Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 80 of 120
Found at i:23372596 original size:43 final size:43
Alignment explanation
Indices: 23372514--23372598 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
23372504 ATTAACATGT
* * *
23372514 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAACTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
23372557 TAAACTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAACTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
23372599 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAACTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:23373097 original size:6 final size:6
Alignment explanation
Indices: 23373086--23373115 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
23373076 GAGCAACAAT
23373086 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
23373116 CATTGGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:23373242 original size:21 final size:21
Alignment explanation
Indices: 23373216--23373262 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
23373206 ACGAGCCATC
*
23373216 GCAATACTTTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
23373237 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCCGG
23373258 GCAAT
1 GCAAT
23373263 TGGACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:23376589 original size:4 final size:4
Alignment explanation
Indices: 23376567--23376641 Score: 53
Period size: 4 Copynumber: 18.5 Consensus size: 4
23376557 AACACATTAC
* * * * * * * *
23376567 CTTT TTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTC CTTC CTTC
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
23376615 CTTT CTTT CTTT CTTTT CTTT CTTT CT
1 CTTT CTTT CTTT C-TTT CTTT CTTT CT
23376642 CGTTTATTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
3 3 0.05
4 49 0.83
5 7 0.12
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:23376599 original size:20 final size:19
Alignment explanation
Indices: 23376573--23376630 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
23376563 TTACCTTTTT
23376573 TTCCTTCTTCTTTCTTTCC
1 TTCCTTCTTCTTTCTTTCC
* *
23376592 TCTCCTTCTTCCTTCCTTCC
1 T-TCCTTCTTCTTTCTTTCC
23376612 TTCCTTTCTTTCTTTCTTT
1 TTCC-TTC-TTCTTTCTTT
23376631 TCTTTCTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 20 0.62
21 8 0.25
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCCTTCTTCTTTCTTTCC
Found at i:23376634 original size:13 final size:13
Alignment explanation
Indices: 23376616--23376641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23376606 CCTTCCTTCC
23376616 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
23376629 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
23376642 CGTTTATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:23377914 original size:39 final size:39
Alignment explanation
Indices: 23377844--23377923 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 39
23377834 TTAATATTTT
23377844 CCCTCCAAAATTTTACTCCCCCATTTATTTTCCCCAAAAA
1 CCCTCCAAAATTTTACTCCCCCA-TTATTTTCCCCAAAAA
* *
23377884 CCCT-CAAAATTTTTACTCCCTC-TTACTTTTCCCCTAAAA
1 CCCTCCAAAA-TTTTACTCCCCCATTA-TTTTCCCCAAAAA
23377923 C
1 C
23377924 TTTTACTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
38 3 0.08
39 18 0.50
40 15 0.42
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.35
Consensus pattern (39 bp):
CCCTCCAAAATTTTACTCCCCCATTATTTTCCCCAAAAA
Found at i:23380073 original size:39 final size:39
Alignment explanation
Indices: 23379979--23380073 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 39
23379969 AAAACTAAAA
* * *
23379979 AAATTAATTAACAATTTAATATAATGATACATGATACAT
1 AAATTAATTAACAATTTAACATAATAATACATGAAACAT
* * * *
23380018 AAAAT-ATACAATAATTTAACATAATAATACATGAAATAT
1 AAATTAAT-TAACAATTTAACATAATAATACATGAAACAT
23380057 AAATTAATGTAA-AATTT
1 AAATTAAT-TAACAATTT
23380074 TAATAGTAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
38 2 0.05
39 38 0.86
40 4 0.09
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (39 bp):
AAATTAATTAACAATTTAACATAATAATACATGAAACAT
Found at i:23380684 original size:20 final size:20
Alignment explanation
Indices: 23380659--23380698 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23380649 GTTATTTATC
*
23380659 ATAATGTATT-TAGTATTTTA
1 ATAATGT-TTATAATATTTTA
23380679 ATAATGTTTATAATATTTTA
1 ATAATGTTTATAATATTTTA
23380699 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
ATAATGTTTATAATATTTTA
Found at i:23381875 original size:9 final size:9
Alignment explanation
Indices: 23381861--23381889 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
23381851 ACAAATGATT
23381861 TTAAAATTA
1 TTAAAATTA
23381870 TTAAAATTA
1 TTAAAATTA
23381879 TTAAAATTA
1 TTAAAATTA
23381888 TT
1 TT
23381890 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:23382485 original size:120 final size:120
Alignment explanation
Indices: 23382337--23382576 Score: 410
Period size: 120 Copynumber: 2.0 Consensus size: 120
23382327 GATCCTCACC
* * *
23382337 TGATGATGATGAAATCATCGATGAACTCTCATAATTCATTAATAAATTTGGATCCGAAAACCCAT
1 TGATGATGATGAAATCATCGATGAACTCTCATAATTCACTAACAAATTCGGATCCGAAAACCCAT
*
23382402 TCTCAGAGAGATTCAGGTTCAAGTTGGGTGTCC-CCATGGTTGAGTTATTATGAAA
66 TCTCAGAGAGATTCAGGTTCAAGTTGGGTG-CCGCCATGGTCGAGTTATTATGAAA
*
23382457 TGATGATGATGAAATCATCGATGAACTCTCATAATTCACTAACAAATTCGGATCTGAAAACCCAT
1 TGATGATGATGAAATCATCGATGAACTCTCATAATTCACTAACAAATTCGGATCCGAAAACCCAT
*
23382522 TCTTAGAGAGATTCAGGTTCAAGTTGGGTGCCGCCATGGTCGAGTTATTATGAAA
66 TCTCAGAGAGATTCAGGTTCAAGTTGGGTGCCGCCATGGTCGAGTTATTATGAAA
23382577 CCAGCTTTGA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
119 2 0.02
120 111 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (120 bp):
TGATGATGATGAAATCATCGATGAACTCTCATAATTCACTAACAAATTCGGATCCGAAAACCCAT
TCTCAGAGAGATTCAGGTTCAAGTTGGGTGCCGCCATGGTCGAGTTATTATGAAA
Found at i:23383273 original size:21 final size:21
Alignment explanation
Indices: 23383248--23383319 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
23383238 ACAAAATATT
**
23383248 ATGTTTGTAGTTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
23383269 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
*
23383290 ATGTTTTGTAACTCTCCTCATT
1 ATG-TTTGTAACTCTCCTCATA
23383312 ATGTTTGT
1 ATGTTTGT
23383320 TTTAAATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 27 0.57
22 20 0.43
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.49
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:23383300 original size:22 final size:22
Alignment explanation
Indices: 23383259--23383317 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
23383249 TGTTTGTAGT
23383259 TCTCCTCATAATG-TTTGTAAC
1 TCTCCTCATAATGTTTTGTAAC
23383280 TCTCCTCATAATGTTTTGTAAC
1 TCTCCTCATAATGTTTTGTAAC
*
23383302 TCTCCTCATTATGTTT
1 TCTCCTCATAATGTTT
23383318 GTTTTAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 13 0.36
22 23 0.64
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (22 bp):
TCTCCTCATAATGTTTTGTAAC
Found at i:23385684 original size:30 final size:30
Alignment explanation
Indices: 23385633--23385690 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
23385623 GAGACAAGAC
* *
23385633 AACCTCTTGGAAATATGGGGGGTGTCTTAG
1 AACCACTTGAAAATATGGGGGGTGTCTTAG
*
23385663 AACCACTTGAAAATGTGGGGGGTGTCTT
1 AACCACTTGAAAATATGGGGGGTGTCTT
23385691 GTTAATGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (30 bp):
AACCACTTGAAAATATGGGGGGTGTCTTAG
Found at i:23387033 original size:22 final size:21
Alignment explanation
Indices: 23386974--23387043 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
23386964 ACAAAACATT
* * *
23386974 ATGTTTGTAACTGTCATCATA
1 ATGTTTATAACTCTCCTCATA
*
23386995 ATGTTTATAACTTTCCTCATA
1 ATGTTTATAACTCTCCTCATA
* * *
23387016 ATATTTTATAGCTCTCCTCATT
1 AT-GTTTATAACTCTCCTCATA
23387038 ATGTTT
1 ATGTTT
23387044 GTTTTAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (21 bp):
ATGTTTATAACTCTCCTCATA
Found at i:23387662 original size:21 final size:22
Alignment explanation
Indices: 23387637--23387690 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
23387627 TAAAATTATT
*
23387637 TAATAATTTTATTATT-TAAGAA
1 TAATAATTTTA-TATTCTAAAAA
23387659 -AATAATTTTATATTCTAAAAA
1 TAATAATTTTATATTCTAAAAA
23387680 TAATAATTTTA
1 TAATAATTTTA
23387691 ATAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 15 0.52
22 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATAATTTTATATTCTAAAAA
Found at i:23390767 original size:30 final size:30
Alignment explanation
Indices: 23390731--23390795 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
23390721 ACTTATTTTA
*
23390731 TTGTTAATTTTGCTATTATTTTAGAGGCAT
1 TTGTTAATTTTGCTACTATTTTAGAGGCAT
*
23390761 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGCTACTATTTTAGAGGCAT
23390791 TTGTT
1 TTGTT
23390796 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTGCTACTATTTTAGAGGCAT
Found at i:23397248 original size:47 final size:47
Alignment explanation
Indices: 23397198--23397287 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
23397188 TTTATGATTT
23397198 TTTTTA-ATATTTTTAT-AAGTTTATATCAATTTTAATGCATTTTATA
1 TTTTTATATATTTTTATGAAGTTTATA-CAATTTTAATGCATTTTATA
* * * * *
23397244 TTTTTATGTTTTTTTATGAATTTTATAGAGTTTTAATGCATTTT
1 TTTTTATATATTTTTATGAAGTTTATACAATTTTAATGCATTTT
23397288 TATAAAGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 6 0.16
47 23 0.62
48 8 0.22
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (47 bp):
TTTTTATATATTTTTATGAAGTTTATACAATTTTAATGCATTTTATA
Found at i:23398053 original size:12 final size:12
Alignment explanation
Indices: 23398027--23398114 Score: 60
Period size: 12 Copynumber: 7.8 Consensus size: 12
23398017 CTGTTTTGGT
*
23398027 TGTTGTTTTCG-
1 TGTTGTTTTTGC
23398038 TGTTGTTTTTGC
1 TGTTGTTTTTGC
* *
23398050 TGTTATTTTTGT
1 TGTTGTTTTTGC
* *
23398062 TGCT-ATTTT--
1 TGTTGTTTTTGC
**
23398071 TGTTGTTTTTAA
1 TGTTGTTTTTGC
*
23398083 TGGTG-TTTTGC
1 TGTTGTTTTTGC
*
23398094 TGTTGTTTTTAC
1 TGTTGTTTTTGC
23398106 TGTTGTTTT
1 TGTTGTTTT
23398115 GATTGTTATT
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
9 3 0.05
10 4 0.07
11 22 0.37
12 31 0.52
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.67
Consensus pattern (12 bp):
TGTTGTTTTTGC
Found at i:23398091 original size:20 final size:21
Alignment explanation
Indices: 23398067--23398114 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
23398057 TTTGTTGCTA
23398067 TTTTTGTTGTTTTTAATGGTG
1 TTTTTGTTGTTTTTAATGGTG
* *
23398088 TTTTGCTGTTGTTTTTACTGTTG
1 TTTT--TGTTGTTTTTAATGGTG
23398111 TTTT
1 TTTT
23398115 GATTGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
23 19 0.83
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69
Consensus pattern (21 bp):
TTTTTGTTGTTTTTAATGGTG
Found at i:23398121 original size:12 final size:12
Alignment explanation
Indices: 23398071--23398126 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
23398061 TTGCTATTTT
* *
23398071 TGTTGTTTTTAA
1 TGTTGTTTTGAC
*
23398083 TGGTGTTTTG-C
1 TGTTGTTTTGAC
*
23398094 TGTTGTTTTTAC
1 TGTTGTTTTGAC
*
23398106 TGTTGTTTTGAT
1 TGTTGTTTTGAC
*
23398118 TGTTATTTT
1 TGTTGTTTT
23398127 TGTTGTTTGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
11 8 0.23
12 27 0.77
ACGTcount: A:0.09, C:0.04, G:0.21, T:0.66
Consensus pattern (12 bp):
TGTTGTTTTGAC
Found at i:23398134 original size:44 final size:43
Alignment explanation
Indices: 23397952--23398134 Score: 114
Period size: 44 Copynumber: 4.2 Consensus size: 43
23397942 AAAAATTATA
*
23397952 TTGTTGTTTTGGTGTT-TTTTTAC---TGTTTTGATTGCTGTTTT
1 TTGTTGTTTTGCTGTTGTTTTTACTGTTGTTTTGATTG-T-TTTT
* * *
23397993 TTATTATTTTTG-TGTTGTTTTCTACTGTT-TTGGTTG-TTGTTTTC
1 TTGTT-GTTTTGCTGTTGTTTT-TACTGTTGTT--TTGATTGTTTTT
* * **
23398037 GTGTTGTTTTTGCTGTTATTTTTGTTGCTAT-TTTTG-TTGTTTTT
1 TTGTTG-TTTTGCTGTTGTTTTTACTG-T-TGTTTTGATTGTTTTT
* *
23398081 AATGGTGTTTTGCTGTTGTTTTTACTGTTGTTTTGATTGTTATTT
1 -TTGTTGTTTTGCTGTTGTTTTTACTGTTGTTTTGATTGTT-TTT
23398126 TTGTTGTTT
1 TTGTTGTTT
23398135 GGATGTTATT
Statistics
Matches: 109, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
41 8 0.07
42 10 0.09
43 9 0.08
44 53 0.49
45 19 0.17
46 7 0.06
47 3 0.03
ACGTcount: A:0.07, C:0.05, G:0.21, T:0.68
Consensus pattern (43 bp):
TTGTTGTTTTGCTGTTGTTTTTACTGTTGTTTTGATTGTTTTT
Found at i:23398148 original size:21 final size:21
Alignment explanation
Indices: 23398106--23398147 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
23398096 TTGTTTTTAC
*
23398106 TGTTGTTTTGATTGTTATTTT
1 TGTTGTTTGGATTGTTATTTT
23398127 TGTTGTTTGGA-TGTTATTTT
1 TGTTGTTTGGATTGTTATTTT
23398147 T
1 T
23398148 TATGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (21 bp):
TGTTGTTTGGATTGTTATTTT
Found at i:23398237 original size:18 final size:19
Alignment explanation
Indices: 23398214--23398249 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23398204 ACTTATATTT
23398214 TATTGT-TAATTTTTTTAC
1 TATTGTATAATTTTTTTAC
*
23398232 TATTGTATTATTTTTTTA
1 TATTGTATAATTTTTTTA
23398250 TTAATACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (19 bp):
TATTGTATAATTTTTTTAC
Found at i:23402121 original size:17 final size:17
Alignment explanation
Indices: 23402099--23402132 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
23402089 ATTAGCAACA
23402099 CCATCATTTCTTTCATT
1 CCATCATTTCTTTCATT
23402116 CCATCATTTCTTTCATT
1 CCATCATTTCTTTCATT
23402133 TTGGGTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (17 bp):
CCATCATTTCTTTCATT
Found at i:23408884 original size:59 final size:58
Alignment explanation
Indices: 23408819--23409214 Score: 367
Period size: 59 Copynumber: 6.8 Consensus size: 58
23408809 CGGGGGGAAT
* * * *
23408819 GTAATTTTGGGAAAATTTGGGGTTAAAAATGGGATTTTAGAAGGTTCAAGGGTAAAATG
1 GTAATTTTGGGAAAA-TTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
* * * * ***
23408878 GTAATTTTTAGTG-AAATCGAGGTTAAAAATGGGATTTCAAAAAGTTTAAGGGTAAAATG
1 GTAA-TTTT-GGGAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
* ** * *
23408937 ATAATTTTTGATAAAATCGGGGTTAAAAGTGGAATTTTGGAAAGTTT-AGAGGTAAAATG
1 GTAA-TTTTGGGAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAG-GGTAAAATG
* *
23408996 GTAATTTTTGGTG-AAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
1 GTAA-TTTTGG-GAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
**
23409055 GTAATTTTTGGTG-AAACCGGGGTT-AAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
1 GTAA-TTTTGG-GAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
* ** *
23409113 GTAATTTTTGGAAGTTTTGGGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGT-AAATG
1 GTAATTTTGGGAA-AATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
* ** * * *
23409170 GTAATTTTTGGAAGTTTTGGGG-TCAAAATGAAATTTTAGAAAGTT
1 GTAATTTTGGGAA-AATTGGGGTTAAAAATGGAATTTTGGAAAGTT
23409215 CGGGGACTAG
Statistics
Matches: 293, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
56 2 0.01
57 52 0.18
58 73 0.25
59 156 0.53
60 8 0.03
61 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.35
Consensus pattern (58 bp):
GTAATTTTGGGAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
Found at i:23409111 original size:58 final size:59
Alignment explanation
Indices: 23408837--23409180 Score: 430
Period size: 59 Copynumber: 5.9 Consensus size: 59
23408827 GGGAAAATTT
* * * * *
23408837 GGGGTTAAAAATGGGATTTTAGAAGGTTCAAGGGTAAAATGGTAATTTTTAGTGAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATC
* * *** * * *
23408896 GAGGTTAAAAATGGGATTTCAAAAAGTTTAAGGGTAAAATGATAATTTTTGATAAAATC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATC
* *
23408955 GGGGTTAAAAGTGGAATTTTGGAAAGTTT-AGAGGTAAAATGGTAATTTTTGGTGAAATT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAG-GGTAAAATGGTAATTTTTGGTGAAATC
* * *
23409014 AGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAACC
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATC
* *
23409073 GGGGTT-AAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT-G-GAAGTTTT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAA--ATC
*
23409131 GGGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGT-AAATGGTAATTTTTGG
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGG
23409181 AAGTTTTGGG
Statistics
Matches: 250, Mismatches: 30, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
56 3 0.01
57 15 0.06
58 78 0.31
59 153 0.61
60 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGGTGAAATC
Found at i:23409219 original size:28 final size:28
Alignment explanation
Indices: 23408955--23409214 Score: 221
Period size: 29 Copynumber: 8.9 Consensus size: 28
23408945 TGATAAAATC
23408955 GGGGTTAAAAGTGGAATTTTGGAAAGTTTA
1 GGGG-TAAAA-TGGAATTTTGGAAAGTTTA
*
23408985 GAGGTAAAATGGTAATTTTTGGTGAAA--TTA
1 GGGGTAAAATGG-AA-TTTT-G-GAAAGTTTA
*
23409015 GGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGT-AAAATGGAATTTTGGAAAGTTTA
**
23409044 GGGGTAAAATGGTAATTTTTGGTGAAA---CC
1 GGGGTAAAATGG-AA-TTTT-G-GAAAGTTTA
23409073 GGGGTTAAAATGGAATTTTGGAAAGTTTA
1 GGGG-TAAAATGGAATTTTGGAAAGTTTA
* *
23409102 AGGGTAAAATGGTAATTTTTGG-AAGTTTT
1 GGGGTAAAATGG-AA-TTTTGGAAAGTTTA
23409131 GGGGTTAAAATGGAATTTTGGAAAGTTTA
1 GGGG-TAAAATGGAATTTTGGAAAGTTTA
*
23409160 GGGGT-AAATGGTAATTTTTGG-AAGTTTT
1 GGGGTAAAATGG-AA-TTTTGGAAAGTTTA
* *
23409188 GGGGTCAAAATGAAATTTTAGAAAGTT
1 GGGGT-AAAATGGAATTTTGGAAAGTT
23409215 CGGGGACTAG
Statistics
Matches: 191, Mismatches: 15, Indels: 49
0.75 0.06 0.19
Matches are distributed among these distances:
26 4 0.02
27 11 0.06
28 48 0.25
29 65 0.34
30 46 0.24
31 9 0.05
32 8 0.04
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.35
Consensus pattern (28 bp):
GGGGTAAAATGGAATTTTGGAAAGTTTA
Found at i:23411150 original size:17 final size:17
Alignment explanation
Indices: 23411128--23411163 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23411118 GTAAATGGAC
* *
23411128 TTTGTAATTGGACTTTA
1 TTTGTAAATGGACATTA
23411145 TTTGTAAATGGACATTA
1 TTTGTAAATGGACATTA
23411162 TT
1 TT
23411164 AATTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (17 bp):
TTTGTAAATGGACATTA
Found at i:23420341 original size:12 final size:12
Alignment explanation
Indices: 23420324--23420349 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23420314 TTATGGATAA
23420324 ACTTTTAAGGCT
1 ACTTTTAAGGCT
23420336 ACTTTTAAGGCT
1 ACTTTTAAGGCT
23420348 AC
1 AC
23420350 CCTTGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (12 bp):
ACTTTTAAGGCT
Found at i:23422377 original size:17 final size:17
Alignment explanation
Indices: 23422351--23422384 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23422341 CATTTGAAAT
23422351 GGGTGGATTTAAATATA
1 GGGTGGATTTAAATATA
* *
23422368 GGGTGTATTTAATTATA
1 GGGTGGATTTAAATATA
23422385 ATTAATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (17 bp):
GGGTGGATTTAAATATA
Found at i:23422816 original size:7 final size:8
Alignment explanation
Indices: 23422798--23422825 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
23422788 AGTAGTTAAT
23422798 AAAATTTA
1 AAAATTTA
23422806 AAAATTTA
1 AAAATTTA
23422814 AAAATTTA
1 AAAATTTA
23422822 AAAA
1 AAAA
23422826 AAAACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAATTTA
Found at i:23431978 original size:2 final size:2
Alignment explanation
Indices: 23431971--23432010 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
23431961 TTTTACCATC
23431971 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23432011 ATCCCTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23435399 original size:22 final size:21
Alignment explanation
Indices: 23435374--23435414 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
23435364 TAACTCTAAA
23435374 TAATTACTTTTTTATTTTTTTC
1 TAATT-CTTTTTTATTTTTTTC
*
23435396 TAATTTTTTTTTATTTTTT
1 TAATTCTTTTTTATTTTTT
23435415 AAGATCACTC
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:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
TAATTCTTTTTTATTTTTTTC
Found at i:23438760 original size:13 final size:13
Alignment explanation
Indices: 23438744--23438768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23438734 ATTCCACATC
23438744 TTCATTTCAAATA
1 TTCATTTCAAATA
23438757 TTCATTTCAAAT
1 TTCATTTCAAAT
23438769 GTCTCTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCATTTCAAATA
Found at i:23442956 original size:113 final size:113
Alignment explanation
Indices: 23442816--23443034 Score: 287
Period size: 113 Copynumber: 1.9 Consensus size: 113
23442806 GAATTGTTTC
* ** *
23442816 AGTAGTAGTCATAAGAGTATAGGTAGTACTCTAACTTGTATTGATAGTTTCGACTCGGATAGT-A
1 AGTAGTAGTCATAAGAGTATAGATAGTACTCTAACTTGTATTGATAGTTGAGACCCGGATA-TCA
* * *
23442880 GTAGAAGTCCAAGGCCAAAACTATTTTGCTTATCGGAGTTTGTTGTGTT
65 GTAGAAGCCCAAGGCCAAAACTACTTTGCATATCGGAGTTTGTTGTGTT
** * * * *
23442929 AGTAGTAGTCATAAGAGTATCTATAGTACTCTGATTTGTATTGATAGTTGAGACCCGGGTATCGG
1 AGTAGTAGTCATAAGAGTATAGATAGTACTCTAACTTGTATTGATAGTTGAGACCCGGATATCAG
* *
23442994 TAGAAGCCCCAGGCCAAAACTACTTTGCATATTGGAGTTTG
66 TAGAAGCCCAAGGCCAAAACTACTTTGCATATCGGAGTTTG
23443035 CTATACCGGT
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
112 1 0.01
113 89 0.99
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (113 bp):
AGTAGTAGTCATAAGAGTATAGATAGTACTCTAACTTGTATTGATAGTTGAGACCCGGATATCAG
TAGAAGCCCAAGGCCAAAACTACTTTGCATATCGGAGTTTGTTGTGTT
Found at i:23446701 original size:21 final size:21
Alignment explanation
Indices: 23446671--23446714 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
23446661 CAAAATTTAT
* *
23446671 ATTTTTAAAAAATTATAAAAA
1 ATTTTAAAAAAAATATAAAAA
*
23446692 ATTTTAAAAAAAATCTAAAAA
1 ATTTTAAAAAAAATATAAAAA
23446713 AT
1 AT
23446715 ATATAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTTTAAAAAAAATATAAAAA
Found at i:23446732 original size:22 final size:21
Alignment explanation
Indices: 23446677--23446726 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
23446667 TTATATTTTT
* *
23446677 AAAAAATTATAAAAAATTTTA
1 AAAAAAATATAAAAAATTATA
*
23446698 AAAAAAATCTAAAAAATATATA
1 AAAAAAATATAAAAAAT-TATA
*
23446720 GAAAAAA
1 AAAAAAA
23446727 GTTAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAAATATAAAAAATTATA
Found at i:23447880 original size:6 final size:6
Alignment explanation
Indices: 23447866--23447903 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
23447856 GATTATAAAA
*
23447866 TGGAAT TGGAGT TGGAGT TGGAGT TGGAGT TGGAGT TG
1 TGGAGT TGGAGT TGGAGT TGGAGT TGGAGT TGGAGT TG
23447904 TATTCCCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.34
Consensus pattern (6 bp):
TGGAGT
Found at i:23451269 original size:38 final size:39
Alignment explanation
Indices: 23451210--23451322 Score: 124
Period size: 38 Copynumber: 2.9 Consensus size: 39
23451200 ATAGAATAAG
* * *
23451210 TCAACACTAGTAG-TAATCATGCTTAACATGTATTCAAT
1 TCAACACTGGCAGATAAACATGCTTAACATGTATTCAAT
* * *
23451248 TCATCACTGGCA-ATTAACATGCTTAACATGTATTCAGT
1 TCAACACTGGCAGATAAACATGCTTAACATGTATTCAAT
* *
23451286 TTAACATTGGCAGATAAACATGCTTTAACA-GTATTCA
1 TCAACACTGGCAGATAAACATGC-TTAACATGTATTCA
23451323 TTAGGGTGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
38 40 0.65
39 16 0.26
40 6 0.10
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (39 bp):
TCAACACTGGCAGATAAACATGCTTAACATGTATTCAAT
Found at i:23453874 original size:23 final size:24
Alignment explanation
Indices: 23453833--23453877 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
23453823 GTTGGATCCA
23453833 AATTAAATTCTAAAAAATAATTTG
1 AATTAAATTCTAAAAAATAATTTG
*
23453857 AATTAAA-TCTAAACAATAATT
1 AATTAAATTCTAAAAAATAATT
23453878 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
AATTAAATTCTAAAAAATAATTTG
Found at i:23453964 original size:13 final size:13
Alignment explanation
Indices: 23453943--23453976 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
23453933 ACAATATAAT
23453943 AATAATAATCCTA
1 AATAATAATCCTA
*
23453956 AATATTAATCCTA
1 AATAATAATCCTA
*
23453969 AAAAATAA
1 AATAATAA
23453977 ACTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:23460125 original size:24 final size:25
Alignment explanation
Indices: 23460073--23460125 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
23460063 TAAATTAATA
*
23460073 AAATCGTATAATTGAATATGTTTAC
1 AAATCGTATAATTGAATATGTTCAC
*
23460098 AAAT-GTATAATTGAATATGTTCAT
1 AAATCGTATAATTGAATATGTTCAC
23460122 AAAT
1 AAAT
23460126 AAATGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (25 bp):
AAATCGTATAATTGAATATGTTCAC
Found at i:23467805 original size:31 final size:31
Alignment explanation
Indices: 23467729--23467805 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
23467719 ATTTAATAAT
* *
23467729 ATAATAATTTATCAATATAATTTATTATTTTA
1 ATAATAATTT-TTAATATAAATTATTATTTTA
*
23467761 ATAA-AACTATTTAATATAGAATT-TTATTTTA
1 ATAATAA-TTTTTAATATA-AATTATTATTTTA
23467792 ATAATAATTTTTAA
1 ATAATAATTTTTAA
23467806 CAGTAACAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (31 bp):
ATAATAATTTTTAATATAAATTATTATTTTA
Found at i:23468484 original size:10 final size:10
Alignment explanation
Indices: 23468466--23468510 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
23468456 AAAATTTTGA
*
23468466 ATTTAAAATT
1 ATTTTAAATT
23468476 ATTTTAAATT
1 ATTTTAAATT
23468486 -TTTTAAGATT
1 ATTTTAA-ATT
*
23468496 ATTTTGAATT
1 ATTTTAAATT
23468506 ATTTT
1 ATTTT
23468511 TTATTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 6 0.19
10 20 0.65
11 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:23468496 original size:20 final size:21
Alignment explanation
Indices: 23468467--23468510 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
23468457 AAATTTTGAA
23468467 TTTAAAATTATTTTAAATT-T
1 TTTAAAATTATTTTAAATTAT
* *
23468487 TTTAAGATTATTTTGAATTAT
1 TTTAAAATTATTTTAAATTAT
23468508 TTT
1 TTT
23468511 TTATTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTAAAATTATTTTAAATTAT
Found at i:23469002 original size:15 final size:16
Alignment explanation
Indices: 23468976--23469005 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23468966 AAACATAAAA
23468976 AAAAATCAATTTTTTC
1 AAAAATCAATTTTTTC
23468992 AAAAATC-ATTTTTT
1 AAAAATCAATTTTTT
23469006 GAAAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATCAATTTTTTC
Found at i:23470375 original size:58 final size:58
Alignment explanation
Indices: 23470307--23470421 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
23470297 AAAGGAATTG
* *
23470307 TTTATGAGTGTTATTT-AGGAATAAAATTATATTTAAATTTAAAAATATTTGGGTTTAA
1 TTTATAAGTGTT-TTTGAAGAATAAAATTATATTTAAATTTAAAAATATTTGGGTTTAA
* ***
23470365 TTTATAAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 TTTATAAGTGTTTTTGAAGAATAAAATTATATTTAAATTTAAAAATATTTGGGTTTA
23470422 GTTTGTTGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 3 0.06
58 47 0.94
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (58 bp):
TTTATAAGTGTTTTTGAAGAATAAAATTATATTTAAATTTAAAAATATTTGGGTTTAA
Found at i:23475221 original size:18 final size:19
Alignment explanation
Indices: 23475171--23475224 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
23475161 ATTTTAAAAT
* *
23475171 AATTCAAAATAATTTTTA-A
1 AATTTAAAAT-ATTTATAGA
23475190 AATTTAAAATATTTATAGA
1 AATTTAAAATATTTATAGA
*
23475209 AATTTCAAA-ATTTATA
1 AATTTAAAATATTTATA
23475225 TTAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTTAAAATATTTATAGA
Found at i:23479801 original size:39 final size:36
Alignment explanation
Indices: 23479738--23479817 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 36
23479728 TAAAAATTGT
* *
23479738 TATAATATTATAATTTTTTTAAAAATTAT-AAAAAAC
1 TATAATATTATAATTTTATGAAAAA-TATGAAAAAAC
*
23479774 TATAATAATTATAATATATTATGAAAAATATGAAATAAC
1 TATAAT-ATTATAAT-T-TTATGAAAAATATGAAAAAAC
23479813 TATAA
1 TATAA
23479818 GAACATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 6 0.16
37 8 0.22
38 4 0.11
39 19 0.51
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (36 bp):
TATAATATTATAATTTTATGAAAAATATGAAAAAAC
Found at i:23482071 original size:10 final size:9
Alignment explanation
Indices: 23482058--23482082 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23482048 AAATAAAAAT
23482058 AAAAAAAGA
1 AAAAAAAGA
23482067 AAAAAAAGA
1 AAAAAAAGA
23482076 AAAAAAA
1 AAAAAAA
23482083 TAAACTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:23482982 original size:2 final size:2
Alignment explanation
Indices: 23482975--23483007 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
23482965 TTTCTTTGCA
*
23482975 TC TC TC TC TC TC TC TC TC TC TC CC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23483008 AACCTTACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:23483385 original size:11 final size:11
Alignment explanation
Indices: 23483369--23483442 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
23483359 CTGAACCCCT
23483369 TTTTAAATTTA
1 TTTTAAATTTA
23483380 TTTT-AA---A
1 TTTTAAATTTA
*
23483387 -TTTAAATTTG
1 TTTTAAATTTA
23483397 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
23483409 ATTTAAATTAA
1 TTTTAAATTTA
*
23483420 GTTTAAATTTA
1 TTTTAAATTTA
23483431 CTTTTAAATTTA
1 -TTTTAAATTTA
23483443 AAATTACTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
10 2 0.04
11 23 0.47
12 18 0.37
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:23483390 original size:6 final size:6
Alignment explanation
Indices: 23483370--23483458 Score: 78
Period size: 6 Copynumber: 15.5 Consensus size: 6
23483360 TGAACCCCTT
* **
23483370 TTTAAA TTT-AT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
23483416 -TTAAG TTTAAA TTTACT TTTAAA TTTAAA ATT-AC TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
23483459 TAAAAGTCCA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
5 14 0.22
6 49 0.78
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:23483390 original size:17 final size:17
Alignment explanation
Indices: 23483370--23483458 Score: 115
Period size: 17 Copynumber: 5.2 Consensus size: 17
23483360 TGAACCCCTT
23483370 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
23483387 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
23483404 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
23483421 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
23483439 TTTAAAATTACTTTAAA
1 TTTAAATTTATTTTAAA
23483456 TTT
1 TTT
23483459 TAAAAGTCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
17 48 0.79
18 13 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:23483407 original size:23 final size:22
Alignment explanation
Indices: 23483381--23483441 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
23483371 TTAAATTTAT
23483381 TTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTTAAATTTG-TTTAAA
*
23483404 TTTAAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAATT-TGTTTAAA
**
23483427 TTTACTTTTAAATTT
1 TTTAAATTTAAATTT
23483442 AAAATTACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTAAATTTAAATTTGTTTAAA
Found at i:23483430 original size:29 final size:29
Alignment explanation
Indices: 23483398--23483458 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
23483388 TTAAATTTGT
*
23483398 TTTAAATTTAAATTT-AAATTAAGTTTAAA
1 TTTAAATTTAAATTTAAAATT-ACTTTAAA
**
23483427 TTTACTTTTAAATTTAAAATTACTTTAAA
1 TTTAAATTTAAATTTAAAATTACTTTAAA
23483456 TTT
1 TTT
23483459 TAAAAGTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTAAATTTAAATTTAAAATTACTTTAAA
Found at i:23484251 original size:27 final size:27
Alignment explanation
Indices: 23484205--23484256 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
23484195 AAATTTATTA
**
23484205 ATAACATTAATATTAATAATAATAAGT
1 ATAACATTAATAACAATAATAATAAGT
*
23484232 ATAACATTAATAACATTAATAATAA
1 ATAACATTAATAACAATAATAATAA
23484257 AATAAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAACATTAATAACAATAATAATAAGT
Found at i:23484669 original size:82 final size:83
Alignment explanation
Indices: 23484518--23484669 Score: 191
Period size: 82 Copynumber: 1.8 Consensus size: 83
23484508 GAATAATATT
* * * * * * * * * *
23484518 TTTTTTTAAAAGGAAAATCTGGGTCAGATCTTAACAGATCTGAACCCAGATCGGTTTTTAAACAG
1 TTTTTTAAAAAAGAAAATCTGGGACAAATCTCAACAAATCTGAACCCAGATCCGTTTTAAAAAAA
23484583 AAGAACAACCAAAATAAG
66 AAGAACAACCAAAATAAG
23484601 TTTTTTAAAAAAG-AAATCTGGGACAAATCTCAACAAATCTGAACCCAGATCCG-TTTAAAATAA
1 TTTTTTAAAAAAGAAAATCTGGGACAAATCTCAACAAATCTGAACCCAGATCCGTTTTAAAA-AA
23484664 AAAGAA
65 AAAGAA
23484670 TGTGAATAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 6 0.10
82 41 0.71
83 11 0.19
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (83 bp):
TTTTTTAAAAAAGAAAATCTGGGACAAATCTCAACAAATCTGAACCCAGATCCGTTTTAAAAAAA
AAGAACAACCAAAATAAG
Found at i:23485402 original size:30 final size:30
Alignment explanation
Indices: 23485367--23485553 Score: 98
Period size: 30 Copynumber: 6.3 Consensus size: 30
23485357 TGAATTGTCC
23485367 AAAAATCATATTTTGACCCCTAAACTTTCA
1 AAAAATCATATTTTGACCCCTAAACTTTCA
* * *
23485397 AAAAATTATATTTT-AACCCTCGAACTTTACA
1 AAAAATCATATTTTGACCCCT-AAACTTT-CA
* * *
23485428 AAAATTACAT-TTTT-AACCCTAAACTTTCC
1 AAAAAT-CATATTTTGACCCCTAAACTTTCA
* * * **
23485457 AAAAATTATATTTTTGACCTCGAATTTTTC-
1 AAAAATCATA-TTTTGACCCCTAAACTTTCA
* * ** **
23485487 AAAAATCACATTTTTACCCAAAAACTTTTT
1 AAAAATCATATTTTGACCCCTAAACTTTCA
* * * *
23485517 AAAATTC-TATTTTTGACCTC-AAATTTTCC
1 AAAAATCATA-TTTTGACCCCTAAACTTTCA
23485546 AAAAATCA
1 AAAAATCA
23485554 CATGTTTACC
Statistics
Matches: 116, Mismatches: 32, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
28 2 0.02
29 36 0.31
30 50 0.43
31 26 0.22
32 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAAATCATATTTTGACCCCTAAACTTTCA
Found at i:23485542 original size:59 final size:59
Alignment explanation
Indices: 23485359--23485621 Score: 221
Period size: 60 Copynumber: 4.5 Consensus size: 59
23485349 GAGGTCCTTG
* * * * * * *
23485359 AATTGTCCAAAAATCATATTTTGACCCCTAAACTTTCAAAAAATTATA-TTTTAACCCTCG
1 AATTTTCCAAAAATCACATTTTTA-CCCAAAACTTTCCAAAAATTATATTTTTGA-CCTCA
* * * * *
23485419 AACTTTACAAAAATTACATTTTTAACCCTAAACTTTCCAAAAATTATATTTTTGACCTCG
1 AATTTTCCAAAAATCACATTTTT-ACCCAAAACTTTCCAAAAATTATATTTTTGACCTCA
* ** *
23485479 AATTTTTCAAAAATCACATTTTTACCCAAAAACTTT-TTAAAATTCTATTTTTGACCTCA
1 AATTTTCCAAAAATCACATTTTTACCC-AAAACTTTCCAAAAATTATATTTTTGACCTCA
* ** * * * * *
23485538 AATTTTCCAAAAATCACATGTTTACCCTTGAAC-TTCTAAAAATTACACTTTTGACTTTA
1 AATTTTCCAAAAATCACATTTTTACCC-AAAACTTTCCAAAAATTATATTTTTGACCTCA
*
23485597 AA-TTTCCAAAATTC-CATTTTTACCC
1 AATTTTCCAAAAATCACATTTTTACCC
23485622 CCGAACTTCA
Statistics
Matches: 170, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
57 10 0.06
58 13 0.08
59 70 0.41
60 71 0.42
61 6 0.04
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (59 bp):
AATTTTCCAAAAATCACATTTTTACCCAAAACTTTCCAAAAATTATATTTTTGACCTCA
Found at i:23485549 original size:29 final size:29
Alignment explanation
Indices: 23485452--23485549 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
23485442 AACCCTAAAC
* *
23485452 TTTCCAAAAATTATATTTTTGACCTCGAAT
1 TTTCC-AAAATTCTATTTTTGACCTCAAAT
* * *
23485482 TTTTCAAAAATCACATTTTT-ACC-CAAAAACT
1 TTTCCAAAATTC-TATTTTTGACCTC--AAA-T
*
23485513 TTT-TAAAATTCTATTTTTGACCTCAAAT
1 TTTCCAAAATTCTATTTTTGACCTCAAAT
23485541 TTTCCAAAA
1 TTTCCAAAA
23485550 ATCACATGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
28 5 0.10
29 21 0.40
30 21 0.40
31 5 0.10
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (29 bp):
TTTCCAAAATTCTATTTTTGACCTCAAAT
Found at i:23485635 original size:28 final size:28
Alignment explanation
Indices: 23485604--23485704 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
23485594 TTAAATTTCC
23485604 AAAATTCCATTTTTACCCCCGAACTTCA
1 AAAATTCCATTTTTACCCCCGAACTTCA
* * *
23485632 AAAATTACAATTTTACCCCCAAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTT-CA
* * *
23485661 AAAATTACCA-TTTTACCCTCGACCTTAA
1 AAAATT-CCATTTTTACCCCCGAACTTCA
*
23485689 AAAAATCACATTTTTA
1 AAAATTC-CATTTTTA
23485705 AACTTAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.02
28 31 0.52
29 26 0.43
30 2 0.03
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCCGAACTTCA
Found at i:23485665 original size:57 final size:57
Alignment explanation
Indices: 23485527--23485771 Score: 153
Period size: 57 Copynumber: 4.2 Consensus size: 57
23485517 AAAATTCTAT
* * * * *
23485527 TTTTGACCTCAAATTTTCCAAAAA-TCACATGTTTACCCTTGAACTTCTAAAAATTACAC
1 TTTTGACCCCAAA-CTTCCAAAAATTC-CATTTTTACCCTCGAACTTC-AAAAATTACAA
*** * *
23485586 TTTTGACTTTAAATTTCC-AAAATTCCATTTTTACCCCCGAACTTCAAAAATTACAA
1 TTTTGACCCCAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCAAAAATTACAA
* * * *
23485642 TTTT-ACCCCCAAACTTCCAAAAATTACCA-TTTTACCCTCGACCTTAAAAAAATCACAT
1 TTTTGA-CCCCAAACTTCCAAAAATT-CCATTTTTACCCTCGAACTT-CAAAAATTACAA
* *** * * * *
23485700 TTTTAAACTTAAAATTTCCAAAAATTAC-TATTTTACCCTCGAA-TGTCCAAAAA-GACCA
1 TTTT-GACCCCAAACTTCCAAAAATTCCAT-TTTTACCCTCGAACT-T-CAAAAATTACAA
23485758 TTTTGACCCCAAAC
1 TTTTGACCCCAAAC
23485772 CTCCGAGAAT
Statistics
Matches: 145, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
55 1 0.01
56 22 0.15
57 46 0.32
58 31 0.21
59 44 0.30
60 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.33
Consensus pattern (57 bp):
TTTTGACCCCAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCAAAAATTACAA
Found at i:23485694 original size:29 final size:28
Alignment explanation
Indices: 23485604--23485692 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 28
23485594 TTAAATTTCC
23485604 AAAATT-CCATTTTTACCCCCGAACTTCA
1 AAAATTACCA-TTTTACCCCCGAACTTCA
* *
23485632 AAAATTACAATTTTACCCCCAAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTT-CA
* * *
23485661 AAAATTACCATTTTACCCTCGACCTTAA
1 AAAATTACCATTTTACCCCCGAACTTCA
23485689 AAAA
1 AAAA
23485693 ATCACATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 26 0.50
29 26 0.50
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAACTTCA
Found at i:23491491 original size:2 final size:2
Alignment explanation
Indices: 23491484--23491600 Score: 234
Period size: 2 Copynumber: 58.5 Consensus size: 2
23491474 TTCAAAATTA
23491484 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23491526 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23491568 TC TC TC 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 TC TC TC T
23491601 TTTCTTCTTT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 115 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:23498818 original size:26 final size:27
Alignment explanation
Indices: 23498788--23498847 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
23498778 TCAGATGACT
*
23498788 ATATAAAAATTTTTAAGA-AATAAAA-A
1 ATATAAAAATTATTAA-ATAATAAAATA
*
23498814 ATATATAAAATTATTAAATATTAAAATA
1 ATATA-AAAATTATTAAATAATAAAATA
23498842 ATATAA
1 ATATAA
23498848 TATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 6 0.21
27 17 0.59
28 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATATAAAAATTATTAAATAATAAAATA
Found at i:23505979 original size:14 final size:14
Alignment explanation
Indices: 23505957--23505986 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23505947 AAAGATAGAA
23505957 ATTTAAAAAAAATT
1 ATTTAAAAAAAATT
*
23505971 ATTTTAAAAAAATT
1 ATTTAAAAAAAATT
23505985 AT
1 AT
23505987 GAAAAAAACT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTAAAAAAAATT
Found at i:23506480 original size:6 final size:6
Alignment explanation
Indices: 23506464--23506498 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
23506454 TTTGGATTTC
23506464 TTTTATA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
23506499 AAAGAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:23515504 original size:22 final size:23
Alignment explanation
Indices: 23515474--23515516 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
23515464 TTTTATAATT
* *
23515474 TTTTGAAAATT-TCATTTTTTAA
1 TTTTAAAAATTATAATTTTTTAA
23515496 TTTTAAAAATTATAATTTTTT
1 TTTTAAAAATTATAATTTTTT
23515517 TCCAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTAAAAATTATAATTTTTTAA
Found at i:23516814 original size:26 final size:26
Alignment explanation
Indices: 23516785--23516856 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
23516775 TTGTACTAAT
* *
23516785 TTAAAATTATATTACGAAAAATCAAA
1 TTAAAATTATATTAAGAAAAATAAAA
* * *
23516811 TTAAAAATA-ATTAAGTAAATTAAAA
1 TTAAAATTATATTAAGAAAAATAAAA
*
23516836 ATAAAATTATATATAA-AAAAA
1 TTAAAATTATAT-TAAGAAAAA
23516857 CTAATTAACA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 19 0.54
26 13 0.37
27 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
TTAAAATTATATTAAGAAAAATAAAA
Found at i:23526654 original size:19 final size:18
Alignment explanation
Indices: 23526601--23526740 Score: 70
Period size: 20 Copynumber: 7.2 Consensus size: 18
23526591 TACATATCTA
23526601 ATAAAAATCATAAAA-ATT
1 ATAAAAAT-ATAAAATATT
* * *
23526619 GTAAAAAGATTGTAAATATT
1 ATAAAAATA-T-AAAATATT
*
23526639 ATAAAAATATTAAAATTTT
1 ATAAAAATA-TAAAATATT
23526658 ATATAAACATAT-AAATAACTT
1 ATA-AAA-ATATAAAAT-A-TT
*
23526679 ATAAAAATATAAAA-CTT
1 ATAAAAATATAAAATATT
* *
23526696 ATAACAATTATTAAAATTTTTT
1 ATAA-AAATA-TAAAA--TATT
23526718 ATATAAAAGTATAAAATATT
1 ATA-AAAA-TATAAAATATT
23526738 ATA
1 ATA
23526741 TACATAAATA
Statistics
Matches: 94, Mismatches: 13, Indels: 28
0.70 0.10 0.21
Matches are distributed among these distances:
17 7 0.07
18 11 0.12
19 25 0.27
20 28 0.30
21 8 0.09
22 12 0.13
23 3 0.03
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAATATAAAATATT
Found at i:23526742 original size:22 final size:21
Alignment explanation
Indices: 23526638--23526767 Score: 66
Period size: 19 Copynumber: 6.4 Consensus size: 21
23526628 TTGTAAATAT
23526638 TATA-AAAATATTAAAAT-TT-
1 TATATAAAATA-TAAAATATTA
*
23526657 TATATAAACATAT-AAATAACT-
1 TATATAAA-ATATAAAAT-ATTA
*
23526678 TATA-AAAATATAAAA-CTTA
1 TATATAAAATATAAAATATTA
* * * *
23526697 TA-A-CAATTATTAAAATTTTT
1 TATATAAAATA-TAAAATATTA
23526717 TATATAAAAGTATAAAATATTA
1 TATATAAAA-TATAAAATATTA
*
23526739 TATACATAAATATAAAA-ATTA
1 TATATA-AAATATAAAATATTA
23526760 T-TATAAAA
1 TATATAAAA
23526768 CTCAATCTGA
Statistics
Matches: 86, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
18 6 0.07
19 22 0.26
20 17 0.20
21 14 0.16
22 22 0.26
23 5 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (21 bp):
TATATAAAATATAAAATATTA
Found at i:23528548 original size:21 final size:20
Alignment explanation
Indices: 23528524--23528572 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
23528514 CAATCCTATA
23528524 AATAGTGAGGTCAAGTTCATG
1 AATAGTGAGGTCAAG-TCATG
* *
23528545 AATAATAAGGTCAAGTCATG
1 AATAGTGAGGTCAAGTCATG
23528565 AATAGTGA
1 AATAGTGA
23528573 TAATATGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (20 bp):
AATAGTGAGGTCAAGTCATG
Found at i:23558001 original size:98 final size:99
Alignment explanation
Indices: 23557831--23558014 Score: 325
Period size: 98 Copynumber: 1.9 Consensus size: 99
23557821 TGGCAAATGC
* * *
23557831 AAATGCCATTTTCTTTTTACCCCTTTAAATTTATATGTTATGAAATATAAAAGCGAGAAGATAAG
1 AAATGCCATTTTCTTTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGCAAGAAGATAAG
23557896 TTATCATTTTCTTTAAAGTGCTCGCCTTTAAAGA
66 TTATCATTTTCTTTAAAGTGCTCGCCTTTAAAGA
23557930 AAATGCCATTTTC-TTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGCAAGAAGATAAG
1 AAATGCCATTTTCTTTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGCAAGAAGATAAG
*
23557994 TTATCATTTTCTTTAATGTGC
66 TTATCATTTTCTTTAAAGTGC
23558015 CCTGTAAAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 68 0.84
99 13 0.16
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (99 bp):
AAATGCCATTTTCTTTTTACCCCCTTAAATTTATATGTTATCAAATATAAAAGCAAGAAGATAAG
TTATCATTTTCTTTAAAGTGCTCGCCTTTAAAGA
Found at i:23559110 original size:3 final size:3
Alignment explanation
Indices: 23559102--23559145 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
23559092 ACATTAGCAT
* *
23559102 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAT CAC CAT CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
23559146 TCATCATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.61, G:0.00, T:0.05
Consensus pattern (3 bp):
CAC
Found at i:23559146 original size:6 final size:6
Alignment explanation
Indices: 23559105--23559160 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
23559095 TTAGCATCAC
* * * * *
23559105 CACCAC CACCAC CACCAC CACCAC CACCAT CACCAT CACCAT CATCAT
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT
*
23559153 CATCAT CA
1 CACCAT CA
23559161 TCGAGTATGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.34, C:0.54, G:0.00, T:0.12
Consensus pattern (6 bp):
CACCAT
Found at i:23560154 original size:10 final size:11
Alignment explanation
Indices: 23560107--23560163 Score: 59
Period size: 10 Copynumber: 5.4 Consensus size: 11
23560097 CGTTTTATGT
23560107 AAAAAATTATGA
1 AAAAAATTAT-A
23560119 AAAAAATTA-A
1 AAAAAATTATA
*
23560129 AAAAAATTCT-
1 AAAAAATTATA
23560139 -AAAAATT-TA
1 AAAAAATTATA
23560148 AAAAAATTATGA
1 AAAAAATTAT-A
23560160 AAAA
1 AAAA
23560164 TACACTACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 1 0.03
9 7 0.18
10 16 0.41
11 1 0.03
12 14 0.36
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:23560164 original size:20 final size:20
Alignment explanation
Indices: 23560107--23560164 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
23560097 CGTTTTATGT
23560107 AAAAAATTATGAAAAAAATTAA
1 AAAAAATTATG--AAAAATTAA
* *
23560129 AAAAAATTCT-AAAAATTTA
1 AAAAAATTATGAAAAATTAA
23560148 AAAAAATTATGAAAAAT
1 AAAAAATTATGAAAAAT
23560165 ACACTACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 17 0.53
20 6 0.19
22 9 0.28
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAAATTATGAAAAATTAA
Found at i:23562239 original size:6 final size:6
Alignment explanation
Indices: 23562221--23562273 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
23562211 ATCAAGATCA
* * * *
23562221 AGATGG -GAGTGG AGATGG AGATGG AGATGA AGATAG AGGTGG AGATGA
1 AGATGG AGA-TGG AGATGG AGATGG AGATGG AGATGG AGATGG AGATGG
23562269 AGATG
1 AGATG
23562274 ATGAGCTAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 2 0.05
6 34 0.89
7 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.17
Consensus pattern (6 bp):
AGATGG
Found at i:23562254 original size:18 final size:18
Alignment explanation
Indices: 23562233--23562273 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
23562223 ATGGGAGTGG
23562233 AGATGGAGATGGAGATGA
1 AGATGGAGATGGAGATGA
* *
23562251 AGATAGAGGTGGAGATGA
1 AGATGGAGATGGAGATGA
23562269 AGATG
1 AGATG
23562274 ATGAGCTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.44, T:0.17
Consensus pattern (18 bp):
AGATGGAGATGGAGATGA
Found at i:23562598 original size:63 final size:64
Alignment explanation
Indices: 23562511--23562650 Score: 205
Period size: 63 Copynumber: 2.2 Consensus size: 64
23562501 AAAAAATGTA
* * * *
23562511 TTGTATTGTATTGTTACATCAATAATCTACTTATTTATATTTTACCAAAAAAT-AATAAATTGT
1 TTGTATTGTATTTTTACATCAATAATCTACTTATTTACATTTTACCAAAAAATGAACAAATTAT
* *
23562574 TTGTATTGTATTTTTACATTAATAATCTACTTATTTACATTTTATCAAAAAATGAACAAATTAT
1 TTGTATTGTATTTTTACATCAATAATCTACTTATTTACATTTTACCAAAAAATGAACAAATTAT
23562638 TTGT-TTGT-TTTTT
1 TTGTATTGTATTTTT
23562651 GTATGTTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
62 5 0.07
63 53 0.76
64 12 0.17
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (64 bp):
TTGTATTGTATTTTTACATCAATAATCTACTTATTTACATTTTACCAAAAAATGAACAAATTAT
Found at i:23563876 original size:18 final size:18
Alignment explanation
Indices: 23563839--23563884 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
23563829 ATTCGAAAAA
*
23563839 AATTCGAGTTGACTCAAAT
1 AATTCGA-TTAACTCAAAT
*
23563858 AATTCGATTAACTCGAAT
1 AATTCGATTAACTCAAAT
*
23563876 AACTCGATT
1 AATTCGATT
23563885 CATTTAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
AATTCGATTAACTCAAAT
Found at i:23581277 original size:29 final size:31
Alignment explanation
Indices: 23581222--23581280 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
23581212 GAGGGTGGGA
* *
23581222 TGAGAGGGGAGTAAATGTTTTAGGGAGAAAG
1 TGAGAGGAGAGTAAAAGTTTTAGGGAGAAAG
23581253 TGAGAGGAG-GTAAAAGTTTT-GGGAGAAA
1 TGAGAGGAGAGTAAAAGTTTTAGGGAGAAA
23581281 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 10 0.38
31 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (31 bp):
TGAGAGGAGAGTAAAAGTTTTAGGGAGAAAG
Found at i:23581456 original size:21 final size:19
Alignment explanation
Indices: 23581423--23581470 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
23581413 GAGAAAAGTA
*
23581423 GGAAAGAGTAAAAGTTTTGTG
1 GGAAA-AGTAAAAGATTTG-G
23581444 GGAAAAGTAAAAAGATTTGG
1 GGAAAAGT-AAAAGATTTGG
23581464 GGTAAAA
1 GG-AAAA
23581471 ATATAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAAGTAAAAGATTTGG
Found at i:23582199 original size:24 final size:24
Alignment explanation
Indices: 23582171--23582233 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
23582161 AGAAATAATC
*
23582171 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* * *
23582195 TTTCAATTAAATTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
23582219 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
23582234 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:23584173 original size:24 final size:24
Alignment explanation
Indices: 23584145--23584207 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
23584135 AGAAATAATC
* * *
23584145 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTACTTAATTA
* *
23584169 TTTCAATTAAACTCTGCTTATTTA
1 TTTCAATTAAACTCTACTTAATTA
23584193 TTTCAATTAAACTCT
1 TTTCAATTAAACTCT
23584208 TATTAGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (24 bp):
TTTCAATTAAACTCTACTTAATTA
Found at i:23584979 original size:26 final size:27
Alignment explanation
Indices: 23584924--23584983 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
23584914 TGGGACTAAT
* ** *
23584924 TTGCTCACACAAGCTGTAAAGTTTGGA
1 TTGCTCACACAAACTGTAAAGTCCGAA
23584951 TTGCTCACACAAACTGT-AAGTCCGAA
1 TTGCTCACACAAACTGTAAAGTCCGAA
23584977 TTGCTCA
1 TTGCTCA
23584984 TATAAGTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (27 bp):
TTGCTCACACAAACTGTAAAGTCCGAA
Found at i:23585389 original size:29 final size:29
Alignment explanation
Indices: 23585347--23585409 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
23585337 TTTTTAATCA
23585347 TATACTAAATTCTTACGAAACTTATTCTG
1 TATACTAAATTCTTACGAAACTTATTCTG
*
23585376 TATACTAAATTCTTACGAGACTTATTCTG
1 TATACTAAATTCTTACGAAACTTATTCTG
23585405 TATAC
1 TATAC
23585410 GTACCATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.41
Consensus pattern (29 bp):
TATACTAAATTCTTACGAAACTTATTCTG
Found at i:23586554 original size:13 final size:13
Alignment explanation
Indices: 23586533--23586566 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
23586523 TAAACAATAT
23586533 AATAATAATCCTA
1 AATAATAATCCTA
*
23586546 AATATTAATCCTA
1 AATAATAATCCTA
*
23586559 AAAAATAA
1 AATAATAA
23586567 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:23591960 original size:2 final size:2
Alignment explanation
Indices: 23591947--23591993 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
23591937 CTTGCTGCCA
*
23591947 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23591989 CT CT C
1 CT CT C
23591994 CCCTCTGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:23592554 original size:7 final size:7
Alignment explanation
Indices: 23592542--23592580 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
23592532 AATCTTAATT
23592542 TTAAAAA
1 TTAAAAA
23592549 TTAAAAA
1 TTAAAAA
23592556 TTAAAAA
1 TTAAAAA
*
23592563 CTTTAAAA
1 -TTAAAAA
*
23592571 TAAAAAA
1 TTAAAAA
23592578 TTA
1 TTA
23592581 TATAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:23592570 original size:15 final size:14
Alignment explanation
Indices: 23592542--23592580 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
23592532 AATCTTAATT
23592542 TTAAAAATTAAAAA
1 TTAAAAATTAAAAA
*
23592556 TTAAAAACTTTAAAA
1 TTAAAAA-TTAAAAA
*
23592571 TAAAAAATTA
1 TTAAAAATTA
23592581 TATAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAATTAAAAA
Found at i:23592718 original size:20 final size:19
Alignment explanation
Indices: 23592684--23592722 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
23592674 ATTTATTTAT
23592684 TAAAATAATTATTTTATAAA
1 TAAAATAATTATTTT-TAAA
23592704 TAAAATAATGT-TTTTTAAA
1 TAAAATAAT-TATTTTTAAA
23592723 ATCCCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 13 0.72
21 1 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TAAAATAATTATTTTTAAA
Found at i:23593910 original size:9 final size:9
Alignment explanation
Indices: 23593896--23593926 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
23593886 AATATATATT
23593896 TTTAAAAAA
1 TTTAAAAAA
23593905 TTT-AAAAA
1 TTTAAAAAA
23593913 TTTAAAAAA
1 TTTAAAAAA
23593922 TTTAA
1 TTTAA
23593927 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:23593918 original size:17 final size:17
Alignment explanation
Indices: 23593896--23593932 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
23593886 AATATATATT
23593896 TTTAAAAAATTTAAAAA
1 TTTAAAAAATTTAAAAA
*
23593913 TTTAAAAAATTTAATAA
1 TTTAAAAAATTTAAAAA
23593930 TTT
1 TTT
23593933 TTTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAAAATTTAAAAA
Found at i:23598888 original size:6 final size:6
Alignment explanation
Indices: 23598879--23598953 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
23598869 GTTTGAATAG
* *
23598879 ATTTAA ATTT-- ATTTAAA ATTTAAA ATTTTTAA ATTTAA ATTT-G CTTTAA
1 ATTTAA ATTTAA ATTT-AA ATTT-AA A--TTTAA ATTTAA ATTTAA ATTTAA
*
23598928 ATTTAA ATTT-A ATTAAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATT
23598954 GATATTAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.07
5 7 0.12
6 31 0.55
7 8 0.14
8 3 0.05
9 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:23598901 original size:17 final size:17
Alignment explanation
Indices: 23598879--23598963 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
23598869 GTTTGAATAG
23598879 ATTTAAATTTATTTAAA
1 ATTTAAATTTATTTAAA
*
23598896 ATTTAAAATT-TTT-AA
1 ATTTAAATTTATTTAAA
*
23598911 ATTTAAATTTGCTTT-AA
1 ATTTAAATTT-ATTTAAA
*
23598928 ATTTAAATTTAATTAAA
1 ATTTAAATTTATTTAAA
*
23598945 ATTTAAATTGATATTAAA
1 ATTTAAATTTAT-TTAAA
23598963 A
1 A
23598964 ACCCAAATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
15 11 0.19
16 5 0.09
17 36 0.62
18 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTAAATTTATTTAAA
Found at i:23600963 original size:29 final size:29
Alignment explanation
Indices: 23600859--23601150 Score: 272
Period size: 29 Copynumber: 9.9 Consensus size: 29
23600849 CCTTGGAGGT
23600859 CCCTAAACTGTCCAAAAATT--ATGTTTTGAC
1 CCCTAAACT-TCCAAAAATTACAT-TTTTG-C
* **
23600889 CCCTAAACTTTACC-TAAATTGTATTTTTGAC
1 CCCTAAAC-TT-CCAAAAATTACATTTTTG-C
* **
23600920 CCCAAAACTTTAAAAAATTACA-TTTTGC
1 CCCTAAACTTCCAAAAATTACATTTTTGC
* *
23600948 CCCTAAATTTCCAAAAATTAAATTTTTGC
1 CCCTAAACTTCCAAAAATTACATTTTTGC
* * * * **
23600977 CCTTAAATTTTCAAAAATTCCATTTTTAA
1 CCCTAAACTTCCAAAAATTACATTTTTGC
*
23601006 CCCTAAAACTTTCAAAAATTACATTTTTG-
1 CCCT-AAACTTCCAAAAATTACATTTTTGC
23601035 CCCTGAAACTTCCAAAAAGTTACATTTTTGC
1 CCCT-AAACTTCCAAAAA-TTACATTTTTGC
*
23601066 CCTCAAAACTTCCAAAAATTACATTTTTGC
1 CC-CTAAACTTCCAAAAATTACATTTTTGC
* * *
23601096 CCCCAAACTTCCAAAAATTATA-TTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTGC
*
23601124 CCCTAAACTTCCAAAAATTCCATTTTT
1 CCCTAAACTTCCAAAAATTACATTTTT
23601151 TACCCAAAAA
Statistics
Matches: 220, Mismatches: 31, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
28 42 0.19
29 75 0.34
30 68 0.31
31 32 0.15
32 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTGC
Found at i:23601139 original size:147 final size:148
Alignment explanation
Indices: 23600911--23601180 Score: 384
Period size: 147 Copynumber: 1.8 Consensus size: 148
23600901 CCTAAATTGT
* * * *
23600911 ATTTTTGACCCCAAAACTTTAAAAAATTACATTTTGCCCCTAAATTTCCAAAAATTAAATTTTTG
1 ATTTTTGACCCCAAAACTTCAAAAAATTACATTTTGCCCCCAAACTTCCAAAAATTAAATTTTTA
* * * * *
23600976 CCCTTAAATTTTCAAAAATTCCATTTTTAACCCTAAAACTTTCAAAAATTA-CATTTTTGCCCTG
66 CCCCTAAACTTCCAAAAATTCCATTTTTAACCCAAAAACTTACAAAAATTACCATTTTTGCCCTG
23601040 AAACTTCCAAAAAGTTAC
131 AAACTTCCAAAAAGTTAC
* *
23601058 ATTTTTG-CCCTCAAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATTATA-TTT
1 ATTTTTGACCC-CAAAACTTCAAAAAATTACA-TTTTGCCCCCAAACTTCCAAAAATTAAATTTT
* *
23601121 TACCCCTAAACTTCCAAAAATTCCATTTTTTACCCAAAAACTTACAAAACTTACCATTTT
64 TACCCCTAAACTTCCAAAAATTCCATTTTTAACCCAAAAACTTACAAAAATTACCATTTT
23601181 ACCCTAGATG
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
146 3 0.03
147 73 0.68
148 31 0.29
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (148 bp):
ATTTTTGACCCCAAAACTTCAAAAAATTACATTTTGCCCCCAAACTTCCAAAAATTAAATTTTTA
CCCCTAAACTTCCAAAAATTCCATTTTTAACCCAAAAACTTACAAAAATTACCATTTTTGCCCTG
AAACTTCCAAAAAGTTAC
Found at i:23601154 original size:30 final size:29
Alignment explanation
Indices: 23600859--23601184 Score: 257
Period size: 30 Copynumber: 11.1 Consensus size: 29
23600849 CCTTGGAGGT
** *
23600859 CCCTAAACTGTCCAAAAATTATGTTTTGAC
1 CCCTAAACT-TCCAAAAATTACATTTTTAC
* **
23600889 CCCTAAACTTTACC-TAAATTGTATTTTTGAC
1 CCCTAAAC-TT-CCAAAAATTACATTTTT-AC
* ** *
23600920 CCCAAAACTTTAAAAAATTACA-TTTTGC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * *
23600948 CCCTAAATTTCCAAAAATTAAATTTTTGC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * * * *
23600977 CCTTAAATTTTCAAAAATTCCATTTTTAA
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* *
23601006 CCCTAAAACTTTCAAAAATTACATTTTT-G
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
*
23601035 CCCTGAAACTTCCAAAAAGTTACATTTTTGC
1 CCCT-AAACTTCCAAAAA-TTACATTTTTAC
* *
23601066 CCTCAAAACTTCCAAAAATTACATTTTTGC
1 CC-CTAAACTTCCAAAAATTACATTTTTAC
* *
23601096 CCCCAAACTTCCAAAAATTATA-TTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
*
23601124 CCCTAAACTTCCAAAAATTCCATTTTTTAC
1 CCCTAAACTTCCAAAAATTACA-TTTTTAC
** * *
23601154 CCAAAAACTTACAAAACTTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
23601183 CC
1 CC
23601185 TAGATGTCTA
Statistics
Matches: 243, Mismatches: 41, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
28 42 0.17
29 78 0.32
30 93 0.38
31 29 0.12
32 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:23601186 original size:58 final size:57
Alignment explanation
Indices: 23600911--23601231 Score: 222
Period size: 57 Copynumber: 5.5 Consensus size: 57
23600901 CCTAAATTGT
* * *
23600911 ATTTTTGACCCCAAAACTTTA-AAAAATTACATTTTGCCCCTAAATTTCCAAAAATTA-
1 ATTTTTTACCCCAAAAC-TTACAAAAATTACATTTT-ACCCTAAACTTCCAAAAATTAC
* * ** * * * *
23600968 AATTTTTGCCCTTAAATTTTCAAAAATTCCATTTTTAACCCTAAAACTTTCAAAAATTAC
1 ATTTTTTACCCCAAAACTTACAAAAATTACA-TTTT-ACCCT-AAACTTCCAAAAATTAC
* ** * *
23601028 A-TTTTTGCCCTGAAACTTCCAAAAAGTTACATTTTTGCCCTCAAAACTTCCAAAAATTAC
1 ATTTTTTACCCCAAAACTTACAAAAA-TTACA-TTTTACCCT--AAACTTCCAAAAATTAC
* * * * *
23601088 A-TTTTTGCCCCCAAACTTCCAAAAATTATATTTTACCCCTAAACTTCCAAAAATTCC
1 ATTTTTTACCCCAAAACTTACAAAAATTACATTTTA-CCCTAAACTTCCAAAAATTAC
* * * * * *
23601145 ATTTTTTACCCAAAAACTTACAAAACTTACCATTTTACCCTAGA-TGTCTAAAAACTCC
1 ATTTTTTACCCCAAAACTTACAAAAATTA-CATTTTACCCTAAACT-TCCAAAAATTAC
* * *
23601203 A-TTTTTAACCCAAAACTTTCAAAATTTAC
1 ATTTTTTACCCCAAAACTTACAAAAATTAC
23601232 CGTTTTACAC
Statistics
Matches: 218, Mismatches: 36, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.01
57 61 0.28
58 51 0.23
59 53 0.24
60 50 0.23
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (57 bp):
ATTTTTTACCCCAAAACTTACAAAAATTACATTTTACCCTAAACTTCCAAAAATTAC
Found at i:23601226 original size:29 final size:29
Alignment explanation
Indices: 23600988--23601226 Score: 175
Period size: 30 Copynumber: 8.2 Consensus size: 29
23600978 CTTAAATTTT
*
23600988 CAAAAATTCCATTTTTAACCCTAAAACTTT
1 CAAAAATTCCATTTTTAACCC-AAAACTTC
* * *
23601018 CAAAAATTACATTTTT-GCCCTGAAACTTC
1 CAAAAATTCCATTTTTAACCC-AAAACTTC
* **
23601047 CAAAAAGTTACATTTTTGCCCTCAAAACTTC
1 CAAAAA-TTCCATTTTTAACC-CAAAACTTC
* ** *
23601078 CAAAAATTACATTTTTGCCCCCAAACTTC
1 CAAAAATTCCATTTTTAACCCAAAACTTC
* *
23601107 CAAAAATT--ATATTTTACCCCTAAACTTC
1 CAAAAATTCCAT-TTTTAACCCAAAACTTC
* *
23601135 CAAAAATTCCATTTTTTACCCAAAAACTTA
1 CAAAAATTCCATTTTTAACCC-AAAACTTC
* * *
23601165 CAAAACTTACCA-TTTT-ACCCTAGA-TGTC
1 CAAAAATT-CCATTTTTAACCCAAAACT-TC
* * *
23601193 TAAAAACTCCATTTTTAACCCAAAACTTT
1 CAAAAATTCCATTTTTAACCCAAAACTTC
23601222 CAAAA
1 CAAAA
23601227 TTTACCGTTT
Statistics
Matches: 173, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.03
28 35 0.20
29 54 0.31
30 59 0.34
31 18 0.10
32 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTAACCCAAAACTTC
Found at i:23601238 original size:57 final size:59
Alignment explanation
Indices: 23601136--23601249 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 59
23601126 CTAAACTTCC
* * *
23601136 AAAAATTCCATTTTTTACCCAAAAACTTACAAAACTTACCATTTTACCCT-AGATGTCT
1 AAAAACTCCATTTTTAACCCAAAAACTTACAAAACTTACCATTTTACACTCAGATGTCT
* * *
23601194 AAAAACTCCATTTTTAACCC-AAAACTTTCAAAATTTACCGTTTTACACTCAGATGT
1 AAAAACTCCATTTTTAACCCAAAAACTTACAAAACTTACCATTTTACACTCAGATGT
23601250 TCGAAAATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 25 0.51
58 24 0.49
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAACTCCATTTTTAACCCAAAAACTTACAAAACTTACCATTTTACACTCAGATGTCT
Found at i:23601265 original size:58 final size:58
Alignment explanation
Indices: 23601136--23601266 Score: 158
Period size: 58 Copynumber: 2.3 Consensus size: 58
23601126 CTAAACTTCC
* *
23601136 AAAAATTCCATTTTTTACCCAAAAACTTACAAAACTTACCATTTTACCCTAGATGTCT
1 AAAAATTCCATTTTTAACCCAAAAACTTACAAAACTTACCATTTTACACTAGATGTCT
* * * *
23601194 AAAAACTCCATTTTTAACCC-AAAACTTTCAAAATTTACCGTTTTACACTCAGATGT-T
1 AAAAATTCCATTTTTAACCCAAAAACTTACAAAACTTACCATTTTACACT-AGATGTCT
* *
23601251 CGAAAATTCTATTTTT
1 -AAAAATTCCATTTTT
23601267 GATCTCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 26 0.42
58 36 0.58
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCCAAAAACTTACAAAACTTACCATTTTACACTAGATGTCT
Found at i:23601397 original size:28 final size:28
Alignment explanation
Indices: 23601342--23601400 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
23601332 AATTTTTCCT
*
23601342 AAATTACCATTTTGCCCTCGAGTGTCCA
1 AAATTACCATTTTGCCCTCGAGTATCCA
* *
23601370 AAATTACCATTTTTCCTTC-AGGTATCCA
1 AAATTACCATTTTGCCCTCGA-GTATCCA
23601398 AAA
1 AAA
23601401 AGTCCCGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTGCCCTCGAGTATCCA
Found at i:23607648 original size:50 final size:50
Alignment explanation
Indices: 23607587--23607820 Score: 153
Period size: 50 Copynumber: 4.6 Consensus size: 50
23607577 CTACAACGGT
* *
23607587 GGATTCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGAC
1 GGATCCAGTACCGCAAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGAC
* * * * *
23607637 GGA-CCGTGTACCTC-AGAAGACACGACAA--GAAAGATCTAAGAC-C-ACAAC
1 GGATCC-AGTACCGCAAAAAGACA--A-AAGGGAAAGATCTAAGTCGCAACGAC
* * *
23607685 AGTAGATTCAGTAACACAAAAAGACAAAAGGGAAAGATCTAAGTCGCAAC-AGC
1 -G--GATCCAGTACCGCAAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGA-C
* * * * * *
23607738 TGA-CCATGTACCTC-AGAAGACACAACGGGAAAGATCTAAGACCGCAACGGC
1 GGATCCA-GTACCGCAAAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGAC
*
23607789 AGATCCAGTACCGCAAAAAGACAAAAGGGAAA
1 GGATCCAGTACCGCAAAAAGACAAAAGGGAAA
23607821 CGTCTTTATC
Statistics
Matches: 139, Mismatches: 25, Indels: 39
0.68 0.12 0.19
Matches are distributed among these distances:
48 4 0.03
49 21 0.15
50 45 0.32
51 44 0.32
52 22 0.16
53 3 0.02
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (50 bp):
GGATCCAGTACCGCAAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGAC
Found at i:23607721 original size:51 final size:51
Alignment explanation
Indices: 23607665--23607820 Score: 167
Period size: 51 Copynumber: 3.1 Consensus size: 51
23607655 GACACGACAA
* * *
23607665 GAAAGATCTAAGACCACAACAGTAGATTCAGTAACACAAAAAGACAAAAGG
1 GAAAGATCTAAGACCGCAACAGTAGATCCAGTACCACAAAAAGACAAAAGG
* * * *
23607716 GAAAGATCTAAG-TCGCAACAGCT-GA-CCATGTACCTC-AGAAGACACAACGG
1 GAAAGATCTAAGACCGCAACAG-TAGATCCA-GTACCACAAAAAGACA-AAAGG
* * *
23607766 GAAAGATCTAAGACCGCAACGGCAGATCCAGTACCGCAAAAAGACAAAAGG
1 GAAAGATCTAAGACCGCAACAGTAGATCCAGTACCACAAAAAGACAAAAGG
23607817 GAAA
1 GAAA
23607821 CGTCTTTATC
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
49 9 0.11
50 30 0.35
51 36 0.42
52 10 0.12
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (51 bp):
GAAAGATCTAAGACCGCAACAGTAGATCCAGTACCACAAAAAGACAAAAGG
Found at i:23607754 original size:101 final size:101
Alignment explanation
Indices: 23607579--23607820 Score: 351
Period size: 101 Copynumber: 2.4 Consensus size: 101
23607569 GGGAAAAACT
* * *
23607579 ACAACGGTGGATTCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGT
1 ACAACGGTAGATTCAGTACCGCAAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGACGGACCAT
*
23607644 GTACCTCAGAAGACACGACAAGAAAGATCTAAGACC
66 GTACCTCAGAAGACACAACAAGAAAGATCTAAGACC
* * * *
23607680 ACAACAGTAGATTCAGTAACACAAAAAGACAAAAGGGAAAGATCTAAGTCGCAAC-AGCTGACCA
1 ACAACGGTAGATTCAGTACCGCAAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGA-CGGACCA
**
23607744 TGTACCTCAGAAGACACAACGGGAAAGATCTAAGACC
65 TGTACCTCAGAAGACACAACAAGAAAGATCTAAGACC
* * *
23607781 GCAACGGCAGATCCAGTACCGCAAAAAGACAAAAGGGAAA
1 ACAACGGTAGATTCAGTACCGCAAAAAGACAAAAGGGAAA
23607821 CGTCTTTATC
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
100 1 0.01
101 123 0.99
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (101 bp):
ACAACGGTAGATTCAGTACCGCAAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGACGGACCAT
GTACCTCAGAAGACACAACAAGAAAGATCTAAGACC
Found at i:23607979 original size:92 final size:92
Alignment explanation
Indices: 23607822--23608433 Score: 1028
Period size: 92 Copynumber: 6.7 Consensus size: 92
23607812 AAAGGGAAAC
* *
23607822 GTCTTTATCTCTCTGAAGTTGTAGTAATAGCAAGATGAAGCTTTAAACATCAATTCCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
*
23607887 TGAAGTTATAGTAAAGTTGGATAGCAA
66 TGAAGTTGTAGTAAAGTTGGATAGCAA
* *
23607914 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAACTCCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
* *
23607979 TAAAGTTGCAGTAAAGTTGGATAGCAA
66 TGAAGTTGTAGTAAAGTTGGATAGCAA
* *
23608006 GTTTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAACCTTCAAACATCAATTCCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
23608071 TGAAGTTGTAGTAAAGTTGGATAGCAA
66 TGAAGTTGTAGTAAAGTTGGATAGCAA
*
23608098 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATTCCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
23608163 TGAAGTTGTAGTAAAGTTGGATAGCAA
66 TGAAGTTGTAGTAAAGTTGGATAGCAA
* * *
23608190 GTCTTTATCTATCTGAAGTTGTAGTAATAGCAAGATAAAGCTTCAAACATCAATTCCTATCCTCT
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
23608255 TGAAGTTGTAGTAAAGTTGGATAGCAA
66 TGAAGTTGTAGTAAAGTTGGATAGCAA
* * * *
23608282 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGTTTCAATCATCAATTCCTATACTCT
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
*
23608347 TGAAGTTGCAGTAAAGTTGGATAGCAA
66 TGAAGTTGTAGTAAAGTTGGATAGCAA
* * *
23608374 GTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTC-GACATCAAATCCTATC
1 GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
23608434 TTCATAAAGA
Statistics
Matches: 489, Mismatches: 31, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
91 12 0.02
92 477 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (92 bp):
GTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCT
TGAAGTTGTAGTAAAGTTGGATAGCAA
Found at i:23608173 original size:52 final size:52
Alignment explanation
Indices: 23608106--23608270 Score: 169
Period size: 52 Copynumber: 3.4 Consensus size: 52
23608096 AAGTCTTTAT
23608106 CTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATTCCTATC
1 CTCTCTGAAGTTGTAGTAA-AGCAAGATAAAGCTTCAAACATCAATTCCTATC
*** *
23608159 CTCT-TGAAGTTGTAGTAAAGTTGGAT--AG---C-AA-GTC--TT--TAT-
1 CTCTCTGAAGTTGTAGTAAAGCAAGATAAAGCTTCAAACATCAATTCCTATC
*
23608198 CTATCTGAAGTTGTAGTAATAGCAAGATAAAGCTTCAAACATCAATTCCTATC
1 CTCTCTGAAGTTGTAGTAA-AGCAAGATAAAGCTTCAAACATCAATTCCTATC
23608251 CTCT-TGAAGTTGTAGTAAAG
1 CTCTCTGAAGTTGTAGTAAAG
23608271 TTGGATAGCA
Statistics
Matches: 88, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
39 3 0.03
40 17 0.19
41 5 0.06
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 2 0.02
47 2 0.02
48 2 0.02
49 2 0.02
50 2 0.02
51 7 0.08
52 31 0.35
53 7 0.08
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (52 bp):
CTCTCTGAAGTTGTAGTAAAGCAAGATAAAGCTTCAAACATCAATTCCTATC
Found at i:23608998 original size:201 final size:201
Alignment explanation
Indices: 23608631--23609067 Score: 721
Period size: 201 Copynumber: 2.2 Consensus size: 201
23608621 AAATGTGATT
* *
23608631 ATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCGACGCTCG
1 ATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACGCCAACTCGACACTCG
23608696 ATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAA
66 ATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAA
* * * *
23608761 ATGGTTAGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTAATGAGATACAGAG
131 ATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAG
23608826 AAGCGA
196 AAGCGA
* *
23608832 ATTGAAACAAATGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTACGCCAACTCGACACTCG
1 ATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACGCCAACTCGACACTCG
* * **
23608897 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAA
66 ATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAA
* *
23608962 ATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATCCAGAG
131 ATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAG
23609027 AAGCGA
196 AAGCGA
* * *
23609033 ATTAAAACAAGTGATGCGGTCATTTTCCTGATGAG
1 ATTAAAACAAATGAGGCGGTCATCTTCCTGATGAG
23609068 TCACTGAGAA
Statistics
Matches: 218, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
201 218 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (201 bp):
ATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACGCCAACTCGACACTCG
ATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAA
ATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAG
AAGCGA
Found at i:23609457 original size:18 final size:17
Alignment explanation
Indices: 23609434--23609487 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
23609424 GTTTGAATAG
* *
23609434 ATTTAAATTTATTGTTAA
1 ATTTAAATTTAAT-TAAA
23609452 ATTTAAATTTAATTAAA
1 ATTTAAATTTAATTAAA
*
23609469 ATTTAAATTGATATTAAA
1 ATTTAAATTTA-ATTAAA
23609487 A
1 A
23609488 ACCCAAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
ATTTAAATTTAATTAAA
Found at i:23611453 original size:30 final size:30
Alignment explanation
Indices: 23611388--23611557 Score: 185
Period size: 29 Copynumber: 5.8 Consensus size: 30
23611378 AAAGGTCCTT
* *
23611388 AAACTGTCTAAAAATTACA-TTTT-CCCCTG
1 AAACT-TCCAAAAATTACATTTTTGACCCTG
* **
23611417 -AACTTCCCAAAATTGTATTTTTGACCCTG
1 AAACTTCCAAAAATTACATTTTTGACCCTG
*
23611446 AAACTTCCAAAAATTACA-TTTT-ACCCCTA
1 AAACTTCCAAAAATTACATTTTTGA-CCCTG
* *
23611475 AAATTTTCAAAAATTACATTTTTG-CCCTG
1 AAACTTCCAAAAATTACATTTTTGACCCTG
23611504 AAACTTCCAAAAATTACATTTTTG--CCTCG
1 AAACTTCCAAAAATTACATTTTTGACCCT-G
23611533 AAACTTCCAAAAATTACATTTTTGA
1 AAACTTCCAAAAATTACATTTTTGA
23611558 TGATATGTTC
Statistics
Matches: 119, Mismatches: 14, Indels: 15
0.80 0.09 0.10
Matches are distributed among these distances:
27 9 0.08
28 12 0.10
29 80 0.67
30 18 0.15
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTGACCCTG
Found at i:23611754 original size:29 final size:27
Alignment explanation
Indices: 23611721--23611851 Score: 122
Period size: 29 Copynumber: 4.6 Consensus size: 27
23611711 AACAAACGCC
23611721 ATTAATTATTTGCCCTCGAAACTTCC-AAA
1 ATTAATT-TTTGCCC-CG-AACTTCCAAAA
**
23611750 ATTAAATTTTCACCCCGAACTTCCAAAA
1 ATT-AATTTTTGCCCCGAACTTCCAAAA
23611778 ATT-ATGTTTTGACCCCGAAACTTCCAAAA
1 ATTAAT-TTTTG-CCCCG-AACTTCCAAAA
*
23611807 ATTACATTTTTACCCCGAACTTCCAAAA
1 ATTA-ATTTTTGCCCCGAACTTCCAAAA
*
23611835 ATTTCATTTTTGACCCC
1 A-TTAATTTTTG-CCCC
23611852 AAAACTTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
26 2 0.02
27 10 0.12
28 31 0.36
29 33 0.38
30 8 0.09
31 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.34
Consensus pattern (27 bp):
ATTAATTTTTGCCCCGAACTTCCAAAA
Found at i:23611822 original size:57 final size:57
Alignment explanation
Indices: 23611729--23611938 Score: 203
Period size: 57 Copynumber: 3.6 Consensus size: 57
23611719 CCATTAATTA
* *
23611729 TTTG-CCCTCGAAACTTCCAAAATTAAATTTTCACCCCGAACTTCCAAAAA-TT-ATGT
1 TTTGACCC-CGAAACTTCCAAAATTACATTTTTACCCCGAACTTCCAAAAATTTCAT-T
23611785 TTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCCGAACTTCCAAAAATTTCATT
1 TTTGACCCCGAAACTTCC-AAAATTACATTTTTACCCCGAACTTCCAAAAATTTCATT
* * * * * * *
23611843 TTTGACCCCAAAACTTGCAAAATTACCA-TTTTACCCCCAAATGTCTAAAAACTCCATT
1 TTTGACCCCGAAACTTCCAAAATTA-CATTTTTACCCCGAACT-TCCAAAAATTTCATT
* * * * **
23611901 TATAATCCCGAAACTTTCAAAATTTACCGTTTTACCCC
1 TTTGACCCCGAAACTTCCAAAA-TTACATTTTTACCCC
23611939 CGATGTTCGA
Statistics
Matches: 131, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
56 14 0.11
57 52 0.40
58 51 0.39
59 14 0.11
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (57 bp):
TTTGACCCCGAAACTTCCAAAATTACATTTTTACCCCGAACTTCCAAAAATTTCATT
Found at i:23611842 original size:28 final size:29
Alignment explanation
Indices: 23611740--23611874 Score: 147
Period size: 28 Copynumber: 4.7 Consensus size: 29
23611730 TTGCCCTCGA
* *
23611740 AACTTCC-AAAATTA-AATTTTCACCCCG
1 AACTTCCAAAAATTACATTTTTGACCCCG
23611767 AACTTCCAAAAATT--ATGTTTTGACCCCG
1 AACTTCCAAAAATTACAT-TTTTGACCCCG
23611795 AAACTTCCAAAAATTACATTTTT-ACCCCG
1 -AACTTCCAAAAATTACATTTTTGACCCCG
* *
23611824 AACTTCCAAAAATTTCATTTTTGACCCCAA
1 AACTTCCAAAAATTACATTTTTGACCCC-G
*
23611854 AACTTGC-AAAATTACCATTTT
1 AACTTCCAAAAATTA-CATTTT
23611875 ACCCCCAAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
27 8 0.09
28 37 0.39
29 31 0.33
30 16 0.17
31 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTGACCCCG
Found at i:23611874 original size:29 final size:28
Alignment explanation
Indices: 23611739--23611879 Score: 144
Period size: 29 Copynumber: 5.0 Consensus size: 28
23611729 TTTGCCCTCG
* *
23611739 AAACTTCC-AAAATTAAATTTTCACCCC
1 AAACTTCCAAAAATTACATTTTGACCCC
* **
23611766 GAACTTCCAAAAATTATGTTTTGACCCC
1 AAACTTCCAAAAATTACATTTTGACCCC
*
23611794 GAAACTTCCAAAAATTACATTTTTACCCC
1 -AAACTTCCAAAAATTACATTTTGACCCC
* *
23611823 GAACTTCCAAAAATTTCATTTTTGACCCC
1 AAACTTCCAAAAATTACA-TTTTGACCCC
*
23611852 AAAACTTGC-AAAATTACCATTTT-ACCCC
1 -AAACTTCCAAAAATTA-CATTTTGACCCC
23611880 CAAATGTCTA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
27 7 0.07
28 37 0.39
29 43 0.45
30 8 0.08
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTGACCCC
Found at i:23611893 original size:58 final size:57
Alignment explanation
Indices: 23611729--23611939 Score: 180
Period size: 58 Copynumber: 3.7 Consensus size: 57
23611719 CCATTAATTA
* * * *
23611729 TTTG-CCCTCGAAACTTCCAAAATTA-AATTTTCACCCCGAACTTCCAAAAA-T-TATGT
1 TTTGACCC-CGAAACTTCCAAAATTACCATTTT-ACCCCCAAATTCCAAAAACTCCAT-T
* * * *
23611785 TTTGACCCCGAAACTTCCAAAAATTA-CATTTTTACCCCGAACTTCCAAAAATTTCATT
1 TTTGACCCCGAAACTTCC-AAAATTACCA-TTTTACCCCCAAATTCCAAAAACTCCATT
* * *
23611843 TTTGACCCCAAAACTTGCAAAATTACCATTTTACCCCCAAATGTCTAAAAACTCCATT
1 TTTGACCCCGAAACTTCCAAAATTACCATTTTACCCCCAAAT-TCCAAAAACTCCATT
* * * * *
23611901 TATAATCCCGAAACTTTCAAAATTTACCGTTTTACCCCC
1 TTTGACCCCGAAACTTCCAAAA-TTACCATTTTACCCCC
23611940 GATGTTCGAA
Statistics
Matches: 132, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
56 14 0.11
57 48 0.36
58 53 0.40
59 17 0.13
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (57 bp):
TTTGACCCCGAAACTTCCAAAATTACCATTTTACCCCCAAATTCCAAAAACTCCATT
Found at i:23612094 original size:28 final size:28
Alignment explanation
Indices: 23612033--23612095 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
23612023 CCTAAATTTT
* * *
23612033 TCCAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAATTACCATTTTACCCCCAAGTA
*
23612061 TCCAAAATTACCATTTTGCCCCCAAGTA
1 TCCAAAATTACCATTTTACCCCCAAGTA
*
23612089 TTCAAAA
1 TCCAAAA
23612096 AGTCCCATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.30
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCCCAAGTA
Done.