Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005315.1 Hibiscus syriacus cultivar Beakdansim tig00012032_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: 85792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9499 original size:15 final size:16
Alignment explanation
Indices: 9479--9512 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9469 GTGGTTAACC
*
9479 AAATTTTT-TTTCTTT
1 AAATTTTTCTTTATTT
9494 AAATTTTTCTTTATTT
1 AAATTTTTCTTTATTT
9510 AAA
1 AAA
9513 AATGCTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
AAATTTTTCTTTATTT
Found at i:11185 original size:20 final size:20
Alignment explanation
Indices: 11160--11222 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
11150 CCGTTAGACA
11160 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
*
11180 GGGGGGGAATCGGTACCCTCT
1 -GGGGGGAATCGGTACCCCCT
*
11201 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
11221 GG
1 GG
11223 ACAATTTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 20 0.51
21 19 0.49
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.17
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:11186 original size:21 final size:21
Alignment explanation
Indices: 11160--11222 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
11150 CCGTTAGACA
11160 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
*
11181 GGGGGGAATCGGTACCCTCT-
1 GGGGGGAATCGGTACCCCCTG
*
11201 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
11222 G
1 G
11223 ACAATTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.17
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:17961 original size:19 final size:19
Alignment explanation
Indices: 17937--17979 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
17927 TTAATTTACG
*
17937 ATTGTGATTGTAAATCTTT
1 ATTGTGATTGTAAATATTT
17956 ATTGTGATTGTAAATATTT
1 ATTGTGATTGTAAATATTT
17975 ATTGT
1 ATTGT
17980 AATTTGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (19 bp):
ATTGTGATTGTAAATATTT
Found at i:26069 original size:60 final size:60
Alignment explanation
Indices: 25976--26103 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
25966 ACAATCGGAT
* * * * *
25976 GATCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGCAACGACCTATGGTCGAGA
1 GATCATTTTGAAACTTTTAATAATCGAGGGACTCAACAAAGCAACGACCTATAGTCAAGA
* * * *
26036 GATCATTTTGAAACTTTTAATAATCCG-GGGACTCAATAAAGTAATGTCCTATAGTCAAGA
1 GATCATTTTGAAACTTTTAATAAT-CGAGGGACTCAACAAAGCAACGACCTATAGTCAAGA
*
26096 GACCATTT
1 GATCATTT
26104 ATGTACTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (60 bp):
GATCATTTTGAAACTTTTAATAATCGAGGGACTCAACAAAGCAACGACCTATAGTCAAGA
Found at i:26159 original size:30 final size:31
Alignment explanation
Indices: 26118--26188 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
26108 ACTTTACCCT
26118 TAAAATT-TAACAATTA-A-ATTATATAAT-
1 TAAAATTATAACAATTAGATATTATATAATA
*
26145 TAATTAATTATAACAATTAGATTTTATATAATA
1 TAA--AATTATAACAATTAGATATTATATAATA
26178 TAAAATTATAA
1 TAAAATTATAA
26189 ACTTTCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
27 3 0.08
29 4 0.11
30 9 0.24
31 9 0.24
32 9 0.24
33 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAAATTATAACAATTAGATATTATATAATA
Found at i:38056 original size:36 final size:36
Alignment explanation
Indices: 38009--38079 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
37999 AGTCTAAAAG
*
38009 AAAATCAGATAATCGGATCGAACTGGAATTTTACAA
1 AAAATCAGATAATCGGATCGAACTAGAATTTTACAA
38045 AAAATCAGATAATCGGATCGAACTAGAATTTTACA
1 AAAATCAGATAATCGGATCGAACTAGAATTTTACA
38080 TAAAGTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (36 bp):
AAAATCAGATAATCGGATCGAACTAGAATTTTACAA
Found at i:42019 original size:24 final size:24
Alignment explanation
Indices: 41992--42040 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
41982 TGCATGACAT
**
41992 TGTACATATTTGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
42016 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
42040 T
1 T
42041 CAGGAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:42469 original size:60 final size:61
Alignment explanation
Indices: 42375--42488 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 61
42365 GAAGATGGAT
* * * *
42375 ACGACCTTATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTAGCATATCCAGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
42436 ACGACCTTATGT-GCATATCCAGATTAGCACTATAGCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTAGCATATCCAGATTAGCACTATAGCGTAAGCTTAGTGCAGGT
42489 TTAGCACTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 37 0.76
61 12 0.24
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (61 bp):
ACGACCTTATGTAGCATATCCAGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:47364 original size:18 final size:18
Alignment explanation
Indices: 47343--47404 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
47333 CATATGTCCC
*
47343 GAAGGACCACTATGTATA
1 GAAGGACCACTATGTACA
* *
47361 GAAGGACCACTATGTCCC
1 GAAGGACCACTATGTACA
* *
47379 GAAGGACCACTATGTCCC
1 GAAGGACCACTATGTACA
47397 GAAGGACC
1 GAAGGACC
47405 GCGTAGACCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.16
Consensus pattern (18 bp):
GAAGGACCACTATGTACA
Found at i:47401 original size:36 final size:36
Alignment explanation
Indices: 47335--47404 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
47325 ATATAACACA
*
47335 TATGTCCCGAAGGACCACTATGTATAGAAGGACCAC
1 TATGTCCCGAAGGACCACTATGTACAGAAGGACCAC
* *
47371 TATGTCCCGAAGGACCACTATGTCCCGAAGGACC
1 TATGTCCCGAAGGACCACTATGTACAGAAGGACC
47405 GCGTAGACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.29, G:0.23, T:0.19
Consensus pattern (36 bp):
TATGTCCCGAAGGACCACTATGTACAGAAGGACCAC
Found at i:52802 original size:48 final size:48
Alignment explanation
Indices: 52750--52854 Score: 192
Period size: 48 Copynumber: 2.2 Consensus size: 48
52740 GTTCAAAGAC
52750 TAAATCTAAACTCTAACTATTCTCACATGACCTAGATTAAAAGAAATA
1 TAAATCTAAACTCTAACTATTCTCACATGACCTAGATTAAAAGAAATA
* *
52798 TAAATCTAAACTCTAACTATTTTCACATGACCTAGATTAAAAGAAATC
1 TAAATCTAAACTCTAACTATTCTCACATGACCTAGATTAAAAGAAATA
52846 TAAATCTAA
1 TAAATCTAA
52855 GGATTTAATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (48 bp):
TAAATCTAAACTCTAACTATTCTCACATGACCTAGATTAAAAGAAATA
Found at i:52908 original size:20 final size:20
Alignment explanation
Indices: 52880--52933 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
52870 TCAAGTGTCT
* *
52880 AAAACTAAATTAGAAATATA
1 AAAAATAAATTAAAAATATA
**
52900 AAAAATAAAGAAAAAATATA
1 AAAAATAAATTAAAAATATA
* *
52920 TATAATAAATTAAA
1 AAAAATAAATTAAA
52934 GGGTTAAATG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAAATAAATTAAAAATATA
Found at i:62384 original size:63 final size:63
Alignment explanation
Indices: 62285--62411 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
62275 GTTTTGAAGA
62285 TTCAAAATTTCCAAATCATCTTCTTAAATTGACAAAAACGCTTTATGGTTTAAAACAATCTCC
1 TTCAAAATTTCCAAATCATCTTCTTAAATTGACAAAAACGCTTTATGGTTTAAAACAATCTCC
62348 TTCAAAATTTCCAAATCATCTTCTTAAATTGACAAAAACGCTTTATGGTTTAAAACAATCTCC
1 TTCAAAATTTCCAAATCATCTTCTTAAATTGACAAAAACGCTTTATGGTTTAAAACAATCTCC
62411 T
1 T
62412 AGAGCTTGGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (63 bp):
TTCAAAATTTCCAAATCATCTTCTTAAATTGACAAAAACGCTTTATGGTTTAAAACAATCTCC
Found at i:63767 original size:22 final size:21
Alignment explanation
Indices: 63737--63817 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 21
63727 TAGAGCAGGA
*
63737 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTGAA-G
* *
63759 GGAACCGATTTCCCCTTTGAATG
1 GGAACCGA-TACCCCCTTGAA-G
* * * *
63782 GGAACTGATTCCCCCATGTAG
1 GGAACCGATACCCCCTTGAAG
*
63803 GGAATCGATACCCCC
1 GGAACCGATACCCCC
63818 CACGAGGTCT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 13 0.28
22 16 0.34
23 18 0.38
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (21 bp):
GGAACCGATACCCCCTTGAAG
Found at i:63778 original size:23 final size:23
Alignment explanation
Indices: 63747--63796 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
63737 GGAATCGATA
*
63747 CCCCCTTGAAGGGGAACCGATTT
1 CCCCCTTGAAGGGGAACCGATTC
* * *
63770 CCCCTTTGAATGGGAACTGATTC
1 CCCCCTTGAAGGGGAACCGATTC
63793 CCCC
1 CCCC
63797 ATGTAGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.24
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:65274 original size:41 final size:41
Alignment explanation
Indices: 65217--65300 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
65207 TCCCCTTTGT
65217 ATAACGGTCAAAATATTTGAATTTTTATACTGCATGAACTG
1 ATAACGGTCAAAATATTTGAATTTTTATACTGCATGAACTG
65258 ATAACGGTCAAAATATTTGAATTTTTATACTGCATGAACTG
1 ATAACGGTCAAAATATTTGAATTTTTATACTGCATGAACTG
65299 AT
1 AT
65301 TCCCTATGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (41 bp):
ATAACGGTCAAAATATTTGAATTTTTATACTGCATGAACTG
Found at i:76734 original size:56 final size:56
Alignment explanation
Indices: 76644--76843 Score: 240
Period size: 56 Copynumber: 3.6 Consensus size: 56
76634 CGCAGGCCCC
* * * * * *
76644 AAAAATAGGGGCCCCGAAATTGATTATATTTATCAGTTGTTGCCATTAATAAGCAT
1 AAAAATAGAGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAAAAGCAT
* * * *
76700 AAAAATAGAGGTCCTGAAATCGAGTATATCTATCAGTTATTGCAATTAAAAAACAT
1 AAAAATAGAGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAAAAGCAT
* * *
76756 AAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAGAAGTAT
1 AAAAATAGAGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAAAAGCAT
* * *
76812 AAAAATA-AGGGTCCTGAAATCGAATATATCTA
1 AAAAATAGA-GGCCCCGAAATCGAGTATATCTA
76844 AAAAATAAAT
Statistics
Matches: 122, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
56 122 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (56 bp):
AAAAATAGAGGCCCCGAAATCGAGTATATCTATCAGTTATTGCCATTAAAAAGCAT
Found at i:77257 original size:132 final size:135
Alignment explanation
Indices: 77078--77349 Score: 347
Period size: 139 Copynumber: 2.0 Consensus size: 135
77068 ATAATATTAT
*
77078 AAAAGATCATTCTTTAGTTTGGACGGAGAATCGTTATTGTAATTCTGT-TTCTTTT-T-AAA-AT
1 AAAAGATCATTCTTTAGTTTGGACGGAGAATCGTTATCGTAATTCTGTATT-TTTTATAAAAGAT
* * * * *
77139 G-ATGGAAATCTGGGTTATAAGCGTCAATCTCCTCTTTTGGTCTCGGTGTATGGTATTAATGTGA
65 GAATGGAAATCAGGGTCATAAGCGTCAATCTCCTCTTTCGGTCTCGGTGTATAGTAGTAATGTGA
77203 GATAAA
130 GATAAA
* * * *
77209 AAAAGATTATTCTTTTAGTTTGGATGGAGAATGGTTATCGTGATTCTGTATTTTTTATAGAAAAA
1 AAAAGATCATTC-TTTAGTTTGGACGGAGAATCGTTATCGTAATTCTGTATTTTTTAT---AAAA
* * *
77274 GATGAATGGAAATCAGGGTCATAGGCGTCAATCTCCTCTTTCGGTCTTGGTGTATAGTAGTGATG
62 GATGAATGGAAATCAGGGTCATAAGCGTCAATCTCCTCTTTCGGTCTCGGTGTATAGTAGTAATG
77339 TGAGATAAA
127 TGAGATAAA
77348 AA
1 AA
77350 TGTGTGAAGT
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
131 11 0.09
132 36 0.30
133 3 0.03
137 3 0.03
138 3 0.03
139 63 0.53
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (135 bp):
AAAAGATCATTCTTTAGTTTGGACGGAGAATCGTTATCGTAATTCTGTATTTTTTATAAAAGATG
AATGGAAATCAGGGTCATAAGCGTCAATCTCCTCTTTCGGTCTCGGTGTATAGTAGTAATGTGAG
ATAAA
Found at i:78451 original size:31 final size:31
Alignment explanation
Indices: 78413--78477 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
78403 ACGACTGAGA
* * *
78413 GACTAAAATCGAACGGATCGATAATGTTATG
1 GACTAAAATCAAACGGATCAATAATGTTAGG
78444 GACTAAAATCAAACGGATCAATAATGTTAGG
1 GACTAAAATCAAACGGATCAATAATGTTAGG
78475 GAC
1 GAC
78478 CATTCCCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (31 bp):
GACTAAAATCAAACGGATCAATAATGTTAGG
Done.