Locus 3397

Sequence ID 2L_DroMel_CAF1
Location 9,834,223 – 9,834,375
Length 152
Max. P 0.982233
window5373 window5374 window5375 window5376 window5377

overview

Window 3

Location 9,834,223 – 9,834,321
Length 98
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 76.16
Mean single sequence MFE -30.16
Consensus MFE -20.68
Energy contribution -20.20
Covariance contribution -0.48
Combinations/Pair 1.12
Mean z-score -1.62
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.827675
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9834223 98 + 22407834
AAGUUUCUGAACCG-------CA--CCCCCUUUUUGGACCACAUCCAUGGGCAGUACGCCCAUGUG-GGAUGG-GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUA
(((((.((....((-------(.--...((.....)).(((..(((((((((.....))))))).)-)..)))-)))((((((((......)))))))).)).))))). ( -34.70)
>DroSec_CAF1 42774 82 + 1
AAGUUUCUAAACCA-------CU--CGCCCU--UUGGAC---------------UACGCCCAUGUGCGGGUGG-GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUA
(((((.((...(((-------((--(((.(.--.(((..---------------.....))).).))))))))-...((((((((......)))))))).)).))))). ( -28.30)
>DroSim_CAF1 45845 82 + 1
AAGUUUCUAAACCA-------CC--CGACCU--UUGGAC---------------UACGCCCAUGUGCGGGUGG-GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUA
(((((.((...(((-------((--((....--.(((..---------------.....)))....)))))))-...((((((((......)))))))).)).))))). ( -28.60)
>DroEre_CAF1 45316 95 + 1
AAGUUUCUGAACUU-------CUCCCCCCUU--UUGGACCGCAAGCA-GAGCACUACGCCCAUG----GGUGGGGCGGGACAAAUGGUGGAAUUUGUCCGAGUAAUUUA
..........((((-------(.(((((((.--.(((..(....)..-..((.....))))).)----)).)))).)((((((((......))))))))))))...... ( -28.30)
>DroYak_CAF1 44832 97 + 1
AAGUUCCUGAACUUACCCAACCCCCCUCCCU--CUGGACCA----CA-GAGCACUACGCCCAUG----GGUGG-GCGGGGCAAAUGGUGAAAUUUGUCCGAGUAAUUUA
(((((....)))))...........(((.((--(((.....----))-))).....((((((..----..)))-)))((((((((......)))))))))))....... ( -30.90)
>consensus
AAGUUUCUGAACCA_______CC__CCCCCU__UUGGACC_____CA_G_GCA_UACGCCCAUGUG_GGGUGG_GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUA
(((((.((....................((.....))...................(((((((......)))).)))((((((((......)))))))).)).))))). (-20.68 = -20.20 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,834,223 – 9,834,321
Length 98
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 76.16
Mean single sequence MFE -29.58
Consensus MFE -11.38
Energy contribution -11.14
Covariance contribution -0.24
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.38
SVM decision value 0.94
SVM RNA-class probability 0.886224
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9834223 98 - 22407834
UAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCAUCC-CACAUGGGCGUACUGCCCAUGGAUGUGGUCCAAAAAGGGGG--UG-------CGGUUCAGAAACUU
..........(((.....)))....((((..((((-((..((-(..((((((.....))))))((((...)))).....)))))--.)-------)))..))))..... ( -31.70)
>DroSec_CAF1 42774 82 - 1
UAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCACCCGCACAUGGGCGUA---------------GUCCAA--AGGGCG--AG-------UGGUUUAGAAACUU
........(((((.....)))((((((((((((((-(((........))))))..---------------......--.)))))--))-------))))...))..... ( -28.80)
>DroSim_CAF1 45845 82 - 1
UAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCACCCGCACAUGGGCGUA---------------GUCCAA--AGGUCG--GG-------UGGUUUAGAAACUU
(((((((((((((.....)))(((.(((((..(((-(((........))))))..---------------)..)))--)))).)--))-------)))))))....... ( -25.60)
>DroEre_CAF1 45316 95 - 1
UAAAUUACUCGGACAAAUUCCACCAUUUGUCCCGCCCCACC----CAUGGGCGUAGUGCUC-UGCUUGCGGUCCAA--AAGGGGGGAG-------AAGUUCAGAAACUU
..........((((...((((.((.((((..((((((((..----..)))).((((....)-)))..))))..)))--).)).)))).-------..))))........ ( -30.40)
>DroYak_CAF1 44832 97 - 1
UAAAUUACUCGGACAAAUUUCACCAUUUGCCCCGC-CCACC----CAUGGGCGUAGUGCUC-UG----UGGUCCAG--AGGGAGGGGGGUUGGGUAAGUUCAGGAACUU
.................((((...((((((((.((-((.((----(..((((.....))))-..----...(((..--..)))))))))).))))))))...))))... ( -31.40)
>consensus
UAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC_CCACCC_CACAUGGGCGUA_UGC_C_UG_____GGUCCAA__AGGGCG__AG_______AGGUUCAGAAACUU
..........((((((((......))))....(((.(((........)))))).................))))......................((((....)))). (-11.38 = -11.14 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,834,244 – 9,834,351
Length 107
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 83.80
Mean single sequence MFE -35.78
Consensus MFE -25.18
Energy contribution -26.02
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.70
SVM decision value 0.57
SVM RNA-class probability 0.784875
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9834244 107 + 22407834
UUUUUGGACCACAUCCAUGGGCAGUACGCCCAUGUG-GGAUGG-GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUACGGAAAAUGCCUGCCUUUUGGUCGUUCGAG
......((((((((((((((((.....))))))...-)))))(-(((((.(((((......)))))((((.........)))).....))))))...)))))....... ( -40.10)
>DroSec_CAF1 42795 91 + 1
U--UUGGAC---------------UACGCCCAUGUGCGGGUGG-GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUACGGAAAAUGCCUGCCUUUUGGUCGGUCGGA
.--((.(((---------------(.(((((((......))))-)))((.((((.((..(.((((.((((.........))))))))..)..)).)))).)))))).)) ( -33.30)
>DroSim_CAF1 45866 91 + 1
U--UUGGAC---------------UACGCCCAUGUGCGGGUGG-GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUACGGAAAAUGCCUGCCUUUUGGUCGGUCGGA
.--((.(((---------------(.(((((((......))))-)))((.((((.((..(.((((.((((.........))))))))..)..)).)))).)))))).)) ( -33.30)
>DroEre_CAF1 45339 101 + 1
U--UUGGACCGCAAGCA-GAGCACUACGCCCAUG----GGUGGGGCGGGACAAAUGGUGGAAUUUGUCCGAGUAAUUUACGGAAAAUGCCUGCCUUUUGGUCGGUCGG-
.--...(((((.(((((-(.(((...(((((...----....)))))((((((((......)))))))).................)))))).))).)))))......- ( -37.10)
>DroYak_CAF1 44862 96 + 1
U--CUGGACCA----CA-GAGCACUACGCCCAUG----GGUGG-GCGGGGCAAAUGGUGAAAUUUGUCCGAGUAAUUUACGGAAAAUGCCUGCCUUUUGGACGGUCGG-
.--...((((.----((-(.(((...((((((..----..)))-)))((((((((......)))))))).................))))))((....))..))))..- ( -35.10)
>consensus
U__UUGGACC_____CA_G_GCA_UACGCCCAUGUG_GGGUGG_GCGGGGCAAAUGGUGGAAUUUGUCCGAGUAAUUUACGGAAAAUGCCUGCCUUUUGGUCGGUCGG_
......((((................(((((((......)))).)))((.((((.(((((.((((.((((.........))))))))..))))).)))).))))))... (-25.18 = -26.02 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,834,244 – 9,834,351
Length 107
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 83.80
Mean single sequence MFE -28.46
Consensus MFE -18.24
Energy contribution -19.00
Covariance contribution 0.76
Combinations/Pair 1.07
Mean z-score -2.60
Structure conservation index 0.64
SVM decision value 1.13
SVM RNA-class probability 0.919654
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9834244 107 - 22407834
CUCGAACGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCAUCC-CACAUGGGCGUACUGCCCAUGGAUGUGGUCCAAAAA
.......(((((...(((.((((......(((...)))..(((.....)))......))))..))-)(((((-...((((((.....))))))))))))))))...... ( -33.40)
>DroSec_CAF1 42795 91 - 1
UCCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCACCCGCACAUGGGCGUA---------------GUCCAA--A
.......(((.....((((((.((((((((.........)))).)))).))......)))).(((-(((........))))))..---------------)))...--. ( -22.30)
>DroSim_CAF1 45866 91 - 1
UCCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCACCCGCACAUGGGCGUA---------------GUCCAA--A
.......(((.....((((((.((((((((.........)))).)))).))......)))).(((-(((........))))))..---------------)))...--. ( -22.30)
>DroEre_CAF1 45339 101 - 1
-CCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGUCCCGCCCCACC----CAUGGGCGUAGUGCUC-UGCUUGCGGUCCAA--A
-..(((((......(((((((((((...............((((((((......))))))))(((((....----...))))).))))).)-))))).)))))...--. ( -37.60)
>DroYak_CAF1 44862 96 - 1
-CCGACCGUCCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUUCACCAUUUGCCCCGC-CCACC----CAUGGGCGUAGUGCUC-UG----UGGUCCAG--A
-..((((...(....)(((((((((...............((.(((((......))))))).(((-(((..----..)))))).))))).)-))----)))))...--. ( -26.70)
>consensus
_CCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC_CCACCC_CACAUGGGCGUA_UGC_C_UG_____GGUCCAA__A
...(((((..((((.((..((.((((((((.........)))).)))).)).)).))))...(((.(((........))))))...............)))))...... (-18.24 = -19.00 +   0.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,834,282 – 9,834,375
Length 93
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.76
Mean single sequence MFE -24.92
Consensus MFE -21.60
Energy contribution -21.52
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -1.86
Structure conservation index 0.87
SVM decision value 1.91
SVM RNA-class probability 0.982233
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9834282 93 - 22407834
CU----GGCAGUCGAAAAGUCGGGCCAACUCGAACGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCAU
..----(((.((((.....(((((....))))).)))).....((((((.((((((((.........)))).)))).))......))))..))-)... ( -23.50)
>DroSec_CAF1 42817 93 - 1
CU----GGCAGUCGAAAAGUCGGGCCAAUCCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCAC
..----(((.((((....((((((....)))))))))).....((((((.((((((((.........)))).)))).))......))))..))-)... ( -25.90)
>DroSim_CAF1 45888 93 - 1
CU----GGCAGUCGAAAAGUCGGGCCAAUCCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC-CCAC
..----(((.((((....((((((....)))))))))).....((((((.((((((((.........)))).)))).))......))))..))-)... ( -25.90)
>DroEre_CAF1 45371 97 - 1
CUAACAGGCAGUCGAAAAGUCGGGCCAA-CCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGUCCCGCCCCAC
......(((.((((....(((((.....-)))))))))((((.((..((.((((((((.........)))).)))).)).)).))))....))).... ( -26.90)
>DroYak_CAF1 44890 96 - 1
CUAACAGGCAGUCGAAAAGUCGGGCCAA-CCGACCGUCCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUUCACCAUUUGCCCCGC-CCAC
......(((....((...(((((.....-)))))..)).....((((((.((((((((.........)))).))))....))...))))..))-)... ( -22.40)
>consensus
CU____GGCAGUCGAAAAGUCGGGCCAA_CCGACCGACCAAAAGGCAGGCAUUUUCCGUAAAUUACUCGGACAAAUUCCACCAUUUGCCCCGC_CCAC
......((((((((....(((((......))))))))).....((..((.((((((((.........)))).)))).)).))...))))......... (-21.60 = -21.52 +  -0.08)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:30 2006