Locus 3500

Sequence ID 2R_DroMel_CAF1
Location 11,734,866 – 11,735,000
Length 134
Max. P 0.863785
window5702 window5703 window5704 window5705

overview

Window 2

Location 11,734,866 – 11,734,979
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.72
Mean single sequence MFE -37.78
Consensus MFE -23.29
Energy contribution -24.97
Covariance contribution 1.68
Combinations/Pair 1.07
Mean z-score -2.06
Structure conservation index 0.62
SVM decision value 0.84
SVM RNA-class probability 0.863785
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734866 113 + 20766785
CA-UUC------AUGUUGGCGAACAAAACGAGUCUUUGCUACAACACAGAUAGCCUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGU
..-...------.((((((((((...........)))))..)))))((((((.(((.((((........))))..))).))))))((((((.....))))))(((((.......))))). ( -34.10)
>DroPse_CAF1 19904 102 + 1
------------------GGAGAGAAAACGGGUCUUUGCGAUAGGACAGCCAGUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGU
------------------((((.(((..(((((((((.......((.(((((((((((....(((((....)))))))))).)))))).)).....)))))))))..)))..)))).... ( -44.40)
>DroSim_CAF1 21231 120 + 1
CAAUUCAGACAAAUGUUGGCGAACAAAACGAGUCUUUGCUACAACACAGACAGCCUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGU
.....((((...((.(((((..((.......((((.((......)).)))).(((........)))...)).))))).)).))))((((((.....))))))(((((.......))))). ( -32.10)
>DroAna_CAF1 20761 111 + 1
-----CAGGCAAU----UGCUAACAAAAUGCUGCUUUGCUUCUGAGUUGCCAAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGU
-----.(((((..----.((.........)))))))..((((((.((.((((((((((....(((((....))))))))))).))))....)).))))))..(((((.......))))). ( -36.40)
>DroPer_CAF1 20592 102 + 1
------------------GGAGAGAAAACGGGUUUUUGCGAUAGGACAGCCAGUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGU
------------------((((.(((..(((((((((.......((.(((((((((((....(((((....)))))))))).)))))).)).....)))))))))..)))..)))).... ( -41.90)
>consensus
_____C____________GCAAACAAAACGAGUCUUUGCUACAGCACAGCCAGUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGU
...............................((((((..........(((((((((((....(((((....)))))))))).))))))........))))))(((((.......))))). (-23.29 = -24.97 +   1.68)

alignment

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secondary structure

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Window 3

Location 11,734,866 – 11,734,979
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.72
Mean single sequence MFE -34.92
Consensus MFE -23.42
Energy contribution -24.22
Covariance contribution 0.80
Combinations/Pair 1.10
Mean z-score -1.60
Structure conservation index 0.67
SVM decision value 0.13
SVM RNA-class probability 0.600019
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734866 113 - 20766785
ACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAGGCUAUCUGUGUUGUAGCAAAGACUCGUUUUGUUCGCCAACAU------GAA-UG
.(((((.......)))))(((((((.(((....))).......((((...)))).......)))))))(((..((((((.(((((((.....)))))))...))))))------..)-)) ( -34.40)
>DroPse_CAF1 19904 102 - 1
ACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUACUGGCUGUCCUAUCGCAAAGACCCGUUUUCUCUCC------------------
...((((...(((..((((...(((..((((.((((((.(((((((..............)))))))))))))......))))..)))))))..))))))).------------------ ( -34.04)
>DroSim_CAF1 21231 120 - 1
ACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAGGCUGUCUGUGUUGUAGCAAAGACUCGUUUUGUUCGCCAACAUUUGUCUGAAUUG
.(((((.......)))))(((((((.(((....))).......((((...)))).......))))))).(.(.((((((.(((((((.....)))))))...))))))..).)....... ( -33.40)
>DroAna_CAF1 20761 111 - 1
ACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUUGGCAACUCAGAAGCAAAGCAGCAUUUUGUUAGCA----AUUGCCUG-----
.(((((.......)))))(((((((((((....(((((.(((((((..............)))))))))))).)))))))))....)).(((..(((....))----).)))...----- ( -39.14)
>DroPer_CAF1 20592 102 - 1
ACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUACUGGCUGUCCUAUCGCAAAAACCCGUUUUCUCUCC------------------
..((((......((((((.....))))))((.((((((.(((((((..............))))))))))))).))............))))..........------------------ ( -33.64)
>consensus
ACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUACUGGCUGUCCUGUAGCAAAGACCCGUUUUGUUCGC____________G_____
.(((((.......)))))(((.....)))...((((((.(((((((..............)))))))))))))............................................... (-23.42 = -24.22 +   0.80)

alignment

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secondary structure

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Window 4

Location 11,734,899 – 11,735,000
Length 101
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 86.12
Mean single sequence MFE -32.20
Consensus MFE -29.52
Energy contribution -29.52
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.92
SVM decision value 0.60
SVM RNA-class probability 0.794976
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734899 101 + 20766785
ACAACACAGAUAGCCUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGAGUACUUUUUUUU
......((((((.(((.((((........))))..))).))))))(((((..((((....(((.(((.......)))))).)))).))))).......... ( -30.80)
>DroVir_CAF1 25966 99 + 1
--AGGGAUUGUAUAAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUACCAUUUUUGGU
--.((((((....))))))..(((((((.(.((((((.....))))))..).((((....(((.(((.......)))))).)))).)).)))))....... ( -33.20)
>DroPse_CAF1 19926 101 + 1
AUAGGACAGCCAGUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGAACACUUUUUUCA
....((.(((((((((((....(((((....)))))))))).)))))).)).((((....(((.(((.......)))))).))))................ ( -35.70)
>DroSim_CAF1 21271 101 + 1
ACAACACAGACAGCCUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGAGUGCUUUUUUUU
.......(((.((((((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))...).))).)))... ( -30.40)
>DroMoj_CAF1 27038 99 + 1
--GGGGAACAUCGCGUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUAUACUUUUUUAU
--.((((..((((...(((...(((((....)))))........(((((((.....))))))).)))..))))))))((((((.....))))))....... ( -31.00)
>DroAna_CAF1 20792 101 + 1
UCUGAGUUGCCAAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUACAUUUUUUUGU
..((((..((((((((((....(((((....))))))))))).)))).))))((((....(((.(((.......)))))).))))................ ( -32.10)
>consensus
ACAGGACAGACAGCAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGAACACUUUUUUGU
...............((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))............... (-29.52 = -29.52 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,734,899 – 11,735,000
Length 101
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 86.12
Mean single sequence MFE -29.78
Consensus MFE -25.75
Energy contribution -25.75
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.86
SVM decision value 0.74
SVM RNA-class probability 0.837783
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11734899 101 - 20766785
AAAAAAAAGUACUCUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAGGCUAUCUGUGUUGU
.......((....((((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))))....))....... ( -29.10)
>DroVir_CAF1 25966 99 - 1
ACCAAAAAUGGUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUUAUACAAUCCCU--
.......(((((..........(((((.......)))))....(((((.(....))))))....((((...)))))))))..((((((....)))))).-- ( -28.30)
>DroPse_CAF1 19926 101 - 1
UGAAAAAAGUGUUCUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUACUGGCUGUCCUAU
..............(((((.....)))))....((((((.....))))))((.((((((.(((((((..............))))))))))))).)).... ( -32.74)
>DroSim_CAF1 21271 101 - 1
AAAAAAAAGCACUCUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAGGCUGUCUGUGUUGU
.......(((((.((((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))))......))))).. ( -32.00)
>DroMoj_CAF1 27038 99 - 1
AUAAAAAAGUAUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGACGCGAUGUUCCCC--
...............((((((((((((.......)))))....(((((.(....))))))....((((...))))....))))))).............-- ( -25.60)
>DroAna_CAF1 20792 101 - 1
ACAAAAAAAUGUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUUGGCAACUCAGA
......................(((((.......)))))....(((((((....(((((.(((((((..............)))))))))))).))))))) ( -30.94)
>consensus
AAAAAAAAGUAUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUGCUAUCUGCCCUGU
...............((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))............... (-25.75 = -25.75 +   0.00)

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 10:57:03 2006