Locus 3575

Sequence ID 2R_DroMel_CAF1
Location 11,897,520 – 11,897,816
Length 296
Max. P 0.973818
window5825 window5826 window5827 window5828

overview

Window 5

Location 11,897,520 – 11,897,637
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.47
Mean single sequence MFE -31.82
Consensus MFE -20.26
Energy contribution -20.95
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value -0.03
SVM RNA-class probability 0.518415
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11897520 117 + 20766785
UUAACUAUAAAUUCUGUGUGGCAAAACAUGCAAACAUGUUUGCGGAAAUACCUGACAGACUCAGGAGGGUCAAACCAAGGGGGGGGGGGGUGUGGUUCGGUGCAGGAAAGAUCA---GGG
...........(((((..(.(((((.((((....)))))))))(((.((((((..(.(((((....)))))...((......)))..))))))..))).)..))))).......---... ( -32.90)
>DroSec_CAF1 38008 110 + 1
UUAACUAUAAAUUCUGUGUGGCAAAACAUGGAAAAAUGUUUGCGGAAAUACCUGACAGACUCAGGAGGGUCAAACCAGGGGGUGGGG------GUUUCGGUGCAGA-AAGAUCA---GGU
...........(((((..(.(((((.(((......)))))))).(((((.(((.((.(((((....)))))...((...)))).)))------))))).)..))))-)......---... ( -29.70)
>DroSim_CAF1 38412 116 + 1
UUAACUAUAAAUUCUGUGUGGCAAAACAUGCAAACAUGUUUGCGGAAAUACCUGACAGACUCAGGAGGGUCAAUCCAGGGGGGGAGG-GGGGUGGUUUGCUGCAGAAAAGAUCA---GGU
...........((((((..((((((...((((((....))))))....(((((..(.(((((....)))))..(((......)))).-.))))).)))))))))))).......---... ( -32.60)
>DroYak_CAF1 38559 115 + 1
UUAACUAUAAAUUCUGUGUGGCAAAACAUGCAAACAUGUUUGCGGAAAUACCUGACAGACUCGGGAGAGUCAACCUAGGGCGGGAGGAGGUG-GGUU-C---CUGAAAAGAUUAAAGGGG
....((......(((.....(((((.((((....)))))))))((((.(((((....(((((....)))))..(((........))))))))-..))-)---).....)))......)). ( -32.10)
>consensus
UUAACUAUAAAUUCUGUGUGGCAAAACAUGCAAACAUGUUUGCGGAAAUACCUGACAGACUCAGGAGGGUCAAACCAGGGGGGGAGG_GGUG_GGUUCGGUGCAGAAAAGAUCA___GGG
...........((((((...(((((.((((....))))))))).......((((...(((((....)))))....))))......................))))))............. (-20.26 = -20.95 +   0.69)

alignment

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secondary structure

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Window 6

Location 11,897,520 – 11,897,637
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.47
Mean single sequence MFE -21.99
Consensus MFE -15.09
Energy contribution -16.15
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.69
SVM decision value -0.00
SVM RNA-class probability 0.531315
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11897520 117 - 20766785
CCC---UGAUCUUUCCUGCACCGAACCACACCCCCCCCCCCCUUGGUUUGACCCUCCUGAGUCUGUCAGGUAUUUCCGCAAACAUGUUUGCAUGUUUUGCCACACAGAAUUUAUAGUUAA
..(---((......((((((..((((((...............))))))(((.(....).))))).)))).......(((((((((....)))).)))))....)))............. ( -22.16)
>DroSec_CAF1 38008 110 - 1
ACC---UGAUCUU-UCUGCACCGAAAC------CCCCACCCCCUGGUUUGACCCUCCUGAGUCUGUCAGGUAUUUCCGCAAACAUUUUUCCAUGUUUUGCCACACAGAAUUUAUAGUUAA
..(---((....(-((((.........------........(((((...(((.(....).)))..))))).......((((((((......))).)))))....)))))....))).... ( -17.80)
>DroSim_CAF1 38412 116 - 1
ACC---UGAUCUUUUCUGCAGCAAACCACCCC-CCUCCCCCCCUGGAUUGACCCUCCUGAGUCUGUCAGGUAUUUCCGCAAACAUGUUUGCAUGUUUUGCCACACAGAAUUUAUAGUUAA
..(---((.....(((((..(((((.((....-........(((((...(((.(....).)))..))))).......(((((....))))).)).)))))....)))))....))).... ( -23.50)
>DroYak_CAF1 38559 115 - 1
CCCCUUUAAUCUUUUCAG---G-AACC-CACCUCCUCCCGCCCUAGGUUGACUCUCCCGAGUCUGUCAGGUAUUUCCGCAAACAUGUUUGCAUGUUUUGCCACACAGAAUUUAUAGUUAA
...((.(((....(((.(---(-((..-.((((....((......))..(((((....)))))....))))..))))(((((((((....)))).)))))......))).))).)).... ( -24.50)
>consensus
ACC___UGAUCUUUUCUGCACCGAACC_CACC_CCCCCCCCCCUGGUUUGACCCUCCUGAGUCUGUCAGGUAUUUCCGCAAACAUGUUUGCAUGUUUUGCCACACAGAAUUUAUAGUUAA
.............(((((.......................(((((...(((.(....).)))..))))).......(((((((((....)))).)))))....)))))........... (-15.09 = -16.15 +   1.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,897,600 – 11,897,716
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.56
Mean single sequence MFE -44.59
Consensus MFE -30.80
Energy contribution -30.68
Covariance contribution -0.12
Combinations/Pair 1.04
Mean z-score -1.91
Structure conservation index 0.69
SVM decision value 0.54
SVM RNA-class probability 0.773556
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11897600 116 + 20766785
GGGGGGGGGGUGUGGUUCGGUGCAGGAAAGAUCA---GGGGAGGUGGCUGGGGAGUGGCACAAUCGAGCAGCCGAGGUGUCAAGCGUUGCAAACACCUUGGUGACAUCGAACC-CUCCGC
((((((..(((((.(((((((((........(((---(.........))))......))))...))))).((((((((((...((...))..)))))))))).)))))...))-)))).. ( -45.24)
>DroSec_CAF1 38088 109 + 1
GGUGGGG------GUUUCGGUGCAGA-AAGAUCA---GGUGAGGUGGCAGGGGAGGGGCACAAUCGAGCAGCCGAGGUGUCAAGCGUUGCAAACACCUUGGUGACAUCGAACC-CUCCAC
.((((((------(.((((((((...-.......---(((...(((.(........).))).))).....((((((((((...((...))..))))))))))).))))))).)-)))))) ( -42.20)
>DroSim_CAF1 38492 115 + 1
GGGGAGG-GGGGUGGUUUGCUGCAGAAAAGAUCA---GGUGAGGUGGCAGGGGAGUGGCACAAUCGAGCAGCCGAGGUGUCAAGCGUUGCAAACACCUUGGUGACAUCGAACC-CUCCAC
..(((((-(.(.((.(((.((((........((.---...))....)))).))).)).)....((((...((((((((((...((...))..))))))))))....)))).))-)))).. ( -42.90)
>DroYak_CAF1 38639 114 + 1
CGGGAGGAGGUG-GGUU-C---CUGAAAAGAUUAAAGGGGGGGGUGGCG-GGGGGUGCCACAAUCGAGCAGCCGAGGUGUCAAGCGUUGCAAACACCUUGGUGACAUCGAACCCCUCGAC
((((((......-..))-)---)))...........((((((.((((((-.....))))))..((((...((((((((((...((...))..))))))))))....)))).))))))... ( -48.00)
>consensus
GGGGAGG_GGUG_GGUUCGGUGCAGAAAAGAUCA___GGGGAGGUGGCAGGGGAGUGGCACAAUCGAGCAGCCGAGGUGUCAAGCGUUGCAAACACCUUGGUGACAUCGAACC_CUCCAC
((((.((....................................(((.(........).)))..((((...((((((((((...((...))..))))))))))....)))).)).)))).. (-30.80 = -30.68 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,897,716 – 11,897,816
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.72
Mean single sequence MFE -21.47
Consensus MFE -16.28
Energy contribution -16.08
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -2.62
Structure conservation index 0.76
SVM decision value 1.72
SVM RNA-class probability 0.973818
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11897716 100 + 20766785
ACAAAGCGAUUCAUUGUUGCGAAAUUUAAUGCGAAAAAUUCAUUAAAAUA-AAA-AACAG------------------CAAACAAACUUUGAAUCCACCGGGAGCCCAAAUUGAAUCGCC
.....((((((((((((((.....(((((((.........)))))))...-...-..)))------------------)))......((((..(((....)))...)))).)))))))). ( -20.22)
>DroSec_CAF1 38197 99 + 1
ACAAAGCGAUUCAUUGUUGCGAAAUUUAAUGCGAAAAACUCAUUAAAAUA-AAA-AA-AG------------------CAAACAAACUUUGAAUCCACCGGGAACCCAAAUUGAAUCGCC
.....(((((((((((((((....(((((((.(.....).)))))))...-...-..-.)------------------).)))))..............((....))....)))))))). ( -20.22)
>DroSim_CAF1 38607 100 + 1
ACAAAGCGAUUCAUUGUUGCGAAAUUUAAUGCGAAAAACUCAUUAAAAUA-AAA-AACAG------------------CAAACAAACUUUGAAUCCACCGGGAGCCCAAAUUGAAUCGCC
.....((((((((((((((.....(((((((.(.....).)))))))...-...-..)))------------------)))......((((..(((....)))...)))).)))))))). ( -21.62)
>DroEre_CAF1 40151 119 + 1
ACAAAGCGAUUCAUUGUUGCGAAAUUUAAUGCGAAAAAUUCAUUAGAAUACAAAAAACAGCUCGGCAGGAGGAAUUGCCAAACAAACUUUGAAUCCACCGGGAGCCCAAAUUGAAU-GCC
.....((((((((..(((......(((((((.........)))))))................(((((......))))).....)))..))))))....((....)).........-)). ( -21.90)
>DroYak_CAF1 38753 119 + 1
ACAAAGCGAUUCAUUGUUGCGAAAUUUAAUGCGAAAAAUUCAUUAAAAUA-AAAAAACACCUCUGCAUGAAGAAUUGCCAAACAAACUUUGAAUCCACCGGGAGUCCAAAUUGAAUCGCC
.....(((((((((((((((((..(((((((.........)))))))...-..........(((......))).))))..)))))..((((..(((....)))...)))).)))))))). ( -23.40)
>consensus
ACAAAGCGAUUCAUUGUUGCGAAAUUUAAUGCGAAAAAUUCAUUAAAAUA_AAA_AACAG__________________CAAACAAACUUUGAAUCCACCGGGAGCCCAAAUUGAAUCGCC
.....((((((((...(((.(...(((((((.(.....).)))))))..............................................(((....)))..))))..)))))))). (-16.28 = -16.08 +  -0.20)

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 10:59:00 2006