Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 42 of 345
Found at i:12200885 original size:15 final size:15
Alignment explanation
Indices: 12200867--12200896 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12200857 TATGTTTTAT
*
12200867 TTGTAAGACATAATG
1 TTGTAAGACACAATG
12200882 TTGTAAGACACAATG
1 TTGTAAGACACAATG
12200897 CTATCGGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (15 bp):
TTGTAAGACACAATG
Found at i:12210230 original size:27 final size:25
Alignment explanation
Indices: 12210171--12210233 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
12210161 CATTATCGCA
12210171 GTTTTGTCCACAGCTTTGTAGTTTT
1 GTTTTGTCCACAGCTTTGTAGTTTT
* ** *
12210196 ATTTTGTCCACATTTTTCGTGGTTTTT
1 GTTTTGTCCACAGCTTT-GTAG-TTTT
12210223 GTTTTGTCCAC
1 GTTTTGTCCAC
12210234 TCTGTTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 14 0.45
26 3 0.10
27 14 0.45
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.54
Consensus pattern (25 bp):
GTTTTGTCCACAGCTTTGTAGTTTT
Found at i:12210796 original size:22 final size:21
Alignment explanation
Indices: 12210733--12210797 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
12210723 ATTTTTCTTT
*
12210733 AAAAAAATGCATACTATTTAAAAA
1 AAAAAAAT--ATAC-ATTCAAAAA
* * *
12210757 AGAAAAATATATAGTCAAAAGA
1 AAAAAAATATACATTCAAAA-A
12210779 AAAAAAATATACATTCAAA
1 AAAAAAATATACATTCAAA
12210798 TTCGGGTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 6 0.18
22 20 0.61
24 7 0.21
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.22
Consensus pattern (21 bp):
AAAAAAATATACATTCAAAAA
Found at i:12214482 original size:11 final size:11
Alignment explanation
Indices: 12214462--12214492 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12214452 TTTTTTAAAA
12214462 ATTA-TATTTT
1 ATTATTATTTT
12214472 ATTATTATTTT
1 ATTATTATTTT
12214483 ATTATTATTT
1 ATTATTATTT
12214493 CATGTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:12222614 original size:29 final size:29
Alignment explanation
Indices: 12222568--12222627 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
12222558 TATATGGTAA
* * *
12222568 TTAATTATGGTTAAAATGGCATGTATAGG
1 TTAATTATGGTCAAAATGGCATATAAAGG
12222597 TTAATT-TGGTCAACAATGGCATATAAAGG
1 TTAATTATGGTCAA-AATGGCATATAAAGG
12222626 TT
1 TT
12222628 TGGTTATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (29 bp):
TTAATTATGGTCAAAATGGCATATAAAGG
Found at i:12224221 original size:36 final size:36
Alignment explanation
Indices: 12224174--12224245 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12224164 TCAAAATGGA
12224174 AATGAAAACTAAGTGAAAAAGGAGACCAAGAGTTTT
1 AATGAAAACTAAGTGAAAAAGGAGACCAAGAGTTTT
12224210 AATGAAAACTAAGTGAAAAAGGAGACCAAGAGTTTT
1 AATGAAAACTAAGTGAAAAAGGAGACCAAGAGTTTT
12224246 TCTTCCAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.19
Consensus pattern (36 bp):
AATGAAAACTAAGTGAAAAAGGAGACCAAGAGTTTT
Found at i:12225915 original size:2 final size:2
Alignment explanation
Indices: 12225908--12225952 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12225898 TTTCCCCCAT
12225908 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12225950 TC T
1 TC T
12225953 GGTACTGCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12226544 original size:48 final size:48
Alignment explanation
Indices: 12226488--12226580 Score: 152
Period size: 48 Copynumber: 1.9 Consensus size: 48
12226478 TTGTAACATC
*
12226488 CCCAACCCTTA-TCTGTCGCCGGAATAGGGTTACGGAGTATTACCAAAG
1 CCCAACCCTTATTC-GTCACCGGAATAGGGTTACGGAGTATTACCAAAG
*
12226536 CCCAACCCTTATTCGTCACTGGAATAGGGTTACGGAGTATTACCA
1 CCCAACCCTTATTCGTCACCGGAATAGGGTTACGGAGTATTACCA
12226581 GACATTTCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 40 0.95
49 2 0.05
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (48 bp):
CCCAACCCTTATTCGTCACCGGAATAGGGTTACGGAGTATTACCAAAG
Found at i:12228360 original size:21 final size:20
Alignment explanation
Indices: 12228317--12228361 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
12228307 CTAATTTCCC
** *
12228317 TTTTTCTTTTCTTTCTTTCT
1 TTTTTCTTTTCTTTCCCTAT
12228337 TTTTCTCTTTTCTTTCCCTAT
1 TTTT-TCTTTTCTTTCCCTAT
12228358 TTTT
1 TTTT
12228362 GTTTTGCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTCTTTCCCTAT
Found at i:12228415 original size:3 final size:3
Alignment explanation
Indices: 12228407--12228459 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
12228397 ATCTTTATTT
*
12228407 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T-A TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12228453 T-A TAA TA
1 TAA TAA TA
12228460 TTTTAATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12228466 original size:16 final size:16
Alignment explanation
Indices: 12228409--12228460 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 16
12228399 CTTTATTTTA
12228409 ATAATAATAATAATAAT
1 ATAATAATAAT-ATAAT
12228426 AATAATAATAATATAAT
1 -ATAATAATAATATAAT
*
12228443 ATAATAATGATATAAT
1 ATAATAATAATATAAT
12228459 AT
1 AT
12228461 TTTAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
16 17 0.52
17 5 0.15
18 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAATAATAATATAAT
Found at i:12231321 original size:11 final size:11
Alignment explanation
Indices: 12231304--12231352 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
12231294 AGATAAATAT
12231304 TATTTTATTAA
1 TATTTTATTAA
* *
12231315 TACTTTAATAAGA
1 TA-TTTTATTA-A
*
12231328 TATTTTATTAT
1 TATTTTATTAA
12231339 TATTTTATTAA
1 TATTTTATTAA
12231350 TAT
1 TAT
12231353 AAAGAAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 15 0.50
12 12 0.40
13 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:12231349 original size:27 final size:27
Alignment explanation
Indices: 12231272--12231351 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
12231262 GAGATATTTT
* *
12231272 GATATTTTATAATTATTTAATTAGATAA
1 GATATTTTATTATTATTTTATTA-ATAA
**
12231300 -ATATTATT-TTATTAATACT-TTAATAA
1 GATATT-TTATTATT-ATTTTATTAATAA
12231326 GATATTTTATTATTATTTTATTAATA
1 GATATTTTATTATTATTTTATTAATA
12231352 TAAAGAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
26 9 0.22
27 28 0.68
28 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (27 bp):
GATATTTTATTATTATTTTATTAATAA
Found at i:12233580 original size:46 final size:46
Alignment explanation
Indices: 12233513--12233719 Score: 274
Period size: 46 Copynumber: 4.7 Consensus size: 46
12233503 ATGGCAACTG
12233513 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
12233559 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
12233597 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
12233643 --TGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * * *
12233687 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
12233720 TCACGTCAAA
Statistics
Matches: 144, Mismatches: 6, Indels: 22
0.84 0.03 0.13
Matches are distributed among these distances:
38 36 0.25
41 2 0.01
43 3 0.02
44 40 0.28
46 63 0.44
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:12233608 original size:38 final size:39
Alignment explanation
Indices: 12233558--12233675 Score: 184
Period size: 38 Copynumber: 2.9 Consensus size: 39
12233548 CTGATATGAA
12233558 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
12233597 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
12233635 ATATGAAATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 --ATG---TGTAAGACCATGGTTGAAAGATACCATGGCAAC
12233676 ATGACAGAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
38 38 0.52
41 2 0.03
44 33 0.45
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:12233639 original size:84 final size:84
Alignment explanation
Indices: 12233465--12233675 Score: 401
Period size: 84 Copynumber: 2.5 Consensus size: 84
12233455 AGTGTGCTCT
12233465 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
12233529 TGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAAC
12233548 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
12233613 TGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAAC
12233632 CTGATATGAAA--TGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
12233676 ATGACAGAAA
Statistics
Matches: 127, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
82 33 0.26
83 45 0.35
84 49 0.39
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (84 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
TGAAAGATACCATGGCAAC
Found at i:12233697 original size:128 final size:121
Alignment explanation
Indices: 12233476--12233719 Score: 355
Period size: 128 Copynumber: 2.0 Consensus size: 121
12233466 TGATATGAAA
12233476 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGTGTGTAAGACCATGGTTGAAAGATACCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGTGTGTAAGACCATGGTTGAAAGATACCA
* * * * *
12233541 TGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
66 TGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTG
12233597 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTAAGACCATGGTTGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CTG---TG---TGTAAGACCATGGTTGAAA
*
12233662 GATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
59 GATACCATGGCAACATGACATG-AAATGAGTAAGACCATAGTTGAAAGACACCATGGCA
12233720 TCACGTCAAA
Statistics
Matches: 109, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
121 34 0.31
122 3 0.03
125 2 0.02
127 1 0.01
128 69 0.63
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (121 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACTGTGTGTAAGACCATGGTTGAAAGATACCA
TGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTG
Found at i:12234023 original size:23 final size:25
Alignment explanation
Indices: 12233978--12234024 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12233968 AATAAATATA
*
12233978 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
12234003 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
12234025 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:12238869 original size:38 final size:38
Alignment explanation
Indices: 12238820--12239057 Score: 343
Period size: 38 Copynumber: 5.9 Consensus size: 38
12238810 TGATATGAAA
12238820 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
12238858 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG
12238901 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CTG
1 ---TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
12238941 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
12238979 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
12239017 ATATGAAATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 ---TG---TGTAAGACCATGGTTGAAAGATACCATGGCAAC
12239058 ATGACAGAAA
Statistics
Matches: 185, Mismatches: 0, Indels: 24
0.89 0.00 0.11
Matches are distributed among these distances:
37 34 0.18
38 77 0.42
40 2 0.01
41 2 0.01
43 2 0.01
44 33 0.18
45 1 0.01
46 34 0.18
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (38 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:12238925 original size:46 final size:45
Alignment explanation
Indices: 12238858--12239101 Score: 281
Period size: 46 Copynumber: 5.7 Consensus size: 45
12238848 TGGCAACCTG
12238858 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATGAAA
12238904 TGTGTAAGACCATGGTTGAAAGATACCATGGCAA-C----TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
12238941 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
12238979 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATGAAA
*
12239025 --TGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATG-AAA
* * * *
12239069 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
12239102 TCACGTCAAA
Statistics
Matches: 180, Mismatches: 6, Indels: 24
0.86 0.03 0.11
Matches are distributed among these distances:
37 34 0.19
38 39 0.22
40 2 0.01
43 3 0.02
44 40 0.22
45 1 0.01
46 61 0.34
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (45 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
Found at i:12239044 original size:44 final size:43
Alignment explanation
Indices: 12238822--12239101 Score: 333
Period size: 38 Copynumber: 6.7 Consensus size: 43
12238812 ATATGAAATG
12238822 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--TG---
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
12238860 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATGAAA
12238904 TGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CTG--TG---
1 --TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
12238943 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--TG---
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
12238981 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATGAAA
*
12239025 TGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATG-AAA
* * *
12239069 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 T--GTAAGACCATGGTTGAAAGATACCATGGCA
12239102 TCACGTCAAA
Statistics
Matches: 219, Mismatches: 5, Indels: 28
0.87 0.02 0.11
Matches are distributed among these distances:
37 32 0.15
38 77 0.35
41 4 0.02
42 2 0.01
43 1 0.00
44 41 0.19
45 3 0.01
46 59 0.27
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (43 bp):
TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAA
Found at i:12240792 original size:79 final size:77
Alignment explanation
Indices: 12240660--12240828 Score: 223
Period size: 79 Copynumber: 2.2 Consensus size: 77
12240650 GAGTCACATC
* ** *
12240660 TCATGTAACTGTAGTAAATCAGGATTACCTTTTAAGTCAAATCCTACCCACCTTAAGTTATCATA
1 TCATGTAACCGTAGCGAATCAGGATTACCTTTTAAGTCAAATCCTACCCACCTTAAGTTACCATA
*
12240725 A-GGAATCATGTA
66 ATGG-ATCATATA
* * * *
12240737 TCGTGTAACCGTAGCGAATCAGGATTATCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCA
1 TCATGTAACCGTAGCGAATCAGGATTA-CCTTTT-AAGTCAAATCCTACCCACCTTAAGTTACCA
12240802 TAATGGATCATATA
64 TAATGGATCATATA
12240816 TCATGTAACCGTA
1 TCATGTAACCGTA
12240829 ATCCTATCCG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 23 0.29
78 6 0.08
79 48 0.61
80 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (77 bp):
TCATGTAACCGTAGCGAATCAGGATTACCTTTTAAGTCAAATCCTACCCACCTTAAGTTACCATA
ATGGATCATATA
Found at i:12240901 original size:40 final size:40
Alignment explanation
Indices: 12240828--12240963 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 40
12240818 ATGTAACCGT
* * * * *
12240828 AATCCTATCCGCCTTAAGTTACCATAGTGAATCAAGAATA
1 AATCCTATCCACTTTAAATTACCACAGTGAATCAAGAACA
* * *
12240868 AATCTTATTCACTTTAAATTACCACAGTGAATCAGGAACA
1 AATCCTATCCACTTTAAATTACCACAGTGAATCAAGAACA
* ** ** * * * *
12240908 AATCCTATCCACTTTGAGGTATTATATTGAATCAGGAACG
1 AATCCTATCCACTTTAAATTACCACAGTGAATCAAGAACA
12240948 AATCCTATCCACTTTA
1 AATCCTATCCACTTTA
12240964 TATTCTCGAG
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (40 bp):
AATCCTATCCACTTTAAATTACCACAGTGAATCAAGAACA
Found at i:12242958 original size:22 final size:22
Alignment explanation
Indices: 12242933--12242976 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12242923 TTATATTTAC
12242933 ACTTTAACCTCTCAAGTTTTGA
1 ACTTTAACCTCTCAAGTTTTGA
12242955 ACTTTAACCTCTCAAGTTTTGA
1 ACTTTAACCTCTCAAGTTTTGA
12242977 GTATTTACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (22 bp):
ACTTTAACCTCTCAAGTTTTGA
Found at i:12244682 original size:26 final size:26
Alignment explanation
Indices: 12244653--12244734 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
12244643 TTGTACAAAT
12244653 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12244679 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
12244705 TGATAATGGCTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12244731 TGAT
1 TGAT
12244735 GGGCATTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:12247582 original size:14 final size:13
Alignment explanation
Indices: 12247565--12247603 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
12247555 AATATAATTA
12247565 TTTGTATATTTTTT
1 TTTGTAT-TTTTTT
*
12247579 TTTGTATTTTTAT
1 TTTGTATTTTTTT
12247592 TTT-TATTTTTTT
1 TTTGTATTTTTTT
12247604 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (13 bp):
TTTGTATTTTTTT
Found at i:12247594 original size:6 final size:6
Alignment explanation
Indices: 12247571--12247611 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
12247561 ATTATTTGTA
*
12247571 TATTTT T-TTTT GTATTTT TATTTT TATTTT T-TTAT TATTTT
1 TATTTT TATTTT -TATTTT TATTTT TATTTT TATTTT TATTTT
12247612 ATAATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.27
6 18 0.60
7 4 0.13
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:12247600 original size:20 final size:20
Alignment explanation
Indices: 12247563--12247606 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12247553 AAAATATAAT
12247563 TATTTGTATATTTTTTTTTG
1 TATTTGTATATTTTTTTTTG
* *
12247583 TATTTTTAT-TTTTATTTTTT
1 TATTTGTATATTTT-TTTTTG
12247603 TATT
1 TATT
12247607 ATTTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.80
Consensus pattern (20 bp):
TATTTGTATATTTTTTTTTG
Found at i:12247622 original size:24 final size:24
Alignment explanation
Indices: 12247569--12247622 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
12247559 TAATTATTTG
* *
12247569 TATATTTTTTTTTGTATTTTTATT
1 TATATTTTTTTATGTATTTTTAAT
*
12247593 TTTATTTTTTTAT-TATTTTATAAT
1 TATATTTTTTTATGTATTTT-TAAT
12247617 TATATT
1 TATATT
12247623 GTATTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (24 bp):
TATATTTTTTTATGTATTTTTAAT
Found at i:12251510 original size:5 final size:5
Alignment explanation
Indices: 12251484--12251542 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
12251474 TAATTATAAA
* **
12251484 ATATAT ATATT AGTAAT ATATT ATATT ATATT ATATT A-ATT -TAAA ATAATT
1 ATAT-T ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATATT AT-ATT
12251535 ATATT ATA
1 ATATT ATA
12251543 AGATATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.09
5 28 0.65
6 11 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (5 bp):
ATATT
Found at i:12251518 original size:15 final size:15
Alignment explanation
Indices: 12251476--12251560 Score: 75
Period size: 16 Copynumber: 5.5 Consensus size: 15
12251466 TTAGATTTTA
*
12251476 ATTATAAAATATATAT
1 ATTATAATATAT-TAT
12251492 ATTAGTAATATATTAT
1 ATTA-TAATATATTAT
*
12251508 ATTATATTATATTA-
1 ATTATAATATATTAT
*
12251522 ATT-TAAAATAATTAT
1 ATTATAATAT-ATTAT
*
12251537 ATTATAAGATATTTAT
1 ATTATAATATA-TTAT
*
12251553 ATGATAAT
1 ATTATAAT
12251561 TAAATTAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.07
14 7 0.12
15 13 0.23
16 26 0.46
17 7 0.12
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
ATTATAATATATTAT
Found at i:12251681 original size:5 final size:5
Alignment explanation
Indices: 12251671--12251699 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12251661 TTATTAAATG
12251671 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
12251700 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:12251765 original size:17 final size:16
Alignment explanation
Indices: 12251720--12251766 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
12251710 AAAGCATGCA
*
12251720 ATAAAAGAAACAAAAC
1 ATAAAAGAAACAGAAC
* *
12251736 ATAAAAAAAACAGAAT
1 ATAAAAGAAACAGAAC
12251752 ATAAAACGAAACAGA
1 ATAAAA-GAAACAGA
12251767 GAAGGAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.72, C:0.11, G:0.09, T:0.09
Consensus pattern (16 bp):
ATAAAAGAAACAGAAC
Found at i:12252961 original size:44 final size:44
Alignment explanation
Indices: 12252913--12252999 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
12252903 TTCGACCTTG
*
12252913 AGTCGATGAGGCACTATAAGTGTCGTACTATTACT-TTGACTTCA
1 AGTCGATGAGGCACCATAAGTGTCGTACTATTACTGTT-ACTTCA
**
12252957 AGTCGATGAGGCACCATGTGTGTCGTACTATTACTGTTACTTC
1 AGTCGATGAGGCACCATAAGTGTCGTACTATTACTGTTACTTC
12253000 GGTTTAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (44 bp):
AGTCGATGAGGCACCATAAGTGTCGTACTATTACTGTTACTTCA
Found at i:12253069 original size:47 final size:47
Alignment explanation
Indices: 12252960--12253079 Score: 118
Period size: 46 Copynumber: 2.5 Consensus size: 47
12252950 GACTTCAAGT
* * ** **
12252960 CGATGAGGCACCATGTGTGTCGTACTATTACTGTTACTTCGGTTTAATT
1 CGATGAGGCA-C-TGAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGC
* *
12253009 CGATGAGG-TCTGAGTATCGTACTGTTACTGTTTACTTCGG-CAAAGC
1 CGATGAGGCACTGAGTGTCGTACTGTTACTG-TTACTTCGGTCAAAGC
*
12253055 CGATGAGGCACTGAGTGCCGTACTG
1 CGATGAGGCACTGAGTGTCGTACTG
12253080 GTGTGTTGGT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
46 27 0.47
47 23 0.40
49 8 0.14
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (47 bp):
CGATGAGGCACTGAGTGTCGTACTGTTACTGTTACTTCGGTCAAAGC
Found at i:12253180 original size:39 final size:40
Alignment explanation
Indices: 12253137--12253218 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 40
12253127 TAAGGGTAAA
12253137 AAAGGTACTGAATGA-TCGACTGTTACTAAATGATATT-AT
1 AAAGGTACTGAATGACT-GACTGTTACTAAATGATATTGAT
* * *
12253176 AAAGGTTCTGAATGACTGACTGTTATTGAATGATATTGAT
1 AAAGGTACTGAATGACTGACTGTTACTAAATGATATTGAT
12253216 AAA
1 AAA
12253219 TTGATTGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.34
Consensus pattern (40 bp):
AAAGGTACTGAATGACTGACTGTTACTAAATGATATTGAT
Found at i:12253221 original size:18 final size:18
Alignment explanation
Indices: 12253200--12253237 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12253190 ACTGACTGTT
*
12253200 ATTGAATGATATTGATAA
1 ATTGAATGATATTGAAAA
*
12253218 ATTGATTGATATTGAAAA
1 ATTGAATGATATTGAAAA
12253236 AT
1 AT
12253238 ATTGACTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (18 bp):
ATTGAATGATATTGAAAA
Found at i:12253322 original size:7 final size:7
Alignment explanation
Indices: 12253312--12253337 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12253302 TTATTGATAT
12253312 TGAACAG
1 TGAACAG
12253319 TGAACAG
1 TGAACAG
12253326 TGAACAG
1 TGAACAG
12253333 TGAAC
1 TGAAC
12253338 TGAAACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (7 bp):
TGAACAG
Found at i:12254130 original size:21 final size:21
Alignment explanation
Indices: 12254100--12254146 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12254090 AACACAGTTG
*
12254100 TGTGACCTAGCGACATGGCCA
1 TGTGACCTAGCGACACGGCCA
* * *
12254121 TGTGATCTAGTGACACGGCCG
1 TGTGACCTAGCGACACGGCCA
12254142 TGTGA
1 TGTGA
12254147 GTCACACGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (21 bp):
TGTGACCTAGCGACACGGCCA
Found at i:12255631 original size:15 final size:16
Alignment explanation
Indices: 12255611--12255644 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12255601 AATAACTCCA
12255611 TTTAAG-AAATATAAT
1 TTTAAGCAAATATAAT
12255626 TTTAAGCAAATATAAT
1 TTTAAGCAAATATAAT
12255642 TTT
1 TTT
12255645 TTATATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTAAGCAAATATAAT
Found at i:12255855 original size:2 final size:2
Alignment explanation
Indices: 12255848--12255874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12255838 CAGTATCCAA
12255848 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 A
12255875 AAGTACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12271322 original size:32 final size:32
Alignment explanation
Indices: 12271281--12271342 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
12271271 TCATATTTTT
* *
12271281 AATTAAATTTGGCCATTAATCTTTTAAAAAAG
1 AATTAAATTTGACCATTAACCTTTTAAAAAAG
12271313 AATTAAATTTGACCATTAACCTTTTAAAAA
1 AATTAAATTTGACCATTAACCTTTTAAAAA
12271343 GAGTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.37
Consensus pattern (32 bp):
AATTAAATTTGACCATTAACCTTTTAAAAAAG
Found at i:12271445 original size:27 final size:27
Alignment explanation
Indices: 12271407--12271460 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12271397 AACATTGTAG
12271407 CCCACATGACAATTCGCATGTAGTTCA
1 CCCACATGACAATTCGCATGTAGTTCA
12271434 CCCACATGACAATTCGCATGTAGTTCA
1 CCCACATGACAATTCGCATGTAGTTCA
12271461 TACTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (27 bp):
CCCACATGACAATTCGCATGTAGTTCA
Found at i:12272376 original size:93 final size:92
Alignment explanation
Indices: 12272214--12272382 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 92
12272204 TCATAACGGT
*
12272214 TGTCATGTCAACATCACTAAAAAATAATAATGTTTTAGTCAACATTTCTATTTAAAAAAAGTGAC
1 TGTCATGTCAACATCACTAAAAAATAATAATGTTTTAGTCAACATTTCTATTTAAAAAAAGCGAC
12272279 TTGACTCTTTTTAATTACCACAATGGC
66 TTGACTCTTTTTAATTACCACAATGGC
* *
12272306 TGTCATGTCAACATCATTAAAAAAATAATAATGTTTTAGTCAATATTT-TCATTTAAAAAAAGCG
1 TGTCATGTCAACATCACT-AAAAAATAATAATGTTTTAGTCAACATTTCT-ATTTAAAAAAAGCG
**
12272370 TTTTGACTCTTTT
64 ACTTGACTCTTTT
12272383 CAAAATGTGA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 18 0.26
93 52 0.74
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (92 bp):
TGTCATGTCAACATCACTAAAAAATAATAATGTTTTAGTCAACATTTCTATTTAAAAAAAGCGAC
TTGACTCTTTTTAATTACCACAATGGC
Found at i:12276561 original size:37 final size:38
Alignment explanation
Indices: 12276511--12276585 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
12276501 TGTGTTAGTG
12276511 TTTGTAATCACCTGTT-TATGATGTGTTAAGATAATAA
1 TTTGTAATCACCTGTTGTATGATGTGTTAAGATAATAA
12276548 TTTGTAATCACCTGTTGTATGATGTGTTAAGATAATAA
1 TTTGTAATCACCTGTTGTATGATGTGTTAAGATAATAA
12276586 ATTATCTCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 16 0.43
38 21 0.57
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (38 bp):
TTTGTAATCACCTGTTGTATGATGTGTTAAGATAATAA
Found at i:12277360 original size:16 final size:17
Alignment explanation
Indices: 12277329--12277361 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12277319 TGCGACAACC
12277329 TAATTTTTTATCTTAAAA
1 TAATTTTTTA-CTTAAAA
12277347 TAATTTTTTA-TTAAA
1 TAATTTTTTACTTAAA
12277362 GCTGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTTTTTACTTAAAA
Found at i:12287903 original size:16 final size:15
Alignment explanation
Indices: 12287852--12287903 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
12287842 AGTATATATA
12287852 AATTTTAATTT-TGTGT
1 AATTTTAATTTAT-T-T
*
12287868 AATTTT-ATTTATTA
1 AATTTTAATTTATTT
12287882 AATTTTAATTTAATTT
1 AATTTTAATTT-ATTT
12287898 AATTTT
1 AATTTT
12287904 TATAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 9 0.29
16 16 0.52
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
AATTTTAATTTATTT
Found at i:12288018 original size:14 final size:14
Alignment explanation
Indices: 12287999--12288028 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12287989 AAGTAAATGC
12287999 ATGTATTCAATTAA
1 ATGTATTCAATTAA
12288013 ATGTATTCAATTAA
1 ATGTATTCAATTAA
12288027 AT
1 AT
12288029 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATGTATTCAATTAA
Found at i:12288062 original size:27 final size:26
Alignment explanation
Indices: 12288026--12288085 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
12288016 TATTCAATTA
* * *
12288026 AATTAAAATTAAAATTTTATGTATGT
1 AATTACAATTAAAATTTTATATATAT
*
12288052 GAATTACAATTCAAATTTTATATATAT
1 -AATTACAATTAAAATTTTATATATAT
12288079 AATTACA
1 AATTACA
12288086 CCAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (26 bp):
AATTACAATTAAAATTTTATATATAT
Found at i:12291087 original size:42 final size:43
Alignment explanation
Indices: 12290992--12291127 Score: 175
Period size: 43 Copynumber: 3.2 Consensus size: 43
12290982 TATATGAACA
* **
12290992 CCGCTAAAGACTAGGACTTATAGCGATGCTTATATAAAAAACG
1 CCGCTAAAGACCAGGACTTATAGCGGCGCTTATATAAAAAACG
* * *
12291035 CCGTTAAAGACCAGGACTTTTAGCGGCACTTATATAAAAAA-G
1 CCGCTAAAGACCAGGACTTATAGCGGCGCTTATATAAAAAACG
* * * *
12291077 CCGCTAAAGACCAAGACTTATAACGGCGCTTTTCTAAAAAACG
1 CCGCTAAAGACCAGGACTTATAGCGGCGCTTATATAAAAAACG
12291120 CCGCTAAA
1 CCGCTAAA
12291128 AATTCTAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 35 0.44
43 44 0.56
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (43 bp):
CCGCTAAAGACCAGGACTTATAGCGGCGCTTATATAAAAAACG
Found at i:12291136 original size:22 final size:22
Alignment explanation
Indices: 12291108--12291171 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
12291098 AACGGCGCTT
12291108 TTCTAAAAAACGCCGCTAAAAA
1 TTCTAAAAAACGCCGCTAAAAA
** *
12291130 TTCTAAAAAACATCGCTAAAAG
1 TTCTAAAAAACGCCGCTAAAAA
12291152 TTCTAAAAAACGCCGCTAAA
1 TTCTAAAAAACGCCGCTAAA
12291172 GACTAGGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.20
Consensus pattern (22 bp):
TTCTAAAAAACGCCGCTAAAAA
Found at i:12291531 original size:21 final size:21
Alignment explanation
Indices: 12291506--12291553 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
12291496 TTCTGTTCTG
*
12291506 CTCCGCCTCCCTCGCTGTTGC
1 CTCCGCCTCCCTCGCTGCTGC
12291527 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
12291548 CTCCGC
1 CTCCGC
12291554 TCTAAGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.00, C:0.56, G:0.19, T:0.25
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGC
Found at i:12291905 original size:41 final size:41
Alignment explanation
Indices: 12291849--12292056 Score: 310
Period size: 41 Copynumber: 5.1 Consensus size: 41
12291839 CGTTTTTACG
* * *
12291849 AAAAA-CAGAGAATTAGCGGCGCTTCTGGCAAAACGCCGTT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCT
* *
12291889 AAAAACCAGAGCATTAGCGGCGCTTCTGGAAAAACGCCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCT
* * *
12291930 AAAAACCATAGCATTAGCGGCGCTTTTGGAAAAACGCCTCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCT
*
12291971 AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGTCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCT
* *
12292012 AAAAACCAGAGCATTAGCAGCGCTTTTGGCAAAACGGCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCT
12292053 AAAA
1 AAAA
12292057 GTCATATAAC
Statistics
Matches: 155, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 5 0.03
41 150 0.97
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (41 bp):
AAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCT
Found at i:12292249 original size:21 final size:21
Alignment explanation
Indices: 12292225--12292305 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
12292215 ATAGTTTATG
*
12292225 GTTTATGGTTTAAGATATATA
1 GTTTAGGGTTTAAGATATATA
* *
12292246 GTTTAGGGTTTAAGATTTTTGA
1 GTTTAGGGTTTAAGATATAT-A
* *
12292268 GTTAACTATGGTTTAAGATATATG
1 GTT---TAGGGTTTAAGATATATA
12292292 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
12292306 GTTTAGGAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 27 0.56
22 4 0.08
24 3 0.06
25 14 0.29
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (21 bp):
GTTTAGGGTTTAAGATATATA
Found at i:12292296 original size:46 final size:46
Alignment explanation
Indices: 12292228--12292321 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
12292218 GTTTATGGTT
**
12292228 TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTTTGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTAGGAGTTAAC
* *
12292274 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTAGGAGTTAAC
12292320 TA
1 TA
12292322 GTATTTGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (46 bp):
TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTAGGAGTTAAC
Found at i:12292400 original size:21 final size:22
Alignment explanation
Indices: 12292371--12292438 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
12292361 ATAATTTAGG
12292371 GTTT-AGGTGTTAGGG-TTGGA
1 GTTTAAGGTGTTAGGGTTTGGA
*
12292391 GTTTAAGGTGTAAGGGTTTGG-
1 GTTTAAGGTGTTAGGGTTTGGA
* *
12292412 GGTTAAGG-GTTAAGGGTTTAGA
1 GTTTAAGGTGTT-AGGGTTTGGA
12292434 GTTTA
1 GTTTA
12292439 GAAAAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 6 0.15
21 25 0.64
22 8 0.21
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (22 bp):
GTTTAAGGTGTTAGGGTTTGGA
Found at i:12292917 original size:39 final size:38
Alignment explanation
Indices: 12292844--12292917 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
12292834 CCTAAACCCA
* *
12292844 ATTTAATATATATATATTTATATTATTTTTAATTTAAT
1 ATTTAATATATATATATGTATATTATTTTAAATTTAAT
* *
12292882 ATTTAATATCCTATATATGTA-ATTGTATTTAAATTT
1 ATTTAATAT-ATATATATGTATATTAT-TTTAAATTT
12292918 TTAATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
38 13 0.43
39 17 0.57
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (38 bp):
ATTTAATATATATATATGTATATTATTTTAAATTTAAT
Found at i:12292956 original size:23 final size:23
Alignment explanation
Indices: 12292895--12292957 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
12292885 TAATATCCTA
*
12292895 TATATGTAATTGTATTTAAATTT
1 TATATGTAATTGTATTAAAATTT
*
12292918 T-TAATTTATATT-TATTAAAATTT
1 TAT-ATGTA-ATTGTATTAAAATTT
12292941 TATATGTAATTGTATTA
1 TATATGTAATTGTATTA
12292958 GCATTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 4 0.12
23 25 0.76
24 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TATATGTAATTGTATTAAAATTT
Found at i:12296383 original size:17 final size:17
Alignment explanation
Indices: 12296358--12296393 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12296348 AAGTTGACTT
* *
12296358 GAACTTAAAACCAATTC
1 GAACATAAAAACAATTC
12296375 GAACATAAAAACAATTC
1 GAACATAAAAACAATTC
12296392 GA
1 GA
12296394 CCAAGTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19
Consensus pattern (17 bp):
GAACATAAAAACAATTC
Found at i:12296417 original size:48 final size:48
Alignment explanation
Indices: 12296346--12296441 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
12296336 CAACCCATAC
* * * *
12296346 CCAAGTTGACTTGAACTTAAAACCAATTCGAACATAAAAACAATTCGA
1 CCAAGTTAACTTGAACTTAAAACCAATCCAAACACAAAAACAATTCGA
*
12296394 CCAAGTTAACTTGAACTTAAAACCAATCCAAACCCAAAAACAATTCGA
1 CCAAGTTAACTTGAACTTAAAACCAATCCAAACACAAAAACAATTCGA
12296442 AAGTAATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (48 bp):
CCAAGTTAACTTGAACTTAAAACCAATCCAAACACAAAAACAATTCGA
Found at i:12296522 original size:11 final size:12
Alignment explanation
Indices: 12296489--12296525 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
12296479 CTCGAAATTG
12296489 ACCGAATCCTTC
1 ACCGAATCCTTC
12296501 ACCGAATCCTTC
1 ACCGAATCCTTC
12296513 ACCG-ATCCTTC
1 ACCGAATCCTTC
12296524 AC
1 AC
12296526 GGAAATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.24, C:0.43, G:0.08, T:0.24
Consensus pattern (12 bp):
ACCGAATCCTTC
Found at i:12299023 original size:43 final size:44
Alignment explanation
Indices: 12298975--12299132 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 44
12298965 AATAAATTTT
*
12298975 TAAAAGGTCAT-ATTTTTAGCGGCGTTTTTAGGAAGAGCGCCGC
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAGAGCGCCGC
* * * *
12299018 TAAAA-GTCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGTCGC
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAGAGCGCCGC
* * * **
12299061 -GAAAGGTCCTGGTCTTTAGCGGCGTTTTTTAAAAAG-GCGCCGC
1 TAAAAGGTCATGATCTTTAGCGGCG-TTTTTAGGAAGAGCGCCGC
* * * *
12299104 T-AAAGGTCCTGGTCTTTAGTGGCCTTTTT
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTT
12299133 TCTAAAAAAC
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 13 0.14
43 76 0.80
44 6 0.06
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (44 bp):
TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAGAGCGCCGC
Found at i:12303293 original size:13 final size:13
Alignment explanation
Indices: 12303275--12303320 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12303265 TTATATGCCC
12303275 ATTTACATGCAGA
1 ATTTACATGCAGA
*
12303288 ATTT--A--CAGT
1 ATTTACATGCAGA
12303297 ATTTACATGCAGA
1 ATTTACATGCAGA
12303310 ATTTACATGCA
1 ATTTACATGCA
12303321 TCAACAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
9 7 0.26
11 2 0.07
13 18 0.67
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (13 bp):
ATTTACATGCAGA
Found at i:12303301 original size:22 final size:22
Alignment explanation
Indices: 12303275--12303316 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12303265 TTATATGCCC
12303275 ATTTACATGCAGAATTTACAGT
1 ATTTACATGCAGAATTTACAGT
12303297 ATTTACATGCAGAATTTACA
1 ATTTACATGCAGAATTTACA
12303317 TGCATCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
ATTTACATGCAGAATTTACAGT
Found at i:12303679 original size:209 final size:209
Alignment explanation
Indices: 12303319--12303724 Score: 785
Period size: 209 Copynumber: 1.9 Consensus size: 209
12303309 AATTTACATG
*
12303319 CATCAACAACATTAATGATATACCTTATTACATGCAGAATTTACAGTATTTAAGCTCCTTAGAAT
1 CATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCTTAGAAT
*
12303384 TATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGCCAGAAA
66 TATACTTTTAAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGCCAGAAA
12303449 ATGAAACAATGTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGA
131 ATGAAACAATGTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGA
12303514 ATAAACACTGCCGT
196 ATAAACACTGCCGT
12303528 CATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCTTAGAAT
1 CATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCTTAGAAT
12303593 TATACTTTTAAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGCCAGAAA
66 TATACTTTTAAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGCCAGAAA
*
12303658 ATGAAATAATGTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGA
131 ATGAAACAATGTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGA
12303723 AT
196 AT
12303725 TATGATTACC
Statistics
Matches: 194, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
209 194 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (209 bp):
CATCAACAACATTAATGATATACCTCATTACATGCAGAATTTACAGTATTTAAGCTCCTTAGAAT
TATACTTTTAAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATGCCAGAAA
ATGAAACAATGTACCATTTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGA
ATAAACACTGCCGT
Found at i:12307467 original size:7 final size:7
Alignment explanation
Indices: 12307455--12307559 Score: 66
Period size: 7 Copynumber: 14.4 Consensus size: 7
12307445 AGTTAACTCC
*
12307455 TAAACCT
1 TAAACCA
*
12307462 TAAACCC
1 TAAACCA
12307469 TAAACCA
1 TAAACCA
* * *
12307476 TATATCT
1 TAAACCA
12307483 TAAACCA
1 TAAACCA
12307490 TAGTTAACTCA
1 TA---AAC-CA
**
12307501 TAAACTT
1 TAAACCA
*
12307508 TAAACCT
1 TAAACCA
12307515 TAAACCA
1 TAAACCA
* * *
12307522 TATATCT
1 TAAACCA
12307529 TAAACCA
1 TAAACCA
12307536 TAAACCA
1 TAAACCA
12307543 TAAACCA
1 TAAACCA
*
12307550 TAAACTA
1 TAAACCA
12307557 TAA
1 TAA
12307560 TGATAATTAA
Statistics
Matches: 75, Mismatches: 19, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
7 65 0.87
8 3 0.04
10 3 0.04
11 4 0.05
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.28
Consensus pattern (7 bp):
TAAACCA
Found at i:12307497 original size:46 final size:46
Alignment explanation
Indices: 12307444--12307537 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
12307434 CTTCAAACAC
*
12307444 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
* *
12307490 TAGTTAACTCATAAACTTTAAACCTTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
12307536 TA
1 TA
12307538 AACCATAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:12307553 original size:21 final size:21
Alignment explanation
Indices: 12307455--12307559 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
12307445 AGTTAACTCC
*
12307455 TAAACCTTAAACCCTAAACCA
1 TAAACCTTAAACCATAAACCA
* *
12307476 TATATCTTAAACCATAGTTAACTCA
1 TAAACCTTAAACCATA---AAC-CA
* *
12307501 TAAACTTTAAACCTTAAACCA
1 TAAACCTTAAACCATAAACCA
* *
12307522 TATATCTTAAACCATAAACCA
1 TAAACCTTAAACCATAAACCA
* *
12307543 TAAACCATAAACTATAA
1 TAAACCTTAAACCATAA
12307560 TGATAATTAA
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
21 45 0.69
22 3 0.05
24 3 0.05
25 14 0.22
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAACCTTAAACCATAAACCA
Found at i:12307782 original size:40 final size:40
Alignment explanation
Indices: 12307720--12307851 Score: 162
Period size: 41 Copynumber: 3.3 Consensus size: 40
12307710 TATGACTTTC
12307720 AGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTT
1 AGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GTTTTT
12307761 AGCGGCGTTTT-CCAAAAGCGCCGCTAATGCTCTGTTTTT
1 AGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTTTTT
* ** *
12307800 CGCGGCGTTTTTTAGTAAAA-C-CCGACTATTGCTCTGTTTTT
1 AGCGGCG--TTTTACCAAAAGCGCCG-CTAATGCTCTGTTTTT
*
12307841 AGTGGCGTTTT
1 AGCGGCGTTTT
12307852 TGGTAAAACG
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
39 16 0.20
40 25 0.31
41 36 0.44
42 4 0.05
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (40 bp):
AGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTTTTT
Found at i:12307809 original size:39 final size:41
Alignment explanation
Indices: 12307716--12307810 Score: 158
Period size: 40 Copynumber: 2.3 Consensus size: 41
12307706 GTTATATGAC
12307716 TTTCAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTT
1 TTTC-GCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTT
*
12307758 TTTAGCGGCGTTTT-CCAAAAGCGCCGCTAATGCTCT-GTT
1 TTTCGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTT
12307797 TTTCGCGGCGTTTT
1 TTTCGCGGCGTTTT
12307811 TTAGTAAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 16 0.31
40 22 0.43
41 10 0.20
42 3 0.06
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (41 bp):
TTTCGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTT
Found at i:12307869 original size:40 final size:40
Alignment explanation
Indices: 12307720--12307882 Score: 154
Period size: 40 Copynumber: 4.0 Consensus size: 40
12307710 TATGACTTTC
***
12307720 AGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTT
1 AGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCT-GTTTTT
**
12307761 AGCGGCG-TTTTCCAAAAGCGCCGCTAATGCTCTGTTTTT
1 AGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCTGTTTTT
* *
12307800 CGCGGCGTTTTTTAGTAAAA-C-CCGACTATTGCTCTGTTTTT
1 AGCGGCG-TTTTT-GTAAAAGCGCCG-CTAATGCTCTGTTTTT
* * *
12307841 AGTGGCGTTTTTGGTAAAA-CGCCGCTATTGCTATGTGTTTT
1 AGCGGCGTTTTT-GTAAAAGCGCCGCTAATGCTCTGT-TTTT
12307882 A
1 A
12307883 CTATTTTTGC
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
39 12 0.11
40 51 0.48
41 40 0.37
42 4 0.04
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.37
Consensus pattern (40 bp):
AGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCTGTTTTT
Found at i:12310968 original size:26 final size:26
Alignment explanation
Indices: 12310931--12311014 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
12310921 TGATACAAAT
*
12310931 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
12310957 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
12310983 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
12311009 TGATAA
1 TGATAA
12311015 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:12313034 original size:137 final size:137
Alignment explanation
Indices: 12312788--12313076 Score: 497
Period size: 137 Copynumber: 2.1 Consensus size: 137
12312778 TTGAGTAGTC
12312788 TCCCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCAT
1 TCCCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCAT
* *
12312853 ACTTTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTA
66 ACTGTCATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTA
12312918 CCACTGT
131 CCACTGT
* * *
12312925 TCCCCAAATGGGCTTGTATATGTTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCAT
1 TCCCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCAT
*
12312990 ACTGTCATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGGCCAGTA
66 ACTGTCATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTA
12313055 CCACTGT
131 CCACTGT
* **
12313062 TACCTGAATGGGCTT
1 TCCCCAAATGGGCTT
12313077 AGGCCCAATA
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
137 143 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
TCCCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATAGGCCTATGGGCCAT
ACTGTCATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTA
CCACTGT
Found at i:12314142 original size:26 final size:25
Alignment explanation
Indices: 12314105--12314264 Score: 257
Period size: 26 Copynumber: 6.2 Consensus size: 25
12314095 TGATACAAAT
12314105 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
12314131 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
12314157 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
12314182 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
12314208 TGATAATGGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
*
12314233 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
12314259 TGATAA
1 TGATAA
12314265 GAATTTCATG
Statistics
Matches: 128, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
25 50 0.39
26 76 0.59
27 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:12314198 original size:77 final size:77
Alignment explanation
Indices: 12314105--12314264 Score: 295
Period size: 77 Copynumber: 2.1 Consensus size: 77
12314095 TGATACAAAT
12314105 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCATGATAATAGGTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATG-TTCATGATAATAGGTTA
12314170 GGTAAATG-TTCA
65 GGTAAATGTTTCA
*
12314182 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCATGATAATGGGTTAG
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCATGATAATAGGTTAG
12314247 GTAAATGTTTCA
66 GTAAATGTTTCA
12314259 TGATAA
1 TGATAA
12314265 GAATTTCATG
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
76 24 0.30
77 57 0.70
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (77 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCATGATAATAGGTTAG
GTAAATGTTTCA
Found at i:12314204 original size:51 final size:51
Alignment explanation
Indices: 12314105--12314264 Score: 284
Period size: 51 Copynumber: 3.1 Consensus size: 51
12314095 TGATACAAAT
12314105 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAATGGGTTAGGTAAATGTTTCA
* *
12314157 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
*
12314208 TGATAATGGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
12314259 TGATAA
1 TGATAA
12314265 GAATTTCATG
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 80 0.78
52 23 0.22
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:12315774 original size:26 final size:26
Alignment explanation
Indices: 12315745--12315797 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12315735 TTTACAGTTT
12315745 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
12315771 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
12315797 T
1 T
12315798 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:12316289 original size:137 final size:135
Alignment explanation
Indices: 12316045--12316329 Score: 534
Period size: 137 Copynumber: 2.1 Consensus size: 135
12316035 GAGTAGTCTC
12316045 CCCAAATGGGCTTGCATATGTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTG
1 CCCAAATGGGCTTGCATATGTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTG
12316110 TTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCAC
66 TTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCAC
12316175 TGTTA
131 TGTTA
12316180 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTA-TGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
12316245 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
64 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
12316310 ACTGTTA
129 ACTGTTA
**
12316317 CCTGAATGGGCTT
1 CCCAAATGGGCTT
12316330 AGGCCCAATG
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
135 20 0.14
136 3 0.02
137 123 0.84
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (135 bp):
CCCAAATGGGCTTGCATATGTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTG
TTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCAC
TGTTA
Found at i:12320043 original size:26 final size:26
Alignment explanation
Indices: 12320006--12320141 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
12319996 TGATACAAAT
*
12320006 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
12320032 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
12320058 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
12320084 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
* *
12320110 TGATAATGGGTTAGGTAAATGTTTCT
1 TGATAATAGGTTAGGTAAATGTTTCA
12320136 TGATAA
1 TGATAA
12320142 GAATTTCATG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 105 1.00
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:12321887 original size:21 final size:21
Alignment explanation
Indices: 12321861--12321908 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12321851 ATTCCCCACA
12321861 TGGAGTGTA-TGGCTGGTAGGG
1 TGGAGTGTAGTGGCTGGT-GGG
*
12321882 TGGAGTGTAGTGGTTGGTGGG
1 TGGAGTGTAGTGGCTGGTGGG
*
12321903 TTGAGT
1 TGGAGT
12321909 AGTCTCCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.12, C:0.02, G:0.52, T:0.33
Consensus pattern (21 bp):
TGGAGTGTAGTGGCTGGTGGG
Found at i:12322160 original size:137 final size:136
Alignment explanation
Indices: 12321915--12322200 Score: 536
Period size: 137 Copynumber: 2.1 Consensus size: 136
12321905 GAGTAGTCTC
*
12321915 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
12321980 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
12322045 CTGTTA
131 CTGTTA
12322051 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
12322116 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
12322181 ACTGTTA
130 ACTGTTA
**
12322188 CCTGAATGGGCTT
1 CCCAAATGGGCTT
12322201 AGGCCCAATG
Statistics
Matches: 146, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 20 0.14
137 126 0.86
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:12323342 original size:9 final size:9
Alignment explanation
Indices: 12323328--12323494 Score: 145
Period size: 9 Copynumber: 17.6 Consensus size: 9
12323318 ATGTATTAGT
12323328 TAAGTTATG
1 TAAGTTATG
12323337 TAAGTTGTTATG
1 TAA---GTTATG
*
12323349 TACGTTATG
1 TAAGTTATG
*
12323358 TGAGTTATG
1 TAAGTTATG
* *
12323367 TAAATTATA
1 TAAGTTATG
12323376 TAAGTTATG
1 TAAGTTATG
*
12323385 TGAGTTATG
1 TAAGTTATG
12323394 TAAGTTGTTATG
1 TAA---GTTATG
*
12323406 TAAATTATG
1 TAAGTTATG
12323415 TAAGTTATG
1 TAAGTTATG
*
12323424 TGAGTTATG
1 TAAGTTATG
12323433 TAAGTTGTTATG
1 TAA---GTTATG
*
12323445 TAAATTATG
1 TAAGTTATG
*
12323454 TAAGTTATA
1 TAAGTTATG
*
12323463 TGAGTTATG
1 TAAGTTATG
12323472 TAAGTTATG
1 TAAGTTATG
* *
12323481 TAATTTATT
1 TAAGTTATG
12323490 TAAGT
1 TAAGT
12323495 AATGATCAAT
Statistics
Matches: 126, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
9 100 0.79
12 26 0.21
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:12323380 original size:39 final size:40
Alignment explanation
Indices: 12323332--12323494 Score: 159
Period size: 39 Copynumber: 4.2 Consensus size: 40
12323322 ATTAGTTAAG
12323332 TTATGTAAGTTGTTATGT-ACGTTATGT-G-AGTTATGTAAA
1 TTATGTAAG-TGTTATGTGA-GTTATGTAGTAGTTATGTAAA
* *
12323371 TTATATAA--GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
*
12323410 TTATGTAA--GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
* *
12323449 TTATGTAA--GTTATATGAGTTATGTA--AGTTATGTAAT
1 TTATGTAAGTGTTATGTGAGTTATGTAGTAGTTATGTAAA
*
12323485 TTATTTAAGT
1 TTATGTAAGT
12323495 AATGATCAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
36 30 0.27
37 1 0.01
38 2 0.02
39 78 0.70
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (40 bp):
TTATGTAAGTGTTATGTGAGTTATGTAGTAGTTATGTAAA
Found at i:12323404 original size:48 final size:44
Alignment explanation
Indices: 12323343--12323482 Score: 165
Period size: 39 Copynumber: 3.4 Consensus size: 44
12323333 TATGTAAGTT
*
12323343 GTTATGTACGTTATGTGAGTTATGTAAATTATATAAGTTATGTGA
1 GTTATGTAAGTTATGT-AGTTATGTAAATTATATAAGTTATGTGA
*
12323388 GTTATGTAAG---T-T-GTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAGTTATGTAGTTATGTAAATTATATAAGTTATGTGA
* *
12323427 GTTATGTAAG---T-T-GTTATGTAAATTATGTAAGTTATATGA
1 GTTATGTAAGTTATGTAGTTATGTAAATTATATAAGTTATGTGA
12323466 GTTATGTAAGTTATGTA
1 GTTATGTAAGTTATGTA
12323483 ATTTATTTAA
Statistics
Matches: 87, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
39 74 0.85
41 1 0.01
42 2 0.02
43 1 0.01
45 9 0.10
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (44 bp):
GTTATGTAAGTTATGTAGTTATGTAAATTATATAAGTTATGTGA
Found at i:12323421 original size:57 final size:57
Alignment explanation
Indices: 12323328--12323494 Score: 187
Period size: 57 Copynumber: 2.9 Consensus size: 57
12323318 ATGTATTAGT
* *
12323328 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATATAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATATAAGTTATG
* * * * *
12323385 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTTGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATATAA---GTTATG
* * * *
12323445 TAAATTATGTAAGTT-ATATG--AGTTATGTAAGTTATGTAATTTATTTAAGT
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATATAAGT
12323495 AATGATCAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
54 2 0.02
57 68 0.73
59 4 0.04
60 19 0.20
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATATAAGTTATG
Found at i:12323483 original size:48 final size:47
Alignment explanation
Indices: 12323330--12323483 Score: 155
Period size: 48 Copynumber: 3.4 Consensus size: 47
12323320 GTATTAGTTA
* * * * * *
12323330 AGTTATGTAAGTTGT-TATGTACGTTATGTGAGTTATGTAAATTATAT
1 AGTTATGTAAGTTATGTAAGT-TGTTATGTAAATTATGTAAGTTATAT
*
12323377 AAGTTATGTGAGTTATGTAAGTTGTTATGTAAATTATGTAAG-T-TAT
1 -AGTTATGTAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATAT
12323423 -G---TG--AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATAT
1 AGTTATGTAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATAT
12323464 GAGTTATGTAAGTTATGTAA
1 -AGTTATGTAAGTTATGTAA
12323484 TTTATTTAAG
Statistics
Matches: 89, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
39 32 0.36
40 1 0.01
41 5 0.06
43 1 0.01
44 1 0.01
46 5 0.06
47 1 0.01
48 39 0.44
49 4 0.04
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (47 bp):
AGTTATGTAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATAT
Found at i:12324079 original size:23 final size:23
Alignment explanation
Indices: 12324053--12324102 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
12324043 GTTCAAGTTT
12324053 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
12324076 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
12324099 ATTT
1 ATTT
12324103 GATTAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
ATTTAAAGGGCTGCAATTCATAC
Found at i:12326636 original size:19 final size:20
Alignment explanation
Indices: 12326597--12326648 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
12326587 TTTCAATTTT
* *
12326597 GATTCGGGGAAATATTTAGG
1 GATTAGGGGAAATAGTTAGG
12326617 GATTAGGGGAAA-AGTTAGG
1 GATTAGGGGAAATAGTTAGG
*
12326636 GATTTGGGGAAAT
1 GATTAGGGGAAAT
12326649 TTGGGTGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.27
Consensus pattern (20 bp):
GATTAGGGGAAATAGTTAGG
Found at i:12327973 original size:29 final size:29
Alignment explanation
Indices: 12327941--12327996 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
12327931 AGAGTTTAGA
12327941 TCATGGGTTATGATCTAGGGGTTAGGCGG
1 TCATGGGTTATGATCTAGGGGTTAGGCGG
*
12327970 TCATGGGTTATGATTTAGGGGTTAGGC
1 TCATGGGTTATGATCTAGGGGTTAGGC
12327997 TTCATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.09, G:0.39, T:0.34
Consensus pattern (29 bp):
TCATGGGTTATGATCTAGGGGTTAGGCGG
Found at i:12328623 original size:41 final size:41
Alignment explanation
Indices: 12328576--12328688 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 41
12328566 ACCTAAAGCA
*
12328576 CCACTATAT-CTCAGTTTTTTGCGGCGTTTTGCATGAAAACG
1 CCACTAT-TGCTCAGTTTTTAGCGGCGTTTTGCATGAAAACG
*
12328617 CTACTATTGCTCAGTTTTTAGCGGCGTTTTGCATGAAAACG
1 CCACTATTGCTCAGTTTTTAGCGGCGTTTTGCATGAAAACG
*
12328658 CCACAATTGCTCAGTTTTTAGCGGCGTTTTG
1 CCACTATTGCTCAGTTTTTAGCGGCGTTTTG
12328689 TTTCAAACGC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 66 0.99
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (41 bp):
CCACTATTGCTCAGTTTTTAGCGGCGTTTTGCATGAAAACG
Found at i:12331496 original size:4 final size:4
Alignment explanation
Indices: 12331487--12331533 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
12331477 ATTTTCATGG
12331487 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
12331534 TACATAAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:12334305 original size:14 final size:14
Alignment explanation
Indices: 12334288--12334314 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12334278 TTCGGGGTTT
12334288 AAAATTTAAGATTC
1 AAAATTTAAGATTC
12334302 AAAATTTAAGATT
1 AAAATTTAAGATT
12334315 AAGGTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATTTAAGATTC
Found at i:12334441 original size:2 final size:2
Alignment explanation
Indices: 12334434--12334464 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12334424 TTCAATCTTA
12334434 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 A
12334465 AAAAGTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12334808 original size:2 final size:2
Alignment explanation
Indices: 12334801--12334830 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12334791 TTGAATGCAC
12334801 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
12334831 GATAATAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12339399 original size:6 final size:6
Alignment explanation
Indices: 12339390--12339429 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
12339380 AGAGTTTTAC
* *
12339390 TATACA TATATA TATATA TATATA TATATA TATATG TATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATA
12339430 AATTACTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:12339404 original size:4 final size:4
Alignment explanation
Indices: 12339390--12339429 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
12339380 AGAGTTTTAC
* *
12339390 TATA CATA TATA TATA TATA TATA TATA TATA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
12339430 AATTACTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (4 bp):
TATA
Found at i:12340253 original size:3 final size:3
Alignment explanation
Indices: 12340245--12340277 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12340235 CAAAGGCTAG
12340245 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12340278 CGAAGTCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12340453 original size:2 final size:2
Alignment explanation
Indices: 12340446--12340471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12340436 TTTTAAAATG
12340446 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
12340472 GACTTACTTT
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:12344785 original size:15 final size:16
Alignment explanation
Indices: 12344765--12344794 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12344755 AAAATATTTG
12344765 TTAAAAT-ATAAAATT
1 TTAAAATCATAAAATT
12344780 TTAAAATCATAAAAT
1 TTAAAATCATAAAAT
12344795 AAGATTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATCATAAAATT
Found at i:12345591 original size:12 final size:13
Alignment explanation
Indices: 12345557--12345595 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
12345547 TTTATGGATA
12345557 ATATATATAAAT-
1 ATATATATAAATG
*
12345569 ATAAATATAAATG
1 ATATATATAAATG
12345582 ATATAT-TAAATG
1 ATATATATAAATG
12345594 AT
1 AT
12345596 GATGATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (13 bp):
ATATATATAAATG
Found at i:12346519 original size:2 final size:2
Alignment explanation
Indices: 12346512--12346541 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12346502 AATTAGAATG
12346512 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
12346542 TTATCACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12350164 original size:20 final size:21
Alignment explanation
Indices: 12350141--12350183 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12350131 CTACATGTGT
*
12350141 ATTTTG-ATGTTTGATGATAG
1 ATTTTGAATGCTTGATGATAG
*
12350161 ATTTTGAATGCTTGTTGATAG
1 ATTTTGAATGCTTGATGATAG
12350182 AT
1 AT
12350184 AAACATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (21 bp):
ATTTTGAATGCTTGATGATAG
Found at i:12352186 original size:19 final size:21
Alignment explanation
Indices: 12352148--12352196 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
12352138 CCTCAGCAGC
*
12352148 TACGCCACGCTTACGCCTCCG
1 TACGCCACGCATACGCCTCCG
12352169 TACGCCA-GCATA-GCCTCCG
1 TACGCCACGCATACGCCTCCG
12352188 TACG-CACGC
1 TACGCCACGC
12352197 CGTGTACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 4 0.15
21 7 0.27
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (21 bp):
TACGCCACGCATACGCCTCCG
Found at i:12364091 original size:79 final size:79
Alignment explanation
Indices: 12363863--12364084 Score: 340
Period size: 79 Copynumber: 2.8 Consensus size: 79
12363853 TGTAGTGGGA
* *
12363863 CAGATCGAAGAAAACAAACCTTAA-CCCCTAAGTAGTAGGGTAACAGGTCAAAGATTACAGATCT
1 CAGATCGAAGAAAACAAACCTTAACCCCCTAAGTAGTAGGGTAACAGGTCGAAGATTGCAGATCT
*
12363927 CGTCTCTAGTGGAG
66 CGTCTCCAGTGGAG
** * *
12363941 CAGATCGAAGAAAACAAACCTTAACCCTTTAAGTAGTAGGGTAACATGTTGAAGATTGCAGATCT
1 CAGATCGAAGAAAACAAACCTTAACCCCCTAAGTAGTAGGGTAACAGGTCGAAGATTGCAGATCT
12364006 CGTCTCCAGTGGAG
66 CGTCTCCAGTGGAG
* *
12364020 CAGATC-AGAGAAAACAAACCTTAACCCCCTAAGTAGTAGGGTAACAGGCCGAAGATTGCAAATC
1 CAGATCGA-AGAAAACAAACCTTAACCCCCTAAGTAGTAGGGTAACAGGTCGAAGATTGCAGATC
12364084 T
65 T
12364085 TATCTCCCTA
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
78 25 0.19
79 104 0.81
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (79 bp):
CAGATCGAAGAAAACAAACCTTAACCCCCTAAGTAGTAGGGTAACAGGTCGAAGATTGCAGATCT
CGTCTCCAGTGGAG
Found at i:12364248 original size:14 final size:14
Alignment explanation
Indices: 12364229--12364258 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12364219 ATCTCCTTGA
12364229 AGTTGCAGTAGAGC
1 AGTTGCAGTAGAGC
12364243 AGTTGCAGTAGAGC
1 AGTTGCAGTAGAGC
12364257 AG
1 AG
12364259 ATTAAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (14 bp):
AGTTGCAGTAGAGC
Found at i:12370028 original size:22 final size:22
Alignment explanation
Indices: 12369998--12370040 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12369988 TTTTTTATGT
*
12369998 ATTACTTATTTAAAATTGTTTC
1 ATTACTTATTTAAAATGGTTTC
* *
12370020 ATTATTTATTTTAAATGGTTT
1 ATTACTTATTTAAAATGGTTT
12370041 TATGTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (22 bp):
ATTACTTATTTAAAATGGTTTC
Found at i:12372040 original size:31 final size:31
Alignment explanation
Indices: 12371992--12372052 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12371982 CATTAGTTGA
*
12371992 GCACTTTTGAAAAGATTTAGTCCTTATTTGG
1 GCACTTTCGAAAAGATTTAGTCCTTATTTGG
* * *
12372023 GCACTTTCGAAAGGATTTTGTTCTTATTTG
1 GCACTTTCGAAAAGATTTAGTCCTTATTTG
12372053 ACCTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (31 bp):
GCACTTTCGAAAAGATTTAGTCCTTATTTGG
Found at i:12372074 original size:44 final size:44
Alignment explanation
Indices: 12372024--12372111 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
12372014 CTTATTTGGG
*
12372024 CACTTTCGAAAGGATTTTGTTCTTATTTGACCTTTTTAAAAGGC
1 CACTTTCGAAAAGATTTTGTTCTTATTTGACCTTTTTAAAAGGC
12372068 CACTTTCGAAAAGATTTTGTTCTTATTTGACCTTTTTAAAAGGC
1 CACTTTCGAAAAGATTTTGTTCTTATTTGACCTTTTTAAAAGGC
12372112 TTGGCTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (44 bp):
CACTTTCGAAAAGATTTTGTTCTTATTTGACCTTTTTAAAAGGC
Found at i:12372800 original size:2 final size:2
Alignment explanation
Indices: 12372793--12372819 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12372783 TAGCCTCTTA
12372793 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 A
12372820 CTTACTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12374332 original size:19 final size:19
Alignment explanation
Indices: 12374293--12374334 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12374283 TCAATCCTTC
* **
12374293 AATTTATTAATATTTTTAA
1 AATTGATTAATATTTCAAA
12374312 AATTGATTAATATTTCAAA
1 AATTGATTAATATTTCAAA
12374331 AATT
1 AATT
12374335 ATTCATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
AATTGATTAATATTTCAAA
Found at i:12381919 original size:17 final size:16
Alignment explanation
Indices: 12381877--12381931 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
12381867 TAGAGTGGAA
12381877 AGAAAACTAGAAGGAT
1 AGAAAACTAGAAGGAT
* *
12381893 -GAAAAATAGAAGGCGT
1 AGAAAACTAGAAGG-AT
12381909 AGAAAACTAGAAGGAT
1 AGAAAACTAGAAGGAT
*
12381925 GGAAAAC
1 AGAAAAC
12381932 ATAAATTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 12 0.38
16 8 0.25
17 12 0.38
ACGTcount: A:0.55, C:0.07, G:0.27, T:0.11
Consensus pattern (16 bp):
AGAAAACTAGAAGGAT
Found at i:12385919 original size:21 final size:21
Alignment explanation
Indices: 12385884--12385944 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
12385874 TTTTCAAACT
12385884 ACAGGGGTCACACGCCCGTGTGG
1 ACAGGGG--ACACGCCCGTGTGG
*
12385907 ACAGGGGACACGCCTGTGTGG
1 ACAGGGGACACGCCCGTGTGG
* *
12385928 -CTATGGGACACACCCGT
1 AC-AGGGGACACGCCCGT
12385945 CCTTCAAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 25 0.76
23 7 0.21
ACGTcount: A:0.20, C:0.30, G:0.36, T:0.15
Consensus pattern (21 bp):
ACAGGGGACACGCCCGTGTGG
Found at i:12387185 original size:25 final size:25
Alignment explanation
Indices: 12387145--12387202 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
12387135 GTGATAAACT
* *
12387145 GTAAGCTCATCTGAGTTGAATATCA
1 GTAAGCTCATCCGAGTTGAATAACA
* *
12387170 GTAAGCTCCTCCGAGTTGAATAACG
1 GTAAGCTCATCCGAGTTGAATAACA
12387195 GTAAGCTC
1 GTAAGCTC
12387203 TTAAGAGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (25 bp):
GTAAGCTCATCCGAGTTGAATAACA
Found at i:12388913 original size:15 final size:14
Alignment explanation
Indices: 12388883--12388928 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
12388873 TTATTATTAC
*
12388883 TATTACTTTTATTAT
1 TATTACTTTT-CTAT
12388898 TATTACTGTTTCTAT
1 TATTACT-TTTCTAT
*
12388913 TATTGCTTTTCTAT
1 TATTACTTTTCTAT
12388927 TA
1 TA
12388929 CCATTTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.32
15 16 0.57
16 3 0.11
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (14 bp):
TATTACTTTTCTAT
Found at i:12388925 original size:14 final size:15
Alignment explanation
Indices: 12388895--12388928 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12388885 TTACTTTTAT
12388895 TATTATTACTGTTTC
1 TATTATTACTGTTTC
*
12388910 TATTATTGCT-TTTC
1 TATTATTACTGTTTC
12388924 TATTA
1 TATTA
12388929 CCATTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTATTACTGTTTC
Found at i:12389125 original size:3 final size:3
Alignment explanation
Indices: 12388957--12389109 Score: 131
Period size: 3 Copynumber: 51.7 Consensus size: 3
12388947 GCACTATTCT
* *
12388957 TTA TT- TTA TTA TTA TTA TTA TT- TTT TTA TTA TT- TTA TCA TTA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
12389002 TCTA TTA TTG TTA TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA CGTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA
*
12389049 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA CT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
12389094 TTA -TA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TT
12389110 GCTATCATCA
Statistics
Matches: 123, Mismatches: 15, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
2 12 0.10
3 103 0.84
4 7 0.06
5 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:12389206 original size:15 final size:15
Alignment explanation
Indices: 12389186--12389215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12389176 ATTTATTTAC
12389186 ATTATTATTACTATT
1 ATTATTATTACTATT
*
12389201 ATTATTATTTCTATT
1 ATTATTATTACTATT
12389216 TTTTTGAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTACTATT
Found at i:12389549 original size:23 final size:23
Alignment explanation
Indices: 12389517--12389568 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
12389507 TAGGTTTTCA
* * *
12389517 CTTATAATATTATTATTGTCATT
1 CTTATTATATGATTATTATCATT
*
12389540 CTTATTATATGGTTATTATCATT
1 CTTATTATATGATTATTATCATT
*
12389563 ATTATT
1 CTTATT
12389569 CTCACCATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
CTTATTATATGATTATTATCATT
Found at i:12391587 original size:38 final size:37
Alignment explanation
Indices: 12391540--12391734 Score: 140
Period size: 38 Copynumber: 5.4 Consensus size: 37
12391530 AAACTCACAA
*
12391540 AACACAATAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAATAATTTATAATAAATTACTAA-AAAATATTT
* * * ***
12391578 AACAAAATAA-TT-T--TACATTACCAAAAACTCACAA
1 AACAAAATAATTTATAATAAATTACTAAAAAAT-ATTT
*
12391612 AACTCAAA-AATTTATAATAAATTACTAACAAAATATTT
1 AAC-AAAATAATTTATAATAAATTACTAA-AAAATATTT
* * ***
12391650 AACAAAAT-ATTT-T--TACATTACTAAAAACTCACAA
1 AACAAAATAATTTATAATAAATTACTAAAAAAT-ATTT
12391684 AACAGAAA-AATTTATAATAAATTACTAGAAAAATATTT
1 AACA-AAATAATTTATAATAAATTACTA-AAAAATATTT
12391722 AACAAAATAATTT
1 AACAAAATAATTT
12391735 TACATTACTA
Statistics
Matches: 116, Mismatches: 25, Indels: 32
0.67 0.14 0.18
Matches are distributed among these distances:
33 8 0.07
34 30 0.26
35 12 0.10
36 4 0.03
37 12 0.10
38 41 0.35
39 9 0.08
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (37 bp):
AACAAAATAATTTATAATAAATTACTAAAAAATATTT
Found at i:12391624 original size:72 final size:72
Alignment explanation
Indices: 12391517--12391753 Score: 413
Period size: 72 Copynumber: 3.3 Consensus size: 72
12391507 TTTAAAAAAA
*
12391517 TTTACATTACTAAAAACTCACAAAACACAATAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTAACAAAATATTTAACA
12391582 AAATAAT
66 AAATAAT
* *
12391589 TTTACATTACCAAAAACTCACAAAACTCAAAAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTAACAAAATATTTAACA
*
12391654 AAATATT
66 AAATAAT
*
12391661 TTTACATTACTAAAAACTCACAAAACAGAAAAATTTATAATAAATTACTAGA-AAAATATTTAAC
1 TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTA-ACAAAATATTTAAC
12391725 AAAATAAT
65 AAAATAAT
12391733 TTTACATTACTAAAAACTCAC
1 TTTACATTACTAAAAACTCAC
12391754 CAAATACTAA
Statistics
Matches: 156, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
72 155 0.99
73 1 0.01
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.30
Consensus pattern (72 bp):
TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTAACAAAATATTTAACA
AAATAAT
Done.