Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006302.1 Hibiscus syriacus cultivar Beakdansim tig00015061_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: 60034
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1415 original size:35 final size:36
Alignment explanation
Indices: 1369--1443 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
1359 TTTCAATTTC
* *
1369 CAATGAAATCTTCAAG-AATCCTCTAGGAAAGCTAT
1 CAATGAAATCTTCAAGAAATCCCCTAAGAAAGCTAT
1404 CAATGAAATCTTCAAGAAATCCCCTAAGAAAGCTAT
1 CAATGAAATCTTCAAGAAATCCCCTAAGAAAGCTAT
1440 CAAT
1 CAAT
1444 TAAAACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 16 0.43
36 21 0.57
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (36 bp):
CAATGAAATCTTCAAGAAATCCCCTAAGAAAGCTAT
Found at i:2512 original size:31 final size:31
Alignment explanation
Indices: 2477--2536 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
2467 AAATCATTAC
*
2477 AAAAATATTAATATTAATA-A-TTTATTTTCT
1 AAAAA-ATAAATATTAATATATTTTATTTTCT
*
2507 AAAAAATAAATCTTAATATATTTTATTTTC
1 AAAAAATAAATATTAATATATTTTATTTTC
2537 GAGCTGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 6 0.23
31 9 0.35
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
AAAAAATAAATATTAATATATTTTATTTTCT
Found at i:5782 original size:18 final size:17
Alignment explanation
Indices: 5746--5796 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
5736 TGTAAAATAC
5746 AATAATTAATAATAA--T
1 AATAA-TAATAATAATTT
5762 AATAATAATAATATATTT
1 AATAATAATAATA-ATTT
* *
5780 AATATTTATAATAATTT
1 AATAATAATAATAATTT
5797 TTAAATTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 8 0.27
16 6 0.20
17 4 0.13
18 12 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATAATAATAATTT
Found at i:6548 original size:17 final size:18
Alignment explanation
Indices: 6520--6565 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
6510 TTTTCAAAGA
*
6520 AATAAAAAATTAAAAAAT
1 AATATAAAATTAAAAAAT
*
6538 -ATATTAAATT-AAAAAT
1 AATATAAAATTAAAAAAT
6554 AATATAAAATTA
1 AATATAAAATTA
6566 TATTTTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATATAAAATTAAAAAAT
Found at i:7138 original size:19 final size:20
Alignment explanation
Indices: 7114--7152 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7104 TACACATCAC
*
7114 TTTAAAA-ATATTAATATCT
1 TTTAAAAGAAATTAATATCT
7133 TTTAAAAGAAATTAATATCT
1 TTTAAAAGAAATTAATATCT
7153 CAAAATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTAAAAGAAATTAATATCT
Found at i:9894 original size:15 final size:15
Alignment explanation
Indices: 9874--9902 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9864 CTCATGGAGG
9874 TGCATCAACATGTTA
1 TGCATCAACATGTTA
9889 TGCATCAACATGTT
1 TGCATCAACATGTT
9903 GATAATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (15 bp):
TGCATCAACATGTTA
Found at i:21942 original size:31 final size:31
Alignment explanation
Indices: 21894--21975 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
21884 TTTAAAACAT
*
21894 AATAA-AATTTATGTACTAAAACGGAACAAA
1 AATAATAATTTAAGTACTAAAACGGAACAAA
* *
21924 AATAATAATTTAAATACTAAAATGGAACAAA
1 AATAATAATTTAAGTACTAAAACGGAACAAA
* *
21955 AATAATAGTTTAGGTACTAAA
1 AATAATAATTTAAGTACTAAA
21976 TGCGTAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 5 0.11
31 40 0.89
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (31 bp):
AATAATAATTTAAGTACTAAAACGGAACAAA
Found at i:28227 original size:16 final size:16
Alignment explanation
Indices: 28206--28248 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
28196 ACAAAGCCTC
28206 TGAATCATTCAGCAAT
1 TGAATCATTCAGCAAT
* *
28222 TGAATCATTCAGTATT
1 TGAATCATTCAGCAAT
28238 TGAATCATTCA
1 TGAATCATTCA
28249 ACGCTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCAAT
Found at i:32586 original size:23 final size:22
Alignment explanation
Indices: 32560--32602 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
32550 GATCTCTCTG
*
32560 ATTTTCTCTCTCTATTTTCTTCT
1 ATTTTCTATCT-TATTTTCTTCT
*
32583 ATTTTCTATCTTTTTTTCTT
1 ATTTTCTATCTTATTTTCTT
32603 TTATAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTCTATCTTATTTTCTTCT
Found at i:33474 original size:15 final size:16
Alignment explanation
Indices: 33442--33480 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
33432 AAATTCAAGC
*
33442 AATATATAAATAATGA
1 AATATAAAAATAATGA
33458 AATATAAAAAT-ATGA
1 AATATAAAAATAATGA
*
33473 AACATAAA
1 AATATAAA
33481 TATGCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (16 bp):
AATATAAAAATAATGA
Found at i:35638 original size:29 final size:30
Alignment explanation
Indices: 35580--35649 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
35570 AACAGTCTCT
* *
35580 AAACTTTTAAAATATTTGTATTTTAGTCATC
1 AAACTTTT-AAATATTTGTATTATAATCATC
*
35611 AAACTTTTAAA-ATTTGTATTATAATCATT
1 AAACTTTTAAATATTTGTATTATAATCATC
35640 AAACTTTTAA
1 AAACTTTTAA
35650 TTTATTTTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 25 0.69
30 3 0.08
31 8 0.22
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (30 bp):
AAACTTTTAAATATTTGTATTATAATCATC
Found at i:35911 original size:55 final size:55
Alignment explanation
Indices: 35815--35926 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
35805 AAGAAGGTTG
* * * *
35815 TAGAACGTAATCACTTATCCAAACTAAAATATTATTATAACATTGACAAACATAA
1 TAGAACCTAACCACTTATCCAAACTAAAATATTATCATAACATTGACAAAAATAA
* * * * *
35870 TAGAACCTAACCATTTATCCAAGCTAAGATGTTATCGTAACATTGACAAAAATAA
1 TAGAACCTAACCACTTATCCAAACTAAAATATTATCATAACATTGACAAAAATAA
35925 TA
1 TA
35927 TTTATATTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (55 bp):
TAGAACCTAACCACTTATCCAAACTAAAATATTATCATAACATTGACAAAAATAA
Found at i:36801 original size:24 final size:23
Alignment explanation
Indices: 36774--36825 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
36764 ACCCTAAATA
*
36774 AACACATTTATAAACATATAAACG
1 AACACATTTACAAACAT-TAAACG
* * *
36798 AACACGTTTACGAACATTAAAGG
1 AACACATTTACAAACATTAAACG
36821 AACAC
1 AACAC
36826 GTTCGTGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (23 bp):
AACACATTTACAAACATTAAACG
Found at i:36841 original size:23 final size:23
Alignment explanation
Indices: 36786--36841 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
36776 CACATTTATA
*
36786 AACATATAAACGAACACGTTTACG
1 AACA-ATAAACGAACACGTTCACG
* * **
36810 AACATTAAAGGAACACGTTCGTG
1 AACAATAAACGAACACGTTCACG
36833 AACAATAAA
1 AACAATAAA
36842 TAATCGAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (23 bp):
AACAATAAACGAACACGTTCACG
Found at i:37364 original size:2 final size:2
Alignment explanation
Indices: 37357--37382 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37347 TTTACCTTTG
37357 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
37383 TGAGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38021 original size:19 final size:20
Alignment explanation
Indices: 37974--38021 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
37964 ATATCCGTTA
37974 ATTTAGATT-TTTTATTAAT
1 ATTTAGATTATTTTATTAAT
*
37993 ATTTATATTATTTT-TTAAT
1 ATTTAGATTATTTTATTAAT
38012 -TTGTAGATTA
1 ATT-TAGATTA
38022 AATTGTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.08
19 19 0.76
20 4 0.16
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
ATTTAGATTATTTTATTAAT
Found at i:43475 original size:15 final size:15
Alignment explanation
Indices: 43455--43488 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43445 TATTTCTAAA
* *
43455 ATTTCTCTTTTCAAT
1 ATTTCTATTTACAAT
43470 ATTTCTATTTACAAT
1 ATTTCTATTTACAAT
43485 ATTT
1 ATTT
43489 TTTGGCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTCTATTTACAAT
Found at i:45985 original size:25 final size:26
Alignment explanation
Indices: 45957--46014 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
45947 GAGCTGCTCA
*
45957 CGAGCTTCAGTTCAT-GATTTCGAGT
1 CGAGCTCCAGTTCATAGATTTCGAGT
* *
45982 CGAGCTCCATTTCATAGTTTTCGAGT
1 CGAGCTCCAGTTCATAGATTTCGAGT
46008 CGAGCTC
1 CGAGCTC
46015 AGCAATACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (26 bp):
CGAGCTCCAGTTCATAGATTTCGAGT
Found at i:49224 original size:16 final size:16
Alignment explanation
Indices: 49189--49226 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
49179 GTTGACCTTA
49189 AAATTTAAAGGTTGCTC
1 AAATTTAAA-GTTGCTC
49206 AAATTTAAA-TTGACTC
1 AAATTTAAAGTTG-CTC
49222 AAATT
1 AAATT
49227 GATCCGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 8 0.40
17 9 0.45
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (16 bp):
AAATTTAAAGTTGCTC
Found at i:49945 original size:77 final size:77
Alignment explanation
Indices: 49852--50019 Score: 327
Period size: 77 Copynumber: 2.2 Consensus size: 77
49842 TTAAATAAAT
49852 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
1 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
49917 ACTAAATCAACC
66 ACTAAATCAACC
*
49929 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGCCA
1 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
49994 ACTAAATCAACC
66 ACTAAATCAACC
50006 AATTTGTGAGCCAC
1 AATTTGTGAGCCAC
50020 ATTGCTTGCT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 90 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (77 bp):
AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
ACTAAATCAACC
Found at i:51621 original size:17 final size:17
Alignment explanation
Indices: 51601--51636 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
51591 AGGTCAACGA
*
51601 TCAACGGTCGGGTCGGG
1 TCAACGGACGGGTCGGG
51618 TCAACGGACGGGTCGGG
1 TCAACGGACGGGTCGGG
51635 TC
1 TC
51637 GGGTCAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.25, G:0.44, T:0.17
Consensus pattern (17 bp):
TCAACGGACGGGTCGGG
Done.