Locus 3851

Sequence ID	2R_DroMel_CAF1
Location	12,723,839 – 12,723,977
Length	138
Max. P	0.855750

overview

Window 3

Location	12,723,839 – 12,723,940
Length	101
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	83.67
Mean single sequence MFE	-26.78
Consensus MFE	-19.35
Energy contribution	-21.60
Covariance contribution	2.25
Combinations/Pair	1.07
Mean z-score	-2.31
Structure conservation index	0.72
SVM decision value	0.39
SVM RNA-class probability	0.717855
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12723839 101 - 20766785
----ACUGGUGCUCAAUGCAUUUUU--UGAGUGGAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCGGUAUCAAGGAGAUGUGAUAAAAAUUAACGACUCCCCG
----((((((((((..((((((((.--.....))))))))(((..............)))..)))))))))).....((((.(((...........))).))))... ( -31.34)
>DroPse_CAF1 74104 99 - 1
CAUGGCUGGCCCCCAAUGCAGUUCUCAGCAUCAGAAUGCAGCCAAAAACAGAGA------CAGA--GACAGGAGAGAAGAGAAGUGAUAAAAAUUAACGACUCCCAU
..((((((.......((((........)))).......))))))..........------....--....((.(((..(.....((((....)))).)..))))).. ( -16.64)
>DroSec_CAF1 70156 101 - 1
----ACUGGUGCUCAAUGCAUUUUU--GGAGUGGAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCAGUAUCAGGGAGAUGUGAUAAAAAUUAACGACUCCCCG
----((((((((((..((((((((.--.....))))))))(((..............)))..))))))))))....(((((.(((...........))).))))).. ( -35.34)
>DroSim_CAF1 76018 101 - 1
----ACUGGUGCUCAAUGCAUUUUU--GGAGUGUAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCAGUAUCAAGGAGAUGUGAUAAAAAUUAACGACUCCCCG
----((((((((((..((((((...--.......))))))(((..............)))..)))))))))).....((((.(((...........))).))))... ( -29.14)
>DroEre_CAF1 71004 99 - 1
------UGGUGCUCAAUGCAUUUUU--GGAGUGGAAUGCAGUCUAAAACAGAGGACCAACCAGAGUACAAGUAUCAAGGAGAUGUGAUAAAAAUUAACGACUCCCCA
------..((((((..((((((((.--.....))))))))((((........))))......)))))).........((((.(((...........))).))))... ( -25.30)
>DroYak_CAF1 77910 99 - 1
------UGGUGCUCAAUGCAUUUUU--AGAGUGGAAUGCAGUCAAAAACAGAGGACCAACAAGACUACCAGUAUCAAGGAGAUGUGAUAAAAAUUAACGACUCCCCA
------((((.(((..((((((((.--.....))))))))((.....)).))).))))...................((((.(((...........))).))))... ( -22.90)
>consensus
____ACUGGUGCUCAAUGCAUUUUU__GGAGUGGAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCAGUAUCAAGGAGAUGUGAUAAAAAUUAACGACUCCCCG
.....(((((((((..((((((((........))))))))(((..........)))......)))))))))......((((.(((...........))).))))... (-19.35 = -21.60 +   2.25)

alignment

secondary structure

dotplot

Window 4

Location	12,723,875 – 12,723,977
Length	102
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.39
Mean single sequence MFE	-30.80
Consensus MFE	-20.85
Energy contribution	-23.10
Covariance contribution	2.25
Combinations/Pair	1.07
Mean z-score	-2.30
Structure conservation index	0.68
SVM decision value	0.81
SVM RNA-class probability	0.855750
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12723875 102 - 20766785
CGUCUCAAGAAAAUGGGCAGACACCUGCUCCACUGGU------ACUGGUGCUCAAUGCAUUUUU--UGAGUGGAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCGG
.............(((((((....)))).)))(((((------((((((.(((..((((((((.--.....))))))))((.....)).))).)))......)))))))) ( -33.30)
>DroPse_CAF1 74140 102 - 1
UGUCUCAAGGAAAUGGCCAAACACCUGCCCCAUGGCUACCAUGGCUGGCCCCCAAUGCAGUUCUCAGCAUCAGAAUGCAGCCAAAAACAGAGA------CAGA--GACAG
((((((.......((((.........(((((((((...))))))..)))......((((.((((.......))))))))))))......))))------))..--..... ( -28.72)
>DroSec_CAF1 70192 102 - 1
CGUCUCAAGAAAAUGGGCAGACACCUGCUCCAAUGGA------ACUGGUGCUCAAUGCAUUUUU--GGAGUGGAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCAG
.............(((((((....)))).))).....------.(((((((((..((((((((.--.....))))))))(((..............)))..))))))))) ( -33.04)
>DroSim_CAF1 76054 102 - 1
CGUCUCAAGAAAAUGGGCAGACACCUGCUCCACUGGA------ACUGGUGCUCAAUGCAUUUUU--GGAGUGUAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCAG
.............(((((((....)))).))).....------.(((((((((..((((((...--.......))))))(((..............)))..))))))))) ( -29.84)
>DroEre_CAF1 71040 96 - 1
CGUCUCAAGGAAAUGGGCAGACACCUGCUCCAC------------UGGUGCUCAAUGCAUUUUU--GGAGUGGAAUGCAGUCUAAAACAGAGGACCAACCAGAGUACAAG
.(((((..((...(((((((....)))).))).------------((((.(((..((((((((.--.....))))))))((.....)).))).)))).)).))).))... ( -30.80)
>DroYak_CAF1 77946 96 - 1
CGUCUCAAGGAAAUGGGCAGACACCUGCUCCAC------------UGGUGCUCAAUGCAUUUUU--AGAGUGGAAUGCAGUCAAAAACAGAGGACCAACAAGACUACCAG
.((((........(((((((....)))).))).------------((((.(((..((((((((.--.....))))))))((.....)).))).))))...))))...... ( -29.10)
>consensus
CGUCUCAAGAAAAUGGGCAGACACCUGCUCCACUGG_______ACUGGUGCUCAAUGCAUUUUU__GGAGUGGAAUGCAGUCAAAAACAGAGGACCGACAAGAGUACCAG
.............(((((((....)))).)))............(((((((((..((((((((........))))))))(((..........)))......))))))))) (-20.85 = -23.10 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:37 2006