Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001226.1 Kokia drynarioides strain JFW-HI SEQ_112582, 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: 28228
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:451 original size:5 final size:5
Alignment explanation
Indices: 441--482 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
431 AAATATAACT
*
441 CATCA CATCA CATTA CATCA CATCA CATCA CATCA CATCA CA
1 CATCA CATCA CATCA CATCA CATCA CATCA CATCA CATCA CA
483 ACATGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (5 bp):
CATCA
Found at i:8996 original size:19 final size:19
Alignment explanation
Indices: 8972--9018 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
8962 GGACTCCTAG
8972 TGTTTAATTAACTTTAAAC
1 TGTTTAATTAACTTTAAAC
8991 TGTTTAATTAACTTTAAAC
1 TGTTTAATTAACTTTAAAC
9010 TGTTTAATT
1 TGTTTAATT
9019 GAATTCATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (19 bp):
TGTTTAATTAACTTTAAAC
Found at i:9971 original size:16 final size:16
Alignment explanation
Indices: 9950--9980 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9940 TGTACTAGTC
*
9950 TCTTGTCTTGTCAATG
1 TCTTGTCTTGACAATG
9966 TCTTGTCTTGACAAT
1 TCTTGTCTTGACAAT
9981 ACTCAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (16 bp):
TCTTGTCTTGACAATG
Found at i:10810 original size:15 final size:16
Alignment explanation
Indices: 10776--10817 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
10766 GAACAACCAT
10776 TGTTTGAGAACAGCTA
1 TGTTTGAGAACAGCTA
* *
10792 TGTTTG-GAATAGTTA
1 TGTTTGAGAACAGCTA
10807 TGTTT-AGAACA
1 TGTTTGAGAACA
10818 ACGTTTCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (16 bp):
TGTTTGAGAACAGCTA
Found at i:26877 original size:30 final size:30
Alignment explanation
Indices: 26819--27103 Score: 185
Period size: 30 Copynumber: 9.6 Consensus size: 30
26809 TCCGGGGGGT
* * *
26819 AAAATGGTACTTTTTGGAAGAATCGGGGTCA
1 AAAATGG-AATTTTTGGAAAAATTGGGGTCA
*
26850 AAAATGGAATTTTTTGAAAAATTGGGGTC-
1 AAAATGGAATTTTTGGAAAAATTGGGGTCA
* ***
26879 -AAATGTAATTTTTGGAAAAATCAAGGT-A
1 AAAATGGAATTTTTGGAAAAATTGGGGTCA
* *
26907 AAAATGGAA-TTTTGG-AAAGTTCGGGGGT-G
1 AAAATGGAATTTTTGGAAAAATT--GGGGTCA
* *
26936 AAAATGCAA-TTTTGGAAAAATTGAGGTCA
1 AAAATGGAATTTTTGGAAAAATTGGGGTCA
** **
26965 AAAATGGAATTTTTGGAAAGTTTAAGGTCA
1 AAAATGGAATTTTTGGAAAAATTGGGGTCA
* *
26995 AAAATGGAATTTTCT-AAAAAATTAAGGGT-A
1 AAAATGGAATTTT-TGGAAAAATT-GGGGTCA
* * ** *
27025 AAAATGTAAATTTTGGAAAGTTTGGGGTTAA
1 AAAATGGAATTTTTGGAAAAATTGGGG-TCA
** *
27056 AAAATGGAA-TTTTGGAAAGTTTGGGGGCTAA
1 AAAATGGAATTTTTGGAAAAATT-GGGG-TCA
*
27087 AAAATGTAATTTTTGGA
1 AAAATGGAATTTTTGGA
27104 CAGTTTAGAG
Statistics
Matches: 204, Mismatches: 36, Indels: 27
0.76 0.13 0.10
Matches are distributed among these distances:
27 4 0.02
28 32 0.16
29 36 0.18
30 89 0.44
31 36 0.18
32 7 0.03
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAAATTGGGGTCA
Found at i:26891 original size:28 final size:28
Alignment explanation
Indices: 26814--26983 Score: 101
Period size: 29 Copynumber: 5.9 Consensus size: 28
26804 AGACATCCGG
* * *
26814 GGGGTAAAATGGTACTTTTTGGAAGAATC
1 GGGGTCAAAT-GTAATTTTTGGAAAAATC
* * *
26843 GGGGTCAAAAATGGAATTTTTTGAAAAATT
1 GGGGTC--AAATGTAATTTTTGGAAAAATC
26873 GGGGTCAAATGTAATTTTTGGAAAAATC
1 GGGGTCAAATGTAATTTTTGGAAAAATC
** * * **
26901 AAGGTAAAAATGGAA-TTTTGGAAAGTTC
1 GGGGT-CAAATGTAATTTTTGGAAAAATC
* * *
26929 GGGGGTGAAAATGCAA-TTTTGGAAAAATT
1 -GGGGT-CAAATGTAATTTTTGGAAAAATC
* *
26958 GAGGTCAAAAATGGAATTTTTGGAAA
1 GGGGTC--AAATGTAATTTTTGGAAA
26984 GTTTAAGGTC
Statistics
Matches: 109, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
28 37 0.34
29 40 0.37
30 28 0.26
31 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (28 bp):
GGGGTCAAATGTAATTTTTGGAAAAATC
Found at i:27059 original size:31 final size:32
Alignment explanation
Indices: 27024--27109 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 32
27014 AATTAAGGGT
*
27024 AAAAATGTAAATTTTGGAAAGTTT-GGGGTTA
1 AAAAATGTAAATTTTGGAAAGTTTGGGGGCTA
*
27055 AAAAATG-GAATTTTGGAAAGTTTGGGGGCTA
1 AAAAATGTAAATTTTGGAAAGTTTGGGGGCTA
* *
27086 AAAAATGTAATTTTTGGACAGTTT
1 AAAAATGTAAATTTTGGAAAGTTT
27110 AGAGACCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 15 0.31
31 20 0.42
32 13 0.27
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (32 bp):
AAAAATGTAAATTTTGGAAAGTTTGGGGGCTA
Done.