Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013325.1 Kokia drynarioides strain JFW-HI SEQ_128347, 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: 16814
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:5534 original size:2 final size:2
Alignment explanation
Indices: 5527--5553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5517 ACGCATTAAG
5527 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5554 CATCCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10010 original size:26 final size:27
Alignment explanation
Indices: 9956--10013 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
9946 TTTAATTAGG
*
9956 AAATATATTTATTTTTAAAATTTATAA
1 AAATATATTTATTTATAAAATTTATAA
9983 AAATATA-TTATTTAATAAAATTTA-AA
1 AAATATATTTATTT-ATAAAATTTATAA
10009 AAATA
1 AAATA
10014 AACACATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATATATTTATTTATAAAATTTATAA
Found at i:11116 original size:5 final size:5
Alignment explanation
Indices: 11106--11151 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
11096 ATGATGTGCA
* * *
11106 AATAT AATAT AATA- AATAT ATTAA AATAT AATAT AATAT GATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
11152 GCAAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:12709 original size:15 final size:15
Alignment explanation
Indices: 12689--12721 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12679 TACCAAATAT
12689 TAACAACTACGAGTC
1 TAACAACTACGAGTC
12704 TAACAACTACGAGTC
1 TAACAACTACGAGTC
12719 TAA
1 TAA
12722 TACTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.21
Consensus pattern (15 bp):
TAACAACTACGAGTC
Found at i:15144 original size:28 final size:30
Alignment explanation
Indices: 15068--15150 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 30
15058 TTCTGATACA
*
15068 CGGGGGCAAAATGGTAATTTTGAGAAAATT
1 CGGGGGTAAAATGGTAATTTTGAGAAAATT
* * *
15098 CGGGGTTAAAAATAG-AATTTT-AG-ACATT
1 CGGGGGT-AAAATGGTAATTTTGAGAAAATT
*
15126 CGGGGGTAAAAGGGTAATTTTGAGA
1 CGGGGGTAAAATGGTAATTTTGAGA
15151 GTTTCGAGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.12
28 16 0.38
29 4 0.10
30 11 0.26
31 6 0.14
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTGAGAAAATT
Found at i:15236 original size:30 final size:29
Alignment explanation
Indices: 15199--15390 Score: 237
Period size: 29 Copynumber: 6.5 Consensus size: 29
15189 GTAAAAGGGT
15199 AATTTTTGGAAGTTTCGGGGTCAAAAATGG
1 AATTTTTGGAAGTTTCGGGGT-AAAAATGG
* * *
15229 GATTTTTGGAAG-CTCGATGGTAAAAATGG
1 AATTTTTGGAAGTTTCG-GGGTAAAAATGG
*
15258 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTCGGGGT-AAAAATGG
* *
15288 GATTTTTGGAAG-TTCGAGGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTAAAAATGG
15316 AATTTTTGGAAGTTTCGGGGTAAAAAATGG
1 AATTTTTGGAAGTTTCGGGGT-AAAAATGG
* *
15346 GATTATTGGAAG-TTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTCG-GGGTAAAAATGG
15375 AATTTTTGGACAGTTT
1 AATTTTTGGA-AGTTT
15391 AGGGACCTTC
Statistics
Matches: 141, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
28 19 0.13
29 60 0.43
30 60 0.43
31 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAGTTTCGGGGTAAAAATGG
Found at i:15254 original size:29 final size:28
Alignment explanation
Indices: 15199--15389 Score: 238
Period size: 30 Copynumber: 6.5 Consensus size: 28
15189 GTAAAAGGGT
*
15199 AATTTTTGGAAGTTTCGGGGTCAAAAATGG
1 AATTTTTGGAAG-TTCGAGGT-AAAAATGG
* *
15229 GATTTTTGGAAGCTCGATGGTAAAAATGG
1 AATTTTTGGAAGTTCGA-GGTAAAAATGG
15258 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGAAG-TTCGAGGT-AAAAATGG
*
15288 GATTTTTGGAAGTTCGAGGTAAAAATGG
1 AATTTTTGGAAGTTCGAGGTAAAAATGG
*
15316 AATTTTTGGAAGTTTCGGGGTAAAAAATGG
1 AATTTTTGGAAG-TTCGAGGT-AAAAATGG
* *
15346 GATTATTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTCGA-GGTAAAAATGG
15375 AATTTTTGGACAGTT
1 AATTTTTGGA-AGTT
15390 TAGGGACCTT
Statistics
Matches: 141, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
28 19 0.13
29 60 0.43
30 62 0.44
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
AATTTTTGGAAGTTCGAGGTAAAAATGG
Found at i:15342 original size:58 final size:59
Alignment explanation
Indices: 15199--15390 Score: 323
Period size: 59 Copynumber: 3.3 Consensus size: 59
15189 GTAAAAGGGT
* *
15199 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGCTCGATGGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
*
15258 AATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* *
15316 AATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTATTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
15375 AATTTTTGGACAGTTT
1 AATTTTTGGA-AGTTT
15391 AGGGACCTTC
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
58 55 0.44
59 66 0.52
60 5 0.04
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:16442 original size:3 final size:3
Alignment explanation
Indices: 16399--16424 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16389 TCATTAATGC
16399 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
16425 AAATAGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Done.