Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 47 of 66
Found at i:16966578 original size:5 final size:5
Alignment explanation
Indices: 16966555--16966630 Score: 68
Period size: 5 Copynumber: 15.2 Consensus size: 5
16966545 ACGTTATAAT
*
16966555 TAAAA TAAAA -AATAT TAAAA TAAAA TATAATA TAAAA T-AAA -AAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TA-AA-A TAAAA TAAAA TAAAA
* * *
16966600 TAAAA TAAAA TAAAA TATAA GAAAT TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
16966631 TTATATAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
4 8 0.14
5 40 0.70
6 6 0.11
7 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:16966630 original size:30 final size:30
Alignment explanation
Indices: 16966570--16966666 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
16966560 TAAAAAATAT
* **
16966570 TAAAATAAAATATAATATAA-AATAAAAAAA
1 TAAAATAAAATAAAATATAAGAA-ATTAAAA
16966600 TAAAATAAAATAAAATATAAGAAATTAAAA
1 TAAAATAAAATAAAATATAAGAAATTAAAA
** * ** *
16966630 T-TTATATAATATAGGTAAAAGAAATTAAAA
1 TAAAATAAAATA-AAATATAAGAAATTAAAA
16966660 TAAAATA
1 TAAAATA
16966667 TATAATATGA
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
29 7 0.13
30 41 0.77
31 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (30 bp):
TAAAATAAAATAAAATATAAGAAATTAAAA
Found at i:16966685 original size:50 final size:48
Alignment explanation
Indices: 16966552--16966725 Score: 140
Period size: 50 Copynumber: 3.6 Consensus size: 48
16966542 GTAACGTTAT
* * *
16966552 AATTAAAATAAAAAATATTAAAATAAAATATAATATAAAATAAAAAAATA
1 AATTAAAATAAAATATA-TAAAATAAAA-ATTATATAAAATAAAAAAAGA
* * * **
16966602 AAATAAAATAAAATATA-AGAAATTAAAATTTATATAATATAGGTAAAAGA
1 AATTAAAATAAAATATATA-AAA-TAAAAATTATATAAAATA-AAAAAAGA
* *
16966652 AATTAAAATAAAATATATAATATGAAAAATTATATTAAAA-AAATAAA-A
1 AATTAAAATAAAATATATAAAAT-AAAAATTATA-TAAAATAAAAAAAGA
* * *
16966700 TATTATAATAAAAAATA-AAAATAAAA
1 AATTAAAATAAAATATATAAAATAAAA
16966726 TATATGACAT
Statistics
Matches: 99, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
46 4 0.04
47 4 0.04
48 16 0.16
49 17 0.17
50 53 0.54
51 5 0.05
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (48 bp):
AATTAAAATAAAATATATAAAATAAAAATTATATAAAATAAAAAAAGA
Found at i:16966712 original size:20 final size:20
Alignment explanation
Indices: 16966676--16966721 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
16966666 ATATAATATG
*
16966676 AAAAATTATATTAAAAAAAT
1 AAAAATTATAATAAAAAAAT
16966696 AAAATATTATAAT-AAAAAAT
1 AAAA-ATTATAATAAAAAAAT
16966716 AAAAAT
1 AAAAAT
16966722 AAAATATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 15 0.62
21 7 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTATAATAAAAAAAT
Found at i:16972276 original size:32 final size:31
Alignment explanation
Indices: 16972226--16972309 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
16972216 GAAAAAATTT
* *
16972226 AAAATAAAATATACAATATAAGAAATTATATTA
1 AAAATAAAA-ATAAAATATAA-AAATTATAATA
* *
16972259 AAAATAAAAATAAAATAT-ATACTTATAATA
1 AAAATAAAAATAAAATATAAAAATTATAATA
16972289 AGAAATGAAAAATAAAATATA
1 A-AAAT-AAAAATAAAATATA
16972310 TTTAATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 9 0.20
31 5 0.11
32 21 0.48
33 9 0.20
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (31 bp):
AAAATAAAAATAAAATATAAAAATTATAATA
Found at i:16972310 original size:32 final size:30
Alignment explanation
Indices: 16972251--16972310 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 30
16972241 ATATAAGAAA
*
16972251 TTATATTAAAAATAAAAATAAAATATATAC
1 TTATAATAAAAATAAAAATAAAATATATAC
16972281 TTATAATAAGAAATGAAAAATAAAATATAT
1 TTATAATAA-AAAT-AAAAATAAAATATAT
16972311 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.30
31 4 0.15
32 15 0.56
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (30 bp):
TTATAATAAAAATAAAAATAAAATATATAC
Found at i:16972554 original size:15 final size:15
Alignment explanation
Indices: 16972505--16972558 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
16972495 ATACCAAACA
* *
16972505 CTGCAATTATCTTTC
1 CTGCAATCATATTTC
* *
16972520 CTGTAATCATATTGC
1 CTGCAATCATATTTC
* *
16972535 TTGCAATCATATTTT
1 CTGCAATCATATTTC
16972550 CTGCAATCA
1 CTGCAATCA
16972559 CATTATCTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (15 bp):
CTGCAATCATATTTC
Found at i:16973240 original size:15 final size:14
Alignment explanation
Indices: 16973217--16973255 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
16973207 TGATTAATAC
16973217 AAATAAAAATTAAA
1 AAATAAAAATTAAA
* *
16973231 AGATTAAAAAATAAA
1 A-AATAAAAATTAAA
16973246 AAATAAAAAT
1 AAATAAAAAT
16973256 AGAGAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAAAATTAAA
Found at i:16973244 original size:22 final size:24
Alignment explanation
Indices: 16973208--16973253 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
16973198 CCTTATTGAT
*
16973208 GATTAATACAAATAAAAATTAAAA
1 GATTAATACAAATAAAAAATAAAA
16973232 GATTAA-A-AAATAAAAAATAAAA
1 GATTAATACAAATAAAAAATAAAA
16973254 ATAGAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 1 0.05
24 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (24 bp):
GATTAATACAAATAAAAAATAAAA
Found at i:16976398 original size:161 final size:158
Alignment explanation
Indices: 16976132--16976438 Score: 578
Period size: 161 Copynumber: 1.9 Consensus size: 158
16976122 ACGGTTGTCA
16976132 TGGGCCCGAGGGAGGTTCCGAGTCGTGACAAATAAATTATTGATGTTTAATGAAAATCAAATTAA
1 TGGGCCCGAGGGAGGTTCCGAGTCGTGACAAATAAATTATTGATGTTTAATGAAAATCAAATTAA
16976197 AAGATTAAGACATGGAAAATACAAATAGAGAAAAATGATTCAAATAATTAAAATTAAAAATTATA
66 AAGATTAAGACATGGAAAATACAAATAGAGAAAAATGATTCAAATAATTAAAATTAAAAATTATA
16976262 TAACTAATTTAAAAATTAAAATTAAATT
131 TAACTAATTTAAAAATTAAAATTAAATT
*
16976290 TNNNGGGCCCGTGGGAGGTTCCGAGTCGTGACAAATAAATTATTGATGTTTAATGAAAATCAAAT
1 T---GGGCCCGAGGGAGGTTCCGAGTCGTGACAAATAAATTATTGATGTTTAATGAAAATCAAAT
16976355 TAAAAGATTAAGACATGGAAAATACAAATAGAGAAAAATGATTCAAATAATTAAAATTAAAAATT
63 TAAAAGATTAAGACATGGAAAATACAAATAGAGAAAAATGATTCAAATAATTAAAATTAAAAATT
16976420 ATATAACTAATTTAAAAAT
128 ATATAACTAATTTAAAAAT
16976439 AAATTATTCA
Statistics
Matches: 145, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
158 1 0.01
161 144 0.99
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.28
Consensus pattern (158 bp):
TGGGCCCGAGGGAGGTTCCGAGTCGTGACAAATAAATTATTGATGTTTAATGAAAATCAAATTAA
AAGATTAAGACATGGAAAATACAAATAGAGAAAAATGATTCAAATAATTAAAATTAAAAATTATA
TAACTAATTTAAAAATTAAAATTAAATT
Found at i:16976451 original size:12 final size:11
Alignment explanation
Indices: 16976415--16976507 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
16976405 TTAAAATTAA
16976415 AAATTATATAACT
1 AAATTA-ATAA-T
* *
16976428 AATTTAAAAAT
1 AAATTAATAAT
*
16976439 AAATTATTCAAT
1 AAATTAAT-AAT
*
16976451 AATTTAATAAT
1 AAATTAATAAT
16976462 AAATTAA-AAT
1 AAATTAATAAT
16976472 --ATTAATAAT
1 AAATTAATAAT
** * *
16976481 TTA-TATTAGT
1 AAATTAATAAT
*
16976491 AATTTAATAAT
1 AAATTAATAAT
16976502 AAATTA
1 AAATTA
16976508 TTAACTTTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
8 5 0.08
9 3 0.05
10 8 0.14
11 26 0.44
12 12 0.20
13 5 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (11 bp):
AAATTAATAAT
Found at i:16976759 original size:48 final size:43
Alignment explanation
Indices: 16976648--16976758 Score: 168
Period size: 43 Copynumber: 2.6 Consensus size: 43
16976638 TAAAATAAAT
* *
16976648 CATAATAACAATTCTTATTCAATTCCATTTCATGAACCAAACTA
1 CATAATAACAATT-TTATTCTATTCAATTTCATGAACCAAACTA
* *
16976692 CATAATAACAATTCTATTCTATTCAATTTCATGAACCAAATTA
1 CATAATAACAATTTTATTCTATTCAATTTCATGAACCAAACTA
*
16976735 CATAATAACAATTTTATTTTATTC
1 CATAATAACAATTTTATTCTATTC
16976759 TTTCTTTAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 48 0.79
44 13 0.21
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.39
Consensus pattern (43 bp):
CATAATAACAATTTTATTCTATTCAATTTCATGAACCAAACTA
Found at i:16986001 original size:19 final size:20
Alignment explanation
Indices: 16985974--16986019 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
16985964 AGGAGACAAG
*
16985974 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
16985993 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
16986012 ATAATATT
1 ATAATATT
16986020 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:16986466 original size:20 final size:20
Alignment explanation
Indices: 16986421--16986458 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16986411 TTTTGGCCCC
16986421 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
16986441 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
16986459 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:16990116 original size:2 final size:2
Alignment explanation
Indices: 16990109--16990134 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16990099 TTAGCATAGC
16990109 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
16990135 TGCATATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16994809 original size:15 final size:15
Alignment explanation
Indices: 16994785--16994829 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
16994775 TTTCAGGGTC
16994785 TTCTTCTTCTTCCTCT
1 TTCTT-TTCTTCCTCT
16994801 TTCTTTTCTTCCTCT
1 TTCTTTTCTTCCTCT
* *
16994816 TCCTCTTCTTCCTC
1 TTCTTTTCTTCCTC
16994830 GGGAGGATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TTCTTTTCTTCCTCT
Found at i:16996548 original size:2 final size:2
Alignment explanation
Indices: 16996543--16996604 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
16996533 ATATTAACAA
** * *
16996543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CN CT AA 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
16996585 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
16996605 CTAACTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16996830 original size:2 final size:2
Alignment explanation
Indices: 16996823--16996847 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16996813 GAAACAAAGA
16996823 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
16996848 TTTTGATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17007631 original size:21 final size:21
Alignment explanation
Indices: 17007605--17007645 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17007595 TTTTAGATCA
*
17007605 TTTTTTTCTTC-CTTTCCTTT
1 TTTTTTTTTTCTCTTTCCTTT
*
17007625 TTTTTTTTTTCTGTTTCCTTT
1 TTTTTTTTTTCTCTTTCCTTT
17007646 AATGGATTAA
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:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTTTTTTTCTCTTTCCTTT
Found at i:17007818 original size:2 final size:2
Alignment explanation
Indices: 17007813--17007839 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17007803 CATATATACC
17007813 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17007840 GTGTTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17009088 original size:17 final size:17
Alignment explanation
Indices: 17009055--17009088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17009045 TCAATTAACT
* *
17009055 AATTAATTAGTTGTTTA
1 AATTAATTACTTATTTA
17009072 AATTAATTACTTATTTA
1 AATTAATTACTTATTTA
17009089 TAAAAAGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTAATTACTTATTTA
Found at i:17011930 original size:31 final size:32
Alignment explanation
Indices: 17011889--17011959 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
17011879 TTCTTTCAAT
* *
17011889 TAAAACAAA-TTATGTTCAAGTGAAAATACAA
1 TAAAAAAAATTTACGTTCAAGTGAAAATACAA
*
17011920 TAAAAAAAATTTACGTTCAAGTGGAAATACAA
1 TAAAAAAAATTTACGTTCAAGTGAAAATACAA
17011952 -AAAAAAAA
1 TAAAAAAAA
17011960 GGTTTATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 16 0.44
32 20 0.56
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (32 bp):
TAAAAAAAATTTACGTTCAAGTGAAAATACAA
Found at i:17031458 original size:18 final size:20
Alignment explanation
Indices: 17031435--17031482 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
17031425 TGAAAATATT
17031435 TAAATATTATTTAA-TAT-A
1 TAAATATTATTTAATTATAA
*
17031453 TTAATATTATTTAATTATAA
1 TAAATATTATTTAATTATAA
17031473 TAAATATTAT
1 TAAATATTAT
17031483 AAAGTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATTATTTAATTATAA
Found at i:17031466 original size:10 final size:10
Alignment explanation
Indices: 17031431--17031505 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
17031421 GAAATGAAAA
17031431 TATTTAAATAT
1 TATTT-AATAT
17031442 TATTTAATA-
1 TATTTAATAT
17031451 TA-TTAATAT
1 TATTTAATAT
17031460 TATTTAAT-T
1 TATTTAATAT
* *
17031469 ATAATAAATAT
1 -TATTTAATAT
**
17031480 TATAAAGTATAT
1 TATTTA--ATAT
17031492 TATTTAATAT
1 TATTTAATAT
17031502 TATT
1 TATT
17031506 GTTTGAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
8 6 0.12
9 5 0.10
10 27 0.52
11 6 0.12
12 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (10 bp):
TATTTAATAT
Found at i:17031692 original size:44 final size:44
Alignment explanation
Indices: 17031571--17031715 Score: 132
Period size: 46 Copynumber: 3.2 Consensus size: 44
17031561 GAAGAATATA
**
17031571 TTTTACTTTTAATATTAAATATTATTTAATTATAATAAAAAGTT-T
1 TTTTA-TTTTAATAGAAAATATTATTTAATTATAATAAAAA-TTAT
** * * *
17031616 AATTAGTCTTTAATATAAAATGTTATTAAATTATAATAAAAATATAT
1 TTTTA-T-TTTAATAGAAAATATTATTTAATTATAATAAAAAT-TAT
* * *
17031663 TTTTATTTTGAT-GAAAATATTATTTAATTATAGTAAAAGTTAT
1 TTTTATTTTAATAGAAAATATTATTTAATTATAATAAAAATTAT
*
17031706 TTTGATTTTA
1 TTTTATTTTA
17031716 TTACTTAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
43 11 0.14
44 23 0.28
45 10 0.12
46 33 0.41
47 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (44 bp):
TTTTATTTTAATAGAAAATATTATTTAATTATAATAAAAATTAT
Found at i:17031752 original size:1 final size:1
Alignment explanation
Indices: 17031748--17031787 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
17031738 TTTATTTTTT
17031748 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17031788 TGTTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17031988 original size:33 final size:34
Alignment explanation
Indices: 17031946--17032014 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
17031936 TTATGAATCA
*
17031946 CTCTATATAATAATTATTTT-TTCTCTATTTTATT
1 CTCTATATAATAACTATTTTATTCTC-ATTTTATT
*
17031980 CTCT-TATAATGACTATTTTATTCTCATTTTATT
1 CTCTATATAATAACTATTTTATTCTCATTTTATT
17032013 CT
1 CT
17032015 TTTCAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 23 0.72
34 9 0.28
ACGTcount: A:0.25, C:0.14, G:0.01, T:0.59
Consensus pattern (34 bp):
CTCTATATAATAACTATTTTATTCTCATTTTATT
Found at i:17040947 original size:28 final size:29
Alignment explanation
Indices: 17040877--17040944 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
17040867 TAATTAAAAT
17040877 AATTTATTTAATTAAAAATAAAAATATAA
1 AATTTATTTAATTAAAAATAAAAATATAA
* * * *
17040906 AACTTGATTGAATT-AATA-AAAAATTTAA
1 AA-TTTATTTAATTAAAAATAAAAATATAA
17040934 AATTTATTTAA
1 AATTTATTTAA
17040945 ATTTTTGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.22
28 11 0.34
29 5 0.16
30 9 0.28
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
AATTTATTTAATTAAAAATAAAAATATAA
Found at i:17041162 original size:34 final size:33
Alignment explanation
Indices: 17041115--17041189 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 33
17041105 GTAGCTAACC
*
17041115 AGCCC-TTTTAATTATTCAAAAAAAAAAGTAAAT
1 AGCCCTTTTTAATTATACAAAAAAAAAA-TAAAT
* *
17041148 AGCCCTTTTTAATTATACCAAAAACAAATAAAT
1 AGCCCTTTTTAATTATACAAAAAAAAAATAAAT
*
17041181 AGGCCTTTT
1 AGCCCTTTT
17041190 AAGCCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 18 0.49
34 19 0.51
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (33 bp):
AGCCCTTTTTAATTATACAAAAAAAAAATAAAT
Found at i:17041171 original size:33 final size:34
Alignment explanation
Indices: 17041115--17041189 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
17041105 GTAGCTAACC
*
17041115 AGCCC-TTTTAATTATTCAAAAAAA-AAAGTAAAT
1 AGCCCTTTTTAATTATACAAAAAAACAAA-TAAAT
*
17041148 AGCCCTTTTTAATTATAC-CAAAAACAAATAAAT
1 AGCCCTTTTTAATTATACAAAAAAACAAATAAAT
*
17041181 AGGCCTTTT
1 AGCCCTTTT
17041190 AAGCCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (34 bp):
AGCCCTTTTTAATTATACAAAAAAACAAATAAAT
Found at i:17042766 original size:15 final size:16
Alignment explanation
Indices: 17042735--17042769 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17042725 ATAATTTTTG
*
17042735 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
17042751 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
17042766 AATT
1 AATT
17042770 CACATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:17042927 original size:13 final size:12
Alignment explanation
Indices: 17042897--17042935 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
17042887 GAGCAAATAG
*
17042897 AATATAATTAAA
1 AATATAAATAAA
17042909 AA-ATAAATAAA
1 AATATAAATAAA
17042920 TAATATAAATAAA
1 -AATATAAATAAA
17042933 AAT
1 AAT
17042936 TTTACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 8 0.33
12 7 0.29
13 9 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AATATAAATAAA
Found at i:17044660 original size:2 final size:2
Alignment explanation
Indices: 17044653--17044684 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17044643 GCGAGCTCTG
17044653 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
17044685 AAATGAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17045192 original size:15 final size:16
Alignment explanation
Indices: 17045158--17045208 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
17045148 TTTTGTATAA
17045158 AATAAAAATAAAAATG
1 AATAAAAATAAAAATG
17045174 AATAAAAGA-AAAAAT-
1 AATAAAA-ATAAAAATG
* *
17045189 AATATAAATAATAAT-
1 AATAAAAATAAAAATG
17045204 AATAA
1 AATAA
17045209 CCAAACTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 1 0.03
15 15 0.50
16 13 0.43
17 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (16 bp):
AATAAAAATAAAAATG
Found at i:17061102 original size:4 final size:4
Alignment explanation
Indices: 17061085--17061120 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
17061075 TTTATGAATT
*
17061085 TACA TACA TGCA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA
17061121 CACACACACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:17078046 original size:29 final size:28
Alignment explanation
Indices: 17077990--17078046 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
17077980 TATTGTAAAA
17077990 ATATTTAATAAATTTTTATTTTTATATT
1 ATATTTAATAAATTTTTATTTTTATATT
17078018 ATATTTAATTAAATTTTTATATTTT-TATT
1 ATATTTAA-TAAATTTTTAT-TTTTATATT
17078047 TCAAATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.30
29 15 0.56
30 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATATTTAATAAATTTTTATTTTTATATT
Found at i:17078109 original size:19 final size:18
Alignment explanation
Indices: 17078068--17078110 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
17078058 AAATTCTTAT
* *
17078068 AATTAATAATCAACTATC
1 AATTATTAATCAAATATC
*
17078086 TATTATTAATCAAAATATC
1 AATTATTAATC-AAATATC
17078105 AATTAT
1 AATTAT
17078111 CATTATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTATTAATCAAATATC
Found at i:17078263 original size:31 final size:31
Alignment explanation
Indices: 17078226--17078302 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
17078216 AATGATTAAT
**
17078226 CATAAAAATTTATTTAATGTAAA-ATAAAAA
1 CATAAAAATTTATTTAACATAAATATAAAAA
* *
17078256 TATTAAAATTTAATTTAACATAAATATAAAAA
1 CATAAAAATTT-ATTTAACATAAATATAAAAA
17078288 CA-AAAAA-TTATTTAA
1 CATAAAAATTTATTTAA
17078303 AATTTCTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 6 0.15
30 11 0.28
31 14 0.36
32 8 0.21
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (31 bp):
CATAAAAATTTATTTAACATAAATATAAAAA
Found at i:17079978 original size:108 final size:108
Alignment explanation
Indices: 17079866--17080074 Score: 310
Period size: 108 Copynumber: 1.9 Consensus size: 108
17079856 TATAAGAAAT
* * * *
17079866 TTTGAGTAAATTTAAATAAAAGGTAAATTGGGTAAAAGTTAAATAGTTTAAAAAAAATGTATGTT
1 TTTGAGTAAATTTAAATAAAAGATAAATTGGGTAAAAATTAAATAATTTAAAAAAAATGTATATT
*
17079931 TGTAAATTGTGAAAGTTGCAACTAAATGAACATATTCTGCTAA
66 TGTAAATTGTGAAAGTTGCAACTAAATCAACATATTCTGCTAA
* * * * * *
17079974 TTTGAGTAAATTTATATAAATGATAAATTGGGTAAAAATTGAATAATTTCAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAATAAAAGATAAATTGGGTAAAAATTAAATAATTTAAAAAAAATGTATATT
*
17080039 TGTAAATTGTGAAAGTTGTAACTAAATCAACATATT
66 TGTAAATTGTGAAAGTTGCAACTAAATCAACATATT
17080075 TGTCATTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAGATAAATTGGGTAAAAATTAAATAATTTAAAAAAAATGTATATT
TGTAAATTGTGAAAGTTGCAACTAAATCAACATATTCTGCTAA
Found at i:17080283 original size:16 final size:16
Alignment explanation
Indices: 17080256--17080289 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17080246 ATATATATAT
17080256 ATTTTTTAACACCATAA
1 ATTTTTTAACACC-TAA
17080273 ATTTTTT-ACACCTAA
1 ATTTTTTAACACCTAA
17080288 AT
1 AT
17080290 ATTTAGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTTTAACACCTAA
Found at i:17080293 original size:17 final size:18
Alignment explanation
Indices: 17080254--17080293 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
17080244 ATATATATAT
17080254 ATATTTTTTAACACCATA
1 ATATTTTTTAACACCATA
17080272 A-ATTTTTT-ACACC-TAA
1 ATATTTTTTAACACCAT-A
17080288 ATATTT
1 ATATTT
17080294 AGCTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.05
16 7 0.35
17 11 0.55
18 1 0.05
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTTTTAACACCATA
Found at i:17086298 original size:18 final size:19
Alignment explanation
Indices: 17086275--17086321 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
17086265 ATATAACTTG
17086275 AAATATTAAACAA-AA-TAA
1 AAATATTAAA-AATAAGTAA
17086293 AAATATTAAAAATAAGTAA
1 AAATATTAAAAATAAGTAA
17086312 AAA-ATTAAAA
1 AAATATTAAAA
17086322 GAGTAGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.07
18 19 0.70
19 6 0.22
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATATTAAAAATAAGTAA
Found at i:17098704 original size:14 final size:15
Alignment explanation
Indices: 17098685--17098725 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
17098675 AAAAACTTTG
17098685 ATTTTTTTA-AATTA
1 ATTTTTTTATAATTA
*
17098699 A-TTTTTTATTATTA
1 ATTTTTTTATAATTA
*
17098713 ATTTTTATATAAT
1 ATTTTTTTATAAT
17098726 ATCATCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTTTTATAATTA
Found at i:17098705 original size:13 final size:14
Alignment explanation
Indices: 17098687--17098725 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
17098677 AAACTTTGAT
17098687 TTTTTTA-AATTAA
1 TTTTTTATAATTAA
*
17098700 TTTTTTATTATTAA
1 TTTTTTATAATTAA
17098714 TTTTTATATAAT
1 TTTTT-TATAAT
17098726 ATCATCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
15 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTATAATTAA
Found at i:17098830 original size:22 final size:20
Alignment explanation
Indices: 17098784--17098944 Score: 66
Period size: 20 Copynumber: 8.4 Consensus size: 20
17098774 TTTTTATAAG
*
17098784 ATTAT-ATTTTTTATTTTTT
1 ATTATAATTTTTTATTTTAT
*
17098803 AATATAATTTTTTATATTATAT
1 ATTATAATTTTTTAT-TT-TAT
17098825 ATTATATTGTAATTTTTTA-TTTAT
1 A-T-TA---TAATTTTTTATTTTAT
** *
17098849 ATTATATAAATTTTAATTT-T
1 ATTATA-ATTTTTTATTTTAT
17098869 -TTAT-A--TTTTATTTTAT
1 ATTATAATTTTTTATTTTAT
*
17098885 -TT-TAATTTTTGATTTTTAT
1 ATTATAATTTTTTA-TTTTAT
*
17098904 ATTAT-ATATTTTA-TTT-T
1 ATTATAATTTTTTATTTTAT
17098921 A--AT-ATTTTTTATTTTA-
1 ATTATAATTTTTTATTTTAT
17098937 ATTATAAT
1 ATTATAAT
17098945 GTTATAAAAT
Statistics
Matches: 110, Mismatches: 10, Indels: 44
0.67 0.06 0.27
Matches are distributed among these distances:
15 18 0.16
16 8 0.07
17 3 0.03
18 9 0.08
19 18 0.16
20 24 0.22
21 6 0.05
22 5 0.05
23 1 0.01
24 6 0.05
25 2 0.02
27 10 0.09
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (20 bp):
ATTATAATTTTTTATTTTAT
Found at i:17098874 original size:48 final size:47
Alignment explanation
Indices: 17098789--17098880 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 47
17098779 ATAAGATTAT
* *
17098789 ATTTTTTATTTTTTAATATAATTTTTTATATTATATATTATATTGTA
1 ATTTTTTATTTTTTAATATAAATTTTAATATTATATATTATATTGTA
* * *
17098836 ATTTTTTATTTATATT-ATATAAATTTTAATTTTTTATATTTTATT
1 ATTTTTTATTT-T-TTAATATAAATTTTAATATTATATATTATATT
17098881 TTATTTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 11 0.29
48 25 0.66
49 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (47 bp):
ATTTTTTATTTTTTAATATAAATTTTAATATTATATATTATATTGTA
Found at i:17098919 original size:33 final size:32
Alignment explanation
Indices: 17098839--17098928 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 32
17098829 TATTGTAATT
*
17098839 TTTTATTTATATTATATAA-ATTTTAATTTTTTATA
1 TTTTATTT-TATT-T-TAATATTTTGA-TTTTTATA
17098874 TTTTATTTTATTTTAAT-TTTTGATTTTTATA
1 TTTTATTTTATTTTAATATTTTGATTTTTATA
17098905 TTATATATTTTATTTTAATATTTT
1 TT-T-TATTTTATTTTAATATTTT
17098929 TTATTTTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
31 10 0.20
32 9 0.18
33 15 0.30
34 8 0.16
35 8 0.16
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (32 bp):
TTTTATTTTATTTTAATATTTTGATTTTTATA
Found at i:17099843 original size:58 final size:58
Alignment explanation
Indices: 17099740--17099853 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
17099730 AAGAAATTTA
* * * * * *
17099740 TGGTTTTTAAGGTAGATATAGTTTCAAATTTTTAGGCTTTCAAATCAAAATATTTTTG
1 TGGTTTTTAAGGCAGATACAGTTTCAAAATTTCAGACCTTCAAATCAAAATATTTTTG
*
17099798 TGGTTTTTAAGGCAGATACAGTTTCAAAATTTCAGACCTTGAAATCAAAATATTTT
1 TGGTTTTTAAGGCAGATACAGTTTCAAAATTTCAGACCTTCAAATCAAAATATTTT
17099854 AGCTTTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (58 bp):
TGGTTTTTAAGGCAGATACAGTTTCAAAATTTCAGACCTTCAAATCAAAATATTTTTG
Found at i:17103437 original size:44 final size:43
Alignment explanation
Indices: 17103389--17103546 Score: 147
Period size: 46 Copynumber: 3.5 Consensus size: 43
17103379 TCAAAATACC
* * *
17103389 TTTTACTATAATTAAATAATATTTTCACCAAAATATAAATATAT
1 TTTTATTATAATTAAATAATATTTT-ACTAAAAGATAAATATAT
** * * * *
17103433 TTTTATTATAATTTCATAATATTTTGTAGTAGAAGATAATTAAACT
1 TTTTATTATAATTAAATAATA-TTT-TACTAAAAGATAAATATA-T
17103479 TTTTATTATAATTAAATAATATTTAATACTAAAAGATAAAATATAT
1 TTTTATTATAATTAAATAATATTT--TACTAAAAGAT-AAATATAT
17103525 TCTTTATTA-AATTTAAATAATA
1 T-TTTATTATAA-TTAAATAATA
17103547 CTATAAAATA
Statistics
Matches: 91, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
44 18 0.20
45 17 0.19
46 34 0.37
47 22 0.24
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (43 bp):
TTTTATTATAATTAAATAATATTTTACTAAAAGATAAATATAT
Found at i:17103554 original size:35 final size:35
Alignment explanation
Indices: 17103514--17103581 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
17103504 ATACTAAAAG
17103514 ATAAAATATATTCTTTATTAAATTTAAATAATACT
1 ATAAAATATATTCTTTATTAAATTTAAATAATACT
17103549 ATAAAATATATTCTTTATTAAATTTAAATAATA
1 ATAAAATATATTCTTTATTAAATTTAAATAATA
17103582 TTAAATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (35 bp):
ATAAAATATATTCTTTATTAAATTTAAATAATACT
Found at i:17103587 original size:10 final size:10
Alignment explanation
Indices: 17103572--17103649 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 10
17103562 TTTATTAAAT
17103572 TTAAATAATA
1 TTAAATAATA
17103582 TTAAATAATA
1 TTAAATAATA
**
17103592 TTTTTTATAATA
1 --TTAAATAATA
* *
17103604 TT-TATTATAA
1 TTAAATAAT-A
17103614 TTAAATAATA
1 TTAAATAATA
17103624 -TAAAT-ATA
1 TTAAATAATA
*
17103632 TTAAATGATA
1 TTAAATAATA
17103642 TTTAAATA
1 -TTAAATA
17103650 TTTCCATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 3 0.05
9 15 0.27
10 19 0.35
11 10 0.18
12 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (10 bp):
TTAAATAATA
Found at i:17103592 original size:35 final size:35
Alignment explanation
Indices: 17103518--17103625 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 35
17103508 TAAAAGATAA
*
17103518 AATATATTCTTTATTAAATTTAAATAATACTATAA-
1 AATATATTCTTTATTAAATTTAAATAATATTA-AAT
17103553 AATATATTCTTTATTAAATTTAAATAATATTAAAT
1 AATATATTCTTTATTAAATTTAAATAATATTAAAT
*
17103588 AATAT-TT-TTTA-TAATATTT--ATTATAATTAAAT
1 AATATATTCTTTATTAA-ATTTAAATAAT-ATTAAAT
17103620 AATATA
1 AATATA
17103626 AATATATTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
31 4 0.06
32 15 0.22
33 8 0.12
34 4 0.06
35 36 0.54
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
AATATATTCTTTATTAAATTTAAATAATATTAAAT
Found at i:17104345 original size:29 final size:28
Alignment explanation
Indices: 17104313--17104367 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
17104303 TAATCAAGTT
* *
17104313 TTTTTACTTTTATTTTTAGTCAAATAAGC
1 TTTTT-CTTTTATTTTGAATCAAATAAGC
*
17104342 TTTTTTTTTTATTTTGAATCAAATAA
1 TTTTTCTTTTATTTTGAATCAAATAA
17104368 ATCCTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTTCTTTTATTTTGAATCAAATAAGC
Found at i:17105143 original size:111 final size:111
Alignment explanation
Indices: 17105004--17105227 Score: 412
Period size: 111 Copynumber: 2.0 Consensus size: 111
17104994 TAGAGTTAAT
*
17105004 TTATGAAAGCTCCAATACTTAAAACACAACATAAAGTAATTAAAATATTAACACAGATGCTAGCT
1 TTATGAAAGCTCCAATACTTAAAACACAACATAAAGCAATTAAAATATTAACACAGATGCTAGCT
17105069 TTAAAATGTTTATAGTTTTGATTATGACAAAATGATCATAATTTGC
66 TTAAAATGTTTATAGTTTTGATTATGACAAAATGATCATAATTTGC
* *
17105115 TTATGAAAGCTCCAATACTTAAAACACAACATAAAGCAATTAGAATATTGACACAGATGCTAGCT
1 TTATGAAAGCTCCAATACTTAAAACACAACATAAAGCAATTAAAATATTAACACAGATGCTAGCT
*
17105180 TTAAAATGTTTATAGTTTTGATTATGACAAAATGATCCTAATTTGC
66 TTAAAATGTTTATAGTTTTGATTATGACAAAATGATCATAATTTGC
17105226 TT
1 TT
17105228 GAATATTATT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (111 bp):
TTATGAAAGCTCCAATACTTAAAACACAACATAAAGCAATTAAAATATTAACACAGATGCTAGCT
TTAAAATGTTTATAGTTTTGATTATGACAAAATGATCATAATTTGC
Found at i:17108227 original size:21 final size:24
Alignment explanation
Indices: 17108177--17108232 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
17108167 ACAAAATCGT
17108177 AACCCTAAATCCCTAATTTATTACCA
1 AACCCTAAATCCCTAA-TTATTA-CA
17108203 AACCCTAAATCCCTAA-T-TT-CA
1 AACCCTAAATCCCTAATTATTACA
17108224 AACCCTAAA
1 AACCCTAAA
17108233 CCTGAAACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.37
23 2 0.07
24 1 0.03
26 16 0.53
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (24 bp):
AACCCTAAATCCCTAATTATTACA
Found at i:17112240 original size:15 final size:15
Alignment explanation
Indices: 17112220--17112249 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17112210 TACTAGAGGA
17112220 ATGAAAAAGGACAAG
1 ATGAAAAAGGACAAG
17112235 ATGAAAAAGGACAAG
1 ATGAAAAAGGACAAG
17112250 GATAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.27, T:0.07
Consensus pattern (15 bp):
ATGAAAAAGGACAAG
Found at i:17127579 original size:153 final size:153
Alignment explanation
Indices: 17127299--17127602 Score: 509
Period size: 153 Copynumber: 2.0 Consensus size: 153
17127289 CCGTTGGCGC
* * *
17127299 TTGCTTCGTTGAAGGTGGTGGACTAGACTTACCTTTACCTTCATTACCTAAGTCCACTTTATAGC
1 TTGCTTCGTTGAAGGTGGTGGACTAGACTAACCTTTACCTTCATTACCTAAATCCACTTTATAAC
* * * *
17127364 AACTATTTATATAGGGATACTGAGTTGCATTGAACAAATTAAATACCATTTCCTTCTTTCCAGCT
66 AACTATCTATATAGGGATACTGAGTTACATTGAACAAATTAAATACCACTTCCTTCTCTCCAGCT
17127429 CTAAAAGTTATTTTGCCATTCGT
131 CTAAAAGTTATTTTGCCATTCGT
* *
17127452 TTGCTTCGTTGAAGGTGGTGGACTAGACTAACCTTTACCTTTATTACGTAAATCCACTTTATAAC
1 TTGCTTCGTTGAAGGTGGTGGACTAGACTAACCTTTACCTTCATTACCTAAATCCACTTTATAAC
*
17127517 AACTATCTGTATAGGGATACTGAGTTACATTGAACAAATTAAATACCACTTCCTTCTCTCCAGCT
66 AACTATCTATATAGGGATACTGAGTTACATTGAACAAATTAAATACCACTTCCTTCTCTCCAGCT
*
17127582 CTGAAAGTTATTTTGCCATTC
131 CTAAAAGTTATTTTGCCATTC
17127603 TTCGCATCAA
Statistics
Matches: 140, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
153 140 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (153 bp):
TTGCTTCGTTGAAGGTGGTGGACTAGACTAACCTTTACCTTCATTACCTAAATCCACTTTATAAC
AACTATCTATATAGGGATACTGAGTTACATTGAACAAATTAAATACCACTTCCTTCTCTCCAGCT
CTAAAAGTTATTTTGCCATTCGT
Found at i:17128547 original size:21 final size:21
Alignment explanation
Indices: 17128497--17128549 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
17128487 GCATTAGTCC
* **
17128497 TTGTCATAAATGCATCGGTCT
1 TTGTCATGAATGCATCAATCT
*
17128518 TTGTTATGAATGCATCAATCT
1 TTGTCATGAATGCATCAATCT
17128539 TTGTCATGAAT
1 TTGTCATGAAT
17128550 TACATGATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGTCATGAATGCATCAATCT
Found at i:17130640 original size:23 final size:23
Alignment explanation
Indices: 17130607--17130666 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
17130597 GGGCTCTTTG
* * * *
17130607 CATGGCGTGTCATAGATTCTCAC
1 CATGGCATGTCACACATTCCCAC
17130630 CATGGCATGTCACACATTCCCAC
1 CATGGCATGTCACACATTCCCAC
17130653 CATGGCATGTCACA
1 CATGGCATGTCACA
17130667 AACTCTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (23 bp):
CATGGCATGTCACACATTCCCAC
Found at i:17130746 original size:23 final size:23
Alignment explanation
Indices: 17130691--17130752 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
17130681 CCGTGTGACA
* *
17130691 GTTGTGTCATATATTCTCACCGT
1 GTTGTGTCACACATTCTCACCGT
** * *
17130714 GCCGTCTCACACATTCTCACCTT
1 GTTGTGTCACACATTCTCACCGT
*
17130737 GTTGTGTCACAGATTC
1 GTTGTGTCACACATTC
17130753 CCTCTATGGC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (23 bp):
GTTGTGTCACACATTCTCACCGT
Found at i:17130865 original size:23 final size:23
Alignment explanation
Indices: 17130808--17130972 Score: 115
Period size: 23 Copynumber: 7.3 Consensus size: 23
17130798 GTGTCACAAC
* *
17130808 CGTGTCACATATGCTCACCATGT
1 CGTGTCACATATTCTCACCATGG
* *
17130831 CGTCTTACATATTCTCACCATGG
1 CGTGTCACATATTCTCACCATGG
* *
17130854 CGTGTCATATATTCACACCATGG
1 CGTGTCACATATTCTCACCATGG
* *
17130877 CATGTCAC--ATTCTCA-CACTAG
1 CGTGTCACATATTCTCACCA-TGG
* *
17130898 CGTGTCACATATTCTCATCATGT
1 CGTGTCACATATTCTCACCATGG
* * * * *
17130921 C--ATCTCATATTCTCTCCAAGC
1 CGTGTCACATATTCTCACCATGG
* * *
17130942 CATGTCACATATTCCCTCCATGG
1 CGTGTCACATATTCTCACCATGG
*
17130965 TGTGTCAC
1 CGTGTCAC
17130973 CAACTCTAAA
Statistics
Matches: 108, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.02
21 30 0.28
23 74 0.69
24 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (23 bp):
CGTGTCACATATTCTCACCATGG
Found at i:17130948 original size:44 final size:43
Alignment explanation
Indices: 17130808--17130955 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 43
17130798 GTGTCACAAC
* * *
17130808 CGTGTCACATATGCTCACCATGTCGTCTTACATATTCTCACCATGG
1 CGTGTCACATATTCTCACCATGTCATC-T-CATATTCTCACCA-AG
* * * * * *
17130854 CGTGTCATATATTCACACCATGGCATGTCACATTCTCACACTAG
1 CGTGTCACATATTCTCACCATGTCATCTCATATTCTCAC-CAAG
* *
17130898 CGTGTCACATATTCTCATCATGTCATCTCATATTCTCTCCAAG
1 CGTGTCACATATTCTCACCATGTCATCTCATATTCTCACCAAG
*
17130941 CCATGTCACATATTC
1 -CGTGTCACATATTC
17130956 CCTCCATGGT
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
43 3 0.04
44 56 0.68
45 2 0.02
46 21 0.26
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (43 bp):
CGTGTCACATATTCTCACCATGTCATCTCATATTCTCACCAAG
Found at i:17131077 original size:23 final size:23
Alignment explanation
Indices: 17131000--17131067 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
17130990 GTGTCACAAC
* *
17131000 CGTGTCACATATTCTCACCATGA
1 CGTGTCACACATTCCCACCATGA
*
17131023 CGTGTCACACATTCCCACCATGT
1 CGTGTCACACATTCCCACCATGA
17131046 CGTGTCACACATTCCCACCATG
1 CGTGTCACACATTCCCACCATG
17131068 GCATTTCACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.24, C:0.37, G:0.13, T:0.26
Consensus pattern (23 bp):
CGTGTCACACATTCCCACCATGA
Found at i:17132417 original size:29 final size:29
Alignment explanation
Indices: 17132356--17132419 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
17132346 TCGACAAGCA
* *
17132356 AAAATAAAAATCGACTGATAATAAGATTT
1 AAAATAAAAATCGACTAATAATAAGATTG
* *
17132385 AAAATAAGAAATTGACTAATTATAA-ATTG
1 AAAATAA-AAATCGACTAATAATAAGATTG
17132414 AAAATA
1 AAAATA
17132420 TGAGTAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (29 bp):
AAAATAAAAATCGACTAATAATAAGATTG
Found at i:17137493 original size:2 final size:2
Alignment explanation
Indices: 17137486--17137519 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
17137476 ATTTATCTAC
17137486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
17137520 CAATAGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17144942 original size:123 final size:123
Alignment explanation
Indices: 17144723--17144967 Score: 447
Period size: 123 Copynumber: 2.0 Consensus size: 123
17144713 ACCTGTGTGT
*
17144723 GTAGGGTCAATAATAGTAGTTGATTTTTATTTATAATATTCTTTTACTTTTAATATACCAAAATA
1 GTAGGGTCAATAATAGTAGTTGATTTTTATTTATAACATTCTTTTACTTTTAATATACCAAAATA
*
17144788 TAATGCAACTTTCAAATAAAAATATTTATTTTACAATTTATCCATAATGAAAATTAGA
66 TAATGCAACTTTCAAACAAAAATATTTATTTTACAATTTATCCATAATGAAAATTAGA
17144846 GTAGGGTCAATAATAGTAGTAT-ATTTTTATTTATAACATTCTTTTACTTTTAATATACCAAAAT
1 GTAGGGTCAATAATAGTAGT-TGATTTTTATTTATAACATTCTTTTACTTTTAATATACCAAAAT
*
17144910 ATAATGCAACTTTCCAACAAAAATATTTATTTTACAATTTATCCATAATGAAAATTAG
65 ATAATGCAACTTTCAAACAAAAATATTTATTTTACAATTTATCCATAATGAAAATTAG
17144968 CTCATAATCG
Statistics
Matches: 118, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
123 117 0.99
124 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (123 bp):
GTAGGGTCAATAATAGTAGTTGATTTTTATTTATAACATTCTTTTACTTTTAATATACCAAAATA
TAATGCAACTTTCAAACAAAAATATTTATTTTACAATTTATCCATAATGAAAATTAGA
Found at i:17146408 original size:29 final size:29
Alignment explanation
Indices: 17146362--17146437 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
17146352 GGTAATAGAA
17146362 AAGAAG-TGTACAAGAATAGGTACAAGAG
1 AAGAAGCTGTACAAGAATAGGTACAAGAG
*
17146390 AAGAAGCTGTACGAGAATAGGTACAAGAG
1 AAGAAGCTGTACAAGAATAGGTACAAGAG
* *
17146419 AATAAGCTGTACATGAATA
1 AAGAAGCTGTACAAGAATA
17146438 AGTATACGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 6 0.14
29 37 0.86
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.17
Consensus pattern (29 bp):
AAGAAGCTGTACAAGAATAGGTACAAGAG
Found at i:17146451 original size:29 final size:29
Alignment explanation
Indices: 17146358--17146453 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
17146348 TAAAGGTAAT
* * *
17146358 AGAAAAGAAG-TGTACAAGAATAGGTACA
1 AGAAAATAAGCTGTACGAGAATAAGTACA
* * *
17146386 AGAGAAGAAGCTGTACGAGAATAGGTACA
1 AGAAAATAAGCTGTACGAGAATAAGTACA
* *
17146415 AGAGAATAAGCTGTAC-ATGAATAAGTATA
1 AGAAAATAAGCTGTACGA-GAATAAGTACA
*
17146444 CGAAAATAAG
1 AGAAAATAAG
17146454 GTAAGAGGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 10 0.17
29 49 0.83
ACGTcount: A:0.50, C:0.08, G:0.25, T:0.17
Consensus pattern (29 bp):
AGAAAATAAGCTGTACGAGAATAAGTACA
Found at i:17146728 original size:35 final size:35
Alignment explanation
Indices: 17146689--17146867 Score: 196
Period size: 35 Copynumber: 5.4 Consensus size: 35
17146679 GTTCTATTTA
* *
17146689 TTCTAGTTATTCTGCCTTAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
17146724 TTCTAGTTGTTCTGCGTGAAGTAGCGCTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
*
17146759 TTC----TA-----CGTGAAGTAGCGCTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
17146785 TTCTACTTATTCTACGTGAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
17146820 TTTTACTTATTCTGCGTGAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
17146855 TTCTGGTTGTTCT
1 TTCTAGTTATTCT
17146868 CTGTACAACA
Statistics
Matches: 123, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
26 24 0.20
30 2 0.02
31 1 0.01
35 96 0.78
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (35 bp):
TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
Found at i:17146767 original size:26 final size:26
Alignment explanation
Indices: 17146730--17146790 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
17146720 CTTGTTCTAG
*
17146730 TTGTTCTGCGTGAAGTAGCGCTTCAC
1 TTGTTCTACGTGAAGTAGCGCTTCAC
17146756 TTGTTCTACGTGAAGTAGCGCTTCAC
1 TTGTTCTACGTGAAGTAGCGCTTCAC
17146782 TTGTTCTAC
1 TTGTTCTAC
17146791 TTATTCTACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TTGTTCTACGTGAAGTAGCGCTTCAC
Found at i:17146782 original size:61 final size:61
Alignment explanation
Indices: 17146707--17146821 Score: 185
Period size: 61 Copynumber: 1.9 Consensus size: 61
17146697 ATTCTGCCTT
* * * *
17146707 AAGTAGCACTTCACTTGTTCTAGTTGTTCTGCGTGAAGTAGCGCTTCACTTGTTCTACGTG
1 AAGTAGCACTTCACTTGTTCTACTTATTCTACGTGAAGTAGCACTTCACTTGTTCTACGTG
*
17146768 AAGTAGCGCTTCACTTGTTCTACTTATTCTACGTGAAGTAGCACTTCACTTGTT
1 AAGTAGCACTTCACTTGTTCTACTTATTCTACGTGAAGTAGCACTTCACTTGTT
17146822 TTACTTATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (61 bp):
AAGTAGCACTTCACTTGTTCTACTTATTCTACGTGAAGTAGCACTTCACTTGTTCTACGTG
Found at i:17147283 original size:40 final size:40
Alignment explanation
Indices: 17147157--17147287 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 40
17147147 TTGTAATGTC
17147157 AATATCTTTTGTAATATTTGATTGATTATGCAATAATATTT
1 AATATC-TTTGTAATATTTGATTGATTATGCAATAATATTT
* * **** *
17147198 AATGTCTTTCGTAATATTTGATTGCATTTTTTTTTAAT-TTC
1 AATATCTTT-GTAATATTTGATTG-ATTATGCAATAATATTT
*
17147239 AATATCTTTGTAATATTTTATTGATTATGCAATAATATTT
1 AATATCTTTGTAATATTTGATTGATTATGCAATAATATTT
17147279 AATATCTTT
1 AATATCTTT
17147288 TTCATAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
39 8 0.11
40 27 0.38
41 29 0.40
42 8 0.11
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (40 bp):
AATATCTTTGTAATATTTGATTGATTATGCAATAATATTT
Found at i:17148232 original size:29 final size:29
Alignment explanation
Indices: 17148194--17148263 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
17148184 AGAAAAGAGG
17148194 TGTACAAGAATAGGTACAAGAGAAGAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
* *
17148223 TGTACGAGAATAGGTACAAGAGAATAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
*
17148252 TGTACATGAATA
1 TGTACAAGAATA
17148264 AGTATACGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.19
Consensus pattern (29 bp):
TGTACAAGAATAGGTACAAGAGAAGAAGC
Found at i:17148572 original size:26 final size:26
Alignment explanation
Indices: 17148543--17148593 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
17148533 AAGTAGTACT
17148543 TGAAGTAGCGCTTCACTTATTCTGCG
1 TGAAGTAGCGCTTCACTTATTCTGCG
*
17148569 TGAAGTAGCGCTTCACTTGTTCTGC
1 TGAAGTAGCGCTTCACTTATTCTGC
17148594 ATTATAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (26 bp):
TGAAGTAGCGCTTCACTTATTCTGCG
Found at i:17152531 original size:102 final size:102
Alignment explanation
Indices: 17152383--17152654 Score: 328
Period size: 102 Copynumber: 2.7 Consensus size: 102
17152373 GAAATGAGCT
* * * * *
17152383 ATAAAGCTTGCGGCCAATAGCATAACATCATTACAGCCAAATTATGAGCGATAAAGCTAGTGGCT
1 ATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGCT
** * * *
17152448 GAAATGTGAATAATAAATTGTGGTCAAAGAATAAGCG
66 GAAATAAGAATAATAAACTATGGTAAAAGAATAAGCG
* * * * * *
17152485 ATAAAGCTTGCGACCAAAAGAAGAATATCATTGCAGCCAAAATATGAGTGGTAAAGCTTGCGGCT
1 ATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGCT
* * *
17152550 GAAGTAAGAATGATGAACTATGGTAAAAGAATAAGCG
66 GAAATAAGAATAATAAACTATGGTAAAAGAATAAGCG
* * * * *
17152587 ATAAAGCTTGCTACCAATAGTATAATATAATTACAGCCAAAATATAAGCGATAAAGCTAGCGGTT
1 ATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGCT
17152652 GAA
66 GAA
17152655 TATGAATTTT
Statistics
Matches: 140, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
102 140 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (102 bp):
ATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGCT
GAAATAAGAATAATAAACTATGGTAAAAGAATAAGCG
Found at i:17153976 original size:29 final size:29
Alignment explanation
Indices: 17153938--17154007 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
17153928 AGAAAAGAAG
17153938 TGTACAAGAATAGGTACAAGAGAAAAAGC
1 TGTACAAGAATAGGTACAAGAGAAAAAGC
* * *
17153967 TGTACGAGAATAGGTACAAGGGAATAAGC
1 TGTACAAGAATAGGTACAAGAGAAAAAGC
*
17153996 TGTACATGAATA
1 TGTACAAGAATA
17154008 AGTATACGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.19
Consensus pattern (29 bp):
TGTACAAGAATAGGTACAAGAGAAAAAGC
Found at i:17154020 original size:29 final size:28
Alignment explanation
Indices: 17153938--17154023 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
17153928 AGAAAAGAAG
*
17153938 TGTACAAGAATAGGTACAAGAGAAAAAGC
1 TGTAC-AGAATAGGTACAAGAGAATAAGC
*
17153967 TGTACGAGAATAGGTACAAGGGAATAAGC
1 TGTAC-AGAATAGGTACAAGAGAATAAGC
* * *
17153996 TGTACATGAATAAGTATACGAGAATAAG
1 TGTACA-GAATAGGTACAAGAGAATAAG
17154024 GTAAGAGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 1 0.02
29 48 0.98
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (28 bp):
TGTACAGAATAGGTACAAGAGAATAAGC
Found at i:17154298 original size:35 final size:35
Alignment explanation
Indices: 17154259--17154411 Score: 189
Period size: 35 Copynumber: 4.4 Consensus size: 35
17154249 GTTCTATTTA
* * *
17154259 TTCTAGTTATTCTACCTTAAGTAGCAGTTCACTTG
1 TTCTAGTTATTCTACGTGAAGTAGCACTTCACTTG
* *
17154294 TTCTAGTTGTTCTACGTGAAGTAGCGCTTCACTTG
1 TTCTAGTTATTCTACGTGAAGTAGCACTTCACTTG
*
17154329 TTCTACTTATTCTACGTGAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTACGTGAAGTAGCACTTCACTTG
* * ** *
17154364 TTTTACTTATTCGGCATGAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTACGTGAAGTAGCACTTCACTTG
* *
17154399 TTCTGGTTGTTCT
1 TTCTAGTTATTCT
17154412 CTGTACAACA
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 101 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (35 bp):
TTCTAGTTATTCTACGTGAAGTAGCACTTCACTTG
Found at i:17163612 original size:98 final size:97
Alignment explanation
Indices: 17163439--17163623 Score: 334
Period size: 98 Copynumber: 1.9 Consensus size: 97
17163429 AGTCTGTGTC
*
17163439 TGTTATGTTTGATAACAACAGTATGCAACAGTAACATCGTAGTGATTTCTGAAGAGAGAAAATGC
1 TGTTATGTTTGATAACAACAGTATGAAACAGTAACATCGTAGTGATTTCTGAAGAGAGAAAATGC
*
17163504 TTGACTTGGTAATGATTTACCAAAAATGTTAA
66 TTCACTTGGTAATGATTTACCAAAAATGTTAA
*
17163536 TGTTGTGTTTGATAACAACAGTATGGAAACAGTAACATCGTAGTGATTTCTGAAGAGAGAAAATG
1 TGTTATGTTTGATAACAACAGTAT-GAAACAGTAACATCGTAGTGATTTCTGAAGAGAGAAAATG
17163601 CTTCACTTGGTAATGATTTACCA
65 CTTCACTTGGTAATGATTTACCA
17163624 CAGAAGTTGA
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
97 23 0.27
98 61 0.73
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (97 bp):
TGTTATGTTTGATAACAACAGTATGAAACAGTAACATCGTAGTGATTTCTGAAGAGAGAAAATGC
TTCACTTGGTAATGATTTACCAAAAATGTTAA
Found at i:17168568 original size:4 final size:4
Alignment explanation
Indices: 17168561--17168598 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
17168551 GATTTATTTA
17168561 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
17168599 ATATGAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:17169463 original size:2 final size:2
Alignment explanation
Indices: 17169452--17169485 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
17169442 ATTTTCAGTT
*
17169452 TA TA TA -A TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17169486 TTCTGGCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17169478 original size:12 final size:12
Alignment explanation
Indices: 17169450--17169487 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
17169440 GTATTTTCAG
17169450 TTTATATA-ATA
1 TTTATATATATA
*
17169461 TATATATATATA
1 TTTATATATATA
17169473 TTTATATATATA
1 TTTATATATATA
17169485 TTT
1 TTT
17169488 CTGGCTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTATATATATA
Found at i:17170166 original size:2 final size:2
Alignment explanation
Indices: 17170159--17170183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17170149 ATAGAGTAAC
17170159 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
17170184 GTAAGAATAA
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:17171755 original size:3 final size:3
Alignment explanation
Indices: 17171739--17171775 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
17171729 TCTTGCTCTT
17171739 TTA TTA TT- TATA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
17171776 ATTTGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17179982 original size:13 final size:14
Alignment explanation
Indices: 17179959--17179987 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17179949 ATTGACTTAT
17179959 TTATATATTTATCA
1 TTATATATTTATCA
17179973 TTAT-TATTTATCA
1 TTATATATTTATCA
17179986 TT
1 TT
17179988 TTTTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATATTTATCA
Found at i:17180215 original size:3 final size:3
Alignment explanation
Indices: 17180207--17180241 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
17180197 TGTATCATGA
17180207 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17180242 TGCAAGTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:17181414 original size:18 final size:17
Alignment explanation
Indices: 17181391--17181434 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
17181381 TTCCTCTTTT
17181391 TTTTA-TTTATATATAATA
1 TTTTATTTTAT-TAT-ATA
*
17181409 TTTTATTTTATTATATT
1 TTTTATTTTATTATATA
17181426 TTTTATTTT
1 TTTTATTTT
17181435 TTTGAGGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 8 0.33
19 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTATTATATA
Found at i:17181650 original size:51 final size:51
Alignment explanation
Indices: 17181594--17181786 Score: 179
Period size: 51 Copynumber: 3.6 Consensus size: 51
17181584 AACAAAAATG
* *
17181594 AAATTTCTAGACTTGATCTAGGCTTGACCCATATTAGAACAAATTCGATTA
1 AAATTTCTAGACTTAATCTAGGCTCGACCCATATTAGAACAAATTCGATTA
* * * * * **
17181645 AAATTTCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAA
1 AAATTTCTAGACTTAATCTAGGCTCGACCCATATTAGAACAAATTCGA-TT-------A
* *
17181704 TTGAAATTTCTAGACTTCATCTAGGCTTGACCCATATTAGAACAAATTCGATTA
1 ---AAATTTCTAGACTTAATCTAGGCTCGACCCATATTAGAACAAATTCGATTA
*
17181758 AAATTTCTAGACTTAATCTTGGCTCGACC
1 AAATTTCTAGACTTAATCTAGGCTCGACC
17181787 TATCTCACAA
Statistics
Matches: 110, Mismatches: 21, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
51 65 0.59
52 2 0.02
54 1 0.01
59 1 0.01
61 2 0.02
62 39 0.35
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (51 bp):
AAATTTCTAGACTTAATCTAGGCTCGACCCATATTAGAACAAATTCGATTA
Found at i:17181711 original size:62 final size:59
Alignment explanation
Indices: 17181645--17182228 Score: 727
Period size: 59 Copynumber: 9.9 Consensus size: 59
17181635 AATTCGATTA
* *
17181645 AAATTTCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT--A-AAAATTG
* * * * * * * **
17181707 AAATTTCTAGACTTCATCTAGGCTTGACCCATATTAGAACAAATTCGA-TT-AAAA-T-
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
* *
17181762 ---TT-CTAGACTTAATCTTGGCTCGACCTATCTCACAACAAGTTCGATTTAAACAAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT--A-AAAATTG
* * * *
17181820 AAATTCCTAAATTTAATTTAGGCTCGACCTATCTCACAACAGGTTCAATTT-AAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
* * *
17181878 AAATTCCTAGACTTAATCTAGGCTTGATCTATCTCACAACAGGTTCGATTTAAAAAAAATTA
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT---AAAAATTG
* * **
17181940 AAATTCCTAAACTTAATTTAGATTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
*
17181999 AAATTCCTAGACTTAATCTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
* * *
17182058 AAATTCTTAGACTTAATCTAGGCTTGACCTATCTCACAACAGGTTTGATTTAAAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
* ***
17182117 AAATTCCTAGACATAATCTAGGCTCGACCTATCTTGTAACAGGTTCGATTTAAAAATTG
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
*
17182176 AAATTCCTAGACTTAATATAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
1 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
17182229 TTCTTTAATG
Statistics
Matches: 451, Mismatches: 56, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
51 34 0.08
52 4 0.01
56 5 0.01
57 5 0.01
58 52 0.12
59 218 0.48
61 4 0.01
62 129 0.29
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
AAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTG
Found at i:17181751 original size:113 final size:117
Alignment explanation
Indices: 17181553--17182228 Score: 646
Period size: 113 Copynumber: 5.8 Consensus size: 117
17181543 ATCGATTTAA
* * * * * *
17181553 GCTCGACTTATCTCAAAATAAGTTCGATTTAAACAAAAATGAAATTTCTAGACTTGATCTAGGCT
1 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTAATCTAGGCT
* * *
17181618 TGACCCATATTAGAACAAATTCGA-TTAAAA-T-TT-CTAAACTTAATCTAG
66 TGACCCATATCACAACAAATTCGATTTAAAATTATTCCTAGACTTAATCTAG
*
17181666 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTCATCTAGGCT
1 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTAATCTAGGCT
* * *
17181731 TGACCCATATTAGAACAAATTCGA-TTAAAA-T-TT-CTAGACTTAATCTTG
66 TGACCCATATCACAACAAATTCGATTTAAAATTATTCCTAGACTTAATCTAG
* * * * *
17181779 GCTCGACCTATCTCACAACAAGTTCGATTTAAACAAAATTGAAATTCCTAAATTTAATTTAGGCT
1 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTAATCTAGGCT
* * * ** *
17181844 CGACCTATCTCACAACAGGTTCAATTTAAAATTGAAATTCCTAGACTTAATCTAG
66 TGACCCATATCACAACAAATTCGATTTAAAATT---ATTCCTAGACTTAATCTAG
* * * * * * * *
17181899 GCTTGATCTATCTCACAACAGGTTCGATTTAAAAAAAATTAAAATTCCTAAACTTAATTTA-GAT
1 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTAATCTAGGCT
* * **
17181963 TCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGACTTAATCTAG
66 T-GACCCATATCACAACAAATTCGATTT-AAAATT---ATTCCTAGACTTAATCTAG
*
17182020 GTTCGACCTATCTCACAACAGGTTCGATTT--A-AAAATTGAAA-TTCTTAGACTTAATCTAGGC
1 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTC-TAGACTTAATCTAGGC
* * ** * *
17182081 TTGACCTATCTCACAACAGGTTTGATTTAAAAATTGAAATTCCTAGACATAATCTAG
65 TTGACCCATATCACAACAAATTCGATTT-AAAATT---ATTCCTAGACTTAATCTAG
*** * *
17182138 GCTCGACCTATCTTGTAACAGGTTCGATTT--A-AAAATTGAAATTCCTAGACTTAATATAGGCT
1 GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTAATCTAGGCT
* * * **
17182200 CGACCTATCTCACAACAGGTTCGATTTAA
66 TGACCCATATCACAACAAATTCGATTTAA
17182229 TTCTTTAATG
Statistics
Matches: 501, Mismatches: 50, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
113 180 0.36
114 6 0.01
115 1 0.00
117 4 0.01
118 151 0.30
119 10 0.02
120 94 0.19
121 55 0.11
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (117 bp):
GCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAATTGAAATTTCTAGACTTAATCTAGGCT
TGACCCATATCACAACAAATTCGATTTAAAATTATTCCTAGACTTAATCTAG
Found at i:17181799 original size:51 final size:51
Alignment explanation
Indices: 17181707--17181807 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
17181697 AACAAAATTG
* * * *
17181707 AAATTTCTAGACTTCATCTAGGCTTGACCCATATTAGAACAAATTCGATTA
1 AAATTTCTAGACTTAATCTAGGCTCGACCCATATCACAACAAATTCGATTA
* * * *
17181758 AAATTTCTAGACTTAATCTTGGCTCGACCTATCTCACAACAAGTTCGATT
1 AAATTTCTAGACTTAATCTAGGCTCGACCCATATCACAACAAATTCGATT
17181808 TAAACAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (51 bp):
AAATTTCTAGACTTAATCTAGGCTCGACCCATATCACAACAAATTCGATTA
Found at i:17190717 original size:13 final size:14
Alignment explanation
Indices: 17190694--17190722 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17190684 ATCGATTTAT
17190694 TTATATATTTATCA
1 TTATATATTTATCA
17190708 TTAT-TATTTATCA
1 TTATATATTTATCA
17190721 TT
1 TT
17190723 TTTTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATATTTATCA
Found at i:17192120 original size:3 final size:3
Alignment explanation
Indices: 17192112--17192139 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17192102 GCATATTCCT
17192112 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17192140 ATATACTATT
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:17197268 original size:2 final size:2
Alignment explanation
Indices: 17197261--17197318 Score: 59
Period size: 2 Copynumber: 30.0 Consensus size: 2
17197251 AAAATTGTTC
* * *
17197261 AT AT AT AT AT AT AT AT AT AC GT AT AT ACT AT AC AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
17197303 AT AT A- AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
17197319 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 3 0.07
2 41 0.89
3 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17197323 original size:2 final size:2
Alignment explanation
Indices: 17197318--17197348 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17197308 ATTATATATA
*
17197318 TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17197349 TTACATAAAA
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:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17199270 original size:2 final size:2
Alignment explanation
Indices: 17199263--17199294 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17199253 TTCTTCTTCT
17199263 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17199295 ACACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17201270 original size:6 final size:7
Alignment explanation
Indices: 17201245--17201269 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17201235 CGTGTTTTTT
17201245 AAAAAGA
1 AAAAAGA
17201252 AAAAAGA
1 AAAAAGA
17201259 AAAAAGA
1 AAAAAGA
17201266 AAAA
1 AAAA
17201270 GTTTCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:17206698 original size:45 final size:45
Alignment explanation
Indices: 17206656--17206745 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
17206646 TATTATATGT
17206656 ATAACTATA-AACA-ATGGATATTGTATTAATATTTACTATATATA
1 ATAA-TATAGAACATATGGATATTGTATTAATATTTACTATATATA
* * * *
17206700 ATTATATAGTATATATGTATATTGTATTAATATATTACTATATATA
1 ATAATATAGAACATATGGATATTGTATTAATAT-TTACTATATATA
17206746 GTTAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 4 0.10
44 5 0.13
45 18 0.46
46 12 0.31
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (45 bp):
ATAATATAGAACATATGGATATTGTATTAATATTTACTATATATA
Found at i:17206791 original size:21 final size:21
Alignment explanation
Indices: 17206754--17206793 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17206744 TAGTTAAAAT
*
17206754 ATACTTATATAGTATATAAGC
1 ATACTTAGATAGTATATAAGC
17206775 ATACTTAGA-AGTCATATAA
1 ATACTTAGATAGT-ATATAA
17206794 TATATATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (21 bp):
ATACTTAGATAGTATATAAGC
Found at i:17211034 original size:11 final size:11
Alignment explanation
Indices: 17211016--17211087 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
17211006 ATTTTTAGTA
17211016 TTATTATTATT
1 TTATTATTATT
*
17211027 TAATTATTTATT
1 TTATTA-TTATT
* *
17211039 TTATTTTTACT
1 TTATTATTATT
17211050 TTATATATT-TT
1 TTAT-TATTATT
17211061 TTATTATTATAT
1 TTATTATTAT-T
17211073 TT-TCTATT-TT
1 TTAT-TATTATT
17211083 TTATT
1 TTATT
17211088 TCTAATTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.16
11 22 0.45
12 19 0.39
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTATT
Found at i:17211065 original size:22 final size:20
Alignment explanation
Indices: 17211016--17211104 Score: 72
Period size: 22 Copynumber: 4.1 Consensus size: 20
17211006 ATTTTTAGTA
*
17211016 TTATTATTATTTAATTATTTATT
1 TTATTTTTATTT-ATTA-TT-TT
17211039 TTATTTTTACTTTATATATTTT
1 TTATTTTTA-TTTAT-TATTTT
17211061 TTATTATTATATTT-TCTATTTT
1 TTATT-TT-TATTTAT-TATTTT
* *
17211083 TTATTTCTAATTATTATTTT
1 TTATTTTTATTTATTATTTT
17211103 TT
1 TT
17211105 TATACCTTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
20 12 0.21
21 2 0.04
22 19 0.33
23 17 0.30
24 7 0.12
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTTATTTATTATTTT
Found at i:17211071 original size:15 final size:15
Alignment explanation
Indices: 17211014--17211107 Score: 61
Period size: 15 Copynumber: 6.2 Consensus size: 15
17211004 CTATTTTTAG
*
17211014 TATTATTATTATTTAAT
1 TATTATTA-TATTT-TT
*
17211031 TATTTATTTTA-TTTT
1 TA-TTATTATATTTTT
17211046 TACTT-TATATATTTTT
1 TA-TTAT-TATATTTTT
*
17211062 TATTATTATATTTTC
1 TATTATTATATTTTT
* *
17211077 TATT-TTTTATTTCT
1 TATTATTATATTTTT
*
17211091 AATTATTAT-TTTTT
1 TATTATTATATTTTT
17211105 TAT
1 TAT
17211108 ACCTTACATT
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
14 17 0.28
15 25 0.42
16 9 0.15
17 4 0.07
18 5 0.08
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATTATATTTTT
Found at i:17211074 original size:35 final size:35
Alignment explanation
Indices: 17211005--17211075 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 35
17210995 TGCAGTTAAC
*
17211005 TATTTTTAGTATTATTATTATTTAATTATTTATTT
1 TATTTTTACTATTATTATTATTTAATTATTTATTT
*
17211040 TATTTTTACT-TTATATATT-TTTTATTATTATATTT
1 TATTTTTACTATTAT-TATTATTTAATTATT-TATTT
17211075 T
1 T
17211076 CTATTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 13 0.41
35 19 0.59
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (35 bp):
TATTTTTACTATTATTATTATTTAATTATTTATTT
Found at i:17211233 original size:4 final size:4
Alignment explanation
Indices: 17211224--17211258 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
17211214 ATTTTTATTA
17211224 TTAT TTAT TTAT TTAT TTAT TT-T TCTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTA
17211259 ATGTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 25 0.86
5 2 0.07
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:17211328 original size:12 final size:12
Alignment explanation
Indices: 17211313--17211371 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
17211303 ATTCGAATTA
17211313 TTATTATTATTT
1 TTATTATTATTT
* *
17211325 TTATCATCATTT
1 TTATTATTATTT
*
17211337 TTTTTATCTATTT
1 TTATTAT-TATTT
17211350 TTA-T-TTATTT
1 TTATTATTATTT
*
17211360 ATTATTTTTATT
1 -TTATTATTATT
17211372 GAGTAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 17 0.46
13 11 0.30
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:17212569 original size:2 final size:2
Alignment explanation
Indices: 17212557--17212586 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17212547 TTTGCCTGCT
17212557 TC TC T- 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 T
17212587 TTACTCTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:17213376 original size:38 final size:37
Alignment explanation
Indices: 17213296--17213717 Score: 386
Period size: 38 Copynumber: 11.5 Consensus size: 37
17213286 TCCTTAAAGT
* * *
17213296 TGAGGCAACGAAACTTTAAAAATGGACTTCTCAAAAT
1 TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAAC
*
17213333 TGAGGCTACGAAACTTTAAAAATGAAACTCCTCAAAAC
1 TGAGGCAACGAAACTTTAAAAATG-AACTCCTCAAAAC
* *
17213371 TGAGGCAACGAAACTTTAAAAATAAAACT-CTCCAAAGC
1 TGAGGCAACGAAACTTTAAAAAT-GAACTCCT-CAAAAC
* *
17213409 TGAGACAAC-ATAACTTTAAAAAT-ATAGCTCCTCAAAGC
1 TGAGGCAACGA-AACTTTAAAAATGA-A-CTCCTCAAAAC
* *
17213447 TGAGGCAAC-ATGACTTTAAAAATGAACTCCTTAAAAC
1 TGAGGCAACGA-AACTTTAAAAATGAACTCCTCAAAAC
* ** * *
17213484 TGAGGCAATGAGATTTTTAAAAATGAACTCCTTAAAAT
1 TGAGGCAACGA-AACTTTAAAAATGAACTCCTCAAAAC
*
17213522 TGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGC
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAAC
* * *
17213560 TGAGGCAATGAAACTTCT-AAAATGAATTCCTCAAAGC
1 TGAGGCAACGAAACTT-TAAAAATGAACTCCTCAAAAC
* *
17213597 TGAGGCAACGAGACTTTTAAAAATGAACTCCTC--AGC
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAAC
** * *
17213633 -GTTGC--C----TTTTAAAAATGAACTCCTCAAAGC
1 TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAAC
* *
17213663 TGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAGC
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAAC
*
17213701 TGAGGCAACGAGACTTT
1 TGAGGCAACGAAACTTT
17213718 TATAAATCTT
Statistics
Matches: 327, Mismatches: 35, Indels: 46
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.06
30 3 0.01
31 3 0.01
33 2 0.01
35 3 0.01
36 4 0.01
37 81 0.25
38 210 0.64
39 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (37 bp):
TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAAC
Found at i:17213379 original size:75 final size:75
Alignment explanation
Indices: 17213296--17213717 Score: 376
Period size: 75 Copynumber: 5.7 Consensus size: 75
17213286 TCCTTAAAGT
* * * *
17213296 TGAGGCAACGAAACTTTAAAAATGGACTTCTCAAAATTGAGGCTACGA-AACTTTAAAAATGAAA
1 TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAACTTTAAAAATG-AA
17213360 CTCCTCAAAAC
65 CTCCTCAAAAC
* * * *
17213371 TGAGGCAACGAAACTTTAAAAATAAAACT-CTCCAAAGCTGAGACAAC-ATAACTTTAAAAAT-A
1 TGAGGCAACGAAACTTTAAAAAT-GAACTCCT-CAAAACTGAGGCAACGAGAACTTTAAAAATGA
*
17213433 TAGCTCCTCAAAGC
64 -A-CTCCTCAAAAC
* * * **
17213447 TGAGGCAAC-ATGACTTTAAAAATGAACTCCTTAAAACTGAGGCAATGAGATTTTTAAAAATGAA
1 TGAGGCAACGA-AACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAACTTTAAAAATGAA
* *
17213511 CTCCTTAAAAT
65 CTCCTCAAAAC
* *
17213522 TGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATGA-AACTTCT-AAAATGA
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAACTT-TAAAAATGA
* *
17213585 ATTCCTCAAAGC
64 ACTCCTCAAAAC
* * ** *
17213597 TGAGGCAACGAGACTTTTAAAAATGAACTCCTC--AGC-GTTGC--C-----TTTTAAAAATGAA
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAACTTTAAAAATGAA
*
17213652 CTCCTCAAAGC
65 CTCCTCAAAAC
* *
17213663 TGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAG-ACTTT
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAACTTT
17213718 TATAAATCTT
Statistics
Matches: 288, Mismatches: 37, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
65 1 0.00
66 53 0.18
68 3 0.01
69 3 0.01
71 1 0.00
72 3 0.01
73 3 0.01
74 1 0.00
75 115 0.40
76 104 0.36
77 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (75 bp):
TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAACTTTAAAAATGAAC
TCCTCAAAAC
Found at i:17213513 original size:113 final size:112
Alignment explanation
Indices: 17213296--17213724 Score: 374
Period size: 113 Copynumber: 3.9 Consensus size: 112
17213286 TCCTTAAAGT
* * * ** * *
17213296 TGAGGCAACGAAAC-TTTAAAAATGGACTTCTCAAAATTGAGGCTACGAAACTTTAAAAATGAAA
1 TGAGACAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATG-AACTTTAAAAATG-AA
* * *
17213360 CTCCTCAAAACTGAGGCAACGA-AACTTTAAAAATAAAACT-CTCCAAAGC
64 CTCCTCAAAACTGAGGCAACGAGAATTTTAAAAAT-GAACTCCT-CAAAAC
17213409 TGAGACAAC-ATAAC-TTTAAAAAT-ATAGCTCCTCAAAGCTGAGGCAACATG-ACTTTAAAAAT
1 TGAGACAACGA-AACTTTTAAAAATGA-A-CTCCTCAAAGCTGAGGC-A-ATGAACTTTAAAAAT
* * * * *
17213470 GAACTCCTTAAAACTGAGGCAATGAGATTTTTAAAAATGAACTCCTTAAAAT
61 GAACTCCTCAAAACTGAGGCAACGAGAATTTTAAAAATGAACTCCTCAAAAC
*
17213522 TGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATGAAACTTCT-AAAATGAA
1 TGAGACAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATG-AACTT-TAAAAATGAA
* * * *
17213586 TTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTC--AGC
64 CTCCTCAAAACTGAGGCAACGAGAATTTTAAAAATGAACTCCTCAAAAC
* *
17213633 -GTTG----C----CTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGA
1 TG-AGACAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATGA-AC-TTTAAAAATGA
* * *
17213689 ACTCCTCAAAGCTGAGGCAACGAGACTTTTATAAAT
63 ACTCCTCAAAACTGAGGCAACGAGAATTTTAAAAAT
17213725 CTTGAAACTA
Statistics
Matches: 271, Mismatches: 28, Indels: 43
0.79 0.08 0.13
Matches are distributed among these distances:
102 1 0.00
103 37 0.14
104 43 0.16
107 1 0.00
110 1 0.00
111 5 0.02
112 2 0.01
113 128 0.47
114 50 0.18
115 1 0.00
116 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (112 bp):
TGAGACAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATGAACTTTAAAAATGAACT
CCTCAAAACTGAGGCAACGAGAATTTTAAAAATGAACTCCTCAAAAC
Found at i:17225904 original size:20 final size:20
Alignment explanation
Indices: 17225868--17225939 Score: 54
Period size: 25 Copynumber: 3.2 Consensus size: 20
17225858 ATTTTTAGTA
17225868 TTATTATTATTTAATTATTT
1 TTATTATTATTTAATTATTT
*
17225888 TTATTTTTACTTTATTATATATTTT
1 TTATTATTA-TTTA--AT-TA-TTT
**
17225913 TTATTATATATTTTTTTATATT
1 TTATTAT-TATTTAATTAT-TT
17225935 TTATT
1 TTATT
17225940 TCTAATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 8 0.20
21 5 0.12
22 9 0.22
23 3 0.07
24 2 0.05
25 12 0.29
26 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTATTATTTAATTATTT
Found at i:17225905 original size:14 final size:14
Alignment explanation
Indices: 17225866--17225958 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
17225856 CTATTTTTAG
17225866 TATTA-TTATTATT
1 TATTATTTATTATT
17225879 TAATTATTT-TTATT
1 T-ATTATTTATTATT
*
17225893 T-TTACTTTATTATA
1 TATTA-TTTATTATT
* *
17225907 TATTTTTTATTATA
1 TATTATTTATTATT
17225921 TATT-TTT-TTATAT
1 TATTATTTATTAT-T
* *
17225934 T-TTATTT-CTAAT
1 TATTATTTATTATT
*
17225946 TATTATTTTTTAT
1 TATTATTTATTAT
17225959 ATCTTACATT
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
12 11 0.17
13 19 0.30
14 30 0.47
15 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTATTATT
Found at i:17225919 original size:17 final size:16
Alignment explanation
Indices: 17225859--17225956 Score: 64
Period size: 17 Copynumber: 6.2 Consensus size: 16
17225849 TAGTTAACTA
*
17225859 TTTTTAGTATTATTAT
1 TTTTTATTATTATTAT
* *
17225875 TATTTAATTATTTTTA-
1 T-TTTTATTATTATTAT
17225891 TTTTTACTTTATTATATAT
1 TTTTTA--TTATTAT-TAT
17225910 TTTTTATTA-TA-TAT
1 TTTTTATTATTATTAT
17225924 TTTTT-TATATT-TTAT
1 TTTTTAT-TATTATTAT
* *
17225939 TTCTAATTATTATT-T
1 TTTTTATTATTATTAT
17225954 TTT
1 TTT
17225957 ATATCTTACA
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
13 1 0.02
14 10 0.16
15 18 0.28
16 7 0.11
17 20 0.31
18 2 0.03
19 6 0.09
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (16 bp):
TTTTTATTATTATTAT
Found at i:17225925 original size:32 final size:32
Alignment explanation
Indices: 17225857--17225927 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
17225847 TGTAGTTAAC
* *
17225857 TATTTTTAGTATTATTATTATTTAATTATTTT
1 TATTTTTACTATTATTATTATTTAATTATTTA
*
17225889 TATTTTTACT-TTATTATATATTT-TTTATTATA
1 TATTTTTACTATTATTAT-TATTTAATTATT-TA
17225921 TATTTTT
1 TATTTTT
17225928 TTATATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (32 bp):
TATTTTTACTATTATTATTATTTAATTATTTA
Found at i:17225929 original size:34 final size:34
Alignment explanation
Indices: 17225866--17225956 Score: 81
Period size: 32 Copynumber: 2.9 Consensus size: 34
17225856 CTATTTTTAG
*
17225866 TATTATTATTATTTAATTATTTTTATTTTTACTT
1 TATTATTATTATTTAATTATTATTATTTTTACTT
*
17225900 TATTA-TA-TATTT-TTTATTATATATTTTT--TT
1 TATTATTATTATTTAATTATTAT-TATTTTTACTT
*
17225930 ATATT-TTATT-TCTAATTATTATT-TTTT
1 -TATTATTATTATTTAATTATTATTATTTT
17225957 ATATCTTACA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
30 6 0.12
31 15 0.31
32 20 0.42
33 2 0.04
34 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (34 bp):
TATTATTATTATTTAATTATTATTATTTTTACTT
Found at i:17225935 original size:42 final size:42
Alignment explanation
Indices: 17225871--17225958 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
17225861 TTTAGTATTA
*
17225871 TTATTATTTAATTATTTTTATTTTTACTT-T-ATTATATATTTT
1 TTATTATATAATTATTTTTA-TTTTACTTCTAATTAT-TATTTT
* *
17225913 TTATTATAT-ATTTTTTTATATTTTATTTCTAATTATTATTTT
1 TTATTATATAATTATTTT-TATTTTACTTCTAATTATTATTTT
17225955 TTAT
1 TTAT
17225959 ATCTTACATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 14 0.35
42 21 0.52
43 5 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (42 bp):
TTATTATATAATTATTTTTATTTTACTTCTAATTATTATTTT
Found at i:17225940 original size:29 final size:27
Alignment explanation
Indices: 17225907--17225974 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
17225897 CTTTATTATA
*
17225907 TATTTTTTATTATATATTTTTTTATATTT
1 TATTTTTTATTAT-TA-TTTTTTATATCT
* *
17225936 TATTTCTAATTATTATTTTTTATATCT
1 TATTTTTTATTATTATTTTTTATATCT
*
17225963 TACATTTTTATT
1 TA-TTTTTTATT
17225975 CTAAGTTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 13 0.41
28 8 0.25
29 11 0.34
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (27 bp):
TATTTTTTATTATTATTTTTTATATCT
Found at i:17225971 original size:42 final size:40
Alignment explanation
Indices: 17225884--17225974 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 40
17225874 TTATTTAATT
*
17225884 ATTTTTATTTTTACTTTATTATATATTTTTTATTATATAT
1 ATTTTTATTTTTACTTTATTATATATTTTTTATTATATAC
* * *
17225924 TTTTTTATATTTTATTTCTAATTAT-TATTTTTTA-TATCTTAC
1 ATTTTTAT-TTTTACTT-T-ATTATATATTTTTTATTAT-ATAC
17225966 ATTTTTATT
1 ATTTTTATT
17225975 CTAAGTTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
40 7 0.17
41 11 0.26
42 19 0.45
43 5 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (40 bp):
ATTTTTATTTTTACTTTATTATATATTTTTTATTATATAC
Found at i:17229645 original size:18 final size:17
Alignment explanation
Indices: 17229622--17229655 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17229612 ACGGTGATTT
*
17229622 TTCTTTGTTTTCTTTCAA
1 TTCTTTCTTTT-TTTCAA
17229640 TTCTTTCTTTTTTTCA
1 TTCTTTCTTTTTTTCA
17229656 CGCTTAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.71
Consensus pattern (17 bp):
TTCTTTCTTTTTTTCAA
Found at i:17243080 original size:13 final size:13
Alignment explanation
Indices: 17243062--17243086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17243052 TAACAAATTC
17243062 TGTTTTTTCTTTT
1 TGTTTTTTCTTTT
17243075 TGTTTTTTCTTT
1 TGTTTTTTCTTT
17243087 GCTTGTCAGT
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:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (13 bp):
TGTTTTTTCTTTT
Found at i:17249996 original size:21 final size:20
Alignment explanation
Indices: 17249962--17250016 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
17249952 AAATAAAAAG
17249962 AAATTA-AA-TTAATATTTT
1 AAATTATAATTTAATATTTT
17249980 AATATTA-AATCTTAATATTTT
1 AA-ATTATAAT-TTAATATTTT
17250001 AAATTATAATTTAATA
1 AAATTATAATTTAATA
17250017 ATAACATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 10 0.30
21 15 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTATAATTTAATATTTT
Done.