Locus 4402

Sequence ID	2L_DroMel_CAF1
Location	12,673,194 – 12,673,300
Length	106
Max. P	0.947766

overview

Window 6

Location	12,673,194 – 12,673,300
Length	106
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.49
Mean single sequence MFE	-22.33
Consensus MFE	-16.31
Energy contribution	-15.23
Covariance contribution	-1.08
Combinations/Pair	1.38
Mean z-score	-2.31
Structure conservation index	0.73
SVM decision value	1.38
SVM RNA-class probability	0.947766
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12673194 106 + 22407834
ACCAAAACAACCA-AAAUCAC---------CAG---AUUCCCCAGAAUCACACCGGUGACCACUCCUUCGUCCGGCACUUUCACGAACGAGAUCGCCUCAUUCGGGAGCACCAGCUCAA
.............-......(---------(.(---((((....))))).....(((((...(((.(((((...........))))).))).)))))......))((((....)))).. ( -24.60)
>DroSec_CAF1 53753 106 + 1
ACCAAAACAACCA-AAACAAC---------CAG---AAUCACCAGAAUCACACCGGUGACCACUCCUUCGUCCGGCACUUUCACGAACGAGAUCGCCUCAUUCGGGAGCACCAGCUCAA
.............-......(---------(.(---(.((....)).)).....(((((...(((.(((((...........))))).))).)))))......))((((....)))).. ( -21.40)
>DroSim_CAF1 55333 97 + 1
ACCAAAA----------CAAC---------CAG---AAUCACCAGAAUCACACCGGUGACCACUCCUUCGUCCGGCACUUUCACGAACGAGAUCGCCUCAUUCGGGAGCACCAGCUCAA
.......----------...(---------(.(---(.((....)).)).....(((((...(((.(((((...........))))).))).)))))......))((((....)))).. ( -21.40)
>DroEre_CAF1 55527 106 + 1
ACCAAAAUCACCA-GAAUCAC---------CAA---AAUCACCAGAACCACACCGGUGACCACUCCUUCGUCCGGCACUUUCACGAACGAGAUCGCCUCAUUCGGGAGCACCAGCUCAA
..........((.-((((...---------...---..(((((...........)))))..............(((..((((......))))..)))..))))))((((....)))).. ( -20.60)
>DroWil_CAF1 6754 117 + 1
CCCAACAUCAACUCCAACUAC-GGCCCCUCCAGCAGCCGCACCAGC-CCUUCCUGGUGAACAUUUGUUCGUUCAACACUUUCACGAAAGGGAUCGUCUCAUACGCGAACAUCAACUCAA
....................(-(((..(....)..))))((((((.-.....))))))......(((((((.....((..((.(....).))..)).......)))))))......... ( -24.00)
>DroYak_CAF1 56273 115 + 1
ACCAAAAUCACCA-GAAUCACCAGCACAACCAA---AAUCACCAAAAUCACACCGGUGACCACUCCUUCGUCCGGCACUUUCACGAACGAGAUCGCCUCAUUCGGGAGCACCAGCUCAA
..........((.-((((.....((........---..(((((...........)))))...(((.(((((...........))))).)))...))...))))))((((....)))).. ( -22.00)
>consensus
ACCAAAAUCACCA_AAACCAC_________CAG___AAUCACCAGAAUCACACCGGUGACCACUCCUUCGUCCGGCACUUUCACGAACGAGAUCGCCUCAUUCGGGAGCACCAGCUCAA
......................................................((((....(((((......(((..((((......))))..)))......)))))))))....... (-16.31 = -15.23 +  -1.08)

alignment

secondary structure

dotplot

Window 7

Location	12,673,194 – 12,673,300
Length	106
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.49
Mean single sequence MFE	-35.63
Consensus MFE	-26.31
Energy contribution	-25.98
Covariance contribution	-0.33
Combinations/Pair	1.29
Mean z-score	-1.43
Structure conservation index	0.74
SVM decision value	0.56
SVM RNA-class probability	0.782460
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12673194 106 - 22407834
UUGAGCUGGUGCUCCCGAAUGAGGCGAUCUCGUUCGUGAAAGUGCCGGACGAAGGAGUGGUCACCGGUGUGAUUCUGGGGAAU---CUG---------GUGAUUU-UGGUUGUUUUGGU
.....((((..(((.((((((((.....)))))))).))..)..)))).(((((.((.((((((((....(((((....))))---)))---------)))))).-...)).))))).. ( -35.40)
>DroSec_CAF1 53753 106 - 1
UUGAGCUGGUGCUCCCGAAUGAGGCGAUCUCGUUCGUGAAAGUGCCGGACGAAGGAGUGGUCACCGGUGUGAUUCUGGUGAUU---CUG---------GUUGUUU-UGGUUGUUUUGGU
..((((....)))).((((((((.....)))))))).((((..(((((((((.(((...((((((((.......)))))))))---)).---------.))).))-))))..))))... ( -34.90)
>DroSim_CAF1 55333 97 - 1
UUGAGCUGGUGCUCCCGAAUGAGGCGAUCUCGUUCGUGAAAGUGCCGGACGAAGGAGUGGUCACCGGUGUGAUUCUGGUGAUU---CUG---------GUUG----------UUUUGGU
.....((((..(((.((((((((.....)))))))).))..)..))))((((.(((...((((((((.......)))))))))---)).---------.)))----------)...... ( -34.00)
>DroEre_CAF1 55527 106 - 1
UUGAGCUGGUGCUCCCGAAUGAGGCGAUCUCGUUCGUGAAAGUGCCGGACGAAGGAGUGGUCACCGGUGUGGUUCUGGUGAUU---UUG---------GUGAUUC-UGGUGAUUUUGGU
.....((((..(((.((((((((.....)))))))).))..)..)))).((..((((((((((((((.......)))))))))---...---------...))))-)..))........ ( -34.80)
>DroWil_CAF1 6754 117 - 1
UUGAGUUGAUGUUCGCGUAUGAGACGAUCCCUUUCGUGAAAGUGUUGAACGAACAAAUGUUCACCAGGAAGG-GCUGGUGCGGCUGCUGGAGGGGCC-GUAGUUGGAGUUGAUGUUGGG
.....(..(((((.((............((((((((((((..((((.....))))....)))))..))))))-)(..((((((((.(....).))))-))).)..).)).)))))..). ( -35.30)
>DroYak_CAF1 56273 115 - 1
UUGAGCUGGUGCUCCCGAAUGAGGCGAUCUCGUUCGUGAAAGUGCCGGACGAAGGAGUGGUCACCGGUGUGAUUUUGGUGAUU---UUGGUUGUGCUGGUGAUUC-UGGUGAUUUUGGU
..((((....)))).((((((((.....)))))))).((((..(((((((....)....((((((((((..(((.........---..)))..))))))))))))-))))..))))... ( -39.40)
>consensus
UUGAGCUGGUGCUCCCGAAUGAGGCGAUCUCGUUCGUGAAAGUGCCGGACGAAGGAGUGGUCACCGGUGUGAUUCUGGUGAUU___CUG_________GUGAUUC_UGGUGAUUUUGGU
....(((((..(((.((((((((.....)))))))).))..)..)))).).........((((((((.......))))))))..................................... (-26.31 = -25.98 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:01 2006