Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003927.1 Hibiscus syriacus cultivar Beakdansim tig00008489_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: 56684
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:324 original size:31 final size:31
Alignment explanation
Indices: 237--358 Score: 131
Period size: 31 Copynumber: 4.0 Consensus size: 31
227 TACAACTGAG
* * * *
237 GGACTAAAATCGAA-TGAATCGATAATATTAA
1 GGACTATAATCGAACAG-ATCGATAACATTAT
* *
268 GGACCATAATC-AACGGATCGATAACATTAT
1 GGACTATAATCGAACAGATCGATAACATTAT
* * *
298 GTATTATAATCGAACAGATCAATAACATTAT
1 GGACTATAATCGAACAGATCGATAACATTAT
*
329 GGACTATAATCGAACAAATCGATAACATTA
1 GGACTATAATCGAACAGATCGATAACATTA
359 GAGACCATGT
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
30 22 0.29
31 53 0.71
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (31 bp):
GGACTATAATCGAACAGATCGATAACATTAT
Found at i:5117 original size:36 final size:32
Alignment explanation
Indices: 5077--5266 Score: 170
Period size: 32 Copynumber: 5.8 Consensus size: 32
5067 TAGATACTCG
*
5077 TATTTTAAGTTGGAACTTGTTTTTAGGTTGCAACCA
1 TATTTTAAGTTGGAACTTG-TTTTA-GAT--AACCA
* * *
5113 TATTTTAGGTTGAAACTTGTTTTAGATACCCA
1 TATTTTAAGTTGGAACTTGTTTTAGATAACCA
*
5145 TATTTTAAGTTGGAACTTGATTTTAGGTTGCAACCA
1 TATTTTAAGTTGGAACTTG-TTTTA-GAT--AACCA
* * * *
5181 TATTGTAGGTTAGAACTTGTTTTAGATACCCA
1 TATTTTAAGTTGGAACTTGTTTTAGATAACCA
*
5213 TATTTTAAGTTGGAACTTGCTTTTGGAT-A-C-
1 TATTTTAAGTTGGAACTTG-TTTTAGATAACCA
* *
5243 TATTTTAGGTTAGAACTTGTTTTA
1 TATTTTAAGTTGGAACTTGTTTTA
5267 AGTTGTAATC
Statistics
Matches: 128, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
29 4 0.03
30 17 0.13
31 1 0.01
32 41 0.32
33 12 0.09
34 6 0.05
35 10 0.08
36 37 0.29
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (32 bp):
TATTTTAAGTTGGAACTTGTTTTAGATAACCA
Found at i:5137 original size:17 final size:17
Alignment explanation
Indices: 5079--5137 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
5069 GATACTCGTA
* *
5079 TTTTAAGTTGGAACTTG
1 TTTTAGGTTGAAACTTG
* * *
5096 TTTTTAGGTTGCAACCATA
1 -TTTTAGGTTG-AAACTTG
5115 TTTTAGGTTGAAACTTG
1 TTTTAGGTTGAAACTTG
5132 TTTTAG
1 TTTTAG
5138 ATACCCATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 10 0.31
18 19 0.59
19 3 0.09
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.47
Consensus pattern (17 bp):
TTTTAGGTTGAAACTTG
Found at i:5155 original size:68 final size:68
Alignment explanation
Indices: 5065--5266 Score: 283
Period size: 68 Copynumber: 3.1 Consensus size: 68
5055 AGGGTGAATG
* * * *
5065 TTTAGATACTCGTATTTTAAGTTGGAACTTGTTTTTAGGTTGCAACCATATTTTAGGTT-GAAAC
1 TTTAGATACCCATATTTTAAGTTGGAACTTGATTTTAGGTTGCAACCATATTGTAGGTTAG-AAC
5129 TTGT
65 TTGT
5133 TTTAGATACCCATATTTTAAGTTGGAACTTGATTTTAGGTTGCAACCATATTGTAGGTTAGAACT
1 TTTAGATACCCATATTTTAAGTTGGAACTTGATTTTAGGTTGCAACCATATTGTAGGTTAGAACT
5198 TGT
66 TGT
* * *
5201 TTTAGATACCCATATTTTAAGTTGGAACTTGCTTTT-GGAT---A-C-TATTTTAGGTTAGAACT
1 TTTAGATACCCATATTTTAAGTTGGAACTTGATTTTAGGTTGCAACCATATTGTAGGTTAGAACT
5260 TGT
66 TGT
5263 TTTA
1 TTTA
5267 AGTTGTAATC
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
62 23 0.18
63 1 0.01
64 1 0.01
67 3 0.02
68 97 0.77
69 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (68 bp):
TTTAGATACCCATATTTTAAGTTGGAACTTGATTTTAGGTTGCAACCATATTGTAGGTTAGAACT
TGT
Found at i:16155 original size:20 final size:20
Alignment explanation
Indices: 16118--16166 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
16108 GGAAGCCTGG
16118 AAATAA-AATTTGTAAAA-T
1 AAATAATAATTTGTAAAATT
*
16136 AAATAATAATGTTTTAAAATT
1 AAATAATAAT-TTGTAAAATT
16157 AAAT-ATAATT
1 AAATAATAATT
16167 GATTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 4 0.15
20 12 0.44
21 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
AAATAATAATTTGTAAAATT
Found at i:16239 original size:16 final size:15
Alignment explanation
Indices: 16201--16248 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
16191 TAATAATTAA
16201 TAATATTTTT-ATATT
1 TAAT-TTTTTAATATT
16216 TAATTTTTTAATATT
1 TAATTTTTTAATATT
16231 TATATTTTTTAA-ATT
1 TA-ATTTTTTAATATT
16246 TAA
1 TAA
16249 AATATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.19
15 16 0.52
16 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATTTTTTAATATT
Found at i:21975 original size:27 final size:27
Alignment explanation
Indices: 21941--21994 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21931 GATGAAAAGT
21941 AAGACTAGCACAGATAGAAGTCATAAG
1 AAGACTAGCACAGATAGAAGTCATAAG
21968 AAGACTAGCACAGATAGAAGTCATAAG
1 AAGACTAGCACAGATAGAAGTCATAAG
21995 CAGATAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (27 bp):
AAGACTAGCACAGATAGAAGTCATAAG
Found at i:26807 original size:20 final size:18
Alignment explanation
Indices: 26784--26827 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
26774 TTATTTTAAA
*
26784 TAAAAATTTAATATTATGTT
1 TAAAAATTTAA-ATT-TCTT
26804 TAAAAA-TTAAATTTCTT
1 TAAAAATTTAAATTTCTT
26821 TAAAAAT
1 TAAAAAT
26828 ACAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 4 0.18
20 6 0.27
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAAAATTTAAATTTCTT
Found at i:45109 original size:23 final size:22
Alignment explanation
Indices: 45061--45109 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
45051 ACAGAATGTC
45061 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
45082 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
45105 AAGGA
1 AAGGA
45110 AGAAATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:46707 original size:23 final size:23
Alignment explanation
Indices: 46639--46699 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
46629 ACATTTTATA
*
46639 TGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
46662 CGGAACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
46685 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
46700 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:51624 original size:23 final size:23
Alignment explanation
Indices: 51594--51653 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
51584 CATTTTATAT
*
51594 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
51617 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
51640 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
51654 TTATACGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Done.