Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013761.1 Kokia drynarioides strain JFW-HI SEQ_128789, 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: 11906
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1913 original size:16 final size:16
Alignment explanation
Indices: 1892--1941 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1882 TGATGGGGAT
1892 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
1908 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
1923 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
1938 ATTA
1 ATTA
1942 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:2234 original size:21 final size:20
Alignment explanation
Indices: 2203--2243 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2193 CTTACTACTG
2203 CTAACAACAAAATAAAATTA
1 CTAACAACAAAATAAAATTA
*
2223 CTAACTAACAAAATTAAATTA
1 CTAAC-AACAAAATAAAATTA
2244 AAGTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (20 bp):
CTAACAACAAAATAAAATTA
Found at i:2622 original size:4 final size:4
Alignment explanation
Indices: 2613--2659 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
2603 CTTCTCCTTC
*
2613 TTCT TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
2660 CTTCAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.85
5 3 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:7459 original size:27 final size:26
Alignment explanation
Indices: 7411--7473 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
7401 ACTCTTGAAC
*
7411 CCCAAACCCTTAAATTTTAAACACGAA
1 CCCAAA-CCTCAAATTTTAAACACGAA
* *
7438 CCCTAAACCTCAAATTTTAAACCCAAA
1 CCC-AAACCTCAAATTTTAAACACGAA
7465 CCCAAACCT
1 CCCAAACCT
7474 TGAACCTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.19
27 23 0.72
28 3 0.09
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.21
Consensus pattern (26 bp):
CCCAAACCTCAAATTTTAAACACGAA
Found at i:9883 original size:31 final size:32
Alignment explanation
Indices: 9836--9923 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 32
9826 ATTATGGGAC
*
9836 TCATTATTAACTTAATTTAATTACGTTATATAA
1 TCATTATTAA-TTAATTTAATTACATTATATAA
*
9869 -CATT-TTAATTTAATTTAATCACATTATATAA
1 TCATTATTAA-TTAATTTAATTACATTATATAA
*
9900 TAATTAATTAATTAATTTAATTAC
1 TCATT-ATTAATTAATTTAATTAC
9924 CATACTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
31 24 0.51
32 7 0.15
33 12 0.26
34 4 0.09
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (32 bp):
TCATTATTAATTAATTTAATTACATTATATAA
Done.