Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 47 of 206
Found at i:13335051 original size:19 final size:21
Alignment explanation
Indices: 13335007--13335051 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
13334997 ATTAATTAAC
13335007 TTTTCTTATTTTTATCAGATTA
1 TTTT-TTATTTTTATCAGATTA
13335029 --TTTTATTTTT-TCA-ATTA
1 TTTTTTATTTTTATCAGATTA
13335046 TTTTTT
1 TTTTTT
13335052 TCAACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.19
18 3 0.14
19 12 0.57
20 2 0.10
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTATTTTTATCAGATTA
Found at i:13343553 original size:18 final size:18
Alignment explanation
Indices: 13343530--13343564 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13343520 ACAACCACGT
*
13343530 CTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTCTTTTTC
13343548 CTTTTTTTTGTCTTTTT
1 CTTTTTTTTGTCTTTTT
13343565 GCATGCATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
CTTTTTTTTGTCTTTTTC
Found at i:13344558 original size:17 final size:17
Alignment explanation
Indices: 13344536--13344587 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
13344526 ATGGAAACAT
* *
13344536 AATCTTCAAGGATATGC
1 AATCTTAAAAGATATGC
*
13344553 AATCTTAGATATGATATGC
1 AATCTTA-A-AAGATATGC
13344572 AATCTTAAAAGATATG
1 AATCTTAAAAGATATG
13344588 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (17 bp):
AATCTTAAAAGATATGC
Found at i:13357270 original size:44 final size:44
Alignment explanation
Indices: 13357207--13357406 Score: 198
Period size: 44 Copynumber: 4.6 Consensus size: 44
13357197 AACCGTTACA
13357207 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* *
13357251 CGGTGGAATTAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * * *** * *
13357295 CGATGGAATCAGTACTTAGCAACCACCTTATAATC-AATGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * *
13357337 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATT--AAGGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACC--TCAC-GTTCAAAGGATCC
*
13357379 CGGTGGAATCAACACTTAGCAACCACCT
1 CGGTGGAATCAGCACTTAGCAACCACCT
13357407 TTATTGTTAG
Statistics
Matches: 132, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.02
41 18 0.14
42 14 0.11
43 25 0.19
44 73 0.55
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (44 bp):
CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
Found at i:13362314 original size:41 final size:40
Alignment explanation
Indices: 13362269--13362345 Score: 127
Period size: 41 Copynumber: 1.9 Consensus size: 40
13362259 CACATTTATA
*
13362269 ATCAATAATTCAGGGAATCTGCACTTAGTAACCCTTTTTTG
1 ATCAATAATTCAGGGAATCTGC-CTTAGCAACCCTTTTTTG
*
13362310 ATCAATGATTCAGGGAATCTGCCTTAGCAACCCTTT
1 ATCAATAATTCAGGGAATCTGCCTTAGCAACCCTTT
13362346 ACATTCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 13 0.38
41 21 0.62
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (40 bp):
ATCAATAATTCAGGGAATCTGCCTTAGCAACCCTTTTTTG
Found at i:13380452 original size:30 final size:30
Alignment explanation
Indices: 13380413--13380487 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
13380403 TTAGGCACAG
*
13380413 AGGACACATGCCCATCTGGCTCATACAGCC
1 AGGAGACATGCCCATCTGGCTCATACAGCC
* * *
13380443 AGGAGACATGCCCGTGTGGCTCATACGGCC
1 AGGAGACATGCCCATCTGGCTCATACAGCC
*
13380473 AGGAGACACGCCCAT
1 AGGAGACATGCCCAT
13380488 GTCTTAGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.33, G:0.27, T:0.15
Consensus pattern (30 bp):
AGGAGACATGCCCATCTGGCTCATACAGCC
Found at i:13386716 original size:25 final size:25
Alignment explanation
Indices: 13386687--13386751 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
13386677 GTCCTATTTG
* *
13386687 TTATTTTTGCTATTAATTAATTTTA
1 TTATTTTTGATATTAATTAATCTTA
*
13386712 TTATTATTT-ATTATT-ATTACTCTTA
1 TTATT-TTTGA-TATTAATTAATCTTA
*
13386737 TTATTATTGATATTA
1 TTATTTTTGATATTA
13386752 TTATTATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
24 6 0.19
25 19 0.59
26 7 0.22
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (25 bp):
TTATTTTTGATATTAATTAATCTTA
Found at i:13386717 original size:3 final size:3
Alignment explanation
Indices: 13386709--13386758 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
13386699 TTAATTAATT
* *
13386709 TTA TTA TTA TTTA TTA TTA TTA CTC TTA TTA TTA TTGA -TA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
13386755 TTA T
1 TTA T
13386759 GTTTGGTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 35 0.88
4 4 0.10
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13386739 original size:15 final size:13
Alignment explanation
Indices: 13386709--13386758 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 13
13386699 TTAATTAATT
13386709 TTATTATTATTTA
1 TTATTATTATTTA
13386722 TTATTATTACTCTTA
1 TTATTATTA-T-TTA
13386737 TTATTATTGATATTA
1 TTATTATT-AT-TTA
13386752 TTATTAT
1 TTATTAT
13386759 GTTTGGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 22 0.67
16 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:13386928 original size:21 final size:22
Alignment explanation
Indices: 13386902--13386950 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
13386892 TTATTATTAG
13386902 TATTA-TAAATTTGTTATGTAT
1 TATTATTAAATTTGTTATGTAT
*
13386923 TATTATCTTAGATTTGTTATGTAT
1 TATTA--TTAAATTTGTTATGTAT
13386947 TATT
1 TATT
13386951 GTTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 5 0.21
24 19 0.79
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (22 bp):
TATTATTAAATTTGTTATGTAT
Found at i:13386990 original size:49 final size:51
Alignment explanation
Indices: 13386893--13386992 Score: 123
Period size: 49 Copynumber: 2.0 Consensus size: 51
13386883 TATAATGTAT
* * * *
13386893 TATTATTAGTATTATAAATTTGTTATGTATTATTATCTTAGATTTGTTATG
1 TATTATTAGTATTATAAATTTATTACGTATTATTATCTTAAATATGTTATG
* * *
13386944 TATTATT-GTTTTA-AAATTTATTACGTATTCTTATTTTAAATATGTTATG
1 TATTATTAGTATTATAAATTTATTACGTATTATTATCTTAAATATGTTATG
13386993 CATCATTACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 30 0.71
50 5 0.12
51 7 0.17
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (51 bp):
TATTATTAGTATTATAAATTTATTACGTATTATTATCTTAAATATGTTATG
Found at i:13387572 original size:19 final size:19
Alignment explanation
Indices: 13387548--13387656 Score: 173
Period size: 19 Copynumber: 5.7 Consensus size: 19
13387538 AATCTTCAGG
13387548 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13387567 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
13387586 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13387605 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
13387624 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13387643 GATATGCAATCTTA
1 GATATGCAATCTTA
13387657 AAAGATATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:13387598 original size:38 final size:38
Alignment explanation
Indices: 13387555--13387656 Score: 195
Period size: 38 Copynumber: 2.7 Consensus size: 38
13387545 AGGGATATGC
13387555 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
13387593 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
13387631 AATCTTAGATATGATATGCAATCTTA
1 AATCTTAGATATGATATGCAATCTTA
13387657 AAAGATATGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:13387983 original size:24 final size:26
Alignment explanation
Indices: 13387956--13388009 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
13387946 CCTTTTAATG
*
13387956 TTTTTGTAA-TTAAGCTTTT-TTTAT
1 TTTTTGTAATTTAACCTTTTATTTAT
* *
13387980 TTTTTTTAATTTACCCTTTTATTTAT
1 TTTTTGTAATTTAACCTTTTATTTAT
13388006 TTTT
1 TTTT
13388010 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.32
25 8 0.32
26 9 0.36
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTGTAATTTAACCTTTTATTTAT
Found at i:13390235 original size:14 final size:14
Alignment explanation
Indices: 13390216--13390243 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13390206 CAAGGAGATC
13390216 CGATCACACCTCAA
1 CGATCACACCTCAA
13390230 CGATCACACCTCAA
1 CGATCACACCTCAA
13390244 AGAAATGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.07, T:0.14
Consensus pattern (14 bp):
CGATCACACCTCAA
Found at i:13396064 original size:46 final size:46
Alignment explanation
Indices: 13395995--13396120 Score: 173
Period size: 46 Copynumber: 2.7 Consensus size: 46
13395985 AAGGAGAAGG
* * * *
13395995 GACCAAGGTGAAAACCTGGAAAGGGTGCTTTAAG-TCCTAAAAAAGA
1 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAGCT-CTAAAAAAAA
*
13396041 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTGAGCTCTAAAAAAAA
1 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAGCTCTAAAAAAAA
* *
13396087 GACCAAGGTGAAAACCCGCAAAGGGCACCTTAAG
1 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAG
13396121 ACCAAAAAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 70 0.99
47 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (46 bp):
GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAGCTCTAAAAAAAA
Found at i:13397420 original size:45 final size:45
Alignment explanation
Indices: 13397356--13397567 Score: 203
Period size: 45 Copynumber: 4.7 Consensus size: 45
13397346 CATTATGGCG
* *
13397356 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGATCATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
* * * * * *
13397401 AATCTTATCTCCCTTAAGTTGTAGTAGAGCAAATTGAAGC-TA-CT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-CATAGCA
* * * * * * * * *
13397445 AATCCTATCTGCCTAAAGTTGTAGTGGAGCGGATTAAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
** *
13397490 AGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
* *
13397535 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
13397568 TTAAAGCTAT
Statistics
Matches: 133, Mismatches: 31, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
44 34 0.26
45 98 0.74
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
Found at i:13397528 original size:89 final size:90
Alignment explanation
Indices: 13397404--13397573 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 90
13397394 CATAGCAAAT
* * * * * * *
13397404 CTTATCTCCCTTAAGTTGTAGTAGAGCAAATTGAAGCTA-CTAATCCTATCTGCCTAAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAAACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCA
* *
13397468 GTGGAGCGGATTAAAGATAGCGAGC
66 GTGGAACAGATTAAAGATAGCGAGC
* * * * *
13397493 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAAACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCA
13397558 GTGGAACAGATTAAAG
66 GTGGAACAGATTAAAG
13397574 CTATAAATTA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
89 33 0.50
90 33 0.50
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (90 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAAACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCA
GTGGAACAGATTAAAGATAGCGAGC
Found at i:13397908 original size:143 final size:142
Alignment explanation
Indices: 13397651--13397958 Score: 442
Period size: 143 Copynumber: 2.2 Consensus size: 142
13397641 AAAGTTGTAG
* *
13397651 GCCTTATCTCCCTAAAGTTGCAGCGGGGCAGACTGAAGACAGCGAAACTTATTCCCTAGCGTTGC
1 GCCTTATCTCCCTAAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAACTTATTCCCTAGCGTTGC
* *
13397716 AGTGGAACAGGTTAAAGCTACAAATTATCGCAGAACTTATCTTCCTGAAGTTGCAGTGGAGCAGA
66 AGTGGAACAGATTAAAGCTACAAATTATCGCAGAACTTATCTTCCTGAAGTTGCAGTGAAGCAGA
*
13397781 TTGAAGCCACCA
131 TTAAAGCCACCA
* *
13397793 GCCTTATCTCCCTAATGTTGCAGCGGAGCAAACTGAAGACAGCGAATCTTATTTCCCTAGCGTTG
1 GCCTTATCTCCCTAAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAACTTA-TTCCCTAGCGTTG
* *
13397858 CAGTGGAATAGATTATAGCTACAAATTAT-G-ACGAATCTTATCTTCCTGAAGTTGCAGTGAAGC
65 CAGTGGAACAGATTAAAGCTACAAATTATCGCA-GAA-CTTATCTTCCTGAAGTTGCAGTGAAGC
*
13397921 AGATTAAAGCCAACAA
128 AGATTAAAGCC-ACCA
* * *
13397937 TCC-TATTTCCCTGAAGTTGCAG
1 GCCTTATCTCCCTAAAGTTGCAG
13397959 TCGAGCGGAT
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
141 1 0.01
142 51 0.34
143 91 0.61
144 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (142 bp):
GCCTTATCTCCCTAAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAACTTATTCCCTAGCGTTGC
AGTGGAACAGATTAAAGCTACAAATTATCGCAGAACTTATCTTCCTGAAGTTGCAGTGAAGCAGA
TTAAAGCCACCA
Found at i:13399416 original size:10 final size:10
Alignment explanation
Indices: 13399401--13399441 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
13399391 TATTAATTAA
13399401 TTTTATTATT
1 TTTTATTATT
13399411 TTTTATTATT
1 TTTTATTATT
13399421 TTTTATTATT
1 TTTTATTATT
13399431 TATTTATTATT
1 T-TTTATTATT
13399442 ACTCTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTATTATT
Found at i:13399419 original size:3 final size:3
Alignment explanation
Indices: 13399403--13399470 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
13399393 TTAATTAATT
* *
13399403 TTA TTA TT- TT- TTA TTA TT- TT- TTA TTA TTTA TTTA TTA TTA CTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA
13399446 TTA TTA TTA TTGA -TA TTA TTA TTA T
1 TTA TTA TTA TT-A TTA TTA TTA TTA T
13399471 GTTTGGTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 9 0.16
3 39 0.70
4 8 0.14
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13399433 original size:24 final size:25
Alignment explanation
Indices: 13399406--13399470 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
13399396 ATTAATTTTA
* *
13399406 TTATTTTTTATTAT-TTTTTATTAT
1 TTATTTATTATTATCTTATTATTAT
13399430 TTATTTATTATTACTCTTATTATTAT
1 TTATTTATTATTA-TCTTATTATTAT
*
13399456 TGATATTATTATTAT
1 TTAT-TTATTATTAT
13399471 GTTTGGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.34
25 1 0.03
26 13 0.37
27 9 0.26
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (25 bp):
TTATTTATTATTATCTTATTATTAT
Found at i:13400665 original size:21 final size:20
Alignment explanation
Indices: 13400618--13400665 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
13400608 CTCAACTCTA
*
13400618 TTTTTAATTTCTCTAATTTT
1 TTTTTAATTTCTCTAATTTG
13400638 TTATTTAATATTCT-TAATTCTG
1 TT-TTTAAT-TTCTCTAATT-TG
13400660 TTTTTA
1 TTTTTA
13400666 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTCTCTAATTTG
Found at i:13401053 original size:24 final size:24
Alignment explanation
Indices: 13400954--13401054 Score: 96
Period size: 24 Copynumber: 4.2 Consensus size: 24
13400944 AATTATAATG
* *
13400954 TATTA-GTATTAGTATTATAAATT
1 TATTACGTATTATTATTTTAAATT
* * * *
13400977 TGTTATGTATTATTATCTTAGATT
1 TATTACGTATTATTATTTTAAATT
* *
13401001 TATTATGTATTATTGTTTTAAAATT
1 TATTACGTATTATTATTTT-AAATT
* *
13401026 TATTACGTATTTTTATTTTAAATA
1 TATTACGTATTATTATTTTAAATT
13401050 TATTA
1 TATTA
13401055 TGCATCATTA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
23 4 0.06
24 39 0.62
25 20 0.32
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
TATTACGTATTATTATTTTAAATT
Found at i:13404929 original size:45 final size:46
Alignment explanation
Indices: 13404880--13404977 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
13404870 AGATAGAAAC
*
13404880 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
13404925 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
13404971 GAAAATA
1 CAAAATA
13404978 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:13408861 original size:45 final size:46
Alignment explanation
Indices: 13408812--13408909 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
13408802 AGATAGAAAC
*
13408812 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
13408857 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
13408903 GAAAATA
1 CAAAATA
13408910 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:13410826 original size:24 final size:25
Alignment explanation
Indices: 13410774--13410837 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 25
13410764 AAAAAGCTTT
*
13410774 TATTTTTATAATTTTT--T-AAAAA
1 TATTTTTATACTTTTTAATAAAAAA
13410796 TATTTTTATACTTTTTAATAAAAAA
1 TATTTTTATACTTTTTAATAAAAAA
*
13410821 TA-TTTTATATTTTTTAA
1 TATTTTTATACTTTTTAA
13410838 CTTTCTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.41
24 15 0.41
25 7 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTTTATACTTTTTAATAAAAAA
Found at i:13410868 original size:6 final size:7
Alignment explanation
Indices: 13410849--13410874 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13410839 TTTCTATATA
13410849 AATTTTT
1 AATTTTT
13410856 AATTTTT
1 AATTTTT
13410863 AATTTTT
1 AATTTTT
13410870 AATTT
1 AATTT
13410875 ATGCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:13413008 original size:278 final size:278
Alignment explanation
Indices: 13412504--13413066 Score: 1108
Period size: 278 Copynumber: 2.0 Consensus size: 278
13412494 AGTCTATCAT
*
13412504 TCAAATATTCAGTTGAGGATCACCCAGCTTCTAAGAAAATAGTCAATGCAGGTTGCTATCTTTAC
1 TCAAATTTTCAGTTGAGGATCACCCAGCTTCTAAGAAAATAGTCAATGCAGGTTGCTATCTTTAC
13412569 AAAACAAACCTTACCACAATTCATATAGTCCAAGTTGGAAACAAGTCCAAAGAATTCAATATTTT
66 AAAACAAACCTTACCACAATTCATATAGTCCAAGTTGGAAACAAGTCCAAAGAATTCAATATTTT
13412634 GTTCATCCCACTGCTTAGCTAAACTTGGCTTATTAATCAAATATATAATGATCTCCCATCTAAAT
131 GTTCATCCCACTGCTTAGCTAAACTTGGCTTATTAATCAAATATATAATGATCTCCCATCTAAAT
13412699 ATTCAACATACAAACTTCTGGTTGCGGATCTCTTTATATGCAATTTTATCCATTATTTTGATTTT
196 ATTCAACATACAAACTTCTGGTTGCGGATCTCTTTATATGCAATTTTATCCATTATTTTGATTTT
13412764 TTTTCTCTCATCTTTATG
261 TTTTCTCTCATCTTTATG
13412782 TCAAATTTTCAGTTGAGGATCACCCAGCTTCTAAGAAAATAGTCAATGCAGGTTGCTATCTTTAC
1 TCAAATTTTCAGTTGAGGATCACCCAGCTTCTAAGAAAATAGTCAATGCAGGTTGCTATCTTTAC
13412847 AAAACAAACCTTACCACAATTCATATAGTCCAAGTTGGAAACAAGTCCAAAGAATTCAATATTTT
66 AAAACAAACCTTACCACAATTCATATAGTCCAAGTTGGAAACAAGTCCAAAGAATTCAATATTTT
*
13412912 GTTCATTCCACTGCTTAGCTAAACTTGGCTTATTAATCAAATATATAATGATCTCCCATCTAAAT
131 GTTCATCCCACTGCTTAGCTAAACTTGGCTTATTAATCAAATATATAATGATCTCCCATCTAAAT
13412977 ATTCAACATACAAACTTCTGGTTGCGGATCTCTTTATATGCAATTTTATCCATTATTTTGATTTT
196 ATTCAACATACAAACTTCTGGTTGCGGATCTCTTTATATGCAATTTTATCCATTATTTTGATTTT
13413042 TTTTCTCTCATCTTTATG
261 TTTTCTCTCATCTTTATG
13413060 TCAAATT
1 TCAAATT
13413067 ACTAGGCAGC
Statistics
Matches: 283, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
278 283 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (278 bp):
TCAAATTTTCAGTTGAGGATCACCCAGCTTCTAAGAAAATAGTCAATGCAGGTTGCTATCTTTAC
AAAACAAACCTTACCACAATTCATATAGTCCAAGTTGGAAACAAGTCCAAAGAATTCAATATTTT
GTTCATCCCACTGCTTAGCTAAACTTGGCTTATTAATCAAATATATAATGATCTCCCATCTAAAT
ATTCAACATACAAACTTCTGGTTGCGGATCTCTTTATATGCAATTTTATCCATTATTTTGATTTT
TTTTCTCTCATCTTTATG
Found at i:13421285 original size:12 final size:12
Alignment explanation
Indices: 13421270--13421301 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
13421260 ACTCATCGTT
13421270 TTTTATTTTTTA
1 TTTTATTTTTTA
13421282 TTTTA-TTTTTA
1 TTTTATTTTTTA
13421293 TTTT-TTTTT
1 TTTTATTTTT
13421302 ACGAATCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:13422208 original size:22 final size:22
Alignment explanation
Indices: 13422164--13422222 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
13422154 ATAAATGTTG
*
13422164 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
13422188 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
13422210 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
13422223 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:13425112 original size:43 final size:43
Alignment explanation
Indices: 13425056--13425291 Score: 211
Period size: 43 Copynumber: 5.4 Consensus size: 43
13425046 ATGCACTTCA
* * *
13425056 TGTGCCAGTATATTTACTTTGGTTCGTCCGATGATGCACTGTG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * * * * *
13425099 TGTGCCAACATATTTGTTTTGGTTCGTTCGATAATGCATTGTG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* *
13425142 TGTGCCAATATATTTGCTTCGGTTCATCCGGTGATTTGCACTGTG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGA--TGCACTGTG
* * * ** * ** * *
13425187 TCTGTCAGTATATTTGCTTCAATTCATGTGATAATGCACTATG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * * * *
13425230 TGTGCCAGTATATTTGCTTCAGTTCGTCCAATGATGCGCTATG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
*
13425273 TGTGCCAATATATTCGCTT
1 TGTGCCAATATATTTGCTT
13425292 TGATTTATCC
Statistics
Matches: 155, Mismatches: 36, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
43 122 0.79
45 33 0.21
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (43 bp):
TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
Found at i:13433960 original size:23 final size:22
Alignment explanation
Indices: 13433917--13433960 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
13433907 TTCTAAGTCG
13433917 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
13433940 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
13433961 TTAGTCGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:13434170 original size:23 final size:23
Alignment explanation
Indices: 13434028--13434172 Score: 227
Period size: 23 Copynumber: 6.3 Consensus size: 23
13434018 ATAAATGCCA
*
13434028 CACTAATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
13434051 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
13434074 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13434097 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13434120 CACTAATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13434143 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13434166 CACTGAT
1 CACTGAT
13434173 CAATAACACT
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 111 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:13439071 original size:23 final size:23
Alignment explanation
Indices: 13439045--13439189 Score: 245
Period size: 23 Copynumber: 6.3 Consensus size: 23
13439035 ATAAATGCCA
13439045 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
13439068 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13439091 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13439114 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13439137 CACTAATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13439160 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13439183 CACTGAT
1 CACTGAT
13439190 CAATAACACT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 114 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:13460129 original size:15 final size:15
Alignment explanation
Indices: 13460109--13460159 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
13460099 AAATTTTTTA
13460109 AAATTATAAAGATAT
1 AAATTATAAAGATAT
13460124 AAATTATTAAAG-TAAT
1 AAATTA-TAAAGAT-AT
* * *
13460140 AACTTATAAAAACAT
1 AAATTATAAAGATAT
13460155 AAATT
1 AAATT
13460160 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (15 bp):
AAATTATAAAGATAT
Found at i:13460394 original size:41 final size:42
Alignment explanation
Indices: 13460322--13460423 Score: 170
Period size: 41 Copynumber: 2.4 Consensus size: 42
13460312 GGCCCATTTT
**
13460322 TATTTTAAAAATTTTAAAAAATTTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAAA
13460365 TATTTTAAAATTAAAAAAAATTT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAAA
13460406 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
13460424 TTAAAAAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
41 36 0.63
42 15 0.26
43 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAAA
Found at i:13460399 original size:30 final size:29
Alignment explanation
Indices: 13460322--13460507 Score: 124
Period size: 30 Copynumber: 6.0 Consensus size: 29
13460312 GGCCCATTTT
*
13460322 TATTTTAAAAAT-TTTAAAAAATTTAAAAAAA
1 TATTTTAAAAATATTT-TAAAA-TT-AAAAAA
13460353 GTATTTTAAAAATATTTTAAAATTAAAAAA
1 -TATTTTAAAAATATTTTAAAATTAAAAAA
* *
13460383 AATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 TATTTTAAAAA-TATTTT--AAA-A--TTAAAA--AA
* ** **
13460420 AAAATTAAAAA-ATTAAAAAATTAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAA
*
13460448 GTATTTTAAAAATATTTTAAAATTTAAAAAG
1 -TATTTTAAAAATATTTTAAAA-TTAAAAAA
* * *
13460479 TATGTAAAAAATATTTTAAACTTAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAA
13460508 ATAAATATAT
Statistics
Matches: 124, Mismatches: 18, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.02
29 24 0.19
30 43 0.35
31 9 0.07
32 20 0.16
33 7 0.06
35 9 0.07
37 10 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (29 bp):
TATTTTAAAAATATTTTAAAATTAAAAAA
Found at i:13460404 original size:11 final size:11
Alignment explanation
Indices: 13460322--13460498 Score: 80
Period size: 11 Copynumber: 16.8 Consensus size: 11
13460312 GGCCCATTTT
13460322 TATTTT-AAAA
1 TATTTTAAAAA
13460332 -ATTTTAAAAA
1 TATTTTAAAAA
*
13460342 -ATTTAAAAAAA
1 TATTT-TAAAAA
13460353 GTATTTTAAAAA
1 -TATTTTAAAAA
13460365 TATTTT--AAA
1 TATTTTAAAAA
*
13460374 -A-TTAAAAAA
1 TATTTTAAAAA
* *
13460383 AATTTAAAAAA
1 TATTTTAAAAA
13460394 GTATTTTAAAAA
1 -TATTTTAAAAA
13460406 TATTTTAAAATTAA
1 TATTTT-AAA--AA
* **
13460420 AAAATTAAAAA
1 TATTTTAAAAA
13460431 -A--TTAAAAA
1 TATTTTAAAAA
*
13460439 -A-TTAAAAAA
1 TATTTTAAAAA
13460448 GTATTTTAAAAA
1 -TATTTTAAAAA
13460460 TATTTT--AAA
1 TATTTTAAAAA
13460469 -A-TTTAAAAA
1 TATTTTAAAAA
* *
13460478 GTATGTAAAAAA
1 -TATTTTAAAAA
13460490 TATTTTAAA
1 TATTTTAAA
13460499 CTTAAAAAAA
Statistics
Matches: 132, Mismatches: 14, Indels: 41
0.71 0.07 0.22
Matches are distributed among these distances:
7 5 0.04
8 10 0.08
9 23 0.17
10 10 0.08
11 42 0.32
12 30 0.23
13 7 0.05
14 5 0.04
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:13460425 original size:8 final size:8
Alignment explanation
Indices: 13460412--13460447 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
13460402 AAAATATTTT
13460412 AAAATTAA
1 AAAATTAA
13460420 AAAATTAA
1 AAAATTAA
13460428 AAAATTAA
1 AAAATTAA
13460436 AAAATTAA
1 AAAATTAA
13460444 AAAA
1 AAAA
13460448 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATTAA
Found at i:13460498 original size:54 final size:50
Alignment explanation
Indices: 13460328--13460498 Score: 137
Period size: 52 Copynumber: 3.4 Consensus size: 50
13460318 TTTTTATTTT
**
13460328 AAAAATTTTAAAA-AATTTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAATAATTT-AAAAAAGTATTTTAAAAATATTTTAAAATT--A
* **
13460380 AAAAATTTAAAAAAGT-ATTTTAAAAA-TATTTT--AAA-ATTAAAAAATTA
1 AAAAA-TTAAAAAA-TAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
13460427 AAAAATT--AAAA-AA-TTAAAAAAGTATTTTAAAAATATTTTAAAATTTA
1 AAAAATTAAAAAATAATTTAAAAAAGTATTTTAAAAATATTTTAAAA-TTA
*
13460474 AAAAGTATGTAAAAAATATTTTAAA
1 AAAA--AT-TAAAAAATAATTTAAA
13460499 CTTAAAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 30
0.71 0.07 0.23
Matches are distributed among these distances:
42 7 0.07
43 7 0.07
44 4 0.04
45 3 0.03
46 9 0.10
47 13 0.14
49 11 0.12
50 4 0.04
52 15 0.16
53 12 0.13
54 9 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (50 bp):
AAAAATTAAAAAATAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:13468725 original size:94 final size:94
Alignment explanation
Indices: 13468464--13468730 Score: 338
Period size: 94 Copynumber: 2.8 Consensus size: 94
13468454 GTGTCACAGT
** * * ** * *
13468464 TTCATCTTGCTCCATTACAACTTCAATGAGATAAGGTTTGTTGTTGTAGTTTCATTCCAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
* * *
13468529 TACAACTTAAGAGGTATAGGATTTGTAGC
66 TACAACTTCAGGGGCATAGGATTTGTAGC
* * * *
13468558 TTCATCTTGCTCCATTGTAACTT-TAGGAAGATAAGATTTTCTATGGTAGCTTCACTCCAACCCA
1 TTCATCTTGCTCCATTGTAACTTCAAGG-AGATAAGATTTACTATTGTAGCTTCATTCCAACCCA
* *
13468622 CTGCCACTTCAGGGGCATAGGATTTGTAGC
65 CTACAACTTCAGGGGCATAGGATTTGTAGC
* * *
13468652 TTCATTTTGCTCCATTGTAACTTCAAGGAGATAAGATTCACTATTGTAGCTTCATTCAAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
13468717 TACAACTTCAGGGG
66 TACAACTTCAGGGG
13468731 GACTGGAGTT
Statistics
Matches: 146, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
93 2 0.01
94 141 0.97
95 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (94 bp):
TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
TACAACTTCAGGGGCATAGGATTTGTAGC
Found at i:13469672 original size:213 final size:213
Alignment explanation
Indices: 13469305--13469719 Score: 803
Period size: 213 Copynumber: 1.9 Consensus size: 213
13469295 CTGTTTTAGG
13469305 TCCTTGTACTATTTAGAAATCTTTCAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
1 TCCTTGTACTATTTAGAAATCTTTCAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
*
13469370 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
66 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAAATAAAATGAAAAAATCTTAACGAAAA
*
13469435 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
131 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTGCCCCA
13469500 GATATCGATATGTAATAA
196 GATATCGATATGTAATAA
*
13469518 TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
1 TCCTTGTACTATTTAGAAATCTTTCAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
13469583 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAAATAAAATGAAAAAATCTTAACGAAAA
66 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAAATAAAATGAAAAAATCTTAACGAAAA
13469648 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTGCCCCA
131 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTGCCCCA
13469713 GATATCG
196 GATATCG
13469720 TATTGTGAGC
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 199 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (213 bp):
TCCTTGTACTATTTAGAAATCTTTCAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAAATAAAATGAAAAAATCTTAACGAAAA
AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTGCCCCA
GATATCGATATGTAATAA
Found at i:13486966 original size:20 final size:20
Alignment explanation
Indices: 13486937--13486988 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
13486927 AATTTTCTCC
13486937 TCTTCCAACTTCTCTATCCT
1 TCTTCCAACTTCTCTATCCT
* *
13486957 TCTTCTAACTTCTCTATCTT
1 TCTTCCAACTTCTCTATCCT
*
13486977 TTTTCCAA-TTCT
1 TCTTCCAACTTCT
13486989 GAACTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (20 bp):
TCTTCCAACTTCTCTATCCT
Found at i:13489833 original size:13 final size:13
Alignment explanation
Indices: 13489817--13489843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13489807 ATTAGTACTT
13489817 ATAATAATTAATG
1 ATAATAATTAATG
13489830 ATAATAATTAATG
1 ATAATAATTAATG
13489843 A
1 A
13489844 CCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAATAATTAATG
Found at i:13490922 original size:7 final size:7
Alignment explanation
Indices: 13490912--13490940 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
13490902 ATATTTTTTG
13490912 TTTTGTT
1 TTTTGTT
13490919 TTTTGTT
1 TTTTGTT
13490926 TTTTGTT
1 TTTTGTT
13490933 TTTTGTT
1 TTTTGTT
13490940 T
1 T
13490941 ATCTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTGTT
Found at i:13492657 original size:9 final size:9
Alignment explanation
Indices: 13492628--13492664 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
13492618 TGAGTTTTCG
13492628 AATTCGAAT
1 AATTCGAAT
*
13492637 AACTCGAAT
1 AATTCGAAT
13492646 AATTCGAAT
1 AATTCGAAT
*
13492655 AATTCAAAT
1 AATTCGAAT
13492664 A
1 A
13492665 TCAAACTATA
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:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:13493124 original size:17 final size:17
Alignment explanation
Indices: 13493097--13493154 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
13493087 CTCTCCCCTA
*
13493097 TTTACTTTCCCTTAAACT
1 TTTATTTTCCC-TAAACT
*
13493115 TTTA-TTTCCCAAAACTT
1 TTTATTTTCCCTAAAC-T
13493132 TTTATTTTTCCCCTAAACT
1 TTTA-TTTT-CCCTAAACT
13493151 TTTA
1 TTTA
13493155 CTTCTCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 4 0.12
19 8 0.24
20 7 0.21
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATTTTCCCTAAACT
Found at i:13495849 original size:21 final size:20
Alignment explanation
Indices: 13495819--13495857 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13495809 GTACATGCAT
13495819 ACATACATTTTTATAATATTG
1 ACATACA-TTTTATAATATTG
*
13495840 ACATATATTTTATAATAT
1 ACATACATTTTATAATAT
13495858 ATATACGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
ACATACATTTTATAATATTG
Found at i:13496367 original size:107 final size:107
Alignment explanation
Indices: 13496176--13496368 Score: 323
Period size: 107 Copynumber: 1.8 Consensus size: 107
13496166 CTAAATAAGA
* * * * *
13496176 CAATGTTTTGAGTTTGGAAAATCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTCTCGTTC
1 CAATATTTTGAGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTC
13496241 GACCAAATAGCCAAATATCCTTTTTAAACTTTCAAAACAAGG
66 GACCAAATAGCCAAATATCCTTTTTAAACTTTCAAAACAAGG
*
13496283 CAATATTTTGCGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTC
1 CAATATTTTGAGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTC
*
13496348 GACTAAATAGCCAAATATCCT
66 GACCAAATAGCCAAATATCCT
13496369 CTTAAATCTC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 79 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (107 bp):
CAATATTTTGAGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTC
GACCAAATAGCCAAATATCCTTTTTAAACTTTCAAAACAAGG
Found at i:13501407 original size:16 final size:17
Alignment explanation
Indices: 13501386--13501423 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13501376 ACAGCAGATT
13501386 TATTTTGATTT-TTTTC
1 TATTTTGATTTCTTTTC
**
13501402 TATTTTTCTTTCTTTTC
1 TATTTTGATTTCTTTTC
13501419 TATTT
1 TATTT
13501424 CGGCTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTGATTTCTTTTC
Found at i:13508951 original size:2 final size:2
Alignment explanation
Indices: 13508944--13508974 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13508934 GAAAAACAAA
*
13508944 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13508975 ACAAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13511259 original size:2 final size:2
Alignment explanation
Indices: 13511254--13511289 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13511244 TCTGTCTCTT
*
13511254 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13511290 AGTTTAATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13514308 original size:20 final size:20
Alignment explanation
Indices: 13514283--13514320 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13514273 GGACTATGCA
*
13514283 AAACAATGTTGTTTTACCCT
1 AAACAATGCTGTTTTACCCT
13514303 AAACAATGCTGTTTTACC
1 AAACAATGCTGTTTTACC
13514321 TTGATCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
AAACAATGCTGTTTTACCCT
Found at i:13515025 original size:9 final size:9
Alignment explanation
Indices: 13515013--13515053 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
13515003 AAAAAGAATT
*
13515013 TTTTTATAA
1 TTTTTAAAA
13515022 TTTTTAAACAA
1 TTTTT-AA-AA
13515033 TTTTTAAAA
1 TTTTTAAAA
13515042 TTTTTAAAA
1 TTTTTAAAA
13515051 TTT
1 TTT
13515054 CAAAAGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 19 0.66
10 3 0.10
11 7 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:13520420 original size:3 final size:3
Alignment explanation
Indices: 13520412--13520535 Score: 221
Period size: 3 Copynumber: 41.3 Consensus size: 3
13520402 CCAATACACT
13520412 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
13520460 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
13520508 GAA GAA TAA GAA GAA GAA GAA AAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
13520536 TCCTTAACTG
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:13525281 original size:5 final size:5
Alignment explanation
Indices: 13525271--13525298 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
13525261 TAAAGCCTCC
13525271 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
13525299 TTACTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:13528219 original size:23 final size:23
Alignment explanation
Indices: 13528173--13528222 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
13528163 GTTTTAAGTT
*
13528173 TTTATATGTATTATTATTTGAAA
1 TTTATATGTATCATTATTTGAAA
13528196 TTTACTATGTATCATTATTT-AAA
1 TTTA-TATGTATCATTATTTGAAA
13528219 TTTA
1 TTTA
13528223 ACATATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTATATGTATCATTATTTGAAA
Found at i:13531870 original size:18 final size:18
Alignment explanation
Indices: 13531807--13531860 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
13531797 ATGAAAAAAC
13531807 AATGATATTTGAAAT-AT
1 AATGATATTTGAAATAAT
** *
13531824 TTTACATATTTGAAATAAT
1 AAT-GATATTTGAAATAAT
13531843 AATGATATTTGAAATAAT
1 AATGATATTTGAAATAAT
13531861 CATTTGATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 1 0.03
18 25 0.86
19 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (18 bp):
AATGATATTTGAAATAAT
Found at i:13532079 original size:13 final size:13
Alignment explanation
Indices: 13532063--13532087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13532053 TAATATATTT
13532063 ATTAATTATAAAC
1 ATTAATTATAAAC
13532076 ATTAATTATAAA
1 ATTAATTATAAA
13532088 TAAAAAAGCT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAATTATAAAC
Found at i:13533005 original size:18 final size:18
Alignment explanation
Indices: 13532982--13533017 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13532972 GTAATATGTT
*
13532982 ATATTATGTTATTTATAA
1 ATATTATGTAATTTATAA
13533000 ATATTATGTAATTTATAA
1 ATATTATGTAATTTATAA
13533018 TACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTATGTAATTTATAA
Found at i:13538545 original size:11 final size:11
Alignment explanation
Indices: 13538529--13538553 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13538519 AAAGTAAAAT
13538529 AAATAAATGAA
1 AAATAAATGAA
13538540 AAATAAATGAA
1 AAATAAATGAA
13538551 AAA
1 AAA
13538554 CTCAAGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATAAATGAA
Found at i:13538547 original size:15 final size:15
Alignment explanation
Indices: 13538503--13538552 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
13538493 TCGAAAGAGG
13538503 AAAAGAAAAAATAAA-
1 AAAAG-AAAAATAAAT
*
13538518 AAAAGTAAAATAAAT
1 AAAAGAAAAATAAAT
*
13538533 AAATGAAAAATAAAT
1 AAAAGAAAAATAAAT
13538548 GAAAA
1 -AAAA
13538553 ACTCAAGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 18 0.62
16 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAGAAAAATAAAT
Found at i:13539412 original size:45 final size:43
Alignment explanation
Indices: 13539361--13539686 Score: 171
Period size: 45 Copynumber: 7.3 Consensus size: 43
13539351 TAATCCGTTT
* *
13539361 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTACTC
1 CACTGCAACTTCAGGGAGATAAGA-TTG-TATCTTCAGTCTACTC
* * * **
13539406 CACTGCAACTCCAAGGAGATAAGACTTGTATCATCAACCTA-TC
1 CACTGCAACTTCAGGGAGATAAGA-TTGTATCTTCAGTCTACTC
* * * *
13539449 CTACTGCAACTTCAGGGATATAAGGATTG-A-CATGA-TCTGCTC
1 C-ACTGCAACTTCAGGGAGATAA-GATTGTATCTTCAGTCTACTC
* * * * * *
13539491 TACTGCAACTTTAGAGAGATAAGATCGATAAT-TTATAGTTTTAATCTGTTC
1 CACTGCAACTTCAGGGAGATAAGATTG-T-ATCTT-CAG-TCT-A-C---TC
* * * *
13539542 CACTGCAACTTTAGGGAAATAAGAGTCGCTATCTTCAGTCTGCTC
1 CACTGCAACTTCAGGGAGATAAGA-TTG-TATCTTCAGTCTACTC
* * *
13539587 CACTGCAACTTCAGGGAGATAAGATTG-GTCGTGA-TCTACTC
1 CACTGCAACTTCAGGGAGATAAGATTGTATCTTCAGTCTACTC
* * * *
13539628 TACTGCAACTTTAGAGAGATAAGATCTACTATCTTCAGTCTACTC
1 CACTGCAACTTCAGGGAGATAAGAT-T-GTATCTTCAGTCTACTC
* *
13539673 TACTGCAACCTCAG
1 CACTGCAACTTCAG
13539687 TAAGAGAAGA
Statistics
Matches: 214, Mismatches: 46, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
40 4 0.02
41 48 0.22
42 11 0.05
43 6 0.03
44 37 0.17
45 69 0.32
46 2 0.01
48 2 0.01
50 2 0.01
51 27 0.13
52 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGATTGTATCTTCAGTCTACTC
Found at i:13539472 original size:44 final size:45
Alignment explanation
Indices: 13539361--13539472 Score: 120
Period size: 44 Copynumber: 2.5 Consensus size: 45
13539351 TAATCCGTTT
* * * **
13539361 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTACTC
1 CACTGCAACTTCAGGGAAATAAGACTTGCTATCATCAACCTACTC
* * *
13539406 CACTGCAACTCCAAGGAGATAAGACTTG-TATCATCAACCTA-TC
1 CACTGCAACTTCAGGGAAATAAGACTTGCTATCATCAACCTACTC
*
13539449 CTACTGCAACTTCAGGGATATAAG
1 C-ACTGCAACTTCAGGGAAATAAG
13539473 GATTGACATG
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.05
44 28 0.51
45 24 0.44
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (45 bp):
CACTGCAACTTCAGGGAAATAAGACTTGCTATCATCAACCTACTC
Found at i:13539611 original size:96 final size:94
Alignment explanation
Indices: 13539304--13539611 Score: 271
Period size: 96 Copynumber: 3.3 Consensus size: 94
13539294 TTGTTATGAC
* * *
13539304 CTGCTCTACTGCAACTTCAAAGAGATAAGATCGGTAATTTATAGCTTTAATCCGTTTCACTGCAA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGATC-GTAATTTATAG-TTTAATCTGTTCCACTGCAA
* *
13539369 CTTCAGGGAAATAAGATTTGCTATCTTTAGT
64 CTTCAGGGAAATAAGAGTTGCTATCTTCAGT
* * * * * * *
13539400 CTACTCCACTGCAACTCCAAGGAGATAAGA-C-T--TGTATCA--TCAACCT-ATCCTACTGCAA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGATCGTAATTTAT-AGTTTAATCTGTTCC-ACTGCAA
* * *
13539458 CTTCAGGGATATAAG-GATTG--A-CATGA-T
64 CTTCAGGGAAATAAGAG-TTGCTATCTTCAGT
* * *
13539485 CTGCTCTACTGCAACTTTAGAGAGATAAGATCGATAATTTATAGTTTTAATCTGTTCCACTGCAA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGATCG-TAATTTATAG-TTTAATCTGTTCCACTGCAA
* *
13539550 CTTTAGGGAAATAAGAGTCGCTATCTTCAGT
64 CTTCAGGGAAATAAGAGTTGCTATCTTCAGT
**
13539581 CTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 CTGCTCCACTGCAACTTCAAAGAGATAAGAT
13539612 TGGTCGTGAT
Statistics
Matches: 163, Mismatches: 32, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
85 25 0.15
86 4 0.02
87 1 0.01
88 3 0.02
89 29 0.18
90 4 0.02
91 4 0.02
92 28 0.17
93 5 0.03
94 1 0.01
95 4 0.02
96 55 0.34
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (94 bp):
CTGCTCCACTGCAACTTCAAAGAGATAAGATCGTAATTTATAGTTTAATCTGTTCCACTGCAACT
TCAGGGAAATAAGAGTTGCTATCTTCAGT
Found at i:13552751 original size:38 final size:38
Alignment explanation
Indices: 13552700--13552775 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
13552690 TTTATAAGTT
13552700 AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
1 AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
*
13552738 AGTTTTTTTTTTCAATTTTCATCTTTCTCCTTTCTTCC
1 AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
13552776 CAAAAAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.11, C:0.25, G:0.03, T:0.62
Consensus pattern (38 bp):
AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
Found at i:13558181 original size:91 final size:91
Alignment explanation
Indices: 13558033--13558291 Score: 326
Period size: 91 Copynumber: 2.9 Consensus size: 91
13558023 ACACTAGATG
* * * * *
13558033 CACATAGTGTAAA-CCTGTAGGCTAAATGTT-TTCCCCGATAACATGCCATATTGCTCATAAGAG
1 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
*
13558096 CTTTCCCGTCGATATAATGCTAAATA
66 CTTTCCCGTCGATATAATGCCAAATA
* *
13558122 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGTTAGATTGCTCATTAGAG
1 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
* * * *
13558187 CTTTCTCG-CTGATATCATGCCAAGTG
66 CTTTCCCGTC-GATATAATGCCAAATA
* * * * *
13558213 TACATAGTGCAAAGCCCGTAGGCTAAATATTCTCCCCCAATAACACGGTAGATTGCTCATAAGAG
1 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
*
13558278 CTTTCCCATCGATA
66 CTTTCCCGTCGATA
13558292 ACACACTAGA
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
89 12 0.08
90 17 0.12
91 116 0.79
92 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (91 bp):
CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
CTTTCCCGTCGATATAATGCCAAATA
Found at i:13563638 original size:13 final size:13
Alignment explanation
Indices: 13563620--13563645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13563610 CGTGTTTCCA
13563620 AAAACCATTTGTT
1 AAAACCATTTGTT
13563633 AAAACCATTTGTT
1 AAAACCATTTGTT
13563646 TGTGTAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:13576526 original size:11 final size:11
Alignment explanation
Indices: 13576500--13576557 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
13576490 CTCTTAGTCT
13576500 TTATTTTATT-
1 TTATTTTATTA
13576510 TTATTTTATTA
1 TTATTTTATTA
13576521 TTATTTCT-TTA
1 TTATTT-TATTA
13576532 TT-TTTTATTA
1 TTATTTTATTA
13576542 GTT-TTTTATTA
1 -TTATTTTATTA
13576553 TTATT
1 TTATT
13576558 CTTAATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.02
10 18 0.42
11 23 0.53
12 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:13576526 original size:21 final size:23
Alignment explanation
Indices: 13576500--13576557 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
13576490 CTCTTAGTCT
13576500 TTATTTTATT-TTATTTTATTA-
1 TTATTTTATTATTATTTTATTAG
13576521 TTATTTCT-TTATT-TTTTATTAG
1 TTATTT-TATTATTATTTTATTAG
13576543 TT-TTTTATTATTATT
1 TTATTTTATTATTATT
13576558 CTTAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.03
21 24 0.75
22 7 0.22
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTATTTTATTATTATTTTATTAG
Found at i:13576531 original size:29 final size:29
Alignment explanation
Indices: 13576497--13576554 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
13576487 CTCCTCTTAG
13576497 TCTTTATTTTATT-TTA-TTTTATTATTATT
1 TCTTTATTTT-TTATTAGTTTT-TTATTATT
13576526 TCTTTATTTTTTATTAGTTTTTTATTATT
1 TCTTTATTTTTTATTAGTTTTTTATTATT
13576555 ATTCTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 2 0.07
29 21 0.78
30 4 0.15
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (29 bp):
TCTTTATTTTTTATTAGTTTTTTATTATT
Found at i:13576539 original size:18 final size:19
Alignment explanation
Indices: 13576508--13576557 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
13576498 CTTTATTTTA
13576508 TTTTATTTTATTATTA-TT
1 TTTTATTTTATTATTAGTT
13576526 TCTTTATTTT-TTATTAGTT
1 T-TTTATTTTATTATTAGTT
13576545 TTTTATTATTATT
1 TTTTATT-TTATT
13576558 CTTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 13 0.46
19 13 0.46
20 2 0.07
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTTTATTATTAGTT
Found at i:13578504 original size:6 final size:6
Alignment explanation
Indices: 13578493--13578535 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
13578483 AGTCTATTTG
* * *
13578493 TTTTAT TTTTAT TTTTA- TTTTAT GTTTAT GTTTAT TGTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
13578536 GCTTAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:13581908 original size:42 final size:42
Alignment explanation
Indices: 13581849--13581942 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
13581839 CTTTCTTTTC
13581849 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
1 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
13581891 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
1 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
*
13581933 CACATGGCCA
1 CACACGGCCA
13581943 TACGACACGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.18
Consensus pattern (42 bp):
CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
Found at i:13593373 original size:12 final size:12
Alignment explanation
Indices: 13593356--13593383 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13593346 CCCCACAGAA
13593356 AATAGACTCATT
1 AATAGACTCATT
13593368 AATAGACTCATT
1 AATAGACTCATT
13593380 AATA
1 AATA
13593384 ATTTAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (12 bp):
AATAGACTCATT
Found at i:13600224 original size:41 final size:41
Alignment explanation
Indices: 13600179--13600414 Score: 224
Period size: 41 Copynumber: 5.8 Consensus size: 41
13600169 GGCATTGAGT
* *
13600179 CTAGCAGGCTTTGTGTCGGTGTGTTATATCAGGCTTTATGC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
* * * * *
13600220 CTAGCAAGCTTCGTGTCAGTGTATTGTATTAAGCTTTATGC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
* * *
13600261 CTAGCAGGCATCGTGCCGGTGTATTATATCAGGCTTTGTGC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
* * * * *
13600302 CTAGCATGCTTTGTG-CTGGTGTATTATATTAGGCATTGTGC
1 CTAGCAGGCTTCGTGTC-GGTGTATTATATCAGGCTTTATGC
* * ** * *
13600343 CTAGCAAGCTTTGTACCGATGTTTTATATCAGGCTTTGA-GC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTT-ATGC
* * *
13600384 CTAGTAGGCTTCGTGTCAGTGTATTGTATCA
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCA
13600415 AGTAAATTGT
Statistics
Matches: 156, Mismatches: 36, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
40 1 0.01
41 154 0.99
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (41 bp):
CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
Found at i:13600303 original size:82 final size:82
Alignment explanation
Indices: 13600179--13600412 Score: 281
Period size: 82 Copynumber: 2.9 Consensus size: 82
13600169 GGCATTGAGT
* * *
13600179 CTAGCAGGCTTTGTGTCGGTGTGTTATATCAGGCTTTATGCCTAGCAAGCTTCGTGTCAGTGTAT
1 CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTCAGTGTAT
*
13600244 TGTATTAAGCTTTATGC
66 TGTATTAAGCATTATGC
* * * * *
13600261 CTAGCAGGCATCGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCATGCTTTGTG-CTGGTGTA
1 CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTC-AGTGTA
* * *
13600325 TTATATTAGGCATTGTGC
65 TTGTATTAAGCATTATGC
* * * * * * *
13600343 CTAGCAAGCTTTGTACCGATGTTTTATATCAGGCTTTGAGCCTAGTAGGCTTCGTGTCAGTGTAT
1 CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTCAGTGTAT
13600408 TGTAT
66 TGTAT
13600413 CAAGTAAATT
Statistics
Matches: 126, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
81 1 0.01
82 124 0.98
83 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (82 bp):
CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTCAGTGTAT
TGTATTAAGCATTATGC
Found at i:13600398 original size:123 final size:122
Alignment explanation
Indices: 13600179--13600414 Score: 271
Period size: 123 Copynumber: 1.9 Consensus size: 122
13600169 GGCATTGAGT
* *
13600179 CTAGCAGGCTTTGTGTCGGTGTGTTATATCAGGCTTTATGCCTAGCAAGCTTCGTGTCAGTGTAT
1 CTAGCAGGCTTTGTGTCGGTGTATTATATCAGGCATTATGCCTAGCAAGCTTC-TGTCAGTGTAT
* * *
13600244 TGTATTAAGCTTTATGCCTAGCAGGCATCGTGCCGGTGTATTATATCAGGCTTTGTGC
65 TATATCAAGCTTTATGCCTAGCAGGCATCGTGCCAGTGTATTATATCAGGCTTTGTGC
* * * *
13600302 CTAGCATGCTTTGTG-CTGGTGTATTATATTAGGCATTGTGCCTAGCAAGCTT-TGTACCGATGT
1 CTAGCAGGCTTTGTGTC-GGTGTATTATATCAGGCATTATGCCTAGCAAGCTTCTGT-CAG-TGT
* * * * * *
13600365 TTTATATCAGGCTTTGA-GCCTAGTAGGCTTCGTGTCAGTGTATTGTATCA
63 ATTATATCAAGCTTT-ATGCCTAGCAGGCATCGTGCCAGTGTATTATATCA
13600415 AGTAAATTGT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
121 3 0.03
122 3 0.03
123 87 0.93
124 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (122 bp):
CTAGCAGGCTTTGTGTCGGTGTATTATATCAGGCATTATGCCTAGCAAGCTTCTGTCAGTGTATT
ATATCAAGCTTTATGCCTAGCAGGCATCGTGCCAGTGTATTATATCAGGCTTTGTGC
Found at i:13608421 original size:13 final size:13
Alignment explanation
Indices: 13608405--13608429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13608395 CCATTGCCAG
13608405 AAATAATAATAAC
1 AAATAATAATAAC
13608418 AAATAATAATAA
1 AAATAATAATAA
13608430 ATATCTAAAC
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:13608746 original size:2 final size:2
Alignment explanation
Indices: 13608739--13608770 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
13608729 TCTCCATGCA
*
13608739 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13608771 TTACTGGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:13627936 original size:19 final size:20
Alignment explanation
Indices: 13627888--13627939 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
13627878 GTATTTGATT
* *
13627888 TTGGATTCTTCTAGATAATG
1 TTGGACTCTTCTAGATAATC
* *
13627908 TAGGAGTCTTCTAG-TAATC
1 TTGGACTCTTCTAGATAATC
13627927 TTGGACTCTTCTA
1 TTGGACTCTTCTA
13627940 ATGCATTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGGACTCTTCTAGATAATC
Found at i:13645294 original size:3 final size:3
Alignment explanation
Indices: 13645288--13645315 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13645278 TAATAATAAT
13645288 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
13645316 GGAGGAGGAG
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:13646112 original size:15 final size:15
Alignment explanation
Indices: 13646092--13646122 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13646082 AAAACAACAT
13646092 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
13646107 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
13646122 A
1 A
13646123 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:13650465 original size:15 final size:15
Alignment explanation
Indices: 13650445--13650475 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13650435 AAAACAACAT
13650445 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
13650460 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
13650475 A
1 A
13650476 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:13651544 original size:111 final size:111
Alignment explanation
Indices: 13651350--13651570 Score: 379
Period size: 111 Copynumber: 2.0 Consensus size: 111
13651340 CTTATTATTT
* * *
13651350 AAATCTTCATTTCGAGAAAACGACACGTCACATCCAATACATTAGGACACGACATATCGAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGAACACGACATATCAAATTCC
*
13651415 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
66 CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTA
* * *
13651461 AAATCTTCATTTCTAGAAAATGACACATCACATCCAATACATTAGAACACGACGTATCAAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGAACACGACATATCAAATTCC
13651526 CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTT
66 CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTT
13651571 TGATTATTTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (111 bp):
AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGAACACGACATATCAAATTCC
CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTA
Found at i:13652009 original size:2 final size:2
Alignment explanation
Indices: 13652002--13652031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13651992 ATCACAAACA
13652002 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
13652032 GCGAATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13653852 original size:44 final size:44
Alignment explanation
Indices: 13653817--13654047 Score: 329
Period size: 44 Copynumber: 5.2 Consensus size: 44
13653807 ACTACTGCTT
* *
13653817 AGGGAGATAGGA-TCCACAATCTTCAACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGCTGGTC
* *
13653861 AGGGAGATAGGACATACAATCTTCCACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * * *
13653905 AGGGAGTTAGGACTTGCGATCTTCAACCTATTCCACTACTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * * *
13653949 AGGGAGTTAGGACTTGCAATCTTCTACCTATTCCTCTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
13653993 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
13654037 AGGGAGCTAGG
1 AGGGAGATAGG
13654048 TTTTGTGATT
Statistics
Matches: 167, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
44 167 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (44 bp):
AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
Found at i:13662562 original size:14 final size:14
Alignment explanation
Indices: 13662543--13662572 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13662533 GGTGGACTCT
13662543 AATGCGAATGCATG
1 AATGCGAATGCATG
13662557 AATGCGAATGCATG
1 AATGCGAATGCATG
13662571 AA
1 AA
13662573 AGCAAAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AATGCGAATGCATG
Found at i:13666008 original size:111 final size:111
Alignment explanation
Indices: 13665814--13666034 Score: 424
Period size: 111 Copynumber: 2.0 Consensus size: 111
13665804 CTTATTATTT
* *
13665814 AAATCTTCATTTCGAGAAAACGACACGTCACATCCAATACATTAGGACACGATGTATCGAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCGAATTCC
13665879 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
66 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
13665925 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCGAATTCC
1 AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCGAATTCC
13665990 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTT
66 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTT
13666035 CGATTATTTA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (111 bp):
AAATCTTCATTTCGAGAAAACGACACATCACATCCAATACATTAGGACACGACGTATCGAATTCC
CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
Found at i:13667913 original size:17 final size:17
Alignment explanation
Indices: 13667891--13667923 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13667881 TTAATTTGGT
13667891 TTTATTTTA-TTTATTTG
1 TTTA-TTTAGTTTATTTG
13667908 TTTATTTAGTTTATTT
1 TTTATTTAGTTTATTT
13667924 CACTAACGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTATTTAGTTTATTTG
Found at i:13674206 original size:30 final size:29
Alignment explanation
Indices: 13674167--13674233 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
13674157 ACCAAAAAAA
*
13674167 GCCGTTTTTTTTCAAAATTTACCGAAATGG
1 GCCGATTTTTTT-AAAATTTACCGAAATGG
** *
13674197 GCCGATTTTTTTATTATTTACCGGAATGG
1 GCCGATTTTTTTAAAATTTACCGAAATGG
13674226 GCC-ATTTT
1 GCCGATTTT
13674234 CCGCGAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 17 0.52
30 11 0.33
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (29 bp):
GCCGATTTTTTTAAAATTTACCGAAATGG
Found at i:13677034 original size:18 final size:19
Alignment explanation
Indices: 13677011--13677053 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
13677001 GAAATGGCAA
13677011 AGATGAGAAATG-AATATG
1 AGATGAGAAATGAAATATG
*
13677029 AGATGATAAATGAAATATG
1 AGATGAGAAATGAAATATG
*
13677048 AAATGA
1 AGATGA
13677054 TGAGATGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (19 bp):
AGATGAGAAATGAAATATG
Found at i:13677047 original size:19 final size:18
Alignment explanation
Indices: 13677011--13677054 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
13677001 GAAATGGCAA
*
13677011 AGATGAGAAATGAATATG
1 AGATGATAAATGAATATG
13677029 AGATGATAAATGAAATATG
1 AGATGATAAATG-AATATG
*
13677048 AAATGAT
1 AGATGAT
13677055 GAGATGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (18 bp):
AGATGATAAATGAATATG
Found at i:13684080 original size:43 final size:43
Alignment explanation
Indices: 13683990--13684094 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 43
13683980 AATGTCATCG
* *
13683990 TCCCAGACGTGGTCTTACATGTAATCACATATCGACGCCACTA
1 TCCCAAACGTGGTCTTACATGTAATCAAATATCGACGCCACTA
* * *
13684033 TCCCAAACAG-GGTCTTACATGTAATCAAATATCGATGTCGAC-G
1 TCCCAAAC-GTGGTCTTACATGTAATCAAATATCGACG-CCACTA
*
13684076 TCCCAGACGTGGTCTTACA
1 TCCCAAACGTGGTCTTACA
13684095 CGAAAACACA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 48 0.91
44 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
TCCCAAACGTGGTCTTACATGTAATCAAATATCGACGCCACTA
Found at i:13685034 original size:28 final size:28
Alignment explanation
Indices: 13684994--13685050 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
13684984 TATGTTTGTT
13684994 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
13685022 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
13685050 T
1 T
13685051 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:13686910 original size:24 final size:24
Alignment explanation
Indices: 13686878--13686935 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
13686868 ATGTCCCAAA
13686878 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
*
13686902 ATTACAGTGAATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
*
13686926 ATTATAGTGG
1 ATTACAGTGG
13686936 GGGCAATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCTTGAAG
Found at i:13687603 original size:44 final size:44
Alignment explanation
Indices: 13687476--13687868 Score: 231
Period size: 44 Copynumber: 8.6 Consensus size: 44
13687466 CTATAACAAG
* *
13687476 TCTTATCTCCCT-AAGGTTGCAGTGGAGTAGACTGAAGATAACCACAAA
1 TCTTATCTCCCTGAA-GTTGCAGTGGAGAAGATTGAAGAT-A-C-C-AA
* * *
13687524 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAA
* * * *
13687568 TCTTATCTCCCTGAAGTTGTAGCGGAGAAGATTGAAGTTACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAA
* * ** * * **
13687612 TCCTATCTCCTTGAAGTTGCAGTGGAGCGGATT-AAAACAATGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGA-TACCAA
* * * * *
13687656 CCCTATAC-CTCTGAAGTTGCAGTAGGTTG--GATT-AAGTCTACCATAACAA
1 TCTTAT-CTCCCTGAAGTTGCAGT-GG-AGAAGATTGAAG------ATACCAA
* *
13687705 GTCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGATAACTACAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGAT-AC--CAA
* * * * * *
13687753 ACTTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGATACAAA
1 TC-TTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAA
* * * * *
13687798 TCTTATCTCTCTGAAGTTGCAGTTGAGCAGATTGAAGTTACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAA
* *
13687842 TCCTATCTCCCTAAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
13687869 TGGATTAAAG
Statistics
Matches: 270, Mismatches: 55, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
43 2 0.01
44 151 0.56
45 9 0.03
46 3 0.01
47 4 0.01
48 68 0.25
49 8 0.03
50 22 0.08
51 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAA
Found at i:13687647 original size:230 final size:230
Alignment explanation
Indices: 13687385--13687975 Score: 896
Period size: 230 Copynumber: 2.6 Consensus size: 230
13687375 TATCAAACTT
*
13687385 TATCT-CTCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCCTATACCTCTGAAGTTGTAGT
1 TATCTCCT-TGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGTAGT
*
13687449 AGGTCGGATTAAGTCTACTATAACAAGTCTTATCTCCCTAAGGTTGCAGTGGAGTAGACTGAAGA
65 AGGTCGGATTAAGTCTACCATAACAAGTCTTATCTCCCTAAGGTTGCAGTGGAGTAGACTGAAGA
* * *
13687514 TAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTCCC
130 TAACCACAAACCTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGATACAAATCTTATCTCCC
*
13687579 TGAAGTTGTAGCGGAGAAGATTGAAGTTACTAATCC
195 TGAAGTTGCAGCGGAGAAGATTGAAGTTACTAATCC
* * *
13687615 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACAATGAACCCTATACCTCTGAAGTTGCAGTA
1 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGTAGTA
* * *
13687680 GGTTGGATTAAGTCTACCATAACAAGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGAT
66 GGTCGGATTAAGTCTACCATAACAAGTCTTATCTCCCTAAGGTTGCAGTGGAGTAGACTGAAGAT
* * *
13687745 AACTACAAACTTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGATACAAATCTTATCTCTCT
131 AACCACAAACCTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGATACAAATCTTATCTCCCT
** *
13687810 GAAGTTGCAGTTGAGCAGATTGAAGTTACTAATCC
196 GAAGTTGCAGCGGAGAAGATTGAAGTTACTAATCC
* * * * * *
13687845 TATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAGCGAAGAATCTTATACCTCTGAAGTTGTAGTA
1 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGTAGTA
* ** * * *
13687910 GGTCGGATTAAATCTACCATAATGAGTCTTATCTCCCTAAAGTTGTAGTGGAGTAGACTGTAGAT
66 GGTCGGATTAAGTCTACCATAACAAGTCTTATCTCCCTAAGGTTGCAGTGGAGTAGACTGAAGAT
13687975 A
131 A
13687976 GCGGATCTTA
Statistics
Matches: 324, Mismatches: 36, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
230 322 0.99
231 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (230 bp):
TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGTAGTA
GGTCGGATTAAGTCTACCATAACAAGTCTTATCTCCCTAAGGTTGCAGTGGAGTAGACTGAAGAT
AACCACAAACCTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGATACAAATCTTATCTCCCT
GAAGTTGCAGCGGAGAAGATTGAAGTTACTAATCC
Found at i:13687888 original size:88 final size:91
Alignment explanation
Indices: 13687701--13687904 Score: 213
Period size: 88 Copynumber: 2.3 Consensus size: 91
13687691 GTCTACCATA
* * * * *
13687701 ACAAGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGATAACTACAAACTTTATCTCCCT
1 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAACTA-AAACTCTATCTCCCT
* *
13687766 AAAGTTACAGTGGAGCAGGTTGAAGAT
65 AAAGTTACAGTGGAGCAGGTTAAAGAG
* * *
13687793 ACAAATCTTATCTCTCTGAAGTTGCAGTTGAGCAGATTGAAG-TTACT-AATC-CTATCTCCCTA
1 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAACTAAAACTCTATCTCCCTA
* * *
13687855 AAGTTGCAGTGGAG-TGGATTAAAGCG
66 AAGTTACAGTGGAGCAGG-TTAAAGAG
13687881 A-AGAATCTTATAC-CTCTGAAGTTG
1 ACA-AATCTTAT-CTCTCTGAAGTTG
13687905 TAGTAGGTCG
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
87 3 0.03
88 48 0.50
89 4 0.04
91 4 0.04
92 37 0.39
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (91 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAACTAAAACTCTATCTCCCTA
AAGTTACAGTGGAGCAGGTTAAAGAG
Found at i:13689653 original size:9 final size:9
Alignment explanation
Indices: 13689639--13689669 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13689629 GTTAAACGAA
13689639 TCGAGTTAT
1 TCGAGTTAT
*
13689648 TCGAGTTAA
1 TCGAGTTAT
13689657 TCGAGTTAT
1 TCGAGTTAT
13689666 TCGA
1 TCGA
13689670 ATCAACTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:13690978 original size:42 final size:43
Alignment explanation
Indices: 13690912--13690994 Score: 116
Period size: 42 Copynumber: 1.9 Consensus size: 43
13690902 GCTCACCCCT
*
13690912 ATATATACATACTTACATTTATTTT-TATGTTTTATAATTTTAAA
1 ATATATACATAC-TACATATATTTTATAT-TTTTATAATTTTAAA
*
13690956 ATATATACATAC-ATATATATTTTATATTTTTATAATTTT
1 ATATATACATACTACATATATTTTATATTTTTATAATTTT
13690995 TATTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 21 0.58
43 3 0.08
44 12 0.33
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (43 bp):
ATATATACATACTACATATATTTTATATTTTTATAATTTTAAA
Found at i:13691499 original size:72 final size:72
Alignment explanation
Indices: 13691382--13691524 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
13691372 TCTTTTCAAA
* *
13691382 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGTATGATCCA
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATAGTGTCCTAACTTACTGGGCATGATCCA
13691447 TTTTTTT
66 TTTTTTT
13691454 CTCAAGTTTTAAACGATCTCGGGAATTAAGAA-ACGATAGTGTCCTAACTTACTGGGCATGATCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGA-GATAGTGTCCTAACTTACTGGGCATGATCC
*
13691518 CTTTTTT
65 ATTTTTT
13691525 AAAGCCAAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 1 0.01
72 66 0.99
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATAGTGTCCTAACTTACTGGGCATGATCCA
TTTTTTT
Found at i:13695918 original size:25 final size:25
Alignment explanation
Indices: 13695888--13695994 Score: 151
Period size: 25 Copynumber: 4.3 Consensus size: 25
13695878 GGACACACCA
* *
13695888 CAGCTTGCATGAGCGTCCCGTTATT
1 CAGCTCGCATGAGCTTCCCGTTATT
*
13695913 CAGCTTGCATGAGCTTCCCGTTATT
1 CAGCTCGCATGAGCTTCCCGTTATT
* *
13695938 CAGCTCGTATGAGCTTCTCGTTATT
1 CAGCTCGCATGAGCTTCCCGTTATT
* *
13695963 CAGCTCGCATGAGCTTTCCATTATT
1 CAGCTCGCATGAGCTTCCCGTTATT
13695988 CAGCTCG
1 CAGCTCG
13695995 GAAAGAGCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.35
Consensus pattern (25 bp):
CAGCTCGCATGAGCTTCCCGTTATT
Found at i:13696018 original size:50 final size:49
Alignment explanation
Indices: 13695906--13696004 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
13695896 ATGAGCGTCC
* * * *
13695906 CGTTATTCAGCTTGCATGAGCTTCCCGTTATTCAGCTCGTATGAGCTTCT
1 CGTTA-TCAGCTCGCATGAGCTTCCCATTATTCAGCTCGAAAGAGCTTCT
*
13695956 CGTTATTCAGCTCGCATGAGCTTTCCATTATTCAGCTCGGAAAGAGCTT
1 CGTTA-TCAGCTCGCATGAGCTTCCCATTATTCAGCTC-GAAAGAGCTT
13696005 ACTGCTTACA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 35 0.81
51 8 0.19
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.35
Consensus pattern (49 bp):
CGTTATCAGCTCGCATGAGCTTCCCATTATTCAGCTCGAAAGAGCTTCT
Found at i:13704073 original size:43 final size:43
Alignment explanation
Indices: 13704012--13704340 Score: 418
Period size: 43 Copynumber: 7.7 Consensus size: 43
13704002 GATATGATTT
* *
13704012 CGTGTAAGACCACGTCTGGGATGTTGGCATAGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
13704055 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
*
13704098 CGTGTAAGACCACGTCTGGAACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
*
13704141 CGTGTAAGACCACGTCTGAGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
* *
13704184 CGCGTAAGACCACGTCTGAGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
* * * *
13704227 CGTGTAAGACCATGTCTGAGACATTGGCATCGTA-TT-TGATT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTTTA
* * * ** *
13704268 CGTGTAAAACC-CTGTCTGGGACAG-TGGAATTGA-TATAAGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTTTA
* *
13704311 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
13704341 TGTACGATAT
Statistics
Matches: 257, Mismatches: 21, Indels: 16
0.87 0.07 0.05
Matches are distributed among these distances:
40 2 0.01
41 25 0.10
42 9 0.04
43 219 0.85
44 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:13707365 original size:16 final size:16
Alignment explanation
Indices: 13707344--13707376 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13707334 TGGTCATAAC
13707344 TACTTCCTATTTTAGG
1 TACTTCCTATTTTAGG
13707360 TACTTCCTATTTTAGG
1 TACTTCCTATTTTAGG
13707376 T
1 T
13707377 TTCTACTCAA
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:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (16 bp):
TACTTCCTATTTTAGG
Found at i:13707443 original size:16 final size:15
Alignment explanation
Indices: 13707420--13707449 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13707410 TTAATATGTT
13707420 TATTTATTCATATCA
1 TATTTATTCATATCA
13707435 TATTGTATTCATATC
1 TATT-TATTCATATC
13707450 GCATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.53
Consensus pattern (15 bp):
TATTTATTCATATCA
Found at i:13709497 original size:69 final size:68
Alignment explanation
Indices: 13709386--13709534 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 68
13709376 TATTATAATT
* * * *
13709386 TTTTTAATGAAATTAGTAAAGAATTGAGCTATAAGAGTATTCTCTGGTCAATGAAGGATTAAAAT
1 TTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTCTAGTCAATG-AGGATTAAAAT
13709451 TAAA
65 TAAA
** * * *
13709455 TTTTTAATGAAAATAGTAAAGAAGTGAACTATGTGAGTATTCTTTAGTCCATGTGGATTAAAATT
1 TTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTCTAGTCAATGAGGATTAAAATT
*
13709520 AAC
66 AAA
*
13709523 TTTTTTATGAAA
1 TTTTTAATGAAA
13709535 GTAGGGAAGA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
68 24 0.35
69 45 0.65
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (68 bp):
TTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTCTAGTCAATGAGGATTAAAATT
AAA
Found at i:13711299 original size:33 final size:33
Alignment explanation
Indices: 13711254--13711322 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
13711244 CAACTTAATC
*
13711254 ATTTCTCTCAAATTCTCTCTAATATT-CTCTCAA
1 ATTTCTCTCAAATTC-CTCTAAAATTCCTCTCAA
*
13711287 ATTTTTCTCAAATTCCTCTAAAATTCCTCTCAA
1 ATTTCTCTCAAATTCCTCTAAAATTCCTCTCAA
13711320 ATT
1 ATT
13711323 ATTTTTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTTCTCTCAAATTCCTCTAAAATTCCTCTCAA
Found at i:13711310 original size:11 final size:11
Alignment explanation
Indices: 13711258--13711322 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
13711248 TTAATCATTT
13711258 CTCTCAAATT-
1 CTCTCAAATTC
13711268 CTCTCTAATATT-
1 CTCTC-AA-ATTC
*
13711280 CTCTCAAATTT
1 CTCTCAAATTC
*
13711291 TTCTCAAATTC
1 CTCTCAAATTC
*
13711302 CTCTAAAATTC
1 CTCTCAAATTC
13711313 CTCTCAAATT
1 CTCTCAAATT
13711323 ATTTTTAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.17
11 31 0.66
12 8 0.17
ACGTcount: A:0.29, C:0.28, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:13711375 original size:29 final size:29
Alignment explanation
Indices: 13711319--13711375 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
13711309 ATTCCTCTCA
* *
13711319 AATTATTTTTAAGAAAGCTTTAATTTTTT
1 AATTATTTTTAAAAAAGCTTTAAATTTTT
13711348 AATTATTTTTAAAAAAG-TTCTAAATTTT
1 AATTATTTTTAAAAAAGCTT-TAAATTTT
13711376 ATTTTTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (29 bp):
AATTATTTTTAAAAAAGCTTTAAATTTTT
Found at i:13713458 original size:21 final size:21
Alignment explanation
Indices: 13713431--13713479 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
13713421 CCCAACACCG
13713431 GCAACCAG-ATCCCCTACCGGA
1 GCAACCAGAATCCCC-ACCGGA
* *
13713452 GGAACCAGAATCCCCGCCGGA
1 GCAACCAGAATCCCCACCGGA
13713473 GCAACCA
1 GCAACCA
13713480 CAACCCTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.31, C:0.41, G:0.22, T:0.06
Consensus pattern (21 bp):
GCAACCAGAATCCCCACCGGA
Found at i:13713860 original size:61 final size:61
Alignment explanation
Indices: 13713743--13713863 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
13713733 AATAGATTAG
* * *
13713743 ATTTTCTATCTACCTATTGTAATTTACTTTTACATTTTTAATATAATAGAAATTCTTTTAC
1 ATTTTCTATCTACCAATTGTAATTTACTTTAACATTTTTAATAGAATAGAAATTCTTTTAC
* * * **
13713804 ATTTTCTATGTACCAATTGTAATTTACTTTAATATTTTTAATAGATTAGATTTTCTTTTA
1 ATTTTCTATCTACCAATTGTAATTTACTTTAACATTTTTAATAGAATAGAAATTCTTTTA
13713864 AATAAGTCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.54
Consensus pattern (61 bp):
ATTTTCTATCTACCAATTGTAATTTACTTTAACATTTTTAATAGAATAGAAATTCTTTTAC
Found at i:13717128 original size:126 final size:126
Alignment explanation
Indices: 13716902--13717320 Score: 705
Period size: 126 Copynumber: 3.3 Consensus size: 126
13716892 GGTCTAACAG
13716902 GAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* *
13716967 CTGCCTAAAGCGTTTTTGATACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTC-A
66 CTGCCTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
**
13717027 GAAGCTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCAT
1 G-AGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCAT
* *
13717092 CCTGCCTAAAGCATTTTTGACACTATTTTCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
65 CCTGCCTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
* **
13717154 GAGTTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* * *
13717219 CTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAA
66 CTGCCTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
*
13717280 GAGCAACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTT
1 GAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTT
13717321 AAATTAACAA
Statistics
Matches: 276, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
125 1 0.00
126 273 0.99
127 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
GAGCTACTGTAGCAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
CTGCCTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
Found at i:13717431 original size:11 final size:11
Alignment explanation
Indices: 13717415--13717441 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13717405 ACCCTAATCC
13717415 AATTTTTAAAT
1 AATTTTTAAAT
13717426 AATTTTTAAAT
1 AATTTTTAAAT
13717437 AATTT
1 AATTT
13717442 ACTCAAGAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTTAAAT
Found at i:13730179 original size:7 final size:7
Alignment explanation
Indices: 13730167--13730196 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
13730157 TATATAAGAC
13730167 TTAAAAT
1 TTAAAAT
13730174 TTAAAAT
1 TTAAAAT
13730181 TTAAAAT
1 TTAAAAT
13730188 TTAATAAT
1 TTAA-AAT
13730196 T
1 T
13730197 ATTTCTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTAAAAT
Found at i:13733191 original size:9 final size:9
Alignment explanation
Indices: 13733177--13733207 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13733167 GTTAAACGAA
13733177 TCGAGTTAT
1 TCGAGTTAT
*
13733186 TCGAGTTAA
1 TCGAGTTAT
13733195 TCGAGTTAT
1 TCGAGTTAT
13733204 TCGA
1 TCGA
13733208 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:13733275 original size:9 final size:9
Alignment explanation
Indices: 13733261--13733288 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13733251 TGAGTTTTCG
13733261 AATTCGAAT
1 AATTCGAAT
13733270 AATTCGAAT
1 AATTCGAAT
13733279 AATTCGAAT
1 AATTCGAAT
13733288 A
1 A
13733289 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:13734322 original size:5 final size:5
Alignment explanation
Indices: 13734312--13734337 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13734302 CTCGAAAATT
13734312 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
13734338 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Done.