Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006989.1 Hibiscus syriacus cultivar Beakdansim tig00018026_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: 51642
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1155 original size:22 final size:23
Alignment explanation
Indices: 1115--1162 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
1105 GAAATGACAA
1115 AGGCAAATACATTTTTTTTGCTT
1 AGGCAAATACATTTTTTTTGCTT
1138 AGGCAAATACA-TTTTTTTGCTT
1 AGGCAAATACATTTTTTTTGCTT
1160 AGG
1 AGG
1163 TTTTTGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (23 bp):
AGGCAAATACATTTTTTTTGCTT
Found at i:1765 original size:2 final size:2
Alignment explanation
Indices: 1758--1788 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1748 TTCTCATTGG
1758 AT AT AT AT AT A- 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
1789 CAATACTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2953 original size:19 final size:19
Alignment explanation
Indices: 2911--2955 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2901 CTAAAAAAAA
* *
2911 CAAAATAAAAAATAAATAT
1 CAAAATTAAAAATAAACAT
*
2930 C-AAATTAAAATTAAACAT
1 CAAAATTAAAAATAAACAT
2948 CAAAATTA
1 CAAAATTA
2956 TATATCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (19 bp):
CAAAATTAAAAATAAACAT
Found at i:3160 original size:19 final size:19
Alignment explanation
Indices: 3122--3166 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3112 TATTATTGTT
3122 AATTAAAATTAAAAAACAA
1 AATTAAAATTAAAAAACAA
* ** *
3141 ATTTAAAATTAATTATCAA
1 AATTAAAATTAAAAAACAA
3160 AATTAAA
1 AATTAAA
3167 TAAAGTCAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAAATTAAAAAACAA
Found at i:5485 original size:31 final size:30
Alignment explanation
Indices: 5444--5530 Score: 120
Period size: 31 Copynumber: 2.9 Consensus size: 30
5434 ACATCTTGTA
* *
5444 AAATAAAAGAAAATAAAATCACATTAATTG
1 AAATACAAGAAAATAAAATCACATAAATTG
5474 AAAGTACAAGAAAATAAAATCACATAAATTG
1 AAA-TACAAGAAAATAAAATCACATAAATTG
** *
5505 AAATATTAGAAAATAAAATTACATAA
1 AAATACAAGAAAATAAAATCACATAA
5531 GTAATGGCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (30 bp):
AAATACAAGAAAATAAAATCACATAAATTG
Found at i:6359 original size:29 final size:34
Alignment explanation
Indices: 6322--6392 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 34
6312 TATTATATAT
6322 ATATAATATTA-ATAA-ATTTA-AT-TTAAATTAA
1 ATAT-ATATTATATAATATTTATATATTAAATTAA
*
6353 A-ATATA-TATATAATATTTATATATTTAATTAA
1 ATATATATTATATAATATTTATATATTAAATTAA
6385 ATATATAT
1 ATATATAT
6393 ATACCTGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
28 2 0.06
29 7 0.21
30 7 0.21
31 3 0.09
32 9 0.27
33 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
ATATATATTATATAATATTTATATATTAAATTAA
Found at i:6414 original size:12 final size:12
Alignment explanation
Indices: 6393--6423 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6383 AAATATATAT
*
6393 ATACCTGGCCCG
1 ATACCCGGCCCG
6405 ATACCCGGCCCG
1 ATACCCGGCCCG
6417 ATACCCG
1 ATACCCG
6424 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:8845 original size:19 final size:19
Alignment explanation
Indices: 8808--8845 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
8798 CGAACTAAAA
*
8808 CAAAATATATATTTCTTAT
1 CAAAATATATATTTATTAT
8827 CAAAATA-ATATTATATTAT
1 CAAAATATATATT-TATTAT
8846 ATGACGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
CAAAATATATATTTATTAT
Found at i:20346 original size:25 final size:26
Alignment explanation
Indices: 20318--20367 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
20308 TGAAAAACTG
* *
20318 ACAATTCAAGG-TTGAAGAAAATGGA
1 ACAATCCAAGGTTTAAAGAAAATGGA
*
20343 ACAATCCAGGGTTTAAAGAAAATGG
1 ACAATCCAAGGTTTAAAGAAAATGG
20368 GCAAATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (26 bp):
ACAATCCAAGGTTTAAAGAAAATGGA
Found at i:22509 original size:75 final size:75
Alignment explanation
Indices: 22393--22564 Score: 204
Period size: 75 Copynumber: 2.3 Consensus size: 75
22383 TTTTCTAGAC
* * * * *
22393 TTAATATTATGGTTCGAGTCTTAAGATTTGACACTTAAATATTATGATTT-TATTAT-AGATTTT
1 TTAATATTGTGGTTTGAGTCTTAAAATTTAACACTTAAATATTATGGTTTAT-TTATGA-ATTTT
*
22456 ATTATTCTAAAA
64 ACTATTCTAAAA
* * *
22468 TTAATATTGTGGTTTGAATCTTAAAATTTAACATTTTAATATTATGGTTTATTTATGAATTTTAC
1 TTAATATTGTGGTTTGAGTCTTAAAATTTAACACTTAAATATTATGGTTTATTTATGAATTTTAC
* *
22533 TGTTCTAAAT
66 TATTCTAAAA
*
22543 TTAATATTGTGATTTGAGTCTT
1 TTAATATTGTGGTTTGAGTCTT
22565 GATATTTGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
75 80 0.98
76 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.51
Consensus pattern (75 bp):
TTAATATTGTGGTTTGAGTCTTAAAATTTAACACTTAAATATTATGGTTTATTTATGAATTTTAC
TATTCTAAAA
Found at i:33033 original size:12 final size:12
Alignment explanation
Indices: 33016--33058 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
33006 AAATTTTGGT
33016 TTTTTTTGTGCC
1 TTTTTTTGTGCC
*
33028 -TTTTTT-TACC
1 TTTTTTTGTGCC
*
33038 TTTTTTTTTGCC
1 TTTTTTTGTGCC
33050 TTTTTTTGT
1 TTTTTTTGT
33059 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 3 0.12
11 12 0.46
12 11 0.42
ACGTcount: A:0.02, C:0.14, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTTTGTGCC
Found at i:33063 original size:22 final size:22
Alignment explanation
Indices: 33009--33068 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
32999 TTTTTTGAAA
* *
33009 TTTTGGTTTTTTTTGTGCCTTT
1 TTTTGCTTTTTTTTTTGCCTTT
* *
33031 TTTTACCTTTTTTTTTGCCTTT
1 TTTTGCTTTTTTTTTTGCCTTT
*
33053 TTTTGTTTTTTTTTTT
1 TTTTGCTTTTTTTTTT
33069 AAAAATAGCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.78
Consensus pattern (22 bp):
TTTTGCTTTTTTTTTTGCCTTT
Found at i:41719 original size:24 final size:24
Alignment explanation
Indices: 41686--41744 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
41676 ATAAACGAAC
*
41686 ATGAATATGTTCGTGAACACATAA
1 ATGAATATGTTCATGAACACATAA
* *
41710 ATGAACATGTTCATGAACATATAA
1 ATGAATATGTTCATGAACACATAA
41734 ATGAATATGTT
1 ATGAATATGTT
41745 TGCGAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (24 bp):
ATGAATATGTTCATGAACACATAA
Found at i:45600 original size:2 final size:2
Alignment explanation
Indices: 45593--45622 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
45583 GTTATATTTA
45593 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45623 AAAATTTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:45676 original size:2 final size:2
Alignment explanation
Indices: 45669--45714 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
45659 AACACGTTGA
45669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45710 AT AT A
1 AT AT A
45715 GTTTTTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45742 original size:35 final size:35
Alignment explanation
Indices: 45701--45903 Score: 171
Period size: 37 Copynumber: 5.5 Consensus size: 35
45691 ATATATATAT
45701 ATATATATTATATAGTTTTTGAAAACATTTTGAAACC
1 ATATATA-TATATAGTTTTTGAAAACATTTTGAAA-C
**
45738 ATATATATATATA-TTTTTGAAAACACTTTCAAAAC
1 ATATATATATATAGTTTTTGAAAACA-TTTTGAAAC
* * * * *
45773 ATATATATATATA-TATATATAT-ATATATATATAT-ATAT
1 ATATATATATATAGT-T-T-T-TGA-AAACAT-TTTGAAAC
45811 ATATATATAATATAGTTTTTGAAAACATTTTAGAAAC
1 ATATATAT-ATATAGTTTTTGAAAACATTTT-GAAAC
*
45848 ATATATATATATAGTTTTTGAAAAACATTTTGAAAGT
1 ATATATATATATAGTTTTTG-AAAACATTTTGAAA-C
*
45885 ATATATAATATATAATTTT
1 ATATAT-ATATATAGTTTT
45904 AAAATGTTTT
Statistics
Matches: 136, Mismatches: 15, Indels: 29
0.76 0.08 0.16
Matches are distributed among these distances:
35 29 0.21
36 34 0.25
37 36 0.26
38 25 0.18
39 11 0.08
40 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (35 bp):
ATATATATATATAGTTTTTGAAAACATTTTGAAAC
Found at i:45780 original size:2 final size:2
Alignment explanation
Indices: 45773--45824 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
45763 CTTTCAAAAC
45773 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
45815 AT AT A- AT AT A
1 AT AT AT AT AT A
45825 GTTTTTGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45810 original size:110 final size:112
Alignment explanation
Indices: 45669--45898 Score: 378
Period size: 110 Copynumber: 2.1 Consensus size: 112
45659 AACACGTTGA
*
45669 ATATATATATATATATATATATATATATATATATATATATTATATAGTTTTTGAAAACATTTT-G
1 ATATATATATATATATATATATATATATATATATATATATAATATAGTTTTTGAAAACATTTTAG
45733 AAACCATATATATATATA-TTTTTG-AAAACACTTTCAAAACATATAT
66 AAA-CATATATATATATAGTTTTTGAAAAACACTTTCAAAACATATAT
45779 ATATATATATATATATATATATATATATATATATATATATAATATAGTTTTTGAAAACATTTTAG
1 ATATATATATATATATATATATATATATATATATATATATAATATAGTTTTTGAAAACATTTTAG
* * **
45844 AAACATATATATATATAGTTTTTGAAAAACATTTTGAAAGTATATAT
66 AAACATATATATATATAGTTTTTGAAAAACACTTTCAAAACATATAT
45891 A-ATATATA
1 ATATATATA
45899 ATTTTAAAAT
Statistics
Matches: 112, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
110 76 0.68
111 17 0.15
112 19 0.17
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (112 bp):
ATATATATATATATATATATATATATATATATATATATATAATATAGTTTTTGAAAACATTTTAG
AAACATATATATATATAGTTTTTGAAAAACACTTTCAAAACATATAT
Found at i:45987 original size:4 final size:4
Alignment explanation
Indices: 45980--46018 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
45970 TATAATTTTT
45980 TTTA TTTA TTT- TCTTA TTTA TTTA TTTA -TTA TTTA TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
46019 CTATTTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 4 0.12
4 27 0.84
5 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:46013 original size:11 final size:11
Alignment explanation
Indices: 45997--46037 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
45987 ATTTTCTTAT
45997 TTATTTATTTA
1 TTATTTATTTA
46008 TTATTTATTTA
1 TTATTTATTTA
* *
46019 CTATTTA-CTA
1 TTATTTATTTA
46029 TT-TTTATTT
1 TTATTTATTT
46038 TTAGATCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
9 4 0.16
10 4 0.16
11 17 0.68
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTATTTA
Done.