Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001225.1 Hibiscus syriacus cultivar Beakdansim tig00002414_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: 52761
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:1824 original size:33 final size:34
Alignment explanation
Indices: 1778--1844 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
1768 AATTAAAAAC
* *
1778 TAATACATTAATCAAAAGAAAAGGGAAAAATAAA
1 TAATACATAAATCAAAAGAAAAAGGAAAAATAAA
** *
1812 TAAT-CATAAATCAATGGAAAAATGAAAAATAAA
1 TAATACATAAATCAAAAGAAAAAGGAAAAATAAA
1845 ATAAATAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.64, C:0.06, G:0.10, T:0.19
Consensus pattern (34 bp):
TAATACATAAATCAAAAGAAAAAGGAAAAATAAA
Found at i:2559 original size:21 final size:21
Alignment explanation
Indices: 2535--2583 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2525 TTTTTATGTG
2535 GTGTTCGTTTGGTTTTGGTTT
1 GTGTTCGTTTGGTTTTGGTTT
** *
2556 GTGTTTTTTTTGTTTTGGTTT
1 GTGTTCGTTTGGTTTTGGTTT
*
2577 GTATTCG
1 GTGTTCG
2584 GGTTTTGATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.04, G:0.29, T:0.65
Consensus pattern (21 bp):
GTGTTCGTTTGGTTTTGGTTT
Found at i:3038 original size:14 final size:14
Alignment explanation
Indices: 3015--3045 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3005 AAAACGAAGG
*
3015 AAAATTAATAAATA
1 AAAATAAATAAATA
3029 AAAATAAATAAATA
1 AAAATAAATAAATA
3043 AAA
1 AAA
3046 GGAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:3136 original size:34 final size:36
Alignment explanation
Indices: 3093--3161 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
3083 TGAAAAATGT
3093 TTTTTAAAA-T-CATATAATATATATTTTCAAAAAA
1 TTTTTAAAATTACATATAATATATATTTTCAAAAAA
* *
3127 TTTTTAAAATTACATATTATATATATTTTCTAAAA
1 TTTTTAAAATTACATATAATATATATTTTCAAAAA
3162 TGTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 9 0.29
35 1 0.03
36 21 0.68
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (36 bp):
TTTTTAAAATTACATATAATATATATTTTCAAAAAA
Found at i:3245 original size:39 final size:38
Alignment explanation
Indices: 3085--3263 Score: 145
Period size: 37 Copynumber: 4.8 Consensus size: 38
3075 ATACGATTTG
** *
3085 AAAAATGTTTTTTAAAATC-ATATAATATAT-ATTTTC
1 AAAAATGTTTTAAAAAAACTATATAATATATAATTTTC
** *
3121 AAAAAAT-TTTTAAAATTAC-ATATTATATAT-ATTTTC
1 -AAAAATGTTTTAAAAAAACTATATAATATATAATTTTC
* *** * *
3157 TAAAATGTTTTTTTTAAAACTATAT-TTATATAGTTTTC
1 AAAAATG-TTTTAAAAAAACTATATAATATATAATTTTC
*** *
3195 AATTTTTTTTTAAAAAAACTATATAATATATAATGTTTC
1 AAAAATGTTTTAAAAAAACTATATAATATATAAT-TTTC
3234 AAAAATGTTTTAAAAAAACTATATAATATA
1 AAAAATGTTTTAAAAAAACTATATAATATA
3264 AATGTTTTCA
Statistics
Matches: 108, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
35 5 0.05
36 23 0.21
37 32 0.30
38 18 0.17
39 30 0.28
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
AAAAATGTTTTAAAAAAACTATATAATATATAATTTTC
Found at i:3385 original size:38 final size:40
Alignment explanation
Indices: 3343--3427 Score: 106
Period size: 38 Copynumber: 2.2 Consensus size: 40
3333 AAAAAAACTT
3343 TATATATAAGTTTC-AAAATGGTTTT-AAAAACTATATA-A
1 TATATATAAGTTTCTAAAAT-GTTTTCAAAAACTATATATA
* * *
3381 TATATAT-ATTTTCTAAAATGTTTTCCAAAATTATATATA
1 TATATATAAGTTTCTAAAATGTTTTCAAAAACTATATATA
3420 TATATATA
1 TATATATA
3428 TATATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 10 0.25
38 22 0.55
39 8 0.20
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (40 bp):
TATATATAAGTTTCTAAAATGTTTTCAAAAACTATATATA
Found at i:3419 original size:2 final size:2
Alignment explanation
Indices: 3412--3440 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3402 TTTCCAAAAT
3412 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3441 GTTTCCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3421 original size:37 final size:36
Alignment explanation
Indices: 3299--3426 Score: 115
Period size: 37 Copynumber: 3.6 Consensus size: 36
3289 TTTTTTAAAA
* **
3299 AAAAACTATATATATAAAT-TTTTCAAAAT-GTTGCAA
1 AAAAACTATATATATATATATTTTCAAAATGGTT--TT
*
3335 AAAAACT-T-TATATATA-AGTTTCAAAATGGTTTT
1 AAAAACTATATATATATATATTTTCAAAATGGTTTT
3368 AAAAACTATATAATATATATATTTTCTAAAAT-GTTTT
1 AAAAACTATAT-ATATATATATTTTC-AAAATGGTTTT
* *
3405 CCAAAATTATATATATATATAT
1 -AAAAACTATATATATATATAT
3427 ATATATATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
33 7 0.09
34 17 0.22
35 5 0.06
36 14 0.18
37 20 0.26
38 14 0.18
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (36 bp):
AAAAACTATATATATATATATTTTCAAAATGGTTTT
Found at i:8932 original size:2 final size:2
Alignment explanation
Indices: 8925--8978 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
8915 AAGTAGTAAC
8925 TA TA TA TA TA TA TA TA TA TA TA TA 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
8967 TA TA TA TA TA TA
1 TA TA TA TA TA TA
8979 CACACAGATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23056 original size:80 final size:79
Alignment explanation
Indices: 22933--23147 Score: 266
Period size: 73 Copynumber: 2.8 Consensus size: 79
22923 ACTTTTAGTG
* * * * *
22933 CTTATTAAAGAAAT--GGGGCCACATTTTATAATTAAATGGTAAGAAAAATGGTACAATAACGTT
1 CTTATTAAATAAATGGGGGGCC-TATTTTATAATTGAATTGTAAGAAAAATTGTACAAT-ACGTT
*
22996 CATGTCTGCCGTAGCA
64 CATGTCTGCCATAGCA
23012 CTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAG--AAATTGTAC----CGTTCA
1 CTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAGAAAAATTGTACAATACGTTCA
**
23071 TGTCTGCCATAGTG
66 TGTCTGCCATAGCA
*
23085 CTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGAAAAATTGTACAATCACGT
1 CTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAGAAAAATTGTACAAT-ACGT
23148 GAATGCAATT
Statistics
Matches: 118, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
73 60 0.51
75 9 0.08
78 8 0.07
79 13 0.11
80 22 0.19
81 6 0.05
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (79 bp):
CTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAGAAAAATTGTACAATACGTTCA
TGTCTGCCATAGCA
Found at i:39725 original size:29 final size:29
Alignment explanation
Indices: 39688--39886 Score: 192
Period size: 29 Copynumber: 7.0 Consensus size: 29
39678 CCTTTGACCG
*
39688 GGTGATATTTTAGTAATTATTTTGAAATT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
39717 GGTGGTATTTTGGTAATTATTTTAAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* *
39746 GGTGCTATTTTTGTAATT-TTTT-AAAA-
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
39772 GAGTGATAATTTCGTAATT-TTTT-AAAGAA
1 G-GTGATATTTTAGTAATTATTTTGAAA-AT
* *
39801 AGTGTTATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
**
39830 GGTTTTATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * * *
39859 GGTGCTATTTTTGTAATTTTTTTAAAAA
1 GGTGATATTTTAGTAATTATTTTGAAAA
39887 AGTGTTAATT
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 25 0.17
28 19 0.13
29 96 0.67
30 3 0.02
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.51
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTATTTTGAAAAT
Found at i:46997 original size:7 final size:7
Alignment explanation
Indices: 46987--47031 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
46977 ATTGACCGAC
46987 CCGTTGA
1 CCGTTGA
46994 CCGTTGA
1 CCGTTGA
**
47001 CC-CCGA
1 CCGTTGA
47007 CCCGTTGA
1 -CCGTTGA
47015 CCGTTGA
1 CCGTTGA
47022 CCGTTGA
1 CCGTTGA
47029 CCG
1 CCG
47032 GGTGATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.13, C:0.38, G:0.27, T:0.22
Consensus pattern (7 bp):
CCGTTGA
Found at i:47006 original size:21 final size:21
Alignment explanation
Indices: 46982--47023 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
46972 CGACCATTGA
46982 CCGACCCGTTGACCGTTGACC
1 CCGACCCGTTGACCGTTGACC
47003 CCGACCCGTTGACCGTTGACC
1 CCGACCCGTTGACCGTTGACC
47024 GTTGACCGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.24, T:0.19
Consensus pattern (21 bp):
CCGACCCGTTGACCGTTGACC
Found at i:47069 original size:29 final size:29
Alignment explanation
Indices: 47032--47178 Score: 133
Period size: 29 Copynumber: 5.1 Consensus size: 29
47022 CCGTTGACCG
* *
47032 GGTGATATTTTATTAATTATTTTGAAATT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* *
47061 GGTGGTATTTTGGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
47090 GGTGCTATTTT-GTAATT-TTTTAAAAAA
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
47117 GAGTGATGA-TTTCGTAATTTTTTTAATGAAAT
1 G-GTGAT-ATTTTAGTAATTATTTTGA--AAAT
47149 --TGATATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
47176 GGT
1 GGT
47179 CTATTTTCGA
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
27 13 0.13
28 14 0.14
29 61 0.63
30 6 0.06
32 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTATTTTGAAAAT
Found at i:47187 original size:57 final size:55
Alignment explanation
Indices: 47033--47201 Score: 139
Period size: 57 Copynumber: 3.0 Consensus size: 55
47023 CGTTGACCGG
* * * * *
47033 GTGATATTTTATTAATTATTTTGAAATTGGTGGTATTTTGGTAATTATTTTGAAAAT
1 GTGATATTTTAGTAATTATTTTGAAAATGGT--TATTTTCGTAATTTTTTTAAAAAT
* * * *
47090 GGTGCTATTTT-GTAATT-TTTTAAAAAAGAGTGATGATTTCGTAATTTTTTTAATGAAAT
1 -GTGATATTTTAGTAATTATTTTGAAAATG-GTTAT--TTTCGTAATTTTTTTAA--AAAT
*
47149 -TGATATTTTAGTAATTATTTTGAAAATGGTCTATTTTCG-ATTTTTTTTAAAAA
1 GTGATATTTTAGTAATTATTTTGAAAATGGT-TATTTTCGTAATTTTTTTAAAAA
47202 GGTGTTAATT
Statistics
Matches: 89, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
54 3 0.03
55 2 0.02
56 18 0.20
57 34 0.38
58 17 0.19
59 15 0.17
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.51
Consensus pattern (55 bp):
GTGATATTTTAGTAATTATTTTGAAAATGGTTATTTTCGTAATTTTTTTAAAAAT
Done.