Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005002.1 Hibiscus syriacus cultivar Beakdansim tig00011223_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: 71987
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7783 original size:6 final size:6
Alignment explanation
Indices: 7774--7807 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
7764 GATTCATCTC
* *
7774 CATCAT CATCAA CATCAG CATCAG CATCAG CATC
1 CATCAG CATCAG CATCAG CATCAG CATCAG CATC
7808 CATTAAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.21
Consensus pattern (6 bp):
CATCAG
Found at i:19465 original size:3 final size:3
Alignment explanation
Indices: 19439--19486 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
19429 TCTTCTTCTT
* * *
19439 CTA CTC CTA CTT CTA CTT CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
19487 ATGCTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (3 bp):
CTA
Found at i:19497 original size:3 final size:3
Alignment explanation
Indices: 19491--19528 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19481 CTACTAATGC
19491 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19529 TTCGTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19899 original size:23 final size:21
Alignment explanation
Indices: 19868--19909 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
19858 AGGGTGTGCT
*
19868 TGGTTGAGTGGAAAGATGGAATA
1 TGGTAGAGT-GAAAG-TGGAATA
19891 TGGTAGAGTGAAAGTGGAA
1 TGGTAGAGTGAAAGTGGAA
19910 ATATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (21 bp):
TGGTAGAGTGAAAGTGGAATA
Found at i:25779 original size:17 final size:17
Alignment explanation
Indices: 25735--25768 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25725 TTAATATTTT
*
25735 GTATTTAATTTATTTAA
1 GTATTTATTTTATTTAA
25752 GTATTTATTTTATTTAA
1 GTATTTATTTTATTTAA
25769 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
GTATTTATTTTATTTAA
Found at i:38140 original size:16 final size:16
Alignment explanation
Indices: 38119--38150 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38109 AATCCGATAA
38119 AATATTATAATGATTT
1 AATATTATAATGATTT
*
38135 AATATTATAATTATTT
1 AATATTATAATGATTT
38151 TTTATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATATTATAATGATTT
Found at i:48014 original size:14 final size:14
Alignment explanation
Indices: 47995--48021 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47985 TCTTTCGAAA
47995 AGAAAAAGCAAAAC
1 AGAAAAAGCAAAAC
48009 AGAAAAAGCAAAA
1 AGAAAAAGCAAAA
48022 AAATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAAAAAGCAAAAC
Found at i:51564 original size:16 final size:17
Alignment explanation
Indices: 51543--51579 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
51533 TTAATTTATA
51543 ATTTTAG-GG-TTAAAT
1 ATTTTAGAGGTTTAAAT
51558 GATTTTAGAGGTTTAAAT
1 -ATTTTAGAGGTTTAAAT
51576 ATTT
1 ATTT
51580 CTTTAGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (17 bp):
ATTTTAGAGGTTTAAAT
Found at i:58972 original size:21 final size:22
Alignment explanation
Indices: 58946--58997 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
58936 TTTGATTTTT
*
58946 TAATAATTTTTAAAAT-TTTAA
1 TAATAATTTATAAAATATTTAA
*
58967 TAATAA-TAATAAAATATTTAA
1 TAATAATTTATAAAATATTTAA
*
58988 TTATAATTTA
1 TAATAATTTA
58998 ATAACATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 16 0.64
22 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATTTATAAAATATTTAA
Found at i:59009 original size:23 final size:21
Alignment explanation
Indices: 58956--59014 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
58946 TAATAATTTT
58956 TAAAA-TTTTAATAATAATAA
1 TAAAATTTTTAATAATAATAA
* *
58976 TAAAATATTTAATTATAATTTAA
1 TAAAATTTTTAATAATAA--TAA
*
58999 TAACATTTTTAGATAA
1 TAAAATTTTTA-ATAA
59015 ATTATGTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.17
21 10 0.33
23 12 0.40
24 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAAATTTTTAATAATAATAA
Found at i:61292 original size:24 final size:23
Alignment explanation
Indices: 61204--61289 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
61194 ACATATTATA
*
61204 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
61227 TGGCACTTCGGTGC-ATCTCTACG
1 TGGCACTTCGGTGCAAT-TCTACG
* *
61250 CGGTC-CTTTGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
61274 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
61290 ATTTATATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
22 3 0.06
23 30 0.59
24 15 0.29
25 3 0.06
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:62824 original size:19 final size:19
Alignment explanation
Indices: 62800--62838 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
62790 TCAAATGCAT
62800 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
62819 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
62838 T
1 T
62839 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:62855 original size:65 final size:64
Alignment explanation
Indices: 62737--62945 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
62727 TATTCAAAGG
* * *
62737 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCAAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
62798 ATTC
61 ATTT
62802 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
62867 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
62931 CATGCATCGATGCAC
1 CATGCACCGATGCAC
62946 ACTTGGTGCA
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:62963 original size:64 final size:65
Alignment explanation
Indices: 62786--62948 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
62776 GAATTAATTG
* * * * *
62786 AACATCAAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
62851 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
62914 A
65 A
62915 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
62949 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:70299 original size:19 final size:19
Alignment explanation
Indices: 70275--70313 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
70265 TCAAATGCAT
70275 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
70294 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
70313 T
1 T
70314 GAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:70376 original size:45 final size:46
Alignment explanation
Indices: 70296--70401 Score: 160
Period size: 45 Copynumber: 2.3 Consensus size: 46
70286 ATGCACTCTC
*
70296 CATGCATCGATGCACTCTGAATATTTTTAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGAATATTTTTAAAACATCGAATGCATTT
* ** *
70342 GATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGAATATTTTTAAAACATCGAATGCATTT
70387 CATGCATCGATGCAC
1 CATGCATCGATGCAC
70402 ACTTGGTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
45 40 0.74
46 14 0.26
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (46 bp):
CATGCATCGATGCACTCAGAATATTTTTAAAACATCGAATGCATTT
Done.