Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007310.1 Hibiscus syriacus cultivar Beakdansim tig00019478_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: 46022
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:574 original size:28 final size:30
Alignment explanation
Indices: 512--567 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
502 TACAATACAA
512 CCCCCAACATTTAGTCTGTTTGCAATATAT
1 CCCCCAACATTTAGTCTGTTTGCAATATAT
542 CCCCCAACATTTAGT-T-TTTGCAATAT
1 CCCCCAACATTTAGTCTGTTTGCAATAT
568 GGTCCCCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 10 0.38
29 1 0.04
30 15 0.58
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (30 bp):
CCCCCAACATTTAGTCTGTTTGCAATATAT
Found at i:5170 original size:20 final size:20
Alignment explanation
Indices: 5145--5187 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5135 CCCAATAAGA
5145 CTTAATAAATACTTTACAAC
1 CTTAATAAATACTTTACAAC
5165 CTTAATAAATACTTTACAAC
1 CTTAATAAATACTTTACAAC
5185 CTT
1 CTT
5188 TAAGGGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (20 bp):
CTTAATAAATACTTTACAAC
Found at i:12421 original size:18 final size:18
Alignment explanation
Indices: 12400--12446 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
12390 TAAAATTGAC
*
12400 ATCGATACTAAAGCCATT
1 ATCGATACTAAAGCCAAT
*
12418 ATCGATACCCTAAGGCCAAT
1 ATCGATA--CTAAAGCCAAT
12438 ATCGATACT
1 ATCGATACT
12447 GATGCCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (18 bp):
ATCGATACTAAAGCCAAT
Found at i:12435 original size:20 final size:20
Alignment explanation
Indices: 12407--12445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12397 GACATCGATA
*
12407 CTAAAGCCATTATCGATACC
1 CTAAAGCCAATATCGATACC
*
12427 CTAAGGCCAATATCGATAC
1 CTAAAGCCAATATCGATAC
12446 TGATGCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (20 bp):
CTAAAGCCAATATCGATACC
Found at i:13190 original size:21 final size:21
Alignment explanation
Indices: 13164--13213 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
13154 CGTTTTGTAA
13164 ACTTAAATTTTATACTTAATT
1 ACTTAAATTTTATACTTAATT
13185 ACTTAAATTTTATACTTAATT
1 ACTTAAATTTTATACTTAATT
*
13206 GCTTAAAT
1 ACTTAAAT
13214 GCAATGGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (21 bp):
ACTTAAATTTTATACTTAATT
Found at i:19811 original size:14 final size:14
Alignment explanation
Indices: 19792--19819 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19782 ATCAATTCAT
19792 GCCCAACTATCTTC
1 GCCCAACTATCTTC
19806 GCCCAACTATCTTC
1 GCCCAACTATCTTC
19820 CTATCACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.07, T:0.29
Consensus pattern (14 bp):
GCCCAACTATCTTC
Found at i:24933 original size:449 final size:449
Alignment explanation
Indices: 24095--24939 Score: 1261
Period size: 449 Copynumber: 1.9 Consensus size: 449
24085 AGTAGTTTTG
* *
24095 TTGGGTTATAGGGTCTAACGATCACCCTTAGGGATTCTATCGTGTATGGACGCGATATCAGGTGC
1 TTGGGTTATAGGGTCCAACGATCAACCTTAGGGATTCTATCGTGTATGGACGCGATATCAGGTGC
* *
24160 TTGACAGCCTAACCTGCCAAGGCACACGTGTTCCTTGCGAAGCCCATAGGCCCGCCCGCAACACG
66 TTGACAGCCTAACCTGCCAAGGCACACGTGTGCATTGCGAAGCCCATAGGCCCGCCCGCAACACG
* *
24225 CTATAGATGTGAGGCTCTGTAATGCTGTGGTGAATTGTGGGGGCTACCCTACAAGAATCCACCTT
131 CTATAGATGCGAGGCTCTGTAATGCTGTGATGAATTGTGGGGGCTACCCTACAAGAATCCACCTT
** * *
24290 GGCTTGGGGGAAACCAGTATCACCCGCTATAAAGATATGAGGTTAAAATGGACCACATGCTTATC
196 AACTTGGGGGAAACCAGTATCACCCGCTACAAAGATATGAGGTTAAAATGGACCACATACTTATC
* *
24355 ACTAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAAGCGTGTTTGA
261 ACCAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAAGCGTGCTTGA
24420 ACCAGAGTAATCCAAGGATGGGTGACCCACTGGAAGTTGTTCAAAAATTGAATGACTCGATCCTA
326 ACCAGAGTAATCCAAGGATGGGTGACCCACTGGAAGTTGTTCAAAAATTGAATGACTCGATCCTA
24485 TCAAGTGGTATCAGAGCAGGTTGTAGGTTCGAATCCCCCAGTTATTGCTGGGGTGATTA
391 TCAAGTGGTATCAGAGCAGGTTGTAGGTTCGAATCCCCCAGTTATTGCTGGGGTGATTA
* *
24544 TTGGGTTATGGGGTCCAACGATCAACCTTAGGGATTCTATCGTGTATGGGCGCGATATCAGGTGC
1 TTGGGTTATAGGGTCCAACGATCAACCTTAGGGATTCTATCGTGTATGGACGCGATATCAGGTGC
* * * * * * *
24609 TTGACAGTCC-AACCTGTCGAGGCCCATGTGTGCATTGCGAATCCTC-TAGGCCCGCCCGTAGCA
66 TTGACAG-CCTAACCTGCCAAGGCACACGTGTGCATTGCGAAGCC-CATAGGCCCGCCCGCAACA
* * * *
24672 CGCTATATATGCGGGGCTCTTTAATG-TCGTGATGAATTGTGGGGG-T-GCCTCACAAGAATCCA
129 CGCTATAGATGCGAGGCTCTGTAATGCT-GTGATGAATTGTGGGGGCTACCCT-ACAAGAATCCA
* * * ** *
24734 CCTTAACTT-GGGGAAACTAGTGATCACCTGTTACAAAGATATGAGGTTAAAATGTCCCACGTAC
192 CCTTAACTTGGGGGAAACCAGT-ATCACCCGCTACAAAGATATGAGGTTAAAATGGACCACATAC
* * *
24798 TTATCACCAATTGGTTTTAAGAAGGAATGGTGATCATTCACTTCAGAACTCTGTAGTTAAGCGTG
256 TTATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAAGCGTG
* * *
24863 CTTGAACCAGAGTAATCTAAGGATGGGTGACCCATTGGAAAGTTGTTCGAAAATTGAATGACTCG
321 CTTGAACCAGAGTAATCCAAGGATGGGTGACCCACTGG-AAGTTGTTCAAAAATTGAATGACTCG
24928 ATCCTATCAAGT
385 ATCCTATCAAGT
24940 TTAACACGGG
Statistics
Matches: 353, Mismatches: 37, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
447 14 0.04
448 151 0.43
449 185 0.52
450 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (449 bp):
TTGGGTTATAGGGTCCAACGATCAACCTTAGGGATTCTATCGTGTATGGACGCGATATCAGGTGC
TTGACAGCCTAACCTGCCAAGGCACACGTGTGCATTGCGAAGCCCATAGGCCCGCCCGCAACACG
CTATAGATGCGAGGCTCTGTAATGCTGTGATGAATTGTGGGGGCTACCCTACAAGAATCCACCTT
AACTTGGGGGAAACCAGTATCACCCGCTACAAAGATATGAGGTTAAAATGGACCACATACTTATC
ACCAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAAGCGTGCTTGA
ACCAGAGTAATCCAAGGATGGGTGACCCACTGGAAGTTGTTCAAAAATTGAATGACTCGATCCTA
TCAAGTGGTATCAGAGCAGGTTGTAGGTTCGAATCCCCCAGTTATTGCTGGGGTGATTA
Found at i:30338 original size:2 final size:2
Alignment explanation
Indices: 30331--30360 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30321 GAGTAGATGA
30331 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
30361 TTAGAAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42680 original size:69 final size:67
Alignment explanation
Indices: 42565--42700 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 67
42555 ATAAAGATTA
* * * *
42565 ATCTCTCAAAAAGGTATAATTTTTGCTTGGTTATAAGCTAATGGGTCACTGTTTTTTTAACTTAG
1 ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAG-TTTTTTAACTT-G
42630 CTTT
64 CTTT
42634 ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAGTTTTTTAACTTGCT
1 ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAGTTTTTTAACTTGCT
42699 TT
66 TT
42701 TTCATTTTCT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 5 0.08
68 11 0.17
69 47 0.75
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (67 bp):
ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAGTTTTTTAACTTGCT
TT
Done.