Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006552.1 Hibiscus syriacus cultivar Beakdansim tig00016014_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: 92463
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1444 original size:48 final size:50
Alignment explanation
Indices: 1391--1494 Score: 194
Period size: 48 Copynumber: 2.1 Consensus size: 50
1381 GCCATCTTTA
1391 TTGTTTAATTGATTAACATGTCT-AGTATCTCAGTTAC-AAAGAACCAAG
1 TTGTTTAATTGATTAACATGTCTAAGTATCTCAGTTACAAAAGAACCAAG
1439 TTGTTTAATTGATTAACATGTCTAAGTATCTCAGTTACAAAAGAACCAAG
1 TTGTTTAATTGATTAACATGTCTAAGTATCTCAGTTACAAAAGAACCAAG
1489 TTGTTT
1 TTGTTT
1495 GGTTGTTTCC
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 23 0.43
49 14 0.26
50 17 0.31
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (50 bp):
TTGTTTAATTGATTAACATGTCTAAGTATCTCAGTTACAAAAGAACCAAG
Found at i:5326 original size:20 final size:21
Alignment explanation
Indices: 5297--5337 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5287 AAATCGTTTA
5297 AATTGGATTT-TGGTTTATTT
1 AATTGGATTTATGGTTTATTT
* *
5317 AATTGTATTTATTGTTTATTT
1 AATTGGATTTATGGTTTATTT
5338 TTTTCTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (21 bp):
AATTGGATTTATGGTTTATTT
Found at i:8863 original size:26 final size:27
Alignment explanation
Indices: 8834--8886 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
8824 TATATTCATA
8834 TAAT-ATACAAAAAATATAT-TATTTTT
1 TAATAATA-AAAAAATATATATATTTTT
* *
8860 TAATAATAAAATAATATCTATATTTTT
1 TAATAATAAAAAAATATATATATTTTT
8887 ATTTACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATAATAAAAAAATATATATATTTTT
Found at i:25523 original size:12 final size:13
Alignment explanation
Indices: 25501--25535 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
25491 GAAATGTTTC
25501 ATTTTTATTTAAT
1 ATTTTTATTTAAT
*
25514 -TTTTTGTTTAAT
1 ATTTTTATTTAAT
25526 ATTTTTATTT
1 ATTTTTATTT
25536 TATGTATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
ATTTTTATTTAAT
Found at i:29048 original size:18 final size:19
Alignment explanation
Indices: 29027--29063 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29017 AAAAATACGA
29027 GAAAAAAGAAAGA-GAAAG
1 GAAAAAAGAAAGATGAAAG
*
29045 GAAAAGAGAAAGATGAAAG
1 GAAAAAAGAAAGATGAAAG
29064 CTTAACTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (19 bp):
GAAAAAAGAAAGATGAAAG
Found at i:39107 original size:28 final size:28
Alignment explanation
Indices: 39076--39130 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
39066 TAATGTTTAG
*
39076 GGTTTAGGATTTAGAGTTTATGTGATAA
1 GGTTTAGGATTTAGAGTTCATGTGATAA
*
39104 GGTTTGGGATTTAGAGTTCATGTGATA
1 GGTTTAGGATTTAGAGTTCATGTGATA
39131 GGATTTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.02, G:0.31, T:0.42
Consensus pattern (28 bp):
GGTTTAGGATTTAGAGTTCATGTGATAA
Found at i:39144 original size:28 final size:28
Alignment explanation
Indices: 39076--39145 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
39066 TAATGTTTAG
* *
39076 GGTTTAGGATTTAGAGTTTATGTGATAA
1 GGTTTAAGATTTAGAGTTCATGTGATAA
**
39104 GGTTTGGGATTTAGAGTTCATGTGAT-A
1 GGTTTAAGATTTAGAGTTCATGTGATAA
*
39131 GGATTTAAGTTTTAG
1 GG-TTTAAGATTTAG
39146 GGTTTAGAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 3 0.08
28 33 0.92
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (28 bp):
GGTTTAAGATTTAGAGTTCATGTGATAA
Found at i:39151 original size:7 final size:7
Alignment explanation
Indices: 39141--39201 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
39131 GGATTTAAGT
39141 TTTAGGG
1 TTTAGGG
*
39148 TTTAGAG
1 TTTAGGG
*
39155 TTTAAGG
1 TTTAGGG
*
39162 TTTA-TG
1 TTTAGGG
39168 TATTAGGG
1 T-TTAGGG
*
39176 ATTAGGG
1 TTTAGGG
* *
39183 ATTAGAG
1 TTTAGGG
39190 TTTAGGG
1 TTTAGGG
39197 TTTAG
1 TTTAG
39202 AATTTAGAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 2 0.05
7 40 0.93
8 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:41215 original size:2 final size:2
Alignment explanation
Indices: 41208--41236 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41198 CCATTACTGT
41208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41237 TAGAATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41833 original size:10 final size:10
Alignment explanation
Indices: 41818--41849 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
41808 ACAGGTAGAA
41818 TGGAATATTT
1 TGGAATATTT
41828 TGGAATATTT
1 TGGAATATTT
41838 TGGAATATTT
1 TGGAATATTT
41848 TG
1 TG
41850 AGTTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (10 bp):
TGGAATATTT
Found at i:42136 original size:13 final size:12
Alignment explanation
Indices: 42105--42138 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42095 TAGGTTCAAA
*
42105 TTCGAGCTTGAG
1 TTCGAGCTCGAG
42117 TTCGAGCTCGAG
1 TTCGAGCTCGAG
42129 TCTCGAGCTC
1 T-TCGAGCTC
42139 CAATCGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (12 bp):
TTCGAGCTCGAG
Found at i:46993 original size:3 final size:3
Alignment explanation
Indices: 46985--47025 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
46975 TTGTAATTAG
46985 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47026 AAAAATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:47430 original size:47 final size:46
Alignment explanation
Indices: 47379--47589 Score: 133
Period size: 47 Copynumber: 4.5 Consensus size: 46
47369 GGCTCCTACG
*
47379 TGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACA
1 TGATGAGGAAGTCTGGTCATCTAAGGGT-GATGACATGGTTCATACA
* * * * * * *
47426 TGATGAAGAACTCTGGCCATCTTTAGGCAGGGTGATAAC-TCGATTCCTACG
1 TGATGAGGAAGTCTGGTCATC--TA---AGGGTGATGACAT-GGTTCATACA
* * * * * * * *
47477 TGATGAGGACGGCTGGTTATCCTAA---TGTTGACACGGCTCCTACG
1 TGATGAGGAAGTCTGGTCAT-CTAAGGGTGATGACATGGTTCATACA
*
47521 TGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACA
1 TGATGAGGAAGTCTGGTCATCTAAGGGT-GATGACATGGTTCATACA
* * *
47568 TGATGAAGAACTCTGGCCATCT
1 TGATGAGGAAGTCTGGTCATCT
47590 TTAGGAAGGG
Statistics
Matches: 120, Mismatches: 32, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
43 4 0.03
44 29 0.24
46 1 0.01
47 49 0.41
49 2 0.02
50 3 0.03
51 26 0.22
52 6 0.05
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (46 bp):
TGATGAGGAAGTCTGGTCATCTAAGGGTGATGACATGGTTCATACA
Found at i:47565 original size:142 final size:142
Alignment explanation
Indices: 47238--47663 Score: 636
Period size: 142 Copynumber: 3.1 Consensus size: 142
47228 GAAACACGAT
* * * ** **
47238 TCCTACGTGATGAGGAAATCT-G--GTC-AA-GG--GATGACACGGCTCATACGCGATGAAGAGT
1 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
* * * * * *
47296 TCTGGTCATCTTTAAGAAGGGTGATAACTAGGTTCCTATGTAATGAGGACGGCTGATTAT-CTAA
66 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
*
47360 GGTTGACACGGC
131 TGTTGACACGGC
47372 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
* *
47437 TCTGGCCATCTTTAGGCAGGGTGATAACTCGATTCCTACGTGATGAGGACGGCTGGTTATCCTAA
66 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
47502 TGTTGACACGGC
131 TGTTGACACGGC
47514 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
47579 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
66 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
*
47644 TGTTGACAC-TC
131 TGTTGACACGGC
47655 TCCTACGTG
1 TCCTACGTG
47664 TCAGGGAGAT
Statistics
Matches: 265, Mismatches: 19, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
134 20 0.08
135 1 0.00
137 3 0.01
138 2 0.01
139 2 0.01
141 85 0.32
142 152 0.57
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (142 bp):
TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
TGTTGACACGGC
Found at i:48650 original size:23 final size:22
Alignment explanation
Indices: 48619--48662 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
48609 CTTTATTTAA
48619 TTTTTTTCTTTTTTCATTTTTC
1 TTTTTTTCTTTTTTCATTTTTC
*
48641 TTTTTCTTCTTTTTTTATTTTT
1 TTTTT-TTCTTTTTTCATTTTT
48663 TTAAGTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTCTTTTTTCATTTTTC
Found at i:62060 original size:3 final size:3
Alignment explanation
Indices: 62052--62092 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
62042 TTGTAATTAG
62052 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
62093 AAAAATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:63004 original size:47 final size:47
Alignment explanation
Indices: 62930--63023 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
62920 CTGAGCAACA
62930 ATATAAAGAAAGAGGCTAATTCTTCATTACCTTCAAAATGAACGAGG
1 ATATAAAGAAAGAGGCTAATTCTTCATTACCTTCAAAATGAACGAGG
* * *
62977 ATATGAAGAAAGAGGCTACTTCTTCATTACCTTGAAAATGAACGAGG
1 ATATAAAGAAAGAGGCTAATTCTTCATTACCTTCAAAATGAACGAGG
63024 TAGCTGATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (47 bp):
ATATAAAGAAAGAGGCTAATTCTTCATTACCTTCAAAATGAACGAGG
Found at i:92219 original size:29 final size:32
Alignment explanation
Indices: 92162--92221 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 32
92152 CCAAGAGTTT
92162 GGAGTTCCTAAGTGAGAAGGACATATTGAATG
1 GGAGTTCCTAAGTGAGAAGGACATATTGAATG
92194 GGAGTTCCT-AGTGAG-A-GACATATTGAAT
1 GGAGTTCCTAAGTGAGAAGGACATATTGAAT
92222 TCACCGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.43
30 1 0.04
31 6 0.21
32 9 0.32
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (32 bp):
GGAGTTCCTAAGTGAGAAGGACATATTGAATG
Done.