Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 26 of 138
Found at i:6587553 original size:21 final size:21
Alignment explanation
Indices: 6587529--6587573 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6587519 AAAAACAATG
* *
6587529 AAGAATCAATCAGTAAAAATA
1 AAGAAACAATCAGTAAAAAAA
* *
6587550 AAGAAAGAATGAGTAAAAAAA
1 AAGAAACAATCAGTAAAAAAA
6587571 AAG
1 AAG
6587574 CAAAAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.67, C:0.04, G:0.16, T:0.13
Consensus pattern (21 bp):
AAGAAACAATCAGTAAAAAAA
Found at i:6588084 original size:4 final size:4
Alignment explanation
Indices: 6588075--6588132 Score: 64
Period size: 4 Copynumber: 14.2 Consensus size: 4
6588065 CATAATTGTC
* * *
6588075 TATT TATT TATT TATT TGTT TATGT TATT TATT TGA-C TATT TATG TATT
1 TATT TATT TATT TATT TATT TAT-T TATT TATT T-ATT TATT TATT TATT
6588124 TATT TATT T
1 TATT TATT T
6588133 GTAAATATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 1 0.02
4 39 0.87
5 5 0.11
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:6588527 original size:19 final size:18
Alignment explanation
Indices: 6588505--6588545 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
6588495 GATTTTTTAA
6588505 AAAAAAAATTAATTTTTTT
1 AAAAAAAA-TAATTTTTTT
*
6588524 AAAAGAAATAATTTTTTT
1 AAAAAAAATAATTTTTTT
6588542 AAAA
1 AAAA
6588546 TCTTACCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAAAAAATAATTTTTTT
Found at i:6589292 original size:24 final size:24
Alignment explanation
Indices: 6589265--6589396 Score: 158
Period size: 24 Copynumber: 5.3 Consensus size: 24
6589255 ATTCGATTTC
*
6589265 ATGATTATTAATGTATTTAATTGT
1 ATGATTATTAATATATTTAATTGT
*
6589289 ATGATTATTAATATATTTATTTGT
1 ATGATTATTAATATATTTAATTGT
* * *
6589313 ATAATTATATTATATTTAATTTAATTGC
1 ATGA-T-TATTA-ATAT-ATTTAATTGT
6589341 ATGATTATTAATATATTTAATTGCT
1 ATGATTATTAATATATTTAATTG-T
*
6589366 -TGATTATTAATATATTTATTTGT
1 ATGATTATTAATATATTTAATTGT
6589389 ATGATTAT
1 ATGATTAT
6589397 ATGTTATTGC
Statistics
Matches: 92, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
23 1 0.01
24 62 0.67
25 4 0.04
26 10 0.11
27 4 0.04
28 11 0.12
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (24 bp):
ATGATTATTAATATATTTAATTGT
Found at i:6589344 original size:76 final size:76
Alignment explanation
Indices: 6589248--6589398 Score: 241
Period size: 76 Copynumber: 2.0 Consensus size: 76
6589238 CATTATGACA
* * *
6589248 ATATTTAATTCGATTTCATGATTATTAATGTATTTAATTG-TATGATTATTAATATATTTATTTG
1 ATATTTAATTCAATTGCATGATTATTAATATATTTAATTGCT-TGATTATTAATATATTTATTTG
6589312 TATAATTATATT
65 TATAATTATATT
*
6589324 ATATTTAATTTAATTGCATGATTATTAATATATTTAATTGCTTGATTATTAATATATTTATTTGT
1 ATATTTAATTCAATTGCATGATTATTAATATATTTAATTGCTTGATTATTAATATATTTATTTGT
*
6589389 ATGATTATAT
66 ATAATTATAT
6589399 GTTATTGCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
76 68 0.99
77 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (76 bp):
ATATTTAATTCAATTGCATGATTATTAATATATTTAATTGCTTGATTATTAATATATTTATTTGT
ATAATTATATT
Found at i:6589351 original size:20 final size:21
Alignment explanation
Indices: 6589325--6589415 Score: 64
Period size: 24 Copynumber: 4.2 Consensus size: 21
6589315 AATTATATTA
6589325 TATTTAATTTAATTGCATGAT
1 TATTTAATTTAATTGCATGAT
*
6589346 TATTAATATATTTAATTGCTTGAT
1 TATT--TA-ATTTAATTGCATGAT
* *
6589370 TATTAATATATTTATTTGTATGAT
1 TATT--TA-ATTTAATTGCATGAT
6589394 TA--T-ATGTT-ATTGCATGAT
1 TATTTAAT-TTAATTGCATGAT
6589412 TATT
1 TATT
6589416 AATGTATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.21
19 2 0.03
20 1 0.02
21 4 0.07
23 2 0.03
24 37 0.64
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (21 bp):
TATTTAATTTAATTGCATGAT
Found at i:6589361 original size:29 final size:29
Alignment explanation
Indices: 6589279--6589362 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
6589269 TTATTAATGT
6589279 ATTTAATTGTATGATTATTAATATATTT-
1 ATTTAATTGTATGATTATTAATATATTTA
* *
6589307 A--T--TTGTATAATTA-TATTATATTTA
1 ATTTAATTGTATGATTATTAATATATTTA
*
6589331 ATTTAATTGCATGATTATTAATATATTTA
1 ATTTAATTGTATGATTATTAATATATTTA
6589360 ATT
1 ATT
6589363 GCTTGATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
23 9 0.20
24 11 0.24
26 2 0.04
28 10 0.22
29 13 0.29
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (29 bp):
ATTTAATTGTATGATTATTAATATATTTA
Found at i:6589372 original size:52 final size:53
Alignment explanation
Indices: 6589279--6589383 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 53
6589269 TTATTAATGT
* * *
6589279 ATTTAATTGTATGATTATTAATATATTTATTTGTATAATTA-TATTATATTTA
1 ATTTAATTGCATGATTATTAATATATTTAATTGTATAATTATTAATATATTTA
*
6589331 ATTTAATTGCATGATTATTAATATATTTAATTGCT-TGATTATTAATATATTTA
1 ATTTAATTGCATGATTATTAATATATTTAATTG-TATAATTATTAATATATTTA
6589384 TTTGTATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
52 36 0.77
53 11 0.23
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (53 bp):
ATTTAATTGCATGATTATTAATATATTTAATTGTATAATTATTAATATATTTA
Found at i:6589410 original size:18 final size:18
Alignment explanation
Indices: 6589376--6589414 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6589366 TGATTATTAA
*
6589376 TATATTTATTTGTATGAT
1 TATATTTATTTGCATGAT
6589394 TATATGTTA-TTGCATGAT
1 TATAT-TTATTTGCATGAT
6589412 TAT
1 TAT
6589415 TAATGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (18 bp):
TATATTTATTTGCATGAT
Found at i:6589448 original size:42 final size:41
Alignment explanation
Indices: 6589355--6589456 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 41
6589345 TTATTAATAT
* * *
6589355 ATTTAATTGCTTGATTATTAATATATTTATTTGTATGATTAT
1 ATTT-ATTGCATGATTATTAATATATTTATTTGTATAATTAA
* *
6589397 ATGTTATTGCATGATTATTAATGTATTTATTTGTGTAATTAA
1 AT-TTATTGCATGATTATTAATATATTTATTTGTATAATTAA
*
6589439 ATTTGATTGCATTATTAT
1 ATTT-ATTGCATGATTAT
6589457 ATATACTTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.04
42 48 0.92
43 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (41 bp):
ATTTATTGCATGATTATTAATATATTTATTTGTATAATTAA
Found at i:6589592 original size:12 final size:12
Alignment explanation
Indices: 6589575--6589601 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6589565 ATATGATTTT
6589575 ATTTATTGCATG
1 ATTTATTGCATG
6589587 ATTTATTGCATG
1 ATTTATTGCATG
6589599 ATT
1 ATT
6589602 CAATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (12 bp):
ATTTATTGCATG
Found at i:6589627 original size:34 final size:35
Alignment explanation
Indices: 6589514--6589644 Score: 153
Period size: 34 Copynumber: 3.8 Consensus size: 35
6589504 ATTTTTGCAA
*
6589514 GCATGATTGATTGCATG-TATGATTTTATATTATT
1 GCATGATTTATTGCATGATATGATTTTATATTATT
** *
6589548 GCACAATTTATAGCATGATATGATTTTAT-TTATT
1 GCATGATTTATTGCATGATATGATTTTATATTATT
*
6589582 GCATGATTTATTGCATGAT-TCAATTTTATATTATT
1 GCATGATTTATTGCATGATAT-GATTTTATATTATT
* * *
6589617 GCATGA-TTATTACCTAATATGATTTTAT
1 GCATGATTTATTGCATGATATGATTTTAT
6589645 TCATAGTATG
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
33 1 0.01
34 57 0.70
35 23 0.28
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (35 bp):
GCATGATTTATTGCATGATATGATTTTATATTATT
Found at i:6589637 original size:68 final size:68
Alignment explanation
Indices: 6589513--6589659 Score: 165
Period size: 68 Copynumber: 2.2 Consensus size: 68
6589503 AATTTTTGCA
* * *
6589513 AGCATGATTGATTGCATGTATGATTTTATATTATTGCACAATTTATAGCATGATATGATTTTATT
1 AGCATGATTTATTGCATGTATAATTTTATATTATTGCACAATTTATAGCATAATATGATTTTATT
*
6589578 TAT
66 CAT
* ** *
6589581 TGCATGATTTATTGCATG-ATTCAATTTTATATTATTGCATGA-TTATTA-CCTAATATGATTTT
1 AGCATGATTTATTGCATGTA-T-AATTTTATATTATTGCACAATTTA-TAGCATAATATGATTTT
6589643 ATTCAT
63 ATTCAT
*
6589649 AGTATGATTTA
1 AGCATGATTTA
6589660 ATATTCATTG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
67 1 0.02
68 46 0.70
69 19 0.29
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (68 bp):
AGCATGATTTATTGCATGTATAATTTTATATTATTGCACAATTTATAGCATAATATGATTTTATT
CAT
Found at i:6590045 original size:22 final size:22
Alignment explanation
Indices: 6590020--6590061 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6590010 TTTATTTGAT
6590020 TTTTGAAGA-TATTATATAATTA
1 TTTTGAAGATTATTA-ATAATTA
*
6590042 TTTTGTAGATTATTAATAAT
1 TTTTGAAGATTATTAATAAT
6590062 AGTATAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTGAAGATTATTAATAATTA
Found at i:6591791 original size:16 final size:16
Alignment explanation
Indices: 6591770--6591800 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6591760 TTAGGATTTT
6591770 GATTTTAGAGTTTTGA
1 GATTTTAGAGTTTTGA
*
6591786 GATTTTAGGGTTTTG
1 GATTTTAGAGTTTTG
6591801 GTTTTAAAAT
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:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (16 bp):
GATTTTAGAGTTTTGA
Found at i:6591841 original size:28 final size:29
Alignment explanation
Indices: 6591758--6591863 Score: 92
Period size: 28 Copynumber: 3.7 Consensus size: 29
6591748 GGTATGAAAG
* * *
6591758 GTTTAGGATTTTGATTTTAGAGTTTTGAGA
1 GTTTAGGGTTTTGA-TTTAAAGATTTGAGA
* *
6591788 TTTTAGGGTTTTGGTTTTAAA-ATTTGAG-
1 GTTTAGGGTTTT-GATTTAAAGATTTGAGA
*
6591816 GTTTAGGGTTTTGATTTAAAGGTTTG-GA
1 GTTTAGGGTTTTGATTTAAAGATTTGAGA
* *
6591844 TTTTAGGGATTTGGATTTAA
1 GTTTAGGG-TTTTGATTTAA
6591864 GGGGTTTAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
27 8 0.13
28 22 0.35
29 16 0.26
30 15 0.24
31 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (29 bp):
GTTTAGGGTTTTGATTTAAAGATTTGAGA
Found at i:6591848 original size:15 final size:15
Alignment explanation
Indices: 6591820--6591891 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
6591810 TTTGAGGTTT
*
6591820 AGGGTTTTGA-TTTA
1 AGGGTTTGGATTTTA
*
6591834 AAGGTTTGGATTTT-
1 AGGGTTTGGATTTTA
6591848 AGGGATTTGGA-TTTA
1 AGGG-TTTGGATTTTA
*
6591863 AGGGGTTTAGATTTTA
1 A-GGGTTTGGATTTTA
*
6591879 GGGGTTTGGATTT
1 AGGGTTTGGATTT
6591892 AAGAATTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
14 14 0.30
15 26 0.55
16 7 0.15
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
AGGGTTTGGATTTTA
Found at i:6591881 original size:30 final size:29
Alignment explanation
Indices: 6591759--6591895 Score: 111
Period size: 30 Copynumber: 4.7 Consensus size: 29
6591749 GTATGAAAGG
* * * *
6591759 TTTAGGATTTTGATTTTAGAGTTTTGAGAT
1 TTTAGGGTTTGGATTTAAGAGGTTT-AGAT
* * *
6591789 TTTAGGGTTTTGGTTTTAA-A-ATTT-GAGG
1 TTTAGGG-TTTGGATTTAAGAGGTTTAGA-T
* *
6591817 TTTAGGGTTTTGATTTAA-AGGTTTGGAT
1 TTTAGGGTTTGGATTTAAGAGGTTTAGAT
*
6591845 TTTAGGGATTTGGATTTAAGGGGTTTAGAT
1 TTTAGGG-TTTGGATTTAAGAGGTTTAGAT
6591875 TTTAGGGGTTTGGATTTAAGA
1 TTTA-GGGTTTGGATTTAAGA
6591896 ATTAGTGTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
27 12 0.14
28 17 0.20
29 15 0.17
30 31 0.36
31 11 0.13
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (29 bp):
TTTAGGGTTTGGATTTAAGAGGTTTAGAT
Found at i:6591920 original size:86 final size:86
Alignment explanation
Indices: 6591759--6591922 Score: 190
Period size: 86 Copynumber: 1.9 Consensus size: 86
6591749 GTATGAAAGG
* * * * * * *
6591759 TTTAGGATTTTGATTTTAGAGTTTTGAGATTTTAGGGTTTTGGTTTTAAAATTTGAGGTTTAGGG
1 TTTAGGATTTGGATTTAAGAGGTTTGAGATTTTAGGGGTTTGGATTTAAAATTTGAGGTTTAAGA
*
6591824 TTTTGATTTAAAGGTTTGGAT
66 TTTCGATTTAAAGGTTTGGAT
*
6591845 TTTAGGGATTTGGATTTAAGGGGTTT-AGATTTTAGGGGTTTGGATTTAAGAA-TT-AGTGTTTA
1 TTTA-GGATTTGGATTTAAGAGGTTTGAGATTTTAGGGGTTTGGATTTAA-AATTTGAG-GTTTA
*
6591907 AGATTTCGTTTTAAAG
63 AGATTTCGATTTAAAG
6591923 AAAATACGAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
85 2 0.03
86 44 0.68
87 19 0.29
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (86 bp):
TTTAGGATTTGGATTTAAGAGGTTTGAGATTTTAGGGGTTTGGATTTAAAATTTGAGGTTTAAGA
TTTCGATTTAAAGGTTTGGAT
Found at i:6592306 original size:8 final size:8
Alignment explanation
Indices: 6592292--6592330 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
6592282 AATAATATAT
6592292 AAAAAATTC
1 AAAAAA-TC
6592301 -AAAAATC
1 AAAAAATC
6592308 AAAAAATC
1 AAAAAATC
6592316 AAAAAATC
1 AAAAAATC
6592324 AAAAAAT
1 AAAAAAT
6592331 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 2 0.07
8 27 0.93
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAATC
Found at i:6599401 original size:3 final size:3
Alignment explanation
Indices: 6599393--6599424 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6599383 AAAATGCAAC
6599393 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6599425 GAAAAAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6600637 original size:18 final size:19
Alignment explanation
Indices: 6600606--6600644 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
6600596 GCAATAACGG
*
6600606 ACCGTTATTACCGCTATTC
1 ACCGTTATTACCGCAATTC
6600625 ACCGTTA-TACCGCAATTC
1 ACCGTTATTACCGCAATTC
6600643 AC
1 AC
6600645 GATCGCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (19 bp):
ACCGTTATTACCGCAATTC
Found at i:6615784 original size:6 final size:7
Alignment explanation
Indices: 6615767--6615794 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
6615757 TTTGACTAAT
6615767 TTTTTTA
1 TTTTTTA
6615774 TTTTTTA
1 TTTTTTA
6615781 TTTTTTA
1 TTTTTTA
6615788 TTTTTTA
1 TTTTTTA
6615795 ATATATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:6622742 original size:24 final size:23
Alignment explanation
Indices: 6622687--6622740 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
6622677 TTTTCTTTTG
6622687 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
6622710 TATTATTATGTATATCT-TTATTCATT
1 TATT-TTATGTAT-TCTATTATT-A-T
6622736 TATTT
1 TATTT
6622741 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 5 0.19
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Found at i:6622799 original size:3 final size:3
Alignment explanation
Indices: 6622791--6622816 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6622781 AGTTATATAT
6622791 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
6622817 TTTGTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6623419 original size:20 final size:20
Alignment explanation
Indices: 6623396--6623439 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
6623386 TGCCCAGTTT
*
6623396 CCGGCGAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
6623416 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
6623436 CCGG
1 CCGG
6623440 TGAATTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.25, T:0.05
Consensus pattern (20 bp):
CCGGCAAAGAATCCCAGAAA
Found at i:6623765 original size:14 final size:15
Alignment explanation
Indices: 6623746--6623787 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
6623736 CCGAGCCGAG
6623746 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
6623760 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
6623773 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
6623787 C
1 C
6623788 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:6623778 original size:13 final size:14
Alignment explanation
Indices: 6623746--6623782 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
6623736 CCGAGCCGAG
6623746 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
6623760 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
6623772 TCCGAGCCGTT
1 -CCGAGCCGTT
6623783 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:6623874 original size:17 final size:17
Alignment explanation
Indices: 6623837--6623886 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
6623827 CTCCAGGTTT
***
6623837 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTGAA
6623854 TTTTTTTTTTTTTTGAA
1 TTTTTTTTTTTTTTGAA
*
6623871 TTTTTTTTTTATTTGA
1 TTTTTTTTTTTTTTGA
6623887 CTTTGATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTTTGAA
Found at i:6623880 original size:1 final size:1
Alignment explanation
Indices: 6623834--6623867 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
6623824 CCGCTCCAGG
6623834 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6623868 GAATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6624203 original size:152 final size:152
Alignment explanation
Indices: 6623917--6624364 Score: 758
Period size: 156 Copynumber: 2.9 Consensus size: 152
6623907 TTTTTTTTCT
6623917 TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTC
1 TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTC
6623982 TTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTCCA
66 TTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTCCA
*
6624047 ATAATTAATTGGATGATTTTGTA
131 ATAATTAATTGGATGATCTTG-A
6624070 TTTTT-TTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTC
1 TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTC
* *
6624134 TTGAGGTGAGGAAATTTTCTCAATTTTCTGTTAAAAGTATTAGAGTCAATTGAGAATAATTTTCG
66 TTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA-TTTC-
* *
6624199 ATAATTAATTAATTGGTTGATCTTGA
129 -CAA-TAATTAATTGGATGATCTTGA
*
6624225 TTTTTCTTTAA-ATAATCCGACGACGGAGCCTCTACAAGTGAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAATA-AATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
6624289 CTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA-AAGTTTC
65 CTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA-TTTC
6624353 CAATAATTAATT
129 CAATAATTAATT
6624365 ACTTGATAAA
Statistics
Matches: 279, Mismatches: 10, Indels: 13
0.92 0.03 0.04
Matches are distributed among these distances:
152 125 0.45
153 11 0.04
155 15 0.05
156 128 0.46
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (152 bp):
TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTC
TTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTCCA
ATAATTAATTGGATGATCTTGA
Found at i:6626546 original size:32 final size:31
Alignment explanation
Indices: 6626500--6626601 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 31
6626490 AGTTGGCGCA
*
6626500 AAAT-TTAAGCCCAATTAAGTTGGCATAAGAT
1 AAATGTTAAGCCCAATTAAGTTGACAT-AGAT
* *
6626531 AAATGTTAAGTCCAATCT-AGTTGTCAT--A-
1 AAATGTTAAGCCCAAT-TAAGTTGACATAGAT
6626559 AAA-GTTAAGCCCAATTAAGTTGACATGAGAT
1 AAATGTTAAGCCCAATTAAGTTGACAT-AGAT
*
6626590 GAATGTTAAGCC
1 AAATGTTAAGCC
6626602 TAATCTAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
26 1 0.02
27 19 0.33
28 3 0.05
29 1 0.02
30 1 0.02
31 6 0.10
32 26 0.45
33 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (31 bp):
AAATGTTAAGCCCAATTAAGTTGACATAGAT
Found at i:6626568 original size:59 final size:57
Alignment explanation
Indices: 6626299--6626828 Score: 298
Period size: 59 Copynumber: 8.9 Consensus size: 57
6626289 ATTTAGAGTC
* * * *
6626299 TAAGCCCAATCTAGCTAGCACAAAAGTTAAGCCCAATTAAGTTGGTAAAAGATAAATAT
1 TAAG-CCAATCTAG-TTGCACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
* * * * * * * * * * *
6626358 CAAGCCTAATCAAGCTAGCAAAAAAGTTAAGCCTAGTTAAGCTAGCATGATATCAATGT
1 TAAGCC-AATCTAG-TTGCACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
* * ** * * * * *
6626417 TAAGCCCAATTTAACTAACACAAAGGTTAAAG-CTAATTAAGTTGACA-AGAGTTGAATGTTT
1 TAAG-CCAATCT-AGTTGCACAAAAGTT-AAGCCCAATTAAGTTGGCATA-AGATAAATG--T
* * * *
6626478 TAAACTTAATCTAGTTGGCGCAAAATTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
1 TAAGC-CAATCTAGTT-GCACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
* * * *
6626537 TAAGTCCAATCTAGTTGTCATAAAAGTTAAGCCCAATTAAGTTGACATGAGATGAATGT
1 TAAG-CCAATCTAGTTG-CACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
* * * * * * * * *
6626596 TAAGCCTAATCTAGTTAGTACAAAAGTTAAGCACAGTTAATTTCGCACAAGGTGAATAT
1 TAAGCC-AATCTAGTT-GCACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
* * * * * *
6626655 TAAAGCCAATCAAGCTAGCAC-AAAGTTAATCCCAGTTAAGTTGGCATTAGATGAATGT
1 T-AAGCCAATCTAG-TTGCACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
* * *
6626713 TAAGCCCAATCTAGCTGGCAC-AAAGTTTTAAGCCCAATTAAGTTAGCATAAGATGAACT-T
1 TAAG-CCAATCTAG-TTGCACAAAAG--TTAAGCCCAATTAAGTTGGCATAAGAT-AAATGT
* * * *
6626773 TAAGCTCCATCTAGCTAGCACAAAAGTTTAAGTCCAATTAAGTTGGCA-CAGATAAA
1 TAAGC-CAATCTAG-TTGCACAAAAG-TTAAGCCCAATTAAGTTGGCATAAGATAAA
6626829 CTCTCGAGCT
Statistics
Matches: 363, Mismatches: 85, Indels: 47
0.73 0.17 0.09
Matches are distributed among these distances:
57 3 0.01
58 55 0.15
59 182 0.50
60 81 0.22
61 41 0.11
62 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (57 bp):
TAAGCCAATCTAGTTGCACAAAAGTTAAGCCCAATTAAGTTGGCATAAGATAAATGT
Found at i:6627171 original size:83 final size:84
Alignment explanation
Indices: 6626985--6627172 Score: 186
Period size: 83 Copynumber: 2.2 Consensus size: 84
6626975 TCCTAGCAAG
* ** * * * * *
6626985 ATTTGTAAGTCTT-TCAAGCTAAATTTATTTTAATGTCAAGATTTATAAAATCTCTAGGCATTAT
1 ATTTGTAAGTCTTCT-AAGCAAAACCTATTTTAATGTCAAGATTTAAAAAACCTCGAGACATAAT
*
6627049 CTCTAAATCCTTCAGGCAAA
65 CTCTAAATCCTTCAGGAAAA
*** * * *
6627069 ATTCCCAAGTTTTCAAAGCAAAACCTA-TTTAGTGTCAAGATTTAAAAAACCTCCGA-ACATAAT
1 ATTTGTAAGTCTTCTAAGCAAAACCTATTTTAATGTCAAGATTTAAAAAACCT-CGAGACATAAT
6627132 CTCTAAATCC-TCTAGGAAAA
65 CTCTAAATCCTTC-AGGAAAA
6627152 ATTTGTAAGTCTTCTAAGCAA
1 ATTTGTAAGTCTTCTAAGCAA
6627173 TATTTGTTTA
Statistics
Matches: 81, Mismatches: 20, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
82 2 0.02
83 59 0.73
84 20 0.25
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (84 bp):
ATTTGTAAGTCTTCTAAGCAAAACCTATTTTAATGTCAAGATTTAAAAAACCTCGAGACATAATC
TCTAAATCCTTCAGGAAAA
Found at i:6627416 original size:46 final size:46
Alignment explanation
Indices: 6627310--6627417 Score: 132
Period size: 46 Copynumber: 2.3 Consensus size: 46
6627300 TCGAATTTCA
* *
6627310 TTTCAATTTGATTTTTAAAGTTATCGAACCTCTAATGAGAAGAGCC
1 TTTCAATTTGATTTTTAAAGTTATCGAACCTCTAATGAAAAAAGCC
*
6627356 -TTCTAGTTTGATTTTTAAAGTTATC-AAGCCTCTAAT-AAAATAAGCC
1 TTTC-AATTTGATTTTTAAAGTTATCGAA-CCTCTAATGAAAA-AAGCC
*
6627402 TTTCAATTTAATTTTT
1 TTTCAATTTGATTTTT
6627418 TCAATATGTC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
45 8 0.15
46 42 0.79
47 3 0.06
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (46 bp):
TTTCAATTTGATTTTTAAAGTTATCGAACCTCTAATGAAAAAAGCC
Found at i:6628527 original size:27 final size:26
Alignment explanation
Indices: 6628486--6628549 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 26
6628476 AAAAGACAAA
*
6628486 AAAAAAAAAACAGTTCCTAACCTTTGCT
1 AAAAAAAAAACAGTTCCT-ACC-TTGCC
*
6628514 AAAAAAAAAA-AGTTCCTAGCTTGCC
1 AAAAAAAAAACAGTTCCTACCTTGCC
6628539 AAAAAAAAAAC
1 AAAAAAAAAAC
6628550 CAAACACCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 14 0.42
26 2 0.06
27 7 0.21
28 10 0.30
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.19
Consensus pattern (26 bp):
AAAAAAAAAACAGTTCCTACCTTGCC
Found at i:6629032 original size:9 final size:10
Alignment explanation
Indices: 6629020--6629073 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 10
6629010 TTTTTCCTTT
6629020 TGTATT-TTA
1 TGTATTATTA
6629029 TGTATT-TTA
1 TGTATTATTA
6629038 T-TATTTATTA
1 TGTA-TTATTA
6629048 T-TATTATTA
1 TGTATTATTA
6629057 TGTATTAATATA
1 TGTATT-AT-TA
6629069 TGTAT
1 TGTAT
6629074 ATCTTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.05
9 19 0.47
10 10 0.25
11 2 0.05
12 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TGTATTATTA
Found at i:6629044 original size:16 final size:16
Alignment explanation
Indices: 6629025--6629156 Score: 60
Period size: 16 Copynumber: 7.9 Consensus size: 16
6629015 CCTTTTGTAT
6629025 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
6629041 TTTATTATTATTATTA
1 TTTATTATTATTATTA
*
6629057 TGTATTAATATATGTA-TA
1 TTTATT-AT-TAT-TATTA
* *
6629075 TCT-TTATTTATT-TTT
1 TTTATTA-TTATTATTA
* *
6629090 TTTGTTAATATT-TATA
1 TTTATTATTATTAT-TA
*
6629106 TGTATT-TTATTTATATA
1 TTTATTATTA-TTAT-TA
*
6629123 GTTATATATTTATTATTA
1 TTTAT-TA-TTATTATTA
6629141 TGTTATTATTATTATT
1 T-TTATTATTATTATT
6629157 TTTTTGTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
15 15 0.17
16 30 0.33
17 20 0.22
18 12 0.13
19 10 0.11
20 3 0.03
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:6629071 original size:40 final size:37
Alignment explanation
Indices: 6629042--6629116 Score: 62
Period size: 40 Copynumber: 1.9 Consensus size: 37
6629032 ATTTTATTAT
* *
6629042 TTATTATTATTATTATGTATTAATATATGTATATCT-TTAT
1 TTATTATTATTATTA-ATATT--TATATGTAT-TTTATTAT
* * *
6629082 TTATTTTTTTTGTTAATATTTATATGTATTTTATT
1 TTATTATTATTATTAATATTTATATGTATTTTATT
6629117 TATATAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
36 2 0.07
37 11 0.38
39 4 0.14
40 12 0.41
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.65
Consensus pattern (37 bp):
TTATTATTATTATTAATATTTATATGTATTTTATTAT
Found at i:6630169 original size:17 final size:16
Alignment explanation
Indices: 6630144--6630202 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 16
6630134 GATTTATTTA
6630144 ATCTTTTTTTATCTTT
1 ATCTTTTTTTATCTTT
*
6630160 ATCTTATTTTTATTTTT
1 ATCTT-TTTTTATCTTT
*
6630177 AT-TTTACTTT-TCTTT
1 ATCTTT-TTTTATCTTT
6630192 AT-TTTTTTTAT
1 ATCTTTTTTTAT
6630203 TTTCACTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 3 0.08
15 11 0.31
16 10 0.28
17 12 0.33
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.76
Consensus pattern (16 bp):
ATCTTTTTTTATCTTT
Found at i:6630226 original size:31 final size:30
Alignment explanation
Indices: 6630155--6630232 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
6630145 TCTTTTTTTA
* *
6630155 TCTTTATCTTATTTTTATTTTTATTTTACTTT
1 TCTTTAT-TT-TTTTTATTTTCATTTTACTTC
6630187 TCTTTATTTTTTTTATTTTCACTTTTA-TTC
1 TCTTTATTTTTTTTATTTTCA-TTTTACTTC
*
6630217 TGTTCTATTTTTTTTA
1 TCTT-TATTTTTTTTA
6630233 AATAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.39
31 18 0.44
32 7 0.17
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.74
Consensus pattern (30 bp):
TCTTTATTTTTTTTATTTTCATTTTACTTC
Found at i:6630409 original size:57 final size:58
Alignment explanation
Indices: 6630245--6630511 Score: 366
Period size: 58 Copynumber: 4.7 Consensus size: 58
6630235 TAAAAAAATT
* * **
6630245 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAATTTAAA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAATTTTCA
* * *
6630303 AAAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCA
* *
6630361 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAA-TTTCC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCA
* *
6630417 AAAAAATATTTTTTAGGGAAAAGTTG-AA-TATCAATTTTTCCTAAAAATAAATTTTC-
1 AAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCA
*
6630473 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
6630512 CCCTACACAA
Statistics
Matches: 187, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
55 23 0.12
56 42 0.22
57 32 0.17
58 86 0.46
59 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (58 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCA
Found at i:6634397 original size:11 final size:11
Alignment explanation
Indices: 6634376--6634483 Score: 58
Period size: 11 Copynumber: 10.5 Consensus size: 11
6634366 ACGATAGATG
6634376 AAAAATG-AGA
1 AAAAATGAAGA
6634386 AAAAATGAAGA
1 AAAAATGAAGA
* *
6634397 AAAGATGATGA
1 AAAAATGAAGA
6634408 AAAAA--AAGGA
1 AAAAATGAA-GA
**
6634418 AAAAAAAAAGGA
1 AAAAATGAA-GA
*
6634430 AAAAA-AAAGA
1 AAAAATGAAGA
6634440 AAGAAA-GAAGA
1 AA-AAATGAAGA
6634451 AAGAAATG-A-A
1 AA-AAATGAAGA
6634461 AAAAAT--A-A
1 AAAAATGAAGA
6634469 AAAAATGAA-A
1 AAAAATGAAGA
6634479 AAAAA
1 AAAAA
6634484 AGATTCAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
8 8 0.09
9 5 0.06
10 28 0.33
11 33 0.39
12 11 0.13
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (11 bp):
AAAAATGAAGA
Found at i:6634419 original size:21 final size:19
Alignment explanation
Indices: 6634375--6634486 Score: 64
Period size: 20 Copynumber: 6.1 Consensus size: 19
6634365 AACGATAGAT
6634375 GAAAAATGAGAAAAAATGAA
1 GAAAAATGAGAAAAAA-GAA
6634395 GAAAAGATGATGAAAAAA-AA
1 GAAAA-ATGA-GAAAAAAGAA
* *
6634415 GGAAAA--A-AAAAAGGAA
1 GAAAAATGAGAAAAAAGAA
*
6634431 -AAAAA-AAGAAAGAAAGAA
1 GAAAAATGAGAAA-AAAGAA
*
6634449 GAAAGAAATGA-AAAAAATAA
1 G-AA-AAATGAGAAAAAAGAA
6634469 -AAAAATGA-AAAAAA-AA
1 GAAAAATGAGAAAAAAGAA
6634485 GA
1 GA
6634487 TTCAAATTGA
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
15 9 0.12
16 5 0.07
17 17 0.23
18 7 0.09
19 1 0.01
20 18 0.24
21 10 0.13
22 8 0.11
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (19 bp):
GAAAAATGAGAAAAAAGAA
Found at i:6634422 original size:12 final size:12
Alignment explanation
Indices: 6634407--6634437 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6634397 AAAGATGATG
6634407 AAAAAAAAGGAA
1 AAAAAAAAGGAA
6634419 AAAAAAAAGGAA
1 AAAAAAAAGGAA
6634431 AAAAAAA
1 AAAAAAA
6634438 GAAAGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:6634472 original size:8 final size:9
Alignment explanation
Indices: 6634420--6634482 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
6634410 AAAAAGGAAA
*
6634420 AAAAAAAGG
1 AAAAAAATG
*
6634429 AAAAAAAAAG
1 -AAAAAAATG
*
6634439 AAAGAAAGAAG
1 AAA-AAA-ATG
*
6634450 AAAGAAATG
1 AAAAAAATG
6634459 AAAAAAAT-
1 AAAAAAATG
6634467 AAAAAAATG
1 AAAAAAATG
6634476 AAAAAAA
1 AAAAAAA
6634483 AAGATTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
8 8 0.17
9 19 0.41
10 13 0.28
11 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAAAATG
Found at i:6636063 original size:42 final size:42
Alignment explanation
Indices: 6636004--6636136 Score: 171
Period size: 42 Copynumber: 3.1 Consensus size: 42
6635994 TGATTGTCAG
* *
6636004 GGAGCAATTTACTTTCCAAAAGTCGTAGTGCTTTTGTTTAGA
1 GGAGCAATTTACTTTCCAAAAGTCGTAGTGCCTCTGTTTAGA
*
6636046 GGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTCCAAAAGTCGTAGTGCCTCTGTTTAGA
* *
6636088 GGAGCAATTTATGTTTCTC-AAAGTCTGTTA-AGCCTCTGTTTAGA
1 GGAGCAATTTA-CTTTC-CAAAAGTC-G-TAGTGCCTCTGTTTAGA
6636132 GGAGC
1 GGAGC
6636137 TTTTGGTAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
42 50 0.62
43 10 0.12
44 20 0.25
45 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (42 bp):
GGAGCAATTTACTTTCCAAAAGTCGTAGTGCCTCTGTTTAGA
Found at i:6636386 original size:3 final size:3
Alignment explanation
Indices: 6636360--6636496 Score: 63
Period size: 3 Copynumber: 44.3 Consensus size: 3
6636350 TTTCCTTTTG
6636360 TAT T-T TAT GTAT T-T TAT TATT TAT TAT TAT TAT TAT TAT TAT GTAT
1 TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * * *
6636406 TAA TA- TAT GTAT T-T TTT TAT TTT TTT TGT TAA TAT T-T ATAT GTAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT
*
6636451 T-T TATT TAT ATAGT TAT ATATT TAT TAT TA- TGT TAT TAT TAT TAT
1 TAT TA-T TAT -TA-T TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT
6636496 T
1 T
6636497 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 34
0.71 0.07 0.23
Matches are distributed among these distances:
2 12 0.11
3 66 0.62
4 27 0.25
5 2 0.02
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6636415 original size:46 final size:45
Alignment explanation
Indices: 6636358--6636495 Score: 122
Period size: 45 Copynumber: 3.0 Consensus size: 45
6636348 TTTTTCCTTT
6636358 TGTATT-T-TATGTATTTTATTATTTATTATTATTATTATTATTA
1 TGTATTATATATGTATTTTATTATTTATTATTATTATTATTATTA
* * * *
6636401 TGTATTAATATATGTATTTTTTTATTT-TTTTTGTTAATATT-TATA
1 TGTATT-ATATATGTATTTTATTATTTATTATTATTATTATTAT-TA
* * * *
6636446 TGTATTTTATTTATATAGTTATATATTTATTATTATGTTATTATTATTA
1 TGTATTATATATGTAT-TTTAT-TATTTATTATTA--TTATTATTATTA
6636495 T
1 T
6636496 TTTTTTGTAA
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
43 6 0.08
44 8 0.11
45 23 0.32
46 21 0.29
47 4 0.05
49 10 0.14
50 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (45 bp):
TGTATTATATATGTATTTTATTATTTATTATTATTATTATTATTA
Found at i:6637370 original size:13 final size:13
Alignment explanation
Indices: 6637352--6637389 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
6637342 TCAAAAATTC
*
6637352 TTTATTTATTTGT
1 TTTATTTATTTAT
6637365 TTTATTTATTTA-
1 TTTATTTATTTAT
6637377 TTT-TTTATTTAT
1 TTTATTTATTTAT
6637389 T
1 T
6637390 AGATTAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 8 0.35
12 4 0.17
13 11 0.48
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:6637405 original size:4 final size:4
Alignment explanation
Indices: 6637352--6637389 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
6637342 TCAAAAATTC
*
6637352 TTTA TTTA TTTGT TTTA TTTA TTTA TTT- TTTA TTTA TT
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TT
6637390 AGATTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.80
5 3 0.10
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:6637456 original size:27 final size:27
Alignment explanation
Indices: 6637412--6637463 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
6637402 TTTAATCTTT
6637412 TTTTATCTTTATCTTATTTTTATTTTTG
1 TTTTATCTTTATCTTATTTTT-TTTTTG
6637440 TTTTA-CTTT-TCTTTATTTTTTTTT
1 TTTTATCTTTATC-TTATTTTTTTTT
6637464 ATTTTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 12 0.52
28 5 0.22
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.79
Consensus pattern (27 bp):
TTTTATCTTTATCTTATTTTTTTTTTG
Found at i:6637466 original size:10 final size:10
Alignment explanation
Indices: 6637428--6637468 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
6637418 CTTTATCTTA
6637428 TTTTTATTTT
1 TTTTTATTTT
*
6637438 TGTTTTACTTT
1 T-TTTTATTTT
*
6637449 TCTTTATTTT
1 TTTTTATTTT
6637459 TTTTTATTTT
1 TTTTTATTTT
6637469 CACTTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:6637474 original size:21 final size:21
Alignment explanation
Indices: 6637430--6637469 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6637420 TTATCTTATT
6637430 TTTATTTTTGTTTTACTTTTC
1 TTTATTTTTGTTTTACTTTTC
6637451 TTTATTTTT-TTTTA-TTTTC
1 TTTATTTTTGTTTTACTTTTC
6637470 ACTTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 9 0.47
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTATTTTTGTTTTACTTTTC
Found at i:6637558 original size:58 final size:56
Alignment explanation
Indices: 6637506--6637779 Score: 315
Period size: 58 Copynumber: 4.8 Consensus size: 56
6637496 AATAAAAAAA
*
6637506 TCAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTAAAAAT-AAATT
1 TCAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
* * *
6637562 TCAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
1 TC-----AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
*
6637624 TCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-AAATT
1 TC-AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
* * *
6637680 TCCAAAAAATATTTTTTAGGGAAAAATTG-AA-TATCAATTTTCCCTAAAAATAAATTT
1 T-CAAAAAATA-TTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
*
6637737 TTAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TCAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCC
6637780 CTACACAAGA
Statistics
Matches: 191, Mismatches: 13, Indels: 27
0.83 0.06 0.12
Matches are distributed among these distances:
55 28 0.15
56 31 0.16
57 37 0.19
58 44 0.23
61 43 0.23
62 8 0.04
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (56 bp):
TCAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
Found at i:6637676 original size:57 final size:57
Alignment explanation
Indices: 6637508--6637779 Score: 354
Period size: 61 Copynumber: 4.7 Consensus size: 57
6637498 TAAAAAAATC
*
6637508 AAAAAATATTTTTG-GGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAA
1 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC----A
* *
6637569 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTCA
* *
6637627 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAATTTCC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
* * * **
6637683 AAAAAATATTTTTTAGGGAAAAATTG-AA-TATCAATTTTCCCTAAAAATAAATTTTT
1 AAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
*
6637739 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
6637780 CTACACAAGA
Statistics
Matches: 191, Mismatches: 14, Indels: 16
0.86 0.06 0.07
Matches are distributed among these distances:
55 22 0.12
56 45 0.24
57 29 0.15
58 43 0.23
61 46 0.24
62 6 0.03
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
Found at i:6638533 original size:19 final size:17
Alignment explanation
Indices: 6638493--6638528 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
6638483 CTTTTAGGTA
6638493 ATTTTATTTATTTATAT
1 ATTTTATTTATTTATAT
6638510 ATTTTATTT-TTTAATAT
1 ATTTTATTTATTT-ATAT
6638527 AT
1 AT
6638529 CTTTTGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTATTTATTTATAT
Found at i:6641348 original size:32 final size:32
Alignment explanation
Indices: 6641307--6641369 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
6641297 GGCACAAAAG
* *
6641307 CATTAAACTACTTCAATTCCTTGTTACTTCTA
1 CATTAAACTACTTAAATTCCTTATTACTTCTA
*
6641339 CATTAAACTACTTAAATTTCTTATTACTTCT
1 CATTAAACTACTTAAATTCCTTATTACTTCT
6641370 TACCCTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.46
Consensus pattern (32 bp):
CATTAAACTACTTAAATTCCTTATTACTTCTA
Found at i:6641655 original size:97 final size:99
Alignment explanation
Indices: 6641549--6641799 Score: 309
Period size: 98 Copynumber: 2.6 Consensus size: 99
6641539 AAATTCAAAA
* * *
6641549 TTAATATTACAAAAATATTAAAGTA-TA-TATATCATCATGTGATCAACAA-TCAAAACATATAC
1 TTAATATTACAAAAATATTAAA-AACAAGTATATCATCATGTGATCAACAATTAAAAACATATAC
* * *
6641611 TTG-AGACATAAAAATTTATTATTAACATGTTTAAT
65 TTGAAG-CATAAAAATATATAATTAACATGCTTAAT
* *
6641646 TTAATATTAC-AAAATATTAAAAACAAGTATATCATCATGTTATCAACAATTAAAAACATATATT
1 TTAATATTACAAAAATATTAAAAACAAGTATATCATCATGTGATCAACAATTAAAAACATATACT
*
6641710 TGAAGCATGAAAATATATAATTAACATGCTTAAT
66 TGAAGCATAAAAATATATAATTAACATGCTTAAT
* * * *
6641744 TTAATGTTAC-AAAACATTAAAAACAAGTATATCATTACGCT-ATCAACAATTAAAAA
1 TTAATATTACAAAAATATTAAAAACAAGTATATCATCATG-TGATCAACAATTAAAAA
6641800 AATTTAGAAC
Statistics
Matches: 136, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
95 1 0.01
96 12 0.09
97 31 0.23
98 89 0.65
99 3 0.02
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (99 bp):
TTAATATTACAAAAATATTAAAAACAAGTATATCATCATGTGATCAACAATTAAAAACATATACT
TGAAGCATAAAAATATATAATTAACATGCTTAAT
Found at i:6641754 original size:98 final size:98
Alignment explanation
Indices: 6641576--6641799 Score: 317
Period size: 98 Copynumber: 2.3 Consensus size: 98
6641566 TTAAAGTATA
* * * *
6641576 TATATCATCATGTGATCAACAA-TCAAAACATATACTTGAGACATAAAAATTTATTATTAACATG
1 TATATCATCATGTTATCAACAATTAAAAACATATACTTGAGACATAAAAATATATAATTAACATG
* *
6641640 TTTAATTTAATATTACAAAATATTAAAAACAAG
66 CTTAATTTAATATTACAAAACATTAAAAACAAG
* *
6641673 TATATCATCATGTTATCAACAATTAAAAACATATATTTGA-AGCATGAAAATATATAATTAACAT
1 TATATCATCATGTTATCAACAATTAAAAACATATACTTGAGA-CATAAAAATATATAATTAACAT
*
6641737 GCTTAATTTAATGTTACAAAACATTAAAAACAAG
65 GCTTAATTTAATATTACAAAACATTAAAAACAAG
* * *
6641771 TATATCATTACGCTATCAACAATTAAAAA
1 TATATCATCATGTTATCAACAATTAAAAA
6641800 AATTTAGAAC
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
97 22 0.19
98 91 0.81
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (98 bp):
TATATCATCATGTTATCAACAATTAAAAACATATACTTGAGACATAAAAATATATAATTAACATG
CTTAATTTAATATTACAAAACATTAAAAACAAG
Found at i:6644486 original size:32 final size:32
Alignment explanation
Indices: 6644395--6644480 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
6644385 ATTTTTTATC
* * * **
6644395 ATAATGGTACAAAACCCATTTACTTTATTTTTT
1 ATAATGG-ATAAAACTCATTTGCTTTATTACTT
*
6644428 ATAATGGATAAAACTTATTTGCTTTATTACTT
1 ATAATGGATAAAACTCATTTGCTTTATTACTT
*
6644460 ATAATATGATAAAACTCATTT
1 ATAAT-GGATAAAACTCATTT
6644481 TTTTATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 24 0.55
33 20 0.45
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (32 bp):
ATAATGGATAAAACTCATTTGCTTTATTACTT
Found at i:6649129 original size:3 final size:3
Alignment explanation
Indices: 6649115--6649175 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
6649105 TTTTTGTTAC
* * * *
6649115 TAT TAC TAT TAT TAT TCT T-G TAT TAT TAT TAT TGT TCAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
6649159 TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
6649176 AGTATAGTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.11
3 40 0.85
4 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:6649144 original size:20 final size:18
Alignment explanation
Indices: 6649115--6649176 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 18
6649105 TTTTTGTTAC
*
6649115 TATTACTATTATTATTCTT
1 TATTA-TATTATTATTCAT
*
6649134 GTATTATTATTATTGTTCAT
1 -TATTA-TATTATTATTCAT
6649154 TATTATATTA-TATT-AT
1 TATTATATTATTATTCAT
6649170 TATTATA
1 TATTATA
6649177 GTATAGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 9 0.24
17 3 0.08
18 5 0.13
19 5 0.13
20 16 0.42
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTATATTATTATTCAT
Found at i:6649164 original size:5 final size:5
Alignment explanation
Indices: 6649154--6649251 Score: 62
Period size: 5 Copynumber: 19.8 Consensus size: 5
6649144 TATTGTTCAT
* * * * *
6649154 TATTA TATTA TATTA TTATTA TAGTA TAGTA TAGTA TAGTA TATTG TATTA
1 TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* *
6649205 TA-TA GTA-TA TAGTA -AGGTA TATTA TTATTA TA-T- TATTA TATTA
1 TATTA -TATTA TATTA TA-TTA TATTA -TATTA TATTA TATTA TATTA
6649248 TATT
1 TATT
6649252 GTTATTTTTA
Statistics
Matches: 80, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
3 2 0.03
4 7 0.09
5 60 0.75
6 11 0.14
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (5 bp):
TATTA
Found at i:6649208 original size:17 final size:17
Alignment explanation
Indices: 6649152--6649214 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 17
6649142 ATTATTGTTC
* *
6649152 ATTATTATATTATAT-T
1 ATTAGTATAGTATATGT
*
6649168 ATTATTATAGTATA-GT
1 ATTAGTATAGTATATGT
6649184 A-TAGTATAGTATATTGT
1 ATTAGTATAGTATA-TGT
6649201 ATTA-TATAGTATAT
1 ATTAGTATAGTATAT
6649215 AGTAAGGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 11 0.27
16 16 0.39
17 12 0.29
18 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (17 bp):
ATTAGTATAGTATATGT
Found at i:6649232 original size:3 final size:3
Alignment explanation
Indices: 6649224--6649418 Score: 127
Period size: 3 Copynumber: 67.3 Consensus size: 3
6649214 TAGTAAGGTA
* * *
6649224 TAT TAT TAT TA- TAT TAT TA- TAT TA- TAT TGT TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * **
6649269 TTT TAT TCT TAC TAT TAT TAT TAT TAT TAT TGT TGT TAT TGT TGT CGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
6649317 TGT TAT TGT TGT TAT T-T TA- CAA TAT AAT ATAT TAT TA- TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * *
6649360 TAC TA- TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6649407 TAT TAT T-T TAT T
1 TAT TAT TAT TAT T
6649419 TTTACTTTTA
Statistics
Matches: 151, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
2 15 0.10
3 134 0.89
4 2 0.01
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6649989 original size:18 final size:19
Alignment explanation
Indices: 6649962--6650000 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6649952 GGAATGAATT
6649962 TTTGAATTTTT-GATAGGA
1 TTTGAATTTTTCGATAGGA
* *
6649980 TTTGAGTTTTTCGATGGGA
1 TTTGAATTTTTCGATAGGA
6649999 TT
1 TT
6650001 CTAGTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (19 bp):
TTTGAATTTTTCGATAGGA
Found at i:6650268 original size:19 final size:19
Alignment explanation
Indices: 6650244--6650284 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
6650234 TCGTAGGTTT
6650244 TTTTTTCATTTTATTTTTA
1 TTTTTTCATTTTATTTTTA
**
6650263 TTTTTTGGTTTTATTTTTA
1 TTTTTTCATTTTATTTTTA
6650282 TTT
1 TTT
6650285 ATTTTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTTCATTTTATTTTTA
Found at i:6650273 original size:30 final size:30
Alignment explanation
Indices: 6650239--6650296 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
6650229 CCTGATCGTA
6650239 GGTTTT-TTTTTCATTTTATTTT-TATTTTTT
1 GGTTTTATTTTT-A-TTTATTTTATATTTTTT
6650269 GGTTTTATTTTTATTTATTTTATATTTT
1 GGTTTTATTTTTATTTATTTTATATTTT
6650297 GCATTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.78
Consensus pattern (30 bp):
GGTTTTATTTTTATTTATTTTATATTTTTT
Found at i:6650303 original size:29 final size:29
Alignment explanation
Indices: 6650253--6650313 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6650243 TTTTTTTCAT
* *
6650253 TTTATTTTTATTTTTTGGTTTTATT-TTTA
1 TTTATTTTTATATTTTGATTTT-TTATTTA
6650282 TTTA-TTTTATATTTTGCATTTTTTATTTA
1 TTTATTTTTATATTTTG-ATTTTTTATTTA
6650311 TTT
1 TTT
6650314 TACTAACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (29 bp):
TTTATTTTTATATTTTGATTTTTTATTTA
Found at i:6650304 original size:25 final size:26
Alignment explanation
Indices: 6650276--6650340 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
6650266 TTTGGTTTTA
6650276 TTTTTATTTATTTTA-T-A-TTTTGCAT
1 TTTTTATTTATTTTACTAACTTTT--AT
6650301 TTTTTATTTATTTTACTAACTTTTAT
1 TTTTTATTTATTTTACTAACTTTTAT
*
6650327 TATTTATTTATTTT
1 TTTTTATTTATTTT
6650341 TACTCAGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 15 0.42
26 16 0.44
27 1 0.03
28 4 0.11
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTATTTATTTTACTAACTTTTAT
Found at i:6650339 original size:26 final size:22
Alignment explanation
Indices: 6650251--6650340 Score: 78
Period size: 25 Copynumber: 3.9 Consensus size: 22
6650241 TTTTTTTTTC
*
6650251 ATTTTATTTTTA-TT-TTTT-G
1 ATTTTATTTTTATTTATTTTAT
*
6650270 GTTTTATTTTTATTTATTTTAT
1 ATTTTATTTTTATTTATTTTAT
6650292 ATTTTGCATTTTTTATTTATTTTACT
1 ATTTT--A-TTTTTATTTATTTTA-T
6650318 AACTTTTATTATTTATTTATTTT
1 -A-TTTTATT-TTTATTTATTTT
6650341 TACTCAGTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
19 11 0.19
20 2 0.03
21 4 0.07
22 4 0.07
24 1 0.02
25 17 0.29
26 14 0.24
27 1 0.02
28 4 0.07
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (22 bp):
ATTTTATTTTTATTTATTTTAT
Found at i:6652017 original size:186 final size:186
Alignment explanation
Indices: 6651703--6652076 Score: 543
Period size: 186 Copynumber: 2.0 Consensus size: 186
6651693 TTAAGATAAA
* * * *
6651703 GTTCATATTATTTTGTATCCTCATTCACACATAGCACATTATTCTTATGCATGAACTCTATACCT
1 GTTCATATTATTATATACCCTCATTCACACATAGCACATTATTCTCATGCATGAACTCTATACCT
* * * *
6651768 AAGTTTCATCTCTTTTAAGAGGGAGTAAAGTATCTATGCTATTATGAGTTGATAACCTTTGCAAT
66 AAGTTTCATCTCTTTTAAAAGGGAGTAAAGTACCTATACTATCATGAGTTGATAACCTTTGCAAT
** * *
6651833 AACAAGTGAAATATGCCCACTCAAATCGAATCATTTTCATTCGTAGCCTATGATAG
131 AACAAGCAAAATATGCCCACTCAAATCGAACCATTTTCATTCATAGCCTATGATAG
* *
6651889 GTTCATATTATTATATACCCTCATTCACACATAGTACATTATTCTCATGCATGATCTCTATA-CT
1 GTTCATATTATTATATACCCTCATTCACACATAGCACATTATTCTCATGCATGAACTCTATACCT
** * *
6651953 CAAGTTTTGTCTCTTTTAAAAGGGAGTAAAGTACCTATATTATCGTGAGTTGATAACCTTTGCAA
66 -AAGTTTCATCTCTTTTAAAAGGGAGTAAAGTACCTATACTATCATGAGTTGATAACCTTTGCAA
* * *
6652018 TAACAAGCAAAATATGCCCACTCAAATTGAACCCTTTTCGTTCATAGCCTATGATAG
130 TAACAAGCAAAATATGCCCACTCAAATCGAACCATTTTCATTCATAGCCTATGATAG
6652075 GT
1 GT
6652077 GAGAATCGAA
Statistics
Matches: 166, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
185 2 0.01
186 164 0.99
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (186 bp):
GTTCATATTATTATATACCCTCATTCACACATAGCACATTATTCTCATGCATGAACTCTATACCT
AAGTTTCATCTCTTTTAAAAGGGAGTAAAGTACCTATACTATCATGAGTTGATAACCTTTGCAAT
AACAAGCAAAATATGCCCACTCAAATCGAACCATTTTCATTCATAGCCTATGATAG
Found at i:6654334 original size:12 final size:12
Alignment explanation
Indices: 6654317--6654343 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6654307 CTCAAATGTG
6654317 CTAGAACCAAAA
1 CTAGAACCAAAA
6654329 CTAGAACCAAAA
1 CTAGAACCAAAA
6654341 CTA
1 CTA
6654344 CCCGAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.26, G:0.07, T:0.11
Consensus pattern (12 bp):
CTAGAACCAAAA
Found at i:6655595 original size:20 final size:20
Alignment explanation
Indices: 6655570--6655609 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6655560 TAAGTGCATG
*
6655570 ATAAAACAATCAAGGAAAAA
1 ATAAAAAAATCAAGGAAAAA
*
6655590 ATAAAAAAATGAAGGAAAAA
1 ATAAAAAAATCAAGGAAAAA
6655610 TGTGGCTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10
Consensus pattern (20 bp):
ATAAAAAAATCAAGGAAAAA
Found at i:6657994 original size:228 final size:230
Alignment explanation
Indices: 6657375--6657995 Score: 643
Period size: 231 Copynumber: 2.7 Consensus size: 230
6657365 TGACTTTTTT
* * *
6657375 TCAAAATCACTAAATGGT-ATTATCCAAGTATTCATGTTTGAATTTCATTAAATTTTTTTTGTGG
1 TCAAAATCACTCAATGGTGA-CATCCAACTATTCATGTTTGAATTTCATT-AATTTTTTTTGTGG
* **
6657439 GAGTTTTCATTAAACAATTTTTTATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCTG-TGG
64 GAGTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTC-GATGG
* * * * * *
6657503 TGATAT-TGAGTATTTATGTTTGAATATCATT--AAAATTTTATCAATGGTGATACTTGAGCCTT
128 TGATATCCGAGTATTCATGTTTGAATATCATTAAAAAAATTTATCAATGATGATACCTGAACCTT
** ** ** * *
6657565 TTAATTAAAATTTTCTCGATGATGTTATTTACGTTTTC
193 TTAATTAAAATTTTCTCGAACATAATATCCAAGCTTTC
** * ** * * * **
6657603 TTGAAATTACTCTGTGGTGATATCCAAGTATTCATGTTTGAGTTTCATTTTTTTTTTTTTTTGGT
1 TCAAAATCACTCAATGGTGACATCCAACTATTCATGTTTGAATTTCA---TTAATTTTTTTT-GT
* * *
6657668 GGGAGTTTTCATTAAACAATTCTCGGTGGTGATAT-CAAGCCTTTACATTAAAACTTACTC-AGT
62 GGGAGTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCGA-T
**
6657731 GGTGATATCCGAGTATTCATGTTTGAATATCATTAAAAAAATTT-T-GGTGATGATATCCT-AAC
126 GGTGATATCCGAGTATTCATGTTTGAATATCATTAAAAAAATTTATCAATGATGATA-CCTGAAC
*
6657793 CTTTTAATTAAAATTTTTTC-AACATCAATATCCAAGCTTTC
190 CTTTTAATTAAAATTTTCTCGAACAT-AATATCCAAGCTTTC
* ** **
6657834 TCAAAATCATTCAATGGTGACATTTAACTATTCATGTTTGAATTTCATTAATTTTTTTTGTTAGA
1 TCAAAATCACTCAATGGTGACATCCAACTATTCATGTTTGAATTTCATTAATTTTTTTTGTGGGA
* * * * ** *
6657899 GTTTTCATAAAACAATTCTAGATGATAATATCCGAGTATTTTCATTAAAACTTACTCGATAGTGA
66 GTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCGATGGTGA
6657964 TATCCGAGTATTCATGTTTGAATATCATTAAA
131 TATCCGAGTATTCATGTTTGAATATCATTAAA
6657996 GTTTCCTCTA
Statistics
Matches: 323, Mismatches: 56, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
227 30 0.09
228 106 0.33
229 2 0.01
230 44 0.14
231 131 0.41
232 3 0.01
233 7 0.02
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (230 bp):
TCAAAATCACTCAATGGTGACATCCAACTATTCATGTTTGAATTTCATTAATTTTTTTTGTGGGA
GTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCGATGGTGA
TATCCGAGTATTCATGTTTGAATATCATTAAAAAAATTTATCAATGATGATACCTGAACCTTTTA
ATTAAAATTTTCTCGAACATAATATCCAAGCTTTC
Found at i:6658054 original size:228 final size:226
Alignment explanation
Indices: 6657375--6658078 Score: 656
Period size: 228 Copynumber: 3.1 Consensus size: 226
6657365 TGACTTTTTT
* * *
6657375 TCAAAATCACTAAATGGT-ATTATCCAAGTATTCATGTTTGAATTTCATTAAATTTTTTTTGTGG
1 TCAAAATCACTCAATGGTGA-CATCCAACTATTCATGTTTGAATTTCATT-AATTTTTTTTGTGG
* **
6657439 GAGTTTTCATTAAACAATTTTTTATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCTG-TGG
64 GAGTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTC-GATGG
* * *
6657503 TGATAT-TGAGTATTTATGTTTGAATATCATTAAAATTTTATCAATGGT-GATACTT-GAGCCTT
128 TGATATCCGAGTATTCATGTTTGAATATCATTAAAA-TTT-TCTAT-GTAGATA-TTCGAGCCTT
* ** * *
6657565 TTAATTAAAATTTTCTCGATGATGTTATTTACGTTTTC
189 TTAATTAAAATTTTCTCGATGATGATATCCAAGCTTTC
** * ** * * * **
6657603 TTGAAATTACTCTGTGGTGATATCCAAGTATTCATGTTTGAGTTTCATTTTTTTTTTTTTTTGGT
1 TCAAAATCACTCAATGGTGACATCCAACTATTCATGTTTGAATTTCA---TTAATTTTTTTT-GT
* * *
6657668 GGGAGTTTTCATTAAACAATTCTCGGTGGTGATAT-CAAGCCTTTACATTAAAACTTACTC-AGT
62 GGGAGTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCGA-T
* * * * *
6657731 GGTGATATCCGAGTATTCATGTTTGAATATCATTAAAAAAATTT-T-GGTGATGATATCCTAACC
126 GGTGATATCCGAGTATTCATGTTTGAATATCATT--AAAATTTTCTATGT-A-GATATTCGAGCC
* ** *
6657794 TTTTAATTAAAATTTTTTC-AACATCAATATCCAAGCTTTC
187 TTTTAATTAAAATTTTCTCGATGAT-GATATCCAAGCTTTC
* ** **
6657834 TCAAAATCATTCAATGGTGACATTTAACTATTCATGTTTGAATTTCATTAATTTTTTTTGTTAGA
1 TCAAAATCACTCAATGGTGACATCCAACTATTCATGTTTGAATTTCATTAATTTTTTTTGTGGGA
* * * * ** *
6657899 GTTTTCATAAAACAATTCTAGATGATAATATCCGAGTATTTTCATTAAAACTTACTCGATAGTGA
66 GTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCGATGGTGA
* * *
6657964 TATCCGAGTATTCATGTTTGAATATCATTAAAGTTTCCTCTATGTAGATATTCGAGGCTTTTAAC
131 TATCCGAGTATTCATGTTTGAATATCATTAAAATTT--TCTATGTAGATATTCGAGCCTTTTAAT
* * *
6658029 TAAAATTTTCTCGGTGGTGATATCCAAACTTT-
194 TAAAATTTTCTCGATGATGATATCCAAGCTTTC
*
6658061 TCCAAAAGCACTCAATGG
1 T-CAAAATCACTCAATGG
6658079 CAATATCTGA
Statistics
Matches: 380, Mismatches: 73, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
226 5 0.01
227 31 0.08
228 157 0.41
229 5 0.01
230 47 0.12
231 129 0.34
232 2 0.01
233 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (226 bp):
TCAAAATCACTCAATGGTGACATCCAACTATTCATGTTTGAATTTCATTAATTTTTTTTGTGGGA
GTTTTCATTAAACAATTCTAGATGGTGATATCCAAGCCTTTTCATTAAAACTTACTCGATGGTGA
TATCCGAGTATTCATGTTTGAATATCATTAAAATTTTCTATGTAGATATTCGAGCCTTTTAATTA
AAATTTTCTCGATGATGATATCCAAGCTTTC
Found at i:6658171 original size:32 final size:33
Alignment explanation
Indices: 6658130--6658201 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
6658120 TGATGGTAAC
* * * *
6658130 ATCCGAGC-TTTTACAAATCATTTGGTAGTGAT
1 ATCCAAGCTTTTTACAAATCACTCGATAGTGAT
*
6658162 ATCCAAGCTTTTTTCAAATCACTCGATAGTGAT
1 ATCCAAGCTTTTTACAAATCACTCGATAGTGAT
6658195 ATCCAAG
1 ATCCAAG
6658202 TATCCAAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (33 bp):
ATCCAAGCTTTTTACAAATCACTCGATAGTGAT
Found at i:6658514 original size:24 final size:25
Alignment explanation
Indices: 6658482--6658543 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 25
6658472 ATTTACTTGA
*
6658482 TGGTGATATCTGAA-TCTTTTTTAG
1 TGGTGATATCTGAAGTCTTTTTCAG
*
6658506 TGGTGATATC-CAAGTCTTTTTCAG
1 TGGTGATATCTGAAGTCTTTTTCAG
6658530 TGGTGATATCTGAA
1 TGGTGATATCTGAA
6658544 ATCATCTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 29 0.88
25 2 0.06
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (25 bp):
TGGTGATATCTGAAGTCTTTTTCAG
Found at i:6658597 original size:81 final size:82
Alignment explanation
Indices: 6658441--6658599 Score: 203
Period size: 81 Copynumber: 2.0 Consensus size: 82
6658431 ATCTTAGCAC
* * * * * **
6658441 TTTTCAGTGGTGATATCCAAAATCATTTTGTATTTACTTGATGGTGATATCTGAATCTTTTTTAG
1 TTTTCAGTGGTGATATCCAAAATCATTCTGCATTCACTCGATAGTGATATCTGAATCCATTTTAG
6658506 TGGTGATATCCAAGTCT
66 TGGTGATATCCAAGTCT
** * * *
6658523 TTTTCAGTGGTGATATCTGAAATCA-TCTGCATTCACTCGATAGTGATATTTGAGTCCATTTTGG
1 TTTTCAGTGGTGATATCCAAAATCATTCTGCATTCACTCGATAGTGATATCTGAATCCATTTTAG
6658587 TGGTGATATCCAA
66 TGGTGATATCCAA
6658600 AATTATTTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
81 42 0.65
82 23 0.35
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (82 bp):
TTTTCAGTGGTGATATCCAAAATCATTCTGCATTCACTCGATAGTGATATCTGAATCCATTTTAG
TGGTGATATCCAAGTCT
Found at i:6658845 original size:22 final size:23
Alignment explanation
Indices: 6658818--6658869 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
6658808 TCAAAAATTC
6658818 AACAAA-ATCCAAAAAAATA-AA
1 AACAAACATCCAAAAAAATATAA
*
6658839 GAACAAACTATCCAAAAATATATAA
1 -AACAAAC-ATCCAAAAAAATATAA
6658864 AACAAA
1 AACAAA
6658870 TAAACAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.23
24 18 0.69
25 2 0.08
ACGTcount: A:0.69, C:0.15, G:0.02, T:0.13
Consensus pattern (23 bp):
AACAAACATCCAAAAAAATATAA
Found at i:6658853 original size:24 final size:24
Alignment explanation
Indices: 6658824--6658869 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6658814 ATTCAACAAA
6658824 ATCCAAAAAAATA-AAGAACAAACT
1 ATCCAAAAAAATATAA-AACAAACT
*
6658848 ATCCAAAAATATATAAAACAAA
1 ATCCAAAAAAATATAAAACAAA
6658870 TAAACAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.15
Consensus pattern (24 bp):
ATCCAAAAAAATATAAAACAAACT
Found at i:6659399 original size:19 final size:18
Alignment explanation
Indices: 6659362--6659410 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6659352 CAATAAAAAT
* *
6659362 TCAAGTCAATTCT-AAGC
1 TCAATTCAATTTTAAAGC
6659379 TCAAATTCAATTTTAAAGC
1 TC-AATTCAATTTTAAAGC
*
6659398 TCAATTTAATTTT
1 TCAATTCAATTTT
6659411 TTTAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 19 0.70
19 6 0.22
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (18 bp):
TCAATTCAATTTTAAAGC
Found at i:6659411 original size:19 final size:19
Alignment explanation
Indices: 6659375--6659410 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6659365 AGTCAATTCT
6659375 AAGCTCAAATTCAATTTTA
1 AAGCTCAAATTCAATTTTA
*
6659394 AAGCTC-AATTTAATTTT
1 AAGCTCAAATTCAATTTT
6659411 TTTAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (19 bp):
AAGCTCAAATTCAATTTTA
Found at i:6663871 original size:8 final size:8
Alignment explanation
Indices: 6663860--6663884 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6663850 TGACAAATTG
6663860 ATGGACAA
1 ATGGACAA
6663868 ATGGACAA
1 ATGGACAA
6663876 ATGGACAA
1 ATGGACAA
6663884 A
1 A
6663885 CAGACAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.24, T:0.12
Consensus pattern (8 bp):
ATGGACAA
Found at i:6664820 original size:14 final size:15
Alignment explanation
Indices: 6664803--6664832 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6664793 CCTCAAAATT
6664803 AAAACAAAAA-AAAA
1 AAAACAAAAATAAAA
6664817 AAAACAAAAATAAAA
1 AAAACAAAAATAAAA
6664832 A
1 A
6664833 TAAAGATACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAACAAAAATAAAA
Found at i:6665561 original size:32 final size:33
Alignment explanation
Indices: 6665504--6665570 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 33
6665494 TAATAATAAA
* * * * *
6665504 ATAAAATTTTAATGATTTGTATATTTTTATTAT
1 ATAAAATATTAATAATTTATATATTTATATCAT
6665537 ATAAAATATTAA-AATTTATATATTTATATCAT
1 ATAAAATATTAATAATTTATATATTTATATCAT
6665569 AT
1 AT
6665571 TTTATATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (33 bp):
ATAAAATATTAATAATTTATATATTTATATCAT
Found at i:6665688 original size:13 final size:13
Alignment explanation
Indices: 6665670--6665699 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6665660 AAATCATATC
*
6665670 ATTTTCATATTTT
1 ATTTTCATATTAT
6665683 ATTTTCATATTAT
1 ATTTTCATATTAT
6665696 ATTT
1 ATTT
6665700 ATATCATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTCATATTAT
Found at i:6665868 original size:18 final size:19
Alignment explanation
Indices: 6665838--6665873 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
6665828 ATAAATTTTT
6665838 AAAATTAATTAATATTTAA
1 AAAATTAATTAATATTTAA
6665857 AAAATTAA-TAATATTTA
1 AAAATTAATTAATATTTA
6665874 TAATAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTAATTAATATTTAA
Found at i:6665899 original size:22 final size:22
Alignment explanation
Indices: 6665873--6665921 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6665863 AATAATATTT
6665873 ATAATAGTTTA-TTAGTAAATA
1 ATAATAGTTTATTTAGTAAATA
* *
6665894 ATTAAT-TTTTATTTATTAAATA
1 A-TAATAGTTTATTTAGTAAATA
6665916 ATAATA
1 ATAATA
6665922 AATTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
ATAATAGTTTATTTAGTAAATA
Found at i:6667220 original size:23 final size:24
Alignment explanation
Indices: 6667188--6667236 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
6667178 AAAGTAAAAG
*
6667188 AAATTGTAAAT-AT-AGTTTTTTT
1 AAATTGTAAATAATAAGTATTTTT
6667210 AAATTAGTAAATAATAAGTATTTTT
1 AAATT-GTAAATAATAAGTATTTTT
6667235 AA
1 AA
6667237 TTCTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 6 0.26
24 2 0.09
25 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (24 bp):
AAATTGTAAATAATAAGTATTTTT
Found at i:6667603 original size:12 final size:13
Alignment explanation
Indices: 6667568--6667598 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
6667558 TTTTATAATG
6667568 TTATGAAAA-TTC
1 TTATGAAAATTTC
6667580 TTATGAAAATTTC
1 TTATGAAAATTTC
6667593 TTATGA
1 TTATGA
6667599 TATTTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (13 bp):
TTATGAAAATTTC
Found at i:6667776 original size:34 final size:34
Alignment explanation
Indices: 6667733--6667839 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 34
6667723 AGGTTTTATT
*
6667733 TAAGTTTAAATAATTTATTGGATATGCATATTTT-A
1 TAAG-TTAAATAATTTATTGAATATGCAT-TTTTGA
* * *
6667768 TAAGTTAAATAACTTATAGAATATGTATTTTTGA
1 TAAGTTAAATAATTTATTGAATATGCATTTTTGA
* * * * * * *
6667802 CAAGCTATATAATTTATTAAAAATGTATATTTGA
1 TAAGTTAAATAATTTATTGAATATGCATTTTTGA
6667836 TAAG
1 TAAG
6667840 GCATTCGATT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
33 4 0.07
34 50 0.86
35 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (34 bp):
TAAGTTAAATAATTTATTGAATATGCATTTTTGA
Found at i:6667887 original size:17 final size:17
Alignment explanation
Indices: 6667867--6667900 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6667857 TATGAATATT
6667867 TAAAAAA-AATTTAAATA
1 TAAAAAATAA-TTAAATA
6667884 TAAAAAATAATTAAATA
1 TAAAAAATAATTAAATA
6667901 ATTTTACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATAATTAAATA
Found at i:6676460 original size:11 final size:13
Alignment explanation
Indices: 6676421--6676458 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
6676411 TTTTTATAAT
**
6676421 ATTATAATAATTA
1 ATTATAATAAAAA
6676434 ATTATAATAAAAA
1 ATTATAATAAAAA
6676447 ATTAT-ATAAAAA
1 ATTATAATAAAAA
6676459 TTCATCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTATAATAAAAA
Found at i:6676658 original size:16 final size:15
Alignment explanation
Indices: 6676637--6676669 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
6676627 TTTATTTTTT
6676637 TAATAAAAATTAAAAA
1 TAATAAAAA-TAAAAA
6676653 TAATAAAAATAAAAA
1 TAATAAAAATAAAAA
6676668 TA
1 TA
6676670 CCAGTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAATAAAAATAAAAA
Found at i:6677313 original size:43 final size:41
Alignment explanation
Indices: 6677214--6677312 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
6677204 GCATTTATAA
* *
6677214 TTTAAA-TTTG-AATAATATTTATTTAAAGATTAAAAAAAT
1 TTTAAATTTTGTAAAAATATTTATTTAAAAATTAAAAAAAT
*
6677253 TTTAAATTTTGTAAAAATATTTATTTAAAAATTTATGAAAAAT
1 TTTAAATTTTGTAAAAATATTTATTTAAAAA-TTA-AAAAAAT
*
6677296 TTTAAAATTTTTTAAAA
1 TTT-AAATTTTGTAAAA
6677313 TTTACATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
39 6 0.12
40 4 0.08
41 17 0.33
42 3 0.06
43 9 0.18
44 12 0.24
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (41 bp):
TTTAAATTTTGTAAAAATATTTATTTAAAAATTAAAAAAAT
Found at i:6677867 original size:12 final size:12
Alignment explanation
Indices: 6677846--6677882 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6677836 GAGTTCGATT
*
6677846 ATTCATACTCGA
1 ATTCAAACTCGA
6677858 ATTCAAACTCGA
1 ATTCAAACTCGA
*
6677870 ATTCGAACTCGA
1 ATTCAAACTCGA
6677882 A
1 A
6677883 ATATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (12 bp):
ATTCAAACTCGA
Found at i:6681813 original size:2 final size:2
Alignment explanation
Indices: 6681806--6681852 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
6681796 ACAGTTTCAA
*
6681806 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6681848 AT AT A
1 AT AT A
6681853 AACACAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6688816 original size:19 final size:19
Alignment explanation
Indices: 6688792--6688836 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
6688782 TTTAATGCAT
6688792 GGTTTTTTAATAAGTCATC
1 GGTTTTTTAATAAGTCATC
6688811 GGTTTTTTAATAAGTCATC
1 GGTTTTTTAATAAGTCATC
6688830 GGTTTTT
1 GGTTTTT
6688837 GCGCACACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (19 bp):
GGTTTTTTAATAAGTCATC
Found at i:6690764 original size:17 final size:18
Alignment explanation
Indices: 6690724--6690764 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
6690714 ATTGAATGTA
6690724 AATTAATTTTATTATATTT
1 AATTAA-TTTATTATATTT
6690743 -A-TAATTTATT-TATTT
1 AATTAATTTATTATATTT
6690758 AATTAAT
1 AATTAAT
6690765 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 7 0.35
18 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTAATTTATTATATTT
Found at i:6691379 original size:18 final size:19
Alignment explanation
Indices: 6691358--6691403 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
6691348 TAATTCGTGA
6691358 ATTTAATTGAATTTTTA-T
1 ATTTAATTGAATTTTTATT
**
6691376 ATTTAATTTTATTTTTATT
1 ATTTAATTGAATTTTTATT
6691395 ATTTTAATT
1 A-TTTAATT
6691404 AATAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.62
19 2 0.08
20 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTAATTGAATTTTTATT
Found at i:6691609 original size:11 final size:11
Alignment explanation
Indices: 6691557--6691591 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
6691547 AAAAATATAA
6691557 AATTT-AATTT
1 AATTTAAATTT
*
6691567 AATTTAAATTA
1 AATTTAAATTT
6691578 AATTTAAATTT
1 AATTTAAATTT
6691589 AAT
1 AAT
6691592 ATCGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:6695316 original size:19 final size:20
Alignment explanation
Indices: 6695294--6695360 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 20
6695284 TGAATTAATC
6695294 TTAAATTATAAT-AAAATAT
1 TTAAATTATAATAAAAATAT
* *
6695313 TTAATATGAT-ATCAAAAT-T
1 TTAA-ATTATAATAAAAATAT
* *
6695332 TTAAA-AATATTTAAAAATAT
1 TTAAATTATA-ATAAAAATAT
6695352 TTAAATTAT
1 TTAAATTAT
6695361 GAATTTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.05
18 1 0.03
19 17 0.46
20 15 0.41
21 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (20 bp):
TTAAATTATAATAAAAATAT
Found at i:6695346 original size:10 final size:10
Alignment explanation
Indices: 6695326--6695356 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
6695316 ATATGATATC
6695326 AAAAT-TTTA
1 AAAATATTTA
6695335 AAAATATTTA
1 AAAATATTTA
6695345 AAAATATTTA
1 AAAATATTTA
6695355 AA
1 AA
6695357 TTATGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATATTTA
Found at i:6696610 original size:29 final size:31
Alignment explanation
Indices: 6696538--6696610 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 31
6696528 TAGTTAATTT
* *
6696538 AAAATATT-GGTTTTATTTAATTAAACCCTT
1 AAAATATTATGTTTTATTTAATTAAACCCTC
*
6696568 AAAATATTAT-TTTTGTTTAATT-AACCC-C
1 AAAATATTATGTTTTATTTAATTAAACCCTC
6696596 AAAAT-TTAGTGTTTT
1 AAAATATTA-TGTTTT
6696611 TCATGCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 3 0.08
28 6 0.16
29 9 0.24
30 19 0.51
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (31 bp):
AAAATATTATGTTTTATTTAATTAAACCCTC
Found at i:6697173 original size:20 final size:22
Alignment explanation
Indices: 6697136--6697176 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
6697126 AAATTTTGTT
6697136 AAAAATTTGTATAAATTTAATAA
1 AAAAATTTGTAT-AATTTAATAA
6697159 AAAAATTT-TAT-ATTTAAT
1 AAAAATTTGTATAATTTAAT
6697177 GTATTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAAATTTGTATAATTTAATAA
Found at i:6702467 original size:12 final size:12
Alignment explanation
Indices: 6702450--6702479 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6702440 AACACGTGTT
*
6702450 TTTCATTTTCCA
1 TTTCATTTTCAA
6702462 TTTCATTTTCAA
1 TTTCATTTTCAA
6702474 TTTCAT
1 TTTCAT
6702480 AAAAAATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCATTTTCAA
Found at i:6703428 original size:17 final size:17
Alignment explanation
Indices: 6703406--6703439 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6703396 TGAATTGATT
*
6703406 TTTATTTAAATTTTTTA
1 TTTATTTAAATTATTTA
*
6703423 TTTATTTTAATTATTTA
1 TTTATTTAAATTATTTA
6703440 ATTAGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTAAATTATTTA
Found at i:6705371 original size:30 final size:30
Alignment explanation
Indices: 6705337--6705396 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
6705327 TCTAATAGCA
6705337 TATCTGTTTAAGTATTTCTTGAAATAAGTC
1 TATCTGTTTAAGTATTTCTTGAAATAAGTC
6705367 TATCTGTTTAAGTATTTCTTGAAATAAGTC
1 TATCTGTTTAAGTATTTCTTGAAATAAGTC
6705397 AGCTATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (30 bp):
TATCTGTTTAAGTATTTCTTGAAATAAGTC
Found at i:6705636 original size:25 final size:25
Alignment explanation
Indices: 6705602--6705654 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
6705592 AAGGTATATT
6705602 TGTTATGTGAGTAT-TGGATTAATCA
1 TGTTATGTGAGTATAT-GATTAATCA
6705627 TGTTATGTGAGTATATGATTAATCA
1 TGTTATGTGAGTATATGATTAATCA
6705652 TGT
1 TGT
6705655 GATTAGCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.45
Consensus pattern (25 bp):
TGTTATGTGAGTATATGATTAATCA
Found at i:6713248 original size:21 final size:21
Alignment explanation
Indices: 6713207--6713249 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6713197 AGATAAACAC
*
6713207 ACAAAAAAATGAAACAAAAAA
1 ACAAAAAAATGAAAAAAAAAA
6713228 ACAAAAAAAT-AAAAAAGAAAA
1 ACAAAAAAATGAAAAAA-AAAA
6713249 A
1 A
6713250 GTTTATTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.05
Consensus pattern (21 bp):
ACAAAAAAATGAAAAAAAAAA
Found at i:6713588 original size:30 final size:29
Alignment explanation
Indices: 6713523--6713588 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
6713513 TTAATTATGT
* *
6713523 ATAAATATTATATTTTTATTAAATAAGATA
1 ATAAATA-TATATTTTTATTAAATAAAAAA
*
6713553 TTAAATA-ATATTTTTATTAATATAAAAAA
1 ATAAATATATATTTTTATTAA-ATAAAAAA
6713582 CATAAAT
1 -ATAAAT
6713589 TAAATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 13 0.43
29 6 0.20
30 11 0.37
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATAAATATATATTTTTATTAAATAAAAAA
Found at i:6714113 original size:16 final size:17
Alignment explanation
Indices: 6714092--6714130 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
6714082 GATCTTACAC
6714092 TAAAAAAT-TCAAAT-AT
1 TAAAAAATAT-AAATAAT
6714108 TAAAAAATATAAATAAT
1 TAAAAAATATAAATAAT
6714125 TAAAAA
1 TAAAAA
6714131 GGAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAAATATAAATAAT
Found at i:6714243 original size:15 final size:16
Alignment explanation
Indices: 6714225--6714256 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6714215 AAAATTATTT
6714225 ATTAAATAT-ATAAAA
1 ATTAAATATAATAAAA
6714240 ATTAAATATAATAAAA
1 ATTAAATATAATAAAA
6714256 A
1 A
6714257 ACAAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTAAATATAATAAAA
Found at i:6714866 original size:11 final size:11
Alignment explanation
Indices: 6714837--6714870 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6714827 TAAAAAATGG
6714837 AAATCTTTA-A
1 AAATCTTTATA
6714847 AAATCTTTATA
1 AAATCTTTATA
*
6714858 AAATTTTTATA
1 AAATCTTTATA
6714869 AA
1 AA
6714871 CTAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATCTTTATA
Found at i:6719632 original size:5 final size:6
Alignment explanation
Indices: 6719557--6719631 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
6719547 TTTCACTAAT
* * * ** *
6719557 AATAAA AACTAAA ATTAAA ACACT-AA AATCAA ATTAAA ACCAAA ATTAAA
1 AATAAA AA-TAAA AATAAA A-A-TAAA AATAAA AATAAA AATAAA AATAAA
*
6719607 ACTAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
6719632 TTTTTGGGCT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 1 0.02
6 45 0.82
7 8 0.15
8 1 0.02
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:6720044 original size:35 final size:35
Alignment explanation
Indices: 6720005--6720102 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 35
6719995 TAAAAATTTT
* * *
6720005 AAGTTTTATAGAGATTTTAGATTCGTAAAGGTTTC
1 AAGTTTCATAGAGATTTCAGATTCGCAAAGGTTTC
* * *
6720040 AAGTTTCGTAGAGATTTCATATTTGCAAAGGTTTC
1 AAGTTTCATAGAGATTTCAGATTCGCAAAGGTTTC
* *
6720075 AAATTTGCA-AG-GATTTCCAGATTTGCAA
1 AAGTTT-CATAGAGATTT-CAGATTCGCAA
6720103 GAATTCAAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
34 5 0.10
35 46 0.88
36 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (35 bp):
AAGTTTCATAGAGATTTCAGATTCGCAAAGGTTTC
Found at i:6720080 original size:17 final size:17
Alignment explanation
Indices: 6720031--6720102 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 17
6720021 TTAGATTCGT
* *
6720031 AAAGGTTTCAAGTTTCGT
1 AAAGGTTTCAAATTT-GC
* * *
6720049 AGAGATTTCATATTTGC
1 AAAGGTTTCAAATTTGC
6720066 AAAGGTTTCAAATTTGC
1 AAAGGTTTCAAATTTGC
*
6720083 -AAGGATTTCCAGATTTGC
1 AAAGG-TTT-CAAATTTGC
6720101 AA
1 AA
6720103 GAATTCAAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
16 4 0.10
17 18 0.43
18 19 0.45
19 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (17 bp):
AAAGGTTTCAAATTTGC
Found at i:6720100 original size:18 final size:18
Alignment explanation
Indices: 6720060--6720144 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 18
6720050 GAGATTTCAT
*
6720060 ATTTGCAAAGG-TTT-CAA
1 ATTTGC-AAGGATTTCCAG
6720077 ATTTGCAAGGATTTCCAG
1 ATTTGCAAGGATTTCCAG
* *
6720095 ATTTGCAA-GAATTCAAAG
1 ATTTGCAAGGATTTC-CAG
* *
6720113 ATTTGCAA-GATTTTCAT
1 ATTTGCAAGGATTTCCAG
* *
6720130 ATTTACAAGAATTTC
1 ATTTGCAAGGATTTC
6720145 ATGTTCGCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
16 4 0.07
17 22 0.41
18 28 0.52
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTTGCAAGGATTTCCAG
Done.