Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007257.1 Hibiscus syriacus cultivar Beakdansim tig00019237_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: 49448
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:5258 original size:25 final size:28
Alignment explanation
Indices: 5221--5283 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
5211 GAGGTACTTG
*
5221 TATTATTT-TAAAATT-TATTCTT-TA-
1 TATTTTTTATAAAATTGTATTCTTATAC
5245 TATTTTTTATAAAATTGTATTCTTATAC
1 TATTTTTTATAAAATTGTATTCTTATAC
*
5273 CATTTTTTATA
1 TATTTTTTATA
5284 TGAAAATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 7 0.21
25 7 0.21
26 7 0.21
27 2 0.06
28 10 0.30
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTTTTTATAAAATTGTATTCTTATAC
Found at i:12722 original size:31 final size:31
Alignment explanation
Indices: 12684--12747 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
12674 TGTTCAATGG
12684 CAGACCAGAATTTTAAAAACCTTTATGACAC
1 CAGACCAGAATTTTAAAAACCTTTATGACAC
*
12715 CAGACCAGACTTTTAAAAACCTTTATGACAC
1 CAGACCAGAATTTTAAAAACCTTTATGACAC
12746 CA
1 CA
12748 TGTCTCACAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (31 bp):
CAGACCAGAATTTTAAAAACCTTTATGACAC
Found at i:23401 original size:42 final size:42
Alignment explanation
Indices: 23354--23515 Score: 215
Period size: 42 Copynumber: 3.9 Consensus size: 42
23344 AGCCCAGGAA
* *
23354 AACTGTAAGGTTTATCCTT-GCACACAGCAAAGGGACTTGGAG
1 AACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACATGGAG
* *
23396 AACTGTAAGGCTTACCCTT-GCAAACAGCAAAGGGACCTGGTA-
1 AACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACATGG-AG
23438 AACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACAT-GAG
1 AACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACATGGAG
*
23479 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGAC
1 -AACTGTAAGGCTTACCTTCGCACACAGCAAAGGGAC
23516 CTGGTAATAC
Statistics
Matches: 109, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
40 1 0.01
41 5 0.05
42 102 0.94
43 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
AACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACATGGAG
Found at i:23461 original size:84 final size:84
Alignment explanation
Indices: 23353--23522 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 84
23343 GAGCCCAGGA
* *
23353 AAACTGTAAGGTTTATCCTTGCACACAGCAAAGGGACTTG-GAGAACTGTAAGGCTTACCCTT-G
1 AAACTGTAAGGCTTATCCTTGCACACAGCAAAGGGACATGAGA-AACTGTAAGGCTTA-CCTTCG
*
23416 CAAACAGCAAAGGGACCTGGT
64 CAAACAACAAAGGGACCTGGT
23437 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACATGAGAAACTGTAAGGCTTACCTTCGC
1 AAACTGTAAGGCTTATCCTT-GCACACAGCAAAGGGACATGAGAAACTGTAAGGCTTACCTTCGC
*
23501 ACACAACAAAGGGACCTGGT
65 AAACAACAAAGGGACCTGGT
23521 AA
1 AA
23523 TACTTCCTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
83 8 0.10
84 69 0.87
85 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (84 bp):
AAACTGTAAGGCTTATCCTTGCACACAGCAAAGGGACATGAGAAACTGTAAGGCTTACCTTCGCA
AACAACAAAGGGACCTGGT
Found at i:24486 original size:28 final size:28
Alignment explanation
Indices: 24455--24516 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
24445 TTAATAGCAC
* *
24455 CATTTTGAAATTAATTACCAAAATAACA
1 CATTTTCAAAATAATTACCAAAATAACA
* *
24483 CATTTTCAAAATAATTACTAAAATATCA
1 CATTTTCAAAATAATTACCAAAATAACA
*
24511 CTTTTT
1 CATTTT
24517 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.39
Consensus pattern (28 bp):
CATTTTCAAAATAATTACCAAAATAACA
Found at i:31833 original size:17 final size:17
Alignment explanation
Indices: 31802--31834 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31792 CATTACAATG
31802 AAAATATAATATAATAA
1 AAAATATAATATAATAA
31819 AAAATTATAAT-TAATA
1 AAAA-TATAATATAATA
31835 TTTTTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATAATATAATAA
Done.