Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000593.1 Hibiscus syriacus cultivar Beakdansim tig00001149_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: 86578
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3568 original size:17 final size:17
Alignment explanation
Indices: 3543--3584 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3533 CAACCAATCA
* *
3543 TCAACATCTTACCTTGG
1 TCAATATCTTACCTAGG
3560 TCAATATCTTACCTAGG
1 TCAATATCTTACCTAGG
3577 TCAATATC
1 TCAATATC
3585 CTAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (17 bp):
TCAATATCTTACCTAGG
Found at i:13365 original size:6 final size:6
Alignment explanation
Indices: 13336--13380 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
13326 AATTTGTTAG
* * *
13336 TTAATT ATTAATT ATAGTT ATAATT TTAATT TTAATT TTAATT TT
1 TTAATT -TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TT
13381 TTTCATCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (6 bp):
TTAATT
Found at i:23366 original size:18 final size:19
Alignment explanation
Indices: 23345--23386 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
23335 GTAACTTGTG
23345 TTGTGTTC-TGTCTTAGAA
1 TTGTGTTCGTGTCTTAGAA
*
23363 TTGTG-TCGTGTCTTATAA
1 TTGTGTTCGTGTCTTAGAA
23381 TTGTGT
1 TTGTGT
23387 ATTAAATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (19 bp):
TTGTGTTCGTGTCTTAGAA
Found at i:27145 original size:2 final size:2
Alignment explanation
Indices: 27140--27167 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27130 AACAGTTTTG
27140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27168 GAGATGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29815 original size:3 final size:3
Alignment explanation
Indices: 29807--29857 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
29797 TTTTTATTTG
29807 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29855 TAT
1 TAT
29858 CAAATATTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:35774 original size:21 final size:21
Alignment explanation
Indices: 35748--35800 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
35738 GTTTCCATAT
*
35748 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCAACTA
*
35769 TCGCAACGCGAACTTCAACTA
1 TCGCAACGCGAACATCAACTA
*
35790 TCGCAATGCGA
1 TCGCAACGCGA
35801 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:35872 original size:44 final size:40
Alignment explanation
Indices: 35796--35875 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 40
35786 ACTATCGCAA
*
35796 TGCGATTTTCCAAATTCGTTGTGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
35836 TGCGATTTATTCCAAATTCGAGTTGCGATAGTCCAAGTTC
1 TGCGA-TT-TTCCAAATTC--GTTGCGATAGTCCAAGTTC
35876 ATTGAGATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 5 0.14
41 2 0.06
42 10 0.29
44 18 0.51
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:35895 original size:63 final size:62
Alignment explanation
Indices: 35804--36058 Score: 236
Period size: 63 Copynumber: 4.1 Consensus size: 62
35794 AATGCGATTT
* *
35804 TCCAAATTCGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGAGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC-AGTTGCGATAG
* * * *
35867 TCCAAGTTCATTGAGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCA-TTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCAGTTGCGATAG
** * * *
35928 TAGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGT-CAAAGTTCGCGTTGCGA
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAA-TTC-AGTTGCGA
*
35988 TTTAT
60 --TAG
* * * *
35993 TCCAAGTTCGTTGCGATAATCGAAGTTCGCGTTGCGATTTATTCCAAGTT-TGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCAGTTGCGATAG
36054 TCCAA
1 TCCAA
36059 AATCGCAACG
Statistics
Matches: 155, Mismatches: 23, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
60 3 0.02
61 37 0.24
62 1 0.01
63 89 0.57
65 22 0.14
66 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (62 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCAGTTGCGATAG
Found at i:35919 original size:42 final size:42
Alignment explanation
Indices: 35867--36055 Score: 306
Period size: 42 Copynumber: 4.5 Consensus size: 42
35857 GTTGCGATAG
*
35867 TCCAAGTTCATTGAGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
35909 TCCAAGTTCATTGCGATAGTAGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
35951 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
35993 TCCAAGTTCGTTGCGATAATCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
**
36035 TCCAAGTTTGTTGCGATAGTC
1 TCCAAGTTCATTGCGATAGTC
36056 CAAAATCGCA
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 138 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:36971 original size:21 final size:20
Alignment explanation
Indices: 36945--37016 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
36935 ATTTTGGACT
36945 ATCGCAACGAACTTGAAATAA
1 ATCGCAACGAACTTG-AATAA
* *
36966 ATCGCAACGCGAACCTCGACT--
1 ATCGCAA--CGAA-CTTGAATAA
*
36987 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTT-GAATAA
37008 ATCGCAACG
1 ATCGCAACG
37017 CGAACTTCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 1 0.03
19 7 0.17
21 23 0.57
23 6 0.15
24 3 0.08
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAACTTGAATAA
Found at i:37007 original size:42 final size:42
Alignment explanation
Indices: 36941--37035 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
36931 TGCAATTTTG
36941 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACCTC
1 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACCTC
* * *
36983 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACCTC
37025 GACTATCGCAA
1 GACTATCGCAA
37036 ATCAGTTTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACCTC
Found at i:37032 original size:21 final size:21
Alignment explanation
Indices: 36966--37035 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
36956 CTTGAAATAA
*
36966 ATCGCAACGCGAACCTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
36987 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
37006 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
37029 ATCGCAA
1 ATCGCAA
37036 ATCAGTTTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.21
21 21 0.55
23 9 0.24
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:38573 original size:22 final size:22
Alignment explanation
Indices: 38547--38591 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
38537 GTGAGTAAAC
*
38547 TTATATAAAAT-TTATAAAAATT
1 TTATAGAAAATATT-TAAAAATT
*
38569 TTATAGAAAGTATTTAAAAATT
1 TTATAGAAAATATTTAAAAATT
38591 T
1 T
38592 GTTAGATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TTATAGAAAATATTTAAAAATT
Found at i:38769 original size:32 final size:32
Alignment explanation
Indices: 38732--38792 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
38722 CAACACCCTC
* * *
38732 AAGACGCCGGGAGATTCCAAACAAGACGCTTG
1 AAGACGCCGGAACATCCCAAACAAGACGCTTG
*
38764 AAGACGCCGGAACATCCCAAGCAAGACGC
1 AAGACGCCGGAACATCCCAAACAAGACGC
38793 CAAAAAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.26, T:0.08
Consensus pattern (32 bp):
AAGACGCCGGAACATCCCAAACAAGACGCTTG
Found at i:39151 original size:3 final size:3
Alignment explanation
Indices: 39143--39168 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39133 AATACAAGTC
39143 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
39169 CATTTTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:40735 original size:35 final size:35
Alignment explanation
Indices: 40682--40752 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
40672 CCCAATTAAA
* * *
40682 ACATGAAAAGAATAGAAATTTAATTGAAGTTTATT
1 ACATGAAAAGAATAGAAATGTAATTAAAGTTAATT
* * *
40717 ACATGAAAATACTGGAAATGTAATTAAAGTTAATT
1 ACATGAAAAGAATAGAAATGTAATTAAAGTTAATT
40752 A
1 A
40753 AATTAAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.32
Consensus pattern (35 bp):
ACATGAAAAGAATAGAAATGTAATTAAAGTTAATT
Found at i:43870 original size:19 final size:20
Alignment explanation
Indices: 43848--43885 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43838 ATCTAACAAA
*
43848 CTAACAAA-TTAATAACTGC
1 CTAACAAACTAAATAACTGC
43867 CTAACAAACTAAATAACTG
1 CTAACAAACTAAATAACTG
43886 AAATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
CTAACAAACTAAATAACTGC
Found at i:49474 original size:2 final size:2
Alignment explanation
Indices: 49469--49516 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
49459 ATTTCAATTC
49469 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
49511 CT CT CT
1 CT CT CT
49517 TTGTTCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:64011 original size:22 final size:22
Alignment explanation
Indices: 63983--64027 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
63973 TGCTATACGG
63983 TTATATCCACTTTGTTCTCCAA
1 TTATATCCACTTTGTTCTCCAA
64005 TTATATCCACTTTGTTCTCCAA
1 TTATATCCACTTTGTTCTCCAA
64027 T
1 T
64028 CATAGAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47
Consensus pattern (22 bp):
TTATATCCACTTTGTTCTCCAA
Found at i:82495 original size:17 final size:17
Alignment explanation
Indices: 82447--82496 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
82437 TTTTTCTAAT
82447 TTAATT-AATTTTAAAA
1 TTAATTAAATTTTAAAA
* * *
82463 CTCATTAAGTTTTAAAA
1 TTAATTAAATTTTAAAA
*
82480 TTAATTAAATTATAAAA
1 TTAATTAAATTTTAAAA
82497 AAAACTTAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAATTAAATTTTAAAA
Found at i:83186 original size:17 final size:15
Alignment explanation
Indices: 83156--83192 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
83146 AACTTTAACC
83156 TTAAACCTATTAATT
1 TTAAACCTATTAATT
83171 TTAAAGCCTAATTAATT
1 TTAAA-CCT-ATTAATT
83188 TTAAA
1 TTAAA
83193 TAAAAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 3 0.15
17 12 0.60
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (15 bp):
TTAAACCTATTAATT
Done.