Locus 3529

Sequence ID 2R_DroMel_CAF1
Location 11,812,473 – 11,812,600
Length 127
Max. P 0.763244
window5743 window5744 window5745

overview

Window 3

Location 11,812,473 – 11,812,573
Length 100
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 81.84
Mean single sequence MFE -40.93
Consensus MFE -29.40
Energy contribution -29.82
Covariance contribution 0.42
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.72
SVM decision value 0.51
SVM RNA-class probability 0.763244
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11812473 100 + 20766785
GCU--GAGGAGAACGCAUCCAGCUGUGCUGCAGCGCCUCGUGUGUCACUUGCCACACACGAACGCCAUUUGGCGAUUGGUGUUGAUGGCCAAUGCGGCGAGC
(((--..(((.......))).((((((((((((((((((((((((........)))))))).((((....))))...))))))).))))....))))).))) ( -41.80)
>DroVir_CAF1 15462 91 + 1
GGGUGGAGGAC---GCGUCCAGCUGUGCCGCAGCGCCUCGUGUGUCAAUGGCCACACACGAACGCCAUUUGGCGCUGGGUGUUGAUGGCCAGCU--------
.......(((.---...)))(((((.(((((((((((((((((((........)))))))).((((....))))...))))))).)))))))))-------- ( -45.00)
>DroPse_CAF1 3113 102 + 1
GAGUGGACGACGACGCUUCCAGCUGUGCUGCAUCGCCUCGUGUGUCACUUGCCACACACGAACGCCAUUUGGCGACUGGUGUUGAUGGCAUAUGCAGAGAAC
(((((........)))))...(((((((((((.((((((((((((........)))))))).((((....))))...)))).)).))))))).))....... ( -38.00)
>DroMoj_CAF1 18297 94 + 1
GGGUGGACGACGUCGCAUCCAGCUGUGCAGCAGCGCCUCGUGUGUCAAUGGCCACACACGAGCCCCAUUUGGAGCUGGGUGUUGAUGGCCAAUG--------
...(((....((((((((((((((((((....))))(((((((((........)))))))))..((....))))))))))).))))).)))...-------- ( -41.50)
>DroAna_CAF1 3068 100 + 1
GGC--GAGGAGAACGCAUCCAGCUGUGUUGCAGCGCCUCGUGUGUCACUUGCCACACACGAACGCCAUUUGGCGAAUGGUGUUGAUGGCCAAUGCAGCGAUC
...--..(((.......))).((((((((((((((((((((((((........)))))))).((((....))))...))))))).....))))))))).... ( -41.30)
>DroPer_CAF1 3197 102 + 1
GAGUGGACGACGACGCUUCCAGCUGUGCUGCAUCGCCUCGUGUGUCACUUGCCACACACGAACGCCAUUUGGCGACUGGUGUUGAUGGCAUAUGCAGAGAAC
(((((........)))))...(((((((((((.((((((((((((........)))))))).((((....))))...)))).)).))))))).))....... ( -38.00)
>consensus
GGGUGGACGACGACGCAUCCAGCUGUGCUGCAGCGCCUCGUGUGUCACUUGCCACACACGAACGCCAUUUGGCGAUUGGUGUUGAUGGCCAAUGCAG_GA_C
..............((.....))...(((((((((((((((((((........)))))))).((((....))))...))))))).))))............. (-29.40 = -29.82 +   0.42)

alignment

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secondary structure

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Window 4

Location 11,812,473 – 11,812,573
Length 100
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 81.84
Mean single sequence MFE -36.48
Consensus MFE -27.31
Energy contribution -28.98
Covariance contribution 1.67
Combinations/Pair 1.20
Mean z-score -1.52
Structure conservation index 0.75
SVM decision value 0.27
SVM RNA-class probability 0.662230
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11812473 100 - 20766785
GCUCGCCGCAUUGGCCAUCAACACCAAUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGCAGCACAGCUGGAUGCGUUCUCCUC--AGC
......((((((.(((............((((....)))).((((((((.(....).)))))))))))((((.....))))..))))))........--... ( -35.90)
>DroVir_CAF1 15462 91 - 1
--------AGCUGGCCAUCAACACCCAGCGCCAAAUGGCGUUCGUGUGUGGCCAUUGACACACGAGGCGCUGCGGCACAGCUGGACGC---GUCCUCCACCC
--------...(((((((..((((..((((((....)))))).))))))))))).........((((((((.((((...)))).).))---).))))..... ( -38.40)
>DroPse_CAF1 3113 102 - 1
GUUCUCUGCAUAUGCCAUCAACACCAGUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGAUGCAGCACAGCUGGAAGCGUCGUCGUCCACUC
(((..((((((.((((............((((....)))).((((((((.(....).))))))))))))))))))...)))(((..(((....))))))... ( -36.40)
>DroMoj_CAF1 18297 94 - 1
--------CAUUGGCCAUCAACACCCAGCUCCAAAUGGGGCUCGUGUGUGGCCAUUGACACACGAGGCGCUGCUGCACAGCUGGAUGCGACGUCGUCCACCC
--------((.(((((((..((((..((((((....)))))).))))))))))).))....((((.((((.(((....))).....))).).))))...... ( -37.40)
>DroAna_CAF1 3068 100 - 1
GAUCGCUGCAUUGGCCAUCAACACCAUUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGCAACACAGCUGGAUGCGUUCUCCUC--GCC
((..((.(((((.(((............((((....)))).((((((((.(....).)))))))))))((((.....))))..)))))))..))...--... ( -34.40)
>DroPer_CAF1 3197 102 - 1
GUUCUCUGCAUAUGCCAUCAACACCAGUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGAUGCAGCACAGCUGGAAGCGUCGUCGUCCACUC
(((..((((((.((((............((((....)))).((((((((.(....).))))))))))))))))))...)))(((..(((....))))))... ( -36.40)
>consensus
G_UC_CUGCAUUGGCCAUCAACACCAAUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGCAGCACAGCUGGAUGCGUCGUCCUCCACCC
........((((((((((..((((....((((....))))...))))))))))))))....((((.(((.(.((((...)))).)))).))))......... (-27.31 = -28.98 +   1.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,812,500 – 11,812,600
Length 100
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -32.20
Consensus MFE -25.34
Energy contribution -25.28
Covariance contribution -0.05
Combinations/Pair 1.14
Mean z-score -1.47
Structure conservation index 0.79
SVM decision value -0.01
SVM RNA-class probability 0.530969
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11812500 100 - 20766785
CCCGAUCUCCUCCAGUCUUUGGUCUCUGCUCGCCGCAUUGGCCAUCAACACCAAUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGC
............((((...(((((..(((.....)))..)))))......((...((((....)))).((((((((.(....).)))))))))).)))). ( -32.70)
>DroPse_CAF1 3142 100 - 1
CUGAAUUGCCUGCUUCUCCUGUUCUCAGUUCUCUGCAUAUGCCAUCAACACCAGUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGAUGC
..((((((...((.......))...))))))...((((.((((............((((....)))).((((((((.(....).)))))))))))))))) ( -33.10)
>DroSim_CAF1 3154 100 - 1
CCCGAUCUCCUCCAGUAUUUGGUCUCUGCUCGCCGCAUUGGCCAUCAACACCAAUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGC
............((((...(((((..(((.....)))..)))))......((...((((....)))).((((((((.(....).)))))))))).)))). ( -33.30)
>DroEre_CAF1 3170 100 - 1
CCCGAUCUCCUCCAGCCUUUGGACUCUGCUCACCGCAUUGGCCAUCAACACCAAUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGC
............((((.......(..(((.....)))..)(((............((((....)))).((((((((.(....).))))))))))))))). ( -31.10)
>DroAna_CAF1 3095 86 - 1
C-------CCCCCAAC-------CUCGGAUCGCUGCAUUGGCCAUCAACACCAUUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGC
.-------.......(-------((((..(((((......(((((..((((....((((....))))...))))))))).)))))....)))))...... ( -29.90)
>DroPer_CAF1 3226 100 - 1
CUGAAUUGCCUGCUUCUCCUGUUCUCAGUUCUCUGCAUAUGCCAUCAACACCAGUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGAUGC
..((((((...((.......))...))))))...((((.((((............((((....)))).((((((((.(....).)))))))))))))))) ( -33.10)
>consensus
CCCGAUCUCCUCCAGCCUUUGGUCUCUGCUCGCCGCAUUGGCCAUCAACACCAAUCGCCAAAUGGCGUUCGUGUGUGGCAAGUGACACACGAGGCGCUGC
............((((...........((.....))....(((............((((....)))).((((((((.(....).))))))))))))))). (-25.34 = -25.28 +  -0.05)

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 10:57:43 2006