Locus 2340

Sequence ID	2L_DroMel_CAF1
Location	6,340,208 – 6,340,320
Length	112
Max. P	0.918094

overview

Window 3

Location	6,340,208 – 6,340,320
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.73
Mean single sequence MFE	-30.18
Consensus MFE	-12.00
Energy contribution	-14.88
Covariance contribution	2.88
Combinations/Pair	1.07
Mean z-score	-2.53
Structure conservation index	0.40
SVM decision value	0.80
SVM RNA-class probability	0.852737
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6340208 112 + 22407834
UUAUGACACCCCAUUAUAGGGUUACCUACCUAUUAAAGC--------UAGACUAUUAGUUCUUCCAAUUAAAGAACCAUUAAAAGGGCAGGUUCCGUAAUGGGAUUACAUUUAAUGGACU
.........((((((((.(((..((((.(((.((((((.--------....))....((((((.......))))))..)))).)))..)))))))))))))))................. ( -24.30)
>DroSec_CAF1 31280 120 + 1
UUAUGAGACCCCAUUAUGGGGUUACCUACCUAUUAAAGACUAUUAUAAAGACUAUUAGUUCUUCCACUUAAAGAACCAUUAAAAGGGUAGGUUCCGUAUUGGGGUUACAUUUAAUGGAUU
..(((.(((((((.((((((...((((((((.....((.((.......)).))....((((((.......))))))........)))))))))))))).))))))).))).......... ( -35.60)
>DroSim_CAF1 33243 112 + 1
UCAUGACACCCCAUUAUGGGGUUACCUACCUAUUAAAGC--------UAGACUAUUAGUUCUUCCACUUAAAGAACCAUUAAAAGGGUAGGUUCCGUAUUGGGGUUACAUUUAAUGGAUU
..(((..((((((.((((((...((((((((.....((.--------....))....((((((.......))))))........)))))))))))))).))))))..))).......... ( -32.40)
>DroEre_CAF1 31942 109 + 1
UUAUGACACCCCAUUAUGGGGUUACCUACCUAGUAAAGC--------UAGACUUCUAGAUCUUCCACUCAAAGUACCGAUAAAAAGCUAAGGUCAGGAUUAGGGUUGC---UGGGUUGGU
.......(((((.....))))).(((.(((((((((..(--------(((..((((.((((((........(((...........)))))))))))))))))..))))---))))).))) ( -31.40)
>DroYak_CAF1 31378 111 + 1
CUAUGAC-CCCCAUUAUGGGGUUACCUACCUAUUAACGC--------UAGACCCUUAGAUCUGCCACACAAAGAACCAUUAAAAGGGUAAGGUCGGUUUUGGGGUUACAUUUAAUUAAUU
...((((-(((......)))))))...............--------..((((((.(((((.(((.(.....).(((........)))..))).))))).)))))).............. ( -27.20)
>consensus
UUAUGACACCCCAUUAUGGGGUUACCUACCUAUUAAAGC________UAGACUAUUAGUUCUUCCACUUAAAGAACCAUUAAAAGGGUAGGUUCCGUAUUGGGGUUACAUUUAAUGGAUU
.......((((((.(((.(((...(((((((................(((....)))((((((.......))))))........))))))).)))))).))))))............... (-12.00 = -14.88 +   2.88)

alignment

secondary structure

dotplot

Window 4

Location	6,340,208 – 6,340,320
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.73
Mean single sequence MFE	-29.13
Consensus MFE	-17.12
Energy contribution	-19.32
Covariance contribution	2.20
Combinations/Pair	1.17
Mean z-score	-2.34
Structure conservation index	0.59
SVM decision value	1.12
SVM RNA-class probability	0.918094
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6340208 112 - 22407834
AGUCCAUUAAAUGUAAUCCCAUUACGGAACCUGCCCUUUUAAUGGUUCUUUAAUUGGAAGAACUAAUAGUCUA--------GCUUUAAUAGGUAGGUAACCCUAUAAUGGGGUGUCAUAA
..........(((..(((((((((..(.(((((((...(((((((((((((.....)))))))))..((....--------.))))))..)))))))....)..)))))))))..))).. ( -31.50)
>DroSec_CAF1 31280 120 - 1
AAUCCAUUAAAUGUAACCCCAAUACGGAACCUACCCUUUUAAUGGUUCUUUAAGUGGAAGAACUAAUAGUCUUUAUAAUAGUCUUUAAUAGGUAGGUAACCCCAUAAUGGGGUCUCAUAA
..........(((..((((((.((.((.(((((((...(((((((((((((.....)))))))))..((.((.......)).))))))..)))))))....)).)).))))))..))).. ( -34.00)
>DroSim_CAF1 33243 112 - 1
AAUCCAUUAAAUGUAACCCCAAUACGGAACCUACCCUUUUAAUGGUUCUUUAAGUGGAAGAACUAAUAGUCUA--------GCUUUAAUAGGUAGGUAACCCCAUAAUGGGGUGUCAUGA
..........(((..((((((.((.((.(((((((...(((((((((((((.....)))))))))..((....--------.))))))..)))))))....)).)).))))))..))).. ( -31.70)
>DroEre_CAF1 31942 109 - 1
ACCAACCCA---GCAACCCUAAUCCUGACCUUAGCUUUUUAUCGGUACUUUGAGUGGAAGAUCUAGAAGUCUA--------GCUUUACUAGGUAGGUAACCCCAUAAUGGGGUGUCAUAA
(((.(((.(---(...((((.......(((.............)))......)).)).(((.((((....)))--------).))).)).))).))).(((((.....)))))....... ( -23.64)
>DroYak_CAF1 31378 111 - 1
AAUUAAUUAAAUGUAACCCCAAAACCGACCUUACCCUUUUAAUGGUUCUUUGUGUGGCAGAUCUAAGGGUCUA--------GCGUUAAUAGGUAGGUAACCCCAUAAUGGGG-GUCAUAG
..........................(((((((((...(((((((((........)))(((((....))))).--------.))))))..))))))...((((.....))))-))).... ( -24.80)
>consensus
AAUCCAUUAAAUGUAACCCCAAUACGGAACCUACCCUUUUAAUGGUUCUUUAAGUGGAAGAACUAAUAGUCUA________GCUUUAAUAGGUAGGUAACCCCAUAAUGGGGUGUCAUAA
..........(((..((((((.((.((.(((((((.......(((((((((.....)))))))))...(.............).......)))))))....)).)).))))))..))).. (-17.12 = -19.32 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:42 2006