Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001775.1 Hibiscus syriacus cultivar Beakdansim tig00003583_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: 52945
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:9302 original size:14 final size:14
Alignment explanation
Indices: 9285--9312 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9275 TCCTAATTAG
9285 AAGATCATGAAAAC
1 AAGATCATGAAAAC
9299 AAGATCATGAAAAC
1 AAGATCATGAAAAC
9313 CTCTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
AAGATCATGAAAAC
Found at i:9717 original size:53 final size:53
Alignment explanation
Indices: 9654--9767 Score: 228
Period size: 53 Copynumber: 2.2 Consensus size: 53
9644 CACCGAGCCA
9654 ATCGCGCGATTACCCAACGTTTTCAGATTCATAGCCGGGCGTGATTGTTCACG
1 ATCGCGCGATTACCCAACGTTTTCAGATTCATAGCCGGGCGTGATTGTTCACG
9707 ATCGCGCGATTACCCAACGTTTTCAGATTCATAGCCGGGCGTGATTGTTCACG
1 ATCGCGCGATTACCCAACGTTTTCAGATTCATAGCCGGGCGTGATTGTTCACG
9760 ATCGCGCG
1 ATCGCGCG
9768 CTATTCTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (53 bp):
ATCGCGCGATTACCCAACGTTTTCAGATTCATAGCCGGGCGTGATTGTTCACG
Found at i:14294 original size:139 final size:139
Alignment explanation
Indices: 14044--14313 Score: 486
Period size: 139 Copynumber: 1.9 Consensus size: 139
14034 TGGGGTATGC
* *
14044 TGATGGAGTAAAGGGGTATCACTTGTGGGATCCCACTGCCCTCAAAGTGATCATTAGCAGGGATG
1 TGATGGAGTAAAGGGGTATCACTTGTGGGATCCCACTGCCCGCAAAGTGATCATTAGCAGAGATG
14109 TTATCTTTGTAGAAGAAAAGATACAAAGAAAAGAAGACGATGATAGTGCTGAAAAGTCAGAGACT
66 TTATCTTTGTAGAAGAAAAGATACAAAGAAAAGAAGACGATGATAGTGCTGAAAAGTCAGAGACT
14174 ATAAGATGT
131 ATAAGATGT
*
14183 TGATGGAGTAAAGGGGTATCGCTTGTGGGATCCCACTGCCCGCAAAGTGATCATTAGCAGAGATG
1 TGATGGAGTAAAGGGGTATCACTTGTGGGATCCCACTGCCCGCAAAGTGATCATTAGCAGAGATG
* * *
14248 TTATCTTTGTAGAAGATAAGCTACAAAGAAAAGAAGATGATGATAGTGCTGAAAAGTCAGAGACT
66 TTATCTTTGTAGAAGAAAAGATACAAAGAAAAGAAGACGATGATAGTGCTGAAAAGTCAGAGACT
14313 A
131 A
14314 CACAGATACT
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 125 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (139 bp):
TGATGGAGTAAAGGGGTATCACTTGTGGGATCCCACTGCCCGCAAAGTGATCATTAGCAGAGATG
TTATCTTTGTAGAAGAAAAGATACAAAGAAAAGAAGACGATGATAGTGCTGAAAAGTCAGAGACT
ATAAGATGT
Found at i:16204 original size:21 final size:20
Alignment explanation
Indices: 16180--16221 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16170 GTCATACAAC
*
16180 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
16201 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
16221 T
1 T
16222 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:19618 original size:35 final size:35
Alignment explanation
Indices: 19572--19681 Score: 175
Period size: 35 Copynumber: 3.1 Consensus size: 35
19562 TGTCACGAAT
19572 AGTAAGGCCCTGAGCACAAAGCCGTGGAGCATGCA
1 AGTAAGGCCCTGAGCACAAAGCCGTGGAGCATGCA
19607 AGTAAGGCCCTGAGCACAAAGCCGTGGAGCATGCA
1 AGTAAGGCCCTGAGCACAAAGCCGTGGAGCATGCA
* * * * *
19642 AGTAAGGCACTGAGAACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGTGGAGCATGCA
19677 AGTAA
1 AGTAA
19682 TCTTCCTCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.35, C:0.25, G:0.30, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGTGGAGCATGCA
Found at i:19769 original size:24 final size:24
Alignment explanation
Indices: 19756--19842 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
19746 AAACATAATT
19756 CAAGTCAAGTATCATATCAGAATC
1 CAAGTCAAGTATCATATCAGAATC
* *
19780 CAAGTCATGTATCATATCAAAATC
1 CAAGTCAAGTATCATATCAGAATC
*
19804 CATGTCAA-TATCATATCAGAATC
1 CAAGTCAAGTATCATATCAGAATC
* *
19827 CAGGTCAGGTATCATA
1 CAAGTCAAGTATCATA
19843 ACATAATTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.36
24 35 0.64
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (24 bp):
CAAGTCAAGTATCATATCAGAATC
Found at i:25365 original size:21 final size:21
Alignment explanation
Indices: 25341--25397 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
25331 TCTGAGTTAC
*
25341 CCGCGACGGCCGCAACAACGT
1 CCGCGACGGCCGCAACAACAT
* * * *
25362 CCGCGACAGCTGCAATAGCAT
1 CCGCGACGGCCGCAACAACAT
*
25383 CCGCGACGACCGCAA
1 CCGCGACGGCCGCAA
25398 TCACGGTAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.40, G:0.26, T:0.07
Consensus pattern (21 bp):
CCGCGACGGCCGCAACAACAT
Found at i:50042 original size:13 final size:13
Alignment explanation
Indices: 50024--50061 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
50014 TCCAGCAGCA
50024 GAGAAGCCCAATG
1 GAGAAGCCCAATG
50037 GAGAAGCCCAATG
1 GAGAAGCCCAATG
* *
50050 GACAAGCTCAAT
1 GAGAAGCCCAAT
50062 TTTAATATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (13 bp):
GAGAAGCCCAATG
Done.