Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001747.1 Hibiscus syriacus cultivar Beakdansim tig00003536_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: 54565
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3703 original size:31 final size:32
Alignment explanation
Indices: 3668--3737 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
3658 TGGCTACGTC
*
3668 TTCTCTTGA-TGTGATCTTAGCAGCTTATGCT
1 TTCTCTTGATTGTGATCTTAGCAGCTTACGCT
3699 TTCTCTTGATTGTGATCTTAGCAGCTTACGCT
1 TTCTCTTGATTGTGATCTTAGCAGCTTACGCT
*
3731 TTATCTT
1 TTCTCTT
3738 AATCTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (32 bp):
TTCTCTTGATTGTGATCTTAGCAGCTTACGCT
Found at i:4198 original size:18 final size:19
Alignment explanation
Indices: 4172--4212 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4162 GGGCAGATTG
4172 CCCAGAGGGAACCGATTCCC
1 CCCAG-GGGAACCGATTCCC
* *
4192 CCCAGGGGTATCGATTCCC
1 CCCAGGGGAACCGATTCCC
4211 CC
1 CC
4213 TGAATGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.41, G:0.24, T:0.15
Consensus pattern (19 bp):
CCCAGGGGAACCGATTCCC
Found at i:12041 original size:14 final size:14
Alignment explanation
Indices: 12022--12065 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
12012 TGACCGGTCT
*
12022 GACCCGACTCGACC
1 GACCCGACCCGACC
12036 GACCCGACCCGACC
1 GACCCGACCCGACC
12050 GTTGACCCGACCCGAC
1 ---GACCCGACCCGAC
12066 TGTTGACCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
17 13 0.50
ACGTcount: A:0.20, C:0.50, G:0.23, T:0.07
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:12058 original size:17 final size:17
Alignment explanation
Indices: 12036--12090 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
12026 CGACTCGACC
*
12036 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
*
12053 GACCCGACCCGACTGTT
1 GACCCGACCCGACAGTT
12070 GACCCGACCCGACAGTT
1 GACCCGACCCGACAGTT
12087 GACC
1 GACC
12091 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:16154 original size:14 final size:14
Alignment explanation
Indices: 16135--16178 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
16125 TGACCGGTCT
*
16135 GACCCGACTCGACC
1 GACCCGACCCGACC
16149 GACCCGACCCGACC
1 GACCCGACCCGACC
16163 GTTGACCCGACCCGAC
1 ---GACCCGACCCGAC
16179 TGTTGACCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
17 13 0.50
ACGTcount: A:0.20, C:0.50, G:0.23, T:0.07
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:16171 original size:17 final size:17
Alignment explanation
Indices: 16149--16203 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
16139 CGACTCGACC
*
16149 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
*
16166 GACCCGACCCGACTGTT
1 GACCCGACCCGACAGTT
16183 GACCCGACCCGACAGTT
1 GACCCGACCCGACAGTT
16200 GACC
1 GACC
16204 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:18920 original size:19 final size:19
Alignment explanation
Indices: 18898--18944 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
18888 CATAATTTAT
18898 TAAAATTTTAAAAGTATT-A
1 TAAAATTTTAAAA-TATTCA
*
18917 TAAAGTTGTTAAAATATTCA
1 TAAAATT-TTAAAATATTCA
*
18937 GAAAATTT
1 TAAAATTT
18945 ATTAAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (19 bp):
TAAAATTTTAAAATATTCA
Found at i:18969 original size:9 final size:10
Alignment explanation
Indices: 18955--18980 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18945 ATTAAAAAGG
18955 TAAAAAAAAT
1 TAAAAAAAAT
18965 TAAAAAAAAT
1 TAAAAAAAAT
18975 TAAAAA
1 TAAAAA
18981 TTATAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:35009 original size:30 final size:29
Alignment explanation
Indices: 34973--35064 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 29
34963 CCTCAAGCTT
*
34973 CTCACCATCATCTTCACTGACTTTAACATC
1 CTCACCA-CATCTTCACTCACTTTAACATC
35003 CTCACCACCATCTTCACTCACTTTAACATCTTC
1 CTCACCA-CATCTTCACTCACTTTAACA---TC
*
35036 CTCACCACTATCTTCACTCACTTCAACAT
1 CTCACCAC-ATCTTCACTCACTTTAACAT
35065 GTTTCTTCTC
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
30 27 0.49
32 1 0.02
33 27 0.49
ACGTcount: A:0.26, C:0.40, G:0.01, T:0.33
Consensus pattern (29 bp):
CTCACCACATCTTCACTCACTTTAACATC
Found at i:35014 original size:33 final size:32
Alignment explanation
Indices: 34973--35064 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 32
34963 CCTCAAGCTT
*
34973 CTCACCATCATCTTCACTGACTTTAACA---TC
1 CTCACCA-CATCTTCACTCACTTTAACATCCTC
*
35003 CTCACCACCATCTTCACTCACTTTAACATCTTC
1 CTCACCA-CATCTTCACTCACTTTAACATCCTC
*
35036 CTCACCACTATCTTCACTCACTTCAACAT
1 CTCACCAC-ATCTTCACTCACTTTAACAT
35065 GTTTCTTCTC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
30 26 0.47
32 1 0.02
33 28 0.51
ACGTcount: A:0.26, C:0.40, G:0.01, T:0.33
Consensus pattern (32 bp):
CTCACCACATCTTCACTCACTTTAACATCCTC
Found at i:40529 original size:15 final size:16
Alignment explanation
Indices: 40504--40585 Score: 79
Period size: 15 Copynumber: 5.4 Consensus size: 16
40494 CGAGTTTGCC
40504 TTATT-TACTTTTACT
1 TTATTATACTTTTACT
*
40519 TTATTAT-CTTTT-TT
1 TTATTATACTTTTACT
40533 ATTATT-TACTTTTACT
1 -TTATTATACTTTTACT
*
40549 TTATTAT-CTTTT-TT
1 TTATTATACTTTTACT
40563 ATTATT-TACTTTTACT
1 -TTATTATACTTTTACT
40579 TTATTAT
1 TTATTAT
40586 TTTGTGAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.07
15 45 0.83
16 5 0.09
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTATACTTTTACT
Found at i:40538 original size:30 final size:30
Alignment explanation
Indices: 40504--40585 Score: 164
Period size: 30 Copynumber: 2.7 Consensus size: 30
40494 CGAGTTTGCC
40504 TTATTTACTTTTACTTTATTATCTTTTTTA
1 TTATTTACTTTTACTTTATTATCTTTTTTA
40534 TTATTTACTTTTACTTTATTATCTTTTTTA
1 TTATTTACTTTTACTTTATTATCTTTTTTA
40564 TTATTTACTTTTACTTTATTAT
1 TTATTTACTTTTACTTTATTAT
40586 TTTGTGAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.70
Consensus pattern (30 bp):
TTATTTACTTTTACTTTATTATCTTTTTTA
Found at i:47862 original size:19 final size:19
Alignment explanation
Indices: 47838--47874 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47828 ATGACCAACA
*
47838 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
47857 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
47875 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:48256 original size:19 final size:19
Alignment explanation
Indices: 48232--48340 Score: 110
Period size: 19 Copynumber: 5.4 Consensus size: 19
48222 TTATTTTGAA
48232 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
48251 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
48273 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
48295 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
48314 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
48333 ATTTTTCA
1 -TTTTTCA
48341 AAATCGCGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
19 44 0.57
20 5 0.06
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:48394 original size:21 final size:21
Alignment explanation
Indices: 48342--48402 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
48332 CATTTTTCAA
*
48342 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
* *
48362 AATCGTGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* *
48383 ATTCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATCTGGA
48403 AACTGAGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:48781 original size:3 final size:3
Alignment explanation
Indices: 48773--48797 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48763 TCTTATTCCT
48773 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
48798 CCTCCCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.