Locus 7141

Sequence ID	2L_DroMel_CAF1
Location	20,007,395 – 20,007,533
Length	138
Max. P	0.991183

overview

Window 8

Location	20,007,395 – 20,007,493
Length	98
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	75.42
Mean single sequence MFE	-33.31
Consensus MFE	-15.45
Energy contribution	-15.78
Covariance contribution	0.34
Combinations/Pair	1.32
Mean z-score	-2.64
Structure conservation index	0.46
SVM decision value	1.94
SVM RNA-class probability	0.983390
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20007395 98 + 22407834
UUGUUGGGCAAUUGUUUGGCUGUUGCCAAACAUCCAGGCAAACAUUCAGCCAACAACGUCGGGCGGCGAGUUGGGAGAACGCCUGCUUUUGCCCAAAU
...((((((((.((((((((....))))))))..(((((.....(((..(((((..((((....)))).)))))..))).)))))...)))))))).. ( -41.80)
>DroSec_CAF1 185149 83 + 1
UUGUUGGGCAAUUGGUUGGCUGUUGCCAAAC------------AUUCAGCC---AACGUCGGGCGGCGAGUUGGGAGAACGCCUGCUUUUGGCCAAAU
...((((.(((..(((((((((.((.....)------------)..)))))---)))..((((((..............)))))))..))).)))).. ( -30.74)
>DroSim_CAF1 187655 83 + 1
UUGUUGGGCAAUUGUUUGGCUGUUGCCAAAC------------AUUCAGCC---AACGUCGGGCGGCGAGUUGGGAGAACGCCUGCUUUUGGCCAAAU
..(((((.....((((((((....)))))))------------).....))---)))....(((.(.((((.((.......)).)))).).))).... ( -30.30)
>DroEre_CAF1 182585 94 + 1
UUGUUGGGCAAAUGUUUGGCUGUUGCCAAACAUCCAGGCAAACAUUCAGCC---AACGGCG-GCCGCAAGUACGGAGAACGCCUGCUUUUGGCCAAAU
((((..((...(((((((((....)))))))))))..)))).......(((---...)))(-((((.(((((.((......))))))).))))).... ( -36.40)
>DroYak_CAF1 183543 95 + 1
UUGUUGGGCAAUUGUUUGGCUGUUGCCAACCAUCCAGGCAAAAAUGCAGUC---AACGGCGGGCCCCAAGUACGGAGAUCGCCUGUUUUUGGCCAAAU
...((((.(((....((((((((((((.........)))).....))))))---)).((((..(.((......)).)..)))).....))).)))).. ( -31.00)
>DroAna_CAF1 179487 84 + 1
UUGUUGGGUAAUUGUUUGGCUGUC-----------UGGCUGUUUGUUGCCU---AACGGAAAGUAGCAAGCAUCGAGAAUGCCAACUUUUGGCCAAAU
...((((.(((..(((.(((..((-----------(.(.((((((((((..---........)))))))))).).)))..))))))..))).)))).. ( -29.60)
>consensus
UUGUUGGGCAAUUGUUUGGCUGUUGCCAAAC____AGGCAAA_AUUCAGCC___AACGGCGGGCGGCAAGUAGGGAGAACGCCUGCUUUUGGCCAAAU
...((((.(((.((((.(((((........................)))))...)))).((((((..............))))))...))).)))).. (-15.45 = -15.78 +   0.34)

alignment

secondary structure

dotplot

Window 9

Location	20,007,395 – 20,007,493
Length	98
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	75.42
Mean single sequence MFE	-31.89
Consensus MFE	-10.02
Energy contribution	-10.93
Covariance contribution	0.92
Combinations/Pair	1.22
Mean z-score	-3.49
Structure conservation index	0.31
SVM decision value	2.25
SVM RNA-class probability	0.991183
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20007395 98 - 22407834
AUUUGGGCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUUGUUGGCUGAAUGUUUGCCUGGAUGUUUGGCAACAGCCAAACAAUUGCCCAACAA
..((((((((..((((((((((..(((((.((.(....).))..)))))..)))))))))).....((((((((....)))))))).))))))))... ( -45.20)
>DroSec_CAF1 185149 83 - 1
AUUUGGCCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUU---GGCUGAAU------------GUUUGGCAACAGCCAACCAAUUGCCCAACAA
..((((.(((....((((((((..((((((((.....))).)))---))..))))------------))))(((....)))......))).))))... ( -26.00)
>DroSim_CAF1 187655 83 - 1
AUUUGGCCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUU---GGCUGAAU------------GUUUGGCAACAGCCAAACAAUUGCCCAACAA
.((..(((((...(.((((..............)))).)...))---)))..))(------------(((((((....))))))))............ ( -28.24)
>DroEre_CAF1 182585 94 - 1
AUUUGGCCAAAAGCAGGCGUUCUCCGUACUUGCGGC-CGCCGUU---GGCUGAAUGUUUGCCUGGAUGUUUGGCAACAGCCAAACAUUUGCCCAACAA
.((..(((((.....((((....((((....)))).-)))).))---)))..))((((.((..(((((((((((....)))))))))))))..)))). ( -37.50)
>DroYak_CAF1 183543 95 - 1
AUUUGGCCAAAAACAGGCGAUCUCCGUACUUGGGGCCCGCCGUU---GACUGCAUUUUUGCCUGGAUGGUUGGCAACAGCCAAACAAUUGCCCAACAA
..((((.(((.(((.((((..(((((....)))))..)))))))---....(((....))).((..((((((....))))))..)).))).))))... ( -32.90)
>DroAna_CAF1 179487 84 - 1
AUUUGGCCAAAAGUUGGCAUUCUCGAUGCUUGCUACUUUCCGUU---AGGCAACAAACAGCCA-----------GACAGCCAAACAAUUACCCAACAA
.((((((....(((.((((((...)))))).))).......(((---.(((........))).-----------))).)))))).............. ( -21.50)
>consensus
AUUUGGCCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUU___GGCUGAAU_UUUGCCU____GUUUGGCAACAGCCAAACAAUUGCCCAACAA
..((((.(((..((.((((...........)))))).................................(((((....)))))....))).))))... (-10.02 = -10.93 +   0.92)

alignment

secondary structure

dotplot

Window 0

Location	20,007,413 – 20,007,533
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.17
Mean single sequence MFE	-42.00
Consensus MFE	-20.16
Energy contribution	-20.47
Covariance contribution	0.31
Combinations/Pair	1.27
Mean z-score	-2.27
Structure conservation index	0.48
SVM decision value	0.61
SVM RNA-class probability	0.800042
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20007413 120 - 22407834
AAGUUGCUGGCCAAGUCGAGUGCCAGUGCACUUGCAGUUCAUUUGGGCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUUGUUGGCUGAAUGUUUGCCUGGAUGUUUGGCAACAGC
.....((((((((((.(((((((....))))))))....((((..(((((......((((((..(((((.((.(....).))..)))))..)))))))))))..)))).)))))..)))) ( -46.60)
>DroSec_CAF1 185167 105 - 1
AAGUUGCUGGCCAAGUCGAGAGCCAGUGCACUUGCAGUUCAUUUGGCCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUU---GGCUGAAU------------GUUUGGCAACAGC
..((((((((((((((...((((...(((....))))))))))))))))....(((((((((..((((((((.....))).)))---))..))))------------))))))))))... ( -44.10)
>DroSim_CAF1 187673 105 - 1
AAGUUGCUGGCCAAGUCGAGAGCCAGUGCACUUGCAGUUCAUUUGGCCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUU---GGCUGAAU------------GUUUGGCAACAGC
..((((((((((((((...((((...(((....))))))))))))))))....(((((((((..((((((((.....))).)))---))..))))------------))))))))))... ( -44.10)
>DroEre_CAF1 182603 116 - 1
AAGUUGUUGGCCAAGUCGAGAGCCAGUGCACUUGCAGUUCAUUUGGCCAAAAGCAGGCGUUCUCCGUACUUGCGGC-CGCCGUU---GGCUGAAUGUUUGCCUGGAUGUUUGGCAACAGC
..(((((((.(((((.((....(((((((....)))((.((((..(((((.....((((....((((....)))).-)))).))---)))..))))...)))))).)))))))))))))) ( -45.50)
>DroYak_CAF1 183561 117 - 1
AAGUUGUUGGCCAAGUCGAGAGCCAGUGCACUUGCAGUUCAUUUGGCCAAAAACAGGCGAUCUCCGUACUUGGGGCCCGCCGUU---GACUGCAUUUUUGCCUGGAUGGUUGGCAACAGC
..(((((..((((...(....)((((.(((..(((((((....((........))((((..(((((....)))))..))))...---)))))))....))))))).))))..)))))... ( -47.20)
>DroAna_CAF1 179505 104 - 1
AAGUUUCUGACAAAGUUAAGAGCCAG--CACUUGCAGUUCAUUUGGCCAAAAGUUGGCAUUCUCGAUGCUUGCUACUUUCCGUU---AGGCAACAAACAGCCA-----------GACAGC
......(((..........((((..(--(....)).)))).((((((....(((.((((((...)))))).))).......(((---.(....).))).))))-----------))))). ( -24.50)
>consensus
AAGUUGCUGGCCAAGUCGAGAGCCAGUGCACUUGCAGUUCAUUUGGCCAAAAGCAGGCGUUCUCCCAACUCGCCGCCCGACGUU___GGCUGAAU_UUUGCCU____GUUUGGCAACAGC
..((((((((((((((.((..((.((....)).))..)).)))))))))...((.((((...........))))))....................................)))))... (-20.16 = -20.47 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:27 2006