Locus 6642

Sequence ID 2L_DroMel_CAF1
Location 18,642,825 – 18,643,005
Length 180
Max. P 0.963205
window10591 window10592 window10593

overview

Window 1

Location 18,642,825 – 18,642,945
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.98
Mean single sequence MFE -31.74
Consensus MFE -23.03
Energy contribution -23.19
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.36
Structure conservation index 0.73
SVM decision value 0.76
SVM RNA-class probability 0.842526
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18642825 120 + 22407834
AAAGGAAACUCACGGAUGGCGAUUCCAUUAUGUAUGUAUGUACAUCCCAGAUUCCGUAUGCACUCAUUCCAAGUGACAAACUUGGCAAACUUGGGCAAUUUCCGCUCCACGGAAAUGUGC
..((....)).((((((((.((........(((((....))))))))))...)))))..((((....(((((((..((....))....)))))))..(((((((.....))))))))))) ( -31.00)
>DroSec_CAF1 115574 111 + 1
AAAGGAAACUCAUGGAUGGCGAUUCUAUUAUGUAUGUACGCACAUCCCAGAUUCCGUAUGCACUCAUUCCAAGUGACAAA---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGC
...((((.((...((((((((((.(......)...)).))).))))).)).))))....((((....(((((((.....)---------))))))..(((((((.....))))))))))) ( -34.30)
>DroSim_CAF1 117201 111 + 1
AAAGGAAACUCAUGGAUGGCGAUUCCAUUAUGUAUGUACGCACAUCCCAGAUUCCGUAUGCACUCAUUCCAAGUGACAAA---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGC
...((((.((...((((((((....(((.....)))..))).))))).)).))))....((((....(((((((.....)---------))))))..(((((((.....))))))))))) ( -35.10)
>DroEre_CAF1 114533 103 + 1
AAAGGAAACUCAUGGAUGGCGAUUCCAUUAUGU--------ACAUCCCCGAUUCCGUAUGUACUCAUUCCAAGUGACAAA---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGC
..((....)).(((((.......)))))...((--------((((...((....)).)))))).....((((((.....)---------)))))((((((((((.....))))))).))) ( -27.70)
>DroYak_CAF1 115967 103 + 1
AGAGGAAACUCAUAGAUGGCGAUUCCAUUAUGU--------ACAUCCCAGAUUCCGUAUGUACUCAUUCCAAGUGACAAA---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGC
.(((....)))...(((((.....)))))..((--------((((.(........).)))))).....((((((.....)---------)))))((((((((((.....))))))).))) ( -30.60)
>consensus
AAAGGAAACUCAUGGAUGGCGAUUCCAUUAUGUAUGUA_G_ACAUCCCAGAUUCCGUAUGCACUCAUUCCAAGUGACAAA_________CUUGGGCAAUUUCCGCUCCACGGAAAUGUGC
...((((.((...(((((........................))))).)).))))....((((....((((((................))))))..(((((((.....))))))))))) (-23.03 = -23.19 +   0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,642,905 – 18,643,005
Length 100
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -26.14
Consensus MFE -21.76
Energy contribution -21.80
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 0.83
SVM decision value 0.63
SVM RNA-class probability 0.804552
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18642905 100 + 22407834
CUUGGCAAACUUGGGCAAUUUCCGCUCCACGGAAAUGUGCACAAUUUAAUUUUGGCCUGCGGUGGCAGGGGUUUGCUCAUUUUUUCCCCC--------GUUUUUCUUU
...((((((((((.((((((((((.....))))))).))).))............(((((....))))))))))))).............--------.......... ( -28.60)
>DroSec_CAF1 115654 93 + 1
---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGCACAAUUUAAUUUUGGCCUGCGGUAGCAGGGGUUUGCUCACUUCCUCCCUGC------UUUUUUUUUUC
---------...((((.(((((((.....))))))).....(((.......))))))).....((((((((.............)))))))------).......... ( -24.42)
>DroSim_CAF1 117281 99 + 1
---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGCACAAUUUAAUUUUGGCCUGCGGUAGCAGGGGUUUGCUCACUUACCCCCUCCCCCCAGCUAUUUUUUUC
---------.(((.((((((((((.....))))))).))).)))........((((.((.((..(..(((((..(....)..)))))..)..))))))))........ ( -28.10)
>DroEre_CAF1 114605 84 + 1
---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGCACAAUUUAAUUUUGGCCUGCGGUGGCAGGGGUUUGCUCAUUUUU-CCCCG---------U-----UUU
---------..(((((((...((.((((((.(....(.((.(((.......))))))..).)))).)).)).))))))).....-.....---------.-----... ( -24.50)
>DroYak_CAF1 116039 85 + 1
---------CUUGGGCAAUUUCCGCUCCACGGAAAUGUGCACAAUUUAAUUUUGGACUGCGGUGGCAGGGGCUUGCUCAUUUUUGCCCCG---------U-----UUU
---------.(((.((((((((((.....))))))).))).)))..............((((.((((((((....)))....))))))))---------)-----... ( -25.10)
>consensus
_________CUUGGGCAAUUUCCGCUCCACGGAAAUGUGCACAAUUUAAUUUUGGCCUGCGGUGGCAGGGGUUUGCUCAUUUUUUCCCCG_________UUUUU_UUU
...........(((((((((((((.....)))))))..((.(((.......))).(((((....))))).)).))))))............................. (-21.76 = -21.80 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,642,905 – 18,643,005
Length 100
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 81.90
Mean single sequence MFE -26.38
Consensus MFE -19.88
Energy contribution -19.88
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.75
SVM decision value 1.55
SVM RNA-class probability 0.963205
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18642905 100 - 22407834
AAAGAAAAAC--------GGGGGAAAAAAUGAGCAAACCCCUGCCACCGCAGGCCAAAAUUAAAUUGUGCACAUUUCCGUGGAGCGGAAAUUGCCCAAGUUUGCCAAG
..........--------...........((.((((((.(((((....)))))...........(((.(((.(((((((.....)))))))))).))))))))))).. ( -28.30)
>DroSec_CAF1 115654 93 - 1
GAAAAAAAAAA------GCAGGGAGGAAGUGAGCAAACCCCUGCUACCGCAGGCCAAAAUUAAAUUGUGCACAUUUCCGUGGAGCGGAAAUUGCCCAAG---------
..........(------((((((.(............))))))))...................(((.(((.(((((((.....)))))))))).))).--------- ( -25.30)
>DroSim_CAF1 117281 99 - 1
GAAAAAAAUAGCUGGGGGGAGGGGGUAAGUGAGCAAACCCCUGCUACCGCAGGCCAAAAUUAAAUUGUGCACAUUUCCGUGGAGCGGAAAUUGCCCAAG---------
...........(((.((...((((((..(....)..))))))....)).)))............(((.(((.(((((((.....)))))))))).))).--------- ( -31.60)
>DroEre_CAF1 114605 84 - 1
AAA-----A---------CGGGG-AAAAAUGAGCAAACCCCUGCCACCGCAGGCCAAAAUUAAAUUGUGCACAUUUCCGUGGAGCGGAAAUUGCCCAAG---------
...-----.---------.((((-.............)))).(((......)))..........(((.(((.(((((((.....)))))))))).))).--------- ( -22.62)
>DroYak_CAF1 116039 85 - 1
AAA-----A---------CGGGGCAAAAAUGAGCAAGCCCCUGCCACCGCAGUCCAAAAUUAAAUUGUGCACAUUUCCGUGGAGCGGAAAUUGCCCAAG---------
...-----.---------.(((((............)))))(((....))).............(((.(((.(((((((.....)))))))))).))).--------- ( -24.10)
>consensus
AAA_AAAAA_________CGGGGAAAAAAUGAGCAAACCCCUGCCACCGCAGGCCAAAAUUAAAUUGUGCACAUUUCCGUGGAGCGGAAAUUGCCCAAG_________
....................(((..............)))((((....))))............(((.(((.(((((((.....)))))))))).))).......... (-19.88 = -19.88 +   0.00)

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 12:16:14 2006