Locus 4613

Sequence ID	2L_DroMel_CAF1
Location	13,193,237 – 13,193,348
Length	111
Max. P	0.998895

overview

Window 5

Location	13,193,237 – 13,193,348
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.94
Mean single sequence MFE	-24.84
Consensus MFE	-20.66
Energy contribution	-22.26
Covariance contribution	1.60
Combinations/Pair	1.06
Mean z-score	-2.44
Structure conservation index	0.83
SVM decision value	1.99
SVM RNA-class probability	0.984959
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13193237 111 + 22407834
AAUUUGUUUAAAUGUAACCCAUAUAUGCGUCAGAAACGACGAGGUCAAAUUAGCAUAACUCGUUUUUAAUCAUUUAUGGAUAUACAUUUAAAUGUGAUGCUUAUAAAAACG---------
.....(((((((((((..(((((.(((.((.((((((((....((.......)).....)))))))).))))).)))))...)))))))))))..................--------- ( -22.30)
>DroSec_CAF1 173 109 + 1
AAUUUGUUUAAAUGUAACCCAUAUAUGCAUCAGAAACGAGGAGGUCAAAUUAGCAUAACUCGUUUUUAAUCAUUUAUGGAUAUACAUUUAAAUGACAUGUUU--UAAAGCG---------
...(..((((((((((..(((((.(((.((.(((((((((...((.......))....))))))))).))))).)))))...))))))))))..).......--.......--------- ( -27.90)
>DroSim_CAF1 173 111 + 1
UAUUUGUUUAAAUGUAACCCAUAUAUGCAUCAGAAACGAGGAGGUCAAAUUAGCAUAACUCGUUUUUAAUCAUUUAUGGAUAUACAUUUAAAUGGCAUGCUUAUAAAAACG---------
...(..((((((((((..(((((.(((.((.(((((((((...((.......))....))))))))).))))).)))))...))))))))))..)................--------- ( -27.90)
>DroEre_CAF1 3478 120 + 1
AAUUUAUUUAAAUGUAACCCAUAUAAGCAUCAGAAACGAGGAGGUCAAAUUAGCAUAACUCGUUGGUAAUCAUUUAUGGUUUUUAAUUUAAAUGUGGUGCUUAUAAAUACCACUAUAAAA
.....((((((((..((.(((((...........((((((...((.......))....))))))..........))))).))...))))))))((((((........))))))....... ( -22.60)
>DroYak_CAF1 565 103 + 1
AACUUAUUUAAAUCUAACCCAUAUAUGCAUCAGAAACGAGGAGGUCUAAUUAGCAUAACUCGUUGGUGAUCAUUUAUGGUUAUAAAUUUA-AUGUGGUGCUUGU----------------
.(((...((((((.((..(((((.(((.((((..((((((...((.......))....))))))..))))))).)))))...)).)))))-)...)))......---------------- ( -23.50)
>consensus
AAUUUGUUUAAAUGUAACCCAUAUAUGCAUCAGAAACGAGGAGGUCAAAUUAGCAUAACUCGUUUUUAAUCAUUUAUGGAUAUACAUUUAAAUGUGAUGCUUAUAAAAACG_________
....((((((((((((..(((((.(((.((.(((((((((...((.......))....))))))))).))))).)))))...)))))))))))).......................... (-20.66 = -22.26 +   1.60)

alignment

secondary structure

dotplot

Window 6

Location	13,193,237 – 13,193,348
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.94
Mean single sequence MFE	-25.54
Consensus MFE	-21.00
Energy contribution	-22.60
Covariance contribution	1.60
Combinations/Pair	1.06
Mean z-score	-3.38
Structure conservation index	0.82
SVM decision value	3.27
SVM RNA-class probability	0.998895
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13193237 111 - 22407834
---------CGUUUUUAUAAGCAUCACAUUUAAAUGUAUAUCCAUAAAUGAUUAAAAACGAGUUAUGCUAAUUUGACCUCGUCGUUUCUGACGCAUAUAUGGGUUACAUUUAAACAAAUU
---------.((((....))))......((((((((((.(((((((.(((.(((.((((((((((........))))....)))))).)))..))).)))))))))))))))))...... ( -25.30)
>DroSec_CAF1 173 109 - 1
---------CGCUUUA--AAACAUGUCAUUUAAAUGUAUAUCCAUAAAUGAUUAAAAACGAGUUAUGCUAAUUUGACCUCCUCGUUUCUGAUGCAUAUAUGGGUUACAUUUAAACAAAUU
---------.......--..........((((((((((.(((((((.(((((((.(((((((.....(......).....))))))).)))).))).)))))))))))))))))...... ( -27.60)
>DroSim_CAF1 173 111 - 1
---------CGUUUUUAUAAGCAUGCCAUUUAAAUGUAUAUCCAUAAAUGAUUAAAAACGAGUUAUGCUAAUUUGACCUCCUCGUUUCUGAUGCAUAUAUGGGUUACAUUUAAACAAAUA
---------.((((....))))......((((((((((.(((((((.(((((((.(((((((.....(......).....))))))).)))).))).)))))))))))))))))...... ( -28.80)
>DroEre_CAF1 3478 120 - 1
UUUUAUAGUGGUAUUUAUAAGCACCACAUUUAAAUUAAAAACCAUAAAUGAUUACCAACGAGUUAUGCUAAUUUGACCUCCUCGUUUCUGAUGCUUAUAUGGGUUACAUUUAAAUAAAUU
.......(((((..........)))))(((((((((((...(((((...(((((..((((((.....(......).....))))))..)))).)...))))).))).))))))))..... ( -21.70)
>DroYak_CAF1 565 103 - 1
----------------ACAAGCACCACAU-UAAAUUUAUAACCAUAAAUGAUCACCAACGAGUUAUGCUAAUUAGACCUCCUCGUUUCUGAUGCAUAUAUGGGUUAGAUUUAAAUAAGUU
----------------............(-((((((((...(((((.(((((((..((((((.....((....)).....))))))..)))).))).)))))..)))))))))....... ( -24.30)
>consensus
_________CGUUUUUAUAAGCAUCACAUUUAAAUGUAUAUCCAUAAAUGAUUAAAAACGAGUUAUGCUAAUUUGACCUCCUCGUUUCUGAUGCAUAUAUGGGUUACAUUUAAACAAAUU
............................((((((((((.(((((((.(((((((.(((((((.....(......).....))))))).)))).))).)))))))))))))))))...... (-21.00 = -22.60 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:38 2006