Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002835.1 Hibiscus syriacus cultivar Beakdansim tig00005833_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: 62311
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:1056 original size:13 final size:13
Alignment explanation
Indices: 1031--1082 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
1021 AATGACGCGC
*
1031 AATGCGCGACATA
1 AATGCGCGTCATA
*
1044 AATGCACGTCATA
1 AATGCGCGTCATA
* * *
1057 AATACGTGTTATA
1 AATGCGCGTCATA
1070 AATGCGCGTCATA
1 AATGCGCGTCATA
1083 GATTTATGAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:5307 original size:4 final size:4
Alignment explanation
Indices: 5298--5332 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5288 CAACTTTTTC
5298 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
5333 AGGGTGTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:20246 original size:35 final size:35
Alignment explanation
Indices: 20205--20299 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
20195 AGAAACTCAA
20205 CATAATTGTATACATAACAAAAACCCTAACAAACT
1 CATAATTGTATACATAACAAAAACCCTAACAAACT
20240 CATAATTGTATTA-ATAA-AATAAACCCTAACAAACT
1 CATAATTGTA-TACATAACAA-AAACCCTAACAAACT
** *
20275 CATAATTACATGCATAACAGAAAAC
1 CATAATTGTATACATAACA-AAAAC
20300 TCTAGCAGTC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
34 3 0.06
35 41 0.79
36 7 0.13
37 1 0.02
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (35 bp):
CATAATTGTATACATAACAAAAACCCTAACAAACT
Found at i:28139 original size:20 final size:20
Alignment explanation
Indices: 28114--28174 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
28104 TTTTGGTGCA
*
28114 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
28134 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
28155 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
28175 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:28183 original size:21 final size:21
Alignment explanation
Indices: 28157--28196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28147 CCCCCTTTGA
*
28157 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
28178 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
28197 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:29839 original size:12 final size:12
Alignment explanation
Indices: 29822--29847 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29812 AGATGAGCTT
29822 GAACAGCCCGAG
1 GAACAGCCCGAG
29834 GAACAGCCCGAG
1 GAACAGCCCGAG
29846 GA
1 GA
29848 GCAAGCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (12 bp):
GAACAGCCCGAG
Found at i:30834 original size:21 final size:21
Alignment explanation
Indices: 30810--30850 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30800 CAGATTGCTC
30810 AGAGGGAACCGATTCCCCCTA
1 AGAGGGAACCGATTCCCCCTA
*
30831 AGAGGGTACCGATTCCCCCT
1 AGAGGGAACCGATTCCCCCT
30851 GAATGGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.17
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCTA
Found at i:30930 original size:19 final size:20
Alignment explanation
Indices: 30900--30944 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
30890 AACCAATTCC
*
30900 CCCCCCAGGGGGTATCGATT
1 CCCCCCAGGGGGTACCGATT
30920 CCCCCCAGGGGGTACCGATT
1 CCCCCCAGGGGGTACCGATT
30940 CCCCC
1 CCCCC
30945 TGTTTAACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.44, G:0.27, T:0.16
Consensus pattern (20 bp):
CCCCCCAGGGGGTACCGATT
Found at i:33948 original size:2 final size:2
Alignment explanation
Indices: 33898--33933 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33888 TTTATATCAA
33898 AT AT AT AT 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 AT AT AT AT
33934 TAACTCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34752 original size:3 final size:3
Alignment explanation
Indices: 34744--34774 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34734 ATGGATCTTT
34744 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34775 GTCATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:36774 original size:25 final size:25
Alignment explanation
Indices: 36742--36815 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
36732 TGCCACATAG
*
36742 ATTTGTCCCAAAGGACCACGTAGAA
1 ATTTGTCCCGAAGGACCACGTAGAA
*
36767 ATTTGTCCCGATGGACCACGTAG-A
1 ATTTGTCCCGAAGGACCACGTAGAA
** *
36791 ATTTGTCATGAAGGACCGCGTAGAA
1 ATTTGTCCCGAAGGACCACGTAGAA
36816 CCCTCGACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 20 0.48
25 22 0.52
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (25 bp):
ATTTGTCCCGAAGGACCACGTAGAA
Found at i:36806 original size:24 final size:24
Alignment explanation
Indices: 36694--36815 Score: 92
Period size: 24 Copynumber: 5.1 Consensus size: 24
36684 CTGCTCATAT
36694 AATTTG-CACTGAAGTG-CCACGTAG
1 AATTTGTCAC-GAAG-GACCACGTAG
* *
36718 AATATG-CACCGAAGTG-CCACATAG
1 AATTTGTCA-CGAAG-GACCACGTAG
* *
36742 -ATTTGTCCCAAAGGACCACGTAG
1 AATTTGTCACGAAGGACCACGTAG
* *
36765 AAATTTGTCCCGATGGACCACGTAG
1 -AATTTGTCACGAAGGACCACGTAG
* *
36790 AATTTGTCATGAAGGACCGCGTAG
1 AATTTGTCACGAAGGACCACGTAG
36814 AA
1 AA
36816 CCCTCGACTT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
22 1 0.01
23 15 0.19
24 43 0.53
25 22 0.27
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (24 bp):
AATTTGTCACGAAGGACCACGTAG
Found at i:36960 original size:14 final size:15
Alignment explanation
Indices: 36941--36979 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
36931 ATCACTTAGC
*
36941 ACATTTTCATATA-G
1 ACATTTTCACATAGG
36955 ACATTTTCACATAGG
1 ACATTTTCACATAGG
*
36970 ATATTTTCAC
1 ACATTTTCAC
36980 TTATAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (15 bp):
ACATTTTCACATAGG
Found at i:43097 original size:25 final size:25
Alignment explanation
Indices: 43067--43140 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
43057 TGCCACATAT
43067 ATTTGTTCCGAAGGACCGCGTAGAA
1 ATTTGTTCCGAAGGACCGCGTAGAA
* * *
43092 ATTTGTCCCAAAGGACCACGTAG-A
1 ATTTGTTCCGAAGGACCGCGTAGAA
*
43116 ATTTG-TCTCGAAGTACCGCGTAGAA
1 ATTTGTTC-CGAAGGACCGCGTAGAA
43141 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.03
24 18 0.45
25 21 0.52
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (25 bp):
ATTTGTTCCGAAGGACCGCGTAGAA
Found at i:43137 original size:24 final size:24
Alignment explanation
Indices: 43067--43140 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
43057 TGCCACATAT
43067 ATTTGT-TCCGAAGGACCGCGTAGAA
1 ATTTGTCT-CGAAGGACCGCGTAG-A
* * *
43092 ATTTGTCCCAAAGGACCACGTAGA
1 ATTTGTCTCGAAGGACCGCGTAGA
*
43116 ATTTGTCTCGAAGTACCGCGTAGA
1 ATTTGTCTCGAAGGACCGCGTAGA
43140 A
1 A
43141 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 22 0.54
25 19 0.46
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (24 bp):
ATTTGTCTCGAAGGACCGCGTAGA
Found at i:43266 original size:14 final size:15
Alignment explanation
Indices: 43244--43281 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
43234 ATCACTTAGC
*
43244 ACATATTCACATA-G
1 ACATTTTCACATAGG
43258 ACATTTTCACATAGG
1 ACATTTTCACATAGG
*
43273 ATATTTTCA
1 ACATTTTCA
43282 TTTATAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAGG
Found at i:47564 original size:20 final size:19
Alignment explanation
Indices: 47539--47577 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
47529 ATCAGTCATG
47539 GGGTATCGATACCAACAGGT
1 GGGTATCGATACCAA-AGGT
47559 GGGTATCGATACCAAAGGT
1 GGGTATCGATACCAAAGGT
47578 TATGTACCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.21
Consensus pattern (19 bp):
GGGTATCGATACCAAAGGT
Found at i:58162 original size:22 final size:22
Alignment explanation
Indices: 58129--58170 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
58119 CTTGTAATTT
*
58129 TATTATTTTATTTTATTTTTTA
1 TATTATTTTATTTTACTTTTTA
58151 TATT-TTTATATTTTACTTTT
1 TATTATTT-TATTTTACTTTT
58171 CTATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
TATTATTTTATTTTACTTTTTA
Found at i:58180 original size:28 final size:28
Alignment explanation
Indices: 58126--58180 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
58116 ATACTTGTAA
* *
58126 TTTTATTATTTTATTTTATTTTTTATAT
1 TTTTATTATTTTATTTTATATTATATAT
*
58154 TTTTA-TATTTTACTTTTCTATTATATA
1 TTTTATTATTTTA-TTTTATATTATATA
58181 ACTTGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTATTATTTTATTTTATATTATATAT
Found at i:60905 original size:31 final size:31
Alignment explanation
Indices: 60867--60930 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
60857 AATATATAAT
* *
60867 ATGTGATCATTTTCGTTTTTAGTTCATTAAG
1 ATGTGATCATGTTCGTTATTAGTTCATTAAG
* *
60898 ATGTGATCATGTTCGTTATTATTTTATTAAG
1 ATGTGATCATGTTCGTTATTAGTTCATTAAG
60929 AT
1 AT
60931 ATGGTCACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.52
Consensus pattern (31 bp):
ATGTGATCATGTTCGTTATTAGTTCATTAAG
Done.