Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012750.1 Kokia drynarioides strain JFW-HI SEQ_127761, 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: 46914
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:2284 original size:2 final size:2
Alignment explanation
Indices: 2277--2316 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2267 TTTTATGTTT
* * *
2277 TA TA TA TA TA TA TA TG TA TA TA TG TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2317 ATTTTTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3282 original size:21 final size:21
Alignment explanation
Indices: 3242--3299 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
3232 CTTATTTATA
* **
3242 TTTTAATTAATCATGTTTTAC
1 TTTTAATTAATCTTAATTTAC
3263 TTTTAATTAATCTTAATTTAC
1 TTTTAATTAATCTTAATTTAC
*
3284 --TTAATTAAGCTTAATT
1 TTTTAATTAATCTTAATT
3300 GTTAATTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTAATTAATCTTAATTTAC
Found at i:4791 original size:3 final size:3
Alignment explanation
Indices: 4783--4833 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
4773 GTCTAGACTT
4783 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4830 ATA A
1 ATA A
4834 CCTCTACTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4808 original size:23 final size:23
Alignment explanation
Indices: 4782--4829 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
4772 TGTCTAGACT
4782 TATAATAATAATAATAATAATAA
1 TATAATAATAATAATAATAATAA
4805 TATAATAATAATAATAATAATAA
1 TATAATAATAATAATAATAATAA
4828 TA
1 TA
4830 ATAACCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TATAATAATAATAATAATAATAA
Found at i:6868 original size:23 final size:23
Alignment explanation
Indices: 6819--6887 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
6809 ATTCAGTAGA
6819 CACACACAGTGCTGAACAG-AAG
1 CACACACAGTGCTGAACAGTAAG
6841 CACACACAGTGCTGAACAGTAAG
1 CACACACAGTGCTGAACAGTAAG
* *
6864 CACACACAGTGCTAAACAATAAG
1 CACACACAGTGCTGAACAGTAAG
6887 C
1 C
6888 GCGCTAATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.42, C:0.28, G:0.19, T:0.12
Consensus pattern (23 bp):
CACACACAGTGCTGAACAGTAAG
Found at i:10627 original size:15 final size:15
Alignment explanation
Indices: 10607--10641 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10597 AATCAATATT
10607 TTTTTACAAAATTTA
1 TTTTTACAAAATTTA
* *
10622 TTTTTATAATATTTA
1 TTTTTACAAAATTTA
10637 TTTTT
1 TTTTT
10642 CTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTACAAAATTTA
Found at i:10646 original size:19 final size:20
Alignment explanation
Indices: 10624--10661 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
10614 AAAATTTATT
*
10624 TTTATAATATTTA-TTTTTC
1 TTTAAAATATTTAGTTTTTC
*
10643 TTTAAAATTTTTAGTTTTT
1 TTTAAAATATTTAGTTTTT
10662 AAATTATGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTAAAATATTTAGTTTTTC
Found at i:11205 original size:42 final size:42
Alignment explanation
Indices: 11158--11242 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
11148 AATTTGTCAC
11158 TTGCGGTGTGTTTTGAAAAGGGTTATTATAAAATTCTGTCCT
1 TTGCGGTGTGTTTTGAAAAGGGTTATTATAAAATTCTGTCCT
11200 TTGCGGTGTGTTTTGAAAAGGGTTATTATAAAATTCTGTCCT
1 TTGCGGTGTGTTTTGAAAAGGGTTATTATAAAATTCTGTCCT
11242 T
1 T
11243 AAACTTATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (42 bp):
TTGCGGTGTGTTTTGAAAAGGGTTATTATAAAATTCTGTCCT
Found at i:12466 original size:15 final size:15
Alignment explanation
Indices: 12448--12481 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12438 ATAAAAACAG
12448 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
**
12463 AAAAAGGAAAAAGAA
1 AAAAAAAAAAAAGAA
12478 AAAA
1 AAAA
12482 CAATGGCGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:12860 original size:3 final size:3
Alignment explanation
Indices: 12852--12881 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12842 CTCATTCCCT
12852 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12882 ATTGCTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:15096 original size:15 final size:17
Alignment explanation
Indices: 15059--15101 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
15049 ATTTCAAAAT
*
15059 TTAAAAATTATATAAAC
1 TTAAAAATAATATAAAC
15076 TTAAAAATAAT-TAAA-
1 TTAAAAATAATATAAAC
15091 TTAAAAA-AATA
1 TTAAAAATAATA
15102 AGGACTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 7 0.29
16 4 0.17
17 10 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAATAATATAAAC
Found at i:20770 original size:4 final size:4
Alignment explanation
Indices: 20745--20780 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
20735 AGAGCATAGG
* *
20745 GAAA GAAT GAAA GAAT GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
20781 TGGGAGAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (4 bp):
GAAA
Found at i:25186 original size:18 final size:18
Alignment explanation
Indices: 25165--25202 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25155 TCTATTTTTT
*
25165 TAATATAAATAACAAAAA
1 TAATAAAAATAACAAAAA
*
25183 TAATAAAAATTACAAAAA
1 TAATAAAAATAACAAAAA
25201 TA
1 TA
25203 GCATAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
TAATAAAAATAACAAAAA
Found at i:29902 original size:36 final size:36
Alignment explanation
Indices: 29854--29952 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
29844 GGTAACAAGA
* *
29854 ATGACCTCTGGGTCAACAGGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAATAGGGAGTAAAATGAGCATC
*
29890 ATGACCTTTGGGTCAATAGAGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAATAGGGAGTAAAATGAGCATC
*
29926 ATGACCTTTGGGTTAATAGGGAGTAAA
1 ATGACCTTTGGGTCAATAGGGAGTAAA
29953 TCAAATATCA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.24
Consensus pattern (36 bp):
ATGACCTTTGGGTCAATAGGGAGTAAAATGAGCATC
Found at i:30733 original size:21 final size:21
Alignment explanation
Indices: 30709--30762 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
30699 AGCTTTACTT
30709 GTATCGGTAGAATTGTCATAG
1 GTATCGGTAGAATTGTCATAG
*
30730 GTATCGATAGAATTGTCATAG
1 GTATCGGTAGAATTGTCATAG
*
30751 GTATCGGAAGAA
1 GTATCGGTAGAA
30763 GTCTGCACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAATTGTCATAG
Found at i:35577 original size:2 final size:2
Alignment explanation
Indices: 35570--35596 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35560 TCTATCCTCC
35570 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35597 TTACATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36570 original size:20 final size:18
Alignment explanation
Indices: 36545--36589 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
36535 TTAATTTAAA
*
36545 TAATATTTTATTTATATTTT
1 TAATATTTT-GTTAT-TTTT
*
36565 TAATATATTGTTATTTTT
1 TAATATTTTGTTATTTTT
36583 TAATATT
1 TAATATT
36590 AATCTCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 4 0.18
20 8 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TAATATTTTGTTATTTTT
Found at i:37777 original size:21 final size:21
Alignment explanation
Indices: 37751--37806 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
37741 ATAATAGCAT
37751 AATCCAAACATAAAGTTTAGA
1 AATCCAAACATAAAGTTTAGA
*
37772 AATCCAAACATAAAGTTTATA
1 AATCCAAACATAAAGTTTAGA
*
37793 AATCCAAAGATAAA
1 AATCCAAACATAAA
37807 ACTTCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.23
Consensus pattern (21 bp):
AATCCAAACATAAAGTTTAGA
Found at i:39671 original size:25 final size:25
Alignment explanation
Indices: 39625--39672 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39615 CTACAATAAT
* *
39625 AATAATAATTTACACTATTAATTAC
1 AATAATAATTTACAATAATAATTAC
* *
39650 AATACTAATTTATAATAATAATT
1 AATAATAATTTACAATAATAATT
39673 GAATTTCTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAATAATTTACAATAATAATTAC
Done.