Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 37 of 226
Found at i:16021307 original size:6 final size:6
Alignment explanation
Indices: 16021296--16021335 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
16021286 TTACTAACAA
16021296 TTAATT TTAATT TT-A-- TTAATTT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAA-TT TTAATT TTAATT TTAATT
16021336 AAAAACGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 2 0.07
4 1 0.03
5 1 0.03
6 22 0.73
7 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:16021308 original size:22 final size:22
Alignment explanation
Indices: 16021281--16021332 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
16021271 AATAATTTGA
16021281 TAATTTTACTAACAATTAATTT
1 TAATTTTACTAACAATTAATTT
* ***
16021303 TAATTTTATTAATTTTTAATTT
1 TAATTTTACTAACAATTAATTT
16021325 TAATTTTA
1 TAATTTTA
16021333 ATTAAAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATTTTACTAACAATTAATTT
Found at i:16021337 original size:16 final size:17
Alignment explanation
Indices: 16021294--16021329 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
16021284 TTTTACTAAC
16021294 AATTAA-TTTTAATTTT
1 AATTAATTTTTAATTTT
16021310 -ATTAATTTTTAATTTT
1 AATTAATTTTTAATTTT
16021326 AATT
1 AATT
16021330 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.28
16 10 0.56
17 3 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTAATTTTTAATTTT
Found at i:16022295 original size:21 final size:21
Alignment explanation
Indices: 16022270--16022310 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16022260 TGTATTTAGG
* *
16022270 AAAAAGAACTAAA-TTGAAAA
1 AAAAAAAACAAAAGTTGAAAA
16022290 AAAAAAAACAAAAGTTGAAAA
1 AAAAAAAACAAAAGTTGAAAA
16022311 TGGTGAAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAAAAAACAAAAGTTGAAAA
Found at i:16022534 original size:48 final size:48
Alignment explanation
Indices: 16022463--16022560 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
16022453 TTGAATTTAG
16022463 AAGGAATTATTAGGTTAATTGGTTTCGAAAACGAGGTATCAAGATCTC
1 AAGGAATTATTAGGTTAATTGGTTTCGAAAACGAGGTATCAAGATCTC
16022511 AAGGAATTATTAGGTTAATTGGTTTCGAAAACGAGGTATCAAGATCTC
1 AAGGAATTATTAGGTTAATTGGTTTCGAAAACGAGGTATCAAGATCTC
16022559 AA
1 AA
16022561 TTTTATAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (48 bp):
AAGGAATTATTAGGTTAATTGGTTTCGAAAACGAGGTATCAAGATCTC
Found at i:16030356 original size:2 final size:2
Alignment explanation
Indices: 16030349--16030485 Score: 50
Period size: 2 Copynumber: 70.5 Consensus size: 2
16030339 CAAATTTCGT
* * * * * *
16030349 TA TA TA TA TA CA TA CA TA CA TT TT TA TA -A TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
16030390 CA TA CA TA TT TT TA TA -A TT TA TT TA TA TA TA TA CA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
16030431 TA TA TA TT TT TA TA T- TT TA TA -A TT TA TA TA CA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
16030471 TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA T
16030486 GCATATTTTT
Statistics
Matches: 98, Mismatches: 31, Indels: 12
0.70 0.22 0.09
Matches are distributed among these distances:
1 5 0.05
2 92 0.94
3 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16030387 original size:31 final size:31
Alignment explanation
Indices: 16030349--16030427 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 31
16030339 CAAATTTCGT
16030349 TATATATATACATACATACATTTTTATAATA
1 TATATATATACATACATACATTTTTATAATA
* *
16030380 TATATATACACATACAT--ATTTTTATAATT
1 TATATATATACATACATACATTTTTATAATA
* *
16030409 TATTTATATATATACATAC
1 TATATATATACATACATAC
16030428 TTATATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 25 0.61
31 16 0.39
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (31 bp):
TATATATATACATACATACATTTTTATAATA
Found at i:16030434 original size:29 final size:29
Alignment explanation
Indices: 16030348--16030445 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
16030338 TCAAATTTCG
16030348 TTATATATATACATACATACATTTTTATAAT
1 TTATATATATACATACATAC--TTTTATAAT
* * *
16030379 ATATATATACACATACATATTTTTATAAT
1 TTATATATATACATACATACTTTTATAAT
* * *
16030408 TTATTTATATATATACATACTTATATATAT
1 TTATATATATACATACATACTTTTATA-AT
*
16030438 TTTTATAT
1 TTATATAT
16030446 TTTATAATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 30 0.55
30 8 0.15
31 17 0.31
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (29 bp):
TTATATATATACATACATACTTTTATAAT
Found at i:16030528 original size:57 final size:53
Alignment explanation
Indices: 16030455--16030591 Score: 141
Period size: 57 Copynumber: 2.5 Consensus size: 53
16030445 TTTTATAATT
* ** **
16030455 TATATACATATCTATATATATATATCTATATGCATATTTTTTTTTCATAAATGTATA
1 TATATACATATATATATATATATATCTATATGC-TATAATTTTTT-AT--ATACATA
* * *
16030512 TATATACATACT-TATATATATTTTTCTATATTCTATAATTTTTTATATACATA
1 TATATACATA-TATATATATATATATCTATATGCTATAATTTTTTATATACATA
*
16030565 TATATACATATATATACATATATATCT
1 TATATACATATATATATATATATATCT
16030592 TTTTATATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
52 1 0.01
53 27 0.40
55 2 0.03
56 9 0.13
57 28 0.41
58 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (53 bp):
TATATACATATATATATATATATATCTATATGCTATAATTTTTTATATACATA
Found at i:16030568 original size:10 final size:10
Alignment explanation
Indices: 16030555--16030589 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
16030545 TATAATTTTT
16030555 TATATACATA
1 TATATACATA
16030565 TATATACATA
1 TATATACATA
16030575 TATATACATA
1 TATATACATA
16030585 TATAT
1 TATAT
16030590 CTTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATACATA
Found at i:16030568 original size:20 final size:20
Alignment explanation
Indices: 16030519--16030599 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
16030509 ATATATATAC
*
16030519 ATACTTATATATATTTTTCTAT
1 ATACATATATATA-TTTT-TAT
*
16030541 ATTC-TATA-AT-TTTTTAT
1 ATACATATATATATTTTTAT
** *
16030558 ATACATATATATACATATAT
1 ATACATATATATATTTTTAT
*
16030578 ATACATATATATCTTTTTAT
1 ATACATATATATATTTTTAT
16030598 AT
1 AT
16030600 TTTTATATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
17 6 0.13
18 8 0.17
19 2 0.04
20 24 0.51
21 4 0.09
22 3 0.06
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
ATACATATATATATTTTTAT
Found at i:16030653 original size:20 final size:19
Alignment explanation
Indices: 16030597--16030655 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
16030587 TATCTTTTTA
*
16030597 TATTTTTA-TATTTTTATT
1 TATTTTTATTATTATTATT
*
16030615 CATTTTT-TTATTTACTTATT
1 TATTTTTATTA-TTA-TTATT
16030635 TATTTTTATTCATTATTATT
1 TATTTTTATT-ATTATTATT
16030655 T
1 T
16030656 TAAGAGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 17 0.52
21 5 0.15
22 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTTATTATTATTATT
Found at i:16030699 original size:24 final size:23
Alignment explanation
Indices: 16030672--16030716 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
16030662 AATATTTTAT
*
16030672 TTTTATTTGCTTATAGATTTGTTA
1 TTTTATATGC-TATAGATTTGTTA
* *
16030696 TTTTGTATGCTATTGATTTGT
1 TTTTATATGCTATAGATTTGT
16030717 CCTTTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.18, C:0.04, G:0.16, T:0.62
Consensus pattern (23 bp):
TTTTATATGCTATAGATTTGTTA
Found at i:16031076 original size:73 final size:73
Alignment explanation
Indices: 16030966--16031109 Score: 261
Period size: 73 Copynumber: 2.0 Consensus size: 73
16030956 TCTTTTCAAA
* * *
16030966 CTCAAGTTTTAAACGATCTCGGGAATTGAGAAGAGATCGTGTCCTAACTTATTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
16031031 TTTTTTTT
66 TTTTTTTT
16031039 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
16031104 TTTTTT
66 TTTTTT
16031110 AAATCCGAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTTT
Found at i:16034548 original size:100 final size:99
Alignment explanation
Indices: 16034366--16034552 Score: 250
Period size: 100 Copynumber: 1.8 Consensus size: 99
16034356 AACATGATGA
* * * *
16034366 GCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTTGCGTCAAAAAGTTCGATGTGTTC
1 GCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAAGTTCAATATATTC
*
16034431 TTAAGAAAAAATTAATAAAATTAGGAGTCTGCTGG
66 TAAAGAAAAAA-TAATAAAATTAGGAGTCTGCTGG
* *
16034466 GCTGAGTAACCGGGGT-AGGGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCAATATATT
1 GCTGAGTAACCGGGGTGA-GGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAAGTTCAATATATT
16034530 CCTAAAGCATAAAAAATAATAAA
65 -CTAAAG---AAAAAATAATAAA
16034553 TAATAAATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
99 1 0.01
100 56 0.75
101 5 0.07
103 7 0.09
104 6 0.08
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (99 bp):
GCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAAGTTCAATATATTC
TAAAGAAAAAATAATAAAATTAGGAGTCTGCTGG
Found at i:16034569 original size:24 final size:24
Alignment explanation
Indices: 16034542--16034587 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
16034532 TAAAGCATAA
16034542 AAAATAATAAAT-AATAAATAAATC
1 AAAATAA-AAATAAATAAATAAATC
*
16034566 AAAATCAAAATAAATAAATAAA
1 AAAATAAAAATAAATAAATAAA
16034588 AGAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAATAAAAATAAATAAATAAATC
Found at i:16034595 original size:20 final size:20
Alignment explanation
Indices: 16034554--16034598 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16034544 AATAATAAAT
**
16034554 AATAAATAAATCAAAATCAA
1 AATAAATAAATCAAAAAAAA
16034574 AATAAATAAAT-AAAAGAAAA
1 AATAAATAAATCAAAA-AAAA
16034594 AATAA
1 AATAA
16034599 TAATTTGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (20 bp):
AATAAATAAATCAAAAAAAA
Found at i:16035176 original size:15 final size:15
Alignment explanation
Indices: 16035151--16035185 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16035141 GACTCTATTT
*
16035151 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
16035165 TAATTAATATTAAGA
1 TAATTAATATTAAGA
16035180 TAATTA
1 TAATTA
16035186 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:16039732 original size:15 final size:15
Alignment explanation
Indices: 16039709--16039752 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
16039699 TATATTATTT
16039709 TATTATATAATATAATA
1 TATTATAT--TATAATA
16039726 TATTATATTATAATA
1 TATTATATTATAATA
16039741 TATTATATTATA
1 TATTATATTATA
16039753 TAAATTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.70
17 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATATTATAATA
Found at i:16039752 original size:20 final size:20
Alignment explanation
Indices: 16039694--16039753 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
16039684 TTTTTATGTT
*
16039694 TTAT-ATATATTATTTTAT-
1 TTATAATATATTATATTATA
*
16039712 TATATAATATAATATATTATA
1 T-TATAATATATTATATTATA
16039733 TTATAATATATTATATTATA
1 TTATAATATATTATATTATA
16039753 T
1 T
16039754 AAATTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 31 0.86
21 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATAATATATTATATTATA
Found at i:16039753 original size:5 final size:5
Alignment explanation
Indices: 16039694--16039753 Score: 63
Period size: 5 Copynumber: 12.2 Consensus size: 5
16039684 TTTTTATGTT
* *
16039694 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTATA ATATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
16039743 TTATA TTATA T
1 TTATA TTATA T
16039754 AAATTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 1 0.02
4 8 0.17
5 33 0.72
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:16049581 original size:24 final size:24
Alignment explanation
Indices: 16049566--16049617 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16049556 AATCAATGTC
16049566 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
** *
16049590 AAATATATTATATTAATAAATACT
1 AAATATATTATGCTAATAAATGCT
16049614 AAAT
1 AAAT
16049618 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:16052853 original size:21 final size:21
Alignment explanation
Indices: 16052826--16052876 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
16052816 AGGTAGGCAA
**
16052826 CTTTTTTTTTTTGC-TTTTTG
1 CTTTTTTTTTACGCTTTTTTG
16052846 CTTTTTTTTTACGCTTTTTTG
1 CTTTTTTTTTACGCTTTTTTG
16052867 CTTTTTTTTT
1 CTTTTTTTTT
16052877 GTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (21 bp):
CTTTTTTTTTACGCTTTTTTG
Found at i:16052883 original size:20 final size:20
Alignment explanation
Indices: 16052826--16052884 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
16052816 AGGTAGGCAA
*
16052826 CTTTTTTTTT-TTGCTTTTTG
1 CTTTTTTTTTGTT-TTTTTTG
*
16052846 CTTTTTTTTTACG-CTTTTTTG
1 CTTTTTTTTT--GTTTTTTTTG
16052867 CTTTTTTTTTGTTTTTTT
1 CTTTTTTTTTGTTTTTTT
16052885 AAAGAATAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 16 0.50
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.80
Consensus pattern (20 bp):
CTTTTTTTTTGTTTTTTTTG
Found at i:16053112 original size:4 final size:4
Alignment explanation
Indices: 16053100--16053130 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
16053090 TAAAATTAGT
16053100 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
16053131 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:16053499 original size:31 final size:32
Alignment explanation
Indices: 16053435--16053499 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
16053425 GGCAAATTAC
*
16053435 AAGAGTAATTGAATCCTAATAAAAATTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
16053467 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
16053498 AA
1 AA
16053500 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:16054208 original size:51 final size:51
Alignment explanation
Indices: 16054148--16054252 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
16054138 CCTGTGTGAA
* *
16054148 GAGGCTTCAATCTAAAGTTGAATTTCATATAGTCCAAAACATTCATAATTT
1 GAGGCTTCAATCCAAAGTTAAATTTCATATAGTCCAAAACATTCATAATTT
16054199 GAGGCTTCAATCCAAAGTTAAATTTCATATAGTCCAAAACATTCATAATTT
1 GAGGCTTCAATCCAAAGTTAAATTTCATATAGTCCAAAACATTCATAATTT
16054250 GAG
1 GAG
16054253 TCTATGCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (51 bp):
GAGGCTTCAATCCAAAGTTAAATTTCATATAGTCCAAAACATTCATAATTT
Found at i:16059461 original size:2 final size:2
Alignment explanation
Indices: 16059454--16059501 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
16059444 GCTTCTGATA
16059454 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
16059496 AG -G AG A
1 AG AG AG A
16059502 TGCTGCAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16068506 original size:14 final size:15
Alignment explanation
Indices: 16068473--16068510 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
16068463 TCTCTCTATA
*
16068473 ATATTTCATTGCTCC
1 ATATTTCCTTGCTCC
16068488 A-ATTTCCTT-CTCC
1 ATATTTCCTTGCTCC
16068501 ATATTTCCTT
1 ATATTTCCTT
16068511 TCTTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 15 0.71
15 1 0.05
ACGTcount: A:0.18, C:0.29, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATTTCCTTGCTCC
Found at i:16070023 original size:2 final size:2
Alignment explanation
Indices: 16070016--16070040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16070006 TATAGTATTG
16070016 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16070041 CAGTTGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16078842 original size:15 final size:14
Alignment explanation
Indices: 16078821--16078856 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
16078811 ATAATCCTTA
*
16078821 ATAATTATCTTAAT
1 ATAATTATCCTAAT
16078835 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
16078850 ATAATTA
1 ATAATTA
16078857 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:16085491 original size:18 final size:16
Alignment explanation
Indices: 16085468--16085508 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
16085458 AAAAATTGTG
16085468 ATAATTACACATTTAAA
1 ATAATTACA-ATTTAAA
*
16085485 TATAATTATAATTTAAA
1 -ATAATTACAATTTAAA
16085502 ATAATTA
1 ATAATTA
16085509 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 8 0.36
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATTACAATTTAAA
Found at i:16085507 original size:16 final size:18
Alignment explanation
Indices: 16085468--16085509 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
16085458 AAAAATTGTG
*
16085468 ATAATTACACATTTAAAT
1 ATAATTATACATTTAAAT
16085486 ATAATTATA-ATTTAAA-
1 ATAATTATACATTTAAAT
16085502 ATAATTAT
1 ATAATTAT
16085510 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTATACATTTAAAT
Found at i:16086821 original size:39 final size:39
Alignment explanation
Indices: 16086710--16086845 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 39
16086700 GCGTTTGGAC
* * *
16086710 AAAAAACGCCACTAAAAATAAAGCAGTAGCGGCGCTTTTG
1 AAAAAACGCCGCTAAAAATAAAGCATTAGCGGCG-TTTTT
* ** ** * *
16086750 GAAAAACGCCGCTAAAGGTCGATCATTTGCGGCGATTTTT
1 AAAAAACGCCGCTAAAAATAAAGCATTAGCGGCG-TTTTT
16086790 AAAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTT
1 AAAAAACGCCGCTAAAAATAAAGCATTAGCGGCGTTTTT
* *
16086828 CCAAAAGCGCCGC-AAAAA
1 -AAAAAACGCCGCTAAAAA
16086846 GCCTAAGCCC
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
38 10 0.13
39 21 0.28
40 45 0.59
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATAAAGCATTAGCGGCGTTTTT
Found at i:16086951 original size:41 final size:41
Alignment explanation
Indices: 16086883--16087083 Score: 325
Period size: 41 Copynumber: 4.9 Consensus size: 41
16086873 AGTTTTTTGG
16086883 GGTCTTTAGCGGCATTTTCTGAA-AAGCGCCGCTAATGATCA
1 GGTCTTTAGCGGCATTTT-TGAATAAGCGCCGCTAATGATCA
** *
16086924 GGTCTTTAGCGGTGTTTTTGAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGATCA
16086965 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAAT-ACTCA
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGA-TCA
16087006 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGATCA
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGATCA
* *
16087047 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATG
1 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATG
16087084 CTCGTACCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
40 4 0.03
41 144 0.97
42 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGATCA
Found at i:16087038 original size:123 final size:123
Alignment explanation
Indices: 16086883--16087120 Score: 374
Period size: 123 Copynumber: 1.9 Consensus size: 123
16086873 AGTTTTTTGG
*
16086883 GGTCTTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGATCAGGTCTTTAGCGGTGTTTTTGAATA
1 GGTCTTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGATCAGGTCTTTAGCGGCGTTTTTGAATA
*
16086948 AGCGCCGCTAATGCTCAGGT-CTTTAGCGGC-ATTTTTGAATAAGCGCCGCTAATACTCA
66 AGCGCCGCTAATGCTC--GTACTTTAGCGGCGATTTTTGAAGAAGCGCCGCTAATACTCA
*
16087006 GGTCTTTAGCGGCATTTT-TGAATAAGCGCCGCTAATGATCAGGTCTTTAGCGGCGTTTTTTAAT
1 GGTCTTTAGCGGCATTTTCTGAA-AAGCGCCGCTAATGATCAGGTCTTTAGCGGCGTTTTTGAAT
* *
16087070 AAGCGCCGCTAATGCTCGTACCTTTAGCGGCGTTTTTTGAGGAAGCGCCGC
65 AAGCGCCGCTAATGCTCGTA-CTTTAGCGGCGATTTTTGAAGAAGCGCCGC
16087121 AAAAACATTT
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
121 2 0.02
122 4 0.04
123 84 0.79
124 16 0.15
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (123 bp):
GGTCTTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGATCAGGTCTTTAGCGGCGTTTTTGAATA
AGCGCCGCTAATGCTCGTACTTTAGCGGCGATTTTTGAAGAAGCGCCGCTAATACTCA
Found at i:16087095 original size:41 final size:40
Alignment explanation
Indices: 16086884--16087120 Score: 298
Period size: 41 Copynumber: 5.8 Consensus size: 40
16086874 GTTTTTTGGG
*
16086884 GTCTTTAGCGGCATTTTCTGAA-AAGCGCCGCTAATGATCA
1 GTCTTTAGCGGCATTTT-TGAATAAGCGCCGCTAATGCTCA
**
16086924 GGTCTTTAGCGGTGTTTTTGAATAAGCGCCGCTAATGCTCA
1 -GTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
*
16086965 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATACTCA
1 -GTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
*
16087006 GGTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGATCA
1 -GTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
* *
16087047 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTC-
1 -GTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
* **
16087087 GTACCTTTAGCGGCGTTTTTTGAGGAAGCGCCGC
1 GT--CTTTAGCGGC-ATTTTTGAATAAGCGCCGC
16087121 AAAAACATTT
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
39 2 0.01
40 4 0.02
41 156 0.88
42 15 0.08
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (40 bp):
GTCTTTAGCGGCATTTTTGAATAAGCGCCGCTAATGCTCA
Found at i:16087598 original size:20 final size:20
Alignment explanation
Indices: 16087563--16087601 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16087553 TAAGGTTTAT
**
16087563 TTAGGGGTTAGGGGTTAGAG
1 TTAGGGGTTAAAGGTTAGAG
16087583 TTAGGGGTTAAAGGTTAGA
1 TTAGGGGTTAAAGGTTAGA
16087602 AGTTTAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.31
Consensus pattern (20 bp):
TTAGGGGTTAAAGGTTAGAG
Found at i:16087713 original size:14 final size:13
Alignment explanation
Indices: 16087688--16087722 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
16087678 ATTAAATAAT
16087688 GTTTAGGGGTTAGG
1 GTTTA-GGGTTAGG
16087702 GATTTAGGGTTAGG
1 G-TTTAGGGTTAGG
16087716 GTTTAGG
1 GTTTAGG
16087723 ATTAATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (13 bp):
GTTTAGGGTTAGG
Found at i:16087837 original size:82 final size:82
Alignment explanation
Indices: 16087637--16087907 Score: 296
Period size: 89 Copynumber: 3.2 Consensus size: 82
16087627 TAGGTTAGAA
* * * * * * *
16087637 TTTAGGGTTTAGACTAATTAATATATTTTATATTATATAATATTAAATAATGTTTAGGGGTTAGG
1 TTTAGGATTTAGATTAATTAGTGTTTTTTA-ATT-TAT-ATATTAAATAATATTTAGGGGTTAGT
* * * *
16087702 GATTTAGGGTTAGGGTTTA-GG
63 GA-TTCGGGGTCGAG-TTAGGG
*
16087723 ATTA--ATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATATTTAGGGGTTAGTGAT
1 TTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATATTTAGGGGTTAGTGAT
16087786 TCGGGGTCGAGTTAGGG
66 TCGGGGTCGAGTTAGGG
*
16087803 TTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGAGGTTAGGGGT
1 TTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA----T--A-TTTAGGGGT
16087868 TAGTGATTCGGGGTCGAGTTAGGG
59 TAGTGATTCGGGGTCGAGTTAGGG
16087892 TTTAGGATTTAGATTA
1 TTTAGGATTTAGATTA
16087908 TGTAACACCC
Statistics
Matches: 161, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
79 3 0.02
80 13 0.08
81 26 0.16
82 44 0.27
83 3 0.02
84 19 0.12
86 4 0.02
88 1 0.01
89 48 0.30
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.45
Consensus pattern (82 bp):
TTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATATTTAGGGGTTAGTGAT
TCGGGGTCGAGTTAGGG
Found at i:16090344 original size:21 final size:21
Alignment explanation
Indices: 16090320--16090362 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16090310 AAATCCCAAA
16090320 TTTTCTTCCTTTCCTTCCCTT
1 TTTTCTTCCTTTCCTTCCCTT
* * * *
16090341 TTTTTTTCTTTTTCTTTCCTT
1 TTTTCTTCCTTTCCTTCCCTT
16090362 T
1 T
16090363 CCTTCTTTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTCCTTTCCTTCCCTT
Found at i:16091154 original size:8 final size:8
Alignment explanation
Indices: 16091143--16091171 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16091133 GGGGTAGGTG
16091143 TTTGGGGT
1 TTTGGGGT
16091151 TTTGGGG-
1 TTTGGGGT
16091158 TTTGGGGT
1 TTTGGGGT
16091166 TTTGGG
1 TTTGGG
16091172 TTAAGGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
TTTGGGGT
Found at i:16091162 original size:15 final size:15
Alignment explanation
Indices: 16091142--16091171 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16091132 AGGGGTAGGT
16091142 GTTTGGGGTTTTGGG
1 GTTTGGGGTTTTGGG
16091157 GTTTGGGGTTTTGGG
1 GTTTGGGGTTTTGGG
16091172 TTAAGGGTTA
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:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (15 bp):
GTTTGGGGTTTTGGG
Found at i:16091390 original size:21 final size:20
Alignment explanation
Indices: 16091351--16091394 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
16091341 GGACAGGACC
16091351 AAAATATAAGAAAAAATAAA
1 AAAATATAAGAAAAAATAAA
16091371 AAAATATAA-AAAGGAAATAAA
1 AAAATATAAGAAA--AAATAAA
16091392 AAA
1 AAA
16091395 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAATATAAGAAAAAATAAA
Found at i:16091425 original size:21 final size:21
Alignment explanation
Indices: 16091401--16091462 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 21
16091391 AAAACTAAAA
16091401 TTTATAATTTTA-TCAAAAACT
1 TTTATAATTTTACT-AAAAACT
* *
16091422 TTTA-AATATTACTTAAAACT
1 TTTATAATTTTACTAAAAACT
*
16091442 TTAATAATTATTTACTAAAAA
1 TTTATAA-T-TTTACTAAAAA
16091463 GTTTAATGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 15 0.47
21 7 0.22
22 1 0.03
23 9 0.28
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTATAATTTTACTAAAAACT
Found at i:16091462 original size:23 final size:22
Alignment explanation
Indices: 16091415--16091469 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
16091405 TAATTTTATC
16091415 AAAAACTTT--TAAATATTACT
1 AAAAACTTTAATAAATATTACT
* *
16091435 TAAAACTTTAATAATTATTTACT
1 AAAAACTTTAATAAATA-TTACT
*
16091458 AAAAAGTTTAAT
1 AAAAACTTTAAT
16091470 GAAAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
22 5 0.18
23 15 0.54
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAACTTTAATAAATATTACT
Found at i:16092578 original size:38 final size:38
Alignment explanation
Indices: 16092535--16092609 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
16092525 AGATAATCCT
*
16092535 GTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCA
1 GTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCCA
16092573 GTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCC
1 GTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCC
16092610 TGTCTGTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (38 bp):
GTCATTTATCCGGTTTGTTTGAATAAATTCAACTTCCA
Found at i:16093921 original size:16 final size:16
Alignment explanation
Indices: 16093900--16093933 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16093890 AATCATGTAG
*
16093900 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAAAT
16093916 AAATAAGTTTGAAAAT
1 AAATAAGTTTGAAAAT
16093932 AA
1 AA
16093934 TGAAAATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (16 bp):
AAATAAGTTTGAAAAT
Found at i:16094004 original size:18 final size:16
Alignment explanation
Indices: 16093962--16093994 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16093952 AAACTTGTAG
16093962 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAGAT
16093978 AAATAAGTTTGAAGAT
1 AAATAAGTTTGAAGAT
16093994 A
1 A
16093995 TAATTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (16 bp):
AAATAAGTTTGAAGAT
Found at i:16094070 original size:9 final size:9
Alignment explanation
Indices: 16094058--16094154 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 9
16094048 TTAAAATAGT
16094058 TAACTTACA
1 TAACTTACA
16094067 TAACTTA-A
1 TAACTTACA
16094075 TTAA-TTA-A
1 -TAACTTACA
* *
16094083 T-ATTATATA
1 TAACT-TACA
16094092 TAACTTACA
1 TAACTTACA
16094101 TAACTTAC-
1 TAACTTACA
16094109 -AACTTACA
1 TAACTTACA
16094117 TAACTTACA
1 TAACTTACA
*
16094126 TTAATATTATACA
1 -T-A-ACT-TACA
*
16094139 TAAATTACA
1 TAACTTACA
16094148 TAACTTA
1 TAACTTA
16094155 ATTAATTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
6 1 0.01
7 9 0.12
8 7 0.10
9 41 0.57
10 5 0.07
11 2 0.03
12 3 0.04
13 4 0.06
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (9 bp):
TAACTTACA
Found at i:16094096 original size:34 final size:34
Alignment explanation
Indices: 16094062--16094281 Score: 175
Period size: 34 Copynumber: 6.2 Consensus size: 34
16094052 AATAGTTAAC
* *
16094062 TTACATAACTTAATTAATTAATATTATATATAAC
1 TTACATAACTTAATTAATTAATATTATACATAAA
*
16094096 TTACATAACTTACAACTTACA-TAACTTACATTAATATTATACATA
1 TTACATAACTT--AA-TTA-ATTAA--T--ATT-ATA-CATA-A-A
* **
16094141 AATTACATAACTTAATTAATTAA-A--ACACAGGAA
1 --TTACATAACTTAATTAATTAATATTATACATAAA
*
16094174 TTACATAACTT-A--CATTAATATTATACATAAA
1 TTACATAACTTAATTAATTAATATTATACATAAA
*
16094205 TTACATTAATATTAATTAATTAATATTATACATAAA
1 TTACA-TAA-CTTAATTAATTAATATTATACATAAA
16094241 TTACATAACTTAATTAATTAATATTATACATAAA
1 TTACATAACTTAATTAATTAATATTATACATAAA
16094275 TTACATA
1 TTACATA
16094282 GCTTGCATTA
Statistics
Matches: 151, Mismatches: 12, Indels: 46
0.72 0.06 0.22
Matches are distributed among these distances:
28 5 0.03
29 1 0.01
30 1 0.01
31 22 0.15
32 3 0.02
33 3 0.02
34 45 0.30
35 4 0.03
36 27 0.18
37 6 0.04
38 1 0.01
39 2 0.01
41 3 0.02
42 3 0.02
43 5 0.03
44 7 0.05
45 2 0.01
47 11 0.07
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (34 bp):
TTACATAACTTAATTAATTAATATTATACATAAA
Found at i:16094114 original size:16 final size:16
Alignment explanation
Indices: 16094093--16094125 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16094083 TATTATATAT
16094093 AACTTACATAACTTAC
1 AACTTACATAACTTAC
16094109 AACTTACATAACTTAC
1 AACTTACATAACTTAC
16094125 A
1 A
16094126 TTAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:16094147 original size:31 final size:31
Alignment explanation
Indices: 16094112--16094304 Score: 210
Period size: 31 Copynumber: 6.0 Consensus size: 31
16094102 AACTTACAAC
16094112 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATACATAAA
* * *
16094143 TTACATAACTTA-ATTAAT-TAAAACACAGGAA
1 TTACATAACTTACATTAATATTATACATA--AA
16094174 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATACATAAA
* *
16094205 TTACATTAATATTAATTAATTAATATTATACATAAA
1 TTACA-TAA-CTT-A--CATTAATATTATACATAAA
*
16094241 TTACATAACTTAATTAATTAATATTATACATAAA
1 TTACATAACTT-A--CATTAATATTATACATAAA
* *
16094275 TTACATAGCTTGCATTAATATTATACATAA
1 TTACATAACTTACATTAATATTATACATAA
16094305 CTTGCATTAA
Statistics
Matches: 141, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
29 6 0.04
30 6 0.04
31 50 0.35
32 9 0.06
33 8 0.06
34 36 0.26
35 3 0.02
36 23 0.16
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (31 bp):
TTACATAACTTACATTAATATTATACATAAA
Found at i:16094147 original size:47 final size:49
Alignment explanation
Indices: 16094059--16094154 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 49
16094049 TAAAATAGTT
* *
16094059 AACTTACATAACTTAATTAATTAATATTATATATAACTTACATAACTTAC
1 AACTTACATAACTTAA-TAATTAATATTATACATAAATTACATAACTTAC
*
16094109 AACTTACATAACTT-A-CATTAATATTATACATAAATTACATAACTTA
1 AACTTACATAACTTAATAATTAATATTATACATAAATTACATAACTTA
16094155 ATTAATTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 28 0.65
49 1 0.02
50 14 0.33
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (49 bp):
AACTTACATAACTTAATAATTAATATTATACATAAATTACATAACTTAC
Found at i:16094200 original size:22 final size:22
Alignment explanation
Indices: 16094175--16094218 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16094165 ACACAGGAAT
*
16094175 TACATAACTTACATTAATATTA
1 TACATAAATTACATTAATATTA
16094197 TACATAAATTACATTAATATTA
1 TACATAAATTACATTAATATTA
16094219 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAAATTACATTAATATTA
Found at i:16094228 original size:14 final size:15
Alignment explanation
Indices: 16094203--16094263 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 15
16094193 ATTATACATA
16094203 AATTACATTAATA-TT
1 AATTA-ATTAATACTT
*
16094218 AATTAATTAATATTAT
1 AATTAATTAATACT-T
*
16094234 ACATAAATTACATAACTT
1 A-ATTAATTA-AT-ACTT
16094252 AATTAATTAATA
1 AATTAATTAATA
16094264 TTATACATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 7 0.18
15 7 0.18
16 4 0.11
17 14 0.37
18 4 0.11
19 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAATTAATACTT
Found at i:16094247 original size:9 final size:9
Alignment explanation
Indices: 16094172--16094281 Score: 52
Period size: 9 Copynumber: 12.0 Consensus size: 9
16094162 AAAACACAGG
16094172 AATTACATA
1 AATTACATA
*
16094181 ACTTACATTA
1 AATTACA-TA
16094191 ATATTATACATA
1 A-A-T-TACATA
16094203 AATTACATTA
1 AATTACA-TA
*
16094213 ATATTA-ATT
1 A-ATTACATA
16094222 AATTA-AT-
1 AATTACATA
*
16094229 ATTATACATA
1 AAT-TACATA
16094239 AATTACATA
1 AATTACATA
* *
16094248 ACTTA-ATT
1 AATTACATA
16094256 AATTA-AT-
1 AATTACATA
*
16094263 ATTATACATA
1 AAT-TACATA
16094273 AATTACATA
1 AATTACATA
16094282 GCTTGCATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
7 4 0.05
8 18 0.23
9 32 0.41
10 12 0.15
11 5 0.06
12 4 0.05
13 4 0.05
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTACATA
Found at i:16097429 original size:66 final size:65
Alignment explanation
Indices: 16097321--16097490 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 65
16097311 GAGCAAATTA
* * *
16097321 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTAAAGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTAAAGTTCAACAAAAG-TATGAAGAACTCCA
16097385 G
65 G
* * * * * *
16097386 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTTCA
1 C-ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTAAAGTTCAACAAAAGTATGAAGAACTCCA
16097451 G
65 G
* *
16097452 CAGCAGCTTAAAGCAGAGGC-GACAGCAAGAGAAGC-AAAG
1 CA-CAACTTAAAGCAGAGGCAG-CAGCGAGAGAAGCTAAAG
16097491 GCGGCAGCGA
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
65 5 0.06
66 77 0.90
67 4 0.05
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (65 bp):
CACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTAAAGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:16097487 original size:21 final size:21
Alignment explanation
Indices: 16097462--16097553 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
16097452 CAGCAGCTTA
*
16097462 AAGCAGAGGCGACAGCAAGAG
1 AAGCAGAGGCGACAGCGAGAG
* *
16097483 AAGCAAAGGCGGCAGCGAGAG
1 AAGCAGAGGCGACAGCGAGAG
* * * *
16097504 AAGTACAGGCTACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAG
* *
16097525 AAGCAGAGGCTACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAG
16097546 AAGCAGAG
1 AAGCAGAG
16097554 CAGCGTCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.38, C:0.18, G:0.40, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAG
Found at i:16097951 original size:43 final size:43
Alignment explanation
Indices: 16097904--16098079 Score: 203
Period size: 43 Copynumber: 4.1 Consensus size: 43
16097894 AGGTGTTGGC
* * **
16097904 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
* ** *
16097947 CTTTAGCGGTGTTTGTGGAAAAAGCGCCACTAAAGATCAA-GGT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGAT-AAGGGT
* *
16097990 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
* * *
16098033 CTATT-GCGGCGTTTGAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
16098076 CTTT
1 CTTT
16098080 CATGGCGTTT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.03
43 107 0.94
44 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATAAGGGT
Found at i:16098087 original size:43 final size:43
Alignment explanation
Indices: 16097924--16098111 Score: 193
Period size: 43 Copynumber: 4.4 Consensus size: 43
16097914 GTTTTTGGTC
* * *
16097924 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGTGTTTGTGGAA
1 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGAGGGA
* * *
16097967 AAAGCGCCACTAAAGATCAA-GGTCTTTAGCGGCGTTTGTGGGG
1 AAAGCGCCGCTAAAGAT-AAGGGTCTTTAGCGGCGTTTGAGGGA
* * *
16098010 AAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGGG
1 AAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGAGGGA
* * * *
16098053 AAAGCGCCGCTAAAGATTAGGTTCTTTCA-TGGCGTTTGAGAGA
1 AAAGCGCCGCTAAAGATAAGGGTCTTT-AGCGGCGTTTGAGGGA
* *
16098096 AAAACGACGCTAAAGA
1 AAAGCGCCGCTAAAGA
16098112 CCCTGATCTT
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
42 3 0.02
43 117 0.94
44 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.23
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGAGGGA
Found at i:16098809 original size:27 final size:26
Alignment explanation
Indices: 16098765--16098818 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
16098755 AATTTAGATT
*
16098765 AATATTTTAATAATAAATATAATTTATA
1 AATATTTTAATAACAAATAT--TTTATA
*
16098793 AATA-TTTAGTAACAAATATTTTATA
1 AATATTTTAATAACAAATATTTTATA
16098818 A
1 A
16098819 CATAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
27 13 0.54
28 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATTTTAATAACAAATATTTTATA
Found at i:16102182 original size:22 final size:23
Alignment explanation
Indices: 16102147--16102189 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
16102137 AGATATTACT
*
16102147 AAAAATTAAGATAAAAGCAAAAC
1 AAAAATTAAAATAAAAGCAAAAC
16102170 AAAAA-TAAAATAAAAGCAAA
1 AAAAATTAAAATAAAAGCAAA
16102190 CGAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (23 bp):
AAAAATTAAAATAAAAGCAAAAC
Found at i:16102282 original size:13 final size:13
Alignment explanation
Indices: 16102249--16102283 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
16102239 TCTTCATTCT
16102249 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
16102262 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
16102275 TTTTGAAAA
1 TTTTGAAAA
16102284 ATTTTGAGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:16121581 original size:84 final size:86
Alignment explanation
Indices: 16121406--16121581 Score: 196
Period size: 86 Copynumber: 2.1 Consensus size: 86
16121396 TTTTTAAAAT
* * *
16121406 AAAATATATTTAAGATAATGATAAATATAAAAATATATATTATATAATTATTATTTTATTTATAT
1 AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
* *
16121471 AAATAAAGTAGTTGTTAATTT
66 AAATAAAATAGTTGTTAATTA
* * * * * ** *
16121492 CAAATATTTTTAACATAATGATATATTTTATTATATA-ATTACATATTTATTATTTGATTT-TAT
1 AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
*
16121555 AAATAAAATATTTAG-TAATTA
66 AAATAAAATAGTT-GTTAATTA
16121576 AAAATA
1 AAAATA
16121582 AAAAATTTGA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 24 0.32
85 21 0.28
86 29 0.39
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (86 bp):
AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
AAATAAAATAGTTGTTAATTA
Found at i:16126388 original size:46 final size:46
Alignment explanation
Indices: 16126321--16126552 Score: 394
Period size: 46 Copynumber: 5.0 Consensus size: 46
16126311 ACAATGCTAT
* * *
16126321 AACTCAGTATGGTTTCCTTCACTGAAACAACATACCTACTTTTCAC
1 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
16126367 AACTCAGTATAGTTTTCTTCACTGAAACAACATACCTACTTTTCAC
1 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
16126413 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
16126459 AACTCAGTAT-GATTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATAG-TTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
16126505 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTATTCAC
1 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
16126551 AA
1 AA
16126553 TTTGCCATGG
Statistics
Matches: 180, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
45 1 0.01
46 178 0.99
47 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (46 bp):
AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:16127821 original size:16 final size:17
Alignment explanation
Indices: 16127775--16127822 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
16127765 AAATTCTTTT
*
16127775 TAAATCGCAAAATTCAC
1 TAAATCACAAAATTCAC
*
16127792 TAAATCACAAAATTTAC
1 TAAATCACAAAATTCAC
*
16127809 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
16127823 TTATAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:16127953 original size:42 final size:42
Alignment explanation
Indices: 16127901--16127980 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
16127891 GATCTCGAAT
*
16127901 CACTGTTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
1 CACTATTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
* *
16127943 CACTATTTCCGACGCCACTGAAAATTGGGCTGTTACAT
1 CACTATTTCCGACACCACTGAAAATTAGGCTGTTACAT
16127981 TTACTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
CACTATTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
Found at i:16134768 original size:27 final size:27
Alignment explanation
Indices: 16134737--16134792 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
16134727 GATTCACTTG
16134737 GAAAATAAAATTACTACTATTTATTAT
1 GAAAATAAAATTACTACTATTTATTAT
16134764 GAAAATAAAATTACTACTATTTATTAT
1 GAAAATAAAATTACTACTATTTATTAT
16134791 GA
1 GA
16134793 TGGAAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (27 bp):
GAAAATAAAATTACTACTATTTATTAT
Found at i:16139635 original size:16 final size:16
Alignment explanation
Indices: 16139606--16139653 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
16139596 TTTTACATGG
16139606 AATTGTTATTAAAATT
1 AATTGTTATTAAAATT
* *
16139622 AATTGCTATCAAAATT
1 AATTGTTATTAAAATT
16139638 AATTGTTATTAAAATT
1 AATTGTTATTAAAATT
16139654 GTATCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (16 bp):
AATTGTTATTAAAATT
Found at i:16139797 original size:83 final size:85
Alignment explanation
Indices: 16139698--16139866 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 85
16139688 TTTGTAAAAT
*
16139698 CTAACATTTTGCTAGTAAAATTATTAATTGTTACTTCTATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTCTATTAATTGTTACTAAAATTATCAAATT
16139763 AT-T-AATTATTAATTGTTA
66 ATATAAATTATTAATTGTTA
* * *
16139781 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTCTATTAATTGTTACTAAAATTATCAAATT
16139846 ATATCAAATTATTAATTGTTA
66 ATAT-AAATTATTAATTGTTA
16139867 ATTGTATTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
83 63 0.80
84 1 0.01
86 15 0.19
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (85 bp):
CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTCTATTAATTGTTACTAAAATTATCAAATT
ATATAAATTATTAATTGTTA
Found at i:16142723 original size:18 final size:18
Alignment explanation
Indices: 16142677--16142723 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
16142667 GCTTACTTAA
*
16142677 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
16142694 TATTTTAGTTATTTATTT
1 TATTTTATTTATTTATTT
16142712 TAATTTT-TTTAT
1 T-ATTTTATTTAT
16142724 CTGACTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:16144832 original size:37 final size:40
Alignment explanation
Indices: 16144737--16144857 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 40
16144727 AACACACCAG
* **
16144737 TTTGGCA-CCTAGTGCCTCATCTGATAATTCGAAGTAATAA
1 TTTGGCACCCT-GTGCCTCATCGGATAAACCGAAGTAATAA
* * *
16144777 TTTGACACCCGGTGCCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGGCACCCTGTGCCTCATCGGATAAACCGAAGTAATAA
* * *
16144815 -TTGGCACCCTGTGCCTCATTGAATTAATCCGAAGTAATGAA
1 TTTGGCACCCTGTGCCTCATCGGA-TAAACCGAAGTAAT-AA
16144856 TT
1 TT
16144858 GACACTCAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
37 18 0.29
38 12 0.19
39 2 0.03
40 26 0.41
41 4 0.06
42 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (40 bp):
TTTGGCACCCTGTGCCTCATCGGATAAACCGAAGTAATAA
Found at i:16145037 original size:17 final size:16
Alignment explanation
Indices: 16144999--16145056 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
16144989 TATTCATTTC
16144999 AATTCAA-ATAATCAATA
1 AATTCAATATAAT--ATA
*
16145016 TATTCAATAT-ATATA
1 AATTCAATATAATATA
16145031 CCAATTCAAT-TAATATA
1 --AATTCAATATAATATA
16145048 AATTCAATA
1 AATTCAATA
16145057 AATTCATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
15 11 0.32
16 1 0.03
17 20 0.59
18 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTCAATATAATATA
Found at i:16145876 original size:21 final size:21
Alignment explanation
Indices: 16145837--16145878 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16145827 AATACATATT
*
16145837 TTATTATTAAATATATATTTA
1 TTATTATTAAACATATATTTA
* *
16145858 TTATTATTACACATGTATTTA
1 TTATTATTAAACATATATTTA
16145879 CCAACACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATTATTAAACATATATTTA
Found at i:16151039 original size:20 final size:20
Alignment explanation
Indices: 16151014--16151052 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16151004 TATTCATTTA
16151014 TTTGTAAATATTTTTATAAT
1 TTTGTAAATATTTTTATAAT
**
16151034 TTTGTATGTATTTTTATAA
1 TTTGTAAATATTTTTATAA
16151053 AATCAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTGTAAATATTTTTATAAT
Found at i:16151268 original size:31 final size:32
Alignment explanation
Indices: 16151233--16151295 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
16151223 TTAGCATTTC
16151233 ATTAATGATTTAACAA-ATAAATGACTAAAAT
1 ATTAATGATTTAACAATATAAATGACTAAAAT
** * *
16151264 ATTAATTTTTTAATAATATTAATGACTAAAAT
1 ATTAATGATTTAACAATATAAATGACTAAAAT
16151296 TGCCAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTAATGATTTAACAATATAAATGACTAAAAT
Found at i:16151858 original size:7 final size:7
Alignment explanation
Indices: 16151846--16151871 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16151836 CTCATCTTTC
16151846 AAATTTT
1 AAATTTT
16151853 AAATTTT
1 AAATTTT
16151860 AAATTTT
1 AAATTTT
16151867 AAATT
1 AAATT
16151872 ATATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:16153833 original size:88 final size:88
Alignment explanation
Indices: 16153724--16153899 Score: 307
Period size: 88 Copynumber: 2.0 Consensus size: 88
16153714 AATTCAGATG
**
16153724 CTTCCAATTATACTCAACATTGTTTTCATGAATACTTGTTTATTCCAACTCCAAACTTTCACCAT
1 CTTCCAATTATACTCAACATTGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
16153789 CCAACAAAGCACAACCATGGACA
66 CCAACAAAGCACAACCATGGACA
* *
16153812 CTTCCAATTATACTCAGCATTGTTTTCATGAATGCTTGTTTAGCCCAACTCCAAACTTTCACCAT
1 CTTCCAATTATACTCAACATTGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
*
16153877 CCAACAAAGGACAACCATGGACA
66 CCAACAAAGCACAACCATGGACA
16153900 ATCATAGAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (88 bp):
CTTCCAATTATACTCAACATTGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
CCAACAAAGCACAACCATGGACA
Found at i:16163605 original size:16 final size:17
Alignment explanation
Indices: 16163574--16163608 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16163564 TAAAAAAATC
*
16163574 CAATTATCATATTTACA
1 CAATTATCACATTTACA
16163591 CAATT-TCACATTTACA
1 CAATTATCACATTTACA
16163607 CA
1 CA
16163609 CACATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATTATCACATTTACA
Found at i:16163617 original size:2 final size:2
Alignment explanation
Indices: 16163612--16163650 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
16163602 TTACACACAC
16163612 AT AT AT AT AT -T CAT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16163651 TCCAATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16164415 original size:16 final size:17
Alignment explanation
Indices: 16164388--16164419 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16164378 CGTTTTAAGC
16164388 TTTCTGTTTCTTTCTTA
1 TTTCTGTTTCTTTCTTA
16164405 TTTCT-TTTCTTTCTT
1 TTTCTGTTTCTTTCTT
16164420 TTGTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTCTGTTTCTTTCTTA
Found at i:16164454 original size:14 final size:16
Alignment explanation
Indices: 16164427--16164460 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
16164417 CTTTTGTTTT
16164427 ATATATATATATAATA
1 ATATATATATATAATA
16164443 ATATA-ATA-ATAATA
1 ATATATATATATAATA
16164457 ATAT
1 ATAT
16164461 TTTAATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 3 0.17
16 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATATATATAATA
Found at i:16166068 original size:23 final size:25
Alignment explanation
Indices: 16166032--16166100 Score: 90
Period size: 23 Copynumber: 2.8 Consensus size: 25
16166022 GGACTCACCA
*
16166032 CAGCTCGTATGAGCTTACCG-TT-T
1 CAGCTCGAATGAGCTTACCGTTTAT
16166055 CAGCTC-AATAGAGCTTACCGTTTAT
1 CAGCTCGAAT-GAGCTTACCGTTTAT
16166080 CAGCTCGGAATGAGCTTACCG
1 CAGCTC-GAATGAGCTTACCG
16166101 ATCATGGCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 2 0.05
23 16 0.40
24 2 0.05
25 7 0.17
26 10 0.25
27 3 0.08
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (25 bp):
CAGCTCGAATGAGCTTACCGTTTAT
Found at i:16166954 original size:7 final size:7
Alignment explanation
Indices: 16166942--16166971 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
16166932 AATTTTTAAA
16166942 AAAAAAG
1 AAAAAAG
16166949 AAAAAAG
1 AAAAAAG
16166956 AAAAAAG
1 AAAAAAG
16166963 AAAAAAG
1 AAAAAAG
16166970 AA
1 AA
16166972 TGAAGTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:16170579 original size:2 final size:2
Alignment explanation
Indices: 16170572--16170598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16170562 CAATTAAAGC
16170572 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 A
16170599 AAATAGGATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16186610 original size:51 final size:51
Alignment explanation
Indices: 16186534--16186650 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
16186524 CAGATCACAT
* * *
16186534 TTATCACTTGCCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACTAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
16186585 TTATCACTTGTTACTTGTCACTGATCGGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
16186636 TTATCACTTGTCACT
1 TTATCACTTGTCACT
16186651 GATCAAAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:16190408 original size:2 final size:2
Alignment explanation
Indices: 16190399--16190433 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16190389 TTACACACTA
16190399 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16190434 TGTTCCACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16191160 original size:9 final size:9
Alignment explanation
Indices: 16191102--16191205 Score: 52
Period size: 9 Copynumber: 11.1 Consensus size: 9
16191092 ATAAAATTTT
16191102 TTATAAAAA
1 TTATAAAAA
*
16191111 TTAT-TAAA
1 TTATAAAAA
16191119 TTATAAAAAA
1 TTAT-AAAAA
* * *
16191129 ATCTAATAAT
1 TTATAA-AAA
*
16191139 TTTTAATAAA
1 TTATAA-AAA
16191149 TTATAAAAA
1 TTATAAAAA
*
16191158 TTATAAAAG
1 TTATAAAAA
*
16191167 TAATAAACATA
1 TTATAAA-A-A
16191178 TT-TAAAATA
1 TTATAAAA-A
*
16191187 TT-TAAAATT
1 TTATAAAA-A
16191196 TTATAAAAA
1 TTATAAAAA
16191205 T
1 T
16191206 ATAGTATAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
8 7 0.09
9 37 0.50
10 29 0.39
11 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (9 bp):
TTATAAAAA
Found at i:16191191 original size:47 final size:47
Alignment explanation
Indices: 16191102--16191205 Score: 113
Period size: 47 Copynumber: 2.2 Consensus size: 47
16191092 ATAAAATTTT
* * *
16191102 TTATAAAAATTATTAAATTATAAAAAAATCTAATAATTTTTAATAA-A
1 TTATAAAAATTATAAAATAATAAAAAAATCTAATAATATTTAA-AATA
* * * *
16191149 TTATAAAAATTATAAAAGTAATAAACATATTTAA-AATATTTAAAATT
1 TTATAAAAATTATAAAA-TAATAAAAAAATCTAATAATATTTAAAATA
16191196 TTATAAAAAT
1 TTATAAAAAT
16191206 ATAGTATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
46 2 0.04
47 34 0.71
48 12 0.25
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (47 bp):
TTATAAAAATTATAAAATAATAAAAAAATCTAATAATATTTAAAATA
Found at i:16197484 original size:31 final size:29
Alignment explanation
Indices: 16197449--16197525 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
16197439 TTAATAGCTC
*
16197449 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
16197480 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
16197509 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
16197526 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:16222514 original size:22 final size:22
Alignment explanation
Indices: 16222472--16222514 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16222462 TCTCACTATT
*
16222472 TTGTTATTATTTCACTGTTATG
1 TTGTTATTATTTCACTATTATG
* *
16222494 TTGTTATTATTTGAGTATTAT
1 TTGTTATTATTTCACTATTAT
16222515 ACAACTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (22 bp):
TTGTTATTATTTCACTATTATG
Found at i:16236293 original size:20 final size:21
Alignment explanation
Indices: 16236252--16236293 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
16236242 TTTCTGCTGC
* *
16236252 CACAATAAAGATATATTATAA
1 CACAATAAAGATAAAATATAA
16236273 CACAATAAA-ATAAAATATAA
1 CACAATAAAGATAAAATATAA
16236293 C
1 C
16236294 CACTGACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (21 bp):
CACAATAAAGATAAAATATAA
Found at i:16238778 original size:29 final size:29
Alignment explanation
Indices: 16238713--16238776 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
16238703 TTTTATAGTG
* *
16238713 TTTTTATAATTTTTAAAAGATTAAATTAAA
1 TTTTTATAA-TTTTAAAAAATTAAAATAAA
16238743 TTTTTATAA-TTTAAAAAATTAAAAATATAA
1 TTTTTATAATTTTAAAAAATT-AAAATA-AA
16238773 TTTT
1 TTTT
16238777 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
29 5 0.17
30 15 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTTATAATTTTAAAAAATTAAAATAAA
Found at i:16238783 original size:28 final size:27
Alignment explanation
Indices: 16238721--16238783 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
16238711 TGTTTTTATA
* *
16238721 ATTTTTAAAAGATTAAATTAAATTTTT
1 ATTTTTAAAAAATTAAAATAAATTTTT
*
16238748 ATAATTTAAAAAATTAAAAATATAA-TTTT
1 AT-TTTTAAAAAATT-AAAATA-AATTTTT
16238777 ATTTTTA
1 ATTTTTA
16238784 TTAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.07
28 14 0.48
29 11 0.38
30 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTTTTAAAAAATTAAAATAAATTTTT
Found at i:16241072 original size:3 final size:3
Alignment explanation
Indices: 16241064--16241123 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
16241054 TCTCTCCTGC
16241064 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16241112 TAT TAT TAT TAT
1 TAT TAT TAT TAT
16241124 CTCAGTTTAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16250597 original size:7 final size:7
Alignment explanation
Indices: 16250573--16250635 Score: 90
Period size: 7 Copynumber: 9.0 Consensus size: 7
16250563 AAAAATAATA
*
16250573 ATTGAGG
1 ATTGAGT
* *
16250580 ATTTAGG
1 ATTGAGT
16250587 ATTGAGT
1 ATTGAGT
*
16250594 ATTGAAT
1 ATTGAGT
16250601 ATTGAGT
1 ATTGAGT
16250608 ATTGAGT
1 ATTGAGT
16250615 ATTGAGT
1 ATTGAGT
16250622 ATTGAGT
1 ATTGAGT
16250629 ATTGAGT
1 ATTGAGT
16250636 TGAAAAGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.30, C:0.00, G:0.29, T:0.41
Consensus pattern (7 bp):
ATTGAGT
Found at i:16251098 original size:15 final size:15
Alignment explanation
Indices: 16251070--16251105 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16251060 AATTAAAAAA
*
16251070 TTAAAAATTTAAACT
1 TTAAAAATTCAAACT
16251085 TTAAAAATTCAAACT
1 TTAAAAATTCAAACT
*
16251100 CTAAAA
1 TTAAAA
16251106 GGCCCGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATTCAAACT
Found at i:16251158 original size:15 final size:15
Alignment explanation
Indices: 16251133--16251162 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16251123 GCTAAACTCG
*
16251133 AAAAAACTCGAACTT
1 AAAAAAATCGAACTT
16251148 AAAAAAATCGAACTT
1 AAAAAAATCGAACTT
16251163 GAGACTAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.20
Consensus pattern (15 bp):
AAAAAAATCGAACTT
Found at i:16261304 original size:9 final size:9
Alignment explanation
Indices: 16261290--16261326 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16261280 TATAGTTTGA
16261290 TATTCGAAT
1 TATTCGAAT
16261299 TATTCGAAT
1 TATTCGAAT
*
16261308 TATTCGAGT
1 TATTCGAAT
*
16261317 TATACGAAT
1 TATTCGAAT
16261326 T
1 T
16261327 CGAAAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16261695 original size:9 final size:9
Alignment explanation
Indices: 16261683--16261737 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
16261673 TATTTAGGAA
16261683 TTTTAAAAC
1 TTTTAAAAC
16261692 TTTTAAAA-
1 TTTTAAAAC
16261700 TTTTAAATTAGGAC
1 TTTT-AA--A--AC
16261714 TTTTAAAAC
1 TTTTAAAAC
16261723 TTTTAAAA-
1 TTTTAAAAC
16261731 TTTTAAA
1 TTTTAAA
16261738 TTAATAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 11 0.28
9 20 0.50
11 2 0.05
13 3 0.08
14 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (9 bp):
TTTTAAAAC
Found at i:16261712 original size:31 final size:31
Alignment explanation
Indices: 16261676--16261740 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
16261666 TTTTTCTTAT
16261676 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
1 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
*
16261707 TTAGGACTTTTAAAACTTTTAAAATTTTAAA
1 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
16261738 TTA
1 TTA
16261741 ATAATGATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAGGAATTTTAAAACTTTTAAAATTTTAAA
Found at i:16263391 original size:7 final size:7
Alignment explanation
Indices: 16263379--16263411 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
16263369 TAGTCGATTG
16263379 GTATTTA
1 GTATTTA
16263386 GTATTTA
1 GTATTTA
16263393 GTATTTA
1 GTATTTA
16263400 GTATTTA
1 GTATTTA
16263407 GTATT
1 GTATT
16263412 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:16265222 original size:18 final size:18
Alignment explanation
Indices: 16265201--16265317 Score: 63
Period size: 18 Copynumber: 6.8 Consensus size: 18
16265191 ACCGAAAATT
16265201 TATTTAAAATTAAAAAAA
1 TATTTAAAATTAAAAAAA
*
16265219 TA-TT----TTAAAAATA
1 TATTTAAAATTAAAAAAA
16265232 T-TTTAAAATT-AAAAAA
1 TATTTAAAATTAAAAAAA
*
16265248 TATTTTAAAATT-TAAAAA
1 TA-TTTAAAATTAAAAAAA
** **
16265266 TA-AAAAAGTATTTTAAAAA
1 TATTTAAA--ATTAAAAAAA
16265285 TATTTTAAAATTAAAAAAA
1 TA-TTTAAAATTAAAAAAA
* *
16265304 AATTTAAAAATAAA
1 TATTTAAAATTAAA
16265318 TATATTTATT
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
13 11 0.14
16 9 0.12
17 4 0.05
18 32 0.42
19 17 0.22
21 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (18 bp):
TATTTAAAATTAAAAAAA
Found at i:16265228 original size:11 final size:11
Alignment explanation
Indices: 16265214--16265294 Score: 60
Period size: 11 Copynumber: 8.4 Consensus size: 11
16265204 TTAAAATTAA
16265214 AAAAATATTTT
1 AAAAATATTTT
16265225 AAAAATATTTT
1 AAAAATATTTT
*
16265236 --AAA-A-TTA
1 AAAAATATTTT
16265243 AAAAATATTTT
1 AAAAATATTTT
16265254 --AAA-A-TTT
1 AAAAATATTTT
16265261 AAAAATA----
1 AAAAATATTTT
16265268 AAAAAGTATTTT
1 AAAAA-TATTTT
16265280 AAAAATATTTT
1 AAAAATATTTT
16265291 AAAA
1 AAAA
16265295 TTAAAAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 24
0.68 0.02 0.29
Matches are distributed among these distances:
7 10 0.18
8 4 0.07
9 12 0.21
10 2 0.04
11 23 0.41
12 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:16265233 original size:29 final size:30
Alignment explanation
Indices: 16265203--16265315 Score: 157
Period size: 29 Copynumber: 4.0 Consensus size: 30
16265193 CGAAAATTTA
16265203 TTTAAAATTAAAAAAATATTTTAAAAATAT
1 TTTAAAATTAAAAAAATATTTTAAAAATAT
16265233 TTTAAAATT-AAAAAATATTTT--AAA-A-
1 TTTAAAATTAAAAAAATATTTTAAAAATAT
* *
16265258 TTTAAAAATAAAAAAGTATTTTAAAAATAT
1 TTTAAAATTAAAAAAATATTTTAAAAATAT
*
16265288 TTTAAAATTAAAAAAA-AATTTAAAAATA
1 TTTAAAATTAAAAAAATATTTTAAAAATA
16265316 AATATATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.11
26 12 0.16
27 3 0.04
28 3 0.04
29 24 0.33
30 23 0.32
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
TTTAAAATTAAAAAAATATTTTAAAAATAT
Found at i:16265264 original size:55 final size:55
Alignment explanation
Indices: 16265202--16265312 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
16265192 CCGAAAATTT
* * *
16265202 ATTTAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAATATTTTAAA
1 ATTTAAAAATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAAATTTAAA
*
16265257 ATTTAAAAATAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAATTTAAA
1 ATTTAAAAATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAAATTTAAA
16265312 A
1 A
16265313 ATAAATATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (55 bp):
ATTTAAAAATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAAATTTAAA
Found at i:16266164 original size:125 final size:125
Alignment explanation
Indices: 16265867--16266243 Score: 585
Period size: 125 Copynumber: 3.0 Consensus size: 125
16265857 CCCAAACATG
* * *
16265867 CTACAGTAGCAAAAGAGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCCAGC
* *
16265932 TAGAAGCGATTTTATACTATTTGCTCCGAAACGTC-AAAAAAAATTATTTATTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
*
16265991 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTTAAATAGCATCCAGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCCAGC
* *
16266056 TAGAAGCGATTTTATACTATTTCCTCAGAAATGTCAAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
* * * *
16266116 CTACTGTAGCAAAAGCGCGTCCAAGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCTAGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCCAGC
* **** *
16266181 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
16266241 CTA
1 CTA
16266244 AAAATCCTAA
Statistics
Matches: 231, Mismatches: 21, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
124 93 0.40
125 138 0.60
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCCAGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
Found at i:16272006 original size:24 final size:24
Alignment explanation
Indices: 16271974--16272046 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 24
16271964 TAAGTGATCA
16271974 TTATTTCTCATGTTCTTTTACCTT
1 TTATTTCTCATGTTCTTTTACCTT
* *
16271998 TTATTTCTCATCCTTTGCCCTTTACCTT
1 TTATTTCTCAT--GTT--CTTTTACCTT
16272026 TTATTTCTCATGTTCTTTTAC
1 TTATTTCTCATGTTCTTTTAC
16272047 TCTCTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 17 0.41
26 4 0.10
28 20 0.49
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59
Consensus pattern (24 bp):
TTATTTCTCATGTTCTTTTACCTT
Found at i:16280333 original size:33 final size:33
Alignment explanation
Indices: 16280296--16280363 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
16280286 AAACTGTAAC
16280296 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
1 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
*
16280329 ATGTGTTTTAGCTAAAATTTCTATGGATTATTG
1 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
16280362 AT
1 AT
16280364 TTTGGATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (33 bp):
ATGTGTTTTAGCTAAAATATCTATGGATTATTG
Found at i:16290329 original size:8 final size:8
Alignment explanation
Indices: 16290280--16290332 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
16290270 CTTAAATTTT
*
16290280 TTTTAATA
1 TTTTAAAA
16290288 TGTTTAAAA
1 T-TTTAAAA
16290297 TTTTAATATA
1 TTTTAA-A-A
*
16290307 TTTTAATA
1 TTTTAAAA
*
16290315 TATTAAAA
1 TTTTAAAA
16290323 TTTTAAAA
1 TTTTAAAA
16290331 TT
1 TT
16290333 AGTTATACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 22 0.59
9 8 0.22
10 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (8 bp):
TTTTAAAA
Found at i:16290388 original size:17 final size:17
Alignment explanation
Indices: 16290352--16290387 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16290342 CAACATTTTC
16290352 TTTAACATATTTAGAAT
1 TTTAACATATTTAGAAT
*
16290369 TTTAATATATTTA-AAT
1 TTTAACATATTTAGAAT
16290385 TTT
1 TTT
16290388 TTAAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAACATATTTAGAAT
Found at i:16290392 original size:71 final size:70
Alignment explanation
Indices: 16290242--16290397 Score: 204
Period size: 71 Copynumber: 2.2 Consensus size: 70
16290232 CTATTAAAAT
* * * * * *
16290242 ATATTTTAAAATTTTGACATTAGTTATACTTAAATTTTTTTTAATATGTTTAAAATTTTAATATA
1 ATATTTTAAAATTTTAAAATTAGTTATACTCAAATTTTCTTTAACATATTTAAAATTTTAATATA
*
16290307 TTTTA
66 TTTAA
* *
16290312 ATATATTAAAATTTTAAAATTAGTTATACTCAACATTTTCTTTAACATATTTAGAATTTTAATAT
1 ATATTTTAAAATTTTAAAATTAGTTATACTCAA-ATTTTCTTTAACATATTTAAAATTTTAATAT
16290377 ATTTAA
65 ATTTAA
* *
16290383 ATTTTTTAAAGTTTT
1 ATATTTTAAAATTTT
16290398 TTAAAATATT
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
70 29 0.40
71 44 0.60
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (70 bp):
ATATTTTAAAATTTTAAAATTAGTTATACTCAAATTTTCTTTAACATATTTAAAATTTTAATATA
TTTAA
Found at i:16290412 original size:9 final size:9
Alignment explanation
Indices: 16290400--16290425 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16290390 AAAGTTTTTT
16290400 AAAATATTA
1 AAAATATTA
16290409 AAAATATTA
1 AAAATATTA
16290418 AAAATATT
1 AAAATATT
16290426 TTTTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATTA
Found at i:16290627 original size:71 final size:71
Alignment explanation
Indices: 16290479--16290628 Score: 214
Period size: 71 Copynumber: 2.1 Consensus size: 71
16290469 TTTAAAATAT
* **
16290479 ATTTTAAAAAATATATTGAATATATTGAAATTTTAAAATTGATTATACTTAGTATTTTTTTAATA
1 ATTTT-AAAAATATATTAAATATATTGAAATTTTAAAATTGATTATACTTAACATTTTTTTAATA
16290544 TATTTAA
65 TATTTAA
* *
16290551 TTTTTAAAAATATATTAAATATATT-AACATTTTAAAATTGGTTATACTTAACA-TTTTTTAATA
1 ATTTTAAAAATATATTAAATATATTGAA-ATTTTAAAATTGATTATACTTAACATTTTTTTAATA
16290614 TATTTAAA
65 TATTT-AA
16290622 ATTTTAA
1 ATTTTAA
16290629 TATATTTAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
70 17 0.24
71 49 0.70
72 4 0.06
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (71 bp):
ATTTTAAAAATATATTAAATATATTGAAATTTTAAAATTGATTATACTTAACATTTTTTTAATAT
ATTTAA
Found at i:16290643 original size:17 final size:17
Alignment explanation
Indices: 16290535--16290645 Score: 68
Period size: 17 Copynumber: 6.4 Consensus size: 17
16290525 ACTTAGTATT
16290535 TTTTTAATATATTT-AA
1 TTTTTAATATATTTAAA
*
16290551 TTTTTAAAAATATATTAAA
1 TTTTT-AATATAT-TTAAA
* *
16290570 TATATTAACAT-TTTAAAA
1 T-TTTTAATATATTT-AAA
** *
16290588 TTGGT--TATACTTAACA
1 TTTTTAATATATTTAA-A
16290604 TTTTTTAATATATTTAAA
1 -TTTTTAATATATTTAAA
* *
16290622 ATTTTAATATATTTAAG
1 TTTTTAATATATTTAAA
16290639 TTTTTAA
1 TTTTTAA
16290646 GTTTTTTAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 19
0.69 0.12 0.18
Matches are distributed among these distances:
15 4 0.06
16 8 0.11
17 34 0.47
18 8 0.11
19 15 0.21
20 3 0.04
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTTAATATATTTAAA
Found at i:16290755 original size:18 final size:17
Alignment explanation
Indices: 16290709--16290747 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
16290699 AAAATATATA
*
16290709 TTAAGTATATTAAAATT
1 TTAAATATATTAAAATT
16290726 TTAAATATATTAAAATT
1 TTAAATATATTAAAATT
16290743 TTAAA
1 TTAAA
16290748 ATTAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAAATT
Found at i:16290782 original size:20 final size:21
Alignment explanation
Indices: 16290749--16290788 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16290739 AATTTTAAAA
*
16290749 TTAATTATACTTAACATTTTT
1 TTAATTATACTTAAAATTTTT
*
16290770 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
16290789 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTATACTTAAAATTTTT
Found at i:16290803 original size:10 final size:11
Alignment explanation
Indices: 16290781--16290807 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16290771 TAATATATTT
16290781 AAAATTTTAAA
1 AAAATTTTAAA
16290792 AAAATTTTAAA
1 AAAATTTTAAA
16290803 AAAAT
1 AAAAT
16290808 CACATTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTTTAAA
Found at i:16290966 original size:2 final size:2
Alignment explanation
Indices: 16290959--16290995 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16290949 TATGAGTCGA
16290959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16290996 ACTTTAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.