Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000197.1 Hibiscus syriacus cultivar Beakdansim tig00000350_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: 55879
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1746 original size:21 final size:21
Alignment explanation
Indices: 1720--1760 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1710 CTTTAACTCC
1720 CATTGACCCCTTCTTCTTCTT
1 CATTGACCCCTTCTTCTTCTT
1741 CATTGACCCCTTCTTCTTCT
1 CATTGACCCCTTCTTCTTCT
1761 CTCCTAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.39, G:0.05, T:0.46
Consensus pattern (21 bp):
CATTGACCCCTTCTTCTTCTT
Found at i:15085 original size:74 final size:74
Alignment explanation
Indices: 14944--15090 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 74
14934 GGGTACAAAT
* * * *
14944 AAAATTTCAGGGTAGATACCATTCATAAAATAGGTAACTAATCGAAGAAAACTTAAATTTCATGG
1 AAAATTTCAAGGTAGACACCATTCATAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGG
*
15009 TGGGCACGA
66 TGGACACGA
* * * ** *
15018 AAAATTTCAAGGTGGACACCA-TCAGTAAAATAAGTAATTAATCGAAGAAAATTTGGATTTTAAG
1 AAAATTTCAAGGTAGACACCATTCA-TAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAG
15082 GTGGACACG
65 GTGGACACG
15091 TGCCCACCCC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 3 0.05
74 58 0.95
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (74 bp):
AAAATTTCAAGGTAGACACCATTCATAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGG
TGGACACGA
Found at i:23750 original size:2 final size:2
Alignment explanation
Indices: 23743--23779 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23733 ATTTAAATAC
23743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23780 GTAGTTTACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25372 original size:20 final size:20
Alignment explanation
Indices: 25347--25418 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
25337 CAAATGAAAT
25347 GATCGATCCCTTTTCAAAAG
1 GATCGATCCCTTTTCAAAAG
* **
25367 GATCGATCCCTCTGGAGAAAG
1 GATCGATCCCTTTTCA-AAAG
* **
25388 AATTAATCCCTTTTCAAAAG
1 GATCGATCCCTTTTCAAAAG
25408 GATCGATCCCT
1 GATCGATCCCT
25419 CGAGGAAAAT
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (20 bp):
GATCGATCCCTTTTCAAAAG
Found at i:25432 original size:21 final size:21
Alignment explanation
Indices: 25403--25442 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25393 ATCCCTTTTC
25403 AAAAGGATC-GATCCCTCGAGG
1 AAAAGGATCAG-TCCCTCGAGG
*
25424 AAAATGATCAGTCCCTCGA
1 AAAAGGATCAGTCCCTCGA
25443 AAGAAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAAGGATCAGTCCCTCGAGG
Found at i:25439 original size:41 final size:41
Alignment explanation
Indices: 25342--25439 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
25332 TCATTCAAAT
*
25342 GAAATGATC-GATCCCTTTTCAAAAGGATCGATCCCTCTGGA
1 GAAATGATCAG-TCCCTTTTCAAAAGGATCGATCCCTCAGGA
* *
25383 GAAA-GAATTAATCCCTTTTCAAAAGGATCGATCCCTCGAGGA
1 GAAATG-ATCAGTCCCTTTTCAAAAGGATCGATCCCTC-AGGA
25425 -AAATGATCAGTCCCT
1 GAAATGATCAGTCCCT
25440 CGAAAGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
40 1 0.02
41 43 0.90
42 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (41 bp):
GAAATGATCAGTCCCTTTTCAAAAGGATCGATCCCTCAGGA
Found at i:29390 original size:21 final size:21
Alignment explanation
Indices: 29357--29396 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29347 TTTTACGTGG
*
29357 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
29378 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
29397 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:34017 original size:22 final size:22
Alignment explanation
Indices: 33992--34034 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33982 GAGGAAAAAG
* *
33992 ACAATGAAAATAAATAAATAAA
1 ACAAAGAAAACAAATAAATAAA
*
34014 ACAAAGAAAACACATAAATAA
1 ACAAAGAAAACAAATAAATAA
34035 CACGAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (22 bp):
ACAAAGAAAACAAATAAATAAA
Found at i:34402 original size:23 final size:23
Alignment explanation
Indices: 34364--34410 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
34354 AAATAATAGT
*
34364 AATAATAAGTATTAAAATAAAAAA
1 AATAATAAGTAAT-AAATAAAAAA
34388 AATAAT-AGTAATAAATAAAAAA
1 AATAATAAGTAATAAATAAAAAA
34410 A
1 A
34411 GAAATAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 5 0.23
24 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AATAATAAGTAATAAATAAAAAA
Found at i:34457 original size:2 final size:2
Alignment explanation
Indices: 34450--34480 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34440 AATCAAAGTA
34450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34481 ATAAAGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35234 original size:17 final size:17
Alignment explanation
Indices: 35209--35243 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35199 AGAACTTAGT
35209 GATAAGAAGCTAGTTAA
1 GATAAGAAGCTAGTTAA
*
35226 GATATGAAGCTAGTTAA
1 GATAAGAAGCTAGTTAA
35243 G
1 G
35244 CCTACTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (17 bp):
GATAAGAAGCTAGTTAA
Done.