Locus 3883

Sequence ID	3R_DroMel_CAF1
Location	10,558,787 – 10,558,884
Length	97
Max. P	0.945960

overview

Window 4

Location	10,558,787 – 10,558,884
Length	97
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	69.45
Mean single sequence MFE	-41.22
Consensus MFE	-27.75
Energy contribution	-26.86
Covariance contribution	-0.88
Combinations/Pair	1.37
Mean z-score	-1.49
Structure conservation index	0.67
SVM decision value	1.36
SVM RNA-class probability	0.945960
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10558787 97 + 27905053
-----------------UUUGCCGCUGCCGUUGCUCUUGGUACCGCCGCCAAAUUUGCUGCUCCUAAUGCUAAUGCCGCU---GCGAAGGCGGUAGCAGCGGCUGCUGCGGCGAAAA
-----------------((((((((.(((((((((...(....)((((((...(((((.((.......((....)).)).---))))))))))))))))))))....)))))))).. ( -44.70)
>DroPse_CAF1 10739 94 + 1
-----------------UGCACGACCCUCGUUCCCCUUGUGACGGCUAUUGUUUUUGUUGAUUUGAAUGCU---GCCACUCAGGCGGAGGCGGCGGCAGCGGCAG---GGGCGCAAU
-----------------((((((.....)))..(((((((..((((..........)))).......((((---(((.(((.....)))..)))))))...))))---))).))).. ( -32.30)
>DroSim_CAF1 7940 97 + 1
-----------------UUUGCCGCUGCCGUUGCUCUUGGUACCGCCGCCAAAUUUGCUGCUCCUAAUGCUAAUGCCGCU---GCGAAGGCGGUAGCAGCGGCUGCUGCGGCGAAAA
-----------------((((((((.(((((((((...(....)((((((...(((((.((.......((....)).)).---))))))))))))))))))))....)))))))).. ( -44.70)
>DroEre_CAF1 16980 114 + 1
ACUCCGAUCCGCUGACGUUUGCCGCUGCUGUUGCUCUUGGUACCGCCGCCAAAUUUGCUGCUCCUAAUGCUAAUGCCGCU---GCGAAGGCGGUAGCAGCGGCUGCUACGGCGAAGA
.........(((((..((..((((((((((..((.(((.(((.(((.((.......)).)).......((....)).).)---)).)))))..)))))))))).))..))))).... ( -44.10)
>DroYak_CAF1 17108 111 + 1
---CCGGUCCGCUGGCGUUUGCCGCCGCUGUUGCUCUUGGUACCGCCGCCAAAUUUGCUGCUCCUAAUGCUAAUGCCGCU---GCGAAGGCGGUAGCAGCGGCUGCAACGGCGAAGA
---.......((.(((....)))))(((((((((....(....)(((((..........((.......))...(((..((---((....))))..)))))))).))))))))).... ( -44.70)
>DroPer_CAF1 10731 94 + 1
-----------------UGCACGACCCUCGUUCCCCUUGUGGCGGCUAUUGUUUUUGUUGAUUUGAAUGCU---GCCACUCAGGCGGAGGCGGCGGCAGCGGCAG---GGGCGCAAU
-----------------(((....((((..(((((((.((((((((....(((......)))......)))---)))))..))).))))((.((....)).))))---))..))).. ( -36.80)
>consensus
_________________UUUGCCGCCGCCGUUGCUCUUGGUACCGCCGCCAAAUUUGCUGCUCCUAAUGCUAAUGCCGCU___GCGAAGGCGGUAGCAGCGGCUGCU_CGGCGAAAA
.................((((((((.(((((((((.........((((((...(((((..........((....)).......)))))))))))))))))))).))...)))))).. (-27.75 = -26.86 +  -0.88)

alignment

secondary structure

dotplot

Window 5

Location	10,558,787 – 10,558,884
Length	97
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	69.45
Mean single sequence MFE	-37.26
Consensus MFE	-23.12
Energy contribution	-23.07
Covariance contribution	-0.05
Combinations/Pair	1.38
Mean z-score	-1.25
Structure conservation index	0.62
SVM decision value	0.47
SVM RNA-class probability	0.747512
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10558787 97 - 27905053
UUUUCGCCGCAGCAGCCGCUGCUACCGCCUUCGC---AGCGGCAUUAGCAUUAGGAGCAGCAAAUUUGGCGGCGGUACCAAGAGCAACGGCAGCGGCAAA-----------------
.....(((((.((.((((((((..........))---))))))....((.((.((.((.((.......)).))....)).)).))....)).)))))...----------------- ( -37.50)
>DroPse_CAF1 10739 94 - 1
AUUGCGCCC---CUGCCGCUGCCGCCGCCUCCGCCUGAGUGGC---AGCAUUCAAAUCAACAAAAACAAUAGCCGUCACAAGGGGAACGAGGGUCGUGCA-----------------
..(((((((---((.((((((((((((........)).)))))---))).......................((.......))))....))))..)))))----------------- ( -29.30)
>DroSim_CAF1 7940 97 - 1
UUUUCGCCGCAGCAGCCGCUGCUACCGCCUUCGC---AGCGGCAUUAGCAUUAGGAGCAGCAAAUUUGGCGGCGGUACCAAGAGCAACGGCAGCGGCAAA-----------------
.....(((((.((.((((((((..........))---))))))....((.((.((.((.((.......)).))....)).)).))....)).)))))...----------------- ( -37.50)
>DroEre_CAF1 16980 114 - 1
UCUUCGCCGUAGCAGCCGCUGCUACCGCCUUCGC---AGCGGCAUUAGCAUUAGGAGCAGCAAAUUUGGCGGCGGUACCAAGAGCAACAGCAGCGGCAAACGUCAGCGGAUCGGAGU
.(((((((((.((.((((((((..........))---))))))....((.((.((.((.((.......)).))....)).)).))....)).)))))...((....))....)))). ( -40.60)
>DroYak_CAF1 17108 111 - 1
UCUUCGCCGUUGCAGCCGCUGCUACCGCCUUCGC---AGCGGCAUUAGCAUUAGGAGCAGCAAAUUUGGCGGCGGUACCAAGAGCAACAGCGGCGGCAAACGCCAGCGGACCGG---
...((((((((((.((((((((..........))---))))))....((.......)).))))...))))))((((.((....((....))((((.....))))...)))))).--- ( -47.30)
>DroPer_CAF1 10731 94 - 1
AUUGCGCCC---CUGCCGCUGCCGCCGCCUCCGCCUGAGUGGC---AGCAUUCAAAUCAACAAAAACAAUAGCCGCCACAAGGGGAACGAGGGUCGUGCA-----------------
..(((((((---((((.((....)).)).(((.(((..(((((---.((......................)).))))).))))))...))))..)))))----------------- ( -31.35)
>consensus
UUUUCGCCG_AGCAGCCGCUGCUACCGCCUUCGC___AGCGGCAUUAGCAUUAGGAGCAGCAAAUUUGGCGGCGGUACCAAGAGCAACGGCAGCGGCAAA_________________
..............(((((((((((((((..(((....)))((....)).....................)))))).....(.....)))))))))).................... (-23.12 = -23.07 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:31 2006