Locus 7624

Sequence ID 2L_DroMel_CAF1
Location 21,164,604 – 21,164,774
Length 170
Max. P 0.972090
window12252 window12253 window12254

overview

Window 2

Location 21,164,604 – 21,164,702
Length 98
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 76.47
Mean single sequence MFE -16.63
Consensus MFE -12.97
Energy contribution -12.92
Covariance contribution -0.05
Combinations/Pair 1.07
Mean z-score -1.60
Structure conservation index 0.78
SVM decision value 1.37
SVM RNA-class probability 0.947539
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21164604 98 - 22407834
ACAAU-UUUAAAGCCAAGAACAGUUUAGUUUAGAGUAGUUUAUAAACUGAUCUACACGUGGCCUAACAUAU---UAUCUAUCAUUACCAUUAAUUAUUCUAA--
.....-......((((.....((.((((((((..........)))))))).)).....)))).........---............................-- ( -12.40)
>DroSim_CAF1 2116 101 - 1
UCAAU-UUUAAAGCCAAGAACAAUUUAGUUUAGAGCAGUUUAUAAACUGAUCUACACAUGGCUUUACAUAUUAUUAUCUAUCAUUACCAUUAAUUAUUCGAA--
.....-..((((((((.((((......))))(((.(((((....))))).))).....))))))))....................................-- ( -17.00)
>DroEre_CAF1 3148 95 - 1
GCAAU-UUUAAAGCCAAGAACAGUUUAGUUUAGAGCAGUUUAUAAACUGAUCUACACGUGGCAUAACAUAUU------CAAUUUUACACCUAAUUAUUACAA--
.....-......((((...........((.((((.(((((....))))).)))).)).))))..........------........................-- ( -13.70)
>DroYak_CAF1 3131 98 - 1
ACAAU-UUUAAAGCCAAGAACAGUUUAGUUUAGAGCAGUUUAUAAACUGAUCUACACGUGGCAUAACAUAUU---AUUUAUAAUUACACUUUAUUAUACUAA--
.....-......((((...........((.((((.(((((....))))).)))).)).))))..........---...((((((........))))))....-- ( -14.80)
>DroMoj_CAF1 3552 96 - 1
GCAAA-GUUAAAGCCAAGAACAGUUCAGUUUAGCGUAGUUUAUAAACUGAUCUACACGUGGCUUGACAUUCA---AUUAAUUGUUUUUGA-AAU---GCAUUCU
(((..-(((((.((((.....((.((((((((..........)))))))).)).....))))))))).((((---(..........))))-).)---))..... ( -23.90)
>DroPer_CAF1 2143 91 - 1
AUAAUCUUUUAAGCCAAGAACAGUUCAGUUUAGAGCAGUCUAUAAACUGAUCUACACGUGGCCUAACA-----------AUAACUACCAUUUACUGUAGAUU--
........(((.((((.....((.((((((((.((....)).)))))))).)).....)))).)))..-----------....((((........))))...-- ( -18.00)
>consensus
ACAAU_UUUAAAGCCAAGAACAGUUUAGUUUAGAGCAGUUUAUAAACUGAUCUACACGUGGCAUAACAUAUU___AU_UAUAAUUACCAUUAAUUAUUCAAA__
............((((.....((.((((((((..........)))))))).)).....)))).......................................... (-12.97 = -12.92 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,164,630 – 21,164,742
Length 112
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 81.51
Mean single sequence MFE -25.19
Consensus MFE -17.44
Energy contribution -17.25
Covariance contribution -0.19
Combinations/Pair 1.16
Mean z-score -1.28
Structure conservation index 0.69
SVM decision value -0.05
SVM RNA-class probability 0.509766
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21164630 112 + 22407834
UA-AUAUGUUAGGCCACGUGUAGAUCAGUUUAUAAACUACUCUAAACUAAACUGUUCUUGGCUUUAAA-AUUGUUCUGGCAGCAUUGUAUCAGCGCUUAGGUAAACGCAUUUAA
..-..((((.((((((.....(((.(((((((...............))))))).)))))))))....-.....((((((.((.........)))).)))).....)))).... ( -17.16)
>DroVir_CAF1 3508 108 + 1
U-AAAAUGUGAGGCCACGUGUAGAUCAGUUUAUAGACUACGCUAAACUGAACUGUUCCUGGCUUC-GU-UUUGCUCUGGCAGCAUUGUAUCAGCGCUCAAAUGAGCUUG---CA
.-..((((((((((((.(..(((.((((((((..........)))))))).)))..).)))))))-..-..(((....))))))))......((((((....))))..)---). ( -33.50)
>DroPse_CAF1 2115 107 + 1
------UGUUAGGCCACGUGUAGAUCAGUUUAUAGACUGUUCUAAACUGAACUGUUCUUGGCUUAAAAGAUUAUUCUGGCAGCAUUGUAUCAGCAUUCAAUUAAGCUUAAU-CG
------..((((((((.(..(((.((((((..((((....)))))))))).)))..).))))))))..(((((..((........(((....)))........))..))))-). ( -26.69)
>DroEre_CAF1 3172 111 + 1
--AAUAUGUUAUGCCACGUGUAGAUCAGUUUAUAAACUGCUCUAAACUAAACUGUUCUUGGCUUUAAA-AUUGCUAUUGCAGCAUUGUAUCAGCGCUUAGAUAAACUCAUUUCA
--.((((((......))))))((((.(((((((.....((.((..((....((((...((((......-...))))..))))....))...)).))....))))))).)))).. ( -19.30)
>DroMoj_CAF1 3576 109 + 1
U-UGAAUGUCAAGCCACGUGUAGAUCAGUUUAUAAACUACGCUAAACUGAACUGUUCUUGGCUUUAAC-UUUGCUCUGGCAGCAUUGUAUCAGCGCUCAAAUAAACUGA---CA
.-....((((((((((.(..(((.((((((((..........)))))))).)))..).))))))..((-..((((.....))))..))...................))---)) ( -26.10)
>DroPer_CAF1 2166 107 + 1
------UGUUAGGCCACGUGUAGAUCAGUUUAUAGACUGCUCUAAACUGAACUGUUCUUGGCUUAAAAGAUUAUUCUGGCAGCAUUGUAUCAGCAUUCAAUUAAGCUUAAU-CG
------..((((((((.(..(((.((((((((.((....)).)))))))).)))..).))))))))..(((((..((........(((....)))........))..))))-). ( -28.39)
>consensus
___A_AUGUUAGGCCACGUGUAGAUCAGUUUAUAAACUACUCUAAACUGAACUGUUCUUGGCUUUAAA_AUUGCUCUGGCAGCAUUGUAUCAGCGCUCAAAUAAACUUA_U_CA
..........((((((.(..(((.((((((((..........)))))))).)))..).))))))........((.(((((......))..))).)).................. (-17.44 = -17.25 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,164,665 – 21,164,774
Length 109
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 76.82
Mean single sequence MFE -26.01
Consensus MFE -21.60
Energy contribution -20.74
Covariance contribution -0.86
Combinations/Pair 1.39
Mean z-score -2.01
Structure conservation index 0.83
SVM decision value 1.69
SVM RNA-class probability 0.972090
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21164665 109 - 22407834
CA----AAACA--AGCAGCAACAAGAAAGUGCUUAGGCUUAAAUGCGUUUACCUAAGCGCUGAUACAAUGCUGCCAGAACAAU-UUUAAAGCCAAGAACAGUUUAGUUUAGAGUAG
..----((((.--.((((((.......((((((((((..((((....)))))))))))))).......))))))..((((..(-(((.......))))..)))).))))....... ( -27.14)
>DroVir_CAF1 3543 101 - 1
--------UCC--AGCAGCAAAAAGAAAGCGUUCAAAUUG---CAAGCUCAUUUGAGCGCUGAUACAAUGCUGCCAGAGCAAA-AC-GAAGCCAGGAACAGUUCAGUUUAGCGUAG
--------((.--.((((((.......(((((((((((.(---....)..))))))))))).......))))))..))((.((-((-..(((........)))..)))).)).... ( -30.34)
>DroPse_CAF1 2145 111 - 1
CA----AUCCGAUGGCAGCAAAAAGAAAGUGUUCAAAUCG-AUUAAGCUUAAUUGAAUGCUGAUACAAUGCUGCCAGAAUAAUCUUUUAAGCCAAGAACAGUUCAGUUUAGAACAG
..----......((((((((.......(((((((((....-...........))))))))).......))))))))......((((.......))))...((((......)))).. ( -25.00)
>DroYak_CAF1 3192 109 - 1
CA----UAAUA--AGCAGCAACAAGAAAGUGCUUAAGUUGAAAUGGGUUUAUCUAAGCGCUGAUACAAUGCUGCCAGAACAAU-UUUAAAGCCAAGAACAGUUUAGUUUAGAGCAG
..----.....--.((((((.......((((((((.(.((((.....)))).))))))))).......)))))).........-......((...((((......))))...)).. ( -22.94)
>DroMoj_CAF1 3611 110 - 1
UGAUGCUAAUC--AGCAGCAACAAGAAAGUCUUCAAAUUG---UCAGUUUAUUUGAGCGCUGAUACAAUGCUGCCAGAGCAAA-GUUAAAGCCAAGAACAGUUCAGUUUAGCGUAG
..(((((((.(--.((((((.......(((.(((((((..---.......))))))).))).......))))))..((((...-(((.........))).)))).).))))))).. ( -25.64)
>DroPer_CAF1 2196 111 - 1
CA----AUCCGAUGGCAGCAAAAAGAAAGUGUUCAAAUCG-AUUAAGCUUAAUUGAAUGCUGAUACAAUGCUGCCAGAAUAAUCUUUUAAGCCAAGAACAGUUCAGUUUAGAGCAG
..----......((((((((.......(((((((((....-...........))))))))).......))))))))......((((.......))))...((((......)))).. ( -25.00)
>consensus
CA____AAACA__AGCAGCAAAAAGAAAGUGUUCAAAUUG_A_UAAGCUUAUUUGAGCGCUGAUACAAUGCUGCCAGAACAAU_UUUAAAGCCAAGAACAGUUCAGUUUAGAGCAG
..............((((((.......(((((((((((............))))))))))).......))))))................((...((((......))))...)).. (-21.60 = -20.74 +  -0.86)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:21 2006