Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006903.1 Hibiscus syriacus cultivar Beakdansim tig00017630_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: 50512
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:7570 original size:20 final size:20
Alignment explanation
Indices: 7525--7574 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
7515 CGATGAACAT
*
7525 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
7546 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
7566 TATCGATAC
1 TATCGATAC
7575 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:8422 original size:20 final size:20
Alignment explanation
Indices: 8397--8436 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8387 TAGATTGTCT
*
8397 AGGGGGTACATATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
*
8417 AGGGGGTACCGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
8437 TGTCTAACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.17
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:9393 original size:24 final size:24
Alignment explanation
Indices: 9348--9436 Score: 119
Period size: 24 Copynumber: 3.8 Consensus size: 24
9338 GAGGGTATGC
*
9348 GGTCCTTCAGGAC-AATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
*
9371 GGTCCTTCGGGACAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTACGT
*
9395 GGTCCTTCGGGACATATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
*
9419 GG-CACTTCGGTACAAATT
1 GGTC-CTTCGGGACAAATT
9437 ATGTGAGCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.22
24 45 0.78
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACGT
Found at i:9427 original size:48 final size:47
Alignment explanation
Indices: 9346--9436 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 47
9336 TTGAGGGTAT
9346 GCGGTCCTTCAGGACAATTCTACGTGGTCCTTCGGGACAAATTCTAC
1 GCGGTCCTTCAGGACAATTCTACGTGGTCCTTCGGGACAAATTCTAC
* *
9393 GCGGTCCTTCGGGACATATTCTACGTGG-CACTTCGGTACAAATT
1 GCGGTCCTTCAGGACA-ATTCTACGTGGTC-CTTCGGGACAAATT
9437 ATGTGAGCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 16 0.40
48 24 0.60
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (47 bp):
GCGGTCCTTCAGGACAATTCTACGTGGTCCTTCGGGACAAATTCTAC
Found at i:11804 original size:22 final size:25
Alignment explanation
Indices: 11755--11805 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 25
11745 ACATTTGATT
11755 TTTCTGTAGATATCATCAATATAATA
1 TTTCTGTAGATATCAT-AATATAATA
*
11781 TTTC-GTAGATAT-AT-ATATATTA
1 TTTCTGTAGATATCATAATATAATA
11803 TTT
1 TTT
11806 GGTTGATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 10 0.42
24 2 0.08
25 8 0.33
26 4 0.17
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (25 bp):
TTTCTGTAGATATCATAATATAATA
Found at i:16097 original size:16 final size:16
Alignment explanation
Indices: 16076--16109 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16066 TCCAACAAAT
16076 GGTCCATGAAGCCAAG
1 GGTCCATGAAGCCAAG
16092 GGTCCATGAAGCCAAG
1 GGTCCATGAAGCCAAG
16108 GG
1 GG
16110 ACCAAAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCCATGAAGCCAAG
Found at i:18877 original size:20 final size:20
Alignment explanation
Indices: 18832--18881 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
18822 CGATGAACAT
*
18832 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
18853 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
18873 TATCGATAC
1 TATCGATAC
18882 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:21108 original size:20 final size:20
Alignment explanation
Indices: 21063--21112 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
21053 CGATGAACAT
*
21063 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
21084 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
21104 TATCGATAC
1 TATCGATAC
21113 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:23341 original size:20 final size:20
Alignment explanation
Indices: 23296--23345 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
23286 CGATGAACAT
*
23296 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
23317 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
23337 TATCGATAC
1 TATCGATAC
23346 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:23918 original size:2 final size:2
Alignment explanation
Indices: 23911--23961 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
23901 ATGGGAATAC
23911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23953 TA TA TA TA T
1 TA TA TA TA T
23962 TATGAATATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24241 original size:24 final size:24
Alignment explanation
Indices: 24212--24266 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
24202 CCTTCAGAAC
* * *
24212 AATTCTACGTTGTCTTTCGGGACA
1 AATTCTACGCTATCCTTCGGGACA
24236 AATTCTACGCTATCCTTCGGGACA
1 AATTCTACGCTATCCTTCGGGACA
*
24260 TATTCTA
1 AATTCTA
24267 TGTGGCACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (24 bp):
AATTCTACGCTATCCTTCGGGACA
Found at i:33937 original size:20 final size:20
Alignment explanation
Indices: 33892--33941 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
33882 CGATGAACAT
*
33892 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
33913 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
33933 TATCGATAC
1 TATCGATAC
33942 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:34784 original size:19 final size:19
Alignment explanation
Indices: 34760--34797 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34750 TAGATTGTCT
*
34760 AGGGGGTACATATTCCCCC
1 AGGGGGTACAGATTCCCCC
*
34779 AGGGGGTACCGATTCCCCC
1 AGGGGGTACAGATTCCCCC
34798 CTGTCTAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.34, G:0.29, T:0.18
Consensus pattern (19 bp):
AGGGGGTACAGATTCCCCC
Found at i:35750 original size:24 final size:24
Alignment explanation
Indices: 35705--35777 Score: 112
Period size: 24 Copynumber: 3.1 Consensus size: 24
35695 GAGGGTATGC
*
35705 GGTCCTTCAGGAC-AATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
*
35728 GGTCCTTCGGGACAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTACGT
*
35752 GGTCCTTCGGGACATATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
35776 GG
1 GG
35778 CACTCGGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 12 0.27
24 33 0.73
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACGT
Found at i:42409 original size:15 final size:16
Alignment explanation
Indices: 42389--42421 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
42379 TCCAACAAAT
42389 GGTCCATGAAG-CAAG
1 GGTCCATGAAGACAAG
42404 GGTCCATGAAGACAAG
1 GGTCCATGAAGACAAG
42420 GG
1 GG
42422 ACCAAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.33, C:0.18, G:0.36, T:0.12
Consensus pattern (16 bp):
GGTCCATGAAGACAAG
Found at i:45172 original size:20 final size:20
Alignment explanation
Indices: 45127--45176 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
45117 CGATGAACAT
*
45127 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
45148 TATCGATACTGATGTGAAG-G
1 TATCGATACTGAT-TGAAGAG
45168 TATCGATAC
1 TATCGATAC
45177 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:50134 original size:2 final size:2
Alignment explanation
Indices: 50127--50180 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
50117 AGATATGGGA
50127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
50168 AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT
50181 TGAATTATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:50452 original size:24 final size:23
Alignment explanation
Indices: 50425--50481 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
50415 TCTTCAGAAC
* *
50425 AATTCTACGTTGTCTTTCGGGACA
1 AATTCTACGTTATC-CTCGGGACA
*
50449 AATTCTACGCTATCCTCGGGACA
1 AATTCTACGTTATCCTCGGGACA
*
50472 TATTCTACGT
1 AATTCTACGT
50482 GGCACTTCGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (23 bp):
AATTCTACGTTATCCTCGGGACA
Done.