Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003434.1 Hibiscus syriacus cultivar Beakdansim tig00007238_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: 54811
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:199 original size:35 final size:34
Alignment explanation
Indices: 136--205 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 34
126 GGATAAAATG
136 AAGTACAGAATGGAAAAAATTGAATTCAAAAGAA
1 AAGTACAGAATGGAAAAAATTGAATTCAAAAGAA
* *
170 AAGTACTGAAT-GAAAGGAAATTGAGTTCAAAAGAA
1 AAGTACAGAATGGAAA--AAATTGAATTCAAAAGAA
205 A
1 A
206 TAAGAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 4 0.12
34 10 0.31
35 18 0.56
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.19
Consensus pattern (34 bp):
AAGTACAGAATGGAAAAAATTGAATTCAAAAGAA
Found at i:8494 original size:37 final size:37
Alignment explanation
Indices: 8448--8827 Score: 367
Period size: 37 Copynumber: 9.9 Consensus size: 37
8438 CATGAAGATG
* *
8448 TTTTAAAAATATTTTCAAAAATTATATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
8485 TTTTCAAAATGA-TTTCAAAAACTATAT-TATATATATA
1 TTTTCAAAAT-ATTTTCAAAAACTATATAT-TATATATA
*
8522 TATTCAAAATATTTTCAAAAACTATATTATATATATATATA
1 TTTTCAAAATATTTTCAAAAAC--TA-TATAT-TATATATA
* * * *
8563 TATTTTAAATTGTTTTCAAAAATTATATATTATATATA
1 T-TTTCAAAATATTTTCAAAAACTATATATTATATATA
* * *
8601 TTTTTTCAGAAACATTTTCAGAAACTATATGTTATATATA
1 --TTTTCA-AAATATTTTCAAAAACTATATATTATATATA
8641 TTTTCAAAATATTTTCAAAAACTATATATTATATATACA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATAT--A
* *
8680 TTTTTAAAATGTTTTCAAAAACTATATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
* *
8717 --TTCAAAATATTTTTAAAAACTATATTATATATATATG
1 TTTTCAAAATATTTTCAAAAACTATA-TAT-TATATATA
** * * *
8754 TTTTCGGAATGTTTTATAAAAAACTATATATTATATATTTG
1 TTTTCAAAAT-ATTT-TCAAAAACTATATATTATATA--TA
*
8795 TTTTCAAAAT-TTTAT-AAAAACTATATACTATAT
1 TTTTCAAAATATTT-TCAAAAACTATATATTATAT
8828 CTTATATATA
Statistics
Matches: 291, Mismatches: 31, Indels: 41
0.80 0.09 0.11
Matches are distributed among these distances:
35 21 0.07
36 5 0.02
37 85 0.29
38 32 0.11
39 63 0.22
40 37 0.13
41 32 0.11
42 16 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTTCAAAATATTTTCAAAAACTATATATTATATATA
Found at i:8547 original size:26 final size:25
Alignment explanation
Indices: 8453--8548 Score: 67
Period size: 26 Copynumber: 3.8 Consensus size: 25
8443 AGATGTTTTA
8453 AAAATATTTTCAAAAATTATATATT-
1 AAAATATTTTCAAAAA-TATATATTC
* *
8478 ATATATATTTTC-AAAAT-GAT-TTC
1 A-AAATATTTTCAAAAATATATATTC
* * *
8501 AAAAACTATATT-ATATATATATATTC
1 -AAAA-TATTTTCAAAAATATATATTC
8527 AAAATATTTTCAAAAACTATAT
1 AAAATATTTTCAAAAA-TATAT
8549 TATATATATA
Statistics
Matches: 52, Mismatches: 10, Indels: 17
0.66 0.13 0.22
Matches are distributed among these distances:
22 2 0.04
23 4 0.08
24 15 0.29
25 14 0.27
26 17 0.33
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (25 bp):
AAAATATTTTCAAAAATATATATTC
Found at i:8588 original size:74 final size:73
Alignment explanation
Indices: 8453--8752 Score: 229
Period size: 77 Copynumber: 3.9 Consensus size: 73
8443 AGATGTTTTA
8453 AAAATATTTTCAAAAATTATATATTATATATATTTTCAAAATGATTTCAAAAACTATATTATATA
1 AAAATATTTTCAAAAATTATATATTATATATATTTTCAAAATGATTTC-AAAAC-ATATTATATA
8518 -TATATATTC
64 TTATATATTC
* * *
8527 AAAATATTTTCAAAAACTATATTATATATATATATATATTTTAAATTGTTTTCAAAA-ATTATAT
1 AAAATATTTTCAAAAA-T-TA-TATAT-TATATATAT-TTTCAAAATGATTTCAAAACA-TAT-T
* *
8591 ATTATATATATTTTTTC
59 A-TATAT-TATATATTC
* * * *
8608 AGAAACATTTTCAGAAACTATATGTTATATATATTTTCAAAAT-ATTTTCAAAA-ACTATATATT
1 A-AAATATTTTCAAAAATTATATATTATATATATTTTCAAAATGA-TTTCAAAACA-TAT-TA-T
* * *
8671 ATATATACATTTTT
61 ATAT-TATATATTC
* * *
8685 AAAATGTTTTCAAAAACTATATATTATATATA--TTCAAAAT-ATTTTTAAAAACTATATTATAT
1 AAAATATTTTCAAAAATTATATATTATATATATTTTCAAAATGA--TTTCAAAAC-ATATTATAT
8747 A-TATAT
63 ATTATAT
8753 GTTTTCGGAA
Statistics
Matches: 189, Mismatches: 22, Indels: 32
0.78 0.09 0.13
Matches are distributed among these distances:
72 4 0.02
74 29 0.15
75 11 0.06
76 33 0.17
77 45 0.24
78 24 0.13
79 20 0.11
80 2 0.01
81 8 0.04
82 13 0.07
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (73 bp):
AAAATATTTTCAAAAATTATATATTATATATATTTTCAAAATGATTTCAAAACATATTATATATT
ATATATTC
Found at i:8765 original size:74 final size:73
Alignment explanation
Indices: 8454--8791 Score: 292
Period size: 76 Copynumber: 4.4 Consensus size: 73
8444 GATGTTTTAA
* * *
8454 AAATATTTTCAAAAATTATATATTATATATATTTTCAAAATGA-TTTCAAAAACTATATTATATA
1 AAATGTTTTCAAAAACTATATATTATATATA--TTCAAAAT-ATTTTTAAAAACTATATTATATA
* *
8518 TATA-TATTCA
63 TATATTTTTCG
* *
8528 AAATATTTTCAAAAACTATATTATATATATATATAT-ATTTTAAAT-TGTTTTCAAAAATTATA-
1 AAATGTTTTCAAAAACTATA-TAT-TATATATAT-TCA----AAATAT-TTTT-AAAAACTATAT
8590 TATTATATATATTTTTTCAG
57 TA-TATATATA-TTTTTC-G
** * * *
8610 AAACATTTTCAGAAACTATATGTTATATATATTTTCAAAATATTTTCAAAAACTATATATTATAT
1 AAATGTTTTCAAAAACTATATATTATATATA--TTCAAAATATTTTTAAAAAC--TATATTATAT
* *
8675 ATACATTTTT-A
62 ATATATTTTTCG
8686 AAATGTTTTCAAAAACTATATATTATATATATTCAAAATATTTTTAAAAACTATATTATATATAT
1 AAATGTTTTCAAAAACTATATATTATATATATTCAAAATATTTTTAAAAACTATATTATATATAT
8751 ATGTTTTCG
66 AT-TTTTCG
* *
8760 GAATGTTTTATAAAAAACTATATATTATATAT
1 AAATG-TTT-TCAAAAACTATATATTATATAT
8792 TTGTTTTCAA
Statistics
Matches: 218, Mismatches: 21, Indels: 48
0.76 0.07 0.17
Matches are distributed among these distances:
72 15 0.07
73 4 0.02
74 44 0.20
75 7 0.03
76 56 0.26
77 5 0.02
78 21 0.10
79 29 0.13
80 10 0.05
81 7 0.03
82 20 0.09
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (73 bp):
AAATGTTTTCAAAAACTATATATTATATATATTCAAAATATTTTTAAAAACTATATTATATATAT
ATTTTTCG
Found at i:8789 original size:39 final size:37
Alignment explanation
Indices: 8549--8827 Score: 251
Period size: 39 Copynumber: 7.3 Consensus size: 37
8539 AAAACTATAT
* * * *
8549 TATATATATATATATATTTT-AAATTGTTTTCAAAAAT
1 TATATAT-TATATATATTTTCAAAATATTTTTAAAAAC
* * *
8586 TATATATTATATATATTTTTTCAGAAACATTTTCAGAAAC
1 TATATATTATATATA--TTTTCA-AAATATTTTTAAAAAC
* *
8626 TATATGTTATATATATTTTCAAAATATTTTCAAAAAC
1 TATATATTATATATATTTTCAAAATATTTTTAAAAAC
* * *
8663 TATATATTATATATACATTTTTAAAATGTTTTCAAAAAC
1 TATATATTATATAT--ATTTTCAAAATATTTTTAAAAAC
8702 TATATATTATATATA--TTCAAAATATTTTTAAAAAC
1 TATATATTATATATATTTTCAAAATATTTTTAAAAAC
* ** *
8737 TATATTATATATATATGTTTTCGGAATGTTTTATAAAAAAC
1 TATA-TAT-TATATATATTTTCAAAATATTTT-T-AAAAAC
* *
8778 TATATATTATATATTTGTTTTCAAAAT-TTTATAAAAAC
1 TATATATTATATA--TATTTTCAAAATATTTTTAAAAAC
*
8816 TATATACTATAT
1 TATATATTATAT
8828 CTTATATATA
Statistics
Matches: 206, Mismatches: 22, Indels: 27
0.81 0.09 0.11
Matches are distributed among these distances:
35 21 0.10
36 11 0.05
37 42 0.20
38 27 0.13
39 53 0.26
40 32 0.16
41 20 0.10
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATATTATATATATTTTCAAAATATTTTTAAAAAC
Found at i:24979 original size:21 final size:21
Alignment explanation
Indices: 24953--24994 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24943 CTAAGATAGG
*
24953 GGGTATTGGTACCT-CTTCATA
1 GGGTATCGGTA-CTACTTCATA
24974 GGGTATCGGTACTACTTCATA
1 GGGTATCGGTACTACTTCATA
24995 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
GGGTATCGGTACTACTTCATA
Found at i:25256 original size:32 final size:29
Alignment explanation
Indices: 25198--25258 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 29
25188 AAACTTTGAA
*
25198 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCAAAAAACATTTTG
25227 TAAATTCAATTCAAGTCTAAAAAAACATTTTG
1 TAAATTCAATT-AAGTC--AAAAAACATTTTG
25259 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.39
30 5 0.18
32 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTAAGTCAAAAAACATTTTG
Found at i:27839 original size:15 final size:16
Alignment explanation
Indices: 27821--27850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27811 AATATCTAAT
27821 AATTAAA-TAAATTTC
1 AATTAAATTAAATTTC
27836 AATTAAATTAAATTT
1 AATTAAATTAAATTT
27851 ATAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAAATTAAATTTC
Found at i:40041 original size:21 final size:20
Alignment explanation
Indices: 40016--40054 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
40006 TATAACAAAG
40016 GTAGTACCGATACTCCCTTTA
1 GTAGTACCGATAC-CCCTTTA
40037 GTAGTACCGATACCCCTT
1 GTAGTACCGATACCCCTT
40055 GGTTTGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (20 bp):
GTAGTACCGATACCCCTTTA
Found at i:41383 original size:12 final size:12
Alignment explanation
Indices: 41348--41388 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
41338 GAGGAAGATG
41348 ATGAAGAAAAGA
1 ATGAAGAAAAGA
*
41360 AGGAA-AATAAGA
1 ATGAAGAA-AAGA
41372 ATGAAGAAAAGA
1 ATGAAGAAAAGA
41384 A-GAAG
1 ATGAAG
41389 GAGGTGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.24
12 17 0.68
13 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.27, T:0.07
Consensus pattern (12 bp):
ATGAAGAAAAGA
Found at i:46951 original size:23 final size:23
Alignment explanation
Indices: 46899--46951 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
46889 ACTGCGCACA
*
46899 CTTTATTTTACCATGACATTTCC
1 CTTTATTTTACCATGACATCTCC
* * *
46922 ATCTATTTTGCCACT-ACATCTCC
1 CTTTATTTTACCA-TGACATCTCC
46945 CTTTATT
1 CTTTATT
46952 GCCACATCAC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.21, C:0.28, G:0.04, T:0.47
Consensus pattern (23 bp):
CTTTATTTTACCATGACATCTCC
Done.