Locus 1718

Sequence ID	X_DroMel_CAF1
Location	4,785,324 – 4,785,467
Length	143
Max. P	0.995843

overview

Window 0

Location	4,785,324 – 4,785,427
Length	103
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	82.18
Mean single sequence MFE	-34.89
Consensus MFE	-21.76
Energy contribution	-25.64
Covariance contribution	3.88
Combinations/Pair	1.12
Mean z-score	-3.66
Structure conservation index	0.62
SVM decision value	2.62
SVM RNA-class probability	0.995843
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4785324 103 + 22224390
AGUGUGAUUAU--GUAUGCAUGUGUGUCUGCAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCAGCC
(((((((....--...((((((.(((.(((((..............)))))))).))))))(((((((........)))))))..)))))))............. ( -37.44)
>DroSec_CAF1 31227 105 + 1
AGUGUGAUUAUAUGUGUGUGUGUGUGUCUGCAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCAGCC
(((((((((((..(((((((((.(((.(((((..............)))))))).)))))))))((((........)))))))).)))))))............. ( -36.64)
>DroEre_CAF1 13784 80 + 1
AGUGUG--UAU--GUGUG----UGUGUGUGCAUCAAAUC-----------------AUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCCCCC
..((((--...--(((((----.((((((((((......-----------------))))))))((((........))))...)).)))))...))))....... ( -27.30)
>DroYak_CAF1 14960 102 + 1
AGUGUAUGCAU--GUGUGUA-GUGUGUGUGCAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGUCUCACAUUUCCAUAGCCCCCA
.(((...((((--(.((((.-(((((((((........)))))))..)).)))).)))))((((((((........))))))))..)))................ ( -38.20)
>consensus
AGUGUGAUUAU__GUGUGUA_GUGUGUCUGCAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCACCC
(((((((((((..(((((((((.(((.(((((..............)))))))).)))))))))((((........)))))))).)))))))............. (-21.76 = -25.64 +   3.88)

alignment

secondary structure

dotplot

Window 1

Location	4,785,324 – 4,785,427
Length	103
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	82.18
Mean single sequence MFE	-32.88
Consensus MFE	-19.58
Energy contribution	-21.20
Covariance contribution	1.62
Combinations/Pair	1.08
Mean z-score	-2.62
Structure conservation index	0.60
SVM decision value	1.18
SVM RNA-class probability	0.926661
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4785324 103 - 22224390
GGCUGGCUAUGGAAAUGUGAGCCACGCACAAGUACAAGUGCGUGUGCAUGAGCGCUGCAAGUGUGUGAUUUGAUGCAGACACACAUGCAUAC--AUAAUCACACU
((((.((.((....)))).))))((((((........))))))((((....)))).......(((((((((((((((........))))).)--).)))))))). ( -39.40)
>DroSec_CAF1 31227 105 - 1
GGCUGGCUAUGGAAAUGUGAGCCACGCACAAGUACAAGUGCGUGUGCAUGAGCGCUGCAAGUGUGUGAUUUGAUGCAGACACACACACACACAUAUAAUCACACU
((((.((.((....)))).))))((((((........))))))((((....)))).....(((((((.((((...)))))))))))................... ( -34.70)
>DroEre_CAF1 13784 80 - 1
GGGGGGCUAUGGAAAUGUGAGCCACGCACAAGUACAAGUGCGUGUGCAU-----------------GAUUUGAUGCACACACA----CACAC--AUA--CACACU
....(..((((....((((......((((........))))((((((((-----------------......)))))))).))----))..)--)))--..)... ( -24.30)
>DroYak_CAF1 14960 102 - 1
UGGGGGCUAUGGAAAUGUGAGACACGCACAAGUACAAGUGCGUGUGCAUGAGCGCUGCAAGUGUGUGAUUUGAUGCACACACAC-UACACAC--AUGCAUACACU
................(((..((((((((........))))))))(((((.((...))..(((((((........)))))))..-......)--))))...))). ( -33.10)
>consensus
GGCGGGCUAUGGAAAUGUGAGCCACGCACAAGUACAAGUGCGUGUGCAUGAGCGCUGCAAGUGUGUGAUUUGAUGCACACACAC_UACACAC__AUAAUCACACU
...............((((.(((((((((........))))))).)).............(((((((.((((...))))))))))).)))).............. (-19.58 = -21.20 +   1.62)

alignment

secondary structure

dotplot

Window 2

Location	4,785,352 – 4,785,467
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	81.61
Mean single sequence MFE	-22.34
Consensus MFE	-16.15
Energy contribution	-16.15
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.72
SVM decision value	1.01
SVM RNA-class probability	0.899691
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4785352 115 + 22224390
CAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCAGCCGCUUCCCCCUCCACGAUCAGUGUUGCUCUUCACCUGCAGC
...............((((((.......((((((((((........))))((((((..(.........)..)))))).................))).))).......)))))). ( -27.24)
>DroSec_CAF1 31257 115 + 1
CAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCAGCCGCUUCCCCCUCCACGAUCAUUGUUGCUCAUCACCUGCAGC
...............((((((.......(((.((((((........))))((((((..(.........)..))))))...................))))).......)))))). ( -23.64)
>DroEre_CAF1 13806 93 + 1
CAUCAAAUC-----------------AUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCCCCCGCU-CCCUCUCC----UUGUUGUUUCUCUUCACCUGCAGC
.........-----------------..((.(((((((........)))))))))............(((.....)))-........----..(((((............))))) ( -17.30)
>DroYak_CAF1 14987 107 + 1
CAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGUCUCACAUUUCCAUAGCCCCCAGCC-CCCUCUCU----UUGUU---ACUUUUCACCUGCAGC
...............((((((.((....))((((((((........))))))))........................-........----.....---.........)))))). ( -21.20)
>consensus
CAUCAAAUCACACACUUGCAGCGCUCAUGCACACGCACUUGUACUUGUGCGUGGCUCACAUUUCCAUAGCCACCCGCU_CCCCCUCC____UCAUUGUUGCUCUUCACCUGCAGC
...........................(((((((((((........)))))))...............((.....))................................)))).. (-16.15 = -16.15 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:25 2006