Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007059.1 Hibiscus syriacus cultivar Beakdansim tig00018314_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: 77969
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:322 original size:2 final size:2
Alignment explanation
Indices: 317--360 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
307 TTAAACGTGT
317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
358 TA T
1 TA T
361 GAAAGTAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1331 original size:64 final size:65
Alignment explanation
Indices: 1228--1371 Score: 202
Period size: 64 Copynumber: 2.2 Consensus size: 65
1218 TTTAAAATTA
* *
1228 AAGTAAATTTAATATTTTTAAAATAAATTAAGGTTTGATTCATTTTATTGTTTTCATTATAATAC
1 AAGTAAATTTAATATTTCTAAAATAAATTAAGATTTGATTCATTTTATTGTTTTCATTATAATAC
* * *
1293 AAGTATATTTAATATTCTCT-AAA-AAATTAAGATTTGATTCATTTTATTGTTTTCGTTGTAATA
1 AAGTAAATTTAATATT-TCTAAAATAAATTAAGATTTGATTCATTTTATTGTTTTCATTATAATA
1356 C
65 C
*
1357 AAGTTAAATATAATA
1 AAG-TAAATTTAATA
1372 CGTTTAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 41 0.59
65 27 0.39
66 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (65 bp):
AAGTAAATTTAATATTTCTAAAATAAATTAAGATTTGATTCATTTTATTGTTTTCATTATAATAC
Found at i:1766 original size:23 final size:22
Alignment explanation
Indices: 1723--1796 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
1713 GGTATATTAT
*
1723 TTTAGTGTTTTTCAACA-TATTCG
1 TTTAGTG-TTTGCAA-ATTATTCG
1746 TTTAGTGTTTGCCAAATTATTCCG
1 TTTAGTGTTTG-CAAATTATT-CG
* * *
1770 TTTAATTTTTGCGAATGTATTCG
1 TTTAGTGTTTGCAAAT-TATTCG
1793 TTTA
1 TTTA
1797 TATGTTTAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 4 0.09
23 24 0.56
24 15 0.35
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (22 bp):
TTTAGTGTTTGCAAATTATTCG
Found at i:6445 original size:100 final size:97
Alignment explanation
Indices: 6284--6461 Score: 270
Period size: 96 Copynumber: 1.8 Consensus size: 97
6274 AATTCAAAAA
* *
6284 AAGATAGATAAAAAGCATTGAAATTAGATATAAAACATACTATTTTTGTAATTTTTCTGATTTTT
1 AAGATAGATAAAAAGCATAGAAATTAGATAAAAAACATACTATTTTTGTAATTTTTCTGATTTTT
6349 T-TATTTTTTTAAATTCAAGTATATTAATTGC
66 TGTATTTTTTTAAATTCAAGTATATTAATTGC
*
6380 AAGATAGATAAAAA-TATAGAAAATTAGATAAATAAACATACTAATTTTTTTGTAATTTTTCTGA
1 AAGATAGATAAAAAGCATAG-AAATTAGATAAA-AAACATACT-A--TTTTTGTAATTTTTCTGA
6444 TTTTTTGTATTTTTTTAA
61 TTTTTTGTATTTTTTTAA
6462 TTTTTTAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
95 3 0.04
96 25 0.34
97 9 0.12
98 1 0.01
100 24 0.33
101 11 0.15
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (97 bp):
AAGATAGATAAAAAGCATAGAAATTAGATAAAAAACATACTATTTTTGTAATTTTTCTGATTTTT
TGTATTTTTTTAAATTCAAGTATATTAATTGC
Found at i:6449 original size:19 final size:18
Alignment explanation
Indices: 6420--6467 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6410 AATAAACATA
6420 CTAATTTTTTTGTAATTTTT
1 CTAA-TTTTTTGT-ATTTTT
*
6440 CTGATTTTTTGTATTTTT
1 CTAATTTTTTGTATTTTT
*
6458 TTAATTTTTT
1 CTAATTTTTT
6468 AAATTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.56
19 8 0.32
20 3 0.12
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
CTAATTTTTTGTATTTTT
Found at i:9204 original size:2 final size:2
Alignment explanation
Indices: 9197--9253 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
9187 TTACCCTTCA
9197 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
*
9239 AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT A
9254 AAGTGGCCTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16504 original size:11 final size:10
Alignment explanation
Indices: 16460--16506 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
16450 TTAAATACGT
16460 TAAAATATAA
1 TAAAATATAA
16470 GTGAAAAT-TAA
1 -T-AAAATATAA
*
16481 TAAAATCTAA
1 TAAAATATAA
16491 TAACAATATAA
1 TAA-AATATAA
16502 TAAAA
1 TAAAA
16507 ATGGTAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 5 0.16
10 9 0.28
11 13 0.41
12 5 0.16
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (10 bp):
TAAAATATAA
Found at i:26672 original size:49 final size:51
Alignment explanation
Indices: 26619--26729 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 51
26609 TAGCGCGGAT
*
26619 CAGGTACCGCG-CTATACCTTTACTCCT-A-ATAATTTTATATAGCGCAGGG
1 CAGGTACCGCGAC-ATACCTTTACTCCTGACATAATTTTATATAGCACAGGG
*
26668 CAGGTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCACGGGG
1 CAGGTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCACAGGG
26719 CAGGTACCGCG
1 CAGGTACCGCG
26730 TTTTGTATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
49 25 0.44
50 2 0.04
51 30 0.53
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (51 bp):
CAGGTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCACAGGG
Found at i:32548 original size:110 final size:111
Alignment explanation
Indices: 32354--32580 Score: 366
Period size: 110 Copynumber: 2.1 Consensus size: 111
32344 ATTACAAAAA
* * * * *
32354 TTAATTCTTAATCTAATAATCATGCAATAAATGAATCAGCTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCAATAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
32419 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* *
32465 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCAATAAATAAATCAACTAAATATTAATAATAATTTAAATTA
32529 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
32575 ATAATT
1 TTAATT
32581 TCCATCCAAG
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 75 0.70
111 32 0.30
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCAATAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:32712 original size:12 final size:10
Alignment explanation
Indices: 32698--32738 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
32688 ACCTTAAAAA
*
32698 GAGAGTATTT
1 GAGAGAATTT
32708 GAGAGAAATTT
1 GAGAG-AATTT
32719 -AGAGAATTT
1 GAGAGAATTT
32728 GAGAGAATTT
1 GAGAGAATTT
32738 G
1 G
32739 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:32941 original size:51 final size:50
Alignment explanation
Indices: 32849--32975 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 50
32839 AGATATACAG
* * * * * **
32849 GTATAGCACGCTGTAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCAACGTGGCGCCAAATCACC
*
32899 GTATAGCGCGGTGCAGGGGGCGCGCTATATCCAACGTGGCGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATA-CCAACGTGGCGCCAAATCACC
*
32950 GTATAGCGCGGTGCAAGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
32976 TTACTGCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 25 0.37
51 42 0.63
ACGTcount: A:0.19, C:0.30, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCAACGTGGCGCCAAATCACC
Found at i:40828 original size:21 final size:22
Alignment explanation
Indices: 40788--40840 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40778 TTTTTCAGAA
* *
40788 TGCTACAGAGGTATCGATACCC-
1 TGCTACAG-TGTACCGATACCCT
40810 TGCTACAGTGTACCGATACCCT
1 TGCTACAGTGTACCGATACCCT
40832 TGCTACAGT
1 TGCTACAGT
40841 AATTTCGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCTACAGTGTACCGATACCCT
Found at i:49437 original size:15 final size:15
Alignment explanation
Indices: 49417--49451 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
49407 CCACCTTACT
49417 AGCAATGAATGAATC
1 AGCAATGAATGAATC
49432 AGCAATGAATGAATC
1 AGCAATGAATGAATC
49447 AGCAA
1 AGCAA
49452 CGAAACCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (15 bp):
AGCAATGAATGAATC
Found at i:52007 original size:46 final size:46
Alignment explanation
Indices: 51937--52029 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
51927 AATTTTTTCT
* * *
51937 GATAAATTTTAAATATAATCTTAATTTTATCTAGAGAGGGGTGGAA
1 GATAAATTCTAAATATAATCTTAATCTTATCTAGAGAGGAGTGGAA
* * *
51983 GATAAATTCTAAATTTAATTTTAATCTTATCTGGAGAGGAGTGGAA
1 GATAAATTCTAAATATAATCTTAATCTTATCTAGAGAGGAGTGGAA
52029 G
1 G
52030 GAGAGACTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (46 bp):
GATAAATTCTAAATATAATCTTAATCTTATCTAGAGAGGAGTGGAA
Found at i:62668 original size:22 final size:23
Alignment explanation
Indices: 62631--62683 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
62621 AGGGGAGTGG
* *
62631 ATAATAAATT-TTTTAAATAATA
1 ATAATAAATTGATTAAAATAATA
*
62653 TTAATAAATTGATTAAAATAATA
1 ATAATAAATTGATTAAAATAATA
62676 ATAA-AAAT
1 ATAATAAAT
62684 GTCACATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAATAAATTGATTAAAATAATA
Found at i:71843 original size:32 final size:32
Alignment explanation
Indices: 71807--71877 Score: 112
Period size: 30 Copynumber: 2.3 Consensus size: 32
71797 TTTGAAAGTG
71807 AATATACAAAAAAAAAAAGTTGACATTGTGAA
1 AATATACAAAAAAAAAAAGTTGACATTGTGAA
*
71839 AATATAC--AAAAAAAAGGTTGACATTGTGAA
1 AATATACAAAAAAAAAAAGTTGACATTGTGAA
71869 AA-ATACAAA
1 AATATACAAA
71878 TGTGGTCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 4 0.11
30 24 0.67
31 1 0.03
32 7 0.19
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (32 bp):
AATATACAAAAAAAAAAAGTTGACATTGTGAA
Found at i:74925 original size:2 final size:2
Alignment explanation
Indices: 74918--74957 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
74908 TTATTATTAT
*
74918 TA TA TA TA TA TG 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
74958 AGGAAATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76550 original size:25 final size:25
Alignment explanation
Indices: 76490--76563 Score: 121
Period size: 26 Copynumber: 2.9 Consensus size: 25
76480 CAGTCTCTTC
*
76490 TAATAAAATAAGGTTTTTTCTTGATT
1 TAATGAAA-AAGGTTTTTTCTTGATT
76516 TAATGAAAAAAGGTTTTTTCTTGATT
1 TAATG-AAAAAGGTTTTTTCTTGATT
76542 TAATGAAAAAGGTTTTTTCTTG
1 TAATGAAAAAGGTTTTTTCTTG
76564 GGTTTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 17 0.37
26 26 0.57
27 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (25 bp):
TAATGAAAAAGGTTTTTTCTTGATT
Done.