Locus 340

Sequence ID	2L_DroMel_CAF1
Location	1,026,353 – 1,026,461
Length	108
Max. P	0.938438

overview

Window 0

Location	1,026,353 – 1,026,461
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	71.16
Mean single sequence MFE	-43.80
Consensus MFE	-21.54
Energy contribution	-22.74
Covariance contribution	1.20
Combinations/Pair	1.22
Mean z-score	-2.00
Structure conservation index	0.49
SVM decision value	1.29
SVM RNA-class probability	0.938438
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1026353 108 + 22407834
------------GGACUUGAGAGGAGCCACAAAGGCCACGAGCCGAGAUUGUUCAGGCUCGACCUUGGAGAUUGGUUUUUCGCAGAGACCUCCGUUGGUAGUCUUGUGAGUAUCUGAUGG
------------((.(((..(((((((((..((((...((((((..((....)).)))))).))))......)))))))))...))).)).((((..(((.((....)).)).)..)))) ( -37.70)
>DroSec_CAF1 8010 120 + 1
CGGGGAGGCAGAUGAUAUGGGAGGAGCCACAAAGGCCACGAGCCGAGAUUGUUCAGGCUCGUCUUUGGAGAUUUCUUUUUCCCAGGAAAGCCCAGUGGCACUCUUGUGAGUAUCUGAUGG
........((((((.((..((((..(((((...(((..((((((..((....)).))))))((((.(((((......))))).))))..)))..))))).))))..))..)))))).... ( -47.40)
>DroSim_CAF1 109 120 + 1
CGGGAGAGCAGAGGAUUUGGGAGGCACCACAAAGGCCACGAGCCGAGAUUGUUCAGGCUCGUCUUUGGAGAUUUGUUUUUCCAAGGGAAGCCCAGUGGCACUCUUGUGAGUAUCUGAUGG
........((((..(((((((((...((((...(((.(((((((..((....)).)))))))(((((((((......)))))))))...)))..))))..)))))..)))).)))).... ( -42.80)
>DroEre_CAF1 6528 102 + 1
G------GCAGGGGAUUUGGGUGGAGGCACAAAGGCCACGAGCCGCGAUAGUUCAGGCUCGUCUCUGGAGAUUUGCGUUUUCC---GAUUCUUAGG---A--CCCU----CAUCUCCUGG
.------.((((((((..((((((((((......)))(((((((..((....)).))))))).)))(((((.......)))))---..........---)--))).----.)))))))). ( -42.50)
>DroYak_CAF1 7883 111 + 1
C------CCAGGGGAUUGGGGAGGAGGCACAAAAGCCACGAGCCGCGAUGGUUCUGGCUCGUCUUUGGAGAUGGGUUCUUUCG---AAUUCUUGGUGGCACUCCCUUGGGCAUCUCCUGG
.------(((((((((.((((((..(((......)))....(((((.(.(((((.(((((((((....))))))))).....)---))))..).))))).)))))).....))))))))) ( -48.60)
>consensus
C______GCAGAGGAUUUGGGAGGAGCCACAAAGGCCACGAGCCGAGAUUGUUCAGGCUCGUCUUUGGAGAUUUGUUUUUCCCAG_GAAGCCCAGUGGCACUCUUGUGAGUAUCUGAUGG
..................(((((...((((.((((..(((((((..((....)).)))))))))))(((((......)))))............))))..)))))............... (-21.54 = -22.74 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	1,026,353 – 1,026,461
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.16
Mean single sequence MFE	-34.54
Consensus MFE	-13.56
Energy contribution	-13.28
Covariance contribution	-0.28
Combinations/Pair	1.21
Mean z-score	-2.00
Structure conservation index	0.39
SVM decision value	1.09
SVM RNA-class probability	0.913856
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1026353 108 - 22407834
CCAUCAGAUACUCACAAGACUACCAACGGAGGUCUCUGCGAAAAACCAAUCUCCAAGGUCGAGCCUGAACAAUCUCGGCUCGUGGCCUUUGUGGCUCCUCUCAAGUCC------------
.................((((......((((((...............)))))).(((.((((((.((......)))))))).((((.....)))))))....)))).------------ ( -26.36)
>DroSec_CAF1 8010 120 - 1
CCAUCAGAUACUCACAAGAGUGCCACUGGGCUUUCCUGGGAAAAAGAAAUCUCCAAAGACGAGCCUGAACAAUCUCGGCUCGUGGCCUUUGUGGCUCCUCCCAUAUCAUCUGCCUCCCCG
....(((((((((....))))(((((.(((((....(((((........)).)))...(((((((.((......))))))))))))))..)))))............)))))........ ( -38.30)
>DroSim_CAF1 109 120 - 1
CCAUCAGAUACUCACAAGAGUGCCACUGGGCUUCCCUUGGAAAAACAAAUCUCCAAAGACGAGCCUGAACAAUCUCGGCUCGUGGCCUUUGUGGUGCCUCCCAAAUCCUCUGCUCUCCCG
....((((........((.(..((((.(((((....(((((..........)))))..(((((((.((......))))))))))))))..))))..))).........))))........ ( -35.93)
>DroEre_CAF1 6528 102 - 1
CCAGGAGAUG----AGGG--U---CCUAAGAAUC---GGAAAACGCAAAUCUCCAGAGACGAGCCUGAACUAUCGCGGCUCGUGGCCUUUGUGCCUCCACCCAAAUCCCCUGC------C
.((((.(((.----.(((--(---..........---(((...((((((...((....((((((((((....))).)))))))))..))))))..)))))))..))).)))).------. ( -33.10)
>DroYak_CAF1 7883 111 - 1
CCAGGAGAUGCCCAAGGGAGUGCCACCAAGAAUU---CGAAAGAACCCAUCUCCAAAGACGAGCCAGAACCAUCGCGGCUCGUGGCUUUUGUGCCUCCUCCCCAAUCCCCUGG------G
(((((.(((......(((((............((---(....))).............(((((((.((....))..)))))))(((......)))..)))))..))).)))))------. ( -39.00)
>consensus
CCAUCAGAUACUCACAAGAGUGCCACUGGGAAUC_CUGGGAAAAACAAAUCUCCAAAGACGAGCCUGAACAAUCUCGGCUCGUGGCCUUUGUGGCUCCUCCCAAAUCCCCUGC______G
.....................................................((((((((((((.((....))..)))))))...)))))............................. (-13.56 = -13.28 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:27 2006