Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 38 of 352
Found at i:12071612 original size:15 final size:13
Alignment explanation
Indices: 12071596--12071648 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
12071586 ATGAATATAT
12071596 TAATACATAATAAA
1 TAATA-ATAATAAA
* *
12071610 TTATTAAAAATATAA
1 -TAATAATAATA-AA
12071625 TAATAATAAT-AA
1 TAATAATAATAAA
12071637 TAATAATAATAA
1 TAATAATAATAA
12071649 TAGAGTGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 12 0.38
13 1 0.03
14 13 0.41
15 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:12071627 original size:3 final size:3
Alignment explanation
Indices: 12071621--12071650 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12071611 TATTAAAAAT
12071621 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12071651 GAGTGGTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12082332 original size:19 final size:19
Alignment explanation
Indices: 12082308--12082352 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
12082298 ATCCAAACAC
12082308 CAGAAAAGTAAATCATTTT
1 CAGAAAAGTAAATCATTTT
12082327 CAGAAAAGTAAATCATTTT
1 CAGAAAAGTAAATCATTTT
12082346 CTAGAAA
1 C-AGAAA
12082353 TCATTTTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
CAGAAAAGTAAATCATTTT
Found at i:12082521 original size:13 final size:13
Alignment explanation
Indices: 12082503--12082527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12082493 TTATATGCAC
12082503 TTTTTTGAATTAT
1 TTTTTTGAATTAT
12082516 TTTTTTGAATTA
1 TTTTTTGAATTA
12082528 ACTATTATAT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTTTTGAATTAT
Found at i:12082607 original size:21 final size:19
Alignment explanation
Indices: 12082567--12082607 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12082557 ATAATTTAAG
*
12082567 ATTATAAAATATTGTAATT
1 ATTATAAAATATTATAATT
12082586 ATTATCAAAATATATATAATT
1 ATTAT-AAAATAT-TATAATT
12082607 A
1 A
12082608 ATTTCTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTATAAAATATTATAATT
Found at i:12083155 original size:21 final size:21
Alignment explanation
Indices: 12083129--12083181 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12083119 TATCATTGGT
* *
12083129 TTTAATCTCACTATTGCAATA
1 TTTAATCTCACTAATACAATA
*
12083150 TTTAATCTCATTAATACAATA
1 TTTAATCTCACTAATACAATA
*
12083171 ATTAATCTCAC
1 TTTAATCTCAC
12083182 AACCATCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAATCTCACTAATACAATA
Found at i:12083489 original size:24 final size:26
Alignment explanation
Indices: 12083462--12083526 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
12083452 CAATGTATTC
* *
12083462 TTTGA-ATTTGAATTGTTTT-TCTAA
1 TTTGATATTTAAATTCTTTTATCTAA
12083486 TTTGATATTTAAATTCTTTTATCTAA
1 TTTGATATTTAAATTCTTTTATCTAA
* * *
12083512 ATTGTTCTTTAAATT
1 TTTGATATTTAAATT
12083527 TATGTTCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 5 0.15
25 12 0.35
26 17 0.50
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTGATATTTAAATTCTTTTATCTAA
Found at i:12084958 original size:8 final size:8
Alignment explanation
Indices: 12084927--12084955 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12084917 AACAAAAAAA
12084927 TTCTTTAT
1 TTCTTTAT
12084935 TTCTTTAT
1 TTCTTTAT
12084943 TTCTTT-T
1 TTCTTTAT
12084950 TTCTTT
1 TTCTTT
12084956 TTTGGCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (8 bp):
TTCTTTAT
Found at i:12087830 original size:13 final size:14
Alignment explanation
Indices: 12087814--12087849 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12087804 CAATCTCATA
12087814 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
12087827 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
12087840 TCTC-ATTTCA
1 TCTCAATTTCA
12087850 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:12087839 original size:18 final size:19
Alignment explanation
Indices: 12087801--12087841 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12087791 TGGTTCATGT
12087801 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
12087820 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
12087838 TTTC
1 TTTC
12087842 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:12088497 original size:15 final size:15
Alignment explanation
Indices: 12088477--12088523 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
12088467 TAATATATAT
12088477 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
12088492 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
12088507 TTCAATCAATATAAA
1 TTCAATCAATATAAA
12088522 TT
1 TT
12088524 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:12089866 original size:15 final size:15
Alignment explanation
Indices: 12089846--12089892 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
12089836 TAATATATAT
12089846 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
12089861 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
12089876 TTCAATCAATATAAA
1 TTCAATCAATATAAA
12089891 TT
1 TT
12089893 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:12090867 original size:31 final size:32
Alignment explanation
Indices: 12090809--12090872 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
12090799 CATACATTTG
* *
12090809 TCATAATTTAATATATTTTTTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
12090841 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
12090872 T
1 T
12090873 TATTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:12091404 original size:13 final size:14
Alignment explanation
Indices: 12091386--12091414 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12091376 GATTAACTTC
12091386 ATAAATATTTT-TA
1 ATAAATATTTTCTA
12091399 ATAAATATTTTCTA
1 ATAAATATTTTCTA
12091413 AT
1 AT
12091415 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:12091675 original size:26 final size:26
Alignment explanation
Indices: 12091633--12091683 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12091623 ATTATGAGAA
12091633 AAATTAAATAAAACAAAAAAATAACTT
1 AAATTAAATAAAACAAAAAAA-AACTT
12091660 AAATTAAA-AAAACAAAAAAAAACT
1 AAATTAAATAAAACAAAAAAAAACT
12091684 AAACATATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.17
26 12 0.50
27 8 0.33
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATTAAATAAAACAAAAAAAAACTT
Found at i:12094176 original size:24 final size:25
Alignment explanation
Indices: 12094130--12094178 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
12094120 TTGCCCGGGC
*
12094130 CCCAACAAGCCCAAAACTAAACCTA
1 CCCAACAAGCCCAAAACCAAACCTA
*
12094155 CCCAAC-AGCCCAAAACCCAACCTA
1 CCCAACAAGCCCAAAACCAAACCTA
12094179 TCCTAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.45, C:0.45, G:0.04, T:0.06
Consensus pattern (25 bp):
CCCAACAAGCCCAAAACCAAACCTA
Found at i:12095329 original size:3 final size:3
Alignment explanation
Indices: 12095321--12095411 Score: 51
Period size: 3 Copynumber: 29.0 Consensus size: 3
12095311 GGATTATCAC
* * * * **
12095321 TAT TAT TAT TAC T-T TAC TAT TAT AAT T-T AAT GTAT TAT CGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
12095365 TAT TATT TATT TATT TATT TATT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TA-T TA-T TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT
12095412 CTTAGGACTA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 2 0.03
3 47 0.67
4 21 0.30
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12095358 original size:41 final size:37
Alignment explanation
Indices: 12095313--12095411 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 37
12095303 ATATACTAGG
*
12095313 ATTATCACTATTATTATTACTTTACTATTA-TAATTTAATGT
1 ATTATCATTATTATTATTA-TTTA-T-TTATTAATTT-AT-T
* *
12095354 ATTATCGTTATTATTATTTATTTATTTATTTATTTATT
1 ATTATCATTATTATTA-TTATTTATTTATTAATTTATT
12095392 ATTATCATTATTATTATTAT
1 ATTATCATTATTATTATTAT
12095412 CTTAGGACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
37 4 0.08
38 16 0.31
39 5 0.10
40 6 0.12
41 18 0.35
42 3 0.06
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (37 bp):
ATTATCATTATTATTATTATTTATTTATTAATTTATT
Found at i:12095376 original size:4 final size:4
Alignment explanation
Indices: 12095367--12095391 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12095357 ATCGTTATTA
12095367 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
12095392 ATTATCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:12095646 original size:15 final size:13
Alignment explanation
Indices: 12095614--12095666 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 13
12095604 GTTGTGTCAT
*
12095614 TATTATTGTTACTGA
1 TATTATTATTA-T-A
12095629 TATTATTCATGTATA
1 TATTATT-AT-TATA
12095644 TATTATTATTAT-
1 TATTATTATTATA
12095656 TATTATTATTA
1 TATTATTATTA
12095667 CCACATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 11 0.31
13 3 0.09
14 2 0.06
15 15 0.43
16 2 0.06
17 2 0.06
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:12095865 original size:39 final size:40
Alignment explanation
Indices: 12095787--12095866 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 40
12095777 ATTACCATTC
12095787 TATTTTCATCTATGTAGATTTTCTCGTTACTTACCTATTTA
1 TATTTTCATCTATGTAGATTTTCTCGTTACTTA-CTATTTA
* * * *
12095828 TATTTTTATCTATTTATATTTTCGTTGTTA-TTA-TATTTA
1 TATTTTCATCTATGTAGATTTTC-TCGTTACTTACTATTTA
12095867 AGCATTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
39 6 0.18
41 23 0.68
42 5 0.15
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (40 bp):
TATTTTCATCTATGTAGATTTTCTCGTTACTTACTATTTA
Found at i:12098346 original size:29 final size:30
Alignment explanation
Indices: 12098287--12098344 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12098277 TCCGAGCCTT
*
12098287 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
12098317 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
12098345 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:12110747 original size:68 final size:68
Alignment explanation
Indices: 12110639--12110914 Score: 435
Period size: 68 Copynumber: 4.1 Consensus size: 68
12110629 CTGGGAATTA
* * * * * *
12110639 CGGATCTCTTCTCCTTGAAATGGCGTTGGAGCGGCTTGAAGCCATAACAGATTTTCTTGAAGTTT
1 CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTT
*
12110704 CAA
66 CAG
* *
12110707 CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTTGAAGCCACAGTAGATCTCCTTGAAGTTT
1 CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTT
*
12110772 CTG
66 CAG
* *
12110775 CGGATCTCTTCTCCCTAAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTT
1 CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTT
12110840 CAG
66 CAG
*
12110843 CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCATAGCAGATCTCCTTGAAGTTT
1 CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTT
12110908 CAG
66 CAG
12110911 CGGA
1 CGGA
12110915 GTAGATTGAA
Statistics
Matches: 192, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 192 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (68 bp):
CGGATCTCTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTT
CAG
Found at i:12110931 original size:34 final size:34
Alignment explanation
Indices: 12110893--12110959 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
12110883 GCCATAGCAG
* * *
12110893 ATCTCCTTGAAGTTTCAGCGGAGTAGATTGAAGT
1 ATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGT
*
12110927 ATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG
1 ATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAG
12110960 ATAGCACATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (34 bp):
ATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGT
Found at i:12111129 original size:41 final size:41
Alignment explanation
Indices: 12111023--12111132 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 41
12111013 CATAGGTTTT
* * * * * * *
12111023 ATCTCTCTGAAGTTGCAGTAGAACAAATCAAAACAAGTCTG
1 ATCTCCCTAAAGTGGCAGTAGAGCAGATCAAAACAAATCTC
* *
12111064 ATCTCCCTAAAGTTGTAGTAGAGCAGATCAAAACAAATCTC
1 ATCTCCCTAAAGTGGCAGTAGAGCAGATCAAAACAAATCTC
*
12111105 ATCTCCCTAAAGTGGCAGTGGAGCAGAT
1 ATCTCCCTAAAGTGGCAGTAGAGCAGAT
12111133 TGAAGTTGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (41 bp):
ATCTCCCTAAAGTGGCAGTAGAGCAGATCAAAACAAATCTC
Found at i:12112487 original size:4 final size:4
Alignment explanation
Indices: 12112478--12112502 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12112468 GTCGTTATTA
12112478 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
12112503 ATTATCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:12115285 original size:40 final size:40
Alignment explanation
Indices: 12115209--12115303 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
12115199 CCATCTCCGA
* * *
12115209 CTAACCCAACACACC-ATGTGGGGATAGAATCGACCCA-C
1 CTAACCCTACACACCAATATGGGGATAGAATCAACCCATC
*
12115247 CTAACCCTACACACCAAGTATGGGGATATAATCAACCCATC
1 CTAACCCTACACACCAA-TATGGGGATAGAATCAACCCATC
12115288 C-AACCCTACACACCAA
1 CTAACCCTACACACCAA
12115304 AAGGTACCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 14 0.28
39 1 0.02
40 33 0.66
41 2 0.04
ACGTcount: A:0.37, C:0.36, G:0.13, T:0.15
Consensus pattern (40 bp):
CTAACCCTACACACCAATATGGGGATAGAATCAACCCATC
Found at i:12120272 original size:31 final size:31
Alignment explanation
Indices: 12120234--12120295 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
12120224 GCTGAAACTG
12120234 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
1 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
12120265 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
1 ATGCCATGTTTCATTTATTTTGTTTAAGCTT
12120296 CTATGTACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (31 bp):
ATGCCATGTTTCATTTATTTTGTTTAAGCTT
Found at i:12135543 original size:19 final size:18
Alignment explanation
Indices: 12135498--12135544 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
12135488 AATTCAAATG
* *
12135498 AAATATTTTAAAATTTTA
1 AAATAATTTAAAATTTAA
12135516 AAATCAATTTAAAATTTAA
1 AAAT-AATTTAAAATTTAA
12135535 ACAATAATTT
1 A-AATAATTT
12135545 GAGAACCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATTTAAAATTTAA
Found at i:12138920 original size:19 final size:18
Alignment explanation
Indices: 12138886--12138921 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12138876 TAACTCTTAG
*
12138886 AAAATAATATATATGATA
1 AAAATAATATAAATGATA
12138904 AAAATATATATAAATGAT
1 AAAATA-ATATAAATGAT
12138922 TAATGGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
AAAATAATATAAATGATA
Found at i:12139253 original size:29 final size:27
Alignment explanation
Indices: 12139196--12139258 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
12139186 AAAATTGAGC
* *
12139196 ATTTAGTTTATCTACTTTTATTTCATCAA
1 ATTTAATTTATCTACTTTTAATT-ATC-A
12139225 ATTTAATTTATCTACTTTTCAGATT-TCA
1 ATTTAATTTATCTACTTTT-A-ATTATCA
12139253 ATTTAA
1 ATTTAA
12139259 ATCCAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 7 0.23
29 20 0.67
30 1 0.03
31 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTTAATTTATCTACTTTTAATTATCA
Found at i:12142182 original size:26 final size:26
Alignment explanation
Indices: 12142146--12142229 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
12142136 CATGAAATTC
12142146 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12142172 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * **
12142198 TTATCATGGAATATTTACCTAACATA
1 TTATCATGAAACATTTACCTAACCCA
12142224 TTATCA
1 TTATCA
12142230 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12147074 original size:24 final size:25
Alignment explanation
Indices: 12147020--12147074 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
12147010 AATAAAATAA
*
12147020 TCAAACTATAATTAAATATTTTTAT
1 TCAAACTATAATTAAATAGTTTTAT
** * *
12147045 AAAAACTTTAATT-ATTAGTTTTAT
1 TCAAACTATAATTAAATAGTTTTAT
12147069 TCAAAC
1 TCAAAC
12147075 AATTTTGTCT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (25 bp):
TCAAACTATAATTAAATAGTTTTAT
Found at i:12158574 original size:49 final size:47
Alignment explanation
Indices: 12158502--12158596 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 47
12158492 TGTATGGTAG
* * * *
12158502 TTGTTATAATTAGTTATTTCATTACTTTCTTTTTACAGATTATTCTTTA
1 TTGTTATAATTAGTAATTCCATTAC-AT-TTTTCACAGATTATTCTTTA
*
12158551 TTGTTATAATTAGTAATTCCATTACATTTTTCCCAGATTATTCTTT
1 TTGTTATAATTAGTAATTCCATTACATTTTTCACAGATTATTCTTT
12158597 CATATAGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 17 0.41
48 1 0.02
49 23 0.56
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.56
Consensus pattern (47 bp):
TTGTTATAATTAGTAATTCCATTACATTTTTCACAGATTATTCTTTA
Found at i:12167580 original size:12 final size:12
Alignment explanation
Indices: 12167563--12167588 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12167553 GAATTTGGAT
12167563 GAGGATGAGGAA
1 GAGGATGAGGAA
12167575 GAGGATGAGGAA
1 GAGGATGAGGAA
12167587 GA
1 GA
12167589 TCCTTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (12 bp):
GAGGATGAGGAA
Found at i:12184427 original size:4 final size:4
Alignment explanation
Indices: 12184418--12184458 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
12184408 TCTTTTCATA
*
12184418 TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
12184459 CAGTGTCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:12199487 original size:40 final size:40
Alignment explanation
Indices: 12199442--12199633 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
12199432 ATAACCACAA
* * *
12199442 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
12199482 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
12199522 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
12199562 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
12199602 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
12199634 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:12199526 original size:80 final size:80
Alignment explanation
Indices: 12199413--12199632 Score: 248
Period size: 80 Copynumber: 2.8 Consensus size: 80
12199403 ACCCAAGTTT
* * * * * * * * *
12199413 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
*
12199476 CAACTCGCACAAATGC
66 C-ACTAGCACAAATGC
* * *
12199492 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
* *
12199556 TCACTAGCATAAATGC
65 GCACTAGCACAAATGC
* *
12199572 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA
12199633 TCATTCAAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 12 0.10
80 98 0.84
81 7 0.06
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
CACTAGCACAAATGC
Found at i:12203659 original size:46 final size:44
Alignment explanation
Indices: 12203642--12203902 Score: 185
Period size: 46 Copynumber: 6.3 Consensus size: 44
12203632 GACAAGTGGA
* * * * *
12203642 AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATA
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGA-C
* *
12203688 AAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
12203733 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 -AAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAGAGAC
*
12203779 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
12203816 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
12203853 AAAGTGAT-AG-G-T-G----GCTACACTTATCTGATC-AGGGAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
12203889 AAGTGATAAGTGAT
1 AAGTGATAAGTGAT
12203903 CATACGTAAG
Statistics
Matches: 201, Mismatches: 8, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
35 7 0.03
36 7 0.03
37 89 0.44
38 1 0.00
42 1 0.00
43 1 0.00
44 1 0.00
46 92 0.46
47 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (44 bp):
AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
Found at i:12203660 original size:52 final size:48
Alignment explanation
Indices: 12203575--12203791 Score: 243
Period size: 46 Copynumber: 4.6 Consensus size: 48
12203565 TTTGAGTACT
* * *
12203575 TCTGATCAAGTG--ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
12203621 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGAC-A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
12203673 TCTGATCAAGTG--ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
12203719 TCTGATCAAGAGAC--AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
12203765 TCTGATCAAGAGAC--AAAGTGATAAGTG
1 TCTGATCAAGAGACATAAAGTGATAAGTG
12203792 GCTACACTTA
Statistics
Matches: 153, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
46 110 0.72
48 1 0.01
49 2 0.01
50 1 0.01
52 39 0.25
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (48 bp):
TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:12203799 original size:37 final size:37
Alignment explanation
Indices: 12203755--12203900 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
12203745 GATAGCTTTA
*
12203755 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12203792 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12203829 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
12203866 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12203901 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:12208410 original size:46 final size:44
Alignment explanation
Indices: 12208393--12208653 Score: 185
Period size: 46 Copynumber: 6.3 Consensus size: 44
12208383 GACAAGTGGA
* * * * *
12208393 AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATA
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGA-C
* *
12208439 AAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
12208484 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 -AAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAGAGAC
*
12208530 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
12208567 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
12208604 AAAGTGAT-AG-G-T-G----GCTACACTTATCTGATC-AGGGAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
12208640 AAGTGATAAGTGAT
1 AAGTGATAAGTGAT
12208654 CATACGTAAG
Statistics
Matches: 201, Mismatches: 8, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
35 7 0.03
36 7 0.03
37 89 0.44
38 1 0.00
42 1 0.00
43 1 0.00
44 1 0.00
46 92 0.46
47 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (44 bp):
AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
Found at i:12208411 original size:52 final size:48
Alignment explanation
Indices: 12208326--12208542 Score: 243
Period size: 46 Copynumber: 4.6 Consensus size: 48
12208316 TTTGAGTACT
* * *
12208326 TCTGATCAAGTG--ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
12208372 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGAC-A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
12208424 TCTGATCAAGTG--ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
12208470 TCTGATCAAGAGAC--AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
12208516 TCTGATCAAGAGAC--AAAGTGATAAGTG
1 TCTGATCAAGAGACATAAAGTGATAAGTG
12208543 GCTACACTTA
Statistics
Matches: 153, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
46 110 0.72
48 1 0.01
49 2 0.01
50 1 0.01
52 39 0.25
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (48 bp):
TCTGATCAAGAGACATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:12208550 original size:37 final size:37
Alignment explanation
Indices: 12208506--12208651 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
12208496 GATAGCTTTA
*
12208506 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12208543 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12208580 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
12208617 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12208652 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:12214831 original size:38 final size:38
Alignment explanation
Indices: 12214789--12214921 Score: 194
Period size: 38 Copynumber: 3.4 Consensus size: 38
12214779 TTAAAGGTCA
12214789 GCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCC
1 GCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCC
12214827 GCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCC
1 GCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCC
* * * *
12214865 GCAGGCTTAGTGCTAGTATTATATTCGAGCTTAAAGTCCC
1 GCAGGCTTCGTGCTGGTATTATATCCG-GGTTAAA-TCCC
* *
12214905 GCAGGTTTTGTGCTGGT
1 GCAGGCTTCGTGCTGGT
12214922 GGCTGGATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 62 0.72
39 6 0.07
40 18 0.21
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (38 bp):
GCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCC
Found at i:12216602 original size:43 final size:42
Alignment explanation
Indices: 12216447--12216608 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 42
12216437 TGTGTTTTCC
* * ** *
12216447 TGTAAGACCACATTTGGGACGTTGGCATCGGCTTATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTATT-TGA-TTACA
* * * *
12216491 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTTCA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACA
** *
12216533 TGTAAGACCTTGTATGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCG-TATTTGATTACA
*
12216576 TGTAAGACCACGTCTGGGACGTTGGCATTGTAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTAT
12216609 GAGCTTTTCA
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
42 32 0.33
43 38 0.39
44 27 0.28
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTACA
Found at i:12216786 original size:18 final size:19
Alignment explanation
Indices: 12216755--12216794 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
12216745 GTACATGTGC
*
12216755 AAGTGATGATATATGATAT
1 AAGTGATGAAATATGATAT
*
12216774 AAGT-ATGAAATATGCTAT
1 AAGTGATGAAATATGATAT
12216792 AAG
1 AAG
12216795 AGTAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (19 bp):
AAGTGATGAAATATGATAT
Found at i:12222599 original size:20 final size:20
Alignment explanation
Indices: 12222574--12222616 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12222564 GATTTACTGC
12222574 GATTGTTTTTCCTTAATTGA
1 GATTGTTTTTCCTTAATTGA
12222594 GATTGTTTTTCCTTAATTGA
1 GATTGTTTTTCCTTAATTGA
12222614 GAT
1 GAT
12222617 ATGCAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (20 bp):
GATTGTTTTTCCTTAATTGA
Found at i:12223381 original size:16 final size:18
Alignment explanation
Indices: 12223360--12223396 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12223350 CCATCAAAAC
12223360 AAATTGA-AAAA-TATAA
1 AAATTGAGAAAATTATAA
12223376 AAATTGAGAAAATTATAA
1 AAATTGAGAAAATTATAA
12223394 AAA
1 AAA
12223397 ATATATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATTGAGAAAATTATAA
Found at i:12223499 original size:18 final size:18
Alignment explanation
Indices: 12223476--12223510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12223466 CATTCTAGAC
12223476 ATATTTTTTAATAATTTT
1 ATATTTTTTAATAATTTT
*
12223494 ATATTTTTTTATAATTT
1 ATATTTTTTAATAATTT
12223511 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTTTTTAATAATTTT
Found at i:12226646 original size:22 final size:22
Alignment explanation
Indices: 12226611--12226663 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12226601 AATAAAATGA
*
12226611 AATTTATTTAATTACTATATATT
1 AATTT-TTAAATTACTATATATT
* *
12226634 AATTTTTAAATTATTATATTTT
1 AATTTTTAAATTACTATATATT
*
12226656 TATTTTTA
1 AATTTTTA
12226664 TAATGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTTTAAATTACTATATATT
Found at i:12226672 original size:23 final size:22
Alignment explanation
Indices: 12226626--12226683 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
12226616 ATTTAATTAC
* * *
12226626 TATATATTAATTTTTAAATTAT
1 TATATTTTTATTTTTAAATGAT
12226648 TATATTTTTATTTTTATAATGAT
1 TATATTTTTATTTTTA-AATGAT
* *
12226671 TAAATTTATATTT
1 TATATTTTTATTT
12226684 ATCATATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTTTTATTTTTAAATGAT
Found at i:12235012 original size:3 final size:3
Alignment explanation
Indices: 12235004--12235032 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12234994 TCTACATTTT
12235004 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
12235033 TTGACTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:12238447 original size:30 final size:30
Alignment explanation
Indices: 12238412--12238469 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
12238402 TAGGCACTTC
*
12238412 CACACGGGT-GATTCACACGCCCGTGTGTGA
1 CACACGGGTAGA-CCACACGCCCGTGTGTGA
12238442 CACACGGGTAGACCACACGCCCGTGTGT
1 CACACGGGTAGACCACACGCCCGTGTGT
12238470 CATGGCCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (30 bp):
CACACGGGTAGACCACACGCCCGTGTGTGA
Found at i:12243678 original size:131 final size:130
Alignment explanation
Indices: 12243189--12243681 Score: 392
Period size: 131 Copynumber: 3.8 Consensus size: 130
12243179 TGGTTTAAGA
* * * * * * * **
12243189 CGAGATTCGATATTTGGCAATTCGCGGAATAGTGCCCTAACGTGTTGGGTTGCAATTTCGCGA-T
1 CGAG-TTCGATGTTTGGCAATTCG-AGAATCGAGCCCTATCGTGCTGGGTTGCGATTTTTC-ATT
* * * * * **
12243253 TGCTCGAAATAATCGAATATCACTTC-AAATTTCACTCATATCTT-TTAAAATCCCTT-AAACGA
63 TGCTCAAAATAATCGAATATCCCTTCGGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACGA
*
12243315 AGA
128 AGG
* * * * * * * *
12243318 CGAGATTTGATGTTTGGCAATTCGAGGAATCGTGCTCTAACGTGTTGGGTCGCAATTTTGCATTT
1 CGAG-TTCGATGTTTGGCAATTCGA-GAATCGAGCCCTATCGTGCTGGGTTGCGATTTTTCATTT
* * * * *
12243383 GCTCAAAATAATCGAATATCACTTCGAAATTCCCCTCATGTCTTCTAAAAATCTTTTAAAACAAA
64 GCTCAAAATAATCGAATATCCCTTCGGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACGAA
12243448 GG
129 GG
* ** * * * **
12243450 CGA-TACTCGGTGTTTGATAATTCGGGAATC-ATGCCCTATCGTGCTAGGTTGTGATTACTCATT
1 CGAGT--TCGATGTTTGGCAATTCGAGAATCGA-GCCCTATCGTGCTGGGTTGCGATTTTTCATT
* * * * *
12243513 TACTCAAAATAATCGAATATTCCATTAGG-TTTTCACTCATGT-TTATTAAAAAT-TTTTCAAAA
63 TGCTCAAAATAATCGAATA-TCCCTTCGGAATTTCACTCATGTCTT-CTAAAAATCTTTT-AAAA
12243575 CGAAGG
125 CGAAGG
* *
12243581 CGACGTTCGATGTTTGGCAATTTGAGAATCGAGCCCTATCGTGCTGGGTTGCGCTTTTTCATTTG
1 CGA-GTTCGATGTTTGGCAATTCGAGAATCGAGCCCTATCGTGCTGGGTTGCGATTTTTCATTTG
* *
12243646 CTCAAAACAATCAAATATCCCTTCGGAATTTCACTC
65 CTCAAAATAATCGAATATCCCTTCGGAATTTCACTC
12243682 GTATTTTCTA
Statistics
Matches: 291, Mismatches: 58, Indels: 28
0.77 0.15 0.07
Matches are distributed among these distances:
128 1 0.00
129 79 0.27
130 29 0.10
131 151 0.52
132 30 0.10
133 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (130 bp):
CGAGTTCGATGTTTGGCAATTCGAGAATCGAGCCCTATCGTGCTGGGTTGCGATTTTTCATTTGC
TCAAAATAATCGAATATCCCTTCGGAATTTCACTCATGTCTTCTAAAAATCTTTTAAAACGAAGG
Found at i:12255270 original size:45 final size:44
Alignment explanation
Indices: 12255221--12255541 Score: 163
Period size: 45 Copynumber: 7.3 Consensus size: 44
12255211 TCTTGTTTCC
*
12255221 CTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTT
1 CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGAATCTTG-CTTT
* * * * * * * **
12255266 CTGAAGTTGCAGTGAAGCAGATTTAAGTC-ACTAACCTAGCTCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGAATCTTGCTTT
* * * **
12255309 CTAAAGTTGTAGTGGAGTAGGTTGAA-ATTAC-AGATCTTG-TTT
1 CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA-ATCTTGCTTT
* * * * * *
12255351 CCCTGAAGTCGCGGTGGAGTAGATCGAAGACGATGAATATTGACTTC
1 --CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGAATCTTG-CTTT
* * * * * * * * **
12255398 CTAAAGTTGCAGTGAAGCAGATTTAAGTC-ACTAACCTAGCTCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGAATCTTGCTTT
* * * **
12255441 CTAAAGTTGTAGTGGAGTAGGTTGAA-ATTAC-ATATCTTG-TTT
1 CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGA-ATCTTGCTTT
*
12255483 CCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTT
1 --CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGAATCTTG-CTTT
*
12255530 CTGATGTTGCAG
1 CTGAAGTTGCAG
12255542 CGAAGCAGAT
Statistics
Matches: 195, Mismatches: 65, Indels: 32
0.67 0.22 0.11
Matches are distributed among these distances:
42 4 0.02
43 58 0.30
44 54 0.28
45 72 0.37
46 2 0.01
47 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGTAGATTGAAGACGACGAATCTTGCTTT
Found at i:12255421 original size:132 final size:133
Alignment explanation
Indices: 12255206--12255858 Score: 870
Period size: 132 Copynumber: 4.9 Consensus size: 133
12255196 GGCGAATCCC
*
12255206 ACAGATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTTCTGAA
1 ACAGATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
* *
12255271 GTTGCAGTGAAGCAGATTTAAGTCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-
66 GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
12255335 ATT
131 ATT
* * * * *
12255338 ACAGATCTTGTTTCCCTGAAGTCGCGGTGGAGTAGATCGAAGACGATGAATATTGACTTCCTAAA
1 ACAGATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
* *
12255403 GTTGCAGTGAAGCAGATTTAAGTCACTAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAA-
66 GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
12255467 ATT
131 ATT
* * *
12255470 ACATATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTTCTGAT
1 ACAGATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
* * *
12255535 GTTGCAGCGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
66 GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
12255600 ATT
131 ATT
* * * * * **
12255603 GCAGATCTTGTTTCTCTG-AGATTGTAGTGGA-TCAGATCGAAGAC-AGCGGATCTAGGTTTCCT
1 ACAGATCTTGTTTCCCTGAAG-TTGCAGTGGAGT-AGATCGAAGACGA-CGAATCTTGACTTCCT
* *
12255665 GATGTTGCAGCGAAGCAGATTTAAGTCACCACCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTG
63 GAAGTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTG
12255730 AAGATT
128 AAGATT
** * * * * * * ** *
12255736 GTAGATCTTGTTTCCCTG-AGATTGCAGTGGAGCAGATTGAAGATGGCGGATCTAGGTTTCTTGA
1 ACAGATCTTGTTTCCCTGAAG-TTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGA
* *
12255800 TA-TTGCAGCGAAGCAGATTTAAGTCACCACCCTAGCTCCCTGAAGTTGTAGTGGAGTAG
65 -AGTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAG
12255859 ACCCAAGATT
Statistics
Matches: 473, Mismatches: 41, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
132 246 0.52
133 227 0.48
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (133 bp):
ACAGATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGACGAATCTTGACTTCCTGAA
GTTGCAGCGAAGCAGATTTAAGTCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAG
ATT
Found at i:12255501 original size:44 final size:45
Alignment explanation
Indices: 12255210--12255506 Score: 141
Period size: 43 Copynumber: 6.7 Consensus size: 45
12255200 AATCCCACAG
* * ** *
12255210 ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGATCGAAGACGAC-GA
1 ATCTTGTTTCCCTAAAGTTGCAGTGGAGTAGATTGAA-ATTACATA
* * * * * *
12255255 ATCTTGACTTT--CTGAAGTTGCAGTGAAGCAGATTTAAGTCAC-TA
1 ATCTTG--TTTCCCTAAAGTTGCAGTGGAGTAGATTGAAATTACATA
* * * * * *
12255299 ACCTAG-CTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTACA-G
1 ATCTTGTTTCCCTAAAGTTGCAGTGGAGTAGATTGAAATTACATA
* * * * *
12255342 ATCTTGTTTCCCTGAAGTCGCGGTGGAGTAGATCG-AA-GACGATGA
1 ATCTTGTTTCCCTAAAGTTGCAGTGGAGTAGATTGAAATTAC-AT-A
* * * * * * *
12255387 ATATTGACTT-CCTAAAGTTGCAGTGAAGCAGATTTAAGTCAC-TA
1 ATCTTG-TTTCCCTAAAGTTGCAGTGGAGTAGATTGAAATTACATA
* * * * *
12255431 ACCTAG-CTCCCTAAAGTTGTAGTGGAGTAGGTTGAAATTACAT-
1 ATCTTGTTTCCCTAAAGTTGCAGTGGAGTAGATTGAAATTACATA
*
12255474 ATCTTGTTTCCCTGAAGTTGCAGTGGAGTAGAT
1 ATCTTGTTTCCCTAAAGTTGCAGTGGAGTAGAT
12255507 CGAAGACGAC
Statistics
Matches: 178, Mismatches: 59, Indels: 31
0.66 0.22 0.12
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 59 0.33
44 55 0.31
45 52 0.29
46 3 0.02
47 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (45 bp):
ATCTTGTTTCCCTAAAGTTGCAGTGGAGTAGATTGAAATTACATA
Found at i:12258964 original size:145 final size:146
Alignment explanation
Indices: 12258675--12258965 Score: 575
Period size: 145 Copynumber: 2.0 Consensus size: 146
12258665 TTCATTGTTT
12258675 CATATCGTCATGTTAATTATTCTCCATGCGTTGTTGTAATCGGATTACATTTTTAGGTTCGCTAT
1 CATATCGTCATGTTAATTATTCTCCATGCGTTGTTGTAATCGGATTACATTTTTAGGTTCGCTAT
12258740 ATGTAATATATTAATTTGTTAGTTGATCACATCTCATATATGTCAATTACCCCATCTTATCGTTT
66 ATGTAATATATTAATTTGTTAGTTGATCACATCTCATATATGTCAATTACCCCATCTTATCGTTT
12258805 TCATTCGATTTTGAAA
131 TCATTCGATTTTGAAA
12258821 CATATCGTCATGTTAATTATTCTCCATGCGTTGTTGTAATCGGATTACATTTTTAGGTTCGCTAT
1 CATATCGTCATGTTAATTATTCTCCATGCGTTGTTGTAATCGGATTACATTTTTAGGTTCGCTAT
12258886 ATGTAAT-TATTAATTTGTTAGTTGATCACATCTCATATATGTCAATTACCCCATCTTATCGTTT
66 ATGTAATATATTAATTTGTTAGTTGATCACATCTCATATATGTCAATTACCCCATCTTATCGTTT
12258950 TCATTCGATTTTGAAA
131 TCATTCGATTTTGAAA
12258966 TTTGGTTTAA
Statistics
Matches: 145, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 73 0.50
146 72 0.50
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (146 bp):
CATATCGTCATGTTAATTATTCTCCATGCGTTGTTGTAATCGGATTACATTTTTAGGTTCGCTAT
ATGTAATATATTAATTTGTTAGTTGATCACATCTCATATATGTCAATTACCCCATCTTATCGTTT
TCATTCGATTTTGAAA
Found at i:12264428 original size:30 final size:30
Alignment explanation
Indices: 12264388--12264477 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
12264378 TAGGCACTTC
* *
12264388 CACACAGGTGATTCATACACCAGTGTGTCA
1 CACACGGGTGATTCACACACCAGTGTGTCA
* * *
12264418 CACACGGGTGATTTACACGCCCGTGTGTCA
1 CACACGGGTGATTCACACACCAGTGTGTCA
* *
12264448 CACACGGGTAGA-CCACACACCCGTGTGTCA
1 CACACGGGT-GATTCACACACCAGTGTGTCA
12264478 TGGCCGTGTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 49 0.96
31 2 0.04
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (30 bp):
CACACGGGTGATTCACACACCAGTGTGTCA
Found at i:12275181 original size:14 final size:14
Alignment explanation
Indices: 12275162--12275190 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12275152 CCCTTTCATG
12275162 AGTCCTAATTAAAA
1 AGTCCTAATTAAAA
12275176 AGTCCTAATTAAAA
1 AGTCCTAATTAAAA
12275190 A
1 A
12275191 CTAAGTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
AGTCCTAATTAAAA
Found at i:12275587 original size:18 final size:18
Alignment explanation
Indices: 12275548--12275645 Score: 146
Period size: 18 Copynumber: 5.5 Consensus size: 18
12275538 AATGATATGT
*
12275548 AATCGTAGATATGA-TAC
1 AATCTTAGATATGATTAC
*
12275565 AATCTTAGATATGATTGC
1 AATCTTAGATATGATTAC
12275583 AATCTTAGATATGA-TAC
1 AATCTTAGATATGATTAC
*
12275600 AATCTTAGATATGATTGC
1 AATCTTAGATATGATTAC
12275618 AATCTTAGATATGATATAC
1 AATCTTAGATATGAT-TAC
12275637 AATCTTAGA
1 AATCTTAGA
12275646 AGATATGATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
17 29 0.40
18 33 0.45
19 11 0.15
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
AATCTTAGATATGATTAC
Found at i:12275593 original size:35 final size:35
Alignment explanation
Indices: 12275539--12275645 Score: 169
Period size: 35 Copynumber: 3.0 Consensus size: 35
12275529 ATAATCTTCA
* *
12275539 ATGATATGTAATCGTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
12275575 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
12275610 ATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATG--ATACAATCTTAGA
12275646 AGATATGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 49 0.73
36 5 0.07
37 13 0.19
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:12275965 original size:12 final size:12
Alignment explanation
Indices: 12275953--12275982 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
12275943 TTTTAATTTA
12275953 TTATATATATTAT
1 TTAT-TATATTAT
12275966 TTATTATATTAT
1 TTATTATATTAT
12275978 TTATT
1 TTATT
12275983 TTCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTATATTAT
Found at i:12275969 original size:16 final size:16
Alignment explanation
Indices: 12275948--12275983 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
12275938 CTTATTTTTA
12275948 ATTTATTATA-TATATT
1 ATTTATTATATTAT-TT
12275964 ATTTATTATATTATTT
1 ATTTATTATATTATTT
12275980 ATTT
1 ATTT
12275984 TCAAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTATATTATTT
Found at i:12277550 original size:36 final size:36
Alignment explanation
Indices: 12277503--12277574 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12277493 CGATTTGAAA
12277503 ACAGGAACAATAACTATAAATGCAAGATCTTTCATG
1 ACAGGAACAATAACTATAAATGCAAGATCTTTCATG
12277539 ACAGGAACAATAACTATAAATGCAAGATCTTTCATG
1 ACAGGAACAATAACTATAAATGCAAGATCTTTCATG
12277575 GAGGTTATAT
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:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (36 bp):
ACAGGAACAATAACTATAAATGCAAGATCTTTCATG
Found at i:12278368 original size:23 final size:23
Alignment explanation
Indices: 12278337--12278391 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
12278327 CTATATGTTT
* * *
12278337 CCCTAGTGGCTTATTTTGTTTGG
1 CCCTTGTGGCGTACTTTGTTTGG
12278360 CCCTTGTGGCGTACTTTGTTTGG
1 CCCTTGTGGCGTACTTTGTTTGG
12278383 CCCTTGTGG
1 CCCTTGTGG
12278392 TGAATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.05, C:0.22, G:0.29, T:0.44
Consensus pattern (23 bp):
CCCTTGTGGCGTACTTTGTTTGG
Found at i:12284562 original size:46 final size:46
Alignment explanation
Indices: 12284394--12284575 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
12284384 TTCGACATGA
* * * * *
12284394 TGCCATAGTATCTTTCAACTATGGTCTTACTCGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACAC-ATTTCATGTCAGGT
* ** * *
12284440 TGCCATGGTATCTTTCCACCATGGTCTTATTCATTTTATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
12284486 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
* *
12284532 TGCTATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAG
12284576 ATAGCACACT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 3 0.03
46 117 0.98
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
Found at i:12285057 original size:23 final size:24
Alignment explanation
Indices: 12284948--12285076 Score: 81
Period size: 23 Copynumber: 5.5 Consensus size: 24
12284938 ATCAGGTAGT
* *
12284948 TCACAAAGAAC-CATATCGTGAAGC
1 TCACAAAGAGCAC-TATCGGGAAGC
* *
12284972 TCACGAAGAGC-CTATTGGGAAGC
1 TCACAAAGAGCACTATCGGGAAGC
* * *
12284995 TC-CGAATG-GCCATATATCGGGAAGT
1 TCAC-AAAGAG-CA-CTATCGGGAAGC
** *
12285020 TCA-AGCGAGCACTATCGGGAGGC
1 TCACAAAGAGCACTATCGGGAAGC
12285043 TCACAAAGAGC-CTATCGGGAAGC
1 TCACAAAGAGCACTATCGGGAAGC
*
12285066 TCACGAAGAGC
1 TCACAAAGAGC
12285077 TGTATTTCGG
Statistics
Matches: 80, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
22 2 0.03
23 47 0.59
24 19 0.24
25 12 0.15
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (24 bp):
TCACAAAGAGCACTATCGGGAAGC
Found at i:12287202 original size:18 final size:18
Alignment explanation
Indices: 12287154--12287202 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
12287144 ATAATATAAT
12287154 TATTTAATTAATAAATATC
1 TATTTAA-TAATAAATATC
*
12287173 TTTTATAAAATAATAAATATC
1 TATT-T--AATAATAAATATC
12287194 TATTTAATA
1 TATTTAATA
12287203 TCTAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 2 0.08
21 14 0.56
22 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTAATAATAAATATC
Found at i:12295429 original size:12 final size:12
Alignment explanation
Indices: 12295412--12295447 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12295402 AAAAAATATC
12295412 AATATTTTTTGA
1 AATATTTTTTGA
12295424 AATATTTTTTGA
1 AATATTTTTTGA
* *
12295436 AAAATTCTTTGA
1 AATATTTTTTGA
12295448 GTACTCGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (12 bp):
AATATTTTTTGA
Found at i:12300338 original size:8 final size:9
Alignment explanation
Indices: 12300297--12300339 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
12300287 CCATTTAGGC
12300297 CTTTTAAAA
1 CTTTTAAAA
*
12300306 TTTTTAAAA
1 CTTTTAAAA
12300315 CTTTTAAAA
1 CTTTTAAAA
12300324 CTTTTAAAA
1 CTTTTAAAA
12300333 -TTTTAAA
1 CTTTTAAA
12300340 CTAGTAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (9 bp):
CTTTTAAAA
Found at i:12300789 original size:14 final size:15
Alignment explanation
Indices: 12300756--12300793 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12300746 ACTATTTTAA
*
12300756 GGTTTATGGATTATG
1 GGTTTAAGGATTATG
*
12300771 GGTTTAAGGGTTA-G
1 GGTTTAAGGATTATG
12300785 GGTTTAAGG
1 GGTTTAAGG
12300794 TTGATGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (15 bp):
GGTTTAAGGATTATG
Found at i:12301591 original size:28 final size:28
Alignment explanation
Indices: 12301531--12301597 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
12301521 ACTAACCTTT
*
12301531 AAACCCATAAACTATAGATCATAAATCCC
1 AAACCC-TAAACTATAGATCATAAATCAC
* *
12301560 AAACTCTAAACTATA-ACTCATAAATCAT
1 AAACCCTAAACTATAGA-TCATAAATCAC
12301588 AAACCCTAAA
1 AAACCCTAAA
12301598 ATCTAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.82
29 5 0.15
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.22
Consensus pattern (28 bp):
AAACCCTAAACTATAGATCATAAATCAC
Found at i:12301781 original size:8 final size:8
Alignment explanation
Indices: 12301746--12301798 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
12301736 TTTATATGTT
*
12301746 AATTTAAA
1 AATTAAAA
12301754 AATTATAAA
1 AATTA-AAA
12301763 AATCTTCAAAA
1 AA--TT-AAAA
12301774 AATTAAAA
1 AATTAAAA
12301782 AATTAAAA
1 AATTAAAA
*
12301790 ACTTAAAA
1 AATTAAAA
12301798 A
1 A
12301799 TGTAATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 24 0.62
9 7 0.18
11 7 0.18
12 1 0.03
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (8 bp):
AATTAAAA
Found at i:12303118 original size:153 final size:154
Alignment explanation
Indices: 12302839--12303145 Score: 580
Period size: 153 Copynumber: 2.0 Consensus size: 154
12302829 GTAAGATAGA
*
12302839 TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAGTTTGCTTCCTTCATCA
1 TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTTCCTTCATCA
12302904 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
66 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
12302969 TTTTATCTTATATTCTGCAGAATG
131 TTTTATCTTATATTCTGCAGAATG
*
12302993 TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTC-AAGAAAAAATTTGCTTCCTTCATCA
1 TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTTCCTTCATCA
*
12303057 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTA
66 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
12303122 TTTTATCTTATATTCTGCAGAATG
131 TTTTATCTTATATTCTGCAGAATG
12303146 GGGATGATTC
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
153 112 0.75
154 38 0.25
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (154 bp):
TTGATTTCACTAATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTTCCTTCATCA
ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGGTGTATAGTTTTTA
TTTTATCTTATATTCTGCAGAATG
Found at i:12305801 original size:152 final size:152
Alignment explanation
Indices: 12305525--12305984 Score: 848
Period size: 152 Copynumber: 3.0 Consensus size: 152
12305515 AAGTTTTGCG
* *
12305525 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCATTTATTTCATTAGCAAACATC
1 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
*
12305590 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTATTG
66 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
*
12305655 CACAGAGGTATATCTATGTGCT
131 CACTGAGGTATATCTATGTGCT
*
12305677 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAGACATC
1 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
*
12305742 GTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTTTTCACTATAAGTTTTGTTG
66 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
*
12305807 CACTGAGGTATATCTATGTACT
131 CACTGAGGTATATCTATGTGCT
*
12305829 CTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
1 CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
12305894 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
66 GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
12305959 CACTGAGGTATATCTATGTGCT
131 CACTGAGGTATATCTATGTGCT
12305981 CTAT
1 CTAT
12305985 AGATATCGTG
Statistics
Matches: 297, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 297 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (152 bp):
CTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATC
GTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTG
CACTGAGGTATATCTATGTGCT
Found at i:12306060 original size:98 final size:98
Alignment explanation
Indices: 12305891--12306082 Score: 357
Period size: 98 Copynumber: 2.0 Consensus size: 98
12305881 ATTAGCAAAC
*
12305891 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
*
12305956 TTGCACTGAGGTATATCTATGTGCTCTATAGAT
66 TTGCACTGAAGTATATCTATGTGCTCTATAGAT
12305989 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
*
12306054 TTGCACTGAAGTATATCTATGTGTTCTAT
66 TTGCACTGAAGTATATCTATGTGCTCTAT
12306083 TGCATGCTGG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (98 bp):
ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
TTGCACTGAAGTATATCTATGTGCTCTATAGAT
Found at i:12306180 original size:250 final size:250
Alignment explanation
Indices: 12305739--12306234 Score: 902
Period size: 250 Copynumber: 2.0 Consensus size: 250
12305729 ATTAGCAGAC
*
12305739 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTTTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTCTTCACTATAAGTTTTG
*
12305804 TTGCACTGAGGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
66 TTGCACTGAAGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
*
12305869 ATCCTTTTTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
131 ATCCTTATTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
*
12305934 CTTTTTTTCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTGCTCTATAGAT
196 CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTGCTCTATAGAT
*
12305989 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTCTTCACTATAAGTTTTG
** *
12306054 TTGCACTGAAGTATATCTATGTGTTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
66 TTGCACTGAAGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
* *
12306119 ATCCTTATTTTCATTAGTAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
131 ATCCTTATTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
12306184 CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTGCTCTAT
196 CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTGCTCTAT
12306235 TGCATGCTGG
Statistics
Matches: 236, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
250 236 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (250 bp):
ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACGCTTTTCTTCACTATAAGTTTTG
TTGCACTGAAGTATATCTATGTACTCTATTGCATGCTAGCTGATCTTTAAAATGATGTTAAGGAT
ATCCTTATTTTCATTAGCAAACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTGCTCTATAGAT
Found at i:12306265 original size:152 final size:152
Alignment explanation
Indices: 12305984--12306341 Score: 644
Period size: 152 Copynumber: 2.4 Consensus size: 152
12305974 ATGTGCTCTA
* *
12305984 TAGATATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAG
1 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAG
* *
12306049 TTTTGTTGCACTGAAGTATATCTATGTGTTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
66 TTTTGTTGCACAGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
12306114 AGGATATCCTTATTTTCATTAG
131 AGGATATCCTTATTTTCATTAG
12306136 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAG
1 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAG
*
12306201 TTTTGTTGCACAGAGGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
66 TTTTGTTGCACAGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
*
12306266 AGGATATCCTTTTTTTCATTAG
131 AGGATATCCTTATTTTCATTAG
* *
12306288 CAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATTTGCTTTTT
1 TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTT
12306342 ACATGAATCC
Statistics
Matches: 198, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 198 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (152 bp):
TAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAG
TTTTGTTGCACAGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTA
AGGATATCCTTATTTTCATTAG
Found at i:12306331 original size:402 final size:402
Alignment explanation
Indices: 12305587--12306341 Score: 1393
Period size: 402 Copynumber: 1.9 Consensus size: 402
12305577 ATTAGCAAAC
*
12305587 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTA
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTA
*
12305652 TTGCACAGAGGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
66 TTGCACAGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
*
12305717 ATCCTTTTTTTCATTAGCAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACG
131 ATCCTTATTTTCATTAGCAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACG
*
12305782 CTTTTTTTCACTATAAGTTTTGTTGCACTGAGGTATATCTATGTACTCTATTGCATGCTAGCTGA
196 CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTACTCTATTGCATGCTAGCTGA
12305847 TCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATCGTGCAATATTTTAACTAA
261 TCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATCGTGCAATATTTTAACTAA
12305912 TACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTGCACTGAGGTATATCTATG
326 TACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTGCACTGAGGTATATCTATG
12305977 TGCTCTATAGAT
391 TGCTCTATAGAT
*
12305989 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTG
1 ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTA
* *
12306054 TTGCACTGAAGTATATCTATGTGTTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
66 TTGCACAGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
* *
12306119 ATCCTTATTTTCATTAGTAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATG
131 ATCCTTATTTTCATTAGCAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACG
* *
12306184 CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTGCTCTATTGCATGCTGGCTGA
196 CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTACTCTATTGCATGCTAGCTGA
*
12306249 TCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAGACATCGTGCAATATTTTAACTAA
261 TCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATCGTGCAATATTTTAACTAA
*
12306314 TACTATTAGCATTTACCATTTGCTTTTT
326 TACTATTAGCATTTACCATATGCTTTTT
12306342 ACATGAATCC
Statistics
Matches: 340, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
402 340 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (402 bp):
ATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATATGCTTTTCTTCACTATAAGTTTTA
TTGCACAGAAGTATATCTATGTGCTCTATTGCATGCTGGCTGATCTTTAAAATGATGTTAAGGAT
ATCCTTATTTTCATTAGCAGACATCGTGCAATATTTTAACTAATACTATTAGCATTTACCATACG
CTTTTTTTCACTATAAGTTTTGTTGCACAGAGGTATATCTATGTACTCTATTGCATGCTAGCTGA
TCTTTAAAATGATGTTAAGGATATCCTTTTTTTCATTAGCAAACATCGTGCAATATTTTAACTAA
TACTATTAGCATTTACCATATGCTTTTTTTCACTATAAGTTTTGTTGCACTGAGGTATATCTATG
TGCTCTATAGAT
Found at i:12307347 original size:43 final size:43
Alignment explanation
Indices: 12307196--12307387 Score: 174
Period size: 43 Copynumber: 4.5 Consensus size: 43
12307186 TTTTTACGGC
* * *
12307196 TCATGACCTTTAGCGGCGTTT-TGGGAAAAGCGCCGCTAAAGG
1 TCATGATCTTTAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGA
* * * * * *
12307238 TCATGGTCTTTAGCAGTGTTTGTGGGAAAAGCGTCGCTAAAGG
1 TCATGATCTTTAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGA
* * * **
12307281 TCAAGGTCTTTAGCGACAATTGCGGGAAAAGCGCCGCTAAAGA
1 TCATGATCTTTAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGA
* * * *
12307324 CCATGACCTTTAGCGGCGTTTGC-GAAAAAGGTGCCGCTAAA-A
1 TCATGATCTTTAGCGGCGTTTGCGGGAAAA-GCGCCGCTAAAGA
*
12307366 GTCATGATTTTTAGCGGCGTTT
1 -TCATGATCTTTAGCGGCGTTT
12307388 TTTTAAATAA
Statistics
Matches: 121, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
42 23 0.19
43 98 0.81
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
TCATGATCTTTAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGA
Found at i:12315874 original size:26 final size:26
Alignment explanation
Indices: 12315833--12315913 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
12315823 TGATATAAAT
12315833 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12315858 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12315884 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12315910 TGAT
1 TGAT
12315914 GGGAATTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 7 0.13
26 48 0.87
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:12322954 original size:29 final size:30
Alignment explanation
Indices: 12322875--12322954 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
12322865 AAAAAATAAA
***
12322875 TTTTAAAGTTTTCTAAATTTTTTTTACTAAT
1 TTTTAAA-TTTTCTAAAGAATTTTTACTAAT
* *
12322906 TTTTATA-TTTGTAAAGAATTTTTAC-AACT
1 TTTTAAATTTTCTAAAGAATTTTTACTAA-T
12322935 TTTTAAATTTTCTAAA-AATT
1 TTTTAAATTTTCTAAAGAATT
12322955 ATATATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 2 0.05
29 25 0.62
30 7 0.17
31 6 0.15
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTTAAATTTTCTAAAGAATTTTTACTAAT
Found at i:12332507 original size:5 final size:5
Alignment explanation
Indices: 12332497--12332529 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
12332487 TTGTGTGTTC
12332497 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
12332530 TCACAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:12343045 original size:22 final size:21
Alignment explanation
Indices: 12343008--12343059 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
12342998 ATCACCCCAA
*
12343008 TTTT-ATTTTATTTTATTTAT
1 TTTTAATTTTATCTTATTTAT
12343028 TTTTAATTGTTATCTTATTTAT
1 TTTTAATT-TTATCTTATTTAT
*
12343050 CTTT-ATTTTA
1 TTTTAATTTTA
12343060 CTAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.25
21 6 0.21
22 15 0.54
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTAATTTTATCTTATTTAT
Found at i:12343160 original size:14 final size:14
Alignment explanation
Indices: 12343143--12343182 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
12343133 ATATTTTTAT
*
12343143 TATTTTTATTTTGG
1 TATTTCTATTTTGG
12343157 TATTTCTATTTTGG
1 TATTTCTATTTTGG
12343171 TATTTCTATTTT
1 TATTTCTATTTT
12343183 TTTTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.70
Consensus pattern (14 bp):
TATTTCTATTTTGG
Found at i:12346350 original size:29 final size:29
Alignment explanation
Indices: 12346316--12346371 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12346306 TTACTTGATA
* * *
12346316 CACACAGCCGTGTCGCAGACCGTGTATGG
1 CACACAACCGTGTCGCAAACCATGTATGG
12346345 CACACAACCGTGTCGCAAACCATGTAT
1 CACACAACCGTGTCGCAAACCATGTAT
12346372 AGCAGACGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (29 bp):
CACACAACCGTGTCGCAAACCATGTATGG
Found at i:12349281 original size:46 final size:46
Alignment explanation
Indices: 12349231--12349583 Score: 539
Period size: 46 Copynumber: 7.7 Consensus size: 46
12349221 GATAGAAAAT
*
12349231 GTGTAAGACCATGGTTGAAAGATACCATGGCAATCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
12349277 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
12349323 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
*
12349369 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
12349415 GTGTAAGACCAT-GTTGAAAGATACCATGGCAACCTGATATGAAAC
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* * * * *
12349460 GTGTAAGACCATGGTTGAAAGGTACCATGACAACGTGACATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
* * *
12349506 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAAC
* * * * *
12349552 GAGTAAAACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
12349584 TCATGTCGAA
Statistics
Matches: 287, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
45 45 0.16
46 242 0.84
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAC
Found at i:12349536 original size:183 final size:184
Alignment explanation
Indices: 12349227--12349583 Score: 574
Period size: 183 Copynumber: 1.9 Consensus size: 184
12349217 CTATGATAGA
*
12349227 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATCTGATATGAAACGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAGACCATGGT
* *
12349292 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGACAACCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
12349357 CTGATATG-AAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
131 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGACACCATGGCAACCTGATATG
12349411 AAATGTGTAAGACCAT-GTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAGACCATGGT
* *
12349475 TGAAAGGTACCATGACAACGTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGACAACCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
12349540 ATGACAGAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCA
131 ATGACAGAAAACGAGTAAAACCATAGTTGAAAGACACCATGGCA
12349584 TCATGTCGAA
Statistics
Matches: 159, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
182 1 0.01
183 142 0.89
184 16 0.10
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.22
Consensus pattern (184 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAGACCATGGT
TGAAAGATACCATGACAACCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
ATGACAGAAAACGAGTAAAACCATAGTTGAAAGACACCATGGCAACCTGATATG
Found at i:12360236 original size:21 final size:21
Alignment explanation
Indices: 12360193--12360243 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
12360183 TAAGAATGTT
**
12360193 ATTAAATTATATATTATTTTA
1 ATTAAATTATATATTATAATA
12360214 ATTAAATTATAT-TTAATAATA
1 ATTAAATTATATATT-ATAATA
*
12360235 ATTAGATTA
1 ATTAAATTA
12360244 AAATATGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAAATTATATATTATAATA
Found at i:12360237 original size:16 final size:16
Alignment explanation
Indices: 12360205--12360291 Score: 56
Period size: 16 Copynumber: 5.5 Consensus size: 16
12360195 TAAATTATAT
*
12360205 ATTAT-TTTAATTA-A
1 ATTATATTTAATAATA
12360219 ATTATATTTAATAATA
1 ATTATATTTAATAATA
*
12360235 ATTAGA-TTAA-AATA
1 ATTATATTTAATAATA
* ** *
12360249 TGATTAAATTTTTTATTAA
1 --ATTATATTTAATAAT-A
12360268 ATTATATTTAATAATA
1 ATTATATTTAATAATA
*
12360284 ATTCTATT
1 ATTATATT
12360292 AAAATTTAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
14 9 0.16
15 11 0.20
16 19 0.35
17 13 0.24
18 2 0.04
19 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTATATTTAATAATA
Found at i:12360244 original size:59 final size:52
Alignment explanation
Indices: 12360197--12360301 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 52
12360187 AATGTTATTA
12360197 AATTATATATTATTTTAATTAAATTATATTTAATAATAATTAGATTAAAATAT
1 AATTATATATTATTTT-ATTAAATTATATTTAATAATAATTAGATTAAAATAT
* ** *
12360250 GATTA-A-ATT-TTTTATTAAATTATATTTAATAATAATTCTATTAAAATTT
1 AATTATATATTATTTTATTAAATTATATTTAATAATAATTAGATTAAAATAT
12360299 AAT
1 AAT
12360302 AACAAACAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 35 0.74
50 4 0.09
51 3 0.06
52 1 0.02
53 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (52 bp):
AATTATATATTATTTTATTAAATTATATTTAATAATAATTAGATTAAAATAT
Found at i:12360484 original size:16 final size:16
Alignment explanation
Indices: 12360463--12360497 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12360453 TGAATTATTG
*
12360463 ATTACAACTCTATTTT
1 ATTACAACTCTATTCT
*
12360479 ATTACAACTTTATTCT
1 ATTACAACTCTATTCT
12360495 ATT
1 ATT
12360498 CCCCCCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:12363598 original size:22 final size:23
Alignment explanation
Indices: 12363572--12363617 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12363562 CAACCAAATC
12363572 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12363594 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12363617 A
1 A
12363618 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12363623 original size:23 final size:23
Alignment explanation
Indices: 12363579--12363623 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12363569 ATCAATTCAA
*
12363579 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12363602 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12363624 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12371260 original size:22 final size:23
Alignment explanation
Indices: 12371235--12371280 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12371225 CAACCAAATC
12371235 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12371257 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12371280 A
1 A
12371281 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12371286 original size:23 final size:23
Alignment explanation
Indices: 12371242--12371286 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12371232 ATCAATTCAA
*
12371242 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12371265 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12371287 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12374035 original size:46 final size:46
Alignment explanation
Indices: 12373985--12374185 Score: 278
Period size: 46 Copynumber: 4.4 Consensus size: 46
12373975 GGCCATTACA
* *
12373985 TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGT
* **
12374031 TGAAAGATACCATGGAAACATGACGGGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGT
* *
12374077 TGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGT
* **
12374123 TGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAAT
1 TGAAAGATACCATGGCAACATGACATG-AAATGAATAAGACCATGGT
* *
12374169 TGAAAGACACTATGGCA
1 TGAAAGATACCATGGCA
12374186 TCAACGTTAA
Statistics
Matches: 137, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 136 0.99
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (46 bp):
TGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGT
Found at i:12374205 original size:92 final size:91
Alignment explanation
Indices: 12374012--12374209 Score: 236
Period size: 92 Copynumber: 2.2 Consensus size: 91
12374002 ACCTGATATG
* * * **
12374012 AAATGAATAAGACCATGGTTGAAAGATACCATGGAAACATGACGGGAAATGAATAAGACCATGGT
1 AAATAAATAAGACCATGGTTGAAAGATACCATGGAAACATGACAGAAAATGAATAAGACCATAAT
* * *
12374077 TGAAAGATACCATGGCAGCGTGACATG
66 TGAAAGACACCATGGCAGCG-AACATA
* * *
12374104 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAAT
1 AAATAAATAAGACCATGGTTGAAAGATACCATGGAAACATGACAGAAAATGAATAAGACCATAAT
* * *
12374169 TGAAAGACACTATGGCATC-AACGTTA
66 TGAAAGACACCATGGCAGCGAAC-ATA
12374195 AAGATAAATAAGACC
1 AA-ATAAATAAGACC
12374210 GTGGATGGGA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
90 2 0.02
91 3 0.03
92 86 0.95
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (91 bp):
AAATAAATAAGACCATGGTTGAAAGATACCATGGAAACATGACAGAAAATGAATAAGACCATAAT
TGAAAGACACCATGGCAGCGAACATA
Found at i:12374490 original size:16 final size:17
Alignment explanation
Indices: 12374469--12374501 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12374459 TTGATGGTGG
12374469 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
*
12374485 ATGAAATGATTTATATA
1 ATGAAATGATTGATATA
12374502 TACTTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:12375826 original size:29 final size:30
Alignment explanation
Indices: 12375779--12375846 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
12375769 TGGCCCAAGA
* * *
12375779 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
12375809 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
12375839 GCAAATAT
1 GTAAATAT
12375847 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:12387284 original size:31 final size:31
Alignment explanation
Indices: 12387242--12387305 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
12387232 CCTTTTCATA
* *
12387242 TTTCATTTTTCATAACACTGGGCCAAAGCCT
1 TTTCATATTTCATAACACTAGGCCAAAGCCT
** *
12387273 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCAAAGCCT
12387304 TT
1 TT
12387306 ACTATAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCAAAGCCT
Found at i:12387605 original size:23 final size:24
Alignment explanation
Indices: 12387499--12387617 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
12387489 GCTTTATCAT
*
12387499 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
12387524 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
*
12387548 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
12387572 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
12387595 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12387618 TTCACTTCCT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 21 0.25
24 52 0.61
25 12 0.14
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12387695 original size:20 final size:20
Alignment explanation
Indices: 12387672--12387734 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
12387662 GAACATCTCG
12387672 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
* *
12387692 TGTGCATATCCTACATGTCA
1 TGTGCATATCATACATATCA
12387712 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
12387732 TGT
1 TGT
12387735 TTATCAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:12387799 original size:25 final size:25
Alignment explanation
Indices: 12387771--12387818 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12387761 ATATATAAAC
* * *
12387771 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12387796 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12387819 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12389027 original size:27 final size:27
Alignment explanation
Indices: 12388976--12389053 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
12388966 GGGCATATTC
* *
12388976 GTCA-TTTACCATACAGGGGTATTACG
1 GTCACTTTACCCTACAGGGGTATTACA
* *
12389002 GTTATTTTACCCTACAGGGGCT-TTACA
1 GTCACTTTACCCTACAGGGG-TATTACA
*
12389029 GTCACTTTACCCTAATAGGGGTATT
1 GTCACTTTACCCT-ACAGGGGTATT
12389054 TTAGTCATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.07
27 30 0.71
28 9 0.21
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGTATTACA
Found at i:12389124 original size:27 final size:27
Alignment explanation
Indices: 12389094--12389145 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
12389084 GTAAATCAAC
12389094 AAACCAA-AGGTATTTC-AGTAATTTTGT
1 AAACCAATA-GTATTTCTA-TAATTTTGT
*
12389121 AAACTAATAGTATTTCTATAATTTT
1 AAACCAATAGTATTTCTATAATTTT
12389146 TAGAAAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (27 bp):
AAACCAATAGTATTTCTATAATTTTGT
Found at i:12389242 original size:54 final size:54
Alignment explanation
Indices: 12389184--12389323 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
12389174 TGTAAATCAG
*
12389184 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACTAA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * *
12389238 GGGTATTTTGGTAATTTTACAAATT-AGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTATAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
* * *
12389292 GGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTA
12389324 AAATAGTAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 1 0.01
54 74 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:12389295 original size:81 final size:81
Alignment explanation
Indices: 12389155--12389308 Score: 202
Period size: 81 Copynumber: 1.9 Consensus size: 81
12389145 TTAGAAAGTC
** * ***
12389155 AAGGGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTATAAATTGAGGGTATTTC
1 AAGGGTATTTCTGTAACTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTC
*
12389220 GGTAATTTCACAAACT
66 AGTAATTTCACAAACT
* *
12389236 AAGGGTATTT-TGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
1 AAGGGTATTTCT-GTAACTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
*
12389300 TAGTAATTT
65 CAGTAATTT
12389309 TGTAAATCGA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
80 1 0.02
81 61 0.98
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.42
Consensus pattern (81 bp):
AAGGGTATTTCTGTAACTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTC
AGTAATTTCACAAACT
Found at i:12389321 original size:27 final size:27
Alignment explanation
Indices: 12389143--12389350 Score: 168
Period size: 27 Copynumber: 7.7 Consensus size: 27
12389133 TTTCTATAAT
*
12389143 TTTTAGAAAGTCAAGGGTATTTCT-GTAA
1 TTTTATAAA-TCAAGGGTATTT-TGGTAA
* * *
12389171 CTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
** *
12389198 TTTTATAAATTGAGGGTATTTCGGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* *
12389225 TTTCACAAA-CTAAGGGTATTTTGGTAA
1 TTTTATAAATC-AAGGGTATTTTGGTAA
* * *
12389252 TTTTACAAATTAGGGGTATTTTGGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* * *
12389279 TTTTACAAACCAAGGGTATTTTAGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* * *** *
12389306 TTTTGTAAATCGAGGGTAAAATAGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* *
12389333 TTCTGTAAATCAAGGGTA
1 TTTTATAAATCAAGGGTA
12389351 AAACAGTAAT
Statistics
Matches: 146, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 139 0.95
28 6 0.04
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (27 bp):
TTTTATAAATCAAGGGTATTTTGGTAA
Found at i:12389351 original size:27 final size:26
Alignment explanation
Indices: 12389301--12389433 Score: 149
Period size: 27 Copynumber: 5.0 Consensus size: 26
12389291 AGGGTATTTT
*
12389301 AGTAATTTTGTAAATCGAGGGTAAAA
1 AGTAATTCTGTAAATCGAGGGTAAAA
*
12389327 TAGTAATTCTGTAAATCAAGGGTAAAA
1 -AGTAATTCTGTAAATCGAGGGTAAAA
* *
12389354 CAGTAATTCTATAAATCGATGGTAAAA
1 -AGTAATTCTGTAAATCGAGGGTAAAA
* *
12389381 CGATAATTCTGTAAATCGATGGTAAAA
1 AG-TAATTCTGTAAATCGAGGGTAAAA
* * *
12389408 CGATAATTTTGTAAGTCGAGGGTAAA
1 AG-TAATTCTGTAAATCGAGGGTAAA
12389434 TCAGGGGTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 93 0.99
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.30
Consensus pattern (26 bp):
AGTAATTCTGTAAATCGAGGGTAAAA
Found at i:12389469 original size:26 final size:26
Alignment explanation
Indices: 12389429--12389492 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
12389419 TAAGTCGAGG
12389429 GTAAATCAGGGGTAAAATGGTAATTAT
1 GTAAATC-GGGGTAAAATGGTAATTAT
*
12389456 GTAAATCGGGGTAAAATGGTAATTCT
1 GTAAATCGGGGTAAAATGGTAATTAT
12389482 GTAAATCGGGG
1 GTAAATCGGGG
12389493 GTACTTTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 29 0.81
27 7 0.19
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (26 bp):
GTAAATCGGGGTAAAATGGTAATTAT
Found at i:12389522 original size:27 final size:26
Alignment explanation
Indices: 12389492--12389590 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 26
12389482 GTAAATCGGG
* *
12389492 GGTACTTTGGTTATTTTACAAGTCGAA
1 GGTA-TTTAGTTATTTTACAAATCGAA
* *
12389519 GGTATTTCAGTAATTTTACAAATCGAG
1 GGTATTT-AGTTATTTTACAAATCGAA
*
12389546 GGTATTTTAG-TATTTTTACAAA-CTAA
1 GGTA-TTTAGTTA-TTTTACAAATCGAA
*
12389572 GCGTATTTCAGTAATTTTA
1 G-GTATTT-AGTTATTTTA
12389591 GTAAACTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
26 10 0.17
27 44 0.76
28 4 0.07
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (26 bp):
GGTATTTAGTTATTTTACAAATCGAA
Found at i:12389542 original size:54 final size:54
Alignment explanation
Indices: 12389484--12389590 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
12389474 GTAATTCTGT
* * *
12389484 AAATCGGGGGTACTTTGGT-TATTTTACAAGTCGAAG-GTATTTCAGTAATTTTAC
1 AAATCGAGGGTACTTTAGTAT-TTTTACAA-ACGAAGCGTATTTCAGTAATTTTAC
* *
12389538 AAATCGAGGGTATTTTAGTATTTTTACAAACTAAGCGTATTTCAGTAATTTTA
1 AAATCGAGGGTACTTTAGTATTTTTACAAACGAAGCGTATTTCAGTAATTTTA
12389591 GTAAACTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 4 0.09
54 41 0.89
55 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (54 bp):
AAATCGAGGGTACTTTAGTATTTTTACAAACGAAGCGTATTTCAGTAATTTTAC
Found at i:12389597 original size:28 final size:27
Alignment explanation
Indices: 12389520--12389599 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
12389510 CAAGTCGAAG
* *
12389520 GTATTTCAGTAATTTTACAAA-TCGAGG
1 GTATTTCAGTAATTTTACAAACT-AAGC
* *
12389547 GTATTTTAGTATTTTTACAAACTAAGC
1 GTATTTCAGTAATTTTACAAACTAAGC
*
12389574 GTATTTCAGTAATTTTAGTAAACTAA
1 GTATTTCAGTAATTTTA-CAAACTAA
12389600 AATATTCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 36 0.82
28 8 0.18
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAACTAAGC
Found at i:12392190 original size:79 final size:79
Alignment explanation
Indices: 12391961--12392192 Score: 315
Period size: 79 Copynumber: 2.9 Consensus size: 79
12391951 GAGTCACATC
* * * *
12391961 TCATGTAACTGTAGTGAATCAAGATTACCC-TTTCAGGTCAAATCCTACCCACCTTAAGTTATCA
1 TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
12392025 TAAG-GAATCATGTA
66 T-AGTGAATCATATA
* * * *
12392039 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACATTAGGTTGCCA
1 TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
12392104 TAATGAATCATATA
66 TAGTGAATCATATA
* * * *
12392118 TCATGTAACCGTAGTGACTCAGGATTACCCTTTTTAGGTCAAATCCTATCCGCCTTAAGTTACCC
1 TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
12392183 TAGTGAATCA
66 TAGTGAATCA
12392193 AGAATAAATC
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
78 28 0.21
79 105 0.79
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (79 bp):
TCATGTAACCGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
TAGTGAATCATATA
Found at i:12392221 original size:40 final size:40
Alignment explanation
Indices: 12392157--12392254 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
12392147 CTTTTTAGGT
* * * *
12392157 CAAATCCTATCCGCCTTAAGTTACCCTAGTGAATCAAGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
* * *
12392197 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
12392237 CAAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
12392255 TATTCTCGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
Found at i:12393845 original size:40 final size:40
Alignment explanation
Indices: 12393801--12393880 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12393791 AGGACCAAAT
12393801 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
1 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
12393841 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
1 TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
12393881 ACATGAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (40 bp):
TGTAAAGAAAAGAAAACTTTCTTTCTTCTATTTTCTTCTA
Found at i:12394943 original size:22 final size:23
Alignment explanation
Indices: 12394905--12394949 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12394895 TGAATTGTGA
12394905 TAGGAATATAAATGAATT-TAGT
1 TAGGAATATAAATGAATTATAGT
*
12394927 TAGGAATA-AATTGGAATTATAGT
1 TAGGAATATAAAT-GAATTATAGT
12394950 AAAAGCTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 13 0.65
23 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (23 bp):
TAGGAATATAAATGAATTATAGT
Done.