Locus 4060

Sequence ID	X_DroMel_CAF1
Location	10,757,517 – 10,757,615
Length	98
Max. P	0.936068

overview

Window 2

Location	10,757,517 – 10,757,615
Length	98
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	82.23
Mean single sequence MFE	-25.98
Consensus MFE	-15.24
Energy contribution	-15.20
Covariance contribution	-0.04
Combinations/Pair	1.06
Mean z-score	-2.29
Structure conservation index	0.59
SVM decision value	0.70
SVM RNA-class probability	0.825265
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10757517 98 + 22224390
AGAUCCUGUCCAUGCACAAGCACUUGCAUAUAGGAUG---CACAUACACGUACGUGCAUGUGCGCAAGGACACGAUGCUGC-UGACGACCAAACAACUCAAU
(((((.(((((.(((....((....)).........(---(((((.(((....))).))))))))).))))).))).))..-.................... ( -28.80)
>DroSec_CAF1 7266 98 + 1
AGAUCCUGUCCAUGCACAAGCACUUGCAUAUGGGAUG---UACAUACACGUGCAUACAUGUACGCAAGGACACGAUGCUGC-UGACGACCAAACAACUCAAU
(((((.(((((.(((....((....))(((((..(((---(((......)))))).)))))..))).))))).))).))..-.................... ( -26.50)
>DroSim_CAF1 4579 98 + 1
AGAUCCUGUCCAUGCACAAGCACUUGCAUAUGGGAUG---UACAUACACGUGCAUACAUGUGCGCAAGGACACGAUGCUGC-UGACGACCAAACAACUCAAU
(((((.(((((.(((....)))...(((((((..(((---(((......)))))).)))))))....))))).))).))..-.................... ( -28.90)
>DroEre_CAF1 6136 82 + 1
ACAUCCUGUCCAUGCACAAGCACUUGCAUAUAGGAUG-------------------CAUGUGCGCAAGGACACGUUGCCAC-UCACGACCAUACAACUCAAU
......(((((.(((....((((.(((((.....)))-------------------)).))))))).))))).((((....-...))))............. ( -22.40)
>DroYak_CAF1 8001 91 + 1
GGAUCCUGUCCAUGCACAAGCACUUGCAUAUAGGAGGAUGUAC-----------UAGAUGUGCGCAAGGACACGAUGCUGCCAUACAAGCAUACAACUCAAU
..(((.(((((.(((....)))...((((((...((......)-----------)..))))))....))))).)))(((........)))............ ( -23.30)
>consensus
AGAUCCUGUCCAUGCACAAGCACUUGCAUAUAGGAUG___UACAUACACGU_C_UACAUGUGCGCAAGGACACGAUGCUGC_UGACGACCAAACAACUCAAU
..(((((((..(((((........))))))))))))......................(((.(....).))).............................. (-15.24 = -15.20 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	10,757,517 – 10,757,615
Length	98
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	82.23
Mean single sequence MFE	-31.88
Consensus MFE	-21.30
Energy contribution	-23.66
Covariance contribution	2.36
Combinations/Pair	1.17
Mean z-score	-2.38
Structure conservation index	0.67
SVM decision value	1.25
SVM RNA-class probability	0.936068
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10757517 98 - 22224390
AUUGAGUUGUUUGGUCGUCA-GCAGCAUCGUGUCCUUGCGCACAUGCACGUACGUGUAUGUG---CAUCCUAUAUGCAAGUGCUUGUGCAUGGACAGGAUCU
.....((((((........)-)))))(((.(((((.(((((((((((((....)))))))))---).........((((....))))))).))))).))).. ( -39.20)
>DroSec_CAF1 7266 98 - 1
AUUGAGUUGUUUGGUCGUCA-GCAGCAUCGUGUCCUUGCGUACAUGUAUGCACGUGUAUGUA---CAUCCCAUAUGCAAGUGCUUGUGCAUGGACAGGAUCU
.....((((((........)-)))))(((.(((((....(((((.....((((.(((((((.---......))))))).)))).)))))..))))).))).. ( -31.40)
>DroSim_CAF1 4579 98 - 1
AUUGAGUUGUUUGGUCGUCA-GCAGCAUCGUGUCCUUGCGCACAUGUAUGCACGUGUAUGUA---CAUCCCAUAUGCAAGUGCUUGUGCAUGGACAGGAUCU
.....((((((........)-)))))(((.(((((.((((((.......((((.(((((((.---......))))))).)))).)))))).))))).))).. ( -34.30)
>DroEre_CAF1 6136 82 - 1
AUUGAGUUGUAUGGUCGUGA-GUGGCAACGUGUCCUUGCGCACAUG-------------------CAUCCUAUAUGCAAGUGCUUGUGCAUGGACAGGAUGU
.....(((((.....(....-)..))))).(((((.(((((((.((-------------------(((.....))))).))))....))).)))))...... ( -27.60)
>DroYak_CAF1 8001 91 - 1
AUUGAGUUGUAUGCUUGUAUGGCAGCAUCGUGUCCUUGCGCACAUCUA-----------GUACAUCCUCCUAUAUGCAAGUGCUUGUGCAUGGACAGGAUCC
.....((((((((....))).)))))(((.(((((.((((((.....(-----------((((................))))))))))).))))).))).. ( -26.89)
>consensus
AUUGAGUUGUUUGGUCGUCA_GCAGCAUCGUGUCCUUGCGCACAUGUA_G_ACGUGUAUGUA___CAUCCUAUAUGCAAGUGCUUGUGCAUGGACAGGAUCU
.....(((((.((.....)).)))))(((.(((((.(((((((((((((....))))))))..............((....))..))))).))))).))).. (-21.30 = -23.66 +   2.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:22 2006