Locus 440

Sequence ID	3R_DroMel_CAF1
Location	1,666,205 – 1,666,321
Length	116
Max. P	0.659080

overview

Window 6

Location	1,666,205 – 1,666,321
Length	116
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	80.70
Mean single sequence MFE	-33.38
Consensus MFE	-19.75
Energy contribution	-22.81
Covariance contribution	3.06
Combinations/Pair	1.15
Mean z-score	-1.92
Structure conservation index	0.59
SVM decision value	0.26
SVM RNA-class probability	0.659080
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1666205 116 + 27905053
CGACUUCUGGCCAGCGAUUCCCAUGUAUUUCAUAUCGCAUUGCCGGUUCCGGAUGGUGUUAACCAGAAAUCGACCAUGUCGAUAUAAGGCACUUAA-GUGCCUACACCGGAGACAUU
......(((((..(((((....(((.....))))))))...)))))((((((.((((....))))...((((((...))))))...((((((....-))))))...))))))..... ( -40.50)
>DroSec_CAF1 5139 114 + 1
CGACUUCUGGCCAGCGAUUCCCAUACAUUUCAUAUCGCAUUGCCGGUUCCGGAUGGUGUUAACCAGAA--UAACCACGUCGAUAUAAGGCACUUAA-GUGCCUACACCGGAGACAUU
......(((((..(((((...............)))))...)))))((((((.((((....))))...--................((((((....-))))))...))))))..... ( -34.96)
>DroSim_CAF1 5148 114 + 1
CGACUUCUGGCCAGUGAUUCCCAUACAUUUCAUAUCGCAUUGCCGGUUCCGGAUGGUGUUAACCAGAA--UAACCACGUCGAUAUAAGGCACUUAA-GUGCCUACACCGGAGACAUU
......(((((..(((((...............)))))...)))))((((((.((((....))))...--................((((((....-))))))...))))))..... ( -33.06)
>DroEre_CAF1 5418 113 + 1
UGACUUCUGGCCUGCGAUUCCCAUGUAUUUC-CAUCGCAGUGCCGGUUCCGGAUGGUGUUAACCAGAA--UAGCCACGUCGAUAUAAGGCACUUAA-GUGCCUACACCGGAGACAUG
......((((((((((((.............-.))))))).)))))((((((.((((....))))...--................((((((....-))))))...))))))..... ( -40.34)
>DroYak_CAF1 5167 100 + 1
UGA--------------UUUCCAUGUAUUUCAUAUUGCAGUGCCGGUUCCGGAUGGUGUUAGCCAGAA--UAACCACGUCGAUAUAAGGCACUUAA-GUGAAUACACCGGAGACAUU
((.--------------(((((.((((((.(((.(((.(((((((....).((((..((((.......--))))..)))).......)))))))))-)))))))))..))))))).. ( -27.40)
>DroAna_CAF1 3891 110 + 1
CGAGCUUGUAAGGGGAAUUCCCAUGUACAUCAUAU-----GGCCAGUUCCGGAUGGCGUUAACCAGAA--CCCCCUGUCCAAUAAAAAACAUUUAAUGUGCGUACACCGGAGACAUU
......(((...(((....)))((((((((...((-----(((((........))))......(((..--....)))............)))...)))))))))))..(....)... ( -24.00)
>consensus
CGACUUCUGGCCAGCGAUUCCCAUGUAUUUCAUAUCGCAUUGCCGGUUCCGGAUGGUGUUAACCAGAA__UAACCACGUCGAUAUAAGGCACUUAA_GUGCCUACACCGGAGACAUU
......(((((..(((((...............)))))...)))))((((((.((((....)))).....................((((((.....))))))...))))))..... (-19.75 = -22.81 +   3.06)

alignment

secondary structure

dotplot

Window 7

Location	1,666,205 – 1,666,321
Length	116
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	80.70
Mean single sequence MFE	-34.35
Consensus MFE	-22.71
Energy contribution	-23.80
Covariance contribution	1.09
Combinations/Pair	1.20
Mean z-score	-1.58
Structure conservation index	0.66
SVM decision value	0.26
SVM RNA-class probability	0.658431
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1666205 116 - 27905053
AAUGUCUCCGGUGUAGGCAC-UUAAGUGCCUUAUAUCGACAUGGUCGAUUUCUGGUUAACACCAUCCGGAACCGGCAAUGCGAUAUGAAAUACAUGGGAAUCGCUGGCCAGAAGUCG
.(((((...(((((((((((-....))))).)))))))))))...(((((((((((((.......(((....)))....((((((((.....)))....)))))))))))))))))) ( -42.70)
>DroSec_CAF1 5139 114 - 1
AAUGUCUCCGGUGUAGGCAC-UUAAGUGCCUUAUAUCGACGUGGUUA--UUCUGGUUAACACCAUCCGGAACCGGCAAUGCGAUAUGAAAUGUAUGGGAAUCGCUGGCCAGAAGUCG
.........(((((((((((-....))))).))))))(((..(((..--.(((((..........))))))))(((...(((((...............)))))..)))....))). ( -36.16)
>DroSim_CAF1 5148 114 - 1
AAUGUCUCCGGUGUAGGCAC-UUAAGUGCCUUAUAUCGACGUGGUUA--UUCUGGUUAACACCAUCCGGAACCGGCAAUGCGAUAUGAAAUGUAUGGGAAUCACUGGCCAGAAGUCG
....(((((((((..(((((-....)))))((((((((.(((.(((.--((((((..........))))))..))).))))))))))).............))))))..)))..... ( -34.60)
>DroEre_CAF1 5418 113 - 1
CAUGUCUCCGGUGUAGGCAC-UUAAGUGCCUUAUAUCGACGUGGCUA--UUCUGGUUAACACCAUCCGGAACCGGCACUGCGAUG-GAAAUACAUGGGAAUCGCAGGCCAGAAGUCA
((((((...(((((((((((-....))))).))))))))))))....--(((((((.........(((....)))..(((((((.-.............)))))))))))))).... ( -42.24)
>DroYak_CAF1 5167 100 - 1
AAUGUCUCCGGUGUAUUCAC-UUAAGUGCCUUAUAUCGACGUGGUUA--UUCUGGCUAACACCAUCCGGAACCGGCACUGCAAUAUGAAAUACAUGGAAA--------------UCA
......((((.((((((((.-...((((((..((......))(((..--.(((((..........))))))))))))))......)).))))))))))..--------------... ( -22.50)
>DroAna_CAF1 3891 110 - 1
AAUGUCUCCGGUGUACGCACAUUAAAUGUUUUUUAUUGGACAGGGGG--UUCUGGUUAACGCCAUCCGGAACUGGCC-----AUAUGAUGUACAUGGGAAUUCCCCUUACAAGCUCG
......(((.(((((((((.......(((((......)))))((.((--((((((..........))))))))..))-----...)).))))))).))).................. ( -27.90)
>consensus
AAUGUCUCCGGUGUAGGCAC_UUAAGUGCCUUAUAUCGACGUGGUUA__UUCUGGUUAACACCAUCCGGAACCGGCAAUGCGAUAUGAAAUACAUGGGAAUCGCUGGCCAGAAGUCG
......(((.((((((((((.....)))))((((((((.....(((...((((((..........))))))..)))....))))))))..))))).))).................. (-22.71 = -23.80 +   1.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:16 2006