Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005265.1 Hibiscus syriacus cultivar Beakdansim tig00011908_pilon, 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: 71980
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:14580 original size:17 final size:17
Alignment explanation
Indices: 14558--14591 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
14548 ACCTTGACCA
14558 AAAAGTCAAATTTTATG
1 AAAAGTCAAATTTTATG
*
14575 AAAAGTCATATTTTATG
1 AAAAGTCAAATTTTATG
14592 TTTTTCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAGTCAAATTTTATG
Found at i:16078 original size:37 final size:37
Alignment explanation
Indices: 15979--16080 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 37
15969 CCTTTTCGTC
*
15979 CTACTAAGATTCAAACTCGTAAAAATAGGATAGAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* *
16016 -T--TAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
16050 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
16081 TCACAAGCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 30 0.55
35 1 0.02
36 1 0.02
37 23 0.42
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:21290 original size:14 final size:14
Alignment explanation
Indices: 21271--21348 Score: 63
Period size: 14 Copynumber: 5.5 Consensus size: 14
21261 ATTCAATCAG
21271 AACAAAAACA-AAAA
1 AACAAAAA-AGAAAA
21285 AACAAAAAAGAAAA
1 AACAAAAAAGAAAA
21299 GAAGCAAAAAAGAAGAA
1 -AA-CAAAAAAGAA-AA
21316 AAC--AAAAGAAAA
1 AACAAAAAAGAAAA
* * *
21328 AAGAAAGAACAAAA
1 AACAAAAAAGAAAA
*
21342 ATCAAAA
1 AACAAAA
21349 TGAAAAAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 4 0.08
13 8 0.15
14 23 0.44
15 3 0.06
16 12 0.23
17 2 0.04
ACGTcount: A:0.79, C:0.09, G:0.10, T:0.01
Consensus pattern (14 bp):
AACAAAAAAGAAAA
Found at i:21311 original size:11 final size:10
Alignment explanation
Indices: 21295--21332 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
21285 AACAAAAAAG
21295 AAAAGAAGCAA
1 AAAAGAAG-AA
21306 AAAAGAAGAA
1 AAAAGAAGAA
21316 AACAA-AAGAA
1 AA-AAGAAGAA
21326 AAAAGAA
1 AAAAGAA
21333 AGAACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.08
10 13 0.52
11 10 0.40
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:21317 original size:24 final size:23
Alignment explanation
Indices: 21281--21325 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
21271 AACAAAAACA
*
21281 AAAAAACAAAAAAGAAAAGAAGC
1 AAAAAACAAAAAACAAAAGAAGC
*
21304 AAAAAAGAAGAAAACAAAAGAA
1 AAAAAACAA-AAAACAAAAGAA
21326 AAAAGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAACAAAAAACAAAAGAAGC
Found at i:21318 original size:31 final size:31
Alignment explanation
Indices: 21274--21332 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21264 CAATCAGAAC
21274 AAAAACAAAAAAACAAAA-AAGAAAAGAAGCA
1 AAAAACAAAAAAACAAAAGAA-AAAAGAAGCA
* *
21305 AAAAAGAAGAAAACAAAAGAAAAAAGAA
1 AAAAACAAAAAAACAAAAGAAAAAAGAA
21333 AGAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (31 bp):
AAAAACAAAAAAACAAAAGAAAAAAGAAGCA
Found at i:21327 original size:19 final size:19
Alignment explanation
Indices: 21274--21341 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
21264 CAATCAGAAC
21274 AAAAACAAAA-AAACAAA-A
1 AAAAACAAAAGAAA-AAAGA
*
21292 AAGAAA-AGAAGCAAAAAAGA
1 AA-AAACAAAAG-AAAAAAGA
21312 AGAAAACAAAAGAAAAAAGA
1 A-AAAACAAAAGAAAAAAGA
*
21332 AAGAACAAAA
1 AAAAACAAAA
21342 ATCAAAATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
18 5 0.12
19 14 0.34
20 17 0.41
21 5 0.12
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAGAAAAAAGA
Found at i:21348 original size:21 final size:20
Alignment explanation
Indices: 21275--21341 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 20
21265 AATCAGAACA
*
21275 AAAACAAAA-AAACAAAAAAG
1 AAAACAAAACAAA-AAAGAAG
* *
21295 AAAA-GAAGCAAAAAAGAAG
1 AAAACAAAACAAAAAAGAAG
*
21314 AAAACAAAAGAAAAAAGAA-
1 AAAACAAAACAAAAAAGAAG
*
21333 AGAACAAAA
1 AAAACAAAA
21342 ATCAAAATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAACAAAACAAAAAAGAAG
Found at i:22034 original size:22 final size:22
Alignment explanation
Indices: 21961--22037 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
21951 GCTACCCCAT
*
21961 CAAACCATTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
21983 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
22005 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
22027 CAAACCTTTGA
1 CAAACCTTTGA
22038 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:23788 original size:106 final size:106
Alignment explanation
Indices: 22836--23787 Score: 1490
Period size: 106 Copynumber: 9.0 Consensus size: 106
22826 GAAGGATATT
* *
22836 GACAACGCTAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
** *
22901 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCGA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
22942 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
23007 AGAGCCAATTTCAACTTCACAGTGAAAGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* *
23048 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
23113 GGAGCCAATTTCAACTTCACATCGAAGGATATTGCACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* * * * *
23154 AACAACGCAAGTTGAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTT
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
** *
23219 AGAGCCAATTTCAACTTCACAATGAAAGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* * *
23260 GACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTT
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
23325 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* *
23366 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
23431 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* *
23472 GACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACAACTTCCAAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
23537 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* ** *
23578 GACGACGCAAGTTCAACTTCAAAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
23643 GGAGACAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* * * * * *
23684 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCC
1 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
23749 AGAGCTAATTTCAACTTCACAACGGAGGATATTGGACTC
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
23788 GGAACAATCC
Statistics
Matches: 780, Mismatches: 66, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 780 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
Found at i:24636 original size:37 final size:37
Alignment explanation
Indices: 24537--24638 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 37
24527 CTTTTTCGTC
24537 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
*
24574 -T--TAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
24608 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
24639 TCACAAGCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 32 0.56
35 1 0.02
36 1 0.02
37 23 0.40
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:24720 original size:21 final size:22
Alignment explanation
Indices: 24691--24734 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
24681 ACACGATTTA
*
24691 CACACAAAACACAGAGG-AAAG
1 CACACAAAACACAAAGGCAAAG
* *
24712 CACAGAAAATACAAAGGCAAAG
1 CACACAAAACACAAAGGCAAAG
24734 C
1 C
24735 TATTGTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.23, G:0.18, T:0.02
Consensus pattern (22 bp):
CACACAAAACACAAAGGCAAAG
Found at i:25152 original size:20 final size:20
Alignment explanation
Indices: 25127--25164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25117 TTTTTTATTA
25127 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
25147 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
25165 TTACTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:28585 original size:55 final size:55
Alignment explanation
Indices: 28509--28899 Score: 483
Period size: 55 Copynumber: 7.2 Consensus size: 55
28499 GTATGGTGAT
*
28509 TTTC-GTATGGGCCCTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * *
28563 TTTCTGTATGGGCACTTGGTGTGAAAAACTAAGAAATTCATACTATGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * *
28618 TTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTTATACAAAGTGTATGAA
1 TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * *
28673 TTT-TCATATGGGCACTTTGTCTTG-AAAACTAAGAAATTCATAATAAGTGTATGAA
1 TTTCT-GTATGGGCACTTTGT-GTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * * *
28728 TTTTTTGTATAGGTACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
1 -TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* *
28784 TTT-TCGTATGGGAACTTTGTGTGTAAAACTAAGAAATT--TA-TAAGTGTATGAA
1 TTTCT-GTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
* * * * *
28836 TTT-TCATATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGTATGTGAA
1 TTTCT-GTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
*
28891 TTTCCGTAT
1 TTTCTGTAT
28900 TGTTGGTGGG
Statistics
Matches: 292, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
52 46 0.16
53 2 0.01
54 7 0.02
55 190 0.65
56 46 0.16
57 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (55 bp):
TTTCTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA
Found at i:28787 original size:111 final size:110
Alignment explanation
Indices: 28507--28899 Score: 535
Period size: 110 Copynumber: 3.6 Consensus size: 110
28497 ATGTATGGTG
* *
28507 ATTTTCGTATGGGCCCTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAA-TTTCTGTA
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTC-GTA
* * *
28571 TGGGCACTTGGTGTGAAAAACTAAGAAATTCATACTATGTGTATGA
65 TGGGCACTTTGTGTGAAAAACTAAGAAATTCATAATAAGTGTATGA
* * * * *
28617 ATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTTATACAAAGTGTATGAATTTTCATAT
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
*
28682 GGGCACTTTGTCTTG-AAAACTAAGAAATTCATAATAAGTGTATGA
66 GGGCACTTTGT-GTGAAAAACTAAGAAATTCATAATAAGTGTATGA
* * *
28727 ATTTTTTGTATAGGTACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTA
1 A-TTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTA
* *
28792 TGGGAACTTTGTGTGTAAAACTAAGAAATT--T-ATAAGTGTATGA
65 TGGGCACTTTGTGTGAAAAACTAAGAAATTCATAATAAGTGTATGA
* * * * *
28835 ATTTTCATATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGTATGTGAATTTCCGTAT
1 ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
28900 TGTTGGTGGG
Statistics
Matches: 252, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
107 56 0.22
108 13 0.05
109 1 0.00
110 96 0.38
111 86 0.34
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (110 bp):
ATTTTCGTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
GGGCACTTTGTGTGAAAAACTAAGAAATTCATAATAAGTGTATGA
Found at i:35814 original size:55 final size:55
Alignment explanation
Indices: 35585--35798 Score: 297
Period size: 55 Copynumber: 3.9 Consensus size: 55
35575 ATGTATGGTG
* *
35585 ATTTCCGTATGGGAACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
1 ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
* * * * *
35640 ATTTCCGTATGGACACTTTCTATGAAAAACTAAGAAATTCATACTAAGTGTATGA
1 ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
*
35695 ATTTTCGTATGGGTACTTTGTGTGCAAAACTAAGAAATGT-ATACTAAGTGTATGA
1 ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAAT-TCATACTAAGTGTATGA
* * *
35750 ATGTGT-GTATGGGCACTTGGTGTGCAAAACTAAGAAATTCATAATAAGT
1 AT-TTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGT
35799 ATGTGATTTT
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
54 1 0.01
55 137 0.97
56 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (55 bp):
ATTTTCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGA
Found at i:37363 original size:32 final size:32
Alignment explanation
Indices: 37325--37405 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
37315 CTAAGGTGAC
*
37325 CCTTGGGTAGGCTCTTAGGCCCCAAGGTACT-
1 CCTTGGGTAGGCTCTTAGGCCCCAAGGCACTA
* *
37356 CCTTTGGGTAGGCTCTAAGGCCCTAAGGCACTA
1 CC-TTGGGTAGGCTCTTAGGCCCCAAGGCACTA
* *
37389 CCTTAGGTTGGCTCTTA
1 CCTTGGGTAGGCTCTTA
37406 TACCCAACGG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.05
32 38 0.90
33 2 0.05
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTTAGGCCCCAAGGCACTA
Found at i:37556 original size:14 final size:14
Alignment explanation
Indices: 37537--37565 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37527 ACTAGACCGC
37537 AATTATGATTTTAA
1 AATTATGATTTTAA
37551 AATTATGATTTTAA
1 AATTATGATTTTAA
37565 A
1 A
37566 GTCACACATT
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:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AATTATGATTTTAA
Found at i:38213 original size:18 final size:19
Alignment explanation
Indices: 38192--38231 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38182 GAAGAGAGAT
38192 AAAA-GAAAGTAGA-AAAAG
1 AAAAGGAAAG-AGACAAAAG
38210 AAAAGGAAAGAGACAAAAG
1 AAAAGGAAAGAGACAAAAG
38229 AAA
1 AAA
38232 GCAAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (19 bp):
AAAAGGAAAGAGACAAAAG
Found at i:38929 original size:28 final size:29
Alignment explanation
Indices: 38886--38954 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
38876 CAAATAAACC
* * * *
38886 AACCCGAAACATATTACCTCC-CCAAATT
1 AACCTGAAACACATTACCACCTCAAAATT
*
38914 AACCTTAAACACATTACCACCTCAAAATT
1 AACCTGAAACACATTACCACCTCAAAATT
38943 AACCTGAAACAC
1 AACCTGAAACAC
38955 GTTAGCTTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (29 bp):
AACCTGAAACACATTACCACCTCAAAATT
Found at i:40351 original size:57 final size:57
Alignment explanation
Indices: 40251--40358 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 57
40241 ATTACTTCCG
* * **
40251 ATGAATTTTTAAAGAAGCTAAGTTTAATTTTTAGGGGTCTCTTGATGATAACTATAA
1 ATGAATTTTTAAAGAAGCCAAGTCTAATTTTTAAAGGTCTCTTGATGATAACTATAA
* * * *
40308 ATGAATTTTTAAAGAAGCCAAGTCTGATTTTTAAATGTTTCTTGTTGATAA
1 ATGAATTTTTAAAGAAGCCAAGTCTAATTTTTAAAGGTCTCTTGATGATAA
40359 GTCCTTTGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (57 bp):
ATGAATTTTTAAAGAAGCCAAGTCTAATTTTTAAAGGTCTCTTGATGATAACTATAA
Found at i:42084 original size:43 final size:43
Alignment explanation
Indices: 42026--42127 Score: 177
Period size: 43 Copynumber: 2.4 Consensus size: 43
42016 AGTTCGTTTC
* *
42026 CATCACATAAGGAGTTAGAACAACACTAATATTTTGGCTCATT
1 CATCGCATATGGAGTTAGAACAACACTAATATTTTGGCTCATT
*
42069 CATCGCATATGGAGTTAGAATAACACTAATATTTTGGCTCATT
1 CATCGCATATGGAGTTAGAACAACACTAATATTTTGGCTCATT
42112 CATCGCATATGGAGTT
1 CATCGCATATGGAGTT
42128 TGATTAGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (43 bp):
CATCGCATATGGAGTTAGAACAACACTAATATTTTGGCTCATT
Found at i:42496 original size:117 final size:116
Alignment explanation
Indices: 42342--42588 Score: 343
Period size: 117 Copynumber: 2.1 Consensus size: 116
42332 CAACATCATC
* *
42342 ACCTTGTTTGATTTCATCACAGAAGGAGCTGGATCGACATTTCCAGTGGAGATTTCATAGTGAAA
1 ACCTTGTTTGATTTCATCACAGAAGGAGCTGGATCGACATTTCCAGTGGAGAGTTCATAATGAAA
*
42407 AGAACTCATCCGAGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
66 AGAACTCATACGAGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
* * * *
42458 CCCTTGGTTTGATTTCATCACAGCAA-GAGGTGGATCGACATTTCTAGTGGAGAGTTCGTAATGA
1 ACCTT-GTTTGATTTCATCACAG-AAGGAGCTGGATCGACATTTCCAGTGGAGAGTTCATAATGA
* * * * *
42522 GAAGAACTCATACGATGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCA
64 AAAGAACTCATACGAGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
*
42575 ACCTTAGATTGATT
1 ACCTT-GTTTGATT
42589 CTATCACCTT
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
116 4 0.04
117 108 0.95
118 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (116 bp):
ACCTTGTTTGATTTCATCACAGAAGGAGCTGGATCGACATTTCCAGTGGAGAGTTCATAATGAAA
AGAACTCATACGAGGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
Found at i:42901 original size:3 final size:3
Alignment explanation
Indices: 42895--42941 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
42885 TTATTATCCT
42895 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42942 TTATTATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:42946 original size:3 final size:3
Alignment explanation
Indices: 42940--42970 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
42930 ATAATAATAA
42940 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42971 TATAGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:44407 original size:16 final size:17
Alignment explanation
Indices: 44375--44414 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
44365 AGATTACCAG
44375 TGGGAATATATGATTAC
1 TGGGAATATATGATTAC
44392 TAGGGAATA-A-GATTAC
1 T-GGGAATATATGATTAC
44408 TGGGAAT
1 TGGGAAT
44415 GTTGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 7 0.32
17 2 0.09
18 7 0.32
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (17 bp):
TGGGAATATATGATTAC
Found at i:47241 original size:23 final size:23
Alignment explanation
Indices: 47209--47266 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
47199 TTATGACATG
*
47209 TTCTCCACCTTTATGGAAC-ATT
1 TTCTCTACCTTTATGGAACGATT
* *
47231 TATCTCTACCTTTGTGGCACGATT
1 T-TCTCTACCTTTATGGAACGATT
*
47255 TTCTCTGCCTTT
1 TTCTCTACCTTT
47267 TGGTAGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 25 0.83
24 4 0.13
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.45
Consensus pattern (23 bp):
TTCTCTACCTTTATGGAACGATT
Found at i:52372 original size:14 final size:14
Alignment explanation
Indices: 52350--52387 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
52340 AAATTTAATA
52350 ATTTAATAATAAAG
1 ATTTAATAATAAAG
*
52364 ATTTGATAATAAAG
1 ATTTAATAATAAAG
52378 ATTTAATAAT
1 ATTTAATAAT
52388 GATTTGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (14 bp):
ATTTAATAATAAAG
Found at i:52413 original size:26 final size:25
Alignment explanation
Indices: 52356--52422 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
52346 AATAATTTAA
*
52356 TAATAAAGATTTGATAATAAAGATT
1 TAATAATGATTTGATAATAAAGATT
* *
52381 TAATAATGATTTGATATTTAATGATT
1 TAATAATGATTTGATA-ATAAAGATT
* *
52407 TAGTAATGATATGATA
1 TAATAATGATTTGATA
52423 GTAGTGATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (25 bp):
TAATAATGATTTGATAATAAAGATT
Found at i:52501 original size:8 final size:8
Alignment explanation
Indices: 52475--52551 Score: 56
Period size: 8 Copynumber: 9.9 Consensus size: 8
52465 CTAATTATTA
52475 ATTTAATG
1 ATTTAATG
*
52483 ATTTTAT-
1 ATTTAATG
52490 ATTTAATG
1 ATTTAATG
52498 ATTTAGTAATG
1 A-TT--TAATG
52509 ATTTAATG
1 ATTTAATG
52517 ATTTAAT-
1 ATTTAATG
* *
52524 A-ATAATT
1 ATTTAATG
52531 ATTTAA--
1 ATTTAATG
*
52537 CTTTAATG
1 ATTTAATG
52545 ATTTAAT
1 ATTTAAT
52552 AATAATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
6 9 0.16
7 8 0.15
8 28 0.51
9 2 0.04
10 2 0.04
11 6 0.11
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (8 bp):
ATTTAATG
Found at i:52514 original size:19 final size:17
Alignment explanation
Indices: 52475--52527 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
52465 CTAATTATTA
52475 ATTTAATGATTT-T-AT
1 ATTTAATGATTTATAAT
52490 ATTTAATGATTTAGTAAT
1 ATTTAATGATTTA-TAAT
52508 GATTTAATGATTTAATAAT
1 -ATTTAATGATTT-ATAAT
52527 A
1 A
52528 ATTATTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 12 0.36
17 1 0.03
18 3 0.09
19 16 0.48
20 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
ATTTAATGATTTATAAT
Found at i:52563 original size:42 final size:42
Alignment explanation
Indices: 52512--52721 Score: 230
Period size: 42 Copynumber: 5.0 Consensus size: 42
52502 AGTAATGATT
*
52512 TAATGATTTAATAATAATTATTTAACTTTAATGATTTAA-TAA
1 TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACT-A
* * * *
52554 TAATTATTTAACT-TTAATGATTTAGCTTTAATAATTTAA-TAA
1 TAATGATTTAA-TAATAATGATTTAACTTTAATGATTTAACT-A
* * ** *
52596 TAATAATTTAACT-TTAATGATTTAACAATAATGATTTAACTT
1 TAATGATTTAA-TAATAATGATTTAACTTTAATGATTTAACTA
* * *
52638 TAATGATTTAATAATAATTATTTAACTTAAATGATTTAACTT
1 TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACTA
*
52680 TAATGATTTAATAATAATAATTTAACTTTAATGATTTAACTA
1 TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACTA
52722 CAGTTGGCGA
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 142 0.98
43 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (42 bp):
TAATGATTTAATAATAATGATTTAACTTTAATGATTTAACTA
Found at i:52719 original size:14 final size:14
Alignment explanation
Indices: 52510--52720 Score: 207
Period size: 14 Copynumber: 15.1 Consensus size: 14
52500 TTAGTAATGA
52510 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
52523 TAATAATTATTTAAC
1 T-TTAATGATTTAAC
52538 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
52551 TAATAATTATTTAAC
1 T-TTAATGATTTAAC
*
52566 TTTAATGATTTAGC
1 TTTAATGATTTAAC
*
52580 TTTAATAATTTAA-
1 TTTAATGATTTAAC
* *
52593 TAATAATAATTTAAC
1 T-TTAATGATTTAAC
52608 TTTAATGATTTAAC
1 TTTAATGATTTAAC
**
52622 AATAATGATTTAAC
1 TTTAATGATTTAAC
52636 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
52649 TAATAATTATTTAAC
1 T-TTAATGATTTAAC
*
52664 TTAAATGATTTAAC
1 TTTAATGATTTAAC
52678 TTTAATGATTTAA-
1 TTTAATGATTTAAC
* *
52691 TAATAATAATTTAAC
1 T-TTAATGATTTAAC
52706 TTTAATGATTTAAC
1 TTTAATGATTTAAC
52720 T
1 T
52721 ACAGTTGGCG
Statistics
Matches: 160, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
13 5 0.03
14 150 0.94
15 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (14 bp):
TTTAATGATTTAAC
Found at i:56229 original size:17 final size:18
Alignment explanation
Indices: 56204--56240 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56194 ACAAATCTAG
56204 ACAAAAAAAGTAAATATT
1 ACAAAAAAAGTAAATATT
*
56222 ACAAAAAAATTAAATATT
1 ACAAAAAAAGTAAATATT
56240 A
1 A
56241 AATGGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
ACAAAAAAAGTAAATATT
Found at i:56683 original size:32 final size:31
Alignment explanation
Indices: 56642--56704 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
56632 GGTCCAAAGC
*
56642 TTATTTCAAATTATGTAACAACATATACATCA
1 TTATTTCAAAGTATGTAACAACATATA-ATCA
*
56674 TTATTTCAAAGTATGTAATAACATATAATCA
1 TTATTTCAAAGTATGTAACAACATATAATCA
56705 CAAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (31 bp):
TTATTTCAAAGTATGTAACAACATATAATCA
Found at i:57190 original size:20 final size:20
Alignment explanation
Indices: 57165--57202 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57155 CAACTCTCTG
*
57165 CTCACCCCATGATTTCCCTA
1 CTCACCCCATGAATTCCCTA
*
57185 CTCACCCCGTGAATTCCC
1 CTCACCCCATGAATTCCC
57203 ACGTCTAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.47, G:0.08, T:0.26
Consensus pattern (20 bp):
CTCACCCCATGAATTCCCTA
Found at i:62808 original size:20 final size:20
Alignment explanation
Indices: 62779--62857 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
62769 CAAGCTGCAA
62779 GAACAATATCGGTACTAGAT
1 GAACAATATCGGTACTAGAT
* * * *
62799 GAACAGTATCGATATTGAGCAA
1 GAACAATATCGGTACT-AG-AT
*
62821 GAACAATATCGGTACTGGAT
1 GAACAATATCGGTACTAGAT
* *
62841 GAACAGTACCGGTACTA
1 GAACAATATCGGTACTA
62858 AGTGCACATA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
20 28 0.62
21 3 0.07
22 14 0.31
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (20 bp):
GAACAATATCGGTACTAGAT
Found at i:68648 original size:20 final size:20
Alignment explanation
Indices: 68623--68697 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 20
68613 ACAAAGGAGC
68623 AGTATCGGTACCATACTAAG
1 AGTATCGGTACCATACTAAG
*
68643 AGTATCGGTACTACCACACTAAG
1 AGTATCGG---TACCATACTAAG
*
68666 TAGTATCGATACCA-A-TAAG
1 -AGTATCGGTACCATACTAAG
*
68685 -GTATCAGTACCAT
1 AGTATCGGTACCAT
68698 TTTAGCATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
17 10 0.22
19 4 0.09
20 9 0.20
21 5 0.11
23 11 0.24
24 7 0.15
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (20 bp):
AGTATCGGTACCATACTAAG
Found at i:71651 original size:20 final size:20
Alignment explanation
Indices: 71628--71668 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
71618 CACTGGTTAT
71628 TATAT-ATGATTTATCATGAA
1 TATATGATG-TTTATCATGAA
*
71648 TATATGATGTTTATTATGAA
1 TATATGATGTTTATCATGAA
71668 T
1 T
71669 GTTATTTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (20 bp):
TATATGATGTTTATCATGAA
Found at i:71923 original size:60 final size:61
Alignment explanation
Indices: 71847--71980 Score: 191
Period size: 60 Copynumber: 2.2 Consensus size: 61
71837 CTATGTGTAT
* * *
71847 GTGGTGGGCACGACTTTATGTGTCATAT-CAGGATCAACA-GAGAGTGTAAACTTAGTGCAG
1 GTGGTGGGCACAACTTTATGTGTCATATCCA-GATCAACACGAGAATGTAAACTTAGTACAG
*
71907 GTGGTGGGCACAACTTTATGTGTCATATCCAGATCAACACTAGAATGTAAACTTAGTACAG
1 GTGGTGGGCACAACTTTATGTGTCATATCCAGATCAACACGAGAATGTAAACTTAGTACAG
* *
71968 GAGATGGGCACAA
1 GTGGTGGGCACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 35 0.53
61 31 0.47
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (61 bp):
GTGGTGGGCACAACTTTATGTGTCATATCCAGATCAACACGAGAATGTAAACTTAGTACAG
Done.