Locus 1383

Sequence ID	3R_DroMel_CAF1
Location	4,041,961 – 4,042,055
Length	94
Max. P	0.978371

overview

Window 0

Location	4,041,961 – 4,042,055
Length	94
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	70.03
Mean single sequence MFE	-27.68
Consensus MFE	-15.82
Energy contribution	-15.66
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-2.03
Structure conservation index	0.57
SVM decision value	1.81
SVM RNA-class probability	0.978371
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4041961 94 + 27905053
UCUUU-----UUUAUUUUUUUUUCUUUGACUGCAGGAAGAUCGAUCUG--GCCGAUCGGUCGGUGCACCUCAUUGACCUCCCUUCAUCU----UCCAGCUCCCU------U
.....-----.....................((.(((((((.((((..--...))))((((((((.....)))))))).......))))----))).)).....------. ( -24.40)
>DroPse_CAF1 28891 92 + 1
UU--------U---------GGUCAGUGAACGGAGGAAGAUCGAUCUGGGGCCGAUCGGUCGGUGCACCUCAUUGACCUCUC--CAUCGCUCUGGCUGUGGCUCUGACUCU
..--------.---------((((((.(.(((((((..(((((..(...)..)))))((((((((.....))))))))))))--)...((....)).))..).)))))).. ( -33.10)
>DroEre_CAF1 31876 88 + 1
UUUUGUGUUUUU-----------GUUUGACUGCAGGAAGAUCGAUCUG--GCCGAUCGGUCGGUGCACCUCAUUGACCUCUCUUCAUCU----GCCAGCUCCCU------U
............-----------....(((((((((((((..((((..--...))))((((((((.....))))))))..)))))..))----).))).))...------. ( -23.60)
>DroYak_CAF1 48460 99 + 1
UGUUUUAUUUUUUGUUAUUUUUGCUUUGACUGCAGGAAGAUCGAUCUG--GCCGAUCGGUCGGUGCACCUCAUUGACCUCUCUUCAUCU----UCCAGUUCCCU------U
.....................(((.......)))(((((((.((((..--...))))((((((((.....)))))))).......))))----)))........------. ( -24.90)
>DroPer_CAF1 29268 86 + 1
UU--------U---------GGUCAGUGAACGGAGGAAGAUCGAUCUGGGGCCGAUCGGUCGGUGCACCUCAUUGACCUCUC--CAUCGCUUUGGCUGUGGCUG------U
..--------.---------(((((((((..((.(.(.((((((((.(....)))))))))..).).)))))))))))...(--(((.((....)).))))...------. ( -32.40)
>consensus
UUUU______UU________GGUCUUUGACUGCAGGAAGAUCGAUCUG__GCCGAUCGGUCGGUGCACCUCAUUGACCUCUCUUCAUCU____GCCAGUUCCCU______U
..................................(((.(((((.........)))))((((((((.....))))))))))).............................. (-15.82 = -15.66 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	4,041,961 – 4,042,055
Length	94
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	70.03
Mean single sequence MFE	-24.86
Consensus MFE	-15.68
Energy contribution	-15.84
Covariance contribution	0.16
Combinations/Pair	1.06
Mean z-score	-1.73
Structure conservation index	0.63
SVM decision value	1.34
SVM RNA-class probability	0.944184
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4041961 94 - 27905053
A------AGGGAGCUGGA----AGAUGAAGGGAGGUCAAUGAGGUGCACCGACCGAUCGGC--CAGAUCGAUCUUCCUGCAGUCAAAGAAAAAAAAAUAAA-----AAAGA
.------.((..((.(((----((((...((..(((((......)).)))..))((((...--..)))).))))))).))..)).................-----..... ( -25.80)
>DroPse_CAF1 28891 92 - 1
AGAGUCAGAGCCACAGCCAGAGCGAUG--GAGAGGUCAAUGAGGUGCACCGACCGAUCGGCCCCAGAUCGAUCUUCCUCCGUUCACUGACC---------A--------AA
.(.(((((.((....))..(((((..(--((.(((((.....(((......)))((((.......))))))))))))..))))).))))))---------.--------.. ( -31.00)
>DroEre_CAF1 31876 88 - 1
A------AGGGAGCUGGC----AGAUGAAGAGAGGUCAAUGAGGUGCACCGACCGAUCGGC--CAGAUCGAUCUUCCUGCAGUCAAAC-----------AAAAACACAAAA
.------...((.(((.(----((..(((((..((((..((.....))..))))((((...--..))))..)))))))))))))....-----------............ ( -21.50)
>DroYak_CAF1 48460 99 - 1
A------AGGGAACUGGA----AGAUGAAGAGAGGUCAAUGAGGUGCACCGACCGAUCGGC--CAGAUCGAUCUUCCUGCAGUCAAAGCAAAAAUAACAAAAAAUAAAACA
.------((....))(((----((((.......((((..((.....))..))))((((...--..)))).)))))))(((.......)))..................... ( -21.80)
>DroPer_CAF1 29268 86 - 1
A------CAGCCACAGCCAAAGCGAUG--GAGAGGUCAAUGAGGUGCACCGACCGAUCGGCCCCAGAUCGAUCUUCCUCCGUUCACUGACC---------A--------AA
.------...(((..((....))..))--)...(((((.(((((....))((.(((((.......))))).)).........))).)))))---------.--------.. ( -24.20)
>consensus
A______AGGGAACUGGC____AGAUGAAGAGAGGUCAAUGAGGUGCACCGACCGAUCGGC__CAGAUCGAUCUUCCUGCAGUCAAAGAAA________AA______AAAA
.......................((((.((..(((((.....(((......)))((((.......)))))))))..)).)).))........................... (-15.68 = -15.84 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:42 2006