Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 167 of 310
Found at i:54786450 original size:16 final size:18
Alignment explanation
Indices: 54786419--54786451 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54786409 AACTCGTCAC
54786419 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
54786437 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
54786452 AATTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:54793713 original size:26 final size:26
Alignment explanation
Indices: 54793682--54793733 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
54793672 TGTGAAGTTA
54793682 TGTGAAAATATTTGATTTACTTATGT
1 TGTGAAAATATTTGATTTACTTATGT
*
54793708 TGTGAAAATATTTTATTTACTTATGT
1 TGTGAAAATATTTGATTTACTTATGT
54793734 ATATGAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (26 bp):
TGTGAAAATATTTGATTTACTTATGT
Found at i:54794017 original size:16 final size:18
Alignment explanation
Indices: 54793986--54794018 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54793976 AACTCGTCAC
54793986 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
54794004 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
54794019 AATTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:54806828 original size:12 final size:12
Alignment explanation
Indices: 54806690--54806832 Score: 58
Period size: 12 Copynumber: 11.3 Consensus size: 12
54806680 TAATTCTGTT
54806690 ATTTATTTATTC
1 ATTTATTTATTC
* * * *
54806702 ATCTACTTGTTT
1 ATTTATTTATTC
54806714 ATTTATTCCTTATTCC
1 ATTTA-T--TTATT-C
54806730 ATTTACTTTATTC
1 ATTTA-TTTATTC
* *
54806743 ATTTATCTGTTC
1 ATTTATTTATTC
* * *
54806755 ATTTACTCATTT
1 ATTTATTTATTC
54806767 ATTTATAAATTATTC
1 ATTTAT---TTATTC
*
54806782 ATTTATTTATTT
1 ATTTATTTATTC
54806794 ATTT-TTGT-TTC
1 ATTTATT-TATTC
* **
54806805 AATCCTTGTATTC
1 ATTTATT-TATTC
54806818 ATTTATTTATT-
1 ATTTATTTATTC
54806829 ATTT
1 ATTT
54806833 CGACATTTTT
Statistics
Matches: 95, Mismatches: 26, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
11 10 0.11
12 47 0.49
13 13 0.14
14 5 0.05
15 14 0.15
16 6 0.06
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.62
Consensus pattern (12 bp):
ATTTATTTATTC
Found at i:54807134 original size:15 final size:16
Alignment explanation
Indices: 54807114--54807156 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
54807104 GCATCTAGCA
54807114 TTTTTATTTTTCA-TT
1 TTTTTATTTTTCATTT
*
54807129 TTTTTATTTTTTATTT
1 TTTTTATTTTTCATTT
54807145 TTATTTATTTTT
1 TT-TTTATTTTT
54807157 ATTACTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 4 0.16
17 9 0.36
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTATTTTTCATTT
Found at i:54807141 original size:22 final size:22
Alignment explanation
Indices: 54807114--54807173 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
54807104 GCATCTAGCA
54807114 TTTTTATTTTTCATTT-TTTTAT
1 TTTTTATTTTT-ATTTATTTTAT
54807136 TTTTTATTTTTATTTATTTTTAT
1 TTTTTATTTTTATTTA-TTTTAT
* *
54807159 TACTTTATTTATATT
1 T-TTTTATTTTTATT
54807174 ATACCATGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 4 0.12
22 11 0.33
23 7 0.21
24 11 0.33
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTATTTTTATTTATTTTAT
Found at i:54807157 original size:10 final size:10
Alignment explanation
Indices: 54807116--54807159 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
54807106 ATCTAGCATT
54807116 TTTATTTTTCA
1 TTTATTTTT-A
* *
54807127 TTTTTTTATTT
1 TTTATTT-TTA
54807138 TTTATTTTTA
1 TTTATTTTTA
54807148 TTTATTTTTA
1 TTTATTTTTA
54807158 TT
1 TT
54807160 ACTTTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 14 0.50
11 12 0.43
12 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:54807165 original size:14 final size:13
Alignment explanation
Indices: 54807113--54807175 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
54807103 GGCATCTAGC
54807113 ATTTTTATT-TTT
1 ATTTTTATTATTT
54807125 CATTTTT-TTATTT
1 -ATTTTTATTATTT
*
54807138 -TTTATTTTTATTT
1 ATTT-TTATTATTT
54807151 ATTTTTATTACTTT
1 ATTTTTATTA-TTT
*
54807165 ATTTATATTAT
1 ATTTTTATTAT
54807176 ACCATGGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
11 3 0.07
12 4 0.09
13 21 0.49
14 15 0.35
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTATTATTT
Found at i:54807165 original size:18 final size:16
Alignment explanation
Indices: 54807116--54807170 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
54807106 ATCTAGCATT
54807116 TTTATTTTTCA-TTTT-
1 TTTATTTTT-ATTTTTA
54807131 TTTATTTTTTATTTTTA
1 TTTA-TTTTTATTTTTA
54807148 TTTATTTTTATTACTTTA
1 TTTATTTTTATT--TTTA
54807166 TTTAT
1 TTTAT
54807171 ATTATACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.14
16 17 0.49
17 4 0.11
18 9 0.26
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:54809267 original size:20 final size:20
Alignment explanation
Indices: 54809244--54809282 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
54809234 TGAAGGAAGA
54809244 TTATAGAAGAATCATGATTT
1 TTATAGAAGAATCATGATTT
54809264 TTATAGAAGAATCATGATT
1 TTATAGAAGAATCATGATT
54809283 AAAGTTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
TTATAGAAGAATCATGATTT
Found at i:54811436 original size:18 final size:18
Alignment explanation
Indices: 54811413--54811448 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54811403 AGAAAGTATG
54811413 ATTGAGTTATGGAAGAGT
1 ATTGAGTTATGGAAGAGT
54811431 ATTGAGTTATGGAAGAGT
1 ATTGAGTTATGGAAGAGT
54811449 GTCTACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (18 bp):
ATTGAGTTATGGAAGAGT
Found at i:54816679 original size:13 final size:13
Alignment explanation
Indices: 54816654--54816679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54816644 GAAATTGTTT
54816654 TTTGAAAATTTTG
1 TTTGAAAATTTTG
54816667 TTTGAAAATTTTG
1 TTTGAAAATTTTG
54816680 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGAAAATTTTG
Found at i:54818402 original size:13 final size:12
Alignment explanation
Indices: 54818381--54818415 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
54818371 GTCTTTTATC
54818381 TTTATTTATTTTA
1 TTTA-TTATTTTA
54818394 TTTACTTATTTTA
1 TTTA-TTATTTTA
54818407 TTTATTATT
1 TTTATTATT
54818416 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:54818512 original size:22 final size:20
Alignment explanation
Indices: 54818494--54818567 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 20
54818484 TATATTTCTG
54818494 AAAT-TATTTTTCTAAATTTT
1 AAATATATTTTT-TAAATTTT
* *
54818514 AAATGTTATTTTTTAAACTTT
1 AAAT-ATATTTTTTAAATTTT
54818535 AAATATCATTTTTTAAATTTT
1 AAATAT-ATTTTTTAAATTTT
54818556 AAATATATTTTT
1 AAATATATTTTT
54818568 AATAATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.23
21 30 0.62
22 7 0.15
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (20 bp):
AAATATATTTTTTAAATTTT
Found at i:54818670 original size:134 final size:135
Alignment explanation
Indices: 54818527--54818827 Score: 364
Period size: 134 Copynumber: 2.2 Consensus size: 135
54818517 TGTTATTTTT
*
54818527 TAAACTTTAAATATCATTTTTTAAATTTTAAA-TAT-ATTTTTAATAATA-TAAAACATTTAA-A
1 TAAATTTTAAATATCATTTTTTAAATTTTAAATTATGATTTTTAA-AATATTAAAA-ATTTAATA
*
54818588 TATTTTAAAGATATGACCTTTCAAATCTATTA-TTAGTTTTATAATATTTTAAATGTATATTTTA
64 T-TTTTAAAGATATGACCTTTCAAATCTATTATTTA-TTTTATAATATTTTAAATATATATTTTA
54818652 AATATTAAA
127 AATATTAAA
* * * * * * *
54818661 T-ATTTTTTAATTTC-TTTTATAATATTTTAAATTATGATTTTTAAATTATTTAAAATTTATTAT
1 TAAATTTTAAATATCATTTTTTAA-ATTTTAAATTATGATTTTTAAAATATTAAAAATTTAATAT
*
54818724 TTTTAAAGATATGACCTTTCAAATTTATTATTTATTTTATAATATTTTAAATATATATTTTAAAT
65 TTTTAAAGATATGACCTTTCAAATCTATTATTTATTTTATAATATTTTAAATATATATTTTAAAT
***
54818789 ATTTTT
130 ATTAAA
*
54818795 TAAATTTTAAATATAATTTTTATAAATTATTAA
1 TAAATTTTAAATATCATTTTT-TAAATT-TTAA
54818828 TTTTAAAATT
Statistics
Matches: 139, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
132 7 0.05
133 17 0.12
134 75 0.54
135 26 0.19
136 7 0.05
137 7 0.05
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (135 bp):
TAAATTTTAAATATCATTTTTTAAATTTTAAATTATGATTTTTAAAATATTAAAAATTTAATATT
TTTAAAGATATGACCTTTCAAATCTATTATTTATTTTATAATATTTTAAATATATATTTTAAATA
TTAAA
Found at i:54818710 original size:24 final size:24
Alignment explanation
Indices: 54818675--54818730 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
54818665 TTTTAATTTC
*
54818675 TTTTATAATATTTTAAA-TTATGAT
1 TTTTA-AATATTTAAAATTTATGAT
*
54818699 TTTTAAATTATTTAAAATTTATTAT
1 TTTTAAA-TATTTAAAATTTATGAT
54818724 TTTTAAA
1 TTTTAAA
54818731 GATATGACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 13 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTAAATATTTAAAATTTATGAT
Found at i:54818783 original size:13 final size:13
Alignment explanation
Indices: 54818765--54818799 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
54818755 TTATTTTATA
54818765 ATATTTTAAATAT
1 ATATTTTAAATAT
54818778 ATATTTTAAATAT
1 ATATTTTAAATAT
54818791 -T-TTTTAAAT
1 ATATTTTAAAT
54818800 TTTAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:54818829 original size:29 final size:31
Alignment explanation
Indices: 54818759--54818846 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 31
54818749 TATTATTTAT
54818759 TTTA-TAATATTTTAAATATATATTTTAAATA
1 TTTATTAA-ATTTTAAATATATATTTTAAATA
*
54818790 TTTTTTAAATTTTAAATATA-ATTTTTATAA-A
1 TTTATTAAATTTTAAATATATA-TTTTA-AATA
*
54818821 -TTATT-AATTTTAAA-ATTTATTTTAAA
1 TTTATTAAATTTTAAATATATATTTTAAA
54818847 GATATTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
27 2 0.04
28 7 0.14
29 10 0.20
30 5 0.10
31 21 0.42
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTATTAAATTTTAAATATATATTTTAAATA
Found at i:54818938 original size:24 final size:23
Alignment explanation
Indices: 54818911--54818955 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
54818901 TTTGTGGAGA
* *
54818911 AATTTAGAATTAATATTATAAAAC
1 AATTTAAAAATAATATT-TAAAAC
54818935 AATTTAAAAATAATATTTAAA
1 AATTTAAAAATAATATTTAAA
54818956 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
AATTTAAAAATAATATTTAAAAC
Found at i:54818962 original size:20 final size:21
Alignment explanation
Indices: 54818937--54819008 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 21
54818927 TATAAAACAA
54818937 TTTAAAAATAAT-ATTTAAAT
1 TTTAAAAATAATAATTTAAAT
*
54818957 TTTAAAAAAAATAATTTAAA-
1 TTTAAAAATAATAATTTAAAT
*
54818977 TTTAAGAA-AATAATTTAAAT
1 TTTAAAAATAATAATTTAAAT
*
54818997 TTAAAAAATAAT
1 TTTAAAAATAAT
54819009 TTAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 11 0.24
20 24 0.53
21 10 0.22
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
TTTAAAAATAATAATTTAAAT
Found at i:54818963 original size:19 final size:18
Alignment explanation
Indices: 54818935--54819044 Score: 104
Period size: 19 Copynumber: 5.9 Consensus size: 18
54818925 ATTATAAAAC
54818935 AATTT-AAAAATAATATTTA
1 AATTTAAAAAAT-A-ATTTA
54818954 AATTTTAAAAAAAATAATTTA
1 AA-TTT--AAAAAATAATTTA
54818975 AATTTAAGAAAATAATTTA
1 AATTTAA-AAAATAATTTA
54818994 AATTTAAAAAATAATTTA
1 AATTTAAAAAATAATTTA
*
54819012 AA---AAATAAT-ATTTAA
1 AATTTAAAAAATAATTT-A
54819027 AATTTTAAAAAATAATTT
1 AA-TTTAAAAAATAATTT
54819045 CAAAAATATA
Statistics
Matches: 78, Mismatches: 2, Indels: 21
0.77 0.02 0.21
Matches are distributed among these distances:
14 4 0.05
15 9 0.12
18 15 0.19
19 26 0.33
20 10 0.13
21 7 0.09
22 1 0.01
23 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
AATTTAAAAAATAATTTA
Found at i:54818973 original size:34 final size:34
Alignment explanation
Indices: 54818930--54819075 Score: 165
Period size: 34 Copynumber: 4.2 Consensus size: 34
54818920 TTAATATTAT
*
54818930 AAAACAATTT-AAAAATAATATTT-AAATTTTAAAA
1 AAAATAATTTAAAAAATAATATTTAAAATTTT--AA
*
54818964 AAAATAATTTAAATTTAAGAAAATAATTT-AAA-TTTAA
1 AAAATAATTTAAA---AA-ATAAT-ATTTAAAATTTTAA
54819001 AAAATAATTTAAAAAATAATATTTAAAATTTTAA
1 AAAATAATTTAAAAAATAATATTTAAAATTTTAA
*
54819035 AAAATAATTTCAAAAATATATATTTAAAATTTTAA
1 AAAATAATTTAAAAAATA-ATATTTAAAATTTTAA
54819070 AAAATA
1 AAAATA
54819076 TATATTATAA
Statistics
Matches: 99, Mismatches: 4, Indels: 17
0.82 0.03 0.14
Matches are distributed among these distances:
32 4 0.04
33 7 0.07
34 33 0.33
35 24 0.24
37 15 0.15
38 2 0.02
39 7 0.07
40 7 0.07
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (34 bp):
AAAATAATTTAAAAAATAATATTTAAAATTTTAA
Found at i:54819049 original size:21 final size:22
Alignment explanation
Indices: 54819008--54819049 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54818998 TAAAAAATAA
*
54819008 TTTAAAAAATAATATTTAAAAT
1 TTTAAAAAATAATATTCAAAAT
54819030 TTTAAAAAATAAT-TTCAAAA
1 TTTAAAAAATAATATTCAAAA
54819050 ATATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAAAATAATATTCAAAAT
Found at i:54819063 original size:14 final size:12
Alignment explanation
Indices: 54818994--54819063 Score: 74
Period size: 12 Copynumber: 5.8 Consensus size: 12
54818984 AAATAATTTA
54818994 AATTTAAAAAAT
1 AATTTAAAAAAT
54819006 AATTTAAAAAAT
1 AATTTAAAAAAT
*
54819018 AATATT-TAAAAT
1 AAT-TTAAAAAAT
54819030 --TTTAAAAAAT
1 AATTTAAAAAAT
54819040 AATTTCAAAAATAT
1 AATTT-AAAAA-AT
54819054 ATATTTAAAA
1 A-ATTTAAAA
54819064 TTTTAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
9 2 0.04
10 6 0.12
12 23 0.47
13 7 0.14
14 7 0.14
15 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTTAAAAAAT
Found at i:54819076 original size:21 final size:19
Alignment explanation
Indices: 54818935--54819078 Score: 96
Period size: 21 Copynumber: 7.8 Consensus size: 19
54818925 ATTATAAAAC
54818935 AATTT-AAAAATAATATTTA
1 AATTTAAAAAAT-ATATTTA
*
54818954 AATTTTAAAAAAAATAATTTA
1 AA-TTTAAAAAATAT-ATTTA
54818975 AATTTAAGAAAATA-ATTTA
1 AATTTAA-AAAATATATTTA
54818994 AATTTAAAAAATA-ATTTA
1 AATTTAAAAAATATATTTA
* *
54819012 AA---AAATAATAT-TTAA
1 AATTTAAAAAATATATTTA
54819027 AATTTTAAAAAATA-ATTT-
1 AA-TTTAAAAAATATATTTA
* *
54819045 CA---AAAATATATATTTAA
1 AATTTAAAAAATATATTT-A
54819062 AATTTTAAAAAATATAT
1 AA-TTTAAAAAATATAT
54819079 ATTATAAAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
14 7 0.07
15 16 0.16
17 1 0.01
18 14 0.14
19 23 0.23
20 10 0.10
21 27 0.28
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (19 bp):
AATTTAAAAAATATATTTA
Found at i:54824230 original size:11 final size:10
Alignment explanation
Indices: 54824195--54824273 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 10
54824185 GGTATTTTTT
54824195 TAAAGAAATTA
1 TAAA-AAATTA
*
54824206 TAATAAAATAA
1 TAA-AAAATTA
54824217 TAAAAAATTCA
1 TAAAAAATT-A
* *
54824228 TAAAACATTG
1 TAAAAAATTA
*
54824238 TAAAAATTTA
1 TAAAAAATTA
*
54824248 TTTAAAAATATA
1 -TAAAAAAT-TA
*
54824260 TAGAAAATTA
1 TAAAAAATTA
54824270 TAAA
1 TAAA
54824274 CATTAATAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
10 17 0.33
11 32 0.62
12 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:54824232 original size:10 final size:9
Alignment explanation
Indices: 54824200--54824381 Score: 59
Period size: 9 Copynumber: 19.2 Consensus size: 9
54824190 TTTTTTAAAG
54824200 AAATTATAATA
1 AAATTAT-A-A
*
54824211 AAATAATAAA
1 AAATTAT-AA
54824221 AAATTCATAA
1 AAATT-ATAA
*
54824231 AACATTGTAA
1 AA-ATTATAA
54824241 AAATTTATTTAA
1 AAA-TTA--TAA
54824253 AAATATATAGA
1 AAAT-TATA-A
54824264 AAATTATAA
1 AAATTATAA
*
54824273 ACATTAATAA
1 AAATT-ATAA
* *
54824283 AAATGACAA
1 AAATTATAA
*
54824292 ATCATTATAA
1 A-AATTATAA
*
54824302 AAA-TACAA
1 AAATTATAA
* *
54824310 AAGA-AAGAA
1 AA-ATTATAA
*
54824319 AAA-TATTA
1 AAATTATAA
54824327 AAA--ATAA
1 AAATTATAA
*
54824334 AAACTATAA
1 AAATTATAA
*
54824343 AAATTATTA
1 AAATTATAA
* *
54824352 GAATTATTTA
1 AAATTA-TAA
*
54824362 AAATTAAAA
1 AAATTATAA
*
54824371 AAATAATAA
1 AAATTATAA
54824380 AA
1 AA
54824382 CAAATTAAAA
Statistics
Matches: 131, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.05
8 12 0.09
9 43 0.33
10 43 0.33
11 19 0.15
12 8 0.06
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (9 bp):
AAATTATAA
Found at i:54824309 original size:18 final size:20
Alignment explanation
Indices: 54824274--54824310 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
54824264 AAATTATAAA
54824274 CATTAATAAAAATGACAAAT
1 CATTAATAAAAATGACAAAT
54824294 CATT-ATAAAAAT-ACAAA
1 CATTAATAAAAATGACAAA
54824311 AGAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (20 bp):
CATTAATAAAAATGACAAAT
Found at i:54824757 original size:29 final size:28
Alignment explanation
Indices: 54824713--54824814 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 28
54824703 AATTGAAAAT
54824713 ATTTTTATAATTTTTTTGTAATCTTATATA
1 ATTTTTATAA-TTTTTT-TAATCTTATATA
** * *
54824743 ATTTTTATAATTTTTTATTTTTTTAAATA
1 ATTTTTATAATTTTTT-TAATCTTATATA
* * *
54824772 ATATTTATAATTTTTTTCA-CTT-TTTA
1 ATTTTTATAATTTTTTTAATCTTATATA
54824798 TATTTTTATAATTTTTT
1 -ATTTTTATAATTTTTT
54824815 AATAATTGCA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
26 2 0.03
27 17 0.29
28 1 0.02
29 29 0.49
30 10 0.17
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (28 bp):
ATTTTTATAATTTTTTTAATCTTATATA
Found at i:54824803 original size:8 final size:9
Alignment explanation
Indices: 54824713--54824870 Score: 79
Period size: 10 Copynumber: 16.6 Consensus size: 9
54824703 AATTGAAAAT
54824713 ATTTTTATA
1 ATTTTTATA
*
54824722 ATTTTTTTGTA
1 A--TTTTTATA
*
54824733 ATCTTATATA
1 AT-TTTTATA
54824743 ATTTTTATA
1 ATTTTTATA
54824752 ATTTTT-TA
1 ATTTTTATA
*
54824760 TTTTTTTAAATA
1 -ATTTTT--ATA
*
54824772 ATATTTATA
1 ATTTTTATA
*
54824781 ATTTTTTTCA
1 ATTTTTAT-A
*
54824791 CTTTTTAT-
1 ATTTTTATA
54824799 ATTTTTATA
1 ATTTTTATA
54824808 ATTTTTTAATA
1 A-TTTTT-ATA
***
54824819 ATTGCAAT-
1 ATTTTTATA
* *
54824827 GTTTTTTTA
1 ATTTTTATA
54824836 ATCTTTTATGA
1 AT-TTTTAT-A
*
54824847 AATTTTATAA
1 ATTTTTAT-A
54824857 ATTTTTATA
1 ATTTTTATA
54824866 ATTTT
1 ATTTT
54824871 GTAATGATAT
Statistics
Matches: 110, Mismatches: 25, Indels: 28
0.67 0.15 0.17
Matches are distributed among these distances:
8 12 0.11
9 38 0.35
10 40 0.36
11 18 0.16
12 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:54826552 original size:29 final size:27
Alignment explanation
Indices: 54826491--54826544 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
54826481 TTCGCTATTT
* *
54826491 AAAACTACATTGGTGAATATTGTAAAA
1 AAAACTACAATGGTGAACATTGTAAAA
54826518 AAAACTACAATGGTGAAGCCATTGTAA
1 AAAACTACAATGGTGAA--CATTGTAA
54826545 GAATAACTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
29 7 0.30
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (27 bp):
AAAACTACAATGGTGAACATTGTAAAA
Found at i:54832931 original size:19 final size:19
Alignment explanation
Indices: 54832885--54832932 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
54832875 GTATATATTT
54832885 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
54832903 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
54832922 TAAGTTTTATT
1 TAAATTTTATT
54832933 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:54832999 original size:43 final size:43
Alignment explanation
Indices: 54832952--54833036 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
54832942 GAAATTTTTA
54832952 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
1 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
* *
54832995 TTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTC
1 TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTC
54833037 CCAATTAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.49
Consensus pattern (43 bp):
TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAACTATTTTCT
Found at i:54837668 original size:19 final size:19
Alignment explanation
Indices: 54837622--54837669 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
54837612 GTATATATTT
54837622 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
54837640 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
54837659 TAAGTTTTATT
1 TAAATTTTATT
54837670 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:54837736 original size:43 final size:43
Alignment explanation
Indices: 54837689--54837773 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
54837679 GAAATTTTTA
*
54837689 TTTTATCTTTTAGTAGTTTACTAAAATAAGGGAATTATTTTCT
1 TTTTATCTTTTAGTAGTTTACTAAAATAAGGGAACTATTTTCT
* * *
54837732 TTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTC
1 TTTTATCTTTTAGTAGTTTACTAAAATAAGGGAACTATTTTC
54837774 CCAATTAGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (43 bp):
TTTTATCTTTTAGTAGTTTACTAAAATAAGGGAACTATTTTCT
Found at i:54839550 original size:12 final size:13
Alignment explanation
Indices: 54839528--54839559 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54839518 GCTGTTTGCA
54839528 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
54839541 TTTC-TTTCTTTC
1 TTTCTTTTCTTTC
54839553 TTT-TTTT
1 TTTCTTTT
54839560 TAAATTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:54845402 original size:12 final size:11
Alignment explanation
Indices: 54845378--54845407 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
54845368 CATTTTGTTC
54845378 TTTAGTTTCTTT
1 TTTA-TTTCTTT
54845390 TTTATTTCTTT
1 TTTATTTCTTT
54845401 TTTATTT
1 TTTATTT
54845408 TTGTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:54848805 original size:17 final size:16
Alignment explanation
Indices: 54848777--54848819 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
54848767 AAAAGTTTAA
* *
54848777 TTTAATTAAATTCATT
1 TTTAATTTAATTCAAT
*
54848793 TTATAATTTAATTTAAT
1 TT-TAATTTAATTCAAT
54848810 TTTAATTTAA
1 TTTAATTTAA
54848820 AAGTATCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATTTAATTCAAT
Found at i:54850127 original size:27 final size:28
Alignment explanation
Indices: 54850097--54850158 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
54850087 AAATAATTTT
*
54850097 TAAAATTCA-AAATATTTATAAAAATTC-
1 TAAAATTCATAAAT-TTTATAAAAAATCA
* *
54850124 TAAAATTTATAAATTTTTTAAAAAATCA
1 TAAAATTCATAAATTTTATAAAAAATCA
54850152 TAAAATT
1 TAAAATT
54850159 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAATTCATAAATTTTATAAAAAATCA
Found at i:54850131 original size:18 final size:19
Alignment explanation
Indices: 54850078--54850136 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
54850068 AATTACAAAA
*
54850078 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
54850097 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
54850116 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
54850134 AAA
1 AAA
54850137 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.37
19 22 0.63
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:54850145 original size:18 final size:18
Alignment explanation
Indices: 54850110--54850165 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
54850100 AATTCAAAAT
* *
54850110 ATTTATAAAAATTCTAAA
1 ATTTATAAAATTTTTAAA
*
54850128 ATTTATAAATTTTTTAAAA
1 ATTTATAAAATTTTT-AAA
* *
54850147 AATCATAAAATTTTTAAA
1 ATTTATAAAATTTTTAAA
54850165 A
1 A
54850166 AAAACTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTATAAAATTTTTAAA
Found at i:54850177 original size:20 final size:20
Alignment explanation
Indices: 54850134--54850175 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54850124 TAAAATTTAT
* *
54850134 AAATTTTTTAAAAAATCATA
1 AAATTTTTAAAAAAAACATA
54850154 AAATTTTTAAAAAAAAC-TA
1 AAATTTTTAAAAAAAACATA
54850173 AAA
1 AAA
54850176 ATATATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTTTAAAAAAAACATA
Found at i:54850714 original size:27 final size:26
Alignment explanation
Indices: 54850679--54850736 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
54850669 GTTGATTTTG
*
54850679 TTTTTTAATT-GGCCAAATAGGTCAATT
1 TTTTTTAATTAGGAC-AATAGGTC-ATT
*
54850706 TTTTTTAATTAGGACAATAGGTCGTT
1 TTTTTTAATTAGGACAATAGGTCATT
54850732 TTTTT
1 TTTTT
54850737 AGAGAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.25
27 18 0.64
28 3 0.11
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.50
Consensus pattern (26 bp):
TTTTTTAATTAGGACAATAGGTCATT
Found at i:54851121 original size:10 final size:10
Alignment explanation
Indices: 54851108--54851133 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54851098 GTTTTTTAAA
54851108 ATTTTAATTT
1 ATTTTAATTT
54851118 ATTTTAATTT
1 ATTTTAATTT
54851128 ATTTTA
1 ATTTTA
54851134 TTTTGTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:54853045 original size:24 final size:24
Alignment explanation
Indices: 54853000--54853046 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
54852990 GAAGGTGATG
* *
54853000 AAGATGAAAACAGAGGTGGAGATA
1 AAGATAAAAACAGAGGTCGAGATA
54853024 AAGATAAAAAC-GATGGTCGAGAT
1 AAGATAAAAACAGA-GGTCGAGAT
54853047 GAATATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.49, C:0.06, G:0.30, T:0.15
Consensus pattern (24 bp):
AAGATAAAAACAGAGGTCGAGATA
Found at i:54856899 original size:16 final size:17
Alignment explanation
Indices: 54856878--54856915 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
54856868 TTTCTTTCCT
*
54856878 ATTTCTGCATTAA-AAA
1 ATTTCTGCACTAATAAA
*
54856894 ATTTCTTCACTAATAAA
1 ATTTCTGCACTAATAAA
54856911 ATTTC
1 ATTTC
54856916 CAATTTGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTCTGCACTAATAAA
Found at i:54857998 original size:24 final size:25
Alignment explanation
Indices: 54857950--54857998 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
54857940 TTAAAACTTG
54857950 AAACACTAAACCCTAATTCCTAAAA
1 AAACACTAAACCCTAATTCCTAAAA
*
54857975 AAACCCTAAA-CCTAA-TCCTAAAA
1 AAACACTAAACCCTAATTCCTAAAA
54857998 A
1 A
54857999 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (25 bp):
AAACACTAAACCCTAATTCCTAAAA
Found at i:54858288 original size:15 final size:15
Alignment explanation
Indices: 54858268--54858297 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54858258 ATAGATAAAA
54858268 AATTTAATATATGTT
1 AATTTAATATATGTT
54858283 AATTTAATATATGTT
1 AATTTAATATATGTT
54858298 GATGTCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
AATTTAATATATGTT
Found at i:54858867 original size:4 final size:4
Alignment explanation
Indices: 54858858--54858882 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
54858848 CATTTCGCTT
54858858 TTGC TTGC TTGC TTGC TTGC TTGC T
1 TTGC TTGC TTGC TTGC TTGC TTGC T
54858883 GGGTGGGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.24, T:0.52
Consensus pattern (4 bp):
TTGC
Found at i:54864639 original size:16 final size:16
Alignment explanation
Indices: 54864618--54864649 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54864608 GCAATTGAAG
54864618 CATTTTCCTTGAAATT
1 CATTTTCCTTGAAATT
54864634 CATTTTCCTTGAAATT
1 CATTTTCCTTGAAATT
54864650 TTTACTTTTT
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:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (16 bp):
CATTTTCCTTGAAATT
Found at i:54866121 original size:85 final size:83
Alignment explanation
Indices: 54865907--54866149 Score: 271
Period size: 85 Copynumber: 2.9 Consensus size: 83
54865897 TAAGTCTTCG
* **
54865907 TTTGGAAATAAATC-AAGATCAAATAATATCTGTTAAACGACGAAAATAAATCCTGAAACAGATT
1 TTTGG-AATAAATCAAAGATGAAATAA-ATCTGTTAAACGACGGGAATAAATCCTGAAACA-ATT
*
54865971 TTATTTAATTTTAATTTCTCA
63 TTATTTAATTTTAATTACTCA
* * * *
54865992 TTTGGCAATAAA--AAA-ATGAAATAAAATTTGTTGAACGGCGGGAATAAATACTGAAACAATTT
1 TTTGG-AATAAATCAAAGATGAAAT-AAATCTGTTAAACGACGGGAATAAATCCTGAAACAATTT
*
54866054 TTTTTAATTTTAA-TACTCA
64 TATTTAATTTTAATTACTCA
*
54866073 TTTGGAGATAAAATCAAAGATGAAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAAT
1 TTTGGA-AT-AAATCAAAGATGAAATAAA-TCTGTTAAACGACGGGAATAAATCCTGAAAC-AAT
*
54866138 TTTATTCAATTT
62 TTTATTTAATTT
54866150 AAAATTTTGT
Statistics
Matches: 132, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
80 1 0.01
81 12 0.09
82 19 0.14
83 33 0.25
84 10 0.08
85 44 0.33
86 13 0.10
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (83 bp):
TTTGGAATAAATCAAAGATGAAATAAATCTGTTAAACGACGGGAATAAATCCTGAAACAATTTTA
TTTAATTTTAATTACTCA
Found at i:54866151 original size:85 final size:84
Alignment explanation
Indices: 54865845--54866149 Score: 270
Period size: 85 Copynumber: 3.7 Consensus size: 84
54865835 AACAAAATCA
* * * * * * * *
54865845 AAATCAAGTCTGTTGAATGACAGGATTAAATCCCGAAACAAA-ATTATTTGA--TTAAGTCTTCG
1 AAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAAGTC-TCA
*
54865907 TTTGGAAATAAATC-AAGATC
65 TTTGG-AATAAATCAAAGATG
** * * *
54865927 AAATAATA-TCTGTTAAACGACGAAAATAAATCCTGAAACAGATTTTATTTAATTTTAATTTCTC
1 AAATAA-AGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAA-GTCTC
54865991 ATTTGGCAATAAA--AAA-ATG
64 ATTTGG-AATAAATCAAAGATG
* * * * * * *
54866010 AAATAAAATTTGTTGAACGGCGGGAATAAATACTGAAAC-AATTTTTTTTAATTTTAA-TACTCA
1 AAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAAGT-CTCA
54866073 TTTGGAGATAAAATCAAAGATG
65 TTTGGA-AT-AAATCAAAGATG
*
54866095 AAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTCAATTT
1 AAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTT
54866150 AAAATTTTGT
Statistics
Matches: 178, Mismatches: 31, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
80 2 0.01
81 11 0.06
82 51 0.29
83 41 0.23
84 5 0.03
85 53 0.30
86 15 0.08
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (84 bp):
AAATAAAGTCTGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTTAAGTCTCAT
TTGGAATAAATCAAAGATG
Found at i:54873293 original size:13 final size:15
Alignment explanation
Indices: 54873269--54873303 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
54873259 ATAAATCCAA
54873269 AAATATAAAATTT-G
1 AAATATAAAATTTAG
54873283 AAATA-AAAATTTAG
1 AAATATAAAATTTAG
54873297 AAATATA
1 AAATATA
54873304 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 11 0.58
15 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AAATATAAAATTTAG
Found at i:54878712 original size:11 final size:11
Alignment explanation
Indices: 54878696--54878721 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54878686 AAAAACAGAG
54878696 TTAACATTTCA
1 TTAACATTTCA
54878707 TTAACATTTCA
1 TTAACATTTCA
54878718 TTAA
1 TTAA
54878722 GATACTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAACATTTCA
Found at i:54902343 original size:20 final size:21
Alignment explanation
Indices: 54902318--54902357 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54902308 ACTCTTGAAC
*
54902318 AGGGC-ACACGCCTGTGTAGA
1 AGGGCAACACGCCCGTGTAGA
54902338 AGGGCAACACGCCCGTGTAG
1 AGGGCAACACGCCCGTGTAG
54902358 CCATTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTAGA
Found at i:54904235 original size:28 final size:28
Alignment explanation
Indices: 54904153--54904302 Score: 187
Period size: 28 Copynumber: 5.4 Consensus size: 28
54904143 GAGATTGGCG
* * * *
54904153 CTAAGTGTGCGGGTTTAAATTGTGCAGCA
1 CTAAGTGTGCGAGTTT-GATTATGTAGCA
* *
54904182 CTAAGTGTGCGA-ATTGAATATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
54904209 CTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
54904237 CTAAGTGTGCGAGTATGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
54904265 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
54904292 CTGAGTGTGCG
1 CTAAGTGTGCG
54904303 GACTTAATAA
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
27 42 0.39
28 54 0.50
29 11 0.10
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:54904243 original size:55 final size:55
Alignment explanation
Indices: 54904178--54904302 Score: 189
Period size: 55 Copynumber: 2.3 Consensus size: 55
54904168 TAAATTGTGC
*
54904178 AGCACTAAGTGTGCGAAT-TGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATATGAATATGTAGCACTAAGTGTGCGAG-TTGACTATAT
* * *
54904233 AGCACTAAGTGTGCGAGTATGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATATGAATATGTAGCACTAAGTGTGCGAGTTGACTATAT
*
54904288 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54904303 GACTTAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 39 0.61
56 25 0.39
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATATGAATATGTAGCACTAAGTGTGCGAGTTGACTATAT
Found at i:54916749 original size:46 final size:47
Alignment explanation
Indices: 54916675--54916836 Score: 147
Period size: 46 Copynumber: 3.5 Consensus size: 47
54916665 GATGCCATGC
* *
54916675 CCCAGACATGGTCTTACACTGAC--ACATCTCGTA-GCCGATGCATAT
1 CCCAGACATAGTCTTACACTGGCTTACATCTCG-AGGCCGATGCATAT
* * *
54916720 CCCAGACAT-GTCTTACACTGGCTTACATCTTGAGGTCGATGCATGT
1 CCCAGACATAGTCTTACACTGGCTTACATCTCGAGGCCGATGCATAT
* * * * * * *
54916766 CCCAAACAT-GTCTTACACTAGCACT-CGTCTCAATGCAGATGCCATAT
1 CCCAGACATAGTCTTACACTGGC-TTACATCTCGAGGCCGATG-CATAT
54916813 CCCAGACATAGTCTTACACTGGCT
1 CCCAGACATAGTCTTACACTGGCT
54916837 CTCATAATGT
Statistics
Matches: 94, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
44 12 0.13
45 10 0.11
46 47 0.50
47 13 0.14
48 12 0.13
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (47 bp):
CCCAGACATAGTCTTACACTGGCTTACATCTCGAGGCCGATGCATAT
Found at i:54916855 original size:48 final size:46
Alignment explanation
Indices: 54916708--54916856 Score: 128
Period size: 46 Copynumber: 3.2 Consensus size: 46
54916698 ACATCTCGTA
** *
54916708 GCCGATGCATATCCCAGACATGTCTTACACTGGCT-TACATCTTGAG
1 GCCGATGCATATCCCAGACATGTCTTACACTGGCTCT-CATAATGTG
* * * *
54916754 GTCGATGCATGTCCCAAACATGTCTTACACTAGCACTCGTC-TCAA--T-
1 GCCGATGCATATCCCAGACATGTCTTACACT-G-GCTC-TCAT-AATGTG
*
54916800 GCAGATGCCATATCCCAGACATAGTCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATATCCCAGACAT-GTCTTACACTGGCTCTCATAATGTG
54916848 GCCGATGCA
1 GCCGATGCA
54916857 CATGTCTTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
45 4 0.05
46 37 0.47
47 17 0.22
48 19 0.24
49 1 0.01
50 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCGATGCATATCCCAGACATGTCTTACACTGGCTCTCATAATGTG
Found at i:54919594 original size:7 final size:7
Alignment explanation
Indices: 54919582--54919611 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
54919572 TGAGATTGAG
54919582 AGAAAAA
1 AGAAAAA
54919589 AGAAAAA
1 AGAAAAA
54919596 AGAAAAA
1 AGAAAAA
54919603 AGAAAAA
1 AGAAAAA
54919610 AG
1 AG
54919612 TGTGTGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:54921074 original size:73 final size:73
Alignment explanation
Indices: 54920987--54921172 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
54920977 ACAACTTGAC
* *
54920987 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAACTCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
54921052 CACTAACA
66 CACTAACA
54921060 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
54921125 CACTAACA
66 CACTAACA
54921133 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
54921173 AATAATAATA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:54921181 original size:3 final size:3
Alignment explanation
Indices: 54921173--54921222 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
54921163 ATTACATCCA
54921173 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54921221 AA
1 AA
54921223 AACATGTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54925558 original size:3 final size:3
Alignment explanation
Indices: 54925550--54925590 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54925540 ATTACATCCA
54925550 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54925591 AACATGTGAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54927447 original size:20 final size:20
Alignment explanation
Indices: 54927422--54927463 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54927412 CAAAGCCAAA
54927422 TAGATCCTAAATATAACATT
1 TAGATCCTAAATATAACATT
54927442 TAGATCCTAAATATAACATT
1 TAGATCCTAAATATAACATT
54927462 TA
1 TA
54927464 ACATATTTAA
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:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (20 bp):
TAGATCCTAAATATAACATT
Found at i:54940159 original size:35 final size:31
Alignment explanation
Indices: 54940079--54940160 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
54940069 CTAAACTTTT
*
54940079 AAAAGTGGCAAATCAATCACTAACATTTATG
1 AAAAGTGACAAATCAATCACTAACATTTATG
* *
54940110 AAAAGTGACAAATCAATCACTAACGTTT-TCT
1 AAAAGTGACAAATCAATCACTAACATTTAT-G
*
54940141 AAAAGTGACAAACCAATCAC
1 AAAAGTGACAAATCAATCAC
54940161 CTAAGCCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 1 0.02
31 45 0.98
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (31 bp):
AAAAGTGACAAATCAATCACTAACATTTATG
Found at i:54947477 original size:46 final size:46
Alignment explanation
Indices: 54947410--54947581 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
54947400 AACCCGCCCC
*
54947410 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
54947456 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
54947504 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
54947549 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
54947582 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 60 0.56
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:54947522 original size:93 final size:93
Alignment explanation
Indices: 54947415--54947585 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
54947405 GCCCCTAAGT
* *
54947415 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54947480 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
54947508 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54947573 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54947586 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54949843 original size:49 final size:48
Alignment explanation
Indices: 54949601--54949860 Score: 229
Period size: 46 Copynumber: 5.5 Consensus size: 48
54949591 AGATATGTGT
*
54949601 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACA-C-ATTG-TGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GACATCAATAGATGAGA
* * * * *
54949647 GCCAGTGTAAGACATGCCTAGGACATGCATTGAC--CACAT-TATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATCA-ATAGATGAGA
* * *
54949693 GCTAGTGTAAGACATGTCTGGGACATGTATTGGCAT---TGAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATCAAT-AGATGAGA
* * * *
54949739 GCTAGTGTAAGACATGTTTGGGACATGCATC-AGCCTCGAGATATA-CA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGA-CATC-A-ATAGATGAGA
*
54949787 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCAATAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGACATCAATAGATGAGA
* *
54949836 GCTAGTGTAAGACCTATCTGGGACA
1 GCTAGTGTAAGACATGTCTGGGACA
54949861 CGACATTGGC
Statistics
Matches: 173, Mismatches: 24, Indels: 31
0.76 0.11 0.14
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 99 0.57
47 4 0.02
48 27 0.16
49 34 0.20
50 3 0.02
51 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACATCAATAGATGAGA
Found at i:54949915 original size:98 final size:97
Alignment explanation
Indices: 54949731--54949919 Score: 256
Period size: 98 Copynumber: 1.9 Consensus size: 97
54949721 ATTGGCATTG
* * *
54949731 AGATGAGAGCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTCGAGATATACAAGCTAGTGTA
1 AGATGAGAGCTAGTGTAAGACATATCTGGGACACGCATCAGCCTCGAGATATACAAGCTAGTGTA
*
54949796 AGACCTGTCTGGGACATGGCATCGACATCAAT
66 AGACCTATCTGGGACATGGCATCGACATCAAT
* ** * *
54949828 AGATGAGAGCTAGTGTAAGACCTATCTGGGACACGACATTGGCCTTGATG-TATGA-AAGTTAGT
1 AGATGAGAGCTAGTGTAAGACATATCTGGGACACG-CATCAGCCTCGA-GATAT-ACAAGCTAGT
54949891 GTAAGACCTATCTGGGACATGGCATCGAC
63 GTAAGACCTATCTGGGACATGGCATCGAC
54949920 TTTGATGTGC
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
97 31 0.39
98 47 0.59
99 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (97 bp):
AGATGAGAGCTAGTGTAAGACATATCTGGGACACGCATCAGCCTCGAGATATACAAGCTAGTGTA
AGACCTATCTGGGACATGGCATCGACATCAAT
Found at i:54949925 original size:49 final size:49
Alignment explanation
Indices: 54949686--54949927 Score: 185
Period size: 49 Copynumber: 5.0 Consensus size: 49
54949676 TTGACCACAT
* * * * * *
54949686 TATGAGAGCTAGTGTAAGACATGTCTGGGACAT-GTATTGGCATTGA-G
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
* * * * * *
54949733 -ATGAGAGCTAGTGTAAGACATGTTTGGGACAT-GCATC-AGCCTCGA-G
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGA-CATTGATG
* **
54949779 ATAT-ACAAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCAATAG
1 -TATGA-AAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGAT-G
* * * * * *
54949830 -ATGAGAGCTAGTGTAAGACCTATCTGGGACACGACATTGGCCTTGATG
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
* *
54949878 TATGAAAGTTAGTGTAAGACCTATCTGGGACATGGCATCGACTTTGATG
1 TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
54949927 T
1 T
54949928 GCTAGCCAGT
Statistics
Matches: 158, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
46 39 0.25
47 1 0.01
48 28 0.18
49 87 0.55
50 2 0.01
51 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (49 bp):
TATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACATTGATG
Found at i:54953079 original size:3 final size:3
Alignment explanation
Indices: 54953031--54953061 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
54953021 GTATCTCCAT
54953031 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54953062 ACCAACTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:54953980 original size:32 final size:32
Alignment explanation
Indices: 54953927--54953996 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
54953917 TACATCCACA
* *
54953927 TGAATTTGGACAAATGGTTATTTAGGTTCA-CT
1 TGAATTTGGACAAAT-GTTATTCAAGTTCATCT
54953959 TGAATTTGGACAACCAT-TTATTCAAGTTCATCT
1 TGAATTTGGACAA--ATGTTATTCAAGTTCATCT
54953992 TGAAT
1 TGAAT
54953997 GTGGTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 24 0.73
33 7 0.21
34 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (32 bp):
TGAATTTGGACAAATGTTATTCAAGTTCATCT
Found at i:54954106 original size:29 final size:29
Alignment explanation
Indices: 54954063--54954123 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
54954053 ATTTATTTTA
*
54954063 AAATTATAAATAATTA-TATCAAATTAGTT
1 AAATTATAAATAATTACT-TAAAATTAGTT
54954092 AAATTATTAAA-AATTACTTAAAATTAGTT
1 AAATTA-TAAATAATTACTTAAAATTAGTT
54954121 AAA
1 AAA
54954124 AATTAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (29 bp):
AAATTATAAATAATTACTTAAAATTAGTT
Found at i:54954114 original size:11 final size:10
Alignment explanation
Indices: 54954031--54954128 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 10
54954021 AAAAATTTAA
54954031 AAAAATTA-T
1 AAAAATTATT
*
54954040 AAAAATTATG
1 AAAAATTATT
* *
54954050 GAAATTTATTT
1 AAAAATTA-TT
*
54954061 TAAAATTA-T
1 AAAAATTATT
54954070 AAATAATTA-T
1 AAA-AATTATT
*
54954080 ATCAAATTAGTT
1 A-AAAATTA-TT
54954092 --AAATTATT
1 AAAAATTATT
54954100 AAAAATTACTT
1 AAAAATTA-TT
54954111 -AAAATTAGTT
1 AAAAATTA-TT
54954121 AAAAATTA
1 AAAAATTA
54954129 GTATTAAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.03
9 17 0.24
10 33 0.47
11 17 0.24
12 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (10 bp):
AAAAATTATT
Found at i:54954137 original size:13 final size:11
Alignment explanation
Indices: 54954083--54954140 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
54954073 TAATTATATC
54954083 AAATTAGTT--
1 AAATTAGTTAA
54954092 AAATTA-TTAA
1 AAATTAGTTAA
*
54954102 AAATTACTT-A
1 AAATTAGTTAA
54954112 AAATTAGTTAA
1 AAATTAGTTAA
54954123 AAATTAGTATTAA
1 AAATTAG--TTAA
54954136 AAATT
1 AAATT
54954141 TCAAATACAC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
8 2 0.05
9 6 0.14
10 15 0.36
11 10 0.24
13 9 0.21
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (11 bp):
AAATTAGTTAA
Found at i:54955610 original size:27 final size:28
Alignment explanation
Indices: 54955568--54955632 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 28
54955558 TCAGGGTATG
54955568 CCACAAAGG-TAGTTCTTTTAGAGTTCA
1 CCACAAAGGCTAGTTCTTTTAGAGTTCA
*
54955595 CCACAAAGGCTA-TTCTTTTAGAGTTCG
1 CCACAAAGGCTAGTTCTTTTAGAGTTCA
54955622 CCACAAAGGCT
1 CCACAAAGGCT
54955633 CACAAAATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (28 bp):
CCACAAAGGCTAGTTCTTTTAGAGTTCA
Found at i:54959529 original size:27 final size:27
Alignment explanation
Indices: 54959499--54959676 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54959489 ATATTGAGTC
* * * *
54959499 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54959526 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54959553 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54959581 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54959608 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54959635 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54959662 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54959677 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54959638 original size:82 final size:81
Alignment explanation
Indices: 54959520--54959675 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54959510 TGCTATATAA
* *
54959520 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54959585 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54959602 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54959666 CACTTAGTGC
65 CACTTAGTGC
54959676 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54968848 original size:27 final size:27
Alignment explanation
Indices: 54968818--54969077 Score: 288
Period size: 27 Copynumber: 9.6 Consensus size: 27
54968808 ATATTGAGCC
* *
54968818 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
54968845 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54968872 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
54968899 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
54968926 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
54968954 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** ** *
54968982 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54969009 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
54969036 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54969063 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
54969078 GTACAATTTA
Statistics
Matches: 201, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
27 151 0.75
28 50 0.25
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54969102 original size:110 final size:110
Alignment explanation
Indices: 54968818--54969077 Score: 276
Period size: 110 Copynumber: 2.4 Consensus size: 110
54968808 ATATTGAGCC
* * * * * * * **
54968818 CGCACACTCAGTGCTATATAATCA-ACTCGCACACTTAGTGCCACGTAATCA-AATCGCACACTT
1 CGCACACTGAGTGCAACATAATCATAATCGCACACTTAGTGCTACATAGTCAGACCCGCACACTT
*
54968881 AGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
66 AGTGCCACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
* * * * *
54968926 CGCACACTTAGTGCTACATAATCATACTCGCACACTTAGTGCTACATAGTCAGACTCGCACTCTT
1 CGCACACTGAGTGCAACATAATCATAATCGCACACTTAGTGCTACATAGTCAGACCCGCACACTT
* * * * **
54968991 AGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTT
66 AGTGCCACATAGTCAACTCGCACACTTAGTGCTA-CATAGTCAACT
* *
54969036 CGCACACTGAGTGCAACATAGTCA-AATCGCACCCTTAGTGCT
1 CGCACACTGAGTGCAACATAATCATAATCGCACACTTAGTGCT
54969078 GTACAATTTA
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
108 22 0.17
109 41 0.32
110 67 0.52
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (110 bp):
CGCACACTGAGTGCAACATAATCATAATCGCACACTTAGTGCTACATAGTCAGACCCGCACACTT
AGTGCCACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
Found at i:54979734 original size:86 final size:86
Alignment explanation
Indices: 54979589--54979760 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
54979579 GGATTTTAAT
54979589 TCTTGAGGTTTCATACCGGAACAACCCTTGTTCCACTGACCAGTAATCTGTTACTGGAAATTGTA
1 TCTTGAGGTTTCATACCGGAACAACCCTTGTTCCACTGACCAGTAATCTGTTACTGGAAATTGTA
54979654 AATGCCACCCCTGCTTCATCA
66 AATGCCACCCCTGCTTCATCA
54979675 TCTTGAGGTTTCATACCGGAACAACCCTTGTTCCACTGACCAGTAATCTGTTACTGGAAATTGTA
1 TCTTGAGGTTTCATACCGGAACAACCCTTGTTCCACTGACCAGTAATCTGTTACTGGAAATTGTA
54979740 AATGCCACCCCTGCTTCATCA
66 AATGCCACCCCTGCTTCATCA
54979761 CAGATTTCTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (86 bp):
TCTTGAGGTTTCATACCGGAACAACCCTTGTTCCACTGACCAGTAATCTGTTACTGGAAATTGTA
AATGCCACCCCTGCTTCATCA
Found at i:54980756 original size:58 final size:58
Alignment explanation
Indices: 54980686--54980801 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
54980676 CTTCTGAGAT
54980686 GGCCATTATTGATTTACATCGTCTCACATGATATCTAGTAGAATTGGTTCCCCCCCCC
1 GGCCATTATTGATTTACATCGTCTCACATGATATCTAGTAGAATTGGTTCCCCCCCCC
**
54980744 GGCCATTATTGATTTACATCGTCTCACATGATATCTAGTAGAATTGGTTTTCCCCCCC
1 GGCCATTATTGATTTACATCGTCTCACATGATATCTAGTAGAATTGGTTCCCCCCCCC
54980802 TTGAGGGCAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (58 bp):
GGCCATTATTGATTTACATCGTCTCACATGATATCTAGTAGAATTGGTTCCCCCCCCC
Found at i:54984891 original size:21 final size:21
Alignment explanation
Indices: 54984858--54984897 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54984848 AAAAGAGATA
* * *
54984858 TTTGATTTGATGAGTGCAGTC
1 TTTGATGTAATGAATGCAGTC
54984879 TTTGATGTAATGAATGCAG
1 TTTGATGTAATGAATGCAG
54984898 CTAATAAAAT
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:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (21 bp):
TTTGATGTAATGAATGCAGTC
Found at i:54986676 original size:43 final size:43
Alignment explanation
Indices: 54986463--54986669 Score: 261
Period size: 43 Copynumber: 4.8 Consensus size: 43
54986453 TTTGAAAAAT
* * * * *
54986463 CTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGATAATGGC
1 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGATCATGAC
* *
54986506 CTTTAGTGACGCTTTTCCCACAAATGCCGCTAAAGATCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGATCATGAC
* * *
54986549 CTTTAGCAGCACTTTTCCCACAAATGCCGCTAAAAATCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGATCATGAC
* ** * *
54986592 CTTTGGCAACGCTTTTCCCACAAACGCCACTAAAGATCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGATCATGAC
* *
54986635 CTTTAGCGGCACTTTTCCTACAAATGCCGCTAAAG
1 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAG
54986670 GCCATGAAAT
Statistics
Matches: 139, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 139 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGATCATGAC
Found at i:54986942 original size:18 final size:19
Alignment explanation
Indices: 54986905--54986945 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54986895 ATTTAGAATC
54986905 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
54986924 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
54986942 AAAA
1 AAAA
54986946 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:54986947 original size:31 final size:31
Alignment explanation
Indices: 54986871--54986944 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
54986861 TCAAGTTATC
*
54986871 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
54986903 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
54986933 TTAAATATAAAA
1 TTAAATATAAAA
54986945 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:54991305 original size:33 final size:33
Alignment explanation
Indices: 54991242--54991314 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
54991232 TCATCTTCAC
54991242 TCTCTTCTTCTTCCTCCTCTCCCGTCTTCT-CT
1 TCTCTTCTTCTTCCTCCTCTCCCGTCTTCTCCT
* * *
54991274 TCCTCTTCTTCTTCTTCTTCTTCC-TCGTTCTCCT
1 T-CTCTTCTTCTTCCTCCTCTCCCGTC-TTCTCCT
54991308 TCTCTTC
1 TCTCTTC
54991315 AATATCTACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.09
33 29 0.83
34 3 0.09
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (33 bp):
TCTCTTCTTCTTCCTCCTCTCCCGTCTTCTCCT
Found at i:54992144 original size:14 final size:14
Alignment explanation
Indices: 54992120--54992172 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
54992110 CATGAACACT
*
54992120 TAACCCTTAACCTC
1 TAACCCCTAACCTC
* *
54992134 TAACCTCTAACCCC
1 TAACCCCTAACCTC
* *
54992148 TAACTCCTAACCCC
1 TAACCCCTAACCTC
54992162 TAACCCCTAAC
1 TAACCCCTAAC
54992173 ACCTAAACCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (14 bp):
TAACCCCTAACCTC
Found at i:54992177 original size:14 final size:14
Alignment explanation
Indices: 54992114--54992178 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
54992104 CTGAATCATG
* *
54992114 AACACTTAACCCTT
1 AACACCTAACCCCT
*
54992128 AAC-CTCTAACCTCT
1 AACAC-CTAACCCCT
* *
54992142 AACCCCTAACTCCT
1 AACACCTAACCCCT
*
54992156 AACCCCTAACCCCT
1 AACACCTAACCCCT
54992170 AACACCTAA
1 AACACCTAA
54992179 ACCTTAAACC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
13 1 0.02
14 40 0.95
15 1 0.02
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.22
Consensus pattern (14 bp):
AACACCTAACCCCT
Found at i:54992177 original size:21 final size:20
Alignment explanation
Indices: 54992120--54992196 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 20
54992110 CATGAACACT
* *
54992120 TAACCCTTAACCTCTAACCTC
1 TAACCCCTAACC-CTAACCCC
54992141 TAACCCCTAACTCCTAACCCC
1 TAACCCCTAAC-CCTAACCCC
* *
54992162 TAACCCCTAACACCTAAACCT
1 TAACCCCTAAC-CCTAACCCC
54992183 TAAACCCC-AACCCT
1 T-AACCCCTAACCCT
54992197 TAAACCATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.06
21 39 0.80
22 7 0.14
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (20 bp):
TAACCCCTAACCCTAACCCC
Found at i:54992202 original size:21 final size:21
Alignment explanation
Indices: 54992163--54992221 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
54992153 CCTAACCCCT
*
54992163 AACCCCTAACACC-TAAACCTTA
1 AACCCC-AAC-CCTTAAACCATA
54992185 AACCCCAACCCTTAAACCATA
1 AACCCCAACCCTTAAACCATA
* * *
54992206 ATCCCTAAACCTTAAA
1 AACCCCAACCCTTAAA
54992222 ATAGTAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.06
21 24 0.75
22 6 0.19
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCCAACCCTTAAACCATA
Found at i:54992813 original size:41 final size:41
Alignment explanation
Indices: 54992747--54993008 Score: 323
Period size: 41 Copynumber: 6.4 Consensus size: 41
54992737 GTTATATGAC
*
54992747 TTTTAGTGGCGTTTTA-CAAATAGCGCCGCTAATACTCTGGT
1 TTTTAGCGGCGTTTTACCAAA-AGCGCCGCTAATACTCTGGT
* *
54992788 TTATAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATACTCTGGT
* * * * *
54992829 TTTTAGCGGCGTTATATCAAAAACGTCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATACTCTGGT
*
54992870 TTTTAGCGGCGTTTTACCAAAAGTGCCGCTAATACTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATACTCTGGT
* *
54992911 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTTCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATACTCTGGT
* ** * * * *
54992951 TTTTAGCGGCGTTTTAACAAAAAATGCCGGTATTGCTC-CGT
1 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATACTCTGGT
54992992 TTTTAGCGGCGTTTTAC
1 TTTTAGCGGCGTTTTAC
54993009 TATTGCTCTG
Statistics
Matches: 196, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
40 19 0.10
41 173 0.88
42 4 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATACTCTGGT
Found at i:54992974 original size:123 final size:123
Alignment explanation
Indices: 54992747--54993008 Score: 377
Period size: 123 Copynumber: 2.1 Consensus size: 123
54992737 GTTATATGAC
*
54992747 TTTTAGTGGCGTTTTA-CAAATAGCGCCGCTAATACTCTGGTTTATAGCGGCGTTTTACCAAAAG
1 TTTTAGCGGCGTTTTACCAAATAGCGCCGCTAATACTCTGGTTTATAGCGGCGTTTTACCAAAAG
* * *
54992811 CGCCGCTAATGCTCTGGTTTTTAGCGGCGTTATATCAAAAACGTCGCTAATGCTCTGGT
66 CGCCGCTAATGCTCTGGTTTTTAGCGGCGTTATAACAAAAACGCCGCTAATGCTC-CGT
* *
54992870 TTTTAGCGGCGTTTTACCAAA-AGTGCCGCTAATACTCTGGTTTTTAGCGGCGTTTTACCAAAAG
1 TTTTAGCGGCGTTTTACCAAATAGCGCCGCTAATACTCTGGTTTATAGCGGCGTTTTACCAAAAG
* * * * * *
54992934 CGCCGCTATTTCTCT-GTTTTTAGCGGCGTTTTAACAAAAAATGCCGGTATTGCTCCGT
66 CGCCGCTAATGCTCTGGTTTTTAGCGGCGTTATAAC-AAAAACGCCGCTAATGCTCCGT
54992992 TTTTAGCGGCGTTTTAC
1 TTTTAGCGGCGTTTTAC
54993009 TATTGCTCTG
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
122 37 0.30
123 84 0.67
124 4 0.03
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (123 bp):
TTTTAGCGGCGTTTTACCAAATAGCGCCGCTAATACTCTGGTTTATAGCGGCGTTTTACCAAAAG
CGCCGCTAATGCTCTGGTTTTTAGCGGCGTTATAACAAAAACGCCGCTAATGCTCCGT
Found at i:54999920 original size:26 final size:26
Alignment explanation
Indices: 54999891--55000726 Score: 1384
Period size: 26 Copynumber: 32.2 Consensus size: 26
54999881 TTAAATGCCC
*
54999891 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
54999917 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
54999943 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
54999969 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
54999995 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000021 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000047 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000073 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000099 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000125 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000151 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000177 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000203 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000229 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000255 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000281 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000307 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000333 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000359 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000385 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000411 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000437 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000463 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000489 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000515 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000541 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000567 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000593 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000619 ATCATGGAATATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
55000645 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55000671 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
55000697 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55000723 ATCA
1 ATCA
55000727 ATTTGTACCA
Statistics
Matches: 750, Mismatches: 60, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 750 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54999951 original size:52 final size:52
Alignment explanation
Indices: 54999891--55000726 Score: 1636
Period size: 52 Copynumber: 16.1 Consensus size: 52
54999881 TTAAATGCCC
* *
54999891 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
54999943 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
54999995 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000047 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000099 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000151 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000203 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000255 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000307 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000359 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000411 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000463 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000515 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000567 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
*
55000619 ATCATGGAATATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
*
55000671 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAATCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
55000723 ATCA
1 ATCA
55000727 ATTTGTACCA
Statistics
Matches: 779, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 779 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (52 bp):
ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
Found at i:55010251 original size:40 final size:40
Alignment explanation
Indices: 55010192--55010269 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
55010182 TGCGGTACCT
* *
55010192 TATGGTGTGTAGGGTTGGATGGGTCAATTATATCCCCATA
1 TATGGTGTGCAGGGATGGATGGGTCAATTATATCCCCATA
* *
55010232 TATGGTGTGCAGGGATGGATGGGTCGATTTTATCCCCA
1 TATGGTGTGCAGGGATGGATGGGTCAATTATATCCCCA
55010270 CATGGTGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.32, T:0.33
Consensus pattern (40 bp):
TATGGTGTGCAGGGATGGATGGGTCAATTATATCCCCATA
Found at i:55010864 original size:26 final size:26
Alignment explanation
Indices: 55010835--55010942 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
55010825 TGGTACAAAT
55010835 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
55010861 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55010887 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
55010913 TGATAATGGTTTAGGGAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55010939 TGAT
1 TGAT
55010943 GGGCATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:55018018 original size:26 final size:26
Alignment explanation
Indices: 55017989--55018149 Score: 313
Period size: 26 Copynumber: 6.2 Consensus size: 26
55017979 TGATAATGGG
55017989 ATGATAATGGATTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
55018015 ATGATAATGGATTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
55018041 ATGATAATGGATTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
55018067 ATGATAATGGATTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
55018093 ATGATAATGGATTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
*
55018119 ATGATAATGGTTTAGGTAAATGTTCC
1 ATGATAATGGATTAGGTAAATGTTCC
55018145 ATGAT
1 ATGAT
55018150 GGGCATTTCA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 134 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
ATGATAATGGATTAGGTAAATGTTCC
Found at i:55024437 original size:12 final size:11
Alignment explanation
Indices: 55024405--55024438 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
55024395 ACTCACTCTC
55024405 CTTCTCCCTCTT
1 CTTCTCCC-CTT
55024417 CTTCTCCCCTT
1 CTTCTCCCCTT
55024428 CATTCTCCCCT
1 C-TTCTCCCCT
55024439 ACTTATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (11 bp):
CTTCTCCCCTT
Found at i:55026100 original size:42 final size:44
Alignment explanation
Indices: 55025996--55026127 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 44
55025986 TTTGATGATA
* *
55025996 CACTTATGTACTAATATGATTGCTTAGGTTTATCCGGTGATGCTTG
1 CACTTATGTGCCAATATGATTGCTTAGGTTTATCC-GTGATGC-TG
55026042 CAC-TATTGTGCCAATATGATTGCTTCA-GTTTAT-C-TGATGGC-G
1 CACTTA-TGTGCCAATATGATTGCTT-AGGTTTATCCGTGAT-GCTG
* * *
55026084 CACTTATGTGCCAATATGATTGCTTTGATTTATTCGATGATGCT
1 CACTTATGTGCCAATATGATTGCTTAGGTTTATCCG-TGATGCT
55026128 CTATGTGTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
42 28 0.38
43 7 0.10
44 4 0.05
45 7 0.10
46 26 0.36
47 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (44 bp):
CACTTATGTGCCAATATGATTGCTTAGGTTTATCCGTGATGCTG
Found at i:55028454 original size:24 final size:24
Alignment explanation
Indices: 55028422--55028471 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
55028412 AGTAGCATAT
55028422 CATACTTGCAACAAAACAAAAGAG
1 CATACTTGCAACAAAACAAAAGAG
55028446 CATACTTGCAACAAAACAAAAGAG
1 CATACTTGCAACAAAACAAAAGAG
55028470 CA
1 CA
55028472 ACAGAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.22, G:0.12, T:0.12
Consensus pattern (24 bp):
CATACTTGCAACAAAACAAAAGAG
Found at i:55031791 original size:16 final size:16
Alignment explanation
Indices: 55031757--55031809 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
55031747 ATGGCATCAG
55031757 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
55031773 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
55031789 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
55031805 TCATG
1 TCATG
55031810 AGTTTATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:55033063 original size:4 final size:4
Alignment explanation
Indices: 55033054--55033134 Score: 83
Period size: 4 Copynumber: 19.0 Consensus size: 4
55033044 TTTCTAATCT
*
55033054 TTTA TTTA TTTA TTTA TTTA TTTA TTTCA TTTA CTTA TTTA TTTTA TTATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA TT-TA
*
55033105 TTTA CTTTA -TTA TTATA TTATA TATA TTTA
1 TTTA -TTTA TTTA TT-TA TT-TA TTTA TTTA
55033135 CTTAAATATG
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.04
4 40 0.60
5 24 0.36
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:55033173 original size:23 final size:22
Alignment explanation
Indices: 55033110--55033183 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
55033100 TTATATTTAC
* *
55033110 TTTATTATTATATTATATATA-
1 TTTATTAATATATAATATATAT
*
55033131 TTTACTTAAATATGTAATATATAT
1 TTTA-TT-AATATATAATATATAT
*
55033155 TTTATTAATATATACATATGTAT
1 TTTATTAATATATA-ATATATAT
*
55033178 ATTATT
1 TTTATT
55033184 TTTAGCATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.09
22 9 0.21
23 26 0.60
24 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTATTAATATATAATATATAT
Found at i:55042241 original size:32 final size:32
Alignment explanation
Indices: 55042205--55042268 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
55042195 TTGATGGGGG
55042205 TTGGGCTGAGGATGTCAATGATCAAGCCTCCA
1 TTGGGCTGAGGATGTCAATGATCAAGCCTCCA
55042237 TTGGGCTGAGGATGTCAATGATCAAGCCTCCA
1 TTGGGCTGAGGATGTCAATGATCAAGCCTCCA
55042269 CTTCTACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (32 bp):
TTGGGCTGAGGATGTCAATGATCAAGCCTCCA
Found at i:55050989 original size:17 final size:17
Alignment explanation
Indices: 55050967--55050999 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55050957 GTCTTTGAAC
55050967 TCACCAA-ATCTGCAAGT
1 TCACCAAGA-CTGCAAGT
55050984 TCACCAAGACTGCAAG
1 TCACCAAGACTGCAAG
55051000 CTTACCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.18
Consensus pattern (17 bp):
TCACCAAGACTGCAAGT
Found at i:55052689 original size:24 final size:24
Alignment explanation
Indices: 55052662--55052707 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
55052652 GAAGATTTAG
*
55052662 TATTTATTAGTATAATATATTTCA
1 TATTTATTAGCATAATATATTTCA
*
55052686 TATTTATTAGCATAATTTATTT
1 TATTTATTAGCATAATATATTT
55052708 GACCTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTTATTAGCATAATATATTTCA
Found at i:55052948 original size:270 final size:271
Alignment explanation
Indices: 55052456--55053002 Score: 864
Period size: 270 Copynumber: 2.0 Consensus size: 271
55052446 AGTATAATAA
**
55052456 AAATATGTGAAACCCATTATAATAAGAATATATATATATAATATTTGTCTAGTTAATGAATTTAT
1 AAATATGTGAAACCCATTATAATAAGAATATATATATATAATATTTGTCTAGTTAATGAACCTAT
*
55052521 TAGATTAAAAATATTTTTAAAAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCTA
66 TAGATTAAAAATATTTTT-AAAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCCA
* **
55052586 AATTCTTGTCAAATAAAATAAGACATTGTTTGCAAGTCAAGTTAAAAAATATATATTTTCTTTCT
130 AATTCTTATCAAATAAAATAAGACATTACTTGCAAGTCAAGTTAAAAAATATATATTTTCTTTCT
* * * **
55052651 AGAAGATTTAGTATTTATTAGTATAATATATTTCATATTTATTAGCATAATTTATTTGACCTATG
195 AAAAGATTTAGTATCTATTAATATAATATATTTCATATTTATTAGCATAATTTATTTGACCTACA
55052716 AATTTAATCTAT
260 AATTTAATCTAT
* * * *
55052728 AAATATGTGAGACCCATTATAATAAGAATATATATATGTAATATTTTTCTAGTTAATGTACCTAT
1 AAATATGTGAAACCCATTATAATAAGAATATATATATATAATATTTGTCTAGTTAATGAACCTAT
*
55052793 TAGATTAAAAATATTTTT-TAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCCAA
66 TAGATTAAAAATATTTTTAAAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCCAA
* *
55052857 ATTCTTATTAAATAAAATAAGAGATTACTTGCAAGTCAAGTTAAACAAA-ATATATTTTCTTTCT
131 ATTCTTATCAAATAAAATAAGACATTACTTGCAAGTCAAGTTAAA-AAATATATATTTTCTTTCT
** *
55052921 AAAAGATTTAGTATCTATTAATATAATATATTTTGTATTTATTAGTATAATTTATTTGACCTACA
195 AAAAGATTTAGTATCTATTAATATAATATATTTCATATTTATTAGCATAATTTATTTGACCTACA
*
55052986 AATTTAGTCTAT
260 AATTTAATCTAT
55052998 AAATA
1 AAATA
55053003 AACACTTTTA
Statistics
Matches: 252, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
270 172 0.68
271 3 0.01
272 77 0.31
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (271 bp):
AAATATGTGAAACCCATTATAATAAGAATATATATATATAATATTTGTCTAGTTAATGAACCTAT
TAGATTAAAAATATTTTTAAAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCCAA
ATTCTTATCAAATAAAATAAGACATTACTTGCAAGTCAAGTTAAAAAATATATATTTTCTTTCTA
AAAGATTTAGTATCTATTAATATAATATATTTCATATTTATTAGCATAATTTATTTGACCTACAA
ATTTAATCTAT
Found at i:55052953 original size:24 final size:24
Alignment explanation
Indices: 55052926--55052977 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
55052916 TTTCTAAAAG
55052926 ATTTAGTATCTATTAATATAATAT
1 ATTTAGTATCTATTAATATAATAT
* * * *
55052950 ATTTTGTATTTATTAGTATAATTT
1 ATTTAGTATCTATTAATATAATAT
55052974 ATTT
1 ATTT
55052978 GACCTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAGTATCTATTAATATAATAT
Found at i:55056637 original size:42 final size:41
Alignment explanation
Indices: 55056578--55056741 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 41
55056568 TAGAGTTAGT
* * *
55056578 TGAGATTACGTGTAAGACCATATCTAGGATATGGCATTGATG
1 TGAGATT-CATGTAAGACCATATCTGGGATATGGCATCGATG
* * *
55056620 TGAGACTTCGTGTAAGACCATATCTGGGATATGTCATCAATG
1 TGAGA-TTCATGTAAGACCATATCTGGGATATGGCATCGATG
* * * *
55056662 TGAGATTTCATATAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGA-TTCATGTAAGACCATATCTGGGATA-TGGCATCGATG
*
55056705 TGAGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGAGAT-TCATGTAAGACCATATCTGGGATATGGCAT
55056742 TGGTATGGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 68 0.66
43 35 0.34
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (41 bp):
TGAGATTCATGTAAGACCATATCTGGGATATGGCATCGATG
Found at i:55080930 original size:12 final size:12
Alignment explanation
Indices: 55080913--55080948 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
55080903 ATTATGCAAA
55080913 CAATCATAAATT
1 CAATCATAAATT
55080925 CAATCATAAATT
1 CAATCATAAATT
*
55080937 CTAAACATAAAT
1 C-AATCATAAAT
55080949 AATAGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (12 bp):
CAATCATAAATT
Found at i:55083954 original size:2 final size:2
Alignment explanation
Indices: 55083947--55083974 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55083937 AGTTATCTTT
55083947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55083975 AAAGATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55092533 original size:31 final size:30
Alignment explanation
Indices: 55092497--55092582 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 30
55092487 GATTAAATCA
*
55092497 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * *
55092527 ACAATTAGAGTTTCAGGTATATAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
*
55092558 AAATTAAAG-TTCATGTATACAATTG
1 AAATTAAAGTTTCAAGTATACAATTG
55092583 CACACTAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 14 0.30
30 8 0.17
31 25 0.53
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:55092575 original size:29 final size:29
Alignment explanation
Indices: 55092497--55092599 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
55092487 GATTAAATCA
* *
55092497 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTC-AGTATACAATTGCACC
* *
55092527 ACAATTAGAGTTTCAGGTATATAATTGCACC
1 A-AATTAAAGTTTCA-GTATACAATTGCACC
55092558 AAATTAAAG-TTCATGTATACAATTGCACAC
1 AAATTAAAGTTTCA-GTATACAATTGCAC-C
*
55092588 TAAATCAAAGTT
1 -AAATTAAAGTT
55092600 CATATATAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
29 17 0.28
30 10 0.17
31 32 0.53
32 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (29 bp):
AAATTAAAGTTTCAGTATACAATTGCACC
Found at i:55092605 original size:29 final size:28
Alignment explanation
Indices: 55092538--55092610 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
55092528 CAATTAGAGT
*
55092538 TTCAGGTATATAATTGCACCAAATTAAAG
1 TTCA-GTATATAATTGCACCAAATCAAAG
*
55092567 TTCATGTATACAATTGCACACTAAATCAAAG
1 TTCA-GTATATAATTGCAC-C-AAATCAAAG
55092598 TTCA-TATATAATT
1 TTCAGTATATAATT
55092611 TTGAGATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 25 0.66
30 1 0.03
31 12 0.32
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (28 bp):
TTCAGTATATAATTGCACCAAATCAAAG
Found at i:55094440 original size:24 final size:25
Alignment explanation
Indices: 55094413--55094461 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
55094403 TTTTTTTTAT
*
55094413 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
55094437 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
55094462 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:55094454 original size:25 final size:23
Alignment explanation
Indices: 55094425--55094489 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
55094415 AATAAAAAAC
*
55094425 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
55094450 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
55094471 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAACAAATA
55094490 AAAAATAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 1 0.03
23 5 0.13
24 3 0.08
25 11 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:55094484 original size:19 final size:20
Alignment explanation
Indices: 55094451--55094489 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
55094441 TCAAATACAT
55094451 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
55094471 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
55094490 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:55095610 original size:23 final size:24
Alignment explanation
Indices: 55095570--55095624 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
55095560 ATTTTATATT
* *
55095570 ATATAATATGTACTAAATATAATT-
1 ATATCATATGTACAAAATA-AATTC
*
55095594 ATGTCATAT-TACAAAATAAATTC
1 ATATCATATGTACAAAATAAATTC
55095617 ATATCATA
1 ATATCATA
55095625 ATATTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 15 0.58
24 7 0.27
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATCATATGTACAAAATAAATTC
Found at i:55099552 original size:5 final size:5
Alignment explanation
Indices: 55099518--55099550 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
55099508 AAACTTGAGT
*
55099518 AGTGG AGTGG AGTGG AGTGG AGTGG AGTTG AGT
1 AGTGG AGTGG AGTGG AGTGG AGTGG AGTGG AGT
55099551 TGGAACTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.55, T:0.24
Consensus pattern (5 bp):
AGTGG
Done.