Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 101 of 216
Found at i:31536047 original size:18 final size:17
Alignment explanation
Indices: 31536013--31536046 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31536003 AAAAAGAAGT
31536013 TTCAGAAGTAAAAAAAA
1 TTCAGAAGTAAAAAAAA
*
31536030 TTCAGAATTAAAAAAAA
1 TTCAGAAGTAAAAAAAA
31536047 AAGAAGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
TTCAGAAGTAAAAAAAA
Found at i:31536962 original size:18 final size:17
Alignment explanation
Indices: 31536950--31536988 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
31536940 GAGAAAATGA
31536950 AAATGAAAAAGAAAAAG
1 AAATGAAAAAGAAAAAG
31536967 AAATG--AAAGAAAAAG
1 AAATGAAAAAGAAAAAG
31536982 AAGATGA
1 AA-ATGA
31536989 GTGTGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (17 bp):
AAATGAAAAAGAAAAAG
Found at i:31536977 original size:15 final size:16
Alignment explanation
Indices: 31536957--31536988 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
31536947 TGAAAATGAA
31536957 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
31536972 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
31536988 A
1 A
31536989 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:31541856 original size:20 final size:20
Alignment explanation
Indices: 31541810--31541856 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31541800 AGCTCGTTTC
*
31541810 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
31541830 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31541850 CAGCTCA
1 CAGCTCA
31541857 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31547006 original size:15 final size:15
Alignment explanation
Indices: 31546986--31547038 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 15
31546976 AGCTTCTTCT
31546986 TTTTTTTCACGAAAA
1 TTTTTTTCACGAAAA
**
31547001 TTTTTTTTTCACGAATT
1 --TTTTTTTCACGAAAA
31547018 TTTTTTTCACG-AAA
1 TTTTTTTCACGAAAA
31547032 TTTTTTT
1 TTTTTTT
31547039 TTGAATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
17 13 0.41
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTTTTTCACGAAAA
Found at i:31547007 original size:17 final size:16
Alignment explanation
Indices: 31546985--31547040 Score: 96
Period size: 15 Copynumber: 3.5 Consensus size: 16
31546975 TAGCTTCTTC
31546985 TTTTTTTTCACGAAAAT
1 TTTTTTTTCACG-AAAT
31547002 TTTTTTTTCACG-AAT
1 TTTTTTTTCACGAAAT
31547017 TTTTTTTTCACGAAAT
1 TTTTTTTTCACGAAAT
31547033 TTTTTTTT
1 TTTTTTTT
31547041 GAATTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.39
16 11 0.29
17 12 0.32
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTTTCACGAAAT
Found at i:31547024 original size:32 final size:28
Alignment explanation
Indices: 31546985--31547051 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 28
31546975 TAGCTTCTTC
31546985 TTTTTTTTCACGAAAATTTTTTTTTCACGAAT
1 TTTTTTTTCACG-AAATTTTTTTTT---GAAT
31547017 TTTTTTTTCACGAAATTTTTTTTTGAAT
1 TTTTTTTTCACGAAATTTTTTTTTGAAT
31547045 TTTTTTT
1 TTTTTTT
31547052 GAATTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.31
31 12 0.34
32 12 0.34
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (28 bp):
TTTTTTTTCACGAAATTTTTTTTTGAAT
Found at i:31547047 original size:11 final size:11
Alignment explanation
Indices: 31547033--31547077 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
31547023 TTCACGAAAT
31547033 TTTTTTTTGAA
1 TTTTTTTTGAA
31547044 TTTTTTTTGAA
1 TTTTTTTTGAA
31547055 TTTTTTTTGAAA
1 TTTTTTTTG-AA
31547067 TTTTTTTTGAA
1 TTTTTTTTGAA
31547078 GAAACTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:31547056 original size:23 final size:23
Alignment explanation
Indices: 31547033--31547077 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31547023 TTCACGAAAT
31547033 TTTTTTTTG-AATTTTTTTTGAA
1 TTTTTTTTGAAATTTTTTTTGAA
31547055 TTTTTTTTGAAATTTTTTTTGAA
1 TTTTTTTTGAAATTTTTTTTGAA
31547078 GAAACTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (23 bp):
TTTTTTTTGAAATTTTTTTTGAA
Found at i:31558486 original size:15 final size:15
Alignment explanation
Indices: 31558458--31558491 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31558448 CCGTATACAA
31558458 TTTT-TTTTCAATTT
1 TTTTCTTTTCAATTT
*
31558472 TTTTCTTTTCGATTT
1 TTTTCTTTTCAATTT
31558487 TTTTC
1 TTTTC
31558492 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTCAATTT
Found at i:31566675 original size:10 final size:10
Alignment explanation
Indices: 31566660--31566721 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
31566650 TTTGAACCAT
*
31566660 TACCAATTCG
1 TACCAATTCA
*
31566670 TACCAAATACCA
1 TACC-AAT-TCA
*
31566682 TACCATTTCA
1 TACCAATTCA
31566692 TACCAATTCCA
1 TACCAATT-CA
* *
31566703 TACCATTTCG
1 TACCAATTCA
31566713 TACCAATTC
1 TACCAATTC
31566722 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:31566705 original size:21 final size:21
Alignment explanation
Indices: 31566660--31566722 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31566650 TTTGAACCAT
* *
31566660 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
31566682 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
31566703 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
31566723 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:31568868 original size:11 final size:11
Alignment explanation
Indices: 31568852--31568893 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
31568842 TAGTTTCTTC
31568852 AAAAAAATTCA
1 AAAAAAATTCA
31568863 AAAAAAATTCA
1 AAAAAAATTCA
31568874 AAAAAAATTCA
1 AAAAAAATTCA
31568885 AAAAAAATT
1 AAAAAAATT
31568894 GGTTTGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:31574134 original size:11 final size:12
Alignment explanation
Indices: 31574104--31574135 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31574094 TTTCACTCTT
31574104 CTCTTTTTCAAA
1 CTCTTTTTCAAA
31574116 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
31574128 TTCTTTTT
1 CTCTTTTT
31574136 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:31574147 original size:27 final size:27
Alignment explanation
Indices: 31574117--31574178 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
31574107 TTTTTCAAAC
*
31574117 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
31574144 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
31574171 TCTTTTTC
1 TCTTTTTC
31574179 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:31574157 original size:13 final size:12
Alignment explanation
Indices: 31574141--31574259 Score: 61
Period size: 12 Copynumber: 10.0 Consensus size: 12
31574131 TTTTTTCGCT
31574141 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
31574154 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
31574168 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
31574179 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
31574193 -TTTCTTTTTC-
1 TTTTCTTTTTCA
* ** *
31574203 TTTGCAATTTCT
1 TTTTCTTTTTCA
* *
31574215 TTTTCTTCTTCG
1 TTTTCTTTTTCA
*
31574227 TTTTCTTTTT-G
1 TTTTCTTTTTCA
31574238 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
31574248 ATTTCTTTTTCA
1 TTTTCTTTTTCA
31574260 ATCTCTTTCT
Statistics
Matches: 81, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 14 0.17
12 40 0.49
13 8 0.10
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:31574170 original size:14 final size:14
Alignment explanation
Indices: 31574119--31574177 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
31574109 TTTCAAACTC
*
31574119 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
31574132 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
31574145 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
31574160 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
31574174 TTTT
1 TTTT
31574178 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:31574258 original size:6 final size:6
Alignment explanation
Indices: 31574139--31574245 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
31574129 TCTTTTTTCG
* * * **
31574139 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
31574190 CGATTT CTTTTT C-TTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
31574237 -GTTTT CTTT
1 CTTTTT CTTT
31574246 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
5 8 0.11
6 51 0.72
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:31575499 original size:20 final size:20
Alignment explanation
Indices: 31575476--31575521 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31575466 CCAGCTCGAA
*
31575476 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
31575496 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
31575516 TTAGCT
1 TTAGCT
31575522 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:31575503 original size:30 final size:30
Alignment explanation
Indices: 31575468--31575541 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
31575458 AGTTTTTCCC
31575468 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
31575498 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
31575528 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
31575542 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:31578138 original size:20 final size:20
Alignment explanation
Indices: 31578115--31578168 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
31578105 AGCTTTTCCC
31578115 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
31578135 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
31578155 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
31578169 TACTTTAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:31578159 original size:30 final size:30
Alignment explanation
Indices: 31578125--31578188 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
31578115 AGCTCAATTT
*
31578125 AGCTCACA-TGAGCTTAATTTAGCTCGTTTG
1 AGCTCA-ATTGAGCTTAATTTAACTCGTTTG
* *
31578155 AGCTCAATTTAGCTTACTTTAACTCGTTTG
1 AGCTCAATTGAGCTTAATTTAACTCGTTTG
31578185 AGCT
1 AGCT
31578189 TGGCTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAACTCGTTTG
Found at i:31581470 original size:52 final size:52
Alignment explanation
Indices: 31581387--31581487 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
31581377 TAAGGAAACG
* *
31581387 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
31581439 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
31581488 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:31582544 original size:15 final size:14
Alignment explanation
Indices: 31582520--31582550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
31582510 TTGCAATTTC
31582520 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
31582534 AAAACAAAAAACAAA
1 AAAA-AAAAAACAAA
31582549 AA
1 AA
31582551 GAGAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:31585131 original size:21 final size:23
Alignment explanation
Indices: 31585086--31585132 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31585076 ACACCTGCAA
* *
31585086 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
31585109 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
31585130 TAA
1 TAA
31585133 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:31588640 original size:21 final size:21
Alignment explanation
Indices: 31588590--31588654 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
31588580 ACCTCTTTGA
*
31588590 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACC-AAT
*
31588613 ACCATACCATTTCATACCAAT
1 ACCATACCATTTCGTACCAAT
*
31588634 TCCATACCATTTCGTACCAAT
1 ACCATACCATTTCGTACCAAT
31588655 CCCCAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 22 0.58
22 12 0.32
23 4 0.11
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (21 bp):
ACCATACCATTTCGTACCAAT
Found at i:31591232 original size:40 final size:40
Alignment explanation
Indices: 31591148--31591330 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
31591138 TTGAATGCTG
* * * *
31591148 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
31591187 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
31591228 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATA-CAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
31591267 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
31591307 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31591331 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:31591299 original size:79 final size:81
Alignment explanation
Indices: 31591148--31591327 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
31591138 TTGAATGCTG
* * * *
31591148 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
* *
31591212 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
31591228 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACAAT-TCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACAATATCCGGACTAAGAT-CCGAAGGCA
31591289 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTTTAAAA
31591307 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
31591328 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 51 0.58
80 25 0.28
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:31591351 original size:39 final size:39
Alignment explanation
Indices: 31591228--31591377 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 39
31591218 AGTTATTAAT
* ** * *
31591228 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAG--ATACAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTCTA-AAA
** *
31591267 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
31591307 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
31591347 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
31591378 GAGCTATATC
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.03
39 52 0.55
40 37 0.39
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:31591351 original size:79 final size:79
Alignment explanation
Indices: 31591201--31591367 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
31591191 GGACTAAGAT
* * * * **
31591201 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAA
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
* *
31591266 TTCCGGGTTAAGTC
66 TACCGGGCTAAGTC
* * *
31591280 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTACT
1 CCGAAGGCATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACA
*
31591343 ATGACCGGGCTATGTC
65 AT-ACCGGGCTAAGTC
31591359 CCGAAGGCA
1 CCGAAGGCA
31591368 CTTGAACGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 14 0.19
79 60 0.81
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
TACCGGGCTAAGTC
Found at i:31596594 original size:21 final size:21
Alignment explanation
Indices: 31596568--31596611 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31596558 GATAACTAGC
31596568 TGAATTGTACGTTTATCAAAT
1 TGAATTGTACGTTTATCAAAT
31596589 TGAATTGTACGTTTATCAAAT
1 TGAATTGTACGTTTATCAAAT
31596610 TG
1 TG
31596612 TGAGATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (21 bp):
TGAATTGTACGTTTATCAAAT
Found at i:31599207 original size:39 final size:39
Alignment explanation
Indices: 31599035--31599216 Score: 156
Period size: 40 Copynumber: 4.6 Consensus size: 39
31599025 TTGAATGCTG
* * * * *
31599035 TCCGGGCTAAGT-CCGAAGGCTTTGTGCTAAGTGAATATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTA-AA
* * *
31599075 -CCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* * **
31599114 TCCGGGTTAAGTCCCAAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
*
31599154 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
*
31599193 -CCGGGCTAATGTCCCGAAGGCATT
1 TCCGGGTTAA-GTCCCGAAGGCATT
31599217 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
38 8 0.07
39 39 0.33
40 62 0.53
41 8 0.07
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:31605076 original size:25 final size:25
Alignment explanation
Indices: 31605040--31605088 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
31605030 TCTCCTAAAT
* *
31605040 TTTAATTTAATTATCAATTTTTTAA
1 TTTAATTGAATTATCAATATTTTAA
*
31605065 TTTAATTGAATTATTAATATTTTA
1 TTTAATTGAATTATCAATATTTTA
31605089 TATTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTAATTGAATTATCAATATTTTAA
Found at i:31609750 original size:16 final size:16
Alignment explanation
Indices: 31609693--31609753 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
31609683 AATTTTATTA
* *
31609693 ATTAAATTAATATTTA
1 ATTAATTTAATATTTT
*
31609709 ATTAATTTAATACTTAT
1 ATTAATTTAATA-TTTT
* *
31609726 CTTGA--TAATATTTT
1 ATTAATTTAATATTTT
31609740 ATTAATTTAATATT
1 ATTAATTTAATATT
31609754 AAGTGATTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 18 0.53
17 5 0.15
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTAATTTAATATTTT
Found at i:31612662 original size:40 final size:40
Alignment explanation
Indices: 31612579--31612729 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
31612569 TTGAATGCTG
* *
31612579 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTA-AGTGACT-AT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* * *
31612617 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
** *
31612658 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
** * *
31612698 TCCGGGTTAAGTCCCGAAAGCATTCGTGCGAG
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAG
31612730 TTTTAAAATC
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
39 11 0.12
40 71 0.76
41 11 0.12
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31612702 original size:80 final size:81
Alignment explanation
Indices: 31612579--31612757 Score: 194
Period size: 80 Copynumber: 2.3 Consensus size: 81
31612569 TTGAATGCTG
* * * *
31612579 TCCGGGCTAAGT-CCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGTAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAG-TCCCGAAAGCAT
* *
31612641 TTGTGCGAGTTATT-AAT
65 TCGTGCGAGTT-TTAAAA
**
31612658 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAGTCCCGAAAGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGTCCCGAAAGCA
31612720 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTTTAAAA
31612738 T-CGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
31612758 ATTGAAGAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
79 34 0.40
80 43 0.50
81 9 0.10
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGTCCCGAAAGCATT
CGTGCGAGTTTTAAAA
Found at i:31612754 original size:39 final size:39
Alignment explanation
Indices: 31612631--31612760 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
31612621 GGACTAAGAT
* *
31612631 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTT-TTAATTCCGGGTTAAGTC
* * **
31612671 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAG-TTTTAATTCCGGGTTAAGTC
* *
31612711 CCGAAAGCATTCGTGCGAGTTTTAAAAT-CGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTTT-AATTCCGGGTTAAGTC
31612750 CCGAAGGCATT
1 CCGAAGGCATT
31612761 GAAGAGTTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 23 0.30
40 53 0.69
41 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTTTAATTCCGGGTTAAGTC
Found at i:31630200 original size:40 final size:40
Alignment explanation
Indices: 31629948--31630199 Score: 369
Period size: 40 Copynumber: 6.3 Consensus size: 40
31629938 TAGTAAAATA
31629948 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
31629988 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCAGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
31630028 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
31630068 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* * * * **
31630108 AGCATTCGTGCTAGTGATATATCTGTGCTAAACCCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* * * * * *
31630148 AGCATTCGTGCTGGTGTTATATCCGGGCTAGGCCCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
31630188 AGCAATCATGCT
1 AGCATTCATGCT
31630200 GATGACGTGT
Statistics
Matches: 194, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 194 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
Found at i:31633611 original size:47 final size:47
Alignment explanation
Indices: 31633554--31633857 Score: 416
Period size: 47 Copynumber: 6.4 Consensus size: 47
31633544 ATTGATGTAC
* * *
31633554 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
31633601 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
31633650 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCGATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31633697 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31633744 ACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31633791 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
31633838 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
31633858 TCCCGAAGGG
Statistics
Matches: 237, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.00
47 195 0.82
49 40 0.17
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:31633735 original size:22 final size:22
Alignment explanation
Indices: 31633708--31633829 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
31633698 CATGTGTATG
31633708 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
31633730 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
31633755 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
31633777 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
31633802 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
31633824 TGTGAT
1 TGTGAT
31633830 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:31636581 original size:10 final size:10
Alignment explanation
Indices: 31636566--31636603 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
31636556 AGTTCACTTG
*
31636566 AGCTCAAGTC
1 AGCTCAATTC
31636576 AGCTC-ATTC
1 AGCTCAATTC
31636585 GAGCTCAATTC
1 -AGCTCAATTC
31636596 AGCTCAAT
1 AGCTCAAT
31636604 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:31643573 original size:12 final size:11
Alignment explanation
Indices: 31643550--31643582 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
31643540 GTTGTAAAGT
31643550 TTTA-TTTTTA
1 TTTATTTTTTA
31643560 TTTATTTATTTA
1 TTTATTT-TTTA
31643572 TTTATTTTTTA
1 TTTATTTTTTA
31643583 CTTAGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:31650312 original size:23 final size:22
Alignment explanation
Indices: 31650261--31650312 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
31650251 CCTCGTCTTT
*
31650261 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
31650283 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
31650306 TTCTTTT
1 TTCTTTT
31650313 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:31659939 original size:30 final size:30
Alignment explanation
Indices: 31659905--31660001 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
31659895 TAAACTAAAA
31659905 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
31659935 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
31659965 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
31659994 ATGAGCTA
1 -TGAGCTA
31660002 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:31662196 original size:12 final size:12
Alignment explanation
Indices: 31662181--31662211 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31662171 TTCTTTTTGC
31662181 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31662193 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31662205 TTTTCAA
1 TTTTCAA
31662212 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:31662288 original size:6 final size:6
Alignment explanation
Indices: 31662272--31662321 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
31662262 TTTCTTTTTA
*
31662272 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
31662321 T
1 T
31662322 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:31662304 original size:37 final size:37
Alignment explanation
Indices: 31662261--31662331 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
31662251 CTTGCCTCTC
31662261 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
31662298 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
31662332 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:31662332 original size:16 final size:16
Alignment explanation
Indices: 31662257--31662317 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
31662247 GCCTCTTGCC
*
31662257 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
31662273 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
31662289 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
31662305 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
31662318 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:31665004 original size:30 final size:30
Alignment explanation
Indices: 31664970--31665066 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
31664960 AAAACTAAAA
31664970 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
31665000 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
31665030 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
31665059 ATGAGCTA
1 -TGAGCTA
31665067 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:31665970 original size:17 final size:15
Alignment explanation
Indices: 31665947--31665990 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
31665937 GAATGAAAAG
31665947 AGAAAAAGAGATTGA
1 AGAAAAAGAGATTGA
*
31665962 GATGAAAAAGAAATTGA
1 -A-GAAAAAGAGATTGA
31665979 AGAAAGAAGAGA
1 AGAAA-AAGAGA
31665991 AAATGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.11
Consensus pattern (15 bp):
AGAAAAAGAGATTGA
Found at i:31665993 original size:23 final size:22
Alignment explanation
Indices: 31665967--31666019 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31665957 ATTGAGATGA
*
31665967 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
31665990 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
31666012 AAAAGAAA
1 AAAAGAAA
31666020 AAACGTGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:31671832 original size:23 final size:22
Alignment explanation
Indices: 31671780--31671832 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31671770 TCCACGTCTT
*
31671780 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
31671802 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
31671825 TTTCTTTT
1 TTTCTTTT
31671833 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:31678810 original size:33 final size:33
Alignment explanation
Indices: 31678772--31678834 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31678762 GATTACTCAC
31678772 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
31678805 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
31678835 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:31678873 original size:18 final size:18
Alignment explanation
Indices: 31678849--31678892 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31678839 TCTTTTTTCG
* *
31678849 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
*
31678867 TTTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
31678885 CTTTTTCA
1 CTTTTTCA
31678893 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:31678888 original size:30 final size:27
Alignment explanation
Indices: 31678852--31678942 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 27
31678842 TTTTTCGCTT
*
31678852 TTTCTTTTTCAATTTTTTTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
31678882 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
31678909 TTTCTTTTTC----TTC-TTT-TTCAA
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
31678930 TTTCTTTTTCAAT
1 TTTCTTTTTCAAT
31678943 CTCTTTCTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
21 14 0.25
22 3 0.05
23 3 0.05
27 13 0.24
28 1 0.02
30 21 0.38
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:31678902 original size:12 final size:12
Alignment explanation
Indices: 31678852--31678948 Score: 77
Period size: 12 Copynumber: 8.6 Consensus size: 12
31678842 TTTTTCGCTT
31678852 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
31678864 TTTTTTTTTC-A
1 TTTCTTTTTCAA
31678875 -TTC----TCAA
1 TTTCTTTTTCAA
31678882 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
31678894 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
31678909 TTTCTTTTTC--
1 TTTCTTTTTCAA
31678919 -TTCTTTTTCAA
1 TTTCTTTTTCAA
31678930 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
31678942 TCTCTTT
1 TTTCTTT
31678949 CTCCTTTTCT
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
6 2 0.03
7 1 0.01
8 3 0.04
9 9 0.13
10 2 0.03
11 1 0.01
12 33 0.48
13 7 0.10
14 7 0.10
15 4 0.06
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:31678912 original size:14 final size:15
Alignment explanation
Indices: 31678893--31678927 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
31678883 TTCTTTTTCA
31678893 ATTTTC-TTTTCTTC
1 ATTTTCTTTTTCTTC
31678907 ATTTTCTTTTTCTTC
1 ATTTTCTTTTTCTTC
*
31678922 TTTTTC
1 ATTTTC
31678928 AATTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTCTTTTTCTTC
Found at i:31678947 original size:27 final size:25
Alignment explanation
Indices: 31678878--31678947 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 25
31678868 TTTTTCATTC
31678878 TCAATTTCTTTTTCAATT-TTCTTTTCT
1 TCAATTTCTTTTTCAATTCTTC--TT-T
*
31678905 TCATTTTCTTTTTC--TTC-T-TTT
1 TCAATTTCTTTTTCAATTCTTCTTT
31678926 TCAATTTCTTTTTCAATCTCTT
1 TCAATTTCTTTTTCAAT-TCTT
31678948 TCTCCTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 1 0.03
24 2 0.06
25 4 0.11
27 13 0.36
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (25 bp):
TCAATTTCTTTTTCAATTCTTCTTT
Found at i:31680018 original size:28 final size:26
Alignment explanation
Indices: 31679958--31680018 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
31679948 TTAAACTTGA
31679958 TTTTTTTTGCTCACCTTTTTTTTCTTT
1 TTTTTTTTGCTCA-CTTTTTTTTCTTT
**
31679985 TCTTTTTTTGCTCGA-TTTTTTTTCACT
1 T-TTTTTTTGCTC-ACTTTTTTTTCTTT
31680012 TTTTTTT
1 TTTTTTT
31680019 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.20
27 12 0.40
28 11 0.37
29 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (26 bp):
TTTTTTTTGCTCACTTTTTTTTCTTT
Found at i:31680054 original size:12 final size:12
Alignment explanation
Indices: 31680039--31680070 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
31680029 TTCAATCAAA
31680039 TTTTTTTTGATT
1 TTTTTTTTGATT
31680051 TTTTTTTT-ATT
1 TTTTTTTTGATT
31680062 TTTTTTTTG
1 TTTTTTTTG
31680071 TTACTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (12 bp):
TTTTTTTTGATT
Found at i:31681666 original size:20 final size:20
Alignment explanation
Indices: 31681634--31681708 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
31681624 AACTTAAGCC
31681634 AAGCTCAAA-CGAGCTAAAGT
1 AAGCT-AAATCGAGCTAAAGT
31681654 AAGCTAAATCGAGCTCAAACG-
1 AAGCTAAATCGAGCT-AAA-GT
** * *
31681675 -AGCTAAATTAAGCTCATGT
1 AAGCTAAATCGAGCTAAAGT
*
31681694 GAGCTAAATCGAGCT
1 AAGCTAAATCGAGCT
31681709 GGGAAAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
20 35 0.80
21 3 0.07
22 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGCTAAATCGAGCTAAAGT
Found at i:31686725 original size:20 final size:20
Alignment explanation
Indices: 31686702--31686748 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31686692 GGGTTAAAAT
*
31686702 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31686722 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31686742 TGAGCTG
1 TGAGCTG
31686749 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31691263 original size:30 final size:30
Alignment explanation
Indices: 31691207--31691263 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
31691197 TGGGCTCAAA
* **
31691207 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
31691237 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
31691264 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:31695975 original size:20 final size:20
Alignment explanation
Indices: 31695950--31695992 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31695940 AAAAGAAAAG
31695950 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
31695970 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
31695990 AAA
1 AAA
31695993 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:31713034 original size:23 final size:23
Alignment explanation
Indices: 31712998--31713041 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31712988 TTTTCTTTTG
31712998 TTCTTTTTCTAACTCATTTTCTC
1 TTCTTTTTCTAACTCATTTTCTC
*
31713021 TTCTTTCTTC-AACTCTTTTTC
1 TTCTTT-TTCTAACTCATTTTC
31713042 AATTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.61
Consensus pattern (23 bp):
TTCTTTTTCTAACTCATTTTCTC
Found at i:31733592 original size:11 final size:10
Alignment explanation
Indices: 31733567--31733627 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
31733557 ACCAATAAAA
31733567 TAAA-TGAGC
1 TAAATTGAGC
*
31733576 TGAATTGTAGC
1 TAAATTG-AGC
31733587 TAAATTGAGC
1 TAAATTGAGC
**
31733597 TCGATTGAGC
1 TAAATTGAGC
31733607 TGAAA-TGAGC
1 T-AAATTGAGC
*
31733617 TCAATTGAGC
1 TAAATTGAGC
31733627 T
1 T
31733628 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:31733628 original size:20 final size:20
Alignment explanation
Indices: 31733568--31733628 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
31733558 CCAATAAAAT
*
31733568 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
31733588 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
31733609 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
31733629 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:31736624 original size:14 final size:14
Alignment explanation
Indices: 31736598--31736656 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
31736588 ATTGTAGATT
31736598 AAAAAAATT--GAA
1 AAAAAAATTGAGAA
31736610 AAAAAAATTGAGAA
1 AAAAAAATTGAGAA
31736624 AAAAAAATTGA-AA
1 AAAAAAATTGAGAA
**
31736637 AAAAAAATTTTGAA
1 AAAAAAATTGAGAA
31736651 AAAAAA
1 AAAAAA
31736657 TTGCATACGG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.21
13 11 0.26
14 22 0.52
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (14 bp):
AAAAAAATTGAGAA
Found at i:31736659 original size:26 final size:26
Alignment explanation
Indices: 31736598--31736656 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
31736588 ATTGTAGATT
31736598 AAAAAAATTGAAAAAAAAATTGAGAA
1 AAAAAAATTGAAAAAAAAATTGAGAA
**
31736624 AAAAAAATTGAAAAAAAAAATTTTGAA
1 AAAAAAATTG-AAAAAAAAATTGAGAA
31736651 AAAAAA
1 AAAAAA
31736657 TTGCATACGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (26 bp):
AAAAAAATTGAAAAAAAAATTGAGAA
Found at i:31743098 original size:11 final size:12
Alignment explanation
Indices: 31743068--31743099 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31743058 TTTCACTCTT
31743068 CTCTTTTTCAAA
1 CTCTTTTTCAAA
31743080 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
31743092 TTCTTTTT
1 CTCTTTTT
31743100 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:31743134 original size:14 final size:14
Alignment explanation
Indices: 31743083--31743141 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
31743073 TTTCAAACTC
*
31743083 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
31743096 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
31743109 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
31743124 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
31743138 TTTT
1 TTTT
31743142 GTTTTCTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:31743146 original size:20 final size:21
Alignment explanation
Indices: 31743118--31743163 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31743108 TCTTTTTCAA
*
31743118 TTTTCTTTTC-TTCATTTTCT
1 TTTTCTTTTCTTTCAATTTCT
*
31743138 TTTTGTTTTCTTTCAATTTCT
1 TTTTCTTTTCTTTCAATTTCT
31743159 TTTTC
1 TTTTC
31743164 AATCTCTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTCTTTTCTTTCAATTTCT
Found at i:31743165 original size:12 final size:12
Alignment explanation
Indices: 31743069--31743172 Score: 52
Period size: 12 Copynumber: 8.4 Consensus size: 12
31743059 TTCACTCTTC
**
31743069 TCTTTTTCAAAC
1 TCTTTTTCAATT
*
31743081 TCTTTTTCAAAT
1 TCTTTTTCAATT
**
31743093 TCTTTTTTCGCTTTT
1 TC-TTTTT--CAATT
31743108 TCTTTTTCAATTT
1 TCTTTTTCAA-TT
*
31743121 TCTTTTCTTCATTT
1 TC-TTT-TTCAATT
*
31743135 TCTTTTT--GTT
1 TCTTTTTCAATT
*
31743145 T-TCTTTCAATT
1 TCTTTTTCAATT
*
31743156 TCTTTTTCAATC
1 TCTTTTTCAATT
31743168 TCTTT
1 TCTTT
31743173 CTCCTTTTCT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
9 4 0.06
10 3 0.04
11 3 0.04
12 29 0.41
13 12 0.17
14 12 0.17
15 8 0.11
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.66
Consensus pattern (12 bp):
TCTTTTTCAATT
Found at i:31744217 original size:19 final size:19
Alignment explanation
Indices: 31744195--31744255 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 19
31744185 TTTAACTCGA
31744195 TTTTTTTTGTCACTTCTTT
1 TTTTTTTTGTCACTTCTTT
*
31744214 TTTTTCCTT-T---TT-TTT
1 TTTTT-TTTGTCACTTCTTT
*
31744229 CTTTTTTTGCTCACTTCTTT
1 TTTTTTTTG-TCACTTCTTT
31744249 TTTTTTT
1 TTTTTTT
31744256 GAATTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 13
0.65 0.08 0.27
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 3 0.10
19 8 0.26
20 11 0.35
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTTTTTGTCACTTCTTT
Found at i:31744269 original size:35 final size:33
Alignment explanation
Indices: 31744196--31744271 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 33
31744186 TTAACTCGAT
* **
31744196 TTTTTTTGTCACTTCTTTTTTTTCCTTTTTTTTC
1 TTTTTTTGTCACTTCTTTTTTTT-CTTATTTTGA
31744230 TTTTTTTGCTCACTTCTTTTTTTT-TTGAATTTTGA
1 TTTTTTTG-TCACTTCTTTTTTTTCTT--ATTTTGA
31744265 TTTTTTT
1 TTTTTTT
31744272 TTGAAACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.06
34 8 0.22
35 26 0.72
ACGTcount: A:0.07, C:0.13, G:0.05, T:0.75
Consensus pattern (33 bp):
TTTTTTTGTCACTTCTTTTTTTTCTTATTTTGA
Found at i:31746677 original size:20 final size:20
Alignment explanation
Indices: 31746630--31746677 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
31746620 AGTAAGCTCG
31746630 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
31746650 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
31746670 GTTGAGCT
1 GTTGAGCT
31746678 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:31747223 original size:20 final size:20
Alignment explanation
Indices: 31747184--31747244 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
31747174 CCAATAAAAT
* *
31747184 AAATGAGCTGAATTGTAGCT-
1 AAATAAGCTCAATTG-AGCTG
*
31747204 AAATTAAGCTCGATTGAGCTG
1 AAA-TAAGCTCAATTGAGCTG
*
31747225 AAATGAGCTCAATTGAGCTG
1 AAATAAGCTCAATTGAGCTG
31747245 GTCAAAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATAAGCTCAATTGAGCTG
Found at i:31749622 original size:30 final size:30
Alignment explanation
Indices: 31749588--31749684 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
31749578 AGCTCACTCC
31749588 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31749618 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
31749648 CAGCTCAACTTTAGCTCACGGGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31749678 TAGCTCA
1 TAGCTCA
31749685 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31752025 original size:20 final size:19
Alignment explanation
Indices: 31751985--31752046 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
31751975 ACCAATAAAA
31751985 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
31752005 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
* *
31752025 TGAAATAAGCTCAATTGAGC
1 T-AAATGAGCTCGATTGAGC
31752045 TA
1 TA
31752047 GTCGGAGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 13 0.35
22 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:31752045 original size:10 final size:10
Alignment explanation
Indices: 31751989--31752045 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
31751979 ATAAAATAAA
*
31751989 TGAGCTGAAT
1 TGAGCTCAAT
*
31751999 TGTAGCTAAAT
1 TG-AGCTCAAT
*
31752010 TGAGCTCGAT
1 TGAGCTCAAT
* *
31752020 TGAGCTGAAA
1 TGAGCTCAAT
*
31752030 TAAGCTCAAT
1 TGAGCTCAAT
31752040 TGAGCT
1 TGAGCT
31752046 AGTCGGAGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (10 bp):
TGAGCTCAAT
Found at i:31756707 original size:19 final size:18
Alignment explanation
Indices: 31756671--31756710 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31756661 TTTCCACTCG
*
31756671 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
31756689 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
31756708 TTT
1 TTT
31756711 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:31757790 original size:13 final size:12
Alignment explanation
Indices: 31757771--31757817 Score: 67
Period size: 12 Copynumber: 3.7 Consensus size: 12
31757761 TAGCTCTCTT
31757771 TTTTTTTTCAAA
1 TTTTTTTTCAAA
31757783 TCTTTTTTTTCACAA
1 --TTTTTTTTCA-AA
31757798 TTTTTTTTCAAA
1 TTTTTTTTCAAA
31757810 TTTTTTTT
1 TTTTTTTT
31757818 TCACAACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.31
13 10 0.31
14 10 0.31
15 2 0.06
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:31757814 original size:26 final size:27
Alignment explanation
Indices: 31757771--31757823 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
31757761 TAGCTCTCTT
31757771 TTTTTTTTCAAATCTTTTTTTTCACAA
1 TTTTTTTTCAAATCTTTTTTTTCACAA
31757798 TTTTTTTTCAAAT-TTTTTTTTCACAA
1 TTTTTTTTCAAATCTTTTTTTTCACAA
31757824 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTTTTCAAATCTTTTTTTTCACAA
Found at i:31757818 original size:13 final size:13
Alignment explanation
Indices: 31757770--31757820 Score: 77
Period size: 13 Copynumber: 3.8 Consensus size: 13
31757760 CTAGCTCTCT
31757770 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
31757783 TCTTTTTTTTCACAA
1 T-TTTTTTTTCA-AA
31757798 -TTTTTTTTCAAA
1 TTTTTTTTTCAAA
31757810 TTTTTTTTTCA
1 TTTTTTTTTCA
31757821 CAACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.06
13 21 0.60
14 10 0.29
15 2 0.06
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:31757889 original size:10 final size:11
Alignment explanation
Indices: 31757863--31757906 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
31757853 GAAACTAGTT
*
31757863 TTTTTTTCAAA
1 TTTTTTTCGAA
*
31757874 TTTTTTTTTGAA
1 -TTTTTTTCGAA
*
31757886 TTTTTTTCGAG
1 TTTTTTTCGAA
31757897 TTTTTTTCGA
1 TTTTTTTCGA
31757907 GAAACTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.68
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:31760019 original size:19 final size:18
Alignment explanation
Indices: 31759983--31760022 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31759973 TTTCCACTCG
*
31759983 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
31760001 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
31760020 TTT
1 TTT
31760023 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:31761097 original size:14 final size:13
Alignment explanation
Indices: 31761078--31761128 Score: 93
Period size: 13 Copynumber: 3.8 Consensus size: 13
31761068 ACTAGCTCTC
31761078 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
31761091 TTTTTTTTTCACAA
1 TTTTTTTTTCA-AA
31761105 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
31761118 TTTTTTTTTCA
1 TTTTTTTTTCA
31761129 CAACTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 24 0.65
14 13 0.35
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:31761110 original size:27 final size:27
Alignment explanation
Indices: 31761078--31761131 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
31761068 ACTAGCTCTC
31761078 TTTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTTCAAATTTTTTTTTCACAA
31761105 TTTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTTCAAATTTTTTTTTCACAA
31761132 CTTGATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTTTTTCAAATTTTTTTTTCACAA
Found at i:31761187 original size:12 final size:12
Alignment explanation
Indices: 31761170--31761213 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
31761160 GGAAACTGGT
31761170 TTTTTTTTCGAA
1 TTTTTTTTCGAA
31761182 TTTTTTTT-GAA
1 TTTTTTTTCGAA
* *
31761193 TTTTTTTTTGAG
1 TTTTTTTTCGAA
31761205 TTTTTTTTC
1 TTTTTTTTC
31761214 AAGAAACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:31763332 original size:19 final size:18
Alignment explanation
Indices: 31763296--31763335 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31763286 TTTCCACTCG
*
31763296 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
31763314 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
31763333 TTT
1 TTT
31763336 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:31764391 original size:13 final size:12
Alignment explanation
Indices: 31764372--31764418 Score: 67
Period size: 12 Copynumber: 3.7 Consensus size: 12
31764362 CTAGCTCTCT
31764372 TTTTTTTTCAAA
1 TTTTTTTTCAAA
31764384 TCTTTTTTTTCACAA
1 --TTTTTTTTCA-AA
31764399 TTTTTTTTCAAA
1 TTTTTTTTCAAA
31764411 TTTTTTTT
1 TTTTTTTT
31764419 TCACAACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.31
13 10 0.31
14 10 0.31
15 2 0.06
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:31764415 original size:26 final size:27
Alignment explanation
Indices: 31764372--31764424 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
31764362 CTAGCTCTCT
31764372 TTTTTTTTCAAATCTTTTTTTTCACAA
1 TTTTTTTTCAAATCTTTTTTTTCACAA
31764399 TTTTTTTTCAAAT-TTTTTTTTCACAA
1 TTTTTTTTCAAATCTTTTTTTTCACAA
31764425 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTTTTCAAATCTTTTTTTTCACAA
Found at i:31764419 original size:13 final size:13
Alignment explanation
Indices: 31764371--31764421 Score: 77
Period size: 13 Copynumber: 3.8 Consensus size: 13
31764361 ACTAGCTCTC
31764371 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
31764384 TCTTTTTTTTCACAA
1 T-TTTTTTTTCA-AA
31764399 -TTTTTTTTCAAA
1 TTTTTTTTTCAAA
31764411 TTTTTTTTTCA
1 TTTTTTTTTCA
31764422 CAACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.06
13 21 0.60
14 10 0.29
15 2 0.06
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:31764481 original size:11 final size:11
Alignment explanation
Indices: 31764465--31764508 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
31764455 AAACTAGTTT
31764465 TTTTTTTCGAA
1 TTTTTTTCGAA
*
31764476 TTTTTTTTGAA
1 TTTTTTTCGAA
*
31764487 TTTTTTTTCGAG
1 -TTTTTTTCGAA
31764499 TTTTTTTCGA
1 TTTTTTTCGA
31764509 GAAACTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.14, C:0.07, G:0.11, T:0.68
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:31764481 original size:12 final size:12
Alignment explanation
Indices: 31764464--31764505 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
31764454 GAAACTAGTT
31764464 TTTTTTTTCGAA
1 TTTTTTTTCGAA
31764476 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
31764487 TTTTTTTTCGAG
1 TTTTTTTTCGAA
31764499 TTTTTTT
1 TTTTTTT
31764506 CGAGAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:31772127 original size:23 final size:22
Alignment explanation
Indices: 31772076--31772127 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
31772066 CCTCGTCTTT
*
31772076 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
31772098 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
31772121 TTCTTTT
1 TTCTTTT
31772128 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:31776189 original size:22 final size:22
Alignment explanation
Indices: 31776139--31776189 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
31776129 CCTCGTCTTT
*
31776139 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
31776161 -TCATTTTCTCTTCTTTTTC-AAC
1 TTC-TTTTCT-TTCTTTTTCTAAC
31776183 TTCTTTT
1 TTCTTTT
31776190 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 12 0.48
23 11 0.44
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:31776201 original size:13 final size:12
Alignment explanation
Indices: 31776148--31776193 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
31776138 TTTCTTTTGT
31776148 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
31776161 -TCATTTTC-TC
1 TTCTTTTTCAAC
31776171 TTCTTTTTCAAC
1 TTCTTTTTCAAC
31776183 TTCTTTTTCAA
1 TTCTTTTTCAA
31776194 TTTTCTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
10 1 0.04
11 7 0.26
12 19 0.70
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:31776218 original size:28 final size:30
Alignment explanation
Indices: 31776163--31776220 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
31776153 TTTCTAACTC
*
31776163 ATTTTCTCTTCTTTTTCAACTTCTTTTTCA
1 ATTTTCTCTTCTTTTTCAACTTCCTTTTCA
31776193 ATTTTCT-TTC-TTTTC-ACATTCCTTTTCA
1 ATTTTCTCTTCTTTTTCAAC-TTCCTTTTCA
31776221 CTCTCAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 14 0.54
29 3 0.12
30 7 0.27
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTCTCTTCTTTTTCAACTTCCTTTTCA
Found at i:31782675 original size:23 final size:22
Alignment explanation
Indices: 31782623--31782675 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
31782613 TCCTTGTCTT
*
31782623 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
31782645 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
31782668 TTTCTTTT
1 TTTCTTTT
31782676 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:31782689 original size:18 final size:18
Alignment explanation
Indices: 31782668--31782707 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31782658 CTTTCTTCAA
* * *
31782668 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
31782686 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
31782704 TTTC
1 TTTC
31782708 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:31791258 original size:23 final size:23
Alignment explanation
Indices: 31791228--31791316 Score: 160
Period size: 23 Copynumber: 3.9 Consensus size: 23
31791218 ATGGTTTGGG
*
31791228 TTTGGTACGAAATGGTAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
31791251 TTTGGTACGAAATGGAAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
31791274 TTTGGTACGAAATGGAAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
*
31791297 TTTGGTTCGAAATGGAAATG
1 TTTGGTACGAAATGGAAATG
31791317 GTTCAAAAAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (23 bp):
TTTGGTACGAAATGGAAATGTAA
Found at i:31792441 original size:45 final size:45
Alignment explanation
Indices: 31792377--31792609 Score: 412
Period size: 45 Copynumber: 5.2 Consensus size: 45
31792367 CATGAAATTA
*
31792377 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
31792422 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
31792467 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
31792512 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
31792557 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
31792602 AGGAAGCA
1 AGGAAGCA
31792610 CCATGGCCGA
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 181 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:31795475 original size:10 final size:10
Alignment explanation
Indices: 31795459--31795516 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
31795449 CAACTCCGAC
31795459 CAGCTCAATT
1 CAGCTCAATT
* *
31795469 GAGCTCATTT
1 CAGCTCAATT
31795479 CAGCTCAA-T
1 CAGCTCAATT
31795488 CGAGCTCAATT
1 C-AGCTCAATT
*
31795499 TAGCTACAATT
1 CAGCT-CAATT
31795510 CAGCTCA
1 CAGCTCA
31795517 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:31795482 original size:20 final size:20
Alignment explanation
Indices: 31795459--31795519 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
31795449 CAACTCCGAC
31795459 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
31795479 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
31795500 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
31795520 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:31796879 original size:15 final size:14
Alignment explanation
Indices: 31796859--31796908 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
31796849 TTGGAGTATC
31796859 AAAAAAATCGAGCAA
1 AAAAAAAT-GAGCAA
31796874 AAAAAAA-GAAAG-AA
1 AAAAAAATG--AGCAA
31796888 AAAAAAAGTGAGCAA
1 AAAAAAA-TGAGCAA
31796903 AAAAAA
1 AAAAAA
31796909 TCAAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
15 17 0.57
16 1 0.03
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (14 bp):
AAAAAAATGAGCAA
Found at i:31797957 original size:11 final size:12
Alignment explanation
Indices: 31797941--31798046 Score: 65
Period size: 12 Copynumber: 8.7 Consensus size: 12
31797931 AAAGAAATTG
31797941 AAAGAAAAC-AA
1 AAAGAAAACGAA
31797952 AAAGAAAACGAA
1 AAAGAAAACGAA
* *
31797964 GAAGAAAAAGAA
1 AAAGAAAACGAA
* *
31797976 ATTACAAAA-GAA
1 A-AAGAAAACGAA
*
31797988 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
31798000 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
31798012 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
31798026 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
31798039 AAAGAAAA
1 AAAGAAAA
31798047 AGCGAAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
11 15 0.20
12 31 0.42
13 16 0.22
14 10 0.14
15 2 0.03
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:31797974 original size:6 final size:6
Alignment explanation
Indices: 31797941--31798048 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
31797931 AAAGAAATTG
* * * * *
31797941 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTA-CA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
** ** * * *
31797988 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
31798039 AAAGAA AAAG
1 AAAGAA AAAG
31798049 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
5 4 0.05
6 57 0.78
7 8 0.11
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:31798002 original size:18 final size:18
Alignment explanation
Indices: 31797945--31798003 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
31797935 AAATTGAAAG
* *
31797945 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
31797963 AGAAGAAAAAGAAAT-TA
1 AAAAGAAAAAGAAATCGA
31797980 CAAAAGAAAAAGAAATCGA
1 -AAAAGAAAAAGAAATCGA
31797999 AAAAG
1 AAAAG
31798004 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:31798030 original size:14 final size:13
Alignment explanation
Indices: 31798009--31798046 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31797999 AAAAGTGAGA
31798009 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31798021 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31798036 GAAAAAGAAAA
1 GAAAAAGAAAA
31798047 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:31798043 original size:13 final size:12
Alignment explanation
Indices: 31797927--31798046 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
31797917 AGAAAGAGAT
*
31797927 TGAAAAAGAAAT
1 TGAAAAAGAAAA
31797939 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
31797949 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
31797960 CGAAGAAGAAAA
1 TGAAAAAGAAAA
* * *
31797972 AGAAATTACAAAA
1 TGAAA-AAGAAAA
31797985 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
31797995 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
31798009 -GAAAAAGAAAA
1 TGAAAAAGAAAA
31798020 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
31798034 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
31798047 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 11 0.13
12 33 0.40
13 15 0.18
14 12 0.14
15 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:31798083 original size:12 final size:12
Alignment explanation
Indices: 31798052--31798083 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31798042 GAAAAAGCGA
*
31798052 AAAAAGAATTTG
1 AAAAAGAGTTTG
31798064 AAAAAGAGTTTG
1 AAAAAGAGTTTG
31798076 AAAAAGAG
1 AAAAAGAG
31798084 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:31799749 original size:10 final size:10
Alignment explanation
Indices: 31799733--31799790 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
31799723 CAACTCCGAC
31799733 CAGCTCAATT
1 CAGCTCAATT
* *
31799743 GAGCTCATTT
1 CAGCTCAATT
31799753 CAGCTCAA-T
1 CAGCTCAATT
31799762 CGAGCTCAATT
1 C-AGCTCAATT
*
31799773 TAGCTACAATT
1 CAGCT-CAATT
31799784 CAGCTCA
1 CAGCTCA
31799791 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:31799756 original size:20 final size:20
Alignment explanation
Indices: 31799733--31799793 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
31799723 CAACTCCGAC
31799733 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
31799753 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
31799774 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
31799794 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:31804620 original size:45 final size:45
Alignment explanation
Indices: 31804556--31804786 Score: 374
Period size: 45 Copynumber: 5.1 Consensus size: 45
31804546 TGAAATTAAG
*
31804556 GAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTGAA
1 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAA
*
31804601 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAG
1 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAA
*
31804646 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAG
1 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAA
31804691 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTT-AA
1 GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAA
* * * * *
31804735 GGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTGAG
1 -GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAA
31804781 GAAGCA
1 GAAGCA
31804787 CCATGGCTGA
Statistics
Matches: 176, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 1 0.01
45 174 0.99
46 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
GAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAA
Found at i:31808350 original size:4 final size:4
Alignment explanation
Indices: 31808332--31808365 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
31808322 TATAAAAATT
31808332 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
31808366 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:31818291 original size:13 final size:12
Alignment explanation
Indices: 31818260--31818314 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
31818250 AATGTGAAAC
*
31818260 AAAAGAAATTGA
1 AAAAGAAGTTGA
31818272 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
31818284 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
31818296 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
31818308 AAAAGAA
1 AAAAGAA
31818315 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:31820186 original size:14 final size:16
Alignment explanation
Indices: 31820167--31820198 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
31820157 CTGTTTTCGA
31820167 TTTCTTT-CTT-TACT
1 TTTCTTTGCTTATACT
31820181 TTTCTTTGCTTATACT
1 TTTCTTTGCTTATACT
31820197 TT
1 TT
31820199 GCCGATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTCTTTGCTTATACT
Found at i:31825820 original size:20 final size:20
Alignment explanation
Indices: 31825797--31825843 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31825787 GGGTTAAGAT
*
31825797 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31825817 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31825837 TGAGCTG
1 TGAGCTG
31825844 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31827557 original size:48 final size:48
Alignment explanation
Indices: 31827502--31827607 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31827492 TTGTCTTTTC
*
31827502 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31827550 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31827598 TTTCTTTTTC
1 TTTCTTTTTC
31827608 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Done.