Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000993.1 Hibiscus syriacus cultivar Beakdansim tig00001987_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: 72146
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2402 original size:42 final size:41
Alignment explanation
Indices: 2328--2479 Score: 214
Period size: 42 Copynumber: 3.6 Consensus size: 41
2318 ATTTTTTGCA
*
2328 TAGGTTTGATGTTTTGCGGCATTTTTCTCACAAATGCCGCAG
1 TAGGTTTGATGTTTTGCGGC-GTTTTCTCACAAATGCCGCAG
* **
2370 TAGGTGTTGATGTTTTGCGGCGTTTTCCCACAAACACCGCAG
1 TAGGT-TTGATGTTTTGCGGCGTTTTCTCACAAATGCCGCAG
*
2412 TAGGTTTTGATGTTTTGCGGCGTTTTCTCACAAATGTCGCAG
1 TAGG-TTTGATGTTTTGCGGCGTTTTCTCACAAATGCCGCAG
*
2454 TAGGTATTGATGTTTTGCAGCGTTTT
1 TAGGT-TTGATGTTTTGCGGCGTTTT
2480 GCTAAAAACG
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 81 0.83
43 16 0.16
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.39
Consensus pattern (41 bp):
TAGGTTTGATGTTTTGCGGCGTTTTCTCACAAATGCCGCAG
Found at i:6476 original size:42 final size:42
Alignment explanation
Indices: 6369--6476 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
6359 AACGAACATA
* * *
6369 CTATTGCAGCGTTTATTACAAAAACGCCACTAAATTACAACT
1 CTATTGCGGCGTTTATTACAAAAACACCACTAAAGTACAACT
6411 CTATTGCGGCGTTTATGT-CAAAAACACCACTAAAGTACAACT
1 CTATTGCGGCGTTTAT-TACAAAAACACCACTAAAGTACAACT
*
6453 -T-TTAGCGGCGTTTGATTAAAAAAA
1 CTATT-GCGGCGTTT-ATTACAAAAA
6477 TGCCGCTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
40 2 0.03
41 11 0.19
42 44 0.76
43 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (42 bp):
CTATTGCGGCGTTTATTACAAAAACACCACTAAAGTACAACT
Found at i:7873 original size:42 final size:41
Alignment explanation
Indices: 7827--8017 Score: 174
Period size: 41 Copynumber: 4.6 Consensus size: 41
7817 ACATTTTGAT
* *
7827 GCGTTTATACAAAAAAATACCACTATTGATT-ACACTATTGTG
1 GCGTTT-T-CAAAAAAATGCCACTATTGATTAACACTATTGCG
* * *
7869 GCGTTTGTTAAAAAAATGCCATTATTGATTAAAACTATTGCG
1 GCGTTT-TCAAAAAAATGCCACTATTGATTAACACTATTGCG
* *
7911 GCGTTTTTC-TAAAAACGCCACTATTGATTAACACTATTGCG
1 GCG-TTTTCAAAAAAATGCCACTATTGATTAACACTATTGCG
* * * * *
7952 GCGTTTGTC-TAAAAATGCCACTATTTATTATCATTATTACG
1 GCGTTT-TCAAAAAAATGCCACTATTGATTAACACTATTGCG
*
7993 GCGTTTT-AAGAATAAACGCCACTAT
1 GCGTTTTCAA-AA-AAATGCCACTAT
8018 ATGTGTAATC
Statistics
Matches: 125, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
40 4 0.03
41 87 0.70
42 31 0.25
43 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (41 bp):
GCGTTTTCAAAAAAATGCCACTATTGATTAACACTATTGCG
Found at i:7882 original size:41 final size:42
Alignment explanation
Indices: 7837--7998 Score: 188
Period size: 41 Copynumber: 3.9 Consensus size: 42
7827 GCGTTTATAC
* *
7837 AAAAAAATACCACTATTGATT-ACACTATTGTGGCGTTTGTT
1 AAAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTT
* *
7878 AAAAAAATGCCATTATTGATTAAAACTATTGCGGCGTTT-TT
1 AAAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTT
** *
7919 CTAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGT-T
* * * *
7962 --AAAAATGCCACTATTTATTATCATTATTACGGCGTTT
1 AAAAAAATGCCACTATTGATTAACACTATTGCGGCGTTT
7999 TAAGAATAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 87 0.84
42 16 0.15
43 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (42 bp):
AAAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTT
Found at i:7971 original size:82 final size:83
Alignment explanation
Indices: 7846--8042 Score: 215
Period size: 82 Copynumber: 2.4 Consensus size: 83
7836 CAAAAAAATA
* * *
7846 CCACTATTGATT-ACACTATTGTGGCGTTTGTTAAAAAAATGCCATTATTGATTAAAACTATTGC
1 CCACTATTGATTAACACTATTGCGGCGTTTGTT-AAAAAATGCCACTATTGATTAAAACTATTAC
***
7910 GGCGTTTTTCTAA-AAACG
65 GGCGTTTTAAGAATAAACG
* ** *
7928 CCACTATTGATTAACACTATTGCGGCGTTTGTCT-AAAAATGCCACTATTTATTATCATTATTAC
1 CCACTATTGATTAACACTATTGCGGCGTTTGT-TAAAAAATGCCACTATTGATTAAAACTATTAC
7992 GGCGTTTTAAGAATAAACG
65 GGCGTTTTAAGAATAAACG
* *
8011 CCACTATATG-TGTAA-TCTATTACGGCGTTTGT
1 CCACTAT-TGAT-TAACACTATTGCGGCGTTTGT
8043 GGTAGAAACA
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
82 46 0.47
83 46 0.47
84 6 0.06
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (83 bp):
CCACTATTGATTAACACTATTGCGGCGTTTGTTAAAAAATGCCACTATTGATTAAAACTATTACG
GCGTTTTAAGAATAAACG
Found at i:8071 original size:42 final size:39
Alignment explanation
Indices: 8025--8166 Score: 119
Period size: 42 Copynumber: 3.5 Consensus size: 39
8015 TATATGTGTA
* *
8025 ATCTATTACGGCGTTTGTGGTAGAAACATCGCTAATTTACC
1 ATCTATTGCGGCGTTTGTGGTA-AAAC-CCGCTAATTTACC
* *
8066 GATCTATTGTGGCGTTT-TGGCTAAAACGCCACTATATGTTA--
1 -ATCTATTGCGGCGTTTGTGG-TAAAAC-CCGCTA-AT-TTACC
*
8107 ATCTATTGCGGCGTTTGTGGTATAAACGCTGCTAATTTACC
1 ATCTATTGCGGCGTTTGTGGTA-AAAC-CCGCTAATTTACC
*
8148 ACTCTATTGCGGTGTTTGT
1 A-TCTATTGCGGCGTTTGT
8167 TAAAAAATGC
Statistics
Matches: 83, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
39 3 0.04
40 19 0.23
41 24 0.29
42 34 0.41
43 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (39 bp):
ATCTATTGCGGCGTTTGTGGTAAAACCCGCTAATTTACC
Found at i:8186 original size:82 final size:82
Alignment explanation
Indices: 8006--8164 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 82
7996 TTTTAAGAAT
*
8006 AAACGCCACTATATGTGTAATCTATTACGGCGTTTGTGGTAGAAACATCGCTAATTTACCGATCT
1 AAACGCCACTATATGT-TAATCTATTGCGGCGTTTGTGGTAGAAACATCGCTAATTTACCGATCT
*
8071 ATTGTGGCGTTTTGGCTA
65 ATTGCGGCGTTTTGGCTA
* *
8089 AAACGCCACTATATGTTAATCTATTGCGGCGTTTGTGGTATAAAC-GCTGCTAATTTACC-ACTC
1 AAACGCCACTATATGTTAATCTATTGCGGCGTTTGTGGTAGAAACATC-GCTAATTTACCGA-TC
*
8152 TATTGCGGTGTTT
64 TATTGCGGCGTTT
8165 GTTAAAAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 2 0.03
82 51 0.74
83 16 0.23
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (82 bp):
AAACGCCACTATATGTTAATCTATTGCGGCGTTTGTGGTAGAAACATCGCTAATTTACCGATCTA
TTGCGGCGTTTTGGCTA
Found at i:10818 original size:20 final size:20
Alignment explanation
Indices: 10790--10842 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
10780 CAAGTCGAGG
*
10790 GTATCGATATTGGCCTTACA
1 GTATTGATATTGGCCTTACA
10810 GTATTGATATTGGCCTTACA
1 GTATTGATATTGGCCTTACA
10830 GTATTGATATTGG
1 GTATTGATATTGG
10843 TCTTTAGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (20 bp):
GTATTGATATTGGCCTTACA
Found at i:11045 original size:20 final size:20
Alignment explanation
Indices: 11017--11067 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
11007 TCTAAAATAT
*
11017 GTATTGATACTACCATGTGA
1 GTATCGATACTACCATGTGA
*
11037 GTATCGATACTACCCTGTGA
1 GTATCGATACTACCATGTGA
11057 GTATCGATACT
1 GTATCGATACT
11068 TGACCCACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATCGATACTACCATGTGA
Found at i:20776 original size:2 final size:2
Alignment explanation
Indices: 20769--20858 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
20759 AAAAATTAAG
20769 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
20811 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
20853 AT AT AT
1 AT AT AT
20859 GCATGCATGC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24208 original size:12 final size:12
Alignment explanation
Indices: 24193--24262 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
24183 GATACATGAC
24193 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
24205 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
24217 ATGGATTCTGTT
1 CTGAATTCTGTT
24229 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
24241 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
24253 TTGATTTCTG
1 CTGAATTCTG
24263 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:24224 original size:24 final size:24
Alignment explanation
Indices: 24194--24266 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
24184 ATACATGACC
24194 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * *
24218 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
24242 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
24266 T
1 T
24267 CTCCGTTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:24242 original size:17 final size:18
Alignment explanation
Indices: 24199--24250 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
24189 TGACCTGAAT
24199 TCTGTTCTGATTTCTGATA
1 TCTGTTCTGA-TTCTGATA
*
24218 T-GGATTCTG-TTCTGATA
1 TCTG-TTCTGATTCTGATA
24235 TCTGTTCTGAATTCTG
1 TCTGTTCTG-ATTCTG
24251 TTTTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 11 0.41
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (18 bp):
TCTGTTCTGATTCTGATA
Found at i:43890 original size:24 final size:24
Alignment explanation
Indices: 43862--43917 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
43852 GCACCACTTT
43862 CACCGAAAGTTTCTCAACAATTTC
1 CACCGAAAGTTTCTCAACAATTTC
43886 CACCGAAAGTTTCTCAACAATTTC
1 CACCGAAAGTTTCTCAACAATTTC
43910 CACCGAAA
1 CACCGAAA
43918 TTAGCCTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (24 bp):
CACCGAAAGTTTCTCAACAATTTC
Found at i:46669 original size:31 final size:31
Alignment explanation
Indices: 46586--46676 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 31
46576 CCTGCACTTT
* *
46586 TAAAATGTTTAATGTGATAGTTA-TCTTTTAA
1 TAAAATATTTAATGTGATATTTATTC-TTTAA
** *
46617 TAAAATATCAAAT-TCGGTATTTATTCTTTAA
1 TAAAATATTTAATGT-GATATTTATTCTTTAA
* *
46648 TAAAATATTTAATGTAATATTTATACTTT
1 TAAAATATTTAATGTGATATTTATTCTTT
46677 TAAAGTTCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.91
32 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (31 bp):
TAAAATATTTAATGTGATATTTATTCTTTAA
Found at i:64863 original size:14 final size:16
Alignment explanation
Indices: 64844--64880 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
64834 CATTCATTCC
64844 CTCTCTCT-ATCTCT-
1 CTCTCTCTAATCTCTG
64858 CTCTCTCTAATCTCTG
1 CTCTCTCTAATCTCTG
64874 CTCTCTC
1 CTCTCTC
64881 GATTCAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 7 0.33
ACGTcount: A:0.08, C:0.43, G:0.03, T:0.46
Consensus pattern (16 bp):
CTCTCTCTAATCTCTG
Found at i:71463 original size:24 final size:24
Alignment explanation
Indices: 71429--71482 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
71419 CTGAAAAATC
71429 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
71453 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
71477 ATCAAA
1 ATCAAA
71483 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:71496 original size:24 final size:24
Alignment explanation
Indices: 71429--71496 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
71419 CTGAAAAATC
* * *
71429 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
71453 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
71477 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
71497 TAGTACTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Done.