Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001552.1 Hibiscus syriacus cultivar Beakdansim tig00003054_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: 59447
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1811 original size:17 final size:17
Alignment explanation
Indices: 1789--1838 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1779 TATTTTTTTC
*
1789 AAAAAAAAAGGCAAAAA
1 AAAAAAAAAGACAAAAA
1806 AAAAAACAAA-ACAAAAA
1 AAAAAA-AAAGACAAAAA
* *
1823 AACAAAAAAGCCAAAA
1 AAAAAAAAAGACAAAA
1839 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGACAAAAA
Found at i:1815 original size:12 final size:12
Alignment explanation
Indices: 1788--1831 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1778 CTATTTTTTT
**
1788 CAAAAAAAAAGG
1 CAAAAAAAAAAA
1800 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1812 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
1825 CAAAAAA
1 CAAAAAA
1832 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:9626 original size:15 final size:15
Alignment explanation
Indices: 9591--9619 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9581 GTGCTTCAAC
9591 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
9605 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
9620 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:9669 original size:29 final size:27
Alignment explanation
Indices: 9614--9672 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
9604 TTTCTTTGCT
* *
9614 TTTCTTCTTTTTGAGTGCTAGATTTTC
1 TTTCTTCTTTTTGAGTGCTACAATTTC
*
9641 TTTCTTTCTTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTT-GAGTGCTACAATTTC
9670 TTT
1 TTT
9673 TATGATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 4 0.15
28 8 0.30
29 15 0.56
ACGTcount: A:0.10, C:0.15, G:0.14, T:0.61
Consensus pattern (27 bp):
TTTCTTCTTTTTGAGTGCTACAATTTC
Found at i:20586 original size:36 final size:36
Alignment explanation
Indices: 20513--20614 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
20503 ATTTAGAAGT
*
20513 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
20548 TGGTGATGATATAGGCCTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
20584 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
20615 AACAAATTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.31
36 43 0.69
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:25071 original size:36 final size:36
Alignment explanation
Indices: 24998--25113 Score: 189
Period size: 36 Copynumber: 3.2 Consensus size: 36
24988 ATTTAGAAGT
*
24998 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
25033 TGGTGATGATGTAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
25069 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
25105 TGGTGATGA
1 TGGTGATGA
25114 ACAGATTGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.26
36 55 0.74
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:30706 original size:10 final size:10
Alignment explanation
Indices: 30681--30761 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
30671 CCTTGGCTTA
30681 CTTTTTTTTT
1 CTTTTTTTTT
*
30691 GATTTTTTTTT
1 -CTTTTTTTTT
30702 CTTTTTCTTTT
1 CTTTTT-TTTT
30713 CTTTTCTTCTTT
1 CTTTT-TT-TTT
**
30725 -TATGATTTTT
1 CT-TTTTTTTT
* *
30735 CTCTTTTTGT
1 CTTTTTTTTT
*
30745 CTTTTTCTTT
1 CTTTTTTTTT
30755 CTTTTTT
1 CTTTTTT
30762 CACTCTAATT
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
10 25 0.47
11 23 0.43
12 5 0.09
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.79
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:30734 original size:17 final size:17
Alignment explanation
Indices: 30714--30760 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
30704 TTTTCTTTTC
30714 TTTTCTTCTTTTATG-AT
1 TTTTCTTCTTTT-TGTAT
*
30731 TTTTC-TCTTTTTGTCT
1 TTTTCTTCTTTTTGTAT
30747 TTTTCTTTCTTTTT
1 TTTTC-TTCTTTTT
30761 TCACTCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 12 0.46
17 5 0.19
18 7 0.27
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTCTTCTTTTTGTAT
Found at i:30748 original size:37 final size:36
Alignment explanation
Indices: 30683--30761 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
30673 TTGGCTTACT
* * *
30683 TTTTTTTTGATTTTTTTTTCTTTTTC-TTTTCTTTTC
1 TTTTTTATGATTTTTTCTTCTTTGTCTTTTTC-TTTC
30719 TTCTTTTATGATTTTTCTCTT-TTTGTCTTTTTCTTTC
1 TT-TTTTATGATTTTT-TCTTCTTTGTCTTTTTCTTTC
30756 TTTTTT
1 TTTTTT
30762 CACTCTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 6 0.16
37 23 0.62
38 8 0.22
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.80
Consensus pattern (36 bp):
TTTTTTATGATTTTTTCTTCTTTGTCTTTTTCTTTC
Found at i:31099 original size:12 final size:12
Alignment explanation
Indices: 31078--31117 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
31068 TTGCGGAATT
31078 ATGGAATTGATG
1 ATGGAATTGATG
*
31090 ATGGACTTGATG
1 ATGGAATTGATG
*
31102 AAGGATATTGATG
1 ATGGA-ATTGATG
31115 ATG
1 ATG
31118 AAATGACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.33
Consensus pattern (12 bp):
ATGGAATTGATG
Found at i:40307 original size:11 final size:11
Alignment explanation
Indices: 40293--40335 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
40283 AAGAAAGAAA
*
40293 AAGACGAAAAG
1 AAGAAGAAAAG
40304 AAGAAGAAAAG
1 AAGAAGAAAAG
40315 AAGAAAAGAAAAG
1 AAG--AAGAAAAG
*
40328 AAAAAGAA
1 AAGAAGAA
40336 TTCAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAG
Found at i:40310 original size:24 final size:23
Alignment explanation
Indices: 40280--40335 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
40270 ATTGGAGTGC
40280 AAAAAGAAAGAA-AAAGACGAAAAG
1 AAAAAGAAAGAAGAAA-A-GAAAAG
*
40304 AAGAAGAAAAGAAGAAAAGAAAAG
1 AAAAAG-AAAGAAGAAAAGAAAAG
40328 AAAAAGAA
1 AAAAAGAA
40336 TTCAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 16 0.57
25 7 0.25
26 3 0.11
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAGAAGAAAAGAAAAG
Found at i:40332 original size:19 final size:19
Alignment explanation
Indices: 40281--40335 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
40271 TTGGAGTGCA
*
40281 AAAAG-AAAGAAAAAGACG
1 AAAAGAAAAGAAAAAGAAG
40299 AAAAGAAGAAG-AAAAGAAG
1 AAAAGAA-AAGAAAAAGAAG
40318 AAAAGAAAAGAAAAAGAA
1 AAAAGAAAAGAAAAAGAA
40336 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 8 0.24
19 22 0.67
20 3 0.09
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAGAAG
Found at i:49164 original size:19 final size:20
Alignment explanation
Indices: 49117--49167 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
49107 GAAACCCCTT
**
49117 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
49137 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
49156 TGAAGATACATG
1 TGAAAATACATG
49168 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:49985 original size:26 final size:25
Alignment explanation
Indices: 49955--50003 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
49945 ATAATATAAG
*
49955 CTAAGTATATGAATTATTATAAAGTA
1 CTAAGAATATGAA-TATTATAAAGTA
* *
49981 CTAAGAATGTGCATATTATAAAG
1 CTAAGAATATGAATATTATAAAG
50004 ATGTCAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
CTAAGAATATGAATATTATAAAGTA
Found at i:52603 original size:23 final size:25
Alignment explanation
Indices: 52577--52631 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
52567 AAATCCAGCA
*
52577 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGAACTCAAAGAGG
* *
52600 AAGAAATTGAAAGAACTCAAAGAGG
1 AAGAAAATCAAAGAACTCAAAGAGG
52625 AAGAAAA
1 AAGAAAA
52632 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGAACTCAAAGAGG
Done.