Locus 2640

Sequence ID 2L_DroMel_CAF1
Location 7,374,308 – 7,374,442
Length 134
Max. P 0.920817
window4201 window4202 window4203 window4204

overview

Window 1

Location 7,374,308 – 7,374,402
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 83.31
Mean single sequence MFE -28.22
Consensus MFE -20.55
Energy contribution -20.14
Covariance contribution -0.42
Combinations/Pair 1.10
Mean z-score -3.00
Structure conservation index 0.73
SVM decision value 0.88
SVM RNA-class probability 0.872929
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7374308 94 + 22407834
CACGGCCAUGUCGACCGUGAUUAACGUCAGCAUUUUUGACAGCCAUUUGACAGCUG------UCAGCGCUGCAUAAGGCAUUUCAAAUAAUGCACUUGAA
(((((.(.....).)))))......(.((((....((((((((.........))))------)))).))))).(((((((((......))))).)))).. ( -28.30)
>DroPse_CAF1 194227 94 + 1
CAUGGCCAUGUCGGCCAUGAUUAACGUCAAC-UUUUUGACAGCCAUUUGACAGCUGCUGUUGCUAUUGCUGCAUAAGGCAUUUAAAAUAUCAUAU-----
(((((((.....)))))))......(((((.-...))))).(((...((.((((.((....))....))))))...)))................----- ( -30.30)
>DroEre_CAF1 163514 94 + 1
CACGGCCAUGUCGACCGUGAUUAACGUCAGCUUUUUUGACAGCCAUUUGACAGCUG------UCAGCGCUGCAUAAGGCAUUUCAAAAAAUGCACUUGAA
(((((.(.....).)))))......(.((((....((((((((.........))))------)))).))))).((((((((((....)))))).)))).. ( -28.40)
>DroYak_CAF1 167108 94 + 1
CACGGCCAUGUCGACCGUGAUUAACGUCAGCUUUUUUGACAGCCAUUUGACAGCUG------UCAGCGCUGCAUAAGGCAUUUCAAAAAAUGCACUUGAA
(((((.(.....).)))))......(.((((....((((((((.........))))------)))).))))).((((((((((....)))))).)))).. ( -28.40)
>DroAna_CAF1 171294 93 + 1
CACGGCCAUGUCGGCCAUGAUUAACGUCAACAUUUUUGACAGCCAUUUGACAGCUG------CCACCGCUGCAUAAGGCAUUUCCACAAAUACACUUUG-
((.((((.....)))).))......(((((.....))))).(((...((.((((..------.....))))))...)))....................- ( -23.60)
>DroPer_CAF1 196387 94 + 1
CAUGGCCAUGUCGGCCAUGAUUAACGUCAAC-UUUUUGACAGCCAUUUGACAGCUGCUGUUGCUAUUGCUGCAUAAGGCAUUUCAAAUAUCAUAU-----
(((((((.....)))))))......(((((.-...))))).(((...((.((((.((....))....))))))...)))................----- ( -30.30)
>consensus
CACGGCCAUGUCGACCAUGAUUAACGUCAAC_UUUUUGACAGCCAUUUGACAGCUG______CCAGCGCUGCAUAAGGCAUUUCAAAAAAUACACUUGA_
(((((.(.....).)))))......(((((.....))))).(((...((.((((.............))))))...)))..................... (-20.55 = -20.14 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,374,308 – 7,374,402
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 83.31
Mean single sequence MFE -30.88
Consensus MFE -24.19
Energy contribution -23.47
Covariance contribution -0.72
Combinations/Pair 1.15
Mean z-score -2.99
Structure conservation index 0.78
SVM decision value 1.14
SVM RNA-class probability 0.920817
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7374308 94 - 22407834
UUCAAGUGCAUUAUUUGAAAUGCCUUAUGCAGCGCUGA------CAGCUGUCAAAUGGCUGUCAAAAAUGCUGACGUUAAUCACGGUCGACAUGGCCGUG
...(((.(((((......))))))))((((((((.(((------(((((((...))))))))))....))))).)))....(((((((.....))))))) ( -33.00)
>DroPse_CAF1 194227 94 - 1
-----AUAUGAUAUUUUAAAUGCCUUAUGCAGCAAUAGCAACAGCAGCUGUCAAAUGGCUGUCAAAAA-GUUGACGUUAAUCAUGGCCGACAUGGCCAUG
-----...((((.........(((...((((((....((....)).)))).))...))).(((((...-.)))))))))..(((((((.....))))))) ( -26.30)
>DroEre_CAF1 163514 94 - 1
UUCAAGUGCAUUUUUUGAAAUGCCUUAUGCAGCGCUGA------CAGCUGUCAAAUGGCUGUCAAAAAAGCUGACGUUAAUCACGGUCGACAUGGCCGUG
...(((.((((((....)))))))))(((((((..(((------(((((((...)))))))))).....)))).)))....(((((((.....))))))) ( -33.70)
>DroYak_CAF1 167108 94 - 1
UUCAAGUGCAUUUUUUGAAAUGCCUUAUGCAGCGCUGA------CAGCUGUCAAAUGGCUGUCAAAAAAGCUGACGUUAAUCACGGUCGACAUGGCCGUG
...(((.((((((....)))))))))(((((((..(((------(((((((...)))))))))).....)))).)))....(((((((.....))))))) ( -33.70)
>DroAna_CAF1 171294 93 - 1
-CAAAGUGUAUUUGUGGAAAUGCCUUAUGCAGCGGUGG------CAGCUGUCAAAUGGCUGUCAAAAAUGUUGACGUUAAUCAUGGCCGACAUGGCCGUG
-..(((.((((((....)))))))))((((((((.(((------(((((((...))))))))))....))))).)))....(((((((.....))))))) ( -32.00)
>DroPer_CAF1 196387 94 - 1
-----AUAUGAUAUUUGAAAUGCCUUAUGCAGCAAUAGCAACAGCAGCUGUCAAAUGGCUGUCAAAAA-GUUGACGUUAAUCAUGGCCGACAUGGCCAUG
-----........(((((...(((...((((((....((....)).)))).))...)))..)))))..-............(((((((.....))))))) ( -26.60)
>consensus
_UCAAGUGCAUUAUUUGAAAUGCCUUAUGCAGCGCUGA______CAGCUGUCAAAUGGCUGUCAAAAA_GCUGACGUUAAUCACGGCCGACAUGGCCGUG
.....................(((...((((((.............)))).))...))).((((.......))))......(((((((.....))))))) (-24.19 = -23.47 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,374,328 – 7,374,442
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 84.61
Mean single sequence MFE -26.35
Consensus MFE -18.81
Energy contribution -20.43
Covariance contribution 1.63
Combinations/Pair 1.07
Mean z-score -2.29
Structure conservation index 0.71
SVM decision value 0.11
SVM RNA-class probability 0.586791
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7374328 114 + 22407834
UUAACGUCAGCAUUUUUGACAGCCAUUUGACAGCUGUCAGCGCUGCAUAAGGCAUUUCAAAUAAUGCACUUGAACAAUUUUCAAGAGGUUUCCCUAUCAAAUAUUUAUGAAAAU
.......((((....((((((((.........)))))))).))))(((((((((((......))))).((((((.....))))))(((....)))........))))))..... ( -27.10)
>DroSec_CAF1 159824 114 + 1
UUAACGUCAGCAUUUUUGACAGCCAUUUGACAGCUGUCAGCGCUGCAUAAGGCAUUUCAAAUAAUGCACUUGAACAAUUUUCAAGGGGGUUCUAUAACAAAUAUUUAUGAUAAU
..(((.((.((((((((((..(((...((.((((.......))))))...)))...))))).))))).((((((.....)))))))).)))....................... ( -26.60)
>DroSim_CAF1 166903 113 + 1
UUAACGUCAGCAUUUUUGACAGCCAUUUGACAGCUGUCAGCGCUGCAUAAGGCAUUUCAAAUAAUGCACUUGAACAAUUUUCAAGGGGGUUCUUUAUCAAAUAUUUAUGAUAA-
..(((.((.((((((((((..(((...((.((((.......))))))...)))...))))).))))).((((((.....)))))))).)))..((((((........))))))- ( -28.80)
>DroEre_CAF1 163534 110 + 1
UUAACGUCAGCUUUUUUGACAGCCAUUUGACAGCUGUCAGCGCUGCAUAAGGCAUUUCAAAAAAUGCACUUGAACAAUUUUCAGGGGU-UUCCUUACCAAAUAUUUAUGAU---
.......((((....((((((((.........)))))))).))))((((((((((((....)))))).((((((.....))))))(((-......))).....))))))..--- ( -28.30)
>DroYak_CAF1 167128 114 + 1
UUAACGUCAGCUUUUUUGACAGCCAUUUGACAGCUGUCAGCGCUGCAUAAGGCAUUUCAAAAAAUGCACUUGAACAUUUUUCAAGGCUCUUCCUGAUCGAAUAUUUAUGAUAAU
....((((((.((((((((..(((...((.((((.......))))))...)))...)))))))).((.((((((.....)))))))).....)))).))............... ( -27.90)
>DroAna_CAF1 171314 97 + 1
UUAACGUCAACAUUUUUGACAGCCAUUUGACAGCUGCCACCGCUGCAUAAGGCAUUUCCACAAAUACACUUUG------------GGGUUUG-----CAAUUUUUCGUAAUAAU
.....(((((.....))))).(((...((.((((.......))))))...)))...(((.((((.....))))------------))).(((-----(........)))).... ( -19.40)
>consensus
UUAACGUCAGCAUUUUUGACAGCCAUUUGACAGCUGUCAGCGCUGCAUAAGGCAUUUCAAAAAAUGCACUUGAACAAUUUUCAAGGGGGUUCCUUAUCAAAUAUUUAUGAUAAU
.......((((....((((((((.........)))))))).))))(((((((((((......))))).((((((.....))))))..................))))))..... (-18.81 = -20.43 +   1.63)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,374,328 – 7,374,442
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 84.61
Mean single sequence MFE -28.22
Consensus MFE -22.38
Energy contribution -22.30
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.40
Structure conservation index 0.79
SVM decision value 0.67
SVM RNA-class probability 0.817660
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7374328 114 - 22407834
AUUUUCAUAAAUAUUUGAUAGGGAAACCUCUUGAAAAUUGUUCAAGUGCAUUAUUUGAAAUGCCUUAUGCAGCGCUGACAGCUGUCAAAUGGCUGUCAAAAAUGCUGACGUUAA
.........(((.((..(.(((....))).)..)).)))....(((.(((((......))))))))((((((((.((((((((((...))))))))))....))))).)))... ( -31.50)
>DroSec_CAF1 159824 114 - 1
AUUAUCAUAAAUAUUUGUUAUAGAACCCCCUUGAAAAUUGUUCAAGUGCAUUAUUUGAAAUGCCUUAUGCAGCGCUGACAGCUGUCAAAUGGCUGUCAAAAAUGCUGACGUUAA
................((((.........((((((.....)))))).(((((.(((((...(((...((((((.......)))).))...)))..))))))))))))))..... ( -27.00)
>DroSim_CAF1 166903 113 - 1
-UUAUCAUAAAUAUUUGAUAAAGAACCCCCUUGAAAAUUGUUCAAGUGCAUUAUUUGAAAUGCCUUAUGCAGCGCUGACAGCUGUCAAAUGGCUGUCAAAAAUGCUGACGUUAA
-((((((........))))))..(((...((((((.....)))))).(((((.(((((...(((...((((((.......)))).))...)))..))))))))))....))).. ( -29.00)
>DroEre_CAF1 163534 110 - 1
---AUCAUAAAUAUUUGGUAAGGAA-ACCCCUGAAAAUUGUUCAAGUGCAUUUUUUGAAAUGCCUUAUGCAGCGCUGACAGCUGUCAAAUGGCUGUCAAAAAAGCUGACGUUAA
---........(((..(((((((..-...)))(((((.(((......))).)))))....))))..)))((((..((((((((((...)))))))))).....))))....... ( -26.80)
>DroYak_CAF1 167128 114 - 1
AUUAUCAUAAAUAUUCGAUCAGGAAGAGCCUUGAAAAAUGUUCAAGUGCAUUUUUUGAAAUGCCUUAUGCAGCGCUGACAGCUGUCAAAUGGCUGUCAAAAAAGCUGACGUUAA
.....(((((.((((...((((((((.((((((((.....)))))).)).))))))))))))..)))))((((..((((((((((...)))))))))).....))))....... ( -31.70)
>DroAna_CAF1 171314 97 - 1
AUUAUUACGAAAAAUUG-----CAAACCC------------CAAAGUGUAUUUGUGGAAAUGCCUUAUGCAGCGGUGGCAGCUGUCAAAUGGCUGUCAAAAAUGUUGACGUUAA
......(((.......(-----((...((------------((((.....)))).))...)))......(((((.((((((((((...))))))))))....))))).)))... ( -23.30)
>consensus
AUUAUCAUAAAUAUUUGAUAAGGAAACCCCUUGAAAAUUGUUCAAGUGCAUUAUUUGAAAUGCCUUAUGCAGCGCUGACAGCUGUCAAAUGGCUGUCAAAAAUGCUGACGUUAA
...........................................(((.(((((......))))))))((((((((.((((((((((...))))))))))....))))).)))... (-22.38 = -22.30 +  -0.08)

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 10:32:35 2006