Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013394.1 Kokia drynarioides strain JFW-HI SEQ_128418, 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: 41777
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:881 original size:19 final size:18
Alignment explanation
Indices: 859--907 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
849 TTACATGGAA
*
859 AAATAAATAAAATTCAAAT
1 AAATAAATAAAA-TAAAAT
878 AAATAAAATAAAATAAAAT
1 AAAT-AAATAAAATAAAAT
*
897 AAATAACTAAA
1 AAATAAATAAA
908 CCTACACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 6 0.22
19 13 0.48
20 8 0.30
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAATAAAAT
Found at i:902 original size:4 final size:5
Alignment explanation
Indices: 858--899 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
848 ATTACATGGA
*
858 AAAAT -AAAT AAAATT CAAAT -AAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA
900 TAACTAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 8 0.24
5 21 0.64
6 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:12427 original size:40 final size:40
Alignment explanation
Indices: 12331--12428 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
12321 ATAATATTTG
* *
12331 AATAAATTATATATTTTTTTATAAGTTTTTATACATTTAA
1 AATAATTTATATATTTTTTTATAAGTTTTAATACATTTAA
* *
12371 AAT-TTTCTATATATTTTTTTATAA-TTTGTAATA-ATTTTAT
1 AATAATT-TATATATTTTTTTATAAGTTT-TAATACA-TTTAA
*
12411 AATAATTTATAAATTTTT
1 AATAATTTATATATTTTT
12429 CATTTTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
39 5 0.10
40 41 0.85
41 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (40 bp):
AATAATTTATATATTTTTTTATAAGTTTTAATACATTTAA
Found at i:28921 original size:7 final size:7
Alignment explanation
Indices: 28911--28938 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28901 AAATTTAGTC
28911 TTTATTT
1 TTTATTT
28918 TTTATTT
1 TTTATTT
28925 TTTATTT
1 TTTATTT
28932 TTTATTT
1 TTTATTT
28939 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:29370 original size:13 final size:13
Alignment explanation
Indices: 29346--29383 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
29336 TTACTATAAA
29346 TTAATT-TTTAAT
1 TTAATTATTTAAT
29358 TTAATTATTTAAT
1 TTAATTATTTAAT
29371 TTAATTATTTAAT
1 TTAATTATTTAAT
29384 AGAGATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTAATTATTTAAT
Found at i:29697 original size:21 final size:21
Alignment explanation
Indices: 29646--29700 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
29636 ATAACGATTA
29646 AATAATTA-TAGAAAAATGTAT
1 AATAATTATTA-AAAAATGTAT
* *
29667 AAAAAATATTAAAAAAT-TAT
1 AATAATTATTAAAAAATGTAT
29687 AAGTAATTATTAAA
1 AA-TAATTATTAAA
29701 TTTTAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.18
21 21 0.75
22 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AATAATTATTAAAAAATGTAT
Found at i:29828 original size:17 final size:18
Alignment explanation
Indices: 29806--29839 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29796 AAACTATAAT
29806 AAATC-ATTAAAAATATC
1 AAATCAATTAAAAATATC
*
29823 AAATCAATTAAGAATAT
1 AAATCAATTAAAAATAT
29840 ATATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATCAATTAAAAATATC
Found at i:29913 original size:10 final size:10
Alignment explanation
Indices: 29879--29913 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
29869 CCCATAATGC
29879 TTAATATTTT
1 TTAATATTTT
*
29889 TTTATGATTTT
1 TTAAT-ATTTT
29900 TTAATATTTT
1 TTAATATTTT
29910 TTAA
1 TTAA
29914 GAAATTACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (10 bp):
TTAATATTTT
Done.