Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007612.1 Hibiscus syriacus cultivar Beakdansim tig00022664_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: 40890
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4105 original size:83 final size:83
Alignment explanation
Indices: 4006--4219 Score: 252
Period size: 83 Copynumber: 2.6 Consensus size: 83
3996 ATGTTTCTTA
*
4006 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAA-TGCCAAAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACT-CCAAAATAGGGATCA
* * *
4070 TTTATGGTGGTACTTTTCT
65 TTTATAGTGGCACTTTTCC
* * * * **
4089 AATAAACGCCGTGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCAT
1 AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
* *
4154 TTATATTGGCATTTTTCC
66 TTATAGTGGCACTTTTCC
* * * *
4172 AACAAATGTCGCGATAGAGTAGTACTTTAA-TGGTGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTAACT-GCGTTTTTATACAAAC
4220 ACGTAATAGG
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
83 108 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (83 bp):
AACAAACGCCGCGATAGAGTAGTACTTTAACTGCGTTTTTATACAAACTCCAAAATAGGGATCAT
TTATAGTGGCACTTTTCC
Found at i:4560 original size:38 final size:40
Alignment explanation
Indices: 4469--4574 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
4459 CTTGTCTTTT
*
4469 GTGGCGCTTTTAAACAAACGCCGCAATAAATCAGTGCAGTA
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-A
* *
4510 GTGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-A
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
*
4548 GTGGTGTTTTTAAATACAAACGCCGCA
1 GTGGCGTTTTT-AA-ACAAACGCCGCA
4575 TGTTTTGGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 11 0.19
39 2 0.03
40 13 0.22
41 33 0.56
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
Found at i:6017 original size:22 final size:22
Alignment explanation
Indices: 5992--6046 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
5982 TTTGTAAAGC
5992 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
6014 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
6036 CTTCTTGATCC
1 CTTCTTGATCC
6047 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:8818 original size:62 final size:62
Alignment explanation
Indices: 8721--8846 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
8711 ACCCGTTTTT
8721 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
8783 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
8845 AT
1 AT
8847 GATACGTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
Found at i:23299 original size:83 final size:83
Alignment explanation
Indices: 23200--23414 Score: 243
Period size: 83 Copynumber: 2.6 Consensus size: 83
23190 GTGTTTCTTA
* * *
23200 AACAAACGCCGCGATAGAGTAGTACTTTAGCTGTGTTTTTATACAAA-TGCCAAAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACT-CCAAAATAGGGATCA
* * *
23264 TTTATGGTGGTACTTTTCT
65 TTTATAGTGGCACTTTTCC
* * * **
23283 AATAAACGCCGTGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCAT
1 AACAAACGCCGCGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCAAAATAGGGATCAT
* *
23348 TTATATTGGCATTTTTCC
66 TTATAGTGGCACTTTTCC
* * ** *
23366 AACAAATGTCGCGATAGAGTAGTACTTTAATGGCCGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTAGCGG-CGTTTTTATACAAAC
23415 ACCGTAATAG
Statistics
Matches: 110, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
83 95 0.86
84 15 0.14
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (83 bp):
AACAAACGCCGCGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCAAAATAGGGATCAT
TTATAGTGGCACTTTTCC
Found at i:23757 original size:38 final size:40
Alignment explanation
Indices: 23666--23771 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
23656 CTTGTCTTTT
*
23666 GTGGCGCTTTTAAACAAACGCCGCAATAAATCAGTGCAGTA
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-A
* *
23707 GTGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-A
1 GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
*
23745 GTGGTGTTTTTAAATACAAACGCCGCA
1 GTGGCGTTTTT-AA-ACAAACGCCGCA
23772 TGTTTTGGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 11 0.19
39 2 0.03
40 13 0.22
41 33 0.56
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
GTGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGA
Found at i:25220 original size:22 final size:22
Alignment explanation
Indices: 25195--25249 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
25185 TTTGTAAAGC
25195 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
25217 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
25239 CTTCTTGATCC
1 CTTCTTGATCC
25250 GTCTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:28025 original size:62 final size:62
Alignment explanation
Indices: 27928--28053 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
27918 ACCCGTTTTT
27928 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
27990 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
28052 AT
1 AT
28054 GATACGTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATGATGTATTTATGTTAATGCATTTCCTA
Done.