Locus 2111

Sequence ID 2L_DroMel_CAF1
Location 5,691,310 – 5,691,469
Length 159
Max. P 0.943082
window3405 window3406 window3407 window3408

overview

Window 5

Location 5,691,310 – 5,691,413
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.29
Mean single sequence MFE -37.34
Consensus MFE -23.82
Energy contribution -25.06
Covariance contribution 1.24
Combinations/Pair 1.10
Mean z-score -2.21
Structure conservation index 0.64
SVM decision value 0.83
SVM RNA-class probability 0.861204
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5691310 103 + 22407834
UGAUUAAGGCCAGGCGGGUGGAAGUGAGCCCCUG--------CUCUGGAGCUCCGGUGCUGUGGACU---------CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCC
............((((((((((.(.((((.((..--------....)).)))))(((.((((((...---------)))))))))..))))))))))....................... ( -36.10)
>DroSec_CAF1 136555 103 + 1
UGAUUAAGGCCAGGCGGGUGGAAGUGAGUCCCUG--------CUCUGGCGCUCCGGAGCUCUGGACU---------CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCC
............((((((((((.((((((((..(--------((((((....)))))))...)))))---------).....))...))))))))))....................... ( -38.60)
>DroSim_CAF1 136038 103 + 1
UGAUUAAGGCCAGGCGGGUGGAAGUGAGCCCCUG--------CUCUGGUGCUCCGGAGCUCUGGACU---------CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCC
............((((((((((.(((((((...(--------((((((....)))))))...)).))---------).....))...))))))))))....................... ( -34.90)
>DroEre_CAF1 139258 97 + 1
UGAUUAAAGCCAGGCGGA-----------------------GCUCCGGAGCUCCGGAGCUCUGGACUCCAUGGACUCCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCGC
............((((((-----------------------(((((((....))))))))))(((((((((((...)))))))...))))....)))....................... ( -40.70)
>DroYak_CAF1 138138 113 + 1
UGAUUAAGGCCAGGCGGAUGGAAGAGAGCCCCUGCUCCAAAGCUCCAAAGCUCCAGAGCUGUGGACUG-------UCCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCGC
............((((((((((.(.((((....)))))..((.((((.((((....)))).))))))(-------((....)))...))))))))))....................... ( -36.40)
>consensus
UGAUUAAGGCCAGGCGGGUGGAAGUGAGCCCCUG________CUCUGGAGCUCCGGAGCUCUGGACU_________CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCC
............((((((((((....................((((((....))))))(..(((............)))..).....))))))))))....................... (-23.82 = -25.06 +   1.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,691,344 – 5,691,453
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.55
Mean single sequence MFE -27.18
Consensus MFE -19.94
Energy contribution -20.54
Covariance contribution 0.60
Combinations/Pair 1.07
Mean z-score -2.86
Structure conservation index 0.73
SVM decision value 1.33
SVM RNA-class probability 0.943082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5691344 109 + 22407834
--CUCUGGAGCUCCGGUGCUGUGGACU---------CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACA
--....((....))(((((((((((..---------...((((....))))((........))....))))))................)))))((((((......))))))........ ( -24.79)
>DroSec_CAF1 136589 109 + 1
--CUCUGGCGCUCCGGAGCUCUGGACU---------CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACA
--...((((..(((((....)))))..---------..(((((....)))))..))))....................................((((((......))))))........ ( -22.70)
>DroSim_CAF1 136072 109 + 1
--CUCUGGUGCUCCGGAGCUCUGGACU---------CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACA
--....((((((((((....)))))..---------..(((((....))))).....................................)))))((((((......))))))........ ( -25.10)
>DroEre_CAF1 139276 119 + 1
-GCUCCGGAGCUCCGGAGCUCUGGACUCCAUGGACUCCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCGCAAUCCCUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACA
-(((((((....)))))))..((((((((((((...)))))))...)))))..(((.(((((.........)))))..))).............((((((......))))))........ ( -38.50)
>DroYak_CAF1 138178 113 + 1
AGCUCCAAAGCUCCAGAGCUGUGGACUG-------UCCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCGCUAUCCCUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACA
.((.....((((....))))((((((.(-------((....)))..))))))..((.(((((.........)))))..)).........))...((((((......))))))........ ( -24.80)
>consensus
__CUCUGGAGCUCCGGAGCUCUGGACU_________CCAUGGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACA
...(((((((((....))))))))).............(((((....))))).(((.(((((.........)))))...................(((((......))))))))...... (-19.94 = -20.54 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,691,344 – 5,691,453
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.55
Mean single sequence MFE -35.31
Consensus MFE -25.64
Energy contribution -25.16
Covariance contribution -0.48
Combinations/Pair 1.11
Mean z-score -2.27
Structure conservation index 0.73
SVM decision value 0.60
SVM RNA-class probability 0.795600
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5691344 109 - 22407834
UGUGAUUGCGCAUAGAAAAAUAUGCGGGUGCGGAAGGAAUGGGAAAAUGUGGAAUAUUCAUUUGGCAGAUGGACAGGUCCAUGG---------AGUCCACAGCACCGGAGCUCCAGAG--
........((((((......))))))((.((....((..(((((...((((((...((((((.....))))))....)))))).---------..))).))...))...)).))....-- ( -31.40)
>DroSec_CAF1 136589 109 - 1
UGUGAUUGCGCAUAGAAAAAUAUGCGGGUGCGGAAGGAAUGGGAAAAUGUGGAAUAUUCAUUUGGCAGAUGGACAGGUCCAUGG---------AGUCCAGAGCUCCGGAGCGCCAGAG--
........((((((......))))))(((((....(((.(.(((...((((((...((((((.....))))))....)))))).---------..)))...).)))...)))))....-- ( -34.80)
>DroSim_CAF1 136072 109 - 1
UGUGAUUGCGCAUAGAAAAAUAUGCGGGUGCGGAAGGAAUGGGAAAAUGUGGAAUAUUCAUUUGGCAGAUGGACAGGUCCAUGG---------AGUCCAGAGCUCCGGAGCACCAGAG--
........((((((......))))))(((((....(((.(.(((...((((((...((((((.....))))))....)))))).---------..)))...).)))...)))))....-- ( -35.20)
>DroEre_CAF1 139276 119 - 1
UGUGAUUGCGCAUAGAAAAAUAUGCGGGUGCGGAGGGAUUGCGAAAAUGUGGAAUAUUCAUUUGGCAGAUGGACAGGUCCAUGGAGUCCAUGGAGUCCAGAGCUCCGGAGCUCCGGAGC-
.(..(((.((((((......)))))(....)...).)))..).....(((.((((....)))).)))..(((((...(((((((...))))))))))))..(((((((....)))))))- ( -42.40)
>DroYak_CAF1 138178 113 - 1
UGUGAUUGCGCAUAGAAAAAUAUGCGGGUGCGGAGGGAUAGCGAAAAUGUGGAAUAUUCAUUUGGCAGAUGGACAGGUCCAUGGA-------CAGUCCACAGCUCUGGAGCUUUGGAGCU
........((((((......))))))..(((.((((((((..............))))).))).)))..(((((..(((....))-------).))))).(((((..(....)..))))) ( -32.74)
>consensus
UGUGAUUGCGCAUAGAAAAAUAUGCGGGUGCGGAAGGAAUGGGAAAAUGUGGAAUAUUCAUUUGGCAGAUGGACAGGUCCAUGG_________AGUCCAGAGCUCCGGAGCUCCAGAG__
........((((((......))))))((.((....(((.........(((.((((....)))).))).(((((....))))).............)))...)).))((....))...... (-25.64 = -25.16 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,691,373 – 5,691,469
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 97.08
Mean single sequence MFE -18.16
Consensus MFE -16.64
Energy contribution -16.64
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.28
Structure conservation index 0.92
SVM decision value 0.36
SVM RNA-class probability 0.705120
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5691373 96 + 22407834
GGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACAACAGAUUGUGUGUUGG
(((....))).....................................((((((..(((((......)))))((((((......))))))))).))) ( -17.70)
>DroSec_CAF1 136618 96 + 1
GGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACAACAGAUUGUGUGUUGG
(((....))).....................................((((((..(((((......)))))((((((......))))))))).))) ( -17.70)
>DroSim_CAF1 136101 96 + 1
GGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACAACAGAUUGUGUGUUGG
(((....))).....................................((((((..(((((......)))))((((((......))))))))).))) ( -17.70)
>DroEre_CAF1 139315 96 + 1
GGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCGCAAUCCCUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACAACAGAUUGUGUGUUGC
(((....)))...(((.(((((.........)))))..)))........((((..(((((......)))))((((((......))))))))))... ( -19.50)
>DroYak_CAF1 138211 96 + 1
GGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCGCUAUCCCUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACAACAGAUUGUGUGUUGC
(((....)))....((.(((((.........)))))..)).........((((..(((((......)))))((((((......))))))))))... ( -18.20)
>consensus
GGACCUGUCCAUCUGCCAAAUGAAUAUUCCACAUUUUCCCAUUCCUUCCGCACCCGCAUAUUUUUCUAUGCGCAAUCACAACAGAUUGUGUGUUGG
(((....))).....................................(.((((..(((((......)))))((((((......)))))))))).). (-16.64 = -16.64 +   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 10:19:50 2006