Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004969.1 Hibiscus syriacus cultivar Beakdansim tig00011162_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: 61018
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:19496 original size:24 final size:24
Alignment explanation
Indices: 19469--19540 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
19459 AAACGGAGAT
*
19469 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
19493 ATCAGATATCAGAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
19517 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
19541 GTAATGTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:19498 original size:12 final size:12
Alignment explanation
Indices: 19471--19540 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
19461 ACGGAGATAT
* *
19471 CAGAAATCAAAA
1 CAGAATTCAGAA
*
19483 CAGAATTCAGAT
1 CAGAATTCAGAA
19495 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
19507 CATAATCCAGAT
1 CAGAATTCAGAA
*
19519 CAGAAATCAGAA
1 CAGAATTCAGAA
19531 CAGAATTCAG
1 CAGAATTCAG
19541 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:19540 original size:48 final size:47
Alignment explanation
Indices: 19469--19577 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 47
19459 AAACGGAGAT
* *
19469 ATCAGAAATCAAAACAGAATTCAGATCA-GATATCAGAACATAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAATG-TATCAGAACATAATCCA
* *
19516 GATCAGAAATCAGAACAGAATTCAGGTAATGTATCAGAACATAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACATAATCCA
*
19564 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
19578 TAAAATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACATAATCCA
Found at i:20726 original size:18 final size:18
Alignment explanation
Indices: 20705--20740 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20695 CTTCCATCCG
*
20705 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
20723 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
20741 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:22069 original size:15 final size:15
Alignment explanation
Indices: 22049--22080 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22039 TCAACGACAA
22049 TCAACGGCCAACGGG
1 TCAACGGCCAACGGG
*
22064 TCAACGGTCAACGGG
1 TCAACGGCCAACGGG
22079 TC
1 TC
22081 GAGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.12
Consensus pattern (15 bp):
TCAACGGCCAACGGG
Found at i:22098 original size:5 final size:5
Alignment explanation
Indices: 22088--22143 Score: 58
Period size: 5 Copynumber: 10.0 Consensus size: 5
22078 GTCGAGTCAA
22088 CGGGT CGGGT CGGGT CGGGT AAACGGGT CGGGT CGGGT CAACGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT CGGGT
22139 CGGGT
1 CGGGT
22144 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 35 0.78
8 10 0.22
ACGTcount: A:0.09, C:0.20, G:0.54, T:0.18
Consensus pattern (5 bp):
CGGGT
Found at i:22098 original size:18 final size:18
Alignment explanation
Indices: 22093--22143 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
22083 GTCAACGGGT
22093 CGGGTCGGGTCGGGTAAA
1 CGGGTCGGGTCGGGTAAA
*
22111 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTAAA
22129 CGGGTCGGGTCGGGT
1 CGGGTCGGGTCGGGT
22144 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.10, C:0.20, G:0.53, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTAAA
Found at i:22112 original size:23 final size:23
Alignment explanation
Indices: 22075--22126 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
22065 CAACGGTCAA
*
22075 CGGGTCGAGTCAACGGGTCGGGT
1 CGGGTCGAGTAAACGGGTCGGGT
*
22098 CGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCGAGTAAACGGGTCGGGT
22121 CGGGTC
1 CGGGTC
22127 AACGGGTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (23 bp):
CGGGTCGAGTAAACGGGTCGGGT
Found at i:22139 original size:13 final size:13
Alignment explanation
Indices: 22069--22121 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
22059 ACGGGTCAAC
22069 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
22082 AGTCAACGGGTCG
1 GGTCAACGGGTCG
22095 GGT---CGGGTCG
1 GGTCAACGGGTCG
*
22105 GGTAAACGGGTCG
1 GGTCAACGGGTCG
22118 GGTC
1 GGTC
22122 GGGTCAACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 10 0.29
13 24 0.71
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:27537 original size:33 final size:33
Alignment explanation
Indices: 27500--27562 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
27490 ATTACGAATT
27500 TGTTAATAATTACCAATAT-AGGCCTTCAATCTA
1 TGTTAATAATTACCAATATGA-GCCTTCAATCTA
**
27533 TGTTAATAATTATTAATATGAGCCTTCAAT
1 TGTTAATAATTACCAATATGAGCCTTCAAT
27563 ATACATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (33 bp):
TGTTAATAATTACCAATATGAGCCTTCAATCTA
Found at i:31010 original size:23 final size:23
Alignment explanation
Indices: 30982--31036 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
30972 CAAAATGATC
30982 ATTTTGATAAAAATTGATAACTA
1 ATTTTGATAAAAATTGATAACTA
31005 ATTTTGATAAAAATTGATAACTA
1 ATTTTGATAAAAATTGATAACTA
31028 ATTTTGATA
1 ATTTTGATA
31037 TAATGCCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (23 bp):
ATTTTGATAAAAATTGATAACTA
Found at i:31013 original size:13 final size:13
Alignment explanation
Indices: 30995--31036 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
30985 TTGATAAAAA
30995 TTGATAACTAATT
1 TTGATAACTAATT
*
31008 TTGATAA--AA-A
1 TTGATAACTAATT
31018 TTGATAACTAATT
1 TTGATAACTAATT
31031 TTGATA
1 TTGATA
31037 TAATGCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (13 bp):
TTGATAACTAATT
Found at i:32720 original size:18 final size:18
Alignment explanation
Indices: 32692--32743 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
32682 GATCAACTCT
32692 GGTCAAAGTCAACGGGTC
1 GGTCAAAGTCAACGGGTC
*
32710 GGGTC-AAGTCAATGGGTC
1 -GGTCAAAGTCAACGGGTC
32728 GGTCAAAGTCAACGGG
1 GGTCAAAGTCAACGGG
32744 ACAGATTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 4 0.13
18 22 0.73
19 4 0.13
ACGTcount: A:0.27, C:0.19, G:0.37, T:0.17
Consensus pattern (18 bp):
GGTCAAAGTCAACGGGTC
Found at i:34056 original size:267 final size:256
Alignment explanation
Indices: 33553--34079 Score: 885
Period size: 267 Copynumber: 2.0 Consensus size: 256
33543 TTTCAGTTGA
*
33553 ATATTGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
1 ATATGGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
33618 AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTTTGGGTGTGACA
66 AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTTTGGGTGTGACA
33683 TTTTTTGTGTGTGTAACAGAATCGATGTGTAGGTCCATTGGGTGTAATCGAGTCGGGAGTTTGAA
131 TTTTTTGTGTGTGTAACAGAATCGATGTGTAGGTCCATTGGGTGTAATCGAGTCGGGAGTTTGAA
*
33748 AACGATAAATTTGAGCTTGTTTCAACCAAACACCAACTTTTAAGTTTGAATACGATTTAAG
196 AACGATAAATTTGAGCTTGCTTCAACCAAACACCAACTTTTAAGTTTGAATACGATTTAAG
33809 ATATGGGTAAATTATGGGGCTAGTCCCTAAAC-TCCTAAACTTTTGAAATTAGCCCAAAATTTTT
1 ATATGGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
*
33873 AGAAACGTATAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTCAAATAAATTTT
66 AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAA-TTT---TAAA--T-AAAT---TTTT
*
33938 GGGGTGTGACATTTTTTGTGTGTGTGACAGAATCGATGTGTAGGTCCATTGGGATGTAATCGAGT
121 -GGGTGTGACATTTTTTGTGTGTGTAACAGAATCGATGTGTAGGTCCATTGGG-TGTAATCGAGT
**
34003 CGGGAGTTTGAAAACGATAAATTTGAGCTTGCTTCAACCAAATGCCAACTTTTAAGTTTGAATAC
184 CGGGAGTTTGAAAACGATAAATTTGAGCTTGCTTCAACCAAACACCAACTTTTAAGTTTGAATAC
34068 GATTTAAG
249 GATTTAAG
34076 ATAT
1 ATAT
34080 AATTCAATTA
Statistics
Matches: 253, Mismatches: 6, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
255 70 0.28
256 34 0.13
259 4 0.02
261 1 0.00
262 4 0.02
265 4 0.02
266 51 0.20
267 85 0.34
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (256 bp):
ATATGGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTTTGGGTGTGACA
TTTTTTGTGTGTGTAACAGAATCGATGTGTAGGTCCATTGGGTGTAATCGAGTCGGGAGTTTGAA
AACGATAAATTTGAGCTTGCTTCAACCAAACACCAACTTTTAAGTTTGAATACGATTTAAG
Found at i:40217 original size:2 final size:2
Alignment explanation
Indices: 40210--40238 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40200 TTAAAAAGTA
40210 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
40239 AATTAAAAAA
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:45967 original size:6 final size:6
Alignment explanation
Indices: 45943--46002 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
45933 TGGAGCTTGG
* *
45943 AGGAGA A-GAGA A-GATGA AGGAGA AGGAAA AGAAGA AGGAGA AGGAGA
1 AGGAGA AGGAGA AGGA-GA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
45990 AGGAGA A-GAGA AG
1 AGGAGA AGGAGA AG
46003 AAAAAGACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 12 0.26
6 33 0.70
7 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (6 bp):
AGGAGA
Found at i:47112 original size:41 final size:41
Alignment explanation
Indices: 47064--47149 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
47054 TTACTGACTT
*
47064 ATTGAAGGCTAATAACAAAGGGTCGATATCGATACTCTTTC
1 ATTGAAGGCTAATAACAAAGGGTCGATATCAATACTCTTTC
* *
47105 ATTGAAGGTTGATAACAAAGGGTCGATATCAATACTCTTTC
1 ATTGAAGGCTAATAACAAAGGGTCGATATCAATACTCTTTC
47146 -TTGA
1 ATTGA
47150 GTATCGATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.10
41 38 0.90
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (41 bp):
ATTGAAGGCTAATAACAAAGGGTCGATATCAATACTCTTTC
Found at i:51642 original size:14 final size:14
Alignment explanation
Indices: 51623--51649 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51613 TTTTTTAGTA
51623 GTATCGATACCATG
1 GTATCGATACCATG
51637 GTATCGATACCAT
1 GTATCGATACCAT
51650 TCAAGTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
GTATCGATACCATG
Found at i:51725 original size:20 final size:20
Alignment explanation
Indices: 51700--51770 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
51690 ATAAGAACAA
*
51700 TATCGATACTACGCTAGTAG
1 TATCGATACTAAGCTAGTAG
* *
51720 TATCGATACCAAGCAAGAGTAG
1 TATCGATACTAAGC--TAGTAG
*
51742 TATCGATACTATG-TGAGTAG
1 TATCGATACTAAGCT-AGTAG
51762 TATCGATAC
1 TATCGATAC
51771 CAAGTGCACA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 26 0.62
22 16 0.38
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (20 bp):
TATCGATACTAAGCTAGTAG
Found at i:51743 original size:22 final size:20
Alignment explanation
Indices: 51715--51774 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
51705 ATACTACGCT
51715 AGTAGTATCGATACCAAGCAAG
1 AGTAGTATCGATACCAAG--AG
* * *
51737 AGTAGTATCGATACTATGTG
1 AGTAGTATCGATACCAAGAG
51757 AGTAGTATCGATACCAAG
1 AGTAGTATCGATACCAAG
51775 TGCACAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
22 16 0.48
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (20 bp):
AGTAGTATCGATACCAAGAG
Found at i:57559 original size:20 final size:21
Alignment explanation
Indices: 57534--57574 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
57524 AACCAAAGGA
57534 GTAGTATC-GATACTAC-ATAG
1 GTAGTATCAG-TACTACTATAG
57554 GTAGTATCAGTACTACTATAG
1 GTAGTATCAGTACTACTATAG
57575 CGTATAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (21 bp):
GTAGTATCAGTACTACTATAG
Done.