Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002559.1 Hibiscus syriacus cultivar Beakdansim tig00005193_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: 55676
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:8105 original size:84 final size:83
Alignment explanation
Indices: 7965--8125 Score: 304
Period size: 84 Copynumber: 1.9 Consensus size: 83
7955 ATACAGGGCA
*
7965 TGCTATTCAGGTTCACATCAATTATATTCCTCAGATGTTCTTTTTTGGTATATTTTGTTTATGTT
1 TGCTATTCAGGTTCACATCAATTATATTCCTCAGATGTTCTGTTTTGGTATATTTTGTTTATGTT
8030 TAATTGAAACTTAAAATG
66 TAATTGAAACTTAAAATG
8048 TGCTATTCAGGTTCACATCAATTATATTTCCTCAGATGTTCTGTTTTGGTATATTTTGTTTATGT
1 TGCTATTCAGGTTCACATCAATTATA-TTCCTCAGATGTTCTGTTTTGGTATATTTTGTTTATGT
8113 TTAATTGAAACTT
65 TTAATTGAAACTT
8126 CTAAATGTTG
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
83 26 0.34
84 50 0.66
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (83 bp):
TGCTATTCAGGTTCACATCAATTATATTCCTCAGATGTTCTGTTTTGGTATATTTTGTTTATGTT
TAATTGAAACTTAAAATG
Found at i:11837 original size:14 final size:15
Alignment explanation
Indices: 11818--11846 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11808 AATATGATGA
11818 TTTTAAAAT-TTATT
1 TTTTAAAATATTATT
11832 TTTTAAAATATTATT
1 TTTTAAAATATTATT
11847 ATATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAATATTATT
Found at i:19497 original size:34 final size:33
Alignment explanation
Indices: 19454--19522 Score: 120
Period size: 34 Copynumber: 2.1 Consensus size: 33
19444 GTATTGATTG
19454 CCCAAGCACAACGGGAAGTTCTACATTGCGGATA
1 CCCAAGCACAACGGGAAGTTCTACATTGCGG-TA
*
19488 CCCAAGCACAACGGGAAGTTTTACATTGCGGTA
1 CCCAAGCACAACGGGAAGTTCTACATTGCGGTA
19521 CC
1 CC
19523 TTTAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 4 0.12
34 30 0.88
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (33 bp):
CCCAAGCACAACGGGAAGTTCTACATTGCGGTA
Found at i:19728 original size:21 final size:21
Alignment explanation
Indices: 19655--19731 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
19645 TAAAGTGTCT
*
19655 AATAATAACAAAACCAGTAGAA
1 AATAATAACAAAACCGGTA-AA
*
19677 AA-AATAACAAAACCGATAAAGCA
1 AATAATAACAAAACCGGT-AA--A
19700 CCCAATAATAACAAAACCGGTAAA
1 ---AATAATAACAAAACCGGTAAA
19724 AATAATAA
1 AATAATAA
19732 TGTTTCCGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
21 22 0.49
22 3 0.07
23 1 0.02
24 1 0.02
26 4 0.09
27 14 0.31
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.13
Consensus pattern (21 bp):
AATAATAACAAAACCGGTAAA
Found at i:21311 original size:7 final size:7
Alignment explanation
Indices: 21299--21330 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
21289 ATAGCATATC
21299 GTTTTAT
1 GTTTTAT
21306 GTTTTAT
1 GTTTTAT
21313 GTTTTAT
1 GTTTTAT
*
21320 GTTTTAA
1 GTTTTAT
21327 GTTT
1 GTTT
21331 ATTTGCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (7 bp):
GTTTTAT
Found at i:22105 original size:20 final size:20
Alignment explanation
Indices: 22080--22121 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
22070 CCGTTACACA
22080 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCTCT
22100 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCTCT
22120 GG
1 GG
22122 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.24, G:0.43, T:0.19
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCTCT
Found at i:22198 original size:36 final size:36
Alignment explanation
Indices: 22157--22228 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
22147 AAATCTGGGG
22157 GGGGAATCGATACCCCCTT-GGGGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCTTGGGGGGGAATCTGTTCCC
*
22193 GGGGAATCGGTACCCCTTGGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCTTGGGGGGGAATCTGTTCCC
22229 TCTGGGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.22
Consensus pattern (36 bp):
GGGGAATCGATACCCCTTGGGGGGGAATCTGTTCCC
Found at i:22457 original size:20 final size:19
Alignment explanation
Indices: 22423--22461 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
22413 ATTTAATCGG
*
22423 ATATATAATTTAAAATTCA
1 ATATAAAATTTAAAATTCA
22442 ATATAAAATCTTAAAATTCA
1 ATATAAAAT-TTAAAATTCA
22462 TTAACACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAAAATTTAAAATTCA
Found at i:25900 original size:19 final size:20
Alignment explanation
Indices: 25876--25915 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25866 TATTTAATCG
*
25876 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
25895 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
25915 A
1 A
25916 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:27139 original size:18 final size:18
Alignment explanation
Indices: 27097--27148 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
27087 TCTCTATGGT
* *
27097 GGATGAATCGACCAAAGGA
1 GGATGAA-CGACCGAAGAA
27116 GG-TGAACGACCGAAGAA
1 GGATGAACGACCGAAGAA
27133 GGATGAACGACCGAAG
1 GGATGAACGACCGAAG
27149 GAGAATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 11 0.37
18 17 0.57
19 2 0.07
ACGTcount: A:0.40, C:0.17, G:0.35, T:0.08
Consensus pattern (18 bp):
GGATGAACGACCGAAGAA
Found at i:27156 original size:18 final size:17
Alignment explanation
Indices: 27098--27157 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
27088 CTCTATGGTG
*
27098 GATGAATCGACCAAAGGA
1 GATGAA-CGACCGAAGGA
* *
27116 GGTGAACGACCGAAGAA
1 GATGAACGACCGAAGGA
27133 GGATGAACGACCGAAGGA
1 -GATGAACGACCGAAGGA
27151 GAATGAA
1 G-ATGAA
27158 TCGATTGTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 10 0.29
18 25 0.71
ACGTcount: A:0.43, C:0.15, G:0.33, T:0.08
Consensus pattern (17 bp):
GATGAACGACCGAAGGA
Found at i:28729 original size:65 final size:63
Alignment explanation
Indices: 28620--28819 Score: 226
Period size: 65 Copynumber: 3.1 Consensus size: 63
28610 TGATGCACAA
* **
28620 ATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCATGCAT
1 ATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATTTCATGCAT
28683 CG
62 CG
* * *
28685 ATGCACATACCATGCATCGATGCACTGAGGGT-TTTATGAAAACATCGAATGCATTTGATGCATC
1 ATGCACA-ACCATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTTCATGCATC
28749 G
63 G
* * *
28750 ATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTTATGCATCG
1 ATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATCG
28814 ATGCAC
1 ATGCAC
28820 TCTTAGTGCA
Statistics
Matches: 118, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 50 0.42
65 58 0.49
66 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
ATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATCG
Found at i:28910 original size:21 final size:21
Alignment explanation
Indices: 28886--28933 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
28876 TGATGCACCG
28886 ATGCACCATGGGTATGCATCA
1 ATGCACCATGGGTATGCATCA
28907 ATGCACCATGGGTATGCATCA
1 ATGCACCATGGGTATGCATCA
28928 ATGCAC
1 ATGCAC
28934 TGACGCTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
ATGCACCATGGGTATGCATCA
Found at i:37331 original size:21 final size:21
Alignment explanation
Indices: 37306--37346 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37296 AACATTAATA
* *
37306 TTTCTATCAGTTTTGTTATTT
1 TTTCTACCAGTTTTATTATTT
*
37327 TTTCTACCGGTTTTATTATT
1 TTTCTACCAGTTTTATTATT
37347 GATAGGTATT
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:0.15, C:0.12, G:0.10, T:0.63
Consensus pattern (21 bp):
TTTCTACCAGTTTTATTATTT
Found at i:45519 original size:21 final size:21
Alignment explanation
Indices: 45493--45532 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
45483 CTATTCATGA
45493 TGGTGGTAGTGATGATGATGG
1 TGGTGGTAGTGATGATGATGG
45514 TGGTGGTAGTGATGATGAT
1 TGGTGGTAGTGATGATGAT
45533 ATAGATAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (21 bp):
TGGTGGTAGTGATGATGATGG
Found at i:52629 original size:28 final size:29
Alignment explanation
Indices: 52573--52644 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
52563 AAAATCGAAT
52573 TAAACGGGGACGGGAAAAAACCGTTTATGC
1 TAAACGGGGACGGG-AAAAACCGTTTATGC
* * *
52603 TAAATGGGGACGGG-AAAACTGTTTATGT
1 TAAACGGGGACGGGAAAAACCGTTTATGC
52631 TAAACGGGGACGGG
1 TAAACGGGGACGGG
52645 GACGGGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 25 0.66
30 13 0.34
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.19
Consensus pattern (29 bp):
TAAACGGGGACGGGAAAAACCGTTTATGC
Done.