Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000034.1 Hibiscus syriacus cultivar Beakdansim tig00000055_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: 26620
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4085 original size:24 final size:25
Alignment explanation
Indices: 4057--4116 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 25
4047 TTGTAGGAAT
4057 TATAGAGA-GATTTGTTACCATTCC
1 TATAGAGATGATTTGTTACCATTCC
4081 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAG--ATGATTTGTTACCATTCC
4108 TATAGAGAT
1 TATAGAGAT
4117 ATGATTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 7 0.21
25 2 0.06
26 1 0.03
27 23 0.70
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (25 bp):
TATAGAGATGATTTGTTACCATTCC
Found at i:4099 original size:27 final size:27
Alignment explanation
Indices: 4065--4123 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
4055 ATTATAGAGA
4065 GATTTGTTACCATTCCTATAGAGATAT
1 GATTTGTTACCATTCCTATAGAGATAT
4092 GATTTGTTACCATTCCTATAGAGATAT
1 GATTTGTTACCATTCCTATAGAGATAT
4119 GATTT
1 GATTT
4124 TGTAAATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (27 bp):
GATTTGTTACCATTCCTATAGAGATAT
Found at i:10586 original size:15 final size:15
Alignment explanation
Indices: 10568--10598 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10558 AAATTTTAAA
10568 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
10583 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
10598 T
1 T
10599 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:13987 original size:27 final size:28
Alignment explanation
Indices: 13934--13987 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
13924 ATTAAAGTAC
* *
13934 TATCCTTCATCAATGTCACTCTTATCAT
1 TATCCTTCATCAATGTCACCCTCATCAT
*
13962 TATCCTT-ATCGATGTCACCCTCATCA
1 TATCCTTCATCAATGTCACCCTCATCA
13988 CACGATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.39
Consensus pattern (28 bp):
TATCCTTCATCAATGTCACCCTCATCAT
Found at i:14814 original size:71 final size:72
Alignment explanation
Indices: 14593--14834 Score: 405
Period size: 72 Copynumber: 3.4 Consensus size: 72
14583 AAGATTAAGT
* * * * *
14593 TCAATTCAATAAAAATATGTAAAATTAAATAGAATTCAAAAGATAATTTTTTAAATAAAGTGGTA
1 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGTTTTTTTAATAAAGTGGTA
14658 TAAATAC
66 TAAATAC
14665 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGGTTTTTTTAATAAAGTGGT
1 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGA-GTTTTTTTAATAAAGTGGT
*
14730 ATAAATGC
65 ATAAATAC
*
14738 TCAATTTAATAAAAATATGT-AAATTAAATAGAATTCAAGAGAGAGTTTTTTTAATAAAGTGCTA
1 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGTTTTTTTAATAAAGTGGTA
14802 TAAATAC
66 TAAATAC
14809 TCAATTTAATAAAAATATGTAAAATT
1 TCAATTTAATAAAAATATGTAAAATT
14835 TAAAATAATA
Statistics
Matches: 160, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
71 45 0.28
72 71 0.44
73 44 0.28
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.35
Consensus pattern (72 bp):
TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGTTTTTTTAATAAAGTGGTA
TAAATAC
Found at i:15399 original size:2 final size:2
Alignment explanation
Indices: 15392--15456 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
15382 TTTCCCCCTT
15392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15434 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
15457 CAAATAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16935 original size:12 final size:12
Alignment explanation
Indices: 16918--16942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16908 AATGTTAAAT
16918 GAATATATTTAC
1 GAATATATTTAC
16930 GAATATATTTAC
1 GAATATATTTAC
16942 G
1 G
16943 GGCATTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (12 bp):
GAATATATTTAC
Found at i:19466 original size:160 final size:161
Alignment explanation
Indices: 19152--19447 Score: 544
Period size: 160 Copynumber: 1.9 Consensus size: 161
19142 GTCGGTCGTG
19152 ATCTCATTAAAATGTTTAAGCTGGTTAGTTACTCTAATCTAATTTATATATATTTTTATTCTTAT
1 ATCTCATTAAAATGTTTAAGCTGGTTAGTTACTCTAATCTAATTTATATATATTTTTATTCTTAT
*
19217 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTTTCT
66 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTATCT
*
19282 CTTATTTAATTTATCGTATTTTTTTACTCTA
131 CTAATTTAATTTATCGTATTTTTTTACTCTA
*
19313 ATCTCATTAAAATGTTTAAGCTGGTTAGTTAC-CTAATCTAATTTTTATATATTTTTATTCTTAT
1 ATCTCATTAAAATGTTTAAGCTGGTTAGTTACTCTAATCTAATTTATATATATTTTTATTCTTAT
19377 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTAT-T
66 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTATCT
19441 -TAATTTA
131 CTAATTTA
19448 TCTTATTTTT
Statistics
Matches: 132, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
158 6 0.05
159 1 0.01
160 93 0.70
161 32 0.24
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (161 bp):
ATCTCATTAAAATGTTTAAGCTGGTTAGTTACTCTAATCTAATTTATATATATTTTTATTCTTAT
TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTATCT
CTAATTTAATTTATCGTATTTTTTTACTCTA
Found at i:19619 original size:20 final size:20
Alignment explanation
Indices: 19567--19612 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
19557 GGTATTTTTT
*
19567 TATTTTTTAAA--CTATTAA
1 TATTTTTTAAATTATATTAA
*
19585 TATTTTTTAAATTATATTTA
1 TATTTTTTAAATTATATTAA
19605 TATTTTTT
1 TATTTTTT
19613 TTATTATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
20 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTTAAATTATATTAA
Found at i:20809 original size:13 final size:13
Alignment explanation
Indices: 20791--20852 Score: 70
Period size: 13 Copynumber: 4.5 Consensus size: 13
20781 TTAAGGCTAG
20791 AGATGACAATTAT
1 AGATGACAATTAT
20804 AGATGACAATTAT
1 AGATGACAATTAT
*
20817 AAGTGGATGATAATTAT
1 -A---GATGACAATTAT
20834 AGATGACAATTAT
1 AGATGACAATTAT
*
20847 AAATGA
1 AGATGA
20853 AGACTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 29 0.69
14 1 0.02
16 1 0.02
17 11 0.26
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (13 bp):
AGATGACAATTAT
Found at i:20832 original size:30 final size:30
Alignment explanation
Indices: 20792--20848 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
20782 TAAGGCTAGA
20792 GATGACAATTATAGATGACAATTATAAGTG
1 GATGACAATTATAGATGACAATTATAAGTG
*
20822 GATGATAATTATAGATGACAATTATAA
1 GATGACAATTATAGATGACAATTATAA
20849 ATGAAGACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.32
Consensus pattern (30 bp):
GATGACAATTATAGATGACAATTATAAGTG
Found at i:21846 original size:27 final size:27
Alignment explanation
Indices: 21815--21880 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
21805 ATAATGGCTC
*
21815 TGAATCATTCAGAATGTACTTCTGTGT
1 TGAATCATTCAGAATGTAATTCTGTGT
*
21842 TGAATCATTAAGAATGTAATTCTGTGT
1 TGAATCATTCAGAATGTAATTCTGTGT
21869 TGAATCATTCAG
1 TGAATCATTCAG
21881 CATTGTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (27 bp):
TGAATCATTCAGAATGTAATTCTGTGT
Found at i:22222 original size:32 final size:32
Alignment explanation
Indices: 22177--22247 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
22167 AATAACAATG
22177 TAAT-ATA-TGTTTATAATCTTTATTAAATAT
1 TAATAATACTGTTTATAATCTTTATTAAATAT
22207 TAATAATACTGTTTATAATCTTTATTAAATAT
1 TAATAATACTGTTTATAATCTTTATTAAATAT
22239 TAATAATAC
1 TAATAATAC
22248 ATATAACTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 4 0.10
31 3 0.08
32 32 0.82
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (32 bp):
TAATAATACTGTTTATAATCTTTATTAAATAT
Done.