAATATAAAAAATTAAAAAATAGTAAA
Found at i:42406793 original size:43 final size:43
Alignment explanation
Indices: 42406716--42406804 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
42406706 TAGAAAAAAT
* *
42406716 ATTAAATTTTAATAAAAATATAAAAAATTAAAAAATTATTAAA
1 ATTAAATTTTAATAAAAATATAAAAAATTAAAAAAATAGTAAA
* *
42406759 ATTAAATTTTTTATAAAAATCGTAAAAAA-T-AAAAAATAGTAAA
1 ATTAAA-TTTTAATAAAAAT-ATAAAAAATTAAAAAAATAGTAAA
42406802 ATT
1 ATT
42406805 TTATAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 20 0.50
44 13 0.32
45 7 0.17
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (43 bp):
ATTAAATTTTAATAAAAATATAAAAAATTAAAAAAATAGTAAA
Found at i:42407120 original size:9 final size:9
Alignment explanation
Indices: 42407030--42407130 Score: 57
Period size: 9 Copynumber: 10.8 Consensus size: 9
42407020 ACTTTATAAA
42407030 ATTTTATAAT
1 ATTTT-TAAT
*
42407040 -TTTTTTAT
1 ATTTTTAAT
*
42407048 ATTTCTATAT
1 ATTTTTA-AT
42407058 ATTTTATAA-
1 ATTTT-TAAT
*
42407067 ATTTTACAAT
1 ATTTT-TAAT
*
42407077 TTTTTATATAT
1 ATTTT-TA-AT
*
42407088 ATTTTTACT
1 ATTTTTAAT
42407097 ATTTTTAAT
1 ATTTTTAAT
42407106 AAATTTTTAAT
1 --ATTTTTAAT
42407117 A-TTTTAAT
1 ATTTTTAAT
42407125 -TTTTTA
1 ATTTTTA
42407131 TTAAAATTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
8 15 0.21
9 26 0.36
10 15 0.21
11 17 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:42407121 original size:19 final size:19
Alignment explanation
Indices: 42407056--42407124 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
42407046 ATATTTCTAT
*
42407056 ATATTTT-ATAAATTTTACA
1 ATATTTTAATAAATTTT-TA
* *
42407075 ATTTTTTATATATATTTTTA
1 ATATTTTA-ATAAATTTTTA
*
42407095 CTATTTTTAATAAATTTTTA
1 ATA-TTTTAATAAATTTTTA
42407115 ATATTTTAAT
1 ATATTTTAAT
42407125 TTTTTATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 13 0.32
20 14 0.35
21 13 0.32
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTAATAAATTTTTA
Found at i:42407398 original size:85 final size:84
Alignment explanation
Indices: 42407221--42407417 Score: 225
Period size: 86 Copynumber: 2.3 Consensus size: 84
42407211 TTAATTGCTC
* * * * *
42407221 TTTTTTTTTAAGTTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTATAA
1 TTTTTTTTTAAGTTTGAGGGT-TTTTTGATACATTTTGAAAGCTCAAGTACCCAAATGAGTACAA
* * **
42407286 AAAAAAGTAGGTGCTTAATT
65 AAAAAAGAACGTAATTAATT
* *
42407306 GTTTTTTTTAAGGTTTGAGGGCTTTTTTGATACATTTTGAAAGCTCAAGTACCCAAATGAGTGCA
1 TTTTTTTTTAA-GTTTGAGGG-TTTTTTGATACATTTTGAAAGCTCAAGTACCCAAATGAGTACA
* *
42407371 AAAAAAA-AACTTAATTAGTGT
64 AAAAAAAGAACGTAATTAAT-T
*
42407392 TTTTTTTTTAAGTTTAAGGGTTTTTT
1 TTTTTTTTTAAGTTTGAGGGTTTTTT
42407418 ACACCCTTAA
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
84 6 0.06
85 24 0.26
86 63 0.67
87 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (84 bp):
TTTTTTTTTAAGTTTGAGGGTTTTTTGATACATTTTGAAAGCTCAAGTACCCAAATGAGTACAAA
AAAAAGAACGTAATTAATT
Found at i:42407992 original size:12 final size:12
Alignment explanation
Indices: 42407975--42407999 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42407965 AACATTTAAT
42407975 ACACATATCAAA
1 ACACATATCAAA
42407987 ACACATATCAAA
1 ACACATATCAAA
42407999 A
1 A
42408000 ATCAATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ACACATATCAAA
Found at i:42417416 original size:50 final size:49
Alignment explanation
Indices: 42417362--42417942 Score: 687
Period size: 50 Copynumber: 11.8 Consensus size: 49
42417352 GGCAATGAGT
* *
42417362 GTGCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCACAGACTGATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* *
42417412 GTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGATAGAGGGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGA--GGA
* * *
42417464 GT-C-AGTGTAAGACCATGTTTGGGACATGGCATCGGCTC-GA-GATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
*
42417509 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
* ** *
42417559 GTGCTAGTGTAAGACCATGTCTGGGACATGGCCTCGGCATGGATAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
* * *** *
42417609 GAG-TCAGTGTAAGACCATGTTTGGGACATGGCATCGG-TTTGA-GATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
* * *
42417656 GTGCCATTGTAAGACCATGTCTGGGACATGGCATCGACACAGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
*
42417706 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGG
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* * * * * *
42417756 GAGTTAGTGTAAAACCATGTCTGGGACATGGCATCAGCTC-GA-GATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
*
42417803 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
* * *
42417853 GTGCTAGTGTAAGACCATGTCTAGGACATGGCATCTGCACGGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
*
42417903 GAG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
42417943 CTATATGCGA
Statistics
Matches: 458, Mismatches: 55, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
45 4 0.01
46 1 0.00
47 107 0.23
48 6 0.01
49 10 0.02
50 325 0.71
51 1 0.00
52 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (49 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
Found at i:42417634 original size:147 final size:147
Alignment explanation
Indices: 42417362--42417940 Score: 915
Period size: 147 Copynumber: 3.9 Consensus size: 147
42417352 GGCAATGAGT
* * * * *
42417362 GTGCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCACAGACTGATGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGAGTGCTAGTGTAAGAC
* * * *
42417427 CATGTTTGGGACATGGCATCGGCACAGATAGAGGGGAGTCAGTGTAAGACCATGTTTGGGACATG
66 CATGTCTGGGACATGGCATCGGCACAGACAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
42417492 GCATCGGCTCGAGATGA
131 GCATCGGCTCGAGATGA
*
42417509 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGAGTGCTAGTGTAAGAC
* ** * *
42417574 CATGTCTGGGACATGGCCTCGGCATGGATAGAGGAGAGTCAGTGTAAGACCATGTTTGGGACATG
66 CATGTCTGGGACATGGCATCGGCACAGACAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
* *
42417639 GCATCGGTTTGAGATGA
131 GCATCGGCTCGAGATGA
* *
42417656 GTGCCATTGTAAGACCATGTCTGGGACATGGCATCGACACAGACAGAGGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGAGTGCTAGTGTAAGAC
* * *
42417721 CATGTCTGGGACATGGCATCGGCACAGACAGAGGGGAGTTAGTGTAAAACCATGTCTGGGACATG
66 CATGTCTGGGACATGGCATCGGCACAGACAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
*
42417786 GCATCAGCTCGAGATGA
131 GCATCGGCTCGAGATGA
*
42417803 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGAGTGCTAGTGTAAGAC
* * *
42417868 CATGTCTAGGACATGGCATCTGCACGGACAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
66 CATGTCTGGGACATGGCATCGGCACAGACAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
42417933 GCATCGGC
131 GCATCGGC
42417941 ACCTATATGC
Statistics
Matches: 397, Mismatches: 35, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
147 397 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (147 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGACCGAGGAGTGCTAGTGTAAGAC
CATGTCTGGGACATGGCATCGGCACAGACAGAGGAGAGTCAGTGTAAGACCATGTCTGGGACATG
GCATCGGCTCGAGATGA
Found at i:42423192 original size:35 final size:35
Alignment explanation
Indices: 42423087--42423249 Score: 168
Period size: 35 Copynumber: 4.6 Consensus size: 35
42423077 GCACATCGTC
* *
42423087 AGTCCAACC-ATAACACGCCAAATGCTCATACGAGCC
1 AGTCCAACCGA-AACACGCC-AATGCTCATAAGAGCT
* * * * *
42423123 AATCGC-TCCAAAACACACCAAATGCTCACAAGAGCT
1 AGTC-CAACCGAAACACGCC-AATGCTCATAAGAGCT
*
42423159 AGTCCAACCGAAACACGCCAATACTCATAAGAGCT
1 AGTCCAACCGAAACACGCCAATGCTCATAAGAGCT
* * *
42423194 AGTACAACTGAAACACGCCAGTGCTCATAAGAGCT
1 AGTCCAACCGAAACACGCCAATGCTCATAAGAGCT
*
42423229 AGTCCAACCAAAACACGCCAA
1 AGTCCAACCGAAACACGCCAA
42423250 ACAGAGAGTA
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
35 63 0.61
36 39 0.38
37 2 0.02
ACGTcount: A:0.40, C:0.33, G:0.14, T:0.13
Consensus pattern (35 bp):
AGTCCAACCGAAACACGCCAATGCTCATAAGAGCT
Found at i:42426222 original size:22 final size:24
Alignment explanation
Indices: 42426180--42426223 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
42426170 TAACTAAGCT
42426180 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
42426204 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
42426224 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:42426704 original size:5 final size:5
Alignment explanation
Indices: 42426694--42426797 Score: 135
Period size: 5 Copynumber: 21.2 Consensus size: 5
42426684 CTATTTAGTT
42426694 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
42426744 ATATA AT-TA ATATA TTATATT ATATT ATATT ATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA ATATA ATATA
42426792 ATATA A
1 ATATA A
42426798 AACATAAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
3 1 0.01
4 12 0.13
5 74 0.81
7 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:42432764 original size:27 final size:28
Alignment explanation
Indices: 42432734--42432792 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
42432724 TCACACCTGG
42432734 AATAATAT-AAATCCT-CCATAACACACA
1 AATAATATCAAATCCTCCCA-AACACACA
* *
42432761 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACA
42432788 AATAA
1 AATAA
42432793 GGCATTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACA
Found at i:42433753 original size:22 final size:22
Alignment explanation
Indices: 42433720--42433766 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
42433710 TCTTCCCCTG
42433720 TTTTCGTCTCTT-TCTCTGTTTC
1 TTTTCGTCTCTTCT-TCTGTTTC
*
42433742 TTTTCTGT-TCTTCTTTTGTTTC
1 TTTTC-GTCTCTTCTTCTGTTTC
42433764 TTT
1 TTT
42433767 ATCTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTCGTCTCTTCTTCTGTTTC
Found at i:42433979 original size:5 final size:5
Alignment explanation
Indices: 42433960--42434035 Score: 88
Period size: 5 Copynumber: 15.4 Consensus size: 5
42433950 TTTACTTATT
42433960 TAATA T-ATAA TAATA TAATA TAATA TAATA TAATA TAAT- TAATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
*
42434009 TATTATA TTATA TAATA -AA-A TAATA TA
1 TA--ATA TAATA TAATA TAATA TAATA TA
42434036 TGTAAAACAT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
3 1 0.02
4 10 0.16
5 45 0.73
6 2 0.03
7 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:42434010 original size:34 final size:30
Alignment explanation
Indices: 42433968--42434035 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
42433958 TTTAATATAT
42433968 AATAATATAATATA--ATATAATATAATATA
1 AATAATATAATATATTATATAATATAATA-A
* *
42433997 ATTAATATAATATATTATATTATATAATAA
1 AATAATATAATATATTATATAATATAATAA
42434027 AATAATATA
1 AATAATATA
42434036 TGTAAAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 13 0.38
30 9 0.26
31 12 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AATAATATAATATATTATATAATATAATAA
Found at i:42434032 original size:39 final size:39
Alignment explanation
Indices: 42433959--42434035 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
42433949 ATTTACTTAT
42433959 TTAATATATAATAATATAATATAATATAATATAATATAA
1 TTAATATATAATAATATAATATAATATAATATAATATAA
* *
42433998 TTAATATAATATATTATATTATATAATA-AA-ATAATATA
1 TTAATAT-ATA-ATAATATAATATAATATAATATAATATA
42434036 TGTAAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 15 0.44
40 5 0.15
41 14 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (39 bp):
TTAATATATAATAATATAATATAATATAATATAATATAA
Found at i:42436332 original size:13 final size:14
Alignment explanation
Indices: 42436309--42436340 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
42436299 TTTAGGTTTT
42436309 AGGTTTAGGGTTCA
1 AGGTTTAGGGTTCA
42436323 AGGTTT-GGGTTCA
1 AGGTTTAGGGTTCA
42436336 AGGTT
1 AGGTT
42436341 AAAGGGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.19, C:0.06, G:0.38, T:0.38
Consensus pattern (14 bp):
AGGTTTAGGGTTCA
Found at i:42436348 original size:21 final size:20
Alignment explanation
Indices: 42436324--42436373 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
42436314 TAGGGTTCAA
42436324 GGTTTGGGTTCAAGGTTAAAG
1 GGTTTGGG-TCAAGGTTAAAG
* *
42436345 GGTTTGGAGTCATGGTTAATG
1 GGTTTGG-GTCAAGGTTAAAG
*
42436366 AGTTTGGG
1 GGTTTGGG
42436374 GCTTGGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.40, T:0.36
Consensus pattern (20 bp):
GGTTTGGGTCAAGGTTAAAG
Found at i:42447113 original size:18 final size:18
Alignment explanation
Indices: 42447092--42447128 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42447082 TGTACATCTT
42447092 TCTGAATTCTCCCCCGAA
1 TCTGAATTCTCCCCCGAA
42447110 TCTGAATTCTCCCCCGAA
1 TCTGAATTCTCCCCCGAA
42447128 T
1 T
42447129 TTTACTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.38, G:0.11, T:0.30
Consensus pattern (18 bp):
TCTGAATTCTCCCCCGAA
Found at i:42448364 original size:30 final size:30
Alignment explanation
Indices: 42448328--42448385 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42448318 CTGGGCATTT
* *
42448328 CCACACGGGCTGGCCACAAGCCCGTGTGAG
1 CCACACGAGCTGGCCACAAGCCCATGTGAG
* *
42448358 CCACACGAGTTGGCCACATGCCCATGTG
1 CCACACGAGCTGGCCACAAGCCCATGTG
42448386 CCAACCCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACAAGCCCATGTGAG
Found at i:42453247 original size:10 final size:10
Alignment explanation
Indices: 42453209--42453255 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
42453199 TTCCTGTCTA
*
42453209 TTATTATTAG
1 TTATTATTAT
42453219 TTA-TATTAT
1 TTATTATTAT
*
42453228 TT-TTCTTTAT
1 TTATT-ATTAT
42453238 TTATTATTAT
1 TTATTATTAT
42453248 TTATTATT
1 TTATTATT
42453256 GTTATTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 8 0.26
10 21 0.68
11 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
TTATTATTAT
Found at i:42455025 original size:6 final size:6
Alignment explanation
Indices: 42455004--42455052 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
42454994 AGTCTATTTG
* *
42455004 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
42455050 TTT
1 TTT
42455053 CTTAGACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:42457751 original size:13 final size:14
Alignment explanation
Indices: 42457728--42457757 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
42457718 TATTGCATTC
42457728 TTAGTTAAATTAGA
1 TTAGTTAAATTAGA
42457742 TTAG-TAAATTAGA
1 TTAGTTAAATTAGA
42457755 TTA
1 TTA
42457758 AAAACAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TTAGTTAAATTAGA
Found at i:42462026 original size:15 final size:16
Alignment explanation
Indices: 42462006--42462039 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42461996 GTTAATAATT
*
42462006 AATTAA-CTAGATGCA
1 AATTAACCTAAATGCA
42462021 AATTAACCTAAATGCA
1 AATTAACCTAAATGCA
42462037 AAT
1 AAT
42462040 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGCA
Found at i:42473394 original size:21 final size:22
Alignment explanation
Indices: 42473350--42473394 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
42473340 GTCAAAAATA
*
42473350 ATAAAAATAATCAAAATTTGAT
1 ATAAAAATAATCAAAATTTCAT
* *
42473372 ATAAAATTAATTAAAA-TTCAT
1 ATAAAAATAATCAAAATTTCAT
42473393 AT
1 AT
42473395 TTTTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAAATAATCAAAATTTCAT
Found at i:42476481 original size:21 final size:20
Alignment explanation
Indices: 42476452--42476493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
42476442 GTGTCTTGAT
42476452 GGTGTGGTGCGA-TAGGCAAG
1 GGTGTGGTGCGAGTA-GCAAG
42476472 GGTGTTGGTGCGAGTAGCAAG
1 GGTG-TGGTGCGAGTAGCAAG
42476493 G
1 G
42476494 CACAGTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.19, C:0.10, G:0.50, T:0.21
Consensus pattern (20 bp):
GGTGTGGTGCGAGTAGCAAG
Found at i:42476918 original size:15 final size:17
Alignment explanation
Indices: 42476883--42476928 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
42476873 TGTTATTAAT
*
42476883 TTATTAAAAATAAATAC
1 TTATTAAATATAAATAC
42476900 TTATTAAATA-AAATA-
1 TTATTAAATATAAATAC
* *
42476915 TTATCAAATTTAAA
1 TTATTAAATATAAA
42476929 CTAATCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.32
16 8 0.32
17 9 0.36
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TTATTAAATATAAATAC
Found at i:42483628 original size:21 final size:22
Alignment explanation
Indices: 42483599--42483644 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
42483589 TTATTTAACA
* *
42483599 TAAATTAAATTGGATTA-AAAT
1 TAAAATAAATTAGATTATAAAT
*
42483620 TAAAATAAATTATATTATAAAT
1 TAAAATAAATTAGATTATAAAT
42483642 TAA
1 TAA
42483645 TACACATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (22 bp):
TAAAATAAATTAGATTATAAAT
Found at i:42488983 original size:22 final size:20
Alignment explanation
Indices: 42488953--42488992 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42488943 AATGATATCA
42488953 CGACCTTGGAAGCTCAATGTTG
1 CGACCTTGG--GCTCAATGTTG
*
42488975 CGACTTTGGGCTCAATGT
1 CGACCTTGGGCTCAATGT
42488993 CGTGACATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.30
Consensus pattern (20 bp):
CGACCTTGGGCTCAATGTTG
Found at i:42498403 original size:27 final size:27
Alignment explanation
Indices: 42498373--42498445 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 27
42498363 TGTCTTGAAT
42498373 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
42498400 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
*
42498432 TTGTTGGATATTGA
1 TTGTTAGATATTGA
42498446 AATGATTGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 14 0.35
32 26 0.65
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:42498425 original size:32 final size:32
Alignment explanation
Indices: 42498386--42498446 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
42498376 TTAGATATTG
42498386 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
*
42498418 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
42498447 ATGATTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:42499849 original size:14 final size:15
Alignment explanation
Indices: 42499811--42499849 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
42499801 AAACACTAGA
42499811 AAAT-ATTTT-CAGT
1 AAATCATTTTCCAGT
42499824 AAATCATTTTCCAG-
1 AAATCATTTTCCAGT
42499838 AAATCATTTTCC
1 AAATCATTTTCC
42499850 GGGAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (15 bp):
AAATCATTTTCCAGT
Found at i:42499860 original size:14 final size:14
Alignment explanation
Indices: 42499811--42499861 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
42499801 AAACACTAGA
* *
42499811 AAAT-ATTTTCAGT
1 AAATCATTTTCCGG
*
42499824 AAATCATTTTCCAG
1 AAATCATTTTCCGG
42499838 AAATCATTTTCCGGG
1 AAATCATTTTCC-GG
42499853 AAAT-ATTTT
1 AAATCATTTT
42499862 ACTGACAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 4 0.12
14 23 0.72
15 5 0.16
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCGG
Found at i:42506333 original size:25 final size:26
Alignment explanation
Indices: 42506302--42506352 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42506292 CTTGTATCAT
*
42506302 TCACATTTGCA-TATCATATCCTGTA
1 TCACATTTGCATTATCATACCCTGTA
*
42506327 TCACATTTGCATTTTCATACCCTGTA
1 TCACATTTGCATTATCATACCCTGTA
42506353 ATTATTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (26 bp):
TCACATTTGCATTATCATACCCTGTA
Found at i:42520895 original size:35 final size:35
Alignment explanation
Indices: 42520846--42520916 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 35
42520836 TGACATCAGA
42520846 TTTAGCTCTGCCAATTATCCTTTT-TAGATATTTTT
1 TTTAGCTCTGCCAATTAT-CTTTTGTAGATATTTTT
*
42520881 TTTAGCTCTTCCAATTATCTTTTGTAGATATTTTT
1 TTTAGCTCTGCCAATTATCTTTTGTAGATATTTTT
42520916 T
1 T
42520917 GTTCTACTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 5 0.15
35 29 0.85
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.56
Consensus pattern (35 bp):
TTTAGCTCTGCCAATTATCTTTTGTAGATATTTTT
Found at i:42524386 original size:5 final size:5
Alignment explanation
Indices: 42524376--42524402 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42524366 CCTCACGGAC
42524376 ATTGG ATTGG ATTGG ATTGG ATTGG AT
1 ATTGG ATTGG ATTGG ATTGG ATTGG AT
42524403 CAGATTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (5 bp):
ATTGG
Found at i:42530685 original size:27 final size:27
Alignment explanation
Indices: 42530647--42530701 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
42530637 AGACTCAATT
42530647 TGCACATTTTATTGAATTTAATTAAAC
1 TGCACATTTTATTGAATTTAATTAAAC
42530674 TGCACATTTTATTGAATTTAATTAAAC
1 TGCACATTTTATTGAATTTAATTAAAC
42530701 T
1 T
42530702 TACTAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (27 bp):
TGCACATTTTATTGAATTTAATTAAAC
Found at i:42533822 original size:24 final size:24
Alignment explanation
Indices: 42533790--42533838 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42533780 ACAGTGATGA
42533790 ACTATGGTATCTGATTTTGAATTG
1 ACTATGGTATCTGATTTTGAATTG
42533814 ACTATGGTATCTGATTTTGAATTG
1 ACTATGGTATCTGATTTTGAATTG
42533838 A
1 A
42533839 TCACAGACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (24 bp):
ACTATGGTATCTGATTTTGAATTG
Found at i:42534148 original size:15 final size:15
Alignment explanation
Indices: 42534130--42534225 Score: 74
Period size: 15 Copynumber: 6.3 Consensus size: 15
42534120 TTTTTTGTCA
42534130 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
* *
42534145 TTTTTTCATCTAGATT
1 TTTTTT-ATTTTGATT
* *
42534161 TTTATT-TTTT-CTT
1 TTTTTTATTTTGATT
*
42534174 CTTTCTTT-TTCTCTCA-T
1 -TTT-TTTATT-T-TGATT
42534191 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
42534206 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
42534221 TTTTT
1 TTTTT
42534226 GTTTTTTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
13 2 0.03
14 7 0.11
15 35 0.55
16 18 0.28
17 2 0.03
ACGTcount: A:0.11, C:0.08, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTTTATTTTGATT
Found at i:42534206 original size:14 final size:14
Alignment explanation
Indices: 42534189--42534230 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
42534179 TTTTTCTCTC
42534189 ATTTTTTTATTTTG
1 ATTTTTTTATTTTG
42534203 ATTTTTTTTATTTTG
1 A-TTTTTTTATTTTG
*
42534218 ATTTTTTTGTTTT
1 ATTTTTTTATTTT
42534231 TTTTAAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (14 bp):
ATTTTTTTATTTTG
Found at i:42534215 original size:23 final size:22
Alignment explanation
Indices: 42534189--42534235 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
42534179 TTTTTCTCTC
42534189 ATTTT-TTTATTTTGATTTTTTTT
1 ATTTTATTT-TTTTG-TTTTTTTT
42534212 ATTTTGATTTTTTTGTTTTTTTT
1 ATTTT-ATTTTTTTGTTTTTTTT
42534235 A
1 A
42534236 AAGGATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 14 0.64
24 5 0.23
25 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (22 bp):
ATTTTATTTTTTTGTTTTTTTT
Found at i:42539017 original size:28 final size:27
Alignment explanation
Indices: 42538986--42539078 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 27
42538976 AATATATGTA
*
42538986 AATTAAAAAGTTAAAATAAATTTGAATG
1 AATTAAAATGTTAAAAT-AATTTGAATG
* * *
42539014 AATTAACAATGTTGAAATAAGTTGAAATA
1 AATTAA-AATGTTAAAATAATTTG-AATG
*
42539043 AATTAAAGATGTTAAAAT-ATTTGAAAG
1 AATTAAA-ATGTTAAAATAATTTGAATG
*
42539070 AAATAAAAT
1 AATTAAAAT
42539079 ATCTAATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
26 2 0.04
27 8 0.15
28 16 0.30
29 27 0.51
ACGTcount: A:0.56, C:0.01, G:0.12, T:0.31
Consensus pattern (27 bp):
AATTAAAATGTTAAAATAATTTGAATG
Found at i:42539257 original size:31 final size:31
Alignment explanation
Indices: 42539219--42539318 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 31
42539209 GGCCCATTTT
42539219 TATTTTAAAATTTTTAAAAAATTAAAAAAAG
1 TATTTTAAAATTTTTAAAAAATTAAAAAAAG
42539250 TATTTTAAAAATATTTTAAAATTAAAAAATTAAAAAAAG
1 TATTTT--AAA-A-TTT----TTAAAAAATTAAAAAAAG
*
42539289 TATTTTTAAAATTTTT-TAAAATTAAAAAAA
1 TA-TTTTAAAATTTTTAAAAAATTAAAAAAA
42539319 ATTAAAAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
31 19 0.32
32 2 0.03
33 3 0.05
34 1 0.02
35 3 0.05
36 3 0.05
37 1 0.02
38 3 0.05
39 20 0.34
40 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
TATTTTAAAATTTTTAAAAAATTAAAAAAAG
Found at i:42539318 original size:41 final size:40
Alignment explanation
Indices: 42539234--42539439 Score: 360
Period size: 40 Copynumber: 5.2 Consensus size: 40
42539224 TAAAATTTTT
*
42539234 AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-
1 AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATTA
*
42539273 AAAAAATTAAAAAAAGTATTTTTAAAATTTTTTAAAATTAA
1 AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATT-A
*
42539314 AAAAAATTAAAAAAAGTATTTTTAAAATTTTTTAAAATTA
1 AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATTA
42539354 AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATTA
1 AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATTA
*
42539394 AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATTA
42539434 AAAAAA
1 AAAAAA
42539440 ATATATTTAT
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 37 0.23
40 85 0.53
41 39 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (40 bp):
AAAAAATTAAAAAAAGTATTTTAAAAATTTTTTAAAATTA
Found at i:42539886 original size:22 final size:22
Alignment explanation
Indices: 42539857--42539904 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42539847 ACAATAATAC
**
42539857 ATAT-AAAATAAAGTAATGCAT
1 ATATAAAAATAAACCAATGCAT
*
42539878 ATATAAAAATAAACCAATGTAT
1 ATATAAAAATAAACCAATGCAT
42539900 ATATA
1 ATATA
42539905 TGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (22 bp):
ATATAAAAATAAACCAATGCAT
Found at i:42549169 original size:13 final size:13
Alignment explanation
Indices: 42549151--42549177 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42549141 AGCTTTTGGT
42549151 TTTGTTATGAAGC
1 TTTGTTATGAAGC
42549164 TTTGTTATGAAGC
1 TTTGTTATGAAGC
42549177 T
1 T
42549178 GAAATATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TTTGTTATGAAGC
Found at i:42552523 original size:48 final size:48
Alignment explanation
Indices: 42552452--42552547 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
42552442 CGAAGATAAC
*
42552452 CACAAAATGCATTAGGATCTTGAATGTAAGAAGAAAAGCTTGGAAAGA
1 CACAAAAGGCATTAGGATCTTGAATGTAAGAAGAAAAGCTTGGAAAGA
42552500 CACAAAAGGCATTAGGATCTTGAATGTAAGAAGAAAAGCTTGGAAAGA
1 CACAAAAGGCATTAGGATCTTGAATGTAAGAAGAAAAGCTTGGAAAGA
42552548 AACTTTGTCC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (48 bp):
CACAAAAGGCATTAGGATCTTGAATGTAAGAAGAAAAGCTTGGAAAGA
Found at i:42555900 original size:20 final size:20
Alignment explanation
Indices: 42555875--42555920 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
42555865 TGAAAAATGA
42555875 TTTCTGGAAAATGAATTACT
1 TTTCTGGAAAATGAATTACT
*
42555895 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATGAATTACT
42555914 TTTCTGG
1 TTTCTGG
42555921 TGTTTGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGAATTACT
Found at i:42556026 original size:20 final size:20
Alignment explanation
Indices: 42556001--42556040 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42555991 TTGTTTTTAC
42556001 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
42556021 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
42556041 TTTTAATTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:42559188 original size:21 final size:19
Alignment explanation
Indices: 42559162--42559202 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
42559152 TATGTCAAAA
*
42559162 TAAATTTTAAAATTAAATATT
1 TAAATTGTAAAA--AAATATT
42559183 TAAATTGTAAAAAAATATT
1 TAAATTGTAAAAAAATATT
42559202 T
1 T
42559203 TATTGTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TAAATTGTAAAAAAATATT
Found at i:42561678 original size:16 final size:18
Alignment explanation
Indices: 42561652--42561685 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42561642 ATTAATTAAC
42561652 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
42561669 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
42561686 CTAATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:42564218 original size:16 final size:17
Alignment explanation
Indices: 42564197--42564254 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
42564187 TAATCACTTT
*
42564197 AATATTAAATTAATA-A
1 AATATTAAATTAAGATA
42564213 AATATT--ATTAAGATA
1 AATATTAAATTAAGATA
* *
42564228 AATATTAAAATAA-ATTT
1 AATATTAAATTAAGA-TA
42564245 AATATTAAAT
1 AATATTAAAT
42564255 CTATTAAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 7 0.21
17 14 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATTAAATTAAGATA
Found at i:42566709 original size:60 final size:60
Alignment explanation
Indices: 42566616--42566732 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
42566606 GAATCTGTTG
* *
42566616 GTAAAAAATAAAAAGTAAAAATCACTAGCAACTATTTTCTACTTTATTTTAATTTTTGAT
1 GTAAAAAATAAAAAATAAAAATCACTAGCAACTATTTTCAACTTTATTTTAATTTTTGAT
* * *
42566676 GTAAAAAATAAAAAATAAAAATTACTAGCAACTATTTTCAATTTTATTTTTATTTTT
1 GTAAAAAATAAAAAATAAAAATCACTAGCAACTATTTTCAACTTTATTTTAATTTTT
42566733 ATTTTTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (60 bp):
GTAAAAAATAAAAAATAAAAATCACTAGCAACTATTTTCAACTTTATTTTAATTTTTGAT
Found at i:42576427 original size:124 final size:125
Alignment explanation
Indices: 42576102--42576452 Score: 614
Period size: 125 Copynumber: 2.8 Consensus size: 125
42576092 TTATTTCGAG
* *
42576102 TTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
42576167 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGTTCATGTAAGAAATAATTTTTTT
66 AAATCGCGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT
* *
42576227 TTGACGTTTCTGAGAAAATACTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
42576292 AAATCGTGCCCTCGTGGATGCGATTTTGCTACAGTTGGTCATGTAAGAAATAA-TTTTTT
66 AAATCGCGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT
42576351 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
42576416 AAATCGCGCCCTCGTGGATGCTATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGATGCGATTTTGCTACAGTAG
42576453 CAAGTTTGGG
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
124 103 0.48
125 110 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT
Found at i:42577183 original size:10 final size:10
Alignment explanation
Indices: 42577168--42577192 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42577158 TAAATCTAAC
42577168 ATTATGTAAA
1 ATTATGTAAA
42577178 ATTATGTAAA
1 ATTATGTAAA
42577188 ATTAT
1 ATTAT
42577193 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:42577237 original size:55 final size:55
Alignment explanation
Indices: 42577176--42577301 Score: 252
Period size: 55 Copynumber: 2.3 Consensus size: 55
42577166 ACATTATGTA
42577176 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
42577231 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
42577286 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
42577302 GGTTAGGGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 71 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:42577390 original size:30 final size:29
Alignment explanation
Indices: 42577327--42577554 Score: 302
Period size: 30 Copynumber: 7.7 Consensus size: 29
42577317 TAGGGTTAGT
*
42577327 GTTTTTAATTAAATTAGGTTAGGG-TTAGG
1 GTTTTTAATTAAATTAGGTTAGGGAGT-GG
42577356 GTTTTTAATTAAATTAGGTTAGGGCAGTGG
1 GTTTTTAATTAAATTAGGTTAGGG-AGTGG
**
42577386 GTTTTTAATTAAATTAGGTTAGGGTTTAGG
1 GTTTTTAATTAAATTAGGTTAGGGAGT-GG
42577416 GTTTTTAATTAAATTAGGTTAGGGTTAGT--
1 GTTTTTAATTAAATTAGGTTAGGG--AGTGG
*
42577445 GTTTTTAATTAAATTAGGTTAGAGCAGTGG
1 GTTTTTAATTAAATTAGGTTAG-GGAGTGG
42577475 GTTTTTAATTAAATTAGGTTAGGGCAGTGG
1 GTTTTTAATTAAATTAGGTTAGGG-AGTGG
*
42577505 GTTTTTAATTAAATTAGGTTAGGG-TTAGG
1 GTTTTTAATTAAATTAGGTTAGGGAGT-GG
42577534 GTTTTTAATTAAATTATGGTT
1 GTTTTTAATTAAATTA-GGTT
42577555 TTTATTACAT
Statistics
Matches: 180, Mismatches: 8, Indels: 21
0.86 0.04 0.10
Matches are distributed among these distances:
28 4 0.02
29 66 0.37
30 108 0.60
31 1 0.01
32 1 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (29 bp):
GTTTTTAATTAAATTAGGTTAGGGAGTGG
Found at i:42577390 original size:59 final size:59
Alignment explanation
Indices: 42577327--42577554 Score: 365
Period size: 59 Copynumber: 3.8 Consensus size: 59
42577317 TAGGGTTAGT
42577327 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGG
1 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGG
*
42577386 GTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGT--
1 GTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGG-CAGTGG
42577445 GTTTTTAATTAAATTAGGTTAGAGCAG-T-GGGTTTTTAATTAAATTAGGTTAGGGCAGTGG
1 GTTTTTAATTAAATTAGGTTAG-G--GTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGG
42577505 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTATGGTT
1 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GGTT
42577555 TTTATTACAT
Statistics
Matches: 157, Mismatches: 2, Indels: 19
0.88 0.01 0.11
Matches are distributed among these distances:
57 1 0.01
58 4 0.03
59 91 0.58
60 57 0.36
61 3 0.02
62 1 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (59 bp):
GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGG
Found at i:42577433 original size:89 final size:88
Alignment explanation
Indices: 42577314--42577554 Score: 403
Period size: 89 Copynumber: 2.7 Consensus size: 88
42577304 TTAGGGTTAG
* *
42577314 GGTTAGGGTTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGA
42577379 GCAGTGGGTTTTTAATTAAATTA
66 GCAGTGGGTTTTTAATTAAATTA
*
42577402 GGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGTGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
42577467 AGCAGTGGGTTTTTAATTAAATTA
65 AGCAGTGGGTTTTTAATTAAATTA
*
42577491 GGTTAGGG-CAGTGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTATGGTT
1 GGTTAGGGTTA--GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GGTT
42577555 TTTATTACAT
Statistics
Matches: 144, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
87 1 0.01
88 8 0.06
89 131 0.91
90 4 0.03
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.44
Consensus pattern (88 bp):
GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGA
GCAGTGGGTTTTTAATTAAATTA
Found at i:42577739 original size:71 final size:70
Alignment explanation
Indices: 42577557--42577738 Score: 296
Period size: 68 Copynumber: 2.6 Consensus size: 70
42577547 TTATGGTTTT
* *
42577557 TATTACATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTAAATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAA-TT
42577622 CTATGCC
64 CTATGCC
*
42577629 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCG-AAAAA-TCT
1 TATTAAATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTCT
*
42577692 ATGCG
66 ATGCC
42577697 TATTAAATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTAAATCAAATAAACTTCTATTTTATTACATCAAATAATA
42577739 AATTTAAATA
Statistics
Matches: 106, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
68 48 0.45
70 5 0.05
71 40 0.38
72 13 0.12
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (70 bp):
TATTAAATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTCT
ATGCC
Found at i:42578167 original size:18 final size:18
Alignment explanation
Indices: 42578140--42578174 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42578130 CGGAAAAGGA
* *
42578140 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
42578158 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
42578175 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:42578836 original size:7 final size:7
Alignment explanation
Indices: 42578826--42578850 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42578816 TTATATACAT
42578826 AATACTA
1 AATACTA
42578833 AATACTA
1 AATACTA
42578840 AATACTA
1 AATACTA
42578847 AATA
1 AATA
42578851 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:42579966 original size:30 final size:31
Alignment explanation
Indices: 42579932--42579995 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
42579922 GCCATTGATG
*
42579932 AAAATATAAAAAAA-ATTAAATTATTTTAAA
1 AAAATATAAAAAAATATAAAATTATTTTAAA
42579962 AAAATATAAAAAAATATAAAATTATTTTAAA
1 AAAATATAAAAAAATATAAAATTATTTTAAA
42579993 AAA
1 AAA
42579996 TAAAATTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (31 bp):
AAAATATAAAAAAATATAAAATTATTTTAAA
Found at i:42580044 original size:29 final size:29
Alignment explanation
Indices: 42580012--42580094 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
42580002 TGAGGGGAAA
42580012 TTGAAATTAAATATGGATTTGAGAGAATT
1 TTGAAATTAAATATGGATTTGAGAGAATT
** *
42580041 TTGAAAGGAAAT-T-GA---GAG-GAA-A
1 TTGAAATTAAATATGGATTTGAGAGAATT
*
42580063 TTGAAATTAAATATGGGTTTGAGAGAATT
1 TTGAAATTAAATATGGATTTGAGAGAATT
42580092 TTG
1 TTG
42580095 GAAGGAAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 10 0.25
23 4 0.10
24 4 0.10
27 5 0.12
28 4 0.10
29 13 0.32
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (29 bp):
TTGAAATTAAATATGGATTTGAGAGAATT
Found at i:42580054 original size:51 final size:51
Alignment explanation
Indices: 42579998--42580102 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
42579988 TTAAAAAATA
*
42579998 AAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGAAAGG
1 AAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGAAAGG
* *
42580049 AAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGAAAGG
42580100 AAA
1 AAA
42580103 GTTGGAAGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.29
Consensus pattern (51 bp):
AAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGAAAGG
Found at i:42580465 original size:21 final size:20
Alignment explanation
Indices: 42580418--42580465 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
42580408 TCCCTATATT
42580418 TAATTTTATATTAAATTGAA
1 TAATTTTATATTAAATTGAA
*
42580438 AACATTTTATTACTTAAATT-AA
1 TA-ATTTTA-TA-TTAAATTGAA
42580460 TAATTT
1 TAATTT
42580466 CGATTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 5 0.22
23 7 0.30
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATTTTATATTAAATTGAA
Found at i:42586342 original size:185 final size:185
Alignment explanation
Indices: 42586030--42586403 Score: 730
Period size: 185 Copynumber: 2.0 Consensus size: 185
42586020 CACAGGTTTA
42586030 AAGCAAACGTAAGATGCTTTGCACATAGCAGTAAAAATCGAAGGGTAGGAATGAAAGCTCAGTAA
1 AAGCAAACGTAAGATGCTTTGCACATAGCAGTAAAAATCGAAGGGTAGGAATGAAAGCTCAGTAA
42586095 TACTGTAGTAAAATGACAAAAACAAACTAGCATTTCACTCCATCTAGTAAAAGCATATTAAATGA
66 TACTGTAGTAAAATGACAAAAACAAACTAGCATTTCACTCCATCTAGTAAAAGCATATTAAATGA
42586160 GTCAAAAAAATGGGATGTGAATACAATTAAAGAAAAGAACATAGAAGAGGAAATG
131 GTCAAAAAAATGGGATGTGAATACAATTAAAGAAAAGAACATAGAAGAGGAAATG
*
42586215 AAGCAAACGTAAGATGCTTTGCACATAGCAGTAAAAATCGAAGGGTAGGAGTGAAAGCTCAGTAA
1 AAGCAAACGTAAGATGCTTTGCACATAGCAGTAAAAATCGAAGGGTAGGAATGAAAGCTCAGTAA
*
42586280 TACTGTAGTAAAATGACAAAAGCAAACTAGCATTTCACTCCATCTAGTAAAAGCATATTAAATGA
66 TACTGTAGTAAAATGACAAAAACAAACTAGCATTTCACTCCATCTAGTAAAAGCATATTAAATGA
42586345 GTCAAAAAAATGGGATGTGAATACAATTAAAGAAAAGAACATAGAAGAGGAAATG
131 GTCAAAAAAATGGGATGTGAATACAATTAAAGAAAAGAACATAGAAGAGGAAATG
42586400 AAGC
1 AAGC
42586404 CAATGCTCTG
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 187 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (185 bp):
AAGCAAACGTAAGATGCTTTGCACATAGCAGTAAAAATCGAAGGGTAGGAATGAAAGCTCAGTAA
TACTGTAGTAAAATGACAAAAACAAACTAGCATTTCACTCCATCTAGTAAAAGCATATTAAATGA
GTCAAAAAAATGGGATGTGAATACAATTAAAGAAAAGAACATAGAAGAGGAAATG
Found at i:42593096 original size:20 final size:22
Alignment explanation
Indices: 42593066--42593109 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
42593056 AAAAAAAGAG
42593066 AAATACAAAAA-AGAATAG-ATC
1 AAATACAAAAAGA-AATAGAATC
42593087 AAAT-CAAAAAGAAATAGAATC
1 AAATACAAAAAGAAATAGAATC
42593108 AA
1 AA
42593110 CGATTTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATACAAAAAGAAATAGAATC
Found at i:42595993 original size:35 final size:32
Alignment explanation
Indices: 42595916--42596139 Score: 268
Period size: 32 Copynumber: 6.7 Consensus size: 32
42595906 AAATAATACA
* *
42595916 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATG
*
42595948 TGAACAGGAGAGATTCCCAGCAACAAAGTAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAA-TAAT--G
* *
42595983 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATG
*
42596015 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAA--TG
* *
42596050 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATG
*
42596082 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACA-AATAAT--G
* *
42596117 TGAACAGGAAATATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAA
42596140 GAAAAGACAA
Statistics
Matches: 167, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
32 73 0.44
33 13 0.08
34 8 0.05
35 73 0.44
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (32 bp):
TGAACAGGAGAGATTCCCTGCAACAAATAATG
Found at i:42596029 original size:67 final size:66
Alignment explanation
Indices: 42595906--42596143 Score: 386
Period size: 67 Copynumber: 3.6 Consensus size: 66
42595896 GTTCAAAAAG
* * * *
42595906 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCAGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
42595971 C
66 C
42595972 AAAGTAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCA
1 AAA-TAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCA
42596037 AC
65 AC
*
42596039 AAAATAATGTGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCA
1 -AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCA
42596104 AC
65 AC
* *
42596106 AGAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 A-AATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
42596144 AGACAAGTGA
Statistics
Matches: 161, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
66 4 0.02
67 154 0.96
68 3 0.02
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (66 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
C
Found at i:42596395 original size:29 final size:29
Alignment explanation
Indices: 42596363--42596435 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
42596353 TTCTCAAGAC
* *
42596363 ATTTAAGTTTTCAAAAATTTAGTTTTTAA
1 ATTTAAGTTTTCAAAAATTAAGTTTTCAA
*
42596392 ATTTCCAAATTTTC--AAATTAAGTTTTCAA
1 ATTT--AAGTTTTCAAAAATTAAGTTTTCAA
* *
42596421 ACTTAAGCTTTCAAA
1 ATTTAAGTTTTCAAA
42596436 TAACAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
27 6 0.18
29 21 0.62
31 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTAAGTTTTCAAAAATTAAGTTTTCAA
Found at i:42596419 original size:13 final size:13
Alignment explanation
Indices: 42596401--42596436 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
42596391 AATTTCCAAA
42596401 TTTTCAAATTAAG
1 TTTTCAAATTAAG
42596414 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
42596428 CTTTCAAAT
1 TTTTCAAAT
42596437 AACAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:42596820 original size:7 final size:7
Alignment explanation
Indices: 42596800--42596843 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
42596790 AAACACATGC
42596800 ATATCAT
1 ATATCAT
42596807 A-ATCAT
1 ATATCAT
42596813 ATATCAT
1 ATATCAT
*
42596820 ACATACAT
1 ATAT-CAT
42596828 ATATCAT
1 ATATCAT
42596835 ATATCAT
1 ATATCAT
42596842 AT
1 AT
42596844 GGCATACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.18
7 21 0.64
8 6 0.18
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (7 bp):
ATATCAT
Found at i:42596833 original size:22 final size:22
Alignment explanation
Indices: 42596799--42596842 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42596789 AAAACACATG
42596799 CATATCATAATCATATATCATA
1 CATATCATAATCATATATCATA
42596821 CATA-CATATATCATATATCATA
1 CATATCATA-ATCATATATCATA
42596843 TGGCATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (22 bp):
CATATCATAATCATATATCATA
Found at i:42596849 original size:29 final size:28
Alignment explanation
Indices: 42596800--42596855 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
42596790 AAACACATGC
*
42596800 ATATCATAATCATATATCATACATACAT
1 ATATCATAATCATATAGCATACATACAT
*
42596828 ATATCATATATCATATGGCATACATACA
1 ATATCATA-ATCATATAGCATACATACA
42596856 CATGTACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (28 bp):
ATATCATAATCATATAGCATACATACAT
Found at i:42598214 original size:15 final size:16
Alignment explanation
Indices: 42598189--42598221 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42598179 ATCAAATTAT
*
42598189 TTAACAATTTACGAAA
1 TTAACAATTTAAGAAA
42598205 TTAA-AATTTAAGAAA
1 TTAACAATTTAAGAAA
42598220 TT
1 TT
42598222 TGGGGCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAACAATTTAAGAAA
Found at i:42599972 original size:43 final size:43
Alignment explanation
Indices: 42599911--42599996 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
42599901 TGCTATGAGT
42599911 ATGTTTCTTGGATTATTATGTAAAAGTCACAACATTACTCGTA
1 ATGTTTCTTGGATTATTATGTAAAAGTCACAACATTACTCGTA
* *
42599954 ATGTTTCTTGGATTATTATGTAATAGTCACTACATTACTCGTA
1 ATGTTTCTTGGATTATTATGTAAAAGTCACAACATTACTCGTA
42599997 GTGATTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (43 bp):
ATGTTTCTTGGATTATTATGTAAAAGTCACAACATTACTCGTA
Found at i:42600793 original size:38 final size:39
Alignment explanation
Indices: 42600743--42600847 Score: 122
Period size: 39 Copynumber: 2.7 Consensus size: 39
42600733 TTATCGAAAT
* *
42600743 CATTGTTATAATTATTGTAATTATAATTTACGA-TCGAA
1 CATTATTATAATTATTGTAATTATAATTTACGAGTCAAA
* * * ***
42600781 TATTTTTATAATTATTGTAATTGTAATTTTTTAGTCAAA
1 CATTATTATAATTATTGTAATTATAATTTACGAGTCAAA
*
42600820 CATTATTATAATTATGGTAATTATAATT
1 CATTATTATAATTATTGTAATTATAATT
42600848 ATTATATTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
38 27 0.49
39 28 0.51
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (39 bp):
CATTATTATAATTATTGTAATTATAATTTACGAGTCAAA
Found at i:42605388 original size:26 final size:26
Alignment explanation
Indices: 42605359--42605408 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
42605349 TGATTAAGAT
42605359 AATAAAATAAGAAA-ATATGAAAAATA
1 AATAAAATAA-AAATATATGAAAAATA
*
42605385 AATAAAATAAAAATATATTAAAAA
1 AATAAAATAAAAATATATGAAAAA
42605409 ATACAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (26 bp):
AATAAAATAAAAATATATGAAAAATA
Found at i:42606322 original size:23 final size:23
Alignment explanation
Indices: 42606284--42606335 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
42606274 TAGATTTTTC
*
42606284 CTAAATACTATTACTAAATAATT
1 CTAAATACTATCACTAAATAATT
*
42606307 CTAAATATTATCACTAAATAATT
1 CTAAATACTATCACTAAATAATT
*
42606330 CAAAAT
1 CTAAAT
42606336 TTAAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATACTATCACTAAATAATT
Found at i:42610760 original size:27 final size:27
Alignment explanation
Indices: 42610739--42610921 Score: 222
Period size: 27 Copynumber: 6.8 Consensus size: 27
42610729 AGGTATAACC
*
42610739 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
42610766 GTCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
42610793 GTCATTTTATCCTATGAGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
42610820 ATCATTTTGCCTTATGAGGCTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
42610847 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** * *
42610874 GTTATTTTACCCTAAAGAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
42610901 GTCATTTTACCCTATGGGGGT
1 GTCATTTTACCCTATGGGGGT
42610922 CTCGGTGCAG
Statistics
Matches: 133, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 133 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:42610769 original size:54 final size:53
Alignment explanation
Indices: 42610710--42610921 Score: 212
Period size: 54 Copynumber: 3.9 Consensus size: 53
42610700 AAGACCATAA
** *
42610710 CAGTCAATTTATCTCCTA-GAGGTATAACCGTCATTTTACCCTATGGGGGTATTT
1 CAGTCAATTTA-C-CCTATGAGGTATTTCGGTCATTTTACCCTATGGGGGTATTT
* * * * *
42610764 CAGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTATCCTATGAGGATATTT
1 CAGTCAATTTACCCTATGA-GGTATTTCGGTCATTTTACCCTATGGGGGTATTT
* * *
42610818 C-GATCATTTTGCCTTATGAGGCTATTTCGGTCATTTTACCCTATGGGGGTATTT
1 CAG-TCAATTTACCCTATGAGG-TATTTCGGTCATTTTACCCTATGGGGGTATTT
* * * * *
42610872 CGGTTATTTTACCCTAAAGAGGTATTTTGGTCATTTTACCCTATGGGGGT
1 CAGTCAATTTACCCT-ATGAGGTATTTCGGTCATTTTACCCTATGGGGGT
42610922 CTCGGTGCAG
Statistics
Matches: 134, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
52 4 0.03
53 6 0.04
54 118 0.88
55 6 0.04
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (53 bp):
CAGTCAATTTACCCTATGAGGTATTTCGGTCATTTTACCCTATGGGGGTATTT
Found at i:42616509 original size:23 final size:23
Alignment explanation
Indices: 42616479--42616536 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
42616469 TACGAAAAAT
*
42616479 AAATAAAATAAA-AATATATTCA-A
1 AAATAAAATAAATAA-AT-TTAAGA
42616502 AAATAAAA-AAATAAATTTAAGA
1 AAATAAAATAAATAAATTTAAGA
42616524 AAATAAAATAAAT
1 AAATAAAATAAAT
42616537 GGATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 3 0.10
22 14 0.45
23 14 0.45
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATAAAATAAATAAATTTAAGA
Found at i:42616531 original size:20 final size:19
Alignment explanation
Indices: 42616483--42616536 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
42616473 AAAAATAAAT
*
42616483 AAAATAAAAATATATTCAA
1 AAAATAAAAATAAATTCAA
* *
42616502 AAATAAAAAAATAAATTTAA
1 AAA-ATAAAAATAAATTCAA
42616522 GAAAAT-AAAATAAAT
1 -AAAATAAAAATAAAT
42616537 GGATAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 12 0.41
20 14 0.48
21 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAAAATAAATTCAA
Found at i:42617394 original size:13 final size:13
Alignment explanation
Indices: 42617376--42617418 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
42617366 TAGATTTTTG
42617376 CTAAATATTATCA
1 CTAAATATTATCA
*
42617389 CTAAATA--AT-T
1 CTAAATATTATCA
42617399 CTAAATATTATCA
1 CTAAATATTATCA
42617412 CTAAATA
1 CTAAATA
42617419 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:42617427 original size:23 final size:23
Alignment explanation
Indices: 42617376--42617425 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
42617366 TAGATTTTTG
42617376 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
42617399 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
42617422 -TAAA
1 CTAAA
42617426 ATTTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:42618005 original size:18 final size:19
Alignment explanation
Indices: 42617982--42618030 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
42617972 AATCGTGTCG
42617982 TTCATTTTCAAAAT-ATTA
1 TTCATTTTCAAAATCATTA
*
42618000 TTCATTTAC-AAATCATTA
1 TTCATTTTCAAAATCATTA
*
42618018 TTCAATTTCAAAA
1 TTCATTTTCAAAA
42618031 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 19 0.73
19 3 0.12
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCATTTTCAAAATCATTA
Found at i:42618440 original size:6 final size:6
Alignment explanation
Indices: 42618429--42618457 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42618419 TAAGCCCTTT
42618429 TCAGTA TCAGTA TCAGTA TCAGTA TCAGT
1 TCAGTA TCAGTA TCAGTA TCAGTA TCAGT
42618458 CCAGTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
TCAGTA
Done.