Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010813.1 Kokia drynarioides strain JFW-HI SEQ_125780, 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: 23551
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Warning! 264 characters in sequence are not A, C, G, or T
Found at i:836 original size:16 final size:15
Alignment explanation
Indices: 817--867 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
807 AAAATATTAA
817 TTTATTAATATATATT
1 TTTATT-ATATATATT
*
833 TTTATT-T-TTTATT
1 TTTATTATATATATT
846 TTTATTAGTATATATT
1 TTTATTA-TATATATT
862 TTTATT
1 TTTATT
868 TTATTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 1 0.03
16 17 0.57
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTATATATATT
Found at i:866 original size:22 final size:22
Alignment explanation
Indices: 829--887 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
819 TATTAATATA
*
829 TATTTTTATTTTTTATTTTTATTAG
1 TATTATTA-TTTTTATTT-TATT-G
854 TA-TA-TATTTTTATTTTATTG
1 TATTATTATTTTTATTTTATTG
874 TATTATTATTTTTA
1 TATTATTATTTTTA
888 AAAATCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 6 0.19
22 17 0.55
23 2 0.06
24 1 0.03
25 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (22 bp):
TATTATTATTTTTATTTTATTG
Found at i:877 original size:16 final size:15
Alignment explanation
Indices: 829--885 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
819 TATTAATATA
829 TATTTTTA-TTT-TT
1 TATTTTTATTTTATT
* *
842 TATTTTTATTAGTATA
1 TATTTTTATT-TTATT
858 TATTTTTATTTTATT
1 TATTTTTATTTTATT
*
873 GTATTATTATTTT
1 -TATTTTTATTTT
886 TAAAAATCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
15 4 0.11
16 22 0.63
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (15 bp):
TATTTTTATTTTATT
Found at i:7905 original size:22 final size:23
Alignment explanation
Indices: 7856--7898 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
7846 GATTACATGA
* *
7856 ATATTTAATTTAAGTGAATTAAT
1 ATATTTAATTAAAGTGAAATAAT
7879 ATATTTAA-TAAAGTGAAATA
1 ATATTTAATTAAAGTGAAATA
7899 TTGTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (23 bp):
ATATTTAATTAAAGTGAAATAAT
Found at i:11991 original size:32 final size:32
Alignment explanation
Indices: 11954--12059 Score: 85
Period size: 32 Copynumber: 3.2 Consensus size: 32
11944 ACTTTAAATT
11954 AATAATGATAAATTTACATTTTAATTCTCAAA
1 AATAATGATAAATTTACATTTTAATTCTCAAA
* *
11986 AATAAT-A-AAAGTTTA-A-TTTAACTTTTTAAATAAA
1 AATAATGATAAA-TTTACATTTTAA--TTCT---CAAA
*
12020 TTAATAATGGTAAATTTACATTTTAATTCTCAAA
1 --AATAATGATAAATTTACATTTTAATTCTCAAA
12054 AATAAT
1 AATAAT
12060 AAAAGTTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 24
0.66 0.06 0.28
Matches are distributed among these distances:
29 5 0.09
30 4 0.07
31 8 0.14
32 12 0.21
34 6 0.11
36 6 0.11
37 7 0.12
38 4 0.07
39 5 0.09
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.42
Consensus pattern (32 bp):
AATAATGATAAATTTACATTTTAATTCTCAAA
Found at i:12005 original size:36 final size:37
Alignment explanation
Indices: 11964--12082 Score: 126
Period size: 37 Copynumber: 3.4 Consensus size: 37
11954 AATAATGATA
11964 AATTT-ACATTTTAATTCTCAAAAATAATAAAAGTTT
1 AATTTAACATTTTAATTCTCAAAAATAATAAAAGTTT
* * * * * *
12000 AATTTAACTTTTTAA--AT--AAATTAAT-AATGGTA
1 AATTTAACATTTTAATTCTCAAAAATAATAAAAGTTT
12032 AATTT-ACATTTTAATTCTCAAAAATAATAAAAGTTT
1 AATTTAACATTTTAATTCTCAAAAATAATAAAAGTTT
*
12068 AATTTAACTTTTTAA
1 AATTTAACATTTTAA
12083 AAATTATAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 13
0.71 0.15 0.15
Matches are distributed among these distances:
31 8 0.13
32 9 0.14
33 8 0.13
35 8 0.13
36 14 0.22
37 16 0.25
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
AATTTAACATTTTAATTCTCAAAAATAATAAAAGTTT
Found at i:12027 original size:68 final size:68
Alignment explanation
Indices: 11948--12083 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
11938 TATAAAACTT
11948 TAAATTAATAATGATAAATTTACATTTTAATTCTCAAAAATAATAAAAGTTTAATTTAACTTTTT
1 TAAATTAATAATGATAAATTTACATTTTAATTCTCAAAAATAATAAAAGTTTAATTTAACTTTTT
12013 AAA
66 AAA
*
12016 TAAATTAATAATGGTAAATTTACATTTTAATTCTCAAAAATAATAAAAGTTTAATTTAACTTTTT
1 TAAATTAATAATGATAAATTTACATTTTAATTCTCAAAAATAATAAAAGTTTAATTTAACTTTTT
12081 AAA
66 AAA
12084 AATTATAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (68 bp):
TAAATTAATAATGATAAATTTACATTTTAATTCTCAAAAATAATAAAAGTTTAATTTAACTTTTT
AAA
Found at i:12092 original size:30 final size:30
Alignment explanation
Indices: 11983--12093 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
11973 TTTAATTCTC
11983 AAAAATAATAAAAGTTTAATTTAACTTTTT
1 AAAAATAATAAAAGTTTAATTTAACTTTTT
* * *
12013 AAATAAATTAATAATGGTAAATTTACATTTTAA-TTCTC
1 -AA-AAA-TAATAA----AAGTTTA-A-TTTAACTTTTT
12051 AAAAATAATAAAAGTTTAATTTAACTTTTT
1 AAAAATAATAAAAGTTTAATTTAACTTTTT
*
12081 AAAAATTATAAAA
1 AAAAATAATAAAA
12094 ATATAAACGA
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
29 5 0.08
30 16 0.25
31 8 0.12
32 3 0.05
33 6 0.09
35 6 0.09
36 3 0.05
37 8 0.12
38 4 0.06
39 5 0.08
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (30 bp):
AAAAATAATAAAAGTTTAATTTAACTTTTT
Found at i:18497 original size:105 final size:105
Alignment explanation
Indices: 18308--18521 Score: 259
Period size: 105 Copynumber: 2.0 Consensus size: 105
18298 GATAATTTTC
* * * * * * * **
18308 CTCACCTTTGTACCTTGAAGATCATTGGTACTTTCACCACTAAATTCACCTGTGTGAATTCAGTA
1 CTCACCCTTGCACCTTGAAGATCATTGATACTCTCACAACTAAATTCACCTCTGTGAACTCAACA
* * * *
18373 AGTAAAACTACAACACAAAAGGTTTTACTATCAATATGCA
66 AGTAAAACCACAACACAAAAGATTTTACTATAAATATACA
* *
18413 CTCACCCTTGCACCTTGAAGATCATTGATACTCTCATAACTAAGTTCA-CTCCTGTGAACTCAAC
1 CTCACCCTTGCACCTTGAAGATCATTGATACTCTCACAACTAAATTCACCT-CTGTGAACTCAAC
* *
18477 AAGTAAAACCATAACCCAAAAGATTTTACTATAAATATACA
65 AAGTAAAACCACAACACAAAAGATTTTACTATAAATATACA
18518 CTCA
1 CTCA
18522 TTGAAAGGTT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 2 0.02
105 89 0.98
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (105 bp):
CTCACCCTTGCACCTTGAAGATCATTGATACTCTCACAACTAAATTCACCTCTGTGAACTCAACA
AGTAAAACCACAACACAAAAGATTTTACTATAAATATACA
Found at i:18534 original size:30 final size:31
Alignment explanation
Indices: 18494--18583 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
18484 ACCATAACCC
* * * *
18494 AAAAGATTTTACTATAAATATACACTCATTG
1 AAAAGGTTTTACTATCAATATGCACTCATAG
*
18525 -AAAGGTTTTACTATCAATATGCACTAATAG
1 AAAAGGTTTTACTATCAATATGCACTCATAG
*
18555 AAAATGTTTTACTATCAATATGCACTCAT
1 AAAAGGTTTTACTATCAATATGCACTCAT
18584 CGTTGCACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.49
31 26 0.51
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (31 bp):
AAAAGGTTTTACTATCAATATGCACTCATAG
Found at i:18567 original size:31 final size:30
Alignment explanation
Indices: 18495--18580 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
18485 CCATAACCCA
* * * * *
18495 AAAGATTTTACTATAAATATACACTCATTG
1 AAAGGTTTTACTATCAATATGCACTAATAG
18525 AAAGGTTTTACTATCAATATGCACTAATAG
1 AAAGGTTTTACTATCAATATGCACTAATAG
*
18555 AAAATGTTTTACTATCAATATGCACT
1 -AAAGGTTTTACTATCAATATGCACT
18581 CATCGTTGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 25 0.51
31 24 0.49
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (30 bp):
AAAGGTTTTACTATCAATATGCACTAATAG
Found at i:18671 original size:166 final size:166
Alignment explanation
Indices: 18389--18688 Score: 420
Period size: 166 Copynumber: 1.8 Consensus size: 166
18379 ACTACAACAC
* * *
18389 AAAAGGTTTTACTATCAATATGCACTCACCCTTGCACCTTGAAGATCATTGATACTCTCATAACT
1 AAAAGGTTTTACTATCAATATGCACTCACCCTTGCACCTTAAAGATAATTGATACTCTCACAACT
* ** * * *
18454 AAGTTCACTCCTGTGAACTCAACAAGTAAAACCATAACCCAAAAGATTTTACTATAAATATACAC
66 AAATTCACTCCAATGAACTCAACAAGTAAAACCACAACACAAAAAATTTTACTATAAATATACAC
18519 TCATTGAAAGGTTTTACTATCAATATGCACTAATAG
131 TCATTGAAAGGTTTTACTATCAATATGCACTAATAG
* * * *
18555 AAAATGTTTTACTATCAATATGCACTCATCGTTGCACCTTAAAGATAATTGATACTCTCACCACT
1 AAAAGGTTTTACTATCAATATGCACTCACCCTTGCACCTTAAAGATAATTGATACTCTCACAACT
* * * * ** *
18620 AAATTCACTCCAATGAATTCAGCAAGTAAAACCACAATATAAAAAATTTTACTATCGATATGCAC
66 AAATTCACTCCAATGAACTCAACAAGTAAAACCACAACACAAAAAATTTTACTATAAATATACAC
18685 TCAT
131 TCAT
18689 GTTGAAAAGT
Statistics
Matches: 114, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
166 114 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (166 bp):
AAAAGGTTTTACTATCAATATGCACTCACCCTTGCACCTTAAAGATAATTGATACTCTCACAACT
AAATTCACTCCAATGAACTCAACAAGTAAAACCACAACACAAAAAATTTTACTATAAATATACAC
TCATTGAAAGGTTTTACTATCAATATGCACTAATAG
Found at i:22241 original size:18 final size:18
Alignment explanation
Indices: 22193--22241 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
22183 TTATTTTAAT
*
22193 TTTGTATTTAATTTTTCA
1 TTTGTATTTATTTTTTCA
*
22211 TTTCT-TTTATTTTTTACA
1 TTTGTATTTATTTTTT-CA
22229 TTTGTATTT-TTTT
1 TTTGTATTTATTTT
22242 ATTAAATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTGTATTTATTTTTTCA
Done.