Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 72 of 171
Found at i:25670481 original size:16 final size:16
Alignment explanation
Indices: 25670426--25670482 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
25670416 TATCTTTTAA
**
25670426 AATTTAAATTTGCTTT
1 AATTTAAATTTGAATT
**
25670442 AATTTTAAATTTTTATCT
1 AA-TTTAAATTTGAAT-T
25670460 AA-TTAAATTTGAATT
1 AATTTAAATTTGAATT
25670475 AATTTAAA
1 AATTTAAA
25670483 ACTTAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 3 0.09
16 17 0.52
17 10 0.30
18 3 0.09
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
AATTTAAATTTGAATT
Found at i:25673925 original size:10 final size:10
Alignment explanation
Indices: 25673907--25673938 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
25673897 AGGTCCTGTA
25673907 TTATATTACT
1 TTATATTACT
*
25673917 TTATTTTACT
1 TTATATTACT
25673927 TTATATTACT
1 TTATATTACT
25673937 TT
1 TT
25673939 TCTTTGGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATTACT
Found at i:25674002 original size:21 final size:22
Alignment explanation
Indices: 25673971--25674014 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
25673961 TTTATATTCC
*
25673971 TTTATTTTACTTTGCTTTGCTT
1 TTTATTTTACTTTGCTTTCCTT
*
25673993 TTTA-TTTACTTTTCTTTCCTT
1 TTTATTTTACTTTGCTTTCCTT
25674014 T
1 T
25674015 GCTTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTATTTTACTTTGCTTTCCTT
Found at i:25674018 original size:66 final size:67
Alignment explanation
Indices: 25673926--25674050 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 67
25673916 TTTATTTTAC
** ** *
25673926 TTTATATTACTTTTCTTTGGTCTGCTTTATATTGCTTTATATTCCTTTATTTTACTTTGCTTTGC
1 TTTATATTACTTTTCTTTCCTCTGCTTTATATAACTTTATATTCCTTTACTTTACTTTGCTTTGC
25673991 TT
66 TT
* * *
25673993 TTTAT-TTACTTTTCTTTCCTTTGCTTTATATAACTTTATATTTCTTTACTTTGCTTTG
1 TTTATATTACTTTTCTTTCCTCTGCTTTATATAACTTTATATTCCTTTACTTTACTTTG
25674051 TTTTACATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 45 0.90
67 5 0.10
ACGTcount: A:0.14, C:0.15, G:0.07, T:0.63
Consensus pattern (67 bp):
TTTATATTACTTTTCTTTCCTCTGCTTTATATAACTTTATATTCCTTTACTTTACTTTGCTTTGC
TT
Found at i:25674045 original size:56 final size:56
Alignment explanation
Indices: 25673950--25674107 Score: 161
Period size: 56 Copynumber: 2.9 Consensus size: 56
25673940 CTTTGGTCTG
* * *
25673950 CTTT-ATATTGCTTTATATTCCTTTAT-TTTACTTTGCTTTGCTTTTTATTTAC-TTTT
1 CTTTAATATTGCTTTATA-TACTTTATATTT-CTTTACTTTGCTTTGT-TTTACATTTT
**
25674006 CTTTCCT-TTGCTTTATATAACTTTATATTTCTTTACTTTGCTTTGTTTTACATTTT
1 CTTTAATATTGCTTTATAT-ACTTTATATTTCTTTACTTTGCTTTGTTTTACATTTT
* *
25674062 CTTTAATATTG---TAT-TACTTTATATTACTTTACTTTGCTTTGCTTTA
1 CTTTAATATTGCTTTATATACTTTATATTTCTTTACTTTGCTTTGTTTTA
25674108 TATATTATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
52 29 0.33
53 1 0.01
54 3 0.03
55 6 0.07
56 43 0.48
57 7 0.08
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.63
Consensus pattern (56 bp):
CTTTAATATTGCTTTATATACTTTATATTTCTTTACTTTGCTTTGTTTTACATTTT
Found at i:25674283 original size:27 final size:27
Alignment explanation
Indices: 25674253--25674308 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
25674243 TGATAGGTGG
*
25674253 ATTTAATT-TATTTAATTACTATTTTTA
1 ATTTAATTATATAT-ATTACTATTTTTA
*
25674280 ATTTAATTATATATATTATTATTTTTA
1 ATTTAATTATATATATTACTATTTTTA
25674307 AT
1 AT
25674309 AATTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTAATTATATATATTACTATTTTTA
Found at i:25675439 original size:30 final size:29
Alignment explanation
Indices: 25675394--25675493 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 29
25675384 AATGTAATTA
* * *
25675394 ATATTATTTTACTTTGGTTTGTTTTGCTTT
1 ATATTACTTTGCTTT-GTTTGCTTTGCTTT
*
25675424 ATATTACTCTGC----TTTGCTTTGCTTT
1 ATATTACTTTGCTTTGTTTGCTTTGCTTT
** *
25675449 ATAAAACTTTGCTTTGATTTGCTTTACTTT
1 ATATTACTTTGCTTTG-TTTGCTTTGCTTT
25675479 ATATTACTTTGCTTT
1 ATATTACTTTGCTTT
25675494 ACTTTATATT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
25 21 0.38
30 34 0.62
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (29 bp):
ATATTACTTTGCTTTGTTTGCTTTGCTTT
Found at i:25675473 original size:15 final size:15
Alignment explanation
Indices: 25675440--25675494 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
25675430 CTCTGCTTTG
**
25675440 CTTTGCTTTATAAAA
1 CTTTGCTTTATATTA
*
25675455 CTTTGCTTTGAT-TTG
1 CTTTGCTTT-ATATTA
*
25675470 CTTTACTTTATATTA
1 CTTTGCTTTATATTA
25675485 CTTTGCTTTA
1 CTTTGCTTTA
25675495 CTTTATATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 2 0.06
15 28 0.88
16 2 0.06
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (15 bp):
CTTTGCTTTATATTA
Found at i:25675488 original size:25 final size:25
Alignment explanation
Indices: 25675397--25675589 Score: 107
Period size: 25 Copynumber: 7.9 Consensus size: 25
25675387 GTAATTAATA
* * * *
25675397 TTATTTTACTTTGGTTTGTTTTGCT
1 TTATATTACTTTGCTTTGCTTTACT
* *
25675422 TTATATTACTCTGCTTTGCTTTGCT
1 TTATATTACTTTGCTTTGCTTTACT
** * *
25675447 TTATAAAACTTTGCTTTGATTTGCT
1 TTATATTACTTTGCTTTGCTTTACT
*
25675472 TTACT-TTA-TATTACTTTGCTTTACT
1 TTA-TATTACT-TTGCTTTGCTTTACT
* * *
25675497 TTATA-T--TGT--TTTGTTTTGCT
1 TTATATTACTTTGCTTTGCTTTACT
*
25675517 TTATATTCCTTTGCTTTGCTTTA-T
1 TTATATTACTTTGCTTTGCTTTACT
* * * *
25675541 ATTGTTTTA-TATTGTTTTGCTTTATT
1 -TTATATTACT-TTGCTTTGCTTTACT
*
25675567 TTATATTCCTTTGCTTTGCTTTA
1 TTATATTACTTTGCTTTGCTTTA
25675590 TATTTTACTT
Statistics
Matches: 129, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
20 14 0.11
21 1 0.01
22 1 0.01
23 3 0.02
24 5 0.04
25 102 0.79
26 3 0.02
ACGTcount: A:0.15, C:0.12, G:0.11, T:0.62
Consensus pattern (25 bp):
TTATATTACTTTGCTTTGCTTTACT
Found at i:25675489 original size:20 final size:20
Alignment explanation
Indices: 25675466--25675543 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
25675456 TTTGCTTTGA
25675466 TTTGCTTTACTTTATATTAC
1 TTTGCTTTACTTTATATTAC
**
25675486 TTTGCTTTACTTTATATTGT
1 TTTGCTTTACTTTATATTAC
* * *
25675506 TTTGTTTTGCTTTATATTCC
1 TTTGCTTTACTTTATATTAC
*
25675526 TTTGCTTTGCTTTATATT
1 TTTGCTTTACTTTATATT
25675544 GTTTTATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.14, C:0.13, G:0.09, T:0.64
Consensus pattern (20 bp):
TTTGCTTTACTTTATATTAC
Found at i:25675539 original size:40 final size:42
Alignment explanation
Indices: 25675465--25675611 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 42
25675455 CTTTGCTTTG
* * * *
25675465 ATTTGCTTTACTTTATATTACTTTGCTTTACTTTATATTG-T
1 ATTTGTTTTGCTTTATATTCCTTTGCTTTGCTTTATATTGTT
25675506 -TTTGTTTTGCTTTATATTCCTTTGCTTTGCTTTATATTGTTTT
1 ATTTGTTTTGCTTTATATTCCTTTGCTTTGCTTTATATTG--TT
25675549 ATATTGTTTTGCTTTATTTTATATTCCTTTGCTTTGCTTTATATT-TT
1 AT-TTGTTTTGC-----TTTATATTCCTTTGCTTTGCTTTATATTGTT
*
25675596 ACTTTGATTTGGCTTT
1 A-TTTG-TTTTGCTTT
25675612 TGTTTTATAT
Statistics
Matches: 89, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
40 35 0.39
43 4 0.04
44 1 0.01
45 9 0.10
47 6 0.07
48 6 0.07
50 28 0.31
ACGTcount: A:0.14, C:0.12, G:0.10, T:0.64
Consensus pattern (42 bp):
ATTTGTTTTGCTTTATATTCCTTTGCTTTGCTTTATATTGTT
Found at i:25675568 original size:10 final size:10
Alignment explanation
Indices: 25675495--25675554 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
25675485 CTTTGCTTTA
25675495 CTTTATATTG
1 CTTTATATTG
* * *
25675505 TTTTGTTTTG
1 CTTTATATTG
*
25675515 CTTTATATTC
1 CTTTATATTG
*
25675525 CTTTGCT-TTG
1 CTTT-ATATTG
25675535 CTTTATATTG
1 CTTTATATTG
*
25675545 TTTTATATTG
1 CTTTATATTG
25675555 TTTTGCTTTA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
9 1 0.03
10 35 0.95
11 1 0.03
ACGTcount: A:0.13, C:0.10, G:0.12, T:0.65
Consensus pattern (10 bp):
CTTTATATTG
Found at i:25675570 original size:20 final size:20
Alignment explanation
Indices: 25675545--25675593 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
25675535 CTTTATATTG
**
25675545 TTTTATATTGTTTTGCTTTA
1 TTTTATATTCCTTTGCTTTA
*
25675565 TTTTATATTCCTTTGCTTTG
1 TTTTATATTCCTTTGCTTTA
*
25675585 CTTTATATT
1 TTTTATATT
25675594 TTACTTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.14, C:0.10, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTATATTCCTTTGCTTTA
Found at i:25675571 original size:50 final size:50
Alignment explanation
Indices: 25675496--25675593 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
25675486 TTTGCTTTAC
* *
25675496 TTTATATTGTTTTGTTTTGCTTTATATTCCTTTGCTTTGCTTTATATTGT
1 TTTATATTGTTTTGCTTTACTTTATATTCCTTTGCTTTGCTTTATATTGT
*
25675546 TTTATATTGTTTTGCTTTATTTTATATTCCTTTGCTTTGCTTTATATT
1 TTTATATTGTTTTGCTTTACTTTATATTCCTTTGCTTTGCTTTATATT
25675594 TTACTTTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.66
Consensus pattern (50 bp):
TTTATATTGTTTTGCTTTACTTTATATTCCTTTGCTTTGCTTTATATTGT
Found at i:25675618 original size:22 final size:22
Alignment explanation
Indices: 25675460--25675611 Score: 73
Period size: 25 Copynumber: 6.6 Consensus size: 22
25675450 TAAAACTTTG
*
25675460 CTTTGATTTGCTTTACTTTATATTA
1 CTTTGATTTGCTTTA---TATTTTA
* * *
25675485 CTTTGCTTTACTTTATATTGT-
1 CTTTGATTTGCTTTATATTTTA
* *
25675506 -TTTGTTTTGCTTTATA--TTC
1 CTTTGATTTGCTTTATATTTTA
*
25675525 CTTTGCTTTGCTTTATATTGTTTTA
1 CTTTGATTTGCTTTATA---TTTTA
*
25675550 -TATTGTTTTGCTTTAT-TTTATA
1 CT-TTGATTTGCTTTATATTT-TA
*
25675572 TTCCTTTGCTTTGCTTTATATTTTA
1 ---CTTTGATTTGCTTTATATTTTA
25675597 CTTTGATTTGGCTTT
1 CTTTGATTT-GCTTT
25675612 TGTTTTATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 32
0.69 0.08 0.22
Matches are distributed among these distances:
18 1 0.01
20 29 0.29
21 3 0.03
22 14 0.14
23 5 0.05
24 1 0.01
25 43 0.43
26 4 0.04
ACGTcount: A:0.14, C:0.12, G:0.11, T:0.64
Consensus pattern (22 bp):
CTTTGATTTGCTTTATATTTTA
Found at i:25675628 original size:39 final size:39
Alignment explanation
Indices: 25675582--25675662 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
25675572 TTCCTTTGCT
25675582 TTGCTTTATA-T-TTTACTTTGATTTGGCTTTTGTTTTATA
1 TTGCTTTATATTATTTACTTTGATTT-G-TTTTGTTTTATA
* *
25675621 TTGCTTTATATTACTTTCCTTTGCTTTGTTTTGTTTTATA
1 TTGCTTTATATTA-TTTACTTTGATTTGTTTTGTTTTATA
25675661 TT
1 TT
25675663 AGTTTGCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 10 0.27
40 15 0.41
41 1 0.03
42 11 0.30
ACGTcount: A:0.14, C:0.10, G:0.11, T:0.65
Consensus pattern (39 bp):
TTGCTTTATATTATTTACTTTGATTTGTTTTGTTTTATA
Found at i:25675705 original size:28 final size:27
Alignment explanation
Indices: 25675665--25675717 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
25675655 TTTATATTAG
25675665 TTTGCTTTGCTTTATTATATTGTTTTGC
1 TTTGCTTTGCTTTA-TATATTGTTTTGC
25675693 TTTGCTTTGCTTTATATATTGTTTT
1 TTTGCTTTGCTTTATATATTGTTTT
25675718 ATATTGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.11, C:0.09, G:0.13, T:0.66
Consensus pattern (27 bp):
TTTGCTTTGCTTTATATATTGTTTTGC
Found at i:25675724 original size:27 final size:28
Alignment explanation
Indices: 25675665--25675727 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
25675655 TTTATATTAG
*
25675665 TTTGCTTTGCTTTATTATATTGTTTTGC
1 TTTGCTTTGCTTTATTATATTGTTTTGA
25675693 TTTGCTTTGCTTTA-TATATTGTTTT-A
1 TTTGCTTTGCTTTATTATATTGTTTTGA
25675719 TATTGCTTT
1 T-TTGCTTT
25675728 ATATATCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.55
28 14 0.42
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (28 bp):
TTTGCTTTGCTTTATTATATTGTTTTGA
Found at i:25675739 original size:42 final size:42
Alignment explanation
Indices: 25675692--25675785 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
25675682 TATTGTTTTG
* * *
25675692 CTTTGCTTTGCTTTATATAT-TGTTTTATATTGCTTTATATAT-
1 CTTTGCTTTGCTTCATATATATCTTTGAT-TTGCTTTATAT-TC
*
25675734 CTTTGCTTTGCTTCATATATATCTTTGCTTTGCTTTATATTC
1 CTTTGCTTTGCTTCATATATATCTTTGATTTGCTTTATATTC
25675776 CTTTGCTTTG
1 CTTTGCTTTG
25675786 GTTTTGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 1 0.02
42 40 0.87
43 5 0.11
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (42 bp):
CTTTGCTTTGCTTCATATATATCTTTGATTTGCTTTATATTC
Found at i:25675744 original size:20 final size:20
Alignment explanation
Indices: 25675692--25675785 Score: 109
Period size: 22 Copynumber: 4.5 Consensus size: 20
25675682 TATTGTTTTG
25675692 CTTTGCTTTGCTTTATATATT
1 CTTTGCTTTGCTTTATATA-T
* **
25675713 GTTTTATATTGCTTTATATAT
1 CTTTGCT-TTGCTTTATATAT
25675734 CTTTGCTTTGCTTCATATATAT
1 CTTTGCTTTGCTT--TATATAT
25675756 CTTTGCTTTGCTTTATAT-T
1 CTTTGCTTTGCTTTATATAT
25675775 CCTTTGCTTTG
1 -CTTTGCTTTG
25675786 GTTTTGTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
19 1 0.02
20 21 0.33
21 9 0.14
22 32 0.51
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (20 bp):
CTTTGCTTTGCTTTATATAT
Found at i:25675752 original size:22 final size:19
Alignment explanation
Indices: 25675692--25675785 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 19
25675682 TATTGTTTTG
25675692 CTTTGCTTTGCTTTATATATT
1 CTTTGCTTTGC-TT-TATATT
* **
25675713 GTTTTATATTGCTTTATATAT
1 CTTTGCT-TTGCTTTATAT-T
25675734 CTTTGCTTTGCTTCATATATAT
1 CTTTGCTTTGCTT--TATAT-T
25675756 CTTTGCTTTGCTTTATATT
1 CTTTGCTTTGCTTTATATT
25675775 CCTTTGCTTTG
1 -CTTTGCTTTG
25675786 GTTTTGTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.02
20 26 0.42
21 11 0.18
22 24 0.39
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (19 bp):
CTTTGCTTTGCTTTATATT
Found at i:25676006 original size:29 final size:27
Alignment explanation
Indices: 25675956--25676014 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 27
25675946 ATGATAGATG
*
25675956 AATTTAATTTATTTAATTATTATTTTT
1 AATTTAATATATTTAATTATTATTTTT
25675983 AATTTAAGTATATTTATATTATTATTTTT
1 AATTTAA-TATATTTA-ATTATTATTTTT
25676012 AAT
1 AAT
25676015 AATCATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 7 0.24
28 7 0.24
29 15 0.52
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
AATTTAATATATTTAATTATTATTTTT
Found at i:25677507 original size:15 final size:15
Alignment explanation
Indices: 25677470--25677510 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25677460 TTGCTTTGCT
*
25677470 TTGCTTTTCTTTATA
1 TTGCTTTGCTTTATA
**
25677485 TTATTTTGCTTTATA
1 TTGCTTTGCTTTATA
25677500 TTGCTTTGCTT
1 TTGCTTTGCTT
25677511 CATCGTTCTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.66
Consensus pattern (15 bp):
TTGCTTTGCTTTATA
Found at i:25679428 original size:15 final size:14
Alignment explanation
Indices: 25679408--25679441 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
25679398 ATCAATGTAA
*
25679408 ATTTTAGTGGTATT
1 ATTTTAGTGATATT
25679422 CATTTTAGTGATATT
1 -ATTTTAGTGATATT
25679437 ATTTT
1 ATTTT
25679442 CATGGTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (14 bp):
ATTTTAGTGATATT
Found at i:25682438 original size:15 final size:14
Alignment explanation
Indices: 25682409--25682458 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
25682399 AATATAAAAT
*
25682409 GCAAAGAAAATCAAA
1 GCAAATAAAA-CAAA
25682424 GCAATATAAAACAAA
1 GCAA-ATAAAACAAA
*
25682439 GCAAATAGAAGCAAA
1 GCAAATA-AAACAAA
25682454 GCAAA
1 GCAAA
25682459 GCACAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.74
16 5 0.16
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.08
Consensus pattern (14 bp):
GCAAATAAAACAAA
Found at i:25682444 original size:25 final size:26
Alignment explanation
Indices: 25682398--25682452 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
25682388 AAAACTATAT
25682398 CAATATAAAATGCAAAGAAAATCA-AAG
1 CAATATAAAA-GCAAAGAAAAT-AGAAG
*
25682425 CAATATAAAA-CAAAGCAAATAGAAG
1 CAATATAAAAGCAAAGAAAATAGAAG
25682450 CAA
1 CAA
25682453 AGCAAAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
27 10 0.38
ACGTcount: A:0.64, C:0.13, G:0.11, T:0.13
Consensus pattern (26 bp):
CAATATAAAAGCAAAGAAAATAGAAG
Found at i:25682481 original size:27 final size:25
Alignment explanation
Indices: 25682451--25682544 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 25
25682441 AAATAGAAGC
25682451 AAAGCAAAGCACAACACATCAATATGA
1 AAAGCAAAGCA-AACA-ATCAATATGA
* *
25682478 AAAG-AACAGCAAGACAATATAAAATGA
1 AAAGCAA-AGCAA-ACAAT-CAATATGA
25682505 AAAGCAAAGCAAAACAATATCAATAT-A
1 AAAGCAAAGC-AAAC-A-ATCAATATGA
25682532 AAAGCAAAGCAAA
1 AAAGCAAAGCAAA
25682545 GCAAAACAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
26 8 0.14
27 37 0.66
28 9 0.16
29 2 0.04
ACGTcount: A:0.62, C:0.16, G:0.12, T:0.11
Consensus pattern (25 bp):
AAAGCAAAGCAAACAATCAATATGA
Found at i:25682495 original size:22 final size:22
Alignment explanation
Indices: 25682470--25682511 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25682460 CACAACACAT
*
25682470 CAATATGAAAA-GAACAGCAAGA
1 CAATAT-AAAATGAAAAGCAAGA
25682492 CAATATAAAATGAAAAGCAA
1 CAATATAAAATGAAAAGCAA
25682512 AGCAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (22 bp):
CAATATAAAATGAAAAGCAAGA
Found at i:25682542 original size:5 final size:5
Alignment explanation
Indices: 25682532--25682742 Score: 92
Period size: 5 Copynumber: 41.4 Consensus size: 5
25682522 TATCAATATA
* * * ** *
25682532 AAAGC AAAGC AAAGC AAAAC AAAGA AAAAC AATATAA AAAGC AAGGC AAAGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AA-A-GC AAAGC AAAGC AAAGC
** * * **
25682584 AATATA AAAGC AAAGC AAAGC AAAGT AAAG- AACAAC AAAGC AATATAA
1 AA-AGC AAAGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AA-A-GC
* * * *
25682632 AAAGC AAAGC AAAGC AAA-A AAAAC AAAAC AAAGC AAATC ATAA-C AAAGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC A-AAGC AAAGC
* * * * * *
25682681 AACGC AAAGC ACATC ACAA-C ATAGC GAAGC ACAA-C ACAA-C ACAGC
1 AAAGC AAAGC AAAGC A-AAGC AAAGC AAAGC A-AAGC A-AAGC AAAGC
25682726 AAAGC AAAGC AAAGC AA
1 AAAGC AAAGC AAAGC AA
25682743 CATGTTGACA
Statistics
Matches: 156, Mismatches: 36, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
4 9 0.06
5 128 0.82
6 14 0.09
7 5 0.03
ACGTcount: A:0.62, C:0.19, G:0.13, T:0.05
Consensus pattern (5 bp):
AAAGC
Found at i:25682594 original size:58 final size:62
Alignment explanation
Indices: 25682510--25682668 Score: 195
Period size: 58 Copynumber: 2.6 Consensus size: 62
25682500 AATGAAAAGC
* * * *
25682510 AAAGCAAAACAATATCAATATAAAAGCAAAGCAAAGCAAA-ACA-AAGAA-AAA-CAATATAA
1 AAAGCAAAGCAA-AGCAATATAAAAGCAAAGCAAAGCAAAGAAAGAACAACAAAGCAATATAA
*
25682569 AAAGCAAGGCAAAGCAATATAAAAGCAAAGCAAAGCAAAGTAAAGAACAACAAAGCAATATAA
1 AAAGCAAAGCAAAGCAATATAAAAGCAAAGCAAAGCAAAG-AAAGAACAACAAAGCAATATAA
* *
25682632 AAAGCAAAGCAAAGCAA-A-AAAAACAAAACAAAGCAAA
1 AAAGCAAAGCAAAGCAATATAAAAGCAAAGCAAAGCAAA
25682669 TCATAACAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
58 26 0.30
59 10 0.11
60 2 0.02
61 21 0.24
62 4 0.05
63 24 0.28
ACGTcount: A:0.67, C:0.14, G:0.12, T:0.07
Consensus pattern (62 bp):
AAAGCAAAGCAAAGCAATATAAAAGCAAAGCAAAGCAAAGAAAGAACAACAAAGCAATATAA
Found at i:25683795 original size:3 final size:3
Alignment explanation
Indices: 25683787--25683814 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25683777 TAAAATTGAT
25683787 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25683815 ATAGGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25689240 original size:23 final size:25
Alignment explanation
Indices: 25689214--25689259 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25689204 CCAATTAGGG
25689214 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
25689237 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
25689260 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:25690381 original size:14 final size:13
Alignment explanation
Indices: 25690360--25690391 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
25690350 AATATTTGCA
25690360 TTTTTAATTTAAT
1 TTTTTAATTTAAT
25690373 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
25690387 TTTTT
1 TTTTT
25690392 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:25693111 original size:6 final size:6
Alignment explanation
Indices: 25693093--25693137 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
25693083 AAATAGTCTA
* * *
25693093 TTTATT TTCATT TTTATT TTTATT TTATTTT TTTAGT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT-TATT TTTATT TTTATT TT
25693138 AATTATGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:25693132 original size:14 final size:13
Alignment explanation
Indices: 25693091--25693137 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
25693081 AAAAATAGTC
25693091 TATTTATTTTCATTT
1 TATTT-TTTT-ATTT
*
25693106 T-TATTTTTATTT
1 TATTTTTTTATTT
25693118 TATTTTTTTAGTTT
1 TATTTTTTTA-TTT
25693132 TATTTT
1 TATTTT
25693138 AATTATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 5 0.18
13 11 0.39
14 11 0.39
15 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:25694096 original size:17 final size:18
Alignment explanation
Indices: 25694076--25694139 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 18
25694066 AAAAAAGTCG
25694076 AAAAGA-AAAATTGAAAA
1 AAAAGACAAAATTGAAAA
*
25694093 AAAA-AGAAAATTAAGAAAA
1 AAAAGACAAAATT--GAAAA
* * *
25694112 AAAAAAGAAAA-AGAAAA
1 AAAAGACAAAATTGAAAA
25694129 AAAAGACAAAA
1 AAAAGACAAAA
25694140 GTGTGTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.03
17 24 0.60
19 9 0.22
20 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAGACAAAATTGAAAA
Found at i:25694129 original size:15 final size:16
Alignment explanation
Indices: 25694110--25694140 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
25694100 AAATTAAGAA
25694110 AAAAAAAAGA-AAAAG
1 AAAAAAAAGACAAAAG
25694125 AAAAAAAAGACAAAAG
1 AAAAAAAAGACAAAAG
25694141 TGTGTTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGACAAAAG
Found at i:25694131 original size:20 final size:20
Alignment explanation
Indices: 25694089--25694132 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
25694079 AGAAAAATTG
** *
25694089 AAAAAAAAAGAAAATTAAGA
1 AAAAAAAAAGAAAAAGAAAA
25694109 AAAAAAAAAGAAAAAGAAAA
1 AAAAAAAAAGAAAAAGAAAA
25694129 AAAA
1 AAAA
25694133 GACAAAAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAGAAAA
Found at i:25694134 original size:26 final size:25
Alignment explanation
Indices: 25694089--25694139 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
25694079 AGAAAAATTG
**
25694089 AAAAAAAAAGAAAATTAAGAAAAAA
1 AAAAAAAAAGAAAAAAAAGAAAAAA
*
25694114 AAAAGAAAAAGAAAAAAAAGACAAAA
1 AAAA-AAAAAGAAAAAAAAGAAAAAA
25694140 GTGTGTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.04
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAAAGAAAAAA
Found at i:25700067 original size:30 final size:28
Alignment explanation
Indices: 25700033--25700125 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 28
25700023 CTGCTTTATA
*
25700033 TTGCTTTATATTCCTTTATTTTACTTTTCT
1 TTGCTTTATATT-CTTTATTTT-CTTTACT
* *
25700063 TTGC-TT-T-TTATTTACTTTTCTTTCCT
1 TTGCTTTATATTCTTTA-TTTTCTTTACT
*
25700089 TTGCTTTATATAACTTTATATTTCTTTACT
1 TTGCTTTATAT-TCTTTAT-TTTCTTTACT
25700119 TTGCTTT
1 TTGCTTT
25700126 GTTTTACATT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
26 14 0.27
27 8 0.15
28 2 0.04
29 4 0.08
30 24 0.46
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.66
Consensus pattern (28 bp):
TTGCTTTATATTCTTTATTTTCTTTACT
Found at i:25700078 original size:21 final size:22
Alignment explanation
Indices: 25700047--25700090 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
25700037 TTTATATTCC
*
25700047 TTTATTTTACTTTTCTTTGCTT
1 TTTATTTTACTTTTCTTTCCTT
25700069 TTTA-TTTACTTTTCTTTCCTT
1 TTTATTTTACTTTTCTTTCCTT
25700090 T
1 T
25700091 GCTTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTTTACTTTTCTTTCCTT
Found at i:25700085 original size:26 final size:25
Alignment explanation
Indices: 25700047--25700142 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 25
25700037 TTTATATTCC
*
25700047 TTTATTTTACTTTTCTTTGCTTTTTA
1 TTTATTTT-CTTTACTTTGCTTTTTA
*
25700073 TTTACTTTTCTTTCCTTTGCTTTATATAA
1 TTTA-TTTTCTTTACTTTGCTTT-T-T-A
25700102 CTTTATATTTCTTTACTTTGCTTTGTT-
1 -TTTAT-TTTCTTTACTTTGCTTT-TTA
*
25700129 TTACATTTTCTTTA
1 TT-TATTTTCTTTA
25700143 ATATTGTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
26 27 0.46
27 7 0.12
28 1 0.02
29 3 0.05
30 21 0.36
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTATTTTCTTTACTTTGCTTTTTA
Found at i:25700106 original size:56 final size:56
Alignment explanation
Indices: 25700033--25700183 Score: 154
Period size: 56 Copynumber: 2.8 Consensus size: 56
25700023 CTGCTTTATA
** * *
25700033 TTGCTTTATATTCCTTTAT-TTTACTTTTCTTTGCTTTTTATTTAC-TTTTCTTTCCT
1 TTGCTTTATATAACTTTATATTT-CTTTACTTTGCTTTGT-TTTACATTTTCTTTCCT
**
25700089 TTGCTTTATATAACTTTATATTTCTTTACTTTGCTTTGTTTTACATTTTCTTTAAT
1 TTGCTTTATATAACTTTATATTTCTTTACTTTGCTTTGTTTTACATTTTCTTTCCT
* *
25700145 ATTG---TAT-T-ACTTTATATTACTTTACTTTGTTTTGTTTTA
1 -TTGCTTTATATAACTTTATATTTCTTTACTTTGCTTTGTTTTA
25700184 TATATCATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
52 29 0.35
53 1 0.01
54 3 0.04
55 5 0.06
56 40 0.48
57 6 0.07
ACGTcount: A:0.17, C:0.13, G:0.05, T:0.65
Consensus pattern (56 bp):
TTGCTTTATATAACTTTATATTTCTTTACTTTGCTTTGTTTTACATTTTCTTTCCT
Found at i:25700359 original size:27 final size:27
Alignment explanation
Indices: 25700329--25700384 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
25700319 TGATAGGTGG
*
25700329 ATTTAATT-TATTTAATTACTATTTTTA
1 ATTTAATTATATAT-ATTACTATTTTTA
*
25700356 ATTTAATTATATATATTATTATTTTTA
1 ATTTAATTATATATATTACTATTTTTA
25700383 AT
1 AT
25700385 AATTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTAATTATATATATTACTATTTTTA
Found at i:25701509 original size:20 final size:20
Alignment explanation
Indices: 25701486--25701559 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
25701476 TATTTTAATT
*
25701486 TGCTTTGCTTTATATTGCTC
1 TGCTTTGCTTTATATTACTC
* *
25701506 TGCTTTACTTTATATTCCTTTGC
1 TGCTTTGCTTTATATTAC--T-C
* *
25701529 TGTTTTGTTTTATATTACTC
1 TGCTTTGCTTTATATTACTC
*
25701549 TGCTTTTCTTT
1 TGCTTTGCTTT
25701560 GTTTTACTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
20 25 0.60
21 1 0.02
22 1 0.02
23 15 0.36
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.61
Consensus pattern (20 bp):
TGCTTTGCTTTATATTACTC
Found at i:25701693 original size:22 final size:21
Alignment explanation
Indices: 25701676--25701728 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
25701666 TTTATATTGT
25701676 TTTGCTTTGCTTCATATATATC
1 TTTGCTTTGCTTCATATAT-TC
* *
25701698 TTTGCTTTGCTTTATATTTTCC
1 TTTGCTTTGCTTCATATATT-C
25701720 TTTGCTTTG
1 TTTGCTTTG
25701729 GCTTTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.60
Consensus pattern (21 bp):
TTTGCTTTGCTTCATATATTC
Found at i:25701722 original size:17 final size:18
Alignment explanation
Indices: 25701692--25701727 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
25701682 TTGCTTCATA
*
25701692 TATATCTTTGCTTTGCTT
1 TATATCTTTCCTTTGCTT
25701710 TATAT-TTTCCTTTGCTT
1 TATATCTTTCCTTTGCTT
25701727 T
1 T
25701728 GGCTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (18 bp):
TATATCTTTCCTTTGCTT
Found at i:25701951 original size:29 final size:27
Alignment explanation
Indices: 25701902--25701959 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 27
25701892 TGATATATGG
*
25701902 ATTTAATTTATTTAATTATTATTTTTA
1 ATTTAATATATTTAATTATTATTTTTA
25701929 ATTTAAGTATATTTATATTATTATTTTTA
1 ATTTAA-TATATTTA-ATTATTATTTTTA
25701958 AT
1 AT
25701960 AATCATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 6 0.21
28 7 0.25
29 15 0.54
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
ATTTAATATATTTAATTATTATTTTTA
Found at i:25704122 original size:15 final size:15
Alignment explanation
Indices: 25704085--25704125 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25704075 TTGCTTTGCT
*
25704085 TTGCTTTTCTTTATA
1 TTGCTTTGCTTTATA
**
25704100 TTATTTTGCTTTATA
1 TTGCTTTGCTTTATA
25704115 TTGCTTTGCTT
1 TTGCTTTGCTT
25704126 CATCGTTCTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.66
Consensus pattern (15 bp):
TTGCTTTGCTTTATA
Found at i:25709025 original size:15 final size:14
Alignment explanation
Indices: 25709005--25709058 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
25708995 AGCAATATAA
25709005 AAAGCAAAGAAAATC
1 AAAGCAAAGAAAA-C
*
25709020 AAAGCAATATAAAAC
1 AAAGCAA-AGAAAAC
*
25709035 AAAGCAAATAAAAGC
1 AAAGCAAAGAAAA-C
25709050 AAAGCAAAG
1 AAAGCAAAG
25709059 CACAACACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 6 0.17
15 24 0.69
16 5 0.14
ACGTcount: A:0.67, C:0.13, G:0.13, T:0.07
Consensus pattern (14 bp):
AAAGCAAAGAAAAC
Found at i:25709043 original size:25 final size:25
Alignment explanation
Indices: 25708973--25709051 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
25708963 AATGTCATAT
** *
25708973 AATATAAAGTAAAGCAAA-CTATAGC
1 AATATAAAACAAAGCAAATC-AAAGC
*
25708998 AATATAAAAAGCAAAGAAAATCAAAGC
1 AATAT-AAAA-CAAAGCAAATCAAAGC
*
25709025 AATATAAAACAAAGCAAATAAAAGC
1 AATATAAAACAAAGCAAATCAAAGC
25709050 AA
1 AA
25709052 AGCAAAGCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 21 0.47
26 7 0.16
27 16 0.36
28 1 0.02
ACGTcount: A:0.65, C:0.11, G:0.10, T:0.14
Consensus pattern (25 bp):
AATATAAAACAAAGCAAATCAAAGC
Found at i:25709080 original size:27 final size:27
Alignment explanation
Indices: 25709042--25709141 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
25709032 AACAAAGCAA
*
25709042 ATAAAA-GCAAAGCAAAGCACAACACAT
1 ATAAAAGGAAAAGCAAAGCACAACA-AT
* * *
25709069 -TAATATGAAAAG-AACAGCACGACAAT
1 ATAAAAGGAAAAGCAA-AGCACAACAAT
*
25709095 ATAAAAGGAAAAGCAAAGCAAAACAAT
1 ATAAAAGGAAAAGCAAAGCACAACAAT
* * *
25709122 ATAAAAAGCAAGGCAAAGCA
1 ATAAAAGGAAAAGCAAAGCA
25709142 ATATAAAAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
26 8 0.14
27 49 0.83
28 2 0.03
ACGTcount: A:0.60, C:0.16, G:0.15, T:0.09
Consensus pattern (27 bp):
ATAAAAGGAAAAGCAAAGCACAACAAT
Found at i:25709114 original size:5 final size:5
Alignment explanation
Indices: 25709104--25709251 Score: 65
Period size: 5 Copynumber: 29.2 Consensus size: 5
25709094 TATAAAAGGA
* ** * **
25709104 AAAGC AAAGC AAAAC AATATA AAAAGC AAGGC AAAGC AATATA AAAGC
1 AAAGC AAAGC AAAGC AA-AGC A-AAGC AAAGC AAAGC AA-AGC AAAGC
* **
25709152 AAAGC TAAA-C AAAGT AAAGC ATAA-C AAAGC AATATAA AAAGC AAAGC
1 AAAGC -AAAGC AAAGC AAAGC A-AAGC AAAGC AA-A-GC AAAGC AAAGC
** * *
25709199 AAAGC AAAAT AAA-- AAA-A AAAGC AAAGC AAAGC ATAA-C AAAGC AACGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC A-AAGC AAAGC AAAGC
25709246 AAAGC A
1 AAAGC A
25709252 CATACAATAT
Statistics
Matches: 108, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
3 3 0.03
4 10 0.09
5 76 0.70
6 16 0.15
7 3 0.03
ACGTcount: A:0.64, C:0.16, G:0.14, T:0.07
Consensus pattern (5 bp):
AAAGC
Found at i:25709128 original size:22 final size:22
Alignment explanation
Indices: 25709103--25709275 Score: 142
Period size: 22 Copynumber: 7.8 Consensus size: 22
25709093 ATATAAAAGG
*
25709103 AAAAGCAAAGCAAAACAATATA
1 AAAAGCAAAGCAAAGCAATATA
*
25709125 AAAAGCAAGGCAAAGCAATAT-
1 AAAAGCAAAGCAAAGCAATATA
25709146 AAAAGCAAAGCTAAA-CAA-AGT-
1 AAAAGCAAAGC-AAAGCAATA-TA
25709167 -AAAGCATAA-CAAAGCAATATA
1 AAAAGCA-AAGCAAAGCAATATA
*
25709188 AAAAGCAAAGCAAAGCAAAATA
1 AAAAGCAAAGCAAAGCAATATA
** *
25709210 AAAAAAAAAGCAAAGCAAAGCATA
1 AAAAGCAAAGCAAAGC-AA-TATA
* *
25709234 ACAAAGCAACGCAAAGCACATACA
1 A-AAAGCAAAGCAAAGCA-ATATA
* *
25709258 ATATAGCAAAGCACAGCA
1 A-AAAGCAAAGCAAAGCA
25709276 CAACACAGCA
Statistics
Matches: 123, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.02
20 12 0.10
21 19 0.15
22 53 0.43
23 2 0.02
24 21 0.17
25 13 0.11
ACGTcount: A:0.62, C:0.17, G:0.13, T:0.08
Consensus pattern (22 bp):
AAAAGCAAAGCAAAGCAATATA
Found at i:25709197 original size:27 final size:27
Alignment explanation
Indices: 25709187--25709238 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
25709177 AAAGCAATAT
*
25709187 AAAAAGCAAAGCAAAGCAAAATAAAAA
1 AAAAAGCAAAGCAAAGCAAAACAAAAA
*
25709214 AAAAAGCAAAGCAAAGCATAACAAA
1 AAAAAGCAAAGCAAAGCAAAACAAA
25709239 GCAACGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.71, C:0.13, G:0.12, T:0.04
Consensus pattern (27 bp):
AAAAAGCAAAGCAAAGCAAAACAAAAA
Found at i:25709285 original size:20 final size:19
Alignment explanation
Indices: 25709244--25709290 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
25709234 ACAAAGCAAC
* * *
25709244 GCAAAGCACATACAATATA
1 GCAAAGCACACACAACACA
25709263 GCAAAGCACAGCACAACACA
1 GCAAAGCACA-CACAACACA
25709283 GCAAAGCA
1 GCAAAGCA
25709291 ATTTAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.51, C:0.28, G:0.15, T:0.06
Consensus pattern (19 bp):
GCAAAGCACACACAACACA
Found at i:25717482 original size:3 final size:3
Alignment explanation
Indices: 25717476--25717509 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
25717466 ATTGTGCTCT
25717476 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25717510 ATAGGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25719050 original size:91 final size:91
Alignment explanation
Indices: 25718895--25719076 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
25718885 ATGAATCATA
25718895 AATCTCAGTTTAAATTGTTCACTAGAAAATATTGAAATTGTTTTAAGAAGCTTATCTGGGTTATT
1 AATCTCAGTTTAAATTGTTCACTAGAAAATATTGAAATTGTTTTAAGAAGCTTATCTGGGTTATT
25718960 ATTTCCTTTTAATGATGGAGGTTTAT
66 ATTTCCTTTTAATGATGGAGGTTTAT
25718986 AATCTCAGTTTAAATTGTTCACTAGAAAATATTGAAATTGTTTTAAGAAGCTTATCTGGGTTATT
1 AATCTCAGTTTAAATTGTTCACTAGAAAATATTGAAATTGTTTTAAGAAGCTTATCTGGGTTATT
25719051 ATTTCCTTTTAATGATGGAGGTTTAT
66 ATTTCCTTTTAATGATGGAGGTTTAT
25719077 CAACTACTTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (91 bp):
AATCTCAGTTTAAATTGTTCACTAGAAAATATTGAAATTGTTTTAAGAAGCTTATCTGGGTTATT
ATTTCCTTTTAATGATGGAGGTTTAT
Found at i:25721270 original size:23 final size:24
Alignment explanation
Indices: 25721206--25721271 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 24
25721196 ATTAATATTA
*
25721206 CTTTACTTTGTTTTATATTACTCTG
1 CTTTGCTTTGTTTTATA-TACTCTG
* * *
25721231 CTTTGCTTTGGTATATA-ACTTTG
1 CTTTGCTTTGTTTTATATACTCTG
* *
25721254 TTTTGTTTTGTTTTATAT
1 CTTTGCTTTGTTTTATAT
25721272 TGATTTATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
23 18 0.56
25 14 0.44
ACGTcount: A:0.15, C:0.11, G:0.12, T:0.62
Consensus pattern (24 bp):
CTTTGCTTTGTTTTATATACTCTG
Found at i:25721838 original size:25 final size:24
Alignment explanation
Indices: 25721781--25721839 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
25721771 AAAAATAGGT
* *
25721781 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
25721804 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
25721828 TATTTTAATAAT
1 TATATT-ATAAT
25721840 AATTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:25721901 original size:57 final size:58
Alignment explanation
Indices: 25721813--25721953 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 58
25721803 ATATATTATA
* * * *
25721813 ATTTTTACT-AATTCATATTTTAATAATAATTATATAAAAATATTATTACATT-A-T-AT
1 ATTTTTATTAAATT-ATA-TTTAATAAGAATTATATAAAAATATAATTAAATTAATTAAT
* * *
25721869 ATTTTATTATTAAATTGTATTTAATAAGAATTATGTTAAAATATAATTAAATTAATTAAT
1 A-TTT-TTATTAAATTATATTTAATAAGAATTATATAAAAATATAATTAAATTAATTAAT
25721929 ATTTTTATTAAATTATATTTAATAA
1 ATTTTTATTAAATTATATTTAATAA
25721954 TAATCATTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
56 1 0.01
57 32 0.45
58 27 0.38
59 8 0.11
60 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAAGAATTATATAAAAATATAATTAAATTAATTAAT
Found at i:25722149 original size:16 final size:16
Alignment explanation
Indices: 25722128--25722183 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
25722118 AGAATTACTG
*
25722128 ATTACAG-TCCTATTTC
1 ATTACAGCT-CTATTCC
25722144 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
25722160 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
25722176 ATTACAGC
1 ATTACAGC
25722184 GAACCAAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:25722296 original size:14 final size:15
Alignment explanation
Indices: 25722278--25722311 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25722268 TTTAATTTCC
25722278 AAATTTA-TATTTTT
1 AAATTTATTATTTTT
*
25722292 GAATTTATTATTTTT
1 AAATTTATTATTTTT
25722307 AAATT
1 AAATT
25722312 CTTCATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
AAATTTATTATTTTT
Found at i:25723115 original size:182 final size:182
Alignment explanation
Indices: 25722758--25723340 Score: 948
Period size: 182 Copynumber: 3.2 Consensus size: 182
25722748 AATACAATTG
* * * *
25722758 CGCACTAAATTCCTGCTATGCATTATTGCAGTAATCACGTTTTAT-TGTTCGCAAAGAATGAACA
1 CGCACTAAATTCCTGCTTTGCATTGTTGCAGTAATCACCTTTTATATGTTCACAAAGAATGAACA
25722822 CGTTGGCTTGGTTACCACTCAACTACTAGAC----TAATTTCTGTACAGTCTCTTTTTCTGACGC
66 CGTTGGCTTGGTTACCACTCAACTACTAGACTGTTTAATTTCTGTACAGTCTC-TTTTCTGACGC
25722883 CTCATACCACTCGACTGCACTATCAGTTTCATAGACGGTCAATGGAGAAATCA
130 CTCATACCACTCGACTGCACTATCAGTTTCATAGACGGTCAATGGAGAAATCA
*
25722936 CGCGCTAAATTCCTGCTTTGCATTGTTGCAGTAATCACCTTTTATATGTTCACAAAGAATGAACA
1 CGCACTAAATTCCTGCTTTGCATTGTTGCAGTAATCACCTTTTATATGTTCACAAAGAATGAACA
* *
25723001 CGCTGGCTTGGTTACCACTCAACTACTAGACTGTTTAATTTCTATACAGTCTCTTTTCCTGACGC
66 CGTTGGCTTGGTTACCACTCAACTACTAGACTGTTTAATTTCTGTACAGTCTCTTTT-CTGACGC
25723066 CTCATA-CACTCGACTGCACTATCAGTTTCATAGACGGTCAATGGAGAAATCA
130 CTCATACCACTCGACTGCACTATCAGTTTCATAGACGGTCAATGGAGAAATCA
*
25723118 CGCACTAAATTCCTGCTTTGCATTGTTGCAGTAATCACGTTTTATATGTTCACAAAGAATGAACA
1 CGCACTAAATTCCTGCTTTGCATTGTTGCAGTAATCACCTTTTATATGTTCACAAAGAATGAACA
* *
25723183 CGTTGGCTTGGTTACCACTCAACTACTAGACTGTTTAATTTCTGTACAGTCTATTTTCTGACGCT
66 CGTTGGCTTGGTTACCACTCAACTACTAGACTGTTTAATTTCTGTACAGTCTCTTTTCTGACGCC
* *
25723248 TCATACCACTCGACTGCACTATCAGTTTCGT--ACGTGATCAATGAAGAAATCA
131 TCATACCACTCGACTGCACTATCAGTTTCATAGACG-G-TCAATGGAGAAATCA
* *
25723300 CGCACTAACTTCCTGCTTTCCATTGTTGCAGTAATCACCTT
1 CGCACTAAATTCCTGCTTTGCATTGTTGCAGTAATCACCTT
25723341 GGTATCAATG
Statistics
Matches: 378, Mismatches: 18, Indels: 14
0.92 0.04 0.03
Matches are distributed among these distances:
178 41 0.11
179 48 0.13
180 3 0.01
181 13 0.03
182 243 0.64
183 30 0.08
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (182 bp):
CGCACTAAATTCCTGCTTTGCATTGTTGCAGTAATCACCTTTTATATGTTCACAAAGAATGAACA
CGTTGGCTTGGTTACCACTCAACTACTAGACTGTTTAATTTCTGTACAGTCTCTTTTCTGACGCC
TCATACCACTCGACTGCACTATCAGTTTCATAGACGGTCAATGGAGAAATCA
Found at i:25731316 original size:18 final size:18
Alignment explanation
Indices: 25731293--25731335 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
25731283 ACCCAAACTT
25731293 GTTGACC-AACCTGAACCC
1 GTTGACCAAACCTG-ACCC
*
25731311 GTTGACCAAACCTGACCT
1 GTTGACCAAACCTGACCC
25731329 GTTGACC
1 GTTGACC
25731336 GTTGTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.21
Consensus pattern (18 bp):
GTTGACCAAACCTGACCC
Found at i:25732014 original size:20 final size:20
Alignment explanation
Indices: 25731989--25732034 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
25731979 CTATATAGAG
*
25731989 ATATTATATTACTTTTCTTT
1 ATATTATATTACTTTGCTTT
* *
25732009 ATATTATTTTGCTTTGCTTT
1 ATATTATATTACTTTGCTTT
25732029 ATATTA
1 ATATTA
25732035 CTTTTCTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (20 bp):
ATATTATATTACTTTGCTTT
Found at i:25732047 original size:20 final size:20
Alignment explanation
Indices: 25732005--25732048 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25731995 TATTACTTTT
*
25732005 CTTTATATTATTTTGCTTTG
1 CTTTATATTATTTTGCTTCG
25732025 CTTTATATTACTTTT-CTTCG
1 CTTTATATTA-TTTTGCTTCG
25732045 CTTT
1 CTTT
25732049 TCTTTGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.14, C:0.16, G:0.07, T:0.64
Consensus pattern (20 bp):
CTTTATATTATTTTGCTTCG
Found at i:25732345 original size:22 final size:23
Alignment explanation
Indices: 25732320--25732364 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
25732310 GATAGGTGAA
* *
25732320 TTTAATTTATTTA-ATTTTTATT
1 TTTAATTTAATTATATTTATATT
25732342 TTTAATTTAATTATATTTATATT
1 TTTAATTTAATTATATTTATATT
25732365 ATTGTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTAATTTAATTATATTTATATT
Found at i:25733137 original size:21 final size:22
Alignment explanation
Indices: 25733086--25733132 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
25733076 TTTTAGTACA
*
25733086 TTTAATATTAGTGAATTTTATT
1 TTTAATATTAGTGAATTTAATT
25733108 TTTAATATTAGTGAATTTAATT
1 TTTAATATTAGTGAATTTAATT
25733130 TTT
1 TTT
25733133 TTATTGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTAATATTAGTGAATTTAATT
Found at i:25736520 original size:25 final size:24
Alignment explanation
Indices: 25736491--25736588 Score: 88
Period size: 25 Copynumber: 3.9 Consensus size: 24
25736481 CATTTCTTTT
*
25736491 TTTGCTTTATATTGTTTTATATTAC
1 TTTGCTTTAT-TTGCTTTATATTAC
* * *
25736516 TTTGCTTTGCTTTGCTTTATACTAG
1 TTTGCTTT-ATTTGCTTTATATTAC
* *
25736541 TTTGCTTTGTTTTGCTTTATATTCC
1 TTTGCTTT-ATTTGCTTTATATTAC
* *
25736566 TTTGCTTTGCTTTACTTTATATT
1 TTTGCTTT-ATTTGCTTTATATT
25736589 GTTTTATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
25 61 0.98
26 1 0.02
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTGCTTTATTTGCTTTATATTAC
Found at i:25736569 original size:50 final size:50
Alignment explanation
Indices: 25736491--25736586 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
25736481 CATTTCTTTT
* *
25736491 TTTGCTTTATATTGTTTTATATTACTTTGCTTTGCTTTGCTTTATACTAG
1 TTTGCTTTATATTGCTTTATATTACTTTGCTTTGCTTTACTTTATACTAG
* * *
25736541 TTTGCTTTGTTTTGCTTTATATTCCTTTGCTTTGCTTTACTTTATA
1 TTTGCTTTATATTGCTTTATATTACTTTGCTTTGCTTTACTTTATA
25736587 TTGTTTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (50 bp):
TTTGCTTTATATTGCTTTATATTACTTTGCTTTGCTTTACTTTATACTAG
Found at i:25736635 original size:25 final size:25
Alignment explanation
Indices: 25736506--25736639 Score: 135
Period size: 25 Copynumber: 5.4 Consensus size: 25
25736496 TTTATATTGT
*
25736506 TTTATATTACTTTGCTTTGCTTTGC
1 TTTATATTAGTTTGCTTTGCTTTGC
* *
25736531 TTTATACTAGTTTGCTTTGTTTTGC
1 TTTATATTAGTTTGCTTTGCTTTGC
** *
25736556 TTTATATTCCTTTGCTTTGCTTTAC
1 TTTATATTAGTTTGCTTTGCTTTGC
** * **
25736581 TTTATATT-GTTTTATATTACTTCAC
1 TTTATATTAGTTTGCT-TTGCTTTGC
* *
25736606 ATTATGTTAGTTTGCTTTGCTTTGC
1 TTTATATTAGTTTGCTTTGCTTTGC
25736631 TTTATATTA
1 TTTATATTA
25736640 ATTACGAAAA
Statistics
Matches: 85, Mismatches: 22, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
24 4 0.05
25 76 0.89
26 5 0.06
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (25 bp):
TTTATATTAGTTTGCTTTGCTTTGC
Found at i:25736851 original size:52 final size:52
Alignment explanation
Indices: 25736793--25736898 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 52
25736783 AGATCAGGTT
*
25736793 ATGGATTTTATTATTAATCTTTTTTTCCTTTTTATTAC-ACCACCATTAATTA
1 ATGGATTTTATTATTAATCTTTATTTCCTTTTTATTACTACC-CCATTAATTA
* *
25736845 ATGGATTTTATTATTAATCTTTATTTCCTTTTTATTGCTACCTCATTAATTA
1 ATGGATTTTATTATTAATCTTTATTTCCTTTTTATTACTACCCCATTAATTA
25736897 AT
1 AT
25736899 TTAATGTCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 47 0.94
53 3 0.06
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (52 bp):
ATGGATTTTATTATTAATCTTTATTTCCTTTTTATTACTACCCCATTAATTA
Found at i:25737705 original size:5 final size:5
Alignment explanation
Indices: 25737697--25738017 Score: 69
Period size: 5 Copynumber: 61.4 Consensus size: 5
25737687 GCTTTTTAAA
* * **
25737697 TTGCT TTGCT TTGCT GTGTT TTGCT TTG-T TGTG-T TGTGCT TTGCT TTTAT
1 TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT T-TGCT T-TGCT TTGCT TTGCT
* * ** * **
25737747 ATTACC TTGCT TTGCTT TTTAT ATTGTT TTGCT TTGCT TTTAT ATTGCT
1 -TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGCT -TTGCT
* ** * * ** *
25737796 TTGCT TTTCTT TTTAT ATTGTT TTACT TTGCT TTGCTT TTTAT ATTGTT
1 TTGCT TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGC-T TTGCT -TTGCT
** * *
25737845 TTGCT TTGCT TTGCTT TTTAT ATTGTT TTTCT TTGCT TTGCT TTG-T TTAGCT
1 TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGCT TTGCT TT-GCT
* * ** * * *
25737897 CTACT TTGCT TTTAT ATTGAT ATT-CTT TTGCA TTGCT TTGCT TTGTT
1 TTGCT TTGCT TTGCT -TTGCT -TTGC-T TTGCT TTGCT TTGCT TTGCT
* * ** * * *
25737944 TTGAT TTGCT TTTCTT TTTAT ATTG-T TGTGCT GTCCT TTGCT TT-AT
1 TTGCT TTGCT TTGC-T TTGCT -TTGCT T-TGCT TTGCT TTGCT TTGCT
* *
25737990 ATTGCT TTGAT TTGCT TTGCT TTACT TT
1 -TTGCT TTGCT TTGCT TTGCT TTGCT TT
25738018 ATATTATATG
Statistics
Matches: 229, Mismatches: 64, Indels: 46
0.68 0.19 0.14
Matches are distributed among these distances:
4 7 0.03
5 171 0.75
6 51 0.22
ACGTcount: A:0.09, C:0.13, G:0.15, T:0.63
Consensus pattern (5 bp):
TTGCT
Found at i:25737769 original size:22 final size:22
Alignment explanation
Indices: 25737733--25737883 Score: 144
Period size: 22 Copynumber: 6.5 Consensus size: 22
25737723 TGTTGTGTTG
* *
25737733 TGCTTTGC-TTTTATATTACCT
1 TGCTTTGCTTTTTATATTGCTT
*
25737754 TGCTTTGCTTTTTATATTGTTT
1 TGCTTTGCTTTTTATATTGCTT
25737776 TGCTTTGC-TTTTATATTGCTT
1 TGCTTTGCTTTTTATATTGCTT
*
25737797 TGCTTTTCTTTTTATATTGTTTTACTT
1 TGCTTTGCTTTTTATATTG-----CTT
25737824 TGCTTTGCTTTTTATATTGTTTTGCTT
1 TGCTTTGCTTTTTATA-----TTGCTT
*
25737851 TGCTTTGCTTTTTATATTGTTT
1 TGCTTTGCTTTTTATATTGCTT
*
25737873 TTCTTTGCTTT
1 TGCTTTGCTTT
25737884 GCTTTGTTTA
Statistics
Matches: 110, Mismatches: 8, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
21 27 0.25
22 43 0.39
27 37 0.34
32 3 0.03
ACGTcount: A:0.09, C:0.13, G:0.12, T:0.66
Consensus pattern (22 bp):
TGCTTTGCTTTTTATATTGCTT
Found at i:25737783 original size:43 final size:43
Alignment explanation
Indices: 25737728--25737829 Score: 159
Period size: 43 Copynumber: 2.4 Consensus size: 43
25737718 TGCTTTGTTG
*
25737728 TGTTGTGCTTTGCTTTTATATTACCTTGCTTTGCTTTTTATAT
1 TGTTTTGCTTTGCTTTTATATTACCTTGCTTTGCTTTTTATAT
* * *
25737771 TGTTTTGCTTTGCTTTTATATTGCTTTGCTTTTCTTTTTATAT
1 TGTTTTGCTTTGCTTTTATATTACCTTGCTTTGCTTTTTATAT
*
25737814 TGTTTTACTTTGCTTT
1 TGTTTTGCTTTGCTTT
25737830 GCTTTTTATA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.65
Consensus pattern (43 bp):
TGTTTTGCTTTGCTTTTATATTACCTTGCTTTGCTTTTTATAT
Found at i:25737785 original size:27 final size:27
Alignment explanation
Indices: 25737680--25738012 Score: 183
Period size: 27 Copynumber: 13.4 Consensus size: 27
25737670 TGTCAACATG
* *
25737680 TTGCTTTGCTTTTTAAATTGCTTTGCT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
* ** *
25737707 TTGCTGTG-TTTTGCT-TTGTTGTG-T
1 TTGCTTTGCTTTTTATATTGTTTTGCT
* *
25737731 TGTGCTTTGC-TTTTATA-----TTACC
1 T-TGCTTTGCTTTTTATATTGTTTTGCT
25737753 TTGCTTTGCTTTTTATATTG---T--T
1 TTGCTTTGCTTTTTATATTGTTTTGCT
*
25737775 TTGCTTTGC-TTTTATATTGCTTTGC-
1 TTGCTTTGCTTTTTATATTGTTTTGCT
*
25737800 TT--T-T-CTTTTTATATTGTTTTACT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
25737823 TTGCTTTGCTTTTTATATTGTTTTGCT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
*
25737850 TTGCTTTGCTTTTTATATTGTTTTTCT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
*
25737877 TTGCTTTGC------T-TTGTTTAGCT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
* * *
25737897 CTACTTTGC-TTTTATATTGATATT-CTT
1 TTGCTTTGCTTTTTATATTG-TTTTGC-T
* ** *
25737924 TTGCATTGC-TTTGCT-TTGTTTTGAT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
* *
25737949 TTGCTTTTCTTTTTATATTGTTGTGCT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
* * * *
25737976 GTCCTTTGC--TTTATATTGCTTTGAT
1 TTGCTTTGCTTTTTATATTGTTTTGCT
25738001 TTGCTTTGCTTT
1 TTGCTTTGCTTT
25738013 ACTTTATATT
Statistics
Matches: 230, Mismatches: 44, Indels: 64
0.68 0.13 0.19
Matches are distributed among these distances:
20 15 0.07
21 21 0.09
22 32 0.14
23 3 0.01
24 4 0.02
25 51 0.22
26 16 0.07
27 88 0.38
ACGTcount: A:0.09, C:0.13, G:0.15, T:0.63
Consensus pattern (27 bp):
TTGCTTTGCTTTTTATATTGTTTTGCT
Found at i:25737967 original size:47 final size:47
Alignment explanation
Indices: 25737840--25737967 Score: 130
Period size: 52 Copynumber: 2.6 Consensus size: 47
25737830 GCTTTTTATA
* * * * *
25737840 TTGTTTTGCTTTGCTTTGCTTTTTATATTGTTTTTCTTTGCTTTGCT
1 TTGTTTTGATTTGCTTTTCTTTTTATATTCTTTTGCATTGCTTTGCT
* * * *
25737887 TTGTTTAGCTCTACTTTGCTTTTATATTGATATTCTTTTGCATTGCTTTGCT
1 TTGTTT---T-GA-TTTGCTTTTCTTTTTATATTCTTTTGCATTGCTTTGCT
25737939 TTGTTTTGATTTGCTTTTCTTTTTATATT
1 TTGTTTTGATTTGCTTTTCTTTTTATATT
25737968 GTTGTGCTGT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
47 23 0.37
48 1 0.02
49 1 0.02
50 1 0.02
52 37 0.59
ACGTcount: A:0.09, C:0.12, G:0.13, T:0.65
Consensus pattern (47 bp):
TTGTTTTGATTTGCTTTTCTTTTTATATTCTTTTGCATTGCTTTGCT
Found at i:25753393 original size:15 final size:15
Alignment explanation
Indices: 25753373--25753406 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25753363 GATTCAGAGG
25753373 CGGCCTCTACTGATA
1 CGGCCTCTACTGATA
*
25753388 CGGCCTCTGCTGATA
1 CGGCCTCTACTGATA
25753403 CGGC
1 CGGC
25753407 TGATTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
CGGCCTCTACTGATA
Found at i:25756255 original size:15 final size:15
Alignment explanation
Indices: 25756231--25756263 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25756221 AAAAATAATA
*
25756231 TAAAGCAAAGCAAAG
1 TAAAGAAAAGCAAAG
25756246 TAAAGAAAAGCAAAG
1 TAAAGAAAAGCAAAG
25756261 TAA
1 TAA
25756264 TATAGAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.09, G:0.18, T:0.09
Consensus pattern (15 bp):
TAAAGAAAAGCAAAG
Found at i:25756275 original size:20 final size:20
Alignment explanation
Indices: 25756226--25756287 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
25756216 TGCAAAAAAA
*
25756226 TAATATAAAGCAAAGCAAAG
1 TAATATAGAGCAAAGCAAAG
25756246 T-A-A-AGA--AAAGCAAAG
1 TAATATAGAGCAAAGCAAAG
25756261 TAATATAGAGCAAAGCAAAG
1 TAATATAGAGCAAAGCAAAG
25756281 TAATATA
1 TAATATA
25756288 AGTCAAGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 10 0.28
16 1 0.03
17 3 0.08
18 4 0.11
19 1 0.03
20 17 0.47
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (20 bp):
TAATATAGAGCAAAGCAAAG
Found at i:25757462 original size:3 final size:3
Alignment explanation
Indices: 25757456--25757502 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
25757446 TTTTTTTTAA
* * *
25757456 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT TAT TAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25757503 GTAAATTCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:25758803 original size:3 final size:3
Alignment explanation
Indices: 25758795--25758836 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
25758785 ATAAACTTAT
*
25758795 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25758837 ATCAGTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 35 0.97
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:25762224 original size:5 final size:5
Alignment explanation
Indices: 25762214--25762321 Score: 62
Period size: 5 Copynumber: 21.6 Consensus size: 5
25762204 GCATTTACAA
* * * * *
25762214 TTTGC TTTGC TTTGT TTTGC TTTAC TTTGT TTTGC TTT-A TATTGT TTTGC
1 TTTGC TTTGC TTTGC TTTGC TTTGC TTTGC TTTGC TTTGC T-TTGC TTTGC
* * ** *
25762264 TTTGC TTTTC TTTTC TTTG- TTTTA TATTGC TTT-C TTTTGC TTT-A TATTGC
1 TTTGC TTTGC TTTGC TTTGC TTTGC T-TTGC TTTGC -TTTGC TTTGC T-TTGC
25762314 TTTGC TTT
1 TTTGC TTT
25762322 ATATTGCTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
4 6 0.08
5 67 0.85
6 6 0.08
ACGTcount: A:0.06, C:0.13, G:0.13, T:0.68
Consensus pattern (5 bp):
TTTGC
Found at i:25762234 original size:15 final size:15
Alignment explanation
Indices: 25762214--25762271 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
25762204 GCATTTACAA
25762214 TTTGCTTTGCTTTGT
1 TTTGCTTTGCTTTGT
*
25762229 TTTGCTTTACTTTGT
1 TTTGCTTTGCTTTGT
*
25762244 TTTGCTTT-ATATTGT
1 TTTGCTTTGCT-TTGT
25762259 TTTGCTTTGCTTT
1 TTTGCTTTGCTTT
25762272 TCTTTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 1 0.03
15 36 0.95
16 1 0.03
ACGTcount: A:0.05, C:0.12, G:0.16, T:0.67
Consensus pattern (15 bp):
TTTGCTTTGCTTTGT
Found at i:25762266 original size:25 final size:25
Alignment explanation
Indices: 25762214--25762341 Score: 89
Period size: 25 Copynumber: 4.9 Consensus size: 25
25762204 GCATTTACAA
* * * * *
25762214 TTTGCTTTGCTTTGTTTTGCTTTAC
1 TTTGTTTTGCTTTATATTGTTTTGC
25762239 TTTGTTTTGCTTTATATTGTTTTGC
1 TTTGTTTTGCTTTATATTGTTTTGC
*
25762264 TTTGCTTTT-CTTT-TCTTTGTTTTATATTGC
1 TTTG-TTTTGCTTTAT-ATTG---T-T-TTGC
* *
25762294 TTTCTTTTGCTTTATATTGCTTTGC
1 TTTGTTTTGCTTTATATTGTTTTGC
* *
25762319 TTTATATTGCTTTATATTGTTTT
1 TTTGTTTTGCTTTATATTGTTTT
25762342 ATATCATAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
24 1 0.01
25 55 0.67
26 5 0.06
28 1 0.01
29 5 0.06
30 14 0.17
31 1 0.01
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.67
Consensus pattern (25 bp):
TTTGTTTTGCTTTATATTGTTTTGC
Found at i:25762288 original size:35 final size:35
Alignment explanation
Indices: 25762220--25762331 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 35
25762210 ACAATTTGCT
*
25762220 TTGCTTTGTTTTGCTTTACTTTGTTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTACTTTGTTTTGCTTTATA
* * *
25762255 TTGTTTTGCTTTGCTTTTCTTT-TCTTTGTTTTATA
1 TTGCTTTGCTTTGCTTTACTTTGT-TTTGCTTTATA
*
25762290 TTGCTTT-CTTTTGCTTTA-TATTGCTTTGCTTTATA
1 TTGCTTTGC-TTTGCTTTACT-TTGTTTTGCTTTATA
25762325 TTGCTTT
1 TTGCTTT
25762332 ATATTGTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.05
35 62 0.95
ACGTcount: A:0.08, C:0.12, G:0.12, T:0.67
Consensus pattern (35 bp):
TTGCTTTGCTTTGCTTTACTTTGTTTTGCTTTATA
Found at i:25762317 original size:15 final size:15
Alignment explanation
Indices: 25762299--25762331 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
25762289 ATTGCTTTCT
25762299 TTTGCTTTATATTGC
1 TTTGCTTTATATTGC
25762314 TTTGCTTTATATTGC
1 TTTGCTTTATATTGC
25762329 TTT
1 TTT
25762332 ATATTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (15 bp):
TTTGCTTTATATTGC
Found at i:25762328 original size:10 final size:10
Alignment explanation
Indices: 25762284--25762345 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
25762274 TTTTCTTTGT
25762284 TTTATATTGC
1 TTTATATTGC
* *
25762294 TTTCTTTTGC
1 TTTATATTGC
25762304 TTTATATTGC
1 TTTATATTGC
25762314 ----T-TTGC
1 TTTATATTGC
25762319 TTTATATTGC
1 TTTATATTGC
*
25762329 TTTATATTGT
1 TTTATATTGC
25762339 TTTATAT
1 TTTATAT
25762346 CATAACAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
9 1 0.02
10 36 0.86
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (10 bp):
TTTATATTGC
Found at i:25762344 original size:20 final size:18
Alignment explanation
Indices: 25762243--25762345 Score: 65
Period size: 20 Copynumber: 5.7 Consensus size: 18
25762233 CTTTACTTTG
*
25762243 TTTTGCTTTATATTGTTT
1 TTTTGCTTTATATTGCTT
*
25762261 TGCTTTGCTTT-TCTT--TT
1 T--TTTGCTTTATATTGCTT
* *
25762278 CTTTGTTTTATATTGCTTT
1 TTTTGCTTTATATTGC-TT
25762297 CTTTTGCTTTATATTGC--
1 -TTTTGCTTTATATTGCTT
25762314 -TTTGCTTTATATTGCTT
1 TTTTGCTTTATATTGCTT
*
25762331 TATATTGTTTTATAT
1 T-T-TTGCTTTATAT
25762346 CATAACAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
15 22 0.33
16 3 0.05
17 2 0.03
18 1 0.02
19 6 0.09
20 32 0.48
ACGTcount: A:0.12, C:0.11, G:0.11, T:0.67
Consensus pattern (18 bp):
TTTTGCTTTATATTGCTT
Found at i:25762380 original size:15 final size:15
Alignment explanation
Indices: 25762357--25762453 Score: 107
Period size: 15 Copynumber: 6.8 Consensus size: 15
25762347 ATAACAAAGA
*
25762357 AAAGTAAAGCAATAT
1 AAAGCAAAGCAATAT
*
25762372 AAAGCAAAGCAATAA
1 AAAGCAAAGCAATAT
*
25762387 AAAG-AACAGTAATAT
1 AAAGCAA-AGCAATAT
25762402 AAAGCAAAGCAATAT
1 AAAGCAAAGCAATAT
25762417 AAAGCAAAGC-A-AT
1 AAAGCAAAGCAATAT
*
25762430 ---GCAAAACAATAT
1 AAAGCAAAGCAATAT
25762442 AAAGCAAAGCAA
1 AAAGCAAAGCAA
25762454 AGCAAAGTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
10 6 0.09
11 1 0.01
12 2 0.03
13 2 0.03
14 3 0.04
15 52 0.76
16 2 0.03
ACGTcount: A:0.62, C:0.12, G:0.13, T:0.12
Consensus pattern (15 bp):
AAAGCAAAGCAATAT
Found at i:25762439 original size:25 final size:25
Alignment explanation
Indices: 25762402--25762476 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
25762392 ACAGTAATAT
25762402 AAAGCAAAGCAATATAAAGCAAAGC
1 AAAGCAAAGCAATATAAAGCAAAGC
* *
25762427 AATGCAAAACAATATAAAGCAAAGC
1 AAAGCAAAGCAATATAAAGCAAAGC
* *
25762452 AAAGCAAAGTACTATAAAGCAAAGC
1 AAAGCAAAGCAATATAAAGCAAAGC
25762477 TGTAACACAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.59, C:0.16, G:0.15, T:0.11
Consensus pattern (25 bp):
AAAGCAAAGCAATATAAAGCAAAGC
Found at i:25762476 original size:5 final size:5
Alignment explanation
Indices: 25762402--25762460 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
25762392 ACAGTAATAT
* * * *
25762402 AAAGC AAAGC AATA-T AAAGC AAAGC AATGC AAAAC AATA-T AAAGC AAAGC
1 AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC
25762452 AAAGC AAAG
1 AAAGC AAAG
25762461 TACTATAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.05
5 39 0.91
6 2 0.05
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.08
Consensus pattern (5 bp):
AAAGC
Found at i:25763036 original size:39 final size:39
Alignment explanation
Indices: 25762993--25763157 Score: 213
Period size: 39 Copynumber: 4.2 Consensus size: 39
25762983 ATATCACCTT
* * * * *
25762993 CAGTTCAATATTTCTTTGCAGTGTTTATAGTGTGACCGC
1 CAGTTCAGTATTTCATTGCAGTGTTTACAGTGTCACTGC
* *
25763032 CAGTTCAGTATTGCATTGCAGTGTTTACAATGTCACTGC
1 CAGTTCAGTATTTCATTGCAGTGTTTACAGTGTCACTGC
* * *
25763071 TAGTTCAGTATTACATTGCAATGTTTACAGTGTCACTGC
1 CAGTTCAGTATTTCATTGCAGTGTTTACAGTGTCACTGC
* *
25763110 CAGTTCAGTATTTCATTGCAGTGCTTGCAGTGTCACTGC
1 CAGTTCAGTATTTCATTGCAGTGTTTACAGTGTCACTGC
*
25763149 CAATTCAGT
1 CAGTTCAGT
25763158 CTAAAATCGA
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 109 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (39 bp):
CAGTTCAGTATTTCATTGCAGTGTTTACAGTGTCACTGC
Found at i:25763041 original size:78 final size:78
Alignment explanation
Indices: 25762957--25763119 Score: 179
Period size: 78 Copynumber: 2.1 Consensus size: 78
25762947 TCACTACCTA
* * * *
25762957 TTCAGTACAGCATT--ATGATGTTTACAATATCACCTTC-AGTTCAATATTTCTTTGCAGTGTTT
1 TTCAGTACAGCATTGCA-G-TGTTTACAATATCA-CTGCTAGTTCAATATTACATTGCAATGTTT
* *
25763019 ATAGTGTGACCGCCAG
63 ACAGTGTCACCGCCAG
** * *
25763035 TTCAGTATTGCATTGCAGTGTTTACAATGTCACTGCTAGTTCAGTATTACATTGCAATGTTTACA
1 TTCAGTACAGCATTGCAGTGTTTACAATATCACTGCTAGTTCAATATTACATTGCAATGTTTACA
*
25763100 GTGTCACTGCCAG
66 GTGTCACCGCCAG
25763113 TTCAGTA
1 TTCAGTA
25763120 TTTCATTGCA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
77 3 0.04
78 66 0.93
79 1 0.01
80 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (78 bp):
TTCAGTACAGCATTGCAGTGTTTACAATATCACTGCTAGTTCAATATTACATTGCAATGTTTACA
GTGTCACCGCCAG
Found at i:25769838 original size:39 final size:39
Alignment explanation
Indices: 25769757--25769980 Score: 173
Period size: 39 Copynumber: 5.7 Consensus size: 39
25769747 ATGGTCTGGT
* * *** *
25769757 AGTGTTTATAATGTCACTACCCA-TTCAGTACAGCATTAC
1 AGTGTTTACAATGTCACT-GCCAGTTCAGTATTTCATTGC
* * * *
25769796 GGTGTTTACAATGTCACTGTCAATTCAGTATTTCTTTGC
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATTTCATTGC
* * * * * **
25769835 GGTGTTTATAGTGTCACCGCCAGTTCAGTATTGCATTAT
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATTTCATTGC
* * * * *
25769874 AGTGTTTATAGTGTGACTACTAGTTCAGTATTGT-ATTGC
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATT-TCATTGC
* * * *
25769913 AGTGTTTACAATGTCACTGCAAGTTTAGTATTCCATTGT
1 AGTGTTTACAATGTCACTGCCAGTTCAGTATTTCATTGC
*
25769952 AGTGTTTGCAATGTCACTGCCAGTTCAGT
1 AGTGTTTACAATGTCACTGCCAGTTCAGT
25769981 CTACAATCGA
Statistics
Matches: 145, Mismatches: 37, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
38 2 0.01
39 143 0.99
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (39 bp):
AGTGTTTACAATGTCACTGCCAGTTCAGTATTTCATTGC
Found at i:25769977 original size:78 final size:78
Alignment explanation
Indices: 25769797--25769980 Score: 199
Period size: 78 Copynumber: 2.4 Consensus size: 78
25769787 CAGCATTACG
* * * * * * *
25769797 GTGTTTACAATGTCACTGTCAATTCAGTATTTCTTTGCGGTGTTTATAGTGTCACCGCCAGTTCA
1 GTGTTTACAATGTCACTGCCAGTTCAGTATTTCATTGCAGTGTTTACAATGTCACCGCAAGTTCA
*
25769862 GTATTGCATTATA
66 GTATTCCATTATA
* * * * * * *
25769875 GTGTTTATAGTGTGACTACTAGTTCAGTATTGT-ATTGCAGTGTTTACAATGTCACTGCAAGTTT
1 GTGTTTACAATGTCACTGCCAGTTCAGTATT-TCATTGCAGTGTTTACAATGTCACCGCAAGTTC
*
25769939 AGTATTCCATTGTA
65 AGTATTCCATTATA
*
25769953 GTGTTTGCAATGTCACTGCCAGTTCAGT
1 GTGTTTACAATGTCACTGCCAGTTCAGT
25769981 CTACAATCGA
Statistics
Matches: 83, Mismatches: 22, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
78 82 0.99
79 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (78 bp):
GTGTTTACAATGTCACTGCCAGTTCAGTATTTCATTGCAGTGTTTACAATGTCACCGCAAGTTCA
GTATTCCATTATA
Found at i:25771348 original size:20 final size:20
Alignment explanation
Indices: 25771323--25771520 Score: 133
Period size: 20 Copynumber: 10.4 Consensus size: 20
25771313 TGCTACAACT
*
25771323 GCAAAGCAATATAAAGGAAA
1 GCAAAGCAATATAAAGCAAA
* *
25771343 GCAAAGAAATATAAAACAAA
1 GCAAAGCAATATAAAGCAAA
25771363 GCAAAATAAAGCAATATAAAGCAAA
1 GC-----AAAGCAATATAAAGCAAA
* *
25771388 TCAAAGTAATATAAAGCAAA
1 GCAAAGCAATATAAAGCAAA
*
25771408 G-AAAGTAATATAAAGCAAA
1 GCAAAGCAATATAAAGCAAA
25771427 GCAAAG-----TAAA-C---
1 GCAAAGCAATATAAAGCAAA
25771438 -CAAAGCAATATAAAGCAAA
1 GCAAAGCAATATAAAGCAAA
* *
25771457 CCAAAGCAGTATAAAG---A
1 GCAAAGCAATATAAAGCAAA
25771474 --AAA-CTAATATAAAGCAAA
1 GCAAAGC-AATATAAAGCAAA
*
25771492 GCAAAGAAATATAAAGCAAA
1 GCAAAGCAATATAAAGCAAA
*
25771512 ACAAAGCAA
1 GCAAAGCAA
25771521 AGCTTCTTTG
Statistics
Matches: 142, Mismatches: 13, Indels: 46
0.71 0.06 0.23
Matches are distributed among these distances:
10 5 0.04
14 2 0.01
15 19 0.13
16 1 0.01
17 1 0.01
18 1 0.01
19 19 0.13
20 77 0.54
25 17 0.12
ACGTcount: A:0.63, C:0.12, G:0.13, T:0.12
Consensus pattern (20 bp):
GCAAAGCAATATAAAGCAAA
Found at i:25771362 original size:15 final size:15
Alignment explanation
Indices: 25771340--25771456 Score: 69
Period size: 15 Copynumber: 7.5 Consensus size: 15
25771330 AATATAAAGG
25771340 AAAGCAAAGAAATAT
1 AAAGCAAAGAAATAT
*
25771355 AAAACAAAGCAAA-AT
1 AAAGCAAAG-AAATAT
* **
25771370 AAAGCAATATAAA-GC
1 AAAGCAA-AGAAATAT
* *
25771385 AAATCAAAGTAATAT
1 AAAGCAAAGAAATAT
25771400 AAAGCAAAGAAAGTAATAT
1 AAAGCAAAG--A--AATAT
*
25771419 AAAGCAAAGCAAA-GT
1 AAAGCAAAG-AAATAT
* *
25771434 AAACCAAAGCAATAT
1 AAAGCAAAGAAATAT
25771449 AAAGCAAA
1 AAAGCAAA
25771457 CCAAAGCAGT
Statistics
Matches: 76, Mismatches: 18, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
14 5 0.07
15 50 0.66
16 6 0.08
18 1 0.01
19 14 0.18
ACGTcount: A:0.64, C:0.11, G:0.12, T:0.13
Consensus pattern (15 bp):
AAAGCAAAGAAATAT
Found at i:25771373 original size:10 final size:10
Alignment explanation
Indices: 25771355--25771456 Score: 64
Period size: 10 Copynumber: 10.3 Consensus size: 10
25771345 AAAGAAATAT
*
25771355 AAAACAAAGC
1 AAAATAAAGC
25771365 AAAATAAAGC
1 AAAATAAAGC
*
25771375 AATATAAAGC
1 AAAATAAAGC
*
25771385 -AAATCAAAGT
1 AAAAT-AAAGC
*
25771395 AATATAAAGC
1 AAAATAAAGC
* *
25771405 -AAAGAAAGT
1 AAAATAAAGC
*
25771414 AATATAAAGC
1 AAAATAAAGC
** *
25771424 AAAGCAAAGT
1 AAAATAAAGC
**
25771434 AAACCAAAGC
1 AAAATAAAGC
*
25771444 AATATAAAGC
1 AAAATAAAGC
25771454 AAA
1 AAA
25771457 CCAAAGCAGT
Statistics
Matches: 67, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
9 9 0.13
10 55 0.82
11 3 0.04
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.13
Consensus pattern (10 bp):
AAAATAAAGC
Found at i:25771373 original size:25 final size:25
Alignment explanation
Indices: 25771345--25771392 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25771335 AAAGGAAAGC
25771345 AAAGAAATATAAAACAAAGCAAAAT
1 AAAGAAATATAAAACAAAGCAAAAT
* * *
25771370 AAAGCAATATAAAGCAAATCAAA
1 AAAGAAATATAAAACAAAGCAAA
25771393 GTAATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.12
Consensus pattern (25 bp):
AAAGAAATATAAAACAAAGCAAAAT
Found at i:25771432 original size:39 final size:40
Alignment explanation
Indices: 25771325--25771435 Score: 125
Period size: 39 Copynumber: 2.7 Consensus size: 40
25771315 CTACAACTGC
* * *
25771325 AAAGCAATATAAAGGAAAGCAAAGAAATATAAAACAAAGCAAAAT
1 AAAGCAATATAAAGCAAAGCAAAGTAATAT-----AAAGCAAAAG
*
25771370 AAAGCAATATAAAGCAAATCAAAGTAATATAAAGC-AAAG
1 AAAGCAATATAAAGCAAAGCAAAGTAATATAAAGCAAAAG
*
25771409 AAAGTAATATAAAGCAAAGCAAAGTAA
1 AAAGCAATATAAAGCAAAGCAAAGTAA
25771436 ACCAAAGCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 28 0.47
40 5 0.08
45 27 0.45
ACGTcount: A:0.64, C:0.09, G:0.14, T:0.14
Consensus pattern (40 bp):
AAAGCAATATAAAGCAAAGCAAAGTAATATAAAGCAAAAG
Found at i:25771483 original size:35 final size:36
Alignment explanation
Indices: 25771375--25771513 Score: 121
Period size: 35 Copynumber: 4.0 Consensus size: 36
25771365 AAAATAAAGC
* * *
25771375 AATATAAAGCAAATCAAAGTAATATAAAGCAAAGAAAGT
1 AATATAAAGCAAACCAAAGAAATATAAAGC--A-AAACT
* * *
25771414 AATATAAAGCAAAGCAAAG-----TAAACCAAAGC-
1 AATATAAAGCAAACCAAAGAAATATAAAGCAAAACT
* *
25771444 AATATAAAGCAAACCAAAGCAGTATAAAG-AAAACT
1 AATATAAAGCAAACCAAAGAAATATAAAGCAAAACT
*
25771479 AATATAAAGCAAAGCAAAGAAATATAAAGCAAAAC
1 AATATAAAGCAAACCAAAGAAATATAAAGCAAAAC
25771514 AAAGCAAAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
30 18 0.22
31 2 0.02
32 1 0.01
34 9 0.11
35 30 0.36
36 5 0.06
39 18 0.22
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (36 bp):
AATATAAAGCAAACCAAAGAAATATAAAGCAAAACT
Found at i:25772624 original size:15 final size:15
Alignment explanation
Indices: 25772603--25772646 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
25772593 CGAAGCAAAG
25772603 CAAAGCAAAGTAATAT
1 CAAAGCAAAGTAA-AT
25772619 -AAAGCAATA-TAAAT
1 CAAAGCAA-AGTAAAT
25772633 CAAAGCAAAGTAAA
1 CAAAGCAAAGTAAA
25772647 GTAATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 21 0.84
16 1 0.04
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.16
Consensus pattern (15 bp):
CAAAGCAAAGTAAAT
Found at i:25772636 original size:25 final size:25
Alignment explanation
Indices: 25772618--25772729 Score: 80
Period size: 25 Copynumber: 4.3 Consensus size: 25
25772608 CAAAGTAATA
*
25772618 TAAAGCAATATAAATCAAAGCAAAG
1 TAAAGCAATATAAACCAAAGCAAAG
* *
25772643 TAAAGTAATATAAACCAAACCAAACCAAAG
1 TAAAGCAATAT-----AAACCAAAGCAAAG
* * *
25772673 CAAGGCAATATAAAGCAAAGCAAAG
1 TAAAGCAATATAAACCAAAGCAAAG
* * ** *
25772698 CAAAGTAATATAAAGAAAAGAAAAG
1 TAAAGCAATATAAACCAAAGCAAAG
25772723 TAAAGCA
1 TAAAGCA
25772730 GTGCAAAATA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
25 48 0.71
30 20 0.29
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.12
Consensus pattern (25 bp):
TAAAGCAATATAAACCAAAGCAAAG
Found at i:25772672 original size:30 final size:30
Alignment explanation
Indices: 25772633--25772705 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
25772623 CAATATAAAT
*
25772633 CAAAGCAAAGTAAAGTAATATAAACCAAAC
1 CAAAGCAAAGTAAAGCAATATAAACCAAAC
* * * * *
25772663 CAAACCAAAGCAAGGCAATATAAAGCAAAG
1 CAAAGCAAAGTAAAGCAATATAAACCAAAC
25772693 CAAAGCAAAGTAA
1 CAAAGCAAAGTAA
25772706 TATAAAGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.59, C:0.18, G:0.14, T:0.10
Consensus pattern (30 bp):
CAAAGCAAAGTAAAGCAATATAAACCAAAC
Found at i:25772728 original size:55 final size:54
Alignment explanation
Indices: 25772622--25772805 Score: 171
Period size: 55 Copynumber: 3.4 Consensus size: 54
25772612 GTAATATAAA
* * ** *
25772622 GCAATATAAATCAAAGCAAAGTAAAGTAATATAAACCAAACCAAACCAAAGCAAG
1 GCAATATAAA-CAAAGCAAAGCAAAGTAATATAAAGCAAAGAAAAGCAAAGCAAG
* *
25772677 GCAATATAAAGCAAAGCAAAGCAAAGTAATATAAAGAAAAGAAAAGTAAAGC-AG
1 GCAATATAAA-CAAAGCAAAGCAAAGTAATATAAAGCAAAGAAAAGCAAAGCAAG
* * * * * *
25772731 TGCAA-A-ATA-ATA-TAAAGCAAAGTAATATAAAGCAATGTAAAGCAAAGCAAA
1 -GCAATATAAACAAAGCAAAGCAAAGTAATATAAAGCAAAGAAAAGCAAAGCAAG
*
25772782 GCAATATAAAACAAGGCAAAGCAA
1 GCAATAT-AAACAAAGCAAAGCAA
25772806 TGCAAAGAAA
Statistics
Matches: 102, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
50 35 0.34
51 4 0.04
53 4 0.04
54 4 0.04
55 55 0.54
ACGTcount: A:0.59, C:0.13, G:0.15, T:0.13
Consensus pattern (54 bp):
GCAATATAAACAAAGCAAAGCAAAGTAATATAAAGCAAAGAAAAGCAAAGCAAG
Found at i:25772756 original size:15 final size:15
Alignment explanation
Indices: 25772732--25772791 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
25772722 GTAAAGCAGT
*
25772732 GCAAAATAATATAAA
1 GCAAAGTAATATAAA
25772747 GCAAAGTAATATAAA
1 GCAAAGTAATATAAA
* *
25772762 GCAATGTAA-AGCAAA
1 GCAAAGTAATA-TAAA
*
25772777 GCAAAGCAATATAAA
1 GCAAAGTAATATAAA
25772792 ACAAGGCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (15 bp):
GCAAAGTAATATAAA
Found at i:25772771 original size:25 final size:25
Alignment explanation
Indices: 25772669--25772780 Score: 91
Period size: 25 Copynumber: 4.5 Consensus size: 25
25772659 AAACCAAACC
* *
25772669 AAAGCAAGGCAATATAAAGCAAAGC
1 AAAGCAAAGCAATATAAAGCAAAGT
* * *
25772694 AAAGCAAAGTAATATAAAGAAAAGA
1 AAAGCAAAGCAATATAAAGCAAAGT
* * ** **
25772719 AAAGTAAAGCAGTGCAAAATAATA-T
1 AAAGCAAAGCAATATAAAGCAA-AGT
* *
25772744 AAAGCAAAGTAATATAAAGCAATGT
1 AAAGCAAAGCAATATAAAGCAAAGT
25772769 AAAGCAAAGCAA
1 AAAGCAAAGCAA
25772781 AGCAATATAA
Statistics
Matches: 64, Mismatches: 21, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
25 63 0.98
26 1 0.02
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.13
Consensus pattern (25 bp):
AAAGCAAAGCAATATAAAGCAAAGT
Found at i:25772778 original size:30 final size:30
Alignment explanation
Indices: 25772744--25772838 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
25772734 AAAATAATAT
* *
25772744 AAAGCAAAGTAATATAAAGCAATGTAAAGC
1 AAAGCAAAGAAATATAAAACAATGTAAAGC
* * *
25772774 AAAGCAAAGCAATATAAAACAAGGCAAAGC
1 AAAGCAAAGAAATATAAAACAATGTAAAGC
* * * *
25772804 AATGCAAAGAAACATAAATCAATATAAAGC
1 AAAGCAAAGAAATATAAAACAATGTAAAGC
25772834 AAAGC
1 AAAGC
25772839 TTCTTTGATA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.59, C:0.14, G:0.15, T:0.13
Consensus pattern (30 bp):
AAAGCAAAGAAATATAAAACAATGTAAAGC
Found at i:25772782 original size:20 final size:20
Alignment explanation
Indices: 25772759--25772838 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
25772749 AAAGTAATAT
*
25772759 AAAGCAATGTAAAGCAAAGC
1 AAAGCAATATAAAGCAAAGC
* *
25772779 AAAGCAATATAAAACAAGGC
1 AAAGCAATATAAAGCAAAGC
**
25772799 AAAGCAATGCAAAG-AAA-C
1 AAAGCAATATAAAGCAAAGC
*
25772817 ATAAATCAATATAAAGCAAAGC
1 --AAAGCAATATAAAGCAAAGC
25772839 TTCTTTGATA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 39 0.85
21 3 0.07
22 1 0.02
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAGCAATATAAAGCAAAGC
Found at i:25772783 original size:35 final size:35
Alignment explanation
Indices: 25772595--25772812 Score: 123
Period size: 35 Copynumber: 6.4 Consensus size: 35
25772585 TACAACGACG
**
25772595 AAGCAAAGCAAAGCAAAGTAATATAAAGCAATATA
1 AAGCAAAGCAAAGCAAAGTAATATAAAGCAATGCA
* * * **
25772630 AATCAAAGCAAAGTAAAGTAATATAAACCAAACCA
1 AAGCAAAGCAAAGCAAAGTAATATAAAGCAATGCA
* * * *
25772665 AACCAAAGCAAGGCAATA-TAA-AGCAAAGCAAAGCA
1 AAGCAAAGCAAAGCAA-AGTAATA-TAAAGCAATGCA
* * * * *
25772700 AAGTAATA-TAAAGAAAAG-AAAAGTAAAGCAGTGCA
1 AAGCAA-AGCAAAGCAAAGTAATA-TAAAGCAATGCA
** * *
25772735 AAATAATA-TAAAGCAAAGTAATATAAAGCAATGTA
1 AAGCAA-AGCAAAGCAAAGTAATATAAAGCAATGCA
*
25772770 AAGCAAAGCAAAGC-AA-T-ATA-AAA-CAAGGCA
1 AAGCAAAGCAAAGCAAAGTAATATAAAGCAATGCA
*
25772800 AAGCAATGCAAAG
1 AAGCAAAGCAAAG
25772813 AAACATAAAT
Statistics
Matches: 145, Mismatches: 31, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
30 17 0.12
31 3 0.02
32 3 0.02
33 1 0.01
34 7 0.05
35 109 0.75
36 5 0.03
ACGTcount: A:0.59, C:0.13, G:0.15, T:0.13
Consensus pattern (35 bp):
AAGCAAAGCAAAGCAAAGTAATATAAAGCAATGCA
Found at i:25773250 original size:15 final size:15
Alignment explanation
Indices: 25773230--25773530 Score: 185
Period size: 15 Copynumber: 19.7 Consensus size: 15
25773220 TACAACGATG
25773230 AAGCAAAGCAATATA
1 AAGCAAAGCAATATA
*
25773245 AAGCAAAGTAATATA
1 AAGCAAAGCAATATA
*
25773260 AAGCAAAGCAA-AGCA
1 AAGCAAAGCAATA-TA
25773275 AAGCAAAAG-AATATA
1 AAGC-AAAGCAATATA
* *
25773290 AAGCAAAACAA-AGGA
1 AAGCAAAGCAATA-TA
*
25773305 AAGCAATAG-AA-AGCA
1 AAGCAA-AGCAATA-TA
25773320 AAGCAAAGCAATAT-
1 AAGCAAAGCAATATA
* *
25773334 AAGCAAAACAA-AGCA
1 AAGCAAAGCAATA-TA
* *
25773349 AAGCAAAAGTAGTATAAAGCA
1 AAGC-AAAGCA--AT--A-TA
25773370 AAGCAAAGCAATATA
1 AAGCAAAGCAATATA
25773385 AAGCAACACAAAGCAATATA
1 AAG-----CAAAGCAATATA
*
25773405 AAGCAAAGTAATATA
1 AAGCAAAGCAATATA
*
25773420 TAGCAAAGCAATATA
1 AAGCAAAGCAATATA
* *
25773435 AAGAAAAGTAATATA
1 AAGCAAAGCAATATA
* * *
25773450 AAGGAAAACAATACA
1 AAGCAAAGCAATATA
* *
25773465 AAGCAAAGCAAAACA
1 AAGCAAAGCAATATA
25773480 AAGCAAAGCAATATA
1 AAGCAAAGCAATATA
*
25773495 AAGTAAAGC-----A
1 AAGCAAAGCAATATA
*
25773505 AAGCAAAGTAATATA
1 AAGCAAAGCAATATA
25773520 AAGCAAAGCAA
1 AAGCAAAGCAA
25773531 AGATAAGTAA
Statistics
Matches: 226, Mismatches: 34, Indels: 52
0.72 0.11 0.17
Matches are distributed among these distances:
10 8 0.04
13 1 0.00
14 17 0.08
15 157 0.69
16 12 0.05
18 3 0.01
20 20 0.09
21 8 0.04
ACGTcount: A:0.61, C:0.13, G:0.15, T:0.11
Consensus pattern (15 bp):
AAGCAAAGCAATATA
Found at i:25773267 original size:5 final size:5
Alignment explanation
Indices: 25773259--25773532 Score: 92
Period size: 5 Copynumber: 54.8 Consensus size: 5
25773249 AAAGTAATAT
* * *
25773259 AAAGC AAAGC AAAGC AAAGC AAAAG- AATA-T AAAGC AAAAC AAAGG AAAGC
1 AAAGC AAAGC AAAGC AAAGC -AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC
* * *
25773309 AATAG- AAAGC AAAGC AAAGC AATA-- TAAGC AAAAC AAAGC AAAGC AAAAGT
1 AA-AGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC -AAAGC
* * * *
25773359 AGTA-T AAAGC AAAGC AAAGC AATA-T AAAGC AACA-C AAAGC AATA-T
1 A-AAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AA-AGC AAAGC AA-AGC
* * * * * * *
25773404 AAAGC AAAGT AATA-T ATAGC AAAGC AATA-T AAAGA AAAGT AATA-T
1 AAAGC AAAGC AA-AGC AAAGC AAAGC AA-AGC AAAGC AAAGC AA-AGC
* * * * *
25773449 AAAGG AAAAC AATA-C AAAGC AAAGC AAAAC AAAGC AAAGC AATA-T AAAGT
1 AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC
* *
25773499 AAAGC AAAGC AAAGT AATA-T AAAGC AAAGC AAAG
1 AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAG
25773533 ATAAGTAATG
Statistics
Matches: 206, Mismatches: 33, Indels: 60
0.69 0.11 0.20
Matches are distributed among these distances:
3 1 0.00
4 16 0.08
5 168 0.82
6 21 0.10
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (5 bp):
AAAGC
Found at i:25773323 original size:50 final size:49
Alignment explanation
Indices: 25773259--25773400 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 49
25773249 AAAGTAATAT
*
25773259 AAAGCAAAGCAAAGCAAAGCAAAAGAATATAAAGCAAAACAAAGGAAAGCA
1 AAAG-AAAGCAAAGCAAAGC-AAAGAATATAAAGCAAAACAAAGCAAAGCA
*
25773310 ATAGAAAGCAAAGCAAAGC----AATAT-AAGCAAAACAAAGCAAAGCA
1 AAAGAAAGCAAAGCAAAGCAAAGAATATAAAGCAAAACAAAGCAAAGCA
* * *
25773354 AAAG-TAGTATAAAGCAAAGCAAAGCAATATAAAGCAACACAAAGCAA
1 AAAGAAAG--CAAAGCAAAGCAAAG-AATATAAAGCAAAACAAAGCAA
25773401 TATAAAGCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
43 2 0.03
44 22 0.29
45 15 0.19
50 20 0.26
51 18 0.23
ACGTcount: A:0.62, C:0.15, G:0.16, T:0.07
Consensus pattern (49 bp):
AAAGAAAGCAAAGCAAAGCAAAGAATATAAAGCAAAACAAAGCAAAGCA
Found at i:25773427 original size:20 final size:20
Alignment explanation
Indices: 25773343--25773532 Score: 107
Period size: 20 Copynumber: 9.7 Consensus size: 20
25773333 TAAGCAAAAC
*
25773343 AAAGCAAAGCAAAAGTAGTAT
1 AAAGCAAAGC-AAAGTAATAT
*
25773364 AAAGCAAAGCAAAGCAATAT
1 AAAGCAAAGCAAAGTAATAT
*
25773384 AAAGCAACA-CAAAGCAATAT
1 AAAGCAA-AGCAAAGTAATAT
25773404 -----AAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
* *
25773419 ATAGCAAAGCAATA-TAA-AGA
1 AAAGCAAAGCAA-AGTAATA-T
* * * * *
25773439 AAAGTAATA-TAAAGGAAAAC
1 AAAGCAA-AGCAAAGTAATAT
* * *
25773459 AATA-CAAAGCAAAGCAAAAC
1 AA-AGCAAAGCAAAGTAATAT
25773479 AAAGCAAAGCAATA-TAA-AGT
1 AAAGCAAAGCAA-AGTAATA-T
25773499 AAAGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
25773519 AAAGCAAAGCAAAG
1 AAAGCAAAGCAAAG
25773533 ATAAGTAATG
Statistics
Matches: 136, Mismatches: 14, Indels: 39
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.01
15 12 0.09
19 6 0.04
20 100 0.74
21 17 0.12
ACGTcount: A:0.61, C:0.12, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAGCAAAGCAAAGTAATAT
Found at i:25773541 original size:25 final size:25
Alignment explanation
Indices: 25773244--25773380 Score: 118
Period size: 25 Copynumber: 5.3 Consensus size: 25
25773234 AAAGCAATAT
25773244 AAAGCAAAGTAATATAAAGCAAAGC
1 AAAGCAAAGTAATATAAAGCAAAGC
* *
25773269 AAAGCAAAGCAAAAGAATATAAAGCAAAAC
1 AAAGCAAAG-----TAATATAAAGCAAAGC
* * *
25773299 AAAGGAAAGCAATAGAAAGCAAAGC
1 AAAGCAAAGTAATATAAAGCAAAGC
*
25773324 AAAGCAATA-TAAGCA-AAA-CAAAGC
1 AAAGCAA-AGTAA-TATAAAGCAAAGC
*
25773348 AAAGCAAAAGTAGTATAAAGCAAAGC
1 AAAGC-AAAGTAATATAAAGCAAAGC
25773374 AAAGCAA
1 AAAGCAA
25773381 TATAAAGCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
24 13 0.14
25 42 0.47
26 13 0.14
30 22 0.24
ACGTcount: A:0.62, C:0.13, G:0.17, T:0.08
Consensus pattern (25 bp):
AAAGCAAAGTAATATAAAGCAAAGC
Found at i:25773545 original size:20 final size:20
Alignment explanation
Indices: 25773479--25773545 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
25773469 AAAGCAAAAC
*
25773479 AAAGCAAAGC-AATATAAAGT
1 AAAGCAAAGCAAAGAT-AAGT
*
25773499 AAAGCAAAGCAAAG-TAATAT
1 AAAGCAAAGCAAAGATAA-GT
25773519 AAAGCAAAGCAAAGATAAGT
1 AAAGCAAAGCAAAGATAAGT
*
25773539 AATGCAA
1 AAAGCAA
25773546 TGCTAGTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 33 0.82
21 5 0.12
ACGTcount: A:0.60, C:0.10, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAGCAAAGCAAAGATAAGT
Found at i:25773632 original size:16 final size:16
Alignment explanation
Indices: 25773611--25773641 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25773601 AAATAAAAAA
25773611 TCAAGATATCATAAAT
1 TCAAGATATCATAAAT
*
25773627 TCAAGATATGATAAA
1 TCAAGATATCATAAA
25773642 ACTTAATAAA
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:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (16 bp):
TCAAGATATCATAAAT
Found at i:25779369 original size:3 final size:3
Alignment explanation
Indices: 25779361--25779386 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25779351 ACAATTCAAA
25779361 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
25779387 AGAAAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.