Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002013.1 Hibiscus syriacus cultivar Beakdansim tig00004113_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: 71026
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:8035 original size:30 final size:30
Alignment explanation
Indices: 8001--8061 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
7991 GCCGAACAGT
*
8001 ATGAAAATATAAGGATACAAGGGATGTATA
1 ATGAAAATATAAGGATACAAAGGATGTATA
8031 ATGAAAATATAAGGATACAAAGGATGTATA
1 ATGAAAATATAAGGATACAAAGGATGTATA
8061 A
1 A
8062 ATGTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.23
Consensus pattern (30 bp):
ATGAAAATATAAGGATACAAAGGATGTATA
Found at i:13002 original size:54 final size:54
Alignment explanation
Indices: 12917--13070 Score: 220
Period size: 54 Copynumber: 2.9 Consensus size: 54
12907 ACCTTTTCTT
* * * * *
12917 ACAGGTATCCCACGATATTGCAAGATAGACATGATTTTCAAGTGCAAGAGCATG
1 ACAGGTATCCGATGTTATTACAAGACAGACATGATTTTCAAGTGCAAGAGCATG
* * *
12971 ACAGGTATCCTATGTTATTACAGGACAGACATGATTTTCAAGCT-CAAGAGCGTG
1 ACAGGTATCCGATGTTATTACAAGACAGACATGATTTTCAAG-TGCAAGAGCATG
13025 ACAGGTATCCGATGTTATTACAAGACAGACATGATTTTCAAGTGCA
1 ACAGGTATCCGATGTTATTACAAGACAGACATGATTTTCAAGTGCA
13071 TGAGAGTGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 87 0.98
55 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (54 bp):
ACAGGTATCCGATGTTATTACAAGACAGACATGATTTTCAAGTGCAAGAGCATG
Found at i:20995 original size:21 final size:21
Alignment explanation
Indices: 20955--20995 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20945 AGCACGGCGA
**
20955 GCTTGACCTTCTTCTTCTTGT
1 GCTTGACCTTCTTCGGCTTGT
*
20976 GCTTGATCTTCTTCGGCTTG
1 GCTTGACCTTCTTCGGCTTG
20996 GTGTAAGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.27, G:0.20, T:0.49
Consensus pattern (21 bp):
GCTTGACCTTCTTCGGCTTGT
Found at i:21688 original size:25 final size:25
Alignment explanation
Indices: 21660--21707 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21650 TAATATTATA
*
21660 TAAATATTTTTTAAATTATTTAAGG
1 TAAATATTTATTAAATTATTTAAGG
* *
21685 TAAATATTTATTAATTTTTTTAA
1 TAAATATTTATTAAATTATTTAA
21708 TTAATTGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TAAATATTTATTAAATTATTTAAGG
Found at i:31342 original size:2 final size:2
Alignment explanation
Indices: 31335--31374 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
31325 GAACTCTCCT
*
31335 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31375 ATTCCCTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39767 original size:2 final size:2
Alignment explanation
Indices: 39762--39790 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39752 CCCATTGTCA
39762 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 A
39791 GTAATCTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44482 original size:2 final size:2
Alignment explanation
Indices: 44475--44521 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
44465 GGTATTGGAT
44475 TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44516 TC TC TC
1 TC TC TC
44522 CTTGCCGACC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:46335 original size:15 final size:15
Alignment explanation
Indices: 46315--46350 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
46305 AATTGGTTTT
46315 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
**
46330 CTGGAATTTGAATTA
1 CTGGAAAATGAATTA
46345 CTGGAA
1 CTGGAA
46351 CTAGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (15 bp):
CTGGAAAATGAATTA
Found at i:46739 original size:23 final size:23
Alignment explanation
Indices: 46710--46754 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
46700 AGTGTTATAT
46710 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
46733 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
46755 AAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:46760 original size:23 final size:23
Alignment explanation
Indices: 46711--46760 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
46701 GTGTTATATT
**
46711 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
46734 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
46757 ATAT
1 ATAT
46761 AATATAACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:46952 original size:43 final size:43
Alignment explanation
Indices: 46870--46973 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
46860 CCAGAAAATC
* *
46870 AATTACGTGAAACAAACA-GGAGAAAATATTTTCCAAAAAACG
1 AATTACGTGAAACAAACACGGAGAAAACATTTTCCAAAAAACA
* * *
46912 AATTACGTGAAACAAACACGGGGAAAACATTTTTCAAAAAATA
1 AATTACGTGAAACAAACACGGAGAAAACATTTTCCAAAAAACA
* *
46955 AATTACATAAAACAAACAC
1 AATTACGTGAAACAAACAC
46974 AAAAATTCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 18 0.33
43 36 0.67
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (43 bp):
AATTACGTGAAACAAACACGGAGAAAACATTTTCCAAAAAACA
Found at i:56626 original size:17 final size:17
Alignment explanation
Indices: 56602--56642 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
56592 TACCCTTTCA
56602 TTAA-TTTTTTTTATAT
1 TTAATTTTTTTTTATAT
*
56618 TTAATTTTTTTTTATTT
1 TTAATTTTTTTTTATAT
56635 TTAATTTT
1 TTAATTTT
56643 GTAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTAATTTTTTTTTATAT
Found at i:58434 original size:17 final size:18
Alignment explanation
Indices: 58401--58434 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58391 CCGTTACTAG
58401 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
58419 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
58435 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:62256 original size:2 final size:2
Alignment explanation
Indices: 62247--62294 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
62237 AAAAAATTAT
62247 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62288 TA TA TA T
1 TA TA TA T
62295 CCCTCAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62929 original size:17 final size:17
Alignment explanation
Indices: 62907--62952 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
62897 GTGAAAATAA
*
62907 ATTAAGTAGGTTAAATT
1 ATTAAGTGGGTTAAATT
62924 ATTAAGTGGGTTAAATT
1 ATTAAGTGGGTTAAATT
62941 ATTAAGTGGGTT
1 ATTAAGTGGGTT
62953 TTTATAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (17 bp):
ATTAAGTGGGTTAAATT
Found at i:64057 original size:76 final size:76
Alignment explanation
Indices: 63931--64079 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 76
63921 TATGGACTTC
63931 TTTTATATCAATTGCATTTGTGAAATTTAAGAGAAAGAATGATTGAATGTTAGCGTAGGGACCAA
1 TTTTATATCAATTGCATTTGTGAAATTTAAGAGAAAGAATGATTGAATGTTAGCGTAGGGACCAA
63996 TTTTACCAATT
66 TTTTACCAATT
* *
64007 TTTTATATCATTTGCTTTTGTGAAATTTAAGAGAAAGAATGATTGAATGTTAGCGTAGGGACCAA
1 TTTTATATCAATTGCATTTGTGAAATTTAAGAGAAAGAATGATTGAATGTTAGCGTAGGGACCAA
64072 TTTTACCA
66 TTTTACCA
64080 TTAAGCATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (76 bp):
TTTTATATCAATTGCATTTGTGAAATTTAAGAGAAAGAATGATTGAATGTTAGCGTAGGGACCAA
TTTTACCAATT
Done.