Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 33 of 82
Found at i:12024397 original size:54 final size:54
Alignment explanation
Indices: 12024333--12024565 Score: 389
Period size: 54 Copynumber: 4.3 Consensus size: 54
12024323 AAAACATTTT
12024333 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACACCAC
12024387 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAG-CTGGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTC-GGACACCAC
* *
12024441 A-CTTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCAC
1 ATC-TCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACACCAC
* * *
12024495 ATCTCACCCATCTCATGTGCATCCTACCACATCGTGCACATATTCGGACACCAC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACACCAC
12024549 ATCTCACCCAGCTCATG
1 ATCTCACCCAGCTCATG
12024566 CACGGTTACA
Statistics
Matches: 168, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.01
54 164 0.98
55 2 0.01
ACGTcount: A:0.26, C:0.40, G:0.14, T:0.20
Consensus pattern (54 bp):
ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACACCAC
Found at i:12024416 original size:30 final size:31
Alignment explanation
Indices: 12024381--12024475 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 31
12024371 CATAGTCGGA
12024381 CACCACATC-TCACCCAGCTCATGTGCATCC
1 CACCACATCGTCACCCAGCTCATGTGCATCC
**
12024411 CACCACATCGTGCACATAG--C-TG-G-A---
1 CACCACATCGT-CACCCAGCTCATGTGCATCC
*
12024435 CACCACA-CTTCACCCAGCTCATGTGCATCC
1 CACCACATCGTCACCCAGCTCATGTGCATCC
12024465 CACCACATCGT
1 CACCACATCGT
12024476 GCACATAGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 21
0.64 0.08 0.28
Matches are distributed among these distances:
22 5 0.10
23 2 0.04
24 8 0.17
25 2 0.04
26 1 0.02
27 2 0.04
28 1 0.02
29 2 0.04
30 17 0.35
31 3 0.06
32 5 0.10
ACGTcount: A:0.25, C:0.43, G:0.13, T:0.19
Consensus pattern (31 bp):
CACCACATCGTCACCCAGCTCATGTGCATCC
Found at i:12029035 original size:37 final size:37
Alignment explanation
Indices: 12028994--12029071 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
12028984 AATGCAATAT
**
12028994 CATCATCATGTGTGCACTTTCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCACACACTTCAA
*
12029031 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCACACACTTCAA
12029068 CATC
1 CATC
12029072 TTCACACAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.36, G:0.09, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCACACACTTCAA
Found at i:12034852 original size:25 final size:25
Alignment explanation
Indices: 12034818--12034868 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12034808 TTCATCTCTA
12034818 ATAAGGCTGGCAAATAACAACGCTG
1 ATAAGGCTGGCAAATAACAACGCTG
*
12034843 ATAATGCTGGCAAATAACAACGCTG
1 ATAAGGCTGGCAAATAACAACGCTG
12034868 A
1 A
12034869 AGTGCAGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (25 bp):
ATAAGGCTGGCAAATAACAACGCTG
Found at i:12042057 original size:14 final size:14
Alignment explanation
Indices: 12042038--12042066 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12042028 TGGGTCTGGT
12042038 TACATCAAAAGCCA
1 TACATCAAAAGCCA
12042052 TACATCAAAAGCCA
1 TACATCAAAAGCCA
12042066 T
1 T
12042067 TTCTTGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (14 bp):
TACATCAAAAGCCA
Found at i:12042221 original size:37 final size:37
Alignment explanation
Indices: 12042180--12042368 Score: 258
Period size: 37 Copynumber: 5.1 Consensus size: 37
12042170 CATATGCATT
12042180 CATCATCATGTGTGCACTCCTTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCGCACACTTCAA
12042217 CATCATCATGTGTGCACTCCTTACTCGCACAC-TCAAA
1 CATCATCATGTGTGCACTCCTTACTCGCACACTTC-AA
* * *
12042254 CATCATCATGTGTACACT-CTCTATTCACACAC-TCTAA
1 CATCATCATGTGTGCACTCCT-TACTCGCACACTTC-AA
*
12042291 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCGCACACTTCAA
* * * *
12042328 GATCATCATGTGTGTACTCCCTACTTGCACACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCGCACACTTCAA
12042365 CATC
1 CATC
12042369 CTCACACAAC
Statistics
Matches: 136, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
36 4 0.03
37 129 0.95
38 3 0.02
ACGTcount: A:0.26, C:0.34, G:0.10, T:0.30
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCTTACTCGCACACTTCAA
Found at i:12052819 original size:18 final size:18
Alignment explanation
Indices: 12052796--12052837 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12052786 ATGACGGGTG
12052796 AAAATAATGTTTTAGAAT
1 AAAATAATGTTTTAGAAT
* **
12052814 AAAATAATTTTTTTTAAT
1 AAAATAATGTTTTAGAAT
12052832 AAAATA
1 AAAATA
12052838 GTATTAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
AAAATAATGTTTTAGAAT
Found at i:12053761 original size:15 final size:15
Alignment explanation
Indices: 12053737--12053811 Score: 98
Period size: 15 Copynumber: 5.0 Consensus size: 15
12053727 CAACAAAGTA
12053737 AAAAGAGAAAGGAAG
1 AAAAGAGAAAGGAAG
* *
12053752 AAAGGAGAAAGAAAG
1 AAAAGAGAAAGGAAG
*
12053767 AAAAGAGAAAGAAAG
1 AAAAGAGAAAGGAAG
*
12053782 AAAGGAGAAA-GAAG
1 AAAAGAGAAAGGAAG
12053796 AAAAAGAGAAAGGAAG
1 -AAAAGAGAAAGGAAG
12053812 GTTCGGCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
14 3 0.06
15 45 0.87
16 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAGGAAG
Found at i:12053765 original size:11 final size:10
Alignment explanation
Indices: 12053749--12053794 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
12053739 AAGAGAAAGG
12053749 AAGAAAGGAGA
1 AAGAAA-GAGA
12053760 AAGAAAGA-A
1 AAGAAAGAGA
12053769 AAGAGAA-AGA
1 AAGA-AAGAGA
12053779 AAGAAAGGAGA
1 AAGAAA-GAGA
12053790 AAGAA
1 AAGAA
12053795 GAAAAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.26
10 9 0.29
11 14 0.45
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAGAAAGAGA
Found at i:12053771 original size:30 final size:30
Alignment explanation
Indices: 12053736--12053811 Score: 127
Period size: 30 Copynumber: 2.5 Consensus size: 30
12053726 ACAACAAAGT
12053736 AAAAAGAGAAAGGAAGAAAGGAGAAAGAA-
1 AAAAAGAGAAAGGAAGAAAGGAGAAAGAAG
*
12053765 AGAAAAGAGAAAGAAAGAAAGGAGAAAGAAG
1 A-AAAAGAGAAAGGAAGAAAGGAGAAAGAAG
12053796 AAAAAGAGAAAGGAAG
1 AAAAAGAGAAAGGAAG
12053812 GTTCGGCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (30 bp):
AAAAAGAGAAAGGAAGAAAGGAGAAAGAAG
Found at i:12054732 original size:20 final size:21
Alignment explanation
Indices: 12054707--12054751 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
12054697 AGCCGAGTCA
12054707 TCATC-ATCACACAACAT-TAT
1 TCATCAAT-ACACAACATATAT
*
12054727 TCATCAATGCACAACATATAT
1 TCATCAATACACAACATATAT
12054748 TCAT
1 TCAT
12054752 GTATATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (21 bp):
TCATCAATACACAACATATAT
Found at i:12059388 original size:77 final size:75
Alignment explanation
Indices: 12059282--12059444 Score: 218
Period size: 77 Copynumber: 2.1 Consensus size: 75
12059272 TGAATTTCTC
* * *
12059282 AAATTAAAATACTATCCTTAATTTTAGGAATTTCTTTTTAAATAGGAAACAATTTCCTATTTTTA
1 AAATTAAAATACTATCCTTAATTTAAGGAATTACTTTTAAAATAGGAAACAATTTCCTATTTTT-
12059347 ATGAATCACCCA
65 -TGAATCACCCA
* * * *
12059359 AAATTAAAATTCTCTCTTTAATTTAAGGAATTACTTTTAAAATAGGAAACAATTTTCTATTTTTT
1 AAATTAAAATACTATCCTTAATTTAAGGAATTACTTTTAAAATAGGAAACAATTTCCTATTTTTT
* *
12059424 TAATCATCCA
66 GAATCACCCA
*
12059434 AAATTAGAATA
1 AAATTAAAATA
12059445 TATGGCATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
75 18 0.24
77 57 0.76
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (75 bp):
AAATTAAAATACTATCCTTAATTTAAGGAATTACTTTTAAAATAGGAAACAATTTCCTATTTTTT
GAATCACCCA
Found at i:12062649 original size:39 final size:38
Alignment explanation
Indices: 12062568--12062664 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 38
12062558 CGTGTGCAAA
* * *
12062568 ATGTGGGGGGATGTACATGATGGCACTAACTATGCACT
1 ATGTGGGGGGATGCACATGATGACACCAACTATGCACT
* *
12062606 ATGTGGGGGGATGCACATGATGACTCCGACTATGTGCAC-
1 ATGTGGGGGGATGCACATGATGACACCAACTA--TGCACT
*
12062645 ATGTGGAGGGATGCACATGA
1 ATGTGGGGGGATGCACATGA
12062665 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
38 27 0.53
39 19 0.37
40 5 0.10
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (38 bp):
ATGTGGGGGGATGCACATGATGACACCAACTATGCACT
Found at i:12069410 original size:43 final size:43
Alignment explanation
Indices: 12069360--12069514 Score: 202
Period size: 43 Copynumber: 3.6 Consensus size: 43
12069350 TATTGACTCG
* * * * *
12069360 GCTATGTGCGAGTAGGGAGTGTGCATAAGCTGATGATGACCCG
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
* * *
12069403 GTTATGTGTGAGTAAGGAGTGCGCATAACCCGGTGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
* * *
12069446 GTTATGTGCGAGTAGGGAGTGCACATAACCCGGTGATGACCTA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
*
12069489 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
12069515 GAGCTGGGAA
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
Found at i:12079586 original size:25 final size:24
Alignment explanation
Indices: 12079557--12079643 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 24
12079547 CAAGTGGTTG
12079557 TAGCCACGTATATCAACCTATGGCC
1 TAGCCACGTATATCAACC-ATGGCC
* *
12079582 TAGCCACATATATCATCCAATGGCC
1 TAGCCACGTATATCAACC-ATGGCC
* * *
12079607 TTGCCGCGTGTAATCACAGACCATGGCC
1 TAGCCACGTAT-AT--CA-ACCATGGCC
12079635 TAGCCACGT
1 TAGCCACGT
12079644 CTAACAGCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
25 29 0.60
26 2 0.04
28 15 0.31
29 2 0.04
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (24 bp):
TAGCCACGTATATCAACCATGGCC
Found at i:12085249 original size:34 final size:35
Alignment explanation
Indices: 12085201--12085287 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 35
12085191 TTGGCTGCTG
*
12085201 AAAATTT-GAGCTGTTTGCTGCCAATTTGTGCA-A
1 AAAATTTGGAGCTGTTTGCTGCCAATTTATGCAGA
* * *
12085234 AAAATTTGGAGCTGTTTGTTGTCGATTTATGCAGA
1 AAAATTTGGAGCTGTTTGCTGCCAATTTATGCAGA
12085269 AAAA-TTGGAGCTGTTTGCT
1 AAAATTTGGAGCTGTTTGCT
12085288 AGTAGTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 7 0.15
34 35 0.74
35 5 0.11
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.38
Consensus pattern (35 bp):
AAAATTTGGAGCTGTTTGCTGCCAATTTATGCAGA
Found at i:12085297 original size:34 final size:33
Alignment explanation
Indices: 12085201--12085311 Score: 107
Period size: 34 Copynumber: 3.3 Consensus size: 33
12085191 TTGGCTGCTG
* * * *
12085201 AAAATTTGAGCTGTTTGCTGCCAATTTGTGCA-A
1 AAAATTGGAGCTGTTTGCTG-TAGTTTATGCAGA
* *
12085234 AAAATTTGGAGCTGTTTGTTGTCGATTTATGCAGA
1 AAAA-TTGGAGCTGTTTGCTGTAG-TTTATGCAGA
* *
12085269 AAAATTGGAGCTGTTTGCTAGTAGTTTATACAGG
1 AAAATTGGAGCTGTTTGCT-GTAGTTTATGCAGA
12085303 AAAATTGGA
1 AAAATTGGA
12085312 CAACATTGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 4 0.06
34 52 0.81
35 8 0.12
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (33 bp):
AAAATTGGAGCTGTTTGCTGTAGTTTATGCAGA
Found at i:12085483 original size:15 final size:15
Alignment explanation
Indices: 12085445--12085483 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12085435 GGAAGAGAGA
*
12085445 AAAATAAAGAAAAAG
1 AAAATAAATAAAAAG
* *
12085460 AAAAAAAATAAATAG
1 AAAATAAATAAAAAG
12085475 AAAATAAAT
1 AAAATAAAT
12085484 GGGCATGACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (15 bp):
AAAATAAATAAAAAG
Found at i:12089026 original size:45 final size:44
Alignment explanation
Indices: 12088962--12089052 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 44
12088952 ACACCTTGGT
12088962 CTCTGTCTATGAGCCTATGTTAAAATCACATTATATATATTCCTC
1 CTCTGTCTATGAGCCTATGTTAAAATCAC-TTATATATATTCCTC
12089007 CTCTGTCTATGAGCCTATGTTAAAATCACTTATATATATTCCTC
1 CTCTGTCTATGAGCCTATGTTAAAATCACTTATATATATTCCTC
12089051 CT
1 CT
12089053 TTGTTCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 17 0.37
45 29 0.63
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (44 bp):
CTCTGTCTATGAGCCTATGTTAAAATCACTTATATATATTCCTC
Found at i:12097000 original size:43 final size:41
Alignment explanation
Indices: 12096893--12097000 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 41
12096883 AAAATCGCAA
* * *
12096893 GAAATGGAGACCTACTCAATCCACTTTACCATAAATCATGG
1 GAAATGGAGACATACTCAATCCACTTGACAATAAATCATGG
*
12096934 GAAATAGAGACATACTCAATCCACTTGACAATAAAATCA-GAG
1 GAAATGGAGACATACTCAATCCACTTGACAAT-AAATCATG-G
* * *
12096976 GAATTTGGAGACTTTCTCAATCCAC
1 GAA-ATGGAGACATACTCAATCCAC
12097001 ATCACAACAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 29 0.52
42 10 0.18
43 17 0.30
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (41 bp):
GAAATGGAGACATACTCAATCCACTTGACAATAAATCATGG
Found at i:12097962 original size:19 final size:19
Alignment explanation
Indices: 12097938--12097980 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
12097928 TCTTCTTCTC
12097938 TTTCATGCTCCCACGCCAT
1 TTTCATGCTCCCACGCCAT
**
12097957 TTTCATGCTCCCATTCCAT
1 TTTCATGCTCCCACGCCAT
12097976 TTTCA
1 TTTCA
12097981 CCCTACCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.37, G:0.07, T:0.40
Consensus pattern (19 bp):
TTTCATGCTCCCACGCCAT
Found at i:12100191 original size:2 final size:2
Alignment explanation
Indices: 12100184--12100218 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12100174 NNNNNNNNNN
12100184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12100219 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12105570 original size:25 final size:25
Alignment explanation
Indices: 12105536--12105591 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
12105526 CAGTCTGTGA
* *
12105536 TTATACGTGGCAAGGCCATGGGTTG
1 TTATACGTGGCAACGCCATGAGTTG
*
12105561 TTATATGTGGCAACGCCATGAGTTG
1 TTATACGTGGCAACGCCATGAGTTG
*
12105586 ATATAC
1 TTATAC
12105592 ATGGTTACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (25 bp):
TTATACGTGGCAACGCCATGAGTTG
Found at i:12110265 original size:25 final size:25
Alignment explanation
Indices: 12110231--12110290 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
12110221 CGGTCTATGA
*
12110231 TTATACGTGGCAAGGCCAC-AGGTTG
1 TTATATGTGGCAAGGCCACTA-GTTG
*
12110256 TTATATGTGGCAAGGTCACTAGTTG
1 TTATATGTGGCAAGGCCACTAGTTG
*
12110281 ATATATGTGG
1 TTATATGTGG
12110291 TTGCAACCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (25 bp):
TTATATGTGGCAAGGCCACTAGTTG
Found at i:12110408 original size:29 final size:32
Alignment explanation
Indices: 12110358--12110418 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
12110348 GGGAATTCGG
*
12110358 TGGAAGGGGGCCTCCTAGATTG-TTAT-TATA
1 TGGAAGGGGGCCTACTAGATTGATTATCTATA
12110388 TGGAAGGGGGTCC-ACT-GATTGATTATCTATA
1 TGGAAGGGGG-CCTACTAGATTGATTATCTATA
12110419 ATTACTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 5 0.19
30 16 0.59
31 6 0.22
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.33
Consensus pattern (32 bp):
TGGAAGGGGGCCTACTAGATTGATTATCTATA
Found at i:12120693 original size:20 final size:21
Alignment explanation
Indices: 12120640--12120693 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
12120630 TATGTTGGTA
12120640 TGTATATATATGAATAAGTGTTG
1 TGTAT-TA-ATGAATAAGTGTTG
*
12120663 TGTATTGATGAATAA-TGTTG
1 TGTATTAATGAATAAGTGTTG
12120683 TGTGA-TAATGA
1 TGT-ATTAATGA
12120694 TGACCCAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 13 0.46
21 9 0.32
22 1 0.04
23 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
TGTATTAATGAATAAGTGTTG
Found at i:12120817 original size:43 final size:43
Alignment explanation
Indices: 12120690--12120825 Score: 184
Period size: 43 Copynumber: 3.2 Consensus size: 43
12120680 TTGTGTGATA
* * * **
12120690 ATGATGACCCAACTATGTGCGATGT-GGGAGTGCACATGAGCTA
1 ATGATGACCCAGCTATGTGCGA-GTAGGGAGTGCGCATAAGCCG
*
12120733 ATGATGACCCAGCTATGTGCGAGTAGGGAATGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
*
12120776 ATGATGACCCAGCTATGTGCGAGTAGGGAGTACGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
*
12120819 ATAATGA
1 ATGATGA
12120826 TGAGCTAGCT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 2 0.02
43 81 0.98
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
Found at i:12126196 original size:22 final size:22
Alignment explanation
Indices: 12126168--12126216 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12126158 AAAAAATGGA
*
12126168 TGCTGATATATTTATGGTACTT
1 TGCTGATATATTCATGGTACTT
* *
12126190 TGCTGATATGTTCATGGTATTT
1 TGCTGATATATTCATGGTACTT
12126212 TGCTG
1 TGCTG
12126217 CTGATAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.22, T:0.49
Consensus pattern (22 bp):
TGCTGATATATTCATGGTACTT
Found at i:12127996 original size:35 final size:35
Alignment explanation
Indices: 12127945--12128115 Score: 263
Period size: 35 Copynumber: 4.9 Consensus size: 35
12127935 AGTGTGGATA
* *
12127945 ATGATATTGAAGTGTGCGAGTTGGGAGTGCACACG
1 ATGATATTGAAATGTGCGAGTAGGGAGTGCACACG
*
12127980 ATGATGTTGAAATGTGCGAGTAGGGAGTGCACACG
1 ATGATATTGAAATGTGCGAGTAGGGAGTGCACACG
*
12128015 ATGATGTTGAAATGTGCGAGTAGGGAGTGCACACG
1 ATGATATTGAAATGTGCGAGTAGGGAGTGCACACG
* * *
12128050 ATGATATTGAAGTGTGTGAGTAGGGAGTGCGCACG
1 ATGATATTGAAATGTGCGAGTAGGGAGTGCACACG
*
12128085 ATGATATAGAAATGTGCGA-TAGGGAGTGCAC
1 ATGATATTGAAATGTGCGAGTAGGGAGTGCAC
12128116 TTGATGATGT
Statistics
Matches: 125, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
34 11 0.09
35 114 0.91
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.24
Consensus pattern (35 bp):
ATGATATTGAAATGTGCGAGTAGGGAGTGCACACG
Found at i:12136231 original size:22 final size:22
Alignment explanation
Indices: 12136201--12136288 Score: 131
Period size: 22 Copynumber: 4.0 Consensus size: 22
12136191 TTAGAGTGGT
* *
12136201 ATCAAAGCTTTTCGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
*
12136223 ATCAGAGCTTTTGATTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
12136245 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
* *
12136267 ATTAGAGCTTTTGGGTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
12136289 TTGTTTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (22 bp):
ATCAGAGCTTTTGGTTTTAAAG
Found at i:12148811 original size:36 final size:35
Alignment explanation
Indices: 12148730--12148819 Score: 112
Period size: 35 Copynumber: 2.5 Consensus size: 35
12148720 CATGGGGAGT
** *
12148730 GGTGTGGGAGTGTGCATGATGATATTGTCGTATGC
1 GGTGTGGGAGTGCACATGATGACATTGTCGTATGC
12148765 GGTGTGGGAGTGCACATGATGACATTAG-C-TATGTAC
1 GGTGTGGGAGTGCACATGATGACATT-GTCGTATG--C
12148801 GGTGTGGGAGTGCACATGA
1 GGTGTGGGAGTGCACATGA
12148820 GCTGGGTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
34 4 0.08
35 24 0.49
36 21 0.43
ACGTcount: A:0.21, C:0.11, G:0.39, T:0.29
Consensus pattern (35 bp):
GGTGTGGGAGTGCACATGATGACATTGTCGTATGC
Found at i:12149288 original size:123 final size:122
Alignment explanation
Indices: 12149117--12149443 Score: 380
Period size: 123 Copynumber: 2.6 Consensus size: 122
12149107 CGTCGTAGCT
* *
12149117 AAATTGATTTTTGACGCGGCGAGAAACTTTTTGCCTTG-GAAGTCACTGTTCTCACTGCAGCCAA
1 AAATTGA-TTTTCAC-CGGCGAGAAACTTTTTGTCTTGAG-AGTCACTGTTCTCACTGCAGCCAA
*
12149181 ATTGATTTTCACCATCGCAA-GA-A-ACTTTCTGTCTTGAAAGTCACTGTTCT-AGCCACAGCC
63 ATTGATTTTC-CC--CGCAATGATAGACTTTCTATCTTGAAAGTCACTGTTCTCA-CCACAGCC
*
12149241 AAATTGATTTTCACCGAGCGAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCGCCT-CAGCCAAA
1 AAATTGATTTTCACCG-GCGAGAAACTTTTTGTCTTGAGAGTCACTGTTCTC-ACTGCAGCCAAA
* * * *
12149305 TTGATTTTCCCCTCAATGATAGACTTTCTATCTTGGAAGTCACTGTTCTCATCGCAGCC
64 TTGATTTTCCCCGCAATGATAGACTTTCTATCTTGAAAGTCACTGTTCTCACCACAGCC
* * **
12149364 AAATTGATTTTCACCGTGGTGAGAAACTTTTTGTCTTGAGAGTCACTATTCT-TGTCGCAGCCAA
1 AAATTGATTTTCACC--GGCGAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCACT-GCAGCCAA
*
12149428 ATTGATTCTCCCCGCA
63 ATTGATTTTCCCCGCA
12149444 GAGAGAAACT
Statistics
Matches: 178, Mismatches: 14, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
120 4 0.02
121 2 0.01
122 6 0.03
123 101 0.57
124 64 0.36
125 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (122 bp):
AAATTGATTTTCACCGGCGAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCACTGCAGCCAAATT
GATTTTCCCCGCAATGATAGACTTTCTATCTTGAAAGTCACTGTTCTCACCACAGCC
Found at i:12149450 original size:62 final size:62
Alignment explanation
Indices: 12149137--12149453 Score: 306
Period size: 62 Copynumber: 5.1 Consensus size: 62
12149127 TTGACGCGGC
* * *
12149137 GAGAAACTTTTTGCCTTG-GAAGTCACTGTTCTCACTGCAGCCAAATTGATTTTCACCATCGC--
1 GAGAAACTTTTTGTCTTGAG-AGTCACTGTTCTCGCCGCAGCCAAATTGATTTTC-CC--CGCAG
12149199 A
62 A
* * * * * *
12149200 -AGAAACTTTCTGTCTTGAAAGTCACTGTTCTAGCCACAGCCAAATTGATTTTCACCG-AGC
1 GAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCGCCGCAGCCAAATTGATTTTCCCCGCAGA
* *
12149260 GAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCGCCTCAGCCAAATTGATTTTCCCCTCA-A
1 GAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCGCCGCAGCCAAATTGATTTTCCCCGCAGA
* * * * ** * ** *
12149321 TGATAGACTTTCTATCTTG-GAAGTCACTGTTCTCATCGCAGCCAAATTGATTTTCACCGTGGT
1 -GAGAAACTTTTTGTCTTGAG-AGTCACTGTTCTCGCCGCAGCCAAATTGATTTTCCCCGCAGA
* * * *
12149384 GAGAAACTTTTTGTCTTGAGAGTCACTATTCTTGTCGCAGCCAAATTGATTCTCCCCGCAGA
1 GAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCGCCGCAGCCAAATTGATTTTCCCCGCAGA
12149446 GAGAAACT
1 GAGAAACT
12149454 CTCTACCTTG
Statistics
Matches: 205, Mismatches: 40, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
59 2 0.01
61 53 0.26
62 149 0.73
63 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (62 bp):
GAGAAACTTTTTGTCTTGAGAGTCACTGTTCTCGCCGCAGCCAAATTGATTTTCCCCGCAGA
Found at i:12153356 original size:19 final size:19
Alignment explanation
Indices: 12153332--12153370 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12153322 GCTAGAGGAA
12153332 AATTTTAGAATAAAATAAT
1 AATTTTAGAATAAAATAAT
* * *
12153351 AATTTTTGGATTAAATAAT
1 AATTTTAGAATAAAATAAT
12153370 A
1 A
12153371 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
AATTTTAGAATAAAATAAT
Found at i:12155566 original size:2 final size:2
Alignment explanation
Indices: 12155532--12155556 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12155522 ATTGTTTTGA
12155532 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12155557 AGTTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12155977 original size:25 final size:25
Alignment explanation
Indices: 12155943--12156002 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
12155933 TCTGTGATAT
**
12155943 ATATATGTGGCAAGGCCACTGGTTG
1 ATATATGTGGCAAGGCCACAAGTTG
*
12155968 ATATATGTGGCTAGGCCACAAGTTG
1 ATATATGTGGCAAGGCCACAAGTTG
*
12155993 ATATACGTGG
1 ATATATGTGG
12156003 TTGCGACAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (25 bp):
ATATATGTGGCAAGGCCACAAGTTG
Found at i:12157637 original size:107 final size:105
Alignment explanation
Indices: 12157448--12157676 Score: 296
Period size: 107 Copynumber: 2.2 Consensus size: 105
12157438 ATTAAGTTGT
* *
12157448 GCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTGATCAATTAAATTGTTTAATTAAGTC
1 GCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATCAATTAAATTGTTTAATTAAATC
12157513 ATCGGGCCTAATTAATTAAATTAAACAATTAAGTTATTAG
66 ATCGGGCCTAATTAATTAAATTAAACAATTAAGTTATTAG
* * * **
12157553 GCCTAATTGATTAAATTCGTTTAATTAAGTCATTGGGCTTAATTGATTAAAATTGTTTAATTAAA
1 GCCTAATTAATTAAATT-GTTTAATTAAATCATTGGGCCTAATCAATT-AAATTGTTTAATTAAA
* * * **** *
12157618 TTATTGGGCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
64 TCATCGGGCCTAATTAATTAAATTAAACAATTAAGTTATTAG
*
12157660 GCCTAATCAATTAAATT
1 GCCTAATTAATTAAATT
12157677 AAACAATTAA
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
105 16 0.15
106 25 0.24
107 64 0.61
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (105 bp):
GCCTAATTAATTAAATTGTTTAATTAAATCATTGGGCCTAATCAATTAAATTGTTTAATTAAATC
ATCGGGCCTAATTAATTAAATTAAACAATTAAGTTATTAG
Found at i:12157692 original size:35 final size:35
Alignment explanation
Indices: 12157428--12157676 Score: 279
Period size: 35 Copynumber: 7.1 Consensus size: 35
12157418 CACTTGATTA
* *
12157428 AAATTATTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
12157460 AAATTGTTTAATTAAATCATTGGGCCTGATCAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* *
12157495 AAATTGTTTAATTAAGTCATCGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
**** * *
12157530 AAATTAAACAATTAAGTTATTAGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
12157565 AAATTCGTTTAATTAAGTCATTGGGCTTAATTGATT
1 AAATT-GTTTAATTAAGTTATTGGGCCTAATTAATT
* *
12157601 AAAATTGTTTAATTAAATTATTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
*
12157637 AAATTGTTTAATTAAGTTATTGGGCCTAATCAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
12157672 AAATT
1 AAATT
12157677 AAACAATTAA
Statistics
Matches: 182, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
32 14 0.08
35 113 0.62
36 50 0.27
37 5 0.03
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:12167693 original size:38 final size:39
Alignment explanation
Indices: 12167594--12167695 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
12167584 ACCCGGCTCA
* *
12167594 TGTACATCCCCCCACATCGTGCACATAGCCGGCACATCG
1 TGTACATCACCCCACATCGTGCACATAGCAGGCACATCG
* * * *
12167633 TGTGCATCTCCCCACATCGTGCACA-ATCAGTGC-CATTG
1 TGTACATCACCCCACATCGTGCACATAGCAG-GCACATCG
12167671 TGTACATCACCCCACATCGTGCACA
1 TGTACATCACCCCACATCGTGCACA
12167696 CAGGCACTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
38 30 0.55
39 25 0.45
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.22
Consensus pattern (39 bp):
TGTACATCACCCCACATCGTGCACATAGCAGGCACATCG
Found at i:12177558 original size:35 final size:35
Alignment explanation
Indices: 12177512--12177580 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
12177502 ATTAAGTTGT
12177512 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
1 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
* *
12177547 GCCTAATTAATTAAATTGTTTAATTAAGTCATTG
1 GCCTAATTAATTAAATTATTTAATTAAATCATTG
12177581 TGTCATGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (35 bp):
GCCTAATTAATTAAATTATTTAATTAAATCATTGG
Found at i:12178410 original size:54 final size:54
Alignment explanation
Indices: 12178329--12178487 Score: 237
Period size: 54 Copynumber: 2.9 Consensus size: 54
12178319 TCATCATGTG
* * *
12178329 CATCTCACCCAACTTATGTGCATCCCACCACATCGTGCACATAGTCGGACATCT
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* * * *
12178383 TATCTCACCCAGCTCATGTGCACCCCACCACATCGTGCACATAACCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
12178437 CATCTCACCCAACTCATGTGCATCCCACCACATCATGCACACAGCCGGACA
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
12178488 GTATCACCAT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.27, C:0.41, G:0.13, T:0.19
Consensus pattern (54 bp):
CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:12180227 original size:35 final size:35
Alignment explanation
Indices: 12180050--12180213 Score: 202
Period size: 35 Copynumber: 4.6 Consensus size: 35
12180040 GGTTTCACAC
****
12180050 ATTGGGCCTAATTAATTAAATTAAACAATTAAGTT
1 ATTGGGCCTAATTAATTAAATTGTTTAATTAAGTT
* *
12180085 ATTGGGCCTAATTGATTAAATTCGTTTAATTAAGTC
1 ATTGGGCCTAATTAATTAAATT-GTTTAATTAAGTT
* * *
12180121 ATTGGGCTTAATTGATTAAAATTGTTTAATTAAATT
1 ATTGGGCCTAATTAATT-AAATTGTTTAATTAAGTT
* *
12180157 TTTGGGCTTAATTAATTAAATTGTTTAATTAAGTT
1 ATTGGGCCTAATTAATTAAATTGTTTAATTAAGTT
*
12180192 ATTGGGCCTAATCAATTAAATT
1 ATTGGGCCTAATTAATTAAATT
12180214 AAACAATTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
35 57 0.51
36 50 0.45
37 5 0.04
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (35 bp):
ATTGGGCCTAATTAATTAAATTGTTTAATTAAGTT
Found at i:12185747 original size:42 final size:42
Alignment explanation
Indices: 12185686--12185769 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
12185676 GTATTGATAT
*
12185686 TGACCCAGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
1 TGACCCAGCTATGTACGAGTAGGAGTGCACATAAGCCGTTGC
* * *
12185728 TGACCCGGCTATGTACGAGTGGGAGTGCGCATAAGCCGTTGC
1 TGACCCAGCTATGTACGAGTAGGAGTGCACATAAGCCGTTGC
12185770 GTATGAGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.21
Consensus pattern (42 bp):
TGACCCAGCTATGTACGAGTAGGAGTGCACATAAGCCGTTGC
Found at i:12185817 original size:2 final size:2
Alignment explanation
Indices: 12185810--12185855 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
12185800 ATGATGAGTG
*
12185810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12185852 AT AT
1 AT AT
12185856 GGTATATGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12194724 original size:21 final size:22
Alignment explanation
Indices: 12194699--12194739 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12194689 CTTAGGTGGA
*
12194699 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
12194720 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
12194740 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:12194740 original size:20 final size:21
Alignment explanation
Indices: 12194699--12194743 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
12194689 CTTAGGTGGA
*
12194699 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
12194720 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
12194740 AAAA
1 AAAA
12194744 AAAGGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:12194744 original size:21 final size:20
Alignment explanation
Indices: 12194697--12194744 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
12194687 ACCTTAGGTG
*
12194697 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
12194717 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
12194739 GAAAAA
1 GAAAAA
12194745 AAGGTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:12197744 original size:73 final size:71
Alignment explanation
Indices: 12197644--12197835 Score: 217
Period size: 72 Copynumber: 2.7 Consensus size: 71
12197634 TGCAGACAAA
* * * **
12197644 GAGC-TCTTAGTCGACTAACTTTCTTCTTGGTTGACTAAGTTGGTTTTGTCTTCTGGTCGCAGAT
1 GAGCATCTTAGTCGACTAACTCT-TTCTTGGTCGACTAAGTTGGTTCTGTCTTCAAGTC-CAGAT
12197708 TCTGGCAG
64 TCTGGCAG
* * *
12197716 AGAGCAT-TTGGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTGTCTTGAAGTCTAGAT
1 -GAGCATCTTAGTCGACTAACTC-TTTCTTGGTCGACTAAGTTGGTTCTGTCTTCAAGTCCAGAT
*
12197780 TTTGGCAG
64 TCTGGCAG
* * *
12197788 TAGCTTCTTAGTCGACTAACTCTTATCTTGGTCAACTAAGTTGGTTCT
1 GAGCATCTTAGTCGACTAACTCTT-TCTTGGTCGACTAAGTTGGTTCT
12197836 ATTTCTCAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
71 6 0.06
72 47 0.46
73 47 0.46
74 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (71 bp):
GAGCATCTTAGTCGACTAACTCTTTCTTGGTCGACTAAGTTGGTTCTGTCTTCAAGTCCAGATTC
TGGCAG
Found at i:12197817 original size:72 final size:73
Alignment explanation
Indices: 12197643--12197835 Score: 223
Period size: 73 Copynumber: 2.7 Consensus size: 73
12197633 TTGCAGACAA
* * * **
12197643 AGAGC-TCTTAGTCGACTAACTTTCTTCTTGGTTGACTAAGTTGGTTTTGTCTTCTGGTCGCAGA
1 AGAGCATCTTAGTCGACTAACTCT-TTCTTGGTCGACTAAGTTGGTTCTGTCTTCAAGTCGCAGA
12197707 TTCTGGCAG
65 TTCTGGCAG
* * *
12197716 AGAGCAT-TTGGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTGTCTTGAAGTC-TAGA
1 AGAGCATCTTAGTCGACTAACTC-TTTCTTGGTCGACTAAGTTGGTTCTGTCTTCAAGTCGCAGA
*
12197779 TTTTGGCAG
65 TTCTGGCAG
* * *
12197788 -TAGCTTCTTAGTCGACTAACTCTTATCTTGGTCAACTAAGTTGGTTCT
1 AGAGCATCTTAGTCGACTAACTCTT-TCTTGGTCGACTAAGTTGGTTCT
12197836 ATTTCTCAAT
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
71 6 0.06
72 47 0.46
73 48 0.47
74 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (73 bp):
AGAGCATCTTAGTCGACTAACTCTTTCTTGGTCGACTAAGTTGGTTCTGTCTTCAAGTCGCAGAT
TCTGGCAG
Found at i:12203381 original size:40 final size:40
Alignment explanation
Indices: 12203321--12203463 Score: 211
Period size: 40 Copynumber: 3.6 Consensus size: 40
12203311 ACTTAGCTCA
* *
12203321 TGTGCATCCCCCCACGTCGTGCATATAGCTGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCATCG
12203361 TGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCATCG
* *
12203401 TGTGCATCCCCCCACATCGTGCACA-AG-T-AATATCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCTGGA-GTCATCG
*
12203439 TGTGCATCCCCCTACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
12203464 AGCAATATCA
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
37 1 0.01
38 31 0.32
39 2 0.02
40 63 0.65
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCATCG
Found at i:12203446 original size:38 final size:38
Alignment explanation
Indices: 12203355--12203475 Score: 172
Period size: 38 Copynumber: 3.1 Consensus size: 38
12203345 ATAGCTGGAG
* *
12203355 TCATCGTGTGCATCCCCCCACATCGTGCACATAGCTGGA-G
1 TCATCGTGTGCATCCCCCCACATCGTGCACA-AG-T-AATA
12203395 TCATCGTGTGCATCCCCCCACATCGTGCACAAGTAATA
1 TCATCGTGTGCATCCCCCCACATCGTGCACAAGTAATA
* *
12203433 TCATCGTGTGCATCCCCCTACATCGTGCACAAGCAATA
1 TCATCGTGTGCATCCCCCCACATCGTGCACAAGTAATA
12203471 TCATC
1 TCATC
12203476 ATCACACTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
37 1 0.01
38 42 0.55
39 2 0.03
40 31 0.41
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (38 bp):
TCATCGTGTGCATCCCCCCACATCGTGCACAAGTAATA
Found at i:12203584 original size:2 final size:2
Alignment explanation
Indices: 12203577--12203601 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12203567 AATGCACAAC
12203577 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12203602 CCAATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12207645 original size:136 final size:134
Alignment explanation
Indices: 12207401--12207670 Score: 504
Period size: 136 Copynumber: 2.0 Consensus size: 134
12207391 TCTGACTAGG
12207401 CTGACGCATAAGGATACAAAATTTGAGTGGTTAGATGCTTGTGAGAATAGCTTTGAGAAGCTTAA
1 CTGACGCATAAGGATACAAAATTTGAGTGGTTAGATGCTTGTGAGAATAGCTTTGAGAAGCTTAA
12207466 GGCATGTCTCACCACAGCTCCAATATTAAGCCTACCGTAAGGCATCAGGGGGTTAAACGATATTT
66 GGCATGTCTCACCACAGCTCCAATATTAAGCCTACCGTAAGGCAT-AGGGGGTTAAACGATATTT
12207531 TGTGA
130 TGTGA
12207536 NCTGACGCATAAGGATACAAAATTTGAGTGGTTAGATGCTTGTGAGAATAGCTTTGAGAAGCTTA
1 -CTGACGCATAAGGATACAAAATTTGAGTGGTTAGATGCTTGTGAGAATAGCTTTGAGAAGCTTA
* *
12207601 AGGCATGTCTCACCACAGCTCCAATATTAAGCCTACCGTAAGGCATAGGGGGTTATACGGTATTT
65 AGGCATGTCTCACCACAGCTCCAATATTAAGCCTACCGTAAGGCATAGGGGGTTAAACGATATTT
12207666 TGTGA
130 TGTGA
12207671 TGCATCACGA
Statistics
Matches: 132, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
135 22 0.17
136 110 0.83
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (134 bp):
CTGACGCATAAGGATACAAAATTTGAGTGGTTAGATGCTTGTGAGAATAGCTTTGAGAAGCTTAA
GGCATGTCTCACCACAGCTCCAATATTAAGCCTACCGTAAGGCATAGGGGGTTAAACGATATTTT
GTGA
Found at i:12210992 original size:35 final size:35
Alignment explanation
Indices: 12210953--12211020 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
12210943 GTGTGGATAG
* *
12210953 TGATGTTGATGTGTGCAAGTAGGGAGTGCACACAA
1 TGATGTTAAAGTGTGCAAGTAGGGAGTGCACACAA
*
12210988 TGATGTTAAAGTGTGCGAGTAGGGAGTGCACAC
1 TGATGTTAAAGTGTGCAAGTAGGGAGTGCACAC
12211021 GATAATATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.25
Consensus pattern (35 bp):
TGATGTTAAAGTGTGCAAGTAGGGAGTGCACACAA
Found at i:12221660 original size:14 final size:15
Alignment explanation
Indices: 12221643--12221675 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12221633 TTTAACAAAA
12221643 AACTAAAATTAA-AC
1 AACTAAAATTAAGAC
*
12221657 AACTTAAATTAAGAC
1 AACTAAAATTAAGAC
12221672 AACT
1 AACT
12221676 CAACATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AACTAAAATTAAGAC
Found at i:12223655 original size:14 final size:14
Alignment explanation
Indices: 12223636--12223662 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12223626 ATAATTTGTC
12223636 TGTATATATATATA
1 TGTATATATATATA
12223650 TGTATATATATAT
1 TGTATATATATAT
12223663 GTTTGCTTAG
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:12223657 original size:12 final size:12
Alignment explanation
Indices: 12223640--12223664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12223630 TTTGTCTGTA
12223640 TATATATATATG
1 TATATATATATG
12223652 TATATATATATG
1 TATATATATATG
12223664 T
1 T
12223665 TTGCTTAGAG
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:12224146 original size:15 final size:15
Alignment explanation
Indices: 12224126--12224161 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
12224116 GGCTTATAGA
12224126 TTGATTATGTT-TTGT
1 TTGATTATGTTGTT-T
12224141 TTGATTATGTTGTTT
1 TTGATTATGTTGTTT
12224156 TTGATT
1 TTGATT
12224162 TCTCATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.14, C:0.00, G:0.19, T:0.67
Consensus pattern (15 bp):
TTGATTATGTTGTTT
Found at i:12227198 original size:19 final size:18
Alignment explanation
Indices: 12227174--12227210 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12227164 TAATGAAAAT
12227174 AAATAAATAAATAAAATAA
1 AAATAAATAAA-AAAATAA
*
12227193 AAATAACTAAAAAAATAA
1 AAATAAATAAAAAAATAA
12227211 GAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAATAAAAAAATAA
Found at i:12227719 original size:21 final size:21
Alignment explanation
Indices: 12227695--12227736 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12227685 TTTAAATAAT
12227695 GGCATC-AGTCTTTGTCATGAA
1 GGCATCTA-TCTTTGTCATGAA
12227716 GGCATCTATCTTTGTCATGAA
1 GGCATCTATCTTTGTCATGAA
12227737 TTGCATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (21 bp):
GGCATCTATCTTTGTCATGAA
Found at i:12238007 original size:29 final size:28
Alignment explanation
Indices: 12237965--12238025 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
12237955 TTTTAAAGTC
*
12237965 AAATAAATAAACTTAAGGAAAAGCCAAAT
1 AAATAAATAAACTTAAAGAAAAG-CAAAT
*
12237994 AAATAAATAAACTTAAAGAAAAGCAACT
1 AAATAAATAAACTTAAAGAAAAGCAAAT
12238022 AAAT
1 AAAT
12238026 GAACTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18
Consensus pattern (28 bp):
AAATAAATAAACTTAAAGAAAAGCAAAT
Found at i:12240194 original size:5 final size:5
Alignment explanation
Indices: 12240180--12240240 Score: 81
Period size: 5 Copynumber: 12.4 Consensus size: 5
12240170 TTCCTTGTTA
* *
12240180 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTA TTTTC TTTTC TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
12240229 -TTTC TTTCTC TT
1 TTTTC TTT-TC TT
12240241 CCTTCTTCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
4 8 0.16
5 38 0.76
6 4 0.08
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:12240458 original size:35 final size:34
Alignment explanation
Indices: 12240372--12240464 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
12240362 ATCTATAAAT
*
12240372 TTTCAGCAGCTAAACCTGCTCCTTTTTACTTCAAA
1 TTTCAGCAGCT-AAGCTGCTCCTTTTTACTTCAAA
* * * *
12240407 -ATCAGCAGCTATGCTGCTCTGTTTTTCCTTCAAA
1 TTTCAGCAGCTAAGCTGCTC-CTTTTTACTTCAAA
*
12240441 TTTCAGCAGCTAAGCTGCACCTTT
1 TTTCAGCAGCTAAGCTGCTCCTTT
12240465 CCTTTAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
33 7 0.15
34 24 0.51
35 16 0.34
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.37
Consensus pattern (34 bp):
TTTCAGCAGCTAAGCTGCTCCTTTTTACTTCAAA
Found at i:12240588 original size:34 final size:34
Alignment explanation
Indices: 12240550--12240638 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
12240540 GCAAAATTCT
* * *
12240550 GCACTTTTTGGCCTCCAAAATTAGCAGAAAAATG
1 GCACTTTTTAGCCTCCAAAACTAACAGAAAAATG
* *
12240584 GCACTTTCTAGCCTCCAAAACTAATAGAAAAATG
1 GCACTTTTTAGCCTCCAAAACTAACAGAAAAATG
* *
12240618 GCTCTTTTCAGCCTCCAAAAC
1 GCACTTTTTAGCCTCCAAAAC
12240639 CAGCCCTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (34 bp):
GCACTTTTTAGCCTCCAAAACTAACAGAAAAATG
Found at i:12247980 original size:21 final size:21
Alignment explanation
Indices: 12247954--12247993 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12247944 TAACCAAAGT
* *
12247954 TTAACCCATTAACCCCTTTGG
1 TTAACCAATTAACACCTTTGG
12247975 TTAACCAATTAACACCTTT
1 TTAACCAATTAACACCTTT
12247994 CTATTTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (21 bp):
TTAACCAATTAACACCTTTGG
Found at i:12249893 original size:21 final size:20
Alignment explanation
Indices: 12249869--12249907 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
12249859 TTGGAAAAAT
12249869 TGTATCGATACATTATGAACA
1 TGTATCGATACATT-TGAACA
12249890 TGTATCGATACATTTGAA
1 TGTATCGATACATTTGAA
12249908 ATAGAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTGAACA
Found at i:12251888 original size:22 final size:22
Alignment explanation
Indices: 12251845--12251889 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12251835 ATTAGATTAA
* *
12251845 TCAAATCTCCATTTAATTAATC
1 TCAAATCTCCAATTAATCAATC
* *
12251867 TCAAATCTCTAATTGATCAATC
1 TCAAATCTCCAATTAATCAATC
12251889 T
1 T
12251890 ATACTCATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (22 bp):
TCAAATCTCCAATTAATCAATC
Found at i:12262133 original size:21 final size:21
Alignment explanation
Indices: 12262095--12262134 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12262085 CACAAAATAG
* *
12262095 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
12262116 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
12262135 ATATATACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:12262506 original size:25 final size:25
Alignment explanation
Indices: 12262473--12262564 Score: 105
Period size: 25 Copynumber: 3.5 Consensus size: 25
12262463 TTATATTTGA
12262473 AGTATATATATACTAAAAATATTTT
1 AGTATATATATACTAAAAATATTTT
* *
12262498 AGTATATATATA-TAATANGTTTATATTTGA
1 AGTATATATATACTAA-A----AATATTT-T
12262528 AGTATATATATACTAAAAATATTTT
1 AGTATATATATACTAAAAATATTTT
12262553 AGTATATATATA
1 AGTATATATATA
12262565 TAATAGTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.05
25 25 0.45
26 6 0.11
29 6 0.11
30 13 0.23
31 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (25 bp):
AGTATATATATACTAAAAATATTTT
Found at i:12262545 original size:55 final size:55
Alignment explanation
Indices: 12262456--12262569 Score: 219
Period size: 55 Copynumber: 2.1 Consensus size: 55
12262446 ATAGAAAGTA
12262456 AATATGTTTATATTTGAAGTATATATATACTAAAAATATTTTAGTATATATATAT
1 AATATGTTTATATTTGAAGTATATATATACTAAAAATATTTTAGTATATATATAT
*
12262511 AATANGTTTATATTTGAAGTATATATATACTAAAAATATTTTAGTATATATATAT
1 AATATGTTTATATTTGAAGTATATATATACTAAAAATATTTTAGTATATATATAT
12262566 AATA
1 AATA
12262570 GTAAATATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (55 bp):
AATATGTTTATATTTGAAGTATATATATACTAAAAATATTTTAGTATATATATAT
Found at i:12262587 original size:29 final size:27
Alignment explanation
Indices: 12262475--12262580 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
12262465 ATATTTGAAG
*
12262475 TATATATATACTAAAAATATTTTAGTA
1 TATATATATAATAAAAATATTTTAGTA
**** *
12262502 TATATATATAATANGTTTATATTT-GAA
1 TATATATATAATAAAAATAT-TTTAGTA
*
12262529 GTATATATATACTAAAAATATTTTAGTA
1 -TATATATATAATAAAAATATTTTAGTA
*
12262557 TATATATATAATAGTAAATATTTT
1 TATATATATAATA-AAAATATTTT
12262581 TCTTATAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
27 32 0.52
28 29 0.48
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (27 bp):
TATATATATAATAAAAATATTTTAGTA
Found at i:12283542 original size:73 final size:72
Alignment explanation
Indices: 12283454--12283591 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 72
12283444 TTTACTTCTA
* * *
12283454 TGTAAAATTGGTTTTAAAGTCAAAAGAATTTGAATCGATTAAAGTTCACTTTAATCGATTAAAAT
1 TGTAAAATTAGTTTTAAAGTCAAAAGAATTTGAATCAATTAAAGTTCACTTCAATCGATTAAAAT
12283519 AGTTTTC
66 AGTTTTC
* * * *
12283526 TGTAAAATTAAGTTTTAAAGTCAAAAGAGTTTTAATCAATTAAATTTCACTTCAATTGATTAAAA
1 TGTAAAATT-AGTTTTAAAGTCAAAAGAATTTGAATCAATTAAAGTTCACTTCAATCGATTAAAA
12283591 T
65 T
12283592 GGTTCTGTGC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
72 9 0.16
73 49 0.84
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (72 bp):
TGTAAAATTAGTTTTAAAGTCAAAAGAATTTGAATCAATTAAAGTTCACTTCAATCGATTAAAAT
AGTTTTC
Found at i:12283708 original size:17 final size:18
Alignment explanation
Indices: 12283688--12283721 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12283678 CCTCTCCCAC
12283688 GATTTCTCTTTA-AAAAT
1 GATTTCTCTTTAGAAAAT
*
12283705 GATTTCTTTTTAGAAAA
1 GATTTCTCTTTAGAAAA
12283722 CATTCAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (18 bp):
GATTTCTCTTTAGAAAAT
Found at i:12286063 original size:71 final size:70
Alignment explanation
Indices: 12285988--12286126 Score: 197
Period size: 71 Copynumber: 2.0 Consensus size: 70
12285978 AGTAACATTG
* * * * * *
12285988 GAAGGGACATTGAGACAAACAAAAAGGTTTTAATTGATTAACACAATGTTTAATTGATTAAATCA
1 GAAGGCACACTGAGACAAACAAAAAGATTTTAATTGACTAACACAAGGTTTAATTGA-TAAAACA
12286053 ACACTA
65 ACACTA
* *
12286059 GAAGGCACACTGAGACAAACAGAAAGATTTTAATTGGCTAACACAAGGTTTAATTGATAAAACAA
1 GAAGGCACACTGAGACAAACAAAAAGATTTTAATTGACTAACACAAGGTTTAATTGATAAAACAA
12286124 CAC
66 CAC
12286127 CATAAGAGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
70 10 0.17
71 50 0.83
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (70 bp):
GAAGGCACACTGAGACAAACAAAAAGATTTTAATTGACTAACACAAGGTTTAATTGATAAAACAA
CACTA
Found at i:12288277 original size:30 final size:29
Alignment explanation
Indices: 12288237--12288293 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
12288227 ATTTGTGTGT
12288237 GAGTGATTTACATGCAAGAAAAACCCTTAA
1 GAGTGATTTACATGCAAG-AAAACCCTTAA
*
12288267 GAGTGGTTTACATGCAAGAAAACCCTT
1 GAGTGATTTACATGCAAGAAAACCCTT
12288294 TTATAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (29 bp):
GAGTGATTTACATGCAAGAAAACCCTTAA
Found at i:12289122 original size:21 final size:21
Alignment explanation
Indices: 12289096--12289137 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12289086 TTGAGTCCTC
12289096 TTCACCCCAATCTCCTCCAAG
1 TTCACCCCAATCTCCTCCAAG
*
12289117 TTCACCTCAATCTCCTCCAAG
1 TTCACCCCAATCTCCTCCAAG
12289138 ATGAAAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.45, G:0.05, T:0.26
Consensus pattern (21 bp):
TTCACCCCAATCTCCTCCAAG
Found at i:12290068 original size:18 final size:18
Alignment explanation
Indices: 12290047--12290081 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12290037 TTAATAAATC
*
12290047 ATTATTAAATTATTAATT
1 ATTATTAAAATATTAATT
12290065 ATTATTAAAATATTAAT
1 ATTATTAAAATATTAAT
12290082 AAAATTGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATTAAAATATTAATT
Found at i:12293352 original size:21 final size:21
Alignment explanation
Indices: 12293318--12293357 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12293308 AATAACTCAA
12293318 TTCAATATATGAGCTCAAATCC
1 TTCAATATATGAGCT-AAATCC
12293340 TTCAATA-ATGAGCTAAAT
1 TTCAATATATGAGCTAAAT
12293358 GCTTACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCAATATATGAGCTAAATCC
Found at i:12295055 original size:28 final size:30
Alignment explanation
Indices: 12295023--12295084 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
12295013 TATAAGTTGA
*
12295023 AAGAA-AACCTTACCACTAA-AATAATTAC
1 AAGAATAACCCTACCACTAATAATAATTAC
*
12295051 AAGAATAGCCCTACCACTAATTAATAATTAC
1 AAGAATAACCCTACCACTAA-TAATAATTAC
12295082 AAG
1 AAG
12295085 GAAGCCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 12 0.41
31 12 0.41
ACGTcount: A:0.50, C:0.21, G:0.06, T:0.23
Consensus pattern (30 bp):
AAGAATAACCCTACCACTAATAATAATTAC
Found at i:12302244 original size:11 final size:12
Alignment explanation
Indices: 12302224--12302278 Score: 64
Period size: 11 Copynumber: 4.8 Consensus size: 12
12302214 TTAAAAAAAA
12302224 TTATTAATAAAT
1 TTATTAATAAAT
12302236 TTATT-ATAAAT
1 TTATTAATAAAT
12302247 TT-TTAATAAATT
1 TTATTAATAAA-T
12302259 GTTATTAA-AAA-
1 -TTATTAATAAAT
12302270 TTATTAATA
1 TTATTAATA
12302279 TTTTAGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.24
11 14 0.37
12 6 0.16
13 5 0.13
14 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TTATTAATAAAT
Found at i:12302246 original size:22 final size:22
Alignment explanation
Indices: 12302221--12302306 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 22
12302211 CTTTTAAAAA
12302221 AAATTATTAATAAATTTATTAT
1 AAATTATTAATAAATTTATTAT
* *
12302243 AAATTTTTAATAAATTGTTATTAA
1 AAATTATTAATAAA-T-TTATTAT
* *
12302267 AAATTATTAAT-ATTTTA-GAT
1 AAATTATTAATAAATTTATTAT
*
12302287 AAATTA-TAA-AAAGTTATTAT
1 AAATTATTAATAAATTTATTAT
12302307 TTTAAATTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
19 7 0.14
20 9 0.18
21 3 0.06
22 14 0.27
23 2 0.04
24 16 0.31
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
AAATTATTAATAAATTTATTAT
Found at i:12302270 original size:24 final size:22
Alignment explanation
Indices: 12302219--12302278 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
12302209 AGCTTTTAAA
12302219 AAAAATTATTAATAAATTTATT
1 AAAAATTATTAATAAATTTATT
* *
12302241 ATAAATTTTTAATAAATTGTTATT
1 AAAAATTATTAATAAA-T-TTATT
12302265 AAAAATTATTAATA
1 AAAAATTATTAATA
12302279 TTTTAGATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 14 0.44
23 1 0.03
24 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAATTATTAATAAATTTATT
Found at i:12302282 original size:33 final size:36
Alignment explanation
Indices: 12302224--12302291 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 36
12302214 TTAAAAAAAA
12302224 TTATTAATAAATTTATTATAAATTTTTA-ATAAATTG
1 TTATTAATAAATTTATTATAAA-TTTTAGATAAATTG
*
12302260 TTATTAA-AAA-TTATTA-ATATTTTAGATAAATT
1 TTATTAATAAATTTATTATAAATTTTAGATAAATT
12302292 ATAAAAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 5 0.17
33 9 0.30
34 6 0.20
35 3 0.10
36 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (36 bp):
TTATTAATAAATTTATTATAAATTTTAGATAAATTG
Found at i:12304190 original size:14 final size:14
Alignment explanation
Indices: 12304171--12304200 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12304161 GGTTTTATGC
*
12304171 TTTAATATTTTGCT
1 TTTAATATTTTACT
12304185 TTTAATATTTTACT
1 TTTAATATTTTACT
12304199 TT
1 TT
12304201 GCATCAGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTAATATTTTACT
Found at i:12304704 original size:2 final size:2
Alignment explanation
Indices: 12304697--12304738 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12304687 CATCTATGTT
12304697 TA TA TA TA 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 TA TA TA TA
12304739 ATTATAGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12313003 original size:30 final size:30
Alignment explanation
Indices: 12312969--12313032 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
12312959 ATTATTAGTA
**
12312969 ATAAAAACTTATTTGATTCAAAACAAAAAT
1 ATAAAAACTTATTTGACACAAAACAAAAAT
* * *
12312999 ATAAAGACTTATTTGACACAAAATAAAAGT
1 ATAAAAACTTATTTGACACAAAACAAAAAT
12313029 ATAA
1 ATAA
12313033 GCACTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (30 bp):
ATAAAAACTTATTTGACACAAAACAAAAAT
Found at i:12314472 original size:9 final size:9
Alignment explanation
Indices: 12314458--12314490 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
12314448 ACACGATTAA
12314458 TAACACGTT
1 TAACACGTT
*
12314467 TAACACGAT
1 TAACACGTT
12314476 TAACACGTT
1 TAACACGTT
12314485 TAACAC
1 TAACAC
12314491 TATTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (9 bp):
TAACACGTT
Found at i:12314472 original size:21 final size:21
Alignment explanation
Indices: 12314448--12314496 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 21
12314438 ATACGACACG
12314448 ACACGATTAATAACACGTTTA
1 ACACGATTAATAACACGTTTA
12314469 ACACGA-T--TAACACGTTTA
1 ACACGATTAATAACACGTTTA
*
12314487 ACACTATTAA
1 ACACGATTAA
12314497 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 16 0.67
19 1 0.04
20 1 0.04
21 6 0.25
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (21 bp):
ACACGATTAATAACACGTTTA
Found at i:12314481 original size:18 final size:18
Alignment explanation
Indices: 12314458--12314496 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12314448 ACACGATTAA
12314458 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
*
12314476 TAACACGTTTAACACTAT
1 TAACACGTTTAACACGAT
12314494 TAA
1 TAA
12314497 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:12314616 original size:26 final size:27
Alignment explanation
Indices: 12314555--12314624 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 27
12314545 TATAATTATA
12314555 AAATAAT-TATAATAAAA--AAATAAT
1 AAATAATATATAATAAAATTAAATAAT
*
12314579 AACATCAA-ATATAATAAAATTTAAT-AT
1 AA-AT-AATATATAATAAAATTAAATAAT
12314606 AAATAATATAT-ATAAAATT
1 AAATAATATATAATAAAATT
12314625 CATTATCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
24 2 0.05
25 12 0.31
26 18 0.46
27 4 0.10
28 3 0.08
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATAATATATAATAAAATTAAATAAT
Found at i:12314779 original size:18 final size:18
Alignment explanation
Indices: 12314736--12314770 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12314726 AACATGTAAT
12314736 GTATACACGTTTAAACAC
1 GTATACACGTTTAAACAC
12314754 GTATACACGTTTAAACA
1 GTATACACGTTTAAACA
12314771 TGATAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (18 bp):
GTATACACGTTTAAACAC
Found at i:12314815 original size:10 final size:10
Alignment explanation
Indices: 12314795--12314828 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12314785 AGTAAACGTA
*
12314795 TTTAAACGTG
1 TTTAAATGTG
12314805 TTTAAATGTG
1 TTTAAATGTG
12314815 TTTTAAATGTG
1 -TTTAAATGTG
12314826 TTT
1 TTT
12314829 GTCGTGTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (10 bp):
TTTAAATGTG
Found at i:12314821 original size:11 final size:11
Alignment explanation
Indices: 12314795--12314828 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12314785 AGTAAACGTA
*
12314795 TTTAAACGTG-
1 TTTAAATGTGT
12314805 TTTAAATGTGT
1 TTTAAATGTGT
12314816 TTTAAATGTGT
1 TTTAAATGTGT
12314827 TT
1 TT
12314829 GTCGTGTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (11 bp):
TTTAAATGTGT
Found at i:12316204 original size:18 final size:19
Alignment explanation
Indices: 12316176--12316212 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12316166 CGTTTATTAT
12316176 AATATTTTATTTTTAATAA
1 AATATTTTATTTTTAATAA
*
12316195 AATA-TTTATTTTTTATAA
1 AATATTTTATTTTTAATAA
12316213 TTTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATTTTATTTTTAATAA
Found at i:12316368 original size:17 final size:16
Alignment explanation
Indices: 12316345--12316437 Score: 53
Period size: 15 Copynumber: 6.2 Consensus size: 16
12316335 AATTGTTATT
12316345 TATTTATAATTTAAACA
1 TATTTATAATTTAAA-A
*
12316362 T-TATTATGA-TTAAAA
1 TAT-TTATAATTTAAAA
12316377 TATTTATAA-TT----
1 TATTTATAATTTAAAA
12316388 TATTTATAATTT-AAA
1 TATTTATAATTTAAAA
*
12316403 TATTAAT-ATTTGAAAA
1 TATTTATAATTT-AAAA
* *
12316419 TTTTTATTA-TTAAAA
1 TATTTATAATTTAAAA
12316434 TATT
1 TATT
12316438 AAAAATTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
11 9 0.15
12 2 0.03
14 4 0.07
15 22 0.36
16 17 0.28
17 7 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (16 bp):
TATTTATAATTTAAAA
Found at i:12325999 original size:21 final size:21
Alignment explanation
Indices: 12325953--12325999 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12325943 GTTTCAGGGT
* *
12325953 TTCAAGTATCGATACTTGTTC
1 TTCAAGTATCGATACTCGATC
*
12325974 ATCAAGTATCGATACTCGATC
1 TTCAAGTATCGATACTCGATC
12325995 TTCAA
1 TTCAA
12326000 ATCCTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCAAGTATCGATACTCGATC
Found at i:12329732 original size:2 final size:2
Alignment explanation
Indices: 12329725--12329787 Score: 117
Period size: 2 Copynumber: 31.0 Consensus size: 2
12329715 TCGTGTTCAC
12329725 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
12329767 NAT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT
12329788 CATGAATGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12331048 original size:15 final size:15
Alignment explanation
Indices: 12331028--12331130 Score: 70
Period size: 15 Copynumber: 6.8 Consensus size: 15
12331018 GATAAGATAA
12331028 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
12331043 ATTTAAATTTAAATT
1 ATTTAAATTTAATTT
* *
12331058 ATCT--A-TTCATTGT
1 ATTTAAATTTAATT-T
12331071 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
** *
12331086 AAATAAAGATT-ATTT
1 ATTTAAA-TTTAATTT
12331101 ATTTTTTAAATTTAATTT
1 A---TTTAAATTTAATTT
*
12331119 GTTTAAATTTAA
1 ATTTAAATTTAA
12331131 AATATCTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
12 4 0.06
13 5 0.08
15 40 0.61
16 7 0.11
17 2 0.03
18 8 0.12
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:12332158 original size:47 final size:47
Alignment explanation
Indices: 12332102--12332212 Score: 195
Period size: 47 Copynumber: 2.4 Consensus size: 47
12332092 AAAATGCTAC
*
12332102 GTAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAATACATGAT
1 GTAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAATACATAAT
* *
12332149 GTATTTATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAAT
1 GTAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAATACATAAT
12332196 GTAATTATTTTACTTAT
1 GTAATTATTTTACTTAT
12332213 GTTGAGTTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (47 bp):
GTAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAATACATAAT
Found at i:12339656 original size:185 final size:192
Alignment explanation
Indices: 12339335--12339708 Score: 555
Period size: 185 Copynumber: 2.0 Consensus size: 192
12339325 ATGACATGGT
12339335 ATGTAGCAATGCAGAATCACACTGACTTAAATCAGAAAATGAATTTGGAAAGGTAGAAAATAAAA
1 ATGTAGCAATGCAGAATCACACTGACTTAAATCAGAAAATGAATTT-G-AAGGTAGAAAATAAAA
* *
12339400 GAAAAACAAAAAGAAAAGTAATAAAGAAATGATGTCAGCTAAACTTGGAAGCCAAATCTAAATGA
64 GAAAAACAAAAAGAAAAGAAATAAAGAAATGATGTCAGCTAAACTTGGAAGCCAAAACTAAATGA
* *
12339465 TCACATCAGTCCCAGCAACACAGAACGGAACAAAAATAAGGCTATATTTGGTTAATTAATTGGC
129 TCACATCACTCCCAGCAACACAGAACAGAACAAAAATAAGGCTATATTTGGTTAATTAATTGGC
* * ***
12339529 ATGTAGCAATGCAGAATCACACTGACTTAAATCAGAAAATGAA-TT-CA-G-A-AAGAT-TGGGA
1 ATGTAGCAATGCAGAATCACACTGACTTAAATCAGAAAATGAATTTGAAGGTAGAAAATAAAAGA
* *
12339588 AAAA-AAAAAGAAAAGAAATAAAGAAATGTTGTCAGCTGAACTTGGAAGCCAAAACTAAATGATC
66 AAAACAAAAAGAAAAGAAATAAAGAAATGATGTCAGCTAAACTTGGAAGCCAAAACTAAATGATC
* * *
12339652 ACATCACTCCTAGCAACACAGAATAGAACAAGAATAAGGCTATATTTGGTTAATTAA
131 ACATCACTCCCAGCAACACAGAACAGAACAAAAATAAGGCTATATTTGGTTAATTAA
12339709 GTCCCTGTTA
Statistics
Matches: 166, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
185 108 0.65
186 6 0.04
187 4 0.02
188 1 0.01
189 1 0.01
190 1 0.01
193 2 0.01
194 43 0.26
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (192 bp):
ATGTAGCAATGCAGAATCACACTGACTTAAATCAGAAAATGAATTTGAAGGTAGAAAATAAAAGA
AAAACAAAAAGAAAAGAAATAAAGAAATGATGTCAGCTAAACTTGGAAGCCAAAACTAAATGATC
ACATCACTCCCAGCAACACAGAACAGAACAAAAATAAGGCTATATTTGGTTAATTAATTGGC
Found at i:12343469 original size:15 final size:15
Alignment explanation
Indices: 12343449--12343478 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12343439 TAATCAAGAT
12343449 TATTAATTTATCGAG
1 TATTAATTTATCGAG
12343464 TATTAATTTATCGAG
1 TATTAATTTATCGAG
12343479 CTTTTACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TATTAATTTATCGAG
Found at i:12344142 original size:3 final size:3
Alignment explanation
Indices: 12344134--12344164 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12344124 ATTTTAAATC
12344134 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12344165 GTATTATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12344209 original size:2 final size:2
Alignment explanation
Indices: 12344204--12344230 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12344194 TTTTTTTTAT
12344204 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
12344231 TACTTAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12347243 original size:18 final size:19
Alignment explanation
Indices: 12347222--12347258 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
12347212 ATACCAAAAG
12347222 AAGATAAAA-AAAAA-GAGA
1 AAGA-AAAAGAAAAATGAGA
12347240 AAGAAAAAGAAAAATGAGA
1 AAGAAAAAGAAAAATGAGA
12347259 GATTTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
AAGAAAAAGAAAAATGAGA
Found at i:12349949 original size:16 final size:17
Alignment explanation
Indices: 12349928--12349970 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
12349918 AAAGAAAAGA
12349928 TATTTTTAAA-AATAAT
1 TATTTTTAAATAATAAT
**
12349944 TATTTTTATAATTTTAAT
1 TATTTTTA-AATAATAAT
12349962 TATTTTTAA
1 TATTTTTAA
12349971 TTAAGTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 3 0.13
18 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTAAATAATAAT
Found at i:12350143 original size:69 final size:69
Alignment explanation
Indices: 12350018--12350188 Score: 188
Period size: 69 Copynumber: 2.5 Consensus size: 69
12350008 CTATGATGTT
*
12350018 ACACGTCATGTACAAAAATC-TGTAACAAGTCATAGTTAGCGTGTAACACGTCATGTACAAAAAT
1 ACACGTCATGTACAAAAA-CATGTGACAAGTCATAGTTAGCGTGTAACACGTCATGTACAAAAA-
*
12350082 C-TTTG
64 CATATG
* * * * *
12350087 ACACTTCATGTACAAAAACATGTGACAAG-CTATGGTTAGCGTGTGACTCG-CTATGTATAAAAA
1 ACACGTCATGTACAAAAACATGTGACAAGTC-ATAGTTAGCGTGTAACACGTC-ATGTACAAAAA
12350150 CATATG
64 CATATG
* * *
12350156 ACACGCCATGTACAAAAACATATGACACGTCAT
1 ACACGTCATGTACAAAAACATGTGACAAGTCAT
12350189 GTATAAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
68 4 0.05
69 81 0.94
70 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (69 bp):
ACACGTCATGTACAAAAACATGTGACAAGTCATAGTTAGCGTGTAACACGTCATGTACAAAAACA
TATG
Found at i:12350205 original size:24 final size:24
Alignment explanation
Indices: 12350063--12350265 Score: 108
Period size: 24 Copynumber: 8.8 Consensus size: 24
12350053 TTAGCGTGTA
*
12350063 ACACGTCATGTACAAAAATC-TTTG
1 ACACGTCATGTACAAAAA-CATGTG
*
12350087 ACACTTCATGTACAAAAACATGTG
1 ACACGTCATGTACAAAAACATGTG
* * * *
12350111 ACAAG-CTATGGT----TAGCGTGTG
1 ACACGTC-AT-GTACAAAAACATGTG
* * *
12350132 ACTCG-CTATGTATAAAAACATATG
1 ACACGTC-ATGTACAAAAACATGTG
* *
12350156 ACACGCCATGTACAAAAACATATG
1 ACACGTCATGTACAAAAACATGTG
*
12350180 ACACGTCATGTATAAAAATC-TGTG
1 ACACGTCATGTACAAAAA-CATGTG
* * *
12350204 ACAAGTCATAGT----TAACGTGTG
1 ACACGTCAT-GTACAAAAACATGTG
12350225 ACAC-TCATGTACAAAAACATGTG
1 ACACGTCATGTACAAAAACATGTG
* *
12350248 ACACATCATGTACGAAAA
1 ACACGTCATGTACAAAAA
12350266 TCTGTGATAA
Statistics
Matches: 139, Mismatches: 24, Indels: 32
0.71 0.12 0.16
Matches are distributed among these distances:
19 2 0.01
20 7 0.05
21 22 0.16
23 13 0.09
24 89 0.64
25 6 0.04
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
ACACGTCATGTACAAAAACATGTG
Found at i:12350223 original size:93 final size:92
Alignment explanation
Indices: 12350063--12350268 Score: 247
Period size: 93 Copynumber: 2.2 Consensus size: 92
12350053 TTAGCGTGTA
* * * *
12350063 ACACGTCATGTACAAAAATCTTTGACACTTCATGTACAAAAACATGTGACAAGCTATGGTTAGCG
1 ACACGTCATGTACAAAAATCTATGACACGTCATGTACAAAAACATGTGACAAGCTATAGTTAACG
* *
12350128 TGTGACTCGCTATGTATAAAAACATATG
66 TGTGACACGC-ATGTACAAAAACATATG
* *
12350156 ACACGCCATGTACAAAAA-CATATGACACGTCATGTATAAAAATC-TGTGACAAG-TCATAGTTA
1 ACACGTCATGTACAAAAATC-TATGACACGTCATGTACAAAAA-CATGTGACAAGCT-ATAGTTA
* *
12350218 ACGTGTGACACTCATGTACAAAAACATGTG
63 ACGTGTGACACGCATGTACAAAAACATATG
* *
12350248 ACACATCATGTACGAAAATCT
1 ACACGTCATGTACAAAAATCT
12350269 GTGATAAGTC
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
92 33 0.34
93 62 0.65
94 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (92 bp):
ACACGTCATGTACAAAAATCTATGACACGTCATGTACAAAAACATGTGACAAGCTATAGTTAACG
TGTGACACGCATGTACAAAAACATATG
Found at i:12350250 original size:68 final size:69
Alignment explanation
Indices: 12350154--12350309 Score: 224
Period size: 68 Copynumber: 2.3 Consensus size: 69
12350144 TAAAAACATA
* * *
12350154 TGACACGCCATGTACAAAAACATATGACACGTCATGTATAAAAATCTGTGACAAGTCATAGTTAA
1 TGACACACCATGTACAAAAACATATGACACATCATGTACAAAAATCTGTGACAAGTCATAGTTAA
12350219 CGTG
66 CGTG
* * * * * *
12350223 TGACAC-TCATGTACAAAAACATGTGACACATCATGTACGAAAATCTGTGATAAGTCATGGTTAG
1 TGACACACCATGTACAAAAACATATGACACATCATGTACAAAAATCTGTGACAAGTCATAGTTAA
12350287 CGTG
66 CGTG
12350291 TGACACACCATGTACAAAA
1 TGACACACCATGTACAAAA
12350310 GCCTGCGACA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
68 60 0.78
69 17 0.22
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (69 bp):
TGACACACCATGTACAAAAACATATGACACATCATGTACAAAAATCTGTGACAAGTCATAGTTAA
CGTG
Found at i:12350294 original size:45 final size:45
Alignment explanation
Indices: 12350244--12350416 Score: 213
Period size: 45 Copynumber: 3.8 Consensus size: 45
12350234 TACAAAAACA
* * *
12350244 TGTGACACATCATGTACGAAAA-TCTGTGATAAGTCATGGTTAGCG
1 TGTGACACACCATGTAC-AAAAGCCTGTGACAAGTCATGGTTAGCG
* *
12350289 TGTGACACACCATGTACAAAAGCCTGCGACAAGCCATGGTTAGCG
1 TGTGACACACCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCG
* *
12350334 TGTTACACGCCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCG
1 TGTGACACACCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCG
* ** * * *
12350379 TGTGATACGTCATATACAAAAGCCTATGACAAGCCATG
1 TGTGACACACCATGTACAAAAGCCTGTGACAAGTCATG
12350417 TACAAAAACC
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
44 4 0.04
45 108 0.96
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (45 bp):
TGTGACACACCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCG
Found at i:12350473 original size:15 final size:14
Alignment explanation
Indices: 12350451--12350480 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12350441 TCTTCTCAAC
12350451 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
12350465 TTTTGTTCTTTTTTT
1 TTTT-TTCTTTTTTT
12350480 T
1 T
12350481 GACAATTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTTTTCTTTTTTT
Found at i:12351182 original size:11 final size:11
Alignment explanation
Indices: 12351166--12351192 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12351156 CATGTTAATA
12351166 TTATGCCCCAC
1 TTATGCCCCAC
12351177 TTATGCCCCAC
1 TTATGCCCCAC
12351188 TTATG
1 TTATG
12351193 AAATATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.37, G:0.11, T:0.33
Consensus pattern (11 bp):
TTATGCCCCAC
Found at i:12351676 original size:13 final size:13
Alignment explanation
Indices: 12351638--12351702 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
12351628 TATAATTTAA
12351638 TAAAATTTTAATT
1 TAAAATTTTAATT
*
12351651 T-AATTTTTAAATT
1 TAAAATTTT-AATT
*
12351664 TAAAATATTAATTTT
1 TAAAATTTTAA--TT
*
12351679 TATAATTTATAA-T
1 TAAAATTT-TAATT
12351692 TAAAATTTTAA
1 TAAAATTTTAA
12351703 ACTTTTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 9 0.22
13 16 0.39
14 5 0.12
15 8 0.20
16 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAAATTTTAATT
Found at i:12351698 original size:22 final size:21
Alignment explanation
Indices: 12351652--12351703 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12351642 ATTTTAATTT
*
12351652 AATTTTTAAATTTAAAATATT
1 AATTTTTAAATTTAAAATATA
*
12351673 AATTTTTATAATTTATAAT-TA
1 AATTTTTA-AATTTAAAATATA
*
12351694 AAATTTTAAA
1 AATTTTTAAA
12351704 CTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 16 0.59
22 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTTAAATTTAAAATATA
Found at i:12351710 original size:52 final size:51
Alignment explanation
Indices: 12351609--12351711 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 51
12351599 ATTTATAGTT
**
12351609 ATTTAAAAGATTAATAATTTATAATTTAATAAAATTTTAATTTAATTTTTAA
1 ATTTAAAAGATTAATAATTTATAATTTAATAAAATTTTAAACT-ATTTTTAA
* *
12351661 ATTTAAAATATTAAT-TTTTATAATTTATAATTAAAATTTTAAACT-TTTTTA
1 ATTTAAAAGATTAATAATTTATAA-TT-TAA-TAAAATTTTAAACTATTTTTA
12351712 TTTTAAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
51 7 0.16
52 22 0.50
53 3 0.07
54 12 0.27
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (51 bp):
ATTTAAAAGATTAATAATTTATAATTTAATAAAATTTTAAACTATTTTTAA
Found at i:12351720 original size:28 final size:27
Alignment explanation
Indices: 12351611--12351720 Score: 77
Period size: 26 Copynumber: 4.1 Consensus size: 27
12351601 TTATAGTTAT
* * *
12351611 TTAAAAGATTAATAATTTATAATTT-AA
1 TTAAAATATTAAT-TTTTATATTTTAAA
* *
12351638 -TAAAATTTTAA-TTTAAT-TTTTAAA
1 TTAAAATATTAATTTTTATATTTTAAA
*
12351662 TTTAAAATATTAATTTTTATAATTTATAA
1 -TTAAAATATTAATTTTTATATTTTA-AA
*
12351691 TTAAAATTTTAAACTTTTT-TATTTTAAA
1 TTAAAATATT-AA-TTTTTATATTTTAAA
12351719 TT
1 TT
12351721 CATTTTTGGT
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
23 3 0.05
24 6 0.09
26 19 0.29
27 5 0.08
28 17 0.26
29 10 0.15
30 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
TTAAAATATTAATTTTTATATTTTAAA
Found at i:12371998 original size:35 final size:35
Alignment explanation
Indices: 12371924--12372003 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
12371914 TTGTACACAG
** *
12371924 AACAACTAGAGCAAGTGAAACGTTACTTCATGTAG
1 AACAACTAGAGCAAGTGAAACGTTACTTCATACAA
*
12371959 AACAATTAGAGCAAGTG-AA-GTTCTACTTCATACAA
1 AACAACTAGAGCAAGTGAAACG-T-TACTTCATACAA
12371994 AACAACTAGA
1 AACAACTAGA
12372004 ATAAATGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 1 0.03
34 3 0.08
35 34 0.89
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (35 bp):
AACAACTAGAGCAAGTGAAACGTTACTTCATACAA
Found at i:12372336 original size:29 final size:28
Alignment explanation
Indices: 12372251--12372346 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 28
12372241 TCACATACAC
* * * *
12372251 CTTCTTTTCTTGTACCTATTCATGTACAA
1 CTTCTTCTCTTATACCTATTCACGTA-TA
* * * *
12372280 CTTCTTCTCTTGTACCTATGCTCATATA
1 CTTCTTCTCTTATACCTATTCACGTATA
*
12372308 GCTTCTTCTCTTATACCTTTTCACGTATA
1 -CTTCTTCTCTTATACCTATTCACGTATA
*
12372337 CCTCTTCTCT
1 CTTCTTCTCT
12372347 ATTACCTTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
28 10 0.19
29 44 0.81
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (28 bp):
CTTCTTCTCTTATACCTATTCACGTATA
Found at i:12385828 original size:22 final size:22
Alignment explanation
Indices: 12385803--12385852 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12385793 TTATCCTTAA
*
12385803 CTTCTTTGTCT-TTCTTCTTCCT
1 CTTCTTT-TCTCTTCTTCTACCT
*
12385825 CTTCTTTTTTCTTCTTCTACCT
1 CTTCTTTTCTCTTCTTCTACCT
12385847 -TTCTTT
1 CTTCTTT
12385853 AAGTCGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (22 bp):
CTTCTTTTCTCTTCTTCTACCT
Found at i:12386700 original size:108 final size:108
Alignment explanation
Indices: 12386509--12386721 Score: 302
Period size: 108 Copynumber: 2.0 Consensus size: 108
12386499 CATTTTTTGT
* * *
12386509 AATCATCACTTTCTCATATTATATTAAACACTGCAAAGTTATCTTTTCAGCAATCACATTCCTAA
1 AATCATCACTTTCTCATATTATACTAAACACTGCAAAGTTATCTTTTCAGCAATCACAATCCCAA
* * *
12386574 CAACATATCAAACTCAACCTAAGTCTTGGATTAATGGTTCTGC
66 CAACATACCAAACACAACCTAACTCTTGGATTAATGGTTCTGC
* ** * * *
12386617 AATCATCA-TTTTTCCATATTATACTAAATGCTGTAAAGTTATCTTTTCAGTAATCATAATCCCA
1 AATCATCACTTTCT-CATATTATACTAAACACTGCAAAGTTATCTTTTCAGCAATCACAATCCCA
12386681 ACAACATACCAAACACAACCTAACTCTTGGATTAATGGTTC
65 ACAACATACCAAACACAACCTAACTCTTGGATTAATGGTTC
12386722 ATTAGTTGGG
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 4 0.04
108 88 0.96
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (108 bp):
AATCATCACTTTCTCATATTATACTAAACACTGCAAAGTTATCTTTTCAGCAATCACAATCCCAA
CAACATACCAAACACAACCTAACTCTTGGATTAATGGTTCTGC
Done.