Locus 4730

Sequence ID	2R_DroMel_CAF1
Location	15,518,640 – 15,518,791
Length	151
Max. P	0.766114

overview

Window 1

Location	15,518,640 – 15,518,758
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.16
Mean single sequence MFE	-30.90
Consensus MFE	-28.67
Energy contribution	-28.42
Covariance contribution	-0.25
Combinations/Pair	1.12
Mean z-score	-1.52
Structure conservation index	0.93
SVM decision value	0.52
SVM RNA-class probability	0.766114
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15518640 118 - 20766785
UCA--AAUAGGUCUGUUAGCCCAUCUCUUCAAGCCCGUUAUAAUAUACGACGGCACUGAAGUGAGCUCAGACUUCUCAAGUGUCUAUAAAGAUACCGAAGAGGGCAUUCGAUUCCAGAAA
...--....((..((...((((.((.(((((.((((((........)))..)))..))))).)).......((((....((((((....)))))).)))).))))...))...))..... ( -29.50)
>DroSec_CAF1 312167 118 - 1
UCA--AAAAGGUCUGUUGGCCCAUCUCUUCAAGCCCGUUAUAAUAUACGACGGUACUGAAGUGAGCUCAGACUUCUCAAGUGUCUACAAAGAUACCGAAGAGGGCAUUCGAUUCCAGAAA
...--....((..((...((((.((.(((((...((((..((...))..))))...))))).)).......((((....((((((....)))))).)))).))))...))...))..... ( -30.50)
>DroSim_CAF1 292075 118 - 1
UCA--AAAAGGUCUGUUGGCCCAUCUCUUCAAGCCCGUUAUAAUAUACGACGGUACCGAAGUGAGCUCAGACUUCUCAGGUGUCUACAAAGAUACCGAAGAGGGCAUUCGAUUCCAGAAA
...--....((..((...((((...(((((....((((..((...))..))))....(((((........)))))...(((((((....))))))))))))))))...))...))..... ( -32.80)
>DroYak_CAF1 309875 120 - 1
UAAACAAUAGGUUUAUUGGCCCAUCUCUUCAAACCUGUUAUUAUAUACGACGGUACUGAAGUGACCUCAGACUUCUCAAGUGUCUAUAAAGAUACCGAGGAGGGCAUUCGGUUCCAGAAU
.........((..(....((((.((.(((((...((((..(.....)..))))...))))).))((((.((....))..((((((....)))))).)))).)))).....)..))..... ( -30.80)
>consensus
UCA__AAAAGGUCUGUUGGCCCAUCUCUUCAAGCCCGUUAUAAUAUACGACGGUACUGAAGUGAGCUCAGACUUCUCAAGUGUCUACAAAGAUACCGAAGAGGGCAUUCGAUUCCAGAAA
.........((...((((((((.((.(((((...((((..(.....)..))))...))))).)).......((((....((((((....)))))).)))).))))...)))).))..... (-28.67 = -28.42 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	15,518,680 – 15,518,791
Length	111
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	86.05
Mean single sequence MFE	-29.12
Consensus MFE	-19.39
Energy contribution	-19.57
Covariance contribution	0.19
Combinations/Pair	1.13
Mean z-score	-1.71
Structure conservation index	0.67
SVM decision value	0.14
SVM RNA-class probability	0.601239
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15518680 111 + 20766785
CUUGAGAAGUCUGAGCUCACUUCAGUGCCGUCGUAUAUUAUAACGGGCUUGAAGAGAUGGGCUAACAGACCUAUU--UGAAAAAGGAAAAGGGUU--U--AGUAUAAGCUUUAUGGA
.....(((((((((((((.((((((.(((..(((........))))))))))))((((((((.....).))))))--)............)))))--)--)).....)))))..... ( -28.30)
>DroSec_CAF1 312207 110 + 1
CUUGAGAAGUCUGAGCUCACUUCAGUACCGUCGUAUAUUAUAACGGGCUUGAAGAGAUGGGCCAACAGACCUUUU--UGAA-AAGAAAAAGGGUU--U--AGUAUAGGCUUUAUGGA
.....((((((((.(((((((((((..((((..((...))..))))..))))))...)))))..(((((((((((--(...-....)))))))))--)--.)).))))))))..... ( -34.00)
>DroSim_CAF1 292115 110 + 1
CCUGAGAAGUCUGAGCUCACUUCGGUACCGUCGUAUAUUAUAACGGGCUUGAAGAGAUGGGCCAACAGACCUUUU--UGAA-AAGGAAAAGGGUU--U--AGUAUAAGCUUUAUGGC
((...(((((.((.(((((((((((..((((..((...))..))))..))))))...)))))))(((((((((((--(...-....)))))))))--)--.))....)))))..)). ( -29.10)
>DroYak_CAF1 309915 113 + 1
CUUGAGAAGUCUGAGGUCACUUCAGUACCGUCGUAUAUAAUAACAGGUUUGAAGAGAUGGGCCAAUAAACCUAUUGUUUAA----AAAAUGUGUUAUUAGAAUAUAAGCUUUACAUA
..((.(((((((((((...)))))).......((((.((((((((.((((.(((.((((((........)))))).)))..----.)))).))))))))..))))..))))).)).. ( -25.10)
>consensus
CUUGAGAAGUCUGAGCUCACUUCAGUACCGUCGUAUAUUAUAACGGGCUUGAAGAGAUGGGCCAACAGACCUAUU__UGAA_AAGAAAAAGGGUU__U__AGUAUAAGCUUUAUGGA
.....(((((.((.(((((((((((..((((..(.....)..))))..))))))...)))))))...((((((((............))))))))............)))))..... (-19.39 = -19.57 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:58 2006