Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004044.1 Hibiscus syriacus cultivar Beakdansim tig00008834_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: 70963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:12641 original size:22 final size:21
Alignment explanation
Indices: 12606--12647 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
12596 TATCTTCGTG
12606 TATATATTTAAAAATAATATTA
1 TATATATTTAAAAAT-ATATTA
* *
12628 TATATCTTTCAAAATATATT
1 TATATATTTAAAAATATATT
12648 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATTTAAAAATATATTA
Found at i:14783 original size:29 final size:30
Alignment explanation
Indices: 14737--14793 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
14727 AAAACAATCT
* *
14737 TAAGTTAAGTTAATAAT-AAATATATTTAA
1 TAAGTTAAGATAAAAATAAAATATATTTAA
*
14766 TAAGTTGAGATAAAAATAAAATATATTT
1 TAAGTTAAGATAAAAATAAAATATATTT
14794 TTAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.39
Consensus pattern (30 bp):
TAAGTTAAGATAAAAATAAAATATATTTAA
Found at i:19233 original size:16 final size:17
Alignment explanation
Indices: 19193--19236 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
19183 GATGATTAGA
19193 TAAATAAAATAATATAT
1 TAAATAAAATAATATAT
**
19210 TTTA-AAAATAATA-AT
1 TAAATAAAATAATATAT
19225 TAAATAAAATAA
1 TAAATAAAATAA
19237 AAAATAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATAAAATAATATAT
Found at i:20788 original size:30 final size:31
Alignment explanation
Indices: 20729--20789 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
20719 AGGTTTAATT
*
20729 AGTGGCGTGACACATACCATATCATCATTTTA
1 AGTGGCGTGACACATACCACA-CATCATTTTA
20761 AGTGGCGTGACACAT--CACACAATCATTTT
1 AGTGGCGTGACACATACCACAC-ATCATTTT
20790 GAATAATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 11 0.41
32 15 0.56
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (31 bp):
AGTGGCGTGACACATACCACACATCATTTTA
Found at i:23388 original size:37 final size:37
Alignment explanation
Indices: 23335--23424 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 37
23325 TTTTGTTCGG
* * * *
23335 GTCGGGTAGGGATTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGATCGA
*
23372 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGATCGG
1 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCAGATCGA
23410 GTCGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
23425 AGGTGAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 10 0.22
38 31 0.67
39 5 0.11
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGATCGA
Found at i:23396 original size:38 final size:39
Alignment explanation
Indices: 23347--23424 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
23337 CGGGTAGGGA
* *
23347 TTTTTAAGTGTGATATTCGGGTCGAGTCGGG-TCGGGTT
1 TTTTTAAGTGTGATATTCAGATCGAGTCGGGTTCGGGTT
*
23385 TTTTTAAGTGTGATATTCAGATCGGGTCGGGTTCGGGTT
1 TTTTTAAGTGTGATATTCAGATCGAGTCGGGTTCGGGTT
23424 T
1 T
23425 AGGTGAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 28 0.78
39 8 0.22
ACGTcount: A:0.14, C:0.10, G:0.35, T:0.41
Consensus pattern (39 bp):
TTTTTAAGTGTGATATTCAGATCGAGTCGGGTTCGGGTT
Found at i:24013 original size:17 final size:18
Alignment explanation
Indices: 23991--24035 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
23981 TATGGAATTG
23991 GATTCCAATTTC-TGACA
1 GATTCCAATTTCATGACA
*
24008 GATTCCAA-TTCATTTACA
1 GATTCCAATTTCA-TGACA
24026 GATTCCAATT
1 GATTCCAATT
24036 CCCTCAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 12 0.50
19 1 0.04
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTCCAATTTCATGACA
Found at i:25713 original size:11 final size:12
Alignment explanation
Indices: 25684--25711 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25674 CCTATATGCC
25684 AAAAATATTAAT
1 AAAAATATTAAT
25696 AAAAATATTAAT
1 AAAAATATTAAT
25708 AAAA
1 AAAA
25712 TAAATCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATATTAAT
Found at i:26529 original size:21 final size:21
Alignment explanation
Indices: 26504--26543 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26494 CTAAAAATGT
*
26504 TAAAAATATTAAAATTTTAAA
1 TAAAAATAATAAAATTTTAAA
*
26525 TAAAAATAATAATATTTTA
1 TAAAAATAATAAAATTTTA
26544 TGTAATTTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAAAATTTTAAA
Found at i:33914 original size:3 final size:3
Alignment explanation
Indices: 33906--33932 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33896 GGTGAATGAG
33906 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
33933 CTATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37206 original size:23 final size:25
Alignment explanation
Indices: 37166--37212 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
37156 TTTAAATAAT
37166 TATATTAAAAAGCTAAAAT-TTTAC
1 TATATTAAAAAGCTAAAATATTTAC
37190 TATA-TAAAAAG-TAAAAATATTTA
1 TATATTAAAAAGCT-AAAATATTTA
37213 TTACCTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.05
23 12 0.57
24 8 0.38
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
TATATTAAAAAGCTAAAATATTTAC
Found at i:39217 original size:67 final size:67
Alignment explanation
Indices: 39109--39242 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
39099 TAAAATTGTG
39109 AGCTTTGACCATACCTAGCGTAGGAGCAAAGCTTCCCGTTGATTCTAATTTACTTGACATTTCCA
1 AGCTTTGACCATACCTAGCGTAGGAGCAAAGCTTCCCGTTGATTCTAATTTACTTGACATTTCCA
39174 AA
66 AA
39176 AGCTTTGACCATACCTAGCGTAGGAGCAAAGCTTCCCGTTGATTCTAATTTACTTGACATTTCCA
1 AGCTTTGACCATACCTAGCGTAGGAGCAAAGCTTCCCGTTGATTCTAATTTACTTGACATTTCCA
39241 AA
66 AA
39243 TCATGAACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (67 bp):
AGCTTTGACCATACCTAGCGTAGGAGCAAAGCTTCCCGTTGATTCTAATTTACTTGACATTTCCA
AA
Found at i:43787 original size:2 final size:2
Alignment explanation
Indices: 43780--43815 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43770 TTGCGCATAC
43780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43816 TCCCTATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44442 original size:35 final size:35
Alignment explanation
Indices: 44396--44465 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
44386 AATGAGAAAG
44396 CTGATGTATTATCTGATGATGATGATATTGTGATC
1 CTGATGTATTATCTGATGATGATGATATTGTGATC
44431 CTGATGTATTATCTGATGATGATGATATTGTGATC
1 CTGATGTATTATCTGATGATGATGATATTGTGATC
44466 TCAGTGAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (35 bp):
CTGATGTATTATCTGATGATGATGATATTGTGATC
Found at i:52023 original size:75 final size:75
Alignment explanation
Indices: 51886--52030 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 75
51876 GGTAGACATA
* * * **
51886 AATAAAATTTCAGGGTGGATATCATCAATAAAATAGGTCATAATCGAATAAATTTTAAAATTTCA
1 AATAAAATTTCAGGGTAGATACCATCAATAAAATAGATCATAATCGAATAAAAATTAAAATTTCA
51951 AGGTGGGTAC
66 AGGTGGGTAC
* * * **
51961 AATAAATTTTTAGGGTAGATACCATCAATAAAATAGATGACTAATCGAA-AAAAATTCGAATTTC
1 AATAAAATTTCAGGGTAGATACCATCAATAAAATAGATCA-TAATCGAATAAAAATTAAAATTTC
*
52025 AGGGTG
65 AAGGTG
52031 AGTCCGGCCC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 50 0.86
76 8 0.14
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (75 bp):
AATAAAATTTCAGGGTAGATACCATCAATAAAATAGATCATAATCGAATAAAAATTAAAATTTCA
AGGTGGGTAC
Found at i:53102 original size:5 final size:5
Alignment explanation
Indices: 53092--53121 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
53082 GTATAACATA
53092 CAGAG CAGAG CAGAG CAGAG CAGAG CAGAG
1 CAGAG CAGAG CAGAG CAGAG CAGAG CAGAG
53122 GATTTCTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
CAGAG
Found at i:58154 original size:32 final size:31
Alignment explanation
Indices: 58111--58194 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
58101 GAAAGTTCGA
* *
58111 GGCCACGGGGCCTACCTAAGAACACATCTTAG
1 GGCCACAGGGCCTACCTAAGAA-ACATCTCAG
** **
58143 GGCCACAGGGCCTACCCGAGAATGATCTCAG
1 GGCCACAGGGCCTACCTAAGAAACATCTCAG
* *
58174 GGCCGCAGAGCCTACCTAAGA
1 GGCCACAGGGCCTACCTAAGA
58195 GTCACATTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 23 0.55
32 19 0.45
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.13
Consensus pattern (31 bp):
GGCCACAGGGCCTACCTAAGAAACATCTCAG
Found at i:62186 original size:3 final size:3
Alignment explanation
Indices: 62178--62253 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
62168 CCCCCACCCT
62178 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
62226 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
62254 GTGTTAAGTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Done.