Locus 4837

Sequence ID 3L_DroMel_CAF1
Location 13,565,820 – 13,565,936
Length 116
Max. P 0.915593
window7627 window7628 window7629

overview

Window 7

Location 13,565,820 – 13,565,911
Length 91
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -26.82
Consensus MFE -18.82
Energy contribution -18.07
Covariance contribution -0.75
Combinations/Pair 1.28
Mean z-score -1.19
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.505619
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13565820 91 + 23771897
---ACUAAGACAGACCUCGACC---UUACCUUUUGGGUGCAAUUUGCUGCGGCAGU------GGCAGUGGCAGCAAUUAAGCCAUAGGGUAGAUUAACAUUAA
---...................---(((((((...(((.....(((((((.((...------....)).)))))))....)))..)))))))........... ( -25.70)
>DroPse_CAF1 55059 91 + 1
AGAGCUGAGACUGCUCUGCUUCUGUUGGCCUUUUGGGUACAAUUUGCAGUGGC------------AGUGGCAGCAAUUAAGCCAUGAGGUAGAUUAACUUGAA
...((((..((((((((((....(((((((.....))).))))..)))).)))------------)))..))))......(((....)))............. ( -30.60)
>DroSec_CAF1 47392 91 + 1
---ACUAAGACAGACCUCGACC---UUGCCUUUUGGGUGCAAUUUGCUGCGGCAGU------GGCAGUGGCAGUAAUUAAGCCACAGGGUAGAUUAACAUUAA
---.............((.(((---(((((.....(.((((......)))).)...------))).(((((.........)))))))))).)).......... ( -23.50)
>DroSim_CAF1 33499 91 + 1
---ACUAAGACAGACCUCGACC---UUACCUUUUGGGUGCAAUUUGCUGCGGCACU------GGCAGUGGCAGCAAUUAAGCCAUAGGGUAGAUUAACAUUAA
---...................---(((((((...(((.....(((((((.((...------....)).)))))))....)))..)))))))........... ( -25.70)
>DroEre_CAF1 48126 91 + 1
---ACUUAGACAGACCUCGACC---UUACCUUUUGGGUGCAAUUUGCGGCGGCAGU------GGCAGUGGCAGCAAUUUAGCCAUGGGGUAGAUUAACAUUAA
---..........(((((.(((---(........))))......(((.((....))------.)))(((((.........))))))))))............. ( -21.70)
>DroPer_CAF1 54818 103 + 1
AGAACUGAGACUGCUCUGCUUCUGUUGGCCUUUUGGGUACAAUUUGCAGUGGCAGUGGCAGUGGCAGUGGCAGCAAUUAAGCCAUGAGGUAGAUUAACUUGAA
...((((..(((((((((((.((((..(((.....))).......)))).))))).))))))..))))(((.........))).(.((((......)))).). ( -33.70)
>consensus
___ACUAAGACAGACCUCGACC___UUACCUUUUGGGUGCAAUUUGCUGCGGCAGU______GGCAGUGGCAGCAAUUAAGCCAUAGGGUAGAUUAACAUUAA
.........................(((((((...(((.....((((.((.((.............)).)).))))....)))..)))))))........... (-18.82 = -18.07 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,565,839 – 13,565,936
Length 97
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -37.48
Consensus MFE -24.30
Energy contribution -25.35
Covariance contribution 1.06
Combinations/Pair 1.15
Mean z-score -2.44
Structure conservation index 0.65
SVM decision value 1.02
SVM RNA-class probability 0.901541
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13565839 97 + 23771897
--UUACCUUUUGGGUGCAAUUUGCUGCGGCAGU------GGCAGUGGCAGCAAUUAAGCCAUAGGGUAGAUUAACAUUAAGCUGCCGCCA--------GAGCGCGAUGCACUU
--...((....))(((((.(.((((((((((((------....(((((.........)))))...((......)).....))))))))..--------.)))).).))))).. ( -32.20)
>DroPse_CAF1 55082 101 + 1
GUUGGCCUUUUGGGUACAAUUUGCAGUGGC------------AGUGGCAGCAAUUAAGCCAUGAGGUAGAUUAACUUGAAGCUGCCGCUGCCUUUGACGAGACAGAUGCGCUC
(((((((.....))).))))((((((.(((------------(((((((((......(((....)))((.....))....)))))))))))).))).)))............. ( -34.10)
>DroSec_CAF1 47411 96 + 1
--UUGCCUUUUGGGUGCAAUUUGCUGCGGCAGU------GGCAGUGGCAGUAAUUAAGCCACAGGGUAGAUUAACAUUAAGCUGCCGCCG--------GAGCGCGAUGCACU-
--...((....))(((((.(.((((.((((...------....(((((.........)))))..(((((.(((....))).)))))))))--------.)))).).))))).- ( -37.60)
>DroEre_CAF1 48145 97 + 1
--UUACCUUUUGGGUGCAAUUUGCGGCGGCAGU------GGCAGUGGCAGCAAUUUAGCCAUGGGGUAGAUUAACAUUAAGCUGCCGCCG--------GGGCAAGAUGCACUU
--...((....))(((((.((((((((((((((------...((((.....((((((.((...)).))))))..))))..))))))))).--------..))))).))))).. ( -39.10)
>DroYak_CAF1 49877 96 + 1
--UUACCUUUUGGGUGCAAUUUGCUGCGGCAGU------GGCAGUGGCAGCAAUUAAGCCACAGGGUAGAUUAACAUUAAGCUGCCGCCG--------GGGCAAGAUGCACU-
--...((....))(((((.((((((.((((...------....(((((.........)))))..(((((.(((....))).)))))))))--------.)))))).))))).- ( -41.80)
>DroPer_CAF1 54841 113 + 1
GUUGGCCUUUUGGGUACAAUUUGCAGUGGCAGUGGCAGUGGCAGUGGCAGCAAUUAAGCCAUGAGGUAGAUUAACUUGAAGCUGCCGCUGCCUUUGACGAGACAGAUGCGCUC
(((((((.....))).))))((((((.((((((((((((..(.(((((.........))))).((((......)))))..)))))))))))).))).)))............. ( -40.10)
>consensus
__UUACCUUUUGGGUGCAAUUUGCUGCGGCAGU______GGCAGUGGCAGCAAUUAAGCCAUAGGGUAGAUUAACAUUAAGCUGCCGCCG________GAGCAAGAUGCACU_
.....((....))(((((.(((((.((((((((..........(((((.........)))))...((......)).....))))))))............))))).))))).. (-24.30 = -25.35 +   1.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,565,839 – 13,565,936
Length 97
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 80.69
Mean single sequence MFE -31.23
Consensus MFE -19.90
Energy contribution -20.35
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -2.59
Structure conservation index 0.64
SVM decision value 1.10
SVM RNA-class probability 0.915593
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13565839 97 - 23771897
AAGUGCAUCGCGCUC--------UGGCGGCAGCUUAAUGUUAAUCUACCCUAUGGCUUAAUUGCUGCCACUGCC------ACUGCCGCAGCAAAUUGCACCCAAAAGGUAA--
..(((((..((((..--------((((((((((.....(((((.(((.....))).))))).))))))...)))------)..).))).......)))))((....))...-- ( -28.10)
>DroPse_CAF1 55082 101 - 1
GAGCGCAUCUGUCUCGUCAAAGGCAGCGGCAGCUUCAAGUUAAUCUACCUCAUGGCUUAAUUGCUGCCACU------------GCCACUGCAAAUUGUACCCAAAAGGCCAAC
(((.((....)))))(((...(((((.((((((...((((((..........))))))....)))))).))------------)))..(((.....))).......))).... ( -30.40)
>DroSec_CAF1 47411 96 - 1
-AGUGCAUCGCGCUC--------CGGCGGCAGCUUAAUGUUAAUCUACCCUGUGGCUUAAUUACUGCCACUGCC------ACUGCCGCAGCAAAUUGCACCCAAAAGGCAA--
-.(((((....(((.--------((((((..((.....((......))...(((((.........))))).)).------.)))))).)))....)))))...........-- ( -30.70)
>DroEre_CAF1 48145 97 - 1
AAGUGCAUCUUGCCC--------CGGCGGCAGCUUAAUGUUAAUCUACCCCAUGGCUAAAUUGCUGCCACUGCC------ACUGCCGCCGCAAAUUGCACCCAAAAGGUAA--
..(((((..((((..--------.((((((((......((......))....((((.........)))).....------.))))))))))))..)))))((....))...-- ( -32.00)
>DroYak_CAF1 49877 96 - 1
-AGUGCAUCUUGCCC--------CGGCGGCAGCUUAAUGUUAAUCUACCCUGUGGCUUAAUUGCUGCCACUGCC------ACUGCCGCAGCAAAUUGCACCCAAAAGGUAA--
-.(((((..((((..--------((((((((((.....(((((.((((...)))).))))).))))))......------...))))..))))..)))))((....))...-- ( -33.10)
>DroPer_CAF1 54841 113 - 1
GAGCGCAUCUGUCUCGUCAAAGGCAGCGGCAGCUUCAAGUUAAUCUACCUCAUGGCUUAAUUGCUGCCACUGCCACUGCCACUGCCACUGCAAAUUGUACCCAAAAGGCCAAC
(((.((....)))))......(((((.((((((...((((((..........))))))....)))))).)))))...(((..(((....)))..(((....)))..))).... ( -33.10)
>consensus
_AGUGCAUCUCGCUC________CGGCGGCAGCUUAAUGUUAAUCUACCCCAUGGCUUAAUUGCUGCCACUGCC______ACUGCCGCAGCAAAUUGCACCCAAAAGGCAA__
..(((((................(((.((((((.....(((((.(((.....))).))))).)))))).)))..........(((....)))...)))))............. (-19.90 = -20.35 +   0.45)

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 11:34:48 2006