Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006397.1 Hibiscus syriacus cultivar Beakdansim tig00015410_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: 80981
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:3134 original size:12 final size:12
Alignment explanation
Indices: 3104--3151 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
3094 ACATACTAAA
3104 AAATATATTTAT
1 AAATATATTTAT
** *
3116 ATTTATATTTCT
1 AAATATATTTAT
*
3128 AAATATA-TTAA
1 AAATATATTTAT
3139 AAATATATTTAT
1 AAATATATTTAT
3151 A
1 A
3152 TTTTTAAACC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATATATTTAT
Found at i:3148 original size:35 final size:36
Alignment explanation
Indices: 3084--3154 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
3074 AGGGCCACAA
3084 ATATTTCTAAACATACTAAAAAATATATTTATATTT
1 ATATTTCTAAACATACTAAAAAATATATTTATATTT
* *
3120 ATATTTCTAAATATA-TTAAAAATATATTTATATTT
1 ATATTTCTAAACATACTAAAAAATATATTTATATTT
3155 TTAAACCTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 19 0.58
36 14 0.42
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (36 bp):
ATATTTCTAAACATACTAAAAAATATATTTATATTT
Found at i:3362 original size:22 final size:22
Alignment explanation
Indices: 3317--3362 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3307 TATCTTTAGG
* **
3317 TTATGTAATTTGAATTTTTTAA
1 TTATGTAATTTGAATTATAAAA
*
3339 TTATTTAATTTGAATTATAAAA
1 TTATGTAATTTGAATTATAAAA
3361 TT
1 TT
3363 TTAAGTTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TTATGTAATTTGAATTATAAAA
Found at i:3542 original size:14 final size:14
Alignment explanation
Indices: 3525--3555 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3515 GTTAGATAAG
*
3525 TGAAAATAGACTAT
1 TGAAAATAGACGAT
3539 TGAAAATAGACGAT
1 TGAAAATAGACGAT
3553 TGA
1 TGA
3556 GATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (14 bp):
TGAAAATAGACGAT
Found at i:8917 original size:28 final size:28
Alignment explanation
Indices: 8871--8925 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
8861 CTTTATTTAC
* * *
8871 ATTATGTCGTCGAGCTAGTGCATGAAAT
1 ATTATGTCATCAAGATAGTGCATGAAAT
*
8899 ATTATGTCATCAAGATAGTGCTTGAAA
1 ATTATGTCATCAAGATAGTGCATGAAA
8926 GTAAAAACAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (28 bp):
ATTATGTCATCAAGATAGTGCATGAAAT
Found at i:10390 original size:2 final size:2
Alignment explanation
Indices: 10385--10415 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10375 TTCTTTTTTA
10385 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10416 ATCTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17443 original size:41 final size:42
Alignment explanation
Indices: 17392--17482 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
17382 GGTACAATAT
* * *
17392 TTTACGGTTG-TAATTTATAGGACACTATGCAATAAATATTA
1 TTTAGGGTTGTTAATTTATACGACACTATGCAATAAATATAA
* * * *
17433 TTTAGGGTTGTTATTTTATACGATATTATGCAATAATTATAA
1 TTTAGGGTTGTTAATTTATACGACACTATGCAATAAATATAA
17475 TTTAGGGT
1 TTTAGGGT
17483 ACAATAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 9 0.21
42 33 0.79
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTAGGGTTGTTAATTTATACGACACTATGCAATAAATATAA
Found at i:18512 original size:42 final size:41
Alignment explanation
Indices: 18439--18606 Score: 178
Period size: 43 Copynumber: 4.0 Consensus size: 41
18429 TCAAGATTCA
* * *
18439 ATGCCCTATTTTTTTAATCTCATTTTTTATCTTTATAGTTG
1 ATGCCCTATTTTTTCAATCTCACTTTTTATCTTTATAATTG
* *
18480 ATGCCCTGATTTTTTCATTCTCACTTTCTATCTTTATAATTG
1 ATGCCCT-ATTTTTTCAATCTCACTTTTTATCTTTATAATTG
* *
18522 AAGCCCCTAATTTGTTTCAATCTCACTTTTTATCTTTATAATCG
1 ATG-CCCT-ATTT-TTTCAATCTCACTTTTTATCTTTATAATTG
*
18566 A-GACCTCTAATTTTTTCAATTTCACTTTTTA-CTTTTATAAT
1 ATG-CC-CT-ATTTTTTCAATCTCACTTTTTATC-TTTATAAT
18607 ATATATCCCT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 7 0.06
42 32 0.29
43 36 0.33
44 35 0.32
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (41 bp):
ATGCCCTATTTTTTCAATCTCACTTTTTATCTTTATAATTG
Found at i:18546 original size:44 final size:43
Alignment explanation
Indices: 18442--18606 Score: 185
Period size: 44 Copynumber: 3.9 Consensus size: 43
18432 AGATTCAATG
* * * *
18442 CCCT-ATTTTTTTAATCTCATTTTTTATCTTTATAGTTGATG-
1 CCCTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAAGC
* * *
18483 CCCTGATTTTTTCATTCTCACTTTCTATCTTTATAATTGAAGC
1 CCCTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAAGC
*
18526 CCCTAATTTGTTTCAATCTCACTTTTTATCTTTATAATCG-AGAC
1 CCCTAATTT-TTTCAATCTCACTTTTTATCTTTATAATTGAAG-C
* *
18570 CTCTAATTTTTTCAATTTCACTTTTTA-CTTTTATAAT
1 CCCTAATTTTTTCAATCTCACTTTTTATC-TTTATAAT
18607 ATATATCCCT
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
41 4 0.04
42 32 0.30
43 35 0.33
44 36 0.34
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.53
Consensus pattern (43 bp):
CCCTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAAGC
Found at i:20324 original size:3 final size:3
Alignment explanation
Indices: 20316--20348 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20306 TGTCCCAACC
20316 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20349 TTTGATTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23611 original size:50 final size:51
Alignment explanation
Indices: 23531--23630 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 51
23521 CTCTCCCCTG
* *
23531 TTCCTTTTGCCACTTAATTTGTTTGTTGTGCACGTTTCTTTTATTACATAA
1 TTCCTTTTGCCACTTAATATGTTTGTTGTGCACGTTTCTTGTATTACATAA
* *
23582 TTCCTTTTGCTACTTGATAT-TTTGTTGTGCACGTTTCTTGTATTACATA
1 TTCCTTTTGCCACTTAATATGTTTGTTGTGCACGTTTCTTGTATTACATA
23631 CATTTGATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 28 0.62
51 17 0.38
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (51 bp):
TTCCTTTTGCCACTTAATATGTTTGTTGTGCACGTTTCTTGTATTACATAA
Found at i:25480 original size:55 final size:54
Alignment explanation
Indices: 25396--25505 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 54
25386 GAAATATTTG
* *
25396 AAAGTTTTAATATTATTGTAGAAGCATTTTAATCCAAAATAATAGGAATTCTTC
1 AAAGTTTTAATATTATTGTAAAAGCATTTTAATCCAAAATAATAAGAATTCTTC
* * * *
25450 AAAGTTTTAGATATTATTGTAAAAGTATTTTAGTTCAAAATAATAAGAATTGTTC
1 AAAGTTTTA-ATATTATTGTAAAAGCATTTTAATCCAAAATAATAAGAATTCTTC
25505 A
1 A
25506 TTGTCTAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
54 9 0.18
55 40 0.82
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (54 bp):
AAAGTTTTAATATTATTGTAAAAGCATTTTAATCCAAAATAATAAGAATTCTTC
Found at i:33203 original size:18 final size:18
Alignment explanation
Indices: 33182--33216 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
33172 TAAAGAAGCA
33182 GCTGCAGCTCAGGCTGCG
1 GCTGCAGCTCAGGCTGCG
33200 GCTGCAGCTCAGGCTGC
1 GCTGCAGCTCAGGCTGC
33217 TTCTTCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.34, G:0.37, T:0.17
Consensus pattern (18 bp):
GCTGCAGCTCAGGCTGCG
Found at i:49815 original size:23 final size:23
Alignment explanation
Indices: 49783--49887 Score: 160
Period size: 23 Copynumber: 4.6 Consensus size: 23
49773 CTTGTATAAA
*
49783 TGCACCGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
49806 TGCACTGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
49829 TGCACTGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
*
49852 TGCACTGTAA-TGCCGCGTAGAAT
1 TGCACTG-AAGTGCCACGTAGAAT
49875 TGCA-TCGAAGTGC
1 TGCACT-GAAGTGC
49888 TATATAAGGT
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.04
23 72 0.94
24 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.22
Consensus pattern (23 bp):
TGCACTGAAGTGCCACGTAGAAT
Found at i:50938 original size:2 final size:2
Alignment explanation
Indices: 50927--50979 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
50917 ACACACACAC
*
50927 AT AT AC 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
50969 AT AT AT A- AT AT
1 AT AT AT AT AT AT
50980 CAATGATTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63560 original size:3 final size:3
Alignment explanation
Indices: 63552--63586 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
63542 AATCTTACAT
63552 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
63587 ACTTTTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:72507 original size:2 final size:2
Alignment explanation
Indices: 72500--72545 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
72490 AGTGAAGTAG
72500 TA TA TA TA TA TA 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 TA TA TA TA TA TA
72542 TA TA
1 TA TA
72546 AGATTTAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.