Locus 3955

Sequence ID 2R_DroMel_CAF1
Location 13,048,926 – 13,049,055
Length 129
Max. P 0.996237
window6385 window6386 window6387 window6388

overview

Window 5

Location 13,048,926 – 13,049,026
Length 100
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 91.10
Mean single sequence MFE -31.42
Consensus MFE -26.20
Energy contribution -26.84
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.50
Structure conservation index 0.83
SVM decision value 2.67
SVM RNA-class probability 0.996237
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13048926 100 + 20766785
GAGAAUGGGCAGCGAUAUCUGCGGCUAAAUAUAACAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCGCUUGAGUCAGCGCUUGGAUGU--------------
.......(((.(((.....))).))).......(((..((((((((((......(((((((((.........))).))))))..))))))))))...)))-------------- ( -33.10)
>DroSec_CAF1 19348 100 + 1
GAGAAUGGGCAGCGAUAUCUGCGGCUAAAUAUAACAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCCCUUGAGUCAGCGCCUCGAUGU--------------
(((....(((.(((.....))).)))..............((((((((.((((..((((..(.......)..))))..))))..))))))))))).....-------------- ( -29.80)
>DroSim_CAF1 19063 100 + 1
GAGAAUGGGCAGCGAUAUCUUCGGCUAAAUAUAACAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCCCCGCUUGAGUCAGCGCCUCGAUGU--------------
(((....(((..(((.....))))))..............((((((((......(((((((((.........)).)))))))..))))))))))).....-------------- ( -30.40)
>DroEre_CAF1 21061 100 + 1
GAGAAUGGGAAGCGAUAUCUGCGGCUAAAUAUAACAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCGCUUGAGUCAGCGACUCGAUGU--------------
.......((..(((.....)))..)).......(((..((((((((((......(((((((((.........))).))))))..)))))).))))..)))-------------- ( -29.90)
>DroYak_CAF1 21693 114 + 1
GAGAAUGGGCAGCGAUAUCUGCGGCUAAAUAUAACAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGUGAGUGCUCCGCUUAAGUCAGCGACUCGAUGUUUAAAUGUUUGAAU
.......(((.(((.....))).)))((((((((((..((((((((((......(((((((((.........))).))))))..)))))).))))..))))...)))))).... ( -33.90)
>consensus
GAGAAUGGGCAGCGAUAUCUGCGGCUAAAUAUAACAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCGCUUGAGUCAGCGCCUCGAUGU______________
.......(((.(((.....))).))).......(((..((((((((((......(((((((((.........))).))))))..))))))).)))..))).............. (-26.20 = -26.84 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,048,926 – 13,049,026
Length 100
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 91.10
Mean single sequence MFE -26.15
Consensus MFE -18.52
Energy contribution -19.52
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.03
Structure conservation index 0.71
SVM decision value 0.91
SVM RNA-class probability 0.879631
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13048926 100 - 20766785
--------------ACAUCCAAGCGCUGACUCAAGCGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUGUUAUAUUUAGCCGCAGAUAUCGCUGCCCAUUCUC
--------------.......((.(((((...((((((.(((.........))))))))).......))))).))....((((....)))).((((......))))........ ( -22.70)
>DroSec_CAF1 19348 100 - 1
--------------ACAUCGAGGCGCUGACUCAAGGGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUGUUAUAUUUAGCCGCAGAUAUCGCUGCCCAUUCUC
--------------(((..(((..(((((...((((..(((...............)))..))))..))))).)))..)))...........((((......))))........ ( -27.56)
>DroSim_CAF1 19063 100 - 1
--------------ACAUCGAGGCGCUGACUCAAGCGGGGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUGUUAUAUUUAGCCGAAGAUAUCGCUGCCCAUUCUC
--------------.....(.((((((((...(((((((.((.........))))))))).......)))))..(((((((((....))).)))))).......))))...... ( -26.70)
>DroEre_CAF1 21061 100 - 1
--------------ACAUCGAGUCGCUGACUCAAGCGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUGUUAUAUUUAGCCGCAGAUAUCGCUUCCCAUUCUC
--------------.....((((.(((((...((((((.(((.........))))))))).......)))))))))...((.((((((......)))))).))........... ( -23.80)
>DroYak_CAF1 21693 114 - 1
AUUCAAACAUUUAAACAUCGAGUCGCUGACUUAAGCGGAGCACUCACUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUGUUAUAUUUAGCCGCAGAUAUCGCUGCCCAUUCUC
.............((((..((((.(((((...((((((.(((.........))))))))).......)))))))))..))))..........((((......))))........ ( -30.00)
>consensus
______________ACAUCGAGGCGCUGACUCAAGCGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUGUUAUAUUUAGCCGCAGAUAUCGCUGCCCAUUCUC
..............(((..(((..(((((...((((((.(((.........))))))))).......))))).)))..)))...........((((......))))........ (-18.52 = -19.52 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,048,960 – 13,049,055
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.33
Mean single sequence MFE -29.92
Consensus MFE -21.76
Energy contribution -22.00
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.73
SVM decision value 0.67
SVM RNA-class probability 0.818455
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13048960 95 + 20766785
CAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCGCUUGAGUCAGCGCUUGGAUGU----------------UUGAA--------UGUUUGAAUG-GGUUUAGCCAUAGG
....((((((((((......(((((((((.........))).))))))..))))))))))..(((.----------------(((((--------(.(......)-.)))))).)))... ( -30.40)
>DroSec_CAF1 19382 103 + 1
CAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCCCUUGAGUCAGCGCCUCGAUGU----------------UUGAAUGUUUGAAUGUUUGAAUG-GGUUUAGCCAUGGG
....((((((((((.((((..((((..(.......)..))))..))))..))))))).)))...((----------------(..(((((....)))))..))).-((.....))..... ( -28.30)
>DroSim_CAF1 19097 95 + 1
CAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCCCCGCUUGAGUCAGCGCCUCGAUGU----------------UUGGA--------UGUUUGAAUG-GGUUUAGCCAUGGG
...((.((((((((......(((((((((.........)).)))))))..))))))))))(.(((.----------------(((((--------(.(......)-.)))))).))).). ( -29.40)
>DroEre_CAF1 21095 95 + 1
CAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCGCUUGAGUCAGCGACUCGAUGU----------------UUGGA--------UGUUUGAAUG-GGUUUAGCAGUGGG
....((((((((((......(((((((((.........))).))))))..)))))).))))..(((----------------(.(((--------(.(......)-.))))))))..... ( -27.80)
>DroYak_CAF1 21727 112 + 1
CAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGUGAGUGCUCCGCUUAAGUCAGCGACUCGAUGUUUAAAUGUUUGAAUGUUUGGA--------UGUUUGAAUGGGGCUUAGCAAUGGG
....((((((((((......(((((((((.........))).))))))..)))))).))))...(((((((((((..(....)..))--------)))))))))....((((....)))) ( -33.70)
>consensus
CAAAGAGUGCUGAUGAAGGAAAGCGGGCAAGAAGAGAGUGCUCCGCUUGAGUCAGCGCCUCGAUGU________________UUGGA________UGUUUGAAUG_GGUUUAGCCAUGGG
....((((((((((......(((((((((.........))).))))))..))))))).)))........................................................... (-21.76 = -22.00 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,048,960 – 13,049,055
Length 95
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.33
Mean single sequence MFE -21.69
Consensus MFE -15.78
Energy contribution -15.98
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.11
Structure conservation index 0.73
SVM decision value 2.16
SVM RNA-class probability 0.989259
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13048960 95 - 20766785
CCUAUGGCUAAACC-CAUUCAAACA--------UUCAA----------------ACAUCCAAGCGCUGACUCAAGCGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUG
...((((......)-))).......--------.....----------------.......((.(((((...((((((.(((.........))))))))).......))))).))..... ( -19.00)
>DroSec_CAF1 19382 103 - 1
CCCAUGGCUAAACC-CAUUCAAACAUUCAAACAUUCAA----------------ACAUCGAGGCGCUGACUCAAGGGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUG
...((((......)-)))....................----------------.((..(((..(((((...((((..(((...............)))..))))..))))).)))..)) ( -23.36)
>DroSim_CAF1 19097 95 - 1
CCCAUGGCUAAACC-CAUUCAAACA--------UCCAA----------------ACAUCGAGGCGCUGACUCAAGCGGGGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUG
...((((......)-))).......--------.....----------------.((..(((..(((((...(((((((.((.........))))))))).......))))).)))..)) ( -22.20)
>DroEre_CAF1 21095 95 - 1
CCCACUGCUAAACC-CAUUCAAACA--------UCCAA----------------ACAUCGAGUCGCUGACUCAAGCGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUG
..............-..........--------.....----------------.((..((((.(((((...((((((.(((.........))))))))).......)))))))))..)) ( -21.60)
>DroYak_CAF1 21727 112 - 1
CCCAUUGCUAAGCCCCAUUCAAACA--------UCCAAACAUUCAAACAUUUAAACAUCGAGUCGCUGACUUAAGCGGAGCACUCACUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUG
.........................--------......................((..((((.(((((...((((((.(((.........))))))))).......)))))))))..)) ( -22.30)
>consensus
CCCAUGGCUAAACC_CAUUCAAACA________UCCAA________________ACAUCGAGGCGCUGACUCAAGCGGAGCACUCUCUUCUUGCCCGCUUUCCUUCAUCAGCACUCUUUG
................................................................(((((...((((((.(((.........))))))))).......)))))........ (-15.78 = -15.98 +   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 11:08:15 2006