Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009842.1 Kokia drynarioides strain JFW-HI SEQ_124569, 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, 969
Length: 1616
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.28
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:816 original size:59 final size:59
Alignment explanation
Indices: 713--1043 Score: 395
Period size: 59 Copynumber: 5.6 Consensus size: 59
703 ATTTAAAACA
* * * * *
713 TTCGAGGGTAAAAAAGGCAATTTTAGG-A-GTTTCGAGGTCGAAAATTGGATTTTTGGAAG
1 TTCGAGGGT-AAAATGGTAATTTTTGGAAGGTTTAG-GGTCAAAAATTGGATTTTTGGAAG
* * *
772 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAA
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATTGGATTTTTGGAAG
* ** * *
831 TT-TAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAA-TGAGATTTTTGGGAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATTG-GATTTTTGGAAG
* *
889 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTT-GAGGTCAAAAATTGGAATTTTGGGAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAG-GGTCAAAAATTGGATTTTTGGAAG
* * * *
948 TTCGGGGGTAAAATGGTAATTTTTGGAAGG-TTCGAGGTTAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAG-GGTCAAAAATTGGATTTTTGGAAG
*
1007 TTCAAGGGTAAAATGGTAATTTTTGGAAGGTTTAGGG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAGGG
1044 ACCTCCAGGG
Statistics
Matches: 236, Mismatches: 28, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.00
58 65 0.28
59 160 0.68
60 10 0.04
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATTGGATTTTTGGAAG
Found at i:1002 original size:118 final size:117
Alignment explanation
Indices: 716--1043 Score: 453
Period size: 118 Copynumber: 2.8 Consensus size: 117
706 TAAAACATTC
* * * * ** * *
716 GAGGGTAAAAAAGGCAATTTTAGG-AGTTTCGAGGTCGAAAATTGGATTTTTGGAAGTTCGGGGG
1 GAGGGT-AAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGG
*
780 TAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAATT
65 TAAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATGGGAATTTTGGAAATT
* * * *
833 TAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGGAGTTCGAGGGT
1 GAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
898 AAAATGGTAATTTTTGGAAGGTTT-GAGGTCAAAAATTGGAATTTTGGGAGTT
66 AAAATGGTAATTTTTGGAAGGTTTAG-GGTCAAAAATGGGAATTTTGGAAATT
* *
950 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCAAGGG
1 -GAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGG
1015 TAAAATGGTAATTTTTGGAAGGTTTAGGG
65 TAAAATGGTAATTTTTGGAAGGTTTAGGG
1044 ACCTCCAGGG
Statistics
Matches: 185, Mismatches: 22, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
116 15 0.08
117 84 0.45
118 85 0.46
119 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (117 bp):
GAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
AAAATGGTAATTTTTGGAAGGTTTAGGGTCAAAAATGGGAATTTTGGAAATT
Found at i:1018 original size:29 final size:29
Alignment explanation
Indices: 761--1035 Score: 255
Period size: 29 Copynumber: 9.4 Consensus size: 29
751 CGAAAATTGG
*
761 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* *
790 ATTTTTGGAAGGTT-TAGGGTCAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGGT--AAAATGGTA
* *
820 ATTTTTGGAAATT-TAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
848 ATTTTTGGAAGGTTCG-GGGTTAAAAAT-G-A
1 ATTTTTGGAA-GTTCGAGGG-T-AAAATGGTA
*
877 GATTTTTGGGAGTTCGAGGGTAAAATGGTA
1 -ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
907 ATTTTTGGAAGGTTTGA-GGTCAAAAATTGG-A
1 ATTTTTGGAA-GTTCGAGGGT--AAAA-TGGTA
* *
938 A-TTTTGGGAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* *
966 ATTTTTGGAAGGTTCGAGGTTAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGGT-AAAATGGTA
*
996 ATTTTTGGAAGTTCAAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1025 ATTTTTGGAAG
1 ATTTTTGGAAG
1036 GTTTAGGGAC
Statistics
Matches: 204, Mismatches: 20, Indels: 44
0.76 0.07 0.16
Matches are distributed among these distances:
27 10 0.05
28 28 0.14
29 77 0.38
30 61 0.30
31 25 0.12
32 3 0.01
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGGTA
Found at i:1325 original size:29 final size:29
Alignment explanation
Indices: 1222--1325 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
1212 NNNNNNNNNN
1222 TTTGGAA-GTTCAAGGGTAAAATGGTAATT
1 TTTGGAAGGTTC-AGGGTAAAATGGTAATT
* *
1251 TTTGGAAGGTTCGGGGTCAAAAATGG-GATT
1 TTTGGAAGGTTCAGGGT--AAAATGGTAATT
*
1281 TTTAGAA-GTTCGAGGGTAAAATGGTAATT
1 TTTGGAAGGTTC-AGGGTAAAATGGTAATT
*
1310 TTTGGAAGGTTTAGGG
1 TTTGGAAGGTTCAGGG
1326 ACCTCCAGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
28 7 0.11
29 28 0.45
30 20 0.32
31 7 0.11
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.34
Consensus pattern (29 bp):
TTTGGAAGGTTCAGGGTAAAATGGTAATT
Done.