Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006343.1 Hibiscus syriacus cultivar Beakdansim tig00015161_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: 58645
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7449 original size:16 final size:16
Alignment explanation
Indices: 7428--7462 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7418 CCTTAATTTT
7428 TATTTAA-TAGAATATA
1 TATTTAATTA-AATATA
7444 TATTTAATTAAATATA
1 TATTTAATTAAATATA
7460 TAT
1 TAT
7463 AAAGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TATTTAATTAAATATA
Found at i:10713 original size:31 final size:30
Alignment explanation
Indices: 10675--10732 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
10665 TTAATCAATT
10675 TTAATAATTATATTATAATTATTTGAAAAAA
1 TTAATAATTATATTATAA-TATTTGAAAAAA
*
10706 TTAATAATTATTTTATAATATTTGAAA
1 TTAATAATTATATTATAATATTTGAAA
10733 GGTCATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAATAATTATATTATAATATTTGAAAAAA
Found at i:18099 original size:37 final size:36
Alignment explanation
Indices: 18058--18132 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 36
18048 GTACATACAG
* *
18058 ATAGTTGAATCACACG-ATTTGAACTAGCAAATATGTA
1 ATAGTTGAA-C-CACGAATTTCAACTAACAAATATGTA
18095 ATAGTTGAACCACGTAATTTCAACTAACAAATATGTA
1 ATAGTTGAACCACG-AATTTCAACTAACAAATATGTA
18132 A
1 A
18133 CTGAATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 4 0.12
36 1 0.03
37 29 0.85
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (36 bp):
ATAGTTGAACCACGAATTTCAACTAACAAATATGTA
Found at i:21185 original size:30 final size:31
Alignment explanation
Indices: 21129--21225 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
21119 GATTAAATTT
*
21129 TAATTTAACCCCTAAA-TTTCAGATAAAATATC
1 TAATTTAA-CCCTAAACTTT-ATATAAAATATC
* * *
21161 -ATTTTAATCTTAAACTTTATATAAAATA-C
1 TAATTTAACCCTAAACTTTATATAAAATATC
*
21190 TAATTTAACCCTAAATTTTATATAAAATAT-
1 TAATTTAACCCTAAACTTTATATAAAATATC
21220 TAATTT
1 TAATTT
21226 GATACTTGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 1 0.02
30 44 0.81
31 9 0.17
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.42
Consensus pattern (31 bp):
TAATTTAACCCTAAACTTTATATAAAATATC
Found at i:44992 original size:18 final size:20
Alignment explanation
Indices: 44954--44994 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44944 TTTTCAATAG
44954 AAAATACATAGATATATTTT
1 AAAATACATAGATATATTTT
*
44974 AAAATATATA-ATA-ATTTT
1 AAAATACATAGATATATTTT
44992 AAA
1 AAA
44995 TTTTCATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATACATAGATATATTTT
Found at i:47814 original size:16 final size:17
Alignment explanation
Indices: 47793--47831 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
47783 TCTTTGTTTC
*
47793 TAGCTTTATAG-CTTTT
1 TAGCTTTATAGCCTTGT
*
47809 TAGCTTTCTAGCCTTGT
1 TAGCTTTATAGCCTTGT
47826 TAGCTT
1 TAGCTT
47832 ATCCCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (17 bp):
TAGCTTTATAGCCTTGT
Found at i:53693 original size:36 final size:36
Alignment explanation
Indices: 53638--53716 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
53628 GAATTAAACG
*
53638 GGGAC-GGGAAAAATCGTTTATGCTAAACGGGGACA
1 GGGACGGGGAAAAATAGTTTATGCTAAACGGGGACA
* * *
53673 GGGACGGGGGAAAATAGTTTATGCTAAATGGGGACG
1 GGGACGGGGAAAAATAGTTTATGCTAAACGGGGACA
53709 GGGACGGG
1 GGGACGGG
53717 TTTGGTAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 5 0.13
36 34 0.87
ACGTcount: A:0.30, C:0.11, G:0.42, T:0.16
Consensus pattern (36 bp):
GGGACGGGGAAAAATAGTTTATGCTAAACGGGGACA
Found at i:53787 original size:2 final size:2
Alignment explanation
Indices: 53780--53875 Score: 73
Period size: 2 Copynumber: 52.0 Consensus size: 2
53770 ATTATTATTT
* * * *
53780 TA TA TA TA T- TA TA TA TA T- TA -A TA AA TT TA -A TT TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
53817 TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA T- TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
53856 TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
53876 CCTGGCCCGA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
1 8 0.11
2 64 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53819 original size:45 final size:44
Alignment explanation
Indices: 53780--53875 Score: 144
Period size: 43 Copynumber: 2.2 Consensus size: 44
53770 ATTATTATTT
53780 TATATATAT-TATAT-ATATTAATAAATTTAATTTAAATTATATA
1 TATATATATATATATAATATTAATAAA-TTAATTTAAATTATATA
* *
53823 TATATATATATATATAATATTTATATATTAATTTAAA-TATATA
1 TATATATATATATATAATATTAATAAATTAATTTAAATTATATA
53866 TATATATATA
1 TATATATATA
53876 CCTGGCCCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
43 25 0.51
44 15 0.31
45 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (44 bp):
TATATATATATATATAATATTAATAAATTAATTTAAATTATATA
Done.