Locus 7703

Sequence ID 3L_DroMel_CAF1
Location 20,602,827 – 20,603,149
Length 322
Max. P 0.999868
window12525 window12526 window12527 window12528 window12529

overview

Window 5

Location 20,602,827 – 20,602,924
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.60
Mean single sequence MFE -27.72
Consensus MFE -22.84
Energy contribution -22.88
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.82
SVM decision value 0.93
SVM RNA-class probability 0.883184
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20602827 97 - 23771897
UAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------CCCGAUCCCCGAGUCACCCCGGACGACCACCAAGUGGACUU
...((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------........(((........)))....((((...)))).... ( -28.60)
>DroSec_CAF1 47724 97 - 1
UAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------CCCAAUCCCCGAGUCACUCCGGACGACCACCAAGUGGACUU
...((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------.......((.(((...))).))....((((...)))).... ( -28.70)
>DroAna_CAF1 69689 115 - 1
UAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAUACUUCGAUACUCGCUACCCCAUACCCAAUACCCGA----UACCCGUUGCCCGCCAAUCCGA-AC
..(((((((((((((.((((((((.......)))))))).....))))))))))))).((((....(((...................)))----.....((((.....)))).)))-). ( -22.31)
>DroSim_CAF1 42513 97 - 1
UAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------CCCAAUCCCCGAGUCAUCCCGGACGACCACCAAGUGGACUU
...((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------........(((........)))....((((...)))).... ( -28.60)
>DroEre_CAF1 40155 96 - 1
UAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------CCCAAUCCCCGUUCCACCCCGGACGACCACCAGUCCG-AUC
...((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------...................(((((........)))))-... ( -30.40)
>consensus
UAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC_______________________CCCAAUCCCCGAGUCACCCCGGACGACCACCAAGUGGACUU
...((((((((((((.((((((((.......)))))))).....))))))))))))...............................(((........)))................... (-22.84 = -22.88 +   0.04)

alignment

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secondary structure

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Window 6

Location 20,602,867 – 20,602,964
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -28.52
Consensus MFE -25.88
Energy contribution -25.92
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.88
Structure conservation index 0.91
SVM decision value 4.31
SVM RNA-class probability 0.999868
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20602867 97 - 23771897
GAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------C
..........((....))...((((.........)))).....((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------. ( -27.80)
>DroSec_CAF1 47764 97 - 1
GAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------C
..........((....))...((((.........)))).....((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------. ( -27.80)
>DroAna_CAF1 69724 120 - 1
GAUAUGAAAAGAGCAACCAAGUGGCAUACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAUACUUCGAUACUCGCUACCCCAUAC
..((((.....(((.......((((.........))))....(((((((((((((.((((((((.......)))))))).....)))))))))))))...........)))....)))). ( -31.40)
>DroSim_CAF1 42553 97 - 1
GAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------C
..........((....))...((((.........)))).....((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------. ( -27.80)
>DroEre_CAF1 40194 97 - 1
GAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC-----------------------C
..........((....))...((((.........)))).....((((((((((((.((((((((.......)))))))).....))))))))))))-----------------------. ( -27.80)
>consensus
GAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCUGAACCGUUUAGUGUAC_______________________C
..........((....))...((((.........)))).....((((((((((((.((((((((.......)))))))).....))))))))))))........................ (-25.88 = -25.92 +   0.04)

alignment

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secondary structure

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Window 7

Location 20,602,884 – 20,603,004
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -32.98
Consensus MFE -31.64
Energy contribution -31.52
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.96
SVM decision value 1.99
SVM RNA-class probability 0.985011
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20602884 120 - 23771897
AGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCU
.((((((((.....)))))).))((((((.(((((((..((((.((.......)))))).))))).........((((...(((..(((...)))..))))))).......)))).)))) ( -33.20)
>DroSec_CAF1 47781 120 - 1
AGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCU
.((((((((.....)))))).))((((((.(((((((..((((.((.......)))))).))))).........((((...(((..(((...)))..))))))).......)))).)))) ( -33.20)
>DroAna_CAF1 69764 120 - 1
AGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGAAGAUAUGAAAAGAGCAACCAAGUGGCAUACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCU
.((((((((.....)))))).)).(((((((.(((.....)))..................((((.........))))..))))))).........((((((((.......)))))))). ( -29.50)
>DroSim_CAF1 42570 120 - 1
AGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCU
.((((((((.....)))))).))((((((.(((((((..((((.((.......)))))).))))).........((((...(((..(((...)))..))))))).......)))).)))) ( -33.20)
>DroEre_CAF1 40211 120 - 1
AGACAGAGUCUGGAACUCUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCU
.((((((((.....)))))).))((((((.(((((((..((((.((.......)))))).))))).........((((...(((..(((...)))..))))))).......)))).)))) ( -35.80)
>consensus
AGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAAUAUGUGCAUUAAAUGUGCAUUGGCAUUAAUCGUCGAUGCU
.(((...((.((..(((((((((....(((((((....))).))))....)))))...))))..)).)).....((((...(((..(((...)))..))))))).......)))...... (-31.64 = -31.52 +  -0.12)

alignment

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secondary structure

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Window 8

Location 20,602,924 – 20,603,038
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.32
Mean single sequence MFE -31.92
Consensus MFE -24.10
Energy contribution -24.10
Covariance contribution -0.00
Combinations/Pair 1.13
Mean z-score -2.56
Structure conservation index 0.76
SVM decision value 1.33
SVM RNA-class probability 0.943068
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20602924 114 - 23771897
ACAGAAUCAGAUUCAGAU------UCGGAUUCAAAGCCGGAGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAA
...((.((((((((...(------((((........)))))....))))))))....((((((....(((((((....))).))))....))))))))...((((.........)))).. ( -32.40)
>DroSec_CAF1 47821 114 - 1
ACAGAAUCAGAUUCAGAU------UCGGAUUCAAAGCCGGAGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAA
...((.((((((((...(------((((........)))))....))))))))....((((((....(((((((....))).))))....))))))))...((((.........)))).. ( -32.40)
>DroAna_CAF1 69804 110 - 1
---GGAUUA-AAACAGAU------UCGAAUUCAAAGUCAGAGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGAAGAUAUGAAAAGAGCAACCAAGUGGCAUACAAAAAGCCAAA
---((....-...(((((------((...(((.......)))...))))))).....((((((....(((((........).))))....))))))))...((((.........)))).. ( -25.20)
>DroSim_CAF1 42610 114 - 1
ACAGAAUCAGAUUCAGAU------UCGGACUCAAAGCCGGAGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAA
...((.((((((((...(------((((........)))))....))))))))....((((((....(((((((....))).))))....))))))))...((((.........)))).. ( -32.40)
>DroEre_CAF1 40251 120 - 1
CCAGAAUCAGAUUUAGAUUCAGACUCGAAUUCAAAGCCGGAGACAGAGUCUGGAACUCUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAA
...(((((.......)))))..((((((.(((...((((.((.((((((.....)))))))))))).(((((((....))).))))....)))...))))))(((.........)))... ( -37.20)
>consensus
ACAGAAUCAGAUUCAGAU______UCGGAUUCAAAGCCGGAGACAGAGUCUGGAACUUUGCUCGGCACGUACGUCACGACGAUAUGAAAAGAGCAAUCGAGUGGCACACAAAAAGCCAAA
........................((((.(((...(((.(((.((((((.....)))))))))))).(((((((....))).))))....)))...)))).((((.........)))).. (-24.10 = -24.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,603,038 – 20,603,149
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.53
Mean single sequence MFE -30.76
Consensus MFE -18.05
Energy contribution -20.70
Covariance contribution 2.65
Combinations/Pair 1.10
Mean z-score -1.84
Structure conservation index 0.59
SVM decision value 0.25
SVM RNA-class probability 0.654944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20603038 111 - 23771897
AAUGUUUUAGCUUGUACUUUUAUAACUGCAGUCAUGUUAUAUCACCUCUCGACAUGACAUCACCGAUCGAUGGGGUUGGGGUUAUUUCGGGGAGCCGAAAC---AGA------AACAUAA
..(((((..((((.(......((((((...((((((((............))))))))....((((((.....))))))))))))....).))))..))))---)..------....... ( -30.90)
>DroSec_CAF1 47935 111 - 1
AAUGUUUUAGCUUGUACUUUUAUAACUGCAGUCAUGUUAUGUCACCUCUCGACAUGACAUCACCGAUCUGCGGGGUUGGGGUUAUUUCGGGGAGCCGAAAC---AGA------AACAUAA
..(((((..((((.(......((((((.((..(((((((((((.......))))))))))..(((.....))))..)).))))))....).))))..))))---)..------....... ( -35.80)
>DroAna_CAF1 69914 98 - 1
UAUGUUUCGUCUUGUAGUUUAAUAACUGAAGCCAUGUUAUAUCACCUCCUGACAUGACAUCAUCC-UCAAUAG---------------GGGGAUCCAAAAUAUCAGA------GGGGUAG
.((((..((((((.(((((....))))))))..)))..)))).(((((((((.((......((((-((.....---------------)))))).....)).)))).------))))).. ( -22.30)
>DroSim_CAF1 42724 111 - 1
AAUGUUUUAGCUUGUACUUUUAUAACUGCAGUCAUGUUAUAUCACCUCUCGACAUGACAUCACCGAUCGGUGGGGUUGGGGUUAUUUCGGGGAGCCGAAAC---AGA------AACAUAA
..(((((..((((.(......((((((.((((((((((............)))))))).(((((....)))))...)).))))))....).))))..))))---)..------....... ( -33.30)
>DroEre_CAF1 40371 112 - 1
-ACGUUUCAGCUUGUACUUUUAUGACUGCAGUCAUGUUAUAUCACCUCUCGACAUGACAUCACCGAUCGGCG-GGUUGGGGUUAU---AGGGAGCCGAAAC---AGAAACAGAAACAUAA
-..(((((.((((.....(((((((((...((((((((............))))))))....((((((....-))))))))))))---))))))).)))))---................ ( -31.50)
>consensus
AAUGUUUUAGCUUGUACUUUUAUAACUGCAGUCAUGUUAUAUCACCUCUCGACAUGACAUCACCGAUCGGUGGGGUUGGGGUUAUUUCGGGGAGCCGAAAC___AGA______AACAUAA
...(((((.((((.(......((((((...((((((((............))))))))....((((((.....))))))))))))....).)))).)))))................... (-18.05 = -20.70 +   2.65)

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 12:54:25 2006