Locus 2001

Sequence ID 3R_DroMel_CAF1
Location 5,678,294 – 5,678,426
Length 132
Max. P 0.978161
window3276 window3277 window3278 window3279

overview

Window 6

Location 5,678,294 – 5,678,393
Length 99
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 83.55
Mean single sequence MFE -38.44
Consensus MFE -24.44
Energy contribution -26.00
Covariance contribution 1.56
Combinations/Pair 1.15
Mean z-score -3.10
Structure conservation index 0.64
SVM decision value 1.81
SVM RNA-class probability 0.978161
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5678294 99 + 27905053
AG-GGGUUGGUUUUCCGCCGUAAUCGCAGUUCCUGCAGGUGGCUACUUAGGGAGUUUCCGUGAAUUCACGGGAAAAACUGCAGUGGCCAAGUUGG------GAAUA
.(-.(((((((.....)))..)))).).((((((.....(((((((((((....((((((((....))))))))...))).))))))))....))------)))). ( -37.60)
>DroSec_CAF1 19689 98 + 1
AG-GGGUGGGUUUUCCGCCGUAAUCGCAGUUCCUGCAGGUGGCUACUUAGGGAGUUUCCCUGAAUGCAGAUGA-AAACUGCAGUGGCCAAGGUGG------GAAUA
..-.(((((.....))))).........(((((..(...(((((((((((((.....)))))).(((((.(..-..)))))))))))))..)..)------)))). ( -44.70)
>DroSim_CAF1 19804 98 + 1
AG-GGGUGGGUUUUCCGCCGUAAUCGCAGUUCCUGCAGGUGGCUACUUAGGGAGUUUCCCUGAAUGCAGCUGA-AAACUGCAGUGGCCAAGUUGG------GAAUA
..-.(((((.....))))).........((((((.....(((((((((((((.....)))))).(((((.(..-..)))))))))))))....))------)))). ( -40.00)
>DroEre_CAF1 16767 85 + 1
GGUGGGUGGGUUUUCCGCAGUAAUCGCGGUUCCUGCAGGUGGCUACUUAGGGAGUUUUCCUGAAUGCAGGGAA-AACCUGCAGUG--------------------A
.....(..((((((((((((.(((....))).)))).....((...(((((((...)))))))..))..))))-))))..)....--------------------. ( -31.10)
>DroYak_CAF1 20332 105 + 1
AGUGGUUGGGUUUUCCGCUGUAAUCGCAGUUCCUGCAGGUGGCUACUUAGGGAGUUUUCCCGAAUGCAGGGCA-AAAUUGCAGUGGCCAAGGUGGGAAUGGGAAUA
(((((.........)))))....((.((.((((..(...(((((((...(((......)))...(((((....-...))))))))))))..)..)))))).))... ( -38.80)
>consensus
AG_GGGUGGGUUUUCCGCCGUAAUCGCAGUUCCUGCAGGUGGCUACUUAGGGAGUUUCCCUGAAUGCAGGGGA_AAACUGCAGUGGCCAAGGUGG______GAAUA
....(((((.....)))))......((((...))))...(((((((((((((.....)))))).(((((........))))))))))))................. (-24.44 = -26.00 +   1.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,678,294 – 5,678,393
Length 99
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 83.55
Mean single sequence MFE -26.10
Consensus MFE -16.06
Energy contribution -15.70
Covariance contribution -0.36
Combinations/Pair 1.24
Mean z-score -2.38
Structure conservation index 0.62
SVM decision value 0.72
SVM RNA-class probability 0.832091
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5678294 99 - 27905053
UAUUC------CCAACUUGGCCACUGCAGUUUUUCCCGUGAAUUCACGGAAACUCCCUAAGUAGCCACCUGCAGGAACUGCGAUUACGGCGGAAAACCAACCC-CU
..(((------((.....)(((..((((((((((.(((((....)))))...........((((....)))))))))))))).....))))))).........-.. ( -25.80)
>DroSec_CAF1 19689 98 - 1
UAUUC------CCACCUUGGCCACUGCAGUUU-UCAUCUGCAUUCAGGGAAACUCCCUAAGUAGCCACCUGCAGGAACUGCGAUUACGGCGGAAAACCCACCC-CU
.....------((.((.((((.(((((((...-....))))....((((.....)))).))).))))..(((((...))))).....)).))...........-.. ( -27.70)
>DroSim_CAF1 19804 98 - 1
UAUUC------CCAACUUGGCCACUGCAGUUU-UCAGCUGCAUUCAGGGAAACUCCCUAAGUAGCCACCUGCAGGAACUGCGAUUACGGCGGAAAACCCACCC-CU
.....------......((((.((((((((..-...)))))....((((.....)))).))).))))..(((((...))))).....((.((.....)).)).-.. ( -28.30)
>DroEre_CAF1 16767 85 - 1
U--------------------CACUGCAGGUU-UUCCCUGCAUUCAGGAAAACUCCCUAAGUAGCCACCUGCAGGAACCGCGAUUACUGCGGAAAACCCACCCACC
(--------------------(.((((((((.-....((((.((..(((....)))..))))))..)))))))))).(((((.....))))).............. ( -25.90)
>DroYak_CAF1 20332 105 - 1
UAUUCCCAUUCCCACCUUGGCCACUGCAAUUU-UGCCCUGCAUUCGGGAAAACUCCCUAAGUAGCCACCUGCAGGAACUGCGAUUACAGCGGAAAACCCAACCACU
..((((..((((.....((((.((((((....-.....)))....((((....))))..))).))))......))))..((.......))))))............ ( -22.80)
>consensus
UAUUC______CCAACUUGGCCACUGCAGUUU_UCCCCUGCAUUCAGGGAAACUCCCUAAGUAGCCACCUGCAGGAACUGCGAUUACGGCGGAAAACCCACCC_CU
.......................((((((.......((((....))))...(((.....)))......))))))...((((.......)))).............. (-16.06 = -15.70 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,678,326 – 5,678,426
Length 100
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 85.60
Mean single sequence MFE -28.70
Consensus MFE -19.80
Energy contribution -21.55
Covariance contribution 1.75
Combinations/Pair 1.18
Mean z-score -2.82
Structure conservation index 0.69
SVM decision value 1.48
SVM RNA-class probability 0.957302
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5678326 100 + 27905053
UGCAGGUGGCUACUUAGGGAGUUUCCGUGAAUUCACGGGAAAAACUGCAGUGGCCAAGUUGG------GAAUACAAUAAAGAAAUGGGU-UUGAAAAAGGGAAAGCU
.((...(((((((((((....((((((((....))))))))...))).)))))))).((((.------.....))))............-..............)). ( -30.10)
>DroSec_CAF1 19721 99 + 1
UGCAGGUGGCUACUUAGGGAGUUUCCCUGAAUGCAGAUGA-AAACUGCAGUGGCCAAGGUGG------GAAUACAAUAAAGAAAUGAGU-CUGAAAAGGGAAAAGCU
.((...(((((((((((((.....)))))).(((((.(..-..)))))))))))))......------....................(-((....))).....)). ( -28.60)
>DroSim_CAF1 19836 99 + 1
UGCAGGUGGCUACUUAGGGAGUUUCCCUGAAUGCAGCUGA-AAACUGCAGUGGCCAAGUUGG------GAAUACAAUAAAGAAAUGGGU-CUGAAAAGGGAAAAGCU
.((...(((((((((((((.....)))))).(((((.(..-..))))))))))))).((((.------.....))))...........(-((....))).....)). ( -30.10)
>DroYak_CAF1 20365 106 + 1
UGCAGGUGGCUACUUAGGGAGUUUUCCCGAAUGCAGGGCA-AAAUUGCAGUGGCCAAGGUGGGAAUGGGAAUACAAAAGGGAAAUGGCUGCUGAAAGGGGGAUAGCU
.((...(((((((...(((......)))...(((((....-...))))))))))))...............................((.((....)).))...)). ( -26.00)
>consensus
UGCAGGUGGCUACUUAGGGAGUUUCCCUGAAUGCAGGGGA_AAACUGCAGUGGCCAAGGUGG______GAAUACAAUAAAGAAAUGGGU_CUGAAAAGGGAAAAGCU
.((...(((((((((((((.....)))))).(((((........))))))))))))..................................((....))......)). (-19.80 = -21.55 +   1.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,678,326 – 5,678,426
Length 100
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 85.60
Mean single sequence MFE -19.47
Consensus MFE -12.21
Energy contribution -13.28
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -2.39
Structure conservation index 0.63
SVM decision value 0.57
SVM RNA-class probability 0.785480
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5678326 100 - 27905053
AGCUUUCCCUUUUUCAA-ACCCAUUUCUUUAUUGUAUUC------CCAACUUGGCCACUGCAGUUUUUCCCGUGAAUUCACGGAAACUCCCUAAGUAGCCACCUGCA
.((..............-.............(((.....------.)))..((((.(((..(((((...(((((....)))))))))).....))).))))...)). ( -17.90)
>DroSec_CAF1 19721 99 - 1
AGCUUUUCCCUUUUCAG-ACUCAUUUCUUUAUUGUAUUC------CCACCUUGGCCACUGCAGUUU-UCAUCUGCAUUCAGGGAAACUCCCUAAGUAGCCACCUGCA
.((............((-(......)))...........------......((((.(((((((...-....))))....((((.....)))).))).))))...)). ( -19.80)
>DroSim_CAF1 19836 99 - 1
AGCUUUUCCCUUUUCAG-ACCCAUUUCUUUAUUGUAUUC------CCAACUUGGCCACUGCAGUUU-UCAGCUGCAUUCAGGGAAACUCCCUAAGUAGCCACCUGCA
.((............((-(......)))...........------......((((.((((((((..-...)))))....((((.....)))).))).))))...)). ( -21.70)
>DroYak_CAF1 20365 106 - 1
AGCUAUCCCCCUUUCAGCAGCCAUUUCCCUUUUGUAUUCCCAUUCCCACCUUGGCCACUGCAAUUU-UGCCCUGCAUUCGGGAAAACUCCCUAAGUAGCCACCUGCA
.(((((..........(((((((.........((......)).........))))....(((....-)))..)))....((((....))))...)))))........ ( -18.47)
>consensus
AGCUUUCCCCUUUUCAG_ACCCAUUUCUUUAUUGUAUUC______CCAACUUGGCCACUGCAGUUU_UCACCUGCAUUCAGGGAAACUCCCUAAGUAGCCACCUGCA
...................................................((((.(((((((........))))....((((.....)))).))).))))...... (-12.21 = -13.28 +   1.06)

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 10:24:54 2006