Locus 89

Sequence ID	4_DroMel_CAF1
Location	669,650 – 669,785
Length	135
Max. P	0.723058

overview

Window 0

Location	669,650 – 669,757
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.51
Mean single sequence MFE	-21.90
Consensus MFE	-18.68
Energy contribution	-18.10
Covariance contribution	-0.58
Combinations/Pair	1.19
Mean z-score	-1.71
Structure conservation index	0.85
SVM decision value	0.40
SVM RNA-class probability	0.723058
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 669650 107 + 1281640
-CAAAUAACUUCUUAGAUAUUU-UUAUUGUGAUUUUAUAA----UGUA----UAGCCGAACUU--UUUCGGUGGGAAUGCUU-UGAUGAAAGCAAAACCGUAAUACGAUUACAACUUCCU
-.(((((.((....)).)))))-...((((((((.(((..----....----..((((((...--.))))))((...(((((-(....))))))...))...))).))))))))...... ( -21.60)
>DroVir_CAF1 6853 112 + 1
CUAAUUUACUUCAUUAGUAUU--UUAUUGUGAGCUAAUUA----UGUAUGUUUAACCGAAUUUUUUUUCGGUGGGAAUGCUU-UAGUGAAAGCAAAACCGUAAU-UGAUUAUAACUUCCU
.(((..((((.....))))..--)))((((((..((((((----(.........((((((......))))))((...(((((-(....))))))...)))))))-)).))))))...... ( -24.10)
>DroPse_CAF1 9023 108 + 1
CUAAAUAACUUCAUUGAUAUUU-UUAUUGUGAUCUAAUAA----UGUA----UAACCGAAUUA--UUUCGGUGGGAAUGCUU-UAAUGAAAGCAAAACCGUAAUAAGAUUAUAACUUCCU
......................-...(((((((((.....----....----..((((((...--.))))))((...(((((-(....))))))...))......)))))))))...... ( -22.40)
>DroWil_CAF1 6423 112 + 1
CUAAUUAACUUCAUUGAUAUU--UUAUUGUGAUCUAAUUAUGUAUGUA----UAACCGAAUCA--UUUCGGUGGGAAUGCUUUUAGUGAAAGCAAAACCGUAAAAAGAUUAUAACUUCCU
.....................--...(((((((((..((((.......----..((((((...--.))))))((...(((((((...)))))))...))))))..)))))))))...... ( -23.30)
>DroAna_CAF1 1585406 101 + 1
----AUAACUUUGUUGAUAUUUUUUAUUUUGAUU---UAA----UGUA----UAACCGAACUU---UUCGGUGGGAAUGCUU-UAACGAAAGCAAAACCGUAAUAAGAUUAGAACUUCCU
----......................((((((((---(..----....----..(((((....---.)))))((...(((((-(....))))))...))......)))))))))...... ( -17.60)
>DroPer_CAF1 15582 108 + 1
CUAAAUAACUUCAUUGAUAUUU-UUAUUGUGAUCUAAUAA----UGUA----UAACCGAAUUA--UUUCGGUGGGAAUGCUU-UAAUGAAAGCAAAACCGUAAUAAGAUUAUAACUUCCU
......................-...(((((((((.....----....----..((((((...--.))))))((...(((((-(....))))))...))......)))))))))...... ( -22.40)
>consensus
CUAAAUAACUUCAUUGAUAUUU_UUAUUGUGAUCUAAUAA____UGUA____UAACCGAAUUA__UUUCGGUGGGAAUGCUU_UAAUGAAAGCAAAACCGUAAUAAGAUUAUAACUUCCU
..........................((((((((....................((((((......))))))((...(((((.......)))))...)).......))))))))...... (-18.68 = -18.10 +  -0.58)

alignment

secondary structure

dotplot

Window 1

Location	669,688 – 669,785
Length	97
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	83.55
Mean single sequence MFE	-18.73
Consensus MFE	-15.22
Energy contribution	-15.72
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.81
SVM decision value	0.17
SVM RNA-class probability	0.617408
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 669688 97 - 1281640
------GAAAAAA-----UACCUGUGUUAUAUUCAUUAGAGGAAGUUGUAAUCGUAUUACGGUUUUGCUUUCAUCA-AAGCAUUCCCACCGAAA--AAGUUCGGCUA----UACA----
------.......-----.....((((...........((((((((...(((((.....)))))..)))))).)).-...........(((((.--...)))))..)----))).---- ( -17.20)
>DroVir_CAF1 6891 108 - 1
CUACAAAAAAAAU-----UACCUGUGUUAUAUACAUAAUAGGAAGUUAUAAUCA-AUUACGGUUUUGCUUUCACUA-AAGCAUUCCCACCGAAAAAAAAUUCGGUUAAACAUACA----
.............-----..(((((............)))))..(((.......-.....((...((((((....)-)))))...))((((((......))))))..))).....---- ( -18.10)
>DroPse_CAF1 9062 101 - 1
--AAAGAAAAAAA-----UACCUGUGUUAUAUACAUUAUAGGAAGUUAUAAUCUUAUUACGGUUUUGCUUUCAUUA-AAGCAUUCCCACCGAAA--UAAUUCGGUUA----UACA----
--...........-----..((((((..........))))))..((.(((((((((((.((((..((((((....)-))))).....)))).))--)))...)))))----))).---- ( -19.50)
>DroWil_CAF1 6461 107 - 1
------AGAAAAAAGUUGAACCUGUGUUAUAUACAUUAUAGGAAGUUAUAAUCUUUUUACGGUUUUGCUUUCACUAAAAGCAUUCCCACCGAAA--UGAUUCGGUUA----UACAUACA
------.(.((((((.(((.((((((..........))))))...)))....)))))).)((...((((((.....))))))...))((((((.--...))))))..----........ ( -20.40)
>DroAna_CAF1 1585439 95 - 1
------GAU-AAU-----UACCUGUGUUAUAUUCAUUAUAGGAAGUUCUAAUCUUAUUACGGUUUUGCUUUCGUUA-AAGCAUUCCCACCGAA---AAGUUCGGUUA----UACA----
------(((-(((-----(.((((((..........)))))).))))...))).......((...((((((....)-)))))...))(((((.---....)))))..----....---- ( -17.70)
>DroPer_CAF1 15621 101 - 1
--AAAGAAAAAAA-----UACCUGUGUUAUAUACAUUAUAGGAAGUUAUAAUCUUAUUACGGUUUUGCUUUCAUUA-AAGCAUUCCCACCGAAA--UAAUUCGGUUA----UACA----
--...........-----..((((((..........))))))..((.(((((((((((.((((..((((((....)-))))).....)))).))--)))...)))))----))).---- ( -19.50)
>consensus
______AAAAAAA_____UACCUGUGUUAUAUACAUUAUAGGAAGUUAUAAUCUUAUUACGGUUUUGCUUUCAUUA_AAGCAUUCCCACCGAAA__AAAUUCGGUUA____UACA____
....................((((((..........))))))..................((...(((((.......)))))...))((((((......)))))).............. (-15.22 = -15.72 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:19 2006