Locus 5609

Sequence ID	2R_DroMel_CAF1
Location	17,873,598 – 17,873,733
Length	135
Max. P	0.686634

overview

Window 3

Location	17,873,598 – 17,873,711
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	94.34
Mean single sequence MFE	-25.61
Consensus MFE	-22.20
Energy contribution	-22.72
Covariance contribution	0.52
Combinations/Pair	1.14
Mean z-score	-1.31
Structure conservation index	0.87
SVM decision value	0.32
SVM RNA-class probability	0.686634
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17873598 113 - 20766785
GUUAUUGGCUUUUUAUCUGGUCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUAUUUGUGGACCGAUCCCAAAGACCAUUGAAUUCAAUCGAAA
.(((.(((((((..(((.((((((...........((((......))))((((((........))))))........)))))))))...)))).))).)))............ ( -29.50)
>DroSec_CAF1 38516 113 - 1
GUUAUUGGCUUUUUAUCUGGUCCAAACGGUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUAUUUGUGGACCGAUCCCAAAGACCAUUGAAUUCAAUCGAAA
.(((.(((((((..(((.((((((...........((((......))))((((((........))))))........)))))))))...)))).))).)))............ ( -29.50)
>DroSim_CAF1 38955 113 - 1
GUUAUUGGCUUUUUAUCUGGUCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUAUUUGUGGAUCGAUCCCAAAGACCAUUGAAUUCAAUCGAAA
.(((.(((((((..(((.((((((...........((((......))))((((((........))))))........)))))))))...)))).))).)))............ ( -26.90)
>DroEre_CAF1 40910 113 - 1
GUUAUUGGCAUUUUAUCUGGCCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCAUUUGAUGGCGAAUAAUAUUUGUGGCCCCCUUCCAAAGACCAUUGAAUUCAAUCGAAA
(((.((((..........((((((((.........((((......))))((((((((...)))).))))....)))).)))).....)))).)))..((((......)))).. ( -21.76)
>DroYak_CAF1 37649 113 - 1
GUUAUUGGCUUUUUAUCUGGCCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCAUUUGAUGGCAAAUAUUAUUUGUGGUCCAAUCCCAAAGACCAUUGAAUUGAAUCGAAA
(((...((((........))))..)))((.......)).((((((..(((....((..(((((.....)))))..))(((((..........))))))))...)))))).... ( -20.40)
>consensus
GUUAUUGGCUUUUUAUCUGGUCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUAUUUGUGGACCGAUCCCAAAGACCAUUGAAUUCAAUCGAAA
.(((.(((((((.....(((((((...........((((......)))).(((((((...)))))))..........))))))).....)))).))).)))............ (-22.20 = -22.72 +   0.52)

alignment

secondary structure

dotplot

Window 4

Location	17,873,638 – 17,873,733
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	96.42
Mean single sequence MFE	-17.84
Consensus MFE	-15.26
Energy contribution	-15.02
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.37
Structure conservation index	0.86
SVM decision value	0.11
SVM RNA-class probability	0.588480
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17873638 95 + 20766785
UAAUAUUCCCCAUCAAACGGGAAUUGCAUAAAUCUGCAUUUAAAGCGUUUGGACCAGAUAAAAAGCCAAUAACAAUUUACGAUGGCCACUGUCAA
............(((((((..((.((((......)))).))....)))))))....((((....((((..............))))...)))).. ( -15.74)
>DroSec_CAF1 38556 95 + 1
UAAUAUUCCCCAUCAAACGGGAAUUGCAUAAAUCUGCAUUUAAACCGUUUGGACCAGAUAAAAAGCCAAUAACAAUUUACGAUGGCCACUGUCAA
............((((((((.((.((((......)))).))...))))))))....((((....((((..............))))...)))).. ( -20.44)
>DroSim_CAF1 38995 95 + 1
UAAUAUUCCCCAUCAAACGGGAAUUGCAUAAAUCUGCAUUUAAAGCGUUUGGACCAGAUAAAAAGCCAAUAACAAUUUACGAUGGCCACUGUCAA
............(((((((..((.((((......)))).))....)))))))....((((....((((..............))))...)))).. ( -15.74)
>DroEre_CAF1 40950 95 + 1
UAUUAUUCGCCAUCAAAUGGGAAUUGCAUAAAUCUGCAUUUAAAGCGUUUGGGCCAGAUAAAAUGCCAAUAACAAUUUACGAUGGCCACUGUCAA
........((((((..........((((......))))..((((..(((..(((..........)))...)))..)))).))))))......... ( -18.70)
>DroYak_CAF1 37689 95 + 1
UAAUAUUUGCCAUCAAAUGGGAAUUGCAUAAAUCUGCAUUUAAAGCGUUUGGGCCAGAUAAAAAGCCAAUAACAAUUUACGAUGGCCACUGUCAA
........((((((..........((((......))))..((((..(((..(((..........)))...)))..)))).))))))......... ( -18.60)
>consensus
UAAUAUUCCCCAUCAAACGGGAAUUGCAUAAAUCUGCAUUUAAAGCGUUUGGACCAGAUAAAAAGCCAAUAACAAUUUACGAUGGCCACUGUCAA
............(((((((..((.((((......)))).))....)))))))....((((....((((..............))))...)))).. (-15.26 = -15.02 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	17,873,638 – 17,873,733
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	96.42
Mean single sequence MFE	-21.82
Consensus MFE	-18.90
Energy contribution	-18.66
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.32
Structure conservation index	0.87
SVM decision value	0.09
SVM RNA-class probability	0.576479
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17873638 95 - 20766785
UUGACAGUGGCCAUCGUAAAUUGUUAUUGGCUUUUUAUCUGGUCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUA
.......((((((..(((((..((.....))..))))).))).)))...........((((......))))((((((........)))))).... ( -20.80)
>DroSec_CAF1 38556 95 - 1
UUGACAGUGGCCAUCGUAAAUUGUUAUUGGCUUUUUAUCUGGUCCAAACGGUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUA
..(((..((((((..(((((..((.....))..))))).))).)))....)))....((((......))))((((((........)))))).... ( -22.10)
>DroSim_CAF1 38995 95 - 1
UUGACAGUGGCCAUCGUAAAUUGUUAUUGGCUUUUUAUCUGGUCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUA
.......((((((..(((((..((.....))..))))).))).)))...........((((......))))((((((........)))))).... ( -20.80)
>DroEre_CAF1 40950 95 - 1
UUGACAGUGGCCAUCGUAAAUUGUUAUUGGCAUUUUAUCUGGCCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCAUUUGAUGGCGAAUAAUA
......(.(((((..(((((.(((.....))).))))).))))))...(((((((((((..((((.....))))..))))))).))))....... ( -23.00)
>DroYak_CAF1 37689 95 - 1
UUGACAGUGGCCAUCGUAAAUUGUUAUUGGCUUUUUAUCUGGCCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCAUUUGAUGGCAAAUAUUA
.........(((((((((((.((((...((((........))))..)))).))))..((((......)))).........)))))))........ ( -22.40)
>consensus
UUGACAGUGGCCAUCGUAAAUUGUUAUUGGCUUUUUAUCUGGUCCAAACGCUUUAAAUGCAGAUUUAUGCAAUUCCCGUUUGAUGGGGAAUAUUA
......(.(((((..(((((..((.....))..))))).))))))............((((......)))).(((((((...)))))))...... (-18.90 = -18.66 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:51 2006