Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000607.1 Hibiscus syriacus cultivar Beakdansim tig00001180_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: 83732
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12377 original size:24 final size:25
Alignment explanation
Indices: 12349--12398 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
12339 GCGAATGTTT
12349 CACACCGAAATACACTATTAATATTA
1 CACA-CGAAATACACTATTAATATTA
* *
12375 CACATCGATATGCACTATTAATAT
1 CACA-CGAAATACACTATTAATAT
12399 GAAATAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (25 bp):
CACACGAAATACACTATTAATATTA
Found at i:14345 original size:24 final size:24
Alignment explanation
Indices: 14318--14365 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
14308 AATGTGGCCT
*
14318 CAAACTTAGAAAACAAACCCAATG
1 CAAACTTAGAAAACAAACACAATG
*
14342 CAAATTTAGAAAACAAACACAATG
1 CAAACTTAGAAAACAAACACAATG
14366 TATCCCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (24 bp):
CAAACTTAGAAAACAAACACAATG
Found at i:14620 original size:16 final size:16
Alignment explanation
Indices: 14601--14653 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
14591 TACTAAAATT
14601 AAAAATTAAATTACTA
1 AAAAATTAAATTACTA
*
14617 AAAAATTAAATATATATTTA
1 AAAAATT-AA-AT-TA-CTA
14637 AAAAATTAAATTACTA
1 AAAAATTAAATTACTA
14653 A
1 A
14654 GGAAACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 4 0.13
19 4 0.13
20 9 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAATTAAATTACTA
Found at i:14621 original size:23 final size:20
Alignment explanation
Indices: 14595--14646 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
14585 TAAAAATACT
14595 AAAATTAAAAATTAAATTACTAA
1 AAAATTAAAAA-TAAATT--TAA
* *
14618 AAAATTAAATATATATTTAA
1 AAAATTAAAAATAAATTTAA
14638 AAAATTAAA
1 AAAATTAAA
14647 TTACTAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 12 0.44
22 5 0.19
23 10 0.37
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTAAAAATAAATTTAA
Found at i:15422 original size:23 final size:23
Alignment explanation
Indices: 15396--15464 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
15386 CACCACAGCT
* *
15396 CGTAAAATTGCACCGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
* * *
15419 CGTAGAATTCCACCGGAGTGCCG
1 CGTAGAATTACACCGAAGTGCCA
*
15442 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
15465 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:25915 original size:21 final size:23
Alignment explanation
Indices: 25892--25934 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25882 CAAATAACCG
25892 AAAAC-TATTATAAAGACAGAGA
1 AAAACGTATTATAAAGACAGAGA
*
25914 AAAACGTGTTATAAAGACAGA
1 AAAACGTATTATAAAGACAGA
25935 ATAATACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (23 bp):
AAAACGTATTATAAAGACAGAGA
Found at i:25935 original size:21 final size:24
Alignment explanation
Indices: 25899--25944 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
25889 CCGAAAACTA
25899 TTATAAAGACAGAGAA-AA-ACGTG
1 TTATAAAGACA-AGAATAATACGTG
25922 TTATAAAGAC-AGAATAATACGTG
1 TTATAAAGACAAGAATAATACGTG
25945 CCAAAAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 2 0.10
23 15 0.71
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.22
Consensus pattern (24 bp):
TTATAAAGACAAGAATAATACGTG
Found at i:25986 original size:11 final size:12
Alignment explanation
Indices: 25970--25998 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25960 TGTTAAGAAT
25970 AAAAAAC-AAGA
1 AAAAAACAAAGA
25981 AAAAAACAAAGA
1 AAAAAACAAAGA
25993 AAAAAA
1 AAAAAA
25999 TAATGAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAGA
Found at i:28764 original size:19 final size:20
Alignment explanation
Indices: 28742--28779 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28732 ACTGTTTTCT
*
28742 TTATATGATC-TTATTTTTA
1 TTATATAATCATTATTTTTA
*
28761 TTATTTAATCATTATTTTT
1 TTATATAATCATTATTTTT
28780 TACGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTATATAATCATTATTTTTA
Found at i:31090 original size:60 final size:60
Alignment explanation
Indices: 31004--31154 Score: 189
Period size: 60 Copynumber: 2.5 Consensus size: 60
30994 ATAAAAAAAA
* * * * *
31004 TAGTCCATAAATTTTTGAATGTTTTAA-TTCTATC-TCCATACTATGTCTCTCATTCTAAAT
1 TAGTCCTTAAACTTTTGAACGTTTTAATTTC-ATCAT-CAGACTATGACTCTCATTCTAAAT
* *
31064 TAGTTCTTAAACTTTTGAACGTTTTAATTTCATCATCAGACTATGACTCTCATTCTATAT
1 TAGTCCTTAAACTTTTGAACGTTTTAATTTCATCATCAGACTATGACTCTCATTCTAAAT
* *
31124 TGGTCCTTAAACTTTTGAACATTTTAATTTC
1 TAGTCCTTAAACTTTTGAACGTTTTAATTTC
31155 TTTACAAACT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
60 75 0.95
61 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (60 bp):
TAGTCCTTAAACTTTTGAACGTTTTAATTTCATCATCAGACTATGACTCTCATTCTAAAT
Found at i:45243 original size:103 final size:103
Alignment explanation
Indices: 45023--45235 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
45013 GGGTCTACGC
*
45023 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
* *
45088 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
45126 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
*
45191 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
45229 GGTCCTT
1 GGTCCTT
45236 ATGGACATTA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:45285 original size:23 final size:23
Alignment explanation
Indices: 45252--45319 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
45242 ATTATTATAT
45252 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
45275 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
45298 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
45320 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:45666 original size:12 final size:12
Alignment explanation
Indices: 45649--45679 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
45639 TGTATGTGAT
45649 ATGTGTGATATG
1 ATGTGTGATATG
45661 ATGTGTGATATG
1 ATGTGTGATATG
45673 ATGTGTG
1 ATGTGTG
45680 CATGATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (12 bp):
ATGTGTGATATG
Found at i:45701 original size:16 final size:16
Alignment explanation
Indices: 45654--45702 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
45644 GTGATATGTG
45654 TGATATGATGTGTGATA
1 TGATAT-ATGTGTGATA
* * **
45671 TGATGTGTGCATGATA
1 TGATATATGTGTGATA
45687 TGATATATGTGTGATA
1 TGATATATGTGTGATA
45703 GGGGTTATGG
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.41
Consensus pattern (16 bp):
TGATATATGTGTGATA
Found at i:48862 original size:32 final size:31
Alignment explanation
Indices: 48829--48931 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
48819 CAGTTCAATA
48829 AAATTTAATGATCATTTTATAATAGTTTGAT
1 AAATTTAATGATCATTTTATAATAGTTTGAT
* *
48860 AAATTGTAATGATCATCTTATAACA-TTTGAT
1 AAATT-TAATGATCATTTTATAATAGTTTGAT
* *
48891 AAATTTAATGA-CTATTTTGTAAT-GTTTGAC
1 AAATTTAATGATC-ATTTTATAATAGTTTGAT
*
48921 AAATTTCATGA
1 AAATTTAATGA
48932 CCAAACTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.02
30 28 0.45
31 16 0.26
32 17 0.27
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (31 bp):
AAATTTAATGATCATTTTATAATAGTTTGAT
Found at i:65472 original size:25 final size:25
Alignment explanation
Indices: 65443--65502 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
65433 TATTTTTGGC
*
65443 ACGTTTTTTTCCCCTATATTTCGGT
1 ACGTTTTTTTCCCCTATATTTCAGT
65468 ACGTTTTTTTCCCCTATATTTCAGT
1 ACGTTTTTTTCCCCTATATTTCAGT
65493 ACGTTTTTTT
1 ACGTTTTTTT
65503 TATCTTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.13, C:0.22, G:0.10, T:0.55
Consensus pattern (25 bp):
ACGTTTTTTTCCCCTATATTTCAGT
Found at i:65812 original size:61 final size:61
Alignment explanation
Indices: 65740--65861 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
65730 GTGATGTAAT
65740 AAGATATATTGACATTTATCTTTATACGAGTTTTTAATTAGGTTTTTAATTTTTTGCTTAC
1 AAGATATATTGACATTTATCTTTATACGAGTTTTTAATTAGGTTTTTAATTTTTTGCTTAC
*
65801 AAGATGTATTGACATTTATCTTTATACGAGTTTTTAATTAGGTTTTTAATTTTTTGCTTAC
1 AAGATATATTGACATTTATCTTTATACGAGTTTTTAATTAGGTTTTTAATTTTTTGCTTAC
65862 GTGATCTTTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.52
Consensus pattern (61 bp):
AAGATATATTGACATTTATCTTTATACGAGTTTTTAATTAGGTTTTTAATTTTTTGCTTAC
Done.