Locus 6088

Sequence ID	X_DroMel_CAF1
Location	15,616,463 – 15,616,733
Length	270
Max. P	0.974381

overview

Window 9

Location	15,616,463 – 15,616,573
Length	110
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	79.94
Mean single sequence MFE	-21.38
Consensus MFE	-16.20
Energy contribution	-18.20
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.76
SVM decision value	0.84
SVM RNA-class probability	0.863454
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15616463 110 + 22224390
UAAACCAACCUAUCUCAAACAUCUUGGGAUCUGGGCUACAACAUCCCAAUUUACUUUGCUAAUAUCGUAUUGUAAGUCGUUAUGGUAAAUACCA-GUACCAUCUAUACUUA
...........(((((((.....)))))))((((.......(((..(.((((((..(((.......)))..)))))).)..))).......)))-)............... ( -19.14)
>DroSec_CAF1 4649 88 + 1
-------------------CAU----GUAUCUGGGCUCCAACAUCCCAAUUCACUUUGCUAAUAUCGUAUCGUAAGUCGUAAUGGUGAGUACCAGGUACCAUCUAUACUUA
-------------------...----((((((((((((...(((..(.(((.((..(((.......)))..)).))).)..)))..)))).))))))))............ ( -20.40)
>DroSim_CAF1 4637 107 + 1
UAAA----UCUGGCUUAAACAUCUUGGGAUCUGGGCUCCAACAUCCCAAUUUACUUUGCUAAUAUCGUAUCGUAAGUCGUAAUGGUGAGUACCAGGUACCAUCUAUACUUA
....----................(((.((((((((((...(((..(.((((((..(((.......)))..)))))).)..)))..)))).)))))).))).......... ( -24.60)
>consensus
UAAA_____CU__CU_AAACAUCUUGGGAUCUGGGCUCCAACAUCCCAAUUUACUUUGCUAAUAUCGUAUCGUAAGUCGUAAUGGUGAGUACCAGGUACCAUCUAUACUUA
........................(((.((((((((((...(((..(.((((((..(((.......)))..)))))).)..)))..)))).)))))).))).......... (-16.20 = -18.20 +   2.00)

alignment

secondary structure

dotplot

Window 0

Location	15,616,573 – 15,616,693
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.61
Mean single sequence MFE	-42.60
Consensus MFE	-38.02
Energy contribution	-38.38
Covariance contribution	0.36
Combinations/Pair	1.09
Mean z-score	-1.47
Structure conservation index	0.89
SVM decision value	0.58
SVM RNA-class probability	0.788811
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15616573 120 + 22224390
UUUUUACUUACUCGAGCUAAGCGCCCGCGUUUAAGAAAAACGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUUUCGAUGGUAUCGUCGGAGAGAUAGUAGCACAGC
....................((((((((((((.....)))))..)))))..(((((((....))))))).(((((((((.(((...(((((((....))))))))))..))))))))))) ( -40.30)
>DroSec_CAF1 4737 120 + 1
UAUUUACUUACUCGCGCUAAGCGCCCGCGUUUGAGAAAAACGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUUUCGAUGGUAUCGUCGGAGAGGUAGUAGCACACC
.............((.....))((((((((((.....)))))..)))))..(((((((....))))))).(((((((((((((...(((((((....))))))))))).))))))))).. ( -47.30)
>DroSim_CAF1 4744 120 + 1
UAUUUACUUACUCGCGCUAAGCGACCGCGUUUGAGAAAAACGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUCUCGAUGGUAUCGUCGGAGAGGUAGUAGCACACC
......((((..((((.........))))..)))).....(((.....)))(((((((....))))))).(((((((((((((..((.(((((....))))))))))).))))))))).. ( -44.50)
>DroEre_CAF1 4957 114 + 1
------CUUACCCGAGCUAACCGUCCACGUUUGAGAAAAACGGUUGGGCCGUCGCGUCCCGAGUUGCGAAUGUGUUGCUCCUUGAUUUCGAUGGUAUCAUCGGAGAGGUAGUAACACAGC
------......((..((((((((...(......)....))))))))..))(((((........))))).(((((((((((((...(((((((....))))))))))).))))))))).. ( -38.80)
>DroYak_CAF1 4430 114 + 1
------CAUACCCGAGCCAAGCGUCCACGUUUGAGGAAAACGGUGGGUCCGUCGCGUCCUGAGUUGCGAAUGUGCUGCUCCUUGAUCUCGAUGGUGUCAUCGGAGAGGUAGUAGCACAGC
------......(((((((((((....))))))((((..((((.....))))....))))..))).))..(((((((((((((..((.(((((....))))))))))).))))))))).. ( -42.10)
>consensus
U_UUUACUUACUCGAGCUAAGCGCCCGCGUUUGAGAAAAACGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUUUCGAUGGUAUCGUCGGAGAGGUAGUAGCACAGC
......................((((.(((((.....)))))...))))..(((((((....))))))).(((((((((((((....((((((....)))))).)))).))))))))).. (-38.02 = -38.38 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	15,616,613 – 15,616,733
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.42
Mean single sequence MFE	-45.85
Consensus MFE	-40.80
Energy contribution	-40.60
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.68
Structure conservation index	0.89
SVM decision value	1.73
SVM RNA-class probability	0.974381
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15616613 120 + 22224390
CGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUUUCGAUGGUAUCGUCGGAGAGAUAGUAGCACAGCUCCAGCUUGCGUACGUCUCCGAACUCGGUUCUAUCGUCCC
.((((((((..(((((((....))))))).(((((((((.(((...(((((((....))))))))))..))))))))))).)))))).(((.......(((....)))......)))... ( -44.12)
>DroSec_CAF1 4777 120 + 1
CGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUUUCGAUGGUAUCGUCGGAGAGGUAGUAGCACACCUCCAGCUUGCGUACGUCUCCGAACUCGGUUCUAUCGUCCC
.(((((((...(((((((....))))))).(((((((((((((...(((((((....))))))))))).)))))))))..))))))).(((.......(((....)))......)))... ( -46.42)
>DroSim_CAF1 4784 120 + 1
CGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUCUCGAUGGUAUCGUCGGAGAGGUAGUAGCACACCUCCAGCUUCCGCACGUCUCCAAACUCGGUUCUAUCGUCCC
((((.(((((((((((((....))))))).(((((((((((((..((.(((((....))))))))))).)))))))))......((....)).............)))))).)))).... ( -45.20)
>DroEre_CAF1 4991 120 + 1
CGGUUGGGCCGUCGCGUCCCGAGUUGCGAAUGUGUUGCUCCUUGAUUUCGAUGGUAUCAUCGGAGAGGUAGUAACACAGCUCCAGCUUUCGCACAUCUCCGAACUCGGUUCUAUCAUCCC
.(((.((((((....((.(.(((.(((((((((((((((((((...(((((((....))))))))))).)))))))))((....)).))))))...))).).)).)))))).)))..... ( -44.90)
>DroYak_CAF1 4464 120 + 1
CGGUGGGUCCGUCGCGUCCUGAGUUGCGAAUGUGCUGCUCCUUGAUCUCGAUGGUGUCAUCGGAGAGGUAGUAGCACAGCUCCAGCUUGCGCACAUCUCCGAACUCGGUUCUAUCGUCCC
(((((((...((.((((...((((((.((.(((((((((((((..((.(((((....))))))))))).)))))))))..))))))))))))))....(((....))).))))))).... ( -48.60)
>consensus
CGGUUGGGCCGUCGCGACCUGAGUUGCGAAUGUGCUGCUCCUUGAUUUCGAUGGUAUCGUCGGAGAGGUAGUAGCACAGCUCCAGCUUGCGCACGUCUCCGAACUCGGUUCUAUCGUCCC
((((.((((((..(((....((((((.((.(((((((((((((....((((((....)))))).)))).)))))))))..)))))))).))).............)))))).)))).... (-40.80 = -40.60 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:52 2006