Locus 81

Sequence ID	2R_DroMel_CAF1
Location	1,335,634 – 1,335,874
Length	240
Max. P	0.998272

overview

Window 6

Location	1,335,634 – 1,335,754
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-36.40
Consensus MFE	-35.14
Energy contribution	-35.14
Covariance contribution	0.00
Combinations/Pair	1.05
Mean z-score	-1.91
Structure conservation index	0.97
SVM decision value	3.05
SVM RNA-class probability	0.998272
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1335634 120 + 20766785
CACAUCGUUUGUCAAUCGUAAACUGCGAUCUGACAGGGACAAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGC
(((....((((((((((((.....))))).))))))).((((((((.........(((((((.((((((((.......)))))))))))))))..))))))))))).............. ( -35.80)
>DroSec_CAF1 54155 120 + 1
CACGUCGUUUGUCAAUCGUAAACUGCGAUCUGACAGGGACAAAUGGCAUUGGAAGUCGCUUUUAUUUGCCGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGC
((((((.((((((((((((.....))))).)))))))))).....(((.(((...(((((((.((((((((.......)))))))))))))))..)))..)))))).............. ( -40.80)
>DroSim_CAF1 32345 120 + 1
CACAUCGUUUGUCAAUCGUAAACUGCGAUCUGACAGGGACAAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGC
(((....((((((((((((.....))))).))))))).((((((((.........(((((((.((((((((.......)))))))))))))))..))))))))))).............. ( -35.80)
>DroEre_CAF1 35688 120 + 1
CACAUCGUUAGUCAAUCGUAAACUGCGAUCUGACAGGGACAAAUGGCAUUGGAAGUCGCUUUUAUUUGCCGGCGAUUAUGGCAAAUGAAGCGAAACUGUUUGUGUGAUUCCUUGUUUGGA
....((((.(((.........)))))))((.((((((((...((.((((....(((((((((.((((((((.......)))))))))))))))..))....)))).)))))))))).)). ( -36.00)
>DroYak_CAF1 22844 120 + 1
CACAUCGUUAGUCAAUCGUAAACUGCGAUCUGACAGGGACAAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGCCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUCUUGUUUAGA
(((.......(((((((((.....))))).))))....((((((((.........(((((((.(((((((.........))))))))))))))..))))))))))).............. ( -33.60)
>consensus
CACAUCGUUUGUCAAUCGUAAACUGCGAUCUGACAGGGACAAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGC
(((....((((((((((((.....))))).))))))).((((((((.........(((((((.((((((((.......)))))))))))))))..))))))))))).............. (-35.14 = -35.14 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	1,335,634 – 1,335,754
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-25.74
Consensus MFE	-22.54
Energy contribution	-22.74
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.30
Structure conservation index	0.88
SVM decision value	0.16
SVM RNA-class probability	0.610884
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1335634 120 - 20766785
GCCAAACAAAAAAUCACACAAACGGUUUCGCUUCAUUUGCCAUAAUCGCCAGCAAAUAAAAGCGACUUCCAAUGCCAUUUGUCCCUGUCAGAUCGCAGUUUACGAUUGACAAACGAUGUG
................((((...((..((((((.((((((...........))))))..))))))...))........((((...((((((.(((.......))))))))).)))))))) ( -24.20)
>DroSec_CAF1 54155 120 - 1
GCCAAACAAAAAAUCACACAAACGGUUUCGCUUCAUUUGCCAUAAUCGCCGGCAAAUAAAAGCGACUUCCAAUGCCAUUUGUCCCUGUCAGAUCGCAGUUUACGAUUGACAAACGACGUG
................(((....((..((((((.(((((((.........)))))))..))))))...))..........(((..((((((.(((.......)))))))))...)))))) ( -29.70)
>DroSim_CAF1 32345 120 - 1
GCCAAACAAAAAAUCACACAAACGGUUUCGCUUCAUUUGCCAUAAUCGCCAGCAAAUAAAAGCGACUUCCAAUGCCAUUUGUCCCUGUCAGAUCGCAGUUUACGAUUGACAAACGAUGUG
................((((...((..((((((.((((((...........))))))..))))))...))........((((...((((((.(((.......))))))))).)))))))) ( -24.20)
>DroEre_CAF1 35688 120 - 1
UCCAAACAAGGAAUCACACAAACAGUUUCGCUUCAUUUGCCAUAAUCGCCGGCAAAUAAAAGCGACUUCCAAUGCCAUUUGUCCCUGUCAGAUCGCAGUUUACGAUUGACUAACGAUGUG
(((......)))....((((..(((((((((((.(((((((.........)))))))..)))))).......(((.(((((.......))))).)))......))))).(....).)))) ( -26.80)
>DroYak_CAF1 22844 120 - 1
UCUAAACAAGAAAUCACACAAACGGUUUCGCUUCAUUUGCCAUAAUCGGCAGCAAAUAAAAGCGACUUCCAAUGCCAUUUGUCCCUGUCAGAUCGCAGUUUACGAUUGACUAACGAUGUG
................((((...((..((((((...(((((......))))).......))))))...))........((((....(((((.(((.......))))))))..)))))))) ( -23.80)
>consensus
GCCAAACAAAAAAUCACACAAACGGUUUCGCUUCAUUUGCCAUAAUCGCCAGCAAAUAAAAGCGACUUCCAAUGCCAUUUGUCCCUGUCAGAUCGCAGUUUACGAUUGACAAACGAUGUG
..............((((((((.(((.((((((.((((((...........))))))..))))))........))).)))))....(((((.(((.......)))))))).......))) (-22.54 = -22.74 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	1,335,674 – 1,335,794
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.75
Mean single sequence MFE	-39.84
Consensus MFE	-31.06
Energy contribution	-32.10
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-2.24
Structure conservation index	0.78
SVM decision value	1.36
SVM RNA-class probability	0.946190
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1335674 120 + 20766785
AAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGCCAGCGCGAAGGACUCGUGCUACCAGACAUUUUUGCGGACA
..........((...(((((((.((((((((.......)))))))))))))))..))(((((((.((.....(((((((..(((((((.....))))))).))))))).)).))))))). ( -41.40)
>DroSec_CAF1 54195 120 + 1
AAAUGGCAUUGGAAGUCGCUUUUAUUUGCCGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGCCAGCGCGAAGGACUCCUGCUGCCGGACAUUUGUGCGGACA
..........((...(((((((.((((((((.......)))))))))))))))..))(((((((..(.....((((((((.((((.((.....)).)))))))))))).)..))))))). ( -44.60)
>DroSim_CAF1 32385 120 + 1
AAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGCCAGCGCGAAGGACUCCUGCUGCCGGACAUUUUUGCGGACA
..........((...(((((((.((((((((.......)))))))))))))))..))(((((((.((.....((((((((.((((.((.....)).)))))))))))).)).))))))). ( -38.80)
>DroEre_CAF1 35728 117 + 1
AAAUGGCAUUGGAAGUCGCUUUUAUUUGCCGGCGAUUAUGGCAAAUGAAGCGAAACUGUUUGUGUGAUUCCUUGUUUGGACAGCGCGAAGGACAACUGCUGCGAGAAGUUUUUGCAG---
....(((((((....(((((((.((((((((.......)))))))))))))))...(.(((((((...(((......)))..))))))).).))).))))((((((...))))))..--- ( -37.80)
>DroYak_CAF1 22884 120 + 1
AAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGCCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUCUUGUUUAGACAACGCGAACGACUCCUGCCGCUCGAAAUGUUUGCGGACA
....((((..(((..(((((((.(((((((.........))))))))))))))...(((((((((....(((.....)))..)))))))))..)))))))((...........))..... ( -36.60)
>consensus
AAAUGGCAUUGGAAGUCGCUUUUAUUUGCUGGCGAUUAUGGCAAAUGAAGCGAAACCGUUUGUGUGAUUUUUUGUUUGGCCAGCGCGAAGGACUCCUGCUGCCAGACAUUUUUGCGGACA
((((.(((((((...(((((((.((((((((.......)))))))))))))))..)))...)))).))))..(((((((.(((((.((.....)).))))))))))))............ (-31.06 = -32.10 +   1.04)

alignment

secondary structure

dotplot

Window 9

Location	1,335,754 – 1,335,874
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.23
Mean single sequence MFE	-43.45
Consensus MFE	-31.55
Energy contribution	-31.99
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-1.64
Structure conservation index	0.73
SVM decision value	0.19
SVM RNA-class probability	0.626312
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1335754 120 - 20766785
AUCAGCCCUGAUUACAUUAGACAUUAAAAGCAGGGAAGCGAGUCAGUGCUUGGCGGUCAGCUGAGGCCACUUCGGUUGGCUGUCCGCAAAAAUGUCUGGUAGCACGAGUCCUUCGCGCUG
((((....))))...((((((((((..(((((..((......))..)))))(((((((((((((((...)))))))))))))))......))))))))))(((.((((...)))).))). ( -42.80)
>DroSec_CAF1 54275 115 - 1
AUCAGCCCUGAUUACAUUAGACAUUAAAAGCAGGG-----AGUCAGUGCUGGGCGGUCAGCCGAGGGCACUUCGGUUGGCUGUCCGCACAAAUGUCCGGCAGCAGGAGUCCUUCGCGCUG
..((((.(((((...))))).........((((((-----(.((.((((.((((((((((((((((...))))))))))))))))))))...(((......))).)).))))).)))))) ( -50.10)
>DroSim_CAF1 32465 114 - 1
AUCA-CCCUGAUUACAUUAGACAUUAAAAGCAGGG-----AGUCAGUGCUGGGCGGUCAGCCGAGGGCACUUCGGUUGGCUGUCCGCAAAAAUGUCCGGCAGCAGGAGUCCUUCGCGCUG
....-..(((((...))))).........((((((-----(.((..((((((((((((((((((((...))))))))))))))))((...........)))))).)).))))).)).... ( -44.40)
>DroYak_CAF1 22964 115 - 1
AUCAGCCCUAAUUACAUUAGGCAUUUAAAGCAGGG-----AGUCAGUGCUUGGCUGUUAGCUGCGGCCACUUUGGUUGGCUGUCCGCAAACAUUUCGAGCGGCAGGAGUCGUUCGCGUUG
..((((((((((...))))))........((.((.-----(((((..((((((((((.....)))))))....)))))))).)).))........((((((((....)))))))).)))) ( -36.50)
>consensus
AUCAGCCCUGAUUACAUUAGACAUUAAAAGCAGGG_____AGUCAGUGCUGGGCGGUCAGCCGAGGCCACUUCGGUUGGCUGUCCGCAAAAAUGUCCGGCAGCAGGAGUCCUUCGCGCUG
.....(((((....................)))))........((((((.((((((((((((((((...))))))))))))))))((..............))...........)))))) (-31.55 = -31.99 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:14 2006