Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003685.1 Hibiscus syriacus cultivar Beakdansim tig00007873_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: 59512
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4145 original size:19 final size:20
Alignment explanation
Indices: 4121--4160 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4111 AATTTAATCG
*
4121 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
4140 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
4160 A
1 A
4161 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:5247 original size:14 final size:14
Alignment explanation
Indices: 5230--5256 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5220 TTATTAAACT
5230 AAATGAATTATTTA
1 AAATGAATTATTTA
5244 AAATGAATTATTT
1 AAATGAATTATTT
5257 TTCTTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
AAATGAATTATTTA
Found at i:6956 original size:18 final size:19
Alignment explanation
Indices: 6922--6959 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6912 AATTTAATCG
*
6922 AATATATAATTTAAAATTC
1 AATATATAATATAAAATTC
6941 AATATA-AATATAAAATTC
1 AATATATAATATAAAATTC
6959 A
1 A
6960 TTAAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATATAATATAAAATTC
Found at i:9845 original size:10 final size:10
Alignment explanation
Indices: 9830--9863 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
9820 AAATATAACT
9830 TAAATGCAAC
1 TAAATGCAAC
9840 TAAATGCAAC
1 TAAATGCAAC
*
9850 TAAATACAAC
1 TAAATGCAAC
9860 TAAA
1 TAAA
9864 ATGTTGTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.56, C:0.18, G:0.06, T:0.21
Consensus pattern (10 bp):
TAAATGCAAC
Found at i:10290 original size:12 final size:12
Alignment explanation
Indices: 10273--10305 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
10263 AGTAAATCAG
10273 GAATCAAGTTTC
1 GAATCAAGTTTC
10285 GAATCAAGTTTC
1 GAATCAAGTTTC
*
10297 AAATCAAGT
1 GAATCAAGT
10306 AGTTTATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (12 bp):
GAATCAAGTTTC
Found at i:10936 original size:23 final size:23
Alignment explanation
Indices: 10909--10956 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
10899 GTCAAACAGT
**
10909 TCGGGGCAGGCTAATGGTTCGGG
1 TCGGGGCAGGCTAACAGTTCGGG
* *
10932 TCGGGTCAGGTTAACAGTTCGGG
1 TCGGGGCAGGCTAACAGTTCGGG
10955 TC
1 TC
10957 AGGTTGGGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.42, T:0.25
Consensus pattern (23 bp):
TCGGGGCAGGCTAACAGTTCGGG
Found at i:15634 original size:18 final size:17
Alignment explanation
Indices: 15603--15640 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
15593 ATTATAAGAC
*
15603 TAATTATAATATTAGTA
1 TAATTATAATATTAGGA
15620 TAATTATATATATTAGGA
1 TAATTATA-ATATTAGGA
15638 TAA
1 TAA
15641 CTTTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TAATTATAATATTAGGA
Found at i:30237 original size:19 final size:19
Alignment explanation
Indices: 30177--30237 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
30167 TTAGTGCAGA
* *
30177 GGGAATCGATACCCTCATG
1 GGGAATCGATACCCCCCTG
* * *
30196 AGGAAACCGAT-TCCCCCTAG
1 -GGGAATCGATACCCCCCT-G
30216 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
30235 GGG
1 GGG
30238 TTCTGGTATT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (19 bp):
GGGAATCGATACCCCCCTG
Found at i:32525 original size:27 final size:27
Alignment explanation
Indices: 32495--32579 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
32485 AAAGGAGAGA
32495 AATGTTAAAAGCGTTTTAAAGAGGAGT
1 AATGTTAAAAGCGTTTTAAAGAGGAGT
* *
32522 AATGTT-AAA--G---TAAGGGGGAGT
1 AATGTTAAAAGCGTTTTAAAGAGGAGT
32543 AAATGTTAAAAGCGTTTTAAAGAGGAGT
1 -AATGTTAAAAGCGTTTTAAAGAGGAGT
*
32571 AGTGTTAAA
1 AATGTTAAA
32580 GTAAGGGGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
21 9 0.20
22 6 0.13
23 3 0.07
24 1 0.02
25 1 0.02
26 3 0.07
27 14 0.30
28 9 0.20
ACGTcount: A:0.41, C:0.02, G:0.28, T:0.28
Consensus pattern (27 bp):
AATGTTAAAAGCGTTTTAAAGAGGAGT
Found at i:32552 original size:49 final size:49
Alignment explanation
Indices: 32494--32592 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
32484 AAAAGGAGAG
32494 AAATGTTAAAAGCGTTTTAAAGAGGAGTAATGTTAAAGTAAGGGGGAGT
1 AAATGTTAAAAGCGTTTTAAAGAGGAGTAATGTTAAAGTAAGGGGGAGT
*
32543 AAATGTTAAAAGCGTTTTAAAGAGGAGTAGTGTTAAAGTAAGGGGGAGT
1 AAATGTTAAAAGCGTTTTAAAGAGGAGTAATGTTAAAGTAAGGGGGAGT
32592 A
1 A
32593 GTATTTTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.26
Consensus pattern (49 bp):
AAATGTTAAAAGCGTTTTAAAGAGGAGTAATGTTAAAGTAAGGGGGAGT
Found at i:37055 original size:24 final size:25
Alignment explanation
Indices: 37009--37060 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
36999 TTCGTCCGAG
37009 TTTTATTATAAATATATTATTATAA
1 TTTTATTATAAATATATTATTATAA
**
37034 TTTTATTATTTAT-TATTATTATAA
1 TTTTATTATAAATATATTATTATAA
37058 TTT
1 TTT
37061 ATAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTATTATAAATATATTATTATAA
Found at i:37062 original size:13 final size:13
Alignment explanation
Indices: 37011--37073 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
37001 CGTCCGAGTT
*
37011 TTATTATAAATATA
1 TTATTAT-AATTTA
37025 TTATTATAATTTTA
1 TTATTATAA-TTTA
37039 TTATT-T-A-TTA
1 TTATTATAATTTA
37049 TTATTATAATTTA
1 TTATTATAATTTA
* *
37062 TAAATATAATTT
1 TTATTATAATTT
37074 TGGTTACAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
10 8 0.19
11 1 0.02
12 2 0.05
13 16 0.38
14 15 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTATAATTTA
Found at i:39142 original size:24 final size:24
Alignment explanation
Indices: 39096--39143 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39086 CGGGTCAATT
**
39096 GGTCAAAGTCAACTGGTTGGGTCA
1 GGTCAAAGTCAACTGGTCAGGTCA
39120 GGTCAAAGTCAAC-GAGTCAGGTCA
1 GGTCAAAGTCAACTG-GTCAGGTCA
39144 AACAGTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (24 bp):
GGTCAAAGTCAACTGGTCAGGTCA
Found at i:42691 original size:13 final size:13
Alignment explanation
Indices: 42675--42720 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
42665 GACGCGCATA
42675 TATGACACACATT
1 TATGACACACATT
*
42688 TATGACACATATT
1 TATGACACACATT
*
42701 TATGACACGCATT
1 TATGACACACATT
42714 TATGACA
1 TATGACA
42721 TTCATTGAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (13 bp):
TATGACACACATT
Found at i:42890 original size:2 final size:2
Alignment explanation
Indices: 42883--42919 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42873 TTTCTTAAAT
42883 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42920 GTAGATTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57925 original size:76 final size:76
Alignment explanation
Indices: 57799--57942 Score: 177
Period size: 76 Copynumber: 1.9 Consensus size: 76
57789 CAAGAAAATA
* *
57799 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TTTAATGC
1 TTATTTAATTAATTCAATT-AATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGC
57863 TTATTTAAAAAC
65 TTATTTAAAAAC
* * * *
57875 TTATTTAATT-ATTCCGAATT-ATATATATTAAAAGAGTTGTAATCTAAATTACATTCTTTTAAT
1 TTATTTAATTAATT-C-AATTAATATACATT-AAAGACTTATAATCTAAATTACAATCTTTTAAT
57938 GCTTA
63 GCTTA
57943 CTTACTATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
75 11 0.19
76 32 0.55
77 15 0.26
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (76 bp):
TTATTTAATTAATTCAATTAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGCT
TATTTAAAAAC
Done.