Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003845.1 Hibiscus syriacus cultivar Beakdansim tig00008247_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: 81063
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3823 original size:54 final size:55
Alignment explanation
Indices: 3741--3848 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 55
3731 TTACGCCAGG
*
3741 CATGTCGGACTTCTACAACCCAACCTTCCTCCAGGATA-TTATGCAATCTTTAAT
1 CATGTCAGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTTTAAT
* * *
3795 CATGTCAGACTTTTACATCCCAACCTTCCTCCAGGATATTTATGCAGTCTTTAA
1 CATGTCAGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTTTAA
3849 CCAGCTCAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 35 0.71
55 14 0.29
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (55 bp):
CATGTCAGACTTCTACAACCCAACCTTCCTCCAGGATATTTATGCAATCTTTAAT
Found at i:9667 original size:15 final size:15
Alignment explanation
Indices: 9649--9691 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9639 TTTTAAGAAA
9649 TTATTAT-TTATGATT
1 TTATTATATTAT-ATT
*
9664 TTATTTTATTATATT
1 TTATTATATTATATT
*
9679 TTATAATATTATA
1 TTATTATATTATA
9692 ACGTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATTATATTATATT
Found at i:10545 original size:18 final size:19
Alignment explanation
Indices: 10496--10547 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
10486 TAGTTTGAAG
*
10496 ATTAATAAATTAAAAATAGT
1 ATTAA-AAATTATAAATAGT
* * *
10516 ATTATAATTTATATATA-T
1 ATTAAAAATTATAAATAGT
10534 ATTAAAAATTATAA
1 ATTAAAAATTATAA
10548 TTAATATTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
18 12 0.48
19 9 0.36
20 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAAAATTATAAATAGT
Found at i:11491 original size:17 final size:17
Alignment explanation
Indices: 11469--11508 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
11459 CCGTGTCCCG
11469 ACCCGGATGTTACGGGT
1 ACCCGGATGTTACGGGT
* *
11486 ACCCGGATTTTGCGGGT
1 ACCCGGATGTTACGGGT
11503 ACCCGG
1 ACCCGG
11509 TAATCGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.23
Consensus pattern (17 bp):
ACCCGGATGTTACGGGT
Found at i:29424 original size:45 final size:45
Alignment explanation
Indices: 29373--29461 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
29363 CTTTTTGGAG
* *
29373 GGTAAGGTCTCCATCCTATATATCGTTTTAAGTTCCTCTTCAGAA
1 GGTAAGGTCCCCATCATATATATCGTTTTAAGTTCCTCTTCAGAA
* * * *
29418 GGTAAGGTCCCCATCATGTTTATCTTTTTGAGTTCCTCTTCAGA
1 GGTAAGGTCCCCATCATATATATCGTTTTAAGTTCCTCTTCAGA
29462 GGGCAAGATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.39
Consensus pattern (45 bp):
GGTAAGGTCCCCATCATATATATCGTTTTAAGTTCCTCTTCAGAA
Found at i:31958 original size:16 final size:16
Alignment explanation
Indices: 31937--31967 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31927 TCTAGTTTTT
31937 CCGAGTACCCAGTTAC
1 CCGAGTACCCAGTTAC
*
31953 CCGAGTACCCGGTTA
1 CCGAGTACCCAGTTA
31968 GTTTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (16 bp):
CCGAGTACCCAGTTAC
Found at i:32253 original size:15 final size:16
Alignment explanation
Indices: 32233--32271 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
32223 CGGAAGTTCT
32233 GGGTACCCGAAAA-TC
1 GGGTACCCGAAAATTC
*
32248 GGGTA-CCAAAAATTC
1 GGGTACCCGAAAATTC
32263 GGGTACCCG
1 GGGTACCCG
32272 GATTTGCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.30
15 12 0.60
16 2 0.10
ACGTcount: A:0.31, C:0.26, G:0.28, T:0.15
Consensus pattern (16 bp):
GGGTACCCGAAAATTC
Found at i:38232 original size:24 final size:24
Alignment explanation
Indices: 38205--38271 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
38195 GGGTACGAAG
* *
38205 GGAGGAAGGAGAGGAGGAAAGGGC
1 GGAGGAAAGAGAGGAGGAAAGGGA
* * *
38229 GGAGGAAATAGCGGCGGAAAGGGA
1 GGAGGAAAGAGAGGAGGAAAGGGA
* *
38253 AGATGAAAGAGAGGAGGAA
1 GGAGGAAAGAGAGGAGGAA
38272 GACACAGAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.04, G:0.51, T:0.03
Consensus pattern (24 bp):
GGAGGAAAGAGAGGAGGAAAGGGA
Found at i:38638 original size:24 final size:24
Alignment explanation
Indices: 38611--38661 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
38601 TCGAGTCCGG
38611 GGATAGGGGCGGCGGAGCTGAGGA
1 GGATAGGGGCGGCGGAGCTGAGGA
* * *
38635 GGATTGTGGTGGCGGAGCTGAGGA
1 GGATAGGGGCGGCGGAGCTGAGGA
38659 GGA
1 GGA
38662 AGAGGAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.57, T:0.14
Consensus pattern (24 bp):
GGATAGGGGCGGCGGAGCTGAGGA
Found at i:42797 original size:18 final size:16
Alignment explanation
Indices: 42738--42802 Score: 55
Period size: 18 Copynumber: 4.0 Consensus size: 16
42728 TAATTGACAC
*
42738 TTATAATTT-TTCTAAT
1 TTATAATTTATT-TTAT
42754 TTAT--TTTATTTTAT
1 TTATAATTTATTTTAT
*
42768 TTATAATATTATATTAT
1 TTATAAT-TTATTTTAT
42785 ATTATATATTTATTTTAT
1 -TTATA-ATTTATTTTAT
42803 CTAAGAATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
15 2 0.05
16 5 0.12
17 8 0.20
18 13 0.32
19 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATAATTTATTTTAT
Found at i:46073 original size:22 final size:22
Alignment explanation
Indices: 46032--46112 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
46022 CTCGTATAAA
46032 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
46055 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46077 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
46099 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
46113 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:46108 original size:13 final size:13
Alignment explanation
Indices: 46046--46108 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
46036 CCGAAGTGCC
46046 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
46059 CC---GAAGTGC-
1 CCGTAGAATTGCA
46068 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
46081 CC---GAAGTGC-
1 CCGTAGAATTGCA
46090 CCGTAGAATTGCA
1 CCGTAGAATTGCA
46103 CCGTAG
1 CCGTAG
46109 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:47664 original size:21 final size:21
Alignment explanation
Indices: 47640--47684 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47630 TCTTGTTCGT
* *
47640 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
47661 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
47682 TTG
1 TTG
47685 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:50895 original size:22 final size:22
Alignment explanation
Indices: 50854--50934 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
50844 CTCGTATAAA
50854 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
50877 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
50899 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
50921 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
50935 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:50930 original size:13 final size:13
Alignment explanation
Indices: 50868--50930 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
50858 CCGAAGTGCC
50868 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
50881 CC---GAAGTGC-
1 CCGTAGAATTGCA
50890 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
50903 CC---GAAGTGC-
1 CCGTAGAATTGCA
50912 CCGTAGAATTGCA
1 CCGTAGAATTGCA
50925 CCGTAG
1 CCGTAG
50931 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:51590 original size:2 final size:2
Alignment explanation
Indices: 51583--51653 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
51573 TCTCTTAAAC
51583 AT AT AT 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 AT AT AT
51625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51654 CATGTTCAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52535 original size:21 final size:21
Alignment explanation
Indices: 52511--52555 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52501 TCTTGTTCGT
* *
52511 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
52532 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
52553 TTG
1 TTG
52556 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:53755 original size:19 final size:19
Alignment explanation
Indices: 53731--53778 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
53721 ACACAGACAT
*
53731 AAACACTTAATCTTTAACA
1 AAACACCTAATCTTTAACA
53750 AAACACCTAATCTTTAACA
1 AAACACCTAATCTTTAACA
53769 AAACACCTAA
1 AAACACCTAA
53779 AGTGCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (19 bp):
AAACACCTAATCTTTAACA
Found at i:61793 original size:27 final size:25
Alignment explanation
Indices: 61755--61837 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 25
61745 GAACGACCGG
*
61755 TTTTTTTACCGGATTAAAAA-TCGGT
1 TTTTTTTACCGGATAAAAAACT-GGT
61780 TTTTTTTAAACCGGATAAAAAACTGGT
1 TTTTTTT--ACCGGATAAAAAACTGGT
* * * *
61807 TTTTTAT-CCGAAAAAAAAATTTGGT
1 TTTTTTTACCGGATAAAAAA-CTGGT
61832 TTTTTT
1 TTTTTT
61838 AAAAAAACCG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 10 0.21
25 16 0.33
27 21 0.44
28 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.45
Consensus pattern (25 bp):
TTTTTTTACCGGATAAAAAACTGGT
Found at i:61798 original size:26 final size:26
Alignment explanation
Indices: 61755--61811 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
61745 GAACGACCGG
*
61755 TTTTTTTACCGGATTAAAAATC-GGT
1 TTTTTTTACCGGATTAAAAAACTGGT
61780 TTTTTTTAAACCGGA-TAAAAAACTGGT
1 TTTTTTT--ACCGGATTAAAAAACTGGT
61807 TTTTT
1 TTTTT
61812 ATCCGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.25
26 7 0.25
27 14 0.50
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (26 bp):
TTTTTTTACCGGATTAAAAAACTGGT
Found at i:70174 original size:21 final size:21
Alignment explanation
Indices: 70148--70187 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
70138 CAGAACCCCA
*
70148 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
70169 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
70188 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Done.