Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014675.1 Kokia drynarioides strain JFW-HI SEQ_129714, 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: 13888
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:325 original size:14 final size:14
Alignment explanation
Indices: 302--387 Score: 61
Period size: 14 Copynumber: 6.0 Consensus size: 14
292 ATATAAATTG
302 TATA-TTTTATACA
1 TATATTTTTATACA
315 TATATTTTTATACA
1 TATATTTTTATACA
*
329 TATATACTGTTAT--A
1 TATAT--TTTTATACA
* *
343 TATATATATATACA
1 TATATTTTTATACA
* *
357 TATCAATTTTAAATCCA
1 TAT--ATTTT-TATACA
374 TATATTTTTATACA
1 TATATTTTTATACA
388 AATAATATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
12 3 0.05
13 4 0.07
14 28 0.51
15 5 0.09
16 8 0.15
17 7 0.13
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (14 bp):
TATATTTTTATACA
Found at i:5008 original size:18 final size:19
Alignment explanation
Indices: 4967--5022 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
4957 TATATTGTTA
*
4967 TTTTTTTT-GTTTTTGGTG
1 TTTTTTTTCTTTTTTGGTG
4985 TGTTTTTTTCTTTTTTGGT-
1 T-TTTTTTTCTTTTTTGGTG
* *
5004 TTTTTTTACTGTTTTGGTG
1 TTTTTTTTCTTTTTTGGTG
5023 CTGCTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 16 0.50
19 8 0.25
20 8 0.25
ACGTcount: A:0.02, C:0.04, G:0.20, T:0.75
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTGGTG
Found at i:5010 original size:20 final size:19
Alignment explanation
Indices: 4967--5010 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
4957 TATATTGTTA
4967 TTTTTTTTGTTTTTGGTGT
1 TTTTTTTTGTTTTTGGTGT
4986 GTTTTTTTCT-TTTTTGGT-T
1 -TTTTTTT-TGTTTTTGGTGT
5005 TTTTTT
1 TTTTTT
5011 ACTGTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 1 0.04
20 15 0.65
21 1 0.04
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (19 bp):
TTTTTTTTGTTTTTGGTGT
Found at i:9744 original size:33 final size:33
Alignment explanation
Indices: 9705--9770 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
9695 GTTGCACGAG
*
9705 CTGCATTTAC-TAGAACTGCAATCGCATAAACTA
1 CTGCATTTACAT-GAACTGCAATCACATAAACTA
* *
9738 CTGCATTTACATGAACTGTAGTCACATAAACTA
1 CTGCATTTACATGAACTGCAATCACATAAACTA
9771 TACATCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (33 bp):
CTGCATTTACATGAACTGCAATCACATAAACTA
Found at i:9756 original size:63 final size:63
Alignment explanation
Indices: 9619--9759 Score: 174
Period size: 63 Copynumber: 2.2 Consensus size: 63
9609 CAGTAGTTTA
* * * * * * ** *
9619 TACATGAACTGCAGTTGCATGAGCTATATTTACAAGAACTGTAGTCACATAAATTGTTTCATT
1 TACATGAACTGTAGTTGCACGAGCTACATTTACAAGAACTGCAATCACATAAACTACTGCATT
* * *
9682 TACATGAACTGTAGTTGCACGAGCTGCATTTACTAGAACTGCAATCGCATAAACTACTGCATT
1 TACATGAACTGTAGTTGCACGAGCTACATTTACAAGAACTGCAATCACATAAACTACTGCATT
9745 TACATGAACTGTAGT
1 TACATGAACTGTAGT
9760 CACATAAACT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (63 bp):
TACATGAACTGTAGTTGCACGAGCTACATTTACAAGAACTGCAATCACATAAACTACTGCATT
Done.