Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 89 of 133
Found at i:17633189 original size:20 final size:20
Alignment explanation
Indices: 17633166--17633215 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
17633156 ATAATTTTTT
* *
17633166 AAATAAAGTTATTTGGTAAA
1 AAATAAAATTATTTAGTAAA
*
17633186 AAATTAAAATTATTTATTAAA
1 AAA-TAAAATTATTTAGTAAA
17633207 AAATAAAAT
1 AAATAAAAT
17633216 CCATATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (20 bp):
AAATAAAATTATTTAGTAAA
Found at i:17649802 original size:17 final size:17
Alignment explanation
Indices: 17649780--17649814 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17649770 TTTGTGCTTA
17649780 TGATTTATTTATGATAT
1 TGATTTATTTATGATAT
17649797 TGATTTATTTATGATAT
1 TGATTTATTTATGATAT
17649814 T
1 T
17649815 TTGATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (17 bp):
TGATTTATTTATGATAT
Found at i:17652498 original size:1 final size:1
Alignment explanation
Indices: 17652492--17652531 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
17652482 GAAAGAATGC
* * *
17652492 AAAAAAAAAAAAAAAAAAACAAAAGAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17652532 TGAATGGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:17652891 original size:16 final size:16
Alignment explanation
Indices: 17652870--17652900 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17652860 GTGTTAATCG
17652870 AAAAAAAAAAGTAAAA
1 AAAAAAAAAAGTAAAA
*
17652886 AAAAAAAAGAGTAAA
1 AAAAAAAAAAGTAAA
17652901 GAAAGATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAAGTAAAA
Found at i:17655200 original size:144 final size:142
Alignment explanation
Indices: 17654843--17655223 Score: 359
Period size: 144 Copynumber: 2.6 Consensus size: 142
17654833 AAAGAAAGTT
* * * *
17654843 AAATTATGAAAATAACCCTAAAGAGCATTTTAGTAATTTCACACCTTTCGAGATACGATA-TAGG
1 AAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACACCTCT-GAGGTACGA-ACAAGG
* * ** **
17654907 TTTTTAATGCATCAAAAATCATAAAATAATTTCAAAACATAATCTAGAGTGTTTCGTGAAAAACC
64 TTTTTAATGTATCAAAAATCATAAAATAATATCAAAACATAATCTAGAGCATTTCGCAAAAAACC
** *
17654972 AACCTCTGAAGGTC
129 AACCTCAAAAGGTA
* ** ** * * * * * ** *
17654986 AAATGACAAAAATATTCCTACAAAGGCATTTTAATAATTTTAAAGCTTCTGAGGTGTGATCAAGG
1 AAATTATGAAAATAACCCTA-AAGGGCATTTTAGTAATTTCACA-CCTCTGAGGTACGAACAAGG
* * * ** *
17655051 CTTTTAATATATCAAAAATCATAAAATGATATCAAATTATGATCTAGAGCATTTCGCAAAAAACC
64 TTTTTAATGTATCAAAAATCATAAAATAATATCAAAACATAATCTAGAGCATTTCGCAAAAAACC
17655116 AACCTCAAAAAGGTA
129 AACCTC-AAAAGGTA
* * *
17655131 AAATTATGAAAATACCCCTAAAGGGCATTGTAGTAATTTCACACCTCCTGAGGTACGAACAAAGT
1 AAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACACCT-CTGAGGTACGAACAAGGT
* * *
17655196 TTTTAATGTACCAATAATCATCAAATAA
65 TTTTAATGTATCAAAAATCATAAAATAA
17655224 CGTTTAAATA
Statistics
Matches: 180, Mismatches: 53, Indels: 9
0.74 0.22 0.04
Matches are distributed among these distances:
143 17 0.09
144 140 0.78
145 23 0.13
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (142 bp):
AAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACACCTCTGAGGTACGAACAAGGTT
TTTAATGTATCAAAAATCATAAAATAATATCAAAACATAATCTAGAGCATTTCGCAAAAAACCAA
CCTCAAAAGGTA
Found at i:17655462 original size:10 final size:10
Alignment explanation
Indices: 17655449--17655495 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
17655439 TTTGATCGAG
17655449 TTTGACCAAA
1 TTTGACCAAA
*
17655459 TTTGACAAAA
1 TTTGACCAAA
**
17655469 TTTGATTAAA
1 TTTGACCAAA
*
17655479 TTTGACCAAG
1 TTTGACCAAA
17655489 TTTGACC
1 TTTGACC
17655496 CGAAGGCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (10 bp):
TTTGACCAAA
Found at i:17656313 original size:20 final size:20
Alignment explanation
Indices: 17656288--17656326 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17656278 TGATTCAATT
*
17656288 TTATATTCTAATTTATTTAG
1 TTATATTATAATTTATTTAG
*
17656308 TTATATTATAATTTTTTTA
1 TTATATTATAATTTATTTA
17656327 TTGATTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATATTATAATTTATTTAG
Found at i:17657410 original size:2 final size:2
Alignment explanation
Indices: 17657403--17657434 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17657393 TATTTGTTTG
*
17657403 GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17657435 ATTTTAAAAT
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17657711 original size:24 final size:24
Alignment explanation
Indices: 17657670--17657726 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
17657660 TCCATATTGC
*
17657670 ATATTTTATTTTGCATAT-ATATAT
1 ATATTTTATTTTGAATATCAT-TAT
17657694 ATATTTTATCTTT-AATATCATTAT
1 ATATTTTAT-TTTGAATATCATTAT
*
17657718 ATTTTTTAT
1 ATATTTTAT
17657727 AATTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTTTATTTTGAATATCATTAT
Found at i:17658560 original size:21 final size:21
Alignment explanation
Indices: 17658517--17658564 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
17658507 CCATGTCAGC
**
17658517 AAAA-AATTTTAAAAATTTAA
1 AAAATAATTTTAAAAAAATAA
*
17658537 AAAATAATTTTAAAAAAATGA
1 AAAATAATTTTAAAAAAATAA
17658558 AAAATAA
1 AAAATAA
17658565 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATAATTTTAAAAAAATAA
Found at i:17658577 original size:17 final size:18
Alignment explanation
Indices: 17658549--17658582 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17658539 AATAATTTTA
17658549 AAAAAATGAAAAATAAAT
1 AAAAAATGAAAAATAAAT
*
17658567 AAAAAAT-AAAAGTAAA
1 AAAAAATGAAAAATAAA
17658583 AGATTAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAAAATGAAAAATAAAT
Found at i:17661505 original size:19 final size:20
Alignment explanation
Indices: 17661481--17661530 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
17661471 TATAATTATA
17661481 TTATTATTAAATT-ATAAAT
1 TTATTATTAAATTAATAAAT
17661500 TTATTA-TAAATTAATAAAT
1 TTATTATTAAATTAATAAAT
*
17661519 TAATCTATTAAA
1 TTAT-TATTAAA
17661531 ATAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 6 0.22
19 15 0.56
20 2 0.07
21 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTATTAAATTAATAAAT
Found at i:17661575 original size:28 final size:28
Alignment explanation
Indices: 17661509--17661576 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
17661499 TTTATTATAA
*
17661509 ATTAATAAATTAATCTATTAAAATAAAT
1 ATTAATAAATTAATCTATCAAAATAAAT
* *
17661537 ATTTATCAATTAAT-TATCACAAAT-AAT
1 ATTAATAAATTAATCTATCA-AAATAAAT
17661564 ATATAATAAATTA
1 AT-TAATAAATTA
17661577 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTAATAAATTAATCTATCAAAATAAAT
Found at i:17666690 original size:16 final size:16
Alignment explanation
Indices: 17666669--17666701 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17666659 ATAAAATCTT
17666669 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17666685 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17666701 A
1 A
17666702 TCTTATATCT
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:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
AATAATCCTTTTTAGA
Found at i:17678039 original size:18 final size:20
Alignment explanation
Indices: 17678018--17678059 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
17678008 ATGAAAAATT
17678018 AAAAAATT-AAAAAA-TGAA
1 AAAAAATTGAAAAAACTGAA
17678036 AAAAAATTGAAAAAACTGAA
1 AAAAAATTGAAAAAACTGAA
17678056 AAAA
1 AAAA
17678060 TGAAAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAATTGAAAAAACTGAA
Found at i:17678048 original size:8 final size:8
Alignment explanation
Indices: 17678003--17678082 Score: 56
Period size: 8 Copynumber: 9.6 Consensus size: 8
17677993 TGGATGAAGA
*
17678003 AAAAAATG
1 AAAAATTG
*
17678011 AAAAATTA
1 AAAAATTG
17678019 AAAAATT-
1 AAAAATTG
*
17678026 AAAAAATG
1 AAAAATTG
17678034 AAAAAAAATTG
1 ---AAAAATTG
*
17678045 AAAAAACTG
1 -AAAAATTG
*
17678054 AAAAAATG
1 AAAAATTG
17678062 AAAAA-TG
1 AAAAATTG
17678069 AAAAATGTG
1 AAAAAT-TG
17678078 AAAAA
1 AAAAA
17678083 AATGAAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
7 13 0.22
8 25 0.42
9 15 0.25
11 7 0.12
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.16
Consensus pattern (8 bp):
AAAAATTG
Found at i:17678050 original size:35 final size:34
Alignment explanation
Indices: 17677996--17678073 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 34
17677986 TCAATAATGG
*
17677996 ATGAAGAAAAAAATGAAAAA-TTAAAAAATTAAAAA
1 ATGAA-AAAAAAATGAAAAACTGAAAAAA-TAAAAA
* *
17678031 ATGAAAAAAAATTGAAAAAACTGAAAAAATGAAAA
1 ATGAAAAAAAAATG-AAAAACTGAAAAAATAAAAA
17678066 ATGAAAAA
1 ATGAAAAA
17678074 TGTGAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 8 0.21
35 23 0.61
36 7 0.18
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.15
Consensus pattern (34 bp):
ATGAAAAAAAAATGAAAAACTGAAAAAATAAAAA
Found at i:17678058 original size:10 final size:9
Alignment explanation
Indices: 17678001--17678108 Score: 70
Period size: 10 Copynumber: 12.4 Consensus size: 9
17677991 AATGGATGAA
17678001 GAAAAAAAT
1 GAAAAAAAT
17678010 G--AAAAAT
1 GAAAAAAAT
*
17678017 -TAAAAAAT
1 GAAAAAAAT
*
17678025 -TAAAAAAT
1 GAAAAAAAT
17678033 GAAAAAAAATT
1 G-AAAAAAA-T
*
17678044 GAAAAAACT
1 GAAAAAAAT
17678053 G-AAAAAAT
1 GAAAAAAAT
17678061 G--AAAAAT
1 GAAAAAAAT
**
17678068 GAAAAATGT
1 GAAAAAAAT
17678077 GAAAAAAAT
1 GAAAAAAAT
*
17678086 GAAGAAAAAG
1 GAA-AAAAAT
17678096 GAAAGAAAA-
1 GAAA-AAAAT
17678105 GAAA
1 GAAA
17678109 GACTCAAATT
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
7 13 0.16
8 21 0.26
9 22 0.27
10 24 0.29
11 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.14, T:0.13
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:17678066 original size:43 final size:44
Alignment explanation
Indices: 17678001--17678084 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
17677991 AATGGATGAA
* *
17678001 GAAAAAAATGAAAAATTAAAAAATTAAAAA-ATGAAAAAAAATT
1 GAAAAAAATGAAAAAATAAAAAATGAAAAATATGAAAAAAAATT
* * *
17678044 GAAAAAACTGAAAAAATGAAAAATGAAAAATGTGAAAAAAA
1 GAAAAAAATGAAAAAATAAAAAATGAAAAATATGAAAAAAA
17678085 TGAAGAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 26 0.74
44 9 0.26
ACGTcount: A:0.73, C:0.01, G:0.11, T:0.15
Consensus pattern (44 bp):
GAAAAAAATGAAAAAATAAAAAATGAAAAATATGAAAAAAAATT
Found at i:17678072 original size:6 final size:7
Alignment explanation
Indices: 17678004--17678075 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 7
17677994 GGATGAAGAA
17678004 AAAAATG
1 AAAAATG
*
17678011 AAAAATTA
1 AAAAA-TG
*
17678019 AAAAATTA
1 AAAAA-TG
17678027 AAAAATG
1 AAAAATG
17678034 -AAAA--
1 AAAAATG
*
17678038 AAAATTG
1 AAAAATG
17678045 AAAAAACTG
1 -AAAAA-TG
17678054 AAAAAATG
1 -AAAAATG
17678062 AAAAATG
1 AAAAATG
17678069 AAAAATG
1 AAAAATG
17678076 TGAAAAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 3 0.05
6 4 0.07
7 20 0.36
8 20 0.36
9 8 0.15
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (7 bp):
AAAAATG
Found at i:17678085 original size:43 final size:42
Alignment explanation
Indices: 17678001--17678099 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
17677991 AATGGATGAA
*
17678001 GAAAAAAATGAAAAATTAAAAAATTAAAAAATGAAAAAAAATT
1 GAAAAAAATGAAAAAATAAAAAATTAAAAAATGAAAAAAAA-T
* * * *
17678044 GAAAAAACTGAAAAAATGAAAAA-TGAAAAATGTGAAAAAAAT
1 GAAAAAAATGAAAAAATAAAAAATTAAAAAATG-AAAAAAAAT
*
17678086 GAAGAAAAAGGAAA
1 GAA-AAAAATGAAA
17678100 GAAAAGAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 12 0.26
43 35 0.74
ACGTcount: A:0.72, C:0.01, G:0.13, T:0.14
Consensus pattern (42 bp):
GAAAAAAATGAAAAAATAAAAAATTAAAAAATGAAAAAAAAT
Found at i:17678857 original size:20 final size:20
Alignment explanation
Indices: 17678832--17678883 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
17678822 CATGTTAGTG
17678832 ACATTTGCATTACATGCATT
1 ACATTTGCATTACATGCATT
17678852 ACATTTTGCATTACATGCATT
1 ACA-TTTGCATTACATGCATT
*
17678873 ACGTTTGCATT
1 ACATTTGCATT
17678884 GTAGTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (20 bp):
ACATTTGCATTACATGCATT
Found at i:17679133 original size:23 final size:23
Alignment explanation
Indices: 17679089--17679133 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
17679079 ATTTTAACTT
* *
17679089 TGATGAAAAATTGAGAATTTTTA
1 TGATAAAAAATTGAGAACTTTTA
**
17679112 TGATAAAAAATTTTGAACTTTT
1 TGATAAAAAATTGAGAACTTTT
17679134 TGAGGAAAGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (23 bp):
TGATAAAAAATTGAGAACTTTTA
Found at i:17679349 original size:14 final size:14
Alignment explanation
Indices: 17679275--17679357 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 14
17679265 TGTCTTTAAG
*
17679275 TTTAAATAAGAATC
1 TTTAAATGAGAATC
17679289 TTT-AA-GA-AAT-
1 TTTAAATGAGAATC
17679299 TTTAAATGAGAATC
1 TTTAAATGAGAATC
*** **
17679313 TTTGTCTTTGAAT-
1 TTTAAATGAGAATC
17679326 TTTAAATGAGAATC
1 TTTAAATGAGAATC
*
17679340 TTTGAATGAGAATC
1 TTTAAATGAGAATC
17679354 TTTA
1 TTTA
17679358 TCTTTGACTT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
10 3 0.06
11 5 0.10
12 3 0.06
13 13 0.25
14 27 0.53
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (14 bp):
TTTAAATGAGAATC
Found at i:17679352 original size:27 final size:27
Alignment explanation
Indices: 17679275--17679357 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
17679265 TGTCTTTAAG
*
17679275 TTTAAATAAGAATCTTT-AA-GA-AAT
1 TTTAAATGAGAATCTTTGAATGAGAAT
** **
17679299 TTTAAATGAGAATCTTTGTCTTTGAAT
1 TTTAAATGAGAATCTTTGAATGAGAAT
17679326 TTTAAATGAGAATCTTTGAATGAGAAT
1 TTTAAATGAGAATCTTTGAATGAGAAT
17679353 CTTTA
1 -TTTA
17679358 TCTTTGACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 16 0.35
27 26 0.57
28 4 0.09
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (27 bp):
TTTAAATGAGAATCTTTGAATGAGAAT
Found at i:17679693 original size:17 final size:17
Alignment explanation
Indices: 17679671--17679735 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
17679661 TTTGATAACG
17679671 TTAAATCCTTGCGAACC
1 TTAAATCCTTGCGAACC
* * *
17679688 TTAAATTCTCGCGAATC
1 TTAAATCCTTGCGAACC
** *
17679705 -TAAAAGCTTGCAAACC
1 TTAAATCCTTGCGAACC
17679721 TTAAA-CTCTTGCGAA
1 TTAAATC-CTTGCGAA
17679736 TTTGAAAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
16 11 0.31
17 25 0.69
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAAATCCTTGCGAACC
Found at i:17680226 original size:3 final size:3
Alignment explanation
Indices: 17680218--17680259 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
17680208 CTTTTCAATT
17680218 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17680260 GTTTTGTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17681158 original size:12 final size:12
Alignment explanation
Indices: 17681143--17681179 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17681133 CCTTTTGTTT
17681143 TGGTTTTTTTTA
1 TGGTTTTTTTTA
17681155 TGGTTTTTATTTA
1 TGGTTTTT-TTTA
17681168 T--TTTTTTTTA
1 TGGTTTTTTTTA
17681178 TG
1 TG
17681180 TTATTATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.22
11 5 0.22
12 8 0.35
13 5 0.22
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.76
Consensus pattern (12 bp):
TGGTTTTTTTTA
Found at i:17681174 original size:22 final size:22
Alignment explanation
Indices: 17681146--17681188 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
17681136 TTTGTTTTGG
*
17681146 TTTTTTTTATGGTTTTTATTTAT
1 TTTTTTTTAT-GTTATTATTTAT
17681169 TTTTTTTTATGTTATTATTT
1 TTTTTTTTATGTTATTATTT
17681189 CCTTTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTTTTTATGTTATTATTTAT
Found at i:17681266 original size:25 final size:23
Alignment explanation
Indices: 17681238--17681283 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
17681228 ATTTTTAGGA
17681238 AAACTATAAAAAAAATATTAAAATT
1 AAAC-ATAAAAAAAAT-TTAAAATT
* *
17681263 AAACATTAATAAAATTTAAAA
1 AAACATAAAAAAAATTTAAAA
17681284 AATAAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 9 0.47
25 4 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAACATAAAAAAAATTTAAAATT
Found at i:17682474 original size:65 final size:64
Alignment explanation
Indices: 17682314--17683033 Score: 229
Period size: 65 Copynumber: 11.2 Consensus size: 64
17682304 TTATCTAGGT
* * * * ** * * * *
17682314 TTTAAGCCTGGTTTAGTTGACACCTAATAAAAATTTAAGCCCAGTGTAGCTGGCACTCAATCAAA
1 TTTAAGCCTAGCTTAGTTGGCACCT-ATGAAGTTTTAAGCCTAGTTTAGCTAGCACT-AATGAAA
17682379 A
64 A
* * ** * * *
17682380 TATAAGCCCAATTTAGTTAGCACCAATGAAGTTTTAAGCCTAGTTTATCTAGCACTAATGAAAA
1 TTTAAGCCTAGCTTAGTTGGCACCTATGAAGTTTTAAGCCTAGTTTAGCTAGCACTAATGAAAA
* ** * *
17682444 TTTAAGCCTAGCTTAGTTGCCACTCTATGAAAATTTAAGCCTAGTATAGCTAGCACCT-A-G--G
1 TTTAAGCCTAGCTTAGTTGGCAC-CTATGAAGTTTTAAGCCTAGTTTAGCTAGCA-CTAATGAAA
*
17682505 T
64 A
* * * * * * *
17682506 TTTAAGCCCACCTTAGCTGGCACCTAT---GTTTTAAGCCCACTTTAGCTGGCACCCAAT-AAAG
1 TTTAAGCCTAGCTTAGTTGGCACCTATGAAGTTTTAAGCCTAGTTTAGCTAGCA-CTAATGAAA-
17682567 A
64 A
* * * * * * * * * *
17682568 TTTAAGCCTAGCTTAGCTAGCATTCAATGAA-ATTTAAGCCTAGATTATCAAACACTTAATGAAG
1 TTTAAGCCTAGCTTAGTTGGCA-CCTATGAAGTTTTAAGCCTAGTTTAGCTAGCAC-TAATGAAA
*
17682632 T
64 A
* * * * * * * *
17682633 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGTTTTAAACCCAATTTAGCTGGCACTGATCAACA
1 TTTAAGCCTAGCTTAGTTGGCACCT-ATGAAGTTTTAAGCCTAGTTTAGCTAGCACTAAT-GA-A
17682698 AA
63 AA
* * * * * * * * * **
17682700 GTTTTAAGCCCAACTTAGCTGACACCTAATGAA-ATTTAAACCCAGTTTAACTGATCTTTAATGA
1 --TTTAAGCCTAGCTTAGTTGGCACCT-ATGAAGTTTTAAGCCTAGTTTAGCT-AGCACTAATGA
17682764 AAA
62 AAA
* * * ** *
17682767 TTTAAGCCTA-ATGTAGTTGGCACCAATAAAGTTTTAAGCCTAGTTTATTTGGCA-TCAATGAAA
1 TTTAAGCCTAGCT-TAGTTGGCACCTATGAAGTTTTAAGCCTAGTTTAGCTAGCACT-AATGAAA
17682830 A
64 A
* * * ** * * *
17682831 TTTAAGCCAAACTTAATTGGCAACC-AGTGAAAATTTAAGCCTAATTTAGATGGCACCT-A-G--
1 TTTAAGCCTAGCTTAGTTGGC-ACCTA-TGAAGTTTTAAGCCTAGTTTAGCTAGCA-CTAATGAA
**
17682891 GT
63 AA
* ** * * * * * *
17682893 TTTAAGCCAAGCTTAACTGGCACCCAATGAAGATTTAAACCTAGCTTAGTTGGCACTTAATG-AA
1 TTTAAGCCTAGCTTAGTTGGCA-CCTATGAAGTTTTAAGCCTAGTTTAGCTAGCAC-TAATGAAA
17682957 A
64 A
* * * * * * * *
17682958 TTTAAACCAAGATTA-TCTGGCACTTAATGAAGTTTTAAGCCCAATTTAGTTGGCACCTAATG-A
1 TTTAAGCCTAGCTTAGT-TGGCACCT-ATGAAGTTTTAAGCCTAGTTTAGCTAGCA-CTAATGAA
17683021 AA
63 AA
*
17683023 TTTAAGTCTAG
1 TTTAAGCCTAG
17683034 TTTCATTGAC
Statistics
Matches: 479, Mismatches: 138, Indels: 75
0.69 0.20 0.11
Matches are distributed among these distances:
58 20 0.04
59 1 0.00
61 6 0.01
62 83 0.17
63 6 0.01
64 60 0.13
65 213 0.44
66 39 0.08
67 5 0.01
68 17 0.04
69 29 0.06
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (64 bp):
TTTAAGCCTAGCTTAGTTGGCACCTATGAAGTTTTAAGCCTAGTTTAGCTAGCACTAATGAAAA
Found at i:17682510 original size:29 final size:29
Alignment explanation
Indices: 17682490--17682558 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
17682480 AAGCCTAGTA
17682490 TAGCTAGCACCTAGGTTTTAAGCCCACCT
1 TAGCTAGCACCTAGGTTTTAAGCCCACCT
* * *
17682519 TAGCTGGCACCTATGTTTTAAGCCCACTT
1 TAGCTAGCACCTAGGTTTTAAGCCCACCT
*
17682548 TAGCTGGCACC
1 TAGCTAGCACC
17682559 CAATAAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (29 bp):
TAGCTAGCACCTAGGTTTTAAGCCCACCT
Found at i:17682664 original size:33 final size:33
Alignment explanation
Indices: 17682314--17683105 Score: 251
Period size: 33 Copynumber: 24.5 Consensus size: 33
17682304 TTATCTAGGT
* * * * *
17682314 TTTAAGCCTGGTTTAGTTGACACCTAATAAAAA
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * * * * *
17682347 TTTAAGCCCAGTGTAGCTGGCACTCAATCAAAA
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * * * * *
17682380 TATAAGCCCAATTTAGTTAGCAC-CAATGAAGT
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* *
17682412 TTTAAGCCTAGTTTA-TCTAGCAC-TAATGAAAA
1 TTTAAGCCTAGTTTAGT-TGGCACTTAATGAAGA
* * *
17682444 TTTAAGCCTAGCTTAGTTGCCACTCT-ATGAAAA
1 TTTAAGCCTAGTTTAGTTGGCACT-TAATGAAGA
* * * * *
17682477 TTTAAGCCTAGTATAGCTAGCACCT-A-G--GT
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* ** * * *
17682506 TTTAAGCCCACCTTAGCTGGCACCT-AT---GT
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * * ** *
17682535 TTTAAGCCCACTTTAGCTGGCACCCAATAAAGA
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * *
17682568 TTTAAGCCTAGCTTAGCTAGCA-TTCAATGAA-A
1 TTTAAGCCTAGTTTAGTTGGCACTT-AATGAAGA
* *** *
17682600 TTTAAGCCTAGATTA-TCAAACACTTAATGAAGT
1 TTTAAGCCTAGTTTAGT-TGGCACTTAATGAAGA
*
17682633 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGT
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * * * ** *
17682666 TTTAAACCCAATTTAGCTGGCACTGATCAACAAAGT
1 TTTAAGCCTAGTTTAGTTGGCACT--T-AATGAAGA
* ** * * *
17682702 TTTAAGCCCAACTTAGCTGACACCTAATGAA-A
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * ** *
17682734 TTTAAACCCAGTTTAACT-G-ATCTTTAATGAAAA
1 TTTAAGCCTAGTTTAGTTGGCA-C-TTAATGAAGA
* * * * *
17682767 TTTAAGCCTAATGTAGTTGGCAC-CAATAAAGT
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * *
17682799 TTTAAGCCTAGTTTATTTGGCA-TCAATGAAAA
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* ** * * * *
17682831 TTTAAGCCAAACTTAATTGGCAAC-CAGTGAAAA
1 TTTAAGCCTAGTTTAGTTGGC-ACTTAATGAAGA
* * * *
17682864 TTTAAGCCTAATTTAGATGGCACCT-A-G--GT
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * ** **
17682893 TTTAAGCCAAGCTTAACTGGCACCCAATGAAGA
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* *
17682926 TTTAAACCTAGCTTAGTTGGCACTTAATGAA-A
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * * *
17682958 TTTAAACCAAGATTA-TCTGGCACTTAATGAAGT
1 TTTAAGCCTAGTTTAGT-TGGCACTTAATGAAGA
* * *
17682991 TTTAAGCCCAATTTAGTTGGCACCTAATGAA-A
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
* * * *
17683023 TTTAAGTCTAGTTTCA-TTGACA-TCTAATTAAAA
1 TTTAAGCCTAGTTT-AGTTGGCACT-TAATGAAGA
* * * * * *
17683056 TTTAAGCCTAGTGTAATTGGTAC-CAATAAAAA
1 TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
*
17683088 TTTAAGCTTAGTTTAGTT
1 TTTAAGCCTAGTTTAGTT
17683106 AGCATAATAG
Statistics
Matches: 579, Mismatches: 142, Indels: 77
0.73 0.18 0.10
Matches are distributed among these distances:
29 65 0.11
30 4 0.01
31 6 0.01
32 217 0.37
33 253 0.44
34 6 0.01
35 2 0.00
36 26 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (33 bp):
TTTAAGCCTAGTTTAGTTGGCACTTAATGAAGA
Found at i:17682808 original size:32 final size:32
Alignment explanation
Indices: 17682759--17683105 Score: 174
Period size: 32 Copynumber: 10.8 Consensus size: 32
17682749 ACTGATCTTT
*
17682759 AATGAAAATTTAAGCCTAATGTAGTTGGCACC
1 AATGAAAATTTAAGCCTAATTTAGTTGGCACC
* * * *
17682791 AAT-AAAGTTTTAAGCCTAGTTTATTTGGCATC
1 AATGAAA-ATTTAAGCCTAATTTAGTTGGCACC
* * *
17682823 AATGAAAATTTAAGCCAAACTTAATTGGCAACC
1 AATGAAAATTTAAGCCTAATTTAGTTGGC-ACC
* *
17682856 AGTGAAAATTTAAGCCTAATTTAGATGGCACC
1 AATGAAAATTTAAGCCTAATTTAGTTGGCACC
*** * **
17682888 --T-AGGTTTTAAGCC-AAGCTTAACTGGCACCC
1 AATGAAAATTTAAGCCTAA-TTTAGTTGGCA-CC
* * ** *
17682918 AATGAAGATTTAAACCTAGCTTAGTTGGCACTT
1 AATGAAAATTTAAGCCTAATTTAGTTGGCAC-C
* * *
17682951 AATG-AAATTTAAACC-AAGATTA-TCTGGCACTT
1 AATGAAAATTTAAGCCTAA-TTTAGT-TGGCAC-C
** *
17682983 AATGAAGTTTTAAGCCCAATTTAGTTGGCACC
1 AATGAAAATTTAAGCCTAATTTAGTTGGCACC
* * * *
17683015 TAATG-AAATTTAAGTCTAGTTTCA-TTGACATCT
1 -AATGAAAATTTAAGCCTAATTT-AGTTGGCA-CC
* * * * *
17683048 AATTAAAATTTAAGCCTAGTGTAATTGGTACC
1 AATGAAAATTTAAGCCTAATTTAGTTGGCACC
* * *
17683080 AATAAAAATTTAAGCTTAGTTTAGTT
1 AATGAAAATTTAAGCCTAATTTAGTT
17683106 AGCATAATAG
Statistics
Matches: 241, Mismatches: 54, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.07
30 3 0.01
31 5 0.02
32 117 0.49
33 93 0.39
34 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
AATGAAAATTTAAGCCTAATTTAGTTGGCACC
Found at i:17682947 original size:62 final size:62
Alignment explanation
Indices: 17682831--17682948 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
17682821 TCAATGAAAA
* * * *
17682831 TTTAAGCCAAACTTAATTGGCAACCAGTGAAAATTTAAGCCTAATTTAGATGGCACCTAGGT
1 TTTAAGCCAAACTTAACTGGCAACCAATGAAAATTTAAACCTAACTTAGATGGCACCTAGGT
* * * * *
17682893 TTTAAGCCAAGCTTAACTGGCACCCAATGAAGATTTAAACCTAGCTTAGTTGGCAC
1 TTTAAGCCAAACTTAACTGGCAACCAATGAAAATTTAAACCTAACTTAGATGGCAC
17682949 TTAATGAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 47 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (62 bp):
TTTAAGCCAAACTTAACTGGCAACCAATGAAAATTTAAACCTAACTTAGATGGCACCTAGGT
Found at i:17683420 original size:29 final size:31
Alignment explanation
Indices: 17683387--17683463 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 31
17683377 TTAAACAAAA
* *
17683387 AAATAAATAATAAAAAT-ATAA-AAATCATT
1 AAATAAATAATAAAAATAATAATAAATAAGT
17683416 AAATAAATAATAATAAATAATAATAAATAAGT
1 AAATAAATAATAA-AAATAATAATAAATAAGT
17683448 AATATAAAT-ATAAAAA
1 AA-ATAAATAATAAAAA
17683464 AAACAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 13 0.31
30 4 0.10
31 7 0.17
32 12 0.29
33 6 0.14
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (31 bp):
AAATAAATAATAAAAATAATAATAAATAAGT
Found at i:17683421 original size:14 final size:14
Alignment explanation
Indices: 17683387--17683457 Score: 62
Period size: 13 Copynumber: 5.4 Consensus size: 14
17683377 TTAAACAAAA
17683387 AAATAAATAATAA-
1 AAATAAATAATAAT
*
17683400 AAAT--ATAAAAAT
1 AAATAAATAATAAT
* *
17683412 CATTAAATAAATAAT
1 AAATAAAT-AATAAT
17683427 -AATAAATAATAAT
1 AAATAAATAATAAT
*
17683440 AAATAAGTAAT-AT
1 AAATAAATAATAAT
17683453 AAATA
1 AAATA
17683458 TAAAAAAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
11 6 0.13
12 2 0.04
13 17 0.36
14 17 0.36
15 5 0.11
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (14 bp):
AAATAAATAATAAT
Found at i:17683430 original size:10 final size:10
Alignment explanation
Indices: 17683388--17683451 Score: 71
Period size: 10 Copynumber: 6.4 Consensus size: 10
17683378 TAAACAAAAA
17683388 AATAAATAAT
1 AATAAATAAT
17683398 AA-AAAT-AT
1 AATAAATAAT
*
17683406 AA-AAATCATT
1 AATAAAT-AAT
17683416 AAATAAATAAT
1 -AATAAATAAT
17683427 AATAAATAAT
1 AATAAATAAT
17683437 AATAAATAAGT
1 AATAAATAA-T
17683448 AATA
1 AATA
17683452 TAAATATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 8 0.17
9 4 0.09
10 22 0.47
11 9 0.19
12 4 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AATAAATAAT
Found at i:17683529 original size:17 final size:18
Alignment explanation
Indices: 17683509--17683552 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
17683499 ATATACAAAT
*
17683509 AAAATATAAATATA-TAA
1 AAAATATAAAGATATTAA
17683526 AAAATATTAAAGATATTAA
1 AAAATA-TAAAGATATTAA
*
17683545 AATATATA
1 AAAATATA
17683553 TATCAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATATAAAGATATTAA
Found at i:17685287 original size:15 final size:15
Alignment explanation
Indices: 17685269--17685326 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
17685259 GAAATTATTA
17685269 AATAAAAAATAAAAT
1 AATAAAAAATAAAAT
* *
17685284 AATAAAAGATTAAAT
1 AATAAAAAATAAAAT
***
17685299 AATAATAATAATATTTT
1 AATAA-AA-AATAAAAT
17685316 AATAAAAAATA
1 AATAAAAAATA
17685327 TATAAAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 22 0.65
16 4 0.12
17 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AATAAAAAATAAAAT
Found at i:17686831 original size:2 final size:2
Alignment explanation
Indices: 17686824--17686865 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
17686814 GATACCAAAG
*
17686824 AT AT AT AT AT AT AT AT CT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17686865 A
1 A
17686866 AGATAAAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17694327 original size:15 final size:16
Alignment explanation
Indices: 17694302--17694331 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17694292 AAAATATTTC
17694302 AAAATATAAAATAAAT
1 AAAATATAAAATAAAT
17694318 AAAA-ATAAAATAAA
1 AAAATATAAAATAAA
17694332 ATGGAAAAAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATATAAAATAAAT
Found at i:17695158 original size:3 final size:3
Alignment explanation
Indices: 17695152--17695291 Score: 96
Period size: 3 Copynumber: 52.0 Consensus size: 3
17695142 TTATTATTAT
** * *
17695152 ATA ATA AT- ATA AT- ATA AT- ATA ATA ACG CT- ATA AT- ATA ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17695195 ATA ATA ATA ATA ATA A-G ATA CT- ATA AT- ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17695239 ACA ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATG ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17695281 ATA AT- ATA ATA
1 ATA ATA ATA ATA
17695292 TACCATACTA
Statistics
Matches: 107, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
2 29 0.27
3 78 0.73
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:17695163 original size:8 final size:8
Alignment explanation
Indices: 17695150--17695291 Score: 105
Period size: 8 Copynumber: 17.0 Consensus size: 8
17695140 TATTATTATT
17695150 ATATAATA
1 ATATAATA
17695158 ATATAATATA
1 ATAT-A-ATA
17695168 ATATAATA
1 ATATAATA
**
17695176 ACGCT-ATA
1 A-TATAATA
17695184 ATATAATA
1 ATATAATA
*
17695192 TTAATAATA
1 AT-ATAATA
17695201 ATAATAATA
1 AT-ATAATA
*
17695210 AGATACTATA
1 ATATA--ATA
17695220 ATATAATA
1 ATATAATA
17695228 ATATAATA
1 ATATAATA
*
17695236 ATAACAATA
1 AT-ATAATA
17695245 ATATAAT-
1 ATATAATA
17695252 ATA-ATATA
1 ATATA-ATA
17695260 ATATAAT-
1 ATATAATA
17695267 ATGATAAT-
1 AT-ATAATA
17695275 ATAATAATA
1 AT-ATAATA
17695284 ATATAATA
1 ATATAATA
17695292 TACCATACTA
Statistics
Matches: 110, Mismatches: 11, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
6 1 0.01
7 8 0.07
8 59 0.54
9 28 0.25
10 14 0.13
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (8 bp):
ATATAATA
Found at i:17695165 original size:5 final size:5
Alignment explanation
Indices: 17695155--17695293 Score: 119
Period size: 5 Copynumber: 27.6 Consensus size: 5
17695145 TTATTATATA
* *
17695155 ATAAT ATAAT ATAAT ATAAT A-ACGCT ATAAT ATAAT ATTA- ATAAT AATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATAAT -ATAAT
* * *
17695206 AATAAG ATACT ATAAT AT-A- ATAAT ATAAT AATAACA ATAAT ATAAT
1 -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAA-T ATAAT ATAAT
*
17695252 ATAAT ATAAT ATAAT AT--G ATAAT ATAAT AATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATA
17695294 CCATACTATA
Statistics
Matches: 110, Mismatches: 12, Indels: 24
0.75 0.08 0.16
Matches are distributed among these distances:
3 4 0.04
4 6 0.05
5 74 0.67
6 25 0.23
7 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:17695612 original size:55 final size:55
Alignment explanation
Indices: 17695523--17695656 Score: 180
Period size: 55 Copynumber: 2.4 Consensus size: 55
17695513 GACTAAGCCG
* * * *
17695523 CAAGTCTGAAAAATGATTTGGACTGAGCCGAGATCGAACAACCGAGATTAAACTA
1 CAAGTTTGAAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAACCA
***
17695578 CAAGTTTGAAAAATGATTTGGACTAAGCCAAGATCGAGTGACCGAGATTAAACCA
1 CAAGTTTGAAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAACCA
17695633 CAAGTTT-AAAAAGTTGATTTGGAC
1 CAAGTTTGAAAAA--TGATTTGGAC
17695657 CAAGTCGAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
54 5 0.07
55 55 0.79
56 10 0.14
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (55 bp):
CAAGTTTGAAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAACCA
Found at i:17697959 original size:2 final size:2
Alignment explanation
Indices: 17697952--17697987 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
17697942 GATACCAAAG
*
17697952 AT AT AT AT AT AT AT CT -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17697988 AGATAAAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17700692 original size:13 final size:14
Alignment explanation
Indices: 17700674--17700702 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17700664 TAGAATTATA
17700674 TTATTT-CAAATTT
1 TTATTTACAAATTT
17700687 TTATTTACAAATTT
1 TTATTTACAAATTT
17700701 TT
1 TT
17700703 TACATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTACAAATTT
Found at i:17705515 original size:11 final size:10
Alignment explanation
Indices: 17705493--17705591 Score: 51
Period size: 10 Copynumber: 9.2 Consensus size: 10
17705483 CAAATTGCTT
17705493 AATAAAAATA
1 AATAAAAATA
17705503 AATAAATAATAA
1 AATAAA-AAT-A
17705515 AAGTTATCAAAATA
1 AA--TA--AAAATA
*
17705529 AATAAAAAATTG
1 AAT-AAAAA-TA
17705541 AATATAAAATA
1 AATA-AAAATA
17705552 ATATAAAAATA
1 A-ATAAAAATA
** *
17705563 TTTCAAAAT-
1 AATAAAAATA
17705572 -AT-AAAATA
1 AATAAAAATA
17705580 AATAAAAATA
1 AATAAAAATA
17705590 AA
1 AA
17705592 ATGGAAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
7 5 0.07
8 1 0.01
9 2 0.03
10 20 0.29
11 16 0.23
12 15 0.21
13 1 0.01
14 5 0.07
15 3 0.04
16 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (10 bp):
AATAAAAATA
Found at i:17705809 original size:21 final size:20
Alignment explanation
Indices: 17705785--17705826 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
17705775 TCTCTCTAAA
*
17705785 AAAACTAAGAATGTTCAATCG
1 AAAACTAAAAATGTTC-ATCG
*
17705806 AAAACTAAAAATTTTCATCG
1 AAAACTAAAAATGTTCATCG
17705826 A
1 A
17705827 TTTCTGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAACTAAAAATGTTCATCG
Found at i:17706409 original size:3 final size:3
Alignment explanation
Indices: 17706392--17706553 Score: 117
Period size: 3 Copynumber: 60.0 Consensus size: 3
17706382 AAGAAAAATG
* *
17706392 ATA A-A ATA A-A ATA ATA ATA ATT ATT AT- ATA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
17706435 AT- ATA ATA AT- GTT ATA AT- ATA ATA GTA ATA ATA ATA ATA ATA A-G
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17706479 ATA CT- ATA AT- ATA AT- ATA ATA ATA ACA ATA AT- ATA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17706521 ATA AT- ATG ATA AT- ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17706554 TACCATACTA
Statistics
Matches: 128, Mismatches: 13, Indels: 36
0.72 0.07 0.20
Matches are distributed among these distances:
2 33 0.26
3 95 0.74
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:17706432 original size:5 final size:5
Alignment explanation
Indices: 17706392--17706555 Score: 113
Period size: 5 Copynumber: 31.6 Consensus size: 5
17706382 AAGAAAAATG
* * *
17706392 ATAAA ATAAA ATAAT AATAAT -TATT AT-AT AATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
** * *
17706442 AATGTT ATAAT ATAAT AGT-A- ATAAT AATAAT AATAAG ATACT ATAAT
1 -ATAAT ATAAT ATAAT A-TAAT ATAAT -ATAAT -ATAAT ATAAT ATAAT
* *
17706489 ATAAT ATAAT AATAACA ATAAT ATAAT ATAAT ATAAT ATGAT A-ATAT
1 ATAAT ATAAT -ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
17706536 AATAAT AATAAT ATAAT ATA
1 -ATAAT -ATAAT ATAAT ATA
17706556 CCATACTATA
Statistics
Matches: 130, Mismatches: 15, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
3 1 0.01
4 6 0.05
5 84 0.65
6 38 0.29
7 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:17706444 original size:32 final size:33
Alignment explanation
Indices: 17706396--17706555 Score: 151
Period size: 32 Copynumber: 5.0 Consensus size: 33
17706386 AAAATGATAA
*
17706396 AATAAAATAATAATAATTATTATATA-ATAATAT
1 AATATAATAATAATAA-TATTATATATATAATAT
*
17706429 AATATAAT-ATAATAATGTTATA-ATATAATAGT
1 AATATAATAATAATAATATTATATATATAATA-T
*
17706461 -A-ATAATAATAATAATA--AGATACTATAATAT
1 AATATAATAATAATAATATTATATA-TATAATAT
* *
17706491 AATATAATAATAACAATAATATA-ATATAATAT
1 AATATAATAATAATAATATTATATATATAATAT
* *
17706523 AATATGATAAT-ATAATAATA-ATAATATAATAT
1 AATATAATAATAATAATATTATAT-ATATAATAT
17706555 A
1 A
17706556 CCATACTATA
Statistics
Matches: 108, Mismatches: 8, Indels: 23
0.78 0.06 0.17
Matches are distributed among these distances:
29 2 0.02
30 9 0.08
31 37 0.34
32 50 0.46
33 8 0.07
34 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (33 bp):
AATATAATAATAATAATATTATATATATAATAT
Found at i:17707451 original size:14 final size:15
Alignment explanation
Indices: 17707420--17707452 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17707410 GTGTTTGCCC
*
17707420 TTTTTTTTGTTTTCA
1 TTTTTTTTGTTGTCA
17707435 TTTTTTTTGTTGT-A
1 TTTTTTTTGTTGTCA
17707449 TTTT
1 TTTT
17707453 CTCAGGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.06, C:0.03, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTTTTTTGTTGTCA
Found at i:17710627 original size:72 final size:72
Alignment explanation
Indices: 17710521--17710667 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 72
17710511 ATGTCTATGG
* * *
17710521 AACCCTCAGATTGTGCATGAACATAAATGCAAAAACCAAATGCATGAATGCAATAAGGAGAATTT
1 AACCCTCAGATGGTGCATGAAAATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
17710586 ACCACAT
66 ACCACAT
* * *
17710593 AACCCTCAGATGGTGCATGAAAATGAATGTAAAAACAAAATGTATGAATGCAATAAGGAGAATTT
1 AACCCTCAGATGGTGCATGAAAATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
17710658 ACCACAT
66 ACCACAT
17710665 AAC
1 AAC
17710668 AATTGTTATC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (72 bp):
AACCCTCAGATGGTGCATGAAAATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
ACCACAT
Found at i:17713674 original size:3 final size:3
Alignment explanation
Indices: 17713662--17713823 Score: 99
Period size: 3 Copynumber: 59.0 Consensus size: 3
17713652 AAGAAAAATG
* *
17713662 ATA A-A ATA ATA ATA ATA ATA ATA CT- ATA AT- ATA ATA ATA A-G ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17713706 CT- ATA AT- ATA AT- ATA ATA AT- ATA ATA ATA ACA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
17713749 AT- ATA TACA AT- ATG AT- ATA A-C ATA AT- ATA ATA CGATA ATA AT-
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA
*
17713791 ATA AT- ATG ATA AT- ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17713824 TACCACACTA
Statistics
Matches: 125, Mismatches: 13, Indels: 42
0.69 0.07 0.23
Matches are distributed among these distances:
2 32 0.26
3 88 0.70
4 2 0.02
5 3 0.02
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17713696 original size:5 final size:5
Alignment explanation
Indices: 17713670--17713825 Score: 102
Period size: 5 Copynumber: 29.6 Consensus size: 5
17713660 TGATAAAATA
* * *
17713670 ATAAT AATAAT AATACT ATAAT ATAAT AATAAG ATACT ATAAT ATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
* * *
17713718 ATAAT A-ATAT AATAAT AACAAT AATAAT ATAAT AT-AT ACAAT ATGAT
1 ATAAT ATA-AT -ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
* ** *
17713765 ATAAC ATAAT ATAAT ACGAT AATAAT ATAAT ATGAT A-ATAT AATAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT -ATAAT
17713812 AATAAT ATAAT ATA
1 -ATAAT ATAAT ATA
17713826 CCACACTATT
Statistics
Matches: 121, Mismatches: 20, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.03
5 76 0.63
6 39 0.32
7 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:17713821 original size:8 final size:8
Alignment explanation
Indices: 17713662--17713823 Score: 102
Period size: 8 Copynumber: 19.4 Consensus size: 8
17713652 AAGAAAAATG
*
17713662 ATAAAATA
1 ATAATATA
17713670 ATAATAATA
1 ATAAT-ATA
17713679 ATAATACT-
1 ATAATA-TA
17713687 ATAATATA
1 ATAATATA
17713695 ATAATA-A
1 ATAATATA
*
17713702 GATACTATAA
1 -ATAATAT-A
17713712 TATAATATA
1 -ATAATATA
17713721 ATAATATA
1 ATAATATA
*
17713729 ATAATAACA
1 ATAAT-ATA
17713738 ATAATA-A
1 ATAATATA
17713745 TATAATATA
1 -ATAATATA
* *
17713754 TACAATATG
1 -ATAATATA
17713763 AT-ATA-A
1 ATAATATA
17713769 CATAATATA
1 -ATAATATA
**
17713778 ATACGATA
1 ATAATATA
17713786 ATAATATA
1 ATAATATA
17713794 AT-ATGATAA
1 ATAAT-AT-A
17713803 TATAATAATA
1 -ATAAT-ATA
17713813 ATAATATA
1 ATAATATA
17713821 ATA
1 ATA
17713824 TACCACACTA
Statistics
Matches: 124, Mismatches: 14, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
7 10 0.08
8 68 0.55
9 32 0.26
10 10 0.08
11 4 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (8 bp):
ATAATATA
Found at i:17715508 original size:29 final size:31
Alignment explanation
Indices: 17715464--17715524 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
17715454 AACCTTACTT
*
17715464 ATCTTTAAAATCATGCAA-TAAACTTAAATTA
1 ATCTTTAAAATCATGCAATTAAAC-CAAATTA
17715495 ATCTTT-AAA-CATGCAATTAAACCAAATTA
1 ATCTTTAAAATCATGCAATTAAACCAAATTA
17715524 A
1 A
17715525 ATCAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.50
30 8 0.29
31 6 0.21
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (31 bp):
ATCTTTAAAATCATGCAATTAAACCAAATTA
Found at i:17715896 original size:13 final size:13
Alignment explanation
Indices: 17715874--17715906 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17715864 TGAACTAGAA
17715874 CAAAAAATT-AAC
1 CAAAAAATTAAAC
17715886 CAAAAAGATTAAAC
1 CAAAAA-ATTAAAC
17715900 CAAAAAA
1 CAAAAAA
17715907 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 4 0.21
14 9 0.47
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (13 bp):
CAAAAAATTAAAC
Found at i:17719376 original size:22 final size:22
Alignment explanation
Indices: 17719322--17719369 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
17719312 GTTAAAGGTA
** *
17719322 GGTTTGATTCAATTTTTGGGTT
1 GGTTTGATTCGGTTTTGGGGTT
*
17719344 GGTTTGGTTCGGTTTTGGGGTT
1 GGTTTGATTCGGTTTTGGGGTT
17719366 GGTT
1 GGTT
17719370 CTATTCGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.06, C:0.04, G:0.38, T:0.52
Consensus pattern (22 bp):
GGTTTGATTCGGTTTTGGGGTT
Found at i:17719404 original size:11 final size:12
Alignment explanation
Indices: 17719384--17719417 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17719374 TCGATTTAAA
17719384 GTTTAGGGTTT-
1 GTTTAGGGTTTG
*
17719395 GTTTAAGGTTTG
1 GTTTAGGGTTTG
17719407 GTTTAGGGTTT
1 GTTTAGGGTTT
17719418 AGAATTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (12 bp):
GTTTAGGGTTTG
Found at i:17719484 original size:7 final size:7
Alignment explanation
Indices: 17719461--17719717 Score: 116
Period size: 7 Copynumber: 38.7 Consensus size: 7
17719451 CTTTAGTATA
17719461 GGTTTAG
1 GGTTTAG
* *
17719468 AGTTT-T
1 GGTTTAG
17719474 GGTTTAG
1 GGTTTAG
* *
17719481 GGTTCAA
1 GGTTTAG
17719488 GGTTTAG
1 GGTTTAG
*
17719495 GATTTAG
1 GGTTTAG
17719502 GGTTTTAG
1 GG-TTTAG
*
17719510 GGTTTAA
1 GGTTTAG
*
17719517 GG-TAAG
1 GGTTTAG
* *
17719523 AGTTT-T
1 GGTTTAG
17719529 GGTTTAG
1 GGTTTAG
*
17719536 GATTT-G
1 GGTTTAG
17719542 GGATTTAG
1 GG-TTTAG
*
17719550 GATTTA-
1 GGTTTAG
17719556 -GTTTAG
1 GGTTTAG
* * *
17719562 GATTCAA
1 GGTTTAG
*
17719569 GGTTT-T
1 GGTTTAG
17719575 GGTTTAG
1 GGTTTAG
* *
17719582 TGTTTGG
1 GGTTTAG
17719589 GGTTTA-
1 GGTTTAG
17719595 GGTTT--
1 GGTTTAG
*
17719600 GATTTAAG
1 GGTTT-AG
*
17719608 GTTTTA-
1 GGTTTAG
* *
17719614 GATTT-T
1 GGTTTAG
17719620 GGTTTAG
1 GGTTTAG
*
17719627 AGTTTAG
1 GGTTTAG
17719634 GGTTTA-
1 GGTTTAG
*
17719640 GGTTT-T
1 GGTTTAG
*
17719646 GGCTTAG
1 GGTTTAG
*
17719653 GGTTT-T
1 GGTTTAG
*
17719659 GGCTTAG
1 GGTTTAG
17719666 GGTTTAG
1 GGTTTAG
17719673 GGTTTAG
1 GGTTTAG
*
17719680 AGTTT-G
1 GGTTTAG
*
17719686 GTTTTAG
1 GGTTTAG
17719693 GGTTTA-
1 GGTTTAG
17719699 GGTTTAG
1 GGTTTAG
17719706 GGTTTAG
1 GGTTTAG
17719713 GGTTT
1 GGTTT
17719718 GCATGTAAAA
Statistics
Matches: 180, Mismatches: 51, Indels: 38
0.67 0.19 0.14
Matches are distributed among these distances:
5 8 0.04
6 54 0.30
7 105 0.58
8 13 0.07
ACGTcount: A:0.17, C:0.02, G:0.34, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:17719491 original size:27 final size:27
Alignment explanation
Indices: 17719460--17719536 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 27
17719450 GCTTTAGTAT
17719460 AGGTTTAGAGTTTTGGTTTAGGGTTCA
1 AGGTTTAGAGTTTTGGTTTAGGGTTCA
* *
17719487 AGGTTTAG-GATTTAGGGTTTTAGGGTTTA
1 AGGTTTAGAG-TTT-TGG-TTTAGGGTTCA
*
17719516 AGG-TAAGAGTTTTGGTTTAGG
1 AGGTTTAGAGTTTTGGTTTAGG
17719537 ATTTGGGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
26 7 0.17
27 13 0.31
28 8 0.19
29 14 0.33
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (27 bp):
AGGTTTAGAGTTTTGGTTTAGGGTTCA
Found at i:17719599 original size:13 final size:13
Alignment explanation
Indices: 17719459--17719713 Score: 139
Period size: 13 Copynumber: 19.3 Consensus size: 13
17719449 GGCTTTAGTA
*
17719459 TAGGTTTAGAGTT
1 TAGGTTTAGGGTT
*
17719472 TTGGTTTAGGGTT
1 TAGGTTTAGGGTT
* *
17719485 CAAGGTTTAGGATT
1 -TAGGTTTAGGGTT
17719499 TAGGGTTTTAGGGTT
1 TA-GG-TTTAGGGTT
* *
17719514 TAAGG-TAAGAGTT
1 T-AGGTTTAGGGTT
* *
17719527 TTGGTTTAGGATT
1 TAGGTTTAGGGTT
* *
17719540 TGGGATTTAGGATT
1 TAGG-TTTAGGGTT
*
17719554 TA-GTTTAGGATT
1 TAGGTTTAGGGTT
* *
17719566 CAAGGTTT-TGGTT
1 -TAGGTTTAGGGTT
*
17719579 TAGTGTTTGGGGTT
1 TAG-GTTTAGGGTT
*
17719593 TAGGTTT--GATT
1 TAGGTTTAGGGTT
*
17719604 TAAGGTTTTA-GATT
1 T-AGG-TTTAGGGTT
* *
17719618 TTGGTTTAGAGTT
1 TAGGTTTAGGGTT
17719631 TAGGGTTTA-GGTT
1 TA-GGTTTAGGGTT
* *
17719644 TTGGCTTAGGGTT
1 TAGGTTTAGGGTT
* *
17719657 TTGGCTTAGGGTT
1 TAGGTTTAGGGTT
*
17719670 TAGGGTTTAGAGTT
1 TA-GGTTTAGGGTT
17719684 T-GGTTTTAGGGTT
1 TAGG-TTTAGGGTT
17719697 TAGGTTTAGGGTT
1 TAGGTTTAGGGTT
17719710 TAGG
1 TAGG
17719714 GTTTGCATGT
Statistics
Matches: 191, Mismatches: 32, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
11 4 0.02
12 27 0.14
13 92 0.48
14 56 0.29
15 11 0.06
16 1 0.01
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.47
Consensus pattern (13 bp):
TAGGTTTAGGGTT
Found at i:17719643 original size:20 final size:20
Alignment explanation
Indices: 17719444--17719717 Score: 152
Period size: 20 Copynumber: 13.6 Consensus size: 20
17719434 CATGGTTATA
* *
17719444 GTTTAGGCTTTA-GTATA-G
1 GTTTAGGGTTTAGGTTTAGG
* *
17719462 GTTTAGAGTTTTGGTTTAGG
1 GTTTAGGGTTTAGGTTTAGG
* *
17719482 GTTCAAGGTTTAGGATTTAGG
1 GTTTAGGGTTTAGG-TTTAGG
* *
17719503 GTTTTAGGGTTTAAGG-TAAGA
1 G-TTTAGGGTTT-AGGTTTAGG
*
17719524 GTTT-TGGTTTAGGATTT-GG
1 GTTTAGGGTTTAGG-TTTAGG
*
17719543 GATTTAGGATTTA-GTTTAGG
1 G-TTTAGGGTTTAGGTTTAGG
* * * * *
17719563 ATTCAAGGTTTTGGTTTAGT
1 GTTTAGGGTTTAGGTTTAGG
*
17719583 GTTTGGGGTTTAGGTTTGATTTAAGG
1 GTTTAGGGTTTA-G---G-TTT-AGG
* * * *
17719609 TTTTA-GATTTTGGTTTAGA
1 GTTTAGGGTTTAGGTTTAGG
*
17719628 GTTTAGGGTTTAGGTTT-TG
1 GTTTAGGGTTTAGGTTTAGG
* * *
17719647 GCTTAGGGTTTTGGCTTAGG
1 GTTTAGGGTTTAGGTTTAGG
17719667 GTTTAGGGTTTAGAGTTT-GG
1 GTTTAGGGTTTAG-GTTTAGG
*
17719687 TTTTAGGGTTTAGGTTTAGG
1 GTTTAGGGTTTAGGTTTAGG
17719707 GTTTAGGGTTT
1 GTTTAGGGTTT
17719718 GCATGTAAAA
Statistics
Matches: 187, Mismatches: 48, Indels: 40
0.68 0.17 0.15
Matches are distributed among these distances:
18 12 0.06
19 45 0.24
20 84 0.45
21 21 0.11
22 8 0.04
23 3 0.02
24 2 0.01
25 7 0.04
26 5 0.03
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.47
Consensus pattern (20 bp):
GTTTAGGGTTTAGGTTTAGG
Found at i:17721417 original size:32 final size:31
Alignment explanation
Indices: 17721352--17721417 Score: 73
Period size: 32 Copynumber: 2.1 Consensus size: 31
17721342 TTTTACTAAT
* *
17721352 TTTTTATTATTTTTATTGTTCTAATTAATAA
1 TTTTTACTATTTTTATTGTTCTAATTAAAAA
17721383 TTTTTACTATTTTTTATT-TT-TAATTTTAAAAA
1 TTTTTACTA-TTTTTATTGTTCTAA--TTAAAAA
17721415 TTT
1 TTT
17721418 ATCAAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 3 0.10
31 10 0.33
32 17 0.57
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTTACTATTTTTATTGTTCTAATTAAAAA
Found at i:17721569 original size:14 final size:14
Alignment explanation
Indices: 17721550--17721582 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
17721540 ATATATTTTA
17721550 TTATTTATTTATTT
1 TTATTTATTTATTT
17721564 TTATTTATTTATTT
1 TTATTTATTTATTT
*
17721578 ATATT
1 TTATT
17721583 ACTATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:17721573 original size:18 final size:17
Alignment explanation
Indices: 17721545--17721579 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
17721535 TAACTATATA
17721545 TTTTATTATTTATTTAT
1 TTTTATTATTTATTTAT
17721562 TTTTATTTATTTATTTAT
1 TTTTA-TTATTTATTTAT
17721580 ATTACTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTATTTATTTAT
Found at i:17721660 original size:21 final size:20
Alignment explanation
Indices: 17721636--17721687 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
17721626 TTAGCATCCA
17721636 TAAATATTAATAATACA-ATTT
1 TAAATATTAATAATA-ATA-TT
*
17721657 TAAATAATAATAATAATATT
1 TAAATATTAATAATAATATT
*
17721677 TAAAAATTAAT
1 TAAATATTAAT
17721688 TCAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATTAATAATAATATT
Found at i:17722482 original size:43 final size:45
Alignment explanation
Indices: 17722435--17722539 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
17722425 CTCCCTAAGT
* * *
17722435 AGAGGTTTAACAACTTTTT-AAAATTT-AAAAAACTCCTCTAAAC
1 AGAGGCTTAACAACTTTTTAAAAATTTAAAAAAACCCCTATAAAC
* * *
17722478 AGAGGCTCAACAACTTTTTAAAAATTTAAAAAAACCCCTATGAAT
1 AGAGGCTTAACAACTTTTTAAAAATTTAAAAAAACCCCTATAAAC
17722523 AGAGGCTTAACAACTTT
1 AGAGGCTTAACAACTTT
17722540 AAAATGCTCC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 17 0.32
44 7 0.13
45 29 0.55
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (45 bp):
AGAGGCTTAACAACTTTTTAAAAATTTAAAAAAACCCCTATAAAC
Found at i:17722691 original size:49 final size:48
Alignment explanation
Indices: 17722640--17723010 Score: 298
Period size: 49 Copynumber: 7.4 Consensus size: 48
17722630 TTCTATACAA
* *
17722640 AGGCTCAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTAAGTAA
1 AGGCTCAACAACTTTAAAAATTTCATCTT-AAAAAGCTCCTCTAAGTAG
* * *
17722689 AGGTTCAACAACTTTCATTGACTTTAAAAATTTCATCTCAAAAAAGCTCCTTTAAGTAG
1 AGG--C-TCAA----CA---ACTTTAAAAATTTCATCT-TAAAAAGCTCCTCTAAGTAG
* * * *
17722748 AGGCTTAACAACTTTAAAAAATTT-ATCATGCAAAAGGCTCCTCTAAGTAA
1 AGGCTCAACAACTTT-AAAAATTTCATC-T-TAAAAAGCTCCTCTAAGTAG
** * * * *
17722798 AGGCTCAATGACTTTAAAAATTTTATCTTGAAAAGTTTCCTCTAAGCAG
1 AGGCTCAACAACTTTAAAAATTTCATCTTAAAAAG-CTCCTCTAAGTAG
* * *
17722847 AGGTTCAACAACTTTAAAAATTTCATTTTAAAAAACTCCTCTAAGTAG
1 AGGCTCAACAACTTTAAAAATTTCATCTTAAAAAGCTCCTCTAAGTAG
* * * *
17722895 AGGCTTAA-AACTTTAAAAA-TTCATCTTGAAAAGGCTCATCTAAGCAG
1 AGGCTCAACAACTTTAAAAATTTCATCTT-AAAAAGCTCCTCTAAGTAG
* * * **
17722942 AGACTCAACAACTTTAAAAATTTCATCTAAAAAAAGTTCCTCTAAACAG
1 AGGCTCAACAACTTTAAAAATTTCATCT-TAAAAAGCTCCTCTAAGTAG
* *
17722991 AGGCTTAACAACTTAAAAAA
1 AGGCTCAACAACTTTAAAAA
17723011 AAATTCATCT
Statistics
Matches: 256, Mismatches: 47, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
46 7 0.03
47 32 0.12
48 32 0.12
49 97 0.38
50 40 0.16
51 1 0.00
52 5 0.02
56 4 0.02
57 1 0.00
59 37 0.14
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (48 bp):
AGGCTCAACAACTTTAAAAATTTCATCTTAAAAAGCTCCTCTAAGTAG
Found at i:17722745 original size:59 final size:59
Alignment explanation
Indices: 17722650--17722762 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
17722640 AGGCTCAACA
***
17722650 ACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTAAGTAAAGG-TTCAACAACTTTCATTG
1 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGCTT-AACAACTTTCATTG
* *
17722709 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTT
1 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGCTTAACAACTTT
17722763 AAAAAATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 46 0.96
60 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (59 bp):
ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGCTTAACAACTTTCATTG
Found at i:17722982 original size:144 final size:148
Alignment explanation
Indices: 17722709--17723010 Score: 400
Period size: 144 Copynumber: 2.1 Consensus size: 148
17722699 ACTTTCATTG
* *
17722709 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTTAAAAAATTTAT
1 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
* * * ** * **
17722774 CATGCAAAAGGCTCCTCTAAGTAAAGGCTCAATGACTTTAAAAATTTTATCTTGAAAAGTTTCCT
66 CATGCAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTAAAAAAGTTTCCT
*
17722839 CTAAGCAGAGG-TTCAACA
131 CTAAACAGAGGCTT-AACA
* *
17722857 ACTTTAAAAATTTCATTTTAAAAAA-CTCCTCTAAGTAGAGGCTTAA-AACTTT-AAAAATTCAT
1 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
* *
17722919 CTTG-AAAAGGCTCATCTAAGCAGAGACTCAACAACTTTAAAAATTTCATCTAAAAAAAG-TTCC
66 CATGCAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCT-AAAAAAGTTTCC
17722982 TCTAAACAGAGGCTTAACA
130 TCTAAACAGAGGCTTAACA
*
17723001 ACTTAAAAAA
1 ACTTTAAAAA
17723011 AAATTCATCT
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
144 68 0.50
145 19 0.14
146 6 0.04
147 20 0.15
148 23 0.17
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (148 bp):
ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
CATGCAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTAAAAAAGTTTCCT
CTAAACAGAGGCTTAACA
Found at i:17729361 original size:13 final size:14
Alignment explanation
Indices: 17729343--17729371 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17729333 TCGAATTATA
17729343 TTATTT-CAAATTT
1 TTATTTACAAATTT
17729356 TTATTTACAAATTT
1 TTATTTACAAATTT
17729370 TT
1 TT
17729372 TACATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTACAAATTT
Found at i:17731591 original size:13 final size:13
Alignment explanation
Indices: 17731561--17731594 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17731551 AAATAAGCTC
17731561 AAAAAGAAATTTTG
1 AAAAA-AAATTTTG
17731575 -AAAAAAATTTTG
1 AAAAAAAATTTTG
17731587 AAAAAAAA
1 AAAAAAAA
17731595 ATTGGCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (13 bp):
AAAAAAAATTTTG
Found at i:17731592 original size:11 final size:12
Alignment explanation
Indices: 17731562--17731593 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
17731552 AATAAGCTCA
17731562 AAAAGAAATTTTG
1 AAAA-AAATTTTG
17731575 AAAAAAATTTTG
1 AAAAAAATTTTG
17731587 AAAAAAA
1 AAAAAAA
17731594 AATTGGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (12 bp):
AAAAAAATTTTG
Found at i:17731592 original size:14 final size:14
Alignment explanation
Indices: 17731561--17731597 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
17731551 AAATAAGCTC
*
17731561 AAAAAGAAATTTTG
1 AAAAAAAAATTTTG
17731575 --AAAAAAATTTTG
1 AAAAAAAAATTTTG
17731587 AAAAAAAAATT
1 AAAAAAAAATT
17731598 GGCATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (14 bp):
AAAAAAAAATTTTG
Found at i:17734106 original size:15 final size:16
Alignment explanation
Indices: 17734078--17734108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17734068 GAAAAGACTT
17734078 TTTCCTTTATTTTTTG
1 TTTCCTTTATTTTTTG
*
17734094 TTTCTTTTATTTTTT
1 TTTCCTTTATTTTTT
17734109 TTTAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTCCTTTATTTTTTG
Found at i:17734182 original size:11 final size:10
Alignment explanation
Indices: 17734160--17734258 Score: 51
Period size: 10 Copynumber: 9.2 Consensus size: 10
17734150 CAAATTGCTT
17734160 AATAAAAATA
1 AATAAAAATA
17734170 AATAAATAATAA
1 AATAAA-AAT-A
17734182 AAGTTAACAAAATA
1 AA--T-A-AAAATA
*
17734196 AATATAAAATTG
1 AATA-AAAA-TA
17734208 AATATAAAATA
1 AATA-AAAATA
17734219 ATATAAAAATA
1 A-ATAAAAATA
** *
17734230 TTTCAAAAT-
1 AATAAAAATA
17734239 -AT-AAAATA
1 AATAAAAATA
17734247 AATAAAAATA
1 AATAAAAATA
17734257 AA
1 AA
17734259 ATGAAAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
7 5 0.07
8 1 0.01
9 2 0.03
10 20 0.28
11 16 0.23
12 17 0.24
14 4 0.06
15 4 0.06
16 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (10 bp):
AATAAAAATA
Found at i:17734265 original size:28 final size:28
Alignment explanation
Indices: 17734191--17734265 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
17734181 AAAGTTAACA
*
17734191 AAATAAATATAAAATTG--AATATAAAAT
1 AAATAAAAATAAAA-TGAAAATATAAAAT
** *
17734218 AATATAAAAAT-ATTTCAAAATATAAAAT
1 AA-ATAAAAATAAAATGAAAATATAAAAT
17734246 AAATAAAAATAAAATGAAAA
1 AAATAAAAATAAAATGAAAA
17734266 AAAAACCCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
26 1 0.03
27 11 0.30
28 25 0.68
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (28 bp):
AAATAAAAATAAAATGAAAATATAAAAT
Found at i:17735072 original size:3 final size:3
Alignment explanation
Indices: 17735055--17735236 Score: 116
Period size: 3 Copynumber: 67.0 Consensus size: 3
17735045 AAGAAAATGG
* * *
17735055 ATA A-A ATA A-A ATA ATA ATA ATT ATT AT- ATA ATA AT- ATA GT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** *
17735098 AT- ATA ATA ATG CT- ATA AT- ATA ATA GCA ATA ATA ATA ATA ATA A-G
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17735142 ATA CT- ATA AT- ATA ATA AT- ATA ATA ATA ACA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17735185 AT- ATA AT- ATA AT- ATA AT- ATA AT- ATG ATA ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
17735226 ATA AT- ATA ATA
1 ATA ATA ATA ATA
17735237 TACCACATTG
Statistics
Matches: 141, Mismatches: 17, Indels: 42
0.70 0.09 0.21
Matches are distributed among these distances:
2 36 0.26
3 102 0.72
4 3 0.02
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:17735102 original size:5 final size:5
Alignment explanation
Indices: 17735055--17735238 Score: 126
Period size: 5 Copynumber: 35.6 Consensus size: 5
17735045 AAGAAAATGG
* * * *
17735055 ATAAA ATAAA ATAAT AATAAT -TATT AT-AT AATAAT ATAGT ATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
** ** * *
17735105 AATGCT ATAAT ATAAT AGCA- ATAAT AATAAT AATAAG ATACT ATAAT
1 -ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT ATAAT
*
17735152 AT-A- ATAAT ATAAT AATAACA ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
17735202 ATAAT ATGAT AATATAT AATAAT AATAAT ATAAT ATA
1 ATAAT ATAAT -ATA-AT -ATAAT -ATAAT ATAAT ATA
17735239 CCACATTGTA
Statistics
Matches: 145, Mismatches: 21, Indels: 26
0.76 0.11 0.14
Matches are distributed among these distances:
3 2 0.01
4 8 0.06
5 91 0.63
6 38 0.26
7 6 0.04
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:17735129 original size:60 final size:58
Alignment explanation
Indices: 17735059--17735236 Score: 172
Period size: 60 Copynumber: 3.1 Consensus size: 58
17735049 AAATGGATAA
* * *
17735059 AATAAAATAATAATAATTATTATATAATAATATAGTATAATATAATAATGCTATAATAT
1 AATACAATAATAATAATTATAATATAATAATATA-TATAATATAATAATACTATAATAT
* * *
17735118 AATAGCAATAATAATAATAATAAGATACTATAATATA-ATAATATAATAATAACAATAATAT
1 AATA-CAATAATAATAATTATAATATA--ATAATATATATAATATAATAAT-ACTATAATAT
* *
17735179 AATATAAT-ATAATATAATATAATATAAT-ATGATA-AT-ATATAATAATA--ATAATAT
1 AATACAATAATAATA-ATTATAATATAATAAT-ATATATAATATAATAATACTATAATAT
17735233 AATA
1 AATA
17735237 TACCACATTG
Statistics
Matches: 103, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
54 11 0.11
56 1 0.01
57 12 0.12
58 7 0.07
59 10 0.10
60 42 0.41
61 12 0.12
62 8 0.08
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (58 bp):
AATACAATAATAATAATTATAATATAATAATATATATAATATAATAATACTATAATAT
Found at i:17735804 original size:55 final size:54
Alignment explanation
Indices: 17735679--17735807 Score: 127
Period size: 55 Copynumber: 2.4 Consensus size: 54
17735669 ATTAAATGAC
* *
17735679 CAGGATTGAATCACAAGTCTAGAAAATGATCTGTATTGAGCCAATATCAAGCGA
1 CAGGATTGAATCACAAGTCTAGAAAATGATCTGTATTAAGCCAAGATCAAGCGA
* * * * * * *
17735733 CTGGGGTTAAACCACAAGTCT-GAAAAGTGATCTAG-ATTAAGCTAAGATCGAGTGA
1 C-AGGATTGAATCACAAGTCTAGAAAA-TGATCT-GTATTAAGCCAAGATCAAGCGA
17735788 TCAGGATTGAATCACAAGTC
1 -CAGGATTGAATCACAAGTC
17735808 AAAAAAACTA
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
54 6 0.10
55 50 0.86
56 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (54 bp):
CAGGATTGAATCACAAGTCTAGAAAATGATCTGTATTAAGCCAAGATCAAGCGA
Found at i:17739030 original size:72 final size:72
Alignment explanation
Indices: 17738910--17739053 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
17738900 GATGCCTATG
* *
17738910 GAACCCTCAGATTGTGCATGAACATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATT
1 GAACCCTCAGATGGTGCATGAAAATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATT
17738975 TACCACA
66 TACCACA
* * * * * *
17738982 GAACCCTTAGATGGTGTATGAAAATGAATGTAAAAACTAAATGTATGAATGCAATAAGGAGAATT
1 GAACCCTCAGATGGTGCATGAAAATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATT
17739047 TACCACA
66 TACCACA
17739054 TAACAATTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (72 bp):
GAACCCTCAGATGGTGCATGAAAATAAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATT
TACCACA
Found at i:17742023 original size:8 final size:8
Alignment explanation
Indices: 17742012--17742091 Score: 52
Period size: 8 Copynumber: 9.1 Consensus size: 8
17742002 AAAGAAAAGA
*
17742012 AAAATGAT
1 AAAATAAT
17742020 AAAATAAT
1 AAAATAAT
17742028 AATAATAAT
1 AA-AATAAT
17742037 AATACTATAAT
1 AA-A--ATAAT
*
17742048 ATAATAAT
1 AAAATAAT
*
17742056 AAGATACTAT
1 AAAATA--AT
*
17742066 AATATAAT
1 AAAATAAT
17742074 AATAATAAT
1 AA-AATAAT
*
17742083 AATATAAT
1 AAAATAAT
17742091 A
1 A
17742092 TATATAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
8 28 0.47
9 17 0.29
10 8 0.14
11 6 0.10
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (8 bp):
AAAATAAT
Found at i:17742030 original size:3 final size:3
Alignment explanation
Indices: 17742018--17742142 Score: 87
Period size: 3 Copynumber: 45.0 Consensus size: 3
17742008 AAGAAAAATG
* *
17742018 ATA A-A ATA ATA ATA ATA ATA ATA CT- ATA AT- ATA ATA ATA A-G ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17742062 CT- ATA AT- ATA ATA ATA ATA ATA AT- ATA AT- ATA TATA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
*
17742103 ATA A-A AT- ATA ATA CGATA AT- ATA ACA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA
17742143 TACCACATTA
Statistics
Matches: 97, Mismatches: 9, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
2 23 0.24
3 68 0.70
4 3 0.03
5 3 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17742110 original size:24 final size:22
Alignment explanation
Indices: 17742026--17742142 Score: 93
Period size: 22 Copynumber: 5.3 Consensus size: 22
17742016 TGATAAAATA
*
17742026 ATAATAATA-ATAATACTATAAT
1 ATAATAATAGATAA-AATATAAT
*
17742048 ATAATAATAAGAT--ACTATAAT
1 ATAATAAT-AGATAAAATATAAT
17742069 ATAATAATA-ATAATAATATAAT
1 ATAATAATAGATAA-AATATAAT
17742091 ATATATAATATGATAAAATATAAT
1 ATA-ATAATA-GATAAAATATAAT
**
17742115 ACGATAAT--ATAACAATAATAAT
1 ATAATAATAGATAA-AAT-ATAAT
17742137 ATAATA
1 ATAATA
17742143 TACCACATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.03
20 5 0.06
21 19 0.24
22 27 0.34
23 12 0.15
24 11 0.14
25 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (22 bp):
ATAATAATAGATAAAATATAAT
Found at i:17742113 original size:46 final size:44
Alignment explanation
Indices: 17742026--17742144 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 44
17742016 TGATAAAATA
* *
17742026 ATAATAATAATAATACTATAATATA-ATAATAAGATACTATAAT
1 ATAATAATAATAATAATATAATATATATAATAAGATAATATAAT
*
17742069 ATAATAATAATAATAATATAATATATATAATATGATAAAATATAAT
1 ATAATAATAATAATAATATAATATATATAATAAGAT--AATATAAT
** *
17742115 ACGATAAT-ATAACAATAATAATATAATATA
1 ATAATAATAATAATAAT-ATAATAT-ATATA
17742145 CCACATTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 24 0.37
44 9 0.14
45 7 0.11
46 20 0.31
47 5 0.08
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (44 bp):
ATAATAATAATAATAATATAATATATATAATAAGATAATATAAT
Found at i:17742122 original size:32 final size:31
Alignment explanation
Indices: 17742018--17742144 Score: 77
Period size: 32 Copynumber: 4.0 Consensus size: 31
17742008 AAGAAAAATG
17742018 ATAAAATAATAATAATAATAATACTATAATATA
1 ATAAAAT-ATAATAATAAT-ATACTATAATATA
* * *
17742051 ATAATAAGATACT-ATAATATAATAATAATAATA
1 ATAA-AATATAATAATAATATACT-ATAAT-ATA
* *
17742084 ATATAATAT-AT-ATAATATGA-TAAAATATA
1 ATAAAATATAATAATAATAT-ACTATAATATA
*
17742113 ATACGATAATATAACAATAATA-A-TATAATATA
1 ATA--A-AATATAATAATAATATACTATAATATA
17742145 CCACATTATT
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
29 6 0.08
30 4 0.05
31 13 0.17
32 29 0.39
33 15 0.20
34 8 0.11
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (31 bp):
ATAAAATATAATAATAATATACTATAATATA
Found at i:17742126 original size:5 final size:5
Alignment explanation
Indices: 17742026--17742115 Score: 83
Period size: 5 Copynumber: 17.2 Consensus size: 5
17742016 TGATAAAATA
* * *
17742026 ATAAT AATAAT AATACT ATAAT ATAAT AATAAG ATACT ATAAT ATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
* *
17742074 AATAAT AATAAT ATAAT AT-AT ATAAT ATGAT AAAAT ATAAT A
1 -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
17742116 CGATAATATA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
4 4 0.06
5 42 0.59
6 25 0.35
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:17743817 original size:29 final size:31
Alignment explanation
Indices: 17743773--17743833 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
17743763 AACCTTACTT
*
17743773 ATCTTTAAAATCATGCAA-TAAACTTAAATTA
1 ATCTTTAAAATCATGCAATTAAAC-CAAATTA
17743804 ATCTTT-AAA-CATGCAATTAAACCAAATTA
1 ATCTTTAAAATCATGCAATTAAACCAAATTA
17743833 A
1 A
17743834 ATCAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.50
30 8 0.29
31 6 0.21
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (31 bp):
ATCTTTAAAATCATGCAATTAAACCAAATTA
Found at i:17747724 original size:11 final size:12
Alignment explanation
Indices: 17747704--17747737 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17747694 TCAATTTAAA
17747704 GTTTAGGGTTT-
1 GTTTAGGGTTTG
*
17747715 GTTTAAGGTTTG
1 GTTTAGGGTTTG
17747727 GTTTAGGGTTT
1 GTTTAGGGTTT
17747738 AGAATTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (12 bp):
GTTTAGGGTTTG
Found at i:17747827 original size:34 final size:32
Alignment explanation
Indices: 17747779--17747999 Score: 100
Period size: 34 Copynumber: 6.4 Consensus size: 32
17747769 GGTTTTAGTA
* *
17747779 TAGGTTTAGAGTTTTGGTTTAGGGTTCAAGGTT
1 TAGGTTTAGGGTTTTGGTTTAGGGTT-AAAGTT
* * *
17747812 TAGGATTTAGGGTTTTAGAGTTTAAGGTAAAACTT
1 TAGG-TTTAGGGTTTT-G-GTTTAGGGTTAAAGTT
* * * *
17747847 TTGGTTTAGGGTTTGGGATTTAGGATTTAAGTT
1 TAGGTTTAGGGTTTTGG-TTTAGGGTTAAAGTT
* * * * **
17747880 TAGGATTCAGGGTTTCGATTTAGTGTTTGGAGTT
1 TAGG-TTTAGGGTTTTGGTTTAG-GGTTAAAGTT
* * * * *
17747914 TAGGTTTGATTTAAGGTTTTAGATTTTGGTTTAGAGTT
1 TA-G---G-TTTAGGGTTTT-GGTTTAGGGTTAAAGTT
***
17747952 TAGGGTTTAGGGTTTTGGTTTAGGGTTTTGGTT
1 TA-GGTTTAGGGTTTTGGTTTAGGGTTAAAGTT
17747985 TAAGGTTTAGGGTTT
1 T-AGGTTTAGGGTTT
17748000 AGAGTTTGGT
Statistics
Matches: 145, Mismatches: 31, Indels: 24
0.73 0.16 0.12
Matches are distributed among these distances:
32 1 0.01
33 47 0.32
34 50 0.34
35 10 0.07
36 8 0.06
38 23 0.16
39 6 0.04
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (32 bp):
TAGGTTTAGGGTTTTGGTTTAGGGTTAAAGTT
Found at i:17747973 original size:13 final size:13
Alignment explanation
Indices: 17747937--17748011 Score: 80
Period size: 13 Copynumber: 5.7 Consensus size: 13
17747927 AGGTTTTAGA
*
17747937 TTTTGGTTTAGAG
1 TTTTGGTTTAGGG
*
17747950 TTTAGGGTTTAGGG
1 TTT-TGGTTTAGGG
17747964 TTTTGGTTTAGGG
1 TTTTGGTTTAGGG
*
17747977 TTTTGGTTTAAGG
1 TTTTGGTTTAGGG
* *
17747990 TTTAGGGTTTAGAG
1 TTT-TGGTTTAGGG
17748004 -TTTGGTTT
1 TTTTGGTTT
17748012 TACGTTTTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
12 5 0.10
13 29 0.56
14 18 0.35
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (13 bp):
TTTTGGTTTAGGG
Found at i:17747981 original size:40 final size:40
Alignment explanation
Indices: 17747928--17748046 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 40
17747918 TTTGATTTAA
17747928 GGTTTTA-GATTTTGGTTTAGAGTTTAGGGTTTAGGGTTTT
1 GGTTTTACG-TTTTGGTTTAGAGTTTAGGGTTTAGGGTTTT
* *
17747968 GG-TTTAGGGTTTTGGTTTA-AGGTTTAGGGTTTAGAG-TTT
1 GGTTTTA-CGTTTTGGTTTAGA-GTTTAGGGTTTAGGGTTTT
*
17748007 GGTTTTACGTTTTAGGTTTTAG-GTTTAGGGTTTAAGGTTT
1 GGTTTTACGTTTT-GG-TTTAGAGTTTAGGGTTTAGGGTTT
17748047 GCATGTAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
39 15 0.22
40 45 0.67
41 7 0.10
ACGTcount: A:0.15, C:0.01, G:0.33, T:0.51
Consensus pattern (40 bp):
GGTTTTACGTTTTGGTTTAGAGTTTAGGGTTTAGGGTTTT
Found at i:17748045 original size:7 final size:7
Alignment explanation
Indices: 17747923--17748046 Score: 55
Period size: 7 Copynumber: 18.4 Consensus size: 7
17747913 TTAGGTTTGA
17747923 TTTAAGG
1 TTTAAGG
* *
17747930 TTTTAGA
1 TTTAAGG
*
17747937 TTT-TGG
1 TTTAAGG
17747943 TTT-AGAG
1 TTTAAG-G
*
17747950 TTTAGGG
1 TTTAAGG
*
17747957 TTTAGGG
1 TTTAAGG
*
17747964 TTT-TGG
1 TTTAAGG
*
17747970 TTTAGGG
1 TTTAAGG
*
17747977 TTT-TGG
1 TTTAAGG
17747983 TTTAAGG
1 TTTAAGG
*
17747990 TTTAGGG
1 TTTAAGG
17747997 TTT-AGAG
1 TTTAAG-G
17748004 TTT--GG
1 TTTAAGG
* *
17748009 TTTTACG
1 TTTAAGG
*
17748016 TTTTAGG
1 TTTAAGG
*
17748023 TTTTAGG
1 TTTAAGG
*
17748030 TTTAGGG
1 TTTAAGG
17748037 TTTAAGG
1 TTTAAGG
17748044 TTT
1 TTT
17748047 GCATGTAAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
5 4 0.04
6 17 0.18
7 71 0.76
8 1 0.01
ACGTcount: A:0.16, C:0.01, G:0.31, T:0.52
Consensus pattern (7 bp):
TTTAAGG
Found at i:17749744 original size:32 final size:31
Alignment explanation
Indices: 17749679--17749744 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
17749669 TTTTACTAAT
* *
17749679 TTTTTATTATTTTTATTGTTTTAATTAATAA
1 TTTTTACTATTTTTATTGTTTTAATTAAAAA
17749710 TTTTTACTATTTTT-TAT-TTTTAATTTTAAAAA
1 TTTTTACTATTTTTAT-TGTTTTAA--TTAAAAA
17749742 TTT
1 TTT
17749745 ATCAAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 7 0.23
31 14 0.47
32 9 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTTTACTATTTTTATTGTTTTAATTAAAAA
Found at i:17749898 original size:18 final size:17
Alignment explanation
Indices: 17749873--17749908 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
17749863 AACAATATAT
*
17749873 TTTATTATTTATTTTTA
1 TTTATTATTTATTATTA
17749890 TTTATTTATTTATTATTA
1 TTTA-TTATTTATTATTA
17749908 T
1 T
17749909 AAAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTATTTATTATTA
Found at i:17749908 original size:14 final size:13
Alignment explanation
Indices: 17749872--17749908 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
17749862 TAACAATATA
17749872 TTTTATTATTTAT
1 TTTTATTATTTAT
17749885 TTTTATTTATTTAT
1 TTTTA-TTATTTAT
17749899 TTATTATTAT
1 TT-TTATTAT
17749909 AAAAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 14 0.64
15 3 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:17750851 original size:44 final size:44
Alignment explanation
Indices: 17750748--17750863 Score: 121
Period size: 44 Copynumber: 2.6 Consensus size: 44
17750738 ATTTGACAAG
* * * *
17750748 CTCCCCTAAGTAGAGGTTTAACAACTTTTTAAAATTTAAAAAAA
1 CTCCTCTAAATAGAGGCTCAACAACTTTTTAAAATTTAAAAAAA
* *
17750792 CTCCTCTAAACAGAGGCTCAACAACTTTTTAAAAATTT-AAAAAG
1 CTCCTCTAAATAGAGGCTCAACAACTTTTT-AAAATTTAAAAAAA
*
17750836 C-CCTTCTGAATAGAGGCTTC-ACAACTTT
1 CTCC-TCTAAATAGAGGC-TCAACAACTTT
17750864 AAAATTCTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 2 0.03
44 50 0.82
45 9 0.15
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (44 bp):
CTCCTCTAAATAGAGGCTCAACAACTTTTTAAAATTTAAAAAAA
Found at i:17751108 original size:49 final size:49
Alignment explanation
Indices: 17751038--17751337 Score: 200
Period size: 49 Copynumber: 6.1 Consensus size: 49
17751028 CATTGACATT
** * *
17751038 AAAAATTTCATCTAAAAAAAGGTCTTTTAAGTAGAGGCTTAACAACTTTA
1 AAAAATTT-ATCTTGAAAAAGGTCCTTTAAGCAGAGGCTTAACAACTTTA
* * * * * * **
17751088 AAAAATTTATCATGCAAAAGGCTCATTTAAGTAAAGGCTCAATGACTTTA
1 AAAAATTTATCTTGAAAAAGG-TCCTTTAAGCAGAGGCTTAACAACTTTA
* * *
17751138 AAAATTTTATCTTG-AAAAGTTTCCTCTAAGCAGAGG-TTCAACAACTTTA
1 AAAAATTTATCTTGAAAAAG-GTCCTTTAAGCAGAGGCTT-AACAACTTTA
* * ** * * *
17751187 AAAATTTTAT-TTTAAAAAACT-CTTCAAGTAGAGGCTTAACAATTTTA
1 AAAAATTTATCTTGAAAAAGGTCCTTTAAGCAGAGGCTTAACAACTTTA
* * * * *
17751234 AAAAATTCATCTTGAAAAAGG-CTTATCTAAGCAAAGACTTAACAGCTTT-
1 AAAAATTTATCTTGAAAAAGGTCCT-T-TAAGCAGAGGCTTAACAACTTTA
* * * *
17751283 AAAAATTTCATC-TCAAAAAGGTTCCTCTAAACAGAGGCTTAACAACTTAA
1 AAAAATTT-ATCTTGAAAAAGG-TCCTTTAAGCAGAGGCTTAACAACTTTA
17751333 AAAAA
1 AAAAA
17751338 AATTCATCTT
Statistics
Matches: 190, Mismatches: 47, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
47 27 0.14
48 14 0.07
49 80 0.42
50 67 0.35
51 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (49 bp):
AAAAATTTATCTTGAAAAAGGTCCTTTAAGCAGAGGCTTAACAACTTTA
Found at i:17751234 original size:146 final size:146
Alignment explanation
Indices: 17751066--17751336 Score: 366
Period size: 146 Copynumber: 1.9 Consensus size: 146
17751056 AAGGTCTTTT
* * * * *
17751066 AAGTAGAGGCTTAACAACTTTAAAAAATTTATCATGCAAAAGGCTCATTTAAGTAAAGGCTCAA-
1 AAGTAGAGGCTTAACAACTTTAAAAAATTCATCATGAAAAAGGCTCATCTAAGCAAAGACTCAAC
* * ** * * *
17751130 TGACTTTAAAAATTTTATCTTGAAAAGTTTCCTCTAAGCAGAGG-TTCAACAACTTTAAAAATTT
66 AG-CTTTAAAAATTTCATCTCAAAAAGGTTCCTCTAAACAGAGGCTT-AACAACTTAAAAAATTT
17751194 TATTTTAAAAAACTCTTC
129 TATTTTAAAAAACTCTTC
* * * *
17751212 AAGTAGAGGCTTAACAATTTTAAAAAATTCATCTTGAAAAAGGCTTATCTAAGCAAAGACTTAAC
1 AAGTAGAGGCTTAACAACTTTAAAAAATTCATCATGAAAAAGGCTCATCTAAGCAAAGACTCAAC
17751277 AGCTTTAAAAATTTCATCTCAAAAAGGTTCCTCTAAACAGAGGCTTAACAACTTAAAAAA
66 AGCTTTAAAAATTTCATCTCAAAAAGGTTCCTCTAAACAGAGGCTTAACAACTTAAAAAA
17751337 AAATTCATCT
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
146 104 0.97
147 3 0.03
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (146 bp):
AAGTAGAGGCTTAACAACTTTAAAAAATTCATCATGAAAAAGGCTCATCTAAGCAAAGACTCAAC
AGCTTTAAAAATTTCATCTCAAAAAGGTTCCTCTAAACAGAGGCTTAACAACTTAAAAAATTTTA
TTTTAAAAAACTCTTC
Found at i:17752195 original size:17 final size:17
Alignment explanation
Indices: 17752173--17752206 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17752163 CTAAGATATA
17752173 TCTCTTT-TTTTTCTTTT
1 TCTCTTTCTTTTT-TTTT
17752190 TCTCTTTCTTTTTTTTT
1 TCTCTTTCTTTTTTTTT
17752207 GTTTTCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTCTTTCTTTTTTTTT
Found at i:17761072 original size:145 final size:143
Alignment explanation
Indices: 17760786--17761124 Score: 373
Period size: 145 Copynumber: 2.3 Consensus size: 143
17760776 TAGTGCCCCA
* ** *
17760786 AAAAAGGTAAAATTACCAAAATACCCTTATGGGGGTATTTTCATAATTTGATCTTCTCAAGCTTA
1 AAAAAGGTGAAATTACCAAAATACCCTTATTAGGGTATTTTCATAATTTGATCTTCTCAAGCTCA
* *
17760851 AATTTTTGTGAAACTTCTCAAATATTAATTTGATAATATTTCATAAATTTTGGTGTATTTAAAAT
66 AATTTTTGTGAAACTTCTCAAATATTAATTTGATAATATTTCATAAATTTTGGTGTATTCAAAAC
*
17760916 CACGATGGTACCTC
131 CACGATAGTACC-C
* * * * *
17760930 AAAAAGGATGAAATTACCAAAATACCCTCATTAGGGTATTTTCATAATTTTACTTTTTTGAA-CT
1 AAAAAGG-TGAAATTACCAAAATACCCTTATTAGGGTATTTTCATAATTTGA-TCTTCTCAAGCT
* * * *
17760994 CAAATTTTTGTGAAACTTTTCAAAT-TTAAATTTTATAATATTTCATGATTTTTGGTG-AGTTCA
64 CAAATTTTTGTGAAACTTCTCAAATATT-AATTTGATAATATTTCATAAATTTTGGTGTA-TTCA
*
17761057 AAGCCAC-AGTAGTACCC
127 AAACCACGA-TAGTACCC
* * * * *
17761074 GAAAAGTGTGATATTACGAAAATAACCTTA-TAGGGGTATTTTCGTAATTTG
1 AAAAAG-GTGAAATTACCAAAATACCCTTATTA-GGGTATTTTCATAATTTG
17761125 GCTTTATCGA
Statistics
Matches: 164, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
143 2 0.01
144 51 0.31
145 105 0.64
146 6 0.04
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (143 bp):
AAAAAGGTGAAATTACCAAAATACCCTTATTAGGGTATTTTCATAATTTGATCTTCTCAAGCTCA
AATTTTTGTGAAACTTCTCAAATATTAATTTGATAATATTTCATAAATTTTGGTGTATTCAAAAC
CACGATAGTACCC
Found at i:17768221 original size:19 final size:19
Alignment explanation
Indices: 17768199--17768242 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17768189 TTTTTTTTCC
17768199 TTTTTTCTTTCATATTTTG
1 TTTTTTCTTTCATATTTTG
* ** *
17768218 TTTTTTTTTTGTTTTTTTG
1 TTTTTTCTTTCATATTTTG
17768237 TTTTTT
1 TTTTTT
17768243 TTGCATTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.05, G:0.07, T:0.84
Consensus pattern (19 bp):
TTTTTTCTTTCATATTTTG
Found at i:17770948 original size:17 final size:17
Alignment explanation
Indices: 17770928--17770962 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17770918 TATTAATCAA
17770928 AATATCATAAATAAATC
1 AATATCATAAATAAATC
17770945 AATATCATAAATAAATC
1 AATATCATAAATAAATC
17770962 A
1 A
17770963 TAAGCACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATCATAAATAAATC
Found at i:17771291 original size:21 final size:21
Alignment explanation
Indices: 17771243--17771282 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17771233 TGATTCAATT
*
17771243 TTATATTCTAATTTATTTTAG
1 TTATATTATAATTTATTTTAG
17771264 TTATATTATAATTT-TTTTA
1 TTATATTATAATTTATTTTA
17771283 TTGATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATATTATAATTTATTTTAG
Found at i:17772264 original size:23 final size:22
Alignment explanation
Indices: 17772184--17772292 Score: 82
Period size: 22 Copynumber: 4.9 Consensus size: 22
17772174 TATTTTAGGC
17772184 TTTATTATATTTTGC-ATTT-GA
1 TTTATTATATTTT-CTATTTAGA
* * * *
17772205 TTTGATTATATATACATATATATA
1 TTT-ATTATATTTTC-TATTTAGA
*
17772229 TATATTACT-TTTT-TAGTTTAGGA
1 TTTATTA-TATTTTCTA-TTTA-GA
*
17772252 TTTATTATATTTTCTATTTAGC
1 TTTATTATATTTTCTATTTAGA
17772274 TTTATTATATTTTCTATTT
1 TTTATTATATTTTCTATTT
17772293 GACTTTAAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
21 6 0.09
22 32 0.47
23 24 0.35
24 6 0.09
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (22 bp):
TTTATTATATTTTCTATTTAGA
Found at i:17773549 original size:18 final size:17
Alignment explanation
Indices: 17773524--17773565 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
17773514 ATAATTTTTT
17773524 AAAA-AAATAAAAAATGA
1 AAAATAAATAAAAAAT-A
17773541 AAAATAAATAAAAAATA
1 AAAATAAATAAAAAATA
*
17773558 AAAGTAAA
1 AAAATAAA
17773566 AGATTAGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAATAAATAAAAAATA
Found at i:17773843 original size:16 final size:17
Alignment explanation
Indices: 17773816--17773848 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
17773806 ATTCTTTTCC
17773816 TTTCATTTTTTTTATTT
1 TTTCATTTTTTTTATTT
17773833 TTTCA-TTTTTTTATTT
1 TTTCATTTTTTTTATTT
17773849 CGAATTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCATTTTTTTTATTT
Found at i:17776158 original size:31 final size:31
Alignment explanation
Indices: 17776115--17776178 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
17776105 TAAATTCAAA
17776115 CACGATGTTAACTTAAAACATGTATTAATAC
1 CACGATGTTAACTTAAAACATGTATTAATAC
*
17776146 CACGGTGTTAACTTAAAACATGTATTAATAC
1 CACGATGTTAACTTAAAACATGTATTAATAC
17776177 CA
1 CA
17776179 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (31 bp):
CACGATGTTAACTTAAAACATGTATTAATAC
Found at i:17791140 original size:17 final size:17
Alignment explanation
Indices: 17791112--17791156 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
17791102 ATGGATGAAG
17791112 AAAAAATT--AAAAATT
1 AAAAAATTAAAAAAATT
17791127 AAAAAATTAAAAAAATT
1 AAAAAATTAAAAAAATT
*
17791144 AAAAAATGAAAAA
1 AAAAAATTAAAAA
17791157 TGAAAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 8 0.30
17 19 0.70
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAAATTAAAAAAATT
Found at i:17791157 original size:7 final size:7
Alignment explanation
Indices: 17791145--17791219 Score: 89
Period size: 7 Copynumber: 10.0 Consensus size: 7
17791135 AAAAAAATTA
17791145 AAAAATG
1 AAAAATG
17791152 AAAAATG
1 AAAAATG
17791159 -AAAATG
1 AAAAATG
17791165 AAAAAAAATG
1 ---AAAAATG
17791175 AAAAATG
1 AAAAATG
17791182 AAAAAGTG
1 AAAAA-TG
17791190 AAAAAGTG
1 AAAAA-TG
17791198 AAAAAATG
1 -AAAAATG
17791206 AAAAATG
1 AAAAATG
17791213 AAAAATG
1 AAAAATG
17791220 TGAAAAAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.10
7 33 0.53
8 12 0.19
9 5 0.08
10 6 0.10
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:17791170 original size:8 final size:8
Alignment explanation
Indices: 17791111--17791237 Score: 95
Period size: 8 Copynumber: 15.9 Consensus size: 8
17791101 AATGGATGAA
17791111 GAAAAAAT
1 GAAAAAAT
*
17791119 -TAAAAAT
1 GAAAAAAT
*
17791126 TAAAAAATT
1 GAAAAAA-T
*
17791135 AAAAAAAT
1 GAAAAAAT
*
17791143 TAAAAAAT
1 GAAAAAAT
17791151 G-AAAAAT
1 GAAAAAAT
17791158 G--AAAAT
1 GAAAAAAT
17791164 GAAAAAAAAT
1 G--AAAAAAT
17791174 G-AAAAAT
1 GAAAAAAT
*
17791181 GAAAAAGT
1 GAAAAAAT
*
17791189 GAAAAAGT
1 GAAAAAAT
17791197 GAAAAAAT
1 GAAAAAAT
17791205 G-AAAAAT
1 GAAAAAAT
*
17791212 GAAAAATGT
1 GAAAAA-AT
17791221 GAAAAAAAT
1 G-AAAAAAT
17791230 GAAGAAAA
1 GAA-AAAA
17791238 AGGAAAGAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
6 6 0.06
7 27 0.27
8 40 0.40
9 15 0.15
10 11 0.11
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.16
Consensus pattern (8 bp):
GAAAAAAT
Found at i:17791170 original size:31 final size:30
Alignment explanation
Indices: 17791113--17791219 Score: 117
Period size: 31 Copynumber: 3.5 Consensus size: 30
17791103 TGGATGAAGA
* * *
17791113 AAAAATTAAAAATTAAAAA-ATTAAAAAAATTA
1 AAAAATGAAAAATGAAAAAGA--AAAAAAA-TG
*
17791145 AAAAATGAAAAATGAAAATGAAAAAAAATG
1 AAAAATGAAAAATGAAAAAGAAAAAAAATG
**
17791175 AAAAATGAAAAAGTGAAAAAGTGAAAAAATG
1 AAAAATGAAAAA-TGAAAAAGAAAAAAAATG
17791206 AAAAATGAAAAATG
1 AAAAATGAAAAATG
17791220 TGAAAAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
30 15 0.23
31 34 0.52
32 16 0.24
33 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (30 bp):
AAAAATGAAAAATGAAAAAGAAAAAAAATG
Found at i:17791214 original size:23 final size:22
Alignment explanation
Indices: 17791137--17791226 Score: 101
Period size: 23 Copynumber: 3.9 Consensus size: 22
17791127 AAAAAATTAA
*
17791137 AAAAATTAAAAAATGAAAAATG
1 AAAAATGAAAAAATGAAAAATG
17791159 -AAAATGAAAAAAAATGAAAAATG
1 AAAAATG--AAAAAATGAAAAATG
*
17791182 AAAAAGTGAAAAAGTGAAAAAATG
1 AAAAA-TGAAAAAATG-AAAAATG
*
17791206 AAAAATGAAAAATGTGAAAAA
1 AAAAATGAAAAA-ATGAAAAA
17791227 AATGAAGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.08
23 34 0.57
24 19 0.32
25 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAATGAAAAAATGAAAAATG
Found at i:17791226 original size:16 final size:15
Alignment explanation
Indices: 17791113--17791217 Score: 97
Period size: 15 Copynumber: 6.8 Consensus size: 15
17791103 TGGATGAAGA
* * *
17791113 AAAAATTAAAAATTA
1 AAAAATGAAAAAATG
* *
17791128 AAAAATTAAAAAAATTA
1 AAAAA-TGAAAAAA-TG
17791145 AAAAATG-AAAAATG
1 AAAAATGAAAAAATG
17791159 -AAAATGAAAAAAAATG
1 AAAAATG--AAAAAATG
*
17791175 AAAAATGAAAAAGTG
1 AAAAATGAAAAAATG
17791190 AAAAAGTGAAAAAATG
1 AAAAA-TGAAAAAATG
17791206 AAAAATGAAAAA
1 AAAAATGAAAAA
17791218 TGTGAAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
13 6 0.08
14 1 0.01
15 29 0.38
16 28 0.36
17 13 0.17
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:17791899 original size:11 final size:12
Alignment explanation
Indices: 17791867--17791899 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
17791857 TTAGTGGACA
17791867 AAATTTGTTATG
1 AAATTTGTTATG
17791879 AAATTTGTTATG
1 AAATTTGTTATG
17791891 AAA-TTGTTA
1 AAATTTGTTA
17791900 GTGCTGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
AAATTTGTTATG
Done.