Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008020.1 Hibiscus syriacus cultivar Beakdansim tig00110488_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: 406994
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:350386 original size:22 final size:21
Alignment explanation
Indices: 350361--350401 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
350351 CGAAATATCT
*
350361 TTCATGATAAAAATCATATATG
1 TTCATAAT-AAAATCATATATG
*
350383 TTCATAATAACATCATATA
1 TTCATAATAAAATCATATA
350402 CAAAAATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (21 bp):
TTCATAATAAAATCATATATG
Found at i:354468 original size:17 final size:17
Alignment explanation
Indices: 354391--354472 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
354381 CATTTAAATA
* *
354391 ATCTAGTTCATTTAGGG
1 ATCTAGTTCATTTATGC
*
354408 AACTAGTTCATTTATGC
1 ATCTAGTTCATTTATGC
* *
354425 ATTTAGATT-ATTTA-GTA
1 ATCTAG-TTCATTTATG-C
* *
354442 AGCTATTTCATTTATGC
1 ATCTAGTTCATTTATGC
354459 ATCTAGTTCATTTA
1 ATCTAGTTCATTTA
354473 ATAAAGTTAG
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
16 3 0.06
17 43 0.88
18 3 0.06
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (17 bp):
ATCTAGTTCATTTATGC
Found at i:354472 original size:34 final size:34
Alignment explanation
Indices: 354391--354472 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
354381 CATTTAAATA
354391 ATCTAGTTCATTTAGGGAACTAGTTCATTTATGC
1 ATCTAGTTCATTTAGGGAACTAGTTCATTTATGC
* * *
354425 ATTTAGATT-ATTTA-GTAAGCTATTTCATTTATGC
1 ATCTAG-TTCATTTAGGGAA-CTAGTTCATTTATGC
354459 ATCTAGTTCATTTA
1 ATCTAGTTCATTTA
354473 ATAAAGTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 5 0.12
34 34 0.83
35 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (34 bp):
ATCTAGTTCATTTAGGGAACTAGTTCATTTATGC
Found at i:354504 original size:17 final size:17
Alignment explanation
Indices: 354461--354541 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
354451 ATTTATGCAT
354461 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
* *
354478 GTTAGCTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
354496 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
354513 CTATTTCATTTA-TAAA
1 CTAGTTCATTAATTAAA
*
354529 CTAATTC-TTAATT
1 CTAGTTCATTAATT
354542 GTTTCATGCG
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
15 3 0.06
16 10 0.20
17 27 0.54
18 10 0.20
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:354962 original size:25 final size:25
Alignment explanation
Indices: 354934--354988 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
354924 AAGCATTCAA
354934 GGCTGATTTAATAATCCAAACCAAG
1 GGCTGATTTAATAATCCAAACCAAG
* *
354959 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATAATCCAAACCAAG
354984 GGCTG
1 GGCTG
354989 TTCATATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATAATCCAAACCAAG
Found at i:357645 original size:180 final size:178
Alignment explanation
Indices: 357334--357666 Score: 410
Period size: 180 Copynumber: 1.8 Consensus size: 178
357324 TGACAAATTT
*
357334 TGTTTGTGATTATATATTTTAATTATAGTGACAAAATGTATAGTCACAAATGATTATCTCCAATT
1 TGTTTGTGATTATATATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTATCTCCAATT
* * *
357399 TTTGGTGCAAAAACAAAATCATATAGTGACATTATTTGTAACTATAGGTTATAATTATTGTTACA
66 TTTGGTACAAAAACAAAATCATATAGTAACAGTATTTGTAACTATAGGTTATAATTA-T-TTACA
357464 AACAA-ATTGTCACAAAAAATAACGAGATTCAAGTTTTTAGTAAAAAAATG
129 AA-AACATTGTCACAAAAAATAACGAGATTCAAGTTTTTAGTAAAAAAATG
* * *
357514 TGTTTGTCG-TTATATGTTTTAATTATAGTGACGAAATATATTGTCACAAA-GATT-TCCCTCCA
1 TGTTTGT-GATTATATATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTAT--CTCCA
* **
357576 TATTTTT-TTACACCAACAAAATCATATAGTAACAAGTA-TTGTAACTATAAGTGTTTATAATTA
63 -ATTTTTGGTACAAAAACAAAATCATATAGTAAC-AGTATTTGTAACTAT-AG-G-TTATAATTA
*
357639 -TTACAAAAACCATTGTCAGAAAAAATAA
123 TTTACAAAAA-CATTGTCACAAAAAATAA
357667 TGGCATTCAG
Statistics
Matches: 132, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
178 1 0.01
179 6 0.05
180 87 0.66
181 28 0.21
182 1 0.01
183 9 0.07
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (178 bp):
TGTTTGTGATTATATATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTATCTCCAATT
TTTGGTACAAAAACAAAATCATATAGTAACAGTATTTGTAACTATAGGTTATAATTATTTACAAA
AACATTGTCACAAAAAATAACGAGATTCAAGTTTTTAGTAAAAAAATG
Found at i:359162 original size:16 final size:19
Alignment explanation
Indices: 359140--359177 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
359130 CAAAAGTTTT
359140 AATATATAAA-CTAA-TTAA
1 AATAT-TAAACCTAACTTAA
359158 AATATTAAACCTAACTTAA
1 AATATTAAACCTAACTTAA
359177 A
1 A
359178 CTGAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AATATTAAACCTAACTTAA
Found at i:361237 original size:198 final size:195
Alignment explanation
Indices: 360830--361262 Score: 525
Period size: 196 Copynumber: 2.2 Consensus size: 195
360820 TTTCATAACT
* * * * *
360830 TATTTTTCACAATAACAAAGTCTAACAAATTTATTTAATTACAATAACATAGTAAATTTAGTCAA
1 TATTTTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACATAGTAAATTTAATCAA
* * *
360895 TATAAAAATATATGCCAAATTTATTTTGTCACAATATTTTGTCAAAATAAAAAATTGTGAGATTT
66 TATAAAAATATATGCCAAATTTATTCTGTCACAATATTTTGTCAAAATAAAAAATTATGAAATTT
* * * * * * *
360960 ATTTAGTAAAAATAATAATTTTTAAAAAATATTAATTTCTCATTATAACAAATTATGACAACTAA
131 ATTTAATAAAAATAACAAATTATAAAAAATATTAATTACACATTATAACAAATTATGACAAATAA
* * * *
361025 TAATCTTTCACAATAAAAAATTGTAACAAAATGATTTAGTTACAATAAC-TAGTTAAGTTTAATC
1 T-ATTTTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACATAG-TAAATTTAATC
* *
361089 AA-AGTAAAAAGT-TATGTCAAATTTATTCT-TC-CTAATATTTTTGTCAAAATGAAAAATTATG
64 AATA-TAAAAA-TATATGCCAAATTTATTCTGTCAC-AATA-TTTTGTCAAAATAAAAAATTATG
* * *
361150 AAAAATTTATTTAATCAAAATAACAAATTATAACAAATATTAATTACACATTATAACAAATTGTG
125 --AAATTTATTTAATAAAAATAACAAATTATAAAAAATATTAATTACACATTATAACAAATTATG
361215 ACAAATAA
188 ACAAATAA
*
361223 TATTTTTCCACAATAACAATTTGTAACAAAATTATTTAGT
1 TATTTTT-CACAATAACAAATTGTAACAAAATTATTTAGT
361263 CATAGTAAAA
Statistics
Matches: 201, Mismatches: 28, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
194 1 0.00
195 11 0.05
196 93 0.46
197 6 0.03
198 90 0.45
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (195 bp):
TATTTTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACATAGTAAATTTAATCAA
TATAAAAATATATGCCAAATTTATTCTGTCACAATATTTTGTCAAAATAAAAAATTATGAAATTT
ATTTAATAAAAATAACAAATTATAAAAAATATTAATTACACATTATAACAAATTATGACAAATAA
Found at i:373997 original size:21 final size:21
Alignment explanation
Indices: 373973--374013 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
373963 ATGCATTCTT
*
373973 ATGATAAAATAAAATATATAA
1 ATGATAAAATAAAAGATATAA
* *
373994 ATGATATAATATAAGATATA
1 ATGATAAAATAAAAGATATA
374014 GTAAGGAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (21 bp):
ATGATAAAATAAAAGATATAA
Found at i:378137 original size:15 final size:15
Alignment explanation
Indices: 378095--378140 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
378085 CCTACTTTGA
378095 TATCA-TTTCATTTCT
1 TATCATTTTC-TTTCT
*
378110 TATCATTTCCTTTCT
1 TATCATTTTCTTTCT
378125 TATCATTTTCTTTCT
1 TATCATTTTCTTTCT
378140 T
1 T
378141 CTTTCATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 25 0.89
16 3 0.11
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (15 bp):
TATCATTTTCTTTCT
Found at i:379239 original size:19 final size:20
Alignment explanation
Indices: 379212--379259 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
379202 CCAATAGCAC
*
379212 GTATCTTCATT-AAAATAAT
1 GTATTTTCATTAAAAATAAT
*
379231 GTATTTTCATTAAAAATCAT
1 GTATTTTCATTAAAAATAAT
379251 GTATTTTCA
1 GTATTTTCA
379260 AAGGGGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (20 bp):
GTATTTTCATTAAAAATAAT
Found at i:380521 original size:17 final size:17
Alignment explanation
Indices: 380499--380532 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
380489 AATAGGCATG
*
380499 TATTTATTCGGTCATCC
1 TATTTATTCGGCCATCC
380516 TATTTATTCGGCCATCC
1 TATTTATTCGGCCATCC
380533 CTTCCAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.44
Consensus pattern (17 bp):
TATTTATTCGGCCATCC
Found at i:381034 original size:15 final size:16
Alignment explanation
Indices: 381008--381039 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
380998 ATAACAACTC
381008 TATCACTTTCATTTCT
1 TATCACTTTCATTTCT
381024 TATCA-TTTCATTTCT
1 TATCACTTTCATTTCT
381039 T
1 T
381040 TCTTAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (16 bp):
TATCACTTTCATTTCT
Found at i:387827 original size:3 final size:3
Alignment explanation
Indices: 387819--387874 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
387809 CTGTAATATG
* * * *
387819 TAA TAA TAA TAA -AT TAA TAA TAA AAA TAA -AA TAA TAA TAA TAG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
387865 TAA TAA TAA T
1 TAA TAA TAA T
387875 TCTTAAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 3 0.07
3 41 0.93
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:387838 original size:14 final size:14
Alignment explanation
Indices: 387819--387873 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
387809 CTGTAATATG
387819 TAATAATAATAAAT
1 TAATAATAATAAAT
387833 TAATAATAA-AAAT
1 TAATAATAATAAAT
* *
387846 AAAATAATAATAATAG
1 -TAATAATAATAA-AT
*
387862 TATTAATAATAA
1 TAATAATAATAA
387874 TTCTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 4 0.12
14 17 0.50
15 12 0.35
16 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:392023 original size:24 final size:25
Alignment explanation
Indices: 391993--392042 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
391983 AAATCAGGAA
* *
391993 AGAAATTGAAGTACTC-AAAAGAAG
1 AGAAATTCAAGCACTCAAAAAGAAG
392017 AGAAATTCAAGCACTCAAAAAGAAG
1 AGAAATTCAAGCACTCAAAAAGAAG
392042 A
1 A
392043 AAAAAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.14
Consensus pattern (25 bp):
AGAAATTCAAGCACTCAAAAAGAAG
Found at i:403159 original size:20 final size:21
Alignment explanation
Indices: 403122--403160 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
403112 ATTTTTTCAA
**
403122 AAAAGCAAAAAAGGCAAAAAC
1 AAAAGCAAAAAAAACAAAAAC
403143 AAAA-CAAAAAAAACAAAA
1 AAAAGCAAAAAAAACAAAA
403161 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (21 bp):
AAAAGCAAAAAAAACAAAAAC
Done.