Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002544.1 Hibiscus syriacus cultivar Beakdansim tig00005166_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: 75227
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11985 original size:2 final size:2
Alignment explanation
Indices: 11978--12010 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11968 TCATATCACC
11978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12011 TCCACATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25849 original size:36 final size:36
Alignment explanation
Indices: 25769--26084 Score: 179
Period size: 36 Copynumber: 8.4 Consensus size: 36
25759 TAATATATAT
*
25769 ATATATATATTAT--GTTTTCAAAAATATTTTTTTTAAA
1 ATATATATATTATACGTTTTC--AAA-ATTATTTTTAAA
* *
25806 A-ATTATATATTATACATTTTCAAAAGTATTTTTAAAATATATA
1 ATA-TATATATTATACGTTTTCAAAATTA-TTTT----TA-A-A
*
25849 TATATATATATTATACGTTTTCAAAAATATTTTTTAAA
1 -ATATATATATTATACGTTTTCAAAATTA-TTTTTAAA
* * *
25887 AAACTATATATTATACGTTTTCAAATTTTTTTTTCAAA
1 ATA-TATATATTATACGTTTTCAAAATTATTTTT-AAA
25925 ACTATATA-ATATATACATGTTTTCGAAAATTATTTTTAAA
1 A-TATATATAT-TATAC--GTTTTC-AAAATTATTTTTAAA
* *
25965 AT-TATATAATATATGTTTTCAAAAATTATTTTTAAA
1 ATATATATATTATACGTTTTC-AAAATTATTTTTAAA
* * * *
26001 ACTATATA-A-TATATGTTTTTAAAACATATTTTCAAA
1 A-TATATATATTATACGTTTTCAAAA-TTATTTTTAAA
* *
26037 ACCATA-ATA-TATA--TTTTCACAAATCAATTTTTAAA
1 A-TATATATATTATACGTTTTCA-AAAT-TATTTTTAAA
26072 AT-TATATATTATA
1 ATATATATATTATA
26085 TGATTTAAAA
Statistics
Matches: 227, Mismatches: 24, Indels: 58
0.73 0.08 0.19
Matches are distributed among these distances:
33 2 0.01
34 8 0.04
35 21 0.09
36 54 0.24
37 29 0.13
38 48 0.21
39 9 0.04
40 12 0.05
41 12 0.05
42 1 0.00
43 1 0.00
44 29 0.13
45 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (36 bp):
ATATATATATTATACGTTTTCAAAATTATTTTTAAA
Found at i:25851 original size:38 final size:38
Alignment explanation
Indices: 25767--26014 Score: 185
Period size: 38 Copynumber: 6.3 Consensus size: 38
25757 TCTAATATAT
*
25767 ATATATATATATTAT--GTTTTCAAAAATATTTTTTTTAAA
1 ATATATATATATTATACGTTTTC--AAA-ATTATTTTTAAA
* *
25806 A-AT-TATATATTATACATTTTCAAAAGTATTTTTAAAATATA
1 ATATATATATATTATACGTTTTCAAAATTATTTTT---A-A-A
*
25847 TATATATATATATTATACGTTTTCAAAAATATTTTTTAAA
1 -ATATATATATATTATACGTTTTCAAAATTA-TTTTTAAA
* *
25887 A-A-ACTATATATTATACGTTTTCAAATTTTTTTTTCAAA
1 ATATA-TATATATTATACGTTTTCAAAATTATTTTT-AAA
25925 ACTATATA-ATA-TATACATGTTTTCGAAAATTATTTTTAAA
1 A-TATATATATATTATAC--GTTTTC-AAAATTATTTTTAAA
*
25965 AT-TATATA-A-TATATGTTTTCAAAAATTATTTTTAAA
1 ATATATATATATTATACGTTTTC-AAAATTATTTTTAAA
26001 ACTATATAATATAT
1 A-TATAT-ATATAT
26015 GTTTTTAAAA
Statistics
Matches: 172, Mismatches: 12, Indels: 48
0.74 0.05 0.21
Matches are distributed among these distances:
36 29 0.17
37 20 0.12
38 46 0.27
39 16 0.09
40 16 0.09
41 13 0.08
42 2 0.01
43 2 0.01
44 23 0.13
45 5 0.03
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (38 bp):
ATATATATATATTATACGTTTTCAAAATTATTTTTAAA
Found at i:31304 original size:103 final size:103
Alignment explanation
Indices: 31134--31332 Score: 380
Period size: 103 Copynumber: 1.9 Consensus size: 103
31124 GAATTACACA
*
31134 AAATGAAATGAACGCCTTTTAAAATTGCTCAAAGTTCTCCCATATATTTCCGAGTATCATTCTCT
1 AAATGAAATGAACGCCTTTTAAAATTGCTCAAAGTTCTCCCATATATTTCAGAGTATCATTCTCT
31199 CATATCCATGCCAAAATATGTGTTGGATGCACAAAACG
66 CATATCCATGCCAAAATATGTGTTGGATGCACAAAACG
*
31237 AAATGAAATGAACGCCTTTTAAAATTGCTCAAAGTTTTCCCATATATTTCAGAGTATCATTCTCT
1 AAATGAAATGAACGCCTTTTAAAATTGCTCAAAGTTCTCCCATATATTTCAGAGTATCATTCTCT
31302 CATATCCATGCCAAAATATGTGTTGGATGCA
66 CATATCCATGCCAAAATATGTGTTGGATGCA
31333 GCCTGTGCGG
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (103 bp):
AAATGAAATGAACGCCTTTTAAAATTGCTCAAAGTTCTCCCATATATTTCAGAGTATCATTCTCT
CATATCCATGCCAAAATATGTGTTGGATGCACAAAACG
Found at i:36276 original size:10 final size:10
Alignment explanation
Indices: 36261--36286 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
36251 CCTTCTCTTA
36261 TCTCTTTCTC
1 TCTCTTTCTC
36271 TCTCTTTCTC
1 TCTCTTTCTC
36281 TCTCTT
1 TCTCTT
36287 GTTAGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TCTCTTTCTC
Found at i:38764 original size:2 final size:2
Alignment explanation
Indices: 38757--38783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38747 GATTCAAGAT
38757 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38784 GCAAAGTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39245 original size:2 final size:2
Alignment explanation
Indices: 39238--39276 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39228 TCCCGACCCG
39238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39277 TTTATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39303 original size:15 final size:15
Alignment explanation
Indices: 39273--39301 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39263 TATATATATA
39273 ATATTTTATTATTTT
1 ATATTTTATTATTTT
39288 ATATTTT-TTATTTT
1 ATATTTTATTATTTT
39302 TAAGTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATATTTTATTATTTT
Found at i:41583 original size:28 final size:28
Alignment explanation
Indices: 41544--41600 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41534 GCAACGCTCA
41544 AAAGAAAGTAGTTCACTTTGAGAAATAC
1 AAAGAAAGTAGTTCACTTTGAGAAATAC
41572 AAAGAAAGTAGTTCACTTTGAGAAATAC
1 AAAGAAAGTAGTTCACTTTGAGAAATAC
41600 A
1 A
41601 TTTGTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (28 bp):
AAAGAAAGTAGTTCACTTTGAGAAATAC
Found at i:43244 original size:122 final size:119
Alignment explanation
Indices: 43025--43281 Score: 270
Period size: 122 Copynumber: 2.1 Consensus size: 119
43015 TTACAGCCAT
* * * * *
43025 TAAGAGCAGGGAAG-TCGAATGTCAATAAGCGCTGTAGGCTTCTTTGGTTTCTTTAAAGCTTCGA
1 TAAGAGCAGGGAAGTTC-TACGTAAATAAGCGCTGGAGGCTTCTTTGGTTTCTTTAAAGCTTAGA
* * * * *
43089 TATGATGTAAGGATTGTAGGCTTCTTTGGTTTCTTTTTAAAGTTGAGTATAGCCTATAA
65 CATGACGTAAGGATTG-AGGCTTCTCTGGTTTC--TTTAAAGTTGAG-AAAACCTATAA
* *
43148 T-AGAGCAGGGAAGTTCTACGTAAATAAGCGCTGGAGGCTTCTTTGGTTTCTTTTAAGTTTAGAC
1 TAAGAGCAGGGAAGTTCTACGTAAATAAGCGCTGGAGGCTTCTTTGGTTTCTTTAAAGCTTAGAC
* * * *
43212 ATGGCGTAAAGGGCA-TG-GGTTTCTCTGGTTTCTTTAAAGTTTAGAAAACCTGTAA
66 ATGACGT-AA-GG-ATTGAGGCTTCTCTGGTTTCTTTAAAGTTGAGAAAACCTATAA
43267 TAAGAGCAGGGAAGT
1 TAAGAGCAGGGAAGT
43282 AGTAGTAGTA
Statistics
Matches: 113, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
119 9 0.08
120 24 0.21
122 70 0.62
123 5 0.04
124 4 0.04
125 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (119 bp):
TAAGAGCAGGGAAGTTCTACGTAAATAAGCGCTGGAGGCTTCTTTGGTTTCTTTAAAGCTTAGAC
ATGACGTAAGGATTGAGGCTTCTCTGGTTTCTTTAAAGTTGAGAAAACCTATAA
Found at i:48542 original size:20 final size:22
Alignment explanation
Indices: 48517--48561 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
48507 TAAAAACAAC
48517 TTTATAATTAATTT-A-TTAAT
1 TTTATAATTAATTTAATTTAAT
* *
48537 TTTATATTTTATTTAATTTAAT
1 TTTATAATTAATTTAATTTAAT
48559 TTT
1 TTT
48562 TCAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATAATTAATTTAATTTAAT
Found at i:50194 original size:24 final size:24
Alignment explanation
Indices: 50158--50250 Score: 114
Period size: 24 Copynumber: 3.7 Consensus size: 24
50148 TTTTAATTTT
*
50158 AATAATAATTTTTTTAAATAAATTA
1 AATATTAA-TTTTTTAAATAAATTA
*
50183 AATATTAATTTTTTAATATTATATTA
1 AATATTAATTTTTTAA-A-TAAATTA
50209 TAGATATTAATTTTTTAAATAAATTA
1 -A-ATATTAATTTTTTAAATAAATTA
*
50235 AATATTAAATTTTTAA
1 AATATTAATTTTTTAA
50251 TATTATATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
24 22 0.37
25 9 0.15
26 12 0.20
27 2 0.03
28 15 0.25
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:50216 original size:28 final size:28
Alignment explanation
Indices: 50184--50275 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
50174 AATAAATTAA
50184 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
*
50212 ATATTAATTTTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTTAATATTATATTATAG
*
50236 ATATTAAATTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
50264 ATATTTAATTTT
1 ATA-TTAATTTT
50276 ATATCATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 14 0.25
25 2 0.04
26 12 0.22
27 2 0.04
28 18 0.33
29 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTAATTTTTTAATATTATATTATAG
Found at i:50227 original size:52 final size:53
Alignment explanation
Indices: 50167--50275 Score: 202
Period size: 52 Copynumber: 2.1 Consensus size: 53
50157 TAATAATAAT
*
50167 TTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA-TTAA
1 TTTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATATTTAA
50219 TTTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATATTTAA
1 TTTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATATTTAA
50272 TTTT
1 TTTT
50276 ATATCATATA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 47 0.85
53 8 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (53 bp):
TTTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATATTTAA
Found at i:50331 original size:20 final size:19
Alignment explanation
Indices: 50271--50332 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
50261 TAGATATTTA
*
50271 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
50290 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
50308 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
50328 ATTTT
1 ATTTT
50333 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:50478 original size:7 final size:7
Alignment explanation
Indices: 50466--50491 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
50456 ATTAAGATTT
50466 TAAAATA
1 TAAAATA
50473 TAAAATA
1 TAAAATA
50480 TAAAATA
1 TAAAATA
50487 TAAAA
1 TAAAA
50492 AATTATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:57660 original size:146 final size:145
Alignment explanation
Indices: 57415--57682 Score: 387
Period size: 146 Copynumber: 1.8 Consensus size: 145
57405 TAGCTTTTAC
* * * *
57415 TTTTTCTTTAGAGAGAAAAGGAGGGAAAAAATTACCTTACGCTGTTGCCGGGGATCGAACACGGT
1 TTTTTCTTTAGAGAGAAAAGGAGCGAAAAAATAACCTTACGCCGTTGCCGGGGATCGAACACGGG
* *
57480 TCACTCGCGTGACAGGCGAGAATACTTACAACTATACTACAACAACTTTGTTGAGAGCAATTTTT
66 TCACCCGCGTGACAGGCGAGAATACTTACAACTATACTACAACAACTTTGCTGAGAGCAATTTTT
57545 ATTTTACAATTGTTA
131 ATTTTACAATTGTTA
* * *
57560 TTTTTTTTTAGATAGAAAAGGAGCG-AAAAATAACAGC-TAGCGCCGTTGCCGGGGATCGAACCC
1 TTTTTCTTTAGAGAGAAAAGGAGCGAAAAAATAAC--CTTA-CGCCGTTGCCGGGGATCGAACAC
* * *
57623 GGGTCACCCGCGTGACAGGCGGGAATACTTACCACTATACTACAACGACTTTGCTGAGAG
63 GGGTCACCCGCGTGACAGGCGAGAATACTTACAACTATACTACAACAACTTTGCTGAGAG
57683 TAAGTTCATT
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
144 8 0.07
145 24 0.22
146 76 0.70
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (145 bp):
TTTTTCTTTAGAGAGAAAAGGAGCGAAAAAATAACCTTACGCCGTTGCCGGGGATCGAACACGGG
TCACCCGCGTGACAGGCGAGAATACTTACAACTATACTACAACAACTTTGCTGAGAGCAATTTTT
ATTTTACAATTGTTA
Found at i:57724 original size:21 final size:19
Alignment explanation
Indices: 57691--57732 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
57681 AGTAAGTTCA
57691 TTATTTTTAT-AAACAATGT
1 TTATTTTTATAAAAC-ATGT
57710 TTATATTTTAGTAAAACATGT
1 TTAT-TTTTA-TAAAACATGT
57731 TT
1 TT
57733 GATGATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 7 0.35
22 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (19 bp):
TTATTTTTATAAAACATGT
Found at i:59809 original size:2 final size:2
Alignment explanation
Indices: 59802--59849 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
59792 ATTCAATTTA
59802 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
59844 AT AT AT
1 AT AT AT
59850 GTTTTTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60435 original size:15 final size:15
Alignment explanation
Indices: 60406--60434 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
60396 AAATTTAATG
60406 AAAACGAATAATTTT
1 AAAACGAATAATTTT
60421 AAAA-GAATAATTTT
1 AAAACGAATAATTTT
60435 TCTGTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (15 bp):
AAAACGAATAATTTT
Found at i:63781 original size:73 final size:73
Alignment explanation
Indices: 63659--63808 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 73
63649 GAATTAGAAC
* * *
63659 TTTGCAACTGAACATATCTTAGATTCTATGAGCAACCTAAATAGCTACATGATATTGTATACCAA
1 TTTGCAACTGAACAAATCTTAGATTCTATGAGCAACCGAAATAGATACATGATATTGTATACCAA
63724 AACAATAT
66 AACAATAT
63732 TTTGCAACTGAACAAATCTTAGATTCTATGAGCAACCGAAATAGATACATGATATTGTATACCAA
1 TTTGCAACTGAACAAATCTTAGATTCTATGAGCAACCGAAATAGATACATGATATTGTATACCAA
63797 AACAATAT
66 AACAATAT
63805 TTTG
1 TTTG
63809 GTGATGCCCA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (73 bp):
TTTGCAACTGAACAAATCTTAGATTCTATGAGCAACCGAAATAGATACATGATATTGTATACCAA
AACAATAT
Done.