Locus 9318

Sequence ID	3R_DroMel_CAF1
Location	24,783,176 – 24,783,391
Length	215
Max. P	0.924891

overview

Window 4

Location	24,783,176 – 24,783,275
Length	99
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	68.91
Mean single sequence MFE	-26.20
Consensus MFE	-11.39
Energy contribution	-10.90
Covariance contribution	-0.49
Combinations/Pair	1.41
Mean z-score	-2.60
Structure conservation index	0.43
SVM decision value	0.86
SVM RNA-class probability	0.868895
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24783176 99 - 27905053
CAUUUCAUAAUCUACUACACUUGAACAAAAGUGCAUAUUU-------------------UUUAGCAGUUCUAGAAUAUCAUUUGA-AAAAUCAUCUUAUUCAGUUA-AGAAUAGGAAUAA
..(((((..........(((((......)))))......(-------------------(((((.....)))))).......)))-)).....((((((((.....-.)))))))).... ( -15.70)
>DroEre_CAF1 23359 118 - 1
UAUUUCAUAAUCUAGUACACUUGCACAAAAGUGCCAAUUUG-ACGCAAGUGGACUUGGUUCUCACAGUUCUGGAAUAUCACUUGGUACGAUAAUCUUAUCAAAGUG-GUGCCAGAAGUAA
........((((.(((.(((((((.((((........))))-..))))))).))).)))).....(.((((((..((((((((((((.(.....).)))).)))))-))))))))).).. ( -32.40)
>DroYak_CAF1 15129 117 - 1
UAUUUCAUAAUCUAGUACACUUGCACAAAAGUGCCCAUUUAUGCGUAAGUGUACUUUGUUCUAACAGUUCUAGAAUUUCACUU---AAGAUAAUCUGAUUCAGCCGAAUGGCAGAAGUAA
((((((...(((((((((((((((.((.((((....)))).)).)))))))))))..((((((.......)))))).......---.))))...........(((....))).)))))). ( -30.50)
>consensus
UAUUUCAUAAUCUAGUACACUUGCACAAAAGUGCCAAUUU___CG_AAGUG_ACUU_GUUCUAACAGUUCUAGAAUAUCACUUG__AAGAUAAUCUUAUUCAGCUG_AUGACAGAAGUAA
((((((....(((((.((....((((....))))........((....))................)).)))))............................(((....))).)))))). (-11.39 = -10.90 +  -0.49)

alignment

secondary structure

dotplot

Window 5

Location	24,783,275 – 24,783,391
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.55
Mean single sequence MFE	-27.70
Consensus MFE	-22.39
Energy contribution	-22.32
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.22
Structure conservation index	0.81
SVM decision value	1.16
SVM RNA-class probability	0.924891
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24783275 116 + 27905053
CCAUAAAAGCUUAUAUGAGG---AAAGUAUGCUUAUGCUGUCUGCAA-AAAAGUUAUUCUUGUUAAGUCUCUCAAGCUUAGCUUAUUCGCAGACACAUCAAGUCAUAUAUAAGAAAGUGA
.(((.....(((((......---...(((((((((((.(((((((.(-(.((((((..((((..........))))..)))))).)).)))))))))).))).))))))))))...))). ( -28.30)
>DroSec_CAF1 14292 119 + 1
CCAUAAAAGCUUAUAUGUUGUUCAAAGUAUGCUUAUGCUGUCUGCAA-AAAAGUUAUUCUUGUUAAGUCUCUCAAGCUUAGCUUAUUCGCAGACACAUCAAGUCAUAUAUAAGAUAGUGU
..............(..(((((....(((((((((((.(((((((.(-(.((((((..((((..........))))..)))))).)).)))))))))).))).)))))....)))))..) ( -29.10)
>DroEre_CAF1 23477 117 + 1
CCAUAUAAGCUUAUGUGAGG---AAACUAUGUUUAUGCUGUCUGGAAAAAAAGUUAUUCUUGUUAAGUCUCUCAAGCGCAGCUUAUUCGCAGACACAUUAAGUCAUAUAUAAGACAGUGA
.(((.....((((((((((.---...)).((((((((.(((((((((...(((((...((((..........))))...))))).))).)))))))).)))).))))))))))...))). ( -24.20)
>DroYak_CAF1 15246 116 + 1
CCAUAAAAGCUUAUGUGAUG---AAAGCAUGCUUAUGUUGUCUGCGA-AAAAGUUAUUCUUGUUAAGUCUCUCAAGCUUAGCUUAUUUGCACACACAUUAGGUCACAUAUAAGAUAGUGA
.(((.....(((((((((((---....)))((((((((.((.(((((-(.((((((..((((..........))))..)))))).)))))).))))).)))))..))))))))...))). ( -29.20)
>consensus
CCAUAAAAGCUUAUAUGAGG___AAAGUAUGCUUAUGCUGUCUGCAA_AAAAGUUAUUCUUGUUAAGUCUCUCAAGCUUAGCUUAUUCGCAGACACAUCAAGUCAUAUAUAAGAUAGUGA
.(((.....((((((((............((((((((.(((((((.....((((((..((((..........))))..))))))....)))))))))).))).))))))))))...))). (-22.39 = -22.32 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:35 2006