Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 174 of 175
Found at i:52552482 original size:59 final size:57
Alignment explanation
Indices: 52552416--52552604 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
52552406 ATTTTATTAA
52552416 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
52552475 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
52552536 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
52552595 ATCATATATT
1 ATCATATATT
52552605 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:52552513 original size:66 final size:64
Alignment explanation
Indices: 52552443--52552641 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
52552433 AAATATATTT
52552443 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
52552508 G
64 G
* * * * * **
52552509 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
52552563 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
52552628 G
64 G
*
52552629 AATATTGATTATT
1 AATATTAATTATT
52552642 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:52552529 original size:120 final size:120
Alignment explanation
Indices: 52552405--52552702 Score: 517
Period size: 120 Copynumber: 2.5 Consensus size: 120
52552395 AATTATTTTA
* * *
52552405 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
52552469 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
52552525 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
52552590 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
52552645 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
52552703 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 161 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:52552545 original size:61 final size:61
Alignment explanation
Indices: 52552478--52552665 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
52552468 TTATAGTATC
52552478 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
52552539 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
52552597 C
61 T
*
52552598 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
52552659 ATATATT
1 ATATATT
52552666 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:52552565 original size:15 final size:15
Alignment explanation
Indices: 52552530--52552581 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52552520 TTAAGAATTT
*
52552530 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52552544 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52552558 TATTTAATAATAAT-
1 TATTTAATTATAATA
52552572 TATGTTAATT
1 TAT-TTAATT
52552582 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52552674 original size:18 final size:17
Alignment explanation
Indices: 52552646--52552680 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52552636 ATTATTAAGA
*
52552646 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52552663 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52552681 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52552910 original size:44 final size:45
Alignment explanation
Indices: 52552845--52552935 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
52552835 ACCTCTATTC
* * *
52552845 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
52552889 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
52552934 CA
1 CA
52552936 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:52552937 original size:16 final size:16
Alignment explanation
Indices: 52552916--52552984 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
52552906 GATTAGCTAT
52552916 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52552932 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
52552949 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52552965 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52552981 TACA
1 TACA
52552985 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:52552958 original size:33 final size:32
Alignment explanation
Indices: 52552916--52552984 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
52552906 GATTAGCTAT
52552916 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
52552949 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
52552981 TACA
1 TACA
52552985 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:52569062 original size:24 final size:23
Alignment explanation
Indices: 52569018--52569063 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
52569008 TTTATTTACG
* * *
52569018 TTTTATTATTTTTATTTTTATTC
1 TTTTATAATTTTTAATATTATTC
52569041 TTTTATAATGTTTTAATATTATT
1 TTTTATAAT-TTTTAATATTATT
52569064 TGTTTGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTATAATTTTTAATATTATTC
Found at i:52569077 original size:12 final size:13
Alignment explanation
Indices: 52569060--52569088 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52569050 GTTTTAATAT
52569060 TATTTG-TTTGTA
1 TATTTGTTTTGTA
52569072 TATTTGTTTTGTA
1 TATTTGTTTTGTA
52569085 TATT
1 TATT
52569089 ATGGGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (13 bp):
TATTTGTTTTGTA
Found at i:52579439 original size:12 final size:12
Alignment explanation
Indices: 52579422--52579446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52579412 TATTTTATAA
52579422 TTTTTAACCTAT
1 TTTTTAACCTAT
52579434 TTTTTAACCTAT
1 TTTTTAACCTAT
52579446 T
1 T
52579447 CTCTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTAACCTAT
Found at i:52590026 original size:15 final size:15
Alignment explanation
Indices: 52590006--52590034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52589996 GTTCTAAGTC
52590006 TGTGTCTGGTTAATT
1 TGTGTCTGGTTAATT
52590021 TGTGTCTGGTTAAT
1 TGTGTCTGGTTAAT
52590035 AAGGTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (15 bp):
TGTGTCTGGTTAATT
Found at i:52596963 original size:27 final size:27
Alignment explanation
Indices: 52596931--52596982 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
52596921 AACTTTTAAA
*
52596931 GGATTAAA-TCACAATTTTATTATTTTG
1 GGATTAAAGT-ACAATTTTATCATTTTG
*
52596958 GGATTAAAGTATAATTTTATCATTT
1 GGATTAAAGTACAATTTTATCATTT
52596983 ACTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.48
Consensus pattern (27 bp):
GGATTAAAGTACAATTTTATCATTTTG
Found at i:52600642 original size:146 final size:143
Alignment explanation
Indices: 52600376--52600645 Score: 391
Period size: 146 Copynumber: 1.9 Consensus size: 143
52600366 GCTTTTGCTC
* * *
52600376 AAATAATAAAATTGATAGAGTAAACTTTAAGGTTTATTAGGTATAAATCCATATGTTTTTTTAGA
1 AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTACTAGATATAAATCCATATGTTTTTTTAGA
*
52600441 TTTATTAAAATATAAAAAGACATAAATATCCTCAAAATAATATTTATTGATTTATAAAATGAAAC
66 TTTATCAAAATATAAAAAGACATAAATATCCTCAAAATAATATTTATTGATTTATAAAATGAAAC
52600506 GAGACTTTTATTA
131 GAGACTTTTATTA
*
52600519 AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTCCTAGAT-TCAAATCCATATGCTTTTTTTC
1 AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTACTAGATAT-AAATCCATATG--TTTTTT-
* * * * *
52600583 TCGATTTATCGAAATATAGAAAGGCATAAATA-CCTTCAAAATAATATTTATTGGTTTATAAAA
62 TAGATTTATCAAAATATAAAAAGACATAAATATCC-TCAAAATAATATTTATTGATTTATAAAA
52600646 CGAATGTGTT
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
142 1 0.01
143 49 0.44
145 8 0.07
146 54 0.48
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (143 bp):
AAATAATAAAATTGAAAGAGTAAACTTTAAGGTTTACTAGATATAAATCCATATGTTTTTTTAGA
TTTATCAAAATATAAAAAGACATAAATATCCTCAAAATAATATTTATTGATTTATAAAATGAAAC
GAGACTTTTATTA
Found at i:52601512 original size:25 final size:25
Alignment explanation
Indices: 52601467--52601515 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
52601457 GATACTGTAT
*
52601467 CAAAAAATGAAATCAATACAAAAATA
1 CAAAAAA-GAAATCAAAACAAAAATA
52601493 CAAAAAA-AAATCAAAAACAAAAA
1 CAAAAAAGAAATC-AAAACAAAAA
52601516 ACATACCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.76, C:0.12, G:0.02, T:0.10
Consensus pattern (25 bp):
CAAAAAAGAAATCAAAACAAAAATA
Found at i:52602712 original size:29 final size:28
Alignment explanation
Indices: 52602652--52602727 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
52602642 CTCTTTCAAA
*
52602652 TATTTTAACATTTTTAATTTATTTCAACT
1 TATTTCAACA-TTTTAATTTATTTCAACT
* *
52602681 TATTTCAATATTGTTAATTTA-TTCAAATT
1 TATTTCAACATT-TTAATTTATTTC-AACT
*
52602710 TATTTTAACATTTTAATT
1 TATTTCAACATTTTAATT
52602728 CATATATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 11 0.28
29 29 0.73
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (28 bp):
TATTTCAACATTTTAATTTATTTCAACT
Found at i:52603790 original size:31 final size:31
Alignment explanation
Indices: 52603737--52603795 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
52603727 ACAATATGGT
* *
52603737 CATTGAATTATTTAAAAATTTTCATTTAAGC
1 CATTGAACTATTCAAAAATTTTCATTTAAGC
*
52603768 CATTGAACTATTCAAAATTTTTCATTTA
1 CATTGAACTATTCAAAAATTTTCATTTA
52603796 GGTCACCAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (31 bp):
CATTGAACTATTCAAAAATTTTCATTTAAGC
Found at i:52612022 original size:6 final size:6
Alignment explanation
Indices: 52612011--52612108 Score: 182
Period size: 6 Copynumber: 16.7 Consensus size: 6
52612001 GGCCAGTAGT
52612011 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
52612059 TACACA TACACA TACACA TACACA TACACA TACAC- -ACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
52612105 TACA
1 TACA
52612109 TTATATAACT
Statistics
Matches: 90, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.04
6 86 0.96
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
TACACA
Found at i:52612157 original size:55 final size:56
Alignment explanation
Indices: 52612094--52612217 Score: 223
Period size: 56 Copynumber: 2.2 Consensus size: 56
52612084 ACACATACAC
* *
52612094 ACACATACACATACATTATATAACTTAAGG-CCAGTAGTTACACAAATAAGAGCAT
1 ACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAGAAT
52612149 ACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAGAAT
1 ACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAGAAT
52612205 ACACATACACATA
1 ACACATACACATA
52612218 GACATACATC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
55 30 0.45
56 36 0.55
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (56 bp):
ACACATACACATACATTATATAACTTAAGGAACAGTAGTTACACAAATAAGAGAAT
Found at i:52614845 original size:12 final size:12
Alignment explanation
Indices: 52614824--52614857 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
52614814 TGTATATACA
*
52614824 TGTATATGTATG
1 TGTATGTGTATG
52614836 TGTATGTGTATG
1 TGTATGTGTATG
52614848 TGTATGTGTA
1 TGTATGTGTA
52614858 CAAGTACGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (12 bp):
TGTATGTGTATG
Found at i:52615105 original size:145 final size:145
Alignment explanation
Indices: 52614842--52615136 Score: 457
Period size: 145 Copynumber: 2.0 Consensus size: 145
52614832 TATGTGTATG
* **
52614842 TGTATGTGTATGTGTACAAGTACGTACATCGCAATGCAACATAATTCTAATTATGTCATGGACAT
1 TGTATGTGTATGTATACAAGTACGTACATCGCAATGCAACATAATTCTAACCATGTCATGGACAT
* * * *
52614907 GAAGGATATGAGGGATAGATGATTCTTTTCGTAAATGTGTTGTTGTTGGTGGTATGATTTGCAGC
66 GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
*
52614972 C-TAGTGAATTCTATA
131 CAT-GTGAATCCTATA
* * * * *
52614987 TGTATTTGTATGTATATATGTACGTATATTGCAATGCAACATAATTCTAACCATGTCATGGACAT
1 TGTATGTGTATGTATACAAGTACGTACATCGCAATGCAACATAATTCTAACCATGTCATGGACAT
52615052 GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
66 GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
52615117 CATGTGAATCCTATA
131 CATGTGAATCCTATA
52615132 TGTAT
1 TGTAT
52615137 ATGTGTACGT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
145 135 0.99
146 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (145 bp):
TGTATGTGTATGTATACAAGTACGTACATCGCAATGCAACATAATTCTAACCATGTCATGGACAT
GAAGGATATGAGGGATAGATGATTCTTTTCCTAAATGTGCTATTGTTGATGGTATGATTTGCAGC
CATGTGAATCCTATA
Found at i:52617712 original size:16 final size:17
Alignment explanation
Indices: 52617691--52617723 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52617681 AATGTTTTGG
*
52617691 TTATTT-ATTTTCTTTT
1 TTATTTGATTTTATTTT
52617707 TTATTTGATTTTATTTT
1 TTATTTGATTTTATTTT
52617724 ATGTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTGATTTTATTTT
Found at i:52620047 original size:29 final size:29
Alignment explanation
Indices: 52619988--52620047 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
52619978 TCGTTCTTAT
* **
52619988 TTTGGTCATCCTAAATTTTTTTTTGTTAA
1 TTTGGTCACCCTAAATTTTTTTTTGCAAA
52620017 TTTGGTCACCCTAAATTTTTTTTAT-CAAA
1 TTTGGTCACCCTAAATTTTTTTT-TGCAAA
52620046 TT
1 TT
52620048 AATCACTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.55
Consensus pattern (29 bp):
TTTGGTCACCCTAAATTTTTTTTTGCAAA
Found at i:52624801 original size:24 final size:24
Alignment explanation
Indices: 52624750--52624805 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
52624740 TATACACCAG
* *
52624750 CACCTCCACCACCAGAACCACCTC
1 CACCACCACCACCAGAACCACCTA
*
52624774 CACCACCACCACCATG-ACCGCCTA
1 CACCACCACCACCA-GAACCACCTA
52624798 CACCACCA
1 CACCACCA
52624806 AAACCTCCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.57, G:0.05, T:0.07
Consensus pattern (24 bp):
CACCACCACCACCAGAACCACCTA
Found at i:52624859 original size:30 final size:30
Alignment explanation
Indices: 52624825--52624903 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 30
52624815 CCAGCTCCTT
52624825 CTCCACCACCATATCCACCTGCA-TGTGCCC
1 CTCCACCACCATATCCACCTGCACT-TGCCC
* *
52624855 CTCCACCACCATATCCTCCTGCACTTGCTC
1 CTCCACCACCATATCCACCTGCACTTGCCC
52624885 CTCCACCACCACT-TCCACC
1 CTCCACCACCA-TATCCACC
52624904 ACCACCTCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 42 0.95
31 2 0.05
ACGTcount: A:0.19, C:0.53, G:0.06, T:0.22
Consensus pattern (30 bp):
CTCCACCACCATATCCACCTGCACTTGCCC
Found at i:52624901 original size:12 final size:12
Alignment explanation
Indices: 52624884--52624913 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52624874 TGCACTTGCT
52624884 CCTCCACCACCA
1 CCTCCACCACCA
*
52624896 CTTCCACCACCA
1 CCTCCACCACCA
52624908 CCTCCA
1 CCTCCA
52624914 TGTCCACCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.63, G:0.00, T:0.13
Consensus pattern (12 bp):
CCTCCACCACCA
Found at i:52625040 original size:3 final size:3
Alignment explanation
Indices: 52625034--52625065 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52625024 AGCTCCGCCG
*
52625034 CCA CCA CTA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
52625066 TCCATGTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.66, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:52625152 original size:135 final size:134
Alignment explanation
Indices: 52625046--52625714 Score: 854
Period size: 135 Copynumber: 5.0 Consensus size: 134
52625036 ACCACTACCA
* * *
52625046 CCACCACCACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCCCCGGCACCACCAGTTCC
1 CCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCACCGGCACCACCAGCTCC
52625111 ACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCAC-CATATCCACCTGCACTAGCT
66 ACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACAC-TATCCACCTGCACTAGCT
52625175 CCACCG
130 -CACCG
*
52625181 CCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCC
1 CCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCACCGGCACCACCAGCTCC
* * *
52625246 GCCTCCTTCGCCACCTCCACCACCATATCCAGAAGCTCCACCAC-CGTATCCACCTGTACTAGCT
66 ACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACAC-TATCCACCTGCACTAGCT
*
52625310 CCGCCG
130 -CACCG
* * *
52625316 CCACCACTACCACCACCACCTCCATGTCCACCTGCACCACCA-GCTCCACCGGCACCACCAGCTC
1 CCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATAC-CCACCGGCACCACCAGCTC
* *
52625380 CACCTCCTTCACCACCCCCACCGCCATATCCAGAAGCTCCACCAC-CATATCCACCTGCACTAGC
65 CACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACAC-TATCCACCTGCACTAGC
*
52625444 T--TCG
129 TCACCG
* * * *
52625448 ---------CCGCCACCACCTCCATGTCCACCTGCACCACCA-GCTCCACCGGCACCACCAGCTC
1 CCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATAC-CCACCGGCACCACCAGCTC
52625503 CACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCAC-CATATCCACCTGCACTAGC
65 CACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACAC-TATCCACCTGCACTAGC
* *
52625567 TCCGCCA
129 T-CACCG
* *
52625574 CCACCACTACCACCACCACCTCCAAT-TCCACCCGCTCCTCCATACCCGCCGGCACCACCAGCTC
1 CCACCACTACCACCACCACCTCC-ATGTCCACCTGCTCCTCCATACCCACCGGCACCACCAGCTC
* * * *
52625638 CGCCTCCTTCACCACCTCCACCACCATATCCAGAAGCTCCACCGC-CATATCCACCTGCACTAGC
65 CACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACAC-TATCCACCTGCACTAGC
*
52625702 TCCACCA
129 T-CACCG
52625709 CCACCA
1 CCACCA
52625715 TTGCCACCTC
Statistics
Matches: 484, Mismatches: 35, Indels: 30
0.88 0.06 0.05
Matches are distributed among these distances:
123 117 0.24
126 1 0.00
132 2 0.00
134 1 0.00
135 360 0.74
136 3 0.01
ACGTcount: A:0.22, C:0.54, G:0.10, T:0.15
Consensus pattern (134 bp):
CCACCACTACCACCACCACCTCCATGTCCACCTGCTCCTCCATACCCACCGGCACCACCAGCTCC
ACCTCCTTCGCCACCTCCACCGCCATATCCAGAAGCTCCACCACACTATCCACCTGCACTAGCTC
ACCG
Found at i:52625200 original size:48 final size:47
Alignment explanation
Indices: 52625001--52625215 Score: 122
Period size: 48 Copynumber: 4.4 Consensus size: 47
52624991 TCCAGAAGCT
*
52625001 CCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCACTACCACCA
1 CCACCACCATATCCACCTGCACT-GCTCCACCGCCACCACTACCACCA
* * * *
52625049 CCACCACCACCA-CCACCTCCA-TG-TCCACCTGCTCCTCCA-TACC-CCC
1 CCACCACCA-TATCCACCTGCACTGCTCCACC-G--CCACCACTACCACCA
* * * * * *
52625095 CGGCACCACCAGT-TCCACCT-C-CTTCGCCACCTCCACCGCCATATCCAGAAGCT
1 C--CACCACCA-TATCCACCTGCACTGCTCCACCGCCACC-AC-TA-CC---ACCA
52625148 CCACCACCATATCCACCTGCACTAGCTCCACCGCCACCACTACCACCA
1 CCACCACCATATCCACCTGCACT-GCTCCACCGCCACCACTACCACCA
* *
52625196 CCACCTCCATGTCCACCTGC
1 CCACCACCATATCCACCTGC
52625216 TCCTCCATAC
Statistics
Matches: 124, Mismatches: 22, Indels: 42
0.66 0.12 0.22
Matches are distributed among these distances:
45 9 0.07
46 5 0.04
47 7 0.06
48 63 0.51
49 3 0.02
50 1 0.01
51 17 0.14
52 3 0.02
53 5 0.04
54 11 0.09
ACGTcount: A:0.22, C:0.54, G:0.08, T:0.15
Consensus pattern (47 bp):
CCACCACCATATCCACCTGCACTGCTCCACCGCCACCACTACCACCA
Found at i:52625353 original size:18 final size:18
Alignment explanation
Indices: 52625342--52625384 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
52625332 CACCTCCATG
52625342 TCCACCTGCACCACCAGC
1 TCCACCTGCACCACCAGC
*
52625360 TCCACCGGCACCACCAGC
1 TCCACCTGCACCACCAGC
52625378 TCCACCT
1 TCCACCT
52625385 CCTTCACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.56, G:0.12, T:0.12
Consensus pattern (18 bp):
TCCACCTGCACCACCAGC
Found at i:52625486 original size:18 final size:18
Alignment explanation
Indices: 52625465--52625507 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
52625455 CACCTCCATG
52625465 TCCACCTGCACCACCAGC
1 TCCACCTGCACCACCAGC
*
52625483 TCCACCGGCACCACCAGC
1 TCCACCTGCACCACCAGC
52625501 TCCACCT
1 TCCACCT
52625508 CCTTCGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.56, G:0.12, T:0.12
Consensus pattern (18 bp):
TCCACCTGCACCACCAGC
Found at i:52625493 original size:258 final size:258
Alignment explanation
Indices: 52625193--52625702 Score: 810
Period size: 258 Copynumber: 2.0 Consensus size: 258
52625183 ACCACTACCA
* * * *
52625193 CCACCACCTCCATGTCCACCTGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCGCC
1 CCACCACCTCCATGTCCACCTGCACCACCATACCCACCGGCACCACCAGCTCCACCTCCTTCGCC
* * *
52625258 ACCTCCACCACCATATCCAGAAGCTCCACCACCGTATCCACCTGTACTAGCTCCGCCGCCACCAC
66 ACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCAC
* *
52625323 TACCACCACCACCTCC-ATGTCCACCTGCACCACCA-GCTCCACCGGCACCACCAGCTCCACCTC
131 TACCACCACCACCTCCAAT-TCCACCCGCACCACCATAC-CCACCGGCACCACCAGCTCCACCTC
*
52625386 CTTCACCACCCCCACCGCCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTTCGCCG
194 CTTCACCACCCCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTTCGCCG
*
52625451 CCACCACCTCCATGTCCACCTGCACCACCA-GCTCCACCGGCACCACCAGCTCCACCTCCTTCGC
1 CCACCACCTCCATGTCCACCTGCACCACCATAC-CCACCGGCACCACCAGCTCCACCTCCTTCGC
*
52625515 CACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCA
65 CACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCA
* * * *
52625580 CTACCACCACCACCTCCAATTCCACCCGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCC
130 CTACCACCACCACCTCCAATTCCACCCGCACCACCATACCCACCGGCACCACCAGCTCCACCTCC
* *
52625645 TTCACCACCTCCACCACCATATCCAGAAGCTCCACCGCCATATCCACCTGCACTAGCT
195 TTCACCACCCCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCT
52625703 CCACCACCAC
Statistics
Matches: 231, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
257 1 0.00
258 227 0.98
259 3 0.01
ACGTcount: A:0.22, C:0.53, G:0.10, T:0.15
Consensus pattern (258 bp):
CCACCACCTCCATGTCCACCTGCACCACCATACCCACCGGCACCACCAGCTCCACCTCCTTCGCC
ACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCAC
TACCACCACCACCTCCAATTCCACCCGCACCACCATACCCACCGGCACCACCAGCTCCACCTCCT
TCACCACCCCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTTCGCCG
Found at i:52625556 original size:69 final size:69
Alignment explanation
Indices: 52625473--52625697 Score: 190
Period size: 69 Copynumber: 3.3 Consensus size: 69
52625463 TGTCCACCTG
** * *
52625473 CACCACCAGCTCCACCGGCACCACCAGCTCCACCTCCTTCGCCACCTCCACCGCCATATCCAGAA
1 CACCACCATATCCACCGGCACCACCAGCTCCACCTCCTTCACCACCTCCACCACCATATCCAGAA
52625538 GCTC
66 GCTC
* * * ** * * * * * *
52625542 CACCACCATATCCACCTGCACTAGCTCCGCCACCACC-ACTACCACCACCACCTCCA-ATTCCAC
1 CACCACCATATCCACCGGCACCACCAGCTCCACCTCCTTC-ACCACCTCCACCACCATA-TCCAG
**
52625605 CCGCT-
64 AAGCTC
* * * *
52625610 --CCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCCAGAA
1 CACCACCATATCCACCGGCACCACCAGCTCCACCTCCTTCACCACCTCCACCACCATATCCAGAA
52625673 GCTC
66 GCTC
* *
52625677 CACCGCCATATCCACCTGCAC
1 CACCACCATATCCACCGGCAC
52625698 TAGCTCCACC
Statistics
Matches: 112, Mismatches: 37, Indels: 14
0.69 0.23 0.09
Matches are distributed among these distances:
66 45 0.40
67 2 0.02
68 2 0.02
69 63 0.56
ACGTcount: A:0.23, C:0.54, G:0.09, T:0.14
Consensus pattern (69 bp):
CACCACCATATCCACCGGCACCACCAGCTCCACCTCCTTCACCACCTCCACCACCATATCCAGAA
GCTC
Found at i:52625732 original size:69 final size:69
Alignment explanation
Indices: 52625514--52625732 Score: 187
Period size: 69 Copynumber: 3.2 Consensus size: 69
52625504 ACCTCCTTCG
* *
52625514 CCACCTCCACCGCCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACC
1 CCACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCACCACC
*
52625579 ACTA
66 ATTA
* * *** * * * * * * ** * * *
52625583 CCACCACCACCTCCA-ATTCCACCCGCT---CCTCCATACCCGCCGGCACCACCAGCTCCGCCTC
1 CCACCTCCACCACCATA-TCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCACCAC
52625644 C-TTCA
65 CATT-A
*
52625649 CCACCTCCACCACCATATCCAGAAGCTCCACCGCCATATCCACCTGCACTAGCTCCACCACCACC
1 CCACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCACCACC
*
52625714 ATTG
66 ATTA
*
52625718 CCACCTCCTCCACCA
1 CCACCTCCACCACCA
52625733 CCTCCATAAC
Statistics
Matches: 108, Mismatches: 35, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
65 1 0.01
66 45 0.42
67 1 0.01
68 1 0.01
69 58 0.54
70 2 0.02
ACGTcount: A:0.23, C:0.53, G:0.08, T:0.15
Consensus pattern (69 bp):
CCACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCACCACC
ATTA
Found at i:52627648 original size:19 final size:20
Alignment explanation
Indices: 52627613--52627650 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52627603 AAAATGAATT
52627613 AAATAAAAATTTCATATATA
1 AAATAAAAATTTCATATATA
*
52627633 AAATTAAAATTT-ATATAT
1 AAATAAAAATTTCATATAT
52627651 GACATTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAAAAATTTCATATATA
Found at i:52633323 original size:26 final size:26
Alignment explanation
Indices: 52633291--52633345 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
52633281 TGACAATTGT
*
52633291 TTACTTAATCAAAT-AATATAATATTA
1 TTACTTAA-AAAATCAATATAATATTA
*
52633317 TTACTTAAAAAATCAATTTAATATTA
1 TTACTTAAAAAATCAATATAATATTA
52633343 TTA
1 TTA
52633346 TACATTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
TTACTTAAAAAATCAATATAATATTA
Found at i:52633935 original size:3 final size:3
Alignment explanation
Indices: 52633929--52633959 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
52633919 ACCAGAGCCG
52633929 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
52633960 TAACACCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:52634076 original size:18 final size:18
Alignment explanation
Indices: 52634055--52634129 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
52634045 ACTCCCGCCA
*
52634055 CCACCACCACCTCCATGT
1 CCACCACCACCTCCATAT
* * *
52634073 CCACTAGCTCCTCCATAT
1 CCACCACCACCTCCATAT
* * *
52634091 CCAGCTCCACCTCCTTCA-
1 CCACCACCACCTCCAT-AT
* *
52634109 CCACCTCCACTTCCATAT
1 CCACCACCACCTCCATAT
52634127 CCA
1 CCA
52634130 GAAGCTCCTC
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
17 1 0.02
18 40 0.95
19 1 0.02
ACGTcount: A:0.21, C:0.52, G:0.04, T:0.23
Consensus pattern (18 bp):
CCACCACCACCTCCATAT
Found at i:52634506 original size:42 final size:42
Alignment explanation
Indices: 52634289--52634506 Score: 135
Period size: 42 Copynumber: 5.3 Consensus size: 42
52634279 ACTAGCTCTG
* * * ** *
52634289 CCTCCACCATTACCGCCACCAGCACCACCTCCATGTCCACCA
1 CCTCCACCATAACCACCACCAGCACCACCTCCTTCACCACCT
* * * *
52634331 GCTCCTCCATAACCACCACCAGCTCCACCTCCTTCGCCACCT
1 CCTCCACCATAACCACCACCAGCACCACCTCCTTCACCACCT
** ** * *
52634373 CCAT-TGCCAT-A-C-CCAGAAGCACCACCTGCAC-T-AGCTCCT
1 CC-TCCACCATAACCACCACCAGCACCACCT-C-CTTCACCACCT
* ** *
52634412 CCTCCACCACT-GCCACCACCAGCACCACCTCCTTGTCCACCG
1 CCTCCACCA-TAACCACCACCAGCACCACCTCCTTCACCACCT
* * *
52634454 GCTCCTCCATAACCACCACCAGCTCCACCTCCTTCACCACCT
1 CCTCCACCATAACCACCACCAGCACCACCTCCTTCACCACCT
*
52634496 CCACCACCATA
1 CCTCCACCATA
52634507 TCCAGAAGCT
Statistics
Matches: 129, Mismatches: 37, Indels: 20
0.69 0.20 0.11
Matches are distributed among these distances:
38 1 0.01
39 21 0.16
40 5 0.04
41 6 0.05
42 95 0.74
43 1 0.01
ACGTcount: A:0.22, C:0.53, G:0.08, T:0.17
Consensus pattern (42 bp):
CCTCCACCATAACCACCACCAGCACCACCTCCTTCACCACCT
Found at i:52634557 original size:18 final size:18
Alignment explanation
Indices: 52634536--52634574 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52634526 TGTCCACCTG
* *
52634536 CACTACCTCCCCCACCAC
1 CACTACCACCACCACCAC
*
52634554 CACTACCACTACCACCAC
1 CACTACCACCACCACCAC
52634572 CAC
1 CAC
52634575 CTCCATGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.62, G:0.00, T:0.10
Consensus pattern (18 bp):
CACTACCACCACCACCAC
Found at i:52634562 original size:123 final size:123
Alignment explanation
Indices: 52634052--52634555 Score: 411
Period size: 123 Copynumber: 4.0 Consensus size: 123
52634042 ACCACTCCCG
* * *
52634052 CCACCACCACCACCTCCATGTCCACTAGCTCCTCCAT----A--TCCAGCTCCACCTCCTTCACC
1 CCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGCTCCACCTCCTTCACC
* * * * * * * *
52634111 ACCTCCACTTCCATATCCAGAAGCTCCTCCACCA-TATCCACCAGCACTAGCTCCTCCACCA
66 ACCTCCACTGCCATACCCAGAAGCACCACCACCACTA-GCTCCA-C-CT-CCACCTCCACCA
* * ** * *
52634172 CCATTGCCACCACCACCTCCGTGTCCATTAGCTCCTTCATAGCCGCCACCACTACCAGCTCCACC
1 CCA---CCAGCACCACCTCCATGTCCACCAGCTCCTCCATA------ACCACCACCAGCTCCACC
* ** ** *
52634237 TCCGTT-GCCACCTCCACTGCCATACCCAGAAGCACCACCTGCACTAGCTCTGCCTCCACCAT-T
57 TCC-TTCACCACCTCCACTGCCATACCCAGAAGCACCACCACCACTAGCTCCACCTCCACC-TCC
*
52634300 ACCG
120 ACCA
*
52634304 CCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGCTCCACCTCCTTCGCC
1 CCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGCTCCACCTCCTTCACC
* ** * * **
52634369 ACCTCCATTGCCATACCCAGAAGCACCACCTGCACTAGCTCCTCCTCCACCACTGCCA
66 ACCTCCACTGCCATACCCAGAAGCACCACCACCACTAGCTCCACCTCCACCTCCACCA
* *
52634427 CCACCAGCACCACCTCCTTGTCCACCGGCTCCTCCATAACCACCACCAGCTCCACCTCCTTCACC
1 CCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGCTCCACCTCCTTCACC
** * * *
52634492 ACCTCCACCACCATATCCAGAAGCTCCACCACCA-T-G-TCCACCTGCACTACCTCCCCCA
66 ACCTCCACTGCCATACCCAGAAGCACCACCACCACTAGCTCCACCT-C-C-ACCTCCACCA
52634550 CCACCA
1 CCACCA
52634556 CTACCACTAC
Statistics
Matches: 316, Mismatches: 45, Indels: 43
0.78 0.11 0.11
Matches are distributed among these distances:
120 9 0.03
121 2 0.01
122 4 0.01
123 207 0.66
129 30 0.09
132 9 0.03
133 4 0.01
134 1 0.00
135 46 0.15
136 4 0.01
ACGTcount: A:0.22, C:0.51, G:0.09, T:0.18
Consensus pattern (123 bp):
CCACCAGCACCACCTCCATGTCCACCAGCTCCTCCATAACCACCACCAGCTCCACCTCCTTCACC
ACCTCCACTGCCATACCCAGAAGCACCACCACCACTAGCTCCACCTCCACCTCCACCA
Found at i:52634647 original size:24 final size:24
Alignment explanation
Indices: 52634601--52634647 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52634591 TTCTCCATAC
*
52634601 CCACTACCACTACCAGCACCACCT
1 CCACTACCACTACCAGAACCACCT
*
52634625 CCACTACCA-TATCCAGAAGCACC
1 CCACTACCACTA-CCAGAACCACC
52634648 ACCTACACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.32, C:0.49, G:0.06, T:0.13
Consensus pattern (24 bp):
CCACTACCACTACCAGAACCACCT
Found at i:52644525 original size:38 final size:37
Alignment explanation
Indices: 52644469--52644550 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 37
52644459 TAATAAATAT
*
52644469 ATATATTTTTTATTTTTTAATTTTAAAATACTTTTAAA
1 ATAT-TTTTTTATTTTTTAATTTTAAAATAATTTTAAA
* **
52644507 ATATTTTTTTATTTTTTTATTTTTAAAATAATTTTTTA
1 ATATTTTTTTA-TTTTTTAATTTTAAAATAATTTTAAA
52644545 ATATTT
1 ATATTT
52644551 ATTAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 7 0.18
38 32 0.82
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (37 bp):
ATATTTTTTTATTTTTTAATTTTAAAATAATTTTAAA
Found at i:52644540 original size:20 final size:22
Alignment explanation
Indices: 52644517--52644557 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
52644507 ATATTTTTTT
52644517 ATTTTTT-TATTT-TTAAAATA
1 ATTTTTTATATTTATTAAAATA
52644537 ATTTTTTAATATTTATTAAAA
1 ATTTTTT-ATATTTATTAAAA
52644558 AATGGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTTATATTTATTAAAATA
Found at i:52649770 original size:5 final size:5
Alignment explanation
Indices: 52649760--52649787 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52649750 ATTAGCTATT
52649760 GTGGA GTGGA GTGGA GTGGA GTGGA GTG
1 GTGGA GTGGA GTGGA GTGGA GTGGA GTG
52649788 ATAAGAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
GTGGA
Found at i:52658541 original size:18 final size:19
Alignment explanation
Indices: 52658509--52658554 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
52658499 TTTAATTTTG
* * *
52658509 TATTATAAATTACATAGTA
1 TATTAGAAATAACATAATA
52658528 TA-TAGAAATAACATAATA
1 TATTAGAAATAACATAATA
52658546 TATTAGAAA
1 TATTAGAAA
52658555 AAAAAAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (19 bp):
TATTAGAAATAACATAATA
Found at i:52664752 original size:19 final size:20
Alignment explanation
Indices: 52664728--52664769 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
52664718 TACTTTGATT
* *
52664728 ATATTATTTATT-TTTATTA
1 ATATTATTGATTCTTTAATA
52664747 ATATTATTGATTCTTTAATA
1 ATATTATTGATTCTTTAATA
52664767 ATA
1 ATA
52664770 AAAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATTATTGATTCTTTAATA
Found at i:52666006 original size:31 final size:29
Alignment explanation
Indices: 52665971--52666051 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
52665961 AATTTGAAAA
* **
52665971 TTATACATGAATTTTGGTTTAATGTGTAATT
1 TTATACATGAATTTTGATTT--TGTACAATT
* *
52666002 TTATACATGAACTTTGATTTTGTACATTT
1 TTATACATGAATTTTGATTTTGTACAATT
52666031 TTATACATGAAATTTTGATTT
1 TTATACATG-AATTTTGATTT
52666052 GATTTAATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 15 0.35
30 10 0.23
31 18 0.42
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (29 bp):
TTATACATGAATTTTGATTTTGTACAATT
Found at i:52678505 original size:27 final size:27
Alignment explanation
Indices: 52678438--52678508 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
52678428 CGGGTGGCGG
*
52678438 CTCATAGGGAGGCACCATTAAAAGTGC
1 CTCATAGGGAGGCGCCATTAAAAGTGC
*
52678465 CTCATAAGGAGGCGCCATTAAAAGTGC
1 CTCATAGGGAGGCGCCATTAAAAGTGC
52678492 CTCATAGGGAGGCGCCA
1 CTCATAGGGAGGCGCCA
52678509 ATGGGTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (27 bp):
CTCATAGGGAGGCGCCATTAAAAGTGC
Found at i:52678562 original size:19 final size:19
Alignment explanation
Indices: 52678513--52679016 Score: 176
Period size: 19 Copynumber: 25.3 Consensus size: 19
52678503 GCGCCAATGG
*
52678513 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
52678532 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
52678553 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
52678572 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
52678595 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
52678615 GT-ATTTTGTATGAATAGT
1 GTAATTTTGTATGAATATT
52678633 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
52678654 GTAATTTTTTATGAATATT
1 GTAATTTTGTATGAATATT
*
52678673 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
52678689 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
52678711 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
*
52678734 GTAATTTTG--T-AATTTT
1 GTAATTTTGTATGAATATT
* *
52678750 GTATGAATATTG--T-AATTTT
1 G--T-AATTTTGTATGAATATT
52678769 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
52678788 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
52678804 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
52678826 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
* *
52678849 ATAATGTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
52678868 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
52678891 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
52678911 GT-ATTTTGTATGGATATT
1 GTAATTTTGTATGAATATT
*
52678929 GT-ATTTTGTATGGATATT
1 GTAATTTTGTATGAATATT
52678947 GTAATATTGTTGTATGAATATT
1 GT-A-ATT-TTGTATGAATATT
52678969 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
52678992 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
52679011 GTAATT
1 GTAATT
52679017 ATTTTATAAT
Statistics
Matches: 380, Mismatches: 40, Indels: 130
0.69 0.07 0.24
Matches are distributed among these distances:
14 4 0.01
15 12 0.03
16 20 0.05
17 15 0.04
18 29 0.08
19 123 0.32
20 33 0.09
21 47 0.12
22 31 0.08
23 31 0.08
24 7 0.02
25 8 0.02
26 4 0.01
27 16 0.04
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:52678691 original size:101 final size:101
Alignment explanation
Indices: 52678516--52678997 Score: 509
Period size: 101 Copynumber: 4.6 Consensus size: 101
52678506 CCAATGGGTA
* * * *
52678516 ATTTTGTATGTATATTGTAACTTTTTGTATGAATATTATAATTTTGTATGAATATTGTAATTATT
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTATT
52678581 TTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
66 TTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
*
52678617 ATTTTGTATGAATAGTGTAATTTTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTATT
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTATT
*
52678682 TTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
66 TTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
52678718 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGA
1 ATTTTGTATGAATATTGTAA---T-T--TTTTGTATGAATATTGTAA-----T--TTTT-TATGA
*
52678783 ATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
52 ATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
* *
52678833 ATTTTGTATGAATATTATAA--TGTTGTATGAATATTGTAATTATTTTAT--A-A-T-TAATT-T
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATT-TTTTATGAATATTGTAATTAT
* * * *
52678890 TGTAT--TTATAGTTTTGGA-TTAGTATTTTGTATGGATATTGT
65 TTTATAATTA-A-TTTTGTATTTA-TA-GTT-T-TGGAT-TAGT
* *
52678931 ATTTTGTATGGATATTGTAATATTGTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAA
1 ATTTTGTATGAATATTGTAAT-TTTTTGTATGAATATTGT-A-ATT-TTT-TATGAATATTGTAA
52678996 TT
61 TT
52678998 TTGTATGAAT
Statistics
Matches: 331, Mismatches: 17, Indels: 58
0.82 0.04 0.14
Matches are distributed among these distances:
92 3 0.01
93 4 0.01
94 13 0.04
95 7 0.02
96 2 0.01
97 5 0.02
98 22 0.07
100 4 0.01
101 134 0.40
102 2 0.01
103 6 0.02
104 4 0.01
105 1 0.00
106 1 0.00
107 38 0.11
108 1 0.00
109 5 0.02
112 1 0.00
114 4 0.01
115 74 0.22
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (101 bp):
ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTATGAATATTGTAATTATT
TTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
Found at i:52678745 original size:8 final size:8
Alignment explanation
Indices: 52678732--52678779 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
52678722 TGTATGAATA
52678732 TTGTAATT
1 TTGTAATT
52678740 TTGTAATT
1 TTGTAATT
*
52678748 TTGTATGAATA
1 TTG--T-AATT
52678759 TTGTAATT
1 TTGTAATT
52678767 TTGTAATT
1 TTGTAATT
52678775 TTGTA
1 TTGTA
52678780 TGAATATTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 27 0.77
9 1 0.03
10 1 0.03
11 6 0.17
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (8 bp):
TTGTAATT
Found at i:52678748 original size:27 final size:27
Alignment explanation
Indices: 52678718--52678793 Score: 152
Period size: 27 Copynumber: 2.8 Consensus size: 27
52678708 TTTGATTAGT
52678718 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
52678745 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
52678772 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
52678794 ATTTTATAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:52678792 original size:115 final size:115
Alignment explanation
Indices: 52678652--52678859 Score: 389
Period size: 115 Copynumber: 1.8 Consensus size: 115
52678642 TGTATGAATA
*
52678652 TTGTAATTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
* *
52678717 TATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATT
66 TATTTTGTATGAATATTATAATGTTGTAATTTTGTATGAATATTGTAATT
52678767 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
52678832 TATTTTGTATGAATATTATAATGTTGTA
66 TATTTTGTATGAATATTATAATGTTGTA
52678860 TGAATATTGT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 90 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (115 bp):
TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
TATTTTGTATGAATATTATAATGTTGTAATTTTGTATGAATATTGTAATT
Found at i:52678865 original size:80 final size:80
Alignment explanation
Indices: 52678770--52678951 Score: 312
Period size: 80 Copynumber: 2.3 Consensus size: 80
52678760 TGTAATTTTG
*
52678770 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
52678835 TTTGTATGAATATTA
66 TTTGTATGAATATTA
*
52678850 TAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
* *
52678915 TTTGTATGGATATTG
66 TTTGTATGAATATTA
*
52678930 T-ATTTTGTATGGATATTGTAAT
1 TAATTTTGTATGAATATTGTAAT
52678952 ATTGTTGTAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 19 0.20
80 77 0.80
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (80 bp):
TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
TTTGTATGAATATTA
Found at i:52678934 original size:18 final size:18
Alignment explanation
Indices: 52678911--52679013 Score: 98
Period size: 18 Copynumber: 5.2 Consensus size: 18
52678901 TTTTGGATTA
*
52678911 GTATTTTGTATGGATATT
1 GTATTTTGTATGAATATT
*
52678929 GTATTTTGTATGGATATT
1 GTATTTTGTATGAATATT
52678947 GTAATATTGTTGTATGAATATT
1 G---TATT-TTGTATGAATATT
52678969 GTAATATTGTTTGTATGAATATT
1 G---TA-T-TTTGTATGAATATT
52678992 GTAATTTTGTATGAATATT
1 GT-ATTTTGTATGAATATT
52679011 GTA
1 GTA
52679014 ATTATTTTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 14
0.84 0.01 0.15
Matches are distributed among these distances:
18 20 0.26
19 16 0.21
20 2 0.03
21 5 0.06
22 18 0.23
23 15 0.19
24 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.52
Consensus pattern (18 bp):
GTATTTTGTATGAATATT
Found at i:52678986 original size:23 final size:23
Alignment explanation
Indices: 52678933--52679015 Score: 122
Period size: 22 Copynumber: 3.8 Consensus size: 23
52678923 GATATTGTAT
*
52678933 TTTGTATGGATATTGTAATATTG
1 TTTGTATGAATATTGTAATATTG
52678956 -TTGTATGAATATTGTAATATTG
1 TTTGTATGAATATTGTAATATTG
52678978 TTTGTATGAATATTGT-A-A-T-
1 TTTGTATGAATATTGTAATATTG
52678997 TTTGTATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
52679016 TATTTTATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
19 16 0.29
20 2 0.04
21 1 0.02
22 22 0.39
23 15 0.27
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (23 bp):
TTTGTATGAATATTGTAATATTG
Found at i:52679090 original size:60 final size:60
Alignment explanation
Indices: 52679010--52679128 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
52679000 GTATGAATAT
* * * * *
52679010 TGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTC
1 TGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTC
52679070 TGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
52679129 TTAGTTTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (60 bp):
TGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTC
Found at i:52679284 original size:15 final size:16
Alignment explanation
Indices: 52679248--52679284 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
52679238 CTCATTTAAT
52679248 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
52679264 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
52679279 TTTTAT
1 TTTTAT
52679285 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:52680666 original size:25 final size:24
Alignment explanation
Indices: 52680638--52680685 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
52680628 AAAATGTTCT
* *
52680638 AAAATTCTGAAAAGAAAATGAAAAA
1 AAAAATCTGAAAA-AAAAAGAAAAA
52680663 AAAAATCTGAAAAAAAAAGAAAA
1 AAAAATCTGAAAAAAAAAGAAAA
52680686 TGACATCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.12
Consensus pattern (24 bp):
AAAAATCTGAAAAAAAAAGAAAAA
Found at i:52685230 original size:19 final size:19
Alignment explanation
Indices: 52685203--52685241 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52685193 TCCGTCTCTT
* * *
52685203 AATATCCAAATACAAGCAA
1 AATAACCAAAGACAACCAA
52685222 AATAACCAAAGACAACCAA
1 AATAACCAAAGACAACCAA
52685241 A
1 A
52685242 CAAGGTACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.23, G:0.05, T:0.10
Consensus pattern (19 bp):
AATAACCAAAGACAACCAA
Found at i:52688543 original size:81 final size:81
Alignment explanation
Indices: 52688408--52688569 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 81
52688398 ATTCTGAAGT
* * * * * * *
52688408 CAACAGCCAAGATACACAAGCATGTGATAAACATCTGCAAAATTTTCCCACTGAAAATTTATTAC
1 CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
*
52688473 AAATTAAAAAATGTAC
66 AAATTAAAAAAGGTAC
*
52688489 CAACAGCCAAGATACACAAGTAAGTGACAAAGAATAT-CAATAA-ATTCCCACTGAAAATCTATC
1 CAACAGCCAAGATACACAAGCAAGTGACAAA-AATATGCAA-AATATTCCCACTGAAAATCTATC
*
52688552 ACAAATTCAAAAAGGTAC
64 ACAAATTAAAAAAGGTAC
52688570 ATTAAGCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 64 0.93
82 5 0.07
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (81 bp):
CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
AAATTAAAAAAGGTAC
Found at i:52691619 original size:11 final size:11
Alignment explanation
Indices: 52691605--52691633 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
52691595 TTAAAAATAA
52691605 AAAATTATTTT
1 AAAATTATTTT
52691616 AAAATTATTTT
1 AAAATTATTTT
52691627 AAAATTA
1 AAAATTA
52691634 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:52691638 original size:19 final size:19
Alignment explanation
Indices: 52691576--52691622 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
52691566 ATTTTTAAAA
52691576 TAAACATTAAAAAATTATTT
1 TAAA-ATTAAAAAATTATTT
*
52691596 TAAAAATAAAAAATTATTT
1 TAAAATTAAAAAATTATTT
52691615 TAAAATTA
1 TAAAATTA
52691623 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATTAAAAAATTATTT
Found at i:52706114 original size:4 final size:4
Alignment explanation
Indices: 52706107--52706132 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
52706097 AAAATAAATA
52706107 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
52706133 ATGATTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:52710858 original size:12 final size:11
Alignment explanation
Indices: 52710836--52710861 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52710826 CCAACCCTTT
52710836 AAAATAAAAAA
1 AAAATAAAAAA
52710847 AAAATAAAAAA
1 AAAATAAAAAA
52710858 AAAA
1 AAAA
52710862 CTATGGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:52715214 original size:6 final size:6
Alignment explanation
Indices: 52715203--52715289 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
52715193 ACAACATCAC
52715203 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
52715251 TATATG TATATG TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TAT
52715290 GGTGGGAAAG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:52727162 original size:31 final size:32
Alignment explanation
Indices: 52727128--52727189 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
52727118 TTAAAAAGAA
52727128 AAAAAATCTT-AATAGCCAAA-TAACTTAAAT
1 AAAAAATCTTGAATAGCCAAAGTAACTTAAAT
* **
52727158 AAAAAATTTTGAATAGTTAAAGTAACTTAAAT
1 AAAAAATCTTGAATAGCCAAAGTAACTTAAAT
52727190 GAATACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 8 0.30
32 10 0.37
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (32 bp):
AAAAAATCTTGAATAGCCAAAGTAACTTAAAT
Found at i:52727706 original size:35 final size:35
Alignment explanation
Indices: 52727667--52727763 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 35
52727657 ACTTGCCTCT
52727667 TCCCATTCTCCCATGCTGTCTGCCACCAGCACCAC
1 TCCCATTCTCCCATGCTGTCTGCCACCAGCACCAC
* *
52727702 TCCCATTCTCCCATGTTGTCTGCCACCAGCGCCAC
1 TCCCATTCTCCCATGCTGTCTGCCACCAGCACCAC
* *
52727737 TCCCACTCTCCCATGCTGTCTACCACC
1 TCCCATTCTCCCATGCTGTCTGCCACC
52727764 TCCACCTCTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.15, C:0.48, G:0.11, T:0.25
Consensus pattern (35 bp):
TCCCATTCTCCCATGCTGTCTGCCACCAGCACCAC
Found at i:52728443 original size:26 final size:26
Alignment explanation
Indices: 52728403--52728470 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
52728393 TAAAATAAAA
52728403 AATAAAAAAGGGGAAAGTTGGTAATGG
1 AATAAAAAA-GGGAAAGTTGGTAATGG
52728430 AATAAAAAAGGGAAAGTTGGTAATGG
1 AATAAAAAAGGGAAAGTTGGTAATGG
*
52728456 AATAAAAAAAGGAAA
1 AATAAAAAAGGGAAA
52728471 TTTTTTTTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 31 0.77
27 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (26 bp):
AATAAAAAAGGGAAAGTTGGTAATGG
Found at i:52729361 original size:3 final size:3
Alignment explanation
Indices: 52729353--52729414 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
52729343 TCGATTTTAC
*
52729353 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
52729401 TAT TAT TTT TAT TA
1 TAT TAT TAT TAT TA
52729415 GTTTATGCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:52729641 original size:20 final size:20
Alignment explanation
Indices: 52729612--52729747 Score: 66
Period size: 20 Copynumber: 6.5 Consensus size: 20
52729602 TTTTATGTTG
52729612 TATTATTATATTTTAATATTA
1 TATTA-TATATTTTAATATTA
*
52729633 TATTATATA-ATT-ATA-TA
1 TATTATATATTTTAATATTA
* *
52729650 TACATATATCTTTTTATATATTA
1 TA-TTATAT-ATTTTA-ATATTA
52729673 TCATTGTATATATTTTAATATTA
1 T-A-T-TATATATTTTAATATTA
* *
52729696 TTAGT-TGTATTTTACACTATTA
1 -TATTATATATTTTA-A-TATTA
* *
52729718 TA-TACATTTTTCTAATATTA
1 TATTATATATTT-TAATATTA
*
52729738 TATTGTATAT
1 TATTATATAT
52729748 ACTATTGTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 28
0.67 0.12 0.22
Matches are distributed among these distances:
17 4 0.05
18 8 0.09
19 2 0.02
20 22 0.26
21 18 0.21
22 10 0.12
23 10 0.12
24 7 0.08
25 5 0.06
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
TATTATATATTTTAATATTA
Found at i:52729746 original size:27 final size:30
Alignment explanation
Indices: 52729716--52729775 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
52729706 TTTACACTAT
*
52729716 TATATAC-ATT-TTTCTA-ATATTATAT-TG
1 TATATACTATTGTTTATATATA-TATATGTG
52729743 TATATACTATTGTTTATATATATATATGTG
1 TATATACTATTGTTTATATATATATATGTG
52729773 TAT
1 TAT
52729776 GTATTTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 7 0.25
28 3 0.11
29 10 0.36
30 8 0.29
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (30 bp):
TATATACTATTGTTTATATATATATATGTG
Found at i:52753983 original size:44 final size:45
Alignment explanation
Indices: 52753920--52754758 Score: 835
Period size: 44 Copynumber: 19.1 Consensus size: 45
52753910 TCATTAAAGT
* * *
52753920 AGATCTTGTCTTCATATATTGG-CGTGAAGTAGCTCGAAGATATC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52753964 AGATCCTATCTTCCTATATTGG-CAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTC-GTGAAGTAGATCGAAGATAGC
* * *
52754007 AGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52754052 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATATC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * *
52754096 AGAT-TCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAAAGC
1 AGATCT-TGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52754140 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATATC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52754184 AGATC-TATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52754226 AGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* *
52754271 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAA-AGTAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-TAGC
* * * *
52754315 AGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * * *
52754358 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52754403 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * *
52754447 AGATCTTATCTTCCTATATTGGTAG-GAAGTAGATCGACGA-CGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * * * * *
52754490 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAAC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* *
52754535 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * * *
52754579 AGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * * * *
52754622 AGATCTTATCTTCCCATATTAGTGGCGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * *
52754667 AGAT-TTGTCTTCCCATA-TGGTGGCGAAGTAGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
* * * * * *
52754709 CGATCTTGTCTTCCCATACTGGTGGTGAAGAAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
52754754 AGATC
1 AGATC
52754759 GACGATGGCG
Statistics
Matches: 654, Mismatches: 115, Indels: 51
0.80 0.14 0.06
Matches are distributed among these distances:
42 11 0.02
43 170 0.26
44 372 0.57
45 101 0.15
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
AGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAGATAGC
Found at i:52754167 original size:132 final size:132
Alignment explanation
Indices: 52753920--52754758 Score: 1018
Period size: 132 Copynumber: 6.4 Consensus size: 132
52753910 TCATTAAAGT
* * * * * * *
52753920 AGATCTTGTCTTCATATATTGG-CGTGAAGTAGCTCGAAGATATCAGATCCTATCTTCCTATATT
1 AGATCTTATCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT-GCAGATCTTATCTTCCCATATT
** * * *** *
52753984 GGCAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAG
64 GGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG
*
52754047 AAAGC
128 ATAGC
* * * * * *
52754052 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATATCAGAT-TCTATCTTCCTATAT
1 AGATCTTATCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT-GCAGATCT-TATCTTCCCATAT
* *
52754115 TGGTAG-GAAGTGGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
63 TGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
*
52754179 ATATC
128 ATAGC
* *
52754184 AGATC-TATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGATCTTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTATCTTCCCATATTGG
*
52754248 TGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-AGT
66 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-T
52754312 AGC
130 AGC
* * *
52754315 AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGATCTTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTATCTTCCCATATTGG
* *
52754380 TGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
66 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
52754445 GC
131 GC
* * * *
52754447 AGATCTTATCTTCCTATATTGGTAGGAAGTAGATCGACGACGCAGATCTTGTCTTCCCATACTGG
1 AGATCTTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTATCTTCCCATATTGG
* *
52754512 TGGCGAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
66 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
52754577 GC
131 GC
* * * *
52754579 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTAG
1 AGATCTTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTATCTTCCCATATTGG
* **
52754644 TGGCGAAGTAGATCGAAGAAAGCAGAT-TTGTCTTCCCATATGGTGGC--GAAGTAGATCGAAGA
66 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT--CATGTATTGGCGTGAAGTAGATCGAAGA
52754706 T-GC
129 TAGC
* * * * * * *
52754709 CGATCTTGTCTTCCCATACTGGTGGTGAAGAAGATCGAAGAAAGCAGATC
1 AGATCTTATCTTCCTATATTGGTAG-GAAGTAGATCGAAG-ATGCAGATC
52754759 GACGATGGCG
Statistics
Matches: 640, Mismatches: 55, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
130 42 0.07
131 128 0.20
132 440 0.69
133 30 0.05
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
AGATCTTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTATCTTCCCATATTGG
TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
GC
Found at i:52754626 original size:351 final size:351
Alignment explanation
Indices: 52753915--52754758 Score: 1132
Period size: 351 Copynumber: 2.4 Consensus size: 351
52753905 TGAAGTCATT
* * *
52753915 AAAGTAGATCTTGTCTTCATATATTGGCGTGAAGTAGCTCGAAGATATCAGATCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
*
52753980 TATTGGCAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGA
66 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGA
*
52754045 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATTCTATCTTCC
131 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATTCTATCTTCC
* ** * *
52754110 TATATTGGTAGGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
196 TATATTGGTAGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGGCGCGAAGTAGATC
* * * * * *
52754175 GAAGATATCAGATCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
261 GAAGAAAACAGATCTATCTTCATATATTGGTAGGAAGTAGATCGAAGATGCAGATCCTATCTTCC
*
52754240 CATATTGGTGGTGAAGTAGATCGAAG
326 CATATTGGTAGTGAAGTAGATCGAAG
*
52754266 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-AGTAGCAGATCCTATCTTCCT
1 AAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGA-TAGCAGATCCTATCTTCCT
*
52754330 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
65 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCG
* *
52754395 CAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGA-TCTTATCTT
130 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATTC-TATCTT
* * * *
52754459 CCTATATTGGTAGGAAGTAGATCGACG-ACGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAG
194 CCTATATTGGTAGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGG-CGCGAAGTAG
* * * * *
52754523 ATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTA
258 ATCGAAGAAAACAGATC-TATCTTCATATATTGGTAG-GAAGTAGATCGAAGAT-GCAGATCCTA
* *
52754587 TCTTCCTATATTGGTAG-GAAGTGGATCGAAG
320 TCTTCCCATATTGGTAGTGAAGTAGATCGAAG
* * * * * *
52754618 -ATGCAGATCTTATCTTCCCATATTAGTGGC--GAAGTAGATCGAAGAAAGCAGAT-TTGTCTTC
1 AAAGCAGATCTTGTCTT--CATA-TATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTC
* * * * * *
52754679 CCATA-TGGTGGCGAAGTAGATCGAAGATGCCGATCTTGTCTTCCCATACTGGTGGTGAAGAAGA
63 CTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGA
52754743 TCGAAGAAAGCAGATC
127 TCGAAGAAAGCAGATC
52754759 GACGATGGCG
Statistics
Matches: 435, Mismatches: 47, Indels: 22
0.86 0.09 0.04
Matches are distributed among these distances:
350 29 0.07
351 313 0.72
352 61 0.14
353 26 0.06
354 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (351 bp):
AAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGA
AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATTCTATCTTCC
TATATTGGTAGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGGCGCGAAGTAGATC
GAAGAAAACAGATCTATCTTCATATATTGGTAGGAAGTAGATCGAAGATGCAGATCCTATCTTCC
CATATTGGTAGTGAAGTAGATCGAAG
Found at i:52754730 original size:219 final size:221
Alignment explanation
Indices: 52753920--52754758 Score: 880
Period size: 219 Copynumber: 3.8 Consensus size: 221
52753910 TCATTAAAGT
* * * * * * *
52753920 AGATCTTGTCTTCATATATTGG-CGTGAAGTAGCTCGAAGATATCAGATCCTATCTTCCTATATT
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCATATT
* * * *
52753984 GGCAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAA
66 AGTAGGAAGTAGATCGAAGAAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAA
** * * *
52754049 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGAT-TCTATCTTCCTAT
131 AGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGAAGAAAGCAGATCT-TATCTTCCTAT
*
52754113 ATTGGTAGGAAGTGGATCGAAGAAAGC
195 ATTGGTAGGAAGTGGATCGAAGATAGC
* * * * * *
52754140 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATATCAGATC-TATCTTCCTATATT
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCATATT
* * *
52754203 GGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAA
66 AGTAGGAAGTAGATCGAAGAAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAA
** * * *
52754268 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-AGTAGCAGATCCTATCTTCCTAT
131 AGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGAAGA-AAGCAGATCTTATCTTCCTAT
52754332 ATTGGTAGGAAGTGGATCGAAGAT-GC
195 ATTGGTAGGAAGTGGATCGAAGATAGC
* * * * * ***
52754358 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCATATT
** * * * * *
52754423 -GGCGTGAAGTAGATCGAAGGTAGCAGATCTTATCTTCCTATATTGGTAG-GAAGTAGATCGACG
66 AGTAG-GAAGTAGATCGAA-GAAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAG
* * * * * * * *
52754486 -ACGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAACAGATCTTGTCTTCAT
129 AAAGCAGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCT
* * *
52754550 GTATTGG-CGTGAAGTAGATCGAAGATAGC
193 ATATTGGTAG-GAAGTGGATCGAAGATAGC
* * * *
52754579 AGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GCAGATCTTATCTTCCCATATT
1 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCATATT
* *
52754642 AGTGGCGAAGTAGATCGAAGAAAGCAGAT-TTGTCTTCCCATA-TGGTGGCGAAGTAGATCGAAG
66 AGTAG-GAAGTAGATCGAAG-AAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAG
* * * * *
52754705 -ATGCCGATCTTGTCTTCCCATACTGGTGGTGAAGAAGATCGAAGAAAGCAGATC
129 AAAGCAGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCGAAGAAAGCAGATC
52754759 GACGATGGCG
Statistics
Matches: 538, Mismatches: 68, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
218 27 0.05
219 297 0.55
220 166 0.31
221 48 0.09
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (221 bp):
AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCATATT
AGTAGGAAGTAGATCGAAGAAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAA
AGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTATCTTCCTATA
TTGGTAGGAAGTGGATCGAAGATAGC
Found at i:52756886 original size:18 final size:20
Alignment explanation
Indices: 52756861--52756904 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
52756851 CCATTTAAAC
52756861 ATATTTTT-TCACACTT-CAT
1 ATATTTTTAT-ACACTTACAT
52756880 A-ATTTTTATACACTTACAT
1 ATATTTTTATACACTTACAT
52756899 ATATTT
1 ATATTT
52756905 ATGCATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 12 0.55
19 6 0.27
20 4 0.18
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTTATACACTTACAT
Found at i:52757536 original size:106 final size:106
Alignment explanation
Indices: 52757400--52757600 Score: 357
Period size: 106 Copynumber: 1.9 Consensus size: 106
52757390 AAAATTTTTC
52757400 TAAATAAGGCAATATTTCGCGTTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
52757465 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
* * *
52757506 TAAATAAGGCGATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
52757571 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
52757601 CTTAAAGCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:52780803 original size:12 final size:12
Alignment explanation
Indices: 52780783--52780819 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
52780773 CCAAAAAACT
52780783 TATGCATATGTA
1 TATGCATATGTA
* *
52780795 TATGTATATGTT
1 TATGCATATGTA
52780807 TATGCATATGTA
1 TATGCATATGTA
52780819 T
1 T
52780820 GGCTAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (12 bp):
TATGCATATGTA
Found at i:52781122 original size:6 final size:6
Alignment explanation
Indices: 52781111--52781146 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
52781101 ACAACATCAC
52781111 TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG
52781147 AATGGTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:52791965 original size:15 final size:16
Alignment explanation
Indices: 52791942--52791971 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52791932 ATATGAAAAA
52791942 ATTTAAATTTAAAATG
1 ATTTAAATTTAAAATG
52791958 ATTT-AATTTAAAAT
1 ATTTAAATTTAAAAT
52791972 TTTTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTAAATTTAAAATG
Found at i:52791965 original size:21 final size:21
Alignment explanation
Indices: 52791940--52791993 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
52791930 ATATATGAAA
52791940 AAATTTAAATTTAAAATGATT
1 AAATTTAAATTTAAAATGATT
* ** *
52791961 TAATTTAAAATTTTTAATTATT
1 AAATTT-AAATTTAAAATGATT
52791983 AAATTTAAATT
1 AAATTTAAATT
52791994 AATGATTCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATTTAAATTTAAAATGATT
Found at i:52792045 original size:16 final size:16
Alignment explanation
Indices: 52792010--52792048 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
52792000 TCGAATATAA
* * *
52792010 AAAATAATTTTAATTT
1 AAAATAATTTAAACTG
52792026 AAAATAATTTAAACTG
1 AAAATAATTTAAACTG
52792042 AAAATAA
1 AAAATAA
52792049 CTTCTCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATAATTTAAACTG
Found at i:52792984 original size:31 final size:30
Alignment explanation
Indices: 52792916--52792984 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
52792906 TTAGCAGCTA
*
52792916 AATAACTTAAATAAAAAATTTTAAATAGTT
1 AATAACTTAAATAAAAAATTTTAAATAATT
* *
52792946 AAGTAACTTAAATAAATACTTTTAAATAATT
1 AA-TAACTTAAATAAAAAATTTTAAATAATT
52792977 CAATAACT
1 -AATAACT
52792985 ATTTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.88
32 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (30 bp):
AATAACTTAAATAAAAAATTTTAAATAATT
Found at i:52805956 original size:25 final size:25
Alignment explanation
Indices: 52805926--52806012 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
52805916 GAAGACTAAG
52805926 AAAATTGAAATCATGTGATCACTTA
1 AAAATTGAAATCATGTGATCACTTA
* ** ** *
52805951 AAAATTGTGAATCAAAATCAGAAGACTAA
1 AAAATTG-AAATC---ATGTGATCACTTA
52805980 GAAAATTGAAATCATGTGATCACTTA
1 -AAAATTGAAATCATGTGATCACTTA
52806006 AAAATTG
1 AAAATTG
52806013 CAATGGCAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
25 14 0.31
26 12 0.27
29 12 0.27
30 7 0.16
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (25 bp):
AAAATTGAAATCATGTGATCACTTA
Found at i:52805967 original size:55 final size:55
Alignment explanation
Indices: 52805903--52806012 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
52805893 TCGTGTATTC
52805903 TGAATCAAAATCAGAAGACTAAGAAAATTGAAATCATGTGATCACTTAAAAATTG
1 TGAATCAAAATCAGAAGACTAAGAAAATTGAAATCATGTGATCACTTAAAAATTG
52805958 TGAATCAAAATCAGAAGACTAAGAAAATTGAAATCATGTGATCACTTAAAAATTG
1 TGAATCAAAATCAGAAGACTAAGAAAATTGAAATCATGTGATCACTTAAAAATTG
52806013 CAATGGCAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (55 bp):
TGAATCAAAATCAGAAGACTAAGAAAATTGAAATCATGTGATCACTTAAAAATTG
Found at i:52811519 original size:29 final size:29
Alignment explanation
Indices: 52811486--52811541 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
52811476 ATATAGATAG
52811486 GATCAAATTAGTCCCTT-TACTATTAAATA
1 GATCAAATTAGT-CCTTATACTATTAAATA
* *
52811515 GATCAATTTAGTCCTTATATTATTAAA
1 GATCAAATTAGTCCTTATACTATTAAA
52811542 AGGAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (29 bp):
GATCAAATTAGTCCTTATACTATTAAATA
Found at i:52813775 original size:7 final size:7
Alignment explanation
Indices: 52813763--52813787 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52813753 TTCCTATATT
52813763 ATTTGAA
1 ATTTGAA
52813770 ATTTGAA
1 ATTTGAA
52813777 ATTTGAA
1 ATTTGAA
52813784 ATTT
1 ATTT
52813788 TGGTCTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (7 bp):
ATTTGAA
Found at i:52814738 original size:95 final size:94
Alignment explanation
Indices: 52814622--52814983 Score: 461
Period size: 93 Copynumber: 3.9 Consensus size: 94
52814612 TTTGGGTTCT
* * *
52814622 TTTTATTTTCTTCTTAAATCGGCTGTGTTTTCCATTGAATTTGAATATGTATATATAACTTCGAA
1 TTTTATTTT-TTCTTTAATCGGCTGTATTTTCCATTGAATTTG-ATATGTATATATAACTTTGAA
52814687 TCGATTTTTCAGCTTCATTGGGATTTTTGGG
64 TCGATTTTTCAGCTTCATTGGGATTTTTGGG
*
52814718 TTTT-TTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGA-ATGTATATATAACTTTGAAC
1 TTTTATTTT-TTCTTTAATCGGCTGTATTTTCCATTGAATTTGATATGTATATATAACTTTGAAT
*
52814781 CGATTTTTCGGCTTCATTGGGATTTTT--G
65 CGATTTTTCAGCTTCATTGGGATTTTTGGG
* * * * *
52814809 -TTT-TTTTTTCTTTAATTGGCTGTATTTTTCTTTGAATTTGA-ATGTATATATAAAAATTTGAG
1 TTTTATTTTTTCTTTAATCGGCTGTATTTTCCATTGAATTTGATATGTATATAT--AACTTTGAA
* * *
52814871 TCAATTTTTAAGCTTCACTGGGATTTTTGGG
64 TCGATTTTTCAGCTTCATTGGGATTTTTGGG
* * *
52814902 TTTTCTTTTTTCCTTTAGTCGGCTGTATTTTCCATTGAATTTG-GATGTATATATAACTTTGAAT
1 TTTTATTTTTT-CTTTAATCGGCTGTATTTTCCATTGAATTTGATATGTATATATAACTTTGAAT
*
52814966 CGATGTTTCAGCTTCATT
65 CGATTTTTCAGCTTCATT
52814984 TGCATGCGGG
Statistics
Matches: 233, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
89 41 0.18
90 7 0.03
91 31 0.13
93 45 0.19
94 26 0.11
95 42 0.18
96 41 0.18
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (94 bp):
TTTTATTTTTTCTTTAATCGGCTGTATTTTCCATTGAATTTGATATGTATATATAACTTTGAATC
GATTTTTCAGCTTCATTGGGATTTTTGGG
Found at i:52814854 original size:22 final size:20
Alignment explanation
Indices: 52814813--52814855 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
52814803 TTTTTGTTTT
**
52814813 TTTTTCTTTAATTGGCTGTA
1 TTTTTCTTTAATTGAATGTA
52814833 TTTTTCTTTGAATTTGAATGTA
1 TTTTTCTTT-AA-TTGAATGTA
52814855 T
1 T
52814856 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (20 bp):
TTTTTCTTTAATTGAATGTA
Found at i:52814956 original size:185 final size:184
Alignment explanation
Indices: 52814627--52814983 Score: 509
Period size: 184 Copynumber: 1.9 Consensus size: 184
52814617 GTTCTTTTTA
* * * * *
52814627 TTTTCTTCTTAAATCGGCTGTGTTTTCCATTGAATTTGAATATGTATATATAACTTCGAATCGAT
1 TTTTCTTCTTAAATCGGCTGTATTTTCCATTGAATTTGAATATATATATAAAAATTCGAATCAAT
* *
52814692 TTTTCAGCTTCATTGGGATTTTTGGGTTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAAT
66 TTTTAAGCTTCACTGGGATTTTTGGGTTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAAT
* *
52814757 TTGAATGTATATATAACTTTGAACCGATTTTTCGGCTTCATTGGGATTTTTGTT
131 TTGAATGTATATATAACTTTGAACCGATGTTTCAGCTTCATTGGGATTTTTGTT
* * * * * * * *
52814811 TTTTTTTCTTTAATTGGCTGTATTTTTCTTTGAATTTGAATGTATATATAAAAATTTGAGTCAAT
1 TTTTCTTCTTAAATCGGCTGTATTTTCCATTGAATTTGAATATATATATAAAAATTCGAATCAAT
*
52814876 TTTTAAGCTTCACTGGGATTTTTGGGTTTTCTTTT-TTCCTTTAGTCGGCTGTATTTTCCATTGA
66 TTTTAAGCTTCACTGGGATTTTTGGGTTTT-TTTTCTT-CTTTAATCGGCTGTATTTTCCATTGA
* *
52814940 ATTTGGATGTATATATAACTTTGAATCGATGTTTCAGCTTCATT
129 ATTTGAATGTATATATAACTTTGAACCGATGTTTCAGCTTCATT
52814984 TGCATGCGGG
Statistics
Matches: 151, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
184 82 0.54
185 69 0.46
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (184 bp):
TTTTCTTCTTAAATCGGCTGTATTTTCCATTGAATTTGAATATATATATAAAAATTCGAATCAAT
TTTTAAGCTTCACTGGGATTTTTGGGTTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAAT
TTGAATGTATATATAACTTTGAACCGATGTTTCAGCTTCATTGGGATTTTTGTT
Found at i:52820793 original size:13 final size:13
Alignment explanation
Indices: 52820775--52820800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52820765 CAATTTTAAA
52820775 AGATTGTAAATAT
1 AGATTGTAAATAT
52820788 AGATTGTAAATAT
1 AGATTGTAAATAT
52820801 TAAAGTGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AGATTGTAAATAT
Found at i:52824617 original size:27 final size:26
Alignment explanation
Indices: 52824563--52824622 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
52824553 ATTTTTTTTT
52824563 ATTTTAATAATTTTTAATTTTTAAAA
1 ATTTTAATAATTTTTAATTTTTAAAA
*
52824589 ATATTTATATATTTTTTGAA-TTTT-AAA
1 AT-TTTA-ATAATTTTT-AATTTTTAAAA
52824616 ATTTTAA
1 ATTTTAA
52824623 AAAAATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 1 0.03
26 6 0.20
27 9 0.30
28 12 0.40
29 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
ATTTTAATAATTTTTAATTTTTAAAA
Found at i:52826054 original size:25 final size:25
Alignment explanation
Indices: 52826008--52826056 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
52825998 AATGTTATTT
*
52826008 TTTAAAGATTTTTGTGTATTTTTTA
1 TTTAAAGATTTTTGTATATTTTTTA
* *
52826033 TTTAAATATTTTT-TATACTTTTTA
1 TTTAAAGATTTTTGTATATTTTTTA
52826057 AATTATTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (25 bp):
TTTAAAGATTTTTGTATATTTTTTA
Found at i:52831244 original size:21 final size:20
Alignment explanation
Indices: 52831207--52831254 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
52831197 AAATTTTAAG
*
52831207 TTTAATTTTTTATTTAAAAAA
1 TTTAATTTATTATTT-AAAAA
*
52831228 TTTAATTTAATTA-TTAAAAT
1 TTTAATTT-ATTATTTAAAAA
52831248 TTTAATT
1 TTTAATT
52831255 ATGTTGCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 10 0.42
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTATTATTTAAAAA
Found at i:52840993 original size:12 final size:12
Alignment explanation
Indices: 52840961--52840998 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
52840951 TATTATTTTA
52840961 ATTACT-TTATT
1 ATTACTATTATT
*
52840972 -TTAATATTATT
1 ATTACTATTATT
52840983 ATTACTATTATT
1 ATTACTATTATT
52840995 ATTA
1 ATTA
52840999 TATATTAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 5 0.22
12 14 0.61
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTACTATTATT
Found at i:52841116 original size:3 final size:3
Alignment explanation
Indices: 52841108--52841137 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
52841098 TGTATTTCTA
52841108 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52841138 ATAGTAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52841318 original size:12 final size:12
Alignment explanation
Indices: 52841301--52841325 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52841291 GTATTATGTT
52841301 TTTTTAATACCA
1 TTTTTAATACCA
52841313 TTTTTAATACCA
1 TTTTTAATACCA
52841325 T
1 T
52841326 GCATGTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTTAATACCA
Found at i:52855553 original size:29 final size:28
Alignment explanation
Indices: 52855500--52855554 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
52855490 TCTTTACAAA
*
52855500 TTTAAAATATAGTCCTTGTACTTTCATT
1 TTTAAAATATAGTCCATGTACTTTCATT
*
52855528 TTTAGAAATTTAGTCCAT-TACATTTCA
1 TTTA-AAATATAGTCCATGTAC-TTTCA
52855555 GATTTCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (28 bp):
TTTAAAATATAGTCCATGTACTTTCATT
Found at i:52875150 original size:16 final size:15
Alignment explanation
Indices: 52875129--52875158 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52875119 GACAATTAAA
52875129 TTAAAATTTTCTATTT
1 TTAAAATTTT-TATTT
52875145 TTAAAATTTTTATT
1 TTAAAATTTTTATT
52875159 ATTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAAAATTTTTATTT
Found at i:52875175 original size:17 final size:17
Alignment explanation
Indices: 52875129--52875172 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
52875119 GACAATTAAA
*
52875129 TTAAAATTTT-CTATTT
1 TTAAAATTTTATTATTT
52875145 TTAAAATTTTTATTATTT
1 TTAAAA-TTTTATTATTT
52875163 TTAATAATTT
1 TTAA-AATTT
52875173 ATTCAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 4 0.17
18 12 0.50
19 2 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAAAATTTTATTATTT
Found at i:52877942 original size:21 final size:19
Alignment explanation
Indices: 52877903--52877947 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
52877893 AATCTTTTAT
52877903 TTTTAAAATAGTAAAAATAA
1 TTTTAAAATAGTAAAAAT-A
* *
52877923 TTTTAAAATATTATATAATA
1 TTTTAAAATAGTA-AAAATA
52877943 TTTTA
1 TTTTA
52877948 TAATTAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTTAAAATAGTAAAAATA
Found at i:52878158 original size:3 final size:3
Alignment explanation
Indices: 52878150--52878190 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
52878140 ATCTAGTTTT
52878150 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
52878191 CAGGTAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52886708 original size:21 final size:20
Alignment explanation
Indices: 52886669--52886708 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52886659 TCCACTTATA
*
52886669 ATTTTTTAATTTTTTAAAAG
1 ATTTTTTAATTTTTCAAAAG
*
52886689 ATTTTTTTATATTTTCAAAA
1 ATTTTTTAAT-TTTTCAAAA
52886709 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
ATTTTTTAATTTTTCAAAAG
Found at i:52905636 original size:16 final size:17
Alignment explanation
Indices: 52905615--52905652 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
52905605 AAAACAAATA
*
52905615 TTATTATATTAA-CCTT
1 TTATTATATTAATACTT
52905631 TTATTATATTAATACTT
1 TTATTATATTAATACTT
52905648 TTATT
1 TTATT
52905653 TAAACCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTATATTAATACTT
Found at i:52905771 original size:29 final size:29
Alignment explanation
Indices: 52905735--52905792 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
52905725 GACTATCTAG
52905735 TTATTAAAATATTACAAAAAAATTATATA
1 TTATTAAAATATTACAAAAAAATTATATA
52905764 TTATTAAAATATTACAAAAAAATTATATA
1 TTATTAAAATATTACAAAAAAATTATATA
52905793 AAAATGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TTATTAAAATATTACAAAAAAATTATATA
Found at i:52913089 original size:67 final size:67
Alignment explanation
Indices: 52912972--52913110 Score: 260
Period size: 67 Copynumber: 2.1 Consensus size: 67
52912962 CGGTGAACTA
* *
52912972 ATATTTTTGAGCTCTTTATTTTAGTGGAAATTAGTGAATGTTCTATATATGATAGATTCTGCTCT
1 ATATATTTGAGCTCTTTATTTTAGTGGAAATTAGTGAATGTTCTAGATATGATAGATTCTGCTCT
52913037 GC
66 GC
52913039 ATATATTTGAGCTCTTTATTTTAGTGGAAATTAGTGAATGTTCTAGATATGATAGATTCTGCTCT
1 ATATATTTGAGCTCTTTATTTTAGTGGAAATTAGTGAATGTTCTAGATATGATAGATTCTGCTCT
52913104 GC
66 GC
52913106 ATATA
1 ATATA
52913111 ATGTGTTAGT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (67 bp):
ATATATTTGAGCTCTTTATTTTAGTGGAAATTAGTGAATGTTCTAGATATGATAGATTCTGCTCT
GC
Found at i:52922583 original size:181 final size:181
Alignment explanation
Indices: 52922270--52922632 Score: 654
Period size: 181 Copynumber: 2.0 Consensus size: 181
52922260 ACCACATTCT
*
52922270 GACGTACATGGACCGGTTTTTATCAGTAGAAATGGATGAAATTTTCAACAAAACGACCAATTTGC
1 GACGTACATGGACCGGTTTTTATAAGTAGAAATGGATGAAATTTTCAACAAAACGACCAATTTGC
*
52922335 TCTTTGCTTTAATGTACAGGGACTAATTTGTCCATTTTTATAGTAAACGAAGCAAAATGCAATCC
66 TCTTTGCTTTAATGTACAGGGACTAATTTGTCCATTTTTATAGTAAACGAAGCAAAAAGCAATCC
52922400 AACTTCTAGTACAAGGGCCTCTATAGCACTTTTCCCCAAACGAACAATATA
131 AACTTCTAGTACAAGGGCCTCTATAGCACTTTTCCCCAAACGAACAATATA
*
52922451 GACGTACATGGACCGGTTTTTATAAGTAGAAATGGATGAAATTTTCAACAAAATGACCAATTTGC
1 GACGTACATGGACCGGTTTTTATAAGTAGAAATGGATGAAATTTTCAACAAAACGACCAATTTGC
* * * *
52922516 TCTTTGCTTTAATGTATAGGGACTAATTTGTCCATTTTTATAGTAAAGGGAGCAAAAAGCGATCC
66 TCTTTGCTTTAATGTACAGGGACTAATTTGTCCATTTTTATAGTAAACGAAGCAAAAAGCAATCC
*
52922581 AACTTCTAGTACAAGGGCCTCTATAGCACTTTTTCCCAAACGAACAATATA
131 AACTTCTAGTACAAGGGCCTCTATAGCACTTTTCCCCAAACGAACAATATA
52922632 G
1 G
52922633 TAAGCATTGG
Statistics
Matches: 174, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 174 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (181 bp):
GACGTACATGGACCGGTTTTTATAAGTAGAAATGGATGAAATTTTCAACAAAACGACCAATTTGC
TCTTTGCTTTAATGTACAGGGACTAATTTGTCCATTTTTATAGTAAACGAAGCAAAAAGCAATCC
AACTTCTAGTACAAGGGCCTCTATAGCACTTTTCCCCAAACGAACAATATA
Found at i:52925365 original size:23 final size:23
Alignment explanation
Indices: 52925309--52925378 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
52925299 TTATTAACAT
* **
52925309 TGTTCGTGAATATGTTCAATTATA
1 TGTTCGTGAACATGTTTGATTA-A
* *
52925333 TGTTCATGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTTGATTAA
52925356 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTTGATTAA
52925379 GTTAAATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.46
Consensus pattern (23 bp):
TGTTCGTGAACATGTTTGATTAA
Found at i:52925388 original size:23 final size:23
Alignment explanation
Indices: 52925327--52925394 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
52925317 AATATGTTCA
*
52925327 ATTATATGTTCATGAACATGTTTG
1 ATTA-ATGTTAATGAACATGTTTG
* **
52925351 TTTAATGTTCGTGAACATGTTTG
1 ATTAATGTTAATGAACATGTTTG
*
52925374 ATTAA-GTTAAATGAATATGTT
1 ATTAATGTT-AATGAACATGTT
52925395 CGTGAACATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.08
23 31 0.84
24 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.46
Consensus pattern (23 bp):
ATTAATGTTAATGAACATGTTTG
Found at i:52926550 original size:43 final size:42
Alignment explanation
Indices: 52926490--52926572 Score: 157
Period size: 43 Copynumber: 2.0 Consensus size: 42
52926480 ACCTGTGCAT
52926490 ACTTACCCTTCTTTCAACAAAGAAAGGTATCACATTCACGAC
1 ACTTACCCTTCTTTCAACAAAGAAAGGTATCACATTCACGAC
52926532 ACTTACCCTTTCTTTCAACAAAGAAAGGTATCACATTCACG
1 ACTTACCC-TTCTTTCAACAAAGAAAGGTATCACATTCACG
52926573 TACTTATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 8 0.20
43 32 0.80
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (42 bp):
ACTTACCCTTCTTTCAACAAAGAAAGGTATCACATTCACGAC
Found at i:52928813 original size:20 final size:18
Alignment explanation
Indices: 52928775--52928813 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
52928765 TAATAGAATC
*
52928775 AAATAGATGATGTCAAAA
1 AAATAGATGATGGCAAAA
52928793 AAATATGATGTATGGCAAAA
1 AAATA-GATG-ATGGCAAAA
52928813 A
1 A
52928814 GAAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (18 bp):
AAATAGATGATGGCAAAA
Found at i:52939027 original size:24 final size:24
Alignment explanation
Indices: 52938996--52939041 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52938986 GCTTCATATT
52938996 TATATATATGCATGTAATTCATCA
1 TATATATATGCATGTAATTCATCA
* *
52939020 TATATATATGTATGTATTTCAT
1 TATATATATGCATGTAATTCAT
52939042 TGTTGAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
TATATATATGCATGTAATTCATCA
Found at i:52953139 original size:29 final size:29
Alignment explanation
Indices: 52953106--52953161 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
52953096 ATATAGATAG
52953106 GATCAAATTAGTCCCTT-TACTATTAAATA
1 GATCAAATTAGT-CCTTGTACTATTAAATA
* *
52953135 GATCAATTTAGTCCTTGTATTATTAAA
1 GATCAAATTAGTCCTTGTACTATTAAA
52953162 AGGAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (29 bp):
GATCAAATTAGTCCTTGTACTATTAAATA
Found at i:52956349 original size:95 final size:93
Alignment explanation
Indices: 52956236--52956502 Score: 412
Period size: 95 Copynumber: 2.9 Consensus size: 93
52956226 GGGTTCTTTT
* *
52956236 TATTTTCTTCTTTAATCGGCTGTGTTTTCCATTGAATTTGAATATGTATATATAACTTCGAATCG
1 TATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
*
52956301 ATTTTTTAGCTTCATTGGGATTTTTGGG
66 ATTTTTCAGCTTCATTGGGATTTTTGGG
* *
52956329 TTCTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAGTATGTATATATAACTTTGAAT
1 -T-ATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAAT
**
52956394 CGCCTTTTCAGCTTCATTGGGATTTTTGGG
64 CGATTTTTCAGCTTCATTGGGATTTTTGGG
**
52956424 TATTTTCCCCTTTAATCGGCTGTATTTTCCATTGAATTTG-A-ATGTATATATAACTTTGAATCG
1 TATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
*
52956487 ATGTTTCAGCTTCATT
66 ATTTTTCAGCTTCATT
52956503 TGCATGCGGG
Statistics
Matches: 158, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
91 35 0.22
93 36 0.23
94 2 0.01
95 85 0.54
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (93 bp):
TATTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
ATTTTTCAGCTTCATTGGGATTTTTGGG
Found at i:52959239 original size:15 final size:14
Alignment explanation
Indices: 52959221--52959268 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
52959211 TTTTAAATAC
52959221 AAAACTTTTAATATT
1 AAAA-TTTTAATATT
*
52959236 AAAATATTACATATT
1 AAAATTTTA-ATATT
52959251 AAAATTTTAA-A-T
1 AAAATTTTAATATT
52959263 AAAATT
1 AAAATT
52959269 CTATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 7 0.23
13 1 0.03
14 5 0.17
15 17 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTTTAATATT
Found at i:52962032 original size:16 final size:16
Alignment explanation
Indices: 52962008--52962041 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52961998 TTTCACGACA
* *
52962008 AACACAAAAAGAAAAG
1 AACAAAAAAAAAAAAG
52962024 AACAAAAAAAAAAAAG
1 AACAAAAAAAAAAAAG
52962040 AA
1 AA
52962042 ACTATGGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAAAAAG
Found at i:52965871 original size:11 final size:11
Alignment explanation
Indices: 52965857--52965897 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
52965847 TGTTTTCTCT
52965857 CTATTTTGCTA
1 CTATTTTGCTA
*
52965868 CTATTTTACTA
1 CTATTTTGCTA
* *
52965879 TTATGTTGCTA
1 CTATTTTGCTA
52965890 CTATTTTG
1 CTATTTTG
52965898 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Done.