Locus 2042

Sequence ID	X_DroMel_CAF1
Location	5,609,216 – 5,609,334
Length	118
Max. P	0.905455

overview

Window 2

Location	5,609,216 – 5,609,334
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.93
Mean single sequence MFE	-25.43
Consensus MFE	-19.93
Energy contribution	-20.37
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-2.07
Structure conservation index	0.78
SVM decision value	1.04
SVM RNA-class probability	0.905455
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5609216 118 + 22224390
GUGGUCCAGUUUUUUUUUUUGGCCACGCGCAGCGAUU-UUAUCUUAUCCGCUUUUCAUUCUCGCC-CGGAUAUAUAUUCCGCAUUAUUACCUGCUCUUCAGCUGAUCGUAUUUACCUUUC
((((.((((.........))))))))(((((((((..-.(((..((((((...............-)))))).))).)).(((........)))......))))..)))........... ( -23.46)
>DroSec_CAF1 10901 108 + 1
GUGGCCCAGUUUUU--UUCUGGCCACGCGCAGCGAUU-UUAUCUUAUCCGCUUGUCUUUCUCGCC-CGGAUAUAUAUCCCGCAUUAUCACCUG--------CUGAUCGUAUUUACCUUUC
((((((.((.....--..)))))))).....((((((-......((((((..((.......))..-))))))........(((........))--------).))))))........... ( -25.30)
>DroSim_CAF1 12619 108 + 1
GUGGCCCAGUUUUU--UUCUGGCCACGCGCAGCGAUU-UUAUCUUAUCCGCUUGUCUUUCUCGCC-CGGAUAUAUAUCCCGCAUUAUCACCUG--------CUGAUCGUAUUUACCUUUC
((((((.((.....--..)))))))).....((((((-......((((((..((.......))..-))))))........(((........))--------).))))))........... ( -25.30)
>DroEre_CAF1 11337 118 + 1
GUGGCCCAGAUUUU--UCCUGGCCACGCGCAGCGAUUUUUAUCUUAUCCGCUCUUGUUUCACGCCCGGGAUAUAUAUCCAGCAUUAUCACCUGCCGUUCAGCUGAUCGUAUUUACCUUUC
((((((..((....--))..))))))((((((((((....)))...................(..((((((....)))).(((........)))))..).))))..)))........... ( -26.40)
>DroYak_CAF1 11474 103 + 1
GUGGCCCAGAUUUU--UCCUGGCCACGCGCAGCGAUU-UUAUCUUAUCCGCC--------------CGGAUAUAUAUCCCGCAUUAUCACCUGCUGUUCAGCUGAUCGUAUUUACCUUUC
((((((..((....--))..))))))(((((((....-......(((((...--------------.)))))........(((........)))......))))..)))........... ( -26.70)
>consensus
GUGGCCCAGUUUUU__UUCUGGCCACGCGCAGCGAUU_UUAUCUUAUCCGCUUGUCUUUCUCGCC_CGGAUAUAUAUCCCGCAUUAUCACCUGC__UUCAGCUGAUCGUAUUUACCUUUC
((((.((((.........))))))))((((((((((....))).((((((................))))))............................))))..)))........... (-19.93 = -20.37 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	5,609,216 – 5,609,334
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.93
Mean single sequence MFE	-27.43
Consensus MFE	-20.76
Energy contribution	-22.56
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.76
SVM decision value	0.01
SVM RNA-class probability	0.536285
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5609216 118 - 22224390
GAAAGGUAAAUACGAUCAGCUGAAGAGCAGGUAAUAAUGCGGAAUAUAUAUCCG-GGCGAGAAUGAAAAGCGGAUAAGAUAA-AAUCGCUGCGCGUGGCCAAAAAAAAAAACUGGACCAC
....(((...((((..((((.((...(((........)))........((((((-...............))))))......-..))))))..)))).(((...........)))))).. ( -22.36)
>DroSec_CAF1 10901 108 - 1
GAAAGGUAAAUACGAUCAG--------CAGGUGAUAAUGCGGGAUAUAUAUCCG-GGCGAGAAAGACAAGCGGAUAAGAUAA-AAUCGCUGCGCGUGGCCAGAA--AAAAACUGGGCCAC
....(((...((((....(--------(((.((((....(.((((....)))).-)((...........))...........-.)))))))).)))).((((..--.....))))))).. ( -25.40)
>DroSim_CAF1 12619 108 - 1
GAAAGGUAAAUACGAUCAG--------CAGGUGAUAAUGCGGGAUAUAUAUCCG-GGCGAGAAAGACAAGCGGAUAAGAUAA-AAUCGCUGCGCGUGGCCAGAA--AAAAACUGGGCCAC
....(((...((((....(--------(((.((((....(.((((....)))).-)((...........))...........-.)))))))).)))).((((..--.....))))))).. ( -25.40)
>DroEre_CAF1 11337 118 - 1
GAAAGGUAAAUACGAUCAGCUGAACGGCAGGUGAUAAUGCUGGAUAUAUAUCCCGGGCGUGAAACAAGAGCGGAUAAGAUAAAAAUCGCUGCGCGUGGCCAGGA--AAAAUCUGGGCCAC
..............((((.(((.....))).)))).(((((((((....))))..))))).......(.((((....(((....))).)))).)((((((.(((--....))).)))))) ( -33.20)
>DroYak_CAF1 11474 103 - 1
GAAAGGUAAAUACGAUCAGCUGAACAGCAGGUGAUAAUGCGGGAUAUAUAUCCG--------------GGCGGAUAAGAUAA-AAUCGCUGCGCGUGGCCAGGA--AAAAUCUGGGCCAC
..............((((.(((.....))).))))...(((((((....)))).--------------(((((.........-..))))).)))((((((.(((--....))).)))))) ( -30.80)
>consensus
GAAAGGUAAAUACGAUCAGCUGAA__GCAGGUGAUAAUGCGGGAUAUAUAUCCG_GGCGAGAAAGAAAAGCGGAUAAGAUAA_AAUCGCUGCGCGUGGCCAGAA__AAAAACUGGGCCAC
..............((((.(((.....))).))))...((.((((....))))................((((....(((....))).))))))((((((((.........)))).)))) (-20.76 = -22.56 +   1.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:51 2006