Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 26 of 27
Found at i:3731317 original size:18 final size:19
Alignment explanation
Indices: 3731296--3731335 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3731286 CTGATTAAGA
* *
3731296 TTAATTAAAGATAT-TATT
1 TTAATAAAAAATATATATT
3731314 TTAATAAAAAATATATATT
1 TTAATAAAAAATATATATT
3731333 TTA
1 TTA
3731336 TATCATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TTAATAAAAAATATATATT
Found at i:3732957 original size:16 final size:17
Alignment explanation
Indices: 3732936--3732975 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3732926 TTATTATTAT
*
3732936 TATTATT-AGTTAAAAA
1 TATTATTAAATTAAAAA
3732952 TATTATTAAATTAAAAA
1 TATTATTAAATTAAAAA
*
3732969 AATTATT
1 TATTATT
3732976 CTTAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TATTATTAAATTAAAAA
Found at i:3732969 original size:19 final size:20
Alignment explanation
Indices: 3732947--3732985 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3732937 ATTATTAGTT
3732947 AAAAA-TATTATTAAATTAA
1 AAAAATTATTATTAAATTAA
* *
3732966 AAAAATTATTCTTAATTTAA
1 AAAAATTATTATTAAATTAA
3732986 TCAACTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTATTATTAAATTAA
Found at i:3735035 original size:18 final size:18
Alignment explanation
Indices: 3735012--3735046 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3735002 TAATTAAATA
3735012 TTTATTTTATTATTTAAT
1 TTTATTTTATTATTTAAT
3735030 TTTATTTTATTATTTAA
1 TTTATTTTATTATTTAA
3735047 AAATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTTATTATTTAAT
Found at i:3735200 original size:16 final size:16
Alignment explanation
Indices: 3735179--3735218 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3735169 AATCATCATC
*
3735179 AAAATTAAAATTGAAA
1 AAAATTAAAATTAAAA
3735195 AAAATTAAAATTAAAA
1 AAAATTAAAATTAAAA
3735211 AAAATTAA
1 AAAATTAA
3735219 TTTCTTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAATTAAAATTAAAA
Found at i:3735486 original size:17 final size:18
Alignment explanation
Indices: 3735464--3735499 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3735454 ATGATATTAA
3735464 AATGAT-TTATTACTTTT
1 AATGATGTTATTACTTTT
*
3735481 AATGATGTTATTTCTTTT
1 AATGATGTTATTACTTTT
3735499 A
1 A
3735500 TATTTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (18 bp):
AATGATGTTATTACTTTT
Found at i:3736144 original size:3 final size:3
Alignment explanation
Indices: 3736115--3736165 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
3736105 AAAATTTAAA
* * * *
3736115 AAT AAA AAT AAC AAT AA- AAA AAT -AT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3736161 AAT AA
1 AAT AA
3736166 AGTACTATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:3736146 original size:22 final size:20
Alignment explanation
Indices: 3736112--3736153 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3736102 ACAAAAATTT
3736112 AAAAATAAAAATAACAATAA
1 AAAAATAAAAATAACAATAA
*
3736132 AAAAATATAATAATAATAATAA
1 AAAAATA-AA-AATAACAATAA
3736154 TAGTAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAATAAAAATAACAATAA
Found at i:3750076 original size:19 final size:19
Alignment explanation
Indices: 3750021--3750076 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
3750011 ATGAATGATA
3750021 AAAAATAATATAATTAA-AT
1 AAAAATAA-ATAATTAATAT
* * *
3750040 AAATAT-ATTAATTTATAT
1 AAAAATAAATAATTAATAT
3750058 AAAAATAAATAATTAATAT
1 AAAAATAAATAATTAATAT
3750077 GTTAGAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 15 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATAAATAATTAATAT
Found at i:3765258 original size:30 final size:31
Alignment explanation
Indices: 3765189--3765260 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
3765179 TTATGTTAAG
*
3765189 ATTTATTTAAATATAAAATAAAAAATAAAAA
1 ATTTATTTAGATATAAAATAAAAAATAAAAA
* *
3765220 A-TTATTTAGATA-CAAATTAAAAATAAAAA
1 ATTTATTTAGATATAAAATAAAAAATAAAAA
3765249 ATTTATTTAGAT
1 ATTTATTTAGAT
3765261 GTGATAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.43
30 20 0.54
31 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (31 bp):
ATTTATTTAGATATAAAATAAAAAATAAAAA
Found at i:3765277 original size:29 final size:28
Alignment explanation
Indices: 3765204--3765260 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 28
3765194 TTTAAATATA
3765204 AAATAAAAAATAAAAAATTATTTAGATAC
1 AAAT-AAAAATAAAAAATTATTTAGATAC
3765233 AAATTAAAAATAAAAAATTTATTTAGAT
1 AAA-TAAAAATAAAAAA-TTATTTAGAT
3765261 GTGATAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (28 bp):
AAATAAAAATAAAAAATTATTTAGATAC
Found at i:3773625 original size:10 final size:10
Alignment explanation
Indices: 3773610--3773640 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3773600 TTCGTAATAT
3773610 TCCCCATTTC
1 TCCCCATTTC
3773620 TCCCCATTTC
1 TCCCCATTTC
3773630 TCCCCATTTC
1 TCCCCATTTC
3773640 T
1 T
3773641 TTAGTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.42
Consensus pattern (10 bp):
TCCCCATTTC
Found at i:3785704 original size:2 final size:2
Alignment explanation
Indices: 3785697--3785723 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3785687 ATGAAGTCCC
3785697 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3785724 AACTAACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3785814 original size:3 final size:3
Alignment explanation
Indices: 3785806--3785844 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3785796 CAATTTTAAA
3785806 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3785845 GATGATCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3787510 original size:19 final size:18
Alignment explanation
Indices: 3787486--3787524 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3787476 AATATGAATT
* *
3787486 ATTAAAATATTTAATTTTA
1 ATTAAAA-ATTAAAATTTA
3787505 ATTAAAAATTAAAATTTA
1 ATTAAAAATTAAAATTTA
3787523 AT
1 AT
3787525 AGTTGAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAAAATTAAAATTTA
Found at i:3795265 original size:21 final size:21
Alignment explanation
Indices: 3795240--3795279 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3795230 TACTTGTATT
3795240 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
3795261 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
3795280 AATTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:3796900 original size:7 final size:7
Alignment explanation
Indices: 3796888--3796913 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3796878 ATTTTTAAAT
3796888 TAAAAAA
1 TAAAAAA
3796895 TAAAAAA
1 TAAAAAA
3796902 TAAAAAA
1 TAAAAAA
3796909 TAAAA
1 TAAAA
3796914 CCTCACCCAC
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:3797263 original size:22 final size:24
Alignment explanation
Indices: 3797201--3797265 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 24
3797191 GTACTTAGGT
3797201 AAATATTTAAATAAATATGTATAAA
1 AAATATTTAAATAAAT-TGTATAAA
** **
3797226 AAATTAAGTATTTAAATT-T-TAAA
1 AAA-TATTTAAATAAATTGTATAAA
3797249 AAATATTTAAATAAATT
1 AAATATTTAAATAAATT
3797266 AATATTAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
22 10 0.32
23 7 0.23
24 1 0.03
25 4 0.13
26 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
AAATATTTAAATAAATTGTATAAA
Found at i:3797905 original size:22 final size:22
Alignment explanation
Indices: 3797877--3797919 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3797867 ATTTTATTGT
3797877 ATTTAAATAATTTTTAATTTAA
1 ATTTAAATAATTTTTAATTTAA
* *
3797899 ATTTAAATGATTTTTATTTTA
1 ATTTAAATAATTTTTAATTTA
3797920 GAAGAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTAAATAATTTTTAATTTAA
Found at i:3799726 original size:2 final size:2
Alignment explanation
Indices: 3799719--3799764 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
3799709 ATTATATTAC
* *
3799719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GAT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
3799762 AT A
1 AT A
3799765 CGAAAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3800671 original size:37 final size:36
Alignment explanation
Indices: 3800574--3800677 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 36
3800564 AGTCGTTATT
* * *
3800574 AAATTGATTAAAT-TAAATTAAATTTATTTATTTTAA
1 AAATTAATTAATTATAAATT-AATTTATTAATTTTAA
** *
3800610 AAATTAATTAATTATAAAAAAATTTATTAATTTTTA
1 AAATTAATTAATTATAAATTAATTTATTAATTTTAA
*
3800646 AAATTAA-TAATTGAATAAATTAATTTTTTAAT
1 AAATTAATTAATT--ATAAATTAATTTATTAAT
3800678 AATATTTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
35 5 0.09
36 32 0.57
37 19 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (36 bp):
AAATTAATTAATTATAAATTAATTTATTAATTTTAA
Found at i:3800695 original size:14 final size:14
Alignment explanation
Indices: 3800676--3800780 Score: 52
Period size: 14 Copynumber: 8.1 Consensus size: 14
3800666 TAATTTTTTA
3800676 ATAATATTTTATAT
1 ATAATATTTTATAT
3800690 ATAATA---TATA-
1 ATAATATTTTATAT
3800700 A-AATATTTT-TAT
1 ATAATATTTTATAT
* *
3800712 ATAATAATTTAAAT
1 ATAATATTTTATAT
*
3800726 ATAA-A-TATA-AT
1 ATAATATTTTATAT
* *
3800737 ATATTACTTATATTAT
1 ATAATA-TTTTA-TAT
*
3800753 ATAATATTGTA-AT
1 ATAATATTTTATAT
3800766 AATAAT-TTTTATAT
1 -ATAATATTTTATAT
3800780 A
1 A
3800781 AAAATAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 27
0.68 0.07 0.26
Matches are distributed among these distances:
9 4 0.06
10 1 0.01
11 11 0.15
12 6 0.08
13 15 0.21
14 23 0.32
15 4 0.06
16 7 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (14 bp):
ATAATATTTTATAT
Found at i:3800701 original size:37 final size:35
Alignment explanation
Indices: 3800670--3800741 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
3800660 ATAAATTAAT
* *
3800670 TTTTTA-ATAATATTTTATATATAATATATAAAATA
1 TTTTTATATAATAATTTAAATATAA-ATATAAAATA
*
3800705 TTTTTATATAATAATTTAAATATAAATATAATATA
1 TTTTTATATAATAATTTAAATATAAATATAAAATA
3800740 TT
1 TT
3800742 ACTTATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTTTATATAATAATTTAAATATAAATATAAAATA
Found at i:3800748 original size:36 final size:36
Alignment explanation
Indices: 3800676--3800749 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
3800666 TAATTTTTTA
* * *
3800676 ATAATATTTTATATATAATATATAAAATATTTTTAT
1 ATAATAATTTAAATATAATATATAAAATATTCTTAT
*
3800712 ATAATAATTTAAATATAA-ATATAATATATTACTTAT
1 ATAATAATTTAAATATAATATATAAAATATT-CTTAT
3800748 AT
1 AT
3800750 TATATAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (36 bp):
ATAATAATTTAAATATAATATATAAAATATTCTTAT
Found at i:3803391 original size:18 final size:18
Alignment explanation
Indices: 3803368--3803411 Score: 81
Period size: 17 Copynumber: 2.5 Consensus size: 18
3803358 GTTGCTAATT
3803368 TTTTATTTTTTTACTATA
1 TTTTATTTTTTTACTATA
3803386 TTTTA-TTTTTTACTATA
1 TTTTATTTTTTTACTATA
3803403 TTTTATTTT
1 TTTTATTTT
3803412 AAGAGCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTACTATA
Found at i:3803608 original size:2 final size:2
Alignment explanation
Indices: 3803601--3803631 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3803591 CTGCTTTAGC
*
3803601 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3803632 GTCGTACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3805611 original size:15 final size:13
Alignment explanation
Indices: 3805566--3805604 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3805556 AATAAAGAGA
3805566 TAATTTTTTTATTT
1 TAATTTTTTT-TTT
*
3805580 CTCATTTTTTTTTT
1 -TAATTTTTTTTTT
3805594 TAATTTTTTTT
1 TAATTTTTTTT
3805605 CCTTTAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 3 0.14
15 9 0.41
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (13 bp):
TAATTTTTTTTTT
Found at i:3805959 original size:24 final size:23
Alignment explanation
Indices: 3805921--3805965 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
3805911 TATTATTATT
3805921 AAAATTTATATAAAATATATAAA
1 AAAATTTATATAAAATATATAAA
*
3805944 AAAATTTAATATAAAATGTATA
1 AAAATTT-ATATAAAATATATA
3805966 GTACTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATTTATATAAAATATATAAA
Found at i:3806419 original size:20 final size:20
Alignment explanation
Indices: 3806388--3806436 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3806378 AGAAAGAATT
*
3806388 GAAGAAGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
3806408 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
3806428 GAAGAGGGA
1 GAAGAGGGA
3806437 GCCTCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.45, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:3806577 original size:27 final size:27
Alignment explanation
Indices: 3806513--3806583 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
3806503 AAACAAGCCT
* *
3806513 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
3806541 CCATTTTTGACAAACACAAA-ATAATCA
1 CCATTTTTGACAAACACAAAGA-AACCA
3806568 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
3806584 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:3808505 original size:21 final size:22
Alignment explanation
Indices: 3808467--3808512 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3808457 ATCTGTTGAA
* **
3808467 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3808488 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3808510 ACT
1 ACT
3808513 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:3810982 original size:20 final size:20
Alignment explanation
Indices: 3810954--3811002 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3810944 AGAAAGAATT
3810954 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
3810974 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
3810994 GAAGAGGGA
1 GAAGAGGGA
3811003 GCCTCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:3811922 original size:3 final size:3
Alignment explanation
Indices: 3811914--3811945 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3811904 ACATTTGATA
3811914 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3811946 ATCAACTTAT
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:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3814941 original size:3 final size:3
Alignment explanation
Indices: 3814933--3814966 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3814923 GATATTCTAT
3814933 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3814967 AACATACGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3815784 original size:2 final size:2
Alignment explanation
Indices: 3815777--3815808 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3815767 ATACAATAAG
3815777 AT AT AT AT AT AT 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 AT
3815809 GGAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3819270 original size:21 final size:21
Alignment explanation
Indices: 3819244--3819297 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3819234 AATAATTAAA
3819244 TATTATATATATTTTTAT-AT
1 TATTATATATATTTTTATGAT
* *
3819264 GTATTATATTTATATTTATGAT
1 -TATTATATATATTTTTATGAT
3819286 T-TTA-ATATATTT
1 TATTATATATATTT
3819298 AATAATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 3 0.11
21 17 0.61
22 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TATTATATATATTTTTATGAT
Found at i:3820149 original size:2 final size:2
Alignment explanation
Indices: 3820142--3820168 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3820132 TCAAGATTGC
3820142 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3820169 ATAATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3820234 original size:20 final size:21
Alignment explanation
Indices: 3820207--3820266 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
3820197 TATTATATTA
**
3820207 AAAT-AATTATT-TTTTTTAT
1 AAATAAATTATTATTTTAAAT
3820226 AAATAAATTATTATTTTAAAT
1 AAATAAATTATTATTTTAAAT
*
3820247 AAA-AAATTATACATTTTAAA
1 AAATAAATTAT-TATTTTAAA
3820267 ATTTAAATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.11
20 14 0.40
21 17 0.49
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATAAATTATTATTTTAAAT
Found at i:3829591 original size:1 final size:1
Alignment explanation
Indices: 3829585--3829612 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3829575 CAAAGTAATT
3829585 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
3829613 AAACGACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3831871 original size:3 final size:3
Alignment explanation
Indices: 3831857--3831906 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
3831847 TGACCATTTC
3831857 CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3831904 CTT
1 CTT
3831907 TTCCTAAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:3832238 original size:2 final size:2
Alignment explanation
Indices: 3832199--3832226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3832189 GAGGTTTGAA
3832199 AT AT AT AT 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
3832227 TTCAGATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3836127 original size:16 final size:16
Alignment explanation
Indices: 3836106--3836139 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3836096 TAACATATAT
3836106 ATATATATATACACAC
1 ATATATATATACACAC
*
3836122 ATATATATATACGCAC
1 ATATATATATACACAC
3836138 AT
1 AT
3836140 GAATGGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATATATATACACAC
Found at i:3842665 original size:28 final size:28
Alignment explanation
Indices: 3842599--3842665 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
3842589 TAAAAATTAC
* *
3842599 GTAAAATCATATAAAAATAATTTAAATTA
1 GTAAAAT-ATATAAAAATAATTAAAATGA
*
3842628 -TAATATTATATAAAAAATAA-TAAAATGA
1 GTAA-AATATAT-AAAAATAATTAAAATGA
3842656 GTAAAATATA
1 GTAAAATATA
3842666 AATATATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
GTAAAATATATAAAAATAATTAAAATGA
Found at i:3842783 original size:20 final size:20
Alignment explanation
Indices: 3842758--3842801 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3842748 TAAATAAAAT
*
3842758 TAATTATTAT-ATTTAATATA
1 TAATTATTATAAATT-ATATA
3842778 TAATTATTATAAATTATATA
1 TAATTATTATAAATTATATA
3842798 TAAT
1 TAAT
3842802 AAAAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTATTATAAATTATATA
Found at i:3843988 original size:2 final size:2
Alignment explanation
Indices: 3843981--3844019 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3843971 AAGCATAGCC
3843981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3844020 GCGTAGCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3844313 original size:2 final size:2
Alignment explanation
Indices: 3844306--3844337 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3844296 AATCAAAACA
*
3844306 CT CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3844338 TATTTTGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3849019 original size:34 final size:34
Alignment explanation
Indices: 3848955--3849019 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
3848945 TAACTATTTT
* * * *
3848955 ATTATTTATTTATATATATAATCTATATGATGTC
1 ATTATATATATATATATAAAATCTAAATGATGTC
3848989 ATTATATATATATATATAAAAT-TAAAATGAT
1 ATTATATATATATATATAAAATCT-AAATGAT
3849020 ATTCTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 1 0.04
34 25 0.96
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (34 bp):
ATTATATATATATATATAAAATCTAAATGATGTC
Found at i:3858825 original size:3 final size:3
Alignment explanation
Indices: 3858819--3858845 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3858809 TTTGGAGGAG
3858819 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
3858846 AGTAGCGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3859203 original size:13 final size:13
Alignment explanation
Indices: 3859185--3859214 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3859175 TGCGGCTGAA
*
3859185 GTTTTTTTTGTTT
1 GTTTTTTATGTTT
3859198 GTTTTTTATGTTT
1 GTTTTTTATGTTT
3859211 GTTT
1 GTTT
3859215 GTTGGTAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (13 bp):
GTTTTTTATGTTT
Found at i:3862174 original size:2 final size:2
Alignment explanation
Indices: 3862167--3862210 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3862157 CAAGTTCAAC
* * *
3862167 CT CT CT CT CC CT CT CT CT CC CT CT CT CT CT CT CG CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3862209 CT
1 CT
3862211 GGCTAATGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.55, G:0.02, T:0.43
Consensus pattern (2 bp):
CT
Found at i:3865555 original size:40 final size:40
Alignment explanation
Indices: 3865502--3865593 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 40
3865492 ATTATAGTAA
*
3865502 TTAATAATTATTTT-AAAAATTTAAAAATAAAATATTATTT
1 TTAATAATTATTTTAAAAAAATTAAAAATAAAAT-TTATTT
*
3865542 TTAATAATTATTTTTAAAAAAATTAAAAATAATATTTATTT
1 TTAATAATTA-TTTTAAAAAAATTAAAAATAAAATTTATTT
*
3865583 ATAAT-ATTATT
1 TTAATAATTATT
3865594 AAATTAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
39 2 0.04
40 14 0.30
41 14 0.30
42 17 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
TTAATAATTATTTTAAAAAAATTAAAAATAAAATTTATTT
Found at i:3865593 original size:16 final size:16
Alignment explanation
Indices: 3865569--3865638 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
3865559 AAAAATTAAA
* *
3865569 AATAATATTTATTTAT
1 AATATTATTAATTTAT
* *
3865585 AATATTATTAAATTAAA
1 AATATTATT-AATTTAT
*
3865602 AATATTATTAATTTTT
1 AATATTATTAATTTAT
* *
3865618 AAAATTATTAAATTTAA
1 AATATTATT-AATTTAT
3865635 AATA
1 AATA
3865639 AAAATAATAT
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 20 0.49
17 21 0.51
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTATTAATTTAT
Found at i:3865601 original size:42 final size:42
Alignment explanation
Indices: 3865503--3865608 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
3865493 TTATAGTAAT
* *
3865503 TAATAATTATT-TT-AAAAATTTAAAAATAAAATATTATTTT
1 TAATAATTATTATTAAAAAAATTAAAAATAAAATATTATTTA
* *
3865543 TAATAATTATTTTTAAAAAAATTAAAAATAATAT-TTATTTA
1 TAATAATTATTATTAAAAAAATTAAAAATAAAATATTATTTA
*
3865584 TAAT-ATTATTAAATTAAAAATATTA
1 TAATAATTATT--ATTAAAAAAATTA
3865609 TTAATTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
40 17 0.30
41 12 0.21
42 28 0.49
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (42 bp):
TAATAATTATTATTAAAAAAATTAAAAATAAAATATTATTTA
Found at i:3865603 original size:33 final size:33
Alignment explanation
Indices: 3865561--3865639 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
3865551 ATTTTTAAAA
* *
3865561 AAATTAAAAATAATATTTATTTATAATATTATT
1 AAATTAAAAATAATATTAATTTATAAAATTATT
* *
3865594 AAATTAAAAATATTATTAATTTTTAAAATTATT
1 AAATTAAAAATAATATTAATTTATAAAATTATT
*
3865627 AAATTTAAAATAA
1 AAATTAAAAATAA
3865640 AAATAATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AAATTAAAAATAATATTAATTTATAAAATTATT
Found at i:3865607 original size:17 final size:17
Alignment explanation
Indices: 3865561--3865638 Score: 79
Period size: 16 Copynumber: 4.7 Consensus size: 17
3865551 ATTTTTAAAA
* *
3865561 AAATTAAAAATAATATT
1 AAATTTAAAATATTATT
* *
3865578 -TATTTATAATATTATT
1 AAATTTAAAATATTATT
*
3865594 AAATTAAAAATATTATT
1 AAATTTAAAATATTATT
* *
3865611 AATTTTTAAA-ATTATT
1 AAATTTAAAATATTATT
3865627 AAATTTAAAATA
1 AAATTTAAAATA
3865639 AAAATAATAT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
16 26 0.55
17 21 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTTAAAATATTATT
Found at i:3866224 original size:21 final size:21
Alignment explanation
Indices: 3866183--3866223 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3866173 ATTTTAATAT
*
3866183 TTATAATTTTTTATCTTAAAA
1 TTATAATTTTTTATCTAAAAA
*
3866204 TTATAATTTTTT-TGTAAAAA
1 TTATAATTTTTTATCTAAAAA
3866224 AAAATCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATAATTTTTTATCTAAAAA
Found at i:3867943 original size:27 final size:27
Alignment explanation
Indices: 3867913--3867973 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
3867903 TTTAATAAAT
*
3867913 AATATAATATA-ATTTATAATA-ATGGTA
1 AATATAATATATATTGATAATATAT--TA
* *
3867940 AATAGATTATATATTGATAATATATTA
1 AATATAATATATATTGATAATATATTA
3867967 AATATAA
1 AATATAA
3867974 ATTTATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
27 16 0.59
28 9 0.33
29 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
AATATAATATATATTGATAATATATTA
Found at i:3867999 original size:22 final size:22
Alignment explanation
Indices: 3867947--3867999 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3867937 GTAAATAGAT
* *
3867947 TATATATTGATAATATATTAAA
1 TATATATTTATAAAATATTAAA
*
3867969 TATAAATTTATAAAAT-TTAAAA
1 TATATATTTATAAAATATT-AAA
3867991 TATATATTT
1 TATATATTT
3868000 GATGTACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATATATTTATAAAATATTAAA
Found at i:3876555 original size:3 final size:3
Alignment explanation
Indices: 3876547--3876579 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3876537 GATCGAGAAA
3876547 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3876580 TAGTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3879799 original size:24 final size:24
Alignment explanation
Indices: 3879763--3879819 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
3879753 AACTTCTACA
*
3879763 ATAATTTTAATTTTTTTTTGTGAT
1 ATAATTTTAATTTTTTGTTGTGAT
*
3879787 ATAATTCTT-ATTTTTTGTTGTTAT
1 ATAATT-TTAATTTTTTGTTGTGAT
3879811 AT-ATTTTAA
1 ATAATTTTAA
3879820 CAAGTGATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 21 0.72
25 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (24 bp):
ATAATTTTAATTTTTTGTTGTGAT
Found at i:3885037 original size:61 final size:61
Alignment explanation
Indices: 3884945--3885062 Score: 186
Period size: 61 Copynumber: 1.9 Consensus size: 61
3884935 GTTTTTGGGC
3884945 GTTTGATTTAATGATAAACATATAAT-TTTTTTTTATTT-GAAAGAAGTAATTTAATTTGGAT
1 GTTTGATTTAATGATAAACATATAATATTTTTTTTATTTAG-AA-AAGTAATTTAATTTGGAT
* *
3885006 GTTTGATTTAATGATGAACATATAATATTTTTTTTATTTAGAAAATTAATTTAATTT
1 GTTTGATTTAATGATAAACATATAATATTTTTTTTATTTAGAAAAGTAATTTAATTT
3885063 TTTTGCCAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 38 0.72
62 14 0.26
63 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (61 bp):
GTTTGATTTAATGATAAACATATAATATTTTTTTTATTTAGAAAAGTAATTTAATTTGGAT
Found at i:3889657 original size:3 final size:3
Alignment explanation
Indices: 3889649--3889684 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3889639 AGGAAGCACT
3889649 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3889685 CATTAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3897844 original size:19 final size:19
Alignment explanation
Indices: 3897816--3897855 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3897806 ATATTTTTAT
3897816 AAAATATAATAAAATAATAA
1 AAAATATAATAAAATAA-AA
*
3897836 AAAAT-TAATATAATAAAA
1 AAAATATAATAAAATAAAA
3897854 AA
1 AA
3897856 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATATAATAAAATAAAA
Found at i:3898239 original size:2 final size:2
Alignment explanation
Indices: 3898232--3898258 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3898222 ATTTACATTT
3898232 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 T
3898259 GTCTTGCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3899363 original size:35 final size:37
Alignment explanation
Indices: 3899310--3899389 Score: 137
Period size: 35 Copynumber: 2.2 Consensus size: 37
3899300 AAGCAATGTT
*
3899310 AGTTTTCTGATCCAATAACCAATTTTTTTAAGTTCCC
1 AGTTTTCTGATCCAATAACCAATTTTTATAAGTTCCC
3899347 AGTTTTCT-A-CCAATAACCAATTTTTATAAGTTCCC
1 AGTTTTCTGATCCAATAACCAATTTTTATAAGTTCCC
3899382 AGTTTTCT
1 AGTTTTCT
3899390 CCTCTGTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
35 33 0.79
36 1 0.02
37 8 0.19
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (37 bp):
AGTTTTCTGATCCAATAACCAATTTTTATAAGTTCCC
Found at i:3904661 original size:2 final size:2
Alignment explanation
Indices: 3904654--3904684 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3904644 TTAAAATGAA
3904654 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3904685 TTAACAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3909154 original size:17 final size:18
Alignment explanation
Indices: 3909128--3909169 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3909118 TGTAAATATT
*
3909128 AAATATAAATATTTTATA
1 AAATATAAATAATTTATA
3909146 AAATA-AAATAATTTATA
1 AAATATAAATAATTTATA
*
3909163 TAATATA
1 AAATATA
3909170 TTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATAAATAATTTATA
Found at i:3909159 original size:18 final size:19
Alignment explanation
Indices: 3909123--3909170 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
3909113 TTAGGTGTAA
*
3909123 ATATTAAATATAAATATTT
1 ATATAAAATATAAATATTT
3909142 -TATAAAATA-AAATAATTT
1 ATATAAAATATAAAT-ATTT
*
3909160 ATATAATATAT
1 ATATAAAATAT
3909171 TATTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAAAATATAAATATTT
Found at i:3909213 original size:3 final size:3
Alignment explanation
Indices: 3909168--3909194 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3909158 TTATATAATA
3909168 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3909195 CGATTGTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3920352 original size:16 final size:15
Alignment explanation
Indices: 3920322--3920366 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
3920312 TTATTATTCA
3920322 ATATTAT-TAAATTT
1 ATATTATATAAATTT
3920336 A-ATTTATATATAATTT
1 ATA-TTATATA-AATTT
3920352 ATATTATATAAATTT
1 ATATTATATAAATTT
3920367 TTATATCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 5 0.19
15 7 0.26
16 13 0.48
17 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATATAAATTT
Found at i:3923119 original size:37 final size:36
Alignment explanation
Indices: 3923063--3923136 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
3923053 CTTCTGGAAA
* *
3923063 TAGTTTATATTCTCCTCTAGGTTT-TAAGGGTAATTGG
1 TAGTTCATATGCTCCTCTAGGTTTGT--GGGTAATTGG
*
3923100 TAGTTCATATGCTCTTCTAGGTTTGTGGGTAATTGG
1 TAGTTCATATGCTCCTCTAGGTTTGTGGGTAATTGG
3923136 T
1 T
3923137 GTATTAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.33
37 21 0.64
38 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46
Consensus pattern (36 bp):
TAGTTCATATGCTCCTCTAGGTTTGTGGGTAATTGG
Found at i:3926080 original size:3 final size:3
Alignment explanation
Indices: 3926072--3926097 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3926062 AATGCAAAGA
3926072 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3926098 GAGAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3926280 original size:14 final size:15
Alignment explanation
Indices: 3926261--3926289 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3926251 TACTCTCGTC
3926261 TTTTTCTTTT-TTTT
1 TTTTTCTTTTCTTTT
3926275 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
3926290 CTATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTCTTTT
Found at i:3926336 original size:3 final size:3
Alignment explanation
Indices: 3926328--3926361 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3926318 AATCAAGGCT
3926328 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3926362 AAACTTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3932870 original size:2 final size:2
Alignment explanation
Indices: 3932863--3932895 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3932853 AGGGGAAAGT
*
3932863 GA GA GA GA GA GA TA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3932896 GAAGTGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
GA
Found at i:3934413 original size:2 final size:2
Alignment explanation
Indices: 3934408--3934433 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3934398 TCGGTTACAA
3934408 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3934434 TAATAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3938494 original size:5 final size:5
Alignment explanation
Indices: 3938484--3938511 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3938474 TAGTACTAGT
3938484 AATTG AATTG AATTG AATTG AATTG AAT
1 AATTG AATTG AATTG AATTG AATTG AAT
3938512 GTCTGTGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (5 bp):
AATTG
Found at i:3939641 original size:3 final size:3
Alignment explanation
Indices: 3939633--3939675 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
3939623 TGCTTCTGTG
* *
3939633 TTA TTA TTA TTA TAA TTA TTA TTG TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3939676 CCGATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3941235 original size:2 final size:2
Alignment explanation
Indices: 3941228--3941260 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3941218 TTGCTTTCCA
3941228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3941261 AAATATAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3943066 original size:28 final size:28
Alignment explanation
Indices: 3943034--3943109 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
3943024 AATGCCACCT
3943034 TTTGTATTTGTCAAATATGGTAGTTTCC
1 TTTGTATTTGTCAAATATGGTAGTTTCC
* *
3943062 TTTGTATTTGTCAAATATGGTGGTTTCT
1 TTTGTATTTGTCAAATATGGTAGTTTCC
*
3943090 TTTGGATTTGTCAAATATGG
1 TTTGTATTTGTCAAATATGG
3943110 AGGCTTGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (28 bp):
TTTGTATTTGTCAAATATGGTAGTTTCC
Found at i:3943129 original size:25 final size:26
Alignment explanation
Indices: 3943038--3943129 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
3943028 CCACCTTTTG
* *
3943038 TATTTGTCAAATATGGTA-GTTTCCTTT
1 TATTTGTCAAATATGG-AGGCTT-CGTT
* * *
3943065 GTATTTGTCAAATATGGTGGTTTCTTT
1 -TATTTGTCAAATATGGAGGCTTCGTT
3943092 TGGATTTGTCAAATATGGAGGCTT-GTT
1 T--ATTTGTCAAATATGGAGGCTTCGTT
3943119 TATTTGTCAAA
1 TATTTGTCAAA
3943130 ATTTGTGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.18
26 1 0.02
27 7 0.12
28 39 0.68
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.48
Consensus pattern (26 bp):
TATTTGTCAAATATGGAGGCTTCGTT
Found at i:3943212 original size:20 final size:20
Alignment explanation
Indices: 3943187--3943232 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3943177 AAATAGAGGC
*
3943187 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
3943207 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
3943227 TCCCTC
1 TCCCTC
3943233 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:3945714 original size:21 final size:22
Alignment explanation
Indices: 3945685--3945730 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3945675 TGTTCAGACA
** *
3945685 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
3945707 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
3945728 AGT
1 AGT
3945731 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:3947666 original size:28 final size:28
Alignment explanation
Indices: 3947634--3947711 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
3947624 CAAATGCCAC
3947634 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
3947662 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
3947690 CCTTTGGATTTGTCAAATATGG
1 CCTTTGTATTTGTCAAATATGG
3947712 AGGCTTGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTAGTTT
Found at i:3947731 original size:25 final size:26
Alignment explanation
Indices: 3947640--3947731 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 26
3947630 CCACCCTTTG
*
3947640 TATTTGTCAAATATGGTA-GTTTCCTTT
1 TATTTGTCAAATATGG-AGGCTTCC-TT
* *
3947667 GTATTTGTCAAATATGGTGGTTTCCTT
1 -TATTTGTCAAATATGGAGGCTTCCTT
*
3947694 TGGATTTGTCAAATATGGAGGCTT-GTT
1 T--ATTTGTCAAATATGGAGGCTTCCTT
3947721 TATTTGTCAAA
1 TATTTGTCAAA
3947732 ATTTGTGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.18
26 1 0.02
27 5 0.09
28 41 0.72
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.47
Consensus pattern (26 bp):
TATTTGTCAAATATGGAGGCTTCCTT
Found at i:3947814 original size:20 final size:20
Alignment explanation
Indices: 3947789--3947834 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3947779 AAATAGAGGC
*
3947789 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
3947809 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
3947829 TCCCTC
1 TCCCTC
3947835 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:3948216 original size:12 final size:14
Alignment explanation
Indices: 3948199--3948232 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3948189 AGAAAATTCA
* *
3948199 ATATATAAATATAT
1 ATATATACACATAT
3948213 ATATATACACATAT
1 ATATATACACATAT
3948227 ATATAT
1 ATATAT
3948233 TTAGTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATACACATAT
Found at i:3948218 original size:14 final size:16
Alignment explanation
Indices: 3948199--3948232 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3948189 AGAAAATTCA
3948199 ATATATA-A-ATATAT
1 ATATATACACATATAT
3948213 ATATATACACATATAT
1 ATATATACACATATAT
3948229 ATAT
1 ATAT
3948233 TTAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATACACATATAT
Found at i:3955279 original size:3 final size:3
Alignment explanation
Indices: 3955271--3955305 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3955261 GAATGTCAAT
3955271 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3955306 TCTCTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3956130 original size:2 final size:2
Alignment explanation
Indices: 3956123--3956165 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3956113 TGAAAGTGTG
3956123 AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
3956165 A
1 A
3956166 CACACACACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3956170 original size:2 final size:2
Alignment explanation
Indices: 3956165--3956197 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3956155 ATATATATAT
*
3956165 AC AC AC AC AC AC AC AC AC AC AC AA AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3956198 TAGATTGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3956963 original size:2 final size:2
Alignment explanation
Indices: 3956956--3956994 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3956946 CATGTGATTT
3956956 TA 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 TA T
3956995 TAATTTGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3961834 original size:2 final size:2
Alignment explanation
Indices: 3961829--3961853 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3961819 CCCCCCCCCC
3961829 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3961854 GTCATTTTCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3961924 original size:2 final size:2
Alignment explanation
Indices: 3961917--3961955 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3961907 TTGTCATTTC
* *
3961917 CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CC CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3961956 CAATCTCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:3965282 original size:5 final size:5
Alignment explanation
Indices: 3965272--3965296 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3965262 CTGTGGAGTG
3965272 TGGAC TGGAC TGGAC TGGAC TGGAC
1 TGGAC TGGAC TGGAC TGGAC TGGAC
3965297 GACCAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
TGGAC
Found at i:3966704 original size:2 final size:2
Alignment explanation
Indices: 3966693--3966726 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3966683 CCAAATCAGC
3966693 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3966727 CCTACGTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3967780 original size:6 final size:6
Alignment explanation
Indices: 3967746--3967776 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3967736 TTATGCCTAT
3967746 ATATAA ATATAA ATATAA ATATAA ATTATAA
1 ATATAA ATATAA ATATAA ATATAA A-TATAA
3967777 TTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:3968159 original size:2 final size:2
Alignment explanation
Indices: 3968152--3968178 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3968142 AGAGCCGAGA
3968152 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3968179 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3968183 original size:2 final size:2
Alignment explanation
Indices: 3968178--3968204 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3968168 ATATATATAT
3968178 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 A
3968205 AGGATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3968336 original size:2 final size:2
Alignment explanation
Indices: 3968329--3968353 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3968319 GCCTTTGGCT
3968329 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
3968354 GCTGAATAAT
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:3968675 original size:28 final size:28
Alignment explanation
Indices: 3968644--3968700 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3968634 TATTTTGTCG
3968644 TCTTCATATATTTTCCTTATTATAATTT
1 TCTTCATATATTTTCCTTATTATAATTT
* **
3968672 TCTTCATATGTTTTTTTTATTATAATTT
1 TCTTCATATATTTTCCTTATTATAATTT
3968700 T
1 T
3968701 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.65
Consensus pattern (28 bp):
TCTTCATATATTTTCCTTATTATAATTT
Found at i:3970174 original size:2 final size:2
Alignment explanation
Indices: 3970167--3970207 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3970157 GAGGAAAGAC
* *
3970167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3970208 ATGGGACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3976447 original size:2 final size:2
Alignment explanation
Indices: 3976440--3976482 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3976430 ATTCCAAAGG
* *
3976440 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3976481 AT
1 AT
3976483 CAATGTTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:3977214 original size:2 final size:2
Alignment explanation
Indices: 3977207--3977234 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3977197 TTTAATAGGA
3977207 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3977235 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3978440 original size:3 final size:3
Alignment explanation
Indices: 3978432--3978457 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3978422 TTATAAAACA
3978432 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3978458 GGTAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3984409 original size:11 final size:12
Alignment explanation
Indices: 3984361--3984447 Score: 54
Period size: 13 Copynumber: 7.2 Consensus size: 12
3984351 TCAAAAGGCC
3984361 ATAAAATATTAT
1 ATAAAATATTAT
*
3984373 AAAAAAATATTATTT
1 -ATAAAATATTA--T
*
3984388 TTAAAATATTAT
1 ATAAAATATTAT
3984400 ATAAAA-ATTAT
1 ATAAAATATTAT
* * *
3984411 -TTAAATTTTTT
1 ATAAAATATTAT
* *
3984422 ATACAATTATAAT
1 ATA-AAATATTAT
3984435 ATAAAAT-TTAT
1 ATAAAATATTAT
3984446 AT
1 AT
3984448 TTAAATTAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
10 4 0.07
11 13 0.24
12 10 0.18
13 18 0.33
14 9 0.16
15 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAAAATATTAT
Found at i:4001964 original size:2 final size:2
Alignment explanation
Indices: 4001959--4001994 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4001949 ACACACACAC
4001959 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
4001995 TACTAGTGTC
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4005345 original size:14 final size:15
Alignment explanation
Indices: 4005328--4005363 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4005318 AAAAAAAAAA
4005328 ATATTTATG-TATTT
1 ATATTTATGTTATTT
4005342 ATATTTATGTTATTT
1 ATATTTATGTTATTT
*
4005357 TTATTTA
1 ATATTTA
4005364 AAATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
ATATTTATGTTATTT
Found at i:4005426 original size:14 final size:14
Alignment explanation
Indices: 4005403--4005441 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
4005393 ATATTAATAA
4005403 ATTTTT-TATGTAT
1 ATTTTTATATGTAT
4005416 ATTTTTATATGTAT
1 ATTTTTATATGTAT
4005430 ATATATTTATAT
1 AT-T-TTTATAT
4005442 CATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 1 0.04
16 7 0.30
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (14 bp):
ATTTTTATATGTAT
Found at i:4005464 original size:17 final size:16
Alignment explanation
Indices: 4005413--4005468 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
4005403 ATTTTTTATG
4005413 TATATTTTTATATGTA
1 TATATTTTTATATGTA
* *
4005429 TATATATTTATATCATA
1 TATATTTTTATAT-GTA
*
4005446 TATATTTTTTTATGT-
1 TATATTTTTATATGTA
4005461 TATATTTT
1 TATATTTT
4005469 AAATATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 8 0.24
16 13 0.38
17 13 0.38
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (16 bp):
TATATTTTTATATGTA
Found at i:4005955 original size:16 final size:17
Alignment explanation
Indices: 4005931--4005963 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4005921 ATTTTTATTA
*
4005931 AAAATAATTACAAATAT
1 AAAATAATTAAAAATAT
4005948 AAAA-AATTAAAAATAT
1 AAAATAATTAAAAATAT
4005964 TATTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAATTAAAAATAT
Found at i:4006605 original size:15 final size:16
Alignment explanation
Indices: 4006584--4006639 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
4006574 ATTTTTAAAT
4006584 AAATTTTATTAATT-A
1 AAATTTTATTAATTAA
*
4006599 TAATTTTATTTAATTAA
1 AAATTTTA-TTAATTAA
* *
4006616 AAATTTTATAAATATTA
1 AAATTTTATTAAT-TAA
4006633 AAATTTT
1 AAATTTT
4006640 CCGGGAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.21
16 10 0.29
17 17 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTTTATTAATTAA
Found at i:4015732 original size:28 final size:26
Alignment explanation
Indices: 4015674--4015763 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 26
4015664 CACCCATTTG
4015674 TTTGTCAAAAATGGTGGTTATTTTGTG-
1 TTTGTCAAAAATGGTGGTT-TTTTG-GA
4015701 TTTGTCAAAAATGGTGGTTTCCTTTGGA
1 TTTGTCAAAAATGGTGGTTT--TTTGGA
* *
4015729 TTTGTCAAATATGGAGGTTTGTTT--A
1 TTTGTCAAAAATGGTGGTTT-TTTGGA
4015754 TTTGTCAAAA
1 TTTGTCAAAA
4015764 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.18
26 1 0.02
27 23 0.41
28 22 0.39
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (26 bp):
TTTGTCAAAAATGGTGGTTTTTTGGA
Found at i:4017570 original size:2 final size:2
Alignment explanation
Indices: 4017563--4017601 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4017553 GCTTGAAATG
4017563 TC TC TC 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
4017602 TTTTTTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4020603 original size:14 final size:14
Alignment explanation
Indices: 4020584--4020611 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4020574 TGGGAGAAGG
4020584 TATGTAAACTTCCA
1 TATGTAAACTTCCA
4020598 TATGTAAACTTCCA
1 TATGTAAACTTCCA
4020612 ACAGCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
TATGTAAACTTCCA
Found at i:4022275 original size:30 final size:29
Alignment explanation
Indices: 4022241--4022309 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 29
4022231 GTTTATCCAT
*
4022241 ATAAGTCCTTATCTTTTGATTTGTACCCAA
1 ATAAG-CCTTATCTATTGATTTGTACCCAA
4022271 ATAAGCCCTTATCTATTGATTTGTACCCAA
1 ATAAG-CCTTATCTATTGATTTGTACCCAA
4022301 ATAAGCCTT
1 ATAAGCCTT
4022310 TATTTCAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (29 bp):
ATAAGCCTTATCTATTGATTTGTACCCAA
Found at i:4022391 original size:31 final size:31
Alignment explanation
Indices: 4022337--4022396 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4022327 AGATTTATGT
* *
4022337 TAAGGGCTTATTTAGGTATAAATTGAAAGGC
1 TAAGGGCTTATTTAGGTACAAATTAAAAGGC
*
4022368 TAAGGGTTTATTT-GGATACAAATTAAAAG
1 TAAGGGCTTATTTAGG-TACAAATTAAAAG
4022397 TCAAGCGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (31 bp):
TAAGGGCTTATTTAGGTACAAATTAAAAGGC
Found at i:4024125 original size:2 final size:2
Alignment explanation
Indices: 4024118--4024147 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4024108 GATATGACTG
4024118 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
4024148 GAGAGAGAGA
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:4024152 original size:2 final size:2
Alignment explanation
Indices: 4024147--4024171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4024137 ATATATATAT
4024147 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 A
4024172 TCCAAAGCAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4028096 original size:2 final size:2
Alignment explanation
Indices: 4028089--4028130 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
4028079 CCGTACAATG
*
4028089 TA TA TA TA TA TA -A TG TA TA TA TA TA TA TA TA TA -A 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
4028129 TA
1 TA
4028131 GCCAACTCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Done.