Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004168.1 Hibiscus syriacus cultivar Beakdansim tig00009114_pilon, whole genome shotgun sequence
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: 252520
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:817 original size:2 final size:2
Alignment explanation
Indices: 810--847 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
800 TACTGGATTA
810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
848 GACTTTAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3142 original size:30 final size:30
Alignment explanation
Indices: 3085--3164 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
3075 AACATATGTA
* * *
3085 ACTGTCCATATG-CTCG-GACATAGGTAAT
1 ACTGTCCATATGTCTCGAAAGACAGGTAAT
3113 ACTGTCCATATGTCTCGAAAGACAGGTAAT
1 ACTGTCCATATGTCTCGAAAGACAGGTAAT
* *
3143 ACTATCCATATGTCTTGAAAGA
1 ACTGTCCATATGTCTCGAAAGA
3165 AATAGGTACC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 12 0.27
29 4 0.09
30 29 0.64
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (30 bp):
ACTGTCCATATGTCTCGAAAGACAGGTAAT
Found at i:4337 original size:20 final size:20
Alignment explanation
Indices: 4312--4385 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
4302 ATTTAAAGTA
4312 GGTATCGGTACCCTCTATAG
1 GGTATCGGTACCCTCTATAG
*
4332 GGTATCGGTACATCCT-TAACTGG
1 GGTATCGGTAC--CCTCT-A-TAG
*
4355 GGTATCGATACCCTCTATAG
1 GGTATCGGTACCCTCTATAG
*
4375 GGTATCAGTAC
1 GGTATCGGTAC
4386 ATCCTTAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 22 0.50
21 5 0.11
22 5 0.11
23 12 0.27
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (20 bp):
GGTATCGGTACCCTCTATAG
Found at i:4361 original size:23 final size:23
Alignment explanation
Indices: 4331--4408 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
4321 ACCCTCTATA
4331 GGGTATCGGTACATCCTTAACTG
1 GGGTATCGGTACATCCTTAACTG
* *
4354 GGGTATCGATAC--CCTCT-A-TA
1 GGGTATCGGTACATCCT-TAACTG
*
4374 GGGTATCAGTACATCCTTAACTG
1 GGGTATCGGTACATCCTTAACTG
4397 GGGTATCGGTAC
1 GGGTATCGGTAC
4409 CCACCCCTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 11 0.25
21 5 0.11
22 5 0.11
23 23 0.52
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
GGGTATCGGTACATCCTTAACTG
Found at i:4373 original size:43 final size:43
Alignment explanation
Indices: 4312--4410 Score: 180
Period size: 43 Copynumber: 2.3 Consensus size: 43
4302 ATTTAAAGTA
*
4312 GGTATCGGTACCCTCTATAGGGTATCGGTACATCCTTAACTGG
1 GGTATCGGTACCCTCTATAGGGTATCAGTACATCCTTAACTGG
*
4355 GGTATCGATACCCTCTATAGGGTATCAGTACATCCTTAACTGG
1 GGTATCGGTACCCTCTATAGGGTATCAGTACATCCTTAACTGG
4398 GGTATCGGTACCC
1 GGTATCGGTACCC
4411 ACCCCTAGGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (43 bp):
GGTATCGGTACCCTCTATAGGGTATCAGTACATCCTTAACTGG
Found at i:4422 original size:43 final size:43
Alignment explanation
Indices: 4312--4424 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
4302 ATTTAAAGTA
* * * *
4312 GGTATCGGTACCCTCTATAGGGTATCGGTACATCCTTAACTGG
1 GGTATCGATACCCCCCATAGGGTATCAGTACATCCTTAACTGG
* *
4355 GGTATCGATACCCTCTATAGGGTATCAGTACATCCTTAACTGG
1 GGTATCGATACCCCCCATAGGGTATCAGTACATCCTTAACTGG
* *
4398 GGTATCGGTACCCACCCCTA-GGTATCA
1 GGTATCGATACCC-CCCATAGGGTATCA
4425 TTACTCTAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 60 0.95
44 3 0.05
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (43 bp):
GGTATCGATACCCCCCATAGGGTATCAGTACATCCTTAACTGG
Found at i:5870 original size:21 final size:21
Alignment explanation
Indices: 5844--5884 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5834 ATTTATAATA
5844 GAGAGTATCGATACTAAGGGG
1 GAGAGTATCGATACTAAGGGG
*
5865 GAGAGTATCGATACTGAGGG
1 GAGAGTATCGATACTAAGGG
5885 CACCTGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.39, T:0.20
Consensus pattern (21 bp):
GAGAGTATCGATACTAAGGGG
Found at i:7088 original size:32 final size:32
Alignment explanation
Indices: 7052--7167 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 32
7042 ATACTAGTAG
*
7052 AGTGTTGCATTCAGATAATTCACAATAGTATC
1 AGTGTTGCATTCAGATAATGCACAATAGTATC
* *
7084 AGTGTTACATTCAGATAATGCACAACAGTATC
1 AGTGTTGCATTCAGATAATGCACAATAGTATC
* *
7116 AGTTTTGCATTAAGATAATGCACAATAG-AGTC
1 AGTGTTGCATTCAGATAATGCACAATAGTA-TC
* *
7148 AATATTGCATTCAGATAATG
1 AGTGTTGCATTCAGATAATG
7168 GACATCAGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 1 0.01
32 72 0.99
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (32 bp):
AGTGTTGCATTCAGATAATGCACAATAGTATC
Found at i:7181 original size:32 final size:32
Alignment explanation
Indices: 7054--7204 Score: 146
Period size: 32 Copynumber: 4.7 Consensus size: 32
7044 ACTAGTAGAG
* *
7054 TGTTGCATTCAGATAATTCACAATAGTATCAG
1 TGTTGCATTCAGATAATGCACAATAGTATCAA
* * *
7086 TGTTACATTCAGATAATGCACAACAGTATCAG
1 TGTTGCATTCAGATAATGCACAATAGTATCAA
* *
7118 TTTTGCATTAAGATAATGCACAATAG-AGTCAA
1 TGTTGCATTCAGATAATGCACAATAGTA-TCAA
* * *
7150 TATTGCATTCAGATAATGGAC-ATCAGTGTCAA
1 TGTTGCATTCAGATAATGCACAAT-AGTATCAA
* *
7182 TGTTGTATGT-AGATAATGTACAA
1 TGTTGCAT-TCAGATAATGCACAA
7205 CAATTACAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
31 3 0.03
32 94 0.95
33 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTTGCATTCAGATAATGCACAATAGTATCAA
Found at i:7196 original size:64 final size:64
Alignment explanation
Indices: 7054--7204 Score: 162
Period size: 64 Copynumber: 2.4 Consensus size: 64
7044 ACTAGTAGAG
* * * * *
7054 TGTTGCATTCAGATAATTCACAATAGTATCAGTGTTACATTCAGATAATGCACAACAGTATCAG
1 TGTTGCATTAAGATAATGCACAATAGTATCAATATTACATTCAGATAATGCACAACAGTATCAA
* * * * *
7118 TTTTGCATTAAGATAATGCACAATAG-AGTCAATATTGCATTCAGATAATGGACATCAGTGTCAA
1 TGTTGCATTAAGATAATGCACAATAGTA-TCAATATTACATTCAGATAATGCACAACAGTATCAA
* *
7182 TGTTGTATGT-AGATAATGTACAA
1 TGTTGCAT-TAAGATAATGCACAA
7205 CAATTACAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 70 0.97
65 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (64 bp):
TGTTGCATTAAGATAATGCACAATAGTATCAATATTACATTCAGATAATGCACAACAGTATCAA
Found at i:9476 original size:34 final size:34
Alignment explanation
Indices: 9412--9476 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
9402 ATCCAATCAG
*
9412 ATATCTTTTAATATTTAAATTTAAATAGATAATA
1 ATATCTTTTAATATTAAAATTTAAATAGATAATA
9446 ATATCTTTTAAT-TTGAAATATTTAAA-AGATA
1 ATATCTTTTAATATT-AAA-ATTTAAATAGATA
9477 TATATACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 2 0.07
34 19 0.68
35 7 0.25
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (34 bp):
ATATCTTTTAATATTAAAATTTAAATAGATAATA
Found at i:10435 original size:16 final size:16
Alignment explanation
Indices: 10414--10445 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10404 TTAATAATTA
10414 CTATTAATTTATTAAT
1 CTATTAATTTATTAAT
*
10430 CTATTAATTTTTTAAT
1 CTATTAATTTATTAAT
10446 AAACAACGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
CTATTAATTTATTAAT
Found at i:18618 original size:2 final size:2
Alignment explanation
Indices: 18611--18673 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
18601 ATTTCACATA
18611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18653 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
18674 ATTAAGATTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19063 original size:45 final size:44
Alignment explanation
Indices: 19003--19094 Score: 175
Period size: 45 Copynumber: 2.1 Consensus size: 44
18993 CTTAACAACA
19003 AAATAGTATTATAATATTATAAATATTTATAATTAAATTTAAAC
1 AAATAGTATTATAATATTATAAATATTTATAATTAAATTTAAAC
19047 AAATAGTATATATAATATTATAAATATTTATAATTAAATTTAAAC
1 AAATAGTAT-TATAATATTATAAATATTTATAATTAAATTTAAAC
19092 AAA
1 AAA
19095 AACTTAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 9 0.19
45 38 0.81
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (44 bp):
AAATAGTATTATAATATTATAAATATTTATAATTAAATTTAAAC
Found at i:21626 original size:15 final size:15
Alignment explanation
Indices: 21606--21634 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21596 TCAAAAGCAC
21606 CATTCATCTTTTGAG
1 CATTCATCTTTTGAG
21621 CATTCATCTTTTGA
1 CATTCATCTTTTGA
21635 CAGAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (15 bp):
CATTCATCTTTTGAG
Found at i:21704 original size:14 final size:14
Alignment explanation
Indices: 21685--21743 Score: 82
Period size: 14 Copynumber: 4.1 Consensus size: 14
21675 GTAATTGGTT
*
21685 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
21699 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
**
21713 TTACTGGAATTTGAA
1 TT-CTGGAAAATGAA
21728 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
21742 TT
1 TT
21744 ACATTTCCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 27 0.69
15 12 0.31
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:21729 original size:29 final size:29
Alignment explanation
Indices: 21687--21745 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
21677 AATTGGTTTT
21687 CTGGAAATTGAATTCTGGAAAATGAATTA
1 CTGGAAATTGAATTCTGGAAAATGAATTA
*
21716 CTGGAATTTGAATTCTGGAAAATGAATTA
1 CTGGAAATTGAATTCTGGAAAATGAATTA
21745 C
1 C
21746 ATTTCCGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (29 bp):
CTGGAAATTGAATTCTGGAAAATGAATTA
Found at i:21787 original size:14 final size:14
Alignment explanation
Indices: 21747--21778 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21737 ATGAATTACA
*
21747 TTTCCGGAAAACGT
1 TTTCCGGAAAATGT
21761 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
21775 TTTC
1 TTTC
21779 TGTAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:22039 original size:23 final size:23
Alignment explanation
Indices: 22011--22058 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
22001 AATAGTGTTA
22011 TATTATATTTTAAAAATATTAAT
1 TATTATATTTTAAAAATATTAAT
* *
22034 TATTATATTTTAAATATATTTAT
1 TATTATATTTTAAAAATATTAAT
22057 TA
1 TA
22059 AAATATTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATATTTTAAAAATATTAAT
Found at i:22064 original size:23 final size:23
Alignment explanation
Indices: 22015--22065 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
22005 GTGTTATATT
**
22015 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* *
22038 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
22061 ATATT
1 ATATT
22066 ATCAGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:22114 original size:39 final size:37
Alignment explanation
Indices: 22027--22125 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 37
22017 ATTTTAAAAA
* * *
22027 TATTAATTATTATATTTTAAATATATTTATTAAAATAT
1 TATTAATTATTATA-TTTAAATAAATATATAAAAATAT
*
22065 TATCAGATTATTATA-TTAATATTAAATATATAAATAATAT
1 TATTA-ATTATTATATTTAA-A-TAAATATATAAA-AATAT
22105 TATTAATTATTAATAATTTAA
1 TATTAATTATT-AT-ATTTAA
22126 TAATATTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
37 4 0.08
38 5 0.10
39 24 0.49
40 11 0.22
41 1 0.02
42 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (37 bp):
TATTAATTATTATATTTAAATAAATATATAAAAATAT
Found at i:22119 original size:27 final size:27
Alignment explanation
Indices: 22078--22158 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
22068 CAGATTATTA
22078 TATTAATATTAAAT-ATATAAATAATAT
1 TATTAATATTAAATAAT-TAAATAATAT
*
22105 TATTAATTATT-AATAATTTAATAATAT
1 TATTAA-TATTAAATAATTAAATAATAT
* ** *
22132 TCTTTCTATGAAATTAA-TAAATAATAT
1 TATTAATATTAAA-TAATTAAATAATAT
22159 AAATTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
26 3 0.07
27 32 0.73
28 9 0.20
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTAATATTAAATAATTAAATAATAT
Found at i:22121 original size:19 final size:18
Alignment explanation
Indices: 22048--22121 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
22038 ATATTTTAAA
*
22048 TATATTTATTAA-AATAT
1 TATAATTATTAATAATAT
22065 TATCAGATTATTATATTAATAT
1 TAT-A-ATTATTA-A-TAATAT
*
22087 TA-AATATATAAATAATAT
1 TATAAT-TATTAATAATAT
22105 TATTAATTATTAATAAT
1 TA-TAATTATTAATAAT
22122 TTAATAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 18 0.39
20 9 0.20
22 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TATAATTATTAATAATAT
Found at i:22230 original size:23 final size:22
Alignment explanation
Indices: 22200--22276 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
22190 AAAATAAAAA
*
22200 TATAATATCTTATATTATATTAT
1 TATAATAT-TTAAATTATATTAT
* *
22223 TATAATATAATT-GATTATTTTAT
1 TATAATAT--TTAAATTATATTAT
* *
22246 TATAATATTTAAAATATAATAT
1 TATAATATTTAAATTATATTAT
*
22268 TATATTATT
1 TATAATATT
22277 AGAAATATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.05
22 15 0.34
23 25 0.57
24 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (22 bp):
TATAATATTTAAATTATATTAT
Found at i:22254 original size:34 final size:33
Alignment explanation
Indices: 22174--22296 Score: 94
Period size: 34 Copynumber: 3.7 Consensus size: 33
22164 TTATTAATAA
* *
22174 TTTATTAT-ATATTATTAAAATAAAAATATAATAT
1 TTTATTATAATATTATTAAAAT-ATAAT-TATTAT
* * *
22208 CTTA-TATTATATTATTATAATATAATTGATTAT
1 TTTATTATAATATTATTAAAATATAATT-ATTAT
22241 TTTATTATAATA-T-TTAAAATATAA-TATTAT
1 TTTATTATAATATTATTAAAATATAATTATTAT
* * *
22271 ATTATTAGAAATATTAATAAATATAT
1 TTTATTA-TAATATTATTAAA-ATAT
22297 TTTAAATATT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
30 11 0.15
31 5 0.07
32 12 0.17
33 19 0.26
34 25 0.35
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (33 bp):
TTTATTATAATATTATTAAAATATAATTATTAT
Found at i:22271 original size:22 final size:22
Alignment explanation
Indices: 22243--22305 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
22233 TTGATTATTT
22243 TATTATAATATTTAAAATATAA
1 TATTATAATATTTAAAATATAA
*
22265 TATTATATTA-TTAGAAATATTAA
1 TATTATAATATTTA-AAATA-TAA
* *
22288 TA-AAT-ATATTTTAAATAT
1 TATTATAATATTTAAAATAT
22306 TTTAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 18 0.53
23 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATAATATTTAAAATATAA
Found at i:25000 original size:17 final size:17
Alignment explanation
Indices: 24978--25034 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
24968 AACGGTCAAC
24978 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
24995 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
25012 GGTCAACGGTCGGGTTG
1 GGTCAACGGTCGGGTCG
25029 GGTCAA
1 GGTCAA
25035 ACCGGTCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:25005 original size:7 final size:7
Alignment explanation
Indices: 24937--24988 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
24927 GGTCAAAGGA
24937 GGTCAAC
1 GGTCAAC
24944 GGTC-AC
1 GGTCAAC
24950 GGT-ATAC
1 GGTCA-AC
24957 GGTCAAC
1 GGTCAAC
*
24964 GGGCAAC
1 GGTCAAC
24971 GGTCAAC
1 GGTCAAC
24978 GGTCAAC
1 GGTCAAC
24985 GGTC
1 GGTC
24989 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
6 5 0.12
7 34 0.85
8 1 0.03
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:25043 original size:9 final size:9
Alignment explanation
Indices: 25029--25097 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
25019 GGTCGGGTTG
25029 GGTCAAACC
1 GGTCAAACC
25038 GGTCAAACC
1 GGTCAAACC
*
25047 GGTTCAGACC
1 GG-TCAAACC
*
25057 GGTCAGACC
1 GGTCAAACC
25066 GGT-ATGAACC
1 GGTCA--AACC
* *
25076 GGTCGATACA
1 GGTC-AAACC
25086 GGTCAAACC
1 GGTCAAACC
25095 GGT
1 GGT
25098 TTTCCAGCTG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
8 1 0.02
9 27 0.55
10 20 0.41
12 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:25076 original size:19 final size:18
Alignment explanation
Indices: 25034--25079 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
25024 GGTTGGGTCA
25034 AACCGGTCAAACCGGTTC
1 AACCGGTCAAACCGGTTC
* *
25052 AGACCGGTCAGACCGGTATG
1 A-ACCGGTCAAACCGGT-TC
25072 AACCGGTC
1 AACCGGTC
25080 GATACAGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.88
20 2 0.08
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.15
Consensus pattern (18 bp):
AACCGGTCAAACCGGTTC
Found at i:32182 original size:9 final size:10
Alignment explanation
Indices: 32159--32191 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
32149 CATGGTTAAC
*
32159 GGTCGGGTCG
1 GGTCGGGTTG
32169 GGTC-GGTTG
1 GGTCGGGTTG
32178 GGTCGGGTTG
1 GGTCGGGTTG
32188 GGTC
1 GGTC
32192 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.00, C:0.15, G:0.58, T:0.27
Consensus pattern (10 bp):
GGTCGGGTTG
Found at i:32225 original size:10 final size:9
Alignment explanation
Indices: 32188--32248 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
32178 GGTCGGGTTG
*
32188 GGTCAGACC
1 GGTCAAACC
32197 GGTCAAACC
1 GGTCAAACC
*
32206 GGTTCGAACC
1 GG-TCAAACC
32216 GGTCAAAACC
1 GGTC-AAACC
*
32226 GATTCAAAACC
1 G-GTC-AAACC
32237 GGTCAAACC
1 GGTCAAACC
32246 GGT
1 GGT
32249 TTTCCAGCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 20 0.45
10 15 0.34
11 9 0.20
ACGTcount: A:0.31, C:0.30, G:0.25, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:32238 original size:21 final size:20
Alignment explanation
Indices: 32194--32243 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
32184 GTTGGGTCAG
* *
32194 ACCGGTC-AAACCGGTTCGA
1 ACCGGTCAAAACCGATTCAA
32213 ACCGGTCAAAACCGATTCAAA
1 ACCGGTCAAAACCGATTC-AA
32234 ACCGGTCAAA
1 ACCGGTCAAA
32244 CCGGTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 7 0.26
20 9 0.33
21 11 0.41
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (20 bp):
ACCGGTCAAAACCGATTCAA
Found at i:34180 original size:237 final size:236
Alignment explanation
Indices: 33766--34241 Score: 844
Period size: 237 Copynumber: 2.0 Consensus size: 236
33756 GCGGGGTGAA
* * **
33766 TGTTAAGAATAGAGTGGTGCCAGTTGGAGAGATTGCCAGCTGGAGTTGTTAGTTACTAACTGTTT
1 TGTTAAGAATAGAGTGGTGCCAGCTAGAGAGATTGCCAGCTGGAGTTGTTAGTTACTAACCATTT
*
33831 CTATTAAGGTTAGTTATTCAGTTAAGCCAGCTTTCTATTGGGTTGAACTTATAGTGTTAACCCGT
66 CTATTAAGGTTAGTTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCGT
*
33896 TAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCTA
131 TAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCAA
33961 CATTTTCTTTCCTTTCACCTCTCTTTACTTCTGGTTTAAAC
196 CATTTTCTTTCCTTTCACCTCTCTTTACTTCTGGTTTAAAC
* * *
34002 TGTTAAGAATAGAGTGGTGTCAGCTAGAGGGATTGTCAGCTGGAGTTGTTAGTTACTAACCATTT
1 TGTTAAGAATAGAGTGGTGCCAGCTAGAGAGATTGCCAGCTGGAGTTGTTAGTTACTAACCATTT
34067 CTATTAAGGTTAGTTTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCG
66 CTATTAAGGTTAG-TTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCG
*
34132 TTAAGAAAAGCATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCA
130 TTAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCA
*
34197 ACATTTTCTTTCCTTTCACTTCTCTTTACTTCTGGTTTAAAC
195 ACATTTTCTTTCCTTTCACCTCTCTTTACTTCTGGTTTAAAC
34239 TGT
1 TGT
34242 GTAGTTAGCA
Statistics
Matches: 228, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
236 71 0.31
237 157 0.69
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (236 bp):
TGTTAAGAATAGAGTGGTGCCAGCTAGAGAGATTGCCAGCTGGAGTTGTTAGTTACTAACCATTT
CTATTAAGGTTAGTTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCGT
TAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCAA
CATTTTCTTTCCTTTCACCTCTCTTTACTTCTGGTTTAAAC
Found at i:56160 original size:19 final size:19
Alignment explanation
Indices: 56136--56177 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
56126 ATAGTCTGAT
56136 GATTATTTTATGATTTGAA
1 GATTATTTTATGATTTGAA
56155 GATTATTTTATGATTTGAA
1 GATTATTTTATGATTTGAA
56174 GATT
1 GATT
56178 CAATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (19 bp):
GATTATTTTATGATTTGAA
Found at i:60124 original size:21 final size:21
Alignment explanation
Indices: 60100--60154 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
60090 ATCATAAGAT
*
60100 AATATCATGTTATTGTTAAAA
1 AATATCATGTCATTGTTAAAA
60121 AATATCATGTCATTGTTAAAA
1 AATATCATGTCATTGTTAAAA
60142 AATATCATAGTCA
1 AATATCAT-GTCA
60155 ACAAGTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (21 bp):
AATATCATGTCATTGTTAAAA
Found at i:69113 original size:16 final size:16
Alignment explanation
Indices: 69073--69115 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 16
69063 CTCTCCCCTC
69073 AATCAATGTACCCTTG
1 AATCAATGTACCCTTG
69089 -A--AA--TACCCTTG
1 AATCAATGTACCCTTG
69100 AATCAATGTACCCTTG
1 AATCAATGTACCCTTG
69116 TAAACAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 10
0.69 0.00 0.31
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 2 0.09
14 2 0.09
15 1 0.05
16 8 0.36
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (16 bp):
AATCAATGTACCCTTG
Found at i:76113 original size:18 final size:18
Alignment explanation
Indices: 76068--76114 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
76058 CACATCAGTA
76068 ATTT-TTAA-AAA-AATT
1 ATTTATTAATAAATAATT
76083 ATTTATTAATAAATAATT
1 ATTTATTAATAAATAATT
* *
76101 ATTTTTTACTAAAT
1 ATTTATTAATAAAT
76115 TAAAAACAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 3 0.11
18 16 0.59
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTAATAAATAATT
Found at i:76790 original size:413 final size:414
Alignment explanation
Indices: 75787--77431 Score: 2463
Period size: 413 Copynumber: 4.0 Consensus size: 414
75777 AAGAGAGACA
* * * * *
75787 TAATGCAAACAAATACCCCCAACATTTGATAATATATGCAATTTTGTCCCAATTATTTTTTTTTG
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
* * * *
75852 AAACATTTGACCCCCACGTTTCATTTTGGATCAAAAAGCACCCTCGTTAGATGAAAACCGTTAGT
66 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTAGATGAAAAACGTTAGT
* * * *
75917 CAACTGACGGTCAACGTCTGAAGTTGACTCAACAAGAACATGTGGAGGGAGATATTGACGTGACA
131 CAACTGACGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGCA
*
75982 TGTCCATATCATAGTAGATTATGACGTGACAGAT-CACGTAGACTAAATGCTGACATGGCATGTC
196 TGTCCATATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGTC
* * *
76046 CACATGTGATGGCACATCAGTAA-TTTTTAAAAAAATTATTTATTAATAAATAATTATTTTTTAC
261 CACGTGTGATGCCACATCAGTAATTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTTAC
* * * *
76110 TAAATTAAAAACAGA-CAATCAGATGCTGTCACATGACATATAGATTTTTTTATTAAATTGAGAT
326 TAAATTAATAACA-ATCAATCAGATGTTGTCACATGACACAT-GAATTTTTTATTAAATTGAGAT
*
76174 AGGAGGGATTAAACATCCACAAATTT
389 AGGAGGGATTAAACCTCCACAAATTT
*
76200 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTA-TAATTTTTTTTG
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
* *
76264 GAACATTTGA-CCCCATGTTTCATTTTGGGTCAAAAAAACACCCTCGTTAGATGAAAAATGTTAG
66 GAACATTTGACCCCCACGTTTCATTTTGGGTC-AAAAAACACCCTCGTTAGATGAAAAACGTTAG
76328 TCAACTGACGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGC
130 TCAACTGACGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGC
* * * * *
76393 ATGTTCATATTACAGTAGATGATGACGTGACAGATCCACATAGACTAAATGTTGACATGGCATGT
195 ATGTCCATATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGT
*
76458 CCACGTGTGATGCCACGTCAGTAATTTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTT
260 CCACGTGTGATGCCACATCAGTAA-TTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTT
76523 ACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATGAATTTTTTATTAAATTGAGAT
324 ACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATGAATTTTTTATTAAATTGAGAT
*
76588 AGGAGGGATTAAACCTCCAAAAATTT
389 AGGAGGGATTAAACCTCCACAAATTT
* * * * * *
76614 TAATGCAAATAAATACTCCTAACGTTTGACAATATATACAATTTT-CCCCTAGTGTTGTTTTTTG
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
* *
76678 GAACATTTGA-CCCCACGTTTCATTTTGGGTCAAAAAACACCATCGTTGGATGAAAAACGTTAGT
66 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTAGATGAAAAACGTTAGT
* * * *
76742 CAACTGACCG-TCAACGTCTGAAGCTGACTCATCAAGAACATGTGGAGGGAGATGCTAATGTGGC
131 CAACTGA-CGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGC
* *
76806 ATGTCCACATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATACTGACATGGCATGT
195 ATGTCCATATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGT
* * * * *
76871 TCACGTGTGATGCCACGTC-GACAATTTTTTTTAAAAAATTAATTAATAATAAATAATTA-TTTT
260 CCACGTGTGATGCCACATCAG-TAA-TTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTT
* * * * *
76934 TACTAAATTAATAACAGTTAATCAGATATTGTCACATGGCACATGGATTTTTTATTAAATTGAGA
323 TACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATGAATTTTTTATTAAATTGAGA
76999 TAGGAGGGATTAAACCTCCACAAATTT
388 TAGGAGGGATTAAACCTCCACAAATTT
* * * *
77026 TAATGCAAATAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCTTATTGTTTTTTTTTT
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
* * * **
77091 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAGCACTCTCGTTGGATGAAAATTGTTAGT
66 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTAGATGAAAAACGTTAGT
* * *
77156 CAACTGACGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGAAGATGCTGATGTGGCA
131 CAACTGACGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGCA
* * *
77221 TGTCCCTATTATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGGCATGGCATGTC
196 TGTCCATATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGTC
77286 CACGTGTGATGCCACATCAGTAATTTTTTAAAAAAA--A--TAATAATAAATAATTATTTTTTAC
261 CACGTGTGATGCCACATCAGTAATTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTTAC
* * *
77347 TAAATTAATAACAACCAATCAGATGTTGTCACACGACACATGTATTTTTTATTAAATTGAGATAG
326 TAAATTAATAACAATCAATCAGATGTTGTCACATGACACATGAATTTTTTATTAAATTGAGATAG
77412 GAGGGATTAAACCTCCACAA
391 GAGGGATTAAACCTCCACAA
77432 TTGAACCTCG
Statistics
Matches: 1126, Mismatches: 93, Indels: 29
0.90 0.07 0.02
Matches are distributed among these distances:
409 16 0.01
410 85 0.08
411 20 0.02
412 275 0.24
413 338 0.30
414 315 0.28
415 77 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (414 bp):
TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTAGATGAAAAACGTTAGT
CAACTGACGATCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGCA
TGTCCATATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGTC
CACGTGTGATGCCACATCAGTAATTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTTAC
TAAATTAATAACAATCAATCAGATGTTGTCACATGACACATGAATTTTTTATTAAATTGAGATAG
GAGGGATTAAACCTCCACAAATTT
Found at i:80219 original size:18 final size:18
Alignment explanation
Indices: 80193--80242 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
80183 TTGAAATCTC
* *
80193 AACTTAAAGGAGATAAAT
1 AACTCAAAGAAGATAAAT
80211 AACTCAAAGTAA-ATAAAT
1 AACTCAAAG-AAGATAAAT
80229 AACTCAAAGAAGAT
1 AACTCAAAGAAGAT
80243 GAACTCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 25 0.89
19 1 0.04
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (18 bp):
AACTCAAAGAAGATAAAT
Found at i:91611 original size:23 final size:25
Alignment explanation
Indices: 91584--91638 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
91574 TATGCAGAAT
91584 TAAATA-TAAATATAAAAGATA-AA
1 TAAATATTAAATATAAAAGATATAA
** *
91607 TAAATTATTGTATATAGAAGATATAA
1 TAAA-TATTAAATATAAAAGATATAA
91633 TAAATA
1 TAAATA
91639 ATATATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 14 0.54
26 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (25 bp):
TAAATATTAAATATAAAAGATATAA
Found at i:91895 original size:31 final size:32
Alignment explanation
Indices: 91819--91898 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
91809 TTAAATGTTG
*
91819 ATGTAAAATTTTAATATATTTTTACATAAATT
1 ATGTAAAATTTTAATATATTTTAACATAAATT
91851 ATGTAAAATTTTAATATATTTTAACATAAATT
1 ATGTAAAATTTTAATATATTTTAACATAAATT
91883 ATGTAAAA-TTTAATAT
1 ATGTAAAATTTTAATAT
91899 TAATTAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 8 0.17
32 39 0.83
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (32 bp):
ATGTAAAATTTTAATATATTTTAACATAAATT
Found at i:92185 original size:20 final size:20
Alignment explanation
Indices: 92149--92186 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92139 ATCATATTCC
**
92149 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
92169 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
92187 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:93531 original size:5 final size:6
Alignment explanation
Indices: 93505--93529 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
93495 TAAGGCCTGT
93505 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
93530 TATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:94461 original size:20 final size:20
Alignment explanation
Indices: 94422--94461 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
94412 GGATAAAGCG
* *
94422 TTATTTAAAATATTATTTTT
1 TTATTAAAAATATTAATTTT
*
94442 TTATTAAAAATGTTAATTTT
1 TTATTAAAAATATTAATTTT
94462 ACTATCTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATTAAAAATATTAATTTT
Found at i:94936 original size:16 final size:17
Alignment explanation
Indices: 94915--94948 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
94905 TTTTGATTTA
94915 TTTTAA-TATTTAAAAT
1 TTTTAATTATTTAAAAT
*
94931 TTTTAATTTTTTAAAAT
1 TTTTAATTATTTAAAAT
94948 T
1 T
94949 AGATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTATTTAAAAT
Found at i:98199 original size:14 final size:14
Alignment explanation
Indices: 98180--98231 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
98170 AATAAGAGAA
98180 AATAAAAAAATATT
1 AATAAAAAAATATT
*
98194 AATAAAATAATAAATT
1 AATAAAA-AA-ATATT
98210 AA-AAAAATAATATT
1 AATAAAAA-AATATT
98224 AATAAAAA
1 AATAAAAA
98232 TAAAAATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 14 0.44
15 12 0.38
16 6 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAAAAAATATT
Found at i:98216 original size:16 final size:16
Alignment explanation
Indices: 98191--98238 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
98181 ATAAAAAAAT
*
98191 ATTAATAAAATAATAA
1 ATTAAAAAAATAATAA
98207 ATTAAAAAAATAAT--
1 ATTAAAAAAATAATAA
98221 ATTAATAAAAATAA-AA
1 ATTAA-AAAAATAATAA
98237 AT
1 AT
98239 CATTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.18
15 8 0.29
16 15 0.54
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTAAAAAAATAATAA
Found at i:98282 original size:38 final size:38
Alignment explanation
Indices: 98233--98421 Score: 124
Period size: 38 Copynumber: 5.3 Consensus size: 38
98223 TAATAAAAAT
* * * *
98233 AAAAATCATTTTTAAAACTATATATTATATATGCT-TTT
1 AAAAATTATTTTTAAAACTATATAATATATAT-ATATTC
* * *
98271 GAAAATTATTTTCAAAACCATATAATATATATATATTC
1 AAAAATTATTTTTAAAACTATATAATATATATATATTC
* *
98309 AAAAATTGTCTTTAAAACTATATAATATATAT-T-TTC
1 AAAAATTATTTTTAAAACTATATAATATATATATATTC
* *
98345 -AAAATTA----T---A-TAT-T-ATATATATTTTTTC
1 AAAAATTATTTTTAAAACTATATAATATATATATATTC
*
98372 -AAAA-TATTTTCAAAAACTATATAATATATATATATTTC
1 AAAAATTATTTT-TAAAACTATATAATATATATATA-TTC
98410 AAAAA-TATTTTT
1 AAAAATTATTTTT
98422 TTTAAAACTC
Statistics
Matches: 118, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
25 8 0.07
26 4 0.03
27 10 0.08
28 1 0.01
31 1 0.01
34 1 0.01
35 9 0.08
36 4 0.03
37 11 0.09
38 59 0.50
39 10 0.08
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (38 bp):
AAAAATTATTTTTAAAACTATATAATATATATATATTC
Found at i:98353 original size:23 final size:24
Alignment explanation
Indices: 98322--98368 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
98312 AATTGTCTTT
98322 AAAACTATATA-ATATATATTTTC
1 AAAACTATATATATATATATTTTC
*
98345 AAAATTATATATTATATATATTTT
1 AAAACTATATA-TATATATATTTT
98369 TTCAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
AAAACTATATATATATATATTTTC
Found at i:98401 original size:39 final size:38
Alignment explanation
Indices: 98337--98420 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 38
98327 TATATAATAT
* * *
98337 ATATTTTCAAAATTATATATTATATATATTTTTTC-AAA
1 ATATTTTCAAAACTATATAATATATATA-TATTTCAAAA
98375 ATATTTTCAAAAACTATATAATATATATATATTTCAAAA
1 ATATTTTC-AAAACTATATAATATATATATATTTCAAAA
98414 ATATTTT
1 ATATTTT
98421 TTTTAAAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
38 13 0.32
39 28 0.68
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (38 bp):
ATATTTTCAAAACTATATAATATATATATATTTCAAAA
Found at i:101652 original size:2 final size:2
Alignment explanation
Indices: 101645--101672 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
101635 AAGTTAAACA
101645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101673 TAAATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102602 original size:12 final size:12
Alignment explanation
Indices: 102582--102619 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
102572 TTTATAAATA
102582 CCTCGCATCTCT
1 CCTCGCATCTCT
*
102594 CCTCACA--TCT
1 CCTCGCATCTCT
102604 CCTCGCATCTCT
1 CCTCGCATCTCT
102616 CCTC
1 CCTC
102620 TCTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.11, C:0.53, G:0.05, T:0.32
Consensus pattern (12 bp):
CCTCGCATCTCT
Found at i:106122 original size:35 final size:34
Alignment explanation
Indices: 106037--106123 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
106027 ATTTGGTATT
*
106037 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
106071 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
106109 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
106124 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:106629 original size:18 final size:18
Alignment explanation
Indices: 106606--106640 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
106596 GGCGATGGCG
106606 GCATCATATATGGCTGCT
1 GCATCATATATGGCTGCT
106624 GCATCATATATGGCTGC
1 GCATCATATATGGCTGC
106641 GGTGGCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (18 bp):
GCATCATATATGGCTGCT
Found at i:108255 original size:111 final size:111
Alignment explanation
Indices: 108061--108393 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
108051 ATTACAAAAA
*
108061 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
108126 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
108172 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAGTAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
108237 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTATCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
108283 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
108348 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
108394 ATGATTTTCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:108535 original size:20 final size:20
Alignment explanation
Indices: 108512--108552 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
108502 AATATACCTT
* *
108512 AAAAATATAGAGTATTTGAG
1 AAAAATATAAAGAATTTGAG
*
108532 AAAAATTTAAAGAATTTGAG
1 AAAAATATAAAGAATTTGAG
108552 A
1 A
108553 GAATTTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (20 bp):
AAAAATATAAAGAATTTGAG
Found at i:110760 original size:41 final size:41
Alignment explanation
Indices: 110715--110796 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
110705 AAATTGAAAA
* *
110715 TAAATTAATAATTTAAAGACCTAATCAAGAAAAATACAAAT
1 TAAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
* *
110756 TAAATTATTAATCTAAAGACCAAATCAAGAAAAGTACAAAT
1 TAAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
110797 ATTGCACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (41 bp):
TAAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
Found at i:114880 original size:18 final size:18
Alignment explanation
Indices: 114857--114891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
114847 TTCCATCCGG
*
114857 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
114875 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
114892 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:116217 original size:18 final size:18
Alignment explanation
Indices: 116194--116234 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
116184 CAACGGTCAA
*
116194 CGGGTCGAGTCAATGGGT
1 CGGGTCGAGTCAACGGGT
*
116212 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
116230 CGGGT
1 CGGGT
116235 AAACGGGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.49, T:0.20
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:116224 original size:31 final size:31
Alignment explanation
Indices: 116188--116247 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
116178 GCCGGTCAAC
* *
116188 GGTCAACGGGTCGAGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
*
116219 GGTCAACGGGTCGGGTAAACGGGTCGGGT
1 GGTCAACGGGTCGAGTAAACGGGTCGGGT
116248 AAACGGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
Found at i:116258 original size:13 final size:13
Alignment explanation
Indices: 116212--116260 Score: 89
Period size: 13 Copynumber: 3.8 Consensus size: 13
116202 GTCAATGGGT
*
116212 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
116225 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
116238 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
116251 CGGGTCGGGT
1 CGGGTCGGGT
116261 CGGGTTGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.16, C:0.18, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:120061 original size:18 final size:18
Alignment explanation
Indices: 120038--120072 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
120028 TTCCATCCGG
*
120038 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
120056 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
120073 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:121405 original size:18 final size:18
Alignment explanation
Indices: 121382--121455 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 18
121372 AACGGGTCAA
* *
121382 CGGGTCGAGTCAATGGGT
1 CGGGTCGAGTAAACGGGT
*
121400 CGGGTCGGGTAAACGGGT
1 CGGGTCGAGTAAACGGGT
121418 C--G--G-GTAAACGGGT
1 CGGGTCGAGTAAACGGGT
*
121431 CGGGTCGGGTAAACGGGT
1 CGGGTCGAGTAAACGGGT
121449 CGGGTCG
1 CGGGTCG
121456 GGTTGTGACC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.23
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 33 0.69
ACGTcount: A:0.16, C:0.18, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCGAGTAAACGGGT
Found at i:121451 original size:31 final size:31
Alignment explanation
Indices: 121374--121453 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
121364 TCAACGACAA
* * * *
121374 CGGGTCAACGGGTCGAGTCAATGGGTCGGGT
1 CGGGTAAACGGGTCGGGTAAACGGGTCGGGT
121405 CGGGTAAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGTAAACGGGTCGGGT
121436 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
121454 CGGGTTGTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.17
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTAAACGGGTCGGGT
Found at i:121453 original size:13 final size:13
Alignment explanation
Indices: 121400--121435 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
121390 GTCAATGGGT
121400 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
121413 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
121426 CGGGTCGGGT
1 CGGGTCGGGT
121436 CGGGTAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:121456 original size:18 final size:18
Alignment explanation
Indices: 121413--121458 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
121403 GTCGGGTAAA
121413 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
121431 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
121449 CGGGTCGGGT
1 CGGGTCGGGT
121459 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:125575 original size:41 final size:41
Alignment explanation
Indices: 125530--125610 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
125520 AATTGAAAAC
* *
125530 AAATTAATAATTTAAAGACCTAATCAAGAAAAATACAAATT
1 AAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAATT
* *
125571 AAATTATTAATCTAAAGACCAAATCAAGAAAAGTACAAAT
1 AAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
125611 ATTGCACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (41 bp):
AAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAATT
Found at i:129716 original size:20 final size:20
Alignment explanation
Indices: 129691--129733 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
129681 ACAGATATTT
* *
129691 TTTCTTTGTATGTCTACTTA
1 TTTCTTTGTATGTATACCTA
129711 TTTCTTTGTATGTATACCTA
1 TTTCTTTGTATGTATACCTA
129731 TTT
1 TTT
129734 GCTTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTCTTTGTATGTATACCTA
Found at i:134720 original size:2 final size:2
Alignment explanation
Indices: 134713--134742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
134703 ATCATAACAC
134713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
134743 ATGGAAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139482 original size:31 final size:31
Alignment explanation
Indices: 139447--139549 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
139437 CCGAAGAAGC
* *
139447 TAGGTAAACTGACCATATATTCCTTAGAACA
1 TAGGTAAACTGTCCATATGTTCCTTAGAACA
* * ***
139478 TAGGTATATTGTCCATATGTCTCGAAAG-ACA
1 TAGGTAAACTGTCCATATGT-TCCTTAGAACA
*
139509 TATGTAAAACTGTCCATATGTT-CTGTAGAACA
1 TAGGT-AAACTGTCCATATGTTCCT-TAGAACA
139541 TAGGTAAAC
1 TAGGTAAAC
139550 CCTCAACTCT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
31 30 0.56
32 24 0.44
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (31 bp):
TAGGTAAACTGTCCATATGTTCCTTAGAACA
Found at i:139830 original size:30 final size:30
Alignment explanation
Indices: 139787--139862 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
139777 CACATTCATA
139787 TCACATGTT-CATATAAGC-TCCTAACTTCTT
1 TCACAT-TTACATATAAGCAT-CTAACTTCTT
* * *
139817 TCACATTTACATATGATCATGTAACTTCTT
1 TCACATTTACATATAAGCATCTAACTTCTT
139847 TCACATTTACATATAA
1 TCACATTTACATATAA
139863 CATGGCTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 2 0.05
30 37 0.93
31 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (30 bp):
TCACATTTACATATAAGCATCTAACTTCTT
Found at i:141811 original size:22 final size:23
Alignment explanation
Indices: 141765--141811 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
141755 TTTGTGAAGA
141765 AGGCTTTTAAAAAGGCTATCAGGCC
1 AGGCTTTTAAAAAGG--ATCAGGCC
*
141790 AGGCTTTTAAACAGG-TCAGGCC
1 AGGCTTTTAAAAAGGATCAGGCC
141812 GAGCCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
25 14 0.67
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (23 bp):
AGGCTTTTAAAAAGGATCAGGCC
Found at i:145373 original size:21 final size:21
Alignment explanation
Indices: 145347--145406 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
145337 CATTAACAAC
145347 AATGAACTCGACGATGATGAA
1 AATGAACTCGACGATGATGAA
**
145368 AATGAA--CGATC-A-GATGCC
1 AATGAACTCGA-CGATGATGAA
*
145386 AACGAACTCGACGATGATGAA
1 AATGAACTCGACGATGATGAA
145407 GAGGAATCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
18 9 0.31
19 5 0.17
20 5 0.17
21 10 0.34
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (21 bp):
AATGAACTCGACGATGATGAA
Found at i:146692 original size:36 final size:38
Alignment explanation
Indices: 146647--146741 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 38
146637 GTATAAATAT
** * *
146647 TTTTATAATTTTTTCTTTTA-TCAA-AATTTT-TATTA
1 TTTTATAATTAATTATTTTATTCAATAATTTTGTATAA
146682 TTTTAGTAATTAATTATTTTATTCAATAATTTTGTATAA
1 TTTTA-TAATTAATTATTTTATTCAATAATTTTGTATAA
*
146721 TTTTATTATT-ATTATTTTATT
1 TTTTATAATTAATTATTTTATT
146742 TAACATTTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.10
36 12 0.24
37 15 0.29
38 10 0.20
39 9 0.18
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (38 bp):
TTTTATAATTAATTATTTTATTCAATAATTTTGTATAA
Found at i:146943 original size:14 final size:14
Alignment explanation
Indices: 146921--146954 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
146911 ATCGAGTATA
*
146921 TATTAATTAGAAAT
1 TATTTATTAGAAAT
*
146935 TATTTATTAGAATT
1 TATTTATTAGAAAT
146949 TATTTA
1 TATTTA
146955 AATAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TATTTATTAGAAAT
Found at i:150284 original size:12 final size:12
Alignment explanation
Indices: 150267--150297 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
150257 ATTAAAATCA
150267 TTAAAATCTATT
1 TTAAAATCTATT
*
150279 TTAAAATTTATT
1 TTAAAATCTATT
150291 TTAAAAT
1 TTAAAAT
150298 ATAGATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:150592 original size:22 final size:22
Alignment explanation
Indices: 150284--150583 Score: 420
Period size: 22 Copynumber: 13.6 Consensus size: 22
150274 CTATTTTAAA
*
150284 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
150306 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
150328 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
** ***
150350 ATTTATTTTAAAATATAAAAAAA
1 ATTTATTTTAAAATAT-GGATTG
* ***
150373 AATTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
150395 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
150417 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
150439 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
150461 AGTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
150483 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
150505 ATTTATTTTAAAATATCGATTG
1 ATTTATTTTAAAATATGGATTG
*
150527 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
* *
150549 ATTTATTTTAAAATATGAATTA
1 ATTTATTTTAAAATATGGATTG
150571 ATTTATTTTAAAA
1 ATTTATTTTAAAA
150584 AATTCATTAT
Statistics
Matches: 252, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
22 235 0.93
23 17 0.07
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:153835 original size:2 final size:2
Alignment explanation
Indices: 153830--153866 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
153820 ATTTTTTTAC
153830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
153867 GTTTGCAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:153922 original size:38 final size:37
Alignment explanation
Indices: 153880--154044 Score: 159
Period size: 38 Copynumber: 4.5 Consensus size: 37
153870 TGCAAATGGT
*
153880 TTTTGAAAATACGTATATAATATATAGCTTTTAAAATA
1 TTTTGAAAATAC-TATATAATATATAGTTTTTAAAATA
153918 TTTTGAAAATA-TATATAATATATAGTTTTTAAAATTA
1 TTTTGAAAATACTATATAATATATAGTTTTTAAAA-TA
**
153955 TTTTTTAAA-ACTTATATAATATATAGTTTTT-AAA-A
1 TTTTGAAAATAC-TATATAATATATAGTTTTTAAAATA
*
153990 --TCG-AAA-ACTTATATAATATATAGTTTTTAAAAAATA
1 TTTTGAAAATAC-TATATAATATATAGTTTTT--AAAATA
154026 TTTTTAGAAAATA-TATATA
1 -TTTT-GAAAATACTATATA
154045 TTTTTTTGAA
Statistics
Matches: 108, Mismatches: 6, Indels: 24
0.78 0.04 0.17
Matches are distributed among these distances:
32 25 0.23
33 1 0.01
35 4 0.04
36 24 0.22
37 12 0.11
38 30 0.28
39 1 0.01
40 7 0.06
41 3 0.03
42 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATACTATATAATATATAGTTTTTAAAATA
Found at i:153998 original size:32 final size:32
Alignment explanation
Indices: 153961--154021 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
153951 ATTATTTTTT
153961 AAAACTTATATAATATATAGTTTTTAAAATCG
1 AAAACTTATATAATATATAGTTTTTAAAATCG
153993 AAAACTTATATAATATATAGTTTTTAAAA
1 AAAACTTATATAATATATAGTTTTTAAAA
154022 AATATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (32 bp):
AAAACTTATATAATATATAGTTTTTAAAATCG
Found at i:154021 original size:70 final size:74
Alignment explanation
Indices: 153893--154030 Score: 196
Period size: 70 Copynumber: 1.9 Consensus size: 74
153883 TGAAAATACG
* *
153893 TATATAATATATAGCTTTTAAAATATTTTGAAAATATATATAATATATAGTTTTT-AAAATTATT
1 TATATAATATATAGCTTTTAAAATA-TTCGAAAATATATATAATATATAGTTTTTAAAAAATATT
153957 TTTTAAAACT
65 TTTTAAAACT
*
153967 TATATAATATATAG-TTTTTAAA-A-TCGAAAACT-TATATAATATATAGTTTTTAAAAAATATT
1 TATATAATATATAGCTTTTAAAATATTCGAAAA-TATATATAATATATAGTTTTTAAAAAATATT
154028 TTT
65 TTT
154031 AGAAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
70 25 0.42
71 12 0.20
72 1 0.02
73 7 0.12
74 14 0.24
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (74 bp):
TATATAATATATAGCTTTTAAAATATTCGAAAATATATATAATATATAGTTTTTAAAAAATATTT
TTTAAAACT
Found at i:154158 original size:22 final size:20
Alignment explanation
Indices: 154133--154214 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
154123 ATATAATATA
154133 TATTTGTTTTTATTATTTGTTT
1 TATTT-TTTTTATTATTT-TTT
154155 TATTTTATTTTTATT-TTATTTT
1 TA-TTT-TTTTTATTATT-TTTT
*
154177 TATTTTATTT-TTATTTATTT
1 TATTTTTTTTATTATTT-TTT
*
154197 TA-TTCTTTTATT-TTTTTT
1 TATTTTTTTTATTATTTTTT
154215 CCAAGTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.06
19 11 0.22
20 13 0.25
21 3 0.06
22 9 0.18
23 12 0.24
ACGTcount: A:0.16, C:0.01, G:0.02, T:0.80
Consensus pattern (20 bp):
TATTTTTTTTATTATTTTTT
Found at i:154168 original size:11 final size:11
Alignment explanation
Indices: 154139--154211 Score: 87
Period size: 11 Copynumber: 6.5 Consensus size: 11
154129 TATATATTTG
154139 TTTTTATTATT-
1 TTTTTATT-TTA
154150 TGTTTTATTTTA
1 T-TTTTATTTTA
154162 TTTTTATTTTA
1 TTTTTATTTTA
154173 TTTTTATTTTA
1 TTTTTATTTTA
154184 TTTTTA-TTTA
1 TTTTTATTTTA
*
154194 TTTTATTCTTTTA
1 -TTT-TTATTTTA
154207 TTTTT
1 TTTTT
154212 TTTCCAAGTC
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
10 4 0.07
11 35 0.62
12 13 0.23
13 4 0.07
ACGTcount: A:0.16, C:0.01, G:0.01, T:0.81
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:154210 original size:5 final size:5
Alignment explanation
Indices: 154152--154200 Score: 64
Period size: 5 Copynumber: 9.4 Consensus size: 5
154142 TTATTATTTG
154152 TTTTA TTTTA TTTTTA TTTTA TTTTTA TTTTA TTTT- TATTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA T-TTTA TTTTA
154199 TT
1 TT
154201 CTTTTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 1 0.03
5 28 0.70
6 11 0.28
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:155408 original size:28 final size:26
Alignment explanation
Indices: 155377--155428 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
155367 GTTTTTATTA
*
155377 TTATTATATTTTTTATTCTTCTTTTCAC
1 TTATTAT-TTTTTTATT-TTCATTTCAC
*
155405 TTATTCTTTTTTTATTTTCATTTC
1 TTATTATTTTTTTATTTTCATTTC
155429 CCTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (26 bp):
TTATTATTTTTTTATTTTCATTTCAC
Found at i:155443 original size:26 final size:26
Alignment explanation
Indices: 155385--155448 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
155375 TATTATTATA
* *
155385 TTTTTTATTCTTCTTTTCACTTATTCT
1 TTTTTTATT-TTCATTTCACCTATTCT
155412 TTTTTTATTTTCATTTC-CCTATT-T
1 TTTTTTATTTTCATTTCACCTATTCT
*
155436 TTTATTTTTTTTC
1 TTT-TTTATTTTC
155449 CTCTCTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 4 0.12
25 13 0.39
26 7 0.21
27 9 0.27
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTATTTTCATTTCACCTATTCT
Found at i:155529 original size:31 final size:32
Alignment explanation
Indices: 155471--155530 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
155461 TTTTATTCAA
* *
155471 TTCTTTTTTTCGTTTTGACTTTTTTATTTATT
1 TTCTTTTTTTCGCTTTGACTTTATTATTTATT
155503 TTCTTTTTGTTC-CTTTGA-TTTATTATTT
1 TTCTTTTT-TTCGCTTTGACTTTATTATTT
155531 TAGTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 9 0.36
32 13 0.52
33 3 0.12
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (32 bp):
TTCTTTTTTTCGCTTTGACTTTATTATTTATT
Found at i:155547 original size:24 final size:25
Alignment explanation
Indices: 155520--155568 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
155510 TGTTCCTTTG
155520 ATTTA-TTATTTTAGTATTA-TATTT
1 ATTTATTTA-TTTAGTATTATTATTT
*
155544 ATTTATTTATTTATTATTATTATTT
1 ATTTATTTATTTAGTATTATTATTT
155569 CTTTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
ATTTATTTATTTAGTATTATTATTT
Found at i:155554 original size:12 final size:13
Alignment explanation
Indices: 155520--155568 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 13
155510 TGTTCCTTTG
155520 ATTTATTAT-TTT
1 ATTTATTATATTT
*
155532 A-GTATTATATTT
1 ATTTATTATATTT
155544 ATTTATT-TATTT
1 ATTTATTATATTT
155556 A-TTATTATTATTT
1 ATTTATTA-TATTT
155569 CTTTTTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 11 0.35
12 11 0.35
13 9 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
ATTTATTATATTT
Found at i:162262 original size:18 final size:19
Alignment explanation
Indices: 162231--162281 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
162221 AACATTCCTA
162231 GTAATCTT--ATTCC-CTG
1 GTAATCTTACATTCCACTG
*
162247 GTGATCTTACATTCCCACTG
1 GTAATCTTACATT-CCACTG
162267 GTAATCTTACATTCC
1 GTAATCTTACATTCC
162282 GCGAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 7 0.24
18 3 0.10
19 4 0.14
20 15 0.52
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (19 bp):
GTAATCTTACATTCCACTG
Found at i:162273 original size:20 final size:20
Alignment explanation
Indices: 162244--162281 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
162234 ATCTTATTCC
*
162244 CTGGTGATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
162264 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
162282 GCGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:164980 original size:36 final size:36
Alignment explanation
Indices: 164896--165108 Score: 277
Period size: 36 Copynumber: 6.0 Consensus size: 36
164886 TGAATAAGAA
* * *
164896 GAACGAAAGGAAACATCGGCACTTTCGATTCAAGT-
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
164931 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* * *
164967 GAACGGAATGAAGCATCGGCACTTTCGATTCAAGAC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* **
165003 GAACGAAAAAAAGCATCGACACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* * *
165039 AAACGGAATGAAGCATCGACACTTTCGATTCAAGTT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* * *
165075 GAACAGAAGGAGGCGTCG-CACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
165109 GTTCATCTTT
Statistics
Matches: 156, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
35 48 0.31
36 108 0.69
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
Found at i:166679 original size:36 final size:35
Alignment explanation
Indices: 166587--166727 Score: 176
Period size: 35 Copynumber: 4.0 Consensus size: 35
166577 GTGAATAAGA
* *
166587 AGAACGAAAGGAAGCATCGCCACTTTCGATTCAAG
1 AGAACGAAAGGAAGCATCGGCACTTTCAATTCAAG
*
166622 TGAAC-AGAAGGAAGCATCGGCACTTTCAATTCAAG
1 AGAACGA-AAGGAAGCATCGGCACTTTCAATTCAAG
*
166657 AAGAACGAAATGAAGCATCGGCACTTTCAATTCAAG
1 -AGAACGAAAGGAAGCATCGGCACTTTCAATTCAAG
* * * * *
166693 TGAACGGAAGAAAGCATCCGCACTTTCGATTCAAG
1 AGAACGAAAGGAAGCATCGGCACTTTCAATTCAAG
166728 TGTTCATCTT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.01
35 59 0.64
36 31 0.34
37 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (35 bp):
AGAACGAAAGGAAGCATCGGCACTTTCAATTCAAG
Found at i:166708 original size:71 final size:71
Alignment explanation
Indices: 166583--166727 Score: 227
Period size: 71 Copynumber: 2.0 Consensus size: 71
166573 GAAGGTGAAT
* * *
166583 AAGAAGAACGAAAGGAAGCATCGCCACTTTCGATTCAAGTGAACAGAAGGAAGCATCGGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGCCACTTTCAATTCAAGTGAACAGAAGAAAGCATCCGCACTTT
166648 CAATTC
66 CAATTC
* * *
166654 AAGAAGAACGAAATGAAGCATCGGCACTTTCAATTCAAGTGAACGGAAGAAAGCATCCGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGCCACTTTCAATTCAAGTGAACAGAAGAAAGCATCCGCACTTT
*
166719 CGATTC
66 CAATTC
166725 AAG
1 AAG
166728 TGTTCATCTT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGCCACTTTCAATTCAAGTGAACAGAAGAAAGCATCCGCACTTT
CAATTC
Found at i:168705 original size:3 final size:3
Alignment explanation
Indices: 168697--168734 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
168687 GTATTTGAAT
168697 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
168735 TTGAATTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:171586 original size:3 final size:3
Alignment explanation
Indices: 171578--171613 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
171568 CAATCTCAGA
171578 TCT TCT TCTT TCT TC- TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
171614 ACGGCTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:172823 original size:18 final size:18
Alignment explanation
Indices: 172800--172842 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
172790 TAAGTACTCA
172800 ATTATTTTATTTTATT-TT
1 ATTATTTTATTTT-TTATT
172818 ATTA-TTTATTTTTTAATT
1 ATTATTTTATTTTTT-ATT
172836 ATTATTT
1 ATTATTT
172843 GATTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 10 0.45
19 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTATTTTATTTTTTATT
Found at i:172840 original size:26 final size:24
Alignment explanation
Indices: 172804--172851 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
172794 TACTCAATTA
*
172804 TTTTATTTTATTTTATTATTTATT
1 TTTTATTTTATTTGATTATTTATT
172828 TTTTAATTATTATTTGATTATTTA
1 TTTT-ATT-TTATTTGATTATTTA
172852 ATTGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 14 0.67
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTGATTATTTATT
Found at i:172883 original size:19 final size:18
Alignment explanation
Indices: 172820--172888 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
172810 TTTATTTTAT
** *
172820 TATTTATTTTTTAATTAT
1 TATTTATTAATTAATTAA
*
172838 TATTTGATTATTTAATTGAA
1 TATTT-ATTAATTAATT-AA
*
172858 AATTTATTTAATTAATTAA
1 TATTTA-TTAATTAATTAA
172877 TATTTATTAATT
1 TATTTATTAATT
172889 GTAGTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.26
19 18 0.42
20 14 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTTATTAATTAATTAA
Found at i:173866 original size:2 final size:2
Alignment explanation
Indices: 173859--173892 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
173849 TTATAGAATG
*
173859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173893 TAAATAGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:181614 original size:27 final size:27
Alignment explanation
Indices: 181552--181624 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 27
181542 GATAATGAGA
* *
181552 ATGATGAGGAGGATGAGGACGATGATG
1 ATGATGAGGAGGAAGAGGACGACGATG
** * **
181579 ACAACGAGGAGGAAGAGGTGGACGATG
1 ATGATGAGGAGGAAGAGGACGACGATG
* *
181606 ATGATGAGGACGAGGAGGA
1 ATGATGAGGAGGAAGAGGA
181625 GCAACATATA
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.36, C:0.07, G:0.45, T:0.12
Consensus pattern (27 bp):
ATGATGAGGAGGAAGAGGACGACGATG
Found at i:182231 original size:4 final size:4
Alignment explanation
Indices: 182222--182255 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
182212 TGAATATTCC
*
182222 CATA CATA CATA TATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
182256 CTGGGGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:190664 original size:22 final size:22
Alignment explanation
Indices: 190636--190683 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
190626 AACCTCAAGA
190636 TTTAAGTAAAACAAATTATATC
1 TTTAAGTAAAACAAATTATATC
190658 TTTAAGTAAAACAAATTATATC
1 TTTAAGTAAAACAAATTATATC
190680 TTTA
1 TTTA
190684 CCTCTAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTAAGTAAAACAAATTATATC
Found at i:201976 original size:31 final size:31
Alignment explanation
Indices: 201930--201993 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
201920 GGGTACATAA
* * *
201930 TCTCTAATGTTATCGATCTATTCGATTTTAG
1 TCTCTAACGTCATCGATCCATTCGATTTTAG
*
201961 TCTCTAACGTCATCGATCCGTTCGATTTTAG
1 TCTCTAACGTCATCGATCCATTCGATTTTAG
201992 TC
1 TC
201994 CCTCAGTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (31 bp):
TCTCTAACGTCATCGATCCATTCGATTTTAG
Found at i:202905 original size:16 final size:17
Alignment explanation
Indices: 202886--202922 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
202876 TAAAATATTA
202886 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
202902 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
202919 TTTT
1 TTTT
202923 TCATCCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:207024 original size:29 final size:28
Alignment explanation
Indices: 206983--207058 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
206973 ATTCTTTAAT
* *
206983 TTCATCC-TCAACTATGATACATTCTAAA
1 TTCATCCATAAACTATGA-ACATTCCAAA
* *
207011 TTGATCCATAAACTTTTGAACATTCCAAA
1 TTCATCCATAAAC-TATGAACATTCCAAA
**
207040 TTCATTTATAAACTATGAA
1 TTCATCCATAAACTATGAA
207059 TCTCATTCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 11 0.29
29 23 0.61
30 4 0.11
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (28 bp):
TTCATCCATAAACTATGAACATTCCAAA
Found at i:207476 original size:19 final size:20
Alignment explanation
Indices: 207452--207490 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
207442 ATAAAAATTT
*
207452 AAAATTATCATATA-TTTTA
1 AAAATTATAATATACTTTTA
*
207471 AAAATTTTAATATACTTTTA
1 AAAATTATAATATACTTTTA
207491 TTACTCTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTATAATATACTTTTA
Found at i:208163 original size:14 final size:14
Alignment explanation
Indices: 208143--208185 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
208133 GCCCTCTGTT
208143 CGAACATAAATGAA
1 CGAACATAAATGAA
*
208157 TGAACATAAATGAA
1 CGAACATAAATGAA
*
208171 CGAACATAAACGAA
1 CGAACATAAATGAA
208185 C
1 C
208186 ATATGATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.56, C:0.16, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:210291 original size:75 final size:75
Alignment explanation
Indices: 210168--210318 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
210158 TTGATTTTTC
* *
210168 AGTGTAAATTATGGTTTATTTGCAGCGATGGACATTTCAGAGACTGGAGTTCAAAAGCCTGGTTC
1 AGTGTAAATTATGGTTTATTTGCAGCGATGGACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
210233 TGCTACTCCA
66 TGCTACTCCA
*
210243 AGTGTAAATTATGGTTTATTTGCAGCGATGTACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
1 AGTGTAAATTATGGTTTATTTGCAGCGATGGACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
210308 TGCTACTCCA
66 TGCTACTCCA
210318 A
1 A
210319 AACTGTAGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (75 bp):
AGTGTAAATTATGGTTTATTTGCAGCGATGGACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
TGCTACTCCA
Found at i:213797 original size:27 final size:27
Alignment explanation
Indices: 213765--213820 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
213755 GATTGAAGAT
213765 TTCTTCAATCTTCACAGATTATCATTC
1 TTCTTCAATCTTCACAGATTATCATTC
213792 TTCTTCAATCTTCACAGATTATCATTC
1 TTCTTCAATCTTCACAGATTATCATTC
213819 TT
1 TT
213821 TTGTTCTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.46
Consensus pattern (27 bp):
TTCTTCAATCTTCACAGATTATCATTC
Found at i:223762 original size:79 final size:78
Alignment explanation
Indices: 223622--223777 Score: 233
Period size: 79 Copynumber: 2.0 Consensus size: 78
223612 ATACTAAGCC
* * *
223622 ACAATAGAAATAAGCGAATCTCCATTTTTTTAAAAAATATTAAATTAATTATTGGGTAAAGAAAA
1 ACAATAGAAATAAGCGAATCTCCA-TTTTTAAAAAAATATTAAATTAATTATCGGGCAAAGAAAA
223687 ATGAAAAAAAAAAA
65 ATGAAAAAAAAAAA
* *
223701 ACAATAGAAATAAGTGCATCTCCA-TTTTAAAAAAATATTAAATTTAATTTATCGGGCAAAGAAA
1 ACAATAGAAATAAGCGAATCTCCATTTTTAAAAAAATATTAAA-TTAA-TTATCGGGCAAAGAAA
223765 AATGAAAAAAAAA
64 AATGAAAAAAAAA
223778 CACTACGTAC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
77 17 0.24
78 4 0.06
79 49 0.70
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (78 bp):
ACAATAGAAATAAGCGAATCTCCATTTTTAAAAAAATATTAAATTAATTATCGGGCAAAGAAAAA
TGAAAAAAAAAAA
Found at i:228631 original size:47 final size:47
Alignment explanation
Indices: 228562--228657 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
228552 ATTGGTAAAC
228562 TTACTTCACTTTTGCTTATAATTATTGGTATTAGTTATATGTTATTG
1 TTACTTCACTTTTGCTTATAATTATTGGTATTAGTTATATGTTATTG
228609 TTACTTCACTTTTGCTTATAATTATTGGTATTAGTTATATGTTATTG
1 TTACTTCACTTTTGCTTATAATTATTGGTATTAGTTATATGTTATTG
228656 TT
1 TT
228658 TTTGTCTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.56
Consensus pattern (47 bp):
TTACTTCACTTTTGCTTATAATTATTGGTATTAGTTATATGTTATTG
Found at i:245294 original size:39 final size:41
Alignment explanation
Indices: 245215--245320 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
245205 ACTGTTTGAA
* * * * *
245215 CAGTGCAAAAAATACTGTGTTGATTCAAACAGTGCTG-AAAAT
1 CAGTGAAAAAAAT-CAGT-TTGGTTCAAACAATGCAGAAAAAT
245257 CAGTG-AAAAAATCAGTTTGGTTCAAACAATGCAGAAAAAT
1 CAGTGAAAAAAATCAGTTTGGTTCAAACAATGCAGAAAAAT
* *
245297 AATTGGAAAAAAATCAGTTTGGTT
1 CAGT-GAAAAAAATCAGTTTGGTT
245321 TGAACTGTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 15 0.27
40 10 0.18
41 8 0.15
42 22 0.40
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.26
Consensus pattern (41 bp):
CAGTGAAAAAAATCAGTTTGGTTCAAACAATGCAGAAAAAT
Found at i:247255 original size:18 final size:18
Alignment explanation
Indices: 247232--247267 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
247222 TTAATTTCCT
247232 TTATTTATTTATTTGAGA
1 TTATTTATTTATTTGAGA
247250 TTATTTATTTATTTGAGA
1 TTATTTATTTATTTGAGA
247268 AGAAATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (18 bp):
TTATTTATTTATTTGAGA
Found at i:247935 original size:24 final size:25
Alignment explanation
Indices: 247908--247963 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
247898 TGTCTAATAG
*
247908 ATAAAAATTGTA-GTTA-GATGAATT
1 ATAAAAATTCTAGGTTATG-TGAATT
247932 ATAAAAATTCTAGTGTTATGTGAATT
1 ATAAAAATTCTAG-GTTATGTGAATT
247958 ATAAAA
1 ATAAAA
247964 GATACATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.39
26 16 0.57
27 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (25 bp):
ATAAAAATTCTAGGTTATGTGAATT
Done.