Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009446.1 Hibiscus syriacus cultivar Beakdansim tig00113545_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: 85786
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6339 original size:31 final size:29
Alignment explanation
Indices: 6275--6332 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
6265 GTTGAGCTGA
* * *
6275 AAATCAGAAATTTAACATTTATATGCCCG
1 AAATCAGAAAATCAACATTTATATGCACG
6304 AAATCAGTAAAATCAACAATTTATATGCA
1 AAATCAG-AAAATCAAC-ATTTATATGCA
6333 ACAAATCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 7 0.29
31 10 0.42
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.29
Consensus pattern (29 bp):
AAATCAGAAAATCAACATTTATATGCACG
Found at i:9427 original size:21 final size:21
Alignment explanation
Indices: 9401--9457 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
9391 GCACCGCAAC
9401 CATTTCAGATGGCACCACAGT
1 CATTTCAGATGGCACCACAGT
* * * *
9422 CGTTTCAGATGGAATCATAGT
1 CATTTCAGATGGCACCACAGT
9443 CATTTCAGATGGCAC
1 CATTTCAGATGGCAC
9458 TAAATCCATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
CATTTCAGATGGCACCACAGT
Found at i:10035 original size:13 final size:13
Alignment explanation
Indices: 10017--10041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10007 GTTGTAACTT
10017 TTTGTATTTAATG
1 TTTGTATTTAATG
10030 TTTGTATTTAAT
1 TTTGTATTTAAT
10042 TATTTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTGTATTTAATG
Found at i:35344 original size:16 final size:16
Alignment explanation
Indices: 35325--35358 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35315 CAATATACGA
35325 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
35341 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
35357 AT
1 AT
35359 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:35432 original size:16 final size:18
Alignment explanation
Indices: 35400--35433 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
35390 TATTAATGTA
35400 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
35418 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
35434 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:36099 original size:130 final size:128
Alignment explanation
Indices: 35897--36142 Score: 420
Period size: 130 Copynumber: 1.9 Consensus size: 128
35887 AATTTTCTTC
*
35897 TAATTAGGTGGTGACATGTGTCACCAATAACATATCATGATCATGTGTTAACACATGTCAGATCC
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATCATGATCATGTGCTAACACATGTCAGATCC
** *
35962 TGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 TAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
36025 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAAT-A-ACATATCATGATCATGTGCTAACACATGTCAGAT
36090 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
64 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
36143 TATATAAAAT
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
128 28 0.25
129 1 0.01
130 81 0.74
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (128 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACATATCATGATCATGTGCTAACACATGTCAGATCC
TAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:36589 original size:35 final size:35
Alignment explanation
Indices: 36539--36614 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
36529 AATTGAATTT
* *
36539 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
36574 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
36609 AATTGA
1 AATTGA
36615 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:38662 original size:2 final size:2
Alignment explanation
Indices: 38655--38679 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38645 ACTTTTATCA
38655 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38680 AACTAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44119 original size:60 final size:61
Alignment explanation
Indices: 44055--44169 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
44045 GTCCCCTGAC
*
44055 TATAGGATACTA-TTTTATTAAGTCCCTCGATTATTAAAAGTTACAAAATAGTCATTAGAT
1 TATAGGATACTACTTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAGTCATTAGAT
** * * * * *
44115 TATAGGATGTTACTTTTTTTTAGTCCCTCGACTATTAGAATTTACAAAATGGTCA
1 TATAGGATACTACTTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAGTCA
44170 CCAACTATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 10 0.22
61 36 0.78
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (61 bp):
TATAGGATACTACTTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAGTCATTAGAT
Found at i:49399 original size:34 final size:36
Alignment explanation
Indices: 49346--49424 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 36
49336 TGACTACATA
*
49346 TTTATATTTATTTCTTTTA-TTGAGAATAA-GTTTTAT
1 TTTAT-TTTATTTCTTTTATTTGAGAA-AATGTTCTAT
*
49382 TTTATTTTTTTTC-TTTATTTGAGAAAATGTTCTAT
1 TTTATTTTATTTCTTTTATTTGAGAAAATGTTCTAT
49417 TTTATTTT
1 TTTATTTT
49425 GACGAGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 6 0.15
35 28 0.72
36 5 0.13
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.65
Consensus pattern (36 bp):
TTTATTTTATTTCTTTTATTTGAGAAAATGTTCTAT
Found at i:50660 original size:17 final size:17
Alignment explanation
Indices: 50635--50673 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
50625 CAATGCAAGG
*
50635 GGCCAGGGAAAATGTAT
1 GGCCCGGGAAAATGTAT
50652 GGCCCGGGAAAATGTAT
1 GGCCCGGGAAAATGTAT
50669 GGCCC
1 GGCCC
50674 TTCAATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.15
Consensus pattern (17 bp):
GGCCCGGGAAAATGTAT
Found at i:54134 original size:51 final size:51
Alignment explanation
Indices: 54054--54153 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
54044 CTTATTATAG
*
54054 ATATTCGATTTATCGTATATATATCAATCACCGATTGATCTAACAAAATAT
1 ATATTCGATTTATCGTATATATATAAATCACCGATTGATCTAACAAAATAT
* *
54105 ATATTCGATTTATC-TAATATATATAAATCACCGGTTGATCTAATAAAAT
1 ATATTCGATTTATCGT-ATATATATAAATCACCGATTGATCTAACAAAAT
54154 GAGATGCTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 1 0.02
51 44 0.98
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (51 bp):
ATATTCGATTTATCGTATATATATAAATCACCGATTGATCTAACAAAATAT
Found at i:54235 original size:25 final size:25
Alignment explanation
Indices: 54204--54253 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
54194 CGTAAACTAA
54204 ATTATTACTACGCAGACATTATATT
1 ATTATTACTACGCAGACATTATATT
54229 ATTATTACTACGCAGACATTATATT
1 ATTATTACTACGCAGACATTATATT
54254 GCACCCGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
ATTATTACTACGCAGACATTATATT
Found at i:54282 original size:19 final size:19
Alignment explanation
Indices: 54260--54297 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54250 TATTGCACCC
54260 GCAAATAAATATATATACT
1 GCAAATAAATATATATACT
54279 GCAAATAAATATATATACT
1 GCAAATAAATATATATACT
54298 TCATAGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
GCAAATAAATATATATACT
Found at i:61554 original size:16 final size:17
Alignment explanation
Indices: 61533--61567 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
61523 TTACTATTCA
61533 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
61549 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
61566 CG
1 CG
61568 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:62334 original size:15 final size:16
Alignment explanation
Indices: 62316--62348 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62306 GTGGCAGATC
62316 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
62331 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
62347 AA
1 AA
62349 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:72953 original size:12 final size:12
Alignment explanation
Indices: 72936--72960 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72926 GTCAAATAAT
72936 TTAGGCACCAAA
1 TTAGGCACCAAA
72948 TTAGGCACCAAA
1 TTAGGCACCAAA
72960 T
1 T
72961 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:76062 original size:68 final size:68
Alignment explanation
Indices: 75953--76097 Score: 238
Period size: 68 Copynumber: 2.1 Consensus size: 68
75943 GACATCGAGA
* * *
75953 ATGATTATTTCTTGATTACTTTCTGCACCTAGTCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
1 ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
76018 TGG
66 TGG
* *
76021 ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCTATCTCGGAAGGCCCT
1 ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
76086 TGG
66 TGG
76089 ATGA-TATTT
1 ATGATTATTT
76098 GGTCATTACC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
67 5 0.07
68 67 0.93
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (68 bp):
ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
TGG
Found at i:79169 original size:12 final size:12
Alignment explanation
Indices: 79152--79177 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
79142 AGTTTTAAGC
79152 TCTTGTTGAGGT
1 TCTTGTTGAGGT
79164 TCTTGTTGAGGT
1 TCTTGTTGAGGT
79176 TC
1 TC
79178 ACCTAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (12 bp):
TCTTGTTGAGGT
Done.