Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 32 of 147
Found at i:6767708 original size:24 final size:24
Alignment explanation
Indices: 6767673--6767734 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
6767663 TTAAATTTAT
6767673 TTATAATT-TTTTTAAAATTTTAAG
1 TTAT-ATTATTTTTAAAATTTTAAG
* *
6767697 TTA-AGTTATTTTTAAAATTTTTAT
1 TTATA-TTATTTTTAAAATTTTAAG
6767721 TTATATTATTTTTA
1 TTATATTATTTTTA
6767735 TATCATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 2 0.06
24 29 0.88
25 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
TTATATTATTTTTAAAATTTTAAG
Found at i:6767731 original size:15 final size:16
Alignment explanation
Indices: 6767713--6767746 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6767703 TATTTTTAAA
*
6767713 ATTTTTAT-TTATATT
1 ATTTTTATATCATATT
6767728 ATTTTTATATCATATT
1 ATTTTTATATCATATT
6767744 ATT
1 ATT
6767747 ATATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATATCATATT
Found at i:6768132 original size:34 final size:35
Alignment explanation
Indices: 6768097--6768164 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
6768087 TGTGTGCCTC
*
6768097 TTATCAACATTTTTGTTTTGGAGCTATGTAACTCT
1 TTATCAACATTTTTGTTTTGGAGCTATGGAACTCT
* * * *
6768132 TTTTCTACCTTTTTGTTTTGGGGCTATGGAACT
1 TTATCAACATTTTTGTTTTGGAGCTATGGAACT
6768165 TTTTCCTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (35 bp):
TTATCAACATTTTTGTTTTGGAGCTATGGAACTCT
Found at i:6768145 original size:35 final size:35
Alignment explanation
Indices: 6768104--6768186 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
6768094 CTCTTATCAA
* *
6768104 CATTTTTGTTTTGGAGCTATGTAACTCTTTTTCTAC
1 CATTTTTGTTTTGGAGCTATGGAACT-TTTTCCTAC
*
6768140 C-TTTTTGTTTTGGGGCTATGGAACTTTTTCCTAC
1 CATTTTTGTTTTGGAGCTATGGAACTTTTTCCTAC
*
6768174 CACTTTTGTTTTG
1 CATTTTTGTTTTG
6768187 TTTTGATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 9 0.21
35 32 0.76
36 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (35 bp):
CATTTTTGTTTTGGAGCTATGGAACTTTTTCCTAC
Found at i:6769482 original size:15 final size:14
Alignment explanation
Indices: 6769462--6769491 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
6769452 AAATTAATAT
6769462 TTTATTATTGTTTTA
1 TTTATTATT-TTTTA
6769477 TTTATTATTTTTTA
1 TTTATTATTTTTTA
6769491 T
1 T
6769492 AAAAGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTATTATTTTTTA
Found at i:6769932 original size:20 final size:19
Alignment explanation
Indices: 6769878--6769940 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
6769868 ATTATAATAC
6769878 ATAAT-TTTTATATAAATT
1 ATAATATTTTATATAAATT
*** *
6769896 ATAATAAAAATACATAAATT
1 ATAAT-ATTTTATATAAATT
6769916 ATTAATATTTTATATAAATT
1 A-TAATATTTTATATAAATT
6769936 CATAA
1 -ATAA
6769941 ATTGTTAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATATTTTATATAAATT
Found at i:6771632 original size:17 final size:17
Alignment explanation
Indices: 6771610--6771644 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6771600 TATAATTAAC
6771610 TTTTTGTATTATATATT
1 TTTTTGTATTATATATT
* *
6771627 TTTTTGTTTTATTTATT
1 TTTTTGTATTATATATT
6771644 T
1 T
6771645 CTTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTGTATTATATATT
Found at i:6774764 original size:2 final size:2
Alignment explanation
Indices: 6774759--6774784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6774749 TTTCAGGTAC
6774759 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
6774785 CACATGAACA
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:6775467 original size:43 final size:46
Alignment explanation
Indices: 6775385--6775472 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 46
6775375 AGAAAGACAA
* * *
6775385 TTTCGTAAACTGGCCTATATTCCCCCATCATCTCGAGAAG-AAAAT
1 TTTCGTAAACTGGCCTATATTCCCCAATCATCCCAAGAAGCAAAAT
6775430 TTTCGT-AACT-GCCTATATTCCCCAAT-ATCCCAAAGAAGCAAAA
1 TTTCGTAAACTGGCCTATATTCCCCAATCATCCC-AAGAAGCAAAA
6775473 AAAGAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 4 0.11
43 20 0.53
44 8 0.21
45 6 0.16
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (46 bp):
TTTCGTAAACTGGCCTATATTCCCCAATCATCCCAAGAAGCAAAAT
Found at i:6776692 original size:22 final size:22
Alignment explanation
Indices: 6776665--6776709 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6776655 TGTCTTTTGA
6776665 ACTAATTAAT-AAATAACAATGC
1 ACTAATTAATGAAA-AACAATGC
*
6776687 ACTAATTAATGAAAAATAATGC
1 ACTAATTAATGAAAAACAATGC
6776709 A
1 A
6776710 ACTTTTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (22 bp):
ACTAATTAATGAAAAACAATGC
Found at i:6785407 original size:24 final size:24
Alignment explanation
Indices: 6785372--6785433 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
6785362 TTAAATTTAT
6785372 TTATAATT-TTTTTAAAATTTTAAG
1 TTAT-ATTATTTTTAAAATTTTAAG
* *
6785396 TTA-AGTTATTTTTAAAATTTTTAT
1 TTATA-TTATTTTTAAAATTTTAAG
6785420 TTATATTATTTTTA
1 TTATATTATTTTTA
6785434 TATCATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 2 0.06
24 29 0.88
25 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
TTATATTATTTTTAAAATTTTAAG
Found at i:6785430 original size:15 final size:16
Alignment explanation
Indices: 6785412--6785445 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6785402 TATTTTTAAA
*
6785412 ATTTTTAT-TTATATT
1 ATTTTTATATCATATT
6785427 ATTTTTATATCATATT
1 ATTTTTATATCATATT
6785443 ATT
1 ATT
6785446 ATATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATATCATATT
Found at i:6785847 original size:35 final size:35
Alignment explanation
Indices: 6785806--6785888 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
6785796 CTCTTATCAA
* *
6785806 CATTTTTGTTTTGGAGCTATATAACTCTTTTTCTAC
1 CATTTTTGTTTTGGAGCTATAGAACT-TTTTCCTAC
* *
6785842 C-TTTTTGTTTTGGGGCTATGGAACTTTTTCCTAC
1 CATTTTTGTTTTGGAGCTATAGAACTTTTTCCTAC
*
6785876 CACTTTTGTTTTG
1 CATTTTTGTTTTG
6785889 TTTTGATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 9 0.22
35 31 0.76
36 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.16, T:0.53
Consensus pattern (35 bp):
CATTTTTGTTTTGGAGCTATAGAACTTTTTCCTAC
Found at i:6787198 original size:15 final size:14
Alignment explanation
Indices: 6787178--6787207 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
6787168 AAATTAATAT
6787178 TTTATTATTGTTTTA
1 TTTATTATT-TTTTA
6787193 TTTATTATTTTTTA
1 TTTATTATTTTTTA
6787207 T
1 T
6787208 AAAAGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTATTATTTTTTA
Found at i:6787667 original size:20 final size:19
Alignment explanation
Indices: 6787613--6787675 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
6787603 ATTATAATAC
6787613 ATAAT-TTTTATATAAATT
1 ATAATATTTTATATAAATT
*** *
6787631 ATAATAAAAATACATAAATT
1 ATAAT-ATTTTATATAAATT
6787651 ATTAATATTTTATATAAATT
1 A-TAATATTTTATATAAATT
6787671 CATAA
1 -ATAA
6787676 ATTGTTAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATATTTTATATAAATT
Found at i:6787878 original size:20 final size:20
Alignment explanation
Indices: 6787862--6787901 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6787852 TAAAATATTA
6787862 AAATTTTAATTTTAATAATT
1 AAATTTTAATTTTAATAATT
*
6787882 AAATTTTAATTTTGATAATT
1 AAATTTTAATTTTAATAATT
6787902 TCAAATACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
AAATTTTAATTTTAATAATT
Found at i:6789398 original size:17 final size:17
Alignment explanation
Indices: 6789376--6789410 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6789366 TATAATTAAC
6789376 TTTTTGTATTATATATT
1 TTTTTGTATTATATATT
* *
6789393 TTTTTGTTTTATTTATT
1 TTTTTGTATTATATATT
6789410 T
1 T
6789411 CTTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTGTATTATATATT
Found at i:6793285 original size:43 final size:44
Alignment explanation
Indices: 6793196--6793289 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
6793186 AATCTATAGA
* * * *
6793196 AAGACAATTTCGTAAACTGCCTAAATTCCCCCATCATCTCGAAG
1 AAGAAAATTTCGTAAACTGCCTAAATTCCCCAATCATCCCAAAG
*
6793240 AAGAAAATTTCGTAAACTGCCTATATTCCCCAAT-ATCCCAAAG
1 AAGAAAATTTCGTAAACTGCCTAAATTCCCCAATCATCCCAAAG
6793283 AAGAAAA
1 AAGAAAA
6793290 AAAGAAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 14 0.31
44 31 0.69
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (44 bp):
AAGAAAATTTCGTAAACTGCCTAAATTCCCCAATCATCCCAAAG
Found at i:6794516 original size:22 final size:22
Alignment explanation
Indices: 6794489--6794533 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6794479 TGTCTTTTGA
6794489 ACTAATTAAT-AAATAACAATGC
1 ACTAATTAATGAAA-AACAATGC
*
6794511 ACTAATTAATGAAAAATAATGC
1 ACTAATTAATGAAAAACAATGC
6794533 A
1 A
6794534 ACTTTTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (22 bp):
ACTAATTAATGAAAAACAATGC
Found at i:6802225 original size:14 final size:15
Alignment explanation
Indices: 6802180--6802226 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
6802170 TTTTGGTAGC
6802180 TTTG-GATTGTGAAAT
1 TTTGAGATT-TGAAAT
*
6802195 TATTGAGATTTGGAAT
1 T-TTGAGATTTGAAAT
6802211 TTTGA-ATTTGAAAT
1 TTTGAGATTTGAAAT
6802225 TT
1 TT
6802227 CCTCACCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.36
15 5 0.18
16 9 0.32
17 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (15 bp):
TTTGAGATTTGAAAT
Found at i:6815095 original size:74 final size:73
Alignment explanation
Indices: 6814974--6815123 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 73
6814964 ATTAAAGGTG
6814974 TTCCCAAATTGGTTTACATGTCTAGTTCTACTGATAAAATCCAATTTCATTGATAATATAATTTG
1 TTCCCAAATTGGTTTACATGTCTAGTTCTACTGATAAAATCCAATTTCATTGATAATATAA-TTG
6815039 AATCCTTGT
65 AATCCTTGT
6815048 TTCCCAAATTGGTTTACATGTCTAGTTCTACTGATAAAATCCAATTTCATTGATAATATAATTGA
1 TTCCCAAATTGGTTTACATGTCTAGTTCTACTGATAAAATCCAATTTCATTGATAATATAATTGA
6815113 ATCCTTGT
66 ATCCTTGT
6815121 TTC
1 TTC
6815124 TGTTTGATAC
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 15 0.20
74 61 0.80
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (73 bp):
TTCCCAAATTGGTTTACATGTCTAGTTCTACTGATAAAATCCAATTTCATTGATAATATAATTGA
ATCCTTGT
Found at i:6820836 original size:15 final size:15
Alignment explanation
Indices: 6820816--6820844 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6820806 TCAAAGAAGA
6820816 TGATTTTCCCATCTT
1 TGATTTTCCCATCTT
6820831 TGATTTTCCCATCT
1 TGATTTTCCCATCT
6820845 GCAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.52
Consensus pattern (15 bp):
TGATTTTCCCATCTT
Found at i:6821538 original size:22 final size:24
Alignment explanation
Indices: 6821512--6821565 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
6821502 AATTATTCAT
6821512 TAAAAAATAAAATTT-TAATTTT-A
1 TAAAAAAT-AAATTTATAATTTTGA
*
6821535 -AAAAAATATATTTATAATTTTGA
1 TAAAAAATAAATTTATAATTTTGA
6821558 TAAAAAAT
1 TAAAAAAT
6821566 TATGTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 14 0.52
23 1 0.04
24 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAAAAATAAATTTATAATTTTGA
Found at i:6821814 original size:2 final size:2
Alignment explanation
Indices: 6821807--6821834 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6821797 ATCCCTCTTT
6821807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6821835 ATGGTATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6823432 original size:39 final size:39
Alignment explanation
Indices: 6823389--6823466 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
6823379 ATAACTAAAC
* * *
6823389 AAATGTATTTAAAGGGTTTTGGTGAACTTTTGAACAATT
1 AAATGCATTTAAAGAGTTTTGGTGAACATTTGAACAATT
*
6823428 AAATGCATTTGAAGAGTTTTGGTGAACATTTGAACAATT
1 AAATGCATTTAAAGAGTTTTGGTGAACATTTGAACAATT
6823467 TTAATATAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (39 bp):
AAATGCATTTAAAGAGTTTTGGTGAACATTTGAACAATT
Found at i:6824915 original size:16 final size:16
Alignment explanation
Indices: 6824896--6824928 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6824886 TGAATAAATA
*
6824896 TGTGTATGTGCATGTG
1 TGTGCATGTGCATGTG
6824912 TGTGCATGTGCATGTG
1 TGTGCATGTGCATGTG
6824928 T
1 T
6824929 CAGACGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.42
Consensus pattern (16 bp):
TGTGCATGTGCATGTG
Found at i:6827281 original size:15 final size:15
Alignment explanation
Indices: 6827261--6827290 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6827251 ATTAATCATG
6827261 AAAATTAAATATATA
1 AAAATTAAATATATA
*
6827276 AAAATTAATTATATA
1 AAAATTAAATATATA
6827291 TATGAAAATT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATTAAATATATA
Found at i:6827291 original size:19 final size:20
Alignment explanation
Indices: 6827263--6827305 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6827253 TAATCATGAA
6827263 AATTAAATATAT-AAAAATT
1 AATTAAATATATGAAAAATT
* *
6827282 AATTATATATATGAAAATTT
1 AATTAAATATATGAAAAATT
6827302 AATT
1 AATT
6827306 TTTACGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AATTAAATATATGAAAAATT
Found at i:6835462 original size:10 final size:11
Alignment explanation
Indices: 6835442--6835511 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 11
6835432 AAAATTATTT
6835442 TTAATAATTAA
1 TTAATAATTAA
6835453 TTAA-AATTAA
1 TTAATAATTAA
*
6835463 TTTAATAAGTAA
1 -TTAATAATTAA
*
6835475 TTGATTAATTGAA
1 TT-AATAATT-AA
* *
6835488 TTAA-ATTTAT
1 TTAATAATTAA
6835498 TTAATAAATTAA
1 TTAAT-AATTAA
6835510 TT
1 TT
6835512 CCATTAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
10 11 0.24
11 13 0.29
12 17 0.38
13 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (11 bp):
TTAATAATTAA
Found at i:6835469 original size:22 final size:23
Alignment explanation
Indices: 6835432--6835476 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
6835422 AAATTTTTAA
* *
6835432 AAAATTATTTTTAATAATTAATT
1 AAAATTATATTTAATAAGTAATT
6835455 AAAATTA-ATTTAATAAGTAATT
1 AAAATTATATTTAATAAGTAATT
6835477 GATTAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTATATTTAATAAGTAATT
Found at i:6836073 original size:22 final size:22
Alignment explanation
Indices: 6836046--6836089 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6836036 TTTATTGGAT
6836046 TTTTATATCTAATAAA-TTAAAA
1 TTTTATATCTAA-AAATTTAAAA
*
6836068 TTTTATATTTAAAAATTTAAAA
1 TTTTATATCTAAAAATTTAAAA
6836090 AAATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTATATCTAAAAATTTAAAA
Found at i:6839005 original size:26 final size:24
Alignment explanation
Indices: 6838950--6839058 Score: 92
Period size: 26 Copynumber: 4.2 Consensus size: 24
6838940 TTAGTATTTG
*
6838950 TATTTTTATTATATATATAGTAAATA
1 TATTTTTATTAAATA-ATA-TAAATA
6838976 TATTTTTATTAAATAATATAAATTA
1 TATTTTTATTAAATAATATAAA-TA
* * * *
6839001 TTATTTTAAATTAAACAAAATTAATA
1 -TATTTT-TATTAAATAATATAAATA
*
6839027 TATTTTTATTTAAAATATATATTAATA
1 TATTTTTA-TT-AAATA-ATATAAATA
6839054 TATTT
1 TATTT
6839059 GTAAAAAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
24 5 0.07
25 13 0.19
26 26 0.38
27 25 0.36
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TATTTTTATTAAATAATATAAATA
Found at i:6839030 original size:25 final size:25
Alignment explanation
Indices: 6838984--6839063 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
6838974 TATATTTTTA
*
6838984 TTAAA-TAATATAAATT-AT-TATT
1 TTAAATTAAAATAAATTAATATATT
6839006 TTAAATTAAACA-AAATTAATATATT
1 TTAAATTAAA-ATAAATTAATATATT
* *
6839031 TTTATTTAAAATATATATTAATATATT
1 TTAAATTAAAATA-A-ATTAATATATT
6839058 TGTAAA
1 T-TAAA
6839064 AAATTACATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 5 0.11
23 8 0.18
24 4 0.09
25 13 0.29
26 1 0.02
27 12 0.27
28 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (25 bp):
TTAAATTAAAATAAATTAATATATT
Found at i:6839516 original size:12 final size:13
Alignment explanation
Indices: 6839496--6839524 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6839486 TTTTAAACTC
6839496 AAACAAAAAAACA
1 AAACAAAAAAACA
6839509 AAAC-AAAAAACA
1 AAACAAAAAAACA
6839521 AAAC
1 AAAC
6839525 GCTCGTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAAAAAAACA
Found at i:6842227 original size:14 final size:15
Alignment explanation
Indices: 6842202--6842233 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
6842192 TTGTGAATAA
6842202 ATTTAGTTTTTATTT
1 ATTTAGTTTTTATTT
6842217 ATTTA-TTTTTATTT
1 ATTTAGTTTTTATTT
6842231 ATT
1 ATT
6842234 ATAATCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
ATTTAGTTTTTATTT
Found at i:6849456 original size:41 final size:41
Alignment explanation
Indices: 6849399--6849479 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
6849389 TCTTCAGGAG
*
6849399 AAATGGAATCTATTTCCATA-GAGTTTTCTTAATTAAACATA
1 AAATGGAATCTATTTCCA-ACCAGTTTTCTTAATTAAACATA
*
6849440 AAATGGAATCTATTTCCAACCAGTTTTGTTAATTAAACAT
1 AAATGGAATCTATTTCCAACCAGTTTTCTTAATTAAACAT
6849480 GACTGACAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (41 bp):
AAATGGAATCTATTTCCAACCAGTTTTCTTAATTAAACATA
Found at i:6849977 original size:22 final size:22
Alignment explanation
Indices: 6849948--6850000 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
6849938 GATATTTTTA
6849948 AATA-TTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
6849969 AATATTTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
6849991 AATATTTTAT
1 AATATTTTAT
6850001 TAATTTCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:6851324 original size:20 final size:19
Alignment explanation
Indices: 6851279--6851321 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6851269 ATATTGTCTA
*
6851279 TATTTAATAAATTAATTTT
1 TATTTAATAAATAAATTTT
6851298 TATTTAATAATATAAA-TTT
1 TATTTAATAA-ATAAATTTT
6851317 TATTT
1 TATTT
6851322 TAAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTAATAAATAAATTTT
Found at i:6852353 original size:16 final size:16
Alignment explanation
Indices: 6852344--6852377 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6852334 ATTTAATTTT
6852344 AAATCAATTTAGATTC
1 AAATCAATTTAGATTC
* *
6852360 AAATCAATATGGATTC
1 AAATCAATTTAGATTC
6852376 AA
1 AA
6852378 TCGAGTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (16 bp):
AAATCAATTTAGATTC
Found at i:6858564 original size:16 final size:16
Alignment explanation
Indices: 6858543--6858576 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6858533 CTGTTGTGAT
6858543 CAATGAAAGCTGATTC
1 CAATGAAAGCTGATTC
6858559 CAATGAAAGCTGATTC
1 CAATGAAAGCTGATTC
6858575 CA
1 CA
6858577 GTACTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (16 bp):
CAATGAAAGCTGATTC
Found at i:6859584 original size:31 final size:33
Alignment explanation
Indices: 6859546--6859619 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
6859536 TATATTTTAT
**
6859546 ATTTTTATATTAAAATAAATTAT-AATATAT-A
1 ATTTTTATATTAAAATAAAGCATAAATATATAA
*
6859577 ATTTTTATA-TAAAATACAGCATAAATATATAA
1 ATTTTTATATTAAAATAAAGCATAAATATATAA
*
6859609 ATTTTAATATT
1 ATTTTTATATT
6859620 TTATACTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.28
31 16 0.44
32 9 0.25
33 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (33 bp):
ATTTTTATATTAAAATAAAGCATAAATATATAA
Found at i:6860150 original size:28 final size:30
Alignment explanation
Indices: 6860090--6860162 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
6860080 TTATTATTAA
* * *
6860090 TTTTTTATTTTATCTCACTAGGCTAGTGTT
1 TTTTTTTTTTTATTTCACTAGGCTAGTGCT
*
6860120 TTTTTTTTTTTATTTCATTAGGCT-G-GCT
1 TTTTTTTTTTTATTTCACTAGGCTAGTGCT
*
6860148 TTTTTTTTTTAATTT
1 TTTTTTTTTTTATTT
6860163 AATTTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 16 0.42
29 1 0.03
30 21 0.55
ACGTcount: A:0.14, C:0.10, G:0.11, T:0.66
Consensus pattern (30 bp):
TTTTTTTTTTTATTTCACTAGGCTAGTGCT
Found at i:6860759 original size:16 final size:17
Alignment explanation
Indices: 6860740--6860771 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6860730 AGTTATTATT
6860740 TAACATATTA-ATTTAA
1 TAACATATTATATTTAA
6860756 TAACATATTATATTTA
1 TAACATATTATATTTA
6860772 TATATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TAACATATTATATTTAA
Found at i:6860779 original size:28 final size:27
Alignment explanation
Indices: 6860744--6860797 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
6860734 ATTATTTAAC
6860744 ATATTAATTTAATAACAT-A-TTATATTT
1 ATATTAA-TTAA-AACATAATTTATATTT
6860771 ATATATAATTAAAACATAATTTATATT
1 ATAT-TAATTAAAACATAATTTATATT
6860798 AAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 5 0.21
27 9 0.38
28 10 0.42
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTAATTAAAACATAATTTATATTT
Found at i:6861044 original size:23 final size:23
Alignment explanation
Indices: 6860992--6861044 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
6860982 CCATGTGGCT
* *
6860992 TCCTATTTGGTTCATTTTCATTT
1 TCCTTTTTGGTTCATTTTCATTA
* *
6861015 TCATTTTTGGTTCTTTTTC-TTGA
1 TCCTTTTTGGTTCATTTTCATT-A
6861038 TCCTTTT
1 TCCTTTT
6861045 ATTTTTAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.64
Consensus pattern (23 bp):
TCCTTTTTGGTTCATTTTCATTA
Found at i:6861439 original size:21 final size:22
Alignment explanation
Indices: 6861391--6861434 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6861381 TGAGAAAGCA
6861391 AAAGTCTTTCACTCATTTTTCT
1 AAAGTCTTTCACTCATTTTTCT
6861413 AAAGTC-TTCTACTCATTTTTCT
1 AAAGTCTTTC-ACTCATTTTTCT
6861435 TAGTCATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (22 bp):
AAAGTCTTTCACTCATTTTTCT
Found at i:6867235 original size:13 final size:14
Alignment explanation
Indices: 6867219--6867250 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6867209 TTGACATTAA
6867219 ATATTATATTTT-T
1 ATATTATATTTTAT
6867232 ATATT-TATTTTAT
1 ATATTATATTTTAT
6867245 ATATTA
1 ATATTA
6867251 AAAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTATATTTTAT
Found at i:6871800 original size:10 final size:10
Alignment explanation
Indices: 6871785--6871810 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6871775 ATAAATTATT
6871785 AATTTAATTA
1 AATTTAATTA
6871795 AATTTAATTA
1 AATTTAATTA
6871805 AATTTA
1 AATTTA
6871811 TAAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTTAATTA
Found at i:6884068 original size:21 final size:20
Alignment explanation
Indices: 6884013--6884070 Score: 53
Period size: 25 Copynumber: 2.6 Consensus size: 20
6884003 CTGTAATACA
6884013 TTTTATATTAGATAAAAAAAT
1 TTTTATATTA-ATAAAAAAAT
*
6884034 TTAATTATTGATTAATAAAATTAAT
1 TT--TTA-T-ATTAATAAAA-AAAT
6884059 TTTTATATTAAT
1 TTTTATATTAAT
6884071 TTTATTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
21 8 0.26
22 1 0.03
23 6 0.19
24 7 0.23
25 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTATATTAATAAAAAAAT
Found at i:6884191 original size:18 final size:16
Alignment explanation
Indices: 6884151--6884193 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
6884141 GAATATAAAT
*
6884151 AAATTATTATTTACAA
1 AAATTATAATTTACAA
*
6884167 AAGTTATAATTATACAAA
1 AAATTATAATT-TAC-AA
6884185 AAATTATAA
1 AAATTATAA
6884194 ATATTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
17 3 0.14
18 10 0.45
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (16 bp):
AAATTATAATTTACAA
Found at i:6884578 original size:19 final size:19
Alignment explanation
Indices: 6884554--6884590 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6884544 CTAATAATGT
6884554 ATAAAATCTATACACTAAC
1 ATAAAATCTATACACTAAC
* *
6884573 ATAAAATTTATATACTAA
1 ATAAAATCTATACACTAA
6884591 TAGTGTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAATCTATACACTAAC
Found at i:6888656 original size:12 final size:13
Alignment explanation
Indices: 6888641--6888669 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6888631 TTAAAATTTC
6888641 AAAAAAAAAA-CT
1 AAAAAAAAAATCT
6888653 AAAAAAAAAATCT
1 AAAAAAAAAATCT
6888666 AAAA
1 AAAA
6888670 CGGTTCTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAATCT
Found at i:6888698 original size:10 final size:9
Alignment explanation
Indices: 6888680--6888744 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
6888670 CGGTTCTAAG
6888680 AAATTTTTA
1 AAATTTTTA
6888689 AAACTTTTTA
1 AAA-TTTTTA
*
6888699 AAATATTTCA
1 AAAT-TTTTA
*
6888709 AAAGTTTTAA
1 AAA-TTTTTA
* *
6888719 AAATTCTAA
1 AAATTTTTA
6888728 AAACTTTTT-
1 AAA-TTTTTA
6888737 AAATTTTT
1 AAATTTTT
6888745 TTTAAATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 5 0.11
9 15 0.32
10 26 0.55
11 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (9 bp):
AAATTTTTA
Found at i:6888716 original size:20 final size:20
Alignment explanation
Indices: 6888688--6888739 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
6888678 AGAAATTTTT
*
6888688 AAAACTTTTTAAAATATT-TC
1 AAAACTTTTTAAAA-ATTCTA
*
6888708 AAAA-GTTTTAAAAATTCTA
1 AAAACTTTTTAAAAATTCTA
6888727 AAAACTTTTTAAA
1 AAAACTTTTTAAA
6888740 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.11
19 13 0.48
20 11 0.41
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAACTTTTTAAAAATTCTA
Found at i:6889164 original size:24 final size:25
Alignment explanation
Indices: 6889110--6889180 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
6889100 TTTTTTAACA
* *
6889110 ATTTTTGAACTTTTAAAATTATCAT
1 ATTTTTTAATTTTTAAAATTATCAT
*
6889135 AATTTTTT-ATTTTTAAAATATTTCAT
1 -ATTTTTTAATTTTTAAAAT-TATCAT
6889161 -TTTTTTAATTTTTATAAATT
1 ATTTTTTAATTTTTA-AAATT
6889181 TTAAAAACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.15
25 18 0.46
26 15 0.38
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (25 bp):
ATTTTTTAATTTTTAAAATTATCAT
Found at i:6889317 original size:10 final size:10
Alignment explanation
Indices: 6889167--6889317 Score: 67
Period size: 10 Copynumber: 14.6 Consensus size: 10
6889157 TCATTTTTTT
*
6889167 AATTTTTATA
1 AATTTTTAAA
6889177 AA-TTTTAAA
1 AATTTTTAAA
*
6889186 AACTTTT--A
1 AATTTTTAAA
* *
6889194 AATTGGTTTTAG
1 AATT--TTTAAA
*
6889206 AATTTTTTAA
1 AATTTTTAAA
6889216 AATTTTTCAAA
1 AATTTTT-AAA
** *
6889227 AAAATTTCAA
1 AATTTTTAAA
6889237 AATTGTTTATAA
1 AATT-TTTA-AA
6889249 AA-TTTTAAA
1 AATTTTTAAA
***
6889258 AATTCTTTTTGG
1 AA-T-TTTTAAA
* *
6889270 AATTTTGAAG
1 AATTTTTAAA
6889280 AATTTTTAAA
1 AATTTTTAAA
*
6889290 ATTTTTTAAA
1 AATTTTTAAA
6889300 GAATTTTTAAAA
1 -AATTTTT-AAA
6889312 AATTTT
1 AATTTT
6889318 GAATTGTTAA
Statistics
Matches: 107, Mismatches: 21, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
8 4 0.04
9 12 0.11
10 50 0.47
11 24 0.22
12 17 0.16
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:6889317 original size:21 final size:20
Alignment explanation
Indices: 6889209--6889317 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 20
6889199 GTTTTAGAAT
*
6889209 TTTTTAAAATTTTTCAAAAAA
1 TTTTAAAAATTTTT-AAAAAA
* * *
6889230 ATTTCAAAATTGTTTATAAAA
1 TTTTAAAAATT-TTTAAAAAA
****
6889251 TTTTAAAAATTCTTTTTGGAA
1 TTTTAAAAATT-TTTAAAAAA
* **
6889272 TTTTGAAGAATTTTTAAAATT
1 TTTT-AAAAATTTTTAAAAAA
6889293 TTTTAAAGAATTTTTAAAAAA
1 TTTTAAA-AATTTTTAAAAAA
6889314 TTTT
1 TTTT
6889318 GAATTGTTAA
Statistics
Matches: 66, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
20 2 0.03
21 55 0.83
22 9 0.14
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTAAAAATTTTTAAAAAA
Found at i:6890652 original size:11 final size:11
Alignment explanation
Indices: 6890633--6890678 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
6890623 AAATTTAACT
*
6890633 TTTTTATATAA
1 TTTTAATATAA
6890644 TTTTAATATAA
1 TTTTAATATAA
6890655 TTTTTAATAT-A
1 -TTTTAATATAA
*
6890666 TTTAAATA-AA
1 TTTTAATATAA
6890676 TTT
1 TTT
6890679 AGATATAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 11 0.35
11 11 0.35
12 9 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAATATAA
Found at i:6890659 original size:12 final size:12
Alignment explanation
Indices: 6890632--6890665 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
6890622 GAAATTTAAC
*
6890632 TTTTTTATATAA
1 TTTTTAATATAA
6890644 -TTTTAATATAA
1 TTTTTAATATAA
6890655 TTTTTAATATA
1 TTTTTAATATA
6890666 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTAATATAA
Found at i:6890677 original size:21 final size:23
Alignment explanation
Indices: 6890623--6890678 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
6890613 TTGGTTTTTG
* *
6890623 AAATTTAACTTTTTTATATAATTT
1 AAATATAA-TTTTTAATATAATTT
*
6890647 TAATATAATTTTTAATAT-ATTT
1 AAATATAATTTTTAATATAATTT
6890669 AAATA-AATTT
1 AAATATAATTT
6890679 AGATATAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.18
22 8 0.29
23 9 0.32
24 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATATAATTTTTAATATAATTT
Found at i:6891374 original size:20 final size:21
Alignment explanation
Indices: 6891349--6891388 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
6891339 TCTCTTTTTT
*
6891349 TTTTTTTTCTA-ATTTTTAAA
1 TTTTTTTTCAAGATTTTTAAA
6891369 TTTTTTTTCAAGATTTTTAA
1 TTTTTTTTCAAGATTTTTAA
6891389 TTGGACGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTTTTTCAAGATTTTTAAA
Found at i:6906862 original size:20 final size:20
Alignment explanation
Indices: 6906838--6906878 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6906828 AAAAAAAATA
*
6906838 AAAAAATAAAAAAAAGCAGAG
1 AAAAAA-AAAAGAAAGCAGAG
*
6906859 AAAAAAAAAAGAAAGGAGAG
1 AAAAAAAAAAGAAAGCAGAG
6906879 TTGGTTGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAGAAAGCAGAG
Found at i:6913922 original size:25 final size:25
Alignment explanation
Indices: 6913894--6913957 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
6913884 TATATTTATA
*
6913894 TTATATTTTATATAAAA-ATTATTT
1 TTATATTTTATATAAAATATAATTT
* *
6913918 GTTATAATTCATATAAAATATAATTT
1 -TTATATTTTATATAAAATATAATTT
6913944 TT-TATTTTAT-TAAA
1 TTATATTTTATATAAA
6913958 TTTATATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 4 0.12
24 6 0.18
25 17 0.52
26 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTATATTTTATATAAAATATAATTT
Found at i:6914022 original size:13 final size:13
Alignment explanation
Indices: 6913973--6914028 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
6913963 ATATAATTAT
6913973 TATTATAATTTTAA
1 TATTAT-ATTTTAA
*
6913987 -ATTATATCATTTTA
1 TATTATAT--TTTAA
*
6914001 TATTTTATTTTAA
1 TATTATATTTTAA
6914014 TATTATATTTATAA
1 TATTATATTT-TAA
6914028 T
1 T
6914029 GTATTATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.06
13 18 0.53
14 8 0.24
15 6 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATATTTTAA
Found at i:6915419 original size:2 final size:2
Alignment explanation
Indices: 6915414--6915441 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6915404 AAAAGTAAAT
6915414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6915442 AATGACTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6925118 original size:41 final size:41
Alignment explanation
Indices: 6925061--6925144 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
6925051 CAGCTAGCAT
*
6925061 AGATCTTTTGGTCCAAATATATAACTATTTTTTAAAATTGG
1 AGATCTTTTGGTCCAAATATATAACTATTTTTCAAAATTGG
* *
6925102 AGATCTTTTGGTCCAAATATATACCTATTTTTCAAGATTGG
1 AGATCTTTTGGTCCAAATATATAACTATTTTTCAAAATTGG
6925143 AG
1 AG
6925145 GCATTCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (41 bp):
AGATCTTTTGGTCCAAATATATAACTATTTTTCAAAATTGG
Found at i:6932345 original size:8 final size:8
Alignment explanation
Indices: 6932332--6932403 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 8
6932322 CTATGCTTGA
6932332 AAAAAAAG
1 AAAAAAAG
6932340 AAAAAAATG
1 AAAAAAA-G
6932349 AGAAAAAATG
1 A-AAAAAA-G
*
6932359 AAAAAATG
1 AAAAAAAG
*
6932367 -AAAAATG
1 AAAAAAAG
*
6932374 ATGAAAAA-
1 A-AAAAAAG
*
6932382 AAAACAA-
1 AAAAAAAG
6932389 AAAAAAAG
1 AAAAAAAG
6932397 AAAAAAA
1 AAAAAAA
6932404 TTGAAAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
7 17 0.32
8 16 0.30
9 11 0.21
10 9 0.17
ACGTcount: A:0.81, C:0.01, G:0.11, T:0.07
Consensus pattern (8 bp):
AAAAAAAG
Found at i:6932346 original size:10 final size:10
Alignment explanation
Indices: 6932329--6932411 Score: 75
Period size: 10 Copynumber: 8.7 Consensus size: 10
6932319 GTACTATGCT
6932329 TGAAAAAAAA
1 TGAAAAAAAA
6932339 -G-AAAAAAA
1 TGAAAAAAAA
*
6932347 TGAGAAAAAA
1 TGAAAAAAAA
6932357 TG--AAAAAA
1 TGAAAAAAAA
**
6932365 TGAAAAATGA
1 TGAAAAAAAA
6932375 TGAAAAAAAA
1 TGAAAAAAAA
**
6932385 ACAAAAAAAA
1 TGAAAAAAAA
* *
6932395 AGAAAAAAAT
1 TGAAAAAAAA
6932405 TGAAAAA
1 TGAAAAA
6932412 TGAAGACTCA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
8 15 0.25
9 2 0.03
10 42 0.71
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.10
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:6932365 original size:18 final size:18
Alignment explanation
Indices: 6932341--6932382 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6932331 AAAAAAAAGA
6932341 AAAAAATGAGAAAA-AATG
1 AAAAAATGA-AAAATAATG
*
6932359 AAAAAATGAAAAATGATG
1 AAAAAATGAAAAATAATG
6932377 AAAAAA
1 AAAAAA
6932383 AAACAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (18 bp):
AAAAAATGAAAAATAATG
Found at i:6933504 original size:41 final size:41
Alignment explanation
Indices: 6933427--6933636 Score: 305
Period size: 41 Copynumber: 5.1 Consensus size: 41
6933417 ATGATTGTCA
* *
6933427 AGGAGCAATTTACTTTTTCAAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTAC--TTTCCAAAGTCGTGGTGCCTCTGTTTAG
6933470 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* *
6933511 AGGAGCAATTTACTTT-CAAAGTCATGGTGCTTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* *
6933551 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* * * *
6933592 AGGAGCAATTTACTTTTCAAAGTCGTTGAGCCTCCGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
6933633 AGGA
1 AGGA
6933637 ACTTTGGTAA
Statistics
Matches: 155, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
40 37 0.24
41 105 0.68
43 13 0.08
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:6933557 original size:81 final size:82
Alignment explanation
Indices: 6933427--6933615 Score: 308
Period size: 81 Copynumber: 2.3 Consensus size: 82
6933417 ATGATTGTCA
*
6933427 AGGAGCAATTTACTTTTTCAAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG
1 AGGAGCAATTTAC-TTTTC-AAAGTCATGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG
6933492 TCGTGGTGCCTCTGTTTAG
64 TCGTGGTGCCTCTGTTTAG
* * * *
6933511 AGGAGCAATTTAC-TTTCAAAGTCATGGTGCTTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
1 AGGAGCAATTTACTTTTCAAAGTCATGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
6933575 GTGGTGCCTCTGTTTAG
66 GTGGTGCCTCTGTTTAG
6933592 AGGAGCAATTTACTTTTCAAAGTC
1 AGGAGCAATTTACTTTTCAAAGTC
6933616 GTTGAGCCTC
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
81 72 0.73
82 14 0.14
84 13 0.13
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (82 bp):
AGGAGCAATTTACTTTTCAAAGTCATGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
GTGGTGCCTCTGTTTAG
Found at i:6933651 original size:1 final size:1
Alignment explanation
Indices: 6933645--6933713 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
6933635 GAACTTTGGT
* * * * * * *
6933645 AAAAAAAAAAAAAAACAAAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAATACAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6933710 AAAA
1 AAAA
6933714 TGACAATATT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.90, C:0.09, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:6933674 original size:21 final size:21
Alignment explanation
Indices: 6933645--6933710 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
6933635 GAACTTTGGT
6933645 AAAAAA-AAAAAAAAAC-A--
1 AAAAAACAAAAAAAAACAAAA
6933662 AAAAAACAAAAAAAAACAAAA
1 AAAAAACAAAAAAAAACAAAA
*
6933683 AAAAAACAAAAAAATACAAAA
1 AAAAAACAAAAAAAAACAAAA
6933704 AACAAAA
1 AA-AAAA
6933711 AAATGACAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 6 0.14
18 10 0.23
19 1 0.02
21 22 0.51
22 4 0.09
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (21 bp):
AAAAAACAAAAAAAAACAAAA
Found at i:6933719 original size:11 final size:10
Alignment explanation
Indices: 6933645--6933705 Score: 83
Period size: 10 Copynumber: 6.3 Consensus size: 10
6933635 GAACTTTGGT
6933645 AAAAAA-AAA
1 AAAAAACAAA
6933654 AAAAAAC--A
1 AAAAAACAAA
6933662 AAAAAACAAA
1 AAAAAACAAA
6933672 AAAAAACAAAA
1 AAAAAAC-AAA
6933683 AAAAAACAAA
1 AAAAAACAAA
*
6933693 AAAATACAAA
1 AAAAAACAAA
6933703 AAA
1 AAA
6933706 CAAAAAAATG
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
8 8 0.17
9 6 0.13
10 23 0.49
11 10 0.21
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:6933974 original size:19 final size:19
Alignment explanation
Indices: 6933946--6933990 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
6933936 TGTATATAGT
*
6933946 TTATTATATTA-TTATTATA
1 TTATTTTATTATTTATT-TA
6933965 TTATTTTATTATTTATTTA
1 TTATTTTATTATTTATTTA
6933984 TTATTTT
1 TTATTTT
6933991 TTTTGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTATTATTTATTTA
Found at i:6933989 original size:11 final size:12
Alignment explanation
Indices: 6933945--6933987 Score: 63
Period size: 11 Copynumber: 3.7 Consensus size: 12
6933935 ATGTATATAG
6933945 TTTATTATATTA
1 TTTATTATATTA
6933957 -TTATTATATTA
1 TTTATTATATTA
6933968 TTTTATTAT-TTA
1 -TTTATTATATTA
6933980 TTTATTAT
1 TTTATTAT
6933988 TTTTTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 19 0.66
12 3 0.10
13 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:6935079 original size:18 final size:18
Alignment explanation
Indices: 6935022--6935096 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 18
6935012 TTATTTAATA
6935022 TTTTTTATCTTTATCTTATTT
1 TTTTTTATC-TT-T-TTATTT
* *
6935043 TTATTTT-T-GTTTTACTT
1 TT-TTTTATCTTTTTATTT
*
6935060 TTCTTTA-CTTTTTATTT
1 TTTTTTATCTTTTTATTT
*
6935077 TTTTTTATTTTTTTATTT
1 TTTTTTATCTTTTTATTT
6935095 TT
1 TT
6935097 CTATTTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
16 3 0.07
17 20 0.47
18 12 0.28
19 1 0.02
21 3 0.07
22 4 0.09
ACGTcount: A:0.12, C:0.07, G:0.01, T:0.80
Consensus pattern (18 bp):
TTTTTTATCTTTTTATTT
Found at i:6935081 original size:10 final size:10
Alignment explanation
Indices: 6935040--6935107 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 10
6935030 CTTTATCTTA
6935040 TTTTTATTTT
1 TTTTTATTTT
*
6935050 TGTTTTACTTT
1 T-TTTTATTTT
*
6935061 TCTTTACTTTT
1 TTTTTA-TTTT
6935072 TATTTT-TTTT
1 T-TTTTATTTT
6935082 TATTTT-TTTAT
1 T-TTTTATTT-T
6935093 TTTTCTATTTT
1 TTTT-TATTTT
6935104 TTTT
1 TTTT
6935108 CTAAATAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
10 21 0.44
11 21 0.44
12 6 0.12
ACGTcount: A:0.10, C:0.06, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:6935089 original size:17 final size:17
Alignment explanation
Indices: 6935020--6935107 Score: 63
Period size: 18 Copynumber: 5.0 Consensus size: 17
6935010 ATTTATTTAA
* *
6935020 TATTTTTTATCTTTATCT
1 TATTTTTTAT-TTTTTTT
6935038 TA-TTTTTATTTTTGTTT
1 TATTTTTTATTTTT-TTT
* **
6935055 TACTTTTCT-TTACTTTT
1 TA-TTTTTTATTTTTTTT
*
6935072 TATTTTTTTTTATTTTTT
1 TATTTTTTATT-TTTTTT
6935090 TATTTTTCTATTTTTTTT
1 TATTTTT-TATTTTTTTT
6935108 CTAAATAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 8 0.15
17 18 0.33
18 22 0.40
19 7 0.13
ACGTcount: A:0.12, C:0.07, G:0.01, T:0.80
Consensus pattern (17 bp):
TATTTTTTATTTTTTTT
Found at i:6935105 original size:16 final size:16
Alignment explanation
Indices: 6935076--6935106 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6935066 ACTTTTTATT
*
6935076 TTTTTTTATTTTTTTA
1 TTTTTCTATTTTTTTA
6935092 TTTTTCTATTTTTTT
1 TTTTTCTATTTTTTT
6935107 TCTAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTCTATTTTTTTA
Found at i:6935198 original size:59 final size:59
Alignment explanation
Indices: 6935113--6935779 Score: 598
Period size: 59 Copynumber: 11.0 Consensus size: 59
6935103 TTTTTCTAAA
** *
6935113 TAAAAATAAA-TTAAAAAAAAAGGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCT
1 TAAAAATAAATTTAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
6935171 TAAAAATAAATTTAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATAAATTTAAAAAAAAAATATTTTTGAGG---A----AAAGTTGAAAGTATCAATTTTCC
6935236 T
59 T
** ** ** *
6935237 TGGAAATCAAAGTTCCAAAAAAAAGGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAA-TTTAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* ** ** *
6935298 TGAAAATCAAGGTT--CCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAATTTAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
6935356 TAGAAATAAATTTTCAAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAA-TTT---AAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** *
6935419 TGGAAATCAAAGTTTCAAAGAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAA-TTT-AAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* ** *
6935481 TAAAAAGTAAATTTTCAAAAAAAAATATTTTTG-GGAAAAAGTCAAAAGTATCAATTTTTCT
1 TAAAAA-TAAA-TTTAAAAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCT
* * ***
6935542 TGAAGATCAAAATTT--CTGAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT--AAATTTAAAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* * * *
6935601 TAGAAATAAATTTTCAAGAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATTAATTTTCCT
1 TAAAAATAAA-TTT--A-AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * * * *
6935664 TGAAAATCAAGGTTT--CAAAAAAATATTCTTGCGGAAAAGTTAAAAGTATCAATTTTCCT
1 TAAAAAT-AA-ATTTAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * *
6935723 TAAAAATAAATTT-CCAAAAAAATATTTTTGGGGAAAAGTTGATAGTATCAATTTTCC
1 TAAAAATAAATTTAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
6935780 CTGCACAAGA
Statistics
Matches: 504, Mismatches: 72, Indels: 66
0.79 0.11 0.10
Matches are distributed among these distances:
57 8 0.02
58 99 0.20
59 103 0.20
60 6 0.01
61 78 0.15
62 58 0.12
63 88 0.17
64 12 0.02
65 1 0.00
66 28 0.06
67 3 0.01
68 20 0.04
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (59 bp):
TAAAAATAAATTTAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:6935580 original size:182 final size:174
Alignment explanation
Indices: 6935213--6935779 Score: 697
Period size: 183 Copynumber: 3.1 Consensus size: 174
6935203 GGAAAAGTTG
* *
6935213 AAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTCCAAAAAAAAGGATTTGTGAGGAAAAG
1 AAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAAAAGATTTGTGAGGAAAAG
* * * *
6935278 TTGAAAGTATCAATTTTCCTTGAAAATCAAGGTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAG
66 TTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTCAAAAAAATATTTTT-GGGAAAAGTTAAAAG
* *
6935343 TATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAAAAAAGATTTTTGAGGA
130 TATCAATTTTCCTT-GAAATAAAATTTC-----AAAAAAATATTTTTG-GGA
* *
6935395 AAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAGAAAAAATATTTTTGAGGAAAA
1 AAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAA-AAAAAAGATTTGTGAGGAAAA
* * *
6935460 GTTGAAAGTATCAATTTTCCTTAAAAAGTAAATTTTCAAAAAAAAATATTTTTGGGAAAAAGTCA
65 GTTGAAAGTATCAATTTTCCTTGAAAA-TAAAGTTTC--AAAAAAATATTTTTGGG-AAAAGTTA
* **
6935525 AAAGTATCAATTTTTCTTGAAGATCAAAATTTCTGAAAAATATTTTTAGGGA
126 AAAGTATCAATTTTCCTTGAA-AT-AAAATTTCAAAAAAATATTTTT-GGGA
* *
6935577 AAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAATTTTCAAGAAAAAAAAAGATTTGTGAGGAA
1 AAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTC---AAAAAAAAAGATTTGTGAGGAA
* * *
6935641 AAGTTGAAAGTATTAATTTTCCTTGAAAATCAAGGTTTCAAAAAAATATTCTTGCGGAAAAGTTA
63 AAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAGTTTCAAAAAAATATTTTTG-GGAAAAGTTA
*
6935706 AAAGTATCAATTTTCCTT-AAAAATAAATTTCCAAAAAAATATTTTTGGGGA
126 AAAGTATCAATTTTCCTTGAAATA-AAATTT-CAAAAAAATATTTTT-GGGA
*
6935757 AAAGTTGATAGTATCAATTTTCC
1 AAAGTTGAAAGTATCAATTTTCC
6935780 CTGCACAAGA
Statistics
Matches: 338, Mismatches: 32, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
178 1 0.00
179 7 0.02
180 41 0.12
181 45 0.13
182 89 0.26
183 95 0.28
184 9 0.03
185 6 0.02
186 38 0.11
187 7 0.02
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (174 bp):
AAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAAAAGATTTGTGAGGAAAAG
TTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTCAAAAAAATATTTTTGGGAAAAGTTAAAAGT
ATCAATTTTCCTTGAAATAAAATTTCAAAAAAATATTTTTGGGA
Found at i:6935599 original size:245 final size:240
Alignment explanation
Indices: 6935125--6935779 Score: 861
Period size: 245 Copynumber: 2.7 Consensus size: 240
6935115 AAAATAAATT
* * * *
6935125 AAAAAAAAAGGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTAAAA
1 AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
* ** *
6935188 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTCC
66 AAAAAATATTTTTGAGG---A----AAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTC
** * *
6935253 AAAAAAAAGGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAGGTTCCAAAA
122 AAAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTCCAAAA
*
6935318 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
186 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
*
6935373 AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAA
1 AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
6935438 GAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAGTAAATTTTCAAAAAA
66 -AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA-TAAA-TTTCAAAAAA
** * * * **
6935503 AAATATTTTTGGGAAAAAGTCAAAAGTATCAATTTTTCTTGAAGATCAAAATTTCTGAAAAATAT
128 AAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAAGTTCCAAAAAATAT
6935568 TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
191 TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
* * * *
6935618 GAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATCAAGGTTTC--A
1 AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
* * * *
6935681 AAAAAATATTCTTGCGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTC-CAAAAAAA
66 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAAA
*
6935745 TATTTTTGGGGAAAAGTTGATAGTATCAATTTTCC
131 TATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCC
6935780 CTGCACAAGA
Statistics
Matches: 365, Mismatches: 35, Indels: 23
0.86 0.08 0.05
Matches are distributed among these distances:
239 34 0.09
240 7 0.02
241 4 0.01
242 45 0.12
243 3 0.01
244 77 0.21
245 120 0.33
248 50 0.14
249 3 0.01
250 6 0.02
251 16 0.04
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (240 bp):
AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAAA
TATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTCCAAAAAATATTTTTA
GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
Found at i:6935700 original size:122 final size:120
Alignment explanation
Indices: 6935125--6935779 Score: 722
Period size: 122 Copynumber: 5.4 Consensus size: 120
6935115 AAAATAAATT
* * * * *
6935125 AAAAAAAAAGGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTAAAA
1 AAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTT--CA
* * *
6935188 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAA-GTTC
64 AAAAAATATTTTTG-GG---A----AAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAATTTTC
6935252 -
120 A
* * * *
6935252 CAAAAAAAAGGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAGGTTCCAA
1 AAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
6935316 AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
66 AAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC-A
* *
6935373 AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAA
1 AAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC--A
*
6935438 GAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAGTAAATTTTC-
64 -AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA-TAAATTTTCA
* * ** * * * **
6935497 -AAAAAAAAATATTTTTG-GGAAAAAGTCAAAAGTATCAATTTTTCTTGAAGATCAAAATTTCTG
1 AAAAAAAAAAGATTTGTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAA
6935560 AAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
65 AAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
* *
6935617 AGAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATCAAGGTTTCAA
1 A-AAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAA
* * *
6935682 AAAAATATTCTTGCGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAA-TTTC-
65 AAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
* * * * *
6935737 --CAAAAAAATATTTTTGGGGAAAAGTTGATAGTATCAATTTTCC
1 AAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCC
6935780 CTGCACAAGA
Statistics
Matches: 462, Mismatches: 47, Indels: 48
0.83 0.08 0.09
Matches are distributed among these distances:
117 37 0.08
118 3 0.01
119 42 0.09
120 44 0.10
121 56 0.12
122 103 0.22
123 54 0.12
124 1 0.00
125 45 0.10
126 23 0.05
127 52 0.11
128 2 0.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (120 bp):
AAAAAAAAAAGATTTGTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
AAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
Found at i:6936769 original size:66 final size:66
Alignment explanation
Indices: 6936637--6936772 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
6936627 ACTATAATCA
* * * *
6936637 ATAAGTTAATAAAAAAAAATTAAGACAAAAGTTATATGCTATAGATTATTATTTTGCCCAAAGAT
1 ATAAGTTAATAAAAAAAAATTAAGACAAAAGCTATATGCTATAGATTAGTAATTTGCACAAAGAT
6936702 T
66 T
*
6936703 ATAAGTTAAT-AAAAAAAATTTAGACCAAAAGCTATATG-TAATA-AGTTAGTAATTTG-ACAAA
1 ATAAGTTAATAAAAAAAAATTAAGA-CAAAAGCTATATGCT-ATAGA-TTAGTAATTTGCACAAA
6936764 TGATT
63 -GATT
6936769 ATAA
1 ATAA
6936773 CCAATTGGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
65 19 0.31
66 42 0.69
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (66 bp):
ATAAGTTAATAAAAAAAAATTAAGACAAAAGCTATATGCTATAGATTAGTAATTTGCACAAAGAT
T
Found at i:6938065 original size:26 final size:26
Alignment explanation
Indices: 6938029--6938079 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6938019 ATCAATATTA
* *
6938029 AAAAAAATTTTCAAATTTTTAAAATT
1 AAAAAAATTTTAAAAATTTTAAAATT
* *
6938055 AAAAAATTTTTAAAAATTTTGAAAT
1 AAAAAAATTTTAAAAATTTTAAAAT
6938080 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAAAAATTTTAAAAATTTTAAAATT
Found at i:6938071 original size:10 final size:10
Alignment explanation
Indices: 6938053--6938091 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
6938043 ATTTTTAAAA
6938053 TTAAAAAATT
1 TTAAAAAATT
*
6938063 TTTAAAAATT
1 TTAAAAAATT
* *
6938073 TTGAAATATT
1 TTAAAAAATT
6938083 TTAAAAAAT
1 TTAAAAAAT
6938092 AAAATATTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:6938094 original size:26 final size:27
Alignment explanation
Indices: 6938065--6938125 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
6938055 AAAAAATTTT
6938065 TAAAAATTTTGAAATA-TTTTAAAAAA
1 TAAAAATTTTGAAATATTTTTAAAAAA
*
6938091 T-AAAATATTTGAAATATTTTTAAAATA
1 TAAAAAT-TTTGAAATATTTTTAAAAAA
6938118 TAAAAATT
1 TAAAAATT
6938126 AAATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 5 0.16
26 10 0.32
27 11 0.35
28 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAAAATTTTGAAATATTTTTAAAAAA
Found at i:6938135 original size:33 final size:33
Alignment explanation
Indices: 6938057--6938158 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 33
6938047 TTAAAATTAA
* *
6938057 AAAAT-TTTTAAAAATTTTGAAATATTTTAAAAAAT
1 AAAATATTTGAAAAATTTTGAAA-A-TAT-AAAAAT
* *
6938092 AAAATATTTGAAATATTTTTAAAATATAAAAAT
1 AAAATATTTGAAAAATTTTGAAAATATAAAAAT
* * *
6938125 TAAATTTTTGAAAAATTTTGAAAATTTAAAAAT
1 AAAATATTTGAAAAATTTTGAAAATATAAAAAT
6938158 A
1 A
6938159 TCTAAAATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 34 0.61
34 2 0.04
35 6 0.11
36 14 0.25
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (33 bp):
AAAATATTTGAAAAATTTTGAAAATATAAAAAT
Found at i:6938169 original size:59 final size:58
Alignment explanation
Indices: 6938071--6938186 Score: 139
Period size: 59 Copynumber: 2.0 Consensus size: 58
6938061 TTTTTAAAAA
* *
6938071 TTTTGAAATATTTTAAAAAATAAAATATTTGAAATATTTTTAAAATATAAAAAT-TAAAT
1 TTTTGAAAAATTTTAAAAAATAAAATATCTGAAATATTTTT--AATATAAAAATCTAAAT
**
6938130 TTTTGAAAAATTTTGAAAATTTAAAAATATCT-AAA-ATTTTTAATATAAAAATCTAAA
1 TTTTGAAAAATTTT-AAAAAAT-AAAATATCTGAAATATTTTTAATATAAAAATCTAAA
6938187 AAACTAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
57 11 0.22
58 4 0.08
59 19 0.38
60 8 0.16
61 8 0.16
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (58 bp):
TTTTGAAAAATTTTAAAAAATAAAATATCTGAAATATTTTTAATATAAAAATCTAAAT
Found at i:6938199 original size:18 final size:18
Alignment explanation
Indices: 6938171--6938214 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6938161 TAAAATTTTT
*
6938171 AATATAAAAA-TCTAAAAA
1 AATAAAAAAATTC-AAAAA
*
6938189 ACTAAAAAAATTCAAAAA
1 AATAAAAAAATTCAAAAA
6938207 AATAAAAA
1 AATAAAAA
6938215 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (18 bp):
AATAAAAAAATTCAAAAA
Found at i:6938213 original size:16 final size:17
Alignment explanation
Indices: 6938174--6938235 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
6938164 AATTTTTAAT
*
6938174 ATAAAAATCT-AAAAAA
1 ATAAAAATTTCAAAAAA
* *
6938190 CTAAAAAAATTCAAAAAA
1 AT-AAAAATTTCAAAAAA
* *
6938208 ATAAAAATTTTAATAAA
1 ATAAAAATTTCAAAAAA
*
6938225 ATAAAATTTTC
1 ATAAAAATTTC
6938236 TTTAAATTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
16 1 0.03
17 27 0.77
18 7 0.20
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATTTCAAAAAA
Found at i:6938477 original size:19 final size:20
Alignment explanation
Indices: 6938455--6938495 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
6938445 AAATCCAAAG
6938455 AATTCAAAAAAT-TATGAAA
1 AATTCAAAAAATATATGAAA
*
6938474 AATTCAAAAAATATATTAAA
1 AATTCAAAAAATATATGAAA
6938494 AA
1 AA
6938496 ATTTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
AATTCAAAAAATATATGAAA
Found at i:6938741 original size:16 final size:15
Alignment explanation
Indices: 6938716--6938749 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6938706 AACTTCTTTA
*
6938716 ATTTT-TTTAAAAAT
1 ATTTTGTTTTAAAAT
6938730 ATTTTGTTTTAAAAT
1 ATTTTGTTTTAAAAT
6938745 ATTTT
1 ATTTT
6938750 ATAATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTGTTTTAAAAT
Found at i:6938778 original size:20 final size:19
Alignment explanation
Indices: 6938736--6938777 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6938726 AAATATTTTG
*
6938736 TTTTAAAATATTTTATAAT
1 TTTTAAAATATTTTAGAAT
6938755 TTTTGAAAATATTTTAG-AT
1 TTTT-AAAATATTTTAGAAT
6938774 TTTT
1 TTTT
6938778 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTAAAATATTTTAGAAT
Found at i:6939798 original size:75 final size:76
Alignment explanation
Indices: 6939709--6939851 Score: 164
Period size: 75 Copynumber: 1.9 Consensus size: 76
6939699 AGATATATGT
** * * *
6939709 TATAGGTTACTATTTAGACTAAAAGTTGTCGTCAA-ATATTAGTAAAAAGAAAAAGTTAGG-TCA
1 TATAGGTTACTATTTAGACTAAAAGTCATAGTCAATAGATTAATAAAAAGAAAAAGTT-GGATCA
6939772 AAGGGTCTAAGC
65 AAGGGTCTAAGC
* * * * * *
6939784 TATATGTTAGTATTTGGGCTAAAGGTCATAGTCAATAGATTAATAAAATGAAAAAGTTGGATCAA
1 TATAGGTTACTATTTAGACTAAAAGTCATAGTCAATAGATTAATAAAAAGAAAAAGTTGGATCAA
6939849 AGG
66 AGG
6939852 CTATACACTA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
75 29 0.53
76 26 0.47
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (76 bp):
TATAGGTTACTATTTAGACTAAAAGTCATAGTCAATAGATTAATAAAAAGAAAAAGTTGGATCAA
AGGGTCTAAGC
Found at i:6939915 original size:14 final size:13
Alignment explanation
Indices: 6939878--6939917 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
6939868 AGTTTTTGGG
6939878 CCAAAAGTTAAAA
1 CCAAAAGTTAAAA
6939891 CCAAAAGTTAAAA
1 CCAAAAGTTAAAA
*
6939904 CCAATGAGTTAAAA
1 CCAA-AAGTTAAAA
6939918 AATGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.57, C:0.15, G:0.10, T:0.17
Consensus pattern (13 bp):
CCAAAAGTTAAAA
Found at i:6943003 original size:18 final size:17
Alignment explanation
Indices: 6942970--6943008 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
6942960 ATTATTATTT
6942970 TATAAAAATCTAAAAAA
1 TATAAAAATCTAAAAAA
6942987 TATAAAAAT-TAATAAAAA
1 TATAAAAATCT-A-AAAAA
6943005 TATA
1 TATA
6943009 TAATTCGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TATAAAAATCTAAAAAA
Found at i:6944194 original size:18 final size:18
Alignment explanation
Indices: 6944171--6944215 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
6944161 TTAAAAATTG
6944171 AAATTATAAGT-ATAATAA
1 AAATTATAA-TAATAATAA
6944189 AAATTATAATAATAATAA
1 AAATTATAATAATAATAA
6944207 AATATTATA
1 AA-ATTATA
6944216 TTTATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.72
19 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATTATAATAATAATAA
Found at i:6946903 original size:20 final size:21
Alignment explanation
Indices: 6946865--6946903 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
6946855 GAATATGAAT
* *
6946865 TTAAATAAAATGATTGAATTA
1 TTAAATAAAATAATAGAATTA
6946886 TTAAA-AAAATAATAGAAT
1 TTAAATAAAATAATAGAAT
6946904 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (21 bp):
TTAAATAAAATAATAGAATTA
Found at i:6947110 original size:27 final size:26
Alignment explanation
Indices: 6947080--6947136 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
6947070 TAAGATAATT
6947080 TAATATCAT-TTAATTTAATTTTATTCA
1 TAATATCATATT-ATTTAATTTTA-TCA
* *
6947107 TAATATTATATTATTTTATTTTATCA
1 TAATATCATATTATTTAATTTTATCA
6947133 TAAT
1 TAAT
6947137 TTTGTGTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 18 0.67
28 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (26 bp):
TAATATCATATTATTTAATTTTATCA
Found at i:6948612 original size:29 final size:29
Alignment explanation
Indices: 6948574--6948664 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
6948564 AAACTATAGT
*
6948574 AAAATATTTAATGTGATATTTAAATTTTA
1 AAAATTTTTAATGTGATATTTAAATTTTA
* * *
6948603 AAAATTTTTAATAT-AGTATCTAAATTATA
1 AAAATTTTTAATGTGA-TATTTAAATTTTA
*
6948632 AATTTATTATTTAATGTGATATTTGAATATTTT
1 AA--AATT-TTTAATGTGATATTT-AA-ATTTT
6948665 TATTTGTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
28 1 0.02
29 25 0.53
31 3 0.06
32 11 0.23
33 3 0.06
34 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.51
Consensus pattern (29 bp):
AAAATTTTTAATGTGATATTTAAATTTTA
Found at i:6954107 original size:2 final size:2
Alignment explanation
Indices: 6954100--6954125 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6954090 CTCACATAAC
6954100 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
6954126 TAAATAGAAA
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:6954907 original size:23 final size:26
Alignment explanation
Indices: 6954881--6954941 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 26
6954871 ATGAAAAAAT
*
6954881 ATAAAAAAATA-ATATAATT-TAA-A
1 ATAAAAAAATATATAAAATTATAACA
6954904 AT-AAAAAATATATAAAATTGATAACA
1 ATAAAAAAATATATAAAATT-ATAACA
6954930 ATAAAAAAATAT
1 ATAAAAAAATAT
6954942 TTTATGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.25
23 9 0.28
25 3 0.09
26 3 0.09
27 9 0.28
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAAAAAAATATATAAAATTATAACA
Found at i:6954932 original size:26 final size:23
Alignment explanation
Indices: 6954884--6954941 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 23
6954874 AAAAAATATA
*
6954884 AAAAAATA-ATATAATTTAAAAT
1 AAAAAATATATAAAATTTAAAAT
6954906 AAAAAATATATAAAATTGATAACAAT
1 AAAAAATATATAAAATT--TAA-AAT
6954932 AAAAAA-ATAT
1 AAAAAATATAT
6954942 TTTATGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 8 0.26
23 7 0.23
25 7 0.23
26 9 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAAATATATAAAATTTAAAAT
Found at i:6960202 original size:16 final size:14
Alignment explanation
Indices: 6960168--6960210 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 14
6960158 GTTGGATTAT
6960168 TAATTTAAAATTTAA
1 TAATTT-AAATTTAA
6960183 TAATTTAAATTTAAAA
1 TAATTTAAATTT--AA
6960199 TAATTTAAATTT
1 TAATTTAAATTT
6960211 GATTACGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTTAAATTTAA
Found at i:6964617 original size:2 final size:2
Alignment explanation
Indices: 6964610--6964644 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6964600 TTACAGCAGA
6964610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6964645 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6964649 original size:2 final size:2
Alignment explanation
Indices: 6964644--6964678 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6964634 ATATATATAT
6964644 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6964679 CTTAATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6974930 original size:22 final size:21
Alignment explanation
Indices: 6974875--6974931 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
6974865 ATATTTATAA
6974875 ATAAATTTT-AATT-A-TTAT
1 ATAAATTTTAAATTAATTTAT
6974893 ATAAATTAATTAAATTAATTTAT
1 ATAAATT--TTAAATTAATTTAT
6974916 ATTAAATTTTAAATTA
1 A-TAAATTTTAAATTA
6974932 TGGTTATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.21
20 2 0.06
21 4 0.12
22 9 0.27
23 5 0.15
24 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAATTTTAAATTAATTTAT
Found at i:6975705 original size:190 final size:189
Alignment explanation
Indices: 6975372--6975744 Score: 550
Period size: 190 Copynumber: 2.0 Consensus size: 189
6975362 TTATCGAGGC
* * *
6975372 TATCCTCAAATGCACGATTTTTATAATATAAAAATTTTATTTTAATTAATATTTATTGTTTTGAA
1 TATCCTCAAATGCACGATTTTTACAATATAAAAATTTTATCTTAATTAATATTTATTGATTTGAA
*
6975437 TGATAAAAAATTTGATTTTTTTTAAATAAGATTTCGATATTAAATTTTGTGAATTAAAAAAATAA
66 TGATAAAAAATTTGATTTTTTTTAAATAAAATTTCGATATTAAATTTTGTGAATTAAAAAAATAA
* * * * * * * *
6975502 ACGTTTGAAAATTTTATTTTTTTATAAGATTTGATATAATTTGATTTTAAAATAGTCAAT
131 ACATTT-AAAAATTTATCTTCTTATAAAATCTGATATAATTTAATTTCAAAATAGTCAAT
* * *
6975562 TATCCTCAAATGCATGATTTTTACAATATACAAATTTTATCTTAATTAATATTTATTGATTTGAG
1 TATCCTCAAATGCACGATTTTTACAATATAAAAATTTTATCTTAATTAATATTTATTGATTTGAA
* *
6975627 TGATAAAAAATTTGATTTTTTTTAAATAAAATTTCGATTTTAAGTTTTGTGAA-TAAAAAAATAA
66 TGATAAAAAATTTGATTTTTTTTAAATAAAATTTCGATATTAAATTTTGTGAATTAAAAAAATAA
* *
6975691 ATATTTAAAAAATTTATCTTCTTATAAAATCTGATCTAATTTAATTTCAAAATA
131 ACATTT-AAAAATTTATCTTCTTATAAAATCTGATATAATTTAATTTCAAAATA
6975745 ATTCAAATTT
Statistics
Matches: 163, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
189 54 0.33
190 109 0.67
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (189 bp):
TATCCTCAAATGCACGATTTTTACAATATAAAAATTTTATCTTAATTAATATTTATTGATTTGAA
TGATAAAAAATTTGATTTTTTTTAAATAAAATTTCGATATTAAATTTTGTGAATTAAAAAAATAA
ACATTTAAAAATTTATCTTCTTATAAAATCTGATATAATTTAATTTCAAAATAGTCAAT
Found at i:6977172 original size:21 final size:21
Alignment explanation
Indices: 6977130--6977174 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6977120 TTGATAAAAG
*
6977130 ATTAAAATCTTAATTTTAATA
1 ATTAAAATCTTAATTATAATA
*
6977151 ATTAAAAT-TTAATTCATGATA
1 ATTAAAATCTTAATT-ATAATA
6977172 ATT
1 ATT
6977175 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAAAATCTTAATTATAATA
Found at i:6977938 original size:2 final size:2
Alignment explanation
Indices: 6977931--6977956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6977921 ATTCACTATG
6977931 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
6977957 TGAATCCATA
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:6983841 original size:11 final size:11
Alignment explanation
Indices: 6983822--6983851 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6983812 TTACTCAAAT
*
6983822 TATTCTAGTAA
1 TATTTTAGTAA
6983833 TATTTTAGTAA
1 TATTTTAGTAA
6983844 TATTTTAG
1 TATTTTAG
6983852 ATTAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (11 bp):
TATTTTAGTAA
Found at i:6993894 original size:13 final size:13
Alignment explanation
Indices: 6993876--6993904 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6993866 CCATTCTTTC
6993876 CAAGCCTTACCTG
1 CAAGCCTTACCTG
6993889 CAAGCCTTACCTG
1 CAAGCCTTACCTG
6993902 CAA
1 CAA
6993905 TCAGGGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (13 bp):
CAAGCCTTACCTG
Found at i:6996434 original size:2 final size:2
Alignment explanation
Indices: 6996429--6996462 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6996419 AAAAATGAGT
6996429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6996463 CCTCAGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6997380 original size:22 final size:22
Alignment explanation
Indices: 6997332--6997382 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
6997322 AATAAGATAC
6997332 ATAAAAAATTTAAGTATTGAAA
1 ATAAAAAATTTAAGTATTGAAA
* *
6997354 A-AAAAAATTTAATTATTTAAA
1 ATAAAAAATTTAAGTATTGAAA
6997375 ATAAAAAA
1 ATAAAAAA
6997383 ATCAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
ATAAAAAATTTAAGTATTGAAA
Found at i:6997728 original size:23 final size:23
Alignment explanation
Indices: 6997699--6997745 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6997689 GGGTTGAACC
* *
6997699 TTTTAAGAGATAAGACTTAGTGT
1 TTTTAAGAAATAAAACTTAGTGT
6997722 TTTTAAGAAATAAAACTTAGTGT
1 TTTTAAGAAATAAAACTTAGTGT
6997745 T
1 T
6997746 GCGTTCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (23 bp):
TTTTAAGAAATAAAACTTAGTGT
Found at i:7001763 original size:21 final size:20
Alignment explanation
Indices: 7001730--7001794 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
7001720 CAAAGATCAT
*
7001730 AATAAAAATATCATGCAAAAA
1 AATAAAAA-ATCATACAAAAA
7001751 AATACAAAAATCATACAAAAA
1 AATA-AAAAATCATACAAAAA
*
7001772 TATCATAATAAATCATACAAAAA
1 -A--ATAAAAAATCATACAAAAA
7001795 TAATCATGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 15 0.39
22 5 0.13
23 15 0.39
24 3 0.08
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.20
Consensus pattern (20 bp):
AATAAAAAATCATACAAAAA
Found at i:7001766 original size:11 final size:11
Alignment explanation
Indices: 7001734--7001795 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 11
7001724 GATCATAATA
*
7001734 AAAATATCATGC
1 AAAA-ATCATAC
*
7001746 AAAAA-AATAC
1 AAAAATCATAC
7001756 AAAAATCATAC
1 AAAAATCATAC
7001767 AAAAATATCATA-
1 -AAAA-ATCATAC
*
7001779 ATAAATCATAC
1 AAAAATCATAC
7001790 AAAAAT
1 AAAAAT
7001796 AATCATGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 14 0.34
11 13 0.32
12 8 0.20
13 6 0.15
ACGTcount: A:0.65, C:0.13, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAAATCATAC
Found at i:7001856 original size:21 final size:21
Alignment explanation
Indices: 7001815--7001859 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7001805 ATCATGAAAA
*
7001815 TAATAAATCATACAAATAAAT
1 TAATAAATCATACAAACAAAT
* *
7001836 TAATAAATCATGCAAGCAAAT
1 TAATAAATCATACAAACAAAT
7001857 TAA
1 TAA
7001860 ATTCAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (21 bp):
TAATAAATCATACAAACAAAT
Done.