Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013057.1 Kokia drynarioides strain JFW-HI SEQ_128075, 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: 26710
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29 TGTGAGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:916 original size:3 final size:3
Alignment explanation
Indices: 908--932 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
898 TTGCCTAAGC
908 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
933 TTTCTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7799 original size:45 final size:45
Alignment explanation
Indices: 7748--7850 Score: 206
Period size: 45 Copynumber: 2.3 Consensus size: 45
7738 ACAACATTTA
7748 CTCTGCAACATTTCAACATCAAAAGAATCCTCGCCTTGGTCTTTC
1 CTCTGCAACATTTCAACATCAAAAGAATCCTCGCCTTGGTCTTTC
7793 CTCTGCAACATTTCAACATCAAAAGAATCCTCGCCTTGGTCTTTC
1 CTCTGCAACATTTCAACATCAAAAGAATCCTCGCCTTGGTCTTTC
7838 CTCTGCAACATTT
1 CTCTGCAACATTT
7851 ACTCTTATTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.32
Consensus pattern (45 bp):
CTCTGCAACATTTCAACATCAAAAGAATCCTCGCCTTGGTCTTTC
Found at i:10997 original size:15 final size:16
Alignment explanation
Indices: 10977--11043 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 16
10967 GTTTTATATA
10977 AAAATTA-TAAAAAAT
1 AAAATTATTAAAAAAT
*
10992 AAAATTATTTAAAAAT
1 AAAATTATTAAAAAAT
** * *
11008 AAAAAAATTATATAA-
1 AAAATTATTAAAAAAT
* *
11023 AAAGTTTTTAAAAAAT
1 AAAATTATTAAAAAAT
11039 AAAAT
1 AAAAT
11044 GGATTGAAGT
Statistics
Matches: 37, Mismatches: 13, Indels: 3
0.70 0.25 0.06
Matches are distributed among these distances:
15 16 0.43
16 21 0.57
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (16 bp):
AAAATTATTAAAAAAT
Found at i:13459 original size:23 final size:22
Alignment explanation
Indices: 13427--13536 Score: 87
Period size: 23 Copynumber: 4.9 Consensus size: 22
13417 GCTGGGGAAA
*
13427 CAGTAAGCACACATAGTGCAAT
1 CAGTAGGCACACATAGTGCAAT
*
13449 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACATAGTGCAAT
* * *
13472 CAATAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACATAGTGC-AAT
* * *
13495 CAGTAAGCGCACGA-AGTGCGAAA
1 CAGTAGGCACAC-ATAGTGC-AAT
* *
13518 CAGTAAGCACACACAGTGC
1 CAGTAGGCACACATAGTGC
13537 TGAACAGTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 16 0.22
23 55 0.76
24 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGTAGGCACACATAGTGCAAT
Found at i:13542 original size:23 final size:21
Alignment explanation
Indices: 13399--13548 Score: 79
Period size: 23 Copynumber: 6.5 Consensus size: 21
13389 CGAAGTACTT
13399 AACAGTAAGCACACAAGTGCTGGGG
1 AACAGTAAGCACACAAGTGC----G
13424 AAACAGTAAGCACACATAGTGC-
1 -AACAGTAAGCACACA-AGTGCG
*
13446 AATCCAGTAGGCACACACAGTGC-
1 AA--CAGTAAGCACACA-AGTGCG
* * * * *
13469 AATCAATAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACA-AGTGCG
*
13492 AATCAGTAAGCGCACGAAGTGCG
1 AA-CAGTAAGCACAC-AAGTGCG
13515 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
13539 AACAGTAAGC
1 AACAGTAAGC
13549 GTGCTAGCTT
Statistics
Matches: 104, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.02
22 16 0.15
23 62 0.60
24 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Found at i:13648 original size:24 final size:26
Alignment explanation
Indices: 13610--13657 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
13600 TCTACATGAG
13610 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
13636 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
13658 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:24666 original size:5 final size:5
Alignment explanation
Indices: 24658--24701 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
24648 TTAATTAAAT
* * *
24658 TAATA TAATA TAATA TAATA TAATT TAAGA TAATTT TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAA-TA TAATA TAA
24702 ATTATTCCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 29 0.91
6 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:26561 original size:12 final size:11
Alignment explanation
Indices: 26540--26592 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
26530 GGGACCAACG
*
26540 AAAAATAAAGGA
1 AAAAAGAAA-GA
26552 AAAAAGAAAGA
1 AAAAAGAAAGA
*
26563 AAAAAGAGA-A
1 AAAAAGAAAGA
26573 AAAAAGAAAGA
1 AAAAAGAAAGA
26584 AAGAAAGAA
1 AA-AAAGAA
26593 GAAGGAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 9 0.25
11 13 0.36
12 14 0.39
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:26563 original size:4 final size:4
Alignment explanation
Indices: 26550--26592 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
26540 AAAAATAAAG
* *
26550 GAAA -AAA GAAA GAAA AAAGA GAAA AAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
26593 GAAGGAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:26565 original size:21 final size:21
Alignment explanation
Indices: 26551--26591 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
26541 AAAATAAAGG
26551 AAAAAAGAAAGAAAAAAGAGA
1 AAAAAAGAAAGAAAAAAGAGA
26572 AAAAAAGAAAGAAAGAAAGA
1 AAAAAAGAAAGAAA-AAAGA
26592 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAGAAAAAAGAGA
Done.