Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009093.1 Hibiscus syriacus cultivar Beakdansim tig00112540_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: 447474
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:5434 original size:14 final size:15
Alignment explanation
Indices: 5417--5446 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5407 TTCTTATTTT
5417 TATTTAA-TTATTAA
1 TATTTAATTTATTAA
5431 TATTTAATTTATTAA
1 TATTTAATTTATTAA
5446 T
1 T
5447 TAACTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTAATTTATTAA
Found at i:8848 original size:32 final size:32
Alignment explanation
Indices: 8812--8885 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
8802 TTGTTTCAAA
*
8812 TCAATATCGGATCGGTT-GATTTTTGGGTATGG
1 TCAATATCGGATCGGTTAGA-TTTTGGGTAGGG
** * *
8844 TCAATATTAGATTGGTTAGATTTTGGGTCGGG
1 TCAATATCGGATCGGTTAGATTTTGGGTAGGG
*
8876 TTAATATCGG
1 TCAATATCGG
8886 GTCGATTCAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.22, C:0.08, G:0.30, T:0.41
Consensus pattern (32 bp):
TCAATATCGGATCGGTTAGATTTTGGGTAGGG
Found at i:10630 original size:23 final size:23
Alignment explanation
Indices: 10593--10663 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
10583 GTCGAGGGTT
* **
10593 CTATGTGGTCATTCGGGGCAATC
1 CTATGTGGTCATTCGGGACAAAA
* *
10616 CTATGTTGTCCTTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
10639 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
10662 CT
1 CT
10664 GTGGTACTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:11851 original size:18 final size:17
Alignment explanation
Indices: 11817--11856 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
11807 ATGGGTCGAG
11817 TATCATATCAAATTTAA
1 TATCATATCAAATTTAA
11834 TTATCATATTCAAA-TTAA
1 -TATCATA-TCAAATTTAA
11852 TATCA
1 TATCA
11857 GGTATTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 11 0.52
19 5 0.24
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
TATCATATCAAATTTAA
Found at i:15312 original size:31 final size:32
Alignment explanation
Indices: 15277--15356 Score: 153
Period size: 31 Copynumber: 2.5 Consensus size: 32
15267 TTATGAGATT
15277 AAAGTATAAATACAAATTCAAGAAAG-AAAGG
1 AAAGTATAAATACAAATTCAAGAAAGAAAAGG
15308 AAAGTATAAATACAAATTCAAGAAAGAAAAGG
1 AAAGTATAAATACAAATTCAAGAAAGAAAAGG
15340 AAAGTATAAATACAAAT
1 AAAGTATAAATACAAAT
15357 AATAATCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.62, C:0.06, G:0.14, T:0.17
Consensus pattern (32 bp):
AAAGTATAAATACAAATTCAAGAAAGAAAAGG
Found at i:23573 original size:15 final size:15
Alignment explanation
Indices: 23555--23584 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23545 CCACGGTGCT
23555 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
23570 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
23585 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:28537 original size:15 final size:15
Alignment explanation
Indices: 28519--28548 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28509 CCACGGTGCT
28519 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
28534 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
28549 GATTATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:33498 original size:15 final size:15
Alignment explanation
Indices: 33480--33509 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33470 CCACGGTGCT
33480 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
33495 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
33510 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:38081 original size:14 final size:14
Alignment explanation
Indices: 38046--38074 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38036 CAACAACCAC
38046 AAAGAAAAAATGAA
1 AAAGAAAAAATGAA
38060 AAAGAAAAAATGAA
1 AAAGAAAAAATGAA
38074 A
1 A
38075 CAAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (14 bp):
AAAGAAAAAATGAA
Found at i:38140 original size:21 final size:21
Alignment explanation
Indices: 38076--38141 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
38066 AAAATGAAAC
* *
38076 AAAAAAGAA-ATCATAGAGAG
1 AAAAAAGAAGATAAAAGAGAG
* *
38096 GAAAAAGAAAGA-AAAAGAAAAG
1 AAAAAAG-AAGATAAAAG-AGAG
38118 AAAAAAGAAGATAAAAGAGAG
1 AAAAAAGAAGATAAAAGAGAG
38139 AAA
1 AAA
38142 TCGAACAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 6 0.17
21 15 0.42
22 15 0.42
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.05
Consensus pattern (21 bp):
AAAAAAGAAGATAAAAGAGAG
Found at i:38285 original size:38 final size:38
Alignment explanation
Indices: 38234--38309 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
38224 AAAGAAAAGA
38234 AAGGTATTATCTTTTTTCTTCTCATTCGAATTTTCTTT
1 AAGGTATTATCTTTTTTCTTCTCATTCGAATTTTCTTT
*
38272 AAGGTATTATCTTTTTTCTTCTCATTTGAATTTTCTTT
1 AAGGTATTATCTTTTTTCTTCTCATTCGAATTTTCTTT
38310 GTTATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.59
Consensus pattern (38 bp):
AAGGTATTATCTTTTTTCTTCTCATTCGAATTTTCTTT
Found at i:40490 original size:2 final size:2
Alignment explanation
Indices: 40485--40510 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40475 TATATCAGAC
40485 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
40511 TGATTTCATT
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
Found at i:41074 original size:2 final size:2
Alignment explanation
Indices: 41067--41110 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
41057 TCAAACATGT
41067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41109 TA
1 TA
41111 CTACCCCCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41392 original size:24 final size:24
Alignment explanation
Indices: 41354--41423 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
41344 CAAAACAGAG
* *
41354 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
41378 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
41402 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
41424 CTATTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:42184 original size:29 final size:29
Alignment explanation
Indices: 42121--42184 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
42111 CATTTTACAC
**
42121 AAATAGCACCCTTTTTTAAATAATTACCA
1 AAATAGCACCCTTTTCGAAATAATTACCA
* * *
42150 ATATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAAATAATTACCA
42179 AAATAG
1 AAATAG
42185 AACCAAAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAGCACCCTTTTCGAAATAATTACCA
Found at i:42243 original size:12 final size:13
Alignment explanation
Indices: 42218--42246 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42208 GAATAGCACC
42218 GGTCAACAGGTCG
1 GGTCAACAGGTCG
42231 GGTCAAC-GGTCG
1 GGTCAACAGGTCG
42243 GGTC
1 GGTC
42247 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:42248 original size:17 final size:17
Alignment explanation
Indices: 42226--42286 Score: 95
Period size: 17 Copynumber: 3.5 Consensus size: 17
42216 CCGGTCAACA
42226 GGTCGGGTCAACGGTCG
1 GGTCGGGTCAACGGTCG
42243 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAAC-GGTCG
* *
42261 GGTTGGGTTAACGGTCG
1 GGTCGGGTCAACGGTCG
42278 GGTCGGGTC
1 GGTCGGGTC
42287 GTGACCGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.10, C:0.20, G:0.49, T:0.21
Consensus pattern (17 bp):
GGTCGGGTCAACGGTCG
Found at i:42310 original size:10 final size:10
Alignment explanation
Indices: 42290--42325 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
42280 TCGGGTCGTG
42290 ACCGGTC-AA
1 ACCGGTCAAA
42299 ACCGGTCAAA
1 ACCGGTCAAA
42309 ACCGGTTCAAA
1 ACCGG-TCAAA
42320 ACCGGT
1 ACCGGT
42326 TTCCAGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:43225 original size:17 final size:17
Alignment explanation
Indices: 43203--43236 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43193 TCATTTATCT
43203 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
43220 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
43237 ATCTGTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (17 bp):
TTCACATTAATCTATAC
Found at i:47758 original size:2 final size:2
Alignment explanation
Indices: 47751--47789 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
47741 ATGGATTGCT
47751 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
47790 TTAGTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48033 original size:13 final size:13
Alignment explanation
Indices: 48012--48063 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
48002 AATAATGCGC
*
48012 AATGAGCGTCATA
1 AATGTGCGTCATA
*
48025 AATGTGCGTAATA
1 AATGTGCGTCATA
* *
48038 AATGCGTGTCATA
1 AATGTGCGTCATA
48051 AATGTGCGTCATA
1 AATGTGCGTCATA
48064 TATTTATGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:48098 original size:28 final size:28
Alignment explanation
Indices: 48058--48118 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
48048 ATAAATGTGC
*
48058 GTCATATATTTATGACGCACAATTACGT
1 GTCATAAATTTATGACGCACAATTACGT
* *
48086 GTCATAAATTTATGATGCACAATTGCGT
1 GTCATAAATTTATGACGCACAATTACGT
48114 GTCAT
1 GTCAT
48119 CTGAGATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (28 bp):
GTCATAAATTTATGACGCACAATTACGT
Found at i:54393 original size:141 final size:142
Alignment explanation
Indices: 54116--54409 Score: 437
Period size: 141 Copynumber: 2.1 Consensus size: 142
54106 ACTAATGGAC
* * **
54116 TAAACCTAAAAGATGGAGGCTCTAATATTAACCCTAATTTATTTTAACCAAATATTGAGTTGAAT
1 TAAACCT-AAAGATGAAGGATCTAATATTAACCCTAATTTATTTTAACCAAATATTGAGTCAAAT
* ** *
54181 AATCAAAATGGTCCCTTGGGCATGTTAATGCGAGAGTCAATTCAAATTACTCCCTAAATTAAAGG
65 AATCAAAATAGTCCCTCAGGCATGTTAATGCGAGAGCCAATTCAAATTACTCCCTAAATTAAAGG
54246 ACTAAAGTGATAT
130 ACTAAAGTGATAT
* * *
54259 TAAACCTAAAG-TGAAGGATCTAATATTAATCCTAATTTATTTTAATCAATTATTGAGTCAAATA
1 TAAACCTAAAGATGAAGGATCTAATATTAACCCTAATTTATTTTAACCAAATATTGAGTCAAATA
* *
54323 ATCAAAATAGTCCCTCAGGTATGTTAATGCGAGAGCCAATTCAAATTATTCCCTAAATTAAAGGA
66 ATCAAAATAGTCCCTCAGGCATGTTAATGCGAGAGCCAATTCAAATTACTCCCTAAATTAAAGGA
*
54388 GTAAAGTGATAT
131 CTAAAGTGATAT
*
54400 TAAAACTAAA
1 TAAACCTAAA
54410 TCTAGAGGTT
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
141 125 0.92
142 4 0.03
143 7 0.05
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (142 bp):
TAAACCTAAAGATGAAGGATCTAATATTAACCCTAATTTATTTTAACCAAATATTGAGTCAAATA
ATCAAAATAGTCCCTCAGGCATGTTAATGCGAGAGCCAATTCAAATTACTCCCTAAATTAAAGGA
CTAAAGTGATAT
Found at i:54611 original size:22 final size:21
Alignment explanation
Indices: 54568--54613 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
54558 AAATCAACAA
54568 TACAAATAAAAAATTAATAATT
1 TACAAATAAAAAA-TAATAATT
54590 TACAAATAACAAAA-AATGAATT
1 TACAAATAA-AAAATAAT-AATT
54612 TA
1 TA
54614 TTAGACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.14
22 15 0.68
23 4 0.18
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
TACAAATAAAAAATAATAATT
Found at i:56197 original size:13 final size:13
Alignment explanation
Indices: 56179--56212 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
56169 GTTGTTATAT
56179 TTTTTATAAATAA
1 TTTTTATAAATAA
*
56192 TTTTTAAAAATAA
1 TTTTTATAAATAA
56205 TATTTTAT
1 T-TTTTAT
56213 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTATAAATAA
Found at i:56239 original size:34 final size:32
Alignment explanation
Indices: 56176--56252 Score: 75
Period size: 34 Copynumber: 2.3 Consensus size: 32
56166 ATAGTTGTTA
* *
56176 TATTTTTTATAAATAATTTTTAAAAATAATATTT
1 TATTTTTTATAAATAATATTT-AAAATAAT-TAT
*
56210 TATTTTTTATTAAAATAATATTT-ATATAATTAT
1 TATTTTTTA-T-AAATAATATTTAAAATAATTAT
56243 TATTTATTTA
1 TATTT-TTTA
56253 ATTTAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 7 0.19
34 19 0.51
35 1 0.03
36 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTTTTTATAAATAATATTTAAAATAATTAT
Found at i:56242 original size:23 final size:22
Alignment explanation
Indices: 56188--56244 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
56178 TTTTTTATAA
*
56188 ATAATTTTTAAAAATAATATTTT
1 ATAATTATT-AAAATAATATTTT
**
56211 ATTTTTTATTAAAATAATATTTAT
1 A-TAATTATTAAAATAATATTT-T
56235 ATAATTATTA
1 ATAATTATTA
56245 TTTATTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTATTAAAATAATATTTT
Found at i:57416 original size:17 final size:17
Alignment explanation
Indices: 57394--57429 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
57384 GCTTGATATA
57394 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
57411 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
57428 AT
1 AT
57430 GTTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:58094 original size:42 final size:40
Alignment explanation
Indices: 57994--58096 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 40
57984 GATGTCACAG
57994 GGGTACATGTCCAGCCCACCAGTTCAGATGCCATCTCTGCAA
1 GGGTACAT-TCCAGCCCACCAGTTCAGATGCCATCTCTGC-A
* * * *
58036 GGGTATATGCCAAGCCCACCAGTTTATATGCCATCTCCT-CA
1 GGGTACATTCC-AGCCCACCAGTTCAGATGCCATCT-CTGCA
58077 GGGTTACATTCCTAGCCCAC
1 GGG-TACATTCC-AGCCCAC
58097 AAGGGTACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 6 0.12
42 43 0.84
43 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (40 bp):
GGGTACATTCCAGCCCACCAGTTCAGATGCCATCTCTGCA
Found at i:63020 original size:25 final size:23
Alignment explanation
Indices: 62967--63029 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
62957 AACCATGGAG
62967 GAAAA-AAAC-AAAAAAAAATGA
1 GAAAAGAAACAAAAAAAAAATGA
*
62988 -AAATGAAACAAAAAAAAAATCTGA
1 GAAAAGAAACAAAAAAAAAA--TGA
*
63012 GAAAAGAAA-AGAAAAAAA
1 GAAAAGAAACAAAAAAAAA
63030 GAAGGGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 9 0.26
24 11 0.32
25 7 0.21
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.06
Consensus pattern (23 bp):
GAAAAGAAACAAAAAAAAAATGA
Found at i:65958 original size:2 final size:2
Alignment explanation
Indices: 65951--65980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
65941 AGTTGTCGCC
65951 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65981 TTAGTGTATA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:66388 original size:17 final size:18
Alignment explanation
Indices: 66352--66389 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
66342 TGAAATTAAA
*
66352 TTATAATTTCTTCAAATT
1 TTATAATTTATTCAAATT
*
66370 TTATGATTTATTC-AATT
1 TTATAATTTATTCAAATT
66387 TTA
1 TTA
66390 AAGATCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATAATTTATTCAAATT
Found at i:70666 original size:9 final size:9
Alignment explanation
Indices: 70641--70688 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
70631 ACTCCTCGCT
*
70641 GTCATCATC
1 GTCATCGTC
*
70650 GTCGTCGTC
1 GTCATCGTC
*
70659 GTCATCGTT
1 GTCATCGTC
*
70668 ATCATCGTC
1 GTCATCGTC
*
70677 GTCGTCGTC
1 GTCATCGTC
70686 GTC
1 GTC
70689 CTGAGCAGGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.10, C:0.31, G:0.23, T:0.35
Consensus pattern (9 bp):
GTCATCGTC
Found at i:71084 original size:18 final size:18
Alignment explanation
Indices: 71027--71084 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
71017 GAAGGCGATG
71027 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
* *
71045 GCGACATCATATATGGTT
1 GCGGCATCATATATGGCT
71063 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
71081 GCGG
1 GCGG
71085 TGGCTGCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:72501 original size:13 final size:13
Alignment explanation
Indices: 72483--72508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72473 CCATTTATCA
72483 TTTTAAAACACAC
1 TTTTAAAACACAC
72496 TTTTAAAACACAC
1 TTTTAAAACACAC
72509 ACTTCTCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TTTTAAAACACAC
Found at i:82285 original size:111 final size:111
Alignment explanation
Indices: 82148--82480 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
82138 ATTACAAAAA
82148 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
82213 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
82259 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
82324 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
82370 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
82435 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
82481 ATGATTTCCA
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 218 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:82562 original size:17 final size:18
Alignment explanation
Indices: 82542--82577 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
82532 GAATTATATT
82542 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
82559 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
82577 A
1 A
82578 TTATATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:82638 original size:10 final size:10
Alignment explanation
Indices: 82623--82663 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
82613 CCTTAAAAGG
82623 GAGAGAATTT
1 GAGAGAATTT
82633 GAGAGAAATTT
1 GAGAG-AATTT
82644 -AGAGAATTT
1 GAGAGAATTT
82653 GAGAGAATTT
1 GAGAGAATTT
82663 G
1 G
82664 GTGTGATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.17
10 19 0.66
11 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:82836 original size:50 final size:50
Alignment explanation
Indices: 82782--82907 Score: 198
Period size: 50 Copynumber: 2.5 Consensus size: 50
82772 AGATACCTAG
82782 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGACACCAAATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGACACCAAATCACC
* ** * *
82832 GTATATCGCGGGGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAGC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGACACCAAATCACC
*
82882 GTATAGCGCGGTTCAGGGGGCGCGCT
1 GTATAGCGCGGATCAGGGGGCGCGCT
82908 TTACTGCTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.15
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGACACCAAATCACC
Found at i:91132 original size:4 final size:4
Alignment explanation
Indices: 91123--91413 Score: 582
Period size: 4 Copynumber: 72.8 Consensus size: 4
91113 GAGTCATGAC
91123 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
91171 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
91219 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
91267 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
91315 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
91363 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
91411 TGT
1 TGT
91414 GTGTGTGTGT
Statistics
Matches: 287, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 287 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:96783 original size:30 final size:30
Alignment explanation
Indices: 96718--96800 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
96708 TAAAATATAT
* *
96718 AACTTTTCAAAATTATAATTTTGGTCCTTA
1 AACTTTTCAAAATTATAATTTAGCTCCTTA
* * *
96748 TACTTTTCAAAATTTATACTTTAGCTTC-TA
1 AACTTTTCAAAA-TTATAATTTAGCTCCTTA
*
96778 AAC-TTTCAAAACTTATATTTTAG
1 AACTTTTCAAAA-TTATAATTTAG
96801 TTACTAGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 18 0.41
30 15 0.34
31 11 0.25
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (30 bp):
AACTTTTCAAAATTATAATTTAGCTCCTTA
Found at i:102567 original size:36 final size:36
Alignment explanation
Indices: 102520--102694 Score: 278
Period size: 36 Copynumber: 4.9 Consensus size: 36
102510 TCGGTGCTGG
* *
102520 ACATTAATACACGAATGTACCAAAGATGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
102556 ACATTGATACACGAATATACCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
102592 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
102628 ACATTGATACACGAATGTATCAAAGCTGATACGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
102664 ACATTGATACGCGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
102695 ATACTCAACT
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 130 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:106268 original size:28 final size:28
Alignment explanation
Indices: 106228--106286 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
106218 TGTATCTTTC
106228 CTTGCTAATATATCTGCTTTATT-ATTTA
1 CTTGCTAATATATCTGCTTTATTGA-TTA
* * *
106256 CTTGCTATTATATTTGTTTTATTGATTA
1 CTTGCTAATATATCTGCTTTATTGATTA
106284 CTT
1 CTT
106287 TTAAATATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (28 bp):
CTTGCTAATATATCTGCTTTATTGATTA
Found at i:114574 original size:10 final size:9
Alignment explanation
Indices: 114547--114572 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
114537 ATCGTAGTTT
114547 ATTTTTTTA
1 ATTTTTTTA
114556 ATTTTTTTA
1 ATTTTTTTA
114565 ATTTTTTT
1 ATTTTTTT
114573 TATCAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:119928 original size:21 final size:21
Alignment explanation
Indices: 119903--119955 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
119893 TCCAAAAGGT
119903 AGTATCAATACCCAAGAGACC
1 AGTATCAATACCCAAGAGACC
*
119924 AGTATCAATACCCAATAGACC
1 AGTATCAATACCCAAGAGACC
* *
119945 AATATCGATAC
1 AGTATCAATAC
119956 TGTTAGGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.19
Consensus pattern (21 bp):
AGTATCAATACCCAAGAGACC
Found at i:126690 original size:21 final size:22
Alignment explanation
Indices: 126664--126719 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
126654 TTCTAGCTGC
*
126664 GAGTATCGATACTCATT-TTAA
1 GAGTATCGATACTCATTCTCAA
*
126685 GAGTATCAATACT--TTCTCAA
1 GAGTATCGATACTCATTCTCAA
*
126705 GGGTATCGATACTCA
1 GAGTATCGATACTCA
126720 AGGGGTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 2 0.07
20 14 0.50
21 12 0.43
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (22 bp):
GAGTATCGATACTCATTCTCAA
Found at i:126918 original size:20 final size:20
Alignment explanation
Indices: 126869--126920 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
126859 CGATGGTATT
* *
126869 GATACCTAAAAGGCAATATC
1 GATAACTAATAGGCAATATC
126889 GATAACTAATAGGCAATATC
1 GATAACTAATAGGCAATATC
126909 GATAACTAATAG
1 GATAACTAATAG
126921 ACCAGTATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (20 bp):
GATAACTAATAGGCAATATC
Found at i:126931 original size:21 final size:20
Alignment explanation
Indices: 126882--126933 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
126872 ACCTAAAAGG
*
126882 CAATATCGATAACTAATAGG
1 CAATATCGATAACTAATAGC
126902 CAATATCGATAACTAATAGAC
1 CAATATCGATAACTAATAG-C
*
126923 CAGTATCGATA
1 CAATATCGATA
126934 CTGTAAGGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (20 bp):
CAATATCGATAACTAATAGC
Found at i:127960 original size:17 final size:17
Alignment explanation
Indices: 127934--127969 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
127924 ATGAGATTGC
127934 TTCAAATGGTAAAATAT
1 TTCAAATGGTAAAATAT
*
127951 TTCAAGTGGTAAAATAT
1 TTCAAATGGTAAAATAT
127968 TT
1 TT
127970 TAATTTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (17 bp):
TTCAAATGGTAAAATAT
Found at i:128491 original size:29 final size:30
Alignment explanation
Indices: 128458--128518 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
128448 AAATTTTGTC
**
128458 TAGTGACTAAAATATAAGTTTTG-AAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
* *
128487 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
128517 TA
1 TA
128519 AGGAACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:134438 original size:12 final size:12
Alignment explanation
Indices: 134421--134445 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
134411 TTGTAAATGC
134421 ACATGACGTTGG
1 ACATGACGTTGG
134433 ACATGACGTTGG
1 ACATGACGTTGG
134445 A
1 A
134446 GAACCATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:136365 original size:21 final size:21
Alignment explanation
Indices: 136339--136391 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
136329 GATATATGAG
*
136339 TGTATCGATACCCCCTTGCTA
1 TGTATCGATACCCCCTCGCTA
*
136360 TGTATCGATACCCCCTCGTTA
1 TGTATCGATACCCCCTCGCTA
136381 TGTATCGATAC
1 TGTATCGATAC
136392 ACTTTGAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (21 bp):
TGTATCGATACCCCCTCGCTA
Found at i:136405 original size:21 final size:21
Alignment explanation
Indices: 136381--136438 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
136371 CCCCTCGTTA
136381 TGTATCGATACACTTTGAATG
1 TGTATCGATACACTTTGAATG
* * *
136402 TGTACCGATATATTCCTTGAATG
1 TGTATCGATACA--CTTTGAATG
136425 TGTATCGATACACT
1 TGTATCGATACACT
136439 CTTAGGTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 11 0.38
23 18 0.62
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACACTTTGAATG
Found at i:137493 original size:15 final size:15
Alignment explanation
Indices: 137473--137501 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
137463 TAACACCTTT
137473 GGTTTAGATAACGAG
1 GGTTTAGATAACGAG
137488 GGTTTAGATAACGA
1 GGTTTAGATAACGA
137502 AAAAGAAATT
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:0.34, C:0.07, G:0.31, T:0.28
Consensus pattern (15 bp):
GGTTTAGATAACGAG
Found at i:138653 original size:12 final size:12
Alignment explanation
Indices: 138636--138662 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
138626 GGGAGTAATT
138636 TTTCAAAAATAA
1 TTTCAAAAATAA
138648 TTTCAAAAATAA
1 TTTCAAAAATAA
138660 TTT
1 TTT
138663 TGAGGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTCAAAAATAA
Found at i:138813 original size:17 final size:19
Alignment explanation
Indices: 138771--138816 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
138761 CTATTGAATT
* *
138771 TTAAAATTTTATATTCGGT
1 TTAAAATTATATATTCGGA
138790 TTAAAATTATATATT-GGA
1 TTAAAATTATATATTCGGA
138808 TT-AAATTAT
1 TTAAAATTAT
138817 TCGAATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 4 0.16
19 14 0.56
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (19 bp):
TTAAAATTATATATTCGGA
Found at i:140699 original size:2 final size:2
Alignment explanation
Indices: 140694--140718 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
140684 ATATGTCTGA
140694 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
140719 GTTAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:140980 original size:28 final size:28
Alignment explanation
Indices: 140940--140998 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
140930 CCTAAACCGA
140940 GCCTATGTTATATAAAAAATATGTGAAT
1 GCCTATGTTATATAAAAAATATGTGAAT
140968 GCCTATGTTATATAAAAAATATGTGAAT
1 GCCTATGTTATATAAAAAATATGTGAAT
140996 GCC
1 GCC
140999 ACTAGGACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (28 bp):
GCCTATGTTATATAAAAAATATGTGAAT
Found at i:146498 original size:27 final size:28
Alignment explanation
Indices: 146440--146551 Score: 140
Period size: 27 Copynumber: 4.1 Consensus size: 28
146430 GAAGATGAAG
* ** * *
146440 AAATGAGAGAGAAAAAAGTAAAAGTTAC
1 AAATGAAAGAGAAATGAGAAAAAGTTAA
146468 AAATGAAAGAGAAATGAG-AAAAGTTAA
1 AAATGAAAGAGAAATGAGAAAAAGTTAA
*
146495 AAATGAAAGAGAAATGA-AAAAGGTTAA
1 AAATGAAAGAGAAATGAGAAAAAGTTAA
*
146522 AAATGAAATAGAAATG-GAAAAAGTTAA
1 AAATGAAAGAGAAATGAGAAAAAGTTAA
146549 AAA
1 AAA
146552 AATTGAGAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
27 60 0.80
28 15 0.20
ACGTcount: A:0.63, C:0.01, G:0.21, T:0.15
Consensus pattern (28 bp):
AAATGAAAGAGAAATGAGAAAAAGTTAA
Found at i:151137 original size:21 final size:21
Alignment explanation
Indices: 151095--151137 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
151085 AAATGAGCTA
* *
151095 TGACTTTGAAGTAAGGCGCCT
1 TGACTATGAAGTAAAGCGCCT
*
151116 TGACTATGAAGTAAAGCTCCT
1 TGACTATGAAGTAAAGCGCCT
151137 T
1 T
151138 TATTCTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (21 bp):
TGACTATGAAGTAAAGCGCCT
Found at i:156296 original size:10 final size:10
Alignment explanation
Indices: 156281--156309 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
156271 GGAGTACCCA
156281 TTTCGATAGT
1 TTTCGATAGT
156291 TTTCGATAGT
1 TTTCGATAGT
156301 TTTCGATAG
1 TTTCGATAG
156310 AGATCTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (10 bp):
TTTCGATAGT
Found at i:160109 original size:13 final size:13
Alignment explanation
Indices: 160091--160155 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
160081 GTCATAAATC
* *
160091 TATGACGCATATT
1 TATGACACACATT
*
160104 TATGACACGCATT
1 TATGACACACATT
160117 TATGACACACATT
1 TATGACACACATT
** *
160130 TATGATGCGCATT
1 TATGACACACATT
*
160143 TATGACACGCATT
1 TATGACACACATT
160156 GAGCGTCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (13 bp):
TATGACACACATT
Found at i:160120 original size:26 final size:26
Alignment explanation
Indices: 160091--160155 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
160081 GTCATAAATC
* *
160091 TATGACGCATATTTATGACACGCATT
1 TATGACACACATTTATGACACGCATT
**
160117 TATGACACACATTTATGATGCGCATT
1 TATGACACACATTTATGACACGCATT
*
160143 TATGACACGCATT
1 TATGACACACATT
160156 GAGCGTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (26 bp):
TATGACACACATTTATGACACGCATT
Found at i:160233 original size:85 final size:84
Alignment explanation
Indices: 160138--160292 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 84
160128 TTTATGATGC
* * *
160138 GCATTTATGACACGCATTG-AGCGTCATTGAAGCCCCCGTCATAAATGAAGATGACACACATTTG
1 GCATGTATGACACACATTGCA-CGTCATTGAAACCCCCGTCATAAATGAAGATGACACACA-TTG
160202 TGTGTCATAAATTTATGACAT
64 TGTGTCATAAATTTATGACAT
** *
160223 GCATGTATGACTTACATTGCATGTCATTGAAACCCCCGTCATAAATGAAGATGACACACATTGTG
1 GCATGTATGACACACATTGCACGTCATTGAAACCCCCGTCATAAATGAAGATGACACACATTGTG
160288 TGTCA
66 TGTCA
160293 GAGAGTATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 10 0.16
85 52 0.83
86 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (84 bp):
GCATGTATGACACACATTGCACGTCATTGAAACCCCCGTCATAAATGAAGATGACACACATTGTG
TGTCATAAATTTATGACAT
Found at i:160292 original size:44 final size:44
Alignment explanation
Indices: 160144--160292 Score: 108
Period size: 44 Copynumber: 3.5 Consensus size: 44
160134 ATGCGCATTT
* * * *
160144 ATGACACGCATTGAGCGTCATTGAAGCCCCCGTCATAAATGAAG
1 ATGACACACATTGTGTGTCATTGAAACCCCCGTCATAAATGAAG
***** * ** *
160188 ATGACACACATTTGTGTGTCA-T-AAATTTATGACATGCATG--T
1 ATGACACACA-TTGTGTGTCATTGAAACCCCCGTCATAAATGAAG
** **
160229 ATGACTTACATTGCATGTCATTGAAACCCCCGTCATAAATGAAG
1 ATGACACACATTGTGTGTCATTGAAACCCCCGTCATAAATGAAG
160273 ATGACACACATTGTGTGTCA
1 ATGACACACATTGTGTGTCA
160293 GAGAGTATAT
Statistics
Matches: 70, Mismatches: 30, Indels: 10
0.64 0.27 0.09
Matches are distributed among these distances:
40 8 0.11
41 9 0.13
42 10 0.14
43 9 0.13
44 26 0.37
45 8 0.11
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
ATGACACACATTGTGTGTCATTGAAACCCCCGTCATAAATGAAG
Found at i:166561 original size:2 final size:2
Alignment explanation
Indices: 166554--166691 Score: 237
Period size: 2 Copynumber: 70.5 Consensus size: 2
166544 ATCGGACCAG
166554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
166596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
166638 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T- TA AA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
166678 TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
166692 TATTTATTTA
Statistics
Matches: 129, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
1 3 0.02
2 126 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:166804 original size:29 final size:30
Alignment explanation
Indices: 166764--166821 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
166754 TCGTCCTCGT
166764 CCCCGTCCCCGTTTAGCATAAACA-TTTTC
1 CCCCGTCCCCGTTTAGCATAAACAGTTTTC
166793 CCCCGTCCCCGTTTAGCATAAACAGTTTT
1 CCCCGTCCCCGTTTAGCATAAACAGTTTT
166822 TTTCCCGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.21, C:0.36, G:0.12, T:0.31
Consensus pattern (30 bp):
CCCCGTCCCCGTTTAGCATAAACAGTTTTC
Found at i:167316 original size:29 final size:31
Alignment explanation
Indices: 167283--167344 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
167273 CTTTATGGAT
*
167283 TTTATGTTGGTACTTTATGTTT-AA-TACTC
1 TTTATGTTGGTACTTAATGTTTGAACTACTC
*
167312 TTTATTTTGGTACTTAATGTTTGAACTACTC
1 TTTATGTTGGTACTTAATGTTTGAACTACTC
167343 TT
1 TT
167345 GTTGATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.69
30 2 0.07
31 7 0.24
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (31 bp):
TTTATGTTGGTACTTAATGTTTGAACTACTC
Found at i:167872 original size:20 final size:20
Alignment explanation
Indices: 167843--167883 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
167833 CAAAAACCCT
*
167843 TGTCAATCTCGCGACCAACA
1 TGTCAATCTCGAGACCAACA
* *
167863 TGTCAGTCTCGATACCAACA
1 TGTCAATCTCGAGACCAACA
167883 T
1 T
167884 TCTAATGGAC
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:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (20 bp):
TGTCAATCTCGAGACCAACA
Found at i:169486 original size:285 final size:286
Alignment explanation
Indices: 168976--169518 Score: 849
Period size: 285 Copynumber: 1.9 Consensus size: 286
168966 GATGACAACG
** * * *
168976 GAAGCAAGGAACAAGTAGGGTTTCATGAAGAAAAGTTTTTTTTAAGAATTGGATTGAGTCCTTGA
1 GAAGCAAGGAACAAGTAGCATTTCATGAAGAAAAGTATGTTTTAAGAACTGGATTGAGTCCTTGA
* ** *
169041 ATGGTGAAAGTAAGAGCGTTCAATTGAGAGAATGATGATGGGAAAAGCACCAGCCTCGATCCAAC
66 ACGGTGAAAGTAAGAGCGGGCAATTAAGAGAATGATGATGGGAAAAGCACCAGCCTCGATCCAAC
* *
169106 TCAAGAACCAGACTAGTTTACTGCCATAGATAAAGTAAATGAGCATCATAAGTGGACCAGCACAA
131 TCAAGAACCAGACTAGTTCACCGCCATAGATAAAGTAAATGAGCATCATAAGTGGACCAGCACAA
* *
169171 TTGCCTATGGAAAGGATGATGTAGTTTATTA-TTAGAATA-GCTTTTATCATAATGTTAGTGTTT
196 TTGCCTATGGAAAGGATGATGTAGTTTATTATTTAGAA-AGGCTTTCATCATAATGGTAGTGTTT
169234 GATTTAGGTTCCTTGCTTTTATTATTA
260 GATTTAGGTTCCTTGCTTTTATTATTA
*
169261 GAAGCAAGGAACAAGTAGCATTTCATGAAGAAAAGTATGTTTTGAGAACTGGATTGAGTCCTTGA
1 GAAGCAAGGAACAAGTAGCATTTCATGAAGAAAAGTATGTTTTAAGAACTGGATTGAGTCCTTGA
* * * *
169326 ACGGTGAAAGTAAGCGCGGGCGATTAAGAGAATGATGATGGGAAAAGCA-CTGATCTCGATCCAA
66 ACGGTGAAAGTAAGAGCGGGCAATTAAGAGAATGATGATGGGAAAAGCACCAG-CCTCGATCCAA
** * *
169390 CTTGAGAACCAGACTAGTTCACCGCCATGGATAAAGTAAATGTGCATCATAAGTGGACCAGCACA
130 CTCAAGAACCAGACTAGTTCACCGCCATAGATAAAGTAAATGAGCATCATAAGTGGACCAGCACA
169455 ATTGCCTATGGAAAGGATGATGTAGTTTATTATTTAGAAAGGCTTTCATCATAATGGTAGTGTT
195 ATTGCCTATGGAAAGGATGATGTAGTTTATTATTTAGAAAGGCTTTCATCATAATGGTAGTGTT
169519 GGGACCGTCG
Statistics
Matches: 233, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
284 2 0.01
285 204 0.88
286 27 0.12
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (286 bp):
GAAGCAAGGAACAAGTAGCATTTCATGAAGAAAAGTATGTTTTAAGAACTGGATTGAGTCCTTGA
ACGGTGAAAGTAAGAGCGGGCAATTAAGAGAATGATGATGGGAAAAGCACCAGCCTCGATCCAAC
TCAAGAACCAGACTAGTTCACCGCCATAGATAAAGTAAATGAGCATCATAAGTGGACCAGCACAA
TTGCCTATGGAAAGGATGATGTAGTTTATTATTTAGAAAGGCTTTCATCATAATGGTAGTGTTTG
ATTTAGGTTCCTTGCTTTTATTATTA
Found at i:172483 original size:39 final size:38
Alignment explanation
Indices: 172417--172521 Score: 126
Period size: 39 Copynumber: 2.8 Consensus size: 38
172407 ATTTTTATAT
172417 TTTATTAAAATAA-AATTATTTTAAATTATATTAATTA
1 TTTATTAAAATAATAATTATTTTAAATTATATTAATTA
*
172454 TTTATTGAAATAATAATATATTATT-AATTATATTAATTA
1 TTTATTAAAATAATAAT-TATT-TTAAATTATATTAATTA
* * *
172493 ATTGTTAAAATAAT-ATTATTGTAATATTA
1 TTTATTAAAATAATAATTATTTTAA-ATTA
172522 AAAACTATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
36 1 0.02
37 17 0.29
38 9 0.16
39 29 0.50
40 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (38 bp):
TTTATTAAAATAATAATTATTTTAAATTATATTAATTA
Found at i:172626 original size:27 final size:25
Alignment explanation
Indices: 172595--172666 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
172585 TAAATATTAC
172595 ATAATTTAATATTATTATTTTATGAA
1 ATAATTTAATATTATTATTTTAT-AA
* * *
172621 ATTAA-TAAATAATATTAATTTTATTA
1 A-TAATTTAATATTATT-ATTTTATAA
*
172647 ATAATTTATTATATATTATT
1 ATAATTTAATAT-TATTATT
172667 ATAATAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
25 3 0.08
26 19 0.53
27 14 0.39
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
ATAATTTAATATTATTATTTTATAA
Found at i:172849 original size:28 final size:27
Alignment explanation
Indices: 172779--172849 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 27
172769 ATTTAATAAT
* *
172779 TAATATTTTCATTAAAATATATTAAAA
1 TAATATTTTAATTAAAATATATAAAAA
* *
172806 TAATATATTAATATTAAATATATAAAACAA
1 TAATATTTTAAT-TAAAATATAT-AAA-AA
172836 TAATATTTTAATTA
1 TAATATTTTAATTA
172850 TTTATGCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 10 0.29
28 9 0.26
29 3 0.09
30 13 0.37
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATATTTTAATTAAAATATATAAAAA
Found at i:176131 original size:2 final size:2
Alignment explanation
Indices: 176124--176167 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
176114 AATATTGACT
*
176124 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
176166 TA
1 TA
176168 AACTCAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:179957 original size:38 final size:38
Alignment explanation
Indices: 179862--179960 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
179852 ACCGTAGCTG
* * * **
179862 ATATGTAGCTGGATTCATGCACTTAACTATTGCCATTA
1 ATATGTAGTTGGATTCATGTATTTAACTATTGCCAGGA
* *
179900 ATATGTAGTTGGATTCATGTATTTAACTCTTGTCAGGA
1 ATATGTAGTTGGATTCATGTATTTAACTATTGCCAGGA
*
179938 ATATATAGTTGGATTCATGTATT
1 ATATGTAGTTGGATTCATGTATT
179961 ATAGAACAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (38 bp):
ATATGTAGTTGGATTCATGTATTTAACTATTGCCAGGA
Found at i:188827 original size:18 final size:18
Alignment explanation
Indices: 188804--188862 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
188794 AAGTTTAATC
*
188804 AATACATAAAGCAACAAA
1 AATACATGAAGCAACAAA
*
188822 AATACACTGAAGTAATC---
1 AATACA-TGAAGCAA-CAAA
188839 AATACATGAAGCAACAAA
1 AATACATGAAGCAACAAA
188857 AATACA
1 AATACA
188863 CCCAGTTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 1 0.03
16 7 0.21
17 6 0.18
18 12 0.36
19 6 0.18
20 1 0.03
ACGTcount: A:0.59, C:0.17, G:0.08, T:0.15
Consensus pattern (18 bp):
AATACATGAAGCAACAAA
Found at i:190135 original size:21 final size:20
Alignment explanation
Indices: 190089--190135 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
190079 TCTGATGATC
190089 ATTTT-ATAATTATTTAAAA
1 ATTTTAATAATTATTTAAAA
** *
190108 AAATTAATAATTATTTTGAAA
1 ATTTTAATAATTA-TTTAAAA
190129 ATTTTAA
1 ATTTTAA
190136 AAAATTAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.14
20 7 0.33
21 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTTAATAATTATTTAAAA
Found at i:190161 original size:29 final size:29
Alignment explanation
Indices: 190097--190161 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
190087 TCATTTTATA
***
190097 ATTATTTAAAAAAATTAATAATTATTTTG
1 ATTATTTAAAAAAATTAATAATTAAACTG
** *
190126 AAAATTTTAAAAAATTAATAATTAAACTG
1 ATTATTTAAAAAAATTAATAATTAAACTG
190155 ATTATTT
1 ATTATTT
190162 GAGTTTAATC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
ATTATTTAAAAAAATTAATAATTAAACTG
Found at i:190315 original size:24 final size:24
Alignment explanation
Indices: 190288--190333 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
190278 AATTAATTAA
190288 TTTTAAAAATAATTATG-ATTTTAT
1 TTTTAAAAA-AATTATGAATTTTAT
*
190312 TTTTGAAAAAATTATGAATTTT
1 TTTTAAAAAAATTATGAATTTT
190334 GGTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (24 bp):
TTTTAAAAAAATTATGAATTTTAT
Found at i:190888 original size:23 final size:22
Alignment explanation
Indices: 190847--190890 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
190837 TGAATGCAAC
* *
190847 ATTAATAAATGTCACATATAAG
1 ATTAATAAATATCAAATATAAG
190869 ATTAATGAAATATCAAATATAA
1 ATTAAT-AAATATCAAATATAA
190891 CATGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (22 bp):
ATTAATAAATATCAAATATAAG
Found at i:191597 original size:29 final size:29
Alignment explanation
Indices: 191565--191621 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
191555 ATTTTAAAAT
191565 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
191594 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
191622 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:191716 original size:20 final size:19
Alignment explanation
Indices: 191677--191718 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
191667 TTTCTTCGAT
191677 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
191696 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
191716 ATT
1 ATT
191719 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:191849 original size:20 final size:19
Alignment explanation
Indices: 191826--191863 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
191816 TAAGATTTTA
191826 ATAAATAAATATTATTTATT
1 ATAAATAAATA-TATTTATT
*
191846 ATAAATATATATATTTAT
1 ATAAATAAATATATTTAT
191864 GGCTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATAAATATATTTATT
Found at i:193238 original size:3 final size:3
Alignment explanation
Indices: 193230--193295 Score: 89
Period size: 3 Copynumber: 21.7 Consensus size: 3
193220 ATATTTAATT
* *
193230 TAA TAA TAA TAA TAA TATA GAA TAA TAA TAA T-A TATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA
193276 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
193296 GAATGAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 50 0.89
4 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:193545 original size:76 final size:76
Alignment explanation
Indices: 193443--193789 Score: 613
Period size: 76 Copynumber: 4.6 Consensus size: 76
193433 GAGGTCTTAA
* * * *
193443 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
193508 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
193519 AAACATCATGCACTGTAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCGAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
193584 AGACTTTTTGG
66 AGGCTTTTTGG
193595 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
193660 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
193671 AAACATCATGTAATGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
193736 AGGCTTTTTGG
66 AGGCTTTTTGG
193747 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
193790 TTGGAAACAT
Statistics
Matches: 257, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 257 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:194098 original size:185 final size:186
Alignment explanation
Indices: 193782--194194 Score: 801
Period size: 185 Copynumber: 2.2 Consensus size: 186
193772 AGATGACCCT
*
193782 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAA
1 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAA
193847 AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
66 AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
193912 ACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACATCAAAAAGCTCCCG
131 ACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACATCAAAAAGCTCCCG
193968 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAATAGTTTACTAAGT-AA
1 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAA
194032 AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
66 AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
*
194097 ACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACATCTAAAAGCTCCCG
131 ACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACATCAAAAAGCTCCCG
194153 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
194195 ACCCTAAGGC
Statistics
Matches: 225, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 164 0.73
186 61 0.27
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (186 bp):
AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAA
AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
ACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACATCAAAAAGCTCCCG
Found at i:194263 original size:76 final size:76
Alignment explanation
Indices: 194135--194422 Score: 504
Period size: 76 Copynumber: 3.8 Consensus size: 76
194125 TCAAAATAAC
* *
194135 AACATCTAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
194200 AAGGCTTTGAA
66 AAGGCTTTGAA
** *
194211 AACATCAAAAAGCTCCTAAAGGCTTTTTGGAAACATCATGCACTGTATGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
194276 AAGGCTTTGAA
66 AAGGCTTTGAA
194287 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
*
194352 AAGGCTTTTAA
66 AAGGCTTTGAA
* *
194363 AACGTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
194423 TGGGAAATAG
Statistics
Matches: 201, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 201 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:195124 original size:22 final size:22
Alignment explanation
Indices: 195096--195150 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
195086 CATAAAGCTT
*
195096 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAACCTA
*
195118 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAACCTA
195140 TCATCTTTGAA
1 TCATCTTTGAA
195151 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACCTA
Found at i:199854 original size:15 final size:14
Alignment explanation
Indices: 199833--199878 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
199823 TTGGTTCAAA
199833 TTTTTTTCCTTTTT
1 TTTTTTTCCTTTTT
199847 TCTTTTTTCCTTATTT
1 T-TTTTTTCCTT-TTT
* *
199863 TTTTCTTCATTTTT
1 TTTTTTTCCTTTTT
199877 TT
1 TT
199879 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.21
15 18 0.64
16 4 0.14
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTCCTTTTT
Found at i:205784 original size:20 final size:19
Alignment explanation
Indices: 205745--205786 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
205735 TTTCTTCGAT
205745 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
205764 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
205784 ATT
1 ATT
205787 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:205897 original size:120 final size:120
Alignment explanation
Indices: 205658--205888 Score: 299
Period size: 120 Copynumber: 1.9 Consensus size: 120
205648 AATATTAGTT
* *
205658 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCTAGGTGCCT
* * *
205723 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCCTTTCTTCAATATCAAAAAATAAATAAATAATTAAAACAATTAA
** * *
205778 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCTAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCTAGGTGC
* * * *
205842 TTTAATACTGC-CCTTTCTT-AATATCGAAAAATAAATAAAT-ATTAAAA
64 CTTAAGACAGCTCCTTTCTTCAATATCAAAAAATAAATAAATAATTAAAA
205889 TAGGATTAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
118 7 0.07
119 24 0.25
120 47 0.49
121 18 0.19
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCTAGGTGCCT
TAAGACAGCTCCTTTCTTCAATATCAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:205954 original size:20 final size:19
Alignment explanation
Indices: 205929--205966 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
205919 TAAGATTTTA
205929 ATAAATAAATATTATTTATT
1 ATAAATAAATA-TATTTATT
*
205949 ATAAATATATATATTTAT
1 ATAAATAAATATATTTAT
205967 GGCTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATAAATATATTTATT
Found at i:207377 original size:3 final size:3
Alignment explanation
Indices: 207364--207442 Score: 54
Period size: 3 Copynumber: 26.7 Consensus size: 3
207354 ATATTTAATT
* * * *
207364 TAA TGA TAA TAA TAA TATA GAA TAA TAA TAA TAA TAA T-A TAT TTA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
207409 T-T TAA TAA TAA TAA TTA TTA TTA TTA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
207443 GAATGAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.92
4 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:207414 original size:22 final size:21
Alignment explanation
Indices: 207369--207442 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
207359 TAATTTAATG
** *
207369 ATAATAATAATATAGAATAATA
1 ATAATAATAAT-TATTATTATA
*
207391 ATAATAATAATATATT-TATTTA
1 ATAATAATAAT-TATTAT-TATA
*
207413 ATAATAATAATTATTATTATT
1 ATAATAATAATTATTATTATA
207434 ATAATAATA
1 ATAATAATA
207443 GAATGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 16 0.36
22 28 0.64
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
ATAATAATAATTATTATTATA
Found at i:212550 original size:15 final size:14
Alignment explanation
Indices: 212528--212557 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
212518 AATTTTTAAA
212528 TTAAATTTATTTAT
1 TTAAATTTATTTAT
212542 TTAATATTTATTTAT
1 TTAA-ATTTATTTAT
212557 T
1 T
212558 AATGAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAAATTTATTTAT
Found at i:213506 original size:21 final size:21
Alignment explanation
Indices: 213482--213590 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 21
213472 ACAGCTCATA
*
213482 ATTTGCACCGATGTGCCACAT
1 ATTTGCACCGAAGTGCCACAT
213503 ATTTGTC-CCGAAG-GACCACAT
1 ATTTG-CACCGAAGTG-CCACAT
* *
213524 AGTTTTACACCGAAGTGTCACAT
1 A--TTTGCACCGAAGTGCCACAT
* *
213547 AGATTGCACCGAAATGCCACAT
1 A-TTTGCACCGAAGTGCCACAT
213569 ATTTGTC-CCGAA-TGACCACAT
1 ATTTG-CACCGAAGTG-CCACAT
213590 A
1 A
213591 AAACCCTCGA
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.04
21 32 0.45
22 20 0.28
23 15 0.21
24 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (21 bp):
ATTTGCACCGAAGTGCCACAT
Found at i:213762 original size:21 final size:21
Alignment explanation
Indices: 213733--213773 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
213723 TATTCATATT
213733 CACTGGTTCAAAGCTCACATC
1 CACTGGTTCAAAGCTCACATC
* *
213754 CACTTGTTCAAAGTTCACAT
1 CACTGGTTCAAAGCTCACAT
213774 TTCCATAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (21 bp):
CACTGGTTCAAAGCTCACATC
Found at i:220417 original size:21 final size:21
Alignment explanation
Indices: 220380--220480 Score: 100
Period size: 21 Copynumber: 4.7 Consensus size: 21
220370 ATAATTTGCA
220380 CCGAAGTGCCA-ATATTTGTC
1 CCGAAGTGCCACATATTTGTC
*
220400 CCGAAG-GACCACATATTTTTGC
1 CCGAAGTG-CCACATATTTGT-C
* * *
220422 ACCAAAGTGCCACATAGATTGTA
1 -CCGAAGTGCCACATA-TTTGTC
220445 CCGAAGTGCCACATATTTGTC
1 CCGAAGTGCCACATATTTGTC
220466 CCGAAG-GACCACATA
1 CCGAAGTG-CCACATA
220481 AACCCTCGAC
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.02
20 10 0.15
21 24 0.36
22 15 0.23
23 12 0.18
24 4 0.06
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (21 bp):
CCGAAGTGCCACATATTTGTC
Found at i:220422 original size:43 final size:45
Alignment explanation
Indices: 220374--220462 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
220364 CAACTCATAA
* * *
220374 TTTGCACCGAAGTGCCA-ATA-TTTGTCCCGAAG-GACCACATATT
1 TTTGCACCAAAGTGCCACATAGATTGTACCGAAGTG-CCACATATT
220417 TTTGCACCAAAGTGCCACATAGATTGTACCGAAGTGCCACATATT
1 TTTGCACCAAAGTGCCACATAGATTGTACCGAAGTGCCACATATT
220462 T
1 T
220463 GTCCCGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 16 0.40
44 3 0.08
45 20 0.50
46 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
TTTGCACCAAAGTGCCACATAGATTGTACCGAAGTGCCACATATT
Found at i:220640 original size:21 final size:21
Alignment explanation
Indices: 220614--220662 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
220604 TAGAGTTTTT
220614 TCACATTCAC-TGATTCAAAGC
1 TCACATTCACTTG-TTCAAAGC
*
220635 TCACATTCACTTGTTCAAAGT
1 TCACATTCACTTGTTCAAAGC
220656 TCACATT
1 TCACATT
220663 TCCATAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (21 bp):
TCACATTCACTTGTTCAAAGC
Found at i:221090 original size:19 final size:22
Alignment explanation
Indices: 221042--221093 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
221032 TACCTTTATA
*
221042 GTACCGATACTTCCCTTCAAGG
1 GTACCGATACCTCCCTTCAAGG
*
221064 GTATCGATACCT-CC-TCAA-G
1 GTACCGATACCTCCCTTCAAGG
221083 GTACCGATACC
1 GTACCGATACC
221094 GAATCAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 2 0.07
22 10 0.37
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (22 bp):
GTACCGATACCTCCCTTCAAGG
Found at i:221199 original size:42 final size:42
Alignment explanation
Indices: 221153--221242 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
221143 CCTAGTATTG
* **
221153 ATACTACCCACACAATATCGATACCCTCTACAATTAGTATCA
1 ATACTACCCACACAATATCGATACCATCTACAACGAGTATCA
* * * *
221195 ATACTACCTACACAGTATCGATACCATCTTCAACGAGTATCG
1 ATACTACCCACACAATATCGATACCATCTACAACGAGTATCA
221237 ATACTA
1 ATACTA
221243 ACCTTAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.27
Consensus pattern (42 bp):
ATACTACCCACACAATATCGATACCATCTACAACGAGTATCA
Found at i:222800 original size:32 final size:32
Alignment explanation
Indices: 222758--222823 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
222748 TTTTACATTT
* *
222758 AAAAATTTGTTAATAATTTACTTCAAAAGCTA
1 AAAAAATTGTTAATAATTTACTTCAAAAACTA
222790 AAAAAATTGTTAATAATTTACTTCAAAAACTA
1 AAAAAATTGTTAATAATTTACTTCAAAAACTA
222822 AA
1 AA
222824 TTAGTCAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.35
Consensus pattern (32 bp):
AAAAAATTGTTAATAATTTACTTCAAAAACTA
Found at i:229121 original size:2 final size:2
Alignment explanation
Indices: 229114--229175 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
229104 ATTAATATGC
229114 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
229156 AT AT AT AT AT AGT AT -T AT AT
1 AT AT AT AT AT A-T AT AT AT AT
229176 CAAAATCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230189 original size:31 final size:32
Alignment explanation
Indices: 230141--230200 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
230131 TGTAAAACTA
230141 CTGACATCAATATTGGCATAC-ATAAAGTTTTC
1 CTGACATCAATATTGGCA-ACAATAAAGTTTTC
230173 CTGACGATC-ATA-TGGCAACAATAAAGTT
1 CTGAC-ATCAATATTGGCAACAATAAAGTT
230201 CATACTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 2 0.08
31 13 0.50
32 8 0.31
33 3 0.12
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (32 bp):
CTGACATCAATATTGGCAACAATAAAGTTTTC
Found at i:232302 original size:23 final size:25
Alignment explanation
Indices: 232257--232318 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
232247 TTTGAAAACA
*
232257 TTTTGAAAACTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
232282 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
232307 TTTGGAAAACAT
1 TTTTGAAAACAT
232319 TTTTGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:232309 original size:62 final size:63
Alignment explanation
Indices: 232228--232353 Score: 168
Period size: 63 Copynumber: 2.0 Consensus size: 63
232218 TTTGAAATAT
* **
232228 ACATATATATAATATAGTTTTTGAAAACA-TTTTG-AAAACTTATATAATATATAGTTTTGAAA
1 ACATATATATAATATAG-TTTGGAAAACATTTTTGAAAAAAATATATAATATATAGTTTTGAAA
* *
232290 ACATATATA-ATATATAGTTTGGAAAACATTTTTGAAAAAAATATATAATATATGGTTTTTAAA
1 ACATATATATA-ATATAGTTTGGAAAACATTTTTGAAAAAAATATATAATATATAGTTTTGAAA
232353 A
1 A
232354 TATTTTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
61 11 0.20
62 20 0.36
63 25 0.45
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (63 bp):
ACATATATATAATATAGTTTGGAAAACATTTTTGAAAAAAATATATAATATATAGTTTTGAAA
Found at i:232338 original size:38 final size:38
Alignment explanation
Indices: 232282--232379 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
232272 TAATATATAG
*
232282 TTTTG-AAAACATATATAATATATAGTTTGGAAAACAT
1 TTTTGAAAAAAATATATAATATATAGTTTGGAAAACAT
* ** *
232319 TTTTGAAAAAAATATATAATATATGGTTTTTAAAATAT
1 TTTTGAAAAAAATATATAATATATAGTTTGGAAAACAT
**
232357 TTTT-AAAACGTATATATAATATA
1 TTTTGAAAA-AAATATATAATATA
232380 GTGAAAACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 9 0.17
38 43 0.83
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTTGAAAAAAATATATAATATATAGTTTGGAAAACAT
Found at i:232484 original size:16 final size:16
Alignment explanation
Indices: 232453--232486 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
232443 GGAAATATAA
* *
232453 TATTTTTATTTTTTAT
1 TATTTTTATATATTAT
232469 TATTTTTATATATTAT
1 TATTTTTATATATTAT
232485 TA
1 TA
232487 ATTAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTATATATTAT
Found at i:233252 original size:55 final size:55
Alignment explanation
Indices: 233181--233301 Score: 179
Period size: 55 Copynumber: 2.2 Consensus size: 55
233171 ACAAAGGGAG
* * * *
233181 GTACCGATACACCCCCAACATCGAATGCATTTTGTGTACCGATACACTCTTTGAT
1 GTACCGATACAACCCCAACATCGAATACATTTTGTGTACCGATACACTCTCTAAT
* * *
233236 GTATCGATACAACCCCAACATCGAATACATTTTGTGTATCGATACACTGTCTAAT
1 GTACCGATACAACCCCAACATCGAATACATTTTGTGTACCGATACACTCTCTAAT
233291 GTACCGATACA
1 GTACCGATACA
233302 CCCATGGCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (55 bp):
GTACCGATACAACCCCAACATCGAATACATTTTGTGTACCGATACACTCTCTAAT
Found at i:239225 original size:20 final size:21
Alignment explanation
Indices: 239153--239230 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 21
239143 ACACTCGTTA
* *
239153 TGTATCGATACACTATGAATG
1 TGTACCGATACACTTTGAATG
*
239174 TGTACCGATACATTCCTTGAATG
1 TGTACCGATACA--CTTTGAATG
* *
239197 TGTATCGATACACTTTGCA-G
1 TGTACCGATACACTTTGAATG
239217 TGTACCGATACACT
1 TGTACCGATACACT
239231 CGTCGGGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
23 18 0.38
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TGTACCGATACACTTTGAATG
Found at i:239593 original size:18 final size:18
Alignment explanation
Indices: 239570--239614 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
239560 TAATTTCTTC
* *
239570 AAAAAACACTATATTTCA
1 AAAAAAAACTAAATTTCA
*
239588 AAAAAAAATTAAATTTCA
1 AAAAAAAACTAAATTTCA
239606 AAATAAAAA
1 AAA-AAAAA
239615 AAATTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAAAACTAAATTTCA
Found at i:239700 original size:13 final size:13
Alignment explanation
Indices: 239677--239715 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
239667 AAAACTACAT
*
239677 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAA
239691 ATTGTTTTCAAAA
1 ATTGTTTTCAAAA
*
239704 ATAGTTTTCAAA
1 ATTGTTTTCAAA
239716 TTTGCCCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAA
Found at i:241193 original size:19 final size:19
Alignment explanation
Indices: 241156--241198 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
241146 TTTTATATAT
* *
241156 ATTTGGTTTTGATTGTTTAA
1 ATTTGGTTTTGAATATTT-A
241176 ATTTGG-TTTGAATATTTA
1 ATTTGGTTTTGAATATTTA
241194 ATTTG
1 ATTTG
241199 AGATTCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (19 bp):
ATTTGGTTTTGAATATTTA
Found at i:241862 original size:55 final size:55
Alignment explanation
Indices: 241772--241916 Score: 211
Period size: 55 Copynumber: 2.6 Consensus size: 55
241762 ACAAAGGGAG
* * *
241772 GTATCAATACACCCTTTGATGTATCGATACACCCCCAACATCGAATGCATTTTGT
1 GTATCGATACACTCTTTGATGTATCGATACACCCCCAAAATCGAATGCATTTTGT
*
241827 TTATCGATACACTCTTTGATGTATCGATACACCCCCAAAATCGAATGCATTTTGT
1 GTATCGATACACTCTTTGATGTATCGATACACCCCCAAAATCGAATGCATTTTGT
* * *
241882 GTATCGATACACTGTCTAATGTA-CTGATACACCCC
1 GTATCGATACACTCTTTGATGTATC-GATACACCCC
241917 TGGCTCGGGA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 1 0.01
55 80 0.99
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (55 bp):
GTATCGATACACTCTTTGATGTATCGATACACCCCCAAAATCGAATGCATTTTGT
Found at i:243501 original size:31 final size:31
Alignment explanation
Indices: 243463--243527 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
243453 AGAGTCGAGG
*
243463 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
243494 GTTTACCTAGGTTCTTCGGGACTTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
243525 GTT
1 GTT
243528 GCCGAGGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:246342 original size:65 final size:64
Alignment explanation
Indices: 246224--246428 Score: 220
Period size: 65 Copynumber: 3.2 Consensus size: 64
246214 TTTCAAAGTG
* * * * **
246224 ATGCACCGATGCACCAATCCATGCATTGATACAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
246287 TT
63 TT
* * * *
246289 ATTCATCGATGCA-CATACCATGCATCGATGCACTCTGGGT-TTTATGAAAACATCGAATGAATT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATT
*
246352 TG
63 TT
*
246354 ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
246418 ATGCATCGATG
1 ATGCATCGATG
246429 TACTCTTAGT
Statistics
Matches: 117, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 45 0.38
65 63 0.54
66 5 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
Found at i:248724 original size:31 final size:31
Alignment explanation
Indices: 248686--248750 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
248676 AGAGTCGAGG
*
248686 GTTTACCTATG-TCTTTCGGGACATATGGACA
1 GTTTACCTAGGTTC-TTCGGGACATATGGACA
*
248717 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACATATGGACA
248748 GTT
1 GTT
248751 GCCGAGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGACATATGGACA
Found at i:249440 original size:21 final size:21
Alignment explanation
Indices: 249411--249483 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
249401 TTACGAAAGT
* *
249411 CACTATAGCAGTGCATCGATG
1 CACTGTAGCAATGCATCGATG
* * *
249432 CACTGTAGCAATGCATTGGTA
1 CACTGTAGCAATGCATCGATG
249453 CACTGTAGCAATGCATCGATG
1 CACTGTAGCAATGCATCGATG
249474 CACTGTAGCA
1 CACTGTAGCA
249484 TAGTTCATGG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
CACTGTAGCAATGCATCGATG
Found at i:250806 original size:16 final size:18
Alignment explanation
Indices: 250768--250824 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
250758 TTTACTCAAT
250768 TATA-TTTATCTTTATTT-
1 TATATTTTATCTTT-TTTA
250785 T-T-TTTTAT-TTTTTTA
1 TATATTTTATCTTTTTTA
*
250800 -ATATTTTTTCTTTTTTA
1 TATATTTTATCTTTTTTA
250817 TATATTTT
1 TATATTTT
250825 GCAATTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 11 0.33
17 8 0.24
18 7 0.21
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (18 bp):
TATATTTTATCTTTTTTA
Done.