Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000201.1 Hibiscus syriacus cultivar Beakdansim tig00000360_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: 46860
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:123 original size:25 final size:23
Alignment explanation
Indices: 51--123 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
41 TAATGAAGGA
*
51 TGCATCGATGCACTA--TA-CAG
1 TGCATCGATGCACTACCTATCGG
* *
71 TGTATCGATGCATTACCTATCGG
1 TGCATCGATGCACTACCTATCGG
94 TGCATCGATGCACTACCTGCATCGG
1 TGCATCGATGCACTACCT--ATCGG
119 TGCAT
1 TGCAT
124 AAATGGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 13 0.30
22 2 0.05
23 18 0.42
25 10 0.23
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (23 bp):
TGCATCGATGCACTACCTATCGG
Found at i:178 original size:21 final size:21
Alignment explanation
Indices: 146--188 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
136 ATTTTGTTTA
146 ATTGAGAGTGCATCAATGCAC
1 ATTGAGAGTGCATCAATGCAC
*
167 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCAATGCAC
188 A
1 A
189 CAACCCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCAATGCAC
Found at i:2676 original size:16 final size:16
Alignment explanation
Indices: 2655--2690 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2645 GTAACAAATA
2655 TATCATACATATATCT
1 TATCATACATATATCT
* *
2671 TATCATTCATATCTCT
1 TATCATACATATATCT
2687 TATC
1 TATC
2691 TCATGTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (16 bp):
TATCATACATATATCT
Found at i:3181 original size:31 final size:31
Alignment explanation
Indices: 3140--3212 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
3130 GAACCTCGAC
* *
3140 AACTGTCCATAGATCCTGACGAACCTAGGTA
1 AACTGTCCATAGATCCCGAAGAACCTAGGTA
* *
3171 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGATCCCGAAGAACCTAGGTA
3202 AACTGTCCATA
1 AACTGTCCATA
3213 TGTCTCGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGATCCCGAAGAACCTAGGTA
Found at i:3231 original size:31 final size:31
Alignment explanation
Indices: 3140--3235 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
3130 GAACCTCGAC
* * * * *
3140 AACTGTCCATAGATCCTGACGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
*
3171 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
* * *
3202 AACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATAGGTCCCGAAGA-ACATAGGTA
3233 AAC
1 AAC
3236 CCTCGACTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (31 bp):
AACTATCCATAGGTCCCGAAGAACATAGGTA
Found at i:4068 original size:23 final size:22
Alignment explanation
Indices: 4041--4086 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
4031 ATTCTATATC
4041 TATATCAGAATAATACATTGATA
1 TATATCAGAATAATA-ATTGATA
* * *
4064 TATATCCGTATACTAATTGATA
1 TATATCAGAATAATAATTGATA
4086 T
1 T
4087 CTTCTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TATATCAGAATAATAATTGATA
Found at i:9211 original size:21 final size:21
Alignment explanation
Indices: 9179--9221 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9169 TGTTTGTTTA
*
9179 ATTGAGAGTGCATTGATGCAC
1 ATTGAGAGTGCATCGATGCAC
9200 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
9221 A
1 A
9222 CAACCCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:9695 original size:14 final size:14
Alignment explanation
Indices: 9676--9703 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9666 CTTGCTCACG
9676 ATGAAGAAGAAGAA
1 ATGAAGAAGAAGAA
9690 ATGAAGAAGAAGAA
1 ATGAAGAAGAAGAA
9704 TATAACTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
ATGAAGAAGAAGAA
Found at i:16267 original size:30 final size:30
Alignment explanation
Indices: 16232--16305 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
16222 TATATGATAT
16232 ATAAAATATATTTTCTAAAG-TAAAATAAGA
1 ATAAAATATATTTT-TAAAGTTAAAATAAGA
*
16262 ATAAAATATA-TTTTAAAGTTAAGATAAGA
1 ATAAAATATATTTTTAAAGTTAAAATAAGA
16291 ATAAAATATATTTTT
1 ATAAAATATATTTTT
16306 TAATGTTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 5 0.12
29 22 0.54
30 14 0.34
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (30 bp):
ATAAAATATATTTTTAAAGTTAAAATAAGA
Found at i:17994 original size:21 final size:21
Alignment explanation
Indices: 17968--18017 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
17958 TTTTATATTT
17968 TAAATTTTGTAAAAAATTATA
1 TAAATTTTGTAAAAAATTATA
17989 TAAATTTTGTAAAAAATTATA
1 TAAATTTTGTAAAAAATTATA
18010 TAAATTTT
1 TAAATTTT
18018 ATGAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAATTTTGTAAAAAATTATA
Found at i:25928 original size:72 final size:73
Alignment explanation
Indices: 25806--25968 Score: 258
Period size: 72 Copynumber: 2.2 Consensus size: 73
25796 ATAGGTACAA
* *
25806 ATAAAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATAGAAGAAAACTTAAATTTC-
1 ATAAAAAATTTCAGGGTGGGACAATCCGTAAAATAAGTAACTAATAGAAGAAAAATTAAATTTCA
25870 AGGATGGAC
66 AGG-TGGAC
*
25879 A-AAAAAATTTCAGGGTGGGACAATCCGTAAAATAAGTAACTAATCGAAGAAAAATTAAATTTCA
1 ATAAAAAATTTCAGGGTGGGACAATCCGTAAAATAAGTAACTAATAGAAGAAAAATTAAATTTCA
25943 AGGTGGAC
66 AGGTGGAC
* *
25951 ATCAAAAATTTCAAGGTG
1 ATAAAAAATTTCAGGGTG
25969 TACACCATAA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
72 65 0.78
73 18 0.22
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (73 bp):
ATAAAAAATTTCAGGGTGGGACAATCCGTAAAATAAGTAACTAATAGAAGAAAAATTAAATTTCA
AGGTGGAC
Found at i:25980 original size:21 final size:21
Alignment explanation
Indices: 25934--25980 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
25924 GAAGAAAAAT
*
25934 TAAATTTCAAGGTGGACATCA
1 TAAATTTCAAGGTGGACACCA
* *
25955 AAAATTTCAAGGTGTACACCA
1 TAAATTTCAAGGTGGACACCA
25976 TAAAT
1 TAAAT
25981 AAAATCAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
TAAATTTCAAGGTGGACACCA
Found at i:26004 original size:72 final size:70
Alignment explanation
Indices: 25808--26004 Score: 175
Period size: 72 Copynumber: 2.7 Consensus size: 70
25798 AGGTACAAAT
* * *** *
25808 AAAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATAGAAGAAAACTTAAATTTCAGG
1 AAAAAATTTCAAGGTGGGACAATAAATAAAATAAGTAACTAATA-AA-AAAAATTAAATTTCAGG
25873 ATGGACA
64 ATGGACA
* *** *
25880 AAAAAATTTCAGGGTGGGACAATCCGTAAAATAAGTAACTAATCGAAGAAAAATTAAATTTCAAG
1 AAAAAATTTCAAGGTGGGACAATAAATAAAATAAGTAACTAAT--AAAAAAAATTAAATTTC-AG
25945 G-TGGACA
63 GATGGACA
* *
25952 TCAAAAATTTCAAGGT-GTACACCATAAATAAAATCAA-TAACTAATAAAAAAAA
1 -AAAAAATTTCAAGGTGGGACA--ATAAATAAAAT-AAGTAACTAATAAAAAAAA
26005 ATTGAATATC
Statistics
Matches: 108, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
72 72 0.67
73 17 0.16
74 17 0.16
75 2 0.02
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (70 bp):
AAAAAATTTCAAGGTGGGACAATAAATAAAATAAGTAACTAATAAAAAAAATTAAATTTCAGGAT
GGACA
Found at i:33244 original size:127 final size:128
Alignment explanation
Indices: 33113--33369 Score: 462
Period size: 127 Copynumber: 2.0 Consensus size: 128
33103 AAAAAATTAT
* *
33113 ATAATTAATATATATACACCTACCTAAAACATGTTTCCAATATATGTTGGCATGCAAGATAGGTC
1 ATAATTAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTC
* *
33178 -TTTAACATCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTTCTTGAGCAAC
66 TTTTAACACCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAAC
33240 ATAATTAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTC
1 ATAATTAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTC
*
33305 TTTTAACACCTTTGATATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAAC
66 TTTTAACACCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAAC
33368 AT
1 AT
33370 TTCTTTTATT
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
127 63 0.51
128 61 0.49
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (128 bp):
ATAATTAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTC
TTTTAACACCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAAC
Found at i:34621 original size:23 final size:23
Alignment explanation
Indices: 34594--34663 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
34584 AGGATTTTTT
*
34594 TAATTTAATATATAA-ATTATTAA
1 TAATTAAATATATAATATTA-TAA
*
34617 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAATATTATAA
34640 TATATATAAA-A-ATAATAATTATAA
1 TA-AT-TAAATATATAAT-ATTATAA
34664 CGGGTATTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 22 0.55
24 14 0.35
25 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
TAATTAAATATATAATATTATAA
Found at i:36155 original size:19 final size:19
Alignment explanation
Indices: 36131--36183 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
36121 ATAAAACCTA
36131 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
36150 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
36169 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
36184 GAAATGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATAGAG
Found at i:42589 original size:20 final size:21
Alignment explanation
Indices: 42564--42612 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
42554 GAAGTTTTAA
42564 GATCATCAATATT-TTTTGAT
1 GATCATCAATATTCTTTTGAT
42584 GATCATCAATATTCTTTTGAT
1 GATCATCAATATTCTTTTGAT
42605 GATCATCA
1 GATCATCA
42613 TGAACTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (21 bp):
GATCATCAATATTCTTTTGAT
Found at i:44727 original size:43 final size:43
Alignment explanation
Indices: 44675--44761 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
44665 TGTGCTCGAT
* *
44675 GCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGTATCG
1 GCATAAAATGCATTCGATGTTTAAAAATAGCCTGAGTGCATCG
*
44718 GCATAAAATGCATTTGATGTTTAAAAATAGCCTGAGTGCATCG
1 GCATAAAATGCATTCGATGTTTAAAAATAGCCTGAGTGCATCG
44761 G
1 G
44762 TGCATTGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (43 bp):
GCATAAAATGCATTCGATGTTTAAAAATAGCCTGAGTGCATCG
Done.