Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011764.1 Kokia drynarioides strain JFW-HI SEQ_126759, 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: 1765
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Found at i:753 original size:59 final size:58
Alignment explanation
Indices: 690--1006 Score: 331
Period size: 59 Copynumber: 5.4 Consensus size: 58
680 AAAATGGTAA
* *
690 TTTT-GGAAGTTTGGGGATAAAATGGTAATTTTTGGAAGATTCAGGGTTAAAAATGAGAT
1 TTTTGGGAA-TTTGGGG-TAAAATGGTAATTTTTGGAAGCTTCAGGGTCAAAAATGAGAT
* * *
749 TTTT-GGAAGTTTGGGGGTTAGATGGTAA-TTTTGGAAGCTTC-GAGGTAAAAAAAAT-AGGAT
1 TTTTGGGAA-TTT-GGGGTAAAATGGTAATTTTTGGAAGCTTCAG-GGT--CAAAAATGA-GAT
* * * *
809 TTTTGGGAATTCGAGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCAAAAATGGGAT
1 TTTTGGGAATTTG-GGGTAAAATGGTAATTTTTGGAAGCTTCAGGGTCAAAAATGAGAT
* * *
868 TTTTGGGAATTTAGGGGTAAAATGGTAA-TTTTGGAAGTTTTAGGGTCAAAAATGGGAT
1 TTTTGGGAATTT-GGGGTAAAATGGTAATTTTTGGAAGCTTCAGGGTCAAAAATGAGAT
* * * *
926 TTTTGGGAATTTGAGGGTAAAACGATAATTTTTGGAAGGTTCGGGGTCAAAAATGAGAT
1 TTTTGGGAATTTG-GGGTAAAATGGTAATTTTTGGAAGCTTCAGGGTCAAAAATGAGAT
*
985 TTTTGGGAATTCGGGAGTAAAA
1 TTTTGGGAATTTGGG-GTAAAA
1007 ATGATATTTT
Statistics
Matches: 222, Mismatches: 22, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
57 2 0.01
58 68 0.31
59 100 0.45
60 31 0.14
61 20 0.09
62 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
TTTTGGGAATTTGGGGTAAAATGGTAATTTTTGGAAGCTTCAGGGTCAAAAATGAGAT
Found at i:1005 original size:117 final size:118
Alignment explanation
Indices: 680--1006 Score: 387
Period size: 119 Copynumber: 2.8 Consensus size: 118
670 ACTCGAGGGT
* * * * *
680 AAAATGGTAATTTT-GGAAGTTTG-GGGATAAAATGGTAATTTTTGGAAGATTCAGGGTTAAAAA
1 AAAATGGGATTTTTGGGAA-TTTGAGGG-TAAAACGGTAATTTTTGGAAGATTCGGGGTCAAAAA
* * * *
743 TGAGATTTTT-GGAAGTTTGGGGGTTAGATGGTAATTTTGGAAGCTTCGAGGTAAAA
64 TGAGATTTTTGGGAAG-TTAGGGGTAAAATGGTAATTTTGGAAGCTTAGAGGT-AAA
* * *
799 AAAATAGGATTTTTGGGAATTCGAGGGTAAAACGGTAATTTTTGGAAGCTTCGGGGTCAAAAATG
1 AAAATGGGATTTTTGGGAATTTGAGGGTAAAACGGTAATTTTTGGAAGATTCGGGGTCAAAAATG
* * * *
864 GGATTTTTGGGAATTTAGGGGTAAAATGGTAATTTTGGAAGTTTTAG-GGT-CA
66 AGATTTTTGGGAAGTTAGGGGTAAAATGGTAATTTTGGAAG-CTTAGAGGTAAA
* *
916 AAAATGGGATTTTTGGGAATTTGAGGGTAAAACGATAATTTTTGGAAGGTTCGGGGTCAAAAATG
1 AAAATGGGATTTTTGGGAATTTGAGGGTAAAACGGTAATTTTTGGAAGATTCGGGGTCAAAAATG
*
981 AGATTTTTGGGAA-TTCGGGAGTAAAA
66 AGATTTTTGGGAAGTTAGGG-GTAAAA
1007 ATGATATTTT
Statistics
Matches: 181, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
116 5 0.03
117 80 0.44
119 82 0.45
120 14 0.08
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (118 bp):
AAAATGGGATTTTTGGGAATTTGAGGGTAAAACGGTAATTTTTGGAAGATTCGGGGTCAAAAATG
AGATTTTTGGGAAGTTAGGGGTAAAATGGTAATTTTGGAAGCTTAGAGGTAAA
Found at i:1024 original size:28 final size:29
Alignment explanation
Indices: 798--1018 Score: 90
Period size: 29 Copynumber: 7.6 Consensus size: 29
788 TCGAGGTAAA
*
798 AAAAAT-AGGATTTTTGGGAATTCGAGGGT-
1 AAAAATGA-GATTTTTAGGAATTCG-GGGTC
**
827 AAAACGGTA-ATTTTT-GGAAGCTTCGGGGTC
1 AAAAATG-AGATTTTTAGGAA--TTCGGGGTC
* * *
857 AAAAATGGGATTTTTGGGAATTTAGGGGT-
1 AAAAATGAGATTTTTAGGAA-TTCGGGGTC
* **
886 -AAAATG-GTAATTTT-GGAAGTTTTAGGGTC
1 AAAAATGAG-ATTTTTAGGAA--TTCGGGGTC
* * *
915 AAAAATGGGATTTTTGGGAATTTGAGGGT-
1 AAAAATGAGATTTTTAGGAATTCG-GGGTC
944 AAAACGAT-A-ATTTTT-GGAAGGTTCGGGGTC
1 AAAA--ATGAGATTTTTAGGAA--TTCGGGGTC
*
974 AAAAATGAGATTTTTGGGAATTCGGGAGT-
1 AAAAATGAGATTTTTAGGAATTCGGG-GTC
*
1003 AAAAATGATATTTTTA
1 AAAAATGAGATTTTTA
1019 TGATTCTCGA
Statistics
Matches: 153, Mismatches: 16, Indels: 46
0.71 0.07 0.21
Matches are distributed among these distances:
27 5 0.03
28 28 0.18
29 52 0.34
30 52 0.34
31 16 0.10
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAAATGAGATTTTTAGGAATTCGGGGTC
Done.