Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000336.1 Hibiscus syriacus cultivar Beakdansim tig00000626_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: 61995
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:10775 original size:53 final size:53
Alignment explanation
Indices: 10712--10817 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
10702 TAATTTACGG
*
10712 CATCAACTTAATAAAATATATTATTATAAATATAAATACTCAAATGAATAACA
1 CATCAACTTAATAAAAGATATTATTATAAATATAAATACTCAAATGAATAACA
*
10765 CATCAACTTAATAAAAGATGTTATTATAAATATAAATACTCAAATGAATAACA
1 CATCAACTTAATAAAAGATATTATTATAAATATAAATACTCAAATGAATAACA
10818 TGTTGTATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.31
Consensus pattern (53 bp):
CATCAACTTAATAAAAGATATTATTATAAATATAAATACTCAAATGAATAACA
Found at i:11958 original size:27 final size:27
Alignment explanation
Indices: 11928--11981 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
11918 GGTAAGCTTC
11928 AGTGTAAACTTTTATTTGAAGGTGTAT
1 AGTGTAAACTTTTATTTGAAGGTGTAT
11955 AGTGTAAACTTTTATTTGAAGGTGTAT
1 AGTGTAAACTTTTATTTGAAGGTGTAT
11982 GTAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (27 bp):
AGTGTAAACTTTTATTTGAAGGTGTAT
Found at i:12697 original size:2 final size:2
Alignment explanation
Indices: 12692--12736 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12682 CCCCAACAAA
12692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
12734 AT A
1 AT A
12737 AATCAAAGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15475 original size:2 final size:2
Alignment explanation
Indices: 15468--15552 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
15458 AGATTTTCTC
15468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
15510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
15552 A
1 A
15553 ATTAAACTAC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28264 original size:12 final size:12
Alignment explanation
Indices: 28238--28291 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
28228 CAATATCGTA
28238 TGAACAGTA--G
1 TGAACAGTACTG
28248 TGAACAGTACTG
1 TGAACAGTACTG
*
28260 TGAACAGTACTA
1 TGAACAGTACTG
*
28272 TAAACAGTACTG
1 TGAACAGTACTG
28284 TGAACAGT
1 TGAACAGT
28292 GTCGAATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
12 29 0.76
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (12 bp):
TGAACAGTACTG
Found at i:29259 original size:23 final size:23
Alignment explanation
Indices: 29225--29268 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29215 ATTACATATA
29225 TGTCCCGAAGGACCA-CGTAGAAT
1 TGTCCCGAAGGA-CAGCGTAGAAT
*
29248 TGTCCCGTAGGACAGCGTAGA
1 TGTCCCGAAGGACAGCGTAGA
29269 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACAGCGTAGAAT
Found at i:33743 original size:45 final size:45
Alignment explanation
Indices: 33679--33807 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 45
33669 GATATATTTT
* ** * *
33679 CTGAAGGAAAGCAATTGGATGACACAATAACTGATGAGACTGTTG
1 CTGAAGGAAAGCATTTGGATGGTACAATAACTGATGACACTGTTA
* * *
33724 CTGAAGGGAAGCATTTGGATGGTACAATAGCTGATGACATTGTTA
1 CTGAAGGAAAGCATTTGGATGGTACAATAACTGATGACACTGTTA
*
33769 CTGAAGGAAAGCATTTGGATGGTACAAAAACTGATGACA
1 CTGAAGGAAAGCATTTGGATGGTACAATAACTGATGACA
33808 ATGATATTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (45 bp):
CTGAAGGAAAGCATTTGGATGGTACAATAACTGATGACACTGTTA
Found at i:38826 original size:18 final size:18
Alignment explanation
Indices: 38800--38837 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38790 TCTCTCTCCG
38800 CGTGATCCAACACTTCCT
1 CGTGATCCAACACTTCCT
* *
38818 CGTGTTCCACCACTTCCT
1 CGTGATCCAACACTTCCT
38836 CG
1 CG
38838 AATTGCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.42, G:0.13, T:0.29
Consensus pattern (18 bp):
CGTGATCCAACACTTCCT
Found at i:46945 original size:17 final size:17
Alignment explanation
Indices: 46923--46980 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
46913 AATTATATTT
*
46923 CAATTCCTAACAAATTC
1 CAATTCCTAACAGATTC
*
46940 CAATTCCTGACAGATTC
1 CAATTCCTAACAGATTC
46957 CAATTCCTAACAGATTC
1 CAATTCCTAACAGATTC
46974 CAATTCC
1 CAATTCC
46981 CTCATAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.29
Consensus pattern (17 bp):
CAATTCCTAACAGATTC
Found at i:47603 original size:17 final size:18
Alignment explanation
Indices: 47567--47607 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
47557 ATATTATGTA
*
47567 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
47585 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
47602 TTTACT
1 TTTACT
47608 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:49964 original size:35 final size:34
Alignment explanation
Indices: 49925--50003 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 34
49915 GTATTTCAGT
*
49925 TAATTTTGTCT-A-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTATCATTTACCATTTAAT-TC--TTATTG
*
49960 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTG-TATCATTTACCATTTAATTCTTATTG
*
49995 TAAGTTTGT
1 TAATTTTGT
50004 TGTATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
34 1 0.03
35 19 0.51
36 2 0.05
37 3 0.08
38 12 0.32
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (34 bp):
TAATTTTGTATCATTTACCATTTAATTCTTATTG
Found at i:53583 original size:21 final size:21
Alignment explanation
Indices: 53557--53596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53547 CAGAACCCCA
*
53557 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
53578 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
53597 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:53631 original size:20 final size:21
Alignment explanation
Indices: 53579--53639 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
53569 TTCCCCTGTG
53579 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
53602 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
53622 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
53640 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Done.