Locus 2995

Sequence ID	2R_DroMel_CAF1
Location	10,326,931 – 10,327,078
Length	147
Max. P	0.795015

overview

Window 5

Location	10,326,931 – 10,327,038
Length	107
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	89.56
Mean single sequence MFE	-26.88
Consensus MFE	-19.08
Energy contribution	-22.07
Covariance contribution	3.00
Combinations/Pair	1.10
Mean z-score	-2.06
Structure conservation index	0.71
SVM decision value	0.36
SVM RNA-class probability	0.703920
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10326931 107 + 20766785
CGGUAGAUCGACGCCACCUGGUCAGGUAGCCACCAUCACCACCACUGGCAUCACCCUGCCUCUGUUCCAUCUACGCUAGAUACACUUUAAAAAAUGUUGGUAAGUAA
.(((.(((....((.((((....)))).))....))))))((((..((((......))))........(((((...)))))................))))...... ( -21.60)
>DroSec_CAF1 41392 107 + 1
CGGUAGAUCGACGCCACCUGGUCAGGUAGCCACCAUCACCACCAUUGGCAUCACCCUGCCUCGGUUCCAUCUACGCUAGCUACACUUUAAAAAGUACUAGCUUGCUA
..((((((.((.(((...((((..(((....)))...)))).....((((......))))..))))).))))))((.(((((.((((....))))..))))).)).. ( -30.80)
>DroSim_CAF1 41584 107 + 1
CGGUAGAUCGACGCCACCUGGUCAGGUAGCCACCAUCACCACCACUGGCAUCACCCUGCCUCUGUUCCAUCUACGCUAGCUACACUUUAAAAAGUACUAGCUUGCAA
..((((((.((.((.((((....)))).))............((..((((......))))..)).)).))))))((.(((((.((((....))))..))))).)).. ( -29.50)
>DroEre_CAF1 41382 107 + 1
CGGUAGAUCGACGCCACCUGGUCAGGUAGCCACCAUCACCACCACCGCCAUCAGCCCGCCUCUGCUCCAUCUACCCUAGCUACACUCUAAAAAAUGCUGUGUAGUAA
.(((((((.((.((....((((..(((....)))...)))).....((.....))........)))).)))))))...(((((((.............))))))).. ( -25.62)
>consensus
CGGUAGAUCGACGCCACCUGGUCAGGUAGCCACCAUCACCACCACUGGCAUCACCCUGCCUCUGUUCCAUCUACGCUAGCUACACUUUAAAAAAUACUAGCUAGCAA
..((((((.((.((.((((....)))).))................((((......)))).....)).))))))(((((((((((((....))))).)))))))).. (-19.08 = -22.07 +   3.00)

alignment

secondary structure

dotplot

Window 6

Location	10,326,931 – 10,327,038
Length	107
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	89.56
Mean single sequence MFE	-37.03
Consensus MFE	-29.85
Energy contribution	-31.97
Covariance contribution	2.12
Combinations/Pair	1.12
Mean z-score	-1.69
Structure conservation index	0.81
SVM decision value	0.44
SVM RNA-class probability	0.735838
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10326931 107 - 20766785
UUACUUACCAACAUUUUUUAAAGUGUAUCUAGCGUAGAUGGAACAGAGGCAGGGUGAUGCCAGUGGUGGUGAUGGUGGCUACCUGACCAGGUGGCGUCGAUCUACCG
......((((............((.((((((...))))))..))...((((......))))..))))((((((.(..(((((((....)))))))..).))).))). ( -32.40)
>DroSec_CAF1 41392 107 - 1
UAGCAAGCUAGUACUUUUUAAAGUGUAGCUAGCGUAGAUGGAACCGAGGCAGGGUGAUGCCAAUGGUGGUGAUGGUGGCUACCUGACCAGGUGGCGUCGAUCUACCG
..((.(((((.(((((....)))))))))).))((((((.((((((.((((......))))..))))..........(((((((....))))))).)).)))))).. ( -41.20)
>DroSim_CAF1 41584 107 - 1
UUGCAAGCUAGUACUUUUUAAAGUGUAGCUAGCGUAGAUGGAACAGAGGCAGGGUGAUGCCAGUGGUGGUGAUGGUGGCUACCUGACCAGGUGGCGUCGAUCUACCG
..((.(((((.(((((....)))))))))).))((((((.((.((..((((......))))..))............(((((((....))))))).)).)))))).. ( -39.40)
>DroEre_CAF1 41382 107 - 1
UUACUACACAGCAUUUUUUAGAGUGUAGCUAGGGUAGAUGGAGCAGAGGCGGGCUGAUGGCGGUGGUGGUGAUGGUGGCUACCUGACCAGGUGGCGUCGAUCUACCG
...((((((.............))))))....(((((((.((((....))..((((.((((((((((.(......).)))))).).)))..)))).)).))))))). ( -35.12)
>consensus
UUACAAGCCAGCACUUUUUAAAGUGUAGCUAGCGUAGAUGGAACAGAGGCAGGGUGAUGCCAGUGGUGGUGAUGGUGGCUACCUGACCAGGUGGCGUCGAUCUACCG
..((((((((.(((((....)))))))))))))((((((.((.....((((......))))................(((((((....))))))).)).)))))).. (-29.85 = -31.97 +   2.12)

alignment

secondary structure

dotplot

Window 7

Location	10,326,967 – 10,327,078
Length	111
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	83.93
Mean single sequence MFE	-24.11
Consensus MFE	-14.02
Energy contribution	-17.28
Covariance contribution	3.25
Combinations/Pair	1.12
Mean z-score	-2.56
Structure conservation index	0.58
SVM decision value	0.60
SVM RNA-class probability	0.795015
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10326967 111 + 20766785
CACCACCACUGGCAUCACCCUGCCUCUGUUCCAUCUACGCUAGAUACACUUUAAAAAAUGUUGGUAAGUAAGAUGGGAUCAUUUAAUCAGCAUUCUAUUCUUUUGCUUUUA
......((..((((......))))..))((((((((((((((...(((.((....)).)))))))..)).))))))))..........((((...........)))).... ( -17.90)
>DroSec_CAF1 41428 111 + 1
CACCACCAUUGGCAUCACCCUGCCUCGGUUCCAUCUACGCUAGCUACACUUUAAAAAGUACUAGCUUGCUAGAUGGGAUCAUUUAAUCAUCAUUCUAUUCUUUUGCUUUCG
..........((((......))))..(((((((((((.((.(((((.((((....))))..))))).)))))))))))))............................... ( -30.60)
>DroSim_CAF1 41620 111 + 1
CACCACCACUGGCAUCACCCUGCCUCUGUUCCAUCUACGCUAGCUACACUUUAAAAAGUACUAGCUUGCAAGAUGGGAUCAUUAAAUCAUCAUUCUAUUCUUUUGCUUUCG
......((..((((......))))..))((((((((..((.(((((.((((....))))..))))).)).))))))))................................. ( -24.30)
>DroEre_CAF1 41418 111 + 1
CACCACCACCGCCAUCAGCCCGCCUCUGCUCCAUCUACCCUAGCUACACUCUAAAAAAUGCUGUGUAGUAAGAUGGGAUCAUUCACUGAUCUUUAUAUCGUUGUGAUUUAG
...(((.((..((((((((........)))............(((((((.............)))))))..)))))(((((.....)))))........)).)))...... ( -23.62)
>consensus
CACCACCACUGGCAUCACCCUGCCUCUGUUCCAUCUACGCUAGCUACACUUUAAAAAAUACUAGCUAGCAAGAUGGGAUCAUUUAAUCAUCAUUCUAUUCUUUUGCUUUCG
..........((((......))))...(((((((((..(((((((((((((....))))).)))))))).)))))))))................................ (-14.02 = -17.28 +   3.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:50 2006