Locus 5837

Sequence ID 2L_DroMel_CAF1
Location 16,556,448 – 16,556,648
Length 200
Max. P 0.998642
window9261 window9262 window9263 window9264 window9265

overview

Window 1

Location 16,556,448 – 16,556,568
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -39.78
Consensus MFE -35.58
Energy contribution -35.46
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.89
SVM decision value 1.79
SVM RNA-class probability 0.977563
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16556448 120 + 22407834
GAAACCGUUGGGCGCUGCCUUUGUGUGCGGAUUGUUUGCUUUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGU
.........((((((((((((((.((.((((..(....)..)))).)).....))))))))))..(((((..((((((....)))))))))))))))(((......)))........... ( -39.00)
>DroSec_CAF1 10974 120 + 1
GAAACCGUUGGGCGCUGCCUUUGUGUGCGGAUUGUUUGCUUUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGU
.........((((((((((((((.((.((((..(....)..)))).)).....))))))))))..(((((..((((((....)))))))))))))))(((......)))........... ( -39.00)
>DroSim_CAF1 10923 120 + 1
GAAACCGUUGGGCGCUGCCUUUGUGUGCGGAUUGUUUGCUUUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGU
.........((((((((((((((.((.((((..(....)..)))).)).....))))))))))..(((((..((((((....)))))))))))))))(((......)))........... ( -39.00)
>DroEre_CAF1 10816 120 + 1
GAAACCGUUGGGCGCUCCCUUUGUGUGCGAAUUGUUUGCUUUUUGGGCCUGUCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCAGCUUAUUUGCCAAAUAAUCUGU
...(((.(((((((..(((.......((((.....)))).....)))..))))))).))).((....)).(((((((((((...(((......))).))))))...)))))......... ( -37.50)
>DroYak_CAF1 10783 120 + 1
GAAACCAUUGGGCGCUCCCUUUGUGUGCGGAUUGUUUGCUUUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCAGGCUUAUUUGCCAAAUAAUCUGU
...((((..(((....)))..)).))(((((((((((((....((((((((((.(((.(..((....))...((((((....))))))).)))))))))))))...).)))))))))))) ( -44.40)
>consensus
GAAACCGUUGGGCGCUGCCUUUGUGUGCGGAUUGUUUGCUUUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGU
...((((..((......))..)).))(((((((((.(((((((...((((......))))...)))))))(((((((((((...(((......))).))))))...)))))))))))))) (-35.58 = -35.46 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,556,488 – 16,556,608
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -40.92
Consensus MFE -38.94
Energy contribution -38.98
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.18
Structure conservation index 0.95
SVM decision value 3.17
SVM RNA-class probability 0.998642
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16556488 120 + 22407834
UUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGGCGCCA
...((((((.(((((..((((((....))...((((((....))))))....))))..(((((((.(((((((((.....))))))))).....))))))).....)))))..))).))) ( -42.10)
>DroSec_CAF1 11014 120 + 1
UUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCGGGCCCCGGCGCCA
....(((((((..(...((((((....))...((((((....))))))....))))..(((((((.(((((((((.....))))))))).....))))))).)..)))))))........ ( -41.50)
>DroSim_CAF1 10963 120 + 1
UUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCGGGCCCCGGCGCCA
....(((((((..(...((((((....))...((((((....))))))....))))..(((((((.(((((((((.....))))))))).....))))))).)..)))))))........ ( -41.50)
>DroEre_CAF1 10856 120 + 1
UUUUGGGCCUGUCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCAGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGUCGCCA
....(((((.(..(...((((((....))...((((((....))))))....))))..(((((((.(((((((((.....))))))))).....))))))).)..).)))))........ ( -36.70)
>DroYak_CAF1 10823 120 + 1
UUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCAGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGGCGCUA
....(((((((((((((.(..((....)).(((((.((((.((((((......))))))...)))))))))..........).))))))))(((.....))).....)))))........ ( -42.80)
>consensus
UUUUGGGCCUGGCCAAAGGUAGCGAAAGCAUUGGUUAAGUUCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGGCGCCA
....(((((((((((((.(..((....)).(((((((((((...(((......))).))))))...)))))..........).))))))))(((.....))).....)))))........ (-38.94 = -38.98 +   0.04)

alignment

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secondary structure

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Window 3

Location 16,556,488 – 16,556,608
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -33.22
Consensus MFE -30.39
Energy contribution -31.39
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.91
SVM decision value 2.24
SVM RNA-class probability 0.990974
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16556488 120 - 22407834
UGGCGCCGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGAACUUAACCAAUGCUUUCGCUACCUUUGGCCAGGCCCAAAA
(((.(((..(((((((..........((((.((((((.((.....)).))))))...((((...(((......))).....))))....))))..........))))))).))))))... ( -36.45)
>DroSec_CAF1 11014 120 - 1
UGGCGCCGGGGCCCGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGAACUUAACCAAUGCUUUCGCUACCUUUGGCCAGGCCCAAAA
(((.(((.(((((((.....((((((.....((((((.((.....)).)))))).)))))).)))))...................((((.((....)).....)))))).))))))... ( -33.20)
>DroSim_CAF1 10963 120 - 1
UGGCGCCGGGGCCCGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGAACUUAACCAAUGCUUUCGCUACCUUUGGCCAGGCCCAAAA
(((.(((.(((((((.....((((((.....((((((.((.....)).)))))).)))))).)))))...................((((.((....)).....)))))).))))))... ( -33.20)
>DroEre_CAF1 10856 120 - 1
UGGCGACGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCUGGGCAAACAAGCCAAGAACUUAACCAAUGCUUUCGCUACCUUUGGACAGGCCCAAAA
........(((((.......((((((.....((((((.((.....)).)))))).))))))((.(((......))).)).......((((.((....)).....))))...))))).... ( -30.00)
>DroYak_CAF1 10823 120 - 1
UAGCGCCGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCUGGCAAACAAGCCAAGAACUUAACCAAUGCUUUCGCUACCUUUGGCCAGGCCCAAAA
..(.(((..(((((((..........((((.((((((.((.....)).))))))...((((..((((......))))....))))....))))..........))))))).))).).... ( -33.25)
>consensus
UGGCGCCGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGAACUUAACCAAUGCUUUCGCUACCUUUGGCCAGGCCCAAAA
(((.(((..(((((((..........((((.((((((.((.....)).))))))...((((...(((......))).....))))....))))..........))))))).))))))... (-30.39 = -31.39 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,556,528 – 16,556,648
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.82
Mean single sequence MFE -39.74
Consensus MFE -33.90
Energy contribution -34.62
Covariance contribution 0.72
Combinations/Pair 1.08
Mean z-score -1.73
Structure conservation index 0.85
SVM decision value 1.29
SVM RNA-class probability 0.938470
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16556528 120 + 22407834
UCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGGCGCCAGUUGACAUAGGCAGGUUGCACUGUGCCUUGCCAUCGACGA
....(((......)))(((((((((.(((((((((.....))))))))).....))))))).((((((((......)))))..)))...((((((..((.....)))))))).....)). ( -37.50)
>DroSec_CAF1 11054 120 + 1
UCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCGGGCCCCGGCGCCAGUUGACAUAGGCAGGUUGCACUGUGUCUUGCCAUCGACGA
...(((((((...((((((((((((.(((((((((.....))))))))).....)))))))....)))))..))).))))(((((....((((((.(((...))).)))))).))))).. ( -41.10)
>DroSim_CAF1 11003 120 + 1
UCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCGGGCCCCGGCGCCAGUUGACAUAGGCAGGUUGCACUGUGUCUUGCCAUCGACGA
...(((((((...((((((((((((.(((((((((.....))))))))).....)))))))....)))))..))).))))(((((....((((((.(((...))).)))))).))))).. ( -41.10)
>DroEre_CAF1 10896 117 + 1
UCUUGGCUUGUUUGCCCAGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGUCGCCAGUUGACAUAGGCAGGUUGGACUGUGUCCCGCCAUCGA---
...((((...((((((..(((((((.(((((((((.....))))))))).....))))))).((((((((......)))))..)))...))))))..((((...)))).))))....--- ( -38.10)
>DroYak_CAF1 10863 117 + 1
UCUUGGCUUGUUUGCCAGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGGCGCUAGUUGACAUAGGCAGGUAGGACUGUGUCUUGCCAUCGA---
..(((((......)))))((((((..(((((((((.....))))))))).......(((.((((.(((....))).)))).)))..)))))).((((((((...)))))))).....--- ( -40.90)
>consensus
UCUUGGCUUGUUUGCCCGGCUUAUUUGCCAAAUAAUCUGUUUGUUUGGCCAUGCAAUAAGUAGUUCUGGCCCCGGCGCCAGUUGACAUAGGCAGGUUGCACUGUGUCUUGCCAUCGACGA
...((((......((((((((((((.(((((((((.....))))))))).....)))))))....)))))......))))(((((....((((((...........)))))).))))).. (-33.90 = -34.62 +   0.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,556,528 – 16,556,648
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.82
Mean single sequence MFE -34.12
Consensus MFE -28.70
Energy contribution -29.22
Covariance contribution 0.52
Combinations/Pair 1.09
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value 0.68
SVM RNA-class probability 0.819693
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16556528 120 - 22407834
UCGUCGAUGGCAAGGCACAGUGCAACCUGCCUAUGUCAACUGGCGCCGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGA
.......((((.(((((..........))))).((((..(((((......))))).....((((((.....((((((.((.....)).)))))).))))))...)))).....))))... ( -33.50)
>DroSec_CAF1 11054 120 - 1
UCGUCGAUGGCAAGACACAGUGCAACCUGCCUAUGUCAACUGGCGCCGGGGCCCGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGA
.......((((..((((.((.((.....)))).))))..(((....))).(((((.....((((((.....((((((.((.....)).)))))).)))))).)))))......))))... ( -35.40)
>DroSim_CAF1 11003 120 - 1
UCGUCGAUGGCAAGACACAGUGCAACCUGCCUAUGUCAACUGGCGCCGGGGCCCGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGA
.......((((..((((.((.((.....)))).))))..(((....))).(((((.....((((((.....((((((.((.....)).)))))).)))))).)))))......))))... ( -35.40)
>DroEre_CAF1 10896 117 - 1
---UCGAUGGCGGGACACAGUCCAACCUGCCUAUGUCAACUGGCGACGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCUGGGCAAACAAGCCAAGA
---....((((.((((...))))....((((((......(((((......))))).....((((((.....((((((.((.....)).)))))).)))))).)))))).....))))... ( -36.40)
>DroYak_CAF1 10863 117 - 1
---UCGAUGGCAAGACACAGUCCUACCUGCCUAUGUCAACUAGCGCCGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCUGGCAAACAAGCCAAGA
---....((((..(((((((......)))....)))).......((((((..........((((((.....((((((.((.....)).)))))).))))))))))))......))))... ( -29.90)
>consensus
UCGUCGAUGGCAAGACACAGUGCAACCUGCCUAUGUCAACUGGCGCCGGGGCCAGAACUACUUAUUGCAUGGCCAAACAAACAGAUUAUUUGGCAAAUAAGCCGGGCAAACAAGCCAAGA
.......((((..((((.((.((.....)))).))))..(((....))).(((((.....((((((.....((((((.((.....)).)))))).)))))).)))))......))))... (-28.70 = -29.22 +   0.52)

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 11:54:15 2006