Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005567.1 Hibiscus syriacus cultivar Beakdansim tig00012914_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: 59856
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:31 original size:12 final size:12
Alignment explanation
Indices: 15--108 Score: 61
Period size: 12 Copynumber: 8.0 Consensus size: 12
5 CGTCGTCGTT
*
15 GTCATCATCGTC
1 GTCATCATCATC
* *
27 TTCATCCTCATC
1 GTCATCATCATC
* *
39 GTC-GCATCTTC
1 GTCATCATCATC
*
50 GTCATCATCTTC
1 GTCATCATCATC
62 GTCATC-T--TC
1 GTCATCATCATC
* *
71 ATCATCATCTTC
1 GTCATCATCATC
83 GTCATCATCACTTC
1 GTCATCATCA--TC
*
97 TTCATCATCATC
1 GTCATCATCATC
109 TGAATCATCG
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 7 0.11
10 1 0.02
11 9 0.14
12 36 0.56
14 11 0.17
ACGTcount: A:0.18, C:0.35, G:0.07, T:0.39
Consensus pattern (12 bp):
GTCATCATCATC
Found at i:2646 original size:34 final size:36
Alignment explanation
Indices: 2607--2673 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2597 TCCTATCAAC
2607 TCAACAAACCCT-A-TT-TTTTACTTCAGTTTAACTT
1 TCAAC-AACCCTAATTTATTTTACTTCAGTTTAACTT
2641 TCAACAACCCTAATTTATTTTACTTCAGTTTAA
1 TCAACAACCCTAATTTATTTTACTTCAGTTTAA
2674 ATTGGCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 6 0.20
34 6 0.20
35 2 0.07
36 16 0.53
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (36 bp):
TCAACAACCCTAATTTATTTTACTTCAGTTTAACTT
Found at i:20329 original size:26 final size:26
Alignment explanation
Indices: 20300--20390 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 26
20290 ATTTAAATTC
*
20300 ATAATATTTTATATTTA-TTAACTTAA
1 ATAATATTTTATATTAACTTAA-TTAA
20326 ATAATATTTTTATATTAAACTT-ATTAA
1 ATAATA-TTTTATATT-AACTTAATTAA
20353 AT-ATATTTTATTATTAACTTAATTTAA
1 ATAATATTTTA-TATTAACTTAA-TTAA
20380 A-AATATTTTAT
1 ATAATATTTTAT
20391 TTTTATTTTC
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
25 10 0.18
26 15 0.26
27 28 0.49
28 2 0.04
29 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (26 bp):
ATAATATTTTATATTAACTTAATTAA
Found at i:20389 original size:27 final size:27
Alignment explanation
Indices: 20302--20412 Score: 97
Period size: 27 Copynumber: 4.2 Consensus size: 27
20292 TTAAATTCAT
* *
20302 AATATTTTA-TATTTA-TTAACTTAAA
1 AATATTTTATTATTAACTTAATTTAAA
20327 TAATATTTT-TATATTAAACTT-A-TTAAA
1 -AATATTTTAT-TATT-AACTTAATTTAAA
*
20354 TATATTTTATTATTAACTTAATTTAAA
1 AATATTTTATTATTAACTTAATTTAAA
* ** *
20381 AATATTTTATTTTTATTTTCATTTAAA
1 AATATTTTATTATTAACTTAATTTAAA
20408 AATAT
1 AATAT
20413 ATATTTTAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.07
26 20 0.28
27 42 0.59
28 2 0.03
29 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
AATATTTTATTATTAACTTAATTTAAA
Found at i:20966 original size:10 final size:10
Alignment explanation
Indices: 20951--20980 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
20941 TTCAAAATCC
20951 ATTCATTTCA
1 ATTCATTTCA
20961 ATTCATTTCA
1 ATTCATTTCA
20971 ATTCCATTTC
1 ATT-CATTTC
20981 TTTGTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTCATTTCA
Found at i:24202 original size:14 final size:14
Alignment explanation
Indices: 24180--24215 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
24170 CCAAACCTTT
24180 ATCTATAATTCTTA
1 ATCTATAATTCTTA
*
24194 ATCTTTAATTCTTA
1 ATCTATAATTCTTA
*
24208 ATATATAA
1 ATCTATAA
24216 ATCTCAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (14 bp):
ATCTATAATTCTTA
Found at i:27059 original size:24 final size:24
Alignment explanation
Indices: 27009--27076 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
26999 TATTATTGTT
**
27009 AAAATATATATGAATTTAAATTCA
1 AAAATATATATGAATTTAAATAAA
*
27033 AAAATATAT-TTAATTTTAAATAAA
1 AAAATATATATGAA-TTTAAATAAA
* *
27057 AAAGT-TAAAT-AATTTAAATA
1 AAAATATATATGAATTTAAATA
27077 TGGTATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 8 0.22
23 7 0.19
24 22 0.59
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (24 bp):
AAAATATATATGAATTTAAATAAA
Found at i:31084 original size:72 final size:71
Alignment explanation
Indices: 30949--31085 Score: 161
Period size: 72 Copynumber: 1.9 Consensus size: 71
30939 GTAATTGTTC
* * * * *
30949 CTAATAACAAGTATTAAAAATAATAAATTTTAAGGGAAACTCCATAATAACAAGTGTTGAAAAAA
1 CTAATAACAAATATTAAAAATAATAAAATTTAA-GGAAACTCCATAATAACAAATATTAAAAAAA
31014 CAAGTCT
65 CAAGTCT
* *
31021 CTAATAACAAATATTAAAAA-AAGTAAAATTTAA-GAATATGTTCATAATAACAAATATTAAAAA
1 CTAATAACAAATATTAAAAATAA-TAAAATTTAAGGAA-A-CTCCATAATAACAAATATTAAAAA
31084 AA
63 AA
31086 ATTGAATCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
70 3 0.05
71 3 0.05
72 49 0.89
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.27
Consensus pattern (71 bp):
CTAATAACAAATATTAAAAATAATAAAATTTAAGGAAACTCCATAATAACAAATATTAAAAAAAC
AAGTCT
Found at i:33189 original size:6 final size:6
Alignment explanation
Indices: 33178--33221 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
33168 TAACCCCTCC
33178 CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CT
1 CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CTCTAA CT
33222 AAAACTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTAA
Found at i:36211 original size:6 final size:6
Alignment explanation
Indices: 36200--36227 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
36190 TCCTAGTTTA
36200 AAATGT AAATGT AAATGT AAATGT AAAT
1 AAATGT AAATGT AAATGT AAATGT AAAT
36228 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (6 bp):
AAATGT
Found at i:42015 original size:2 final size:2
Alignment explanation
Indices: 42008--42043 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41998 CAGAAGTTTC
42008 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
42044 TAGGCTTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47751 original size:39 final size:37
Alignment explanation
Indices: 47705--47779 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
47695 ACGCCACTAG
**
47705 AAACAGAAAAAAATGCGGTGAATTTATTAAAAACGCCAA
1 AAACAGAAAAAAATGCGACG--TTTATTAAAAACGCCAA
* *
47744 AAACAGAAAACATTGCGACGTTTATTAAAAACGCCA
1 AAACAGAAAAAAATGCGACGTTTATTAAAAACGCCA
47780 TTAAAGTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 16 0.50
39 16 0.50
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.19
Consensus pattern (37 bp):
AAACAGAAAAAAATGCGACGTTTATTAAAAACGCCAA
Found at i:47885 original size:42 final size:43
Alignment explanation
Indices: 47808--47907 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 43
47798 TAAAAGGCAC
* *
47808 AAAAATTGCGGCG-TTGTAATTAAAAGTGCCACTAAAGTACTG
1 AAAAATTGCGGCGTTTGTAATTAAAAGAGCCACTAAACTACTG
* * *
47850 AAAAAATGCGGCGTTTGTAGTTAAAA-AGCCGCTAAACTACTG
1 AAAAATTGCGGCGTTTGTAATTAAAAGAGCCACTAAACTACTG
*
47892 AAAAATTACGGCGTTT
1 AAAAATTGCGGCGTTT
47908 AATAAAAACG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 39 0.78
43 11 0.22
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (43 bp):
AAAAATTGCGGCGTTTGTAATTAAAAGAGCCACTAAACTACTG
Found at i:56103 original size:23 final size:22
Alignment explanation
Indices: 56059--56105 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
56049 ATTTTTGTTT
* * *
56059 TTTTATTATAGAAAATCTATAA
1 TTTTATTAAAAAAAATCCATAA
56081 TTTTATTAAAAAAATATCCATAA
1 TTTTATTAAAAAAA-ATCCATAA
56104 TT
1 TT
56106 ACAATGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTTATTAAAAAAAATCCATAA
Done.