Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 21 of 25
Found at i:3226598 original size:23 final size:21
Alignment explanation
Indices: 3226549--3226612 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 21
3226539 TATATATTTA
*
3226549 TATTATATTTATATTTTATTT
1 TATTATATTTATATTTTATTG
*
3226570 TAATTATTTTATATATTTTATTCG
1 T-ATTATATT-TATATTTTATT-G
3226594 TATTATATAATTATATTTT
1 TATTATAT--TTATATTTT
3226613 TCATATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 1 0.03
22 7 0.20
23 17 0.49
24 9 0.26
25 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTATATTTATATTTTATTG
Found at i:3227262 original size:20 final size:19
Alignment explanation
Indices: 3227216--3227262 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3227206 TATATTTGTA
*
3227216 TTAT-TTAAATTTTAATAT
1 TTATATTAAATATTAATAT
*
3227234 ATATAATTAAATATTAATAAT
1 TTAT-ATTAAATATTAAT-AT
3227255 TTATATTA
1 TTATATTA
3227263 TATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
20 15 0.65
21 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATTAAATATTAATAT
Found at i:3227267 original size:11 final size:11
Alignment explanation
Indices: 3227253--3227304 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
3227243 AATATTAATA
3227253 ATTTATATTAT
1 ATTTATATTAT
*
3227264 ATTTATTTTAT
1 ATTTATATTAT
* *
3227275 TTTTATGTTAT
1 ATTTATATTAT
3227286 A-TTATATT-T
1 ATTTATATTAT
3227295 -TTTATATTAT
1 ATTTATATTAT
3227305 TTAATTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 8 0.24
10 7 0.21
11 19 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:3227275 original size:27 final size:28
Alignment explanation
Indices: 3227244--3227322 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
3227234 ATATAATTAA
*
3227244 ATATTAATAATTTATATTATATTTATTT
1 ATATTATTAATTTATATTATATTTATTT
*
3227272 -TATT-TTTATGTTATATTATATTT-TTT
1 ATATTATTAAT-TTATATTATATTTATTT
*
3227298 ATATTATTTAATTT-TATCATATTTA
1 ATATTA-TTAATTTATATTATATTTA
3227323 AAATTACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 6 0.14
27 30 0.71
28 2 0.05
29 4 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
ATATTATTAATTTATATTATATTTATTT
Found at i:3227279 original size:22 final size:22
Alignment explanation
Indices: 3227254--3227314 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 22
3227244 ATATTAATAA
3227254 TTTATATTATATTTATTTTATT
1 TTTATATTATATTTATTTTATT
* *
3227276 TTTATGTTATA-TTA-TAT-TT
1 TTTATATTATATTTATTTTATT
*
3227295 TTTATATTAT-TTAATTTTAT
1 TTTATATTATATTTATTTTAT
3227315 CATATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 4 0.13
22 10 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATATTATATTTATTTTATT
Found at i:3227311 original size:17 final size:17
Alignment explanation
Indices: 3227260--3227312 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
3227250 ATAATTTATA
*
3227260 TTATATTTATTTTA-TTT
1 TTATA-TTATTTAATTTT
*
3227277 TTATGTTATATTATATTTT
1 TTATATTAT-TTA-ATTTT
3227296 TTATATTATTTAATTTT
1 TTATATTATTTAATTTT
3227313 ATCATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.13
17 11 0.37
18 4 0.13
19 11 0.37
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATATTATTTAATTTT
Found at i:3227538 original size:5 final size:5
Alignment explanation
Indices: 3227523--3227553 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
3227513 AAATATTTTT
3227523 ATTTAA ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA
3227554 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:3227613 original size:19 final size:19
Alignment explanation
Indices: 3227591--3227627 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3227581 TAAAAAATTA
3227591 TTTTTAT-ATTAATATTTAT
1 TTTTTATAATTAA-ATTTAT
3227610 TTTTTATAATTAAATTTA
1 TTTTTATAATTAAATTTA
3227628 AATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATAATTAAATTTAT
Found at i:3232596 original size:21 final size:21
Alignment explanation
Indices: 3232572--3232617 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3232562 TTCCTTTTTC
3232572 TTTGGG-TCTCTTTT-TATGGTG
1 TTTGGGCTC-CTTTTGTATGG-G
3232593 TTTGGGCTCCTTTTGTATGGG
1 TTTGGGCTCCTTTTGTATGGG
3232614 TTTG
1 TTTG
3232618 TTAGGCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.04, C:0.11, G:0.30, T:0.54
Consensus pattern (21 bp):
TTTGGGCTCCTTTTGTATGGG
Found at i:3237651 original size:35 final size:37
Alignment explanation
Indices: 3237543--3237653 Score: 181
Period size: 37 Copynumber: 3.1 Consensus size: 37
3237533 CAAGTGTCGT
3237543 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
*
3237580 ACATTACCTTGTGGAATGGGGTGGGATTGAGAGGTAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
* *
3237617 ACATCAACTTGTGGAAT-GGG-GGGATTGAGTGGTAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
3237652 AC
1 AC
3237654 TTGGCTTTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 16 0.23
36 3 0.04
37 51 0.73
ACGTcount: A:0.26, C:0.08, G:0.40, T:0.26
Consensus pattern (37 bp):
ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
Found at i:3241417 original size:2 final size:2
Alignment explanation
Indices: 3241412--3241447 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3241402 ATATATATAT
3241412 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
3241448 CAAATTAGCT
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:3241660 original size:17 final size:17
Alignment explanation
Indices: 3241634--3241767 Score: 55
Period size: 18 Copynumber: 7.6 Consensus size: 17
3241624 AAATTTAACA
3241634 TAAAAA-TAATAAATAT
1 TAAAAATTAATAAATAT
3241650 TAAAAATTAATATAA-AT
1 TAAAAATTAATA-AATAT
*
3241667 ATAATATAAAT-ATAAATATT
1 -TAA-A-AATTAATAAATA-T
* * *
3241687 TTAAAATTTATAAA-AA
1 TAAAAATTAATAAATAT
* *
3241703 TATAAATT-ATTAATAT
1 TAAAAATTAATAAATAT
3241719 ATAAAAATTTATATAAA-AT
1 -TAAAAA-TTA-ATAAATAT
* *
3241738 TAAAAAATATTATAATAT
1 TAAAAATTAATA-AATAT
*
3241756 AATAAAATTAAT
1 TA-AAAATTAAT
3241768 TAATTAATAC
Statistics
Matches: 87, Mismatches: 15, Indels: 29
0.66 0.11 0.22
Matches are distributed among these distances:
15 4 0.05
16 15 0.17
17 20 0.23
18 24 0.28
19 16 0.18
20 8 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTAATAAATAT
Found at i:3241669 original size:6 final size:6
Alignment explanation
Indices: 3241637--3241685 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
3241627 TTTAACATAA
* *
3241637 AAATAAT AAATATT AAAAAT TAATAT AAATAT -AATAT AAATAT AAATAT
1 AAAT-AT AAATA-T AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
3241686 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 22 0.61
7 9 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATAT
Found at i:3241673 original size:11 final size:11
Alignment explanation
Indices: 3241653--3241681 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3241643 TAAATATTAA
3241653 AAAT-TAATAT
1 AAATATAATAT
3241663 AAATATAATAT
1 AAATATAATAT
3241674 AAATATAA
1 AAATATAA
3241682 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3241691 original size:26 final size:25
Alignment explanation
Indices: 3241634--3241726 Score: 66
Period size: 26 Copynumber: 3.6 Consensus size: 25
3241624 AAATTTAACA
* * *
3241634 TAAAAATAATAAATATTAAAAATTAAT
1 TAAATATAATAAA-AATATAAATT-AT
* *
3241661 ATAAATATAATATAAATATAAATATTT
1 -TAAATATAATAAAAATATAAAT-TAT
*
3241688 TAAA-ATTTATAAAAATATAAATTAT
1 TAAATA-TAATAAAAATATAAATTAT
3241713 T-AATAT-ATAAAAAT
1 TAAATATAATAAAAAT
3241727 TTATATAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
23 8 0.15
24 3 0.06
25 5 0.09
26 18 0.33
27 8 0.15
28 12 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAATATAATAAAAATATAAATTAT
Found at i:3241726 original size:33 final size:33
Alignment explanation
Indices: 3241637--3241741 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 33
3241627 TTTAACATAA
*
3241637 AAATAATAAATAT-TAAAAATTAATATAAATATAATAT
1 AAAT-ATAAATATATAAAAATT--TAT--ATAAAATAT
* *
3241674 AAATATAAATATTTTAAAATTTATA-AAAATAT
1 AAATATAAATATATAAAAATTTATATAAAATAT
*
3241706 AAATTATTAATATATAAAAATTTATATAAAAT-T
1 AAA-TATAAATATATAAAAATTTATATAAAATAT
3241739 AAA
1 AAA
3241742 AAATATTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
32 9 0.15
33 24 0.40
34 5 0.08
35 3 0.05
36 8 0.13
37 11 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
AAATATAAATATATAAAAATTTATATAAAATAT
Found at i:3241761 original size:20 final size:20
Alignment explanation
Indices: 3241708--3241762 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3241698 AAAAATATAA
3241708 ATTATTAATAT-AT-AAAAAT
1 ATTA-TAATATAATAAAAAAT
*
3241727 -TTAT-ATAAAATTAAAAAAT
1 ATTATAATATAA-TAAAAAAT
3241746 ATTATAATATAATAAAA
1 ATTATAATATAATAAAA
3241763 TTAATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.10
17 2 0.07
18 4 0.14
19 6 0.21
20 9 0.31
21 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATAATATAATAAAAAAT
Found at i:3243543 original size:12 final size:12
Alignment explanation
Indices: 3243514--3243605 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
3243504 TTTTAATAAA
3243514 TATATATTTATAAT
1 TATAT-TTTAT-AT
* *
3243528 TTTATATTATAT
1 TATATTTTATAT
* *
3243540 TTTATTTTAAAT
1 TATATTTTATAT
3243552 TATATTTTA-AT
1 TATATTTTATAT
3243563 TAT-TTTTATCA-
1 TATATTTTAT-AT
*
3243574 TATA-TATATA-
1 TATATTTTATAT
*
3243584 TATATTTTTTAT
1 TATATTTTATAT
3243596 TATATGTTTA
1 TATAT-TTTA
3243606 AAATTATGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
10 10 0.16
11 16 0.25
12 26 0.41
13 7 0.11
14 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:3243546 original size:17 final size:17
Alignment explanation
Indices: 3243510--3243560 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
3243500 TTAATTTTAA
3243510 TAAATATATATTTATAATTT
1 TAAAT-TATATTT-T-ATTT
*
3243530 TATATTATATTTTATTT
1 TAAATTATATTTTATTT
3243547 TAAATTATATTTTA
1 TAAATTATATTTTA
3243561 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 17 0.59
18 1 0.03
19 7 0.24
20 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAAATTATATTTTATTT
Found at i:3243553 original size:62 final size:62
Alignment explanation
Indices: 3243487--3243605 Score: 136
Period size: 62 Copynumber: 1.9 Consensus size: 62
3243477 ATAAATTAAT
*
3243487 AATTA-ATGTCATATTAATTTTAATAA-ATATATATTTATAATTTTATATTATAT-TTTATTTTA
1 AATTATATGTCA-ATT-ATTTTAATAATATATATATATAT-ATTTTATATTATATGTTTATTTTA
* * * * *
3243549 AATTATATTTTAATTATTTTTATCATATATATATATATATTTTTTATTATATGTTTA
1 AATTATATGTCAATTATTTTAATAATATATATATATATATTTTATATTATATGTTTA
3243606 AAATTATGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
61 21 0.44
62 23 0.48
63 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (62 bp):
AATTATATGTCAATTATTTTAATAATATATATATATATATTTTATATTATATGTTTATTTTA
Found at i:3243976 original size:22 final size:21
Alignment explanation
Indices: 3243948--3244037 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 21
3243938 AAGCAGATAG
*
3243948 TATTTATATAATTTTTTTATTA
1 TATTTATATAA-ATTTTTATTA
* *
3243970 TAATTATATTTAAATTATTA-TA
1 T-ATT-TATATAAATTTTTATTA
3243992 TATTTATATAAATTTTTATT-
1 TATTTATATAAATTTTTATTA
* *
3244012 TATTTATATTATTTTTTA-TA
1 TATTTATATAAATTTTTATTA
3244032 T-TTTAT
1 TATTTAT
3244038 TTTGATTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.11
20 29 0.51
21 4 0.07
22 4 0.07
23 8 0.14
24 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTATATAAATTTTTATTA
Found at i:3243987 original size:20 final size:20
Alignment explanation
Indices: 3243964--3244079 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
3243954 TATAATTTTT
3243964 TTATTATA-ATTATATTTAAA
1 TTATTATATATT-TATTTAAA
*
3243984 TTATTATATATTTATATAAA
1 TTATTATATATTTATTTAAA
* * *
3244004 TTTTTATTTATTTATATT-AT
1 TTATTATATATTTAT-TTAAA
* **
3244024 TTTTTATAT-TTTATTTTGA
1 TTATTATATATTTATTTAAA
* *
3244043 TTATTTTATATTTTATTTATA
1 TTATTATATA-TTTATTTAAA
3244064 TTA-TATA-ATTATATTT
1 TTATTATATATT-TATTT
3244080 TTTCATGTGA
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
18 4 0.05
19 18 0.23
20 40 0.52
21 15 0.19
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.66
Consensus pattern (20 bp):
TTATTATATATTTATTTAAA
Found at i:3244011 original size:16 final size:17
Alignment explanation
Indices: 3243986--3244032 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
3243976 TATTTAAATT
*
3243986 ATTATATATTTATATAA
1 ATTATTTATTTATATAA
* *
3244003 ATT-TTTATTTATTTAT
1 ATTATTTATTTATATAA
3244019 ATTATTT-TTTATAT
1 ATTATTTATTTATAT
3244033 TTTATTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTATTTATATAA
Found at i:3244039 original size:14 final size:14
Alignment explanation
Indices: 3244005--3244058 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
3243995 TTATATAAAT
3244005 TTTTATTTATTTATA
1 TTTTATTT-TTTATA
3244020 --TTATTTTTTATA
1 TTTTATTTTTTATA
*
3244032 TTTTA-TTTTGATTA
1 TTTTATTTTTTA-TA
*
3244046 TTTTATATTTTAT
1 TTTTATTTTTTAT
3244059 TTATATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.19
13 11 0.34
14 11 0.34
15 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTATTTTTTATA
Found at i:3244045 original size:23 final size:21
Alignment explanation
Indices: 3243992--3244067 Score: 86
Period size: 21 Copynumber: 3.6 Consensus size: 21
3243982 AATTATTATA
*
3243992 TATTTATATAAATTTT-TA-TT
1 TATTTATAT-TATTTTATATTT
3244012 TATTTATATTATTTTTTATATTT
1 TATTTATATTA--TTTTATATTT
3244035 TATTT-TGATTATTTTATATTT
1 TATTTAT-ATTATTTTATATTT
3244056 TATTTATATTAT
1 TATTTATATTAT
3244068 ATAATTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.02
20 9 0.18
21 24 0.49
22 4 0.08
23 11 0.22
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (21 bp):
TATTTATATTATTTTATATTT
Found at i:3244046 original size:16 final size:17
Alignment explanation
Indices: 3243992--3244069 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 17
3243982 AATTATTATA
**
3243992 TATTTATATAAAT-TTT
1 TATTTATATTTATATTT
3244008 TA-TT-TATTTATATTAT
1 TATTTATATTTATATT-T
*
3244024 TTTTTATATTT-TATTT
1 TATTTATATTTATATTT
3244040 TGA-TTAT-TTTATATTT
1 T-ATTTATATTTATATTT
3244056 TATTTATA-TTATAT
1 TATTTATATTTATAT
3244070 AATTATATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 5 0.10
15 8 0.16
16 26 0.52
17 6 0.12
18 5 0.10
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (17 bp):
TATTTATATTTATATTT
Found at i:3244093 original size:44 final size:42
Alignment explanation
Indices: 3244003--3244096 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 42
3243993 ATTTATATAA
** * *
3244003 ATTTTTATTTATTTATATTATTTTTTATATTTTATTTTGATT
1 ATTTTTATTTATTTATATTATTAATTATATTTTATTATGATG
3244045 ATTTTATATTTTATTTATATTATATAATTATATTTT-TTCATG-TG
1 ATTTT-TA-TTTATTTATATTAT-TAATTATATTTTATT-ATGATG
3244089 ATTTTTAT
1 ATTTTTAT
3244097 GTTAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
42 6 0.14
43 4 0.09
44 22 0.50
45 12 0.27
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (42 bp):
ATTTTTATTTATTTATATTATTAATTATATTTTATTATGATG
Found at i:3244751 original size:5 final size:5
Alignment explanation
Indices: 3244741--3244805 Score: 63
Period size: 5 Copynumber: 14.4 Consensus size: 5
3244731 ATTTAAATAT
*
3244741 TTATA TTATA TT-TA TTTTA TT-T- TTATA TTATA TTATA TT-T- TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
3244786 TTAT- TTA-A TTATA TCATA TT
1 TTATA TTATA TTATA TTATA TT
3244806 TAAAATTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
3 4 0.08
4 14 0.27
5 33 0.65
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (5 bp):
TTATA
Found at i:3244753 original size:11 final size:11
Alignment explanation
Indices: 3244737--3244779 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
3244727 AAATATTTAA
3244737 ATATTTATATT
1 ATATTTATATT
*
3244748 ATATTTATTTT
1 ATATTTATATT
*
3244759 ATTTTTATATT
1 ATATTTATATT
3244770 ATA-TTATATT
1 ATATTTATATT
3244780 TTTATATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATATTTATATT
Found at i:3244779 original size:18 final size:18
Alignment explanation
Indices: 3244746--3244789 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3244736 AATATTTATA
*
3244746 TTATATT-TATTTTATTT
1 TTATATTATATTATATTT
3244763 TTATATTATATTATATTT
1 TTATATTATATTATATTT
3244781 TTATATTAT
1 TTATATTAT
3244790 TTAATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATTATATTATATTT
Found at i:3244814 original size:65 final size:64
Alignment explanation
Indices: 3244690--3244821 Score: 160
Period size: 65 Copynumber: 2.0 Consensus size: 64
3244680 CAAGAAAATT
* *
3244690 TTTTATTTTTATACTATATAAATTTTAATATATATTTAAATATTTAAATATTTATATTATATTTA
1 TTTTATTTTTATACTATATAAATTTTAATATATATTTAAATATATAAATATTTAAATTAT-TTTA
* * * * *
3244755 TTTTATTTTTATATTATATTATATTTTTATAT-TATTTAATTATAT-CATATTTAAAATTATTTT
1 TTTTATTTTTATACTATA-TAAATTTTAATATATATTTAAATATATAAATATTT-AAATTATTTT
3244818 A
64 A
3244819 TTT
1 TTT
3244822 ACGTGTAAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
64 13 0.22
65 34 0.59
66 11 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (64 bp):
TTTTATTTTTATACTATATAAATTTTAATATATATTTAAATATATAAATATTTAAATTATTTTA
Found at i:3244818 original size:26 final size:28
Alignment explanation
Indices: 3244761--3244819 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
3244751 TTTATTTTAT
* * *
3244761 TTTTATATTATATTATATTTTTATATTA
1 TTTTATATTATATCATATTTTAAAATTA
3244789 -TTTA-ATTATATCATA-TTTAAAATTA
1 TTTTATATTATATCATATTTTAAAATTA
3244814 TTTTAT
1 TTTTAT
3244820 TTACGTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTATATTATATCATATTTTAAAATTA
Found at i:3245037 original size:20 final size:20
Alignment explanation
Indices: 3245014--3245066 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
3245004 TTTTATTTAA
3245014 ATTTAAATTTAAATTGATTT
1 ATTTAAATTTAAATTGATTT
** **
3245034 ATTTTGATTTATTTTGATTT
1 ATTTAAATTTAAATTGATTT
3245054 A--TAAATTTAAATT
1 ATTTAAATTTAAATT
3245067 ATTATTTTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTAAATTTAAATTGATTT
Found at i:3245040 original size:10 final size:10
Alignment explanation
Indices: 3245027--3245055 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3245017 TAAATTTAAA
3245027 TTGATTTATT
1 TTGATTTATT
3245037 TTGATTTATT
1 TTGATTTATT
3245047 TTGATTTAT
1 TTGATTTAT
3245056 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (10 bp):
TTGATTTATT
Found at i:3245081 original size:16 final size:16
Alignment explanation
Indices: 3245062--3245101 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3245052 TTATAAATTT
*
3245062 AAATTATTATTTTAAA
1 AAATTATTATATTAAA
**
3245078 AAATTAAAATATTAAA
1 AAATTATTATATTAAA
3245094 AAATTATT
1 AAATTATT
3245102 TTTATATTAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTATTATATTAAA
Found at i:3245084 original size:21 final size:21
Alignment explanation
Indices: 3245051--3245091 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3245041 TTTATTTTGA
* * *
3245051 TTTATAAATTTAAATTATTAT
1 TTTAAAAAATTAAAATATTAT
3245072 TTTAAAAAATTAAAATATTA
1 TTTAAAAAATTAAAATATTA
3245092 AAAAATTATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAAAAATTAAAATATTAT
Found at i:3245136 original size:20 final size:20
Alignment explanation
Indices: 3245098--3245137 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3245088 ATTAAAAAAT
*
3245098 TATTTTTATATTATTATTTA
1 TATTTTTATATTATAATTTA
3245118 TATTTTTATAATTA-AATTTA
1 TATTTTTAT-ATTATAATTTA
3245138 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTATATTATAATTTA
Found at i:3248099 original size:19 final size:19
Alignment explanation
Indices: 3248054--3248099 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
3248044 TTACAATTTT
3248054 ATTGATAAAAATAATATCAA
1 ATTGAT-AAAATAATATCAA
* *
3248074 AAT-ATAAAATATTATCAA
1 ATTGATAAAATAATATCAA
3248092 ATTGATAA
1 ATTGATAA
3248100 CGTAGTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 14 0.64
19 6 0.27
20 2 0.09
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
ATTGATAAAATAATATCAA
Found at i:3249920 original size:21 final size:21
Alignment explanation
Indices: 3249896--3249941 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3249886 TTCCTTTTTC
* *
3249896 TTTGGG-TCTTTTTTTATGGTG
1 TTTGGGCTCATTTTGTATGG-G
3249917 TTTGGGCTCATTTTGTATGGG
1 TTTGGGCTCATTTTGTATGGG
3249938 TTTG
1 TTTG
3249942 TTAGGCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.57
Consensus pattern (21 bp):
TTTGGGCTCATTTTGTATGGG
Found at i:3253826 original size:37 final size:37
Alignment explanation
Indices: 3253776--3253952 Score: 216
Period size: 37 Copynumber: 4.8 Consensus size: 37
3253766 TAAGTGTCGT
* *
3253776 ACATTAACTTGTGGAATGGGGTGAGATTGAGAGATAG
1 ACATTACCTTGTGGAATGGGGTGGGATTGAGAGATAG
* *
3253813 ACATTACCTTGTGGAATGGGGTGGGATTGAGTGGTAG
1 ACATTACCTTGTGGAATGGGGTGGGATTGAGAGATAG
* * *
3253850 AC-TTGGCTTTTTGGAATGGGGTGGGATTGAGAGATAG
1 ACATT-ACCTTGTGGAATGGGGTGGGATTGAGAGATAG
* *
3253887 ACATTACCTTATGGAATGGGGTGGGATTGAGAGGTAG
1 ACATTACCTTGTGGAATGGGGTGGGATTGAGAGATAG
* * *
3253924 ACATCAACTTGTAGAAT-GGG-GGGATTGAG
1 ACATTACCTTGTGGAATGGGGTGGGATTGAG
3253953 TGGTAGACTT
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
35 9 0.07
36 5 0.04
37 105 0.87
38 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.38, T:0.28
Consensus pattern (37 bp):
ACATTACCTTGTGGAATGGGGTGGGATTGAGAGATAG
Found at i:3253941 original size:74 final size:74
Alignment explanation
Indices: 3253776--3253952 Score: 252
Period size: 74 Copynumber: 2.4 Consensus size: 74
3253766 TAAGTGTCGT
* *
3253776 ACATTAACTTGTGGAATGGGGTGAGATTGAGAGATAGACATTACCTTGTGGAATGGGGTGGGATT
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGATAGACATTACCTTATGGAATGGGGTGGGATT
*
3253841 GAGTGGTAG
66 GAGAGGTAG
** *
3253850 AC-TTGGCTTTTTGGAATGGGGTGGGATTGAGAGATAGACATTACCTTATGGAATGGGGTGGGAT
1 ACATTAAC-TTGTGGAATGGGGTGGGATTGAGAGATAGACATTACCTTATGGAATGGGGTGGGAT
3253914 TGAGAGGTAG
65 TGAGAGGTAG
* *
3253924 ACATCAACTTGTAGAAT-GGG-GGGATTGAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAG
3253953 TGGTAGACTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
72 9 0.10
73 6 0.07
74 73 0.81
75 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.38, T:0.28
Consensus pattern (74 bp):
ACATTAACTTGTGGAATGGGGTGGGATTGAGAGATAGACATTACCTTATGGAATGGGGTGGGATT
GAGAGGTAG
Found at i:3257696 original size:2 final size:2
Alignment explanation
Indices: 3257689--3257714 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3257679 TTCTGTATTT
3257689 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
3257715 GAGAGAGAGA
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:3257719 original size:2 final size:2
Alignment explanation
Indices: 3257714--3257739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3257704 ATATATATAT
3257714 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
3257740 CAAATTAGCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3257952 original size:17 final size:17
Alignment explanation
Indices: 3257926--3258059 Score: 55
Period size: 18 Copynumber: 7.6 Consensus size: 17
3257916 AAATTTAACA
3257926 TAAAAA-TAATAAATAT
1 TAAAAATTAATAAATAT
3257942 TAAAAATTAATATAA-AT
1 TAAAAATTAATA-AATAT
*
3257959 ATAATATAAAT-ATAAATATT
1 -TAA-A-AATTAATAAATA-T
* * *
3257979 TTAAAATTTATAAA-AA
1 TAAAAATTAATAAATAT
* *
3257995 TATAAATT-ATTAATAT
1 TAAAAATTAATAAATAT
3258011 ATAAAAATTTATATAAA-AT
1 -TAAAAA-TTA-ATAAATAT
* *
3258030 TAAAAAATATTATAATAT
1 TAAAAATTAATA-AATAT
*
3258048 AATAAAATTAAT
1 TA-AAAATTAAT
3258060 TAATTAATAC
Statistics
Matches: 87, Mismatches: 15, Indels: 29
0.66 0.11 0.22
Matches are distributed among these distances:
15 4 0.05
16 15 0.17
17 20 0.23
18 24 0.28
19 16 0.18
20 8 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTAATAAATAT
Found at i:3257961 original size:6 final size:6
Alignment explanation
Indices: 3257929--3257977 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
3257919 TTTAACATAA
* *
3257929 AAATAAT AAATATT AAAAAT TAATAT AAATAT -AATAT AAATAT AAATAT
1 AAAT-AT AAATA-T AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
3257978 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 22 0.61
7 9 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATAT
Found at i:3257965 original size:11 final size:11
Alignment explanation
Indices: 3257945--3257973 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3257935 TAAATATTAA
3257945 AAAT-TAATAT
1 AAATATAATAT
3257955 AAATATAATAT
1 AAATATAATAT
3257966 AAATATAA
1 AAATATAA
3257974 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3257983 original size:26 final size:25
Alignment explanation
Indices: 3257926--3258018 Score: 66
Period size: 26 Copynumber: 3.6 Consensus size: 25
3257916 AAATTTAACA
* * *
3257926 TAAAAATAATAAATATTAAAAATTAAT
1 TAAATATAATAAA-AATATAAATT-AT
* *
3257953 ATAAATATAATATAAATATAAATATTT
1 -TAAATATAATAAAAATATAAAT-TAT
*
3257980 TAAA-ATTTATAAAAATATAAATTAT
1 TAAATA-TAATAAAAATATAAATTAT
3258005 T-AATAT-ATAAAAAT
1 TAAATATAATAAAAAT
3258019 TTATATAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
23 8 0.15
24 3 0.06
25 5 0.09
26 18 0.33
27 8 0.15
28 12 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAATATAATAAAAATATAAATTAT
Found at i:3258018 original size:33 final size:33
Alignment explanation
Indices: 3257929--3258033 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 33
3257919 TTTAACATAA
*
3257929 AAATAATAAATAT-TAAAAATTAATATAAATATAATAT
1 AAAT-ATAAATATATAAAAATT--TAT--ATAAAATAT
* *
3257966 AAATATAAATATTTTAAAATTTATA-AAAATAT
1 AAATATAAATATATAAAAATTTATATAAAATAT
*
3257998 AAATTATTAATATATAAAAATTTATATAAAAT-T
1 AAA-TATAAATATATAAAAATTTATATAAAATAT
3258031 AAA
1 AAA
3258034 AAATATTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
32 9 0.15
33 24 0.40
34 5 0.08
35 3 0.05
36 8 0.13
37 11 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
AAATATAAATATATAAAAATTTATATAAAATAT
Found at i:3258053 original size:20 final size:20
Alignment explanation
Indices: 3258000--3258054 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3257990 AAAAATATAA
3258000 ATTATTAATAT-AT-AAAAAT
1 ATTA-TAATATAATAAAAAAT
*
3258019 -TTAT-ATAAAATTAAAAAAT
1 ATTATAATATAA-TAAAAAAT
3258038 ATTATAATATAATAAAA
1 ATTATAATATAATAAAA
3258055 TTAATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.10
17 2 0.07
18 4 0.14
19 6 0.21
20 9 0.31
21 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATAATATAATAAAAAAT
Found at i:3259750 original size:20 final size:20
Alignment explanation
Indices: 3259713--3259751 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3259703 TTTTATTTTT
*
3259713 TATTATAATTATATATAAAA
1 TATTATAATTATAAATAAAA
3259733 TATTATATATT-TAAATAAA
1 TATTATA-ATTATAAATAAA
3259752 TTATCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTATAATTATAAATAAAA
Found at i:3259789 original size:17 final size:17
Alignment explanation
Indices: 3259769--3259848 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
3259759 AAATTAATAA
3259769 TTAATATTATATTAATT
1 TTAATATTATATTAATT
*
3259786 TTAATCAATATA-T-ATT
1 TTAAT-ATTATATTAATT
* *
3259802 TTTATTTTAT-TTATATT
1 TTAATATTATATTA-ATT
* *
3259819 TTTATATTATATTTTATT
1 TTAATATTATA-TTAATT
3259837 TTAA-ATTATATT
1 TTAATATTATATT
3259849 TTAATTGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 4 0.08
16 9 0.18
17 24 0.48
18 11 0.22
19 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATATTATATTAATT
Found at i:3259826 original size:19 final size:18
Alignment explanation
Indices: 3259794--3259876 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 18
3259784 TTTTAATCAA
*
3259794 TATATATTTTTATTTTATT
1 TATAT-TTTTTATTATATT
3259813 TATATTTTTATATTATATT
1 TATATTTTT-TATTATATT
**
3259832 T-TATTTTAAATTATATT
1 TATATTTTTTATTATATT
* *
3259849 T-TAATTGTT-TT-TA-T
1 TATATTTTTTATTATATT
3259863 TATATTTTTTATTA
1 TATATTTTTTATTA
3259877 GCGTGTTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
14 2 0.04
15 8 0.16
16 4 0.08
17 13 0.25
18 10 0.20
19 14 0.27
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (18 bp):
TATATTTTTTATTATATT
Found at i:3262938 original size:3 final size:3
Alignment explanation
Indices: 3262930--3262954 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3262920 TATCATAAGA
3262930 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3262955 CAATACGAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3263999 original size:21 final size:20
Alignment explanation
Indices: 3263973--3264013 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3263963 AGATCAAAAA
*
3263973 AATTAATTTAAATTATTATTT
1 AATTAATAT-AATTATTATTT
*
3263994 AATTAATATAATTTTTATTT
1 AATTAATATAATTATTATTT
3264014 TTATTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTAATATAATTATTATTT
Found at i:3264745 original size:26 final size:25
Alignment explanation
Indices: 3264715--3264782 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
3264705 TAAATGATTT
* *
3264715 AATTTGATACTTAAATTTTTTTTATC
1 AATTTAATA-TTAAATATTTTTTATC
*
3264741 AATTTAATATTTAATATTTTTTATC
1 AATTTAATATTAAATATTTTTTATC
*
3264766 AA-AT-ATATT-AATATTTT
1 AATTTAATATTAAATATTTT
3264783 AAATGAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.21
23 5 0.13
24 1 0.03
25 16 0.42
26 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (25 bp):
AATTTAATATTAAATATTTTTTATC
Found at i:3265049 original size:17 final size:17
Alignment explanation
Indices: 3265029--3265061 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3265019 ATTAATATTT
3265029 TAAAATATCAAATAAAA
1 TAAAATATCAAATAAAA
*
3265046 TAAAATATTAAATAAA
1 TAAAATATCAAATAAA
3265062 TATTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATATCAAATAAAA
Found at i:3265999 original size:20 final size:21
Alignment explanation
Indices: 3265954--3266003 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3265944 TCGTTTAGAT
*
3265954 TTATTTATTAAATTAAATAAA
1 TTATTTATTTAATTAAATAAA
*
3265975 -AATTTATTTAA-TAAATAAA
1 TTATTTATTTAATTAAATAAA
3265994 TTATTT-TTTA
1 TTATTTATTTA
3266004 TTTATATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTATTTAATTAAATAAA
Found at i:3266153 original size:23 final size:23
Alignment explanation
Indices: 3266126--3266174 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3266116 TTTAAATTTA
3266126 ATTAATTATAAA-AATATATAAAT
1 ATTAA-TATAAATAATATATAAAT
* *
3266149 ATTAATATAAATAATATTTTAAT
1 ATTAATATAAATAATATATAAAT
3266172 ATT
1 ATT
3266175 TTTTTAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAATATAAATAATATATAAAT
Found at i:3266497 original size:26 final size:26
Alignment explanation
Indices: 3266461--3266514 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3266451 TTTTAATTAC
3266461 TAATTGTTGGTGTGTGTGTATATATA
1 TAATTGTTGGTGTGTGTGTATATATA
3266487 TAATTGTTGGTGTGTGTGTATATATA
1 TAATTGTTGGTGTGTGTGTATATATA
3266513 TA
1 TA
3266515 TATATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (26 bp):
TAATTGTTGGTGTGTGTGTATATATA
Found at i:3266545 original size:15 final size:15
Alignment explanation
Indices: 3266525--3266562 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
3266515 TATATATATG
3266525 TAATTATTCAAAAAA
1 TAATTATTCAAAAAA
3266540 TAATTATTCAAAAAA
1 TAATTATTCAAAAAA
3266555 TAATTATT
1 TAATTATT
3266563 TTATATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATTATTCAAAAAA
Found at i:3271275 original size:2 final size:2
Alignment explanation
Indices: 3271268--3271386 Score: 130
Period size: 2 Copynumber: 59.5 Consensus size: 2
3271258 TATGAACATA
* * * *
3271268 AT AT AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
3271310 AT AT AT AT AT AT GT AT AT GT AT AT AT TT AT AT GT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3271352 AT AT AT AT AT AT GT AT AT AT TT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3271387 CACAAACACT
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3272273 original size:5 final size:6
Alignment explanation
Indices: 3272250--3272280 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3272240 TTTTCACATC
3272250 ATTTTAT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTT-T ATTTTT ATTTTT ATTTTT ATTTTT
3272281 CATATCAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:3273643 original size:20 final size:20
Alignment explanation
Indices: 3273614--3273651 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3273604 TGTGGCAAAA
3273614 ATTAGAAAATGATTTTAAGT
1 ATTAGAAAATGATTTTAAGT
* *
3273634 ATTAGCAAATGTTTTTAA
1 ATTAGAAAATGATTTTAA
3273652 ACATCGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTAGAAAATGATTTTAAGT
Found at i:3275276 original size:2 final size:2
Alignment explanation
Indices: 3275238--3275267 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3275228 ATTTTTTTAT
*
3275238 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3275268 CCTATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3276091 original size:8 final size:8
Alignment explanation
Indices: 3276078--3276106 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3276068 AGCTCTGTTC
3276078 TATCAACA
1 TATCAACA
3276086 TATCAACA
1 TATCAACA
3276094 TATCAACA
1 TATCAACA
3276102 TATCA
1 TATCA
3276107 GTTATTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TATCAACA
Found at i:3276522 original size:20 final size:22
Alignment explanation
Indices: 3276499--3276542 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3276489 AAATGAATTT
*
3276499 ATTAA-AA-TATTTTTATTTAA
1 ATTAATAATTATTATTATTTAA
3276519 ATTAATTAATTATTATTATTTAA
1 ATTAA-TAATTATTATTATTTAA
3276542 A
1 A
3276543 AATTGAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATAATTATTATTATTTAA
Found at i:3277483 original size:29 final size:32
Alignment explanation
Indices: 3277447--3277526 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 32
3277437 AATTTAGTTA
3277447 TATATTAATATAATTA-ATTT-T-TTTATATT
1 TATATTAATATAATTATATTTATATTTATATT
* * *
3277476 TATTTTAAAATATTTATATTTAATATTTATATT
1 TATATTAATATAATTATATTT-ATATTTATATT
* *
3277509 TATATGAATATAAATATA
1 TATATTAATATAATTATA
3277527 AATCTTTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 13 0.33
30 4 0.10
32 1 0.03
33 21 0.54
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATATTAATATAATTATATTTATATTTATATT
Found at i:3277488 original size:14 final size:14
Alignment explanation
Indices: 3277471--3277510 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3277461 TAATTTTTTT
3277471 ATATTTAT-TTTAAA
1 ATATTTATATTT-AA
3277485 ATATTTATATTT-A
1 ATATTTATATTTAA
3277498 ATATTTATATTTA
1 ATATTTATATTTA
3277511 TATGAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.54
14 8 0.33
15 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATTTATATTTAA
Found at i:3277891 original size:17 final size:18
Alignment explanation
Indices: 3277848--3277906 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
3277838 TTAAATATTA
*
3277848 AATTTAA-TATTAAATAT
1 AATTTAATTAATAAATAT
3277865 AATTAATAATTAATAAATAT
1 AATT--TAATTAATAAATAT
*
3277885 -ATTTAATTTAAT-TATAT
1 AATTTAA-TTAATAAATAT
3277902 AATTT
1 AATTT
3277907 TTATATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 11 0.31
18 9 0.26
19 6 0.17
20 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTAATTAATAAATAT
Found at i:3280105 original size:27 final size:26
Alignment explanation
Indices: 3280075--3280126 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3280065 TTTTACTTTT
*
3280075 AAAATAACTATCCATTTTTTTAAAAAA
1 AAAATAACTAT-AATTTTTTTAAAAAA
*
3280102 AAAATACCTATAATTTTTTTAAAAA
1 AAAATAACTATAATTTTTTTAAAAA
3280127 TATTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAACTATAATTTTTTTAAAAAA
Found at i:3282458 original size:2 final size:2
Alignment explanation
Indices: 3282451--3282488 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3282441 ATTAATGGAA
*
3282451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3282489 TTGTAGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3284413 original size:5 final size:5
Alignment explanation
Indices: 3284391--3284425 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
3284381 TGACATACCC
3284391 AAAAT GAAAAT GAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT AAA
3284426 TAGCTTTCAG
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:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3284729 original size:47 final size:49
Alignment explanation
Indices: 3284654--3284747 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 49
3284644 TCAATTTTGA
*
3284654 ATTAAATAATTTTTTATTTTAAATT-T-TATTTTTATTATTTAAAATAT
1 ATTAAATAATTTTTTATATTAAATTATATATTTTTATTATTTAAAATAT
3284701 ATTAAA-AATTATTTTATATTAATATTTATATATTTTTATTATTTAAA
1 ATTAAATAATT-TTTTATATTAA-A-TTATATATTTTTATTATTTAAA
3284748 TAATAATTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
46 4 0.10
47 16 0.39
48 1 0.02
49 2 0.05
50 1 0.02
51 17 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (49 bp):
ATTAAATAATTTTTTATATTAAATTATATATTTTTATTATTTAAAATAT
Found at i:3285659 original size:6 final size:6
Alignment explanation
Indices: 3285658--3285686 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3285648 AATATTTTTA
3285658 TTTAAT TTTAAT TTTAAT TTTAAT TTTAA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAA
3285687 AATTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTAAT
Found at i:3287464 original size:17 final size:16
Alignment explanation
Indices: 3287433--3287473 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
3287423 TTATTTAAAT
3287433 TTAATTATAAAAATATA
1 TTAA-TATAAAAATATA
*
3287450 TTAATATAAATAATATT
1 TTAATATAAA-AATATA
3287467 TTAATAT
1 TTAATAT
3287474 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATATAAAAATATA
Found at i:3287508 original size:16 final size:16
Alignment explanation
Indices: 3287487--3287520 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3287477 TAAATAATAA
3287487 AATAAATAATTAAA-TT
1 AATAAA-AATTAAACTT
3287503 AATAAAAATTAAACTT
1 AATAAAAATTAAACTT
3287519 AA
1 AA
3287521 ATTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAAAATTAAACTT
Found at i:3287940 original size:18 final size:19
Alignment explanation
Indices: 3287919--3287960 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3287909 TTTATTAATT
*
3287919 TTTTAAATATAT-TATAAA
1 TTTTAAATACATATATAAA
*
3287937 TTTT-ATTACATATATAAA
1 TTTTAAATACATATATAAA
3287955 TTTTAA
1 TTTTAA
3287961 TTTAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 14 0.70
19 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAAATACATATATAAA
Found at i:3287949 original size:21 final size:20
Alignment explanation
Indices: 3287892--3287951 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
3287882 TTATTTCAAC
* *
3287892 TATAAATATTTTAATTAT-T
1 TATAAATTTTTTAAATATAT
*
3287911 TATTAATTTTTTAAATATAT
1 TATAAATTTTTTAAATATAT
*
3287931 TATAAATTTTATTACATATAT
1 TATAAATTTT-TTAAATATAT
3287952 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 15 0.44
20 10 0.29
21 9 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TATAAATTTTTTAAATATAT
Found at i:3288068 original size:21 final size:22
Alignment explanation
Indices: 3288027--3288072 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
3288017 TTACATCCAA
3288027 AATTTTAACTATATCTATTATT
1 AATTTTAACTATATCTATTATT
3288049 AATTTTAATCTA-AT-TATTATT
1 AATTTTAA-CTATATCTATTATT
3288070 AAT
1 AAT
3288073 ACCTTCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.43
22 10 0.43
23 3 0.13
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTAACTATATCTATTATT
Found at i:3288266 original size:5 final size:5
Alignment explanation
Indices: 3288256--3288280 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3288246 CTTTCTTTGC
3288256 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
3288281 GCTCTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3296532 original size:29 final size:29
Alignment explanation
Indices: 3296490--3296551 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
3296480 TCCCAAAATG
*
3296490 AAGAAAAATTTTCTATATTTGAGTATCCC
1 AAGAAAAATTTTCTATATTTGAGAATCCC
3296519 AAGAAAAGA-TTTCTATATTTGAGAATCCC
1 AAGAAAA-ATTTTCTATATTTGAGAATCCC
3296548 AAGA
1 AAGA
3296552 CGCACCCACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
AAGAAAAATTTTCTATATTTGAGAATCCC
Found at i:3296885 original size:13 final size:13
Alignment explanation
Indices: 3296867--3296891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3296857 ACCTGAAATT
3296867 TTGTAGAAAAAGG
1 TTGTAGAAAAAGG
3296880 TTGTAGAAAAAG
1 TTGTAGAAAAAG
3296892 CATAACAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (13 bp):
TTGTAGAAAAAGG
Found at i:3301586 original size:2 final size:2
Alignment explanation
Indices: 3301581--3301605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3301571 AAAAAAAAAA
3301581 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3301606 ATTTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3301941 original size:15 final size:16
Alignment explanation
Indices: 3301923--3301959 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3301913 AATTTAATTT
3301923 TAATAAAATTAA-AAA
1 TAATAAAATTAATAAA
*
3301938 TAATAATATTAATAAA
1 TAATAAAATTAATAAA
3301954 -AATAAA
1 TAATAAA
3301960 TATTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 16 0.84
16 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATAAAATTAATAAA
Found at i:3302148 original size:20 final size:21
Alignment explanation
Indices: 3302123--3302162 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3302113 AAATAATAAT
3302123 TTTAAT-ATAAATA-ATTAAAA
1 TTTAATGA-AAATATATTAAAA
3302143 TTTAATGAAAATATATTAAA
1 TTTAATGAAAATATATTAAA
3302163 TAATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TTTAATGAAAATATATTAAAA
Found at i:3303062 original size:27 final size:26
Alignment explanation
Indices: 3303032--3303124 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 26
3303022 TGAATACTCA
*
3303032 TTAAAATTTATTAAATTATATTTATGT
1 TTAAAA-TAATTAAATTATATTTATGT
* *
3303059 TTAAAAATGATTAAAATTAT-TTTAT-A
1 TT-AAAATAATT-AAATTATATTTATGT
*
3303085 TT-AAATAATAAAATTATATTTATGT
1 TTAAAATAATTAAATTATATTTATGT
* *
3303110 TGAATTATAATTAAA
1 TTAA-AATAATTAAA
3303125 AATTATTGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
23 7 0.13
24 11 0.21
25 1 0.02
26 3 0.06
27 19 0.37
28 11 0.21
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
TTAAAATAATTAAATTATATTTATGT
Found at i:3303088 original size:26 final size:27
Alignment explanation
Indices: 3303031--3303108 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
3303021 TTGAATACTC
* *
3303031 ATTAAAATTTATTAAATTATATTTATG
1 ATTAAAAATGATTAAATTATATTTATG
*
3303058 TTTAAAAATGATTAAAATTAT-TTTAT-
1 ATTAAAAATGATT-AAATTATATTTATG
3303084 ATTAAATAAT-A--AAATTATATTTATG
1 ATTAAA-AATGATTAAATTATATTTATG
3303109 TTGAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
23 7 0.16
24 5 0.12
26 6 0.14
27 18 0.42
28 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
ATTAAAAATGATTAAATTATATTTATG
Found at i:3303104 original size:88 final size:93
Alignment explanation
Indices: 3302998--3303201 Score: 226
Period size: 88 Copynumber: 2.2 Consensus size: 93
3302988 TATATAATAA
* * * *
3302998 AAATAAATAAAGTTATATTTATATTGAA-TACTCATTAAAATTTATTAAATTATAT-TTATGTTT
1 AAAT-AATAAAATTATATTTATATTGAATTA-TAATTAAAAATTATTAAATTATATGTT-T-ATT
*
3303061 AAAA-AT-GA-T-T-AAAATTAT-TTTATATT
62 AAAATATAAATTATCAAAATTATATTTATATT
* *
3303087 AAATAATAAAATTATATTTATGTTGAATTATAATTAAAAATTATTGAATTATATGTTTATTAAAA
1 AAATAATAAAATTATATTTATATTGAATTATAATTAAAAATTATTAAATTATATGTTTATTAAAA
*
3303152 TATAAATTATCAAAATTATATTTATCTT
66 TATAAATTATCAAAATTATATTTATATT
* *
3303180 AAATAATAAAAATATATATATA
1 AAATAATAAAATTATATTTATA
3303202 ATTCAAAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
87 6 0.06
88 45 0.47
89 9 0.09
90 1 0.01
91 1 0.01
92 8 0.08
93 26 0.27
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (93 bp):
AAATAATAAAATTATATTTATATTGAATTATAATTAAAAATTATTAAATTATATGTTTATTAAAA
TATAAATTATCAAAATTATATTTATATT
Found at i:3303543 original size:18 final size:19
Alignment explanation
Indices: 3303492--3303545 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
3303482 ATAATATCAC
*
3303492 ATAATTTATTAATTA-TAT
1 ATAATTTATTAAATATTAT
*
3303510 ATAAATTTA-TATATATTA-
1 AT-AATTTATTAAATATTAT
3303528 ATAATTTATTAAATATTA
1 ATAATTTATTAAATATTA
3303546 GCTTTTGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.20
18 16 0.53
19 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATTTATTAAATATTAT
Found at i:3303643 original size:3 final size:3
Alignment explanation
Indices: 3303635--3303662 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3303625 ACTATGTTCG
3303635 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3303663 AAATTTTATG
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:3306270 original size:53 final size:54
Alignment explanation
Indices: 3306190--3306296 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 54
3306180 ATTTGTATAT
3306190 TATATTGGTGTGTCTATGTTTACAAGATTGATATG-AAAAAAACCACGAAATAC
1 TATATTGGTGTGTCTATGTTTACAAGATTGATATGAAAAAAAACCACGAAATAC
3306243 TATATTGGTGTGTCTATGTTTACAAGATTGATATGAAAAAAAACCACGAAATAC
1 TATATTGGTGTGTCTATGTTTACAAGATTGATATGAAAAAAAACCACGAAATAC
3306297 GGTATGTGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 35 0.66
54 18 0.34
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (54 bp):
TATATTGGTGTGTCTATGTTTACAAGATTGATATGAAAAAAAACCACGAAATAC
Found at i:3308667 original size:1 final size:1
Alignment explanation
Indices: 3308657--3308701 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
3308647 CCCCTACGCT
* *
3308657 CCCCCTCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3308702 ACTCCCCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.96, G:0.00, T:0.04
Consensus pattern (1 bp):
C
Found at i:3308680 original size:20 final size:20
Alignment explanation
Indices: 3308665--3308708 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3308655 CTCCCCCTCC
*
3308665 CCCCCCCCCCCCCCCCCCCT
1 CCCCCCCCCCCCCCCCCACT
3308685 CCCCCCCCCCCCCCCCCACT
1 CCCCCCCCCCCCCCCCCACT
3308705 CCCC
1 CCCC
3308709 ACTCTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.93, G:0.00, T:0.05
Consensus pattern (20 bp):
CCCCCCCCCCCCCCCCCACT
Found at i:3308681 original size:21 final size:22
Alignment explanation
Indices: 3308657--3308701 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3308647 CCCCTACGCT
3308657 CCCCCTCCCCCCCCCCCCCCCC
1 CCCCCTCCCCCCCCCCCCCCCC
3308679 CCCCCTCCCCCCCCCCCCCCCC
1 CCCCCTCCCCCCCCCCCCCCCC
3308701 C
1 C
3308702 ACTCCCCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.96, G:0.00, T:0.04
Consensus pattern (22 bp):
CCCCCTCCCCCCCCCCCCCCCC
Found at i:3310725 original size:2 final size:2
Alignment explanation
Indices: 3310718--3310746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3310708 TTTAGCAGAC
3310718 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 A
3310747 CACACACACG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3312134 original size:43 final size:44
Alignment explanation
Indices: 3312086--3312178 Score: 145
Period size: 43 Copynumber: 2.1 Consensus size: 44
3312076 GGCTAAATTC
*
3312086 TAAATTTCTTATGTTTTTATATTCAAATTTGATCTACTC-A-TTT
1 TAAATTTCTTATGTTTTTATATTCAAATTTAATCTA-TCAACTTT
*
3312129 TAAATTTTTTATGTTTTTATATTCAAATTTAATCTATCAACTTT
1 TAAATTTCTTATGTTTTTATATTCAAATTTAATCTATCAACTTT
3312173 TAAATT
1 TAAATT
3312179 AGATATTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 2 0.04
43 35 0.76
44 9 0.20
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (44 bp):
TAAATTTCTTATGTTTTTATATTCAAATTTAATCTATCAACTTT
Found at i:3314735 original size:29 final size:29
Alignment explanation
Indices: 3314693--3314754 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
3314683 TCCCAAAATG
*
3314693 AAGAAAAATTTTCTATATTTGAGTATCCC
1 AAGAAAAATTTTCTATATTTGAGAATCCC
3314722 AAGAAAAGA-TTTCTATATTTGAGAATCCC
1 AAGAAAA-ATTTTCTATATTTGAGAATCCC
3314751 AAGA
1 AAGA
3314755 CGCACCCACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
AAGAAAAATTTTCTATATTTGAGAATCCC
Found at i:3315088 original size:13 final size:13
Alignment explanation
Indices: 3315070--3315094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3315060 ACCTGAAATT
3315070 TTGTAGAAAAAGG
1 TTGTAGAAAAAGG
3315083 TTGTAGAAAAAG
1 TTGTAGAAAAAG
3315095 CATAACAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (13 bp):
TTGTAGAAAAAGG
Found at i:3322333 original size:27 final size:29
Alignment explanation
Indices: 3322303--3322359 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
3322293 AATTTACTAT
3322303 TTAAATATAAA-AAAAT-TATT-TTTATAA
1 TTAAATATAAATAAAATATATTATTT-TAA
*
3322330 TTAAATTTAAATAAAATATATTATTTTAA
1 TTAAATATAAATAAAATATATTATTTTAA
3322359 T
1 T
3322360 ATTTAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 5 0.19
29 8 0.31
30 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAATATAAATAAAATATATTATTTTAA
Found at i:3322366 original size:32 final size:33
Alignment explanation
Indices: 3322301--3322367 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
3322291 TGAATTTACT
*
3322301 ATTTAAATATAAAAAAATTATTTTTATAATTAA
1 ATTTAAATATAAAAAAATTATTTTAATAATTAA
* * *
3322334 ATTTAAATA-AAATATATTATTTTAATATTTAA
1 ATTTAAATATAAAAAAATTATTTTAATAATTAA
3322366 AT
1 AT
3322368 AATGATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTAAATATAAAAAAATTATTTTAATAATTAA
Found at i:3322786 original size:18 final size:18
Alignment explanation
Indices: 3322735--3322823 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 18
3322725 TAATATTTAT
* *
3322735 ATATAAATTTAAATAAAA
1 ATATTAATTTAAATTAAA
* *
3322753 ATAATAA-TTATTATTAAA
1 ATATTAATTTA-AATTAAA
3322771 ATATTAATTTAAATTAAA
1 ATATTAATTTAAATTAAA
* *
3322789 TTAAATTAATTTATATTAAAA
1 --ATATTAATTTAAATT-AAA
*
3322810 AAATT-ATTTAAATT
1 ATATTAATTTAAATT
3322824 TAACTTAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
17 3 0.05
18 30 0.53
19 8 0.14
20 13 0.23
21 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAATTTAAATTAAA
Found at i:3322788 original size:41 final size:40
Alignment explanation
Indices: 3322704--3322823 Score: 99
Period size: 41 Copynumber: 3.0 Consensus size: 40
3322694 TAATATTAAA
* *
3322704 AAATAAAAAT--TAGTTATATATTAATAT-TTATATATAAATTT
1 AAATAAAAATAATA-TTAT-TATTAAAATATTA-ATTTAAA-TT
3322745 AAATAAAAATAATAATTATTATTAAAATATTAATTTAAATT
1 AAATAAAAATAAT-ATTATTATTAAAATATTAATTTAAATT
* * *
3322786 AAATTAAATTAAT-TTA-TATTAAAAAAATT-ATTTAAATT
1 AAATAAAAATAATATTATTATT-AAAATATTAATTTAAATT
3322824 TAACTTAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
38 13 0.19
39 10 0.14
41 23 0.33
42 14 0.20
43 8 0.12
44 1 0.01
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (40 bp):
AAATAAAAATAATATTATTATTAAAATATTAATTTAAATT
Found at i:3322815 original size:24 final size:26
Alignment explanation
Indices: 3322786--3322842 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
3322776 AATTTAAATT
3322786 AAATTAAATT-AATTTATA-TTAA-AA
1 AAATTAAATTAAATTTA-ACTTAATAA
*
3322810 AAATT-ATTTAAATTTAACTTAATAA
1 AAATTAAATTAAATTTAACTTAATAA
3322835 AAATTAAA
1 AAATTAAA
3322843 CTTATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 4 0.15
24 15 0.56
25 7 0.26
26 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATTAAATTAAATTTAACTTAATAA
Found at i:3323193 original size:29 final size:28
Alignment explanation
Indices: 3323120--3323194 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
3323110 ATTAATTAAA
*
3323120 ATAATATTTT-TTATTTTAATTTAATTT
1 ATAATATTTTATTATATTAATTTAATTT
* * * *
3323147 ATAAAAATATATAAATATTAATTTAATTTT
1 ATAATATTTTAT-TATATTAATTTAA-TTT
*
3323177 TTAATATTTTATTATATT
1 ATAATATTTTATTATATT
3323195 TTAAATAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
27 7 0.20
28 1 0.03
29 16 0.46
30 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATAATATTTTATTATATTAATTTAATTT
Found at i:3323334 original size:145 final size:145
Alignment explanation
Indices: 3323184--3323475 Score: 548
Period size: 145 Copynumber: 2.0 Consensus size: 145
3323174 TTTTTAATAT
3323184 TTTATTATATTTTAAATAATAATAATTTAACTCATCAAATTAAATTAAATTCAATCTTAAATTTA
1 TTTATTATATTTTAAATAATAATAATTTAACTCATCAAATTAAATTAAATTCAATCTTAAATTTA
*
3323249 AATTTAATTTTTTAAACTTATAACTCAAATATAAATACTTCGTGTTAAAATATTTTAAAAATAAG
66 AATTTAATTTTTTAAACTTATAACTCAAATATAAATACTTCATGTTAAAATATTTTAAAAATAAG
*
3323314 TAAGATTAATTGATG
131 TAAAATTAATTGATG
*
3323329 TTTATTATATTTTAAATAATAATAATTTAACTCATCAAATTAAATTGAATTCAATCTTAAATTTA
1 TTTATTATATTTTAAATAATAATAATTTAACTCATCAAATTAAATTAAATTCAATCTTAAATTTA
*
3323394 AATTTAATTTTTTAAACTTATAACTCAAATATAAATACTTTATGTTAAAATATTTTAAAAATAAG
66 AATTTAATTTTTTAAACTTATAACTCAAATATAAATACTTCATGTTAAAATATTTTAAAAATAAG
3323459 TAAAATTAATTGATG
131 TAAAATTAATTGATG
3323474 TT
1 TT
3323476 AATATCGAAA
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (145 bp):
TTTATTATATTTTAAATAATAATAATTTAACTCATCAAATTAAATTAAATTCAATCTTAAATTTA
AATTTAATTTTTTAAACTTATAACTCAAATATAAATACTTCATGTTAAAATATTTTAAAAATAAG
TAAAATTAATTGATG
Found at i:3325346 original size:25 final size:25
Alignment explanation
Indices: 3325274--3325347 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
3325264 TGAATTATGA
3325274 TTAAAAATT-TTTT-TATTTAAA--
1 TTAAAAATTATTTTATATTTAAATT
* *
3325295 TT-AAAATTAATTTA-ATTTAATTAT
1 TTAAAAATTATTTTATATTTAAAT-T
*
3325319 TTAAAAATTATTTTATAATTAAATT
1 TTAAAAATTATTTTATATTTAAATT
3325344 TTAA
1 TTAA
3325348 TAAAAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 6 0.15
21 11 0.27
24 2 0.05
25 16 0.39
26 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAAAATTATTTTATATTTAAATT
Found at i:3325786 original size:17 final size:18
Alignment explanation
Indices: 3325764--3325807 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
3325754 CATTAATACG
3325764 TAATTATAAATATA-ATA
1 TAATTATAAATATATATA
*
3325781 TAATTAAAAATATATATA
1 TAATTATAAATATATATA
*
3325799 TAATAATAA
1 TAATTATAA
3325808 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTATAAATATATATA
Found at i:3327868 original size:27 final size:25
Alignment explanation
Indices: 3327798--3327869 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 25
3327788 ATGATTGGTA
*
3327798 ATATAATAATAATAAAA-AAATTTT
1 ATATATTAATAATAAAATAAATTTT
* * * **
3327822 AAAAATTATTAATATGATAATTATTTT
1 ATATATTAATAATAAAATAA--ATTTT
3327849 ATATATTAATAATAAAATAAA
1 ATATATTAATAATAAAATAAA
3327870 AAGATTTTAT
Statistics
Matches: 34, Mismatches: 11, Indels: 5
0.68 0.22 0.10
Matches are distributed among these distances:
24 11 0.32
25 3 0.09
27 20 0.59
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (25 bp):
ATATATTAATAATAAAATAAATTTT
Found at i:3327933 original size:4 final size:4
Alignment explanation
Indices: 3327924--3327949 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3327914 AATATATTAA
3327924 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
3327950 TTTATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3327985 original size:20 final size:20
Alignment explanation
Indices: 3327950--3327998 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
3327940 AAATAAATAA
3327950 TTTATATATTATATTTTTAAT
1 TTTAT-TATTATATTTTTAAT
*
3327971 TTTAATTATTA-ATTTTTTAT
1 TTT-ATTATTATATTTTTAAT
3327991 TTTATTAT
1 TTTATTAT
3327999 CGGTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 5 0.19
20 11 0.42
21 8 0.31
22 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTATTATATTTTTAAT
Found at i:3328330 original size:31 final size:32
Alignment explanation
Indices: 3328267--3328330 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3328257 AAAGTATATA
* *
3328267 AATATTTTAATATTTATATAAAATAAATTATT
1 AATATATTAAAATTTATATAAAATAAATTATT
* *
3328299 AATATATTAAAATTTATGT-AAATGAATTATT
1 AATATATTAAAATTTATATAAAATAAATTATT
3328330 A
1 A
3328331 TTTTATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
AATATATTAAAATTTATATAAAATAAATTATT
Found at i:3333885 original size:2 final size:2
Alignment explanation
Indices: 3333880--3333921 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3333870 ACAAACACTC
3333880 AG AG AG 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 AG AG AG
3333922 CAAATAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3336360 original size:3 final size:3
Alignment explanation
Indices: 3336354--3336395 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3336344 TCTACAACAA
3336354 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3336396 TAAAACTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3336518 original size:16 final size:17
Alignment explanation
Indices: 3336497--3336533 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3336487 TTGACACAGT
3336497 TTTTTAAATATA-ATTA
1 TTTTTAAATATATATTA
*
3336513 TTTTTAAATTTATATTA
1 TTTTTAAATATATATTA
3336530 TTTT
1 TTTT
3336534 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTAAATATATATTA
Found at i:3336753 original size:22 final size:22
Alignment explanation
Indices: 3336728--3336793 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
3336718 TAAAATAAAA
3336728 AAAAATATTTAAAT-TTAA-TT
1 AAAAATATTTAAATATTAATTT
*
3336748 ATAAAATATATAAATATTAATTT
1 A-AAAATATTTAAATATTAATTT
* *
3336771 AAAAATATTGTATATATTTATTT
1 AAAAATATT-TAAATATTAATTT
3336794 TAACAATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 11 0.29
23 14 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAATATTTAAATATTAATTT
Found at i:3336900 original size:18 final size:18
Alignment explanation
Indices: 3336866--3336902 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3336856 ATCCAAATTT
* *
3336866 AATTAAAAATTACATAAA
1 AATTAAAAATAAAATAAA
3336884 AATTAAAAATAAAATAAA
1 AATTAAAAATAAAATAAA
3336902 A
1 A
3336903 TCATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AATTAAAAATAAAATAAA
Found at i:3341584 original size:2 final size:2
Alignment explanation
Indices: 3341577--3341630 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
3341567 TATTTTTACT
* * * * *
3341577 TA TA TA TA TA TA TA CA TA CA 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
3341619 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3341631 CATACGTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:3341643 original size:18 final size:18
Alignment explanation
Indices: 3341578--3341634 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
3341568 ATTTTTACTT
3341578 ATATATATATATACATAC
1 ATATATATATATACATAC
*
3341596 ATATATATATATACACAC
1 ATATATATATATACATAC
*
3341614 ATATATATATATATATAC
1 ATATATATATATACATAC
3341632 ATA
1 ATA
3341635 CGTACATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATATATATACATAC
Found at i:3344056 original size:40 final size:39
Alignment explanation
Indices: 3344006--3344081 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
3343996 TTTATAACGT
*
3344006 ATGTTTTTTAATTTATGTTTTCTCCAAATAATGTTTATA
1 ATGTTTTTTAATGTATGTTTTCTCCAAATAATGTTTATA
3344045 ATGTATTTTTAATGTATGTTTTCTCCAAATAATGTTT
1 ATGT-TTTTTAATGTATGTTTTCTCCAAATAATGTTT
3344082 TTTCTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (39 bp):
ATGTTTTTTAATGTATGTTTTCTCCAAATAATGTTTATA
Found at i:3346081 original size:28 final size:28
Alignment explanation
Indices: 3346050--3346127 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 28
3346040 GTAAAGTCAG
* *
3346050 TATTTTTTTTTAAATAATATTA-TATTAA
1 TATTTTTATTT-AATAATATTATTATAAA
3346078 TA--TTTATTTAATAATATTATTATAAA
1 TATTTTTATTTAATAATATTATTATAAA
*
3346104 TATTTATATATTTAATAAAATTAT
1 TATTT-T-TATTTAATAATATTAT
3346128 AAATTAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 10 0.24
26 13 0.31
28 3 0.07
29 1 0.02
30 15 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTTTTATTTAATAATATTATTATAAA
Done.