Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001296.1 Kokia drynarioides strain JFW-HI SEQ_112696, 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: 26938
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:804 original size:18 final size:20
Alignment explanation
Indices: 769--805 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
759 TATATTTTTA
769 ATATTTACATTCTACACATT
1 ATATTTACATTCTACACATT
789 ATATTTA-ATT-TACACAT
1 ATATTTACATTCTACACAT
806 AATGTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTACATTCTACACATT
Found at i:4442 original size:12 final size:12
Alignment explanation
Indices: 4414--4445 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4404 AACAAAACAG
4414 AGAAAT-AAAAT
1 AGAAATAAAAAT
4425 -GAAATAAAAAT
1 AGAAATAAAAAT
4436 AGAAATAAAA
1 AGAAATAAAA
4446 TAATATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 5 0.26
12 9 0.47
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (12 bp):
AGAAATAAAAAT
Found at i:4445 original size:11 final size:11
Alignment explanation
Indices: 4414--4447 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
4404 AACAAAACAG
4414 AGAAATAAAAT
1 AGAAATAAAAT
4425 -GAAATAAAAAT
1 AGAAAT-AAAAT
4436 AGAAATAAAAT
1 AGAAATAAAAT
4447 A
1 A
4448 ATATATTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (11 bp):
AGAAATAAAAT
Found at i:7619 original size:16 final size:16
Alignment explanation
Indices: 7600--7630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7590 TTTAACTTAT
*
7600 TTCTATTTAAATTTAA
1 TTCTATTCAAATTTAA
7616 TTCTATTCAAATTTA
1 TTCTATTCAAATTTA
7631 CTTTAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTCTATTCAAATTTAA
Found at i:9717 original size:42 final size:42
Alignment explanation
Indices: 9658--9738 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
9648 CAATTGATGT
9658 GATTGAAATGTTGATGTTAATGATATGTTATTTAGTTTTCGG
1 GATTGAAATGTTGATGTTAATGATATGTTATTTAGTTTTCGG
*
9700 GATTGAAATTTTGATGTTAATGATATGTTATTTAGTTTT
1 GATTGAAATGTTGATGTTAATGATATGTTATTTAGTTTT
9739 TGGCCTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.51
Consensus pattern (42 bp):
GATTGAAATGTTGATGTTAATGATATGTTATTTAGTTTTCGG
Found at i:12438 original size:4 final size:4
Alignment explanation
Indices: 12429--12459 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
12419 TCTATGTTGG
12429 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
12460 GTCTTGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:17377 original size:10 final size:10
Alignment explanation
Indices: 17355--17387 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
17345 TCTCTTTCAA
17355 CATTTTC-TT
1 CATTTTCTTT
17364 CATTTTCTTT
1 CATTTTCTTT
17374 CATTTTTCTTT
1 CA-TTTTCTTT
17385 CAT
1 CAT
17388 GTAAAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 5 0.23
11 10 0.45
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (10 bp):
CATTTTCTTT
Found at i:20558 original size:22 final size:22
Alignment explanation
Indices: 20533--20575 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20523 TATTCAAATA
20533 ATAACAATAAAATAG-CAGCAAC
1 ATAACAATAAAAT-GTCAGCAAC
* *
20555 ATAATAGTAAAATGTCAGCAA
1 ATAACAATAAAATGTCAGCAA
20576 AACAATGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.56, C:0.14, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAATAAAATGTCAGCAAC
Done.