Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 65 of 127
Found at i:12650524 original size:22 final size:22
Alignment explanation
Indices: 12650450--12650734 Score: 81
Period size: 22 Copynumber: 12.8 Consensus size: 22
12650440 ATCATCACAA
* *
12650450 ATTTATTACTAAATTAACTATG
1 ATTTATTATTAAATTATCTATG
* * *
12650472 ATTTATTATCAATTTAT-TACTA
1 ATTTATTATTAAATTATCTA-TG
*
12650494 ATTTA-TATTAAATTATCCATG
1 ATTTATTATTAAATTATCTATG
*
12650515 ATTTATTATTAAGTTAT-TATTG
1 ATTTATTATTAAATTATCTA-TG
* * * *
12650537 ATTAACTACTACTAAGTTATAT-TG
1 ATT---TATTATTAAATTATCTATG
* * *
12650561 ATTTTTTTTTAAGTT-TCCTATG
1 ATTTATTATTAAATTAT-CTATG
* *
12650583 ATTAACTATTAAATTATC-ATTG
1 ATTTATTATTAAATTATCTA-TG
* * * *
12650605 ATTTACTATTAAGTTATTTATT
1 ATTTATTATTAAATTATCTATG
* * *
12650627 ATTTACTACTAAGTTTAT-TA-G
1 ATTTATTATTAA-ATTATCTATG
**
12650648 -TTTATTACTATTAAATTA-AAATTG
1 ATTTA-T--TATTAAATTATCTA-TG
* * *
12650672 ATTTACTATTAAGTTATC-ACTA
1 ATTTATTATTAAATTATCTA-TG
*
12650694 ATTTATTATTTAAGTTATC-ATTG
1 ATTTATTA-TTAAATTATCTA-TG
*
12650717 ATTTATTATTAAGTTATC
1 ATTTATTATTAAATTATC
12650735 AATTATTATC
Statistics
Matches: 198, Mismatches: 42, Indels: 46
0.69 0.15 0.16
Matches are distributed among these distances:
20 5 0.03
21 28 0.14
22 111 0.56
23 31 0.16
24 6 0.03
25 16 0.08
26 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (22 bp):
ATTTATTATTAAATTATCTATG
Found at i:12650735 original size:22 final size:22
Alignment explanation
Indices: 12650494--12650757 Score: 175
Period size: 22 Copynumber: 11.9 Consensus size: 22
12650484 TTTATTACTA
*
12650494 ATTTA-TATTAAATTATCCA-TG
1 ATTTACTATTAAGTTAT-CATTG
* *
12650515 ATTTATTATTAAGTTATTATTG
1 ATTTACTATTAAGTTATCATTG
*
12650537 ATTAACTACTACTAAGTTAT-ATTG
1 ATT---TACTATTAAGTTATCATTG
** * *
12650561 ATTTTTTTTTAAGTT-TCCTATG
1 ATTTACTATTAAGTTATCAT-TG
* *
12650583 ATTAACTATTAAATTATCATTG
1 ATTTACTATTAAGTTATCATTG
*
12650605 ATTTACTATTAAGTTATTTATT-
1 ATTTACTATTAAGTTA-TCATTG
* * *
12650627 ATTTACTACTAAGTTTATTAGTTT
1 ATTTACTATTAAG-TTATCA-TTG
* **
12650651 A-TTACTATTAAATTAAAATTG
1 ATTTACTATTAAGTTATCATTG
* *
12650672 ATTTACTATTAAGTTATCACTA
1 ATTTACTATTAAGTTATCATTG
*
12650694 ATTTATTATTTAAGTTATCATTG
1 ATTTACTA-TTAAGTTATCATTG
*
12650717 ATTTATTATTAAGTTATCAATT-
1 ATTTACTATTAAGTTATC-ATTG
*
12650739 A-TTATCTACTAAGTTATCA
1 ATTTA-CTATTAAGTTATCA
12650758 CTTTTTTTAA
Statistics
Matches: 193, Mismatches: 34, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.01
21 22 0.11
22 106 0.55
23 44 0.23
24 8 0.04
25 12 0.06
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.51
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCATTG
Found at i:12651131 original size:22 final size:22
Alignment explanation
Indices: 12651032--12651162 Score: 100
Period size: 22 Copynumber: 5.9 Consensus size: 22
12651022 AAAATATATA
* * *
12651032 TATCAATGATTGACAATTAAGT
1 TATCAATGATTTACTATTAAAT
* * * *
12651054 TATTAATTATTTACTACTAAAA
1 TATCAATGATTTACTATTAAAT
* *
12651076 TATCAATAATTTACTACTAAAT
1 TATCAATGATTTACTATTAAAT
** *
12651098 TATCAAAAATTTACTATTAATT
1 TATCAATGATTTACTATTAAAT
* * *
12651120 TATGAATGATTTGCCATTAAAT
1 TATCAATGATTTACTATTAAAT
* *
12651142 TATGAATGATTTTACCATTAA
1 TATCAATGA-TTTACTATTAA
12651163 TTGTTCTTTA
Statistics
Matches: 88, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
22 78 0.89
23 10 0.11
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (22 bp):
TATCAATGATTTACTATTAAAT
Found at i:12651372 original size:22 final size:19
Alignment explanation
Indices: 12651325--12651363 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12651315 TTATTAGTAG
*
12651325 TTTACTACTAAGTTATCAA
1 TTTACTACTAAATTATCAA
12651344 TTTACTACTAAATTATCAA
1 TTTACTACTAAATTATCAA
12651363 T
1 T
12651364 AATTTACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (19 bp):
TTTACTACTAAATTATCAA
Found at i:12651525 original size:22 final size:22
Alignment explanation
Indices: 12651500--12651564 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
12651490 TACTGACTTA
12651500 TATTAAATTATGCATGATTTAC
1 TATTAAATTATGCATGATTTAC
* * *
12651522 TATTAAAGTAT-CACTGATTAAT
1 TATTAAATTATGCA-TGATTTAC
*
12651544 TATTATATTATTG-ATGATTTA
1 TATTAAATTA-TGCATGATTTA
12651565 TTACTAGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (22 bp):
TATTAAATTATGCATGATTTAC
Found at i:12651576 original size:22 final size:21
Alignment explanation
Indices: 12651558--12651635 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 21
12651548 ATATTATTGA
* *
12651558 TGATTTATTACTAGGTTATAC
1 TGATTTACTACTAAGTTATAC
* * *
12651579 TAATTTACTACTAATTTATGAT
1 TGATTTACTACTAAGTTAT-AC
* *
12651601 TGATTTATTATTAAGTTAATTA-
1 TGATTTACTACTAAGTT-A-TAC
12651623 TGATTTACTACTA
1 TGATTTACTACTA
12651636 TCAATTAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
21 15 0.35
22 25 0.58
23 2 0.05
24 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (21 bp):
TGATTTACTACTAAGTTATAC
Found at i:12651746 original size:22 final size:22
Alignment explanation
Indices: 12651680--12651747 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
12651670 CTACTAAATT
12651680 ATAATTAATCTACTATAAGTTATCA
1 ATAATTAA-CTAC--TAAGTTATCA
* * * * * *
12651705 TTGATTTATTATTAAATTATCA
1 ATAATTAACTACTAAGTTATCA
12651727 ATAATTAACTACTAAGTTATC
1 ATAATTAACTACTAAGTTATC
12651748 TCTTATTTTT
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
22 24 0.77
24 2 0.06
25 5 0.16
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (22 bp):
ATAATTAACTACTAAGTTATCA
Found at i:12651746 original size:44 final size:46
Alignment explanation
Indices: 12651680--12651770 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 46
12651670 CTACTAAATT
12651680 ATAATTAATCTACTATAAGTTATCAT-TGATTTATTATTAAATTATCA
1 ATAATTAATCTAC-ATAAGTTATC-TCTGATTTATTATTAAATTATCA
* * *
12651727 ATAATTAA-CTAC-TAAGTTATCTCTTATTTTTTATTAAGTTATCA
1 ATAATTAATCTACATAAGTTATCTCTGATTTATTATTAAATTATCA
12651771 TTGATTTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
43 1 0.03
44 27 0.68
46 4 0.10
47 8 0.20
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.48
Consensus pattern (46 bp):
ATAATTAATCTACATAAGTTATCTCTGATTTATTATTAAATTATCA
Found at i:12651777 original size:22 final size:22
Alignment explanation
Indices: 12651695--12651778 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
12651685 TAATCTACTA
12651695 TAAGTTATCATTGATTTATTAT
1 TAAGTTATCATTGATTTATTAT
* * * * * *
12651717 TAAATTATCAATAATTAACTAC
1 TAAGTTATCATTGATTTATTAT
* *
12651739 TAAGTTATC-TCTTATTTTTTAT
1 TAAGTTATCAT-TGATTTATTAT
12651761 TAAGTTATCATTGATTTA
1 TAAGTTATCATTGATTTA
12651779 GTACTATATT
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (22 bp):
TAAGTTATCATTGATTTATTAT
Found at i:12651901 original size:22 final size:21
Alignment explanation
Indices: 12651863--12651932 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
12651853 TACTAAAAGG
*
12651863 TTATCAATTATTAATTACTAAA
1 TTAT-AATTATTTATTACTAAA
* *
12651885 TTATAATTCATTTATTATTAAG
1 TTATAATT-ATTTATTACTAAA
**
12651907 TTATCTTTAATTT-TTCACTAAA
1 TTATAATT-ATTTATT-ACTAAA
12651929 TTAT
1 TTAT
12651933 CAATAAGGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.16
22 32 0.84
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (21 bp):
TTATAATTATTTATTACTAAA
Found at i:12653579 original size:32 final size:31
Alignment explanation
Indices: 12653536--12653597 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
12653526 AAAAAGATAC
12653536 TATATTTTAATTGTTGTTTCATTCTTATTAT
1 TATATTTTAATTGTTGTTTCATTCTTATTAT
*
12653567 TATATTTTTAATTGTTGTTTCATTTTTATTA
1 TATA-TTTTAATTGTTGTTTCATTCTTATTA
12653598 CTATTATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.66
Consensus pattern (31 bp):
TATATTTTAATTGTTGTTTCATTCTTATTAT
Found at i:12655557 original size:27 final size:27
Alignment explanation
Indices: 12655504--12655557 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
12655494 TTTATTTAAT
* **
12655504 ATGACAAATCATTTTTTTTTATGAAAA
1 ATGAAAAATCATTTTTACTTATGAAAA
12655531 ATGAAAAATCA-TTTTACTTATGAAAA
1 ATGAAAAATCATTTTTACTTATGAAAA
12655557 A
1 A
12655558 GAGTCTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (27 bp):
ATGAAAAATCATTTTTACTTATGAAAA
Found at i:12655823 original size:15 final size:15
Alignment explanation
Indices: 12655805--12655852 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
12655795 TTAGTTGATT
12655805 TAAATTAAATTTAAA
1 TAAATTAAATTTAAA
12655820 TAAATT-AA--T-AA
1 TAAATTAAATTTAAA
*
12655831 -AATTTAAATTTAAA
1 TAAATTAAATTTAAA
12655845 TAAATTAA
1 TAAATTAA
12655853 CAAAAGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 1 0.04
13 1 0.04
14 4 0.15
15 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTAAATTTAAA
Found at i:12655838 original size:25 final size:26
Alignment explanation
Indices: 12655809--12655871 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 26
12655799 TTGATTTAAA
*
12655809 TTAAATTTAAATAAATTAATAAAA-T
1 TTAAATTTAAATAAATTAACAAAAGT
12655834 TTAAATTTAAATAAATTAACAAAAGT
1 TTAAATTTAAATAAATTAACAAAAGT
*
12655860 TATATATTTAAA
1 T-TAAATTTAAA
12655872 GATAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 23 0.68
26 2 0.06
27 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (26 bp):
TTAAATTTAAATAAATTAACAAAAGT
Found at i:12672525 original size:15 final size:15
Alignment explanation
Indices: 12672476--12672529 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
12672466 ACTAAATTGC
12672476 ATTTTAAAAAATAAT
1 ATTTTAAAAAATAAT
*
12672491 AATTGTAAAAAA-AAT
1 -ATTTTAAAAAATAAT
* *
12672506 TTTTTAAAAAATTAT
1 ATTTTAAAAAATAAT
12672521 ATTTTAAAA
1 ATTTTAAAA
12672530 TTTTTCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.28
15 13 0.41
16 10 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTTTAAAAAATAAT
Found at i:12673541 original size:29 final size:30
Alignment explanation
Indices: 12673487--12673544 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
12673477 AAAATATAAA
*
12673487 AATCATTAAAATTTTGGGTAACTTACTAAG
1 AATCATTAAAATTTTGGATAACTTACTAAG
12673517 AATCATTAAAA-TTTGGATAACTTACTAA
1 AATCATTAAAATTTTGGATAACTTACTAA
12673545 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
AATCATTAAAATTTTGGATAACTTACTAAG
Found at i:12676612 original size:23 final size:23
Alignment explanation
Indices: 12676582--12676625 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
12676572 GTATTGACTT
12676582 ATATTTGTATTTCAAAAGCAATG
1 ATATTTGTATTTCAAAAGCAATG
12676605 ATATTTGTATTTCAAAAGCAA
1 ATATTTGTATTTCAAAAGCAA
12676626 AGAATCAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (23 bp):
ATATTTGTATTTCAAAAGCAATG
Found at i:12679710 original size:14 final size:14
Alignment explanation
Indices: 12679691--12679725 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12679681 ACAAATCAAA
12679691 TACAAATTCATCTT
1 TACAAATTCATCTT
*
12679705 TACAAATTTATCTT
1 TACAAATTCATCTT
*
12679719 TTCAAAT
1 TACAAAT
12679726 ATAGTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (14 bp):
TACAAATTCATCTT
Found at i:12679799 original size:19 final size:17
Alignment explanation
Indices: 12679761--12679810 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
12679751 ATTAAAAGAT
*
12679761 AACAAAAAAAAAATCAA
1 AACAAAAAAAAAACCAA
*
12679778 AACTAAAAGAAAAAACCCA
1 AAC-AAAA-AAAAAACCAA
12679797 AACAAAAAATAAAA
1 AACAAAAAA-AAAA
12679811 AAATTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 12 0.43
19 11 0.39
ACGTcount: A:0.78, C:0.14, G:0.02, T:0.06
Consensus pattern (17 bp):
AACAAAAAAAAAACCAA
Found at i:12680115 original size:23 final size:25
Alignment explanation
Indices: 12680040--12680127 Score: 60
Period size: 27 Copynumber: 3.4 Consensus size: 25
12680030 TATCTTAATT
12680040 ATATATAAATATAATATTTTAAA-ATAA
1 ATATATAAATA-AA-A-TTTAAACATAA
*
12680067 ATATATTAAATAATAACTTATTAACAT-A
1 ATATA-TAAATAA-AA-TT-TAAACATAA
12680095 ATATATAAATAAAA-TTAAACA-AA
1 ATATATAAATAAAATTTAAACATAA
*
12680118 AAATA-AAATA
1 ATATATAAATA
12680128 TATATTCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
22 5 0.10
23 10 0.19
24 1 0.02
26 2 0.04
27 16 0.31
28 16 0.31
29 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATATAAATAAAATTTAAACATAA
Found at i:12681030 original size:15 final size:16
Alignment explanation
Indices: 12681012--12681063 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
12681002 ATAATAATTT
12681012 TATTAATATA-AAATA
1 TATTAATATATAAATA
*
12681027 TATTAATATATAATTA
1 TATTAATATATAAATA
* *
12681043 AATTAATAATATATATA
1 TATTAAT-ATATAAATA
12681060 TATT
1 TATT
12681064 GATCGAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 10 0.33
16 10 0.33
17 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATATATAAATA
Found at i:12681124 original size:14 final size:14
Alignment explanation
Indices: 12681105--12681133 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12681095 ATTTGATCTT
12681105 AATTTTTTTTAAAA
1 AATTTTTTTTAAAA
12681119 AATTTTTTTTAAAA
1 AATTTTTTTTAAAA
12681133 A
1 A
12681134 TATTAACTCA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTTTTTTAAAA
Found at i:12689072 original size:20 final size:20
Alignment explanation
Indices: 12689043--12689081 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12689033 TCTTTTATAC
12689043 TTATTCGAATAACTGTAAAA
1 TTATTCGAATAACTGTAAAA
* *
12689063 TTATTTGAATAATTGTAAA
1 TTATTCGAATAACTGTAAA
12689082 TCCCTTTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TTATTCGAATAACTGTAAAA
Found at i:12699623 original size:14 final size:14
Alignment explanation
Indices: 12699588--12699616 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12699578 CCTCTAACAC
12699588 TACCTTTTTGCCCT
1 TACCTTTTTGCCCT
12699602 TACCTTTTTGCCCT
1 TACCTTTTTGCCCT
12699616 T
1 T
12699617 TTTTTTTATA
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:0.07, C:0.34, G:0.07, T:0.52
Consensus pattern (14 bp):
TACCTTTTTGCCCT
Found at i:12701267 original size:9 final size:9
Alignment explanation
Indices: 12701253--12701282 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12701243 ATACATATTG
12701253 ATATAATTT
1 ATATAATTT
*
12701262 ATATAATAT
1 ATATAATTT
12701271 ATATAATTT
1 ATATAATTT
12701280 ATA
1 ATA
12701283 AGTATTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATAATTT
Found at i:12701452 original size:17 final size:17
Alignment explanation
Indices: 12701432--12701464 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12701422 ATTTAGTTAT
12701432 GTTATTT-TATTGATTAG
1 GTTATTTGT-TTGATTAG
12701449 GTTATTTGTTTGATTA
1 GTTATTTGTTTGATTA
12701465 TTATGCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (17 bp):
GTTATTTGTTTGATTAG
Found at i:12707182 original size:38 final size:38
Alignment explanation
Indices: 12707122--12707198 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
12707112 TAAACAATGC
*
12707122 ATGGCAAAACTCCTCCTCAATTTGTGCATCCTAATCCA
1 ATGGCAAAACTCCTCCTCAATTTATGCATCCTAATCCA
** *
12707160 ATGGCAAAACTTTTCCTTAATTTATGCATCCTAATCCA
1 ATGGCAAAACTCCTCCTCAATTTATGCATCCTAATCCA
12707198 A
1 A
12707199 CACAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.32
Consensus pattern (38 bp):
ATGGCAAAACTCCTCCTCAATTTATGCATCCTAATCCA
Found at i:12707830 original size:16 final size:16
Alignment explanation
Indices: 12707811--12707845 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12707801 ATTAAAGCTT
*
12707811 ATACCAATTATTAAGG
1 ATACCAATTATTAAAG
*
12707827 ATACCAATTGTTAAAG
1 ATACCAATTATTAAAG
12707843 ATA
1 ATA
12707846 TGTTATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (16 bp):
ATACCAATTATTAAAG
Found at i:12712753 original size:19 final size:19
Alignment explanation
Indices: 12712717--12712754 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12712707 TATTAAGTCC
*
12712717 AAAATAAATAATTCACTTT
1 AAAATAAATAATTAACTTT
12712736 AAAA-AAATAATTGAACTTT
1 AAAATAAATAATT-AACTTT
12712755 CATTTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAATAAATAATTAACTTT
Found at i:12716589 original size:26 final size:26
Alignment explanation
Indices: 12716532--12716589 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
12716522 AAAAACATTA
*
12716532 AATTAAAATATGAATATAATAAATTT
1 AATTAAAATATGAATATAATAAATAT
* * *
12716558 ATTTAAAGTTTGAATATAAT-AATAT
1 AATTAAAATATGAATATAATAAATAT
12716583 AGATTAA
1 A-ATTAA
12716590 TGTTATTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (26 bp):
AATTAAAATATGAATATAATAAATAT
Found at i:12716651 original size:19 final size:19
Alignment explanation
Indices: 12716627--12716663 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12716617 TTAATAATGT
* *
12716627 TTATTTATTTCATTATTTA
1 TTATTTATGTAATTATTTA
12716646 TTATTTATGTAATTATTT
1 TTATTTATGTAATTATTT
12716664 TATTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTATGTAATTATTTA
Found at i:12717696 original size:31 final size:31
Alignment explanation
Indices: 12717649--12717707 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12717639 TAATAATAAA
12717649 TAATAACATATATAATAATATTTTTATTATTT
1 TAATAACATATATAATAATA-TTTTATTATTT
*
12717681 TAATAATA-ATATAATAATATTTTATTA
1 TAATAACATATATAATAATATTTTATTA
12717708 AGAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.31
31 11 0.42
32 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TAATAACATATATAATAATATTTTATTATTT
Found at i:12717704 original size:22 final size:22
Alignment explanation
Indices: 12717634--12717731 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
12717624 ACTATATTAT
12717634 TATTTTAATAATAA-ATAATAA
1 TATTTTAATAATAATATAATAA
* * ** *
12717655 CA-TAT-ATAATAATATTTTTAT
1 TATTTTAATAATAATA-TAATAA
12717676 TATTTTAATAATAATATAATAA
1 TATTTTAATAATAATATAATAA
* * ** *
12717698 TATTTTATTAAGAATATTTTAT
1 TATTTTAATAATAATATAATAA
12717720 TATTTTAATAAT
1 TATTTTAATAAT
12717732 TAATTTTAAA
Statistics
Matches: 56, Mismatches: 17, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
19 7 0.12
20 3 0.05
21 5 0.09
22 32 0.57
23 9 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
TATTTTAATAATAATATAATAA
Found at i:12717963 original size:25 final size:25
Alignment explanation
Indices: 12717933--12717982 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12717923 ATATTTTAAT
*
12717933 AGTAGAAATATTTTAGTAATAAATA
1 AGTAGAAATATTTTAGCAATAAATA
12717958 AGTAGAAATATTTTAGCAATAAATA
1 AGTAGAAATATTTTAGCAATAAATA
12717983 TTACTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (25 bp):
AGTAGAAATATTTTAGCAATAAATA
Found at i:12721215 original size:27 final size:27
Alignment explanation
Indices: 12721185--12721236 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12721175 CTCTTAATCT
12721185 TTTATTTTCATTTTTGTT-TATTTTTGC
1 TTTATTTTCATTTTT-TTATATTTTTGC
*
12721212 TTTATTTTGATTTTTTTATATTTTT
1 TTTATTTTCATTTTTTTATATTTTT
12721237 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (27 bp):
TTTATTTTCATTTTTTTATATTTTTGC
Found at i:12722531 original size:13 final size:13
Alignment explanation
Indices: 12722513--12722554 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
12722503 AGATGTTTTT
12722513 ATAATTAGACTAAA
1 ATAATT-GACTAAA
12722527 A-AATTG-CTAAAA
1 ATAATTGACT-AAA
12722539 ATAATTGACTAAA
1 ATAATTGACTAAA
12722552 ATA
1 ATA
12722555 CCCTAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.08
12 5 0.20
13 15 0.60
14 3 0.12
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
ATAATTGACTAAA
Found at i:12727935 original size:22 final size:22
Alignment explanation
Indices: 12727899--12727950 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
12727889 GTAAACATCA
*
12727899 ATAACTT-GTAGTAAATCAATG
1 ATAACTTAATAGTAAATCAATG
*
12727920 ATAACTTAATAGTAAATGAATG
1 ATAACTTAATAGTAAATCAATG
12727942 ATAA-TTAAT
1 ATAACTTAAT
12727951 TTAGTAGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCAATG
Found at i:12728013 original size:22 final size:22
Alignment explanation
Indices: 12727977--12728076 Score: 60
Period size: 22 Copynumber: 4.5 Consensus size: 22
12727967 GATTACTTTT
* *
12727977 TAATAAATTAGTAATAATATAA
1 TAATAAATCAATAATAATATAA
* *
12727999 TAATAAATGC-ATAATACTTTAA
1 TAATAAAT-CAATAATAATATAA
* * *
12728021 TAGTAAATCAATTATAATATAG
1 TAATAAATCAATAATAATATAA
** * *
12728043 TTGTAAAT-ACATAACAATATAG
1 TAATAAATCA-ATAATAATATAA
*
12728065 TACTAAATCAAT
1 TAATAAATCAAT
12728077 GAGAGCTTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
21 2 0.03
22 57 0.95
23 1 0.02
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (22 bp):
TAATAAATCAATAATAATATAA
Found at i:12728243 original size:22 final size:22
Alignment explanation
Indices: 12728218--12728265 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12728208 TTGATAGTGA
*
12728218 AAATT-ATAAATAACTTAGTAGT
1 AAATTAAT-AATAAATTAGTAGT
12728240 AAATTAATAATAAATTAGTAGT
1 AAATTAATAATAAATTAGTAGT
12728262 AAAT
1 AAAT
12728266 AAGTGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
AAATTAATAATAAATTAGTAGT
Found at i:12728264 original size:11 final size:11
Alignment explanation
Indices: 12728232--12728265 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12728222 TATAAATAAC
12728232 TTAGTAGTAAA
1 TTAGTAGTAAA
* *
12728243 TTAATAATAAA
1 TTAGTAGTAAA
12728254 TTAGTAGTAAA
1 TTAGTAGTAAA
12728265 T
1 T
12728266 AAGTGATGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (11 bp):
TTAGTAGTAAA
Found at i:12728279 original size:22 final size:21
Alignment explanation
Indices: 12728226--12728293 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
12728216 GAAAATTATA
*
12728226 AATAACTTAGTAGTAAATTAAT
1 AATAAATTAGTAGTAAA-TAAT
12728248 AATAAATTAGTAGTAAATAAGT
1 AATAAATTAGTAGTAAATAA-T
* * * *
12728270 GATGATTTAGTAGTTAATAA-
1 AATAAATTAGTAGTAAATAAT
12728290 AATA
1 AATA
12728294 GTAGTAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 33 0.87
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.35
Consensus pattern (21 bp):
AATAAATTAGTAGTAAATAAT
Found at i:12728288 original size:37 final size:37
Alignment explanation
Indices: 12728247--12728324 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
12728237 AGTAAATTAA
* *
12728247 TAATAAATTAGTAGTAAATAAGTGATGATTTAGTAGT
1 TAATAAAATAGTAGTAAATAAGTGATGATCTAGTAGT
*
12728284 TAATAAAATAGTAGTAAATAATTGATGATCTAGTAGT
1 TAATAAAATAGTAGTAAATAAGTGATGATCTAGTAGT
12728321 TAAT
1 TAAT
12728325 CACTAAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.01, G:0.17, T:0.37
Consensus pattern (37 bp):
TAATAAAATAGTAGTAAATAAGTGATGATCTAGTAGT
Found at i:12728397 original size:22 final size:22
Alignment explanation
Indices: 12728332--12728456 Score: 78
Period size: 22 Copynumber: 5.8 Consensus size: 22
12728322 AATCACTAAA
*
12728332 AACATAAAAGTAAATTAGT-AT
1 AACATAATAGTAAATTAGTAAT
* *
12728353 AACTTAGTAGTAAATTA-TCAAT
1 AACATAATAGTAAATTAGT-AAT
*
12728375 AACATAATAGTTAATTAGTAAT
1 AACATAATAGTAAATTAGTAAT
** * *
12728397 AATTTAATAATAAATCA-TGAAT
1 AACATAATAGTAAATTAGT-AAT
** *
12728419 AATTTAAT-TTAAATTAGTAAT
1 AACATAATAGTAAATTAGTAAT
* * *
12728440 AACTTGATAGTGAATTA
1 AACATAATAGTAAATTA
12728457 TAGATAATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.01
21 30 0.37
22 49 0.60
23 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.37
Consensus pattern (22 bp):
AACATAATAGTAAATTAGTAAT
Found at i:12728818 original size:44 final size:44
Alignment explanation
Indices: 12728748--12728856 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
12728738 TAAATCAAGA
* * * * *
12728748 ATAACTTAACAAAAAAT-AAGTGATAACTTAGTAGTTAATT-GTTG
1 ATAACTTAATAATAAATCAA-TAATAACTTAATAGTAAATTAG-TG
*
12728792 ATAACTTATTAATAAATCAATAATAACTTAATAGTAAATTAGTG
1 ATAACTTAATAATAAATCAATAATAACTTAATAGTAAATTAGTG
* *
12728836 ATAATTTAATAGTAAATCAAT
1 ATAACTTAATAATAAATCAAT
12728857 TTTAGTTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 51 0.94
45 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (44 bp):
ATAACTTAATAATAAATCAATAATAACTTAATAGTAAATTAGTG
Found at i:12728839 original size:22 final size:22
Alignment explanation
Indices: 12728761--12728852 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
12728751 ACTTAACAAA
* *
12728761 AAATAAGTGATAACTTAGTAGT
1 AAATTAGTGATAACTTAATAGT
* * *
12728783 TAATT-GTTGATAACTTATTAAT
1 AAATTAG-TGATAACTTAATAGT
* * *
12728805 AAATCAATAATAACTTAATAGT
1 AAATTAGTGATAACTTAATAGT
*
12728827 AAATTAGTGATAATTTAATAGT
1 AAATTAGTGATAACTTAATAGT
12728849 AAAT
1 AAAT
12728853 CAATTTTAGT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 53 0.98
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (22 bp):
AAATTAGTGATAACTTAATAGT
Found at i:12728921 original size:22 final size:22
Alignment explanation
Indices: 12728896--12729008 Score: 95
Period size: 22 Copynumber: 5.2 Consensus size: 22
12728886 TAAATTATAA
*
12728896 ATAAATTAGTAATAAATCATTG
1 ATAAATTAGTAGTAAATCATTG
*
12728918 ATAAATTAGTAGTAAATAATTG
1 ATAAATTAGTAGTAAATCATTG
* * * * *
12728940 ATGATTTAATAGTTAATTATTG
1 ATAAATTAGTAGTAAATCATTG
** * *
12728962 A-AAATTTAAAAATAGATCATT-
1 ATAAA-TTAGTAGTAAATCATTG
*
12728983 ATAACTTAGTAGTAAATCATTG
1 ATAAATTAGTAGTAAATCATTG
12729005 ATAA
1 ATAA
12729009 CATAATTCTT
Statistics
Matches: 69, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
21 14 0.20
22 55 0.80
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.38
Consensus pattern (22 bp):
ATAAATTAGTAGTAAATCATTG
Found at i:12729046 original size:65 final size:66
Alignment explanation
Indices: 12728906--12729046 Score: 158
Period size: 65 Copynumber: 2.2 Consensus size: 66
12728896 ATAAATTAGT
* ** * * *
12728906 AATAAATCATTGATAAATTAGTAGTAAATAATTGATGATTTAATAGTTAATTATTGAAAATTTAA
1 AATAAATCATTGATAAATTAGTAGTAAATAATTGATAACATAATACTTAATTAATGAAAACTTAA
12728971 A
66 A
* * * * *
12728972 AATAGATCATT-ATAACTTAGTAGTAAATCATTGATAACATAATTCTTAATTAATGATAACTTAA
1 AATAAATCATTGATAAATTAGTAGTAAATAATTGATAACATAATACTTAATTAATGAAAACTTAA
*
12729036 T
66 A
*
12729037 AGTAAATCAT
1 AATAAATCAT
12729047 GCATAATTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
65 51 0.84
66 10 0.16
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (66 bp):
AATAAATCATTGATAAATTAGTAGTAAATAATTGATAACATAATACTTAATTAATGAAAACTTAA
A
Found at i:12729052 original size:22 final size:21
Alignment explanation
Indices: 12728908--12729064 Score: 73
Period size: 22 Copynumber: 7.2 Consensus size: 21
12728898 AAATTAGTAA
* *
12728908 TAAATCATTGATAAATTAGTAG
1 TAAATCA-TGATAACTTAATAG
* * *
12728930 TAAATAATTGATGATTTAATAG
1 TAAATCA-TGATAACTTAATAG
* * * * * *
12728952 TTAATTATTGAAAATTTAAAAA
1 TAAATCA-TGATAACTTAATAG
* * *
12728974 TAGATCATTATAACTTAGTAG
1 TAAATCATGATAACTTAATAG
* **
12728995 TAAATCATTGATAACATAATTCT
1 TAAATCA-TGATAACTTAA-TAG
* *
12729018 TAATTAATGATAACTTAATAG
1 TAAATCATGATAACTTAATAG
*
12729039 TAAATCATGCATAATTTAATA-
1 TAAATCATG-ATAACTTAATAG
12729060 TAAAT
1 TAAAT
12729065 TAGTAATAGC
Statistics
Matches: 99, Mismatches: 33, Indels: 7
0.71 0.24 0.05
Matches are distributed among these distances:
21 27 0.27
22 66 0.67
23 6 0.06
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (21 bp):
TAAATCATGATAACTTAATAG
Found at i:12729148 original size:21 final size:20
Alignment explanation
Indices: 12729122--12729193 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
12729112 GATAATTTTG
12729122 TAGTAAATAATAAAAAATAA
1 TAGTAAATAATAAAAAATAA
* * *
12729142 GCAGTAAATCAATGATAACATAA
1 -TAGTAAAT-AAT-AAAAAATAA
*
12729165 TAGTAAGTATATAAAAAATAA
1 TAGTAAATA-ATAAAAAATAA
12729186 TAGTAAAT
1 TAGTAAAT
12729194 CTTTGATAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 22 0.55
22 11 0.28
23 7 0.17
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.26
Consensus pattern (20 bp):
TAGTAAATAATAAAAAATAA
Found at i:12729150 original size:43 final size:41
Alignment explanation
Indices: 12729103--12729217 Score: 104
Period size: 43 Copynumber: 2.7 Consensus size: 41
12729093 TAATTTGTGA
*
12729103 TAAATTGATGATAATTTTGTAGTAAATAATAAAAAATAAGCAG
1 TAAATT-ATGATAATTTAGTAGTAAATAATAAAAAATAA-CAG
* ** * * *
12729146 TAAATCAATGATAACATAATAGTAAGTATATAAAAAATAATAG
1 TAAAT-TATGATAATTTAGTAGTAAATA-ATAAAAAATAACAG
* *
12729189 TAAATCTTTGATAATTTAGTTGTAAATAA
1 TAAAT-TATGATAATTTAGTAGTAAATAA
12729218 CTAATAACGT
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
42 1 0.02
43 44 0.79
44 11 0.20
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (41 bp):
TAAATTATGATAATTTAGTAGTAAATAATAAAAAATAACAG
Found at i:12729224 original size:22 final size:21
Alignment explanation
Indices: 12729199--12729281 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
12729189 TAAATCTTTG
*
12729199 ATAATTTAGTTGTAAATAACTA
1 ATAATTTAGTAGTAAAT-ACTA
** * * *
12729221 ATAACGTAATAATAAGTTACTA
1 ATAATTTAGTAGTAA-ATACTA
* * *
12729243 ATAATTTAGTTGTAAACTAGTG
1 ATAATTTAGTAGTAAA-TACTA
12729265 ATAATTTAGTAGTAAAT
1 ATAATTTAGTAGTAAAT
12729282 TAATTAATGA
Statistics
Matches: 44, Mismatches: 15, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
21 1 0.02
22 42 0.95
23 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.39
Consensus pattern (21 bp):
ATAATTTAGTAGTAAATACTA
Found at i:12729365 original size:22 final size:22
Alignment explanation
Indices: 12729339--12729409 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
12729329 TAAGTTAATT
12729339 ATAACTTTATAATAAATCATCA
1 ATAACTTTATAATAAATCATCA
*
12729361 ATAACTTTATGATAAATCA--A
1 ATAACTTTATAATAAATCATCA
* *
12729381 ATTTAATTTTATTATAAATCATCA
1 A--TAACTTTATAATAAATCATCA
12729405 ATAAC
1 ATAAC
12729410 ATAGTAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.05
22 37 0.90
24 2 0.05
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.39
Consensus pattern (22 bp):
ATAACTTTATAATAAATCATCA
Found at i:12729456 original size:21 final size:21
Alignment explanation
Indices: 12729432--12729522 Score: 76
Period size: 22 Copynumber: 4.2 Consensus size: 21
12729422 CACTAACAAT
12729432 TTAATAGAAATCATTCATAAC
1 TTAATAGAAATCATTCATAAC
* * * *
12729453 TTAATGGTAATCAATCATAAT
1 TTAATAGAAATCATTCATAAC
* *
12729474 TTAAT-GATAATTCATTAATAAT
1 TTAATAGA-AA-TCATTCATAAC
* *
12729496 TTAGTAGTAAATCATTGATAAC
1 TTAATAG-AAATCATTCATAAC
12729518 TTAAT
1 TTAAT
12729523 TGTCAGTCAT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 24 0.44
22 26 0.47
23 3 0.05
24 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.40
Consensus pattern (21 bp):
TTAATAGAAATCATTCATAAC
Found at i:12729497 original size:22 final size:21
Alignment explanation
Indices: 12729419--12729541 Score: 72
Period size: 22 Copynumber: 5.7 Consensus size: 21
12729409 CATAGTAGTA
* *
12729419 AATCACTAACAATTTAATAGA-
1 AATCATTAATAATTTAAT-GAT
* * *
12729440 AATCATTCATAACTTAATGGT
1 AATCATTAATAATTTAATGAT
* *
12729461 AATCAATCATAATTTAATGAT
1 AATCATTAATAATTTAATGAT
*
12729482 AATTCATTAATAATTTAGT-AGT
1 AA-TCATTAATAATTTAATGA-T
* *
12729504 AAATCATTGATAACTTAATTG-T
1 -AATCATTAATAATTTAA-TGAT
*
12729526 CAGTCATTAATAATTT
1 -AATCATTAATAATTT
12729542 TTTTATACTT
Statistics
Matches: 78, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 35 0.45
22 39 0.50
23 3 0.04
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (21 bp):
AATCATTAATAATTTAATGAT
Found at i:12729857 original size:22 final size:22
Alignment explanation
Indices: 12729832--12729879 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
12729822 AGTATTTAAT
*
12729832 CAATGATAACTCAATAATAAAC
1 CAATAATAACTCAATAATAAAC
* * *
12729854 CAATAATAATTTAATAATAAAT
1 CAATAATAACTCAATAATAAAC
12729876 CAAT
1 CAAT
12729880 TTTAGTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (22 bp):
CAATAATAACTCAATAATAAAC
Found at i:12729955 original size:21 final size:20
Alignment explanation
Indices: 12729901--12729960 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
12729891 AGTAATTAAT
*
12729901 TAATA-AACTTATTAGTAAA
1 TAATATAACTTAGTAGTAAA
*
12729920 TAATAAATAATTTAGTAGTAAA
1 TAAT--ATAACTTAGTAGTAAA
12729942 TCAATATAACTTAGTAGTA
1 T-AATATAACTTAGTAGTA
12729961 GTTAATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.12
21 14 0.41
22 13 0.38
23 3 0.09
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (20 bp):
TAATATAACTTAGTAGTAAA
Found at i:12730336 original size:22 final size:22
Alignment explanation
Indices: 12729857--12730415 Score: 160
Period size: 22 Copynumber: 25.2 Consensus size: 22
12729847 AATAAACCAA
* *
12729857 TAATAATTTAATAATAAATCAAT
1 TAATAATTTAGTAGTAAATC-AT
* * * * *
12729880 T-TTAGTTTAATAGTAATTAAT
1 TAATAATTTAGTAGTAAATCAT
* * *
12729901 TAATAAACTTATTAGTAAATAAT
1 TAAT-AATTTAGTAGTAAATCAT
* *
12729924 AAATAATTTAGTAGTAAATCAA
1 TAATAATTTAGTAGTAAATCAT
* *
12729946 T-ATAACTTAGTAGTAGTTAATTAT
1 TAATAA-TT--TAGTAGTAAATCAT
* *
12729970 CAATAATTTA-TAGTTAATCAT
1 TAATAATTTAGTAGTAAATCAT
* * *
12729991 GT-ATAATTTAATA-TAAATAAG
1 -TAATAATTTAGTAGTAAATCAT
* * * * *
12730012 TGATAACTT-GATAATGAATTAT
1 TAATAATTTAG-TAGTAAATCAT
*** * * *
12730034 GGTTAAATTAGTAATAAAT-TT
1 TAATAATTTAGTAGTAAATCAT
* *
12730055 ATAATAATTTTGTAGTAAATAAAT
1 -TAATAATTTAGTAGTAAAT-CAT
* * * * *
12730079 GAA-AACTAAGTGGTAAATCAA
1 TAATAATTTAGTAGTAAATCAT
* ** *
12730100 TGATAACATAGTAGGAAATGCA-
1 TAATAATTTAGTAGTAAAT-CAT
* *
12730122 TAATAATGTAATAGTAAATCAT
1 TAATAATTTAGTAGTAAATCAT
*
12730144 TAATAATTTAG-ATGTAAATTAT
1 TAATAATTTAGTA-GTAAATCAT
* * * * ** * *
12730166 TGACAACTAAACAGTAAACCAC
1 TAATAATTTAGTAGTAAATCAT
* * * *
12730188 TAATAACTTAATTGTAAATTGA-
1 TAATAATTTAGTAGTAAA-TCAT
* * *
12730210 TGATAATTTAGTAATAAATTAAT
1 TAATAATTTAGTAGTAAA-TCAT
*
12730233 TATTGATAACTTT-GTAATAAATCAT
1 TA---ATAA-TTTAGTAGTAAATCAT
* *
12730258 TGATAATTTAATAGTAAA-CTAGT
1 TAATAATTTAGTAGTAAATC-A-T
*
12730281 T-ATAACTTTA-TAATAAATCAT
1 TAATAA-TTTAGTAGTAAATCAT
* * *
12730302 AAAT-ATTTGGTAGTAAGTCAT
1 TAATAATTTAGTAGTAAATCAT
* *
12730323 CAATAATTTAGTAGTAAATTAT
1 TAATAATTTAGTAGTAAATCAT
12730345 TAATAATTTAGTAGTAAATCAT
1 TAATAATTTAGTAGTAAATCAT
* * *
12730367 TTATAAATTAGTAGTAAATTAT
1 TAATAATTTAGTAGTAAATCAT
* * *
12730389 TGATAATATAGTAGTACATCAT
1 TAATAATTTAGTAGTAAATCAT
12730411 TAATA
1 TAATA
12730416 GCTTATAATA
Statistics
Matches: 393, Mismatches: 109, Indels: 69
0.69 0.19 0.12
Matches are distributed among these distances:
20 4 0.01
21 62 0.16
22 257 0.65
23 33 0.08
24 14 0.04
25 8 0.02
26 12 0.03
27 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (22 bp):
TAATAATTTAGTAGTAAATCAT
Found at i:12730384 original size:11 final size:11
Alignment explanation
Indices: 12730330--12730387 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
12730320 CATCAATAAT
12730330 TTAGTAGTAAA
1 TTAGTAGTAAA
* * *
12730341 TTATTAATAAT
1 TTAGTAGTAAA
12730352 TTAGTAGTAAA
1 TTAGTAGTAAA
* *
12730363 TCATTTA-TAAA
1 TTA-GTAGTAAA
12730374 TTAGTAGTAAA
1 TTAGTAGTAAA
12730385 TTA
1 TTA
12730388 TTGATAATAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
10 2 0.06
11 31 0.89
12 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (11 bp):
TTAGTAGTAAA
Found at i:12730814 original size:21 final size:22
Alignment explanation
Indices: 12730767--12730815 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
12730757 GAAAGTTAAT
*
12730767 AAAATTATATTAAGAGGTTACC
1 AAAATTATATTAAGAGATTACC
* *
12730789 AAAATTTTATTAA-AGATTATC
1 AAAATTATATTAAGAGATTACC
12730810 AAAATT
1 AAAATT
12730816 GTATCAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (22 bp):
AAAATTATATTAAGAGATTACC
Found at i:12732326 original size:63 final size:64
Alignment explanation
Indices: 12732256--12732647 Score: 363
Period size: 63 Copynumber: 6.2 Consensus size: 64
12732246 AAAGACTAGT
* * ** ** *
12732256 AACGCAGTAATTGATTATTTTTAAAA-AATTATAATGATTAATTATTGCATTATAAAATGAAGT
1 AACGCAGTAATTGATTATTTTTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * *
12732319 AATGCAGTAATTGATT-GTTTTAAAACAATTACAATGATCAATTATTATGTTATAAAATAAAGC
1 AACGCAGTAATTGATTATTTTTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * * * * * *
12732382 AATGTAGTAATTGATT-GTTTGAAAAAAATTATAATGATTAATTAGTGTGTTATAAAACAAAGC
1 AACGCAGTAATTGATTATTTTTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * * * * *
12732445 AACGCAGTAATTGATCATTTGATT--AA-AATTATAATTACCAATTGTTGCGTTATAAAACAAAA
1 AACGCAGTAATTGATTATTT--TTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAG
12732507 C
64 C
* * * *
12732508 AACGCAGTAATTGATTA-TTTTAAAACAATTACAATTATC-ATTGTTATGTTATAAAACAAAGT
1 AACGCAGTAATTGATTATTTTTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * *
12732570 AATGCAGTAATTGA--ATGTTTTAAAATAATTACAATGATCAATTACTGTGTTATAAAACAAAGT
1 AACGCAGTAATTGATTAT-TTTTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* *
12732633 AACACAGCAATTGAT
1 AACGCAGTAATTGAT
12732648 CATTGTAATT
Statistics
Matches: 273, Mismatches: 45, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.01
62 64 0.23
63 201 0.74
64 4 0.01
66 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (64 bp):
AACGCAGTAATTGATTATTTTTAAAACAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
Found at i:12732408 original size:126 final size:125
Alignment explanation
Indices: 12732256--12732676 Score: 439
Period size: 126 Copynumber: 3.4 Consensus size: 125
12732246 AAAGACTAGT
* ** **
12732256 AACGCAGTAATTGATTATTTTTAAAAAATTATAATGATTAATTATTGCATTATAAAATGAAGTAA
1 AACGCAGTAATTGATTATTTTAAAAAAATTATAATGATTAATTATTGTGTTATAAAACAAAGTAA
* *
12732321 TGCAGTAATTGATTGTTTTAAAACAATTACAATGATCAATTATTATGTTATAAAATAAAGC
66 TGCAGTAATTGATTGTTTTAAAA-AATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * * * *
12732382 AATGTAGTAATTGATTGTTTGAAAAAAATTATAATGATTAATTAGTGTGTTATAAAACAAAGCAA
1 AACGCAGTAATTGATTATTTTAAAAAAATTATAATGATTAATTATTGTGTTATAAAACAAAGTAA
* ** * * * * * * * *
12732447 CGCAGTAATTGATCATTTGATTAAAATTATAATTACCAATTGTTGCGTTATAAAACAAAAC
66 TGCAGTAATTGATTGTTTTA-AAAAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * * * *
12732508 AACGCAGTAATTGATTATTTTAAAACAATTACAATTA-TCATTGTTATGTTATAAAACAAAGTAA
1 AACGCAGTAATTGATTATTTTAAAAAAATTATAATGATTAATTATTGTGTTATAAAACAAAGTAA
* * *
12732572 TGCAGTAATTGAATGTTTTAAAATAATTACAATGATCAATTACTGTGTTATAAAACAAAGT
66 TGCAGTAATTGATTGTTTTAAAA-AATTACAATGATCAATTATTGTGTTATAAAACAAAGC
* * * * ** * *
12732633 AACACAGCAATTGATCATTGTAATTAAATTATAATTATCAATTA
1 AACGCAGTAATTGATTATTTTAAAAAAATTATAATGATTAATTA
12732677 CTACATTTCA
Statistics
Matches: 231, Mismatches: 61, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
124 2 0.01
125 95 0.41
126 132 0.57
127 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (125 bp):
AACGCAGTAATTGATTATTTTAAAAAAATTATAATGATTAATTATTGTGTTATAAAACAAAGTAA
TGCAGTAATTGATTGTTTTAAAAAATTACAATGATCAATTATTGTGTTATAAAACAAAGC
Found at i:12732651 original size:188 final size:189
Alignment explanation
Indices: 12732322--12732675 Score: 532
Period size: 188 Copynumber: 1.9 Consensus size: 189
12732312 ATGAAGTAAT
* * *
12732322 GCAGTAATTGATTGTTTTAAAACAATTACAATGATCAATTATTATGTTATAAAATAAAGCAATGT
1 GCAGTAATTGATTATTTTAAAACAATTACAATGATCAATTATTATGTTATAAAACAAAGCAATGC
* * * * *
12732387 AGTAATTGATTGTTTGAAAAAAATTATAATGATTAATTAGTGTGTTATAAAACAAAGCAACGCAG
66 AGTAATTGAATGTTTGAAAAAAATTACAATGATCAATTACTGTGTTATAAAACAAAGCAACACAG
* *
12732452 TAATTGATCATT-TGATTAAAATTATAATTACCAATTGTTGCGTTATAAAACAAAACAAC
131 CAATTGATCATTGTAATT-AAATTATAATTACCAATTGTTGCGTTATAAAACAAAACAAC
* * *
12732511 GCAGTAATTGATTATTTTAAAACAATTACAATTATC-ATTGTTATGTTATAAAACAAAGTAATGC
1 GCAGTAATTGATTATTTTAAAACAATTACAATGATCAATTATTATGTTATAAAACAAAGCAATGC
* * *
12732575 AGTAATTGAATGTTTTAAAATAATTACAATGATCAATTACTGTGTTATAAAACAAAGTAACACAG
66 AGTAATTGAATGTTTGAAAAAAATTACAATGATCAATTACTGTGTTATAAAACAAAGCAACACAG
*
12732640 CAATTGATCATTGTAATTAAATTATAATTATCAATT
131 CAATTGATCATTGTAATTAAATTATAATTACCAATT
12732676 ACTACATTTC
Statistics
Matches: 147, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
188 109 0.74
189 38 0.26
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36
Consensus pattern (189 bp):
GCAGTAATTGATTATTTTAAAACAATTACAATGATCAATTATTATGTTATAAAACAAAGCAATGC
AGTAATTGAATGTTTGAAAAAAATTACAATGATCAATTACTGTGTTATAAAACAAAGCAACACAG
CAATTGATCATTGTAATTAAATTATAATTACCAATTGTTGCGTTATAAAACAAAACAAC
Found at i:12740402 original size:2 final size:2
Alignment explanation
Indices: 12740395--12740423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12740385 ACCCACTACG
12740395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12740424 TTATTTATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12740807 original size:37 final size:38
Alignment explanation
Indices: 12740741--12740813 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
12740731 TACTAAGTAC
12740741 TAATGTTAATAAAAAAAATTTATACTTGATACATATAT
1 TAATGTTAATAAAAAAAATTTATACTTGATACATATAT
*
12740779 TAATGTTAATAAAAAAAA-TTATATTTGATACATAT
1 TAATGTTAATAAAAAAAATTTATACTTGATACATAT
12740814 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 16 0.47
38 18 0.53
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (38 bp):
TAATGTTAATAAAAAAAATTTATACTTGATACATATAT
Found at i:12741774 original size:30 final size:29
Alignment explanation
Indices: 12741738--12741806 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
12741728 TATTGAATTG
*
12741738 TATAAAATATTA-TATT-TATATTATATTTTA
1 TATAAAA-ATTACTATTATA-ATT-TATATTA
12741768 TATAAAAATTACGTATTATAATTTATATTA
1 TATAAAAATTAC-TATTATAATTTATATTA
12741798 TATAAAAAT
1 TATAAAAAT
12741807 ATAAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 4 0.11
30 22 0.63
31 7 0.20
32 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TATAAAAATTACTATTATAATTTATATTA
Found at i:12741869 original size:29 final size:29
Alignment explanation
Indices: 12741813--12741870 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12741803 AAATATAAAA
* **
12741813 TATAATTTTTTAATTTTATTAAATATATT
1 TATAATTTTATAAAATTATTAAATATATT
12741842 TATAATTTTATAAAATT-TTAAATAATATT
1 TATAATTTTATAAAATTATTAAAT-ATATT
12741871 ATTTTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TATAATTTTATAAAATTATTAAATATATT
Found at i:12742545 original size:23 final size:23
Alignment explanation
Indices: 12742493--12742543 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12742483 ATTTTTATTT
*
12742493 TAAAATATCTAAATCAAATAAAT
1 TAAAATATCTAAATCAAATAAAA
* *
12742516 TAAAATATCTAATTTAATATAAAA
1 TAAAATATCTAAATCAA-ATAAAA
12742540 TAAA
1 TAAA
12742544 TAATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAATATCTAAATCAAATAAAA
Found at i:12761238 original size:21 final size:22
Alignment explanation
Indices: 12761214--12761274 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
12761204 GAGTCTCACA
12761214 TTAAGAAAATT-TTAAA-ATATT
1 TTAAGAAAATTATTAAATAT-TT
12761235 TTAA-AAAATTATTAAATATTT
1 TTAAGAAAATTATTAAATATTT
*
12761256 TTAAAGAAAA-AATTAAATA
1 TT-AAGAAAATTATTAAATA
12761275 GGCAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 6 0.17
21 13 0.37
22 12 0.34
23 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
TTAAGAAAATTATTAAATATTT
Found at i:12761242 original size:20 final size:21
Alignment explanation
Indices: 12761214--12761274 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
12761204 GAGTCTCACA
12761214 TTAAGAAAATT-TTAAAATATT
1 TTAAGAAAATTATT-AAATATT
12761235 TTAA-AAAATTATTAAATATTT
1 TTAAGAAAATTATTAAATA-TT
*
12761256 TTAAAGAAAA-AATTAAATA
1 TT-AAGAAAATTATTAAATA
12761275 GGCAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 11 0.31
21 10 0.29
22 10 0.29
23 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
TTAAGAAAATTATTAAATATT
Found at i:12761273 original size:22 final size:20
Alignment explanation
Indices: 12761228--12761274 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
12761218 GAAAATTTTA
**
12761228 AAATATTTTAAAAAATTATT
1 AAATATTTTAAAAAAAAATT
12761248 AAATATTTTTAAAGAAAAAATT
1 AAATA-TTTTAAA-AAAAAATT
12761270 AAATA
1 AAATA
12761275 GGCAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATATTTTAAAAAAAAATT
Found at i:12762723 original size:2 final size:2
Alignment explanation
Indices: 12762716--12762759 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12762706 CATTTTCATC
12762716 TA TA TA TA TA 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 TA TA TA TA TA
12762758 TA
1 TA
12762760 CACACCTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12762832 original size:24 final size:21
Alignment explanation
Indices: 12762777--12762833 Score: 53
Period size: 24 Copynumber: 2.6 Consensus size: 21
12762767 TAAAACATAC
12762777 AAAAT-AAAAATTATTTAAAT
1 AAAATAAAAAATTATTTAAAT
* *
12762797 AAACTATTAAAATATGATTTAAATT
1 AAA--A-TAAAAAATTATTTAAA-T
12762822 AAAATAAAAAAT
1 AAAATAAAAAAT
12762834 CCCCGACGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 3 0.10
22 8 0.28
23 2 0.07
24 12 0.41
25 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATAAAAAATTATTTAAAT
Found at i:12764163 original size:15 final size:16
Alignment explanation
Indices: 12764136--12764165 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12764126 AATTATTATT
12764136 AAATATATAAAAAAAG
1 AAATATATAAAAAAAG
12764152 AAATAT-TAAAAAAA
1 AAATATATAAAAAAA
12764166 AAAACCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATATATAAAAAAAG
Found at i:12765510 original size:22 final size:21
Alignment explanation
Indices: 12765472--12765513 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12765462 TTTATTAATT
*
12765472 AAAAAAAAAAGTCAAGAAAAC
1 AAAAAAAAAAGTAAAGAAAAC
*
12765493 AAAAAAAAATGTAAAAGAAAA
1 AAAAAAAAAAGT-AAAGAAAA
12765514 AAGAAGCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAGTAAAGAAAAC
Found at i:12770301 original size:2 final size:2
Alignment explanation
Indices: 12770294--12770318 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12770284 TAAAATAACA
12770294 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 A
12770319 ACATTCCATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12770647 original size:2 final size:2
Alignment explanation
Indices: 12770640--12770684 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12770630 TAGAAGGAAA
12770640 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12770682 AG A
1 AG A
12770685 CAAAAAAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12771425 original size:21 final size:21
Alignment explanation
Indices: 12771401--12771442 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12771391 TCATGTGAAT
12771401 AATACGTGAGTCACATATAAC
1 AATACGTGAGTCACATATAAC
12771422 AATACGTGAGTCACATATAAC
1 AATACGTGAGTCACATATAAC
12771443 GTCAAGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (21 bp):
AATACGTGAGTCACATATAAC
Found at i:12773796 original size:24 final size:26
Alignment explanation
Indices: 12773769--12773824 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
12773759 TAAAAATTAA
*
12773769 AAATCAATTA-TATTAAAATTG-ACT
1 AAATCAATAATTATTAAAATTGAACT
12773793 AAATCAATAATTATTAAAATTGAACT
1 AAATCAATAATTATTAAAATTGAACT
12773819 -AATCAA
1 AAATCAA
12773825 ATCAACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.31
25 17 0.59
26 3 0.10
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (26 bp):
AAATCAATAATTATTAAAATTGAACT
Found at i:12779671 original size:20 final size:20
Alignment explanation
Indices: 12779626--12779664 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12779616 TAAAACTGTC
* *
12779626 GGTAATAATAAAATTCTATA
1 GGTAATAAAAAAAATCTATA
12779646 GGTAATAAAAAAAATCTAT
1 GGTAATAAAAAAAATCTAT
12779665 TAGTAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (20 bp):
GGTAATAAAAAAAATCTATA
Found at i:12779673 original size:32 final size:33
Alignment explanation
Indices: 12779637--12779704 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
12779627 GTAATAATAA
*
12779637 AATTCTATAGGTAATAA-AAAAAATCTATTAGT
1 AATTCTATAGGTAATAATAAAAAATCAATTAGT
* * *
12779669 AATTCTATCGGTAATAATTAAAATTCAATTAGT
1 AATTCTATAGGTAATAATAAAAAATCAATTAGT
12779702 AAT
1 AAT
12779705 AATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (33 bp):
AATTCTATAGGTAATAATAAAAAATCAATTAGT
Found at i:12779693 original size:21 final size:20
Alignment explanation
Indices: 12779669--12779713 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
12779659 ATCTATTAGT
* *
12779669 AATTCTATCGGTAATAATTAA
1 AATTCAATCAGTAATAA-TAA
*
12779690 AATTCAATTAGTAATAATAA
1 AATTCAATCAGTAATAATAA
12779710 AATT
1 AATT
12779714 TTGTTGGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (20 bp):
AATTCAATCAGTAATAATAA
Found at i:12779946 original size:18 final size:18
Alignment explanation
Indices: 12779905--12779944 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12779895 GTAAATTACA
*
12779905 ATTTAAATATGTGTAATT
1 ATTTAAATATGTATAATT
*
12779923 ATTTAAATATGCTATTATT
1 ATTTAAATATG-TATAATT
12779942 ATT
1 ATT
12779945 AATTAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (18 bp):
ATTTAAATATGTATAATT
Found at i:12782219 original size:48 final size:48
Alignment explanation
Indices: 12782154--12782251 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 48
12782144 ATATAGAACA
*
12782154 AAAGCATTCGATCAATATTCCAATAAAACC-AGCAAAAAATAAATATAT
1 AAAGCATTCCATCAATATTCCAATAAAACCAAG-AAAAAATAAATATAT
* *
12782202 AAAGCATTCCATCAATATTCTAATAAACCCAAGAAAAAATAAATATAT
1 AAAGCATTCCATCAATATTCCAATAAAACCAAGAAAAAATAAATATAT
12782250 AA
1 AA
12782252 TGTTACTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 44 0.96
49 2 0.04
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.23
Consensus pattern (48 bp):
AAAGCATTCCATCAATATTCCAATAAAACCAAGAAAAAATAAATATAT
Found at i:12782439 original size:9 final size:9
Alignment explanation
Indices: 12782425--12782500 Score: 86
Period size: 9 Copynumber: 8.8 Consensus size: 9
12782415 GTCACGTGTT
12782425 TCATCATTA
1 TCATCATTA
*
12782434 TCATCATCA
1 TCATCATTA
12782443 TCATCATTA
1 TCATCATTA
12782452 TCATCATTA
1 TCATCATTA
* *
12782461 GCATC---G
1 TCATCATTA
12782467 TCATCATTA
1 TCATCATTA
* *
12782476 TCATTATCA
1 TCATCATTA
12782485 TCATCATTA
1 TCATCATTA
12782494 TCATCAT
1 TCATCAT
12782501 CTTCTTCTTC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 4 0.07
9 50 0.93
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.41
Consensus pattern (9 bp):
TCATCATTA
Found at i:12782442 original size:6 final size:6
Alignment explanation
Indices: 12782425--12782501 Score: 82
Period size: 6 Copynumber: 12.8 Consensus size: 6
12782415 GTCACGTGTT
* * * * *
12782425 TCATCA TTATCA TCATCA TCATCA TTATCA TCATTA GCATCG TCATCA
1 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA
* * *
12782473 TTATCA TTATCA TCATCA TTATCA TCATC
1 TCATCA TCATCA TCATCA TCATCA TCATC
12782502 TTCTTCTTCT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (6 bp):
TCATCA
Found at i:12787583 original size:54 final size:53
Alignment explanation
Indices: 12787481--12787585 Score: 122
Period size: 54 Copynumber: 2.0 Consensus size: 53
12787471 GGCGGGTTTG
* * * * *
12787481 AAATTTTTAATTTTAGTGATGGTTTTATTGACGAAATTTCTATTGGTAATGAA
1 AAATTTTTAATTTTAGTGATGATTTTATCGACGAAACTTCCATCGGTAATGAA
* *
12787534 AAATTTTTAACTTTTA-TCGATGATTTTATCGATGGAACTTCCATCGGTAATG
1 AAATTTTTAA-TTTTAGT-GATGATTTTATCGACGAAACTTCCATCGGTAATG
12787586 TCGAAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
53 11 0.26
54 32 0.74
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (53 bp):
AAATTTTTAATTTTAGTGATGATTTTATCGACGAAACTTCCATCGGTAATGAA
Found at i:12797699 original size:11 final size:11
Alignment explanation
Indices: 12797677--12797718 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
12797667 CTTACAAAAA
*
12797677 AAAAAAAAAGG
1 AAAAAGAAAGG
*
12797688 AAAGAGAAAGG
1 AAAAAGAAAGG
12797699 AAAAAG-AAGG
1 AAAAAGAAAGG
12797709 AAAAATGAAA
1 AAAAA-GAAA
12797719 CAACGATGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.35
11 15 0.58
12 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGG
Found at i:12802975 original size:30 final size:30
Alignment explanation
Indices: 12802941--12803002 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
12802931 TATTTGAAGA
12802941 CTATGGAGTCTGTTAGGGAGAAGAAGCAAT
1 CTATGGAGTCTGTTAGGGAGAAGAAGCAAT
12802971 CTATGGAGTCTGTTAGGGAGAAGAAGCAAT
1 CTATGGAGTCTGTTAGGGAGAAGAAGCAAT
12803001 CT
1 CT
12803003 TTTGATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.24
Consensus pattern (30 bp):
CTATGGAGTCTGTTAGGGAGAAGAAGCAAT
Found at i:12803151 original size:108 final size:107
Alignment explanation
Indices: 12802962--12803180 Score: 384
Period size: 108 Copynumber: 2.0 Consensus size: 107
12802952 GTTAGGGAGA
* * *
12802962 AGAAGCAATCTATGGAGTCTGTTAGGGAGAAGAAGCAATCTTTTGATTCAAACAGAGGCAATTCC
1 AGAAGCAATCTATGGAGTCTGTTAGGGAGAAGAACCAATCTTTTAAATCAAACAGAGGCAATTCC
*
12803027 AGTGAAAGATTAAATAGAGGCAAGTTAAAGGATGATTCAAAGG
66 AGTGAAAGATTAAATAGAGGCAAGTCAAAGGATGATTCAAA-G
12803070 AGAAGCAATCTATGGAGTCTGTTAGGGAGAAGAACCAATCTTTTAAATCAAACAGAGGCAATTCC
1 AGAAGCAATCTATGGAGTCTGTTAGGGAGAAGAACCAATCTTTTAAATCAAACAGAGGCAATTCC
*
12803135 AGTGAAAGATTAAATAGAGGCAAGTCGAAGGATGATTCAAAG
66 AGTGAAAGATTAAATAGAGGCAAGTCAAAGGATGATTCAAAG
12803177 AGAA
1 AGAA
12803181 ATTTTGGGGA
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 5 0.05
108 101 0.95
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (107 bp):
AGAAGCAATCTATGGAGTCTGTTAGGGAGAAGAACCAATCTTTTAAATCAAACAGAGGCAATTCC
AGTGAAAGATTAAATAGAGGCAAGTCAAAGGATGATTCAAAG
Found at i:12803480 original size:2 final size:2
Alignment explanation
Indices: 12803475--12803505 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12803465 TCTCTCTCTC
12803475 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12803506 TGTTTTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12806520 original size:17 final size:17
Alignment explanation
Indices: 12806498--12806534 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
12806488 ATGCAGTACT
12806498 ATTGGTGCATATAAAGA
1 ATTGGTGCATATAAAGA
12806515 ATTGGTGCATATAAAGA
1 ATTGGTGCATATAAAGA
12806532 ATT
1 ATT
12806535 TTCATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (17 bp):
ATTGGTGCATATAAAGA
Found at i:12815537 original size:28 final size:22
Alignment explanation
Indices: 12815458--12815534 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
12815448 GTAATTGATC
*
12815458 AAGCTCAAGCTGATACAACATT
1 AAGCTCGAGCTGATACAACATT
12815480 AAGCTCGAGCTGATACAACATT
1 AAGCTCGAGCTGATACAACATT
12815502 AAGCTCGAGCTGATACAACATT
1 AAGCTCGAGCTGATACAACATT
12815524 AAGCTCGAGCT
1 AAGCTCGAGCT
12815535 CGACTTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (22 bp):
AAGCTCGAGCTGATACAACATT
Found at i:12815740 original size:9 final size:9
Alignment explanation
Indices: 12815726--12815755 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
12815716 GATATTTTAT
12815726 TAATTAAAA
1 TAATTAAAA
12815735 TAATTAAAA
1 TAATTAAAA
12815744 TATATTAAAA
1 TA-ATTAAAA
12815754 TA
1 TA
12815756 TAAAAGCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:12815752 original size:10 final size:10
Alignment explanation
Indices: 12815728--12815757 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12815718 TATTTTATTA
12815728 ATTAAAATA-
1 ATTAAAATAT
12815737 ATTAAAATAT
1 ATTAAAATAT
12815747 ATTAAAATAT
1 ATTAAAATAT
12815757 A
1 A
12815758 AAAGCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:12821868 original size:102 final size:103
Alignment explanation
Indices: 12821733--12821943 Score: 334
Period size: 102 Copynumber: 2.0 Consensus size: 103
12821723 ATGTATTTAT
*
12821733 TTGGATTCACTTGAAGCCCCAAATGCAAAATGCAATCGCATATTTCTTTTATGATTGGTTAG-TT
1 TTGGATTCACTTGAAGCCCCAAATGCAAAATGCAATCACATATTTCTTTTATGATTGGTTAGTTT
*
12821797 ATCCCATACATTTATGATTGGTTAGTTATTTATCATCA
66 ATCCCATACATCTATGATTGGTTAGTTATTTATCATCA
*
12821835 TTGGATTCACTTGAAGCTCCAAATGCAAAATGCAATCACATATTTCTTTTATGATTGGTTAGTTA
1 TTGGATTCACTTGAAGCCCCAAATGCAAAATGCAATCACATATTTCTTTTATGATTGGTTAG---
* * *
12821900 TTTATCCTATGCCTCTATGATTGGTTAGTTATTTATCATCA
63 TTTATCCCATACATCTATGATTGGTTAGTTATTTATCATCA
12821941 TTG
1 TTG
12821944 TAATTTCAAG
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
102 60 0.61
106 39 0.39
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (103 bp):
TTGGATTCACTTGAAGCCCCAAATGCAAAATGCAATCACATATTTCTTTTATGATTGGTTAGTTT
ATCCCATACATCTATGATTGGTTAGTTATTTATCATCA
Found at i:12824789 original size:44 final size:44
Alignment explanation
Indices: 12824701--12824814 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
12824691 TGCTAACCCT
* * *
12824701 AAATAATCAAATAAATTGGTACACATATAAAATCAAAATATACA
1 AAATAAACAAATAAATTAGTACACATATAAAATCAAAAGATACA
* * * *
12824745 AAATAAACAAATAAATTAGTACGCATA-AAGACTCAGAAGCTACA
1 AAATAAACAAATAAATTAGTACACATATAA-AATCAAAAGATACA
* **
12824789 AAATAAATAAATAGGTTAGTACACAT
1 AAATAAACAAATAAATTAGTACACAT
12824815 GAAAATCCAC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 2 0.03
44 56 0.97
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (44 bp):
AAATAAACAAATAAATTAGTACACATATAAAATCAAAAGATACA
Found at i:12825546 original size:26 final size:24
Alignment explanation
Indices: 12825497--12825574 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 24
12825487 TTATAATCAT
*
12825497 TCATGCAAAAATATCACAATAAAA
1 TCATGCAAAAATATCACAAAAAAA
*
12825521 TCATGCAATTAAATATCATAAAAAAA
1 TCATGCAA--AAATATCACAAAAAAA
* *
12825547 --A-GCAAAAA-ATCATAAAAACA
1 TCATGCAAAAATATCACAAAAAAA
12825567 -CATGCAAA
1 TCATGCAAA
12825575 TAAAACTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 11 0.23
21 4 0.09
22 5 0.11
23 4 0.09
24 9 0.19
26 14 0.30
ACGTcount: A:0.60, C:0.15, G:0.05, T:0.19
Consensus pattern (24 bp):
TCATGCAAAAATATCACAAAAAAA
Found at i:12825703 original size:21 final size:22
Alignment explanation
Indices: 12825679--12825725 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
12825669 TAAATATATT
*
12825679 AAAAAATTAAAA-AAAAAACAA
1 AAAAAATCAAAATAAAAAACAA
* *
12825700 AAAAAATCAAAATCAAAATCAA
1 AAAAAATCAAAATAAAAAACAA
12825722 AAAA
1 AAAA
12825726 TAAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (22 bp):
AAAAAATCAAAATAAAAAACAA
Found at i:12826154 original size:18 final size:18
Alignment explanation
Indices: 12826124--12826173 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
12826114 AAAATTCAAC
*
12826124 CCAAATTCC-AAAATA-A
1 CCAAAATCCAAAAATATA
*
12826140 TCCAAAATCCAAAAATCTA
1 -CCAAAATCCAAAAATATA
*
12826159 CCAAAACCCAAAAAT
1 CCAAAATCCAAAAAT
12826174 TAAAACCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.29
18 19 0.68
19 1 0.04
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (18 bp):
CCAAAATCCAAAAATATA
Found at i:12827272 original size:3 final size:3
Alignment explanation
Indices: 12827264--12827295 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12827254 TAGGACATTA
12827264 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12827296 AGTAAATTTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12827700 original size:3 final size:3
Alignment explanation
Indices: 12827694--12827721 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12827684 AAAAAATGAG
12827694 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12827722 AATCTCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12830607 original size:239 final size:239
Alignment explanation
Indices: 12830187--12830626 Score: 781
Period size: 239 Copynumber: 1.8 Consensus size: 239
12830177 CACCTCTGAC
* *
12830187 TCTGCCATTCGACTAACACCTTCTTTGATTGACATATTCCTGTTATGCCATACAACCCGGCTTAG
1 TCTGCCATTCGACTAACACCTTCTTTGATTGACATATTCCTGTTATGCCATACAACACAGCTTAG
* * * * *
12830252 GACCAAACCAAATTCCCAGTCTTGTGTATCAGTCTTGTTTGTAATCTCTTCCAGATACCCATGAT
66 GACCAAACCAAATTCCCAATCTTGTGTATCAGTCTTGTTGGTAATCTCCTCAAGAAACCCATGAT
* *
12830317 CCTCTAGCCCTCGTGCGTCTGTCCATCTTGTAGAAACACCTGCACATCTCCATATCTCATTCACT
131 CCTCTAGCCCTCGTGCGTCTGTCCATCTTGAAGAAACACCCGCACATCTCCATATCTCATTCACT
12830382 TGTTCAAGATACAAACACCTTCTTTGATTAACACCTCCTTTGAG
196 TGTTCAAGATACAAACACCTTCTTTGATTAACACCTCCTTTGAG
12830426 TCTGCCATTCGACTAACACCTTCTTTGATTGACATATTCCTGTTATGCCATACAACACAGCTTAG
1 TCTGCCATTCGACTAACACCTTCTTTGATTGACATATTCCTGTTATGCCATACAACACAGCTTAG
*
12830491 GACCAAACCAAATTCCCAATCTTGTGTATCAGTCTTGTTGGTAATCTCCTCAAGAAACCCGTGAT
66 GACCAAACCAAATTCCCAATCTTGTGTATCAGTCTTGTTGGTAATCTCCTCAAGAAACCCATGAT
*
12830556 CCTCTAGCCCTCGTGCGTCTGTCCATCTTGAAGAAACACCCGCATATCTCCATATCTCATTCACT
131 CCTCTAGCCCTCGTGCGTCTGTCCATCTTGAAGAAACACCCGCACATCTCCATATCTCATTCACT
12830621 TGTTCA
196 TGTTCA
12830627 CACTCTCATA
Statistics
Matches: 190, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
239 190 1.00
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (239 bp):
TCTGCCATTCGACTAACACCTTCTTTGATTGACATATTCCTGTTATGCCATACAACACAGCTTAG
GACCAAACCAAATTCCCAATCTTGTGTATCAGTCTTGTTGGTAATCTCCTCAAGAAACCCATGAT
CCTCTAGCCCTCGTGCGTCTGTCCATCTTGAAGAAACACCCGCACATCTCCATATCTCATTCACT
TGTTCAAGATACAAACACCTTCTTTGATTAACACCTCCTTTGAG
Found at i:12847171 original size:14 final size:14
Alignment explanation
Indices: 12847152--12847181 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12847142 ATATATATAT
*
12847152 AGAGAGAGAAAGAG
1 AGAGAGAGAAACAG
12847166 AGAGAGAGAAACAG
1 AGAGAGAGAAACAG
12847180 AG
1 AG
12847182 GAATCATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.40, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAAACAG
Found at i:12848055 original size:3 final size:3
Alignment explanation
Indices: 12848047--12848094 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
12848037 GAATCACCAC
12848047 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
12848093 TT
1 TT
12848095 TATCTAATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12850006 original size:16 final size:15
Alignment explanation
Indices: 12849985--12850018 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12849975 TATGACCTTC
*
12849985 AAGGAAGAAGAAAGAA
1 AAGGAAGAA-AAAAAA
12850001 AAGGAAGAAAAAAAA
1 AAGGAAGAAAAAAAA
12850016 AAG
1 AAG
12850019 AAAAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAGGAAGAAAAAAAA
Found at i:12852295 original size:21 final size:23
Alignment explanation
Indices: 12852271--12852318 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
12852261 TCTTTAACTT
* *
12852271 TTTTTTTAATT-TTAATAA-ATA
1 TTTTTATAATTATAAATAATATA
12852292 TTTTTATAATTATAAATAATATA
1 TTTTTATAATTATAAATAATATA
12852315 TTTT
1 TTTT
12852319 CAAAGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTATAATTATAAATAATATA
Found at i:12852535 original size:24 final size:24
Alignment explanation
Indices: 12852487--12852542 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
12852477 ACTTTTTCTT
* *
12852487 TTTTTAAATAATTTTTAATAAATA
1 TTTTTAAATAATTATAAATAAATA
12852511 TTTTTAAA-AATTATAAATAATATA
1 TTTTTAAATAATTATAAATAA-ATA
12852535 TTTTTAAA
1 TTTTTAAA
12852543 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTTAAATAATTATAAATAAATA
Found at i:12853067 original size:17 final size:16
Alignment explanation
Indices: 12853017--12853069 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
12853007 TTTTTACCCA
*
12853017 TTTTAAATTTTTTCTTT
1 TTTTAAATTTTAT-TTT
*
12853034 TTTTAAATTATAAATTTT
1 TTTTAAATT-T-TATTTT
12853052 TTTTAAGATTTTATTTT
1 TTTTAA-ATTTTATTTT
12853069 T
1 T
12853070 CATATGTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.50
18 11 0.37
19 4 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTAAATTTTATTTT
Found at i:12853347 original size:20 final size:17
Alignment explanation
Indices: 12853311--12853356 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
12853301 GCCATTTTAC
12853311 TTCTTTTTTTTTTGTTT
1 TTCTTTTTTTTTTGTTT
12853328 TTCTTTTTTCTGTTTAGTTT
1 TTCTTTTTT-T-TTT-GTTT
*
12853348 TCCTTTTTT
1 TTCTTTTTT
12853357 GCTTTTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 1 0.04
19 3 0.12
20 12 0.48
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (17 bp):
TTCTTTTTTTTTTGTTT
Found at i:12853795 original size:9 final size:9
Alignment explanation
Indices: 12853758--12853787 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
12853748 ATTTTTTTAC
12853758 TTTCATTTT
1 TTTCATTTT
12853767 TTCTCATTTT
1 TT-TCATTTT
12853777 TTTCATTTT
1 TTTCATTTT
12853786 TT
1 TT
12853788 ATCTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCATTTT
Found at i:12854620 original size:23 final size:24
Alignment explanation
Indices: 12854574--12854620 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
12854564 GTATTTCATT
*
12854574 TTTTATATAAATTATAATACATAAC
1 TTTTATATAAA-TATAAAACATAAC
*
12854599 TTTTATATAAA-ATAAAATATAA
1 TTTTATATAAATATAAAACATAA
12854621 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTATATAAATATAAAACATAAC
Found at i:12855596 original size:11 final size:11
Alignment explanation
Indices: 12855580--12855604 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12855570 TTGAAAATCG
12855580 GGGGTCGGGTC
1 GGGGTCGGGTC
12855591 GGGGTCGGGTC
1 GGGGTCGGGTC
12855602 GGG
1 GGG
12855605 TAGGATGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (11 bp):
GGGGTCGGGTC
Found at i:12855773 original size:21 final size:22
Alignment explanation
Indices: 12855747--12855799 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12855737 GATATTTTTA
*
12855747 AATATTTTATATTT-AAAAATT
1 AATATTTTATATTTAAAAAAAT
12855768 AATATTTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
12855790 AATATTTTAT
1 AATATTTTAT
12855800 TAATTTCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:12856423 original size:2 final size:2
Alignment explanation
Indices: 12856407--12856444 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
12856397 TGTTAAAGCC
* *
12856407 TA TA TA AA TA AA 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 TA TA TA
12856445 AAACTTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12861340 original size:39 final size:40
Alignment explanation
Indices: 12861273--12861369 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 40
12861263 AAAATTCATT
*
12861273 TTAATAAATAATTTTTATATTATAATAATAAT-AATAAATA
1 TTAATAATTAATTTTTATATTATAATAAT-ATCAATAAATA
* * *
12861313 TTAATAATTAA-TTTTATTTTA-ATATAATATCAGTAAATT
1 TTAATAATTAATTTTTATATTATA-ATAATATCAATAAATA
12861352 TTAATAATT--TTTTTATAT
1 TTAATAATTAATTTTTATAT
12861370 AATTTTGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
38 10 0.20
39 29 0.59
40 10 0.20
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (40 bp):
TTAATAATTAATTTTTATATTATAATAATATCAATAAATA
Found at i:12861443 original size:21 final size:21
Alignment explanation
Indices: 12861395--12861471 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
12861385 TAGCCTTTGT
* *
12861395 TAAAATTTTGGTAACTTA-TGA
1 TAAAATTTTAGTAA-TTATTAA
*
12861416 TATAATTTTAGTAATTATTAA
1 TAAAATTTTAGTAATTATTAA
** * *
12861437 TGCAATTTTAGTAATTTTTGA
1 TAAAATTTTAGTAATTATTAA
12861458 TAAAATTTTAGTAA
1 TAAAATTTTAGTAA
12861472 CCTCTTTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
20 3 0.07
21 43 0.93
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (21 bp):
TAAAATTTTAGTAATTATTAA
Found at i:12861520 original size:21 final size:21
Alignment explanation
Indices: 12861495--12861534 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12861485 TTTTAGTAAT
*
12861495 TTTTTGATAACTTA-TGATATA
1 TTTTTAATAA-TTACTGATATA
12861516 TTTTTAATAATTACTGATA
1 TTTTTAATAATTACTGATA
12861535 AAATTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTTAATAATTACTGATATA
Found at i:12861824 original size:22 final size:22
Alignment explanation
Indices: 12861783--12861958 Score: 124
Period size: 22 Copynumber: 8.0 Consensus size: 22
12861773 TTAAAAAAAT
* *
12861783 TTATCAATGATTGA-TAATTAAA
1 TTATCAATGATTTACT-ACTAAA
* * **
12861805 TTATCATTGATTTACTATTATG
1 TTATCAATGATTTACTACTAAA
* *
12861827 TTATCAGTGATTTACTACTAAGC
1 TTATCAATGATTTACTACTAA-A
* * * *
12861850 TT-TCAATAATATATTGCTAAA
1 TTATCAATGATTTACTACTAAA
* *
12861871 TTATCAATGATTTATTATTAAA
1 TTATCAATGATTTACTACTAAA
* * *
12861893 TTAGCATTGATTTACTACTAAT
1 TTATCAATGATTTACTACTAAA
* * *
12861915 TTATGAATGATTTACTAGTAAG
1 TTATCAATGATTTACTACTAAA
12861937 TTAT-AACTGATTTACTACTAAA
1 TTATCAA-TGATTTACTACTAAA
12861959 GTGTTGATAA
Statistics
Matches: 120, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
21 4 0.03
22 113 0.94
23 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATCAATGATTTACTACTAAA
Found at i:12861990 original size:22 final size:21
Alignment explanation
Indices: 12861934--12862054 Score: 72
Period size: 22 Copynumber: 5.7 Consensus size: 21
12861924 ATTTACTAGT
* *
12861934 AAGTTATAACTGATTTACTACTA
1 AAGTTATAA-TAATTTATTA-TA
*
12861957 AAGTGT-TGATAATTTATTACT-
1 AAGT-TATAATAATTTATTA-TA
*
12861978 AAGTTACTAATAATTTGTTATA
1 AAGTTA-TAATAATTTATTATA
* *
12862000 AAGTTATAACTAATTTACTATT
1 AAGTTATAA-TAATTTATTATA
* *
12862022 AA--T-TGATAATTTACTATA
1 AAGTTATAATAATTTATTATA
12862040 AAGTTATCAATAATT
1 AAGTTAT-AATAATT
12862055 AACTAATTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
18 13 0.17
19 2 0.03
20 3 0.04
21 9 0.12
22 44 0.56
23 6 0.08
24 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (21 bp):
AAGTTATAATAATTTATTATA
Found at i:12862012 original size:33 final size:33
Alignment explanation
Indices: 12861933--12862025 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
12861923 GATTTACTAG
* * **
12861933 TAAGTTATAACTGATTTACTACTAAAGTGTTGA
1 TAAGTTATAACTAATTTACTAATAATTTGTTGA
* * *
12861966 TAATTTATTACTAAGTTACTAATAATTTGTT-A
1 TAAGTTATAACTAATTTACTAATAATTTGTTGA
*
12861998 TAAAGTTATAACTAATTTACTATTAATT
1 T-AAGTTATAACTAATTTACTAATAATT
12862026 GATAATTTAC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.45
Consensus pattern (33 bp):
TAAGTTATAACTAATTTACTAATAATTTGTTGA
Done.