Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002183.1 Hibiscus syriacus cultivar Beakdansim tig00004450_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: 55108
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:13625 original size:2 final size:2
Alignment explanation
Indices: 13618--13759 Score: 68
Period size: 2 Copynumber: 74.0 Consensus size: 2
13608 AGTATTTTAT
* * *
13618 TA TA TA TA TA TA TA TA TA T- TA TA TT TA CA TA T- TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
13657 TA TA TA GTA TT TA TA T- TT TA GTA TG TA TA TA TG TG TG TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
13700 TA T- TA GTA TA TG TA TA TA -A TA TT TA TA T- TA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
13739 TA TT TA AA AA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
13760 CATTATTTTA
Statistics
Matches: 108, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
1 9 0.08
2 93 0.86
3 6 0.06
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13740 original size:14 final size:14
Alignment explanation
Indices: 13615--13759 Score: 80
Period size: 13 Copynumber: 10.6 Consensus size: 14
13605 AGTAGTATTT
13615 TATTATATA-TATA
1 TATTATATATTATA
13628 TA-TATATATTATA
1 TATTATATATTATA
*
13641 T-TTACATATTAT-
1 TATTATATATTATA
13653 T-TTATATA-TAGTA
1 TATTATATATTA-TA
13666 T-TTATAT-TT-TA
1 TATTATATATTATA
* *
13677 GTATGTATATATGTGTG
1 -TAT-TATATAT-TATA
13694 TA-TATATATTAGTA
1 TATTATATATTA-TA
*
13708 TATGTATATAATATTTA
1 TAT-TATAT-AT-TATA
13725 TATTATATATTATA
1 TATTATATATTATA
**
13739 TATT-TA-AAAATA
1 TATTATATATTATA
13751 TATTATATA
1 TATTATATA
13760 CATTATTTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 35
0.70 0.06 0.23
Matches are distributed among these distances:
11 4 0.04
12 23 0.22
13 30 0.29
14 23 0.22
15 3 0.03
16 13 0.12
17 8 0.08
18 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.54
Consensus pattern (14 bp):
TATTATATATTATA
Found at i:13758 original size:26 final size:25
Alignment explanation
Indices: 13723--13810 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 25
13713 ATATAATATT
13723 TATATTATATATTATATATTTAAAAA
1 TATATTATATA-TATATATTTAAAAA
*
13749 TATATTATATACAT-TATTTTAAAAA
1 TATATTATATATATATA-TTTAAAAA
*
13774 -A-A--ATATAGTATATATTTTAAAA
1 TATATTATATA-TATATATTTAAAAA
13796 TATATTATA-ATATAT
1 TATATTATATATATAT
13811 GTTTTGGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
21 5 0.10
22 9 0.17
23 4 0.08
24 9 0.17
25 11 0.21
26 14 0.27
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TATATTATATATATATATTTAAAAA
Found at i:13809 original size:24 final size:24
Alignment explanation
Indices: 13723--13815 Score: 91
Period size: 24 Copynumber: 3.8 Consensus size: 24
13713 ATATAATATT
*
13723 TATATTATATATTATATATTTAAAAA
1 TATATTATA-A-TATATATTTTAAAA
*
13749 TATATTAT-ATACATTATTTTAAAA
1 TATATTATAATATA-TATTTTAAAA
* * *
13773 -AAAATATAGTATATATTTTAAAA
1 TATATTATAATATATATTTTAAAA
*
13796 TATATTATAATATATGTTTT
1 TATATTATAATATATATTTT
13816 GGAAAAAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
23 18 0.33
24 28 0.52
26 8 0.15
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (24 bp):
TATATTATAATATATATTTTAAAA
Found at i:13843 original size:2 final size:2
Alignment explanation
Indices: 13838--13878 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
13828 TAGGCATTCC
13838 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
13879 TTATTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16832 original size:20 final size:19
Alignment explanation
Indices: 16735--16833 Score: 55
Period size: 20 Copynumber: 5.2 Consensus size: 19
16725 TATTTAATAG
16735 TATTT-TATTATATATATA
1 TATTTATATTATATATATA
*
16753 TA-TTAT-TTATA-ATTTTA
1 TATTTATATTATATA-TATA
* * *
16770 GTATATATATAATATAGTACA
1 -TATTTATATTATATA-TATA
* * *
16791 CA-TTATAATATATACATAA
1 TATTTATATTATATATAT-A
16810 TATTTATATTATATAGTATA
1 TATTTATATTATATA-TATA
16830 TATT
1 TATT
16834 ATTTTTGAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 16
0.65 0.17 0.18
Matches are distributed among these distances:
16 1 0.02
17 10 0.18
18 6 0.11
19 14 0.25
20 21 0.37
21 5 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (19 bp):
TATTTATATTATATATATA
Found at i:16897 original size:37 final size:41
Alignment explanation
Indices: 16814--16898 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
16804 ACATAATATT
*
16814 TATATTATATAGTATATATTATTTTTGAAAACACGTATAATA
1 TATATTATATAGTAGATATTATTTTTGAAAACAC-TATAATA
*
16856 TATATTATATA-TAGA-A-TATTTTT-AAAACA-TATTATA
1 TATATTATATAGTAGATATTATTTTTGAAAACACTATAATA
16892 GTATATT
1 -TATATT
16899 TTTTGTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 6 0.15
37 6 0.15
38 6 0.15
39 7 0.17
40 1 0.03
41 3 0.08
42 11 0.28
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (41 bp):
TATATTATATAGTAGATATTATTTTTGAAAACACTATAATA
Found at i:17064 original size:2 final size:2
Alignment explanation
Indices: 16993--17044 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
16983 CCTGATTAAA
*
16993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17035 -T AT AGT AT AT
1 AT AT A-T AT AT
17045 GTTTTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20113 original size:10 final size:10
Alignment explanation
Indices: 20098--20125 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20088 ATGGTTTTAT
20098 GTCTTCAAAG
1 GTCTTCAAAG
20108 GTCTTCAAAG
1 GTCTTCAAAG
20118 GTCTTCAA
1 GTCTTCAA
20126 GAACAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (10 bp):
GTCTTCAAAG
Found at i:20339 original size:14 final size:15
Alignment explanation
Indices: 20183--20345 Score: 220
Period size: 15 Copynumber: 10.5 Consensus size: 15
20173 TAATAAGGTT
20183 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
20198 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
20213 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
20228 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
20243 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
20258 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
20273 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
20288 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
20307 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
20325 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
20339 ATTTATT
1 ATTTATT
20346 AGTATGAATT
Statistics
Matches: 135, Mismatches: 6, Indels: 15
0.87 0.04 0.10
Matches are distributed among these distances:
14 12 0.09
15 102 0.76
16 4 0.03
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 4 0.03
22 7 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:20364 original size:22 final size:22
Alignment explanation
Indices: 20348--20390 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20338 AATTTATTAG
20348 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
20370 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
20391 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:20364 original size:32 final size:31
Alignment explanation
Indices: 20325--20476 Score: 151
Period size: 32 Copynumber: 5.4 Consensus size: 31
20315 TTTTAAAATA
20325 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
20357 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
20379 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
20411 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
20433 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
20465 ATTTATTTTAAA
1 ATTTATTTTAAA
20477 ATATGGATTG
Statistics
Matches: 100, Mismatches: 0, Indels: 40
0.71 0.00 0.29
Matches are distributed among these distances:
22 27 0.27
23 5 0.05
24 4 0.04
26 6 0.06
27 4 0.04
28 6 0.06
30 4 0.04
31 4 0.04
32 40 0.40
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:20379 original size:69 final size:67
Alignment explanation
Indices: 20243--20400 Score: 230
Period size: 69 Copynumber: 2.3 Consensus size: 67
20233 TTATAAAATA
20243 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
20308 TG
66 TG
* * * * *
20310 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATG
20374 GATTG
63 GATTG
20379 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
20401 GTATGGATTG
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
66 13 0.16
67 22 0.27
68 13 0.16
69 34 0.41
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
TG
Found at i:20391 original size:54 final size:54
Alignment explanation
Indices: 20325--20493 Score: 329
Period size: 54 Copynumber: 3.1 Consensus size: 54
20315 TTTTAAAATA
*
20325 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
20379 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
20433 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
20487 ATTTATT
1 ATTTATT
20494 ATTGTAGTTG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 114 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:20427 original size:22 final size:22
Alignment explanation
Indices: 20402--20444 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20392 AATTTATTAG
20402 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
20424 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
20445 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:20524 original size:80 final size:80
Alignment explanation
Indices: 20424--20573 Score: 300
Period size: 80 Copynumber: 1.9 Consensus size: 80
20414 TATTTTAAAA
20424 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
20489 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
20504 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
20569 TTATT
66 TTATT
20574 TTAAATAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:20561 original size:22 final size:22
Alignment explanation
Indices: 20536--20578 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20526 AATTTATTAG
20536 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
20558 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
20579 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:23482 original size:31 final size:31
Alignment explanation
Indices: 23447--23523 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 31
23437 TTCAACGTTC
* *
23447 AAGTGACTAAAACTTAATAAAACGATAACGT
1 AAGTGACTAAAACTTAATAAAACAATAACGA
23478 AAGTGACT-AAACTTAATAAAACAATAACGA
1 AAGTGACTAAAACTTAATAAAACAATAACGA
23508 AAGTGA-TCAAAACTTA
1 AAGTGACT-AAAACTTA
23524 TGTTCTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 1 0.02
30 26 0.62
31 15 0.36
ACGTcount: A:0.53, C:0.13, G:0.12, T:0.22
Consensus pattern (31 bp):
AAGTGACTAAAACTTAATAAAACAATAACGA
Found at i:25209 original size:51 final size:51
Alignment explanation
Indices: 25149--25256 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
25139 ATATTCTGCA
* *
25149 ATTAGTTATCACATGAAAAATAAAGCACATATACATAATCTTAATAATTAG
1 ATTAGTTATCACATGAAAAATAAAGCACATAAACATAATCTTAATAAGTAG
* *
25200 ATTAGTTATCACATGAAAAATATAGCACATAAACATAATCTTTATAAGTAG
1 ATTAGTTATCACATGAAAAATAAAGCACATAAACATAATCTTAATAAGTAG
*
25251 AATAGT
1 ATTAGT
25257 AAAGATTCGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (51 bp):
ATTAGTTATCACATGAAAAATAAAGCACATAAACATAATCTTAATAAGTAG
Found at i:34350 original size:21 final size:21
Alignment explanation
Indices: 34311--34351 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34301 GCAAGAATTT
*
34311 ATGGCTTTAATAAAAACTTTC
1 ATGGCTTTAACAAAAACTTTC
* *
34332 ATGGCTTTAACCAATACTTT
1 ATGGCTTTAACAAAAACTTT
34352 GATACATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
ATGGCTTTAACAAAAACTTTC
Found at i:42791 original size:21 final size:19
Alignment explanation
Indices: 42763--42803 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
42753 CATTGCAGGA
42763 ATTTATGGCTTCGAAAAAAG
1 ATTTATGGCTTC-AAAAAAG
*
42783 ATTTCATGGCTTCAACAAAG
1 ATTT-ATGGCTTCAAAAAAG
42803 A
1 A
42804 CCTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (19 bp):
ATTTATGGCTTCAAAAAAG
Done.