Locus 140

Sequence ID 3R_DroMel_CAF1
Location 742,558 – 742,781
Length 223
Max. P 0.938346
window227 window228 window229 window230

overview

Window 7

Location 742,558 – 742,673
Length 115
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 86.52
Mean single sequence MFE -35.65
Consensus MFE -27.86
Energy contribution -30.18
Covariance contribution 2.31
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.78
SVM decision value 0.52
SVM RNA-class probability 0.767158
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 742558 115 + 27905053
CUUUUCGGGGCCCGUCAUACCCGAUCGGCCUGGACAAGCGGUGCACGGGAAACCAGAUAGAGAAACUGAACUUCCAUUUGAUUUGCCGCUUUUCCAGCCAAAACCAUUUCUCUUG
....(((((..........)))))..(((.((((.(((((((....((....))((((.(((.........))).)))).....))))))).)))))))................ ( -35.70)
>DroSec_CAF1 9894 115 + 1
CUUUUCGGGGCCCGUCAAACCCGAUCGGUCUGGACAGGCGGUGCACGGCAAACCAGAUGGAGAAAACGAAGUUCCAUUUGAUUUGCCGCCUUUCCACCCAAAACCAUUUCUCUUG
......((((((.(((......))).))).((((.(((((.....)((((((.(((((((((.........))))))))).)))))))))).)))))))................ ( -40.50)
>DroSim_CAF1 9858 115 + 1
CUUUUCGGGGCCCGUCAAACCCGAUCGGUCUGGACAGGCGGUGCACGGCAAACCAGAUGGAGAAAACGAAGUUCCAUUUGAUUUGCCGCCUUUCCACCCAAAACCAUUUCUCUUG
......((((((.(((......))).))).((((.(((((.....)((((((.(((((((((.........))))))))).)))))))))).)))))))................ ( -40.50)
>DroEre_CAF1 10208 98 + 1
CUUUUCGGGGCCCGUCAAACCCGAUCGGCCUGG-----------------AAGCAGAUGGAGAAAACGAAGUUCCAUUUGAUUUGCCGCCUGUCCAGCCAGAACAAUUUCUCUUG
..((((.(((((.(((......))).))))).)-----------------)))(((((((((.........))))))))).........(((......))).............. ( -25.90)
>consensus
CUUUUCGGGGCCCGUCAAACCCGAUCGGCCUGGACAGGCGGUGCACGGCAAACCAGAUGGAGAAAACGAAGUUCCAUUUGAUUUGCCGCCUUUCCACCCAAAACCAUUUCUCUUG
......((((((.(((......))).))))((((.(((((.....)((((((.(((((((((.........))))))))).)))))))))).)))).))................ (-27.86 = -30.18 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 742,558 – 742,673
Length 115
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 86.52
Mean single sequence MFE -38.75
Consensus MFE -28.91
Energy contribution -32.85
Covariance contribution 3.94
Combinations/Pair 1.09
Mean z-score -1.57
Structure conservation index 0.75
SVM decision value 0.20
SVM RNA-class probability 0.630295
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 742558 115 - 27905053
CAAGAGAAAUGGUUUUGGCUGGAAAAGCGGCAAAUCAAAUGGAAGUUCAGUUUCUCUAUCUGGUUUCCCGUGCACCGCUUGUCCAGGCCGAUCGGGUAUGACGGGCCCCGAAAAG
............((((((..((....((((.((((((.(((((.(........)))))).)))))).))))...))(((((((...(((.....)))..))))))).)))))).. ( -33.10)
>DroSec_CAF1 9894 115 - 1
CAAGAGAAAUGGUUUUGGGUGGAAAGGCGGCAAAUCAAAUGGAACUUCGUUUUCUCCAUCUGGUUUGCCGUGCACCGCCUGUCCAGACCGAUCGGGUUUGACGGGCCCCGAAAAG
............(((((((.((....(((((((((((.(((((...........))))).)))))))))))...))(((((((.(((((.....))))))))))))))))))).. ( -48.70)
>DroSim_CAF1 9858 115 - 1
CAAGAGAAAUGGUUUUGGGUGGAAAGGCGGCAAAUCAAAUGGAACUUCGUUUUCUCCAUCUGGUUUGCCGUGCACCGCCUGUCCAGACCGAUCGGGUUUGACGGGCCCCGAAAAG
............(((((((.((....(((((((((((.(((((...........))))).)))))))))))...))(((((((.(((((.....))))))))))))))))))).. ( -48.70)
>DroEre_CAF1 10208 98 - 1
CAAGAGAAAUUGUUCUGGCUGGACAGGCGGCAAAUCAAAUGGAACUUCGUUUUCUCCAUCUGCUU-----------------CCAGGCCGAUCGGGUUUGACGGGCCCCGAAAAG
....((((....))))(((((((..(((((........(((((...........)))))))))))-----------------))).)))..(((((..........))))).... ( -24.50)
>consensus
CAAGAGAAAUGGUUUUGGCUGGAAAGGCGGCAAAUCAAAUGGAACUUCGUUUUCUCCAUCUGGUUUGCCGUGCACCGCCUGUCCAGACCGAUCGGGUUUGACGGGCCCCGAAAAG
............(((((((.......(((((((((((.(((((...........))))).))))))))))).....(((((((.(((((.....))))))))))))))))))).. (-28.91 = -32.85 +   3.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 742,633 – 742,750
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 86.50
Mean single sequence MFE -22.51
Consensus MFE -18.20
Energy contribution -18.45
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.81
SVM decision value 1.27
SVM RNA-class probability 0.938346
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 742633 117 + 27905053
AUUUGAUUUGCCGCUUUUCCAGCCAAAACCAUUUCUCUUGUUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAUUUUCACAGGUGGCCCACUAAUUUCUUCCUACCAUUCCUC
......((((..(((.....))))))).......................(((((((((((.(((...............))).)))))))))))...................... ( -21.66)
>DroSec_CAF1 9969 104 + 1
AUUUGAUUUGCCGCCUUUCCACCCAAAACCAUUUCUCUUGCUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAUUUUCUUAGGUGGCCCACUAAUUUC-------------UC
.........(((((((....(((((....(((...........))).....))))).((((.....))))..............)))))))...........-------------.. ( -20.80)
>DroSim_CAF1 9933 104 + 1
AUUUGAUUUGCCGCCUUUCCACCCAAAACCAUUUCUCUUGCUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAUUUUCUUAGGUGGCCCACUAAUUUC-------------UC
.........(((((((....(((((....(((...........))).....))))).((((.....))))..............)))))))...........-------------.. ( -20.80)
>DroEre_CAF1 10266 115 + 1
AUUUGAUUUGCCGCCUGUCCAGCCAGAACAAUUUCUCUUGUUUAUGCCCCGUGGGUCGCU-UUGAUAAGCUUAUUUAUUUUC-AAGGUGGCCCACUAAUUUUUUCCCACCACAUUUC
....((..((...........((..((((((......))))))..))...((((((((((-((((...............))-))))))))))))................))..)) ( -26.76)
>consensus
AUUUGAUUUGCCGCCUUUCCACCCAAAACCAUUUCUCUUGCUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAUUUUCUUAGGUGGCCCACUAAUUUC_____________UC
..................................................(((((((((((..((((((....)))))).....)))))))))))...................... (-18.20 = -18.45 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 742,673 – 742,781
Length 108
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 73.65
Mean single sequence MFE -22.91
Consensus MFE -12.13
Energy contribution -13.93
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.53
SVM decision value 0.48
SVM RNA-class probability 0.751142
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 742673 108 + 27905053
UUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAU---UUUCACAGGUGGCCCACUAAUUUCUUCCUACCAUUCCUCAAUGUAGGUCUCUUUCGGU---UGUAGAUUGUGA
(((((..((.(((((((((((.(((.............---..))).))))))))))).........(((((.(((....))))))))........)).---.)))))...... ( -28.46)
>DroSec_CAF1 10009 95 + 1
CUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAU---UUUCUUAGGUGGCCCACUAAUUUC-------------UCAAUGUAGGUCUCUUUCGGU---UGUAGAUUGUCA
..........(((((((((((..((.............---..))..))))))))))).....((-------------(((((...((......)).))---)).)))...... ( -21.96)
>DroSim_CAF1 9973 95 + 1
CUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAU---UUUCUUAGGUGGCCCACUAAUUUC-------------UCAAUGUAGGUCUCUUUCGGU---UGUAGAUUGUGA
..........(((((((((((..((.............---..))..))))))))))).....((-------------.((((.((.(.((.....)).---).)).)))).)) ( -23.36)
>DroEre_CAF1 10306 109 + 1
UUUAUGCCCCGUGGGUCGCU-UUGAUAAGCUUAUUUAU---UUUC-AAGGUGGCCCACUAAUUUUUUCCCACCACAUUUCUAUUUAGGUCUCUUUUAUUAUGCUUAUAUUGUGA
..........((((((((((-((((.............---..))-))))))))))))..............((((........(((((............)))))...)))). ( -25.06)
>DroYak_CAF1 10831 97 + 1
------GUCAGUGGG-------UGAUAAGCUUAUAUAUAUAUUUA-CAGGUGGCCCAAUAAUUUCCUACUAUCAUUUCAAAAUUUAGACUCCUUUCGGU---CAUAGAUUGUGA
------.....((((-------(.((......(((....)))...-...)).)))))...................(((.((((((((((......)))---).)))))).))) ( -15.70)
>consensus
CUUAUGCCCCGUGGGUCGCUUUUGAUAAGCUUAUUUAU___UUUC_CAGGUGGCCCACUAAUUUC_U_C_A_CA____UCAAUGUAGGUCUCUUUCGGU___UGUAGAUUGUGA
..........(((((((((((..((..................))..)))))))))))........................................................ (-12.13 = -13.93 +   1.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:15 2006