Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 44 of 135
Found at i:11370512 original size:67 final size:67
Alignment explanation
Indices: 11370440--11370570 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
11370430 TATTTGTTTA
*
11370440 AGTCAAACTCTTATTAGTCGAGATTATTTTATTATTATTTAAACTTGGAATTTAGCCTATATATT
1 AGTCAAACTCTTATTAGTCGAGATTATTGTATTATTATTTAAACTTGGAATTTAGCCTATATATT
11370505 TG
66 TG
* * * *
11370507 AGTCAAATTCTTATTAGTCTAGATTATTGTATTATTATTTGACCTTGGAATTTAGCCTATATAT
1 AGTCAAACTCTTATTAGTCGAGATTATTGTATTATTATTTAAACTTGGAATTTAGCCTATATAT
11370571 AGGCTCTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (67 bp):
AGTCAAACTCTTATTAGTCGAGATTATTGTATTATTATTTAAACTTGGAATTTAGCCTATATATT
TG
Found at i:11372565 original size:25 final size:25
Alignment explanation
Indices: 11372531--11372588 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
11372521 AAACCAAATG
11372531 TATTAGGTTAGTGGAATGGCATGAA
1 TATTAGGTTAGTGGAATGGCATGAA
* *
11372556 TATTAGGTTAGTGGAATGGTATGAT
1 TATTAGGTTAGTGGAATGGCATGAA
11372581 TATTAGGT
1 TATTAGGT
11372589 GAATATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (25 bp):
TATTAGGTTAGTGGAATGGCATGAA
Found at i:11373735 original size:35 final size:36
Alignment explanation
Indices: 11373689--11373789 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
11373679 GGTAATAGGC
* **
11373689 ATGACCTTTGAGTCAA-AGGGAG-AGAAATGAGCATA
1 ATGACCCTTGAGTCAACAGGGAGTA-AAACAAGCATA
* *
11373724 ATGACCCTTGAGTCAATAGAGAGTAAAACAAGCATA
1 ATGACCCTTGAGTCAACAGGGAGTAAAACAAGCATA
11373760 ATGACCCTTGAGGTCAACAGGGAGTAAAAC
1 ATGACCCTTGA-GTCAACAGGGAGTAAAAC
11373790 GAATAACGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 15 0.26
36 25 0.44
37 17 0.30
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (36 bp):
ATGACCCTTGAGTCAACAGGGAGTAAAACAAGCATA
Found at i:11375550 original size:3 final size:3
Alignment explanation
Indices: 11375528--11375576 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
11375518 AAGAAGGAAT
*
11375528 TTC TTC ATTT TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC -TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
11375575 TT
1 TT
11375577 TCTCTCATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.88
4 5 0.12
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:11376336 original size:18 final size:18
Alignment explanation
Indices: 11376313--11376371 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
11376303 TCAAAAGAAG
11376313 GCATATGTCTCGGTTAGA
1 GCATATGTCTCGGTTAGA
** * *
11376331 GCATAT-TGCTATGAT-GTT
1 GCATATGT-CTCGGTTAG-A
11376349 GCATATGTCTCGGTTAGA
1 GCATATGTCTCGGTTAGA
11376367 GCATA
1 GCATA
11376372 CTGCTATGAT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (18 bp):
GCATATGTCTCGGTTAGA
Found at i:11376360 original size:36 final size:36
Alignment explanation
Indices: 11376313--11376403 Score: 146
Period size: 36 Copynumber: 2.5 Consensus size: 36
11376303 TCAAAAGAAG
*
11376313 GCATATGTCTCGGTTAGAGCATATTGCTATGATGTT
1 GCATATGTCTCGGTTAGAGCATACTGCTATGATGTT
11376349 GCATATGTCTCGGTTAGAGCATACTGCTATGATGTT
1 GCATATGTCTCGGTTAGAGCATACTGCTATGATGTT
* * *
11376385 TCATACGACTCGGTTAGAG
1 GCATATGTCTCGGTTAGAG
11376404 TGTAATGCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.35
Consensus pattern (36 bp):
GCATATGTCTCGGTTAGAGCATACTGCTATGATGTT
Found at i:11376413 original size:36 final size:36
Alignment explanation
Indices: 11376313--11376481 Score: 137
Period size: 36 Copynumber: 4.7 Consensus size: 36
11376303 TCAAAAGAAG
* *
11376313 GCATATGTCTCGGTTAGAGCATATTGCTATGATGTT
1 GCATACGTCTCGGTTAGAGCATAATGCTATGATGTT
* *
11376349 GCATATGTCTCGGTTAGAGCATACTGCTATGATGTT
1 GCATACGTCTCGGTTAGAGCATAATGCTATGATGTT
* * ** * *
11376385 TCATACGACTCGGTTAGAGTGTAATGCTAAGGAAG-T
1 GCATACGTCTCGGTTAGAGCATAATGCT-ATGATGTT
* * * *
11376421 GCGTACGTCTCGGTTAGA-CTGTAATGCTAAGGAAG-T
1 GCATACGTCTCGGTTAGAGC-ATAATGCT-ATGATGTT
** *
11376457 GCATGTGTCTCGGTTAGAGCGTAAT
1 GCATACGTCTCGGTTAGAGCATAAT
11376482 AGTAAGAAAG
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
36 109 0.96
37 5 0.04
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (36 bp):
GCATACGTCTCGGTTAGAGCATAATGCTATGATGTT
Found at i:11376469 original size:72 final size:72
Alignment explanation
Indices: 11376393--11376548 Score: 181
Period size: 72 Copynumber: 2.2 Consensus size: 72
11376383 TTTCATACGA
* * * *
11376393 CTCGGTTAGAGTGTAAT-GCTAAGGAAGTGCGTACGTCTCGGTTAGA-CTGTAATGCTAAGGAAG
1 CTCGGTTAGAGCGTAATAG-TAAGAAAGTGCGTACATCTCGATTAGAGC-GTAATGCTAAGGAAG
*
11376456 TGCATGTGT
64 TGCATATGT
* * * *
11376465 CTCGGTTAGAGCGTAATAGTAAGAAAGTGCTTACATCTCGATTAGAGCGTAATGTTAAGTAATTG
1 CTCGGTTAGAGCGTAATAGTAAGAAAGTGCGTACATCTCGATTAGAGCGTAATGCTAAGGAAGTG
*
11376530 CTTATGT
66 CATATGT
*
11376537 CTCGATTAGAGC
1 CTCGGTTAGAGC
11376549 ATAAGGCCAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
72 69 0.97
73 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (72 bp):
CTCGGTTAGAGCGTAATAGTAAGAAAGTGCGTACATCTCGATTAGAGCGTAATGCTAAGGAAGTG
CATATGT
Found at i:11376493 original size:36 final size:36
Alignment explanation
Indices: 11376388--11376548 Score: 164
Period size: 36 Copynumber: 4.5 Consensus size: 36
11376378 TGATGTTTCA
* * *
11376388 TACGACTCGGTTAGAGTGTAATGCTAAGGAAGTGCG
1 TACGTCTCGGTTAGAGCGTAATGCTAAGGAAGTGCT
*
11376424 TACGTCTCGGTTAGA-CTGTAATGCTAAGGAAGTGCA
1 TACGTCTCGGTTAGAGC-GTAATGCTAAGGAAGTGCT
** *
11376460 TGTGTCTCGGTTAGAGCGTAATAG-TAAGAAAGTGCT
1 TACGTCTCGGTTAGAGCGTAAT-GCTAAGGAAGTGCT
* * * * *
11376496 TACATCTCGATTAGAGCGTAATGTTAAGTAATTGCT
1 TACGTCTCGGTTAGAGCGTAATGCTAAGGAAGTGCT
* *
11376532 TATGTCTCGATTAGAGC
1 TACGTCTCGGTTAGAGC
11376549 ATAAGGCCAT
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.01
36 103 0.97
37 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (36 bp):
TACGTCTCGGTTAGAGCGTAATGCTAAGGAAGTGCT
Found at i:11377642 original size:26 final size:26
Alignment explanation
Indices: 11377606--11377658 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
11377596 AACATGGAAC
*
11377606 ATAAGAAATTAACATCAGAATATAAA
1 ATAAAAAATTAACATCAGAATATAAA
*
11377632 ATAAAAAATTAACATTAGAATATAAA
1 ATAAAAAATTAACATCAGAATATAAA
11377658 A
1 A
11377659 CAAATAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (26 bp):
ATAAAAAATTAACATCAGAATATAAA
Found at i:11378046 original size:50 final size:50
Alignment explanation
Indices: 11377967--11378119 Score: 245
Period size: 50 Copynumber: 3.1 Consensus size: 50
11377957 ATACAAAAAA
* * *
11377967 AAAAATATATACAAGTATAATTCAATGATAAAAGAATAAGCGATACTATG
1 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGCGATACTATG
11378017 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGC-AGTACTATG
1 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGCGA-TACTATG
* *
11378067 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGCGTTAGTATG
1 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGCGATACTATG
11378117 AAA
1 AAA
11378120 TAAACCAGTG
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
49 1 0.01
50 95 0.99
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (50 bp):
AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGCGATACTATG
Found at i:11380750 original size:21 final size:21
Alignment explanation
Indices: 11380726--11380766 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11380716 ACATATATAC
*
11380726 TCATATATATTTTGTATTTCA
1 TCATATATATTTTCTATTTCA
* *
11380747 TCATCTATTTTTTCTATTTC
1 TCATATATATTTTCTATTTC
11380767 GAAAATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.15, G:0.02, T:0.61
Consensus pattern (21 bp):
TCATATATATTTTCTATTTCA
Found at i:11387994 original size:22 final size:22
Alignment explanation
Indices: 11387929--11387995 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 22
11387919 GTTTTCTTAA
**
11387929 AAATTAAACCCTTTCATTTTTT
1 AAATTAAACCCTTTTGTTTTTT
* * *
11387951 TAATTAATCCTTTTATTCGTTTTTT
1 AAATTAAACC-CTT-TT-GTTTTTT
11387976 AAATTAAACCCTTTTGTTTT
1 AAATTAAACCCTTTTGTTTT
11387996 AAGATTTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
22 13 0.38
23 4 0.12
24 3 0.09
25 14 0.41
ACGTcount: A:0.27, C:0.15, G:0.03, T:0.55
Consensus pattern (22 bp):
AAATTAAACCCTTTTGTTTTTT
Found at i:11387995 original size:20 final size:21
Alignment explanation
Indices: 11387972--11388016 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11387962 TTTATTCGTT
*
11387972 TTTTAA-ATTAAACCCTTTTG
1 TTTTAAGATTAAACCATTTTG
* *
11387992 TTTTAAGATTTAATCATTTTG
1 TTTTAAGATTAAACCATTTTG
11388013 TTTT
1 TTTT
11388017 TATTTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTAAGATTAAACCATTTTG
Found at i:11388073 original size:25 final size:26
Alignment explanation
Indices: 11388034--11388082 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
11388024 TTTAAAATTC
11388034 CCTTTTTATTCTTTTTT-ATTTAAAT
1 CCTTTTTATTCTTTTTTAATTTAAAT
11388059 CCTTTTATATT-TTTTTTAATTTAA
1 CCTTTT-TATTCTTTTTTAATTTAA
11388083 GCCCATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (26 bp):
CCTTTTTATTCTTTTTTAATTTAAAT
Found at i:11393868 original size:27 final size:28
Alignment explanation
Indices: 11393800--11393888 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
11393790 AGGCAAATCC
* * * *
11393800 TTGTGGTGATTTTCATAAAGAACAACCC
1 TTGTGGCGATTTTCGTAAAGAACAGCCT
* * *
11393828 TTATGGCAATTTTTGTAAAGAACAGCCT
1 TTGTGGCGATTTTCGTAAAGAACAGCCT
11393856 TTGTGGCGATTTTCGTAAAGAA-AGCCT
1 TTGTGGCGATTTTCGTAAAGAACAGCCT
11393883 TTGTGG
1 TTGTGG
11393889 TTAAATTCTG
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 11 0.22
28 40 0.78
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (28 bp):
TTGTGGCGATTTTCGTAAAGAACAGCCT
Found at i:11393901 original size:28 final size:29
Alignment explanation
Indices: 11393815--11393903 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 29
11393805 GTGATTTTCA
* * * * *
11393815 TAAAGAACAACCCTTATGGC-AATTTTTG
1 TAAAGAACAGCCTTTGTGGCGAAATTCTG
**
11393843 TAAAGAACAGCCTTTGTGGCGATTTTC-G
1 TAAAGAACAGCCTTTGTGGCGAAATTCTG
**
11393871 TAAAGAA-AGCCTTTGTGGTTAAATTCTG
1 TAAAGAACAGCCTTTGTGGCGAAATTCTG
11393899 TAAAG
1 TAAAG
11393904 TGAGCATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
27 15 0.30
28 31 0.62
29 4 0.08
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (29 bp):
TAAAGAACAGCCTTTGTGGCGAAATTCTG
Found at i:11394703 original size:17 final size:18
Alignment explanation
Indices: 11394683--11394717 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11394673 CTTAGTAAAT
11394683 TTAGG-TTTAGTTATTTC
1 TTAGGTTTTAGTTATTTC
11394700 TTAGGTTTTAGTTATTTC
1 TTAGGTTTTAGTTATTTC
11394718 ATTTTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (18 bp):
TTAGGTTTTAGTTATTTC
Found at i:11395684 original size:27 final size:27
Alignment explanation
Indices: 11395646--11395700 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
11395636 CTCAAAAGAA
*
11395646 AGAAATAGTCACTTGAGTTTAGACCTC
1 AGAAACAGTCACTTGAGTTTAGACCTC
11395673 AGAAACAGTCACTTGAGTTTAGACCTC
1 AGAAACAGTCACTTGAGTTTAGACCTC
11395700 A
1 A
11395701 AATCTAGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (27 bp):
AGAAACAGTCACTTGAGTTTAGACCTC
Found at i:11398599 original size:20 final size:20
Alignment explanation
Indices: 11398558--11398599 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
11398548 CATCTTTAGA
*
11398558 TTTTTTAAAATTATCATTAAT
1 TTTTTTAAAACTATCA-TAAT
11398579 TTTTTTAAAAACTATCA-AAT
1 TTTTTT-AAAACTATCATAAT
11398599 T
1 T
11398600 GATCTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTTAAAACTATCATAAT
Found at i:11401964 original size:26 final size:26
Alignment explanation
Indices: 11401926--11401978 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
11401916 AGAGATAAGC
* *
11401926 GGTTAGAACATACTGAGTGCAAGTAT
1 GGTTAGAAAATACAGAGTGCAAGTAT
*
11401952 GGTTAGAAAATACAGAGTGCATGTAT
1 GGTTAGAAAATACAGAGTGCAAGTAT
11401978 G
1 G
11401979 CCTTTTTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.26
Consensus pattern (26 bp):
GGTTAGAAAATACAGAGTGCAAGTAT
Found at i:11405447 original size:17 final size:18
Alignment explanation
Indices: 11405425--11405465 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
11405415 GAAGATATGC
11405425 ATGATAAA-AAAGTGACG
1 ATGATAAAGAAAGTGACG
11405442 ATGATAAAGAAAGTGACG
1 ATGATAAAGAAAGTGACG
11405460 ATGATA
1 ATGATA
11405466 GTGAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (18 bp):
ATGATAAAGAAAGTGACG
Found at i:11410770 original size:12 final size:12
Alignment explanation
Indices: 11410753--11410779 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11410743 TGCTCTCTTT
11410753 CTTTACCTTTTA
1 CTTTACCTTTTA
11410765 CTTTACCTTTTA
1 CTTTACCTTTTA
11410777 CTT
1 CTT
11410780 GTGTGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (12 bp):
CTTTACCTTTTA
Found at i:11416268 original size:41 final size:41
Alignment explanation
Indices: 11416160--11416280 Score: 119
Period size: 41 Copynumber: 3.0 Consensus size: 41
11416150 GAATAGCGTA
* *
11416160 TCTTCAATCTACCCTCTGATTAGGGT-AAGAGATTG-TCTGG
1 TCTTCAATCTGCCCTCT-ATTAGGGTAAAGAGATTGATGTGG
*
11416200 TCTTCAATCTGCCC-C-ATGGTCGAGGTAAAGAGATTGATGT-G
1 TCTTCAATCTGCCCTCTAT--TAG-GGTAAAGAGATTGATGTGG
11416241 TCTTCAATCTGCCCTCTAATTAGGGTAAA-AGATTGGATGT
1 TCTTCAATCTGCCCTCT-ATTAGGGTAAAGAGATT-GATGT
11416281 TTTAATTGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
37 2 0.03
39 3 0.04
40 21 0.31
41 35 0.51
42 5 0.07
44 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (41 bp):
TCTTCAATCTGCCCTCTATTAGGGTAAAGAGATTGATGTGG
Found at i:11416385 original size:39 final size:39
Alignment explanation
Indices: 11416161--11416742 Score: 317
Period size: 39 Copynumber: 14.8 Consensus size: 39
11416151 AATAGCGTAT
* * * **
11416161 CTTCAATCTACCCTCTGATTAGGGTAAGAGATTGTCTGG
1 CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
* * * *
11416200 TCTTCAATCTGCCCCATGGTCGAGGTAAAGAGATT-GATGTG
1 -CTTCAATCTGCCCTATGATTGGGGT-AAGAGATTGGATG-G
* * * *
11416241 TCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGAT-G
1 -CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
* * * * * *
11416280 TTTTAAT-TG-CTTCATGATCGGAGTAAAAGATTGGATGATG
1 CTTCAATCTGCCCT-ATGATTGGGGTAAGAGATTGGATG--G
* * * * *
11416320 CCTGT-AACCTACCCCATGATCGGGGTAAGAGATTGGGTGG
1 -CT-TCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
*
11416360 CTTCAATCTGCCCTATGATTAGGGTAAGAGATTGGATGG
1 CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
* * * *
11416399 TTTTCAATCTGCCCAATGATCGGGGTAAGAGATTGGATGAT
1 -CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATG-G
* * * * *
11416440 TTTCAATCT-ACCTCATGATCGGGGTAAGAGATTAGACGG
1 CTTCAATCTGCCCT-ATGATTGGGGTAAGAGATTGGATGG
* * * * *
11416479 TTTTAATTTGCCTCT-TGATTGGGGTAAGAGATTGGCGTGT
1 CTTCAATCTGCC-CTATGATTGGGGTAAGAGATTGG-ATGG
* ** * **
11416519 CTTCAATCTACTTTTTGATTAAGGTAA-AGATTGGAT-G
1 CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
* *** **
11416556 CTTTCAATCTGCCCTATGATCGGGGTAAGAGATTATTTAT
1 C-TTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
* * * *
11416596 CTTTAATCTACCCTTTGATTAGGGTCAA-AGATTGGAT-G
1 CTTCAATCTGCCCTATGATTGGGGT-AAGAGATTGGATGG
* * * ** *
11416634 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGCCTGT
1 CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
* * * *
11416673 CTTCAATCTGCCTTCTGATTAGGGTAAAAGATTTGGAT-G
1 CTTCAATCTGCCCTATGATTGGGGTAAGAGA-TTGGATGG
*
11416712 CTTCAATCTGTCCC-ATGATCGGGGTAAGAGA
1 CTTCAATCTG-CCCTATGATTGGGGTAAGAGA
11416743 CCTGTAAAAT
Statistics
Matches: 403, Mismatches: 112, Indels: 55
0.71 0.20 0.10
Matches are distributed among these distances:
36 2 0.00
37 23 0.06
38 51 0.13
39 145 0.36
40 122 0.30
41 36 0.09
42 23 0.06
43 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
CTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGG
Found at i:11416626 original size:78 final size:77
Alignment explanation
Indices: 11416335--11416742 Score: 407
Period size: 77 Copynumber: 5.2 Consensus size: 77
11416325 AACCTACCCC
* * * * *
11416335 ATGATCGGGGTAAGAGATTGGGTGGCTTCAATCTGCCCTATGATTAGGGTAAGAGATTGGATGGT
1 ATGATCGGGGTAAGAGATTGCGTGTCTTCAATCTACCCTTTGATTAGGGTAA-AGATTGGAT-GC
*
11416400 TTTCAATCTGCCCA
64 TTTCAATCTGCCCT
* * ** * *
11416414 ATGATCGGGGTAAGAGATTG-GATGATTTTCAATCTA-CCTCATGATCGGGGTAAGAGATTAGAC
1 ATGATCGGGGTAAGAGATTGCG-TG-TCTTCAATCTACCCT-TTGATTAGGGTAA-AGATTGGAT
* * *
11416477 GGTTTTAATTTGCCTCT
62 GCTTTCAATCTGCC-CT
* ** *
11416494 -TGATTGGGGTAAGAGATTGGCGTGTCTTCAATCTACTTTTTGATTAAGGTAAAGATTGGATGCT
1 ATGATCGGGGTAAGAGATT-GCGTGTCTTCAATCTACCCTTTGATTAGGGTAAAGATTGGATGCT
11416558 TTCAATCTGCCCT
65 TTCAATCTGCCCT
*** * *
11416571 ATGATCGGGGTAAGAGATTATTTATCTTTAATCTACCCTTTGATTAGGGTCAAAGATTGGATG-T
1 ATGATCGGGGTAAGAGATTGCGTGTCTTCAATCTACCCTTTGATTAGGGT-AAAGATTGGATGCT
*
11416635 TTCAATCTGCCCC
65 TTCAATCTGCCCT
* *
11416648 ATGATCGGGGTAAGAGATTGCCTGTCTTCAATCT-GCCTTCTGATTAGGGTAAAAGATTTGGATG
1 ATGATCGGGGTAAGAGATTGCGTGTCTTCAATCTACCCTT-TGATTAGGGT-AAAGA-TTGGATG
11416712 C-TTCAATCTGTCCC-
63 CTTTCAATCTG-CCCT
11416726 ATGATCGGGGTAAGAGA
1 ATGATCGGGGTAAGAGA
11416743 CCTGTAAAAT
Statistics
Matches: 275, Mismatches: 41, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
76 4 0.01
77 82 0.30
78 81 0.29
79 75 0.27
80 32 0.12
81 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (77 bp):
ATGATCGGGGTAAGAGATTGCGTGTCTTCAATCTACCCTTTGATTAGGGTAAAGATTGGATGCTT
TCAATCTGCCCT
Found at i:11425213 original size:15 final size:14
Alignment explanation
Indices: 11425176--11425218 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
11425166 TCAAGAGCCA
11425176 AAGGGTCAGCAAAC
1 AAGGGTCAGCAAAC
*
11425190 AATGGGTCAGCAATC
1 AA-GGGTCAGCAAAC
11425205 AAGGAGTCAG-AAAC
1 AAGG-GTCAGCAAAC
11425219 TGACGGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.42, C:0.19, G:0.28, T:0.12
Consensus pattern (14 bp):
AAGGGTCAGCAAAC
Found at i:11425696 original size:18 final size:18
Alignment explanation
Indices: 11425667--11425706 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 18
11425657 ATAATTTTAA
11425667 AAAGTAAAAATTAAAAAAT
1 AAAGTAAAAATT-AAAAAT
11425686 AAAGT-AAAATTAAAAAT
1 AAAGTAAAAATTAAAAAT
11425703 AAAG
1 AAAG
11425707 AGAGTAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAGTAAAAATTAAAAAT
Found at i:11426193 original size:21 final size:23
Alignment explanation
Indices: 11426154--11426200 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
11426144 TTTAATTAAA
**
11426154 TAAATTTAATTAATTG-AAATTT
1 TAAATTTAATTAAAAGAAAATTT
11426176 TAAA-TTAATTAAAAGAAAATTT
1 TAAATTTAATTAAAAGAAAATTT
11426198 TAA
1 TAA
11426201 TTTGGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAATTTAATTAAAAGAAAATTT
Found at i:11428567 original size:23 final size:23
Alignment explanation
Indices: 11428514--11428567 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
11428504 TTTAGGGGGC
*
11428514 AAAATT-AAATTGTAATTTTTAA
1 AAAATTAAAAATGTAATTTTTAA
* * *
11428536 GATAGTAAAAATGTAATTTTTAA
1 AAAATTAAAAATGTAATTTTTAA
11428559 AAAATTAAA
1 AAAATTAAA
11428568 TTGAAGTTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
AAAATTAAAAATGTAATTTTTAA
Found at i:11439889 original size:15 final size:15
Alignment explanation
Indices: 11439853--11439883 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11439843 TTTAACACCA
11439853 TTAAAAATGAGTTGT
1 TTAAAAATGAGTTGT
11439868 TTAAAAATGAGTTGT
1 TTAAAAATGAGTTGT
11439883 T
1 T
11439884 ACAAAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (15 bp):
TTAAAAATGAGTTGT
Found at i:11439889 original size:16 final size:15
Alignment explanation
Indices: 11439855--11439891 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
11439845 TAACACCATT
*
11439855 AAAAATGAGTTGTTT
1 AAAAATGAGTTGTTC
11439870 AAAAATGAGTTGTTAC
1 AAAAATGAGTTGTT-C
11439886 AAAAAT
1 AAAAAT
11439892 CTTAACCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (15 bp):
AAAAATGAGTTGTTC
Found at i:11450249 original size:52 final size:54
Alignment explanation
Indices: 11450170--11450290 Score: 133
Period size: 52 Copynumber: 2.3 Consensus size: 54
11450160 CTACTTTACA
* * **
11450170 TAAAAATCCAAAC-TTTTATTTCGAAATAGTTAAAAAAAATCAAA-ATTT-TGTT
1 TAAAAATCTAAACTTTTTATTTCAAAATAACTAAAAAAAAT-AAATATTTATGTT
* * * *
11450222 TAAAAATTTAAACTTTTTATTT-AAAATAACTAAAATAAATAAATTTTTATTTT
1 TAAAAATCTAAACTTTTTATTTCAAAATAACTAAAAAAAATAAATATTTATGTT
11450275 TAAAAATCTAAACTTT
1 TAAAAATCTAAACTTT
11450291 CTCTTTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
51 3 0.05
52 28 0.49
53 26 0.46
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
TAAAAATCTAAACTTTTTATTTCAAAATAACTAAAAAAAATAAATATTTATGTT
Found at i:11450296 original size:150 final size:150
Alignment explanation
Indices: 11450003--11450371 Score: 465
Period size: 150 Copynumber: 2.4 Consensus size: 150
11449993 TGATTAAAAC
* *
11450003 AAAATCACTACTTTACTTCAAAATCAAAATTTTTATTTCGAAATAGCTAAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTCAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTT
* * * * *
11450068 AATTGAAAAATTTAAACTTTTTCTTTAAAATCATTAAAAACAGATTTTTATTTTTTAAAAATCTA
66 TATTGAAAAATTTAAACTTTTTATTTAAAATAATAAAAAACAAATTTTTATTTTTTAAAAATCTA
*
11450133 AACTTTATTTC-TTTTTAATG
131 AACTTTATCTCTTTTTTAA-G
* * * *
11450153 AAAATCACTACTTTACATAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTT
1 AAAATCACTACTTTACTTCAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTT
* * *
11450218 TGTTTAAAAATTTAAACTTTTTATTTAAAATAACTAAAATAAATAAATTTTTA-TTTTTAAAAAT
66 TATTGAAAAATTTAAACTTTTTATTTAAAATAA-T-AAA-AAACAAATTTTTATTTTTTAAAAAT
*
11450282 CTAAACTTTCTCT-TTTTTTAAG
128 CTAAACTTTATCTCTTTTTTAAG
* * * * * *
11450304 AAAATAACTAATTTTCTTCAAAATCAAAATTTTTATTTTGAAATTGTTTAAAAAAAAACTAAAAT
1 AAAATCACTACTTTACTTCAAAATCAAAATTTTTATTTCGAAATAG-TTAAAAAAAATC-AAAAT
11450369 TTT
64 TTT
11450372 TCCCAAAATC
Statistics
Matches: 187, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
150 87 0.47
151 39 0.21
152 42 0.22
153 19 0.10
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (150 bp):
AAAATCACTACTTTACTTCAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTT
TATTGAAAAATTTAAACTTTTTATTTAAAATAATAAAAAACAAATTTTTATTTTTTAAAAATCTA
AACTTTATCTCTTTTTTAAG
Found at i:11450792 original size:3 final size:3
Alignment explanation
Indices: 11450784--11450814 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11450774 CATAAAACCC
*
11450784 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11450815 TTGGGCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11451271 original size:42 final size:41
Alignment explanation
Indices: 11451204--11451772 Score: 638
Period size: 42 Copynumber: 13.6 Consensus size: 41
11451194 ATGAGAATGC
* * *
11451204 AAATAGACCT-CACACTTGGACCTCTAAATGGAATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAATGG-ATGAAAAGT
* * * * *
11451245 AAATGAAACTCCACACCTGGGACTCTAAATGCAATGAAAATT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* * *
11451287 AAATAGACCTCCACACCTGAGTCTCTAAATGTGATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* * * *
11451329 AAATAGACCTCCACACTTGGGCCTCTAAATACGATAAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAAT-GGATGAAAAGT
11451371 AAATGGACCTCCACACCTGGGCCTCTAAATGCGATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* * * *
11451413 AAATGGGCCTCCACACTTGGGCCTCTAAATGCAATGAAAAAT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* *
11451455 AAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGA
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* * * * *
11451497 AAATGGGCCTTCACACTTAGGCCTCTAAATGCGATGAAAAAT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* *
11451539 AAATGGACCTCTACACCTGGGCCTCTAAATGCAATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* * *
11451581 AAAT-GAGTCTCCACACCTGAGCCTCTAAATGCAATGAAAAGT
1 AAATGGA-CCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* * *
11451623 AAATGGGCCTCCACACCTGTGCCTCTAAATACGATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAAT-GGATGAAAAGT
* **
11451665 AAATGGGCCTCCACACCTACGCCTCTAAATGCGATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
* *
11451707 AAATGGGCCTCCACACCTTGGCCTCTAAATGCGATGAAAAGT
1 AAATGGACCTCCACACCTGGGCCTCTAAATG-GATGAAAAGT
*
11451749 AAATGGACCTCCACACCTAGGCCT
1 AAATGGACCTCCACACCTGGGCCT
11451773 TTAATGTAAT
Statistics
Matches: 458, Mismatches: 62, Indels: 15
0.86 0.12 0.03
Matches are distributed among these distances:
41 9 0.02
42 448 0.98
43 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (41 bp):
AAATGGACCTCCACACCTGGGCCTCTAAATGGATGAAAAGT
Found at i:11451313 original size:84 final size:83
Alignment explanation
Indices: 11451204--11451785 Score: 720
Period size: 84 Copynumber: 7.0 Consensus size: 83
11451194 ATGAGAATGC
* * *** *
11451204 AAATAGACCT-CACACTTGGACCTCTAAATG-GAATGAAAAGTAAATGAAACTCCACACCTGGGA
1 AAATGGACCTCCACACCTGG-CCTCTAAATGCG-ATGAAAAGTAAATGGGCCTCCACACCTGGGC
*
11451267 CTCTAAATGCAATGAAAATT
64 CTCTAAATGCAATGAAAAGT
* * * * * *
11451287 AAATAGACCTCCACACCTGAGTCTCTAAATGTGATGAAAAGTAAATAGACCTCCACACTTGGGCC
1 AAATGGACCTCCACACCTG-GCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCC
* * *
11451352 TCTAAATACGATAAAAAGT
65 TCTAAATGCAATGAAAAGT
*
11451371 AAATGGACCTCCACACCTGGGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACTTGGGCC
1 AAATGGACCTCCACACCT-GGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCC
*
11451436 TCTAAATGCAATGAAAAAT
65 TCTAAATGCAATGAAAAGT
* * * *
11451455 AAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGAAAATGGGCCTTCACACTTAGGCC
1 AAATGGACCTCCACACCT-GGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCC
* *
11451520 TCTAAATGCGATGAAAAAT
65 TCTAAATGCAATGAAAAGT
* * * * *
11451539 AAATGGACCTCTACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGAGTCTCCACACCTGAGCC
1 AAATGGACCTCCACACCT-GGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCC
11451604 TCTAAATGCAATGAAAAGT
65 TCTAAATGCAATGAAAAGT
* * **
11451623 AAATGGGCCTCCACACCTGTGCCTCTAAATACGATGAAAAGTAAATGGGCCTCCACACCTACGCC
1 AAATGGACCTCCACACCTG-GCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCC
*
11451688 TCTAAATGCGATGAAAAGT
65 TCTAAATGCAATGAAAAGT
* * *
11451707 AAATGGGCCTCCACACCTTGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCC
1 AAATGGACCTCCACACC-TGGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCC
* *
11451772 T-TTAATGTAATGAA
65 TCTAAATGCAATGAA
11451786 TGCTTTCCTT
Statistics
Matches: 441, Mismatches: 52, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
83 21 0.05
84 415 0.94
85 5 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (83 bp):
AAATGGACCTCCACACCTGGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTGGGCCT
CTAAATGCAATGAAAAGT
Found at i:11451385 original size:126 final size:126
Alignment explanation
Indices: 11451204--11451772 Score: 716
Period size: 126 Copynumber: 4.5 Consensus size: 126
11451194 ATGAGAATGC
* * * *
11451204 AAATAGACCT-CACACTTGGACCTCTAAATG-GAATGAAAAGTAAATGAAACTCCACACCTGGGA
1 AAATAGACCTCCACACTTGGGCCTCTAAATGCG-ATGAAAAGTAAATGGACCTCCACACCTGGGC
* * * * **
11451267 CTCTAAATGCAATGAAAATTAAATAGACCTCCACACCTGAGTCTCTAAATGTGATGAAAAGT
65 CTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGT
* *
11451329 AAATAGACCTCCACACTTGGGCCTCTAAATACGATAAAAAGTAAATGGACCTCCACACCTGGGCC
1 AAATAGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGCC
* * * *
11451394 TCTAAATGCGATGAAAAGTAAATGGGCCTCCACACTTGGGCCTCTAAATGCAATGAAAAAT
66 TCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGT
* * * * * * * *
11451455 AAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGAAAATGGGCCTTCACACTTAGGCC
1 AAATAGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGCC
* * *
11451520 TCTAAATGCGATGAAAAATAAATGGACCTCTACACCTGGGCCTCTAAATGCAATGAAAAGT
66 TCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGT
* * * * * *
11451581 AAAT-GAGTCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGTGC
1 AAATAGA-CCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGC
* * *
11451645 CTCTAAATACGATGAAAAGTAAATGGGCCTCCACACCT-ACGCCTCTAAATGCGATGAAAAGT
65 CTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGA-GCCTCTAAATGCAATGAAAAGT
* * *
11451707 AAATGGGCCTCCACACCTT-GGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGC
1 AAATAGACCTCCACA-CTTGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGC
11451771 CT
65 CT
11451773 TTAATGTAAT
Statistics
Matches: 384, Mismatches: 54, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
125 12 0.03
126 368 0.96
127 4 0.01
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (126 bp):
AAATAGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGGGCC
TCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGT
Found at i:11453915 original size:24 final size:24
Alignment explanation
Indices: 11453882--11453936 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
11453872 GTTAAGAGTA
* *
11453882 AAAATTGTCAATGCAATTGTAATAC
1 AAAA-TGTCAATGCAACTGAAATAC
* *
11453907 AAAATGTCAGTGCAACTGAAATAT
1 AAAATGTCAATGCAACTGAAATAC
11453931 AAAATG
1 AAAATG
11453937 AATTGATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (24 bp):
AAAATGTCAATGCAACTGAAATAC
Found at i:11456001 original size:17 final size:16
Alignment explanation
Indices: 11455938--11456003 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
11455928 ATACTATACA
*
11455938 AAAATAATGAAAATGC
1 AAAACAATGAAAATGC
* *
11455954 AACTACAATGCAAATGC
1 AA-AACAATGAAAATGC
11455971 TAAAACAA-GTAAAATGC
1 -AAAACAATG-AAAATGC
*
11455988 AGAGACAATGAAAATG
1 A-AAACAATGAAAATG
11456004 TAATGACAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.10
17 32 0.82
18 3 0.08
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (16 bp):
AAAACAATGAAAATGC
Found at i:11457280 original size:24 final size:24
Alignment explanation
Indices: 11457220--11457310 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
11457210 TTTCAGAAAT
* * *
11457220 TTAGCTCATACAAGCCCAGACAAAA
1 TTAGCTCTTACGAGCCCAGA-TAAA
* **
11457245 TTAGCTCATACGAGCCCAGATAGG
1 TTAGCTCTTACGAGCCCAGATAAA
*
11457269 TTAGCTCTTACGAGCCTAGATAAA
1 TTAGCTCTTACGAGCCCAGATAAA
11457293 TTAGCTCATT-CGAGCCCA
1 TTAGCTC-TTACGAGCCCA
11457311 TACAGAGTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
24 35 0.62
25 21 0.38
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGATAAA
Found at i:11459400 original size:21 final size:21
Alignment explanation
Indices: 11459354--11459405 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
11459344 CGGGGCAATA
* *
11459354 CTTTCTTCTTCTTCCTTTTCTT
1 CTTTC-TCTTCTTCCTTTGCTC
11459376 CTTTCTCTTCTT-CTCTTGCTC
1 CTTTCTCTTCTTCCT-TTGCTC
*
11459397 CTTTATCTT
1 CTTTCTCTT
11459406 GTGCTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.63
Consensus pattern (21 bp):
CTTTCTCTTCTTCCTTTGCTC
Found at i:11472694 original size:149 final size:151
Alignment explanation
Indices: 11472325--11472684 Score: 503
Period size: 152 Copynumber: 2.4 Consensus size: 151
11472315 AAACAAATAT
* * * * *
11472325 ACTACTTTGCTTCAAAATCAAAACATTTATTTCGAAATAGCTAAAAAAAATCAAAACTTTGTTTA
1 ACTATTTTACTTCAAAATCAAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTTTATTTA
* * * * *
11472390 AAAATTTTAAC-TTTTTCTTTAAAATCATTAAAAAACAGATTTTTATTTTTTTAAAAATCTACAC
65 AAAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA-TTTTTTAAAAATATAAAC
* *
11472454 TTTCTTTCTTTTTAATGAAAATC
129 TTTCTCTCTTTTTAAAGAAAATC
* * *
11472477 ACTATTTTACTTTAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTATTTAA
1 ACTATTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTATTTAA
*
11472542 AAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACATATTTTTA-TTTTTAAAAATATAAACTT
66 AAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAAATATAAACTT
11472606 TCTCT-TTTTTAAAGAAAATC
131 TCTCTCTTTTTAAAGAAAATC
* *
11472626 ACTATTTTTCTTCAAAATCAAAACTTTTATTTCGAAATTGTTTAAAAAAA-CAAAACTTT
1 ACTATTTTACTTCAAAATCAAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTTT
11472685 TTCCCAAAAT
Statistics
Matches: 185, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
149 58 0.31
150 30 0.16
151 32 0.17
152 65 0.35
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (151 bp):
ACTATTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTATTTAA
AAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAAATATAAACTT
TCTCTCTTTTTAAAGAAAATC
Found at i:11473699 original size:24 final size:23
Alignment explanation
Indices: 11473672--11473758 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
11473662 TCATTAACAT
*
11473672 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
** * *
11473696 TGTTTATGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
11473719 TGTTCGTTAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
11473742 -GTTAAATGAACATGTTC
1 TGTT-CGTGAACATGTTC
11473759 TTGAACATTA
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 3 0.06
23 29 0.59
24 17 0.35
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:11475371 original size:189 final size:189
Alignment explanation
Indices: 11475051--11475429 Score: 740
Period size: 189 Copynumber: 2.0 Consensus size: 189
11475041 CTCGAGTTGA
11475051 TGGGAAATATAGCCCTCGTAAGACCTAAAAAGATCCTCCCTGCTTCCTGCTTCCATTGCATGATT
1 TGGGAAATATAGCCCTCGTAAGACCTAAAAAGATCCTCCCTGCTTCCTGCTTCCATTGCATGATT
*
11475116 TGGAAAAAGGTTTTACCCTTTGCTTCATCCTTTCGCACGAAAGGTGATGAATTTCTGTAAGATAG
66 TGGAAAAAGGTTTTACCCTTTGCTTCATCCTTTCACACGAAAGGTGATGAATTTCTGTAAGATAG
11475181 CTCTCAGGCAGCTATCCAGAACTGCCTAGTGGATACTAATTGGTTTCATCATCCTCTGC
131 CTCTCAGGCAGCTATCCAGAACTGCCTAGTGGATACTAATTGGTTTCATCATCCTCTGC
*
11475240 TGGGAAATATAGCCCTCGTAAGATCTAAAAAGATCCTCCCTGCTTCCTGCTTCCATTGCATGATT
1 TGGGAAATATAGCCCTCGTAAGACCTAAAAAGATCCTCCCTGCTTCCTGCTTCCATTGCATGATT
11475305 TGGAAAAAGGTTTTACCCTTTGCTTCATCCTTTCACACGAAAGGTGATGAATTTCTGTAAGATAG
66 TGGAAAAAGGTTTTACCCTTTGCTTCATCCTTTCACACGAAAGGTGATGAATTTCTGTAAGATAG
11475370 CTCTCAGGCAGCTATCCAGAACTGCCTAGTGGATACTAATTGGTTTCATCATCCTCTGC
131 CTCTCAGGCAGCTATCCAGAACTGCCTAGTGGATACTAATTGGTTTCATCATCCTCTGC
11475429 T
1 T
11475430 AAGAGAAGGG
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (189 bp):
TGGGAAATATAGCCCTCGTAAGACCTAAAAAGATCCTCCCTGCTTCCTGCTTCCATTGCATGATT
TGGAAAAAGGTTTTACCCTTTGCTTCATCCTTTCACACGAAAGGTGATGAATTTCTGTAAGATAG
CTCTCAGGCAGCTATCCAGAACTGCCTAGTGGATACTAATTGGTTTCATCATCCTCTGC
Found at i:11479774 original size:26 final size:26
Alignment explanation
Indices: 11479744--11479793 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11479734 AAAATAAATG
11479744 GTACTGAAAAGTAAATGATAAACTAA
1 GTACTGAAAAGTAAATGATAAACTAA
* *
11479770 GTACTGAAAGGTAAATGGTAAACT
1 GTACTGAAAAGTAAATGATAAACT
11479794 GTAAATGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (26 bp):
GTACTGAAAAGTAAATGATAAACTAA
Found at i:11491000 original size:25 final size:26
Alignment explanation
Indices: 11490920--11491000 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 26
11490910 ATTCTGTGTT
* * **
11490920 TGGCTCGAATAAGCCATTTTCTGTTC
1 TGGCTCGAATAAGCTATATTCTGTAA
*
11490946 TGGGCTCGAATGAGCTATATTCTGTAA
1 T-GGCTCGAATAAGCTATATTCTGTAA
* *
11490973 TGGCTCGAATAATCT-TATTCTGTCA
1 TGGCTCGAATAAGCTATATTCTGTAA
11490998 TGG
1 TGG
11491001 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 12 0.26
26 13 0.28
27 21 0.46
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (26 bp):
TGGCTCGAATAAGCTATATTCTGTAA
Found at i:11495243 original size:42 final size:42
Alignment explanation
Indices: 11495197--11495298 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
11495187 ATTCCGAGTA
11495197 ATGAGTCTTCCTTTAATCATATTCTAATTATCATCCCGAGAC
1 ATGAGTCTTCCTTTAATCATATTCTAATTATCATCCCGAGAC
* * * * *
11495239 ATGAGTTTTCCCTTAATCATATTCTCATTCTCATCCTGAGAC
1 ATGAGTCTTCCTTTAATCATATTCTAATTATCATCCCGAGAC
11495281 ATGAGTCTTCCTTTAATC
1 ATGAGTCTTCCTTTAATC
11495299 TATCCTGATG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (42 bp):
ATGAGTCTTCCTTTAATCATATTCTAATTATCATCCCGAGAC
Found at i:11502356 original size:41 final size:42
Alignment explanation
Indices: 11502172--11502347 Score: 189
Period size: 42 Copynumber: 4.2 Consensus size: 42
11502162 CCAAGTCATA
* * * *
11502172 AGTCTTCCTTTTTAAACATAATCTCACGCTCATTCCGAGTCATG
1 AGTCTTCC--TTTAATCATATTCTCATGCTCATTCCGAGACATG
* *
11502216 AGTCTTTCTTTAATCATATTCTCATTCTCA-TCTCGAGACATG
1 AGTCTTCCTTTAATCATATTCTCATGCTCATTC-CGAGACATG
*
11502258 AGTCTTCCTTTAATCATATTCTC-TTCTC-TTCCTGAGACATG
1 AGTCTTCCTTTAATCATATTCTCATGCTCATTCC-GAGACATG
* * * *
11502299 AGTCTTCCTTTAAT-ATATCCTCATGCTCATTTCGAGTCACG
1 AGTCTTCCTTTAATCATATTCTCATGCTCATTCCGAGACATG
11502340 AGTCTTCC
1 AGTCTTCC
11502348 ATTCATATAA
Statistics
Matches: 115, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
40 8 0.07
41 49 0.43
42 51 0.44
44 7 0.06
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (42 bp):
AGTCTTCCTTTAATCATATTCTCATGCTCATTCCGAGACATG
Found at i:11516933 original size:16 final size:16
Alignment explanation
Indices: 11516906--11516939 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11516896 AAATGCATAA
11516906 ATGCAATAATGTATGC
1 ATGCAATAATGTATGC
11516922 ATGCAATAATGTATGC
1 ATGCAATAATGTATGC
11516938 AT
1 AT
11516940 TTACTATATA
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:0.12, G:0.18, T:0.32
Consensus pattern (16 bp):
ATGCAATAATGTATGC
Found at i:11522238 original size:24 final size:22
Alignment explanation
Indices: 11522199--11522245 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
11522189 GATTAAAATT
* *
11522199 TGAAGATAAATCTGAATTTTTC
1 TGAAGATAAATATGAAATTTTC
11522221 TGAAGATAAAAATATGAAATTTTC
1 TGAAGAT--AAATATGAAATTTTC
11522245 T
1 T
11522246 TATTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (22 bp):
TGAAGATAAATATGAAATTTTC
Found at i:11523102 original size:14 final size:14
Alignment explanation
Indices: 11523083--11523112 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11523073 TTTTTGAATT
11523083 TTGAGTTAATCGAA
1 TTGAGTTAATCGAA
*
11523097 TTGAGTTATTCGAA
1 TTGAGTTAATCGAA
11523111 TT
1 TT
11523113 ATTCGTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (14 bp):
TTGAGTTAATCGAA
Found at i:11523308 original size:19 final size:19
Alignment explanation
Indices: 11523280--11523331 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
11523270 AAAAATTACA
*
11523280 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
11523299 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
11523318 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
11523332 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:11523377 original size:9 final size:9
Alignment explanation
Indices: 11523363--11523414 Score: 54
Period size: 8 Copynumber: 5.8 Consensus size: 9
11523353 TAAATTTTTA
*
11523363 AAAAAATCT
1 AAAAAATAT
11523372 AAAAAATATAT
1 -AAAAA-ATAT
*
11523383 AAAAAAGAT
1 AAAAAATAT
11523392 AAAAAAT-T
1 AAAAAATAT
11523400 AAAAAA-AT
1 AAAAAATAT
11523408 AAAAAAT
1 AAAAAAT
11523415 TATTAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
8 14 0.39
9 9 0.25
10 10 0.28
11 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAAATAT
Found at i:11523386 original size:20 final size:18
Alignment explanation
Indices: 11523360--11523413 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
11523350 TTATAAATTT
*
11523360 TTAAAAAAATCTAAAAAA
1 TTAAAAAAATATAAAAAA
*
11523378 TATATAAAAAAGATAAAAAA
1 T-TA-AAAAAATATAAAAAA
11523398 TTAAAAAAATA-AAAAA
1 TTAAAAAAATATAAAAA
11523414 TTATTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 5 0.16
18 8 0.26
19 4 0.13
20 14 0.45
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
TTAAAAAAATATAAAAAA
Found at i:11523409 original size:16 final size:17
Alignment explanation
Indices: 11523382--11523416 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
11523372 AAAAAATATA
11523382 TAAAAAAGATAAAAAAT
1 TAAAAAAGATAAAAAAT
11523399 TAAAAAA-ATAAAAAAT
1 TAAAAAAGATAAAAAAT
11523415 TA
1 TA
11523417 TTAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
TAAAAAAGATAAAAAAT
Found at i:11523419 original size:19 final size:18
Alignment explanation
Indices: 11523360--11523421 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 18
11523350 TTATAAATTT
11523360 TTAAAAAAATCTAAAAAATA
1 TTAAAAAAA--TAAAAAATA
11523380 TATAAAAAAGAT-AAAAA-A
1 T-TAAAAAA-ATAAAAAATA
11523398 TTAAAAAAATAAAAAATTA
1 TTAAAAAAATAAAAAA-TA
11523417 TTAAA
1 TTAAA
11523422 TAATAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.05
17 12 0.32
18 2 0.05
19 11 0.30
20 2 0.05
21 7 0.19
22 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
TTAAAAAAATAAAAAATA
Found at i:11523737 original size:21 final size:21
Alignment explanation
Indices: 11523713--11523753 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11523703 ACTTTTTCTA
11523713 AAGTTAAAA-GTCAAAACTATC
1 AAGTTAAAAGGT-AAAACTATC
11523734 AAGTTAAAAGGTAAAACTAT
1 AAGTTAAAAGGTAAAACTAT
11523754 ATCGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATC
Found at i:11527811 original size:22 final size:22
Alignment explanation
Indices: 11527770--11527814 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11527760 TCTGATACCA
*
11527770 TGAAGATAAATCTCATTTTTTC
1 TGAAGATAAATCTCAATTTTTC
* *
11527792 TGAAGATAAATTTGAATTTTTC
1 TGAAGATAAATCTCAATTTTTC
11527814 T
1 T
11527815 TATTCTTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (22 bp):
TGAAGATAAATCTCAATTTTTC
Found at i:11530992 original size:30 final size:30
Alignment explanation
Indices: 11530958--11531021 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
11530948 TTTAACCTTC
* * *
11530958 TAAATCCTTCACTTTTTAA-TTATATCTAAA
1 TAAAT-CTTCAATCTTTAATTTATACCTAAA
*
11530988 TAAATCTTTAATCTTTAATTTATACCTAAA
1 TAAATCTTCAATCTTTAATTTATACCTAAA
11531018 TAAA
1 TAAA
11531022 CTTTCATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAATCTTCAATCTTTAATTTATACCTAAA
Found at i:11531007 original size:29 final size:29
Alignment explanation
Indices: 11530972--11531030 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
11530962 TCCTTCACTT
*
11530972 TTTAA-TTATATCTAAATAAATCTTTAATC
1 TTTAATTTATACCTAAATAAA-CTTTAATC
*
11531001 TTTAATTTATACCTAAATAAACTTTCATC
1 TTTAATTTATACCTAAATAAACTTTAATC
11531030 T
1 T
11531031 AAATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAATTTATACCTAAATAAACTTTAATC
Found at i:11538748 original size:12 final size:12
Alignment explanation
Indices: 11538715--11538748 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11538705 TATATATATA
*
11538715 TGTGTGTGTGTG
1 TGTGTGTATGTG
11538727 TGTGTGTATGTG
1 TGTGTGTATGTG
*
11538739 TGTGTTTATG
1 TGTGTGTATG
11538749 ATGATAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (12 bp):
TGTGTGTATGTG
Found at i:11542523 original size:37 final size:37
Alignment explanation
Indices: 11542462--11542680 Score: 269
Period size: 37 Copynumber: 5.9 Consensus size: 37
11542452 GCATCTAAGT
*
11542462 AAATCAGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
1 AAATCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
* * * * *
11542499 AATTCGGGCTATGTGCCTAACAGGCTTTGTGTCGTTG
1 AAATCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
*
11542536 AAATCGGGCTATGTGCGTAGCAGGCTTCGTGCCGGTG
1 AAATCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
* *
11542573 AAATCGAGCTATGTGCCTAGCAGGCTTCGTGTCGGTG
1 AAATCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
* * * *
11542610 TATTCGGGCTATGTGCCTAGCAGACTTCATGCCGGTG
1 AAATCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
* * * *
11542647 TAATCAGGC-ATATGCCTAGCAGGCCTTTGTGCCG
1 AAATCGGGCTATGTGCCTAGCAGG-CTTCGTGCCG
11542681 ATGATTAAAA
Statistics
Matches: 154, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
36 12 0.08
37 142 0.92
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.28
Consensus pattern (37 bp):
AAATCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTG
Found at i:11554292 original size:17 final size:17
Alignment explanation
Indices: 11554270--11554317 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
11554260 CCCACAAAAC
*
11554270 AGAAATGAAATAACAAA
1 AGAAATGAAAAAACAAA
11554287 AGAAATGAAAAAACAAA
1 AGAAATGAAAAAACAAA
*
11554304 GGAAATGAAGAAAA
1 AGAAATGAA-AAAA
11554318 TGACTGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (17 bp):
AGAAATGAAAAAACAAA
Found at i:11561048 original size:3 final size:3
Alignment explanation
Indices: 11561031--11561096 Score: 57
Period size: 3 Copynumber: 22.0 Consensus size: 3
11561021 TGCAATCAAT
* * *
11561031 GAA GAA GCAA G-A GAA GAA GGA GAA -AGA GAA GAA GAA AAA AAA GAA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA
11561076 G-A GAA GAAA GAA GAA GAA GAA
1 GAA GAA G-AA GAA GAA GAA GAA
11561097 ATTGCCTCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 5 0.09
3 41 0.77
4 7 0.13
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11561049 original size:15 final size:15
Alignment explanation
Indices: 11561031--11561096 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
11561021 TGCAATCAAT
*
11561031 GAAGAAGCAAGAGAA
1 GAAGAAGAAAGAGAA
*
11561046 GAAGGAGAAAGAGAA
1 GAAGAAGAAAGAGAA
* *
11561061 GAAGAAAAAAAAGAA
1 GAAGAAGAAAGAGAA
11561076 G-AGAAGAAAGAAGAA
1 GAAGAAGAAAG-AGAA
11561091 GAAGAA
1 GAAGAA
11561097 ATTGCCTCGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 7 0.17
15 31 0.74
16 4 0.10
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAAGAGAA
Found at i:11571079 original size:3 final size:3
Alignment explanation
Indices: 11571046--11571114 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
11571036 TGTAGCCGAT
*
11571046 GAA GAA GCAA G-A GAA G-A GGA GAA -AGA GAA GAA GAA GAA GAA -AA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA
11571089 -AA GAA G-A GAA GAAA GAA GAA GAA GAA
1 GAA GAA GAA GAA G-AA GAA GAA GAA GAA
11571115 ATTGCCTCGA
Statistics
Matches: 57, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
2 11 0.19
3 39 0.68
4 7 0.12
ACGTcount: A:0.65, C:0.01, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11571105 original size:28 final size:28
Alignment explanation
Indices: 11571046--11571115 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
11571036 TGTAGCCGAT
* * *
11571046 GAAGAAGCAAGAGAAGAGGAGAAAGAGAA
1 GAAGAAG-AAGAAAAAAGAAGAAAGAGAA
11571075 GAAGAAGAAGAAAAAAGAAGAGAAGA-AA
1 GAAGAAGAAGAAAAAAGAAGA-AAGAGAA
11571103 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
11571116 TTGCCTCGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 26 0.70
29 11 0.30
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (28 bp):
GAAGAAGAAGAAAAAAGAAGAAAGAGAA
Found at i:11573066 original size:25 final size:25
Alignment explanation
Indices: 11573038--11573088 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
11573028 TCTCTTATTC
*
11573038 ATTTTTGAAGATAGCTGCCATGGAA
1 ATTTTTGAAAATAGCTGCCATGGAA
11573063 ATTTTTGAAAATAGCTGCCATGGAA
1 ATTTTTGAAAATAGCTGCCATGGAA
11573088 A
1 A
11573089 CCTAACTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (25 bp):
ATTTTTGAAAATAGCTGCCATGGAA
Found at i:11575010 original size:21 final size:21
Alignment explanation
Indices: 11574980--11575033 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
11574970 GCATACTCAA
*
11574980 ATGCATCCACAATA-AAGCTAG
1 ATGCAACCACAATAGAAGC-AG
* * *
11575001 ATGCAACCACACTAGAATCGG
1 ATGCAACCACAATAGAAGCAG
11575022 ATGCAACCACAA
1 ATGCAACCACAA
11575034 CACTCTTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.15
Consensus pattern (21 bp):
ATGCAACCACAATAGAAGCAG
Found at i:11581013 original size:21 final size:21
Alignment explanation
Indices: 11580980--11581028 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
11580970 TCAAGAAGAG
** *
11580980 CATGTTGCTGAGGAGGAAATTC
1 CATGTTGGAGAGGAAGAAA-TC
11581002 C-TGTTGGAGAGGAAGAAATC
1 CATGTTGGAGAGGAAGAAATC
11581022 CATGTTG
1 CATGTTG
11581029 AGGATGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 19 0.83
22 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.27
Consensus pattern (21 bp):
CATGTTGGAGAGGAAGAAATC
Found at i:11584349 original size:61 final size:58
Alignment explanation
Indices: 11584199--11584352 Score: 200
Period size: 61 Copynumber: 2.6 Consensus size: 58
11584189 CGGCATATTA
* *
11584199 GAAAGCCTTTGTGGTGAGTACTAAATGTTAATGAATGTTTGTGGAAAAACTTGGATAG
1 GAAAGCCTTTGTGGTGAGTACTAAATGTTAAGGAATGTTTGTGGAAAAACTTAGATAG
* * *
11584257 GAAAACCTTTTTGGTGAGTACTAAATGTTAAGGAATGCCTTTGTGGCAAAACTCTAGATAG
1 GAAAGCCTTTGTGGTGAGTACTAAATGTTAAGGAATG--TTTGTGGAAAAACT-TAGATAG
* * * *
11584318 GAAAGCCTTTGTGGCGAGTATTGAATATTAAGGAA
1 GAAAGCCTTTGTGGTGAGTACTAAATGTTAAGGAA
11584353 CACCTTTATG
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
58 34 0.41
60 13 0.16
61 35 0.43
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (58 bp):
GAAAGCCTTTGTGGTGAGTACTAAATGTTAAGGAATGTTTGTGGAAAAACTTAGATAG
Found at i:11584486 original size:28 final size:28
Alignment explanation
Indices: 11584407--11584504 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
11584397 ACTGAATGGA
* * *
11584407 AAAGGAA-GCCTTCGTGGTTGTCTCTAT
1 AAAGGAATGCCTTCGTGGCTATCTCTGT
* * *
11584434 AAAGGAAATGCCTTTGTGACAATCTCTGTT
1 AAAGG-AATGCCTTCGTGGCTATCTCTG-T
**
11584464 AAAGGAA-GCCTTCGTGGCTATCTAAGT
1 AAAGGAATGCCTTCGTGGCTATCTCTGT
11584491 AAAGGAATGCCTTC
1 AAAGGAATGCCTTC
11584505 ACGGCGAACT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 13 0.23
28 22 0.39
29 15 0.27
30 6 0.11
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (28 bp):
AAAGGAATGCCTTCGTGGCTATCTCTGT
Found at i:11588433 original size:38 final size:38
Alignment explanation
Indices: 11588352--11588435 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
11588342 TGAGTCTAAT
* * *
11588352 TAGAATTGCACCCAGAATTGTCACTACATGACGATGTC
1 TAGAATTGCACCCAAAATTATCACTACATAACGATGTC
* * *
11588390 CAGAATTGCACCCAAAATTATCACTGCCTAA-GCATGTC
1 TAGAATTGCACCCAAAATTATCACTACATAACG-ATGTC
11588428 TAGAATTG
1 TAGAATTG
11588436 TCGTTGTAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.03
38 37 0.97
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (38 bp):
TAGAATTGCACCCAAAATTATCACTACATAACGATGTC
Found at i:11592036 original size:27 final size:28
Alignment explanation
Indices: 11591998--11592065 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
11591988 CTACTGCGGT
*
11591998 GAACTTTGAAGAAGACGTCA-TTATGGC
1 GAACTTTGAAGAAGACGCCACTTATGGC
* *
11592025 GAACTCTGAAGAAGATGCCACTTATGGC
1 GAACTTTGAAGAAGACGCCACTTATGGC
11592053 -ACACTTTGAAGAA
1 GA-ACTTTGAAGAA
11592066 ATGGTACTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (28 bp):
GAACTTTGAAGAAGACGCCACTTATGGC
Found at i:11592498 original size:23 final size:23
Alignment explanation
Indices: 11592467--11592513 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11592457 AGATGTGAAG
*
11592467 GGTAAGACAAGATTTCAAGGTAA
1 GGTAAGACAAGATTTCAAAGTAA
* * *
11592490 GGTATGACATGTTTTCAAAGTAA
1 GGTAAGACAAGATTTCAAAGTAA
11592513 G
1 G
11592514 TACGACGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (23 bp):
GGTAAGACAAGATTTCAAAGTAA
Found at i:11596465 original size:22 final size:22
Alignment explanation
Indices: 11596440--11596486 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11596430 AAGAGAGAAA
11596440 TGAGAGAG-GATTGAGAATAAAT
1 TGAGAGAGAG-TTGAGAATAAAT
* *
11596462 TGAGAGAGAGTTGAGAGTGAAT
1 TGAGAGAGAGTTGAGAATAAAT
11596484 TGA
1 TGA
11596487 AAAAGTGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.23
Consensus pattern (22 bp):
TGAGAGAGAGTTGAGAATAAAT
Found at i:11596486 original size:11 final size:11
Alignment explanation
Indices: 11596417--11596486 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
11596407 AACTGTGAGG
*
11596417 ATTGAGTGA-A
1 ATTGAGAGAGA
*
11596427 ATTAAGAGAGA
1 ATTGAGAGAGA
* *
11596438 AATGAGAGAGG
1 ATTGAGAGAGA
*
11596449 ATTGAGA-ATAA
1 ATTGAGAGA-GA
11596460 ATTGAGAGAGA
1 ATTGAGAGAGA
* *
11596471 GTTGAGAGTGA
1 ATTGAGAGAGA
11596482 ATTGA
1 ATTGA
11596487 AAAAGTGGGA
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
10 8 0.18
11 36 0.80
12 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (11 bp):
ATTGAGAGAGA
Found at i:11596684 original size:28 final size:28
Alignment explanation
Indices: 11596644--11596704 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
11596634 ACCCTCTCTC
*
11596644 CAAAATCGACCTAATCCGATAAATTTAA
1 CAAAATCAACCTAATCCGATAAATTTAA
** *
11596672 CAAAATCAACCTAATTTGATAATTTTAA
1 CAAAATCAACCTAATCCGATAAATTTAA
*
11596700 TAAAA
1 CAAAA
11596705 AATGAGCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (28 bp):
CAAAATCAACCTAATCCGATAAATTTAA
Found at i:11598879 original size:31 final size:32
Alignment explanation
Indices: 11598844--11598911 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 32
11598834 TTATATAGAT
*
11598844 AAATTCATGTACCAATTAAATA-TTTTTTGAC
1 AAATTCAAGTACCAATTAAATATTTTTTTGAC
* *** *
11598875 AAATTTAAGTTGTAATTAAATATTTTTTTGAG
1 AAATTCAAGTACCAATTAAATATTTTTTTGAC
11598907 AAATT
1 AAATT
11598912 TAAAAAAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (32 bp):
AAATTCAAGTACCAATTAAATATTTTTTTGAC
Found at i:11599248 original size:18 final size:18
Alignment explanation
Indices: 11599225--11599260 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11599215 GACACCTATG
*
11599225 TATTTTTTTTAAATACAA
1 TATTTTATTTAAATACAA
*
11599243 TATTTTATTTATATACAA
1 TATTTTATTTAAATACAA
11599261 AAATACGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTATTTAAATACAA
Found at i:11599532 original size:84 final size:82
Alignment explanation
Indices: 11599385--11599549 Score: 260
Period size: 84 Copynumber: 2.0 Consensus size: 82
11599375 TTTCAGAAAA
* *
11599385 AAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTTTCGAGAAAAAA
1 AAAAAAATTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTCTCG-G-AAAAA
*
11599450 ATTGCATTTTTTGGTGTTC
64 ATTGCATTTTTGGGTGTTC
*
11599469 AAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTC-GAAAAAA
1 AAAAAAATTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACACC-CCTTTTCTCGGAAAAAA
11599533 TTGCATTTTTGGGTGTT
65 TTGCATTTTTGGGTGTT
11599550 GGCCATCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
82 22 0.29
83 1 0.01
84 45 0.59
85 8 0.11
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (82 bp):
AAAAAAATTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTCTCGGAAAAAAT
TGCATTTTTGGGTGTTC
Found at i:11599614 original size:61 final size:57
Alignment explanation
Indices: 11599469--11599868 Score: 378
Period size: 61 Copynumber: 6.9 Consensus size: 57
11599459 TTTGGTGTTC
* * * *
11599469 AAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCG-
1 AAAAAAATTC-AAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTC-AGA
11599527 -AAAAAATTGC--ATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGA
1 AAAAAAATT-CAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTTCAGA
*
11599583 AAAAGAAATTTCAAACTTCTTT-GGTGTTGGCCATCAAATGGCCGACACCCCCCTTTTCTTG-
1 AAAA-AAA-TTCAAA-TT-TTTGGGTGTTGGCCATCAAATGGCCGACA-CCCCCTTTTC-AGA
* * *
11599644 AAAAAAATT-ACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTCA-A
1 AAAAAAATTCAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTTCAGA
* * *
11599700 AAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCGAA
1 AAAAAAATTCAAA--TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTC-AG-A
* *
11599761 AAAAAAATT-ACATTTTTGGGTGTTGGTCATCAAA-----GACACCCCCTATTTCAGAAA
1 AAAAAAATTCAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTTCAG--A
* * * *
11599815 AAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTT
1 AAAAAAATTCAAA-TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTTTT
11599869 TTCGAGAAAA
Statistics
Matches: 287, Mismatches: 25, Indels: 58
0.78 0.07 0.16
Matches are distributed among these distances:
53 11 0.04
54 15 0.05
55 38 0.13
56 40 0.14
57 43 0.15
58 30 0.10
59 37 0.13
60 9 0.03
61 54 0.19
62 10 0.03
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (57 bp):
AAAAAAATTCAAATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCAGA
Found at i:11599708 original size:116 final size:113
Alignment explanation
Indices: 11599469--11599898 Score: 546
Period size: 116 Copynumber: 3.7 Consensus size: 113
11599459 TTTGGTGTTC
* * *
11599469 AAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCG-AAAAAA
1 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAAA
*
11599533 TTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGA
66 TTACATTTTTGGGTGTTGGCCATCAAATGG-CGACACCCCCTGTTTCA-A
* * *
11599583 AAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTTTTCTTGAAAA
1 AAAA-AAA-TTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCCCTTTTCTCGAAAA
*
11599648 AAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTCAA
63 AAATTACATTTTTGGGTGTTGGCCATCAAATGGC-GACACCCCCTGTTTCAA
*
11599700 AAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAA
1 AAAAAAATTCAAATTTTTTT-GGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCG--AAAA
* *
11599765 AAATTACATTTTTGGGTGTTGGTCATCAAA----GACACCCCCTATTTCAGAAA
63 AAATTACATTTTTGGGTGTTGGCCATCAAATGGCGACACCCCCTGTTTC---AA
* * * *
11599815 AAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTTTTCGAGAAAAA
1 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTC--GAAAAA
* *
11599880 AATTGCATTTTTTGGTGTT
64 AATTACATTTTTGGGTGTT
11599899 CAAAAAAATT
Statistics
Matches: 282, Mismatches: 21, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
112 13 0.05
114 58 0.21
115 48 0.17
116 63 0.22
117 50 0.18
118 50 0.18
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (113 bp):
AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAAA
TTACATTTTTGGGTGTTGGCCATCAAATGGCGACACCCCCTGTTTCAA
Found at i:11599980 original size:83 final size:84
Alignment explanation
Indices: 11599815--11599981 Score: 266
Period size: 85 Copynumber: 2.0 Consensus size: 84
11599805 ATTTCAGAAA
* *
11599815 AAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTTTTCGAGAAAAA
1 AAAAAAATTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTTCTC-AGAAAAA
*
11599880 AATTGCATTTTTTGGTGTTC
65 AATTGCATTTTTGGGTGTTC
*
11599900 AAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCTCC-TTTTCTC-GAAAAA
1 AAAAAAATTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACACC-CCTTTTTCTCAGAAAAA
11599963 AATTGCATTTTTGGGTGTT
65 AATTGCATTTTTGGGTGTT
11599982 GGCCATCAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
83 24 0.31
85 51 0.66
86 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (84 bp):
AAAAAAATTCAAAATTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTTCTCAGAAAAAA
ATTGCATTTTTGGGTGTTC
Found at i:11600047 original size:202 final size:198
Alignment explanation
Indices: 11599700--11600099 Score: 552
Period size: 202 Copynumber: 2.0 Consensus size: 198
11599690 GCTGTTTCAA
*
11599700 AAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAA
1 AAAAAAATTCAAAATTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCG-AAAAA
* *
11599765 AAATTACATTTTTGGGTGTTGGTCATCAAAGACACCCCCTATTTCAGAAAAAAAAAATTCAAATT
65 AAATTACATTTTTGGGTGTTGGCCATCAAAGACACCCCCTATTTCAGAAAAAAAAAATTCAAACT
* * ** * *
11599830 TTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTTTTTCGAGAAAAAAATTGCATTTTTTGG
130 TCTTTGGTATTGGCCATCAAATGGCCGACACCCC-CCTTTTCGAGAAAAAAATTACATTTTTGGG
11599895 TGTTC
194 TGTTC
* * *
11599900 AAAAAAATTCAAAATTTTTT-GGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCG-AAAAA
1 AAAAAAATTCAAAATTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAA
* * * *
11599963 AATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGAAAAAGAAATTTCA
66 AATTACATTTTTGGGTGTTGGCCATCAAA-----GACACCCCCTATTTCAGAAAAAAAAAATTCA
* **
11600028 AACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTTTTCTTGAAAAAAATTACATTTTT
126 AACTTCTTTGGTATTGGCCATCAAATGGCCGACACCCCCCTTTTCGAGAAAAAAATTACATTTTT
11600093 GGGTGTT
191 GGGTGTT
11600100 GGCCATCAAA
Statistics
Matches: 176, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
197 32 0.18
199 35 0.20
200 19 0.11
201 28 0.16
202 62 0.35
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (198 bp):
AAAAAAATTCAAAATTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTTTCTCGAAAAAA
AATTACATTTTTGGGTGTTGGCCATCAAAGACACCCCCTATTTCAGAAAAAAAAAATTCAAACTT
CTTTGGTATTGGCCATCAAATGGCCGACACCCCCCTTTTCGAGAAAAAAATTACATTTTTGGGTG
TTC
Found at i:11600050 original size:61 final size:59
Alignment explanation
Indices: 11599900--11600302 Score: 430
Period size: 61 Copynumber: 6.8 Consensus size: 59
11599890 TTTGGTGTTC
* * * *
11599900 AAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCG-
1 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTAGA
*
11599958 AAAAAAATTGC--A-TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTC-AGA
1 AAAAAAATT-CAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTTCTAGA
* * *
11600015 AAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTTTTCTTG-
1 AAAA-AAA-TTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCCCTTTTCTAGA
* * * *
11600076 AAAAAAATT-ACA-TTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTC-AGA
1 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTTCTAGA
*
11600133 AAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTATTCTCGAGA
1 AAAAAAATTCAAATTTTTTT-GGTGTTGGCCATCAAATGGCCGACACCCCCTT-TTCT--AGA
* * * * * *
11600196 AAAAAATTTTAATTTTTTTTTGTGTCGGCCATCAAATGGCCGACACCCCCTTTTCTCAAA
1 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCT-AGA
* *
11600256 TAAAAAAATTCTAAA-TTTCTTGGTGTTGGCCATCAAATGACCGACAC
1 -AAAAAAATTC-AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACAC
11600303 AAACTTCTCC
Statistics
Matches: 291, Mismatches: 33, Indels: 39
0.80 0.09 0.11
Matches are distributed among these distances:
56 41 0.14
57 50 0.17
58 17 0.06
59 11 0.04
60 37 0.13
61 77 0.26
62 38 0.13
63 20 0.07
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (59 bp):
AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTAGA
Found at i:11600119 original size:118 final size:115
Alignment explanation
Indices: 11599900--11600302 Score: 506
Period size: 118 Copynumber: 3.4 Consensus size: 115
11599890 TTTGGTGTTC
* * *
11599900 AAAAAAATTCAAAATTT-TTTGGTGTTGGCCATCAAATGGTCGACACCTCCTTTTCTCGAAAAAA
1 AAAAAAATTC-AAATTTCTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTAGAAAAAA
*
11599964 ATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGA
65 ATTACATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGA
* *
11600015 AAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTTTTCTTGAAAA
1 AAAA-AAA-TTCAAATTTCTTTGGTGTTGGCCATCAAATGGCCGACA-CCCCCTTTTCTAGAAAA
* *
11600080 AAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTCAGA
63 AAATTACATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGA
* *
11600133 AAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATGGCCGACACCCCCTTATTCTCGAGAAA
1 AAAAAAATTCAAATTTCTTT-GGTGTTGGCCATCAAATGGCCGACACCCCCTT-TTCT--AGAAA
** * * *
11600198 AAAATTTTA-ATTTTTTTTTGTGTCGGCCATCAAATGGCCGACACCCCCTTTTCTCAAA
62 AAAA--TTACA--TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTT-TCAGA
*
11600256 TAAAAAAATTCTAAATTTC-TTGGTGTTGGCCATCAAATGACCGACAC
1 -AAAAAAATTC-AAATTTCTTTGGTGTTGGCCATCAAATGGCCGACAC
11600303 AAACTTCTCC
Statistics
Matches: 252, Mismatches: 21, Indels: 22
0.85 0.07 0.07
Matches are distributed among these distances:
115 4 0.02
116 26 0.10
117 61 0.24
118 69 0.27
119 8 0.03
120 1 0.00
121 3 0.01
122 34 0.13
123 28 0.11
124 12 0.05
125 6 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (115 bp):
AAAAAAATTCAAATTTCTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTAGAAAAAAA
TTACATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTTCAGA
Found at i:11600123 original size:432 final size:432
Alignment explanation
Indices: 11599308--11600203 Score: 1742
Period size: 432 Copynumber: 2.1 Consensus size: 432
11599298 CCATTGCATC
11599308 GCCGACACCCCCTTTTCTCGAAAAAAAAATTACATTTTTGGGTGTTGGTCATCAAAGACACCCCC
1 GCCGACACCCCCTTTTCTCGAAAAAAAAATTACATTTTTGGGTGTTGGTCATCAAAGACACCCCC
11599373 TATTTCAGAAAAAAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTT
66 TATTTCAGAAAAAAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTT
11599438 TTCGAGAAAAAAATTGCATTTTTTGGTGTTCAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCA
131 TTCGAGAAAAAAATTGCATTTTTTGGTGTTCAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCA
11599503 AATGGTCGACACCTCCTTTTCTCGAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGAC
196 AATGGTCGACACCTCCTTTTCTCGAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGAC
11599568 ACCCCCTGTTTCAGAAAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCC
261 ACCCCCTGTTTCAGAAAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCC
11599633 CCCTTTTCTTGAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTC
326 CCCTTTTCTTGAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTC
11599698 A-AAAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATG
391 AGAAAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATG
11599739 GCCGACACCCCCTTTTCTCGAAAAAAAAATTACATTTTTGGGTGTTGGTCATCAAAGACACCCCC
1 GCCGACACCCCCTTTTCTCGAAAAAAAAATTACATTTTTGGGTGTTGGTCATCAAAGACACCCCC
11599804 TATTTCAG-AAAAAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTT
66 TATTTCAGAAAAAAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCC-TTT
11599868 TTTCGAGAAAAAAATTGCATTTTTTGGTGTTCAAAAAAATTCAAAATTTTTTGGTGTTGGCCATC
130 TTTCGAGAAAAAAATTGCATTTTTTGGTGTTCAAAAAAATTCAAAATTTTTTGGTGTTGGCCATC
11599933 AAATGGTCGACACCTCCTTTTCTCGAAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCG
195 AAATGGTCGACACCTCCTTTTCTCG-AAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCG
11599998 ACACCCCCTGTTTCAGAAAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACAC
259 ACACCCCCTGTTTCAGAAAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACAC
11600063 CCCCCTTTTCTTGAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTT
324 CCCCCTTTTCTTGAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTT
11600128 TCAGAAAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATG
389 TCAGAAAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATG
*
11600172 GCCGACACCCCCTTATTCTCGAGAAAAAAATT
1 GCCGACACCCCCTT-TTCTCGAAAAAAAAATT
11600204 TTAATTTTTT
Statistics
Matches: 460, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
430 52 0.11
431 166 0.36
432 172 0.37
433 54 0.12
434 16 0.03
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (432 bp):
GCCGACACCCCCTTTTCTCGAAAAAAAAATTACATTTTTGGGTGTTGGTCATCAAAGACACCCCC
TATTTCAGAAAAAAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGTCGACACCCCTTTT
TTCGAGAAAAAAATTGCATTTTTTGGTGTTCAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCA
AATGGTCGACACCTCCTTTTCTCGAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGAC
ACCCCCTGTTTCAGAAAAAGAAATTTCAAACTTCTTTGGTGTTGGCCATCAAATGGCCGACACCC
CCCTTTTCTTGAAAAAAATTACATTTTTGGGTGTTGGCCATCAAATGGCTGACACCCGCTGTTTC
AGAAAAAAAATTCAAATTTTTTTAGGTGTTAGCCATCAAATG
Found at i:11604066 original size:11 final size:12
Alignment explanation
Indices: 11604026--11604074 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
11604016 ATTTGTGTAA
11604026 AAAATTAATTTG
1 AAAATTAATTTG
11604038 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
11604052 TTGAAATTAATTTG
1 --AAAATTAATTTG
11604066 AAAATTAAT
1 AAAATTAAT
11604075 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:11604362 original size:84 final size:84
Alignment explanation
Indices: 11604205--11604357 Score: 229
Period size: 84 Copynumber: 1.8 Consensus size: 84
11604195 AAAAAGATAG
*
11604205 TTATTATATTACAATTTATATCAAATATTGTATTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTATATCAAATAATGTATTAATTTGACAATACATTATTTATCAAATTTTC
11604270 ATATTTAAAGTACAAATTA
66 ATATTTAAAGTACAAATTA
* * * * * *
11604289 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-TAATTTT-
1 TTATTATATTACAATTTATATCAAATAATGTATTAATTTGACAATACATTATTTATCAAATTTTC
11604352 ATATTT
66 ATATTT
11604358 TTAAATAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 6 0.10
83 6 0.10
84 50 0.81
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (84 bp):
TTATTATATTACAATTTATATCAAATAATGTATTAATTTGACAATACATTATTTATCAAATTTTC
ATATTTAAAGTACAAATTA
Found at i:11604441 original size:66 final size:66
Alignment explanation
Indices: 11604299--11604431 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
11604289 TTATTATATT
* *
11604299 ATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATTTTTAAAT
1 ATAATTTTTATCATATAATGTGTTGATTTAACAATACATTATTTATTAATTTTATATCTTTAAAT
11604364 A
66 A
11604365 ATAATTTTTATCATATAATGTGTTGATTTAACAATACATTATTTATTAATTTTATATCTTTAAAT
1 ATAATTTTTATCATATAATGTGTTGATTTAACAATACATTATTTATTAATTTTATATCTTTAAAT
11604430 A
66 A
11604431 A
1 A
11604432 ATTTTTTTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (66 bp):
ATAATTTTTATCATATAATGTGTTGATTTAACAATACATTATTTATTAATTTTATATCTTTAAAT
A
Found at i:11604499 original size:88 final size:85
Alignment explanation
Indices: 11604367--11604636 Score: 349
Period size: 88 Copynumber: 3.2 Consensus size: 85
11604357 TTTAAATAAT
11604367 AATTTTTATCATATAATGTGTTGATTT-A-ACAATACATTATTTATTAATTTTATATCTTTAAAT
1 AATTTTTATCATATAATGTGTTGATTTGATACAATACATTATTTATTAATTTTATATCTTTAAAT
11604430 AAATTTTTTTATTATATTAC
66 AAATTTTTTTATTATATTAC
* *
11604450 AATATTTATCATATAATGTGTTGATTTGACTTGACAATACATTATTTATTAATTCTATATCTTTA
1 AATTTTTATCATATAATGTGTTGATTTGA--T-ACAATACATTATTTATTAATTTTATATCTTTA
****
11604515 AATAAAAAAATTTATTATA-TAC
63 AATAAATTTTTTTATTATATTAC
11604537 AATTTTTATCATAT-A--TGTTGATTTGAT--AATACATTATTTATTAATTTTATATCTTTAAAT
1 AATTTTTATCATATAATGTGTTGATTTGATACAATACATTATTTATTAATTTTATATCTTTAAAT
11604597 AAAAATTATTATTATTATTATATTAC
66 --AAA-T-TT-TT-TTATTATATTAC
11604623 AATTTTTATCATAT
1 AATTTTTATCATAT
11604637 TTTAAATTTA
Statistics
Matches: 163, Mismatches: 12, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
79 32 0.20
81 3 0.02
82 1 0.01
83 26 0.16
84 13 0.08
85 8 0.05
86 18 0.11
87 16 0.10
88 46 0.28
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (85 bp):
AATTTTTATCATATAATGTGTTGATTTGATACAATACATTATTTATTAATTTTATATCTTTAAAT
AAATTTTTTTATTATATTAC
Found at i:11604826 original size:20 final size:20
Alignment explanation
Indices: 11604797--11604848 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
11604787 AACGTCCCGA
11604797 GACCGCCGTTGACC-ACTGTT
1 GACCGCCGTTGACCGACT-TT
*
11604817 GACCGTCGTTGACCGACTTT
1 GACCGCCGTTGACCGACTTT
*
11604837 GTCCGCCGTTGA
1 GACCGCCGTTGA
11604849 TCGAGTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (20 bp):
GACCGCCGTTGACCGACTTT
Found at i:11607187 original size:147 final size:147
Alignment explanation
Indices: 11606920--11607215 Score: 583
Period size: 147 Copynumber: 2.0 Consensus size: 147
11606910 AACGTTGACA
*
11606920 CCATCGAGGATGAGGTGACAAACACCAATGTAGCGCCTCCTGAACAAGCTGTACTACGGCCTCGG
1 CCATCGAGGATGAGGCGACAAACACCAATGTAGCGCCTCCTGAACAAGCTGTACTACGGCCTCGG
11606985 CCTCGCCGAGCCTGAAGGAAGCCGGACTGTTACACACCAGCGCCGGGGACGTCACCGGGATCTAC
66 CCTCGCCGAGCCTGAAGGAAGCCGGACTGTTACACACCAGCGCCGGGGACGTCACCGGGATCTAC
11607050 TCAATTTTGATTTTTTT
131 TCAATTTTGATTTTTTT
11607067 CCATCGAGGATGAGGCGACAAACACCAATGTAGCGCCTCCTGAACAAGCTGTACTACGGCCTCGG
1 CCATCGAGGATGAGGCGACAAACACCAATGTAGCGCCTCCTGAACAAGCTGTACTACGGCCTCGG
11607132 CCTCGCCGAGCCTGAAGGAAGCCGGACTGTTACACACCAGCGCCGGGGACGTCACCGGGATCTAC
66 CCTCGCCGAGCCTGAAGGAAGCCGGACTGTTACACACCAGCGCCGGGGACGTCACCGGGATCTAC
11607197 TCAATTTTGATTTTTTT
131 TCAATTTTGATTTTTTT
11607214 CC
1 CC
11607216 CTTTACTTTT
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 148 1.00
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.21
Consensus pattern (147 bp):
CCATCGAGGATGAGGCGACAAACACCAATGTAGCGCCTCCTGAACAAGCTGTACTACGGCCTCGG
CCTCGCCGAGCCTGAAGGAAGCCGGACTGTTACACACCAGCGCCGGGGACGTCACCGGGATCTAC
TCAATTTTGATTTTTTT
Found at i:11607257 original size:30 final size:31
Alignment explanation
Indices: 11607223--11607314 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 31
11607213 TCCCTTTACT
*
11607223 TTTTAAATTTAATTTGTAATTTCATT-TTTA
1 TTTTAAATTTAATTTGTAATTTCATTGTATA
11607253 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
1 TTTTAAATTTAATTT-GTAATTTCATTGTATA
* ** *
11607283 TTTTAATTTTTCTTTCTAATTTCA-TGTATA
1 TTTTAAATTTAATTTGTAATTTCATTGTATA
11607313 TT
1 TT
11607315 CTAATTATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.04
30 50 0.94
31 1 0.02
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (31 bp):
TTTTAAATTTAATTTGTAATTTCATTGTATA
Found at i:11608321 original size:56 final size:52
Alignment explanation
Indices: 11608184--11608346 Score: 179
Period size: 51 Copynumber: 3.1 Consensus size: 52
11608174 ATTTGGAATT
* * *
11608184 TTTTTATTCGAGAAAAGGGGATGTCGGCCATTTGATGGCCAACACC--GAATT
1 TTTTT-TTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAATA
* * *
11608235 TTTTTTCTCGAGAATAGGGGGTGTCAGCCATATGATGGCCAACACCTAAAAATGCAA
1 TTTTTT-TCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACC-AAAAAT---A
* *
11608292 TTTTTTTCGATAAAAGGGGGTGTCGGCCATTTGATGGGCAACACCAAAAA-A
1 TTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAATA
11608343 TTTT
1 TTTT
11608347 AAAATTTTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
50 1 0.01
51 45 0.48
54 3 0.03
55 5 0.05
56 34 0.36
57 6 0.06
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (52 bp):
TTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAATA
Found at i:11608454 original size:60 final size:59
Alignment explanation
Indices: 11608292--11608665 Score: 262
Period size: 59 Copynumber: 6.3 Consensus size: 59
11608282 AAAAATGCAA
* * * * * **
11608292 TTTTTTTCGATAAAAGGGGGTGTCGGCCATTTGATGGGCAACACCAAAAAATTTTAAAAT
1 TTTTTTTTGA-AACAGGAGGTGTCGACCATTTGATGGCCAACACCAAAAAAAATTAAAAT
* * *
11608352 TTTTTTCTCAAGAAA-AGGAGGTATCGATCATTTGAT-GCCAACACCCAAAAAAAATTAAAAT
1 TTTTTT-T--TGAAACAGGAGGTGTCGACCATTTGATGGCCAACA-CCAAAAAAAATTAAAAT
* * * ** *
11608413 TTTTTTTTGAAACAGGAGGTGTCGGCCATTTGATGGTCAACACGAAAAAATTTTGAAAT
1 TTTTTTTTGAAACAGGAGGTGTCGACCATTTGATGGCCAACACCAAAAAAAATTAAAAT
** *** * * *
11608472 TTTTTTTCTGAAACAAGG-GGTGTCGGTCATGCAATGGCCTACACC--CAAAAA-TACAAT
1 TTTTTTT-TGAAAC-AGGAGGTGTCGACCATTTGATGGCCAACACCAAAAAAAATTAAAAT
* * * * * * *
11608529 CTTTTTCTCGAGAA-AAGAGGGCGTCGATCATTTGATGGTCAACACC-AAAAAAATTTAAAT
1 -TTTTTTTTGA-AACAGGA-GGTGTCGACCATTTGATGGCCAACACCAAAAAAAATTAAAAT
** *
11608589 TTTTTTTCTGAAACAGG-GGTTGTCGACCATTTGATGGCCAACACCAAAAAATTTTGAAAT
1 TTTTTTT-TGAAACAGGAGG-TGTCGACCATTTGATGGCCAACACCAAAAAAAATTAAAAT
11608649 GTTTTTTTTGAAACAGG
1 -TTTTTTTTGAAACAGG
11608666 CCAACATCCT
Statistics
Matches: 244, Mismatches: 51, Indels: 38
0.73 0.15 0.11
Matches are distributed among these distances:
56 2 0.01
57 6 0.02
58 37 0.15
59 73 0.30
60 73 0.30
61 49 0.20
62 2 0.01
63 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (59 bp):
TTTTTTTTGAAACAGGAGGTGTCGACCATTTGATGGCCAACACCAAAAAAAATTAAAAT
Found at i:11611349 original size:18 final size:20
Alignment explanation
Indices: 11611318--11611355 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11611308 TGTAGATCAC
11611318 CTTTAATGGAAGG-TGAGGT
1 CTTTAATGGAAGGTTGAGGT
*
11611337 CTTT-ATGGCAGGTTGAGGT
1 CTTTAATGGAAGGTTGAGGT
11611356 TGGTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.21, C:0.08, G:0.37, T:0.34
Consensus pattern (20 bp):
CTTTAATGGAAGGTTGAGGT
Found at i:11612393 original size:31 final size:31
Alignment explanation
Indices: 11612357--11612438 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
11612347 GTTTGGGTTA
*
11612357 GGACTAAAATT-TCAAAATTTAAAAAGTAAAG
1 GGACTAAAATTGTC-AAATTCAAAAAGTAAAG
*
11612388 GGACTAAAATTGTCCAATTCAAAAAGTATAA-
1 GGACTAAAATTGTCAAATTCAAAAAGTA-AAG
11612419 -GATCTAAAATTGATCAAATT
1 GGA-CTAAAATTG-TCAAATT
11612439 ATAGAAACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 2 0.05
31 32 0.73
32 10 0.23
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (31 bp):
GGACTAAAATTGTCAAATTCAAAAAGTAAAG
Found at i:11616138 original size:27 final size:27
Alignment explanation
Indices: 11616108--11616160 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
11616098 TTTAAAATAC
11616108 GTGTTTTCTTACATGTATAAGCATAAT
1 GTGTTTTCTTACATGTATAAGCATAAT
*
11616135 GTGTTTTTTTACATGTATAAGCATAA
1 GTGTTTTCTTACATGTATAAGCATAA
11616161 AAAAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (27 bp):
GTGTTTTCTTACATGTATAAGCATAAT
Found at i:11617494 original size:17 final size:17
Alignment explanation
Indices: 11617472--11617507 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
11617462 AGAGAGCCAT
11617472 ACTTTTTTCCAGTACAA
1 ACTTTTTTCCAGTACAA
11617489 ACTTTTTTCCAGTACAA
1 ACTTTTTTCCAGTACAA
11617506 AC
1 AC
11617508 GTCTTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (17 bp):
ACTTTTTTCCAGTACAA
Found at i:11624587 original size:12 final size:12
Alignment explanation
Indices: 11624570--11624597 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11624560 AAAATCTCTA
11624570 AAATATTTTCTT
1 AAATATTTTCTT
11624582 AAATATTTTCTT
1 AAATATTTTCTT
11624594 AAAT
1 AAAT
11624598 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATATTTTCTT
Found at i:11627195 original size:30 final size:30
Alignment explanation
Indices: 11627146--11627397 Score: 241
Period size: 30 Copynumber: 8.5 Consensus size: 30
11627136 TTTTAGAGAA
* * *
11627146 TTTA-GGGTCAAAATGTAATTTTTGAAAAA
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* *
11627175 TTTAGGGGTTAAAATATAATTTTATG-AAAG
1 TTTAGGGGTTAAAATGTAATTTT-GGAAAAG
* *
11627205 TTT-GAGGGTTAAAATGTGATTTTTGGGAAA-
1 TTTAG-GGGTTAAAATGT-AATTTTGGAAAAG
* *
11627235 TTTAGAGGG-CAAAATGTGATTTTGGAAAAG
1 TTTAG-GGGTTAAAATGTAATTTTGGAAAAG
*
11627265 TTTAGGGGTTAAAATGTAATTTTGG-GAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * *
11627294 TTTAAGGGTAAAAATGCAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* *
11627324 TTTAGGGGTTAAAACGTAATTTTGGAAAGG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * *
11627354 TTT-GGGGTCAAAATGTGATTTTGGAAAGG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
11627383 TTT-GGAGGTTAAAAT
1 TTTAGG-GGTTAAAAT
11627398 ATAGTTTTAA
Statistics
Matches: 187, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
29 70 0.37
30 102 0.55
31 15 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (30 bp):
TTTAGGGGTTAAAATGTAATTTTGGAAAAG
Found at i:11627219 original size:60 final size:59
Alignment explanation
Indices: 11627146--11627397 Score: 194
Period size: 59 Copynumber: 4.2 Consensus size: 59
11627136 TTTTAGAGAA
* * *
11627146 TTTAGGGTCAAAATGTAATTTTTGAAAAATTTAG-GGGTTAAAATATAATTTTATG-AAAG
1 TTTAGGGTTAAAATGTAATTTTTGAAAAATTTAGAGGG-CAAAATATAATTTT-GGAAAAG
* ** * *
11627205 TTTGAGGGTTAAAATGTGATTTTTGGGAAATTTAGAGGGCAAAATGTGATTTTGGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTTGAAAAATTTAGAGGGCAAAATATAATTTTGGAAAAG
** * *
11627265 TTTAGGGGTTAAAATGTAA-TTTTGGGAAGTTTA-AGGGTAAAA-ATGCAATTTTGGAAAAG
1 TTTA-GGGTTAAAATGTAATTTTTGAAAAATTTAGAGGGCAAAATAT--AATTTTGGAAAAG
* * ** * * *
11627324 TTTAGGGGTTAAAACGTAATTTTGGAAAGGTTT-G-GGGTCAAAATGTGATTTTGGAAAGG
1 TTTA-GGGTTAAAATGTAATTTTTGAAAAATTTAGAGGG-CAAAATATAATTTTGGAAAAG
*
11627383 TTTGGAGGTTAAAAT
1 TTTAG-GGTTAAAAT
11627398 ATAGTTTTAA
Statistics
Matches: 158, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.01
58 9 0.06
59 73 0.46
60 71 0.45
61 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
TTTAGGGTTAAAATGTAATTTTTGAAAAATTTAGAGGGCAAAATATAATTTTGGAAAAG
Found at i:11627317 original size:59 final size:58
Alignment explanation
Indices: 11627201--11627397 Score: 236
Period size: 59 Copynumber: 3.3 Consensus size: 58
11627191 TAATTTTATG
* *
11627201 AAAGTTTGAGGGTTAAAATGTGATTTTTGGGAAATTTAGAGGG-CAAAATGTGATTTTGGA
1 AAAGTTTG-GGGTTAAAATGT-AATTTTGGGAAGTTTA-AGGGTCAAAATGTGATTTTGGA
* **
11627261 AAAGTTTAGGGGTTAAAATGTAATTTTGGGAAGTTTAAGGGTAAAAATGCAATTTTGGA
1 AAAGTTT-GGGGTTAAAATGTAATTTTGGGAAGTTTAAGGGTCAAAATGTGATTTTGGA
* * *
11627320 AAAGTTTAGGGGTTAAAACGTAATTTTGGAAAGGTTT-GGGGTCAAAATGTGATTTTGGA
1 AAAGTTT-GGGGTTAAAATGTAATTTTGGGAA-GTTTAAGGGTCAAAATGTGATTTTGGA
*
11627379 AAGGTTTGGAGGTTAAAAT
1 AAAGTTTGG-GGTTAAAAT
11627398 ATAGTTTTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
58 6 0.05
59 90 0.75
60 23 0.19
61 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (58 bp):
AAAGTTTGGGGTTAAAATGTAATTTTGGGAAGTTTAAGGGTCAAAATGTGATTTTGGA
Found at i:11629559 original size:48 final size:48
Alignment explanation
Indices: 11629502--11629624 Score: 149
Period size: 48 Copynumber: 2.6 Consensus size: 48
11629492 GATTTGGTCT
* * * **
11629502 ACTTTTCTGTATCTTATTAGGAAGGTGACCGCCTCATTG-TTTCAATTC
1 ACTTCTCTGTATCTTATCAGGAAGATGACCGCCTCATTGCTTT-AACCC
* * * *
11629550 ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTTAACCC
1 ACTTCTCTGTATCTTATCAGGAAGATGACCGCCTCATTGCTTTAACCC
11629598 ACTTCTCTGTATCTTATCAGGAAGATG
1 ACTTCTCTGTATCTTATCAGGAAGATG
11629625 GGGTTTGATG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 61 0.95
49 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (48 bp):
ACTTCTCTGTATCTTATCAGGAAGATGACCGCCTCATTGCTTTAACCC
Found at i:11629941 original size:50 final size:50
Alignment explanation
Indices: 11629803--11630535 Score: 485
Period size: 49 Copynumber: 14.9 Consensus size: 50
11629793 TCAATTTTTT
* * * * *
11629803 CATCATAT-TTCTTAGGTACCGGGTTTGCCGTTACGGCCTCAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * *
11629852 CTTCATATCTTC-ATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
*
11629901 CATCACATCTTCTAAGGTA-CGGGATCCGCCGTTGCGGCCTCAATCC-TTCC
1 CATCACATCTTCTAAGGTATCGGG-TTCGCCGTTGCGGCCTCAA-CCTTTCC
* * * * ***
11629951 CTTCAAATCTTC-ATGGTATCGGGTTCACCGTTATAGCCTCAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * *
11630000 CATCATATCTTCTAAGG-ATCGAGTTCGCTGTTGCGGCCTCAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
** * *
11630049 TTTCATATCTTCGT--GGTATCAGGTTCGCCGTTGCGGCCTCAACCTTTCC
1 CATCACATCTTC-TAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * *** * * *
11630098 CATCGCATCTTTTAAGGTATCAAATTTGCCGTTGTGACCTCAATCC-TT-C
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCC
* * * * * * *
11630147 CATTCAAACCCTC-ATA-GTAGCGGGTTCACCATTGTGGCCTCAACCTTTCC
1 CA-TCACATCTTCTA-AGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * * ** * *
11630197 CATAACATCTTTTAAGGTATCGAGTTCGCCGTTACGGTGTCCATCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * * * *
11630247 CTTCATATCTTC-ATGGTATCGAGTTCGCTGTTGCGGCCACAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * * * * * *
11630296 CATCGCATCTTTTAAGGTA-CTAGATTGGCCGTTACAGCCACAATCC-TTCC
1 CATCACATCTTCTAAGGTATC-GGGTTCGCCGTTGCGGCCTCAA-CCTTTCC
* * * * * ** * * * *
11630346 CTTCAAATCCT-TATGGTACCAAGTTCACTGTTACGGCCTTAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * *
11630395 TATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * * *
11630445 CATCACATCTTTTAAGGTACCGGGTTCACCATTGTGGCCTCAACCTTTCC
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * ** *
11630495 CTTCATATCTTC-AGGGTAT-TAGTTTGCCGTTGCGGCCTCAA
1 CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA
11630536 TCTTCCCTGT
Statistics
Matches: 530, Mismatches: 130, Indels: 49
0.75 0.18 0.07
Matches are distributed among these distances:
48 25 0.05
49 264 0.50
50 235 0.44
51 6 0.01
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (50 bp):
CATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
Found at i:11629990 original size:99 final size:99
Alignment explanation
Indices: 11629829--11630549 Score: 661
Period size: 99 Copynumber: 7.3 Consensus size: 99
11629819 TACCGGGTTT
* * *
11629829 GCCGTTACGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCA
1 GCCGTTGCGGCCTCAATCC-TTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCA
* * *
11629893 ACCTTTCCCATCACATCTTCTAAGGTA-CGGGATCC
65 ACCTTTCCCATCACATCTTTTAAGGTATCGAG-TTC
* ***
11629928 GCCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTATCGGGTTCACCGTTATAGCCTCAA
1 GCCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAA
* *
11629993 CCTTTCCCATCATATCTTCTAAGG-ATCGAGTTC
66 CCTTTCCCATCACATCTTTTAAGGTATCGAGTTC
* * * * * * *
11630026 GCTGTTGCGGCCTCAA-CCTTTCCTTTCATATCTTCGTGGTATCAGGTTCGCCGTTGCGGCCTCA
1 GCCGTTGCGGCCTCAATCC-TTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCA
* * * *
11630090 ACCTTTCCCATCGCATCTTTTAAGGTATCAAATTT
65 ACCTTTCCCATCACATCTTTTAAGGTATCGAGTTC
* * * * * * * * *
11630125 GCCGTTGTGACCTCAATCCTTCCATTCAAACCCTCATAGTAGCGGGTTCACCATTGTGGCCTCAA
1 GCCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAA
*
11630190 CCTTTCCCATAACATCTTTTAAGGTATCGAGTTC
66 CCTTTCCCATCACATCTTTTAAGGTATCGAGTTC
* ** * * * * * * * *
11630224 GCCGTTACGGTGTCCATCTTTCCCTTCATATCTTCATGGTATCGAGTTCGCTGTTGCGGCCACAA
1 GCCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAA
* * *
11630289 CCTTTCCCATCGCATCTTTTAAGGTA-CTAGATTG
66 CCTTTCCCATCACATCTTTTAAGGTATCGAG-TTC
* * * ** * * *
11630323 GCCGTTACAGCCACAATCCTTCCCTTCAAATCCTT-ATGGTACCAAGTTCACTGTTACGGCCTTA
1 GCCGTTGCGGCCTCAATCCTTCCCTTCAAAT-CTTCATGGTACCGGGTTCACCGTTGCGGCCTCA
* * *
11630387 ACCTTTCCTATCACATCTTTTAAGGTACCGGGTTC
65 ACCTTTCCCATCACATCTTTTAAGGTATCGAGTTC
* * * * * * *
11630422 ACCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTTTAAGGTACCGGGTTCACCATTGTGGCCTC
1 GCCGTTGCGGCCTCAATCC-TTCCCTTCAAATC-TTCATGGTACCGGGTTCACCGTTGCGGCCTC
* * * * * *
11630486 AACCTTTCCCTTCATATC-TTCAGGGTAT-TAGTTT
64 AACCTTTCCCATCACATCTTTTAAGGTATCGAGTTC
11630520 GCCGTTGCGGCCTCAAT-CTTCCCTGTCAAA
1 GCCGTTGCGGCCTCAATCCTTCCCT-TCAAA
11630550 CCTGTAGAAT
Statistics
Matches: 498, Mismatches: 111, Indels: 27
0.78 0.17 0.04
Matches are distributed among these distances:
97 7 0.01
98 106 0.21
99 341 0.68
100 44 0.09
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (99 bp):
GCCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAA
CCTTTCCCATCACATCTTTTAAGGTATCGAGTTC
Found at i:11630342 original size:198 final size:197
Alignment explanation
Indices: 11629829--11630495 Score: 755
Period size: 198 Copynumber: 3.4 Consensus size: 197
11629819 TACCGGGTTT
* *
11629829 GCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAA
1 GCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGAGTTCGCCGTTGCGGCCTCAA
* * ** * *
11629894 CCTTTCCCATCACATCTTCTAAGGTACGGGATCCGCCGTTGCGGCCTCAATCCTTCCCTTCAAAT
66 CCTTTCCCATCGCATCTTTTAAGGTACTAGATTCGCCGTT-CAGCCTCAATCCTTCCCTTCAAAT
* * * * *
11629959 CTTCATGGTATCGGGTTCACCGTTATAGCCTCAACCTTTCCCATCATATCTTCTAAGG-ATCGAG
130 CCTCATGGTACCGGGTTCACCGTTATGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCGAG
11630023 TTC
195 TTC
* * * *
11630026 GCTGTTGCGGCCTCAACCTTTCCTTTCATATCTTCGTGGTATC-AGGTTCGCCGTTGCGGCCTCA
1 GCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGA-GTTCGCCGTTGCGGCCTCA
* * ** *
11630090 ACCTTTCCCATCGCATCTTTTAAGGTA-TCAAATTTGCCGTTGTGACCTCAATCCTTCCATTCAA
65 ACCTTTCCCATCGCATCTTTTAAGGTACT-AGATTCGCCGTTCAG-CCTCAATCCTTCCCTTCAA
* * * * * *
11630154 ACCCTCATAGTAGCGGGTTCACCATTGTGGCCTCAACCTTTCCCATAACATCTTTTAAGGTATCG
128 ATCCTCATGGTACCGGGTTCACCGTTATGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCG
11630219 AGTTC
193 AGTTC
** * * * *
11630224 GCCGTTACGGTGTCCATCTTTCCCTTCATATCTTCATGGTATCGAGTTCGCTGTTGCGGCCACAA
1 GCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGAGTTCGCCGTTGCGGCCTCAA
* *
11630289 CCTTTCCCATCGCATCTTTTAAGGTACTAGATTGGCCGTTACAGCCACAATCCTTCCCTTCAAAT
66 CCTTTCCCATCGCATCTTTTAAGGTACTAGATTCGCCGTT-CAGCCTCAATCCTTCCCTTCAAAT
* ** * * * * * *
11630354 CCTTATGGTACCAAGTTCACTGTTACGGCCTTAACCTTTCCTATCACATCTTTTAAGGTACCGGG
130 CCTCATGGTACCGGGTTCACCGTTATGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCGAG
11630419 TTC
195 TTC
* * * * * * * * * * *
11630422 ACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGGTTCACCATTGTGGCCTCA
1 GCCGTTACGGCCTCAACCTTTCCCTTCATATC-TTCATGGTATCGAGTTCGCCGTTGCGGCCTCA
11630487 ACCTTTCCC
65 ACCTTTCCC
11630496 TTCATATCTT
Statistics
Matches: 388, Mismatches: 74, Indels: 14
0.82 0.16 0.03
Matches are distributed among these distances:
196 1 0.00
197 158 0.41
198 194 0.50
199 35 0.09
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.33
Consensus pattern (197 bp):
GCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGAGTTCGCCGTTGCGGCCTCAA
CCTTTCCCATCGCATCTTTTAAGGTACTAGATTCGCCGTTCAGCCTCAATCCTTCCCTTCAAATC
CTCATGGTACCGGGTTCACCGTTATGGCCTCAACCTTTCCCATCACATCTTTTAAGGTATCGAGT
TC
Found at i:11634776 original size:29 final size:29
Alignment explanation
Indices: 11634746--11635043 Score: 214
Period size: 30 Copynumber: 10.1 Consensus size: 29
11634736 TTTCAGAGAA
* *
11634746 TTTAGGGTTAAAATGTAATTTTAGAAAAA
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
*
11634775 TTTAGAGGTTAAAATGTAATTTTAGG-TAAG
1 TTTAG-GGTTAAAATGTAATTTT-GGAAAAG
* * * *
11634805 TTTAGGGGTAAAAATGTGATTTTAGG-GAAC
1 TTTA-GGGTTAAAATGTAATTTT-GGAAAAG
* *
11634835 TTTAAGTGG-TAGAATGCT-ATTTTGGGAAAG
1 TTT-AG-GGTTAAAATG-TAATTTTGGAAAAG
* * *
11634865 TTTGAGGGTCAAAATGTGATTTTGG-GAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
* * * * *
11634894 TTTAAGGATGAAAACGTGATTTT-GAGGAAG
1 TTT-AGGGTTAAAATGTAATTTTGGA-AAAG
* *
11634924 TTTTGGGTTAAAATGTGATTTTGGAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
*
11634953 TTTGGGGGTTAAAATGTAATTTTGGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
*
11634983 TTTAGGGGTTAAAATATAA-TTTGGAAAAG
1 TTTA-GGGTTAAAATGTAATTTTGGAAAAG
* ** *
11635012 TTTAGGGTGAAAATAAAATTTTGGAAAGG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
11635041 TTT
1 TTT
11635044 GGGGGTCAAA
Statistics
Matches: 223, Mismatches: 31, Indels: 30
0.79 0.11 0.11
Matches are distributed among these distances:
28 13 0.06
29 79 0.35
30 125 0.56
31 6 0.03
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.36
Consensus pattern (29 bp):
TTTAGGGTTAAAATGTAATTTTGGAAAAG
Found at i:11634817 original size:59 final size:59
Alignment explanation
Indices: 11634746--11635074 Score: 219
Period size: 59 Copynumber: 5.6 Consensus size: 59
11634736 TTTCAGAGAA
* * * *
11634746 TTTAGGGTTAAAATGTAATTTTAGAAAAATTTAGAGGTTAAAATGTAATTTTAGGTAAG
1 TTTAGGGGTAAAATGTGATTTTAGAAAAGTTTAGAGGTTAAAATGTAATTTTAGGAAAG
** * * * *
11634805 TTTAGGGGTAAAAATGTGATTTTAGGGAACTTTA-AGTGGTAGAATGCT-ATTTTGGGAAAG
1 TTTAGGGGT-AAAATGTGATTTTAGAAAAGTTTAGAG-GTTAAAATG-TAATTTTAGGAAAG
** * * *
11634865 TTT-GAGGGTCAAAATGTGATTTT-GGGAAGTTTA-AGGATGAAAACGTGATTTTGAGG-AAG
1 TTTAG-GGGT-AAAATGTGATTTTAGAAAAGTTTAGAGG-TTAAAATGTAATTTT-AGGAAAG
* * * * *
11634924 TTTTGGGTTAAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTT-GGAAAAG
1 TTTAGGGGTAAAATGTGATTTTAGAAAAGTTTAGAGGTTAAAATGTAATTTTAGG-AAAG
* * * * **
11634983 TTTAGGGGTTAAAATAT-AATTTGGAAAAGTTTAG-GGTGAAAATAAAATTTT-GGAAAGG
1 TTTAGGGG-TAAAATGTGATTTTAGAAAAGTTTAGAGGTTAAAATGTAATTTTAGGAAA-G
* * * *
11635041 TTTGGGGGTCAAAATATGATTTTATAAAGGTTTA
1 TTTAGGGGT-AAAATGTGATTTTAGAAAAGTTTA
11635075 AGGGTCAAAA
Statistics
Matches: 217, Mismatches: 37, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
57 6 0.03
58 46 0.21
59 95 0.44
60 69 0.32
61 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
TTTAGGGGTAAAATGTGATTTTAGAAAAGTTTAGAGGTTAAAATGTAATTTTAGGAAAG
Found at i:11635049 original size:58 final size:59
Alignment explanation
Indices: 11634928--11635062 Score: 164
Period size: 58 Copynumber: 2.3 Consensus size: 59
11634918 AGGAAGTTTT
* * * * **
11634928 GGGTTAAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATAT-AATTTGGAAAAGTTTGAGGGTGAAAATAAAATTTTGGAAAAGTTTAG
* *
11634988 GGGTTAAAATATAATTTGGAAAAGTTT-AGGGTGAAAATAAAATTTTGGAAAGGTTTGG
1 GGGTTAAAATATAATTTGGAAAAGTTTGAGGGTGAAAATAAAATTTTGGAAAAGTTTAG
* *
11635046 GGGTCAAAATATGATTT
1 GGGTTAAAATATAATTT
11635063 TATAAAGGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 40 0.62
59 14 0.22
60 11 0.17
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (59 bp):
GGGTTAAAATATAATTTGGAAAAGTTTGAGGGTGAAAATAAAATTTTGGAAAAGTTTAG
Found at i:11635063 original size:30 final size:29
Alignment explanation
Indices: 11634853--11635087 Score: 152
Period size: 30 Copynumber: 8.0 Consensus size: 29
11634843 GTAGAATGCT
* *
11634853 ATTTTGGGAAAGTTTGAGGGTCAAAATGTG
1 ATTTT-GGAAAGTTTAAGGGTCAAAATATG
* * * **
11634883 ATTTTGGGAAGTTTAAGGATGAAAACGTG
1 ATTTTGGAAAGTTTAAGGGTCAAAATATG
* * * *
11634912 ATTTTGAGGAAGTTT-TGGGTTAAAATGTG
1 ATTTTG-GAAAGTTTAAGGGTCAAAATATG
** * * *
11634941 ATTTTGGAAAAGTTTGGGGGTTAAAATGTA
1 ATTTTGG-AAAGTTTAAGGGTCAAAATATG
* *
11634971 ATTTTGGAAAAGTTTAGGGGTTAAAATAT-
1 ATTTTGG-AAAGTTTAAGGGTCAAAATATG
* * **
11635000 AATTTGGAAAAGTTT-AGGGTGAAAATAAA
1 ATTTTGG-AAAGTTTAAGGGTCAAAATATG
**
11635029 ATTTTGGAAAGGTTTGGGGGTCAAAATATG
1 ATTTTGGAAA-GTTTAAGGGTCAAAATATG
**
11635059 ATTTTATAAAGGTTTAAGGGTCAAAATAT
1 ATTTTGGAAA-GTTTAAGGGTCAAAATAT
11635088 AGCTTTTAAA
Statistics
Matches: 172, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
28 14 0.08
29 71 0.41
30 87 0.51
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (29 bp):
ATTTTGGAAAGTTTAAGGGTCAAAATATG
Found at i:11638895 original size:14 final size:15
Alignment explanation
Indices: 11638876--11638905 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11638866 AGTTTGATTG
11638876 AAAATAA-AGAAATA
1 AAAATAATAGAAATA
11638890 AAAATAATAGAAATA
1 AAAATAATAGAAATA
11638905 A
1 A
11638906 TGGATATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAATAATAGAAATA
Found at i:11639246 original size:3 final size:3
Alignment explanation
Indices: 11639238--11639262 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11639228 GCGGGCTTGG
11639238 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
11639263 AATATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11639851 original size:5 final size:5
Alignment explanation
Indices: 11639841--11639866 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11639831 GAACAAATAT
11639841 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
11639867 ATTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:11652507 original size:20 final size:19
Alignment explanation
Indices: 11652471--11652516 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
11652461 GAGGAAGGGG
11652471 AGGAAG-AAGAGAAAAGAA
1 AGGAAGAAAGAGAAAAGAA
11652489 AGGAAGAAAGAGAAAAAGAA
1 AGGAAGAAAGAG-AAAAGAA
*
11652509 AAGAAGAA
1 AGGAAGAA
11652517 GAATTTCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.24
19 5 0.20
20 14 0.56
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AGGAAGAAAGAGAAAAGAA
Found at i:11665151 original size:25 final size:25
Alignment explanation
Indices: 11665123--11665171 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11665113 AAGTCGTAGC
*
11665123 AAGAGAAATTGAAGAAGTTCAGAAA
1 AAGAGAAATTGAACAAGTTCAGAAA
*
11665148 AAGAGAAATTGAACAAGTTGAGAA
1 AAGAGAAATTGAACAAGTTCAGAA
11665172 GATATAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.16
Consensus pattern (25 bp):
AAGAGAAATTGAACAAGTTCAGAAA
Found at i:11666913 original size:19 final size:20
Alignment explanation
Indices: 11666879--11666916 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11666869 AGAAATGAGA
11666879 GAATAGAAGAGATGATTAAT
1 GAATAGAAGAGATGATTAAT
*
11666899 GAATGGAAG-GATGATTAA
1 GAATAGAAGAGATGATTAA
11666917 GAAGTGAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (20 bp):
GAATAGAAGAGATGATTAAT
Done.