Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007031.1 Kokia drynarioides strain JFW-HI SEQ_121639, 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: 35776
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:2201 original size:19 final size:19
Alignment explanation
Indices: 2177--2220 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2167 ATAGCATATG
*
2177 TCACAACATCT-CATGTTTT
1 TCACAACAT-TACATATTTT
*
2196 TCACAATATTACATATTTT
1 TCACAACATTACATATTTT
2215 TCACAA
1 TCACAA
2221 TCATATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (19 bp):
TCACAACATTACATATTTT
Found at i:21446 original size:70 final size:67
Alignment explanation
Indices: 21350--21482 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
21340 TCCGAATAAA
* ** *
21350 AAAAGGCAAAACTACGTCGTTTTGATAAATGTTTACTCTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTAC-CCAT-T-AAGTTAAAAGGCAAAACCATT
21415 AAGTT
63 AAGTT
* * *
21420 AAAAGGTAAAATTATGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
21483 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 2 0.04
70 32 0.57
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (67 bp):
AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:26785 original size:31 final size:31
Alignment explanation
Indices: 26747--26814 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
26737 ATTTCAATAT
26747 TTTAAATTTTAAATA-A-TTAAATAATTTTTAA
1 TTTAAATTTTAAATATAGTTAAAT--TTTTTAA
*
26778 TTTAAATTTTAAATATAGTTTAATTTTTTAA
1 TTTAAATTTTAAATATAGTTAAATTTTTTAA
26809 TTTAAA
1 TTTAAA
26815 AAATAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 28 0.82
32 1 0.03
33 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTAAATTTTAAATATAGTTAAATTTTTTAA
Found at i:30687 original size:33 final size:32
Alignment explanation
Indices: 30649--30716 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
30639 ATTTTTATTA
30649 TATTTTATTAT-ACATTTTTTTTTTGTAATTTTC
1 TATTTTATTATGA-A-TTTTTTTTTGTAATTTTC
* *
30682 TATTTTTTTTTGAATTTTTTTTTGTAATTTTC
1 TATTTTATTATGAATTTTTTTTTGTAATTTTC
30714 TAT
1 TAT
30717 AATTTTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 21 0.66
33 10 0.31
34 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (32 bp):
TATTTTATTATGAATTTTTTTTTGTAATTTTC
Found at i:30705 original size:32 final size:32
Alignment explanation
Indices: 30664--30725 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
30654 TATTATACAT
**
30664 TTTTTTTTTGTAATTTTCTATTTTTTTTTGAA
1 TTTTTTTTTGTAATTTTCTATAATTTTTTGAA
30696 TTTTTTTTTGTAATTTTCTATAATTTTTTG
1 TTTTTTTTTGTAATTTTCTATAATTTTTTG
30726 GTTAATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.74
Consensus pattern (32 bp):
TTTTTTTTTGTAATTTTCTATAATTTTTTGAA
Found at i:30710 original size:13 final size:12
Alignment explanation
Indices: 30683--30712 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
30673 GTAATTTTCT
30683 ATTTTTTTTTGA
1 ATTTTTTTTTGA
30695 ATTTTTTTTTGTA
1 ATTTTTTTTTG-A
30708 ATTTT
1 ATTTT
30713 CTATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:31226 original size:18 final size:17
Alignment explanation
Indices: 31196--31230 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31186 ATTTGTATAA
*
31196 ATTTTTTTGTAAATTTT
1 ATTTTTTTATAAATTTT
31213 ATTTATTTTATAAATTTT
1 ATTT-TTTTATAAATTTT
31231 CAAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTTTTTATAAATTTT
Found at i:35411 original size:25 final size:26
Alignment explanation
Indices: 35383--35431 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
35373 ATATTTTACA
*
35383 AAACCCAAAAA-TAAAAAAAAACCCT
1 AAACCAAAAAATTAAAAAAAAACCCT
* *
35408 AAACTAAAAAATTGAAAAAAAACC
1 AAACCAAAAAATTAAAAAAAAACC
35432 TAATAATTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.69, C:0.18, G:0.02, T:0.10
Consensus pattern (26 bp):
AAACCAAAAAATTAAAAAAAAACCCT
Found at i:35416 original size:17 final size:18
Alignment explanation
Indices: 35382--35418 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35372 AATATTTTAC
35382 AAAACCCAAAAATAAAAA
1 AAAACCCAAAAATAAAAA
* *
35400 AAAACCCTAAACTAAAAA
1 AAAACCCAAAAATAAAAA
35418 A
1 A
35419 TTGAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.19, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAACCCAAAAATAAAAA
Done.