Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 16 of 24
Found at i:3226522 original size:18 final size:19
Alignment explanation
Indices: 3226494--3226549 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
3226484 TTAAATTTAT
*
3226494 AATTTTAAATATAAATAAA
1 AATTATAAATATAAATAAA
* *
3226513 TA-TATAAATATAAAAAAA
1 AATTATAAATATAAATAAA
*
3226531 AATTATATACTATAAATAA
1 AATTATA-AATATAAATAA
3226550 TTAATTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 15 0.52
19 5 0.17
20 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTATAAATATAAATAAA
Found at i:3226533 original size:24 final size:24
Alignment explanation
Indices: 3226478--3226548 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
3226468 ATCATTAACC
* * * *
3226478 AAAAAATTAAATTTATAATTTTAA
1 AAAAAAATAAATATATAAATATAA
* *
3226502 ATATAAATAAATATATAAATATAA
1 AAAAAAATAAATATATAAATATAA
*
3226526 AAAAAAATTATATACTATAAATA
1 AAAAAAA-TAAATA-TATAAATA
3226549 ATTAATTTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 23 0.64
25 5 0.14
26 8 0.22
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAAAATAAATATATAAATATAA
Found at i:3226606 original size:21 final size:19
Alignment explanation
Indices: 3226581--3226623 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
3226571 AATGAAAATT
*
3226581 AAATATAATTATTAATATATA
1 AAATATAAATA-TAATATA-A
3226602 AAATATAAATATAATATAA
1 AAATATAAATATAATATAA
3226621 AAA
1 AAA
3226624 CGCGTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATAAATATAATATAA
Found at i:3227088 original size:26 final size:25
Alignment explanation
Indices: 3227002--3227088 Score: 83
Period size: 26 Copynumber: 3.5 Consensus size: 25
3226992 CTATATAATT
* *
3227002 TATTTATTTATTTATTTTTAATTAA
1 TATTTATTTATTAATTTTTTATTAA
*
3227027 -ATTTATATTATTAA---ATTATTAA
1 TATTTAT-TTATTAATTTTTTATTAA
*
3227049 TATTAATTTAATTAATTTTTTATTAA
1 TATTTATTT-ATTAATTTTTTATTAA
3227075 TATTTATATTATTA
1 TATTTAT-TTATTA
3227089 TTAAAACCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
22 8 0.16
23 10 0.20
24 6 0.12
25 6 0.12
26 17 0.35
27 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTATTTATTAATTTTTTATTAA
Found at i:3227397 original size:16 final size:17
Alignment explanation
Indices: 3227371--3227402 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3227361 TTTATCTTTC
3227371 TAAAAATATAATAATTT
1 TAAAAATATAATAATTT
3227388 TAAAAA-ATAATAATT
1 TAAAAATATAATAATT
3227403 ATTTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATATAATAATTT
Found at i:3227400 original size:19 final size:18
Alignment explanation
Indices: 3227372--3227427 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
3227362 TTATCTTTCT
3227372 AAAAATATAATAATTTTA
1 AAAAATATAATAATTTTA
*
3227390 AAAAATAATAATTATTTTA
1 AAAAAT-ATAATAATTTTA
*
3227409 ATTAAAATATAAAAATTTT
1 A--AAAATATAATAATTTT
3227428 TACTATACGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 6 0.19
19 12 0.38
20 9 0.28
21 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATATAATAATTTTA
Found at i:3227878 original size:17 final size:19
Alignment explanation
Indices: 3227846--3227886 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 19
3227836 TAAATATAAA
3227846 TATAAATATGATAAATATT
1 TATAAATATGATAAATATT
3227865 TATAAAT-T-ATAAATATT
1 TATAAATATGATAAATATT
3227882 TATAA
1 TATAA
3227887 TTGAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TATAAATATGATAAATATT
Found at i:3228009 original size:17 final size:18
Alignment explanation
Indices: 3227977--3228015 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3227967 TATATTATTA
3227977 TTAAAAATAATATTAAAAT
1 TTAAAAAT-ATATTAAAAT
*
3227996 TTAAAAAT-TATTAATAT
1 TTAAAAATATATTAAAAT
3228013 TTA
1 TTA
3228016 TAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAAATATATTAAAAT
Found at i:3228762 original size:4 final size:4
Alignment explanation
Indices: 3228753--3228779 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3228743 CTCACCTGCA
3228753 CTTT CTTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTT
3228780 GCTTGCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:3231797 original size:20 final size:19
Alignment explanation
Indices: 3231759--3231801 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
3231749 AAAAAATAAA
* *
3231759 AAATTATATATTAATTATT
1 AAATTAAATATTAAATATT
3231778 AAATTAAATATTTAAATATT
1 AAATTAAATA-TTAAATATT
3231798 AAAT
1 AAAT
3231802 ACTTAACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTAAATATTAAATATT
Found at i:3233493 original size:24 final size:22
Alignment explanation
Indices: 3233466--3233513 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
3233456 AAAATAATTT
3233466 TTAATAAT-AATTTAAATTATTAAA
1 TTAA-AATAAATTTAAA-TA-TAAA
*
3233490 TTAAATTAAATTTAAATATAAA
1 TTAAAATAAATTTAAATATAAA
3233512 TT
1 TT
3233514 TAGATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 6 0.27
23 4 0.18
24 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATAAATTTAAATATAAA
Found at i:3233500 original size:18 final size:17
Alignment explanation
Indices: 3233424--3233513 Score: 58
Period size: 18 Copynumber: 5.1 Consensus size: 17
3233414 TAAATTTTAT
*
3233424 TTAAATTTAATTATAAAA
1 TTAAATTTAAATAT-AAA
**
3233442 TATAAATAGAAATA-AAA
1 T-TAAATTTAAATATAAA
* * * *
3233459 ATAATTTTTAATAATAAT
1 TTAAATTTAAAT-ATAAA
3233477 TTAAATTATTAAAT-TAAA
1 TTAAA-T-TTAAATATAAA
3233495 TTAAATTTAAATATAAA
1 TTAAATTTAAATATAAA
3233512 TT
1 TT
3233514 TAGATTAATT
Statistics
Matches: 53, Mismatches: 13, Indels: 13
0.67 0.16 0.16
Matches are distributed among these distances:
16 13 0.25
17 11 0.21
18 14 0.26
19 10 0.19
20 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAATATAAA
Found at i:3234299 original size:2 final size:2
Alignment explanation
Indices: 3234292--3234321 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3234282 AGAAAAGGTT
3234292 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
3234322 GTTTCTGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3235643 original size:27 final size:27
Alignment explanation
Indices: 3235603--3235656 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3235593 CAGCAACGAT
*
3235603 GACAATAATAACAAGAGAAGTGAAGAC
1 GACAATAATAACAAGACAAGTGAAGAC
* *
3235630 GACAATAATCACAAGACAATTGAAGAC
1 GACAATAATAACAAGACAAGTGAAGAC
3235657 TATGTTGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.15, G:0.19, T:0.13
Consensus pattern (27 bp):
GACAATAATAACAAGACAAGTGAAGAC
Found at i:3240973 original size:7 final size:7
Alignment explanation
Indices: 3240961--3240986 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3240951 AGTATACTTT
3240961 TTATTAA
1 TTATTAA
3240968 TTATTAA
1 TTATTAA
3240975 TTATTAA
1 TTATTAA
3240982 TTATT
1 TTATT
3240987 TTTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:3240995 original size:14 final size:13
Alignment explanation
Indices: 3240958--3240992 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3240948 ATAAGTATAC
3240958 TTTTTATTAATTA
1 TTTTTATTAATTA
*
3240971 TTAATTATTAATTA
1 TT-TTTATTAATTA
3240985 TTTTTATT
1 TTTTTATT
3240993 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTATTAATTA
Found at i:3241073 original size:27 final size:27
Alignment explanation
Indices: 3241038--3241098 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3241028 TTAATTTTAG
*
3241038 AATTATATTTAGTTAT-TGTTAAATTA
1 AATTATATTAAGTTATATGTTAAATTA
* *
3241064 AATTATTATTAAGTTATATTTTAATTTA
1 AATTA-TATTAAGTTATATGTTAAATTA
3241092 AA-TATAT
1 AATTATAT
3241099 GTTAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.27
27 12 0.40
28 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
AATTATATTAAGTTATATGTTAAATTA
Found at i:3241124 original size:37 final size:36
Alignment explanation
Indices: 3241077--3241149 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
3241067 TATTATTAAG
*
3241077 TTATATTTTAATTTAAATATATGTTAAATATTTTAAAT
1 TTATATTTTAATTTAAATATATATT-AA-ATTTTAAAT
*
3241115 TTAT-TTTTAATTTAATTATATATTAAATTTTAAAT
1 TTATATTTTAATTTAAATATATATTAAATTTTAAAT
3241150 GAATTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 9 0.27
36 2 0.06
37 18 0.55
38 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (36 bp):
TTATATTTTAATTTAAATATATATTAAATTTTAAAT
Found at i:3241267 original size:9 final size:9
Alignment explanation
Indices: 3241227--3241268 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
3241217 CTGATTAAAG
3241227 AAAA-ATAA
1 AAAATATAA
3241235 AAAA-ATAA
1 AAAATATAA
*
3241243 AAAATATCA
1 AAAATATAA
*
3241252 AACATATAA
1 AAAATATAA
3241261 AAAATATA
1 AAAATATA
3241269 TTTTATCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 12 0.41
9 17 0.59
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATATAA
Found at i:3241436 original size:26 final size:25
Alignment explanation
Indices: 3241388--3241441 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3241378 TATCTTTAAA
* * *
3241388 ATTTTAAAATAATAATAATTAATTT
1 ATTTTAAAATAAAAATAAATAATAT
*
3241413 ATTTTTAAATAAAAATAACATAATAT
1 ATTTTAAAATAAAAATAA-ATAATAT
3241439 ATT
1 ATT
3241442 AATATTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTTAAAATAAAAATAAATAATAT
Found at i:3241644 original size:5 final size:5
Alignment explanation
Indices: 3241634--3241667 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
3241624 CGCTTACTTA
*
3241634 AATTT AATTT AATTT AATTAT ATTTT AATTT AAT
1 AATTT AATTT AATTT AATT-T AATTT AATTT AAT
3241668 AATAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:3241676 original size:10 final size:10
Alignment explanation
Indices: 3241663--3241725 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
3241653 ATATTTTAAT
*
3241663 TTAATAATAA
1 TTAAAAATAA
*
3241673 TTAAAAATAT
1 TTAAAAATAA
*
3241683 TTAAAAAAAA
1 TTAAAAATAA
3241693 TTAAAAATTAA
1 TTAAAAA-TAA
3241704 --AATAAATAA
1 TTAA-AAATAA
3241713 TTAATAAA-AA
1 TTAA-AAATAA
3241723 TTA
1 TTA
3241726 TATTTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 5 0.11
10 31 0.70
11 8 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:3241686 original size:20 final size:20
Alignment explanation
Indices: 3241661--3241700 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3241651 TTATATTTTA
* *
3241661 ATTTAATAATAATTAAAAAT
1 ATTTAAAAAAAATTAAAAAT
3241681 ATTTAAAAAAAATTAAAAAT
1 ATTTAAAAAAAATTAAAAAT
3241701 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTAAAAAAAATTAAAAAT
Found at i:3241714 original size:20 final size:20
Alignment explanation
Indices: 3241668--3241716 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3241658 TTAATTTAAT
*
3241668 AATAATTAAAAATATTTAAAA
1 AATAATT-AAAATATTAAAAA
3241689 AA-AATTAAAA-ATTAAAATA
1 AATAATTAAAATATTAAAA-A
3241708 AATAATTAA
1 AATAATTAA
3241717 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 7 0.28
20 10 0.40
21 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAATTAAAATATTAAAAA
Found at i:3241902 original size:23 final size:23
Alignment explanation
Indices: 3241857--3241902 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3241847 ATTAATAGAC
*
3241857 ATAATAATATTTTTTATTAAAAA
1 ATAATAATATTTTTGATTAAAAA
*
3241880 ATAATAAT-TTTTTAGATTTAAAA
1 ATAATAATATTTTT-GATTAAAAA
3241903 TTCCTTTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAATAATATTTTTGATTAAAAA
Found at i:3248727 original size:69 final size:71
Alignment explanation
Indices: 3248664--3248820 Score: 210
Period size: 74 Copynumber: 2.2 Consensus size: 71
3248654 TAATTTAATC
** * *
3248664 AATTTTTATTTGATGC-A-CAGTTTGGATAATAATTAAAATGAATAATTTGGTCTGGATAATAAT
1 AATTTTTATTAAATGCAATCAGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAATAAT
3248727 TAATTT
66 TAATTT
* * *
3248733 ATTTTTTATTAAATTCAATTTGGAGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAAT
1 AATTTTTATTAAATGCAA--T-CAGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAAT
3248798 AATTAATTT
63 AATTAATTT
3248807 AATTTTTATTAAAT
1 AATTTTTATTAAAT
3248821 TTGATTCATA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
69 12 0.16
70 1 0.01
74 62 0.83
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (71 bp):
AATTTTTATTAAATGCAATCAGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAATAAT
TAATTT
Found at i:3248769 original size:74 final size:74
Alignment explanation
Indices: 3248682--3248821 Score: 253
Period size: 74 Copynumber: 1.9 Consensus size: 74
3248672 TTTGATGCAC
* * *
3248682 AGTTTGGATAATAATTAAAATGAATAATTTGGTCTGGATAATAATTAATTTATTTTTTATTAAAT
1 AGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAATAATTAATTTAATTTTTATTAAAT
3248747 TCAATTTGG
66 TCAATTTGG
3248756 AGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAATAATTAATTTAATTTTTATTAAAT
1 AGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAATAATTAATTTAATTTTTATTAAAT
3248821 T
66 T
3248822 TGATTCATAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (74 bp):
AGTTTGAATAATAATTAAAATGAATAATTGGGTCTGGATAATAATTAATTTAATTTTTATTAAAT
TCAATTTGG
Found at i:3258881 original size:2 final size:2
Alignment explanation
Indices: 3258874--3258903 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3258864 GAATCCATAA
*
3258874 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3258904 TACCTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3258885 original size:10 final size:10
Alignment explanation
Indices: 3258870--3258902 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3258860 CATTGAATCC
3258870 ATAAATATAT
1 ATAAATATAT
3258880 ATAAATATAT
1 ATAAATATAT
*
3258890 ATATATATAT
1 ATAAATATAT
3258900 ATA
1 ATA
3258903 TTACCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAAATATAT
Found at i:3260480 original size:16 final size:16
Alignment explanation
Indices: 3260424--3260481 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
3260414 GAATAGAATC
3260424 ATAATTTAAAATTTAAA
1 ATAATTT-AAATTTAAA
** *
3260441 ATTTTTTAAA-TCAAA
1 ATAATTTAAATTTAAA
3260456 ATGAA-TTAAATTTAAA
1 AT-AATTTAAATTTAAA
3260472 ATAATTTAAA
1 ATAATTTAAA
3260482 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 13 0.41
16 14 0.44
17 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATTTAAATTTAAA
Found at i:3266493 original size:2 final size:2
Alignment explanation
Indices: 3266486--3266515 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3266476 AGGGTTGCGT
3266486 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3266516 AGATAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3266800 original size:2 final size:2
Alignment explanation
Indices: 3266793--3266829 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3266783 TGGTAAAGAC
3266793 TA TA TA 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 TA TA TA T
3266830 GTGATCAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3267194 original size:45 final size:48
Alignment explanation
Indices: 3267145--3267257 Score: 109
Period size: 45 Copynumber: 2.4 Consensus size: 48
3267135 TTTAAAAAAA
3267145 TATTAAAATATTAAAATAAATAAT-TTTTTA-TAA-AATTTAAT-ATTT
1 TATTAAAATATTAAAATAAATAATATTTTTATTAATAA-TTAATAATTT
*
3267190 TATTATCAAAT-TT-ATATAAA-AATATTTTTATTAATTAATTAATAATTT
1 TATTA--AAATATTAAAATAAATAATATTTTTATTAA-TAATTAATAATTT
3267238 T-TTAAAATA-TAAATATAAAT
1 TATTAAAATATTAAA-ATAAAT
3267258 TATAAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
44 3 0.05
45 22 0.40
46 6 0.11
47 17 0.31
48 7 0.13
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (48 bp):
TATTAAAATATTAAAATAAATAATATTTTTATTAATAATTAATAATTT
Found at i:3268405 original size:20 final size:20
Alignment explanation
Indices: 3268377--3268414 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3268367 ATTTAAATTT
*
3268377 TTAATATTTTTAATTTTAAA
1 TTAAAATTTTTAATTTTAAA
*
3268397 TTAAAATTTTTATTTTTA
1 TTAAAATTTTTAATTTTA
3268415 TTATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAAAATTTTTAATTTTAAA
Found at i:3268421 original size:13 final size:12
Alignment explanation
Indices: 3268405--3268438 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
3268395 AATTAAAATT
3268405 TTTATTTTTATTA
1 TTTATTTTTA-TA
3268418 TTTATTTATTATA
1 TTTATTT-TTATA
3268431 TTTATTTT
1 TTTATTTT
3268439 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 16 0.80
14 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTTATA
Found at i:3269040 original size:3 final size:3
Alignment explanation
Indices: 3269034--3269070 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3269024 CATCATCATC
3269034 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3269071 CTTGTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3269585 original size:27 final size:29
Alignment explanation
Indices: 3269554--3269619 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 29
3269544 AATTAATCAA
*
3269554 ATTTTGATTAAAAATTA-TT-TAAT-TATT
1 ATTTT-ATTAAAAAATATTTATAATATATT
3269581 A-TTT-TTAAAAAATATTTATAATATATT
1 ATTTTATTAAAAAATATTTATAATATATT
3269608 ATTTTTATTAAA
1 A-TTTTATTAAA
3269620 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
24 9 0.28
25 2 0.06
26 7 0.22
27 6 0.19
29 3 0.09
30 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTTTATTAAAAAATATTTATAATATATT
Found at i:3269589 original size:24 final size:27
Alignment explanation
Indices: 3269561--3269614 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3269551 CAAATTTTGA
*
3269561 TTAAAAATTA-TT-TAAT-TATTATTT
1 TTAAAAAATATTTATAATATATTATTT
3269585 TTAAAAAATATTTATAATATATTATTT
1 TTAAAAAATATTTATAATATATTATTT
3269612 TTA
1 TTA
3269615 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.35
25 2 0.08
26 4 0.15
27 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAAAAAATATTTATAATATATTATTT
Found at i:3269620 original size:27 final size:27
Alignment explanation
Indices: 3269554--3269620 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
3269544 AATTAATCAA
* * *
3269554 ATTTTGATTAAAAATTATTTAATTATT
1 ATTTTTATTAAATATTATATAATTATT
**
3269581 ATTTTTAAAAAATATT-TATAATATATT
1 ATTTTTATTAAATATTATATAAT-TATT
3269608 ATTTTTATTAAAT
1 ATTTTTATTAAAT
3269621 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
ATTTTTATTAAATATTATATAATTATT
Found at i:3273847 original size:28 final size:26
Alignment explanation
Indices: 3273816--3273870 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
3273806 TTAATTTAAA
*
3273816 ATAAAAATAAATTTTTATTTATTTATTT
1 ATAAAAATAAA-TTTGATTT-TTTATTT
3273844 ATAAAAATAAATTTGATTTTTTATTT
1 ATAAAAATAAATTTGATTTTTTATTT
3273870 A
1 A
3273871 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.31
27 7 0.27
28 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATAAAAATAAATTTGATTTTTTATTT
Found at i:3273874 original size:12 final size:12
Alignment explanation
Indices: 3273851--3273909 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
3273841 TTTATAAAAA
*
3273851 TAAATTTGATTT
1 TAAATTTAATTT
**
3273863 TTTATTTAATTT
1 TAAATTTAATTT
3273875 TAAATTTAATTAT
1 TAAATTTAATT-T
* *
3273888 TCATTATTAATTT
1 TAAAT-TTAATTT
3273901 TAAATTTAA
1 TAAATTTAA
3273910 ATTAAAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
12 22 0.61
13 8 0.22
14 6 0.17
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
TAAATTTAATTT
Found at i:3273929 original size:20 final size:19
Alignment explanation
Indices: 3273896--3273989 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 19
3273886 ATTCATTATT
*
3273896 AATTTTAAATTTAAATTAAA
1 AATTTTATA-TTAAATTAAA
3273916 AATTTTATTATT-AATTAAA
1 AATTTTA-TATTAAATTAAA
**
3273935 AA-AATATATTAAATATAAAA
1 AATTTTATATTAAAT-T-AAA
*
3273955 AATTTTA-ATTAAATTTATA
1 AATTTTATATTAAA-TTAAA
3273974 AA--TTAT-TTAAATTAAA
1 AATTTTATATTAAATTAAA
3273990 TATTAAAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
16 4 0.07
17 12 0.20
18 5 0.08
19 14 0.23
20 21 0.35
21 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTTATATTAAATTAAA
Found at i:3273946 original size:17 final size:16
Alignment explanation
Indices: 3273922--3273967 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
3273912 TAAAAATTTT
3273922 ATTATTAATTAAAAAA
1 ATTATTAATTAAAAAA
*
3273938 ATATATTAAATATAAAAA
1 AT-TATTAATTA-AAAAA
3273956 ATT-TTAATTAAA
1 ATTATTAATTAAA
3273968 TTTATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 8 0.31
17 9 0.35
18 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATTAATTAAAAAA
Found at i:3273984 original size:37 final size:36
Alignment explanation
Indices: 3273904--3273989 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 36
3273894 TTAATTTTAA
3273904 ATTTAAATT-AAAAATTTTATTATTAATTAAAAAAAT
1 ATTTAAATTAAAAAATTTTATTA-TAATTAAAAAAAT
* * *
3273940 ATATTAAATATAAAAAATTTTAATTA-AATTTATAAATT
1 AT-TTAAAT-TAAAAAATTTT-ATTATAATTAAAAAAAT
3273978 ATTTAAATTAAA
1 ATTTAAATTAAA
3273990 TATTAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
36 6 0.14
37 12 0.28
38 12 0.28
39 9 0.21
40 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
ATTTAAATTAAAAAATTTTATTATAATTAAAAAAAT
Found at i:3274067 original size:28 final size:27
Alignment explanation
Indices: 3274026--3274078 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3274016 ATAACATCTT
*
3274026 AAATTATTCAAATTTAAGTTTAATTTAA
1 AAATTATTCAAA-TTAAATTTAATTTAA
**
3274054 AAATTATTTTAATTAAATTTAATTT
1 AAATTATTCAAATTAAATTTAATTT
3274079 TTTTAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
AAATTATTCAAATTAAATTTAATTTAA
Found at i:3274093 original size:20 final size:19
Alignment explanation
Indices: 3274055--3274094 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3274045 TTAATTTAAA
*
3274055 AATTATTTTAATTAAATTT
1 AATTATTTTAATAAAATTT
*
3274074 AATTTTTTTAATCAAAATTT
1 AATTATTTTAAT-AAAATTT
3274094 A
1 A
3274095 GGGTTAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTATTTTAATAAAATTT
Found at i:3274617 original size:2 final size:2
Alignment explanation
Indices: 3274610--3274645 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3274600 CTCAACTCAA
3274610 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3274646 TAAGTTCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3277237 original size:2 final size:2
Alignment explanation
Indices: 3277232--3277274 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3277222 AAAAACTACA
3277232 TC TC TC TC TC 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
3277274 T
1 T
3277275 TTATTTCCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3281291 original size:2 final size:2
Alignment explanation
Indices: 3281279--3281317 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3281269 GTTTCCCGTT
*
3281279 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3281318 GCTACTGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3281647 original size:15 final size:17
Alignment explanation
Indices: 3281627--3281666 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
3281617 TATAAATTTT
3281627 TTTAAAAAAT-TAT-AA
1 TTTAAAAAATATATCAA
3281642 TTTAAAAAATATATCAA
1 TTTAAAAAATATATCAA
3281659 TATTAAAA
1 T-TTAAAA
3281667 TTTTAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 3 0.14
17 3 0.14
18 6 0.27
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAAAAAATATATCAA
Found at i:3281687 original size:15 final size:15
Alignment explanation
Indices: 3281669--3281703 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3281659 TATTAAAATT
3281669 TTAAACATTATATTA
1 TTAAACATTATATTA
* *
3281684 TTAAATATTATATTT
1 TTAAACATTATATTA
3281699 TTAAA
1 TTAAA
3281704 AATATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAACATTATATTA
Found at i:3283136 original size:63 final size:63
Alignment explanation
Indices: 3283058--3283186 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 63
3283048 ATTTTTTAAT
*
3283058 TATTATTAAATTTATGGATAAATATATTTAATATTTATCAAATTAATAA-ATA-ATTTTATTTTA
1 TATTATTAAATTTATGAATAAATATA-TTAA-ATTTATCAAATTAATAACATACATTTTATTTTA
* *
3283121 TATTATTAAATTTATGAATAATTATATTAAATTTATCAAATTTATAATCATACCATTTTATTTTA
1 TATTATTAAATTTATGAATAAATATATTAAATTTATCAAATTAATAA-CATA-CATTTTATTTTA
3283186 T
1 T
3283187 TTTTGGATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
61 16 0.27
62 4 0.07
63 27 0.46
65 12 0.20
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (63 bp):
TATTATTAAATTTATGAATAAATATATTAAATTTATCAAATTAATAACATACATTTTATTTTA
Found at i:3283141 original size:31 final size:31
Alignment explanation
Indices: 3283052--3283165 Score: 122
Period size: 32 Copynumber: 3.6 Consensus size: 31
3283042 AATAAAATTT
* * *
3283052 TTTAATTATTATTAAATTTATGGATAAATATA
1 TTTAA-TATTATCAAATTTATGAATAATTATA
* * *
3283084 TTTAATATTTATCAAATTAATAAATAATTTTA
1 TTTAATA-TTATCAAATTTATGAATAATTATA
* *
3283116 TTTTATATTATTAAATTTATGAATAATTATA
1 TTTAATATTATCAAATTTATGAATAATTATA
*
3283147 TTAAAT-TTATCAAATTTAT
1 TTTAATATTATCAAATTTAT
3283166 AATCATACCA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
30 12 0.18
31 26 0.39
32 29 0.43
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTAATATTATCAAATTTATGAATAATTATA
Found at i:3283655 original size:14 final size:14
Alignment explanation
Indices: 3283636--3283665 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3283626 TCATATTCAT
3283636 ATTTAATATTTTTA
1 ATTTAATATTTTTA
3283650 ATTTAATATTTTTA
1 ATTTAATATTTTTA
3283664 AT
1 AT
3283666 GCATTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTAATATTTTTA
Found at i:3283775 original size:2 final size:2
Alignment explanation
Indices: 3283768--3283803 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3283758 GAACAAAGAG
3283768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3283804 ACTTGTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3286831 original size:12 final size:12
Alignment explanation
Indices: 3286804--3286836 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3286794 GTGATAGAAC
3286804 TAAAAT-TATAA
1 TAAAATATATAA
*
3286815 AAAAATATATAA
1 TAAAATATATAA
3286827 TAAAATATAT
1 TAAAATATAT
3286837 TATTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAATATATAA
Found at i:3286858 original size:24 final size:25
Alignment explanation
Indices: 3286817--3286871 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
3286807 AATTATAAAA
3286817 AAATATATAATAAAATATATTATTT
1 AAATATATAATAAAATATATTATTT
* *
3286842 AAATTTAT-ATAATATATATTA-TT
1 AAATATATAATAAAATATATTATTT
3286865 -AATATAT
1 AAATATAT
3286872 TAAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 2 0.07
24 12 0.44
25 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATATAATAAAATATATTATTT
Found at i:3286870 original size:20 final size:17
Alignment explanation
Indices: 3286857--3286907 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 17
3286847 TATATAATAT
3286857 ATATTATTAATATATTAAA
1 ATATTATTAA-ATA-TAAA
3286876 AT-TTATATAAATATAAA
1 ATATTAT-TAAATATAAA
3286893 ATATT-TTAAATATAA
1 ATATTATTAAATATAA
3286908 TTATAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 9 0.30
19 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTATTAAATATAAA
Found at i:3286881 original size:18 final size:17
Alignment explanation
Indices: 3286842--3286907 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 17
3286832 TATATTATTT
3286842 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
*
3286857 ATA-TTAT-TAATATATTA
1 AAATTTATATAA-ATA-TA
3286874 AAATTTATATAAATATA
1 AAATTTATATAAATATA
3286891 AAATATT-T-TAAATATA
1 AAAT-TTATATAAATATA
3286907 A
1 A
3286908 TTATAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 5 0.12
16 10 0.24
17 9 0.21
18 9 0.21
19 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:3286934 original size:22 final size:23
Alignment explanation
Indices: 3286821--3286936 Score: 69
Period size: 24 Copynumber: 5.0 Consensus size: 23
3286811 ATAAAAAAAT
* *
3286821 ATATAATAAAATATATTATTTAAA
1 ATAT-ATAAAATATAATATATAAA
* * * *
3286845 TTTATATAATATATATTAT-TAAT
1 -ATATATAAAATATAATATATAAA
*
3286868 ATAT-TAAAATTTATATAAATATAAA
1 ATATATAAAA--TATA-ATATATAAA
* *
3286893 ATATTTTAAATATAAT-TATAAA
1 ATATATAAAATATAATATATAAA
*
3286915 ATA-ATAAAATATACTATATAAA
1 ATATATAAAATATAATATATAAA
3286937 TATTAGAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
21 13 0.18
22 18 0.25
23 8 0.11
24 19 0.26
25 10 0.14
26 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATAAAATATAATATATAAA
Found at i:3292125 original size:7 final size:7
Alignment explanation
Indices: 3292113--3292175 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
3292103 AAAGTGAGTG
3292113 AAATAAA
1 AAATAAA
3292120 AAATAAA
1 AAATAAA
3292127 AAATAAA
1 AAATAAA
*
3292134 AAAT-AT
1 AAATAAA
3292140 AAATAAA
1 AAATAAA
*
3292147 AAAGTGAGTA
1 AAA-T-A-AA
3292157 AAATAAA
1 AAATAAA
*
3292164 AAATTAA
1 AAATAAA
3292171 AAATA
1 AAATA
3292176 TAGGTAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 5 0.11
7 33 0.72
8 2 0.04
9 2 0.04
10 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:3292191 original size:24 final size:23
Alignment explanation
Indices: 3292161--3292237 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
3292151 TGAGTAAAAT
3292161 AAAAAATTAAAAATATAGGTAAA
1 AAAAAATTAAAAATATAGGTAAA
* * **
3292184 AAAGAAATTACAAATAAAAAT-AA
1 AAA-AAATTAAAAATATAGGTAAA
*
3292207 AAAAAATCTAAAAAGTATAGGTGAA
1 AAAAAAT-TAAAAA-TATAGGTAAA
3292232 AAAAAA
1 AAAAAA
3292238 GGAGTGGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 4 0.10
23 13 0.31
24 17 0.40
25 8 0.19
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAAATTAAAAATATAGGTAAA
Found at i:3292199 original size:38 final size:37
Alignment explanation
Indices: 3292119--3292210 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
3292109 AGTGAAATAA
**
3292119 AAAATAAAAAATAAAAAATATAAATAAAAAAGTGAGT
1 AAAATAAAAAATAAAAAATATAAATAAAAAAGAAAGT
* ** *
3292156 AAAATAAAAAATTAAAAATATAGGTAAAAAAGAAATT
1 AAAATAAAAAATAAAAAATATAAATAAAAAAGAAAGT
3292193 ACAAAT-AAAAATAAAAAA
1 A-AAATAAAAAATAAAAAA
3292211 AATCTAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 43 0.91
38 4 0.09
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (37 bp):
AAAATAAAAAATAAAAAATATAAATAAAAAAGAAAGT
Found at i:3292362 original size:12 final size:12
Alignment explanation
Indices: 3292327--3292362 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
3292317 TTAAAAAAAT
*
3292327 TAATTATTAATA
1 TAATTTTTAATA
3292339 TAATTTTATAATA
1 TAATTTT-TAATA
3292352 TAATTTTTAAT
1 TAATTTTTAAT
3292363 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TAATTTTTAATA
Found at i:3300689 original size:12 final size:12
Alignment explanation
Indices: 3300672--3300701 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3300662 CTTATATCTA
3300672 TGAATTCATTAT
1 TGAATTCATTAT
*
3300684 TGAATTCCTTAT
1 TGAATTCATTAT
3300696 TGAATT
1 TGAATT
3300702 TCTTGTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
TGAATTCATTAT
Found at i:3304000 original size:22 final size:24
Alignment explanation
Indices: 3303972--3304015 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3303962 TTTATCAAAA
*
3303972 TATTAAT-ATTTTAAA-AAAAATT
1 TATTAATAAATTTAAATAAAAATT
3303994 TATTAATAAATTTAAATAAAAA
1 TATTAATAAATTTAAATAAAAA
3304016 ATTTTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TATTAATAAATTTAAATAAAAATT
Found at i:3308685 original size:26 final size:26
Alignment explanation
Indices: 3308656--3308726 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
3308646 AATTCGATTT
3308656 ATTTTTTAATTATATAATATATATTA
1 ATTTTTTAATTATATAATATATATTA
* *
3308682 ATTTTATATTTATAT-ATA-ATA-TA
1 ATTTTTTAATTATATAATATATATTA
* *
3308705 A-TTTTT-ATCATATAAAATATAT
1 ATTTTTTAATTATATAATATATAT
3308727 CATATTATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.14
22 6 0.17
23 6 0.17
24 3 0.08
25 3 0.08
26 13 0.36
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTTTAATTATATAATATATATTA
Found at i:3308717 original size:21 final size:23
Alignment explanation
Indices: 3308672--3308725 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
3308662 TAATTATATA
*
3308672 ATATAT-AT-TAATTTTATATTT
1 ATATATAATATAATTTTATATTC
3308693 ATATATAATATAATTTT-TA-TC
1 ATATATAATATAATTTTATATTC
*
3308714 ATATAAAATATA
1 ATATATAATATA
3308726 TCATATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 18 0.62
22 4 0.14
23 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATAATATAATTTTATATTC
Found at i:3308821 original size:15 final size:14
Alignment explanation
Indices: 3308796--3308842 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
3308786 TGAAAATTAT
*
3308796 TAAAATTTAAAAAA
1 TAAATTTTAAAAAA
3308810 TATAATTTTAAAAAA
1 TA-AATTTTAAAAAA
3308825 TAAA--TTAAAAATA
1 TAAATTTTAAAAA-A
3308838 TAAAT
1 TAAAT
3308843 AAACTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 4 0.14
15 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATTTTAAAAAA
Found at i:3308827 original size:13 final size:14
Alignment explanation
Indices: 3308799--3308840 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3308789 AAATTATTAA
*
3308799 AATTTAAAAAATAT
1 AATTTTAAAAATAT
3308813 AATTTTAAAAA-AT
1 AATTTTAAAAATAT
*
3308826 AA-ATTAAAAATAT
1 AATTTTAAAAATAT
3308839 AA
1 AA
3308841 ATAAACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.28
13 8 0.32
14 10 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTTTAAAAATAT
Found at i:3308841 original size:13 final size:13
Alignment explanation
Indices: 3308805--3308842 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3308795 TTAAAATTTA
*
3308805 AAAAATATAATTTT
1 AAAAATATAA-ATT
3308819 AAAAA-ATAAATT
1 AAAAATATAAATT
3308831 AAAAATATAAAT
1 AAAAATATAAAT
3308843 AAACTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 10 0.45
14 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATATAAATT
Found at i:3311085 original size:2 final size:2
Alignment explanation
Indices: 3311078--3311108 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3311068 GCCCCACCCA
3311078 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3311109 AATAGGTGGC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3311345 original size:79 final size:79
Alignment explanation
Indices: 3311214--3311372 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
3311204 GCTATTGGCT
3311214 GCCATTCTTGAGCATATTGAAACTCTTAAGGTCCTGGTTCAGATACTACATCAACAATCTAAAAG
1 GCCATTCTTGAGCATATTGAAACTCTTAAGGTCCTGGTTCAGATACTACATCAACAATCTAAAAG
3311279 TTCAGAGAAAGCCA
66 TTCAGAGAAAGCCA
*
3311293 GCCATTCTTGAGCATATTGAACCTCTTAAGGTCCTGGTTCAGATACTACATCAACAATCTAAAAG
1 GCCATTCTTGAGCATATTGAAACTCTTAAGGTCCTGGTTCAGATACTACATCAACAATCTAAAAG
3311358 TTCAGAGAAAGCCA
66 TTCAGAGAAAGCCA
3311372 G
1 G
3311373 AATTGATATA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (79 bp):
GCCATTCTTGAGCATATTGAAACTCTTAAGGTCCTGGTTCAGATACTACATCAACAATCTAAAAG
TTCAGAGAAAGCCA
Found at i:3318995 original size:21 final size:20
Alignment explanation
Indices: 3318952--3318996 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3318942 TCATAAATAT
* *
3318952 GAATTTAATAATATTTCAAA
1 GAATTTAATAATATGTAAAA
3318972 GAATTTAATAATATCGTAAAA
1 GAATTTAATAATAT-GTAAAA
3318993 GAAT
1 GAAT
3318997 AAAATACGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (20 bp):
GAATTTAATAATATGTAAAA
Found at i:3320564 original size:2 final size:2
Alignment explanation
Indices: 3320557--3320586 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3320547 TATATTAGAT
3320557 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
3320587 AGATTTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3324758 original size:188 final size:188
Alignment explanation
Indices: 3324441--3324810 Score: 643
Period size: 188 Copynumber: 2.0 Consensus size: 188
3324431 CAAAGGAAAT
*
3324441 ATTTCATCACCTAATAATTAGTTTAGCCAGTTCTCTTCTCCACAGGCTTTCTAGATTGGAGGTGG
1 ATTTCATCACCTAATAATTAGTTTAGCCAATTCTCTTCTCCACAGGCTTTCTAGATTGGAGGTGG
* *
3324506 AATTGAAACGAGATGGAAGTAGGGATTTCTTTATTTATTTTTATTTTATTTTTGTATAAATATTG
66 AATGGAAACGAGATGGAAGTAGGGATTTCTTTATCTATTTTTATTTTATTTTTGTATAAATATTG
* * *
3324571 TAAATGTTTATTTTTATAGA-TCTCAGTTATATTTATAATATTTTATTTTATTGCAAGA
131 TAAATGTTTATTTTTATA-ATTCTCAGATACATTAATAATATTTTATTTTATTGCAAGA
* *
3324629 ATTTCATCACTTAATAATTAGTTTAGCCAATTCTCTTTTCCACAGGCTTTCTAGATTGGAGGTGG
1 ATTTCATCACCTAATAATTAGTTTAGCCAATTCTCTTCTCCACAGGCTTTCTAGATTGGAGGTGG
3324694 AATGGAAACGAGATGGAAGTAGGGATTTCTTTATCTATTTTTATTTTATTTTTGTATAAATATTG
66 AATGGAAACGAGATGGAAGTAGGGATTTCTTTATCTATTTTTATTTTATTTTTGTATAAATATTG
*
3324759 TAAATGTTTATTTTTATAATTGTCAGATACATTAATAATATTTTATTTTATT
131 TAAATGTTTATTTTTATAATTCTCAGATACATTAATAATATTTTATTTTATT
3324811 TTTTATTAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
187 1 0.01
188 171 0.99
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (188 bp):
ATTTCATCACCTAATAATTAGTTTAGCCAATTCTCTTCTCCACAGGCTTTCTAGATTGGAGGTGG
AATGGAAACGAGATGGAAGTAGGGATTTCTTTATCTATTTTTATTTTATTTTTGTATAAATATTG
TAAATGTTTATTTTTATAATTCTCAGATACATTAATAATATTTTATTTTATTGCAAGA
Found at i:3325347 original size:19 final size:19
Alignment explanation
Indices: 3325323--3325360 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3325313 ATAAAATAAT
3325323 AATTCA-AATAAAATCTTAA
1 AATTCACAA-AAAATCTTAA
*
3325342 AATTCACAAAAAGTCTTAA
1 AATTCACAAAAAATCTTAA
3325361 TCCTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (19 bp):
AATTCACAAAAAATCTTAA
Found at i:3325825 original size:14 final size:15
Alignment explanation
Indices: 3325806--3325834 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3325796 ATATTATTCA
3325806 AATTTAT-TTTTATG
1 AATTTATATTTTATG
3325820 AATTTATATTTTATG
1 AATTTATATTTTATG
3325835 TAAGAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
AATTTATATTTTATG
Found at i:3325953 original size:25 final size:25
Alignment explanation
Indices: 3325914--3326003 Score: 91
Period size: 25 Copynumber: 3.6 Consensus size: 25
3325904 TTTAATTCAG
*
3325914 ATTTAAATTTGGATAATAATGTATGA
1 ATTTAAATTTAGATAATAAT-TATGA
*
3325940 ATTT-AATTTAGATAATAA--ATAA
1 ATTTAAATTTAGATAATAATTATGA
3325962 ATTTAAATTTTA-A-AATAATTTTATGA
1 ATTTAAA-TTTAGATAATAA--TTATGA
3325988 ATTTAAATTTAGATAA
1 ATTTAAATTTAGATAA
3326004 ATTATAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 12 0.23
23 3 0.06
24 4 0.08
25 17 0.32
26 15 0.28
27 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (25 bp):
ATTTAAATTTAGATAATAATTATGA
Found at i:3326219 original size:20 final size:18
Alignment explanation
Indices: 3326155--3326212 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
3326145 AATTTTAAAT
*
3326155 ATTTAATTTAAAATTAATTA
1 ATTTAATTAAAAATT--TTA
* *
3326175 ATGATAAATAAAAATTTTA
1 AT-TTAATTAAAAATTTTA
3326194 ATTTAATTAAAAATTTTA
1 ATTTAATTAAAAATTTTA
3326212 A
1 A
3326213 AATTTAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 15 0.47
19 5 0.16
20 2 0.06
21 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTAATTAAAAATTTTA
Found at i:3326412 original size:9 final size:8
Alignment explanation
Indices: 3326406--3326482 Score: 59
Period size: 9 Copynumber: 9.1 Consensus size: 8
3326396 AGATATTTCA
*
3326406 TATATTTT
1 TATATATT
3326414 TATTATATT
1 TA-TATATT
*
3326423 TGTATATTT
1 TATATA-TT
3326432 TATAATATT
1 TAT-ATATT
3326441 TA-ATATAT
1 TATATAT-T
3326449 TATATATT
1 TATATATT
3326457 TATAATAATT
1 TAT-AT-ATT
3326467 TATAT-TT
1 TATATATT
*
3326474 TATAAATT
1 TATATATT
3326482 T
1 T
3326483 TGATAATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
7 10 0.18
8 16 0.28
9 22 0.39
10 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (8 bp):
TATATATT
Found at i:3326430 original size:8 final size:7
Alignment explanation
Indices: 3326416--3326547 Score: 58
Period size: 9 Copynumber: 17.6 Consensus size: 7
3326406 TATATTTTTA
3326416 TTATATT
1 TTATATT
3326423 TGTATATT
1 T-TATATT
3326431 TTATAATAT
1 TTAT-AT-T
3326440 TTAATATAT
1 TT-ATAT-T
3326449 TATATATT
1 T-TATATT
*
3326457 TATAATAAT
1 T-T-ATATT
3326466 TTATATT
1 TTATATT
3326473 TTATAAATT
1 TTAT--ATT
3326482 TTGATAATT
1 TT-AT-ATT
3326491 TTAT-TT
1 TTATATT
*
3326497 TTAGA--
1 TTATATT
3326502 TTATATT
1 TTATATT
3326509 TATATTATT
1 T-TA-TATT
*
3326518 TTTTATT
1 TTATATT
3326525 TTATA--
1 TTATATT
*
3326530 TAATATT
1 TTATATT
*
3326537 TTATTTT
1 TTATATT
3326544 TTAT
1 TTAT
3326548 TATGTTATTT
Statistics
Matches: 100, Mismatches: 9, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
5 8 0.08
6 5 0.05
7 30 0.30
8 19 0.19
9 33 0.33
10 5 0.05
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (7 bp):
TTATATT
Found at i:3326447 original size:19 final size:18
Alignment explanation
Indices: 3326398--3326531 Score: 79
Period size: 18 Copynumber: 7.6 Consensus size: 18
3326388 CTAATGTTAG
*
3326398 ATATTTCATATATTTTTATT
1 ATATTT-ATATA-TTTTATA
*
3326418 ATATTTGTATATTTTATA
1 ATATTTATATATTTTATA
*
3326436 ATATTTA-ATATATTAT-
1 ATATTTATATATTTTATA
*
3326452 ATATTTATAATAATTTAT-
1 ATATTTAT-ATATTTTATA
*
3326470 AT-TTTATAAATTTTGATA
1 ATATTTATATATTTT-ATA
* *
3326488 AT-TTTAT-T-TTTAGATT
1 ATATTTATATATTT-TATA
*
3326504 ATATTTATATTATTTT-TT
1 ATATTTATA-TATTTTATA
3326522 AT-TTTATATA
1 ATATTTATATA
3326532 ATATTTTATT
Statistics
Matches: 93, Mismatches: 12, Indels: 22
0.73 0.09 0.17
Matches are distributed among these distances:
16 21 0.23
17 26 0.28
18 32 0.34
19 5 0.05
20 9 0.10
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTTTATA
Found at i:3326458 original size:25 final size:25
Alignment explanation
Indices: 3326416--3326491 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
3326406 TATATTTTTA
*
3326416 TTATAT-TTGTATATTTTATAAT-AT
1 TTATATATTATATA-TTTATAATAAT
3326440 TTAATATATTATATATTTATAATAAT
1 TT-ATATATTATATATTTATAATAAT
* * *
3326466 TTATATTTTATAAATTT-TGATAAT
1 TTATATATTATATATTTATAATAAT
3326490 TT
1 TT
3326492 TATTTTTAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.22
25 25 0.56
26 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (25 bp):
TTATATATTATATATTTATAATAAT
Found at i:3326527 original size:17 final size:17
Alignment explanation
Indices: 3326502--3326550 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3326492 TATTTTTAGA
*
3326502 TTATATTTATATTATTTT
1 TTAT-TTTATATTATATT
*
3326520 TTATTTTATATAATATT
1 TTATTTTATATTATATT
*
3326537 TTATTTTTTATTAT
1 TTATTTTATATTAT
3326551 GTTATTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTATATTATATT
Found at i:3326536 original size:19 final size:19
Alignment explanation
Indices: 3326509--3326547 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3326499 AGATTATATT
*
3326509 TATATTATTTT-TTATTTTA
1 TATAATATTTTATT-TTTTA
3326528 TATAATATTTTATTTTTTA
1 TATAATATTTTATTTTTTA
3326547 T
1 T
3326548 TATGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATAATATTTTATTTTTTA
Found at i:3326540 original size:24 final size:23
Alignment explanation
Indices: 3326488--3326548 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
3326478 AATTTTGATA
** *
3326488 ATTTTA-TTTTTAGATTATATTT
1 ATTTTATTTTTTATTTTATATAT
*
3326510 ATATTATTTTTTATTTTATATAAT
1 ATTTTATTTTTTATTTTATAT-AT
3326534 ATTTTATTTTTTATT
1 ATTTTATTTTTTATT
3326549 ATGTTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.16
23 12 0.38
24 15 0.47
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTTATTTTTTATTTTATATAT
Found at i:3326550 original size:22 final size:21
Alignment explanation
Indices: 3326488--3326550 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
3326478 AATTTTGATA
* *
3326488 ATTTTATTTTTAGATTATATTT
1 ATTTTATTTTT-TATTATATAT
*
3326510 ATATTATTTTTTATTTTATATAAT
1 ATTTTATTTTTTA--TTATAT-AT
3326534 ATTTTATTTTTTATTAT
1 ATTTTATTTTTTATTAT
3326551 GTTATTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 6 0.18
24 13 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTATTTTTTATTATATAT
Found at i:3326560 original size:54 final size:51
Alignment explanation
Indices: 3326446--3326560 Score: 115
Period size: 52 Copynumber: 2.2 Consensus size: 51
3326436 ATATTTAATA
3326446 TATTATATATTTATAATAATTTATATTTTATAAATTTTGATAATTTTATTTT
1 TATT-TATATTTATAATAATTTATATTTTATAAATTTTGATAATTTTATTTT
* * * * * *
3326498 TAGATTATATTTATATTATTTTTTATTTTATATAATATTTTAT-TTTTTATTATGT
1 TA-TTTATATTTATAATAATTTATATTTTATA-AAT-TTTGATAATTTTATT-T-T
3326553 TATTTATA
1 TATTTATA
3326561 AATCATATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
52 26 0.51
53 11 0.22
54 11 0.22
55 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (51 bp):
TATTTATATTTATAATAATTTATATTTTATAAATTTTGATAATTTTATTTT
Found at i:3326923 original size:12 final size:11
Alignment explanation
Indices: 3326906--3326932 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3326896 GTTGTAAGCC
3326906 AAAAAAAAAAG
1 AAAAAAAAAAG
3326917 AAAAAAAAAAG
1 AAAAAAAAAAG
3326928 AAAAA
1 AAAAA
3326933 TAGTTCTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3326960 original size:165 final size:164
Alignment explanation
Indices: 3326708--3327037 Score: 597
Period size: 165 Copynumber: 2.0 Consensus size: 164
3326698 TCTTCATGTG
** **
3326708 CTCAAGCAAATTAATCCTATTTGAGTTGTAAGCCAAAAAAAAAATTAAAAAAAAGAAAAATAGTT
1 CTCAAGCAAATTAAAACTATTTGAGTTGTAAGCCAAAAAAAAAAAAAAAAAAAAGAAAAATAGTT
*
3326773 CTTAGTGATAATATTTGAAAATAAAAATTAATACATTTCATATAATAATTGTTAAGATAACATAT
66 CTTAGTGATAATATTTGAAAATAAAAATTAATACATTTCATATAATAATTGTCAAGATAACATAT
3326838 TTATTTCAAGATTTTTTTGTCCCCTATATTTCTA
131 TTATTTCAAGATTTTTTTGTCCCCTATATTTCTA
3326872 CTCAAGCAAATTAAAACTATTTGAGTTGTAAGCCAAAAAAAAAAGAAAAAAAAAAGAAAAATAGT
1 CTCAAGCAAATTAAAACTATTTGAGTTGTAAGCCAAAAAAAAAA-AAAAAAAAAAGAAAAATAGT
*
3326937 TCTTAGTGATGATATTTGAAAATAAAAATTAATACATTTCATATAATAATTGTCAAGATAACATA
65 TCTTAGTGATAATATTTGAAAATAAAAATTAATACATTTCATATAATAATTGTCAAGATAACATA
3327002 TTTATTTCAAGATTTTTTTGTCCCCTATATTTCTA
130 TTTATTTCAAGATTTTTTTGTCCCCTATATTTCTA
3327037 C
1 C
3327038 CTTTATCTTC
Statistics
Matches: 159, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
164 42 0.26
165 117 0.74
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (164 bp):
CTCAAGCAAATTAAAACTATTTGAGTTGTAAGCCAAAAAAAAAAAAAAAAAAAAGAAAAATAGTT
CTTAGTGATAATATTTGAAAATAAAAATTAATACATTTCATATAATAATTGTCAAGATAACATAT
TTATTTCAAGATTTTTTTGTCCCCTATATTTCTA
Found at i:3328655 original size:17 final size:19
Alignment explanation
Indices: 3328633--3328668 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
3328623 TTTATCAATT
3328633 ATATAAAT-A-TAAATATA
1 ATATAAATGATTAAATATA
3328650 ATATAAATGATTAAATATA
1 ATATAAATGATTAAATATA
3328669 TCAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
ATATAAATGATTAAATATA
Found at i:3329169 original size:17 final size:18
Alignment explanation
Indices: 3329136--3329171 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3329126 TATTACGTAA
*
3329136 ATTTATATTTGATATATT
1 ATTTAAATTTGATATATT
3329154 ATTTAAATTT-ATATATT
1 ATTTAAATTTGATATATT
3329171 A
1 A
3329172 ATAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTAAATTTGATATATT
Found at i:3329183 original size:24 final size:24
Alignment explanation
Indices: 3329133--3329185 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3329123 TTTTATTACG
* * *
3329133 TAAATTTATATTTGATATATTATT
1 TAAATTTATATTTAATATATAAAT
3329157 TAAATTTATATATTAATA-ATAAAT
1 TAAATTTATAT-TTAATATATAAAT
3329181 TAAAT
1 TAAAT
3329186 CATATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAAATTTATATTTAATATATAAAT
Found at i:3341720 original size:2 final size:2
Alignment explanation
Indices: 3341715--3341748 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3341705 AAAAGAAGAA
3341715 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
3341749 GGCAATAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3344301 original size:22 final size:21
Alignment explanation
Indices: 3344254--3344352 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 21
3344244 TGATTTAATT
*
3344254 TTTTTAAATTATATTATTTA-A
1 TTTTTAAA-TATATAATTTATA
* *
3344275 -ATTTAAGTATATAATTATATA
1 TTTTTAAATATATAATT-TATA
3344296 TTTTTAAATATATAATTTATAA
1 TTTTTAAATATATAATTTAT-A
* *
3344318 TTTATTTAAATTATTTAAATTCATA
1 -TT-TTTAAA-TATAT-AATTTATA
*
3344343 ATTTTAAATA
1 TTTTTAAATA
3344353 AAAAATTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
19 8 0.13
20 7 0.11
21 4 0.06
22 17 0.27
23 8 0.13
24 7 0.11
25 5 0.08
26 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTTTAAATATATAATTTATA
Found at i:3344808 original size:2 final size:2
Alignment explanation
Indices: 3344795--3344824 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3344785 AACCAGGGAG
*
3344795 TA TA TT 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
3344825 ATACACTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3345780 original size:30 final size:28
Alignment explanation
Indices: 3345734--3345792 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
3345724 TGGATTGAGC
*
3345734 ATTAAATTTTTAATTTTAATAATTAAAA
1 ATTAAATTTTTAATTTTAATAATGAAAA
*
3345762 ATTAAATTTTAATAATTTTAATCATGAAAA
1 ATTAAATTTT--TAATTTTAATAATGAAAA
3345792 A
1 A
3345793 AATTGGGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 10 0.37
30 17 0.63
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTAAATTTTTAATTTTAATAATGAAAA
Found at i:3349998 original size:12 final size:12
Alignment explanation
Indices: 3349978--3350020 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3349968 TTTGTTAATG
3349978 AATATTTTAAAAT
1 AATA-TTTAAAAT
*
3349991 ATTATTTAAAATT
1 AATATTTAAAA-T
*
3350004 AATATATAAAAT
1 AATATTTAAAAT
3350016 AATAT
1 AATAT
3350021 ATTCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 13 0.50
13 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATATTTAAAAT
Found at i:3356571 original size:12 final size:11
Alignment explanation
Indices: 3356542--3356575 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3356532 ATGATATTAT
3356542 ATTTTAAAAAA
1 ATTTTAAAAAA
*
3356553 TTTTTAAATAAA
1 ATTTTAAA-AAA
3356565 ATTTTAAAAAA
1 ATTTTAAAAAA
3356576 TTGAATGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:3364836 original size:15 final size:16
Alignment explanation
Indices: 3364816--3364845 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3364806 TATTTTAAAT
3364816 TTATATA-TAATTTTA
1 TTATATATTAATTTTA
3364831 TTATATATTAATTTT
1 TTATATATTAATTTT
3364846 GAGGTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATATTAATTTTA
Found at i:3365900 original size:25 final size:25
Alignment explanation
Indices: 3365872--3365945 Score: 91
Period size: 24 Copynumber: 3.0 Consensus size: 25
3365862 AGCATTATAT
3365872 TATTAAAATATTATTTTTATATTAA
1 TATTAAAATATTATTTTTATATTAA
*
3365897 TATTAAAATATT-TTTATA-ATTAAA
1 TATTAAAATATTATTTTTATATT-AA
*
3365921 TTTTAAAA-ATTATTTTTATTATTAA
1 TATTAAAATATTATTTTTA-TATTAA
3365946 ATAATAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.14
24 19 0.45
25 14 0.33
26 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTAAAATATTATTTTTATATTAA
Found at i:3365954 original size:23 final size:24
Alignment explanation
Indices: 3365881--3365954 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 24
3365871 TTATTAAAAT
3365881 ATTATTTTTA-TATTAATATTAA-A
1 ATTATTTTTATTATTAA-ATTAATA
* *
3365904 A-TATTTTTATAATTAAATTTTAAAA
1 ATTATTTTTATTATTAAA--TTAATA
3365929 ATTATTTTTATTATTAAA-TAATA
1 ATTATTTTTATTATTAAATTAATA
3365952 ATT
1 ATT
3365955 TAAATTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 9 0.21
23 13 0.30
24 4 0.09
25 2 0.05
26 15 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATTTTTATTATTAAATTAATA
Found at i:3365961 original size:20 final size:19
Alignment explanation
Indices: 3365912--3365961 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
3365902 AAATATTTTT
3365912 ATAA-TTAAATT-TTAAAA
1 ATAATTTAAATTATTAAAA
* **
3365929 ATTATTTTTATTATTAAATA
1 ATAATTTAAATTATTAAA-A
3365949 ATAATTTAAATTA
1 ATAATTTAAATTA
3365962 ACTCAAATAC
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 5 0.21
20 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAATTTAAATTATTAAAA
Found at i:3367332 original size:14 final size:15
Alignment explanation
Indices: 3367300--3367339 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3367290 AATTTTTTTT
*
3367300 TTAAAAATATA-TAA
1 TTAAAAATAAATTAA
3367314 TTAAAAATAAATTAA
1 TTAAAAATAAATTAA
3367329 -T-AAAATAAATT
1 TTAAAAATAAATT
3367340 TTTTAGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 10 0.42
14 11 0.46
15 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAAATAAATTAA
Found at i:3372334 original size:16 final size:16
Alignment explanation
Indices: 3372305--3372347 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3372295 ATATATATTT
*
3372305 AACAAAAGAATAAAAGA
1 AACAAAA-AATAAAAAA
3372322 AACAAAAAATAAAAAA
1 AACAAAAAATAAAAAA
*
3372338 AACATAAAAT
1 AACAAAAAAT
3372348 TGATTCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (16 bp):
AACAAAAAATAAAAAA
Found at i:3373450 original size:127 final size:127
Alignment explanation
Indices: 3373302--3373533 Score: 356
Period size: 127 Copynumber: 1.8 Consensus size: 127
3373292 AAAAATAATA
* * * *
3373302 AATAAAGATTAATCAATATTTTAATTTAATAAAAAATCATTAATAAAAAATTACTTAATATTAAT
1 AATAAAAAATAATCAACATTTTAATTTAATAAAAAATCATTAATAAAAAATAACTTAATATTAAT
* * *
3373367 AAAAGATATATCAATAAAAAAGATTTTACATTATTAAAAATTCTGAATAAGACTTCAAGATT
66 AAAAGATATACCAATAAAAAAGAGTTTACATTAATAAAAATTCTGAATAAGACTTCAAGATT
* * *
3373429 AATAAAAAATAATCAACATTTTAATTTAATTAAAATTCATTAATAAAAAATAAGTTAATATTAAT
1 AATAAAAAATAATCAACATTTTAATTTAATAAAAAATCATTAATAAAAAATAACTTAATATTAAT
* *
3373494 AAAAGATATACCAATAAGAAAGGGTTTACATTAATAAAAA
66 AAAAGATATACCAATAAAAAAGAGTTTACATTAATAAAAA
3373534 ATAAATAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
127 93 1.00
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (127 bp):
AATAAAAAATAATCAACATTTTAATTTAATAAAAAATCATTAATAAAAAATAACTTAATATTAAT
AAAAGATATACCAATAAAAAAGAGTTTACATTAATAAAAATTCTGAATAAGACTTCAAGATT
Found at i:3374176 original size:2 final size:2
Alignment explanation
Indices: 3374169--3374193 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3374159 TTTCATTGAG
3374169 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
3374194 TAGAAATCTT
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:3374441 original size:24 final size:23
Alignment explanation
Indices: 3374397--3374441 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3374387 TTATAAATTT
* *
3374397 ATATATTTTTAATAAATTAAATA
1 ATATAATTTTAATAAAATAAATA
*
3374420 ATATAATTTTATTAAAAATAAA
1 ATATAATTTTAAT-AAAATAAA
3374442 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAATTTTAATAAAATAAATA
Found at i:3376106 original size:2 final size:2
Alignment explanation
Indices: 3376099--3376145 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3376089 AGCTATTAAA
3376099 TC TC TC TC TC 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
3376141 TC TC T
1 TC TC T
3376146 ATCTATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3380291 original size:2 final size:2
Alignment explanation
Indices: 3380284--3380326 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3380274 CCCAAGAGTG
3380284 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
3380326 T
1 T
3380327 GAATGGTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3383365 original size:14 final size:14
Alignment explanation
Indices: 3383346--3383376 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3383336 ATTGTCAAAT
*
3383346 TAATATTACAATAA
1 TAATATTAAAATAA
3383360 TAATATTAAAATAA
1 TAATATTAAAATAA
3383374 TAA
1 TAA
3383377 CAAAGTCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATATTAAAATAA
Found at i:3384199 original size:50 final size:50
Alignment explanation
Indices: 3384124--3384416 Score: 354
Period size: 50 Copynumber: 5.9 Consensus size: 50
3384114 ATTATTATTT
*
3384124 ACCAACCTTTGATAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
1 ACCAACCTTTGACAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
* * *
3384174 ACCAACCTTTGACAATCGAGAGAGGTAACCGTAATTGTTGATTATTCTTT
1 ACCAACCTTTGACAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
* * *
3384224 ACTAACCTTTGACAGTCGAGAGAGGTAGTCGTAATTGTTGACTATTCTTC
1 ACCAACCTTTGACAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
* * * * *** *
3384274 ACCAACATTTGATAGTCGAAAGAGGTGGCCGTAATTGTTGACTATTTTTC
1 ACCAACCTTTGACAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
* ** **
3384324 ACCAACCTTTGACAGTCGAGAGAGGTGGTTATAATTGTTGACTATTCTTC
1 ACCAACCTTTGACAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
* * * *
3384374 ACCAACCTTTGACAATAGAGAAATGTGA-CTGTAATTGTTGACT
1 ACCAACCTTTGACAATCGAGAGAGGTAATC-GTAATTGTTGACT
3384417 TTAAGCATAT
Statistics
Matches: 211, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
50 211 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (50 bp):
ACCAACCTTTGACAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTC
Found at i:3384285 original size:100 final size:99
Alignment explanation
Indices: 3384111--3384414 Score: 419
Period size: 100 Copynumber: 3.0 Consensus size: 99
3384101 GCAAAGTGAT
* * *
3384111 TTGATTATTATTTACCAACCTTTGATAATCGAGAGAGGTAATCGTAATTGTTGACTATTCTTCAC
1 TTGATTATT-TTTACCAACCTTTGACAGTCGAGAGAGGTAGTCGTAATTGTTGACTATTCTTCAC
*
3384176 CAACCTTTGACAATCGAGAGAGGTAACCGTAATTG
65 CAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
*
3384211 TTGATTATTCTTTACTAACCTTTGACAGTCGAGAGAGGTAGTCGTAATTGTTGACTATTCTTCAC
1 TTGATTATT-TTTACCAACCTTTGACAGTCGAGAGAGGTAGTCGTAATTGTTGACTATTCTTCAC
* * * * *
3384276 CAACATTTGATAGTCGAAAGAGGTGGCCGTAATTG
65 CAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * **
3384311 TTGACTATTTTTCACCAACCTTTGACAGTCGAGAGAGGTGGTTATAATTGTTGACTATTCTTCAC
1 TTGATTATTTTT-ACCAACCTTTGACAGTCGAGAGAGGTAGTCGTAATTGTTGACTATTCTTCAC
* * * *
3384376 CAACCTTTGACAATAGAGAAATGTGACTGTAATTG
65 CAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
3384411 TTGA
1 TTGA
3384415 CTTTAAGCAT
Statistics
Matches: 178, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 3 0.02
100 175 0.98
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (99 bp):
TTGATTATTTTTACCAACCTTTGACAGTCGAGAGAGGTAGTCGTAATTGTTGACTATTCTTCACC
AACCTTTGACAATCGAGAGAGGTGACCGTAATTG
Found at i:3384690 original size:19 final size:19
Alignment explanation
Indices: 3384654--3384690 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3384644 TGGTTGTCGA
**
3384654 GGTACTGTTCACGTATACG
1 GGTACTGTTCACACATACG
3384673 GGTACTGTTCACACATAC
1 GGTACTGTTCACACATAC
3384691 AGTTACTTGC
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:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (19 bp):
GGTACTGTTCACACATACG
Found at i:3384697 original size:19 final size:19
Alignment explanation
Indices: 3384653--3384697 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3384643 TTGGTTGTCG
**
3384653 AGGTACTGTTCACGTATAC
1 AGGTACTGTTCACACATAC
*
3384672 GGGTACTGTTCACACATAC
1 AGGTACTGTTCACACATAC
*
3384691 AGTTACT
1 AGGTACT
3384698 TGCACGTGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (19 bp):
AGGTACTGTTCACACATAC
Found at i:3388862 original size:50 final size:50
Alignment explanation
Indices: 3388787--3389036 Score: 349
Period size: 50 Copynumber: 5.0 Consensus size: 50
3388777 AAGTGATTTG
* * *
3388787 ACTATTCTTTATCAACCTTTGACAATCAAGAGAGGTGGCCGTAATTGTTA
1 ACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
* * *
3388837 ACTATTCTTTATCAACCTTTGACAATCGAGAGATGTGACCGTAATTGTTG
1 ACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
* * *
3388887 ACTATT-TTTCACCAACCTTTTACAATCGAGAGAGGTGACCATAATTGTTG
1 ACTATTCTTT-ACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
* * *
3388937 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCATAATTATTA
1 ACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
* * *
3388987 ACTATTCTTCACCAACCTTTGACAATAGAGAAAGGTGACCGTAATTGTTA
1 ACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
3389037 CCCCTAAGCA
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 3 0.02
50 177 0.97
51 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (50 bp):
ACTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTA
Found at i:3390305 original size:18 final size:18
Alignment explanation
Indices: 3390282--3390324 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3390272 AGATACGTAT
*
3390282 AAAAAATAT-TAAAAGATG
1 AAAAAATATATAAAAG-TA
3390300 AAAAAA-ATATAAAAGTA
1 AAAAAATATATAAAAGTA
3390317 AAAAAATA
1 AAAAAATA
3390325 GATATGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (18 bp):
AAAAAATATATAAAAGTA
Found at i:3390306 original size:19 final size:16
Alignment explanation
Indices: 3390282--3390324 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 16
3390272 AGATACGTAT
3390282 AAAAAATATTAAAAGATGA
1 AAAAAATA-TAAAAG-T-A
3390301 AAAAAATATAAAAGTA
1 AAAAAATATAAAAGTA
3390317 AAAAAATA
1 AAAAAATA
3390325 GATATGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.38
17 1 0.04
18 6 0.25
19 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
AAAAAATATAAAAGTA
Found at i:3394740 original size:40 final size:39
Alignment explanation
Indices: 3394641--3394740 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
3394631 ATGTAATTAG
* * *
3394641 TTAATTGATATAAATTCTTTTGAGAAGATGGTTTTTATAC
1 TTAATTAATATAAATT-TTTTCAGAAAATGGTTTTTATAC
*** *
3394681 TTAATTAATAATTTTTTTTTTCAGAAAATGATTTTTTATAC
1 TTAATTAAT-ATAAATTTTTTCAGAAAATG-GTTTTTATAC
3394722 TTAATTAATATAAATTTTT
1 TTAATTAATATAAATTTTT
3394741 ATTTGCTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
40 26 0.54
41 22 0.46
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (39 bp):
TTAATTAATATAAATTTTTTCAGAAAATGGTTTTTATAC
Done.