Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008593.1 Hibiscus syriacus cultivar Beakdansim tig00111542_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: 1058705
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 5 of 5
Found at i:1033366 original size:30 final size:30
Alignment explanation
Indices: 1033298--1033373 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
1033288 CTTTTAAAAC
**
1033298 TTACAATACAGTCCCCAACATTTAGTCCGT
1 TTACAATATGGTCCCCAACATTTAGTCCGT
* *
1033328 TTACAATATGGTCCCCAATATTTAGTCTGT
1 TTACAATATGGTCCCCAACATTTAGTCCGT
*
1033358 TTGCAATATGGTCCCC
1 TTACAATATGGTCCCC
1033374 GGCCATTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (30 bp):
TTACAATATGGTCCCCAACATTTAGTCCGT
Found at i:1041158 original size:20 final size:20
Alignment explanation
Indices: 1041129--1041171 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1041119 TGTAATTATT
*
1041129 ATAATATTTTAAAATTAATA
1 ATAATATTTTAAAATAAATA
* *
1041149 ATAATTTTTTATAATAAATA
1 ATAATATTTTAAAATAAATA
1041169 ATA
1 ATA
1041172 TTAATTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATATTTTAAAATAAATA
Found at i:1041215 original size:22 final size:23
Alignment explanation
Indices: 1041158--1041202 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1041148 AATAATTTTT
*
1041158 TATAATAAAT-AATATTAATTAA
1 TATATTAAATAAATATTAATTAA
1041180 TATATTAAATAAATA-TAATTAA
1 TATATTAAATAAATATTAATTAA
1041202 T
1 T
1041203 CATTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATATTAAATAAATATTAATTAA
Found at i:1044327 original size:138 final size:138
Alignment explanation
Indices: 1044079--1044682 Score: 967
Period size: 138 Copynumber: 4.4 Consensus size: 138
1044069 ACTATTCATA
* * * * *
1044079 TCCATTATTTTTTCAGATAATATTTTATTATTGCCCTATTATGCCACTCATGTCCCCCGGAGAAC
1 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGAGAAC
1044144 TATTCATGTAAGTACCTATTATTTCTGATGG-GACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGG
66 TATTCATGTAAGTACCTATTATTTCTGA-GGAGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGG
*
1044208 GGCGAGCCT
130 GGCGCGCCT
*
1044217 TCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGAGAAC
1 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGAGAAC
*
1044282 TATTCATGTAAGTACCTATTATTTCTGAGGAGACTTGGCAAAGTGGTGAAAGTGCGTTCCCGGGG
66 TATTCATGTAAGTACCTATTATTTCTGAGGAGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGG
1044347 GCGCGCCT
131 GCGCGCCT
* * *
1044355 TCCATTATTTTATCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGTCCCTCGGAGAAC
1 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGAGAAC
* * * *
1044420 TATTCACGTCAGTACCTATTATTTCTGAGTAGACTTGGCAAAGTAGTGAAAGCGCGTTCCCGGGG
66 TATTCATGTAAGTACCTATTATTTCTGAGGAGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGG
1044485 GCGCGCCT
131 GCGCGCCT
* * * *
1044493 TCCATTATTTTGTCTGAGAATATGCTATCATTGCCCTATTATGTCACTCATGTCACCCGAAGAAC
1 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGAGAAC
* * * * * *
1044558 TATTTATATCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGTGTTCCCGAGG
66 TATTCATGTAAGTACCTATTATTTCTGAGGAGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGG
1044623 GCGCGCCT
131 GCGCGCCT
1044631 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
1 TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
1044683 CGAAATTGGA
Statistics
Matches: 434, Mismatches: 31, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
137 2 0.00
138 432 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (138 bp):
TCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGAGAAC
TATTCATGTAAGTACCTATTATTTCTGAGGAGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGG
GCGCGCCT
Found at i:1044754 original size:23 final size:23
Alignment explanation
Indices: 1044728--1044813 Score: 138
Period size: 23 Copynumber: 3.7 Consensus size: 23
1044718 ATGTGAAGTT
1044728 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
1044751 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
1044774 T-AGATAAATTGGATAAAATGTTA
1 TGA-ATAAATTGGATAAAATGTTA
* *
1044797 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
1044814 TGTGAAGTGA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.02
23 58 0.98
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:1044853 original size:63 final size:63
Alignment explanation
Indices: 1044777--1044898 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
1044767 AATGTTATAG
*
1044777 ATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGA
1 ATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGA
*
1044840 ATAAATTGTATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGT
1 ATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGT
1044899 GAGCATTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (63 bp):
ATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGA
Found at i:1044888 original size:23 final size:23
Alignment explanation
Indices: 1044840--1044889 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1044830 GGTTGTTTGA
* * *
1044840 ATAAATTGTATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
1044863 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
1044886 ATAA
1 ATAA
1044890 GTTGGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:1044983 original size:14 final size:14
Alignment explanation
Indices: 1044964--1044993 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1044954 TGATAAGTTG
*
1044964 GTTTTAATTTATAT
1 GTTTTAATGTATAT
1044978 GTTTTAATGTATAT
1 GTTTTAATGTATAT
1044992 GT
1 GT
1044994 CTTCGGCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:1045270 original size:21 final size:21
Alignment explanation
Indices: 1045246--1045306 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
1045236 ATAAAACCCT
1045246 GCGGGCTA-GACATGTAACCTA
1 GCGGGCTAGGA-ATGTAACCTA
*
1045267 GCGGGCTAGGAATGTAACCTT
1 GCGGGCTAGGAATGTAACCTA
*
1045288 GAGGGCTAGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
1045307 CTGCGTAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTA
Found at i:1045336 original size:42 final size:42
Alignment explanation
Indices: 1045288--1045378 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 42
1045278 ATGTAACCTT
* ** *
1045288 GAGGGCTAGGAATGTAACCCTGCGTAGATGACATATAAACTG
1 GAGGGCTAGGAATATAACCCTAAGGAGATGACATATAAACTG
* * * * *
1045330 GTGGGCTTGGCATATACCCCTAAGGAGATGACATCTAAACTG
1 GAGGGCTAGGAATATAACCCTAAGGAGATGACATATAAACTG
1045372 GAGGGCT
1 GAGGGCT
1045379 GGGCATCATC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (42 bp):
GAGGGCTAGGAATATAACCCTAAGGAGATGACATATAAACTG
Found at i:1047115 original size:18 final size:18
Alignment explanation
Indices: 1047069--1047116 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
1047059 TTTAAATAAA
* *
1047069 TAATAATTATATAAATAT
1 TAATATTTATATAAAAAT
1047087 T-AT-TTTA-ATAAAAAT
1 TAATATTTATATAAAAAT
1047102 TAATATTTATATAAA
1 TAATATTTATATAAA
1047117 TATAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 6 0.24
18 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATTTATATAAAAAT
Found at i:1047122 original size:17 final size:17
Alignment explanation
Indices: 1047068--1047123 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1047058 ATTTAAATAA
*
1047068 ATAATAATTATATAAAT
1 ATAATATTTATATAAAT
* *
1047085 ATTAT-TTTA-ATAAAA
1 ATAATATTTATATAAAT
1047100 ATTAATATTTATATAAAT
1 A-TAATATTTATATAAAT
1047118 ATAATA
1 ATAATA
1047124 ATAGAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 13 0.42
18 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATATTTATATAAAT
Found at i:1049296 original size:29 final size:29
Alignment explanation
Indices: 1049261--1049342 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1049251 AAACTAAATT
* *
1049261 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1049290 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1049319 GATGTCATTGCTTATATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1049343 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1053978 original size:29 final size:29
Alignment explanation
Indices: 1053943--1054024 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1053933 AAACTAAATT
* *
1053943 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1053972 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
1054001 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1054025 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Done.