Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 16 of 105
Found at i:3244811 original size:22 final size:22
Alignment explanation
Indices: 3244784--3244827 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3244774 AACTTAATAT
3244784 TTTTCAAGTAGAATCGGACAAA
1 TTTTCAAGTAGAATCGGACAAA
* *
3244806 TTTTCAAGTTGAATTGGACAAA
1 TTTTCAAGTAGAATCGGACAAA
3244828 AAGCTCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (22 bp):
TTTTCAAGTAGAATCGGACAAA
Found at i:3249092 original size:18 final size:18
Alignment explanation
Indices: 3249069--3249104 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3249059 AAGTGATCTG
3249069 ATGCTAAGTTCAAGGATT
1 ATGCTAAGTTCAAGGATT
3249087 ATGCTAAGTTCAAGGATT
1 ATGCTAAGTTCAAGGATT
3249105 TTGCAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
ATGCTAAGTTCAAGGATT
Found at i:3249673 original size:16 final size:17
Alignment explanation
Indices: 3249652--3249686 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3249642 TTTGCGTTTG
*
3249652 TCTTC-TTCTTTTCTTT
1 TCTTCTTTCTTTCCTTT
3249668 TCTTCTTTCTTTCCTTT
1 TCTTCTTTCTTTCCTTT
3249685 TC
1 TC
3249687 CTTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TCTTCTTTCTTTCCTTT
Found at i:3252152 original size:2 final size:2
Alignment explanation
Indices: 3252145--3252185 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3252135 TGCAATTGTT
* *
3252145 TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3252186 TCCATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3253310 original size:22 final size:23
Alignment explanation
Indices: 3253272--3253318 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3253262 AATTTTAGTT
*
3253272 AAGGCATCTCCT-AAAAATGTCCA
1 AAGGCATATCCTAAAAAAT-TCCA
3253295 AAGGCATAT-CTAAAAAATTCCA
1 AAGGCATATCCTAAAAAATTCCA
3253317 AA
1 AA
3253319 AATTTTATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (23 bp):
AAGGCATATCCTAAAAAATTCCA
Found at i:3254572 original size:28 final size:29
Alignment explanation
Indices: 3254541--3254606 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
3254531 TTTATTAAAA
* * *
3254541 TTATTTTAAA-TATATAAATTTTAATTA-T
1 TTATTTTAAATTAT-TAAATATGAAATATT
3254569 TTATTTTAAATTATTAAATATGAAATATT
1 TTATTTTAAATTATTAAATATGAAATATT
3254598 TTATTTTAA
1 TTATTTTAA
3254607 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 20 0.61
29 13 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
TTATTTTAAATTATTAAATATGAAATATT
Found at i:3254582 original size:14 final size:14
Alignment explanation
Indices: 3254541--3254583 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3254531 TTTATTAAAA
3254541 TTATTTTAAATATAT
1 TTATTTTAAAT-TAT
**
3254556 AAATTTT-AATTAT
1 TTATTTTAAATTAT
3254569 TTATTTTAAATTAT
1 TTATTTTAAATTAT
3254583 T
1 T
3254584 AAATATGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.35
14 10 0.43
15 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTTTAAATTAT
Found at i:3265541 original size:23 final size:23
Alignment explanation
Indices: 3265512--3265564 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3265502 AATATTTATA
3265512 AAATTTTTTGAG-ATTCAAATCCT
1 AAATTTTTTGAGAATT-AAATCCT
* *
3265535 AAATTTTTTGGGAATTAAATTCT
1 AAATTTTTTGAGAATTAAATCCT
3265558 AAATTTT
1 AAATTTT
3265565 CAAGAGCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (23 bp):
AAATTTTTTGAGAATTAAATCCT
Found at i:3270900 original size:22 final size:22
Alignment explanation
Indices: 3270873--3270914 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3270863 GATTTAAAAT
*
3270873 TTTAACAAAAACAATAAATAAA
1 TTTAACAAAAACAAAAAATAAA
*
3270895 TTTAACAAAATCAAAAAATA
1 TTTAACAAAAACAAAAAATA
3270915 TAACTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
TTTAACAAAAACAAAAAATAAA
Found at i:3271015 original size:33 final size:30
Alignment explanation
Indices: 3270971--3271037 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 30
3270961 TATAAAATAT
*
3270971 AATATATATACACAAATTATCAATATTTTATAA
1 AATATAAATACACAAATTATC-ATA-TTTA-AA
*
3271004 AATATAAATACATAAATTATCATATTTAAA
1 AATATAAATACACAAATTATCATATTTAAA
3271034 AATA
1 AATA
3271038 AATTATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 6 0.19
31 4 0.12
32 3 0.09
33 19 0.59
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.37
Consensus pattern (30 bp):
AATATAAATACACAAATTATCATATTTAAA
Found at i:3274332 original size:9 final size:10
Alignment explanation
Indices: 3274306--3274344 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3274296 TATCTAAAAA
3274306 TTAAAATATTT
1 TTAAAA-ATTT
3274317 TTAAAAATTT
1 TTAAAAATTT
*
3274327 TTAAAAATAT
1 TTAAAAATTT
*
3274337 TAAAAAAT
1 TTAAAAAT
3274345 ATAAGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAAAATTT
Found at i:3274336 original size:38 final size:37
Alignment explanation
Indices: 3274291--3274365 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
3274281 GATTTTTTAG
* *
3274291 AAAAATATCTAAAAATTAAAATATTTTTAAAAATTTTT
1 AAAAATAT-TAAAAAATAAAAGATTTTTAAAAATTTTT
* * *
3274329 AAAAATATTAAAAAATATAAGATTTTTTAGAATTTTT
1 AAAAATATTAAAAAATAAAAGATTTTTAAAAATTTTT
3274366 CCATATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 24 0.75
38 8 0.25
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (37 bp):
AAAAATATTAAAAAATAAAAGATTTTTAAAAATTTTT
Found at i:3274400 original size:16 final size:14
Alignment explanation
Indices: 3274371--3274405 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
3274361 TTTTTCCATA
3274371 TTTTTAAATTTAAT
1 TTTTTAAATTTAAT
3274385 TTTTTAATATTTTAAT
1 TTTTTAA-A-TTTAAT
3274401 TTTTT
1 TTTTT
3274406 TTTGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 1 0.05
16 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTAAATTTAAT
Found at i:3274613 original size:8 final size:8
Alignment explanation
Indices: 3274602--3274626 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3274592 AATTTTCCCA
3274602 AAAATTTT
1 AAAATTTT
3274610 AAAATTTT
1 AAAATTTT
3274618 AAAATTTT
1 AAAATTTT
3274626 A
1 A
3274627 TTTTAAAAAT
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:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:3283963 original size:17 final size:18
Alignment explanation
Indices: 3283931--3283969 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3283921 TATCAAATTA
*
3283931 TATATTTTTATTAATTTT
1 TATATTTTTATAAATTTT
3283949 TATATTTTTA-AAATTTT
1 TATATTTTTATAAATTTT
3283966 TATA
1 TATA
3283970 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATTTTTATAAATTTT
Found at i:3284762 original size:18 final size:19
Alignment explanation
Indices: 3284749--3284819 Score: 76
Period size: 18 Copynumber: 3.8 Consensus size: 19
3284739 TTATTTCGAA
3284749 TTAAATTTAAATTTTAAAT
1 TTAAATTTAAATTTTAAAT
*
3284768 TTAAA-TCAAATTTTAAAT
1 TTAAATTTAAATTTTAAAT
* *
3284786 AATAAATTTTAAA--TTGAAT
1 -TTAAA-TTTAAATTTTAAAT
3284805 TTAAATTTAAATTTT
1 TTAAATTTAAATTTT
3284820 TTATTATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 6 0.14
18 16 0.38
19 16 0.38
21 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTAAATTTAAATTTTAAAT
Found at i:3284766 original size:7 final size:6
Alignment explanation
Indices: 3284749--3284818 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 6
3284739 TTATTTCGAA
* *
3284749 TTAAAT TTAAATT TTAAAT TTAAA- TCAAATT TTAAAT AATAAATT TTAAA-
1 TTAAAT TTAAA-T TTAAAT TTAAAT TTAAA-T TTAAAT -TTAAA-T TTAAAT
*
3284799 TTGAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TT
3284819 TTTATTATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.15
6 25 0.48
7 18 0.35
8 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:3284811 original size:32 final size:31
Alignment explanation
Indices: 3284756--3284816 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
3284746 GAATTAAATT
*
3284756 TAAATTTTAAATTTAAATCAAATTTTAAATAA
1 TAAATTTTAAATTGAAATCAAA-TTTAAATAA
* *
3284788 TAAATTTTAAATTGAATTTAAATTTAAAT
1 TAAATTTTAAATTGAAATCAAATTTAAAT
3284817 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (31 bp):
TAAATTTTAAATTGAAATCAAATTTAAATAA
Found at i:3284820 original size:25 final size:24
Alignment explanation
Indices: 3284747--3284819 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
3284737 TTTTATTTCG
3284747 AATTAAATTTAAATTTTAAA-TTTA
1 AATTAAATTTAAA-TTTAAATTTTA
* *
3284771 AATCAAATTTTAAATAATAAATTTTA
1 AATTAAA-TTTAAAT-TTAAATTTTA
*
3284797 AATTGAATTTAAATTTAAATTTT
1 AATTAAATTTAAATTTAAATTTT
3284820 TTATTATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 15 0.37
25 17 0.41
26 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
AATTAAATTTAAATTTAAATTTTA
Found at i:3286678 original size:18 final size:19
Alignment explanation
Indices: 3286657--3286703 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
3286647 AATATTAAAT
3286657 TAAAAAATAATATA-GAAA
1 TAAAAAATAATATAGGAAA
**
3286675 TAAAAAA-AAGGTAGGAAA
1 TAAAAAATAATATAGGAAA
*
3286693 TAATAAATAAT
1 TAAAAAATAAT
3286704 GAAACTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 17 0.74
19 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
TAAAAAATAATATAGGAAA
Found at i:3293642 original size:3 final size:3
Alignment explanation
Indices: 3293634--3293665 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3293624 TAAATTTATC
3293634 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3293666 TTCTAATGGA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3293874 original size:2 final size:2
Alignment explanation
Indices: 3293867--3293891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3293857 AACCTAACTT
3293867 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3293892 CACTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3294047 original size:2 final size:2
Alignment explanation
Indices: 3294040--3294064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3294030 TTACCATTAT
3294040 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3294065 GTACTTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3295039 original size:20 final size:20
Alignment explanation
Indices: 3294993--3295038 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3294983 TAAATCAACA
*
3294993 TTTATAATTTATTTTTTGTT
1 TTTAAAATTTATTTTTTGTT
3295013 TTTAAAATTT-TTTTTT-TT
1 TTTAAAATTTATTTTTTGTT
3295031 TTGTAAAA
1 TT-TAAAA
3295039 AATTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTAAAATTTATTTTTTGTT
Found at i:3295369 original size:2 final size:2
Alignment explanation
Indices: 3295362--3295388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3295352 ATTCTCATAA
3295362 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3295389 AAAGTCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3299756 original size:120 final size:118
Alignment explanation
Indices: 3299617--3299923 Score: 318
Period size: 120 Copynumber: 2.6 Consensus size: 118
3299607 TTCAAAGACC
* *
3299617 ACAAGACTACATTTTTTAAAGT-GAAA-ATATGGTTTTTAATTG-AAAGCACAAA-TAAACATAC
1 ACAAGACTACATTTTTTAAAGTAGAAACATA--ATCTTTAATTGAAAAG-A-AAATTAAACATAC
* *
3299678 AAAAACTACATTTCTTAAAGTAGAAACGTGATCTTTAATTGAAAAAAAAATTAAACAT
62 AAAAACTACATTTCTTAAACTAGAAACGTGATCTTCAATTGAAAAAAAAA-TAAACAT
* *
3299736 ACAAGGACTATATTTTTTAAAGTAGAAACATAATCTTTAATTGAAAAGAAAATTAAACATACAAG
1 ACAA-GACTACATTTTTTAAAGTAGAAACATAATCTTTAATTGAAAAGAAAATTAAACATACAAA
* * * * * **
3299801 GACTACGTTTCTTAAACTGGAAACTTGGTCTTCAATTGAAAAAAAAATGGACAT
65 AACTACATTTCTTAAACTAGAAACGTGATCTTCAATTGAAAAAAAAATAAACAT
* * * * * *** *
3299855 ACAAAGACTACATTTTTTAAACTGGAAACGTGATCTATAATTTTTAA-AAGATTAAACATACAAA
1 AC-AAGACTACATTTTTTAAAGTAGAAACATAATCTTTAATTGAAAAGAAAATTAAACATACAAA
3299919 AACTA
65 AACTA
3299924 TGCTTTTTAT
Statistics
Matches: 157, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
118 19 0.12
119 47 0.30
120 80 0.51
121 8 0.05
122 3 0.02
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (118 bp):
ACAAGACTACATTTTTTAAAGTAGAAACATAATCTTTAATTGAAAAGAAAATTAAACATACAAAA
ACTACATTTCTTAAACTAGAAACGTGATCTTCAATTGAAAAAAAAATAAACAT
Found at i:3299876 original size:59 final size:59
Alignment explanation
Indices: 3299619--3299923 Score: 279
Period size: 60 Copynumber: 5.1 Consensus size: 59
3299609 CAAAGACCAC
* * * * *
3299619 AAGACTACATTTTTTAAAGT-GAAAATATGGTTTTTAATTGAAAGCACAAATAAACATACA
1 AAGACTACATTTTTTAAAGTAGAAACT-TGATCTTTAATTGAAA-AAAAAATAAACATACA
* * *
3299679 AAAACTACATTTCTTAAAGTAGAAACGTGATCTTTAATTGAAAAAAAAATTAAACATACA
1 AAGACTACATTTTTTAAAGTAGAAACTTGATCTTTAATTGAAAAAAAAA-TAAACATACA
* * * * *
3299739 AGGACTATATTTTTTAAAGTAGAAACATAATCTTTAATTGAAAAGAAAATTAAACATACA
1 AAGACTACATTTTTTAAAGTAGAAACTTGATCTTTAATTGAAAA-AAAAATAAACATACA
* * * * * * * **
3299799 AGGACTACGTTTCTTAAACTGGAAACTTGGTCTTCAATTGAAAAAAAAATGGACATACA
1 AAGACTACATTTTTTAAAGTAGAAACTTGATCTTTAATTGAAAAAAAAATAAACATACA
* * * * *** * *
3299858 AAGACTACATTTTTTAAACTGGAAACGTGATCTATAATTTTTAAAAGATTAAACATACA
1 AAGACTACATTTTTTAAAGTAGAAACTTGATCTTTAATTGAAAAAAAAATAAACATACA
*
3299917 AAAACTA
1 AAGACTA
3299924 TGCTTTTTAT
Statistics
Matches: 200, Mismatches: 42, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
59 67 0.34
60 125 0.62
61 8 0.04
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (59 bp):
AAGACTACATTTTTTAAAGTAGAAACTTGATCTTTAATTGAAAAAAAAATAAACATACA
Found at i:3311148 original size:18 final size:19
Alignment explanation
Indices: 3311125--3311162 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3311115 GTTCAGGTAA
*
3311125 AAATTTTTT-TTGTTTTTT
1 AAATTTTTTCTTATTTTTT
3311143 AAATTTTTTCTTATTTTTT
1 AAATTTTTTCTTATTTTTT
3311162 A
1 A
3311163 TATATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (19 bp):
AAATTTTTTCTTATTTTTT
Found at i:3311159 original size:19 final size:18
Alignment explanation
Indices: 3311125--3311176 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
3311115 GTTCAGGTAA
*
3311125 AAATTTTTTTTGTTTTTT
1 AAATTTTTTTTATTTTTT
3311143 AAATTTTTTCTTATTTTTT
1 AAATTTTTT-TTATTTTTT
* *
3311162 ATATATTATTTTATT
1 AAAT-TTTTTTTATT
3311177 AAAATTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.31
19 16 0.55
20 4 0.14
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
AAATTTTTTTTATTTTTT
Found at i:3311289 original size:24 final size:23
Alignment explanation
Indices: 3311262--3311306 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3311252 ATTAATTTTT
3311262 TAAAAATAAACTTTAAAAATAAAA
1 TAAAAATAAA-TTTAAAAATAAAA
*
3311286 TAAAAATAAATTTAATAATAA
1 TAAAAATAAATTTAAAAATAA
3311307 TATTAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAAATAAATTTAAAAATAAAA
Found at i:3311512 original size:18 final size:18
Alignment explanation
Indices: 3311482--3311531 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3311472 TTTCTTTTAT
3311482 AAAAT-AGTAATAAATGA
1 AAAATGAGTAATAAATGA
* * *
3311499 AAATTGATTAATAAATTA
1 AAAATGAGTAATAAATGA
3311517 AAAATGAGTAATAAA
1 AAAATGAGTAATAAA
3311532 AATGAGAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (18 bp):
AAAATGAGTAATAAATGA
Found at i:3323564 original size:11 final size:11
Alignment explanation
Indices: 3323548--3323576 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3323538 GGTAAAAAAA
3323548 AATTTTTTTTG
1 AATTTTTTTTG
3323559 AA-TTTTTTTG
1 AATTTTTTTTG
3323569 AATTTTTT
1 AATTTTTT
3323577 ATATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:3323566 original size:10 final size:10
Alignment explanation
Indices: 3323551--3323576 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3323541 AAAAAAAAAT
3323551 TTTTTTTGAA
1 TTTTTTTGAA
3323561 TTTTTTTGAA
1 TTTTTTTGAA
3323571 TTTTTT
1 TTTTTT
3323577 ATATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:3323935 original size:18 final size:18
Alignment explanation
Indices: 3323905--3323954 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
3323895 TTTCTTGTAT
3323905 AAAAT-AGTAATAAA-TA
1 AAAATGAGTAATAAATTA
*
3323921 AAAATTGATTAATAAATTA
1 AAAA-TGAGTAATAAATTA
3323940 AAAATGAGTAATAAA
1 AAAATGAGTAATAAA
3323955 AATGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 4 0.14
17 1 0.03
18 18 0.62
19 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
AAAATGAGTAATAAATTA
Found at i:3326801 original size:20 final size:20
Alignment explanation
Indices: 3326776--3326823 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
3326766 TCTAACAGAG
3326776 GAAGAAAAGATAATTTTATT
1 GAAGAAAAGATAATTTTATT
3326796 GAAGAAAAGATAATTTTATT
1 GAAGAAAAGATAATTTTATT
3326816 GAAGAAAA
1 GAAGAAAA
3326824 ACATGATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (20 bp):
GAAGAAAAGATAATTTTATT
Found at i:3331514 original size:2 final size:2
Alignment explanation
Indices: 3331507--3331568 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
3331497 ACCATAGGCA
*
3331507 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3331549 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
3331569 AATATCACAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3341085 original size:19 final size:18
Alignment explanation
Indices: 3341023--3341084 Score: 81
Period size: 19 Copynumber: 3.4 Consensus size: 18
3341013 AATGTATATA
3341023 TAATAAAAATTT-TAAAT
1 TAATAAAAATTTATAAAT
* *
3341040 TATTTAAAATTTATAAAAT
1 TAATAAAAATTTAT-AAAT
3341059 TAATAAATAATTTATAAAT
1 TAATAAA-AATTTATAAAT
3341078 TAATAAA
1 TAATAAA
3341085 TTATTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 10 0.26
18 1 0.03
19 20 0.53
20 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAAAATTTATAAAT
Found at i:3349939 original size:9 final size:8
Alignment explanation
Indices: 3349923--3349947 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3349913 TTTTTATTAA
3349923 TATTTTTT
1 TATTTTTT
3349931 TATTTTTT
1 TATTTTTT
3349939 TATTTTTT
1 TATTTTTT
3349947 T
1 T
3349948 GTTTGAAAAT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:3350093 original size:26 final size:25
Alignment explanation
Indices: 3350039--3350093 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
3350029 CTTACCTAAG
*
3350039 AATTTTATAAAAATTTACCATTTGA
1 AATTTTATAAAAATTTACCATTGGA
* *
3350064 AATTTCTAT-AAATTTTATCATTGGA
1 AATTT-TATAAAAATTTACCATTGGA
3350089 TAATT
1 -AATT
3350094 AATATTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (25 bp):
AATTTTATAAAAATTTACCATTGGA
Found at i:3352589 original size:358 final size:352
Alignment explanation
Indices: 3351920--3352663 Score: 985
Period size: 358 Copynumber: 2.1 Consensus size: 352
3351910 TTTTCTTAGC
* * * * * *
3351920 AAACACCTTCTATAACCACCGTGGTATGTTAAAGGCGTTTTATAATAAAAGATGCCTTTAATAAT
1 AAACACCTTCTATAACCATCGTGGTATATTGAAGGCATTTTATAACAAAAGATGCATTTAATAAT
** * * * *
3351985 CCCAAAATTTTTTTTAATGAAATAATTGAAAGCGTTGCTATCTGCAACTGTCTTTACTAATTATT
66 CCCAAAAAATTTTTTAATGAAATAATTGAAAGCGTTGCTATCTGCAAATGTCTTGACTAACTATC
*
3352050 TACAAAATCTAATAGCAAATATTAGCATTTTTCTTGAAAATACACATCAATAACCATGTTAAAAT
131 TACAAAATCTAATAACAAATATTAGCATTTTTCTTGAAAATACACATCAATAACCATGTTAAAAT
*** * * * *
3352115 TTATGTGGTGATATATTAAAAGTATTTTATAGTAAAAGCTGCTTTTAATAATGCCCAAAATTTTT
196 TTATGTGACAATATATTAAAAGCATTTTACAGTAAAAGCTACCTTTAATAATGCCCAAAATTTTT
*** *
3352180 AGAGGGAAAATATTGAAGGCATCTATTATTAACAAACATCTTCAATAATGGATTACTAAGTTTAA
261 AGAAAAAAAATATTGAAGGCATCCATTATTAACAAACATCTTCAATAATGGATTACTAAGTTTAA
3352245 -AGGTATATTGAAAGCACT-TTTTTGAAT
326 CA-GTATATTGAAAGCA-TATTTTTGAAT
**
3352272 AAATGCCTTCTATAACCATCGTGGTATATTGAAGGCATTTTATAACAAAAGATGCATTTAATAAT
1 AAACACCTTCTATAACCATCGTGGTATATTGAAGGCATTTTATAACAAAAGATGCATTTAATAAT
* *
3352337 CTCTCAAAAAATTTTTTAATGAAATTATTGAAGGCGTTGCTATCTGCAAATG-CATTGACTAACT
66 C-C-CAAAAAATTTTTTAATGAAATAATTGAAAGCGTTGCTATCTGCAAATGTC-TTGACTAACT
* * *
3352401 ATCTACAAAATCTAATAACAAATATTAAAGGCATTTTTCTTGAATATACGCCTTCAATAACCATG
128 ATCTACAAAATCTAATAACAAATATT--A-GCATTTTTCTTGAAAATAC-ACATCAATAACCATG
* * *
3352466 TTAAAATTTATGTGACAATATATT-GAAGACATTTTACAGTAGAAGAC-ACCTTTAATAATGCCT
189 TTAAAATTTATGTGACAATATATTAAAAG-CATTTTACAGTAAAAG-CTACCTTTAATAATGCCC
** **
3352529 AAAATTTTTAGAAAAAAAATATTGAAGGCATCCATTATTAACAAATGTCTTCTGTAATGGATTAC
252 AAAATTTTTAGAAAAAAAATATTGAAGGCATCCATTATTAACAAACATCTTCAATAATGGATTAC
*
3352594 TAAGTTTAACAGTATATTGAAGGCATATTTTTGAAT
317 TAAGTTTAACAGTATATTGAAAGCATATTTTTGAAT
* *
3352630 AAACACCTTCTATAACTATCATGGTATATTGAAG
1 AAACACCTTCTATAACCATCGTGGTATATTGAAG
3352664 ATATTTTACT
Statistics
Matches: 338, Mismatches: 43, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
352 58 0.17
353 2 0.01
354 75 0.22
356 1 0.00
357 22 0.07
358 178 0.53
359 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (352 bp):
AAACACCTTCTATAACCATCGTGGTATATTGAAGGCATTTTATAACAAAAGATGCATTTAATAAT
CCCAAAAAATTTTTTAATGAAATAATTGAAAGCGTTGCTATCTGCAAATGTCTTGACTAACTATC
TACAAAATCTAATAACAAATATTAGCATTTTTCTTGAAAATACACATCAATAACCATGTTAAAAT
TTATGTGACAATATATTAAAAGCATTTTACAGTAAAAGCTACCTTTAATAATGCCCAAAATTTTT
AGAAAAAAAATATTGAAGGCATCCATTATTAACAAACATCTTCAATAATGGATTACTAAGTTTAA
CAGTATATTGAAAGCATATTTTTGAAT
Found at i:3367731 original size:3 final size:3
Alignment explanation
Indices: 3367723--3367767 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3367713 CAAAATTAAC
3367723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3367768 TCGAATTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3368241 original size:4 final size:4
Alignment explanation
Indices: 3368234--3368263 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
3368224 TATATATATA
3368234 TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
3368264 AAAAAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:3369614 original size:27 final size:28
Alignment explanation
Indices: 3369584--3369640 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
3369574 TTTTTTATTT
*
3369584 TTTTTTACTTTTTTCT-TTTTTTTAAGA
1 TTTTTTACTTTTGTCTCTTTTTTTAAGA
3369611 TTTTTTACTTTTGTCTCTTTTTTTAAGA
1 TTTTTTACTTTTGTCTCTTTTTTTAAGA
3369639 TT
1 TT
3369641 AATAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (28 bp):
TTTTTTACTTTTGTCTCTTTTTTTAAGA
Found at i:3369646 original size:3 final size:3
Alignment explanation
Indices: 3369640--3369686 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3369630 TTTTTAAGAT
3369640 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3369687 TAAAAAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3372507 original size:30 final size:31
Alignment explanation
Indices: 3372460--3372518 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
3372450 AAAGTCTTGA
*
3372460 TTTTTAGGATATAGTTGGTAGTAGATGTTGG
1 TTTTTAGGATATAGTTGGTAATAGATGTTGG
*
3372491 TTTTTAGGAT-TAGTTGGTAATAGTTGTT
1 TTTTTAGGATATAGTTGGTAATAGATGTT
3372519 AAATATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (31 bp):
TTTTTAGGATATAGTTGGTAATAGATGTTGG
Found at i:3373211 original size:29 final size:29
Alignment explanation
Indices: 3373146--3373228 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
3373136 ACGTTAAAAA
* * *
3373146 TAAATATTATATTAATTAACATATTTATAATT
1 TAAATATTATATT-A--AATATTTTTAAAATT
*
3373178 CAAATATTATATTAAATATTTTTAAAATT
1 TAAATATTATATTAAATATTTTTAAAATT
* *
3373207 TAAATATCACATTAAATATTTT
1 TAAATATTATATTAAATATTTT
3373229 ATCATAATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 31 0.70
31 1 0.02
32 12 0.27
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAATATTATATTAAATATTTTTAAAATT
Found at i:3375358 original size:16 final size:16
Alignment explanation
Indices: 3375330--3375373 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3375320 AATTATTCAA
3375330 AAATAAT-TTTTTATG
1 AAATAATATTTTTATG
*
3375345 GAATAATATTTTTATG
1 AAATAATATTTTTATG
3375361 AAATAATTATTTT
1 AAATAA-TATTTT
3375374 CGAAACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 13 0.52
17 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (16 bp):
AAATAATATTTTTATG
Found at i:3387972 original size:186 final size:195
Alignment explanation
Indices: 3387502--3388059 Score: 548
Period size: 200 Copynumber: 2.9 Consensus size: 195
3387492 TACATGCACC
* * * *
3387502 ATAA-ATGATCGATTGAATAACATTGACCTAAATGATGATTTTGCCTTGTTATTTTTTGA-TTCT
1 ATAATATGATTGATTGAAAAACATTAACCTAAATGATGATTTTGCCTTGTTATTTTCTGATTTC-
* * * * *
3387565 GCCAACGATCTAGATTAGAAAAGCTCATAAATCAATAAGAAAATTCAATTTTTTTTCTTTTATTA
65 GCCATCAATCTAGATAAAAAAAGCTCACAAATCAATAAGAAAATTCAA---TTTTTCTTTTATTA
* *
3387630 CAAATAAAAGTTTAAGATTTTGACAAATGGGTATGTGCTTTTATTAGGGATCTTGTAGTTAATGA
127 CAAAGAAAAATTTAAGATTTTGACAAATGGGTATGTGCTTTTATTAGGGATCTTGTAGTT-ATGA
*
3387695 TGATG
191 TGAAG
* * * * * * *
3387700 ATAATGATGATTGATTAAAAAACATCAACCTAATTGATGATTTTGCCTTATTATTTCCTTATTCC
1 ATAAT-ATGATTGATTGAAAAACATTAACCTAAATGATGATTTTGCCTTGTTATTTTCTGATTTC
** * *
3387765 TTCATTAATCTAGATAAAAAAAACTCACAAATCAATAAGAAAATTCAA-TTTT-TTTT-TTACAA
65 GCCATCAATCTAGATAAAAAAAGCTCACAAATCAATAAGAAAATTCAATTTTTCTTTTATTACAA
* * * * *
3387827 AGAAAAATTTAAGATTTTGAC-AATGGGTATGTGTTTTTGTTAGGGTTCTTGTTG-T-TGTTGAA
130 AGAAAAATTTAAGATTTTGACAAATGGGTATGTGCTTTTATTAGGGATCTTGTAGTTATGATGAA
3387889 G
195 G
* * * **
3387890 CT-AT-T-ATTGATTGAAGAACATTAACCCAAATGATGATTTCACCTTGTTATTTTCTGATTTCG
1 ATAATATGATTGATTGAAAAACATTAACCTAAATGATGATTTTGCCTTGTTATTTTCTGATTTCG
* * *
3387952 CCATCAACCTA-ATAAAAAAAAGCTCACAAATCAACAAGAAAATTCAAAATTTTTTCTTTTTTTT
66 CCATCAATCTAGAT-AAAAAAAGCTCACAAATCAATAAGAAAATTC--AA-TTTTTC--TTTTAT
* ** *
3388016 TACAAA-AAAAATTTTAAGATTTTGATAAATAAGTATGTGTTTTT
125 TACAAAGAAAAA-TTTAAGATTTTGACAAATGGGTATGTGCTTTT
3388060 TTTTTTATTC
Statistics
Matches: 297, Mismatches: 49, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
185 2 0.01
186 82 0.28
187 1 0.00
188 2 0.01
189 2 0.01
190 11 0.04
192 1 0.00
193 38 0.13
194 45 0.15
195 19 0.06
196 4 0.01
198 4 0.01
200 84 0.28
201 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (195 bp):
ATAATATGATTGATTGAAAAACATTAACCTAAATGATGATTTTGCCTTGTTATTTTCTGATTTCG
CCATCAATCTAGATAAAAAAAGCTCACAAATCAATAAGAAAATTCAATTTTTCTTTTATTACAAA
GAAAAATTTAAGATTTTGACAAATGGGTATGTGCTTTTATTAGGGATCTTGTAGTTATGATGAAG
Found at i:3391479 original size:20 final size:21
Alignment explanation
Indices: 3391456--3391494 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3391446 TATATAATGA
*
3391456 AATCCTTGCTTA-CATAATTG
1 AATCCATGCTTAGCATAATTG
3391476 AATCCATGCTTAGCATAAT
1 AATCCATGCTTAGCATAAT
3391495 CAGGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (21 bp):
AATCCATGCTTAGCATAATTG
Found at i:3396011 original size:16 final size:16
Alignment explanation
Indices: 3395990--3396021 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3395980 AATTATAAAA
*
3395990 ATTATTTTATTATAGT
1 ATTATTGTATTATAGT
3396006 ATTATTGTATTATAGT
1 ATTATTGTATTATAGT
3396022 TTTGGTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTATTGTATTATAGT
Found at i:3400271 original size:2 final size:2
Alignment explanation
Indices: 3400264--3400294 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3400254 ACTGTATCAC
3400264 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3400295 ATCGCACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3405830 original size:71 final size:71
Alignment explanation
Indices: 3405750--3405922 Score: 242
Period size: 71 Copynumber: 2.5 Consensus size: 71
3405740 ACATGAAATT
3405750 ACAACTATAAACATCATTTTGTTTTAAAGCATAATAAGATAAATAGAAACAGTAGAAACAACCTT
1 ACAACTATAAACATCATTTTGTTTTAAAGCATAATAAGATAAATAGAAACAGTAGAAACAACCTT
3405815 AACCTC
66 AACCTC
* * * ** *
3405821 ACAACTATAATCATCATTTTGTTCTAAAGCACAATAAGATAAATAGAAACAGTAGAAAGGACTTT
1 ACAACTATAAACATCATTTTGTTTTAAAGCATAATAAGATAAATAGAAACAGTAGAAACAACCTT
*
3405886 AACCTT
66 AACCTC
* *
3405892 ACATA-TGTAAACATCATTTTG-TTCAAAGCAT
1 ACA-ACTATAAACATCATTTTGTTTTAAAGCAT
3405923 TGTATACACA
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
70 7 0.08
71 81 0.91
72 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (71 bp):
ACAACTATAAACATCATTTTGTTTTAAAGCATAATAAGATAAATAGAAACAGTAGAAACAACCTT
AACCTC
Found at i:3408601 original size:2 final size:2
Alignment explanation
Indices: 3408596--3408627 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3408586 TGTGTGTGTG
3408596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3408628 ATTTACCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3409921 original size:15 final size:16
Alignment explanation
Indices: 3409894--3409924 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3409884 TATTTATTTA
3409894 TTTATTGTTTTGGATG
1 TTTATTGTTTTGGATG
3409910 TTTATT-TTTTGGATG
1 TTTATTGTTTTGGATG
3409925 AATTTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.65
Consensus pattern (16 bp):
TTTATTGTTTTGGATG
Found at i:3415592 original size:20 final size:20
Alignment explanation
Indices: 3415554--3415593 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3415544 ATCTCTCAAA
3415554 AGAAAACCAATACAACATATC
1 AGAAAACCAATA-AACATATC
3415575 AGAAAACCAGAT-AACATAT
1 AGAAAACCA-ATAAACATAT
3415594 ATTAAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 9 0.50
22 2 0.11
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.15
Consensus pattern (20 bp):
AGAAAACCAATAAACATATC
Found at i:3415923 original size:13 final size:13
Alignment explanation
Indices: 3415905--3415953 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
3415895 TTTAATTCGA
3415905 ATTAAATTTAAAT
1 ATTAAATTTAAAT
* *
3415918 ATTAAATGTATAT
1 ATTAAATTTAAAT
*
3415931 ATTAAATTT-GA-
1 ATTAAATTTAAAT
3415942 ATTAAATTTAAA
1 ATTAAATTTAAA
3415954 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 19 0.63
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:3416069 original size:22 final size:22
Alignment explanation
Indices: 3416044--3416108 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 22
3416034 ATAAAAATAA
3416044 TAAATTTATGTAAAAATTTA-TT
1 TAAATTTAT-TAAAAATTTATTT
*
3416066 TAAATTTA-TAAAAAATTATTT
1 TAAATTTATTAAAAATTTATTT
3416087 TAAATTAATATATAAAAATTTA
1 TAAATT--TAT-TAAAAATTTA
3416109 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 9 0.25
21 8 0.22
22 8 0.22
23 2 0.06
25 9 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATTTATTAAAAATTTATTT
Found at i:3416081 original size:21 final size:22
Alignment explanation
Indices: 3416044--3416108 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
3416034 ATAAAAATAA
*
3416044 TAAATTTATGTAAAAATTTA-TT
1 TAAATTTAT-AAAAAATTTATTT
3416066 TAAATTTATAAAAAA-TTATTT
1 TAAATTTATAAAAAATTTATTT
3416087 TAAATTAATATATAAAAATTTA
1 TAAATT--TATA-AAAAATTTA
3416109 AATTTAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 3 0.08
21 13 0.35
22 9 0.24
23 4 0.11
24 5 0.14
25 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATTTATAAAAAATTTATTT
Found at i:3418017 original size:10 final size:10
Alignment explanation
Indices: 3417993--3418021 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3417983 TTCAAAATTG
3417993 TAAATAAAA-
1 TAAATAAAAT
3418002 TAAATAAAAT
1 TAAATAAAAT
3418012 TAAATAAAAT
1 TAAATAAAAT
3418022 CACTTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAATAAAAT
Found at i:3425495 original size:31 final size:32
Alignment explanation
Indices: 3425456--3425524 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
3425446 TTAGTACTAT
3425456 TAAA-ATTTAAAT-TAAAATA-ATATATTATTA
1 TAAATATTTAAATATAAAATATATATATT-TTA
* * *
3425486 TAAATATTTAAGTATAAATTATATATATTTTT
1 TAAATATTTAAATATAAAATATATATATTTTA
3425518 TAAATAT
1 TAAATAT
3425525 CAATTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 4 0.12
31 7 0.21
32 15 0.45
33 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
TAAATATTTAAATATAAAATATATATATTTTA
Found at i:3430262 original size:20 final size:20
Alignment explanation
Indices: 3430237--3430278 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3430227 CTAAATTTAA
3430237 AAAAAAAAAAAAAAAAACTG
1 AAAAAAAAAAAAAAAAACTG
* *
3430257 AAAAAAAAAAAACAAAATTG
1 AAAAAAAAAAAAAAAAACTG
3430277 AA
1 AA
3430279 GTACTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.83, C:0.05, G:0.05, T:0.07
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAACTG
Found at i:3433824 original size:36 final size:34
Alignment explanation
Indices: 3433754--3433829 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 34
3433744 AAAAATATAA
*
3433754 AAATATATTTTTAATTTTTATTAAAATATTAAATT
1 AAAT-TATTTTTAATTTTTATTAAAATATCAAATT
*
3433789 AAATTATTTTTATATTATATT-TTAAATTATCAAATT
1 AAATTATTTTTA-ATT-T-TTATTAAAATATCAAATT
*
3433825 TAATT
1 AAATT
3433830 TTAAAGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.23
35 7 0.20
36 18 0.51
37 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
AAATTATTTTTAATTTTTATTAAAATATCAAATT
Found at i:3438282 original size:1 final size:1
Alignment explanation
Indices: 3438276--3438309 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
3438266 AGCAAACCAG
3438276 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3438310 CCCTAACTGA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3441447 original size:15 final size:15
Alignment explanation
Indices: 3441423--3441453 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3441413 TAAAAAAACC
*
3441423 AATAATTAAATAATA
1 AATAACTAAATAATA
3441438 AATAACTAAATAATA
1 AATAACTAAATAATA
3441453 A
1 A
3441454 TAAGATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAACTAAATAATA
Found at i:3441454 original size:18 final size:17
Alignment explanation
Indices: 3441430--3441477 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
3441420 ACCAATAATT
3441430 AAATAATAAATA-ACTAA
1 AAATAATAAATATA-TAA
3441447 ATAATAATAAGATATATAA
1 A-AATAATAA-ATATATAA
3441466 AAATAGATAAAT
1 AAATA-ATAAAT
3441478 CAAGGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.04
18 14 0.52
19 11 0.41
20 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
AAATAATAAATATATAA
Found at i:3447638 original size:27 final size:27
Alignment explanation
Indices: 3447598--3447671 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 27
3447588 ACCTCAAGGT
* * **
3447598 AAAATAATATATAAATATTTAAAAAGA
1 AAAAAAATAAATAAATATAAAAAAAGA
3447625 AAAAAAATAAAT-AATGATAAAAAAAGA
1 AAAAAAATAAATAAAT-ATAAAAAAAGA
*
3447652 AAAACAA-AAA-AAA-ATAAAAA
1 AAAAAAATAAATAAATATAAAAA
3447672 GAAAATAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.17
26 8 0.20
27 25 0.62
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (27 bp):
AAAAAAATAAATAAATATAAAAAAAGA
Found at i:3447662 original size:16 final size:16
Alignment explanation
Indices: 3447643--3447676 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3447633 AAATAATGAT
3447643 AAAAAAAGAAAAACAA
1 AAAAAAAGAAAAACAA
* *
3447659 AAAAAAATAAAAAGAA
1 AAAAAAAGAAAAACAA
3447675 AA
1 AA
3447677 TAACTTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAAAAACAA
Found at i:3447676 original size:27 final size:27
Alignment explanation
Indices: 3447618--3447676 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
3447608 ATAAATATTT
* *
3447618 AAAAAGAAAAAAAATAAATAATGATAA
1 AAAAAGAAAAAAAATAAAAAATGAAAA
3447645 AAAAAGAAAAACAAA-AAAAAAT-AAAA
1 AAAAAGAAAAA-AAATAAAAAATGAAAA
3447671 AGAAAA
1 A-AAAA
3447677 TAACTTGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 21 0.75
28 3 0.11
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAAAATAAAAAATGAAAA
Found at i:3450255 original size:13 final size:13
Alignment explanation
Indices: 3450237--3450267 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3450227 TTTAAATTTC
3450237 AATTATTGATGAT
1 AATTATTGATGAT
3450250 AATTATTGATGAT
1 AATTATTGATGAT
3450263 AATTA
1 AATTA
3450268 ATTAATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
AATTATTGATGAT
Found at i:3450767 original size:80 final size:80
Alignment explanation
Indices: 3450634--3450798 Score: 303
Period size: 80 Copynumber: 2.1 Consensus size: 80
3450624 TACAAGCATG
*
3450634 ACTATGAGTCGGCTATACTCAAACCTTGTTATCTTCACATTGACCTTCAACCAGATTTGGTAACA
1 ACTATGAATCGGCTATACTCAAACCTTGTTATCTTCACATTGACCTTCAACCAGATTTGGTAACA
3450699 AGTCATTTTCTTATT
66 AGTCATTTTCTTATT
* *
3450714 ACTATGAATCGGCTATACTCAAACCTTGTTATCTTCACCTTGAGCTTCAACCAGATTTGGTAACA
1 ACTATGAATCGGCTATACTCAAACCTTGTTATCTTCACATTGACCTTCAACCAGATTTGGTAACA
3450779 AGTCATTTTCTTATT
66 AGTCATTTTCTTATT
3450794 ACTAT
1 ACTAT
3450799 TTGAGATTTC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (80 bp):
ACTATGAATCGGCTATACTCAAACCTTGTTATCTTCACATTGACCTTCAACCAGATTTGGTAACA
AGTCATTTTCTTATT
Found at i:3451976 original size:17 final size:17
Alignment explanation
Indices: 3451954--3451994 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3451944 TGTTTAAAAA
3451954 TTAAAATTTAATATTTTT
1 TTAAAATTTAA-ATTTTT
*
3451972 TAAAAATTTAAATTTTT
1 TTAAAATTTAAATTTTT
3451989 TTAAAA
1 TTAAAA
3451995 AATTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAATTTAAATTTTT
Found at i:3451995 original size:19 final size:19
Alignment explanation
Indices: 3451956--3452006 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3451946 TTTAAAAATT
3451956 AAAATTT-AATATTTTTTA
1 AAAATTTAAATATTTTTTA
3451974 AAAATTTAAAT-TTTTTTAA
1 AAAATTTAAATATTTTTT-A
*
3451993 AAAATTAAAATATT
1 AAAATTTAAATATT
3452007 AAAAAAGTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.45
19 14 0.48
20 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATTTAAATATTTTTTA
Found at i:3452064 original size:18 final size:18
Alignment explanation
Indices: 3451956--3452065 Score: 71
Period size: 18 Copynumber: 5.8 Consensus size: 18
3451946 TTTAAAAATT
*
3451956 AAAATTTAATATTTTTTAA
1 AAAATTAAATA-TTTTTAA
* *
3451975 AAATTTAAATTTTTTTAA
1 AAAATTAAATATTTTTAA
*
3451993 AAAATTAAA-A-TATTAA
1 AAAATTAAATATTTTTAA
*
3452009 AAAAGTACATTTATTATTTTTAA
1 AAAATTA-A---A-TATTTTTAA
* *
3452032 AAAAGTAAAAAATTTTTAA
1 AAAA-TTAAATATTTTTAA
*
3452051 AAAATTCAATATTTT
1 AAAATTAAATATTTT
3452066 GAATTTTTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
16 11 0.16
17 1 0.01
18 23 0.33
19 20 0.29
20 2 0.03
22 1 0.01
23 10 0.14
24 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAATTAAATATTTTTAA
Found at i:3452081 original size:36 final size:37
Alignment explanation
Indices: 3452040--3452116 Score: 138
Period size: 36 Copynumber: 2.1 Consensus size: 37
3452030 AAAAAAGTAA
3452040 AAAATTTTTAAAAAATTCAATATTTTGAA-TTTTTTT
1 AAAATTTTTAAAAAATTCAATATTTTGAATTTTTTTT
*
3452076 AAAATTTTTTAAAAATTCAATATTTTGAATTTTTTTT
1 AAAATTTTTAAAAAATTCAATATTTTGAATTTTTTTT
3452113 AAAA
1 AAAA
3452117 ATTAAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 28 0.72
37 11 0.28
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (37 bp):
AAAATTTTTAAAAAATTCAATATTTTGAATTTTTTTT
Found at i:3452085 original size:37 final size:37
Alignment explanation
Indices: 3452039--3452119 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
3452029 TAAAAAAGTA
3452039 AAAAATTTTTAAAAAATTCAATATTTTGAA-TTTTTTT
1 AAAAATTTTT-AAAAATTCAATATTTTGAATTTTTTTT
*
3452076 AAAATTTTTTAAAAATTCAATATTTTGAATTTTTTTT
1 AAAAATTTTTAAAAATTCAATATTTTGAATTTTTTTT
3452113 AAAAATT
1 AAAAATT
3452120 AAAATTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 19 0.46
37 22 0.54
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (37 bp):
AAAAATTTTTAAAAATTCAATATTTTGAATTTTTTTT
Found at i:3452101 original size:26 final size:24
Alignment explanation
Indices: 3452072--3452178 Score: 76
Period size: 27 Copynumber: 4.3 Consensus size: 24
3452062 TTTTGAATTT
3452072 TTTTAAAATTTTTTAAAAATTCAATA
1 TTTTAAAATTTTTTAAAAATT-AA-A
**
3452098 TTTTGAATTTTTTTTAAAAATTAAA
1 TTTT-AAAATTTTTTAAAAATTAAA
* *
3452123 ATTT--AATTTTTTAAAAAATAAA
1 TTTTAAAATTTTTTAAAAATTAAA
** *
3452145 -AATAAGATTTTTTAAAAAATTAAAA
1 TTTTAAAATTTTTT-AAAAATT-AAA
3452170 TATTTAAAA
1 T-TTTAAAA
3452179 ATATTAAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
21 1 0.02
22 15 0.25
23 7 0.11
24 6 0.10
25 7 0.11
26 6 0.10
27 19 0.31
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTAAAATTTTTTAAAAATTAAA
Found at i:3452130 original size:24 final size:23
Alignment explanation
Indices: 3452080--3452170 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 23
3452070 TTTTTTAAAA
*
3452080 TTTTTTAAAAATTCAATATTTTGAATT
1 TTTTTTAAAAATT-AA-AATTT-AA-T
3452107 TTTTTTAAAAATTAAAATTTAA-
1 TTTTTTAAAAATTAAAATTTAAT
* * *
3452129 TTTTTTAAAAAATAAAAATAAGAT
1 TTTTTTAAAAATTAAAATTTA-AT
*
3452153 TTTTTAAAAAATTAAAAT
1 TTTTTTAAAAATTAAAAT
3452171 ATTTAAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
22 18 0.33
23 1 0.02
24 17 0.31
25 4 0.07
26 2 0.04
27 13 0.24
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTTTAAAAATTAAAATTTAAT
Found at i:3452139 original size:23 final size:23
Alignment explanation
Indices: 3452078--3452170 Score: 91
Period size: 23 Copynumber: 3.9 Consensus size: 23
3452068 ATTTTTTTAA
*
3452078 AATTTTTT-AAAAATTCAATATTTT
1 AATTTTTTAAAAAATT-AA-AATTT
*
3452102 GAATTTTTTTTAAAAATTAAAATTT
1 -AA-TTTTTTAAAAAATTAAAATTT
* *
3452127 AATTTTTTAAAAAA-TAAAAATA
1 AATTTTTTAAAAAATTAAAATTT
3452149 AGATTTTTTAAAAAATTAAAAT
1 A-ATTTTTTAAAAAATTAAAAT
3452171 ATTTAAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
22 7 0.12
23 24 0.41
24 7 0.12
25 6 0.10
26 8 0.14
27 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTTTTAAAAAATTAAAATTT
Found at i:3452200 original size:22 final size:22
Alignment explanation
Indices: 3452109--3452209 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 22
3452099 TTTGAATTTT
*
3452109 TTTTAAAAAT-TAAAATTTAATT
1 TTTTAAAAATATAAAA-TTAATA
* *
3452131 TTTTAAAAA-ATAAAAATAAGATT
1 TTTTAAAAATAT-AAAATTA-ATA
*
3452154 TTTTAAAAA-AT-TAA--AATA
1 TTTTAAAAATATAAAATTAATA
*
3452172 -TTTAAAAATATTAAATTAATA
1 TTTTAAAAATATAAAATTAATA
3452193 TTTTAAAAATATGAAAA
1 TTTTAAAAATAT-AAAA
3452210 ATTTCTTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
17 8 0.12
18 4 0.06
19 3 0.05
21 6 0.09
22 23 0.35
23 21 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTTAAAAATATAAAATTAATA
Found at i:3453026 original size:31 final size:31
Alignment explanation
Indices: 3452971--3453035 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3452961 ATATTTAATA
3452971 ATTTATATTATCATATGATATAAAA-TATTAT
1 ATTTATATTATCATATGATATAAAATTATT-T
* *
3453002 ATTTATATTAT-ATTTTATACTAAAATTATTT
1 ATTTATATTATCATATGATA-TAAAATTATTT
3453033 ATT
1 ATT
3453036 ATAATTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.20
31 20 0.67
32 4 0.13
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (31 bp):
ATTTATATTATCATATGATATAAAATTATTT
Found at i:3453130 original size:11 final size:11
Alignment explanation
Indices: 3453116--3453171 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
3453106 AAATTTTAAA
3453116 TTATATTATTT
1 TTATATTATTT
3453127 TTATA-TATTTT
1 TTATATTA-TTT
3453138 ATTCATATTATTT
1 -TT-ATATTATTT
*
3453151 TTATATCATATT
1 TTATATTAT-TT
*
3453163 TTAAATTAT
1 TTATATTAT
3453172 CATACTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.05
11 14 0.38
12 13 0.35
13 6 0.16
14 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTATTT
Found at i:3458829 original size:22 final size:22
Alignment explanation
Indices: 3458803--3458869 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
3458793 TATCATTAAT
3458803 TAATTAAAATATATTATATTTA
1 TAATTAAAATATATTATATTTA
*
3458825 TAATT-AAATGATATTAATAATTA
1 TAATTAAAAT-ATATT-ATATTTA
3458848 T-ATTATTAAATAT-TT-TATTTA
1 TAATTA--AAATATATTATATTTA
3458869 T
1 T
3458870 TTTCTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
21 10 0.26
22 13 0.34
23 9 0.24
24 2 0.05
25 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TAATTAAAATATATTATATTTA
Found at i:3470097 original size:16 final size:17
Alignment explanation
Indices: 3470057--3470095 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3470047 GATCCTTGAT
3470057 TTTTTTCTTTTTTTAAA
1 TTTTTTCTTTTTTTAAA
*
3470074 TTTTTTCTTTTTTTATA
1 TTTTTTCTTTTTTTAAA
3470091 TTTTT
1 TTTTT
3470096 CTATGTACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCTTTTTTTAAA
Found at i:3470470 original size:15 final size:15
Alignment explanation
Indices: 3470452--3470485 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3470442 TCCCACCTGT
3470452 TTTCATCCATTTAAC
1 TTTCATCCATTTAAC
* *
3470467 TTTCATCTATTTAGC
1 TTTCATCCATTTAAC
3470482 TTTC
1 TTTC
3470486 TTCCTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTCATCCATTTAAC
Found at i:3477046 original size:17 final size:15
Alignment explanation
Indices: 3477026--3477072 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3477016 TTTTAACATA
3477026 TTGTTAGTTATTATATT
1 TTGTT-GTTA-TATATT
3477043 TTGTTGTTATATATT
1 TTGTTGTTATATATT
*
3477058 AT-TTGTTA-ATATT
1 TTGTTGTTATATATT
3477071 TT
1 TT
3477073 ATTATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 7 0.25
16 4 0.14
17 5 0.18
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
TTGTTGTTATATATT
Found at i:3477731 original size:21 final size:21
Alignment explanation
Indices: 3477698--3477760 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
3477688 ACAACATTTT
*
3477698 TTGAGTTGAAAGCTGTTGTGA
1 TTGAGCTGAAAGCTGTTGTGA
* *
3477719 TTGAGCTGGAAGCTGTTGTGT
1 TTGAGCTGAAAGCTGTTGTGA
*
3477740 TTGAACTGAAAGCTGTTGTGA
1 TTGAGCTGAAAGCTGTTGTGA
3477761 GGTCTTGTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.08, G:0.33, T:0.37
Consensus pattern (21 bp):
TTGAGCTGAAAGCTGTTGTGA
Found at i:3482390 original size:46 final size:46
Alignment explanation
Indices: 3482337--3482425 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
3482327 ATCAAAATAG
* * *
3482337 TGGCATTATAGTATCATCATAAAGTTGATTACAAGCTAGCACATCA
1 TGGCATTACAGTATCATCATAAAGTTGATAACAAGCAAGCACATCA
* * * *
3482383 TGGCATTACATTATCATCATCAATTTGATAATAAGCAAGCACA
1 TGGCATTACAGTATCATCATAAAGTTGATAACAAGCAAGCACA
3482426 ACTGCAGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (46 bp):
TGGCATTACAGTATCATCATAAAGTTGATAACAAGCAAGCACATCA
Found at i:3484313 original size:54 final size:54
Alignment explanation
Indices: 3484205--3484424 Score: 230
Period size: 54 Copynumber: 4.1 Consensus size: 54
3484195 CCGTGTTCCC
* * * * * *
3484205 CATACTCGGGTCTCCGGCCATGCCCAGATCCAAATTCAG--G-AGGAGGCTGCT
1 CATATTCGGGTCTCCGGCCATACCCGGAACCAAACTCAGATGTAGGTGGCTGCT
* **
3484256 CATATTCGGGTCTCCGTCCATACCCGGAATTAAACTCAGATGTAGGTGGCTGCT
1 CATATTCGGGTCTCCGGCCATACCCGGAACCAAACTCAGATGTAGGTGGCTGCT
* * * *
3484310 CATATTCGGGTCTCCGGCCATACCCAGAACCCAACTCCGGTGTAGGTGGCTGCT
1 CATATTCGGGTCTCCGGCCATACCCGGAACCAAACTCAGATGTAGGTGGCTGCT
* * * * * * *
3484364 CATATTCGGGTCTCCGGCCATAACCGGATCCAAAATCCGGTGAAGGTGACTGCT
1 CATATTCGGGTCTCCGGCCATACCCGGAACCAAACTCAGATGTAGGTGGCTGCT
*
3484418 CAAATTC
1 CATATTC
3484425 AGGTTTTCGG
Statistics
Matches: 142, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
51 31 0.22
53 1 0.01
54 110 0.77
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Consensus pattern (54 bp):
CATATTCGGGTCTCCGGCCATACCCGGAACCAAACTCAGATGTAGGTGGCTGCT
Found at i:3484441 original size:54 final size:54
Alignment explanation
Indices: 3484299--3484451 Score: 153
Period size: 54 Copynumber: 2.8 Consensus size: 54
3484289 ACTCAGATGT
* * * * * * * * *
3484299 AGGTGGCTGCTCATATTCGGGTCTCCGGCCATACCCAGAACCCAACTCCGGTGT
1 AGGTGACTGCTCAAATTCAGGTCTCCGGCAATAACCAGATCCAAAATCCGGTGA
* * * * *
3484353 AGGTGGCTGCTCATATTCGGGTCTCCGGCCATAACCGGATCCAAAATCCGGTGA
1 AGGTGACTGCTCAAATTCAGGTCTCCGGCAATAACCAGATCCAAAATCCGGTGA
* * *
3484407 AGGTGACTGCTCAAATTCAGGTTTTCGGCAATAACCAGATTCAAA
1 AGGTGACTGCTCAAATTCAGGTCTCCGGCAATAACCAGATCCAAA
3484452 TTCGGATCCG
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 85 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (54 bp):
AGGTGACTGCTCAAATTCAGGTCTCCGGCAATAACCAGATCCAAAATCCGGTGA
Found at i:3484445 original size:108 final size:108
Alignment explanation
Indices: 3484249--3484445 Score: 252
Period size: 108 Copynumber: 1.8 Consensus size: 108
3484239 TTCAGGAGGA
* * * * * * *
3484249 GGCTGCTCATATTCGGGTCTCCGTCCATACCCGGAATTAAACTCAGATGTAGGTGGCTGCTCATA
1 GGCTGCTCATATTCGGGTCTCCGGCCATAACCGGAATCAAAATCAGATGAAGGTGACTGCTCAAA
* * *
3484314 TTCGGGTCTCCGGCCATACCCAGAACCCAACTCCGGTGTAGGT
66 TTCAGGTCTCCGGCAATAACCAGAACCCAACTCCGGTGTAGGT
* *
3484357 GGCTGCTCATATTCGGGTCTCCGGCCATAACCGG-ATCCAAAATCCGGTGAAGGTGACTGCTCAA
1 GGCTGCTCATATTCGGGTCTCCGGCCATAACCGGAAT-CAAAATCAGATGAAGGTGACTGCTCAA
* *
3484421 ATTCAGGTTTTCGGCAATAACCAGA
65 ATTCAGGTCTCCGGCAATAACCAGA
3484446 TTCAAATTCG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
107 2 0.03
108 72 0.97
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (108 bp):
GGCTGCTCATATTCGGGTCTCCGGCCATAACCGGAATCAAAATCAGATGAAGGTGACTGCTCAAA
TTCAGGTCTCCGGCAATAACCAGAACCCAACTCCGGTGTAGGT
Found at i:3493651 original size:30 final size:29
Alignment explanation
Indices: 3493617--3493706 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
3493607 TTTAATTTTT
* *
3493617 TTTATTCTGAATCAATTGAATCCTCAAATA
1 TTTATT-TTAATCAATTGAATCCTTAAATA
* *
3493647 TTTATTTTCATCAAATTGAATCTTTAAATA
1 TTTATTTTAATC-AATTGAATCCTTAAATA
* *
3493677 TTTATTTTTACTCAATTAAATCCTTAAATA
1 TTTA-TTTTAATCAATTGAATCCTTAAATA
3493707 GATAAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.08
30 40 0.80
31 6 0.12
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTATTTTAATCAATTGAATCCTTAAATA
Found at i:3495116 original size:18 final size:19
Alignment explanation
Indices: 3495081--3495130 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
3495071 TATGATATTT
*
3495081 AAATATAACATAATTACATA
1 AAATAAAACATAATTACA-A
*
3495101 ATATAAAA-ATAA-TACAA
1 AAATAAAACATAATTACAA
3495118 AAATAAAACATAA
1 AAATAAAACATAA
3495131 AAAACGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 4 0.15
20 6 0.23
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAACATAATTACAA
Found at i:3501638 original size:6 final size:6
Alignment explanation
Indices: 3501629--3501653 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3501619 TCGATGTTGG
3501629 ACTTGA ACTTGA ACTTGA ACTTGA A
1 ACTTGA ACTTGA ACTTGA ACTTGA A
3501654 TGAGACACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ACTTGA
Found at i:3504841 original size:22 final size:22
Alignment explanation
Indices: 3504801--3504843 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3504791 AAACAATAAA
*
3504801 AAAATTATTAAATTTTAAATAT
1 AAAATTATTAAATTATAAATAT
3504823 AAAATTA-TAAATTAATAAATA
1 AAAATTATTAAATT-ATAAATA
3504844 ACAAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTATTAAATTATAAATAT
Found at i:3507407 original size:29 final size:29
Alignment explanation
Indices: 3507369--3507424 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3507359 AATAAAAAAA
* *
3507369 ATAAAGATTTATTTAAATATAATAAAACT
1 ATAAAAATTTATTTAAAAATAATAAAACT
3507398 ATAAAAATTTATTTAAAAATAATAAAA
1 ATAAAAATTTATTTAAAAATAATAAAA
3507425 TAATTCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
ATAAAAATTTATTTAAAAATAATAAAACT
Found at i:3514502 original size:16 final size:17
Alignment explanation
Indices: 3514477--3514517 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3514467 ATAAAATGGA
* *
3514477 TAATTTTATAT-ATTTT
1 TAATTATATATAAGTTT
3514493 TAATTATATATAAGTTT
1 TAATTATATATAAGTTT
3514510 T-ATTATAT
1 TAATTATAT
3514518 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTATATATAAGTTT
Found at i:3514614 original size:22 final size:20
Alignment explanation
Indices: 3514589--3514654 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
3514579 TAAAATTTTT
3514589 ATAATTAATCAAAATTAATTTA
1 ATAATTAATC--AATTAATTTA
*
3514611 ATAATCAATCAATTAATTTA
1 ATAATTAATCAATTAATTTA
*
3514631 ATTCAATTAATTTAATT-ATTTA
1 A-T-AATTAA-TCAATTAATTTA
3514653 AT
1 AT
3514655 TCGATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 11 0.29
21 2 0.05
22 20 0.53
23 5 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTAATCAATTAATTTA
Found at i:3514638 original size:14 final size:14
Alignment explanation
Indices: 3514619--3514647 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3514609 TAATAATCAA
3514619 TCAATTAATTTAAT
1 TCAATTAATTTAAT
3514633 TCAATTAATTTAAT
1 TCAATTAATTTAAT
3514647 T
1 T
3514648 ATTTAATTCG
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:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TCAATTAATTTAAT
Found at i:3516103 original size:45 final size:45
Alignment explanation
Indices: 3516039--3516140 Score: 177
Period size: 45 Copynumber: 2.3 Consensus size: 45
3516029 GGGCATTGGA
*
3516039 TTTCCAGTTTGTGGATGATATTGGATCATCTTGTTACTATTCTGC
1 TTTCCAGTTTGCGGATGATATTGGATCATCTTGTTACTATTCTGC
3516084 TTTCCAGTTTGCGGATGATATTGGATCATCTTGTTACTATTCTGC
1 TTTCCAGTTTGCGGATGATATTGGATCATCTTGTTACTATTCTGC
* *
3516129 TTTTCAGATTGC
1 TTTCCAGTTTGC
3516141 TGAAGAGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.46
Consensus pattern (45 bp):
TTTCCAGTTTGCGGATGATATTGGATCATCTTGTTACTATTCTGC
Found at i:3517166 original size:15 final size:15
Alignment explanation
Indices: 3517146--3517178 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3517136 ATGTTTAGTC
*
3517146 TTGGCTTTATTGGAT
1 TTGGCTTTATCGGAT
3517161 TTGGCTTTATCGGAT
1 TTGGCTTTATCGGAT
3517176 TTG
1 TTG
3517179 ATCAAAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.27, T:0.52
Consensus pattern (15 bp):
TTGGCTTTATCGGAT
Found at i:3522126 original size:37 final size:37
Alignment explanation
Indices: 3522084--3522158 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
3522074 CATATTGCAG
3522084 GAATGTTCGTTTCAGTGCGGGTCATAATGAAAGGAAA
1 GAATGTTCGTTTCAGTGCGGGTCATAATGAAAGGAAA
* *
3522121 GAATGTTTGTTTCAGTGCGGGTCATAATGATAGGAAA
1 GAATGTTCGTTTCAGTGCGGGTCATAATGAAAGGAAA
3522158 G
1 G
3522159 GAAACAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (37 bp):
GAATGTTCGTTTCAGTGCGGGTCATAATGAAAGGAAA
Found at i:3531087 original size:23 final size:23
Alignment explanation
Indices: 3531042--3531087 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3531032 AGAGGTTTTA
*
3531042 AAGATTAGGATTTCAAGATTTTG
1 AAGATTAGGATTTCAAGAGTTTG
* * *
3531065 AAGATTCGGATTTTAAGGGTTTG
1 AAGATTAGGATTTCAAGAGTTTG
3531088 GATTTAAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.39
Consensus pattern (23 bp):
AAGATTAGGATTTCAAGAGTTTG
Found at i:3531090 original size:15 final size:15
Alignment explanation
Indices: 3531072--3531252 Score: 56
Period size: 15 Copynumber: 12.0 Consensus size: 15
3531062 TTGAAGATTC
3531072 GGATTTTAAGGGTTT
1 GGATTTTAAGGGTTT
3531087 GGA-TTTAA--GTTT
1 GGATTTTAAGGGTTT
* * *
3531099 TGATGGTTTTATGGTTT
1 GGAT--TTTAAGGGTTT
3531116 GG-TTTTAA-GGTATT
1 GGATTTTAAGGGT-TT
* * *
3531130 GAAGGTTTAA-GTTTT
1 GGA-TTTTAAGGGTTT
*
3531145 TGA-TTTAAGGGTTT
1 GGATTTTAAGGGTTT
* **
3531159 GGATTTAAAAGATTTT
1 GGATTT-TAAGGGTTT
3531175 GGATTTT-AGGAGTTT
1 GGATTTTAAGG-GTTT
* **
3531190 CAGATTTTAAGATTTT
1 -GGATTTTAAGGGTTT
* *
3531206 GAATTTT-AGGATTTT
1 GGATTTTAAGG-GTTT
*
3531221 GGATTTTAGGGGATTTT
1 GGATTTTAAGGG--TTT
*
3531238 GGATTTTAGGGGTTT
1 GGATTTTAAGGGTTT
3531253 TAGAAACCTA
Statistics
Matches: 122, Mismatches: 26, Indels: 36
0.66 0.14 0.20
Matches are distributed among these distances:
12 6 0.05
13 8 0.07
14 22 0.18
15 33 0.27
16 31 0.25
17 22 0.18
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.49
Consensus pattern (15 bp):
GGATTTTAAGGGTTT
Found at i:3531181 original size:7 final size:7
Alignment explanation
Indices: 3531169--3531244 Score: 53
Period size: 7 Copynumber: 9.9 Consensus size: 7
3531159 GGATTTAAAA
3531169 GATTTTG
1 GATTTTG
3531176 GATTTTAG
1 GATTTT-G
**
3531184 GAGTTTCA
1 GA-TTTTG
*
3531192 GATTTTAA
1 GATTTT-G
3531200 GATTTTG
1 GATTTTG
*
3531207 AATTTTAG
1 GATTTT-G
3531215 GATTTTG
1 GATTTTG
3531222 GATTTTAGGG
1 GATTTT---G
3531232 GATTTTG
1 GATTTTG
3531239 GATTTT
1 GATTTT
3531245 AGGGGTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
7 28 0.50
8 18 0.32
9 3 0.05
10 7 0.12
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.51
Consensus pattern (7 bp):
GATTTTG
Found at i:3531189 original size:46 final size:45
Alignment explanation
Indices: 3531139--3531248 Score: 103
Period size: 46 Copynumber: 2.4 Consensus size: 45
3531129 TGAAGGTTTA
* *
3531139 AGTTTTTGATTTAAGGGTTTGGATTTAAAAGATTTTGGATTTTAGG
1 AGTTTTAGATTTAAGGGTTTGAATTT-AAAGATTTTGGATTTTAGG
* ** * *
3531185 AGTTTCAGATTTTAAGATTTTGAATTTTAGGATTTTGGATTTTAGG
1 AGTTTTAGA-TTTAAGGGTTTGAATTTAAAGATTTTGGATTTTAGG
* * *
3531231 GGATTTTGGATTTTAGGG
1 AG-TTTTAGATTTAAGGG
3531249 GTTTTAGAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
46 30 0.61
47 19 0.39
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.48
Consensus pattern (45 bp):
AGTTTTAGATTTAAGGGTTTGAATTTAAAGATTTTGGATTTTAGG
Found at i:3531236 original size:17 final size:17
Alignment explanation
Indices: 3531169--3531253 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 17
3531159 GGATTTAAAA
*
3531169 GATTTTGGATTTTAGGA
1 GATTTTGGATTTTAGGG
** *
3531186 G-TTTCAGATTTTA--A
1 GATTTTGGATTTTAGGG
*
3531200 GATTTTGAATTTTA--G
1 GATTTTGGATTTTAGGG
3531215 GATTTTGGATTTTAGGG
1 GATTTTGGATTTTAGGG
3531232 GATTTTGGATTTTAGGG
1 GATTTTGGATTTTAGGG
3531249 G-TTTT
1 GATTTT
3531254 AGAAACCTAG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
14 2 0.03
15 22 0.38
16 14 0.24
17 20 0.34
ACGTcount: A:0.21, C:0.01, G:0.27, T:0.51
Consensus pattern (17 bp):
GATTTTGGATTTTAGGG
Found at i:3531683 original size:12 final size:12
Alignment explanation
Indices: 3531666--3531717 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
3531656 TATCATGCAT
3531666 AAATATATAAAA
1 AAATATATAAAA
3531678 AAATAT-TAAAA
1 AAATATATAAAA
3531689 ATAATA-A-AAATA
1 A-AATATATAAA-A
3531701 ATAATATATAAAA
1 A-AATATATAAAA
3531714 AAAT
1 AAAT
3531718 TCAAAAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.26
12 20 0.57
13 3 0.09
14 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATATATAAAA
Found at i:3531690 original size:9 final size:9
Alignment explanation
Indices: 3531672--3531717 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3531662 GCATAAATAT
3531672 ATAA-AAAA
1 ATAATAAAA
*
3531680 ATATTAAAA
1 ATAATAAAA
3531689 ATAATAAAA
1 ATAATAAAA
*
3531698 ATAATAATAT
1 ATAATAA-AA
3531708 ATAA-AAAA
1 ATAATAAAA
3531716 AT
1 AT
3531718 TCAAAAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 21 0.66
10 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
ATAATAAAA
Found at i:3532761 original size:15 final size:15
Alignment explanation
Indices: 3532743--3532772 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3532733 ATATATTATT
*
3532743 ATTATTATTATTAAA
1 ATTATTAATATTAAA
3532758 ATTATTAATATTAAA
1 ATTATTAATATTAAA
3532773 CTTAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTAATATTAAA
Found at i:3533213 original size:34 final size:34
Alignment explanation
Indices: 3533120--3533205 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
3533110 CTAAAGATTA
*
3533120 GGATTAAACCGTGAATCAGAGAATAAAACGATCG
1 GGATTAAACCGCGAATCAGAGAATAAAACGATCG
* **
3533154 AGATTAAACTTCGAATCAGAGAATAAAGA-GA-CTG
1 GGATTAAACCGCGAATCAGAGAATAAA-ACGATC-G
3533188 GGATTAAACCGCGAATCA
1 GGATTAAACCGCGAATCA
3533206 AAAAATAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.02
34 41 0.95
35 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (34 bp):
GGATTAAACCGCGAATCAGAGAATAAAACGATCG
Found at i:3533462 original size:174 final size:171
Alignment explanation
Indices: 3533165--3533682 Score: 563
Period size: 174 Copynumber: 3.0 Consensus size: 171
3533155 GATTAAACTT
* * * *
3533165 CGAATCAGAGAATAAAGAGACTGGGATTAAACCGCGAATCAAAAAATAATGTTAACTTGGATTAA
1 CGAATCAGAGAATAAAAAGAC-GAGATTAAA-CGCGAGTCAAAAAATAACGTTAACTTGGATTAA
* * * *
3533230 ATCATAAGTCAGAAAATAAGAAA-ACAAGGAATAAACCATGAGTCAGAAGTTAACAACAATAATC
64 ATCACAAGTCAGAAAATAAAAAAGACAA-GAATAAACCACGAGTCAGAGGTTAACAACAA-AATC
3533294 GAGATTAAACTGTAATTTTAAATTAAAGAGATCGGAATTGAACCA-
127 GAGATTAAACT-TAATTTTAAATTAAAGAGATCGGAATTGAACCAG
* * *
3533339 CGAATCGGAGAATAAAAAGATCGAGATTAAATCGCGAGTTAAAAAATAACGTTAACTTGGATT-T
1 CGAATCAGAGAATAAAAAGA-CGAGATTAAA-CGCGAGTCAAAAAATAACGTTAACTTGGATTAA
** *
3533403 ATCACAAGTCAGAAAATAAAAAAGATCGAA-AATAAATGACAAGTCAGAGGTTAACAACAACAAT
64 ATCACAAGTCAGAAAATAAAAAAGA-C-AAGAATAAACCACGAGTCAGAGGTTAACAACAA-AAT
* * *
3533467 CGATATTAAAC-TACGATTTTAAATTAAAGAGATAGGGATTGAA-CAG
126 CGAGATTAAACTTA--ATTTTAAATTAAAGAGATCGGAATTGAACCAG
* ** * *
3533513 CGAATCAGAGAATAAAAAGACAAGGATTAAACTGCGAGTCAAAAAATGTCGTTAACTTAGATTGA
1 CGAATCAGAGAATAAAAAGACGA-GATTAAAC-GCGAGTCAAAAAATAACGTTAACTTGGATTAA
* * *
3533578 ATCACAAGTCAAAAAAT-AAGAAGACCAAGAATAAACCACGAGTCAGAGGTTAACAAC--AATCA
64 ATCACAAGTCAGAAAATAAAAAAGA-CAAGAATAAACCACGAGTCAGAGGTTAACAACAAAATCG
*
3533640 AGATTAAA-TTACGATTTTAAATTAAAGATATC-GAGATTGAACC
128 AGATTAAACTTA--ATTTTAAATTAAAGAGATCGGA-ATTGAACC
3533683 GTAAATTAAC
Statistics
Matches: 293, Mismatches: 37, Indels: 30
0.81 0.10 0.08
Matches are distributed among these distances:
170 1 0.00
171 38 0.13
172 3 0.01
173 28 0.10
174 203 0.69
175 18 0.06
176 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (171 bp):
CGAATCAGAGAATAAAAAGACGAGATTAAACGCGAGTCAAAAAATAACGTTAACTTGGATTAAAT
CACAAGTCAGAAAATAAAAAAGACAAGAATAAACCACGAGTCAGAGGTTAACAACAAAATCGAGA
TTAAACTTAATTTTAAATTAAAGAGATCGGAATTGAACCAG
Found at i:3534530 original size:21 final size:22
Alignment explanation
Indices: 3534474--3534530 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
3534464 TGCAGACGAC
*
3534474 ATTTTTTATAAAAAATATATTAA
1 ATTTTTT-TAAAAATTATATTAA
* * *
3534497 AATTTTTT-GAAATTATA-TCA
1 ATTTTTTTAAAAATTATATTAA
3534517 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
3534531 AAGAAAACTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 9 0.33
21 11 0.41
22 1 0.04
23 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTTTTAAAAATTATATTAA
Found at i:3535009 original size:1 final size:1
Alignment explanation
Indices: 3535003--3535032 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3534993 GTTCAATGTG
3535003 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3535033 CCTAACCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3536338 original size:23 final size:25
Alignment explanation
Indices: 3536307--3536352 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
3536297 CATTTATATA
*
3536307 TTTAGTTAA-ATATTT-TTAAAATT
1 TTTAATTAATATATTTATTAAAATT
*
3536330 TTTAATTAATTTATTTATTAAAA
1 TTTAATTAATATATTTATTAAAA
3536353 AATAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 5 0.26
25 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTAATTAATATATTTATTAAAATT
Found at i:3538421 original size:17 final size:18
Alignment explanation
Indices: 3538399--3538434 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3538389 CCATCCATAA
3538399 ATTTTTATATT-ATATTT
1 ATTTTTATATTCATATTT
3538416 ATTTTTATATTCATATTT
1 ATTTTTATATTCATATTT
3538434 A
1 A
3538435 ATAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATATTCATATTT
Found at i:3538610 original size:28 final size:27
Alignment explanation
Indices: 3538558--3538621 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
3538548 TTTTATTTTG
*
3538558 TATAT-TTAA-ATAATTTTTTTATAAA
1 TATATATTAATATAATTTTTTAATAAA
3538583 TATATATTAATATATATTTTTTAATAAA
1 TATATATTAATATA-ATTTTTTAATAAA
*
3538611 AATATATTAAT
1 TATATATTAAT
3538622 TTTAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 3 0.09
28 22 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TATATATTAATATAATTTTTTAATAAA
Found at i:3538620 original size:14 final size:14
Alignment explanation
Indices: 3538578--3538621 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3538568 TAATTTTTTT
3538578 ATAAATATATATTA
1 ATAAATATATATTA
* * *
3538592 ATATATATTTTTTA
1 ATAAATATATATTA
*
3538606 ATAAAAATATATTA
1 ATAAATATATATTA
3538620 AT
1 AT
3538622 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATATATATTA
Found at i:3538661 original size:25 final size:24
Alignment explanation
Indices: 3538590--3538673 Score: 62
Period size: 27 Copynumber: 3.3 Consensus size: 24
3538580 AAATATATAT
* *
3538590 TAATATATATTTTTTAAT-AAAAA
1 TAATTTATATTATTTAATAAAAAA
* * *
3538613 TATATTAATTTTAATTAATCTAAAATAA
1 TA-ATTTATATTATTTAA--TAAAA-AA
3538641 TAATTTATATTATTTAATAAAAAAA
1 TAATTTATATTATTTAAT-AAAAAA
*
3538666 TTATTTAT
1 TAATTTAT
3538674 TAAATATATA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
23 2 0.04
24 10 0.22
25 10 0.22
26 5 0.11
27 15 0.33
28 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTTATATTATTTAATAAAAAA
Found at i:3540175 original size:17 final size:16
Alignment explanation
Indices: 3540148--3540190 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
3540138 CTCAAATTCG
*
3540148 AATTCAAAATATTTTATA
1 AATT-AAAATATATTA-A
3540166 AATTAAAATATATTAA
1 AATTAAAATATATTAA
3540182 AATATAAAA
1 AAT-TAAAA
3540191 ATTCGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAAAATATATTAA
Found at i:3549725 original size:20 final size:20
Alignment explanation
Indices: 3549656--3549726 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
3549646 ATAAACTTTA
*
3549656 TAAATAATACATTAATAAATATTT
1 TAAATAA-A-ATTTATAAATA--T
* **
3549680 TAAATAAATTTTATTATTTAT
1 TAAATAAAATTTA-TAAATAT
3549701 T-AATAAAATTTATAAATAT
1 TAAATAAAATTTATAAATAT
3549720 TAAATAA
1 TAAATAA
3549727 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.16
20 15 0.39
21 2 0.05
22 3 0.08
23 5 0.13
24 7 0.18
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATAAAATTTATAAATAT
Done.