Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000825.1 Hibiscus syriacus cultivar Beakdansim tig00001596_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: 51544
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1255 original size:29 final size:29
Alignment explanation
Indices: 1222--1322 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 29
1212 TGTATTACTT
* *
1222 ATTCTACATGGGATTATATCCCTGTCTTG
1 ATTCTGCATGAGATTATATCCCTGTCTTG
* *
1251 ATTCTGCATGAGATTATATCCCCGTCCTG
1 ATTCTGCATGAGATTATATCCCTGTCTTG
* * **
1280 ATTCTGTATGTGATTATATTTCTGTCTTG
1 ATTCTGCATGAGATTATATCCCTGTCTTG
* *
1309 TTTCTGCGTGAGAT
1 ATTCTGCATGAGAT
1323 CATCTACGGA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (29 bp):
ATTCTGCATGAGATTATATCCCTGTCTTG
Found at i:10561 original size:2 final size:2
Alignment explanation
Indices: 10556--10580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10546 CGTGTGTGTG
10556 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10581 TATCATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11349 original size:2 final size:2
Alignment explanation
Indices: 11344--11373 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11334 CAATTAATAG
11344 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
11374 ACGTAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13207 original size:17 final size:17
Alignment explanation
Indices: 13169--13213 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
13159 TTCAAAAGAT
*
13169 ATATTATAAAATTTAAAA
1 ATATTA-AAAATTAAAAA
13187 ATATTAAAAA-TAAAAA
1 ATATTAAAAATTAAAAA
13203 GATATTAAAAA
1 -ATATTAAAAA
13214 ATTATTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 14 0.56
18 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATTAAAAATTAAAAA
Found at i:15405 original size:3 final size:3
Alignment explanation
Indices: 15397--15421 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
15387 CATTCATGTA
15397 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
15422 ATGTTCCATT
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
Found at i:25947 original size:10 final size:11
Alignment explanation
Indices: 25922--25946 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25912 CAGCAATTCG
25922 AAAAGAAAAAA
1 AAAAGAAAAAA
25933 AAAAGAAAAAA
1 AAAAGAAAAAA
25944 AAA
1 AAA
25947 GCTGTTCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:25955 original size:33 final size:35
Alignment explanation
Indices: 25902--25972 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
25892 CTCCATCGAG
25902 AGAAAAAAAACAGCAATTCG-AAAAGAAAAAAAAA
1 AGAAAAAAAACAGCAATTCGAAAAAGAAAAAAAAA
** *
25936 AGAAAAAAAA-AGCTGTTCGAAAAAGAAGAAAAAA
1 AGAAAAAAAACAGCAATTCGAAAAAGAAAAAAAAA
25970 AGA
1 AGA
25973 CATGAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (35 bp):
AGAAAAAAAACAGCAATTCGAAAAAGAAAAAAAAA
Found at i:40743 original size:20 final size:20
Alignment explanation
Indices: 40718--40763 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
40708 ACTCACGTTA
40718 GCACACTCCTATGGAGACCT
1 GCACACTCCTATGGAGACCT
*
40738 GCACACTCCTATGGAGACTT
1 GCACACTCCTATGGAGACCT
40758 GCACAC
1 GCACAC
40764 ATTAGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.20
Consensus pattern (20 bp):
GCACACTCCTATGGAGACCT
Found at i:43130 original size:13 final size:13
Alignment explanation
Indices: 43112--43139 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43102 CGAAGAGAAA
43112 ATCTTATTCGATG
1 ATCTTATTCGATG
43125 ATCTTATTCGATG
1 ATCTTATTCGATG
43138 AT
1 AT
43140 ATAAAGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
ATCTTATTCGATG
Found at i:45028 original size:21 final size:21
Alignment explanation
Indices: 45002--45056 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
44992 ACTAATGAGG
*
45002 TTTATTTTCTTTGA-ATTTTTC
1 TTTATTTTCTTTGACA-TTATC
*
45023 TTTATTTACTTT-ACATTATC
1 TTTATTTTCTTTGACATTATC
*
45043 TTTGTTTTCTTTGA
1 TTTATTTTCTTTGA
45057 GTGTTGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTATTTTCTTTGACATTATC
Found at i:48975 original size:19 final size:19
Alignment explanation
Indices: 48953--48991 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
48943 GTAAGAACGC
48953 TCATAATTAGGAAGAATGT
1 TCATAATTAGGAAGAATGT
48972 TCATAATTAGGAAGAATGT
1 TCATAATTAGGAAGAATGT
48991 T
1 T
48992 TACCTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (19 bp):
TCATAATTAGGAAGAATGT
Found at i:49977 original size:24 final size:22
Alignment explanation
Indices: 49931--49977 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
49921 ATTATGACGA
49931 ATTATCTTTTAGGATTAGATTT
1 ATTATCTTTTAGGATTAGATTT
* *
49953 ATTATTTTATTAGGAATTAGTTTT
1 ATTATCTT-TTAGG-ATTAGATTT
49977 A
1 A
49978 GTTAAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 5 0.24
24 9 0.43
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (22 bp):
ATTATCTTTTAGGATTAGATTT
Done.