Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007533.1 Kokia drynarioides strain JFW-HI SEQ_122158, 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: 10888
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1962 original size:44 final size:46
Alignment explanation
Indices: 1910--1995 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
1900 AAATCCATCT
*
1910 ATAACCATTATTGA-G-GAGATAGAACATGAAATGAAAATTAAAAC
1 ATAACCATTATTGAGGAGAGAGAGAACATGAAATGAAAATTAAAAC
*
1954 ATAACCATTATTGAGGAGAGAGAGAACATGAGATGAAAATTA
1 ATAACCATTATTGAGGAGAGAGAGAACATGAAATGAAAATTA
1996 GAAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 14 0.37
45 1 0.03
46 23 0.61
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (46 bp):
ATAACCATTATTGAGGAGAGAGAGAACATGAAATGAAAATTAAAAC
Found at i:2813 original size:16 final size:16
Alignment explanation
Indices: 2789--2838 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2779 AATTTTACCA
*
2789 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
**
2805 TTATAAATTTTAAAAGA
1 TTATAAA-TTTAAAATT
2822 TT-TAAA-TTAAAATT
1 TTATAAATTTAAAATT
2836 TTA
1 TTA
2839 CCATTTTAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 8 0.30
16 10 0.37
17 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:7393 original size:27 final size:28
Alignment explanation
Indices: 7333--7402 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
7323 TAAAGCTACC
**
7333 AAAAAAATATAAAAAATATTAAATTTTA
1 AAAAAAATATAAAAAATATTAAATAGTA
*
7361 ATAAAAATATAAAAAA-ATTAAA-AGTA
1 AAAAAAATATAAAAAATATTAAATAGTA
7387 GAAAAAAATTATAAAA
1 -AAAAAAA-TATAAAA
7403 TGCATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.06
27 12 0.33
28 22 0.61
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (28 bp):
AAAAAAATATAAAAAATATTAAATAGTA
Found at i:7629 original size:10 final size:10
Alignment explanation
Indices: 7610--7640 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
7600 TTTTCATGAA
7610 TTTTAT-ATT
1 TTTTATAATT
7619 TTTTATAATT
1 TTTTATAATT
7629 TTTTATAATT
1 TTTTATAATT
7639 TT
1 TT
7641 CTTACGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATAATT
Found at i:7632 original size:19 final size:19
Alignment explanation
Indices: 7610--7686 Score: 54
Period size: 19 Copynumber: 4.1 Consensus size: 19
7600 TTTTCATGAA
7610 TTTTAT-ATTTTTTATAATT
1 TTTTATAATTTTTTAT-ATT
*
7629 TTTTATAATTTTCTTACGA--
1 TTTTATAATTTT-TTA-TATT
* **
7648 CTTTATAAAATTTTATATT
1 TTTTATAATTTTTTATATT
7667 TTTTATATATTTTTTA-ATT
1 TTTTATA-ATTTTTTATATT
7686 T
1 T
7687 AAAATATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 25 0.57
20 11 0.25
21 4 0.09
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTATATT
Found at i:7706 original size:30 final size:29
Alignment explanation
Indices: 7662--7736 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
7652 ATAAAATTTT
7662 ATATTTTTTATATATTTTTT-AATTTAAA
1 ATATTTTTTATATATTTTTTAAATTTAAA
7690 ATATTTTCTATATATATTTTTTAAATTT--A
1 ATATTTT-T-TATATATTTTTTAAATTTAAA
*
7719 ATAGTTTTTATA-ATTTTT
1 ATATTTTTTATATATTTTT
7737 ATTGATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 6 0.14
27 4 0.09
28 8 0.19
29 8 0.19
30 12 0.28
31 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (29 bp):
ATATTTTTTATATATTTTTTAAATTTAAA
Found at i:7735 original size:9 final size:9
Alignment explanation
Indices: 7589--7748 Score: 60
Period size: 9 Copynumber: 16.9 Consensus size: 9
7579 TAGTGCAATG
*
7589 ATTTTAATA
1 ATTTTTATA
7598 ATTTTTCATGA
1 ATTTTT-AT-A
7609 A-TTTTATA
1 ATTTTTATA
*
7617 TTTTTTATA
1 ATTTTTATA
7626 ATTTTTTATA
1 A-TTTTTATA
7636 ATTTTCT-TA
1 ATTTT-TATA
*
7645 CGA-CTTTATAA
1 --ATTTTTAT-A
*
7656 AATTTTATA
1 ATTTTTATA
*
7665 TTTTTTATA
1 ATTTTTATA
7674 TATTTTT-TA
1 -ATTTTTATA
* *
7683 A-TTTAAAA
1 ATTTTTATA
7691 TATTTTCTATA
1 -ATTTT-TATA
*
7702 TATATTTTTTA
1 -AT-TTTTATA
* *
7713 AATTTAATA
1 ATTTTTATA
*
7722 GTTTTTATA
1 ATTTTTATA
*
7731 ATTTTTATTG
1 ATTTTTA-TA
7741 ATTTTTAT
1 ATTTTTAT
7749 TTTTATCATT
Statistics
Matches: 113, Mismatches: 21, Indels: 34
0.67 0.12 0.20
Matches are distributed among these distances:
7 3 0.03
8 3 0.03
9 51 0.45
10 41 0.36
11 12 0.11
12 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:8522 original size:70 final size:67
Alignment explanation
Indices: 8429--8561 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
8419 TTCGAATAAA
* * *
8429 AAAAGGCAAAACTATGTCGTTTTGATAAATATTTACCCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTATGTCATTTTGATAAATATTTACCC-AT-T-AAGTTAAAAGGCAAAACCATT
8494 AAATT
63 AAATT
* * *
8499 AAAAGGTAAAATTATGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGCAAAACTATGTCATTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTA
8562 TATTGTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 21 0.37
68 1 0.02
69 1 0.02
70 34 0.60
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (67 bp):
AAAAGGCAAAACTATGTCATTTTGATAAATATTTACCCATTAAGTTAAAAGGCAAAACCATTAAA
TT
Done.