Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000506.1 Hibiscus syriacus cultivar Beakdansim tig00000963_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: 89512
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:195 original size:2 final size:2
Alignment explanation
Indices: 190--225 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
180 CATAAGTTCT
190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226 ATCGGTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17342 original size:21 final size:21
Alignment explanation
Indices: 17316--17388 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
17306 CGAATATGTA
17316 AATCGCAATGCGATAATACAT
1 AATCGCAATGCGATAATACAT
* **
17337 AATCGCAATACGATTCTGAC-T
1 AATCGCAATGCGATAAT-ACAT
** *
17358 -ATCGCGTTGCGATAATACAA
1 AATCGCAATGCGATAATACAT
17378 AATCGCAATGC
1 AATCGCAATGC
17389 AATTTTCAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
19 2 0.05
20 11 0.29
21 23 0.61
22 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (21 bp):
AATCGCAATGCGATAATACAT
Found at i:17344 original size:41 final size:41
Alignment explanation
Indices: 17294--17388 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
17284 GCAATTTTAG
17294 AAAATCGCAATGCGAATATGTA-AATCGCAATGCGATAATAC
1 AAAATCGCAATGCGAATATG-ACAATCGCAATGCGATAATAC
* * * * * **
17335 ATAATCGCAATACGATTCTGACTATCGCGTTGCGATAATAC
1 AAAATCGCAATGCGAATATGACAATCGCAATGCGATAATAC
17376 AAAATCGCAATGC
1 AAAATCGCAATGC
17389 AATTTTCAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.02
41 43 0.98
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAATGCGAATATGACAATCGCAATGCGATAATAC
Found at i:17566 original size:22 final size:22
Alignment explanation
Indices: 17536--17586 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
17526 CTACGGCGAT
*
17536 ATCCATCCCCATCTCCGAAGAA
1 ATCCGTCCCCATCTCCGAAGAA
**
17558 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGAAGAA
17580 ATCCGTC
1 ATCCGTC
17587 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGAAGAA
Found at i:17988 original size:19 final size:19
Alignment explanation
Indices: 17964--18012 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
17954 AGTCAAATTC
17964 GCGTTGCGATTTTCATTTT
1 GCGTTGCGATTTTCATTTT
17983 GCGTTGCGATTTTCATTTT
1 GCGTTGCGATTTTCATTTT
18002 GCGTTGCGATT
1 GCGTTGCGATT
18013 ATCTCGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
GCGTTGCGATTTTCATTTT
Found at i:18042 original size:20 final size:20
Alignment explanation
Indices: 18017--18066 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
18007 GCGATTATCT
18017 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
18037 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
18057 CGTTTCGATA
1 CGTTGCGATA
18067 ATTATTTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:18106 original size:20 final size:20
Alignment explanation
Indices: 17961--18108 Score: 71
Period size: 20 Copynumber: 7.8 Consensus size: 20
17951 GATAGTCAAA
*
17961 TTCGCGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
17981 TT-GCGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
18000 TT-GCGTTGCGA--TT-A-T
1 TTCGTGTTGCGATTTTCATT
* ** **
18015 CTC--GTTGCGATAGTCAAA
1 TTCGTGTTGCGATTTTCATT
* ** **
18033 TTCGCGTTGCGATAGTCAAA
1 TTCGTGTTGCGATTTTCATT
* * *
18053 TTCGCGTTTCGATAATT-ATT
1 TTCGTGTTGCGAT-TTTCATT
18073 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
18093 TTCTTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
18109 AAGTTTAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
14 7 0.07
15 2 0.02
16 2 0.02
17 3 0.03
18 2 0.02
19 30 0.28
20 59 0.55
21 2 0.02
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.47
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:20051 original size:20 final size:20
Alignment explanation
Indices: 20026--20074 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
20016 AAACTTAAAA
*
20026 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
20046 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
20066 ATCACAACG
1 ATCGCAACG
20075 GGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:20162 original size:19 final size:19
Alignment explanation
Indices: 20134--20183 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20124 AAAATGAAAA
*
20134 TCGCAATGCGA-ATTTAGTT
1 TCGCATTGCGATATTTA-TT
* *
20153 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATATTTATT
20172 TCGCATTGCGAT
1 TCGCATTGCGAT
20184 TATCTCGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATATTTATT
Found at i:20184 original size:19 final size:20
Alignment explanation
Indices: 20146--20184 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
20136 GCAATGCGAA
*
20146 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
20166 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
20185 ATCTCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:20237 original size:20 final size:20
Alignment explanation
Indices: 20214--20257 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
20204 ATTTGTGTTG
20214 CGATAGTCATTTTCGCGTTA
1 CGATAGTCATTTTCGCGTTA
*
20234 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCGTTA
20254 CGAT
1 CGAT
20258 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTA
Found at i:20844 original size:21 final size:20
Alignment explanation
Indices: 20753--20856 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 20
20743 GACTCACCTG
*
20753 TCATCGTTCAAGAGGCCTCT
1 TCATCGTTCAAGAGGCCCCT
* *
20773 CCTATCGTTTAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCCCT
** *
20794 ATCATCCCTCAAGAGTCCCCT
1 -TCATCGTTCAAGAGGCCCCT
* *
20815 TCCACCGTTTAAGAGGCCCCT
1 T-CATCGTTCAAGAGGCCCCT
* *
20836 GTCATCGTTGAAGAGGTCCCT
1 -TCATCGTTCAAGAGGCCCCT
20857 CCCACCATTC
Statistics
Matches: 64, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
20 2 0.03
21 60 0.94
22 2 0.03
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:20862 original size:42 final size:42
Alignment explanation
Indices: 20749--20871 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
20739 GCCTGACTCA
* *
20749 CCTGTCATCGTTCAAGAGG-CCTCTCCTATCGTTTAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCC-CTCCCACCGTTTAAGAGGCC
* ** *
20791 CCTATCATCCCTCAAGA-GTCCCCTTCCACCGTTTAAGAGGCC
1 CCTGTCATCGTTCAAGAGGT-CCCTCCCACCGTTTAAGAGGCC
* * *
20833 CCTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTTAAGAG
20872 CCCGATTCAT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 60 0.92
43 4 0.06
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTTAAGAGGCC
Found at i:22254 original size:14 final size:14
Alignment explanation
Indices: 22235--22271 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
22225 GCTTGTTTAA
22235 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
22249 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
22263 TTGATTTGT
1 TTGATTTGT
22272 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:22315 original size:36 final size:35
Alignment explanation
Indices: 22268--22379 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 35
22258 AAAAGTTGAT
22268 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
* * *
22303 CTTGTTTAATTGATTTGT-AA-AAGT-TGA----T-
1 -TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
22331 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
*
22366 ATTATTTAATTGAT
1 -TTGTTTAATTGAT
22380 TGAAATGTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
27 16 0.27
28 2 0.03
29 4 0.07
30 2 0.03
33 2 0.03
34 4 0.07
35 2 0.03
36 28 0.47
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.54
Consensus pattern (35 bp):
TTGTTTAATTGATGTGTAAATAATTCTTATTTGTG
Found at i:22348 original size:63 final size:63
Alignment explanation
Indices: 22249--22380 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
22239 TTTGTAAAAG
* *
22249 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGATTATTTAA
22312 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGATTATTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGATTATTTAA
22375 TTGATT
1 TTGATT
22381 GAAATGTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (63 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGATTATTTAA
Found at i:22499 original size:20 final size:20
Alignment explanation
Indices: 22470--22530 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
22460 CGCTAAACTC
22470 AAATCGCAATGCGAAAGTCA
1 AAATCGCAATGCGAAAGTCA
* *
22490 AAATCACAATGCGAAAGCCA
1 AAATCGCAATGCGAAAGTCA
*
22510 AAATCGCAACGCGAAAGTCA
1 AAATCGCAATGCGAAAGTCA
22530 A
1 A
22531 TTCGCGTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (20 bp):
AAATCGCAATGCGAAAGTCA
Found at i:22594 original size:20 final size:20
Alignment explanation
Indices: 22569--22679 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 20
22559 GCGATTTTCT
*
22569 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
22589 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
22609 CGTTACGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
* * *
22629 CATTGCGAT--T---TTTGA
1 CGTTGCGATAGTCAAATTCA
*
22644 -GTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
22663 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
22680 GAATGTGTAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
14 7 0.10
15 3 0.04
16 1 0.01
18 1 0.01
19 2 0.03
20 59 0.81
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:22620 original size:74 final size:74
Alignment explanation
Indices: 22520--22679 Score: 207
Period size: 74 Copynumber: 2.2 Consensus size: 74
22510 AAATCGCAAC
* * * * * *
22520 GCGAAAGTC-AATTCGCGTTGCAATAGTCTAATACGCTTTGCGATTTTCT-CGTTGCGATAGTCA
1 GCGATAGTCAAATTCGCGTTACAATAGTCAAATACACATTGCGATTTT-TGAGTTGCGATAGTCA
22583 AATTCCCGTT
65 AATTCCCGTT
* *
22593 GCGATAGTCAAATTCGCGTTACGATAGTCAAATTCACATTGCGATTTTTGAGTTGCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTACAATAGTCAAATACACATTGCGATTTTTGAGTTGCGATAGTCAA
*
22658 ATTCGCGTT
66 ATTCCCGTT
*
22667 GCGATATTCAAAT
1 GCGATAGTCAAAT
22680 GAATGTGTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
73 9 0.12
74 66 0.88
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (74 bp):
GCGATAGTCAAATTCGCGTTACAATAGTCAAATACACATTGCGATTTTTGAGTTGCGATAGTCAA
ATTCCCGTT
Found at i:22873 original size:18 final size:18
Alignment explanation
Indices: 22850--22884 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22840 AAGCCGGTTG
*
22850 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
22868 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
22885 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:24939 original size:14 final size:14
Alignment explanation
Indices: 24920--24946 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24910 TCCAGTGGCA
24920 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
24934 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
24947 TTTCTTCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:24952 original size:12 final size:13
Alignment explanation
Indices: 24921--24953 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
24911 CCAGTGGCAT
24921 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
24934 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
24947 TTTCTTC
1 TTTCTTC
24954 TTATTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:25213 original size:24 final size:24
Alignment explanation
Indices: 25162--25213 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
25152 ATCTGAGTAT
** *
25162 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
25186 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
25210 TGAC
1 TGAC
25214 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:26122 original size:21 final size:21
Alignment explanation
Indices: 26098--26158 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
26088 ATTTACATAT
26098 TCGCATTGCGAATTTAGAAAA
1 TCGCATTGCGAATTTAGAAAA
*
26119 TCGCAATGCG-A--TAGTCAAAA
1 TCGCATTGCGAATTTAG--AAAA
* *
26139 TCGCGTTGCGAATTTGGAAA
1 TCGCATTGCGAATTTAGAAA
26159 TTGATTTGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
18 3 0.10
20 13 0.42
21 13 0.42
23 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGAATTTAGAAAA
Found at i:26199 original size:19 final size:19
Alignment explanation
Indices: 26175--26211 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
26165 TGCGATACTG
*
26175 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
26194 GAGATCGCATTGTGATTT
1 GAGATCGCATTGCGATTT
26212 TGTTGATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:29454 original size:230 final size:227
Alignment explanation
Indices: 29048--29492 Score: 782
Period size: 230 Copynumber: 1.9 Consensus size: 227
29038 TTATCTATCC
* *
29048 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATA
1 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATA
**
29113 TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGT
66 TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGT
*
29178 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
131 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATT-AAAAAAATTGAAAC
29243 ATAAATTACATAACTTTCAAAAAAGTATATATTA
195 ATAAATTACATAACTTT-AAAAAAGTATATATTA
*
29277 TTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGTTAAT
1 TTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAGTTAAT
*
29342 ATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
65 ATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
* *
29407 TAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTGAAAC
130 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAAC
29472 ATAAATTACATAACTTTAAAA
195 ATAAATTACATAACTTTAAAA
29493 GCAGTTTTAA
Statistics
Matches: 206, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 62 0.30
230 140 0.68
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (227 bp):
TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATA
TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGT
AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACA
TAAATTACATAACTTTAAAAAAGTATATATTA
Found at i:29747 original size:20 final size:19
Alignment explanation
Indices: 29724--29770 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
29714 CGATATAACA
*
29724 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
29744 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
29764 GGTAAAA
1 GGTAAAA
29771 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:32331 original size:14 final size:14
Alignment explanation
Indices: 32314--32360 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
32304 AAAATATGAA
32314 GAAGAAAAGAGGAG
1 GAAGAAAAGAGGAG
32328 GAAGAAGAAGA-GATG
1 GAAGAA-AAGAGGA-G
*
32343 GAAGAAATGAGGAG
1 GAAGAAAAGAGGAG
32357 GAAG
1 GAAG
32361 GAGAGGCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.04
Consensus pattern (14 bp):
GAAGAAAAGAGGAG
Found at i:33949 original size:19 final size:19
Alignment explanation
Indices: 33905--33948 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
33895 AATGTCGAGT
33905 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
33924 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
33943 T-ATTTT
1 TAATTTT
33949 TTTTATGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:34416 original size:198 final size:199
Alignment explanation
Indices: 34032--35447 Score: 2583
Period size: 198 Copynumber: 7.1 Consensus size: 199
34022 TGAAGGGTCA
*
34032 TGTCGATACTAATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
34096 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34161 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34226 AATG
196 AATG
34230 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
34295 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
34360 TAATATGTAA-TTTTCAATATAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34424 AATG
196 AATG
* *
34428 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
*
34493 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34558 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34623 AATG
196 AATG
34627 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
34692 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34757 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34821 AATG
196 AATG
34825 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
34890 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34954 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
35019 AATG
196 AATG
* * *
35023 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
**
35088 CCTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
35153 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGCCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
35218 AATG
196 AATG
* *
35222 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
* *
35286 CATAAAGTGTCGATCCATATAT-AAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
35350 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
35415 AATG
196 AATG
*
35419 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
35448 CTAATTTAAA
Statistics
Matches: 1187, Mismatches: 27, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
197 157 0.13
198 591 0.50
199 439 0.37
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:34782 original size:397 final size:397
Alignment explanation
Indices: 34032--35447 Score: 2597
Period size: 397 Copynumber: 3.6 Consensus size: 397
34022 TGAAGGGTCA
* * *
34032 TGTCGATACTAATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
34096 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34161 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34226 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
34291 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
34356 AATGTAATATGTAATTTTCAATATAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 AATGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
34421 AATAATG
391 AATAATG
34428 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
34493 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34558 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34623 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
34688 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
34753 AATGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 AATGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
34818 AATAATG
391 AATAATG
* *
34825 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
34890 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34954 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
* *
35019 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
* **
35084 CACCCCTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
35149 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGCCT
326 AATGTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
35214 AAATAATG
390 AAATAATG
35222 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
35286 CATAAAGTGTCGATCCATATAT-AAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
35350 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
35415 AATGTGTCGACACTAATATATTTTGTGTCGATA
196 AATGTGTCGACACTAATATAGTTTGTGTCGATA
35448 CTAATTTAAA
Statistics
Matches: 991, Mismatches: 26, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
395 29 0.03
396 374 0.38
397 588 0.59
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (397 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
AATAATG
Found at i:35175 original size:595 final size:595
Alignment explanation
Indices: 34032--35447 Score: 2633
Period size: 595 Copynumber: 2.4 Consensus size: 595
34022 TGAAGGGTCA
*
34032 TGTCGATACTAATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
34096 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34161 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34226 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
34291 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
260 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
34356 AATGTAATATGTAATTTTCAATATAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
325 AATGTAATATGTAATTTTCAATATAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTA
*
34421 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAG
390 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAG
34486 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
455 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
*
34551 TATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
520 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
*
34616 TCTAAATAATG
585 CCTAAATAATG
34627 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
34692 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34757 TAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 TAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
34822 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGC
34887 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATA
261 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
* *
34951 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTA
326 ATGTAATATGTAA-TTTTCAATATAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTA
35016 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAG
390 AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAG
*
35081 GTGCACCCCTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
455 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
*
35146 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
520 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
35211 CCTAAATAATG
585 CCTAAATAATG
* *
35222 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
* *
35286 CATAAAGTGTCGATCCATATAT-AAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
35350 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
35415 AATGTGTCGACACTAATATATTTTGTGTCGATA
195 AATGTGTCGACACTAATATAGTTTGTGTCGATA
35448 CTAATTTAAA
Statistics
Matches: 802, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
593 56 0.07
594 135 0.17
595 489 0.61
596 122 0.15
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (595 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGC
ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTCAATATAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAA
ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGG
TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGC
CTAAATAATG
Found at i:36934 original size:12 final size:12
Alignment explanation
Indices: 36917--37008 Score: 76
Period size: 12 Copynumber: 7.4 Consensus size: 12
36907 GGTCGCAGAA
*
36917 GATGAAGCTGAC
1 GATGAAGATGAC
36929 GATGAAGATGAC
1 GATGAAGATGAC
36941 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
36956 GATGAAGCTGGC
1 GATGAAGATGAC
*
36968 GATGAAGATGAT
1 GATGAAGATGAC
* * *
36980 GACGATGATGAT
1 GATGAAGATGAC
* *
36992 GATGATGATGAA
1 GATGAAGATGAC
37004 GATGA
1 GATGA
37009 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
12 54 0.81
13 1 0.01
14 1 0.01
15 11 0.16
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:36938 original size:6 final size:6
Alignment explanation
Indices: 36914--37008 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
36904 ATCGGTCGCA
* * * * *
36914 GAAGAT GAAGCT GACGAT GAAGAT GACGATGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT
** * * * * *
36965 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
37009 TGATCCAAAC
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
6 63 0.91
8 1 0.01
9 5 0.07
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:36953 original size:15 final size:15
Alignment explanation
Indices: 36929--37011 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
36919 TGAAGCTGAC
*
36929 GATGAAGATGACGAT
1 GATGATGATGACGAT
36944 GATGATGATGACGAT
1 GATGATGATGACGAT
* *
36959 GA--A-GCTGGCGAT
1 GATGATGATGACGAT
*
36971 GAAGATGATGACGAT
1 GATGATGATGACGAT
*
36986 GATGATGATGATGAT
1 GATGATGATGACGAT
*
37001 GAAGATGATGA
1 GATGATGATGA
37012 TCCAAACAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 1 0.02
15 46 0.81
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:36955 original size:27 final size:27
Alignment explanation
Indices: 36925--37008 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
36915 AAGATGAAGC
36925 TGACGATGAAGATGACGATGATGATGA
1 TGACGATGAAGATGACGATGATGATGA
* * *
36952 TGACGATGAAGCTGGCGATGAAGATGA
1 TGACGATGAAGATGACGATGATGATGA
* * *
36979 TGACGATGATGATGATGATGATGAAGA
1 TGACGATGAAGATGACGATGATGATGA
37006 TGA
1 TGA
37009 TGATCCAAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (27 bp):
TGACGATGAAGATGACGATGATGATGA
Found at i:38690 original size:183 final size:184
Alignment explanation
Indices: 38379--39230 Score: 1604
Period size: 183 Copynumber: 4.7 Consensus size: 184
38369 CTTTCAACAT
**
38379 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38444 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
38509 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
38563 ATTATAATGTAATAGATAATTTTGTAATATAACTGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38628 -GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
38692 AATGTGTCGATACAATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
38745 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38810 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
38874 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
38928 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38993 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
39057 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
39111 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
39176 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
39231 CCATTTAAAA
Statistics
Matches: 655, Mismatches: 9, Indels: 8
0.97 0.01 0.01
Matches are distributed among these distances:
182 158 0.24
183 404 0.62
184 93 0.14
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:41819 original size:23 final size:23
Alignment explanation
Indices: 41788--41850 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
41778 ATAGGTAAAC
*
41788 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
41811 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
41834 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
41851 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:41858 original size:23 final size:23
Alignment explanation
Indices: 41788--41860 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
41778 ATAGGTAAAC
* * **
41788 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
41811 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
41834 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
41857 ATAT
1 ATAT
41861 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:42248 original size:23 final size:23
Alignment explanation
Indices: 42217--42279 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
42207 ATAGGTAAAC
*
42217 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
42240 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
42263 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
42280 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:42287 original size:23 final size:23
Alignment explanation
Indices: 42217--42289 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
42207 ATAGGTAAAC
* * **
42217 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
42240 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
42263 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
42286 ATAT
1 ATAT
42290 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:42710 original size:23 final size:23
Alignment explanation
Indices: 42646--42711 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
42636 AATAGGTAAA
* *
42646 TATATGATGTAATAGGTAGCCCT
1 TATATAATGTAATAGGTATCCCT
**
42669 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTATCCCT
42692 TATATAATGTAATAGGTATC
1 TATATAATGTAATAGGTATC
42712 TATCTCGCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (23 bp):
TATATAATGTAATAGGTATCCCT
Found at i:42936 original size:18 final size:18
Alignment explanation
Indices: 42915--42951 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42905 GTAATTGGAG
42915 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
42933 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
42951 T
1 T
42952 ATATATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:50222 original size:2 final size:2
Alignment explanation
Indices: 50215--50246 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50205 TAAAAATCAA
50215 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
50247 TAAATATGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50523 original size:19 final size:19
Alignment explanation
Indices: 50495--50532 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
50485 GCTTCATTAC
*
50495 TTTAATGAAAATATTAAAT
1 TTTAAAGAAAATATTAAAT
*
50514 TTTAAAGAAAGTATTAAAT
1 TTTAAAGAAAATATTAAAT
50533 ATATAAAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (19 bp):
TTTAAAGAAAATATTAAAT
Found at i:51711 original size:3 final size:3
Alignment explanation
Indices: 51703--51741 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
51693 AAAGAAAAAC
51703 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51742 GATCAAAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51767 original size:21 final size:20
Alignment explanation
Indices: 51732--51782 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
51722 TAATAATAAT
51732 AATAATAATAGATCAAAAGGAGA
1 AATAA-AATAGATC-AAAGGA-A
*
51755 AA-AAAATATATCAAAGGAA
1 AATAAAATAGATCAAAGGAA
51774 AATAAAATA
1 AATAAAATA
51783 AAATAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 7 0.27
22 2 0.08
23 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (20 bp):
AATAAAATAGATCAAAGGAA
Found at i:51835 original size:3 final size:3
Alignment explanation
Indices: 51829--51875 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
51819 AAAAAATGTA
51829 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
51876 ATCAAAAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51908 original size:14 final size:15
Alignment explanation
Indices: 51889--51929 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
51879 AAAAGATAAA
51889 AAAATAAATAAAG-G
1 AAAATAAATAAAGAG
51903 AAAATAAATCAAAGAG
1 AAAATAAAT-AAAGAG
51919 AAAA-AAATAAA
1 AAAATAAATAAA
51930 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.48
15 8 0.32
16 5 0.20
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (15 bp):
AAAATAAATAAAGAG
Found at i:51949 original size:9 final size:9
Alignment explanation
Indices: 51827--51957 Score: 67
Period size: 9 Copynumber: 14.4 Consensus size: 9
51817 GAAAAAAATG
51827 TAAATAATAA
1 TAAA-AATAA
*
51837 TAATAATAA
1 TAAAAATAA
*
51846 TAATAATAA
1 TAAAAATAA
*
51855 TAATAATAA
1 TAAAAATAA
*
51864 TAATAATAA
1 TAAAAATAA
*
51873 TAAATCAAAAGA
1 TAAA--AATA-A
51885 TAAAAA-AA
1 TAAAAATAA
*
51893 TAAATA-AA
1 TAAAAATAA
**
51901 GGAAAATAAA
1 TAAAAAT-AA
* *
51911 TCAAAGAGAA
1 T-AAAAATAA
51921 -AAAAATAA
1 TAAAAATAA
51929 -AATAAA-AA
1 TAA-AAATAA
51937 TAAAAATAA
1 TAAAAATAA
51946 T-AAAATAA
1 TAAAAATAA
51954 TAAA
1 TAAA
51958 TGAATCAAAG
Statistics
Matches: 98, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
8 32 0.33
9 46 0.47
10 9 0.09
11 6 0.06
12 5 0.05
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (9 bp):
TAAAAATAA
Found at i:51949 original size:15 final size:15
Alignment explanation
Indices: 51828--51950 Score: 67
Period size: 15 Copynumber: 8.1 Consensus size: 15
51818 AAAAAAATGT
*
51828 AAATAATAATAATAA
1 AAATAAAAATAATAA
* *
51843 TAATAATAATAATAA
1 AAATAAAAATAATAA
* *
51858 TAATAATAATAATAA
1 AAATAAAAATAATAA
51873 TAAATCAAAAGATAA-AA
1 -AAAT-AAAA-ATAATAA
* **
51890 AAATAAATA-AAGGA
1 AAATAAAAATAATAA
*
51904 AAATAAATCAA-AGAGAA
1 AAATAAA--AATA-ATAA
*
51921 AAA-AATAA-AATAA
1 AAATAAAAATAATAA
51934 AAATAAAAATAATAA
1 AAATAAAAATAATAA
51949 AA
1 AA
51951 TAATAAATGA
Statistics
Matches: 89, Mismatches: 10, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
13 8 0.09
14 16 0.18
15 39 0.44
16 11 0.12
17 11 0.12
18 4 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (15 bp):
AAATAAAAATAATAA
Found at i:52034 original size:13 final size:12
Alignment explanation
Indices: 52002--52039 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
51992 TTAAGGGACC
*
52002 AAAATAAAATGA
1 AAAATAATATGA
52014 AAAA-AATATGA
1 AAAATAATATGA
52025 AACAATAATATGA
1 AA-AATAATATGA
52038 AA
1 AA
52040 TAAACACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 8 0.35
12 6 0.26
13 9 0.39
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (12 bp):
AAAATAATATGA
Found at i:52884 original size:21 final size:20
Alignment explanation
Indices: 52842--52911 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 20
52832 TATATAATAT
52842 TATATATTATACATGTAT-ATA
1 TATATATT-TA-ATGTATCATA
52863 TATATATTTAATGTATGCATA
1 TATATATTTAATGTAT-CATA
*
52884 T-TATAATATAATCGTATCATA
1 TATAT-ATTTAAT-GTATCATA
52905 TACTATA
1 TA-TATA
52912 AATATGTCAC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
19 6 0.14
20 5 0.12
21 23 0.55
22 5 0.12
23 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATATTTAATGTATCATA
Found at i:53736 original size:84 final size:84
Alignment explanation
Indices: 53601--54451 Score: 1040
Period size: 84 Copynumber: 10.1 Consensus size: 84
53591 ACTCGACGTT
* * * * * **
53601 TTTTATTGACAGATAACCCTTCTTGCCTTGAGCTAAGCTGTGAATGATGTGCCTTTGG-GCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAG
* * *
53665 TGTAATCGAACTCGAATGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * * * *
53685 TTTGGTTGGTAGATAACCTTTCTCGCCTTAAGTTATGCTGCAAATGTTGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
53750 GTAATCAAACTCGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* ** * *
53769 TTTTGTTGGAAGATAACCCTTCTAGCCTTGAGTTATAATGCAAAAGACGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
53834 GTAGTCAAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * *
53853 TTTTGTTGGTAAATAACCCTTATTGCCTTAAGATATGTTGCAAATAATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
53918 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
53937 TTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATACTGCAAATGATATG-CTTATGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAG
*
54001 CGTAGTCAAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * * *
54021 TTTTGTTGGCAAATAACCTTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
54086 GTAGTCAAACTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
* *
54105 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGATGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
54170 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * *
54189 TTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGTCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
54254 GTAGTCGAACTCGAAGATT
66 GTAGTCGAACTCGAAGGTC
* * * * *
54273 TTTTGTTGGCAAATATCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGACC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
54338 GTAGTCTAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * **
54357 GTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATATTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
54422 GTAGTCGAACTCGAAGGTT
66 GTAGTCGAACTCGAAGGTC
*
54441 TTTTATTGGCA
1 TTTTGTTGGCA
54452 AATAGCCTTT
Statistics
Matches: 655, Mismatches: 109, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
83 6 0.01
84 646 0.99
85 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:53940 original size:252 final size:251
Alignment explanation
Indices: 53601--54477 Score: 1191
Period size: 252 Copynumber: 3.5 Consensus size: 251
53591 ACTCGACGTT
* * * * * * * **
53601 TTTTATTGACAGATAACCCTTCTTGCCTTGAGCTAAGCTGTGAATGATGTGCCTTTGG-GCTGAG
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGTTGCAAATGATGTGCC-TTGGAGCTGAG
* * * * * *
53665 TGTAATCGAACTCGAATGTCTTTGGTTGGTAGATAACCTTTCTCGCCTTAAGTTATGCTGCAAAT
65 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAAT
* * * *
53730 GTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTTGTTGG-AAGATAACCCTTCTAG
130 GATATG-CTTTGAGCTGAGTGTAGTCAAACTCGAAGGTATTTTGTTGGCAA-ATAACCCTTCTTG
* * * *
53794 CCTTGAGTTATAATGCAAAAGACGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
193 CCTTGAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
* * * * * *
53853 TTTTGTTGGTAAATAACCCTTATTGCCTTAAGATATGTTGCAAATAATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
*
53918 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATACTGCAAATG
66 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATG
* * *
53983 ATATGCTTATGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAACCTTTCTTGCC
131 ATATGCTT-TGAGCTGAGTGTAGTCAAACTCGAAGGTATTTTGTTGGCAAATAACCCTTCTTGCC
* *
54048 TTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTC
195 TTGAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
* *
54105 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGATGAGC
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* *
54170 GTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
66 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATG
* * * *
54235 ATATGTCTTTGAGCTGAGTGTAGTCGAACTCGAAGATTTTTTGTTGGCAAATATCCCTTCTTGCC
131 ATATG-CTTTGAGCTGAGTGTAGTCAAACTCGAAGGTATTTTGTTGGCAAATAACCCTTCTTGCC
* * *
54300 TTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGACCGTAGTCTAACTCGAAGGTC
195 TTGAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
* *
54357 GTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATATTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* ** * * * * *
54422 GTAGTCGAACTCGAAGGTTTTTTATTGGCAAATAGCCTTTCTTGCATTGAGCTATG
66 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATG
54478 TTTCAAATAA
Statistics
Matches: 554, Mismatches: 67, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
251 7 0.01
252 542 0.98
253 5 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (251 bp):
TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATG
ATATGCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTATTTTGTTGGCAAATAACCCTTCTTGCCT
TGAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
Found at i:54695 original size:124 final size:123
Alignment explanation
Indices: 54489--54851 Score: 557
Period size: 124 Copynumber: 2.9 Consensus size: 123
54479 TTCAAATAAA
* * * *
54489 CACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCATTGTGAAGTTGAGCCTTGA
1 CACGAT-TCATTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * * ** **
54554 ATTGGATATCATTCGTCGTGAAGTTGAAATCAAATATAAAGATGAATGTTGTTGGTGGG
65 ATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAC
54613 CACGATTCCATTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATT-CATTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
*
54678 ATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAATATGAATGTTACTGGTGAC
65 ATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAC
* *
54737 CACGATTCACTTCGTCGTGAAGTTGAAACTGTGGATGGCCCATTCGTTGTGAAGTTGAGCATTGA
1 CACGATTCA-TTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
54802 ATTGGATATCCTTT-GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
65 ATTGGATAT-CTTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
54852 TCTTCGAGTC
Statistics
Matches: 221, Mismatches: 15, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
123 3 0.01
124 214 0.97
125 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (123 bp):
CACGATTCATTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAA
TTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAC
Found at i:56184 original size:99 final size:98
Alignment explanation
Indices: 55985--56251 Score: 403
Period size: 99 Copynumber: 2.7 Consensus size: 98
55975 AGCTAGCTGG
* * *
55985 ATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAA-TATCATTGTATAGAT
1 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGT-TTATTGTATAGAT
56049 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
65 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
56083 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGAT
1 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTATAGAT
56148 ATTATAATCACCTTTATCAGGCTAGCAT-AATATT
65 ATTATAATCACCTTTATCAGGCTAGC-TGAATATT
* * * *
56182 ATCCATAAAGATGGGGCGTTTAAGCAATTGCTTTAGAGGGACAACTCAAGATTTATTGTATATAT
1 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTATAGAT
56247 ATTAT
65 ATTAT
56252 TATAATCTGG
Statistics
Matches: 155, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
98 46 0.30
99 107 0.69
100 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (98 bp):
ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTATTGTATAGATA
TTATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:67945 original size:17 final size:17
Alignment explanation
Indices: 67920--67963 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
67910 ACTTAGGCAT
*
67920 CAAGTTCACACTTGAGC
1 CAAGGTCACACTTGAGC
67937 CAAGGTCACACTTGAGC
1 CAAGGTCACACTTGAGC
67954 CAAGGTCACA
1 CAAGGTCACA
67964 TAATGCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (17 bp):
CAAGGTCACACTTGAGC
Found at i:72059 original size:8 final size:8
Alignment explanation
Indices: 72048--72121 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
72038 GGGAAAATGT
72048 AAAAATAA
1 AAAAATAA
72056 AAAAATAA
1 AAAAATAA
72064 AATAAA-ATA
1 AA-AAATA-A
* *
72073 ATAAATCA
1 AAAAATAA
*
72081 AAAGATAA
1 AAAAATAA
*
72089 ATAAATAA
1 AAAAATAA
*
72097 ATAAATAA
1 AAAAATAA
* **
72105 ATAAAGGA
1 AAAAATAA
72113 AAAAATAA
1 AAAAATAA
72121 A
1 A
72122 GGAAAAAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
8 46 0.90
9 5 0.10
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (8 bp):
AAAAATAA
Found at i:72078 original size:12 final size:12
Alignment explanation
Indices: 72050--72105 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
72040 GAAAATGTAA
*
72050 AAATAAAAAAAT
1 AAATAAAATAAT
72062 AAAATAAAATAAT
1 -AAATAAAATAAT
*
72075 AAATCAAAA-GAT
1 AAAT-AAAATAAT
72087 AAAT-AAATAAAT
1 AAATAAAAT-AAT
72099 AAATAAA
1 AAATAAA
72106 TAAAGGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.08
12 16 0.44
13 17 0.47
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:72094 original size:4 final size:4
Alignment explanation
Indices: 72050--72109 Score: 61
Period size: 4 Copynumber: 14.8 Consensus size: 4
72040 GAAAATGTAA
* *
72050 AAAT AAAA AAAT AAAAT AAA- ATAAT AAAT CAAA- AGAT AAAT AAAT AAAT
1 AAAT AAAT AAAT -AAAT AAAT A-AAT AAAT -AAAT AAAT AAAT AAAT AAAT
72099 AAAT AAAT AAA
1 AAAT AAAT AAA
72110 GGAAAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
3 3 0.06
4 36 0.77
5 8 0.17
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:72130 original size:13 final size:12
Alignment explanation
Indices: 72103--72156 Score: 81
Period size: 12 Copynumber: 4.2 Consensus size: 12
72093 ATAAATAAAT
72103 AAATAAAGGAAA
1 AAATAAAGGAAA
72115 AAATAAAGGAAAA
1 AAATAAAGG-AAA
72128 AAATAAAGGAAA
1 AAATAAAGGAAA
72140 AAATCAAAGAGAAA
1 AAAT-AAAG-GAAA
72154 AAA
1 AAA
72157 ATTAAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.41
13 16 0.41
14 7 0.18
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (12 bp):
AAATAAAGGAAA
Found at i:73085 original size:2 final size:2
Alignment explanation
Indices: 73073--73119 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
73063 AAATAACATA
* *
73073 AT AT AT GT AT AT A- AT AT -T AT AT AT -T AT AC 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
73112 AT AT AT AT
1 AT AT AT AT
73120 TTAACGTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79227 original size:21 final size:21
Alignment explanation
Indices: 79201--79347 Score: 116
Period size: 21 Copynumber: 6.8 Consensus size: 21
79191 ATTATTCGGG
79201 ACATATATGTGGTCATTTGGA
1 ACATATATGTGGTCATTTGGA
* *
79222 ACATATATGCGGTCCTTTGGA
1 ACATATATGTGGTCATTTGGA
* * *
79243 ATATATATTTGGTCCTTTGGA
1 ACATATATGTGGTCATTTGGA
* *
79264 ACATATATGTGGTTC-TTAGGG
1 ACATATATGTGG-TCATTTGGA
* * * *
79285 ACAATTCTATGTGGTCCTTCGGG
1 AC-A-TATATGTGGTCATTTGGA
* *
79308 ACATATATGTGGTCATTCGGG
1 ACATATATGTGGTCATTTGGA
*
79329 ACATTTCTATGTGGTCATT
1 ACA--TATATGTGGTCATT
79348 CGGGATAATT
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
21 72 0.68
22 6 0.06
23 28 0.26
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (21 bp):
ACATATATGTGGTCATTTGGA
Found at i:79295 original size:23 final size:23
Alignment explanation
Indices: 79269--79361 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 23
79259 TTGGAACATA
*
79269 TATGTGGTTC-TTAGGGACAATTC
1 TATGTGG-TCATTCGGGACAATTC
* *
79292 TATGTGGTCCTTCGGGAC-A-TA
1 TATGTGGTCATTCGGGACAATTC
*
79313 TATGTGGTCATTCGGGACATTTC
1 TATGTGGTCATTCGGGACAATTC
*
79336 TATGTGGTCATTCGGGATAATTC
1 TATGTGGTCATTCGGGACAATTC
79359 TAT
1 TAT
79362 ATGGCACTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 18 0.30
22 3 0.05
23 39 0.65
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (23 bp):
TATGTGGTCATTCGGGACAATTC
Found at i:79315 original size:44 final size:44
Alignment explanation
Indices: 79252--79352 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
79242 AATATATATT
* *
79252 TGGTCCTTTGGAACATATATGTGGTTC-TTAGGGACAATTCTATG
1 TGGTCCTTCGGGACATATATGTGG-TCATTAGGGACAATTCTATG
* *
79296 TGGTCCTTCGGGACATATATGTGGTCATTCGGGACATTTCTATG
1 TGGTCCTTCGGGACATATATGTGGTCATTAGGGACAATTCTATG
*
79340 TGGTCATTCGGGA
1 TGGTCCTTCGGGA
79353 TAATTCTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 2 0.04
44 49 0.96
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.37
Consensus pattern (44 bp):
TGGTCCTTCGGGACATATATGTGGTCATTAGGGACAATTCTATG
Found at i:79618 original size:21 final size:21
Alignment explanation
Indices: 79567--79627 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
79557 ATTCAGGTAA
*
79567 GATATGAAAGTATGTGACTGTAT
1 GATATGAAAGTATGT-A-AGTAT
*
79590 GATATGAAAGTATGTAAGTGT
1 GATATGAAAGTATGTAAGTAT
*
79611 GTTATGAAAGTATGTAA
1 GATATGAAAGTATGTAA
79628 CTGCATGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 19 0.54
22 1 0.03
23 15 0.43
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (21 bp):
GATATGAAAGTATGTAAGTAT
Found at i:80196 original size:13 final size:13
Alignment explanation
Indices: 80178--80207 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
80168 GACTTTTTTT
80178 GTCAAAGTCAACG
1 GTCAAAGTCAACG
80191 GTCAAAGTCAACG
1 GTCAAAGTCAACG
80204 GTCA
1 GTCA
80208 TGTCAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:80214 original size:18 final size:19
Alignment explanation
Indices: 80191--80226 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
80181 AAAGTCAACG
80191 GTCAAAGTCAACG-GTCAT
1 GTCAAAGTCAACGTGTCAT
80209 GTCAAAGTCAACGTGTCA
1 GTCAAAGTCAACGTGTCA
80227 GAACGATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (19 bp):
GTCAAAGTCAACGTGTCAT
Found at i:80261 original size:20 final size:20
Alignment explanation
Indices: 80238--80286 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
80228 AACGATTCGG
**
80238 GTTGACTCAGTTCAGTCCGA
1 GTTGACTCAGAACAGTCCGA
* *
80258 GTTGACTAAGAACAGTTCGA
1 GTTGACTCAGAACAGTCCGA
80278 GTTGACTCA
1 GTTGACTCA
80287 AACTGGTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
GTTGACTCAGAACAGTCCGA
Found at i:81880 original size:21 final size:21
Alignment explanation
Indices: 81837--81890 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
81827 GTATGAACAA
81837 TATCGATACCATATGGAAGAGG
1 TATCGATACC-TATGGAAGAGG
* *
81859 TTTCGATACCTATGTGGA-AGG
1 TATCGATACCTATG-GAAGAGG
81880 TATCGATACCT
1 TATCGATACCT
81891 GGGGAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
TATCGATACCTATGGAAGAGG
Found at i:82836 original size:28 final size:28
Alignment explanation
Indices: 82761--82839 Score: 108
Period size: 26 Copynumber: 2.9 Consensus size: 28
82751 AGAGTCGAGG
* *
82761 GTTCTATGTGGTCTTTTGGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
* *
82789 G-T-TACGTGGTCCTTCAGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
82815 GTTCTATGTGGTCCTTCGGGACATA
1 GTTCTATGTGGTCCTTCGGGACATA
82840 GTGGTCATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 21 0.49
27 2 0.05
28 20 0.47
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.39
Consensus pattern (28 bp):
GTTCTATGTGGTCCTTCGGGACATATGT
Found at i:87642 original size:2 final size:2
Alignment explanation
Indices: 87635--87660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
87625 AATTGCTATC
87635 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
87661 TCATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.