Locus 775

Sequence ID 2R_DroMel_CAF1
Location 3,738,376 – 3,738,572
Length 196
Max. P 0.990590
window1352 window1353 window1354 window1355 window1356

overview

Window 2

Location 3,738,376 – 3,738,492
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.65
Mean single sequence MFE -38.43
Consensus MFE -34.22
Energy contribution -34.33
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -3.30
Structure conservation index 0.89
SVM decision value 1.58
SVM RNA-class probability 0.965657
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738376 116 + 20766785
UACACUUGUUACGCACAAGAAAUCCAAAUCGGCCCAAGAAACGCAGAUAGCUGGGUCCAUUCAGGACCU----AUUUUUGUUUUGGCUGUGAGAAACGCAGCCGAUUUGAAUUUGCCGAU
....(((((.....)))))........((((((.((((((..((.....))(((((((.....))))))----)))))))..(((((((((.....))))))))).........)))))) ( -39.20)
>DroSim_CAF1 1136 119 + 1
UACACUUGUUACCCACAAGAAAUCCAAAUCGGCCCAAGAAACGCAGAUAGCUGGGUCCAUUCAGGACCUACAUAUUUUUGU-UUGGCUGUGAGAAAAGCAGCCGAUUUGAAUUUGCCGAU
....(((((.....)))))........((((((.....(((((.(((((..(((((((.....)))))))..))))).)))-))((((((.......))))))...........)))))) ( -38.60)
>DroYak_CAF1 1129 115 + 1
UACACUUGUUACCCACAAGAAAUCCAAAUCGGCCCAAGAAACGCAGAUAGCUGGGUCCAUUCAGGACCU----AUUUCGGU-UUGGCUGUGAGAAAUGCAGCCGAUUUGAAUUUGCCGAU
....(((((.....)))))........((((((.........((.....))(((((((.....))))))----).(((((.-((((((((.......)))))))).)))))...)))))) ( -37.50)
>consensus
UACACUUGUUACCCACAAGAAAUCCAAAUCGGCCCAAGAAACGCAGAUAGCUGGGUCCAUUCAGGACCU____AUUUUUGU_UUGGCUGUGAGAAAAGCAGCCGAUUUGAAUUUGCCGAU
....(((((.....)))))........((((((.........(((((.....((((((.....)))))).......))))).((((((((.......)))))))).........)))))) (-34.22 = -34.33 +   0.11)

alignment

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secondary structure

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Window 3

Location 3,738,376 – 3,738,492
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.65
Mean single sequence MFE -36.53
Consensus MFE -34.73
Energy contribution -34.73
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.95
SVM decision value 1.43
SVM RNA-class probability 0.953382
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738376 116 - 20766785
AUCGGCAAAUUCAAAUCGGCUGCGUUUCUCACAGCCAAAACAAAAAU----AGGUCCUGAAUGGACCCAGCUAUCUGCGUUUCUUGGGCCGAUUUGGAUUUCUUGUGCGUAACAAGUGUA
....((((((((((((((((((.(.....).)).(((((((......----.(((((.....)))))..((.....)))))..))))))))))))))))).(((((.....)))))))). ( -36.30)
>DroSim_CAF1 1136 119 - 1
AUCGGCAAAUUCAAAUCGGCUGCUUUUCUCACAGCCAA-ACAAAAAUAUGUAGGUCCUGAAUGGACCCAGCUAUCUGCGUUUCUUGGGCCGAUUUGGAUUUCUUGUGGGUAACAAGUGUA
....((((((((((((((((((((........))).((-((...........(((((.....)))))..((.....))))))....)))))))))))))).(((((.....)))))))). ( -36.60)
>DroYak_CAF1 1129 115 - 1
AUCGGCAAAUUCAAAUCGGCUGCAUUUCUCACAGCCAA-ACCGAAAU----AGGUCCUGAAUGGACCCAGCUAUCUGCGUUUCUUGGGCCGAUUUGGAUUUCUUGUGGGUAACAAGUGUA
....(((((((((((((((((((..........))...-...(((((----.(((((.....)))))..((.....)))))))...)))))))))))))).(((((.....)))))))). ( -36.70)
>consensus
AUCGGCAAAUUCAAAUCGGCUGCAUUUCUCACAGCCAA_ACAAAAAU____AGGUCCUGAAUGGACCCAGCUAUCUGCGUUUCUUGGGCCGAUUUGGAUUUCUUGUGGGUAACAAGUGUA
....(((((((((((((((((((..........))(((.((...........(((((.....)))))..((.....))))...))))))))))))))))).(((((.....)))))))). (-34.73 = -34.73 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,738,416 – 3,738,532
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.21
Mean single sequence MFE -37.37
Consensus MFE -33.70
Energy contribution -33.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.90
SVM decision value 0.05
SVM RNA-class probability 0.560643
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738416 116 + 20766785
ACGCAGAUAGCUGGGUCCAUUCAGGACCU----AUUUUUGUUUUGGCUGUGAGAAACGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGC
..((((((...(((((((.....))))))----)...(((..(((((((((.....)))))))))..)))))))))...((((.(((.....(((((.......)))))..))))))).. ( -37.60)
>DroSim_CAF1 1176 119 + 1
ACGCAGAUAGCUGGGUCCAUUCAGGACCUACAUAUUUUUGU-UUGGCUGUGAGAAAAGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGC
(((.(((((..(((((((.....)))))))..))))).)))-...((((..(((((((.....((..((.(((..(((.(((....)))..)))))).))..))...)))))))..)))) ( -36.80)
>DroYak_CAF1 1169 115 + 1
ACGCAGAUAGCUGGGUCCAUUCAGGACCU----AUUUCGGU-UUGGCUGUGAGAAAUGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGC
..((((((...(((((((.....))))))----)..((((.-((((((((.......)))))))).))))))))))...((((.(((.....(((((.......)))))..))))))).. ( -37.70)
>consensus
ACGCAGAUAGCUGGGUCCAUUCAGGACCU____AUUUUUGU_UUGGCUGUGAGAAAAGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGC
..((((((....((((((.....)))))).............((((((((.......)))))))).....))))))...((((.(((.....(((((.......)))))..))))))).. (-33.70 = -33.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,738,452 – 3,738,572
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.61
Mean single sequence MFE -38.13
Consensus MFE -37.47
Energy contribution -37.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.98
SVM decision value 0.95
SVM RNA-class probability 0.888408
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738452 120 + 20766785
UUUUGGCUGUGAGAAACGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGCAGAAAAGGAUCACAGGGGCAUAUUCAAAAUGUGUGUGUGG
..(((((((((.....)))))))))(((((((.((((..(((....))).(((..(....)..)((((((((((......))))))))))....)))))).)))))))............ ( -39.50)
>DroSim_CAF1 1216 119 + 1
U-UUGGCUGUGAGAAAAGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGCAGAAAAGGAUCACAGGGGCAUAUUCAAAAUGUGUGUGUGG
.-((((((((.......))))))))(((((((.((((..(((....))).(((..(....)..)((((((((((......))))))))))....)))))).)))))))............ ( -37.50)
>DroYak_CAF1 1205 119 + 1
U-UUGGCUGUGAGAAAUGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGCAGAAAAGGAUCACAGGGGCAUAUUCAAAAUGUGUGUGUGG
.-((((((((.......))))))))(((((((.((((..(((....))).(((..(....)..)((((((((((......))))))))))....)))))).)))))))............ ( -37.40)
>consensus
U_UUGGCUGUGAGAAAAGCAGCCGAUUUGAAUUUGCCGAUGCACAGGUAGCCGGGAUACAUUUCAUCCUUUUCUUGCAGCAGAAAAGGAUCACAGGGGCAUAUUCAAAAUGUGUGUGUGG
..((((((((.......))))))))(((((((.((((..(((....))).(((..(....)..)((((((((((......))))))))))....)))))).)))))))............ (-37.47 = -37.47 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,738,452 – 3,738,572
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.61
Mean single sequence MFE -35.53
Consensus MFE -35.00
Energy contribution -35.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.71
Structure conservation index 0.98
SVM decision value 2.22
SVM RNA-class probability 0.990590
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3738452 120 - 20766785
CCACACACACAUUUUGAAUAUGCCCCUGUGAUCCUUUUCUGCUGCAAGAAAAGGAUGAAAUGUAUCCCGGCUACCUGUGCAUCGGCAAAUUCAAAUCGGCUGCGUUUCUCACAGCCAAAA
............(((((((.((((....(.((((((((((......)))))))))).).((((((...((...)).)))))).)))).)))))))..(((((.(.....).))))).... ( -36.60)
>DroSim_CAF1 1216 119 - 1
CCACACACACAUUUUGAAUAUGCCCCUGUGAUCCUUUUCUGCUGCAAGAAAAGGAUGAAAUGUAUCCCGGCUACCUGUGCAUCGGCAAAUUCAAAUCGGCUGCUUUUCUCACAGCCAA-A
............(((((((.((((....(.((((((((((......)))))))))).).((((((...((...)).)))))).)))).)))))))..(((((.........)))))..-. ( -35.00)
>DroYak_CAF1 1205 119 - 1
CCACACACACAUUUUGAAUAUGCCCCUGUGAUCCUUUUCUGCUGCAAGAAAAGGAUGAAAUGUAUCCCGGCUACCUGUGCAUCGGCAAAUUCAAAUCGGCUGCAUUUCUCACAGCCAA-A
............(((((((.((((....(.((((((((((......)))))))))).).((((((...((...)).)))))).)))).)))))))..(((((.........)))))..-. ( -35.00)
>consensus
CCACACACACAUUUUGAAUAUGCCCCUGUGAUCCUUUUCUGCUGCAAGAAAAGGAUGAAAUGUAUCCCGGCUACCUGUGCAUCGGCAAAUUCAAAUCGGCUGCAUUUCUCACAGCCAA_A
............(((((((.((((....(.((((((((((......)))))))))).).((((((...((...)).)))))).)))).)))))))..(((((.........))))).... (-35.00 = -35.00 +   0.00)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:59 2006