Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001831.1 Hibiscus syriacus cultivar Beakdansim tig00003703_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: 61134
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:8949 original size:23 final size:22
Alignment explanation
Indices: 8889--8998 Score: 93
Period size: 23 Copynumber: 5.0 Consensus size: 22
8879 TAGCTCGTAA
8889 TTTGCACCGAAGTACCACATA-
1 TTTGCACCGAAGTACCACATAG
* * *
8910 ATTGTC-TCGAAGGACCACATAGG
1 TTTG-CACCGAAGTACCACATA-G
8933 TTTGCACCGAAGTACCACATAAG
1 TTTGCACCGAAGTACCACAT-AG
* *
8956 TTTGCACCAAAGTGCCACATA-
1 TTTGCACCGAAGTACCACATAG
* *
8977 ATTGTC-CCGAAGGACCACATAG
1 TTTG-CACCGAAGTACCACATAG
8999 AACCCTTGAC
Statistics
Matches: 70, Mismatches: 12, Indels: 13
0.74 0.13 0.14
Matches are distributed among these distances:
21 31 0.44
22 4 0.06
23 34 0.49
24 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (22 bp):
TTTGCACCGAAGTACCACATAG
Found at i:13494 original size:64 final size:64
Alignment explanation
Indices: 13378--13578 Score: 230
Period size: 64 Copynumber: 3.1 Consensus size: 64
13368 ATTCAAGGTG
* * * * * *
13378 ATGCACCGATGCATCAAACCATGCATCGATGCACCTATGAT-TTAATT-GAACATCAAATGCATT
1 ATGCATCGATG-AACAAGCCATGCATCGATGCACC-AGGATATT-TTTCAAACATCAAATGCATT
13441 TC
63 TC
*
13443 ATGCATCGATGAACAAGCCATGCATCGATGCACTC-GGA-ATATTTTCAAACATCGAATGCATTT
1 ATGCATCGATGAACAAGCCATGCATCGATGCAC-CAGGATAT-TTTTCAAACATCAAATGCATTT
*
13506 G
64 C
* * *
13507 ATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCAAACATCAAATGCACTTC
1 ATGCATCGATGAACAAGCCATGCATCGATGCACCAGGATATTTTTCAAACATCAAATGCATTTC
13571 ATGCATCG
1 ATGCATCG
13579 TTGCACTCTT
Statistics
Matches: 117, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 6 0.05
64 98 0.84
65 13 0.11
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGAACAAGCCATGCATCGATGCACCAGGATATTTTTCAAACATCAAATGCATTTC
Found at i:13584 original size:64 final size:64
Alignment explanation
Indices: 13426--13584 Score: 232
Period size: 64 Copynumber: 2.5 Consensus size: 64
13416 GATTTAATTG
*
13426 AACATCAAATGCATTTCATGCATCGATGAACAAGCCATGCATCGATGCACTCGGAATATTTTCA
1 AACATCAAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCGGAATATTTTCA
* * *
13490 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGG-CTATTTTTC
1 AACATCAAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTC-GGAATA-TTTTC
13553 A
64 A
* *
13554 AACATCAAATGCACTTCATGCATCGTTGCAC
1 AACATCAAATGCATTTCATGCATCGATGCAC
13585 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 3 0.04
64 82 0.96
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (64 bp):
AACATCAAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCGGAATATTTTCA
Found at i:22164 original size:64 final size:63
Alignment explanation
Indices: 22048--22190 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 63
22038 ATTCAAGGTG
* * * *
22048 ATGCACCGATGCATCAAACCATGCATCGATGCACCTATGATTTAATTGAACATCGAATGCATTTC
1 ATGCATCGATGCA-CAAACCATGCATCGATGCACCTAGGATTT-ATTAAACATCGAATGCACTTC
*
22113 ATGCATCGATGCACAAGCCATGCATCGATGCACC-AGGCTATTT-TTCAAACATCGAATGCACTT
1 ATGCATCGATGCACAAACCATGCATCGATGCACCTAGG--ATTTATT-AAACATCGAATGCACTT
22176 C
63 C
22177 ATGCATCGATGCAC
1 ATGCATCGATGCAC
22191 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 4 0.06
64 50 0.71
65 16 0.23
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACAAACCATGCATCGATGCACCTAGGATTTATTAAACATCGAATGCACTTC
Found at i:22190 original size:17 final size:19
Alignment explanation
Indices: 22162--22210 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
22152 ATTTTTCAAA
22162 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
22180 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
22199 CACCGATGCACT
1 CATCGATGCACT
22211 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:26290 original size:22 final size:22
Alignment explanation
Indices: 26258--26314 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
26248 ACTCACCACT
26258 CAGTATCGATACCCTATACAAC
1 CAGTATCGATACCCTATACAAC
*
26280 CAGTATTGATACCCTATACAAC
1 CAGTATCGATACCCTATACAAC
*
26302 CAGTACCGATACC
1 CAGTATCGATACC
26315 ACCCTTCGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.23
Consensus pattern (22 bp):
CAGTATCGATACCCTATACAAC
Found at i:34491 original size:20 final size:19
Alignment explanation
Indices: 34447--34483 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34437 ATACCAAAAG
*
34447 CTTCACAATTTTTGTCATT
1 CTTCACAATCTTTGTCATT
34466 CTTCACAATCTTT-TCATT
1 CTTCACAATCTTTGTCATT
34484 TCCTTCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.22, C:0.24, G:0.03, T:0.51
Consensus pattern (19 bp):
CTTCACAATCTTTGTCATT
Found at i:36759 original size:23 final size:23
Alignment explanation
Indices: 36725--36779 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
36715 ATGTAATTTA
36725 AATA-TTT-TTTTTATATTTTATT
1 AATATTTTATTTTTAT-TTTTATT
36747 AATATTTTATTTTTATTTTTATT
1 AATATTTTATTTTTATTTTTATT
*
36770 AAAATTTTAT
1 AATATTTTAT
36780 AAATTCCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 4 0.13
23 19 0.63
24 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
AATATTTTATTTTTATTTTTATT
Found at i:38065 original size:24 final size:25
Alignment explanation
Indices: 38005--38065 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
37995 TCGGGCCGGG
38005 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
38028 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
38052 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
38066 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:42814 original size:2 final size:2
Alignment explanation
Indices: 42807--42832 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42797 CGTCGATGTA
42807 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
42833 TACTTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46059 original size:148 final size:146
Alignment explanation
Indices: 45770--46050 Score: 438
Period size: 145 Copynumber: 1.9 Consensus size: 146
45760 GTTCTTATTC
* ****
45770 GTCAATGGTACCTGTGCAGTCCAGGGGCCTCCAGTGTTTGTGCTTAATACAAAGCAATTTTTTTT
1 GTCAATGGTACATGTGCAGTCCAGGGGCCTCCAGTGTTTGTGCTTAATACAAAGCAA--TAAAAT
* * *
45835 TTTTTTTTTTCAGAATTATAGAAGAATTTAGTTCTATGTTCTTGCTTAACTCTTAATACATGCAG
64 TTTCTTTTTGCAGAATTATAGAAGAATTTAGTTCTATGTTCTTGCTTAACTCTTAATACATGCAA
*
45900 ACGATTTTAAAAACAATA
129 ACAATTTTAAAAACAATA
*
45918 GTCAATGGTTCATGTGCAGTCCAGGGGCCTCCAGTGTTTGTGCTTAATACAAAGCAA-AAAATTT
1 GTCAATGGTACATGTGCAGTCCAGGGGCCTCCAGTGTTTGTGCTTAATACAAAGCAATAAAATTT
*
45982 TCTTTTTGCAGAATTATAGAAGAATTTAGTTCTATGTTCTTGTTTAACTCTTAATACATGCAAAC
66 TCTTTTTGCAGAATTATAGAAGAATTTAGTTCTATGTTCTTGCTTAACTCTTAATACATGCAAAC
46047 AATT
131 AATT
46051 GTTTTAAAAG
Statistics
Matches: 122, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
145 67 0.55
148 55 0.45
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (146 bp):
GTCAATGGTACATGTGCAGTCCAGGGGCCTCCAGTGTTTGTGCTTAATACAAAGCAATAAAATTT
TCTTTTTGCAGAATTATAGAAGAATTTAGTTCTATGTTCTTGCTTAACTCTTAATACATGCAAAC
AATTTTAAAAACAATA
Found at i:47952 original size:109 final size:109
Alignment explanation
Indices: 47758--47958 Score: 307
Period size: 109 Copynumber: 1.8 Consensus size: 109
47748 AGTGCATGGT
* *
47758 GGACATTATTATGCATTTATCAGACCGGCTCTTTCTGATCTATGGTACAGATCATACCAATGCAT
1 GGACATTATCATGCATTTATCAGACCGGCTCTTTCTGATCAATGGTACAGATCATACCAATGCAT
47823 AAAATTTATACTATGCAAAAAAAAAAAGGTTATTAATTATTTTC
66 AAAATTTATACTATGCAAAAAAAAAAAGGTTATTAATTATTTTC
* * * * *
47867 GGACATTATCATGCATTTATGAGGCTGGCAT-TTTCTGATCAATGGTACCGATCATGCCAATGCA
1 GGACATTATCATGCATTTATCAGACCGGC-TCTTTCTGATCAATGGTACAGATCATACCAATGCA
47931 T-AAATTTATACTATGCAAAAAATAAAAA
65 TAAAATTTATACTATGCAAAAAA-AAAAA
47959 TAAAAAGAAG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
108 21 0.25
109 61 0.73
110 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (109 bp):
GGACATTATCATGCATTTATCAGACCGGCTCTTTCTGATCAATGGTACAGATCATACCAATGCAT
AAAATTTATACTATGCAAAAAAAAAAAGGTTATTAATTATTTTC
Found at i:58289 original size:21 final size:22
Alignment explanation
Indices: 58265--58306 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
58255 TTAAGGTATA
58265 TTTT-ATTATATTTAA-TATTTG
1 TTTTAATT-TATTTAAGTATTTG
58286 TTTTAATTTATTTAAGTATTT
1 TTTTAATTTATTTAAGTATTT
58307 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTTAATTTATTTAAGTATTTG
Done.