Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 171 of 313
Found at i:53344395 original size:26 final size:26
Alignment explanation
Indices: 53344314--53344397 Score: 88
Period size: 24 Copynumber: 3.4 Consensus size: 26
53344304 AACCATGTAA
* * *
53344314 CGGGAAGCTCCGGATATCC-ATTAA-
1 CGGGAAGCTCCAGAGAGCCAATTAAT
*
53344338 CGGGAAGCT-CATACGAGCCAA-T-AT
1 CGGGAAGCTCCAGA-GAGCCAATTAAT
53344362 CGGGAAGCTCCAGAGAGCCAATTAAT
1 CGGGAAGCTCCAGAGAGCCAATTAAT
53344388 CGGGAAGCTC
1 CGGGAAGCTC
53344398 ATGAAAGAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
23 3 0.06
24 29 0.59
25 5 0.10
26 12 0.24
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (26 bp):
CGGGAAGCTCCAGAGAGCCAATTAAT
Found at i:53344455 original size:25 final size:25
Alignment explanation
Indices: 53344338--53344457 Score: 102
Period size: 25 Copynumber: 4.7 Consensus size: 25
53344328 TATCCATTAA
*
53344338 CGGGAAGCTCATACGAGCCAAT-AT
1 CGGGAAGCTCATAAGAGCCAATAAT
*
53344362 CGGGAAGCTCCA-GAGAGCCAATTAAT
1 CGGGAAGCT-CATAAGAGCCAA-TAAT
**
53344388 CGGGAAGCTCATGAAAGAGCCTTTAAT
1 CGGGAAGCTCAT--AAGAGCCAATAAT
* **
53344415 CAGGAAGCTCCGAAGAGCC-ATATAT
1 CGGGAAGCTCATAAGAGCCAATA-AT
*
53344440 CGGGACGCTCATAAGAGC
1 CGGGAAGCTCATAAGAGC
53344458 TGCGGTGTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
24 18 0.24
25 28 0.37
26 11 0.14
27 13 0.17
28 6 0.08
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAATAAT
Found at i:53344535 original size:24 final size:25
Alignment explanation
Indices: 53344496--53344554 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
53344486 CACAACCAAT
***
53344496 CGGGAAGCTCCGAAGAGTTAT-TAA
1 CGGGAAGCTCCGAAGAACCATATAA
53344520 CGGGAAGCTCAC-AAGAACCATATAA
1 CGGGAAGCTC-CGAAGAACCATATAA
53344545 CGGGAAGCTC
1 CGGGAAGCTC
53344555 GTGAGAGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.15
Consensus pattern (25 bp):
CGGGAAGCTCCGAAGAACCATATAA
Found at i:53344584 original size:25 final size:25
Alignment explanation
Indices: 53344517--53344587 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
53344507 GAAGAGTTAT
** *
53344517 TAACGGGAAGCTCACAAGAACCATA
1 TAACGGGAAGCTCATGAGAGCCATA
*
53344542 TAACGGGAAGCTCGTGAGAGCCATA
1 TAACGGGAAGCTCATGAGAGCCATA
* * *
53344567 TATCGGGATGCTTATGAGAGC
1 TAACGGGAAGCTCATGAGAGC
53344588 TAATAATGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (25 bp):
TAACGGGAAGCTCATGAGAGCCATA
Found at i:53344800 original size:22 final size:23
Alignment explanation
Indices: 53344748--53344800 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
53344738 ACATGGCACT
*
53344748 TATAC-ATTTCAAATACATAACA
1 TATACAATTTAAAATACATAACA
*
53344770 T-T-CAATTTAAAATATATAA-A
1 TATACAATTTAAAATACATAACA
53344790 TATACAATTTA
1 TATACAATTTA
53344801 GTGACACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.12
21 15 0.58
22 8 0.31
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (23 bp):
TATACAATTTAAAATACATAACA
Found at i:53346532 original size:3 final size:3
Alignment explanation
Indices: 53346524--53346557 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
53346514 TTTACCTTGT
* *
53346524 TTA TTA TTA TTA TTA TTA TTA TTG GTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53346558 ATTGTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:53348804 original size:20 final size:20
Alignment explanation
Indices: 53348779--53348816 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53348769 GACAAGATGT
*
53348779 ATGGGTAGAAGTGGACTTGA
1 ATGGGTAGAAGTGAACTTGA
53348799 ATGGGTAGAAGTGAACTT
1 ATGGGTAGAAGTGAACTT
53348817 TTACAGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.37, T:0.26
Consensus pattern (20 bp):
ATGGGTAGAAGTGAACTTGA
Found at i:53351591 original size:31 final size:31
Alignment explanation
Indices: 53351556--53351624 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
53351546 TGAATACTTT
* *
53351556 AGTTCAGACCCCAATAT-ACAAATAATTGTCA
1 AGTTCAAACCACAATATGA-AAATAATTGTCA
* *
53351587 AGTTCAAATCACAATATGAGAATAATTGTCA
1 AGTTCAAACCACAATATGAAAATAATTGTCA
*
53351618 AATTCAA
1 AGTTCAA
53351625 GGATTAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (31 bp):
AGTTCAAACCACAATATGAAAATAATTGTCA
Found at i:53358645 original size:14 final size:14
Alignment explanation
Indices: 53358626--53358656 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53358616 ATTACTAGTA
53358626 TTTCTTGCATGATT
1 TTTCTTGCATGATT
53358640 TTTCTTGCATGATT
1 TTTCTTGCATGATT
53358654 TTT
1 TTT
53358657 GGATTTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (14 bp):
TTTCTTGCATGATT
Found at i:53360152 original size:11 final size:11
Alignment explanation
Indices: 53360136--53360176 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
53360126 ATTTTAAAAA
53360136 TAAAAAAATTT
1 TAAAAAAATTT
53360147 TAAAAAAAGTATTT
1 T-AAAAAA--ATTT
53360161 TAAAAAAATTT
1 TAAAAAAATTT
53360172 TAAAA
1 TAAAA
53360177 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.37
12 6 0.22
13 6 0.22
14 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:53360653 original size:33 final size:31
Alignment explanation
Indices: 53360595--53360655 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
53360585 CCCAATTATA
* *
53360595 TTTATTTTTTTATTTTGGTATTTAAATTTTT
1 TTTATTTTTTTAATTTGGTACTTAAATTTTT
53360626 TTTATTTTGCTTTAATTTGGTACTTAAATT
1 TTTATTTT--TTTAATTTGGTACTTAAATT
53360656 ATCATCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 8 0.31
33 18 0.69
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.67
Consensus pattern (31 bp):
TTTATTTTTTTAATTTGGTACTTAAATTTTT
Found at i:53369043 original size:57 final size:57
Alignment explanation
Indices: 53368968--53369099 Score: 183
Period size: 57 Copynumber: 2.3 Consensus size: 57
53368958 TTGAGACTTG
* * * *
53368968 TTGAATGTCGCGACTTTGCTGCTGTTTGGGATCAACTTCCATCTTCAGGCTACTGGC
1 TTGAATGTTGTGACTTTGCTACTGTTTGGGATCAACTTCCATCTTCAAGCTACTGGC
* * *
53369025 TTGAATGTTGTGATTTTGCTATTGTTTGGGATCAACTTCCATCTTCAAGCTATTGGC
1 TTGAATGTTGTGACTTTGCTACTGTTTGGGATCAACTTCCATCTTCAAGCTACTGGC
* *
53369082 TTGACTATTGTGACTTTG
1 TTGAATGTTGTGACTTTG
53369100 GTGAGTGGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (57 bp):
TTGAATGTTGTGACTTTGCTACTGTTTGGGATCAACTTCCATCTTCAAGCTACTGGC
Found at i:53369139 original size:21 final size:22
Alignment explanation
Indices: 53369115--53369164 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
53369105 TGGATGTCGT
53369115 GACTTTG-TAGGCCAATGTTGC
1 GACTTTGATAGGCCAATGTTGC
* *
53369136 GACTTTGATCGTCCAATGTTGC
1 GACTTTGATAGGCCAATGTTGC
*
53369158 AACTTTG
1 GACTTTG
53369165 GGTCCAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (22 bp):
GACTTTGATAGGCCAATGTTGC
Found at i:53369171 original size:20 final size:21
Alignment explanation
Indices: 53369126--53369172 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
53369116 ACTTTGTAGG
*
53369126 CCAATGTTGCGACTTTGATCGT
1 CCAATGTTGCAACTTTGA-CGT
*
53369148 CCAATGTTGCAACTTTG-GGT
1 CCAATGTTGCAACTTTGACGT
53369168 CCAAT
1 CCAAT
53369173 AAGCTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (21 bp):
CCAATGTTGCAACTTTGACGT
Found at i:53373736 original size:44 final size:44
Alignment explanation
Indices: 53373653--53373740 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
53373643 CTTGCCTTCA
* * *
53373653 GTCTGCCATTTTGGCTTACACCCACTCGAGGTTGTATTTAGACT
1 GTCTGCCACTTTGGCGTACACCCACTCGAGGTTGGATTTAGACT
*
53373697 GTCTGCCACTTTGGCGTAC-CCTCATTC-AGGTTTGGATTTAGACT
1 GTCTGCCACTTTGGCGTACACC-CACTCGAGG-TTGGATTTAGACT
53373741 ATTCACCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 5 0.13
44 33 0.87
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (44 bp):
GTCTGCCACTTTGGCGTACACCCACTCGAGGTTGGATTTAGACT
Found at i:53373794 original size:16 final size:16
Alignment explanation
Indices: 53373753--53373797 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
53373743 TCACCACTTT
* *
53373753 GGCTTGCAATTCGACA
1 GGCTTGCACTTTGACA
**
53373769 GGCTCACACTTTGACA
1 GGCTTGCACTTTGACA
53373785 GGCTTGCACTTTG
1 GGCTTGCACTTTG
53373798 CTTACTGTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (16 bp):
GGCTTGCACTTTGACA
Found at i:53387540 original size:61 final size:60
Alignment explanation
Indices: 53387444--53387626 Score: 178
Period size: 59 Copynumber: 3.0 Consensus size: 60
53387434 ATTATATTTA
* * *
53387444 ATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAT
1 ATAAGAATTATTTTAAATTAAATTTTATAATATTATATATTATGATTTTAGTAAATTCAT
* ** * * *
53387504 ATAAGAA-TA-TTTAATATTAAGAATTTTATTAA-ATTATATATTTTTG-TTAAATTATATTTA-
1 ATAAGAATTATTTTAA-ATT-A-AATTTTA-TAATATTATATA-TTATGATTTTAGTAAATTCAT
* * *
53387564 ATAATAATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
1 ATAAGAATTATTTTAAATTAAATTTTATAATATTATATATTATGATTTTAGTAAATTCAT
53387624 ATA
1 ATA
53387627 TTTTATTAAA
Statistics
Matches: 95, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
58 11 0.12
59 28 0.29
60 17 0.18
61 28 0.29
62 11 0.12
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (60 bp):
ATAAGAATTATTTTAAATTAAATTTTATAATATTATATATTATGATTTTAGTAAATTCAT
Found at i:53387548 original size:18 final size:17
Alignment explanation
Indices: 53387526--53387660 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 17
53387516 AATATTAAGA
53387526 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
53387543 ATTTTTGTTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
53387559 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
53387573 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* *
53387592 AATATTA-TATATTATA-
1 -ATTTTATTAAATTATAT
*
53387608 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
53387626 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53387643 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
53387661 TTAATAATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 9 0.10
16 9 0.10
17 20 0.22
18 41 0.45
19 1 0.01
20 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53387555 original size:120 final size:120
Alignment explanation
Indices: 53387405--53387626 Score: 426
Period size: 120 Copynumber: 1.9 Consensus size: 120
53387395 AAGAATATTT
53387405 AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
* *
53387470 ATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
66 ATAATATTATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
53387525 AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
53387590 ATAATATTATATATTATAATTTTAGTAAATTCATATA
66 ATAATATTATATATTATAATTTTAGTAAATTCATATA
53387627 TTTTATTAAA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
ATAATATTATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
Found at i:53387579 original size:26 final size:25
Alignment explanation
Indices: 53387541--53387680 Score: 85
Period size: 26 Copynumber: 5.5 Consensus size: 25
53387531 ATTAAATTAT
*
53387541 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
53387567 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
* * * *
53387593 ATATTATATATTATAATTTTAGTAAATTC
1 ATATTAT-T-TTA-AATTATATTTAA-TA
*
53387622 ATA-TATTTT--ATTA-AATT-AT-
1 ATATTATTTTAAATTATATTTAATA
*
53387641 ATATTTTTATTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
53387667 ATAATTATGTTAAA
1 AT-ATTATTTTAAA
53387681 ATATGATTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
19 3 0.03
20 4 0.05
21 3 0.03
22 2 0.02
23 7 0.08
24 3 0.03
25 7 0.08
26 30 0.34
27 13 0.15
28 11 0.13
29 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:53387598 original size:15 final size:15
Alignment explanation
Indices: 53387554--53387609 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
53387544 TTTTTGTTAA
*
53387554 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
53387569 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
53387580 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
53387595 ATTATATATTATAAT
1 ATTATATTTTATAAT
53387610 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:53387627 original size:41 final size:41
Alignment explanation
Indices: 53387404--53387645 Score: 138
Period size: 41 Copynumber: 6.0 Consensus size: 41
53387394 TAAGAATATT
* *
53387404 TAATTTTATTAAATTATATATTTTTGTTAA-ATTATAT-TTAA
1 TAATTTTAGTAAATTATATA-TTTT-ATAATATTATATATTAA
** *
53387445 TAATAATTATTTTAAA-T-TATATTTTATAGTATTATATATT-A
1 TAAT--TT-TAGTAAATTATATATTTTATAATATTATATATTAA
* *
53387486 TGATTTTAGTAAATTCATATA----AGAATATT-TAATATTAA
1 TAATTTTAGTAAATT-ATATATTTTATAATATTAT-ATATTAA
* * *
53387524 GAATTTTATTAAATTATATATTTTTGTTAA-ATTATAT-TTAA
1 TAATTTTAGTAAATTATATA-TTTT-ATAATATTATATATTAA
**
53387565 TAATAATTATTTTAAA-T-TATATTTTATAATATTATATATT-A
1 TAAT--TT-TAGTAAATTATATATTTTATAATATTATATATTAA
53387606 TAATTTTAGTAAATTCATATATTTTATTAA-ATTATATATT
1 TAATTTTAGTAAATT-ATATATTTTA-TAATATTATATATT
53387646 TTTATTAAAT
Statistics
Matches: 157, Mismatches: 18, Indels: 52
0.69 0.08 0.23
Matches are distributed among these distances:
36 1 0.01
37 16 0.10
38 23 0.15
39 6 0.04
40 5 0.03
41 65 0.41
42 20 0.13
43 9 0.06
44 12 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (41 bp):
TAATTTTAGTAAATTATATATTTTATAATATTATATATTAA
Found at i:53387880 original size:44 final size:45
Alignment explanation
Indices: 53387817--53387914 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
53387807 CTATTACAAC
* *
53387817 TCCATTCCATTCAACCAAACACAAGA-TTACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACACAAGATTTACTATTACACCTCTAT
*** *
53387861 TCCATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTAT
1 TCCATTACATTCAACCAAACACAAGATTTACTATTACACCTCTAT
53387906 TCCATTACA
1 TCCATTACA
53387915 CCTCTATTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 22 0.47
45 25 0.53
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACACAAGATTTACTATTACACCTCTAT
Found at i:53387914 original size:16 final size:16
Alignment explanation
Indices: 53387893--53387962 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
53387883 TTGATTTGCT
*
53387893 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
53387909 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
53387925 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
53387941 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
53387957 AATACA
1 ATTACA
53387963 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:53388197 original size:32 final size:32
Alignment explanation
Indices: 53388161--53388233 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 32
53388151 TAGTTGTAAT
* * * *
53388161 ATAATAGTACAATGACAACAAATAGCAGCAAA
1 ATAATAGTAAAATGACAACAAACAACAACAAA
*
53388193 ATAATA-TCAAAATGGCAACAAACAACAACAAA
1 ATAATAGT-AAAATGACAACAAACAACAACAAA
*
53388225 ACAATAGTA
1 ATAATAGTA
53388234 GACAACAGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.03
32 31 0.94
33 1 0.03
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.15
Consensus pattern (32 bp):
ATAATAGTAAAATGACAACAAACAACAACAAA
Found at i:53404584 original size:22 final size:20
Alignment explanation
Indices: 53404542--53404593 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
53404532 TAAATAATTG
*
53404542 AAATT-TTTAATATTTTATT
1 AAATTATTTAAAATTTTATT
53404561 AAATTATTTAAAATTTTAAGTT
1 AAATTATTTAAAATTTT-A-TT
53404583 AAATTAATTTA
1 AAATT-ATTTA
53404594 GTAACTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.18
20 10 0.36
21 1 0.04
22 7 0.25
23 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AAATTATTTAAAATTTTATT
Found at i:53406504 original size:27 final size:27
Alignment explanation
Indices: 53406474--53406720 Score: 325
Period size: 27 Copynumber: 9.1 Consensus size: 27
53406464 GATATAACAG
53406474 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
53406501 TCATTTTAACCTATAGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
53406527 GTCATTCTACCCTTTGGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
*
53406555 TCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * * *
53406582 TCATTCTACCCTATGAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
53406609 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
*
53406636 TCATTTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCGA
** * *
53406663 TCATTTTACCCTATATGGATATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
*
53406690 TCATTTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
53406717 TCAT
1 TCAT
53406721 AACAATGTAA
Statistics
Matches: 190, Mismatches: 28, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 188 0.99
28 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:53406581 original size:81 final size:81
Alignment explanation
Indices: 53406474--53406720 Score: 361
Period size: 81 Copynumber: 3.0 Consensus size: 81
53406464 GATATAACAG
* * *
53406474 TCATTTTACCCTATGGGGGTATTTCGATCATTTTAACCTATAGGGGTATTTCAGTCATTCTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCC
*
53406539 TTTGGGGGTATTTCGA
66 TATGGGGGTATTTCGA
* * *
53406555 TCATTTTACCCTATAGGGGTATTTCGATCATTCTACCCTAT-GAGGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAG-GGGTATTTCGGTCATTTTACC
* *
53406619 CTATGGGGGTATTTTGG
65 CTATGGGGGTATTTCGA
* * *
53406636 TCATTTTACCCTATGGGGGTATTTCAATCATTTTACCCTATATGGATATTTCGGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCC
*
53406701 TATGAGGGTATTTCGA
66 TATGGGGGTATTTCGA
53406717 TCAT
1 TCAT
53406721 AACAATGTAA
Statistics
Matches: 146, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 145 0.99
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCC
TATGGGGGTATTTCGA
Found at i:53409301 original size:18 final size:17
Alignment explanation
Indices: 53409251--53409301 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
53409241 GTTTTCTATT
53409251 TAAAATCATTAAAAATTA
1 TAAAAT-ATTAAAAATTA
*
53409269 TAAAGATATGAAAAATTA
1 TAAA-ATATTAAAAATTA
53409287 TAAAATATTACAAAA
1 TAAAATATTA-AAAA
53409302 AATTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 22 0.76
19 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (17 bp):
TAAAATATTAAAAATTA
Found at i:53409304 original size:20 final size:20
Alignment explanation
Indices: 53409279--53409334 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
53409269 TAAAGATATG
53409279 AAAAATTATAAAATATTACA
1 AAAAATTATAAAATATTACA
* * *
53409299 AAAAATTA-AAAAAAGTATA
1 AAAAATTATAAAATATTACA
*
53409318 ATAAAAATATAAAATAT
1 A-AAAATTATAAAATAT
53409335 CTATAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 9 0.32
20 14 0.50
21 5 0.18
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATTATAAAATATTACA
Found at i:53413671 original size:25 final size:25
Alignment explanation
Indices: 53413643--53413712 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
53413633 TGGACAAACC
53413643 ACAGCTTGTATGAGCTTCCCGATTT
1 ACAGCTTGTATGAGCTTCCCGATTT
* *
53413668 ACAGCTCGTATGAGCTTCCTGATTT
1 ACAGCTTGTATGAGCTTCCCGATTT
*
53413693 GCAGCTTGTATGAGCTTCCC
1 ACAGCTTGTATGAGCTTCCC
53413713 AATTCACAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
ACAGCTTGTATGAGCTTCCCGATTT
Found at i:53413740 original size:50 final size:50
Alignment explanation
Indices: 53413644--53413741 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
53413634 GGACAAACCA
* * * * * *
53413644 CAGCTTGTATGAGCTTCCCGATTTACAGCTCGTATGAGCTTCCTGATTTG
1 CAGCTTGTATGAGCTTCCCAATTCACAACTCGTATGAACATACTGATTTG
53413694 CAGCTTGTATGAGCTTCCCAATTCACAACTCGTGA-GAACATACTGATT
1 CAGCTTGTATGAGCTTCCCAATTCACAACTCGT-ATGAACATACTGATT
53413742 CTTAGCTCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (50 bp):
CAGCTTGTATGAGCTTCCCAATTCACAACTCGTATGAACATACTGATTTG
Found at i:53419318 original size:14 final size:14
Alignment explanation
Indices: 53419299--53419328 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53419289 ACACGGGGTT
53419299 GATTTGATTCGTGA
1 GATTTGATTCGTGA
53419313 GATTTGATTCGTGA
1 GATTTGATTCGTGA
53419327 GA
1 GA
53419329 CTGAGGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (14 bp):
GATTTGATTCGTGA
Found at i:53421134 original size:25 final size:25
Alignment explanation
Indices: 53421100--53421209 Score: 103
Period size: 25 Copynumber: 4.3 Consensus size: 25
53421090 CGGACACACC
*
53421100 ACAGCACGTATGAGCTTCCCGATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
**
53421125 ACAGCTCGTATGAGCTTCTTGATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
* * * *
53421150 GCAGCTTGTAGTATGAGCTTCTCAATTT
1 ACAGC---TCGTATGAGCTTCCCGATTT
* * *
53421178 GCAGCTCGTATGAGCTTCCTGATTC
1 ACAGCTCGTATGAGCTTCCCGATTT
53421203 ACAGCTC
1 ACAGCTC
53421210 ATGAGAGCAT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
25 47 0.68
28 22 0.32
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCCCGATTT
Found at i:53421208 original size:53 final size:53
Alignment explanation
Indices: 53421107--53421208 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
53421097 ACCACAGCAC
* * **
53421107 GTATGAGCTTCCCGATTTACAGCTCGTATGAGCTTCTTGATTTGCAGCTTGTA
1 GTATGAGCTTCCCAATTTACAGCTCGTATGAGCTTCCTGATTCACAGCTTGTA
* *
53421160 GTATGAGCTTCTCAATTTGCAGCTCGTATGAGCTTCCTGATTCACAGCT
1 GTATGAGCTTCCCAATTTACAGCTCGTATGAGCTTCCTGATTCACAGCT
53421209 CATGAGAGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (53 bp):
GTATGAGCTTCCCAATTTACAGCTCGTATGAGCTTCCTGATTCACAGCTTGTA
Found at i:53421245 original size:25 final size:25
Alignment explanation
Indices: 53421179--53421246 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
53421169 TCTCAATTTG
* * *
53421179 CAGCTCGTATGAGCTTCCTGATTCA
1 CAGCTCGTATGAACATACTGATTCA
53421204 CAGCTC--ATGAGAGCATACTGATTCA
1 CAGCTCGTATGA-A-CATACTGATTCA
*
53421229 TAGCTCGTATGAACATAC
1 CAGCTCGTATGAACATAC
53421247 ATGAATACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.11
25 26 0.74
26 1 0.03
27 4 0.11
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (25 bp):
CAGCTCGTATGAACATACTGATTCA
Found at i:53426710 original size:102 final size:102
Alignment explanation
Indices: 53426589--53426789 Score: 314
Period size: 102 Copynumber: 2.0 Consensus size: 102
53426579 AAATATAAAG
* * * *
53426589 GGGGTTGCTAAGTGCTGATTTCCCAATTCATTGGTGGTTGCGAAGTGCTGATTCCATCA-TATTT
1 GGGGTTGCTAAGTGATGATTCCCCAATTCATTGGTGGTTGCGAAGTGCTGATCCCA-CAGTATCT
*
53426653 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
65 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
* * *
53426691 GGGGTTGTTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACAGTATCTT
1 GGGGTTGCTAAGTGATGATTCCCCAATTCATTGGTGGTTGCGAAGTGCTGATCCCACAGTATCTT
53426756 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
53426790 GATTCATTGG
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 2 0.02
102 88 0.98
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (102 bp):
GGGGTTGCTAAGTGATGATTCCCCAATTCATTGGTGGTTGCGAAGTGCTGATCCCACAGTATCTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:53426730 original size:33 final size:33
Alignment explanation
Indices: 53426666--53426902 Score: 139
Period size: 33 Copynumber: 6.8 Consensus size: 33
53426656 ATGTGAAGGG
*
53426666 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
53426693 GGTTGTTAAGTGATGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
53426726 GGTTGCTAAGTGCTGA-TCCCACAGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCC-C-G-A--TT-CAT-TG---GT
53426768 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
53426801 GGTTGCTAAGTGCTGATTCCACCG-TATCATTGAATGT
1 GGTTGCTAAGTGCTGATTCC-CCGAT-TCATTG---GT
* * *
53426838 GAAAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
53426877 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
53426903 AACGGATAAC
Statistics
Matches: 165, Mismatches: 15, Indels: 53
0.71 0.06 0.23
Matches are distributed among these distances:
27 20 0.12
31 2 0.01
32 6 0.04
33 55 0.33
34 14 0.08
35 1 0.01
36 2 0.01
37 6 0.04
38 4 0.02
39 4 0.02
40 1 0.01
41 1 0.01
42 26 0.16
43 23 0.14
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:53426812 original size:75 final size:76
Alignment explanation
Indices: 53426689--53426892 Score: 329
Period size: 75 Copynumber: 2.7 Consensus size: 76
53426679 TGATTCCCCC
*
53426689 AAGGGGTTGTTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACAGTATC
1 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACAGTATC
53426754 -TTAAATGTGA
66 ATTAAATGTGA
* * *
53426764 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACAGTATC
*
53426829 ATTGAATGTGA
66 ATTAAATGTGA
* * *
53426840 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGA
53426893 ATCCACCGAT
Statistics
Matches: 120, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 61 0.51
76 59 0.49
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACAGTATC
ATTAAATGTGA
Found at i:53426880 original size:76 final size:75
Alignment explanation
Indices: 53426689--53426900 Score: 334
Period size: 76 Copynumber: 2.8 Consensus size: 75
53426679 TGATTCCCCC
* * *
53426689 AAGGGGTTGTTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACAGTATC
1 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
53426754 TTAAATGTGA
66 TTAAATGTGA
*
53426764 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
53426829 ATTGAATGTGA
66 -TTAAATGTGA
* * * *
53426840 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
53426901 ATAACGGATA
Statistics
Matches: 127, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
75 61 0.48
76 66 0.52
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:53434212 original size:102 final size:102
Alignment explanation
Indices: 53434086--53434286 Score: 348
Period size: 102 Copynumber: 2.0 Consensus size: 102
53434076 GAATATAAAG
* *
53434086 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
* **
53434151 AAATGTGAAGGGGGTTGGTAAGTGCTGATTCCCCCAA
66 AAATGTGAAAGGGGTTACTAAGTGCTGATTCCCCCAA
*
53434188 GGGGTTGGTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
53434253 AAATGTGAAAGGGGTTACTAAGTGCTGATTCCCC
66 AAATGTGAAAGGGGTTACTAAGTGCTGATTCCCC
53434287 GATTCATTGG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
AAATGTGAAAGGGGTTACTAAGTGCTGATTCCCCCAA
Found at i:53434380 original size:76 final size:75
Alignment explanation
Indices: 53434186--53434397 Score: 352
Period size: 76 Copynumber: 2.8 Consensus size: 75
53434176 TGATTCCCCC
* *
53434186 AAGGGGTTGGTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
53434251 TTAAATGTGA
66 TTAAATGTGA
*
53434261 AAGGGGTTACTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
53434326 ATTGAATGTGA
66 -TTAAATGTGA
* * *
53434337 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
53434398 ATAACAGATA
Statistics
Matches: 128, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 62 0.48
76 66 0.52
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:53437146 original size:5 final size:6
Alignment explanation
Indices: 53437114--53437156 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
53437104 TAAGTTTAAG
* * *
53437114 AAAATA ACATTA AACATA AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A
53437157 TAGACTAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:53449208 original size:20 final size:21
Alignment explanation
Indices: 53449180--53449221 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
53449170 AGGGGTTAAA
53449180 TTGAGAAATGTG-CAAATTGT
1 TTGAGAAATGTGTCAAATTGT
* *
53449200 TTGATAAATGTGTTAAATTGT
1 TTGAGAAATGTGTCAAATTGT
53449221 T
1 T
53449222 AAATGTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.43
Consensus pattern (21 bp):
TTGAGAAATGTGTCAAATTGT
Found at i:53450861 original size:12 final size:12
Alignment explanation
Indices: 53450844--53450874 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53450834 CTAGTAGCTT
*
53450844 CACACGGCCTAG
1 CACACGACCTAG
53450856 CACACGACCTAG
1 CACACGACCTAG
53450868 CACACGA
1 CACACGA
53450875 GCATGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.42, G:0.19, T:0.06
Consensus pattern (12 bp):
CACACGACCTAG
Found at i:53455437 original size:27 final size:25
Alignment explanation
Indices: 53455381--53455445 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 25
53455371 TTTGTATATG
*
53455381 ATTATTTTAACTTGCTTTATAGATT
1 ATTATTTTAAGTTGCTTTATAGATT
*
53455406 ATTATTTTAAGTTGCTTTATATATT
1 ATTATTTTAAGTTGCTTTATAGATT
53455431 ATTTTATTTTAAGTT
1 A--TTATTTTAAGTT
53455446 ATTCTACATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 24 0.67
27 12 0.33
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.60
Consensus pattern (25 bp):
ATTATTTTAAGTTGCTTTATAGATT
Found at i:53455456 original size:27 final size:26
Alignment explanation
Indices: 53455407--53455468 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
53455397 TTATAGATTA
* * *
53455407 TTATTTTAAGTTGCTTTATATATTATT
1 TTATTTTAAGTTGATTTACATATT-TC
53455434 TTATTTTAAGTT-ATTCTACATATTTC
1 TTATTTTAAGTTGATT-TACATATTTC
53455460 TTATTTTAA
1 TTATTTTAA
53455469 AATTAACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.39
27 19 0.61
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTGATTTACATATTTC
Found at i:53461716 original size:18 final size:19
Alignment explanation
Indices: 53461680--53461716 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53461670 TTTAGCATGT
*
53461680 CAAATTACCAATTACTGAA
1 CAAATTACCAATTAATGAA
53461699 CAAATTACC-ATTAATGAA
1 CAAATTACCAATTAATGAA
53461717 TAAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (19 bp):
CAAATTACCAATTAATGAA
Found at i:53461722 original size:19 final size:19
Alignment explanation
Indices: 53461681--53461722 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
53461671 TTAGCATGTC
* *
53461681 AAATTACCAATTACTGAAC
1 AAATTACCAATTAATGAAA
53461700 AAATTACC-ATTAATGAATA
1 AAATTACCAATTAATGAA-A
53461719 AAAT
1 AAAT
53461723 ATTTGTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATTACCAATTAATGAAA
Found at i:53466492 original size:29 final size:29
Alignment explanation
Indices: 53466442--53466501 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53466432 CCTATGAATA
* *
53466442 CCTCTAATAGATAGGATTACTTACATGGT
1 CCTCTAATAGATAAGATGACTTACATGGT
53466471 CCTCTAATAGATAAGATGACTTACATGGT
1 CCTCTAATAGATAAGATGACTTACATGGT
53466500 CC
1 CC
53466502 GAAGAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (29 bp):
CCTCTAATAGATAAGATGACTTACATGGT
Found at i:53469949 original size:34 final size:34
Alignment explanation
Indices: 53469878--53469995 Score: 123
Period size: 34 Copynumber: 3.5 Consensus size: 34
53469868 TTCAATGCGT
* * **
53469878 TGGTGAGGTGTAGTTACTGCTC-GCCAGAGCAA-C
1 TGGTGTGGTGTAGTTACTACTCTAACA-AGCAATC
* * * *
53469911 TGGTGTGGTTTAGTTATTACTCTGACAATCAATC
1 TGGTGTGGTGTAGTTACTACTCTAACAAGCAATC
* *
53469945 TGGTGTGGTGTAGTTACTACTGTAACGAGCAATC
1 TGGTGTGGTGTAGTTACTACTCTAACAAGCAATC
53469979 TGGTGTGGTGTAGTTAC
1 TGGTGTGGTGTAGTTAC
53469996 CCGTGTATCC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
33 22 0.31
34 49 0.69
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (34 bp):
TGGTGTGGTGTAGTTACTACTCTAACAAGCAATC
Found at i:53470611 original size:33 final size:33
Alignment explanation
Indices: 53470574--53470647 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
53470564 TTGGTAAATG
53470574 TGTTTGGAGTTTTGAATGGTAACTAAAATAGCA
1 TGTTTGGAGTTTTGAATGGTAACTAAAATAGCA
53470607 TGTTTGGAGTTTTGAATGGTAACTAAAATAGCA
1 TGTTTGGAGTTTTGAATGGTAACTAAAATAGCA
53470640 TGTTTGGA
1 TGTTTGGA
53470648 CATGGATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (33 bp):
TGTTTGGAGTTTTGAATGGTAACTAAAATAGCA
Found at i:53477644 original size:41 final size:41
Alignment explanation
Indices: 53477580--53477835 Score: 381
Period size: 41 Copynumber: 6.2 Consensus size: 41
53477570 ATGTTCTGAG
*
53477580 GGCGTTTTTATGTAAGCGACGCTAATGTTCTGGGCTTTAGC
1 GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
* *
53477621 GGCGTTTTTATCTAAACGCCGCTAATGTTCTGGGCTTTAGC
1 GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
*
53477662 GGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGCTTTAGC
1 GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
*
53477703 GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGC
1 GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
* *
53477744 GGCATTTTTAAGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
1 GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
* * *
53477785 GGCGTTTTTAT-TGATGCGCCGCTAAT-TCTCAGGCCTTTAGC
1 GGCGTTTTTATGT-AAGCGCCGCTAATGT-TCTGGGCTTTAGC
53477826 GGCGCTTTTT
1 GGCG-TTTTT
53477836 TAAAAAACGC
Statistics
Matches: 197, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
40 2 0.01
41 190 0.96
42 5 0.03
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (41 bp):
GGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGCTTTAGC
Found at i:53477752 original size:123 final size:123
Alignment explanation
Indices: 53477536--53477835 Score: 427
Period size: 123 Copynumber: 2.5 Consensus size: 123
53477526 GACTTTTCGG
*
53477536 GGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCT--G----AG-GGCGTTTTTATGTA
1 GGGCTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATGTA
* * *
53477594 AGCGACGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATCTAAACGCCGCTAATGTTCT
66 AGCGACGCTAATGTTCTGGGATTTAGCGGCATTTTTAACTAAACGCCGCTAATGTTCT
53477652 GGGCTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATGTA
1 GGGCTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATGTA
* * *
53477717 AGCGCCGCTAATGTTCTGGGATTTAGCGGCATTTTTAAGTAAGCGCCGCTAATGTTCT
66 AGCGACGCTAATGTTCTGGGATTTAGCGGCATTTTTAACTAAACGCCGCTAATGTTCT
* * * *
53477775 GGGCTTTAGCGGCGTTTTTATTGATGCGCCGCTAAT-TCTCAGGCCTTTAGCGGCGCTTTTT
1 GGGCTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGT-TCTGGGCTTTAGCGGCG-TTTTT
53477836 TAAAAAACGC
Statistics
Matches: 164, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
116 40 0.24
118 1 0.01
122 3 0.02
123 115 0.70
124 5 0.03
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.37
Consensus pattern (123 bp):
GGGCTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATGTA
AGCGACGCTAATGTTCTGGGATTTAGCGGCATTTTTAACTAAACGCCGCTAATGTTCT
Found at i:53477864 original size:123 final size:123
Alignment explanation
Indices: 53477536--53477875 Score: 362
Period size: 123 Copynumber: 2.8 Consensus size: 123
53477526 GACTTTTCGG
* **
53477536 GGGCTTTAGCGGCGTTTTTA-TGTAAGCGCCGCTAATGTT-----C-TGAG-GGCGTTTTTATGT
1 GGGCTTTAGCGGCGTTTTTATTG-AAGCGCCGCTAATGTTCAGGCCTTTAGCGGCGTTTTTATAA
* * * * *
53477593 AAGCGACGCTAATGTTCTGGGC-TTTAGCGGCGTTTTTATCTAAACGCCGCTAATGTTCT
65 AAACGCCGCTAATGCTCT-GGCATTTAGCGGCATTTTTAACTAAACGCCGCTAATGTTCT
* * * **
53477652 GGGCTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATGTA
1 GGGCTTTAGCGGCGTTTTTATTGAAGCGCCGCTAATGTTCAGGCCTTTAGCGGCGTTTTTATAAA
* * * * *
53477717 AGCGCCGCTAATGTTCTGGGATTTAGCGGCATTTTTAAGTAAGCGCCGCTAATGTTCT
66 AACGCCGCTAATGCTCTGGCATTTAGCGGCATTTTTAACTAAACGCCGCTAATGTTCT
*
53477775 GGGCTTTAGCGGCGTTTTTATTGATGCGCCGCTAAT-TCTCAGGCCTTTAGCGGCGCTTTTT-TA
1 GGGCTTTAGCGGCGTTTTTATTGAAGCGCCGCTAATGT-TCAGGCCTTTAGCGGCG-TTTTTAT-
* *
53477838 AAAAACGCCGCTAATGCTCT-TCATTTAGTGGCATTTTT
63 AAAAACGCCGCTAATGCTCTGGCATTTAGCGGCATTTTT
53477876 GGAAAGCGCC
Statistics
Matches: 193, Mismatches: 19, Indels: 17
0.84 0.08 0.07
Matches are distributed among these distances:
116 36 0.19
117 1 0.01
121 1 0.01
122 6 0.03
123 128 0.66
124 21 0.11
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (123 bp):
GGGCTTTAGCGGCGTTTTTATTGAAGCGCCGCTAATGTTCAGGCCTTTAGCGGCGTTTTTATAAA
AACGCCGCTAATGCTCTGGCATTTAGCGGCATTTTTAACTAAACGCCGCTAATGTTCT
Found at i:53478202 original size:23 final size:23
Alignment explanation
Indices: 53478174--53478249 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
53478164 GTTTAAGGGC
*
53478174 TATAGTATGTAGTCTAAGGGTTT
1 TATAGTATGTAGTTTAAGGGTTT
*
53478197 TATAGT-T-TAATGTTTAA-TGTTT
1 TATAGTATGT-A-GTTTAAGGGTTT
53478219 ACTATAGTATGTAGTTTAAGGGTTT
1 --TATAGTATGTAGTTTAAGGGTTT
53478244 TATAGT
1 TATAGT
53478250 TTATGGTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
21 1 0.02
22 6 0.14
23 17 0.40
24 12 0.28
25 6 0.14
26 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (23 bp):
TATAGTATGTAGTTTAAGGGTTT
Found at i:53482470 original size:29 final size:29
Alignment explanation
Indices: 53482428--53482485 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
53482418 TAAATCTTCT
53482428 TCCATTTGTCAACTATTTCATTTCCAAAA
1 TCCATTTGTCAACTATTTCATTTCCAAAA
53482457 TCCATTTGTCAACTATTTCATTTCCAAAA
1 TCCATTTGTCAACTATTTCATTTCCAAAA
53482486 ATATATTTTG
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:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (29 bp):
TCCATTTGTCAACTATTTCATTTCCAAAA
Found at i:53482633 original size:16 final size:16
Alignment explanation
Indices: 53482614--53482662 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
53482604 TTAAGTTCAA
* *
53482614 ATTTCATAACTTACGT
1 ATTTCATAATTTACAT
53482630 ATTTTACATAATTTACAT
1 A-TTT-CATAATTTACAT
*
53482648 AATTCATAATTTACA
1 ATTTCATAATTTACA
53482663 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 12 0.43
17 5 0.18
18 11 0.39
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTTCATAATTTACAT
Found at i:53482644 original size:9 final size:9
Alignment explanation
Indices: 53482613--53482669 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
53482603 TTTAAGTTCA
53482613 AATTT-CAT
1 AATTTACAT
* *
53482621 AACTTACGT
1 AATTTACAT
*
53482630 ATTTTACAT
1 AATTTACAT
53482639 AATTTACAT
1 AATTTACAT
53482648 AA-TT-CAT
1 AATTTACAT
*
53482655 AATTTACAA
1 AATTTACAT
53482664 AATTTA
1 AATTTA
53482670 AATATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.13
8 8 0.21
9 26 0.67
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (9 bp):
AATTTACAT
Found at i:53482667 original size:16 final size:16
Alignment explanation
Indices: 53482636--53482667 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53482626 ACGTATTTTA
*
53482636 CATAATTTACATAATT
1 CATAATTTACAAAATT
53482652 CATAATTTACAAAATT
1 CATAATTTACAAAATT
53482668 TAAATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
CATAATTTACAAAATT
Found at i:53486738 original size:28 final size:29
Alignment explanation
Indices: 53486693--53486754 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
53486683 GACAGGAATT
53486693 GGATCTTCGAATGCTCCGATTATACCTGA
1 GGATCTTCGAATGCTCCGATTATACCTGA
*
53486722 GGAT-TTCGAATGTTCCGATTATACCTGA
1 GGATCTTCGAATGCTCCGATTATACCTGA
53486750 GGATC
1 GGATC
53486755 CTACAGAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (29 bp):
GGATCTTCGAATGCTCCGATTATACCTGA
Found at i:53487406 original size:324 final size:324
Alignment explanation
Indices: 53486817--53487467 Score: 1239
Period size: 324 Copynumber: 2.0 Consensus size: 324
53486807 AATTGGTTTA
53486817 TTTTTTAAAATCTTATATTATAATATACCGTTTTTCACCTGAAAATGGTAGGACGCGCAGAGGTC
1 TTTTTTAAAATCTTATATTATAATATACCGTTTTTCACCTGAAAATGGTAGGACGCGCAGAGGTC
* *
53486882 GAGGTTGTACGCTACTTAGCGAGTTGTACGAGTTAGATCCAGTCGAGCGTGTCAAAGTATGCAGA
66 GAGGTCGTACGCTACTTAGCGAGTTGTACGAGTTAGATCCAGTCGAGCGTGTCAAAGTATCCAGA
53486947 AACAGTTTTGGTCAGCCTGTTGGAACAGAAGCTCGACTATTAGCAGGATACATGGGCATTTTAGC
131 AACAGTTTTGGTCAGCCTGTTGGAACAGAAGCTCGACTATTAGCAGGATACATGGGCATTTTAGC
* * *
53487012 ACGAAATGCGAATATGTTGCCTATCAACTACGAGTCATGGCATCAAATGCCCGATAGTAACAAAA
196 ACAAAATGCGAATATGTTACCTATCAACTACGAGTCATGGCATCAAATGCCCAATAGTAACAAAA
53487077 ATCAAGCCCTCGATAATATTAAGGTAACAAAACGTTAATGTCATCTGTAATACTTAGGAATTAG
261 ATCAAGCCCTCGATAATATTAAGGTAACAAAACGTTAATGTCATCTGTAATACTTAGGAATTAG
*
53487141 TTTTTTAAAATCTTATATTATAATATACCGTTTTTCAGCTGAAAATGGTAGGACGCGCAGAGGTC
1 TTTTTTAAAATCTTATATTATAATATACCGTTTTTCACCTGAAAATGGTAGGACGCGCAGAGGTC
53487206 GAGGTCGTACGCTACTTAGCGAGTTGTACGAGTTAGATCCAGTCGAGCGTGTCAAAGTATCCAGA
66 GAGGTCGTACGCTACTTAGCGAGTTGTACGAGTTAGATCCAGTCGAGCGTGTCAAAGTATCCAGA
*
53487271 AACAGTTTTGGTCAGCCTGTTGGAATAGAAGCTCGACTATTAGCAGGATACATGGGCATTTTAGC
131 AACAGTTTTGGTCAGCCTGTTGGAACAGAAGCTCGACTATTAGCAGGATACATGGGCATTTTAGC
53487336 ACAAAATGCGAATATGTTACCTATCAACTACGAGTCATGGCATCAAATGCCCAATAGTAACAAAA
196 ACAAAATGCGAATATGTTACCTATCAACTACGAGTCATGGCATCAAATGCCCAATAGTAACAAAA
53487401 ATCAAGCCCTCGATAATATTAAGGTAACAAAACGTTAATGTCATCTGTAATACTTAGGAATTAG
261 ATCAAGCCCTCGATAATATTAAGGTAACAAAACGTTAATGTCATCTGTAATACTTAGGAATTAG
53487465 TTT
1 TTT
53487468 CAGTTATATT
Statistics
Matches: 320, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
324 320 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (324 bp):
TTTTTTAAAATCTTATATTATAATATACCGTTTTTCACCTGAAAATGGTAGGACGCGCAGAGGTC
GAGGTCGTACGCTACTTAGCGAGTTGTACGAGTTAGATCCAGTCGAGCGTGTCAAAGTATCCAGA
AACAGTTTTGGTCAGCCTGTTGGAACAGAAGCTCGACTATTAGCAGGATACATGGGCATTTTAGC
ACAAAATGCGAATATGTTACCTATCAACTACGAGTCATGGCATCAAATGCCCAATAGTAACAAAA
ATCAAGCCCTCGATAATATTAAGGTAACAAAACGTTAATGTCATCTGTAATACTTAGGAATTAG
Found at i:53488797 original size:43 final size:43
Alignment explanation
Indices: 53488744--53488962 Score: 307
Period size: 43 Copynumber: 5.1 Consensus size: 43
53488734 AACAAATAGT
* *
53488744 GGCGTTTGTGTAAAAAGCGCCACTAAAGAACATTAGCTTTAGC
1 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACATTATCTTTAGC
* * * *
53488787 GGCGTTTGTGTTAGAAGCGCCGCTAAAGAACATGAACTTTAGC
1 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACATTATCTTTAGC
* * *
53488830 GGCGTTTGTGTTAAAAGCGCCGCTAAAGAACATGACCTTTAGC
1 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACATTATCTTTAGC
*
53488873 GGCGTTTGTGTAAAAAGCGCTGCTAAAGAACATGT-TCTTTAGC
1 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACAT-TATCTTTAGC
*
53488916 GGCGTTTGTGTAAAAAGTGCCGCTAAAGAACATGT-TCTTTAGC
1 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACAT-TATCTTTAGC
53488959 GGCG
1 GGCG
53488963 CTTTTAAAAA
Statistics
Matches: 162, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACATTATCTTTAGC
Found at i:53493615 original size:17 final size:18
Alignment explanation
Indices: 53493590--53493623 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53493580 GGATTTGAAC
*
53493590 TATATAATTT-ATTTTTT
1 TATACAATTTGATTTTTT
53493607 TATACAATTTGATTTTT
1 TATACAATTTGATTTTT
53493624 CTACTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TATACAATTTGATTTTTT
Found at i:53494089 original size:41 final size:41
Alignment explanation
Indices: 53494037--53494222 Score: 254
Period size: 41 Copynumber: 4.5 Consensus size: 41
53494027 TAACGGCGTT
* * *
53494037 TTTTTGAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCG
1 TTTTTGGGAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCG
53494078 TTTTTGGGAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCG
1 TTTTTGGGAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCG
* *
53494119 TTTTTGGGAAAGCGCCGCTAATGATCAAGGATTTAGCGGCG
1 TTTTTGGGAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCG
53494160 TTTTT--GAAGTAGCGCCGCTAAT-ACTCAGGGCTTTAGCGGCG
1 TTTTTGGGAA--AGCGCCGCTAATGA-TCAGGGCTTTAGCGGCG
*
53494201 TTTTT-GAAGAAGCGCCGCTAAT
1 TTTTTGGGA-AAGCGCCGCTAAT
53494223 TCTCTATTTT
Statistics
Matches: 132, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
39 3 0.02
40 1 0.01
41 126 0.95
42 1 0.01
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (41 bp):
TTTTTGGGAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCG
Found at i:53494246 original size:82 final size:81
Alignment explanation
Indices: 53494037--53494275 Score: 250
Period size: 82 Copynumber: 2.9 Consensus size: 81
53494027 TAACGGCGTT
* * * * **
53494037 TTTTTGAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGA
1 TTTTTGAGAAAGCGCCGCTAATGATCAAGGATTTAGCGGCGTTTTT-AAAAAGCGCCGCTAAT-A
53494102 -TCAGGGCTTTAGCGGCG
64 CTCAGGGCTTTAGCGGCG
* **
53494119 TTTTTGGGAAAGCGCCGCTAATGATCAAGGATTTAGCGGCGTTTTTGAAGTAGCGCCGCTAATAC
1 TTTTTGAGAAAGCGCCGCTAATGATCAAGGATTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATAC
53494184 TCAGGGCTTTAGCGGCG
65 TCAGGGCTTTAGCGGCG
** * ** * * *
53494201 TTTTTGA-AGAAGCGCCGCTAATTCTCTA-TTTTTAGTGGCATTTTTTAAAAAGCGCCGCTAATG
1 TTTTTGAGA-AAGCGCCGCTAATGATCAAGGATTTAGCGGC-GTTTTTAAAAAGCGCCGCTAATA
*
53494264 CTCAGGGATTTA
64 CTCAGGGCTTTA
53494276 ATATAATCTA
Statistics
Matches: 133, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
81 35 0.26
82 98 0.74
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (81 bp):
TTTTTGAGAAAGCGCCGCTAATGATCAAGGATTTAGCGGCGTTTTTAAAAAGCGCCGCTAATACT
CAGGGCTTTAGCGGCG
Found at i:53495694 original size:43 final size:43
Alignment explanation
Indices: 53495625--53495896 Score: 298
Period size: 43 Copynumber: 6.3 Consensus size: 43
53495615 TTTTTAATAG
*
53495625 AAGCGTCGCTAAAGGTCA-TGAG-CTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGT-ATTG-GTCTTTAGCGGCGTTTGTGGGAA
** *
53495668 AAGCATCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGCAA
1 AAGCGCCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGGAA
* * ** * * *
53495711 AAGCCCCGCTAAATGTCCTGATCTTTAGCGGTGATTGTGGGAA
1 AAGCGCCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGGAA
* * * *
53495754 AAGCGCCGCTAAAGTTACTT-GTCTTTAGCGGTGCTTGTGAGAA
1 AAGCGCCGCTAAAGGTA-TTGGTCTTTAGCGGCGTTTGTGGGAA
* * * *
53495797 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGACGTTTATTGGAA
1 AAGCGCCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGGAA
**
53495840 AAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGGAA
*
53495883 AAGCGTCGCTAAAG
1 AAGCGCCGCTAAAG
53495897 TTAGCAACGC
Statistics
Matches: 193, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
42 4 0.02
43 188 0.97
44 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:53495792 original size:129 final size:129
Alignment explanation
Indices: 53495647--53495899 Score: 364
Period size: 129 Copynumber: 2.0 Consensus size: 129
53495637 AGGTCATGAG
* * * *
53495647 CTTTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGGTATTGGTCTTTAGCGGCGTTT-GTGGCAA
1 CTTTAGCGGCGCTTGTGAGAAAAGCACCGCTAAAGGTATTGGTCTTTAGCGACGTTTAGTGG-AA
* *
53495711 AAGCCCCGCTAAATGTCCTGATCTTTAGCGGTGATTGTGGGAAAAGCGCCGCTAAAGTTACTTGT
65 AAGCCCCGCTAAAGGTCCTGATCTTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGTTACTTGT
* * * *
53495776 CTTTAGCGGTGCTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGACGTTTATTGGAAA
1 CTTTAGCGGCGCTTGTGAGAAAAGCACCGCTAAAGGTATTGGTCTTTAGCGACGTTTAGTGGAAA
* * * *
53495841 AGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGTTA
66 AGCCCCGCTAAAGGTCCTGATCTTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGTTA
53495900 GCAACGCGGT
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
129 106 0.97
130 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (129 bp):
CTTTAGCGGCGCTTGTGAGAAAAGCACCGCTAAAGGTATTGGTCTTTAGCGACGTTTAGTGGAAA
AGCCCCGCTAAAGGTCCTGATCTTTAGCGGCGATTGTGGGAAAAGCGCCGCTAAAGTTACTTGT
Found at i:53498153 original size:21 final size:19
Alignment explanation
Indices: 53498101--53498154 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
53498091 GGTACAATTA
53498101 TTTAAAATTATTATTAACATG
1 TTTAAAA-T-TTATTAACATG
* *
53498122 TTTAGAGTTTATTAACATTG
1 TTTAAAATTTATTAACA-TG
53498142 TTTTAAAATTTAT
1 -TTTAAAATTTAT
53498155 CCTTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 9 0.33
20 3 0.11
21 15 0.56
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTAAAATTTATTAACATG
Found at i:53498661 original size:15 final size:16
Alignment explanation
Indices: 53498641--53498670 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53498631 ATGTTTCAAC
53498641 TTAAT-AATGTTGTTA
1 TTAATAAATGTTGTTA
53498656 TTAATAAATGTTGTT
1 TTAATAAATGTTGTT
53498671 GTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (16 bp):
TTAATAAATGTTGTTA
Found at i:53500700 original size:2 final size:2
Alignment explanation
Indices: 53500693--53500723 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53500683 AGTGCAGCTT
53500693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53500724 CGGTGCGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53501097 original size:13 final size:13
Alignment explanation
Indices: 53501081--53501105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53501071 TTTAAATTTA
53501081 TTTTATAGAAAAT
1 TTTTATAGAAAAT
53501094 TTTTATAGAAAA
1 TTTTATAGAAAA
53501106 ATAATTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTATAGAAAAT
Found at i:53504666 original size:26 final size:27
Alignment explanation
Indices: 53504630--53504733 Score: 108
Period size: 26 Copynumber: 4.0 Consensus size: 27
53504620 GTCAGCAATT
*
53504630 CTGTTACT-GACAGTTTTGCTGCGATA
1 CTGTTACTCGACAGCTTTGCTGCGATA
* **
53504656 CTGTTACT-GACAGTTTTGCTGTAATA
1 CTGTTACTCGACAGCTTTGCTGCGATA
* *
53504682 CTGTTACTCG-CAGCTTTGTTACGATA
1 CTGTTACTCGACAGCTTTGCTGCGATA
* *
53504708 CTATTA-TCGGCAGCTTTGCTGCGATA
1 CTGTTACTCGACAGCTTTGCTGCGATA
53504734 TTGGTGTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
25 3 0.05
26 62 0.94
27 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
CTGTTACTCGACAGCTTTGCTGCGATA
Found at i:53506787 original size:17 final size:17
Alignment explanation
Indices: 53506765--53506798 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53506755 AAATATATAT
*
53506765 TTTTAAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
53506782 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
53506799 AATAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:53509462 original size:24 final size:24
Alignment explanation
Indices: 53509435--53509482 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
53509425 AAGATTTAGT
53509435 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAGTATAATATATTTGAC
* *
53509459 ATTTATTAGTATAGTTTATTTGAC
1 ATTTATTAGTATAATATATTTGAC
53509483 TTACTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGAC
Found at i:53511434 original size:70 final size:68
Alignment explanation
Indices: 53511314--53511451 Score: 197
Period size: 70 Copynumber: 2.0 Consensus size: 68
53511304 TATCTCGGAT
* * * *
53511314 TTTAAAAAAAAGGTCATTCCCAGTAAGTTAGGACACGATCTTTTATTAATTCCCGAGATCGTTTA
1 TTTAAAAAAAAGATCATACCCAGTAAGTTAGGACACGATCTCTCATTAATTCCCGAGATCGTTTA
53511379 AAA
66 AAA
*
53511382 TTTAAGAAAAAGAGATCATACCCAGTAAGTTAGGACACGATCTCCTCA-TAATTCTCGAGATCGT
1 TTTAA-AAAAA-AGATCATACCCAGTAAGTTAGGACACGATCT-CTCATTAATTCCCGAGATCGT
53511446 TTAAAA
63 TTAAAA
53511452 CTTGAGTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 5 0.08
69 5 0.08
70 50 0.81
71 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (68 bp):
TTTAAAAAAAAGATCATACCCAGTAAGTTAGGACACGATCTCTCATTAATTCCCGAGATCGTTTA
AAA
Found at i:53511862 original size:25 final size:26
Alignment explanation
Indices: 53511834--53511891 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
53511824 AGAGATATAC
53511834 ATGTATATAGATATAAATTA-AAAAT
1 ATGTATATAGATATAAATTATAAAAT
* * * *
53511859 ATGTATGTATATGTGAATTATAAAAT
1 ATGTATATAGATATAAATTATAAAAT
*
53511885 ATATATA
1 ATGTATA
53511892 AAAATATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (26 bp):
ATGTATATAGATATAAATTATAAAAT
Found at i:53511891 original size:11 final size:11
Alignment explanation
Indices: 53511877--53511911 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
53511867 ATATGTGAAT
53511877 TATAAAATATA
1 TATAAAATATA
53511888 TATAAAA-ATA
1 TATAAAATATA
53511898 TATAAAATATA
1 TATAAAATATA
53511909 TAT
1 TAT
53511912 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAAATATA
Found at i:53511902 original size:21 final size:21
Alignment explanation
Indices: 53511877--53511936 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
53511867 ATATGTGAAT
53511877 TATAAAATATATATAAAAATA
1 TATAAAATATATATAAAAATA
*
53511898 TATAAAATATATATTTTAAAATA
1 TATAAAATATATA--TAAAAATA
53511921 TA-AAGAATATATATAA
1 TATAA-AATATATATAA
53511937 GTATGTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 15 0.44
22 2 0.06
23 17 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAAAATATATATAAAAATA
Found at i:53513680 original size:2 final size:2
Alignment explanation
Indices: 53513673--53513702 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53513663 TGACACATAA
53513673 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
53513703 GTGAGGGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53515238 original size:9 final size:9
Alignment explanation
Indices: 53515186--53515246 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
53515176 CCGGTTCAAG
53515186 TTTTTATATA
1 TTTTTA-ATA
* *
53515196 TTTTTTACA
1 TTTTTAATA
*
53515205 TTTTTTATAA
1 TTTTTAAT-A
* *
53515215 CTTTAAATCA
1 TTTTTAAT-A
53515225 TTTTTAATA
1 TTTTTAATA
53515234 TTTTTAATA
1 TTTTTAATA
53515243 TTTT
1 TTTT
53515247 CATAAAAACT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
9 23 0.56
10 18 0.44
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTAATA
Found at i:53518151 original size:15 final size:14
Alignment explanation
Indices: 53518126--53518164 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
53518116 TAAATATAAA
53518126 AAATTTTATATATT
1 AAATTTTATATATT
53518140 AAATTATTATATATTT
1 AAATT-TTATATA-TT
*
53518156 ACATTTTAT
1 AAATTTTAT
53518165 GCAATTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATTTTATATATT
Found at i:53519205 original size:30 final size:32
Alignment explanation
Indices: 53519146--53519207 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
53519136 GTATTCATTT
*
53519146 CTTTAAATGTGTACAATTGAATTAAAATCAAA
1 CTTTAAATGTGTACAATTGAATCAAAATCAAA
* *
53519178 CTTT-AATGTGTATAATTGCA-CAAAATCAAA
1 CTTTAAATGTGTACAATTGAATCAAAATCAAA
53519208 TATTATGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 14 0.52
32 4 0.15
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (32 bp):
CTTTAAATGTGTACAATTGAATCAAAATCAAA
Found at i:53521018 original size:9 final size:9
Alignment explanation
Indices: 53520964--53521068 Score: 63
Period size: 9 Copynumber: 11.7 Consensus size: 9
53520954 TTACATCTCC
*
53520964 AAAAATTAT
1 AAAAAATAT
* *
53520973 AAAAAGTGT
1 AAAAAATAT
53520982 AAAAGAAT-T
1 AAAA-AATAT
*
53520991 AATATAATAT
1 AA-AAAATAT
* *
53521001 ATAATATAT
1 AAAAAATAT
53521010 AAAAAATAT
1 AAAAAATAT
*
53521019 AAAAACTAT
1 AAAAAATAT
*
53521028 --AATATAT
1 AAAAAATAT
53521035 AAAAAATAT
1 AAAAAATAT
*
53521044 AAAAAAAACT
1 AAAAAATA-T
* *
53521054 ATAATATAT
1 AAAAAATAT
53521063 AAAAAA
1 AAAAAA
53521069 AAAACAAATC
Statistics
Matches: 71, Mismatches: 19, Indels: 12
0.70 0.19 0.12
Matches are distributed among these distances:
7 5 0.07
9 55 0.77
10 11 0.15
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAAATAT
Found at i:53521031 original size:25 final size:26
Alignment explanation
Indices: 53521000--53521068 Score: 113
Period size: 28 Copynumber: 2.6 Consensus size: 26
53520990 TAATATAATA
53521000 TATAATATATAAAAAATAT-AAAAAC
1 TATAATATATAAAAAATATAAAAAAC
53521025 TATAATATATAAAAAATATAAAAAAAAC
1 TATAATATATAAAAAATAT--AAAAAAC
53521053 TATAATATATAAAAAA
1 TATAATATATAAAAAA
53521069 AAAACAAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 19 0.46
28 22 0.54
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (26 bp):
TATAATATATAAAAAATATAAAAAAC
Found at i:53524509 original size:14 final size:15
Alignment explanation
Indices: 53524482--53524510 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53524472 AAACCGGCCG
53524482 GGTTAGTAGAAATCA
1 GGTTAGTAGAAATCA
53524497 GGTTAGT-GAAATCA
1 GGTTAGTAGAAATCA
53524511 AGAGTGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (15 bp):
GGTTAGTAGAAATCA
Found at i:53525644 original size:41 final size:41
Alignment explanation
Indices: 53525569--53525674 Score: 104
Period size: 41 Copynumber: 2.6 Consensus size: 41
53525559 AGACCATATG
** * *
53525569 GGTCACACGACCGTGTGGTAGGCCGTGTAACAGACAATGGG
1 GGTCACACGGTCGTGTGGTTGGCCGTGTAACAGACAATGGA
* * ** * *
53525610 GGTCATACGGTCGTGTGGTTGGTCGTGTGCCAGACCATGTA
1 GGTCACACGGTCGTGTGGTTGGCCGTGTAACAGACAATGGA
* *
53525651 GGTTACATGGTCGTGTGGTTGGCC
1 GGTCACACGGTCGTGTGGTTGGCC
53525675 AGCCTATATG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.20, G:0.38, T:0.25
Consensus pattern (41 bp):
GGTCACACGGTCGTGTGGTTGGCCGTGTAACAGACAATGGA
Found at i:53528166 original size:20 final size:20
Alignment explanation
Indices: 53528143--53528183 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53528133 ATGGCTAGGA
53528143 AGTTATTAAGTTTATTTAGT
1 AGTTATTAAGTTTATTTAGT
* *
53528163 AGTTCTTAAGTTTGTTTAGT
1 AGTTATTAAGTTTATTTAGT
53528183 A
1 A
53528184 AGTTGTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (20 bp):
AGTTATTAAGTTTATTTAGT
Found at i:53528289 original size:20 final size:20
Alignment explanation
Indices: 53528264--53528314 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
53528254 ATCTTTTTAC
*
53528264 TCTTGGTTTTAATCAATTGT
1 TCTTGGTTTCAATCAATTGT
*
53528284 TCTTGGTTTCAATCATTTGT
1 TCTTGGTTTCAATCAATTGT
*
53528304 TCTTAGTTTCA
1 TCTTGGTTTCA
53528315 GTTGATTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (20 bp):
TCTTGGTTTCAATCAATTGT
Found at i:53529394 original size:11 final size:11
Alignment explanation
Indices: 53529380--53529455 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
53529370 GATAATCACT
53529380 TTAATATTAAA
1 TTAATATTAAA
53529391 TTAATA--AAA
1 TTAATATTAAA
* *
53529400 -TACTACTAAGA
1 TTAATATTAA-A
53529411 -TAAGTATTAAA
1 TTAA-TATTAAA
53529422 TTAATATTAATA
1 TTAATATTAA-A
53529434 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
53529447 ATAATATTA
1 TTAATATTA
53529456 TATTTAGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 2 0.04
11 21 0.40
12 13 0.25
13 4 0.08
14 6 0.11
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:53531615 original size:33 final size:33
Alignment explanation
Indices: 53531564--53531772 Score: 132
Period size: 33 Copynumber: 5.7 Consensus size: 33
53531554 TTATCCGTTA
* *
53531564 TCGGTGAATTCAGCACTTAGCAACCACCAGTGAT
1 TCGGGGAA-TCAGCACTTAGCAACCACCAATGAT
*
53531598 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGAT
1 TCGGGGAATCAGCACTTAGCAACCAC---CA-A--T--GAT
* *
53531639 ACGGTGGAATCAGCACTTAGCAACCACCAATGAA
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
53531673 TCGGGGAATCAGTACTTAGCAACCCCCTTTATATTCCAAGAT
1 TCGGGGAATCAGCACTTAGCAACCACC---A-A-T----GAT
*
53531715 AT-GGTGGAATCAGCACTTAGCAACCACCAATGAA
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
53531749 TCAGGGAATTAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
53531773 CCTTTTATAT
Statistics
Matches: 139, Mismatches: 15, Indels: 43
0.71 0.08 0.22
Matches are distributed among these distances:
33 58 0.42
34 15 0.11
36 4 0.03
37 1 0.01
38 3 0.02
39 4 0.03
40 1 0.01
41 6 0.04
42 25 0.18
43 22 0.16
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:53531661 original size:42 final size:41
Alignment explanation
Indices: 53531602--53531739 Score: 132
Period size: 42 Copynumber: 3.5 Consensus size: 41
53531592 AGTGATTCGG
53531602 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCA-ATTTAAGATACGGT
* *
53531644 GGAATCAGCACTTAGCAACCAC---CAA--TGA-AT-CGG-
1 GGAATCAGCACTTAGCAACCCCTTTCAATTTAAGATACGGT
* * *
53531677 GGAATCAGTACTTAGCAACCCCCTTT-ATATTCCAAGATATGGT
1 GGAATCAGCACTTAGCAA-CCCCTTTCA-ATT-TAAGATACGGT
53531720 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
53531740 ACCAATGAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
33 17 0.22
34 6 0.08
35 2 0.03
36 3 0.04
37 1 0.01
38 1 0.01
39 2 0.03
40 1 0.01
41 2 0.03
42 25 0.32
43 17 0.22
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTTCAATTTAAGATACGGT
Found at i:53531742 original size:76 final size:76
Alignment explanation
Indices: 53531565--53531784 Score: 320
Period size: 76 Copynumber: 2.9 Consensus size: 76
53531555 TATCCGTTAT
* *
53531565 CGGT-GAATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAA-CCCCTTTC
1 CGGTGGAA-TCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTT-
* *
53531628 ACATT-TAAGATA
64 ATATTCCAAGATA
*
53531640 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGTACTTAGCAACCCCCTTTAT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAT
53531705 ATTCCAAGATA
66 ATTCCAAGATA
* * * *
53531716 TGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGCAACCCCTTTTAT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAT
53531781 ATTC
66 ATTC
53531785 AATATACTCC
Statistics
Matches: 132, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
75 52 0.39
76 80 0.61
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAT
ATTCCAAGATA
Found at i:53533713 original size:16 final size:16
Alignment explanation
Indices: 53533692--53533722 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53533682 CTATGCATGC
*
53533692 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
53533708 AAAATACAAAAGACA
1 AAAATACAAAAGACA
53533723 ATAGTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:53537577 original size:20 final size:20
Alignment explanation
Indices: 53537552--53537591 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53537542 AGTGGGTTTT
* *
53537552 ATTTTATTTTATTTTTCAAA
1 ATTTTAATTTAGTTTTCAAA
*
53537572 ATTTTAATTTGGTTTTCAAA
1 ATTTTAATTTAGTTTTCAAA
53537592 GAACTGTACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTTAATTTAGTTTTCAAA
Found at i:53540091 original size:5 final size:5
Alignment explanation
Indices: 53540074--53540103 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
53540064 TATACAATAT
53540074 AATTA AA-TA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA A
53540104 CTATTTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:53542043 original size:21 final size:21
Alignment explanation
Indices: 53542017--53542060 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53542007 ATTAACTTCA
53542017 ACGTACTAACATCAATATCTG
1 ACGTACTAACATCAATATCTG
53542038 ACGTACTAACATCAATATCTG
1 ACGTACTAACATCAATATCTG
53542059 AC
1 AC
53542061 ATTAAACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (21 bp):
ACGTACTAACATCAATATCTG
Found at i:53543231 original size:42 final size:42
Alignment explanation
Indices: 53543116--53543337 Score: 295
Period size: 42 Copynumber: 5.3 Consensus size: 42
53543106 TTTTTAAACA
*
53543116 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGGTC
1 TTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCCGGGTC
* * *
53543157 TATAGCGGCGTTTTCGTCTAAGCGCCACTAATGCTCCGAGTC
1 TTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCCGGGTC
* * * * *
53543199 TTTAGCAGCGCTTTCGTCTAAACGCCGGTAATGCTCCGAGTC
1 TTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCCGGGTC
* *
53543241 TTTAGCGGCGTTTTTGTCTAAGCGTCGCTAATGCTCCGGGTC
1 TTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCCGGGTC
* ** *
53543283 TATAGCGGCGTTTTCGAATATGCGCCGCTAATGCT-CGGGTC
1 TTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCCGGGTC
53543324 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
53543338 TATATATGCG
Statistics
Matches: 156, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 51 0.33
42 105 0.67
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCCGGGTC
Found at i:53543345 original size:41 final size:42
Alignment explanation
Indices: 53543116--53543437 Score: 292
Period size: 41 Copynumber: 7.8 Consensus size: 42
53543106 TTTTTAAACA
53543116 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGGTC
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
* * * *
53543157 TATAGCGGCGTTTTCGTCTAAGCGCCACTAATGCTCCGAGTC
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
* * * * * *
53543199 TTTAGCAGCGCTTTCGTCTAAACGCCGGTAATGCTCCGAGTC
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
*
53543241 TTTAGCGGCGTTTTTGTCTAAGCGTCGCTAATGCTCCGGGTC
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
* * ** *
53543283 TATAGCGGCGTTTTCGAATATGCGCCGCTAATGCT-CGGGTC
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
* * * * * * * *
53543324 TTTAGCGGCGTTTTTATATATGCGCTGCTAGTTCTCC-TGTA
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
* * * * ******
53543365 TTCAGCGGCGTTTGTATCTAAGCGCCGCGAATG-TATTAACC
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
* *
53543406 TTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
53543438 AGTAACAAAA
Statistics
Matches: 226, Mismatches: 52, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
40 1 0.00
41 119 0.53
42 106 0.47
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.33
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGGGTC
Found at i:53545537 original size:25 final size:22
Alignment explanation
Indices: 53545483--53545539 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
53545473 CACGATTTCA
*
53545483 TTTCCCCAATTTCCCAACTTCT
1 TTTCCCCAATTTCCCAACTTAT
*
53545505 TTTCCCCCAATTTCCCCCAAGTTAT
1 TTT-CCCCAATTT--CCCAACTTAT
53545530 TCTTCCCCAA
1 T-TTCCCCAA
53545540 AGTATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
25 15 0.52
26 2 0.07
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTCCCCAATTTCCCAACTTAT
Found at i:53545551 original size:14 final size:15
Alignment explanation
Indices: 53545515--53545553 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
53545505 TTTCCCCCAA
*
53545515 TTTCCCCCAAGTTAT
1 TTTCCCCAAAGTTAT
53545530 TCTTCCCCAAAG-TAT
1 T-TTCCCCAAAGTTAT
53545545 TTTCCCCAA
1 TTTCCCCAA
53545554 TTTCCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
TTTCCCCAAAGTTAT
Found at i:53545817 original size:33 final size:33
Alignment explanation
Indices: 53545775--53545842 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
53545765 CATCTATGTT
*
53545775 ATTCGAGTTAAATGAGATGAGTGTTGGGTATGA
1 ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
*
53545808 ATTCGAGTTAAATGAGATTAGTGTTAGGTATGA
1 ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
53545841 AT
1 AT
53545843 ATATGTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (33 bp):
ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
Found at i:53546105 original size:17 final size:17
Alignment explanation
Indices: 53546083--53546120 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
53546073 ATCCCAGGAA
53546083 CTTGCAGCCTCTACTTC
1 CTTGCAGCCTCTACTTC
*
53546100 CTTGCAGCCTTTACTTC
1 CTTGCAGCCTCTACTTC
53546117 CTTG
1 CTTG
53546121 TGAACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.37, G:0.13, T:0.39
Consensus pattern (17 bp):
CTTGCAGCCTCTACTTC
Found at i:53547619 original size:24 final size:24
Alignment explanation
Indices: 53547592--53547644 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
53547582 TATTTGTATA
53547592 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
*
53547616 ATATTTGTATCTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
53547640 ATATT
1 ATATT
53547645 ATAAAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAATATT
Found at i:53547796 original size:22 final size:22
Alignment explanation
Indices: 53547751--53547796 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53547741 AACTTAATTA
*
53547751 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTGAC
53547773 ATTAATATTATACATAGA-TGAC
1 ATTAATATTATACATA-ACTGAC
53547795 AT
1 AT
53547797 AACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAACTGAC
Found at i:53547852 original size:22 final size:22
Alignment explanation
Indices: 53547807--53547852 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
53547797 AACTTAATTA
* *
53547807 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATGAC
53547829 ATTAATATTATACATAAATGAC
1 ATTAATATTATACATAAATGAC
53547851 AT
1 AT
53547853 AACTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAAATGAC
Found at i:53547872 original size:34 final size:34
Alignment explanation
Indices: 53547829--53548037 Score: 150
Period size: 34 Copynumber: 6.7 Consensus size: 34
53547819 CATAACTTAC
*
53547829 ATTAATATTATACATAAATGACATAACTTAATTA
1 ATTAATATTATACATAAATTACATAACTTAATTA
*
53547863 ATTAATATTATACATAACTTAC---A-TTAA-T-
1 ATTAATATTATACATAAATTACATAACTTAATTA
* * * *
53547891 ATT-ATA-CATAAATGACA-T--A-AC-TTAATTA
1 ATTAATATTATACAT-AAATTACATAACTTAATTA
* *
53547919 ATTAATATTATACATAACTTACATAAATTAATTA
1 ATTAATATTATACATAAATTACATAACTTAATTA
* *
53547953 GTT-A-A-TATACATAAATTACATAACTT-A--C
1 ATTAATATTATACATAAATTACATAACTTAATTA
* * *
53547981 ATTAATATGATACATAAATGACATAACTTAGTTA
1 ATTAATATTATACATAAATTACATAACTTAATTA
*
53548015 ATTAATATTATACATAACTTACA
1 ATTAATATTATACATAAATTACA
53548038 ACTTACATAA
Statistics
Matches: 133, Mismatches: 24, Indels: 36
0.69 0.12 0.19
Matches are distributed among these distances:
26 10 0.08
27 5 0.04
28 8 0.06
29 6 0.05
30 12 0.09
31 39 0.29
32 2 0.02
33 2 0.02
34 49 0.37
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (34 bp):
ATTAATATTATACATAAATTACATAACTTAATTA
Found at i:53547908 original size:22 final size:22
Alignment explanation
Indices: 53547863--53547908 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
53547853 AACTTAATTA
* *
53547863 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATGAC
53547885 ATTAATATTATACATAAATGAC
1 ATTAATATTATACATAAATGAC
53547907 AT
1 AT
53547909 AACTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAAATGAC
Found at i:53547943 original size:9 final size:9
Alignment explanation
Indices: 53547929--53548157 Score: 60
Period size: 9 Copynumber: 26.7 Consensus size: 9
53547919 ATTAATATTA
53547929 TACATAACT
1 TACATAACT
*
53547938 TACATAAAT
1 TACATAACT
* *
53547947 TA-ATTAGT
1 TACATAACT
53547955 TA-AT-A-T
1 TACATAACT
*
53547961 -ACATAAAT
1 TACATAACT
53547969 TACATAACT
1 TACATAACT
*
53547978 TACATTAATAT
1 TACA-TAA-CT
*
53547989 GATACATAAAT
1 --TACATAACT
*
53548000 GACATAACT
1 TACATAACT
**
53548009 TAGTTAA-T
1 TACATAACT
*
53548017 TA-AT-ATT
1 TACATAACT
53548024 ATACATAACT
1 -TACATAACT
53548034 TAC--AACT
1 TACATAACT
53548041 TACATAACT
1 TACATAACT
**
53548050 TACATATTTT
1 TACATA-ACT
*
53548060 TA-ATTA-T
1 TACATAACT
* *
53548067 T-CGTAAAT
1 TACATAACT
53548075 TACATAACT
1 TACATAACT
* *
53548084 TACTTAATT
1 TACATAACT
*
53548093 TTCATAA--
1 TACATAACT
*
53548100 TAAATAACT
1 TACATAACT
*
53548109 TACATAAAT
1 TACATAACT
* *
53548118 AAC-T-TCT
1 TACATAACT
53548125 TACATAACT
1 TACATAACT
** *
53548134 TATGTGACT
1 TACATAACT
53548143 TACATAACT
1 TACATAACT
53548152 TACATA
1 TACATA
53548158 GCATAATTTT
Statistics
Matches: 159, Mismatches: 39, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 23 0.14
8 18 0.11
9 95 0.60
10 8 0.05
11 3 0.02
12 3 0.02
13 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:53547966 original size:56 final size:56
Alignment explanation
Indices: 53547736--53547942 Score: 405
Period size: 56 Copynumber: 3.7 Consensus size: 56
53547726 TATTGTAAGG
*
53547736 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAGAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
53547792 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
53547848 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
53547904 GACATAACTTAATTAATTAATATTATACATAACTTACAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACAT
53547943 AAATTAATTA
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 150 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.39
Consensus pattern (56 bp):
GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
Found at i:53548006 original size:96 final size:90
Alignment explanation
Indices: 53547829--53548037 Score: 310
Period size: 96 Copynumber: 2.3 Consensus size: 90
53547819 CATAACTTAC
* * * *
53547829 ATTAATATTATACATAAATGACATAACTTAATTAATTAATATTATACATAACTTACATTAATATT
1 ATTAATATTATACATAACTTACATAAATTAATTAATTAATATTATACATAACTTACATTAATATG
53547894 ATACATAAATGACATAACTTAATTA
66 ATACATAAATGACATAACTTAATTA
*
53547919 ATTAATATTATACATAACTTACATAAATTAATTAGTTAATATACATAAATTACATAACTTACATT
1 ATTAATATTATACATAACTTACATAAATTAATTAATTAATAT---T--A-TACATAACTTACATT
*
53547984 AATATGATACATAAATGACATAACTTAGTTA
60 AATATGATACATAAATGACATAACTTAATTA
53548015 ATTAATATTATACATAACTTACA
1 ATTAATATTATACATAACTTACA
53548038 ACTTACATAA
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
90 38 0.36
93 1 0.01
95 1 0.01
96 67 0.63
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (90 bp):
ATTAATATTATACATAACTTACATAAATTAATTAATTAATATTATACATAACTTACATTAATATG
ATACATAAATGACATAACTTAATTA
Found at i:53548112 original size:34 final size:34
Alignment explanation
Indices: 53548037--53548115 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
53548027 CATAACTTAC
* * ***
53548037 AACTTACATAACTTACATATTTTTAATTATTCGT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
* * *
53548071 AAATTACATAACTTACTTAATTTTCATAATAAAT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
53548105 AACTTACATAA
1 AACTTACATAA
53548116 ATAACTTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (34 bp):
AACTTACATAACTTACATAATTTTAATAATAAAT
Found at i:53548188 original size:25 final size:25
Alignment explanation
Indices: 53548159--53548214 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
53548149 ACTTACATAG
* *
53548159 CATAATTTTCATAATACACAACTTA
1 CATAATTTGCATAATAAACAACTTA
** *
53548184 CATAATTTGGGTAATAAATAACTTA
1 CATAATTTGCATAATAAACAACTTA
53548209 CATAAT
1 CATAAT
53548215 ACATAACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (25 bp):
CATAATTTGCATAATAAACAACTTA
Found at i:53548214 original size:16 final size:16
Alignment explanation
Indices: 53548195--53548228 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53548185 ATAATTTGGG
53548195 TAATAAATAACTTACA
1 TAATAAATAACTTACA
*
53548211 TAATACATAACTTACA
1 TAATAAATAACTTACA
53548227 TA
1 TA
53548229 GCTTAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAAATAACTTACA
Found at i:53553750 original size:66 final size:65
Alignment explanation
Indices: 53553656--53553826 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
53553646 GAGCAAATTA
* * * * *
53553656 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
53553720 G
65 G
*
53553721 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
53553786 G
65 G
* * * * *
53553787 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
53553827 CGACAGCGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:53553824 original size:21 final size:21
Alignment explanation
Indices: 53553798--53553909 Score: 82
Period size: 21 Copynumber: 5.3 Consensus size: 21
53553788 AGCAGCTTAG
*
53553798 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
*
53553819 AGCAGAGGCGACAGCGAA-AGA
1 AGCAGAGGCGGCAGC-AAGAGA
* * * *
53553840 AGAACAGGCTGCAGCAAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
*** * *
53553861 AGCAGAGGCTAAAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
* * *
53553882 AGCAGAGGCTGCAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
53553903 AGCAGAG
1 AGCAGAG
53553910 CAGCGTCAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 2 0.03
21 71 0.95
22 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.41, T:0.04
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:53553867 original size:42 final size:42
Alignment explanation
Indices: 53553808--53553909 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
53553798 AGCAGATGCG
* *
53553808 GCAGCAAGAGAAGCAGAGGCGACAGCGAAAGAAGAACAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAAAGAAGAACAGGCT
* ** * *
53553850 GCAGCAAGGGAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAAAGAAGAACAGGCT
*
53553892 GCAGCGAGGGAAGCAGAG
1 GCAGCAAGGGAAGCAGAG
53553910 CAGCGTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.38, C:0.18, G:0.41, T:0.03
Consensus pattern (42 bp):
GCAGCAAGGGAAGCAGAGGCGAAAGCGAAAGAAGAACAGGCT
Found at i:53554643 original size:24 final size:24
Alignment explanation
Indices: 53554611--53554660 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
53554601 GATTCATATA
*
53554611 TTTCTATTGCTTTTGGACTACTTT
1 TTTCTATTGATTTTGGACTACTTT
*
53554635 TTTCTATTGATTTTGGACTGCTTT
1 TTTCTATTGATTTTGGACTACTTT
53554659 TT
1 TT
53554661 CTTTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTCTATTGATTTTGGACTACTTT
Found at i:53557396 original size:105 final size:105
Alignment explanation
Indices: 53557268--53557726 Score: 451
Period size: 105 Copynumber: 4.4 Consensus size: 105
53557258 TCTTCTTCGA
* * *
53557268 AATGATAAAGCAAGGCATTAAGCCTAATGTCGTCACATATAGTATATTGATCGATGCGCTTTGCA
1 AATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATCGATTCGCTTTGCA
* * *
53557333 AGCAA-GGAATGATATCTAAAGCCGAAGATATTGTTGGCAT
66 AG-AATGGTATGGTTTCTAAAGCCGAAGATATTGTTGGCAT
* * * * *
53557373 AATGACAAAGCAAGGCATTAAGCCTAATGTTGTCACATATGGTATATTCATCGATACTCTTTGCA
1 AATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATCGATTCGCTTTGCA
* * * * *
53557438 AG-ATGGGGGA-GGTTTCTAAAGCCGAAGTTGTTGTTGACGT
66 AGAAT--GGTATGGTTTCTAAAGCCGAAGATATTGTTGGCAT
* * ** * *
53557478 GATGAGAAAGCAAGGCATCGAA-CCTAATGTTGTCATGTATAGTACATTGATAGATTCGCTTTGC
1 AATGAGAAAGCAAGGCAT-TAAGCCTAATGTTGTCACATATAGTATATTGATCGATTCGCTTTGC
* * ** * *
53557542 AAGAATGGTATGGTTTCTGAAGCTGAATTTATTGTTTGCAC
65 AAGAATGGTATGGTTTCTAAAGCCGAAGATATTGTTGGCAT
* * * * * * * *
53557583 GATGAGAAAGCAAGGCGCTGAA-CCTAATGTTATCACGTATAATATATTGATGGATTCACTTTGC
1 AATGAGAAAGCAAGGC-ATTAAGCCTAATGTTGTCACATATAGTATATTGATCGATTCGCTTTGC
* * * * *
53557647 AAGAATAGTATGGTTTCTGAAGCTGAAGATATTTTTGGCAG
65 AAGAATGGTATGGTTTCTAAAGCCGAAGATATTGTTGGCAT
* *
53557688 AATGAGAAAGCAAGGCATTTAGCCTGATGTTGTCACATA
1 AATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCACATA
53557727 CAACACTCTG
Statistics
Matches: 293, Mismatches: 53, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
103 1 0.00
104 5 0.02
105 279 0.95
106 8 0.03
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (105 bp):
AATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATCGATTCGCTTTGCA
AGAATGGTATGGTTTCTAAAGCCGAAGATATTGTTGGCAT
Found at i:53572361 original size:60 final size:60
Alignment explanation
Indices: 53572279--53572411 Score: 196
Period size: 60 Copynumber: 2.2 Consensus size: 60
53572269 TGTAACCTTA
* * * *
53572279 TCTTGTGAGCTT-GCTTTACGAGCTGTGCCTGCGATCCTGCCTTATGAGCTCGCGTAAGGT
1 TCTTGTGAG-TTGGCTCTACGAGCTGTACCTGCGATCCTACCTTATGAGCTCGCGCAAGGT
* *
53572339 TCTTGTGAGTTGGCTCTGCGAGCTGTACCTGGGATCCTACCTTATGAGCTCGCGCAAGGT
1 TCTTGTGAGTTGGCTCTACGAGCTGTACCTGCGATCCTACCTTATGAGCTCGCGCAAGGT
53572399 TCTTGTGAGTTGG
1 TCTTGTGAGTTGG
53572412 GTTTGTAGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 2 0.03
60 64 0.97
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33
Consensus pattern (60 bp):
TCTTGTGAGTTGGCTCTACGAGCTGTACCTGCGATCCTACCTTATGAGCTCGCGCAAGGT
Done.