Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005127.1 Hibiscus syriacus cultivar Beakdansim tig00011537_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: 84837
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:5348 original size:19 final size:19
Alignment explanation
Indices: 5324--5378 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
5314 AAAAATAATA
5324 TAAATATATTATATAATT-T
1 TAAATATATTATA-AATTAT
*
5343 TAAATAATATT-TAATTTAT
1 TAAAT-ATATTATAAATTAT
5362 TAAATATTATTATAAAT
1 TAAATA-TATTATAAAT
5379 CTTTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 4 0.13
19 17 0.57
20 9 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATATATTATAAATTAT
Found at i:5894 original size:2 final size:2
Alignment explanation
Indices: 5887--5912 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5877 ATACAATAAC
5887 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
5913 GAACGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8719 original size:2 final size:2
Alignment explanation
Indices: 8714--8749 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8704 ACACACGCTC
8714 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
8750 GCATACATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9524 original size:13 final size:13
Alignment explanation
Indices: 9508--9542 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
9498 ATTAATCTAT
9508 ATTATTTATTATA
1 ATTATTTATTATA
9521 ATTA-TTATTATA
1 ATTATTTATTATA
*
9533 AATATTTATT
1 ATTATTTATT
9543 CTATATTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATTTATTATA
Found at i:10486 original size:5 final size:5
Alignment explanation
Indices: 10457--10548 Score: 125
Period size: 5 Copynumber: 18.8 Consensus size: 5
10447 TATAAATAAT
* * * *
10457 ATATT ATATT ATATC ATATT ATATC ATATC ATACC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
*
10507 ATATC A-ATC ATTTC ATATC ATATC ATATC ATATC ATAT- ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
10549 GATAAAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
4 8 0.10
5 71 0.90
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATC
Found at i:26358 original size:15 final size:16
Alignment explanation
Indices: 26332--26363 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
26322 TTATAAATAT
26332 AATAATATTTTTAAAA
1 AATAATATTTTTAAAA
26348 AATAA-ATTTTTAAAA
1 AATAATATTTTTAAAA
26363 A
1 A
26364 TATCAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATATTTTTAAAA
Found at i:26692 original size:16 final size:15
Alignment explanation
Indices: 26671--26703 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
26661 TTGTGAATTT
26671 TTTTAATTAATTTATA
1 TTTTAATTAATTT-TA
26687 TTTTAATTAATTTTA
1 TTTTAATTAATTTTA
26702 TT
1 TT
26704 CGACCAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATTAATTTTA
Found at i:28970 original size:19 final size:19
Alignment explanation
Indices: 28946--29010 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
28936 TATACAAAAC
28946 TTTTATTGAATATAAACGA
1 TTTTATTGAATATAAACGA
*
28965 TTTTATTTGTGAACATAAAC--
1 TTTTA--T-TGAATATAAACGA
*
28985 TTTTATTGAATATAAATGA
1 TTTTATTGAATATAAACGA
29004 TTTTATT
1 TTTTATT
29011 TGTGAACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 9 0.24
18 1 0.03
19 12 0.32
20 5 0.13
21 1 0.03
22 10 0.26
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (19 bp):
TTTTATTGAATATAAACGA
Found at i:28977 original size:22 final size:22
Alignment explanation
Indices: 28952--29022 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
28942 AAACTTTTAT
*
28952 TGAATATAAACGATTTTATTTG
1 TGAACATAAACGATTTTATTTG
28974 TGAACATAAAC--TTTTA--T-
1 TGAACATAAACGATTTTATTTG
* *
28991 TGAATATAAATGATTTTATTTG
1 TGAACATAAACGATTTTATTTG
29013 TGAACATAAA
1 TGAACATAAA
29023 AGAACAATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 9 0.22
18 1 0.03
19 5 0.12
20 5 0.12
21 1 0.03
22 19 0.47
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAACATAAACGATTTTATTTG
Found at i:28996 original size:39 final size:39
Alignment explanation
Indices: 28942--29022 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
28932 AGTATATACA
28942 AAACTTTTATTGAATATAAACGATTTTATTTGTGAACAT
1 AAACTTTTATTGAATATAAACGATTTTATTTGTGAACAT
*
28981 AAACTTTTATTGAATATAAATGATTTTATTTGTGAACAT
1 AAACTTTTATTGAATATAAACGATTTTATTTGTGAACAT
29020 AAA
1 AAA
29023 AGAACAATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (39 bp):
AAACTTTTATTGAATATAAACGATTTTATTTGTGAACAT
Found at i:28999 original size:17 final size:17
Alignment explanation
Indices: 28942--29000 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
28932 AGTATATACA
28942 AAACTTTTATTGAATAT
1 AAACTTTTATTGAATAT
*
28959 AAACGATTTTATTTGTGAACAT
1 AAAC--TTTTA--T-TGAATAT
28981 AAACTTTTATTGAATAT
1 AAACTTTTATTGAATAT
28998 AAA
1 AAA
29001 TGATTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 13 0.37
18 1 0.03
19 5 0.14
20 5 0.14
21 1 0.03
22 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (17 bp):
AAACTTTTATTGAATAT
Found at i:53550 original size:18 final size:17
Alignment explanation
Indices: 53523--53557 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53513 TCACAGGTTG
*
53523 AAGTCCCATAACATAATT
1 AAGTCACATAACA-AATT
53541 AAGTCACATAACAAATT
1 AAGTCACATAACAAATT
53558 CTTGGTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (17 bp):
AAGTCACATAACAAATT
Found at i:55868 original size:31 final size:31
Alignment explanation
Indices: 55802--55954 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
55792 CCCGAAGGAC
* *
55802 CAGTCCATA-GATTCCGAAGAACCTAGGT-AA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
55832 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
55863 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
55894 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
55925 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
55955 CCCTCGACCC
Statistics
Matches: 119, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
30 24 0.20
31 95 0.80
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:57177 original size:12 final size:12
Alignment explanation
Indices: 57160--57185 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57150 ATATATATCA
57160 TTTAATTATATT
1 TTTAATTATATT
57172 TTTAATTATATT
1 TTTAATTATATT
57184 TT
1 TT
57186 CAAGTCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTAATTATATT
Found at i:60204 original size:31 final size:31
Alignment explanation
Indices: 60166--60319 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
60156 CCCGAAGGAC
* *
60166 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
60197 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
60228 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
60259 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
60290 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
60320 CCCTCGACCC
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:65176 original size:22 final size:22
Alignment explanation
Indices: 65135--65201 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
65125 CTCGTATAAA
65135 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
65158 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
65180 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
65202 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:66915 original size:21 final size:21
Alignment explanation
Indices: 66891--66935 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66881 TCTAGTTCGT
* *
66891 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
66912 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
66933 TTG
1 TTG
66936 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:70116 original size:22 final size:22
Alignment explanation
Indices: 70075--70163 Score: 160
Period size: 22 Copynumber: 4.0 Consensus size: 22
70065 CTCGTATAAA
70075 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
70098 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70120 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
70142 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70164 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 53 0.82
23 12 0.18
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:70151 original size:13 final size:13
Alignment explanation
Indices: 70089--70151 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
70079 CCGAAGTGCC
70089 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
70102 CC---GAAGTGC-
1 CCGTAGAATTGCA
70111 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
70124 CC---GAAGTGC-
1 CCGTAGAATTGCA
70133 CCGTAGAATTGCA
1 CCGTAGAATTGCA
70146 CCGTAG
1 CCGTAG
70152 TGCCCGTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:71870 original size:21 final size:21
Alignment explanation
Indices: 71846--71890 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
71836 TCTAGTTCGT
* *
71846 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
71867 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
71888 TTG
1 TTG
71891 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.