Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010543.1 Kokia drynarioides strain JFW-HI SEQ_125462, 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: 7908
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.31
Warning! 386 characters in sequence are not A, C, G, or T
Found at i:6824 original size:89 final size:86
Alignment explanation
Indices: 6744--7126 Score: 359
Period size: 89 Copynumber: 4.3 Consensus size: 86
6734 TTCAAGGTCA
*
6744 AAAATGGGATTTTTGGAAGTTTGAGGGGT-AAAATGGTAATTTGTGGAAAGTTTGGGGTCAAAAA
1 AAAATGGAATTTTTGGAAGTTT-AGGGGTAAAAATGG-AATTT-TGGAAAGTTTGGGGTCAAAAA
6808 TGGGATTTTTGGAAGTTCGAGGGT
63 TGGGATTTTTGGAAGTTCGAGGGT
* * * * ** *
6832 AAAATGGTAATTTTTGGAAGGTTAGGGGTTAAAAATAGGATTTTTAGAAGGTTCAGGATCAAAAA
1 AAAATGG-AATTTTTGGAAGTTTAGGGG-TAAAAAT-GGAATTTTGGAAAGTTTGGGGTCAAAAA
* *
6897 TGAGATTTTGGGAAGTTCG-GAGGT
63 TGGGATTTTTGGAAGTTCGAG-GGT
* * * *
6921 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTGGGAAGTTTGGGGGT--AAAA
1 AAAATGG-AATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTGGAAAGTTT-GGGGTCAAAAA
*
6984 TGGTAATTTTTTGGAAGGTTCG-GGGTT
63 TGG-GA-TTTTTGGAA-GTTCGAGGG-T
* *
7011 AAAAATGTG-ATTTTTGGAAGTTTGGGGGT-AAAACGGTAATTCTTGG-AAGATTTGGGGTCAAA
1 -AAAATG-GAATTTTTGGAAGTTTAGGGGTAAAAATGG-AATT-TTGGAAAG-TTTGGGGTCAAA
7073 AATGGGATTTTTGGAAGTTCGAGGGT
61 AATGGGATTTTTGGAAGTTCGAGGGT
*
7099 AAAATGGTAGTTTTTGGAAGGTTTAGGG
1 AAAATGG-AATTTTTGGAA-GTTTAGGG
7127 ACCTCCGGGG
Statistics
Matches: 244, Mismatches: 29, Indels: 43
0.77 0.09 0.14
Matches are distributed among these distances:
86 1 0.00
87 12 0.05
88 47 0.19
89 126 0.52
90 42 0.17
91 15 0.06
92 1 0.00
ACGTcount: A:0.30, C:0.03, G:0.34, T:0.33
Consensus pattern (86 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTGGAAAGTTTGGGGTCAAAAATGG
GATTTTTGGAAGTTCGAGGGT
Found at i:6866 original size:59 final size:59
Alignment explanation
Indices: 6681--6881 Score: 269
Period size: 60 Copynumber: 3.4 Consensus size: 59
6671 ATGTTCGAAA
* * * *
6681 TCAAAAATGAGATTTTTTGAAGTTCGAGGGTAAAAAGGGTAATTTGTGGAAAGTTCA-AGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTGTGGAAAGTT-AGGGG
* *
6741 TCAAAAATGGGATTTTTGGAAGTTTGAGGGGTAAAATGGTAATTTGTGGAAAGTTTGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTGTGGAAAGTTAGGGG
* *
6801 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTAGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTGTGGAAAGTTAGGGG
* * *
6860 TTAAAAATAGGATTTTTAGAAG
1 TCAAAAATGGGATTTTTGGAAG
6882 GTTCAGGATC
Statistics
Matches: 126, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
59 48 0.38
60 74 0.59
61 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (59 bp):
TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTGTGGAAAGTTAGGGG
Found at i:6906 original size:59 final size:58
Alignment explanation
Indices: 6744--7121 Score: 306
Period size: 59 Copynumber: 6.4 Consensus size: 58
6734 TTCAAGGTCA
* * * *
6744 AAAATGGGATTTTTGGAAGTTTGAGGGGT--AAAATG-GTAATTTGTGGAAAGTTT-GGGGT
1 AAAATGGAATTTTTGGAAGGTT-CGGGGTCAAAAATGAG--ATTT-TGGGAAGTTTGGGGGT
* * * *
6802 CAAAAATGGGATTTTTGGAA-GTTCGAGGGT--AAAATG-GTAATTTTTGGAAGGTTAGGGGTT
1 --AAAATGGAATTTTTGGAAGGTTCG-GGGTCAAAAATGAG--ATTTTGGGAA-GTTTGGGGGT
* * * * *
6862 AAAAATAGG-ATTTTTAGAAGGTTCAGGATCAAAAATGAGATTTTGGGAAGTTCGGAGGT
1 -AAAAT-GGAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTGGGAAGTTTGGGGGT
*
6921 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTGGGAAGTTTGGGGGT
1 AAAATGG-AATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTGGGAAGTTTGGGGGT
* * *
6980 AAAATGGTAATTTTTTGGAAGGTTCGGGGTTAAAAATGTGATTTTTGGAAGTTTGGGGGT
1 AAAATGG-AA-TTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTGGGAAGTTTGGGGGT
* * * * * * * *
7040 AAAACGGTAATTCTTGGAAGATTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGG-AATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTGGGAAGTTTGGGGGT
*
7099 AAAATGGTAGTTTTTGGAAGGTT
1 AAAATGG-AATTTTTGGAAGGTT
7122 TAGGGACCTC
Statistics
Matches: 273, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.01
58 10 0.04
59 162 0.59
60 92 0.34
61 6 0.02
62 1 0.00
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTGGGAAGTTTGGGGGT
Found at i:7090 original size:119 final size:118
Alignment explanation
Indices: 6872--7121 Score: 347
Period size: 119 Copynumber: 2.1 Consensus size: 118
6862 AAAAATAGGA
* * *
6872 TTTTTAGAAGGTTCAGGATCAAAAATGAGATTTTGGGAAGTTCGGAGGTAAAATGGTAATTTTTG
1 TTTTTGGAAGGTTCAGGATCAAAAATGAGATTTTGGGAAGTTCGGAGGTAAAACGGTAATTCTTG
* * * *
6937 GAAGGTTCGGGGTCAAAAATGGGATTTTGGGAAGTTTGGGGGTAAAATGGTAAT
66 GAAGATTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGAGGGTAAAATGGT-AG
* * * * * * *
6991 TTTTTGGAAGGTTCGGGGTTAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAACGGTAATTCTTG
1 TTTTTGGAAGGTTCAGGATCAAAAATGAGATTTTGGGAAGTTCGGAGGTAAAACGGTAATTCTTG
* *
7056 GAAGATTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAG
66 GAAGATTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGAGGGTAAAATGGTAG
7109 TTTTTGGAAGGTT
1 TTTTTGGAAGGTT
7122 TAGGGACCTC
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
118 14 0.12
119 101 0.88
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (118 bp):
TTTTTGGAAGGTTCAGGATCAAAAATGAGATTTTGGGAAGTTCGGAGGTAAAACGGTAATTCTTG
GAAGATTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGAGGGTAAAATGGTAG
Done.