Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008266.1 Kokia drynarioides strain JFW-HI SEQ_122931, 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: 3985
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Found at i:2731 original size:6 final size:6
Alignment explanation
Indices: 2715--2818 Score: 75
Period size: 6 Copynumber: 16.3 Consensus size: 6
2705 TTCAATGAAT
*
2715 AAAGAAA AAAGAA AAAGAAGA AGAAGAA AATGAA AAAGAA AAAGAA AAAGAAA
1 AAAG-AA AAAGAA AAAG-A-A A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-AA
* * * * **
2768 AAAGAGGA AAACAA AAAGAA AAACAA AAA-TA GAAGAA ATGGAA AAAGAA
1 AAAGA--A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
2817 AA
1 AA
2819 GGAGAGGTCG
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
5 3 0.04
6 50 0.65
7 13 0.17
8 8 0.10
9 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:2749 original size:21 final size:19
Alignment explanation
Indices: 2715--2818 Score: 84
Period size: 21 Copynumber: 5.1 Consensus size: 19
2705 TTCAATGAAT
2715 AAAGAAAAAAGAAAAAGAAGA
1 AAAG-AAAAAGAAAAAGAA-A
*
2736 AGAAGAAAATGAAAAAG-AA
1 A-AAGAAAAAGAAAAAGAAA
*
2755 AAAGAAAAAGAAAAAAGAGGA
1 AAAGAAAAAG-AAAAAGA-AA
* *
2776 AAACAAAAAGAAAAACAAA
1 AAAGAAAAAGAAAAAGAAA
2795 AATAGAAGAAATGGAAAAAGAAA
1 AA-AGAA-AAA--GAAAAAGAAA
2818 A
1 A
2819 GGAGAGGTCG
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.12
19 11 0.16
20 10 0.15
21 25 0.37
22 3 0.04
23 10 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAGAAA
Found at i:2757 original size:27 final size:25
Alignment explanation
Indices: 2715--2818 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 25
2705 TTCAATGAAT
*
2715 AAAGAAAAAAGAAAAAGAAGAAGAAGA
1 AAAG-AAAAAGAAAAAGAAAAAGAA-A
2742 AAATGAAAAAGAAAAAGAAAAAGAAA
1 AAA-GAAAAAGAAAAAGAAAAAGAAA
* *
2768 AAAGAGGAAAACAAAAAGAAAAACAAA
1 AAAGA--AAAAGAAAAAGAAAAAGAAA
2795 AATAGAAGAAATGGAAAAAGAAAA
1 AA-AGAA-AAA--GAAAAAGAAAA
2819 GGAGAGGTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.03
26 5 0.08
27 45 0.68
28 4 0.06
29 10 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAGAAAAAGAAA
Found at i:2761 original size:33 final size:33
Alignment explanation
Indices: 2708--2804 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
2698 ACTCGGATTC
2708 AATGAATAAAGAAAAAAGAAAAAGAAGAAGAAGAA
1 AATGAA-AAAG-AAAAAGAAAAAGAAGAAGAAGAA
* *
2743 AATGAAAAAGAAAAAGAAAAAGAAAAAAGAGGAA
1 AATGAAAAAGAAAAAGAAAAAG-AAGAAGAAGAA
* * *
2777 AA-CAAAAAGAAAAACAAAAA-TAGAAGAA
1 AATGAAAAAGAAAAAGAAAAAGAAGAAGAA
2805 ATGGAAAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 5 0.09
33 28 0.52
34 15 0.28
35 6 0.11
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (33 bp):
AATGAAAAAGAAAAAGAAAAAGAAGAAGAAGAA
Found at i:3875 original size:49 final size:49
Alignment explanation
Indices: 3822--3983 Score: 170
Period size: 49 Copynumber: 3.3 Consensus size: 49
3812 AAAAGCATGA
* * *
3822 AGGGAAAGATTTAAGCCGCAACGGTGAATGCAGAACCACGAAGATATAG
1 AGGGAAAGATTTAAGCCGCAACGGCGAATGCAGTACCACGAAGACATAG
* ** * *
3871 AGGGAAAGATTTAAGTCGCAATAGCGAACCTTGTA-TATCA-G-AGACAT-G
1 AGGGAAAGATTTAAGCCGCAACGGCGAA---TGCAGTACCACGAAGACATAG
*
3919 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAG
1 -AGGGAAAGATTTAAGCCGCAACGGCGAATGCAGTACCACGAAGACATAG
*
3969 AGGGAAAGGTTTAAG
1 AGGGAAAGATTTAAG
3984 TC
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
46 2 0.02
47 4 0.04
48 2 0.02
49 74 0.82
50 2 0.02
51 3 0.03
52 3 0.03
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.17
Consensus pattern (49 bp):
AGGGAAAGATTTAAGCCGCAACGGCGAATGCAGTACCACGAAGACATAG
Found at i:3942 original size:98 final size:98
Alignment explanation
Indices: 3773--3985 Score: 311
Period size: 98 Copynumber: 2.2 Consensus size: 98
3763 GACGATTTGA
* *
3773 AGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACAGCAAACCTTGTACATCAAAAGCATGAAGGGAAAGATTTAAGC
* * *
3838 CGCAACGGTGAATGCAGAACCACGAAGATATAG
66 CGCAACGGCGAATCCAGAACCACGAAGACATAG
* * * * *
3871 AGGGAAAGATTTAAGTCGCAATAGCGAACCTTGTATATC-AGAGACATGAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACAGCAAACCTTGTACATCAAAAG-CATGAAGGGAAAGATTTAAG
*
3935 CCGCAACGGCGAATCCAGTACCACGAAGACATAG
65 CCGCAACGGCGAATCCAGAACCACGAAGACATAG
3969 AGGGAAAGGTTTAAGTC
1 AGGGAAAGGTTTAAGTC
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
97 3 0.03
98 99 0.97
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACAGCAAACCTTGTACATCAAAAGCATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGAACCACGAAGACATAG
Done.