Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003541.1 Hibiscus syriacus cultivar Beakdansim tig00007469_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: 85601
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:844 original size:23 final size:22
Alignment explanation
Indices: 812--855 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
802 TCTGAAAATC
*
812 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCG-ATATTGACCAAT
*
835 ATCAAGTCCGATATTGACCAA
1 ATCAAATCCGATATTGACCAA
856 GACCAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (22 bp):
ATCAAATCCGATATTGACCAAT
Found at i:1563 original size:20 final size:20
Alignment explanation
Indices: 1535--1624 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
1525 AAATTTCAGT
* *
1535 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1555 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
1575 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1595 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
1615 ATTGCGATTT
1 GTTGCGATTT
1625 TGTTGGTCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1933 original size:10 final size:10
Alignment explanation
Indices: 1918--1943 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1908 ATTTTAAAAT
1918 TTTATATAAA
1 TTTATATAAA
1928 TTTATATAAA
1 TTTATATAAA
1938 TTTATA
1 TTTATA
1944 AATTTGGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATATAAA
Found at i:4547 original size:4 final size:4
Alignment explanation
Indices: 4540--4577 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
4530 CAATGTATGT
4540 ATAA AT-A ATGAA ATAA AT-A ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATA
4578 CATAGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.19
4 22 0.71
5 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:4561 original size:15 final size:15
Alignment explanation
Indices: 4540--4577 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4530 CAATGTATGT
4540 ATAAATAATGAAATAA
1 ATAAATAAT-AAATAA
4556 AT-AATAAATAAATAA
1 ATAAAT-AATAAATAA
4571 ATAAATA
1 ATAAATA
4578 CATAGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAAATAATAAATAA
Found at i:4564 original size:19 final size:19
Alignment explanation
Indices: 4540--4577 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4530 CAATGTATGT
4540 ATAAAT-AATGAAATAAATA
1 ATAAATAAAT-AAATAAATA
4559 ATAAATAAATAAATAAATA
1 ATAAATAAATAAATAAATA
4578 CATAGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAAATAAATAAATAAATA
Found at i:23895 original size:51 final size:51
Alignment explanation
Indices: 23826--24000 Score: 217
Period size: 51 Copynumber: 3.4 Consensus size: 51
23816 TAGAACGAGG
* *
23826 GTCATAGTTTGGGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGA
1 GTCATAATTTGAGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGA
* ** * * *
23877 GTCATAATTTGAGTATGAAATATTCAA-ATGTTTGAGGACCAATTTAAAATGA
1 GTCATAATTTGAGGATGAAAT-TGGAATAT-TTTAAGGACTAATTTAGAATGA
** * *
23929 GTCATGGTTTGGGGATGAAATTGGAATGTTTTAAGGACTAATTTAGAATGA
1 GTCATAATTTGAGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGA
23980 GTCATAATTTGAGGATGAAAT
1 GTCATAATTTGAGGATGAAAT
24001 ATTCAAATGT
Statistics
Matches: 100, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
51 60 0.60
52 40 0.40
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (51 bp):
GTCATAATTTGAGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGA
Found at i:23928 original size:52 final size:52
Alignment explanation
Indices: 23859--24036 Score: 225
Period size: 52 Copynumber: 3.4 Consensus size: 52
23849 GAATATTTTA
* * *
23859 AGGACTAATTTAGAATGAGTCATAATTTGAGTATGAAATATTCAAATGTTTG
1 AGGACCAATTTAAAATGAGTCATAATTTGAGGATGAAATATTCAAATGTTTG
** * ** *
23911 AGGACCAATTTAAAATGAGTCATGGTTTGGGGATG-AA-ATTGGAATGTTTTA
1 AGGACCAATTTAAAATGAGTCATAATTTGAGGATGAAATATTCAAATG-TTTG
* *
23962 AGGACTAATTTAGAATGAGTCATAATTTGAGGATGAAATATTCAAATGTTTG
1 AGGACCAATTTAAAATGAGTCATAATTTGAGGATGAAATATTCAAATGTTTG
*
24014 AGGACCAGTTTAAAATGAGTCAT
1 AGGACCAATTTAAAATGAGTCAT
24037 GGTTTGGGGA
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
50 7 0.07
51 35 0.34
52 54 0.52
53 7 0.07
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (52 bp):
AGGACCAATTTAAAATGAGTCATAATTTGAGGATGAAATATTCAAATGTTTG
Found at i:23944 original size:103 final size:103
Alignment explanation
Indices: 23826--24046 Score: 406
Period size: 103 Copynumber: 2.1 Consensus size: 103
23816 TAGAACGAGG
* *
23826 GTCATAGTTTGGGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGAGTCATAATTTGAGT
1 GTCATGGTTTGGGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGAGTCATAATTTGAGG
23891 ATGAAATATTCAAATGTTTGAGGACCAATTTAAAATGA
66 ATGAAATATTCAAATGTTTGAGGACCAATTTAAAATGA
*
23929 GTCATGGTTTGGGGATGAAATTGGAATGTTTTAAGGACTAATTTAGAATGAGTCATAATTTGAGG
1 GTCATGGTTTGGGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGAGTCATAATTTGAGG
*
23994 ATGAAATATTCAAATGTTTGAGGACCAGTTTAAAATGA
66 ATGAAATATTCAAATGTTTGAGGACCAATTTAAAATGA
24032 GTCATGGTTTGGGGA
1 GTCATGGTTTGGGGA
24047 CATGTGATGC
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (103 bp):
GTCATGGTTTGGGGATGAAATTGGAATATTTTAAGGACTAATTTAGAATGAGTCATAATTTGAGG
ATGAAATATTCAAATGTTTGAGGACCAATTTAAAATGA
Found at i:35440 original size:25 final size:25
Alignment explanation
Indices: 35412--35464 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
35402 TAGGCTATGA
*
35412 AAACATAAAC-TAAAGCTATGAAAGC
1 AAACATAAACAT-AAGCTAAGAAAGC
35437 AAACATAAACATAAGCTAAGAAAGC
1 AAACATAAACATAAGCTAAGAAAGC
35462 AAA
1 AAA
35465 GCTATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.11, T:0.13
Consensus pattern (25 bp):
AAACATAAACATAAGCTAAGAAAGC
Found at i:37425 original size:3 final size:3
Alignment explanation
Indices: 37417--37460 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
37407 TAAACCTTAC
37417 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37461 CTAAAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38423 original size:21 final size:21
Alignment explanation
Indices: 38397--38437 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38387 ACAATCACGT
38397 AAAATAAATAAATAAATTATG
1 AAAATAAATAAATAAATTATG
* *
38418 AAAATAAATAATTAATTTAT
1 AAAATAAATAAATAAATTAT
38438 TGATAATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAATAAATAAATAAATTATG
Found at i:41916 original size:28 final size:29
Alignment explanation
Indices: 41858--41922 Score: 114
Period size: 28 Copynumber: 2.3 Consensus size: 29
41848 GACTCATTAG
*
41858 AATTTTATAAGTTTAAGTTTACCCTCTAA
1 AATTATATAAGTTTAAGTTTACCCTCTAA
41887 AATTATATAAGTTTAAG-TTACCCTCTAA
1 AATTATATAAGTTTAAGTTTACCCTCTAA
41915 AATTATAT
1 AATTATAT
41923 TTTAAAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 19 0.54
29 16 0.46
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (29 bp):
AATTATATAAGTTTAAGTTTACCCTCTAA
Found at i:43115 original size:32 final size:32
Alignment explanation
Indices: 42979--43116 Score: 154
Period size: 32 Copynumber: 4.3 Consensus size: 32
42969 GCTTGAGAAT
42979 CTACCCAAAGG-AGTACCTTAGGGCCTAAGAGC
1 CTACCC-AAGGAAGTACCTTAGGGCCTAAGAGC
* * * *
43011 TTACCCAAGGAAGTACATTAGGGTCTAAGAAC
1 CTACCCAAGGAAGTACCTTAGGGCCTAAGAGC
* *
43043 CTACCCAATGAAGTACCTTGGGGCCTTAA-AGC
1 CTACCCAAGGAAGTACCTTAGGGCC-TAAGAGC
* * *
43075 CTACCCAAGGAAATACCTTGGGGCCTCAGAGC
1 CTACCCAAGGAAGTACCTTAGGGCCTAAGAGC
*
43107 TTACCCAAGG
1 CTACCCAAGG
43117 TCACCATAGG
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
31 6 0.07
32 80 0.90
33 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (32 bp):
CTACCCAAGGAAGTACCTTAGGGCCTAAGAGC
Found at i:55833 original size:29 final size:31
Alignment explanation
Indices: 55790--55849 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
55780 TTTAAGGCTA
* *
55790 GTTCCATAATAACAAATATTGAAA-AAAAGT
1 GTTCCATAAAAACAAATATTAAAAGAAAAGT
55820 GTTCC-TAAAAACAAATATTAAAAGAAAAGT
1 GTTCCATAAAAACAAATATTAAAAGAAAAGT
55850 AAATTTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (31 bp):
GTTCCATAAAAACAAATATTAAAAGAAAAGT
Found at i:57693 original size:22 final size:24
Alignment explanation
Indices: 57659--57702 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
57649 CAACCCAATT
57659 TCCTATTATTTTTTTAAAAATTCG
1 TCCTATTATTTTTTTAAAAATTCG
57683 TCCT-TTA-TTTTTTAAAAATT
1 TCCTATTATTTTTTTAAAAATT
57703 TGAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (24 bp):
TCCTATTATTTTTTTAAAAATTCG
Found at i:58373 original size:60 final size:60
Alignment explanation
Indices: 58306--58418 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 60
58296 TCATGTGATC
* *
58306 ATTTTATAACTTTTAATGGGTCTAGGGACTTAACAAAGTAACATTCTAT-GTCGAAGGACT
1 ATTTTATAACTTTTAAT-AGTCTAGGAACTTAACAAAGTAACATTCTATAGTCGAAGGACT
* **
58366 ATTTTATAACTTTTAATAGTCTAGGAACTTAATAAAGTAGTATTCTATAGTCG
1 ATTTTATAACTTTTAATAGTCTAGGAACTTAACAAAGTAACATTCTATAGTCG
58419 GGGAACCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 26 0.55
60 21 0.45
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCTAGGAACTTAACAAAGTAACATTCTATAGTCGAAGGACT
Found at i:62992 original size:87 final size:90
Alignment explanation
Indices: 62815--63027 Score: 301
Period size: 87 Copynumber: 2.4 Consensus size: 90
62805 AGAGTTCATC
* * *
62815 TCAAATGATTGA-AAGTTATTTTTAAAAAGATATTGCTTTATACTAACCTTAAATTAATAAAATA
1 TCAAATGGTTGAGAA-TTATTTTTAAACAGATATTGCTTTATACTAACCTCAAATTAATAAAATA
*
62879 AATAAATAAATAGTCTGTGATGATTG
65 AATAAATAAATAGTCTATGATGATTG
* *
62905 TCAAATGGTTGAGAATTATTTTT-AACAGATATTG-TCTTATACTTATCTCAAATTAAT-AAA-A
1 TCAAATGGTTGAGAATTATTTTTAAACAGATATTGCT-TTATACTAACCTCAAATTAATAAAATA
62966 AATAAATAAATAGTCTATGATGATTG
65 AATAAATAAATAGTCTATGATGATTG
* *
62992 TCAAATGGTTGAGAGTTATTTTTGAACAGATATTGC
1 TCAAATGGTTGAGAATTATTTTTAAACAGATATTGC
63028 CTTTCGAGTA
Statistics
Matches: 112, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
87 48 0.43
88 15 0.13
89 28 0.25
90 19 0.17
91 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (90 bp):
TCAAATGGTTGAGAATTATTTTTAAACAGATATTGCTTTATACTAACCTCAAATTAATAAAATAA
ATAAATAAATAGTCTATGATGATTG
Found at i:78243 original size:21 final size:21
Alignment explanation
Indices: 78219--78263 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
78209 TTTTTAAAAA
78219 AAAAATAAAAGTTTAGGTACT
1 AAAAATAAAAGTTTAGGTACT
* * *
78240 AAAATTGATAGTTTAGGTACT
1 AAAAATAAAAGTTTAGGTACT
78261 AAA
1 AAA
78264 TGCATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (21 bp):
AAAAATAAAAGTTTAGGTACT
Found at i:78798 original size:4 final size:4
Alignment explanation
Indices: 78789--78837 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
78779 GAATTAATAC
78789 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
78837 C
1 C
78838 GCGCGCACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.51, G:0.24, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:79770 original size:18 final size:18
Alignment explanation
Indices: 79744--79784 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
79734 GAAATGTAAA
*
79744 ATTATCGGTGGGAATAAG
1 ATTACCGGTGGGAATAAG
*
79762 ATTACCGGTTGGAATAAG
1 ATTACCGGTGGGAATAAG
79780 ATTAC
1 ATTAC
79785 TGGGAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (18 bp):
ATTACCGGTGGGAATAAG
Found at i:80005 original size:36 final size:36
Alignment explanation
Indices: 79933--80005 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
79923 ATTCTACTAT
**
79933 AATTTATATATTTTCTTTAAAAAATTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTAAAAACATAA
* *
79969 AATTTATATAATTTT-TTTACAAAATTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTAAAAACATAA
80005 A
1 A
80006 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 27 0.84
37 5 0.16
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
AATTTATATATTTTCTTTAAAAAATTAAAAACATAA
Found at i:81062 original size:14 final size:14
Alignment explanation
Indices: 81045--81072 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
81035 ATCATAACAA
81045 AATTATATAACTAT
1 AATTATATAACTAT
81059 AATTATATAACTAT
1 AATTATATAACTAT
81073 TATTTCACTT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Done.