Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007978.1 Hibiscus syriacus cultivar Beakdansim tig00110415_pilon, whole genome shotgun sequence
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: 1479011
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 6 of 7
Found at i:1240890 original size:20 final size:20
Alignment explanation
Indices: 1240828--1241021 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1240818 CGATTTTCCA
* ** *
1240828 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1240848 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1240868 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1240888 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1240908 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1240928 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1240948 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1240968 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1240988 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1241009 AAATCGCAACGCG
1 AAATCGCAACGCG
1241022 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1240912 original size:60 final size:60
Alignment explanation
Indices: 1240828--1241021 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1240818 CGATTTTCCA
* ** * *
1240828 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1240888 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1240948 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1241009 AAATCGCAACGCG
1 AAATCGCAACGCG
1241022 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1241441 original size:33 final size:33
Alignment explanation
Indices: 1241402--1241472 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1241392 TTCACTTAGA
*
1241402 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1241435 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1241468 TTTCA
1 TTTCA
1241473 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1241612 original size:14 final size:14
Alignment explanation
Indices: 1241593--1241647 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1241583 AGAATGACTG
1241593 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1241607 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
1241626 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1241640 TCGCAACG
1 TCGCAACG
1241648 CGAAACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1241685 original size:19 final size:18
Alignment explanation
Indices: 1241658--1241775 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
1241648 CGAAACAAAA
*
1241658 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
1241677 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
1241691 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
1241710 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
1241724 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
1241742 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
1241757 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
1241775 T
1 T
1241776 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:1241699 original size:14 final size:14
Alignment explanation
Indices: 1241680--1241769 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1241670 TTTCATTTCG
1241680 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1241694 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1241713 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1241727 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1241744 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1241760 CGTTGCGATT
1 CGTTGCGATT
1241770 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1241705 original size:33 final size:33
Alignment explanation
Indices: 1241663--1241777 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1241653 CAAAATCGCA
1241663 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1241696 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1241729 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1241762 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1241778 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1243701 original size:185 final size:186
Alignment explanation
Indices: 1243471--1243852 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
1243461 TAGATTGCTT
1243471 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243536 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1243601 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1243656 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243721 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1243786 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243842 AGTAAATTTAT
1 AGTAAATTTAT
1243853 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1243785 original size:93 final size:93
Alignment explanation
Indices: 1243471--1243850 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
1243461 TAGATTGCTT
*
1243471 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243536 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243564 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243628 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243656 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243721 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243749 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243814 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243842 AGTAAATTT
1 AGTAAATTT
1243851 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1243934 original size:19 final size:19
Alignment explanation
Indices: 1243894--1244022 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1243884 TAGTTTACTT
* *
1243894 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1243914 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1243933 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1243952 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1243966 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1243985 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1243999 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1244018 TCGCA
1 TCGCA
1244023 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1243973 original size:33 final size:32
Alignment explanation
Indices: 1243930--1244022 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1243920 CGCGAAACCA
**
1243930 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1243962 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1243995 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1244023 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1244020 original size:52 final size:52
Alignment explanation
Indices: 1243894--1244022 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1243884 TAGTTTACTT
**
1243894 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1243946 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1243999 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1244023 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1244040 original size:19 final size:19
Alignment explanation
Indices: 1244018--1244152 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1244008 GAAACCAAAA
*
1244018 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1244037 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1244053 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1244070 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1244086 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1244103 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1244122 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1244142 TCGTGTTGCGA
1 TCGCGTTGCGA
1244153 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1244059 original size:14 final size:14
Alignment explanation
Indices: 1244040--1244096 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1244030 TTTCATTTCG
1244040 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1244054 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1244071 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1244087 CGTTGCGATT
1 CGTTGCGATT
1244097 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1244065 original size:33 final size:33
Alignment explanation
Indices: 1244023--1244115 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1244013 CAAAATCGCA
*
1244023 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1244056 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1244089 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1244116 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1246011 original size:38 final size:38
Alignment explanation
Indices: 1245968--1246040 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1245958 AATTGATTGT
*
1245968 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1246006 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1246041 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:1246027 original size:19 final size:19
Alignment explanation
Indices: 1245963--1246027 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1245953 AGTTTAATTG
*
1245963 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1245982 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1246000 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1246020 ATTGATTT
1 ATTGATTT
1246028 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:1246041 original size:14 final size:14
Alignment explanation
Indices: 1246022--1246057 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1246012 ATTGTTTAAT
1246022 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1246036 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1246050 TGATTTGT
1 TGATTTGT
1246058 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1246180 original size:19 final size:19
Alignment explanation
Indices: 1246164--1246264 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
1246154 AAAAATGACT
1246164 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1246183 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1246201 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1246215 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1246234 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1246254 ATCGCAATGCG
1 ATCGCAATGCG
1246265 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
13 1 0.01
14 9 0.12
16 4 0.05
18 10 0.14
19 30 0.41
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1246317 original size:19 final size:19
Alignment explanation
Indices: 1246293--1246590 Score: 402
Period size: 19 Copynumber: 16.7 Consensus size: 19
1246283 GATTATCTCG
1246293 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246312 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246331 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1246345 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246364 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246383 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1246402 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246421 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246440 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1246454 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246473 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246492 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1246506 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246525 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246544 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1246558 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1246578 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1246591 GTTGGGATTT
Statistics
Matches: 248, Mismatches: 10, Indels: 41
0.83 0.03 0.14
Matches are distributed among these distances:
14 24 0.10
16 29 0.12
17 27 0.11
18 2 0.01
19 153 0.62
20 13 0.05
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1246536 original size:161 final size:157
Alignment explanation
Indices: 1246271--1246590 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
1246261 TGCGTTTATA
1246271 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
1246336 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1246401 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
1246432 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1246497 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
1246562 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
1246589 AT
1 AT
1246591 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:1246562 original size:33 final size:33
Alignment explanation
Indices: 1246312--1246617 Score: 271
Period size: 33 Copynumber: 8.8 Consensus size: 33
1246302 TCATTTCGCA
*
1246312 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1246345 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1246381 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
1246419 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1246454 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1246490 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1246525 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1246558 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1246592 TTGGGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1246618 GTATTTTCCG
Statistics
Matches: 234, Mismatches: 20, Indels: 39
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 16 0.07
33 84 0.36
34 20 0.09
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1246617 original size:52 final size:52
Alignment explanation
Indices: 1246271--1246590 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
1246261 TGCGTTTATA
*
1246271 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1246323 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1246375 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1246432 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1246484 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1246536 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1246589 AT
1 AT
1246591 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1248938 original size:12 final size:12
Alignment explanation
Indices: 1248921--1248945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1248911 TCTTCGGGGA
1248921 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1248933 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1248945 C
1 C
1248946 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1249154 original size:24 final size:24
Alignment explanation
Indices: 1249120--1249166 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1249110 CTGAAACATC
1249120 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1249144 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1249167 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1249868 original size:20 final size:20
Alignment explanation
Indices: 1249840--1250248 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
1249830 AAATTTCAGT
* * * *
1249840 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1249860 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1249880 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1249900 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1249920 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1249940 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1249960 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1249980 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1250000 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1250020 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250040 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250060 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1250080 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1250100 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250120 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1250140 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1250160 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1250180 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1250200 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1250220 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1250240 GTTGCGATT
1 GTTGCGATT
1250249 ATGGAAAATC
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 331 0.97
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1250632 original size:18 final size:19
Alignment explanation
Indices: 1250598--1250642 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1250588 ATTTTCAATG
1250598 ATTAATTTATCATATTTTTA
1 ATTAATTTATCATA-TTTTA
1250618 ATTAATTT-T-ATATTTTA
1 ATTAATTTATCATATTTTA
1250635 ATTTAATT
1 A-TTAATT
1250643 AGTTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 9 0.38
19 1 0.04
20 8 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAATTTATCATATTTTA
Found at i:1250642 original size:22 final size:21
Alignment explanation
Indices: 1250614--1250657 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1250604 TTATCATATT
1250614 TTTAATTAATTTTATATTTTAA
1 TTTAATTAATTTTA-ATTTTAA
*
1250636 TTTAATTAGTTTTAATTTTAA
1 TTTAATTAATTTTAATTTTAA
1250657 T
1 T
1250658 ATTTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAATTAATTTTAATTTTAA
Found at i:1250663 original size:15 final size:14
Alignment explanation
Indices: 1250619--1250662 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
1250609 ATATTTTTAA
1250619 TTAATTTT-ATATT
1 TTAATTTTAATATT
1250632 TTAA-TTTAATTAGTT
1 TTAATTTTAA-TA-TT
1250647 TTAATTTTAATATT
1 TTAATTTTAATATT
1250661 TT
1 TT
1250663 TGAAATTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.11
13 5 0.19
14 6 0.22
15 8 0.30
16 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTAATTTTAATATT
Found at i:1260123 original size:2 final size:2
Alignment explanation
Indices: 1260116--1260149 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1260106 GAAGGTAGAC
1260116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1260150 TAATAGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276171 original size:18 final size:18
Alignment explanation
Indices: 1276113--1276190 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 18
1276103 CAACCCATTA
1276113 TTATTTTT-ATTTTCATTT
1 TTATTTTTGATTTT-ATTT
*
1276131 GTTCAATTTTT-ATTTTCAATT
1 -TT--ATTTTTGATTTT-ATTT
1276152 TTATTTTCTGA-TTTATTT
1 TTATTTT-TGATTTTATTT
* *
1276170 TTGTTTTTTATTTTATTT
1 TTATTTTTGATTTTATTT
1276188 TTA
1 TTA
1276191 GATACATCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
17 2 0.04
18 23 0.47
19 6 0.12
20 3 0.06
21 15 0.31
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (18 bp):
TTATTTTTGATTTTATTT
Found at i:1276456 original size:53 final size:53
Alignment explanation
Indices: 1276399--1276579 Score: 123
Period size: 53 Copynumber: 3.2 Consensus size: 53
1276389 GTTCGAATTG
1276399 TGCAGAAAAGTTCAAACAGAACAATGCGAAAAAAACTGATTTGGTTCAAACAA
1 TGCAGAAAAGTTCAAACAGAACAATGCGAAAAAAACTGATTTGGTTCAAACAA
* * * *
1276452 TGCAGGAAAA-TACATAACAAATTCAAAACAATGCAGTGCAGAAAAAAACAGATTTGATTCGAAC
1 TGCA-GAAAAGT---T--CAAA--CAGAAC-A---A-TGC-GAAAAAAACTGATTTGGTTCAAAC
*
1276516 TA
52 AA
* * * * *
1276518 TGTAGAAAAGTTCGAACAGAACAGTGC-AGAAAAAATTGATTTGGTTCAAACAG
1 TGCAGAAAAGTTCAAACAGAACAATGCGA-AAAAAACTGATTTGGTTCAAACAA
1276571 TGCAGAAAA
1 TGCAGAAAA
1276580 AAATTGATTT
Statistics
Matches: 96, Mismatches: 16, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
52 1 0.01
53 31 0.32
54 8 0.08
56 1 0.01
58 5 0.05
59 5 0.05
60 5 0.05
61 4 0.04
63 1 0.01
64 1 0.01
65 8 0.08
66 26 0.27
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (53 bp):
TGCAGAAAAGTTCAAACAGAACAATGCGAAAAAAACTGATTTGGTTCAAACAA
Found at i:1276570 original size:34 final size:34
Alignment explanation
Indices: 1276527--1276610 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 34
1276517 ATGTAGAAAA
1276527 GTTCGAACAGAACAGTGCAG-AAAAAATTGATTTG
1 GTTC-AACAGAACAGTGCAGAAAAAAATTGATTTG
1276561 GTT---CA-AACAGTGCAGAAAAAAATTGATTTG
1 GTTCAACAGAACAGTGCAGAAAAAAATTGATTTG
1276591 GTT---CA-AACAGTGCAGAAAAA
1 GTTCAACAGAACAGTGCAGAAAAA
1276611 TACACAGCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
29 10 0.20
30 36 0.73
34 3 0.06
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (34 bp):
GTTCAACAGAACAGTGCAGAAAAAAATTGATTTG
Found at i:1276583 original size:30 final size:30
Alignment explanation
Indices: 1276537--1276610 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
1276527 GTTCGAACAG
1276537 AACAGTGCAG-AAAAAATTGATTTGGTTCA
1 AACAGTGCAGAAAAAAATTGATTTGGTTCA
1276566 AACAGTGCAGAAAAAAATTGATTTGGTTCA
1 AACAGTGCAGAAAAAAATTGATTTGGTTCA
1276596 AACAGTGCAGAAAAA
1 AACAGTGCAGAAAAA
1276611 TACACAGCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 10 0.23
30 34 0.77
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (30 bp):
AACAGTGCAGAAAAAAATTGATTTGGTTCA
Found at i:1276597 original size:119 final size:117
Alignment explanation
Indices: 1276367--1276583 Score: 287
Period size: 119 Copynumber: 1.9 Consensus size: 117
1276357 ATTGTTCAGA
* * * *
1276367 CAGTGCAGGAAAAAAAGACTTGGTTCGAATTGTGCAGAAAAGTTCAAACAGAACAATGCGAAAAA
1 CAGTGCAGAAAAAAAAGACTTGATTCGAACTATGCAGAAAAGTTCAAACAGAACAATGCGAAAAA
*
1276432 AACTGATTTGGTTCAAACAATGCAGGAAAATACATAACAAATTCAAAACAATG
66 AACTGATTTGGTTCAAACAATGCAGGAAAATAAATAACAAATTC-AAACAATG
* * * *
1276485 CAGTGCAGAAAAAAACAGATTTGATTCGAACTATGTAGAAAAGTTCGAACAGAACAGTGC-AGAA
1 CAGTGCAGAAAAAAA-AGACTTGATTCGAACTATGCAGAAAAGTTCAAACAGAACAATGCGA-AA
* *
1276549 AAAATTGATTTGGTTCAAACAGTGCA-GAAAA-AAAT
64 AAAACTGATTTGGTTCAAACAATGCAGGAAAATAAAT
1276584 TGATTTGGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
117 3 0.03
118 20 0.23
119 63 0.73
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.20
Consensus pattern (117 bp):
CAGTGCAGAAAAAAAAGACTTGATTCGAACTATGCAGAAAAGTTCAAACAGAACAATGCGAAAAA
AACTGATTTGGTTCAAACAATGCAGGAAAATAAATAACAAATTCAAACAATG
Found at i:1276689 original size:28 final size:28
Alignment explanation
Indices: 1276640--1276697 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1276630 GTGCAATGTA
* *
1276640 AAAAAAATAGCAGCACAGTTTTGGTTCG
1 AAAAAAATAACAGCACAATTTTGGTTCG
*
1276668 AAAAAAATAACAGTACAATTTTGGTTCG
1 AAAAAAATAACAGCACAATTTTGGTTCG
1276696 AA
1 AA
1276698 CAATGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (28 bp):
AAAAAAATAACAGCACAATTTTGGTTCG
Found at i:1286468 original size:62 final size:63
Alignment explanation
Indices: 1286330--1286474 Score: 150
Period size: 62 Copynumber: 2.3 Consensus size: 63
1286320 ATTAAATTAT
* * * * *
1286330 TGACGTGACATATATTAAATTATTATTTTGAGTGACGTTATACACATTACATCATCACTTTAA
1 TGACATGACATATATTATATTATTATTTTGAGTGACGTAATACACAATAAATCATCACTTTAA
* * * * * * *
1286393 TGACATAATATATATTATATT-TTATTTTTATTGATG-AATACATAATAAATCATCATTTTAAA
1 TGACATGACATATATTATATTATTATTTTGAGTGACGTAATACACAATAAATCATCACTTT-AA
*
1286455 TGACATGACATATAATATAT
1 TGACATGACATATATTATAT
1286475 CAATGATTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
61 18 0.27
62 31 0.47
63 17 0.26
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (63 bp):
TGACATGACATATATTATATTATTATTTTGAGTGACGTAATACACAATAAATCATCACTTTAA
Found at i:1290853 original size:16 final size:16
Alignment explanation
Indices: 1290832--1290863 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1290822 TAAAAAATTT
1290832 TGAGTTATTCGAGTTG
1 TGAGTTATTCGAGTTG
1290848 TGAGTTATTCGAGTTG
1 TGAGTTATTCGAGTTG
1290864 ACGAGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (16 bp):
TGAGTTATTCGAGTTG
Found at i:1291665 original size:14 final size:14
Alignment explanation
Indices: 1291648--1291680 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1291638 ATTTCTATGT
*
1291648 AGGGAATTATTTGC
1 AGGGAATTATTTAC
1291662 AGGGAATTATTTAC
1 AGGGAATTATTTAC
1291676 AGGGA
1 AGGGA
1291681 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:1296701 original size:20 final size:20
Alignment explanation
Indices: 1296678--1296724 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1296668 GTTTCCAAAT
*
1296678 TCGCAACGTGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1296698 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1296718 TCGCAAC
1 TCGCAAC
1296725 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:1296752 original size:18 final size:19
Alignment explanation
Indices: 1296718--1296881 Score: 126
Period size: 20 Copynumber: 8.4 Consensus size: 19
1296708 AATTTGTAAA
1296718 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
1296738 TCGCAACAC-AAGTCAAAT
1 TCGCAACACGAAGTCAAAT
*
1296756 TCGCAACGC-AA-T-AAAT
1 TCGCAACACGAAGTCAAAT
*
1296772 TCGCAACGCGATAG-CAAAT
1 TCGCAACACGA-AGTCAAAT
1296791 TCGCAACACTGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* *
1296811 TCGCAACGCGTAAATGCAAAGT
1 TCGCAACACG-AAGT-CAAA-T
*
1296833 AATCGCAACGCGAATTTGT-AAA-
1 --TCGCAACACGAA---GTCAAAT
1296855 TCGCAACACTGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
1296875 TCGCAAC
1 TCGCAAC
1296882 GCGCCAAATA
Statistics
Matches: 121, Mismatches: 6, Indels: 34
0.75 0.04 0.21
Matches are distributed among these distances:
16 13 0.11
17 2 0.02
18 22 0.18
19 18 0.15
20 42 0.35
21 7 0.06
22 1 0.01
23 2 0.02
24 13 0.11
26 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:1296773 original size:16 final size:18
Alignment explanation
Indices: 1296729--1296819 Score: 107
Period size: 18 Copynumber: 5.0 Consensus size: 18
1296719 CGCAACACAG
*
1296729 AAGTCAAATTCGCAACAC
1 AAGTCAAATTCGCAACGC
1296747 AAGTCAAATTCGCAACGC
1 AAGTCAAATTCGCAACGC
1296765 AA-T-AAATTCGCAACGC
1 AAGTCAAATTCGCAACGC
*
1296781 GATAG-CAAATTCGCAACAC
1 -A-AGTCAAATTCGCAACGC
1296800 TGAAGTCAAATTCGCAACGC
1 --AAGTCAAATTCGCAACGC
1296820 GTAAATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
16 13 0.20
17 2 0.03
18 20 0.31
19 14 0.22
20 15 0.23
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (18 bp):
AAGTCAAATTCGCAACGC
Found at i:1296973 original size:19 final size:19
Alignment explanation
Indices: 1296899--1296967 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
1296889 ATAACACGAA
1296899 AAATTTGCAACTGAATTTC
1 AAATTTGCAACTGAATTTC
1296918 AAATTTGCAACTGAATTTC
1 AAATTTGCAACTGAATTTC
1296937 AAATTTGCAACTGAATTTC
1 AAATTTGCAACTGAATTTC
*
1296956 AAATTCGCAACT
1 AAATTTGCAACT
1296968 CGATTTTCGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (19 bp):
AAATTTGCAACTGAATTTC
Found at i:1297201 original size:14 final size:15
Alignment explanation
Indices: 1297161--1297200 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1297151 TCCCCATCTC
*
1297161 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1297176 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1297192 TAATTTTTT
1 TAATTTTTT
1297201 CAATGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1300176 original size:18 final size:18
Alignment explanation
Indices: 1300150--1300190 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1300140 AAGCAAAAGG
*
1300150 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
*
1300168 AAATTAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
*
1300186 CAATC
1 AAATC
1300191 GGCTTCACCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1300696 original size:66 final size:65
Alignment explanation
Indices: 1300614--1300789 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 65
1300604 AATTTAAAAC
1300614 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
1300679 A
65 A
* * *
1300680 AACAAATCAACTTTTACAAATCAATTAAGCAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
1300744 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
1300790 GTGTACCACA
Statistics
Matches: 99, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 33 0.33
68 4 0.04
69 15 0.15
70 6 0.06
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:1302135 original size:21 final size:21
Alignment explanation
Indices: 1302108--1302178 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1302098 GTGAATCGGA
1302108 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* ** *
1302129 C-CATTGAACGATGACAGGGGC
1 CTC-TTGAACGGTGGGAGGGAC
*
1302150 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGAC
1302171 CTCTTGAA
1 CTCTTGAA
1302179 ATGAGAGGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Found at i:1302167 original size:42 final size:40
Alignment explanation
Indices: 1302108--1302199 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 40
1302098 GTGAATCGGA
*
1302108 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTC-TTGAA--ATGACAGGAGC
* *
1302150 CTCTTGAACGGTGGGAGGGGCCTCTTGAAATGAGAGGAGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAAATGACAGGAGC
1302190 CTCTTGAACG
1 CTCTTGAACG
1302200 ATGATGTGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 19 0.41
42 26 0.57
43 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.37, T:0.20
Consensus pattern (40 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAAATGACAGGAGC
Found at i:1304383 original size:14 final size:14
Alignment explanation
Indices: 1304364--1304390 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1304354 ACGCGAAAAT
1304364 GAAAATCGCAACGA
1 GAAAATCGCAACGA
1304378 GAAAATCGCAACG
1 GAAAATCGCAACG
1304391 CAAAACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1305008 original size:20 final size:20
Alignment explanation
Indices: 1304983--1305234 Score: 221
Period size: 20 Copynumber: 12.6 Consensus size: 20
1304973 TAAACGCGTT
*
1304983 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGTG
* *
1305003 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
1305023 TTGCGAATTTGA-TTATCGTG
1 TTGCGAATTTGACTT-TCGTG
*
1305043 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
**
1305063 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GTG
* *
1305084 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
* *
1305104 TTGCAAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
* **
1305124 TTGTGAATTTGACTTTTATG
1 TTGCGAATTTGACTTTCGTG
* * *
1305144 TTGTG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC--TTTCGTG
1305164 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
*
1305184 TTACGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
*
1305204 TTGCG-ATTT-ACATATTCGCG
1 TTGCGAATTTGAC-T-TTCGTG
1305224 TTGCGAATTTG
1 TTGCGAATTTG
1305235 GAAACTGAGT
Statistics
Matches: 192, Mismatches: 27, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
18 4 0.02
19 12 0.06
20 144 0.75
21 30 0.16
22 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGTG
Found at i:1305175 original size:60 final size:60
Alignment explanation
Indices: 1304983--1305234 Score: 260
Period size: 60 Copynumber: 4.2 Consensus size: 60
1304973 TAAACGCGTT
* * * *** * *
1304983 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTT-GAT-TATCGTG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTATGTTGCG-ATTTACATAT-TCGCG
** *
1305043 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAC-TA-TCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTA-TGTTGCG-ATTT-ACATATTCGCG
* * * *
1305104 TTGCAAATTTGACTTTTGTGTTGTGAATTTGACTTTTATGTTGTGATTTACAGATTCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTATGTTGCGATTTACATATTCGCG
* * * *
1305164 TTGCGAATTTGACTTCTGTGTTACGAATTTGACTTCTGTGTTGCGATTTACATATTCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTATGTTGCGATTTACATATTCGCG
1305224 TTGCGAATTTG
1 TTGCGAATTTG
1305235 GAAACTGAGT
Statistics
Matches: 162, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
58 2 0.01
59 5 0.03
60 106 0.65
61 48 0.30
62 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (60 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTATGTTGCGATTTACATATTCGCG
Found at i:1305267 original size:60 final size:60
Alignment explanation
Indices: 1305143--1305269 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
1305133 TGACTTTTAT
* ** * * *
1305143 GTTGTGATTTACAGATTCGCGTTGCGAATTTGACTTCTGTGTTACGAATTTGACTTCTGT
1 GTTGCGATTTACAGATTCGCGTTGCGAATTTGACAACTGAGTTACGAATTAGACTTCTGC
* * *
1305203 GTTGCGATTTACATATTCGCGTTGCGAATTTGGA-AACTGAGTTGCGAAATTAGAGTTC-GC
1 GTTGCGATTTACAGATTCGCGTTGCGAATTT-GACAACTGAGTTACG-AATTAGACTTCTGC
1305263 GTTGCGA
1 GTTGCGA
1305270 ATTTGTTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 45 0.80
61 11 0.20
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (60 bp):
GTTGCGATTTACAGATTCGCGTTGCGAATTTGACAACTGAGTTACGAATTAGACTTCTGC
Found at i:1325265 original size:20 final size:20
Alignment explanation
Indices: 1325214--1325289 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
1325204 GCTTGGAGCG
1325214 TGGGGGGAATCGGTACCCCCT
1 TGGGGGGAATCGGTA-CCCCT
***
1325235 CATGGGGAATCGGTACCCCT
1 TGGGGGGAATCGGTACCCCT
* **
1325255 TGGGGGTAATCGGTACTTTCT
1 TGGGGGGAATCGGTAC-CCCT
1325276 TGGGGGGAATCGGT
1 TGGGGGGAATCGGT
1325290 TCTATCTGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.16, C:0.21, G:0.38, T:0.25
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCCT
Found at i:1328636 original size:18 final size:19
Alignment explanation
Indices: 1328601--1328637 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1328591 CAAGGAATGT
1328601 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1328621 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1328638 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1328861 original size:37 final size:37
Alignment explanation
Indices: 1328788--1328862 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1328778 GTCGGAAAAT
* *
1328788 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
1328825 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
1328862 A
1 A
1328863 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1334174 original size:16 final size:16
Alignment explanation
Indices: 1334153--1334186 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1334143 GATGTTTAGG
*
1334153 AAATGAGTTTAAGATT
1 AAATGAATTTAAGATT
1334169 AAATGAATTTAAGATT
1 AAATGAATTTAAGATT
1334185 AA
1 AA
1334187 TTTATTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (16 bp):
AAATGAATTTAAGATT
Found at i:1334527 original size:20 final size:21
Alignment explanation
Indices: 1334488--1334543 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1334478 CCTAAAACTA
* *
1334488 ATCCCTTTCATTTGTGCCTTC
1 ATCCCCTTCATTTATGCCTTC
1334509 ATCCCCTTCA-TTATGCCTTC
1 ATCCCCTTCATTTATGCCTTC
*
1334529 ATCCCCTTCCTTTAT
1 ATCCCCTTCATTTAT
1334544 CCCTCTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.12, C:0.38, G:0.05, T:0.45
Consensus pattern (21 bp):
ATCCCCTTCATTTATGCCTTC
Found at i:1336110 original size:11 final size:13
Alignment explanation
Indices: 1336083--1336107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1336073 TTCTCAATCT
1336083 TCTTCTCATTATA
1 TCTTCTCATTATA
1336096 TCTTCTCATTAT
1 TCTTCTCATTAT
1336108 CTTTTCCTAC
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:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTTCTCATTATA
Found at i:1341025 original size:23 final size:23
Alignment explanation
Indices: 1340999--1341048 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1340989 ATCTAGCACA
*
1340999 ATAACATATTAGGTAACACTTAT
1 ATAACATAATAGGTAACACTTAT
** *
1341022 ATAATGTAATAGGTAGCACTTAT
1 ATAACATAATAGGTAACACTTAT
1341045 ATAA
1 ATAA
1341049 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:1341055 original size:23 final size:23
Alignment explanation
Indices: 1341008--1341055 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1340998 AATAACATAT
**
1341008 TAGGTAACACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
*
1341031 TAGGTAGCACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
1341054 TA
1 TA
1341056 TGTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:1341112 original size:23 final size:23
Alignment explanation
Indices: 1341086--1341133 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1341076 ATCAAGCACA
*
1341086 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
** *
1341109 ATAATGTAATATGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
1341132 AT
1 AT
1341134 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGTTTAT
Found at i:1341132 original size:87 final size:87
Alignment explanation
Indices: 1340894--1341133 Score: 336
Period size: 87 Copynumber: 2.8 Consensus size: 87
1340884 TCATTTAATC
* * * * * *
1340894 GAAATATTATCAAGTAAAATAACAAATTAGGTAGCACTTATATAATGTAATAGGTAGTGCATATA
1 GAAACATTATCAAGCACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATA
**
1340959 TAATAAAATATGTTAATTACTT
66 TAATAAAATATGTTAATTACAA
* * * *
1340981 TAAACATTATCTAGCACAATAACATATTAGGTAACACTTATATAATGTAATAGGTAGCACTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATA
1341046 TAATAAAATATGTTAATTACAA
66 TAATAAAATATGTTAATTACAA
** * *
1341068 GAAACATTATCAAGCACAATAACATATTAGGTAGCGTTTATATAATGTAATATGTAGCGTTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATA
1341133 T
66 T
1341134 TGACCTATTT
Statistics
Matches: 133, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 133 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (87 bp):
GAAACATTATCAAGCACAATAACATATTAGGTAGCACTTATATAATGTAATAGGTAGCGCTTATA
TAATAAAATATGTTAATTACAA
Found at i:1341585 original size:199 final size:199
Alignment explanation
Indices: 1341135--1341652 Score: 756
Period size: 199 Copynumber: 2.6 Consensus size: 199
1341125 CGTTTATATT
* * *
1341135 GACCTATTTTCTAACT-AAACTGATATATTTCTACCGGGTACATTGTAAATTTACCTATTACATT
1 GACCTATTTTCTAA-TAAAACCGGTATATTTCTACCGGATACATTGTAAATTTACCTATTACATT
* *
1341199 ATAATTATCGGTTTCGATTCTTTTGGGATCGATACTTTTAATAAATGTATCGACATTTTATGTGT
65 ATAATTATCGGTTTCGATT-TTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
*
1341264 GCATCTCGTTGGGCATTCATTCTGGAAAAAAGGTATCGACACAAACTTAAAACGTGTCGATACAT
129 GCATCTCATTGGGCATTCATTCTGGAAAAAAGGTATCGACACAAACTTAAAACGTGTCGATACAT
1341329 TATGTA
194 TATGTA
* * * *
1341335 GATCTATTTTCTTATAAAACCGGTATATTTCTACCGGATACATTATAAATTTACCTATTGCATTG
1 GACCTATTTTCTAATAAAACCGGTATATTTCTACCGGATACATTGTAAATTTACCTATTACATT-
* *
1341400 A-AATTATCGGTTTCAATGTTTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
65 ATAATTATCGGTTTCGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
* * * *
1341464 GCATCTCATTTGGCATTTATTTTGGAAAAAA-GTATCGACACAAACTTAAAATGTGTCGATACAT
129 GCATCTCATTGGGCATTCATTCTGGAAAAAAGGTATCGACACAAACTTAAAACGTGTCGATACAT
*
1341528 TATTTA
194 TATGTA
* **
1341534 GACCTATTTTCTCATAAAACCGGTATATTTCTACAAGATACATTGTAAATTTACCTATTACATTA
1 GACCTATTTTCTAATAAAACCGGTATATTTCTACCGGATACATTGTAAATTTACCTATTACATTA
* *
1341599 TAATTATCAGTTTCGATCTTTTTGGGATCGACACTTTTAGA-AAATGTATCGACA
66 TAATTATCGGTTTCGAT-TTTTTGGGATCGATACTTTTA-ATAAATGTATCGACA
1341653 AATATGTTTA
Statistics
Matches: 285, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
198 1 0.00
199 142 0.50
200 140 0.49
201 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
GACCTATTTTCTAATAAAACCGGTATATTTCTACCGGATACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGC
ATCTCATTGGGCATTCATTCTGGAAAAAAGGTATCGACACAAACTTAAAACGTGTCGATACATTA
TGTA
Found at i:1341940 original size:21 final size:21
Alignment explanation
Indices: 1341902--1341941 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1341892 TAAAAATTAC
* *
1341902 CTAAAACATTATTATTTTTAT
1 CTAAAACATCAATATTTTTAT
*
1341923 CTAAAACATCAATGTTTTT
1 CTAAAACATCAATATTTTT
1341942 TAACATTTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (21 bp):
CTAAAACATCAATATTTTTAT
Found at i:1342213 original size:125 final size:125
Alignment explanation
Indices: 1341986--1342245 Score: 340
Period size: 125 Copynumber: 2.1 Consensus size: 125
1341976 ACAGTTAAAA
* * * * * * *
1341986 AATAACAAAACCGGTAGCGCTTTTACCGGTTTTGTTAAGAAACCGGGTAATATGCCAAAATAATA
1 AATAACAAAACCGGCAGCGCTTTTACCGGTTTTATTAAAAAACCCGATAAAATACCAAAATAATA
* ** * * * *
1342051 ATAAAACCGGTAGAAATAATGATGTTTTCGATAATTTTTACCTGTTTTATTGTGCACAAC
66 ACAAAACCAATAAAAATAATAATATTTTCGATAATTTTTACCAGTTTTATTGTGCACAAC
* *
1342111 AATAACAAAACCGGCAGCGCTTTTATCGGTTTTATTAAAAAACCCGATAAAATACCAAAATATTA
1 AATAACAAAACCGGCAGCGCTTTTACCGGTTTTATTAAAAAACCCGATAAAATACCAAAATAATA
* * * *
1342176 ACAAAATCAATAAAAATAATAATATTTTCGGTCATTTTTACCAGTTTTATTGTGTACAAC
66 ACAAAACCAATAAAAATAATAATATTTTCGATAATTTTTACCAGTTTTATTGTGCACAAC
1342236 AATAACAAAA
1 AATAACAAAA
1342246 TCAGAACCGT
Statistics
Matches: 115, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
125 115 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (125 bp):
AATAACAAAACCGGCAGCGCTTTTACCGGTTTTATTAAAAAACCCGATAAAATACCAAAATAATA
ACAAAACCAATAAAAATAATAATATTTTCGATAATTTTTACCAGTTTTATTGTGCACAAC
Found at i:1347415 original size:68 final size:66
Alignment explanation
Indices: 1347336--1347468 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 66
1347326 TTGATAAATA
* *
1347336 AAAAATTAATATCTGTAAACAAAC-AGTCTAAAAATAATAATAAAATAAAATAAAACTTCTAATG
1 AAAAATGAATATCTGTAAACAAACGA-TCTAAAAATAATAAT-AAA-AAAATAAAACTTATAATG
1347400 TAAT
63 TAAT
* *
1347404 AAAAATGAATATCTTTAAATAAACGATCTAAAAATAATAATAAAAAAATAAAACTTATAATGTAA
1 AAAAATGAATATCTGTAAACAAACGATCTAAAAATAATAATAAAAAAATAAAACTTATAATGTAA
1347469 ACACCTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 20 0.33
67 3 0.05
68 36 0.60
69 1 0.02
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.28
Consensus pattern (66 bp):
AAAAATGAATATCTGTAAACAAACGATCTAAAAATAATAATAAAAAAATAAAACTTATAATGTAA
T
Found at i:1347775 original size:14 final size:12
Alignment explanation
Indices: 1347753--1347794 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
1347743 AATATTAATA
1347753 TTTTAAAATATT
1 TTTTAAAATATT
1347765 TTTGATAAAATATT
1 TTT--TAAAATATT
*
1347779 ATTTAAAATATT
1 TTTTAAAATATT
1347791 TTTT
1 TTTT
1347795 TTATCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTTAAAATATT
Found at i:1351620 original size:10 final size:10
Alignment explanation
Indices: 1351581--1351620 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1351571 TTCATCATAC
1351581 CAAATTCTCT
1 CAAATTCTCT
*
1351591 CAATTTCTCT
1 CAAATTCTCT
*
1351601 CAACTTCTCT
1 CAAATTCTCT
*
1351611 CAAATACTCT
1 CAAATTCTCT
1351621 TTATTATCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1351678 original size:9 final size:9
Alignment explanation
Indices: 1351666--1351699 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1351656 TAATATTTTG
1351666 TATTTAATT
1 TATTTAATT
*
1351675 TATTTAA-G
1 TATTTAATT
1351683 TATTTAATT
1 TATTTAATT
1351692 TATTTAAT
1 TATTTAAT
1351700 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1351705 original size:17 final size:17
Alignment explanation
Indices: 1351665--1351703 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1351655 TTAATATTTT
1351665 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1351682 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1351699 -TATTT
1 GTATTT
1351704 TACTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1353759 original size:3 final size:3
Alignment explanation
Indices: 1353751--1353782 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1353741 AGCTACTCAG
*
1353751 GAC GAC GAC GAC GAC GAC GAC GAC GAT GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1353783 TTATGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.34, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:1359300 original size:17 final size:18
Alignment explanation
Indices: 1359274--1359318 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1359264 TATGAAATTT
*
1359274 GATTCAAATTCC-TGACA
1 GATTCAAATTCCTTCACA
*
1359291 GATTCCAATTCCTTCACA
1 GATTCAAATTCCTTCACA
*
1359309 GATTCTAATT
1 GATTCAAATT
1359319 TACTCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCAAATTCCTTCACA
Found at i:1365215 original size:22 final size:21
Alignment explanation
Indices: 1365187--1365252 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
1365177 ATTATATGGT
*
1365187 ATGAACAGTATCGTGAACATTA
1 ATGAACAGTA-CGTGAACAGTA
* *
1365209 ATGAACAATACTGTAAACAGTA
1 ATGAACAGTAC-GTGAACAGTA
1365231 ATGAACAGTACCGTGAACAGTA
1 ATGAACAGTA-CGTGAACAGTA
1365253 CCGACTACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (21 bp):
ATGAACAGTACGTGAACAGTA
Found at i:1365311 original size:21 final size:21
Alignment explanation
Indices: 1365286--1365328 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1365276 TGCTATAGGG
*
1365286 GTATCGATACCTTGCTACAGT
1 GTATCGATACCCTGCTACAGT
1365307 GTATCGATACCCTGCTACAGT
1 GTATCGATACCCTGCTACAGT
1365328 G
1 G
1365329 ATTTCGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (21 bp):
GTATCGATACCCTGCTACAGT
Found at i:1366085 original size:32 final size:32
Alignment explanation
Indices: 1366008--1366104 Score: 144
Period size: 31 Copynumber: 3.1 Consensus size: 32
1365998 GCTCGTATAA
* *
1366008 TAAT-TTGTCCATATGTCCCTAAGAACATAGA
1 TAATCTTGTCCATATGTCCCGAAGAACATAGG
*
1366039 TAAAC-TGTCCATATGTCCCGAAGAACATAGG
1 TAATCTTGTCCATATGTCCCGAAGAACATAGG
*
1366070 TAATCTTGTCCATATGTTCCGAAGAACATAGG
1 TAATCTTGTCCATATGTCCCGAAGAACATAGG
1366102 TAA
1 TAA
1366105 CCCTCGACTC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (32 bp):
TAATCTTGTCCATATGTCCCGAAGAACATAGG
Found at i:1370289 original size:18 final size:18
Alignment explanation
Indices: 1370257--1370293 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1370247 TATCACAAAT
1370257 ATTATAATAATTTAATCA
1 ATTATAATAATTTAATCA
1370275 ATTA-AATAATATTAATCA
1 ATTATAATAAT-TTAATCA
1370293 A
1 A
1370294 CGTAGAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAATAATTTAATCA
Found at i:1375826 original size:21 final size:22
Alignment explanation
Indices: 1375787--1375844 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
1375777 AAAGAATAAA
1375787 TAAATTGAATTT-T-ATTAATT
1 TAAATTGAATTTATAATTAATT
1375807 T-AATTGAATTTATAATTAATT
1 TAAATTGAATTTATAATTAATT
*
1375828 TAAATT-ACTTTATAATT
1 TAAATTGAATTTATAATT
1375845 TAAAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 18 0.53
22 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (22 bp):
TAAATTGAATTTATAATTAATT
Found at i:1375829 original size:11 final size:11
Alignment explanation
Indices: 1375807--1375844 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1375797 TTTATTAATT
1375807 TAATTGAATTTA
1 TAATT-AATTTA
1375819 TAATTAATTTA
1 TAATTAATTTA
*
1375830 -AATTACTTTA
1 TAATTAATTTA
1375840 TAATT
1 TAATT
1375845 TAAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 10 0.42
12 5 0.21
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATTAATTTA
Found at i:1375901 original size:22 final size:22
Alignment explanation
Indices: 1375876--1375920 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1375866 AAAATTTTGA
*
1375876 TTAT-AATATGATTTTTAAAAAT
1 TTATCAAT-TGATATTTAAAAAT
*
1375898 TTATCACTTGATATTTAAAAAT
1 TTATCAATTGATATTTAAAAAT
1375920 T
1 T
1375921 CTAAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TTATCAATTGATATTTAAAAAT
Found at i:1381890 original size:16 final size:16
Alignment explanation
Indices: 1381863--1381902 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1381853 AAAAAAAGCG
1381863 AAGATAAATAAATAAAT
1 AAGAT-AATAAATAAAT
*
1381880 AAGATAATAAATTAAT
1 AAGATAATAAATAAAT
*
1381896 AAAATAA
1 AAGATAA
1381903 AAACAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAGATAATAAATAAAT
Found at i:1382154 original size:23 final size:22
Alignment explanation
Indices: 1382110--1382156 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1382100 CCGAAAATAG
*
1382110 AAAAAGGGATACGAATTTAAAA
1 AAAAAAGGATACGAATTTAAAA
*
1382132 AAAAAAGGATAC-AGATTTGAAA
1 AAAAAAGGATACGA-ATTTAAAA
1382154 AAA
1 AAA
1382157 GGATAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAAAAGGATACGAATTTAAAA
Found at i:1382169 original size:19 final size:19
Alignment explanation
Indices: 1382132--1382169 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1382122 GAATTTAAAA
*
1382132 AAAAAAGGATACAGATTTG
1 AAAAAAGGATAAAGATTTG
*
1382151 AAAAAAGGATAAAGGTTTG
1 AAAAAAGGATAAAGATTTG
1382170 GTCAGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (19 bp):
AAAAAAGGATAAAGATTTG
Found at i:1382446 original size:25 final size:25
Alignment explanation
Indices: 1382418--1382465 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1382408 AACGTATATA
1382418 AAAAGAATAGA-AATATAAATAAAAG
1 AAAAGAATA-ATAATATAAATAAAAG
*
1382443 AAAATAATAATAATATAAATAAA
1 AAAAGAATAATAATATAAATAAA
1382466 TAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAAGAATAATAATATAAATAAAAG
Found at i:1382462 original size:15 final size:15
Alignment explanation
Indices: 1382432--1382504 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 15
1382422 GAATAGAAAT
*
1382432 ATAAATAAAAGA-AA
1 ATAAATAAAATATAA
1382446 AT-AATAATAATATAA
1 ATAAATAA-AATATAA
1382461 ATAAATAAAATATTAA
1 ATAAATAAAATA-TAA
* *
1382477 GAAAAATATACATATAA
1 -ATAAATA-AAATATAA
1382494 ATAAAATAAAA
1 AT-AAATAAAA
1382505 CAAATAGATG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 8 0.17
16 11 0.23
17 14 0.30
18 4 0.09
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAATAAAATATAA
Found at i:1383924 original size:20 final size:20
Alignment explanation
Indices: 1383901--1383942 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1383891 GAATCCTTCG
1383901 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
1383921 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
1383941 TC
1 TC
1383943 AGAGTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGTGAAGTTGAAATCGAAC
Found at i:1384214 original size:193 final size:193
Alignment explanation
Indices: 1383987--1384878 Score: 1381
Period size: 193 Copynumber: 4.6 Consensus size: 193
1383977 GCCAAAGATA
* *
1383987 CTTCGTTGTGAAGCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGACGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1384052 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAT
* ** * *
1384117 AAGTTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATC
131 TAGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATC
1384180 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1384245 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTT
66 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAT
** * *
1384310 TAGTTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATC
131 TAGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATC
*
1384373 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * *
1384438 TGAACTTGCATTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGG----GAAATTGTT
66 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAT
* * **
1384499 TA-TTGACAACCAGCGGTCCCTTTGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
131 TAGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATC
1384561 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 CTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
1384626 AAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAAT
62 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
* **
1384687 T-ATTGGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
127 TGATTAGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTGGAGTCCAATA
1384751 TC
192 TC
* *
1384753 CTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGTCTCTTCGTCGTG
1 CTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
1384818 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTATGAAGTTGAAATTGGCTCTG
62 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1384879 GGTAAAACCT
Statistics
Matches: 661, Mismatches: 29, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
188 75 0.11
189 11 0.02
191 2 0.00
192 270 0.41
193 302 0.46
196 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (193 bp):
CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAT
TAGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATC
Found at i:1384260 original size:94 final size:94
Alignment explanation
Indices: 1383987--1384873 Score: 1342
Period size: 94 Copynumber: 9.2 Consensus size: 94
1383977 GCCAAAGATA
* *
1383987 CTTCGTTGTGAAGCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGACGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1384052 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
*** **
1384081 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGACAGTCAGCGGTCCCTTCGTCGT
1 CTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTA-TTGACAACCAGCGGTCCCTTCGTCGT
*** *
1384146 GAAGTTGAACTTGTACTGTCTTGAGTCCAATATC
61 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
1384180 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1384245 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
**
1384274 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTAGTTGACAGTCAGCGGTCCCTTCGTCGT
1 CTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTA-TTGACAACCAGCGGTCCCTTCGTCGT
*** *
1384339 GAAGTTGAACTTGTACTGTCTTGAGTCCAATATC
61 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
*
1384373 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1384438 TGAACTTGCATTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
* * *
1384467 CTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTTGTCGTAAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1384532 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
1384561 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 CTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
1384626 AAGTTGAACTTGCGTTGTCTTGAGTCCAATATC
62 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* **
1384659 CTTCGTTGTGAAGTTGAAATTGGGAAATTATTGGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1384724 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
* *
1384753 CTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGTCTCTTCGTCGTG
1 CTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1384818 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
62 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* *
1384851 CTTCATTATGAAGTTGAAATTGG
1 CTTCGTTGTGAAGTTGAAATTGG
1384874 CTCTGGGTAA
Statistics
Matches: 724, Mismatches: 51, Indels: 32
0.90 0.06 0.04
Matches are distributed among these distances:
94 353 0.49
95 19 0.03
98 199 0.27
99 153 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (94 bp):
CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATC
Found at i:1384676 original size:43 final size:43
Alignment explanation
Indices: 1384615--1384770 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
1384605 ACCAGCGGTC
1384615 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
* * * * * ** ***
1384658 CCTTCGTTGTGAAGTTGAAATTGGGAAATTATTGGTTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TT-GT-CTTGA-GTCCA-ATAT
*
1384708 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
* *
1384752 CCTTCATTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
1384771 ATTGGCTCTG
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 39 0.48
44 1 0.01
45 3 0.04
46 5 0.06
47 2 0.02
48 6 0.07
49 3 0.04
50 1 0.01
51 22 0.27
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
Found at i:1385710 original size:12 final size:11
Alignment explanation
Indices: 1385689--1385717 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1385679 ACCCTAAACA
1385689 TTTTTCTTTTT
1 TTTTTCTTTTT
1385700 TTTTTCTTTTT
1 TTTTTCTTTTT
1385711 TTTTTCT
1 TTTTTCT
1385718 ACTTAGGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1385730 original size:64 final size:65
Alignment explanation
Indices: 1385626--1385749 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 65
1385616 TTTTCCTTCA
* *
1385626 TTTCGTTTGTTTTTCTATTTTTTTTTCAATTTAGAGCGCCCTTTCGGGTTTTCACCCTAAACATT
1 TTTCGTTTGTTTTTCTATTTTTTTTTCAACTTAGAGCGCCCTCTCGGGTTTTCACCCTAAACATT
* * * *
1385691 TTTCTTTTTTTTTTCT-TTTTTTTTTCTACTTAG-GACGCCCTCTCGGGTTTTCATCCTAA
1 TTTCGTTTGTTTTTCTATTTTTTTTTCAACTTAGAG-CGCCCTCTCGGGTTTTCACCCTAA
1385750 GCGAAATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.02
64 37 0.71
65 14 0.27
ACGTcount: A:0.13, C:0.21, G:0.11, T:0.55
Consensus pattern (65 bp):
TTTCGTTTGTTTTTCTATTTTTTTTTCAACTTAGAGCGCCCTCTCGGGTTTTCACCCTAAACATT
Found at i:1385763 original size:64 final size:65
Alignment explanation
Indices: 1385635--1385763 Score: 147
Period size: 64 Copynumber: 2.0 Consensus size: 65
1385625 ATTTCGTTTG
* * ** *
1385635 TTTTTCTATTTTTTTTTCAATTTAGAGCGCCCTTTCGGGTTTTCACCCTAAACATTTTTCTTTTT
1 TTTTTCTATTTTTTTTTCAACTTAGAGCGCCCTCTCGGGTTTTCACCCTAAACAAATATCTTTTT
* * *
1385700 TTTTTCT-TTTTTTTTTCTACTTAG-GACGCCCTCTCGGGTTTTCATCCTAAGCGAAATAT-TTT
1 TTTTTCTATTTTTTTTTCAACTTAGAG-CGCCCTCTCGGGTTTTCACCCTAAAC-AAATATCTTT
1385762 TT
64 TT
1385764 GACTGCGTCC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
63 1 0.02
64 43 0.80
65 10 0.19
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (65 bp):
TTTTTCTATTTTTTTTTCAACTTAGAGCGCCCTCTCGGGTTTTCACCCTAAACAAATATCTTTTT
Found at i:1392312 original size:20 final size:21
Alignment explanation
Indices: 1392279--1392319 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1392269 TGATCTTCTA
*
1392279 ATATTTTTATCTTT-TCTTCC
1 ATATTTTTAGCTTTATCTTCC
*
1392299 ATATTTTTGGCTTTATCTTCC
1 ATATTTTTAGCTTTATCTTCC
1392320 TCATCAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.61
Consensus pattern (21 bp):
ATATTTTTAGCTTTATCTTCC
Found at i:1395147 original size:11 final size:10
Alignment explanation
Indices: 1395119--1395153 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1395109 AAGGTTAGTA
*
1395119 AAATAGAAAT
1 AAATAAAAAT
1395129 AAATAAAAAT
1 AAATAAAAAT
1395139 AAATAAAAAAT
1 AAAT-AAAAAT
1395150 AAAT
1 AAAT
1395154 GGTAAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1396169 original size:16 final size:16
Alignment explanation
Indices: 1396142--1396181 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1396132 AAAAAAAGCG
1396142 AAGATAAATAAATAAAT
1 AAGAT-AATAAATAAAT
*
1396159 AAGATAATAAATTAAT
1 AAGATAATAAATAAAT
*
1396175 AAAATAA
1 AAGATAA
1396182 AAACAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAGATAATAAATAAAT
Found at i:1396284 original size:26 final size:22
Alignment explanation
Indices: 1396238--1396292 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 22
1396228 AAGCGAAAGT
1396238 AAAAAAAATATAAATACAAATA
1 AAAAAAAATATAAATACAAATA
1396260 CAGAAAAAAATGGATAGAATA-AAATA
1 -A-AAAAAAAT--ATA-AATACAAATA
1396286 AAAAAAA
1 AAAAAAA
1396293 TAGTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
23 1 0.04
24 14 0.50
25 1 0.04
26 8 0.29
27 4 0.14
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.15
Consensus pattern (22 bp):
AAAAAAAATATAAATACAAATA
Found at i:1396444 original size:6 final size:5
Alignment explanation
Indices: 1396425--1396511 Score: 54
Period size: 5 Copynumber: 16.4 Consensus size: 5
1396415 ATATAAAAAG
* *
1396425 AATAGA AATAA AATATA AATAA AAGAA AATAA TAATAA TAT-A AAT-A
1 AATA-A AATAA AATA-A AATAA AATAA AATAA -AATAA AATAA AATAA
*
1396471 AATAA AATATTA AGA-AA AATATA CATATA AATAA AATAA AA
1 AATAA AATA--A A-ATAA AATA-A AATA-A AATAA AATAA AA
1396512 CAAATAGATG
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
4 8 0.12
5 32 0.48
6 23 0.34
7 3 0.04
8 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:1396471 original size:15 final size:15
Alignment explanation
Indices: 1396415--1396511 Score: 63
Period size: 17 Copynumber: 6.1 Consensus size: 15
1396405 ATATTAACGT
*
1396415 ATATAAAAAGAATAGAA
1 ATATAAATA-AATA-AA
*
1396432 ATAAAATATAAATAAA
1 ATATAA-ATAAATAAA
*
1396448 AGA-AAAT-AATAATA
1 ATATAAATAAATAA-A
1396462 ATATAAATAAATAAA
1 ATATAAATAAATAAA
* *
1396477 ATATTAAGAAAAATATAC
1 ATA-TAA-ATAAATA-AA
1396495 ATATAAATAAAATAAA
1 ATATAAAT-AAATAAA
1396511 A
1 A
1396512 CAAATAGATG
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
13 5 0.08
14 5 0.08
15 10 0.16
16 15 0.23
17 23 0.36
18 6 0.09
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (15 bp):
ATATAAATAAATAAA
Found at i:1400671 original size:2 final size:2
Alignment explanation
Indices: 1400664--1400695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1400654 CATGAGAAGA
1400664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1400696 TATGTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1402526 original size:39 final size:39
Alignment explanation
Indices: 1402482--1402621 Score: 201
Period size: 39 Copynumber: 3.6 Consensus size: 39
1402472 TTTGAATGGA
* * *
1402482 GTACTAAAATGAAATAAAAACTAGAGTTTTTAAGGGCGG
1 GTACTAAAATAAAACAAAAACTATAGTTTTTAAGGGCGG
* *
1402521 GTACTAAAATAAAACAAAAACTATAATTTTTAAGGACGG
1 GTACTAAAATAAAACAAAAACTATAGTTTTTAAGGGCGG
*
1402560 GTACTAAAATAAAACAAAAACTATAGTTTTT-AGGGTGGG
1 GTACTAAAATAAAACAAAAACTATAGTTTTTAAGGG-CGG
*
1402599 GTACTAAAATGAAACAAAAACTA
1 GTACTAAAATAAAACAAAAACTA
1402622 AACTTTAAGT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 3 0.03
39 88 0.97
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (39 bp):
GTACTAAAATAAAACAAAAACTATAGTTTTTAAGGGCGG
Found at i:1409082 original size:31 final size:31
Alignment explanation
Indices: 1409040--1409116 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
1409030 AACGGTGGAA
* *
1409040 TGACAATTTTGTTACAAATTGATAACGCTAG
1 TGACAATTTTGTTACAAACTGATAACACTAG
*
1409071 TGACTATTTTGTTACAAACTGATAACACTAG
1 TGACAATTTTGTTACAAACTGATAACACTAG
*
1409102 TGACCATTTTGTTAC
1 TGACAATTTTGTTAC
1409117 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (31 bp):
TGACAATTTTGTTACAAACTGATAACACTAG
Found at i:1409816 original size:25 final size:25
Alignment explanation
Indices: 1409788--1409835 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1409778 GTTAGGAGTG
* *
1409788 AACTTATATAATTTTAGGAGGATAT
1 AACTTATAAAATTATAGGAGGATAT
1409813 AACTTATAAAATTATAGGAGGAT
1 AACTTATAAAATTATAGGAGGAT
1409836 GAAAACATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
AACTTATAAAATTATAGGAGGATAT
Found at i:1410437 original size:3 final size:3
Alignment explanation
Indices: 1410429--1410460 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1410419 AAGTAAATTT
1410429 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1410461 TGTGTTTCGT
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1410693 original size:3 final size:3
Alignment explanation
Indices: 1410685--1410718 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1410675 TAGATTTCGC
1410685 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1410719 ACATAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1411981 original size:74 final size:72
Alignment explanation
Indices: 1411860--1411995 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 72
1411850 GGGCCTACTG
*** * * *
1411860 AATTATCATATTTTTGGGTTTTTTAAATAAAAAATGATGTTTAAAAATATTTTTTTTAATTATTG
1 AATTATCATATTTTAAAGTATTTGAAATAAAAAATGATATTTAAAAATA--TTTTTTAATTATTG
1411925 GGATCACTA
64 GGATCACTA
1411934 AATTATCATATTTTAAAGTATTTGAAATAAAAATAT-ATATTTAAAAATATTTTTTAATTATT
1 AATTATCATATTTTAAAGTATTTGAAATAAAAA-ATGATATTTAAAAATATTTTTTAATTATT
1411996 AAACTTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 13 0.24
74 40 0.73
75 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (72 bp):
AATTATCATATTTTAAAGTATTTGAAATAAAAAATGATATTTAAAAATATTTTTTAATTATTGGG
ATCACTA
Found at i:1415471 original size:20 final size:20
Alignment explanation
Indices: 1415446--1415497 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1415436 ATGCAGGTAG
1415446 AGTATCGATACTATAGGGAT
1 AGTATCGATACTATAGGGAT
1415466 AGTATCGATACTATAGGGAT
1 AGTATCGATACTATAGGGAT
* *
1415486 AATACCGATACT
1 AGTATCGATACT
1415498 TGTTCTTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTATAGGGAT
Found at i:1422524 original size:17 final size:17
Alignment explanation
Indices: 1422502--1422538 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1422492 AATCTTTATC
1422502 ATTCAAATCAAAACATT
1 ATTCAAATCAAAACATT
1422519 ATTCAAATCAAAACATT
1 ATTCAAATCAAAACATT
1422536 ATT
1 ATT
1422539 TTAGTGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTCAAATCAAAACATT
Found at i:1422666 original size:7 final size:6
Alignment explanation
Indices: 1422655--1422684 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1422645 TTAAGTATTA
1422655 AAATTG ACAATTG AAATTG AAATTG AAATT
1 AAATTG A-AATTG AAATTG AAATTG AAATT
1422685 TTAGTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (6 bp):
AAATTG
Found at i:1423278 original size:12 final size:13
Alignment explanation
Indices: 1423261--1423289 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1423251 TAACATGTTG
1423261 CCTTA-CACAAAA
1 CCTTACCACAAAA
1423273 CCTTACCACAAAA
1 CCTTACCACAAAA
1423286 CCTT
1 CCTT
1423290 GGATAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (13 bp):
CCTTACCACAAAA
Found at i:1425116 original size:2 final size:2
Alignment explanation
Indices: 1425111--1425154 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1425101 AACTATTTAA
1425111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1425153 AT
1 AT
1425155 GAAAAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1426168 original size:149 final size:148
Alignment explanation
Indices: 1425899--1426192 Score: 453
Period size: 149 Copynumber: 2.0 Consensus size: 148
1425889 TTCTTTGGGT
*
1425899 TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCTTTGGATTCGAGTTTAAAGC
1 TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCCTTGGATTCGAGTTTAAAGC
* * * ** *
1425964 TCTTATTGTTGGTAATTCCGCGTTTTTAGGATTTAATTACTGGATTAACTAGTTGAACATCATGT
66 TCTTATGGTCGGTAATTCCACGCATTTAGGATTTAATTACTGGATTAACTAGTTGAACATAATGT
1426029 ATTTGTTGATTGATACTG
131 ATTTGTTGATTGATACTG
* * * *
1426047 TTTTTGCTTATTGAAGAACCTGAATTATGTGATGTAAAATTTGCCCTTGGATTCGAGCTTTAAAG
1 TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCCTTGGATTCGAG-TTTAAAG
* * *
1426112 CTCTTATGGTCGGTAATTCCACGCATTTAGGATTTCATTACTGGGTTAACTGGTTGAACATAATG
65 CTCTTATGGTCGGTAATTCCACGCATTTAGGATTTAATTACTGGATTAACTAGTTGAACATAATG
1426177 TATTTGTTGATTGATA
130 TATTTGTTGATTGATA
1426193 TATTACTCTT
Statistics
Matches: 131, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
148 52 0.40
149 79 0.60
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (148 bp):
TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCCTTGGATTCGAGTTTAAAGC
TCTTATGGTCGGTAATTCCACGCATTTAGGATTTAATTACTGGATTAACTAGTTGAACATAATGT
ATTTGTTGATTGATACTG
Found at i:1428315 original size:60 final size:60
Alignment explanation
Indices: 1428251--1428401 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 60
1428241 TGGCAACATA
* * * *
1428251 CATCCCCAAACTATGACTTTTATTCTAAATTGGTCC-CTAAACATTTGAACATTTCAATTT
1 CATCCCCAAACTATGACTCTTATTCTAAATTGGTCCAC-AAACATTTGAACATTCCAAATC
** * * *
1428311 CATCCCTC-AACTATGACTCCCATTCTAAATTGGTCCACAAGCTTTTTAACATTCCAAATC
1 CATCCC-CAAACTATGACTCTTATTCTAAATTGGTCCACAAACATTTGAACATTCCAAATC
* *
1428371 CATCCTCAAACTATGACCCTTATTCTAAATT
1 CATCCCCAAACTATGACTCTTATTCTAAATT
1428402 AGCCCCAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 1 0.01
60 72 0.96
61 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (60 bp):
CATCCCCAAACTATGACTCTTATTCTAAATTGGTCCACAAACATTTGAACATTCCAAATC
Found at i:1428416 original size:60 final size:59
Alignment explanation
Indices: 1428251--1428427 Score: 151
Period size: 60 Copynumber: 2.9 Consensus size: 59
1428241 TGGCAACATA
* ** * * * * * *
1428251 CATCCCCAAACTATGACTTTTATTCTAAATTGGTCCCTAAACATTTGAACATTTCAATTT
1 CATCCTCAAACTATGACCCTTATTCTAAATT-GCCCCAAAACTTTTGAACATTCCAAATC
* ** * *
1428311 CATCCCTC-AACTATGACTCC-CATTCTAAATTGGTCCACAAGCTTTTTAACATTCCAAATC
1 CAT-CCTCAAACTATGAC-CCTTATTCTAAATTGCCCCA-AAACTTTTGAACATTCCAAATC
* *
1428371 CATCCTCAAACTATGACCCTTATTCTAAATTAGCCCCAAAACTTTTGATCACTCCAA
1 CATCCTCAAACTATGACCCTTATTCTAAATT-GCCCCAAAACTTTTGAACATTCCAA
1428428 TAATATCCCT
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
59 9 0.10
60 75 0.82
61 7 0.08
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (59 bp):
CATCCTCAAACTATGACCCTTATTCTAAATTGCCCCAAAACTTTTGAACATTCCAAATC
Found at i:1429011 original size:3 final size:3
Alignment explanation
Indices: 1429003--1429028 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1428993 TGACAAAAAA
1429003 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1429029 ATTACCGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1429257 original size:13 final size:14
Alignment explanation
Indices: 1429228--1429257 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1429218 TGGATTTGCC
1429228 AAAATGACCAACAA
1 AAAATGACCAACAA
1429242 AAAATGACCAACAA
1 AAAATGACCAACAA
1429256 AA
1 AA
1429258 CCGCAATGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAATGACCAACAA
Found at i:1429390 original size:21 final size:21
Alignment explanation
Indices: 1429312--1429432 Score: 65
Period size: 21 Copynumber: 5.9 Consensus size: 21
1429302 AATCAGTTCC
*
1429312 CAGAATTGCAACGCGATTATGA
1 CAGAATCGCAACGCGATTAT-A
*
1429334 -AGAATCGCAATGCGA-TAGTA
1 CAGAATCGCAACGCGATTA-TA
** * *
1429354 CA-AATTCGCATTGCGATTTTT
1 CAGAA-TCGCAACGCGATTATA
*
1429375 CAGAATCGCAACGCGAATATGA
1 CAGAATCGCAACGCGATTAT-A
**
1429397 -A-AATCGCAACGCGAACATA
1 CAGAATCGCAACGCGATTATA
* *
1429416 TA-AATTGCAACGCGATT
1 CAGAATCGCAACGCGATT
1429433 CTGACTATCG
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.01
20 34 0.44
21 40 0.51
22 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
CAGAATCGCAACGCGATTATA
Found at i:1429403 original size:20 final size:20
Alignment explanation
Indices: 1429378--1429430 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1429368 GATTTTTCAG
*
1429378 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
1429398 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
*
1429418 AATTGCAACGCGA
1 AATCGCAACGCGA
1429431 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:1429484 original size:41 final size:40
Alignment explanation
Indices: 1429439--1429588 Score: 176
Period size: 41 Copynumber: 3.7 Consensus size: 40
1429429 GATTCTGACT
* * * *
1429439 ATCGCAACGAGTATCCGTAAAATCACAACGTGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCACAACGAGAATACGTAA
*
1429480 ATCGCAACGCGTATCTGTAAATCACAACGAGAATACGT-A
1 ATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAA
* * * *
1429519 ATCACAATGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCACAACGAGAATACGT-AA
* *
1429560 ATCGCAATGCGTATCCGTAAATCGCAACG
1 ATCGCAACGCGTATCCGTAAATCACAACG
1429589 CGATTTTTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 34 0.35
40 17 0.18
41 45 0.47
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAA
Found at i:1429487 original size:20 final size:20
Alignment explanation
Indices: 1429439--1429588 Score: 140
Period size: 20 Copynumber: 7.5 Consensus size: 20
1429429 GATTCTGACT
1429439 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
1429460 ATCACAACGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1429480 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
1429500 ATCACAACGAGAATACGT-A
1 ATCGCAACGAGTATCCGTAA
* * *
1429519 ATCACAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
1429539 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
1429560 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
1429580 ATCGCAACG
1 ATCGCAACG
1429589 CGATTTTTAA
Statistics
Matches: 101, Mismatches: 26, Indels: 5
0.77 0.20 0.04
Matches are distributed among these distances:
19 15 0.15
20 55 0.54
21 31 0.31
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:1429523 original size:19 final size:19
Alignment explanation
Indices: 1429499--1429558 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1429489 CGTATCTGTA
1429499 AATCACAACGAGAATACGT
1 AATCACAACGAGAATACGT
* * * *
1429518 AATCACAATGCGTATCCGT
1 AATCACAACGAGAATACGT
* *
1429537 AAATCGCAACGACAATACGT
1 -AATCACAACGAGAATACGT
1429557 AA
1 AA
1429559 AATCGCAATG
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.18
Consensus pattern (19 bp):
AATCACAACGAGAATACGT
Found at i:1430174 original size:20 final size:20
Alignment explanation
Indices: 1430149--1430218 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1430139 TTCTAAACTT
*
1430149 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
1430169 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * * *
1430189 ACTATCTCAACGCG-AAATA
1 AAAATCGCAACACGAAAATG
1430208 AAAATCGCAAC
1 AAAATCGCAAC
1430219 GAGATAATTG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Done.