Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003046.1 Hibiscus syriacus cultivar Beakdansim tig00006339_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: 50152
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:146 original size:15 final size:15
Alignment explanation
Indices: 128--159 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
118 TAAATTCAAG
128 TTTAGGAATTATCTT
1 TTTAGGAATTATCTT
*
143 TTTAGGATTTATCTT
1 TTTAGGAATTATCTT
158 TT
1 TT
160 GTATTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTAGGAATTATCTT
Found at i:17768 original size:39 final size:39
Alignment explanation
Indices: 17714--17804 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
17704 AAAATAGCAA
** *
17714 TAGTTTAGATTAACTAGAGTTCTATCTTACTTGATTTAG
1 TAGTTTAGATTAACTAGAACTCTATCATACTTGATTTAG
*
17753 TAGTTTAGATTAACTAGAACTCTATCATATTTGATTTAG
1 TAGTTTAGATTAACTAGAACTCTATCATACTTGATTTAG
*
17792 TAGTTTAAATTAA
1 TAGTTTAGATTAA
17805 TTATAACTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (39 bp):
TAGTTTAGATTAACTAGAACTCTATCATACTTGATTTAG
Found at i:21921 original size:19 final size:19
Alignment explanation
Indices: 21899--21957 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
21889 AAAGTTGAAA
21899 AGATTTAATAAAATAAAAT
1 AGATTTAATAAAATAAAAT
* *
21918 AGATAATAAT-AAATAAAAG
1 AGAT-TTAATAAAATAAAAT
* *
21937 GGAAATTAATAAAATAAAAT
1 AG-ATTTAATAAAATAAAAT
21957 A
1 A
21958 AAATAATAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AGATTTAATAAAATAAAAT
Found at i:25918 original size:19 final size:19
Alignment explanation
Indices: 25894--25952 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
25884 GTAAAGTTGG
*
25894 AAAGATTTAATAAAATAAA
1 AAAGATATAATAAAATAAA
*
25913 ATAGATAATAAT-AAATAAA
1 AAAGAT-ATAATAAAATAAA
*
25932 AAAGAAAATAATAAAATAAA
1 AAAG-ATATAATAAAATAAA
25952 A
1 A
25953 CAATAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (19 bp):
AAAGATATAATAAAATAAA
Found at i:25926 original size:20 final size:20
Alignment explanation
Indices: 25901--25952 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
25891 TGGAAAGATT
* *
25901 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAAAGAAAA
25921 TAAT-AAATAAAAAAGAAAA
1 TAATAAAATAAAAAAGAAAA
25940 TAATAAAATAAAA
1 TAATAAAATAAAA
25953 CAATAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (20 bp):
TAATAAAATAAAAAAGAAAA
Found at i:25940 original size:12 final size:13
Alignment explanation
Indices: 25901--25959 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
25891 TGGAAAGATT
*
25901 TAATAAAATAAAA
1 TAATAAAAGAAAA
*
25914 TAGATAATAA-TAAA
1 TA-ATAA-AAGAAAA
25928 TAA-AAAAGAAAA
1 TAATAAAAGAAAA
*
25940 TAATAAAATAAAA
1 TAATAAAAGAAAA
*
25953 CAATAAA
1 TAATAAA
25960 TAATAGTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 17 0.45
14 9 0.24
15 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (13 bp):
TAATAAAAGAAAA
Found at i:25960 original size:20 final size:19
Alignment explanation
Indices: 25901--25964 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
25891 TGGAAAGATT
25901 TAATAAAATAAAATAGAT-AA
1 TAATAAAATAAAA-A-ATAAA
*
25921 TAAT-AAATAAAAAAGAAAA
1 TAATAAAATAAAAAA-TAAA
25940 TAATAAAATAAAACAATAAA
1 TAATAAAATAAAA-AATAAA
25960 TAATA
1 TAATA
25965 GTAGTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 14 0.37
20 20 0.53
21 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (19 bp):
TAATAAAATAAAAAATAAA
Found at i:26037 original size:17 final size:18
Alignment explanation
Indices: 26007--26044 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
25997 TTTTTAAAAG
26007 AAAATATAAGAATTAAAT
1 AAAATATAAGAATTAAAT
*
26025 AAAA-ATAATAATTAAAT
1 AAAATATAAGAATTAAAT
26042 AAA
1 AAA
26045 TAATTTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAATATAAGAATTAAAT
Found at i:32890 original size:29 final size:29
Alignment explanation
Indices: 32847--32929 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
32837 CTCACTTAAC
32847 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
32877 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
32906 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
32930 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:37581 original size:29 final size:29
Alignment explanation
Indices: 37548--37620 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
37538 TAAATATATG
37548 TAAGCAATGACATCATTACTTAAATGATA
1 TAAGCAATGACATCATTACTTAAATGATA
* * *
37577 TAAGCAATGACAGCTTTACTTAAATGATG
1 TAAGCAATGACATCATTACTTAAATGATA
37606 TAAGCAATGACATCA
1 TAAGCAATGACATCA
37621 ATTTAGTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (29 bp):
TAAGCAATGACATCATTACTTAAATGATA
Found at i:39876 original size:13 final size:15
Alignment explanation
Indices: 39850--39896 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
39840 GTCGATAGAT
39850 TATTTAA-AAAATTA
1 TATTTAAGAAAATTA
39864 TATTT-AG-AAATTA
1 TATTTAAGAAAATTA
*
39877 TTTTTAAGATAAATTA
1 TATTTAAGA-AAATTA
39893 TATT
1 TATT
39897 AGTGCTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.41
14 7 0.26
16 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
TATTTAAGAAAATTA
Found at i:40228 original size:6 final size:6
Alignment explanation
Indices: 40217--40290 Score: 148
Period size: 6 Copynumber: 12.3 Consensus size: 6
40207 TCCTCTTTCG
40217 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
40265 ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT AT
40291 AAATTAATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:40406 original size:2 final size:2
Alignment explanation
Indices: 40399--40430 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40389 TATTTATTAT
40399 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
40431 ATTTGTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43999 original size:59 final size:59
Alignment explanation
Indices: 43915--44029 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
43905 AAACTATGAC
** *
43915 TCTCATTTTAAATTAGTCTCTAAACTTTTAAATATTATAATTTCATCCTCAAACTAATA
1 TCTCATTCCAAATTAGTCTCTAAACTTTTAAACATTATAATTTCATCCTCAAACTAATA
* *
43974 TCTCATTCCAAATTAGTC-CTCAAACTTTTGAACATTCTAATTTCATCCTCAAACTA
1 TCTCATTCCAAATTAGTCTCT-AAACTTTTAAACATTATAATTTCATCCTCAAACTA
44030 TGACCCTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 2 0.04
59 48 0.96
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (59 bp):
TCTCATTCCAAATTAGTCTCTAAACTTTTAAACATTATAATTTCATCCTCAAACTAATA
Found at i:49829 original size:20 final size:21
Alignment explanation
Indices: 49777--49831 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
49767 GATTCTACTA
*
49777 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
49798 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
49819 TCGCG-TGCGATTT
1 TCGCGTTGCGATTT
49832 AAATCGCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 8 0.24
21 25 0.76
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:49864 original size:20 final size:20
Alignment explanation
Indices: 49852--49904 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
49842 ATTTTCTAAT
49852 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
49872 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
49892 TCGCAATGCGATT
1 TCGCAATGCGATT
49905 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:50094 original size:22 final size:21
Alignment explanation
Indices: 50069--50129 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 21
50059 AGCGACATCC
50069 TCCCCATCTCTGACGAAATCAG
1 TCCCCATCTC-GACGAAATCAG
*
50091 TCCCCA---CGACGATATCAG
1 TCCCCATCTCGACGAAATCAG
* *
50109 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCT-CGACGAAATCA
50130 TTCACGGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
22 15 0.48
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (21 bp):
TCCCCATCTCGACGAAATCAG
Done.