Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009258.1 Kokia drynarioides strain JFW-HI SEQ_123963, 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: 16751
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6907 original size:59 final size:59
Alignment explanation
Indices: 6792--7402 Score: 827
Period size: 59 Copynumber: 10.4 Consensus size: 59
6782 GCACATGGGC
* * *
6792 AAAATGGTAA-TTTTAAAAGGTTC-GGGTCAAAAACGGGATTTTTGG-AGATTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTTGGGGGT
* * *
6849 AAAATGGTAATTTTTAAAAGGTTCGGGG-CTAAAAATGGGATTTTTTGAAGTTTAGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTC-AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * *
6908 AAATTGGTAATTTTTAGAAGGTTTGGGGTCAAACATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * * *
6967 AAATTGGTGATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
7026 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * * *
7084 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGAATTTTTAGATGTTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* * *
7143 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* * *
7202 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTTGGAAATTCGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGA-TTTTTGGAAGTTTGGGGGT
* * *
7262 AAAATGGTAATTTTAAGAAGGTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * * * *
7321 AAAATGTTAATTTTTAGAAGGTTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
7380 AAAATGGTAATTTTTAGAAGGTT
1 AAAATGGTAATTTTTAGAAGGTT
7403 TAGGGACCTT
Statistics
Matches: 499, Mismatches: 48, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
57 10 0.02
58 66 0.13
59 368 0.74
60 55 0.11
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
Found at i:7407 original size:29 final size:29
Alignment explanation
Indices: 6844--7403 Score: 382
Period size: 29 Copynumber: 19.0 Consensus size: 29
6834 TGGAGATTCG
* *
6844 GGGGTAAAATGGTAATTTTTAAAAGGTTC
1 GGGGTAAAATGGTAATTTTTAGAAGGTTT
* *
6873 GGGGCTAAAAATGG-GATTTTTTGAA-GTTT
1 GGGG-T-AAAATGGTAATTTTTAGAAGGTTT
*
6902 AGGGGTAAATTGGTAATTTTTAGAAGGTTT
1 -GGGGTAAAATGGTAATTTTTAGAAGGTTT
* * *
6932 GGGGTCAAACATGG-GATTTTTGGAA-GTTCG
1 GGGGT-AAA-ATGGTAATTTTTAGAAGGTT-T
* * *
6962 GGGGTAAATTGGTGATTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTAGAAGGTTT
* * * *
6991 GAGGTCAAAAATGG-GATTTTTGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTAGAAGGTTT
* *
7020 GAGGGTAAAATGGTGATTTTTAGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTAGAAGGTTT
* * *
7050 GGGGTCAAAAATGG-GATTTTTGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTAGAAGGTTT
* *
7079 GGGGTAAAATGGTGATTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTAGAAGGTTT
* *
7108 GGGGTCAAAAATGG-AATTTTTAG-ATGTTCG
1 GGGGT--AAAATGGTAATTTTTAGAAGGTT-T
* *
7138 GGGGTAAAATGGTGATTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTAGAAGGTTT
*
7167 GGGGTCAAAAATGG-AATTTTTGGAA-GTTT
1 GGGGT--AAAATGGTAATTTTTAGAAGGTTT
*
7196 GAGGGTAAAATGGTAATTTTTAGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTAGAAGGTTT
* * * *
7226 GGGGTCAAAAATGAG-ATTTTTTGGAA-ATTCG
1 GGGGT--AAAATG-GTAATTTTTAGAAGGTT-T
* *
7257 GGGGTAAAATGGTAATTTTAAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTAGAAGGTTT
* *
7286 GAGGTCAAAAATGG-AATTTTTGGAA-GTTT
1 GGGGT--AAAATGGTAATTTTTAGAAGGTTT
* *
7315 GGGGGTAAAATGTTAATTTTTAGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTAGAAGGTTT
* * *
7345 GAGGTTAAAAATGG-AATTTTTGGAA-GTTC
1 G-GGGT-AAAATGGTAATTTTTAGAAGGTTT
7374 GAGGGTAAAATGGTAATTTTTAGAAGGTTT
1 G-GGGTAAAATGGTAATTTTTAGAAGGTTT
7404 AGGGACCTTC
Statistics
Matches: 432, Mismatches: 55, Indels: 87
0.75 0.10 0.15
Matches are distributed among these distances:
27 7 0.02
28 54 0.12
29 165 0.38
30 135 0.31
31 70 0.16
32 1 0.00
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTAGAAGGTTT
Found at i:9742 original size:27 final size:28
Alignment explanation
Indices: 9702--9784 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 28
9692 CATTTAATTA
*
9702 ATTTTTAAAATTTTAAAAT-ATTTTTAT-
1 ATTTTT-AAATTTTAAAATAATTTTAATG
* **
9729 ATTTTTATACTTTTTGAATAATTTTAATG
1 ATTTTTA-AATTTTAAAATAATTTTAATG
*
9758 ATTTTTAATTTTTAAAAATAACTTTTA
1 ATTTTTAAATTTT-AAAATAA-TTTTA
9785 TAATATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.02
27 14 0.32
28 12 0.27
29 12 0.27
30 5 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTAAATTTTAAAATAATTTTAATG
Found at i:9971 original size:27 final size:27
Alignment explanation
Indices: 9918--9972 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9908 AGATGATTTG
* **
9918 AAATAAAATATAAATTTAAAATCTAAA
1 AAATAAAAAATAAATAAAAAATCTAAA
9945 AAATAAAAAATTAAATAAAAAAT-TAAA
1 AAATAAAAAA-TAAATAAAAAATCTAAA
9972 A
1 A
9973 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (27 bp):
AAATAAAAAATAAATAAAAAATCTAAA
Found at i:9973 original size:13 final size:13
Alignment explanation
Indices: 9944--9975 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
9934 TAAAATCTAA
9944 AAAATAAAAAATT
1 AAAATAAAAAATT
9957 -AAATAAAAAATT
1 AAAATAAAAAATT
9969 AAAATAA
1 AAAATAA
9976 TTTTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:11082 original size:2 final size:2
Alignment explanation
Indices: 11075--11104 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11065 ATAGTATAAA
11075 AT 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 AT
11105 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11665 original size:20 final size:21
Alignment explanation
Indices: 11642--11680 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11632 TATATAATGT
11642 ATTTT-AT-TATTATATTTAAA
1 ATTTTAATATATTA-ATTTAAA
11662 ATTTTAATATATTAATTTA
1 ATTTTAATATATTAATTTA
11681 TATATACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTAATATATTAATTTAAA
Found at i:13790 original size:20 final size:21
Alignment explanation
Indices: 13752--13791 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13742 ATTATATTAC
13752 TGTTTTGGTGCTCTTTTTTAT
1 TGTTTTGGTGCTCTTTTTTAT
*
13773 TGTTTTGGTGCTTTTTTTT
1 TGTTTTGGTGCTCTTTTTT
13792 TTGCTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.07, G:0.20, T:0.70
Consensus pattern (21 bp):
TGTTTTGGTGCTCTTTTTTAT
Found at i:13800 original size:44 final size:44
Alignment explanation
Indices: 13751--13835 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
13741 AATTATATTA
* * *
13751 CTGTTTTGGTGCT-CTTTTTTATTGTTTTGGTGCTTTTTTTTTTG
1 CTGTTTTGGTACTACTTTTTTACTATTTTGGTG-TTTTTTTTTTG
* *
13795 CTGTTTTGGTATTATTTTTTTACTATTTTGGTGTTTTTTTT
1 CTGTTTTGGTACTACTTTTTTACTATTTTGGTGTTTTTTTT
13836 ACTGTTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 19 0.54
45 16 0.46
ACGTcount: A:0.06, C:0.07, G:0.18, T:0.69
Consensus pattern (44 bp):
CTGTTTTGGTACTACTTTTTTACTATTTTGGTGTTTTTTTTTTG
Found at i:13812 original size:22 final size:21
Alignment explanation
Indices: 13748--13842 Score: 84
Period size: 22 Copynumber: 4.4 Consensus size: 21
13738 AAAAATTATA
** *
13748 TTACTGTTTTGGTGCTCTTTT
1 TTACTGTTTTGGTATTTTTTT
* *
13769 TTATTGTTTTGGTGCTTTTTTTT
1 TTACTGTTTTGGT--ATTTTTTT
*
13792 TTGCTGTTTTGGTATTATTTTT
1 TTACTGTTTTGGTATT-TTTTT
* *
13814 TTACTATTTTGGT-GTTTTTT
1 TTACTGTTTTGGTATTTTTTT
13834 TTACTGTTT
1 TTACTGTTT
13843 CAAAGTTGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.22
21 15 0.25
22 16 0.27
23 16 0.27
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.68
Consensus pattern (21 bp):
TTACTGTTTTGGTATTTTTTT
Found at i:13875 original size:15 final size:15
Alignment explanation
Indices: 13848--13888 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
13838 TGTTTCAAAG
13848 TTGTTATTT-TTGTTA
1 TTGTT-TTTGTTGTTA
13863 TTGTTTTTGTTGTTA
1 TTGTTTTTGTTGTTA
13878 TT-TTTATTGTT
1 TTGTTT-TTGTT
13889 TTGCTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.10, C:0.00, G:0.15, T:0.76
Consensus pattern (15 bp):
TTGTTTTTGTTGTTA
Found at i:13881 original size:12 final size:12
Alignment explanation
Indices: 13847--13925 Score: 60
Period size: 12 Copynumber: 6.9 Consensus size: 12
13837 CTGTTTCAAA
13847 GTTGTTATTTTT
1 GTTGTTATTTTT
* *
13859 GTTATTGTTTTT
1 GTTGTTATTTTT
13871 GTTGTTATTTTT
1 GTTGTTATTTTT
*
13883 ATTG----TTTT
1 GTTGTTATTTTT
*
13891 GCTGTTATTTTT
1 GTTGTTATTTTT
* *
13903 GTTGCT-GTTTT
1 GTTGTTATTTTT
13914 GATTGTTATTTT
1 G-TTGTTATTTT
13926 GATGGTTTGG
Statistics
Matches: 49, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
8 6 0.12
11 5 0.10
12 35 0.71
13 3 0.06
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.71
Consensus pattern (12 bp):
GTTGTTATTTTT
Found at i:13896 original size:20 final size:20
Alignment explanation
Indices: 13860--13948 Score: 79
Period size: 20 Copynumber: 4.2 Consensus size: 20
13850 GTTATTTTTG
13860 TTATTGTTTTTGTTGTTATTT
1 TTATTG-TTTTGTTGTTATTT
*
13881 TTATTGTTTTGCTGTTATTT
1 TTATTGTTTTGTTGTTATTT
*
13901 TTGTTGCTGTTTTGATTGTTATTT
1 TT-AT--TGTTTTG-TTGTTATTT
* * * *
13925 TGATGGTTTGGATGTTATTT
1 TTATTGTTTTGTTGTTATTT
13945 TTAT
1 TTAT
13949 GCGTTTTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
20 26 0.47
21 12 0.22
23 8 0.15
24 9 0.16
ACGTcount: A:0.11, C:0.02, G:0.19, T:0.67
Consensus pattern (20 bp):
TTATTGTTTTGTTGTTATTT
Found at i:13899 original size:44 final size:44
Alignment explanation
Indices: 13849--13946 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
13839 GTTTCAAAGT
* * * * *
13849 TGTTATTTTTGTTATTGTTTTTG-TTGTTATTTTTATTGTTTTGC
1 TGTTATTTTTGTTACTG-TTTTGATTGTTATTTTGATGGTTTGGA
*
13893 TGTTATTTTTGTTGCTGTTTTGATTGTTATTTTGATGGTTTGGA
1 TGTTATTTTTGTTACTGTTTTGATTGTTATTTTGATGGTTTGGA
13937 TGTTATTTTT
1 TGTTATTTTT
13947 ATGCGTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 5 0.11
44 42 0.89
ACGTcount: A:0.10, C:0.02, G:0.19, T:0.68
Consensus pattern (44 bp):
TGTTATTTTTGTTACTGTTTTGATTGTTATTTTGATGGTTTGGA
Found at i:16739 original size:26 final size:26
Alignment explanation
Indices: 16680--16739 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
16670 CTAATGTCTA
*
16680 ATTTTTTAAAAACACTTGTCAAAATC
1 ATTTTTTAAAAACACTTGTCAAAAGC
* * *
16706 ATTTTTTAACAACACTTTTTAAAAGC
1 ATTTTTTAAAAACACTTGTCAAAAGC
16732 -TTTGTTTA
1 ATTT-TTTA
16740 GCAATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (26 bp):
ATTTTTTAAAAACACTTGTCAAAAGC
Done.