Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006232.1 Hibiscus syriacus cultivar Beakdansim tig00014853_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: 66334
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:9818 original size:25 final size:25
Alignment explanation
Indices: 9744--9866 Score: 70
Period size: 26 Copynumber: 4.8 Consensus size: 25
9734 AGAGTGATTT
*
9744 TAGGTTAAAGTGGTATAGGGTTCGTTA
1 TAGGTTAAAGTGGTTTAGGGTT--TTA
* * ** * *
9771 -AGGTGAAAGTGATGAAAGATTTTA
1 TAGGTTAAAGTGGTTTAGGGTTTTA
*
9795 TAGGTTAAAGTGGTTTAGGGTTTTT
1 TAGGTTAAAGTGGTTTAGGGTTTTA
* * * *
9820 TAAGG-TAAGAGCGGTTAAGGGTTGTC
1 T-AGGTTAA-AGTGGTTTAGGGTTTTA
* *
9846 TATGATAAAGTGGTTTAGGGT
1 TAGGTTAAAGTGGTTTAGGGT
9867 AAGGTTCGAT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
24 3 0.04
25 34 0.47
26 35 0.49
ACGTcount: A:0.28, C:0.02, G:0.33, T:0.36
Consensus pattern (25 bp):
TAGGTTAAAGTGGTTTAGGGTTTTA
Found at i:13239 original size:2 final size:2
Alignment explanation
Indices: 13232--13256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13222 ATGAACAGGG
13232 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
13257 GAACTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18433 original size:23 final size:23
Alignment explanation
Indices: 18403--18448 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18393 CTACTAAACC
18403 TTTTCGCAGAACATAATCAATAA
1 TTTTCGCAGAACATAATCAATAA
18426 TTTTCGCAGAACATAATCAATAA
1 TTTTCGCAGAACATAATCAATAA
18449 GATTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
TTTTCGCAGAACATAATCAATAA
Found at i:23866 original size:60 final size:60
Alignment explanation
Indices: 23751--23867 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
23741 ACAAATGGTC
* *** *
23751 CTCCAACTATAGGATATTATTTTGTTGAGTCATTTGATTATAAAAAATTACAAAATGATT
1 CTCCAACTATAGGATATTACTTTGTTGAGTCATCAAACTATAAAAAATTACAAAATGATT
* * * * * *
23811 CTCCAACTATAGGATGTTGCTTTGTTGAGTCCTCAAACTATTAAAAGTTATAAAATG
1 CTCCAACTATAGGATATTACTTTGTTGAGTCATCAAACTATAAAAAATTACAAAATG
23868 GTCATTCAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (60 bp):
CTCCAACTATAGGATATTACTTTGTTGAGTCATCAAACTATAAAAAATTACAAAATGATT
Found at i:27020 original size:27 final size:27
Alignment explanation
Indices: 26988--27086 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 27
26978 TTTGATCGGG
26988 TCGGGTCGGGTTTTTTAAGTGTGATATTT
1 TCGGGTCGGGTTTTTTAAGTGTGATA--T
27017 GGGTCGGGTCGGGTTTTTTAAGTGTGATAT
1 ---TCGGGTCGGGTTTTTTAAGTGTGATAT
* *
27047 TCGGGTCGAGTTTTTTAAGTGTAATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
27074 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
27087 AGGATGAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 37 0.58
30 1 0.02
32 26 0.41
ACGTcount: A:0.14, C:0.08, G:0.34, T:0.43
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:27021 original size:32 final size:32
Alignment explanation
Indices: 26985--27084 Score: 138
Period size: 32 Copynumber: 3.3 Consensus size: 32
26975 TATTTTGATC
26985 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTT
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTT
27017 GGGTCGGGTCGGGTTTTTTAAGTGTGATA--T
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTT
* * *
27047 ---TCGGGTCGAGTTTTTTAAGTGTAATATTC
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTT
27076 GGGTCGGGT
1 GGGTCGGGT
27085 TTAGGATGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
27 24 0.40
30 1 0.02
32 35 0.58
ACGTcount: A:0.14, C:0.08, G:0.37, T:0.41
Consensus pattern (32 bp):
GGGTCGGGTCGGGTTTTTTAAGTGTGATATTT
Found at i:27661 original size:16 final size:16
Alignment explanation
Indices: 27640--27686 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
27630 GTTTTAGATT
27640 CAGATTCCAATTCCTA
1 CAGATTCCAATTCCTA
27656 CAGATTCCAATTCCTA
1 CAGATTCCAATTCCTA
27672 CAGATTCCAATTCCT
1 CAGATTCCAATTCCT
27687 TCACAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (16 bp):
CAGATTCCAATTCCTA
Found at i:30047 original size:15 final size:15
Alignment explanation
Indices: 30023--30056 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30013 CCGTAGGACC
30023 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
30038 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
30053 ACTA
1 ACTA
30057 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:30737 original size:63 final size:64
Alignment explanation
Indices: 30593--30737 Score: 145
Period size: 64 Copynumber: 2.3 Consensus size: 64
30583 ATGCATTGAA
* * * * * *
30593 GCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTATTATTAATGGGATGCATCGAT
1 GCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATAAAAGAGATGCATCAAT
* * * *
30657 GCA-TTCCTTATGCATCGATTCACT-AATTGCATTCGATGTTTTTATT-TAAAAGAG-TGCATCA
1 GCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTTTATTATAAAAGAGATGCATCA
30718 AT
63 AT
30720 GCACTACCTGTGCATCGA
1 GCACTACCTGTGCATCGA
30738 CACACCTTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
63 22 0.34
64 35 0.54
65 8 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
GCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATAAAAGAGATGCATCAAT
Found at i:35624 original size:81 final size:81
Alignment explanation
Indices: 35489--35650 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
35479 CCTTCAACCG
*
35489 AGGACGTAACCCCTCTATAAACCACTCACAAGTATCCTTCTCCGTAGGAACTAGCTCGGCAGCAA
1 AGGACATAACCCCTCTATAAACCACTCACAAGTATCCTTCTCCGTAGGAACTAGCTCGGCAGCAA
*
35554 AACGGCTCATCTTATT
66 AACGGCTCAACTTATT
*
35570 AGGACATAACCCCTCTATAAACCACTCACAAGTATCCTTCTCTGTAGGAACTAGCTCGGCAGCAA
1 AGGACATAACCCCTCTATAAACCACTCACAAGTATCCTTCTCCGTAGGAACTAGCTCGGCAGCAA
*
35635 AGCGGCTCAACTTATT
66 AACGGCTCAACTTATT
35651 GAATTCACAC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (81 bp):
AGGACATAACCCCTCTATAAACCACTCACAAGTATCCTTCTCCGTAGGAACTAGCTCGGCAGCAA
AACGGCTCAACTTATT
Found at i:37052 original size:15 final size:15
Alignment explanation
Indices: 37028--37061 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
37018 CCGTAGGACC
37028 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
37043 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
37058 ACTA
1 ACTA
37062 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:37661 original size:64 final size:64
Alignment explanation
Indices: 37588--37743 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 64
37578 TAATGAAGGT
* * * *
37588 ATGCATCGATGCATTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCATTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TAAAAGA
37651 G
64 G
** * *
37652 ATGCATCGATGCATGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTAAAAGAG
1 ATGCATCGATGCATTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTAAAAGAG
* *
37716 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCATTACTTGTGCATCGAT
37744 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
63 23 0.30
64 46 0.60
65 8 0.10
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCATTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTAAAAGAG
Found at i:46002 original size:16 final size:16
Alignment explanation
Indices: 45957--46009 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
45947 AATTTATTTT
*
45957 ATAATATATATTTAAA
1 ATAATATATTTTTAAA
*
45973 ATACATGAATATTTTTATA
1 ATA-AT--ATATTTTTAAA
45992 ATAATATATTTTTAAA
1 ATAATATATTTTTAAA
46008 AT
1 AT
46010 TTAAGTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 15 0.48
17 2 0.06
18 2 0.06
19 12 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
ATAATATATTTTTAAA
Found at i:47421 original size:18 final size:19
Alignment explanation
Indices: 47395--47438 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
47385 TAGAATGACT
*
47395 ATATTTAAA-ATTAATATA
1 ATATATAAACATTAATATA
*
47413 ATATATAAACATTGATATA
1 ATATATAAACATTAATATA
47432 AT-TATAA
1 ATATATAA
47439 TCGTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATATAAACATTAATATA
Found at i:47540 original size:2 final size:2
Alignment explanation
Indices: 47529--47559 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47519 GAAAACAACC
47529 AT AT -T 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
47560 GAGGCTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.