Locus 1753

Sequence ID	3L_DroMel_CAF1
Location	5,045,050 – 5,045,267
Length	217
Max. P	0.965593

overview

Window 6

Location	5,045,050 – 5,045,160
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	94.10
Mean single sequence MFE	-22.31
Consensus MFE	-18.96
Energy contribution	-18.64
Covariance contribution	-0.32
Combinations/Pair	1.09
Mean z-score	-1.52
Structure conservation index	0.85
SVM decision value	0.75
SVM RNA-class probability	0.839860
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5045050 110 - 23771897
GCAAAGCG-----UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGGAGGCAAAUAAACGAGCCGGCAGC----AGAAUCAGCAUCA
((((((((-----(........))...((((....))))))))).(((...(((..........((((.......)))).(((..........))).)))))----)......)).... ( -21.20)
>DroSec_CAF1 251571 110 - 1
GCAAAGCG-----UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGGAGGCAAAUAAACGAGCCGGCAGC----AGAAUCAGCAUCA
((((((((-----(........))...((((....))))))))).(((...(((..........((((.......)))).(((..........))).)))))----)......)).... ( -21.20)
>DroSim_CAF1 272472 110 - 1
GCAAAGCG-----UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGGAGGCAAAUAAACGAGCCGGCAGC----AGAAUCAGCAUCA
((((((((-----(........))...((((....))))))))).(((...(((..........((((.......)))).(((..........))).)))))----)......)).... ( -21.20)
>DroEre_CAF1 255000 115 - 1
GGAAAGCGUAGAACAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGGAGGCAAAUAAGCGAGCUGGCAGC----AGAAUCAGCAUCA
.....((...............))...((........(((((((((((....))))))).....((((.......))))..........))))(((((....----....))))).)). ( -22.96)
>DroYak_CAF1 261394 114 - 1
GAAAAGCG-----CAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGGAGGCAAAUAAGCGAGUCGGCAGCAGGCAGAAUCAGCAGCA
.....(((-----(........((...((((....))))(((((((((....))))))......((((.......)))).)))......))((.((.((.....)).)).)).)).)). ( -25.00)
>consensus
GCAAAGCG_____UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGGAGGCAAAUAAACGAGCCGGCAGC____AGAAUCAGCAUCA
......................((...((((....))))(((((((((....))))))).....((((.......)))).(((..........))).))..............)).... (-18.96 = -18.64 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	5,045,086 – 5,045,191
Length	105
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.17
Mean single sequence MFE	-19.50
Consensus MFE	-17.54
Energy contribution	-17.26
Covariance contribution	-0.28
Combinations/Pair	1.07
Mean z-score	-1.16
Structure conservation index	0.90
SVM decision value	-0.05
SVM RNA-class probability	0.509186
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5045086 105 + 23771897
CCACUUGGUCUGUGGUAUUUUUUAUGCAUUUGCAUAAAGCGAAAUGUAUUUCUAUGCUAUGUUCUA-----CGCUUUGCCAACAUUUUCACUACUGUUUUUUCUGGCGCU
.....(((..((((((((.....((((((((((.....)).))))))))....))))))))..)))-----......((((.......((....)).......))))... ( -19.94)
>DroSec_CAF1 251607 105 + 1
CCACUUGGUCUGUGGUAUUUUUUAUGCAUUUGCAUAAAGCGAAAUGUAUUUCUAUGCUAUGUUCUA-----CGCUUUGCCAACAUUUUCACUACUGUUUUUUCUGGCGCU
.....(((..((((((((.....((((((((((.....)).))))))))....))))))))..)))-----......((((.......((....)).......))))... ( -19.94)
>DroSim_CAF1 272508 105 + 1
CCACUUGGUCUGUGGUAUUUUUUAUGCAUUUGCAUAAAGCGAAAUGUAUUUCUAUGCUAUGUUCUA-----CGCUUUGCCAACAUUUUCACUACUGUUUUUUCUGGCGCU
.....(((..((((((((.....((((((((((.....)).))))))))....))))))))..)))-----......((((.......((....)).......))))... ( -19.94)
>DroEre_CAF1 255036 110 + 1
CCACUUGGUCUGUGGUAUUUUUUAUGCAUUUGCAUAAAGCGAAAUGUAUUUCUAUGCUAUGUUCUGUUCUACGCUUUCCCAACAUUUUCACUACUGUUUUUUCUGGCGCU
......((..((((((((.....((((((((((.....)).))))))))....))))))))..))......((((.....((((..........))))......)))).. ( -18.80)
>DroYak_CAF1 261434 105 + 1
CCACUUGGUCUGUGGUAUUUUUUAUGCAUUUGCAUAAAGCGAAAUGUAUUUCUAUGCUAUGUUCUG-----CGCUUUUCCAACAUUUUCACUACUGUUUUUUCUGGGUCU
..(((..(.(.(((((....(((((((....)))))))(((((..((((....))))....))).)-----).................))))).)......)..))).. ( -18.90)
>consensus
CCACUUGGUCUGUGGUAUUUUUUAUGCAUUUGCAUAAAGCGAAAUGUAUUUCUAUGCUAUGUUCUA_____CGCUUUGCCAACAUUUUCACUACUGUUUUUUCUGGCGCU
.....(((..((((((((.....((((((((((.....)).))))))))....))))))))..)))...........((((.......((....)).......))))... (-17.54 = -17.26 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	5,045,086 – 5,045,191
Length	105
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.17
Mean single sequence MFE	-18.96
Consensus MFE	-16.32
Energy contribution	-16.32
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.86
SVM decision value	0.49
SVM RNA-class probability	0.755586
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5045086 105 - 23771897
AGCGCCAGAAAAAACAGUAGUGAAAAUGUUGGCAAAGCG-----UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGG
.(((((((.....((....)).......)))))...((.-----.........))...((((....))))))(((((((....))))))).....((((.......)))) ( -20.20)
>DroSec_CAF1 251607 105 - 1
AGCGCCAGAAAAAACAGUAGUGAAAAUGUUGGCAAAGCG-----UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGG
.(((((((.....((....)).......)))))...((.-----.........))...((((....))))))(((((((....))))))).....((((.......)))) ( -20.20)
>DroSim_CAF1 272508 105 - 1
AGCGCCAGAAAAAACAGUAGUGAAAAUGUUGGCAAAGCG-----UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGG
.(((((((.....((....)).......)))))...((.-----.........))...((((....))))))(((((((....))))))).....((((.......)))) ( -20.20)
>DroEre_CAF1 255036 110 - 1
AGCGCCAGAAAAAACAGUAGUGAAAAUGUUGGGAAAGCGUAGAACAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGG
...................(((((((((((.....)))))................((....))..))))))(((((((....))))))).....((((.......)))) ( -16.80)
>DroYak_CAF1 261434 105 - 1
AGACCCAGAAAAAACAGUAGUGAAAAUGUUGGAAAAGCG-----CAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGG
...................((((((..(((.....)))(-----(........))...........))))))(((((((....))))))).....((((.......)))) ( -17.40)
>consensus
AGCGCCAGAAAAAACAGUAGUGAAAAUGUUGGCAAAGCG_____UAGAACAUAGCAUAGAAAUACAUUUCGCUUUAUGCAAAUGCAUAAAAAAUACCACAGACCAAGUGG
...................((((((.(((.......((...............))........)))))))))(((((((....))))))).....((((.......)))) (-16.32 = -16.32 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	5,045,160 – 5,045,267
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	98.88
Mean single sequence MFE	-29.40
Consensus MFE	-26.81
Energy contribution	-27.41
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.91
SVM decision value	1.58
SVM RNA-class probability	0.965593
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5045160 107 - 23771897
GGUGCCCAUCGCCGGGCGCUCAUUAAAAUGCAACUGUGUGCGGUAAUGGCCAAAAAGGGAAACGUGCAAUAAAAGCAGCGCCAGAAAAAACAGUAGUGAAAAUGUUG
.((((((......))))))((((((........(((.(((((((....)))......(....).(((.......)))))))))).........))))))........ ( -30.03)
>DroSec_CAF1 251681 107 - 1
GGUGCCCAUCGCCGGGCGCUCAUUAAAAUGCAACUGUGUGCGGUAAUGGCCAAAAAGGGAAACGUGCAAUAAAAGCAGCGCCAGAAAAAACAGUAGUGAAAAUGUUG
.((((((......))))))((((((........(((.(((((((....)))......(....).(((.......)))))))))).........))))))........ ( -30.03)
>DroSim_CAF1 272582 107 - 1
GGUGCCCAUCGCCGGGCGCUCAUUAAAAUGCAACUGUGUGCGGUAAUGGCCAAAAAGGGAAACGUGCAAUAAAAGCAGCGCCAGAAAAAACAGUAGUGAAAAUGUUG
.((((((......))))))((((((........(((.(((((((....)))......(....).(((.......)))))))))).........))))))........ ( -30.03)
>DroEre_CAF1 255115 107 - 1
GGUGCCCAUCGCCGGGCGCUCAUUAAAAUGCAACUGUGUGCGGUAAUGGGCAAAAAGGGAAACGUGCAAUAAAAGCAGCGCCAGAAAAAACAGUAGUGAAAAUGUUG
(((((((((..(((.((((................)))).)))..))))))......(....).(((.......)))..)))......((((..........)))). ( -30.89)
>DroYak_CAF1 261508 107 - 1
GGUGCCCAUCGCCGGGCGCUCAUUAAAAUGCAACUGUGUGCGGUAAUGGCCAAAAAGGGAAACGUGCAAUAAAAGCAGACCCAGAAAAAACAGUAGUGAAAAUGUUG
(((((((......))))))).........((.(((((....(((....))).....(((...(.(((.......)))).))).......))))).)).......... ( -26.00)
>consensus
GGUGCCCAUCGCCGGGCGCUCAUUAAAAUGCAACUGUGUGCGGUAAUGGCCAAAAAGGGAAACGUGCAAUAAAAGCAGCGCCAGAAAAAACAGUAGUGAAAAUGUUG
.((((((......))))))((((((........(((.(((((((....)))......(....).(((.......)))))))))).........))))))........ (-26.81 = -27.41 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:23 2006