Locus 3416

Sequence ID	3L_DroMel_CAF1
Location	10,016,428 – 10,016,541
Length	113
Max. P	0.965769

overview

Window 9

Location	10,016,428 – 10,016,527
Length	99
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	81.56
Mean single sequence MFE	-31.88
Consensus MFE	-24.09
Energy contribution	-23.57
Covariance contribution	-0.53
Combinations/Pair	1.15
Mean z-score	-1.60
Structure conservation index	0.76
SVM decision value	0.41
SVM RNA-class probability	0.725946
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10016428 99 + 23771897
CCACCCAGCG-----------------U--UUUCCCGCAAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCA
.......(((-----------------(--((....((((((((...(((((((((((((.((((....))..)))))))))...(....)))))))...))))).)))..)))))). ( -30.70)
>DroVir_CAF1 70317 101 + 1
GGCCGGUUUC-----------------CCGCAGGCCGCAAAUGGACCGCAAAUGGCAGCGUGCGGAAAUCCAUGCUGCAGCUUUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCA
((((.((...-----------------..)).))))((((((((...(((((((((((((((........)))))))).((....))...)))))))...))))).)))......... ( -38.80)
>DroPse_CAF1 74565 101 + 1
GUCCCCCCUC-----------------UCGACUGCCGCAAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCCGCCAUUAUGCAUGAAUGCA
(((.......-----------------..))).((.(((((((....((((.((((((((.((((....))..))))))))))))))...)))))))..)).....((((....)))) ( -26.80)
>DroGri_CAF1 69113 118 + 1
AGCCACUUCCUUUCUCUGGCAUGCAGGCUGCAGGCCACAAAUGGACCGCAAAUGGCAGCAUGCGGAAAUCCAUGCUGCAGCUUUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCA
.((((...........))))((((((((((..(((((....))).))(((((((((((((((........)))))))).((....))...))))))))))))....)))))....... ( -42.00)
>DroAna_CAF1 68154 101 + 1
UGCCCCCUCC-----------------UCACUUGCCGCAAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCA
..........-----------------......((.(((((((....((((.((((((((.((((....))..))))))))))))))...)))))))..)).....((((....)))) ( -26.80)
>DroPer_CAF1 74370 101 + 1
GUCCCCCCUC-----------------UCGACUACCGCAAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCCGCCAUUAUGCAUGAAUGCA
(((.......-----------------..)))....(((((((....((((.((((((((.((((....))..))))))))))))))...))))))).........((((....)))) ( -26.20)
>consensus
GGCCCCCUCC_________________UCGCAUGCCGCAAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCA
....................................((((((((...(((((((((((((.((((....))..)))))))))...(....)))))))...))))).)))......... (-24.09 = -23.57 +  -0.53)

alignment

secondary structure

dotplot

Window 0

Location	10,016,447 – 10,016,541
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.55
Mean single sequence MFE	-27.27
Consensus MFE	-24.94
Energy contribution	-24.25
Covariance contribution	-0.69
Combinations/Pair	1.14
Mean z-score	-2.29
Structure conservation index	0.91
SVM decision value	1.59
SVM RNA-class probability	0.965769
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10016447 94 + 23771897
AAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCAUAGAAAUAGAAA-AC-------------------------
.(((((...(((((((((((((.((((....))..)))))))))...(....)))))))...)))))(((((....)))))...........-..------------------------- ( -25.10)
>DroVir_CAF1 70338 119 + 1
AAAUGGACCGCAAAUGGCAGCGUGCGGAAAUCCAUGCUGCAGCUUUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCAUAGAAAUACGUA-GUGUCACACUUAUACCAACACACACUC
.(((((...(((((((((((((((........)))))))).((....))...)))))))...)))))(((((....)))))........((.-((((.............)))))).... ( -32.62)
>DroGri_CAF1 69151 101 + 1
AAAUGGACCGCAAAUGGCAGCAUGCGGAAAUCCAUGCUGCAGCUUUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCAUAGAAAUACAUG-AUGUCACAC------------------
.(((((...(((((((((((((((........)))))))).((....))...)))))))...)))))(((((....)))))...........-.........------------------ ( -30.60)
>DroEre_CAF1 71204 94 + 1
AAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCAUAGAAAUAGAAU-UC-------------------------
.(((((...(((((((((((((.((((....))..)))))))))...(....)))))))...)))))(((((....)))))...........-..------------------------- ( -25.10)
>DroYak_CAF1 70973 94 + 1
AAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCCGCCAUUAUGCAUGAAUGCAUAGAAAUAGAAU-AC-------------------------
.(((((...(((((((((((((.((((....))..)))))))))...(....)))))))...)))))(((((....)))))...........-..------------------------- ( -25.10)
>DroAna_CAF1 68175 95 + 1
AAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCAUAGAAAUAGAAAAAC-------------------------
.(((((...(((((((((((((.((((....))..)))))))))...(....)))))))...)))))(((((....)))))..............------------------------- ( -25.10)
>consensus
AAAUGGACCGCAAAUGGUAACGUGCGGAAAUCCAUGCUGUUGCCAUUGUAAACGUUUGCCAGCCAUUAUGCAUGAAUGCAUAGAAAUAGAAA_AC_________________________
.(((((...(((((((((((((.((((....))..)))))))))...(....)))))))...)))))(((((....)))))....................................... (-24.94 = -24.25 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:38 2006