Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000556.1 Hibiscus syriacus cultivar Beakdansim tig00001086_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: 359109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:284035 original size:21 final size:21
Alignment explanation
Indices: 284009--284057 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
283999 CATATTTGCA
*
284009 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTACAAGTTCGCG
*
284030 TTGCGATAGTAGAAGTTCGCG
1 TTGCGATAGTACAAGTTCGCG
284051 TTGCGAT
1 TTGCGAT
284058 TTATTCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTACAAGTTCGCG
Found at i:285024 original size:16 final size:17
Alignment explanation
Indices: 284994--285026 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
284984 AGTATAAAAT
284994 AAAAAATAATATTATAA
1 AAAAAATAATATTATAA
*
285011 AAAAAATTAT-TTATAA
1 AAAAAATAATATTATAA
285027 TTAAAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAATAATATTATAA
Found at i:295478 original size:74 final size:76
Alignment explanation
Indices: 295357--295504 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 76
295347 TTCGAATCAG
295357 TGGCGTGGAGACTGCGGCTCAAAAGGTCACTGTGCGCTCTATGG-TT-TCGGCTGGGGAATGGGA
1 TGGCGTGGAGACTGCGGCTCAAAAGGTCACTGTGCGCTCTATGGTTTCTCGGCTGGGGAATGGGA
295420 GTGGCATTTCA
66 GTGGCATTTCA
295431 TGGCGTGGAGACTGCGGCTCAAAAGGTCACTGTGCGCTCTATGGTTTCTCGGCTGGGGAATGGGA
1 TGGCGTGGAGACTGCGGCTCAAAAGGTCACTGTGCGCTCTATGGTTTCTCGGCTGGGGAATGGGA
295496 GTGGCATTT
66 GTGGCATTT
295505 AGTTCGGCAT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 44 0.61
75 2 0.03
76 26 0.36
ACGTcount: A:0.17, C:0.19, G:0.38, T:0.26
Consensus pattern (76 bp):
TGGCGTGGAGACTGCGGCTCAAAAGGTCACTGTGCGCTCTATGGTTTCTCGGCTGGGGAATGGGA
GTGGCATTTCA
Found at i:298127 original size:20 final size:22
Alignment explanation
Indices: 298081--298128 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
298071 AAAACAATTA
298081 AGATA-TATATATTTTATAAAT
1 AGATATTATATATTTTATAAAT
298102 A-A-ATTAT-TATTTT-TAAAT
1 AGATATTATATATTTTATAAAT
298120 AGATATTAT
1 AGATATTAT
298129 CTTGAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 6 0.25
19 8 0.33
20 9 0.38
21 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
AGATATTATATATTTTATAAAT
Found at i:306387 original size:5 final size:5
Alignment explanation
Indices: 306377--306402 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
306367 AAGATACATG
306377 TGATA TGATA TGATA TGATA TGATA T
1 TGATA TGATA TGATA TGATA TGATA T
306403 ACATGACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42
Consensus pattern (5 bp):
TGATA
Found at i:306759 original size:21 final size:22
Alignment explanation
Indices: 306724--306765 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
306714 CATCCTTCAG
306724 GATGACAGGTCCTTCAGGACACA
1 GATGACA-GTCCTTCAGGACACA
*
306747 GATGACA-TCCTTCGGGACA
1 GATGACAGTCCTTCAGGACA
306766 TTTGTACGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (22 bp):
GATGACAGTCCTTCAGGACACA
Found at i:306955 original size:20 final size:20
Alignment explanation
Indices: 306919--307068 Score: 80
Period size: 20 Copynumber: 8.1 Consensus size: 20
306909 TGACATGATT
*
306919 TATATATATGTCATATTGAAA
1 TATATACATG-CATATTGAAA
306940 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
*
306960 TGT-T--ATG---ATT-AAA
1 TATATACATGCATATTGAAA
* *
306973 TGGTA-AGAATGCATATTGAAA
1 T-ATATA-CATGCATATTGAAA
306994 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
*
307014 TGT-T--ATG---ATT-AAA
1 TATATACATGCATATTGAAA
* *
307027 TGGTA-AGAATGCATATTGAAA
1 T-ATATA-CATGCATATTGAAA
307048 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
307068 T
1 T
307069 GTTATGATTA
Statistics
Matches: 102, Mismatches: 7, Indels: 41
0.68 0.05 0.27
Matches are distributed among these distances:
13 8 0.08
14 10 0.10
17 12 0.12
19 2 0.02
20 51 0.50
21 19 0.19
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TATATACATGCATATTGAAA
Found at i:306993 original size:54 final size:54
Alignment explanation
Indices: 306930--307097 Score: 336
Period size: 54 Copynumber: 3.1 Consensus size: 54
306920 ATATATATGT
306930 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
306984 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
307038 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
307092 CATATT
1 CATATT
307098 CATGAAATCT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 114 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (54 bp):
CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
Found at i:308876 original size:3 final size:3
Alignment explanation
Indices: 308868--308905 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
308858 GAATATATAT
308868 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
308906 TTGATTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:313023 original size:38 final size:38
Alignment explanation
Indices: 312964--313055 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 38
312954 TATAAGACAT
* * * *
312964 ATGATAGGTCCTACGGGACACAGATTACATTCTTCAGG
1 ATGATAGGTCCTTCGGCACACAGATGACATCCTTCAGG
* *
313002 ATGACAGGTCCTTCGGCACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGCACACAGATGACATCCTTCAGG
313040 ATGATAGGTCCTTCGG
1 ATGATAGGTCCTTCGG
313056 GACATTTGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGCACACAGATGACATCCTTCAGG
Found at i:313249 original size:20 final size:21
Alignment explanation
Indices: 313213--313254 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
313203 TGACATGATT
*
313213 TATATATATGTCATATTAAAA
1 TATATACATGTCATATTAAAA
*
313234 TATATACATG-CATATTGAAA
1 TATATACATGTCATATTAAAA
313254 T
1 T
313255 GTTATGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
TATATACATGTCATATTAAAA
Found at i:313888 original size:197 final size:197
Alignment explanation
Indices: 313548--313943 Score: 747
Period size: 197 Copynumber: 2.0 Consensus size: 197
313538 AATTAAAGTA
*
313548 TTTTGTTTTAAACAAAGTTTTAAATTCCCCGGGGTTTTTCTTTAAGTGTCAAGGTTTGAAAAGTC
1 TTTTATTTTAAACAAAGTTTTAAATTCCCCGGGGTTTTTCTTTAAGTGTCAAGGTTTGAAAAGTC
*
313613 AATGTGACACCTCAGACTCTTATTCGGGTCGGGTACGGGTTGGGGTGTTACATATCCGACACTTT
66 AATGTGACACCTCAGACTCGTATTCGGGTCGGGTACGGGTTGGGGTGTTACATATCCGACACTTT
*
313678 TACCCGAGTCCAATTAACATTGGATAGCCGAATTGCCCTTTGGTTTAAGTATTTTGGTCTAATTT
131 TACCCGAGTCCAATTAACATTGGATAGCCGAATTGCCCTTTGGTTTAACTATTTTGGTCTAATTT
313743 TG
196 TG
*
313745 TTTTATTTTAAACAAAGTTTTAAATTCCCCGGGGTTTTTCTTTAAGTGTCAAGGTTTGGAAAGTC
1 TTTTATTTTAAACAAAGTTTTAAATTCCCCGGGGTTTTTCTTTAAGTGTCAAGGTTTGAAAAGTC
313810 AATGTGACACCTCAGACTCGTATTCGGGTCGGGTACGGGTTGGGGTGTTACATATCCGACACTTT
66 AATGTGACACCTCAGACTCGTATTCGGGTCGGGTACGGGTTGGGGTGTTACATATCCGACACTTT
*
313875 TACCCGAGTCCAATTAACATTGGGTAGCCGAATTGCCCTTTGGTTTAACTATTTTGGTCTAATTT
131 TACCCGAGTCCAATTAACATTGGATAGCCGAATTGCCCTTTGGTTTAACTATTTTGGTCTAATTT
313940 TG
196 TG
313942 TT
1 TT
313944 GTTGCAGATC
Statistics
Matches: 194, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
197 194 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (197 bp):
TTTTATTTTAAACAAAGTTTTAAATTCCCCGGGGTTTTTCTTTAAGTGTCAAGGTTTGAAAAGTC
AATGTGACACCTCAGACTCGTATTCGGGTCGGGTACGGGTTGGGGTGTTACATATCCGACACTTT
TACCCGAGTCCAATTAACATTGGATAGCCGAATTGCCCTTTGGTTTAACTATTTTGGTCTAATTT
TG
Found at i:316342 original size:13 final size:14
Alignment explanation
Indices: 316324--316354 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
316314 GTATCATATT
316324 TCACATA-TTCATA
1 TCACATAGTTCATA
316337 TCACATAGTTCATA
1 TCACATAGTTCATA
316351 TCAC
1 TCAC
316355 TTGCATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:318418 original size:21 final size:21
Alignment explanation
Indices: 318378--318420 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
318368 TTTTCAAAAC
* *
318378 TTAAAATTAATATGAGATAAA
1 TTAAAATTAAAATGAAATAAA
*
318399 TTAAAATTAAAATTAAATAAA
1 TTAAAATTAAAATGAAATAAA
318420 T
1 T
318421 AAATAATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
TTAAAATTAAAATGAAATAAA
Found at i:321239 original size:21 final size:20
Alignment explanation
Indices: 321208--321247 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
321198 GGTTTTGGTT
321208 TAATACATGTATTATCATGA
1 TAATACATGTATTATCATGA
321228 TAATACCATGTATTATCATG
1 TAATA-CATGTATTATCATG
321248 CCCTGCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
TAATACATGTATTATCATGA
Found at i:334126 original size:33 final size:33
Alignment explanation
Indices: 334084--334151 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
334074 TTTGCAAAAG
334084 AACCAAACTTCTGGCTCTGCATTTTCAAAGCAT
1 AACCAAACTTCTGGCTCTGCATTTTCAAAGCAT
334117 AACCAAACTTCTGGCTCTGCATTTTCAAAGCAT
1 AACCAAACTTCTGGCTCTGCATTTTCAAAGCAT
334150 AA
1 AA
334152 ACAACATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (33 bp):
AACCAAACTTCTGGCTCTGCATTTTCAAAGCAT
Found at i:352889 original size:22 final size:20
Alignment explanation
Indices: 352864--352956 Score: 69
Period size: 21 Copynumber: 4.3 Consensus size: 20
352854 CACCACAGCT
352864 CACATAATTTGCACTGAAGTAC
1 CACAT-ATTTGC-CTGAAGTAC
* *
352886 CACATATTTGTCTCGAAGTGC
1 CACATATTTGCCT-GAAGTAC
* *
352907 CACATATTTGTCCCGAAGGAC
1 CACATATTTG-CCTGAAGTAC
* *
352928 CACATAGGTTTGTCCCGAAGGAC
1 CACATA--TTTG-CCTGAAGTAC
352951 CACATA
1 CACATA
352957 AGACCCTCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
20 2 0.03
21 32 0.52
22 6 0.10
23 21 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
CACATATTTGCCTGAAGTAC
Found at i:352943 original size:23 final size:21
Alignment explanation
Indices: 352879--352956 Score: 104
Period size: 21 Copynumber: 3.6 Consensus size: 21
352869 AATTTGCACT
* *
352879 GAAGTACCACATATTTGTCTC
1 GAAGGACCACATATTTGTCCC
352900 GAAGTG-CCACATATTTGTCCC
1 GAAG-GACCACATATTTGTCCC
352921 GAAGGACCACATAGGTTTGTCCC
1 GAAGGACCACATA--TTTGTCCC
352944 GAAGGACCACATA
1 GAAGGACCACATA
352957 AGACCCTCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.02
21 29 0.57
23 21 0.41
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GAAGGACCACATATTTGTCCC
Found at i:353083 original size:14 final size:15
Alignment explanation
Indices: 353064--353096 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
353054 GTATATCTTG
353064 TTCACAT-AAGCACT
1 TTCACATCAAGCACT
*
353078 TTCACATCAAGCATT
1 TTCACATCAAGCACT
353093 TTCA
1 TTCA
353097 TAAAGCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (15 bp):
TTCACATCAAGCACT
Found at i:357643 original size:23 final size:23
Alignment explanation
Indices: 357583--357645 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
357573 AATAGTTAGG
357583 TAATTATACATTTTAATTAAATTA
1 TAATTATACA-TTTAATTAAATTA
* * **
357607 TATTTAAATTTTTAATT-AATTCA
1 TAATTATACATTTAATTAAATT-A
357630 TAATTATACATTTAAT
1 TAATTATACATTTAAT
357646 ATTCTATAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
22 4 0.13
23 20 0.67
24 6 0.20
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTATACATTTAATTAAATTA
Done.