Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003458.1 Hibiscus syriacus cultivar Beakdansim tig00007307_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: 110590
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5768 original size:23 final size:22
Alignment explanation
Indices: 5715--5774 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
5705 TAAGGTGTCA
5715 TTTTGAAAGGTGTCAAAACTTT
1 TTTTGAAAGGTGTCAAAACTTT
5737 TTTTGAAAGGTGTCAAAAC-TT
1 TTTTGAAAGGTGTCAAAACTTT
5758 TTTTGAAAAAGGTGTCA
1 TTTTG--AAAGGTGTCA
5775 TTTTCTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.19
22 19 0.53
23 10 0.28
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (22 bp):
TTTTGAAAGGTGTCAAAACTTT
Found at i:6492 original size:15 final size:14
Alignment explanation
Indices: 6462--6520 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
6452 ATTAAATTAT
* *
6462 AAACAAAAACTCTA
1 AAACATAAACCCTA
*
6476 AAACCATAAACCTTA
1 AAA-CATAAACCCTA
6491 AAACATAAACCCTA
1 AAACATAAACCCTA
* * *
6505 AATCTTATACCCTA
1 AAACATAAACCCTA
6519 AA
1 AA
6521 CTCAAAACCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACATAAACCCTA
Found at i:6560 original size:14 final size:14
Alignment explanation
Indices: 6541--6568 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6531 AAAACTCTAC
6541 TAAACCTTAACCTT
1 TAAACCTTAACCTT
6555 TAAACCTTAACCTT
1 TAAACCTTAACCTT
6569 AAATATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAACCTTAACCTT
Found at i:12415 original size:33 final size:32
Alignment explanation
Indices: 12363--12431 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
12353 TTTATTTTGT
*
12363 TCGGGTCGGATTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGATTTTTTAAGTGTCATATTCGGG
*
12395 TCGGGTCGAGTTTTTTTAAGTGTCATATTCGGG
1 TCGGGTCG-GATTTTTTAAGTGTCATATTCGGG
12428 TCGG
1 TCGG
12432 TAACATTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.41
Consensus pattern (32 bp):
TCGGGTCGGATTTTTTAAGTGTCATATTCGGG
Found at i:13908 original size:3 final size:3
Alignment explanation
Indices: 13900--13951 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
13890 TGTAAATCAA
13900 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13948 AAT A
1 AAT A
13952 GAGTTTACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21978 original size:14 final size:14
Alignment explanation
Indices: 21955--22010 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
21945 TGTTTGTGAA
21955 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
21969 CGTTCTGTTATG-T
1 CGTTCGGTTATGTT
*
21982 --TT-GTTTATGTT
1 CGTTCGGTTATGTT
21993 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
22007 CGTT
1 CGTT
22011 TATGTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 5 0.15
11 3 0.09
13 3 0.09
14 23 0.68
ACGTcount: A:0.07, C:0.12, G:0.25, T:0.55
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:21994 original size:24 final size:24
Alignment explanation
Indices: 21962--22031 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
21952 GAACGTTCGG
21962 TTATGTTCGTTCTGTTATGTTTGT
1 TTATGTTCGTTCTGTTATGTTTGT
* *
21986 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCTGTTATGTTTGT
*
22010 TTATGTTCATTCAT-TTATGTTT
1 TTATGTTCGTTC-TGTTATGTTT
22032 AACCCAATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (24 bp):
TTATGTTCGTTCTGTTATGTTTGT
Found at i:22027 original size:38 final size:37
Alignment explanation
Indices: 21955--22030 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
21945 TGTTTGTGAA
* **
21955 CGTTCGGTTATGTTCGTTCTGTTATGTTTGTTTATGTT
1 CGTTCGGTTATGTTCGTTATGTTA-GTTCATTTATGTT
21993 CGTTCGGTTATGTTCGTTTATGTTCA-TTCATTTATGTT
1 CGTTCGGTTATGTTCG-TTATGTT-AGTTCATTTATGTT
22031 TAACCCAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 26 0.79
39 6 0.18
40 1 0.03
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.57
Consensus pattern (37 bp):
CGTTCGGTTATGTTCGTTATGTTAGTTCATTTATGTT
Found at i:22846 original size:11 final size:11
Alignment explanation
Indices: 22830--22881 Score: 86
Period size: 11 Copynumber: 4.6 Consensus size: 11
22820 TGGGGCAATG
22830 TCGAGCTTGAA
1 TCGAGCTTGAA
22841 TCGAGCTTAGAA
1 TCGAGCTT-GAA
*
22853 TTGAGCTTGAA
1 TCGAGCTTGAA
22864 TCGAGCTTGAA
1 TCGAGCTTGAA
22875 TCGAGCT
1 TCGAGCT
22882 CAAGTCTCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:22862 original size:23 final size:22
Alignment explanation
Indices: 22830--22881 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
22820 TGGGGCAATG
22830 TCGAGCTTGAATCGAGCTTAGAA
1 TCGAGCTTGAATCGAGCTT-GAA
*
22853 TTGAGCTTGAATCGAGCTTGAA
1 TCGAGCTTGAATCGAGCTTGAA
22875 TCGAGCT
1 TCGAGCT
22882 CAAGTCTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (22 bp):
TCGAGCTTGAATCGAGCTTGAA
Found at i:23137 original size:16 final size:16
Alignment explanation
Indices: 23116--23164 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
23106 CCAACGTTTA
23116 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23132 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
**
23148 TGCGCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23164 T
1 T
23165 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.06, C:0.14, G:0.27, T:0.53
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:23168 original size:10 final size:10
Alignment explanation
Indices: 23110--23148 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
23100 GGGTCTCCAA
23110 CGTTTATGTT
1 CGTTTATGTT
23120 CGTTTATGTT
1 CGTTTATGTT
23130 CG----TGTT
1 CGTTTATGTT
23136 CGTTTATGTT
1 CGTTTATGTT
23146 CGT
1 CGT
23149 GCGCGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.24
10 19 0.76
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:23254 original size:16 final size:16
Alignment explanation
Indices: 23233--23263 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23223 AAAAAAAAAT
23233 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23249 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
23264 CTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:24081 original size:30 final size:32
Alignment explanation
Indices: 24038--24110 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 32
24028 AATATTGAAA
24038 TAATTTATCTATTTTATTTAAATAA-AAATATTG
1 TAATTT-T-TATTTTATTTAAATAATAAATATTG
* *
24071 T-ATTTTTATTTTATTTAAATAATAATTATTT
1 TAATTTTTATTTTATTTAAATAATAAATATTG
24102 TAATTTTTA
1 TAATTTTTA
24111 ATAATATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 16 0.44
31 8 0.22
32 11 0.31
33 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (32 bp):
TAATTTTTATTTTATTTAAATAATAAATATTG
Found at i:24572 original size:31 final size:31
Alignment explanation
Indices: 24536--24598 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
24526 CTAATATCAA
24536 ATTGATATTCTATTTAAATTTCAGGGGTGAT
1 ATTGATATTCTATTTAAATTTCAGGGGTGAT
*
24567 ATTGATATTTTATTTAAATTTCAGGGGTGAT
1 ATTGATATTCTATTTAAATTTCAGGGGTGAT
24598 A
1 A
24599 ATAAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (31 bp):
ATTGATATTCTATTTAAATTTCAGGGGTGAT
Found at i:27076 original size:20 final size:20
Alignment explanation
Indices: 27039--27075 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
27029 AGGTTGGTTG
27039 TATTAAAAATAATATTTTAA
1 TATTAAAAATAATATTTTAA
*
27059 TATTAAATA-AATATTTT
1 TATTAAAAATAATATTTT
27076 TTTGATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAAAATAATATTTTAA
Found at i:27456 original size:16 final size:16
Alignment explanation
Indices: 27431--27465 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27421 GGCATCGTTC
*
27431 ATCTTCGCATTTGTAT
1 ATCTTCGCATTTGCAT
*
27447 ATCTTTGCATTTGCAT
1 ATCTTCGCATTTGCAT
27463 ATC
1 ATC
27466 CAAGCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (16 bp):
ATCTTCGCATTTGCAT
Found at i:28450 original size:54 final size:53
Alignment explanation
Indices: 28367--28477 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
28357 TCTAAATCTT
* * *
28367 ATAAACCCTGATTAACTAAGTTCCTAGTTCACTGCACCCAA-AACCCTAAATACA
1 ATAAACCCCGATTAACTAAATTCCGAGTTCACTG--CCCAACAACCCTAAATACA
* * *
28421 ATAAACCCCGGTTAATTAAATTCCGAGTTCACTGCCCAACAACCCTAAATCCA
1 ATAAACCCCGATTAACTAAATTCCGAGTTCACTGCCCAACAACCCTAAATACA
28474 ATAA
1 ATAA
28478 CAGTTGTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 5 0.10
53 16 0.32
54 29 0.58
ACGTcount: A:0.39, C:0.30, G:0.08, T:0.23
Consensus pattern (53 bp):
ATAAACCCCGATTAACTAAATTCCGAGTTCACTGCCCAACAACCCTAAATACA
Found at i:30770 original size:2 final size:2
Alignment explanation
Indices: 30763--30791 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30753 TTAAATTATT
30763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30792 TCTTTAACAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36189 original size:89 final size:88
Alignment explanation
Indices: 36034--36197 Score: 256
Period size: 89 Copynumber: 1.9 Consensus size: 88
36024 TGCATCCAAA
* * *
36034 TTGAATTCGGTTAATGTATATTTTTAATTGCTTTGATTTACTTTAAATTGTCATTTTTATGAACT
1 TTGAATTCGGTTAATGTAGAATTTTAATTGCTTTAATTTACTTTAAATTGTCATTTTTATGAACT
36099 TATTTGGTGATGGTGAACGCATT
66 TATTTGGTGATGGTGAACGCATT
* ** *
36122 TTGAATTCGTTTAATGTAGAATTTTAATTGCTTTAAATTTGTTTTAAATTTTCATTTTTATGAAC
1 TTGAATTCGGTTAATGTAGAATTTTAATTGCTTT-AATTTACTTTAAATTGTCATTTTTATGAAC
36187 TTATTTGGTGA
65 TTATTTGGTGA
36198 ACACTCTCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
88 31 0.46
89 37 0.54
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (88 bp):
TTGAATTCGGTTAATGTAGAATTTTAATTGCTTTAATTTACTTTAAATTGTCATTTTTATGAACT
TATTTGGTGATGGTGAACGCATT
Found at i:41912 original size:207 final size:207
Alignment explanation
Indices: 41631--42025 Score: 603
Period size: 207 Copynumber: 1.9 Consensus size: 207
41621 GAAAGTGCCA
* * * *
41631 AAGGTGTCACCGCCTCGTAGAAAAGCAACAAGAGAAGAAAAACCAGTGAAGATGAGGAATATGGC
1 AAGGTGTCACCACCTCGTAGAAAAACAACAAGAGAAGAAAAACCAGAGAAGATGAGAAATATGGC
* * *
41696 CAAGAAAGATGGTGGAAGTTCTGATTTGTCCACTTCAAACTCTAGGCAAGCGAATGCTGTTAATA
66 CAAGAAAGATGGAGGAAGATCTGATTTGTCCACTTCAAACTCTAGGCAAGCGAACGCTGTTAATA
* * **
41761 ATTATGAAGCAAATAACTTTGGATATAGACAATATGATCCCGAGCCTCCCACTGATGATACAGAA
131 ATTATGAAACAAATAACGTTACATATAGACAATATGATCCCGAGCCTCCCACTGATGATACAGAA
41826 GAGAAAGTAATG
196 GAGAAAGTAATG
*
41838 AAGGTGTCACCACCTCGTAGAAAAACAA-ATAGAGAAGAAAAACCGGAGAAGATGAGAAATATGG
1 AAGGTGTCACCACCTCGTAGAAAAACAACA-AGAGAAGAAAAACCAGAGAAGATGAGAAATATGG
* * ** *
41902 CCATGAAAGATGGAGGAGGATCTGATTTGTCTGCTTCAAACTCTAGGCAGGCGAACGCTGTTAAT
65 CCAAGAAAGATGGAGGAAGATCTGATTTGTCCACTTCAAACTCTAGGCAAGCGAACGCTGTTAAT
* *
41967 AATTATGAAACAAGTAACGTTACATATAGACAATATGATCCTGAGCCTCCCACTGATGA
130 AATTATGAAACAAATAACGTTACATATAGACAATATGATCCCGAGCCTCCCACTGATGA
42026 GAATATCAAT
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
206 1 0.01
207 167 0.99
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (207 bp):
AAGGTGTCACCACCTCGTAGAAAAACAACAAGAGAAGAAAAACCAGAGAAGATGAGAAATATGGC
CAAGAAAGATGGAGGAAGATCTGATTTGTCCACTTCAAACTCTAGGCAAGCGAACGCTGTTAATA
ATTATGAAACAAATAACGTTACATATAGACAATATGATCCCGAGCCTCCCACTGATGATACAGAA
GAGAAAGTAATG
Found at i:63978 original size:22 final size:22
Alignment explanation
Indices: 63944--63991 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
63934 ATTAACTTAA
*
63944 AAATAAAATTTATATAATA-AT
1 AAATAAAAGTTATATAATATAT
*
63965 AAATAAAAAGTTATTTAATATAT
1 AAAT-AAAAGTTATATAATATAT
63988 AAAT
1 AAAT
63992 TTTAATTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATAAAAGTTATATAATATAT
Found at i:96970 original size:17 final size:17
Alignment explanation
Indices: 96921--96962 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
96911 ATATTTTTAT
*
96921 TTAATTATAATAATTAAA
1 TTAATAATAATAA-TAAA
96939 TTAATAATAATAATAAA
1 TTAATAATAATAATAAA
96956 TTAATAA
1 TTAATAA
96963 ATATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAATAATAATAATAAA
Found at i:106952 original size:14 final size:14
Alignment explanation
Indices: 106933--106965 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
106923 TGGGGAGTAA
*
106933 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
106947 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
106961 TCCCT
1 TCCCT
106966 ACATAGAAAT
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:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Done.