Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010574.1 Kokia drynarioides strain JFW-HI SEQ_125497, 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: 11997
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:833 original size:18 final size:18
Alignment explanation
Indices: 783--837 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
773 TATTTCATAT
783 TTCGAAAAAGTGAAAAAAA
1 TTCGAAAAA-TGAAAAAAA
*
802 TTCGAAAAAAGAAAAAAA
1 TTCGAAAAATGAAAAAAA
*
820 -TCGAAATATTGAAAAAAA
1 TTCGAAA-AATGAAAAAAA
838 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.19
18 17 0.53
19 9 0.28
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.16
Consensus pattern (18 bp):
TTCGAAAAATGAAAAAAA
Found at i:836 original size:27 final size:26
Alignment explanation
Indices: 806--874 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
796 AAAAAATTCG
806 AAAAAAGAAAAAAATCGAAA-TATTGAA
1 AAAAAAGAAAAAAATC-AAAGT-TTGAA
*
833 AAAAAATAAAAAAAATCAAAGTTTGAA
1 AAAAAA-GAAAAAAATCAAAGTTTGAA
*
860 AAATAAGAAGAAAAA
1 AAAAAAGAA-AAAAA
875 AATTCGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.06
27 24 0.67
28 10 0.28
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAAAGAAAAAAATCAAAGTTTGAA
Found at i:837 original size:28 final size:28
Alignment explanation
Indices: 806--909 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 28
796 AAAAAATTCG
806 AAAAAAGAAAAAAATCGAAA-TATTGAAA
1 AAAAAAGAAAAAAATCGAAAGT-TTGAAA
834 AAAAATA-AAAAAAATC-AAAGTTTGAAA
1 AAAAA-AGAAAAAAATCGAAAGTTTGAAA
861 AATAAGAAGAAAAAAATTCG-AA--TT-AAA
1 AA-AA-AAGAAAAAAA-TCGAAAGTTTGAAA
888 AAAAGAA-AAAAAGAATCGAAAG
1 AAAA-AAGAAAAA-AATCGAAAG
910 CAGAAAAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 21
0.76 0.00 0.24
Matches are distributed among these distances:
25 8 0.12
26 9 0.14
27 16 0.24
28 20 0.30
29 9 0.14
30 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (28 bp):
AAAAAAGAAAAAAATCGAAAGTTTGAAA
Found at i:906 original size:25 final size:27
Alignment explanation
Indices: 858--907 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
848 TCAAAGTTTG
858 AAAAATAAGAAGAAAAAAATTCGAATT
1 AAAAATAAGAAGAAAAAAATTCGAATT
885 AAAAA-AAGAA-AAAAAGAA-TCGAA
1 AAAAATAAGAAGAAAAA-AATTCGAA
908 AGCAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (27 bp):
AAAAATAAGAAGAAAAAAATTCGAATT
Found at i:3384 original size:17 final size:17
Alignment explanation
Indices: 3364--3396 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3354 TTTAAGGACT
3364 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
3381 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
3397 TAAGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:3703 original size:50 final size:51
Alignment explanation
Indices: 3590--3713 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 51
3580 TGACATCCAT
* * * *
3590 TAACTCTCATGATTAGTTAAGTTTGCATCACAAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCACAAAATAATGACATGCATTAAC
* ** *
3642 TAACTTACATGTTAGTTAAATATGCATCAC-AAATCCT-ATCATGCATTATC
1 TAACTCACATGTTAGTTAAATATGCATCACAAAATAATGA-CATGCATTAAC
*
3692 TAACTCCCATGTTAGTTAAATA
1 TAACTCACATGTTAGTTAAATA
3714 CATCATTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 34 0.56
51 17 0.28
52 9 0.15
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (51 bp):
TAACTCACATGTTAGTTAAATATGCATCACAAAATAATGACATGCATTAAC
Found at i:4756 original size:18 final size:18
Alignment explanation
Indices: 4706--4760 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
4696 TATTTCATAT
4706 TTCGAAAAAGTGAAAAAAA
1 TTCGAAAAA-TGAAAAAAA
*
4725 TTCGAAAAAAGAAAAAAA
1 TTCGAAAAATGAAAAAAA
*
4743 -TCGAAATATTGAAAAAAA
1 TTCGAAA-AATGAAAAAAA
4761 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.19
18 17 0.53
19 9 0.28
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.16
Consensus pattern (18 bp):
TTCGAAAAATGAAAAAAA
Found at i:4759 original size:27 final size:26
Alignment explanation
Indices: 4729--4797 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
4719 AAAAAATTCG
4729 AAAAAAGAAAAAAATCGAAA-TATTGAA
1 AAAAAAGAAAAAAATC-AAAGT-TTGAA
*
4756 AAAAAATAAAAAAAATCAAAGTTTGAA
1 AAAAAA-GAAAAAAATCAAAGTTTGAA
*
4783 AAATAAGAAGAAAAA
1 AAAAAAGAA-AAAAA
4798 AATTCGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.06
27 24 0.67
28 10 0.28
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAAAGAAAAAAATCAAAGTTTGAA
Found at i:4760 original size:28 final size:28
Alignment explanation
Indices: 4729--4832 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 28
4719 AAAAAATTCG
4729 AAAAAAGAAAAAAATCGAAA-TATTGAAA
1 AAAAAAGAAAAAAATCGAAAGT-TTGAAA
4757 AAAAATA-AAAAAAATC-AAAGTTTGAAA
1 AAAAA-AGAAAAAAATCGAAAGTTTGAAA
4784 AATAAGAAGAAAAAAATTCG-AA--TT-AAA
1 AA-AA-AAGAAAAAAA-TCGAAAGTTTGAAA
4811 AAAAGAA-AAAAAGAATCGAAAG
1 AAAA-AAGAAAAA-AATCGAAAG
4833 CAGAAAAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 21
0.76 0.00 0.24
Matches are distributed among these distances:
25 8 0.12
26 9 0.14
27 16 0.24
28 20 0.30
29 9 0.14
30 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (28 bp):
AAAAAAGAAAAAAATCGAAAGTTTGAAA
Found at i:4829 original size:25 final size:27
Alignment explanation
Indices: 4781--4830 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
4771 TCAAAGTTTG
4781 AAAAATAAGAAGAAAAAAATTCGAATT
1 AAAAATAAGAAGAAAAAAATTCGAATT
4808 AAAAA-AAGAA-AAAAAGAA-TCGAA
1 AAAAATAAGAAGAAAAA-AATTCGAA
4831 AGCAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (27 bp):
AAAAATAAGAAGAAAAAAATTCGAATT
Found at i:7307 original size:17 final size:17
Alignment explanation
Indices: 7287--7319 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7277 TTTAAGGACT
7287 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
7304 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
7320 TAAGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:7626 original size:50 final size:51
Alignment explanation
Indices: 7513--7636 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 51
7503 TGACATCCAT
* * * *
7513 TAACTCTCATGATTAGTTAAGTTTGCATCACAAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCACAAAATAATGACATGCATTAAC
* ** *
7565 TAACTTACATGTTAGTTAAATATGCATCAC-AAATCCT-ATCATGCATTATC
1 TAACTCACATGTTAGTTAAATATGCATCACAAAATAATGA-CATGCATTAAC
*
7615 TAACTCCCATGTTAGTTAAATA
1 TAACTCACATGTTAGTTAAATA
7637 CATCATTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 34 0.56
51 17 0.28
52 9 0.15
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (51 bp):
TAACTCACATGTTAGTTAAATATGCATCACAAAATAATGACATGCATTAAC
Found at i:8907 original size:18 final size:18
Alignment explanation
Indices: 8857--8911 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
8847 TATTTCATAT
8857 TTCGAAAAAGTGAAAAAAA
1 TTCGAAAAA-TGAAAAAAA
*
8876 TTCGAAAAAAGAAAAAAA
1 TTCGAAAAATGAAAAAAA
*
8894 -TCGAAATATTGAAAAAAA
1 TTCGAAA-AATGAAAAAAA
8912 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.19
18 17 0.53
19 9 0.28
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.16
Consensus pattern (18 bp):
TTCGAAAAATGAAAAAAA
Found at i:8910 original size:27 final size:26
Alignment explanation
Indices: 8880--8948 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
8870 AAAAAATTCG
8880 AAAAAAGAAAAAAATCGAAA-TATTGAA
1 AAAAAAGAAAAAAATC-AAAGT-TTGAA
*
8907 AAAAAATAAAAAAAATCAAAGTTTGAA
1 AAAAAA-GAAAAAAATCAAAGTTTGAA
*
8934 AAATAAGAAGAAAAA
1 AAAAAAGAA-AAAAA
8949 AATTCGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.06
27 24 0.67
28 10 0.28
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAAAGAAAAAAATCAAAGTTTGAA
Found at i:8911 original size:28 final size:28
Alignment explanation
Indices: 8880--8983 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 28
8870 AAAAAATTCG
8880 AAAAAAGAAAAAAATCGAAA-TATTGAAA
1 AAAAAAGAAAAAAATCGAAAGT-TTGAAA
8908 AAAAATA-AAAAAAATC-AAAGTTTGAAA
1 AAAAA-AGAAAAAAATCGAAAGTTTGAAA
8935 AATAAGAAGAAAAAAATTCG-AA--TT-AAA
1 AA-AA-AAGAAAAAAA-TCGAAAGTTTGAAA
8962 AAAAGAA-AAAAAGAATCGAAAG
1 AAAA-AAGAAAAA-AATCGAAAG
8984 CAGAAAAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 21
0.76 0.00 0.24
Matches are distributed among these distances:
25 8 0.12
26 9 0.14
27 16 0.24
28 20 0.30
29 9 0.14
30 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (28 bp):
AAAAAAGAAAAAAATCGAAAGTTTGAAA
Found at i:8980 original size:25 final size:27
Alignment explanation
Indices: 8932--8981 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
8922 TCAAAGTTTG
8932 AAAAATAAGAAGAAAAAAATTCGAATT
1 AAAAATAAGAAGAAAAAAATTCGAATT
8959 AAAAA-AAGAA-AAAAAGAA-TCGAA
1 AAAAATAAGAAGAAAAA-AATTCGAA
8982 AGCAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (27 bp):
AAAAATAAGAAGAAAAAAATTCGAATT
Found at i:11458 original size:17 final size:17
Alignment explanation
Indices: 11438--11470 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11428 TTTAAGGACT
11438 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
11455 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
11471 TAAGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:11777 original size:50 final size:51
Alignment explanation
Indices: 11664--11787 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 51
11654 TGACATCCAT
* * * *
11664 TAACTCTCATGATTAGTTAAGTTTGCATCACAAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCACAAAATAATGACATGCATTAAC
* ** *
11716 TAACTTACATGTTAGTTAAATATGCATCAC-AAATCCT-ATCATGCATTATC
1 TAACTCACATGTTAGTTAAATATGCATCACAAAATAATGA-CATGCATTAAC
*
11766 TAACTCCCATGTTAGTTAAATA
1 TAACTCACATGTTAGTTAAATA
11788 CATCATTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 34 0.56
51 17 0.28
52 9 0.15
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (51 bp):
TAACTCACATGTTAGTTAAATATGCATCACAAAATAATGACATGCATTAAC
Done.