Locus 3992

Sequence ID	2R_DroMel_CAF1
Location	13,206,398 – 13,206,550
Length	152
Max. P	0.904120

overview

Window 5

Location	13,206,398 – 13,206,517
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.20
Mean single sequence MFE	-36.43
Consensus MFE	-18.65
Energy contribution	-18.85
Covariance contribution	0.20
Combinations/Pair	1.36
Mean z-score	-2.20
Structure conservation index	0.51
SVM decision value	0.94
SVM RNA-class probability	0.886535
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13206398 119 - 20766785
UACUUGAUUUGUC-AUCAGAUCAGUGACAUAAAUCCGCUGCGGGACAAUCCCCACUACCGCCACGUUGUGGAUAUGCAGCUGGAGAACAAUCAGAUAUCCAAUGUGGACAACUUGGAGGA
...((((((((..-..))))))))(((......(((((((((((......)))....((((......))))....))))).)))......)))....(((((.((.....)))))))... ( -35.20)
>DroPse_CAF1 449 116 - 1
UCCUCCC---CUU-UCCAGAUCAGCGACAUAAAACCGCUACGGGAUAAUCCCCAUUACCGCCAUGUGGUGGAUGUGCAUCUGGAGAACAACCGCAUCUCCAAUGUGGACGACCUGGAGAA
..((((.---.((-(((((((..((.((((...........(((......)))....(((((....))))))))))))))))))))....((((((.....)))))).......)))).. ( -40.50)
>DroGri_CAF1 7986 117 - 1
CAUUU-AUC-AUU-UAUAGAUCAGCGACAUAAAUCCACUGCGCGAUAAUCCGCAUUAUAAGCAUGUGGUCGAUGUGCAGCUGGAAAACAAUCGGAUCUCGAACAUUGAUGUCCUGGAGGA
.....-...-...-......((((.(((((...(((((((((((.....((((((.......))))))....))))))).))))......(((.....)))......))))))))).... ( -32.00)
>DroYak_CAF1 449 119 - 1
CACUAUAUUCGUU-AUCAGAUCAGUGAUAUAAAUCCGCUGCGAGACAAUCCCCACUACCGCCACGUGGUGGAUAUGCAGCUGGAGAACAAUCACAUAUCCAAUGUGGACAACUUGGAGGA
.............-.........(((((.....((((((((((.....)).(((((((......)))))))....))))).))).....)))))...(((((.((.....)))))))... ( -33.70)
>DroMoj_CAF1 1442 118 - 1
CACAA-CGC-AAUUUGCAGAUCAGUGAUAUUAAUCCGCUGCGGGACAAUCCCCACUAUCACCACGUGGUGGACGUGCAGCUGGAGAACAAUUUGAUCUCAAACAUCGACGUGCUGGAGGA
(((..-((.-..((((.(((((((.........(((((((((((......))).(((((((...)))))))....))))).))).......)))))))))))...))..)))........ ( -36.69)
>DroPer_CAF1 449 116 - 1
UCCUCCC---CUU-UCCAGAUCAGCGACAUAAAUCCGCUACGGGAUAAUCCCCAUUACCGCCAUGUGGUGGAUGUGCAUCUGGAGAACAACCGCAUCUCCAAUGUGGACGACCUGGAGAA
..((((.---.((-(((((((..((.((((...........(((......)))....(((((....))))))))))))))))))))....((((((.....)))))).......)))).. ( -40.50)
>consensus
CACUA_AU__AUU_UCCAGAUCAGCGACAUAAAUCCGCUGCGGGACAAUCCCCACUACCGCCACGUGGUGGAUGUGCAGCUGGAGAACAAUCGCAUCUCCAAUGUGGACGACCUGGAGGA
..............(((((.(((((..((((..(((((((((((......)))...........))))))))))))..)))))..............(((.....)))....)))))... (-18.65 = -18.85 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	13,206,438 – 13,206,550
Length	112
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.49
Mean single sequence MFE	-26.09
Consensus MFE	-18.76
Energy contribution	-18.73
Covariance contribution	-0.02
Combinations/Pair	1.35
Mean z-score	-1.72
Structure conservation index	0.72
SVM decision value	1.03
SVM RNA-class probability	0.904120
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13206438 112 - 20766785
UAUGAGCAUAUUAAAGCUCAAUGAAAAGUAACUUACUUGAUUUGUCAUCAGAUCAGUGACAUAAAUCCGCUGCGGGACAAUCCCCACUACCGCCACGUUGUGGAUAUGCAGC
..(((((........)))))............(((((.((((((....))))))))))).........((((((((......)))....((((......))))....))))) ( -32.20)
>DroGri_CAF1 8026 96 - 1
UU---UUGU--------C---UGAUACACAAGUCAUUU-AUC-AUUUAUAGAUCAGCGACAUAAAUCCACUGCGCGAUAAUCCGCAUUAUAAGCAUGUGGUCGAUGUGCAGC
..---(((.--------(---((((....((((.....-...-))))....))))))))..........(((((((.....((((((.......))))))....))))))). ( -20.50)
>DroSec_CAF1 489 100 - 1
UAU------------GCUCAAUGAAACGUAACUUACUUGAUUUGUCAUCAGAUCAGUGACUUAAAUCCGCUGCGGGACAAUCCCCACUAUCGCCACGUUGUGGAUAUGCAGC
...------------.............(((.(((((.((((((....))))))))))).))).....((((((((......))).......((((...))))....))))) ( -25.60)
>DroSim_CAF1 309 100 - 1
UAU------------GCCCAAUGAAACGUAACUUACUUGAUUUGUCAUCAGAUCAGUGACUUAAAUCCGCUGCGGGACAAUCCCCACUAUCGCCACGUUGUGGAUAUGCAGC
...------------.............(((.(((((.((((((....))))))))))).))).....((((((((......))).......((((...))))....))))) ( -25.60)
>DroEre_CAF1 493 100 - 1
UGU------------GCUCAAUGGAACCUAACUCACUAGAUUUGUUAACAGAUCAGUGACAUAAAUCCGCUGCGGGACAAUCCCCACUACCGUCACGUUGUGGAUAUGCAGC
...------------.......(((.......(((((.((((((....)))))))))))......)))((((((((.....)))(((.((......)).))).....))))) ( -28.72)
>DroYak_CAF1 489 100 - 1
UGU------------GUUCAAUGAAACAUAACUCACUAUAUUCGUUAUCAGAUCAGUGAUAUAAAUCCGCUGCGAGACAAUCCCCACUACCGCCACGUGGUGGAUAUGCAGC
(((------------(((......))))))..(((((....((.......))..))))).........(((((((.....)).(((((((......)))))))....))))) ( -23.90)
>consensus
UAU____________GCUCAAUGAAACGUAACUCACUUGAUUUGUCAUCAGAUCAGUGACAUAAAUCCGCUGCGGGACAAUCCCCACUACCGCCACGUUGUGGAUAUGCAGC
................................(((((.((((((....))))))))))).........((((((((......)))....((((......))))....))))) (-18.76 = -18.73 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:11 2006