Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003671.1 Kokia drynarioides strain JFW-HI SEQ_116589, 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: 18137
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:224 original size:6 final size:6
Alignment explanation
Indices: 215--292 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
205 CTTTTTTTAT
* * *
215 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
262 -TTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
293 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.24
6 38 0.66
7 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:235 original size:17 final size:17
Alignment explanation
Indices: 215--324 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 17
205 CTTTTTTTAT
*
215 TTTAAATTTATAATAAT
1 TTTAAATTTATAATAAA
*
232 TTTAAATTTGAAAATAAA
1 TTTAAATTT-ATAATAAA
*
250 TTTAAACTTA-AATTAAA
1 TTTAAATTTATAA-TAAA
**
267 TTTAAATTTATTTTAAA
1 TTTAAATTTATAATAAA
* *
284 TTTAAATTTTTAAACAAA
1 TTTAAATTTAT-AATAAA
* *
302 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTATAATAAA
319 TTTAAA
1 TTTAAA
325 ATGAGTTTGG
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
16 2 0.03
17 48 0.66
18 23 0.32
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTATAATAAA
Found at i:271 original size:11 final size:11
Alignment explanation
Indices: 233--291 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
223 TATAATAATT
233 TTAAATTTGAAA
1 TTAAATTT-AAA
*
245 ATAAATTTAAA
1 TTAAATTTAAA
256 CTTAAA-TTAAA
1 -TTAAATTTAAA
**
267 TTTAAATTTATT
1 -TTAAATTTAAA
279 TTAAATTTAAA
1 TTAAATTTAAA
290 TT
1 TT
292 TTTAAACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 24 0.63
12 14 0.37
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:272 original size:52 final size:52
Alignment explanation
Indices: 215--324 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
205 CTTTTTTTAT
* * * *
215 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTATAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
** ** *
267 TTTAAATTTATTTTAAATTTAAATTTTTAAACAAATTTAATCCTAAAATAAA
1 TTTAAATTTATAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
319 TTTAAA
1 TTTAAA
325 ATGAGTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (52 bp):
TTTAAATTTATAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
Found at i:9645 original size:45 final size:45
Alignment explanation
Indices: 9564--9654 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
9554 ATAGAAATAA
* * *
9564 AGAAATGGAAAACATTCGGAAATGATTATGGTTTTCTTCGAAATGG
1 AGAAATGGAAAACATTCGGAAATGAATATGATTTTC-TCAAAATGG
* * *
9610 AGAAATGG-AATCATTTGGAAATGAATGTGATTTTCTCAAAATGG
1 AGAAATGGAAAACATTCGGAAATGAATATGATTTTCTCAAAATGG
9654 A
1 A
9655 AATGAAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 9 0.23
45 22 0.56
46 8 0.21
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (45 bp):
AGAAATGGAAAACATTCGGAAATGAATATGATTTTCTCAAAATGG
Found at i:12556 original size:11 final size:12
Alignment explanation
Indices: 12533--12561 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
12523 ATTCACTAAA
12533 AAATAATTATCT
1 AAATAATTATCT
12545 AAATAA-TATCT
1 AAATAATTATCT
12556 AAATAA
1 AAATAA
12562 AATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATAATTATCT
Found at i:17529 original size:22 final size:21
Alignment explanation
Indices: 17491--17534 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
17481 TTTTGAGCAA
17491 TTTAATTTTTTCCTTTTATTTT
1 TTTAATTTTTTCCTTTT-TTTT
*
17513 TTTAACTTTTT--TTTTTTTT
1 TTTAATTTTTTCCTTTTTTTT
17532 TTT
1 TTT
17535 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
22 10 0.48
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTAATTTTTTCCTTTTTTTT
Done.