Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005522.1 Hibiscus syriacus cultivar Beakdansim tig00012756_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: 55870
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:11895 original size:25 final size:26
Alignment explanation
Indices: 11860--11921 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
11850 ATAAAAACAT
* *
11860 AAAAAACTAAAGAAAT-AGTCAAATA
1 AAAAAATTAAAGAAATAAGTAAAATA
*
11885 AAAAAATTAAATAAATAAGTAAAATA
1 AAAAAATTAAAGAAATAAGTAAAATA
*
11911 AATTAAATTAA
1 AA-AAAATTAA
11922 TAAAATACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 14 0.45
26 10 0.32
27 7 0.23
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAAAATTAAAGAAATAAGTAAAATA
Found at i:11916 original size:22 final size:21
Alignment explanation
Indices: 11883--11924 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
11873 AATAGTCAAA
11883 TAAAAAAATTAAATAAATAAG
1 TAAAAAAATTAAATAAATAAG
*
11904 TAAAATAAATTAAATTAATAA
1 TAAAA-AAATTAAATAAATAA
11925 AATACTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAAAATTAAATAAATAAG
Found at i:11917 original size:18 final size:17
Alignment explanation
Indices: 11887--11928 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
11877 GTCAAATAAA
11887 AAAATTAAATAAA-TAAGT
1 AAAA-TAAATAAATTAA-T
11905 AAAATAAATTAAATTAAT
1 AAAATAAA-TAAATTAAT
11923 AAAATA
1 AAAATA
11929 CTAATGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 15 0.68
19 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATAAATAAATTAAT
Found at i:11996 original size:10 final size:9
Alignment explanation
Indices: 11951--11994 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
11941 GGAAAAAAGT
*
11951 AATAAAATA
1 AATAAAACA
*
11960 AATAAATCA
1 AATAAAACA
*
11969 AATAAGACAA
1 AATAAAAC-A
11979 AATAAAACA
1 AATAAAACA
11988 AATAAAA
1 AATAAAA
11995 ACCTAAGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (9 bp):
AATAAAACA
Found at i:13274 original size:16 final size:16
Alignment explanation
Indices: 13253--13283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13243 CCGTGTCTTC
13253 TTTGTAACTGGGCTTG
1 TTTGTAACTGGGCTTG
*
13269 TTTGTATCTGGGCTT
1 TTTGTAACTGGGCTT
13284 TAGGGTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.29, T:0.48
Consensus pattern (16 bp):
TTTGTAACTGGGCTTG
Found at i:14192 original size:30 final size:27
Alignment explanation
Indices: 14149--14211 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
14139 TTTATAGACG
*
14149 TATGGTTAATCGATTCAAAAAAATATAATA
1 TATGGTCAATCGATT-AAAAAAATAT--TA
* *
14179 TATGGTCACTCGATTTAAAAAATATTA
1 TATGGTCAATCGATTAAAAAAATATTA
14206 TATGGT
1 TATGGT
14212 TACTTTCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 8 0.27
29 9 0.30
30 13 0.43
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37
Consensus pattern (27 bp):
TATGGTCAATCGATTAAAAAAATATTA
Found at i:27628 original size:23 final size:23
Alignment explanation
Indices: 27602--27678 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
27592 TTCTACGCGA
27602 TCCTTCGGGATAATTCTACATGG
1 TCCTTCGGGATAATTCTACATGG
* * *
27625 TCCTTCGGGACATTTATACATGG
1 TCCTTCGGGATAATTCTACATGG
* * **
27648 TCTTTCGGGATAATACTATGTGG
1 TCCTTCGGGATAATTCTACATGG
27671 TCCTTCGG
1 TCCTTCGG
27679 AACATTCTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
TCCTTCGGGATAATTCTACATGG
Found at i:29245 original size:18 final size:19
Alignment explanation
Indices: 29222--29257 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29212 AATTTTAAGA
*
29222 TTAATTTT-TATTCGATTT
1 TTAATTTTAAATTCGATTT
29240 TTAATTTTAAATTCGATT
1 TTAATTTTAAATTCGATT
29258 CAATCGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
TTAATTTTAAATTCGATTT
Found at i:30026 original size:38 final size:38
Alignment explanation
Indices: 29984--30059 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
29974 ATATCAAGAA
* *
29984 TTTGGGATATAATTCTTGAGGGAGTTGTAAGATTACAC
1 TTTGGGATATAATTCTTAAGGGAGTTATAAGATTACAC
30022 TTTGGGATATAATTCTTAAGGGAGTTATAAGATTACAC
1 TTTGGGATATAATTCTTAAGGGAGTTATAAGATTACAC
30060 CTTGTTCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (38 bp):
TTTGGGATATAATTCTTAAGGGAGTTATAAGATTACAC
Found at i:30505 original size:30 final size:30
Alignment explanation
Indices: 30446--30533 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
30436 ATATTTTGTC
* * *
30446 TAGTGACTAAAGTGTAAGTTTTG-AAAGTT
1 TAGTGGCTAAAATGTAAATTTTGAAAAGTT
*
30475 TAGTGGCTAAAATATAAATTTTGAAAAGTT
1 TAGTGGCTAAAATGTAAATTTTGAAAAGTT
* *
30505 TAG-GGACCAAAATGT-AATTTTTAAAAGTT
1 TAGTGG-CTAAAATGTAAATTTTGAAAAGTT
30534 ATATATTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 34 0.68
30 16 0.32
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (30 bp):
TAGTGGCTAAAATGTAAATTTTGAAAAGTT
Found at i:32714 original size:22 final size:23
Alignment explanation
Indices: 32686--32742 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 23
32676 TTTAAGAATG
*
32686 GAGAAGAAATGATGAAGAAA-GAA
1 GAGAAGAAATGAAG-AGAAATGAA
32709 -AGAAGAAAATGAAGAGAAATGAA
1 GAGAAG-AAATGAAGAGAAATGAA
32732 GATGAAGAAAT
1 GA-GAAGAAAT
32743 AAAAAGTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 10 0.34
23 10 0.34
24 5 0.17
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (23 bp):
GAGAAGAAATGAAGAGAAATGAA
Found at i:34109 original size:3 final size:3
Alignment explanation
Indices: 34101--34134 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
34091 ATATTTCTCA
34101 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34135 ATTGAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34122 original size:14 final size:14
Alignment explanation
Indices: 34105--34133 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34095 TTCTCAAATA
34105 ATAATAATAATAAT
1 ATAATAATAATAAT
34119 ATAATAATAATAAT
1 ATAATAATAATAAT
34133 A
1 A
34134 AATTGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:34122 original size:17 final size:17
Alignment explanation
Indices: 34102--34134 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34092 TATTTCTCAA
34102 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
34119 ATAATAATAATAATAA
1 ATAATAATAATAATAA
34135 ATTGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Done.