Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005732.1 Kokia drynarioides strain JFW-HI SEQ_119970, 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, 809
Length: 1349
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Found at i:513 original size:59 final size:59
Alignment explanation
Indices: 412--870 Score: 344
Period size: 59 Copynumber: 7.8 Consensus size: 59
402 GGAGTCCCGA
* **
412 GGGT-AAAAATGGTAA-TTTTGG--ATTCTCGGGGATGAAATGGTAATTTTGGGAAAATTCG
1 GGGTCAAAAATGG-AATTTTTGGACATT-TCGGGG-TAAAATGGTAATTTTGGGAAGTTTCG
* * * * * *
470 GGGTTAAAAATGGAATTTTTAGACATTTAGGGGTAAAAGGGTAATTTTGAG-AGTTTCA
1 GGGTCAAAAATGGAATTTTTGGACATTTCGGGGTAAAATGGTAATTTTGGGAAGTTTCG
* * * * *
528 AGGTCGAAAATGGAGTTTTTGGACA-TTCGGGGTAAAATGGTAATTTTAGGAAGTTACG
1 GGGTCAAAAATGGAATTTTTGGACATTTCGGGGTAAAATGGTAATTTTGGGAAGTTTCG
* ** * * * *
586 AGGTTGAAAATGGAGTTTTTGGACATCTGGGGGTAAAATGGTAATTTTAGGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGACATTTCGGGGTAAAATGGTAATTTTGGGAAGTTTCG
* * *
645 GAGTCAAAAATGAAATTTTTGGA-AGTTCGGGGCTAAAATGG-AATTTTGGGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGACATTTCGGGG-TAAAATGGTAATTTTGGGAAGTTTCG
* * *
703 GGGTCAAAAATGGGATTTTTGGA-AGTTT-GGAGCTAAAAATGG-AATTTTTGGAAGTTT-G
1 GGGTCAAAAATGGAATTTTTGGACA-TTTCGG-GGT-AAAATGGTAATTTTGGGAAGTTTCG
* * *
761 GGG-CTAAAAATGGAA-TTTTGGAAAGTTTCGGGGTCAAAAATGG-GATTTTTGGAAG-TTCG
1 GGGTC-AAAAATGGAATTTTTGGACA-TTTCGGGGT--AAAATGGTAATTTTGGGAAGTTTCG
* * * *
820 AGG-CTGAAAATGAAATTTTTGGA-AGTTCGGGGGTAAAAATGG-AATATTTGG
1 GGGTC-AAAAATGGAATTTTTGGACATTTC-GGGGT-AAAATGGTAAT-TTTGG
871 ACAGCTTAGG
Statistics
Matches: 335, Mismatches: 48, Indels: 35
0.80 0.11 0.08
Matches are distributed among these distances:
57 29 0.09
58 140 0.42
59 151 0.45
60 12 0.04
61 3 0.01
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (59 bp):
GGGTCAAAAATGGAATTTTTGGACATTTCGGGGTAAAATGGTAATTTTGGGAAGTTTCG
Found at i:682 original size:29 final size:29
Alignment explanation
Indices: 534--871 Score: 293
Period size: 29 Copynumber: 11.6 Consensus size: 29
524 TTCAAGGTCG
*
534 AAAATGGAGTTTTTGGACA-TTCGGGG-T-
1 AAAATGGAATTTTTGGA-AGTTCGGGGCTA
* * * *
561 AAAATGGTAATTTTAGGAAGTTACGAGGTTG
1 AAAATGG-AATTTTTGGAAGTT-CGGGGCTA
* *
592 AAAATGGAGTTTTTGGACA--TCTGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTC-GGGGCTA
* *
620 AAAATGGTAATTTTAGGAAGTTTCGGAG-TCA
1 AAAATGG-AATTTTTGGAAG-TTCGGGGCT-A
*
651 AAAATGAAATTTTTGGAAGTTCGGGGCT-
1 AAAATGGAATTTTTGGAAGTTCGGGGCTA
*
679 AAAATGGAATTTTGGGAAGTTTCGGGG-TCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGCT-A
* * *
709 AAAATGGGATTTTTGGAAGTTTGGAGCTA
1 AAAATGGAATTTTTGGAAGTTCGGGGCTA
*
738 AAAATGGAATTTTTGGAAGTTTGGGGCTA
1 AAAATGGAATTTTTGGAAGTTCGGGGCTA
767 AAAATGGAA-TTTTGGAAAGTTTCGGGG-TCA
1 AAAATGGAATTTTTGG-AAG-TTCGGGGCT-A
* * *
797 AAAATGGGATTTTTGGAAGTTCGAGGCTG
1 AAAATGGAATTTTTGGAAGTTCGGGGCTA
* *
826 AAAATGAAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGCTA
*
855 AAAATGGAATATTTGGA
1 AAAATGGAATTTTTGGA
872 CAGCTTAGGG
Statistics
Matches: 256, Mismatches: 32, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
27 8 0.03
28 43 0.17
29 122 0.48
30 61 0.24
31 22 0.09
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGGGGCTA
Found at i:770 original size:58 final size:59
Alignment explanation
Indices: 446--871 Score: 292
Period size: 58 Copynumber: 7.3 Consensus size: 59
436 CTCGGGGATG
* ** * * * * *
446 AAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATGGAATTTTTAGACATTTAGGGG-T-A
1 AAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGAAATTTTTGGA-AGTTCGGGGCTAA
* ** * * *
505 AAAGGGTAA-TTTT-GAGAGTTTCAAGGTCGAAAATGGAGTTTTTGGACA-TTCGGGG-T-A
1 AAATGG-AATTTTTGGA-AGTTTCGGGGTCAAAAATGAAATTTTTGGA-AGTTCGGGGCTAA
* * * ** * * *
562 AAATGGTAATTTTAGGAAGTTACGAGGTTGAAAATGGAGTTTTTGGACA--TCTGGGGGT-A
1 AAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGAAATTTTTGGA-AGTTC-GGGGCTAA
* *
621 AAATGGTAATTTTAGGAAGTTTCGGAGTCAAAAATGAAATTTTTGGAAGTTCGGGGCT-A
1 AAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGAAATTTTTGGAAGTTCGGGGCTAA
* ** * *
680 AAATGGAATTTTGGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGCTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGAAATTTTTGGAAGTTCGGGGCTAA
*
739 AAATGGAATTTTTGGAAGTTT-GGGG-CTAAAAATGGAA-TTTTGGAAAGTTTCGGGG-TCAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTC-AAAAATGAAATTTTTGG-AAG-TTCGGGGCT-AA
* * * *
798 AAATGGGATTTTTGGAAG-TTCGAGG-CTGAAAATGAAATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTC-AAAAATGAAATTTTTGGAAGTTCGGGGCTAA
*
856 AAATGGAATATTTGGA
1 AAATGGAATTTTTGGA
872 CAGCTTAGGG
Statistics
Matches: 312, Mismatches: 40, Indels: 31
0.81 0.10 0.08
Matches are distributed among these distances:
57 27 0.09
58 151 0.48
59 126 0.40
60 8 0.03
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (59 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGAAATTTTTGGAAGTTCGGGGCTAA
Found at i:787 original size:88 final size:88
Alignment explanation
Indices: 620--871 Score: 366
Period size: 88 Copynumber: 2.8 Consensus size: 88
610 ATCTGGGGGT
* *
620 AAAATGGTAATTTTAGGAAGTTTCGGAG-TCAAAAATGAAATTTTTGGAAGTTCGGGGCT-AAAA
1 AAAATGG-GATTTTTGGAAGTTT-GGAGCT-AAAAATGAAATTTTTGGAAGTTCGGGGCTAAAAA
*
683 TGGAATTTTGGGAAGTTTCGGGGTCA
63 TGGAATTTTGGAAAGTTTCGGGGTCA
* *
709 AAAATGGGATTTTTGGAAGTTTGGAGCTAAAAATGGAATTTTTGGAAGTTTGGGGCTAAAAATGG
1 AAAATGGGATTTTTGGAAGTTTGGAGCTAAAAATGAAATTTTTGGAAGTTCGGGGCTAAAAATGG
774 AATTTTGGAAAGTTTCGGGGTCA
66 AATTTTGGAAAGTTTCGGGGTCA
* * *
797 AAAATGGGATTTTTGGAAG-TTCGAGGCTGAAAATGAAATTTTTGGAAGTTCGGGGGTAAAAATG
1 AAAATGGGATTTTTGGAAGTTTGGA-GCTAAAAATGAAATTTTTGGAAGTTCGGGGCTAAAAATG
861 GAATATTTGGA
65 GAAT-TTTGGA
872 CAGCTTAGGG
Statistics
Matches: 149, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
87 35 0.23
88 101 0.68
89 13 0.09
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (88 bp):
AAAATGGGATTTTTGGAAGTTTGGAGCTAAAAATGAAATTTTTGGAAGTTCGGGGCTAAAAATGG
AATTTTGGAAAGTTTCGGGGTCA
Found at i:1016 original size:34 final size:34
Alignment explanation
Indices: 977--1041 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
967 AAGGAAAATT
977 TATGGGGTAATTTTGTAATTAAAGCGAACCTTTG
1 TATGGGGTAATTTTGTAATTAAAGCGAACCTTTG
1011 TATGGGGTAATTTTGTAATTAAAGCGAACCT
1 TATGGGGTAATTTTGTAATTAAAGCGAACCT
1042 GATTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (34 bp):
TATGGGGTAATTTTGTAATTAAAGCGAACCTTTG
Done.