Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003099.1 Hibiscus syriacus cultivar Beakdansim tig00006472_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: 86817
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3966 original size:21 final size:19
Alignment explanation
Indices: 3921--3969 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3911 TACCATATGT
*
3921 TAAAAGATAGATTATAAATA
1 TAAAAGAT-GATCATAAATA
3941 T-AAAGATGATCATAATAATA
1 TAAAAGATGATCAT-A-AATA
3961 TAAAAGATG
1 TAAAAGATG
3970 TAAAAGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 7 0.28
20 6 0.24
21 7 0.28
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (19 bp):
TAAAAGATGATCATAAATA
Found at i:9739 original size:20 final size:19
Alignment explanation
Indices: 9697--9741 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
9687 CCAAGAGCAT
* * *
9697 GTATTTTCATTTATGTCAT
1 GTATTTTCATTAAAGTCAA
9716 GTATTTTCATTAAAAGTCAA
1 GTATTTTCATT-AAAGTCAA
9736 GTATTT
1 GTATTT
9742 CAAAGGGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (19 bp):
GTATTTTCATTAAAGTCAA
Found at i:16012 original size:17 final size:17
Alignment explanation
Indices: 15990--16041 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
15980 TAATAAAGTT
15990 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
16007 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
16024 TAGTT-ATTTATTAAAC
1 TAGTTCATTAATTAAAC
16040 TA
1 TA
16042 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 11 0.35
17 20 0.65
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:18895 original size:17 final size:17
Alignment explanation
Indices: 18875--18910 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
18865 TTAATAAATT
18875 TAGTTC-ATTAATTAAAC
1 TAGTTCAATT-ATTAAAC
18892 TAGTTCAATTATTAAAC
1 TAGTTCAATTATTAAAC
18909 TA
1 TA
18911 AATCTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCAATTATTAAAC
Found at i:24073 original size:17 final size:17
Alignment explanation
Indices: 24026--24078 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
24016 ATTAAAGTGT
* *
24026 TAGTTAGATTAATGCAC
1 TAGTTTGATTAATGAAC
* * *
24043 TAGCTTAATAAATGAAC
1 TAGTTTGATTAATGAAC
24060 TAGTTTGATTAATGAAC
1 TAGTTTGATTAATGAAC
24077 TA
1 TA
24079 AATGCATGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTGATTAATGAAC
Found at i:35283 original size:21 final size:20
Alignment explanation
Indices: 35241--35288 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
35231 ACTACCAACT
35241 TTTCA-TTAATTCATTTTCA
1 TTTCATTTAATTCATTTTCA
* *
35260 TTTCATTTACTTCAGTTTTTA
1 TTTCATTTAATTCA-TTTTCA
35281 TTTCATTT
1 TTTCATTT
35289 TATTTCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 13 0.52
ACGTcount: A:0.21, C:0.15, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTCATTTAATTCATTTTCA
Found at i:48486 original size:1 final size:1
Alignment explanation
Indices: 48482--48526 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
48472 TAATTTTGGC
* * * *
48482 TTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48527 GAAAAAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:48495 original size:9 final size:9
Alignment explanation
Indices: 48483--48526 Score: 70
Period size: 9 Copynumber: 4.8 Consensus size: 9
48473 AATTTTGGCT
48483 TTTTTTTTG
1 TTTTTTTTG
48492 TTTTTTTTG
1 TTTTTTTTG
*
48501 TTTTTTTGTT
1 TTTTTTT-TG
48511 TTTTTTTTG
1 TTTTTTTTG
48520 TTTTTTT
1 TTTTTTT
48527 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:48499 original size:29 final size:28
Alignment explanation
Indices: 48465--48526 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
48455 TCGTTTTCAA
48465 TTTTTTGTAATTTTGGCTTTTTTTTTGTT
1 TTTTTTGT-ATTTTGGCTTTTTTTTTGTT
* * *
48494 TTTTTTGTTTTTTTGTTTTTTTTTTGTT
1 TTTTTTGTATTTTGGCTTTTTTTTTGTT
48522 TTTTT
1 TTTTT
48527 GAAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.03, C:0.02, G:0.11, T:0.84
Consensus pattern (28 bp):
TTTTTTGTATTTTGGCTTTTTTTTTGTT
Found at i:48515 original size:19 final size:20
Alignment explanation
Indices: 48482--48527 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
48472 TAATTTTGGC
48482 TTTTTTT-TTGTTTTTTTTG
1 TTTTTTTGTTGTTTTTTTTG
48501 TTTTTTTGTT-TTTTTTTTG
1 TTTTTTTGTTGTTTTTTTTG
48520 TTTTTTTG
1 TTTTTTTG
48528 AAAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (20 bp):
TTTTTTTGTTGTTTTTTTTG
Found at i:53580 original size:19 final size:19
Alignment explanation
Indices: 53539--53581 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
53529 AATTTTAACT
* **
53539 TTTTTGGCTTTTTTTTGTT
1 TTTTTGCCTTTTTTTTGCC
53558 TTTTTGCCTTTTTTTTGCC
1 TTTTTGCCTTTTTTTTGCC
53577 TTTTT
1 TTTTT
53582 TTTGTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77
Consensus pattern (19 bp):
TTTTTGCCTTTTTTTTGCC
Found at i:53592 original size:11 final size:11
Alignment explanation
Indices: 53538--53585 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
53528 AAATTTTAAC
*
53538 TTTTTTGGCTT
1 TTTTTTGCCTT
53549 TTTTTTG---T
1 TTTTTTGCCTT
53557 TTTTTTGCCTT
1 TTTTTTGCCTT
53568 TTTTTTGCCTT
1 TTTTTTGCCTT
53579 TTTTTTG
1 TTTTTTG
53586 TTTTTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.24
11 26 0.76
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.77
Consensus pattern (11 bp):
TTTTTTGCCTT
Found at i:53593 original size:19 final size:19
Alignment explanation
Indices: 53538--53574 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53528 AAATTTTAAC
*
53538 TTTTTTGGCTTTTTTTTGT
1 TTTTTTGCCTTTTTTTTGT
53557 TTTTTTGCCTTTTTTTTG
1 TTTTTTGCCTTTTTTTTG
53575 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (19 bp):
TTTTTTGCCTTTTTTTTGT
Found at i:58072 original size:22 final size:23
Alignment explanation
Indices: 58020--58072 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
58010 TAGTATAATA
* *
58020 ATTAAAAAAATTATAATTTTTTT
1 ATTAAAATAATTATAATTTTATT
* *
58043 ATTCAAATATTTATAA-TTTATT
1 ATTAAAATAATTATAATTTTATT
58065 ATTAAAAT
1 ATTAAAAT
58073 TATATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTAAAATAATTATAATTTTATT
Found at i:58080 original size:2 final size:2
Alignment explanation
Indices: 58073--58103 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58063 TTATTAAAAT
58073 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
58104 CACAACGATA
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:58080 original size:23 final size:23
Alignment explanation
Indices: 58031--58080 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
58021 TTAAAAAAAT
* * *
58031 TATAATTTTTTTATTCAAATATT
1 TATAATTTTATTATTAAAATATA
58054 TATAA-TTTATTATTAAAATTATA
1 TATAATTTTATTATTAAAA-TATA
58077 TATA
1 TATA
58081 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATAATTTTATTATTAAAATATA
Found at i:58420 original size:29 final size:30
Alignment explanation
Indices: 58382--58445 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
58372 TTTTTTTAAA
*
58382 TTTTATAAA-TTAACACCTAAAAATATATTT
1 TTTTATAAATTTAACACC-AAAAATAAATTT
*
58412 TTTTA-AAATTTAACACCCAAAATAAATTT
1 TTTTATAAATTTAACACCAAAAATAAATTT
58441 TTTTA
1 TTTTA
58446 CACCTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTTATAAATTTAACACCAAAAATAAATTT
Found at i:63245 original size:24 final size:25
Alignment explanation
Indices: 63210--63264 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
63200 ACTTGGAGCC
*
63210 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
63234 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
63258 TCAAGTG
1 TCAAGTG
63265 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:66354 original size:20 final size:20
Alignment explanation
Indices: 66329--66368 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
66319 TACGTTTACA
66329 TATGTTTTACAT-TCATTTAT
1 TATG-TTTACATATCATTTAT
*
66349 TATGTTTGCATATCATTTAT
1 TATGTTTACATATCATTTAT
66369 ATAACATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (20 bp):
TATGTTTACATATCATTTAT
Found at i:67944 original size:19 final size:17
Alignment explanation
Indices: 67905--67955 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
67895 TTGGAGTGCA
*
67905 AAAAGAAAGAAAAAGAC
1 AAAAGAAAGAAAAACAC
*
67922 AAAAGAAGAGAAAAATCAG
1 AAAAGAA-AGAAAAA-CAC
67941 AAAAGAAAAGAAAAA
1 AAAAG-AAAGAAAAA
67956 GGAAAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 13 0.45
20 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAAAACAC
Found at i:67969 original size:25 final size:25
Alignment explanation
Indices: 67914--67973 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
67904 AAAAAGAAAG
* *
67914 AAAAAGACAAAAGAAGAGAAAAATC
1 AAAAAGAAAAAAAAAGAGAAAAATC
*
67939 AGAAAAGAAAAGAAAAAG-GAAAATTC
1 A-AAAAGAAAA-AAAAAGAGAAAAATC
67965 AAAAAGAAA
1 AAAAAGAAA
67974 GCAAGCCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.30
26 16 0.53
27 5 0.17
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAGAGAAAAATC
Found at i:80825 original size:41 final size:42
Alignment explanation
Indices: 80780--80861 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
80770 TTCATTTCTG
80780 ATTGAAATCAGAAACAAA-TTCTCAAAATTCCTTCCTCTCGC
1 ATTGAAATCAGAAACAAATTTCTCAAAATTCCTTCCTCTCGC
80821 ATTGAAATCAGAAACAAATTTCTCAAAATTCCTTCCTCTCG
1 ATTGAAATCAGAAACAAATTTCTCAAAATTCCTTCCTCTCG
80862 TACCCTCCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 18 0.45
42 22 0.55
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (42 bp):
ATTGAAATCAGAAACAAATTTCTCAAAATTCCTTCCTCTCGC
Done.