Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011888.1 Kokia drynarioides strain JFW-HI SEQ_126885, 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: 11924
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1503 original size:2 final size:2
Alignment explanation
Indices: 1496--1557 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1486 ATTCATATTA
1496 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
1538 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1558 TCATATTCGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1698 original size:24 final size:24
Alignment explanation
Indices: 1666--1903 Score: 289
Period size: 24 Copynumber: 9.9 Consensus size: 24
1656 GTTTAGTACA
*
1666 TTTACGCTCGTCAGCTAAGATACG
1 TTTACGCTCGTCAGCTAATATACG
** *
1690 TTTACGCTCACCAGCTAATATGCG
1 TTTACGCTCGTCAGCTAATATACG
1714 TTTACGCTCGTCAGCTAATATACG
1 TTTACGCTCGTCAGCTAATATACG
*
1738 TTTACGCTCG-CAAGCTAATATGCG
1 TTTACGCTCGTC-AGCTAATATACG
* *
1762 TTTACGCTCGCCAGCTAATATATG
1 TTTACGCTCGTCAGCTAATATACG
* *
1786 TTTACTCTCGTCAGCTAATATGCG
1 TTTACGCTCGTCAGCTAATATACG
* ** *
1810 TTTATGCTCACCAGCTAATATATG
1 TTTACGCTCGTCAGCTAATATACG
* *
1834 TTTACGCGCGTCAGCTAATATGCG
1 TTTACGCTCGTCAGCTAATATACG
* * *
1858 TTTACGCTTGCCAGCTAATATATG
1 TTTACGCTCGTCAGCTAATATACG
*
1882 TTTACGCTCATCAGCTAATATA
1 TTTACGCTCGTCAGCTAATATA
1904 AGAAACATTG
Statistics
Matches: 178, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
23 1 0.01
24 176 0.99
25 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTAATATACG
Found at i:1722 original size:48 final size:48
Alignment explanation
Indices: 1666--1902 Score: 341
Period size: 48 Copynumber: 4.9 Consensus size: 48
1656 GTTTAGTACA
* * * **
1666 TTTACGCTCGTCAGCTAAGATACGTTTACGCTCACCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATATGTTTACGCTCGTCAGCTAATATGCG
* *
1714 TTTACGCTCGTCAGCTAATATACGTTTACGCTCG-CAAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATATGTTTACGCTCGTC-AGCTAATATGCG
*
1762 TTTACGCTCGCCAGCTAATATATGTTTACTCTCGTCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATATGTTTACGCTCGTCAGCTAATATGCG
* * *
1810 TTTATGCTCACCAGCTAATATATGTTTACGCGCGTCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATATGTTTACGCTCGTCAGCTAATATGCG
* *
1858 TTTACGCTTGCCAGCTAATATATGTTTACGCTCATCAGCTAATAT
1 TTTACGCTCGCCAGCTAATATATGTTTACGCTCGTCAGCTAATAT
1903 AAGAAACATT
Statistics
Matches: 173, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
47 1 0.01
48 171 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (48 bp):
TTTACGCTCGCCAGCTAATATATGTTTACGCTCGTCAGCTAATATGCG
Found at i:5252 original size:41 final size:41
Alignment explanation
Indices: 5207--5312 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
5197 AGAAACTCGA
* * *
5207 TATATTAAAGGAAGGCCCATGTCTTGGGATGAGAATTAGAT
1 TATATTAAAGGAAGACTCATGTCTTGGGATGAGAATGAGAT
*
5248 TATATTAAAGGAAGACTCATGTCTTTGGATGAGAATGAGAT
1 TATATTAAAGGAAGACTCATGTCTTGGGATGAGAATGAGAT
5289 TATATTAAAGGAAGACTCATGTCT
1 TATATTAAAGGAAGACTCATGTCT
5313 CAAAATGAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (41 bp):
TATATTAAAGGAAGACTCATGTCTTGGGATGAGAATGAGAT
Found at i:5359 original size:47 final size:47
Alignment explanation
Indices: 5295--5399 Score: 210
Period size: 47 Copynumber: 2.2 Consensus size: 47
5285 AGATTATATT
5295 AAAGGAAGACTCATGTCTCAAAATGAGCGTTAGGTTTGTTTTTTATA
1 AAAGGAAGACTCATGTCTCAAAATGAGCGTTAGGTTTGTTTTTTATA
5342 AAAGGAAGACTCATGTCTCAAAATGAGCGTTAGGTTTGTTTTTTATA
1 AAAGGAAGACTCATGTCTCAAAATGAGCGTTAGGTTTGTTTTTTATA
5389 AAAGGAAGACT
1 AAAGGAAGACT
5400 TATGACTCGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (47 bp):
AAAGGAAGACTCATGTCTCAAAATGAGCGTTAGGTTTGTTTTTTATA
Found at i:8317 original size:52 final size:52
Alignment explanation
Indices: 8234--8428 Score: 259
Period size: 52 Copynumber: 3.8 Consensus size: 52
8224 GCTATAAACA
* * * * *
8234 AAAGGGTTCGATGACTAAGTGTTATCATGAGTAAACGAATCCTTTACGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
*
8286 AAAGGGTCCGATGACTAAGTGTCATCTTGAGTAAATGAATCCTTTATGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * *
8338 AAAGGGTCCGATGATTAAGT-TCCATAGTGAGTAAATGAATCCATGATGGATT
1 AAAGGGTCCGATGACTAAGTGT-CATCGTGAGTAAATGAATCCTTTATGGATT
* *
8390 AAA-GGTCCGATGACTCAGTGTCATCGTGAGTATATGAAT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
8429 TTCTATAAGG
Statistics
Matches: 127, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
51 31 0.24
52 96 0.76
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (52 bp):
AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:8474 original size:104 final size:103
Alignment explanation
Indices: 8261--8455 Score: 250
Period size: 104 Copynumber: 1.9 Consensus size: 103
8251 AGTGTTATCA
* * *
8261 TGAGTAAACGAATCCTTTACGGATTAAAGGGTCCGATGACTAAGTGTCATCTTGAGTAAATGAAT
1 TGAGTAAACGAATCCATGACGGATTAAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
* *
8326 CCTTTATGGATTAAAGGGTCCGATGATTAAGTTCCATAG
66 CCTATAAGGA-TAAAGGGTCCGATGATTAAGTTCCATAG
* * * *
8365 TGAGTAAATGAATCCATGATGGATTAAA-GGTCCGATGACTCAGTGTCATCGTGAGTATATGAAT
1 TGAGTAAACGAATCCATGACGGATTAAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-
*
8429 TTCTATAAGGA-ACAAGAGGTCCGATGA
65 TCCTATAAGGATA-AAG-GGTCCGATGA
8456 CTATATGTCA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
102 1 0.01
103 35 0.45
104 42 0.54
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (103 bp):
TGAGTAAACGAATCCATGACGGATTAAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
CCTATAAGGATAAAGGGTCCGATGATTAAGTTCCATAG
Found at i:10078 original size:25 final size:24
Alignment explanation
Indices: 10050--10154 Score: 108
Period size: 23 Copynumber: 4.4 Consensus size: 24
10040 GCTGGGCAAC
* *
10050 AGAGAGCACACACAGTGCTAA-AT
1 AGAGAGCACACAAAGTGCTAATAG
* * *
10073 AGAGAGTACACAAAGTACTAAT-C
1 AGAGAGCACACAAAGTGCTAATAG
10096 AGAGAGCACACAAAGTGCTAATCAG
1 AGAGAGCACACAAAGTGCTAAT-AG
*
10121 AGAGCA-CACACAAAGTGCTAATAAC
1 AGAG-AGCACACAAAGTGCTAAT-AG
10146 AGAGAGCAC
1 AGAGAGCAC
10155 GAGACGTGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 38 0.56
24 1 0.01
25 28 0.41
26 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (24 bp):
AGAGAGCACACAAAGTGCTAATAG
Found at i:10083 original size:23 final size:23
Alignment explanation
Indices: 10050--10179 Score: 104
Period size: 23 Copynumber: 5.5 Consensus size: 23
10040 GCTGGGCAAC
10050 AGAGAGCACACACAGTGCTAAAT
1 AGAGAGCACACACAGTGCTAAAT
* * *
10073 AGAGAGTACACAAAGTACT-AAT
1 AGAGAGCACACACAGTGCTAAAT
*
10095 CAGAGAGCACACAAAGTGCT-AAT
1 -AGAGAGCACACACAGTGCTAAAT
*
10118 CAGAGAGCACACACAAAGTGCTAATAAC
1 -AGAGAGCACACAC--AGTGCT-A-AAT
* *
10146 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAGTGCTAAAT
*
10169 AGAGAGTACAC
1 AGAGAGCACAC
10180 TAGTGTTCCT
Statistics
Matches: 90, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
22 4 0.04
23 60 0.67
24 1 0.01
25 11 0.12
27 9 0.10
28 5 0.06
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAT
Found at i:10116 original size:46 final size:47
Alignment explanation
Indices: 10048--10179 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 47
10038 GTGCTGGGCA
*
10048 ACAGAGAGCACACACAGTGCTAAATAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACAAAGTGCTAAATAGAGAGTACACAAAGTACTAAT
* *
10095 -CAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAAAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAAT-AGAGAG--TACACAAAGTACTAAT
* * *
10143 AACAGAGAGCACGA-GACGTGCTAAACAGAGAGTACAC
1 -ACAGAGAGCAC-ACAAAGTGCTAAATAGAGAGTACAC
10180 TAGTGTTCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
45 3 0.04
46 25 0.35
48 18 0.25
50 22 0.31
51 3 0.04
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (47 bp):
ACAGAGAGCACACAAAGTGCTAAATAGAGAGTACACAAAGTACTAAT
Done.