Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006773.1 Hibiscus syriacus cultivar Beakdansim tig00017122_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: 64834
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6635 original size:17 final size:17
Alignment explanation
Indices: 6598--6646 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
6588 AGTTTGATTG
* *
6598 TTTTTATTTTATTCCTA
1 TTTTTATTTTTTTCATA
* *
6615 TTTTCATTTTTTT-ATT
1 TTTTTATTTTTTTCATA
6631 TTTTTATTTTTTTCAT
1 TTTTTATTTTTTTCAT
6647 GATTGCTTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTTCATA
Found at i:7353 original size:131 final size:131
Alignment explanation
Indices: 7136--7463 Score: 451
Period size: 131 Copynumber: 2.5 Consensus size: 131
7126 GTTTTGGTTG
* * * *
7136 GAGTAATAGATGATTGCTTTAAGGCATGAGAGGTTATTTATTCTCGATTGGAAATAATCAGATAT
1 GAGTAATAAATGATTTCTTTAAGGCATGAGAGGTAATTTATTCTCGATTGGAAATAATTAGATAT
* * * * ** *
7201 TACCGTTTTCTCTGGAGTCAATATTGATTTTTAAGACGGAATAGTGATATCTCTTCATTTCGATT
66 TACCGTTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTCTTCATTTCAATT
7266 A
131 A
* * *
7267 GAGTAATAAATGATTTCTTTAAGGCATGAGAGGTCATTTATTCTCGTTTGGAAATCATTAGATAT
1 GAGTAATAAATGATTTCTTTAAGGCATGAGAGGTAATTTATTCTCGATTGGAAATAATTAGATAT
7332 TACCGTTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTCTTCATTTCAATT
66 TACCGTTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTCTTCATTTCAATT
*
7397 G
131 A
* * * * * *
7398 GGGTAATAAATGAATGT-TTAAAGGCATGAAAGGTAAATTATTCTCAATTGGAAATAATTAGATA
1 GAGTAATAAATG-ATTTCTTTAAGGCATGAGAGGTAATTTATTCTCGATTGGAAATAATTAGATA
7462 TT
65 TT
7464 GTCGTTTCTC
Statistics
Matches: 173, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
131 170 0.98
132 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (131 bp):
GAGTAATAAATGATTTCTTTAAGGCATGAGAGGTAATTTATTCTCGATTGGAAATAATTAGATAT
TACCGTTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTCTTCATTTCAATT
A
Found at i:13912 original size:33 final size:33
Alignment explanation
Indices: 13875--13942 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
13865 TTCTCTTATC
13875 TCCTTTGTTTCTTGTCG-AAGTGCATGAATTGTT
1 TCCTTTGTTTCTTGTCGCAA-TGCATGAATTGTT
* *
13908 TCCTTTGTTTCTTGTTGCAATGCCTGAATTGTT
1 TCCTTTGTTTCTTGTCGCAATGCATGAATTGTT
13941 TC
1 TC
13943 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.50
Consensus pattern (33 bp):
TCCTTTGTTTCTTGTCGCAATGCATGAATTGTT
Found at i:16566 original size:19 final size:19
Alignment explanation
Indices: 16542--16588 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16532 AAATGATTTC
* *
16542 TTTTGAAAAGAAAATTTAA-
1 TTTTGAAAACAAAA-TGAAG
16561 TTTTGAAAACAAAATGAAG
1 TTTTGAAAACAAAATGAAG
16580 TTTTGAAAA
1 TTTTGAAAA
16589 ATGATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAG
Found at i:16746 original size:24 final size:25
Alignment explanation
Indices: 16719--16768 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
16709 GTGATTTCTA
*
16719 AAAAAATTGTGTT-TTATAA-ATTTT
1 AAAAAATGGTGTTATTA-AATATTTT
*
16743 AAAATATGGTGTTATTAAATATTTT
1 AAAAAATGGTGTTATTAAATATTTT
16768 A
1 A
16769 TAAATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (25 bp):
AAAAAATGGTGTTATTAAATATTTT
Found at i:27944 original size:19 final size:19
Alignment explanation
Indices: 27904--27952 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
27894 AGGTCAAGAG
*
27904 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAAT
27923 CATGT-TTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
27942 CATGTCATTTT
1 CATGT-ATTTT
27953 AGGAAGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
21 4 0.15
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:29930 original size:24 final size:21
Alignment explanation
Indices: 29896--29938 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
29886 TCCACAAGAT
*
29896 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
29918 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
29939 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:37961 original size:27 final size:25
Alignment explanation
Indices: 37929--37978 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
37919 AAAGAAATTG
37929 AAGCACTCCAAAAGAAGAAGAAAAATC
1 AAGCACT-CAAAA-AAGAAGAAAAATC
*
37956 AAGCACTCAAAAAGGAAGAAAAA
1 AAGCACTCAAAAAAGAAGAAAAA
37979 GAAAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 5 0.23
27 7 0.32
ACGTcount: A:0.62, C:0.16, G:0.16, T:0.06
Consensus pattern (25 bp):
AAGCACTCAAAAAAGAAGAAAAATC
Found at i:40438 original size:22 final size:23
Alignment explanation
Indices: 40395--40438 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40385 TTTGAAATGA
*
40395 TTTGAAATACTTTGTAAAATTAT
1 TTTGAAATAATTTGTAAAATTAT
*
40418 TTTGAAATAATTT-TAAGATTA
1 TTTGAAATAATTTGTAAAATTA
40439 AAACTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTGAAATAATTTGTAAAATTAT
Found at i:41034 original size:17 final size:17
Alignment explanation
Indices: 40981--41046 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
40971 GAAATATAAG
*
40981 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
40997 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
41013 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
41030 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
41046 T
1 T
41047 ATCCAAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:42978 original size:22 final size:22
Alignment explanation
Indices: 42911--42991 Score: 101
Period size: 23 Copynumber: 3.7 Consensus size: 22
42901 AGAACCCCAT
* *
42911 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTTCAA
*
42932 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
42955 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
42977 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
42992 TGCTACACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 17 0.32
22 15 0.28
23 21 0.40
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:47681 original size:20 final size:19
Alignment explanation
Indices: 47641--47682 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
47631 TCTTTATTTC
*
47641 ATTTCATTCTTATTCTTTT
1 ATTTCATTCTTATTCTATT
47660 ATTTCATTACTTATAT-TATT
1 ATTTCATT-CTTAT-TCTATT
47680 ATT
1 ATT
47683 CCCTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 11 0.55
21 1 0.05
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTCATTCTTATTCTATT
Found at i:47961 original size:20 final size:21
Alignment explanation
Indices: 47938--47994 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
47928 ATTGGAGTGC
*
47938 AAAAAAGAAAAGAGAAGACAA
1 AAAAAAGAAAAGAAAAGACAA
* **
47959 AAAGAAGAAAA-AAAATTCAA
1 AAAAAAGAAAAGAAAAGACAA
47979 AAAAAAGAAAAGAAAA
1 AAAAAAGAAAAGAAAA
47995 AGAAGTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.04
Consensus pattern (21 bp):
AAAAAAGAAAAGAAAAGACAA
Found at i:47983 original size:23 final size:25
Alignment explanation
Indices: 47957--48007 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
47947 AAGAGAAGAC
47957 AAAAAG-AAGAAAAA-AAATTCAAA
1 AAAAAGAAAGAAAAAGAAATTCAAA
*
47980 AAAAAGAAAAGAAAAAGAAGTTCAAA
1 AAAAAG-AAAGAAAAAGAAATTCAAA
48006 AA
1 AA
48008 GAGAAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
25 8 0.33
26 10 0.42
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.08
Consensus pattern (25 bp):
AAAAAGAAAGAAAAAGAAATTCAAA
Found at i:62655 original size:23 final size:22
Alignment explanation
Indices: 62629--62681 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
62619 TTTCTTTCTT
62629 TTTCTTTTTCAAGTGCTTTTGAA
1 TTTCTTTTTCAAGTGCTTTTG-A
** *
62652 TTTCTTCTTTTGAGTGCTTTTGT
1 TTTCTT-TTTCAAGTGCTTTTGA
62675 TTTCTTT
1 TTTCTTT
62682 GCTGAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 12 0.46
24 13 0.50
ACGTcount: A:0.09, C:0.13, G:0.13, T:0.64
Consensus pattern (22 bp):
TTTCTTTTTCAAGTGCTTTTGA
Done.