Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006218.1 Hibiscus syriacus cultivar Beakdansim tig00014810_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: 59833
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:11684 original size:15 final size:16
Alignment explanation
Indices: 11666--11699 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11656 TATGAACATC
11666 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
11681 AAATAGAATAACAATA
1 AAATAAAATAACAATA
11697 AAA
1 AAA
11700 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:11933 original size:21 final size:22
Alignment explanation
Indices: 11907--11948 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11897 TGCAAATGAC
*
11907 AAATAA-AATATTTACAATATT
1 AAATAAGAACATTTACAATATT
*
11928 AAATAAGAACATTTACTATAT
1 AAATAAGAACATTTACAATAT
11949 ATGCATAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATAAGAACATTTACAATATT
Found at i:13846 original size:3 final size:3
Alignment explanation
Indices: 13838--13877 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
13828 TGTAATTAAT
**
13838 TAA TAA TAA TAAA TAA CGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13878 AAAAAAGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:24581 original size:19 final size:19
Alignment explanation
Indices: 24549--24594 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
24539 CGGTCCAAAC
*
24549 CGGTCTGAACCGGTTTAAT
1 CGGTCCGAACCGGTTTAAT
* *
24568 CGGTCCGAATCGGTTTGAT
1 CGGTCCGAACCGGTTTAAT
24587 CGGTCCGA
1 CGGTCCGA
24595 CCCGACCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
CGGTCCGAACCGGTTTAAT
Found at i:24730 original size:58 final size:58
Alignment explanation
Indices: 24609--24771 Score: 206
Period size: 58 Copynumber: 2.8 Consensus size: 58
24599 ACCTGATACA
* * * *
24609 GTGACATTCT-GGAAATTTTTGTGAAAAAGGTGATATTCTGGGAAATATTTTTAAAAAAG
1 GTGACATTCTGGGAAATTTTT-TGAAAAATGTGACATT-TGGGAATTATTTTAAAAAAAG
*
24668 GTGACATTCTGGGAAATTTTTTGAAAAAATATGACA-TTGGGAATTATTTTAAAAAAAG
1 GTGACATTCTGGGAAATTTTTTG-AAAAATGTGACATTTGGGAATTATTTTAAAAAAAG
*
24726 GTGACATGCTGGG-AATTATTTTGAAAAATGTGACATTTTGGGAATT
1 GTGACATTCTGGGAAATT-TTTTGAAAAATGTGACA-TTTGGGAATT
24772 TTCGAATATG
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
57 15 0.16
58 36 0.39
59 22 0.24
60 19 0.21
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.36
Consensus pattern (58 bp):
GTGACATTCTGGGAAATTTTTTGAAAAATGTGACATTTGGGAATTATTTTAAAAAAAG
Found at i:24770 original size:29 final size:29
Alignment explanation
Indices: 24609--24771 Score: 163
Period size: 30 Copynumber: 5.6 Consensus size: 29
24599 ACCTGATACA
*
24609 GTGACATTCTGGAAATT-TTTGTGAAAAAG
1 GTGACATTCTGGGAATTATTT-TGAAAAAG
* * *
24638 GTGATATTCTGGGAAATATTTTTAAAAAAG
1 GTGACATTCTGGGAATTA-TTTTGAAAAAG
*
24668 GTGACATTCTGGGAAATT-TTTTGAAAAAAT
1 GTGACATTCTGGG-AATTATTTTG-AAAAAG
* *
24698 ATGACA-T-TGGGAATTATTTTAAAAAAAG
1 GTGACATTCTGGGAATTATTTT-GAAAAAG
* *
24726 GTGACATGCTGGGAATTATTTTGAAAAAT
1 GTGACATTCTGGGAATTATTTTGAAAAAG
*
24755 GTGACATTTTGGGAATT
1 GTGACATTCTGGGAATT
24772 TTCGAATATG
Statistics
Matches: 109, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
27 4 0.04
28 18 0.17
29 39 0.36
30 42 0.39
31 6 0.06
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.36
Consensus pattern (29 bp):
GTGACATTCTGGGAATTATTTTGAAAAAG
Found at i:29783 original size:29 final size:29
Alignment explanation
Indices: 29740--29822 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
29730 CTCACCTAAC
29740 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
29770 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
29799 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
29823 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34545 original size:29 final size:29
Alignment explanation
Indices: 34502--34584 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
34492 CTCACCTAAC
34502 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
34532 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
34561 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
34585 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:38767 original size:21 final size:21
Alignment explanation
Indices: 38727--38771 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
38717 GGGCTCTCAG
*
38727 ATCATATCATATCCATTCATTA
1 ATCATATCATATCCAATCA-TA
*
38749 ATCATA-CATTTCCAATCATA
1 ATCATATCATATCCAATCATA
38769 ATC
1 ATC
38772 TTTTTCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
ATCATATCATATCCAATCATA
Found at i:41566 original size:23 final size:23
Alignment explanation
Indices: 41540--41607 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
41530 TCTATGCGGT
*
41540 CCTTCGGGACAATTCTACGTGGA
1 CCTTCGGGACATTTCTACGTGGA
* * *
41563 CCTTCAGGACATTTCTACGCGGT
1 CCTTCGGGACATTTCTACGTGGA
* *
41586 CCTTCGGAACATTTCTATGTGG
1 CCTTCGGGACATTTCTACGTGG
41608 CACTTTGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
CCTTCGGGACATTTCTACGTGGA
Found at i:41881 original size:2 final size:2
Alignment explanation
Indices: 41798--41873 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
41788 GATGATATGC
41798 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
41840 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
41874 GCATATATGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58870 original size:19 final size:19
Alignment explanation
Indices: 58846--58884 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
58836 AACTTATACA
*
58846 ATTTCATAAAAAATTTAAT
1 ATTTCATAAAAAAATTAAT
58865 ATTTCATAAAAAAATTAAT
1 ATTTCATAAAAAAATTAAT
58884 A
1 A
58885 CATACCTGTA
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:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTCATAAAAAAATTAAT
Done.