Locus 935

Sequence ID 2R_DroMel_CAF1
Location 4,070,033 – 4,070,192
Length 159
Max. P 0.943399
window1653 window1654 window1655

overview

Window 3

Location 4,070,033 – 4,070,152
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.11
Mean single sequence MFE -32.20
Consensus MFE -25.16
Energy contribution -25.04
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.21
Structure conservation index 0.78
SVM decision value 1.33
SVM RNA-class probability 0.943399
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4070033 119 - 20766785
UUGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGCUUGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAAAAGUGCAACAA-AAAGAAUUCGAGAUAGAAAUCAAUUUUU
....((((..(.....(((((((.....)))))))((((((((((..(((....)))...)).))))))))...........)..))))..-...((.(((......))).))....... ( -34.30)
>DroSec_CAF1 52686 118 - 1
CCGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGC-UGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAAAACUGCAACAA-AAAGAAUUUGAGAUAGAAAUCAAUUUUU
.(((((((.((...(((((((((.....)))))))))(-((((((..(((....)))...)).))))))))))))))..............-..((((.((((........)))).)))) ( -32.50)
>DroSim_CAF1 60864 118 - 1
UCGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGC-UGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAAAACUGCAACAA-AAAGAAUUCGAGAUAGAAAUCAAUUUUU
((((((((.((...(((((((((.....)))))))))(-((((((..(((....)))...)).))))))))))))))).............-...((.(((......))).))....... ( -34.20)
>DroEre_CAF1 54058 120 - 1
UUGCGUUGCGCAACUUCAGUUUAAAAACUAAACGGGGCUUGCUGUCUGCCUCUGGGCAAAACAAUUAGGCCAACGCGGAAAAAUGCACCAAAAAAGUAUCCGGGAUAGAAAUCAAUUUUU
..(((((((((((((((.(((((.....))))))))).))))(((.((((....))))..))).....).))))))(((....(((.........))))))..(((....)))....... ( -26.30)
>DroYak_CAF1 56717 118 - 1
UUGCGUUGUGCAACUUCAGUUCAAAAACUGAACGGGGCGGGCUGUCUGCCUUUGGGCA-AACAAUUAGGCCAACGCGGAAAAGUGCAACAA-AAAGUAUCCGAGAUAGCAAUCAAUUUUU
((((((((..(...(((((((....)))))))((.(...((((((.((((....))))-.)).....))))..).)).....)..))))..-....((((...))))))))......... ( -33.70)
>consensus
UUGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGC_UGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAAAACUGCAACAA_AAAGAAUUCGAGAUAGAAAUCAAUUUUU
((((((((.((...(((((((((.....))))))))).....(((..(((....)))...))).....)))))))))).........................(((....)))....... (-25.16 = -25.04 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,070,072 – 4,070,192
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -32.38
Consensus MFE -25.98
Energy contribution -26.22
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.80
SVM decision value 0.58
SVM RNA-class probability 0.787311
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4070072 120 + 20766785
UUUCGCGUUGGCCUAAUUGUUUGGCCCAAAGGCAGACAUCAAGCCCCGUUUAGUUUUUAAACGGAAGUUGCACAACGCAAGAAAUAAAAGGCUGAAAGGAUUUAGAACAUGGCAAAAAGU
....((..((..((((.((((((.((....))))))))(((.(((((((((((...))))))))...((((.....)))).........))))))......))))..))..))....... ( -29.60)
>DroSec_CAF1 52725 119 + 1
UUUCGCGUUGGCCUAAUUGUUUGGCCCAAAGGCAGACAUCA-GCCCCGUUUAGUUUUUAAACGGAAGUUGCACAACGCGGAAAACAAAAGGCUGAAAGGAUUUUGAACAUGGCAAAAAGU
((((((((((.......((((((.((....)))))))).((-((.((((((((...))))))))..))))..))))))))))..(((((..((....)).)))))............... ( -34.80)
>DroSim_CAF1 60903 119 + 1
UUUCGCGUUGGCCUAAUUGUUUGGCCCAAAGGCAGACAUCA-GCCCCGUUUAGUUUUUAAACGGAAGUUGCACAACGCGAAAAACAAAAGGCUGAAAGGAUUUUGAACAUGGCAAAAAGU
((((((((((.......((((((.((....)))))))).((-((.((((((((...))))))))..))))..))))))))))..(((((..((....)).)))))............... ( -35.30)
>DroEre_CAF1 54098 119 + 1
UUCCGCGUUGGCCUAAUUGUUUUGCCCAGAGGCAGACAGCAAGCCCCGUUUAGUUUUUAAACUGAAGUUGCGCAACGCAAAAAC-CAAAGGCUGAAAGGAUUUUCAACAUGGCAAAAAGU
.(((...(..((((..((((((((((....))))))..))))......(((((((....))))))).(((((...)))))....-...))))..)..))).................... ( -28.60)
>DroYak_CAF1 56756 119 + 1
UUCCGCGUUGGCCUAAUUGUU-UGCCCAAAGGCAGACAGCCCGCCCCGUUCAGUUUUUGAACUGAAGUUGCACAACGCAAAAAACAAAACGCUGAAAGGAUUUUGAAUAUGGCAAAAAGU
..((((((((((....(((((-((((....))))))))).........(((((((....)))))))...)).))))))......(((((..((....)).))))).....))........ ( -33.60)
>consensus
UUUCGCGUUGGCCUAAUUGUUUGGCCCAAAGGCAGACAUCA_GCCCCGUUUAGUUUUUAAACGGAAGUUGCACAACGCAAAAAACAAAAGGCUGAAAGGAUUUUGAACAUGGCAAAAAGU
....((...(((.....(((((.(((....))))))))....)))((.((((((((((.(((....)))((.....))........)))))))))).))............))....... (-25.98 = -26.22 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,070,072 – 4,070,192
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.58
Mean single sequence MFE -32.26
Consensus MFE -25.68
Energy contribution -25.76
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.80
SVM decision value 0.86
SVM RNA-class probability 0.868226
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4070072 120 - 20766785
ACUUUUUGCCAUGUUCUAAAUCCUUUCAGCCUUUUAUUUCUUGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGCUUGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAA
........................................(((((((.........(((((((.....)))))))((((((((((..(((....)))...)).))))))))))))))).. ( -30.10)
>DroSec_CAF1 52725 119 - 1
ACUUUUUGCCAUGUUCAAAAUCCUUUCAGCCUUUUGUUUUCCGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGC-UGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAA
.........................................(((((((.((...(((((((((.....)))))))))(-((((((..(((....)))...)).))))))))))))))... ( -30.20)
>DroSim_CAF1 60903 119 - 1
ACUUUUUGCCAUGUUCAAAAUCCUUUCAGCCUUUUGUUUUUCGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGC-UGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAA
......................................((((((((((.((...(((((((((.....)))))))))(-((((((..(((....)))...)).))))))))))))))))) ( -32.70)
>DroEre_CAF1 54098 119 - 1
ACUUUUUGCCAUGUUGAAAAUCCUUUCAGCCUUUG-GUUUUUGCGUUGCGCAACUUCAGUUUAAAAACUAAACGGGGCUUGCUGUCUGCCUCUGGGCAAAACAAUUAGGCCAACGCGGAA
.......((((.(((((((....)))))))...))-))(((((((((((((((((((.(((((.....))))))))).))))(((.((((....))))..))).....).)))))))))) ( -35.90)
>DroYak_CAF1 56756 119 - 1
ACUUUUUGCCAUAUUCAAAAUCCUUUCAGCGUUUUGUUUUUUGCGUUGUGCAACUUCAGUUCAAAAACUGAACGGGGCGGGCUGUCUGCCUUUGGGCA-AACAAUUAGGCCAACGCGGAA
...............((((((.(.....).))))))..(((((((((.(((..((((((((....))))))).)..)))((((((.((((....))))-.)).....))))))))))))) ( -32.40)
>consensus
ACUUUUUGCCAUGUUCAAAAUCCUUUCAGCCUUUUGUUUUUUGCGUUGUGCAACUUCCGUUUAAAAACUAAACGGGGC_UGAUGUCUGCCUUUGGGCCAAACAAUUAGGCCAACGCGAAA
......................................((((((((((.((...(((((((((.....))))))))).....(((..(((....)))...))).....)))))))))))) (-25.68 = -25.76 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:53 2006