Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 21 of 27
Found at i:3535961 original size:17 final size:16
Alignment explanation
Indices: 3535921--3535963 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3535911 AAATAATTTA
*
3535921 AAATTTTTAAAAATTG
1 AAATTTTAAAAAATTG
*
3535937 AATTTTTTAAAAAATTG
1 AA-ATTTTAAAAAATTG
3535954 ATAATTTTAA
1 A-AATTTTAA
3535964 CATTGAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
AAATTTTAAAAAATTG
Found at i:3537051 original size:3 final size:3
Alignment explanation
Indices: 3537043--3537070 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3537033 GATTCATAGC
3537043 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3537071 AATAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3545955 original size:43 final size:43
Alignment explanation
Indices: 3545894--3545978 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
3545884 GGAAGCAGCC
* **
3545894 TAAATCATGAAAACGGGGTCATGAGAGCGCAATAAAAGCGTCG
1 TAAATCATGAAAACGGGGTCATGAAAAAGCAATAAAAGCGTCG
* *
3545937 TAAATCGTGAAAACGGGGTCATGAAAAAGCTATAAAAGCGTC
1 TAAATCATGAAAACGGGGTCATGAAAAAGCAATAAAAGCGTC
3545979 ATACTGCTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (43 bp):
TAAATCATGAAAACGGGGTCATGAAAAAGCAATAAAAGCGTCG
Found at i:3548966 original size:14 final size:14
Alignment explanation
Indices: 3548947--3548981 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3548937 GAGGTAAGAA
3548947 AAATAGAGAATCAG
1 AAATAGAGAATCAG
3548961 AAATAGAGAATCAG
1 AAATAGAGAATCAG
*
3548975 AATTAGA
1 AAATAGA
3548982 TAGAATAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
AAATAGAGAATCAG
Found at i:3563976 original size:5 final size:5
Alignment explanation
Indices: 3563957--3564173 Score: 80
Period size: 5 Copynumber: 43.4 Consensus size: 5
3563947 TTAAATTTAA
* * **
3563957 ATTAA ATTAA ATTAT ATTATT ATTAT AAAAT ATTTAAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTA-T ATTAT ATTAT A-TT-AT ATTAT ATTAT
* * * * *
3564005 ACTT-T AATT-T AATAT -TTATT ATTAT AATAA ATTAAA ATTAA ATT-T
1 A-TTAT -ATTAT ATTAT ATTA-T ATTAT ATTAT ATT-AT ATTAT ATTAT
* *
3564050 AATA- ATTCAT A-TAT -TTAT ATTAT ATTAT ATTAT ATATTT ATTAT ATT-T
1 ATTAT ATT-AT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT
* * * * *
3564098 ATTAT -TATAT ATT-T ATTAT ATTTT ATTTT ATATAA ATTTT AATAT ATTA-
1 ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT
* *
3564147 ATAAT -TTAT ATTAT ATATAT TTTAT AT
1 ATTAT ATTAT ATTAT AT-TAT ATTAT AT
3564174 AATACAAAAT
Statistics
Matches: 162, Mismatches: 27, Indels: 46
0.69 0.11 0.20
Matches are distributed among these distances:
4 28 0.17
5 100 0.62
6 31 0.19
7 3 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:3564039 original size:23 final size:22
Alignment explanation
Indices: 3563940--3564090 Score: 79
Period size: 23 Copynumber: 6.9 Consensus size: 22
3563930 TTTTAAATGA
*
3563940 ATAAT-AATTAA-ATTTAAATT
1 ATAATAAATTAATATTTATATT
3563960 A-AATTAAATT-ATA-TTATTATT
1 ATAA-TAAATTAATATTTA-TATT
3563981 ATAA-AATATTTAATA-TTATATT
1 ATAATAA-A-TTAATATTTATATT
* *
3564003 ATACTTTAATTTAATATTTATTATT
1 ATA--ATAAATTAATATTTA-TATT
* *
3564028 ATAATAAATTAA-AATTAAATT
1 ATAATAAATTAATATTTATATT
3564049 -TAAT-AATTCATATATTTATATT
1 ATAATAAATT-A-ATATTTATATT
* *
3564071 ATATTATATTATATATTTAT
1 ATAATAAATTA-ATATTTAT
3564091 TATATTTATT
Statistics
Matches: 102, Mismatches: 11, Indels: 33
0.70 0.08 0.23
Matches are distributed among these distances:
19 6 0.06
20 13 0.13
21 14 0.14
22 22 0.22
23 32 0.31
24 6 0.06
25 9 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATAAATTAATATTTATATT
Found at i:3564096 original size:9 final size:9
Alignment explanation
Indices: 3564064--3564120 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
3564054 ATTCATATAT
3564064 TTATATTATA
1 TTATATT-TA
3564074 TTATA-TTA
1 TTATATTTA
3564082 -TATATTTA
1 TTATATTTA
3564090 TTATATTTA
1 TTATATTTA
3564099 -T-TA-TTA
1 TTATATTTA
3564105 -TATATTTA
1 TTATATTTA
3564113 TTATATTT
1 TTATATTT
3564121 TATTTTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
6 4 0.10
7 8 0.19
8 9 0.21
9 16 0.38
10 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATATTTA
Found at i:3564103 original size:23 final size:23
Alignment explanation
Indices: 3564058--3564131 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 23
3564048 TTAATAATTC
3564058 ATATATTTA-TATTATATTA-TATT
1 ATATATTTATTA-TAT-TTATTATT
3564081 ATATATTTATTATATTTATTATT
1 ATATATTTATTATATTTATTATT
3564104 ATATATTTATTATATTTTATT-TT
1 ATATATTTATTATA-TTTATTATT
3564127 ATATA
1 ATATA
3564132 AATTTTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
22 3 0.06
23 37 0.77
24 8 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATATTTATTATATTTATTATT
Found at i:3564118 original size:32 final size:31
Alignment explanation
Indices: 3564059--3564173 Score: 113
Period size: 32 Copynumber: 3.9 Consensus size: 31
3564049 TAATAATTCA
3564059 TATATTTATATTATATTATATTA-TATATTTAT
1 TATATTTATATTATA-TATATTATTATA-TTAT
3564091 TATATTTATTATTATATAT-TTATTATATT-T
1 TATATTTA-TATTATATATATTATTATATTAT
* * *
3564121 TAT-TTTATA-TA-A-ATTTTAATATATTAA
1 TATATTTATATTATATATATTATTATATTAT
3564148 TA-ATTTATATTATATATATT-TTATAT
1 TATATTTATATTATATATATTATTATAT
3564174 AATACAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
25 2 0.03
26 10 0.14
27 10 0.14
28 4 0.06
29 10 0.14
30 8 0.11
31 5 0.07
32 15 0.21
33 7 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATATTTATATTATATATATTATTATATTAT
Found at i:3564216 original size:16 final size:16
Alignment explanation
Indices: 3564058--3564217 Score: 100
Period size: 16 Copynumber: 9.9 Consensus size: 16
3564048 TTAATAATTC
*
3564058 ATATAT-TTATATTAT
1 ATATATATTATATTTT
3564073 AT-TATATTATATATTT
1 ATATATATTATAT-TTT
3564089 AT-TATATT-TATTATT
1 ATATATATTATATT-TT
3564104 ATATATTTATTATATTTT
1 ATATA--TATTATATTTT
* *
3564122 AT-TTTATATAAATTTT
1 ATATATAT-TATATTTT
*
3564138 A-ATATATTAATAATTT
1 ATATATATT-ATATTTT
3564154 ATAT-TATATATATTTT
1 ATATATAT-TATATTTT
** * * *
3564170 ATATAATACAAAATATC
1 ATAT-ATATTATATTTT
* *
3564187 ATATATTTTGTATTTT
1 ATATATATTATATTTT
3564203 ATATATATTATATTT
1 ATATATATTATATTT
3564218 ATAAAAAATT
Statistics
Matches: 110, Mismatches: 21, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
14 4 0.04
15 19 0.17
16 61 0.55
17 12 0.11
18 10 0.09
19 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (16 bp):
ATATATATTATATTTT
Found at i:3564882 original size:15 final size:15
Alignment explanation
Indices: 3564860--3564903 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
3564850 AGTGGTCTTA
3564860 AAAT-TATTAATAAT
1 AAATATATTAATAAT
3564874 AAATATATT-ATAA-
1 AAATATATTAATAAT
3564887 AAA-ATATTAAT-AT
1 AAATATATTAATAAT
3564900 AAAT
1 AAAT
3564904 TTAATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 8 0.31
15 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATATTAATAAT
Found at i:3565191 original size:10 final size:10
Alignment explanation
Indices: 3565174--3565214 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
3565164 AATTAAATAA
3565174 ATAT-AAATT
1 ATATAAAATT
3565183 ATATAAAATT
1 ATATAAAATT
* *
3565193 TTATAAAAAT
1 ATATAAAATT
3565203 ATATAAAATT
1 ATATAAAATT
3565213 AT
1 AT
3565215 CACGTCTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
9 4 0.15
10 23 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATAAAATT
Found at i:3567469 original size:14 final size:14
Alignment explanation
Indices: 3567446--3567475 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3567436 TTATTATAAA
*
3567446 TATATTTAAAATTT
1 TATATGTAAAATTT
3567460 TATATGTAAAATTT
1 TATATGTAAAATTT
3567474 TA
1 TA
3567476 AATATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TATATGTAAAATTT
Found at i:3567505 original size:18 final size:17
Alignment explanation
Indices: 3567444--3567503 Score: 72
Period size: 18 Copynumber: 3.6 Consensus size: 17
3567434 TTTTATTATA
3567444 AATATATTTAAAA-TTT
1 AATATATTTAAAATTTT
*
3567460 --TATATGTAAAATTTT
1 AATATATTTAAAATTTT
3567475 AAATATATTTATAAATTTT
1 -AATATATTTA-AAATTTT
3567494 AATATATTTA
1 AATATATTTA
3567504 TATATTTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.27
15 3 0.08
18 17 0.46
19 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
AATATATTTAAAATTTT
Found at i:3567512 original size:19 final size:19
Alignment explanation
Indices: 3567470--3567540 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
3567460 TATATGTAAA
*
3567470 ATTTTAAATATATTTATA-
1 ATTTTTAATATATTTATAT
*
3567488 AATTTTAATATATTTATAT
1 ATTTTTAATATATTTATAT
**
3567507 ATTTTTGTTATATTTATAT
1 ATTTTTAATATATTTATAT
* *
3567526 TTTTTTATTATATTT
1 ATTTTTAATATATTT
3567541 TATTAATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
18 16 0.36
19 29 0.64
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (19 bp):
ATTTTTAATATATTTATAT
Found at i:3567549 original size:11 final size:10
Alignment explanation
Indices: 3567489--3567545 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
3567479 ATATTTATAA
*
3567489 ATTTTAATAT
1 ATTTTATTAT
3567499 A-TTTA-TAT
1 ATTTTATTAT
*
3567507 ATTTTTGTTAT
1 A-TTTTATTAT
3567518 ATTTATATT-T
1 ATTT-TATTAT
3567528 -TTTTATTAT
1 ATTTTATTAT
3567537 ATTTTATTA
1 ATTTTATTA
3567546 ATATATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 16 0.41
11 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:3567662 original size:2 final size:2
Alignment explanation
Indices: 3567657--3567683 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3567647 TGGGCGTGTG
3567657 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
3567684 TGAAATACAC
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:3567749 original size:18 final size:16
Alignment explanation
Indices: 3567734--3567766 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3567724 ATTAAATATT
*
3567734 TATTTTAAATTTAATA
1 TATTATAAATTTAATA
3567750 -ATTATAAATTTAATA
1 TATTATAAATTTAATA
3567765 TA
1 TA
3567767 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 2
0.83 0.06 0.11
Matches are distributed among these distances:
15 14 0.93
16 1 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATAAATTTAATA
Found at i:3568173 original size:20 final size:20
Alignment explanation
Indices: 3568150--3568190 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3568140 TAATCATATT
3568150 TAAATTATT-ATATATTTATA
1 TAAATT-TTGATATATTTATA
*
3568170 TAAATTTTGATATGTTTATA
1 TAAATTTTGATATATTTATA
3568190 T
1 T
3568191 TTTATGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TAAATTTTGATATATTTATA
Found at i:3568228 original size:11 final size:11
Alignment explanation
Indices: 3568212--3568251 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3568202 TAGATTTTAA
3568212 TATATTTATAT
1 TATATTTATAT
3568223 TATATTTATAT
1 TATATTTATAT
* *
3568234 TATTTTTTATGT
1 TA-TATTTATAT
3568246 TATATT
1 TATATT
3568252 ATGCAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3572313 original size:21 final size:19
Alignment explanation
Indices: 3572289--3572328 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
3572279 ATAAAAATAT
*
3572289 TTTAATTTTTATATTATTAAA
1 TTTAATATTTA-ATT-TTAAA
3572310 TTTAATATTTAATTTTAAA
1 TTTAATATTTAATTTTAAA
3572329 ATTATGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATATTTAATTTTAAA
Found at i:3572382 original size:20 final size:20
Alignment explanation
Indices: 3572359--3572413 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
3572349 ATTAAAAATA
3572359 TTAAAAAAATATTTAAATTT
1 TTAAAAAAATATTTAAATTT
*
3572379 TTAACTTAAAAT-TTTAAATTT
1 TTAA--AAAAATATTTAAATTT
*
3572400 TATCAAAAAATATT
1 T-TAAAAAAATATT
3572414 CATTTTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 9 0.32
21 12 0.43
22 7 0.25
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAAAATATTTAAATTT
Found at i:3572450 original size:40 final size:40
Alignment explanation
Indices: 3572360--3572444 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
3572350 TTAAAAATAT
*
3572360 TAAAAAAATATTTAAATTTTTAACTTAAAATTTTAAATTTTA
1 TAAAAAAATA-TT-CATTTTTAACTTAAAATTTTAAATTTTA
* * *
3572402 TCAAAAAATATTCATTTTTAACTTATAA-TTT-AATTTTT
1 TAAAAAAATATTCATTTTTAACTTAAAATTTTAAATTTTA
3572440 TAAAA
1 TAAAA
3572445 TAAAATTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
38 10 0.26
39 3 0.08
40 14 0.37
41 2 0.05
42 9 0.24
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (40 bp):
TAAAAAAATATTCATTTTTAACTTAAAATTTTAAATTTTA
Found at i:3573008 original size:18 final size:18
Alignment explanation
Indices: 3572981--3573021 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
3572971 ATCAAATATT
3572981 TAAA-TGTAATATTTTTA
1 TAAATTGTAATATTTTTA
3572998 TAAATTGTAATATTTTTA
1 TAAATTGTAATATTTTTA
3573016 TAAATT
1 TAAATT
3573022 ATTTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TAAATTGTAATATTTTTA
Found at i:3573094 original size:2 final size:2
Alignment explanation
Indices: 3573087--3573125 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3573077 TAAAATATTT
3573087 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
3573126 CATTTACGCA
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:3573867 original size:21 final size:20
Alignment explanation
Indices: 3573831--3573888 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3573821 ATATGATAAA
3573831 AAAATTTAACTTATAAAACTT
1 AAAATTTAA-TTATAAAACTT
* *
3573852 ATAAATTTGATTATAAAATTT
1 A-AAATTTAATTATAAAACTT
*
3573873 AAAATTTAATTTTAAA
1 AAAATTTAATTATAAA
3573889 TTATGAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.41
21 12 0.38
22 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTTAATTATAAAACTT
Found at i:3576895 original size:18 final size:19
Alignment explanation
Indices: 3576862--3576897 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3576852 TAATATATTT
3576862 TTTATTCGTATTATGTTTA
1 TTTATTCGTATTATGTTTA
*
3576881 TTTATTTGT-TTATGTTT
1 TTTATTCGTATTATGTTT
3576898 TTTGATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69
Consensus pattern (19 bp):
TTTATTCGTATTATGTTTA
Found at i:3582102 original size:117 final size:117
Alignment explanation
Indices: 3581884--3582236 Score: 494
Period size: 117 Copynumber: 3.0 Consensus size: 117
3581874 CTACTAAAAT
*
3581884 CCCATGTAACTTAAACCTTAAGTCCTTAACCAGTTCCCGCTCCCCGTT-TCTGGAAACAAAA-TT
1 CCCATGTAACTTAAACCTTAAGTCCTTAACCAGTTCCCGCTCCTCGTTAT-TGGAAACAAAACTT
* * *
3581947 CAGTCACTGCAGGAGACGGACAACGAACTTAGTTCGTTCACCGAGTGAACTTTC
65 -AGTTACTGCAGGAGACAGACAACGAACTGAGTTCGTTCACCGAGTGAACTTTC
* *
3582001 CCCATGTAACTTAAACCTTAAGGCCTTAACCAGTTCCCTCTCCTCGTTATTGGAAACAAAACTTA
1 CCCATGTAACTTAAACCTTAAGTCCTTAACCAGTTCCCGCTCCTCGTTATTGGAAACAAAACTTA
* * ** * * * *
3582066 GTTAATGCAGGAAACAGACGGCGTACTGAGTCCGTTCACCGAGTGAACCTTG
66 GTTACTGCAGGAGACAGACAACGAACTGAGTTCGTTCACCGAGTGAACTTTC
* * * * *
3582118 CCCATGTAACTTAAACCTTAAAGTCCTTAACCGGTTCCCGCTTCTCGTTATCGGGAACAAAACCT
1 CCCATGTAACTTAAACCTT-AAGTCCTTAACCAGTTCCCGCTCCTCGTTATTGGAAACAAAACTT
3582183 AGTTACTGCAGGAGACAGACAACGAACTGAGTTCGTTCACCGAGTGAACTTTC
65 AGTTACTGCAGGAGACAGACAACGAACTGAGTTCGTTCACCGAGTGAACTTTC
3582236 C
1 C
3582237 GGCAATGGAC
Statistics
Matches: 204, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
117 117 0.57
118 87 0.43
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (117 bp):
CCCATGTAACTTAAACCTTAAGTCCTTAACCAGTTCCCGCTCCTCGTTATTGGAAACAAAACTTA
GTTACTGCAGGAGACAGACAACGAACTGAGTTCGTTCACCGAGTGAACTTTC
Found at i:3593803 original size:177 final size:176
Alignment explanation
Indices: 3593497--3593828 Score: 565
Period size: 177 Copynumber: 1.9 Consensus size: 176
3593487 GTCCAGTTCA
*
3593497 CAAAATGCTAAGCATCAATGGCGTTGAAGGAGAGTGCAGTTGCTATGCGGTTGACATACCTGGAT
1 CAAAATGCTAAGCATCAATGGCGTTGAAGGAGAGTGCAGTTGCTATGCGGTTGACATACATGGAT
*
3593562 TAACAATTGAAGCTCGGATTAGCAGGCTTGAGAAACTGGTTGAAGAGCTAAAAGCAATGAGATCT
66 TAACAATTGAAGCTCGGATTAGCAGGCTTGAGAAACTGGTTGAAGAGCTAAAAGCAACGAGATCT
*
3593627 GCTTGCAAGTAGTCTCTAGCAATTAGCATTGAGATGTACTTATACT
131 GCTTGCAAGCAGTCTCTAGCAATTAGCATTGAGATGTACTTATACT
*
3593673 CAAAATCGCTAAGCATCAATGGTGTTGAAGGAGAGTGCAGTTGCTATGCGGTTGACATACATGGA
1 CAAAAT-GCTAAGCATCAATGGCGTTGAAGGAGAGTGCAGTTGCTATGCGGTTGACATACATGGA
* * *
3593738 TTAACACTTGAAGCTCGGATTAGCAGGCTTGAGAAACTGGTTGAAGAGTTAAAAGCGACGAGATC
65 TTAACAATTGAAGCTCGGATTAGCAGGCTTGAGAAACTGGTTGAAGAGCTAAAAGCAACGAGATC
* * *
3593803 TGCTTGGAAGCAGTCTTTAGCCATTA
130 TGCTTGCAAGCAGTCTCTAGCAATTA
3593829 ACATCAACAT
Statistics
Matches: 145, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
176 6 0.04
177 139 0.96
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (176 bp):
CAAAATGCTAAGCATCAATGGCGTTGAAGGAGAGTGCAGTTGCTATGCGGTTGACATACATGGAT
TAACAATTGAAGCTCGGATTAGCAGGCTTGAGAAACTGGTTGAAGAGCTAAAAGCAACGAGATCT
GCTTGCAAGCAGTCTCTAGCAATTAGCATTGAGATGTACTTATACT
Found at i:3600157 original size:25 final size:23
Alignment explanation
Indices: 3600128--3600176 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
3600118 AAATTTAAAA
*
3600128 TTTAAATTTTAATATTTATAATTTT
1 TTTAAATTTTAA-A-TAATAATTTT
*
3600153 TTTAATTTTTAAATAATAATTTT
1 TTTAAATTTTAAATAATAATTTT
3600176 T
1 T
3600177 GATAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 1 0.05
25 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTAAATTTTAAATAATAATTTT
Found at i:3605935 original size:18 final size:19
Alignment explanation
Indices: 3605902--3605939 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3605892 CGATTATAAC
3605902 TTAAATATAATATAAAAAA
1 TTAAATATAATATAAAAAA
*
3605921 TTAAA-ATATTATAAAAAA
1 TTAAATATAATATAAAAAA
3605939 T
1 T
3605940 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAATATAATATAAAAAA
Found at i:3605967 original size:27 final size:28
Alignment explanation
Indices: 3605906--3606000 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 28
3605896 TATAACTTAA
* *
3605906 ATATAATATA-AAAAATTAAAATATTAT
1 ATATAATATATTAAAATTAAAATATAAT
* * *
3605933 AAAAAATATATTAAAATTAATATA-AAT
1 ATATAATATATTAAAATTAAAATATAAT
* **
3605960 ATATAATATTTTAAATAAAAAAATTATAAT
1 ATATAATATATTAAA-ATTAAAA-TATAAT
*
3605990 ATAAAATATAT
1 ATATAATATAT
3606001 AAATATAATA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
27 22 0.43
28 15 0.29
29 2 0.04
30 12 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATATAATATATTAAAATTAAAATATAAT
Found at i:3605995 original size:14 final size:16
Alignment explanation
Indices: 3605952--3606023 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 16
3605942 ATTAAAATTA
*
3605952 ATATAAATAT-ATAAT
1 ATATAAATATAAAAAT
* *
3605967 ATTTTAAATAAAAAAAT
1 A-TATAAATATAAAAAT
3605984 -TAT-AATAT-AAAAT
1 ATATAAATATAAAAAT
*
3605997 ATATAAATATAATAAAA
1 ATATAAATATAA-AAAT
*
3606014 ATATTAATAT
1 ATATAAATAT
3606024 TATCCGGTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
13 5 0.11
14 7 0.16
15 8 0.18
16 8 0.18
17 16 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAATATAAAAAT
Found at i:3606005 original size:15 final size:15
Alignment explanation
Indices: 3605952--3606008 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
3605942 ATTAAAATTA
*
3605952 ATATAAATATATAAT
1 ATATAAATATAAAAT
* *
3605967 ATTTTAAATA-AAAAA
1 A-TATAAATATAAAAT
3605982 AT-TATAATATAAAAT
1 ATATA-AATATAAAAT
3605997 ATATAAATATAA
1 ATATAAATATAA
3606009 TAAAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 2 0.06
14 5 0.15
15 18 0.53
16 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAATATAAAAT
Found at i:3606023 original size:17 final size:20
Alignment explanation
Indices: 3605903--3606017 Score: 84
Period size: 20 Copynumber: 6.0 Consensus size: 20
3605893 GATTATAACT
*
3605903 TAAATATAATATAAAAAAT-
1 TAAATATAATATAAAATATA
* *
3605922 TAAAATATTATAAAAAATATA
1 T-AAATATAATATAAAATATA
3605943 TTAAA-ATTAATAT-AAATATA
1 -TAAATA-TAATATAAAATATA
* *
3605963 T-AATAT--T-TTAAATAAA
1 TAAATATAATATAAAATATA
*
3605979 AAAATTATAATATAAAATATA
1 TAAA-TATAATATAAAATATA
3606000 TAAATATAATA-AAAATAT
1 TAAATATAATATAAAATAT
3606018 TAATATTATC
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
15 1 0.01
16 7 0.09
17 2 0.03
18 6 0.08
19 10 0.13
20 31 0.41
21 17 0.23
22 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATATAATATAAAATATA
Found at i:3606626 original size:30 final size:30
Alignment explanation
Indices: 3606569--3606626 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3606559 TGATTCTCTG
* *
3606569 TTTTTTTTCCTGCAGTATCCCAGGTGTTAA
1 TTTTTTTTCCTGCAGAAACCCAGGTGTTAA
** *
3606599 TTTTTTTTTTTGCAGAAACCCATGTGTT
1 TTTTTTTTCCTGCAGAAACCCAGGTGTT
3606627 TTTTTACTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (30 bp):
TTTTTTTTCCTGCAGAAACCCAGGTGTTAA
Found at i:3613780 original size:11 final size:11
Alignment explanation
Indices: 3613748--3613780 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3613738 TAAATTTTTT
*
3613748 ATTAAATAAAA
1 ATTAAAAAAAA
3613759 ATT-AAAAAAA
1 ATTAAAAAAAA
3613769 ATTAAAAAAAA
1 ATTAAAAAAAA
3613780 A
1 A
3613781 AGTAAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
ATTAAAAAAAA
Found at i:3613788 original size:10 final size:10
Alignment explanation
Indices: 3613748--3613779 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
3613738 TAAATTTTTT
3613748 ATTAAATAAAA
1 ATTAAA-AAAA
3613759 ATTAAAAAAA
1 ATTAAAAAAA
3613769 ATTAAAAAAA
1 ATTAAAAAAA
3613779 A
1 A
3613780 AAGTAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:3616582 original size:2 final size:2
Alignment explanation
Indices: 3616575--3616604 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3616565 AAAACATGTC
*
3616575 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3616605 GAAGGATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3621887 original size:2 final size:2
Alignment explanation
Indices: 3621880--3621914 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3621870 TATTTGTTGC
3621880 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 T
3621915 TTCTGATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3631161 original size:261 final size:260
Alignment explanation
Indices: 3630524--3631307 Score: 1410
Period size: 261 Copynumber: 3.0 Consensus size: 260
3630514 TTCCATGGTG
* *
3630524 AAGATGACTGGGAAGAATAGTTTGCCTATTCCTCCCGGCAAAAGAAACCGACCAAGGA-CCAAGG
1 AAGACGACTGGGAAGAATAGTTTGCCTATTCCTCCCGGCAAAACAAACCGACCAAGGACCCAAGG
* *
3630588 ACCCTACTCAAATATGGAAGATTGGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGGGTTGTATT
66 ACCCTACTCAAATATGGAAGATTTGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGAGTTGTATT
*
3630653 ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATTCAATGACAGTAAAC
131 ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATACAATGACAGTAAAC
*
3630718 ATGTAACATGGGCAACCCTGACGACCTCTTATGTTTATGCTGACTTGGCT-AAAAATGGAAATAG
196 ATGTAACATGGGCAACCCTGACGACCTCTTATGTTTATGCTGACTTGGCTAAAAAATGGAAATAA
*
3630782 AAGACGACTGGGAAGAATAGTTTGCCTATCCCTCCCGGCAAAACAAACCGACCAAGGACCCAAGG
1 AAGACGACTGGGAAGAATAGTTTGCCTATTCCTCCCGGCAAAACAAACCGACCAAGGACCCAAGG
3630847 ACCCTACTCAAATATGGAAGATTTGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGAGTTGTATT
66 ACCCTACTCAAATATGGAAGATTTGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGAGTTGTATT
3630912 ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATACAATGACAGTAAAC
131 ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATACAATGACAGTAAAC
*
3630977 ATGTAACATGGGCAACCCTGACGACCTCTTATGTTGTAAGCTGACTTGGCTAAAAAATGGAAATA
196 ATGTAACATGGGCAACCCTGACGACCTCTTATGTT-TATGCTGACTTGGCTAAAAAATGGAAATA
3631042 A
260 A
3631043 AAGACGACTGGGAAGAATAGTTTGCCTATTCCTCCCGGCAAAACAAACCGACCAAGGACCCAAGG
1 AAGACGACTGGGAAGAATAGTTTGCCTATTCCTCCCGGCAAAACAAACCGACCAAGGACCCAAGG
*
3631108 GCCCTACTCAAATATGGAAGATTTGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGAGTTGTATT
66 ACCCTACTCAAATATGGAAGATTTGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGAGTTGTATT
3631173 ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATACAATGACAGTAAAC
131 ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATACAATGACAGTAAAC
* * * * *
3631238 ATGTAACATGGGCGACCTTGACGGCCTCTTATGTTTATGCTGACTTGACTAAATAATGGAAATAC
196 ATGTAACATGGGCAACCCTGACGACCTCTTATGTTTATGCTGACTTGGCTAAAAAATGGAAATA-
3631303 A
260 A
3631304 AAGA
1 AAGA
3631308 GAATTGTTAT
Statistics
Matches: 506, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
258 55 0.11
259 168 0.33
260 40 0.08
261 243 0.48
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (260 bp):
AAGACGACTGGGAAGAATAGTTTGCCTATTCCTCCCGGCAAAACAAACCGACCAAGGACCCAAGG
ACCCTACTCAAATATGGAAGATTTGGATCCGTAAAAAGCTTCTTCACTAGTAGAAGAGTTGTATT
ACTTCGCCATTTATGGCAGAGGCAACCTTGAGAGACATGTAATCTGTCATACAATGACAGTAAAC
ATGTAACATGGGCAACCCTGACGACCTCTTATGTTTATGCTGACTTGGCTAAAAAATGGAAATAA
Found at i:3631610 original size:79 final size:79
Alignment explanation
Indices: 3631474--3631631 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 79
3631464 ATCAAAAATT
* *
3631474 CTTAAAAGATTGTTAGACGTAAAGTCCATTCAGGAGGAAAATTTCACATAATATTACTTTTCCAT
1 CTTAAAAGATTGTTAGACGTAAAGTCCATTCAGAAGGAAAATTTAACATAATATTACTTTTCCAT
3631539 ATTTCATTTATATA
66 ATTTCATTTATATA
* * *
3631553 CTTAAAAGATTGTTAGACGTAAAGTTCATTCAGAAGGCAAAA-TTAACATAATGTTACTTTTCCG
1 CTTAAAAGATTGTTAGACGTAAAGTCCATTCAGAAGG-AAAATTTAACATAATATTACTTTTCCA
3631617 TATTTCATTTATATA
65 TATTTCATTTATATA
3631632 TATATATATA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 69 0.95
80 4 0.05
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (79 bp):
CTTAAAAGATTGTTAGACGTAAAGTCCATTCAGAAGGAAAATTTAACATAATATTACTTTTCCAT
ATTTCATTTATATA
Found at i:3633690 original size:32 final size:32
Alignment explanation
Indices: 3633653--3633736 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 32
3633643 TAATACTATT
*
3633653 TTAAATAA-TAATATAAATTTTCA-GATTTAAAC
1 TTAAATAAGTAA-A-AAATTTTAATGATTTAAAC
*
3633685 TTAAATAAGTAAAAAATTTTAATTGATTTAGAC
1 TTAAATAAGTAAAAAATTTTAA-TGATTTAAAC
*
3633718 TTAAA-AAGAAAAAGAATTT
1 TTAAATAAGTAAAA-AATTT
3633737 CGAACTACAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
31 8 0.18
32 16 0.36
33 21 0.47
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (32 bp):
TTAAATAAGTAAAAAATTTTAATGATTTAAAC
Found at i:3633807 original size:2 final size:2
Alignment explanation
Indices: 3633800--3633826 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3633790 ACAGATTAAT
3633800 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
3633827 GTACAAATTT
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:3635390 original size:22 final size:22
Alignment explanation
Indices: 3635365--3635410 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3635355 CTTAAAGTAT
3635365 TATTTTTA-TATTAATATTTATA
1 TATTTTTATTATTAA-ATTTATA
3635387 TATTTTTATTATTAAATTTATA
1 TATTTTTATTATTAAATTTATA
3635409 TA
1 TA
3635411 AAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTATTATTAAATTTATA
Found at i:3641433 original size:15 final size:15
Alignment explanation
Indices: 3641413--3641460 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
3641403 TAAAAAATAT
3641413 TTAAATATATTTATA
1 TTAAATATATTTATA
3641428 TTAAATATATTTATA
1 TTAAATATATTTATA
*
3641443 TT---TATATTTATT
1 TTAAATATATTTATA
3641455 TTAAAT
1 TTAAAT
3641461 TTAAATAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 11 0.38
15 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATATATTTATA
Found at i:3644563 original size:2 final size:2
Alignment explanation
Indices: 3644556--3644587 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3644546 AACTTGTTCC
3644556 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
3644588 TCCGTAGCAG
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:3652548 original size:20 final size:21
Alignment explanation
Indices: 3652509--3652549 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3652499 TTAGGCAAAG
* *
3652509 AAAATTAGTTTACCAAACTTC
1 AAAATTAGTTAACAAAACTTC
3652530 AAAATTA-TTAACAAAACTTC
1 AAAATTAGTTAACAAAACTTC
3652550 TTTTACATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATTAGTTAACAAAACTTC
Found at i:3659224 original size:17 final size:16
Alignment explanation
Indices: 3659202--3659261 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
3659192 ATTTTTTAGA
3659202 TTTAATTATGATTAAAT
1 TTTAATTAT-ATTAAAT
*
3659219 TTTAA-TATATTAATAA
1 TTTAATTATATTAA-AT
3659235 TTTATATTATA-TAAAT
1 TTTA-ATTATATTAAAT
3659251 TTTAA-TATATT
1 TTTAATTATATT
3659262 TATTTATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.11
15 7 0.19
16 13 0.35
17 9 0.24
18 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAATTATATTAAAT
Found at i:3661506 original size:23 final size:23
Alignment explanation
Indices: 3661454--3661508 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3661444 TCCCCCCACC
*
3661454 TCATTTTCTATCTCTTTTTTCCT
1 TCATTTTCTATCTCTTTTTCCCT
*
3661477 TCATTTTCTCTCTCTTTTTCCCAT
1 TCATTTTCTATCTCTTTTTCCC-T
*
3661501 TCTTTTTC
1 TCATTTTC
3661509 CCTGGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (23 bp):
TCATTTTCTATCTCTTTTTCCCT
Found at i:3666721 original size:4 final size:4
Alignment explanation
Indices: 3666698--3666735 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
3666688 TAAAAACCCA
* *
3666698 CTTT CTCT CTTT CCTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
3666736 CCATATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:3668240 original size:2 final size:2
Alignment explanation
Indices: 3668233--3668287 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
3668223 TGTATATGTT
* * * *
3668233 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TG TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3668275 TA TA -A GTA TA TA T
1 TA TA TA -TA TA TA T
3668288 TCTTGGATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3673654 original size:10 final size:11
Alignment explanation
Indices: 3673635--3673663 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3673625 AAGTCACAAA
3673635 AAAGAAAAAAG
1 AAAGAAAAAAG
3673646 AAA-AAAAAAG
1 AAAGAAAAAAG
3673656 AAAGAAAA
1 AAAGAAAA
3673664 CAACTCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:3674485 original size:3 final size:3
Alignment explanation
Indices: 3674477--3674507 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3674467 AAATTAAATT
3674477 TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3674508 TTTGCGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:3674490 original size:11 final size:11
Alignment explanation
Indices: 3674474--3674507 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
3674464 TAAAAATTAA
3674474 ATTTTATTATT
1 ATTTTATTATT
3674485 ATTTTATTATT
1 ATTTTATTATT
3674496 ATTATTATTATT
1 ATT-TTATTATT
3674508 TTTGCGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:3681777 original size:22 final size:22
Alignment explanation
Indices: 3681741--3681820 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
3681731 AATTATATAT
3681741 AATAGTTTTTT-AAAATAAATA
1 AATAGTTTTTTAAAAATAAATA
*
3681762 AGTTA-TTTTTTAAAAATAAATA
1 A-ATAGTTTTTTAAAAATAAATA
*
3681784 AATAGTTTTTTAAAAAT--ATT
1 AATAGTTTTTTAAAAATAAATA
*
3681804 AATATTTTTTTAAAAAT
1 AATAGTTTTTTAAAAAT
3681821 TATTATAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
20 18 0.35
21 9 0.17
22 25 0.48
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
AATAGTTTTTTAAAAATAAATA
Found at i:3681807 original size:20 final size:20
Alignment explanation
Indices: 3681735--3681825 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 20
3681725 GAAAAAAATT
3681735 ATATATAATAGTTTTTT-AAA
1 ATAT-TAATAGTTTTTTAAAA
*
3681755 ATAAATAAGTTA-TTTTTTAAAA
1 AT-ATTAA--TAGTTTTTTAAAA
*
3681777 ATAAATAAATAGTTTTTTAAAA
1 AT--ATTAATAGTTTTTTAAAA
*
3681799 ATATTAATATTTTTTTAAAA
1 ATATTAATAGTTTTTTAAAA
3681819 ATTATTA
1 A-TATTA
3681826 TAATAAAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
20 22 0.37
21 14 0.24
22 19 0.32
23 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
ATATTAATAGTTTTTTAAAA
Found at i:3681819 original size:21 final size:21
Alignment explanation
Indices: 3681735--3681825 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 21
3681725 GAAAAAAATT
3681735 ATATATAATAGTTTTTTAAAATA
1 ATAT-TAATAGTTTTTTAAAA-A
3681758 A-A-TAAGTTA-TTTTTTAAAAA
1 ATATTAA--TAGTTTTTTAAAAA
* *
3681778 TAAATAAATAGTTTTTT-AAAA
1 -ATATTAATAGTTTTTTAAAAA
*
3681799 ATATTAATATTTTTTTAAAAA
1 ATATTAATAGTTTTTTAAAAA
*
3681820 TTATTA
1 ATATTA
3681826 TAATAAAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
20 17 0.30
21 26 0.46
22 10 0.18
23 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
ATATTAATAGTTTTTTAAAAA
Found at i:3682320 original size:2 final size:2
Alignment explanation
Indices: 3682315--3682356 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3682305 GGTTTTTTAT
* *
3682315 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3682357 CCCCATTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3691261 original size:28 final size:31
Alignment explanation
Indices: 3691223--3691288 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 31
3691213 GTTTTTATAA
3691223 TTTAAAATTTTAAAAATAA-TTT-AT-TATT
1 TTTAAAATTTTAAAAATAATTTTCATATATT
* * *
3691251 TTTAAATTTTTTACAATAATTTTCATATATT
1 TTTAAAATTTTAAAAATAATTTTCATATATT
3691282 TTTAAAA
1 TTTAAAA
3691289 ACATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 16 0.52
29 3 0.10
30 2 0.06
31 10 0.32
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTAAAATTTTAAAAATAATTTTCATATATT
Found at i:3693802 original size:8 final size:8
Alignment explanation
Indices: 3693789--3693822 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
3693779 GGGCCGTACC
3693789 AAAAATAA
1 AAAAATAA
3693797 AAAAATAA
1 AAAAATAA
3693805 AAAAATAA
1 AAAAATAA
3693813 AAAAATAA
1 AAAAATAA
3693821 AA
1 AA
3693823 GGGAAGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:3693915 original size:8 final size:8
Alignment explanation
Indices: 3693899--3693928 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3693889 GGAAAGAGAG
3693899 TCGCTCTC
1 TCGCTCTC
*
3693907 TCTCTCTC
1 TCGCTCTC
3693915 TCGCTCTC
1 TCGCTCTC
3693923 TCGCTC
1 TCGCTC
3693929 GCTTTCGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.10, T:0.40
Consensus pattern (8 bp):
TCGCTCTC
Found at i:3699376 original size:30 final size:30
Alignment explanation
Indices: 3699340--3699401 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3699330 GAACGCATTT
3699340 GGGGGTGGATTTGAGAGGAGAGAGAGAGGA
1 GGGGGTGGATTTGAGAGGAGAGAGAGAGGA
3699370 GGGGGTGGATTTGAGAGGAGAGAGAGAGGA
1 GGGGGTGGATTTGAGAGGAGAGAGAGAGGA
3699400 GG
1 GG
3699402 TGGATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.58, T:0.13
Consensus pattern (30 bp):
GGGGGTGGATTTGAGAGGAGAGAGAGAGGA
Found at i:3699406 original size:27 final size:28
Alignment explanation
Indices: 3699342--3699408 Score: 109
Period size: 30 Copynumber: 2.4 Consensus size: 28
3699332 ACGCATTTGG
3699342 GGGTGGATTTGAGAGGAGAGAGAGAGGA
1 GGGTGGATTTGAGAGGAGAGAGAGAGGA
3699370 GGGGGTGGATTTGAGAGGAGAGAGAGAGGA
1 --GGGTGGATTTGAGAGGAGAGAGAGAGGA
3699400 -GGTGGATTT
1 GGGTGGATTT
3699409 TTTGATTCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 9 0.24
30 28 0.76
ACGTcount: A:0.28, C:0.00, G:0.54, T:0.18
Consensus pattern (28 bp):
GGGTGGATTTGAGAGGAGAGAGAGAGGA
Found at i:3699992 original size:2 final size:2
Alignment explanation
Indices: 3699981--3700034 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
3699971 AGAATATCGC
3699981 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3700022 TA TA TG TA TA TA T
1 TA TA TA TA TA TA T
3700035 TGTTTAAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3702221 original size:2 final size:2
Alignment explanation
Indices: 3702214--3702243 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3702204 CCCAATTCTT
3702214 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3702244 TATGGAATGA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3703262 original size:2 final size:2
Alignment explanation
Indices: 3703255--3703290 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3703245 ATTTGGTGAC
3703255 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
3703291 CAATTCCATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3705236 original size:2 final size:2
Alignment explanation
Indices: 3705229--3705264 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3705219 CTTTGATGCC
3705229 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
3705265 CCCATAAGTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3705839 original size:25 final size:22
Alignment explanation
Indices: 3705774--3705842 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
3705764 CAATTAGAGG
3705774 ATTTTGAACATGAGATAACCTC
1 ATTTTGAACATGAGATAACCTC
* *
3705796 -TTTTGAAAACAAGACATAACAACTTC
1 ATTTTG--AACATGAGATAAC--C-TC
3705822 ATTTTGAACATGAGATAACCT
1 ATTTTGAACATGAGATAACCT
3705843 TTTCTATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
21 5 0.14
22 1 0.03
23 12 0.32
25 12 0.32
26 2 0.05
27 5 0.14
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (22 bp):
ATTTTGAACATGAGATAACCTC
Found at i:3712208 original size:33 final size:33
Alignment explanation
Indices: 3712162--3712288 Score: 130
Period size: 33 Copynumber: 3.8 Consensus size: 33
3712152 ACTAACACTC
** * * *
3712162 CCACATCCTCCTGAGGTCCACCCTCACTTGCAA
1 CCACATCGACCTGAGGCCCAACCTCACTTGGAA
*
3712195 CCACATCGACCTGAGACCCAACCTCACTTGGAA
1 CCACATCGACCTGAGGCCCAACCTCACTTGGAA
* * * * *
3712228 -CAGCATCGTCCTGTGGTCCAATCTCACCTGGAA
1 CCA-CATCGACCTGAGGCCCAACCTCACTTGGAA
*
3712261 GCACATCGACCTGAGGCCCAACCTCACT
1 CCACATCGACCTGAGGCCCAACCTCACT
3712289 CAGAACAGCA
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
32 2 0.03
33 71 0.95
34 2 0.03
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (33 bp):
CCACATCGACCTGAGGCCCAACCTCACTTGGAA
Found at i:3712320 original size:66 final size:66
Alignment explanation
Indices: 3712165--3712326 Score: 209
Period size: 66 Copynumber: 2.5 Consensus size: 66
3712155 AACACTCCCA
* * **
3712165 CATCCTCCTGAGGTCCACCCTCACTTGCAACCACATCGACCTGAGACCCAACCTCACTTGGAACA
1 CATCCTCCTGAGGTCCAACCTCACTTGGAACCACATCGACCTGAGACCCAACCTCACTCAGAACA
3712230 G
66 G
* * * * * *
3712231 CATCGTCCTGTGGTCCAATCTCACCTGGAAGCACATCGACCTGAGGCCCAACCTCACTCAGAACA
1 CATCCTCCTGAGGTCCAACCTCACTTGGAACCACATCGACCTGAGACCCAACCTCACTCAGAACA
3712296 G
66 G
*
3712297 CATCCTCGC-GAGGTCTAACCTCACTTGGAA
1 CATCCTC-CTGAGGTCCAACCTCACTTGGAA
3712327 TCCCAATAGC
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
66 79 0.99
67 1 0.01
ACGTcount: A:0.25, C:0.38, G:0.18, T:0.19
Consensus pattern (66 bp):
CATCCTCCTGAGGTCCAACCTCACTTGGAACCACATCGACCTGAGACCCAACCTCACTCAGAACA
G
Found at i:3712967 original size:2 final size:2
Alignment explanation
Indices: 3712960--3712988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3712950 AAAATATAAT
3712960 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3712989 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3713870 original size:23 final size:24
Alignment explanation
Indices: 3713824--3713872 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
3713814 AAATATGATA
* *
3713824 TATATATATATATATTAAATATAT
1 TATATATATATATATCAAACATAT
*
3713848 TATAT-TATATTTATCAAACATAT
1 TATATATATATATATCAAACATAT
3713871 TA
1 TA
3713873 AGGAGCCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATATATATATATCAAACATAT
Found at i:3726870 original size:33 final size:33
Alignment explanation
Indices: 3726833--3726907 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
3726823 AATTTATAAT
* * * *
3726833 ATAAAATAAAATATAAGATCTTATTTTTAAAAA
1 ATAAAATAAAAAATAAAATCTTAGTTTAAAAAA
*
3726866 ATAAAATAAAAAATAAAATTTTAGTTTAAAAAA
1 ATAAAATAAAAAATAAAATCTTAGTTTAAAAAA
3726899 ATAAAATAA
1 ATAAAATAA
3726908 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAAAATAAAAAATAAAATCTTAGTTTAAAAAA
Found at i:3726877 original size:12 final size:12
Alignment explanation
Indices: 3726860--3726884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3726850 ATCTTATTTT
3726860 TAAAAAATAAAA
1 TAAAAAATAAAA
3726872 TAAAAAATAAAA
1 TAAAAAATAAAA
3726884 T
1 T
3726885 TTTAGTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:3727071 original size:25 final size:26
Alignment explanation
Indices: 3727042--3727099 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
3727032 TTCAAAAAAA
*
3727042 TTTTAAAATT-TAT-TTTTTATATATT
1 TTTTAAAATTATATGTTATTA-ATATT
*
3727067 TTTT-AAATTATATGTTATTAATTTT
1 TTTTAAAATTATATGTTATTAATATT
3727092 TTTTAAAA
1 TTTTAAAA
3727100 AATCATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 5 0.18
25 15 0.54
26 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTAAAATTATATGTTATTAATATT
Found at i:3727531 original size:19 final size:21
Alignment explanation
Indices: 3727499--3727545 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3727489 CTTAAAAATT
*
3727499 AATTTTTATAATTAA-AATAA
1 AATTATTATAATTAACAATAA
3727519 AATTATTAT-ATTAACAATAA
1 AATTATTATAATTAACAATAA
3727539 AA-TATTA
1 AATTATTA
3727546 AATGTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTATTATAATTAACAATAA
Found at i:3727910 original size:16 final size:17
Alignment explanation
Indices: 3727885--3727918 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3727875 AGCAAAAGTT
*
3727885 AAAATCAATTTAATTAA
1 AAAATCAATTAAATTAA
3727902 AAAAT-AATTAAATTAA
1 AAAATCAATTAAATTAA
3727918 A
1 A
3727919 TTTAAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATCAATTAAATTAA
Found at i:3728089 original size:23 final size:23
Alignment explanation
Indices: 3728033--3728104 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
3728023 TAACTGAATT
3728033 AATAT-TTAAAATATATTTAAT-A
1 AATATATT-AAATATATTTAATAA
3728055 AATATA-T--A-ATATTTAATAA
1 AATATATTAAATATATTTAATAA
3728074 AATATATTAAATATATTTAATAA
1 AATATATTAAATATATTTAATAA
3728097 AATATATT
1 AATATATT
3728105 TAAAACCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
18 9 0.20
19 8 0.18
20 1 0.02
22 7 0.16
23 19 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATATATTAAATATATTTAATAA
Found at i:3728099 original size:14 final size:14
Alignment explanation
Indices: 3728039--3728107 Score: 67
Period size: 14 Copynumber: 5.0 Consensus size: 14
3728029 AATTAATATT
3728039 TAAAATATATTTAA
1 TAAAATATATTTAA
3728053 TAAATATATAATATTTAA
1 T-AA-A-AT-ATATTTAA
3728071 TAAAATATA--T--
1 TAAAATATATTTAA
3728081 T-AAATATATTTAA
1 TAAAATATATTTAA
3728094 TAAAATATATTTAA
1 TAAAATATATTTAA
3728108 AACCAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
9 7 0.15
10 1 0.02
11 1 0.02
12 1 0.02
13 1 0.02
14 16 0.35
15 4 0.09
16 2 0.04
17 4 0.09
18 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:3729288 original size:21 final size:21
Alignment explanation
Indices: 3729264--3729339 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
3729254 AGATCTGGAC
3729264 GCGGTGGGTCTGGTTACGGTG
1 GCGGTGGGTCTGGTTACGGTG
* * * *
3729285 GCGGTGGCTCCGGTGGCTATGGAG
1 GCGGTGGGT-C--TGGTTACGGTG
*
3729309 GCGGTGGATCTGGTTACGGTG
1 GCGGTGGGTCTGGTTACGGTG
3729330 GCGGTGGGTC
1 GCGGTGGGTC
3729340 CGGTGGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 25 0.58
22 1 0.02
23 1 0.02
24 16 0.37
ACGTcount: A:0.07, C:0.17, G:0.51, T:0.25
Consensus pattern (21 bp):
GCGGTGGGTCTGGTTACGGTG
Found at i:3729315 original size:45 final size:45
Alignment explanation
Indices: 3729259--3729362 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
3729249 CCTCGAGATC
*
3729259 TGGACGCGGTGGGTCTGGTTACGGTGGCGGTGGCTCCGGTGGCTA
1 TGGAGGCGGTGGGTCTGGTTACGGTGGCGGTGGCTCCGGTGGCTA
* * *
3729304 TGGAGGCGGTGGATCTGGTTACGGTGGCGGTGGGTCCGGTGGTTA
1 TGGAGGCGGTGGGTCTGGTTACGGTGGCGGTGGCTCCGGTGGCTA
*
3729349 TGGAGGTGGTGGGT
1 TGGAGGCGGTGGGT
3729363 ACGGTGGTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.08, C:0.14, G:0.52, T:0.26
Consensus pattern (45 bp):
TGGAGGCGGTGGGTCTGGTTACGGTGGCGGTGGCTCCGGTGGCTA
Found at i:3729359 original size:24 final size:24
Alignment explanation
Indices: 3729259--3729370 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
3729249 CCTCGAGATC
*
3729259 TGGACGCGGTGGGT-C--TGGTTA
1 TGGAGGCGGTGGGTCCGGTGGTTA
* * * *
3729280 CGGTGGCGGTGGCTCCGGTGGCTA
1 TGGAGGCGGTGGGTCCGGTGGTTA
*
3729304 TGGAGGCGGTGGAT-C--TGGTTA
1 TGGAGGCGGTGGGTCCGGTGGTTA
* *
3729325 CGGTGGCGGTGGGTCCGGTGGTTA
1 TGGAGGCGGTGGGTCCGGTGGTTA
* *
3729349 TGGAGGTGGTGGGTACGGTGGT
1 TGGAGGCGGTGGGTCCGGTGGT
3729371 GGTGGAAGGA
Statistics
Matches: 69, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
21 26 0.38
22 2 0.03
23 1 0.01
24 40 0.58
ACGTcount: A:0.08, C:0.14, G:0.52, T:0.26
Consensus pattern (24 bp):
TGGAGGCGGTGGGTCCGGTGGTTA
Found at i:3729396 original size:21 final size:21
Alignment explanation
Indices: 3729370--3729417 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3729360 GGTACGGTGG
3729370 TGGTGGAAGGACAGGTGGGTA
1 TGGTGGAAGGACAGGTGGGTA
* * *
3729391 TGGTGGAGGGACCGGTGGTTA
1 TGGTGGAAGGACAGGTGGGTA
*
3729412 TAGTGG
1 TGGTGG
3729418 CGGCGGAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.06, G:0.52, T:0.23
Consensus pattern (21 bp):
TGGTGGAAGGACAGGTGGGTA
Found at i:3730242 original size:51 final size:51
Alignment explanation
Indices: 3730186--3730286 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
3730176 CCCTTTTCGC
* *
3730186 AGGTTTCTTTTATTTGTTTGTTTTCAACTTTTCGTAGATGAGTAGGGACGT
1 AGGTTTCTTATATTTGTTTGTTTTCAACCTTTCGTAGATGAGTAGGGACGT
* * *
3730237 AGGTTTCTTATGTTTGTTTGTTTTCAACCTTTCTTAGATGTGTAGGGACG
1 AGGTTTCTTATATTTGTTTGTTTTCAACCTTTCGTAGATGAGTAGGGACG
3730287 AAATTGCGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.49
Consensus pattern (51 bp):
AGGTTTCTTATATTTGTTTGTTTTCAACCTTTCGTAGATGAGTAGGGACGT
Found at i:3731699 original size:2 final size:2
Alignment explanation
Indices: 3731692--3731721 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3731682 AATTTCAGCA
3731692 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
3731722 TCTTCTCCCT
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):
AT
Found at i:3734066 original size:170 final size:170
Alignment explanation
Indices: 3733784--3734097 Score: 574
Period size: 170 Copynumber: 1.8 Consensus size: 170
3733774 TCCCTGCATG
* *
3733784 TCAGTAATTCTTCATTAATTACCAACTAATGCTACCGGTATTTATGTAGTATGTTCATCATTTCT
1 TCAGTAATTCTTCATTAATTACCAACTAATGCAACCAGTATTTATGTAGTATGTTCATCATTTCT
* *
3733849 CAAGTTCTATAGTAGCAGAGTTTTAATTAGGGCCTGGAAAAGCTCTGCCCTACGCTGATTAATAT
66 CAAGTTCAATAGTAGCAGAGTTTTAATTAGAGCCTGGAAAAGCTCTGCCCTACGCTGATTAATAT
3733914 TGGGTTTTGGGCCTCCCCCCCCCCCCCCCACCAAAAAAAA
131 TGGGTTTTGGGCCTCCCCCCCCCCCCCCCACCAAAAAAAA
*
3733954 TCAGTAATTCTTCATTAATTACCAATTAATGCAACCAGTATTTATGTAGTATGTTCATCATTTCT
1 TCAGTAATTCTTCATTAATTACCAACTAATGCAACCAGTATTTATGTAGTATGTTCATCATTTCT
*
3734019 CAAGTTCAATAGTAGCAGAGTTTTAATTAGAGCCTGGAAAAGCTCTGCCTTACGCTGATTAATAT
66 CAAGTTCAATAGTAGCAGAGTTTTAATTAGAGCCTGGAAAAGCTCTGCCCTACGCTGATTAATAT
3734084 TGGGTTTTGGGCCT
131 TGGGTTTTGGGCCT
3734098 TAAGCAACCG
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 138 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (170 bp):
TCAGTAATTCTTCATTAATTACCAACTAATGCAACCAGTATTTATGTAGTATGTTCATCATTTCT
CAAGTTCAATAGTAGCAGAGTTTTAATTAGAGCCTGGAAAAGCTCTGCCCTACGCTGATTAATAT
TGGGTTTTGGGCCTCCCCCCCCCCCCCCCACCAAAAAAAA
Found at i:3736191 original size:2 final size:2
Alignment explanation
Indices: 3736184--3736215 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3736174 ACATAGAGGG
3736184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3736216 CAAACGACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3738392 original size:4 final size:4
Alignment explanation
Indices: 3738385--3738414 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3738375 AATTATACAT
3738385 TTTA TTTA TTTA TTTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3738415 TTAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3742800 original size:16 final size:15
Alignment explanation
Indices: 3742775--3742808 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3742765 TTATGTTTAG
*
3742775 ATAAACAATAATAAAA
1 ATAAAAAATAA-AAAA
3742791 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
3742806 ATA
1 ATA
3742809 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
ATAAAAAATAAAAAA
Found at i:3744665 original size:20 final size:21
Alignment explanation
Indices: 3744640--3744689 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3744630 TTTTAATTTT
3744640 TTTTTATAT-TTA-ATATATAA
1 TTTTTATATATTATATATAT-A
*
3744660 TTTTTAT-TATTATTTATATA
1 TTTTTATATATTATATATATA
3744680 TTTTTATATA
1 TTTTTATATA
3744690 AGAATGACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATATATTATATATATA
Found at i:3744669 original size:23 final size:23
Alignment explanation
Indices: 3744621--3744680 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
3744611 CAAAATTATC
*
3744621 TTATT-TTTAT-TTTAATTTTT-
1 TTATTATTTATATATAATTTTTA
*
3744641 TTTTATATTTAATATATAATTTTTA
1 TTAT-TATTT-ATATATAATTTTTA
3744666 TTATTATTTATATAT
1 TTATTATTTATATAT
3744681 TTTTATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.09
21 1 0.03
22 3 0.09
23 8 0.25
24 14 0.44
25 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATTTATATATAATTTTTA
Found at i:3755033 original size:27 final size:28
Alignment explanation
Indices: 3754961--3755035 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 28
3754951 AGGGTACATA
3754961 ATTT-ATATATTTAATTATATTATAAATAT
1 ATTTAATATA-TTAATTAT-TTATAAATAT
**
3754990 ATTTAAT-TATTTTTTATTTATATAA-AT
1 ATTTAATATATTAATTATTTATA-AATAT
3755017 A-TTAATATATTAATTATTT
1 ATTTAATATATTAATTATTT
3755036 TTATTATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 5 0.13
27 18 0.46
28 8 0.21
29 6 0.15
30 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTAATATATTAATTATTTATAAATAT
Found at i:3756072 original size:19 final size:18
Alignment explanation
Indices: 3756050--3756106 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
3756040 AATTTTAATA
3756050 TTTAAAATAAAAATAATTT
1 TTTAAAAT-AAAATAATTT
* * *
3756069 TTTATAATTTAAATATTTAT
1 TTTA-AAATAAAATAATT-T
*
3756089 TTTTAAATAAAATAATTT
1 TTTAAAATAAAATAATTT
3756107 CACTACATTC
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 1 0.03
19 21 0.72
20 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAATAAAATAATTT
Found at i:3756165 original size:18 final size:17
Alignment explanation
Indices: 3756120--3756157 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3756110 TACATTCATA
3756120 TTTTTAA-A-TTTATAT
1 TTTTTAATATTTTATAT
3756135 TTTTTAATATTTTA-AT
1 TTTTTAATATTTTATAT
3756151 TTTTTAA
1 TTTTTAA
3756158 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAATATTTTATAT
Found at i:3756746 original size:17 final size:18
Alignment explanation
Indices: 3756724--3756765 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
3756714 AACACTAAAA
3756724 TAAAAATTAAGATA-TT-T
1 TAAAAATTAA-ATATTTAT
3756741 TAAAAA-TAAATATTTAT
1 TAAAAATTAAATATTTAT
3756758 TAAAAATT
1 TAAAAATT
3756766 TTCATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 13 0.59
18 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAAATTAAATATTTAT
Found at i:3758599 original size:16 final size:15
Alignment explanation
Indices: 3758580--3758722 Score: 79
Period size: 16 Copynumber: 9.7 Consensus size: 15
3758570 TCATTCAATC
3758580 ATATTATATATTTTAA
1 ATATTATATATTTT-A
*
3758596 ATATAATATATTTTA
1 ATATTATATATTTTA
3758611 AT-TTA-AT-TTTTA
1 ATATTATATATTTTA
*
3758623 ATAATTTTATATTTTA
1 AT-ATTATATATTTTA
* *
3758639 ATTTTATTAAATTATATA
1 ATATTA-TATATT-T-TA
* * *
3758657 ATA-AAAATAATTTA
1 ATATTATATATTTTA
3758671 ATA-TAT-T-TTTTAA
1 ATATTATATATTTT-A
*
3758684 ATATT-TATATTATA
1 ATATTATATATTTTA
*
3758698 ATACTATATATATTTA
1 ATATTATATAT-TTTA
3758714 ATA-TATATA
1 ATATTATATA
3758723 ATATAAACTA
Statistics
Matches: 97, Mismatches: 17, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
12 10 0.10
13 8 0.08
14 17 0.18
15 22 0.23
16 34 0.35
17 2 0.02
18 4 0.04
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATATATTTTA
Found at i:3758606 original size:23 final size:23
Alignment explanation
Indices: 3758580--3758697 Score: 59
Period size: 23 Copynumber: 5.3 Consensus size: 23
3758570 TCATTCAATC
3758580 ATATTATATATTTTAAATATAAT
1 ATATTATATATTTTAAATATAAT
* * *
3758603 ATATT-T-TAATTTAATTTTTAAT
1 ATATTATATATTTTAA-ATATAAT
* * * *
3758625 A-ATTTTATATTTTAATTTTATT
1 ATATTATATATTTTAAATATAAT
* * *
3758647 AAATTATATA--ATAAAAATAAT
1 ATATTATATATTTTAAATATAAT
* * * *
3758668 TTAATATATTTTTTAAATAT-TT
1 ATATTATATATTTTAAATATAAT
3758690 ATATTATA
1 ATATTATA
3758698 ATACTATATA
Statistics
Matches: 69, Mismatches: 20, Indels: 13
0.68 0.20 0.13
Matches are distributed among these distances:
21 22 0.32
22 22 0.32
23 25 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTATATATTTTAAATATAAT
Found at i:3758624 original size:22 final size:23
Alignment explanation
Indices: 3758586--3758643 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
3758576 AATCATATTA
* *
3758586 TATATTTTAA-ATATAATATATTT
1 TATATTTTAATTTTTAATA-ATTT
3758609 TA-A-TTTAATTTTTAATAATTT
1 TATATTTTAATTTTTAATAATTT
3758630 TATATTTTAATTTT
1 TATATTTTAATTTT
3758644 ATTAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 11 0.37
22 8 0.27
23 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATTTTAATTTTTAATAATTT
Found at i:3760019 original size:16 final size:17
Alignment explanation
Indices: 3759998--3760030 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3759988 CTATTAATAT
*
3759998 TTAAATTTTAA-ATTTA
1 TTAAATATTAATATTTA
3760014 TTAAATATTAATATTTA
1 TTAAATATTAATATTTA
3760031 ATATCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAATATTAATATTTA
Found at i:3763981 original size:20 final size:21
Alignment explanation
Indices: 3763915--3763981 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
3763905 TGTTTGACTA
3763915 AAATA-ATTAAAATATTATAT
1 AAATATATTAAAATATTATAT
*
3763935 AAA-AT-TATAAAATATGAATTAT
1 AAATATAT-TAAAATAT-TA-TAT
*
3763957 TAATATATTAAAAT-TTATAT
1 AAATATATTAAAATATTATAT
3763977 AAATA
1 AAATA
3763982 ATAATATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 2 0.05
20 18 0.49
21 2 0.05
22 6 0.16
23 8 0.22
24 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
AAATATATTAAAATATTATAT
Found at i:3770093 original size:14 final size:16
Alignment explanation
Indices: 3770066--3770097 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3770056 AAGTAAAATG
3770066 TTTATAAATATTAAAA
1 TTTATAAATATTAAAA
3770082 TTTA-AAAT-TTAAAA
1 TTTATAAATATTAAAA
3770096 TT
1 TT
3770098 ATTAGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTATAAATATTAAAA
Found at i:3777555 original size:19 final size:19
Alignment explanation
Indices: 3777504--3777559 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
3777494 AGGGTAGTTT
3777504 ATACAAAACTTATGTATCG
1 ATACAAAACTTATGTATCG
*
3777523 --A-AACA-TTA--TATCG
1 ATACAAAACTTATGTATCG
3777536 ATACAAAACTTATGTATCG
1 ATACAAAACTTATGTATCG
3777555 ATACA
1 ATACA
3777560 TTTATTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
13 5 0.17
15 4 0.14
16 6 0.21
17 4 0.14
19 10 0.34
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (19 bp):
ATACAAAACTTATGTATCG
Found at i:3778540 original size:29 final size:31
Alignment explanation
Indices: 3778504--3778567 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
3778494 TAATGAATAA
**
3778504 AATATTTTAGTTTTTATATTATT-AAATT-T
1 AATATTTTAACTTTTATATTATTGAAATTAT
*
3778533 AATATTTTAACTTTTATATTTTTGAAATTAT
1 AATATTTTAACTTTTATATTATTGAAATTAT
3778564 AATA
1 AATA
3778568 AATAAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 20 0.67
30 5 0.17
31 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (31 bp):
AATATTTTAACTTTTATATTATTGAAATTAT
Found at i:3778555 original size:15 final size:15
Alignment explanation
Indices: 3778515--3778561 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
3778505 ATATTTTAGT
*
3778515 TTTTATATTATTAAA
1 TTTTATATTTTTAAA
* *
3778530 TTTAATA-TTTTAAC
1 TTTTATATTTTTAAA
3778544 TTTTATATTTTTGAAA
1 TTTTATATTTTT-AAA
3778560 TT
1 TT
3778562 ATAATAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.44
15 10 0.40
16 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTATATTTTTAAA
Found at i:3785267 original size:17 final size:16
Alignment explanation
Indices: 3785223--3785275 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
3785213 TAAAATTAAT
3785223 TTAAATAT-ATAAATA
1 TTAAATATAATAAATA
* *
3785238 TTAAATAAAAATAAATT
1 TTAAAT-ATAATAAATA
3785255 TTAAAATATAATAAAATA
1 TT-AAATATAAT-AAATA
3785273 TTA
1 TTA
3785276 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 13 0.43
18 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATATAATAAATA
Found at i:3785284 original size:35 final size:31
Alignment explanation
Indices: 3785211--3785284 Score: 76
Period size: 35 Copynumber: 2.3 Consensus size: 31
3785201 GATTTATTTT
*
3785211 ATTAAAATTAATTTAAATATATAAATATTAA
1 ATTAAAATAAATTTAAATATATAAATATTAA
* *
3785242 ATAAAAATAAATTTTAAAATATAATAAAATATTAT
1 ATTAAAATAAA-TTT-AAATAT-AT-AAATATTAA
*
3785277 TTTAAAAT
1 ATTAAAAT
3785285 TTTAATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 9 0.26
32 3 0.09
33 6 0.18
34 2 0.06
35 14 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
ATTAAAATAAATTTAAATATATAAATATTAA
Found at i:3785323 original size:17 final size:17
Alignment explanation
Indices: 3785283--3785320 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3785273 TTATTTTAAA
3785283 ATTTTAATAAAAAATAT
1 ATTTTAATAAAAAATAT
* *
3785300 ATATTAATATAAAATA-
1 ATTTTAATAAAAAATAT
3785316 ATTTT
1 ATTTT
3785321 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTTAATAAAAAATAT
Found at i:3785545 original size:22 final size:24
Alignment explanation
Indices: 3785517--3785569 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3785507 ATATTTGTTT
**
3785517 TTTATTTAAAATT-T-TTTAATTA
1 TTTATTTAAAATTCTCTCAAATTA
*
3785539 TTTATTTTAAATTCTCTCAAATTA
1 TTTATTTAAAATTCTCTCAAATTA
3785563 TTTATTT
1 TTTATTT
3785570 TGATGGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 12 0.46
23 1 0.04
24 13 0.50
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTAAAATTCTCTCAAATTA
Found at i:3788028 original size:7 final size:7
Alignment explanation
Indices: 3788012--3788045 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
3788002 TAACCTGTGC
3788012 TTTTCTT
1 TTTTCTT
*
3788019 TTTGCTT
1 TTTTCTT
3788026 TTTTCTT
1 TTTTCTT
3788033 TTTTCTT
1 TTTTCTT
3788040 TTTTCT
1 TTTTCT
3788046 AATAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:3792043 original size:22 final size:21
Alignment explanation
Indices: 3792003--3792044 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3791993 AGTTTTTTTA
* *
3792003 ATAAATTAAAAATGTGTAAAT
1 ATAAATTAAAAAAGGGTAAAT
3792024 ATAAATTTAAAAAAGGGTAAA
1 ATAAA-TTAAAAAAGGGTAAA
3792045 AAAGGAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
ATAAATTAAAAAAGGGTAAAT
Found at i:3792601 original size:19 final size:21
Alignment explanation
Indices: 3792564--3792603 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3792554 ACTTAAAAAA
*
3792564 ATATACTATAAAATAATATTT
1 ATATAATATAAAATAATATTT
3792585 ATATAATAT-AAAT-ATATTT
1 ATATAATATAAAATAATATTT
3792604 TGTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAATATAAAATAATATTT
Found at i:3792619 original size:18 final size:19
Alignment explanation
Indices: 3792564--3792619 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
3792554 ACTTAAAAAA
*
3792564 ATATACTATAAAATAATATTT
1 ATATAATAT-AAA-AATATTT
*
3792585 ATATAATATAAATATATTT
1 ATATAATATAAAAATATTT
* *
3792604 -TGTAATTTAAAAATAT
1 ATATAATATAAAAATAT
3792620 AATTAAATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 13 0.43
19 6 0.20
20 3 0.10
21 8 0.27
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATATAATATAAAAATATTT
Found at i:3792903 original size:18 final size:17
Alignment explanation
Indices: 3792880--3792932 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
3792870 TTAAATAAAG
*
3792880 ATTAAATAAAAGTATAAT
1 ATTAAATAAAAAT-TAAT
3792898 ATTAAATATAAAATTAAT
1 ATTAAATA-AAAATTAAT
* *
3792916 AATAAATAATAATTAAT
1 ATTAAATAAAAATTAAT
3792933 TTTTAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.26
18 19 0.61
19 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTAAATAAAAATTAAT
Found at i:3794104 original size:3 final size:3
Alignment explanation
Indices: 3794089--3794146 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
3794079 GTTGATACCA
3794089 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3794135 TAT TAT TAT TAT
1 TAT TAT TAT TAT
3794147 CAAAACCCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3794543 original size:2 final size:2
Alignment explanation
Indices: 3794536--3794571 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3794526 TCCAAGAATA
*
3794536 AT AT AT AT AC 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
3794572 GACAATCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3794949 original size:28 final size:28
Alignment explanation
Indices: 3794924--3794984 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
3794914 GTATTATAAG
3794924 TATACTTAAGATATT-ATATATTTATATA
1 TATACTTAAGATATTAATA-ATTTATATA
* *
3794952 TATATTTAATATATTAATAATTTATATTA
1 TATACTTAAGATATTAATAATTTATA-TA
3794981 TATA
1 TATA
3794985 TAAATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TATACTTAAGATATTAATAATTTATATA
Found at i:3794998 original size:34 final size:36
Alignment explanation
Indices: 3794940--3795019 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 36
3794930 TAAGATATTA
*
3794940 TATATT-TATATATATATTTAATAT-ATTAATA-ATT
1 TATATTATATATAAATATTTAATATAATT-ATAGATT
*
3794974 TATATTATATATAAAT-TTTGATATAATTATAGTATT
1 TATATTATATATAAATATTTAATATAATTATAG-ATT
3795010 TATATTATAT
1 TATATTATAT
3795020 TTATACATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 16 0.40
35 11 0.28
36 13 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (36 bp):
TATATTATATATAAATATTTAATATAATTATAGATT
Found at i:3795374 original size:3 final size:3
Alignment explanation
Indices: 3795366--3795402 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3795356 ATGCCACCTT
3795366 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3795403 AATCGTGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3795523 original size:2 final size:2
Alignment explanation
Indices: 3795518--3795551 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3795508 ACCAAAAAAT
3795518 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3795552 ATGGAAAAAT
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):
TA
Done.