Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003435.1 Hibiscus syriacus cultivar Beakdansim tig00007239_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: 56422
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:10791 original size:19 final size:20
Alignment explanation
Indices: 10767--10809 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
10757 AGCATTTATC
*
10767 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
10786 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
10806 TTCA
1 TTCA
10810 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:12687 original size:19 final size:20
Alignment explanation
Indices: 12663--12705 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
12653 AGCATTTATC
12663 TTCATTAAAAAT-ATGTATT
1 TTCATTAAAAATCATGTATT
*
12682 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
12702 TTCA
1 TTCA
12706 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:17293 original size:10 final size:10
Alignment explanation
Indices: 17280--17324 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
17270 AAATTTTGGC
17280 TTTTTTGTTT
1 TTTTTTGTTT
*
17290 TTTTTTGTGT
1 TTTTTTGTTT
**
17300 TTTTTTG-CC
1 TTTTTTGTTT
17309 TTTTTTGTTT
1 TTTTTTGTTT
17319 TTTTTT
1 TTTTTT
17325 TGTAGAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.84
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:18099 original size:17 final size:20
Alignment explanation
Indices: 18074--18113 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
18064 AAGGTCCTAA
*
18074 ATAACTAATGAA-TAAA-AT
1 ATAACTAATAAACTAAACAT
18092 ATAA-TAATAAACTAAACAT
1 ATAACTAATAAACTAAACAT
18111 ATA
1 ATA
18114 TTAACTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAACTAATAAACTAAACAT
Found at i:24049 original size:13 final size:11
Alignment explanation
Indices: 24033--24112 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 11
24023 ATACTATTTC
24033 CATCACCATAGT
1 CATCACCATA-T
*
24045 CCATCTTCCATTAT
1 -CATC-ACCA-TAT
24059 CAT-ACCTATAT
1 CATCACC-ATAT
24070 CATCACCATAGTT
1 CATCACCATA--T
24083 CATCACCATAT
1 CATCACCATAT
*
24094 CA-CGCCTATAT
1 CATCACC-ATAT
24105 CATCACCA
1 CATCACCA
24113 AATTCTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
10 3 0.05
11 21 0.38
12 7 0.13
13 18 0.33
14 4 0.07
15 2 0.04
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:24102 original size:35 final size:37
Alignment explanation
Indices: 24033--24112 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
24023 ATACTATTTC
* *
24033 CATCACCATAGTCCATCTTCCATTATCATACCTATAT
1 CATCACCATAGTCCATCTACCATTATCACACCTATAT
* *
24070 CATCACCATAGTTCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAGTCCATCTACCATTATCACACCTATAT
24105 CATCACCA
1 CATCACCA
24113 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (37 bp):
CATCACCATAGTCCATCTACCATTATCACACCTATAT
Found at i:29630 original size:33 final size:33
Alignment explanation
Indices: 29586--29654 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
29576 CATCACCATA
*
29586 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
29619 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
29652 TTC
1 TTC
29655 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:39375 original size:35 final size:37
Alignment explanation
Indices: 39306--39383 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 37
39296 ATACTATTCC
*
39306 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTGCCATTATCACGCCTATAT
*
39343 CATCACCATAGTCCATC-GCCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTGCCATTATCACGCCTATAT
39378 CATCAC
1 CATCAC
39384 GAAATTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTGCCATTATCACGCCTATAT
Found at i:39863 original size:14 final size:15
Alignment explanation
Indices: 39832--39873 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39822 TTTGGAGTGC
39832 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
39847 AAAAG-AAGAATA-A
1 AAAAGAAAGAAAAGA
39860 AAAAGCAAAGAAAA
1 AAAAG-AAAGAAAA
39874 AGTGAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:47168 original size:25 final size:25
Alignment explanation
Indices: 47139--47202 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
47129 CTTGGCTTGC
47139 TTTTCTCTTTT-TAAAATCTTT-TTCT
1 TTTTCTCTTTTCT-AAAT-TTTCTTCT
*
47164 TTTTCTTCTTTTCTGAATTTTCTTCT
1 TTTTC-TCTTTTCTAAATTTTCTTCT
*
47190 TTTTGTCTTTTCT
1 TTTTCTCTTTTCT
47203 TTCTTTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 16 0.47
26 17 0.50
27 1 0.03
ACGTcount: A:0.09, C:0.17, G:0.03, T:0.70
Consensus pattern (25 bp):
TTTTCTCTTTTCTAAATTTTCTTCT
Found at i:47206 original size:17 final size:15
Alignment explanation
Indices: 47155--47211 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
47145 CTTTTTAAAA
*
47155 TCTTTTTCTTTTTCT
1 TCTTTTTGTTTTTCT
*
47170 TCTTTTCTGAATTTTCT
1 TCTTTT-TG-TTTTTCT
47187 TCTTTTTGTCTTTTCTT
1 TCTTTTTGT-TTTTC-T
47204 TCTTTTTG
1 TCTTTTTG
47212 CACTCCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 21 0.60
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.74
Consensus pattern (15 bp):
TCTTTTTGTTTTTCT
Found at i:49310 original size:19 final size:19
Alignment explanation
Indices: 49274--49322 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
49264 GGCCAAGAGC
* **
49274 ATGTATCTTCATTTAAATA
1 ATGTATTTTCATAAAAATA
*
49293 ATGTATTTTCATAAAAATC
1 ATGTATTTTCATAAAAATA
49312 ATGTATTTTCA
1 ATGTATTTTCA
49323 AAGGGGTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (19 bp):
ATGTATTTTCATAAAAATA
Found at i:49729 original size:35 final size:37
Alignment explanation
Indices: 49660--49739 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
49650 ATACTATTCC
*
49660 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
49697 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
49732 CATCACCA
1 CATCACCA
49740 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:53754 original size:35 final size:37
Alignment explanation
Indices: 53685--53764 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
53675 ATACTATTTC
*
53685 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
53722 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
53757 CATCACCA
1 CATCACCA
53765 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:54275 original size:43 final size:46
Alignment explanation
Indices: 54175--54279 Score: 128
Period size: 49 Copynumber: 2.3 Consensus size: 46
54165 AGGATCAGAT
* *
54175 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACAATAGTTTAGTTA
54224 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-AT-GTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATAGTTTAG-TTA
54267 TTATTATTTTATT
1 TTATTATTTTATT
54280 CTTTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
42 5 0.09
43 18 0.34
44 9 0.17
48 1 0.02
49 20 0.38
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATAGTTTAGTTA
Found at i:54927 original size:15 final size:15
Alignment explanation
Indices: 54907--54936 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54897 GAAACAAGCA
54907 ATCTTGCTTGTTCTT
1 ATCTTGCTTGTTCTT
54922 ATCTTGCTTGTTCTT
1 ATCTTGCTTGTTCTT
54937 GCACTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.13, T:0.60
Consensus pattern (15 bp):
ATCTTGCTTGTTCTT
Done.