Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004008.1 Hibiscus syriacus cultivar Beakdansim tig00008737_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: 207271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:176800 original size:20 final size:20
Alignment explanation
Indices: 176743--176800 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
176733 TCGCATTACA
* *
176743 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
176763 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
176783 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
176801 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:177887 original size:24 final size:24
Alignment explanation
Indices: 177860--177913 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
177850 GTATTCGAAA
* *
177860 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
177884 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
177908 TTTGAT
1 TTTGAT
177914 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:178105 original size:12 final size:12
Alignment explanation
Indices: 178088--178112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
178078 ATATAATCCT
178088 GAAGAAGAAAAA
1 GAAGAAGAAAAA
178100 GAAGAAGAAAAA
1 GAAGAAGAAAAA
178112 G
1 G
178113 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:180498 original size:19 final size:19
Alignment explanation
Indices: 180407--180504 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
180397 GGAAATTACT
*
180407 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
180426 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
180440 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
180459 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
180473 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
180492 ATCGCAACGCGAA
1 ATCGCAATGCGAA
180505 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:180507 original size:33 final size:33
Alignment explanation
Indices: 180408--180507 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
180398 GAAATTACTA
* * *
180408 TCGCAATACGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
180441 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
180474 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
180507 T
1 T
180508 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:180522 original size:19 final size:20
Alignment explanation
Indices: 180500--180542 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
180490 AAATCGCAAC
180500 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
180519 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
180539 GCGA
1 GCGA
180543 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:180527 original size:14 final size:14
Alignment explanation
Indices: 180528--180561 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
180518 TGCGATTTTC
180528 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
180542 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
180556 ATTTTC
1 ATTTTC
180562 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:180702 original size:14 final size:14
Alignment explanation
Indices: 180683--180719 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
180673 CATCAATTAA
180683 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
180697 ACAAATCACCTTTT
1 ACAAATCAACTTTT
*
180711 ATAAATCAA
1 ACAAATCAA
180720 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:182110 original size:21 final size:21
Alignment explanation
Indices: 182077--182172 Score: 54
Period size: 21 Copynumber: 4.6 Consensus size: 21
182067 GTGAATCAGG
* *
182077 CTCTTGAATGATGAGAGGGAC
1 CTCTTCAACGATGAGAGGGAC
*
182098 CTCTTCAACGATGACAGTGG-C
1 CTCTTCAACGATGAGAG-GGAC
* * *
182119 CTCTTGAACGGTGGGAGGGGA-
1 CTCTTCAACGATGAGA-GGGAC
* * * *
182140 CTC-TCGAGGAATGATAGGGGC
1 CTCTTCAACG-ATGAGAGGGAC
182161 CTCTTCAACGAT
1 CTCTTCAACGAT
182173 AGGAGTGGAC
Statistics
Matches: 53, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
20 6 0.11
21 40 0.75
22 7 0.13
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (21 bp):
CTCTTCAACGATGAGAGGGAC
Found at i:182162 original size:42 final size:42
Alignment explanation
Indices: 182116--182199 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
182106 CGATGACAGT
* * *
182116 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
182158 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
182200 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:184233 original size:20 final size:19
Alignment explanation
Indices: 184202--184262 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
184192 TCTTTTGGTT
184202 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
184221 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
184242 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
184261 GA
1 GA
184263 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:184284 original size:33 final size:34
Alignment explanation
Indices: 184227--184303 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
184217 ACGAGATAAT
*
184227 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCA
*
184261 GAGAATCGCAACGC-GAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCA
*
184294 GACAATCGCA
1 GAGAATCGCA
184304 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.38, C:0.26, G:0.25, T:0.12
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCA
Found at i:184914 original size:20 final size:21
Alignment explanation
Indices: 184885--184937 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
184875 GCGCTATGTA
184885 AATC-GCGTTGCGAAAGTCAG
1 AATCTGCGTTGCGAAAGTCAG
184905 AAT-TGCGTTGCGAAAGTCAG
1 AATCTGCGTTGCGAAAGTCAG
*
184925 TATCT-CGTTGCGA
1 AATCTGCGTTGCGA
184938 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (21 bp):
AATCTGCGTTGCGAAAGTCAG
Found at i:184998 original size:41 final size:41
Alignment explanation
Indices: 184905--185041 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 41
184895 CGAAAGTCAG
* * * * **
184905 AATT-GCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-GT
1 AATTCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCC
* *
184944 ATTATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCC
1 AAT-TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCC
* ** *
184986 AATTCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCTC
1 AATTCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCC
185027 AATTCGCGTTGCGAT
1 AATTCGCGTTGCGAT
185042 TTACTTATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.03
40 5 0.06
41 71 0.89
42 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
AATTCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCC
Found at i:185012 original size:20 final size:20
Alignment explanation
Indices: 184968--185060 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
184958 ATAGTAAGTA
* **
184968 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
184989 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* *
185009 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-TAT
*
185030 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
185050 TCGCATTGCGA
1 TCGCATTGCGA
185061 ATTGGGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:185042 original size:41 final size:41
Alignment explanation
Indices: 184968--185060 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
184958 ATAGTAAGTA
184968 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
185009 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
185050 TCGCATTGCGA
1 TCGCATTGCGA
185061 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:189489 original size:20 final size:22
Alignment explanation
Indices: 189464--189504 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
189454 CGAGACTGGA
189464 AAGTGTTTTGA-C-TAAAAATC
1 AAGTGTTTTGAGCTTAAAAATC
189484 AAGTGTTTTGAGCTTAAAAAT
1 AAGTGTTTTGAGCTTAAAAAT
189505 GATATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (22 bp):
AAGTGTTTTGAGCTTAAAAATC
Found at i:194082 original size:20 final size:20
Alignment explanation
Indices: 194053--194091 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
194043 TTTCCACCAC
*
194053 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
194073 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
194092 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:198753 original size:24 final size:22
Alignment explanation
Indices: 198726--198772 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
198716 AAAGATATGG
*
198726 AAAATAACAAGTAAAACTATAAAA
1 AAAATAAAAAGTAAAA-TA-AAAA
198750 AAAATAAAAAGTAAAATAAAAA
1 AAAATAAAAAGTAAAATAAAAA
198772 A
1 A
198773 TGCTATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 2 0.09
24 15 0.68
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAATAAAAAGTAAAATAAAAA
Found at i:198771 original size:12 final size:12
Alignment explanation
Indices: 198726--198771 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
198716 AAAGATATGG
*
198726 AAAATAACAAGT
1 AAAATAAAAAGT
198738 AAAACTATAAAA--
1 AAAA-TA-AAAAGT
198750 AAAATAAAAAGT
1 AAAATAAAAAGT
198762 AAAATAAAAA
1 AAAATAAAAA
198772 ATGCTATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
10 4 0.14
11 2 0.07
12 18 0.62
13 2 0.07
14 3 0.10
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAGT
Found at i:205107 original size:2 final size:2
Alignment explanation
Indices: 205100--205143 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
205090 CATGAGTTGA
205100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205142 AT
1 AT
205144 TAAATGACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.