Locus 333

Sequence ID 3R_DroMel_CAF1
Location 1,263,246 – 1,263,383
Length 137
Max. P 0.963843
window557 window558

overview

Window 7

Location 1,263,246 – 1,263,366
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.00
Mean single sequence MFE -47.97
Consensus MFE -40.74
Energy contribution -42.27
Covariance contribution 1.53
Combinations/Pair 1.06
Mean z-score -2.55
Structure conservation index 0.85
SVM decision value 1.56
SVM RNA-class probability 0.963843
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1263246 120 + 27905053
AGAACAAGUGCAUCUCGGCAUAGCGCAUCACUCUGGAGGGUGGUGCGGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCGUUUUUGGGGGCUACUGGGGUCGGCAAAACAAGCAUAC
.......((((.....(((....((((((((((....))))))))))..)))(((..((((.((((((((((..(((((...))))).))))))).))).))))))).......)))).. ( -56.00)
>DroVir_CAF1 19501 120 + 1
AAAAUAAGUGCAUUUCGGCAUAGCGUAUCACUCUGGAGGGUGGUGGAGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCAGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAU
.......((((.....(((.(..(.((((((((....)))))))))..))))(((..(((.((..(((((((..(((......)))..)))))))....)))))))).......)))).. ( -44.50)
>DroGri_CAF1 33744 120 + 1
AAAAUAAGUGCAUUUCGGCAUAGCGUAUCACUCUGGAGGGUGGUGCAGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCUGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAU
.......((((.....(((.....(((((((((....)))))))))...)))(((..(((.((..(((((((..(((......)))..)))))))....)))))))).......)))).. ( -46.80)
>DroSec_CAF1 40095 120 + 1
AGAACAAGUUCAUCUCGGCAUAGCGCAUCACUCUGGAGGGUGGUGCGGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCGUUUUUGGGGGCUACUGGGGUCGGCAAAACAAGCAUAC
.(((....))).....(((....((((((((((....))))))))))..)))(((..((((.((((((((((..(((((...))))).))))))).))).)))))))............. ( -52.40)
>DroWil_CAF1 26116 111 + 1
AAAAUAAGUGCAUUUCGGCAUAGCGCAUCACUCUGGAG---------GAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCAUUUUUGGGGGCUACUGGCGUUGGCAAAACAAGCAUAU
.......((((......((.((((((............---------.((((.....)))).((((((((((..(((......)))..))))))).))))))))))).......)))).. ( -38.12)
>DroMoj_CAF1 29261 120 + 1
AAAACAAGUGCAUUUCGGCAUAGCGUAUCACUCUGGAGGGUGGUGCAGAGCCCCCAUGGCUGCAGGGCCCCCUUAAAGCAGCAUUUUUGGGGGCUUCUGGCGUCGGCAAAACAAGCAUAU
.......((((......((...(((((((((((....))))))))).(((((((((..((((((((....)))....))))).....)))))))))...))....)).......)))).. ( -50.02)
>consensus
AAAACAAGUGCAUUUCGGCAUAGCGCAUCACUCUGGAGGGUGGUGCAGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAU
.......((((.....(((.....(((((((((....)))))))))...)))(((..(((..((((((((((..(((......)))..))))))).)))..)))))).......)))).. (-40.74 = -42.27 +   1.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,263,286 – 1,263,383
Length 97
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.38
Mean single sequence MFE -39.27
Consensus MFE -28.00
Energy contribution -28.03
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -2.05
Structure conservation index 0.71
SVM decision value 0.96
SVM RNA-class probability 0.889964
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1263286 97 + 27905053
UGGUGCGGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCGUUUUUGGGGGCUACUGGGGUCGGCAAAACAAGCAUACUACAGGUGAG-UCCAAAC---------------------
......(((..((((.(((((.((((((((((..(((((...))))).))))))).))).)))))((.......))........))))..-)))....--------------------- ( -38.70)
>DroVir_CAF1 19541 107 + 1
UGGUGGAGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCAGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAUUACAGGUAAG-UGUUAUCUUCA--------CAUAUA---
..((((((((((((....)).((..(((((((..(((......)))..)))))))....))...)))......(((((.(((....))))-)))).))))))--------).....--- ( -39.00)
>DroGri_CAF1 33784 110 + 1
UGGUGCAGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCUGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAUUACAAGUAUG-UAUUUACUGCA--------AACAUAUGU
...(((((.(((((....)).((..(((((((..(((......)))..)))))))....))...))).......((((((.....)))))-).....)))))--------......... ( -38.80)
>DroYak_CAF1 52694 117 + 1
UGGUGCGGAGCCGCCAUGGCUGCAGGGCCCCCUUAAGGCCGCGUUUUUGGGGGCUACUGGGGUCGGCAAAACAAGCAUACUACAGGUGAG-UCCAAAU-UUACCAUGGUUCACCUAUGU
..(((((....)(((..((((.((((((((((..(((((...))))).))))))).))).))))))).......)))).....(((((((-.(((...-......)))))))))).... ( -45.70)
>DroMoj_CAF1 29301 103 + 1
UGGUGCAGAGCCCCCAUGGCUGCAGGGCCCCCUUAAAGCAGCAUUUUUGGGGGCUUCUGGCGUCGGCAAAACAAGCAUAUUACAGGUAAACUGA-----UAA--------UACGUA---
.(..((((((((((((..((((((((....)))....))))).....))))))).))).))..)..........((.((((((((.....))).-----)))--------)).)).--- ( -40.20)
>DroAna_CAF1 39175 106 + 1
UGGUGCGGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAUUACAGGUAAG-CGUAAAA-U-----------UAUUUUUU
((.(((.(((((((....)).....(((((((..(((......)))..)))))))...))).)).)))...)).((.(((.....))).)-)......-.-----------........ ( -33.20)
>consensus
UGGUGCAGAGCCGCCAUGGCUGCAGGGCCCCCUUAAAGCCGCAUUUUUGGGGGCUACUGGCGUCGGCAAAACAAGCAUAUUACAGGUAAG_UGUAAAC_U_A_________ACAUA___
.(((.....)))(((..(((..((((((((((..(((......)))..))))))).)))..)))))).................................................... (-28.00 = -28.03 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:39 2006