Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013423.1 Kokia drynarioides strain JFW-HI SEQ_128449, 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: 25204
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:658 original size:40 final size:40
Alignment explanation
Indices: 603--739 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
593 GTAGTCTAGT
* * *
603 AGTGTTTACACTGTCACGA-CTAGTTCAGTAATAATATTGC
1 AGTGTTTACAATGTCACGATC-AATTCAGTAATAATATCGC
* * *
643 AGTGTTTATAATGTCACTATCAATTCAGTAGTAATATCGC
1 AGTGTTTACAATGTCACGATCAATTCAGTAATAATATCGC
* * * * * *
683 GGTGTTTACAATGTCACTATCAATTCAATGATAGTATTGC
1 AGTGTTTACAATGTCACGATCAATTCAGTAATAATATCGC
* *
723 AGCGTTTACAGTGTCAC
1 AGTGTTTACAATGTCAC
740 TGCTAATTCA
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 79 0.99
41 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (40 bp):
AGTGTTTACAATGTCACGATCAATTCAGTAATAATATCGC
Found at i:814 original size:42 final size:40
Alignment explanation
Indices: 626--823 Score: 146
Period size: 40 Copynumber: 4.9 Consensus size: 40
616 TCACGACTAG
* * * * * **
626 TTCAGTAATAATATTGCAGTGTTTATAATGTCACTATCAA
1 TTCAATAATAGTATTGCAGCGTTTACAGTGTCACTGCCAA
* * * * * * * **
666 TTCAGTAGTAATATCGCGGTGTTTACAATGTCACTATCAA
1 TTCAATAATAGTATTGCAGCGTTTACAGTGTCACTGCCAA
* *
706 TTCAATGATAGTATTGCAGCGTTTACAGTGTCACTGCTAA
1 TTCAATAATAGTATTGCAGCGTTTACAGTGTCACTGCCAA
* * *
746 TTCAATAATAGTATTGCAACGTTTACAGTGTCATTGCCAG
1 TTCAATAATAGTATTGCAGCGTTTACAGTGTCACTGCCAA
* * *
786 TT-AGTAATAGTAATATTGCAGTGTTTACAGTCTCACTG
1 TTCAATAATAG---TATTGCAGCGTTTACAGTGTCACTG
824 TCGATTCGGT
Statistics
Matches: 130, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
39 7 0.05
40 102 0.78
42 21 0.16
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (40 bp):
TTCAATAATAGTATTGCAGCGTTTACAGTGTCACTGCCAA
Found at i:10621 original size:21 final size:22
Alignment explanation
Indices: 10595--10666 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
10585 GAAGTTTTTA
*
10595 GTATCGGTAGAGGTAAT-ACTT
1 GTATCGGTAGAAGTAATCACTT
*
10616 GTATCGGTAGAAG-AGTCACTT
1 GTATCGGTAGAAGTAATCACTT
* *
10637 TTATCGGTAGAACT-ATCACTT
1 GTATCGGTAGAAGTAATCACTT
10658 GTATCGGTA
1 GTATCGGTA
10667 ATAGTCTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.05
21 41 0.95
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (22 bp):
GTATCGGTAGAAGTAATCACTT
Found at i:11588 original size:14 final size:15
Alignment explanation
Indices: 11569--11597 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11559 TTTAATGAAA
11569 AATTTTAAA-AATAT
1 AATTTTAAATAATAT
11583 AATTTTAAATAATAT
1 AATTTTAAATAATAT
11598 TTTTTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAAATAATAT
Found at i:18642 original size:23 final size:25
Alignment explanation
Indices: 18616--18661 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18606 CCAATTAGGG
18616 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
18639 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
18662 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:21727 original size:23 final size:23
Alignment explanation
Indices: 21686--21742 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
21676 GTTAATAGAG
21686 ACTTTCAATTTACAATTCA-TATC
1 ACTTTCAA-TTACAATTCACTATC
* * *
21709 ACTTTCAATTCCAATTTCACTTTT
1 ACTTTCAATTACAA-TTCACTATC
21733 ACTTTCAATT
1 ACTTTCAATT
21743 TTGATCACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.17
23 12 0.41
24 12 0.41
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (23 bp):
ACTTTCAATTACAATTCACTATC
Found at i:22857 original size:30 final size:33
Alignment explanation
Indices: 22821--22880 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
22811 CACACATTAG
*
22821 CTTTCTCC-T-TT-CCTTTTTCTTCAATTTGGT
1 CTTTCTCCTTCTTCCCTCTTTCTTCAATTTGGT
22851 CTTTCTCCTTCTTCCCTCTTTCTTCAATTT
1 CTTTCTCCTTCTTCCCTCTTTCTTCAATTT
22881 CATACAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 1 0.04
32 2 0.08
33 15 0.58
ACGTcount: A:0.07, C:0.32, G:0.03, T:0.58
Consensus pattern (33 bp):
CTTTCTCCTTCTTCCCTCTTTCTTCAATTTGGT
Found at i:24508 original size:29 final size:29
Alignment explanation
Indices: 24474--24677 Score: 182
Period size: 29 Copynumber: 7.0 Consensus size: 29
24464 AATTTGAGTT
24474 TAAAAAGGGAATTTTTGGAAGTTTCGGGG
1 TAAAAAGGGAATTTTTGGAAGTTTCGGGG
* * * *
24503 TCAAAAA-TGAGATTTTTGAAATTTTGGGGG
1 T-AAAAAGGGA-ATTTTTGGAAGTTTCGGGG
* * *
24533 TAAAAATGGAATTTTTGGAAGTTTTGAGGT
1 TAAAAAGGGAATTTTTGGAAGTTTCG-GGG
* * *
24563 TAAAATGGG-ATTTTTGGAATTTTGGGGG
1 TAAAAAGGGAATTTTTGGAAGTTTCGGGG
* * **
24591 TAAAAATGGAATTTTTGTAAGTTTCAAGG
1 TAAAAAGGGAATTTTTGGAAGTTTCGGGG
24620 TCAAAAATGGG-ATTTTTGGAAGTTT-GAGGG
1 T-AAAAA-GGGAATTTTTGGAAGTTTCG-GGG
* *
24650 TAAAAACGAAATTTTTGGAAGTTTCGGG
1 TAAAAAGGGAATTTTTGGAAGTTTCGGG
24678 ACCTTCAGGG
Statistics
Matches: 138, Mismatches: 27, Indels: 20
0.75 0.15 0.11
Matches are distributed among these distances:
28 10 0.07
29 71 0.51
30 55 0.40
31 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
TAAAAAGGGAATTTTTGGAAGTTTCGGGG
Found at i:24518 original size:59 final size:59
Alignment explanation
Indices: 24446--24675 Score: 275
Period size: 59 Copynumber: 3.9 Consensus size: 59
24436 ACCCGGGGGT
* * ** * *
24446 AAAATGGTAATTTTGGGAAATTTGAGTTTAAAAAGGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGG-GATTTTTGGAAATTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * * *
24506 AAAATGAGATTTTT-GAAATTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGT-T
1 AAAATGGGATTTTTGGAAA-TTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * * *
24564 AAAATGGGATTTTTGGAATTTTGGGGGTAAAAATGGAATTTTTGTAAGTTTCAAGGTCA
1 AAAATGGGATTTTTGGAAATTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
* * *
24623 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAACGAAATTTTTGGAAGTTTCG
1 AAAATGGGATTTTTGGAAATTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCG
24676 GGACCTTCAG
Statistics
Matches: 145, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
58 52 0.36
59 87 0.60
60 6 0.04
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAATTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
Done.