Locus 4379

Sequence ID	2R_DroMel_CAF1
Location	14,397,561 – 14,397,659
Length	98
Max. P	0.858845

overview

Window 5

Location	14,397,561 – 14,397,659
Length	98
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	77.67
Mean single sequence MFE	-29.70
Consensus MFE	-19.33
Energy contribution	-20.11
Covariance contribution	0.78
Combinations/Pair	1.35
Mean z-score	-1.46
Structure conservation index	0.65
SVM decision value	0.47
SVM RNA-class probability	0.748790
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14397561 98 + 20766785
AAGUCAGCUUUACUGGAGCUGACUGUCACUUCAACUCCGGCGAUAUGGGAGAUUUCCUCUUGACAGACUGUUCUGCCAAGGGU-----ACGCC-AGCAAAGACU
.(((((((((.....)))))))))(((.......((((.(.....).)))).....((((((.((((....)))).)))))).-----.....-......))). ( -31.60)
>DroSec_CAF1 29725 98 + 1
AAGUCAGCUUUGCUGGAGCUGGCUGUCACUUCAACUCCGGCGAAAUGGAAGAUUUCCUCUUGACAGAUUGUUCUGCCAAAGGU-----ACGCA-GGCAAAGACU
..(((.((((((((((((.(((........))).))))))))))...........(((.(((.((((....)))).)))))).-----..)).-)))....... ( -28.80)
>DroSim_CAF1 33084 98 + 1
AAGUCAGCUUUACUGGAGCUGGCUGUCACUUCAACUGCGGCGAUAUGGGAGAUUUCCUCUUGACAGACUGUUCUGCCAAGGGU-----ACGCC-AGCAAAGACU
.(((((((((.....)))))))))...........(((((((.((((((......)))((((.((((....)))).)))).))-----)))))-.)))...... ( -32.50)
>DroEre_CAF1 31491 95 + 1
AAGUCAGCUUUACUGGAGCUGGCUGUCACUUCAACUCCGGCGAUAUGGGAGAUUUCCUCUUGACAGACUGCUAUGCCAUAUG---------CGAAGCAAAGACU
.(((((((((.....)))))))))(((.......((((.(.....).)))).................((((.(((.....)---------)).))))..))). ( -26.90)
>DroYak_CAF1 30908 98 + 1
AAGUCAGCUUUACUGGAGCUGGCUGUCACUUCAACUCCGGCGAUAUGGGAGAUUUCCUCUUGACAGACUGCUCUGCCAAGGGA-----ACACG-AGCAACGACU
.(((((((((.....)))))))))(((.......((((.(.....).))))..((((.((((.((((....)))).)))))))-----)....-......))). ( -32.90)
>DroPer_CAF1 30468 94 + 1
-AGCUGG-----CUG--CCUGGCUGUCACUUCAACAUUUGUGAUAUGGCAGAUGUUUUUUCCCCAAAU-GUCUCCCCAAAUACCCUUAACGAA-GGGACAGGCC
-......-----..(--((((..((((((..........)))))).((.((((((((.......))))-)))).))......(((((....))-))).))))). ( -25.50)
>consensus
AAGUCAGCUUUACUGGAGCUGGCUGUCACUUCAACUCCGGCGAUAUGGGAGAUUUCCUCUUGACAGACUGUUCUGCCAAAGGU_____ACGCA_AGCAAAGACU
.(((((((((.....)))))))))(((.((((...............)))).....((((((.((((....)))).))))))..................))). (-19.33 = -20.11 +   0.78)

alignment

secondary structure

dotplot

Window 6

Location	14,397,561 – 14,397,659
Length	98
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	77.67
Mean single sequence MFE	-31.35
Consensus MFE	-18.79
Energy contribution	-19.63
Covariance contribution	0.84
Combinations/Pair	1.38
Mean z-score	-1.86
Structure conservation index	0.60
SVM decision value	0.82
SVM RNA-class probability	0.858845
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14397561 98 - 20766785
AGUCUUUGCU-GGCGU-----ACCCUUGGCAGAACAGUCUGUCAAGAGGAAAUCUCCCAUAUCGCCGGAGUUGAAGUGACAGUCAGCUCCAGUAAAGCUGACUU
((.(((((((-((((.-----...(((((((((....))))))))).(((....))).....))))((((((((........)))))))))))))))))..... ( -39.70)
>DroSec_CAF1 29725 98 - 1
AGUCUUUGCC-UGCGU-----ACCUUUGGCAGAACAAUCUGUCAAGAGGAAAUCUUCCAUUUCGCCGGAGUUGAAGUGACAGCCAGCUCCAGCAAAGCUGACUU
((.((((((.-.(((.-----...(((((((((....))))))))).(((.....)))....))).(((((((..........))))))).))))))))..... ( -32.00)
>DroSim_CAF1 33084 98 - 1
AGUCUUUGCU-GGCGU-----ACCCUUGGCAGAACAGUCUGUCAAGAGGAAAUCUCCCAUAUCGCCGCAGUUGAAGUGACAGCCAGCUCCAGUAAAGCUGACUU
((.(((((((-((.((-----.(((((((((((....))))))))).))............((((..(....)..))))......)).)))))))))))..... ( -32.10)
>DroEre_CAF1 31491 95 - 1
AGUCUUUGCUUCG---------CAUAUGGCAUAGCAGUCUGUCAAGAGGAAAUCUCCCAUAUCGCCGGAGUUGAAGUGACAGCCAGCUCCAGUAAAGCUGACUU
((((...((((..---------(....(((.......(((....)))(((....)))......)))(((((((..........))))))).)..)))).)))). ( -28.40)
>DroYak_CAF1 30908 98 - 1
AGUCGUUGCU-CGUGU-----UCCCUUGGCAGAGCAGUCUGUCAAGAGGAAAUCUCCCAUAUCGCCGGAGUUGAAGUGACAGCCAGCUCCAGUAAAGCUGACUU
(((((..(((-....(-----((((((((((((....))))))))).))))............((.(((((((..........))))))).))..)))))))). ( -32.70)
>DroPer_CAF1 30468 94 - 1
GGCCUGUCCC-UUCGUUAAGGGUAUUUGGGGAGAC-AUUUGGGGAAAAAACAUCUGCCAUAUCACAAAUGUUGAAGUGACAGCCAGG--CAG-----CCAGCU-
(((.((((.(-((((......((.....((.(((.-.(((.......)))..))).)).....))......))))).))))))).((--(..-----...)))- ( -23.20)
>consensus
AGUCUUUGCU_CGCGU_____ACCCUUGGCAGAACAGUCUGUCAAGAGGAAAUCUCCCAUAUCGCCGGAGUUGAAGUGACAGCCAGCUCCAGUAAAGCUGACUU
((((...((.............(((((((((((....))))))))).))..............((.(((((((..........))))))).))...)).)))). (-18.79 = -19.63 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:14 2006