Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004250.1 Hibiscus syriacus cultivar Beakdansim tig00009318_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: 394940
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
File 2 of 2
Found at i:338197 original size:35 final size:36
Alignment explanation
Indices: 338103--338207 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
338093 GATACAATCT
* *
338103 GTCCATCACCATTATTACGCCTATATCATCACCTTA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
338139 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
338175 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
338208 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:342088 original size:36 final size:36
Alignment explanation
Indices: 342048--342152 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
342038 GATACAATCT
342048 GTCCATCACCATTATCACGCCTATATAATCACCATA
1 GTCCATCACCATTATCACGCCTATATAATCACCATA
*
342084 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATAATCACCATA
* *
342120 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATAATCACCA
342153 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATAATCACCATA
Found at i:342093 original size:13 final size:11
Alignment explanation
Indices: 342051--342135 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
342041 ACAATCTGTC
342051 CATCACCATTAT
1 CATCACCA-TAT
*
342063 CA-CGCCTATAT
1 CATCACC-ATAT
*
342074 AATCACCATAGT
1 CATCACCATA-T
342086 CCATCACCATTAT
1 -CATCACCA-TAT
*
342099 CA-CGCCTATAT
1 CATCACC-ATAT
342110 CATCACCATATT
1 CATCACCATA-T
342122 CCATCACCATAT
1 -CATCACCATAT
342134 CA
1 CA
342136 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.40
12 15 0.26
13 18 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:346511 original size:19 final size:20
Alignment explanation
Indices: 346478--346525 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
346468 ACCCCTTTGG
*
346478 AAATACATGATTTTTGATGA
1 AAATACATGATTTTTAATGA
346498 AAATACATGA-TTTTAATGA
1 AAATACATGATTTTTAATGA
*
346517 AGATACATG
1 AAATACATG
346526 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (20 bp):
AAATACATGATTTTTAATGA
Found at i:352604 original size:19 final size:20
Alignment explanation
Indices: 352580--352630 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
352570 CGGCCAAGAG
* *
352580 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
352599 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
352619 CATGTATTTTCA
1 CATGTATTTTCA
352631 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:365188 original size:13 final size:11
Alignment explanation
Indices: 365147--365231 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
365137 ACAATCTGTC
365147 CATCACCATTAT
1 CATCACCA-TAT
*
365159 CA-CGCCTATAT
1 CATCACC-ATAT
365170 CATCACCATAGT
1 CATCACCATA-T
365182 CCATCACCATTAT
1 -CATCACCA-TAT
*
365195 CA-CGCCTATAT
1 CATCACC-ATAT
365206 CATCACCATATT
1 CATCACCATA-T
365218 CCATCACCATAT
1 -CATCACCATAT
365230 CA
1 CA
365232 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:365191 original size:36 final size:36
Alignment explanation
Indices: 365144--365248 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
365134 GATACAATCT
365144 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
365180 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
365216 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
365249 ACTGATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:365619 original size:35 final size:37
Alignment explanation
Indices: 365564--365643 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
365554 TATGAGAATT
* *
365564 TGGTAATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
365599 TGGTGATGTTATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
365636 TGGTGATG
1 TGGTGATG
365644 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 19 0.49
36 4 0.10
37 16 0.41
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:369867 original size:24 final size:24
Alignment explanation
Indices: 369840--369890 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
369830 TGCTGCAACA
369840 AAAGCAAC-AAAAGAGAAAA-AAAAG
1 AAAG-AACAAAAAGA-AAAAGAAAAG
369864 AAAGAACAAAAAGAAAAAGAAAAG
1 AAAGAACAAAAAGAAAAAGAAAAG
369888 AAA
1 AAA
369891 AAGACTCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAGAACAAAAAGAAAAAGAAAAG
Found at i:369893 original size:11 final size:11
Alignment explanation
Indices: 369848--369894 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
369838 CAAAAGCAAC
369848 AAAAGAGAAAA-
1 AAAAGA-AAAAG
*
369859 AAAAGAAAGAACA
1 AAAAGAAA-AA-G
369872 AAAAGAAAAAG
1 AAAAGAAAAAG
369883 AAAAGAAAAAG
1 AAAAGAAAAAG
369894 A
1 A
369895 CTCCTACATC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.06
11 20 0.62
12 2 0.06
13 8 0.25
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:384177 original size:14 final size:14
Alignment explanation
Indices: 384158--384189 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
384148 AAATTTTGGC
384158 TTTTTTGGCTTTTT
1 TTTTTTGGCTTTTT
*
384172 TTTTTTTGCTTTTT
1 TTTTTTGGCTTTTT
384186 TTTT
1 TTTT
384190 GCCTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (14 bp):
TTTTTTGGCTTTTT
Found at i:392937 original size:25 final size:27
Alignment explanation
Indices: 392898--392956 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
392888 ATTCATCTTG
*
392898 AAAAAAAAGAGAATTCC-AAAATTAAA
1 AAAAAAAACAGAATTCCGAAAATTAAA
**
392924 AAAAAAAACA-AATTCCGAAAATTTTA
1 AAAAAAAACAGAATTCCGAAAATTAAA
392950 AAAAAAA
1 AAAAAAA
392957 GAAAAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.17
Consensus pattern (27 bp):
AAAAAAAACAGAATTCCGAAAATTAAA
Done.