Locus 6835

Sequence ID	X_DroMel_CAF1
Location	17,004,594 – 17,004,737
Length	143
Max. P	0.994680

overview

Window 3

Location	17,004,594 – 17,004,705
Length	111
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	64.52
Mean single sequence MFE	-35.92
Consensus MFE	-13.98
Energy contribution	-12.66
Covariance contribution	-1.32
Combinations/Pair	1.50
Mean z-score	-2.85
Structure conservation index	0.39
SVM decision value	2.50
SVM RNA-class probability	0.994680
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17004594 111 + 22224390
UUUACUACUAUUUCUGUUUAUUGCCAUUAAGGUACCACU-GUACCUUAAGCGGGGGCGAUG-CUCUUUGCCCAGCUAGAGAGGGAGAGAGAGAGAGCAACGCCGCUCUUU-UUU
....((.((.((((((((.....((.(((((((((....-)))))))))..))((((((..-....))))))))).))))).)))).((((((((((......)))))))-))) ( -39.70)
>DroSec_CAF1 9550 109 + 1
AUUGCUUUUAUAUCUGGUUACUGUUAUUAAGGUACCACU-GUACUUUAAGCGGGGGCGAUG-CUCUUUGCCCAGCUAGCGAGGGCGAAA--GAGAGCAACGCCGCUCUUU-UUU
...((((((....((((((.((((..(((((((((....-)))))))))))))((((((..-....)))))))))))).))))))((((--((((((......)))))))-))) ( -41.50)
>DroSim_CAF1 4609 110 + 1
AUUGCUGGAAUGCCUGGAAAUUGA-AUAAAAGGACCACCCUUAUUUUUUGGGGGGGCCCUAACUUUCUUCCGGGGGGCCGAGGNNNNNN--NNNNNNNNNNNNNNNNNNN-NNN
....((.(..(.(((((((...((-(....(((.((.((((((.....)))))))).)))....)))))))))).)..).)).......--...................-... ( -28.50)
>DroEre_CAF1 9342 102 + 1
AUUGCUAUUAUUUCUGGUUAGAGAUGCAAAGGUAUCACU-GUACUUUUAGCGGGGGCGAUG-CUCUUUGCGCAGUGAGAGAGG----------GAGCAACGCCGCUCUUUUUUU
(((((....((((((....))))))(((((((((((.((-((.......))))....))))-).))))))))))).(((((((----------((((......))))))))))) ( -34.00)
>DroYak_CAF1 10230 99 + 1
AUUACUAUUAUUUCUGCUUAAAGAUGUUGAGGUACCACU-GUACUUUGAGCGGGGGCGAUG-CUCUUUGCCCAGUGAGAGA------------GAGCAACACCGCUCUUU-UUC
...(((.......((((((((((((..((......))..-)).))))))))))((((((..-....)))))))))((((((------------((((......)))))))-))) ( -35.90)
>consensus
AUUGCUAUUAUUUCUGGUUAUUGAUAUUAAGGUACCACU_GUACUUUAAGCGGGGGCGAUG_CUCUUUGCCCAGCGAGAGAGG__________GAGCAACGCCGCUCUUU_UUU
.............(((...........((((((((.....)))))))).(((((((.......))))))).)))...................((((......))))....... (-13.98 = -12.66 +  -1.32)

alignment

secondary structure

dotplot

Window 4

Location	17,004,633 – 17,004,737
Length	104
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	82.54
Mean single sequence MFE	-37.88
Consensus MFE	-21.88
Energy contribution	-22.88
Covariance contribution	1.00
Combinations/Pair	1.09
Mean z-score	-2.85
Structure conservation index	0.58
SVM decision value	1.23
SVM RNA-class probability	0.933180
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17004633 104 + 22224390
GUACCUUAAGCGGGGGCGAUGCUCUUUGCCCAGCUAGAGAGGGAGAGAGAGAGAGCAACGCCGCUCUUU-UUUGCAUGCCUGUCGCACAUUUUGCUCUCGUAUUU
((((....(((..((((((......)))))).))).(((((.((((((((((((((......)))))))-)))...(((.....)))..)))).))))))))).. ( -38.90)
>DroSec_CAF1 9589 102 + 1
GUACUUUAAGCGGGGGCGAUGCUCUUUGCCCAGCUAGCGAGGGCGAAA--GAGAGCAACGCCGCUCUUU-UUUGCAUGCCUGUCGCACAUUUUGCUCUCUUAUUU
........(((..((((((......)))))).)))(((((((((((((--((((((......)))))))-))))).(((.....)))..)))))))......... ( -37.80)
>DroEre_CAF1 9381 94 + 1
GUACUUUUAGCGGGGGCGAUGCUCUUUGCGCAGUGAGAGAGG----------GAGCAACGCCGCUCUUUUUUUGCAUGGCUGCCGCUCAUUUGACUCUCUCAUU-
((......(((((.(((.((((.....))((((.(((((((.----------(.((...))).))))))).)))))).))).)))))......)).........- ( -32.70)
>DroYak_CAF1 10269 92 + 1
GUACUUUGAGCGGGGGCGAUGCUCUUUGCCCAGUGAGAGA------------GAGCAACACCGCUCUUU-UUCGCAUGCCUGCCGCUCGUUUUGCUCUCUCAUUU
(((...(((((((((((((......)))))).((((((((------------((((......)))))))-))))).......)))))))...))).......... ( -42.10)
>consensus
GUACUUUAAGCGGGGGCGAUGCUCUUUGCCCAGCGAGAGAGG__________GAGCAACGCCGCUCUUU_UUUGCAUGCCUGCCGCACAUUUUGCUCUCUCAUUU
.........((..((((((......)))))).))(((((((...........((((......)))).......(((....)))...........))))))).... (-21.88 = -22.88 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:07 2006