Locus 6704

Sequence ID	2L_DroMel_CAF1
Location	18,732,640 – 18,732,792
Length	152
Max. P	0.998231

overview

Window 3

Location	18,732,640 – 18,732,752
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.49
Mean single sequence MFE	-44.54
Consensus MFE	-35.96
Energy contribution	-38.56
Covariance contribution	2.60
Combinations/Pair	1.00
Mean z-score	-3.26
Structure conservation index	0.81
SVM decision value	3.04
SVM RNA-class probability	0.998231
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18732640 112 + 22407834
CCAUCGUUGUCGGUUCCACAUUGCACCACUGGGUUUUUAAAGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGAGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAA
.....(((((((.((((((((((((((.((..(((.....)))..)).).))))((((((((((....))))))))..((((.....))))--------))))))))))))))))))... ( -42.80)
>DroSec_CAF1 25189 112 + 1
CCAUGGUUGUCGGUUCCACAUUGCACCACUGGGUUUUAAAAGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAA
.....(((((((.((((((((((((((.((..(((.....)))..)).).))))((((((((((....))))))))))((((.....))))--------..))))))))))))))))... ( -47.10)
>DroSim_CAF1 23731 112 + 1
CCAUGGUUGUCGGUUCCACAUUGCACCACUGGGUUUUAAAAGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAA
.....(((((((.((((((((((((((.((..(((.....)))..)).).))))((((((((((....))))))))))((((.....))))--------..))))))))))))))))... ( -47.10)
>DroEre_CAF1 25286 108 + 1
CCAU----GGCGGUUCCACUGUGCACCACUGGGUUGUAAAAGCGAAGAGUGUGCCCCAGCAGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAA
....----.((.(((((((...((((.(((...((((....))))..)))))))((((((.(((....))).))))))((((.....))))--------.....))))))).))...... ( -38.50)
>DroYak_CAF1 25254 120 + 1
CCAUCGUUGUCGGUUCCACUGUGCUCCAGUGGGUUUUAAAAGCGAAGUGUGUGCCCCAGCAGAAAAGAUUCAGUUGGGUGGCUAUCUGCCACCCAAUGUGGAAUGUGGAAUGGCGGCAAA
...(((((......(((((((.....))))))).......)))))......(((((((.......(.((((.((((((((((.....))))))))))...)))).)....))).)))).. ( -47.22)
>consensus
CCAUCGUUGUCGGUUCCACAUUGCACCACUGGGUUUUAAAAGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA________GGAAUGUGGAAUGGCGGCAAA
.....(((((((.((((((((((((((.((..(((.....)))..)).).))))((((((((((....))))))))))((((.....))))..........))))))))))))))))... (-35.96 = -38.56 +   2.60)

alignment

secondary structure

dotplot

Window 4

Location	18,732,640 – 18,732,752
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.49
Mean single sequence MFE	-32.79
Consensus MFE	-25.65
Energy contribution	-26.89
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-1.79
Structure conservation index	0.78
SVM decision value	0.64
SVM RNA-class probability	0.809487
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18732640 112 - 22407834
UUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACUCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCUUUAAAAACCCAGUGGUGCAAUGUGGAACCGACAACGAUGG
.(((.((...(((((((((..--------((((.....))))((((.(((((....))))).))))(((((((.................))).))))))))))))).)).)))...... ( -30.93)
>DroSec_CAF1 25189 112 - 1
UUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACCCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCUUUUAAAACCCAGUGGUGCAAUGUGGAACCGACAACCAUGG
.(((.((...(((((((((..--------((((.....))))((((.(((((....))))).))))(((((((.................))).))))))))))))).)).)))...... ( -33.93)
>DroSim_CAF1 23731 112 - 1
UUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACCCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCUUUUAAAACCCAGUGGUGCAAUGUGGAACCGACAACCAUGG
.(((.((...(((((((((..--------((((.....))))((((.(((((....))))).))))(((((((.................))).))))))))))))).)).)))...... ( -33.93)
>DroEre_CAF1 25286 108 - 1
UUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACCCAACUGAAUCUUUUCUGCUGGGGCACACUCUUCGCUUUUACAACCCAGUGGUGCACAGUGGAACCGCC----AUGG
......((..((((((...((--------..(((((.....................)))))..))(((((((.................))).))))...))))))..)).----.... ( -28.43)
>DroYak_CAF1 25254 120 - 1
UUUGCCGCCAUUCCACAUUCCACAUUGGGUGGCAGAUAGCCACCCAACUGAAUCUUUUCUGCUGGGGCACACACUUCGCUUUUAAAACCCACUGGAGCACAGUGGAACCGACAACGAUGG
..((((.(((..............(((((((((.....)))))))))..(((....)))...)))))))....(.(((..........((((((.....)))))).........))).). ( -36.71)
>consensus
UUUGCCGCCAUUCCACAUUCC________UGGCAGAUAGCCACCCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCUUUUAAAACCCAGUGGUGCAAUGUGGAACCGACAACCAUGG
.(((.((...((((((.............((((.....))))((((.(((((....))))).))))(((((((.................))).))))...)))))).)).)))...... (-25.65 = -26.89 +   1.24)

alignment

secondary structure

dotplot

Window 5

Location	18,732,680 – 18,732,792
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.01
Mean single sequence MFE	-40.54
Consensus MFE	-36.84
Energy contribution	-37.44
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.91
SVM decision value	2.98
SVM RNA-class probability	0.997984
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18732680 112 + 22407834
AGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGAGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAAGAGACGAGCCGUAACGAACAUGGCUAUCUUUACGGCACCC
..........(((((.((((((((....)))))))).((.((((((..(..--------.....)..).))))).))(((((....((((((.......)))))).)))))..))))).. ( -37.90)
>DroSec_CAF1 25229 112 + 1
AGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAAGAGACGAGCCGUAACGAACAUGGCUAUCUUUACGGCACCC
..........((((((((((((((....)))))))))((.((((((..(..--------.....)..).))))).))(((((....((((((.......)))))).)))))..))))).. ( -41.20)
>DroSim_CAF1 23771 112 + 1
AGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAAGAGACGAGCCGUAACGAACAUGGCUAUCUUUACGGCACCC
..........((((((((((((((....)))))))))((.((((((..(..--------.....)..).))))).))(((((....((((((.......)))))).)))))..))))).. ( -41.20)
>DroEre_CAF1 25322 112 + 1
AGCGAAGAGUGUGCCCCAGCAGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA--------GGAAUGUGGAAUGGCGGCAAAGAGACGAGCCGUAACGAACAUGGCUAUCUUUACGGCACCC
..........((((((((((.(((....))).)))))((.((((((..(..--------.....)..).))))).))(((((....((((((.......)))))).)))))..))))).. ( -35.90)
>DroYak_CAF1 25294 120 + 1
AGCGAAGUGUGUGCCCCAGCAGAAAAGAUUCAGUUGGGUGGCUAUCUGCCACCCAAUGUGGAAUGUGGAAUGGCGGCAAAGAGACGAGCCGUAACGAACAUGGCUAUCUUUACGGCACCC
......((((.(((((((.......(.((((.((((((((((.....))))))))))...)))).)....))).)))).(((((..((((((.......)))))).)))))...)))).. ( -46.50)
>consensus
AGCGAAGAGUGUGCCCCAGCUGAAAAGAUUCAGUUGGGUGGCUAUCUGCCA________GGAAUGUGGAAUGGCGGCAAAGAGACGAGCCGUAACGAACAUGGCUAUCUUUACGGCACCC
..........((((((((((((((....)))))))))((.((((((..(...............)..).))))).))(((((....((((((.......)))))).)))))..))))).. (-36.84 = -37.44 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	18,732,680 – 18,732,792
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.01
Mean single sequence MFE	-34.70
Consensus MFE	-31.80
Energy contribution	-32.24
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.92
SVM decision value	1.56
SVM RNA-class probability	0.964022
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18732680 112 - 22407834
GGGUGCCGUAAAGAUAGCCAUGUUCGUUACGGCUCGUCUCUUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACUCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCU
(((((..(((((((.((((.((.....)).))))....))))))).(((............--------((((.....)))).(((.(((((....))))).)))))).)))))...... ( -32.30)
>DroSec_CAF1 25229 112 - 1
GGGUGCCGUAAAGAUAGCCAUGUUCGUUACGGCUCGUCUCUUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACCCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCU
(((((..(((((((.((((.((.....)).))))....))))))).(((............--------((((.....)))).(((.(((((....))))).)))))).)))))...... ( -35.30)
>DroSim_CAF1 23771 112 - 1
GGGUGCCGUAAAGAUAGCCAUGUUCGUUACGGCUCGUCUCUUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACCCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCU
(((((..(((((((.((((.((.....)).))))....))))))).(((............--------((((.....)))).(((.(((((....))))).)))))).)))))...... ( -35.30)
>DroEre_CAF1 25322 112 - 1
GGGUGCCGUAAAGAUAGCCAUGUUCGUUACGGCUCGUCUCUUUGCCGCCAUUCCACAUUCC--------UGGCAGAUAGCCACCCAACUGAAUCUUUUCUGCUGGGGCACACUCUUCGCU
(((((..(((((((.((((.((.....)).))))....))))))).(((............--------((((.....)))).(((.(.(((....))).).)))))).)))))...... ( -30.70)
>DroYak_CAF1 25294 120 - 1
GGGUGCCGUAAAGAUAGCCAUGUUCGUUACGGCUCGUCUCUUUGCCGCCAUUCCACAUUCCACAUUGGGUGGCAGAUAGCCACCCAACUGAAUCUUUUCUGCUGGGGCACACACUUCGCU
..((((((((((((.((((.((.....)).))))....)))))))..............((((((((((((((.....)))))))))..(((....))))).)))))))).......... ( -39.90)
>consensus
GGGUGCCGUAAAGAUAGCCAUGUUCGUUACGGCUCGUCUCUUUGCCGCCAUUCCACAUUCC________UGGCAGAUAGCCACCCAACUGAAUCUUUUCAGCUGGGGCACACUCUUCGCU
(((((..(((((((.((((.((.....)).))))....))))))).(((....................((((.....)))).(((.(((((....))))).)))))).)))))...... (-31.80 = -32.24 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:59 2006