Locus 4108

Sequence ID	X_DroMel_CAF1
Location	10,842,306 – 10,842,492
Length	186
Max. P	0.987732

overview

Window 1

Location	10,842,306 – 10,842,413
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.62
Mean single sequence MFE	-31.82
Consensus MFE	-22.54
Energy contribution	-22.60
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-1.58
Structure conservation index	0.71
SVM decision value	0.10
SVM RNA-class probability	0.585057
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10842306 107 + 22224390
CCAACAAUUCACACCCAACGACGAAUUGCCAGUGGAUU-GAAGUGGCCAGAAGCCAACG-------GGCACAUGGGCGAUGGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAAAC-----
((..((((((((...(((.......)))...)))))))-)...((((.....))))..)-------).......((((.(((.(..((((.....)))).).))).)))).....----- ( -29.50)
>DroSec_CAF1 21078 97 + 1
-----AAU-----CCCAACGACGAAUCGCCAGUGGAUU-GGAGUGGCCAGAGGCCAACG-------GGCACAUGGGCGAUGGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAACC-----
-----..(-----((((........(((((.(((..((-(...(((((...))))).))-------)...))).))))))))))..((((.....((....))....))))....----- ( -31.30)
>DroSim_CAF1 1969 104 + 1
-CA--AAUUCGCACCCAACGACAAAUCGCCAGUGGAUU-GGAGUGGCCAGAGGCCAACG-------GGCACAUGGGCGAUGGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAAAC-----
-..--.(((.(((((((........(((((.(((..((-(...(((((...))))).))-------)...))).)))))))))...((((.....)))).))).)))........----- ( -32.20)
>DroYak_CAF1 10076 114 + 1
-C--CAAUUCGCACCCAAC---GAAUCACCAGUGGAAUGGGAGUGGACAGAGGCCAAUGGCCCAGAGGCACAUGGGCGCUGGGAAAUGGCCAAAAGCCAAUGCCAAUGCUAAAGCCAAAG
-.--...(((((.((((..---...(((....)))..)))).)))))....(((.....(((((........)))))((..((...((((.....))))...))...))....))).... ( -34.30)
>consensus
_C___AAUUCGCACCCAACGACGAAUCGCCAGUGGAUU_GGAGUGGCCAGAGGCCAACG_______GGCACAUGGGCGAUGGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAAAC_____
...........................((((.(........).))))((...(((...........)))...))((((.(((.(..((((.....)))).).))).)))).......... (-22.54 = -22.60 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	10,842,378 – 10,842,492
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.45
Mean single sequence MFE	-42.38
Consensus MFE	-37.81
Energy contribution	-38.12
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-4.17
Structure conservation index	0.89
SVM decision value	2.09
SVM RNA-class probability	0.987732
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10842378 114 + 22224390
GGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAAAC------UAAAGCCAAAGCUAGAGCUAAAGCCCAGCUAACUAGCCCGUUUGCCACUCGCUAAUAGUUGGCGUUGGCCAUUUCCUGG
(((((((((((((..((((((......((......------..((((....(((((((((.......))))..)))))..)))).......)).....)))))).))))))))))))).. ( -41.56)
>DroSec_CAF1 21140 114 + 1
GGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAACC------AAAGGCCAAAGCUAAAGCUAAAGCCCUGCUAACUAGCCCGUUUGCCACUCACUAAUAGUUGGCGUUGGCCAUUUCCCGG
(((((((((((((..((((((((....))(((((.------...(((...(((....)))...)))..(((....)))..))))).............)))))).))))))))))))).. ( -43.70)
>DroSim_CAF1 2038 114 + 1
GGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAAAC------UAAAGCCAAAGCUAGAGCUAAAGCCCUGCUAACUAGCCCGUUUGCCACUCGCUAAUAGUUGGCGUUGGCCAUUUCCCGG
(((((((((((((..((((((......((......------..((((....((((((((.........)))..)))))..)))).......)).....)))))).))))))))))))).. ( -43.36)
>DroYak_CAF1 10150 120 + 1
GGGAAAUGGCCAAAAGCCAAUGCCAAUGCUAAAGCCAAAGCCAAAGCCAAAGCCAAAGCCAAAGCCCUGCUAACUAGCCCGUUUGCCACUCGCUAAUAGUUGGCGUUGGCCAUUUCCCGG
(((((((((((((..((((((......(((...((....))...)))...(((....((..((((...(((....)))..)))))).....)))....)))))).))))))))))))).. ( -40.90)
>consensus
GGGAAAUGGCCAAAAGCCAAUGCCAAUGCCAAAAC______UAAAGCCAAAGCUAAAGCUAAAGCCCUGCUAACUAGCCCGUUUGCCACUCGCUAAUAGUUGGCGUUGGCCAUUUCCCGG
(((((((((((((..((((((......((................((...(((....)))...))...((.(((......))).)).....)).....)))))).))))))))))))).. (-37.81 = -38.12 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	10,842,378 – 10,842,492
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.45
Mean single sequence MFE	-54.15
Consensus MFE	-47.61
Energy contribution	-47.80
Covariance contribution	0.19
Combinations/Pair	1.07
Mean z-score	-5.46
Structure conservation index	0.88
SVM decision value	1.08
SVM RNA-class probability	0.911500
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10842378 114 - 22224390
CCAGGAAAUGGCCAACGCCAACUAUUAGCGAGUGGCAAACGGGCUAGUUAGCUGGGCUUUAGCUCUAGCUUUGGCUUUA------GUUUUGGCAUUGGCAUUGGCUUUUGGCCAUUUCCC
...((((((((((((.(((((......((.((((.(((((.((((((..((((((((....)).))))))))))))...------).)))).)))).)).)))))..)))))))))))). ( -51.70)
>DroSec_CAF1 21140 114 - 1
CCGGGAAAUGGCCAACGCCAACUAUUAGUGAGUGGCAAACGGGCUAGUUAGCAGGGCUUUAGCUUUAGCUUUGGCCUUU------GGUUUGGCAUUGGCAUUGGCUUUUGGCCAUUUCCC
..(((((((((((((.(((((......((.((((.((((((((((((..((((((((....))))).))))))))))..------.))))).)))).)).)))))..))))))))))))) ( -55.30)
>DroSim_CAF1 2038 114 - 1
CCGGGAAAUGGCCAACGCCAACUAUUAGCGAGUGGCAAACGGGCUAGUUAGCAGGGCUUUAGCUCUAGCUUUGGCUUUA------GUUUUGGCAUUGGCAUUGGCUUUUGGCCAUUUCCC
..(((((((((((((.(((((......((.((((.(((((.((((((..((((((((....))))).)))))))))...------).)))).)))).)).)))))..))))))))))))) ( -53.60)
>DroYak_CAF1 10150 120 - 1
CCGGGAAAUGGCCAACGCCAACUAUUAGCGAGUGGCAAACGGGCUAGUUAGCAGGGCUUUGGCUUUGGCUUUGGCUUUGGCUUUGGCUUUAGCAUUGGCAUUGGCUUUUGGCCAUUUCCC
..(((((((((((((.((((((..((.((.....)).))..)((((((..((((((((..((((..(((....)))..))))..)))))).)))))))).)))))..))))))))))))) ( -56.00)
>consensus
CCGGGAAAUGGCCAACGCCAACUAUUAGCGAGUGGCAAACGGGCUAGUUAGCAGGGCUUUAGCUCUAGCUUUGGCUUUA______GUUUUGGCAUUGGCAUUGGCUUUUGGCCAUUUCCC
..(((((((((((((.(((((......((.((((.((((...(((....)))((((((..(((....)))..)))))).........)))).)))).)).)))))..))))))))))))) (-47.61 = -47.80 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:34 2006