Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005553.1 Hibiscus syriacus cultivar Beakdansim tig00012873_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: 60684
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8553 original size:72 final size:72
Alignment explanation
Indices: 8466--8610 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 72
8456 AATAGAAATC
8466 GTTGAAAGTAACAAATTTATTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
1 GTTGAAAGTAACAAATTTATTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
8531 AAATTTT
66 AAATTTT
* *
8538 GTTGAAAGTAACAAATTTGTTACTAGTTTCTAACTAAATTGTTTTTGGTGGAATAAACCAAAATT
1 GTTGAAAGTAACAAATTTATTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
8603 AAATTTT
66 AAATTTT
8610 G
1 G
8611 GTTTATTGTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (72 bp):
GTTGAAAGTAACAAATTTATTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
AAATTTT
Found at i:10064 original size:12 final size:12
Alignment explanation
Indices: 10047--10074 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10037 TTAATGCATC
10047 TTTTTGTTAATT
1 TTTTTGTTAATT
10059 TTTTTGTTAATT
1 TTTTTGTTAATT
10071 TTTT
1 TTTT
10075 CTCTTATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTGTTAATT
Found at i:11352 original size:23 final size:22
Alignment explanation
Indices: 11305--11352 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
11295 ATATAATATA
** *
11305 AATATAATTTATCATTATCTTG
1 AATATAATTTATCATTAAATAG
11327 AATATAATTTTATCATTAAATAG
1 AATATAA-TTTATCATTAAATAG
11350 AAT
1 AAT
11353 TTATTAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
AATATAATTTATCATTAAATAG
Found at i:22508 original size:23 final size:23
Alignment explanation
Indices: 22470--22517 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
22460 ATACGTGCAA
* *
22470 AAACTCTTAACCAATTGACAATG
1 AAACTCTCAACCAATTAACAATG
* *
22493 AAACTCTCAACTAATTAATAATG
1 AAACTCTCAACCAATTAACAATG
22516 AA
1 AA
22518 CACTTATACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (23 bp):
AAACTCTCAACCAATTAACAATG
Found at i:25530 original size:19 final size:19
Alignment explanation
Indices: 25506--25542 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
25496 TGACTAAATT
25506 AGCCG-CCCATTAATGTTGA
1 AGCCGCCCCATT-ATGTTGA
25525 AGCCGCCCCATTATGTTG
1 AGCCGCCCCATTATGTTG
25543 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (19 bp):
AGCCGCCCCATTATGTTGA
Found at i:32023 original size:21 final size:21
Alignment explanation
Indices: 31999--32043 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31989 TTTTGTTCGT
* *
31999 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32020 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32041 TTG
1 TTG
32044 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37205 original size:4 final size:4
Alignment explanation
Indices: 37196--37229 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
37186 ATTTTTTCAT
37196 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
37230 ATCTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.47, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:38023 original size:10 final size:10
Alignment explanation
Indices: 38008--38032 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
37998 GCCTCCAAAG
38008 GGAAGCTGAA
1 GGAAGCTGAA
38018 GGAAGCTGAA
1 GGAAGCTGAA
38028 GGAAG
1 GGAAG
38033 GAAGTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (10 bp):
GGAAGCTGAA
Found at i:58810 original size:20 final size:21
Alignment explanation
Indices: 58787--58831 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
58777 ATTTTTCAAA
*
58787 TAAAAATCATA-ATTATTTTT
1 TAAAAATAATATATTATTTTT
*
58807 T-AAAATAATATTTTATTTTT
1 TAAAAATAATATATTATTTTT
58827 TAAAA
1 TAAAA
58832 GAATAGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 8 0.38
20 10 0.48
21 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAAATAATATATTATTTTT
Found at i:58836 original size:20 final size:20
Alignment explanation
Indices: 58799--58836 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58789 AAAATCATAA
*
58799 TTATTTTTTAAAATAATATT
1 TTATTTTTTAAAAGAATATT
58819 TTATTTTTTAAAAGAATA
1 TTATTTTTTAAAAGAATA
58837 GTTATGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTTTTTAAAAGAATATT
Found at i:58841 original size:19 final size:20
Alignment explanation
Indices: 58799--58841 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
58789 AAAATCATAA
* *
58799 TTATTTTTTAAAATAATATT
1 TTATTTTTTAAAAGAATATG
58819 TTATTTTTTAAAAGAATA-G
1 TTATTTTTTAAAAGAATATG
58838 TTAT
1 TTAT
58842 GACAGTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTATTTTTTAAAAGAATATG
Done.