Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003142.1 Hibiscus syriacus cultivar Beakdansim tig00006613_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: 553945
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:520358 original size:21 final size:21
Alignment explanation
Indices: 520328--520385 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
520318 AAAATGAGTA
520328 TTTTAACAAGAAGTTTTGAAAC
1 TTTT-ACAAGAAGTTTTGAAAC
*
520350 TTTTACAAG-ATTTTTGAAAC
1 TTTTACAAGAAGTTTTGAAAC
*
520370 -TTTCCAAGACAGTTTT
1 TTTTACAAGA-AGTTTT
520386 CCAAAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.23
20 10 0.32
21 10 0.32
22 4 0.13
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (21 bp):
TTTTACAAGAAGTTTTGAAAC
Found at i:522928 original size:43 final size:43
Alignment explanation
Indices: 522860--522961 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
522850 CGTTCAAAGA
* *
522860 ATCTCTCGACGTCTTCAGCACAAAAATTTACATGCATTA-TTGG
1 ATCTCTCGACGTCTTCAGCACAAAAATTTACATACA-AACTTGG
* *
522903 ATCTCTCGACGTCTTCATTCA-AAAAATTTCCATACAAACTTGG
1 ATCTCTCGACGTCTTCA-GCACAAAAATTTACATACAAACTTGG
522946 AT-TGCTCGACGTCTTC
1 ATCT-CTCGACGTCTTC
522962 TATGCAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.04
43 48 0.92
44 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (43 bp):
ATCTCTCGACGTCTTCAGCACAAAAATTTACATACAAACTTGG
Found at i:528522 original size:12 final size:12
Alignment explanation
Indices: 528505--528529 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
528495 CATCTCATTC
528505 TTAAAAATCTTA
1 TTAAAAATCTTA
528517 TTAAAAATCTTA
1 TTAAAAATCTTA
528529 T
1 T
528530 CTTAGAGGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAAATCTTA
Found at i:538942 original size:33 final size:33
Alignment explanation
Indices: 538905--539012 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
538895 ACACGCTGGA
*
538905 CATCCGAGGCCATCCGACCGAGCTATGCGAGAG
1 CATCCGAGGCCATCCGACCGAGCTATGCGAGGG
* * *
538938 CATCCGAGGCCATCCGACCGCGGCTATCCAAGGG
1 CATCCGAGGCCATCCGACCG-AGCTATGCGAGGG
* ** * *
538972 AATCCGAGGGTAGCCGAGCGAGCTATGCGAGGG
1 CATCCGAGGCCATCCGACCGAGCTATGCGAGGG
539005 CATCCGAG
1 CATCCGAG
539013 CGAGCTATGC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 37 0.61
34 24 0.39
ACGTcount: A:0.23, C:0.31, G:0.33, T:0.12
Consensus pattern (33 bp):
CATCCGAGGCCATCCGACCGAGCTATGCGAGGG
Found at i:539011 original size:23 final size:23
Alignment explanation
Indices: 538976--539063 Score: 158
Period size: 23 Copynumber: 3.8 Consensus size: 23
538966 CAAGGGAATC
* *
538976 CGAGGGTAGCCGAGCGAGCTATG
1 CGAGGGCATCCGAGCGAGCTATG
538999 CGAGGGCATCCGAGCGAGCTATG
1 CGAGGGCATCCGAGCGAGCTATG
539022 CGAGGGCATCCGAGCGAGCTATG
1 CGAGGGCATCCGAGCGAGCTATG
539045 CGAGGGCATCCGAGCGAGC
1 CGAGGGCATCCGAGCGAGC
539064 GAGCAAGGGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.22, C:0.26, G:0.41, T:0.11
Consensus pattern (23 bp):
CGAGGGCATCCGAGCGAGCTATG
Found at i:539107 original size:29 final size:29
Alignment explanation
Indices: 539074--539129 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
539064 GAGCAAGGGT
*
539074 AGGTCGCCCGGAGAGCATGGCGACCTACA
1 AGGTCGCCCGAAGAGCATGGCGACCTACA
* * *
539103 AGGTCGTCTGAAGGGCATGGCGACCTA
1 AGGTCGCCCGAAGAGCATGGCGACCTA
539130 TGTGTTGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGAAGAGCATGGCGACCTACA
Found at i:543999 original size:17 final size:17
Alignment explanation
Indices: 543973--544013 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
543963 AGAGAATTGG
543973 AATCTATGAAGGAATGA
1 AATCTATGAAGGAATGA
* *
543990 AATCTGTGAATGAATGA
1 AATCTATGAAGGAATGA
544007 AATCTAT
1 AATCTAT
544014 CAGGAATTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (17 bp):
AATCTATGAAGGAATGA
Found at i:549394 original size:16 final size:16
Alignment explanation
Indices: 549373--549409 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
549363 TTTGGTTAAA
549373 GGAATAAAAGATAATT
1 GGAATAAAAGATAATT
*
549389 GGAATAAAAGATTATT
1 GGAATAAAAGATAATT
549405 GGAAT
1 GGAAT
549410 GTATATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (16 bp):
GGAATAAAAGATAATT
Found at i:549498 original size:38 final size:37
Alignment explanation
Indices: 549463--549533 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
549453 TACAAATTGT
*
549463 AAAATATTTATAT-ATTTTCTTTAAAAAAATTAAATTC
1 AAAATACTTATATAATTTT-TTTAAAAAAATTAAATTC
* * *
549500 ATAATACTTATATAATTTTTTTTACAAAATTAAA
1 AAAATACTTATATAATTTTTTTAAAAAAATTAAA
549534 AATATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (37 bp):
AAAATACTTATATAATTTTTTTAAAAAAATTAAATTC
Done.