Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005613.1 Hibiscus syriacus cultivar Beakdansim tig00013051_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: 72894
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5387 original size:17 final size:17
Alignment explanation
Indices: 5351--5394 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
5341 TCAAACATTC
*
5351 AACACACAAAATATCCA
1 AACACATAAAATATCCA
5368 AACA-ATAAAATATCCAA
1 AACACATAAAATATCC-A
5385 AACACATAAA
1 AACACATAAA
5395 TCCATCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.64, C:0.23, G:0.00, T:0.14
Consensus pattern (17 bp):
AACACATAAAATATCCA
Found at i:5395 original size:17 final size:16
Alignment explanation
Indices: 5354--5395 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5344 AACATTCAAC
5354 ACACA-AAATATCCAA
1 ACACATAAATATCCAA
5369 ACA-ATAAAATATCCAAA
1 ACACAT-AAATATCC-AA
5386 ACACATAAAT
1 ACACATAAAT
5396 CCATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 3 0.13
16 8 0.35
17 9 0.39
18 2 0.09
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (16 bp):
ACACATAAATATCCAA
Found at i:6797 original size:12 final size:13
Alignment explanation
Indices: 6780--6812 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6770 AATGGGCAAA
*
6780 TTTGAAAACT-AT
1 TTTGAAAACTAAG
6792 TTTGAAAACTAAG
1 TTTGAAAACTAAG
6805 TTTGAAAA
1 TTTGAAAA
6813 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACTAAG
Found at i:16857 original size:2 final size:2
Alignment explanation
Indices: 16808--16837 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16798 GGTCTATTTA
16808 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16838 AAGTTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16941 original size:39 final size:36
Alignment explanation
Indices: 16842--16978 Score: 193
Period size: 39 Copynumber: 3.7 Consensus size: 36
16832 AATATAAAGT
* *
16842 TTTTGAATATATATATAATATACAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
16878 TTTTGAAAATATATATAATATATAGCTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACA
*
16915 TTTTGAACACCTATATATAATATATAGTTTTTGAAAACA
1 TTTTGAA-A-ATATATATAATATATAG-TTTTGAAAACA
*
16954 TTTTGAATATATATATATATATATA
1 TTTTGAAAATATATATA-ATATATA
16979 TATATATATA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
36 23 0.25
37 26 0.29
38 8 0.09
39 34 0.37
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:16967 original size:2 final size:2
Alignment explanation
Indices: 16960--17026 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
16950 AACATTTTGA
16960 AT AT AT 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 AT AT AT
*
17002 AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17027 GAATGAGGGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19565 original size:16 final size:16
Alignment explanation
Indices: 19546--19578 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19536 CAACTTTAAA
19546 ATTTGATTT-TTTTATT
1 ATTT-ATTTATTTTATT
19562 ATTTATTTATTTTATT
1 ATTTATTTATTTTATT
19578 A
1 A
19579 GTTGTGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTATTTATTTTATT
Found at i:32837 original size:78 final size:77
Alignment explanation
Indices: 32683--32839 Score: 253
Period size: 78 Copynumber: 2.0 Consensus size: 77
32673 TGGGTGGGAA
32683 AAAATATTAAAATTTTTAAAATTTCAAAGTTAAAAATAATATCAAACTTTTCGAAAATTTTAACA
1 AAAATATTAAAATTTTTAAAATTTCAAAGTTAAAAATAATATCAAACTTTTC-AAAATTTTAACA
32748 AATTTGAATTTTT
65 AATTTGAATTTTT
*
32761 AAAATATTAAAATTTTTAAAATTTCGAAGTTAAAAATAATATCAAACTTTT-AAAATTTATTTAA
1 AAAATATTAAAATTTTTAAAATTTCAAAGTTAAAAATAATATCAAACTTTTCAAAA--T-TTTAA
*
32825 CAAATTTGATTTTTT
63 CAAATTTGAATTTTT
32840 TTTAAATTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
76 4 0.05
78 51 0.69
79 19 0.26
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (77 bp):
AAAATATTAAAATTTTTAAAATTTCAAAGTTAAAAATAATATCAAACTTTTCAAAATTTTAACAA
ATTTGAATTTTT
Found at i:32841 original size:64 final size:63
Alignment explanation
Indices: 32773--32896 Score: 196
Period size: 64 Copynumber: 2.0 Consensus size: 63
32763 AATATTAAAA
* *
32773 TTTTTAAAATTTCGAAGTTAAAAATAATATCAAACTTTTA-AAATTTATTTAACAAATTTGATTT
1 TTTTTAAAATTTCGAAATTAAAAATAATATCAAACATTTAGAAA-TT-TTTAACAAATTTGATTT
*
32837 TTTTTTAAATTTCGAAATTAAAAATAATATCAAACATTTAGAAATTTTTAACAAATTTGA
1 TTTTTAAAATTTCGAAATTAAAAATAATATCAAACATTTAGAAATTTTTAACAAATTTGA
32897 AAAAAAATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 14 0.25
64 39 0.70
65 3 0.05
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (63 bp):
TTTTTAAAATTTCGAAATTAAAAATAATATCAAACATTTAGAAATTTTTAACAAATTTGATTT
Found at i:33335 original size:32 final size:32
Alignment explanation
Indices: 33299--33368 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
33289 GATTTTGGTT
* *
33299 AGATGAAACA-AGTTTGTTGCGTAAGAGATTGA
1 AGATGAAA-AGAGTGTGTTACGTAAGAGATTGA
*
33331 AGATGAAAAGAGTGTGTTATGTAAGAGATTGA
1 AGATGAAAAGAGTGTGTTACGTAAGAGATTGA
33363 AGATGA
1 AGATGA
33369 TGTGCACGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.27
Consensus pattern (32 bp):
AGATGAAAAGAGTGTGTTACGTAAGAGATTGA
Found at i:35093 original size:14 final size:15
Alignment explanation
Indices: 35060--35094 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
35050 CACATCCTAA
35060 AAATGTGTAATTATT
1 AAATGTGTAATTATT
35075 AAATGTGTAATTA-T
1 AAATGTGTAATTATT
35089 AAATGT
1 AAATGT
35095 ACTAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (15 bp):
AAATGTGTAATTATT
Found at i:49150 original size:21 final size:21
Alignment explanation
Indices: 49124--49167 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49114 AAATCGAAGT
49124 TATAGAGAAATTTATTCTCTA
1 TATAGAGAAATTTATTCTCTA
49145 TATAGAGAAATTTATTCTCTA
1 TATAGAGAAATTTATTCTCTA
49166 TA
1 TA
49168 AACAAGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (21 bp):
TATAGAGAAATTTATTCTCTA
Found at i:53265 original size:3 final size:3
Alignment explanation
Indices: 53259--53303 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
53249 GTAGTAGTAG
53259 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53304 TTGGATCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:53879 original size:118 final size:116
Alignment explanation
Indices: 53625--53880 Score: 338
Period size: 116 Copynumber: 2.2 Consensus size: 116
53615 CTGTTCCAAC
* * * *
53625 TCTTTATGTGATGGAATCGAGCTAAGTTTGAATAAGTTTTTCTCATTAGGAACTTTTCTCCCTTA
1 TCTTT-TGTGATGGAATCGAACCAAGTTTGAACAAGTTTTTCTCATTAGGAACTTTTCTCCCTCA
* *
53690 TCGGATGAGTTCTTCTCATTACAAACCTTCCATTAAATATTTTGATCCACCT
65 TCGGACGAGTTCTTCTCATTACAAACCTTCCATTAAATATGTTGATCCACCT
* * *
53742 TCTTCTGTGATGGACTCGAACCAA-TGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCCCTC
1 TCTTTTGTGATGGAATCGAACCAAGT-TTGAACAAGTTTTTCTCATTAGGAACTT-TTCTCCCTC
* *
53806 ATCGGACGAGTTCTTCTCATTACGAACCCTTCCATTTGAA-ATGTTGATCCA-CT
64 ATCGGACGAGTTCTTCTCATTAC-AAACCTTCCA-TTAAATATGTTGATCCACCT
53859 TCCTTTTGTGATGGAATCGAAC
1 T-CTTTTGTGATGGAATCGAAC
53881 GTAGCACTGG
Statistics
Matches: 121, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
115 1 0.01
116 42 0.35
117 37 0.31
118 37 0.31
119 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (116 bp):
TCTTTTGTGATGGAATCGAACCAAGTTTGAACAAGTTTTTCTCATTAGGAACTTTTCTCCCTCAT
CGGACGAGTTCTTCTCATTACAAACCTTCCATTAAATATGTTGATCCACCT
Found at i:65501 original size:20 final size:21
Alignment explanation
Indices: 65463--65501 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
65453 CATCAAGGTC
65463 TTTGTCGAAGCCATGAAATCT
1 TTTGTCGAAGCCATGAAATCT
*
65484 TTTGTCGATGCCAT-AAAT
1 TTTGTCGAAGCCATGAAAT
65502 TTATGTAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTGTCGAAGCCATGAAATCT
Done.