Locus 2943

Sequence ID	2R_DroMel_CAF1
Location	10,169,321 – 10,169,445
Length	124
Max. P	0.966025

overview

Window 6

Location	10,169,321 – 10,169,413
Length	92
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	78.03
Mean single sequence MFE	-16.10
Consensus MFE	-9.55
Energy contribution	-10.80
Covariance contribution	1.25
Combinations/Pair	1.11
Mean z-score	-1.79
Structure conservation index	0.59
SVM decision value	0.06
SVM RNA-class probability	0.563382
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10169321 92 - 20766785
UGGCAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAUUGUUGUUGUUAUCAUUCGUAUACACUCAUAUUU-------AUUAUAGCUAUUUUCUAUGU-UU
....((((((.......(((.(((.((((...)))).))).)))(((((.((..((((......))))..-------)).))))).......)))))-). ( -13.00)
>DroSec_CAF1 9115 93 - 1
UGGAAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAAUGUGGUUUUAAUCAUUCGUAUUCACUCAUAUUU-------GUUAUAGCUAUUUCCUAUACCUU
.(((((...........(((..(((((((...)))))))..)))..........((....((........-------))....))..)))))........ ( -15.90)
>DroSim_CAF1 8934 93 - 1
UGGCAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAAUGUGGUUUUAAUCAUUCGUAUUCACUCAUAUUU-------GUUAUAGCUAUUUCCUAUACCUU
((((.............(((..(((((((...)))))))..)))................((........-------))....))))............. ( -15.00)
>DroYak_CAF1 9522 91 - 1
UGGCAUCAUAUUUAAUUAAAUGCAUU-UCUUUGAGAAUGUGGUUUUAAUCAUCUGGGGUCAUGAAAAUGACAUCUUUUCGAUAGCCAUUUCC--------
(((((((((((((..(((((......-..))))))))))))))....(((....((((((((....))))).)))....))).)))).....-------- ( -20.50)
>consensus
UGGCAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAAUGUGGUUUUAAUCAUUCGUAUUCACUCAUAUUU_______GUUAUAGCUAUUUCCUAUAC_UU
((((.((..........((((((((((((...))))))))))))..........)).))))....................................... ( -9.55 = -10.80 +   1.25)

alignment

secondary structure

dotplot

Window 7

Location	10,169,340 – 10,169,445
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.20
Mean single sequence MFE	-14.40
Consensus MFE	-3.54
Energy contribution	-4.18
Covariance contribution	0.64
Combinations/Pair	1.19
Mean z-score	-1.79
Structure conservation index	0.25
SVM decision value	0.55
SVM RNA-class probability	0.779814
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10169340 105 + 20766785
AAU-------AAAUAUGAGUGUAUACGAAUGAUAACAACAACAAUCUCAAAGAGAAUGCAGUUAAUUAAAUAUGUUGCCACCAUAUCAAUGAAUACAA----CUCAUCA---CAAUCC-A
...-------....((((((((((.((..(((((....(((((.((((...)))).....(((.....))).)))))......))))).)).)))).)----)))))..---......-. ( -14.50)
>DroSec_CAF1 9135 105 + 1
AAC-------AAAUAUGAGUGAAUACGAAUGAUUAAAACCACAUUCUCAAAGAGAAUGCAGUUAAUUAAAUAUGUUUCCAGCAUAUCAAUGAAUACAA----CUCAUCA---CAAUCC-A
...-------....((((((.........(((((((.....(((((((...)))))))...))))))).((((((.....))))))...........)----)))))..---......-. ( -18.10)
>DroSim_CAF1 8954 105 + 1
AAC-------AAAUAUGAGUGAAUACGAAUGAUUAAAACCACAUUCUCAAAGAGAAUGCAGUUAAUUAAAUAUGUUGCCACCAUAUCAAUGAAUACAA----CUCAUCA---CAAUCC-A
...-------........((((.......(((((((.....(((((((...)))))))...))))))).....((((....(((....)))....)))----)...)))---).....-. ( -16.30)
>DroEre_CAF1 9115 92 + 1
CGAAACG--GAAAUUUUAAUGACCACGGAUGAUUAAAACCACAUGCUCAAAGA-----------------UAUGAUGCCACCAUAUCAAUGAAUACAA----AUCAUCA---CAACCC--
.......--..................(((((((.................((-----------------((((.......))))))..((....)))----)))))).---......-- ( -11.30)
>DroYak_CAF1 9534 119 + 1
CGAAAAGAUGUCAUUUUCAUGACCCCAGAUGAUUAAAACCACAUUCUCAAAGA-AAUGCAUUUAAUUAAAUAUGAUGCCACCAUGUUAAUGAAUACAACCCAAUCACCAAUUCAACUCCA
......(((.(((((..((((......................(((.....))-)..(((((...........)))))...))))..)))))..........)))............... ( -11.80)
>consensus
AAA_______AAAUAUGAGUGAAUACGAAUGAUUAAAACCACAUUCUCAAAGAGAAUGCAGUUAAUUAAAUAUGUUGCCACCAUAUCAAUGAAUACAA____CUCAUCA___CAAUCC_A
..........................((.((..........(((((((...)))))))...........(((((.......)))))..........................)).))... ( -3.54 =  -4.18 +   0.64)

alignment

secondary structure

dotplot

Window 8

Location	10,169,340 – 10,169,445
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.20
Mean single sequence MFE	-24.81
Consensus MFE	-9.18
Energy contribution	-11.78
Covariance contribution	2.60
Combinations/Pair	1.10
Mean z-score	-2.20
Structure conservation index	0.37
SVM decision value	1.59
SVM RNA-class probability	0.966025
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10169340 105 - 20766785
U-GGAUUG---UGAUGAG----UUGUAUUCAUUGAUAUGGUGGCAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAUUGUUGUUGUUAUCAUUCGUAUACACUCAUAUUU-------AUU
.-......---..(((((----(.((((....(((.((((((((((((.............(((.((((...)))).)))))))))))))))))).))))))))))....-------... ( -26.81)
>DroSec_CAF1 9135 105 - 1
U-GGAUUG---UGAUGAG----UUGUAUUCAUUGAUAUGCUGGAAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAAUGUGGUUUUAAUCAUUCGUAUUCACUCAUAUUU-------GUU
.-.(((..---..(((((----(.((((....((((....((....)).........(((..(((((((...)))))))..)))...))))...))))..))))))....-------))) ( -24.30)
>DroSim_CAF1 8954 105 - 1
U-GGAUUG---UGAUGAG----UUGUAUUCAUUGAUAUGGUGGCAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAAUGUGGUUUUAAUCAUUCGUAUUCACUCAUAUUU-------GUU
(-((((..---.((((((----((((..((((....))))..)))))..........(((..(((((((...)))))))..)))....)))))...))))).........-------... ( -25.90)
>DroEre_CAF1 9115 92 - 1
--GGGUUG---UGAUGAU----UUGUAUUCAUUGAUAUGGUGGCAUCAUA-----------------UCUUUGAGCAUGUGGUUUUAAUCAUCCGUGGUCAUUAAAAUUUC--CGUUUCG
--(((...---(((((((----.....((((..((((((((...))))))-----------------))..))))((((.(((.......)))))))))))))).....))--)...... ( -21.30)
>DroYak_CAF1 9534 119 - 1
UGGAGUUGAAUUGGUGAUUGGGUUGUAUUCAUUAACAUGGUGGCAUCAUAUUUAAUUAAAUGCAUU-UCUUUGAGAAUGUGGUUUUAAUCAUCUGGGGUCAUGAAAAUGACAUCUUUUCG
..(((..((...((((((((..(..(((((.((((...((..((((.............))))...-)).)))))))))..)..).)))))))....(((((....))))).))..))). ( -25.72)
>consensus
U_GGAUUG___UGAUGAG____UUGUAUUCAUUGAUAUGGUGGCAACAUAUUUAAUUAACUGCAUUCUCUUUGAGAAUGUGGUUUUAAUCAUUCGUAUUCACUCAUAUUU_______GUU
............(((((......................(((....)))........((((((((((((...))))))))))))....)))))........................... ( -9.18 = -11.78 +   2.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:27 2006