Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002919.1 Hibiscus syriacus cultivar Beakdansim tig00006035_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: 56340
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2065 original size:30 final size:30
Alignment explanation
Indices: 2030--2099 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
2020 GGGTGATATA
2030 AAACATGTCACACATCACTTCTG-TGACATG
1 AAACATGTCACACATCACTT-TGATGACATG
* *
2060 AAACATGTCACGCCTCACTTTGATGACATG
1 AAACATGTCACACATCACTTTGATGACATG
2090 AAACATGTCA
1 AAACATGTCA
2100 TATCATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (30 bp):
AAACATGTCACACATCACTTTGATGACATG
Found at i:3952 original size:28 final size:27
Alignment explanation
Indices: 3899--3959 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
3889 AATTAAAAAA
*
3899 ATATTTAAGGTCTTAGAATAAAAGTAAT
1 ATATTTCAGGTCTTAGAATAAAAGT-AT
*
3927 ATATTTCAGGTGCTTAGAA-AATAGTAT
1 ATATTTCAGGT-CTTAGAATAAAAGTAT
3954 AT-TTTC
1 ATATTTC
3960 TGTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.13
27 4 0.13
28 15 0.50
29 7 0.23
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
ATATTTCAGGTCTTAGAATAAAAGTAT
Found at i:8721 original size:21 final size:21
Alignment explanation
Indices: 8656--8741 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
8646 AATACCTTGA
* *
8656 AGGGGAATCGATTCCCCCTTTGA
1 AGGGGAACCGATTCCCCC--TGT
*
8679 AGGGGAACCAATTCCTCCCTGT
1 AGGGGAACCGATTCC-CCCTGT
8701 AGGGGAACCGATTCCCCCTGT
1 AGGGGAACCGATTCCCCCTGT
* *
8722 AGGGGAATCGATACCCCCTG
1 AGGGGAACCGATTCCCCCTG
8742 GAGGTTTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
21 24 0.43
22 16 0.29
23 13 0.23
24 3 0.05
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (21 bp):
AGGGGAACCGATTCCCCCTGT
Found at i:10112 original size:18 final size:19
Alignment explanation
Indices: 10076--10123 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
10066 ATTAGTAAAA
*
10076 ATATAAAAATTATTTAAATT
1 ATATAAAAA-TATTAAAATT
10096 ATATAAAAAT-TTAAAATT
1 ATATAAAAATATTAAAATT
*
10114 TTA-AAAAATA
1 ATATAAAAATA
10124 ATAATGTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 1 0.04
20 9 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAAAATATTAAAATT
Found at i:11775 original size:58 final size:60
Alignment explanation
Indices: 11656--11797 Score: 182
Period size: 58 Copynumber: 2.4 Consensus size: 60
11646 GTGTATACGT
* * *
11656 ATGGTTTGGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACTAATATAGAATGAAGGTC
1 ATGGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGAGGACTAATATAGAATGAAAGTC
* *
11716 ATGGTTTGGGATGCAA-TGAAATGTTC-AAAAGTTTGAGGACTAATGTAGAAT-AATAGTC
1 ATGGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGAGGACTAATATAGAATGAA-AGTC
* *
11774 ATAGTTTAGGGATGAAATTAAAAT
1 ATGGTTT-GGGATGAAATTGAAAT
11798 ATTTAAAAGT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.03
58 32 0.45
59 17 0.24
60 20 0.28
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (60 bp):
ATGGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGAGGACTAATATAGAATGAAAGTC
Found at i:12888 original size:15 final size:14
Alignment explanation
Indices: 12868--12898 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
12858 GGAAATTAAA
12868 AATAAAGATAAAGAT
1 AATAAAGAT-AAGAT
12883 AATAAAGATAAGAT
1 AATAAAGATAAGAT
12897 AA
1 AA
12899 AGATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (14 bp):
AATAAAGATAAGAT
Found at i:12900 original size:11 final size:11
Alignment explanation
Indices: 12872--12904 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12862 ATTAAAAATA
12872 AAGATAAAGAT
1 AAGATAAAGAT
12883 -A-ATAAAGAT
1 AAGATAAAGAT
12892 AAGATAAAGAT
1 AAGATAAAGAT
12903 AA
1 AA
12905 AATACAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.40
10 2 0.10
11 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (11 bp):
AAGATAAAGAT
Found at i:15628 original size:26 final size:26
Alignment explanation
Indices: 15593--15643 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
15583 TGTTAGAGGA
*
15593 ATGAATTTATAAAATTTTAAAGGGGT
1 ATGAACTTATAAAATTTTAAAGGGGT
*
15619 ATGAACTTATAAAATTTTAAGGGGG
1 ATGAACTTATAAAATTTTAAAGGGG
15644 CGAAAACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (26 bp):
ATGAACTTATAAAATTTTAAAGGGGT
Found at i:25854 original size:11 final size:10
Alignment explanation
Indices: 25829--25853 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25819 TCGGTTCTCC
25829 TTTTTCTTTT
1 TTTTTCTTTT
25839 TTTTTCTTTT
1 TTTTTCTTTT
25849 TTTTT
1 TTTTT
25854 TTACGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:32975 original size:20 final size:20
Alignment explanation
Indices: 32952--32992 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
32942 CCAGAACCTC
32952 TAGGTAGAATAATATTCTCT
1 TAGGTAGAATAATATTCTCT
32972 TAGGTAGAATAATATTCTCT
1 TAGGTAGAATAATATTCTCT
32992 T
1 T
32993 TTACCATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
TAGGTAGAATAATATTCTCT
Found at i:33558 original size:2 final size:2
Alignment explanation
Indices: 33551--33598 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
33541 GATAATTTTG
33551 AT AT AT 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
33593 AT AT AT
1 AT AT AT
33599 TGCTTTTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33936 original size:26 final size:27
Alignment explanation
Indices: 33884--33942 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
33874 ACATTCACCT
*
33884 TATTTCTTTAAATATTTTTCAAAACAA
1 TATTTCTTTAAATATTTTTAAAAACAA
*
33911 TATTTCTTT-AA-CTTTTTAAAACACAA
1 TATTTCTTTAAATATTTTTAAAA-ACAA
33937 TATTTC
1 TATTTC
33943 ACTAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 12 0.41
27 9 0.31
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTTCTTTAAATATTTTTAAAAACAA
Found at i:53270 original size:61 final size:60
Alignment explanation
Indices: 53166--53283 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
53156 ATGCAAACAA
* *
53166 TCCCTCGACTATAAGGCGTTGCTTTGTTGAATCCCTCGACTATTGAAAGTTACAAAATGG
1 TCCCTCGACTATAAGACGTTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATGG
* ** * * *
53226 TCCCTCGATTATAAGACGATTTTTTTGTTGTATCCCTCGGCTATTAAAAGTTATAAAA
1 TCCCTCGACTATAAGACG-TTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAA
53284 CGATCACCCG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 16 0.33
61 33 0.67
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
TCCCTCGACTATAAGACGTTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATGG
Done.