Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006997.1 Hibiscus syriacus cultivar Beakdansim tig00018043_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: 61774
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:9869 original size:21 final size:20
Alignment explanation
Indices: 9815--9883 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
9805 CGACTTATTC
9815 TTTTT-TAATTTTTTAATTAT
1 TTTTTATAATTTTTTAATT-T
**
9835 TTTACAATATATTTGTTTAATTT
1 TTT-TTATA-ATTT-TTTAATTT
*
9858 TTTTTATAATTTATATAATTT
1 TTTTTATAATTT-TTTAATTT
9879 TTTTT
1 TTTTT
9884 TATTATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 3 0.08
21 16 0.41
22 5 0.13
23 8 0.21
24 7 0.18
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (20 bp):
TTTTTATAATTTTTTAATTT
Found at i:12861 original size:21 final size:21
Alignment explanation
Indices: 12837--12878 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12827 AAATCTAATT
*
12837 ATTTTTTCTTT-TCCAAATATC
1 ATTTTTTATTTAT-CAAATATC
12858 ATTTTTTATTTATCAAATATC
1 ATTTTTTATTTATCAAATATC
12879 CTTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTATTTATCAAATATC
Found at i:19153 original size:15 final size:15
Alignment explanation
Indices: 19135--19185 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
19125 GTAGGGACTA
19135 AAAAGTGTAAATTTC
1 AAAAGTGTAAATTTC
****
19150 AAAAGT-TCAAGGACC
1 AAAAGTGT-AAATTTC
19165 AAAAGTGTAAATTTC
1 AAAAGTGTAAATTTC
19180 AAAAGT
1 AAAAGT
19186 ATGTATTTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (15 bp):
AAAAGTGTAAATTTC
Found at i:22031 original size:177 final size:177
Alignment explanation
Indices: 21698--22047 Score: 504
Period size: 177 Copynumber: 2.0 Consensus size: 177
21688 AGTATGATGA
* * * * * *
21698 TTATCGATCGATTTGGTTTGATTCATTATTTCGTTCTTGTAGTAGTACATTTGTTTTACTATGGC
1 TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
* * * *
21763 ACTATGTGTGCTAGGATGGTGTTCATAATGAATTACCACTCTGTAATTGTTAGTATAATGTCGTT
66 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCACTATGGAATTGTTAGTATAATGTCCTT
* * * *
21828 GTGTACTACAATTCCTATATGTCATTGTAGCACTTAAGTACTACATG
131 GTGGACTAAAATACCTATACGTCATTGTAGCACTTAAGTACTACATG
* * * *
21875 TTATCTATCGATTTTGTTTAATGCATTATTGCGTTTTTGTAGTAGTATATTTGTTGTACCATAGC
1 TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
*
21940 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCATTATGGAATTGTTAGTATAGA-GTCCT
66 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCACTATGGAATTGTTAGTATA-ATGTCCT
*
22004 TGTGGACTAAAATACCTATACGTCATTGTAGCACTTAGGTACTA
130 TGTGGACTAAAATACCTATACGTCATTGTAGCACTTAAGTACTA
22048 ATTGTGTACC
Statistics
Matches: 152, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
177 151 0.99
178 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (177 bp):
TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCACTATGGAATTGTTAGTATAATGTCCTT
GTGGACTAAAATACCTATACGTCATTGTAGCACTTAAGTACTACATG
Found at i:24893 original size:79 final size:79
Alignment explanation
Indices: 24762--25157 Score: 568
Period size: 79 Copynumber: 5.1 Consensus size: 79
24752 AAAACAAATG
* *
24762 AAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
24827 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* * *
24841 AAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATTCAATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
24906 TACATTGTCAGCAT
66 TACATTGTCAGCAT
*
24920 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
24985 TAAATTGTCAGCAT
66 TACATTGTCAGCAT
* * *
24999 AAAAGAATAATTCATATGGGTGAATTATTGGCATGAATGGATGCCATAACTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* *
25064 TACATTTTCAGTAT
66 TACATTGTCAGCAT
* * * ** *
25078 AAAAGAATAAAT-CATAT---TG-GTTATTGGCATGAAAAGATGCCATCGCTGAAATACATATGA
1 AAAAGAAT-AATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
* *
25138 GTGCATTATCAGCAT
65 GTACATTGTCAGCAT
25153 AAAAG
1 AAAAG
25158 TATATTTTAT
Statistics
Matches: 290, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
75 50 0.17
76 2 0.01
79 235 0.81
80 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
TACATTGTCAGCAT
Found at i:29142 original size:30 final size:30
Alignment explanation
Indices: 29106--29168 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
29096 GAAATCAAAG
29106 ACTTTGAAATAAAAGTGGATGGATGTCTAT
1 ACTTTGAAATAAAAGTGGATGGATGTCTAT
29136 ACTTTGAAATAAAAGTGGATGGATGTCTAT
1 ACTTTGAAATAAAAGTGGATGGATGTCTAT
29166 ACT
1 ACT
29169 ATAAGGGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (30 bp):
ACTTTGAAATAAAAGTGGATGGATGTCTAT
Found at i:29860 original size:15 final size:15
Alignment explanation
Indices: 29840--29870 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29830 TCAAGTATTC
29840 TAATAGGGCGAGCCA
1 TAATAGGGCGAGCCA
29855 TAATAGGGCGAGCCA
1 TAATAGGGCGAGCCA
29870 T
1 T
29871 TCAGAGCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (15 bp):
TAATAGGGCGAGCCA
Found at i:37994 original size:79 final size:79
Alignment explanation
Indices: 37858--38099 Score: 394
Period size: 79 Copynumber: 3.1 Consensus size: 79
37848 AAAACGAATG
* * *
37858 AAAATAATAATGCATATGGGGGTATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
37923 TACATTGTCAGTAT
66 TACATTGTCAGCAT
*
37937 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
38002 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* * *
38016 AAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCATCGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* *
38081 TGCATTATCAGCAT
66 TACATTGTCAGCAT
38095 AAAAG
1 AAAAG
38100 TATATATTTT
Statistics
Matches: 152, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 152 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
TACATTGTCAGCAT
Found at i:39321 original size:62 final size:62
Alignment explanation
Indices: 39220--39347 Score: 202
Period size: 62 Copynumber: 2.1 Consensus size: 62
39210 GAAGTATCAG
*
39220 TACTCTCTACAAGGGTATCGATACTCGTGGTCCAATATCAATACTCAAAGGGTCAATATCGA
1 TACTCTCTACAAGGGTATCGATACTCGTGATCCAATATCAATACTCAAAGGGTCAATATCGA
* * * * *
39282 TACTCTCTATAAGGGTATCTATACTCGTGATCCAGTATCAATACTCAGAGGGTCAGTATCGA
1 TACTCTCTACAAGGGTATCGATACTCGTGATCCAATATCAATACTCAAAGGGTCAATATCGA
39344 TACT
1 TACT
39348 GAGGCATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (62 bp):
TACTCTCTACAAGGGTATCGATACTCGTGATCCAATATCAATACTCAAAGGGTCAATATCGA
Found at i:41320 original size:59 final size:58
Alignment explanation
Indices: 41246--41700 Score: 583
Period size: 59 Copynumber: 7.8 Consensus size: 58
41236 TTCCCCATAC
* *
41246 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAATGTGCCCAATAA
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAA-GTGCCCTATAT
* ** ** *
41305 GGAAATTCATACACTTAATATGAATTTCTTATCATTTTAGCACATGAGCACCCTATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAGTGCCCTATAT
* * *
41363 GAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGACCTATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC-AAGTGCCCTATAT
* *
41422 AGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTACCCTATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC-AAGTGCCCTATAT
* * **
41481 GGAAATTCATACACTTAGTATGAAATTCTTATCATTTTAGCACATGAAGTGTTCTATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACA-CAAGTGCCCTATAT
* * *
41540 GGAAATTCATACACTTTA-TATGCATTTCTTATCATTTTAGCACACAAATTGCCTTATAT
1 GGAAATTCATACAC-TTAGTATGAATTTCTTATCATTTTAGCACAC-AAGTGCCCTATAT
* * * * *
41599 GAAAATTCATACACTTAATATGAATTTCTTATCATTTTTGCACACGATGTGCCC--TAC
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC-AAGTGCCCTATAT
* *
41656 GGAAATTTATACACTTAGTATGAATTTCTTATCATTTTAGTACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC
41701 TTAGTGCCAT
Statistics
Matches: 346, Mismatches: 45, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
57 42 0.12
58 52 0.15
59 249 0.72
60 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAGTGCCCTATAT
Found at i:42078 original size:22 final size:20
Alignment explanation
Indices: 42033--42084 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
42023 TTGTTCCTCA
*
42033 GTATCGATACTGCCACCATG
1 GTATCGATACTACCACCATG
*
42053 GTATCGATACTACTCTACTATG
1 GTATCGATACTAC-C-ACCATG
*
42075 GTATCAATAC
1 GTATCGATAC
42085 CCCCTTCTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 14 0.52
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACCACCATG
Found at i:42178 original size:95 final size:95
Alignment explanation
Indices: 42031--42255 Score: 265
Period size: 95 Copynumber: 2.4 Consensus size: 95
42021 TCTTGTTCCT
* * * *
42031 CAGTATCGATACTGCC--ACCATGGTATCGATACTACTCTACTATGGTATCAATACCCCCTTCTG
1 CAGTATCGATAC--CCTTACCATGGTATCGATACTACTATACTATGATACCAATACCCCCTTATG
* * * *
42094 GTATGGTTACCAAAATTAGATTCGATATGGCC
64 GTATCGATACCAAAATTAGATTCAATATGACC
* *
42126 CAGTATCGATACCCTTACCATGGTATCGATATTACTATACTATGATACCAATACCCCTTTATGGT
1 CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGATACCAATACCCCCTTATGGT
* * * *
42191 ATCGATACCAAAATTAGGTTTAATGTTACC
66 ATCGATACCAAAATTAGATTCAATATGACC
** *
42221 TGGTATCGATACCCTTACTATGGTATCGATACTAC
1 CAGTATCGATACCCTTACCATGGTATCGATACTAC
42256 CTCGTCGGTA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
93 2 0.02
95 108 0.98
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (95 bp):
CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGATACCAATACCCCCTTATGGT
ATCGATACCAAAATTAGATTCAATATGACC
Found at i:43535 original size:2 final size:2
Alignment explanation
Indices: 43528--43574 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
43518 GCAAAAGTTA
43528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43570 AT AT A
1 AT AT A
43575 AAATATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50092 original size:27 final size:26
Alignment explanation
Indices: 50054--50111 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
50044 AGAACATATA
*
50054 TAAAACTGCCTAAACACTGCCTAATT
1 TAAAACTACCTAAACACTGCCTAATT
50080 TAAAGACTACCTAAACACTGCCTAATT
1 TAAA-ACTACCTAAACACTGCCTAATT
50107 TAAAA
1 TAAAA
50112 ACCAATTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (26 bp):
TAAAACTACCTAAACACTGCCTAATT
Found at i:52670 original size:29 final size:29
Alignment explanation
Indices: 52602--52674 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
52592 AAAACTATAT
* * *
52602 TTTTGGTCCCTAAATTTTCAAAAGTTTATA
1 TTTTGGTCACT-AACTTTCAAAAGTTTACA
* *
52632 CTTT-GACACTGAACTTTCAAAA-TTTACA
1 TTTTGGTCACT-AACTTTCAAAAGTTTACA
52660 TTTTGGTCACTAACT
1 TTTTGGTCACTAACT
52675 AAAATTTGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 12 0.35
29 19 0.56
30 3 0.09
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTTGGTCACTAACTTTCAAAAGTTTACA
Found at i:56768 original size:15 final size:15
Alignment explanation
Indices: 56748--56796 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
56738 AAGAAAACCT
56748 ATTAAAAATGGATAA
1 ATTAAAAATGGATAA
56763 ATT-AAAAT-GACT--
1 ATTAAAAATGGA-TAA
56775 ATTAAAAATGGATAA
1 ATTAAAAATGGATAA
56790 ATTAAAA
1 ATTAAAA
56797 TATTATCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 3 0.10
13 8 0.28
14 8 0.28
15 10 0.34
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (15 bp):
ATTAAAAATGGATAA
Found at i:56771 original size:14 final size:14
Alignment explanation
Indices: 56752--56797 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
56742 AAACCTATTA
56752 AAAATGGATAAATT
1 AAAATGGATAAATT
56766 AAAAT-GACT--ATT
1 AAAATGGA-TAAATT
56778 AAAAATGGATAAATT
1 -AAAATGGATAAATT
56793 AAAAT
1 AAAAT
56798 ATTATCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 13 0.48
15 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (14 bp):
AAAATGGATAAATT
Found at i:56777 original size:27 final size:27
Alignment explanation
Indices: 56746--56797 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
56736 GGAAGAAAAC
56746 CTATTAAAAATGGATAAATTAAAATGA
1 CTATTAAAAATGGATAAATTAAAATGA
56773 CTATTAAAAATGGATAAATTAAAAT
1 CTATTAAAAATGGATAAATTAAAAT
56798 ATTATCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.31
Consensus pattern (27 bp):
CTATTAAAAATGGATAAATTAAAATGA
Done.