Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 28 of 29
Found at i:4838503 original size:28 final size:28
Alignment explanation
Indices: 4838451--4838512 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
4838441 ATATAGTATT
*
4838451 TTAAGTATAATTATAAATTATAAAATTA
1 TTAAATATAATTATAAATTATAAAATTA
4838479 TATAAATATAA-TATAAA-TATAAAAATTA
1 T-TAAATATAATTATAAATTAT-AAAATTA
4838507 TTAAAT
1 TTAAAT
4838513 TTATTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 8 0.26
28 15 0.48
29 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
TTAAATATAATTATAAATTATAAAATTA
Found at i:4839903 original size:2 final size:2
Alignment explanation
Indices: 4839896--4839931 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4839886 CTGCTATAAG
4839896 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
4839932 AACCAAAAAC
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):
TA
Found at i:4842515 original size:24 final size:24
Alignment explanation
Indices: 4842488--4842574 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
4842478 AGGTGGACTG
*
4842488 GAAGGCTCAGGTGCAACAGGACCA
1 GAAGGCTCAGGTGCAAGAGGACCA
* ***
4842512 GAAGGCTCAGGTGCAAGTGGAATG
1 GAAGGCTCAGGTGCAAGAGGACCA
* *
4842536 GAAGGCTCGGGTGCAAGAGGACCC
1 GAAGGCTCAGGTGCAAGAGGACCA
*
4842560 GAATGCTCAGGTGCA
1 GAAGGCTCAGGTGCA
4842575 GTAATAGGGG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.38, T:0.13
Consensus pattern (24 bp):
GAAGGCTCAGGTGCAAGAGGACCA
Found at i:4842551 original size:48 final size:48
Alignment explanation
Indices: 4842480--4842574 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
4842470 TCATCATCAG
*
4842480 GTGGACTGGAAGGCTCAGGTGCAACAGGACCAGAAGGCTCAGGTGCAA
1 GTGGAATGGAAGGCTCAGGTGCAACAGGACCAGAAGGCTCAGGTGCAA
* * * *
4842528 GTGGAATGGAAGGCTCGGGTGCAAGAGGACCCGAATGCTCAGGTGCA
1 GTGGAATGGAAGGCTCAGGTGCAACAGGACCAGAAGGCTCAGGTGCA
4842575 GTAATAGGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.39, T:0.14
Consensus pattern (48 bp):
GTGGAATGGAAGGCTCAGGTGCAACAGGACCAGAAGGCTCAGGTGCAA
Found at i:4844408 original size:2 final size:2
Alignment explanation
Indices: 4844401--4844430 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4844391 ATTATTTCTC
4844401 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
4844431 TATTCAGTTT
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:4845048 original size:31 final size:31
Alignment explanation
Indices: 4845010--4845073 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
4845000 AACTCAACTC
*
4845010 AACTCAATCCAAAATGAACAAGAAAATAAAA
1 AACTCAATCCAAAATGAACAAAAAAATAAAA
4845041 AACTCAATCCAAAATGAACAAAAAAATAAAA
1 AACTCAATCCAAAATGAACAAAAAAATAAAA
4845072 AA
1 AA
4845074 ATTTTACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.12
Consensus pattern (31 bp):
AACTCAATCCAAAATGAACAAAAAAATAAAA
Found at i:4850011 original size:18 final size:19
Alignment explanation
Indices: 4849985--4850020 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4849975 TTTGTATTTT
*
4849985 TTAACTTTAAAT-TTTTAA
1 TTAAATTTAAATATTTTAA
4850003 TTAAATTTAAATATTTTA
1 TTAAATTTAAATATTTTA
4850021 TTTTACTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAATTTAAATATTTTAA
Found at i:4850389 original size:2 final size:2
Alignment explanation
Indices: 4850382--4850406 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4850372 TGTTTAGTTT
4850382 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4850407 GGATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4851101 original size:20 final size:20
Alignment explanation
Indices: 4851078--4851115 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4851068 TATTTATTAT
4851078 TTTTAAT-TAATATTATAAAA
1 TTTTAATATAA-ATTATAAAA
4851098 TTTTAATATAAATTATAA
1 TTTTAATATAAATTATAA
4851116 TTTAAGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAATATAAATTATAAAA
Found at i:4851507 original size:24 final size:21
Alignment explanation
Indices: 4851480--4851531 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 21
4851470 GAAAATATTT
4851480 TTATAATATATTTATAAATTATCA
1 TTATAA-ATATTT-TAAATT-TCA
*
4851504 TTATAAATATTTTAAATTTTA
1 TTATAAATATTTTAAATTTCA
4851525 TTATAAA
1 TTATAAA
4851532 AATCTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.33
22 6 0.22
23 6 0.22
24 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAAATATTTTAAATTTCA
Found at i:4851534 original size:23 final size:21
Alignment explanation
Indices: 4851472--4851549 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 21
4851462 AGACAAGAGA
4851472 AAATATTT-TTATAATATATTTAT
1 AAAT-TTTATTATAA-ATATTT-T
*
4851495 AAATTATCATTATAAATATTTT
1 AAATT-TTATTATAAATATTTT
*
4851517 AAATTTTATTATAAAAATCTTT
1 AAATTTTATTATAAATAT-TTT
*
4851539 GAAATTGTATT
1 -AAATTTTATT
4851550 TATAGTAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
21 11 0.23
22 10 0.21
23 20 0.43
24 6 0.13
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
AAATTTTATTATAAATATTTT
Found at i:4852322 original size:32 final size:30
Alignment explanation
Indices: 4852245--4852322 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 30
4852235 AATAGTTATA
*
4852245 TATAAAAATTATA-ATTAATATATATTTTT
1 TATAAAAATAATATATTAATATATATTTTT
4852274 TATAAAAAAGTAAATATATTAA-ATATATTTTT
1 TAT-AAAAA-T-AATATATTAATATATATTTTT
4852306 TACATAATAAATAATAT
1 T--ATAA-AAATAATAT
4852323 TTGAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
29 3 0.07
30 5 0.12
31 1 0.02
32 19 0.46
33 8 0.20
34 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
TATAAAAATAATATATTAATATATATTTTT
Found at i:4855754 original size:13 final size:14
Alignment explanation
Indices: 4855721--4855771 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
4855711 ATAATATATT
4855721 TAAATATTTAAA-TA
1 TAAATA-TTAAATTA
* *
4855735 TATATATT-GATTA
1 TAAATATTAAATTA
4855748 TAAATATTAAATT-
1 TAAATATTAAATTA
4855761 TAAATATTAAA
1 TAAATATTAAA
4855772 AAAATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 22 0.71
14 8 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATTAAATTA
Found at i:4856583 original size:15 final size:15
Alignment explanation
Indices: 4856558--4856601 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4856548 AGTATAAGAT
4856558 AAATTTATAAATATTA
1 AAATTT-TAAATATTA
*
4856574 AAATTTTAAATTTTA
1 AAATTTTAAATATTA
*
4856589 AAATATTAAATAT
1 AAATTTTAAATAT
4856602 ATATAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTTAAATATTA
Found at i:4857292 original size:6 final size:7
Alignment explanation
Indices: 4857273--4857298 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4857263 CATTCATATA
4857273 AATTTTT
1 AATTTTT
4857280 AATTTTT
1 AATTTTT
4857287 AATTTTT
1 AATTTTT
4857294 AATTT
1 AATTT
4857299 ATAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:4857316 original size:30 final size:30
Alignment explanation
Indices: 4857280--4857348 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
4857270 ATAAATTTTT
* *
4857280 AATTTTTAATTTTTAATTTATAAATAAATA
1 AATTTTTAATATTTAATATATAAATAAATA
**
4857310 AATTTTTAATATTTAATATATACTTAAATA
1 AATTTTTAATATTTAATATATAAATAAATA
*
4857340 AATTCTTAA
1 AATTTTTAA
4857349 CATAAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTTTTAATATTTAATATATAAATAAATA
Found at i:4863155 original size:12 final size:12
Alignment explanation
Indices: 4863138--4863171 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
4863128 GCTTCGTCCG
4863138 AGAAGAACAAGA
1 AGAAGAACAAGA
4863150 AGAAGAA-AGAGA
1 AGAAGAACA-AGA
4863162 AGAAGAACAA
1 AGAAGAACAA
4863172 AAAAATGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAGAACAAGA
Found at i:4863965 original size:2 final size:2
Alignment explanation
Indices: 4863958--4863990 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4863948 TCTTTTATTT
4863958 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 T
4863991 TTGATGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4874107 original size:6 final size:6
Alignment explanation
Indices: 4874098--4874134 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
4874088 AAGTCATGCA
4874098 CAGGCT CAGGCT CAGGCT CAGGCT CAGGCT CAGGCT C
1 CAGGCT CAGGCT CAGGCT CAGGCT CAGGCT CAGGCT C
4874135 GACCCACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CAGGCT
Found at i:4877499 original size:6 final size:6
Alignment explanation
Indices: 4877488--4877546 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
4877478 TTTTAAAATT
* *
4877488 TTAAAA TTAAAA TTAAAT TTAAAA TT-ATA -TAAAA TT-AAA TT-AAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
*
4877532 TTAAATT TTAAAA TT
1 TTAAA-A TTAAAA TT
4877547 TTTAAATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 1 0.02
5 14 0.33
6 23 0.53
7 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAAAA
Found at i:4877507 original size:27 final size:25
Alignment explanation
Indices: 4877479--4877546 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 25
4877469 TATATAATAT
4877479 TTTAAAATTTTAAAATTAAAATTAAA
1 TTTAAAATTTTAAAATT-AAATTAAA
4877505 TTTAAAATTATATAAAATTAAATTAAA
1 TTTAAAATT-T-TAAAATTAAATTAAA
4877532 -TT-AAATTTTAAAATT
1 TTTAAAATTTTAAAATT
4877547 TTTAAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.17
24 1 0.03
25 5 0.12
26 11 0.28
27 9 0.22
28 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTAAAATTTTAAAATTAAATTAAA
Found at i:4877529 original size:5 final size:5
Alignment explanation
Indices: 4877491--4877538 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
4877481 TAAAATTTTA
* *
4877491 AAATT AAAATT AAATTT AAAATT ATATA AAATT AAATT AAATT AAATT
1 AAATT -AAATT AAA-TT -AAATT AAATT AAATT AAATT AAATT AAATT
4877539 TTAAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 24 0.67
6 9 0.25
7 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:4877538 original size:10 final size:11
Alignment explanation
Indices: 4877491--4877538 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
4877481 TAAAATTTTA
4877491 AAATTAAAATT
1 AAATTAAAATT
4877502 AAATTTAAAATT
1 AAA-TTAAAATT
*
4877514 ATA-TAAAATT
1 AAATTAAAATT
4877524 AAATT-AAATT
1 AAATTAAAATT
4877534 AAATT
1 AAATT
4877539 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 19 0.58
11 4 0.12
12 10 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:4877572 original size:11 final size:11
Alignment explanation
Indices: 4877556--4877596 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
4877546 TTTTAAATAT
4877556 ATATTTTTATA
1 ATATTTTTATA
4877567 ATA-TTTTA-A
1 ATATTTTTATA
4877576 A-ATTTTTATA
1 ATATTTTTATA
*
4877586 TTATTTTTATA
1 ATATTTTTATA
4877597 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 1 0.04
9 7 0.27
10 6 0.23
11 12 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTTTATA
Found at i:4877573 original size:33 final size:30
Alignment explanation
Indices: 4877536--4877596 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 30
4877526 ATTAAATTAA
4877536 ATTTTAAAATTTTTAAATATATATTTTTATAAT
1 ATTTTAAAATTTTT--ATAT-TATTTTTATAAT
4877569 ATTTTAAAATTTTTATATTATTTTTATA
1 ATTTTAAAATTTTTATATTATTTTTATA
4877597 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 10 0.36
31 4 0.14
33 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTTAAAATTTTTATATTATTTTTATAAT
Found at i:4877597 original size:11 final size:11
Alignment explanation
Indices: 4877552--4877600 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
4877542 AAATTTTTAA
4877552 ATATATATTTTT
1 ATAT-TATTTTT
*
4877564 ATAATA-TTTT
1 ATATTATTTTT
*
4877574 A-A-AATTTTT
1 ATATTATTTTT
4877583 ATATTATTTTT
1 ATATTATTTTT
4877594 ATATTAT
1 ATATTAT
4877601 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.03
9 6 0.19
10 6 0.19
11 15 0.48
12 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:4877646 original size:21 final size:22
Alignment explanation
Indices: 4877607--4877650 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4877597 TTATAAAAAT
*
4877607 TAAAAATTAATTTAAAATTAAA
1 TAAAAATCAATTTAAAATTAAA
*
4877629 TAAAAATCAATTT-TAATTAAA
1 TAAAAATCAATTTAAAATTAAA
4877650 T
1 T
4877651 TCAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAATCAATTTAAAATTAAA
Found at i:4877656 original size:21 final size:20
Alignment explanation
Indices: 4877607--4877666 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
4877597 TTATAAAAAT
*
4877607 TAAAAATTAATTTAAAATTAAA
1 TAAAAA-TAA-TTATAATTAAA
*
4877629 TAAAAATCAATTTTAATTAAA
1 TAAAAAT-AATTATAATTAAA
**
4877650 TTCAAATAATTATAATT
1 TAAAAATAATTATAATT
4877667 TTTTAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 9 0.28
21 15 0.47
22 8 0.25
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAATAATTATAATTAAA
Found at i:4888818 original size:2 final size:2
Alignment explanation
Indices: 4888806--4888836 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4888796 TTGCATATGC
*
4888806 AT AT AT GT 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 A
4888837 CGTCATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4888980 original size:15 final size:16
Alignment explanation
Indices: 4888960--4888989 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4888950 CGTGTGGTAT
4888960 AAATTAAGC-AATTTC
1 AAATTAAGCTAATTTC
4888975 AAATTAAGCTAATTT
1 AAATTAAGCTAATTT
4888990 AGATACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (16 bp):
AAATTAAGCTAATTTC
Found at i:4889101 original size:11 final size:11
Alignment explanation
Indices: 4889085--4889122 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4889075 CGTATATATC
4889085 ATATAAAAATT
1 ATATAAAAATT
*
4889096 ATATAAAAATA
1 ATATAAAAATT
*
4889107 AT-TAAAATTT
1 ATATAAAAATT
4889117 ATATAA
1 ATATAA
4889123 TATAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:4889138 original size:18 final size:17
Alignment explanation
Indices: 4889104--4889163 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
4889094 TTATATAAAA
*
4889104 ATAAT-TAAAATTT-AT
1 ATAATATAAATTTTAAT
4889119 ATAATATAAATTATTAAT
1 ATAATATAAATT-TTAAT
* *
4889137 ATATTAAAAATTTTAAT
1 ATAATATAAATTTTAAT
4889154 ATAATTATAA
1 ATAA-TATAA
4889164 CAAAAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.14
16 5 0.14
17 10 0.28
18 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATATAAATTTTAAT
Found at i:4890445 original size:270 final size:270
Alignment explanation
Indices: 4889941--4890457 Score: 666
Period size: 270 Copynumber: 1.9 Consensus size: 270
4889931 CTTACTAATT
* * *
4889941 TAAAAGTTAATCAAATTTAAAATATCGTAATCTTTGCTTATAATAATTATATTAACAATATGAAA
1 TAAAAGTTAATCAAATTTAAAATATAGTAATATTTGCTTATAATAATTACATTAACAATATGAAA
*
4890006 GTAAAAAAATTTGATTATTGATTTCAACATAACAAAAAAGTATTATTAATCTCAAGAATTATAAT
66 GTAAAAAAATTTGATCATTGATTTCAACATAACAAAAAAGTATTATTAATCTCAAGAATTATAAT
* * * * * * *
4890071 ATTTTTAATTATCAAATCTGTTTGACTCTCATAATGATAGATTACTCTATGCATAATTTTTAAGT
131 ACTTTTAATTACCAAACCTCTTTGACTCTCATAATGATAGATTACTCGATACATAATTTTCAAGT
* * *
4890136 TTTGACAAATAATTATATTTTTAAAAAAGTCTCTTCGCATTAAAATTATGTTGATTTAAAAAATA
196 TTTGACAAATAATCATATTTTAAAAAAAATCTCTTCGCATTAAAATTATGTTGATTTAAAAAATA
4890201 TCAAATAAGC
261 TCAAATAAGC
* * * * *
4890211 TAAAAGTTAATCAAGTTTAAAATATAGTAATATTTGCTTATAATAATTACATTGATATTATTAAA
1 TAAAAGTTAATCAAATTTAAAATATAGTAATATTTGCTTATAATAATTACATTAACAATATGAAA
* *
4890276 GTGAAAAATTTTGATCATTGATTTCAACATAACAAGAAAA-TATTATTAATCTCAAGAATTATAA
66 GTAAAAAAATTTGATCATTGATTTCAACATAACAA-AAAAGTATTATTAATCTCAAGAATTATAA
* * * * ** * * *
4890340 TACTTTTAATTGCCAAACCTCTTTGAC-CGTTA-AATGGTTGATTGTTGGATATATAGTTTTCAA
130 TACTTTTAATTACCAAACCTCTTTGACTC-TCATAATGATAGATTACTCGATACATAATTTTCAA
* *
4890403 GCTTTT-ATAAA-AGATCATATTTTAAAAAAAAATCTTTTCGCATTAAAATTATGTT
194 G-TTTTGACAAATA-ATCATATTTT-AAAAAAAATCTCTTCGCATTAAAATTATGTT
4890458 AACTTACGAA
Statistics
Matches: 210, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
268 1 0.00
269 36 0.17
270 169 0.80
271 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (270 bp):
TAAAAGTTAATCAAATTTAAAATATAGTAATATTTGCTTATAATAATTACATTAACAATATGAAA
GTAAAAAAATTTGATCATTGATTTCAACATAACAAAAAAGTATTATTAATCTCAAGAATTATAAT
ACTTTTAATTACCAAACCTCTTTGACTCTCATAATGATAGATTACTCGATACATAATTTTCAAGT
TTTGACAAATAATCATATTTTAAAAAAAATCTCTTCGCATTAAAATTATGTTGATTTAAAAAATA
TCAAATAAGC
Found at i:4892500 original size:3 final size:3
Alignment explanation
Indices: 4892492--4892521 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4892482 CTTTTCTACC
4892492 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4892522 TCCGTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4896065 original size:67 final size:67
Alignment explanation
Indices: 4895940--4896071 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 67
4895930 TACCACGGCG
* * *
4895940 AAATTATTTTCTACAGTTGAAATTGACTTTGTCTCTCAAATCAATGAAAAGATGAGGACACGACA
1 AAATTATTTTCTACAGTTGAAACTGACTTTGTCTCTCAAATCAATGAAAACATAAGGACACGACA
4896005 GC
66 GC
*
4896007 AAATTATTTTCTACAGTTGAAACTGACTTTGTCTCTCAAAATCATTGAAAACA-AAGGACACGAC
1 AAATTATTTTCTACAGTTGAAACTGACTTTGTCTCTC-AAATCAATGAAAACATAAGGACACGAC
4896071 A
65 A
4896072 AGGTAACTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 47 0.78
68 13 0.22
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (67 bp):
AAATTATTTTCTACAGTTGAAACTGACTTTGTCTCTCAAATCAATGAAAACATAAGGACACGACA
GC
Found at i:4897336 original size:8 final size:8
Alignment explanation
Indices: 4897323--4897351 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4897313 TCTTTGAAAC
4897323 CTTTTTTT
1 CTTTTTTT
4897331 C-TTTTTT
1 CTTTTTTT
4897338 CTTTTTTT
1 CTTTTTTT
4897346 CTTTTT
1 CTTTTT
4897352 CTAAGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
CTTTTTTT
Found at i:4897343 original size:15 final size:15
Alignment explanation
Indices: 4897323--4897351 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4897313 TCTTTGAAAC
4897323 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
4897338 CTTTTTTTCTTTTT
1 CTTTTTTTCTTTTT
4897352 CTAAGCTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
CTTTTTTTCTTTTTT
Found at i:4900465 original size:479 final size:470
Alignment explanation
Indices: 4899218--4901023 Score: 1960
Period size: 479 Copynumber: 3.8 Consensus size: 470
4899208 AAGTTCTTTA
* * *
4899218 AACCATGCACTAATGAGTTGTATCGAAATACATCTAACCAATTAGTAACTTAAAGAATTTATCTA
1 AACCATGCAC-AATGAGTTGTATCGAAACACATCCAACCAATTAATAACTTAAAGAATTTATCTA
*
4899283 GCCTTTTAAATCCTTCAAGGATTTATCCAAGC-TTTTTTCCCTTCTAAAAAGGGTTAAATCCTTA
65 GCCTTTTAAATCCTTCAAGGATTTGTCCAAGCGTTTTTTCCCTTCTAAAAAGGGTTAAATCCTTA
* * * * *
4899347 ATTTCTTATTGTTTAACTTCTTAAAGATAAGTATT-TTTTTAAAAAAAGTCAATTTGATAATATA
130 ACTTCTCATTGTTTAACTTCTTAAAAATAAGT-TTCTTTTAAAAAAAAGTCAAATTGATAATATA
* * *
4899411 ATAATAATAACATTAAATTAAAAATATTTAGATTATTAAAATTTAAAAAATAATTATCTAATAAA
194 ATAATAATAAAATTAAATTAAAAATATTTAAATTATTAAAATTTAAAAAATAATTATCCAATAAA
*
4899476 AACAACCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCTATTTTTCTTTTAAAAT
259 AACAACCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCTATTTTTC--TT---CT
* * *
4899541 ATTATATATATATATATATATTCTTTTAAGAGTTATTTTTTTAACCCAAAAAATGAATCTTAAAA
319 A--A-A-ATAT-CATATATATTCTTTTAAGAGCTA-TTTTTT-ACCCAAAAAATGAATGTTAAAA
* * * * *
4899606 GTTATAGTATTGACAATTATTCATTAAAATCATATAAAAAGATTGATTAAGTTTGATATTATGAA
377 ATTTTAGTATTAACAATTATTCATT--AA-CATATAAAAGGATT-AAT-AGTTTGATATTATGAA
*
4899671 TTAAGTGGCTTAAAAAATGTATTATTTAATGTTTTTTAAACCACGGCCAATCATGG
437 -T-A----C-T------TG---------ATGTTTTTTAAACCACAGCCAATCATGG
* *
4899727 GACCATGCACTAATCG-GTTGTATCGAAACACATCCAACCAATTAGTAACTT---G-----A---
1 AACCATGCAC-AAT-GAGTTGTATCGAAACACATCCAACCAATTAATAACTTAAAGAATTTATCT
* * * * * *
4899780 AG-------AA---TTCAAGGATTTGTTCAAGCGTTTTTTTCCTTTTAAAAAAGGCTAAATTCTT
64 AGCCTTTTAAATCCTTCAAGGATTTGTCCAAGCGTTTTTTCCCTTCTAAAAAGGGTTAAATCCTT
* *
4899835 AACTTCTCCTTGTTTAAGCTTCTTAAAAATAAGCTTCTTTTAAAAGAAAAGTCAAATTGATAATA
129 AACTTCTCATTGTTTAA-CTTCTTAAAAATAAGTTTCTTTTAAAA-AAAAGTCAAATTGATAATA
* **
4899900 TAATAATAGTAAAATTAAATTAAAGGTATTTAAATTATTAAAATTTTAAAAAATAATTATCCAAT
192 TAATAATAATAAAATTAAATTAAAAATATTTAAATTATTAAAA-TTTAAAAAATAATTATCCAAT
*
4899965 AAAAACAACCTACTCACTTAAAAAATATATCTTTATTTTTT-ATTTTAATCTATTTTTCTTTTAA
256 AAAAACAACCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCTATTTTTCTTCTAA
** * *
4900029 AATATCATATATATATTCTTTTAAGAGCTATTTTTTACTTAAAAAATGAATATTAAAAATTTTAA
321 AATATC--ATATATATTCTTTTAAGAGCTATTTTTTACCCAAAAAATGAATGTTAAAAATTTTAG
4900094 TATTAACAATTATTCATTAACCATATAAAAGGATTAACTGAGTTTGATATTATGAATACTTGATG
384 TATTAACAATTATTCATTAA-CATATAAAAGGATTAA-T-AGTTTGATATTATGAATACTTGATG
*
4900159 TTTTTTAAACTACAGCCAATCATGG
446 TTTTTTAAACCACAGCCAATCATGG
* * * *
4900184 AACCATGCAC-ATGGGTTGTATCGAAACACATCCGATCAATTAATAACTTGAAGAATTTATCTAG
1 AACCATGCACAATGAGTTGTATCGAAACACATCCAACCAATTAATAACTTAAAGAATTTATCTAG
4900248 CCTTTTAAATCCTTCAAGGATTTGTCCAAGC-TTTTTTCCCTTCTAAAAAGGGTTAAATCCTTAA
66 CCTTTTAAATCCTTCAAGGATTTGTCCAAGCGTTTTTTCCCTTCTAAAAAGGGTTAAATCCTTAA
* *
4900312 CTTCTCATTGTTTAACTTCTTAAAAAGAAGTCTTTTTTTTTAAAAAAAAAGTCAAATTGATAATA
131 CTTCTCATTGTTTAACTTCTTAAAAATAAG---TTTCTTTT-AAAAAAAAGTCAAATTGATAATA
* * * * *
4900377 AAATAATAAAAAAATTAAATTAAAAGTATTTAAATTATTTTAAAATTTTTAAAAGTAATTATCCA
192 TAATAATAATAAAATTAAATTAAAAATATTTAAATTA--TTAAAA-TTTAAAAAATAATTATCCA
* * * *
4900442 ATAAAACCTACCTACTTACTT-AAAAATATATCTTTATTTTTTAATTTTAATCTAACTTTTCTTC
254 ATAAAAACAACCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCT-ATTTTTCTTC
* *
4900506 TAAAATATCATAGATATTCTTTTAAGAGCTATTTTTTAATCCAAAAAATGAATGTTAAAAATTTT
318 TAAAATATCATATATATTCTTTTAAGAGCTATTTTTT-ACCCAAAAAATGAATGTTAAAAATTTT
* *
4900571 AGTATTAACAATTA-T--TT----TGT--AAGTGACTTAA-A--ATGCATA-T-T--A-A-TTGA
382 AGTATTAACAATTATTCATTAACATATAAAAG-GA-TTAATAGTTTG-ATATTATGAATACTTGA
* *
4900618 TGTTCTTTAAACCACAGCTAATCATGG
444 TGTTTTTTAAACCACAGCCAATCATGG
* * * *
4900645 GACCATGCACTAATAAGTTGTATCGAAACAAATCCAACAAATTAATAACTTAAAGAATTTATCTA
1 AACCATGCAC-AATGAGTTGTATCGAAACACATCCAACCAATTAATAACTTAAAGAATTTATCTA
** * * * * **
4900710 ATCTTTTAAATCTTTCAAAGATTTGTTCAAGCTTTTTTTCCCTTCTAAAAAGGGTTAAATATTTA
65 GCCTTTTAAATCCTTCAAGGATTTGTCCAAGCGTTTTTTCCCTTCTAAAAAGGGTTAAATCCTTA
*
4900775 ATTTCTCATTGTTTAACTTCTTAAAAATAAGTTTCTTTTAAAAAAAA-TCAAATTGATAATATAA
130 ACTTCTCATTGTTTAACTTCTTAAAAATAAGTTTCTTTTAAAAAAAAGTCAAATTGATAATATAA
* *
4900839 TAATAATAACATTAAATTAAAAATATTTAGATTATTAAAATTTAAAAAATAATTATCCAATAAAA
195 TAATAATAAAATTAAATTAAAAATATTTAAATTATTAAAATTTAAAAAATAATTATCCAATAAAA
** * *
4900904 ATTATCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCTATTTTTCTTCTAAAGTA
260 ACAACCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCTATTTTTCTTCTAAAATA
* *
4900969 TCATATATATTCTTTTAAAAGCTATTTTTTACCCAGAAAATGAATGTTAAAAATT
325 TCATATATATTCTTTTAAGAGCTATTTTTTACCCAAAAAATGAATGTTAAAAATT
4901024 GAATCTAAAT
Statistics
Matches: 1140, Mismatches: 110, Indels: 148
0.82 0.08 0.11
Matches are distributed among these distances:
454 1 0.00
455 57 0.05
456 77 0.07
457 73 0.06
458 1 0.00
459 46 0.04
460 8 0.01
461 44 0.04
462 1 0.00
463 75 0.07
464 59 0.05
465 1 0.00
466 7 0.01
467 3 0.00
468 1 0.00
469 3 0.00
470 2 0.00
471 6 0.01
472 1 0.00
473 3 0.00
474 14 0.01
475 42 0.04
476 20 0.02
477 59 0.05
478 55 0.05
479 120 0.11
480 17 0.01
481 40 0.04
482 10 0.01
483 22 0.02
484 1 0.00
486 2 0.00
488 17 0.01
489 44 0.04
490 21 0.02
491 75 0.07
492 61 0.05
498 2 0.00
501 1 0.00
506 1 0.00
509 46 0.04
510 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (470 bp):
AACCATGCACAATGAGTTGTATCGAAACACATCCAACCAATTAATAACTTAAAGAATTTATCTAG
CCTTTTAAATCCTTCAAGGATTTGTCCAAGCGTTTTTTCCCTTCTAAAAAGGGTTAAATCCTTAA
CTTCTCATTGTTTAACTTCTTAAAAATAAGTTTCTTTTAAAAAAAAGTCAAATTGATAATATAAT
AATAATAAAATTAAATTAAAAATATTTAAATTATTAAAATTTAAAAAATAATTATCCAATAAAAA
CAACCTACTCACTTAAAAAATATATCTTTATTTTTTAATTTTAATCTATTTTTCTTCTAAAATAT
CATATATATTCTTTTAAGAGCTATTTTTTACCCAAAAAATGAATGTTAAAAATTTTAGTATTAAC
AATTATTCATTAACATATAAAAGGATTAATAGTTTGATATTATGAATACTTGATGTTTTTTAAAC
CACAGCCAATCATGG
Found at i:4901734 original size:6 final size:6
Alignment explanation
Indices: 4901723--4901786 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
4901713 TTTTATGATC
* *
4901723 TATATT TATATT TATATT TAT-TT TAT-TT TAT-TT TATTTT TATTAAT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TA-TATT
*
4901769 TATTTT TA-ATT TAATATT
1 TATATT TATATT T-ATATT
4901787 ATAAAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
5 18 0.37
6 24 0.49
7 7 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATATT
Found at i:4901749 original size:5 final size:5
Alignment explanation
Indices: 4901727--4901761 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
4901717 ATGATCTATA
4901727 TTTAT ATTTAT ATTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT -TTTAT -TTTAT TTTAT TTTAT TTTAT TTT
4901762 TATTAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:4901776 original size:19 final size:16
Alignment explanation
Indices: 4901727--4901765 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4901717 ATGATCTATA
4901727 TTTATATTTATATTTA-T
1 TTTAT-TTTAT-TTTATT
4901744 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
4901760 TTTATT
1 TTTATT
4901766 AATTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:4901832 original size:19 final size:19
Alignment explanation
Indices: 4901808--4901858 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4901798 ATTAAAATTT
4901808 ATTTATAAATATAATTTTA
1 ATTTATAAATATAATTTTA
*
4901827 ATTTATAAAT-T-TTTTTA
1 ATTTATAAATATAATTTTA
4901844 ATATTATACAATATA
1 AT-TTATA-AATATA
4901859 TATTCAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 13 0.48
20 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATAAATATAATTTTA
Found at i:4901944 original size:11 final size:9
Alignment explanation
Indices: 4901901--4901935 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
4901891 TATATATACT
4901901 AAAAATATA
1 AAAAATATA
4901910 AAAAATATA
1 AAAAATATA
4901919 AAAAATATA
1 AAAAATATA
4901928 AAAAATAT
1 AAAAATAT
4901936 TTAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATATA
Found at i:4904594 original size:2 final size:2
Alignment explanation
Indices: 4904589--4904617 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4904579 TTCAACCCAA
4904589 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4904618 AGAATAGAAA
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:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4910990 original size:16 final size:16
Alignment explanation
Indices: 4910966--4910999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4910956 ACTTTGATAC
* *
4910966 TTTTTAAAATTTTTTA
1 TTTTAAAAATCTTTTA
4910982 TTTTAAAAATCTTTTA
1 TTTTAAAAATCTTTTA
4910998 TT
1 TT
4911000 AAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAAAATCTTTTA
Found at i:4914091 original size:19 final size:19
Alignment explanation
Indices: 4914069--4914124 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4914059 AAAATCATAT
4914069 TTATAAATAATAATTAAAG
1 TTATAAATAATAATTAAAG
** * * *
4914088 TTATTTATAAAAATTATAT
1 TTATAAATAATAATTAAAG
4914107 TTATAAATAATAATTAAA
1 TTATAAATAATAATTAAA
4914125 ACTATATTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTATAAATAATAATTAAAG
Found at i:4914094 original size:38 final size:38
Alignment explanation
Indices: 4914051--4914124 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
4914041 TATATTAATA
4914051 TATTTATAAAAATCATATTTATAAATAATAATTAAAGT
1 TATTTATAAAAATCATATTTATAAATAATAATTAAAGT
*
4914089 TATTTATAAAAATTATATTTATAAATAATAATTAAA
1 TATTTATAAAAATCATATTTATAAATAATAATTAAA
4914125 ACTATATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
TATTTATAAAAATCATATTTATAAATAATAATTAAAGT
Found at i:4914716 original size:20 final size:21
Alignment explanation
Indices: 4914691--4914730 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4914681 TTCTATCAGA
*
4914691 TTAAATTATAATTAA-AAATT
1 TTAAATAATAATTAATAAATT
*
4914711 TTAAATAATATTTAATAAAT
1 TTAAATAATAATTAATAAAT
4914731 CGAGTGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATAATAATTAATAAATT
Found at i:4932210 original size:12 final size:12
Alignment explanation
Indices: 4932193--4932222 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4932183 TCAATCCAAG
4932193 TCAACAACAACA
1 TCAACAACAACA
4932205 TCAACAACAACA
1 TCAACAACAACA
*
4932217 ACAACA
1 TCAACA
4932223 GGAGGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.33, G:0.00, T:0.07
Consensus pattern (12 bp):
TCAACAACAACA
Found at i:4932702 original size:26 final size:25
Alignment explanation
Indices: 4932662--4932715 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
4932652 CAATAATTTT
*
4932662 TTAATTTTTTAATTTAAATA-TAAA
1 TTAATTTTTTAATTTAAAAATTAAA
4932686 TTAATTTAATTTAATTTAAAAATTAAA
1 TTAATTT--TTTAATTTAAAAATTAAA
4932713 TTA
1 TTA
4932716 TTATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.27
26 12 0.46
27 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATTTTTTAATTTAAAAATTAAA
Found at i:4932727 original size:19 final size:22
Alignment explanation
Indices: 4932670--4932730 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 22
4932660 TTTTAATTTT
* *
4932670 TTAATTTAA-ATATAAATTAAT
1 TTAATTTAATTTATAAATTAAA
*
4932691 TTAATTTAATTTAAAAATTAAA
1 TTAATTTAATTTATAAATTAAA
4932713 TT-A-TT-ATTTATAAATTAA
1 TTAATTTAATTTATAAATTAA
4932731 TAAAAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.34
20 2 0.06
21 10 0.29
22 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATTTAATTTATAAATTAAA
Found at i:4932764 original size:22 final size:22
Alignment explanation
Indices: 4932739--4932799 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
4932729 AATAAAAAAT
*
4932739 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAATATTTAAA
4932761 TATTTTTATAATTAA-ATTTAAA
1 TATTTTTAT-ATTAATATTTAAA
4932783 TAATTTTT-TATT-ATATT
1 T-ATTTTTATATTAATATT
4932800 AAACTTCACA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 1 0.03
21 6 0.17
22 17 0.49
23 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATATTAATATTTAAA
Found at i:4933015 original size:22 final size:21
Alignment explanation
Indices: 4932973--4933037 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 21
4932963 TCATTTTATT
4932973 AAAAT-TTTTTATAAATAAATATA
1 AAAATATTTTTA-AAAT-AATA-A
4932996 AATAA-ATTTTTAAAATAATAA
1 AA-AATATTTTTAAAATAATAA
4933017 AAAATATGTTTTAATAATAAT
1 AAAATAT-TTTTAA-AATAAT
4933038 TTATAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 10 0.27
23 12 0.32
24 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATATTTTTAAAATAATAA
Found at i:4938264 original size:31 final size:31
Alignment explanation
Indices: 4938226--4938287 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
4938216 TGGGTGCACC
*
4938226 TTTAACCAAGACAAACACTAGCACGATCAAG
1 TTTAACCAAAACAAACACTAGCACGATCAAG
4938257 TTTAACCAAAACAAACACTAGCACGATCAAG
1 TTTAACCAAAACAAACACTAGCACGATCAAG
4938288 ATCCACTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (31 bp):
TTTAACCAAAACAAACACTAGCACGATCAAG
Found at i:4939440 original size:2 final size:2
Alignment explanation
Indices: 4939428--4939464 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4939418 AGTCTATTTA
4939428 AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4939465 AAATAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4939452 original size:19 final size:19
Alignment explanation
Indices: 4939428--4939464 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4939418 AGTCTATTTA
4939428 ATATATAATATATATATAT
1 ATATATAATATATATATAT
*
4939447 ATATATATTATATATATA
1 ATATATAATATATATATA
4939465 AAATAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATAATATATATATAT
Found at i:4953317 original size:33 final size:31
Alignment explanation
Indices: 4953278--4953351 Score: 103
Period size: 33 Copynumber: 2.3 Consensus size: 31
4953268 CCAACACAAT
*
4953278 TTTATAAATTTAAACAATATTTTATAACTATAA
1 TTTATAAATTTAAACAATA-TTTATAACCA-AA
*
4953311 TTTATAAATTTAAATAATATTTATAACCAAA
1 TTTATAAATTTAAACAATATTTATAACCAAA
*
4953342 ATTATAAATT
1 TTTATAAATT
4953352 AAAAAAATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 11 0.29
32 9 0.24
33 18 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTATAAATTTAAACAATATTTATAACCAAA
Found at i:4953945 original size:2 final size:2
Alignment explanation
Indices: 4953926--4953981 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
4953916 CCAAGTGATT
* * * * *
4953926 TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA CA CA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4953968 TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA
4953982 GTTTTATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:4954717 original size:17 final size:19
Alignment explanation
Indices: 4954676--4954717 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
4954666 AAAAAAGTTA
*
4954676 AATTTTAAATTTATTAAAT
1 AATTTTAAATTTATAAAAT
4954695 -ATTTTAAA-TTA-AAAAT
1 AATTTTAAATTTATAAAAT
4954711 AATTTTA
1 AATTTTA
4954718 TGAGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 9 0.43
18 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTTAAATTTATAAAAT
Found at i:4957860 original size:27 final size:27
Alignment explanation
Indices: 4957801--4957890 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 27
4957791 CTTCTATAGT
4957801 TTATATTTATATAAT-TTTTATATATTATAA
1 TTATATTTA-A-AATATTTTATAT-TTAT-A
4957831 TTATATTTAAAATATTTTATATTTATA
1 TTATATTTAAAATATTTTATATTTATA
* *
4957858 TTA-ATTT-TAATATATTAATACTTTATA
1 TTATATTTAAAATAT-TTTATA-TTTATA
4957885 TTATAT
1 TTATAT
4957891 AAATTTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.09
26 9 0.17
27 13 0.24
28 9 0.17
29 9 0.17
30 9 0.17
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATATTTAAAATATTTTATATTTATA
Found at i:4957873 original size:14 final size:15
Alignment explanation
Indices: 4957853--4957899 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
4957843 TATTTTATAT
4957853 TTATATTAATTTTAA
1 TTATATTAATTTTAA
4957868 -TATATTAATACTTTATA
1 TTATATTAAT--TTTA-A
*
4957885 TTATATAAATTTTAA
1 TTATATTAATTTTAA
4957900 AAATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 8 0.30
17 1 0.04
18 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTAATTTTAA
Found at i:4957898 original size:16 final size:16
Alignment explanation
Indices: 4957800--4957898 Score: 59
Period size: 17 Copynumber: 6.2 Consensus size: 16
4957790 ACTTCTATAG
*
4957800 TTTATATTTATATAATT
1 TTTATA-TTATATAAAT
4957817 TTTATA-TAT-TATAA-
1 TTTATATTATATA-AAT
*
4957831 -TTATATT-TAAAATAT
1 TTTATATTATATAA-AT
*
4957846 TTTATATTTATATTAAT
1 TTTATA-TTATATAAAT
*
4957863 TTTA-A-TATATTAATAC
1 TTTATATTATA-TAA-AT
4957879 TTTATATTATATAAAT
1 TTTATATTATATAAAT
4957895 TTTA
1 TTTA
4957899 AAAATATATT
Statistics
Matches: 63, Mismatches: 7, Indels: 25
0.66 0.07 0.26
Matches are distributed among these distances:
13 7 0.11
14 9 0.14
15 6 0.10
16 16 0.25
17 18 0.29
18 7 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATATTATATAAAT
Found at i:4957913 original size:23 final size:24
Alignment explanation
Indices: 4957881--4957938 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
4957871 ATTAATACTT
4957881 TATA-TTATATAAATTTTA-AAAA
1 TATATTTATATAAATTTTATAAAA
* * *
4957903 TATATTTATAT-TATTTTATATAT
1 TATATTTATATAAATTTTATAAAA
4957926 TATATTTATATAA
1 TATATTTATATAA
4957939 TCATATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTTATATAAATTTTATAAAA
Found at i:4957921 original size:38 final size:39
Alignment explanation
Indices: 4957879--4957974 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 39
4957869 ATATTAATAC
4957879 TTTATATTATATAAATTTTA-AAAAT-ATATTT-ATATTAT
1 TTTATA-TAT-TAAATTTTATAAAATCATATTTAATATTAT
* *
4957917 TTTATATATTATA-TTTATATAATCATATTTAATATTAT
1 TTTATATATTAAATTTTATAAAATCATATTTAATATTAT
*
4957955 TATTAAATATTAAATTTTAT
1 T-TTATATATTAAATTTTAT
4957975 CTCATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
35 4 0.08
36 7 0.14
37 9 0.18
38 14 0.29
39 10 0.20
40 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (39 bp):
TTTATATATTAAATTTTATAAAATCATATTTAATATTAT
Found at i:4957944 original size:14 final size:13
Alignment explanation
Indices: 4957904--4957951 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
4957894 TTTTAAAAAT
4957904 ATATTTATAT-T-
1 ATATTTATATATC
*
4957915 AT-TTTATATATT
1 ATATTTATATATC
4957927 ATATTTATATAATC
1 ATATTTATAT-ATC
4957941 ATATTTA-ATAT
1 ATATTTATATAT
4957952 TATTATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 7 0.22
11 3 0.09
12 4 0.12
13 9 0.28
14 9 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTTATATATC
Found at i:4958301 original size:22 final size:21
Alignment explanation
Indices: 4958265--4958305 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
4958255 TTTATTTAAT
4958265 TAATATATTAAAAATAATAAA
1 TAATATATTAAAAATAATAAA
*
4958286 TAATATTATTATAAATAATA
1 TAATA-TATTAAAAATAATA
4958306 TCGTATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATATATTAAAAATAATAAA
Found at i:4960125 original size:21 final size:22
Alignment explanation
Indices: 4960100--4960149 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
4960090 TAAATTTTAT
*
4960100 ATTTTTATTAT-ATTTAAATAA
1 ATTTTAATTATAATTTAAATAA
*
4960121 ATTTTAATTTTAATTTAAAT-A
1 ATTTTAATTATAATTTAAATAA
4960142 A-TTTAATT
1 ATTTTAATT
4960150 TGTATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAATTATAATTTAAATAA
Found at i:4960148 original size:20 final size:22
Alignment explanation
Indices: 4960110--4960160 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 22
4960100 ATTTTTATTA
4960110 TATTTAAATAAATTTTAATTT-
1 TATTTAAATAAATTTTAATTTG
4960131 TAATTTAAAT-AA-TTTAATTTG
1 T-ATTTAAATAAATTTTAATTTG
4960152 TATTTAAAT
1 TATTTAAAT
4960161 TAGTCGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 16 0.57
21 4 0.14
22 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTAAATAAATTTTAATTTG
Found at i:4962200 original size:2 final size:2
Alignment explanation
Indices: 4962193--4962229 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4962183 GAAGCCACCT
4962193 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4962230 TCATCTTATC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4968430 original size:3 final size:3
Alignment explanation
Indices: 4968424--4968448 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4968414 ATAACGATAG
4968424 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
4968449 TTATTAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4969985 original size:40 final size:42
Alignment explanation
Indices: 4969898--4969983 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
4969888 CTGAAAACCC
*
4969898 ATATTAATATTTAAAATAATATTAAAAAATAAAAATTATTTT
1 ATATTAATATTTAAAATAATATTAAAAAACAAAAATTATTTT
* * * * *
4969940 ATATTAATATTTATAATTAA-ATTTAAATACAAATATTTTTTT
1 ATATTAATATTTA-AAATAATATTAAAAAACAAAAATTATTTT
4969982 AT
1 AT
4969984 TATAATGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (42 bp):
ATATTAATATTTAAAATAATATTAAAAAACAAAAATTATTTT
Found at i:4971368 original size:17 final size:18
Alignment explanation
Indices: 4971313--4971373 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
4971303 AATATTATCA
4971313 TAAATATAATACAATATATT
1 TAAATATAATA-AA-ATATT
*
4971333 TAAATATAAT-TAATA--
1 TAAATATAATAAAATATT
4971348 TAAA-ATAATAAAATATT
1 TAAATATAATAAAATATT
4971365 TAAAATATA
1 T-AAATATA
4971374 TTTCGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
17 4 0.12
18 4 0.12
19 3 0.09
20 10 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATAATAAAATATT
Found at i:4975878 original size:2 final size:2
Alignment explanation
Indices: 4975873--4975903 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4975863 AAAAAAAAAA
4975873 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 A
4975904 CATAATGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4985776 original size:71 final size:71
Alignment explanation
Indices: 4985698--4985839 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
4985688 TATACATTAT
*
4985698 ACTGTGAGACTGCTTAAATTATTGTGTTTCTTTTTCTTCTAAAAATTAGTGCAATCTAGTTACTA
1 ACTGTGAGACTGCTTAAATTATTGTGTTTCTTTTTCTTCTAAAAATTAGTACAATCTAGTTACTA
4985763 TGATTG
66 TGATTG
*
4985769 ACTGTGAGACTGCTTAACTTATTGTGTTTCTTTTTCTTCTAAAAATTAGTACAATCTAGTTACTA
1 ACTGTGAGACTGCTTAAATTATTGTGTTTCTTTTTCTTCTAAAAATTAGTACAATCTAGTTACTA
4985834 TGATTG
66 TGATTG
4985840 TTTTTCTTCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (71 bp):
ACTGTGAGACTGCTTAAATTATTGTGTTTCTTTTTCTTCTAAAAATTAGTACAATCTAGTTACTA
TGATTG
Found at i:4992681 original size:16 final size:15
Alignment explanation
Indices: 4992644--4992684 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4992634 TCACCGTTTG
* *
4992644 ATAAAATTTGTAAAA
1 ATAATATTTATAAAA
4992659 ATAATATTTATAAAA
1 ATAATATTTATAAAA
4992674 ATATATATTTA
1 ATA-ATATTTA
4992685 AAATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATAATATTTATAAAA
Found at i:4992720 original size:18 final size:17
Alignment explanation
Indices: 4992699--4992743 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
4992689 ATTATTTTTA
*
4992699 ATTAAATAAAAATAATGT
1 ATTAAATAAAAA-AATAT
4992717 ATTAAATATAAAAAATAT
1 ATTAAATA-AAAAAATAT
*
4992735 ATAAAATAA
1 ATTAAATAA
4992744 TCATTAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 19 0.79
19 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATTAAATAAAAAAATAT
Found at i:4992925 original size:21 final size:20
Alignment explanation
Indices: 4992896--4992965 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
4992886 TATTGTATTT
*
4992896 ATATATTATAATTTATTTAAA
1 ATATATTAT-ATTTATATAAA
*
4992917 ATATTTTATATTTATATAAA
1 ATATATTATATTTATATAAA
*
4992937 AT-T-TTATATTT-TAATAAT
1 ATATATTATATTTAT-ATAAA
*
4992955 TTATATTATAT
1 ATATATTATAT
4992966 AAATTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 1 0.02
18 13 0.31
19 2 0.05
20 18 0.43
21 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATATTTATATAAA
Found at i:4992931 original size:20 final size:19
Alignment explanation
Indices: 4992896--4992947 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
4992886 TATTGTATTT
* *
4992896 ATATATTATAATTTATTTAAA
1 ATATTTTAT-ATTTATAT-AA
4992917 ATATTTTATATTTATATAA
1 ATATTTTATATTTATATAA
4992936 A-ATTTTATATTT
1 ATATTTTATATTT
4992948 TAATAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 3 0.10
20 7 0.24
21 8 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTTATATTTATATAA
Found at i:4992942 original size:18 final size:18
Alignment explanation
Indices: 4992919--4992968 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
4992909 TATTTAAAAT
4992919 ATTTTATATTTATATAAA
1 ATTTTATATTTATATAAA
*
4992937 ATTTTATATTT-TA-ATA
1 ATTTTATATTTATATAAA
4992953 A-TTTATA-TTATATAAA
1 ATTTTATATTTATATAAA
4992969 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 8 0.29
16 5 0.18
17 2 0.07
18 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTATATTTATATAAA
Found at i:4992970 original size:15 final size:15
Alignment explanation
Indices: 4992921--4992972 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
4992911 TTTAAAATAT
4992921 TTTATATTTATATAAAA
1 TTTATA-TTATAT-AAA
*
4992938 TTTTATATTTTA-ATAA
1 -TTTATATTATATA-AA
4992954 TTTATATTATATAAA
1 TTTATATTATATAAA
4992969 TTTA
1 TTTA
4992973 AAAATTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 17 0.57
16 3 0.10
17 4 0.13
18 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:4993006 original size:22 final size:22
Alignment explanation
Indices: 4992976--4993017 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4992966 AAATTTAAAA
4992976 ATTTCATATATTAATATTATTT
1 ATTTCATATATTAATATTATTT
* * *
4992998 ATTTTATATTTTTATATTAT
1 ATTTCATATATTAATATTAT
4993018 GTAATTACGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTCATATATTAATATTATTT
Found at i:4993050 original size:18 final size:18
Alignment explanation
Indices: 4993029--4993068 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4993019 TAATTACGTG
*
4993029 ATATATAGGTATCATAAA
1 ATATATAGATATCATAAA
*
4993047 ATATCTAGATATCATAAA
1 ATATATAGATATCATAAA
4993065 ATAT
1 ATAT
4993069 CAATAATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (18 bp):
ATATATAGATATCATAAA
Found at i:4993093 original size:2 final size:2
Alignment explanation
Indices: 4993086--4993130 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4993076 GTATGAACAA
4993086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4993128 AT A
1 AT A
4993131 ATGAAGGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4994225 original size:251 final size:250
Alignment explanation
Indices: 4993708--4994198 Score: 894
Period size: 251 Copynumber: 2.0 Consensus size: 250
4993698 TTAATTATAA
* *
4993708 AATAAAAATTAATTAAAAATATTTATAAATTTAATCATAGTTTTAAATTTTTTTAATTTTTATTA
1 AATAAAAATTAATTAAAAAAATATATAAATTTAATCATAGTTTTAAATTTTTTTAATTTTTATTA
4993773 TATTTAAATCAAATTTGATTCAATTTTAAAATTTAAATTATTATTTAAAAAATATATATATTTTA
66 TATTTAAATCAAATTTGATTCAATTTTAAAATTTAAATTATTATTTAAAAAATATATATATTTTA
*
4993838 TAATAATTATTCAGATTAAATTTATCGTATTGGATGAAACAGTTTTACTCCTAAGACTATGGGAT
131 TAATAATTATTCAGATTAAATTTATCGTATTGAATGAAACAGTTTTACTCCTAAGACTATGGGAT
**
4993903 GTTTTAAACCAGATCTTAATGAATCCTTAGCAGCAGGATTAGATAACTTAATTAT
196 GTTTTAAACCAGATCTTAATGAATCCTTAGCAGCAGGATTAGATAACTTAAGCAT
4993958 AAAATAAAAATTAATTAAAAAAATATATAAATTTAATCATAGTTTTAAATTTTTTTAATTTTTAT
1 --AATAAAAATTAATTAAAAAAATATATAAATTTAATCATAGTTTTAAATTTTTTTAATTTTTAT
*
4994023 TATATTTAAATCAAATTTGATTCAATTTTAAAATTTAAATTATTATTTAAAAGA-ATATATATTT
64 TATATTTAAATCAAATTTGATTCAATTTTAAAATTTAAATTATTATTTAAAAAATATATATATTT
4994087 TATAATAATTATTCAGATTAAATTTATCGTATTGAATGAAACAGTTTTACTCCTAAGACTATGGG
129 TATAATAATTATTCAGATTAAATTTATCGTATTGAATGAAACAGTTTTACTCCTAAGACTATGGG
*
4994152 ATGTTTTTAACCAGATCTTAATGAATCCTTAGCAGCAGGATTAGATA
194 ATGTTTTAAACCAGATCTTAATGAATCCTTAGCAGCAGGATTAGATA
4994199 CTTGCAACGC
Statistics
Matches: 234, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
251 120 0.51
252 114 0.49
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (250 bp):
AATAAAAATTAATTAAAAAAATATATAAATTTAATCATAGTTTTAAATTTTTTTAATTTTTATTA
TATTTAAATCAAATTTGATTCAATTTTAAAATTTAAATTATTATTTAAAAAATATATATATTTTA
TAATAATTATTCAGATTAAATTTATCGTATTGAATGAAACAGTTTTACTCCTAAGACTATGGGAT
GTTTTAAACCAGATCTTAATGAATCCTTAGCAGCAGGATTAGATAACTTAAGCAT
Found at i:4994627 original size:2 final size:2
Alignment explanation
Indices: 4994620--4994660 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4994610 CTGGTGAAGG
4994620 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4994661 TCCACATGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4995512 original size:2 final size:2
Alignment explanation
Indices: 4995505--4995530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4995495 TCAAATTGTT
4995505 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
4995531 GAGATAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5007427 original size:2 final size:2
Alignment explanation
Indices: 5007382--5007409 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5007372 ATCATATACC
5007382 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
5007410 CCTCTATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5007774 original size:10 final size:10
Alignment explanation
Indices: 5007759--5007829 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
5007749 TTTAAAATAT
5007759 TATATTTTTA
1 TATATTTTTA
5007769 TATATTTTT-
1 TATATTTTTA
* *
5007778 TATATATTAA
1 TATATTTTTA
5007788 TA-ATTTATT-
1 TATATTT-TTA
*
5007797 T-TATTTAATA
1 TATATTT-TTA
5007807 TATATTTTTA
1 TATATTTTTA
* *
5007817 TATGTATTTA
1 TATATTTTTA
5007827 TAT
1 TAT
5007830 TTATATTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 17 0.35
10 26 0.54
11 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (10 bp):
TATATTTTTA
Found at i:5007799 original size:31 final size:29
Alignment explanation
Indices: 5007728--5007801 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
5007718 ATTTATTTGT
*
5007728 TTATATTTGTATTATTTTTTATTTAAAATA
1 TTATATTT-TATTATTTTTTATATAAAATA
*
5007758 TTATATTTTTATATATTTTTTATATATTAATAA
1 TTATA-TTTTAT-TATTTTTTATATA-AAAT-A
5007791 TT-TATTTTATT
1 TTATATTTTATT
5007802 TAATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 9 0.24
31 21 0.55
32 5 0.13
33 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATATTTTATTATTTTTTATATAAAATA
Found at i:5007844 original size:21 final size:21
Alignment explanation
Indices: 5007814--5007860 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5007804 ATATATATTT
*
5007814 TTATATGTATTTATATTTATA
1 TTATACGTATTTATATTTATA
*
5007835 TTATACGTATTTATTTTTATA
1 TTATACGTATTTATATTTATA
5007856 TTATA
1 TTATA
5007861 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TTATACGTATTTATATTTATA
Found at i:5007974 original size:15 final size:15
Alignment explanation
Indices: 5007954--5008011 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
5007944 AGCTGACAAA
5007954 GAAAGAAAGAAAAAG
1 GAAAGAAAGAAAAAG
*
5007969 GAAAG-AAGAGAAAG
1 GAAAGAAAGAAAAAG
*
5007983 GAGAAAAGAAGAAAAAG
1 GA-AAGA-AAGAAAAAG
5008000 GAACA-AAAGAAA
1 GAA-AGAAAGAAA
5008012 GAAGAGAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.28
15 13 0.36
16 2 0.06
17 11 0.31
ACGTcount: A:0.71, C:0.02, G:0.28, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAAG
Found at i:5007977 original size:14 final size:14
Alignment explanation
Indices: 5007954--5008002 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 14
5007944 AGCTGACAAA
5007954 GAAAGAAAGAAAAAG
1 GAAAG-AAGAAAAAG
5007969 GAAAGAAGAGAAAGGAG
1 GAAAGAAGA-AAA--AG
*
5007986 AAAAGAAGAAAAAG
1 GAAAGAAGAAAAAG
5008000 GAA
1 GAA
5008003 CAAAAGAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
16 3 0.10
17 10 0.34
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
GAAAGAAGAAAAAG
Found at i:5007992 original size:17 final size:17
Alignment explanation
Indices: 5007970--5008023 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
5007960 AAGAAAAAGG
5007970 AAAGAAGAGAAAGGAGA
1 AAAGAAGAGAAAGGAGA
* *
5007987 AAAGAAGAAAAAGGAACA
1 AAAGAAGAGAAAGG-AGA
5008005 AAAGAA-AG-AAGAGAGA
1 AAAGAAGAGAAAG-GAGA
5008021 AAA
1 AAA
5008024 ATTTATTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 8 0.26
17 15 0.48
18 8 0.26
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAGAAGAGAAAGGAGA
Found at i:5008105 original size:31 final size:29
Alignment explanation
Indices: 5008034--5008107 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
5008024 ATTTATTTGT
*
5008034 TTATATTTGTATTATTTTTTATTTAAAATA
1 TTATATTT-TATTATTTTTTATATAAAATA
*
5008064 TTATATTTTTATATATTTTTTATATATTAATAA
1 TTATA-TTTTAT-TATTTTTTATATA-AAAT-A
5008097 TT-TATTTTATT
1 TTATATTTTATT
5008108 TAATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 9 0.24
31 21 0.55
32 5 0.13
33 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATATTTTATTATTTTTTATATAAAATA
Found at i:5008115 original size:306 final size:307
Alignment explanation
Indices: 5007561--5008177 Score: 1200
Period size: 306 Copynumber: 2.0 Consensus size: 307
5007551 TATCTACTAT
5007561 ATATCTAATTTGAACTACATACATAGGTGAGGAATTGACACCTGTCCATGCCTTTTTTTACTTTT
1 ATATCTAATTTGAACTACATACATAGGTGAGGAATTGACACCTGTCCATGCCTTTTTTTACTTTT
*
5007626 TTTTTTTCGTTCAGCTGACAAAGAAAGAAAGAAAAAAGAAAGGAGAGAAAGGAGAAAAGAAGAAA
66 TTTTTTTCGTTCAGCTGACAAAGAAAGAAAGAAAAAAGAAAGAAGAGAAAGGAGAAAAGAAGAAA
5007691 AAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTTGTATTATTTTTTATTTAAAA
131 AAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTTGTATTATTTTTTATTTAAAA
5007756 TATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTATTTAATATATATTTTTATATG
196 TATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTATTTAATATATATTTTTATATG
*
5007821 TATTTATATTTATATTATACGTATTTATTTTTATATTATATTTTTAA
261 TATGTATATTTATATTATACGTATTTATTTTTATATTATATTTTTAA
5007868 ATATCTAATTTGAACTACATACATAGGTGAGGAATTGACACCTGTCCATGCCTTTTTTTAC-TTT
1 ATATCTAATTTGAACTACATACATAGGTGAGGAATTGACACCTGTCCATGCCTTTTTTTACTTTT
*
5007932 TTTTTTTCGTTCAGCTGACAAAGAAAGAAAGAAAAAGGAAAGAAGAGAAAGGAGAAAAGAAGAAA
66 TTTTTTTCGTTCAGCTGACAAAGAAAGAAAGAAAAAAGAAAGAAGAGAAAGGAGAAAAGAAGAAA
5007997 AAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTTGTATTATTTTTTATTTAAAA
131 AAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTTGTATTATTTTTTATTTAAAA
5008062 TATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTATTTAATATATATTTTTATATG
196 TATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTATTTAATATATATTTTTATATG
5008127 TATGTATATTTATATTATACGTATTTATTTTTATATTATATTTTTAA
261 TATGTATATTTATATTATACGTATTTATTTTTATATTATATTTTTAA
5008174 ATAT
1 ATAT
5008178 TTTTTATAAA
Statistics
Matches: 307, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
306 246 0.80
307 61 0.20
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (307 bp):
ATATCTAATTTGAACTACATACATAGGTGAGGAATTGACACCTGTCCATGCCTTTTTTTACTTTT
TTTTTTTCGTTCAGCTGACAAAGAAAGAAAGAAAAAAGAAAGAAGAGAAAGGAGAAAAGAAGAAA
AAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTTGTATTATTTTTTATTTAAAA
TATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTATTTAATATATATTTTTATATG
TATGTATATTTATATTATACGTATTTATTTTTATATTATATTTTTAA
Found at i:5008150 original size:21 final size:21
Alignment explanation
Indices: 5008120--5008166 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5008110 ATATATATTT
*
5008120 TTATATGTATGTATATTTATA
1 TTATACGTATGTATATTTATA
* *
5008141 TTATACGTATTTATTTTTATA
1 TTATACGTATGTATATTTATA
5008162 TTATA
1 TTATA
5008167 TTTTTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATACGTATGTATATTTATA
Found at i:5009619 original size:20 final size:17
Alignment explanation
Indices: 5009588--5009653 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
5009578 ATTTATTTGA
5009588 ATAATT-TATTTATCAAATT
1 ATAATTATATTTA--AAA-T
5009607 ATAATTATATTTAAAAT
1 ATAATTATATTTAAAAT
* *
5009624 ATTATAATATTTAAAAT
1 ATAATTATATTTAAAAT
*
5009641 ATTATTATATTTA
1 ATAATTATATTTA
5009654 TATATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 28 0.65
18 3 0.07
19 6 0.14
20 6 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATTATATTTAAAAT
Found at i:5009635 original size:17 final size:17
Alignment explanation
Indices: 5009613--5009653 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
5009603 AATTATAATT
5009613 ATATTTAAAATATTATA
1 ATATTTAAAATATTATA
*
5009630 ATATTTAAAATATTATT
1 ATATTTAAAATATTATA
5009647 ATATTTA
1 ATATTTA
5009654 TATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTTAAAATATTATA
Found at i:5009686 original size:20 final size:20
Alignment explanation
Indices: 5009638--5009689 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
5009628 TAATATTTAA
5009638 AATATTATTATATTTATATAT
1 AATATTA-TATATTTATATAT
* *
5009659 ATTTTTATATATTTATA-ATT
1 AATATTATATATTTATATA-T
5009679 AATATTATATA
1 AATATTATATA
5009690 AATTTTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTATATATTTATATAT
Found at i:5009697 original size:60 final size:58
Alignment explanation
Indices: 5009610--5009739 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
5009600 TCAAATTATA
* *
5009610 ATTATA-TTTAA--AATATTATAATATTTAAAATATTATTATATT-TATATATATTTTT
1 ATTATATTTTAATTAATATTATAAAATTTAAAATATT-TAATATTATATATATATTTTT
* * *
5009665 A-TATATTTATAATTAATATTATATAAATTTTAAAGTATTTAATATTATATTTTTATTTTT
1 ATTATATTT-TAATTAATATTATA-AAA-TTTAAAATATTTAATATTATATATATATTTTT
5009725 ATTATATTTTAATTA
1 ATTATATTTTAATTA
5009740 TTTTTTATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
54 4 0.06
55 3 0.05
56 3 0.05
58 9 0.15
59 8 0.13
60 28 0.45
61 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (58 bp):
ATTATATTTTAATTAATATTATAAAATTTAAAATATTTAATATTATATATATATTTTT
Found at i:5009732 original size:11 final size:11
Alignment explanation
Indices: 5009718--5009751 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5009708 ATTATATTTT
5009718 TATTTTTATTA
1 TATTTTTATTA
*
5009729 TATTTTAATTA
1 TATTTTTATTA
5009740 T-TTTTTATTA
1 TATTTTTATTA
5009750 TA
1 TA
5009752 ATGATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:5009740 original size:20 final size:20
Alignment explanation
Indices: 5009642--5009751 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 20
5009632 ATTTAAAATA
5009642 TTATTATA-TTTATATATATTT
1 TTATTATATTTTA-AT-TATTT
* *
5009663 TTA-TATATTTATAATTAATA
1 TTATTATATTT-TAATTATTT
* *
5009683 TTATATAAATTTTAAAGTATTT
1 TTAT-TATATTTT-AATTATTT
*
5009705 AATATTATA-TTT--TTATTT
1 -TTATTATATTTTAATTATTT
5009723 TTATTATATTTTAATTATTTT
1 TTATTATATTTTAATTA-TTT
5009744 TTATTATA
1 TTATTATA
5009752 ATGATAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.10
18 8 0.12
20 13 0.19
21 22 0.32
22 16 0.23
23 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATTATATTTTAATTATTT
Found at i:5009856 original size:4 final size:4
Alignment explanation
Indices: 5009849--5009883 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
5009839 TATGTAGTGG
*
5009849 GAAA GAAA GAAA GAAA AAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
5009884 AAAAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:5009871 original size:16 final size:17
Alignment explanation
Indices: 5009850--5009885 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
5009840 ATGTAGTGGG
5009850 AAAGAAAGAAAGAA-AA
1 AAAGAAAGAAAGAAGAA
5009866 AAAGAAAGAAAGAAGAA
1 AAAGAAAGAAAGAAGAA
5009883 AAA
1 AAA
5009886 AAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAGAA
Found at i:5009942 original size:24 final size:24
Alignment explanation
Indices: 5009915--5009983 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 24
5009905 ATGTTTGTAT
5009915 TTATATTTTTTTATTTTTAAAATA
1 TTATATTTTTTTATTTTTAAAATA
* *
5009939 TTATATTTTGTATATTTTTAACATA
1 TTATATTTT-TTTATTTTTAAAATA
5009964 TTAATAATTTATTTTATTTT
1 TT-AT-ATTT-TTTTATTTT
5009984 ATGTATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 9 0.24
25 15 0.39
26 2 0.05
27 11 0.29
28 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (24 bp):
TTATATTTTTTTATTTTTAAAATA
Found at i:5010092 original size:17 final size:17
Alignment explanation
Indices: 5010057--5010094 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5010047 TATTATTTAA
5010057 AATATTATAAATTTATGT
1 AATATTATAAA-TTATGT
5010075 AATATTTATAAA-TATGT
1 AATA-TTATAAATTATGT
5010092 AAT
1 AAT
5010095 TATATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATTATAAATTATGT
Found at i:5012373 original size:11 final size:10
Alignment explanation
Indices: 5012343--5012398 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
5012333 TTAATATCAT
5012343 AAATTAAATA
1 AAATTAAATA
5012353 ATAATT--ATA
1 A-AATTAAATA
5012362 AAATTAACATA
1 AAATTAA-ATA
5012373 AAATTAAAATA
1 AAATT-AAATA
5012384 AAATTATAATA
1 AAATTA-AATA
5012395 AAAT
1 AAAT
5012399 AATTTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 2 0.05
11 28 0.70
12 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAATA
Found at i:5013382 original size:13 final size:13
Alignment explanation
Indices: 5013364--5013390 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5013354 TCATTCTCTA
5013364 CATAGAAGTATAG
1 CATAGAAGTATAG
5013377 CATAGAAGTATAG
1 CATAGAAGTATAG
5013390 C
1 C
5013391 TATCTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (13 bp):
CATAGAAGTATAG
Found at i:5014497 original size:21 final size:21
Alignment explanation
Indices: 5014468--5014508 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5014458 ATTTATTATC
**
5014468 TTTTGATTTTATTTAAATAAA
1 TTTTGATTTTAAATAAATAAA
*
5014489 TTTTTATTTTAAATAAATAA
1 TTTTGATTTTAAATAAATAA
5014509 TTGATTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTGATTTTAAATAAATAAA
Found at i:5014501 original size:17 final size:16
Alignment explanation
Indices: 5014474--5014506 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5014464 TATCTTTTGA
5014474 TTTTATTTAAATAAAT
1 TTTTATTTAAATAAAT
5014490 TTTTATTTTAAATAAAT
1 TTTTA-TTTAAATAAAT
5014507 AATTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATTTAAATAAAT
Found at i:5014747 original size:29 final size:29
Alignment explanation
Indices: 5014708--5014820 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
5014698 AAAGATTTAT
5014708 TTTAATATAAATTAAAAATTAAAATATTA
1 TTTAATATAAATTAAAAATTAAAATATTA
* *
5014737 TTTAATATAAATTAAAAATTAAAAAAATA
1 TTTAATATAAATTAAAAATTAAAATATTA
* * * *
5014766 TAT-ATGTAAATTTAAAATTAATAA-CTTA
1 TTTAATATAAATTAAAAATTAA-AATATTA
5014794 TTTAA-ATATAA-TAAAAA-TATAAATATT
1 TTTAATATA-AATTAAAAATTA-AAATATT
5014821 TATCTACAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.06
28 30 0.44
29 34 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
TTTAATATAAATTAAAAATTAAAATATTA
Found at i:5018835 original size:2 final size:2
Alignment explanation
Indices: 5018830--5018863 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5018820 AGAGAGAATG
5018830 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
5018864 ATTTTGTTCT
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
Found at i:5019776 original size:6 final size:6
Alignment explanation
Indices: 5019765--5019802 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
5019755 GTTGTCAGCG
5019765 TACATA TACATA TACATA TACATA TACATA TACATA TA
1 TACATA TACATA TACATA TACATA TACATA TACATA TA
5019803 TATTATATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:5021598 original size:2 final size:2
Alignment explanation
Indices: 5021591--5021626 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5021581 GACCTCCGAC
5021591 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5021627 GCTGACTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5024167 original size:28 final size:26
Alignment explanation
Indices: 5024115--5024167 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
5024105 TTATGTGTTT
* *
5024115 TTTTTTATATATTCAATTTTTTAATA
1 TTTTTTATATATTCAATATTATAATA
*
5024141 TTTTTTATATATTTAATAAATTATAAT
1 TTTTTTATATATTCAAT--ATTATAAT
5024168 TTTATATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 16 0.73
28 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTTATATATTCAATATTATAATA
Found at i:5024768 original size:22 final size:21
Alignment explanation
Indices: 5024721--5024760 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5024711 ACGAATTATT
*
5024721 AATATATTA-ATATTTATATA
1 AATATATTATATATTTAAATA
5024741 AATATATTATAT-TTTAAATA
1 AATATATTATATATTTAAATA
5024761 CGAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATATTATATATTTAAATA
Found at i:5025131 original size:34 final size:34
Alignment explanation
Indices: 5025085--5025302 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
5025075 GTAAAAACCA
*
5025085 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
5025119 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
5025153 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
5025187 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
5025220 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
5025254 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
5025287 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
5025303 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:5025199 original size:68 final size:67
Alignment explanation
Indices: 5025083--5025302 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
5025073 TGGTAAAAAC
* * *
5025083 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
5025148 AT
66 AT
* * *
5025150 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
5025215 AAT
65 AAT
* * * * * *
5025218 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
5025283 AT
66 AT
5025285 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
5025303 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:5029395 original size:19 final size:19
Alignment explanation
Indices: 5029368--5029430 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
5029358 TCACGTGTAC
* *
5029368 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
5029387 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
5029406 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
5029425 AGTACC
1 AGTACC
5029431 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:5029781 original size:34 final size:34
Alignment explanation
Indices: 5029735--5029950 Score: 260
Period size: 34 Copynumber: 6.4 Consensus size: 34
5029725 GTAAAAACCA
*
5029735 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
5029769 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
5029803 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
5029837 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
5029870 CTATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
5029904 CCATTTAATCAACAATGATAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
5029937 CCATTTAATCAACA
1 CCATTTAATCAACA
5029951 GTTGACAGCT
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
33 42 0.27
34 113 0.72
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Done.