Locus 1429

Sequence ID 2L_DroMel_CAF1
Location 3,809,238 – 3,809,496
Length 258
Max. P 0.967697
window2326 window2327 window2328 window2329

overview

Window 6

Location 3,809,238 – 3,809,348
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.61
Mean single sequence MFE -21.70
Consensus MFE -18.84
Energy contribution -18.88
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.28
Structure conservation index 0.87
SVM decision value 0.28
SVM RNA-class probability 0.667912
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3809238 110 + 22407834
GGGGGGGAGCCGGAAAA----------CGAAACUGUCGCAGCGACAGUUGAAAAGCAGUAAAAUUAUGUGUUUAAUGUACAACAUAAAAUAGCAAGCUAUUUUAUACACAAUAUUCAAUU
...((....)).(((..----------...((((((((...)))))))).................(((((............(((((((((....))))))))))))))...))).... ( -21.90)
>DroSec_CAF1 18513 109 + 1
-GGGGGGAGCCGGAAAA----------CGAAUCUGUCGCAGCGACAGUUGAAAAACAGUAAAAUUAUGUGUUUUAUGUACAACAUAAGAUAGCAAGCUAUUUUAUACACAAUAUUCAAUU
-..((....))......----------.....((((((...))))))(((((..(((.((((((.....))))))))).....(((((((((....)))))))))........))))).. ( -20.80)
>DroSim_CAF1 18513 109 + 1
-GGGGGGAGCCGGAAAA----------CGAAACUGUCGCAGCGACAGUUGAAAAACAGUAAAAUUAUGUGUUUAAUGUACAACAUAAAAUAGCAAGCUAUUUUAUACACAAUAUUCAAUU
-..((....)).(((..----------...((((((((...)))))))).................(((((............(((((((((....))))))))))))))...))).... ( -21.90)
>DroEre_CAF1 20006 108 + 1
-G--GGGAGCCGGAAAA---------UCGAAACUGUCGCAGCGACAGUUUAAAAGCAGUAAAAUUAUGUGUUUAAUGUACAACAUAAAAUAGCAAGCUAUUUUAUACACAAUAUUCAAUU
-(--(....)).(((..---------...(((((((((...)))))))))................(((((............(((((((((....))))))))))))))...))).... ( -22.90)
>DroYak_CAF1 20377 118 + 1
-G-AGGGAGCCGGAAAACGAAACGAAACGAAACUGUCGCAGCGACAGUUGAAAAUCAGUAAAAUUAUGUGUUUAAUGUACAACAUAAAAUAGCAAGCUAUUUUAUACACAAUAUUCAAUU
-.-...............(((..((.....((((((((...)))))))).....))..........(((((............(((((((((....))))))))))))))...))).... ( -21.00)
>consensus
_GGGGGGAGCCGGAAAA__________CGAAACUGUCGCAGCGACAGUUGAAAAACAGUAAAAUUAUGUGUUUAAUGUACAACAUAAAAUAGCAAGCUAUUUUAUACACAAUAUUCAAUU
............(((...............((((((((...)))))))).................(((((............(((((((((....))))))))))))))...))).... (-18.84 = -18.88 +   0.04)

alignment

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secondary structure

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Window 7

Location 3,809,238 – 3,809,348
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.61
Mean single sequence MFE -21.12
Consensus MFE -19.62
Energy contribution -20.02
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.93
SVM decision value 1.61
SVM RNA-class probability 0.967697
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3809238 110 - 22407834
AAUUGAAUAUUGUGUAUAAAAUAGCUUGCUAUUUUAUGUUGUACAUUAAACACAUAAUUUUACUGCUUUUCAACUGUCGCUGCGACAGUUUCG----------UUUUCCGGCUCCCCCCC
...((((.((((((((((((((((....)))))))))(((........))))))))))))))..((.....((((((((...)))))))).((----------.....))))........ ( -21.40)
>DroSec_CAF1 18513 109 - 1
AAUUGAAUAUUGUGUAUAAAAUAGCUUGCUAUCUUAUGUUGUACAUAAAACACAUAAUUUUACUGUUUUUCAACUGUCGCUGCGACAGAUUCG----------UUUUCCGGCUCCCCCC-
....((((.((((((((((.((((....))))......)))))))))).........................((((((...)))))))))).----------................- ( -18.30)
>DroSim_CAF1 18513 109 - 1
AAUUGAAUAUUGUGUAUAAAAUAGCUUGCUAUUUUAUGUUGUACAUUAAACACAUAAUUUUACUGUUUUUCAACUGUCGCUGCGACAGUUUCG----------UUUUCCGGCUCCCCCC-
...((((.((((((((((((((((....)))))))))(((........)))))))))))))).........((((((((...))))))))...----------................- ( -21.00)
>DroEre_CAF1 20006 108 - 1
AAUUGAAUAUUGUGUAUAAAAUAGCUUGCUAUUUUAUGUUGUACAUUAAACACAUAAUUUUACUGCUUUUAAACUGUCGCUGCGACAGUUUCGA---------UUUUCCGGCUCCC--C-
((((((..((((((((((((((((....)))))))))(((........)))))))))).............((((((((...))))))))))))---------))...........--.- ( -22.90)
>DroYak_CAF1 20377 118 - 1
AAUUGAAUAUUGUGUAUAAAAUAGCUUGCUAUUUUAUGUUGUACAUUAAACACAUAAUUUUACUGAUUUUCAACUGUCGCUGCGACAGUUUCGUUUCGUUUCGUUUUCCGGCUCCCU-C-
...((((.((((((((((((((((....)))))))))(((........))))))))))))))..((.....((((((((...)))))))).....))....................-.- ( -22.00)
>consensus
AAUUGAAUAUUGUGUAUAAAAUAGCUUGCUAUUUUAUGUUGUACAUUAAACACAUAAUUUUACUGCUUUUCAACUGUCGCUGCGACAGUUUCG__________UUUUCCGGCUCCCCCC_
...((((.((((((((((((((((....)))))))))(((........)))))))))))))).........((((((((...)))))))).............................. (-19.62 = -20.02 +   0.40)

alignment

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secondary structure

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Window 8

Location 3,809,348 – 3,809,460
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -28.56
Consensus MFE -22.12
Energy contribution -22.72
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.77
SVM decision value 0.45
SVM RNA-class probability 0.741814
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3809348 112 - 22407834
GUUGUCCACCAAGCAAUCAUCAAUCAU-AUUGUUUAAACUAAAGAGCUUUAAUCGUAUG----CAUGAGUGUUGAUGGCAGCUUUUUGGUUU---AAAUCGUUUCUCUUAGAUGUGGAUA
..(((((((..................-...(((((((((((((((((...((((.(((----(....))))))))...)))))))))))))---))))....((.....)).))))))) ( -29.40)
>DroSec_CAF1 18622 112 - 1
GUUGUCCACCAAGCAAUCAUCAAUCAU-AUUGGUAAAACUAAAGAGCUUUAAUCGUAUG----CAUGAGUGUUGAUGGCACCUUUUUGGUUU---AAAUCGUUUCUCUUAGAUGUGGAUA
..(((((((.........((((((...-)))))).(((((((((((.....((((.(((----(....)))))))).....)))))))))))---..................))))))) ( -22.80)
>DroSim_CAF1 18622 112 - 1
GUUGUCCACCAAGCAAUCAUCAAUCAU-AUUGGUAAAACUAAAGAGCUUUAAUCGUAUG----CAUGAGUGUUGAUGGCAGCUUUUUGGUUU---AAAUCGUUUCUCUUAGAUGUGGAUA
..(((((((.........((((((...-)))))).(((((((((((((...((((.(((----(....))))))))...)))))))))))))---..................))))))) ( -28.10)
>DroEre_CAF1 20114 116 - 1
GUUGUCCACCAAGCAAUCAUCAAUCAA-AUUGGUGAAACUAAAGAGCUUUAAUCGUAUGCAUGCAUGAGUGUUGAUGGCAGCUUUUUGGUUU---UAAUCGUUUCUCUUAAAUGUGGAUA
..(((((((.......((((((((...-))))))))((((((((((((...((((...((((......))))))))...)))))))))))).---..................))))))) ( -31.40)
>DroYak_CAF1 20495 116 - 1
GCUGUCCACCAAGCAAUCAACAAUCAAUAUUGGUGAAACUAAAGAGCUUUAAUCGUAUG----CAUGAGUGUUGAUGGCAGCUUUUUGGUUUCGUUAAUCGUUUCUCUUAAAUGUGGAUA
..(((((((...................(((..(((((((((((((((...((((.(((----(....))))))))...)))))))))))))))..))).((((.....))))))))))) ( -31.10)
>consensus
GUUGUCCACCAAGCAAUCAUCAAUCAU_AUUGGUAAAACUAAAGAGCUUUAAUCGUAUG____CAUGAGUGUUGAUGGCAGCUUUUUGGUUU___AAAUCGUUUCUCUUAGAUGUGGAUA
..(((((((.........((((((....)))))).(((((((((((((...((((((((....)))).....))))...))))))))))))).....................))))))) (-22.12 = -22.72 +   0.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,809,385 – 3,809,496
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.24
Mean single sequence MFE -23.65
Consensus MFE -21.05
Energy contribution -21.45
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.89
SVM decision value 0.67
SVM RNA-class probability 0.819031
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3809385 111 + 22407834
UGCCAUCAACACUCAUG----CAUACGAUUAAAGCUCUUUAGUUUAAACAAU-AUGAUUGAUGAUUGCUUGGUGGACAACUAGUAAGCGCAACAACUAAAC---AAUUGGCAAAUGUU-U
((((((((.((.(((((----.....(((((((....))))))).......)-)))).)).)))..(((((.(((....))).))))).............---...)))))......-. ( -22.70)
>DroSec_CAF1 18659 111 + 1
UGCCAUCAACACUCAUG----CAUACGAUUAAAGCUCUUUAGUUUUACCAAU-AUGAUUGAUGAUUGCUUGGUGGACAACUAGUAAGCGCAACAACUAAAC---AAUUGGCAAAUGUU-U
((((((((.((.(((((----..((.(((((((....))))))).))....)-)))).)).)))..(((((.(((....))).))))).............---...)))))......-. ( -23.00)
>DroSim_CAF1 18659 111 + 1
UGCCAUCAACACUCAUG----CAUACGAUUAAAGCUCUUUAGUUUUACCAAU-AUGAUUGAUGAUUGCUUGGUGGACAACUAGUAAGCGCAACAACUAAAC---AAUUGGCAAAUGUU-U
((((((((.((.(((((----..((.(((((((....))))))).))....)-)))).)).)))..(((((.(((....))).))))).............---...)))))......-. ( -23.00)
>DroEre_CAF1 20151 116 + 1
UGCCAUCAACACUCAUGCAUGCAUACGAUUAAAGCUCUUUAGUUUCACCAAU-UUGAUUGAUGAUUGCUUGGUGGACAACUAGUAAGCGCAACAACUAAAC---AAUUGGCAAAUGUUUU
(((((.........(((....))).........(((..(((((((((((((.-..((((...))))..))))))))..)))))..))).............---...)))))........ ( -23.20)
>DroYak_CAF1 20535 115 + 1
UGCCAUCAACACUCAUG----CAUACGAUUAAAGCUCUUUAGUUUCACCAAUAUUGAUUGUUGAUUGCUUGGUGGACAGCUAUUAAGCGCAACAACUAAACAACAAUUGGCAAAUGUU-U
(((((((((((.(((..----.....(((((((....)))))))..........))).))))))..(((((((((....)))))))))...................)))))......-. ( -26.33)
>consensus
UGCCAUCAACACUCAUG____CAUACGAUUAAAGCUCUUUAGUUUCACCAAU_AUGAUUGAUGAUUGCUUGGUGGACAACUAGUAAGCGCAACAACUAAAC___AAUUGGCAAAUGUU_U
((((((((.((.((((..........(((((((....))))))).........)))).)).)))..(((((.(((....))).)))))...................)))))........ (-21.05 = -21.45 +   0.40)

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 10:02:26 2006