Locus 7711

Sequence ID 3R_DroMel_CAF1
Location 20,712,295 – 20,712,460
Length 165
Max. P 0.976624
window12437 window12438 window12439

overview

Window 7

Location 20,712,295 – 20,712,391
Length 96
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 85.17
Mean single sequence MFE -20.59
Consensus MFE -14.03
Energy contribution -14.70
Covariance contribution 0.67
Combinations/Pair 1.14
Mean z-score -2.40
Structure conservation index 0.68
SVM decision value 0.49
SVM RNA-class probability 0.755883
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20712295 96 + 27905053
CUCCGAUAGUGGUACUUACCAUAUGCACUAAAAACUAUCUGCUAUCU-AACUAGCAUUCUAAGGUAUAUGCUUUAUAUGUAUCUUUCAUGAUAUAUU
....(((((((((....))).............))))))(((((...-...)))))...((((((....)))))).(((((((......))))))). ( -16.51)
>DroSec_CAF1 8765 96 + 1
CCCAGAUAGUGGUACUUACCAUAUGCACUAAAAACUAUCUGCAAACU-AACUAGGCUACUAAGGUGUUUACUCAUUAUAUAUCCUUCAGGAUAUAUU
.....(((((((((..((((...((((............))))....-...(((....))).))))..))).))))))((((((....))))))... ( -20.50)
>DroSim_CAF1 9638 97 + 1
CUGAGAUAGUGGUACUUACCAUAUGCACUAAAAACUAUCUGCUAACUUAGUUAGCCUUCUAAGGUGUAUGCUGAUUAUAUAUCCUUCGGGAUAUAUU
........(((((....)))))(((((((...........((((((...)))))).......))))))).......((((((((....)))))))). ( -24.77)
>consensus
CUCAGAUAGUGGUACUUACCAUAUGCACUAAAAACUAUCUGCUAACU_AACUAGCCUUCUAAGGUGUAUGCUCAUUAUAUAUCCUUCAGGAUAUAUU
..........((((..((((....(((............))).........(((....))).))))..))))....((((((((....)))))))). (-14.03 = -14.70 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,712,330 – 20,712,427
Length 97
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 76.84
Mean single sequence MFE -18.00
Consensus MFE -10.73
Energy contribution -9.97
Covariance contribution -0.77
Combinations/Pair 1.35
Mean z-score -2.42
Structure conservation index 0.60
SVM decision value 1.77
SVM RNA-class probability 0.976624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20712330 97 + 27905053
UAUCUGCUAUCU-AACUAGCAUUCUAAGGUAUAUGCUUUAUAUGUAUCUUUCAUGAUAUAUUCAGAUUCAGAUGUGAUUUCCUUCCAAAUAGAAUUCA
((((((..((((-....(((((..........)))))....(((((((......)))))))..)))).))))))(((.(((..........))).))) ( -16.50)
>DroSec_CAF1 8800 88 + 1
UAUCUGCAAACU-AACUAGGCUACUAAGGUGUUUACUCAUUAUAUAUCCUUCAGGAUAUAUUCCAAUUCAGAU-UGAUUUCCUUCUAAUU--------
.(((((.((((.-..((((....)).))..)))).......((((((((....)))))))).......)))))-................-------- ( -13.40)
>DroSim_CAF1 9673 90 + 1
UAUCUGCUAACUUAGUUAGCCUUCUAAGGUGUAUGCUGAUUAUAUAUCCUUCGGGAUAUAUUCCAAUUCAGGUAUGAUUUCCUUCUAAUU--------
.....((((((...)))))).....((((..((((((((..((((((((....))))))))......))).)))))....))))......-------- ( -24.10)
>consensus
UAUCUGCUAACU_AACUAGCCUUCUAAGGUGUAUGCUCAUUAUAUAUCCUUCAGGAUAUAUUCCAAUUCAGAU_UGAUUUCCUUCUAAUU________
((((((.....................((((((((.....)))))))).....(((.....)))....))))))........................ (-10.73 =  -9.97 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,712,351 – 20,712,460
Length 109
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 74.68
Mean single sequence MFE -17.47
Consensus MFE -8.15
Energy contribution -9.60
Covariance contribution 1.45
Combinations/Pair 1.17
Mean z-score -2.89
Structure conservation index 0.47
SVM decision value 0.73
SVM RNA-class probability 0.834336
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20712351 109 + 27905053
UCUAAGGUAUAUGCUUUAUAUGUAUCUUUCAUGAUAUAUUCAGAUUCAGAUGUGAUUUCCUUCCAAAUAGAAUUCAAUUCACAUUUUUCCAUCAUUCGUAAAUUCUCUC
..((((((....)))))).(((((((......)))))))...(((..((((((((.....(((......)))......))))))))....)))................ ( -15.10)
>DroSec_CAF1 8821 97 + 1
ACUAAGGUGUUUACUCAUUAUAUAUCCUUCAGGAUAUAUUCCAAUUCAGAU-UGAUUUCCUUCUAAUU-----------AAUCUAUGCCCAUCAUUCGUAACUUUUCUC
.....((((..........((((((((....))))))))........((((-(((((.......))))-----------))))).....))))................ ( -16.90)
>DroSim_CAF1 9695 98 + 1
UCUAAGGUGUAUGCUGAUUAUAUAUCCUUCGGGAUAUAUUCCAAUUCAGGUAUGAUUUCCUUCUAAUU-----------AAUCUAUGCCCAUCAUUCGUUACUACUCAC
.....((((.....(((..((((((((....))))))))......)))(((((((((...........-----------)))).)))))))))................ ( -20.40)
>consensus
UCUAAGGUGUAUGCUCAUUAUAUAUCCUUCAGGAUAUAUUCCAAUUCAGAU_UGAUUUCCUUCUAAUU___________AAUCUAUGCCCAUCAUUCGUAACUUCUCUC
.....((.(((((......((((((((....))))))))......(((....)))............................)))))))................... ( -8.15 =  -9.60 +   1.45)

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 12:52:44 2006