Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005370.1 Hibiscus syriacus cultivar Beakdansim tig00012208_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: 42952
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1531 original size:2 final size:2
Alignment explanation
Indices: 1518--1570 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1508 TTTATTCCCT
* * *
1518 TA TA TT TA TA TA TA TA TT TA TA TT TA TA TA TA TA TA 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
1560 TA TA TA TA TA T
1 TA TA TA TA TA T
1571 TTAGCATACG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:12462 original size:13 final size:13
Alignment explanation
Indices: 12455--12487 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12445 GAAAAAAGAG
12455 AGAAAAAAACAAA
1 AGAAAAAAACAAA
12468 AGAAAAAAACAAA
1 AGAAAAAAACAAA
12481 AGAAAAA
1 AGAAAAA
12488 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AGAAAAAAACAAA
Found at i:12495 original size:24 final size:23
Alignment explanation
Indices: 12423--12497 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 23
12413 CCCTAAATTG
*
12423 AAAAAAAAAGAAAAGGAAAAGAGA
1 AAAAAAAAAGAAAAAGAAAAGA-A
*
12447 AAAAAGAGAGAA-AAAAACAAAAGAA
1 AAAAA-A-A-AAGAAAAAGAAAAGAA
12472 AAAAACAAAAGAAAAAGAAAAGAA
1 AAAAA-AAAAGAAAAAGAAAAGAA
12496 AA
1 AA
12498 TAAGGTGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.47
25 8 0.19
26 11 0.26
27 2 0.05
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAGAAAAAGAAAAGAA
Found at i:16138 original size:49 final size:49
Alignment explanation
Indices: 16085--16182 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
16075 CTCACGATAA
16085 CAAAATAAGTTAATTACTTATAATGTAATATAAATTCTCTACAATATAT
1 CAAAATAAGTTAATTACTTATAATGTAATATAAATTCTCTACAATATAT
*
16134 CAAAATAAGTTAATTACTTATAATGTAATATAGATTCTCTACAATATAT
1 CAAAATAAGTTAATTACTTATAATGTAATATAAATTCTCTACAATATAT
16183 TCGGTTGTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (49 bp):
CAAAATAAGTTAATTACTTATAATGTAATATAAATTCTCTACAATATAT
Found at i:16546 original size:54 final size:54
Alignment explanation
Indices: 16441--16928 Score: 415
Period size: 54 Copynumber: 8.9 Consensus size: 54
16431 TTATTCCATT
* * * * *
16441 TTATAAGGTAACCGATAAAAAAAACAAAACAAAGCACAACCGATAACGTTACTCCTAC
1 TTATAAGGTAACCGAT---TAAAA-ATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* * *
16499 TTATAAGGTTACCGATTGAAAATAACAAGGCGCAACCGTTAAAGTTACTCCTAC
1 TTATAAGGTAACCGATTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* * * * *
16553 TTATAAGGTAACAGGTTAAAAATAACAAGGAGCAACCGTTAACGTTACTCATTC
1 TTATAAGGTAACCGATTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* *
16607 TTATAAGGTAACC-AGTTAAAAATAACAAGCCGTAACCGTTAACGTTACTCCTAC
1 TTATAAGGTAACCGA-TTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* * * * * * *
16661 TTATAAAGTAACCGGTTAAAAATAACAAGGTGCAACCGTCACCTTTACTCTTAC
1 TTATAAGGTAACCGATTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* * * * * * * * **
16715 TTATAAGGTTACTGGTTAAATAAAACACAAGGCACAACCATAAACTTTACTTATAC
1 TTATAAGGTAACCGATTAAA-AATA-ACAAGGCGCAACCGTTAACGTTACTCCTAC
* * * * * ***
16771 TTATAAGATAATCGGTTGAAAATAAAAAATTGCAACCGTTAACGTTACTCCTAC
1 TTATAAGGTAACCGATTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* * * * * *
16825 TTATAAGGTAATCGATAAAAAAACAAAACAAGACACAACCGTAAACGTTACTCCTAC
1 TTATAAGGTAACCGAT--TAAAA-ATAACAAGGCGCAACCGTTAACGTTACTCCTAC
* *
16882 TTATAAGGTAACC-AGTTAAAAATAACATGGCACAACC-TATAACGTTA
1 TTATAAGGTAACCGA-TTAAAAATAACAAGGCGCAACCGT-TAACGTTA
16929 TTCAAGAATG
Statistics
Matches: 345, Mismatches: 76, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
53 1 0.00
54 235 0.68
55 13 0.04
56 42 0.12
57 39 0.11
58 15 0.04
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (54 bp):
TTATAAGGTAACCGATTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTAC
Found at i:17037 original size:19 final size:19
Alignment explanation
Indices: 17013--17056 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
17003 TATCGGAACT
*
17013 TTGTTATGAGGATCGAAAC
1 TTGTTATGAGGATAGAAAC
*
17032 TTGTTATGATGATAGAAAC
1 TTGTTATGAGGATAGAAAC
17051 TTGTTA
1 TTGTTA
17057 AAAATAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.39
Consensus pattern (19 bp):
TTGTTATGAGGATAGAAAC
Found at i:17257 original size:55 final size:50
Alignment explanation
Indices: 17173--17338 Score: 187
Period size: 48 Copynumber: 3.3 Consensus size: 50
17163 ATACTTTGCG
* * * *
17173 GAAAAGT-TTGATACTTTGCAGCCTTCTCATTTTCTATGTTTTTTAATATTTTT
1 GAAAAGTATCGATACTTTGCAGTCTTCTCATTTTCCAT-TTTTTTAA-A--TTC
*
17226 GTAAAAGTATCGATACTTTACAGTCTTCTCATTTTCCATTTTTTT-AATTC
1 G-AAAAGTATCGATACTTTGCAGTCTTCTCATTTTCCATTTTTTTAAATTC
*
17276 G-AAAGTATCGATACTTTGCATTCTTCTCATTTTCCATTTTTTTTAAATTC
1 GAAAAGTATCGATACTTTGCAGTCTTCTCATTTTCCA-TTTTTTTAAATTC
*
17326 G-ATAGTATCGATA
1 GAAAAGTATCGATA
17339 GTATCGATAC
Statistics
Matches: 101, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
48 33 0.33
49 7 0.07
50 20 0.20
52 1 0.01
53 2 0.02
54 12 0.12
55 26 0.26
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.49
Consensus pattern (50 bp):
GAAAAGTATCGATACTTTGCAGTCTTCTCATTTTCCATTTTTTTAAATTC
Found at i:18135 original size:3 final size:3
Alignment explanation
Indices: 18127--18151 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18117 GGATGAATTT
18127 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
18152 CAAGCCGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:25768 original size:121 final size:123
Alignment explanation
Indices: 25618--25863 Score: 462
Period size: 121 Copynumber: 2.0 Consensus size: 123
25608 TTTATAACTT
25618 AAGATTGATAAGATTGAACACAAAGCTAACAAATATAAATGTGAAATCA-TTATCACTTATAATT
1 AAGATTGATAAGATTGAACACAAAGCTAACAAATATAAATGTGAAATCATTTATCAC-TATAATT
25682 TGTTAAGTAAAATTTGATAAATATTTTTTTAT-AAA-ATATTCTTGCACCCATGGCGTG
65 TGTTAAGTAAAATTTGATAAATATTTTTTTATAAAATATATTCTTGCACCCATGGCGTG
25739 AAGATTGATAAGATTGAACACAAAGCTAACAAATATAAATGTGAAATCATTTATCACTATAATTT
1 AAGATTGATAAGATTGAACACAAAGCTAACAAATATAAATGTGAAATCATTTATCACTATAATTT
25804 GTTAAGTAAAATTTGATAAATATTTTTTTATAAAATATATTCTTGCACCCATGGCGTG
66 GTTAAGTAAAATTTGATAAATATTTTTTTATAAAATATATTCTTGCACCCATGGCGTG
25862 AA
1 AA
25864 TTCGGGGTGT
Statistics
Matches: 122, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
121 88 0.72
122 10 0.08
123 24 0.20
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (123 bp):
AAGATTGATAAGATTGAACACAAAGCTAACAAATATAAATGTGAAATCATTTATCACTATAATTT
GTTAAGTAAAATTTGATAAATATTTTTTTATAAAATATATTCTTGCACCCATGGCGTG
Found at i:28377 original size:3 final size:3
Alignment explanation
Indices: 28360--28401 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
28350 ACTTTATCCA
*
28360 TAT TA- TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28402 GATTGTGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29218 original size:25 final size:25
Alignment explanation
Indices: 29184--29234 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29174 ATCATTGATG
29184 ATATATTAAGTAATCTAAGTGACAA
1 ATATATTAAGTAATCTAAGTGACAA
29209 ATATATTAAGTAATCTAAGTGACAA
1 ATATATTAAGTAATCTAAGTGACAA
29234 A
1 A
29235 AAGGAGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (25 bp):
ATATATTAAGTAATCTAAGTGACAA
Found at i:29708 original size:46 final size:46
Alignment explanation
Indices: 29641--29827 Score: 293
Period size: 46 Copynumber: 4.1 Consensus size: 46
29631 TACCACGTTT
*
29641 TTCCGATCATCACCTCTAAGCTATATTAAACCCTCAGCCTCCATTG
1 TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGCCTCCATTG
* *
29687 TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGACTCCGTTG
1 TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGCCTCCATTG
* * * * *
29733 ATCCGATCATCATCTTTAAGGTATTTTAAACCCTCAGCTTCCATTG
1 TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGCCTCCATTG
*
29779 TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGTCTCCATTG
1 TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGCCTCCATTG
29825 TTC
1 TTC
29828 TCTCATTCAT
Statistics
Matches: 125, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (46 bp):
TTCCGATCATCATCTCTAAGCTATATTAAACCCTCAGCCTCCATTG
Found at i:30529 original size:2 final size:2
Alignment explanation
Indices: 30522--30552 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30512 TCATAAAATT
30522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30553 TTACAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38362 original size:2 final size:2
Alignment explanation
Indices: 38355--38381 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38345 TGATTATAAT
38355 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38382 TAATTGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.