Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001262.1 Hibiscus syriacus cultivar Beakdansim tig00002480_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: 38225
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1815 original size:24 final size:24
Alignment explanation
Indices: 1788--1843 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
1778 AAAAATGATA
1788 AAAAAATTGAATAAAAA-ATAATTT
1 AAAAAA-TGAATAAAAACATAATTT
1812 AAAAAA-GAATAAAAACGATAATTT
1 AAAAAATGAATAAAAAC-ATAATTT
1836 AAAGAAAT
1 AAA-AAAT
1844 AGTAAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 9 0.32
24 16 0.57
25 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (24 bp):
AAAAAATGAATAAAAACATAATTT
Found at i:2989 original size:13 final size:13
Alignment explanation
Indices: 2971--3027 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
2961 GGGAAAAACA
2971 AAAAATAAGTAAT
1 AAAAATAAGTAAT
2984 AAAAATAA-TAAT
1 AAAAATAAGTAAT
2996 AATAAATAATGATAAT
1 AA-AAATAA-G-TAAT
* *
3012 AATAATAAATAAT
1 AAAAATAAGTAAT
3025 AAA
1 AAA
3028 TAAATAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 6 0.16
13 20 0.54
15 5 0.14
16 6 0.16
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (13 bp):
AAAAATAAGTAAT
Found at i:2995 original size:3 final size:3
Alignment explanation
Indices: 2974--3026 Score: 61
Period size: 3 Copynumber: 16.7 Consensus size: 3
2964 AAAAACAAAA
* *
2974 AAT AAGT AAT AAA AAT AAT AAT AAT AAAT AAT GAT AAT AAT AAT AAAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT
3022 AAT AA
1 AAT AA
3027 ATAAATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
3 34 0.79
4 9 0.21
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2996 original size:19 final size:19
Alignment explanation
Indices: 2981--3026 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2971 AAAAATAAGT
*
2981 AATAAAAATAATAATAATA
1 AATAATAATAATAATAATA
*
3000 AATAATGATAATAATAATA
1 AATAATAATAATAATAATA
3019 AATAATAA
1 AATAATAA
3027 ATAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:3005 original size:22 final size:26
Alignment explanation
Indices: 2973--3030 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
2963 GAAAAACAAA
* *
2973 AAATAAGTAATAAAAATAAT-AATAAT
1 AAATAA-TGATAATAATAATAAATAAT
2999 AAATAATGATAATAATAATAAATAAT
1 AAATAATGATAATAATAATAAATAAT
3025 AAATAA
1 AAATAA
3031 ATAAAACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (26 bp):
AAATAATGATAATAATAATAAATAAT
Found at i:3146 original size:31 final size:29
Alignment explanation
Indices: 3084--3179 Score: 117
Period size: 31 Copynumber: 3.3 Consensus size: 29
3074 TAAACTATAT
*
3084 ACTATATAAATTTC--AAAT-TTTTAAAAAA
1 ACTATATAATTTTCAAAAATGTTTT--AAAA
3112 ACTATATAATTTTCAAAAAATGTTTTCAAAA
1 ACTATATAATTTTC-AAAAATGTTTT-AAAA
3143 ACTATATAATTTTCAAAAATGTTTTAAAA
1 ACTATATAATTTTCAAAAATGTTTTAAAA
*
3172 ATTATATA
1 ACTATATA
3180 TTATATATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
28 13 0.21
29 11 0.18
30 11 0.18
31 22 0.36
32 4 0.07
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (29 bp):
ACTATATAATTTTCAAAAATGTTTTAAAA
Found at i:3188 original size:38 final size:38
Alignment explanation
Indices: 3145--3293 Score: 171
Period size: 38 Copynumber: 3.9 Consensus size: 38
3135 TTTCAAAAAC
3145 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
*
3183 TATATAAGTTTTC-AAAATGCTTTAAAAATTATATA-T-
1 TATATAA-TTTTCAAAAATGTTTTAAAAATTATATATTA
* **
3219 TATATAGTTTTCAAAAATGATTTTAAAAACCATATATTA
1 TATATAATTTTCAAAAATG-TTTTAAAAATTATATATTA
* * *
3258 TATAT-TTTTTCTAAAAATATTTTAAAACTATATATA
1 TATATAATTTTC-AAAAATGTTTTAAAAAT-TATATA
3294 CCCGTTTTCA
Statistics
Matches: 94, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
35 5 0.05
36 12 0.13
37 14 0.15
38 42 0.45
39 21 0.22
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (38 bp):
TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
Found at i:29238 original size:63 final size:64
Alignment explanation
Indices: 29083--29243 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
29073 TTCCCTTGAA
* * *
29083 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACTTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACTTTCGATGTTTCCATTTTAAGGGG
* * * *
29147 GTGTATCGATGCAC-TCCTTATGCATCGATGCACTAATTGCA-TTT-GATGTTTCCATTTTAA-T
1 GTGCATCGATGCACTTCC-TATGCATCGATACAC-AAAT-CACTTTCGATGTTTCCATTTTAAGG
29208 GG
63 GG
*
29210 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTTCCTATGCATCGATACACA
29244 CTGAACAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 30 0.36
64 44 0.53
65 6 0.07
66 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACTTTCGATGTTTCCATTTTAAGGGG
Found at i:30296 original size:32 final size:32
Alignment explanation
Indices: 30255--30361 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 32
30245 AGTCAAGGGT
*
30255 TTACCTATGTTCTACGGAATATATAAACAGAA
1 TTACCTATGTTCTACGGAACATATAAACAGAA
* * * *
30287 TTACCTATG-TCTTTCGGGACATATGAACAGTA
1 TTACCTATGTTC-TACGGAACATATAAACAGAA
** * *
30319 -TACCTATGTTCTAATGAACATATAGACA-AT
1 TTACCTATGTTCTACGGAACATATAAACAGAA
*
30349 TTACCTAGGTTCT
1 TTACCTATGTTCT
30362 TCGGGACCTA
Statistics
Matches: 58, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
31 32 0.55
32 26 0.45
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATAAACAGAA
Found at i:30379 original size:62 final size:63
Alignment explanation
Indices: 30256--30379 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 63
30246 GTCAAGGGTT
* * *
30256 TACCTATGTTCTACGGAATATATAAACAGAATTACCTATGTCTTTCGGGACATATGAACAGTA
1 TACCTATGTTCTAAGGAACATATAAACAGAATTACCTAGGTCTTTCGGGACATATGAACAGTA
* * * * *
30319 TACCTATGTTCTAATGAACATATAGACA-ATTTACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATAAACAGAATTACCTAGGTCT-TTCGGGACATATGAACAGT
30380 TGCCGAGGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.52
63 24 0.46
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TACCTATGTTCTAAGGAACATATAAACAGAATTACCTAGGTCTTTCGGGACATATGAACAGTA
Found at i:35666 original size:2 final size:2
Alignment explanation
Indices: 35659--35689 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35649 ATATTGGGAT
35659 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
35690 TCATCATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:37969 original size:25 final size:23
Alignment explanation
Indices: 37930--37985 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 23
37920 TAAAAAGTAA
* *
37930 AAATATTTAATTATAATATAATTAT
1 AAATATTAAAATAT-ATAT-ATTAT
*
37955 AAATATTAAAATATATATTTTAT
1 AAATATTAAAATATATATATTAT
37978 -AATATTAA
1 AAATATTAA
37986 CTAAATGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 4 0.14
25 12 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTAAAATATATATATTAT
Found at i:37981 original size:22 final size:20
Alignment explanation
Indices: 37939--37985 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
37929 AAAATATTTA
*
37939 ATTATAATATAATTATAAAT
1 ATTAAAATATAATTATAAAT
*
37959 ATTAAAATATATATTTTATAAT
1 ATTAAAATATA-ATTATA-AAT
37981 ATTAA
1 ATTAA
37986 CTAAATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAAATATAATTATAAAT
Done.