Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009100.1 Hibiscus syriacus cultivar Beakdansim tig00112556_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: 94155
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:8664 original size:4 final size:4
Alignment explanation
Indices: 8655--8706 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
8645 GATGGTTATG
8655 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
8703 CATA
1 CATA
8707 TTGACAGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:17722 original size:2 final size:2
Alignment explanation
Indices: 17715--17752 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
17705 GGTTATTACT
*
17715 TA TA TA TA TG 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 TA TA TA TA TA
17753 AAAGAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19141 original size:2 final size:2
Alignment explanation
Indices: 19130--19161 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19120 TCGAGAACAG
19130 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19162 TACTATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27284 original size:30 final size:30
Alignment explanation
Indices: 27250--27324 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
27240 TCACATTAAC
27250 AATAGTATAAGGACTATATTTCAAATTGAG
1 AATAGTATAAGGACTATATTTCAAATTGAG
*
27280 AATAGTATAAGGACTATATTTCAAATTTAG
1 AATAGTATAAGGACTATATTTCAAATTGAG
27310 AATAGTATAAGGACT
1 AATAGTATAAGGACT
27325 GATACCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (30 bp):
AATAGTATAAGGACTATATTTCAAATTGAG
Found at i:37640 original size:2 final size:2
Alignment explanation
Indices: 37633--37671 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
37623 TAAATTCATA
*
37633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37672 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:38233 original size:29 final size:29
Alignment explanation
Indices: 38199--38257 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
38189 CCTAAATTAA
*
38199 TTTGATTTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
38228 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
38257 T
1 T
38258 AGGCGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:42839 original size:29 final size:29
Alignment explanation
Indices: 42805--42863 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42795 CCTAAATTAA
42805 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
42834 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
42863 T
1 T
42864 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:44849 original size:29 final size:29
Alignment explanation
Indices: 44815--44873 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
44805 CCTAAATTAA
44815 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
44844 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
44873 T
1 T
44874 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:53618 original size:92 final size:92
Alignment explanation
Indices: 53511--53684 Score: 240
Period size: 92 Copynumber: 1.9 Consensus size: 92
53501 CATTATTGTT
* * *
53511 TTTATAGCAGTTGGTTTGATTATCGACCTGGAGATTTAGTTGCACTTGGTTTTTAGACATATTAG
1 TTTATAGCAGTTGGTTTGATTATCGACATGAAGATTTAGTTGCACTTGATTTTTAGACATATTAG
53576 CTTACCATTATTATTTTTATTGTTATC
66 CTTACCATTATTATTTTTATTGTTATC
* * * ** * * *
53603 TTTATATCATTTGGTTTGATTATTGGTATGAATATTTTGTTGCACTTGATTTTTAGATATATTAG
1 TTTATAGCAGTTGGTTTGATTATCGACATGAAGATTTAGTTGCACTTGATTTTTAGACATATTAG
*
53668 CTTACCATTATTGTTTT
66 CTTACCATTATTATTTT
53685 CATTATTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
92 70 1.00
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (92 bp):
TTTATAGCAGTTGGTTTGATTATCGACATGAAGATTTAGTTGCACTTGATTTTTAGACATATTAG
CTTACCATTATTATTTTTATTGTTATC
Found at i:54446 original size:5 final size:5
Alignment explanation
Indices: 54436--54462 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
54426 ACAATGATAA
54436 ACATT ACATT ACATT ACATT ACATT AC
1 ACATT ACATT ACATT ACATT ACATT AC
54463 TACTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (5 bp):
ACATT
Found at i:63286 original size:27 final size:25
Alignment explanation
Indices: 63255--63313 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
63245 ATTTAACAAA
63255 AAGGGGGAGAAGAATAAGTGTTAAAGT
1 AAGGGGGAG-AGAA-AAGTGTTAAAGT
*
63282 AA-GGGG-GAGTAAAGTGTTAAAGT
1 AAGGGGGAGAGAAAAGTGTTAAAGT
63305 AAGGGGGAG
1 AAGGGGGAG
63314 TAATTTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 14 0.48
24 7 0.24
25 2 0.07
26 4 0.14
27 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.42, T:0.17
Consensus pattern (25 bp):
AAGGGGGAGAGAAAAGTGTTAAAGT
Found at i:63296 original size:23 final size:23
Alignment explanation
Indices: 63270--63316 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
63260 GGAGAAGAAT
63270 AAGTGTTAAAGTAAGGGGGAGTA
1 AAGTGTTAAAGTAAGGGGGAGTA
63293 AAGTGTTAAAGTAAGGGGGAGTA
1 AAGTGTTAAAGTAAGGGGGAGTA
63316 A
1 A
63317 TTTCTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.21
Consensus pattern (23 bp):
AAGTGTTAAAGTAAGGGGGAGTA
Found at i:74514 original size:35 final size:35
Alignment explanation
Indices: 74475--74546 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
74465 CCATAGATGG
74475 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
1 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
74510 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
1 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
74545 AA
1 AA
74547 ATATTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (35 bp):
AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
Found at i:74623 original size:28 final size:28
Alignment explanation
Indices: 74591--74660 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
74581 GTAATTTAGT
74591 CTCTCCTATCTTCTAATCCCAATTCCAC
1 CTCTCCTATCTTCTAATCCCAATTCCAC
74619 CTCTCCTATCTTCTAATCCCAATTCCAC
1 CTCTCCTATCTTCTAATCCCAATTCCAC
74647 CTCTCCTATCTTCT
1 CTCTCCTATCTTCT
74661 TAAATTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.39
Consensus pattern (28 bp):
CTCTCCTATCTTCTAATCCCAATTCCAC
Found at i:77139 original size:27 final size:27
Alignment explanation
Indices: 77109--77166 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
77099 GTTATTTTTT
* *
77109 AGACATATTTTGTTCTACTTGGTGTTG
1 AGACATACTTTGTTCTACTTGATGTTG
*
77136 AGACATACTTTGTTCTACTTGATTTTG
1 AGACATACTTTGTTCTACTTGATGTTG
77163 AGAC
1 AGAC
77167 TTCTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (27 bp):
AGACATACTTTGTTCTACTTGATGTTG
Found at i:77317 original size:90 final size:91
Alignment explanation
Indices: 77176--77457 Score: 323
Period size: 92 Copynumber: 3.1 Consensus size: 91
77166 CTTCTTTTTA
* * *
77176 TTTTCATTGTTGTTTTTATAGTAGTTAGTTTAATTATTGGTTTAGATATTTTGCTGTACTTGATT
1 TTTTCATTGTTG-TTTTATAGTAGTTAGTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATT
*
77241 TTTAGACATATTAACTTATTATTATTG
65 TTTAGACATATTAGCTTATTATTATTG
* * * * * **
77268 TTTTTATTGTTGTTTTATAATAGTT-GATTGATTATTGGTCTGGATATTTTGTTATACACGATTT
1 TTTTCATTGTTGTTTTATAGTAGTTAGTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATTT
* *
77332 TTAGACATATTGGCTTATTATTATTA
66 TTAGACATATTAGCTTATTATTATTG
* * * * * * * * *
77358 TTTTCATTGTTACTTTTATAGCAGTTGGTTTGATTATCGATCTAAAAATTTAGTTGCACTTGATT
1 TTTTCATTGTT-GTTTTATAGTAGTTAGTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATT
**
77423 TTTAGACATATTAGCTTACCATTATTG
65 TTTAGACATATTAGCTTATTATTATTG
77450 TTTTCATT
1 TTTTCATT
77458 ATTTTTTGAA
Statistics
Matches: 156, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
90 64 0.41
91 23 0.15
92 69 0.44
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (91 bp):
TTTTCATTGTTGTTTTATAGTAGTTAGTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATTT
TTAGACATATTAGCTTATTATTATTG
Found at i:84742 original size:30 final size:31
Alignment explanation
Indices: 84677--84743 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
84667 ATCATAATTC
* *
84677 AAATGAGTCTTTATGTGAAAAAATATTGATA
1 AAATGAGTCATTATATGAAAAAATATTGATA
* * *
84708 AAATGGGTCATTATATGAAAAATTA-TGATT
1 AAATGAGTCATTATATGAAAAAATATTGATA
84738 AAATGA
1 AAATGA
84744 ACTATTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (31 bp):
AAATGAGTCATTATATGAAAAAATATTGATA
Found at i:86889 original size:18 final size:18
Alignment explanation
Indices: 86857--86891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
86847 ATTTAAAATT
* *
86857 TAGGGTTAGTTTTTAGAG
1 TAGGGTTAATATTTAGAG
86875 TAGGGTTAATATTTAGA
1 TAGGGTTAATATTTAGA
86892 ATTTAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (18 bp):
TAGGGTTAATATTTAGAG
Found at i:87211 original size:30 final size:30
Alignment explanation
Indices: 87177--87233 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
87167 TCTAGTTATA
* *
87177 AAATAATCATTAAAGTTTA-TAAATTATTAC
1 AAAT-ATCATTAAAATTGATTAAATTATTAC
87207 AAATATCATTAAAATTGATTAAATTAT
1 AAATATCATTAAAATTGATTAAATTAT
87234 CTCAAAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATATCATTAAAATTGATTAAATTATTAC
Found at i:90430 original size:14 final size:14
Alignment explanation
Indices: 90411--90439 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90401 TTATCTTATG
90411 AATCTCATCAGAAA
1 AATCTCATCAGAAA
90425 AATCTCATCAGAAA
1 AATCTCATCAGAAA
90439 A
1 A
90440 TACTCGCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AATCTCATCAGAAA
Done.