Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003664.1 Hibiscus syriacus cultivar Beakdansim tig00007824_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: 50713
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8416 original size:20 final size:20
Alignment explanation
Indices: 8391--8445 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
8381 TAAAAGAATG
8391 AGAAATAGAGAGAAAACTAA
1 AGAAATAGAGAGAAAACTAA
** *
8411 AGAAATA-AGAGTGAAGTAA
1 AGAAATAGAGAGAAAACTAA
* *
8430 AGAAAAAGAGATAAAA
1 AGAAATAGAGAGAAAA
8446 AAGTGGGTGG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.65, C:0.02, G:0.22, T:0.11
Consensus pattern (20 bp):
AGAAATAGAGAGAAAACTAA
Found at i:15035 original size:22 final size:22
Alignment explanation
Indices: 15007--15057 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
14997 TAATGCTACG
15007 GCAATACCTCTCAGCATGAACT
1 GCAATACCTCTCAGCATGAACT
*
15029 GCAATACCTCTTAGCATGAACT
1 GCAATACCTCTCAGCATGAACT
15051 GCAATAC
1 GCAATAC
15058 TAGCCTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (22 bp):
GCAATACCTCTCAGCATGAACT
Found at i:29615 original size:385 final size:383
Alignment explanation
Indices: 28846--29615 Score: 1035
Period size: 382 Copynumber: 2.0 Consensus size: 383
28836 AGGAAGTTTT
* *
28846 TTATTGATGAAGAAGTGTTTCAATCCTTTGCGACAATCAAGAAGAAGCTAGTGAATGCCCCTGTT
1 TTATTGACGAAGAAGTGCTTCAATCCTTTGCGACAATCAAGAAGAAGCTAGTGAATG-CCC----
* * *
28911 ATTATGGCACCTGATTGAAATTTTCGCTATGAATTAATGTGTTATGTTAATGATTTTATTGGAGA
61 -TTATGGCACCTGATTGAAATTTTCGCTATGAATTAATATGTAATGCTAATGATTTTATTGGAGA
* *
28976 AGCAGTGCTAGGGCAACGAAAGGATAAAATGTTTCACGCGATAAATTATGCAAGTAGGACATTAA
125 AGCAGTACTAGGGCAACGAAAGGATAAAATGTTTCACGCGATAAATTATGAAAGTAGGACATTAA
* * * ** * *
29041 ATGAAGCTAGGTTAACTACATCGCAACTGAAAAGAAGTTGCTTATTATGGTGTTTGCTTTTGACT
190 ATGAAGCCAGGTTAACTACACCACAACTGAAAAGAAGTTGCTTATTATACTGTTTGCTTTCGACA
*
29106 AATTTCGTTCATATCTGGTGCGTGCGAAAGTGATCGTCTATACTGACCACTCAGCGCTGAAGCAT
255 AATTTCGTTCATATATGGTGCGT-CGAAAGTGATCGTCTATACTGACCACTCAGCGCTGAAGCAT
*
29171 TTATTTTCCAAGAAGGATACAAAACCTTGTTTAATTCGATGGGTACTTTTACTCCAAGAAGATTG
319 TTATTTTCCAAGAAGGATACAAAACCTCGTTTAATTCGATGGGTACTTTTACTCCAAGAAGATTG
*
29236 TTATTGACGAAGAAGTGCTTCAATCTTTTGCGACAATCAAGAAGAAGCTAGTGAATG-CC-TATG
1 TTATTGACGAAGAAGTGCTTCAATCCTTTGCGACAATCAAGAAGAAGCTAGTGAATGCCCTTATG
* * * * * * **
29299 GCATCTGATTGGAATTTTC-CATTTGAATTAATATGTAATGCTAGTGATTTTGTTGTAGGTGCAG
66 GCACCTGATTGAAATTTTCGC-TATGAATTAATATGTAATGCTAATGATTTTATTGGAGAAGCAG
* * *
29363 TACTAGGGCAACGAAAGGATAAAATGTTTCACGTGATACATTATGAAAGTAGGACATTAAATTAA
130 TACTAGGGCAACGAAAGGATAAAATGTTTCACGCGATAAATTATGAAAGTAGGACATTAAATGAA
* * * * * *
29428 GCCCAGGTTAACTGCACCATAATTGAAAAGAAGTTGTTTGTTGTACTGTTTGCTTTCGACAAATT
195 G-CCAGGTTAACTACACCACAACTGAAAAGAAGTTGCTTATTATACTGTTTGCTTTCGACAAATT
* *
29493 TTGTTCATATATATGGTGGACGT-GAAAGTGATTGTCTATACTGACCACTCAGCGCTGAAGCATT
259 TCGTTC--ATATATGGT-G-CGTCGAAAGTGATCGTCTATACTGACCACTCAGCGCTGAAGCATT
* * * *
29557 TATTTTCCAAGAATGATAGAATACCTCGTTTAATTTGATGGGTACTTTTACTCCAAGAA
320 TATTTTCCAAGAAGGATACAAAACCTCGTTTAATTCGATGGGTACTTTTACTCCAAGAA
29616 TTTGATATTG
Statistics
Matches: 334, Mismatches: 40, Indels: 17
0.85 0.10 0.04
Matches are distributed among these distances:
381 1 0.00
382 116 0.35
383 55 0.16
385 102 0.31
386 1 0.00
387 3 0.01
388 2 0.01
390 54 0.16
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (383 bp):
TTATTGACGAAGAAGTGCTTCAATCCTTTGCGACAATCAAGAAGAAGCTAGTGAATGCCCTTATG
GCACCTGATTGAAATTTTCGCTATGAATTAATATGTAATGCTAATGATTTTATTGGAGAAGCAGT
ACTAGGGCAACGAAAGGATAAAATGTTTCACGCGATAAATTATGAAAGTAGGACATTAAATGAAG
CCAGGTTAACTACACCACAACTGAAAAGAAGTTGCTTATTATACTGTTTGCTTTCGACAAATTTC
GTTCATATATGGTGCGTCGAAAGTGATCGTCTATACTGACCACTCAGCGCTGAAGCATTTATTTT
CCAAGAAGGATACAAAACCTCGTTTAATTCGATGGGTACTTTTACTCCAAGAAGATTG
Found at i:30190 original size:77 final size:81
Alignment explanation
Indices: 30104--30256 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 81
30094 AAATAAAATA
* *
30104 TTATTTAATTAATTCAAATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACA-AATTTTA
1 TTATATAATTAATTCAAATTAAATATATCAATTAAAAGACTTATAAACTAAATTACATAATTTTA
*
30165 ATGTTTATTTAAAAAC
66 ATGCTTATTTAAAAAC
* * * * **
30181 TTATATAATTATTTCAAATTATATATATCAATTAAAAGAGTTGTAAACTAAATTACATTCTTTTA
1 TTATATAATTAATTCAAATTAAATATATCAATTAAAAGACTTATAAACTAAATTACATAATTTTA
30246 ATGCTTATTTA
66 ATGCTTATTTA
30257 CTATATTCAG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 24 0.38
78 1 0.02
79 3 0.05
80 20 0.32
81 15 0.24
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (81 bp):
TTATATAATTAATTCAAATTAAATATATCAATTAAAAGACTTATAAACTAAATTACATAATTTTA
ATGCTTATTTAAAAAC
Found at i:38840 original size:18 final size:18
Alignment explanation
Indices: 38817--38863 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
38807 CAAGTCAATG
38817 GAAGGTGAAGAGGAAGTT
1 GAAGGTGAAGAGGAAGTT
38835 GAAGGTGAAGAGGAAGTT
1 GAAGGTGAAGAGGAAGTT
38853 GAAGGTGAAGA
1 GAAGGTGAAGA
38864 AGAAAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (18 bp):
GAAGGTGAAGAGGAAGTT
Found at i:39862 original size:42 final size:42
Alignment explanation
Indices: 39800--39882 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
39790 AAAAGATATA
*
39800 AATCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAT
1 AATCTTAGGGAATAAGTTGGGTAATGCTGGTAATAACTCCAT
* * *
39842 AATCTTAGGGAATAATTTGGGTGATGTTGGTAATAACTCCA
1 AATCTTAGGGAATAAGTTGGGTAATGCTGGTAATAACTCCA
39883 ACATAGTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (42 bp):
AATCTTAGGGAATAAGTTGGGTAATGCTGGTAATAACTCCAT
Found at i:41804 original size:20 final size:20
Alignment explanation
Indices: 41775--41838 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
41765 GGTAATACCT
*
41775 ATACTACTAAGGCAGTATCG
1 ATACTGCTAAGGCAGTATCG
41795 ATACTGCTAAGGCAGTATCG
1 ATACTGCTAAGGCAGTATCG
41815 ATACTGCTAAGGCAGTATCG
1 ATACTGCTAAGGCAGTATCG
41835 ATAC
1 ATAC
41839 CGTGCTTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (20 bp):
ATACTGCTAAGGCAGTATCG
Found at i:41882 original size:18 final size:18
Alignment explanation
Indices: 41859--41893 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41849 GAACCTCAAA
41859 ATGGTACCGATACCATGC
1 ATGGTACCGATACCATGC
*
41877 ATGGTATCGATACCATG
1 ATGGTACCGATACCATG
41894 TTAATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (18 bp):
ATGGTACCGATACCATGC
Found at i:43455 original size:15 final size:15
Alignment explanation
Indices: 43431--43461 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43421 AAAAAAGAAG
*
43431 AAGATCAAGAAAATA
1 AAGATAAAGAAAATA
43446 AAGATAAAGAAAATA
1 AAGATAAAGAAAATA
43461 A
1 A
43462 GGAAATGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.13, T:0.13
Consensus pattern (15 bp):
AAGATAAAGAAAATA
Found at i:47527 original size:22 final size:21
Alignment explanation
Indices: 47477--47536 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
47467 ATTTTGTGCA
47477 CTTAGTATCGATATTGTTCAT
1 CTTAGTATCGATATTGTTCAT
* *
47498 -ATAGTATCGATATTGTTCTT
1 CTTAGTATCGATATTGTTCAT
*
47518 GCTTAGTATCGATACTGTT
1 -CTTAGTATCGATATTGTT
47537 TATCCAGTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 18 0.55
22 15 0.45
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (21 bp):
CTTAGTATCGATATTGTTCAT
Done.