Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004759.1 Hibiscus syriacus cultivar Beakdansim tig00010738_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: 59568
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:8116 original size:40 final size:40
Alignment explanation
Indices: 8067--8188 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
8057 TGTATGTTTA
*
8067 TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
8107 TAATACACTTCGGTGTATATGGTAGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
8147 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
8187 TA
1 TA
8189 GCACTATGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:8381 original size:44 final size:45
Alignment explanation
Indices: 8281--8419 Score: 208
Period size: 45 Copynumber: 3.1 Consensus size: 45
8271 GTTTCTAGTT
*
8281 TATTGGTAAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAATA
* * *
8326 TATTGGAAAAATAAGCTTACGAGCTTATGGAAT-AATGGTAATTA
1 TATTGGTAAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAATA
* * *
8370 TATTGGTAAAATAAGCTTATGAGCTTATGGGATAAATAGTAAATA
1 TATTGGTAAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAATA
8415 TATTG
1 TATTG
8420 ATAAGAAATG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
44 40 0.47
45 45 0.53
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (45 bp):
TATTGGTAAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAATA
Found at i:13326 original size:52 final size:52
Alignment explanation
Indices: 13248--13350 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
13238 TTATAATATT
13248 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
13300 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
13351 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:17922 original size:52 final size:52
Alignment explanation
Indices: 17844--17946 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
17834 TTATAATATT
17844 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
17896 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
17947 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:29841 original size:23 final size:20
Alignment explanation
Indices: 29790--29849 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
29780 TTTTGGTGCA
*
29790 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
29809 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
29830 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
29850 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:40504 original size:54 final size:54
Alignment explanation
Indices: 40418--40864 Score: 562
Period size: 54 Copynumber: 8.3 Consensus size: 54
40408 TTACCAAATA
*
40418 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGAAGAACAACCTTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCTTTTC
* * * *
40472 GGCCCTAAGTGTGTAATTCACAGAATTCATCATATGTTGTTGAACAACCGTTTT-
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACC-TTTTC
* ** *
40526 GGCACTAAGTGTGCAATTCACAGAATTTGTCATATGTTGATGAACAACAGTTTT-
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAAC-CTTTTC
* * * *
40580 GGCACTAAGTGTGCAATTCACGAAATTAATTATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCTTTTC
* * ** **
40634 GGAACTAAGTATGCAATTCACGGAATTTGTCATATGTTGATGAACAATAGTTTT-
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAA-CCTTTTC
* *
40688 GGCACTAAGTGTGCAATTCACGGAATTAATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCTTTTC
* * * * *
40742 GGAACTAAGTATACAATTCACGGAATTCATCATAGGTTGATGAACAA-CTGTTTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCT-TTTC
* *
40796 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTCATGAACAA-CTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCT-TTTC
40850 GGCACTAAGTGTGCA
1 GGCACTAAGTGTGCA
40865 TCTCAACGAA
Statistics
Matches: 339, Mismatches: 48, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
53 7 0.02
54 325 0.96
55 7 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCTTTTC
Found at i:40615 original size:108 final size:108
Alignment explanation
Indices: 40418--40864 Score: 628
Period size: 108 Copynumber: 4.1 Consensus size: 108
40408 TTACCAAATA
* * *
40418 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGAAGAACAAC-CTTTTCGGCCCTAAGT
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACAGTTTT-GGCACTAAGT
* * * *
40482 GTGTAATTCACAGAATTCATCATATGTTGTTGAACAACCGTTTT
65 GTGCAATTCACAGAATTAATCATATGTTGATGAACAACCGTTTC
* **
40526 GGCACTAAGTGTGCAATTCACAGAATTTGTCATATGTTGATGAACAACAGTTTTGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACAGTTTTGGCACTAAGTG
*
40591 TGCAATTCAC-GAAATTAATTATATGTTGATGAACAACCGTTTC
66 TGCAATTCACAG-AATTAATCATATGTTGATGAACAACCGTTTC
* * ** *
40634 GGAACTAAGTATGCAATTCACGGAATTTGTCATATGTTGATGAACAATAGTTTTGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACAGTTTTGGCACTAAGTG
*
40699 TGCAATTCACGGAATTAATCATATGTTGATGAACAACCGTTTC
66 TGCAATTCACAGAATTAATCATATGTTGATGAACAACCGTTTC
* * * * * *
40742 GGAACTAAGTATACAATTCACGGAATTCATCATAGGTTGATGAACAACTGTTTGGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACAGTTTTGGCACTAAGTG
* * *
40807 TGCAATTCACAGAATTCATCATATGTTCATGAACAACTGTTTC
66 TGCAATTCACAGAATTAATCATATGTTGATGAACAACCGTTTC
40850 GGCACTAAGTGTGCA
1 GGCACTAAGTGTGCA
40865 TCTCAACGAA
Statistics
Matches: 306, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.00
108 300 0.98
109 5 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (108 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACAGTTTTGGCACTAAGTG
TGCAATTCACAGAATTAATCATATGTTGATGAACAACCGTTTC
Found at i:40689 original size:162 final size:161
Alignment explanation
Indices: 40418--40864 Score: 624
Period size: 162 Copynumber: 2.8 Consensus size: 161
40408 TTACCAAATA
* * *
40418 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGAAGAACAACCTTTTCGGCCCTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
* * *
40483 TGTAATTCACAGAATTCATCATATGTTGTTGAACAACCGTTTTGGCACTAAGTGTGCAATTCACA
66 TGCAATTCACAGAATTCATCATATGTTGATGAACAA-TGTTTTGGCACTAAGTGTGCAATTCACA
** *
40548 GAATTTGTCATATGTTGATGAACAACAGTTTT
130 GAATTAATCATATGTTGATGAACAACAGTTTC
* * * * *
40580 GGCACTAAGTGTGCAATTCACGAAATTAATTATATGTTGATGAACAACCGTTTCGGAACTAAGTA
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
* ** *
40645 TGCAATTCACGGAATTTGTCATATGTTGATGAACAATAGTTTTGGCACTAAGTGTGCAATTCACG
66 TGCAATTCACAGAATTCATCATATGTTGATGAACAAT-GTTTTGGCACTAAGTGTGCAATTCACA
*
40710 GAATTAATCATATGTTGATGAACAACCGTTTC
130 GAATTAATCATATGTTGATGAACAACAGTTTC
* * * * * *
40742 GGAACTAAGTATACAATTCACGGAATTCATCATAGGTTGATGAACAACTGTTTGGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
* *
40807 TGCAATTCACAGAATTCATCATATGTTCATGAACAACTGTTTCGGCACTAAGTGTGCA
66 TGCAATTCACAGAATTCATCATATGTTGATGAACAA-TGTTTTGGCACTAAGTGTGCA
40865 TCTCAACGAA
Statistics
Matches: 248, Mismatches: 35, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
162 247 1.00
163 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (161 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
TGCAATTCACAGAATTCATCATATGTTGATGAACAATGTTTTGGCACTAAGTGTGCAATTCACAG
AATTAATCATATGTTGATGAACAACAGTTTC
Found at i:52282 original size:36 final size:36
Alignment explanation
Indices: 52242--52373 Score: 153
Period size: 36 Copynumber: 3.8 Consensus size: 36
52232 GATAGCTATA
*
52242 AAAGATAAGGCTGGAATTTGAATTTGATTAGCTGCT
1 AAAGATAAGGCTGGAATTTGAATTTTATTAGCTGCT
* * * *
52278 AAAGATAAGGTTGTAATTTGATTTTTATTAGCCGCT
1 AAAGATAAGGCTGGAATTTGAATTTTATTAGCTGCT
* * *
52314 GAAGATAAGGTTGGAATTTGAATTTTATT---TACT
1 AAAGATAAGGCTGGAATTTGAATTTTATTAGCTGCT
* *
52347 AAAGATAAAGCTGAAATTTGAATTTTA
1 AAAGATAAGGCTGGAATTTGAATTTTA
52374 AATAAAATTG
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
33 25 0.30
36 57 0.70
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (36 bp):
AAAGATAAGGCTGGAATTTGAATTTTATTAGCTGCT
Done.