Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007517.1 Hibiscus syriacus cultivar Beakdansim tig00020943_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: 77156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2214 original size:75 final size:75
Alignment explanation
Indices: 2068--2217 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
2058 GTTGAGCATA
* *** * ** *
2068 AATAAAATTTCAGGGTGGACACCATTTGTAAAATATGTGACTAATCGAAGAAAATTTATCTTTGA
1 AATAAAATTTCAGGATGGACACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
2133 GGGTAGACAC
66 GGGTAGACAC
*
2143 AATAAAATTTCAGGATGGGCACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
1 AATAAAATTTCAGGATGGACACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
*
2208 GTGTAGACAC
66 GGGTAGACAC
2218 GTGCCCACCT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (75 bp):
AATAAAATTTCAGGATGGACACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
GGGTAGACAC
Found at i:3593 original size:17 final size:17
Alignment explanation
Indices: 3553--3600 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3543 ATGTCCTTTA
3553 ATAATA-ATATTCA-AT
1 ATAATATATATTCACAT
*
3568 ATCATATATATTCACAT
1 ATAATATATATTCACAT
*
3585 TTAATATATATTCACA
1 ATAATATATATTCACA
3601 CTGAATTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 16 0.57
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATATATTCACAT
Found at i:7609 original size:16 final size:17
Alignment explanation
Indices: 7577--7609 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7567 AATTTCTAAT
7577 TTTTGGTATCCAAATTC
1 TTTTGGTATCCAAATTC
*
7594 TTTTGGT-TCCATATTC
1 TTTTGGTATCCAAATTC
7610 ATTAGTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (17 bp):
TTTTGGTATCCAAATTC
Found at i:10134 original size:65 final size:64
Alignment explanation
Indices: 9951--10142 Score: 205
Period size: 65 Copynumber: 3.0 Consensus size: 64
9941 AGTGCATCGG
* * *
9951 TGCATTCGATGTTTCA-AAATAGCCA-GAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAA
1 TGCATTCGATGTTTCATAAA-A-TCATTAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAA
10014 A
64 A
* *
10015 TGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATGGTAT-GTGCATCGATGCATGAA
1 TGCATTCGATG-TTTCATAAAATCATTAGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAA
10079 A
64 A
* * * *
10080 TGCATTCGATG-TTCAATTTAATTCATT-GTGCATCGATGCATGGATTGGTACATCGGTGCATCA
1 TGCATTCGATGTTTC-A-TAAAATCATTAGTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
10143 CTTTGATAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
63 3 0.03
64 30 0.28
65 72 0.66
66 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
TGCATTCGATGTTTCATAAAATCATTAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAA
Found at i:17962 original size:2 final size:2
Alignment explanation
Indices: 17957--17981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17947 AACGAAACTG
17957 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
17982 CAACTAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28932 original size:92 final size:94
Alignment explanation
Indices: 28753--28935 Score: 239
Period size: 92 Copynumber: 2.0 Consensus size: 94
28743 TCTAAGGATG
* *
28753 ATTAGAGTTAAATTTAAAATTTATTAAAAAAATATTTTTCGTGTTTATAATATTTGTCCTTTACC
1 ATTAGAGTTAAATTTAAAATTTATCAAAAAAATAATTTTCGTGTTTATAATATTTGTCCTTTACC
28818 GAATTGAACATGAATATCAACAATATACA
66 GAATTGAACATGAATATCAACAATATACA
* * * * *
28847 ATTAGGGTTAAATTTAGAATTTGTCAAGAAAAGTTAATTTTCGTG-TT-T-ATATTTGTCTTTTA
1 ATTAGAGTTAAATTTAAAATTTATCAA-AAAA-ATAATTTTCGTGTTTATAATATTTGTCCTTTA
* *
28909 -CGGATTGAACGTGAATATCAACAATAT
64 CCGAATTGAACATGAATATCAACAATAT
28936 CTAGAGTATA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
92 25 0.32
93 13 0.17
94 24 0.31
95 6 0.08
96 10 0.13
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (94 bp):
ATTAGAGTTAAATTTAAAATTTATCAAAAAAATAATTTTCGTGTTTATAATATTTGTCCTTTACC
GAATTGAACATGAATATCAACAATATACA
Found at i:42087 original size:2 final size:2
Alignment explanation
Indices: 42080--42118 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42070 TACCTTCTGA
42080 AT AT AT AT 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 AT AT AT AT A
42119 CAATACCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48872 original size:21 final size:21
Alignment explanation
Indices: 48848--48901 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
48838 CATACCCCAA
* *
48848 GTATCGATATTCCTTGAAGAG
1 GTATCGATACTCCTCGAAGAG
48869 GTATCGATACTCCTCGAAGAG
1 GTATCGATACTCCTCGAAGAG
48890 GTATCGATACTC
1 GTATCGATACTC
48902 ACCCTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCCTCGAAGAG
Found at i:51590 original size:3 final size:3
Alignment explanation
Indices: 51582--51614 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
51572 TTTAATTAAA
51582 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51615 TGAAAACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:60880 original size:2 final size:2
Alignment explanation
Indices: 60873--60911 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
60863 TTTAACAGAA
60873 AT AT AT AT 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 AT AT AT AT A
60912 GATTTCAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62988 original size:31 final size:31
Alignment explanation
Indices: 62931--62989 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
62921 TTCAAGTTTT
*
62931 TTTGAGTTTAAGTCGAGCTTCAAATTTTGAC
1 TTTGAGTTTAAGTCGAGCTTAAAATTTTGAC
* *
62962 TTTGAGTTTGAGTTGA-CTTAACAATTTT
1 TTTGAGTTTAAGTCGAGCTTAA-AATTTT
62990 AAGTTTGCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
TTTGAGTTTAAGTCGAGCTTAAAATTTTGAC
Found at i:68267 original size:5 final size:5
Alignment explanation
Indices: 68257--68281 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
68247 AGTTATAAAC
68257 TGGGG TGGGG TGGGG TGGGG TGGGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG
68282 ATGACAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
TGGGG
Found at i:75060 original size:22 final size:25
Alignment explanation
Indices: 75034--75089 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
75024 GTGATCCTAC
75034 ACTTGCC-ACAA-A-CATTAACTCT
1 ACTTGCCGACAACATCATTAACTCT
*
75056 ACTTGCCTCGGCAACATCATTAACTCT
1 ACTTG-C-CGACAACATCATTAACTCT
75083 ACTTGCC
1 ACTTGCC
75090 TCGACAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.18
23 1 0.04
24 1 0.04
25 4 0.14
26 2 0.07
27 15 0.54
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (25 bp):
ACTTGCCGACAACATCATTAACTCT
Found at i:75081 original size:27 final size:27
Alignment explanation
Indices: 75046--75097 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
75036 TTGCCACAAA
*
75046 CATTAACTCTACTTGCCTCGGCAACAT
1 CATTAACTCTACTTGCCTCGACAACAT
75073 CATTAACTCTACTTGCCTCGACAAC
1 CATTAACTCTACTTGCCTCGACAAC
75098 TTCACTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.35, G:0.10, T:0.29
Consensus pattern (27 bp):
CATTAACTCTACTTGCCTCGACAACAT
Found at i:75377 original size:37 final size:36
Alignment explanation
Indices: 75250--75391 Score: 250
Period size: 36 Copynumber: 3.9 Consensus size: 36
75240 ACTAATCTTC
75250 AATAAG-AAAATACCCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
75285 AATAAGAAAAATACTCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
75321 AATAAGAAAAATACTCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
75357 AATAAGAAAAAATACCCAAATTTCTTATGAAACCT
1 AATAAG-AAAAATACCCAAATTTCTTATGAAACCT
75392 AAATTGGTGA
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
35 6 0.06
36 70 0.68
37 27 0.26
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (36 bp):
AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
Done.