Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002237.1 Kokia drynarioides strain JFW-HI SEQ_114239, 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: 11192
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:1990 original size:23 final size:25
Alignment explanation
Indices: 1964--2009 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1954 CCAATTAGGG
1964 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
1987 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
2010 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:2222 original size:58 final size:58
Alignment explanation
Indices: 2131--2247 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
2121 TATTATTGAA
*
2131 GGAAACAATTGAAGAAACACCATAGAAGTCATCTTTGAAGCCGATTTCCATGAAGATT
1 GGAAACAATTGAAGAAACACCATAGAAGCCATCTTTGAAGCCGATTTCCATGAAGATT
2189 GGAAACAATTGAAGAAACACCATAGAAGCCATCTTTGAAGCCGATTTCCATGAAGATT
1 GGAAACAATTGAAGAAACACCATAGAAGCCATCTTTGAAGCCGATTTCCATGAAGATT
2247 G
1 G
2248 AAGACCTCTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (58 bp):
GGAAACAATTGAAGAAACACCATAGAAGCCATCTTTGAAGCCGATTTCCATGAAGATT
Found at i:3170 original size:13 final size:13
Alignment explanation
Indices: 3140--3183 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
3130 CATTTTTTTG
3140 TTTTACTATTTACAT
1 TTTTA-TATTTA-AT
3155 TTTTA-ATTTAAT
1 TTTTATATTTAAT
*
3167 TTTTATATTTTAT
1 TTTTATATTTAAT
3180 TTTT
1 TTTT
3184 CCGTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 15 0.56
15 5 0.19
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATATTTAAT
Found at i:6030 original size:13 final size:12
Alignment explanation
Indices: 6012--6059 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
6002 AGTATATTTA
6012 TTTCATTTTCATT
1 TTTCATTTT-ATT
6025 TTTCATTTTATT
1 TTTCATTTTATT
6037 TTT-AGTTTTA-T
1 TTTCA-TTTTATT
6048 TTT-ATTTTATT
1 TTTCATTTTATT
6059 T
1 T
6060 ATTCCTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.15
11 8 0.24
12 11 0.33
13 9 0.27
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTCATTTTATT
Found at i:6062 original size:4 final size:5
Alignment explanation
Indices: 6008--6059 Score: 50
Period size: 5 Copynumber: 9.4 Consensus size: 5
5998 AATTAGTATA
*
6008 TTTAT TTCAT TTTCATT TTTCAT TTTATT TTTAGT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTT-A-T TTT-AT TTTA-T TTTA-T TTTAT TTTAT TTTAT
6058 TT
1 TT
6060 ATTCCTATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
5 20 0.49
6 15 0.37
7 6 0.15
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:6994 original size:19 final size:18
Alignment explanation
Indices: 6970--7041 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 18
6960 TATTATTTAG
6970 AAAAAGAACAAAATGAAAA
1 AAAAAGAA-AAAATGAAAA
6989 AAAAAGTCGAAAAAAATGAAAA
1 AAAAA---G-AAAAAATGAAAA
7011 AAGAAA-AAAATAATTG-AAA
1 AA-AAAGAAAA-AA-TGAAAA
7030 AAAAAGAAAAAA
1 AAAAAGAAAAAA
7042 AATTGGAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
18 9 0.20
19 16 0.36
20 2 0.04
22 13 0.29
23 5 0.11
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAAAGAAAAAATGAAAA
Found at i:7016 original size:29 final size:29
Alignment explanation
Indices: 6970--7041 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
6960 TATTATTTAG
6970 AAAAAGAACAAAATGAAAAAAA-AAGTCGAA
1 AAAAAGAA-AAAATGAAAAAAATAA-TCGAA
*
7000 AAAAATGAAAAAA-GAAAAAAATAATTGAAA
1 AAAAA-GAAAAAATGAAAAAAATAATCG-AA
7030 AAAAAGAAAAAA
1 AAAAAGAAAAAA
7042 AATTGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 17 0.45
30 18 0.47
31 3 0.08
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (29 bp):
AAAAAGAAAAAATGAAAAAAATAATCGAA
Found at i:7019 original size:30 final size:29
Alignment explanation
Indices: 6970--7041 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
6960 TATTATTTAG
*
6970 AAAAAGAACAAAATGAAAAAAAAAGTCGAAA
1 AAAAAGAA-AAAA-GAAAAAAAAAATCGAAA
* * *
7001 AAAATGAAAAAAGAAAAAAATAATTGAAA
1 AAAAAGAAAAAAGAAAAAAAAAATCGAAA
7030 AAAAAGAAAAAA
1 AAAAAGAAAAAA
7042 AATTGGAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 25 0.69
30 4 0.11
31 7 0.19
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (29 bp):
AAAAAGAAAAAAGAAAAAAAAAATCGAAA
Found at i:7028 original size:20 final size:21
Alignment explanation
Indices: 6998--7067 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
6988 AAAAAAGTCG
6998 AAAAAAA-TGAAAAAAGAA-A
1 AAAAAAATTGAAAAAAGAAGA
*
7017 AAAATAATTGAAAAAA-AAGA
1 AAAAAAATTGAAAAAAGAAGA
7037 AAAAAAATTGGAAAAAAGAAGA
1 AAAAAAATT-GAAAAAAGAAGA
7059 AGAAAAAAT
1 A-AAAAAAT
7068 AAAAATGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.18
20 17 0.39
21 7 0.16
22 5 0.11
23 7 0.16
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (21 bp):
AAAAAAATTGAAAAAAGAAGA
Found at i:7064 original size:21 final size:20
Alignment explanation
Indices: 6997--7065 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 20
6987 AAAAAAAGTC
6997 GAAAAAAA-TGAAAAAAGAA
1 GAAAAAAATTGAAAAAAGAA
7016 -AAAAATAATTGAAAAAA-AA
1 GAAAAA-AATTGAAAAAAGAA
7035 GAAAAAAAATTGGAAAAAAGAA
1 G-AAAAAAATT-GAAAAAAGAA
7057 GAAGAAAAA
1 GAA-AAAAA
7066 ATAAAAATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
18 5 0.12
19 4 0.09
20 12 0.28
21 14 0.33
22 8 0.19
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
GAAAAAAATTGAAAAAAGAA
Found at i:7071 original size:20 final size:20
Alignment explanation
Indices: 6979--7072 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 20
6969 GAAAAAGAAC
* *
6979 AAAATGAAAAAAAAAGTCGAAA
1 AAAATGAAAAAAGAAG--AAAA
7001 AAAATGAAAAAAGAA-AAAA
1 AAAATGAAAAAAGAAGAAAA
*
7020 ATAATTGAAAAAA-AAGAAAA
1 A-AAATGAAAAAAGAAGAAAA
7040 AAAATTGGAAAAAAGAAGAAGAA
1 AAAA-T-GAAAAAAGAAGAA-AA
7063 AAAAT-AAAAA
1 AAAATGAAAAA
7073 TGTGTTTGAG
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
19 8 0.13
20 21 0.34
21 7 0.11
22 20 0.32
23 6 0.10
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAATGAAAAAAGAAGAAAA
Found at i:8079 original size:23 final size:25
Alignment explanation
Indices: 8053--8098 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
8043 CCAATTAGGG
8053 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
8076 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
8099 TGGATCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Done.