Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006838.1 Kokia drynarioides strain JFW-HI SEQ_121437, 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, 848
Length: 1414
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Found at i:58 original size:18 final size:20
Alignment explanation
Indices: 37--85 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
27 AATGTTTCGA
37 TAATAATAATAA-TAAT-AT
1 TAATAATAATAATTAATAAT
*
55 TAATAATTATTAATTAATAAT
1 TAATAA-TAATAATTAATAAT
76 TAATTAATAA
1 TAA-TAATAA
86 AAAAAAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 6 0.24
19 5 0.20
20 4 0.16
21 7 0.28
22 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATAATAATAATTAATAAT
Found at i:68 original size:7 final size:7
Alignment explanation
Indices: 37--79 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
27 AATGTTTCGA
37 TAATAA-
1 TAATAAT
43 TAATAA-
1 TAATAAT
49 TAAT-AT
1 TAATAAT
55 TAATAAT
1 TAATAAT
*
62 TATTAAT
1 TAATAAT
69 TAATAAT
1 TAATAAT
76 TAAT
1 TAAT
80 TAATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 1 0.03
6 14 0.42
7 18 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:77 original size:11 final size:10
Alignment explanation
Indices: 37--85 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
27 AATGTTTCGA
37 TAATAATAA-
1 TAATAATAAT
46 TAATAAT-AT
1 TAATAATAAT
*
55 TAATAATTAT
1 TAATAATAAT
65 TAATTAATAAT
1 TAA-TAATAAT
76 TAATTAATAA
1 TAA-TAATAA
86 AAAAAAACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 1 0.03
9 14 0.39
10 5 0.14
11 16 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATAATAAT
Found at i:531 original size:29 final size:30
Alignment explanation
Indices: 498--677 Score: 205
Period size: 29 Copynumber: 6.1 Consensus size: 30
488 AATTGTCTAG
**
498 AAATCCCATTTTTGACCTTGAA-CTTCCAA
1 AAATCCCATTTTTGACCCCGAACCTTCCAA
527 AAATCCCATTTTTGACCCCGAACCTTCCAA
1 AAATCCCATTTTTGACCCCGAACCTTCCAA
* *
557 AAATTACCA-TTTT-ACCATCGAA-CTTCCAA
1 AAA-TCCCATTTTTGACC-CCGAACCTTCCAA
*
586 AAATCTCATTTTTGACCCCGAACCTTCCAA
1 AAATCCCATTTTTGACCCCGAACCTTCCAA
* *
616 AAATTACCA--TTTCACCCCCGAA-CTTCCAA
1 AAA-TCCCATTTTTGA-CCCCGAACCTTCCAA
645 AAAT-CCATTTTTGACCCCGAACCTTCCAA
1 AAATCCCATTTTTGACCCCGAACCTTCCAA
674 AAAT
1 AAAT
678 TATCATTTTA
Statistics
Matches: 129, Mismatches: 11, Indels: 22
0.80 0.07 0.14
Matches are distributed among these distances:
27 3 0.02
28 11 0.09
29 70 0.54
30 38 0.29
31 7 0.05
ACGTcount: A:0.33, C:0.32, G:0.06, T:0.29
Consensus pattern (30 bp):
AAATCCCATTTTTGACCCCGAACCTTCCAA
Found at i:714 original size:58 final size:58
Alignment explanation
Indices: 517--695 Score: 297
Period size: 59 Copynumber: 3.1 Consensus size: 58
507 TTTTGACCTT
517 GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCAT-C
1 GAACTTCCAAAAAT-CCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACC-TCC
* *
576 GAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCC
1 GAACTTCCAAAAATC-CATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCTCC
*
635 GAACTTCCAAAAATCCATTTTTGACCCCGAACCTTCCAAAAATTATCATTTTACCTCC
1 GAACTTCCAAAAATCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCTCC
693 GAA
1 GAA
696 TGTTTGAAAT
Statistics
Matches: 113, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
58 44 0.39
59 69 0.61
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (58 bp):
GAACTTCCAAAAATCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCTCC
Done.