Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005414.1 Hibiscus syriacus cultivar Beakdansim tig00012412_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: 52093
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4091 original size:12 final size:12
Alignment explanation
Indices: 4074--4100 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4064 TCCTGTTCCT
4074 CCAGTGCCAATG
1 CCAGTGCCAATG
4086 CCAGTGCCAATG
1 CCAGTGCCAATG
4098 CCA
1 CCA
4101 ACTCCAGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.37, G:0.22, T:0.15
Consensus pattern (12 bp):
CCAGTGCCAATG
Found at i:16509 original size:19 final size:20
Alignment explanation
Indices: 16487--16527 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16477 ATTATTTTTC
*
16487 AAAAAAAATCTAAAAT-CTT
1 AAAAAAAATCCAAAATCCTT
*
16506 AAAAAAATTCCAAAATCCTT
1 AAAAAAAATCCAAAATCCTT
16526 AA
1 AA
16528 TCTCAAAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAAAATCCAAAATCCTT
Found at i:19342 original size:25 final size:25
Alignment explanation
Indices: 19292--19342 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
19282 TACAATCTTT
* * *
19292 TAAAATTTTAAAAATAATACATTTA
1 TAAAATTTTAAAAAGAATAAAATTA
19317 TAAAATTTTAAGAAAGAA-AAAATTA
1 TAAAATTTTAA-AAAGAATAAAATTA
19342 T
1 T
19343 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAAATTTTAAAAAGAATAAAATTA
Found at i:19379 original size:20 final size:20
Alignment explanation
Indices: 19351--19389 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19341 ATTAATTAAA
19351 AATACGTAA-AAAATGTTTAT
1 AATACGTAATAAAAT-TTTAT
*
19371 AATATGTAATAAAATTTTA
1 AATACGTAATAAAATTTTA
19390 AAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
AATACGTAATAAAATTTTAT
Found at i:25944 original size:19 final size:19
Alignment explanation
Indices: 25920--25966 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
25910 TTTTCCCGAT
25920 ATATCACCGGTTATCGGTA
1 ATATCACCGGTTATCGGTA
25939 ATATCACCGGTTATCGGTA
1 ATATCACCGGTTATCGGTA
*
25958 ATATTACCG
1 ATATCACCG
25967 ATCTAACACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (19 bp):
ATATCACCGGTTATCGGTA
Found at i:26080 original size:50 final size:50
Alignment explanation
Indices: 26026--26143 Score: 148
Period size: 50 Copynumber: 2.4 Consensus size: 50
26016 AAGTGCGCCT
* ** *
26026 CCTGCACCACGCTATACGATGATTTGGCGTCACGTGAGGTATAGCGC-ACC
1 CCTGCACCGCGCTATACGATGAGCTGGCGCCACGTG-GGTATAGCGCGACC
* * *
26076 CCTGCATCGCGCTATACGGTGAGCTGGCGCCACGTGGGTATAGCGCGGCC
1 CCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTATAGCGCGACC
*
26126 CCTGCAGCGCGCTATACG
1 CCTGCACCGCGCTATACG
26144 CCACGTAGGG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
49 10 0.17
50 49 0.83
ACGTcount: A:0.18, C:0.32, G:0.31, T:0.19
Consensus pattern (50 bp):
CCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTATAGCGCGACC
Found at i:29939 original size:16 final size:16
Alignment explanation
Indices: 29905--29943 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
29895 AGAAATAAAG
*
29905 TAAAAAAATTATAATT
1 TAAAAAAATTACAATT
29921 TAACAAAAATTACAA-T
1 TAA-AAAAATTACAATT
29937 TAAAAAA
1 TAAAAAA
29944 CAAAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAAAATTACAATT
Found at i:32180 original size:110 final size:111
Alignment explanation
Indices: 31983--32203 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
31973 ATTACAAAAA
* * * *
31983 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
* *
32048 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
*
32094 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
32158 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
32204 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 70 0.68
111 33 0.32
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:36690 original size:29 final size:28
Alignment explanation
Indices: 36610--36702 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
36600 ATAAAATTAT
*
36610 ATATTTATTTTAATAAAAGATATTTTAA
1 ATATTTATTTTAATAAAAGATAATTTAA
** * * *
36638 ATATTTAAATAAACAAAATTATAATTTAA
1 ATATTTATTTTAATAAAA-GATAATTTAA
* *
36667 ATATTTATTTTAATTAAAGAATAATCTAA
1 ATATTTATTTTAATAAAAG-ATAATTTAA
36696 ATATTTA
1 ATATTTA
36703 AAGGGTTACA
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
28 14 0.28
29 36 0.72
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATTTATTTTAATAAAAGATAATTTAA
Found at i:38382 original size:22 final size:22
Alignment explanation
Indices: 38349--38401 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
38339 GAGTAATCAA
38349 GTTATG-GTTACCTAGGAGTGG
1 GTTATGAGTTACCTAGGAGTGG
38370 GTTATGAGTTACCTAGGAGTGG
1 GTTATGAGTTACCTAGGAGTGG
38392 GTTATGAGTT
1 GTTATGAGTT
38402 GGGGGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.21, C:0.08, G:0.36, T:0.36
Consensus pattern (22 bp):
GTTATGAGTTACCTAGGAGTGG
Found at i:44960 original size:2 final size:2
Alignment explanation
Indices: 44955--44982 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44945 TTTCTACGTC
44955 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44983 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46647 original size:18 final size:18
Alignment explanation
Indices: 46620--46656 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46610 TATATTAATA
*
46620 AAATATTATGTTAAATTG
1 AAATAATATGTTAAATTG
*
46638 AAATAATATGTTCAATTG
1 AAATAATATGTTAAATTG
46656 A
1 A
46657 TAATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (18 bp):
AAATAATATGTTAAATTG
Done.