Locus 708

Sequence ID	3L_DroMel_CAF1
Location	2,123,578 – 2,123,698
Length	120
Max. P	0.804789

overview

Window 3

Location	2,123,578 – 2,123,698
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.24
Mean single sequence MFE	-24.78
Consensus MFE	-18.93
Energy contribution	-19.75
Covariance contribution	0.81
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.76
SVM decision value	0.36
SVM RNA-class probability	0.706576
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2123578 120 + 23771897
UCCAGACCCACCUGAAUCGCACAACAAACGUAAAGAAACUCUUUAUAAAGCAUUUCGGUCUAUAAGUUUUUUGUCGAACCAUGUUUGUAUAAAGAUUUUCGAUUCGUAGGUAGUCUGAUU
..(((((..(((((((((.....((....))...((((.(((((((((((((((((((.(............))))))..)))))).)))))))).)))))))))..)))).)))))... ( -30.90)
>DroSec_CAF1 175823 119 + 1
UCCAGACCCACCUGAAUCGCACAACAAACGUAAAGAAACUCUUUAUAAAGCAUUUCGGUCUAUAA-UUUUUUGUCGAACCAUUUUUGUAUAAAGAUUUUCGAUUCGUAGGUAGUCUGAUU
..(((((..(((((((((.....((....))...((((.((((((((.........((((.((((-....)))).).))).......)))))))).)))))))))..)))).)))))... ( -27.39)
>DroEre_CAF1 180514 119 + 1
ACUAGACUCACCUCAAUCGCACAACAUACGUAAAGAAACUCUUUAUAAAGCAUUUCGGUCCAUCA-AUUUUUGUCGAACCAUUUUUGUAUAAAGAUUUUCGGUUCGUAGGUAGUCUGAUU
..((((((.(((((((((.....((....))...((((.((((((((.........(((.(..((-.....))..).))).......)))))))).)))))))).).))))))))))... ( -23.99)
>DroYak_CAF1 173426 115 + 1
-UUAG---UACCUGAAUCACACAACAUACGUAAAGAAACUCCUUAUAAAGCAUUUCGGUCUACAA-AUUUUUCUCGAACCAUUUUUGUAUACAGAAUUUCGAUUCGUAGGUAGUCUGAUU
-....---......(((((.((.((.((((....((((.((..(((((((...(((((.......-.......)))))....)))))))....)).))))....)))).)).)).))))) ( -16.84)
>consensus
UCCAGACCCACCUGAAUCGCACAACAAACGUAAAGAAACUCUUUAUAAAGCAUUUCGGUCUAUAA_AUUUUUGUCGAACCAUUUUUGUAUAAAGAUUUUCGAUUCGUAGGUAGUCUGAUU
..(((((..(((((((((.....((....))...((((.((((((((......(((((...............))))).........)))))))).)))))))))..)))).)))))... (-18.93 = -19.75 +   0.81)

alignment

secondary structure

dotplot

Window 4

Location	2,123,578 – 2,123,698
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.24
Mean single sequence MFE	-27.86
Consensus MFE	-22.57
Energy contribution	-23.75
Covariance contribution	1.19
Combinations/Pair	1.08
Mean z-score	-1.83
Structure conservation index	0.81
SVM decision value	0.63
SVM RNA-class probability	0.804789
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2123578 120 - 23771897
AAUCAGACUACCUACGAAUCGAAAAUCUUUAUACAAACAUGGUUCGACAAAAAACUUAUAGACCGAAAUGCUUUAUAAAGAGUUUCUUUACGUUUGUUGUGCGAUUCAGGUGGGUCUGGA
..(((((((((((..((((((...........((((((..((((................))))(((((.(((....))).))))).....))))))....)))))))))).))))))). ( -29.95)
>DroSec_CAF1 175823 119 - 1
AAUCAGACUACCUACGAAUCGAAAAUCUUUAUACAAAAAUGGUUCGACAAAAAA-UUAUAGACCGAAAUGCUUUAUAAAGAGUUUCUUUACGUUUGUUGUGCGAUUCAGGUGGGUCUGGA
..(((((((((((..(((((((((.((((((((......(((((..........-.....)))))........)))))))).))))..((((.....)))).))))))))).))))))). ( -29.20)
>DroEre_CAF1 180514 119 - 1
AAUCAGACUACCUACGAACCGAAAAUCUUUAUACAAAAAUGGUUCGACAAAAAU-UGAUGGACCGAAAUGCUUUAUAAAGAGUUUCUUUACGUAUGUUGUGCGAUUGAGGUGAGUCUAGU
....(((((((((.(((...((((.((((((((......(((((((.((.....-)).)))))))........)))))))).))))....(((((...))))).))))))).)))))... ( -29.94)
>DroYak_CAF1 173426 115 - 1
AAUCAGACUACCUACGAAUCGAAAUUCUGUAUACAAAAAUGGUUCGAGAAAAAU-UUGUAGACCGAAAUGCUUUAUAAGGAGUUUCUUUACGUAUGUUGUGUGAUUCAGGUA---CUAA-
(((((.((.((.((((.(..((((((((.((((......(((((((((.....)-)))..)))))........)))).))))))))..).)))).)).)).)))))......---....- ( -22.34)
>consensus
AAUCAGACUACCUACGAAUCGAAAAUCUUUAUACAAAAAUGGUUCGACAAAAAA_UUAUAGACCGAAAUGCUUUAUAAAGAGUUUCUUUACGUAUGUUGUGCGAUUCAGGUGGGUCUAGA
..(((((((((((..(((((((((.((((((((......(((((................)))))........)))))))).))))..((((.....)))).)))))))))).)))))). (-22.57 = -23.75 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:05 2006