Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001974.1 Kokia drynarioides strain JFW-HI SEQ_113819, 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: 11160
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:1009 original size:17 final size:17
Alignment explanation
Indices: 987--1065 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
977 GGACATTCAA
*
987 AATAAAATTAAATTTAT
1 AATAAATTTAAATTTAT
1004 AATAAATTTAAATTTCA-
1 AATAAATTTAAATTT-AT
**
1021 GCTAAATTTAAATTTAT
1 AATAAATTTAAATTTAT
* * * *
1038 AATAAACTCAATTTTAA
1 AATAAATTTAAATTTAT
1055 AATAAATTTAA
1 AATAAATTTAA
1066 GTTAATTGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
16 1 0.02
17 47 0.96
18 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (17 bp):
AATAAATTTAAATTTAT
Found at i:1061 original size:34 final size:34
Alignment explanation
Indices: 985--1065 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
975 TTGGACATTC
* * *
985 AAAATAAAATTAAATTTATAATAAATTTAAATTT
1 AAAATAAATTTAAATTTATAATAAACTCAAATTT
* ** *
1019 CAGCTAAATTTAAATTTATAATAAACTCAATTTT
1 AAAATAAATTTAAATTTATAATAAACTCAAATTT
1053 AAAATAAATTTAA
1 AAAATAAATTTAA
1066 GTTAATTGGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (34 bp):
AAAATAAATTTAAATTTATAATAAACTCAAATTT
Found at i:1939 original size:195 final size:194
Alignment explanation
Indices: 1597--1989 Score: 759
Period size: 195 Copynumber: 2.0 Consensus size: 194
1587 TCCTCCAAGC
*
1597 ACAATTTTAAAGTCCCATATTTGATATGGCTGATAAAATTTTTCTTTTTCAGCAATACCAATTAG
1 ACAATTTTAAAGTCCCATATTTGATATGGCTGATAAAATTCTTCTTTTTCAGCAATACCAATTAG
1662 GCTGTGAATTTGATATGAAAATACTTTATATAATCTTGATCTTTAGTCTACTTGATTAGCATTGT
66 GCTGTGAATTTGATATGAAAATACTTTATATAATCTTGATCTTTAGTCTACTTGATTAGCATTGT
1727 TTTTATAAAAGCTGGAAAATCTTTTGTTAGATGGAAAGAAAGATTTTGTACTGTAAGTTCTTTT
131 TTTTATAAAAGCTGGAAAATCTTTTGTTAGATGGAAAGAAAGATTTTGTACTGTAAGTTCTTTT
1791 ACAATTTTAAAGTCCCATATTTGATATGGCTGATAAAATTCTTCTTTTTCAGCAATACCAATTAG
1 ACAATTTTAAAGTCCCATATTTGATATGGCTGATAAAATTCTTCTTTTTCAGCAATACCAATTAG
*
1856 GCTGTGAATATTGATATGAAAATACTTTATATAATCTTGATCTTTAGTCTGCTTGATTAGCATTG
66 GCTGTGAAT-TTGATATGAAAATACTTTATATAATCTTGATCTTTAGTCTACTTGATTAGCATTG
1921 TTTTTATAAAAGCTGGAAAATCTTTTGTTAGATGGAAAGAAAGATTTTGTACTGTAAGTTCTTTT
130 TTTTTATAAAAGCTGGAAAATCTTTTGTTAGATGGAAAGAAAGATTTTGTACTGTAAGTTCTTTT
1986 ACAA
1 ACAA
1990 AACCCCATTC
Statistics
Matches: 196, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
194 73 0.37
195 123 0.63
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (194 bp):
ACAATTTTAAAGTCCCATATTTGATATGGCTGATAAAATTCTTCTTTTTCAGCAATACCAATTAG
GCTGTGAATTTGATATGAAAATACTTTATATAATCTTGATCTTTAGTCTACTTGATTAGCATTGT
TTTTATAAAAGCTGGAAAATCTTTTGTTAGATGGAAAGAAAGATTTTGTACTGTAAGTTCTTTT
Found at i:5399 original size:11 final size:11
Alignment explanation
Indices: 5383--5412 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5373 TATAAATACC
5383 CCTCATTTCTA
1 CCTCATTTCTA
5394 CCTCATTTCTA
1 CCTCATTTCTA
5405 CCTCATTT
1 CCTCATTT
5413 TGATCAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.47
Consensus pattern (11 bp):
CCTCATTTCTA
Done.