Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 134 of 230
Found at i:39062518 original size:15 final size:16
Alignment explanation
Indices: 39062498--39062531 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39062488 TTAAATTAAA
*
39062498 ATTTTAAAT-TTATTT
1 ATTTTAAATATTATAT
39062513 ATTTTAAATATTATAT
1 ATTTTAAATATTATAT
39062529 ATT
1 ATT
39062532 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAAATATTATAT
Found at i:39065144 original size:24 final size:24
Alignment explanation
Indices: 39065116--39065163 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39065106 AGCTTATGTA
39065116 ATAAAATAAAAATTTCTGAGAATT
1 ATAAAATAAAAATTTCTGAGAATT
39065140 ATAAAATAAAAATTTCTGAGAATT
1 ATAAAATAAAAATTTCTGAGAATT
39065164 TAGCGTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (24 bp):
ATAAAATAAAAATTTCTGAGAATT
Found at i:39066377 original size:12 final size:12
Alignment explanation
Indices: 39066360--39066384 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39066350 GATCAAACTG
39066360 ATAAAAATGTAA
1 ATAAAAATGTAA
39066372 ATAAAAATGTAA
1 ATAAAAATGTAA
39066384 A
1 A
39066385 CGTTAAAGGT
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATAAAAATGTAA
Found at i:39068681 original size:17 final size:17
Alignment explanation
Indices: 39068664--39068696 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39068654 ATAATATTAT
39068664 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
39068680 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
39068697 CTTATCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:39068725 original size:57 final size:57
Alignment explanation
Indices: 39068658--39068856 Score: 141
Period size: 68 Copynumber: 3.2 Consensus size: 57
39068648 CCCAAAATAA
* *
39068658 TATTATTTTAATAAATTTAATATTTAATTTAATTTAATACTTATCTTGATAGTATTT
1 TATTAATTTAATAAATTTAATATTAAATTTAATTTAATACTTATCTTGATAGTATTT
* *
39068715 TATTAATTTAATATCAAAGTGATTATCTTAATATTAAATTAAATTTAATATTTATCTT-ATAGAT
1 TATTAATTT-A-AT---A---A--AT-TTAATATTAAATTTAATTTAATACTTATCTTGATAG-T
39068779 AAATATT
54 --AT-TT
* * * * * *
39068786 CTATTACTTTAATAGA-TTAATATTAAATTTAATCTAATACTTTTCTTGATAAGAATTA
1 -TATTAATTTAATAAATTTAATATTAAATTTAATTTAATACTTATCTTGAT-AGTATTT
39068844 TATTAATTTAATA
1 TATTAATTTAATA
39068857 TTAAAGTGAT
Statistics
Matches: 111, Mismatches: 13, Indels: 36
0.69 0.08 0.22
Matches are distributed among these distances:
57 20 0.18
58 2 0.02
59 4 0.04
60 27 0.24
61 2 0.02
62 4 0.04
65 1 0.01
67 7 0.06
68 29 0.26
70 4 0.04
71 3 0.03
72 8 0.07
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (57 bp):
TATTAATTTAATAAATTTAATATTAAATTTAATTTAATACTTATCTTGATAGTATTT
Found at i:39080869 original size:29 final size:29
Alignment explanation
Indices: 39080827--39080889 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
39080817 ATCAACAATT
39080827 GAAAAGGGATAGCTTCGGCTATCGAATAC
1 GAAAAGGGATAGCTTCGGCTATCGAATAC
* * *
39080856 GAAAAGGGATAGCTTCGGTTATCGATTAT
1 GAAAAGGGATAGCTTCGGCTATCGAATAC
39080885 GAAAA
1 GAAAA
39080890 TTGATGGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.24
Consensus pattern (29 bp):
GAAAAGGGATAGCTTCGGCTATCGAATAC
Found at i:39080927 original size:30 final size:30
Alignment explanation
Indices: 39080893--39080951 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39080883 ATGAAAATTG
* *
39080893 ATGGTGAAGGCCATCGAACTATGAAAAGGA
1 ATGGTGAAGACCATCAAACTATGAAAAGGA
* *
39080923 ATGGTGACGACCATCAAATTATGAAAAGG
1 ATGGTGAAGACCATCAAACTATGAAAAGG
39080952 GATAGCTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (30 bp):
ATGGTGAAGACCATCAAACTATGAAAAGGA
Found at i:39082413 original size:23 final size:23
Alignment explanation
Indices: 39082378--39082421 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
39082368 AATGGACAAT
39082378 ATGTGTGTTTTGA-ATTGATTTTA
1 ATGTGTGTTTTGATA-TGATTTTA
39082401 ATGTGT-TTATTGATATGATTT
1 ATGTGTGTT-TTGATATGATTT
39082422 GAAAAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.11
23 16 0.84
24 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (23 bp):
ATGTGTGTTTTGATATGATTTTA
Found at i:39084304 original size:8 final size:8
Alignment explanation
Indices: 39084291--39084330 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
39084281 TAGAATAAAT
39084291 TAAAAAAA
1 TAAAAAAA
39084299 TAAAAAAA
1 TAAAAAAA
*
39084307 TAAAAAAC
1 TAAAAAAA
*
39084315 TAATAAAA
1 TAAAAAAA
39084323 TAATAAAA
1 TAA-AAAA
39084331 GTTTCCTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 24 0.89
9 3 0.11
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:39088129 original size:21 final size:21
Alignment explanation
Indices: 39088104--39088146 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39088094 TGGGACTTAA
39088104 AAGTTAAAA-GTAAAGTAAATC
1 AAGTTAAAATGTAAA-TAAATC
*
39088125 AAGTTAAAATTTAAATAAATC
1 AAGTTAAAATGTAAATAAATC
39088146 A
1 A
39088147 TGCAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (21 bp):
AAGTTAAAATGTAAATAAATC
Found at i:39088859 original size:10 final size:10
Alignment explanation
Indices: 39088846--39088884 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
39088836 AGGTTAAAAG
39088846 ACTAAAATTA
1 ACTAAAATTA
39088856 ACTAAAATTA
1 ACTAAAATTA
*
39088866 ACTAAAA-AA
1 ACTAAAATTA
39088875 ACTAAAATTA
1 ACTAAAATTA
39088885 TAAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (10 bp):
ACTAAAATTA
Found at i:39092371 original size:79 final size:79
Alignment explanation
Indices: 39092236--39092394 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
39092226 TGAAAAGATC
*
39092236 GTCCTATTTTTATGATGCTTTTATTGGTCTTGCATTGTATCTTTTACACTTCACATTCAAGCTAA
1 GTCCTATTTTTATGATGCTTTTATTGCTCTTGCATTGTATCTTTTACACTTCACATTCAAGCTAA
39092301 AAATGAATATGAAA
66 AAATGAATATGAAA
*
39092315 GTCCTATTTTTATGATGCTTTTATTGCTCTTGCATTGTATCTTTTACACTTTACATTCAAGCTAA
1 GTCCTATTTTTATGATGCTTTTATTGCTCTTGCATTGTATCTTTTACACTTCACATTCAAGCTAA
39092380 AAATGAATATGAAA
66 AAATGAATATGAAA
39092394 G
1 G
39092395 AGACATCAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (79 bp):
GTCCTATTTTTATGATGCTTTTATTGCTCTTGCATTGTATCTTTTACACTTCACATTCAAGCTAA
AAATGAATATGAAA
Found at i:39094428 original size:19 final size:19
Alignment explanation
Indices: 39094392--39094433 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
39094382 CTAAAATATG
*
39094392 TTAAGTAATTAAGATTT-A
1 TTAAGTAATTAACATTTAA
*
39094410 TTAAGTTAATTAACCTTTAA
1 TTAAG-TAATTAACATTTAA
39094430 TTAA
1 TTAA
39094434 CATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 10 0.50
20 5 0.25
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (19 bp):
TTAAGTAATTAACATTTAA
Found at i:39099353 original size:12 final size:12
Alignment explanation
Indices: 39099334--39099365 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39099324 GGACACATAG
39099334 CCGTGTCCCATC
1 CCGTGTCCCATC
*
39099346 CTGTGTCCCATC
1 CCGTGTCCCATC
39099358 CCGTGTCC
1 CCGTGTCC
39099366 TCACACATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.47, G:0.19, T:0.28
Consensus pattern (12 bp):
CCGTGTCCCATC
Found at i:39112669 original size:23 final size:23
Alignment explanation
Indices: 39112643--39112700 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
39112633 AAACATTGTT
* *
39112643 AATTGATA-TGTTAAAGTGCTGCA
1 AATTGA-AGTGTTAAAGTACTACA
39112666 AATTGAAGTGTTAAAGTACTACA
1 AATTGAAGTGTTAAAGTACTACA
*
39112689 AATAGAAGTGTT
1 AATTGAAGTGTT
39112701 TAGTTGCTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (23 bp):
AATTGAAGTGTTAAAGTACTACA
Found at i:39112776 original size:23 final size:22
Alignment explanation
Indices: 39112730--39112873 Score: 141
Period size: 23 Copynumber: 6.4 Consensus size: 22
39112720 TGTTTTATCA
*
39112730 TTGT-AATTGAGGTGTATAAATG
1 TTGTAAATTGAAGTGT-TAAATG
*
39112752 TTGTTAATT-AAGATGTTAAAGTG
1 TTGTAAATTGAAG-TGTTAAA-TG
* *
39112775 TTGCAAATTGAAGTGTTTAAATA
1 TTGTAAATTGAAGTG-TTAAATG
39112798 TTGTAAATTGAAGTGTTAAAGTG
1 TTGTAAATTGAAGTGTTAAA-TG
39112821 TTGTAAATTGAAGTGTTTAAATG
1 TTGTAAATTGAAGTG-TTAAATG
* * *
39112844 TTGTGAATTAAAGTATTAAAGTG
1 TTGTAAATTGAAGTGTTAAA-TG
39112867 TT-TAAAT
1 TTGTAAAT
39112874 GTTGTATATT
Statistics
Matches: 104, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
22 24 0.23
23 67 0.64
24 13 0.12
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.42
Consensus pattern (22 bp):
TTGTAAATTGAAGTGTTAAATG
Found at i:39112784 original size:114 final size:115
Alignment explanation
Indices: 39112564--39112791 Score: 334
Period size: 114 Copynumber: 2.0 Consensus size: 115
39112554 AGCCCTATTT
* * * * *
39112564 AAGTACTGCAATTTGAAGTGTTTAGTTGTTGGAAATTAAGATGTTTTATTTCTGTAAATTGAGGT
1 AAGTACTACAAATAGAAGTGTTTAGTTGCTGGAAATTAAGATGTTTTATATCTGTAAATTGAGGT
* *
39112629 GTATAAACATTGTTAATTGATATGTTAAAGTGCTGCAAATTGAAGTGTTA
66 GTATAAACATTGTTAATTAAGATGTTAAAGTGCTGCAAATTGAAGTGTTA
*
39112679 AAGTACTACAAATAGAAGTGTTTAGTTGCTGGAAATTGAGATGTTTTATCAT-TGT-AATTGAGG
1 AAGTACTACAAATAGAAGTGTTTAGTTGCTGGAAATTAAGATGTTTTAT-ATCTGTAAATTGAGG
** *
39112742 TGTATAAATGTTGTTAATTAAGATGTTAAAGTGTTGCAAATTGAAGTGTT
65 TGTATAAACATTGTTAATTAAGATGTTAAAGTGCTGCAAATTGAAGTGTT
39112792 TAAATATTGT
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
114 53 0.52
115 47 0.47
116 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (115 bp):
AAGTACTACAAATAGAAGTGTTTAGTTGCTGGAAATTAAGATGTTTTATATCTGTAAATTGAGGT
GTATAAACATTGTTAATTAAGATGTTAAAGTGCTGCAAATTGAAGTGTTA
Found at i:39112796 original size:46 final size:46
Alignment explanation
Indices: 39112734--39112868 Score: 175
Period size: 46 Copynumber: 2.9 Consensus size: 46
39112724 TTATCATTGT
* * *
39112734 AATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGTTGCA
1 AATTGAAGTGTTTAAATGTTGTAAATTAAGATGTTAAAGTGTTGCA
* *
39112780 AATTGAAGTGTTTAAATATTGTAAATTGAAG-TGTTAAAGTGTTGTA
1 AATTGAAGTGTTTAAATGTTGTAAATT-AAGATGTTAAAGTGTTGCA
* *
39112826 AATTGAAGTGTTTAAATGTTGTGAATTAA-AGTATTAAAGTGTT
1 AATTGAAGTGTTTAAATGTTGTAAATTAAGA-TGTTAAAGTGTT
39112869 TAAATGTTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
45 2 0.03
46 73 0.94
47 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (46 bp):
AATTGAAGTGTTTAAATGTTGTAAATTAAGATGTTAAAGTGTTGCA
Found at i:39113027 original size:23 final size:23
Alignment explanation
Indices: 39112972--39113028 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
39112962 AAATGTTGTT
* *
39112972 AATTGGGATGTTAAAGTGTTGTA
1 AATTGGGGTGTTAAAGTGTTGCA
** * *
39112995 TGTTGAGGTGTTTAAGTGTTGCA
1 AATTGGGGTGTTAAAGTGTTGCA
39113018 AATTGGGGTGT
1 AATTGGGGTGT
39113029 ACAAACGAGT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.02, G:0.35, T:0.40
Consensus pattern (23 bp):
AATTGGGGTGTTAAAGTGTTGCA
Found at i:39113922 original size:5 final size:5
Alignment explanation
Indices: 39113912--39113942 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
39113902 TGAACCTTTG
39113912 TTTAT TTTAT TTTAT TTTAT TTTA- TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
39113943 CCTTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:39117164 original size:15 final size:16
Alignment explanation
Indices: 39117144--39117176 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39117134 TAAGTAAATG
39117144 AAATGGAAAG-TAAGT
1 AAATGGAAAGATAAGT
*
39117159 AAATGGAATGATAAGT
1 AAATGGAAAGATAAGT
39117175 AA
1 AA
39117177 GTAAATGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (16 bp):
AAATGGAAAGATAAGT
Found at i:39117184 original size:20 final size:20
Alignment explanation
Indices: 39117134--39117185 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
39117124 AAGCTTGTGC
*
39117134 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
39117154 TAAGTAAATGGAAT-GATAAG
1 TAAGTAAATGGAATGGA-AAG
39117174 TAAGTAAATGGA
1 TAAGTAAATGGA
39117186 GTGGTTCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:39118904 original size:40 final size:39
Alignment explanation
Indices: 39118867--39119043 Score: 162
Period size: 39 Copynumber: 4.5 Consensus size: 39
39118857 ATATCCGGAC
*
39118867 TAAGATCCGAAGGCTTTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGT
* *
39118907 TAAGCCCCGAAGGCCTTT-TGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * **
39118946 TAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * * * *
39118986 TATGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
39119025 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
39119044 AACGAGGAGC
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
39 64 0.55
40 53 0.45
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:39118943 original size:39 final size:39
Alignment explanation
Indices: 39118820--39119041 Score: 189
Period size: 40 Copynumber: 5.6 Consensus size: 39
39118810 TTGAATGCTG
* * * * *
39118820 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
** *
39118860 TCCGGACTAAGAT-CCGAAGGCTTTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGC-ATTGTGCGAGATACTAAA
* * *
39118899 TTCCGGGTTAAGCCCCGAAGGCCTTTTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* **
39118939 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
39118979 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
39119018 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39119042 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
39 70 0.45
40 73 0.47
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:39118968 original size:79 final size:79
Alignment explanation
Indices: 39118873--39119041 Score: 196
Period size: 79 Copynumber: 2.1 Consensus size: 79
39118863 GGACTAAGAT
* * * *
39118873 CCGAAGGCTTTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTTGCGAGATACTA
1 CCGAAGGCATTCGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTA
* *
39118937 AATCCGGGTTAAGTC
65 AAACCGGGCTAAGTC
* ** * * * *
39118952 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTCGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
39119017 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
39119031 CCGAAGGCATT
1 CCGAAGGCATT
39119042 TGAACGAGGA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
79 72 0.96
80 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:39119061 original size:79 final size:79
Alignment explanation
Indices: 39118900--39119076 Score: 194
Period size: 79 Copynumber: 2.3 Consensus size: 79
39118890 AGATACAAAT
* * * * *
39118900 TCCGGGTTAAGCCCCGAAGGCCTTTTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
** ** *
39118965 TGCGAGTTGTTAAA
66 AACGAGGAGCTAAA
* * * * *
39118979 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
*
39119044 AACGAGGAGCTATA
66 AACGAGGAGCTAAA
*
39119058 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39119077 TACGTGATTT
Statistics
Matches: 80, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
78 14 0.17
79 66 0.82
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGGAGCTAAA
Found at i:39122677 original size:20 final size:20
Alignment explanation
Indices: 39122654--39122759 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
39122644 GGGCGCTAAA
*
39122654 GTGCAATCAGGGGCACGAGT
1 GTGCAATCAGGGGCACGAAT
* * *
39122674 GTGCAAACAGGGGTACCAGA-
1 GTGCAATCAGGGGCACGA-AT
* *
39122694 GTGTATTCAGGGGCACGAAT
1 GTGCAATCAGGGGCACGAAT
* *
39122714 GTGCTATCAGGGGCATC-AAA
1 GTGCAATCAGGGGCA-CGAAT
* *
39122734 GTGCATTCAGGGGCATGAAT
1 GTGCAATCAGGGGCACGAAT
39122754 GTGCAA
1 GTGCAA
39122760 ATAGGGACAC
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 1 0.02
20 62 0.97
21 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (20 bp):
GTGCAATCAGGGGCACGAAT
Found at i:39122704 original size:40 final size:40
Alignment explanation
Indices: 39122651--39122776 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
39122641 TAAGGGCGCT
* * *
39122651 AAAGTGCAATCAGGGGCACGAGTGTGCAAACAGGGGTACC
1 AAAGTGCATTCAGGGGCACGAATGTGCAAACAGGGGCACC
* * * * *
39122691 AGAGTGTATTCAGGGGCACGAATGTGCTATCAGGGGCATC
1 AAAGTGCATTCAGGGGCACGAATGTGCAAACAGGGGCACC
* * *
39122731 AAAGTGCATTCAGGGGCATGAATGTGCAAATAGGGACACC
1 AAAGTGCATTCAGGGGCACGAATGTGCAAACAGGGGCACC
39122771 AAAGTG
1 AAAGTG
39122777 TTTATAGGGG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.32, C:0.17, G:0.33, T:0.17
Consensus pattern (40 bp):
AAAGTGCATTCAGGGGCACGAATGTGCAAACAGGGGCACC
Found at i:39122786 original size:40 final size:40
Alignment explanation
Indices: 39122742--39122820 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
39122732 AAGTGCATTC
* *
39122742 AGGGGCAT-GAATGTGCAAATAGGGACACCAAAGTGTTTAT
1 AGGGGCATAG-ATGTGCAAACAAGGACACCAAAGTGTTTAT
* * *
39122782 AGGGGTATAGTTGTGCAAACAAGGACACCGAAGTGTTTA
1 AGGGGCATAGATGTGCAAACAAGGACACCAAAGTGTTTA
39122821 CAAGGGCACC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (40 bp):
AGGGGCATAGATGTGCAAACAAGGACACCAAAGTGTTTAT
Found at i:39137619 original size:51 final size:51
Alignment explanation
Indices: 39137497--39137676 Score: 159
Period size: 51 Copynumber: 3.5 Consensus size: 51
39137487 AAAGTGATGG
* * * * * * * *
39137497 TCACGTGTGTAGTACTTTGTGCAGGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGCGTATCGGATAGTGA-CGA
* * *
39137547 TCGCATCTGTAGTACTATGTGTAGGCTACTACGCGTA-CTGGATAGTTACGA
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGCGTATC-GGATAGTGACGA
* * * * * *
39137598 TCACGTGTGTGGTACTATGTGTAGGCTACTACGTGTATCGGATGGTGATGG
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGCGTATCGGATAGTGACGA
*
39137649 TCACATGTGTAGTACTATGTGCAGGCTA
1 TCACATGTGTAGTACTATGTGTAGGCTA
39137677 TTATGTGAAC
Statistics
Matches: 104, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 33 0.32
51 67 0.64
52 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGTAGGCTACTACGCGTATCGGATAGTGACGA
Found at i:39137739 original size:45 final size:45
Alignment explanation
Indices: 39137690--39137778 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
39137680 TGTGAACCAA
* *
39137690 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
39137735 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
39137779 AGTATATGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:39140819 original size:41 final size:41
Alignment explanation
Indices: 39140771--39141080 Score: 350
Period size: 41 Copynumber: 7.5 Consensus size: 41
39140761 GAGTGTAAAC
* * * *
39140771 AGGGGCACGTATGTGCTATTCAAGGGTATCGAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * * * *
39140812 AGTGGCACATATGTGGAATTTAGGGGTACCAAAGTACAAAA
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* *
39140853 AGGGGCACATATGTGCAATTTAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * *
39140894 AGTGGCACGTATGTTCAATTTAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * * * * *
39140935 AGTGGCACGTATGTTCAATTTAGGGATACTAAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * * *
39140976 ATGGGGCATGTATGTGTAATTCAGGGGTACCGAAGTGCAAAT
1 A-GGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * *
39141018 AGGGGCACGTGTGTGCAATTCAGGGGTACCGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
39141059 AGGGGCACACGTATGTGCAATT
1 AGGGG--CACGTATGTGCAATT
39141081 TAGTGGTTAA
Statistics
Matches: 232, Mismatches: 34, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
41 187 0.81
42 31 0.13
43 14 0.06
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
Found at i:39141096 original size:21 final size:21
Alignment explanation
Indices: 39141070--39141112 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
39141060 GGGGCACACG
39141070 TATGTGCAATTTAGTGGTTAA
1 TATGTGCAATTTAGTGGTTAA
39141091 TATGTGCAATTTAGTGGTTAA
1 TATGTGCAATTTAGTGGTTAA
39141112 T
1 T
39141113 TAACTATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (21 bp):
TATGTGCAATTTAGTGGTTAA
Found at i:39142410 original size:27 final size:27
Alignment explanation
Indices: 39142337--39142417 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
39142327 ACCGAATGCA
* ** *
39142337 CCTCGATAGGTAAAATTACCAAAATAC
1 CCTCGATGGGTAAAATTACTGAAACAC
* *
39142364 CCTCAATGGGTAATATTACTGAAACAC
1 CCTCGATGGGTAAAATTACTGAAACAC
39142391 CCTCGATGGGTAAAATTACTGAAACAC
1 CCTCGATGGGTAAAATTACTGAAACAC
39142418 AAAATTACCG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (27 bp):
CCTCGATGGGTAAAATTACTGAAACAC
Found at i:39142679 original size:26 final size:26
Alignment explanation
Indices: 39142643--39142737 Score: 93
Period size: 26 Copynumber: 3.7 Consensus size: 26
39142633 TTGCCACAAA
* *
39142643 TACTGTTACTGGTAGCTTTGTTATGT
1 TACTGATACTGGTAGCTTTGTTGTGT
* * **
39142669 TACTGATACTGGTAGCTCTGCTGCAT
1 TACTGATACTGGTAGCTTTGTTGTGT
**
39142695 TACTTTTACTGGTAGCTTTGTTGTGT
1 TACTGATACTGGTAGCTTTGTTGTGT
*
39142721 TACT-ATTACTGGCAGCT
1 TACTGA-TACTGGTAGCT
39142738 CTGCTGCATT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (26 bp):
TACTGATACTGGTAGCTTTGTTGTGT
Found at i:39142707 original size:52 final size:52
Alignment explanation
Indices: 39142643--39142758 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
39142633 TTGCCACAAA
*
39142643 TACTGTTACTGGTAGCTTTGTTATGTTACTGA-TACTGGTAGCTCTGCTGCAT
1 TACTGTTACTGGTAGCTTTGTTATGTTACT-ATTACTGGCAGCTCTGCTGCAT
* *
39142695 TACTTTTACTGGTAGCTTTGTTGTGTTACTATTACTGGCAGCTCTGCTGCAT
1 TACTGTTACTGGTAGCTTTGTTATGTTACTATTACTGGCAGCTCTGCTGCAT
39142747 TACTGTTACTGG
1 TACTGTTACTGG
39142759 CATATTGCTG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 1 0.02
52 58 0.98
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.43
Consensus pattern (52 bp):
TACTGTTACTGGTAGCTTTGTTATGTTACTATTACTGGCAGCTCTGCTGCAT
Found at i:39142749 original size:26 final size:26
Alignment explanation
Indices: 39142675--39142760 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
39142665 ATGTTACTGA
* *
39142675 TACTGGTAGCTCTGCTGCATTACTTT
1 TACTGGCAGCTCTGCTGCATTACTAT
* * * **
39142701 TACTGGTAGCTTTGTTGTGTTACTAT
1 TACTGGCAGCTCTGCTGCATTACTAT
*
39142727 TACTGGCAGCTCTGCTGCATTACTGT
1 TACTGGCAGCTCTGCTGCATTACTAT
39142753 TACTGGCA
1 TACTGGCA
39142761 TATTGCTGCG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (26 bp):
TACTGGCAGCTCTGCTGCATTACTAT
Found at i:39142912 original size:30 final size:29
Alignment explanation
Indices: 39142876--39142962 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 29
39142866 ACTGCATTTG
39142876 CACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCT-AGGCCCACA
* * *
39142906 CTCTGTTACTGTATTGGGCTTGGCCTACA
1 CACTGTTACTGTATTGGGCTAGGCCCACA
* *
39142935 CACTGCTACTGTATAGGGCTTAGGCCCA
1 CACTGTTACTGTATTGGGC-TAGGCCCA
39142963 GACTGATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (29 bp):
CACTGTTACTGTATTGGGCTAGGCCCACA
Found at i:39142944 original size:29 final size:29
Alignment explanation
Indices: 39142876--39142962 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
39142866 ACTGCATTTG
*
39142876 CACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCT-TGGCCCACA
* *
39142906 CTCTGTTACTGTATTGGGCTTGGCCTACA
1 CACTGTTACTGTATTGGGCTTGGCCCACA
* *
39142935 CACTGCTACTGTATAGGGCTTAGGCCCA
1 CACTGTTACTGTATTGGGCTT-GGCCCA
39142963 GACTGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 25 0.51
30 24 0.49
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (29 bp):
CACTGTTACTGTATTGGGCTTGGCCCACA
Found at i:39149577 original size:20 final size:20
Alignment explanation
Indices: 39149517--39149612 Score: 63
Period size: 21 Copynumber: 4.7 Consensus size: 20
39149507 AATTTAGCAA
39149517 TACTGAAGTACAAGCAGGGG
1 TACTGAAGTACAAGCAGGGG
* * *
39149537 CACAT-ATGTGA-AATTCAGGGG
1 TAC-TGAAGT-ACAA-GCAGGGG
39149558 TACTGAAGTACAAGCAGGGG
1 TACTGAAGTACAAGCAGGGG
* * *
39149578 CAC-GTATGTTCAATGCAGGGG
1 TACTG-AAGTACAA-GCAGGGG
*
39149599 TACCGAAGTACAAG
1 TACTGAAGTACAAG
39149613 TAAAGGTATG
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
19 1 0.02
20 24 0.43
21 30 0.54
22 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (20 bp):
TACTGAAGTACAAGCAGGGG
Found at i:39149597 original size:41 final size:41
Alignment explanation
Indices: 39149411--39149612 Score: 233
Period size: 41 Copynumber: 4.9 Consensus size: 41
39149401 GTGTAAAAAA
* * *
39149411 GGGCACGTATGTACAATTTAGGGGTACTGAAGTACAAACAG
1 GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAGCAG
* * * * * *
39149452 GGGAACGCATGTGCATTTCAAGGCTACTGAAGTACAAACAG
1 GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAGCAG
* * ***
39149493 GGGCACGTATGTGAAATTTAGCAATACTGAAGTACAAGCAG
1 GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAGCAG
* *
39149534 GGGCACATATGTGAAATTCAGGGGTACTGAAGTACAAGCAG
1 GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAGCAG
* * *
39149575 GGGCACGTATGTTCAATGCAGGGGTACCGAAGTACAAG
1 GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAG
39149613 TAAAGGTATG
Statistics
Matches: 134, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 134 1.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (41 bp):
GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAGCAG
Found at i:39154276 original size:8 final size:8
Alignment explanation
Indices: 39154263--39154299 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
39154253 GTGAATCGGC
*
39154263 AAAAGCCG
1 AAAAGCCA
39154271 AAAAGCCA
1 AAAAGCCA
39154279 AAAAGCCA
1 AAAAGCCA
39154287 AAAAGCCA
1 AAAAGCCA
39154295 AAAAG
1 AAAAG
39154300 TAATAAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.62, C:0.22, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAGCCA
Found at i:39157967 original size:16 final size:16
Alignment explanation
Indices: 39157946--39158006 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
39157936 GTGAATCGAA
39157946 AAAAGCCGAAAAGATG
1 AAAAGCCGAAAAGATG
* *
39157962 AAAAGCCGAAAAGTTA
1 AAAAGCCGAAAAGATG
* *
39157978 AAAAGTC-AAAAAATTG
1 AAAAGCCGAAAAGA-TG
*
39157994 AAAAGCCAAAAAG
1 AAAAGCCGAAAAG
39158007 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 4 0.11
16 27 0.77
17 4 0.11
ACGTcount: A:0.61, C:0.11, G:0.18, T:0.10
Consensus pattern (16 bp):
AAAAGCCGAAAAGATG
Found at i:39158013 original size:16 final size:16
Alignment explanation
Indices: 39157944--39158013 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
39157934 CTGTGAATCG
*
39157944 AAAAAAGCCGAAAAG-
1 AAAAAAGCCAAAAAGT
* *
39157959 ATGAAAAGCCGAAAAGT
1 A-AAAAAGCCAAAAAGT
* * *
39157976 TAAAAAGTCAAAAAAT
1 AAAAAAGCCAAAAAGT
**
39157992 TGAAAAGCCAAAAAGT
1 AAAAAAGCCAAAAAGT
39158008 AAAAAA
1 AAAAAA
39158014 TATGGAAATT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
15 1 0.02
16 41 0.98
ACGTcount: A:0.64, C:0.10, G:0.16, T:0.10
Consensus pattern (16 bp):
AAAAAAGCCAAAAAGT
Found at i:39160075 original size:18 final size:18
Alignment explanation
Indices: 39160033--39160075 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39160023 CCCCATTCCG
*
39160033 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
39160051 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
39160069 AAGTATG
1 AAGTATG
39160076 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:39160597 original size:27 final size:28
Alignment explanation
Indices: 39160513--39160610 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
39160503 CATGAGTTTG
* * *
39160513 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
39160542 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
39160570 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
39160597 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
39160611 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:39160624 original size:29 final size:27
Alignment explanation
Indices: 39160541--39160624 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
39160531 TAAATTGTTC
* *
39160541 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
39160569 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
39160596 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
39160625 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:39163705 original size:21 final size:21
Alignment explanation
Indices: 39163657--39163699 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39163647 GGTAATTTTG
**
39163657 AAATTAATTTGAAATTAAAAC
1 AAATTAAAGTGAAATTAAAAC
39163678 AAATTAAAGTGAAATTAAAAC
1 AAATTAAAGTGAAATTAAAAC
39163699 A
1 A
39163700 TTTTAACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATTAAAGTGAAATTAAAAC
Found at i:39164691 original size:40 final size:40
Alignment explanation
Indices: 39164636--39164913 Score: 317
Period size: 40 Copynumber: 7.0 Consensus size: 40
39164626 ACGCGTTTTG
* * *
39164636 GTTGGATCAGCTCTTATGAGCTTCTGCTTGGCATGTTTCA
1 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
39164676 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
1 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
* * *
39164716 GTTGGATAAACTCTTATGAGCTTCTGTTTGTCGTGTTTTA
1 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
* * * * * *
39164756 GTTGGATCAGCTATTATGAGATTTTATTTGGTGTGTTTCA
1 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
* * * * * * *
39164796 ATTTGATTAGCTCTTATGAGCTTTTGTTTGGTGTTTTTCG
1 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
* *
39164836 GTTGGATTAGCTCTTATGAGCTTTTGTTTGGCGTGTTTC-
1 GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
* *
39164875 GATTGGATGAA-CTCTTATGAGCTTCTATTTGGTGTGTTT
1 G-TTGGAT-AAGCTCTTATGAGCTTCTGTTTGGCGTGTTT
39164914 GGTTGATCTG
Statistics
Matches: 205, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 1 0.00
40 203 0.99
41 1 0.00
ACGTcount: A:0.15, C:0.13, G:0.25, T:0.47
Consensus pattern (40 bp):
GTTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCA
Found at i:39164850 original size:120 final size:120
Alignment explanation
Indices: 39164630--39164913 Score: 354
Period size: 120 Copynumber: 2.4 Consensus size: 120
39164620 TATTCGACGC
* ** ** *
39164630 GTTTTGGTTGGATCAGCTCTTATGAGCTTCTGCTTGGCATGTTTCAGTTGGATAAGCTCTTATGA
1 GTTTTAGTTGGATCAGCTCTTATGAGCTTCTATTTGGTGTGTTTCAATTGGATAAGCTCTTATGA
*
39164695 GCTTCTGTTTGGCGTGTTTCAGTTGGATAAACTCTTATGAGCTTCTGTTTGTCGT
66 GCTTCTGTTTGGCGTGTTTCAGTTGGATAAACTCTTATGAGCTTCTGTTTGGCGT
* * * * *
39164750 GTTTTAGTTGGATCAGCTATTATGAGATTTTATTTGGTGTGTTTCAATTTGATTAGCTCTTATGA
1 GTTTTAGTTGGATCAGCTCTTATGAGCTTCTATTTGGTGTGTTTCAATTGGATAAGCTCTTATGA
* * * * * * *
39164815 GCTTTTGTTTGGTGTTTTTCGGTTGGATTAGCTCTTATGAGCTTTTGTTTGGCGT
66 GCTTCTGTTTGGCGTGTTTCAGTTGGATAAACTCTTATGAGCTTCTGTTTGGCGT
* * *
39164870 G-TTTCGATTGGATGAACTCTTATGAGCTTCTATTTGGTGTGTTT
1 GTTTTAG-TTGGATCAGCTCTTATGAGCTTCTATTTGGTGTGTTT
39164914 GGTTGATCTG
Statistics
Matches: 138, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
119 4 0.03
120 134 0.97
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.47
Consensus pattern (120 bp):
GTTTTAGTTGGATCAGCTCTTATGAGCTTCTATTTGGTGTGTTTCAATTGGATAAGCTCTTATGA
GCTTCTGTTTGGCGTGTTTCAGTTGGATAAACTCTTATGAGCTTCTGTTTGGCGT
Found at i:39165478 original size:16 final size:16
Alignment explanation
Indices: 39165457--39165493 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
39165447 AGCTTATGCT
39165457 AAGTAAATGGAACAAA
1 AAGTAAATGGAACAAA
39165473 AAGTAAATGGAACAAA
1 AAGTAAATGGAACAAA
39165489 AAGTA
1 AAGTA
39165494 GGTACGTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.19, T:0.14
Consensus pattern (16 bp):
AAGTAAATGGAACAAA
Found at i:39171889 original size:50 final size:50
Alignment explanation
Indices: 39171769--39172007 Score: 253
Period size: 50 Copynumber: 4.6 Consensus size: 50
39171759 ATTTGGGTAA
* * * *
39171769 AGAGATCCCATGTAAGACCATGTCTTGGACATGGCATTGACATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAG---ATG
* * *
39171825 ATAGGTCCCCTGTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * * *
39171875 AGAGGTCCCATGTAAGACCATGACTGAGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * * *
39171925 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCAACATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
** *
39171975 AGAACATCCCATGTAAGACCATGTGTGGGACAT
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACAT
39172008 AGCTTTGGCA
Statistics
Matches: 156, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
50 90 0.58
51 26 0.17
53 3 0.02
55 2 0.01
56 35 0.22
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:39171957 original size:100 final size:103
Alignment explanation
Indices: 39171769--39171997 Score: 295
Period size: 100 Copynumber: 2.2 Consensus size: 103
39171759 ATTTGGGTAA
* *
39171769 AGAGATCCCATGTAAGACCATGTCTTGGACATGGCATTGACATCCTTGAGATCATGATAGGTCCC
1 AGAGATCCCATGTAAGACCATGACTTGGACATGGCATTGACATCC-TGAGA--ATGAGAGGTCCC
* * *
39171834 CTGTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATG
63 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
* * *
39171875 AGAGGTCCCATGTAAGACCATGAC-TGAGACATGGCGTTGGCA-CC-GAG-ATGAGAGGTCCCCT
1 AGAGATCCCATGTAAGACCATGACTTG-GACATGGCATTGACATCCTGAGAATGAGAGGTCCCCT
*
39171936 GTAAGACCATGTCTGGGACATGGCATGGGCACCAACATT
65 GTAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
*
39171975 AGAACATCCCATGTAAGACCATG
1 AG-AGATCCCATGTAAGACCATG
39171998 TGTGGGACAT
Statistics
Matches: 110, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
100 50 0.45
101 18 0.16
103 3 0.03
105 4 0.04
106 35 0.32
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGACTTGGACATGGCATTGACATCCTGAGAATGAGAGGTCCCCTG
TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
Found at i:39178652 original size:56 final size:50
Alignment explanation
Indices: 39178579--39178822 Score: 299
Period size: 50 Copynumber: 4.7 Consensus size: 50
39178569 GGTAAAAAGA
* *
39178579 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCTTGAGATCATGATAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATGAGAGG
* * *
39178635 TCCCTTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
39178685 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
39178735 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGG
*
39178786 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39178823 TGTTTTTACC
Statistics
Matches: 166, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
50 94 0.57
51 34 0.20
53 3 0.02
55 2 0.01
56 33 0.20
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:39178764 original size:100 final size:104
Alignment explanation
Indices: 39178578--39178823 Score: 338
Period size: 100 Copynumber: 2.4 Consensus size: 104
39178568 GGGTAAAAAG
* * **
39178578 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCTTGAGATCATGATAGGTCCCTTAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA--ATGAGAGGTCCCCCAT
* * *
39178643 AAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAG-AG
63 AAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGAAC
* * *
39178684 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAG-ATGAGAGGTCCCCCGTAAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCCCATAAG
39178746 ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAAC
66 ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAAC
*
39178785 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39178824 GTTTTTACCA
Statistics
Matches: 126, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
100 49 0.39
101 37 0.29
103 3 0.02
105 2 0.02
106 35 0.28
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (104 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCCCATAAG
ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAAC
Found at i:39200360 original size:39 final size:40
Alignment explanation
Indices: 39200266--39200487 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
39200256 GGGTGTTACA
*
39200266 TCCGGGCTAAGT-CCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
39200303 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
39200344 TCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39200383 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
39200422 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
39200461 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39200488 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
38 10 0.06
39 83 0.51
40 57 0.35
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39200509 original size:79 final size:79
Alignment explanation
Indices: 39200317--39200520 Score: 204
Period size: 79 Copynumber: 2.6 Consensus size: 79
39200307 GGACTAAGAT
** * * *
39200317 CCGAAGGCATTTGTGCGAGAT-ACTAATTCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT
*
39200380 AATTCCGGGCTAAGC
65 AATACCGGGCTAAGC
** *
39200395 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACT
*
39200459 -ATAACCGGGCTATGTC
65 AAT-ACCGGGCTAAG-C
* * *
39200475 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
39200521 TACGTGATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 36 0.33
79 47 0.43
80 25 0.23
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:39208330 original size:39 final size:41
Alignment explanation
Indices: 39208235--39208417 Score: 206
Period size: 40 Copynumber: 4.6 Consensus size: 41
39208225 TTGAATGATG
*
39208235 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
39208274 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
39208314 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
39208353 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
39208393 ACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTT
39208418 TAACGAGGAG
Statistics
Matches: 125, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 60 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:39208370 original size:79 final size:81
Alignment explanation
Indices: 39208235--39208417 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
39208225 TTGAATGATG
39208235 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
39208298 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
39208313 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
39208374 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
39208393 ACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTT
39208418 TAACGAGGAG
Statistics
Matches: 91, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.64
80 22 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:39208440 original size:79 final size:79
Alignment explanation
Indices: 39208236--39208451 Score: 191
Period size: 79 Copynumber: 2.7 Consensus size: 79
39208226 TGAATGATGT
**
39208236 CCGGGCTAAGTCCCGAAGGC-TTGTGCTA--AGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 CCGGGCTAAG-CCCGAAGGCATT-TG-TACGAGTGACTAA-ATCCGGGTTAA-ATCCCGAAGGCA
*
39208296 TTTGTGCGAGATACTAATT
61 TTTGTGCGAGATACTAATA
* * *
39208315 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGTACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
39208380 GCGA-ATTACT-ATAA
66 GCGAGA-TACTAAT-A
* * *
39208394 CCGGGCTATGTCCCGAAGGCATTT-TAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGT-ACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
39208452 TACGTGATTT
Statistics
Matches: 115, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
77 1 0.01
78 15 0.13
79 73 0.63
80 26 0.23
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGTACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:39230215 original size:13 final size:13
Alignment explanation
Indices: 39230197--39230224 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39230187 TTGTTTGATG
39230197 CATCGATCCCTAT
1 CATCGATCCCTAT
39230210 CATCGATCCCTAT
1 CATCGATCCCTAT
39230223 CA
1 CA
39230225 CATGATCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.39, G:0.07, T:0.29
Consensus pattern (13 bp):
CATCGATCCCTAT
Found at i:39247029 original size:13 final size:13
Alignment explanation
Indices: 39247011--39247036 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39247001 ACTTGTCGTG
39247011 TGTGAATGTGTAA
1 TGTGAATGTGTAA
39247024 TGTGAATGTGTAA
1 TGTGAATGTGTAA
39247037 GTATACACGT
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:0.31, T:0.38
Consensus pattern (13 bp):
TGTGAATGTGTAA
Found at i:39259493 original size:22 final size:22
Alignment explanation
Indices: 39259468--39259512 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
39259458 ATTATGATGA
39259468 TTGATATGT-TGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
39259490 TTGATATGTATGCGATTATATT
1 TTGATATGTATGAGATTATATT
39259512 T
1 T
39259513 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:39263465 original size:40 final size:41
Alignment explanation
Indices: 39263402--39263482 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
39263392 CAGACAGAAC
* * *
39263402 CTCATAAGAGTTAATCCAACCGAAATATGCCAAACA-AAAG
1 CTCATAAGAGCTAATCCAACCGAAACAGGCCAAACAGAAAG
* *
39263442 CTCATAAGAGCTAGTCCACCCGAAACAGGCCAAACAGAAAG
1 CTCATAAGAGCTAATCCAACCGAAACAGGCCAAACAGAAAG
39263483 TATAACACGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (41 bp):
CTCATAAGAGCTAATCCAACCGAAACAGGCCAAACAGAAAG
Found at i:39272284 original size:14 final size:14
Alignment explanation
Indices: 39272265--39272291 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39272255 CTTTATTTAT
39272265 TTAAATAAAATATC
1 TTAAATAAAATATC
39272279 TTAAATAAAATAT
1 TTAAATAAAATAT
39272292 TAAAGAAATT
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:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAATAAAATATC
Found at i:39272478 original size:29 final size:29
Alignment explanation
Indices: 39272424--39272479 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
39272414 GCTTTTAAAG
* *
39272424 ATATTTACAAAAAGAGACAGCTAATTTCA
1 ATATTTACAAAAAGAGACACCAAATTTCA
39272453 ATATTTACAAAAAGA-ACAACCAAATTT
1 ATATTTACAAAAAGAGAC-ACCAAATTT
39272480 TGCACATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (29 bp):
ATATTTACAAAAAGAGACACCAAATTTCA
Found at i:39283449 original size:50 final size:50
Alignment explanation
Indices: 39283342--39283588 Score: 287
Period size: 50 Copynumber: 4.8 Consensus size: 50
39283332 TTAAGGGAAT
**
39283342 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTTCATTGAGATTATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG---CACCGAG---ATGA
* *
39283398 GAGGTCCCATGTAAGACCATGTCTGCGACATGGCGTTGGCACCGAGATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
* *
39283448 GAGGTCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCGAGATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
** * * *
39283498 GAGGTCCCCCGTAAGACCATGTCTGAGACATGGCATGGGCACCGATATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
** * * * *
39283548 GAACTCCCAGGTAAAACCATATCTGGGATATGGCATTGGCA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39283589 GTACAGAAAA
Statistics
Matches: 169, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 127 0.75
53 5 0.03
56 37 0.22
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
Found at i:39286685 original size:36 final size:36
Alignment explanation
Indices: 39286644--39286719 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
39286634 CCATTAACTA
39286644 GTATTATTACAAGCACTAATTTCTTTGTTAACTCTT
1 GTATTATTACAAGCACTAATTTCTTTGTTAACTCTT
*
39286680 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTT
1 GTATTATTACAAGCACTAATTTCTTTGTTAACTCTT
39286716 GTAT
1 GTAT
39286720 CATATTCAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.49
Consensus pattern (36 bp):
GTATTATTACAAGCACTAATTTCTTTGTTAACTCTT
Found at i:39286765 original size:59 final size:59
Alignment explanation
Indices: 39286680--39286836 Score: 314
Period size: 59 Copynumber: 2.7 Consensus size: 59
39286670 GTTAACTCTT
39286680 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTATCATATTCAGCCATTAACTA
1 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTATCATATTCAGCCATTAACTA
39286739 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTATCATATTCAGCCATTAACTA
1 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTATCATATTCAGCCATTAACTA
39286798 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTA
1 GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTA
39286837 GGGAAGCCAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 98 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (59 bp):
GTATTATTACAAGCACTAATTTCTTTTTTAACTCTTGTATCATATTCAGCCATTAACTA
Found at i:39287276 original size:53 final size:53
Alignment explanation
Indices: 39287218--39287326 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
39287208 ACACTCATGC
*
39287218 ACATTAATTAATTGAACATGCAACTTAAATCTCCTTATTTAAAATGAAAATAA
1 ACATTAATTAATTGAACATGCAACTTAAATCACCTTATTTAAAATGAAAATAA
39287271 ACATTAATTAATTGAACATGCAACTTAAATCACCTTATTTAAAATGAAAATAA
1 ACATTAATTAATTGAACATGCAACTTAAATCACCTTATTTAAAATGAAAATAA
39287324 ACA
1 ACA
39287327 CACTTTAACT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.32
Consensus pattern (53 bp):
ACATTAATTAATTGAACATGCAACTTAAATCACCTTATTTAAAATGAAAATAA
Found at i:39287519 original size:52 final size:50
Alignment explanation
Indices: 39287454--39287569 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
39287444 ATGAACAAAT
* * * *
39287454 GAGTTACTTAATGCATAACTTAATTTAATGATGCCAACTTTAACTAACATGG
1 GAGTTACATAATGCATAACATAATTT-ATGATGCAAAC-TTAACTAACATGA
* ** *
39287506 GAGTTGCATAATGCATGTCATAGTTTATGATGCAAACTTAACTAACATGA
1 GAGTTACATAATGCATAACATAATTTATGATGCAAACTTAACTAACATGA
39287556 GAGTTACATAATGC
1 GAGTTACATAATGC
39287570 GTGACTTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 25 0.45
51 10 0.18
52 20 0.36
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (50 bp):
GAGTTACATAATGCATAACATAATTTATGATGCAAACTTAACTAACATGA
Found at i:39299283 original size:74 final size:74
Alignment explanation
Indices: 39299155--39299302 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
39299145 TAACTGATTC
*
39299155 CAACCAAATAGTCACCTGCAAGCATTTATTAACAAACACACTAAAACACATTTTAACACACTAAA
1 CAACCAAATAGTCACCTGCAAGCATGTATTAACAAACACACTAAAACACATTTTAACACACTAAA
39299220 CTTAATAAG
66 CTTAATAAG
* * * *
39299229 CAACTAAATAGTCATCTGCAAGCATGTATTAACAAACACATTAAAACACTTTTTAACACACTAAA
1 CAACCAAATAGTCACCTGCAAGCATGTATTAACAAACACACTAAAACACATTTTAACACACTAAA
39299294 CTTAATAAG
66 CTTAATAAG
39299303 TTTAATTAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (74 bp):
CAACCAAATAGTCACCTGCAAGCATGTATTAACAAACACACTAAAACACATTTTAACACACTAAA
CTTAATAAG
Found at i:39302044 original size:50 final size:50
Alignment explanation
Indices: 39301924--39302164 Score: 209
Period size: 50 Copynumber: 4.7 Consensus size: 50
39301914 GGTAAATAGA
*
39301924 TCCCATGTAAGACCATGTCT-GGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
*
39301979 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * ** * * **
39302029 TCCCCCGTAAGACCATGTCTAGGACATTACATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
39302079 TCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
39302128 TCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39302165 TGTTATTATC
Statistics
Matches: 153, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 76 0.50
53 3 0.02
55 21 0.14
56 15 0.10
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:39305272 original size:15 final size:15
Alignment explanation
Indices: 39305240--39305281 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
39305230 TCACCTTTTC
* *
39305240 CTTTTTTTT-TCATT
1 CTTTTTTTTCTTATA
39305254 CTTTTTTTTCTTATA
1 CTTTTTTTTCTTATA
39305269 CTTTTTCTTTCTT
1 CTTTTT-TTTCTT
39305282 TTCTTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTTTTCTTATA
Found at i:39308370 original size:74 final size:74
Alignment explanation
Indices: 39308273--39308420 Score: 242
Period size: 74 Copynumber: 2.0 Consensus size: 74
39308263 TAACTGATTC
* * *
39308273 CAACCAAATAGTCACCTGGAAGCATTTATTAACAAACACATTAAAACACATTTAAACACACTAAA
1 CAACCAAATAGTCACCTGCAAGCAGTTATTAACAAACACATTAAAACACATTTAAACACACAAAA
39308338 CTTAATAAG
66 CTTAATAAG
* *
39308347 CAACTAAATAGTCACCTGCAAGCAGTTATTAACAAACACATTAAAACACATTTTAACACACAAAA
1 CAACCAAATAGTCACCTGCAAGCAGTTATTAACAAACACATTAAAACACATTTAAACACACAAAA
*
39308412 CTTATTAAG
66 CTTAATAAG
39308421 TTTAATTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.24
Consensus pattern (74 bp):
CAACCAAATAGTCACCTGCAAGCAGTTATTAACAAACACATTAAAACACATTTAAACACACAAAA
CTTAATAAG
Found at i:39317832 original size:27 final size:28
Alignment explanation
Indices: 39317781--39317842 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 28
39317771 AAATTAAATT
*
39317781 TATAAAACCCTAAAATTAACAACATTAA
1 TATAAAACCCTAAAATCAACAACATTAA
39317809 TATAAAACCCT-AAATCATAC-ACATTAA
1 TATAAAACCCTAAAATCA-ACAACATTAA
39317836 TATAAAA
1 TATAAAA
39317843 TTATTATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (28 bp):
TATAAAACCCTAAAATCAACAACATTAA
Found at i:39317996 original size:51 final size:51
Alignment explanation
Indices: 39317890--39317992 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 51
39317880 TATTTTTTTG
* * * **
39317890 AATTTTTTAGAATTAGGATTAAATTGAGACTACTTGTAAATTTTAAGGGTT
1 AATTTTTTAAAATTAGGACTAAATTGAGACTAATTGTAAAAGTTAAGGGTT
* *
39317941 AATTTTTTAAAATTATGACTAAATTGATA-TAATATGTAAAAGTTAA-GGTT
1 AATTTTTTAAAATTAGGACTAAATTGAGACTAAT-TGTAAAAGTTAAGGGTT
39317991 AA
1 AA
39317993 ATTTATTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 9 0.20
51 35 0.80
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.42
Consensus pattern (51 bp):
AATTTTTTAAAATTAGGACTAAATTGAGACTAATTGTAAAAGTTAAGGGTT
Found at i:39318284 original size:18 final size:17
Alignment explanation
Indices: 39318244--39318285 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
39318234 TTAAAGAAAT
39318244 TATTTTTATCATATTAA
1 TATTTTTATCATATTAA
39318261 TAATTTTTAT-AGTAATTAA
1 T-ATTTTTATCA-T-ATTAA
39318280 TATTTT
1 TATTTT
39318286 AAAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTTTTATCATATTAA
Found at i:39340055 original size:26 final size:27
Alignment explanation
Indices: 39340006--39340062 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
39339996 AAATGTTGTT
39340006 AAATGACCAAAATACCCTCAAAGGGTA
1 AAATGACCAAAATACCCTCAAAGGGTA
*
39340033 AAATGACCAAAATACCC-CTAAGGGTA
1 AAATGACCAAAATACCCTCAAAGGGTA
39340059 AAAT
1 AAAT
39340063 TACCGTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATACCCTCAAAGGGTA
Found at i:39343103 original size:34 final size:34
Alignment explanation
Indices: 39343060--39343135 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
39343050 AGATTTAAAC
39343060 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
39343094 AAATTAATTACTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
39343128 AAGTTAAT
1 AAATTAAT
39343136 GAACTAACTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:39345075 original size:6 final size:6
Alignment explanation
Indices: 39345066--39345119 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
39345056 TCGCTTGCAA
* * **
39345066 TTTCTT TTTCTT TTTCAT TTTCTA TTTCTT TTTCAC TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
39345114 TTTCTT
1 TTTCTT
39345120 CCTCTTTGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:39345087 original size:18 final size:17
Alignment explanation
Indices: 39345039--39345117 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 17
39345029 TTTTCTCTCA
39345039 CTTTTTCGATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
** *
39345057 CGCTTGCAATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
39345075 CTTTTTCATTTTCTATTT
1 CTTTTTCA-TTTCTTTTT
39345093 CTTTTTCACTTTCTTTTT
1 CTTTTTCA-TTTCTTTTT
39345111 CTTTTTC
1 CTTTTTC
39345118 TTCCTCTTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
17 1 0.02
18 49 0.98
ACGTcount: A:0.08, C:0.20, G:0.04, T:0.68
Consensus pattern (17 bp):
CTTTTTCATTTCTTTTT
Found at i:39347647 original size:37 final size:33
Alignment explanation
Indices: 39347575--39347639 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
39347565 TTAAACAAAT
39347575 TAATTACTAACACTTATTTAAGCTGAACTAAAA
1 TAATTACTAACACTTATTTAAGCTGAACTAAAA
*
39347608 TAATTACTAACACTTATTTGAGCTGAACTAAA
1 TAATTACTAACACTTATTTAAGCTGAACTAAA
39347640 GTTAATAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (33 bp):
TAATTACTAACACTTATTTAAGCTGAACTAAAA
Found at i:39357032 original size:28 final size:27
Alignment explanation
Indices: 39356975--39357126 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
39356965 TAAATTGTGC
*
39356975 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
39357002 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
39357030 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
39357057 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
39357085 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
39357112 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39357127 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:39357039 original size:55 final size:55
Alignment explanation
Indices: 39356975--39357126 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
39356965 TAAATTGTGC
*
39356975 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
39357030 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
39357085 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
39357127 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:39369330 original size:17 final size:17
Alignment explanation
Indices: 39369301--39369333 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39369291 TAGAATTCGT
39369301 TTGAGTAAATTATTTAA
1 TTGAGTAAATTATTTAA
39369318 TTGAG-AAATTTATTTA
1 TTGAGTAAA-TTATTTA
39369334 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTGAGTAAATTATTTAA
Found at i:39384308 original size:22 final size:22
Alignment explanation
Indices: 39384263--39384308 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
39384253 CGTATGCTAA
* * * *
39384263 ATTTGTGATAAATATGTTTTTG
1 ATTTGTGATAAAAAAGATTATG
39384285 ATTTGTGATAAAAAAGATTATG
1 ATTTGTGATAAAAAAGATTATG
39384307 AT
1 AT
39384309 GTGATGAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (22 bp):
ATTTGTGATAAAAAAGATTATG
Found at i:39385620 original size:30 final size:30
Alignment explanation
Indices: 39385584--39385645 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
39385574 AATTGGTAAA
39385584 ATTAACAAAAGATAAATAAAAGAATAGAAG
1 ATTAACAAAAGATAAATAAAAGAATAGAAG
39385614 ATTAACAAAAGATAAATAAAAGAATAGAAG
1 ATTAACAAAAGATAAATAAAAGAATAGAAG
39385644 AT
1 AT
39385646 AAAGATAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.66, C:0.03, G:0.13, T:0.18
Consensus pattern (30 bp):
ATTAACAAAAGATAAATAAAAGAATAGAAG
Found at i:39385824 original size:29 final size:29
Alignment explanation
Indices: 39385769--39385824 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
39385759 ATTTTTATTT
*
39385769 ATTTGAAGTGACTAAATTGAGAAAAATAA
1 ATTTGAAGTGACTAAATTAAGAAAAATAA
*
39385798 ATTTGAAGTGACCTAAA-TAAGACAAAT
1 ATTTGAAGTGA-CTAAATTAAGAAAAAT
39385825 CATATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (29 bp):
ATTTGAAGTGACTAAATTAAGAAAAATAA
Found at i:39395494 original size:15 final size:16
Alignment explanation
Indices: 39395476--39395505 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39395466 TTTCGCCCTT
39395476 TTCATTTTCA-TTTTC
1 TTCATTTTCACTTTTC
39395491 TTCATTTTCACTTTT
1 TTCATTTTCACTTTT
39395506 ATTTTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCATTTTCACTTTTC
Found at i:39398743 original size:23 final size:22
Alignment explanation
Indices: 39398713--39398770 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
39398703 ATATGAATCA
*
39398713 AAAT-TAATTATAATAATTAACC
1 AAATATAATAATAATAATT-ACC
*
39398735 AAATATAATAATTATAATTACC
1 AAATATAATAATAATAATTACC
39398757 ATAATTATAATAAT
1 A-AA-TATAATAAT
39398771 GTTTGACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 8 0.26
23 14 0.45
24 9 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATAATAATAATAATTACC
Found at i:39404467 original size:39 final size:40
Alignment explanation
Indices: 39404376--39404634 Score: 298
Period size: 39 Copynumber: 6.6 Consensus size: 40
39404366 TCCTCGTTCA
* * * *
39404376 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39404414 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39404454 AATGCCATC-GGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39404493 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39404532 AATGCCTTCGGGACTTAACCC-GATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
39404571 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
39404611 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39404635 CAGCATTCAA
Statistics
Matches: 192, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
38 30 0.16
39 103 0.54
40 51 0.27
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39412070 original size:40 final size:40
Alignment explanation
Indices: 39412022--39412285 Score: 361
Period size: 40 Copynumber: 6.6 Consensus size: 40
39412012 CTCCTGTTCA
* * *
39412022 AATGCCTTCGGGACATAGCCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39412062 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39412102 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39412142 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39412182 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
39412222 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
39412262 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39412286 CAGCATTCAA
Statistics
Matches: 205, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 3 0.01
40 194 0.95
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39415153 original size:17 final size:16
Alignment explanation
Indices: 39415130--39415168 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
39415120 ATTGTAACAC
*
39415130 CCCAAAAATCTCGAAA
1 CCCAAAAATCTCAAAA
39415146 CCCAAAAATCTCAAAA
1 CCCAAAAATCTCAAAA
*
39415162 TCCAAAA
1 CCCAAAA
39415169 CTTTTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.31, G:0.03, T:0.13
Consensus pattern (16 bp):
CCCAAAAATCTCAAAA
Found at i:39416690 original size:21 final size:21
Alignment explanation
Indices: 39416637--39416677 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39416627 AATGAGTATA
*
39416637 TCATAGCATATCATGTGCATC
1 TCATAACATATCATGTGCATC
39416658 TCATAACATATCATGTGCAT
1 TCATAACATATCATGTGCAT
39416678 ACCATGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
TCATAACATATCATGTGCATC
Found at i:39418507 original size:19 final size:20
Alignment explanation
Indices: 39418483--39418520 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39418473 CACAACCCAA
39418483 TACCAAATT-TTAAAAATTC
1 TACCAAATTCTTAAAAATTC
*
39418502 TACCAAATTCTTGAAAATT
1 TACCAAATTCTTAAAAATT
39418521 ACGAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (20 bp):
TACCAAATTCTTAAAAATTC
Found at i:39430380 original size:39 final size:39
Alignment explanation
Indices: 39430294--39430502 Score: 248
Period size: 39 Copynumber: 5.4 Consensus size: 39
39430284 TCCTCGTTCA
* * ** *
39430294 AATGCCTTCGGGACATAGCCCGG-TTTAGTAACTCACAC-
1 AATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCACG
39430332 AATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACG
39430371 AATGCCTTCGGACTTAACCCGGATTT---AACTCGCACG
1 AATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACG
*
39430407 AATGCCTTCGGACTTAACCCGGATTTAACAACTCTCACG
1 AATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACG
* ** * *
39430446 AATGCCTTCGGGACTTAACCCGAATTTAGTATCTCGCACA
1 AATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCACG
*
39430486 AAGGCCTTCGGATCTTA
1 AATGCCTTCGGA-CTTA
39430503 GTCCGGATAT
Statistics
Matches: 151, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
36 36 0.24
37 11 0.07
38 21 0.14
39 47 0.31
40 36 0.24
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:39430423 original size:75 final size:75
Alignment explanation
Indices: 39430294--39430502 Score: 276
Period size: 75 Copynumber: 2.7 Consensus size: 75
39430284 TCCTCGTTCA
* * * *
39430294 AATGCCTTCGGGACATAGCCCGGTTTAGTAACTCACACAATGCCTTCGGACTTAACCCGGATTTA
1 AATGCCTTCGGGACTTAACCCGGATT--TAACTCGCACAATGCCTTCGGACTTAACCCGGATTTA
39430359 ACAACTCGCACG
64 ACAACTCGCACG
39430371 AATGCCTTC-GGACTTAACCCGGATTTAACTCGCACGAATGCCTTCGGACTTAACCCGGATTTAA
1 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCAC-AATGCCTTCGGACTTAACCCGGATTTAA
*
39430435 CAACTCTCACG
65 CAACTCGCACG
* *
39430446 AATGCCTTCGGGACTTAACCCGAATTTAGTATCTCGCACAAAGGCCTTCGGATCTTA
1 AATGCCTTCGGGACTTAACCCGGATTTA--A-CTCGCAC-AATGCCTTCGGA-CTTA
39430503 GTCCGGATAT
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
74 9 0.08
75 47 0.40
76 30 0.25
77 9 0.08
78 1 0.01
79 18 0.15
80 4 0.03
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (75 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACAATGCCTTCGGACTTAACCCGGATTTAAC
AACTCGCACG
Found at i:39430558 original size:41 final size:41
Alignment explanation
Indices: 39430481--39430558 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39430471 TTAGTATCTC
* * *
39430481 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39430522 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39430559 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39438302 original size:40 final size:40
Alignment explanation
Indices: 39438211--39438420 Score: 305
Period size: 40 Copynumber: 5.3 Consensus size: 40
39438201 TCCTCGTTCA
* * * ** *
39438211 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
39438250 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
39438290 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
39438330 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCTCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
39438370 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
39438410 AAGGCCTTCGG
1 AATGCCTTCGG
39438421 ATCTTAGTCC
Statistics
Matches: 157, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 33 0.21
40 124 0.79
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:39438433 original size:120 final size:119
Alignment explanation
Indices: 39438211--39438473 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
39438201 TCCTCGTTCA
* * **
39438211 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * *
39438276 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
39438329 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCTCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
39438394 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
39438450 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39438474 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 36 0.30
120 80 0.66
121 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:39438457 original size:80 final size:80
Alignment explanation
Indices: 39438214--39438473 Score: 260
Period size: 80 Copynumber: 3.3 Consensus size: 80
39438204 TCGTTCAAAT
* * * ** * * *
39438214 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
39438278 ACAACTCGCACGAAT
66 ACAACTCTCACGAAA
* * *
39438293 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
*
39438358 ACAACTCTCACGAAT
66 ACAACTCTCACGAAA
** * **
39438373 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
*
39438437 ATTC-ACT-TAGCAC-AAA
65 A-ACAACTCT--CACGAAA
*
39438453 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
39438474 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
79 34 0.22
80 120 0.76
81 4 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ACAACTCTCACGAAA
Found at i:39438482 original size:41 final size:41
Alignment explanation
Indices: 39438405--39438482 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39438395 TTAGTATCTC
* * *
39438405 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39438446 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39438483 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39441544 original size:20 final size:18
Alignment explanation
Indices: 39441519--39441561 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
39441509 TGATATGTTT
*
39441519 TTAATACTTTTTTATTAATA
1 TTAATA-TTTATTATTAA-A
39441539 TTAATATTTATTATTAAA
1 TTAATATTTATTATTAAA
39441557 TTAAT
1 TTAAT
39441562 CATATAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATATTTATTATTAAA
Found at i:39461636 original size:20 final size:20
Alignment explanation
Indices: 39461611--39461656 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39461601 AATTAAACCG
39461611 AGCTCAAATGAGCTGAATTA
1 AGCTCAAATGAGCTGAATTA
** *
39461631 AGCTCATGTGAGTTGAATTA
1 AGCTCAAATGAGCTGAATTA
*
39461651 AACTCA
1 AGCTCA
39461657 TGTGAGCTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (20 bp):
AGCTCAAATGAGCTGAATTA
Found at i:39461657 original size:20 final size:20
Alignment explanation
Indices: 39461619--39461664 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
39461609 CGAGCTCAAA
*
39461619 TGAGCTGAATTAAGCTCATG
1 TGAGCTGAATTAAACTCATG
*
39461639 TGAGTTGAATTAAACTCATG
1 TGAGCTGAATTAAACTCATG
39461659 TGAGCT
1 TGAGCT
39461665 AAACCGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (20 bp):
TGAGCTGAATTAAACTCATG
Found at i:39469519 original size:41 final size:41
Alignment explanation
Indices: 39469460--39469608 Score: 244
Period size: 41 Copynumber: 3.6 Consensus size: 41
39469450 CATTGAATGT
* * * *
39469460 AAGGGGTTGCTAAATGCAGATTCCTTGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCTGAAACTCTGATCAAA
39469501 AAGGGGTTGCTAAGTGCAGATTCCCTGAAACTCTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCTGAAACTCTGATCAAA
*
39469542 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCTGAAACTCTGATCAAA
*
39469583 AAGGGGTAGCTAAGTGCAGATTCCCT
1 AAGGGGTTGCTAAGTGCAGATTCCCT
39469609 AAGGGGTTGC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 101 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCTGAAACTCTGATCAAA
Found at i:39469620 original size:26 final size:26
Alignment explanation
Indices: 39469583--39469633 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
39469573 TCTGATCAAA
39469583 AAGGGGTAGCTAAGTGCAGATTCCCT
1 AAGGGGTAGCTAAGTGCAGATTCCCT
* *
39469609 AAGGGGTTGCTAAGTGCTGATTCCC
1 AAGGGGTAGCTAAGTGCAGATTCCC
39469634 CGAATTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (26 bp):
AAGGGGTAGCTAAGTGCAGATTCCCT
Found at i:39474413 original size:56 final size:58
Alignment explanation
Indices: 39474279--39474414 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 58
39474269 TATTCCAAAA
* * *
39474279 ATACTATTATTTTAATAGTTTTAATATTTAATTTAATTTAATAATTATCTTAGAGATAAGT
1 ATACTATTAATTTAATA-TTTTAATATTAAATTTAATTGAATAATTATCTT--AGATAAGT
**
39474340 ATACTATTAATTTAATATATTTAATATTAAATTTAATTGAATGTTTATCTT-GATAAGT
1 ATACTATTAATTTAATAT-TTTAATATTAAATTTAATTGAATAATTATCTTAGATAAGT
39474398 AT--TA-TATATTTAATATT
1 ATACTATTA-ATTTAATATT
39474415 AAAGTGATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
55 3 0.04
56 11 0.16
58 9 0.13
60 1 0.01
61 44 0.65
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (58 bp):
ATACTATTAATTTAATATTTTAATATTAAATTTAATTGAATAATTATCTTAGATAAGT
Found at i:39475882 original size:9 final size:9
Alignment explanation
Indices: 39475868--39475953 Score: 84
Period size: 9 Copynumber: 9.4 Consensus size: 9
39475858 TTTGGTTAAA
39475868 AATTACCCG
1 AATTACCCG
*
39475877 AATTACCTG
1 AATTACCCG
39475886 AATTACCCG
1 AATTACCCG
*
39475895 AATTACCTG
1 AATTACCCG
* *
39475904 AATTAACCA
1 AATTACCCG
*
39475913 AATTAACCG
1 AATTACCCG
39475922 AATTA-CCG
1 AATTACCCG
*
39475930 AAAAATACCCG
1 --AATTACCCG
*
39475941 AATTACCCA
1 AATTACCCG
39475950 AATT
1 AATT
39475954 TTTTTTTATT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
8 3 0.05
9 54 0.84
10 4 0.06
11 3 0.05
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:39488189 original size:18 final size:18
Alignment explanation
Indices: 39488162--39488201 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
39488152 ACTGTTGTTC
*
39488162 AGAA-TTGTTGCTGTAGA
1 AGAAGTTGTTGCTGAAGA
39488179 AGAAGTTGTTGCTGAAGA
1 AGAAGTTGTTGCTGAAGA
39488197 AGAAG
1 AGAAG
39488202 AAGTTGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (18 bp):
AGAAGTTGTTGCTGAAGA
Found at i:39488207 original size:18 final size:18
Alignment explanation
Indices: 39488168--39488212 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
39488158 GTTCAGAATT
* **
39488168 GTTGCTGTAGAAGAAGTT
1 GTTGCTGAAGAAGAAGAA
39488186 GTTGCTGAAGAAGAAGAA
1 GTTGCTGAAGAAGAAGAA
*
39488204 GTTGTTGAA
1 GTTGCTGAA
39488213 AATGAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (18 bp):
GTTGCTGAAGAAGAAGAA
Found at i:39499438 original size:20 final size:20
Alignment explanation
Indices: 39499413--39499466 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
39499403 TTAACCCTTC
39499413 CATTTACTTACTTTCCATTG
1 CATTTACTTACTTTCCATTG
39499433 CATTTACTTACTTTCCATTG
1 CATTTACTTACTTTCCATTG
*
39499453 TATTTACTTACTTT
1 CATTTACTTACTTT
39499467 AGCTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (20 bp):
CATTTACTTACTTTCCATTG
Found at i:39513274 original size:7 final size:7
Alignment explanation
Indices: 39513243--39513284 Score: 57
Period size: 7 Copynumber: 5.6 Consensus size: 7
39513233 GGAGGAAAAG
39513243 AAATGAAA
1 AAAT-AAA
39513251 AAATAATA
1 AAATAA-A
39513259 AAATGAAA
1 AAAT-AAA
39513267 AAATAAA
1 AAATAAA
39513274 AAATAAA
1 AAATAAA
39513281 AAAT
1 AAAT
39513285 GTAAAGCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 16 0.50
8 14 0.44
9 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:39513289 original size:16 final size:16
Alignment explanation
Indices: 39513243--39513284 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
39513233 GGAGGAAAAG
39513243 AAATGAAAAAATAATA
1 AAATGAAAAAATAATA
39513259 AAATGAAAAAATAA-A
1 AAATGAAAAAATAATA
39513274 AAAT-AAAAAAT
1 AAATGAAAAAAT
39513285 GTAAAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
16 14 0.54
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (16 bp):
AAATGAAAAAATAATA
Found at i:39513827 original size:18 final size:18
Alignment explanation
Indices: 39513792--39513834 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
39513782 GTTGGGTTCT
*
39513792 GAAATAAAAATAAATTAA
1 GAAATAAAAACAAATTAA
*
39513810 -AAATTAAAACAAATTTAA
1 GAAATAAAAACAAA-TTAA
39513828 GAAATAA
1 GAAATAA
39513835 TTTCACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 11 0.55
18 4 0.20
19 5 0.25
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
GAAATAAAAACAAATTAA
Found at i:39518699 original size:34 final size:34
Alignment explanation
Indices: 39518656--39518735 Score: 128
Period size: 34 Copynumber: 2.4 Consensus size: 34
39518646 ACTCTACATT
*
39518656 GCTTAATCAATCTTCCATGATCTCCAATTCGTCC
1 GCTTAATCAAGCTTCCATGATCTCCAATTCGTCC
39518690 GCTTAATCAAGCTTCCATGATCTCCAATTCGT-C
1 GCTTAATCAAGCTTCCATGATCTCCAATTCGTCC
*
39518723 -CTTGATCAAGCTT
1 GCTTAATCAAGCTT
39518736 GGAACTTCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 12 0.27
33 1 0.02
34 31 0.70
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (34 bp):
GCTTAATCAAGCTTCCATGATCTCCAATTCGTCC
Found at i:39527106 original size:21 final size:21
Alignment explanation
Indices: 39527049--39527113 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
39527039 ATATAATATT
*
39527049 AATTTAGTTATAATTTAAAAA
1 AATTTAATTATAATTTAAAAA
* * *
39527070 AATAATT-ATTAAAATTTACAAC
1 AAT--TTAATTATAATTTAAAAA
*
39527092 AATTTAATTATAATTTTAAAA
1 AATTTAATTATAATTTAAAAA
39527113 A
1 A
39527114 TTCAAAGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.06
21 15 0.45
22 14 0.42
23 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTTAATTATAATTTAAAAA
Found at i:39527166 original size:20 final size:19
Alignment explanation
Indices: 39527130--39527180 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
39527120 GAAATATATA
*
39527130 AAAATATCTA-AATATTTT
1 AAAATATATATAATATTTT
*
39527148 CAAATATATATAATAATTTT
1 AAAATATATATAAT-ATTTT
*
39527168 AAAAAATATATAA
1 AAAATATATATAA
39527181 AAATAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.30
19 3 0.11
20 16 0.59
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATATATATAATATTTT
Found at i:39527243 original size:50 final size:49
Alignment explanation
Indices: 39527121--39527223 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 49
39527111 AAATTCAAAG
** *
39527121 AAATATATAAAAATATCTAAATATTTTCAAATATATATAATAATTTTAAA
1 AAATATATAAAAATAAATAAATATTTTCAAATATATATAATAAATTT-AA
39527171 AAATATATAAAAATAAATAAATATTTTCAAAATATTATAATAATAAATTTAA
1 AAATATATAAAAATAAATAAATATTTTC-AAATA-TAT-ATAATAAATTTAA
39527223 A
1 A
39527224 TTTTATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
50 26 0.55
51 5 0.11
52 6 0.13
53 10 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (49 bp):
AAATATATAAAAATAAATAAATATTTTCAAATATATATAATAAATTTAA
Done.