Locus 3544

Sequence ID	3R_DroMel_CAF1
Location	9,590,741 – 9,590,880
Length	139
Max. P	0.934729

overview

Window 6

Location	9,590,741 – 9,590,840
Length	99
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	90.03
Mean single sequence MFE	-22.16
Consensus MFE	-18.98
Energy contribution	-19.54
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.86
SVM decision value	0.37
SVM RNA-class probability	0.709948
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9590741 99 - 27905053
UAAAACUUU-UUUUGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAAGCACUUGUGGGCGAUCCACUGAGCCACAAGAGUCACGAUUAUGCU
.........-..(((((.(((....((((((((.......))))))))..........(((((((.((......))..)))))))))))))))....... ( -23.10)
>DroSec_CAF1 67045 100 - 1
UACAACUUUUUUUAGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAACCACUUGUGGGCGAUCCACUGAGCCACAAGAGUCAUGAUUAUGCU
..........(((((((........((((((((.......)))))))))))))))...(((((((.((......))..)))))))............... ( -24.00)
>DroSim_CAF1 77228 99 - 1
UACAACUUU-UUUAGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAACCACUUGUGGGCGAUCCACUGAGCCACAAGAGUCACGAUUAUGCU
.........-(((((((........((((((((.......)))))))))))))))...(((((((.((......))..)))))))............... ( -24.00)
>DroEre_CAF1 69871 97 - 1
UGAAU-UUU-UCGAGUGCAUUAAUUAUAGCCAAACCA-AUUCAGCUAUCACUAAACUACUUGUGGGCGAUCCACUGAGCCACAAGAGUCACGAUUAUGCU
.....-...-......((((.(((((((((.......-.....)))))......(((.(((((((.((......))..))))))))))...)))))))). ( -17.70)
>DroYak_CAF1 67739 98 - 1
UGAAUCUUU-UUGAGUGCAUUAAUUAUAGCGCAGCCA-AUUCGGCUAUCACUAAACCACUUGUGGGCGAUCCCCUGAGCCACAAGAGUCACGAUUAUGCU
..((((...-.(((((((..........))))((((.-....)))).)))........(((((((.((......))..)))))))......))))..... ( -22.00)
>consensus
UAAAACUUU_UUUAGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAACCACUUGUGGGCGAUCCACUGAGCCACAAGAGUCACGAUUAUGCU
................((((.((((((((((((.......))))))))..........(((((((.((......))..)))))))......)))))))). (-18.98 = -19.54 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	9,590,778 – 9,590,880
Length	102
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	70.30
Mean single sequence MFE	-14.42
Consensus MFE	-8.64
Energy contribution	-9.04
Covariance contribution	0.40
Combinations/Pair	1.13
Mean z-score	-1.78
Structure conservation index	0.60
SVM decision value	1.24
SVM RNA-class probability	0.934729
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9590778 102 - 27905053
CUAACCGUGUUGAAAUUGUUCAAAUUUGGCCACUUGUAUAUAAAACUUU-UUUUGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAAGCACUUGU
....(((..(((((....)))))...)))....................-....((((.(((.(.((((((((.......)))))))).).))).)))).... ( -19.30)
>DroSec_CAF1 67082 84 - 1
CUAA-------------------UUUUGCCAACUUCUAUAUACAACUUUUUUUAGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAACCACUUGU
....-------------------..................((((.....(((((((........((((((((.......)))))))))))))))....)))) ( -14.40)
>DroSim_CAF1 77265 83 - 1
CUAA-------------------UUUUGCCAACUUCUAUAUACAACUUU-UUUAGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAACCACUUGU
....-------------------..................((((....-(((((((........((((((((.......)))))))))))))))....)))) ( -15.00)
>DroEre_CAF1 69908 99 - 1
-UAACCUUAAUAAAAUAGUUAAAUUCAAGCAUUUUCUAUAUGAAU-UUU-UCGAGUGCAUUAAUUAUAGCCAAACCA-AUUCAGCUAUCACUAAACUACUUGU
-..............(((((........((((((((.....))..-...-..)))))).......(((((.......-.....))))).....)))))..... (  -8.61)
>DroYak_CAF1 67776 87 - 1
--------------ACAGUAAAAGUCAAGCAAUUUCUUGAUGAAUCUUU-UUGAGUGCAUUAAUUAUAGCGCAGCCA-AUUCGGCUAUCACUAAACCACUUGU
--------------(((((....((((((......))))))........-.(((((((..........))))((((.-....)))).))).......)).))) ( -14.80)
>consensus
CUAA__________A__GU__AAUUUUGGCAACUUCUAUAUAAAACUUU_UUUAGUGUAUUAAUUAUAGCCAAUCCAAAUUUGGCUAUCACUGAACCACUUGU
......................................................(((..(((.(.((((((((.......)))))))).).)))..))).... ( -8.64 =  -9.04 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:51 2006