Locus 3296

Sequence ID X_DroMel_CAF1
Location 8,778,359 – 8,778,463
Length 104
Max. P 0.998840
window5395 window5396

overview

Window 5

Location 8,778,359 – 8,778,463
Length 104
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 75.76
Mean single sequence MFE -29.77
Consensus MFE -18.08
Energy contribution -18.63
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.58
Structure conservation index 0.61
SVM decision value 0.06
SVM RNA-class probability 0.564925
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8778359 104 + 22224390
UAGGGCAAGCCC-----UAUUUCUAUUUUGUAUUUUCUUGGCUCUAUUUGCUUGGCCAGCACUGUGCGCU-GCGUCCAUGGUCCAGUUGCAGACCAUGUGCUCGUCCUGC---
((((((.(((..-----............((((....((((((..........))))))....))))...-.....(((((((........))))))).))).)))))).--- ( -29.10)
>DroSec_CAF1 26926 109 + 1
UGGGGCCAACCAUUACUUUUUUUUUUUUUGUAUUUUCUUGGCUCUAUUUGCAUGCCCAGCACUGUGCGCU-GCGUCCAUGGUCCAGUUGCAGACCAUGUGCUCGUGCUCC---
(((((((((....(((.............))).....)))))))))...(((((..((((.......)))-).(..(((((((........)))))))..).)))))...--- ( -32.92)
>DroYak_CAF1 23593 93 + 1
UAAGUGAAA--------------------CUGUUUUCUUGGUUCUAUUUGCUUGGCCAGCACUGUGCGCUGGCGUCCAUGGUCCAGUUGCAGACCAUGUUCUCGUGCUCCUGC
.(((((.((--------------------(((......))))).)))))((.((((((((.......))))))(..(((((((........)))))))..).)).))...... ( -27.30)
>consensus
UAGGGCAAACC______U_UUU_U_UUUUGUAUUUUCUUGGCUCUAUUUGCUUGGCCAGCACUGUGCGCU_GCGUCCAUGGUCCAGUUGCAGACCAUGUGCUCGUGCUCC___
......................................(((((..........)))))((((...((....))(..(((((((........)))))))..)..))))...... (-18.08 = -18.63 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 8,778,359 – 8,778,463
Length 104
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 75.76
Mean single sequence MFE -31.83
Consensus MFE -19.09
Energy contribution -19.53
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -2.91
Structure conservation index 0.60
SVM decision value 3.25
SVM RNA-class probability 0.998840
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8778359 104 - 22224390
---GCAGGACGAGCACAUGGUCUGCAACUGGACCAUGGACGC-AGCGCACAGUGCUGGCCAAGCAAAUAGAGCCAAGAAAAUACAAAAUAGAAAUA-----GGGCUUGCCCUA
---..(((.(((((.((((((((......))))))))....(-(((((...)))))).((..((.......))...............((....))-----))))))).))). ( -31.60)
>DroSec_CAF1 26926 109 - 1
---GGAGCACGAGCACAUGGUCUGCAACUGGACCAUGGACGC-AGCGCACAGUGCUGGGCAUGCAAAUAGAGCCAAGAAAAUACAAAAAAAAAAAAAGUAAUGGUUGGCCCCA
---((.((.(((.((((((((((......)))))))).((.(-(((((...))))))(((...........))).......................))..)).))))).)). ( -32.20)
>DroYak_CAF1 23593 93 - 1
GCAGGAGCACGAGAACAUGGUCUGCAACUGGACCAUGGACGCCAGCGCACAGUGCUGGCCAAGCAAAUAGAACCAAGAAAACAG--------------------UUUCACUUA
...(((((....(..((((((((......))))))))..)((((((((...))))))))........................)--------------------))))..... ( -31.70)
>consensus
___GGAGCACGAGCACAUGGUCUGCAACUGGACCAUGGACGC_AGCGCACAGUGCUGGCCAAGCAAAUAGAGCCAAGAAAAUACAAAA_A_AAA_A______GGUUUGCCCUA
......((.(.((((((((((((......)))))))(..((....))..).))))).)))..................................................... (-19.09 = -19.53 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:49 2006