Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 19 of 221
Found at i:5492442 original size:21 final size:21
Alignment explanation
Indices: 5492418--5492462 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5492408 TGAATTTTTA
* *
5492418 TTTCTTTAC-ATTTTTTATAAT
1 TTTC-TTACAATTTTATAAAAT
5492439 TTTCTTACAATTTTATAAAAT
1 TTTCTTACAATTTTATAAAAT
5492460 TTT
1 TTT
5492463 ACCATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTCTTACAATTTTATAAAAT
Found at i:5492508 original size:20 final size:19
Alignment explanation
Indices: 5492466--5492511 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
5492456 AAATTTTACC
** *
5492466 ATTTTTATAATTGTTTTTG
1 ATTTTTATAATTGTTAATA
5492485 ATTTTTATAATTTGTTAATA
1 ATTTTTATAA-TTGTTAATA
5492505 ATTTTTA
1 ATTTTTA
5492512 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
ATTTTTATAATTGTTAATA
Found at i:5492527 original size:8 final size:9
Alignment explanation
Indices: 5492387--5492558 Score: 75
Period size: 9 Copynumber: 18.2 Consensus size: 9
5492377 TTTTGATACG
5492387 ATAATTTTT
1 ATAATTTTT
*
5492396 ATATTTTTTT
1 ATA-ATTTTT
5492406 AATGAATTTTT
1 -AT-AATTTTT
5492417 AT--TTCTTT
1 ATAATT-TTT
* *
5492425 ACATTTTTT
1 ATAATTTTT
5492434 ATAATTTTCT
1 ATAATTTT-T
*
5492444 -TACAATTTT
1 ATA-ATTTTT
*
5492453 ATAAAATTTT
1 AT-AATTTTT
**
5492463 ACCATTTTT
1 ATAATTTTT
5492472 ATAATTGTTT
1 ATAATT-TTT
* *
5492482 TTGATTTTT
1 ATAATTTTT
5492491 ATAATTTGTT
1 ATAATTT-TT
5492501 AATAATTTTT
1 -ATAATTTTT
5492511 A-ATATTTTT
1 ATA-ATTTTT
5492520 AT-ATTTTT
1 ATAATTTTT
* *
5492528 ATTAAAATTTA
1 A-T-AATTTTT
*
5492539 ATAATGTTT
1 ATAATTTTT
*
5492548 ATAACTTTT
1 ATAATTTTT
5492557 AT
1 AT
5492559 TGATTTTTGT
Statistics
Matches: 123, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
7 2 0.02
8 12 0.10
9 54 0.44
10 34 0.28
11 20 0.16
12 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5492867 original size:87 final size:89
Alignment explanation
Indices: 5492737--5492907 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 89
5492727 TATAAAAAAA
* * *
5492737 GGTTTAATTGCTTTTTTCTGAAAAGTTTGAGGGCTTTTTTGATGTATTTTGA-AAGTTTAAATA-
1 GGTTTAATTGCTTTTTTCTGAAAAGTTTGAGAGCTTTTTTGATGCATTTTGACAA-TTCAAATAC
5492800 CTCAATTGAATGCAAAAAAAAGCAGG
65 CT-AATTGAATGCAAAAAAAAGCAGG
** *
5492826 GGTTTAATTGCTTTTTT-T-TTAAGTTTGAGAGTTTTTTTGATGCATTTTGACAATTCAAATACC
1 GGTTTAATTGCTTTTTTCTGAAAAGTTTGAGAGCTTTTTTGATGCATTTTGACAATTCAAATACC
*
5492889 TAATTGAGTGCAAAAAAAA
66 TAATTGAATGCAAAAAAAA
5492908 AAGAGAGCAG
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 51 0.70
88 5 0.07
89 17 0.23
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (89 bp):
GGTTTAATTGCTTTTTTCTGAAAAGTTTGAGAGCTTTTTTGATGCATTTTGACAATTCAAATACC
TAATTGAATGCAAAAAAAAGCAGG
Found at i:5496116 original size:21 final size:21
Alignment explanation
Indices: 5496091--5496136 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5496081 AGTTTACAAA
5496091 AAAAAATTTAAAATAATTTTC
1 AAAAAATTTAAAATAATTTTC
* * *
5496112 AAAAAGTTTTAAATAATTTTT
1 AAAAAATTTAAAATAATTTTC
5496133 AAAA
1 AAAA
5496137 TTCAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAAATTTAAAATAATTTTC
Found at i:5496890 original size:16 final size:17
Alignment explanation
Indices: 5496860--5496897 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
5496850 TTTATGAAAA
5496860 TATAAAAATCAATTTTT
1 TATAAAAATCAATTTTT
5496877 TATAAAAATC-ATTTTT
1 TATAAAAATCAATTTTT
5496893 TATAA
1 TATAA
5496898 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAAAAATCAATTTTT
Found at i:5499058 original size:29 final size:29
Alignment explanation
Indices: 5499012--5499076 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
5499002 ACAACACTTT
* *
5499012 AACATAAGTGACTAAAATGTAACAATTCA
1 AACATAAATGACTAAAATATAACAATTCA
* * * *
5499041 AACATAAATGGCTGAAATATAATAATTGA
1 AACATAAATGACTAAAATATAACAATTCA
*
5499070 AATATAA
1 AACATAA
5499077 GTAACTATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (29 bp):
AACATAAATGACTAAAATATAACAATTCA
Found at i:5500601 original size:20 final size:20
Alignment explanation
Indices: 5500576--5500613 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5500566 GTTAACATGC
5500576 ATAATG-AAATAATAAATACG
1 ATAATGTAAATAA-AAATACG
5500596 ATAATGTAAATAAAAATA
1 ATAATGTAAATAAAAATA
5500614 ATACGAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATAATGTAAATAAAAATACG
Found at i:5503432 original size:26 final size:26
Alignment explanation
Indices: 5503403--5503461 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
5503393 TACCCTTACC
*
5503403 AAAATTTTGATGATTTTGCCACTGGT
1 AAAATTTTAATGATTTTGCCACTGGT
*
5503429 AAAATTTTAATGATTTTGCCCCTGGT
1 AAAATTTTAATGATTTTGCCACTGGT
5503455 AAAATTT
1 AAAATTT
5503462 CGAGAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (26 bp):
AAAATTTTAATGATTTTGCCACTGGT
Found at i:5504660 original size:19 final size:19
Alignment explanation
Indices: 5504636--5504674 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5504626 TTTGTACTAC
5504636 GATCTGACCACGTAATACT
1 GATCTGACCACGTAATACT
5504655 GATCTGACCACGTAATACT
1 GATCTGACCACGTAATACT
5504674 G
1 G
5504675 CTTAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (19 bp):
GATCTGACCACGTAATACT
Found at i:5505462 original size:20 final size:18
Alignment explanation
Indices: 5505412--5505521 Score: 66
Period size: 19 Copynumber: 5.9 Consensus size: 18
5505402 TTATAGGATA
5505412 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
5505429 AATATTAAGA-TAATTACTTT
1 AATATTAA-ATTAA-TA-TTT
**
5505449 AATATTAAATTAATAAAAT
1 AATATTAAATTAAT-ATTT
* *
5505468 ACTATTAAGA-TAAGTATTA
1 AATATTAA-ATTAA-TATTT
* *
5505487 AAT-TTAATTTAATATTA
1 AATATTAAATTAATATTT
*
5505504 AACTATTAAAATAATATT
1 AA-TATTAAATTAATATT
5505522 ATTTTTGGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
17 18 0.25
18 9 0.12
19 28 0.39
20 17 0.24
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:5505509 original size:37 final size:37
Alignment explanation
Indices: 5505410--5505522 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 37
5505400 ATTTATAGGA
*
5505410 TAAATATTAAATTAA-ATTTAA-TATTAAGATAATTACT
1 TAAATATTAAATTAATATTAAACTATTAAGATAA-TA-T
* *
5505447 TTAATATTAAATTAATA-AAATACTATTAAGATAAGTAT
1 TAAATATTAAATTAATATTAA-ACTATTAAGATAA-TAT
* *
5505485 TAAAT-TTAATTTAATATTAAACTATTAAAATAATAT
1 TAAATATTAAATTAATATTAAACTATTAAGATAATAT
5505521 TA
1 TA
5505523 TTTTTGGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
36 5 0.08
37 37 0.58
38 9 0.14
39 13 0.20
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (37 bp):
TAAATATTAAATTAATATTAAACTATTAAGATAATAT
Found at i:5510473 original size:20 final size:20
Alignment explanation
Indices: 5510448--5510495 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5510438 TCATTTCCAA
5510448 GTGTTT-ATAACTTGGGTTTT
1 GTGTTTAATAA-TTGGGTTTT
*
5510468 GTGTTTAATTATTGGGTTTT
1 GTGTTTAATAATTGGGTTTT
5510488 -T-TTTAATA
1 GTGTTTAATA
5510496 GGATGTTCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 6 0.24
19 1 0.04
20 15 0.60
21 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (20 bp):
GTGTTTAATAATTGGGTTTT
Found at i:5529861 original size:5 final size:5
Alignment explanation
Indices: 5529851--5529881 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5529841 TTCCATCTTT
*
5529851 TTTAA TTTAA TTTAA TTTAA TTTAA CTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
5529882 GGATTTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TTTAA
Found at i:5531635 original size:17 final size:19
Alignment explanation
Indices: 5531609--5531652 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
5531599 AAAGTTTTTG
5531609 AAAA-AAATTATTT-TAT-
1 AAAATAAATTATTTATATA
5531625 AAAATAAATTATTTATATA
1 AAAATAAATTATTTATATA
5531644 AAAATAAAT
1 AAAATAAAT
5531653 GAATCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.16
17 9 0.36
18 3 0.12
19 9 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAAATTATTTATATA
Found at i:5540190 original size:20 final size:20
Alignment explanation
Indices: 5540162--5540200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5540152 TGTTGTATTG
* *
5540162 GATTTGAAAACGATTAATTC
1 GATTCGAAAACGAGTAATTC
*
5540182 GATTCGAAATCGAGTAATT
1 GATTCGAAAACGAGTAATT
5540201 AAATAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
GATTCGAAAACGAGTAATTC
Found at i:5540550 original size:13 final size:13
Alignment explanation
Indices: 5540532--5540557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5540522 TAAATGGGTG
5540532 GTCAAAAGTCAAA
1 GTCAAAAGTCAAA
5540545 GTCAAAAGTCAAA
1 GTCAAAAGTCAAA
5540558 TGATTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
GTCAAAAGTCAAA
Found at i:5547277 original size:125 final size:123
Alignment explanation
Indices: 5547044--5547295 Score: 423
Period size: 125 Copynumber: 2.0 Consensus size: 123
5547034 AAATCCTTGT
* *
5547044 AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGTATTTATCAATTCAT
1 AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGAATTTATCAAATCAT
*
5547109 AGCCATGCTTTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAATCATCA
66 AGCCATGCTTTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCA
* *
5547167 AACTCGTTCATAGACAACTGTTTTCAACTATCTGATCATGGTTTTAGCTTCGAATTTATTAAATC
1 AACTCGTTCAT--ACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGAATTTATCAAATC
* *
5547232 ATATCCATGCTTTCATAGACAACATTGTTAGGAATTAGTATGATGAGAATGAAACCATCA
64 ATAGCCATGCTTTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCA
5547292 AACT
1 AACT
5547296 AGGACCTGGT
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
123 11 0.09
125 109 0.91
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (123 bp):
AACTCGTTCATACAACTGTTTTCAACTATCTGATCATGGTTTTAACTTCGAATTTATCAAATCAT
AGCCATGCTTTCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCA
Found at i:5550673 original size:37 final size:37
Alignment explanation
Indices: 5550626--5550696 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
5550616 AGTATTACTT
*
5550626 AATATTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
5550663 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
5550697 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:5550701 original size:19 final size:19
Alignment explanation
Indices: 5550632--5550700 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
5550622 ACTTAATATT
5550632 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
5550651 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
5550669 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
5550688 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
5550701 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:5550832 original size:27 final size:27
Alignment explanation
Indices: 5550776--5550861 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
5550766 TTTTTTTTCC
* *
5550776 TTTGGCACCA-TGGAGCCGCCAA-TGA
1 TTTGGCACCATTGGTGCCGCCAATTTA
5550801 CTTTGGCACCATTGGTGCCGCCAATTTA
1 -TTTGGCACCATTGGTGCCGCCAATTTA
*
5550829 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACCATTGGTGCCGCCAATTTA
*
5550856 ATTGGC
1 TTTGGC
5550862 TTGATCAGGC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
26 10 0.19
27 42 0.78
28 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATTTA
Found at i:5550960 original size:27 final size:26
Alignment explanation
Indices: 5550902--5550970 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
5550892 TTTGTTTTTT
*
5550902 TTATATATTTTGGTAAATAAAAAATA
1 TTATATATTTTGGTAAATAAAAAAAA
*
5550928 TATATATTTTTTGGTAAATAAAAAAAA
1 T-TATATATTTTGGTAAATAAAAAAAA
*
5550955 GTTATAACATTTTGGT
1 -TTAT-ATATTTTGGT
5550971 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 26 0.72
28 9 0.25
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.43
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAA
Found at i:5555314 original size:4 final size:4
Alignment explanation
Indices: 5555305--5555338 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
5555295 AAATATCTAT
5555305 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
5555339 ACATACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.47, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:5559327 original size:27 final size:27
Alignment explanation
Indices: 5559272--5559335 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
5559262 AAAATATTAT
5559272 AATTAAATTATAAAATTTTAAATGGTTA
1 AATT-AATTATAAAATTTTAAATGGTTA
**
5559300 AATTAATT-TAAAATTTTACAATTTTTA
1 AATTAATTATAAAATTTTA-AATGGTTA
*
5559327 AAATAATTA
1 AATTAATTA
5559336 AATTATAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 10 0.32
27 17 0.55
28 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
AATTAATTATAAAATTTTAAATGGTTA
Found at i:5560589 original size:18 final size:19
Alignment explanation
Indices: 5560568--5560603 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5560558 AACTTAAACT
*
5560568 TTAAATTGA-ATATTAAAA
1 TTAAATTCATATATTAAAA
5560586 TTAAATTCATATATTAAA
1 TTAAATTCATATATTAAA
5560604 TGATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAAATTCATATATTAAAA
Found at i:5564685 original size:15 final size:16
Alignment explanation
Indices: 5564661--5564709 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
5564651 AGTTTAGAAT
5564661 AATAAGTATAACTATA
1 AATAAGTATAACTATA
*
5564677 AATAA-TATATGCTAT-
1 AATAAGTATA-ACTATA
*
5564692 AATAATTATAACTA-A
1 AATAAGTATAACTATA
5564707 AAT
1 AAT
5564710 TAGATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (16 bp):
AATAAGTATAACTATA
Found at i:5566348 original size:27 final size:27
Alignment explanation
Indices: 5566299--5566397 Score: 77
Period size: 27 Copynumber: 3.9 Consensus size: 27
5566289 TATAATACAT
* ** *
5566299 ATACATTTTTTTTCCATTTTATAATTC
1 ATACATTTTCTTTATATTATATAATTC
5566326 ATACATTTTCTTTATATTATAT-A--C
1 ATACATTTTCTTTATATTATATAATTC
**
5566350 ATACAGATTTTC-ACATA-TATA-AATT-
1 ATAC--ATTTTCTTTATATTATATAATTC
5566375 ATACATTTTCTTTATATTATATA
1 ATACATTTTCTTTATATTATATA
5566398 CATACAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
23 6 0.11
24 13 0.23
25 11 0.20
26 8 0.14
27 18 0.32
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (27 bp):
ATACATTTTCTTTATATTATATAATTC
Found at i:5566352 original size:24 final size:24
Alignment explanation
Indices: 5566325--5566403 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
5566315 TTTTATAATT
5566325 CATACATTTTCTTTATATTATATA
1 CATACATTTTCTTTATATTATATA
** *
5566349 CATACAGATTTTC-ACATA-TATAAA
1 CATAC--ATTTTCTTTATATTATATA
*
5566373 TTATACATTTTCTTTATATTATATA
1 -CATACATTTTCTTTATATTATATA
5566398 CATACA
1 CATACA
5566404 AATTTTCACA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
23 6 0.14
24 18 0.43
25 12 0.29
26 6 0.14
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (24 bp):
CATACATTTTCTTTATATTATATA
Found at i:5566361 original size:49 final size:49
Alignment explanation
Indices: 5566321--5566419 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
5566311 TCCATTTTAT
*
5566321 AATTCATACATTTTCTTTATATTATATACATACAGATTTTCACATATATA
1 AATT-ATACATTTTCTTTATATTATATACATACAAATTTTCACATATATA
5566371 AATTATACATTTTCTTTATATTATATACATACAAATTTTCACATATATA
1 AATTATACATTTTCTTTATATTATATACATACAAATTTTCACATATATA
5566420 TATTTTCCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 44 0.92
50 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.46
Consensus pattern (49 bp):
AATTATACATTTTCTTTATATTATATACATACAAATTTTCACATATATA
Found at i:5566453 original size:13 final size:12
Alignment explanation
Indices: 5566435--5566464 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5566425 TCCCATAGTT
5566435 TATTTATATATTA
1 TATTTATATA-TA
5566448 TATTTATATATA
1 TATTTATATATA
5566460 TATTT
1 TATTT
5566465 TGTTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATATATA
Found at i:5569449 original size:6 final size:6
Alignment explanation
Indices: 5569440--5569472 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5569430 AGAAGTTAGG
5569440 AAATAA AAATAA AAAT-A AAAT-A AAATAA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA
5569473 TATGTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:5569466 original size:16 final size:17
Alignment explanation
Indices: 5569440--5569472 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5569430 AGAAGTTAGG
5569440 AAATAAAAATAAAAATA
1 AAATAAAAATAAAAATA
5569457 AAAT-AAAATAAAAATA
1 AAATAAAAATAAAAATA
5569473 TATGTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAAATAAAAATA
Found at i:5570834 original size:19 final size:20
Alignment explanation
Indices: 5570794--5570834 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5570784 AAGTTTGAAA
5570794 TTTAAAAATCTAGTGAATTT
1 TTTAAAAATCTAGTGAATTT
5570814 TTTAAAAATCTAGTGAATTT
1 TTTAAAAATCTAGTGAATTT
5570834 T
1 T
5570835 ATTTTTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTAAAAATCTAGTGAATTT
Found at i:5573801 original size:9 final size:9
Alignment explanation
Indices: 5573787--5573823 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5573777 TATAGTTTGA
5573787 TATTCGAAT
1 TATTCGAAT
5573796 TATTCGAAT
1 TATTCGAAT
*
5573805 TATTCGAGT
1 TATTCGAAT
5573814 TATTCGAAT
1 TATTCGAAT
5573823 T
1 T
5573824 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5577548 original size:921 final size:921
Alignment explanation
Indices: 5575762--5577610 Score: 3644
Period size: 921 Copynumber: 2.0 Consensus size: 921
5575752 TTTAAAAAAT
5575762 ATAACTACTAAGAATTATCTAATTAGAAAATATGGACTAAATCTATAACTTTACTGATAATACAG
1 ATAA-TACTAAGAATTATCTAATTAGAAAATATGGACTAAATCTATAACTTTACTGATAATACAG
5575827 AATTAATAGCATAATTAACCAAACATATTTAATTGTAACCATTTGGTCTAAGACTAAAATTTTGA
65 AATTAATAGCATAATTAACCAAACATATTTAATTGTAACCATTTGGTCTAAGACTAAAATTTTGA
5575892 AATATGAAAAGTACAAGAGCTGAAATTGATTAAATTAAAGTACAATTACTAAATCTACAACTTAC
130 AATATGAAAAGTACAAGAGCTGAAATTGATTAAATTAAAGTACAATTACTAAATCTACAACTTAC
5575957 ATAAAGTACAAGGTTTAATAGCAAAATTTACTAATAAATAAATCCAATAGCCTCAAATGGGCCAA
195 ATAAAGTACAAGGTTTAATAGCAAAATTTACTAATAAATAAATCCAATAGCCTCAAATGGGCCAA
5576022 AGAAGCCTGCACCGACCATCATTGAACTTTGACTAGTCGTGAAGCAACGACAGAAGAAGGTACGC
260 AGAAGCCTGCACCGACCATCATTGAACTTTGACTAGTCGTGAAGCAACGACAGAAGAAGGTACGC
5576087 GACGAATCCCTAGATCTGTTAAGCTCCGACTAGTGATGAACCAATGTAGCAGGGGCACCAACCAA
325 GACGAATCCCTAGATCTGTTAAGCTCCGACTAGTGATGAACCAATGTAGCAGGGGCACCAACCAA
5576152 CCAAAGTACTGGGGTTGCCGGTAAGGAAACCAAGGGACTAGCCAACGCTAACCATAGACCCCCAC
390 CCAAAGTACTGGGGTTGCCGGTAAGGAAACCAAGGGACTAGCCAACGCTAACCATAGACCCCCAC
5576217 AAGGCGGTTGGAAATAAAAGCCTCGCAAAATGATGACCAAATGGTTGAAGAAGGGGGCAAAATTC
455 AAGGCGGTTGGAAATAAAAGCCTCGCAAAATGATGACCAAATGGTTGAAGAAGGGGGCAAAATTC
*
5576282 AAACCTTATTCTGCTTTTCAAGGGAATGCGACTCCTTCAGAAGAAGTCTTTGAACTCTTGATAAA
520 AAACCTTATTATGCTTTTCAAGGGAATGCGACTCCTTCAGAAGAAGTCTTTGAACTCTTGATAAA
*
5576347 GGCGGGAACAATACTTTCAGTTGTTGAGAGACAGAATGATTACTTAGTCGATGACACTTCAATAC
585 GGCGGGAACAATACTTTCAGTTGTTGAGAGACAGAATGATTACTTAGTCGACGACACTTCAATAC
5576412 TTCTCTCAAAAGAGTTACCCTCAACAATGCTGAAAGATAAAAGAAATAAAAAAATAAACAATTAA
650 TTCTCTCAAAAGAGTTACCCTCAACAATGCTGAAAGATAAAAGAAATAAAAAAATAAACAATTAA
5576477 ATTGAAAAGAAAAGCCTCTCAAAACGACAACCATAAGGTCAAAGAAGAGAAAGGGGGCGGGATCC
715 ATTGAAAAGAAAAGCCTCTCAAAACGACAACCATAAGGTCAAAGAAGAGAAAGGGGGCGGGATCC
*
5576542 AAATTATATTTATATCGAAAGATGAAAGAAAAGAAACAAAAAACAACTAAACAAAAAAGATATGG
780 AAATTATATTTATATCGAAAGATGAAAGAAAAGAAACAAAAAACAACTAAACAAAAAAGATATAG
5576607 CACTACTTTTATCTTTATAGATGGGTTTTGTGTATAGGAATAATACACGGTAAGTGACTTTCATA
845 CACTACTTTTATCTTTATAGATGGGTTTTGTGTATAGGAATAATACACGGTAAGTGACTTTCATA
5576672 TATAATCAATGA
910 TATAATCAATGA
5576684 ATAATACTAAGAATTATCTAATTAGAAAATATGGACTAAATCTATAACTTTACTGATAATACAGA
1 ATAATACTAAGAATTATCTAATTAGAAAATATGGACTAAATCTATAACTTTACTGATAATACAGA
5576749 ATTAATAGCATAATTAACCAAACATATTTAATTGTAACCATTTGGTCTAAGACTAAAATTTTGAA
66 ATTAATAGCATAATTAACCAAACATATTTAATTGTAACCATTTGGTCTAAGACTAAAATTTTGAA
5576814 ATATGAAAAGTACAAGAGCTGAAATTGATTAAATTAAAGTACAATTACTAAATCTACAACTTACA
131 ATATGAAAAGTACAAGAGCTGAAATTGATTAAATTAAAGTACAATTACTAAATCTACAACTTACA
5576879 TAAAGTACAAGGTTTAATAGCAAAATTTACTAATAAATAAATCCAATAGCCTCAAATGGGCCAAA
196 TAAAGTACAAGGTTTAATAGCAAAATTTACTAATAAATAAATCCAATAGCCTCAAATGGGCCAAA
5576944 GAAGCCTGCACCGACCATCATTGAACTTTGACTAGTCGTGAAGCAACGACAGAAGAAGGTACGCG
261 GAAGCCTGCACCGACCATCATTGAACTTTGACTAGTCGTGAAGCAACGACAGAAGAAGGTACGCG
5577009 ACGAATCCCTAGATCTGTTAAGCTCCGACTAGTGATGAACCAATGTAGCAGGGGCACCAACCAAC
326 ACGAATCCCTAGATCTGTTAAGCTCCGACTAGTGATGAACCAATGTAGCAGGGGCACCAACCAAC
5577074 CAAAGTACTGGGGTTGCCGGTAAGGAAACCAAGGGACTAGCCAACGCTAACCATAGACCCCCACA
391 CAAAGTACTGGGGTTGCCGGTAAGGAAACCAAGGGACTAGCCAACGCTAACCATAGACCCCCACA
5577139 AGGCGGTTGGAAATAAAAGCCTCGCAAAATGATGACCAAATGGTTGAAGAAGGGGGCAAAATTCA
456 AGGCGGTTGGAAATAAAAGCCTCGCAAAATGATGACCAAATGGTTGAAGAAGGGGGCAAAATTCA
*
5577204 AACCTTATTATGCTTTTCAAGGGAATGCGACTCCTTTAGAAGAAGTCTTTGAACTCTTGATAAAG
521 AACCTTATTATGCTTTTCAAGGGAATGCGACTCCTTCAGAAGAAGTCTTTGAACTCTTGATAAAG
5577269 GCGGGAACAATACTTTCAGTTGTTGAGAGACAGAATGATTACTTAGTCGACGACACTTCAATACT
586 GCGGGAACAATACTTTCAGTTGTTGAGAGACAGAATGATTACTTAGTCGACGACACTTCAATACT
5577334 TCTCTCAAAAGAGTTACCCTCAACAATGCTGAAAGATAAAAGAAATAAAAAAATAAACAATTAAA
651 TCTCTCAAAAGAGTTACCCTCAACAATGCTGAAAGATAAAAGAAATAAAAAAATAAACAATTAAA
5577399 TTGAAAAGAAAAGCCTCTCAAAACGACAACCATAAGGTCAAAGAAGAGAAAGGGGGCGGGATCCA
716 TTGAAAAGAAAAGCCTCTCAAAACGACAACCATAAGGTCAAAGAAGAGAAAGGGGGCGGGATCCA
*
5577464 AATTATATTTATATCGAAAGATGAAAGAAGAGAAACAAAAAACAACTAAACAAAAAAGATATAGC
781 AATTATATTTATATCGAAAGATGAAAGAAAAGAAACAAAAAACAACTAAACAAAAAAGATATAGC
5577529 ACTACTTTTATCTTTATAGATGGGTTTTGTGTATAGGAATAATACACGGTAAGTGACTTTCATAT
846 ACTACTTTTATCTTTATAGATGGGTTTTGTGTATAGGAATAATACACGGTAAGTGACTTTCATAT
5577594 ATAATCAATGA
911 ATAATCAATGA
5577605 ATAATA
1 ATAATA
5577611 GCATAACACT
Statistics
Matches: 922, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
921 918 1.00
922 4 0.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (921 bp):
ATAATACTAAGAATTATCTAATTAGAAAATATGGACTAAATCTATAACTTTACTGATAATACAGA
ATTAATAGCATAATTAACCAAACATATTTAATTGTAACCATTTGGTCTAAGACTAAAATTTTGAA
ATATGAAAAGTACAAGAGCTGAAATTGATTAAATTAAAGTACAATTACTAAATCTACAACTTACA
TAAAGTACAAGGTTTAATAGCAAAATTTACTAATAAATAAATCCAATAGCCTCAAATGGGCCAAA
GAAGCCTGCACCGACCATCATTGAACTTTGACTAGTCGTGAAGCAACGACAGAAGAAGGTACGCG
ACGAATCCCTAGATCTGTTAAGCTCCGACTAGTGATGAACCAATGTAGCAGGGGCACCAACCAAC
CAAAGTACTGGGGTTGCCGGTAAGGAAACCAAGGGACTAGCCAACGCTAACCATAGACCCCCACA
AGGCGGTTGGAAATAAAAGCCTCGCAAAATGATGACCAAATGGTTGAAGAAGGGGGCAAAATTCA
AACCTTATTATGCTTTTCAAGGGAATGCGACTCCTTCAGAAGAAGTCTTTGAACTCTTGATAAAG
GCGGGAACAATACTTTCAGTTGTTGAGAGACAGAATGATTACTTAGTCGACGACACTTCAATACT
TCTCTCAAAAGAGTTACCCTCAACAATGCTGAAAGATAAAAGAAATAAAAAAATAAACAATTAAA
TTGAAAAGAAAAGCCTCTCAAAACGACAACCATAAGGTCAAAGAAGAGAAAGGGGGCGGGATCCA
AATTATATTTATATCGAAAGATGAAAGAAAAGAAACAAAAAACAACTAAACAAAAAAGATATAGC
ACTACTTTTATCTTTATAGATGGGTTTTGTGTATAGGAATAATACACGGTAAGTGACTTTCATAT
ATAATCAATGA
Found at i:5584680 original size:17 final size:17
Alignment explanation
Indices: 5584642--5584690 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
5584632 GGGTGAGAAG
5584642 TAAAAGTTTAGGGGAAAA
1 TAAAAGTTTAGGGG-AAA
*
5584660 TAAAAAGTTTTGGGG-AA
1 T-AAAAGTTTAGGGGAAA
5584677 TAAAAGTTTGAGGG
1 TAAAAGTTT-AGGG
5584691 AAAGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 1 0.04
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (17 bp):
TAAAAGTTTAGGGGAAA
Found at i:5585071 original size:9 final size:9
Alignment explanation
Indices: 5585054--5585087 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5585044 AATTTGATAG
5585054 TCGAATTAT
1 TCGAATTAT
*
5585063 TCAAATTAT
1 TCGAATTAT
*
5585072 TCGAGTTAT
1 TCGAATTAT
5585081 TCGAATT
1 TCGAATT
5585088 CGAAAACTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (9 bp):
TCGAATTAT
Found at i:5592057 original size:14 final size:15
Alignment explanation
Indices: 5592038--5592098 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
5592028 AACCCAAATT
5592038 AACCC-ACTAGCCTA
1 AACCCAACTAGCCTA
*
5592052 AACCCAATTAGCCTA
1 AACCCAACTAGCCTA
* *
5592067 AGCCCAAC-ACCCT-
1 AACCCAACTAGCCTA
*
5592080 AGCCCAACTAGCCTA
1 AACCCAACTAGCCTA
5592095 AACC
1 AACC
5592099 AGAAATCAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
13 8 0.21
14 13 0.34
15 17 0.45
ACGTcount: A:0.36, C:0.43, G:0.08, T:0.13
Consensus pattern (15 bp):
AACCCAACTAGCCTA
Found at i:5592424 original size:11 final size:10
Alignment explanation
Indices: 5592408--5592449 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
5592398 ATTTTATAAG
5592408 AAAAAAATAC
1 AAAAAAATAC
*
5592418 AAAAAAATTC
1 AAAAAAATAC
5592428 AAAAAAA-AC
1 AAAAAAATAC
5592437 AAGAAAGAATAC
1 AA-AAA-AATAC
5592449 A
1 A
5592450 TCGTTTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.11
10 19 0.70
11 2 0.07
12 3 0.11
ACGTcount: A:0.76, C:0.10, G:0.05, T:0.10
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:5593202 original size:3 final size:3
Alignment explanation
Indices: 5593194--5593249 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5593184 ATTAAACCTT
5593194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5593242 TTA TTA TT
1 TTA TTA TT
5593250 TTCGTACTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5593575 original size:16 final size:16
Alignment explanation
Indices: 5593556--5593586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5593546 TCATATACAC
*
5593556 ATTCTTTAATATTTTT
1 ATTCTATAATATTTTT
5593572 ATTCTATAATATTTT
1 ATTCTATAATATTTT
5593587 ACTTTAATTT
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:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTCTATAATATTTTT
Found at i:5596224 original size:51 final size:51
Alignment explanation
Indices: 5596164--5596267 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
5596154 ATTTATACTT
5596164 AAATTTCTGGATTCACCCCGTTTCGATGTGTTTGAATGGTTTATGAAATTC
1 AAATTTCTGGATTCACCCCGTTTCGATGTGTTTGAATGGTTTATGAAATTC
5596215 AAATTTCTGGATTCACCCCGTTTCGATGTGTTTGAATGGTTTATGAAATTC
1 AAATTTCTGGATTCACCCCGTTTCGATGTGTTTGAATGGTTTATGAAATTC
5596266 AA
1 AA
5596268 GTTAAAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (51 bp):
AAATTTCTGGATTCACCCCGTTTCGATGTGTTTGAATGGTTTATGAAATTC
Found at i:5598312 original size:19 final size:19
Alignment explanation
Indices: 5598288--5598367 Score: 94
Period size: 18 Copynumber: 4.2 Consensus size: 19
5598278 ACTCTCAACA
5598288 AAAATTACAAAATAATTTT
1 AAAATTACAAAATAATTTT
*
5598307 AAAATTTTCAAAATAATTTTT
1 AAAA-TTACAAAATAA-TTTT
*
5598328 AAAGTT-CAAAATAATTTT
1 AAAATTACAAAATAATTTT
5598346 AAAATTA-AAAAT-ATTTAT
1 AAAATTACAAAATAATTT-T
5598364 AAAA
1 AAAA
5598368 ATTTCAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
17 4 0.07
18 19 0.35
19 12 0.22
20 12 0.22
21 7 0.13
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (19 bp):
AAAATTACAAAATAATTTT
Found at i:5598318 original size:20 final size:20
Alignment explanation
Indices: 5598295--5598351 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
5598285 ACAAAAATTA
5598295 CAAAATAATTTTAAAATTTT
1 CAAAATAATTTTAAAATTTT
* *
5598315 CAAAATAATTTTTAAA-GTT
1 CAAAATAATTTTAAAATTTT
5598334 CAAAATAATTTTAAAATT
1 CAAAATAATTTTAAAATT
5598352 AAAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (20 bp):
CAAAATAATTTTAAAATTTT
Found at i:5601792 original size:3 final size:3
Alignment explanation
Indices: 5601784--5601818 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5601774 ACGCTACCGC
* *
5601784 TGT TGT TGT TAT TTT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
5601819 CCACCTTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
TGT
Found at i:5607486 original size:59 final size:60
Alignment explanation
Indices: 5607371--5607512 Score: 150
Period size: 59 Copynumber: 2.4 Consensus size: 60
5607361 TAGCATTTTT
* *
5607371 TTTTTCC--AATTTGATACCTAAACTTTGTTGGGTCCAATTTGGTATCTAACCTTGACA-C
1 TTTTTCCTTAATTTGATACCTAAACTTTGTTGGGCCCAATTTGGTACCTAA-CTTGACATC
* * * *
5607429 TTTTT-CTTAATTTGATATCTAAACTTTTTTTGGCCCAATTTGGTACCTGAA-TGTGACATT
1 TTTTTCCTTAATTTGATACCTAAACTTTGTTGGGCCCAATTTGGTACCT-AACT-TGACATC
* *
5607489 TTTTTCCTTAATTTGGTACGTAAA
1 TTTTTCCTTAATTTGATACCTAAA
5607513 TTTATTAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 6 0.09
59 40 0.58
60 7 0.10
61 15 0.22
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (60 bp):
TTTTTCCTTAATTTGATACCTAAACTTTGTTGGGCCCAATTTGGTACCTAACTTGACATC
Found at i:5607877 original size:26 final size:27
Alignment explanation
Indices: 5607848--5607908 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
5607838 AATGTTTGAC
5607848 AAGTTCAAGTACCAAATCA-AAAAAAA
1 AAGTTCAAGTACCAAATCAGAAAAAAA
* * * *
5607874 AAGTT-AGGTATCAAATTAGGAAAAAA
1 AAGTTCAAGTACCAAATCAGAAAAAAA
5607900 AAG-TCAAGT
1 AAGTTCAAGT
5607909 TTAGATACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (27 bp):
AAGTTCAAGTACCAAATCAGAAAAAAA
Found at i:5607977 original size:31 final size:31
Alignment explanation
Indices: 5607942--5608101 Score: 159
Period size: 31 Copynumber: 5.3 Consensus size: 31
5607932 AAAGGATTAA
* *
5607942 GTACCAACTTAAGAAAAAATGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
5607973 GTACCAAATTAAG-AAAAGTGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
** *
5608003 GTATAAAATTAGGAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
* ** **
5608034 ATACCAAATTGGGCCAAA----CAAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTC-AAGTTTAG
* *
5608062 GTACCAAATTATGAAAAAGTGTCAAATTTAG
1 GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
*
5608093 GTACTAAAT
1 GTACCAAAT
5608102 GTTATATTAA
Statistics
Matches: 105, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 21 0.20
30 26 0.25
31 56 0.53
32 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAAGTGTCAAGTTTAG
Found at i:5608081 original size:59 final size:59
Alignment explanation
Indices: 5607873--5608101 Score: 187
Period size: 61 Copynumber: 3.8 Consensus size: 59
5607863 ATCAAAAAAA
* * *
5607873 AAAG-TTAGGTATCAAATTAGGAAAAAAAAGTCAAGTTTAGATACCAAATTAGATCCCAAA-
1 AAAGTTTAGGTACCAAATTAGG-AAAAAATGTCAAGTTTAGATACCAAATT-GA-GCCAAAC
* * * * * * * *
5607933 AAGGATTAAGTACCAACTTAAGAAAAAATGTCAAGTTTAGGTACCAAATTAAG-AAAAGTGTC
1 AAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAGATACCAAATTGAGCCAAA----C
** * *
5607995 -AAGTTTAGGTATAAAATTAGGAAAAAGTGTCAAGTTTAGATACCAAATTGGGCCAAAC
1 AAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAGATACCAAATTGAGCCAAAC
* * * * *
5608053 AAAGTTTAGGTACCAAATTATGAAAAAGTGTCAAATTTAGGTACTAAAT
1 AAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAGATACCAAAT
5608102 GTTATATTAA
Statistics
Matches: 133, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
57 3 0.02
58 1 0.01
59 43 0.32
60 29 0.22
61 54 0.41
62 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.26
Consensus pattern (59 bp):
AAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAGATACCAAATTGAGCCAAAC
Found at i:5608094 original size:120 final size:122
Alignment explanation
Indices: 5607877--5608101 Score: 303
Period size: 120 Copynumber: 1.9 Consensus size: 122
5607867 AAAAAAAAAG
* * *
5607877 TTAGGTATCAAATTAGGAAAAAAAAGTCAAGTTTAGATACCAAATTAGATCCCAAAAAGGATTAA
1 TTAGGTATAAAATTAGGAAAAAAAAGTCAAGTTTAGATACCAAATTAGAGCCCAAAAAAGATTAA
* *
5607942 GTACCAACTTAAGAAAAAATGTCAAGTTTAGGTACCAAATTAAGAAAAGTGTCAAGT
66 GTACCAAATTAAGAAAAAATGTCAAATTTAGGTACCAAATTAAGAAAAGTGTCAAGT
** * *
5607999 TTAGGTATAAAATTAGG-AAAAAGTGTCAAGTTTAGATACCAAATT-G-GGCCAAACAAAGTTTA
1 TTAGGTATAAAATTAGGAAAAAAAAGTCAAGTTTAGATACCAAATTAGAGCCCAAA-AAAGATTA
* * * *
5608061 GGTACCAAATTATGAAAAAGTGTCAAATTTAGGTACTAAAT
65 AGTACCAAATTAAGAAAAAATGTCAAATTTAGGTACCAAAT
5608102 GTTATATTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
119 5 0.06
120 42 0.47
121 26 0.29
122 16 0.18
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (122 bp):
TTAGGTATAAAATTAGGAAAAAAAAGTCAAGTTTAGATACCAAATTAGAGCCCAAAAAAGATTAA
GTACCAAATTAAGAAAAAATGTCAAATTTAGGTACCAAATTAAGAAAAGTGTCAAGT
Found at i:5620242 original size:19 final size:18
Alignment explanation
Indices: 5620195--5620240 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5620185 CCAAAAAAGT
*
5620195 AATTTTTTTTTCCTTTTC
1 AATTTTTTTTTCATTTTC
5620213 AATTTTTTTTTCATTTT-
1 AATTTTTTTTTCATTTTC
*
5620230 TATTTTTTTTT
1 AATTTTTTTTT
5620241 TTGTCAGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (18 bp):
AATTTTTTTTTCATTTTC
Found at i:5624743 original size:21 final size:21
Alignment explanation
Indices: 5624692--5624732 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5624682 TTCAAATCTT
* *
5624692 AAACCCTGAATCTTGAATCAC
1 AAACTCTGAATCTCGAATCAC
5624713 AAACTCTGAATCTCGAATCA
1 AAACTCTGAATCTCGAATCA
5624733 TAAATCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (21 bp):
AAACTCTGAATCTCGAATCAC
Found at i:5629434 original size:17 final size:17
Alignment explanation
Indices: 5629267--5629444 Score: 116
Period size: 17 Copynumber: 10.4 Consensus size: 17
5629257 GTTTTTTTTT
* *
5629267 AACACGAGAATTTTGAA
1 AACACGAAAATTTTTAA
* *
5629284 AACACGAGAATTTGT-A
1 AACACGAAAATTTTTAA
5629300 AACACG-AAA-TTTTAA
1 AACACGAAAATTTTTAA
5629315 AACACGAAAATTTTTAGA
1 AACACGAAAATTTTTA-A
5629333 AA-ACGAAAATTTTTAA
1 AACACGAAAATTTTTAA
* **
5629349 AACAAGACATTTTTTTTTGAA
1 AACACGA-A--AATTTTT-AA
** *
5629370 AACACGGGAATTTTAAAA
1 AACACGAAAATTTT-TAA
* *
5629388 AACAGGGAAA--TTTAGA
1 AACACGAAAATTTTTA-A
5629404 AACACGAAAATTTTTAA
1 AACACGAAAATTTTTAA
* * *
5629421 AACACGACATTTTTTGA
1 AACACGAAAATTTTTAA
5629438 AACACGA
1 AACACGA
5629445 TGTAAAAAAC
Statistics
Matches: 127, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.02
15 10 0.08
16 24 0.19
17 56 0.44
18 22 0.17
20 5 0.04
21 7 0.06
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (17 bp):
AACACGAAAATTTTTAA
Found at i:5629668 original size:19 final size:17
Alignment explanation
Indices: 5629601--5629684 Score: 78
Period size: 17 Copynumber: 4.7 Consensus size: 17
5629591 TTTTTTAAAA
5629601 AAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
* * * * *
5629618 GAAACGCCAGAATTTTG
1 AAAACACGAAAATTTTT
*
5629635 AAAACACGAAGATTTTT
1 AAAACACGAAAATTTTT
5629652 AAAACAAACGAAAATTTTT
1 AAAAC--ACGAAAATTTTT
5629671 GCAAAACACGAAAA
1 --AAAACACGAAAA
5629685 CACAAAATTG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
17 28 0.55
19 18 0.35
21 5 0.10
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (17 bp):
AAAACACGAAAATTTTT
Found at i:5629678 original size:21 final size:19
Alignment explanation
Indices: 5629628--5629670 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5629618 GAAACGCCAG
*
5629628 AATTTTGAAAAC--ACGAA
1 AATTTTTAAAACAAACGAA
*
5629645 GATTTTTAAAACAAACGAA
1 AATTTTTAAAACAAACGAA
5629664 AATTTTT
1 AATTTTT
5629671 GCAAAACACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (19 bp):
AATTTTTAAAACAAACGAA
Found at i:5642832 original size:20 final size:20
Alignment explanation
Indices: 5642807--5642845 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5642797 AGGGCATTTG
*
5642807 ATGGGACACGACGAGAAGTC
1 ATGGGACACGACGAAAAGTC
5642827 ATGGGACACGACGAAAAGT
1 ATGGGACACGACGAAAAGT
5642846 GGGGCCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.33, T:0.10
Consensus pattern (20 bp):
ATGGGACACGACGAAAAGTC
Found at i:5647353 original size:1 final size:1
Alignment explanation
Indices: 5647349--5647438 Score: 63
Period size: 1 Copynumber: 90.0 Consensus size: 1
5647339 AAAAGTAGAC
* * * * * * * ** *
5647349 AAAAAACAAAAAAAAACAAAAACAACAAAAAAAACAACAAAAAAAAAACAAAAAAACCAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
5647414 AAAAAGAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5647439 TCAATATGAA
Statistics
Matches: 65, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:5647376 original size:26 final size:25
Alignment explanation
Indices: 5647347--5647418 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
5647337 AAAAAAGTAG
5647347 ACAAAAAACAAAAAAAAACAAAAACA
1 ACAAAAAACAAAAAAAAA-AAAAACA
5647373 ACAAAAAA-AACAACAAAAAAAAAACA
1 ACAAAAAACAA-AA-AAAAAAAAAACA
* *
5647399 A-AAAAACCAAAAAGAAAAAA
1 ACAAAAAACAAAAAAAAAAAA
5647419 GAAAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 7 0.17
25 9 0.22
26 20 0.49
27 5 0.12
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (25 bp):
ACAAAAAACAAAAAAAAAAAAAACA
Found at i:5647380 original size:21 final size:19
Alignment explanation
Indices: 5647349--5647438 Score: 90
Period size: 21 Copynumber: 4.4 Consensus size: 19
5647339 AAAAGTAGAC
*
5647349 AAAAAACAAAAAAAAACAA
1 AAAAAAAAAAAAAAAACAA
*
5647368 AAACAACAAAAAAAACAACAA
1 AAA-AA-AAAAAAAAAAACAA
*
5647389 AAAAAAAACAAAAAAACCAA
1 AAAAAAAA-AAAAAAAACAA
*
5647409 AAAGAAAAAAGAAAAAAAGAA
1 AAA-AAAAAA-AAAAAAACAA
5647430 AAAGAAAAA
1 AAA-AAAAA
5647439 TCAATATGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.10
20 17 0.28
21 37 0.62
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAACAA
Found at i:5647392 original size:32 final size:31
Alignment explanation
Indices: 5647349--5647432 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 31
5647339 AAAAGTAGAC
5647349 AAAAAAC-AAAAAAAAACAAAAACAA-CAAAA
1 AAAAAACAAAAAAAAAACAAAAA-AACCAAAA
5647379 AAAACAACAAAAAAAAAACAAAAAAACCAAAA
1 AAAA-AACAAAAAAAAAACAAAAAAACCAAAA
* * *
5647411 AGAAAA-AAGAAAAAAAGAAAAA
1 AAAAAACAAAAAAAAAACAAAAA
5647433 GAAAAATCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 18 0.38
31 7 0.15
32 23 0.48
ACGTcount: A:0.86, C:0.11, G:0.04, T:0.00
Consensus pattern (31 bp):
AAAAAACAAAAAAAAAACAAAAAAACCAAAA
Found at i:5647425 original size:15 final size:14
Alignment explanation
Indices: 5647349--5647438 Score: 83
Period size: 15 Copynumber: 6.2 Consensus size: 14
5647339 AAAAGTAGAC
5647349 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
* *
5647363 AACAAAA-ACAACAA
1 AA-AAAACAAAAAAA
*
5647377 AAAAAACAACAAAA
1 AAAAAACAAAAAAA
5647391 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
* *
5647405 CCAAAAAGAAAAAAGA
1 -AAAAAACAAAAAA-A
*
5647421 AAAAAAGAAAAAGAA
1 AAAAAACAAAAA-AA
5647436 AAA
1 AAA
5647439 TCAATATGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.06
14 26 0.42
15 30 0.48
16 2 0.03
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAAAA
Found at i:5647433 original size:14 final size:13
Alignment explanation
Indices: 5647349--5647438 Score: 76
Period size: 14 Copynumber: 6.4 Consensus size: 13
5647339 AAAAGTAGAC
5647349 AAAAAACAAAAAA
1 AAAAAACAAAAAA
5647362 AAACAAA-AACAACAA
1 AAA-AAACAA-AA-AA
5647377 AAAAAACAACAAAA
1 AAAAAACAA-AAAA
5647391 AAAAAACAAAAAA
1 AAAAAACAAAAAA
*
5647404 ACCAAAAAGAAAAAA
1 A--AAAAACAAAAAA
5647419 GAAAAAA-AGAAAAA
1 -AAAAAACA-AAAAA
5647433 GAAAAA
1 -AAAAA
5647439 TCAATATGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
13 11 0.16
14 35 0.51
15 21 0.31
16 1 0.01
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAA
Found at i:5648654 original size:164 final size:162
Alignment explanation
Indices: 5648290--5649622 Score: 1657
Period size: 164 Copynumber: 8.4 Consensus size: 162
5648280 TCTTTTAAGA
*
5648290 ATTT-TTTTTCAATTTCT-ATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTCTTTTT-AATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* ** *
5648353 GAGTCACG-TCGAGGTA-TT---TTTA-AATT-TCT-ATTTTCAAAAAATCAACTCATATTGCGA
65 GGGTCACGCT-GAGGTATTTCAATTTATGTTTCTCTGTTTTTCAAAAAATCAACTCATATTGCGA
5648410 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
129 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
* *
5648444 ATTTTCTTTTAAATCTCTG-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 A-TTTCTTTTTAATTTCTGTTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
5648508 CGGGTCACGCTGAGGTATCTTCAATTTATGTTTCTCTGTTTTTCAAAAAAATCAACTTATATTGC
64 CGGGTCACGCTGAGGTAT-TTCAATTTATGTTTCTCTGTTTTTC-AAAAAATCAACTCATATTGC
*
5648573 GAGAAGTGAGTTGGGCCTCGGGTCGCACGCTGAGGT
127 GAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
*
5648609 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCG
1 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * *
5648674 GGTCACGCTGAGGTATTTTCAATTTATGTTTTTCTATTTTTCAAAAAAATCAACTCATATTGTGA
66 GGTCACGCTGAGGTA-TTTCAATTTATGTTTCTCTGTTTTTC-AAAAAATCAACTCATATTGCGA
5648739 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
129 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
* * *
5648773 ATTTTCTTTTAAATCTCTG-TTTTTCAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 A-TTTCTTTTTAATTTCTGTTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5648837 CGGGTCACGCTGAGGTATCTTCAATTTATGTTTCTCTGTTTTTCAAAAAAATCAACTCATATTGC
64 CGGGTCACGCTGAGGTAT-TTCAATTTATGTTTCTCTGTTTTTC-AAAAAATCAACTCATATTGC
*
5648902 GAGAAGTGAGTTGGGCCTCGGGTCGCACGCTGAGGT
127 GAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
5648938 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* *
5649003 GGTCATGCTGAGGTATCTTCAATTTATGTTTCTCTGTTTTTCAAAAAAATCAACTTATATTGCGA
66 GGTCACGCTGAGGTAT-TTCAATTTATGTTTCTCTGTTTTTC-AAAAAATCAACTCATATTGCGA
*
5649068 GAAGTGAGTTGGGCCTCGGGTCGCACGCTGAGGT
129 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
* *
5649102 ATTTCTTTTTAATTTCTGTTTTTTCAAAAATTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
1 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * * *
5649167 GGTCACGCTGAGATATTTTTAATTTATG--TCT-T-TTTTT---AAAATCAACTCATAATAC-AG
66 GGTCACGCTGAGGTA-TTTCAATTTATGTTTCTCTGTTTTTCAAAAAATCAACTCATATTGCGAG
*
5649224 AGGTGAGTTGAGCCTCGGGT--CACGCTGAGGT
130 AAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
* * * * *
5649255 A----TTTTTAATTTATGTCTTTTT--TAAAATCAACTCATA-TAC-AGAGGTGAGTTGAGCTTT
1 ATTTCTTTTTAATTTCTGT-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
** * * * **
5649312 GGACCATGCCGAGGTATTTC-TTTTAAATTTCT-T-TTTTTC-AAAAATCAACTCATATTGCGA-
65 GGGTCACGCTGAGGTATTTCAATTTATGTTTCTCTGTTTTTCAAAAAATCAACTCATATTGCGAG
* *
5649372 AAGGTGAGTTGAGCCTCGGGTCACAC-C-GATGT
130 AA-GTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
* * * * *
5649404 ATTTCTTTTAAATTTATGTTTTTTAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTT
1 ATTTCTTTTTAATTTCTGTTTTTT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
** * * **
5649469 GGACCATGCCGAGGTATTTC-ATTTA-AATT-TCTGTTTTTC-AAAAATCAACTCATATTGCGAG
65 GGGTCACGCTGAGGTATTTCAATTTATGTTTCTCTGTTTTTCAAAAAATCAACTCATATTGCGAG
* *
5649530 AGGTGAGTTGAGCCTCGGGT--CACGCCGAGGT
130 AAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
*
5649561 A-TTC--TTCAA-TTCATG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTCTTTTTAATTTC-TGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
5649620 GGG
65 GGG
5649623 GCACATGTCG
Statistics
Matches: 1061, Mismatches: 73, Indels: 93
0.86 0.06 0.08
Matches are distributed among these distances:
144 4 0.00
145 3 0.00
146 36 0.03
147 2 0.00
148 30 0.03
149 37 0.03
150 6 0.01
151 41 0.04
152 5 0.00
153 32 0.03
154 7 0.01
155 52 0.05
156 81 0.08
157 92 0.09
158 3 0.00
160 5 0.00
161 5 0.00
162 5 0.00
163 3 0.00
164 396 0.37
165 216 0.20
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (162 bp):
ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
GGTCACGCTGAGGTATTTCAATTTATGTTTCTCTGTTTTTCAAAAAATCAACTCATATTGCGAGA
AGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
Found at i:5648901 original size:329 final size:324
Alignment explanation
Indices: 5648290--5649656 Score: 1705
Period size: 329 Copynumber: 4.3 Consensus size: 324
5648280 TCTTTTAAGA
*
5648290 ATTT-TTTTTCAATTTCT-ATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTCTTTTT-AATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
5648353 GAGTCACG-TCGAGGTATTTTTAA---A----TTTCTA-TTTTCAAAAAATCAACTCATATTGCG
65 GGGTCACGCT-GAGGTATTTTCAATTTATGTTTTTCTATTTTTCAAAAAATCAACTCATATTGCG
5648409 AGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCTTTTAAATCTCTG-TTTTTCAAAA
129 AGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTCTTTTAAATCTCTGTTTTTTCAAAA
5648473 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATG
193 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATG
* *
5648538 TTTCTCTGTTTTTCAAAAAAATCAACTTATATTGCGAGAAGTGAGTTGGGCCTCGGGTCGCACGC
258 TTTCTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGT--CACGC
5648603 TGAGGT
319 TGAGGT
*
5648609 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCG
1 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
*
5648674 GGTCACGCTGAGGTATTTTCAATTTATGTTTTTCTATTTTTCAAAAAAATCAACTCATATTGTGA
66 GGTCACGCTGAGGTATTTTCAATTTATGTTTTTCTATTTTTC-AAAAAATCAACTCATATTGCGA
5648739 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCTTTTAAATCTCTG-TTTTTCAAAAA
130 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTCTTTTAAATCTCTGTTTTTTCAAAAA
*
5648803 AATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATGT
194 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATGT
*
5648868 TTCTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGGGCCTCGGGTCGCACGCT
259 TTCTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGT--CACGCT
5648933 GAGGT
320 GAGGT
5648938 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * * * *
5649003 GGTCATGCTGAGGTATCTTCAATTTATGTTTCTCTGTTTTTCAAAAAAATCAACTTATATTGCGA
66 GGTCACGCTGAGGTATTTTCAATTTATGTTTTTCTATTTTTC-AAAAAATCAACTCATATTGCGA
* * *
5649068 GAAGTGAGTTGGGCCTCGGGTCGCACGCTGAGGTATTTCTTTTTAATTTCTGTTTTTTC-AAAAA
130 GAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATCTCTGTTTTTTCAAAAAA
* * * * *
5649132 TTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGATATTTTTAATTTATG--
195 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATGTT
* * *
5649195 TCT-T-TTTTT--AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
260 TCTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGT
* * * * *
5649255 A----TTTTTAATTTATGTCTTTTT--TAAAATCAACTCATA-TAC-AGAGGTGAGTTGAGCTTT
1 ATTTCTTTTTAATTTCTGT-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
** * * *** *
5649312 GGACCATGCCGAGGTA-TTTC--TTT-TAAATTTCTTTTTTTC-AAAAATCAACTCATATTGCGA
65 GGGTCACGCTGAGGTATTTTCAATTTATGTTTTTCTATTTTTCAAAAAATCAACTCATATTGCGA
* * * * *
5649372 -AAGGTGAGTTGAGCCTCGGGTCACAC-C-GATGTATTTCTTTTAAATTTATGTTTTTTAAAAAA
130 GAA-GTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATCTCTGTTTTTTCAAAAA
* * ** * * **
5649434 AATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTAT-TTC-ATTTA-AA
194 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATGT
* *
5649496 TT-TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGG
259 TTCTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGG
5649560 T
324 T
*
5649561 A-TTC--TTCAA-TTCATG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTCTTTTTAATTTC-TGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
5649620 GGGGCACATG-TCGAGGTATTTTCGATTTTTGTTTTTC
65 GGGTCAC--GCT-GAGGTATTTTCAATTTATGTTTTTC
5649657 GAAGATCAAC
Statistics
Matches: 936, Mismatches: 75, Indels: 79
0.86 0.07 0.07
Matches are distributed among these distances:
301 6 0.01
302 30 0.03
303 55 0.06
304 41 0.04
305 21 0.02
306 60 0.06
307 11 0.01
308 20 0.02
309 3 0.00
310 36 0.04
311 6 0.01
312 14 0.01
313 16 0.02
314 10 0.01
317 12 0.01
319 31 0.03
320 84 0.09
321 1 0.00
323 1 0.00
324 5 0.01
325 1 0.00
326 3 0.00
327 6 0.01
328 82 0.09
329 381 0.41
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (324 bp):
ATTTCTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
GGTCACGCTGAGGTATTTTCAATTTATGTTTTTCTATTTTTCAAAAAATCAACTCATATTGCGAG
AAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATCTCTGTTTTTTCAAAAAAA
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATCTTCAATTTATGTTT
CTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGT
Found at i:5649720 original size:75 final size:74
Alignment explanation
Indices: 5649035--5649734 Score: 511
Period size: 75 Copynumber: 9.2 Consensus size: 74
5649025 TTTATGTTTC
* * * *
5649035 TCTGTTTTTCAAAAAAATCAACTTATATTGCGAGAAGTGAGTTGGGCCTCGGGTCGCACGCTGAG
1 TCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCCGAG
**
5649100 GTATTTCTTTTTAATT
63 GTA-TTC---TCGATT
* * *
5649116 TCTGTTTTTTCAAAAATTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGA
1 TCTG-TTTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGG
* **
5649180 TATTTTTAATT
64 TATTCTCGATT
* ** * * *
5649191 TATGTCTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGG
1 TCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGG
* **
5649254 TATTTTTAATT
64 TATTCTCGATT
* ** * ** * *
5649265 TATGTCTTTTTTAAAATCAACTCATA-TAC-AGAGGTGAGTTGAG-CTTTGGACCATGCCGAGGT
1 TCTGT-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGT
**
5649327 ATTTCTTTTAAATT
65 A-TTC---TCGATT
* * * *
5649341 TCTTTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGT-CACACCGATGTA
1 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTA
**
5649405 TTTCTTTTAAATT
66 -TTC---TCGATT
* * * * * *
5649418 TATGTTTTTTAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGACCATGCCGAG
1 TCTG-TTTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAG
**
5649482 GTATTTCATTTAAATT
63 GTA-TTC---TCGATT
5649498 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-CACGCCGAGGTA
1 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTA
*
5649562 TTCTTC-AAT
66 TTC-TCGATT
* * *
5649571 TCATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGG
1 TC-TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCCGAGG
*
5649636 TATTTTCGATT
64 TATTCTCGATT
* * * * * * * *
5649647 TTTGTTTTTCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTCGCACGCCGAGCT
1 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCCGAGGT
*
5649712 GTTCTCGATT
65 ATTCTCGATT
*
5649722 TCTGCTTTTCAAA
1 TCTGTTTTTCAAA
5649735 TAAAGAGGAA
Statistics
Matches: 526, Mismatches: 72, Indels: 48
0.81 0.11 0.07
Matches are distributed among these distances:
71 4 0.01
72 28 0.05
73 26 0.05
74 97 0.18
75 112 0.21
76 37 0.07
77 84 0.16
78 13 0.02
79 18 0.03
80 64 0.12
81 37 0.07
82 6 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (74 bp):
TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCCGAGGTA
TTCTCGATT
Found at i:5649951 original size:32 final size:31
Alignment explanation
Indices: 5649887--5649948 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
5649877 TTTTTAAATT
*
5649887 TTTTTGCATTTTGACCCCAAACTTTTCTAAA
1 TTTTTACATTTTGACCCCAAACTTTTCTAAA
5649918 TTTTTACATTTTGACCCCAAAAC-TTTCTAAA
1 TTTTTACATTTTGACCCC-AAACTTTTCTAAA
5649949 ATTATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTTTACATTTTGACCCCAAACTTTTCTAAA
Found at i:5649971 original size:29 final size:30
Alignment explanation
Indices: 5649894--5650000 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 30
5649884 ATTTTTTTGC
* *
5649894 ATTTTGACCCC-AAACTTT-TCTAAATTTTTAC
1 ATTTTGACCCCAAAACTTTCTC-AAA--ATTAT
5649925 ATTTTGACCCCAAAACTTTCT-AAAATTAT
1 ATTTTGACCCCAAAACTTTCTCAAAATTAT
** *
5649954 ATTTTGACCCTTAGACTTTCTCAAAATT-T
1 ATTTTGACCCCAAAACTTTCTCAAAATTAT
* *
5649983 CACTTTGACCCCTAAACT
1 -ATTTTGACCCCAAAACT
5650001 CTTAAGAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
29 22 0.34
30 20 0.31
31 14 0.22
32 7 0.11
33 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (30 bp):
ATTTTGACCCCAAAACTTTCTCAAAATTAT
Found at i:5650490 original size:14 final size:15
Alignment explanation
Indices: 5650462--5650505 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
5650452 CAATCAAATA
5650462 AAGAAAAGAGAAGAG
1 AAGAAAAGAGAAGAG
5650477 AAGAAAAG-GAAGAG
1 AAGAAAAGAGAAGAG
** *
5650491 GGGAAGAGAGAAGAG
1 AAGAAAAGAGAAGAG
5650506 CCCGTCCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAGAAGAG
Found at i:5650612 original size:14 final size:13
Alignment explanation
Indices: 5650579--5650636 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
5650569 ATTCGGCCCG
5650579 AAGAAGAGGAAGAAA
1 AAGAA-AGGAA-AAA
5650594 AAGAAAGGAAAAA
1 AAGAAAGGAAAAA
5650607 AGAGAAA-GAAAAA
1 A-AGAAAGGAAAAA
*
5650620 GAAAAAAGGGAAAAA
1 -AAGAAA-GGAAAAA
5650635 AA
1 AA
5650637 TATAAGAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 14 0.37
14 13 0.34
15 11 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAAGGAAAAA
Found at i:5650625 original size:19 final size:19
Alignment explanation
Indices: 5650588--5650636 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
5650578 GAAGAAGAGG
* *
5650588 AAGAAAAAG-AAAGGAAAA
1 AAGAGAAAGAAAAAGAAAA
5650606 AAGAGAAAGAAAAAGAAAA
1 AAGAGAAAGAAAAAGAAAA
*
5650625 AAGGGAAA-AAAA
1 AAGAGAAAGAAAA
5650637 TATAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AAGAGAAAGAAAAAGAAAA
Found at i:5651519 original size:17 final size:17
Alignment explanation
Indices: 5651464--5651519 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5651454 TTCGTGTTTC
*
5651464 TTTCTAAAAAAATCGTGT
1 TTTC-AAAAAATTCGTGT
* *
5651482 TTTCAAAAATTCTCATG-
1 TTTCAAAAAAT-TCGTGT
5651499 TTTCAAAAAATTCGTGT
1 TTTCAAAAAATTCGTGT
5651516 TTTC
1 TTTC
5651520 GTGTTTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.13
17 19 0.61
18 8 0.26
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (17 bp):
TTTCAAAAAATTCGTGT
Found at i:5651650 original size:18 final size:18
Alignment explanation
Indices: 5651629--5652052 Score: 177
Period size: 17 Copynumber: 24.6 Consensus size: 18
5651619 AAATTTTGTG
5651629 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
5651647 TTTTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
5651664 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
5651682 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
5651699 TTTTCGTGTTTTTTTTAAAAAA
1 TTTTCGTG----TTTTCAAAAA
* * *
5651721 ATTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
** *
5651739 TTTTCG-CATTTCATAAA
1 TTTTCGTGTTTTCAAAAA
*
5651756 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
5651774 -CTCCG-GTGTTTC-AAAG
1 TTTTCGTGT-TTTCAAAAA
* *
5651790 TTTTCATGTGTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
5651808 TTCTCGCG-TTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
5651825 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
5651843 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
5651857 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
5651872 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
5651887 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
5651904 TTTTCGTG-TTTC-TAAA
1 TTTTCGTGTTTTCAAAAA
* *
5651920 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
5651937 TTCCCGTG-TTTCAAAAAAAA
1 TTTTCGTGTTTTC---AAAAA
* * *
5651957 ATGTCTTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
5651974 TTTTCGTG-TTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
5651992 TTTTCGTGTTTT-TAAAA
1 TTTTCGTGTTTTCAAAAA
*
5652009 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
5652025 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
5652043 TTCTCGTGTT
1 TTTTCGTGTT
5652053 AAAAAAAAAC
Statistics
Matches: 298, Mismatches: 70, Indels: 76
0.67 0.16 0.17
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 6 0.02
16 36 0.12
17 120 0.40
18 91 0.31
19 6 0.02
20 9 0.03
21 3 0.01
22 14 0.05
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:5651673 original size:43 final size:43
Alignment explanation
Indices: 5651589--5651676 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
5651579 TTTGATATTA
* *
5651589 TCGTGTTTTCAAAAAAATTCCGTGTTCGACAAATTTTGTGTTT
1 TCGTGTTTTCAAAAAAATTCCGTGTTCGAAAAATTTCGTGTTT
* * **
5651632 TCGTGTTTTC-AAAAATTTTCGTGTTTTAAAAATCTTCGTGTTT
1 TCGTGTTTTCAAAAAAATTCCGTGTTCGAAAAAT-TTCGTGTTT
5651675 TC
1 TC
5651677 AAAAATTCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 18 0.47
43 20 0.53
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.48
Consensus pattern (43 bp):
TCGTGTTTTCAAAAAAATTCCGTGTTCGAAAAATTTCGTGTTT
Found at i:5651677 original size:35 final size:33
Alignment explanation
Indices: 5651630--5652052 Score: 182
Period size: 35 Copynumber: 12.3 Consensus size: 33
5651620 AATTTTGTGT
5651630 TTTCGTGTTTTCAAAAATTTTCGTGTTTTAAAAA
1 TTTCGTG-TTTCAAAAATTTTCGTGTTTTAAAAA
* * * *
5651664 TCTTCGTGTTTTCAAAAATTCTGGCGTTTCAAAAA
1 T-TTCGTG-TTTCAAAAATTTTCGTGTTTTAAAAA
* * * *
5651699 TTTTCGTGTTTTTTTTAAAAAAATTACGTGTTTTCACAAAT
1 -TTTCGTG-----TTTCAAAAATTTTCGTGTTTT-A-AAAA
** * *
5651740 TTTCGCATTTCATAAATTCTCGTGTTTTCAAAAA
1 TTTCGTGTTTCAAAAATTTTCGTGTTTT-AAAAA
* * * * *
5651774 CTCCGGTGTTTC-AAAGTTTTCATGTGTTCAAAAA
1 TTTC-GTGTTTCAAAAATTTTCGTGT-TTTAAAAA
* * ** *
5651808 TTCTCGCGTTTAAAAAAAATTCGTGTTTCAAAATA
1 TT-TCGTGTTTCAAAAATTTTCGTGTTTTAAAA-A
** **
5651843 TTCTCGCATTTC---AATTTT--TGTTTTTTAAA
1 TT-TCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
* *
5651872 --TCGTGTTTCAAAAAAATGTCGTGTTTTAAAAA
1 TTTCGTGTTTC-AAAAATTTTCGTGTTTTAAAAA
* * *
5651904 TTTTCGTGTTTC-TAAATTTCCCTGTTTTAAAAA
1 -TTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
* * * *
5651937 TTCCCGTGTTTCAAAAAAAAATGTCTTGTTTTAAAAA
1 TT-TCGTGTTTC---AAAAATTTTCGTGTTTTAAAAA
*
5651974 TTTTCGTGTTTCTAAAAATTTTCGTGTTTTTAAAAT
1 -TTTCGTGTTTC-AAAAATTTTCGTG-TTTTAAAAA
* *
5652010 TTTCGTGTTT-ACAAATTCTCGTGTTTTCAAAAA
1 TTTCGTGTTTCAAAAATTTTCGTGTTTT-AAAAA
5652043 TTCTCGTGTT
1 TT-TCGTGTT
5652053 AAAAAAAAAC
Statistics
Matches: 288, Mismatches: 70, Indels: 62
0.69 0.17 0.15
Matches are distributed among these distances:
26 7 0.02
29 1 0.00
30 11 0.04
32 19 0.07
33 41 0.14
34 40 0.14
35 110 0.38
36 9 0.03
37 24 0.08
38 2 0.01
39 15 0.05
40 6 0.02
41 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (33 bp):
TTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
Found at i:5651751 original size:57 final size:56
Alignment explanation
Indices: 5651638--5651767 Score: 151
Period size: 57 Copynumber: 2.4 Consensus size: 56
5651628 GTTTTCGTGT
** * *
5651638 TTTCAAAAATTTTCGTG----TTTTAAAAATCTTCGTGTTTTCAAAAATTCTGGCG
1 TTTCAAAAATTTTCGTGTTTTTTTTAAAAAAATTCGTGTTTTCAAAAATTCTCGCA
* *
5651690 TTTCAAAAATTTTCGTGTTTTTTTTAAAAAAATTACGTGTTTTCACAAATTTTCGCA
1 TTTCAAAAATTTTCGTGTTTTTTTTAAAAAAATT-CGTGTTTTCAAAAATTCTCGCA
* *
5651747 TTTCATAAATTCTCGTGTTTT
1 TTTCAAAAATTTTCGTGTTTT
5651768 CAAAAACTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
52 17 0.26
56 11 0.17
57 37 0.57
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (56 bp):
TTTCAAAAATTTTCGTGTTTTTTTTAAAAAAATTCGTGTTTTCAAAAATTCTCGCA
Found at i:5652057 original size:16 final size:16
Alignment explanation
Indices: 5652005--5652058 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5651995 TCGTGTTTTT
* *
5652005 AAAATTTTCGTGTTTA
1 AAAATTCTCGTGTTAA
* *
5652021 CAAATTCTCGTGTTTTCA
1 AAAATTCTCGTG--TTAA
5652039 AAAATTCTCGTGTTAA
1 AAAATTCTCGTGTTAA
5652055 AAAA
1 AAAA
5652059 AAACTTTCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 17 0.55
18 14 0.45
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (16 bp):
AAAATTCTCGTGTTAA
Found at i:5652059 original size:18 final size:18
Alignment explanation
Indices: 5652022--5652079 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
5652012 TCGTGTTTAC
***
5652022 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTGTTAAAAA
5652040 AAATTCTCGTGTTAAAAAA
1 AAATTCTCGTGTT-AAAAA
*
5652059 AAACTT-TCGTTTTAAAAA
1 AAA-TTCTCGTGTTAAAAA
5652077 AAA
1 AAA
5652080 AGAAATACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 21 0.62
19 11 0.32
20 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (18 bp):
AAATTCTCGTGTTAAAAA
Found at i:5652078 original size:105 final size:105
Alignment explanation
Indices: 5651872--5652076 Score: 269
Period size: 105 Copynumber: 2.0 Consensus size: 105
5651862 GTTTTTTAAA
5651872 TCGTGTTTCAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAATTTCCCTGTTTTAAAAA
1 TCGTGTTTCAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAATTTCCCTGTTTTAAAAA
*
5651937 TTCCCGTGTTTCAAAAAAAAATGTCTTGTTTTAAAAATTT
66 TTCCCGTGTTTCAAAAAAAAATGTCTCGTTTTAAAAATTT
* * * * *
5651977 TCGTGTTTCTAAAAATTTTCGTGTTTTTAAAATTTTCGTGTTTAC-AAA-TTCTCGTGTTTTCAA
1 TCGTGTTTCAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTT-CTAAATTTC-CCTGTTTT-AA
*
5652040 AAATTCTCGTG-TT-AAAAAAAAACT-T-TCGTTTTAAAAA
63 AAATTCCCGTGTTTCAAAAAAAAA-TGTCTCGTTTTAAAAA
5652077 AAAAGAAATA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
103 11 0.12
104 13 0.15
105 52 0.58
106 13 0.15
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (105 bp):
TCGTGTTTCAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAATTTCCCTGTTTTAAAAA
TTCCCGTGTTTCAAAAAAAAATGTCTCGTTTTAAAAATTT
Found at i:5656696 original size:21 final size:22
Alignment explanation
Indices: 5656668--5656717 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
5656658 TTTTGAAACC
5656668 CAAG-TTCAAGA-TTTATGATT
1 CAAGATTCAAGAGTTTATGATT
* *
5656688 CGAGATTC-AGAGTTTGTGATT
1 CAAGATTCAAGAGTTTATGATT
5656709 CAAGATTCA
1 CAAGATTCA
5656718 GGGTTTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (22 bp):
CAAGATTCAAGAGTTTATGATT
Found at i:5656729 original size:21 final size:21
Alignment explanation
Indices: 5656679--5656729 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5656669 AAGTTCAAGA
*
5656679 TTTATGATTCGAGATTCAGAG
1 TTTATGATTCAAGATTCAGAG
* *
5656700 TTTGTGATTCAAGATTCAGGG
1 TTTATGATTCAAGATTCAGAG
*
5656721 TTTAAGATT
1 TTTATGATT
5656730 TGAAGTTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (21 bp):
TTTATGATTCAAGATTCAGAG
Found at i:5661319 original size:23 final size:22
Alignment explanation
Indices: 5661286--5661338 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 22
5661276 ATAGTCTGAC
5661286 AAAAAAAAAATTAAAAAAGTGA
1 AAAAAAAAAATTAAAAAAGTGA
*
5661308 AAAGAAAAAAATTGAAAAAGTGA
1 AAA-AAAAAAATTAAAAAAGTGA
5661331 AAAAAAAA
1 AAAAAAAA
5661339 TTACTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (22 bp):
AAAAAAAAAATTAAAAAAGTGA
Found at i:5673695 original size:31 final size:31
Alignment explanation
Indices: 5673652--5673810 Score: 159
Period size: 30 Copynumber: 5.3 Consensus size: 31
5673642 TTAATATAAC
* * *
5673652 ATTTAGTACCTAAATTTGACACTTTTTCATA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
** *
5673683 ATTTGGTACCTAAACTTTG----TTTGGCCCA
1 ATTTGGTACCTAAAC-TTGACACTTTTTCCTA
*
5673711 ATTTGGTATCTAAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
** *
5673742 ATTTTATACCTAAACTTGACAC-TTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
5673772 ATTTGGTACCTAAACTTGACA-TTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
5673802 AGTTGGTAC
1 ATTTGGTAC
5673811 TTAATCCTTT
Statistics
Matches: 105, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
27 3 0.03
28 19 0.18
30 42 0.40
31 38 0.36
32 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:5673878 original size:120 final size:120
Alignment explanation
Indices: 5673652--5673875 Score: 299
Period size: 120 Copynumber: 1.9 Consensus size: 120
5673642 TTAATATAAC
* * *
5673652 ATTTAGTACCTAAATTTGACACTTTTTCATAATTTGGTACCTAAACTTTGTTTGGCCCAATTTGG
1 ATTTAGTACCTAAACTTGACACTTTTTCATAAGTTGGTACCTAAACTTTGTTGGGCCCAATTTGG
*
5673717 TATCTAAACTTGACACTTTTTCCTAATTTTATACCTAAACTTGACACTTTTCTTA
66 TATCTAAACTTGACACTTTTTCCTAATTTGATACCTAAACTTGACACTTTTCTTA
* * * * * *
5673772 ATTTGGTACCTAAACTTGACA-TTTTTCTTAAGTTGGTACTTAATCCTTT-TTGGGATCTAATTT
1 ATTTAGTACCTAAACTTGACACTTTTTCATAAGTTGGTACCTAA-ACTTTGTTGGG-CCCAATTT
**
5673835 GGTATCTAAACTTGACTTTTTTTTCCTAATTTGATACCTAA
64 GGTATCTAAACTTGAC-ACTTTTTCCTAATTTGATACCTAA
5673876 CTTTTTTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
119 23 0.26
120 45 0.51
121 21 0.24
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (120 bp):
ATTTAGTACCTAAACTTGACACTTTTTCATAAGTTGGTACCTAAACTTTGTTGGGCCCAATTTGG
TATCTAAACTTGACACTTTTTCCTAATTTGATACCTAAACTTGACACTTTTCTTA
Found at i:5673880 original size:59 final size:58
Alignment explanation
Indices: 5673652--5673882 Score: 140
Period size: 59 Copynumber: 3.9 Consensus size: 58
5673642 TTAATATAAC
* * * * * * * * *
5673652 ATTTAGTACCTAAATTTGACACTTTTTCATAATTTGGTACCTAAACTTTGTTTGG-CCCA
1 ATTTGGTACCTAAACTTGACA-TTTTTCCTAAGTTGATACCTAACCTTT-TTGGGATCTA
* * * * *******
5673711 ATTTGGTATCTAAACTTGACACTTTTTCCTAATTTTATACCTAAACTTGACACTTTTCTTA
1 ATTTGGTACCTAAACTTGACA-TTTTTCCTAAGTTGATACCTAACCTT-TTTGGGATC-TA
* * *
5673772 ATTTGGTACCTAAACTTGACATTTTTCTTAAGTTGGTACTTAATCCTTTTTGGGATCTA
1 ATTTGGTACCTAAACTTGACATTTTTCCTAAGTTGATACCTAA-CCTTTTTGGGATCTA
* * * *
5673831 ATTTGGTATCTAAACTTGACTTTTTTTTCCTAATTTGATACCTAACTTTTTT
1 ATTTGGTACCTAAACTTGAC--ATTTTTCCTAAGTTGATACCTAACCTTTTT
5673883 TTTTGATTTG
Statistics
Matches: 131, Mismatches: 35, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
59 63 0.48
60 26 0.20
61 42 0.32
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (58 bp):
ATTTGGTACCTAAACTTGACATTTTTCCTAAGTTGATACCTAACCTTTTTGGGATCTA
Found at i:5673903 original size:26 final size:27
Alignment explanation
Indices: 5673844--5673904 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
5673834 TGGTATCTAA
5673844 ACTTG-ACTTTTTTTTCCTAATTTGAT
1 ACTTGAACTTTTTTTTCCTAATTTGAT
* * * *
5673870 ACCT-AACTTTTTTTT-TTGATTTGGT
1 ACTTGAACTTTTTTTTCCTAATTTGAT
5673895 ACTTGAACTT
1 ACTTGAACTT
5673905 GTCAAACATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (27 bp):
ACTTGAACTTTTTTTTCCTAATTTGAT
Found at i:5692469 original size:46 final size:45
Alignment explanation
Indices: 5692402--5692743 Score: 209
Period size: 44 Copynumber: 7.8 Consensus size: 45
5692392 ATTATACAGG
*
5692402 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
5692448 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * * * *
5692492 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG------GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
* ** * *
5692531 TCTTATCTCTCTGA-AGTTACAGTATAGA-AGATC--A-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATTCAGA
*
5692572 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
5692618 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * * **
5692662 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * *
5692706 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA
5692744 CACTATCCTA
Statistics
Matches: 228, Mismatches: 44, Indels: 48
0.71 0.14 0.15
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 22 0.10
40 1 0.00
41 27 0.12
42 2 0.01
43 4 0.02
44 88 0.39
45 5 0.02
46 75 0.33
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
Found at i:5692783 original size:87 final size:85
Alignment explanation
Indices: 5692445--5692821 Score: 325
Period size: 87 Copynumber: 4.4 Consensus size: 85
5692435 AAAGAATTTC
* * *
5692445 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAGGATAGTAATCCTATCTCCTTG-AGA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGGACACTAATCCTATCTCCCTGAAG-
*
5692508 TTACAATGGAGCGGATTAAAG
65 TTACAGTGGAGCGGATTAAAG
* *** * * *
5692529 -GATCTTATCTCTCTGA-AGTTACAGTATAGAAGATC-----ACA-TCAGGTCTTATCTCCCTG-
1 AGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGGACACT-A-ATCCTATCTCCCTGA
* * **
5692585 AGATTACAGTGGAACAGACCAAAG
63 AG-TTACAGTGGAGCGGATTAAAG
* *
5692609 AATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAGGATAGTAATCCTATCTCCC
1 ------AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGGACACTAATCCTATCTCCC
5692673 TGAAGTTACAGTGGAGCGGATTAAAATAAG
60 TGAAGTTACAGTGGAGCGGATT---A-AAG
5692703 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAA-GACACT-ATCCTATCTCCCTGAAGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGGACACTAATCCTATCTCCCTGAAGT
5692766 TACAGTGGAGCGGATTAAAG
66 TACAGTGGAGCGGATTAAAG
* * * *
5692786 -GATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
5692822 CATCAAGTCT
Statistics
Matches: 239, Mismatches: 32, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
78 1 0.00
79 3 0.01
80 30 0.13
82 33 0.14
83 31 0.13
84 1 0.00
87 62 0.26
88 41 0.17
89 2 0.01
90 25 0.10
91 5 0.02
92 1 0.00
93 1 0.00
94 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (85 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGGACACTAATCCTATCTCCCTGAAGT
TACAGTGGAGCGGATTAAAG
Found at i:5692792 original size:170 final size:164
Alignment explanation
Indices: 5692405--5692820 Score: 419
Period size: 170 Copynumber: 2.4 Consensus size: 164
5692395 ATACAGGTCT
5692405 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAACAGACCAAAG------AGATCTTATCTCCCTGAGATTACAG
*
5692470 CGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTT
60 CGGAGCAGATCAAGGATAGTAATCCTATCTCCCTGAGATTACAATGGAGCGGATTAAAGGATCTT
* * * * * *
5692535 ATCTCTCTGAAGTTACAGTATAGAAGATCACATCAGGTCT
125 ATCTCCCTGAAGTTACAGCAGAGAAGATCACAACAGATCC
5692575 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAACAGACCAAAG------AGATCTTATCTCCCTGAGATTACAG
*
5692640 CGGAGCAGATCAAGGATAGTAATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAGA
60 CGGAGCAGATCAAGGATAGTAATCCTATCTCCCTGAGA-TTACAATGGAGCGGATT---A-AAG-
* * *
5692704 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGA-AGACACTATCC
119 GATCTTATCTCCCTGAAG-TTACAGCAGAGAAGATC-ACA-ACA-GATCC
* * ** * * *
5692752 TATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAG-GATCTTATCTCTCTGAGGTTACAGCAGAG
1 TATCTCCCTGAGA-TTACAGTGGAACAGACCAAAGAGATCTTATCTCCCTGAGATTACAGCGGAG
*
5692815 TAGATC
65 CAGATC
5692821 GCATCAAGTC
Statistics
Matches: 216, Mismatches: 19, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
169 1 0.00
170 147 0.68
173 1 0.00
174 5 0.02
175 28 0.13
176 4 0.02
177 30 0.14
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (164 bp):
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAGATCTTATCTCCCTGAGATTACAGCGGAGC
AGATCAAGGATAGTAATCCTATCTCCCTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCC
CTGAAGTTACAGCAGAGAAGATCACAACAGATCC
Found at i:5693130 original size:87 final size:87
Alignment explanation
Indices: 5693061--5693677 Score: 297
Period size: 89 Copynumber: 7.0 Consensus size: 87
5693051 GGGGCAAGTT
*
5693061 GAAGATATGAGTCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAGGATCTTATCTCTC
1 GAAGACATGAGTCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAGGATCTTATCTCTC
* *
5693126 TGAAGTTACAGTAGAGTAGATC
66 TGAAGTTACAGTGGAGCAGATC
* * * * * ** *
5693148 GCA-CCA-G-GTCTTATCTCCTTG-AGATTATAGTGGAGCAGACCGAAGAATTTCA-GATCTTAT
1 GAAGACATGAGTCCTATCTCCCTGAAG-TTATAGTGGAGCGGA-TTAA-AA--TAAGGATCTTAT
* *
5693208 CTCTCTGAGGTTACAGCGGAGCAGATC
61 CTCTCTGAAGTTACAGTGGAGCAGATC
* *
5693235 GAAGACAT-AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCT
1 GAAGACATGAGTCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAAT-AAGGATCTTATCTCT
* * *
5693299 CTGAAGTTACAGTAGAGTAGATT
65 CTGAAGTTACAGTGGAGCAGATC
* * * * * * * ** *
5693322 GCA-TCA-G-GTCTTATCTCCCTG-AGATTACAGTGGAGCAGATTGAAGA-CACTATCTTATTTC
1 GAAGACATGAGTCCTATCTCCCTGAAG-TTATAGTGGAGCGGATT-AAAATAAGGATCTTATCTC
* *
5693382 CCTG-AGATTACAGTGGAACAGATC
64 TCTGAAG-TTACAGTGGAGCAGATC
* * ** * * * * ***
5693406 GAAGA-ATTTCAGATCTTATCTCATTG-AGATTACAGCGGAGCAGATTGAAGCCAGAGAT-TTAT
1 GAAGACA--TGAG-TCCTATCTCCCTGAAG-TTATAGTGGAGCGGATTAAAATAAG-GATCTTAT
* * *
5693468 CTCCCT-AAGATTACAGCGGAGCAAATC
61 CTCTCTGAAG-TTACAGTGGAGCAGATC
* * * *
5693495 AAAGACACT-A-TCCTATCTCCCT-AAATTA-AGGTGGAGCGGATTGAAATAAAAGATCTTATCT
1 GAAGACA-TGAGTCCTATCTCCCTGAAGTTATA-GTGGAGCGGATTAAAAT-AAGGATCTTATCT
* * *
5693556 CTCTAAAGTTACAGCAGAGTAGATCGTATCAGATT
63 CTCTGAAGTT--A-C--AGT-G---G-AGCAGATC
* * *
5693591 GAAGCCA-GAGATCTTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCT
1 GAAGACATGAG-TCCTATCTCCCTGAAG-TTATAGTGGAGCGGATTAAAAT-AAGGATCTTATCT
* *
5693654 CTCTGAAGTTACAGTAGAGTAGAT
63 CTCTGAAGTTACAGTGGAGCAGAT
5693678 TGTATTAGGT
Statistics
Matches: 399, Mismatches: 85, Indels: 91
0.69 0.15 0.16
Matches are distributed among these distances:
83 4 0.01
84 58 0.15
85 51 0.13
86 31 0.08
87 72 0.18
88 15 0.04
89 89 0.22
90 5 0.01
91 2 0.01
92 1 0.00
93 3 0.01
95 3 0.01
96 11 0.03
97 12 0.03
98 41 0.10
99 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (87 bp):
GAAGACATGAGTCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAGGATCTTATCTCTC
TGAAGTTACAGTGGAGCAGATC
Found at i:5693357 original size:128 final size:128
Alignment explanation
Indices: 5693197--5693579 Score: 395
Period size: 128 Copynumber: 3.0 Consensus size: 128
5693187 CCGAAGAATT
* * *
5693197 TCAGATCTTATCTCTCTGAGGTTACAGCGGAGCAGATCGAAGACA-TAATCCTATCTCCCTGAAG
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAAG
* *
5693261 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGCA-
65 TTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATTGAAG
* * * *
5693325 TCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACACTATCTTATTTCCCTG-AGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAG-
* * * ** * *
5693389 TTACAGTGGAACAGATCGAAGAATTTCAGATCTTATCTCAT-TG-AGATTACAGCGGAGCAGATT
65 TTACAGTGGAGCGGAT-TAA-AA-TAAAGATCTTATCTC-TCTGAAG-TTACAGCAGAGTAGATT
5693452 GAAG
125 GAAG
* * * *
5693456 CCAGAGAT-TTATCTCCCTAAGATTACAGCGGAGCAAATCAAAGACACTATCCTATCTCCCT-AA
1 TCAG-G-TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAA
* * *
5693519 ATTA-AGGTGGAGCGGATTGAAATAAAAGATCTTATCTCTCTAAAGTTACAGCAGAGTAGAT
64 GTTACA-GTGGAGCGGATTAAAAT-AAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGAT
5693580 CGTATCAGAT
Statistics
Matches: 206, Mismatches: 34, Indels: 29
0.77 0.13 0.11
Matches are distributed among these distances:
127 2 0.01
128 68 0.33
129 34 0.17
130 35 0.17
131 18 0.09
132 48 0.23
133 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (128 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGT
TACAGTGGAGCGGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATTGAAG
Found at i:5693386 original size:43 final size:44
Alignment explanation
Indices: 5693156--5693539 Score: 222
Period size: 43 Copynumber: 8.8 Consensus size: 44
5693146 TCGCACCAGG
* * **
5693156 TCTTATCTCCTTGAGATTATAGTGGAGCAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA--TC-GA
* * * * *
5693202 TCTTATCTCTCTGAGGTTACAGCGGAGCAGATCGAAGACAT-AA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACATCGA
* * * * **
5693245 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGA-CATCGA
* * * *
5693289 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATT---G-CATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACATC-GA
*
5693330 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACATCGA
* * *
5693373 TCTTATTTCCCTGAGATTACAGTGGAACAGATCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA--TC-GA
** * * **
5693419 TCTTATCTCATTGAGATTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACATCGA
* * * ** *
5693463 T-TTATCTCCCTAAGATTACAGCGGAGCAAATCAAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACATCGA
* * *
5693505 TCCTATCTCCCT-AAATTA-AGGTGGAGCGGATTGAA
1 TCTTATCTCCCTGAGATTACA-GTGGAGCAGATTGAA
5693540 ATAAAAGATC
Statistics
Matches: 260, Mismatches: 61, Indels: 38
0.72 0.17 0.11
Matches are distributed among these distances:
40 1 0.00
41 30 0.12
42 22 0.08
43 103 0.40
44 34 0.13
45 4 0.02
46 64 0.25
47 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACATCGA
Found at i:5693439 original size:46 final size:43
Alignment explanation
Indices: 5693075--5693490 Score: 230
Period size: 43 Copynumber: 9.6 Consensus size: 43
5693065 ATATGAGTCC
* * * *
5693075 TATCTCCCTGA-AGTTATAGTGGAGCGGATT-AAAATAAGGATCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGATCA-GATCT
* * * * * * *
5693118 TATCTCTCTGA-AGTTACAGTAGAGTAGATCG--CACCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGATCAGATCT
* * **
5693159 TATCTCCTTGAGATTATAGTGGAGCAGACCGAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-A--TCAGATCT
* * * * * *
5693205 TATCTCTCTGAGGTTACAGCGGAGCAGATCGAAGA-CATAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATCA-GATCT
* * *
5693248 TATCTCCCTGA-AGTTACAGTGGAGCGGATT-AAAATAAAGGATCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGAT-CA-GATCT
* * * * *
5693292 TATCTCTCTGA-AGTTACAGTAGAGTAGATTG--CATCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGATCAGATCT
*
5693333 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGA-CACTATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATCA-GATCT
* * *
5693376 TATTTCCCTGAGATTACAGTGGAACAGATCGAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-A--TCAGATCT
** * *
5693422 TATCTCATTGAGATTACAGCGGAGCAGATTGAAGCCA-GAGAT-T
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--ATCAGATCT
* *
5693465 TATCTCCCTAAGATTACAGCGGAGCA
1 TATCTCCCTGAGATTACAGTGGAGCA
5693491 AATCAAAGAC
Statistics
Matches: 287, Mismatches: 65, Indels: 42
0.73 0.16 0.11
Matches are distributed among these distances:
41 57 0.20
42 12 0.04
43 112 0.39
44 36 0.13
45 1 0.00
46 66 0.23
47 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATCAGATCT
Found at i:5695249 original size:3 final size:3
Alignment explanation
Indices: 5695241--5695277 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
5695231 CAATTTTATG
* *
5695241 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5695278 ATATATATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5695319 original size:14 final size:13
Alignment explanation
Indices: 5695292--5695320 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5695282 ATATCTTTGT
5695292 TATTCTCATTATA
1 TATTCTCATTATA
5695305 TATTCTCATT-TA
1 TATTCTCATTATA
5695317 TATT
1 TATT
5695321 TACTTGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTCTCATTATA
Found at i:5695395 original size:12 final size:12
Alignment explanation
Indices: 5695380--5695404 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5695370 TATATTTGCT
5695380 TATATATGTATA
1 TATATATGTATA
5695392 TATATATGTATA
1 TATATATGTATA
5695404 T
1 T
5695405 GTATTTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATGTATA
Found at i:5695626 original size:15 final size:17
Alignment explanation
Indices: 5695594--5695634 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5695584 TCTCACATGC
*
5695594 ATATTTTTTATATGTAT
1 ATATTATTTATATGTAT
5695611 ATATTATTTAT-T-TAT
1 ATATTATTTATATGTAT
*
5695626 ATAATATTT
1 ATATTATTT
5695635 GTACGCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTATTTATATGTAT
Found at i:5696916 original size:24 final size:24
Alignment explanation
Indices: 5696901--5696952 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5696891 AATCAAAGTC
5696901 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
5696925 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
5696949 AAAT
1 AAAT
5696953 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:5699394 original size:3 final size:3
Alignment explanation
Indices: 5699388--5699422 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5699378 TGCTTCTGCT
5699388 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
5699423 TAAATCATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:5707612 original size:19 final size:19
Alignment explanation
Indices: 5707585--5707637 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
5707575 AAATTTCTAA
*
5707585 TTATGTATATCTTTAAATT
1 TTATATATATCTTTAAATT
*
5707604 TTATATATATATTTTAAATT
1 TTATATATAT-CTTTAAATT
**
5707624 TCCTATA-ATCTTTA
1 TTATATATATCTTTA
5707638 CTATATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 13 0.46
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.57
Consensus pattern (19 bp):
TTATATATATCTTTAAATT
Found at i:5707630 original size:20 final size:21
Alignment explanation
Indices: 5707590--5707630 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5707580 TCTAATTATG
*
5707590 TATATCTTTAAATTTTATATA
1 TATATCTTTAAATTTCATATA
*
5707611 TATAT-TTTAAATTTCCTATA
1 TATATCTTTAAATTTCATATA
5707631 ATCTTTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATCTTTAAATTTCATATA
Found at i:5709905 original size:24 final size:24
Alignment explanation
Indices: 5709873--5709922 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5709863 CTCCTATTGG
5709873 CCTTAACCCCTTTCAATAGTCATT
1 CCTTAACCCCTTTCAATAGTCATT
5709897 CCTTAACCCCTTTCAATAGTCATT
1 CCTTAACCCCTTTCAATAGTCATT
5709921 CC
1 CC
5709923 CTAATTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.36, G:0.04, T:0.36
Consensus pattern (24 bp):
CCTTAACCCCTTTCAATAGTCATT
Found at i:5713463 original size:110 final size:108
Alignment explanation
Indices: 5713247--5713585 Score: 524
Period size: 109 Copynumber: 3.1 Consensus size: 108
5713237 TGGATTGAGA
* **
5713247 TTTAAAAGGATATTTGGCTATTTGGTCAAACGAG--AAATCGAAACCCAGCACATTAGGGCATAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAA-CCAGCACATTAGGGCACGT
5713310 TTT-T-GAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATT
65 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATT
*
5713352 TTCTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATTGAAATCCAGCACATTAGGGCACG
1 TT-TAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAA-CCAGCACATTAGGGCACG
* * *
5713417 TTTTCTCGAATTTCCAAACGCAAAATATTCCCTTATTTTGAAATT
64 TTTTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATT
* *
5713462 TTTAAAAGAATATTTGGCTATTTGGTCGAACAAGAAAAATCGAAACCTAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACC-AGCACATTAGGGCACGT
5713527 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTT
65 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAA-TT
5713572 TTTAAAAGGATATT
1 TTTAAAAGGATATT
5713586 AATATGCGTA
Statistics
Matches: 212, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
105 2 0.01
106 31 0.15
108 30 0.14
109 97 0.46
110 52 0.25
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (108 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCAGCACATTAGGGCACGTT
TTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATT
Found at i:5715506 original size:11 final size:11
Alignment explanation
Indices: 5715484--5715516 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
5715474 AACTAATCCT
5715484 CTCTCAAATTTC
1 CTCTC-AATTTC
5715496 CTCTCAATTTC
1 CTCTCAATTTC
5715507 CTCTCAATTT
1 CTCTCAATTT
5715517 TGGTGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:5715621 original size:27 final size:26
Alignment explanation
Indices: 5715591--5715641 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5715581 ACTAAAGCAT
* *
5715591 ATTGACGATAAAGTTAAAAATAAATAA
1 ATTGA-GAGAAAGTTAAAAAAAAATAA
*
5715618 ATTGAGAGAAATTTAAAAAAAAAT
1 ATTGAGAGAAAGTTAAAAAAAAAT
5715642 TAGAGTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (26 bp):
ATTGAGAGAAAGTTAAAAAAAAATAA
Found at i:5715851 original size:6 final size:7
Alignment explanation
Indices: 5715836--5715864 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5715826 CTTTTTAAGG
5715836 AAAAGAA
1 AAAAGAA
5715843 AAAAGAA
1 AAAAGAA
5715850 AAAAG-A
1 AAAAGAA
5715856 AAAAGAA
1 AAAAGAA
5715863 AA
1 AA
5715865 GCATTCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:5715858 original size:13 final size:14
Alignment explanation
Indices: 5715836--5715864 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5715826 CTTTTTAAGG
5715836 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
5715850 AAAAG-AAAAAGAA
1 AAAAGAAAAAAGAA
5715863 AA
1 AA
5715865 GCATTCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:5716166 original size:24 final size:23
Alignment explanation
Indices: 5716128--5716173 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
5716118 TTTGGTGCTC
*
5716128 TTATTTTTCTGTTGTTTTTGTTG
1 TTATTTTTCTATTGTTTTTGTTG
5716151 TTATTTTTGCTATTGTTTTTGTT
1 TTATTTTT-CTATTGTTTTTGTT
5716174 ATTTATACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (23 bp):
TTATTTTTCTATTGTTTTTGTTG
Found at i:5717327 original size:22 final size:21
Alignment explanation
Indices: 5717298--5717368 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 21
5717288 ATTCAAAATA
5717298 ATTTTTAAAATCAAAATTTAT
1 ATTTTTAAAATCAAAATTTAT
5717319 ATTTCTT---A--AAAATTTAT
1 ATTT-TTAAAATCAAAATTTAT
* *
5717336 GTTTTTAAAATTCAAAATTCAT
1 ATTTTTAAAA-TCAAAATTTAT
5717358 ATTTTTTAAAA
1 A-TTTTTAAAA
5717369 AATATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 2 0.05
17 12 0.31
19 2 0.05
21 4 0.10
22 10 0.26
23 9 0.23
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (21 bp):
ATTTTTAAAATCAAAATTTAT
Found at i:5718016 original size:19 final size:19
Alignment explanation
Indices: 5717989--5718037 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5717979 CCTAAACATG
5717989 AACCTTGAACCCTAAAT-TA
1 AACCTTGAACCC-AAATCTA
*
5718008 GAA-CTTGAATCCAAATCTA
1 -AACCTTGAACCCAAATCTA
5718027 AACCTTGAACC
1 AACCTTGAACC
5718038 TTGGGTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (19 bp):
AACCTTGAACCCAAATCTA
Found at i:5719309 original size:27 final size:27
Alignment explanation
Indices: 5719255--5719309 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5719245 AAAAAACGTC
* ***
5719255 AAATTTAGATATCAAATTTGACCCAAA
1 AAATTTAAATATCAAATTTGAAAAAAA
*
5719282 AAATTTAAATATCAAATTTTAAAAAAA
1 AAATTTAAATATCAAATTTGAAAAAAA
5719309 A
1 A
5719310 TATCGAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (27 bp):
AAATTTAAATATCAAATTTGAAAAAAA
Found at i:5731221 original size:30 final size:30
Alignment explanation
Indices: 5731185--5731267 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
5731175 CATGTACATA
*
5731185 TATAAAAAA-ATTATATACATATATATAGAT
1 TATAAAAAAGATAAT-TACATATATATAGAT
5731215 TATAAAAAAGATAATTACATATATAT--A-
1 TATAAAAAAGATAATTACATATATATAGAT
*
5731242 TATAAACAAATAATAATTACATATAT
1 TATAAA-AAA-GATAATTACATATAT
5731268 TAAAATTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 6 0.12
28 4 0.08
29 14 0.29
30 20 0.42
31 4 0.08
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (30 bp):
TATAAAAAAGATAATTACATATATATAGAT
Found at i:5731564 original size:3 final size:3
Alignment explanation
Indices: 5731556--5731594 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
5731546 GTATATATAG
* * *
5731556 TAA TAA TAA TAA TAA TGA TAA TGA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5731595 CTTAATAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5731604 original size:20 final size:20
Alignment explanation
Indices: 5731579--5731636 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
5731569 AATGATAATG
5731579 ATAACAATAATAATAACTTA
1 ATAACAATAATAATAACTTA
* *
5731599 ATAACAAGAA-AATCAAATTTA
1 ATAACAATAATAAT--AACTTA
*
5731620 ATAAAAATAAATAATAA
1 ATAACAAT-AATAATAA
5731637 ATAAAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 3 0.10
20 9 0.30
21 13 0.43
22 2 0.07
23 3 0.10
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
ATAACAATAATAATAACTTA
Found at i:5731940 original size:23 final size:24
Alignment explanation
Indices: 5731910--5731956 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5731900 AAATTAAATC
5731910 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
5731933 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
5731957 AAGACTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:5732543 original size:23 final size:24
Alignment explanation
Indices: 5732514--5732561 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5732504 TTCTATGTTG
5732514 TAAA-AATAATATTTTTATTCATAAA
1 TAAATAATAAT-TTTTTATT-ATAAA
*
5732539 TAAATTATAATTTTTTATTATAA
1 TAAATAATAATTTTTTATTATAA
5732562 CTTATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATAATAATTTTTTATTATAAA
Found at i:5733789 original size:7 final size:7
Alignment explanation
Indices: 5733779--5733808 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5733769 ATAAATAATA
5733779 AAAAATT
1 AAAAATT
5733786 AAAAATT
1 AAAAATT
5733793 AAAAATT
1 AAAAATT
5733800 AAAAATT
1 AAAAATT
5733807 AA
1 AA
5733809 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:5736832 original size:27 final size:25
Alignment explanation
Indices: 5736738--5736832 Score: 84
Period size: 27 Copynumber: 3.6 Consensus size: 25
5736728 CTCTTTTATC
* *
5736738 ATTATTTATTTTAATTTTTTTACATTT
1 ATTATTTATTTAAATTTTTTT--ATAT
*
5736765 ATTATTTATTTGAAACTGTTTTTATAT
1 ATTATTTATTT-AAA-TTTTTTTATAT
*
5736792 -TAAATTTATTTAAATTTCTTTTATAT
1 AT-TATTTATTTAAATTT-TTTTATAT
5736818 ATTATTTATTGTAAA
1 ATTATTTATT-TAAA
5736833 CTTATGTATG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.04
26 19 0.34
27 27 0.48
28 2 0.04
29 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (25 bp):
ATTATTTATTTAAATTTTTTTATAT
Found at i:5738068 original size:12 final size:12
Alignment explanation
Indices: 5738051--5738075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5738041 ATTTTCCAAG
5738051 AAAATGAAAATA
1 AAAATGAAAATA
5738063 AAAATGAAAATA
1 AAAATGAAAATA
5738075 A
1 A
5738076 CCTTTGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:5738528 original size:14 final size:14
Alignment explanation
Indices: 5738509--5738537 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5738499 GACCTCAGTT
5738509 TTCTAAAGTGTTGA
1 TTCTAAAGTGTTGA
5738523 TTCTAAAGTGTTGA
1 TTCTAAAGTGTTGA
5738537 T
1 T
5738538 GGAGCCACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TTCTAAAGTGTTGA
Found at i:5740181 original size:21 final size:21
Alignment explanation
Indices: 5740157--5740201 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5740147 CTTAAAGCGA
5740157 AGGTAGCATCGAGAGAAGCAG
1 AGGTAGCATCGAGAGAAGCAG
5740178 AGGTAGCATCGAGAGAAGCAG
1 AGGTAGCATCGAGAGAAGCAG
5740199 AGG
1 AGG
5740202 CTCAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.40, T:0.09
Consensus pattern (21 bp):
AGGTAGCATCGAGAGAAGCAG
Done.