Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 132 of 150
Found at i:39691132 original size:18 final size:18
Alignment explanation
Indices: 39691109--39691148 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39691099 TACTCGGAAA
* *
39691109 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
39691127 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
39691145 AGGA
1 AGGA
39691149 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:39693033 original size:12 final size:12
Alignment explanation
Indices: 39692982--39693026 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
39692972 ATTAAATATG
39692982 AATTTGAGAG-A
1 AATTTGAGAGAA
*
39692993 AATTTG-GAAGGA
1 AATTTGAG-AGAA
39693005 AA-TTGAGAGAA
1 AATTTGAGAGAA
39693016 AATTTGAGAGA
1 AATTTGAGAGA
39693027 GGATTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGAA
Found at i:39703844 original size:18 final size:17
Alignment explanation
Indices: 39703802--39703851 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
39703792 TAATATCGAT
39703802 TATTCAAATAA-AAAAG
1 TATTCAAATAACAAAAG
*
39703818 TATTTAAATAACAAAA-
1 TATTCAAATAACAAAAG
*
39703834 TAAATTCAAATTACAAAA
1 T--ATTCAAATAACAAAA
39703852 AAAAGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 11 0.39
17 4 0.14
18 13 0.46
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (17 bp):
TATTCAAATAACAAAAG
Found at i:39705867 original size:30 final size:30
Alignment explanation
Indices: 39705831--39705893 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
39705821 ACTTATTTTA
39705831 TTGTTAATTTTATTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
* *
39705861 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
39705891 TTG
1 TTG
39705894 CTTGTTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:39706031 original size:11 final size:11
Alignment explanation
Indices: 39706015--39706045 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
39706005 TATATATATT
39706015 TAAAAATTATA
1 TAAAAATTATA
39706026 TAAAAATTATA
1 TAAAAATTATA
39706037 TAAAAATTA
1 TAAAAATTA
39706046 ATACGGGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:39712199 original size:31 final size:32
Alignment explanation
Indices: 39712164--39712223 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
39712154 ATGTGTATGA
*
39712164 TTGAATCAAAATTAAAA-TTTCAT-GTATACAT
1 TTGAACCAAAA-TAAAAGTTTCATGGTATACAT
*
39712195 TTGAACCATAATAAAAGTTTCATGGTATA
1 TTGAACCAAAATAAAAGTTTCATGGTATA
39712224 ATTACACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 15 0.60
32 5 0.20
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (32 bp):
TTGAACCAAAATAAAAGTTTCATGGTATACAT
Found at i:39712257 original size:29 final size:29
Alignment explanation
Indices: 39712223--39712286 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
39712213 TTCATGGTAT
*
39712223 AATTACAC-CAAATCAAAATTCATGTATCA
1 AATTACACACAAATCAAAATTCATATAT-A
*
39712252 AATTACACATTAAATCAAAATTCATATATA
1 AATTACACA-CAAATCAAAATTCATATATA
39712282 AATTA
1 AATTA
39712287 AAATTTCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 8 0.26
30 6 0.19
31 17 0.55
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.31
Consensus pattern (29 bp):
AATTACACACAAATCAAAATTCATATATA
Found at i:39722914 original size:26 final size:27
Alignment explanation
Indices: 39722864--39722914 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
39722854 TTTTAAATGT
*
39722864 TCGTGTTCATTAATTTTAAATTTATGC
1 TCGTGTTCATTAATTTTAAAATTATGC
*
39722891 TCGTGTTCATTTA-TTTAAAATTAT
1 TCGTGTTCATTAATTTTAAAATTAT
39722915 ATATTTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (27 bp):
TCGTGTTCATTAATTTTAAAATTATGC
Found at i:39727820 original size:6 final size:6
Alignment explanation
Indices: 39727776--39727816 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
39727766 TTGTAGTTGG
* * *
39727776 AAATGG AAATGA AAATGA AAATGA AAATAA AAATGG AAATG
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATG
39727817 GAAACTTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AAATGA
Found at i:39728007 original size:26 final size:25
Alignment explanation
Indices: 39727964--39728035 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
39727954 AAATTTCTCG
*
39727964 AAAA-TTTACTAGGGGTAAAATCGTC
1 AAAATTTTACTA-GAGTAAAATCGTC
*
39727989 AAAATTTTA-TCATGAGTAAAATCGTT
1 AAAATTTTACT-A-GAGTAAAATCGTC
39728015 AAAATTTTACTAGAGTAAAAT
1 AAAATTTTACTAGAGTAAAAT
39728036 TGGGATGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 14 0.34
26 26 0.63
27 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (25 bp):
AAAATTTTACTAGAGTAAAATCGTC
Found at i:39729564 original size:13 final size:13
Alignment explanation
Indices: 39729522--39729606 Score: 66
Period size: 13 Copynumber: 6.4 Consensus size: 13
39729512 TTTAGTGTTA
39729522 TTTTATTATTTAT
1 TTTTATTATTTAT
*
39729535 TTTTCTTAATGTTTAT
1 TTTTATT-A--TTTAT
39729551 TTATT-TTATTTAT
1 TT-TTATTATTTAT
*
39729564 TTTTATTTTTTAT
1 TTTTATTATTTAT
**
39729577 TTTTATT-TTGGT
1 TTTTATTATTTAT
* *
39729589 TTTTATTTTTTCT
1 TTTTATTATTTAT
39729602 TTTTA
1 TTTTA
39729607 CACGTTCTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
12 12 0.20
13 35 0.58
14 1 0.02
15 1 0.02
16 9 0.15
17 2 0.03
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:39729568 original size:19 final size:18
Alignment explanation
Indices: 39729527--39729599 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
39729517 TGTTATTTTA
*
39729527 TTATTTATTTTTCTTAATGT
1 TTATTTATTTTT-TT-ATTT
39729547 TTATTTATTTTATTTATTT
1 TTATTTATTTT-TTTATTT
*
39729566 TTATTTTTTATTTTTATTT
1 TTATTTATT-TTTTTATTT
*
39729585 TGGTTTTTATTTTTT
1 T--TATTTATTTTTT
39729600 CTTTTTACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 19 0.42
20 19 0.42
21 7 0.16
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.78
Consensus pattern (18 bp):
TTATTTATTTTTTTATTT
Found at i:39729570 original size:6 final size:6
Alignment explanation
Indices: 39729546--39729598 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
39729536 TTTCTTAATG
**
39729546 TTTATT TATT-TT ATTTATT TTTATTT TTTATT TTTATT TTGGTT TTTATT
1 TTTATT T-TTATT -TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT
39729596 TTT
1 TTT
39729599 TCTTTTTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 28 0.72
7 11 0.28
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:39730243 original size:21 final size:21
Alignment explanation
Indices: 39730217--39730271 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
39730207 ACAGGCAACT
39730217 CACACGGGCGTGTGTCCCCTC
1 CACACGGGCGTGTGTCCCCTC
**
39730238 CACACGGGCGTGTGTGGCCTC
1 CACACGGGCGTGTGTCCCCTC
**
39730259 CACATAGGCGTGT
1 CACACGGGCGTGT
39730272 AGACCCCCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.13, C:0.35, G:0.33, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTGTGTCCCCTC
Found at i:39733128 original size:14 final size:14
Alignment explanation
Indices: 39733109--39733144 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39733099 TCATTTAATC
*
39733109 ACCAAAATTATTAA
1 ACCAAAATTATCAA
*
39733123 ACCAAAATTATCAG
1 ACCAAAATTATCAA
39733137 ACCAAAAT
1 ACCAAAAT
39733145 CTAATATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (14 bp):
ACCAAAATTATCAA
Found at i:39743056 original size:21 final size:21
Alignment explanation
Indices: 39743030--39743183 Score: 98
Period size: 21 Copynumber: 7.3 Consensus size: 21
39743020 CTGAAGGCTT
*
39743030 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * *
39743051 AACAGAAACCCATAA-AGGTTG
1 AACAGAAGCTCATAAGA-GCTA
* *
39743072 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
39743093 AAC-GACAACACATAAGGGTTA
1 AACAGA-AGCTCATAAGAGCTA
*
39743114 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
39743135 AACATAAACTCATATGAGTTG
1 AACAGAAGCTCATAAGAGCTA
*
39743156 AACAGAAGCTTATGAA-AGCTA
1 AACAGAAGCTCAT-AAGAGCTA
39743177 AACAGAA
1 AACAGAA
39743184 AGTAAATACG
Statistics
Matches: 96, Mismatches: 32, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
20 3 0.03
21 89 0.93
22 4 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:39743090 original size:42 final size:42
Alignment explanation
Indices: 39743030--39743184 Score: 163
Period size: 42 Copynumber: 3.7 Consensus size: 42
39743020 CTGAAGGCTT
* *
39743030 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAAGGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACACATAAAGGTTG
* * * *
39743072 AACAGAAGCTCGTAAGAGCTGAAC-GACAACACATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGA-AACACATAAAGGTTG
* * * *
39743114 AACAGAAGCTCAAAAGAGCTAAACATAAACTCAT-ATGAGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACACATAAAG-GTTG
*
39743156 AACAGAAGCTTATGAA-AGCTAAACAGAAA
1 AACAGAAGCTCAT-AAGAGCTAAACAGAAA
39743185 GTAAATACGA
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.04
42 86 0.92
43 3 0.03
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACACATAAAGGTTG
Found at i:39744706 original size:21 final size:21
Alignment explanation
Indices: 39744676--39744790 Score: 133
Period size: 21 Copynumber: 5.5 Consensus size: 21
39744666 CGTGTTTTAC
39744676 TTTCTGTTCAACTCTTATGAG
1 TTTCTGTTCAACTCTTATGAG
* * *
39744697 TTTATGTTCAGCTCTTACGAG
1 TTTCTGTTCAACTCTTATGAG
*
39744718 CTTT-TGTTTAACTCTTATGAG
1 -TTTCTGTTCAACTCTTATGAG
*
39744739 TTTCTGTTCAACTCTTATAAG
1 TTTCTGTTCAACTCTTATGAG
* *
39744760 TTTCTGTTCAGCTCTTACGAG
1 TTTCTGTTCAACTCTTATGAG
* *
39744781 CTTCTATTCA
1 TTTCTGTTCA
39744791 GGTTTTGAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 3 0.04
21 73 0.92
22 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (21 bp):
TTTCTGTTCAACTCTTATGAG
Found at i:39744791 original size:21 final size:21
Alignment explanation
Indices: 39744677--39744807 Score: 104
Period size: 21 Copynumber: 6.3 Consensus size: 21
39744667 GTGTTTTACT
* * *
39744677 TTCTGTTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
*
39744698 TTATGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * * *
39744719 TTTTGTTTAACTCTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
* ** *
39744740 TTCTGTTCAACTCTTATAAGT
1 TTCTGTTCAGCTCTTACGAGC
39744761 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * *
39744782 TTCTATTCAGGT-TT-TGAGC
1 TTCTGTTCAGCTCTTACGAGC
39744801 TTCTGTT
1 TTCTGTT
39744808 AACAATGTAC
Statistics
Matches: 90, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 10 0.11
20 2 0.02
21 78 0.87
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:39747769 original size:11 final size:13
Alignment explanation
Indices: 39747749--39747780 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39747739 AATAAATTAA
39747749 TAAAATATCAT-T
1 TAAAATATCATAT
39747761 TAAAA-ATCATAT
1 TAAAATATCATAT
39747773 TAAAATAT
1 TAAAATAT
39747781 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:39750363 original size:2 final size:2
Alignment explanation
Indices: 39750278--39750344 Score: 116
Period size: 2 Copynumber: 32.5 Consensus size: 2
39750268 TGAAATCAAG
39750278 TA TA TA TCA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39750322 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
39750345 CGTCATTATA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 59 0.94
3 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39750682 original size:2 final size:2
Alignment explanation
Indices: 39750479--39750666 Score: 243
Period size: 2 Copynumber: 93.0 Consensus size: 2
39750469 NNNNNNNNNN
* *
39750479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * ** * *
39750521 CAC AC ACT CAC AT -T CT AT CT AT AT AT AT AT AT AT CG CT CT AT
1 -AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39750563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39750605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39750647 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
39750667 CATTATAAAA
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.01
2 165 0.99
4 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39753640 original size:216 final size:217
Alignment explanation
Indices: 39753241--39753867 Score: 1003
Period size: 216 Copynumber: 2.9 Consensus size: 217
39753231 TCTAATTGAT
* *
39753241 GCAATATTTAGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
*
39753305 TTCAACCAAATGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTCTGCGTTTGGAA
66 TTCAACCAAATGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAA
39753370 ATTCGAGGAACGTGCCCTAAGGTGTTGGGTTGCGATTTCTCGTTCAACCAAATGGCTTAATATCC
131 ATTCGAGGAACGTGCCCTAAGGTGTTGGGTTGCGATTTCTCGTTCAACCAAATGGCTTAATATCC
*
39753435 TTTTCAAAAATCTCAATATATG
196 TTTTCAAAAATCTCAAAATATG
*
39753457 GCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
* *
39753522 TTCAACCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAATGTAATGTTTTGCGTTTGGAA
66 TTCAACCAAATGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAA
*
39753587 ATT-GAGGAACGTGCCCTAAGGTGCTGGGTTGCGATTTCTCGTTCAACCAAATGGCTTAATATCC
131 ATTCGAGGAACGTGCCCTAAGGTGTTGGGTTGCGATTTCTCGTTCAACCAAATGGCTTAATATCC
39753651 TTTTCAAAAATCTCAAAATATG
196 TTTTCAAAAATCTCAAAATATG
* * * *
39753673 GCAATGTTTTGCGTTTGGAGATTCGAGATAACATGCCCTAAGGTGCTGGATGTCGATTTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
* * * * * *
39753738 TTCAACTAAATAGCTAAATATC-CTTTCAAAAATTAT-AAAATGAGGCAATGTTTTGCGTTTGGA
66 TTCAACCAAATGGCTTAATATCTTTTTCAAAAATT-TCAAAATAAGGTAATGTTTTGCGTTTGGA
* * * *
39753801 ATTTCGAGGAACGTGCCCTAAGGTGTTGGGTTTCGATTTCTCGTTTAACCAAATTG-TTAAATAT
130 AATTCGAGGAACGTGCCCTAAGGTGTTGGGTTGCGATTTCTCGTTCAACCAAATGGCTT-AATAT
39753865 CCT
194 CCT
39753868 CTTGAATTTT
Statistics
Matches: 381, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
215 40 0.10
216 239 0.63
217 102 0.27
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (217 bp):
GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
TTCAACCAAATGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAA
ATTCGAGGAACGTGCCCTAAGGTGTTGGGTTGCGATTTCTCGTTCAACCAAATGGCTTAATATCC
TTTTCAAAAATCTCAAAATATG
Found at i:39765718 original size:87 final size:88
Alignment explanation
Indices: 39765539--39766134 Score: 457
Period size: 87 Copynumber: 6.8 Consensus size: 88
39765529 TGAATATTAG
** * ** * *
39765539 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
1 AGATCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAAGTCA-GGTCTTATCTCCCTGAGGTT
** ** **
39765603 ACAGTGGAGCGGA-TTAA-AA-TAA
64 ACAGTGGAGTAGACCGAAGAATTTC
* * *
39765625 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCAGGTCTTATCTCCCTGAGGTTA
1 A-GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAAGTCAGGTCTTATCTCCCTGAGGTTA
39765689 CAGTGGAGTAGACCGAAGAATTTC
65 CAGTGGAGTAGACCGAAGAATTTC
* ** * ** * *
39765713 AGATCTTATCTCCCCG-AGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
1 AGATCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAAGTCA-GGTCTTATCTCCCTGAGGTT
** ** **
39765777 ACAGTGGAGCGGA-TTAA-AA-TAA
64 ACAGTGGAGTAGACCGAAGAATTTC
* * * *
39765799 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCAGGTCTTATCTCCCTAAGGTTA
1 A-GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAAGTCAGGTCTTATCTCCCTGAGGTTA
*
39765863 CAGTGGAGTCGACCGAAGAATTTC
65 CAGTGGAGTAGACCGAAGAATTTC
* ** * ** * *
39765887 AGATCTTATCTCCCCG-AGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
1 AGATCTTATCTCCCTGAAG-TTACAGTAGAGCAGATCGAAGTCA-GGTCTTATCTCCCTGAGGTT
** ** **
39765951 ACAGTGGAGCGGA-TTAA-AA-TAA
64 ACAGTGGAGTAGACCGAAGAATTTC
* * *
39765973 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCAGGTCTTATCTCCCTGAGGTTA
1 A-GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAAGTCAGGTCTTATCTCCCTGAGGTTA
*
39766037 CAGTGGAGTAGACCGATGAATTTC
65 CAGTGGAGTAGACCGAAGAATTTC
* * * * * *
39766061 AGATCTTATCTCCCTGAGGTTACAGTGGAACAGATTGAAGCCAGAGATCTTATCTCCCTGAGATT
1 AGATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAAGTCAG-G-TCTTATCTCCCTGAGGTT
39766126 ACAGTGGAG
64 ACAGTGGAG
39766135 CAGATCACAT
Statistics
Matches: 390, Mismatches: 96, Indels: 44
0.74 0.18 0.08
Matches are distributed among these distances:
85 80 0.21
86 20 0.05
87 187 0.48
88 23 0.06
89 54 0.14
90 26 0.07
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (88 bp):
AGATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGAAGTCAGGTCTTATCTCCCTGAGGTTAC
AGTGGAGTAGACCGAAGAATTTC
Found at i:39765722 original size:46 final size:45
Alignment explanation
Indices: 39765539--39766140 Score: 344
Period size: 44 Copynumber: 13.8 Consensus size: 45
39765529 TGAATATTAG
* * *
39765539 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * ** * **
39765581 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAA-AATAA
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * *
39765625 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA-TC
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* *
39765667 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAA-TTC
* * * *
39765713 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAG-A--C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * ** * **
39765755 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAA-AATAA
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * *
39765799 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA-TC
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * *
39765841 AGGTCTTATCTCCCTAAGGTTACAGTGGAGTCGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAA-TTC
* * * *
39765887 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAG-A--C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * ** * **
39765929 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAA-AATAA
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * * *
39765973 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA-TC
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
* * *
39766015 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGATGAATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAA-TTC
** * * *
39766061 AGATCTTATCTCCCTGAGGTTACAGTGGAACAGATTGAAGCCA--G
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG-AATTC
* *
39766105 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATC
39766141 ACATCAAGTC
Statistics
Matches: 425, Mismatches: 101, Indels: 66
0.72 0.17 0.11
Matches are distributed among these distances:
41 88 0.21
42 17 0.04
43 85 0.20
44 126 0.30
45 2 0.00
46 106 0.25
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATTC
Found at i:39766201 original size:348 final size:348
Alignment explanation
Indices: 39765539--39766203 Score: 984
Period size: 348 Copynumber: 1.9 Consensus size: 348
39765529 TGAATATTAG
*
39765539 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
39765604 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
39765669 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCCGAGATT
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCCGAGATT
* ** *
39765734 ACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
196 ACAGCGGAACAGATCGAAGACAAGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
* * * * ** * * * *
39765799 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTTAC
261 AGGATCTTATCTCCCTGAAGTAACAGGAGAGTAAAAAGAACCAGATCCTATCTCCCTAAGGTTAC
39765864 AGTGGAGTCGACCGAAGAATTTC
326 AGTGGAGTCGACCGAAGAATTTC
39765887 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
39765952 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* * *
39766017 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGATGAATTTCAGATCTTATCTCCCTGAGGTT
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCCGAGATT
* * * * * *
39766082 ACAGTGGAACAGATTGAAGCCAGAGATCTTATCTCCCTG-AGATTACAGTGGAGCAGA-TCACAT
196 ACAGCGGAACAGATCGAAGACA-AGATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAAT
* *
39766145 CAA-G-TCTTATCTCCCTAAGCAGTAAC-GGAGCAG-ACAAAAGAAACCA-ATCCTATCTCCCT
259 AAAGGATCTTATCTCCCT--GAAGTAACAGGAG-AGTA-AAAAG-AACCAGATCCTATCTCCCT
39766204 GAGCAGCAGT
Statistics
Matches: 284, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
346 11 0.04
347 5 0.02
348 238 0.84
349 30 0.11
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (348 bp):
AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCCGAGATT
ACAGCGGAACAGATCGAAGACAAGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
AGGATCTTATCTCCCTGAAGTAACAGGAGAGTAAAAAGAACCAGATCCTATCTCCCTAAGGTTAC
AGTGGAGTCGACCGAAGAATTTC
Found at i:39766206 original size:174 final size:174
Alignment explanation
Indices: 39765539--39766135 Score: 1052
Period size: 174 Copynumber: 3.4 Consensus size: 174
39765529 TGAATATTAG
*
39765539 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
39765604 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
39765669 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
39765713 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
39765778 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
39765843 GTCTTATCTCCCTAAGGTTACAGTGGAGTCGACCGAAGAATTTC
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
39765887 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
39765952 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
39766017 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGATGAATTTC
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
* * * * * * ** *
39766061 AGATCTTATCTCCCTGAGGTTACAGTGGAACAGATTGAAGCCAGAGATCTTATCTCCCTG-AGAT
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCTCCCTGAAG-T
39766125 TACAGTGGAGC
64 TACAGTGGAGC
39766136 AGATCACATC
Statistics
Matches: 406, Mismatches: 15, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
174 381 0.94
175 25 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (174 bp):
AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
Found at i:39768774 original size:109 final size:108
Alignment explanation
Indices: 39768475--39769087 Score: 758
Period size: 109 Copynumber: 5.7 Consensus size: 108
39768465 TCTAATTGAT
* *
39768475 GCAATATTTAGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGAT-TTTCTCGT
* * *
39768540 TCAAGCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAG
65 TCAACCAAACGGCTTAATATCCTTTTCAAAAATCTCAAAATAAG
* * * * *
39768584 GTAATGTTCTGCGTTTGGAAATTTGAGGAACGTGCCCTAAGGTGCTGGGT-TACGA-TTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGT-CGATTTTCTCGT
* * *
39768647 TCAACCAAAAGGCTTAATATCCTTTT-AAAAATCTCAATATATG
65 TCAACCAAACGGCTTAATATCCTTTTCAAAAATCTCAAAATAAG
* *
39768690 GCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCTAGGTGTCGATCTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGTCGAT-TTTCTCG
* *
39768755 TTCAACCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAG
64 TTCAACCAAACGGCTTAATATCCTTTTCAAAAATCTCAAAATAAG
* * * *
39768800 GTAATGTTCTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGT-TGCGA-TTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGT-CGATTTTCTCGT
* * *
39768863 TAAACCAAATGGCTTAATATCCTTTTCAAAAATCTCAAAATATG
65 TCAACCAAACGGCTTAATATCCTTTTCAAAAATCTCAAAATAAG
* *
39768907 GCAATGTTTTGCGTTTGGAGATTCGAGATAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGA-AACATGCCCTAAGGTGCTGGGTGTCGA-TTTTCTCG
** * * *
39768972 TTCAACCAAATAGCTAAATATCC-TTTCAAAAAT-TATAAAATGAG
64 TTCAACCAAACGGCTTAATATCCTTTTCAAAAATCT-CAAAATAAG
* * * *
39769016 GCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTTAGGTGTTGGGT-TCCGA-TTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGT-CGATTTTCTCGT
*
39769079 TTAACCAAA
65 TCAACCAAA
39769088 TTGTTAAATA
Statistics
Matches: 436, Mismatches: 55, Indels: 29
0.84 0.11 0.06
Matches are distributed among these distances:
106 52 0.12
107 126 0.29
108 50 0.11
109 144 0.33
110 64 0.15
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (108 bp):
GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCTCGTT
CAACCAAACGGCTTAATATCCTTTTCAAAAATCTCAAAATAAG
Found at i:39768879 original size:216 final size:217
Alignment explanation
Indices: 39768475--39769101 Score: 967
Period size: 216 Copynumber: 2.9 Consensus size: 217
39768465 TCTAATTGAT
* *
39768475 GCAATATTTAGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
*
39768539 TTCAAGCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTCTGCGTTTGGAA
66 TTCAACCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTCTGCGTTTGGAA
* * *
39768604 ATTTGAGGAACGTGCCCTAAGGTGCTGGGTTACGATTTCTCGTTCAACCAAAAGGCTTAATATCC
131 ATTCGAGGAACGTGCCCTAAGGTGCTGGGTTACGATTTCTCGTTAAACCAAATGGCTTAATATCC
*
39768669 TTTT-AAAAATCTCAATATATG
196 TTTTCAAAAATCTCAAAATATG
* *
39768690 GCAATGTTTTGCGTTTGGAAATTCAAGAAAACATGCCCTAAGGTGCTAGGTGTCGATCTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
39768755 TTCAACCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTCTGCGTTTGGAA
66 TTCAACCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTCTGCGTTTGGAA
*
39768820 ATTCGAGGAACGTGCCCTAAGGTGCTGGGTTGCGATTTCTCGTTAAACCAAATGGCTTAATATCC
131 ATTCGAGGAACGTGCCCTAAGGTGCTGGGTTACGATTTCTCGTTAAACCAAATGGCTTAATATCC
39768885 TTTTCAAAAATCTCAAAATATG
196 TTTTCAAAAATCTCAAAATATG
* * * *
39768907 GCAATGTTTTGCGTTTGGAGATTCGAGATAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
** * * * * *
39768972 TTCAACCAAATAGCTAAATATC-CTTTCAAAAATTAT-AAAATGAGGCAATGTTTTGCGTTTGGA
66 TTCAACCAAACGGCTTAATATCTTTTTCAAAAATT-TCAAAATAAGGTAATGTTCTGCGTTTGGA
* * * * *
39769035 AATTCGAGGAACGTGCCCTTAGGTGTTGGGTTCCGATTTCTCGTTTAACCAAATTG-TTAAATAT
130 AATTCGAGGAACGTGCCCTAAGGTGCTGGGTTACGATTTCTCGTTAAACCAAATGGCTT-AATAT
39769099 CCT
194 CCT
39769102 CTTGAATTTT
Statistics
Matches: 380, Mismatches: 28, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
215 26 0.07
216 259 0.68
217 95 0.25
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (217 bp):
GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATCTTTCTCG
TTCAACCAAACGGCTTAATATCTTTTTCAAAAATTTCAAAATAAGGTAATGTTCTGCGTTTGGAA
ATTCGAGGAACGTGCCCTAAGGTGCTGGGTTACGATTTCTCGTTAAACCAAATGGCTTAATATCC
TTTTCAAAAATCTCAAAATATG
Found at i:39769922 original size:23 final size:24
Alignment explanation
Indices: 39769876--39769921 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39769866 ATGTTCATAT
*
39769876 ATTTTCACATGTTATTTCCTTTTA
1 ATTTCCACATGTTATTTCCTTTTA
*
39769900 ATTTCCACGTGTTATTTCCTTT
1 ATTTCCACATGTTATTTCCTTT
39769922 ACTTTCCGAT
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:0.17, C:0.20, G:0.07, T:0.57
Consensus pattern (24 bp):
ATTTCCACATGTTATTTCCTTTTA
Found at i:39781185 original size:21 final size:22
Alignment explanation
Indices: 39781152--39781193 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
39781142 TCCATATTTG
39781152 TATATTAATTTTAATATTATTA
1 TATATTAATTTTAATATTATTA
39781174 TATATT-ATTTTAATATTATT
1 TATATTAATTTTAATATTATT
39781194 TTTTCTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATTAATTTTAATATTATTA
Found at i:39781191 original size:11 final size:11
Alignment explanation
Indices: 39781153--39781195 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
39781143 CCATATTTGT
39781153 ATATTAATTTTA
1 ATATT-ATTTTA
*
39781165 ATATTATTAT-
1 ATATTATTTTA
39781175 ATATTATTTTA
1 ATATTATTTTA
39781186 ATATTATTTT
1 ATATTATTTT
39781196 TTCTAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 14 0.50
12 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTTTA
Found at i:39787751 original size:12 final size:12
Alignment explanation
Indices: 39787721--39787754 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
39787711 TATATATTTT
39787721 AAAATT-ATATA
1 AAAATTAATATA
39787732 AAAA-TAATATA
1 AAAATTAATATA
39787743 AAAATTAATATA
1 AAAATTAATATA
39787755 GGCGGGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 13 0.62
12 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:39788165 original size:17 final size:17
Alignment explanation
Indices: 39788149--39788181 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39788139 AATTGGGTTG
39788149 GAAAAATT-ATTTAGTT
1 GAAAAATTAATTTAGTT
*
39788165 GATAAATTAATTTAGTT
1 GAAAAATTAATTTAGTT
39788182 AATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
GAAAAATTAATTTAGTT
Found at i:39788185 original size:9 final size:9
Alignment explanation
Indices: 39788169--39788218 Score: 75
Period size: 9 Copynumber: 5.7 Consensus size: 9
39788159 TTAGTTGATA
39788169 AATTAATTT
1 AATTAATTT
*
39788178 AGTTAATTT
1 AATTAATTT
39788187 AATTAATTT
1 AATTAATTT
*
39788196 AATTAATTA
1 AATTAATTT
39788205 AATTAATTT
1 AATTAATTT
39788214 -ATTAA
1 AATTAA
39788219 ATAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
8 5 0.14
9 32 0.86
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
AATTAATTT
Found at i:39788201 original size:13 final size:13
Alignment explanation
Indices: 39788169--39788224 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
39788159 TTAGTTGATA
* *
39788169 AATTAATTTAGTT
1 AATTAATTAAATT
*
39788182 AATTTAATTAATTT
1 AA-TTAATTAAATT
39788196 AATTAATTAAATT
1 AATTAATTAAATT
*
39788209 AATTTATTAAA-T
1 AATTAATTAAATT
39788221 AATT
1 AATT
39788225 TTTTTGGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 5 0.13
13 22 0.58
14 11 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
AATTAATTAAATT
Found at i:39788660 original size:52 final size:52
Alignment explanation
Indices: 39788598--39788705 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
39788588 TGAGAATAAA
39788598 TTCTCTCTATTTTTCGACATAGTAACAATCTCTCAAAGTTGTGTGTAAATAG
1 TTCTCTCTATTTTTCGACATAGTAACAATCTCTCAAAGTTGTGTGTAAATAG
39788650 TTCTCTCTATTTTTCGACATAGTAACAATCTCTCAAAGTTGTGTGTAAATAG
1 TTCTCTCTATTTTTCGACATAGTAACAATCTCTCAAAGTTGTGTGTAAATAG
39788702 TTCT
1 TTCT
39788706 ACCTGTGCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (52 bp):
TTCTCTCTATTTTTCGACATAGTAACAATCTCTCAAAGTTGTGTGTAAATAG
Found at i:39789004 original size:22 final size:21
Alignment explanation
Indices: 39788975--39789132 Score: 77
Period size: 20 Copynumber: 7.8 Consensus size: 21
39788965 TTTTTATTTT
39788975 AAAA-ATTTTAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
**
39788995 AAATATATTTTAAAAATATTTTA
1 AAA-ATATTTTAAAAA-ATTAAA
39789018 AAAATATTTT--AAAATTAAA
1 AAAATATTTTAAAAAATTAAA
* **
39789037 AAAA-A--TTAAAAAAATATTT
1 AAAATATTTTAAAAAATTA-AA
* *
39789056 TAAA-A-TTAAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
**
39789075 AAAAGTATTTTAAAAATATT-TT
1 AAAA-TATTTTAAAAA-ATTAAA
**
39789097 AAAAT-TTAAAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
* *
39789117 AAAGTA-TGTAAAAAAT
1 AAAATATTTTAAAAAAT
39789133 ATTTTAAAAT
Statistics
Matches: 102, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
16 2 0.02
18 7 0.07
19 18 0.18
20 34 0.33
21 3 0.03
22 28 0.27
23 10 0.10
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAATATTTTAAAAAATTAAA
Found at i:39789011 original size:13 final size:13
Alignment explanation
Indices: 39788993--39789024 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39788983 TAAAAAATTA
39788993 AAAAATATATTTT
1 AAAAATATATTTT
39789006 -AAAA-ATATTTT
1 AAAAATATATTTT
39789017 AAAAATAT
1 AAAAATAT
39789025 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.41
12 8 0.47
13 2 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAAATATATTTT
Found at i:39789066 original size:28 final size:29
Alignment explanation
Indices: 39789017--39789089 Score: 130
Period size: 29 Copynumber: 2.5 Consensus size: 29
39789007 AAAATATTTT
39789017 AAAAATATTTTAAAATTAAAAAAAATTAA
1 AAAAATATTTTAAAATTAAAAAAAATTAA
39789046 AAAAATATTTTAAAATT-AAAAAAATTAA
1 AAAAATATTTTAAAATTAAAAAAAATTAA
39789074 AAAAAGTATTTTAAAA
1 AAAAA-TATTTTAAAA
39789090 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 16 0.37
29 27 0.63
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAAATATTTTAAAATTAAAAAAAATTAA
Found at i:39789068 original size:8 final size:9
Alignment explanation
Indices: 39789028--39789078 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
39789018 AAAATATTTT
39789028 AAAATTAAAA
1 AAAATT-AAA
39789038 AAAATTAAA
1 AAAATTAAA
***
39789047 AAAATATTTT
1 AAAAT-TAAA
39789057 AAAATTAAA
1 AAAATTAAA
39789066 AAAATTAAA
1 AAAATTAAA
39789075 AAAA
1 AAAA
39789079 GTATTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 22 0.65
10 12 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAATTAAA
Found at i:39789071 original size:80 final size:81
Alignment explanation
Indices: 39788969--39789153 Score: 236
Period size: 80 Copynumber: 2.3 Consensus size: 81
39788959 GGCCCATTTT
* **
39788969 TATTTTAAAAATTTTAAAAAATTAAAAAATA-TATTTTAAAAATATTTTAAAAATATT-TTAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAA-AGTATTTTAAAAATATTTT-AAAAT-TTAAAAAAA
39789032 TTAAAAAA-AAT-TAAAAAAA
62 TTAAAAAAGAATGT-AAAAAA
39789051 TATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAATTA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTT-AAAAAAATTA
*
39789115 AAAAAGTATGTAAAAAA
65 AAAAAGAATGTAAAAAA
39789132 TATTTTAAAATTTTAAAAAAAT
1 TATTTTAAAA-TTTAAAAAAAT
39789154 AAATATATTT
Statistics
Matches: 92, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
78 2 0.02
79 6 0.07
80 45 0.49
81 22 0.24
82 7 0.08
83 10 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (81 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
AAAAGAATGTAAAAAA
Found at i:39789141 original size:11 final size:11
Alignment explanation
Indices: 39788969--39789100 Score: 81
Period size: 11 Copynumber: 12.9 Consensus size: 11
39788959 GGCCCATTTT
39788969 TATTTT-AAAA
1 TATTTTAAAAA
39788979 -ATTTTAAAAA
1 TATTTTAAAAA
**
39788989 -ATTAAAAAATA
1 TATTTTAAAA-A
39789000 TATTTTAAAAA
1 TATTTTAAAAA
39789011 TATTTTAAAAA
1 TATTTTAAAAA
39789022 TATTTT--AAA
1 TATTTTAAAAA
*
39789031 -A-TTAAAAAA
1 TATTTTAAAAA
* **
39789040 AATTAAAAAAA
1 TATTTTAAAAA
39789051 TATTTT--AAA
1 TATTTTAAAAA
39789060 -A--TTAAAAA
1 TATTTTAAAAA
* **
39789068 AATTAAAAAAA
1 TATTTTAAAAA
39789079 GTATTTTAAAAA
1 -TATTTTAAAAA
39789091 TATTTTAAAA
1 TATTTTAAAA
39789101 TTTAAAAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 5 0.05
9 15 0.16
10 12 0.13
11 44 0.46
12 15 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:39789152 original size:11 final size:11
Alignment explanation
Indices: 39788975--39789153 Score: 58
Period size: 10 Copynumber: 17.5 Consensus size: 11
39788965 TTTTTATTTT
39788975 AAAAATTTT-A
1 AAAAATTTTAA
*
39788985 AAAAA-TTAAA
1 AAAAATTTTAA
39788995 AAATATATTTTAA
1 AAA-A-ATTTTAA
*
39789008 AAATATTTTAA
1 AAAAATTTTAA
*
39789019 AAATATTTT--
1 AAAAATTTTAA
39789028 -AAAA--TTAA
1 AAAAATTTTAA
*
39789036 AAAAA-ATTAA
1 AAAAATTTTAA
39789046 AAAAATATTT--
1 AAAAAT-TTTAA
*
39789056 TAAAA--TTAA
1 AAAAATTTTAA
*
39789065 AAAAA-TTAAA
1 AAAAATTTTAA
39789075 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
39789088 AAATATTTT--
1 AAAAATTTTAA
39789097 -AAAA-TTTAA
1 AAAAATTTTAA
*
39789106 AAAAA-ATTAA
1 AAAAATTTTAA
* *
39789116 AAAAGTATGTAA
1 AAAAAT-TTTAA
39789128 AAAATATTTT--
1 AAAA-ATTTTAA
39789138 -AAAATTTTAA
1 AAAAATTTTAA
39789148 AAAAAT
1 AAAAAT
39789154 AAATATATTT
Statistics
Matches: 127, Mismatches: 17, Indels: 49
0.66 0.09 0.25
Matches are distributed among these distances:
6 2 0.02
7 5 0.04
8 11 0.09
9 13 0.10
10 41 0.32
11 27 0.21
12 13 0.10
13 15 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:39789737 original size:6 final size:7
Alignment explanation
Indices: 39789712--39789744 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
39789702 TGCAAATGAA
39789712 TCATTTC
1 TCATTTC
39789719 TCATTTC
1 TCATTTC
39789726 TCATTT-
1 TCATTTC
39789732 TCATTT-
1 TCATTTC
39789738 TCATTTC
1 TCATTTC
39789745 CATATTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (7 bp):
TCATTTC
Found at i:39789800 original size:45 final size:46
Alignment explanation
Indices: 39789751--39789840 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
39789741 TTTCCATATT
*
39789751 GAGAAAATCA-AATTCATTTCTAAAT-TATTCAATTTCTCCATTTCG
1 GAGAAAACCATAA-TCATTTCTAAATGTATTCAATTTCTCCATTTCG
* * * *
39789796 GAGAAAACCATAATCATTTCTGAATGTTTTCCATTTCTCTATTTC
1 GAGAAAACCATAATCATTTCTAAATGTATTCAATTTCTCCATTTC
39789841 TATTCATTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (46 bp):
GAGAAAACCATAATCATTTCTAAATGTATTCAATTTCTCCATTTCG
Found at i:39791607 original size:2 final size:2
Alignment explanation
Indices: 39791600--39791631 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39791590 CTTTCCTCCT
39791600 TA TA 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 TA TA
39791632 ACCTAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39798173 original size:3 final size:3
Alignment explanation
Indices: 39798167--39798214 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
39798157 ATCGGAATTT
* * * *
39798167 TTA TTA TTA TCA TTG TTA TTA TTA ATA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39798215 CTTTTTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:39801781 original size:69 final size:69
Alignment explanation
Indices: 39801697--39801844 Score: 251
Period size: 69 Copynumber: 2.1 Consensus size: 69
39801687 GAAAAGGGTG
* * *
39801697 AGCTAAAAGTTAGAGTGGCTGAACTTGAGAAAACTTTTTATCGGTATCGAAATCGTAAATCTGTA
1 AGCTAAGAGCTAGAGTGGCTGAACTTGAGAAAACTTTTTATCGGTATCGAAATCATAAATCTGTA
39801762 ATGA
66 ATGA
*
39801766 AGCTAAGAGCTAGAGTGGCTGAACTTGAGAAAACTTTTTATCGGTATCGAAATCATAATTCTGTA
1 AGCTAAGAGCTAGAGTGGCTGAACTTGAGAAAACTTTTTATCGGTATCGAAATCATAAATCTGTA
*
39801831 ATGG
66 ATGA
39801835 AGCTAAGAGC
1 AGCTAAGAGC
39801845 GATTTTAGAC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (69 bp):
AGCTAAGAGCTAGAGTGGCTGAACTTGAGAAAACTTTTTATCGGTATCGAAATCATAAATCTGTA
ATGA
Found at i:39810162 original size:12 final size:12
Alignment explanation
Indices: 39810145--39810169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39810135 AAATTGAGAC
39810145 TATCCCTTCAGA
1 TATCCCTTCAGA
39810157 TATCCCTTCAGA
1 TATCCCTTCAGA
39810169 T
1 T
39810170 TTTGTTGTCA
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:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:39811027 original size:132 final size:131
Alignment explanation
Indices: 39810790--39811134 Score: 528
Period size: 132 Copynumber: 2.6 Consensus size: 131
39810780 GTGTATTAAA
*
39810790 GAAGACTGTGAATCTTATCTTCCCAAGGAAGTAAGGAAGCAAATTTAAGCCACCAGTCCTATCTC
1 GAAGACGGTGAATCTTATCTTCCCAAGGAAGT-AGGAAGCAAATTTAAGCCACCAGTCCTATCTC
* *
39810855 CCTAAGCAGCAGTGGAGTAGGTTGAATATTGTAGATCCTGTATCCCTAAGCAGTAGTGGAGCAGA
65 CCTGAGCAGCAGTGGAGTAGGTTGAATATTGTAGATCCTGTATCCCTAAGCAATAGTGGAGCAGA
39810920 TC
130 TC
* * *
39810922 GAAGACGGTGAATCTTATCTTCCCAAAGAAGTAGGAAATCAAATTTAAGCCACCAGTTCTATCTC
1 GAAGACGGTGAATCTTATCTTCCCAAGGAAGTAGG-AAGCAAATTTAAGCCACCAGTCCTATCTC
* * *
39810987 CCTGAGCAACAGTGGAGTAGGTTGAATATTGTAGATCCTGTCTCCCTAAGCAATAGTGGAGTAGA
65 CCTGAGCAGCAGTGGAGTAGGTTGAATATTGTAGATCCTGTATCCCTAAGCAATAGTGGAGCAGA
39811052 TC
130 TC
** * *
39811054 GAAGACGGTGGCTCTTATCTTCCCAAGGAAGTAGGGAAGCAGATTTAAGCCATCAGTCCTATCTC
1 GAAGACGGTGAATCTTATCTTCCCAAGGAAGTA-GGAAGCAAATTTAAGCCACCAGTCCTATCTC
* *
39811119 CTTGAGTAGCAGTGGA
65 CCTGAGCAGCAGTGGA
39811135 ATAGNNNNNN
Statistics
Matches: 192, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
131 3 0.02
132 187 0.97
133 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (131 bp):
GAAGACGGTGAATCTTATCTTCCCAAGGAAGTAGGAAGCAAATTTAAGCCACCAGTCCTATCTCC
CTGAGCAGCAGTGGAGTAGGTTGAATATTGTAGATCCTGTATCCCTAAGCAATAGTGGAGCAGAT
C
Found at i:39813248 original size:20 final size:20
Alignment explanation
Indices: 39813205--39813248 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
39813195 CTAAAGGTTG
* *
39813205 AAAATTAAAACTTTAGGGGG
1 AAAATAAAAACTTTAGGGGA
* *
39813225 AAAATAAAAAGTTTTGGGGA
1 AAAATAAAAACTTTAGGGGA
39813245 AAAA
1 AAAA
39813249 AAGTTCGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (20 bp):
AAAATAAAAACTTTAGGGGA
Found at i:39813845 original size:9 final size:9
Alignment explanation
Indices: 39813831--39813867 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39813821 TATAGTTTGA
39813831 TATTCGAAT
1 TATTCGAAT
39813840 TATTCGAAT
1 TATTCGAAT
*
39813849 TATTCGAGT
1 TATTCGAAT
39813858 TATTCGAAT
1 TATTCGAAT
39813867 T
1 T
39813868 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:39813938 original size:9 final size:9
Alignment explanation
Indices: 39813921--39813951 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39813911 TCGAGTTGAT
39813921 TCGAATAAC
1 TCGAATAAC
*
39813930 TCGATTAAC
1 TCGAATAAC
39813939 TCGAATAAC
1 TCGAATAAC
39813948 TCGA
1 TCGA
39813952 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:39814578 original size:3 final size:3
Alignment explanation
Indices: 39814572--39814622 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
39814562 TCAGATTTTT
* * * *
39814572 TTA TTA TCA TTG TTA TTA TTA ATA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39814620 TTA
1 TTA
39814623 GTTTTTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:39814592 original size:15 final size:15
Alignment explanation
Indices: 39814572--39814622 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
39814562 TCAGATTTTT
*
39814572 TTATTATCATTGTTA
1 TTATTATCATTATTA
39814587 TTATTAAT-ATTATTA
1 TTATT-ATCATTATTA
39814602 TTATTATCATTATTA
1 TTATTATCATTATTA
39814617 TTATTA
1 TTATTA
39814623 GTTTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 2 0.06
15 29 0.88
16 2 0.06
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (15 bp):
TTATTATCATTATTA
Found at i:39817675 original size:26 final size:26
Alignment explanation
Indices: 39817646--39817700 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39817636 ATAATTATAT
*
39817646 TTTAAAATATTAAAATTTAATACTTA
1 TTTAAAATATTAAAATTTAATAATTA
** *
39817672 TTTAGTATATTTAAATTTAATAATTA
1 TTTAAAATATTAAAATTTAATAATTA
39817698 TTT
1 TTT
39817701 TCATACACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTAAAATATTAAAATTTAATAATTA
Found at i:39821870 original size:17 final size:18
Alignment explanation
Indices: 39821830--39821890 Score: 86
Period size: 19 Copynumber: 3.3 Consensus size: 18
39821820 TATACACATT
39821830 AAAATATATAAAAATAAA
1 AAAATATATAAAAATAAA
39821848 ATAAATATATAAAAATAAA
1 A-AAATATATAAAAATAAA
**
39821867 AAATATATATAAATCTAAA
1 AAA-ATATATAAAAATAAA
39821886 AAAAT
1 AAAAT
39821891 TGTAAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.13
19 34 0.87
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATATAAAAATAAA
Found at i:39822118 original size:19 final size:20
Alignment explanation
Indices: 39822094--39822138 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
39822084 TTAATTACTT
39822094 TTTTTATAATATT-TTTCGA-
1 TTTTTAT-ATATTATTTCGAC
*
39822113 TTTTTATATATTATTTTGAC
1 TTTTTATATATTATTTCGAC
39822133 TTTTTA
1 TTTTTA
39822139 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTATATATTATTTCGAC
Found at i:39822129 original size:20 final size:21
Alignment explanation
Indices: 39822090--39822138 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
39822080 AAATTTAATT
*
39822090 ACTTTTTTTATAATATTTTTCG
1 ACTTTTTATATAATATTTTT-G
*
39822112 A-TTTTTATATATTA-TTTTG
1 ACTTTTTATATAATATTTTTG
39822131 ACTTTTTA
1 ACTTTTTA
39822139 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 11 0.46
22 1 0.04
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (21 bp):
ACTTTTTATATAATATTTTTG
Found at i:39822375 original size:19 final size:18
Alignment explanation
Indices: 39822331--39822379 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
39822321 AATATTATAA
39822331 TTTA-TTTTTATAATATT
1 TTTATTTTTTATAATATT
*
39822348 TTTCCATTTTTGTATATTATT
1 TTT--ATTTTT-TATAATATT
39822369 TTTATTTTTTA
1 TTTATTTTTTA
39822380 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 7 0.26
20 4 0.15
21 11 0.41
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTATTTTTTATAATATT
Found at i:39822391 original size:22 final size:23
Alignment explanation
Indices: 39822366--39822408 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39822356 TTTGTATATT
*
39822366 ATTTTTAT-TTTTTAAAATTTAA
1 ATTTATATATTTTTAAAATTTAA
39822388 ATTTATATATTTTTAAAATTT
1 ATTTATATATTTTTAAAATTT
39822409 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTATATATTTTTAAAATTTAA
Found at i:39822402 original size:16 final size:15
Alignment explanation
Indices: 39822383--39822442 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 15
39822373 TTTTTTAAAA
39822383 TTTAAATTTATATATT
1 TTTAAATTT-TATATT
*
39822399 TTTAAAATTTTTTATT
1 TTT-AAATTTTATATT
*
39822415 TTTAAACTTT-T-TT
1 TTTAAATTTTATATT
* *
39822428 TTAAAATTATATATT
1 TTTAAATTTTATATT
39822443 ACAATTGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
13 9 0.25
14 2 0.06
15 8 0.22
16 11 0.31
17 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAAATTTTATATT
Found at i:39822408 original size:17 final size:16
Alignment explanation
Indices: 39822386--39822425 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
39822376 TTTAAAATTT
39822386 AAATTTATATATTTTTA
1 AAATTT-TATATTTTTA
*
39822403 AAATTTTTTATTTTTA
1 AAATTTTATATTTTTA
*
39822419 AACTTTT
1 AAATTTT
39822426 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATTTTATATTTTTA
Found at i:39822428 original size:17 final size:16
Alignment explanation
Indices: 39822395--39822427 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39822385 TAAATTTATA
39822395 TATTTTTAAAATTTTT
1 TATTTTTAAAATTTTT
*
39822411 TATTTTTAAACTTTTT
1 TATTTTTAAAATTTTT
39822427 T
1 T
39822428 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTAAAATTTTT
Found at i:39823979 original size:24 final size:24
Alignment explanation
Indices: 39823926--39823971 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
39823916 TCTTTGTAGA
*
39823926 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGTATTTATTAGCATAAT
39823950 ATATTTAGTATTTATTAGCATA
1 ATATTTAGTATTTATTAGCATA
39823972 GTTTATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (24 bp):
ATATTTAGTATTTATTAGCATAAT
Found at i:39833583 original size:15 final size:16
Alignment explanation
Indices: 39833553--39833585 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39833543 TAGTCATTCT
*
39833553 ATTAAAAATTTCATCC
1 ATTAAAAATTTAATCC
39833569 ATTAAAAA-TTAATCC
1 ATTAAAAATTTAATCC
39833584 AT
1 AT
39833586 ATATGTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAAAATTTAATCC
Found at i:39836381 original size:25 final size:25
Alignment explanation
Indices: 39836344--39836411 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
39836334 CGGACACACC
*
39836344 ACAGCTCGTATGAGCTTC-AGATTTTT
1 ACAGCTCGCATGAGCTTCTAGA--TTT
*
39836370 A-AGCTCGCATGAGCTTCTCGATTT
1 ACAGCTCGCATGAGCTTCTAGATTT
39836394 ACAGCTCGCATGAGCTTC
1 ACAGCTCGCATGAGCTTC
39836412 CCTTTATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 4 0.11
25 31 0.82
26 3 0.08
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCTAGATTT
Found at i:39836423 original size:25 final size:26
Alignment explanation
Indices: 39836345--39836425 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 26
39836335 GGACACACCA
* *
39836345 CAGCTCGTATGAGCTTCAGATTT-TT
1 CAGCTCGCATGAGCTTCACATTTATT
* *
39836370 AAGCTCGCATGAGCTTCTCGATTTA--
1 CAGCTCGCATGAGCTTCAC-ATTTATT
*
39836395 CAGCTCGCATGAGCTTC-CCTTTATT
1 CAGCTCGCATGAGCTTCACATTTATT
39836420 CAGCTC
1 CAGCTC
39836426 ACATATGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 4 0.09
24 1 0.02
25 37 0.80
26 4 0.09
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.35
Consensus pattern (26 bp):
CAGCTCGCATGAGCTTCACATTTATT
Found at i:39836425 original size:50 final size:49
Alignment explanation
Indices: 39836344--39836457 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 49
39836334 CGGACACACC
* * *
39836344 ACAGCTCGTATGAGCTTCAGATTTTTAAGCTCGCATGA-GCTTCTCGATTT
1 ACAGCTCGTATGAGCTTCACATTTTTAAGCTCACAT-ATGCTTCCCG-TTT
* * * *
39836394 ACAGCTCGCATGAGCTTC-CCTTTATTCAGCTCACATATGTTTCCCGTTT
1 ACAGCTCGTATGAGCTTCACATTT-TTAAGCTCACATATGCTTCCCGTTT
39836443 ACAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
39836458 ATACATGTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
49 21 0.39
50 33 0.61
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (49 bp):
ACAGCTCGTATGAGCTTCACATTTTTAAGCTCACATATGCTTCCCGTTT
Found at i:39845932 original size:28 final size:26
Alignment explanation
Indices: 39845884--39845938 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
39845874 TATCCTTTTG
*
39845884 TAACTTTTTATAAATAATTAATAATT
1 TAACTTTTTATAAATAATTAAGAATT
**
39845910 TAACATTTTTATATAATTTTTAAGAATT
1 TAAC-TTTTTATA-AATAATTAAGAATT
39845938 T
1 T
39845939 TATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 8 0.33
28 12 0.50
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
TAACTTTTTATAAATAATTAAGAATT
Found at i:39848149 original size:22 final size:22
Alignment explanation
Indices: 39848123--39848164 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39848113 GTAGCTGCTG
*
39848123 TTTGCTGCCATTTTGATATTGT
1 TTTGCTACCATTTTGATATTGT
* *
39848145 TTTGCTATCATTTTGCTATT
1 TTTGCTACCATTTTGATATT
39848165 ATATTACTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (22 bp):
TTTGCTACCATTTTGATATTGT
Found at i:39848174 original size:22 final size:22
Alignment explanation
Indices: 39848131--39848181 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
39848121 TGTTTGCTGC
* * *
39848131 CATTTTGATATTGTTTTGCTAT
1 CATTTTGATATTATATTACTAT
*
39848153 CATTTTGCTATTATATTACTAT
1 CATTTTGATATTATATTACTAT
*
39848175 TATTTTG
1 CATTTTG
39848182 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (22 bp):
CATTTTGATATTATATTACTAT
Found at i:39850078 original size:42 final size:42
Alignment explanation
Indices: 39850019--39850102 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
39850009 CACTTTCGTC
39850019 CATGCAAAATATGTATAAATGTTGTTTCAACACCAATCGGTT
1 CATGCAAAATATGTATAAATGTTGTTTCAACACCAATCGGTT
* *
39850061 CATGCAGAATGTGTATAAATGTTGTTTCAACACCAATCGGTT
1 CATGCAAAATATGTATAAATGTTGTTTCAACACCAATCGGTT
39850103 AGCTAGAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (42 bp):
CATGCAAAATATGTATAAATGTTGTTTCAACACCAATCGGTT
Found at i:39851495 original size:24 final size:25
Alignment explanation
Indices: 39851430--39851495 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
39851420 AGATTAATAT
* *
39851430 TTATAAA-TATGAAATTTATTTTTA
1 TTATAAATTATGAAATTTATTATAA
* * *
39851454 TTAATAACTAATGCAATTT-TTATAA
1 TT-ATAAATTATGAAATTTATTATAA
39851479 TTATAAATTATGAAATT
1 TTATAAATTATGAAATT
39851496 GATATTGTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
24 14 0.44
25 10 0.31
26 8 0.25
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (25 bp):
TTATAAATTATGAAATTTATTATAA
Found at i:39851870 original size:27 final size:27
Alignment explanation
Indices: 39851838--39851890 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
39851828 ATTGTAAGTT
39851838 AACCAACTTATTTTAATTAAGGCAATG
1 AACCAACTTATTTTAATTAAGGCAATG
39851865 AACCAACTTATTTTAATTAAGGCAAT
1 AACCAACTTATTTTAATTAAGGCAAT
39851891 AACTTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (27 bp):
AACCAACTTATTTTAATTAAGGCAATG
Found at i:39852401 original size:20 final size:20
Alignment explanation
Indices: 39852378--39852493 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
39852368 TCTCAACAAA
*
39852378 AATTACAAAAAATTCAAAAT
1 AATTATAAAAAATTCAAAAT
* *
39852398 AATTTTTAAAAATTCAAAAT
1 AATTATAAAAAATTCAAAAT
*
39852418 ATTTAT-AAAAATTACAAAAATT
1 AATTATAAAAAATT-C-AAAA-T
* * *
39852440 ATATTTTTAAAAAATTGTAAAAA
1 A-A-TTATAAAAAATT-CAAAAT
*
39852463 AATATATAAATAAATTTAAAA-
1 AAT-TATAAA-AAATTCAAAAT
39852484 AATTA-AAAAA
1 AATTATAAAAA
39852494 TTTCTAGAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.03
19 10 0.13
20 24 0.31
21 8 0.10
22 13 0.17
23 6 0.08
24 7 0.09
25 7 0.09
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (20 bp):
AATTATAAAAAATTCAAAAT
Found at i:39852421 original size:19 final size:20
Alignment explanation
Indices: 39852385--39852436 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
39852375 AAAAATTACA
*
39852385 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTAT
39852405 AAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTAT
39852424 AAAAATTACAAAA
1 AAAAATT-CAAAA
39852437 ATTATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:39852467 original size:24 final size:23
Alignment explanation
Indices: 39852413--39852467 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
39852403 TTAAAAATTC
39852413 AAAATATTTATAAAAATTACAAA
1 AAAATATTTATAAAAATTACAAA
* * **
39852436 AATTATATTTTTAAAAAATTGTAAA
1 AA-AATATTTAT-AAAAATTACAAA
39852461 AAAATAT
1 AAAATAT
39852468 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 11 0.44
25 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATATTTATAAAAATTACAAA
Found at i:39853898 original size:116 final size:116
Alignment explanation
Indices: 39853694--39853925 Score: 464
Period size: 116 Copynumber: 2.0 Consensus size: 116
39853684 TAAACACGAA
39853694 AAGATATTAAAATTGGTTTAAAATATTGTACCAACCGATACGTATTGGTCGAAACGGTAATAATA
1 AAGATATTAAAATTGGTTTAAAATATTGTACCAACCGATACGTATTGGTCGAAACGGTAATAATA
39853759 CATCGAAATATTAGCTGAAATTATTTGCCACTCCTCCGCTCTTTTAACAAG
66 CATCGAAATATTAGCTGAAATTATTTGCCACTCCTCCGCTCTTTTAACAAG
39853810 AAGATATTAAAATTGGTTTAAAATATTGTACCAACCGATACGTATTGGTCGAAACGGTAATAATA
1 AAGATATTAAAATTGGTTTAAAATATTGTACCAACCGATACGTATTGGTCGAAACGGTAATAATA
39853875 CATCGAAATATTAGCTGAAATTATTTGCCACTCCTCCGCTCTTTTAACAAG
66 CATCGAAATATTAGCTGAAATTATTTGCCACTCCTCCGCTCTTTTAACAAG
39853926 GTTTCAGACT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (116 bp):
AAGATATTAAAATTGGTTTAAAATATTGTACCAACCGATACGTATTGGTCGAAACGGTAATAATA
CATCGAAATATTAGCTGAAATTATTTGCCACTCCTCCGCTCTTTTAACAAG
Found at i:39857529 original size:11 final size:11
Alignment explanation
Indices: 39857489--39857670 Score: 94
Period size: 11 Copynumber: 17.9 Consensus size: 11
39857479 GGCCCATTTT
39857489 TATTTT-AAAA
1 TATTTTAAAAA
39857499 -ATTTTAAAAA
1 TATTTTAAAAA
**
39857509 -ATTAAAAAAA
1 TATTTTAAAAA
39857519 GTATTTTAAAAA
1 -TATTTTAAAAA
39857531 TATTTTAAAAA
1 TATTTTAAAAA
39857542 TATTTT--AAA
1 TATTTTAAAAA
39857551 -A--TTAAAAA
1 TATTTTAAAAA
* *
39857559 AATTTAAAAAA
1 TATTTTAAAAA
* *
39857570 AAATTTAAAAA
1 TATTTTAAAAA
*
39857581 AATTTT--AAA
1 TATTTTAAAAA
39857590 -A--TTAAAAA
1 TATTTTAAAAA
* **
39857598 AATTAAAAAAA
1 TATTTTAAAAA
39857609 GTATTTTAAAAA
1 -TATTTTAAAAA
39857621 TATTTT--AAA
1 TATTTTAAAAA
39857630 -ATTTTAAAAA
1 TATTTTAAAAA
* *
39857640 -AATTAAAAAA
1 TATTTTAAAAA
*
39857650 GTA-TGTAAAAA
1 -TATTTTAAAAA
39857661 TATTTTAAAA
1 TATTTTAAAA
39857671 TTAAAAAAAT
Statistics
Matches: 135, Mismatches: 18, Indels: 37
0.71 0.09 0.19
Matches are distributed among these distances:
6 4 0.03
8 13 0.10
9 16 0.12
10 25 0.19
11 60 0.44
12 17 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:39857570 original size:40 final size:40
Alignment explanation
Indices: 39857489--39857680 Score: 232
Period size: 40 Copynumber: 4.8 Consensus size: 40
39857479 GGCCCATTTT
* **
39857489 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATATTT-TAAAATTAAAAAAA-T-TTAAAAAAA
39857531 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAA
* *
39857571 -AATTTAAAAAAATTTTAAAATTAAAAAAA-TTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAA
*
39857609 GTATTTTAAAAATATTTTAAAATTTTAAAAAAA-TTAAAAAAG
1 -TATTTTAAAAATATTTTAAAA--TTAAAAAAATTTAAAAAAA
*
39857651 TA-TGTAAAAATATTTTAAAATTAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAT
39857681 AAATATATTT
Statistics
Matches: 135, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
38 18 0.13
39 27 0.20
40 42 0.31
41 3 0.02
42 42 0.31
43 3 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAA
Found at i:39857571 original size:12 final size:12
Alignment explanation
Indices: 39857554--39857582 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
39857544 TTTTAAAATT
39857554 AAAAAAATTTAA
1 AAAAAAATTTAA
39857566 AAAAAAATTTAA
1 AAAAAAATTTAA
39857578 AAAAA
1 AAAAA
39857583 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAATTTAA
Found at i:39857598 original size:17 final size:17
Alignment explanation
Indices: 39857535--39857601 Score: 71
Period size: 17 Copynumber: 3.6 Consensus size: 17
39857525 TAAAAATATT
*
39857535 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTTAAAA
*
39857552 TTAAAAAAATTTAAAAAAAAA
1 TTAAAAAAATTT----TAAAA
39857573 TTTAAAAAAATTTTAAAA
1 -TTAAAAAAATTTTAAAA
39857591 TTAAAAAAATT
1 TTAAAAAAATT
39857602 AAAAAAAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
17 22 0.52
18 4 0.10
21 4 0.10
22 12 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:39858434 original size:17 final size:18
Alignment explanation
Indices: 39858400--39858434 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39858390 ACTGCACGAC
39858400 CTCATGCAAATTACCAAAG
1 CTCATGCAAA-TACCAAAG
39858419 CTCATGCAAA-ACCAAA
1 CTCATGCAAATACCAAA
39858435 ATGAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.29, G:0.09, T:0.17
Consensus pattern (18 bp):
CTCATGCAAATACCAAAG
Found at i:39859205 original size:10 final size:11
Alignment explanation
Indices: 39859171--39859204 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
39859161 CTGGCCCGCC
39859171 TATATTAATTTT
1 TATA-TAATTTT
39859183 TATATAATTTT
1 TATATAATTTT
39859194 TATATAATTTT
1 TATATAATTTT
39859205 AAAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATAATTTT
Found at i:39860902 original size:2 final size:2
Alignment explanation
Indices: 39860895--39860928 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39860885 NNNNNNNNNG
39860895 TA TA TA 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 TA TA TA
39860929 CTTCAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39868765 original size:17 final size:18
Alignment explanation
Indices: 39868734--39868771 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
39868724 ATCTTCCACA
39868734 TTTTAATCTTATTATT-T
1 TTTTAATCTTATTATTGT
39868751 TTTTAATC-TATTTATTGT
1 TTTTAATCTTA-TTATTGT
39868769 TTT
1 TTT
39868772 GAATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 13 0.68
18 4 0.21
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAATCTTATTATTGT
Found at i:39869616 original size:6 final size:6
Alignment explanation
Indices: 39869605--39869645 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
39869595 TCTTAAAAAC
*
39869605 TATAAA TATAAA TATAAA TA-AAA TGTAAA TATAAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
39869646 AACATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
TATAAA
Found at i:39869633 original size:17 final size:17
Alignment explanation
Indices: 39869608--39869641 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39869598 TAAAAACTAT
39869608 AAATATAAATATAAATA
1 AAATATAAATATAAATA
*
39869625 AAATGTAAATATAAATA
1 AAATATAAATATAAATA
39869642 TAAAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATATAAATATAAATA
Found at i:39873688 original size:15 final size:15
Alignment explanation
Indices: 39873668--39873699 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39873658 AAACCTATAA
*
39873668 AAATTAAATTAAACT
1 AAATTAAATAAAACT
39873683 AAATTAAATAAAACT
1 AAATTAAATAAAACT
39873698 AA
1 AA
39873700 TAAGTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTAAATAAAACT
Found at i:39879877 original size:44 final size:44
Alignment explanation
Indices: 39879827--39879917 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
39879817 GTAGGTAAAA
* *
39879827 TAATATTAAAATAACCTATACTAATTAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
39879871 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
39879915 TAA
1 TAA
39879918 AAACAGAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
Found at i:39879944 original size:25 final size:25
Alignment explanation
Indices: 39879896--39879944 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39879886 CTACACTAAT
* * **
39879896 CAGAGTTTAAGTGGGAAACTAAAAA
1 CAGAGTTTAACTAGGAAAAGAAAAA
39879921 CAGAGTTTAACTAGGAAAAGAAAA
1 CAGAGTTTAACTAGGAAAAGAAAA
39879945 GCTGAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.18
Consensus pattern (25 bp):
CAGAGTTTAACTAGGAAAAGAAAAA
Found at i:39886398 original size:9 final size:9
Alignment explanation
Indices: 39886381--39886417 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39886371 TGAGTTTTCG
39886381 AATTCGAAT
1 AATTCGAAT
*
39886390 AACTCGAAT
1 AATTCGAAT
39886399 AATTCGAAT
1 AATTCGAAT
39886408 AATTCGAAT
1 AATTCGAAT
39886417 A
1 A
39886418 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39887460 original size:5 final size:5
Alignment explanation
Indices: 39887443--39887473 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
39887433 CTCGAAAATT
*
39887443 TTCGA TTCAA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
39887474 CGAATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:39922467 original size:19 final size:20
Alignment explanation
Indices: 39922443--39922485 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39922433 GCTAAAATAA
*
39922443 TATCGATA-CTAAATAAAAG
1 TATCGATACCTAAAGAAAAG
*
39922462 TATCGATACCTAAAGGAAAG
1 TATCGATACCTAAAGAAAAG
39922482 TATC
1 TATC
39922486 AGTACTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (20 bp):
TATCGATACCTAAAGAAAAG
Found at i:39927137 original size:30 final size:30
Alignment explanation
Indices: 39927101--39927162 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
39927091 AGAAGATAAA
39927101 AAGAGATTAGGTTGCTTAGTGATCTTCAAC
1 AAGAGATTAGGTTGCTTAGTGATCTTCAAC
39927131 AAGAGATTAGGTTGCTTAGTGATCTTCAAC
1 AAGAGATTAGGTTGCTTAGTGATCTTCAAC
39927161 AA
1 AA
39927163 TTATAACCAA
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:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (30 bp):
AAGAGATTAGGTTGCTTAGTGATCTTCAAC
Found at i:39927877 original size:13 final size:13
Alignment explanation
Indices: 39927859--39927901 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
39927849 AAATTTGAAT
39927859 TATTTAGTGATAA
1 TATTTAGTGATAA
*
39927872 TATTTAG-G--AC
1 TATTTAGTGATAA
39927882 TATTTAGTGATAA
1 TATTTAGTGATAA
39927895 TATTTAG
1 TATTTAG
39927902 GAAAAGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.32
11 1 0.04
12 1 0.04
13 15 0.60
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:39927885 original size:23 final size:23
Alignment explanation
Indices: 39927859--39927903 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
39927849 AAATTTGAAT
39927859 TATTTAGTGATAATATTTAGGAC
1 TATTTAGTGATAATATTTAGGAC
39927882 TATTTAGTGATAATATTTAGGA
1 TATTTAGTGATAATATTTAGGA
39927904 AAAGTCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (23 bp):
TATTTAGTGATAATATTTAGGAC
Found at i:39928499 original size:19 final size:19
Alignment explanation
Indices: 39928475--39928515 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
39928465 GACCCACGCG
39928475 GTTAAGGCCGTTGATTCGA
1 GTTAAGGCCGTTGATTCGA
39928494 GTTAAGGCCGTTGATTCGA
1 GTTAAGGCCGTTGATTCGA
39928513 GTT
1 GTT
39928516 GGGATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.34
Consensus pattern (19 bp):
GTTAAGGCCGTTGATTCGA
Found at i:39930483 original size:15 final size:15
Alignment explanation
Indices: 39930463--39930494 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39930453 ATGCAAGTGT
39930463 TGTGACCTTAAAAGA
1 TGTGACCTTAAAAGA
39930478 TGTGACCTTAAAAGA
1 TGTGACCTTAAAAGA
39930493 TG
1 TG
39930495 GAACAGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (15 bp):
TGTGACCTTAAAAGA
Found at i:39936517 original size:124 final size:123
Alignment explanation
Indices: 39936296--39936550 Score: 393
Period size: 124 Copynumber: 2.1 Consensus size: 123
39936286 AAATAGTGGG
** * * * *
39936296 AAATCGCTTTTACCAGGATGCTATTTGAGAAGAAATTGTTAAATCGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
*
39936361 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTGACGTTTTCTTAGCAAATAGTATA
66 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTGACG-TTTCTGAGCAAATAGTATA
39936420 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
* * * *
39936485 TCGCTACAATTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTAC-AGTGGTCATGTAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
39936544 AAATCGC
1 AAATCGC
39936551 GCCCTCGTGG
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
124 89 0.75
125 30 0.25
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (123 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:39938238 original size:51 final size:51
Alignment explanation
Indices: 39938165--39938496 Score: 475
Period size: 51 Copynumber: 6.4 Consensus size: 51
39938155 ATGCGGTTAG
*
39938165 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA
* * *
39938216 GGTTAGGATTTTTAATTAAATTAAATTAGGTTAGGATTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA
*
39938267 GGTTAGGGTTTTTAATTAAATTAAATTAGGGTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT-AATTAAATTA
* * **
39938323 GGGTAGGGTTTTTAATTAAATTAAACTAGGTTAGGGTTTTTAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA
* * **
39938374 AGTTAGGGTTTTTAATTAAAATAGGTTAGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA
* *
39938425 GGTTAGGGTTTTTAATTAAGTTAAATTAGGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA
*
39938476 GGTTAGGGTTTTTAATCAAAT
1 GGTTAGGGTTTTTAATTAAAT
39938497 AATGTCAAAA
Statistics
Matches: 247, Mismatches: 29, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
51 195 0.79
52 2 0.01
53 3 0.01
54 3 0.01
55 2 0.01
56 42 0.17
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (51 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA
Found at i:39938482 original size:28 final size:28
Alignment explanation
Indices: 39938165--39938475 Score: 356
Period size: 28 Copynumber: 11.8 Consensus size: 28
39938155 ATGCGGTTAG
39938165 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
*
39938193 GGTTAGGG--TTT--TT-AACTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
*
39938216 GGTTAGGATTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
* *
39938244 GGTTA-GG-ATTT--TT-AATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
39938267 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
*
39938295 GGGTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
* *
39938323 GGGTAGGGTTTTTAATTAAATTAAACTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
**
39938351 GGTTAGGGTTTTTAATTAGGTT--A--A
1 GGTTAGGGTTTTTAATTAAATTAAATTA
* **
39938375 -GTTAGGGTTTTTAATTAAAATAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
39938402 GGTTAGGG--TTT--TT-AATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
*
39938425 GGTTAGGGTTTTTAATTAAGTTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAAATTA
*
39938453 GGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
39938476 GGTTAGGGTT
Statistics
Matches: 240, Mismatches: 23, Indels: 40
0.79 0.08 0.13
Matches are distributed among these distances:
23 63 0.26
24 9 0.04
25 9 0.04
26 10 0.04
27 8 0.03
28 141 0.59
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
GGTTAGGGTTTTTAATTAAATTAAATTA
Found at i:39940925 original size:30 final size:30
Alignment explanation
Indices: 39940884--39940941 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
39940874 TGAAGGAAAA
*
39940884 TGAGAGGATTTTGGAAGGAATTTGAGAGTT
1 TGAGAGAATTTTGGAAGGAATTTGAGAGTT
39940914 TGAGAGAATTTTGGAAGGAATTTGAGAG
1 TGAGAGAATTTTGGAAGGAATTTGAGAG
39940942 AATTTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TGAGAGAATTTTGGAAGGAATTTGAGAGTT
Found at i:39940937 original size:22 final size:22
Alignment explanation
Indices: 39940912--39940977 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
39940902 AATTTGAGAG
*
39940912 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
39940934 TTTGAGAGAATTTTTGAACGGAA
1 TTTGAGAGAATTTTTGAA-GGAA
39940957 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
39940978 ATTAATATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.81
23 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:39946178 original size:20 final size:20
Alignment explanation
Indices: 39946153--39946194 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39946143 TCAGTGGAGT
39946153 AGTTACTGTGCCATCAAGAA
1 AGTTACTGTGCCATCAAGAA
39946173 AGTTACTGTGCCATCAAGAA
1 AGTTACTGTGCCATCAAGAA
39946193 AG
1 AG
39946195 CCAGTCAAGT
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:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (20 bp):
AGTTACTGTGCCATCAAGAA
Found at i:39957199 original size:23 final size:22
Alignment explanation
Indices: 39957173--39957215 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
39957163 TACTAAAACA
*
39957173 TGTAGGTTGTGGATAAACCACCT
1 TGTAGGTCGTGGAT-AACCACCT
39957196 TGTAGGTCGTGGATAACCAC
1 TGTAGGTCGTGGATAACCAC
39957216 TAAATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (22 bp):
TGTAGGTCGTGGATAACCACCT
Found at i:39958154 original size:14 final size:11
Alignment explanation
Indices: 39958125--39958166 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
39958115 TCGGTTTCAG
39958125 TGTGGTGGTGA
1 TGTGGTGGTGA
*
39958136 TGTGGTGGTGC
1 TGTGGTGGTGA
*
39958147 TATGGTGGTGA
1 TGTGGTGGTGA
*
39958158 TTTGGTGGT
1 TGTGGTGGT
39958167 TTGGGGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.07, C:0.02, G:0.50, T:0.40
Consensus pattern (11 bp):
TGTGGTGGTGA
Found at i:39960541 original size:54 final size:54
Alignment explanation
Indices: 39960483--39960605 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
39960473 TCATAAACCG
* ** *
39960483 TGTAACTCACTAACTA-AGGTCACACAG-TCGTGTCGTAGGCCGTGTGCCAGACCA
1 TGTAACTCACTAACTAGA-GTCACACGGCT-GTGTCACAGACCGTGTGCCAGACCA
* * *
39960537 TGTAACTCACTAACTTGATTCACACGGCTGTGTCACAGACGGTGTGCCAGACCA
1 TGTAACTCACTAACTAGAGTCACACGGCTGTGTCACAGACCGTGTGCCAGACCA
*
39960591 TGTGACTCACTAACT
1 TGTAACTCACTAACT
39960606 TGATACACAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 57 0.97
55 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (54 bp):
TGTAACTCACTAACTAGAGTCACACGGCTGTGTCACAGACCGTGTGCCAGACCA
Found at i:39962400 original size:18 final size:17
Alignment explanation
Indices: 39962377--39962410 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39962367 CAAAAATCAC
39962377 TTAACAAAACAAGTTTAT
1 TTAAC-AAACAAGTTTAT
*
39962395 TTAACAACCAAGTTTA
1 TTAACAAACAAGTTTA
39962411 ATAATCTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAACAAACAAGTTTAT
Found at i:39986583 original size:3 final size:3
Alignment explanation
Indices: 39986575--39986631 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
39986565 AGGAATACTG
* * *
39986575 TAA TAA TAA TAA -CA TAA TTA TAA TTAA TAT TAA TAA TCACA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T-A-A TAA TAA
39986622 TAA TAA TAA T
1 TAA TAA TAA T
39986632 GAGGAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 1 0.02
3 36 0.82
4 5 0.11
5 2 0.05
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:39986616 original size:27 final size:26
Alignment explanation
Indices: 39986578--39986629 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
39986568 AATACTGTAA
*
39986578 TAATAATAACATAATTATAATTAATAT
1 TAATAATAACATAATAATAA-TAATAT
*
39986605 TAATAATCACATAATAATAATAATA
1 TAATAATAACATAATAATAATAATA
39986630 ATGAGGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAATAACATAATAATAATAATAT
Found at i:39990006 original size:24 final size:24
Alignment explanation
Indices: 39989919--39989992 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
39989909 AGGATCCACC
*
39989919 TCCGGCTTCGGCTCTGACTCTGAG
1 TCCGGCTTCGGCTCCGACTCTGAG
*
39989943 TCCGGCTTCGGCTCCGACTCCGAG
1 TCCGGCTTCGGCTCCGACTCTGAG
39989967 TCCGGCTTCGGCTCCGACTCTGAG
1 TCCGGCTTCGGCTCCGACTCTGAG
39989991 TC
1 TC
39989993 TGACTTCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.08, C:0.38, G:0.28, T:0.26
Consensus pattern (24 bp):
TCCGGCTTCGGCTCCGACTCTGAG
Found at i:39990035 original size:60 final size:60
Alignment explanation
Indices: 39989931--39990048 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
39989921 CGGCTTCGGC
* * *
39989931 TCTGACTCTGAGTCCGGCTTCGGCTCCGACTCCGAGTCCGGCTTCGGCTCCGACTCTGAG
1 TCTGACTCTGAGTCCGGCTCCGGCTCCGACTCCGAGTCCAGCTTCAGCTCCGACTCTGAG
* * *
39989991 TCTGACT-TCGAGTCCGGCTCCGGCTCCGAGTCCG-GCTTCAGCTTCAGCTCCGGCTCTG
1 TCTGACTCT-GAGTCCGGCTCCGGCTCCGACTCCGAG-TCCAGCTTCAGCTCCGACTCTG
39990049 CCATTAGAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.09, C:0.37, G:0.28, T:0.25
Consensus pattern (60 bp):
TCTGACTCTGAGTCCGGCTCCGGCTCCGACTCCGAGTCCAGCTTCAGCTCCGACTCTGAG
Found at i:39998713 original size:7 final size:7
Alignment explanation
Indices: 39998701--39998743 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
39998691 TTAATATGTG
39998701 TTTGATT
1 TTTGATT
39998708 TTTGATT
1 TTTGATT
39998715 TTTGATT
1 TTTGATT
39998722 TTTGATT
1 TTTGATT
*
39998729 TTTTATT
1 TTTGATT
*
39998736 TTTTATT
1 TTTGATT
39998743 T
1 T
39998744 AAAAATGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (7 bp):
TTTGATT
Found at i:40003457 original size:24 final size:24
Alignment explanation
Indices: 40003430--40003475 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
40003420 TGACTACTCT
40003430 CATTGATTCTTCTATAATACCTCC
1 CATTGATTCTTCTATAATACCTCC
*
40003454 CATTGATTCTTCTGTAATACCT
1 CATTGATTCTTCTATAATACCT
40003476 ATCACTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (24 bp):
CATTGATTCTTCTATAATACCTCC
Found at i:40003486 original size:24 final size:24
Alignment explanation
Indices: 40003435--40003486 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
40003425 ACTCTCATTG
* * *
40003435 ATTCTTCTATAATACCTCCCATTG
1 ATTCTTCTATAATACCTACCACTA
* *
40003459 ATTCTTCTGTAATACCTATCACTA
1 ATTCTTCTATAATACCTACCACTA
40003483 ATTC
1 ATTC
40003487 ACTTACACCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTCTTCTATAATACCTACCACTA
Found at i:40008241 original size:51 final size:51
Alignment explanation
Indices: 40008142--40008357 Score: 304
Period size: 51 Copynumber: 4.4 Consensus size: 51
40008132 TGAGTACTTC
* *
40008142 TGATCAGTGACAAGTGATAAGTGGTAG-TTTAGCTACATTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
40008192 TGATACGTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
*
40008243 TGATAAGTGAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC--
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
40008292 -G----GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATTTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
*
40008338 TGACAAGTGACAAGTGATAA
1 TGATAAGTGACAAGTGATAA
40008358 ATGTGATCCG
Statistics
Matches: 148, Mismatches: 10, Indels: 15
0.86 0.06 0.09
Matches are distributed among these distances:
44 40 0.27
47 1 0.01
48 1 0.01
50 25 0.17
51 81 0.55
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
Found at i:40008258 original size:44 final size:44
Alignment explanation
Indices: 40008198--40008353 Score: 195
Period size: 44 Copynumber: 3.4 Consensus size: 44
40008188 TCAGTGATAC
* *
40008198 GTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATCAGTGATAA
1 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATC-------A
* * *
40008249 GTGAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCG
1 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATCA
*
40008293 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATTTGATCA
1 GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATCA
40008337 GTGACAAGTGACAAGTG
1 GTGACAAGTGACAAGTG
40008354 ATAAATGTGA
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
44 57 0.58
51 41 0.42
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (44 bp):
GTGACAAGTGACAAGTGGTAGCTTTAGCTACACTTATCTGATCA
Done.