Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004262.1 Hibiscus syriacus cultivar Beakdansim tig00009337_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: 73508
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:330 original size:19 final size:20
Alignment explanation
Indices: 303--341 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
293 AAAATTTATT
303 TTATAATATGAAATTTTAAA
1 TTATAATATGAAATTTTAAA
**
323 TTAT-ATATGTTATTTTAAA
1 TTATAATATGAAATTTTAAA
342 AAATTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATAATATGAAATTTTAAA
Found at i:906 original size:18 final size:18
Alignment explanation
Indices: 883--919 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
873 TTAATTTATT
*
883 AAAATTAAATATTATATA
1 AAAATTAAATATAATATA
*
901 AAAATTAGATATAATATA
1 AAAATTAAATATAATATA
919 A
1 A
920 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATTAAATATAATATA
Found at i:5651 original size:2 final size:2
Alignment explanation
Indices: 5644--5672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5634 TATGTCATTA
5644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5673 AAAGAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9237 original size:15 final size:15
Alignment explanation
Indices: 9217--9247 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9207 CAACAGATAG
9217 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
9232 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
9247 A
1 A
9248 TTTAGAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:12927 original size:20 final size:19
Alignment explanation
Indices: 12899--12968 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
12889 CACATACAGG
12899 TTCGAAACTTTGAAGAAAGT
1 TTCGAAACTTTG-AGAAAGT
* *
12919 TTTGAAACTTTTGAGAAAGA
1 TTCGAAAC-TTTGAGAAAGT
*
12939 TTGGAAACTTTGTA-AAAGT
1 TTCGAAACTTTG-AGAAAGT
*
12958 ATCGAAACTTT
1 TTCGAAACTTT
12969 TAAACGTACT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 17 0.40
20 21 0.50
21 4 0.10
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.34
Consensus pattern (19 bp):
TTCGAAACTTTGAGAAAGT
Found at i:13191 original size:20 final size:20
Alignment explanation
Indices: 13168--13205 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13158 TATTTAAAAA
13168 ACTTTAAACACATTTTAAAC
1 ACTTTAAACACATTTTAAAC
*
13188 ACTTTAAACATATTTTAA
1 ACTTTAAACACATTTTAA
13206 TTAACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (20 bp):
ACTTTAAACACATTTTAAAC
Found at i:15021 original size:19 final size:21
Alignment explanation
Indices: 14978--15026 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
14968 TCTAAATTCT
* *
14978 TTTTCAAAATTTCATTTTTGA
1 TTTTCAAAATTCCATTTTAGA
14999 TTTTCAAAA-TCCATTTTAG-
1 TTTTCAAAATTCCATTTTAGA
15018 TTTTCAAAA
1 TTTTCAAAA
15027 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
21 9 0.35
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTCAAAATTCCATTTTAGA
Found at i:15917 original size:27 final size:21
Alignment explanation
Indices: 15864--15915 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
15854 ACTAATTTGT
15864 TCTTACCTTTCAAGGATAAGG
1 TCTTACCTTTCAAGGATAAGG
15885 TCTTACCTTTCAAGGATAAGG
1 TCTTACCTTTCAAGGATAAGG
* *
15906 TGTAACCTTT
1 TCTTACCTTT
15916 ACAACTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (21 bp):
TCTTACCTTTCAAGGATAAGG
Found at i:16252 original size:20 final size:20
Alignment explanation
Indices: 16229--16266 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16219 TGCAGTTTAG
16229 AAACTTTGAAGAAAGTTTCA
1 AAACTTTGAAGAAAGTTTCA
*
16249 AAACTTTTAAGAAAGTTT
1 AAACTTTGAAGAAAGTTT
16267 GTGAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (20 bp):
AAACTTTGAAGAAAGTTTCA
Found at i:16544 original size:20 final size:20
Alignment explanation
Indices: 16517--16562 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
16507 TTGTTTCATA
16517 TTTAAAAAGCTTTAAACACAT
1 TTTAAAAA-CTTTAAACACAT
*
16538 TTTAAAAACTTTAAACATAT
1 TTTAAAAACTTTAAACACAT
16558 TTTAA
1 TTTAA
16563 GTAACTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTAAAAACTTTAAACACAT
Found at i:20520 original size:31 final size:30
Alignment explanation
Indices: 20485--20559 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
20475 ATTCAGGGGT
* * * * *
20485 TAATATGAGAAAAGTAGCTAAATTTAATGAC
1 TAATATGAGAAAA-AAACGAAATTCAATAAC
20516 TAATATG-GAACAAAAACGAAATTCAATAAC
1 TAATATGAGAA-AAAAACGAAATTCAATAAC
20546 TAATATGAGAAAAA
1 TAATATGAGAAAAA
20560 TAAACAATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (30 bp):
TAATATGAGAAAAAAACGAAATTCAATAAC
Found at i:27262 original size:30 final size:30
Alignment explanation
Indices: 27226--27288 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
27216 TATTTCTGTT
27226 GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
1 GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
*
27256 GGTCCAGTGTGTCCTGGTCCTGGTAGTGGG
1 GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
27286 GGT
1 GGT
27289 TTGATCCGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.08, C:0.19, G:0.44, T:0.29
Consensus pattern (30 bp):
GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
Found at i:29593 original size:17 final size:17
Alignment explanation
Indices: 29571--29615 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
29561 AGATGTTAGG
29571 TAAAATTTTGAGAAAAA
1 TAAAATTTTGAGAAAAA
29588 TAAAATTTTGAGAAAAA
1 TAAAATTTTGAGAAAAA
29605 TAAAATTTTGA
1 TAAAATTTTGA
29616 TACTAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (17 bp):
TAAAATTTTGAGAAAAA
Found at i:32465 original size:13 final size:15
Alignment explanation
Indices: 32433--32467 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
32423 ATTTTTAATG
32433 AATATTAAATAAAAT
1 AATATTAAATAAAAT
32448 AATATTAAA-AAAAT
1 AATATTAAATAAAAT
32462 -ATATTA
1 AATATTA
32468 TTAGTGGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 5 0.25
15 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATTAAATAAAAT
Found at i:39466 original size:21 final size:21
Alignment explanation
Indices: 39440--39479 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39430 CAGAACCCCA
*
39440 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
39461 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
39480 TCAAAAGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:46785 original size:13 final size:13
Alignment explanation
Indices: 46767--46793 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46757 ATGAGTAAGG
46767 TTATAAACATGAT
1 TTATAAACATGAT
46780 TTATAAACATGAT
1 TTATAAACATGAT
46793 T
1 T
46794 GTGTTTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTATAAACATGAT
Found at i:47382 original size:13 final size:13
Alignment explanation
Indices: 47364--47389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47354 AGTCTCTACT
47364 TATTATATATAGA
1 TATTATATATAGA
47377 TATTATATATAGA
1 TATTATATATAGA
47390 AATGATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATTATATATAGA
Found at i:51458 original size:45 final size:45
Alignment explanation
Indices: 51404--51530 Score: 182
Period size: 46 Copynumber: 2.8 Consensus size: 45
51394 AATAAATGAT
51404 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCA
* *
51449 TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTTGAATAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGTTTA-TTTTTCGAACAAGCA
* * * *
51495 TGCAAATTAGATATCATGTGGTTAGGATTTCTTTTT
1 TGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT
51531 GTGGATAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
45 30 0.41
46 41 0.55
47 3 0.04
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (45 bp):
TGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCA
Found at i:55100 original size:23 final size:23
Alignment explanation
Indices: 55074--55122 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
55064 TTACAGCAGG
*
55074 AGAAATGATTGAAATGGCGATTA
1 AGAAATGATTGAAATGGCAATTA
55097 AGAAATGATTGAAATGGCAATTA
1 AGAAATGATTGAAATGGCAATTA
55120 AGA
1 AGA
55123 GTGGAAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (23 bp):
AGAAATGATTGAAATGGCAATTA
Found at i:59430 original size:31 final size:31
Alignment explanation
Indices: 59392--59547 Score: 253
Period size: 31 Copynumber: 5.0 Consensus size: 31
59382 AGGGTCGAGG
59392 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
59423 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
59454 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
59485 GTTTACCTATG-TCTTTCGGGACATATGGACT
1 GTTTACCTATGTTC-TTCGGGACATATGGACT
* * *
59516 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
59547 G
1 G
59548 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
30 2 0.02
31 114 0.96
32 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:63782 original size:17 final size:17
Alignment explanation
Indices: 63756--63808 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
63746 AAGAAGAAAT
63756 AAAA-GAGAAAAAATGA
1 AAAATGAGAAAAAATGA
63772 AAAATGAG-AAAAA-GA
1 AAAATGAGAAAAAATGA
63787 AAAATGATGGAAAAAATGA
1 AAAATGA--GAAAAAATGA
63806 AAA
1 AAA
63809 GAAAAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.28
16 9 0.28
17 4 0.12
18 5 0.16
19 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (17 bp):
AAAATGAGAAAAAATGA
Found at i:65247 original size:24 final size:24
Alignment explanation
Indices: 65220--65326 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
65210 AAACGGAGAT
*
65220 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
65244 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
65268 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
65292 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
65316 ATCAGAAATCA
1 ATCAGAAATCA
65327 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:65326 original size:48 final size:48
Alignment explanation
Indices: 65220--65328 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
65210 AAACGGAGAT
* * * *
65220 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
65268 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
65316 ATCAGAAATCAGA
1 ATCAGAAATCAGA
65329 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:67797 original size:7 final size:7
Alignment explanation
Indices: 67785--67822 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
67775 TGGTCAACTC
67785 CGGTCAA
1 CGGTCAA
67792 CGGTCAA
1 CGGTCAA
67799 CGGTCAA
1 CGGTCAA
67806 CGGTCAA
1 CGGTCAA
67813 CGGTCAA
1 CGGTCAA
67820 CGG
1 CGG
67823 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:67832 original size:13 final size:13
Alignment explanation
Indices: 67814--67842 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
67804 AACGGTCAAC
67814 GGTCAACGGGTCG
1 GGTCAACGGGTCG
67827 GGTCAACGGGTCG
1 GGTCAACGGGTCG
67840 GGT
1 GGT
67843 GAGGTCAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:67890 original size:18 final size:18
Alignment explanation
Indices: 67820--67892 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
67810 CAACGGTCAA
67820 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
67838 CGGGT-GAGGTCAA-----
1 CGGGTCG-GGTCAACGGGT
*
67851 C-GGTC-GGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
67867 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
67885 CGGGTCGG
1 CGGGTCGG
67893 TTGTGACCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
11 5 0.11
12 3 0.07
13 1 0.02
16 1 0.02
17 5 0.11
18 29 0.66
ACGTcount: A:0.14, C:0.21, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:69558 original size:55 final size:54
Alignment explanation
Indices: 69393--69855 Score: 486
Period size: 55 Copynumber: 8.6 Consensus size: 54
69383 TTTATGAAGA
* * * *
69393 TCGAG-TCTTATACTCTCTGAAGGAATAGGGAGCGGACATGTTTGTTAAAGA--T
1 TCGAGTTC-TATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
*
69445 T-GAGTCCTATACTCTCTGAAAGAATAGGGA---GACCTGTTTATTGAAGATTT
1 TCGAGTTCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
*
69495 TCCAAGTTCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
1 T-CGAGTTCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
*
69550 TCCGAGTTCTATACTTTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
1 T-CGAGTTCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
* * * *
69605 TCCGAGTTCTATACTCTCTGAATA-AATAGAGAGCGGACCCGTTTTATGGAAAATTGT
1 T-CGAGTTCTATACTCTCTGAA-AGAATAGGGAGCGGACCTG-TTTATTGAAGATT-T
* * *
69662 TCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-GTTTATTGAAGA---
1 TCGAGTTCTATACTCTCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTT
* * * *
69713 TCGAG-TCTTATACTCTCTGAAGGAATATGGAGCGGACCCGATTATTGAAGATTAT
1 TCGAGTTC-TATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATT-T
* * * * *
69768 TCGAGTTCTATACTCTCTGAAGGAATAGAGACCGGACCCGTTTGTTGAAGATTAT
1 TCGAGTTCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATT-T
* * *
69823 TTGAG-TCTTATACTCTCTGAATGAATAGAGAGC
1 TCGAGTTC-TATACTCTCTGAAAGAATAGGGAGC
69856 AGACACATTT
Statistics
Matches: 358, Mismatches: 32, Indels: 39
0.83 0.07 0.09
Matches are distributed among these distances:
48 14 0.04
50 4 0.01
51 68 0.19
52 29 0.08
54 2 0.01
55 192 0.54
56 46 0.13
57 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (54 bp):
TCGAGTTCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTT
Found at i:69775 original size:162 final size:160
Alignment explanation
Indices: 69383--69861 Score: 527
Period size: 162 Copynumber: 3.0 Consensus size: 160
69373 AGCAAACTCA
* * *
69383 TTTA-TGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACATGTTTGTT-AA-A-GA
1 TTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTA
* * * *
69444 TT-GAGTCCTATACTCTCTGAAAGAATAG-G-G-AGACCTG-TTTATTGAAGATTTTCCAAGTTC
66 TTCGAGTTCTATACTCTCTGAAA-AATAGAGAGCGGACCCGTTTTA-TGAAGATTTT-CAAGTCC
69504 TATACTCTCTGAAAGAATAGGGAGCGGAC-CTG
128 TATACTCTCTGAAAGAATAGGGAGCGGACACTG
* *
69536 TTTATTGAAGATTTTCCGAGT-TCTATACTTTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAA
1 TTTATTGAAGA---T-CGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAA
*
69600 GATT-TTCCGAGTTCTATACTCTCTGAATAAATAGAGAGCGGACCCGTTTTATGGAAAATTGTTC
61 GATTATT-CGAGTTCTATACTCTCTGAA-AAATAGAGAGCGGACCCGTTTTAT-GAAGATT-TTC
*
69664 AAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-G
122 AAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACTG
* * *
69702 TTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATATGGAGCGGACCCGATTATTGAAGATTA
1 TTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTA
* * ** *
69767 TTCGAGTTCTATACTCTCTGAAGGAATAGAGACCGGACCCGTTTGT-TGAAGATTATTTGAGTCT
66 TTCGAGTTCTATACTCTCTGAA-AAATAGAGAGCGGACCCGTTT-TATGAAGATT-TTCAAGTCC
* * *
69831 TATACTCTCTGAATGAATAGAGAGCAGACAC
128 TATACTCTCTGAAAGAATAGGGAGCGGACAC
69862 ATTTTGAAGA
Statistics
Matches: 277, Mismatches: 27, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
153 4 0.01
154 6 0.02
157 2 0.01
158 39 0.14
159 2 0.01
160 3 0.01
161 40 0.14
162 108 0.39
163 7 0.03
164 1 0.00
165 6 0.02
166 56 0.20
167 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (160 bp):
TTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTA
TTCGAGTTCTATACTCTCTGAAAAATAGAGAGCGGACCCGTTTTATGAAGATTTTCAAGTCCTAT
ACTCTCTGAAAGAATAGGGAGCGGACACTG
Found at i:69775 original size:217 final size:216
Alignment explanation
Indices: 69447--69855 Score: 553
Period size: 217 Copynumber: 1.9 Consensus size: 216
69437 TTAAAGATTG
69447 AGTCCTATACTCTCTGAAAGAATAGGGAGACCTGTTTATTGAAGATTTTCCAAGTTCTATACTCT
1 AGTCCTATACTCTCTGAAAGAATAGGGAGACCTGTTTATTGAAGA--TTCCAAGTTCTATACTCT
* * *
69512 CTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTCCGAGTTCTATACTTTCTGAAAGAAT
64 CTGAAAGAATAGGGAGCGGACCCGATTATTGAAGATTTTCCGAGTTCTATACTCTCTGAAAGAAT
* * *
69577 AGGGAGCGGACCTGTTTATTGAAGATT-TTCCGAGT-TCTATACTCTCTGAATAAATAGAGAGCG
129 AGAGACCGGACCCGTTTATTGAAGATTATT-CGAGTCT-TATACTCTCTGAATAAATAGAGAGCG
69640 GACCCGTTTTATGGAAAATTGTTCA
192 GACCCGTTTTATGGAAAATTGTTCA
* *
69665 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-GTTTATTGAAGA-T-CGAG-TCTTATAC
1 AGTCCTATACTCTCTGAAAGAATAGGGA---GAC-CTGTTTATTGAAGATTCCAAGTTC-TATAC
* * *
69726 TCTCTGAAGGAATATGGAGCGGACCCGATTATTGAAGATTATT-CGAGTTCTATACTCTCTGAAG
61 TCTCTGAAAGAATAGGGAGCGGACCCGATTATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAA
* * *
69790 GAATAGAGACCGGACCCGTTTGTTGAAGATTATTTGAGTCTTATACTCTCTGAATGAATAGAGAG
125 GAATAGAGACCGGACCCGTTTATTGAAGATTATTCGAGTCTTATACTCTCTGAATAAATAGAGAG
69855 C
190 C
69856 AGACACATTT
Statistics
Matches: 169, Mismatches: 14, Indels: 17
0.85 0.07 0.09
Matches are distributed among these distances:
216 2 0.01
217 118 0.70
218 33 0.20
221 15 0.09
222 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (216 bp):
AGTCCTATACTCTCTGAAAGAATAGGGAGACCTGTTTATTGAAGATTCCAAGTTCTATACTCTCT
GAAAGAATAGGGAGCGGACCCGATTATTGAAGATTTTCCGAGTTCTATACTCTCTGAAAGAATAG
AGACCGGACCCGTTTATTGAAGATTATTCGAGTCTTATACTCTCTGAATAAATAGAGAGCGGACC
CGTTTTATGGAAAATTGTTCA
Found at i:69897 original size:162 final size:160
Alignment explanation
Indices: 69393--69914 Score: 511
Period size: 162 Copynumber: 3.2 Consensus size: 160
69383 TTTATGAAGA
** * * * *
69393 TCGAGTCTTATAC-TCTCTGAAGGAATAGGGAGCGGACATGTTTGTTAAAGA--TT--GAGTCCT
1 TCGAGTCTT-TACTTC-CTGAAGGAATAGGGAGCGGACCCGATTATTGAAGATTTTCCGAGTTCT
* *
69453 ATACTCTCTGAAAGAATAGGGA--GACCTGTTTATTGAAGATTTTCCAAGT-TCTATACTCTCTG
64 ATACTCTCTGAAAGAATAGAGACGGACCCGTTT-TTGAAGATTTT-CAAGTCT-TATACTCTCTG
69515 AAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTT
126 AAAGAATAGGGAGCGGACAC-GTTTATTGAAGATTT
* * * * *
69550 TCCGAGTTCTATACTTTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTCCGAGTTCT
1 T-CGAG-TCTTTACTTCCTGAAGGAATAGGGAGCGGACCCGATTATTGAAGATTTTCCGAGTTCT
* *
69615 ATACTCTCTGAATA-AATAGAGAGCGGACCCGTTTTATGGAAAATTGTTCAAGTCCTATACTCTC
64 ATACTCTCTGAA-AGAATAGAGA-CGGACCCGTTTT-T-GAAGATT-TTCAAGTCTTATACTCTC
*
69679 TGAAGGAATAGGGAGCGGACACGTTTATTGAAGA---
124 TGAAAGAATAGGGAGCGGACACGTTTATTGAAGATTT
*
69713 TCGAGTCTTATAC-TCTCTGAAGGAATATGGAGCGGACCCGATTATTGAAGATTATT-CGAGTTC
1 TCGAGTCTT-TACTTC-CTGAAGGAATAGGGAGCGGACCCGATTATTGAAGATT-TTCCGAGTTC
* **
69776 TATACTCTCTGAAGGAATAGAGACCGGACCCGTTTGTTGAAGATTATTTGAGTCTTATACTCTCT
63 TATACTCTCTGAAAGAATAGAGA-CGGACCCGTTT-TTGAAGATT-TTCAAGTCTTATACTCTCT
* * * *
69841 GAATGAATAGAGAGCAGACAC-ATT-TTGAAGATTGT
125 GAAAGAATAGGGAGCGGACACGTTTATTGAAGATT-T
* *
69876 TCGAGTCTTTACTTCCTGAAGGAATGGGGAGCAGACCCG
1 TCGAGTCTTTACTTCCTGAAGGAATAGGGAGCGGACCCG
69915 CCATTTGAAG
Statistics
Matches: 307, Mismatches: 32, Indels: 47
0.80 0.08 0.12
Matches are distributed among these distances:
157 1 0.00
158 38 0.12
159 11 0.04
160 4 0.01
161 44 0.14
162 129 0.42
163 16 0.05
164 1 0.00
165 9 0.03
166 51 0.17
167 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (160 bp):
TCGAGTCTTTACTTCCTGAAGGAATAGGGAGCGGACCCGATTATTGAAGATTTTCCGAGTTCTAT
ACTCTCTGAAAGAATAGAGACGGACCCGTTTTTGAAGATTTTCAAGTCTTATACTCTCTGAAAGA
ATAGGGAGCGGACACGTTTATTGAAGATTT
Done.