Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 377 of 378
Found at i:112473516 original size:41 final size:41
Alignment explanation
Indices: 112473471--112473570 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 41
112473461 AAACGCCACA
* *
112473471 AAAAACTGAGCAATAGCGATGTTTTT-GATCCAAACGCAGCT
1 AAAAACTGAGCAATAGCGACGTTTTTAG-TCAAAACGCAGCT
* * * *
112473512 AAAAA-TAGAGCAATAGTGGCGTTTTTAGTTAAAACGCCGCT
1 AAAAACT-GAGCAATAGCGACGTTTTTAGTCAAAACGCAGCT
*
112473553 AAAAACTGAACAATAGCG
1 AAAAACTGAGCAATAGCG
112473571 GCGCTTTTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
40 1 0.02
41 45 0.94
42 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (41 bp):
AAAAACTGAGCAATAGCGACGTTTTTAGTCAAAACGCAGCT
Found at i:112473694 original size:122 final size:123
Alignment explanation
Indices: 112473566--112473824 Score: 360
Period size: 122 Copynumber: 2.1 Consensus size: 123
112473556 AACTGAACAA
* *
112473566 TAGCGGCGCTTTTGAAAAAACGCCGCTATAGATCGAGCTTTTAGCGGTGCTTTT-GGAAAAACAC
1 TAGCGGCGCTTTTGAAAAAACGCCACTATAGATCGAGCTTTTAGCGGCGCTTTTAGG-AAAACAC
* * * * * *
112473630 CACTATAGATCGATGTTTTAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTC-AGTTTT
65 CACTATAGATCAAGGTTTTAGCGGCACTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* * * *
112473688 TAGCGGCGCTTTTGGAAAAACGGCACTATAGATCGAGGTTTTAGCGGCGCTTTTAGGAAAACGCC
1 TAGCGGCGCTTTTGAAAAAACGCCACTATAGATCGAGCTTTTAGCGGCGCTTTTAGGAAAACACC
* *
112473753 ACTATAGATTAAGGTTTTAGCGGCACTTTTGGGAAAACGCCGCTATAGATCGAGGTTT
66 ACTATAGATCAAGGTTTTAGCGGCACTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
*
112473811 TAGTGGCGCTTTTG
1 TAGCGGCGCTTTTG
112473825 GGAAAATGCC
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
122 100 0.83
123 20 0.17
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (123 bp):
TAGCGGCGCTTTTGAAAAAACGCCACTATAGATCGAGCTTTTAGCGGCGCTTTTAGGAAAACACC
ACTATAGATCAAGGTTTTAGCGGCACTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
Found at i:112473836 original size:41 final size:41
Alignment explanation
Indices: 112473566--112473836 Score: 348
Period size: 41 Copynumber: 6.6 Consensus size: 41
112473556 AACTGAACAA
* *
112473566 TAGCGGCGCTTTTGAAAAAACGCCGCTATAGATCGAGCTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* * * *
112473607 TAGCGGTGCTTTTGGAAAAACACCACTATAGATCGATGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* * *
112473648 TAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTC-AGTTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* *
112473688 TAGCGGCGCTTTTGGAAAAACGGCACTATAGATCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* **
112473729 TAGCGGCGCTTTTAGG-AAAACGCCACTATAGATTAAGGTTT
1 TAGCGGCGCTTTT-GGAAAAACGCCGCTATAGATCGAGGTTT
* *
112473770 TAGCGGCACTTTTGGGAAAACGCCGCTATAGATCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* * *
112473811 TAGTGGCGCTTTTGGGAAAATGCCGC
1 TAGCGGCGCTTTTGGAAAAACGCCGC
112473837 AAAAAATTAA
Statistics
Matches: 199, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
40 36 0.18
41 161 0.81
42 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
Found at i:112474257 original size:21 final size:21
Alignment explanation
Indices: 112474211--112474262 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
112474201 TTAATTATCA
* *
112474211 TTATAGTTTAGGGTTTATAGT
1 TTATGGTTAAGGGTTTATAGT
*
112474232 ATATGGTTAAGGGTTTA-ATGT
1 TTATGGTTAAGGGTTTATA-GT
112474253 TTATGAGTTA
1 TTATG-GTTA
112474263 CTATTTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (21 bp):
TTATGGTTAAGGGTTTATAGT
Found at i:112474303 original size:6 final size:7
Alignment explanation
Indices: 112474286--112474350 Score: 60
Period size: 7 Copynumber: 9.0 Consensus size: 7
112474276 TATGAATTAT
112474286 GGGTTAA
1 GGGTTAA
112474293 GGGTT-A
1 GGGTTAA
112474299 GGGTTTAA
1 GGG-TTAA
**
112474307 GTTTTAGA
1 GGGTTA-A
*
112474315 GGGGTTGA
1 -GGGTTAA
*
112474323 GGTTTAA
1 GGGTTAA
112474330 GGGTTAA
1 GGGTTAA
112474337 GGGTTAA
1 GGGTTAA
112474344 GGGTTAA
1 GGGTTAA
112474351 AGATTTATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
6 4 0.09
7 35 0.76
8 4 0.09
9 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.34
Consensus pattern (7 bp):
GGGTTAA
Found at i:112480669 original size:22 final size:23
Alignment explanation
Indices: 112480627--112480669 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
112480617 TTTCAAAAAT
*
112480627 TAAACATAATATAATATTTAACA
1 TAAAAATAATATAATATTTAACA
*
112480650 TAAAAATAA-ATATTATTTAA
1 TAAAAATAATATAATATTTAA
112480670 TTAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAATAATATAATATTTAACA
Found at i:112480690 original size:22 final size:22
Alignment explanation
Indices: 112480624--112480691 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
112480614 AAATTTCAAA
* * *
112480624 AATTAAACATAATATAATATTTA
1 AATTAAA-ATAAAATAATTTTTT
* *
112480647 ACATAAAAAT-AAAT-ATTATTT
1 A-ATTAAAATAAAATAATTTTTT
112480668 AATTAAAATAAAATAATTTTTT
1 AATTAAAATAAAATAATTTTTT
112480690 AA
1 AA
112480692 AGTTCATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
20 7 0.20
21 9 0.26
22 11 0.31
23 3 0.09
24 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAAAATAAAATAATTTTTT
Found at i:112480751 original size:43 final size:43
Alignment explanation
Indices: 112480703--112480886 Score: 217
Period size: 43 Copynumber: 4.3 Consensus size: 43
112480693 GTTCATAATT
* *
112480703 TTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGCGAGAAAAGCACCGCTAAAGGTCATGGTC
* * *
112480746 TTTAGCGGCGTTTGCGGGAAAAGCACTGCTAGAGGTCATGGTC
1 TTTAGCGGCGTTTGCGAGAAAAGCACCGCTAAAGGTCATGGTC
* ** * *
112480789 TTTAGCTGCGTTT-TTAGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGCGAGAAAAGCACCGCTAAAGGTCATGGTC
* ** * * *
112480831 TTTAGCAGCGTTTGTAAAAAAAGCATCGCTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGCGAGAAAAGCACCGCTAAAGGTCATGGTC
112480874 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
112480887 TTTTAAATAA
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 34 0.29
43 85 0.71
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGCGAGAAAAGCACCGCTAAAGGTCATGGTC
Found at i:112480853 original size:85 final size:85
Alignment explanation
Indices: 112480703--112480888 Score: 239
Period size: 85 Copynumber: 2.2 Consensus size: 85
112480693 GTTCATAATT
** * ***
112480703 TTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGCGGGAAAA
1 TTTAGCGGCGTTT-TTAGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTGCAAAAAAA
* *
112480768 GCA-CTGCTAGAGGTCATGGTC
65 GCATC-GCTAAAAGTCATGGTC
* * * *
112480789 TTTAGCTGCGTTTTTAGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCAGCGTTTGTAAAAAAAG
1 TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTGCAAAAAAAG
112480854 CATCGCTAAAAGTCATGGTC
66 CATCGCTAAAAGTCATGGTC
112480874 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
112480889 TTAAATAAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 73 0.85
86 13 0.15
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (85 bp):
TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTGCAAAAAAAG
CATCGCTAAAAGTCATGGTC
Found at i:112493308 original size:265 final size:266
Alignment explanation
Indices: 112492792--112493314 Score: 836
Period size: 265 Copynumber: 1.9 Consensus size: 266
112492782 AATGAAGTCT
112492792 TCCTGTATTTTTATGTAATAACAAGGTTCCAGCATATATATATATACATATATGGATGGAAAAGC
1 TCCTGTATTTTTATGTAATAACAAGGTTCCAGCATATATATATATACATATATGGATGGAAAAGC
*
112492857 AGATACTAGTAGCACTCAAGTGGCAGCTCCCAATCTATGGTGGGTCAATCCTTCCACCGAAGAAA
66 AGATACTAGTAGCACTCAAGTGGCAGCTCCCAATCTATGGTGGGTCAACCCTTCCACCGAAGAAA
* *
112492922 TTCATGTCGACCATGTGCCTTTTTTCAAATCGACCATAATTTTGCTTGACAAATACAATGTACTG
131 TTCATGTCGA-CA---G-C-TATTTCAAATCGACCATAATTTAGCTTGACAAATACAATGTACTG
* *
112492987 ATTAACTTGACCCTTATAGCCGACACAACACGTAATATAAACAACATGTAAACATCATCTTCAAC
190 ATTAACTTGACCCGTATAGCCGACACAACACGTAATATAAACAACACGTAAACATCATCTTCAAC
112493052 CAAATATCATCG
255 CAAATATCATCG
112493064 TCCTGTATTTTTATGTAATAACAAGGTTCCAGCATATATATATATACACATATATGGATGGAAAA
1 TCCTGTATTTTTATGTAATAACAAGGTTCCAGCATATATATATAT--ACATATATGGATGGAAAA
* * * * *
112493129 GCATATATTAGTAGCAGTCAAGTGGCAGTTCCTAATCTATGGTGGGTCAACCCTTCCACCGAAGA
64 GCAGATACTAGTAGCACTCAAGTGGCAGCTCCCAATCTATGGTGGGTCAACCCTTCCACCGAAGA
* *
112493194 AATTCATGTCGA-A-C-ATTTCAAATCTACCATAATTTAGCTTGACAAATACAATGTATTGATTA
129 AATTCATGTCGACAGCTATTTCAAATCGACCATAATTTAGCTTGACAAATACAATGTACTGATTA
*
112493256 ACTTGACCCGTATAGCCGACACAACACGTTATATAAACAACACGTAAACATCATCTTCA
194 ACTTGACCCGTATAGCCGACACAACACGTAATATAAACAACACGTAAACATCATCTTCA
112493315 TCTAATATTA
Statistics
Matches: 236, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
265 100 0.42
267 1 0.00
272 46 0.19
274 89 0.38
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (266 bp):
TCCTGTATTTTTATGTAATAACAAGGTTCCAGCATATATATATATACATATATGGATGGAAAAGC
AGATACTAGTAGCACTCAAGTGGCAGCTCCCAATCTATGGTGGGTCAACCCTTCCACCGAAGAAA
TTCATGTCGACAGCTATTTCAAATCGACCATAATTTAGCTTGACAAATACAATGTACTGATTAAC
TTGACCCGTATAGCCGACACAACACGTAATATAAACAACACGTAAACATCATCTTCAACCAAATA
TCATCG
Found at i:112495293 original size:20 final size:19
Alignment explanation
Indices: 112495257--112495294 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
112495247 ATGTATAGAT
*
112495257 GCATTTTTTAGTTAATTTA
1 GCATTTTTTAGTAAATTTA
112495276 GCATTTTTTAGTCAAATTT
1 GCATTTTTTAGT-AAATTT
112495295 CACTGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (19 bp):
GCATTTTTTAGTAAATTTA
Found at i:112495670 original size:19 final size:20
Alignment explanation
Indices: 112495629--112495672 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
112495619 TATCAATGTA
112495629 TTTTAGATATAATTTAACTT
1 TTTTAGATATAATTTAACTT
112495649 TTTTAGATATAATTTAACTT
1 TTTTAGATATAATTTAACTT
112495669 TTTT
1 TTTT
112495673 TTATTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTAGATATAATTTAACTT
Found at i:112496144 original size:14 final size:15
Alignment explanation
Indices: 112496120--112496149 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
112496110 CATTATATTC
112496120 ATTTTTCTTTTTTTA
1 ATTTTTCTTTTTTTA
112496135 ATTTTT-TTTTTTTA
1 ATTTTTCTTTTTTTA
112496149 A
1 A
112496150 ACAGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTCTTTTTTTA
Found at i:112497720 original size:24 final size:24
Alignment explanation
Indices: 112497688--112497737 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
112497678 AGTTTCTGGC
112497688 TATTATTGATATATGTATTTTTGG
1 TATTATTGATATATGTATTTTTGG
112497712 TATTATTGATATATGTATTTTTGG
1 TATTATTGATATATGTATTTTTGG
112497736 TA
1 TA
112497738 GTAGGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (24 bp):
TATTATTGATATATGTATTTTTGG
Found at i:112501256 original size:27 final size:28
Alignment explanation
Indices: 112501218--112501275 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
112501208 CCAATTTACT
* * *
112501218 ATGTTTTTTTAATCT-ACAAGGATTAAA
1 ATGTCTTTTTAAACTAAAAAGGATTAAA
*
112501245 ATGTCTTTTTAAAGTAAAAAGGATTAAA
1 ATGTCTTTTTAAACTAAAAAGGATTAAA
112501273 ATG
1 ATG
112501276 AACTTCTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (28 bp):
ATGTCTTTTTAAACTAAAAAGGATTAAA
Found at i:112503232 original size:2 final size:2
Alignment explanation
Indices: 112503225--112503261 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
112503215 TAAATGAGGC
112503225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112503262 GCGTATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112507814 original size:7 final size:7
Alignment explanation
Indices: 112507802--112507831 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
112507792 TTTCTATACT
112507802 TTTCAAA
1 TTTCAAA
112507809 TTTCAAA
1 TTTCAAA
*
112507816 TTTTAAA
1 TTTCAAA
112507823 TTTCAAA
1 TTTCAAA
112507830 TT
1 TT
112507832 CAGTTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (7 bp):
TTTCAAA
Found at i:112510102 original size:39 final size:41
Alignment explanation
Indices: 112510032--112510111 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 41
112510022 TAAAAGTAGA
112510032 TAGTTTAATTTTTAAATGTGTGAAGAATACAAGCAATTAAG
1 TAGTTTAATTTTTAAATGTGTGAAGAATACAAGCAATTAAG
112510073 TAGTTTAATTTTT-AA-GTGTGAAGAATACAAGCAATTAAG
1 TAGTTTAATTTTTAAATGTGTGAAGAATACAAGCAATTAAG
112510112 CAGAGAAGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 24 0.62
40 2 0.05
41 13 0.33
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (41 bp):
TAGTTTAATTTTTAAATGTGTGAAGAATACAAGCAATTAAG
Found at i:112517804 original size:11 final size:12
Alignment explanation
Indices: 112517776--112517809 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
112517766 GGATGGTTGA
112517776 ATTAAATAAATT
1 ATTAAATAAATT
*
112517788 ATTAAATAATTT
1 ATTAAATAAATT
*
112517800 ATAAAATAAA
1 ATTAAATAAA
112517810 AATATATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTAAATAAATT
Found at i:112520970 original size:22 final size:24
Alignment explanation
Indices: 112520930--112520973 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
112520920 AATAAAGTTT
*
112520930 AATTTTATTTATATATAATATGGA
1 AATTTTATATATATATAATATGGA
112520954 AATTTTATATA-AT-TAATATG
1 AATTTTATATATATATAATATG
112520974 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
AATTTTATATATATATAATATGGA
Found at i:112521548 original size:20 final size:18
Alignment explanation
Indices: 112521522--112521570 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
112521512 GTTATTATTA
112521522 ATTATTTTTAAATTATAT
1 ATTATTTTTAAATTATAT
112521540 ATTTTATTTTT--ATTATAT
1 A--TTATTTTTAAATTATAT
112521558 ATTATTTTTAAAT
1 ATTATTTTTAAAT
112521571 ACATACACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.30
18 11 0.41
20 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTTTTAAATTATAT
Found at i:112521554 original size:18 final size:19
Alignment explanation
Indices: 112521523--112521568 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 19
112521513 TTATTATTAA
112521523 TTATTTTTAAATTATATATT
1 TTATTTTT-AATTATATATT
112521543 TTATTTTT-ATTATATA--
1 TTATTTTTAATTATATATT
112521559 TTATTTTTAA
1 TTATTTTTAA
112521569 ATACATACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 8 0.32
20 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTAATTATATATT
Found at i:112523793 original size:2 final size:2
Alignment explanation
Indices: 112523786--112523811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112523776 TTAAAGTTCT
112523786 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
112523812 AATACACAAT
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):
TA
Found at i:112534433 original size:19 final size:19
Alignment explanation
Indices: 112534409--112534445 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
112534399 AAATTATGAG
* *
112534409 TTAAATTTTAAAGTAGTCT
1 TTAAATTTCAAAATAGTCT
112534428 TTAAATTTCAAAATAGTC
1 TTAAATTTCAAAATAGTC
112534446 CAATTGAGTC
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:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (19 bp):
TTAAATTTCAAAATAGTCT
Found at i:112540895 original size:5 final size:5
Alignment explanation
Indices: 112540885--112540910 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
112540875 ACAGTCGAAC
112540885 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
112540911 GCGTCGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:112543513 original size:3 final size:3
Alignment explanation
Indices: 112543507--112543531 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
112543497 GTCGTCGTCC
112543507 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
112543532 TTAATGGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:112547060 original size:17 final size:16
Alignment explanation
Indices: 112547032--112547081 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
112547022 TCTAGTTCGA
112547032 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGGG
* *
112547048 TCAATTTTAGGTTCT-AG
1 TC-ATTTTGGGTT-TGGG
112547065 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGGG
112547081 T
1 T
112547082 TTGAGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 12 0.44
18 1 0.04
ACGTcount: A:0.12, C:0.08, G:0.30, T:0.50
Consensus pattern (16 bp):
TCATTTTGGGTTTGGG
Found at i:112547072 original size:33 final size:32
Alignment explanation
Indices: 112546997--112547081 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 32
112546987 TAAAATTTAC
* *
112546997 CGATCATTTT-GATTCTGTGTCAATTTCTAGTT
1 CGATCATTTTGGGTT-TGGGTCAATTTCTAGTT
112547029 CGATCATTTTGGGTTTGGGTCAATTT-TAGGTT
1 CGATCATTTTGGGTTTGGGTCAATTTCTA-GTT
*
112547061 CTAGTCATTTTGGGTTTGGGT
1 CGA-TCATTTTGGGTTTGGGT
112547082 TTGAGTTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
31 2 0.04
32 25 0.53
33 20 0.43
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (32 bp):
CGATCATTTTGGGTTTGGGTCAATTTCTAGTT
Found at i:112547076 original size:16 final size:16
Alignment explanation
Indices: 112547032--112547078 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
112547022 TCTAGTTCGA
*
112547032 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGAG
*
112547048 TCAATTTTAGGTTCT-AG
1 TC-ATTTTGGGTT-TGAG
112547065 TCATTTTGGGTTTG
1 TCATTTTGGGTTTG
112547079 GGTTTGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 12 0.48
18 1 0.04
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.51
Consensus pattern (16 bp):
TCATTTTGGGTTTGAG
Found at i:112548941 original size:22 final size:23
Alignment explanation
Indices: 112548902--112548944 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
112548892 GTAACCTAAT
112548902 TTAAAATTAATAAAAATTAAACC
1 TTAAAATTAATAAAAATTAAACC
*
112548925 TTAAAGTTAA-AAAAATTAAA
1 TTAAAATTAATAAAAATTAAA
112548945 AGAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAAATTAATAAAAATTAAACC
Found at i:112556098 original size:21 final size:21
Alignment explanation
Indices: 112556074--112556117 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
112556064 CATCTATAGT
*
112556074 AATATAT-AATATTATAATGTA
1 AATATATAAATATTA-AATATA
*
112556095 AATATTTAAATATTAAATATA
1 AATATATAAATATTAAATATA
112556116 AA
1 AA
112556118 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATATAAATATTAAATATA
Found at i:112559384 original size:21 final size:21
Alignment explanation
Indices: 112559367--112559409 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
112559357 TTTAAAATCT
112559367 AAAACCTAAAAATCAAAACCC
1 AAAACCTAAAAATCAAAACCC
* *
112559388 AAAATCTAAAACTCAAAACCC
1 AAAACCTAAAAATCAAAACCC
112559409 A
1 A
112559410 GACCTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAACCTAAAAATCAAAACCC
Found at i:112559404 original size:14 final size:14
Alignment explanation
Indices: 112559360--112559405 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
112559350 TTCAAAATTT
*
112559360 AAAATCTAAAACCTA
1 AAAATCTAAAA-CTC
*
112559375 AAAATC-AAAACCC
1 AAAATCTAAAACTC
112559388 AAAATCTAAAACTC
1 AAAATCTAAAACTC
112559402 AAAA
1 AAAA
112559406 CCCAGACCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 14 0.52
15 6 0.22
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATCTAAAACTC
Found at i:112560568 original size:26 final size:26
Alignment explanation
Indices: 112560532--112560667 Score: 220
Period size: 26 Copynumber: 5.2 Consensus size: 26
112560522 TGATACAAAT
112560532 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
112560558 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
112560584 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
112560610 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
112560636 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
112560662 TGATAA
1 TGATAA
112560668 GAATTTAATG
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 1 0.01
26 106 0.99
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:112564294 original size:36 final size:36
Alignment explanation
Indices: 112564254--112564325 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
112564244 TTGATACATA
* *
112564254 ATTTTGATTTTG-TGCAATTATACACGTGAAACTTTC
1 ATTTTGATTATGATGCAAATATACACGT-AAACTTTC
* *
112564290 ATTTTGATTATGATTCAAATATATACGTAAACTTTC
1 ATTTTGATTATGATGCAAATATACACGTAAACTTTC
112564326 TTTCGCACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 19 0.61
37 12 0.39
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (36 bp):
ATTTTGATTATGATGCAAATATACACGTAAACTTTC
Found at i:112566570 original size:31 final size:31
Alignment explanation
Indices: 112566535--112566601 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
112566525 ATAAAATGGG
112566535 ATTTTAGGTTCC-TTAAAAGTTGGAAAAAAAA
1 ATTTTAGG-TCCTTTAAAAGTTGGAAAAAAAA
*
112566566 ATTTTAGGTCCTTTAAAAGTTGGTAAAAAAA
1 ATTTTAGGTCCTTTAAAAGTTGGAAAAAAAA
112566597 ATTTT
1 ATTTT
112566602 GGCCCCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (31 bp):
ATTTTAGGTCCTTTAAAAGTTGGAAAAAAAA
Found at i:112566754 original size:14 final size:12
Alignment explanation
Indices: 112566724--112566754 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
112566714 GCCAAGCTTG
112566724 AATATATTCTTA
1 AATATATTCTTA
*
112566736 AATATATTTTTA
1 AATATATTCTTA
112566748 AATATAT
1 AATATAT
112566755 GGAAAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATATTCTTA
Found at i:112577926 original size:12 final size:12
Alignment explanation
Indices: 112577905--112577937 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
112577895 TTTTCGTTTT
*
112577905 TAATTGATTTAA
1 TAATTAATTTAA
112577917 TAATTAATTTAA
1 TAATTAATTTAA
112577929 TAATTAATT
1 TAATTAATT
112577938 AATTACAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (12 bp):
TAATTAATTTAA
Found at i:112579737 original size:13 final size:13
Alignment explanation
Indices: 112579719--112579744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
112579709 TACAGCTACA
112579719 TATATATATATAT
1 TATATATATATAT
112579732 TATATATATATAT
1 TATATATATATAT
112579745 AGAATAGACT
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:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:112583800 original size:30 final size:30
Alignment explanation
Indices: 112583766--112583851 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
112583756 AAAACCCTAG
112583766 CCACCTTGCCTCCCACTTGTACCTACTCCA
1 CCACCTTGCCTCCCACTTGTACCTACTCCA
112583796 CCACCTTGCCTCCCACTTGTACCTACTCCA
1 CCACCTTGCCTCCCACTTGTACCTACTCCA
** *
112583826 CCACCTTATCTCCCACTTGCACCTAC
1 CCACCTTGCCTCCCACTTGTACCTAC
112583852 ACCATCAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.17, C:0.50, G:0.06, T:0.27
Consensus pattern (30 bp):
CCACCTTGCCTCCCACTTGTACCTACTCCA
Found at i:112584765 original size:2 final size:2
Alignment explanation
Indices: 112584760--112584793 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
112584750 GTATTTCTAT
* *
112584760 TA TA TA CA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112584794 GTATTACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112592331 original size:18 final size:18
Alignment explanation
Indices: 112592295--112592332 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
112592285 AAAAAAAAAT
*
112592295 ATCAAATTAAATATTTAA
1 ATCAAATTAAATATCTAA
112592313 ATCAAATTTAAATA-CTAA
1 ATCAAA-TTAAATATCTAA
112592331 AT
1 AT
112592333 AATATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
ATCAAATTAAATATCTAA
Found at i:112601903 original size:2 final size:2
Alignment explanation
Indices: 112601896--112601929 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
112601886 TGAACTCGTA
112601896 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
112601930 CAATTGTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112605359 original size:2 final size:2
Alignment explanation
Indices: 112605352--112605377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112605342 GTATGATACA
112605352 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
112605378 TCAAAGGATG
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:112605878 original size:21 final size:20
Alignment explanation
Indices: 112605820--112605896 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 20
112605810 CGTATTTTCT
*
112605820 TTTGAGATTTAAAATTTA-G
1 TTTGAAATTTAAAATTTAGG
* **
112605839 TTTATAAGATTTATTATTTAGG
1 TTT-GAA-ATTTAAAATTTAGG
112605861 ATTTGAAATTTAAAATTTAGAG
1 -TTTGAAATTTAAAATTTAG-G
*
112605883 TTTAGAATTTTAAA
1 TTT-GAAATTTAAA
112605897 TTCCAACATT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 24 0.55
22 13 0.30
23 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (20 bp):
TTTGAAATTTAAAATTTAGG
Found at i:112609668 original size:20 final size:22
Alignment explanation
Indices: 112609614--112609656 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
112609604 CATCCACCAA
112609614 ACACTAC-AATTAGAGAGTTTG
1 ACACTACAAATTAGAGAGTTTG
112609635 ACACTACAAATTAGAGAGTTTG
1 ACACTACAAATTAGAGAGTTTG
112609657 TATCCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (22 bp):
ACACTACAAATTAGAGAGTTTG
Found at i:112621334 original size:56 final size:57
Alignment explanation
Indices: 112621233--112621342 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 57
112621223 ATTATATTGA
* ** *
112621233 GATTTAATTTTTTTATTCTAGTTAGGCCTTAAACTTGACAGTTATTCCCACATTAGG
1 GATTTAATTTTTTTATTCTAGTTAGACCTTAAACTCAACAATTATTCCCACATTAGG
* *
112621290 GATTTAATTTTTTT-TT-TAAGTTAGACCTTAAACTCAATAATTATTCTCACATT
1 GATTTAATTTTTTTATTCT-AGTTAGACCTTAAACTCAACAATTATTCCCACATT
112621343 GTGGCCTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 1 0.02
56 31 0.67
57 14 0.30
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (57 bp):
GATTTAATTTTTTTATTCTAGTTAGACCTTAAACTCAACAATTATTCCCACATTAGG
Found at i:112622064 original size:19 final size:19
Alignment explanation
Indices: 112622034--112622078 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
112622024 AGTATTGTGA
112622034 AATTTATAATTTAATCTATTT
1 AATTT-TAATTTAATCT-TTT
112622055 -ATTTTAATTTAATCTTTT
1 AATTTTAATTTAATCTTTT
112622073 AATTTT
1 AATTTT
112622079 TTAAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTAATTTAATCTTTT
Found at i:112633012 original size:33 final size:32
Alignment explanation
Indices: 112632947--112633012 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
112632937 ATATTCAAAA
* *
112632947 CATGTTAGGAATAGCTCTTGTTAAGAACAACT
1 CATGTTAGGAATAGATCTTATTAAGAACAACT
* * *
112632979 CATGTTTGGAGTAGATCTTATTCAAGAATAACT
1 CATGTTAGGAATAGATCTTATT-AAGAACAACT
112633012 C
1 C
112633013 TTATTCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (32 bp):
CATGTTAGGAATAGATCTTATTAAGAACAACT
Found at i:112637760 original size:27 final size:28
Alignment explanation
Indices: 112637730--112637869 Score: 184
Period size: 27 Copynumber: 5.2 Consensus size: 28
112637720 ATGACGAAGT
112637730 CACCAGATACAGAT-ATTGTGGCAGAGC
1 CACCAGATACAGATAATTGTGGCAGAGC
* *
112637757 CACCTGA-ACAGAT-ATATGTGACAGAGC
1 CACCAGATACAGATAAT-TGTGGCAGAGC
* *
112637784 CACCAGAT-CAGATAATCGTGGCATAGC
1 CACCAGATACAGATAATTGTGGCAGAGC
112637811 CACCAGA-ACAGATAATTGTGGCAGAGC
1 CACCAGATACAGATAATTGTGGCAGAGC
*
112637838 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGATAATTGTGGCAGAGC
112637865 CACCA
1 CACCA
112637870 AGACGCTTCC
Statistics
Matches: 99, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.08
27 89 0.90
28 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (28 bp):
CACCAGATACAGATAATTGTGGCAGAGC
Found at i:112637805 original size:54 final size:54
Alignment explanation
Indices: 112637730--112637869 Score: 212
Period size: 54 Copynumber: 2.6 Consensus size: 54
112637720 ATGACGAAGT
* *
112637730 CACCAGATACAGAT-ATTGTGGCAGAGCCACCTGAACAGAT-ATATGTGACAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATAAT-TGTGACAGAGC
* *
112637784 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATAATTGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATAATTGTGACAGAGC
112637838 CACCAGATCAGATAATTGTGGCATAGCCACCA
1 CACCAGATCAGATAATTGTGGCATAGCCACCA
112637870 AGACGCTTCC
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
53 5 0.06
54 72 0.91
55 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATAATTGTGACAGAGC
Found at i:112639410 original size:46 final size:44
Alignment explanation
Indices: 112639351--112639465 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
112639341 ACAGGACAGA
* *
112639351 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
112639397 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
112639441 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
112639466 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:112639446 original size:44 final size:45
Alignment explanation
Indices: 112639351--112639484 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
112639341 ACAGGACAGA
* *
112639351 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
112639397 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
112639441 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
112639485 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:112645541 original size:46 final size:44
Alignment explanation
Indices: 112645482--112645596 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
112645472 ACAGGACAGA
* *
112645482 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
112645528 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
112645572 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
112645597 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:112645577 original size:44 final size:45
Alignment explanation
Indices: 112645482--112645615 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
112645472 ACAGGACAGA
* *
112645482 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
112645528 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
112645572 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
112645616 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:112651674 original size:46 final size:44
Alignment explanation
Indices: 112651615--112651729 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
112651605 ACAGGACAGA
* *
112651615 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
112651661 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
112651705 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
112651730 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:112651710 original size:44 final size:45
Alignment explanation
Indices: 112651615--112651748 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
112651605 ACAGGACAGA
* *
112651615 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
112651661 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
112651705 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
112651749 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:112654553 original size:26 final size:26
Alignment explanation
Indices: 112654522--112654628 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
112654512 TGAAATGCCC
112654522 ATCATAGAACATTTACCTAAACCATT
1 ATCATAGAACATTTACCTAAACCATT
*
112654548 ATCATAGAACATTTACCTAACCCATT
1 ATCATAGAACATTTACCTAAACCATT
* *
112654574 ATCATAGAATATTTACCTAATCCATT
1 ATCATAGAACATTTACCTAAACCATT
*
112654600 ATCATGGAACATTTACCT-AACCATT
1 ATCATAGAACATTTACCTAAACCATT
112654625 ATCA
1 ATCA
112654629 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
25 10 0.13
26 65 0.87
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (26 bp):
ATCATAGAACATTTACCTAAACCATT
Found at i:112655914 original size:2 final size:2
Alignment explanation
Indices: 112655863--112655897 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
112655853 GGTATTTAAA
112655863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112655898 GTATTTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112656516 original size:15 final size:15
Alignment explanation
Indices: 112656496--112656530 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
112656486 TTTTGGTAGG
112656496 TTTTTCTTT-TTCTTT
1 TTTTTCTTTGTT-TTT
112656511 TTTTTCTTTGTTTTT
1 TTTTTCTTTGTTTTT
112656526 TTTTT
1 TTTTT
112656531 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:112657280 original size:88 final size:83
Alignment explanation
Indices: 112657173--112657750 Score: 299
Period size: 88 Copynumber: 7.0 Consensus size: 83
112657163 AACAGACATT
** * *
112657173 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
112657238 TTGATTTTTTGAAACTTAACTTG
65 TTGATTTTTTGAAA---AAC-TG
* * * ** *
112657261 AAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGGAGGTTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
112657325 GTTGA-TTTTTGAAAAACAG
64 GTTGATTTTTTGAAAAACTG
* * * * ** *** *
112657344 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAAT
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAAT
112657405 ATGAGTTGAATTTTTTTG-AAAA---
60 ATGAGTTG-A-TTTTTTGAAAAACTG
** * *
112657427 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
112657492 TTGA-TTTTTGAAAACAGAATTTG
65 TTGATTTTTTG--AA-A-AA-CTG
* * * * * *
112657515 AAAAACAGATTTTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
112657580 TTGATTTTTTTGAAAAA-T-
65 TTGA-TTTTTTGAAAAACTG
* *** *** * *
112657598 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
112657658 GTTGATTTTTTTG--AAA--G
64 GTTGA-TTTTTTGAAAAACTG
* * * * * * *
112657675 ATAGA-A-A--TTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
112657736 TTGATTTTTTGAAAA
65 TTGATTTTTTGAAAA
112657751 CAGAAATTGA
Statistics
Matches: 384, Mismatches: 69, Indels: 84
0.72 0.13 0.16
Matches are distributed among these distances:
76 9 0.02
77 47 0.12
78 2 0.01
79 64 0.17
80 3 0.01
81 11 0.03
82 38 0.10
83 14 0.04
84 41 0.11
85 9 0.02
86 6 0.02
87 19 0.05
88 115 0.30
90 6 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (83 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAACTG
Found at i:112657377 original size:30 final size:30
Alignment explanation
Indices: 112657341--112657402 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
112657331 TTTTGAAAAA
112657341 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
112657371 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
112657401 CA
1 CA
112657403 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:112657521 original size:14 final size:14
Alignment explanation
Indices: 112657498--112657532 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
112657488 TGAGTTGATT
112657498 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
112657511 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
112657525 TTTGAAAA
1 TTTGAAAA
112657533 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:112657833 original size:72 final size:73
Alignment explanation
Indices: 112657550--112658080 Score: 411
Period size: 72 Copynumber: 6.8 Consensus size: 73
112657540 ACATGTAACC
* * * *
112657550 CGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG--AAAATAC
* *
112657615 CTCAGTGTGTGAT
62 CTCAGCGTGT-CT
* * *
112657628 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGC
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
112657693 TCAGCGCATGAGC-
63 TCAGCG--TG-TCT
* * *
112657706 CAAGGGTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
112657771 ACGTGTCT
66 GCGTGTCT
* ** * * *
112657779 TGAGGCTCAACTCATTTCTCACAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
112657843 GCGTGTCC
66 GCGTGTCT
*
112657851 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTTTGAAAGCAGAAATTGAAAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-------TTTTTTGAAAACAGAAATTG----
** ** *
112657916 ATGGAAATTGAAAATACCTCGACGTGTGAT
55 A---AAA-T--ACCT-CAGC---GTGT-CT
* * *
112657946 CTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTTTGACAACAGAAATTGAAATTACCT
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
112658011 CAGCGTGTC-
64 CAGCGTGTCT
* *
112658020 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAAAAATTGAAAA
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAA
112658081 ACGGAAATTG
Statistics
Matches: 366, Mismatches: 56, Indels: 65
0.75 0.11 0.13
Matches are distributed among these distances:
72 65 0.18
73 29 0.08
74 43 0.12
75 32 0.09
76 14 0.04
77 41 0.11
78 5 0.01
79 51 0.14
80 19 0.05
82 1 0.00
83 2 0.01
84 1 0.00
86 1 0.00
87 2 0.01
88 1 0.00
90 20 0.05
91 2 0.01
94 4 0.01
95 1 0.00
96 32 0.09
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (73 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
GCGTGTCT
Found at i:112658031 original size:170 final size:168
Alignment explanation
Indices: 112657747--112658223 Score: 718
Period size: 165 Copynumber: 2.9 Consensus size: 168
112657737 TGATTTTTTG
* * * ** * *
112657747 AAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCACAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
112657810 TGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
66 TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
*
112657874 ATATGAGTTGATTTTTTTTTTTTTGAAA-GCAGAAATTGA
131 ATATGAGTTGA--TTTTTTTTTTTGAAAGGCAAAAATTGA
*
112657913 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
112657978 TGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
112658043 AATATGAGTTGA----TTTTTTTGAAAGGCAAAAATTGA
130 AATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
* * * *
112658078 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
112658143 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
112658208 AATATGAGTTGATTTT
130 AATATGAGTTGATTTT
112658224 GAAAAAGTAG
Statistics
Matches: 284, Mismatches: 18, Indels: 15
0.90 0.06 0.05
Matches are distributed among these distances:
164 11 0.04
165 146 0.51
166 27 0.10
167 1 0.00
168 30 0.11
170 69 0.24
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (168 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
Found at i:112658042 original size:74 final size:75
Alignment explanation
Indices: 112657919--112658080 Score: 222
Period size: 74 Copynumber: 2.1 Consensus size: 75
112657909 TTGAAAAATG
*
112657919 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
112657984 TTTTGACAACA
65 TTTTGACAACA
* * *
112657995 GAAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
112658058 TTTTGA-AAGGCA
65 TTTTGACAA--CA
*
112658070 AAAATTGAAAA
1 GAAATTGAAAA
112658081 ACGGAAATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
73 2 0.03
74 42 0.55
75 12 0.16
76 21 0.27
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (75 bp):
GAAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAACA
Found at i:112658209 original size:74 final size:75
Alignment explanation
Indices: 112658084--112658223 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 75
112658074 TTGAAAAACG
* *
112658084 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
112658149 TTTTGACAACA
65 TTTTGACAACA
* * *
112658160 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
112658224 GAAAAAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 37 0.63
76 22 0.37
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTGACAACA
Found at i:112658412 original size:212 final size:208
Alignment explanation
Indices: 112658023--112658623 Score: 652
Period size: 212 Copynumber: 2.9 Consensus size: 208
112658013 GCGTGTCCTG
* *
112658023 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAA--AAATTGAAAAACGGA
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGA---TTTTG-AA--CAACTAAATTG-AAAACAGA
* * * *
112658086 AATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTTT
59 AATTGAAAATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
*** * *
112658151 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
121 AAAAC-ACAAAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
112658216 TTGATTTTGAAAAAGTAGAAATTAAA
184 TTGATTTTGAAAAA-CAAAAATTAAA
112658242 AGG-TTCAAC-CTACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAAT
1 AGGCTT-AACTC-ACCTCTCGCAATATGAGTTGATT-TTGAACAAC-TAAATTGAAAACAGAAAT
**
112658305 TGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACA
62 TGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACA
* *
112658370 CAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTT
127 CAAAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
112658435 TGAAAAACAAAAATTAAA
191 TGAAAAACAAAAATTAAA
* * *
112658453 AGGCTTAACTCACCTCTCGCAATATGA---G----T---CAA-T---TT-AAAACATAAACTAAA
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACTAAATTGAAAACAGAAATTGAA
* * * *
112658503 AATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-ACAAA
66 AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACACAAA
* *
112658567 AATT-AAAATACCTCAACGTGTCTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATT
131 AATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
112658624 AAAACACAAA
Statistics
Matches: 343, Mismatches: 31, Indels: 45
0.82 0.07 0.11
Matches are distributed among these distances:
190 20 0.06
191 14 0.04
192 15 0.04
193 9 0.03
194 65 0.19
195 2 0.01
198 1 0.00
200 3 0.01
203 1 0.00
208 1 0.00
211 31 0.09
212 71 0.21
213 4 0.01
214 40 0.12
216 28 0.08
217 9 0.03
218 2 0.01
219 27 0.08
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (208 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACTAAATTGAAAACAGAAATTGAA
AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACACAAA
AATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA
AACAAAAATTAAA
Found at i:112658422 original size:72 final size:71
Alignment explanation
Indices: 112658288--112658453 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
112658278 TGAACAACGT
* * * *
112658288 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
112658353 GAGTTG
66 GAGTTG
*
112658359 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
112658424 TGAGTTG
65 TGAGTTG
**
112658431 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
112658454 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:112658548 original size:122 final size:122
Alignment explanation
Indices: 112658328--112658826 Score: 586
Period size: 122 Copynumber: 4.0 Consensus size: 122
112658318 GCGTGACCTG
* * *
112658328 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTAAAACACAAAAACTGAAAATACCTCAGCG
112658393 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
64 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * *
112658453 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAA-ACATAAACTAAAAATACCTCAGCGTG
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTAAAACACAAAAACTGAAAATACCTCAGCGTG
* *
112658517 CCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCA
66 CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATT---A-A----A
* * ** *
112658582 ACGTGTCTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACC
1 A-G-G-CTTA-ACTC-A--C-CTCTCGCAATATGAGTCAATTAAAACACAAAAACTGAAAATACC
112658647 TCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAA
58 TCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAA
112658712 A
122 A
*
112658713 AGGCTTAACTCACCTCTCGCAATATGAGTCAATT-------TAAAACT-AAAA-ACCTCAGCGTG
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTAAAACACAAAAACTGAAAATACCTCAGCGTG
* * * *
112658769 TCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAACAATTAAA
66 CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
112658826 A
1 A
112658827 ATACCTCAAC
Statistics
Matches: 328, Mismatches: 28, Indels: 48
0.81 0.07 0.12
Matches are distributed among these distances:
113 15 0.05
114 50 0.15
115 4 0.01
116 5 0.02
121 12 0.04
122 63 0.19
123 26 0.08
124 3 0.01
125 28 0.09
126 1 0.00
127 3 0.01
128 3 0.01
129 3 0.01
130 2 0.01
131 3 0.01
132 3 0.01
133 3 0.01
134 1 0.00
135 1 0.00
136 2 0.01
137 22 0.07
138 63 0.19
139 12 0.04
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (122 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTCAATTAAAACACAAAAACTGAAAATACCTCAGCGTG
CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:112658594 original size:69 final size:70
Alignment explanation
Indices: 112658453--112658713 Score: 345
Period size: 69 Copynumber: 3.8 Consensus size: 70
112658443 AAAAATTAAA
* * * * *
112658453 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACA-AAAATTAAAATACCTCAGCGT
112658516 GCCCCG
65 GCCCCG
* *
112658522 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAACGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAGCGTG
* *
112658587 -TCTG
66 CCCCG
*
112658591 AGGCTCAACTCA-CTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATT-AAAATACCTCAGCG
112658653 TGCCCCG
64 TGCCCCG
*
112658660 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
112658714 GGCTTAACTC
Statistics
Matches: 167, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
66 5 0.03
67 9 0.05
68 33 0.20
69 54 0.32
70 42 0.25
71 10 0.06
72 11 0.07
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (70 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAATACCTCAGCGTG
CCCCG
Found at i:112658660 original size:260 final size:254
Alignment explanation
Indices: 112658291--112658878 Score: 991
Period size: 260 Copynumber: 2.3 Consensus size: 254
112658281 ACAACGTAAA
* * * *
112658291 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTG-TCTGAGGCTCAACTCACCTCTCGCAATATGAG
112658356 TTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
65 TTG--ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
112658421 ATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAT
128 ATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAT
112658486 TTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
193 TT-----A-AAACT-AAAA-ACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
112658551 TGATT
250 TGATT
112658556 TTGAAAACAAAAATT-AAAATACCTCAACGTGTCTGAGGCTCAACTCA-CTCTCGCAATATGAGT
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGT
112658619 TGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
66 TGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
112658684 TGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTA
131 TGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTA
*
112658749 AAACTAAAAACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
196 AAACTAAAAACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
* *
112658808 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTC-TGAGGCTCAACTCACCTCTCGCAATATGAG
112658873 TTGATT
65 TTGATT
112658879 TTCCTTGAAA
Statistics
Matches: 315, Mismatches: 5, Indels: 16
0.94 0.01 0.05
Matches are distributed among these distances:
252 63 0.20
253 22 0.07
254 19 0.06
255 22 0.07
260 127 0.40
262 18 0.06
263 15 0.05
264 15 0.05
265 14 0.04
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (254 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
TGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTA
AAACTAAAAACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
Found at i:112665593 original size:11 final size:12
Alignment explanation
Indices: 112665571--112665605 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
112665561 TGGAATATGC
*
112665571 AATGAATGAATG
1 AATGCATGAATG
112665583 AATGCAT-AATG
1 AATGCATGAATG
112665594 AATGCATGAATG
1 AATGCATGAATG
112665606 TTAAATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.26
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:112667294 original size:2 final size:2
Alignment explanation
Indices: 112667287--112667315 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
112667277 CATAAAATAC
112667287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112667316 AAAGTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:112667760 original size:10 final size:10
Alignment explanation
Indices: 112667745--112667775 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
112667735 CGCCCGTCGT
112667745 CGGCCACCGC
1 CGGCCACCGC
112667755 CGGCCACCGC
1 CGGCCACCGC
112667765 CGGCCACCGC
1 CGGCCACCGC
112667775 C
1 C
112667776 ACGGTGGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.61, G:0.29, T:0.00
Consensus pattern (10 bp):
CGGCCACCGC
Found at i:112668180 original size:28 final size:28
Alignment explanation
Indices: 112668117--112668182 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
112668107 GTTAGGTGGC
112668117 TAGGTTTTTTTATCTTTTTTTGTTAGGT
1 TAGGTTTTTTTATCTTTTTTTGTTAGGT
*** * *
112668145 TTTCTTTTTTCT-TCTTTTTTTTTTGGGT
1 TAGGTTTTTT-TATCTTTTTTTGTTAGGT
112668173 TAGGTTTTTT
1 TAGGTTTTTT
112668183 GGTAGGTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.73
Consensus pattern (28 bp):
TAGGTTTTTTTATCTTTTTTTGTTAGGT
Found at i:112668208 original size:16 final size:16
Alignment explanation
Indices: 112668189--112668223 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
112668179 TTTTGGTAGG
112668189 TTTTTCTTT-TTCTTTT
1 TTTTTCTTTGTT-TTTT
112668205 TTTTTCTTTGTTTTTT
1 TTTTTCTTTGTTTTTT
112668221 TTT
1 TTT
112668224 GGGTTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTTCTTTGTTTTTT
Found at i:112670415 original size:20 final size:20
Alignment explanation
Indices: 112670392--112670443 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 20
112670382 AAATCCAAAT
112670392 TAAAATACTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
112670412 TAAAAT-CTTGAAATTCAGGA
1 TAAAATAC-TGAAATTCAGGA
112670432 TAAGAATACTGA
1 TAA-AATACTGA
112670444 TATGGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 21 0.72
21 6 0.21
22 1 0.03
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (20 bp):
TAAAATACTGAAATTCAGGA
Found at i:112673335 original size:30 final size:30
Alignment explanation
Indices: 112673299--112673359 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
112673289 TCCTTAACTC
112673299 AAACTTTGGAAAATTTACAATTTTGCCCCT
1 AAACTTTGGAAAATTTACAATTTTGCCCCT
* * * *
112673329 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAATTTACAATTTTGCCCCT
112673359 A
1 A
112673360 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAAAATTTACAATTTTGCCCCT
Found at i:112678762 original size:29 final size:29
Alignment explanation
Indices: 112678728--112678786 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
112678718 TAAATGAAAC
112678728 ATAGTTTTTATGTGGCATAGTTTAAAAGA
1 ATAGTTTTTATGTGGCATAGTTTAAAAGA
112678757 ATAGTTTTTATGTGGCATAGTTTAAAAGA
1 ATAGTTTTTATGTGGCATAGTTTAAAAGA
112678786 A
1 A
112678787 AAATACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (29 bp):
ATAGTTTTTATGTGGCATAGTTTAAAAGA
Found at i:112691157 original size:48 final size:48
Alignment explanation
Indices: 112691065--112691163 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
112691055 AAAAGTTATT
* *
112691065 TAATGTTTTAATTCAAAATATTATCAATTCTGAATAAAATTAGTTAAG
1 TAATGTTTTAATTCAAAAGATTATCAATTCTGAATAAAACTAGTTAAG
** *
112691113 TAATGTTTTAATTCAAAAGATTATCAATT-TCGAATAAGGCTAGTTATG
1 TAATGTTTTAATTCAAAAGATTATCAATTCT-GAATAAAACTAGTTAAG
112691161 TAA
1 TAA
112691164 CCTACGTAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
47 1 0.02
48 44 0.98
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (48 bp):
TAATGTTTTAATTCAAAAGATTATCAATTCTGAATAAAACTAGTTAAG
Found at i:112693214 original size:12 final size:12
Alignment explanation
Indices: 112693197--112693221 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112693187 CTTTTCCATC
112693197 TATTTTCTTTAT
1 TATTTTCTTTAT
112693209 TATTTTCTTTAT
1 TATTTTCTTTAT
112693221 T
1 T
112693222 GTTCTAATAT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTCTTTAT
Found at i:112696939 original size:46 final size:46
Alignment explanation
Indices: 112696819--112696945 Score: 218
Period size: 46 Copynumber: 2.8 Consensus size: 46
112696809 TGTAACCCGC
* * * *
112696819 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
112696865 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
112696911 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
112696946 AATGCCCAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:112699747 original size:54 final size:54
Alignment explanation
Indices: 112699633--112699790 Score: 203
Period size: 54 Copynumber: 3.0 Consensus size: 54
112699623 GTATATCATA
* * * * * * *
112699633 CCGATGCCATATCCCGGATATGGTCTTACACGG-GAGCACTTATCACTT-ATCT
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGATATCACTTATCACTTGTTCT
* *
112699685 CCGATGCCATAGCCCAGCTATGGTCTTATACGGATATCACTTATCAATTGTTTT
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGATATCACTTATCACTTGTTCT
* *
112699739 CCGATGCCATAGCCCAGCTATAGTCTTATACAGATATCACTTATCACTTGTT
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGATATCACTTATCACTTGTT
112699791 GCCACGGTCC
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 29 0.32
53 12 0.13
54 51 0.55
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (54 bp):
CCGATGCCATAGCCCAGCTATGGTCTTATACGGATATCACTTATCACTTGTTCT
Found at i:112711012 original size:41 final size:41
Alignment explanation
Indices: 112710952--112711039 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
112710942 GAAAACCCTT
*
112710952 TCGAGAAAAAATCACGGGTAGAGGAGAAGATAATTTACTATG
1 TCGA-AAAAAACCACGGGTAGAGGAGAAGATAATTTACTATG
112710994 TCGAAAAAAACCACGGGTAGAGGAGAAGATAATTTACTATG
1 TCGAAAAAAACCACGGGTAGAGGAGAAGATAATTTACTATG
112711035 TCGAA
1 TCGAA
112711040 TTTGAATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.20
Consensus pattern (41 bp):
TCGAAAAAAACCACGGGTAGAGGAGAAGATAATTTACTATG
Found at i:112711251 original size:18 final size:16
Alignment explanation
Indices: 112711220--112711255 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
112711210 TCAATATTGA
112711220 TTTACTTTTATTTTAT
1 TTTACTTTTATTTTAT
112711236 TTTACTATTGTATTTTAT
1 TTTACT-TT-TATTTTAT
112711254 TT
1 TT
112711256 CAATAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTACTTTTATTTTAT
Found at i:112711510 original size:2 final size:2
Alignment explanation
Indices: 112711503--112711578 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
112711493 AAAATCTGGC
112711503 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
112711545 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
112711579 TTTATTCTCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:112713696 original size:16 final size:15
Alignment explanation
Indices: 112713671--112713718 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
112713661 CTATTTTAAG
112713671 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
112713686 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
112713703 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
112713718 T
1 T
112713719 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:112719303 original size:77 final size:80
Alignment explanation
Indices: 112719175--112719357 Score: 223
Period size: 77 Copynumber: 2.3 Consensus size: 80
112719165 GCTACTCGTT
* * *
112719175 CAAATGCCTTCGGGACATATCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-AATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
112719239 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
* ** *
112719255 CAAATGCCTTC-GG-CTTAGCCCGGAATAGTAACTCGCACGAATGCCTTCGGATCTTAGTCTGGA
1 CAAATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
112719318 TATAGTCACTTAGCA
66 TATAGTAACTTAGCA
112719333 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
112719358 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
76 3 0.03
77 44 0.49
78 18 0.20
79 13 0.15
80 11 0.12
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:112719351 original size:40 final size:39
Alignment explanation
Indices: 112719156--112719357 Score: 214
Period size: 40 Copynumber: 5.1 Consensus size: 39
112719146 CGGAGTTTAA
** * *
112719156 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATATC
1 CCGGATATAG-TAACTCGCACAAATGCCTTC-GGACTTAGC
* *
112719196 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTC-GGACTTAGC
*
112719236 CCGGATTTAGTAACTCGCACAAATGCCTTCGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGC
* *
112719274 CCGGA-ATAGTAACTCGCACGAATGCCTTCGGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGA-CTTAGC
* * *
112719313 CTGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTC-GGACTTAGC
112719353 CCGGA
1 CCGGA
112719358 CATCATTCGA
Statistics
Matches: 139, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
37 24 0.17
38 10 0.07
39 12 0.09
40 83 0.60
41 10 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGC
Found at i:112722099 original size:16 final size:15
Alignment explanation
Indices: 112722073--112722121 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 15
112722063 TCTATTTTAA
112722073 ATTTATTTTAATTTT
1 ATTTATTTTAATTTT
112722088 ATTTATTTTTAATTATT
1 ATTTA-TTTTAATT-TT
112722105 A-TTATTTTAGATTTT
1 ATTTATTTTA-ATTTT
112722120 AT
1 AT
112722122 ATTAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.43
16 14 0.47
17 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
ATTTATTTTAATTTT
Found at i:112726068 original size:54 final size:55
Alignment explanation
Indices: 112725932--112726070 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 55
112725922 TTGAAAATTT
* * * *
112725932 TTTGGTGCTAGCCTGTCAATGGTCAGCACCAAAATACGAATTTTCAAAAAAAAAA
1 TTTGGTGCTGGCCTGTCAATGGCCGGCACCAAAATACGAAGTTTCAAAAAAAAAA
* * *
112725987 TTT-GTGCTGGCCTGTTAATGGCAGGCACCAAAATACGAGGTTT-AAAAAAAAAA
1 TTTGGTGCTGGCCTGTCAATGGCCGGCACCAAAATACGAAGTTTCAAAAAAAAAA
112726040 TTTGGTGCTGGCCTGTCAATGGCCGGCACCA
1 TTTGGTGCTGGCCTGTCAATGGCCGGCACCA
112726071 GTATTAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
53 13 0.18
54 58 0.78
55 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (55 bp):
TTTGGTGCTGGCCTGTCAATGGCCGGCACCAAAATACGAAGTTTCAAAAAAAAAA
Found at i:112726170 original size:57 final size:53
Alignment explanation
Indices: 112726040--112726180 Score: 176
Period size: 53 Copynumber: 2.6 Consensus size: 53
112726030 AAAAAAAAAA
* *
112726040 TTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTAAAAAAAATTGAAAATT
1 TTTGGTGCTGTCCTGTCAATGGCCGACACCAGTATTAAAAAAAATTGAAAATT
*
112726093 TTTGGTGCTGTCCTGTCAATGGCCGACACCAGTATTAAAAAAGAAAATTTGAAATTT
1 TTTGGTGCTGTCCTGTCAATGGCCGACACCAGTATT--AAAA-AAAA-TTGAAAATT
** *
112726150 TTTTTTGCTGGT-TTGTCAATGGCCGACACCA
1 TTTGGTGCT-GTCCTGTCAATGGCCGACACCA
112726181 AAATACGAGT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
53 34 0.44
55 4 0.05
56 4 0.05
57 33 0.43
58 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (53 bp):
TTTGGTGCTGTCCTGTCAATGGCCGACACCAGTATTAAAAAAAATTGAAAATT
Found at i:112726200 original size:162 final size:158
Alignment explanation
Indices: 112725854--112726290 Score: 468
Period size: 162 Copynumber: 2.7 Consensus size: 158
112725844 TTGGTATACA
* * *
112725854 AAAATACGAGTTTTCAAAAAAAAATTTGGTGCCGGCCTGTCAATGGCCGACAACAGTATTAAAAA
1 AAAATACGAGTTTT-AAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTAAAAA
* * * * *
112725919 AATTTGAAAATTTTTTGGTGCTAGCCTGTCAATGGTCAGCACCAAAATACGAATTTTCAAAAAAA
65 AAATTGAAAA-TTTTTGGTGCTAGCCTGTCAATGGCCAGCACCAAAAAAAGAAATTT--AAAAAA
* *
112725984 AAATTTGTGCTGGCCTGTTAATGGCAGGCACC
127 AAATTTGTGCTGGCCTGTCAATGGCAGACACC
*
112726016 AAAATACGAGGTTTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTAAAAA
1 AAAATACGA-GTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTAAAAA
112726081 AAATTGAAAATTTTTGGTGCT-GTCCTGTCAATGGCC-GACACCAGTATTAAAAAAGAAAATTT-
65 AAATTGAAAATTTTTGGTGCTAG-CCTGTCAATGGCCAG-CACC---A--AAAAAAG-AAATTTA
* **** * ** *
112726143 GAAATTTTTTTTTGCTGGTTTGTCAATGGCCGACACC
122 AAAAAAAATTTGTGCTGGCCTGTCAATGGCAGACACC
* * *
112726180 AAAATACGAGTTTTAAAAAAAAAATTGGTGCTAGCCTGTCAATGGCAGGCACCAGTATTAAAAAA
1 AAAATACGAGTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTAAAAAA
* * * *
112726245 AATTGAAATTTTTTTGGT-ATTGACCTATCAATGGCCAGCACCAAAA
66 AATTGAAA-ATTTTTGGTGCTAG-CCTGTCAATGGCCAGCACCAAAA
112726291 TACGAGTTTT
Statistics
Matches: 235, Mismatches: 28, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
159 3 0.01
160 2 0.01
161 28 0.12
162 65 0.28
163 65 0.28
164 61 0.26
165 1 0.00
166 5 0.02
167 5 0.02
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (158 bp):
AAAATACGAGTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTAAAAAA
AATTGAAAATTTTTGGTGCTAGCCTGTCAATGGCCAGCACCAAAAAAAGAAATTTAAAAAAAAAT
TTGTGCTGGCCTGTCAATGGCAGACACC
Found at i:112726297 original size:107 final size:107
Alignment explanation
Indices: 112725854--112726319 Score: 343
Period size: 107 Copynumber: 4.3 Consensus size: 107
112725844 TTGGTATACA
* * * *
112725854 AAAATACGAGTTTTCAAAAAAAAATTTGGTGCCGGCCTGTCAATGGCCGACAACAGTATTAAAAA
1 AAAATACGAGTTTT-AAAAAAAAAATTGGTGCTGGCCTGTCAATGGCAGACACCAGTATTAAAAA
* * *
112725919 AATTTGAAAATTTTTTGGTGCT-AGCCTGTCAATGGTCAGCACC
65 AAATTGAAATTTTTTTGGTGCTGA-CCTGTCAATGGCCAGCACC
* * * * *
112725962 AAAATACGAATTTTCAAAAAAAAAATTTGTGCTGGCCTGTTAATGGCAGGCACCAAAATACGAGG
1 AAAATACGAGTTTT-AAAAAAAAAATTGGTGCTGGCCTGTCAATGGCAGACACC--AGT---A--
* * *
112726027 TTTAAAAAAA---AAA----TTTGGTGCTGGCCTGTCAATGGCCGGCACC
58 TTAAAAAAAATTGAAATTTTTTTGGTGCTGACCTGTCAATGGCCAGCACC
* ** * *
112726070 --AGT---A-TTAAAAAAAATTGAAAATTTTTGGTGCTGTCCTGTCAATGGCCGACACCAGTATT
1 AAAATACGAGTTTTAAAAAA---AAAA---TTGGTGCTGGCCTGTCAATGGCAGACACCAGTATT
* ***
112726129 AAAAAAGAAAATTTGAAATTTTTTT-TTGCTGGTTTGTCAATGGCC-GACACC
60 --AAAA-AAAA-TTGAAATTTTTTTGGTGCTGACCTGTCAATGGCCAG-CACC
* *
112726180 AAAATACGAGTTTTAAAAAAAAAATTGGTGCTAGCCTGTCAATGGCAGGCACCAGTATTAAAAAA
1 AAAATACGAGTTTTAAAAAAAAAATTGGTGCTGGCCTGTCAATGGCAGACACCAGTATTAAAAAA
** *
112726245 AATTGAAATTTTTTTGGTATTGACCTATCAATGGCCAGCACC
66 AATTGAAATTTTTTTGGTGCTGACCTGTCAATGGCCAGCACC
* **
112726287 AAAATACGAGTTTTCAAAAAAATTTTGGTGCTG
1 AAAATACGAGTTTTAAAAAAAAAATTGGTGCTG
112726320 AAATTTTTTT
Statistics
Matches: 279, Mismatches: 45, Indels: 69
0.71 0.11 0.18
Matches are distributed among these distances:
100 2 0.01
101 6 0.02
102 6 0.02
103 5 0.02
104 4 0.01
105 2 0.01
106 15 0.05
107 77 0.28
108 77 0.28
109 1 0.00
110 54 0.19
111 3 0.01
112 5 0.02
113 5 0.02
115 9 0.03
116 8 0.03
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (107 bp):
AAAATACGAGTTTTAAAAAAAAAATTGGTGCTGGCCTGTCAATGGCAGACACCAGTATTAAAAAA
AATTGAAATTTTTTTGGTGCTGACCTGTCAATGGCCAGCACC
Found at i:112731001 original size:19 final size:19
Alignment explanation
Indices: 112730977--112731029 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
112730967 ATTTTATGCA
112730977 TATTTTGAATTTTAAAAAT
1 TATTTTGAATTTTAAAAAT
*
112730996 TATTTT-ATATTTCTTAAAAT
1 TATTTTGA-ATTT-TAAAAAT
112731016 TATTTTGTAATTTT
1 TATTTTG-AATTTT
112731030 TATTAAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
20 13 0.45
21 4 0.14
22 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
TATTTTGAATTTTAAAAAT
Found at i:112737801 original size:1 final size:1
Alignment explanation
Indices: 112737795--112737819 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
112737785 CTGTAAGTGG
112737795 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
112737820 AAATCTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:112737996 original size:31 final size:29
Alignment explanation
Indices: 112737958--112738022 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
112737948 ATTAGTAAAA
*
112737958 ATAAAATTACATTTTAGTCTCTTTAAAAATG
1 ATAAAATTACA-TTTAATCT-TTTAAAAATG
** *
112737989 ATAAAATTTGATTTAATCTTTTAAAAATT
1 ATAAAATTACATTTAATCTTTTAAAAATG
112738018 ATAAA
1 ATAAA
112738023 TATATAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 7 0.23
31 9 0.30
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (29 bp):
ATAAAATTACATTTAATCTTTTAAAAATG
Found at i:112743475 original size:16 final size:16
Alignment explanation
Indices: 112743450--112743488 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
112743440 TTATTTGTTC
* *
112743450 AAATTCTTTTAATTTT
1 AAATTATTTTAAATTT
112743466 AAATTATTTTAAATTT
1 AAATTATTTTAAATTT
112743482 AAATTAT
1 AAATTAT
112743489 CTCGAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:112744124 original size:29 final size:29
Alignment explanation
Indices: 112744055--112744132 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 29
112744045 TAGAATATCA
*
112744055 AATTTATATATTAATTTTGATTTAATTTGT
1 AATTTATATATAAATTTTGATTTAA-TTGT
* *
112744085 AATTTTGTATATAAATTTTGATTTGA-TGT
1 AA-TTTATATATAAATTTTGATTTAATTGT
112744114 AATTATATATATTAAATTT
1 AATT-TATATA-TAAATTT
112744133 AAATTATGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 2 0.05
29 10 0.24
30 9 0.22
31 20 0.49
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (29 bp):
AATTTATATATAAATTTTGATTTAATTGT
Found at i:112744185 original size:31 final size:29
Alignment explanation
Indices: 112744084--112744186 Score: 82
Period size: 31 Copynumber: 3.4 Consensus size: 29
112744074 ATTTAATTTG
* *
112744084 TAATTTTGTATATAAATTTTGA-TTTGAT
1 TAATTTTATATATAAATTTTAATTTTGAT
* * * *
112744112 GTAATTATATATATTAAATTTAAATTATGGT
1 -TAATTTTATATA-TAAATTTTAATTTTGAT
* *
112744143 TTATATGTATATATAAAATTTTAATTTTGAT
1 TAAT-TTTATATAT-AAATTTTAATTTTGAT
112744174 TCAATTTTATATA
1 T-AATTTTATATA
112744187 GCGGTGAAGT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 10 0.18
30 12 0.21
31 32 0.57
32 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (29 bp):
TAATTTTATATATAAATTTTAATTTTGAT
Found at i:112745562 original size:6 final size:6
Alignment explanation
Indices: 112745553--112745615 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
112745543 ATTTATATAC
* * *
112745553 ATATGT ATATGG ATATGG ATATGG ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
112745601 ATATGT ATATGT ATA
1 ATATGT ATATGT ATA
112745616 ATCATAATAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (6 bp):
ATATGT
Found at i:112745705 original size:9 final size:9
Alignment explanation
Indices: 112745693--112745789 Score: 86
Period size: 9 Copynumber: 10.6 Consensus size: 9
112745683 TTATTGTTGA
112745693 TATTAATAT
1 TATTAATAT
*
112745702 TATTAATAA
1 TATTAATAT
*
112745711 TATTAATAA
1 TATTAATAT
* *
112745720 TAATAATAA
1 TATTAATAT
*
112745729 TAATAATAAT
1 TATTAAT-AT
*
112745739 ATATTATTAT
1 -TATTAATAT
*
112745749 TATTATTAT
1 TATTAATAT
*
112745758 TATTATTAT
1 TATTAATAT
*
112745767 TATTATTAT
1 TATTAATAT
*
112745776 TATTATTAT
1 TATTAATAT
112745785 TATTA
1 TATTA
112745790 TTTTGAACAT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
9 73 0.90
10 3 0.04
11 5 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTAATAT
Found at i:112745711 original size:3 final size:3
Alignment explanation
Indices: 112745705--112745739 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
112745695 TTAATATTAT
*
112745705 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
112745740 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:112745746 original size:3 final size:3
Alignment explanation
Indices: 112745740--112745791 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
112745730 AATAATAATA
112745740 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
112745788 TAT T
1 TAT T
112745792 TTGAACATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:112746252 original size:24 final size:23
Alignment explanation
Indices: 112746208--112746272 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 23
112746198 AAAAATAAAT
112746208 AAATATTTATTATTATATTTTAA
1 AAATATTTATTATTATATTTTAA
112746231 AAATATTTATTTATTCAT-TTTT--
1 AAATATTTA-TTATT-ATATTTTAA
112746253 -AA-ATTTATTATTATATTTTA
1 AAATATTTATTATTATATTTTA
112746273 TTGAAACTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.05
19 9 0.24
20 5 0.13
21 2 0.05
23 9 0.24
24 9 0.24
25 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
AAATATTTATTATTATATTTTAA
Found at i:112746766 original size:2 final size:2
Alignment explanation
Indices: 112746761--112746799 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
112746751 TTTTTTGCAG
112746761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112746800 CTGTGTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112748072 original size:13 final size:13
Alignment explanation
Indices: 112748054--112748079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
112748044 AGCGTAACGA
112748054 TGAGGCATGCTGC
1 TGAGGCATGCTGC
112748067 TGAGGCATGCTGC
1 TGAGGCATGCTGC
112748080 ACTCTAAATG
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:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
TGAGGCATGCTGC
Found at i:112761963 original size:22 final size:25
Alignment explanation
Indices: 112761920--112761969 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
112761910 TTTTAGTAAA
*
112761920 GAAAAAAAATATAGGTACCT-AATT
1 GAAAAAAAATATAGATACCTAAATT
*
112761944 GAAAAAAATTA-AGATA-CTAAATT
1 GAAAAAAAATATAGATACCTAAATT
112761967 GAA
1 GAA
112761970 CATTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 2 0.09
23 11 0.48
24 10 0.43
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (25 bp):
GAAAAAAAATATAGATACCTAAATT
Found at i:112764327 original size:15 final size:16
Alignment explanation
Indices: 112764307--112764345 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
112764297 TTATTAATGC
*
112764307 AAAATAAT-ATTATTT
1 AAAATAATAATTAATT
112764322 AAAATAATAATTAATT
1 AAAATAATAATTAATT
*
112764338 AACATAAT
1 AAAATAAT
112764346 TAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATAATAATTAATT
Found at i:112764453 original size:21 final size:22
Alignment explanation
Indices: 112764389--112764453 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 22
112764379 TAGTGTTCAT
*
112764389 AAAAAATTTCTAAT-TATTGTT
1 AAAAAATTTCTAATATATTGTA
** * * *
112764410 AAAGCATTTGTAAAAT-TTATA
1 AAAAAATTTCTAATATATTGTA
112764431 AAAAAATTT-TAATATATTGTA
1 AAAAAATTTCTAATATATTGTA
112764452 AA
1 AA
112764454 TTAAACTCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
20 5 0.16
21 26 0.81
22 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (22 bp):
AAAAAATTTCTAATATATTGTA
Found at i:112772593 original size:26 final size:26
Alignment explanation
Indices: 112772537--112772593 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
112772527 AGATCATGTC
*
112772537 AATTTAAATTTTCAAAGTTGTTGGAT
1 AATTTAAATTTTCAAAGTTGTTGAAT
* *
112772563 AATTTAAGATTTTTAGAGTT-TTGAAT
1 AATTTAA-ATTTTCAAAGTTGTTGAAT
*
112772589 TATTT
1 AATTT
112772594 GGGGTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (26 bp):
AATTTAAATTTTCAAAGTTGTTGAAT
Found at i:112772631 original size:32 final size:33
Alignment explanation
Indices: 112772565--112772632 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
112772555 TGTTGGATAA
* * *
112772565 TTTAAGATTTTTAGAGTTTTGAATTATTTGGGG
1 TTTAAAATTTTTAAAGTTTTGAATCATTTGGGG
*
112772598 TTTAAAATTTTTAAAG-TTTGAATCATTTTGGG
1 TTTAAAATTTTTAAAGTTTTGAATCATTTGGGG
112772630 TTT
1 TTT
112772633 GGATAGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.53
Consensus pattern (33 bp):
TTTAAAATTTTTAAAGTTTTGAATCATTTGGGG
Found at i:112775847 original size:20 final size:20
Alignment explanation
Indices: 112775819--112775858 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
112775809 TTTTTACTCA
* *
112775819 AAACTTTAAATCTTGAACTT
1 AAACCTTAAACCTTGAACTT
112775839 AAACCTTAAACCTTGAACTT
1 AAACCTTAAACCTTGAACTT
112775859 CAAGTGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (20 bp):
AAACCTTAAACCTTGAACTT
Found at i:112776219 original size:13 final size:13
Alignment explanation
Indices: 112776201--112776225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112776191 AAACATCAAT
112776201 TCGGATACAAGAA
1 TCGGATACAAGAA
112776214 TCGGATACAAGA
1 TCGGATACAAGA
112776226 TAAAAGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (13 bp):
TCGGATACAAGAA
Found at i:112778796 original size:258 final size:257
Alignment explanation
Indices: 112778418--112778938 Score: 611
Period size: 256 Copynumber: 2.0 Consensus size: 257
112778408 GTTAACTTCT
* * *
112778418 TAATGTTGTTTTAAGTTGATTGGCATTGCTAGTTTCTGATACTAAGTTAGTTGGTAAGTAGCTTT
1 TAATGTTGTTTTAAGTTGATTGGCATTGCTAGTTTCTAATACTAAG-TA-TTGATAAATAGCTTT
* ** ** *
112778483 GGATGTGCAGACATGGTGGGGTATAATGTGGTTTATTGTTTAAAAGCTCTTCATATATATACATG
64 GAACATGCAGACATGGCCGGGTATAATGTAGTTTATTGTTTAAAAGCTCTTCATATATATACAT-
* ** * * * *
112778548 CACACGCACACGTGCGTGCATGCATGCATACATTTATATGTATATATAGAAGTGGGATCTAATGA
128 -ACACACACACGCACATGCATGCATGCATACATATATATGTATATATAGAAATGGGATCTAACGA
* * * * * *
112778613 TTCATTAATGTCCCCGAAA-ATGTTAAACTCCCCCTTTATGAACTTCATTTTGCTGCTTAGATGT
192 TTCACTAATGCCCCCCAAATATGTTAAA-T-CCCCTTAAGGAACTTCATTTTGCTACTTAGATGT
112778677 GGA
255 GGA
*
112778680 TAATGTTGTTTTAATTTGATTGGCATTGCTAGTTTCTAACT-CTAA-T-TTGATAAATAGCTTTG
1 TAATGTTGTTTTAAGTTGATTGGCATTGCTAGTTTCTAA-TACTAAGTATTGATAAATAGCTTTG
* * *
112778742 AACATGCAGGCATGGCCGGGTATAATGTAGTTTTTTGTTTAAAAGCAT-TTCATATATATATATA
65 AACATGCAGACATGGCCGGGTATAATGTAGTTTATTGTTTAAAAGC-TCTTCATATATATACATA
* * * * * * *
112778806 TATATACATGCACATGCGTGCATGCATACATATATATGTGTATATGGAAATGGGATCTAACGATT
129 CACACACACGCACATGCATGCATGCATACATATATATGTATATATAGAAATGGGATCTAACGATT
** *
112778871 CACTAATGCCCCCCAAATATGTTAAATCCCCTTAAGGGTCTTCATTTTGCTACTTTGATGTGGA
194 CACTAATGCCCCCCAAATATGTTAAATCCCCTTAAGGAACTTCATTTTGCTACTTAGATGTGGA
112778935 TAAT
1 TAAT
112778939 ATAGTCTTGA
Statistics
Matches: 220, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
255 35 0.16
256 67 0.30
257 8 0.04
258 66 0.30
259 1 0.00
260 1 0.00
262 41 0.19
263 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (257 bp):
TAATGTTGTTTTAAGTTGATTGGCATTGCTAGTTTCTAATACTAAGTATTGATAAATAGCTTTGA
ACATGCAGACATGGCCGGGTATAATGTAGTTTATTGTTTAAAAGCTCTTCATATATATACATACA
CACACACGCACATGCATGCATGCATACATATATATGTATATATAGAAATGGGATCTAACGATTCA
CTAATGCCCCCCAAATATGTTAAATCCCCTTAAGGAACTTCATTTTGCTACTTAGATGTGGA
Found at i:112779034 original size:266 final size:255
Alignment explanation
Indices: 112778568--112779042 Score: 585
Period size: 256 Copynumber: 1.8 Consensus size: 255
112778558 CGTGCGTGCA
* * * * * *
112778568 TGCATGCATACATTTATATGTATATATAGAAGTGGGATCTAATGATTCATTAATGTCCCCGAAAA
1 TGCATGCATACATATATATGTATATATAGAAATGGGATCTAACGATTCACTAATGCCCCCCAAAA
* * * ** *
112778633 TGTTAAACTCCCCCTTTATGAACTTCATTTTGCTGCTTAGATGTGGATAATGTTGTTTTAATTTG
66 TGTTAAACTCCCCCTTAAGGAACTTCATTTTGCTACTTAGATGTGGATAATGTTGTACTAAGTTG
* * * * *
112778698 ATTGGCATTGCTAGTTTCTAACTCTAATTTGATAAATAGCTTTGAACATGCAGGCATGGCCGGGT
131 ATTAGCATTGCTAGTTTCGAACTCTAATTTGATAAACAGCTTTGAACATGCAGGCATGGCAGGAT
112778763 ATAATGTAGTTTTTTGTTTAAAAGCATTTCATATATATATATATATATACATGCACATGCG
196 ATAATGT-GTTTTTTGTTTAAAAGCATTTCATATATATATATATATATACATGCACATGCG
* *
112778824 TGCATGCATACATATATATGTGTATATGGAAATGGGATCTAACGATTCACTAATGCCCCCCAAAT
1 TGCATGCATACATATATATGTATATATAGAAATGGGATCTAACGATTCACTAATGCCCCCCAAA-
** *
112778889 ATGTTAAA-T-CCCCTTAAGGGTCTTCATTTTGCTACTTTGATGTGGATAATATAGTCTTGAGTA
65 ATGTTAAACTCCCCCTTAAGGAACTTCATTTTGCTACTTAGATGTGGAT-A-AT-G--TT--GTA
* * * *
112778952 CTAAGTTGATTAGCATTGCTAGTTTTCGACACTAGGTTATTTGATAAACGGCTTTGGACATGCAG
123 CTAAGTTGATTAGCATTGCTAG-TTTCGA-ACT--CTAATTTGATAAACAGCTTTGAACATGCAG
112779017 GCATGGCAGGATATAATGTGTTTTTT
184 GCATGGCAGGATATAATGTGTTTTTT
112779043 TTTTGTTTGT
Statistics
Matches: 181, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
255 32 0.18
256 58 0.32
257 10 0.06
258 1 0.01
260 2 0.01
262 21 0.12
263 5 0.03
264 3 0.02
265 7 0.04
266 42 0.23
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (255 bp):
TGCATGCATACATATATATGTATATATAGAAATGGGATCTAACGATTCACTAATGCCCCCCAAAA
TGTTAAACTCCCCCTTAAGGAACTTCATTTTGCTACTTAGATGTGGATAATGTTGTACTAAGTTG
ATTAGCATTGCTAGTTTCGAACTCTAATTTGATAAACAGCTTTGAACATGCAGGCATGGCAGGAT
ATAATGTGTTTTTTGTTTAAAAGCATTTCATATATATATATATATATACATGCACATGCG
Found at i:112781108 original size:30 final size:30
Alignment explanation
Indices: 112781074--112781166 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
112781064 GTTGATCTCT
112781074 ATTGAAGATTAAACAAGCAGGCAAGGTTTC
1 ATTGAAGATTAAACAAGCAGGCAAGGTTTC
* * *
112781104 ATTGAAG--T-AA-ATGAATG-AA--TTAATC
1 ATTGAAGATTAAACAAGCAGGCAAGGTT--TC
112781129 TATTGAAGATTAAACAAGCAGGCAAGGTTTC
1 -ATTGAAGATTAAACAAGCAGGCAAGGTTTC
112781160 ATTGAAG
1 ATTGAAG
112781167 TAAATGAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
23 2 0.04
25 4 0.09
26 11 0.23
27 2 0.04
28 2 0.04
29 2 0.04
30 18 0.38
31 4 0.09
33 2 0.04
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (30 bp):
ATTGAAGATTAAACAAGCAGGCAAGGTTTC
Found at i:112781157 original size:56 final size:56
Alignment explanation
Indices: 112781071--112781185 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
112781061 CAGGTTGATC
112781071 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
1 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
112781127 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
1 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
112781183 TCT
1 TCT
112781186 TGTGATATGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.30
Consensus pattern (56 bp):
TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
Found at i:112781741 original size:22 final size:23
Alignment explanation
Indices: 112781716--112781758 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
112781706 TCAAAATATT
112781716 TAAATTC-AAAAAAATAAAAAAC
1 TAAATTCTAAAAAAATAAAAAAC
*
112781738 TAAATTCTTAAAAAATAAAAA
1 TAAATTCTAAAAAAATAAAAA
112781759 TATAGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAATTCTAAAAAAATAAAAAAC
Done.