Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 32 of 39
Found at i:4566039 original size:28 final size:28
Alignment explanation
Indices: 4565986--4566040 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
4565976 ACTAAATATG
* * *
4565986 ATAATTTATGTATTGATATTATATTTAT
1 ATAATTTATATATTGATATCAAATTTAT
4566014 ATAATTTATATATT-ATAGTCAAATTTA
1 ATAATTTATATATTGATA-TCAAATTTA
4566041 AAATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (28 bp):
ATAATTTATATATTGATATCAAATTTAT
Found at i:4567390 original size:22 final size:22
Alignment explanation
Indices: 4567354--4567399 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4567344 TCAAATATGA
*
4567354 ATATTATATTATAATCTT-TAAT
1 ATATTATATCATAAT-TTATAAT
*
4567376 ATATTATATCGTAATTTATAAT
1 ATATTATATCATAATTTATAAT
4567398 AT
1 AT
4567400 CTTAACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATATCATAATTTATAAT
Found at i:4568463 original size:24 final size:23
Alignment explanation
Indices: 4568412--4568475 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
4568402 TAATACAACA
4568412 TTATAA-TTAT-TATTTTATAAT
1 TTATAATTTATATATTTTATAAT
*
4568433 TTTTAATTTATATATTATTA-ATAT
1 TTATAATTTATATATT-TTATA-AT
*
4568457 TTATAATTAATAT-TTTTAT
1 TTATAATTTATATATTTTAT
4568476 CGTAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 5 0.14
22 7 0.20
23 7 0.20
24 16 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATAATTTATATATTTTATAAT
Found at i:4569674 original size:17 final size:16
Alignment explanation
Indices: 4569647--4569682 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4569637 AATTATATAT
*
4569647 TATATTTATATCTAAA
1 TATATTTATATATAAA
4569663 TATATGTTATATATAAA
1 TATAT-TTATATATAAA
4569680 TAT
1 TAT
4569683 TAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TATATTTATATATAAA
Found at i:4570109 original size:27 final size:25
Alignment explanation
Indices: 4570079--4570192 Score: 67
Period size: 27 Copynumber: 4.3 Consensus size: 25
4570069 ATATTGATAG
4570079 TTTATATATTTATTATAATCATATAAT
1 TTTATATATTTATTATAAT-ATA-AAT
*
4570106 TTTATCATATTATAATTAT-ATTTAAAT
1 TTTAT-ATATT-T-ATTATAATATAAAT
*
4570133 TATTATATA-TTATTATAAATTTTAATAT
1 T-TTATATATTTATTAT-AA-TATAA-AT
*
4570161 ATTA-ATAATTTATT-T-ATATAAAT
1 TTTATAT-ATTTATTATAATATAAAT
4570184 TTTAATATA
1 TTT-ATATA
4570193 ATCGAGTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 27
0.70 0.04 0.26
Matches are distributed among these distances:
23 4 0.06
24 11 0.15
25 4 0.06
26 4 0.06
27 22 0.31
28 18 0.25
29 3 0.04
30 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTATATATTTATTATAATATAAAT
Found at i:4570151 original size:20 final size:21
Alignment explanation
Indices: 4570113--4570164 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
4570103 AATTTTATCA
*
4570113 TATTATA-ATTATATTTAAAT
1 TATTATATATTATATATAAAT
4570133 TATTATATATTAT-TATAAAT
1 TATTATATATTATATATAAAT
4570153 T-TTAATATATTA
1 TATT-ATATATTA
4570165 ATAATTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATATATTATATATAAAT
Found at i:4570223 original size:19 final size:20
Alignment explanation
Indices: 4570199--4570239 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
4570189 TATAATCGAG
*
4570199 TTTTTATATTAT-GTTTATT
1 TTTTTATATTATAGTATATT
4570218 TTTTTATATTATAGTATATT
1 TTTTTATATTATAGTATATT
4570238 TT
1 TT
4570240 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTATATTATAGTATATT
Found at i:4570236 original size:29 final size:27
Alignment explanation
Indices: 4570203--4570266 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
4570193 ATCGAGTTTT
**
4570203 TATATTATGTTTATTTTTTTATATTATA
1 TATATTATAATTA-TTTTTTATATTATA
*
4570231 GTATATTTTAATTATTTTTTATATTATA
1 -TATATTATAATTATTTTTTATATTATA
4570259 TA-ATTATA
1 TATATTATA
4570267 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 5 0.16
27 2 0.06
28 14 0.45
29 10 0.32
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
TATATTATAATTATTTTTTATATTATA
Found at i:4571490 original size:16 final size:15
Alignment explanation
Indices: 4571467--4571526 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
4571457 AAGTATATTC
4571467 ATTTT-TATTTATAT
1 ATTTTATATTTATAT
*
4571481 ATTTTAT-TATATCAT
1 ATTTTATATTTAT-AT
* *
4571496 AATTTTAT-TTAAAAT
1 -ATTTTATATTTATAT
4571511 ATTTTATATTTATAT
1 ATTTTATATTTATAT
4571526 A
1 A
4571527 AAATTTTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 16 0.44
15 11 0.31
16 9 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTATATTTATAT
Found at i:4571522 original size:20 final size:20
Alignment explanation
Indices: 4571499--4571540 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4571489 ATATCATAAT
*
4571499 TTTATTTAAAATATTT-TATA
1 TTTATATAAAAT-TTTATATA
4571519 TTTATATAAAATTTTATATA
1 TTTATATAAAATTTTATATA
4571539 TT
1 TT
4571541 AATAACTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATATAAAATTTTATATA
Found at i:4571583 original size:12 final size:12
Alignment explanation
Indices: 4571569--4571618 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
4571559 TATGTTAATA
* *
4571569 TTATATTTTATA
1 TTATATTATATT
*
4571581 TTATTTTATATT
1 TTATATTATATT
4571593 TTATATTATATT
1 TTATATTATATT
4571605 TTA-ATTAT-TT
1 TTATATTATATT
4571615 TTAT
1 TTAT
4571619 GTTTTACAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 5 0.15
11 5 0.15
12 23 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATATTATATT
Found at i:4571591 original size:17 final size:17
Alignment explanation
Indices: 4571569--4571601 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4571559 TATGTTAATA
4571569 TTATATTTTATATTATT
1 TTATATTTTATATTATT
4571586 TTATATTTTATATTAT
1 TTATATTTTATATTAT
4571602 ATTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATATTTTATATTATT
Found at i:4571603 original size:29 final size:29
Alignment explanation
Indices: 4571566--4571624 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
4571556 TATTATGTTA
4571566 ATATTATATTTTATATTA-TTTTATATTTT
1 ATATTATATTTTA-ATTATTTTTATATTTT
*
4571595 ATATTATATTTTAATTATTTTTATGTTTT
1 ATATTATATTTTAATTATTTTTATATTTT
4571624 A
1 A
4571625 CAGGGCAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (29 bp):
ATATTATATTTTAATTATTTTTATATTTT
Found at i:4572186 original size:201 final size:201
Alignment explanation
Indices: 4571965--4572384 Score: 777
Period size: 201 Copynumber: 2.1 Consensus size: 201
4571955 TTTATAATTA
* *
4571965 AAATTTTAAACTATATTTTCATTATATATGTTAATTTAAAACTTAATAATGATGATGTAATATTT
1 AAATTTTAAACTATATTTTCATTATATATATTAATTTAAAACTTAATAATGATGATGCAATATTT
* *
4572030 TTTATCAATAAAATTATGACGCATGATATTATTCACGTGTAAATAATTAAAAAATATTTTATTTT
66 TTTATCAATAAAATTATGACACATGATATTATTCACATGTAAATAATTAAAAAATATTTTATTTT
4572095 TATTTATTTTTAAATTTAAAATTTTAAATCTCATAATTTTATTAATAAAAAATTATCATATCATC
131 TATTTATTTTTAAATTTAAAATTTTAAATCTCATAATTTTATTAATAAAAAATTATCATATCATC
4572160 ACTATT
196 ACTATT
4572166 AAATTTTAAACTATATTTTCATTATATATATTAATTTAAAACTTAATAATGATGATGCAATATTT
1 AAATTTTAAACTATATTTTCATTATATATATTAATTTAAAACTTAATAATGATGATGCAATATTT
*
4572231 TTTGTCAATAAAATTATGACACATGATATTATTCACATGTAAATAATTAAAAAATATTTTATTTT
66 TTTATCAATAAAATTATGACACATGATATTATTCACATGTAAATAATTAAAAAATATTTTATTTT
*
4572296 TATTTATTTTTAAATTTAAAATTTTAAATCTCATAATTTTATTAATAAAAAATTATCATATCATT
131 TATTTATTTTTAAATTTAAAATTTTAAATCTCATAATTTTATTAATAAAAAATTATCATATCATC
4572361 ACTATT
196 ACTATT
4572367 AAATTTTAAACTAATATT
1 AAATTTTAAACT-ATATT
4572385 ATAATAAAAA
Statistics
Matches: 212, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
201 207 0.98
202 5 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (201 bp):
AAATTTTAAACTATATTTTCATTATATATATTAATTTAAAACTTAATAATGATGATGCAATATTT
TTTATCAATAAAATTATGACACATGATATTATTCACATGTAAATAATTAAAAAATATTTTATTTT
TATTTATTTTTAAATTTAAAATTTTAAATCTCATAATTTTATTAATAAAAAATTATCATATCATC
ACTATT
Found at i:4575224 original size:32 final size:33
Alignment explanation
Indices: 4575188--4575271 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
4575178 TTCATATTAC
* * *
4575188 ATTTATATTATATAAATTTTAATATA-ATAATA
1 ATTTATATAAAATAAATTTTAATACATATAATA
*
4575220 ATTTATATAAAATAAATTTTGATACATATAATA
1 ATTTATATAAAATAAATTTTAATACATATAATA
*
4575253 A-ATA-ATAAAATAAAATTTT
1 ATTTATATAAAAT-AAATTTT
4575272 CAATCGATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
31 7 0.16
32 31 0.69
33 7 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
ATTTATATAAAATAAATTTTAATACATATAATA
Found at i:4580064 original size:21 final size:22
Alignment explanation
Indices: 4580038--4580123 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 22
4580028 TAATTTATAA
4580038 TATTTTATAATA-TAAAAATTT
1 TATTTTATAATATTAAAAATTT
4580059 TATTTT-TAA-ATTAATAAA-TT
1 TATTTTATAATATTAA-AAATTT
* * *
4580079 TCTTTTAAAATATTATAAAATAT
1 TATTTTATAATATTA-AAAATTT
*
4580102 T-TTTTA-AAT-TAAAAAATTT
1 TATTTTATAATATTAAAAATTT
4580121 TAT
1 TAT
4580124 AAACTTAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
19 8 0.15
20 16 0.30
21 14 0.26
22 12 0.23
23 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTTATAATATTAAAAATTT
Found at i:4580086 original size:19 final size:18
Alignment explanation
Indices: 4580061--4580138 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 18
4580051 AAAAATTTTA
4580061 TTTTTAAATTAATAAATT
1 TTTTTAAATTAATAAATT
*
4580079 TCTTTTAAAATATTATAAAATAT
1 T-TTTT-AAAT-TAAT-AAAT-T
*
4580102 TTTTTAAATTAA-AAAAT
1 TTTTTAAATTAATAAATT
*
4580119 TTTATAAACTTAATAAATT
1 TTTTTAAA-TTAATAAATT
4580138 T
1 T
4580139 AAATCAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
17 8 0.17
18 8 0.17
19 9 0.19
20 6 0.12
21 7 0.15
22 8 0.17
23 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAATTAATAAATT
Found at i:4580139 original size:17 final size:17
Alignment explanation
Indices: 4580094--4580138 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4580084 TAAAATATTA
* *
4580094 TAAAATATTTTTTAAAT
1 TAAAAAATTTTATAAAT
4580111 TAAAAAATTTTATAAACT
1 TAAAAAATTTTATAAA-T
*
4580129 TAATAAATTT
1 TAAAAAATTT
4580139 AAATCAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAAATTTTATAAAT
Found at i:4591930 original size:123 final size:124
Alignment explanation
Indices: 4591691--4592031 Score: 591
Period size: 123 Copynumber: 2.8 Consensus size: 124
4591681 TTGTGATTTT
* * * **
4591691 ATTTTCTCACTTATCATTCCAATTAGATATTACATTTACTTCAAACATTATGCAAATCATGTCGA
1 ATTTTCTCAGTTATCATTCCAATTAGATATTATATTTACGTCAAACATCGTGCAAATCATGTCGA
*
4591756 ATTTTAAATGAGTTTCATAGTCAAATGAAAGGAATGAAAGGGAACTAAGGGGCCAGTTA
66 ATTTTAAAAGAGTTTCATAGTCAAATGAAAGGAATGAAAGGGAACTAAGGGGCCAGTTA
4591815 ATTTTCTCAGTTATCATTCCAATTAGATATTATATTTACGTCAAACATCGTGCAAATCAT-TCGA
1 ATTTTCTCAGTTATCATTCCAATTAGATATTATATTTACGTCAAACATCGTGCAAATCATGTCGA
*
4591879 ATTTTAAAAGAGTTTCATAGTCAAATGAAAGGAATGAAAGGGAACTAAGGGGCCATTTA
66 ATTTTAAAAGAGTTTCATAGTCAAATGAAAGGAATGAAAGGGAACTAAGGGGCCAGTTA
4591938 ATTTTCTCAGTTATCATTCCAATTAGATATTATATTTACGTC--A-ATCGTGCAAATCATGTCGA
1 ATTTTCTCAGTTATCATTCCAATTAGATATTATATTTACGTCAAACATCGTGCAAATCATGTCGA
4592000 ATTTTAAAAGAGTTTCATAGTCAAATGAAAGG
66 ATTTTAAAAGAGTTTCATAGTCAAATGAAAGG
4592032 GAACTAAGGG
Statistics
Matches: 209, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
120 14 0.07
121 37 0.18
123 103 0.49
124 55 0.26
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (124 bp):
ATTTTCTCAGTTATCATTCCAATTAGATATTATATTTACGTCAAACATCGTGCAAATCATGTCGA
ATTTTAAAAGAGTTTCATAGTCAAATGAAAGGAATGAAAGGGAACTAAGGGGCCAGTTA
Found at i:4593015 original size:136 final size:137
Alignment explanation
Indices: 4592770--4593050 Score: 415
Period size: 136 Copynumber: 2.1 Consensus size: 137
4592760 TTTACAAGAG
** * *
4592770 ATAATTTTAGATATGAGTAAAAAAATCACTGAACGGGCATAGAGAAAAAAACTACAAAAGTGTAG
1 ATAATTTTAGATATGAGTAAAAAAATCACTGAACGAACATAGAAAAAAAAACTACAAAAGTATAG
** * *
4592835 AGAATTTTTTTTTAGATGTAAAAAGAAATATAACTCGTAAATAAAAAAATCTTAAATATTATCAT
66 AGAATTTTTTTTTAGAAATAAAAAGAAATATAACTCGTAAATAAAAAAATATTAAATATTACCAT
*
4592900 TCGAATT
131 TCAAATT
*
4592907 ATAATTTT-GATATGAGTAAAAAAATCACTGAACGAACATA-AAAAAAAGAACTATAAAAGTATA
1 ATAATTTTAGATATGAGTAAAAAAATCACTGAACGAACATAGAAAAAAA-AACTACAAAAGTATA
* *
4592970 GAGATTTTTTTTTTAGAAATAAAAA-AAGATATAACTTGTAAATAAAAAAATATTAAATATTACC
65 GAGAATTTTTTTTTAGAAATAAAAAGAA-ATATAACTCGTAAATAAAAAAATATTAAATATTACC
4593034 ATTCAAATT
129 ATTCAAATT
4593043 ATAATTTT
1 ATAATTTT
4593051 TTTTCCTTCT
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
135 8 0.06
136 114 0.88
137 8 0.06
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (137 bp):
ATAATTTTAGATATGAGTAAAAAAATCACTGAACGAACATAGAAAAAAAAACTACAAAAGTATAG
AGAATTTTTTTTTAGAAATAAAAAGAAATATAACTCGTAAATAAAAAAATATTAAATATTACCAT
TCAAATT
Found at i:4596958 original size:13 final size:13
Alignment explanation
Indices: 4596940--4596964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4596930 ACACATATTT
4596940 AAATATAAATATA
1 AAATATAAATATA
4596953 AAATATAAATAT
1 AAATATAAATAT
4596965 TTAAATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATA
Found at i:4606423 original size:8 final size:8
Alignment explanation
Indices: 4606414--4606482 Score: 84
Period size: 8 Copynumber: 8.6 Consensus size: 8
4606404 TAGTCACAAA
*
4606414 AGAGACAA
1 AGAGACAG
*
4606422 AGAGAGAG
1 AGAGACAG
*
4606430 AGAGAGAG
1 AGAGACAG
4606438 AGAGACAG
1 AGAGACAG
4606446 AGAGACAG
1 AGAGACAG
*
4606454 AGAGAGAG
1 AGAGACAG
*
4606462 AGAGAGAG
1 AGAGACAG
*
4606470 AGAGAGAG
1 AGAGACAG
4606478 AGAGA
1 AGAGA
4606483 GAGACGACTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 57 1.00
ACGTcount: A:0.52, C:0.04, G:0.43, T:0.00
Consensus pattern (8 bp):
AGAGACAG
Found at i:4606429 original size:2 final size:2
Alignment explanation
Indices: 4606422--4606486 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
4606412 AAAGAGACAA
* *
4606422 AG AG AG AG AG AG AG AG AG AG AC AG AG AG AC AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4606464 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
4606487 CGACTCCTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4608220 original size:22 final size:23
Alignment explanation
Indices: 4608174--4608222 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4608164 TATTATTATT
*
4608174 ATTTTTTAAAAAAATCAAATTAA
1 ATTTTTTAAAAAAATCAAATCAA
* *
4608197 ATTTTTTTAAAAAAT-TAATCAA
1 ATTTTTTAAAAAAATCAAATCAA
4608219 ATTT
1 ATTT
4608223 AATGTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTTTTAAAAAAATCAAATCAA
Found at i:4609917 original size:18 final size:17
Alignment explanation
Indices: 4609894--4609937 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4609884 TAATATTTTA
* *
4609894 AAAAAATTTTAAATATAT
1 AAAAAATATTAAAAAT-T
*
4609912 AAAAAAAATTAAAAATT
1 AAAAAATATTAAAAATT
4609929 AAAAAATAT
1 AAAAAATAT
4609938 CTATATCGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAATATTAAAAATT
Found at i:4611138 original size:31 final size:32
Alignment explanation
Indices: 4611076--4611148 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
4611066 AATATTTTAT
*
4611076 TTTATTTATTAATTTTATAAAAATGATTAATA
1 TTTATTTATTAATTTAATAAAAATGATTAATA
4611108 TTTATTT-TTAA-TTAATAATAATATGA-TAATAA
1 TTTATTTATTAATTTAATAA-AA-ATGATTAAT-A
*
4611140 TATATTTAT
1 TTTATTTAT
4611149 GTTAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
30 6 0.17
31 10 0.29
32 18 0.51
33 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (32 bp):
TTTATTTATTAATTTAATAAAAATGATTAATA
Found at i:4611195 original size:20 final size:21
Alignment explanation
Indices: 4611168--4611213 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4611158 TGTAATTTAT
*
4611168 TTAA-ATTTTATTT-ATCATA
1 TTAATATTTTATTTAATAATA
4611187 TTAATA-TTTATTTAATAATA
1 TTAATATTTTATTTAATAATA
4611207 TTAATAT
1 TTAATAT
4611214 AAAATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATATTTTATTTAATAATA
Found at i:4611207 original size:14 final size:14
Alignment explanation
Indices: 4611188--4611227 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4611178 TTTATCATAT
4611188 TAATATTTATTTAA
1 TAATATTTATTTAA
* *
4611202 TAATATTAATATAA
1 TAATATTTATTTAA
4611216 -AATATTTATTTA
1 TAATATTTATTTA
4611228 TATTTAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTATTTAA
Found at i:4611221 original size:13 final size:14
Alignment explanation
Indices: 4611188--4611244 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
4611178 TTTATCATAT
* *
4611188 TAATATTTATTTAA
1 TAATATTAATATAA
4611202 TAATATTAATATAA
1 TAATATTAATATAA
* *
4611216 -AATATTTAT-TTA
1 TAATATTAATATAA
4611228 T-AT-TTAATATAA
1 TAATATTAATATAA
4611240 TAATA
1 TAATA
4611245 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
11 4 0.12
12 7 0.21
13 10 0.30
14 12 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATATTAATATAA
Found at i:4611225 original size:27 final size:25
Alignment explanation
Indices: 4611172--4611249 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 25
4611162 ATTTATTTAA
*
4611172 ATTT-TATTT-ATCATATTAATATTT
1 ATTTATATTTAAT-ATAATAATATTT
4611196 ATTTAATAATATTAATATAA-AATATTT
1 ATTT-AT-AT-TTAATATAATAATATTT
4611223 ATTTATATTTAATATAATAATAATTT
1 ATTTATATTTAATATAATAAT-ATTT
4611249 A
1 A
4611250 AATATTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
24 13 0.28
25 5 0.11
26 8 0.17
27 13 0.28
28 5 0.11
29 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTATATTTAATATAATAATATTT
Found at i:4611232 original size:33 final size:33
Alignment explanation
Indices: 4611184--4611265 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
4611174 TTTATTTATC
* *
4611184 ATATTAATATTTATTT-A-ATAATATTAATATAAA
1 ATATTTAT-TTTATTTAATATAATAATAAT-TAAA
*
4611217 ATATTTATTTATATTTAATATAATAATAATTTAA
1 ATATTTATTT-TATTTAATATAATAATAATTAAA
4611251 ATATTTATTTTATTT
1 ATATTTATTTTATTT
4611266 TTTAAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 17 0.40
34 14 0.33
35 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTTATTTTATTTAATATAATAATAATTAAA
Found at i:4611254 original size:24 final size:23
Alignment explanation
Indices: 4611195--4611257 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
4611185 TATTAATATT
4611195 TATTTAATAATA-TTAATATAAAA
1 TATTT-ATAATATTTAATATAAAA
*
4611218 TATTTATTTATATTTAATATAATAA
1 TATTTA-TAATATTTAATATAA-AA
4611243 TAATTTA-AATATTTA
1 T-ATTTATAATATTTA
4611258 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 9 0.26
24 16 0.47
25 3 0.09
26 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTATAATATTTAATATAAAA
Found at i:4611284 original size:33 final size:33
Alignment explanation
Indices: 4611185--4611284 Score: 94
Period size: 33 Copynumber: 2.9 Consensus size: 33
4611175 TTATTTATCA
*
4611185 TATTAATATTTATTTAATAATATTAATATAAAATATT
1 TATTTATATTT-TTTAA-AATATTAAT-T-AAATATT
** * *
4611222 TATTTATATTTAATATAATAATAATTTAAATATT
1 TATTTATATTTTTTAAAATATTAA-TTAAATATT
4611256 TATTT-TATTTTTTAAAATATTTAATTAAA
1 TATTTATATTTTTTAAAATA-TTAATTAAA
4611285 AATAATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
33 16 0.31
34 15 0.29
35 8 0.15
36 3 0.06
37 10 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATTTATATTTTTTAAAATATTAATTAAATATT
Found at i:4611288 original size:35 final size:35
Alignment explanation
Indices: 4611185--4611288 Score: 97
Period size: 34 Copynumber: 2.9 Consensus size: 35
4611175 TTATTTATCA
*
4611185 TATTAATATTTATTTAATAATATTAA-TATAAAATATT
1 TATTTATATTT-TTTAA-AATATTAATTA-AAAATATT
** * * *
4611222 TATTTATATTTAATATAATAATAATT-TAAATATT
1 TATTTATATTTTTTAAAATATTAATTAAAAATATT
4611256 TATTT-TATTTTTTAAAATATTTAATTAAAAATA
1 TATTTATATTTTTTAAAATA-TTAATTAAAAATA
4611289 ATATAATATA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
33 11 0.21
34 17 0.32
35 12 0.23
36 3 0.06
37 10 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TATTTATATTTTTTAAAATATTAATTAAAAATATT
Found at i:4611765 original size:23 final size:26
Alignment explanation
Indices: 4611716--4611765 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
4611706 TATCAAACAC
*
4611716 ATAAATACTTTACACTAATATCATTAA
1 ATAAATACTTAACACTAATAT-ATTAA
4611743 ATAAATA-TTAACA-TAATAT-TTAA
1 ATAAATACTTAACACTAATATATTAA
4611766 TATCTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
25 6 0.27
26 5 0.23
27 7 0.32
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (26 bp):
ATAAATACTTAACACTAATATATTAA
Found at i:4611866 original size:19 final size:20
Alignment explanation
Indices: 4611835--4611894 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 20
4611825 ATTATGATTT
4611835 TATTAA-ATGTTAAATATTA-
1 TATTAATAT-TTAAATATTAG
*
4611854 TATTAATATTTAATGATTTTAG
1 TATTAATATTTAA--ATATTAG
*
4611876 TATATAATATTTACATATT
1 TAT-TAATATTTAAATATT
4611895 TAATAAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.30
20 2 0.06
21 9 0.27
22 3 0.09
23 9 0.27
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
TATTAATATTTAAATATTAG
Found at i:4612523 original size:2 final size:2
Alignment explanation
Indices: 4612514--4612549 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4612504 ATTGTGTGCG
*
4612514 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4612550 TTAGCTGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4613876 original size:28 final size:26
Alignment explanation
Indices: 4613812--4613878 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
4613802 TCTAACTTAA
* *
4613812 AATAATATTTAATAATAAAAATTTTT
1 AATATTATTTAAAAATAAAAATTTTT
4613838 -AT-TTAATTTTAAAATATAAAAATATTTT
1 AATATT-A-TTTAAAA-ATAAAAAT-TTTT
4613866 AATATTATTTAAA
1 AATATTATTTAAA
4613879 CAGTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
24 1 0.03
25 3 0.09
26 6 0.18
27 8 0.24
28 10 0.30
29 3 0.09
30 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATTATTTAAAAATAAAAATTTTT
Found at i:4614350 original size:14 final size:14
Alignment explanation
Indices: 4614331--4614358 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4614321 TCATTTTTAT
4614331 TTTTAAAAAAATAA
1 TTTTAAAAAAATAA
4614345 TTTTAAAAAAATAA
1 TTTTAAAAAAATAA
4614359 ATCGATATAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTTAAAAAAATAA
Found at i:4615787 original size:24 final size:24
Alignment explanation
Indices: 4615717--4615791 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
4615707 ATTTATAGTA
* *
4615717 ATTAAATT-TAATATTAATTTTTT
1 ATTAAATTATATTATTAAATTTTT
* * *
4615740 AATAAATTATAATTTTTTAA-TTTT
1 ATTAAATTAT-ATTATTAAATTTTT
*
4615764 ATTAAATTATATTACTAAATTTTT
1 ATTAAATTATATTATTAAATTTTT
4615788 ATTA
1 ATTA
4615792 TTAAAAAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
23 13 0.32
24 22 0.55
25 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTAAATTATATTATTAAATTTTT
Found at i:4616129 original size:23 final size:23
Alignment explanation
Indices: 4616082--4616139 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 23
4616072 CTTAATTCAC
*
4616082 TATTTATTATATTAATAAAATAT
1 TATTTATTATATTAATAAAAAAT
4616105 TATTTA-TAT-TTGAATACAAAAATT
1 TATTTATTATATT-AATA-AAAAA-T
4616129 ATATTTATTAT
1 -TATTTATTAT
4616140 TAAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 10 0.34
24 1 0.03
25 6 0.21
26 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTATTATATTAATAAAAAAT
Found at i:4616878 original size:18 final size:19
Alignment explanation
Indices: 4616839--4616879 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4616829 TCCAAAAACC
* *
4616839 TTAATAAAATATTTATTTT
1 TTAAAAAAATATTTATTAT
4616858 TTAAAAAAATATTTA-TAT
1 TTAAAAAAATATTTATTAT
4616876 TTAA
1 TTAA
4616880 TATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAAAAATATTTATTAT
Found at i:4617237 original size:17 final size:17
Alignment explanation
Indices: 4617213--4617260 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
4617203 TTTTTAAAAA
4617213 ATAA-ATATATTTATAT
1 ATAATATATATTTATAT
*
4617229 -TAAATATATATTTACAT
1 AT-AATATATATTTATAT
*
4617246 ATAATATTTATTTAT
1 ATAATATATATTTAT
4617261 GTTTAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 2 0.08
17 22 0.85
18 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATATATATTTATAT
Found at i:4618132 original size:2 final size:2
Alignment explanation
Indices: 4618125--4618161 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4618115 ATTCTATACG
*
4618125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4618162 GCAAACTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4619119 original size:26 final size:26
Alignment explanation
Indices: 4619088--4619141 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
4619078 CAATTTAAAA
* *
4619088 TTTTATTTTATTATTTAAAATAATAT
1 TTTTATATTAATATTTAAAATAATAT
* *
4619114 TTTTATATTAATATTTATAATTATAT
1 TTTTATATTAATATTTAAAATAATAT
4619140 TT
1 TT
4619142 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTATATTAATATTTAAAATAATAT
Found at i:4622214 original size:2 final size:2
Alignment explanation
Indices: 4622207--4622231 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4622197 GGAAAAACAG
4622207 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4622232 AAATCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4624653 original size:36 final size:36
Alignment explanation
Indices: 4624605--4624674 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
4624595 GGCAGATGTT
* *
4624605 GAAGGTGTTGAAGGAGGTGATTTTGGGATTGTTGAA
1 GAAGATGTTGAAGGAGGTGATCTTGGGATTGTTGAA
4624641 GAAGATGTTGAAGGAGGTGATCTTGGGATTGTTG
1 GAAGATGTTGAAGGAGGTGATCTTGGGATTGTTG
4624675 GTGAAGACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.01, G:0.41, T:0.33
Consensus pattern (36 bp):
GAAGATGTTGAAGGAGGTGATCTTGGGATTGTTGAA
Found at i:4624681 original size:36 final size:36
Alignment explanation
Indices: 4624604--4624681 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
4624594 AGGCAGATGT
* *
4624604 TGAAGGTGTTGAAGGAGGTGATTTTGGGATTGTTGA
1 TGAAGATGTTGAAGGAGGTGATCTTGGGATTGTTGA
* *
4624640 AGAAGATGTTGAAGGAGGTGATCTTGGGATTGTTGG
1 TGAAGATGTTGAAGGAGGTGATCTTGGGATTGTTGA
4624676 TGAAGA
1 TGAAGA
4624682 CTTTCAGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.01, G:0.41, T:0.32
Consensus pattern (36 bp):
TGAAGATGTTGAAGGAGGTGATCTTGGGATTGTTGA
Found at i:4627858 original size:7 final size:7
Alignment explanation
Indices: 4627795--4627863 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
4627785 CGCGTAGTAA
4627795 TTTATAT
1 TTTATAT
4627802 ATTTATAT
1 -TTTATAT
4627810 TTTAT-T
1 TTTATAT
4627816 TTTATAAT
1 TTTAT-AT
*
4627824 TTTTTAT
1 TTTATAT
*
4627831 ATTATA-
1 TTTATAT
* *
4627837 ATCATAT
1 TTTATAT
4627844 TTAATATAT
1 TT--TATAT
4627853 TTTATAT
1 TTTATAT
4627860 TTTA
1 TTTA
4627864 ATTAATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 11 0.22
7 21 0.42
8 12 0.24
9 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTATAT
Found at i:4628274 original size:27 final size:28
Alignment explanation
Indices: 4628213--4628280 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
4628203 ATTATGATCC
4628213 AAACAAA-CCAAATTGAAATTAAAAAAA
1 AAACAAACCCAAATTGAAATTAAAAAAA
* * *
4628240 AAAAAAACCCAAATTGAAA-TCAATAAA
1 AAACAAACCCAAATTGAAATTAAAAAAA
*
4628267 AACCAAACCCAAAT
1 AAACAAACCCAAAT
4628281 CTAATCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.66, C:0.18, G:0.03, T:0.13
Consensus pattern (28 bp):
AAACAAACCCAAATTGAAATTAAAAAAA
Found at i:4628844 original size:23 final size:23
Alignment explanation
Indices: 4628818--4628866 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4628808 TTTTTAAAAA
4628818 TTTT-TAGTTTAAAATTTTTTTAT
1 TTTTATAGTTTAAAA-TTTTTTAT
**
4628841 TTTTATTTTTTAAAATTTTTTAT
1 TTTTATAGTTTAAAATTTTTTAT
4628864 TTT
1 TTT
4628867 CACAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATAGTTTAAAATTTTTTAT
Found at i:4629012 original size:19 final size:17
Alignment explanation
Indices: 4628966--4629019 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
4628956 TATAATTTAA
*
4628966 AAAATTATAATTTATAAT
1 AAAATTAAAATTTA-AAT
*
4628984 AAAATAAAAATTTAAAT
1 AAAATTAAAATTTAAAT
*
4629001 ATCAAATTAAAAATTAAAT
1 A--AAATTAAAATTTAAAT
4629020 TAAGGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.13
18 12 0.40
19 14 0.47
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTAAAATTTAAAT
Found at i:4629248 original size:20 final size:20
Alignment explanation
Indices: 4629215--4629271 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
4629205 ATTTAAAAAA
*
4629215 TTATAATAAATAAAAAATAAT
1 TTATAAT-ATTAAAAAATAAT
*
4629236 TTATAATATTAAAAAATTAT
1 TTATAATATTAAAAAATAAT
4629256 TTA-AATATTAAAAAAT
1 TTATAATATTAAAAAAT
4629272 TTAGATGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.38
20 14 0.41
21 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATAATATTAAAAAATAAT
Found at i:4629249 original size:19 final size:19
Alignment explanation
Indices: 4629225--4629271 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
4629215 TTATAATAAA
4629225 TAAAAAATAATTTATAATAT
1 TAAAAAATAATTTA-AATAT
*
4629245 TAAAAAATTATTTAAATAT
1 TAAAAAATAATTTAAATAT
4629264 TAAAAAAT
1 TAAAAAAT
4629272 TTAGATGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATAATTTAAATAT
Found at i:4629272 original size:19 final size:20
Alignment explanation
Indices: 4629196--4629272 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 20
4629186 TTAATATTTT
4629196 AATT-TTTAT-AT-TTAAAA
1 AATTATTTATAATATTAAAA
*
4629213 AATTA-TAATAA-A-TAAAA
1 AATTATTTATAATATTAAAA
*
4629230 AATAATTTATAATATTAAAA
1 AATTATTTATAATATTAAAA
4629250 AATTATTTA-AATATTAAAA
1 AATTATTTATAATATTAAAA
4629269 AATT
1 AATT
4629273 TAGATGTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 16 0.32
18 6 0.12
19 15 0.30
20 13 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATTTATAATATTAAAA
Found at i:4629288 original size:19 final size:19
Alignment explanation
Indices: 4629266--4629309 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4629256 TTAAATATTA
*
4629266 AAAAATTTAGATGTAATAT
1 AAAAATTTAAATGTAATAT
* * *
4629285 AAAATTTTAAATTTTATAT
1 AAAAATTTAAATGTAATAT
4629304 AAAAAT
1 AAAAAT
4629310 ATCTACATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAAATTTAAATGTAATAT
Found at i:4629393 original size:19 final size:18
Alignment explanation
Indices: 4629371--4629428 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
4629361 ATATTTCAAA
4629371 TAATACATTAATATTTTAT
1 TAATACATTAATATTTT-T
*
4629390 TAATA-TTTAAATAATTTTT
1 TAATACATT-AAT-ATTTTT
4629409 TAATATCATTAATATTTTT
1 TAATA-CATTAATATTTTT
4629428 T
1 T
4629429 TATAAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 21 0.64
20 8 0.24
21 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATACATTAATATTTTT
Found at i:4629487 original size:14 final size:14
Alignment explanation
Indices: 4629436--4629488 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
4629426 TTTTATAAGT
* *
4629436 TTTAATATATAAAT
1 TTTAAAATATAAAA
* *
4629450 TTTAAATTATTAAA
1 TTTAAAATATAAAA
4629464 TTTAATAATATAAAA
1 TTTAA-AATATAAAA
*
4629479 ATTAAAATAT
1 TTTAAAATAT
4629489 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAAATATAAAA
Found at i:4629917 original size:34 final size:33
Alignment explanation
Indices: 4629855--4629920 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
4629845 ATAAATTTAA
4629855 TTTTAAATTTTTATTTAATAATAAAAATAATAC
1 TTTTAAATTTTTATTTAATAATAAAAATAATAC
4629888 TTTTATAATATTTTA-TTAAT-ATAATAAATAATA
1 TTTTA-AAT-TTTTATTTAATAATAA-AAATAATA
4629921 AAATAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 9 0.30
34 16 0.53
35 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (33 bp):
TTTTAAATTTTTATTTAATAATAAAAATAATAC
Found at i:4630216 original size:21 final size:21
Alignment explanation
Indices: 4630186--4630228 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4630176 GATCAATTTG
*
4630186 ATTTATTTAAATTAAAAATTA
1 ATTTAATTAAATTAAAAATTA
* *
4630207 ATTTAATTAAATTTAATATTA
1 ATTTAATTAAATTAAAAATTA
4630228 A
1 A
4630229 AATTAATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAATTAAATTAAAAATTA
Found at i:4630220 original size:27 final size:27
Alignment explanation
Indices: 4630190--4630241 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
4630180 AATTTGATTT
*
4630190 ATTTAA-ATTAAAAATTAATTTAATTAA
1 ATTTAATATT-AAAATTAATTGAATTAA
4630217 ATTTAATATTAAAATTAATTGAATT
1 ATTTAATATTAAAATTAATTGAATT
4630242 GATTGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTTAATATTAAAATTAATTGAATTAA
Found at i:4630234 original size:22 final size:21
Alignment explanation
Indices: 4630192--4630241 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4630182 TTTGATTTAT
*
4630192 TTAAATTAAAAATTAATTTAA
1 TTAAATTAAAAATTAAATTAA
* *
4630213 TTAAATTTAATATTAAAATTAA
1 TTAAATTAAAAATT-AAATTAA
*
4630235 TTGAATT
1 TTAAATT
4630242 GATTGAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTAAATTAAAAATTAAATTAA
Found at i:4633751 original size:33 final size:33
Alignment explanation
Indices: 4633714--4633992 Score: 441
Period size: 33 Copynumber: 8.5 Consensus size: 33
4633704 AATATACAAA
* * *
4633714 CCTCCACCAGTTCCAGTTTATGAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
* *
4633747 CCTCCGCCAGTTCCAGTTTATGAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
*
4633780 CCTCCGCCAGTTCCAGTATACAAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
4633813 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
*
4633846 CCTCCGCCAGTTCCAGTATACAAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
*
4633879 CCTCCGCCAGTTCCAGTATACAAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
4633912 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
* * *
4633945 CCTCCACCAGTTCCAGTGTATAATAAACCACTT
1 CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
* *
4633978 CCTCCTCCCGTTCCA
1 CCTCCGCCAGTTCCA
4633993 ATCTACAAGC
Statistics
Matches: 234, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 234 1.00
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (33 bp):
CCTCCGCCAGTTCCAGTATATAAGAAACCACTT
Found at i:4634623 original size:9 final size:9
Alignment explanation
Indices: 4634608--4634641 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
4634598 AACAAAATAA
4634608 TTTATTATT
1 TTTATTATT
*
4634617 ATTATTATT
1 TTTATTATT
*
4634626 TTTATAATT
1 TTTATTATT
4634635 TTTATTA
1 TTTATTA
4634642 CTTTAAACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTATTATT
Found at i:4635094 original size:4 final size:4
Alignment explanation
Indices: 4635087--4635113 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4635077 TATATATATA
4635087 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
4635114 CTGTCGAAGG
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:4637578 original size:223 final size:223
Alignment explanation
Indices: 4637187--4637635 Score: 749
Period size: 223 Copynumber: 2.0 Consensus size: 223
4637177 GGTTTGTAGA
* *
4637187 AATATAGACAGCTAATCGGACTGTGTTCATTAAGATGGTTGATTATGTCCATACATGTTTAGTTG
1 AATATAGACAGCTAATCGGACTGTGTTCATTAAGATGGCTGATTATGTCCACACATGTTTAGTTG
*
4637252 TATGTTCTGAAGTATATTTTGTCACTCTTATTATGTGCATTTTGAGATGAAATGCATTAATTTCA
66 TATGTTCTGAAGTATATTTTGTCACTATTATTATGTGCATTTTGAGATGAAATGCATTAATTTCA
*
4637317 TTAGGAGATGCAAGAATAGATATTAGCTTAGTTATATAATTTA-TTTTTATTTTTAT-TTTTGGC
131 TTAGGAGATGCAAGAATAGATATTAGCTTAGCTATATAATTTATTTTTTATTTTT-TCTTTTGGC
*
4637380 TGTTGTTATGCTTTAGCCTTCTAACATTT
195 TGTTGTTATGCTTAAGCCTTCTAACATTT
* * *
4637409 AATATAGACAGCTAATCTGAGTGTGTTCATTAAGATGGCTGATTATGTCTCACGCATGTTTAGTT
1 AATATAGACAGCTAATCGGACTGTGTTCATTAAGATGGCTGATTATGTC-CACACATGTTTAGTT
* * * *
4637474 GTATGTTCTGAAGTATCTTTTGTTACTATTATTATGTGCATTTTGAGATGGAATGTATTAATTTC
65 GTATGTTCTGAAGTATATTTTGTCACTATTATTATGTGCATTTTGAGATGAAATGCATTAATTTC
*
4637539 ATTAGGAGATGCAAGAATAGATATTAGCTTAGCTATATAATTTATTTTTTATTTTTTCTTTTTGC
130 ATTAGGAGATGCAAGAATAGATATTAGCTTAGCTATATAATTTATTTTTTATTTTTTCTTTTGGC
4637604 TGTTGTTATGCTTAAGCCTTCTAACATTT
195 TGTTGTTATGCTTAAGCCTTCTAACATTT
4637633 AAT
1 AAT
4637636 GTACATTTTG
Statistics
Matches: 211, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
222 46 0.22
223 117 0.55
224 48 0.23
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.45
Consensus pattern (223 bp):
AATATAGACAGCTAATCGGACTGTGTTCATTAAGATGGCTGATTATGTCCACACATGTTTAGTTG
TATGTTCTGAAGTATATTTTGTCACTATTATTATGTGCATTTTGAGATGAAATGCATTAATTTCA
TTAGGAGATGCAAGAATAGATATTAGCTTAGCTATATAATTTATTTTTTATTTTTTCTTTTGGCT
GTTGTTATGCTTAAGCCTTCTAACATTT
Found at i:4643172 original size:21 final size:21
Alignment explanation
Indices: 4643119--4643173 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 21
4643109 TATTAATTTA
4643119 TTGACTTCATGCATTTTTCTC
1 TTGACTTCATGCATTTTTCTC
* *
4643140 TTG-GTT--TGCATTTTTCTG
1 TTGACTTCATGCATTTTTCTC
4643158 TTGACTTCATGCATTT
1 TTGACTTCATGCATTT
4643174 GTGATCTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 14 0.50
19 2 0.07
20 2 0.07
21 10 0.36
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.55
Consensus pattern (21 bp):
TTGACTTCATGCATTTTTCTC
Found at i:4643369 original size:174 final size:172
Alignment explanation
Indices: 4643081--4643422 Score: 564
Period size: 174 Copynumber: 2.0 Consensus size: 172
4643071 ATTGGTGGTA
*
4643081 GTTGGTGTTCTTTTGAAGGGATATTGATTATTAATTTATTGACTTCATGCATTTTTCTCTTGGTT
1 GTTGGTGTCCTTTTGAAGGGATATTGATTATTAATTTATTGACTTCATGCATTTTTCTCTTGGTT
*
4643146 TGCATTTTTCTGTTGACTTCATGCATTTGTGATCTGTACTTTGGATATTCTTTACAGTGGATCAT
66 TGCATTTTTCTGTTGACTTCATGCATGTGTGATCTGTACTTTGGATATTCTTTACAGTGGATCAT
*
4643211 GGTTGCTATCTGGAAAGTTGTCAAAGATGCTTTTAATTCAAT
131 GGTTGCTATCTGGAAAGTTGGCAAAGATGCTTTTAATTCAAT
*
4643253 GTTGGTGTCCTTTTGAAGGGATATTGATTATTAATTTATT-A-TTAATCTGTTTC-TTTTTCTCT
1 GTTGGTGTCCTTTTGAAGGGATATTGATTATTAATTTATTGACTTCA--TG---CATTTTTCTCT
*
4643315 TGGTTTGCATTTTTCTGTTGACTTCATTCATGTGTGATCTGTACTTTGGATATTCTTTACAGTGG
61 TGGTTTGCATTTTTCTGTTGACTTCATGCATGTGTGATCTGTACTTTGGATATTCTTTACAGTGG
*
4643380 ATCATGGTTGCTATCTGGCAAGTTGGCAAAGATGCTTTTAATT
126 ATCATGGTTGCTATCTGGAAAGTTGGCAAAGATGCTTTTAATT
4643423 GATAGTGAGC
Statistics
Matches: 159, Mismatches: 6, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
170 3 0.02
171 1 0.01
172 41 0.26
174 113 0.71
175 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (172 bp):
GTTGGTGTCCTTTTGAAGGGATATTGATTATTAATTTATTGACTTCATGCATTTTTCTCTTGGTT
TGCATTTTTCTGTTGACTTCATGCATGTGTGATCTGTACTTTGGATATTCTTTACAGTGGATCAT
GGTTGCTATCTGGAAAGTTGGCAAAGATGCTTTTAATTCAAT
Found at i:4654001 original size:7 final size:7
Alignment explanation
Indices: 4653989--4654025 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
4653979 GTTCAATCTC
4653989 AATTTAA
1 AATTTAA
4653996 AATTTAA
1 AATTTAA
4654003 AATTT--
1 AATTTAA
4654008 -ATTTAA
1 AATTTAA
4654014 AATTTAA
1 AATTTAA
4654021 AATTT
1 AATTT
4654026 GATTCGATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.15
7 23 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
AATTTAA
Found at i:4654013 original size:18 final size:18
Alignment explanation
Indices: 4653990--4654025 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4653980 TTCAATCTCA
4653990 ATTTAAAATTTAAAATTT
1 ATTTAAAATTTAAAATTT
4654008 ATTTAAAATTTAAAATTT
1 ATTTAAAATTTAAAATTT
4654026 GATTCGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAAATTTAAAATTT
Found at i:4655864 original size:258 final size:258
Alignment explanation
Indices: 4655407--4655921 Score: 976
Period size: 258 Copynumber: 2.0 Consensus size: 258
4655397 GCCTTGGCTG
4655407 GTGGTTCAGCATTAGGCACCAGTTTAATTTTGTGATCCACCTCTCTCTTAGGTGGTAGCTTCTTC
1 GTGGTTCAGCATTAGGCACCAGTTTAATTTTGTGATCCACCTCTCTCTTAGGTGGTAGCTTCTTC
*
4655472 GGCAATTATGCAGGCATCACATCATTGAAGGATTGTAGCACCTCCAAAGGGGTTTCTTCTATGGG
66 GGCAATTATGCAGGCATCACATCATTGAAGGATTGTAGCACCTCCAAAGGGGCTTCTTCTATGGG
* **
4655537 TTTTTGAAGCTCATCAATTTTCAAAGTTGTTAAATAAGTGACTTCATCTCTACGTACACCCTTGG
131 TTCTTGAAGCTCATCAATTTTCAAAGTTGCCAAATAAGTGACTTCATCTCTACGTACACCCTTGG
*
4655602 CAAACTGGATTGAGGACAACACCTTGGCTTTAACACTCATTTCTCGATTCACTGGCACAATAT
196 CAAACTGGATTGAGGACAACACCTTGGCTTTAACACTCATTTCTCGATTCACCGGCACAATAT
4655665 GTGGTTCAGCATTAGGCACCAGTTTAATTTTGTGATCCACCTCTCTCTTAGGTGGTAGCTTCTTC
1 GTGGTTCAGCATTAGGCACCAGTTTAATTTTGTGATCCACCTCTCTCTTAGGTGGTAGCTTCTTC
*
4655730 GGCAATTCTGCAGGCATCACATCATTGAAGGATTGTAGCACCTCCAAAGGGGCTTCTTCTATGGG
66 GGCAATTATGCAGGCATCACATCATTGAAGGATTGTAGCACCTCCAAAGGGGCTTCTTCTATGGG
4655795 TTCTTGAAGCTCATCAATTTTCAAAGTTGCCAAATAAGTGACTTCATCTCTACGTACACCCTTGG
131 TTCTTGAAGCTCATCAATTTTCAAAGTTGCCAAATAAGTGACTTCATCTCTACGTACACCCTTGG
4655860 CAAACTGGATTGAGGACAACACCTTGGCTTTAACACTCATTTCTCGATTCACCGGCACAATA
196 CAAACTGGATTGAGGACAACACCTTGGCTTTAACACTCATTTCTCGATTCACCGGCACAATA
4655922 CATTGATAGC
Statistics
Matches: 251, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 251 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (258 bp):
GTGGTTCAGCATTAGGCACCAGTTTAATTTTGTGATCCACCTCTCTCTTAGGTGGTAGCTTCTTC
GGCAATTATGCAGGCATCACATCATTGAAGGATTGTAGCACCTCCAAAGGGGCTTCTTCTATGGG
TTCTTGAAGCTCATCAATTTTCAAAGTTGCCAAATAAGTGACTTCATCTCTACGTACACCCTTGG
CAAACTGGATTGAGGACAACACCTTGGCTTTAACACTCATTTCTCGATTCACCGGCACAATAT
Found at i:4659574 original size:2 final size:2
Alignment explanation
Indices: 4659569--4659601 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4659559 ATAAATATGA
*
4659569 TC TC TC CC 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 T
4659602 TTGATATGCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:4659832 original size:18 final size:18
Alignment explanation
Indices: 4659800--4659876 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
4659790 TTAAATTAAT
4659800 ATAAAATTCAT-TTAATTA
1 ATAAAATT-ATATTAATTA
*
4659818 ATAAAATTATATTAA-AA
1 ATAAAATTATATTAATTA
* * * *
4659835 AT-TAATTAAATTGATTG
1 ATAAAATTATATTAATTA
*
4659852 ATATAATTA-ATTAAATTA
1 ATAAAATTATATT-AATTA
4659870 ATAAAAT
1 ATAAAAT
4659877 AAAAAATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
16 9 0.20
17 10 0.22
18 27 0.59
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAAAATTATATTAATTA
Found at i:4661032 original size:18 final size:18
Alignment explanation
Indices: 4661009--4661044 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4660999 ATCAATTTTG
* *
4661009 AAATAATAATTTAAAATT
1 AAATAAAAATATAAAATT
4661027 AAATAAAAATATAAAATT
1 AAATAAAAATATAAAATT
4661045 TTTTAAACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAAAATATAAAATT
Found at i:4661128 original size:1 final size:1
Alignment explanation
Indices: 4661122--4661149 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
4661112 TTTCAATCTT
4661122 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
4661150 CATCACGATA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4661619 original size:2 final size:2
Alignment explanation
Indices: 4661608--4661645 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4661598 CGGAACTTAT
*
4661608 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4661646 GAATTAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4667610 original size:25 final size:24
Alignment explanation
Indices: 4667563--4667626 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
4667553 ATATATAACA
4667563 TAAATAT-AATATTTAAAAGTAAT
1 TAAATATAAATATTTAAAAGTAAT
* **
4667586 TAAAATATAAATATTTTAATTTAAT
1 T-AAATATAAATATTTAAAAGTAAT
* *
4667611 TTAATATAAAAATTTA
1 TAAATATAAATATTTA
4667627 TAAATATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 1 0.03
24 18 0.55
25 14 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAATATAAATATTTAAAAGTAAT
Found at i:4670005 original size:16 final size:17
Alignment explanation
Indices: 4669984--4670019 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4669974 TTCTAATATG
4669984 TTGAGTTGA-TTAAGAC
1 TTGAGTTGATTTAAGAC
4670000 TTGAGTTGATTTAAGAC
1 TTGAGTTGATTTAAGAC
4670017 TTG
1 TTG
4670020 TTTATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.42
Consensus pattern (17 bp):
TTGAGTTGATTTAAGAC
Found at i:4674103 original size:19 final size:19
Alignment explanation
Indices: 4674064--4674119 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
4674054 TACATAAATT
* *
4674064 TTTTATTTTAATTATTTAAA
1 TTTTATTATAAATA-TTAAA
4674084 TTTTATTATAAATATTAAA
1 TTTTATTATAAATATTAAA
4674103 TATTTA-TATAAAT-TTAA
1 T-TTTATTATAAATATTAA
4674120 CGTAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 13 0.39
20 16 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTATTATAAATATTAAA
Found at i:4674221 original size:12 final size:12
Alignment explanation
Indices: 4674204--4674252 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
4674194 TATATTATAA
4674204 TATATTATATTT
1 TATATTATATTT
*
4674216 TATATTATCTTT
1 TATATTATATTT
* *
4674228 TATTTTTTATTT
1 TATATTATATTT
*
4674240 ATATAATATATTT
1 -TATATTATATTT
4674253 AATAATATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TATATTATATTT
Found at i:4679146 original size:113 final size:113
Alignment explanation
Indices: 4678948--4679171 Score: 394
Period size: 113 Copynumber: 2.0 Consensus size: 113
4678938 AGACAAAACA
*
4678948 TTAAACCGAATATCGACAAATGAGGTGTTGCTGCCAAGGGAAATCGTCCAAGAAAAGTTGACAGG
1 TTAAACCGAATATCGACAAATGAGGTGTTGCTGCCAAGGAAAATCGTCCAAGAAAAGTTGACAGG
*
4679013 TTGATACTCGGTGAAAAGTAAATGGATGACATGTTTTATCAGCCTACT
66 TTGATACTCGGTGAAAAGTAAATGGATGACATGCTTTATCAGCCTACT
* * * *
4679061 TTAAACCTAATATCGACAAATGAGGTGTTGCTGCCAAGGAAAATCGTCCGAGAAAAGTTGTCTGG
1 TTAAACCGAATATCGACAAATGAGGTGTTGCTGCCAAGGAAAATCGTCCAAGAAAAGTTGACAGG
4679126 TTGATACTCGGTGAAAAGTAAATGGATGACATGCTTTATCAGCCTA
66 TTGATACTCGGTGAAAAGTAAATGGATGACATGCTTTATCAGCCTA
4679172 GTGTAAAATG
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 105 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (113 bp):
TTAAACCGAATATCGACAAATGAGGTGTTGCTGCCAAGGAAAATCGTCCAAGAAAAGTTGACAGG
TTGATACTCGGTGAAAAGTAAATGGATGACATGCTTTATCAGCCTACT
Found at i:4684039 original size:11 final size:12
Alignment explanation
Indices: 4683992--4684039 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4683982 TTTACAGTCG
4683992 TTTTAAAATATAAA
1 TTTTAAAA-A-AAA
* * *
4684006 TATTAAATATAA
1 TTTTAAAAAAAA
4684018 TTTTAAAAAAAA
1 TTTTAAAAAAAA
4684030 TTTTAAAAAA
1 TTTTAAAAAA
4684040 TTAAATATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 21 0.75
13 1 0.04
14 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTTTAAAAAAAA
Found at i:4690372 original size:28 final size:28
Alignment explanation
Indices: 4690335--4690396 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
4690325 TTAAATATGA
* *
4690335 ATATAAAAAAATTTTATAAATATTTTAAAT
1 ATATAAAAATATTTTA-AAA-AATTTAAAT
4690365 ATATAAAAATATTTTAAAAAATTTAAAT
1 ATATAAAAATATTTTAAAAAATTTAAAT
4690393 ATAT
1 ATAT
4690397 TTATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 12 0.40
29 3 0.10
30 15 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATAAAAATATTTTAAAAAATTTAAAT
Found at i:4690383 original size:10 final size:10
Alignment explanation
Indices: 4690340--4690398 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 10
4690330 TATGAATATA
*
4690340 AAAAAATTTT
1 AAAATATTTT
4690350 ATAAATATTTT
1 A-AAATATTTT
* *
4690361 -AAATATATA
1 AAAATATTTT
4690370 AAAATATTTT
1 AAAATATTTT
*
4690380 AAAA-AATTT
1 AAAATATTTT
4690389 AAATATATTT
1 AAA-ATATTT
4690399 ATATTAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
9 14 0.37
10 13 0.34
11 11 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATATTTT
Found at i:4693455 original size:27 final size:27
Alignment explanation
Indices: 4693411--4693475 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
4693401 AAAAATGAGG
* * **
4693411 TTGGAATATCCTTCGAAATTGATGGGA
1 TTGGAGTATCCTTCGAAAATGATAAGA
*
4693438 TTGGAGTATCTCTT-GAAAATGGTAAGA
1 TTGGAGTATC-CTTCGAAAATGATAAGA
4693465 TTGGAGTATCC
1 TTGGAGTATCC
4693476 CTTAAAGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.88
28 3 0.09
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (27 bp):
TTGGAGTATCCTTCGAAAATGATAAGA
Found at i:4693789 original size:79 final size:78
Alignment explanation
Indices: 4693706--4693877 Score: 184
Period size: 79 Copynumber: 2.2 Consensus size: 78
4693696 GGAGATAGTG
* * * *
4693706 GGGTTGCAGTATCTCCAATGGTG-AAATTTTGATATTTTGGAAGTAAAAATGAGGTTAGAGCATC
1 GGGTTGCAGTATC-CCAATAGTGAAAAATTCGATATTTTAGAAGTAAAAATGAGGTTAGAGCATC
**
4693770 TTCTCAGAAATAAT
65 CCCTCAGAAATAAT
* * * * * *
4693784 AGGGTTGGATTATCCCAATAGTGAAAAATTCGATATTTTAGAATTAAAATTGAGGTTGGAGTATC
1 -GGGTTGCAGTATCCCAATAGTGAAAAATTCGATATTTTAGAAGTAAAAATGAGGTTAGAGCATC
*
4693849 CCCTCAGAAATGAT
65 CCCTCAGAAATAAT
**
4693863 GGGTTAAAGTATCCC
1 GGGTTGCAGTATCCC
4693878 CGATGGAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
78 20 0.26
79 56 0.74
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (78 bp):
GGGTTGCAGTATCCCAATAGTGAAAAATTCGATATTTTAGAAGTAAAAATGAGGTTAGAGCATCC
CCTCAGAAATAAT
Found at i:4696227 original size:51 final size:50
Alignment explanation
Indices: 4696140--4696309 Score: 214
Period size: 50 Copynumber: 3.3 Consensus size: 50
4696130 TACATTGAAG
* * * *
4696140 AATGTATCAATATATTTGGGTAAAAAACTCAAAATATATCGATACAATAAAA
1 AATGTATCAATACATTTAGGT-TAAAACCCAAAATATATCGATACAAT-AAA
* * *
4696192 AATGTATCGATACATTTAGGTTAAAACCCAGAATATATCGATACAATGAA
1 AATGTATCAATACATTTAGGTTAAAACCCAAAATATATCGATACAATAAA
* * *
4696242 AATATATCGATACATTTAGGTTAAAACCCAAAATGTATCGATACAATGAAA
1 AATGTATCAATACATTTAGGTTAAAACCCAAAATATATCGATACAAT-AAA
*
4696293 AATGTATCAATAGATTT
1 AATGTATCAATACATTT
4696310 TCTTTTTAGA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
50 46 0.45
51 39 0.38
52 18 0.17
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (50 bp):
AATGTATCAATACATTTAGGTTAAAACCCAAAATATATCGATACAATAAA
Found at i:4697298 original size:6 final size:6
Alignment explanation
Indices: 4697287--4697340 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
4697277 AATATAAATC
* *
4697287 ATATTT ATATTT AAAATTT A-A-AT ATATTT ATGATTT ATA-TT ATATTT
1 ATATTT ATATTT -ATATTT ATATTT ATATTT AT-ATTT ATATTT ATATTT
4697334 ATATTT A
1 ATATTT A
4697341 AATAAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.05
5 7 0.17
6 20 0.50
7 11 0.28
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
ATATTT
Found at i:4697312 original size:17 final size:17
Alignment explanation
Indices: 4697292--4697344 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
4697282 AAATCATATT
4697292 TATATTTAAAATTTAAA
1 TATATTTAAAATTTAAA
** *
4697309 TATATTTATGATTTATAT
1 TATATTTAAAATTTA-AA
*
4697327 TATATTT-ATATTTAAA
1 TATATTTAAAATTTAAA
4697343 TA
1 TA
4697345 AATAATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 3 0.10
17 18 0.62
18 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TATATTTAAAATTTAAA
Found at i:4702996 original size:24 final size:24
Alignment explanation
Indices: 4702953--4703006 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4702943 AGGTGGAGGT
*
4702953 GGTGGATATGGAGGGAGTGGATCC
1 GGTGGATATGGAGGGAGTGGATAC
* *
4702977 GGTGGTTATGGAGGCG-GTGGGTAC
1 GGTGGATATGGAGG-GAGTGGATAC
4703001 GGTGGA
1 GGTGGA
4703007 GGAAGGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.54, T:0.22
Consensus pattern (24 bp):
GGTGGATATGGAGGGAGTGGATAC
Found at i:4703042 original size:21 final size:21
Alignment explanation
Indices: 4703014--4703062 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
4703004 GGAGGAAGGA
*
4703014 GAGGTGGGTATGGTGGTGGTG
1 GAGGTGGGTATGGCGGTGGTG
*
4703035 GCGGTGGGTATGGCGGTGGTG
1 GAGGTGGGTATGGCGGTGGTG
4703056 GAGGTGG
1 GAGGTGG
4703063 AGGTGGTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.04, G:0.63, T:0.24
Consensus pattern (21 bp):
GAGGTGGGTATGGCGGTGGTG
Found at i:4706600 original size:15 final size:14
Alignment explanation
Indices: 4706557--4706605 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 14
4706547 CCCCACTTTT
4706557 TATTTTT-TTTAAA
1 TATTTTTATTTAAA
*
4706570 TATTTATATTT-AA
1 TATTTTTATTTAAA
4706583 TATTTTTATTTAATA
1 TATTTTTATTTAA-A
4706598 TATTTTTA
1 TATTTTTA
4706606 AATATGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 18 0.58
14 4 0.13
15 9 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATTTAAA
Found at i:4706806 original size:2 final size:2
Alignment explanation
Indices: 4706799--4706825 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4706789 ATCTTCGGTT
4706799 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 T
4706826 CAATCAGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4706987 original size:2 final size:2
Alignment explanation
Indices: 4706980--4707013 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4706970 CTCTAGTACC
4706980 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
4707014 TAAGTATGCT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4713044 original size:12 final size:13
Alignment explanation
Indices: 4713013--4713047 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
4713003 TCTCTTCAAA
4713013 ATATTT-ATATTT
1 ATATTTAATATTT
4713025 ATATTTAATATTT
1 ATATTTAATATTT
4713038 AT-TTTAATAT
1 ATATTTAATAT
4713048 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:4714109 original size:64 final size:67
Alignment explanation
Indices: 4713965--4714109 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 67
4713955 CTGTTCTCAC
* * * *
4713965 TAAAATTTATTAAAAAATTTTGAGATATTCAAAATAAAAATATAATTTTTTATAATATTTATATA
1 TAAAATTTATTAAAAAATTATGAAATATTCAAAATAAAAATATAATTTTTTATAATAATAATATA
4714030 TA
66 TA
* ** *
4714032 TATAAA--TA-AAAAAAATTAT-AAATATT-AAAATTTTAATTATAATTTTTT-TAATAATAAT-
1 TA-AAATTTATTAAAAAATTATGAAATATTCAAAA-TAAAAATATAATTTTTTATAATAATAATA
4714090 TATA
64 TATA
4714094 TAAAATTTATTAAAAA
1 TAAAATTTATTAAAAA
4714110 TAAGCTCAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
61 3 0.05
62 6 0.09
63 14 0.22
64 25 0.39
65 9 0.14
66 2 0.03
67 2 0.03
68 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (67 bp):
TAAAATTTATTAAAAAATTATGAAATATTCAAAATAAAAATATAATTTTTTATAATAATAATATA
TA
Found at i:4714281 original size:18 final size:19
Alignment explanation
Indices: 4714260--4714298 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
4714250 CTTATTAAAT
4714260 TAATTTTATATATT-TTTA
1 TAATTTTATATATTATTTA
*
4714278 TAATTTTTTATATTATTTA
1 TAATTTTATATATTATTTA
4714297 TA
1 TA
4714299 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TAATTTTATATATTATTTA
Found at i:4714303 original size:10 final size:10
Alignment explanation
Indices: 4714264--4714339 Score: 72
Period size: 10 Copynumber: 7.7 Consensus size: 10
4714254 TTAAATTAAT
4714264 TTTATATATT-
1 TTTATAT-TTA
4714274 TTTATAATTT-
1 TTTAT-ATTTA
4714284 TTTATA-TTA
1 TTTATATTTA
4714293 TTTATATTTA
1 TTTATATTTA
4714303 TTTA-ATTTA
1 TTTATATTTA
*
4714312 ATTATCATTT-
1 TTTAT-ATTTA
4714322 TTTATTATTTA
1 TTTA-TATTTA
4714333 TTTATAT
1 TTTATAT
4714340 AAATAATACA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
8 2 0.04
9 15 0.26
10 29 0.51
11 11 0.19
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATATTTA
Found at i:4715722 original size:17 final size:18
Alignment explanation
Indices: 4715692--4715730 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
4715682 TCTAAATTAT
4715692 TATTTATATAATTAAAAA
1 TATTTATATAATTAAAAA
*
4715710 TATTTAT-TAATTATAAA
1 TATTTATATAATTAAAAA
4715727 TATT
1 TATT
4715731 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTATATAATTAAAAA
Found at i:4717185 original size:11 final size:10
Alignment explanation
Indices: 4717160--4717184 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4717150 TGTGCTTTCC
4717160 TTTTTCTTTT
1 TTTTTCTTTT
4717170 TTTTTCTTTT
1 TTTTTCTTTT
4717180 TTTTT
1 TTTTT
4717185 TTGCTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:4721089 original size:18 final size:18
Alignment explanation
Indices: 4721066--4721100 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4721056 TCGTATCTAA
4721066 AATCCATAATAGCATGTC
1 AATCCATAATAGCATGTC
* *
4721084 AATCCATGATGGCATGT
1 AATCCATAATAGCATGT
4721101 GAGCGGGCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (18 bp):
AATCCATAATAGCATGTC
Found at i:4722786 original size:18 final size:19
Alignment explanation
Indices: 4722751--4722788 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4722741 TTAGTTAATT
*
4722751 ATAAAAATTATATTTATTA
1 ATAAAAATTATATATATTA
*
4722770 ATAATAATT-TATATATTA
1 ATAAAAATTATATATATTA
4722788 A
1 A
4722789 AATGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAAAAATTATATATATTA
Found at i:4723335 original size:21 final size:23
Alignment explanation
Indices: 4723309--4723358 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
4723299 TTAATTAAAA
4723309 ATAAATAATTT-AATTAAAT-TT
1 ATAAATAATTTAAATTAAATATT
*
4723330 ATAAATTATTTAAATTAAATATT
1 ATAAATAATTTAAATTAAATATT
4723353 A-AAATA
1 ATAAATA
4723359 TTATATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 12 0.48
23 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAAATAATTTAAATTAAATATT
Found at i:4723360 original size:21 final size:20
Alignment explanation
Indices: 4723309--4723373 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
4723299 TTAATTAAAA
4723309 ATAAATAATTTAATTAAATTT
1 ATAAAT-ATTTAATTAAATTT
4723330 ATAAATTATTTAAATTAAATATT
1 ATAAA-TATTT-AATTAAAT-TT
*
4723353 A-AAATA-TTATATTTAATTT
1 ATAAATATTTA-ATTAAATTT
4723372 AT
1 AT
4723374 TTAATAACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.11
20 8 0.21
21 11 0.29
22 12 0.32
23 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAATATTTAATTAAATTT
Found at i:4723372 original size:31 final size:35
Alignment explanation
Indices: 4723337--4723406 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 35
4723327 TTTATAAATT
4723337 ATTTAAATTAAAT-A-TTAAAATATTAT-ATTT-A
1 ATTTAAATTAAATAACTTAAAATATTATAATTTGA
* *
4723368 ATTT--ATTTAATAACTTAAATTATTATAATTTGA
1 ATTTAAATTAAATAACTTAAAATATTATAATTTGA
4723401 ATTTAA
1 ATTTAA
4723407 TTTTATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
29 6 0.19
30 1 0.03
31 15 0.48
32 4 0.13
33 5 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (35 bp):
ATTTAAATTAAATAACTTAAAATATTATAATTTGA
Found at i:4723511 original size:30 final size:28
Alignment explanation
Indices: 4723475--4723572 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 28
4723465 AACAAAAATA
4723475 TATATATGATAATTAAAATTTTTTTATTAT
1 TATATATGAT-A-TAAAATTTTTTTATTAT
4723505 TATATATTGATAT-AAATTTTTTTAATT-T
1 TATATA-TGATATAAAATTTTTTT-ATTAT
4723533 TATAAGTATGATCA-AAAATTATTCATTTATTAT
1 TAT-A-TATGAT-ATAAAATT-TT--TTTATTAT
4723566 TATATAT
1 TATATAT
4723573 TTAAAAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
28 14 0.24
29 9 0.16
30 15 0.26
31 9 0.16
32 4 0.07
33 7 0.12
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (28 bp):
TATATATGATATAAAATTTTTTTATTAT
Found at i:4723521 original size:28 final size:29
Alignment explanation
Indices: 4723489--4723573 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 29
4723479 TATGATAATT
4723489 AAAATTTTTTTATTATTATATATTGAT-A
1 AAAATTTTTTTATTATTATATATTGATCA
*
4723517 TAAATTTTTTTAATT-TTATA-AGTATGATCA
1 AAAATTTTTTT-ATTATTATATA-T-TGATCA
4723547 AAAATTATTCATTTATTATTATATATT
1 AAAATT-TT--TTTATTATTATATATT
4723574 TAAAAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
27 1 0.02
28 16 0.35
29 7 0.15
30 6 0.13
31 2 0.04
32 4 0.09
33 9 0.20
34 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (29 bp):
AAAATTTTTTTATTATTATATATTGATCA
Found at i:4727709 original size:2 final size:2
Alignment explanation
Indices: 4727702--4727738 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4727692 TGGCCCCTTC
4727702 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 A
4727739 ACCCTAACCT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4728575 original size:3 final size:3
Alignment explanation
Indices: 4728567--4728597 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4728557 TTTTAGTGTC
4728567 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4728598 ATGTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4728834 original size:13 final size:14
Alignment explanation
Indices: 4728818--4728847 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4728808 ATTTTTATAT
4728818 ATTTAAATAA-TAA
1 ATTTAAATAATTAA
4728831 ATTTAAATAATTAA
1 ATTTAAATAATTAA
4728845 ATT
1 ATT
4728848 ACAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTAAATAATTAA
Found at i:4729208 original size:24 final size:25
Alignment explanation
Indices: 4729167--4729228 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
4729157 AAAAGAAAGT
4729167 AATATTGATATTTATTTA-ATATAAA
1 AATATTGATATTTATTTATAT-TAAA
* *
4729192 AATATTTA-ATTTTTTTATATTAAA
1 AATATTGATATTTATTTATATTAAA
4729216 AA-ATT-ATATTTAT
1 AATATTGATATTTAT
4729229 ATTTAAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.03
23 8 0.25
24 14 0.44
25 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATTGATATTTATTTATATTAAA
Found at i:4729216 original size:23 final size:25
Alignment explanation
Indices: 4729167--4729228 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
4729157 AAAAGAAAGT
4729167 AATATTGATATTTATTTAATATAAA
1 AATATTGATATTTATTTAATATAAA
* *
4729192 AATATTTA-ATTT-TTTTATATTAAA
1 AATATTGATATTTATTTAATA-TAAA
4729216 AA-ATT-ATATTTAT
1 AATATTGATATTTAT
4729229 ATTTAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 13 0.41
24 11 0.34
25 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATTGATATTTATTTAATATAAA
Found at i:4733870 original size:21 final size:22
Alignment explanation
Indices: 4733836--4733877 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4733826 TATTAATATG
4733836 AAAATAATTTTTTAAAATAATA
1 AAAATAATTTTTTAAAATAATA
*
4733858 AAAATAA-TTTTTAAATTAAT
1 AAAATAATTTTTTAAAATAAT
4733878 CTAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATAATTTTTTAAAATAATA
Found at i:4734037 original size:39 final size:40
Alignment explanation
Indices: 4733994--4734069 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
4733984 AATTAATATT
*
4733994 TAAAAATATATA-ATTAATACATTATTTTAT-TAAATTTAA
1 TAAAAATA-ATACATAAATACATTATTTTATATAAATTTAA
* *
4734033 TAAAAATAATACATAAATATATTATTTTTTATAAATT
1 TAAAAATAATACATAAATACATTATTTTATATAAATT
4734070 ATCTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.09
39 23 0.72
40 6 0.19
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (40 bp):
TAAAAATAATACATAAATACATTATTTTATATAAATTTAA
Found at i:4734300 original size:21 final size:20
Alignment explanation
Indices: 4734265--4734303 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4734255 CCATATATTT
4734265 ATTTATATATAATATAATAA
1 ATTTATATATAATATAATAA
*
4734285 ATTTATATTTTAATATAAT
1 ATTTATA-TATAATATAAT
4734304 TTTATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATATATAATATAATAA
Found at i:4738147 original size:21 final size:21
Alignment explanation
Indices: 4738123--4738163 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4738113 AGGTAAATGA
4738123 TATTTTAAAATT-TTTATTAAT
1 TATTTTAAAATTATTT-TTAAT
4738144 TATTTTAAAATTATTTTTAA
1 TATTTTAAAATTATTTTTAA
4738164 AAAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTAAAATTATTTTTAAT
Found at i:4742484 original size:13 final size:13
Alignment explanation
Indices: 4742466--4742490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4742456 GGCTTGGGAG
4742466 TGACTAAAAGAAA
1 TGACTAAAAGAAA
4742479 TGACTAAAAGAA
1 TGACTAAAAGAA
4742491 TATTGGCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (13 bp):
TGACTAAAAGAAA
Found at i:4742580 original size:13 final size:14
Alignment explanation
Indices: 4742564--4742594 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4742554 AAAATTTAAA
4742564 AATATTTT-AAATC
1 AATATTTTAAAATC
4742577 AATATTTTAAAATC
1 AATATTTTAAAATC
4742591 AATA
1 AATA
4742595 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATTTTAAAATC
Found at i:4742905 original size:22 final size:21
Alignment explanation
Indices: 4742880--4742921 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
4742870 ATATTAAAAA
4742880 TTATTCTTA-AATTAATATTTAT
1 TTATT-TTATAATTAA-ATTTAT
4742902 TTATTTTATAATTAAATTTA
1 TTATTTTATAATTAAATTTA
4742922 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTTTATAATTAAATTTAT
Found at i:4744166 original size:28 final size:26
Alignment explanation
Indices: 4744129--4744200 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 26
4744119 GACTAAATTC
4744129 AATAATTTTAAATATAATATAAATATT
1 AATAATTTTAAATATAATA-AAATATT
* * *
4744156 ATATAAATTTATATATAATAAATTATT
1 A-ATAATTTTAAATATAATAAAATATT
*
4744183 AAT-ATTTTAAAAATAATA
1 AATAATTTTAAATATAATA
4744201 CGATATAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 12 0.32
26 2 0.05
27 8 0.21
28 16 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAATTTTAAATATAATAAAATATT
Done.