Locus 6397

Sequence ID 2R_DroMel_CAF1
Location 20,009,257 – 20,009,402
Length 145
Max. P 0.996469
window10207 window10208 window10209 window10210

overview

Window 7

Location 20,009,257 – 20,009,368
Length 111
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 79.75
Mean single sequence MFE -35.40
Consensus MFE -25.26
Energy contribution -25.90
Covariance contribution 0.64
Combinations/Pair 1.26
Mean z-score -2.88
Structure conservation index 0.71
SVM decision value 2.70
SVM RNA-class probability 0.996469
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20009257 111 + 20766785
UAGGGGGAUGCACUGAGAGAACAGUUCUUAACUUUUUCGAAAGGGCAGGAAAAAGUAUGCAUGAGUAUUUUGUGGUUUGCAACUCAGCUCAUUCACUGCAUACUUUUCCCU--------
...((((((((.((..(((((.(((.....))))))))...)).)))....(((((((((((((((...((((.....))))....))))).....)))))))))))))))-------- ( -31.60)
>DroSec_CAF1 26019 111 + 1
UAAGGGGCUUCACUGAGAGAACAGUUGCUAACUUUUUCGAAAGGGAAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCUGCUCUCUCAUUGCAUACUUUUCCCU--------
..(((((((((.((..(((((.(((.....))))))))...)).))))).(((((((((((((((((..(((((...)))))...)))))).....)))))))))))))))-------- ( -37.50)
>DroSim_CAF1 26191 111 + 1
CAAGGGGCUGCACUGAGAGAACAGUUCCUAACUUUUUCGAAUGAGCAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCUGCUCUCUCAUUGCAUACUUUUUCCU--------
...((((((((.(...(((((.(((.....))))))))....).)))))((((((((((((((((((..(((((...)))))...)))))).....)))))))))))))))-------- ( -35.10)
>DroEre_CAF1 31961 110 + 1
UG-GGGGCUGCACUGAGGGAAUAGUUCCCAACUUCUUUGCUGGCACAGCAAAAAGUAUGCAAGGGUAUUUUGUGGUUCGCUACCCAGCUCCUUCACUGCAUACUUUUCCCC--------
.(-(((((((((..((((((.....))))....))..))).)))......(((((((((((((((....(((.(((.....))))))..))))...)))))))))))))))-------- ( -36.70)
>DroYak_CAF1 31349 118 + 1
UA-GUGGCUGCACUGAGGAAAUAGUUCUGCACUUCUUUGAAAGCACAGCAAAAAGUAUGCAAGAGUGUUUUGUGGUGUGCCACCCAAGUUAUUCACUGCAUACUUUUUCCCUUUUCUCA
.(-(((....))))(((((((..(((.(((............))).)))((((((((((((.(((((.((((.((((...)))))))).)))))..))))))))))))...))))))). ( -36.10)
>consensus
UA_GGGGCUGCACUGAGAGAACAGUUCCUAACUUUUUCGAAAGCGCAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCAGCUCAUUCACUGCAUACUUUUCCCU________
...((((((((.((..(((((.(((.....))))))))...)).))))).((((((((((((((((...((((.....))))....))))).....))))))))))))))......... (-25.26 = -25.90 +   0.64)

alignment

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secondary structure

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Window 8

Location 20,009,257 – 20,009,368
Length 111
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 79.75
Mean single sequence MFE -33.26
Consensus MFE -20.75
Energy contribution -20.19
Covariance contribution -0.56
Combinations/Pair 1.22
Mean z-score -2.73
Structure conservation index 0.62
SVM decision value 2.21
SVM RNA-class probability 0.990356
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20009257 111 - 20766785
--------AGGGAAAAGUAUGCAGUGAAUGAGCUGAGUUGCAAACCACAAAAUACUCAUGCAUACUUUUUCCUGCCCUUUCGAAAAAGUUAAGAACUGUUCUCUCAGUGCAUCCCCCUA
--------(((((((((((((((((......))(((((...............))))))))))))))))))))((.((((....))))......((((......))))))......... ( -27.26)
>DroSec_CAF1 26019 111 - 1
--------AGGGAAAAGUAUGCAAUGAGAGAGCAGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUUCCCUUUCGAAAAAGUUAGCAACUGUUCUCUCAGUGAAGCCCCUUA
--------((((....((...((.(((((((((((((((((((..............))))).)))..(((((...((((....))))..)))))))))))))))).))..)))))).. ( -31.64)
>DroSim_CAF1 26191 111 - 1
--------AGGAAAAAGUAUGCAAUGAGAGAGCAGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUGCUCAUUCGAAAAAGUUAGGAACUGUUCUCUCAGUGCAGCCCCUUG
--------((((((((((((((((.(((...((......))(.....)......))))))))))))))))(((((...(((..........)))((((......))))))))).))).. ( -30.70)
>DroEre_CAF1 31961 110 - 1
--------GGGGAAAAGUAUGCAGUGAAGGAGCUGGGUAGCGAACCACAAAAUACCCUUGCAUACUUUUUGCUGUGCCAGCAAAGAAGUUGGGAACUAUUCCCUCAGUGCAGCCCC-CA
--------(((((((((((((((((......)))(((((.............)))))..)))))))))).((((..(.(((......)))((((.....))))...)..)))))))-). ( -40.82)
>DroYak_CAF1 31349 118 - 1
UGAGAAAAGGGAAAAAGUAUGCAGUGAAUAACUUGGGUGGCACACCACAAAACACUCUUGCAUACUUUUUGCUGUGCUUUCAAAGAAGUGCAGAACUAUUUCCUCAGUGCAGCCAC-UA
.(((.(((.(((((((((((((((.((.....(((((((...)))).))).....))))))))))))))).(((..((((....))))..)))..)).))).)))((((....)))-). ( -35.90)
>consensus
________AGGGAAAAGUAUGCAGUGAAAGAGCUGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUGCCCUUUCGAAAAAGUUAGGAACUGUUCUCUCAGUGCAGCCCC_UA
.........(((((((((((((((..........((((...............)))))))))))))))))(((((...........(((.....)))...........))))))).... (-20.75 = -20.19 +  -0.56)

alignment

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secondary structure

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Window 9

Location 20,009,297 – 20,009,402
Length 105
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 81.33
Mean single sequence MFE -31.06
Consensus MFE -17.24
Energy contribution -17.96
Covariance contribution 0.72
Combinations/Pair 1.23
Mean z-score -2.22
Structure conservation index 0.56
SVM decision value 0.61
SVM RNA-class probability 0.797454
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20009297 105 + 20766785
AAGGGCAGGAAAAAGUAUGCAUGAGUAUUUUGUGGUUUGCAACUCAGCUCAUUCACUGCAUACUUUUCCCU--------GUGUAGGCAGUGCUCUUCCUCACCGGGUUAUGUA
..(((((((.((((((((((((((((...((((.....))))....))))).....))))))))))).)))--------))(.(((.((....)).)))).)).......... ( -32.10)
>DroSec_CAF1 26059 105 + 1
AAGGGAAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCUGCUCUCUCAUUGCAUACUUUUCCCU--------GUGUAGACAGUGCUCUUCCUCACCGGGUUAUGUA
.((((((((((((((((((((((((((..(((((...)))))...)))))).....)))))))))))..((--------((....)))))))).))))).............. ( -30.60)
>DroSim_CAF1 26231 105 + 1
AUGAGCAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCUGCUCUCUCAUUGCAUACUUUUUCCU--------GUGUAGGCAGUGCUCUUCCUCACCUGGUUAUGUA
((((.(((.((((((((((((((((((..(((((...)))))...)))))).....))))))))))))...--------(((.(((.((....)).))))))))).))))... ( -31.30)
>DroEre_CAF1 32000 105 + 1
UGGCACAGCAAAAAGUAUGCAAGGGUAUUUUGUGGUUCGCUACCCAGCUCCUUCACUGCAUACUUUUCCCC--------GUGCAGCGAGUGCUUCUGCUCACCGCGUUAUGUA
..((((.(..(((((((((((((((....(((.(((.....))))))..))))...)))))))))))..).--------)))).(((.(((........))))))........ ( -32.70)
>DroYak_CAF1 31388 113 + 1
AAGCACAGCAAAAAGUAUGCAAGAGUGUUUUGUGGUGUGCCACCCAAGUUAUUCACUGCAUACUUUUUCCCUUUUCUCAGUGUACUUAGUACUUUUCCUCACCGCGUUAUGUA
..(((.(((((((((((((((.(((((.((((.((((...)))))))).)))))..)))))))))))).............((((...)))).............))).))). ( -28.60)
>consensus
AAGCGCAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCAGCUCAUUCACUGCAUACUUUUCCCU________GUGUAGGCAGUGCUCUUCCUCACCGGGUUAUGUA
....(((...((((((((((((((((...((((.....))))....))))).....)))))))))))............(((.(((.((....)).)))))).......))). (-17.24 = -17.96 +   0.72)

alignment

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secondary structure

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Window 0

Location 20,009,297 – 20,009,402
Length 105
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 81.33
Mean single sequence MFE -31.22
Consensus MFE -20.04
Energy contribution -19.04
Covariance contribution -1.00
Combinations/Pair 1.26
Mean z-score -2.45
Structure conservation index 0.64
SVM decision value 1.42
SVM RNA-class probability 0.952719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20009297 105 - 20766785
UACAUAACCCGGUGAGGAAGAGCACUGCCUACAC--------AGGGAAAAGUAUGCAGUGAAUGAGCUGAGUUGCAAACCACAAAAUACUCAUGCAUACUUUUUCCUGCCCUU
.........(((((........)))))......(--------(((((((((((((((((......))(((((...............)))))))))))))))))))))..... ( -30.56)
>DroSec_CAF1 26059 105 - 1
UACAUAACCCGGUGAGGAAGAGCACUGUCUACAC--------AGGGAAAAGUAUGCAAUGAGAGAGCAGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUUCCCUU
.............((((..((((.((((....))--------)).(((((((((((((.(((...((......))(.....)......)))))))))))))))))))).)))) ( -28.70)
>DroSim_CAF1 26231 105 - 1
UACAUAACCAGGUGAGGAAGAGCACUGCCUACAC--------AGGAAAAAGUAUGCAAUGAGAGAGCAGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUGCUCAU
...........((((((.((.((...)))).).(--------((.(((((((((((((.(((...((......))(.....)......)))))))))))))))).)))))))) ( -28.60)
>DroEre_CAF1 32000 105 - 1
UACAUAACGCGGUGAGCAGAAGCACUCGCUGCAC--------GGGGAAAAGUAUGCAGUGAAGGAGCUGGGUAGCGAACCACAAAAUACCCUUGCAUACUUUUUGCUGUGCCA
........((((((((........))))))))((--------((.((((((((((((((......)))(((((.............)))))..))))))))))).)))).... ( -39.42)
>DroYak_CAF1 31388 113 - 1
UACAUAACGCGGUGAGGAAAAGUACUAAGUACACUGAGAAAAGGGAAAAAGUAUGCAGUGAAUAACUUGGGUGGCACACCACAAAACACUCUUGCAUACUUUUUGCUGUGCUU
.......((((((........((((...)))).............(((((((((((((.((.....(((((((...)))).))).....)))))))))))))))))))))... ( -28.80)
>consensus
UACAUAACCCGGUGAGGAAGAGCACUGCCUACAC________AGGGAAAAGUAUGCAGUGAAAGAGCUGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUGCCCUU
..........((((........))))................((.(((((((((((((..........((((...............))))))))))))))))).))...... (-20.04 = -19.04 +  -1.00)

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 12:10:00 2006