Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008735.1 Hibiscus syriacus cultivar Beakdansim tig00111808_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: 58451
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:16774 original size:17 final size:16
Alignment explanation
Indices: 16752--16785 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16742 TAAAGACAGT
16752 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
16769 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
16785 A
1 A
16786 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:27014 original size:17 final size:16
Alignment explanation
Indices: 26992--27025 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
26982 TAAAGACAGT
26992 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
27009 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
27025 A
1 A
27026 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:27544 original size:24 final size:24
Alignment explanation
Indices: 27500--27549 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27490 ATAAAGAACC
*
27500 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
27524 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
27548 AA
1 AA
27550 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:28908 original size:24 final size:24
Alignment explanation
Indices: 28864--28913 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28854 ATAAAGAACC
*
28864 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
28888 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
28912 AA
1 AA
28914 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:34737 original size:64 final size:65
Alignment explanation
Indices: 34689--34848 Score: 261
Period size: 65 Copynumber: 2.5 Consensus size: 65
34679 TGCACTAAGA
* * *
34689 GTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCC-TGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAA-CCTTGAGTGCATCGATGCATGGTA
34752 T
65 T
*
34753 GTGCATCGATACATCAAATGTATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
34818 GTGCATCGATGCATCAAATGTATTCGATGTT
1 GTGCATCGATGCATCAAATGTATTCGATGTT
34849 CAACTAAATC
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
64 33 0.37
65 56 0.63
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
Found at i:34838 original size:19 final size:19
Alignment explanation
Indices: 34799--34838 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34789 AAAACCTTGA
***
34799 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAAT
34818 GTGCATCGATGCATCAAAT
1 GTGCATCGATGCATCAAAT
34837 GT
1 GT
34839 ATTCGATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATCAAAT
Found at i:34888 original size:65 final size:64
Alignment explanation
Indices: 34689--34896 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 64
34679 TGCACTAAGA
* * * *
34689 GTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCCT-GAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGTATTCGATG-TTTCATAAAA-CATCGAGTGCATCGATGCATGGTA
34752 T
64 T
* * *
34753 GTGCATCGATACATCAAATGTATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGTATTCGATG-TTTCATAAAACATCGAGTGCATCGATGCATGGTAT
* * * *
34818 GTGCATCGATGCATCAAATGTATTCGATG-TTCAACTAAATCATCG-GTTCATCGATGCATAGTT
1 GTGCATCGATGCATCAAATGTATTCGATGTTTC-A-TAAAACATCGAGTGCATCGATGCATGGTA
34881 T
64 T
*
34882 GATGCATCGGTGCAT
1 G-TGCATCGATGCAT
34897 GCCTTTGAAT
Statistics
Matches: 127, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
63 3 0.02
64 52 0.41
65 72 0.57
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGTATTCGATGTTTCATAAAACATCGAGTGCATCGATGCATGGTAT
Found at i:35369 original size:2 final size:2
Alignment explanation
Indices: 35362--35392 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35352 AATTGATTAA
35362 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
35393 GCTTAAGCTG
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:43011 original size:65 final size:64
Alignment explanation
Indices: 42877--43033 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 64
42867 TGCACTAAGA
* * * * * **
42877 GTGCATAGATGCATAAAATGCATTTGATGTTTTGAAAAAGGCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATATTTTCAAAAACCCTGAGTGCATCGATGCATGGTAT
*
42941 ATGCATCGATGCATCAAATGCATTCGATATTTTCATAAAACCCTGAGTGCATCGATGCAAT-GTA
1 GTGCATCGATGCATCAAATGCATTCGATATTTTCA-AAAACCCTGAGTGCATCGATGC-ATGGTA
43005 T
64 T
43006 GTGCATCGATGCATCAAATGCATTCGAT
1 GTGCATCGATGCATCAAATGCATTCGAT
43034 GTTCAATTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 29 0.35
65 51 0.62
66 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATATTTTCAAAAACCCTGAGTGCATCGATGCATGGTAT
Found at i:43076 original size:65 final size:65
Alignment explanation
Indices: 42919--43084 Score: 198
Period size: 65 Copynumber: 2.6 Consensus size: 65
42909 TGAAAAAGGC
* *
42919 TGAGTGCATCGATGCATGGTAT-ATGCATCGATGCATCAAATGCATTCGATATTTTCATAAAACC
1 TGAGTGCATCGATGCATAGTATGATGCATCGATGCATCAAATGCATTCGA-ATGTTCATAAAACC
*
42983 C
65 A
* *
42984 TGAGTGCATCGATGCA-ATGTATG-TGCATCGATGCATCAAATGCATTCG-ATGTTCAATTAAAT
1 TGAGTGCATCGATGCATA-GTATGATGCATCGATGCATCAAATGCATTCGAATGTTC-ATAAAAC
43046 CA
64 CA
* *
43048 TCGA-TGCATCGATGCATAGTTTGATGCATCGGTGCAT
1 T-GAGTGCATCGATGCATAGTATGATGCATCGATGCAT
43085 GCCTTTGAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
63 5 0.06
64 23 0.26
65 60 0.68
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (65 bp):
TGAGTGCATCGATGCATAGTATGATGCATCGATGCATCAAATGCATTCGAATGTTCATAAAACCA
Found at i:49200 original size:26 final size:26
Alignment explanation
Indices: 49171--49221 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
49161 ACAAATATAT
* **
49171 AAATGAAAATGTAGGGATGCAAGTGC
1 AAATGAAAATGCAAAGATGCAAGTGC
*
49197 AAATGTAAATGCAAAGATGCAAGTG
1 AAATGAAAATGCAAAGATGCAAGTG
49222 AATGCGTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.08, G:0.27, T:0.20
Consensus pattern (26 bp):
AAATGAAAATGCAAAGATGCAAGTGC
Found at i:49683 original size:14 final size:15
Alignment explanation
Indices: 49638--49685 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
49628 CAAAGAAAAG
49638 AAAA-AAAGAGTTAGT
1 AAAATAAAGAG-TAGT
*
49653 AAGAATAATGAGTAGT
1 AA-AATAAAGAGTAGT
49669 AAAATAAAG-GTAGT
1 AAAATAAAGAGTAGT
49683 AAA
1 AAA
49686 TTGTACCTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
16 8 0.28
17 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
AAAATAAAGAGTAGT
Found at i:53038 original size:18 final size:18
Alignment explanation
Indices: 53015--53059 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
53005 AGAAAATTAG
53015 TGAATATTTTTGAAAATT
1 TGAATATTTTTGAAAATT
* *
53033 TGAATAAATTTTGAATATT
1 TGAAT-ATTTTTGAAAATT
53052 T-AATATTT
1 TGAATATTT
53060 AAAATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TGAATATTTTTGAAAATT
Done.