Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000760.1 Hibiscus syriacus cultivar Beakdansim tig00001477_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: 80581
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3227 original size:12 final size:12
Alignment explanation
Indices: 3207--3236 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3197 TTTATTTTAT
*
3207 TATTATACCTTC
1 TATTTTACCTTC
3219 TATTTTACCTTC
1 TATTTTACCTTC
3231 TATTTT
1 TATTTT
3237 TTTCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTACCTTC
Found at i:3293 original size:16 final size:16
Alignment explanation
Indices: 3271--3304 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3261 AATTTAACAC
3271 TTTT-TTTTAT-TTTA
1 TTTTGTTTTATCTTTA
3285 TTTTGTTTTATCTTTA
1 TTTTGTTTTATCTTTA
3301 TTTT
1 TTTT
3305 ACCACTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 6 0.33
16 8 0.44
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTGTTTTATCTTTA
Found at i:4515 original size:23 final size:23
Alignment explanation
Indices: 4469--4516 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
4459 TTATTAATGA
* * *
4469 TATAATTTTATATTTTGAAGTTT
1 TATAATTTTATATCTTAAAATTT
4492 TATAATTTTATATCTTAAAATTT
1 TATAATTTTATATCTTAAAATTT
4515 TA
1 TA
4517 ATTTAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TATAATTTTATATCTTAAAATTT
Found at i:8436 original size:12 final size:12
Alignment explanation
Indices: 8419--8444 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8409 GTGTTACATT
8419 TTTTTTTTGTTA
1 TTTTTTTTGTTA
8431 TTTTTTTTGTTA
1 TTTTTTTTGTTA
8443 TT
1 TT
8445 ATTATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGTTA
Found at i:9132 original size:36 final size:37
Alignment explanation
Indices: 9060--9133 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
9050 GTTGAAAAAT
* * *
9060 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTCTCTTTAAAAAATTGAAAATCATAAA
*
9097 ATTTATATAATTCT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTCTCTTTAAAAAATTGAAAATCATAAA
9133 A
1 A
9134 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 22 0.69
38 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTCTCTTTAAAAAATTGAAAATCATAAA
Found at i:14586 original size:19 final size:20
Alignment explanation
Indices: 14536--14590 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
14526 AGATGAAATT
14536 TATATTTAAAATAATAATAA
1 TATATTTAAAATAATAATAA
14556 TAATTCATTTAAAA-AATAATAA
1 T-A-T-ATTTAAAATAATAATAA
*
14578 TATAATTAAAATA
1 TATATTTAAAATA
14591 TAGAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 2 0.07
22 10 0.33
23 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATTTAAAATAATAATAA
Found at i:15501 original size:2 final size:2
Alignment explanation
Indices: 15494--15527 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15484 GTGATCATAC
15494 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
15528 TACCAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21898 original size:54 final size:54
Alignment explanation
Indices: 21814--21989 Score: 253
Period size: 54 Copynumber: 3.3 Consensus size: 54
21804 GGGTCAAGCA
* * * * * * * *
21814 CAGGGTTGGCAACATTGGGTCCCGTCGGAATCGGACCCGTGTTTGCTCCCAGAC
1 CAGGGTTGGCAACATTGGCTCCTGTGGGAATCGGACCTGTGGTAGCACCCACAC
*
21868 CAGGGTTCGCAACATTGGCTCCTGTGGGAATCGGACCTGTGGTAGCACCCACAC
1 CAGGGTTGGCAACATTGGCTCCTGTGGGAATCGGACCTGTGGTAGCACCCACAC
* *
21922 CAGGGTTGGCAACATTAGCTCCTGTGGGAATGGGACCTGTGGTAGCACCCACAC
1 CAGGGTTGGCAACATTGGCTCCTGTGGGAATCGGACCTGTGGTAGCACCCACAC
21976 CAGGGTTGGCAACA
1 CAGGGTTGGCAACA
21990 GCAGCCCCTG
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.20
Consensus pattern (54 bp):
CAGGGTTGGCAACATTGGCTCCTGTGGGAATCGGACCTGTGGTAGCACCCACAC
Found at i:22029 original size:54 final size:54
Alignment explanation
Indices: 21861--22018 Score: 167
Period size: 54 Copynumber: 2.9 Consensus size: 54
21851 CGTGTTTGCT
* * *** * *
21861 CCCAGACCAGGGTTCGCAACATTGGCTCCTGTGGGAATCGG-ACCTGTGGTAGCA
1 CCCACACCAGGGTTGGCAACAGCAGCCCCTGTGGGAAT-GGAACCAGTGGTAGCA
** * * *
21915 CCCACACCAGGGTTGGCAACATTAGCTCCTGTGGGAATGGGACCTGTGGTAGCA
1 CCCACACCAGGGTTGGCAACAGCAGCCCCTGTGGGAATGGAACCAGTGGTAGCA
*
21969 CCCACACCAGGGTTGGCAACAGCAGCCCCTGAT-GGATTGGAACCAGTGGT
1 CCCACACCAGGGTTGGCAACAGCAGCCCCTG-TGGGAATGGAACCAGTGGT
22019 TTCAGCCACA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.02
54 90 0.97
55 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (54 bp):
CCCACACCAGGGTTGGCAACAGCAGCCCCTGTGGGAATGGAACCAGTGGTAGCA
Found at i:26155 original size:15 final size:15
Alignment explanation
Indices: 26137--26179 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
26127 GAAAGGAATA
26137 AAAACCCAGAAAATG
1 AAAACCCAGAAAATG
*
26152 AAAACCAAGAAAATG
1 AAAACCCAGAAAATG
*
26167 AAATCCCAGAAAA
1 AAAACCCAGAAAA
26180 AGAAGGGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.63, C:0.19, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAACCCAGAAAATG
Found at i:26777 original size:3 final size:3
Alignment explanation
Indices: 26769--26806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
26759 TATAAATGAG
26769 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
26807 GCTTGATCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38878 original size:37 final size:36
Alignment explanation
Indices: 38808--38894 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
38798 GGGCCAACCC
* * *
38808 GACCGGACCCGAAAATTTTATATCCTTCACCGACCT
1 GACCCGACCCGAAAAATATATATCCTTCACCGACCT
*
38844 GACCCGACCCGAAAAATATATA-CCTT--CC-ACCC
1 GACCCGACCCGAAAAATATATATCCTTCACCGACCT
*
38876 GACCCGACTCGAAATAATA
1 GACCCGACCCGAAA-AATA
38895 ATAATAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 16 0.36
33 6 0.13
35 4 0.09
36 19 0.42
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.20
Consensus pattern (36 bp):
GACCCGACCCGAAAAATATATATCCTTCACCGACCT
Found at i:52663 original size:60 final size:60
Alignment explanation
Indices: 52577--52703 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
52567 CATATGTCCT
* * * * ** *
52577 CAAAGTATGACCTTCATTTTAGATTGATCCTTAAAC-TTTTGAACATTTCAATTTCATCTC
1 CAAACTATGACATTCATTCTAAATTGATCCCCAAACTTTTTGAACATTCCAATTTCAT-TC
52637 CAAACTATGACATTCATTCTAAATTGATCCCCAAACTTTTTGAACATTCCAATTTCATTC
1 CAAACTATGACATTCATTCTAAATTGATCCCCAAACTTTTTGAACATTCCAATTTCATTC
52697 CAAACTA
1 CAAACTA
52704 ATTATTATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 39 0.66
61 20 0.34
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (60 bp):
CAAACTATGACATTCATTCTAAATTGATCCCCAAACTTTTTGAACATTCCAATTTCATTC
Found at i:66471 original size:29 final size:29
Alignment explanation
Indices: 66429--66486 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
66419 GACGTGAGTT
66429 GGTGTTTTGATGTACGAAATAAGTCGATC
1 GGTGTTTTGATGTACGAAATAAGTCGATC
* *
66458 GGTGTTTTGATGTACGAAGTGAGTCGATC
1 GGTGTTTTGATGTACGAAATAAGTCGATC
66487 TGAATTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.34
Consensus pattern (29 bp):
GGTGTTTTGATGTACGAAATAAGTCGATC
Found at i:74911 original size:15 final size:15
Alignment explanation
Indices: 74891--74920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
74881 TTCCGAAGAA
*
74891 GGAAAGAGGCTAAAC
1 GGAAAGAAGCTAAAC
74906 GGAAAGAAGCTAAAC
1 GGAAAGAAGCTAAAC
74921 ATTTCCAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.30, T:0.07
Consensus pattern (15 bp):
GGAAAGAAGCTAAAC
Found at i:76744 original size:21 final size:21
Alignment explanation
Indices: 76720--76795 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
76710 TTAAAATTAA
76720 ATTTTATTATTGATCAGTCAT
1 ATTTTATTATTGATCAGTCAT
* * * * *
76741 ATTTTATTGTGATTTGTTAAAATTAA
1 ATTTTA-T-T-A-TTGAT-CAGTCAT
76767 ATTTTATTATTGATCAGTCAT
1 ATTTTATTATTGATCAGTCAT
76788 ATTTTATT
1 ATTTTATT
76796 GTTCTTATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
21 17 0.43
22 5 0.12
23 2 0.05
24 2 0.05
25 5 0.12
26 9 0.22
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTTTATTATTGATCAGTCAT
Found at i:77871 original size:113 final size:113
Alignment explanation
Indices: 77673--77899 Score: 382
Period size: 113 Copynumber: 2.0 Consensus size: 113
77663 ACATACGAAA
** *
77673 TCTTAGGATTTTGTCGCTAAAAACGACGTCGTGGGTAGTAATATCACGCCCCAACTTTTAAACTT
1 TCTTAGGATTTTGTCGCTAAAAACGACGTCGTGCCTAGTAATATCACACCCCAACTTTTAAACTT
77738 AATTTTAAATGTTTAATTAGTATATTTTGGGGACCAAATTGAAAGATC
66 AATTTTAAATGTTTAATTAGTATATTTTGGGGACCAAATTGAAAGATC
* * * *
77786 TCTTAGGATTTTGTCGCTAAAAACGACGTTGTGCCTAGTAATGTCACACGCTAACTTTTAAACTT
1 TCTTAGGATTTTGTCGCTAAAAACGACGTCGTGCCTAGTAATATCACACCCCAACTTTTAAACTT
*
77851 AATTTTAAATGTTTAATTAGTATATTTTGGGGACCGAATTGAAAGATC
66 AATTTTAAATGTTTAATTAGTATATTTTGGGGACCAAATTGAAAGATC
77899 T
1 T
77900 TAAAGATGTA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (113 bp):
TCTTAGGATTTTGTCGCTAAAAACGACGTCGTGCCTAGTAATATCACACCCCAACTTTTAAACTT
AATTTTAAATGTTTAATTAGTATATTTTGGGGACCAAATTGAAAGATC
Done.