Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000476.1 Hibiscus syriacus cultivar Beakdansim tig00000888_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: 64951
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4102 original size:13 final size:14
Alignment explanation
Indices: 4081--4110 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4071 CCACTATTTT
*
4081 AATTTTTTTAAATC
1 AATTTTTTAAAATC
4095 AATTTTTTAAAATC
1 AATTTTTTAAAATC
4109 AA
1 AA
4111 CTCATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTTTTAAAATC
Found at i:12195 original size:29 final size:29
Alignment explanation
Indices: 12152--12234 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
12142 CTCACCTAAC
12152 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
12182 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
12211 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
12235 ATTTAGCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:15618 original size:15 final size:15
Alignment explanation
Indices: 15598--15627 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15588 CTTTCTCATA
15598 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
15613 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
15628 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:16965 original size:29 final size:29
Alignment explanation
Indices: 16922--17004 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
16912 CTCACCTAAC
16922 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
16952 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
16981 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
17005 ATTTAGCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:17715 original size:18 final size:18
Alignment explanation
Indices: 17687--17748 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
17677 ATAAGATTGC
17687 ACTAA-TAGACTATGCAA
1 ACTAATTAGACTATGCAA
* *
17704 ACTAATTAGACTATGGAG
1 ACTAATTAGACTATGCAA
*
17722 A--AACT--ACTATGCAA
1 ACTAATTAGACTATGCAA
17736 ACTAATTAGACTA
1 ACTAATTAGACTA
17749 CAGAGAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
14 8 0.24
16 6 0.18
17 5 0.15
18 15 0.44
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (18 bp):
ACTAATTAGACTATGCAA
Found at i:17733 original size:32 final size:32
Alignment explanation
Indices: 17695--17759 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
17685 GCACTAATAG
**
17695 ACTATGCAAACTAATTAGACTATGGAGAAACT
1 ACTATGCAAACTAATTAGACTACAGAGAAACT
17727 ACTATGCAAACTAATTAGACTACAGAGAAACT
1 ACTATGCAAACTAATTAGACTACAGAGAAACT
17759 A
1 A
17760 ATTAGGCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (32 bp):
ACTATGCAAACTAATTAGACTACAGAGAAACT
Found at i:19426 original size:4 final size:4
Alignment explanation
Indices: 19417--19450 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
19407 TTTTTAATAG
*
19417 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
19451 TATTGGGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:24398 original size:65 final size:65
Alignment explanation
Indices: 24193--24381 Score: 308
Period size: 65 Copynumber: 2.9 Consensus size: 65
24183 GTACCAGTAT
* * *
24193 AGATCACTCATATGACTCATGTACGTTTGTGGCGCCTGAGGTGGAGTGATAATTGAATACAATAC
1 AGATCACTCATATGACTCATGTACGTTTGTAGTGCATGAGGTGGAGTGATAATTGAATACAATAC
*
24258 AGATCACTCATATGACTCATGTACGTTTGTAGTGCATGAGGTGGAGTGATAATTGAATACAATAT
1 AGATCACTCATATGACTCATGTACGTTTGTAGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* *
24323 ATATCACTCATATGACTCATGTATC-TTTGTAGTGCATGAGGTGAAGTGATAATTGAATA
1 AGATCACTCATATGACTCATGTA-CGTTTGTAGTGCATGAGGTGGAGTGATAATTGAATA
24382 TTGCACAGAC
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
65 116 0.99
66 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (65 bp):
AGATCACTCATATGACTCATGTACGTTTGTAGTGCATGAGGTGGAGTGATAATTGAATACAATAC
Found at i:29436 original size:22 final size:23
Alignment explanation
Indices: 29411--29457 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
29401 TGAATTATAC
29411 TTTTACTAATAT-AAAATTCTGA
1 TTTTACTAATATGAAAATTCTGA
* * *
29433 TTTTACTGATCTGAAATTTCTGA
1 TTTTACTAATATGAAAATTCTGA
29456 TT
1 TT
29458 GTCTGATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (23 bp):
TTTTACTAATATGAAAATTCTGA
Found at i:32821 original size:20 final size:20
Alignment explanation
Indices: 32796--32842 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
32786 CGATTAACCT
32796 GTTGACCCGTTTACTTGACC
1 GTTGACCCGTTTACTTGACC
*
32816 GTTGACTCGTTTACTTGACC
1 GTTGACCCGTTTACTTGACC
32836 GTTGACC
1 GTTGACC
32843 ATTGACTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGACCCGTTTACTTGACC
Found at i:32854 original size:20 final size:20
Alignment explanation
Indices: 32808--32850 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
32798 TGACCCGTTT
* *
32808 ACTTGACCGTTGACTCGTTT
1 ACTTGACCGTTGACTCATTG
32828 ACTTGACCGTTGAC-CATTG
1 ACTTGACCGTTGACTCATTG
32847 ACTT
1 ACTT
32851 TGACTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (20 bp):
ACTTGACCGTTGACTCATTG
Found at i:33387 original size:22 final size:23
Alignment explanation
Indices: 33357--33408 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
33347 TTTTTTGAAC
* *
33357 TCTGCTTTTACGGATATGAAA-T
1 TCTGATTTTACGGATATAAAACT
* *
33379 TCTGATTTTACTGATCTAAAACT
1 TCTGATTTTACGGATATAAAACT
33402 TCTGATT
1 TCTGATT
33409 GTCTGATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (23 bp):
TCTGATTTTACGGATATAAAACT
Found at i:35350 original size:40 final size:40
Alignment explanation
Indices: 35299--35377 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
35289 AGAGCATGTT
* * *
35299 TATGTATGTTTTTTGCATGTTTCATG-TCATCATCATCATG
1 TATGTATGTTTTGTACATGTGTCATGCT-ATCATCATCATG
*
35339 TATGTATGTTTTGTATATGTGTCATGCTATCATCATCAT
1 TATGTATGTTTTGTACATGTGTCATGCTATCATCATCAT
35378 CATTGTTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (40 bp):
TATGTATGTTTTGTACATGTGTCATGCTATCATCATCATG
Found at i:35499 original size:178 final size:169
Alignment explanation
Indices: 35231--35627 Score: 526
Period size: 178 Copynumber: 2.3 Consensus size: 169
35221 GTTATATGGT
* * *
35231 TTGCATGCATCATGCATTTACCGTCTTCAGTCGATGATGTGCTTTCTGTTAGAATGTGAGAGCAT
1 TTGCATGCATCATGCAATTACCGTCTTCA-TCGATGATATGCTTGCTGTTAGAATGTGAGAGCAT
* * * *
35296 GTTTATGTATGTTTTTTGCATGTTTCATGTCATCATCATCATGTATGTATGTTTTGTATATGTGT
65 GTATATGTAAGTTTTTTCCATGTTTCATGTCATCATCATCATGTATGTATG---T-T-TATGTAT
* *
35361 CATGCTATCATCATCATCATTGTTGTTGTTA-TTATTGTATGTTCTGCAA
125 CATGCTACCATCATCATCATTGTTGTTG--ACTTATTGT-TG-TATG-AA
* * * *
35410 TTGCATGCATCATGCAATTACCGTCTTCATAGTTGATTTGGTTGCTGTTAGAATGTGAGAGCATG
1 TTGCATGCATCATGCAATTACCGTCTTCATCGATGATATGCTTGCTGTTAGAATGTGAGAGCATG
35475 TATATGTAAGTTTTTTCCATGTTTCATGTCATCATCATCATGTATGTATGTTTATGTATCATGCT
66 TATATGTAAGTTTTTTCCATGTTTCATGTCATCATCATCATGTATGTATGTTTATGTATCATGCT
* **
35540 ACCATCATCATCATTGTTGTTGACTTCTTGTTGTATGGT
131 ACCATCATCATCATTGTTGTTGACTTATTGTTGTATGAA
* *
35579 TTGCATGCATCATGCAATTACCATCTTCATCGCTGATATGCTTGCTGTT
1 TTGCATGCATCATGCAATTACCGTCTTCATCGATGATATGCTTGCTGTT
35628 TATGCTTTTT
Statistics
Matches: 197, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
169 44 0.22
170 3 0.02
171 3 0.02
172 6 0.03
173 33 0.17
174 1 0.01
175 1 0.01
178 78 0.40
179 28 0.14
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (169 bp):
TTGCATGCATCATGCAATTACCGTCTTCATCGATGATATGCTTGCTGTTAGAATGTGAGAGCATG
TATATGTAAGTTTTTTCCATGTTTCATGTCATCATCATCATGTATGTATGTTTATGTATCATGCT
ACCATCATCATCATTGTTGTTGACTTATTGTTGTATGAA
Found at i:36087 original size:17 final size:17
Alignment explanation
Indices: 36057--36091 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
36047 AAACTTCGTT
36057 TCATTTCGAGTTTATAAA
1 TCATTTCGAGTTTA-AAA
36075 TCATTTC-AGTTTAAAA
1 TCATTTCGAGTTTAAAA
36091 T
1 T
36092 TCGAGTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (17 bp):
TCATTTCGAGTTTAAAA
Found at i:38568 original size:60 final size:60
Alignment explanation
Indices: 38499--38668 Score: 200
Period size: 60 Copynumber: 2.9 Consensus size: 60
38489 TATTTGGATG
* * * * * *
38499 AATTTGGGGATAAAATTGGAAGATGT-AAAAGTTTAGGGACTGATTTAGAATGATATTCAT
1 AATTTGGGGATAAAATTGAAAGAT-TCAAAAGTTTAAGGACTAATTTAAAATGACAGTCAT
* *
38559 AGTTTGGGGATAAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAAAATGACAGTCAT
1 AATTTGGGGATAAAATTGAAAGATTCAAAAGTTTAAGGACTAATTTAAAATGACAGTCAT
* * * * *
38619 AATTTTGAGATAAAATTAAAATATTTAAAAG-TTAAGGACTAATTTAAAAT
1 AATTTGGGGATAAAATTGAAAGATTCAAAAGTTTAAGGACTAATTTAAAAT
38669 TAGGGACATA
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
59 20 0.21
60 76 0.79
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (60 bp):
AATTTGGGGATAAAATTGAAAGATTCAAAAGTTTAAGGACTAATTTAAAATGACAGTCAT
Found at i:38665 original size:19 final size:19
Alignment explanation
Indices: 38641--38687 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
38631 AAATTAAAAT
38641 ATTTAAAAGTTAAGGAC-TA
1 ATTTAAAA-TTAAGGACATA
*
38660 ATTTAAAATTAGGGACATA
1 ATTTAAAATTAAGGACATA
38679 ATTTGAAAA
1 ATTT-AAAA
38688 CATATAGTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 14 0.56
20 4 0.16
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (19 bp):
ATTTAAAATTAAGGACATA
Found at i:40184 original size:20 final size:21
Alignment explanation
Indices: 40160--40223 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 21
40150 ACTTGAATTT
40160 AAAAAAATCAAAAAAAAATAC
1 AAAAAAATCAAAAAAAAATAC
*
40181 AAAAAAAT-ACAAAAAAATAC
1 AAAAAAATCAAAAAAAAATAC
* *
40201 -AAAAAATC-AGAAAAATTAC
1 AAAAAAATCAAAAAAAAATAC
40220 AAAA
1 AAAA
40224 CAATTAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.41
20 14 0.38
21 8 0.22
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAAAATCAAAAAAAAATAC
Found at i:40223 original size:9 final size:10
Alignment explanation
Indices: 40160--40223 Score: 78
Period size: 10 Copynumber: 6.4 Consensus size: 10
40150 ACTTGAATTT
*
40160 AAAAAAATCAA
1 AAAAAAAT-AC
40171 AAAAAAATAC
1 AAAAAAATAC
40181 AAAAAAATAC
1 AAAAAAATAC
40191 AAAAAAATAC
1 AAAAAAATAC
40201 -AAAAAAT-C
1 AAAAAAATAC
*
40209 AGAAAAATTAC
1 A-AAAAAATAC
40220 AAAA
1 AAAA
40224 CAATTAGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
8 1 0.02
9 7 0.15
10 30 0.62
11 10 0.21
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:44031 original size:21 final size:21
Alignment explanation
Indices: 43990--44031 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43980 ATTACATCAA
*
43990 AGTACTTAAAATATTAGTTTT
1 AGTACTTAAAATATTAATTTT
* *
44011 AGTACTTAAACTTTTAATTTT
1 AGTACTTAAAATATTAATTTT
44032 TTCAAAATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
AGTACTTAAAATATTAATTTT
Found at i:47292 original size:36 final size:35
Alignment explanation
Indices: 47252--47335 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
47242 TTCAAAACTT
47252 AATTAAATTTTGAAC-GGGATACTAAAATGAAACAAA
1 AATTAAATTTT-AACAGGG-TACTAAAATGAAACAAA
* * *
47288 AATTAAGCTTTTAACATGGTACTAAAATGGAACAAA
1 AATTAA-ATTTTAACAGGGTACTAAAATGAAACAAA
* *
47324 AACTAAACTTTA
1 AATTAAATTTTA
47336 GGTATGGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 4 0.10
36 30 0.75
37 6 0.15
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (35 bp):
AATTAAATTTTAACAGGGTACTAAAATGAAACAAA
Found at i:53661 original size:2 final size:2
Alignment explanation
Indices: 53654--53680 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53644 ATAATTAATA
53654 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 A
53681 CACTATTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62601 original size:64 final size:64
Alignment explanation
Indices: 62467--62624 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
62457 TTATCATTGG
* * * * * *
62467 GATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGAATTTGATGTTTCCTTATTAATGG
1 GATGCATCGATGCACT-ACTTATGCATCGATGCACGAATTGAATTCGATGTTTCATTATTAAAGA
* *
62531 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTCGATGT-TTCATTATTAAAGA
**
62594 GAGTGCATCGATGCACTACCAATGCATCGAT
1 GA-TGCATCGATGCACTACTTATGCATCGAT
62625 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.91
65 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTCGATGTTTCATTATTAAAGA
Done.