Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003286.1 Hibiscus syriacus cultivar Beakdansim tig00006914_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: 63069
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:3102 original size:90 final size:90
Alignment explanation
Indices: 2943--3106 Score: 301
Period size: 90 Copynumber: 1.8 Consensus size: 90
2933 TTAATTTTAA
*
2943 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAACCTGGA
1 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACCTGGA
3008 TATAAAAGGATTATTAAATTCCAAT
66 TATAAAAGGATTATTAAATTCCAAT
* *
3033 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACTTGGC
1 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACCTGGA
3098 TATAAAAGG
66 TATAAAAGG
3107 GTGTATTGGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (90 bp):
TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACCTGGA
TATAAAAGGATTATTAAATTCCAAT
Found at i:6216 original size:18 final size:19
Alignment explanation
Indices: 6187--6222 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
6177 AGACCGAACA
6187 TAAATGTTTTATTAAAATT
1 TAAATGTTTTATTAAAATT
6206 TAAAT-TTTTATTAAAAT
1 TAAATGTTTTATTAAAAT
6223 AATATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TAAATGTTTTATTAAAATT
Found at i:29375 original size:31 final size:31
Alignment explanation
Indices: 29311--29387 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
29301 CTTTTAAAAC
* **
29311 TTGCAATAAT-GTCCCCAAATATTTAGTTTGT
1 TTGCAAT-ATGGTCCCCAAACATTTAGTCCGT
*
29342 TTGCAATATGGTCCCCTAACATTTAGTCCGT
1 TTGCAATATGGTCCCCAAACATTTAGTCCGT
* *
29373 TTGTAATATGTTCCC
1 TTGCAATATGGTCCC
29388 TGACGTAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (31 bp):
TTGCAATATGGTCCCCAAACATTTAGTCCGT
Found at i:35205 original size:21 final size:23
Alignment explanation
Indices: 35153--35214 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
35143 CGATACCATT
* *
35153 TATGGTATCGATACTACTTAGTG
1 TATGGTACCGATACTACTTAGCG
*
35176 TAGTAGTACCGATACT-CTTAGCG
1 TA-TGGTACCGATACTACTTAGCG
35199 -ATGGTACCGATACTAC
1 TATGGTACCGATACTAC
35215 CTTTTTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 12 0.36
22 2 0.06
23 8 0.24
24 11 0.33
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (23 bp):
TATGGTACCGATACTACTTAGCG
Found at i:43578 original size:24 final size:23
Alignment explanation
Indices: 43533--43579 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
43523 AAATTCCAGT
* *
43533 ATACTAAAATGGTAGTATCGATA
1 ATACTAAAATAGTAGTACCGATA
43556 ATACTAAATATAGTAGTACCGATA
1 ATACTAAA-ATAGTAGTACCGATA
43580 CCCTTGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (23 bp):
ATACTAAAATAGTAGTACCGATA
Found at i:48280 original size:31 final size:32
Alignment explanation
Indices: 48245--48314 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
48235 CTTTTAAAAC
* *
48245 TTGCAATAAT-GTCCCAAAATATTTAGTCTGT
1 TTGCAATAATGGTCCCAAAACATTTAGTCCGT
**
48276 TTGCAAT-ATGGTCCCCTAACATTTAGTCCGT
1 TTGCAATAATGGTCCCAAAACATTTAGTCCGT
48307 TTGCAATA
1 TTGCAATA
48315 TGTTCCCCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (32 bp):
TTGCAATAATGGTCCCAAAACATTTAGTCCGT
Found at i:50846 original size:31 final size:31
Alignment explanation
Indices: 50771--50835 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
50761 GTTATGTCGA
**
50771 GGACCATATTACAAACAGACTAAATGTTAGG
1 GGACCATATTGTAAACAGACTAAATGTTAGG
*
50802 GGACCATATTGTAAACAGACTAAATGTTGGG
1 GGACCATATTGTAAACAGACTAAATGTTAGG
50833 GGA
1 GGA
50836 TTGTATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (31 bp):
GGACCATATTGTAAACAGACTAAATGTTAGG
Found at i:55105 original size:19 final size:19
Alignment explanation
Indices: 55067--55120 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
55057 GTTGAAAATG
**
55067 ATTTGATTTTGAAAGCAAA
1 ATTTGATTTTGAAAAAAAA
55086 ATTTGATTTTGAAAAAAAA
1 ATTTGATTTTGAAAAAAAA
***
55105 ATGAAATTTTGAAAAA
1 ATTTGATTTTGAAAAA
55121 TGATTTTGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (19 bp):
ATTTGATTTTGAAAAAAAA
Found at i:61341 original size:36 final size:36
Alignment explanation
Indices: 61294--61383 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
61284 GTACATTCAC
*
61294 AGGGCACTGAATGTGACGCATCTACGGT-GCAATCAA
1 AGGGCACTGAATGTGACACATCTACGGTAG-AATCAA
* * *
61330 AGGGCATTGAATGTGTCACATCTACGGTAGAATCAC
1 AGGGCACTGAATGTGACACATCTACGGTAGAATCAA
*
61366 ATGGCACTGAATGTGACA
1 AGGGCACTGAATGTGACA
61384 TACCTATTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
36 45 0.98
37 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (36 bp):
AGGGCACTGAATGTGACACATCTACGGTAGAATCAA
Found at i:62020 original size:31 final size:32
Alignment explanation
Indices: 61983--62044 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
61973 CCCGATTATA
61983 TATATATAATATTTTAT-TTTGTATATTAATT
1 TATATATAATATTTTATATTTGTATATTAATT
*
62014 TATATATAATATTTTATATTTTTATATTAAT
1 TATATATAATATTTTATATTTGTATATTAAT
62045 AACAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
TATATATAATATTTTATATTTGTATATTAATT
Done.