Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002553.1 Hibiscus syriacus cultivar Beakdansim tig00005180_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: 40734
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:6983 original size:18 final size:18
Alignment explanation
Indices: 6938--6986 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
6928 AGAAAATAAG
*
6938 GATCGAGAGAAGGAGAGG
1 GATCGAGAGAAGGAGAGA
** * *
6956 GAAGGTGAGAAGGATAGA
1 GATCGAGAGAAGGAGAGA
6974 GATCGAGAGAAGG
1 GATCGAGAGAAGG
6987 GAAAGGAGAG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.47, T:0.08
Consensus pattern (18 bp):
GATCGAGAGAAGGAGAGA
Found at i:8020 original size:29 final size:29
Alignment explanation
Indices: 7981--8037 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
7971 AACCCCCTTC
7981 ATAATTGTCAGAGAGCCAAGAGGGCAATA
1 ATAATTGTCAGAGAGCCAAGAGGGCAATA
*
8010 ATAATTGTCAGAGAGCCAAGGGGGCAAT
1 ATAATTGTCAGAGAGCCAAGAGGGCAAT
8038 CTAACAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.18
Consensus pattern (29 bp):
ATAATTGTCAGAGAGCCAAGAGGGCAATA
Found at i:11222 original size:3 final size:3
Alignment explanation
Indices: 11209--11240 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
11199 CCCTCTTTTC
*
11209 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11241 AAAGAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14380 original size:21 final size:22
Alignment explanation
Indices: 14356--14398 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14346 ATTACAAATG
* *
14356 AATGTTAT-TTTGATTAAAAAA
1 AATGATATATTTGAGTAAAAAA
14377 AATGATATATTTGAGTAAAAAA
1 AATGATATATTTGAGTAAAAAA
14399 GCCTCCTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
AATGATATATTTGAGTAAAAAA
Found at i:20926 original size:21 final size:21
Alignment explanation
Indices: 20900--20942 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20890 TTTTCGGGCT
* *
20900 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
20921 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
20942 A
1 A
20943 CGAACATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:21002 original size:66 final size:67
Alignment explanation
Indices: 20922--21071 Score: 230
Period size: 66 Copynumber: 2.3 Consensus size: 67
20912 ACCCATTCAA
* *
20922 GGGGAACCGATACCCCTTCAACGAACATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAACATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
20986 GG
66 GG
* * * *
20988 GGGGAACCGATACCCCCTCAACGCATATGAATTCCAGAATGCTTGTGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAACATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
21053 GG
66 GG
*
21055 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
21072 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
66 58 0.76
67 18 0.24
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAACATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
GG
Found at i:21408 original size:29 final size:29
Alignment explanation
Indices: 21371--21442 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
21361 CATATTATGA
* *
21371 TACAGGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
21400 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
21429 TACATGACATGAAT
1 TACATGACATGAAT
21443 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:21884 original size:149 final size:149
Alignment explanation
Indices: 21612--21913 Score: 568
Period size: 149 Copynumber: 2.0 Consensus size: 149
21602 GAGTAGAGGG
21612 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
* *
21677 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTACGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTACGGACATCATTA
21742 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
21761 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGGAAGACACAT
1 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
*
21826 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTACGGACATCATTA
21891 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
21910 TCTA
1 TCTA
21914 CGGGGCACTT
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (149 bp):
TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTACGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:21938 original size:23 final size:23
Alignment explanation
Indices: 21894--21938 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21884 ATCATTATAT
*
21894 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
21917 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
21939 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:28005 original size:21 final size:21
Alignment explanation
Indices: 27972--28012 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27962 TTCGGGCTAT
* *
27972 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
27993 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
28013 CGAACATGAT
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:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:28069 original size:65 final size:66
Alignment explanation
Indices: 27992--28140 Score: 219
Period size: 65 Copynumber: 2.3 Consensus size: 66
27982 ACCCATTCAA
* *
27992 GGGGAACCGATACCCCTTCAACGAACATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAACATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
28056 G
66 G
* * * *
28057 GGGGAACCGATACCCCCTCAACGCATATGAATTCCAGAATGCTTGTGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAACATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA-
28122 GG
65 GG
*
28124 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
28141 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
65 58 0.77
67 17 0.23
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAACATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
G
Found at i:28477 original size:29 final size:29
Alignment explanation
Indices: 28440--28511 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
28430 CATATTATGA
* *
28440 TACAGGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
28469 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
28498 TACATGACATGAAT
1 TACATGACATGAAT
28512 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:29005 original size:23 final size:23
Alignment explanation
Indices: 28961--29005 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28951 ATCATTATAT
*
28961 GGCACTACAGTGCAATTCTACGG
1 GGCACTACAGTGCAATTATACGG
* * *
28984 GGCACTTCGGTGCATTTATACG
1 GGCACTACAGTGCAATTATACG
29006 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGG
Found at i:32101 original size:98 final size:100
Alignment explanation
Indices: 31918--32102 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 100
31908 AACAAACCAC
* * * * *
31918 TGAGAAAACAGAACAAAGACAATCTAGAAAGGCTGGCTACATTAAATCAATATGTTGCTTAACTG
1 TGAGAAAACAGAACAAAGACAATCCAGAAAGACTGACTAAATTAAATCAATATGTTGCTAAACTG
* *
31983 TGCCATAGGCAGGACAGTAGGGACATAGAGACCTT
66 TGCCAAAGACAGGACAGTAGGGACATAGAGACCTT
* * *
32018 TGAGAAAACA-AA-AAAGACAATCCAGAAAGACTGACTAAATTAGATCAATATGTTTCTAAATTG
1 TGAGAAAACAGAACAAAGACAATCCAGAAAGACTGACTAAATTAAATCAATATGTTGCTAAACTG
32081 TGCCAAAGACAGGACAGTAGGG
66 TGCCAAAGACAGGACAGTAGGG
32103 GATTTTCAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
98 63 0.84
99 2 0.03
100 10 0.13
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (100 bp):
TGAGAAAACAGAACAAAGACAATCCAGAAAGACTGACTAAATTAAATCAATATGTTGCTAAACTG
TGCCAAAGACAGGACAGTAGGGACATAGAGACCTT
Found at i:34919 original size:7 final size:7
Alignment explanation
Indices: 34909--34989 Score: 63
Period size: 7 Copynumber: 11.6 Consensus size: 7
34899 CGGAAAGTGG
34909 CGGCGGA
1 CGGCGGA
34916 CGGCGGA
1 CGGCGGA
* *
34923 TGTCGGA
1 CGGCGGA
*
34930 CGGCAGA
1 CGGCGGA
34937 CGGCGGA
1 CGGCGGA
34944 CGGCGGA
1 CGGCGGA
* *
34951 TGTCGGA
1 CGGCGGA
* **
34958 CGACAAA
1 CGGCGGA
*
34965 CGGCGGC
1 CGGCGGA
34972 CGGCGGA
1 CGGCGGA
* *
34979 TGTCGGA
1 CGGCGGA
34986 CGGC
1 CGGC
34990 AAACGGCGGC
Statistics
Matches: 53, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.17, C:0.27, G:0.48, T:0.07
Consensus pattern (7 bp):
CGGCGGA
Found at i:34931 original size:14 final size:14
Alignment explanation
Indices: 34912--34989 Score: 75
Period size: 14 Copynumber: 5.6 Consensus size: 14
34902 AAAGTGGCGG
34912 CGGACGGCGGATGT
1 CGGACGGCGGATGT
* * *
34926 CGGACGGCAGACGG
1 CGGACGGCGGATGT
34940 CGGACGGCGGATGT
1 CGGACGGCGGATGT
* ** * *
34954 CGGACGACAAACGG
1 CGGACGGCGGATGT
*
34968 CGGCCGGCGGATGT
1 CGGACGGCGGATGT
34982 CGGACGGC
1 CGGACGGC
34990 AAACGGCGGC
Statistics
Matches: 46, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.18, C:0.27, G:0.47, T:0.08
Consensus pattern (14 bp):
CGGACGGCGGATGT
Found at i:35002 original size:28 final size:28
Alignment explanation
Indices: 34909--34998 Score: 153
Period size: 28 Copynumber: 3.2 Consensus size: 28
34899 CGGAAAGTGG
*
34909 CGGCGGACGGCGGATGTCGGACGGCAGA
1 CGGCGGACGGCGGATGTCGGACGGCAAA
*
34937 CGGCGGACGGCGGATGTCGGACGACAAA
1 CGGCGGACGGCGGATGTCGGACGGCAAA
*
34965 CGGCGGCCGGCGGATGTCGGACGGCAAA
1 CGGCGGACGGCGGATGTCGGACGGCAAA
34993 CGGCGG
1 CGGCGG
34999 CCGGAGGACA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.19, C:0.27, G:0.48, T:0.07
Consensus pattern (28 bp):
CGGCGGACGGCGGATGTCGGACGGCAAA
Found at i:37915 original size:36 final size:36
Alignment explanation
Indices: 37868--37936 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
37858 ATATCTAAAT
*
37868 TCAAAATTCATAAAAATATCTATAAAGAGCAAAGTA
1 TCAAAATTCATAAAAATATCTATAAAGAACAAAGTA
37904 TCAAAATTCATAAAAATATCTATAAAGAACAAA
1 TCAAAATTCATAAAAATATCTATAAAGAACAAA
37937 AAGACATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.25
Consensus pattern (36 bp):
TCAAAATTCATAAAAATATCTATAAAGAACAAAGTA
Done.