Locus 8007

Sequence ID 3R_DroMel_CAF1
Location 21,472,200 – 21,472,333
Length 133
Max. P 0.987156
window12888 window12889 window12890 window12891

overview

Window 8

Location 21,472,200 – 21,472,307
Length 107
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 83.18
Mean single sequence MFE -33.88
Consensus MFE -29.43
Energy contribution -29.19
Covariance contribution -0.25
Combinations/Pair 1.08
Mean z-score -2.83
Structure conservation index 0.87
SVM decision value 1.62
SVM RNA-class probability 0.968302
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21472200 107 + 27905053
----UCGUGAUCUGAUUUUCAGCCGAAUAUAAAUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUCGAAU-AAACAUUGCACUUGUCCCGGCCUAUGGGC
----(((.(..(((.....)))))))................((((((((.((((((((((.(((.((((..(.....)...-)))).)))))))).))))).)))))))). ( -34.40)
>DroGri_CAF1 67643 97 + 1
AUAUUCUUAAACGUGU---------------ACCAUAAAUUGCUUGCAGGACGGGAAGGUGUCAACGUUUUGCAUUUUGAAUCAAACAUUGCACUUGUCCCGGCCUAUGAGC
................---------------..........((((..(((.((((((((((.(((.((((..(.....)....)))).)))))))).))))).)))..)))) ( -25.20)
>DroSim_CAF1 64110 107 + 1
----UCGUGAUCUUGUUUUCAGCCGAAUAAAAAUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUCGAAU-AAACAUUGCACUUGUCCCGGCCUAUGGGC
----(((((.(.((((((......)))))).).)))))....((((((((.((((((((((.(((.((((..(.....)...-)))).)))))))).))))).)))))))). ( -35.20)
>DroEre_CAF1 80147 107 + 1
----UCGUGAUCUUGUUUUCGGCCGAAUAUGAAUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUCGAAU-AAACAUUGCACUUGUCCCGGCCUAUGGGC
----(((((.((.(((((......))))).)).)))))....((((((((.((((((((((.(((.((((..(.....)...-)))).)))))))).))))).)))))))). ( -37.30)
>DroYak_CAF1 70784 107 + 1
----UCGUGAUCUUGUUUUCGUUCGAAUAUGAAUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUUGAAU-AAACAUUGCACUUGUCCCGGCCUAUGGGC
----(((((.((.(((((......))))).)).)))))....((((((((.((((((((((.(((.((((..(.....)...-)))).)))))))).))))).)))))))). ( -37.60)
>DroAna_CAF1 158305 105 + 1
----UCCUCGUAGCAUUUUCCAUCGAAUAU-AAUACAAAUUUCCCGUAGGACGGGAAGGUGUCAAGGUUUUGAAUU-AAAUU-AAACAUUGCACUUGUCCCGGCCUAUGGGC
----.....(((..((.(((....))).))-..)))......((((((((.((((((((((.(((.((((......-.....-)))).)))))))).))))).)))))))). ( -33.60)
>consensus
____UCGUGAUCUUGUUUUCAGCCGAAUAU_AAUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUCGAAU_AAACAUUGCACUUGUCCCGGCCUAUGGGC
..........................................((((((((.((((((((((.(((.((((.............)))).)))))))).))))).)))))))). (-29.43 = -29.19 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,472,200 – 21,472,307
Length 107
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 83.18
Mean single sequence MFE -30.10
Consensus MFE -27.25
Energy contribution -27.17
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -2.70
Structure conservation index 0.91
SVM decision value 1.83
SVM RNA-class probability 0.979319
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21472200 107 - 27905053
GCCCAUAGGCCGGGACAAGUGCAAUGUUU-AUUCGAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAUUUAUAUUCGGCUGAAAAUCAGAUCACGA----
.(((.((((.(((((...(((((((((((-............)))))))).)))..))))).)))).)))................(((.(((.....)))....)))---- ( -33.10)
>DroGri_CAF1 67643 97 - 1
GCUCAUAGGCCGGGACAAGUGCAAUGUUUGAUUCAAAAUGCAAAACGUUGACACCUUCCCGUCCUGCAAGCAAUUUAUGGU---------------ACACGUUUAAGAAUAU
(((..((((.(((((...(((((((((((.............)))))))).)))..))))).))))..)))..........---------------................ ( -27.82)
>DroSim_CAF1 64110 107 - 1
GCCCAUAGGCCGGGACAAGUGCAAUGUUU-AUUCGAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAUUUUUAUUCGGCUGAAAACAAGAUCACGA----
.(((.((((.(((((...(((((((((((-............)))))))).)))..))))).)))).)))................(((.((.......))....)))---- ( -30.00)
>DroEre_CAF1 80147 107 - 1
GCCCAUAGGCCGGGACAAGUGCAAUGUUU-AUUCGAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAUUCAUAUUCGGCCGAAAACAAGAUCACGA----
.......(((((((....(((((((((((-............)))))))).))).((((((.....)))))).............)))))))................---- ( -29.80)
>DroYak_CAF1 70784 107 - 1
GCCCAUAGGCCGGGACAAGUGCAAUGUUU-AUUCAAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAUUCAUAUUCGAACGAAAACAAGAUCACGA----
.(((.((((.(((((...(((((((((((-............)))))))).)))..))))).)))).)))...............(((....))).............---- ( -29.30)
>DroAna_CAF1 158305 105 - 1
GCCCAUAGGCCGGGACAAGUGCAAUGUUU-AAUUU-AAUUCAAAACCUUGACACCUUCCCGUCCUACGGGAAAUUUGUAUU-AUAUUCGAUGGAAAAUGCUACGAGGA----
.(((.((((.(((((...((((((.((((-.....-......)))).))).)))..))))).)))).)))...((((((.(-((.(((....))).))).))))))..---- ( -30.60)
>consensus
GCCCAUAGGCCGGGACAAGUGCAAUGUUU_AUUCGAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAUU_AUAUUCGGCCGAAAACAAGAUCACGA____
.(((.((((.(((((...(((((((((((.............)))))))).)))..))))).)))).))).......................................... (-27.25 = -27.17 +  -0.08)

alignment

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secondary structure

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Window 0

Location 21,472,228 – 21,472,333
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.60
Mean single sequence MFE -37.02
Consensus MFE -31.58
Energy contribution -30.22
Covariance contribution -1.36
Combinations/Pair 1.22
Mean z-score -4.01
Structure conservation index 0.85
SVM decision value 1.47
SVM RNA-class probability 0.956368
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21472228 105 + 27905053
AUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUCGAAU-AAACAUUGCACUUGUCCCGGCCUAUGGGCGGUUUGUAAUA-AACAACUA-------------AAAUCUA
.((..(((..((((((((.((((((((((.(((.((((..(.....)...-)))).)))))))).))))).))))))))..)))..))...-........-------------....... ( -38.00)
>DroVir_CAF1 80434 101 + 1
UCACAAACUGCUUGCAGGACGGGAAGGUGUCAACGUUUUGCUUUAUGAAUCAAACAUUGCACUUGUCCCGGCCUAUGAGCGGUUUGUGCCACAACAAACG-------------A------
.((((((((((((..(((.((((((((((.(((.((((..(.....)....)))).)))))))).))))).)))..))))))))))))............-------------.------ ( -39.80)
>DroGri_CAF1 67660 101 + 1
CCAUAAAUUGCUUGCAGGACGGGAAGGUGUCAACGUUUUGCAUUUUGAAUCAAACAUUGCACUUGUCCCGGCCUAUGAGCGGUUUGUGCAUCUACAACUG-------------G------
.((((((((((((..(((.((((((((((.(((.((((..(.....)....)))).)))))))).))))).)))..))))))))))))............-------------.------ ( -35.50)
>DroYak_CAF1 70812 105 + 1
AUAUGAAUUUCCCGUAGGACGGGAAGGUGUCAACGUUUUGCAUUUUGAAU-AAACAUUGCACUUGUCCCGGCCUAUGGGCGGUUUGUAAUA-AACAACUA-------------AAAUGCA
.((..(((..((((((((.((((((((((.(((.((((..(.....)...-)))).)))))))).))))).))))))))..)))..))...-........-------------....... ( -38.30)
>DroMoj_CAF1 66516 107 + 1
UCAUAAAUUGCUUGCAGGACGGGAAGGUGUCAACGUUUUACCUUUUGAUUCAAACAUUGCACUUGUCCCGGCCUAUGAGCGGUUUAUCUUACAACAAUCA-------------GGUCCAA
..(((((((((((..(((.((((((((((.(((.((((.............)))).)))))))).))))).)))..))))))))))).............-------------....... ( -32.32)
>DroAna_CAF1 158332 117 + 1
AUACAAAUUUCCCGUAGGACGGGAAGGUGUCAAGGUUUUGAAUU-AAAUU-AAACAUUGCACUUGUCCCGGCCUAUGGGCGGUUUGUCAAA-CACAUCGAUACAUAUUUUUAGAAAUAUU
..((((((..((((((((.((((((((((.(((.((((......-.....-)))).)))))))).))))).))))))))..))))))....-...........((((((....)))))). ( -38.20)
>consensus
ACAUAAAUUGCCCGCAGGACGGGAAGGUGUCAACGUUUUGCAUUUUGAAU_AAACAUUGCACUUGUCCCGGCCUAUGAGCGGUUUGUAAUA_AACAACUA_____________AAAU__A
.((((((((.((((.(((.((((((((((.(((.((((.............)))).)))))))).))))).))).)))).))))))))................................ (-31.58 = -30.22 +  -1.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,472,228 – 21,472,333
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.60
Mean single sequence MFE -31.66
Consensus MFE -24.08
Energy contribution -23.52
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -2.99
Structure conservation index 0.76
SVM decision value 2.07
SVM RNA-class probability 0.987156
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21472228 105 - 27905053
UAGAUUU-------------UAGUUGUU-UAUUACAAACCGCCCAUAGGCCGGGACAAGUGCAAUGUUU-AUUCGAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAU
..((.((-------------(..((((.-....))))....(((.((((.(((((...(((((((((((-............)))))))).)))..))))).)))).)))))).)).... ( -30.80)
>DroVir_CAF1 80434 101 - 1
------U-------------CGUUUGUUGUGGCACAAACCGCUCAUAGGCCGGGACAAGUGCAAUGUUUGAUUCAUAAAGCAAAACGUUGACACCUUCCCGUCCUGCAAGCAGUUUGUGA
------.-------------............(((((((.(((..((((.(((((...(((((((((((.............)))))))).)))..))))).))))..))).))))))). ( -37.42)
>DroGri_CAF1 67660 101 - 1
------C-------------CAGUUGUAGAUGCACAAACCGCUCAUAGGCCGGGACAAGUGCAAUGUUUGAUUCAAAAUGCAAAACGUUGACACCUUCCCGUCCUGCAAGCAAUUUAUGG
------(-------------((.((((......))))...(((..((((.(((((...(((((((((((.............)))))))).)))..))))).))))..)))......))) ( -30.12)
>DroYak_CAF1 70812 105 - 1
UGCAUUU-------------UAGUUGUU-UAUUACAAACCGCCCAUAGGCCGGGACAAGUGCAAUGUUU-AUUCAAAAUGCAAAACGUUGACACCUUCCCGUCCUACGGGAAAUUCAUAU
.......-------------...((((.-....))))....(((.((((.(((((...(((((((((((-............)))))))).)))..))))).)))).))).......... ( -29.90)
>DroMoj_CAF1 66516 107 - 1
UUGGACC-------------UGAUUGUUGUAAGAUAAACCGCUCAUAGGCCGGGACAAGUGCAAUGUUUGAAUCAAAAGGUAAAACGUUGACACCUUCCCGUCCUGCAAGCAAUUUAUGA
.......-------------.............(((((..(((..((((.(((((...(((((((((((..(((....))).)))))))).)))..))))).))))..)))..))))).. ( -30.50)
>DroAna_CAF1 158332 117 - 1
AAUAUUUCUAAAAAUAUGUAUCGAUGUG-UUUGACAAACCGCCCAUAGGCCGGGACAAGUGCAAUGUUU-AAUUU-AAUUCAAAACCUUGACACCUUCCCGUCCUACGGGAAAUUUGUAU
...........((((((((....)))))-))).(((((...(((.((((.(((((...((((((.((((-.....-......)))).))).)))..))))).)))).)))...))))).. ( -31.20)
>consensus
U__AUUU_____________UAGUUGUU_UAUCACAAACCGCCCAUAGGCCGGGACAAGUGCAAUGUUU_AUUCAAAAUGCAAAACGUUGACACCUUCCCGUCCUACAAGAAAUUUAUAU
.......................((((......))))....((..((((.(((((...(((((((((((.............)))))))).)))..))))).))))..)).......... (-24.08 = -23.52 +  -0.56)

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 13:00:14 2006