Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006538.1 Hibiscus syriacus cultivar Beakdansim tig00015965_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: 65504
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:11718 original size:3 final size:3
Alignment explanation
Indices: 11712--11812 Score: 112
Period size: 3 Copynumber: 33.0 Consensus size: 3
11702 CATCATCATC
* * * *
11712 ATT ATT ATT ATC ATT ATT ATT ATT GTT TTT ATT ATT ATC ATT ATT AGTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * *
11761 TTT AATT CTT CTT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11807 ATT ATT
1 ATT ATT
11813 CATTGAATCA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
3 79 0.95
4 4 0.05
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:14991 original size:10 final size:9
Alignment explanation
Indices: 14958--14992 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
14948 TTTAATCAAT
*
14958 AAATCTATC
1 AAATCTGTC
14967 AAATCTGTC
1 AAATCTGTC
14976 AAATCTGTC
1 AAATCTGTC
14985 GAAATCTG
1 -AAATCTG
14993 GGATTTGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (9 bp):
AAATCTGTC
Found at i:24364 original size:324 final size:318
Alignment explanation
Indices: 23745--24386 Score: 1011
Period size: 324 Copynumber: 2.0 Consensus size: 318
23735 AGCCTGATCG
* * *
23745 AATTGAGGTTAATGAAGCATTAGAACTTCAAAATAGGATCATTGTACTGGAGAAAGAAAATCAAC
1 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
*
23810 ATGCTGATAGCAAGGTGCATGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAGT
66 ATGCTGATAGCAAGGTGCAGGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAGT
* *
23875 TCCGAGAAAGAAAAAGCTAGTTTGAAGCAGAAGCAGTTTTATGATAAAATTCAAGATTTGCAGTG
131 TCCGAGAAAGAAAAAGCTAGTATGAAGCAGAAGCAGTTTTATGAGAAAATTCAAGATTTGCAGTG
* *
23940 TCAGCTCGATACAGCCCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAAGCAATT
196 TCAACTCGATACAGCCCAAAGAGAAATTGTGGAGTTGAAACTAGAGCTTGCTGAGAGAAGCAATT
* *
24005 GCATTAAAGTCTTGAATGAAAGCCTTGAGACTTCAAAATCGGAGAGCAACAGGCTTAA
261 GCATTAAAGTCTTAAATGAAAGCCTTGAGACTTCAAAATCGGAAAGCAACAGGCTTAA
24063 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
1 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
* * * * *
24128 TTGTTGATAGCAAGAG-GCAGGCATTGTTGGAAGAGTTATGTATTACTAAAGAAATGCTCTAGTG
66 ATGCTGATAGCAAG-GTGCAGGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAG
*
24192 TTCCGAGAAAGAAAATGCTAGTATGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATT
130 TTCCGAGAAAGAAAAAGCTAGTATGAAG-----C-AGAAGCAGTTTTATGAGAAAATTCAAGATT
*
24257 TGCAGTGTCAACTCGATAC-GTCTCAAAGAGAAATTGTGGAGTTGAAACTAGAGCTTGCTGAGAG
189 TGCAGTGTCAACTCGATACAG-CCCAAAGAGAAATTGTGGAGTTGAAACTAGAGCTTGCTGAGAG
* *
24321 AAGCAGTTGCATTAAAGTCTTAAATG-AAGACCTTGAGACTTCAAAATCGGAAAGCAACGGGCTT
253 AAGCAATTGCATTAAAGTCTTAAATGAAAG-CCTTGAGACTTCAAAATCGGAAAGCAACAGGCTT
24385 AA
317 AA
24387 GAGCAAAATG
Statistics
Matches: 296, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
318 144 0.49
319 1 0.00
323 5 0.02
324 146 0.49
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (318 bp):
AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
ATGCTGATAGCAAGGTGCAGGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAGT
TCCGAGAAAGAAAAAGCTAGTATGAAGCAGAAGCAGTTTTATGAGAAAATTCAAGATTTGCAGTG
TCAACTCGATACAGCCCAAAGAGAAATTGTGGAGTTGAAACTAGAGCTTGCTGAGAGAAGCAATT
GCATTAAAGTCTTAAATGAAAGCCTTGAGACTTCAAAATCGGAAAGCAACAGGCTTAA
Found at i:33991 original size:36 final size:32
Alignment explanation
Indices: 33933--34140 Score: 213
Period size: 32 Copynumber: 6.2 Consensus size: 32
33923 CATATTTTGA
33933 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGATCAG
1 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGG----G
*
33970 TCGGGTCGGGTTTTTTAAGTGTGATATTCGAG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
34002 TC-GGTCGGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
* * * * *
34033 TCAGATCGAGTTTTTTGAGTGTGATATTCAGG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
34065 TCGGGTCGGGTCTGATTTGTTTAAGTGTGATATTCGGG
1 TCGGGTC-GG---G-TTT-TTTAAGTGTGATATTCGGG
** *
34103 TCGGGTATGGTTTTTTAAGTGTGACAATT-GGG
1 TCGGGTCGGGTTTTTTAAGTGTGA-TATTCGGG
34135 TCGGGT
1 TCGGGT
34141 TTAGGGTGAA
Statistics
Matches: 149, Mismatches: 14, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
31 30 0.20
32 53 0.36
33 7 0.05
34 1 0.01
36 21 0.14
37 14 0.09
38 23 0.15
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (32 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
Found at i:34098 original size:101 final size:100
Alignment explanation
Indices: 33944--34126 Score: 262
Period size: 99 Copynumber: 1.8 Consensus size: 100
33934 CGGGTCGGGT
* *
33944 TTTTTTAAGTGTGATATTCGGATCAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGAGTC-GGTC
1 TTTTTTAAGTGTGATATTCGGATCAGTCGGGTCGGATTTTTTAAGTGTGATATTCGAGTCGGGTA
34008 GGGTTTTTTAAGTGTGATATTCGGGTCAGATCGAG
66 GGGTTTTTTAAGTGTGATATTCGGGTCAGATCGAG
* * * *
34043 TTTTTTGAGTGTGATATTCAGG-TCGGGTCGGGTCTGATTTGTTTAAGTGTGATATTCGGGTCGG
1 TTTTTTAAGTGTGATATTC-GGATC-AGTCGGGTCGGATTT-TTTAAGTGTGATATTCGAGTCGG
*
34107 GTATGGTTTTTTAAGTGTGA
63 GTAGGGTTTTTTAAGTGTGA
34127 CAATTGGGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
99 20 0.27
100 14 0.19
101 20 0.27
102 19 0.26
ACGTcount: A:0.17, C:0.09, G:0.32, T:0.42
Consensus pattern (100 bp):
TTTTTTAAGTGTGATATTCGGATCAGTCGGGTCGGATTTTTTAAGTGTGATATTCGAGTCGGGTA
GGGTTTTTTAAGTGTGATATTCGGGTCAGATCGAG
Found at i:37418 original size:31 final size:31
Alignment explanation
Indices: 37383--37445 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
37373 AGTTTGAATC
*
37383 TTTACATTGTTAATAGAATAATAAGTTGGGT
1 TTTACATTGTTAATAGAATAATAAGTCGGGT
37414 TTTACATTGTTAATAGAATAATAAGTCGGGT
1 TTTACATTGTTAATAGAATAATAAGTCGGGT
37445 T
1 T
37446 GGAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (31 bp):
TTTACATTGTTAATAGAATAATAAGTCGGGT
Found at i:39263 original size:34 final size:34
Alignment explanation
Indices: 39225--39359 Score: 229
Period size: 34 Copynumber: 4.0 Consensus size: 34
39215 AAGTATTTTG
*
39225 ATGTTATGTCTTTTTAAAGAGATTGGTTTACTTT
1 ATGTTATGTCTCTTTAAAGAGATTGGTTTACTTT
39259 ATGTTATGTCTCTTTAAAGAGATTGGTTTACTTT
1 ATGTTATGTCTCTTTAAAGAGATTGGTTTACTTT
*
39293 ATGTTA--TCTCTTTAAAGAGATTGGTTTACTTC
1 ATGTTATGTCTCTTTAAAGAGATTGGTTTACTTT
*
39325 ATGTTATGTCTCTTTAAAGAGACTGGTTTACTTT
1 ATGTTATGTCTCTTTAAAGAGATTGGTTTACTTT
39359 A
1 A
39360 GGAATAAAGT
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
32 31 0.33
34 64 0.67
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (34 bp):
ATGTTATGTCTCTTTAAAGAGATTGGTTTACTTT
Found at i:42207 original size:3 final size:3
Alignment explanation
Indices: 42199--42228 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42189 TAGTGTACCC
42199 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42229 ACGAGAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48074 original size:2 final size:2
Alignment explanation
Indices: 48067--48092 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48057 TATGGAGTTC
48067 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
48093 CATTCAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50226 original size:32 final size:32
Alignment explanation
Indices: 50181--50243 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
50171 AGCAACAGAC
50181 CCATAGTTCGGTCCTTCACTTTCGTTTGAGAA
1 CCATAGTTCGGTCCTTCACTTTCGTTTGAGAA
50213 CCATAGCTT-GGTCCTTCACTTTCGTTTGAGA
1 CCATAG-TTCGGTCCTTCACTTTCGTTTGAGA
50244 CCCACTCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (32 bp):
CCATAGTTCGGTCCTTCACTTTCGTTTGAGAA
Found at i:59833 original size:18 final size:17
Alignment explanation
Indices: 59801--59846 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
59791 AATTTATATT
59801 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
59818 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
59836 ATTAAATATAT
1 AGTAAA-ATAT
59847 CATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:63927 original size:2 final size:2
Alignment explanation
Indices: 63920--63944 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63910 TGTCAGTTTT
63920 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
63945 TATATAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.