Locus 4816

Sequence ID 2L_DroMel_CAF1
Location 13,738,960 – 13,739,160
Length 200
Max. P 0.990432
window7617 window7618 window7619 window7620 window7621

overview

Window 7

Location 13,738,960 – 13,739,069
Length 109
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 89.69
Mean single sequence MFE -27.83
Consensus MFE -22.31
Energy contribution -22.38
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.80
SVM decision value 0.98
SVM RNA-class probability 0.893228
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13738960 109 + 22407834
AAUUUACAUAAAUACAAUAUGGUGCGUGCUUCCCGGCGCCAUUUUAUUUGCACAACACAUACGCA--GCUCUAUACAUAUGUGUGUGUGAAUGGAAAUGCACACACACACA
.................(((((.(((((((....))))).........(((...........)))--)).)))))....((((((((((.((....)).)))))))))).. ( -29.60)
>DroSec_CAF1 2799 103 + 1
AAUUUACAUAAAUACAAUAUGGUGCGUGCUUCUCGGCGCCAUUUUAUUUGCACAACACAUACGCGCGGCUCUAUAC--AUGUGUGCGUGAAUGGGCAUGCACACA------
.................(((((.(((((((....))))).........(((.(.........).))))).))))).--.((((((((((......))))))))))------ ( -27.10)
>DroSim_CAF1 4456 107 + 1
AAUUUACAUAAAUACAAUAUGGUGCGUGCUUCUCGGCGCCAUUUUAUUUGCACAACACAUACGCGGUGCUCUAUAC--AUGUGUGCGUGAAUGGAAAUGCACACACAUA--
.........(((((....(((((((..........)))))))..)))))((((..(......)..)))).......--.(((((((((........)))))))))....-- ( -28.50)
>DroEre_CAF1 4338 103 + 1
AAUUUACAUAAAUACAAUAUGGUGCGUGCUUCUCGGCGCCAUUUUACUUGCACAACAUAUACGGG--UGUCUAUAC--AUGUGUGCGUGAAUGGAAAUGCACACACA----
......((((.......))))(((((((((....))).((((((....((((((.(((.((..(.--...)..)).--))))))))).))))))..)))))).....---- ( -26.10)
>consensus
AAUUUACAUAAAUACAAUAUGGUGCGUGCUUCUCGGCGCCAUUUUAUUUGCACAACACAUACGCG__GCUCUAUAC__AUGUGUGCGUGAAUGGAAAUGCACACACA____
........((((((....(((((((..........)))))))..)))))).............................(((((((((........)))))))))...... (-22.31 = -22.38 +   0.06)

alignment

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secondary structure

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Window 8

Location 13,739,000 – 13,739,093
Length 93
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 80.51
Mean single sequence MFE -19.88
Consensus MFE -12.36
Energy contribution -12.18
Covariance contribution -0.19
Combinations/Pair 1.11
Mean z-score -2.08
Structure conservation index 0.62
SVM decision value 0.72
SVM RNA-class probability 0.833421
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739000 93 + 22407834
AUUUUAUUUGCACAACACAUACGCA--GCUCUAUACAUAUGUGUGUGUGAAUGGAAAUGCACACACACACA--CGCACACACCCAUGAAACAUAUUU
.((((((((((...........)))--)...........((((((((((.((....)).))))))))))..--...........))))))....... ( -18.90)
>DroSec_CAF1 2839 81 + 1
AUUUUAUUUGCACAACACAUACGCGCGGCUCUAUAC--AUGUGUGCGUGAAUGGGCAUGCACACA------------CA--CACAUGGAACAUAUUU
.......((((.(.........).)))).(((((..--.((((((((((......))))))))))------------..--...)))))........ ( -18.20)
>DroSim_CAF1 4496 89 + 1
AUUUUAUUUGCACAACACAUACGCGGUGCUCUAUAC--AUGUGUGCGUGAAUGGAAAUGCACACACAUA----CGCACA--CACAUGGAACAUAUUU
.........((((..(......)..))))(((((..--.((((((((((..((..........))..))----))))))--)).)))))........ ( -23.80)
>DroEre_CAF1 4378 87 + 1
AUUUUACUUGCACAACAUAUACGGG--UGUCUAUAC--AUGUGUGCGUGAAUGGAAAUGCACACACA----CACACGCA--CAAGCGAAACAUAUUU
.......((((....(......).(--(((......--.(((((((((........)))))))))..----.....)))--)..))))......... ( -18.64)
>consensus
AUUUUAUUUGCACAACACAUACGCG__GCUCUAUAC__AUGUGUGCGUGAAUGGAAAUGCACACACA______CGCACA__CACAUGAAACAUAUUU
.......................................(((((((((........)))))))))................................ (-12.36 = -12.18 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,739,036 – 13,739,133
Length 97
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 86.06
Mean single sequence MFE -31.25
Consensus MFE -23.40
Energy contribution -23.65
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -3.43
Structure conservation index 0.75
SVM decision value 2.21
SVM RNA-class probability 0.990432
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739036 97 + 22407834
AUGUGUGUGUGAAUGGAAAUGCACACACACACA--CGCACACACCCAUGAAACAUAUUUGCACCAAAGUGCGUAUUGAUUUGCGGCAUAUGCGUGUGAA
..(((((((((.((....)).)))))))))(((--((((.....((..(((.((....(((((....)))))...)).)))..))....)))))))... ( -35.00)
>DroSec_CAF1 2875 85 + 1
AUGUGUGCGUGAAUGGGCAUGCACACA------------CA--CACAUGGAACAUAUUUGCACCGAAGUGCGUAUUGAUUUGCGGCAUAUGCAUGUGAA
.((((((((((......))))))))))------------..--((((((...(((((..((((....))))(((......)))...))))))))))).. ( -30.10)
>DroSim_CAF1 4532 93 + 1
AUGUGUGCGUGAAUGGAAAUGCACACACAUA----CGCACA--CACAUGGAACAUAUUUGCACCGAAGUGCGUAUUGAUUUGCGGCAUAUGCAUGUGAA
.(((((((((........))))))))).(((----(((((.--....(((..((....))..)))..))))))))...((..((((....)).))..)) ( -28.20)
>DroEre_CAF1 4412 93 + 1
AUGUGUGCGUGAAUGGAAAUGCACACACA----CACACGCA--CAAGCGAAACAUAUUUGCACCGAAGUGCGUAUUGAUUUGCGGCAUAUGCAUGUGAA
.(((((((((........)))))))))..----((((.(((--...(((((.((....(((((....)))))...)).)))))......))).)))).. ( -31.70)
>consensus
AUGUGUGCGUGAAUGGAAAUGCACACACA______CGCACA__CACAUGAAACAUAUUUGCACCGAAGUGCGUAUUGAUUUGCGGCAUAUGCAUGUGAA
.(((((((((........)))))))))................((((((...(((((..((((....))))(((......)))...))))))))))).. (-23.40 = -23.65 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,739,036 – 13,739,133
Length 97
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 86.06
Mean single sequence MFE -33.15
Consensus MFE -17.36
Energy contribution -17.93
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -4.76
Structure conservation index 0.52
SVM decision value 0.35
SVM RNA-class probability 0.701963
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739036 97 - 22407834
UUCACACGCAUAUGCCGCAAAUCAAUACGCACUUUGGUGCAAAUAUGUUUCAUGGGUGUGUGCG--UGUGUGUGUGUGCAUUUCCAUUCACACACACAU
...(((((((((((((............((((....))))...((((...))))))))))))))--)))(((((((((.((....)).))))))))).. ( -39.70)
>DroSec_CAF1 2875 85 - 1
UUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUCCAUGUG--UG------------UGUGUGCAUGCCCAUUCACGCACACAU
...((((((.......))..........((((....))))....)))).....(((--((------------((((((.((....)).))))))))))) ( -26.30)
>DroSim_CAF1 4532 93 - 1
UUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUCCAUGUG--UGUGCG----UAUGUGUGUGCAUUUCCAUUCACGCACACAU
.......(((((((((((..........((((....))))..(((((...))))))--)).)))----)))))((((((............)))))).. ( -31.90)
>DroEre_CAF1 4412 93 - 1
UUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUUCGCUUG--UGCGUGUG----UGUGUGUGCAUUUCCAUUCACGCACACAU
...(((((((((.((.(.((((......((((....))))......))))))).))--)))))))(----((((((((.((....)).))))))))).. ( -34.70)
>consensus
UUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUCCAUGUG__UGUGCG______UGUGUGUGCAUUUCCAUUCACGCACACAU
...((((((.......))..........((((....))))....))))......................((((((((.((....)).))))))))... (-17.36 = -17.93 +   0.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,739,069 – 13,739,160
Length 91
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 89.11
Mean single sequence MFE -24.15
Consensus MFE -17.19
Energy contribution -17.25
Covariance contribution 0.06
Combinations/Pair 1.12
Mean z-score -1.77
Structure conservation index 0.71
SVM decision value 0.18
SVM RNA-class probability 0.623777
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739069 91 - 22407834
UUU-UUUGUAUCGAAACGAGGAAAGCAUUUCACACGCAUAUGCCGCAAAUCAAUACGCACUUUGGUGCAAAUAUGUUUCAUGGGUGUGUGCG--
(((-(((((......))))))))...........((((((((((............((((....))))...((((...))))))))))))))-- ( -23.40)
>DroSec_CAF1 2902 86 - 1
UUUUUUUGUAUCGGAACGAGGAAAGCAUUUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUCCAUGUG--UG------
............((((((.((...((((.....)))).....))............((((....)))).....)))))).....--..------ ( -21.20)
>DroSim_CAF1 4563 90 - 1
UUUUUUUGUAUCGGAACGAGGAAAGCAUUUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUCCAUGUG--UGUGCG--
(((((((((......)))))))))((((..(((((((((((...(.....).....((((....))))..)))))...))))))--.)))).-- ( -25.00)
>DroEre_CAF1 4441 91 - 1
UUU-UUUGUAUCGGAACGAGGAAAACAUUUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUUCGCUUG--UGCGUGUG
(((-(((((......)))))))).......((((((((((.((.(.((((......((((....))))......))))))).))--)))))))) ( -27.00)
>consensus
UUU_UUUGUAUCGGAACGAGGAAAGCAUUUCACAUGCAUAUGCCGCAAAUCAAUACGCACUUCGGUGCAAAUAUGUUCCAUGUG__UGUGCG__
............((((((.((...((((.....)))).....))............((((....)))).....))))))............... (-17.19 = -17.25 +   0.06)

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 11:28:07 2006