Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005663.1 Hibiscus syriacus cultivar Beakdansim tig00013240_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: 67427
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:6695 original size:9 final size:10
Alignment explanation
Indices: 6676--6716 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
6666 TATTCACAAC
6676 TTCATTTTTT
1 TTCATTTTTT
6686 TTCA-TTTTT
1 TTCATTTTTT
6695 TTCAATTTTTTT
1 TTC-A-TTTTTT
6707 TTCATTTTTT
1 TTCATTTTTT
6717 AGTGGGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.29
10 11 0.39
11 1 0.04
12 8 0.29
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (10 bp):
TTCATTTTTT
Found at i:6705 original size:12 final size:11
Alignment explanation
Indices: 6676--6716 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 11
6666 TATTCACAAC
6676 TTCA-TTTTTT
1 TTCATTTTTTT
6686 TTCA--TTTTT
1 TTCATTTTTTT
6695 TTCAATTTTTTT
1 TTC-ATTTTTTT
6707 TTCATTTTTT
1 TTCATTTTTT
6717 AGTGGGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.29
10 5 0.18
11 7 0.25
12 8 0.29
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCATTTTTTT
Found at i:12243 original size:43 final size:42
Alignment explanation
Indices: 12149--12247 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
12139 ATTGCGACGT
* *
12149 ATAAAAAAATGCCGCTATATACCAACCTTTAGCGGCGTTTGT
1 ATAAAAAAACGCCGCTATATACCAACCTTTAGCGGCGTTTGC
** * *
12191 ATCCTAAAAACGTCGCTATATACTAGACCTATT-GCGGCGTTTGC
1 AT-AAAAAAACGCCGCTATATACCA-ACCT-TTAGCGGCGTTTGC
12235 ATAAAAAAACGCC
1 ATAAAAAAACGCC
12248 ACTAAATCTC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
42 2 0.04
43 25 0.56
44 16 0.36
45 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (42 bp):
ATAAAAAAACGCCGCTATATACCAACCTTTAGCGGCGTTTGC
Found at i:12268 original size:44 final size:44
Alignment explanation
Indices: 12220--12364 Score: 127
Period size: 43 Copynumber: 3.3 Consensus size: 44
12210 ATACTAGACC
*
12220 TATTGCGGCGTTTGCATAAAAAAACGCCACTAAATCTCAAAACT
1 TATTGCGGCGTTTGCATAAAAAAACGCCGCTAAATCTCAAAACT
* * * *
12264 TATTGCAGCGTTTGTGAT-AAAAAAC-CCGTTAAATCTCAACACT
1 TATTGCGGCGTTTG-CATAAAAAAACGCCGCTAAATCTCAAAACT
* * * * * * **
12307 TATTACGGCATTT--TTAAGACAAAGGCCGCTAAATATCAGTACT
1 TATTGCGGCGTTTGCATAA-AAAAACGCCGCTAAATCTCAAAACT
12350 TATTGCGGCGTTTGC
1 TATTGCGGCGTTTGC
12365 TATATATCGT
Statistics
Matches: 78, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 4 0.05
43 50 0.64
44 20 0.26
45 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (44 bp):
TATTGCGGCGTTTGCATAAAAAAACGCCGCTAAATCTCAAAACT
Found at i:18757 original size:6 final size:6
Alignment explanation
Indices: 18743--18788 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
18733 CATATAAGAT
* *
18743 ATATAC ATATGC ATATACAC ATATAC ATACAC ATATAC ATATAC AT
1 ATATAC ATATAC ATAT--AC ATATAC ATATAC ATATAC ATATAC AT
18789 GCACATGCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 29 0.85
8 5 0.15
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (6 bp):
ATATAC
Found at i:18764 original size:14 final size:13
Alignment explanation
Indices: 18741--18787 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
18731 ACCATATAAG
*
18741 ATATATACATATGC
1 ATATACACATAT-C
18755 ATATACACATAT-
1 ATATACACATATC
*
18767 ACATACACATATAC
1 ATATACACATAT-C
18781 ATATACA
1 ATATACA
18788 TGCACATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
14 17 0.61
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (13 bp):
ATATACACATATC
Found at i:18768 original size:20 final size:20
Alignment explanation
Indices: 18743--18794 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
18733 CATATAAGAT
**
18743 ATATACATATGCATATACAC
1 ATATACATACACATATACAC
18763 ATATACATACACATAT--AC
1 ATATACATACACATATACAC
*
18781 ATATACATGCACAT
1 ATATACATACACAT
18795 GCACATGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.52
20 14 0.48
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (20 bp):
ATATACATACACATATACAC
Found at i:18800 original size:18 final size:18
Alignment explanation
Indices: 18743--18800 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
18733 CATATAAGAT
*
18743 ATATACATATGCATATACAC
1 ATATACATA--CACATACAC
*
18763 ATATACATACACATATAC
1 ATATACATACACATACAC
* *
18781 ATATACATGCACATGCAC
1 ATATACATACACATACAC
18799 AT
1 AT
18801 GCACGTGCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 24 0.73
20 9 0.27
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.28
Consensus pattern (18 bp):
ATATACATACACATACAC
Found at i:18825 original size:6 final size:6
Alignment explanation
Indices: 18802--18846 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
18792 CATGCACATG
* ** *
18802 CACGTG CACGTA CACGTA CACGTA CATATA CACATA CACGTA CAC
1 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CAC
18847 ATATTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.33, G:0.13, T:0.18
Consensus pattern (6 bp):
CACGTA
Found at i:18847 original size:12 final size:12
Alignment explanation
Indices: 18757--18849 Score: 69
Period size: 12 Copynumber: 7.8 Consensus size: 12
18747 ACATATGCAT
*
18757 ATACACATATAC
1 ATACACATACAC
*
18769 ATACACATATAC
1 ATACACATACAC
* *
18781 ATATACATGCAC
1 ATACACATACAC
* *
18793 ATGCACATGCAC
1 ATACACATACAC
* * *
18805 GTGCACGTACAC
1 ATACACATACAC
* * *
18817 GTACACGTACAT
1 ATACACATACAC
18829 ATACACATACAC
1 ATACACATACAC
*
18841 GTACACATA
1 ATACACATA
18850 TTTCTTTATA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.22
Consensus pattern (12 bp):
ATACACATACAC
Found at i:26090 original size:30 final size:30
Alignment explanation
Indices: 26047--26107 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
26037 GGACCTGTCT
* *
26047 AGAGGTTACAAAGAACCCCGGTAACTATCC
1 AGAGGTCACAAAGAACCCCGGCAACTATCC
* * *
26077 AGAGGTCATAAAGATCCTCGGCAACTATCC
1 AGAGGTCACAAAGAACCCCGGCAACTATCC
26107 A
1 A
26108 TATGTTCCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (30 bp):
AGAGGTCACAAAGAACCCCGGCAACTATCC
Found at i:32821 original size:13 final size:13
Alignment explanation
Indices: 32803--32829 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32793 ACTGTGAAGC
32803 TCGACAGAAGCTT
1 TCGACAGAAGCTT
32816 TCGACAGAAGCTT
1 TCGACAGAAGCTT
32829 T
1 T
32830 TCTTGTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (13 bp):
TCGACAGAAGCTT
Found at i:38488 original size:32 final size:32
Alignment explanation
Indices: 38452--38523 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
38442 AATAATGGCG
* *
38452 TAATACATATTATATGTACATAAGTAATGATA
1 TAATACATATCATATGTACATAAATAATGATA
* *
38484 TAATATATATCATATGTACATAAATGATGATA
1 TAATACATATCATATGTACATAAATAATGATA
38516 TAATACAT
1 TAATACAT
38524 GTCACATACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (32 bp):
TAATACATATCATATGTACATAAATAATGATA
Found at i:39746 original size:49 final size:50
Alignment explanation
Indices: 39664--39762 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 50
39654 TAAACCCTAA
39664 AAACCAATGGGAAAAGTGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
1 AAACCAATGGGAAAAGTGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
*
39714 AAACCAATGGGAAAA-TGTCATGTGAGGTAGGCAGCTACAGCTGTCTTAT
1 AAACCAATGGGAAAAGTGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
39763 TATTATTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 33 0.69
50 15 0.31
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.23
Consensus pattern (50 bp):
AAACCAATGGGAAAAGTGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
Found at i:39825 original size:15 final size:15
Alignment explanation
Indices: 39805--39837 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
39795 GAAGCAATCA
39805 AAATTTAAAGCTATT
1 AAATTTAAAGCTATT
39820 AAATTTAAAGCTATT
1 AAATTTAAAGCTATT
39835 AAA
1 AAA
39838 ACGTATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
AAATTTAAAGCTATT
Found at i:47091 original size:2 final size:2
Alignment explanation
Indices: 47084--47147 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
47074 AATAAACAAT
47084 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
47126 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
47148 AAGTTTAGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52889 original size:19 final size:20
Alignment explanation
Indices: 52865--52912 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
52855 AATGATTTTC
* * *
52865 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
52884 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
52904 TTTTGAAAA
1 TTTTGAAAA
52913 ATAATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:57823 original size:2 final size:2
Alignment explanation
Indices: 57814--57874 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
57804 TATTTTTTAT
57814 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- 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
57854 TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
57875 ATAATTTCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:57838 original size:21 final size:21
Alignment explanation
Indices: 57814--57874 Score: 104
Period size: 23 Copynumber: 2.8 Consensus size: 21
57804 TATTTTTTAT
57814 TATAATATATATATATATATA
1 TATAATATATATATATATATA
57835 TATATATTATATATATATATATA
1 TATA-A-TATATATATATATATA
57858 TATAATATATATATATA
1 TATAATATATATATATA
57875 ATAATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.42
22 2 0.05
23 20 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAATATATATATATATATA
Found at i:57942 original size:36 final size:36
Alignment explanation
Indices: 57889--58015 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 36
57879 TTTCAAACAT
** * ***
57889 TATTTTTGAAAGTATATAGTATAT-GCTTTGAAGCCG
1 TATTTTTGAAAACATATAATATATAGCTTTGAA-AAA
* *
57925 TATTTTTGAAAACATATAATATATAGTTTTTAAAAA
1 TATTTTTGAAAACATATAATATATAGCTTTGAAAAA
** *
57961 TATTTTTGAAAACATATAATATATATATTTTAAAAAA
1 TATTTTTGAAAACATATAATATATA-GCTTTGAAAAA
*
57998 CGATTTTTGAAAACATAT
1 -TATTTTTGAAAACATAT
58016 TTTTTTGAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
36 46 0.60
37 15 0.19
38 16 0.21
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (36 bp):
TATTTTTGAAAACATATAATATATAGCTTTGAAAAA
Found at i:58004 original size:38 final size:36
Alignment explanation
Indices: 57926--58015 Score: 137
Period size: 36 Copynumber: 2.4 Consensus size: 36
57916 TTGAAGCCGT
*
57926 ATTTTTGAAAACATATAATATATAGTTTTTAAAAAT
1 ATTTTTGAAAACATATAATATATAGTTTTTAAAAAG
57962 ATTTTTGAAAACATATAATATATA-TATTTTAAAAAACG
1 ATTTTTGAAAACATATAATATATAGT-TTTT-AAAAA-G
58000 ATTTTTGAAAACATAT
1 ATTTTTGAAAACATAT
58016 TTTTTTGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
35 1 0.02
36 28 0.56
37 5 0.10
38 16 0.32
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (36 bp):
ATTTTTGAAAACATATAATATATAGTTTTTAAAAAG
Found at i:58051 original size:4 final size:4
Alignment explanation
Indices: 58042--58090 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
58032 TATGGGTTAT
58042 TTTA TTTA TTTA TTTA TTTCA TTTTA TTT- TTTA -TT- TTTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTT-A -TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
58090 T
1 T
58091 AGGTCCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
3 7 0.18
4 23 0.59
5 6 0.15
6 3 0.08
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:58069 original size:18 final size:19
Alignment explanation
Indices: 58038--58090 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
58028 ACATTATGGG
58038 TTATTTT-A-TTTATTTAT
1 TTATTTTCATTTTATTTAT
58055 TTA-TTTCATTTTATTT-T
1 TTATTTTCATTTTATTTAT
*
58072 TTATTTTTATTTTATTTAT
1 TTATTTTCATTTTATTTAT
58091 AGGTCCAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 3 0.10
17 8 0.26
18 19 0.61
19 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (19 bp):
TTATTTTCATTTTATTTAT
Found at i:62156 original size:15 final size:15
Alignment explanation
Indices: 62114--62160 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
62104 GATATTTTGC
* *
62114 TGTAATTTGATACGT
1 TGTAATTTGATTCGA
62129 TGTAATTTGATTCGA
1 TGTAATTTGATTCGA
*
62144 TGTAATTTAATTCGA
1 TGTAATTTGATTCGA
62159 TG
1 TG
62161 ATGTTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (15 bp):
TGTAATTTGATTCGA
Done.