Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 27 of 109
Found at i:4677494 original size:19 final size:20
Alignment explanation
Indices: 4677472--4677515 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
4677462 TATTTTAATT
4677472 TATAAAAATTTAA-AAAA-TA
1 TATAAAAA-TTAATAAAAGTA
4677491 TATAAAAATTAATAAAAGTA
1 TATAAAAATTAATAAAAGTA
4677511 TATAA
1 TATAA
4677516 TTTAATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TATAAAAATTAATAAAAGTA
Found at i:4677520 original size:18 final size:18
Alignment explanation
Indices: 4677472--4677521 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
4677462 TATTTTAATT
*
4677472 TATAAAAATTTAA-AAAA
1 TATATAAATTTAATAAAA
*
4677489 TATATAAAAATTAATAAAA
1 TATAT-AAATTTAATAAAA
4677508 GTATAT-AATTTAAT
1 -TATATAAATTTAAT
4677522 TTGGTTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 14 0.52
19 4 0.15
20 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TATATAAATTTAATAAAA
Found at i:4679323 original size:95 final size:96
Alignment explanation
Indices: 4679222--4679400 Score: 213
Period size: 95 Copynumber: 1.9 Consensus size: 96
4679212 TAAATTTTTC
* *
4679222 AATAATTTAATAAG-ATTTAACTCGAGATTTAAATCTTTC-AATAATTTGATAGGATTGAAAAAA
1 AATAATTTAAT-AGTACTTAACTCGAGATTTAAAT-TTTCAAATAATTTGATAAGATT-AAAAAA
4679285 T-ATTT-TTTTAAAAAAAATTTATTAAGTACTCT
63 TAATTTATTTTAAAAAAAATTTATTAAGTACTCT
* ** * * *
4679317 AATAATTTGATAGTACTTAGTTCGATATTTAAATTTTCAAATCATTTGGTAAGATTAAAAAATAA
1 AATAATTTAATAGTACTTAACTCGAGATTTAAATTTTCAAATAATTTGATAAGATTAAAAAATAA
**
4679382 TTTATTTTTCAAAAAATTT
66 TTTATTTTAAAAAAAATTT
4679401 TGTTATGAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
94 13 0.19
95 44 0.63
96 13 0.19
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.42
Consensus pattern (96 bp):
AATAATTTAATAGTACTTAACTCGAGATTTAAATTTTCAAATAATTTGATAAGATTAAAAAATAA
TTTATTTTAAAAAAAATTTATTAAGTACTCT
Found at i:4679564 original size:29 final size:29
Alignment explanation
Indices: 4679523--4679579 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4679513 TTTTTTTTAT
* *
4679523 AAAATATCCATTAACA-CAAATAAAATAA
1 AAAATATCAATTAAAATCAAATAAAATAA
*
4679551 AAAATTATCAATTAAAATCAATTAAAATA
1 AAAA-TATCAATTAAAATCAAATAAAATA
4679580 CGCAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 10 0.42
30 10 0.42
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAATATCAATTAAAATCAAATAAAATAA
Found at i:4679625 original size:21 final size:23
Alignment explanation
Indices: 4679587--4679629 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
4679577 ATACGCAAAT
4679587 TTAAATAAATAAATAAAATTACA
1 TTAAATAAATAAATAAAATTACA
*
4679610 TTAAA-AATTAAA-AAAATTAC
1 TTAAATAAATAAATAAAATTAC
4679630 CAAAATGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAAATAAATAAATAAAATTACA
Found at i:4680681 original size:4 final size:4
Alignment explanation
Indices: 4680672--4680752 Score: 62
Period size: 4 Copynumber: 20.8 Consensus size: 4
4680662 CCATAAAAAC
* * * *
4680672 AAAT AAAT AAAAT AATT AAAT AAA- AAAG AGAT AAA- GAAT AAAT AAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
4680719 AAAT ATGAT AAA- CAA- AAAT AAAT AAAT AAAT AAA
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
4680753 ATTCAATCAG
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
3 9 0.15
4 45 0.74
5 7 0.11
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:4680730 original size:35 final size:34
Alignment explanation
Indices: 4680672--4680752 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 34
4680662 CCATAAAAAC
*
4680672 AAATAAATAAAATAATTAAATAAA-AAAGAGATAAA-
1 AAATAAAT-AAATAAATAAATAAACAAA-A-ATAAAT
* *
4680707 GAATAAATAAATAAATATGATAAACAAAAATAAAT
1 AAATAAATAAATAAATA-AATAAACAAAAATAAAT
4680742 AAATAAATAAA
1 AAATAAATAAA
4680753 ATTCAATCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
34 13 0.33
35 23 0.59
36 3 0.08
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (34 bp):
AAATAAATAAATAAATAAATAAACAAAAATAAAT
Found at i:4680741 original size:23 final size:23
Alignment explanation
Indices: 4680688--4680752 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
4680678 ATAAAATAAT
* *
4680688 TAAATAAA-AAAGAGATAAAGAA
1 TAAATAAATAAATAGATAAACAA
4680710 TAAATAAATAAATATGATAAACAA
1 TAAATAAATAAATA-GATAAACAA
*
4680734 -AAATAAATAAATAAATAAA
1 TAAATAAATAAATAGATAAA
4680753 ATTCAATCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 13 0.34
23 17 0.45
24 8 0.21
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (23 bp):
TAAATAAATAAATAGATAAACAA
Found at i:4685794 original size:21 final size:21
Alignment explanation
Indices: 4685734--4685794 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
4685724 AGTAGTGGGT
* *
4685734 TGAGGAGAAGGAGAAGAAGGT
1 TGAGGAGCAGGAGAAGAAGGC
* **
4685755 TGAGGGGCA-GAGGTTGAAGGC
1 TGAGGAGCAGGA-GAAGAAGGC
*
4685776 TGAGGAGCAGGAGACGAAG
1 TGAGGAGCAGGAGAAGAAG
4685795 CTGCAGCACT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.34, C:0.07, G:0.49, T:0.10
Consensus pattern (21 bp):
TGAGGAGCAGGAGAAGAAGGC
Found at i:4690988 original size:30 final size:29
Alignment explanation
Indices: 4690940--4691034 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 29
4690930 TAATTTTTTT
4690940 AAAATT-AAAAAAA-TAAAAATTTTAATA
1 AAAATTAAAAAAAATTAAAAATTTTAATA
*
4690967 AAAATCT-CAAAAAATTCAAAAAGTTTT--TGA
1 AAAAT-TAAAAAAAATT-AAAAA-TTTTAAT-A
4690997 AAAATTGAAAAAAAATT-AAAATTTTAATA
1 AAAATT-AAAAAAAATTAAAAATTTTAATA
4691026 AAAA-TAAAA
1 AAAATTAAAA
4691035 TTTTCTTCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
27 9 0.16
28 12 0.21
29 12 0.21
30 12 0.21
31 12 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAATTAAAAAAAATTAAAAATTTTAATA
Found at i:4691221 original size:20 final size:20
Alignment explanation
Indices: 4691177--4691223 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4691167 ACAATTTTAT
4691177 TTTTTTTATATATTTTATGA
1 TTTTTTTATATATTTTATGA
* *
4691197 CTTTTTTATAT-TTTTTTGGA
1 TTTTTTTATATATTTTAT-GA
4691217 TTTTTTT
1 TTTTTTT
4691224 TCTAAAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTTTTTATATATTTTATGA
Found at i:4691316 original size:18 final size:18
Alignment explanation
Indices: 4691258--4691316 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
4691248 TAAATAACTT
* *
4691258 TTTTAGAATATTTCAAAA
1 TTTTAGAATTTTTAAAAA
* **
4691276 TTTTAGATTTTTTAAATT
1 TTTTAGAATTTTTAAAAA
4691294 TTTTAGAATTTTTAAAAA
1 TTTTAGAATTTTTAAAAA
*
4691312 ATTTA
1 TTTTA
4691317 AAGAAAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTTAGAATTTTTAAAAA
Found at i:4691349 original size:19 final size:19
Alignment explanation
Indices: 4691276--4691368 Score: 62
Period size: 19 Copynumber: 4.7 Consensus size: 19
4691266 TATTTCAAAA
*
4691276 TTTTAGATTTTTTA-AATT
1 TTTTAGATTTTTTATAAAT
* *
4691294 TTTTAGAATTTTTAAAAAAT
1 TTTTAG-ATTTTTTATAAAT
**
4691314 TTAAAGAAAATTTTTTTATAAAT
1 TTTTAG---A-TTTTTTATAAAT
* *
4691337 TTTTAGATTTTTTTTAAAA
1 TTTTAGATTTTTTATAAAT
*
4691356 TATTAGATTTTTT
1 TTTTAGATTTTTT
4691369 TTAATCTCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
18 6 0.10
19 29 0.49
20 8 0.14
22 2 0.03
23 14 0.24
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTAGATTTTTTATAAAT
Found at i:4691369 original size:19 final size:19
Alignment explanation
Indices: 4691323--4691372 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
4691313 TTTAAAGAAA
* *
4691323 ATTTTTTTATAAATTTTTAG
1 ATTTTTTT-TAAAATATTAG
4691343 ATTTTTTTTAAAATATTAG
1 ATTTTTTTTAAAATATTAG
4691362 ATTTTTTTTAA
1 ATTTTTTTTAA
4691373 TCTCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTTTTTAAAATATTAG
Found at i:4691549 original size:20 final size:18
Alignment explanation
Indices: 4691527--4691589 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 18
4691517 TCTTTTTTAA
4691527 TTTTTATAATTTTAAAATT
1 TTTTTA-AATTTTAAAATT
* *
4691546 ATTTCAAATTTTTAAAAATT
1 TTTTTAAA-TTTT-AAAATT
4691566 TTTTTAAAAATTTTAAAATT
1 TTTTT--AAATTTTAAAATT
4691586 TTTT
1 TTTT
4691590 ATTTAATACT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 2 0.06
19 8 0.22
20 19 0.53
21 4 0.11
22 3 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAAATTTTAAAATT
Found at i:4691571 original size:12 final size:12
Alignment explanation
Indices: 4691554--4691579 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4691544 TTATTTCAAA
4691554 TTTTTAAAAATT
1 TTTTTAAAAATT
4691566 TTTTTAAAAATT
1 TTTTTAAAAATT
4691578 TT
1 TT
4691580 AAAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTAAAAATT
Found at i:4697619 original size:21 final size:22
Alignment explanation
Indices: 4697594--4697636 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4697584 AATAAAAACT
4697594 TAATTAATAAAATTTT-TTTAA
1 TAATTAATAAAATTTTATTTAA
* *
4697615 TAATTATTAAATTTTTATTTAA
1 TAATTAATAAAATTTTATTTAA
4697637 GGATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATTAATAAAATTTTATTTAA
Found at i:4701145 original size:26 final size:26
Alignment explanation
Indices: 4701109--4701161 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4701099 TTCTCTGAAG
4701109 TATGACATAAAAATAAGTAATAAACC
1 TATGACATAAAAATAAGTAATAAACC
4701135 TATGACATAAAAATAAGTAATAAACC
1 TATGACATAAAAATAAGTAATAAACC
4701161 T
1 T
4701162 GTAGGTATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (26 bp):
TATGACATAAAAATAAGTAATAAACC
Found at i:4702393 original size:14 final size:14
Alignment explanation
Indices: 4702374--4702402 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4702364 AAAACTTGTT
4702374 ATTATGATTTTTGG
1 ATTATGATTTTTGG
4702388 ATTATGATTTTTGG
1 ATTATGATTTTTGG
4702402 A
1 A
4702403 CTTTAAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (14 bp):
ATTATGATTTTTGG
Found at i:4703062 original size:4 final size:4
Alignment explanation
Indices: 4703053--4703093 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
4703043 GGTACCACTG
4703053 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT C
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT C
4703094 CATCCACCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (4 bp):
CTAT
Found at i:4711653 original size:24 final size:24
Alignment explanation
Indices: 4711624--4711669 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4711614 ACAAAAAAAG
4711624 AACAAAAAAGA-AAGAAAGAAGACA
1 AACAAAAAAGACAAGAAA-AAGACA
*
4711648 AACAAAAAATACAAGAAAAAGA
1 AACAAAAAAGACAAGAAAAAGA
4711670 AAAAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (24 bp):
AACAAAAAAGACAAGAAAAAGACA
Found at i:4711672 original size:18 final size:18
Alignment explanation
Indices: 4711628--4711676 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
4711618 AAAAAGAACA
* *
4711628 AAAAAGAAAGAA-AGAAG
1 AAAAAGAAAAAATACAAG
* *
4711645 ACAAACAAAAAATACAAG
1 AAAAAGAAAAAATACAAG
4711663 AAAAAGAAAAAATA
1 AAAAAGAAAAAATA
4711677 AAGCAGGGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAATACAAG
Found at i:4713418 original size:20 final size:20
Alignment explanation
Indices: 4713363--4713424 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
4713353 GGGATTTTTA
4713363 TTTATTTTTATTTTA-GATT
1 TTTATTTTTATTTTATGATT
* *
4713382 TTT-TTATTTCACATTTATCATT
1 TTTATT-TTT-A-TTTTATGATT
4713404 TTTATTTTTATTTTATGATT
1 TTTATTTTTATTTTATGATT
4713424 T
1 T
4713425 ATTTTCTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 10 0.29
21 5 0.15
22 9 0.26
23 2 0.06
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTATTTTTATTTTATGATT
Found at i:4714487 original size:8 final size:8
Alignment explanation
Indices: 4714474--4714499 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4714464 TCAGGTGCAA
4714474 GGTAACCT
1 GGTAACCT
4714482 GGTAACCT
1 GGTAACCT
4714490 GGTAACCT
1 GGTAACCT
4714498 GG
1 GG
4714500 AGGTGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (8 bp):
GGTAACCT
Found at i:4716023 original size:115 final size:114
Alignment explanation
Indices: 4715802--4716080 Score: 346
Period size: 115 Copynumber: 2.4 Consensus size: 114
4715792 AAATAAAATG
* * * * * * *
4715802 ATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAATAAATT
1 ATAAATTTTCCAAAAAA-GTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGT
* * * *
4715867 TTCTAAAAATATTTTTTAAAAAAAGTTGAAAGTATCAATTTTCTTTAAAA
65 TTCAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
* * *
4715917 ATAAATTTTCCAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAGGTT
1 ATAAATTTTCCAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTT
**
4715982 TCAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
66 TC-AAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
* *
4716032 TTAAAGTTTT-C-AAAAAGTATTTTGAGAAAAAGTTAAAAGTATCAATTTT
1 ATAAA-TTTTCCAAAAAAGT-TTTTGAGAAAAAGTTGAAAGTATCAATTTT
4716081 TCTTACACAA
Statistics
Matches: 143, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
114 49 0.34
115 90 0.63
116 4 0.03
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (114 bp):
ATAAATTTTCCAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTT
TCAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
Found at i:4716082 original size:58 final size:58
Alignment explanation
Indices: 4715802--4716080 Score: 350
Period size: 57 Copynumber: 4.9 Consensus size: 58
4715792 AAATAAAATG
* * * *
4715802 ATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTAAAA
1 ATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
* * * * *
4715860 ATAAATTTTC-TAAAAATATTTTTTAAAAAAAGTTGAAAGTATCAATTTTCTTTAAAA
1 ATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
* * *
4715917 ATAAATTTTCCAAAAAA-GTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAA
1 ATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
* ** *
4715974 TTAAGGTTTCAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
1 ATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
* * *
4716032 TTAAAGTTTTC-AAAAAGTA-TTTTGAGAAAAAGTTAAAAGTATCAATTTT
1 ATAAA-TTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
4716081 TCTTACACAA
Statistics
Matches: 192, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
57 126 0.66
58 62 0.32
59 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (58 bp):
ATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAA
Found at i:4722336 original size:35 final size:35
Alignment explanation
Indices: 4722297--4722383 Score: 138
Period size: 35 Copynumber: 2.5 Consensus size: 35
4722287 ATTTTTTTTG
*
4722297 AAAAGATATTTGCATTTCATGTGCATCATTTTAAA
1 AAAAGATATTTGTATTTCATGTGCATCATTTTAAA
* **
4722332 AAAAGACATTTGTATTTCATGTGCATCATTTTAGG
1 AAAAGATATTTGTATTTCATGTGCATCATTTTAAA
4722367 AAAAGATATTTGTATTT
1 AAAAGATATTTGTATTT
4722384 GCATCCTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (35 bp):
AAAAGATATTTGTATTTCATGTGCATCATTTTAAA
Found at i:4722411 original size:33 final size:34
Alignment explanation
Indices: 4722296--4722411 Score: 119
Period size: 35 Copynumber: 3.4 Consensus size: 34
4722286 TATTTTTTTT
* *
4722296 GAAAAGATATTTGCATTTCATGTGCATCATTTTAA
1 GAAAAGACATTTGTATTTCA-GTGCATCATTTTAA
* *
4722331 AAAAAGACATTTGTATTTCATGTGCATCATTTTAG
1 GAAAAGACATTTGTATTTCA-GTGCATCATTTTAA
* * *
4722366 GAAAAGATATTTGTATTTGCA-T-CCTTATTTTAA
1 GAAAAGACATTTGTATTT-CAGTGCATCATTTTAA
*
4722399 GAGAAGACATTTG
1 GAAAAGACATTTG
4722412 CATCATAATG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 19 0.28
34 1 0.01
35 47 0.68
36 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (34 bp):
GAAAAGACATTTGTATTTCAGTGCATCATTTTAA
Found at i:4722626 original size:48 final size:48
Alignment explanation
Indices: 4722564--4722810 Score: 163
Period size: 48 Copynumber: 5.1 Consensus size: 48
4722554 ATTTGAATAT
*
4722564 ATTTGCA-TCTTCTCGGTGGTGATATCCGAGTTTAAAGTTTGAATTTAC
1 ATTTGCATTC-TCTCGATGGTGATATCCGAGTTTAAAGTTTGAATTTAC
*
4722612 ATTTGCATTCTCTCGATGGTGATATCCGAGTATTAAAGCTTGAA-TTAC
1 ATTTGCATTCTCTCGATGGTGATATCCGAGT-TTAAAGTTTGAATTTAC
* ** *** *
4722660 A-TT---TT-T-TCGATGGTGATATTCGAGTTCCCTTCAGTGACAATATCTGAAGAT
1 ATTTGCATTCTCTCGATGGTGATATCCGAGTT---TAAAGTTTGAAT-T-T----AC
* * * *
4722711 ATTTGCATAT-TCTCGGTGGTGATAACCAAGTTTAAAGTTTGAATTTGC
1 ATTTGCAT-TCTCTCGATGGTGATATCCGAGTTTAAAGTTTGAATTTAC
* * *
4722759 ATTTGCATTCTCTCGATGGTGATGTCTGAGTATTAAAGCTTGAA-TTAC
1 ATTTGCATTCTCTCGATGGTGATATCCGAGT-TTAAAGTTTGAATTTAC
4722807 ATTT
1 ATTT
4722811 TCTCGATGGT
Statistics
Matches: 151, Mismatches: 28, Indels: 40
0.69 0.13 0.18
Matches are distributed among these distances:
41 1 0.01
42 18 0.12
43 1 0.01
44 7 0.05
46 1 0.01
47 4 0.03
48 63 0.42
49 24 0.16
51 2 0.01
52 3 0.02
53 1 0.01
54 7 0.05
55 1 0.01
56 2 0.01
57 16 0.11
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (48 bp):
ATTTGCATTCTCTCGATGGTGATATCCGAGTTTAAAGTTTGAATTTAC
Found at i:4722689 original size:147 final size:147
Alignment explanation
Indices: 4722482--4722886 Score: 609
Period size: 147 Copynumber: 2.8 Consensus size: 147
4722472 ACATACTCAG
* * *
4722482 TGGTGATATCTGAG-ATTAAAGTTTGAATTACATTTTCTAGATGGTGATATTCGAGTTCCCTTTG
1 TGGTGATATCTGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTCCCTTCG
* * *
4722546 GTGACGATATTTGAATATATTTGCATCTTCTCGGTGGTGATATCCGAGTTTAAAGTTTGAATTTA
66 GTGACAATATCTGAATATATTTGCATCTTCTCGGTGGTGATATCCAAGTTTAAAGTTTGAATTTA
4722611 CATTTGCATTCTCTCGA
131 CATTTGCATTCTCTCGA
* * *
4722628 TGGTGATATCCGAGTATTAAAGCTTGAATTACATTTTTTCGATGGTGATATTCGAGTTCCCTTCA
1 TGGTGATATCTGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTCCCTTCG
* * * *
4722693 GTGACAATATCTGAAGATATTTGCATATTCTCGGTGGTGATAACCAAGTTTAAAGTTTGAATTTG
66 GTGACAATATCTGAATATATTTGCATCTTCTCGGTGGTGATATCCAAGTTTAAAGTTTGAATTTA
4722758 CATTTGCATTCTCTCGA
131 CATTTGCATTCTCTCGA
* *
4722775 TGGTGATGTCTGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCG
1 TGGTGATATCTGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTCCCTTCG
* * * *
4722840 ATGGCAATATCCGAAGT-CA-TTGCATCTTCTCGGTGGTGATATCCAAG
66 GTGACAATATCTGAA-TATATTTGCATCTTCTCGGTGGTGATATCCAAG
4722887 ATTATTTATC
Statistics
Matches: 232, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
146 39 0.17
147 193 0.83
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (147 bp):
TGGTGATATCTGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTCCCTTCG
GTGACAATATCTGAATATATTTGCATCTTCTCGGTGGTGATATCCAAGTTTAAAGTTTGAATTTA
CATTTGCATTCTCTCGA
Found at i:4723102 original size:51 final size:49
Alignment explanation
Indices: 4722938--4723156 Score: 205
Period size: 49 Copynumber: 4.4 Consensus size: 49
4722928 AATGATTTAA
* * *
4722938 TTTAAAGTTGTTAAGCCTTTGCTGAGAGAAGCTTTGTTCAAGATGATAA-
1 TTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCTTT-TTCAAGATGAAAAT
* * * *
4722987 TTTAAAGTTATTGAGCCTTTGCTGATAGAAGCTTTTTTCAAGAT-AAGAT
1 TTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGC-TTTTTCAAGATGAAAAT
* *
4723036 TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTTCTAGATGAAAATTT
1 TTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCT-TTTTCAAGATGAAAA--T
* **
4723088 TTTAAA-TTGTTGAGCTTCTGCTGAGATGAA-CTTTTTTC-AGATTTTAAAT
1 TTTAAAGTTGTTGAGCCTCTGCTGAGA-GAAGC-TTTTTCAAGA-TGAAAAT
4723137 TTTCAAAAGTTGTTGAGCCT
1 TTT--AAAGTTGTTGAGCCT
4723157 TGAGTAAGAT
Statistics
Matches: 142, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
48 3 0.02
49 78 0.55
50 9 0.06
51 32 0.23
52 20 0.14
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (49 bp):
TTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCTTTTTCAAGATGAAAAT
Found at i:4723392 original size:14 final size:13
Alignment explanation
Indices: 4723373--4723416 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
4723363 ATAATAATAC
4723373 AAAAAAAGAACAAA
1 AAAAAAAG-ACAAA
4723387 AAAAAAAGACAAA
1 AAAAAAAGACAAA
* *
4723400 CAAAAAATACAAGA
1 AAAAAAAGACAA-A
4723414 AAA
1 AAA
4723417 GGAAAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.82, C:0.09, G:0.07, T:0.02
Consensus pattern (13 bp):
AAAAAAAGACAAA
Found at i:4723731 original size:19 final size:20
Alignment explanation
Indices: 4723686--4723734 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
4723676 GATCCTGCCA
4723686 AAAAAAAAAAGAAGTTCCAG
1 AAAAAAAAAAGAAGTTCCAG
*
4723706 AATAAAAAAAA-AA-TTCCTG
1 AA-AAAAAAAAGAAGTTCCAG
4723725 CAAAAAAAAA
1 -AAAAAAAAA
4723735 CCATTCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 12 0.46
20 6 0.23
21 8 0.31
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAGAAGTTCCAG
Found at i:4724288 original size:30 final size:30
Alignment explanation
Indices: 4724245--4724318 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
4724235 TGAGCAGGAA
* * * *
4724245 CCAAATCGTTGAACCTGATCCAGACCGAAC
1 CCAAACCGCTGAACCCGAGCCAGACCGAAC
* * * *
4724275 CCGAACCGCTGAACCCGAGCTAGATCGATC
1 CCAAACCGCTGAACCCGAGCCAGACCGAAC
4724305 CCAAACCGCTGAAC
1 CCAAACCGCTGAAC
4724319 GTGACTAGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.36, G:0.19, T:0.14
Consensus pattern (30 bp):
CCAAACCGCTGAACCCGAGCCAGACCGAAC
Found at i:4724768 original size:20 final size:23
Alignment explanation
Indices: 4724728--4724769 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
4724718 GTTATAAAAT
4724728 AATAAGTTAATTAATAAATTAAG
1 AATAAGTTAATTAATAAATTAAG
4724751 AATAAG-TAA-TAA-AAATTAA
1 AATAAGTTAATTAATAAATTAA
4724770 AAAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 3 0.16
23 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (23 bp):
AATAAGTTAATTAATAAATTAAG
Found at i:4726187 original size:25 final size:25
Alignment explanation
Indices: 4726156--4726213 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
4726146 TATTAATATA
*
4726156 ATTATTATAATAT-TTAAAATTATTT
1 ATTATTAAAATATATT-AAATTATTT
4726181 ATTATTAAAATATATTAAATTATTT
1 ATTATTAAAATATATTAAATTATTT
4726206 ATTATTAA
1 ATTATTAA
4726214 TATTAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATTAAAATATATTAAATTATTT
Found at i:4726233 original size:25 final size:22
Alignment explanation
Indices: 4726143--4726239 Score: 83
Period size: 25 Copynumber: 4.2 Consensus size: 22
4726133 TTTTTTAAAA
* *
4726143 TAATATTAATA-TAATTATTA-
1 TAATATTAAAATTATTTATTAT
4726163 TAATATTTAAAATTATTTATTAT
1 TAATA-TTAAAATTATTTATTAT
*
4726186 TAAAATATATTAAATTATTTATTAT
1 T--AATAT-TAAAATTATTTATTAT
4726211 TAATATTAAAATATAATTATATT-T
1 TAATATTAAAAT-T-ATT-TATTAT
4726235 TAATA
1 TAATA
4726240 ATTATATTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
20 5 0.08
21 5 0.08
22 13 0.20
23 7 0.11
24 10 0.16
25 24 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATTAAAATTATTTATTAT
Found at i:4726251 original size:13 final size:14
Alignment explanation
Indices: 4726223--4726252 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4726213 ATATTAAAAT
4726223 ATAATTATATTTTA
1 ATAATTATATTTTA
4726237 ATAATTATA-TTTA
1 ATAATTATATTTTA
4726250 ATA
1 ATA
4726253 TTAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATTATATTTTA
Found at i:4726280 original size:20 final size:20
Alignment explanation
Indices: 4726240--4726277 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4726230 TATTTTAATA
*
4726240 ATTATATTTAATATTAAAAT
1 ATTATATTTAATATAAAAAT
4726260 ATTATA-TTAATATAAAAA
1 ATTATATTTAATATAAAAA
4726278 ATACTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATATTTAATATAAAAAT
Found at i:4730642 original size:19 final size:18
Alignment explanation
Indices: 4730604--4730640 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4730594 TTTATAAAAA
* *
4730604 TAATTTTTATTTATTTTT
1 TAATTTTAAATTATTTTT
4730622 TAATTTTAAATTATTTTT
1 TAATTTTAAATTATTTTT
4730640 T
1 T
4730641 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TAATTTTAAATTATTTTT
Found at i:4731362 original size:28 final size:28
Alignment explanation
Indices: 4731288--4731353 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
4731278 AAAGGTATTT
* ** *
4731288 TTATTTTTCAAATTTTATTTGAATTAAA
1 TTATTTTTTAAAAATTATTTAAATTAAA
*
4731316 TTATTTTTTAAAAAATATTTAAATTAAA
1 TTATTTTTTAAAAATTATTTAAATTAAA
4731344 TTATTATTTT
1 TTATT-TTTT
4731354 TAAGTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTATTTTTTAAAAATTATTTAAATTAAA
Found at i:4731820 original size:13 final size:13
Alignment explanation
Indices: 4731802--4731848 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
4731792 TATTTTCATG
4731802 TAATTTTTATTTT
1 TAATTTTTATTTT
* *
4731815 TAATTTATATATATA
1 TAATTT-T-TATTTT
4731830 TAATTTTTATTTT
1 TAATTTTTATTTT
4731843 TAATTT
1 TAATTT
4731849 ATATATATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 16 0.57
14 2 0.07
15 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAATTTTTATTTT
Found at i:4731833 original size:28 final size:28
Alignment explanation
Indices: 4731802--4731856 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
4731792 TATTTTCATG
4731802 TAATTTTTATTTTTAATTTATATATATA
1 TAATTTTTATTTTTAATTTATATATATA
4731830 TAATTTTTATTTTTAATTTATATATAT
1 TAATTTTTATTTTTAATTTATATATAT
4731857 GTGAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TAATTTTTATTTTTAATTTATATATATA
Found at i:4742873 original size:58 final size:58
Alignment explanation
Indices: 4742801--4743240 Score: 491
Period size: 58 Copynumber: 7.7 Consensus size: 58
4742791 TTGTACAGGA
* * *
4742801 AAAATTGATACTTTCAACTTTTCTC-CAAAAATATTTTTTAAAATTTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAA-GTTTATTTTCAAGG
* * * * *
4742859 AAAATTGATTCTTTCAACTTTTC-CTCAAAAATTCACTTTTGAAAACTTGT-TTTT-AAGT
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAA-T-ATTTTTTAAAAGTT-TATTTTCAAGG
* * *
4742917 AAAATTGATACTTTCAACTTTTC-CTCAAAAGTTCATTTTTGAAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCTCTCAAAA-AT-ATTTTTTAAAAGTTTATTTTCAAGG
* * *
4742975 AAAATTGATACTTTCAACTTTTC-CCCAAAAATATTTTTTTTGAAAAGCTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAATA--TTTTTT-AAAAGTTTATTTTCAAGG
4743035 AAAATTGATAC-TTCAACTTTT-TCTC-AAAATA-TTTTTAGAAAGTTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTA-AAAGTTTATTTTCAAGG
4743090 AAAATTGATACTTTCAACTTTT-TCTCAAAAA-ATTTTTTAGAAAGTTTATTTTCAA-G
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTA-AAAGTTTATTTTCAAGG
* * *
4743146 AAAATTTATACTTTCAACTTTT-TCTCAAAAA-ATTTTTTAGAAAGCTTATTTTCCAAAG
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTA-AAAGTTTATTTT-CAAGG
4743204 AAAATTGATACTTTCAACTTTTCT-TCAAAAATATTTT
1 AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTT
4743241 GAATTTTATT
Statistics
Matches: 339, Mismatches: 23, Indels: 39
0.85 0.06 0.10
Matches are distributed among these distances:
54 1 0.00
55 31 0.09
56 68 0.20
57 37 0.11
58 143 0.42
59 28 0.08
60 31 0.09
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAAGTTTATTTTCAAGG
Found at i:4743197 original size:29 final size:29
Alignment explanation
Indices: 4743109--4743202 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 29
4743099 ACTTTCAACT
*
4743109 TTTTCTCAAAAAATTTTTTAGAAAGTTTA
1 TTTTCTCAAAAAATTTTTTAGAAAGCTTA
**
4743138 -TTT-TCAAGAAAATTTATACTT-TCAA-C-T-
1 TTTTCTCAA-AAAATTT-T--TTAGAAAGCTTA
4743165 TTTTCTCAAAAAATTTTTTAGAAAGCTTA
1 TTTTCTCAAAAAATTTTTTAGAAAGCTTA
4743194 TTTTC-CAAA
1 TTTTCTCAAA
4743203 GAAAATTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 21
0.66 0.07 0.28
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 6 0.12
28 26 0.52
29 10 0.20
30 2 0.04
31 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTTCTCAAAAAATTTTTTAGAAAGCTTA
Found at i:4743272 original size:10 final size:9
Alignment explanation
Indices: 4743257--4743294 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
4743247 TATTTAAAGA
4743257 AAATAAATAT
1 AAATAAA-AT
4743267 AAATAAAAT
1 AAATAAAAT
4743276 AAAATAAAAT
1 -AAATAAAAT
4743286 AAA-AAAAT
1 AAATAAAAT
4743294 A
1 A
4743295 TCAAACATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.22
9 5 0.19
10 16 0.59
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:4743274 original size:15 final size:15
Alignment explanation
Indices: 4743251--4743295 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4743241 GAATTTTATT
*
4743251 TAAAGAAAATAAATA
1 TAAATAAAATAAATA
4743266 TAAATAAAATAAA-A
1 TAAATAAAATAAATA
4743280 TAAAATAAAA-AAATA
1 T-AAATAAAATAAATA
4743295 T
1 T
4743296 CAAACATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAATAAAATAAATA
Found at i:4743277 original size:5 final size:5
Alignment explanation
Indices: 4743256--4743289 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
4743246 TTATTTAAAG
4743256 AAAAT -AAAT ATAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
4743290 AAATATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:4743863 original size:14 final size:14
Alignment explanation
Indices: 4743844--4743875 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
4743834 TCGAAATCTG
4743844 AAAATTTTTCAAAA
1 AAAATTTTTCAAAA
4743858 AAAA--TTTCAAAA
1 AAAATTTTTCAAAA
4743870 AAAATT
1 AAAATT
4743876 CTCCAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 4
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.75
14 4 0.25
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTTTTCAAAA
Found at i:4743870 original size:13 final size:12
Alignment explanation
Indices: 4743850--4743875 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4743840 TCTGAAAATT
4743850 TTTCAAAAAAAA
1 TTTCAAAAAAAA
4743862 TTTCAAAAAAAA
1 TTTCAAAAAAAA
4743874 TT
1 TT
4743876 CTCCAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
TTTCAAAAAAAA
Found at i:4744201 original size:17 final size:17
Alignment explanation
Indices: 4744168--4744208 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4744158 TTAATAGATA
* *
4744168 ATAAA-AAAATAATTAG
1 ATAAATAAAAGAAATAG
4744184 ATAAATAAAAGAAATAG
1 ATAAATAAAAGAAATAG
4744201 ATAAATAA
1 ATAAATAA
4744209 TAATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (17 bp):
ATAAATAAAAGAAATAG
Found at i:4744265 original size:7 final size:7
Alignment explanation
Indices: 4744195--4744335 Score: 77
Period size: 6 Copynumber: 20.4 Consensus size: 7
4744185 TAAATAAAAG
4744195 AAATAGAT
1 AAATA-AT
4744203 AAATAAT
1 AAATAAT
4744210 -AATAAT
1 AAATAAT
4744216 -AATAAT
1 AAATAAT
*
4744222 AACAAAAT
1 AA-ATAAT
*
4744230 AAAAGCAGAT
1 -AAA-TA-AT
4744240 AAATAAT
1 AAATAAT
4744247 AAA-AAT
1 AAATAAT
*
4744253 -ATTAAT
1 AAATAAT
*
4744259 AGATAAT
1 AAATAAT
4744266 AAATAAAT
1 AAAT-AAT
4744274 AAATAA-
1 AAATAAT
4744280 AAATAA-
1 AAATAAT
4744286 AAA-AAT
1 AAATAAT
*
4744292 ATATTAAT
1 A-AATAAT
*
4744300 AAATAGAC
1 AAATA-AT
4744308 AAATAAT
1 AAATAAT
4744315 AAA-AAT
1 AAATAAT
4744321 AAA-AAT
1 AAATAAT
*
4744327 GAA-AAT
1 AAATAAT
4744333 AAA
1 AAA
4744336 ACTAAAAGCC
Statistics
Matches: 108, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
5 3 0.03
6 44 0.41
7 25 0.23
8 28 0.26
9 6 0.06
10 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (7 bp):
AAATAAT
Found at i:4744270 original size:40 final size:39
Alignment explanation
Indices: 4744165--4744304 Score: 113
Period size: 37 Copynumber: 3.7 Consensus size: 39
4744155 ATATTAATAG
*
4744165 ATAATAAAAA-AATAATTAGATAAATAAA-AGAAATAGATAA
1 ATAATAAAAATAATAA-TAGAT-AATAAATA-AAACAGATAA
* *
4744205 ATAATAATAATAATAATA-A-CA-AAATAAAAGCAGATAA
1 ATAATAAAAATAATAATAGATAATAAATAAAA-CAGATAA
*
4744242 ATAATAAAAATATTAATAGATAATAAATAAATA-A-ATAA
1 ATAATAAAAATAATAATAGATAATAAATAAA-ACAGATAA
*
4744280 A-AATAAAAA-AAT-ATA-TTAATAAATA
1 ATAATAAAAATAATAATAGATAATAAATA
4744305 GACAAATAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
34 9 0.11
35 3 0.04
36 8 0.09
37 32 0.38
38 6 0.07
39 3 0.04
40 18 0.21
41 6 0.07
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (39 bp):
ATAATAAAAATAATAATAGATAATAAATAAAACAGATAA
Found at i:4744276 original size:34 final size:35
Alignment explanation
Indices: 4744238--4744326 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 35
4744228 ATAAAAGCAG
**
4744238 ATAAATAATAAAAATATTAATAGA-TAATAAATAA
1 ATAAATAATAAAAATAAAAATAGATTAATAAATAA
* *
4744272 ATAAATAA-AAATAA-AAAAATATATTAATAAATAG
1 ATAAATAATAAA-AATAAAAATAGATTAATAAATAA
*
4744306 ACAAATAATAAAAATAAAAAT
1 ATAAATAATAAAAATAAAAAT
4744327 GAAAATAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 9 0.20
34 28 0.61
35 9 0.20
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (35 bp):
ATAAATAATAAAAATAAAAATAGATTAATAAATAA
Found at i:4744289 original size:38 final size:37
Alignment explanation
Indices: 4744240--4744325 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 37
4744230 AAAAGCAGAT
*
4744240 AAATAATAAAAATATTAATAGAT-AATAAATAAATAAATAA
1 AAATAA-AAAAATA-TAATA-ATAAATAAACAAAT-AATAA
* *
4744280 AAATAAAAAAATATATTAATAAATAGACAAATAATAA
1 AAATAAAAAAATATAATAATAAATAAACAAATAATAA
4744317 AAATAAAAA
1 AAATAAAAA
4744326 TGAAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 16 0.38
38 13 0.31
39 7 0.17
40 6 0.14
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (37 bp):
AAATAAAAAAATATAATAATAAATAAACAAATAATAA
Found at i:4744316 original size:41 final size:41
Alignment explanation
Indices: 4744240--4744336 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 41
4744230 AAAAGCAGAT
* * *
4744240 AAATAATAAAAATATTAATAGATAATAAATAAAT-AAATAA
1 AAATAAAAAAAATATTAATAAATAACAAATAAATAAAATAA
4744280 AAATAAAAAAATATATTAATAAATAGACAAAT-AATAAAAATAA
1 AAATAAAAAAA-ATATTAATAAATA-ACAAATAAAT-AAAATAA
4744323 AAATGAAAATAAAA
1 AAAT-AAAA-AAAA
4744337 CTAAAAGCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 10 0.21
41 15 0.31
42 5 0.10
43 10 0.21
44 5 0.10
45 3 0.06
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (41 bp):
AAATAAAAAAAATATTAATAAATAACAAATAAATAAAATAA
Found at i:4744673 original size:44 final size:42
Alignment explanation
Indices: 4744619--4744803 Score: 197
Period size: 36 Copynumber: 4.5 Consensus size: 42
4744609 TATAAACAAA
4744619 GCTCCTCTAATCAGAGGCTCAACAATTTTTGAAAAAA-AAATAAG
1 GCTCCTCTAATCAGAGGCTCAACAA-TTTTGAAAAAATAAAT--G
* *
4744663 GCTCCTCTAATCAAAGGCTCAACGATTTTGAAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACAATTTTGAAAAAATAAATG
* * * *
4744705 GCTCCTTTAATCAGAGGCTCAACGACTTTG-GAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACAATTTTGAAAAAATAAATG
*
4744746 GCT-C-C---TCAGAGGCTCAACGATTTTG-AAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACAATTTTGAAAAAATAAATG
* * *
4744782 GCTTCTCTAATTAGAAGCTCAA
1 GCTCCTCTAATCAGAGGCTCAA
4744804 ATGGCTCCTC
Statistics
Matches: 124, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
36 32 0.26
37 1 0.01
38 1 0.01
40 1 0.01
41 23 0.19
42 28 0.23
43 11 0.09
44 27 0.22
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (42 bp):
GCTCCTCTAATCAGAGGCTCAACAATTTTGAAAAAATAAATG
Found at i:4744710 original size:42 final size:41
Alignment explanation
Indices: 4744574--4744803 Score: 218
Period size: 44 Copynumber: 5.5 Consensus size: 41
4744564 TTTGATCAAA
* * * * **
4744574 GCTCCTCTAAGCAGATGCTTAACGACTTTGAGAAATATAAACAAA
1 GCTCCTCTAATCAGAGGCTCAACGATTTTGA-AAA-AT-AA-ATG
* *
4744619 GCTCCTCTAATCAGAGGCTCAACAATTTTTGAAAAAAAAATAAG
1 GCTCCTCTAATCAGAGGCTCAACGA-TTTTGAAAAATAAAT--G
*
4744663 GCTCCTCTAATCAAAGGCTCAACGATTTTGAAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGATTTTG-AAAAATAAATG
* * *
4744705 GCTCCTTTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGATTTTGAAAAATAAATG
4744746 GCT-C-C---TCAGAGGCTCAACGATTTTGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGATTTTGAAAAATAAATG
* * *
4744782 GCTTCTCTAATTAGAAGCTCAA
1 GCTCCTCTAATCAGAGGCTCAA
4744804 ATGGCTCCTC
Statistics
Matches: 156, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
36 32 0.21
37 1 0.01
38 1 0.01
40 1 0.01
41 23 0.15
42 29 0.19
43 7 0.04
44 33 0.21
45 24 0.15
46 5 0.03
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGATTTTGAAAAATAAATG
Found at i:4744805 original size:25 final size:25
Alignment explanation
Indices: 4744777--4744828 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
4744767 TTTGAAAAAT
* *
4744777 AAATGGCTTCTCTAATTAGAAGCTC
1 AAATGGCTCCTCTAATCAGAAGCTC
*
4744802 AAATGGCTCCTCTAATCAGAGGCTC
1 AAATGGCTCCTCTAATCAGAAGCTC
4744827 AA
1 AA
4744829 CAACTTTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
AAATGGCTCCTCTAATCAGAAGCTC
Found at i:4744940 original size:42 final size:41
Alignment explanation
Indices: 4744802--4745142 Score: 391
Period size: 42 Copynumber: 8.2 Consensus size: 41
4744792 TTAGAAGCTC
* *
4744802 AAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAAT
1 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAT
* * * * *
4744843 AAATGGCTCATCTTATCATAGGCTCTATGACTTTTGAAAAT
1 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAT
* * * **
4744884 AAATGGCTCATCTAATCAAAGGCTCGATAACTTTTGAGAAAT
1 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGA-AAAT
4744926 AAATGGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAT
1 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAT
* * * *
4744966 AAATAAAGCTCCTCTAAACAGATGCTCAACGACTTTCGAAAAAT
1 AAAT--GGCTCCTCTAATCAGAGGCTCAACGACTTTTG-AAAAT
*
4745010 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTT-AAATT
1 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAT
* * *
4745050 AAATAAAGCTCCTCTAAGCAGAAGCTCAACGACTTTTGAAAAAT
1 AAAT--GGCTCCTCTAATCAGAGGCTCAACGACTTTTG-AAAAT
* * *
4745094 AAATGGCTCTTCTAATCAGAGGCTCAACAAC-TTTAAAAAT
1 AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAT
4745134 AAATGGCTC
1 AAATGGCTC
4745143 ATTGACGATT
Statistics
Matches: 256, Mismatches: 35, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
40 30 0.12
41 75 0.29
42 131 0.51
43 3 0.01
44 17 0.07
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (41 bp):
AAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAT
Found at i:4745499 original size:43 final size:42
Alignment explanation
Indices: 4745441--4745525 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
4745431 TTTGGCAAAC
*
4745441 TTGGAATTCATATCCAAAAA-TCTAAAGCTTTTCATTTAAATT
1 TTGGAATTCACATCCAAAAATTC-AAAGCTTTTCATTTAAATT
* *
4745483 TTGGAGATTCACATCCAGAAATTCAAAGCTTTTCATTTGAATT
1 TTGGA-ATTCACATCCAAAAATTCAAAGCTTTTCATTTAAATT
4745526 CAAAGTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 5 0.13
43 31 0.82
44 2 0.05
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAGCTTTTCATTTAAATT
Found at i:4745753 original size:22 final size:21
Alignment explanation
Indices: 4745704--4745764 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
4745694 AAGGTTTCAC
4745704 TTCTCAAAGATTCTCATTTTGA
1 TTCTCAAAGATTCTCA-TTTGA
**
4745726 AACTCAAAGATTCTCATTTGA
1 TTCTCAAAGATTCTCATTTGA
*
4745747 GTTCTCAAAAATTCTCAT
1 -TTCTCAAAGATTCTCAT
4745765 CAAAATATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (21 bp):
TTCTCAAAGATTCTCATTTGA
Found at i:4746950 original size:20 final size:22
Alignment explanation
Indices: 4746907--4746952 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4746897 TCTTTTTTTT
*
4746907 CTTTTTTTTTAATTTATTTTAC
1 CTTTTTTTTTAATTTATTTCAC
*
4746929 CTTTTTTTTT-CTTT-TTTCAC
1 CTTTTTTTTTAATTTATTTCAC
4746949 CTTT
1 CTTT
4746953 CACCATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (22 bp):
CTTTTTTTTTAATTTATTTCAC
Found at i:4746985 original size:32 final size:34
Alignment explanation
Indices: 4746929--4746992 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
4746919 TTTATTTTAC
*
4746929 CTTTTTTTTTCTTTTTTCACCTTTCA-CCATTTT
1 CTTTTCTTTTCTTTTTTCACCTTTCATCCATTTT
*
4746962 CTTTTCTTTTC-TTTTTCATCTTTCATCCATT
1 CTTTTCTTTTCTTTTTTCACCTTTCATCCATT
4746993 GTTGATATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (34 bp):
CTTTTCTTTTCTTTTTTCACCTTTCATCCATTTT
Found at i:4750994 original size:60 final size:59
Alignment explanation
Indices: 4750928--4751246 Score: 211
Period size: 58 Copynumber: 5.7 Consensus size: 59
4750918 TTGTACAGGA
* *
4750928 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTTG-AAACTT-TTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTTGAAAACTTGTT--TTT-AAAG
**
4750988 AAAATTGATACTTTCAAC--TTTTCCTAAAAA-ATTCACTTTTGAAAACTTGTTTTTAAAG
1 AAAATTGATACTTTCAACTTTTTTCC-AAAAATATT-TTTTTTGAAAACTTGTTTTTAAAG
* *
4751046 AAAATTGATACTTTCAACTTTTTTTCAAAAATA--TTTTTT-AAAA--AGTTTATT----
1 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTTGAAAACTTGTTT-TTAAAG
* * * * * *
4751097 ----TTCA-ACTTTCAAC-TTTTCCTCAAAAATA-TTTTTTAGAAAGCTT-ATTTTCAAG
1 AAAATTGATACTTTCAACTTTTTTC-CAAAAATATTTTTTTTGAAAACTTGTTTTTAAAG
* * * * *
4751149 TAAAATTGATACTTTCAACTTTTTTTCAAAAATA-TTTTTTAGAAAGCTT-ATTTTCAAG
1 -AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTTGAAAACTTGTTTTTAAAG
*
4751207 AAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
1 -AAAATTGATACTTTCAACTTTTTTC-CAAAAATATTTTTT
4751247 GAATTTTACT
Statistics
Matches: 212, Mismatches: 21, Indels: 53
0.74 0.07 0.19
Matches are distributed among these distances:
45 4 0.02
46 17 0.08
47 8 0.04
48 5 0.02
49 2 0.01
54 4 0.02
55 2 0.01
56 4 0.02
57 11 0.05
58 96 0.45
59 27 0.13
60 30 0.14
61 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTTGAAAACTTGTTTTTAAAG
Found at i:4751106 original size:104 final size:104
Alignment explanation
Indices: 4750997--4751205 Score: 309
Period size: 104 Copynumber: 2.0 Consensus size: 104
4750987 GAAAATTGAT
*
4750997 ACTTTCAACTTTTCCT-AAAAA-ATTCACTTTT-GAAAACTTGTTTTTAAAG-AAAATTGATACT
1 ACTTTCAACTTTTCCTCAAAAATATT---TTTTAGAAAACTT-ATTTTAAAGTAAAATTGATACT
*
4751058 TTCAACTTTTTTTCAAAAATATTTTTTAAAAAGTTTATTTTCA
62 TTCAACTTTTTTTCAAAAATATTTTTTAAAAAGCTTATTTTCA
* *
4751101 ACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGTAAAATTGATACTTTCA
1 ACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTAAAGTAAAATTGATACTTTCA
*
4751166 ACTTTTTTTCAAAAATATTTTTTAGAAAGCTTATTTTCA
66 ACTTTTTTTCAAAAATATTTTTTAAAAAGCTTATTTTCA
4751205 A
1 A
4751206 GAAAAATTGA
Statistics
Matches: 96, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
103 11 0.11
104 77 0.80
105 5 0.05
106 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (104 bp):
ACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTTAAAGTAAAATTGATACTTTCA
ACTTTTTTTCAAAAATATTTTTTAAAAAGCTTATTTTCA
Found at i:4751108 original size:46 final size:46
Alignment explanation
Indices: 4751055--4751147 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
4751045 GAAAATTGAT
** *
4751055 ACTTTCAACTTTTTTTCAAAAATATTTTTTAAAAAGTTTATTTTCA
1 ACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAGCTTATTTTCA
*
4751101 ACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTATTTTCA
1 ACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAGCTTATTTTCA
4751147 A
1 A
4751148 GTAAAATTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (46 bp):
ACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAGCTTATTTTCA
Found at i:4751214 original size:162 final size:161
Alignment explanation
Indices: 4750937--4751246 Score: 396
Period size: 162 Copynumber: 1.9 Consensus size: 161
4750927 AAAAATTGAT
* * *
4750937 ACTTTCAACTTTTTTCCAAAAATATTTTTTTTGAAACTTTTAATTTCGAGGAAAATTGATACTTT
1 ACTTTCAACTTTTCTCCAAAAATATTTTTTTAGAAAC-TTTAATTTCAAGGAAAATTGATACTTT
* *
4751002 CAACTTTTCCTAAAAAATTCACTTTTGAAAACTTGTTTTTAAAGAAAATTGATACTTTCAACTTT
65 CAACTTTTCCTAAAAAATT--CTTTTGAAAACTTATTTTCAAAGAAAATTGATACTTTCAACTTT
**
4751067 TTTTCAAAAATATTTTTTAAAAAGTTTATTTTCA
128 TCCTCAAAAATATTTTTTAAAAAGTTTATTTTCA
* *
4751101 ACTTTCAACTTTTC-CTCAAAAATA-TTTTTTAGAAAGC-TTATTTTCAAGTAAAATTGATACTT
1 ACTTTCAACTTTTCTC-CAAAAATATTTTTTTAGAAA-CTTTAATTTCAAGGAAAATTGATACTT
** *
4751163 TCAACTTTTTTTCAAAAATATT-TTTTAGAAAGCTTATTTTC-AAGAAAAATTGATACTTTCAAC
64 TCAACTTTTCCT-AAAAA-ATTCTTTT-GAAAACTTATTTTCAAAG-AAAATTGATACTTTCAAC
4751226 TTTTCCTCAAAAATATTTTTT
125 TTTTCCTCAAAAATATTTTTT
4751247 GAATTTTACT
Statistics
Matches: 128, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
161 7 0.05
162 80 0.62
163 16 0.12
164 25 0.20
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (161 bp):
ACTTTCAACTTTTCTCCAAAAATATTTTTTTAGAAACTTTAATTTCAAGGAAAATTGATACTTTC
AACTTTTCCTAAAAAATTCTTTTGAAAACTTATTTTCAAAGAAAATTGATACTTTCAACTTTTCC
TCAAAAATATTTTTTAAAAAGTTTATTTTCA
Found at i:4751324 original size:4 final size:4
Alignment explanation
Indices: 4751315--4751348 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
4751305 TAATAATAAT
4751315 AATA AATA AATA AATA AAT- AA-A AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
4751349 CATGAGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.14
4 24 0.86
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:4752204 original size:15 final size:15
Alignment explanation
Indices: 4752186--4752273 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 15
4752176 AGCAGATAAT
*
4752186 ATAAAAATAT-TATA
1 ATAAAAATATAAATA
4752200 GATAAAAA-ATAAATA
1 -ATAAAAATATAAATA
*
4752215 ATAAAAATATATATTA
1 ATAAAAATATA-AATA
* * *
4752231 ATAAATAGACAAATA
1 ATAAAAATATAAATA
4752246 ATAAAAATA-AAA-A
1 ATAAAAATATAAATA
*
4752259 ATGAAAATA-AAATA
1 ATAAAAATATAAATA
4752273 A
1 A
4752274 AGCCCATTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
13 12 0.20
14 14 0.23
15 23 0.38
16 11 0.18
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAAAATATAAATA
Found at i:4752222 original size:13 final size:13
Alignment explanation
Indices: 4752204--4752269 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 13
4752194 ATTATAGATA
4752204 AAAAATAAATAAT
1 AAAAATAAATAAT
4752217 AAAAATATATATTAAT
1 AAAAATA-A-A-TAAT
*
4752233 AAATAGACAAATAAT
1 AAA-A-ATAAATAAT
*
4752248 AAAAATAAAAAAT
1 AAAAATAAATAAT
*
4752261 GAAAATAAA
1 AAAAATAAA
4752270 ATAAAGCCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 22 0.50
14 2 0.05
15 8 0.18
16 8 0.18
17 2 0.05
18 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:4752245 original size:31 final size:29
Alignment explanation
Indices: 4752186--4752254 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
4752176 AGCAGATAAT
*
4752186 ATAAAAATATTATAGATAAAAAATAAATA
1 ATAAAAATATTATAGATAAAAAACAAATA
*
4752215 ATAAAAATATATATTA-ATAAATAGACAAATA
1 ATAAAAATAT-TA-TAGATAAA-AAACAAATA
4752246 ATAAAAATA
1 ATAAAAATA
4752255 AAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 10 0.29
30 7 0.20
31 18 0.51
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAAAATATTATAGATAAAAAACAAATA
Found at i:4758863 original size:8 final size:8
Alignment explanation
Indices: 4758850--4758898 Score: 89
Period size: 8 Copynumber: 6.0 Consensus size: 8
4758840 TTTGTATTTC
4758850 ATTTTTTA
1 ATTTTTTA
4758858 ATTTTTTA
1 ATTTTTTA
4758866 ATTTTTTA
1 ATTTTTTA
4758874 ATTTTTTA
1 ATTTTTTA
4758882 ATTTTTTA
1 ATTTTTTA
4758890 ATTTCTTTA
1 ATTT-TTTA
4758899 TTTATTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 36 0.90
9 4 0.10
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTTA
Found at i:4762091 original size:2 final size:2
Alignment explanation
Indices: 4762086--4762125 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4762076 TTAGTGTGTG
4762086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4762126 AACCTAGCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4762945 original size:2 final size:2
Alignment explanation
Indices: 4762938--4762975 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4762928 CCACATGACC
4762938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4762976 GGTAGATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4764981 original size:11 final size:11
Alignment explanation
Indices: 4764965--4765009 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
4764955 ATTTATACAA
*
4764965 ATAAAACAAAT
1 ATAAAAAAAAT
4764976 ATAAAAAAAAT
1 ATAAAAAAAAT
4764987 AATAAATAAAGAAT
1 -ATAAA-AAA-AAT
4765001 ATAAAAAAA
1 ATAAAAAAA
4765010 TCAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 11 0.37
12 8 0.27
13 8 0.27
14 3 0.10
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:4766250 original size:8 final size:8
Alignment explanation
Indices: 4766232--4766272 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
4766222 TAAATAAAAT
4766232 AAATA-AA
1 AAATATAA
4766239 AAATATAA
1 AAATATAA
*
4766247 AAATACAA
1 AAATATAA
4766255 AAATATAA
1 AAATATAA
4766263 AAATATAA
1 AAATATAA
4766271 AA
1 AA
4766273 CATAAAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 5 0.16
8 26 0.84
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATATAA
Found at i:4766256 original size:16 final size:15
Alignment explanation
Indices: 4766232--4766285 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
4766222 TAAATAAAAT
4766232 AAATAAAAAATATAA
1 AAATAAAAAATATAA
4766247 AAATACAAAAATATAA
1 AAATA-AAAAATATAA
* *
4766263 AAATATAAAACATAA
1 AAATAAAAAATATAA
*
4766278 AAGTAAAA
1 AAATAAAA
4766286 TGAGTAATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 19 0.56
16 15 0.44
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.19
Consensus pattern (15 bp):
AAATAAAAAATATAA
Found at i:4767760 original size:15 final size:16
Alignment explanation
Indices: 4767742--4767771 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4767732 TTCACTTATT
4767742 TTTTTTCTTT-TTTTC
1 TTTTTTCTTTCTTTTC
4767757 TTTTTTCTTTCTTTT
1 TTTTTTCTTTCTTTT
4767772 TTTATCCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTCTTTCTTTTC
Found at i:4773823 original size:17 final size:16
Alignment explanation
Indices: 4773801--4773832 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4773791 GTTATTTATA
4773801 GTAGGGTAATAGGTGGG
1 GTAGGGTAAT-GGTGGG
4773818 GTAGGGTAATGGTGG
1 GTAGGGTAATGGTGG
4773833 ATAAGGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.00, G:0.53, T:0.25
Consensus pattern (16 bp):
GTAGGGTAATGGTGGG
Found at i:4777860 original size:13 final size:13
Alignment explanation
Indices: 4777842--4777884 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
4777832 TTAAATTTTA
*
4777842 TTTTTATTTTAAT
1 TTTTTAGTTTAAT
4777855 TTTTTAGTTTAA-
1 TTTTTAGTTTAAT
* *
4777867 TTTTTGGATTAAT
1 TTTTTAGTTTAAT
4777880 TTTTT
1 TTTTT
4777885 TTTAGTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTTTAGTTTAAT
Found at i:4778507 original size:20 final size:18
Alignment explanation
Indices: 4778484--4778520 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
4778474 ATTTTTTTTT
4778484 TTTGCATGACTAATATTATA
1 TTTGCATGA-TAAT-TTATA
4778504 TTTGCATGATAATTTAT
1 TTTGCATGATAATTTAT
4778521 TTGCCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTGCATGATAATTTATA
Found at i:4782433 original size:59 final size:59
Alignment explanation
Indices: 4782369--4782819 Score: 525
Period size: 58 Copynumber: 7.7 Consensus size: 59
4782359 TTTTGTACAG
* * * *
4782369 GAAAAAATGATACTTTCAACTTTTCTC-CAAAAATATTTTTTAAAAATTTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAAA-GTTTATTTTCAA
* * * *
4782428 GAAAAATTGATTCTTTCAACTTTTC-CTCAAAAATTCACTTTTGAAAAACTTGT-TTTT-AA
1 GAAAAATTGATACTTTCAACTTTTCTCTCAAAAA-T-ATTTTTTAAAAAGTT-TATTTTCAA
* * * *
4782487 GTAAAATTGATACTTTCAACTTTTC-CTCAAAAGT-TCATTTTTGAAAA-TTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCTCTCAAAAATAT--TTTTTAAAAAGTTTATTTTCAA
* * * *
4782545 GGAAAATTGATACTTTCAACTTTTC-CCCAAAAATATTTTTTTTGAAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCTCTCAAAAATA--TTTTTTAAAAAGTTTATTTTCAA
*
4782605 -AGAAAATTGATACTTTCAACTTTT-TCTCAAAAATATTTTTTAGAAAGTTTATTTTCAA
1 GA-AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAA
* *
4782663 GGAAAATTGATACTTTCAACTTTT-TCTCAAAAATATTTTTTAGAAAGTTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAA
* *
4782721 GAAAAATTGATACTTTCAACTTTT-TCTCAAAAATATTTTTTAGAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAA
4782779 -AGAAAATTGATACTTTCAACTTTTCT-TCAAAAATATTTTTT
1 GA-AAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTT
4782820 GAATTTTATT
Statistics
Matches: 349, Mismatches: 26, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
56 1 0.00
57 7 0.02
58 212 0.61
59 71 0.20
60 46 0.13
61 12 0.03
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAA
Found at i:4782518 original size:118 final size:114
Alignment explanation
Indices: 4782371--4782818 Score: 503
Period size: 118 Copynumber: 3.9 Consensus size: 114
4782361 TTGTACAGGA
* * * *
4782371 AAAAATGATACTTTCAAC-TTTTCTCCAAAAATATTTTTTAAAAATTTTTAATTTCGAGAAAAAT
1 AAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTAAAAA-GTTTATTTTCAAGAAAAAT
* *
4782435 TGATTCTTTCAACTTTTCCTCAAAAATTCACTTTTGAAAAACTTGTTTTTAAG
64 TGATACTTTCAACTTTTCCTCAAAAATT-ATTTTTGAAAAACTT-TTTTTAAG
* * * * *
4782488 TAAAATTGATACTTTCAACTTTTCCTCAAAAGT-TCATTTTTGAAAA-TTTATTTTTAAGGAAAA
1 -AAAATTGATACTTTCAACTTTTTCTCAAAAATAT--TTTTTAAAAAGTTTATTTTCAAGAAAAA
* * * *
4782551 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAAGCTTATTTTCAAAG
63 TTGATACTTTCAACTTTTCCTC-AAAA-ATTATTTTTGAAAAACTT-TTTT-TAAG
* *
4782607 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGTTTATTTTCAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAAGAAAAATTG
* * * *
4782672 ATACTTTCAACTTTTTCTCAAAAA-TATTTTTTAGAAAGTTTATTTTCAAG
66 ATACTTTCAACTTTTCCTCAAAAATTATTTTTGAAAAACTTT-TTTT-AAG
* *
4782722 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGCTTATTTTCAA-AGAAAAT
1 -AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAAGA-AAAAT
*
4782786 TGATACTTTCAACTTTTCTTCAAAAA-TATTTTT
64 TGATACTTTCAACTTTTCCTCAAAAATTATTTTT
4782819 TGAATTTTAT
Statistics
Matches: 286, Mismatches: 32, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
114 1 0.00
115 17 0.06
116 92 0.32
117 46 0.16
118 109 0.38
119 21 0.07
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAGTTTATTTTCAAGAAAAATTG
ATACTTTCAACTTTTCCTCAAAAATTATTTTTGAAAAACTTTTTTTAAG
Found at i:4782671 original size:176 final size:174
Alignment explanation
Indices: 4782369--4782819 Score: 565
Period size: 176 Copynumber: 2.6 Consensus size: 174
4782359 TTTTGTACAG
* * * ** * *
4782369 GAAAAAATGATACTTTCAACTTTTCTCCAAAAATA-TTTTTTAAAAATTTTTAATTTC-GAGAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAA-GCTTATTTTCAAAG-AA
* * * * *
4782432 AATTGATTCTTTCAACTTTTCCTCAAAAATTCACTTTTGAAAAACTTGTTTTTAAGTAAAATTGA
64 AATTGATACTTTCAACTTTTTCTCAAAAA-T-ATTTTTTAAAAACTTGTTTTTAAGGAAAATTGA
* *
4782497 TACTTTCAACTTTTCCTCAAAAGT-TCATTTTT-GAAAATTTATTTTTAA
127 TACTTTCAACTTTTCCTCAAAAATAT--TTTTTAGAAAATTTATTTTCAA
*
4782545 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAAGCTTATTTTCAAAGAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAAGCTTATTTTCAAAGAAA
* *
4782610 ATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGTT-TATTTTCAAGGAAAATTGAT
65 ATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTGT-TTTT-AAGGAAAATTGAT
* *
4782674 ACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGTTTATTTTCAA
128 ACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAATTTATTTTCAA
* * *
4782721 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAG-AAAGCTTATTTTCAAAGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAAGCTTATTTTCAAAGAAAA
4782785 TTGATACTTTCAAC-TTTTCTTCAAAAATATTTTTT
66 TTGATACTTTCAACTTTTTC-TCAAAAATATTTTTT
4782820 GAATTTTATT
Statistics
Matches: 244, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
173 5 0.02
174 51 0.21
175 27 0.11
176 112 0.46
177 37 0.15
178 12 0.05
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (174 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAAGCTTATTTTCAAAGAAAA
TTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTGTTTTTAAGGAAAATTGATACT
TTCAACTTTTCCTCAAAAATATTTTTTAGAAAATTTATTTTCAA
Found at i:4782843 original size:5 final size:5
Alignment explanation
Indices: 4782835--4782878 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
4782825 TTATTTAAAG
4782835 AAAAT AAAAT --AAT AAAAT AAAAT AAAAT AAAAAT AAAA- AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT A
4782879 TTAAACAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.09
4 4 0.11
5 23 0.66
6 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:4782853 original size:13 final size:13
Alignment explanation
Indices: 4782835--4782859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4782825 TTATTTAAAG
4782835 AAAATAAAATAAT
1 AAAATAAAATAAT
4782848 AAAATAAAATAA
1 AAAATAAAATAA
4782860 AATAAAAATA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:4782858 original size:18 final size:18
Alignment explanation
Indices: 4782835--4782883 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
4782825 TTATTTAAAG
4782835 AAAATAAAATAATAAAAT
1 AAAATAAAATAATAAAAT
4782853 AAAATAAAAT-A-AAAAT
1 AAAATAAAATAATAAAAT
*
4782869 AAAA-AAAATATTAAA
1 AAAATAAAATAATAAA
4782884 CAATTCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 9 0.32
17 4 0.14
18 10 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAATAATAAAAT
Found at i:4782860 original size:10 final size:10
Alignment explanation
Indices: 4782835--4782878 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 10
4782825 TTATTTAAAG
4782835 AAAATAAAAT
1 AAAATAAAAT
4782845 --AATAAAAT
1 AAAATAAAAT
4782853 AAAATAAAAT
1 AAAATAAAAT
4782863 AAAAATAAAA-
1 -AAAATAAAAT
4782873 AAAATA
1 AAAATA
4782879 TTAAACAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.26
9 6 0.19
10 8 0.26
11 9 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:4782911 original size:4 final size:4
Alignment explanation
Indices: 4782902--4782927 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4782892 ATTTAATAAT
4782902 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
4782928 ACATGAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:4783461 original size:12 final size:13
Alignment explanation
Indices: 4783435--4783459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4783425 TCTGAAAATT
4783435 TTTCAAAAAAAAA
1 TTTCAAAAAAAAA
4783448 TTTCAAAAAAAA
1 TTTCAAAAAAAA
4783460 TTCTCCAAAA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
TTTCAAAAAAAAA
Found at i:4783787 original size:17 final size:17
Alignment explanation
Indices: 4783754--4783794 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4783744 TTAATAGATA
* *
4783754 ATAAA-AAAATAATTAG
1 ATAAATAAAAGAAATAG
4783770 ATAAATAAAAGAAATAG
1 ATAAATAAAAGAAATAG
4783787 ATAAATAA
1 ATAAATAA
4783795 TAATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (17 bp):
ATAAATAAAAGAAATAG
Found at i:4783816 original size:40 final size:38
Alignment explanation
Indices: 4783772--4783888 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 38
4783762 ATAATTAGAT
*
4783772 AAATAAAAGAAATAGATAAATAATAATAATAATAATAACA
1 AAATAAAAGAAATA-ATAAATAAAAATAATAATAATAA-A
* *
4783812 AAATAAAAGCAGATAA-ATAATAAAAATATTAATAGATAAA
1 AAATAAAAG-AAATAATA-AATAAAAATAATAATA-ATAAA
* *
4783852 AAAT-AAATAAATAA-AAATAAAAATATATATTAATAAA
1 AAATAAAAGAAATAATAAATAAAAATA-ATAATAATAAA
4783889 TAGACAAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
37 15 0.23
38 10 0.15
39 4 0.06
40 29 0.44
41 8 0.12
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (38 bp):
AAATAAAAGAAATAATAAATAAAAATAATAATAATAAA
Found at i:4783852 original size:15 final size:15
Alignment explanation
Indices: 4783824--4783872 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
4783814 ATAAAAGCAG
4783824 ATAAAT-AATAAAAA
1 ATAAATAAATAAAAA
* *
4783838 TATTAATAGATAAAAA
1 -ATAAATAAATAAAAA
4783854 ATAAATAAAT-AAAA
1 ATAAATAAATAAAAA
4783868 ATAAA
1 ATAAA
4783873 AATATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 9 0.31
15 13 0.45
16 7 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
ATAAATAAATAAAAA
Found at i:4783862 original size:34 final size:33
Alignment explanation
Indices: 4783753--4783907 Score: 91
Period size: 37 Copynumber: 4.4 Consensus size: 33
4783743 ATTAATAGAT
*
4783753 AATAA-AAAAATAATTAGATAAATAAAAGAAATAGATA
1 AATAATAAAAAT-ATTA-AT-AAT-AAA-AAATAAATA
* * * *
4783790 AATAATAATAATAATAATAACAAAATAAAAGCAGATA
1 AATAATAAAAATATTAATAATAAAA-AATA--A-ATA
4783827 AATAATAAAAATATTAATAGATAAAAAATAAATA
1 AATAATAAAAATATTAATA-ATAAAAAATAAATA
* * * *
4783861 AATAAAAATAAAAATA-T-ATATTAATAAATAGACA
1 AAT---AATAAAAATATTAATAATAAAAAATAAATA
4783895 AATAATAAAAATA
1 AATAATAAAAATA
4783908 AAAATGAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
31 10 0.10
33 1 0.01
34 25 0.26
35 6 0.06
36 3 0.03
37 41 0.43
38 10 0.10
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.24
Consensus pattern (33 bp):
AATAATAAAAATATTAATAATAAAAAATAAATA
Found at i:4783871 original size:37 final size:36
Alignment explanation
Indices: 4783789--4783912 Score: 117
Period size: 37 Copynumber: 3.3 Consensus size: 36
4783779 AGAAATAGAT
* *
4783789 AAATAATAATAATAATAATAACAAAATAAA-AGCAGATAA
1 AAATAAAAATATTAATAATAA-AAAATAAATA--A-ATAA
4783828 ATAATAAAAATATTAATAGATAAAAAATAAATAAATAA
1 A-AATAAAAATATTAATA-ATAAAAAATAAATAAATAA
* * *
4783866 AAATAAAAATATATATTAATAAATAGACAAAT-AATAA
1 AAATAAAAATAT-TAATAATAAA-AAATAAATAAATAA
4783903 AAATAAAAAT
1 AAATAAAAAT
4783913 GAAAATAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
37 31 0.41
38 15 0.20
39 2 0.03
40 22 0.29
41 5 0.07
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (36 bp):
AAATAAAAATATTAATAATAAAAAATAAATAAATAA
Found at i:4783922 original size:5 final size:6
Alignment explanation
Indices: 4783850--4783928 Score: 52
Period size: 6 Copynumber: 12.7 Consensus size: 6
4783840 TTAATAGATA
* * * * *
4783850 AAAAAT AAATAAAT AAAAAT AAAAAT ATATATT AATAAAT AGACA- AATAAT
1 AAAAAT -AA-AAAT AAAAAT AAAAAT A-AAAAT AA-AAAT AAAAAT AAAAAT
* *
4783901 AAAAAT AAAAAT GAAAAT AAAACT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
4783929 GCCTATTGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
5 2 0.04
6 38 0.69
7 11 0.20
8 4 0.07
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:4784136 original size:11 final size:11
Alignment explanation
Indices: 4784120--4784154 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4784110 CGTGACACAT
4784120 TTTTGTTTTTG
1 TTTTGTTTTTG
*
4784131 TTTTGTTTTTA
1 TTTTGTTTTTG
*
4784142 TTTTTTTTTTG
1 TTTTGTTTTTG
4784153 TT
1 TT
4784155 AAAATTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:4784145 original size:17 final size:17
Alignment explanation
Indices: 4784119--4784154 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4784109 ACGTGACACA
*
4784119 TTTTTGTTTTTGTTTTG
1 TTTTTATTTTTGTTTTG
*
4784136 TTTTTATTTTTTTTTTG
1 TTTTTATTTTTGTTTTG
4784153 TT
1 TT
4784155 AAAATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (17 bp):
TTTTTATTTTTGTTTTG
Found at i:4784312 original size:42 final size:41
Alignment explanation
Indices: 4784170--4784636 Score: 451
Period size: 42 Copynumber: 11.1 Consensus size: 41
4784160 TTTGATCAAA
* * * **
4784170 GCTCCTCTAAGCAGATGCTTAACGACTTTGAGAAATATAAACAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGA-AAA-AT-AA-ATG
* * *
4784215 GCTCCTCTAATCAGAGGCTCAACAATTTTTGAAAAAAAAATAAG
1 GCTCCTCTAATCAGAGGCTCAACGA-CTTTGAAAAATAAAT--G
* *
4784259 GCTCCTCTAATCAAAGGCTCAACGATTTTGGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTT-GAAAAATAAATG
* * *
4784301 GCTCATTTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
* * * * *
4784342 GCTCATCTTATCATAGGCTCTATGACTTTTG-AAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAATG
* * * ** *
4784383 GCTCATCTAATCAAAGGCTCGATAACTTTTGAGAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAATG
4784425 GCTCCTCTAATCAGAGGCTCAACGACTTTGATAATAAATAAA--
1 GCTCCTCTAATCAGAGGCTCAACGACTTTG--AA-AAATAAATG
* *
4784467 GCTCCTCTAAACAGATGCTCAACGACTTTCGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTT-GAAAAATAAATG
4784509 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAATTAAATAAA--
1 GCTCCTCTAATCAGAGGCTCAACGACTTTG-AA--AAATAAATG
* *
4784551 GCTCCTCTAAGCAGAAGCTCAACGACTTTTGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAATG
* * *
4784593 GCTCTTCTAATCAGAGGTTCAACAACTTT-AAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
4784633 GCTC
1 GCTC
4784637 ATTGACGATT
Statistics
Matches: 361, Mismatches: 43, Indels: 41
0.81 0.10 0.09
Matches are distributed among these distances:
40 29 0.08
41 79 0.22
42 164 0.45
43 12 0.03
44 48 0.13
45 24 0.07
46 5 0.01
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
Found at i:4784993 original size:43 final size:42
Alignment explanation
Indices: 4784935--4785019 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
4784925 TTTGGCAAAC
*
4784935 TTGGAATTCATATCCAAAAA-TCTAAAGCTTTTCATTTAAATT
1 TTGGAATTCACATCCAAAAATTC-AAAGCTTTTCATTTAAATT
*
4784977 TTGGAGATTCACATCCAAAAATTCAAAGCTTTTCATTTGAATT
1 TTGGA-ATTCACATCCAAAAATTCAAAGCTTTTCATTTAAATT
4785020 CAAAGTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
42 5 0.13
43 32 0.82
44 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAGCTTTTCATTTAAATT
Found at i:4785247 original size:22 final size:21
Alignment explanation
Indices: 4785198--4785258 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
4785188 AAGGTTTCAC
4785198 TTCTCAAAGATTCTCATTTTGA
1 TTCTCAAAGATTCTCA-TTTGA
**
4785220 AACTCAAAGATTCTCATTTGA
1 TTCTCAAAGATTCTCATTTGA
*
4785241 GTTCTCAAAAATTCTCAT
1 -TTCTCAAAGATTCTCAT
4785259 CAAAATATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (21 bp):
TTCTCAAAGATTCTCATTTGA
Found at i:4786439 original size:20 final size:21
Alignment explanation
Indices: 4786399--4786441 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4786389 CTTTTTTTTC
*
4786399 TTTTTTTTATTTATTTTACCT
1 TTTTTTTTATTTATTTCACCT
*
4786420 TTTTTTTTCTTT-TTTCACCT
1 TTTTTTTTATTTATTTCACCT
4786440 TT
1 TT
4786442 CACCTTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTTTATTTATTTCACCT
Found at i:4790480 original size:58 final size:59
Alignment explanation
Indices: 4790414--4790569 Score: 185
Period size: 59 Copynumber: 2.7 Consensus size: 59
4790404 TTTGTACAGA
* **
4790414 AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTTTG-AAACTT-TAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCCAAAAATATTTTTTTTGAAAACTTGT-ATTTAAAG
* ** *
4790472 GAAAATTGATACTTTCAAC-TTTTCCTAAAAA-ATTCACTTTTGAAAACTTGTTTTTAAAG
1 AAAAATTGATACTTTCAACTTTTTCC-AAAAATATT-TTTTTTGAAAACTTGTATTTAAAG
*
4790531 AAAAATTGATACTTTCAACTTTTTTCAAAAATATTTTTT
1 AAAAATTGATACTTTCAACTTTTTCCAAAAATATTTTTT
4790570 AAAAAGTTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
57 9 0.11
58 27 0.33
59 36 0.44
60 9 0.11
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (59 bp):
AAAAATTGATACTTTCAACTTTTTCCAAAAATATTTTTTTTGAAAACTTGTATTTAAAG
Found at i:4790593 original size:45 final size:45
Alignment explanation
Indices: 4790541--4790631 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
4790531 AAAAATTGAT
* *
4790541 ACTTTCAACTTTTTTCAAAAATATTTTTTAAAAAGTTTATTTTCA
1 ACTTTCAACTTTTCTCAAAAATATTTTTTAAAAAGCTTATTTTCA
*
4790586 ACTTTCAACTTTTCTCAAAAATATTTTTTAGAAAGCTTATTTTCA
1 ACTTTCAACTTTTCTCAAAAATATTTTTTAAAAAGCTTATTTTCA
4790631 A
1 A
4790632 GAAAATTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (45 bp):
ACTTTCAACTTTTCTCAAAAATATTTTTTAAAAAGCTTATTTTCA
Found at i:4790744 original size:17 final size:17
Alignment explanation
Indices: 4790724--4790762 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
4790714 CTAATCTAAT
4790724 AATAAT-AATAATAAATA
1 AATAATAAAT-ATAAATA
4790741 AATAATAAATATAAATA
1 AATAATAAATATAAATA
4790758 AATAA
1 AATAA
4790763 ATACATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATAAATATAAATA
Found at i:4790761 original size:14 final size:13
Alignment explanation
Indices: 4790727--4790765 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
4790717 ATCTAATAAT
*
4790727 AATAATAATAAATA
1 AATAATAA-ATATA
4790741 AATAATAAATATA
1 AATAATAAATATA
4790754 AATAAATAAATA
1 AAT-AATAAATA
4790766 CATGAGAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAATAAATATA
Found at i:4791629 original size:23 final size:23
Alignment explanation
Indices: 4791603--4791647 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4791593 AAATAAAAGC
*
4791603 AGATAAATAATAAA-AATATTAAT
1 AGATAAAAAATAAATAA-ATTAAT
4791626 AGATAAAAAATAAATAAATTAA
1 AGATAAAAAATAAATAAATTAA
4791648 AATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
AGATAAAAAATAAATAAATTAAT
Found at i:4791663 original size:31 final size:30
Alignment explanation
Indices: 4791605--4791682 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
4791595 ATAAAAGCAG
4791605 ATAAATAATAAAAATATTAATAGATAAAAA
1 ATAAATAATAAAAATATTAATAGATAAAAA
* * *
4791635 ATAAATAAATTAAAATATATATTA-ATAAATAG
1 ATAAAT-AATAAAAATAT-TAATAGATAAA-AA
*
4791667 ACAAATAATAAAAATA
1 ATAAATAATAAAAATA
4791683 AAAATGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 6 0.15
31 24 0.60
32 10 0.25
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (30 bp):
ATAAATAATAAAAATATTAATAGATAAAAA
Found at i:4791684 original size:6 final size:6
Alignment explanation
Indices: 4791673--4791703 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4791663 ATAGACAAAT
*
4791673 AATAAA AATAAA AATGAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
4791704 GCCCATTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:4792579 original size:19 final size:19
Alignment explanation
Indices: 4792555--4792594 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4792545 TAAAGTTGTC
*
4792555 TCAG-TTTCAAACATGCCTT
1 TCAGTTTTCAAA-AAGCCTT
4792574 TCAGTTTTCAAAAAGCCTT
1 TCAGTTTTCAAAAAGCCTT
4792593 TC
1 TC
4792595 TCTTTCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (19 bp):
TCAGTTTTCAAAAAGCCTT
Found at i:4798280 original size:9 final size:8
Alignment explanation
Indices: 4798259--4798291 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
4798249 TTTGTATTTC
4798259 ATTTTTTA
1 ATTTTTTA
4798267 ATTTTTTA
1 ATTTTTTA
4798275 ATTTTTTA
1 ATTTTTTA
4798283 ATTTCTTTA
1 ATTT-TTTA
4798292 TTTATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTTA
Found at i:4802307 original size:2 final size:2
Alignment explanation
Indices: 4802300--4802325 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4802290 CCACATGACC
4802300 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4802326 GGTAGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4804330 original size:26 final size:22
Alignment explanation
Indices: 4804301--4804352 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
4804291 AAATTTATAC
4804301 AAATAAAACAAATATAAAAAAATAA
1 AAAT-AAA-AAATAT-AAAAAATAA
*
4804326 TAAATAAAGAATATAAAAAATAA
1 -AAATAAAAAATATAAAAAATAA
4804349 AAAT
1 AAAT
4804353 TAATTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 9 0.36
24 5 0.20
25 3 0.12
26 4 0.16
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAAAATATAAAAAATAA
Found at i:4805575 original size:8 final size:8
Alignment explanation
Indices: 4805557--4805589 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4805547 TAAATAAAAT
4805557 AAATA-AA
1 AAATATAA
*
4805564 AAATACAA
1 AAATATAA
4805572 AAATATAA
1 AAATATAA
4805580 AAATATAA
1 AAATATAA
4805588 AA
1 AA
4805590 CATAAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 5 0.21
8 19 0.79
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (8 bp):
AAATATAA
Found at i:4805581 original size:16 final size:15
Alignment explanation
Indices: 4805557--4805596 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
4805547 TAAATAAAAT
4805557 AAATAAAAAATACAA
1 AAATAAAAAATACAA
*
4805572 AAATATAAAAATATAA
1 AAATA-AAAAATACAA
4805588 AACATAAAA
1 AA-ATAAAA
4805597 GTAAAATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 14 0.64
17 3 0.14
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAAAATACAA
Found at i:4805964 original size:39 final size:38
Alignment explanation
Indices: 4805823--4805989 Score: 154
Period size: 39 Copynumber: 4.3 Consensus size: 38
4805813 GACATATGAC
** * * *
4805823 TAAAGAATAAAGGCTCTTCATAATAGATGCACATGACTT
1 TAAA-AATAAAGGCTCCCCATAATTGAGGCACATAACTT
* * * *
4805862 CAAAGAATAAAGGCTCTTCCATAACTGAGGCACATGACTT
1 TAAA-AATAAAGGCTC-CCCATAATTGAGGCACATAACTT
*
4805902 TAAAAATTAAGGCTTCCCCATAATTGAGGCACATAACTT
1 TAAAAATAAAGGC-TCCCCATAATTGAGGCACATAACTT
* ** * *
4805941 TGAAAATAAAGGCTCCCCTATAATAAAGGCACACAAATT
1 TAAAAATAAAGGCTCCCC-ATAATTGAGGCACATAACTT
4805980 TAAAAATAAA
1 TAAAAATAAA
4805990 TACTCAAAAG
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
38 5 0.05
39 79 0.73
40 24 0.22
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (38 bp):
TAAAAATAAAGGCTCCCCATAATTGAGGCACATAACTT
Found at i:4807078 original size:15 final size:16
Alignment explanation
Indices: 4807060--4807089 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4807050 TTCACTTATT
4807060 TTTTTTCTTT-TTTTC
1 TTTTTTCTTTCTTTTC
4807075 TTTTTTCTTTCTTTT
1 TTTTTTCTTTCTTTT
4807090 TTTATCCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTCTTTCTTTTC
Found at i:4817173 original size:14 final size:14
Alignment explanation
Indices: 4817154--4817184 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4817144 TTAAATTTTA
*
4817154 TTTTTATTTTAATT
1 TTTTTAGTTTAATT
4817168 TTTTTAGTTTAATT
1 TTTTTAGTTTAATT
4817182 TTT
1 TTT
4817185 GGATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTAGTTTAATT
Found at i:4817820 original size:20 final size:18
Alignment explanation
Indices: 4817795--4817831 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
4817785 TATTTTTTTT
4817795 TTTGCATGACTAATATTATA
1 TTTGCATGA-TAAT-TTATA
4817815 TTTGCATGATAATTTAT
1 TTTGCATGATAATTTAT
4817832 TTGCCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTGCATGATAATTTATA
Done.