Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009188.1 Hibiscus syriacus cultivar Beakdansim tig00112761_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: 189620
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:139714 original size:40 final size:40
Alignment explanation
Indices: 139637--139716 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
139627 TTATATATAC
* *
139637 TTTCAAAAACTATATATTATATATATTTTTTTCAAAAAAT
1 TTTCAAAAACTATATATTATATATATTATATTCAAAAAAT
*
139677 TTTCAAAAACTATACTA-TAT-TATTATATATATTAAAAAAA
1 TTTCAAAAACTATA-TATTATATA-TAT-TATATTCAAAAAA
139717 ATCCAGACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 2 0.06
40 20 0.59
41 12 0.35
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (40 bp):
TTTCAAAAACTATATATTATATATATTATATTCAAAAAAT
Found at i:140426 original size:59 final size:59
Alignment explanation
Indices: 140317--140442 Score: 166
Period size: 59 Copynumber: 2.1 Consensus size: 59
140307 TAAAATCCAC
* * * *
140317 AAATGGTCCCCAAACTATAGGATGATTTTGTTGAGTCACTTGACTGTTAAAAGTTA-TA
1 AAATGGTCCCCAAACTATAGGATGACTTTGTTGAGTCACTTGACTATTAAAAATTACAA
* *
140375 AAATGGTCCCCTAACTATAGGTATTACTTTGTTGAGTC-CATTGACTATTAAAAATTACAA
1 AAATGGTCCCCAAACTATAGG-ATGACTTTGTTGAGTCAC-TTGACTATTAAAAATTACAA
140435 AAATGGTC
1 AAATGGTC
140443 ATCTGACTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
58 21 0.36
59 29 0.49
60 9 0.15
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (59 bp):
AAATGGTCCCCAAACTATAGGATGACTTTGTTGAGTCACTTGACTATTAAAAATTACAA
Found at i:143435 original size:13 final size:13
Alignment explanation
Indices: 143413--143452 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
143403 TTACAAACTC
*
143413 GCATATGAAGACT
1 GCATAAGAAGACT
*
143426 GCATAAGAAGACC
1 GCATAAGAAGACT
143439 GCATAAGAAGACT
1 GCATAAGAAGACT
143452 G
1 G
143453 TTCAACTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.15
Consensus pattern (13 bp):
GCATAAGAAGACT
Found at i:151589 original size:36 final size:36
Alignment explanation
Indices: 151548--151622 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
151538 ATCCAATTTG
151548 ATTATCCGAAAATCAAAAAATTGATCGGATATCCAA
1 ATTATCCGAAAATCAAAAAATTGATCGGATATCCAA
*
151584 ATTATCTGAAAATCAAAAAATTGATCGGATATCCAA
1 ATTATCCGAAAATCAAAAAATTGATCGGATATCCAA
151620 ATT
1 ATT
151623 TTTGGATCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (36 bp):
ATTATCCGAAAATCAAAAAATTGATCGGATATCCAA
Found at i:159195 original size:12 final size:12
Alignment explanation
Indices: 159176--159218 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
159166 ACATCAATTT
159176 AGTTAGGTGAAG
1 AGTTAGGTGAAG
*
159188 AATTAGGTGAAG
1 AGTTAGGTGAAG
*
159200 AGGTAGGTG-AG
1 AGTTAGGTGAAG
159211 AGTTAGGT
1 AGTTAGGT
159219 ATTTATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.26
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:163880 original size:12 final size:12
Alignment explanation
Indices: 163863--163917 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
163853 ACATCAATTT
*
163863 AGTTTGGTGAAG
1 AGTTAGGTGAAG
* *
163875 AGTTTGGTTAAG
1 AGTTAGGTGAAG
*
163887 AATTAGGTGAAG
1 AGTTAGGTGAAG
163899 AGTTAGGTG-AG
1 AGTTAGGTGAAG
*
163910 AATTAGGT
1 AGTTAGGT
163918 ATTTGTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:163915 original size:23 final size:24
Alignment explanation
Indices: 163868--163917 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
163858 AATTTAGTTT
*
163868 GGTGAAGAGTTTGGTTAAGAATTA
1 GGTGAAGAGTTAGGTTAAGAATTA
*
163892 GGTGAAGAGTTAGG-TGAGAATTA
1 GGTGAAGAGTTAGGTTAAGAATTA
163915 GGT
1 GGT
163918 ATTTGTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (24 bp):
GGTGAAGAGTTAGGTTAAGAATTA
Found at i:165821 original size:18 final size:18
Alignment explanation
Indices: 165798--165847 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
165788 ATATAGAGAT
165798 AATAATATCATGTTAATG
1 AATAATATCATGTTAATG
165816 AATAATATCATGTTAATG
1 AATAATATCATGTTAATG
165834 AATAATATCATGTT
1 AATAATATCATGTT
165848 GTGCATAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (18 bp):
AATAATATCATGTTAATG
Found at i:169159 original size:17 final size:17
Alignment explanation
Indices: 169137--169172 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
169127 TGAAATATGT
169137 ATTTTATAAA-ATTTAAA
1 ATTTTA-AAATATTTAAA
169154 ATTTTAAAATATTTAAA
1 ATTTTAAAATATTTAAA
169171 AT
1 AT
169173 AATTGTAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTAAAATATTTAAA
Found at i:173788 original size:19 final size:19
Alignment explanation
Indices: 173764--173819 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
173754 GAACGCTGGA
173764 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
173783 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
173804 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
173820 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:173799 original size:11 final size:11
Alignment explanation
Indices: 173764--173812 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
173754 GAACGCTGGA
173764 AACCGGTTTTG
1 AACCGGTTTTG
173775 -ACCGG-TTT-
1 AACCGGTTTTG
173783 AACCGGTTTTG
1 AACCGGTTTTG
173794 AACCGGTTTTG
1 AACCGGTTTTG
173805 -ACCGGTTT
1 AACCGGTTT
173813 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:173815 original size:9 final size:10
Alignment explanation
Indices: 173765--173819 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
173755 AACGCTGGAA
173765 ACCGGTTTTG
1 ACCGGTTTTG
*
173775 ACCGG-TTTA
1 ACCGGTTTTG
173784 ACCGGTTTTG
1 ACCGGTTTTG
173794 AACCGGTTTTG
1 -ACCGGTTTTG
173805 ACCGG-TTTG
1 ACCGGTTTTG
173814 ACCGGT
1 ACCGGT
173820 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:173873 original size:13 final size:13
Alignment explanation
Indices: 173832--173862 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
173822 CGACCCGTTT
*
173832 ACCCGTTTACCCG
1 ACCCGTTGACCCG
173845 ACCCGTTGACCCG
1 ACCCGTTGACCCG
173858 ACCCG
1 ACCCG
173863 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:173942 original size:29 final size:29
Alignment explanation
Indices: 173881--173956 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
173871 ACCGTTGACC
*** *
173881 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
173910 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
173939 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
173957 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:181048 original size:10 final size:10
Alignment explanation
Indices: 181033--181076 Score: 65
Period size: 9 Copynumber: 4.6 Consensus size: 10
181023 AACGCTGGAA
181033 ACCGGTTTTG
1 ACCGGTTTTG
*
181043 ACCGG-TTTA
1 ACCGGTTTTG
181052 ACCGGTTTTG
1 ACCGGTTTTG
181062 ACCGG-TTTG
1 ACCGGTTTTG
181071 ACCGGT
1 ACCGGT
181077 CACGACCCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 17 0.57
10 13 0.43
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:181056 original size:19 final size:19
Alignment explanation
Indices: 181032--181076 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
181022 GAACGCTGGA
181032 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
181051 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
*
181070 GACCGGT
1 AACCGGT
181077 CACGACCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:181083 original size:19 final size:19
Alignment explanation
Indices: 181042--181089 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
181032 AACCGGTTTT
***
181042 GACCGGTTTAACCGGTTTT
1 GACCGGTTTAACCGGTCAC
*
181061 GACCGGTTTGACCGGTCAC
1 GACCGGTTTAACCGGTCAC
*
181080 GACCCGTTTA
1 GACCGGTTTA
181090 CCCGTTTACC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (19 bp):
GACCGGTTTAACCGGTCAC
Found at i:181130 original size:13 final size:13
Alignment explanation
Indices: 181089--181119 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
181079 CGACCCGTTT
*
181089 ACCCGTTTACCCG
1 ACCCGTTGACCCG
181102 ACCCGTTGACCCG
1 ACCCGTTGACCCG
181115 ACCCG
1 ACCCG
181120 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:181199 original size:29 final size:29
Alignment explanation
Indices: 181138--181213 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
181128 ACCGTTGACC
*** *
181138 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
181167 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
181196 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
181214 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:182596 original size:19 final size:19
Alignment explanation
Indices: 182558--182597 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
182548 GACATATTTG
*
182558 TATTATATATTATGTTCTA
1 TATTATATATTATGTCCTA
182577 TATTATAT-TTATCGTCCTA
1 TATTATATATTAT-GTCCTA
182596 TA
1 TA
182598 AGTGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (19 bp):
TATTATATATTATGTCCTA
Done.