Locus 5743

Sequence ID 2R_DroMel_CAF1
Location 18,194,062 – 18,194,202
Length 140
Max. P 0.998915
window9196 window9197 window9198

overview

Window 6

Location 18,194,062 – 18,194,162
Length 100
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 82.54
Mean single sequence MFE -28.94
Consensus MFE -22.18
Energy contribution -22.22
Covariance contribution 0.04
Combinations/Pair 1.22
Mean z-score -3.18
Structure conservation index 0.77
SVM decision value 2.82
SVM RNA-class probability 0.997223
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18194062 100 + 20766785
----------UGCGUUUUACUAGUAUAC------AAAAGUCCCUUUUACAAAAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAAC-UUCAGGUCAUGUAAAAGGGACU-UUACCU
----------..................------.(((((((((((((((....(((((((.....)))))))...(((.((......-)))))....)))))))))))))-)).... ( -28.00)
>DroSec_CAF1 19353 106 + 1
----------UGAGUAUUAUUAGUCUACAUUUGCAAAAGUCCCUUUUACAAGAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAAC-UUCAGGUCGUGUAAAAGGGGCU-UUACCU
----------.((.((....)).))..........(((((((((((((((.((.((..(((((....(((.......)))...)))))-...)).)).)))))))))))))-)).... ( -30.10)
>DroSim_CAF1 19394 106 + 1
----------UGAGUAUUACUAGUCUACAUUUGCAAAAGUCCCUUUUACAAAAGCUUUGUUUUCUAAGCAUAGAAACUGCAACGAAAC-UUCAGGUCUUGUAAAAGGGACU-UUACCU
----------.........................((((((((((((((((.(.((..(((((....(((.......)))...)))))-...)).).))))))))))))))-)).... ( -27.80)
>DroEre_CAF1 19923 118 + 1
AUUAAGCUAUUGCGUUUUACUAGUACACAUUUGCAAGAGUCCCUUUUACAAAAGCUACGUUUUCUAAGCACAGAAACUGCAAUAAAAAUUUCAGGUUGUGUAAAGGGGGCUUUUACCU
.....((...((.((.........)).))...))(((((((((((((((....(((..........)))((((...(((.(((....))).))).))))))))))))))))))).... ( -29.80)
>DroYak_CAF1 20735 107 + 1
----------UAAGUUUUACUAGUAUGCAUUUGCAAAAGCCCCUUCUACAAAAGCUAUGUUUUCUCAGCAUGGAAACUGCAAUAAAAC-UUUAGGUGGUGCAAAGGGGGCUUUUACCU
----------................((....))(((((((((((...((..(.(((.(((((....(((.(....))))...)))))-..))).)..))...))))))))))).... ( -29.00)
>consensus
__________UGAGUUUUACUAGUAUACAUUUGCAAAAGUCCCUUUUACAAAAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAAC_UUCAGGUCGUGUAAAAGGGGCU_UUACCU
.....................................(((((((((((((....(((((((.....)))))))...(((............)))....)))))))))))))....... (-22.18 = -22.22 +   0.04)

alignment

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secondary structure

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Window 7

Location 18,194,062 – 18,194,162
Length 100
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 82.54
Mean single sequence MFE -29.70
Consensus MFE -25.62
Energy contribution -26.14
Covariance contribution 0.52
Combinations/Pair 1.24
Mean z-score -3.26
Structure conservation index 0.86
SVM decision value 3.28
SVM RNA-class probability 0.998915
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18194062 100 - 20766785
AGGUAA-AGUCCCUUUUACAUGACCUGAA-GUUUCGUUGCAGUUUCUAUGCUUAGAAAACAUAGCUUUUGUAAAAGGGACUUUU------GUAUACUAGUAAAACGCA----------
.(((((-(((((((((((((.((.(((..-.((((...(((.......)))...))))...))).)).))))))))))))))..------...))))...........---------- ( -29.70)
>DroSec_CAF1 19353 106 - 1
AGGUAA-AGCCCCUUUUACACGACCUGAA-GUUUCGUUGCAGUUUCUAUGCUUAGAAAACAUAGCUCUUGUAAAAGGGACUUUUGCAAAUGUAGACUAAUAAUACUCA----------
..((((-((.((((((((((.((.(((..-.((((...(((.......)))...))))...))).)).)))))))))).).)))))......................---------- ( -27.60)
>DroSim_CAF1 19394 106 - 1
AGGUAA-AGUCCCUUUUACAAGACCUGAA-GUUUCGUUGCAGUUUCUAUGCUUAGAAAACAAAGCUUUUGUAAAAGGGACUUUUGCAAAUGUAGACUAGUAAUACUCA----------
..((((-((((((((((((((((.((...-.((((...(((.......)))...))))....)).))))))))))))))).))))).......((.((....)).)).---------- ( -34.80)
>DroEre_CAF1 19923 118 - 1
AGGUAAAAGCCCCCUUUACACAACCUGAAAUUUUUAUUGCAGUUUCUGUGCUUAGAAAACGUAGCUUUUGUAAAAGGGACUCUUGCAAAUGUGUACUAGUAAAACGCAAUAGCUUAAU
..((((.((.(((.((((((.((.(((...((((((..((((...))))...))))))...))).)).)))))).))).)).))))...(((((.........))))).......... ( -23.80)
>DroYak_CAF1 20735 107 - 1
AGGUAAAAGCCCCCUUUGCACCACCUAAA-GUUUUAUUGCAGUUUCCAUGCUGAGAAAACAUAGCUUUUGUAGAAGGGGCUUUUGCAAAUGCAUACUAGUAAAACUUA----------
..(((((((((((.((((((....(((..-(((((....((((......))))..))))).)))....)))))).)))))))))))...(((......))).......---------- ( -32.60)
>consensus
AGGUAA_AGCCCCUUUUACACGACCUGAA_GUUUCGUUGCAGUUUCUAUGCUUAGAAAACAUAGCUUUUGUAAAAGGGACUUUUGCAAAUGUAUACUAGUAAAACUCA__________
..((((.(((((((((((((.((.(((....((((...(((.......)))...))))...))).)).))))))))))))).))))................................ (-25.62 = -26.14 +   0.52)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,194,086 – 18,194,202
Length 116
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 86.11
Mean single sequence MFE -24.62
Consensus MFE -19.22
Energy contribution -19.90
Covariance contribution 0.68
Combinations/Pair 1.14
Mean z-score -1.89
Structure conservation index 0.78
SVM decision value 0.72
SVM RNA-class probability 0.831628
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18194086 116 + 20766785
CCCUUUUACAAAAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAAC-UUCAGGUCAUGUAAAAGGGACU-UUACCUAACUUUGAAGGACCGAAUGUUCUCAAAUAAACUCAAAUAA
((((((((((....(((((((.....)))))))...(((.((......-)))))....))))))))))...-.........(((((.((((.....)))))))))............. ( -25.10)
>DroSec_CAF1 19383 108 + 1
CCCUUUUACAAGAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAAC-UUCAGGUCGUGUAAAAGGGGCU-UUACCUAACUUUGGAGGACCGAAUGUUCUCAAAUAAA--------A
((((((((((.((.((..(((((....(((.......)))...)))))-...)).)).))))))))))...-.............((((((.....)))))).......--------. ( -28.60)
>DroSim_CAF1 19424 108 + 1
CCCUUUUACAAAAGCUUUGUUUUCUAAGCAUAGAAACUGCAACGAAAC-UUCAGGUCUUGUAAAAGGGACU-UUACCUAACUUUGGAGGACCGAAUGUUCUCAAAUAAA--------A
(((((((((((.(.((..(((((....(((.......)))...)))))-...)).).)))))))))))...-.............((((((.....)))))).......--------. ( -26.30)
>DroEre_CAF1 19963 110 + 1
CCCUUUUACAAAAGCUACGUUUUCUAAGCACAGAAACUGCAAUAAAAAUUUCAGGUUGUGUAAAGGGGGCUUUUACCUAACCUUGAAGGACCGAAUCUUCUCAAAUAAA--------A
(((((((((....(((..........)))((((...(((.(((....))).))).)))))))))))))................(((((......))))).........--------. ( -21.10)
>DroYak_CAF1 20765 109 + 1
CCCUUCUACAAAAGCUAUGUUUUCUCAGCAUGGAAACUGCAAUAAAAC-UUUAGGUGGUGCAAAGGGGGCUUUUACCUAACCUUGGAGAACUGAGUGUUCACAAAUAAU--------A
.............(((..((((((.(((((.(....))))........-.((((((((.((.......))..))))))))...))))))))..))).............--------. ( -22.00)
>consensus
CCCUUUUACAAAAGCUAUGUUUUCUAAGCAUAGAAACUGCAACGAAAC_UUCAGGUCGUGUAAAAGGGGCU_UUACCUAACUUUGGAGGACCGAAUGUUCUCAAAUAAA________A
((((((((((....(((((((.....)))))))...(((............)))....))))))))))..............(((.(((((.....)))))))).............. (-19.22 = -19.90 +   0.68)

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 11:53:15 2006