Locus 4323

Sequence ID 2L_DroMel_CAF1
Location 12,373,977 – 12,374,107
Length 130
Max. P 0.942375
window6811 window6812 window6813

overview

Window 1

Location 12,373,977 – 12,374,067
Length 90
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 85.80
Mean single sequence MFE -22.07
Consensus MFE -17.24
Energy contribution -18.30
Covariance contribution 1.06
Combinations/Pair 1.10
Mean z-score -2.64
Structure conservation index 0.78
SVM decision value 0.60
SVM RNA-class probability 0.795004
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12373977 90 + 22407834
AAGCCAUCCCA--ACCACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAAC
...........--.............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))... ( -22.80)
>DroVir_CAF1 245995 88 + 1
-CGCCACCCCCGCAGCACCAACUUCAGCAGCA---GCAGCCCACAAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAAC
-.(((......((.((..........)).)).---.............(((((((....)))))))..(((((.....)))))...)))... ( -22.30)
>DroSec_CAF1 198036 90 + 1
AAGCCAUCCCA--ACCAUCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAAC
...........--.............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))... ( -22.80)
>DroSim_CAF1 203286 90 + 1
AAGCCAUCCCA--ACCAUCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAAC
...........--.............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))... ( -22.80)
>DroWil_CAF1 254962 84 + 1
--GUCAUCGCC--CCCUCCGAC----GCCCUCAUCGAUGUCCGCAAACAUGACCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACAGCGAC
--((.((((((--......(((----(.(......).)))).((((..(((.(((....))).)))...))))....)))))).))...... ( -18.90)
>DroYak_CAF1 206114 90 + 1
AAGCCAUCCCA--ACCACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAAC
...........--.............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))... ( -22.80)
>consensus
AAGCCAUCCCA__ACCACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAAC
..........................(((((..((...(((.((((..(((((((....)))))))...))))....)))))..)))))... (-17.24 = -18.30 +   1.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,373,990 – 12,374,107
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.35
Mean single sequence MFE -31.10
Consensus MFE -21.69
Energy contribution -22.25
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.83
Structure conservation index 0.70
SVM decision value 0.52
SVM RNA-class probability 0.767466
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12373990 117 + 22407834
CACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCGCCGAAUCCGGCGCCAUAUUUAGUU
...........((((............((((..(((((((....)))))))...))))...((((....(((....)))...(((....)))))))....))))............. ( -36.70)
>DroVir_CAF1 246009 114 + 1
CACCAACUUCAGCAGCA---GCAGCCCACAAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACCAAAUCCGGCGCCAUAUUUAGUU
....((((......((.---((((((.......(((((((....)))))))..(((((.....))))).(((....)))...)))))).(((.........))))).......)))) ( -35.72)
>DroGri_CAF1 252910 97 + 1
--------------------ACAGUCCACAAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUACCGCCACCAAAUCCGGCGCCAUAUUUAGUU
--------------------.........(((.(((((......((((((...(((((.....))))).(((....)))..))))))..(((.........)))))))).))).... ( -27.30)
>DroWil_CAF1 254973 113 + 1
CUCCGAC----GCCCUCAUCGAUGUCCGCAAACAUGACCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACAGCGACCUAUUGGCUACCCCCACCGAAUCCGGCGCCAUAUUUAGUU
....(.(----(((....(((((((......)))).........((((((...((((((((....))).))))).......)))))).......)))....)))).).......... ( -22.60)
>DroMoj_CAF1 250797 97 + 1
--------------------GCAGCCCACUAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACCAAAUCCGGCGCCAUAUUUAGUU
--------------------((((((.......(((((((....)))))))..(((((.....))))).(((....)))...))))))((((.........))))............ ( -34.10)
>DroAna_CAF1 185452 117 + 1
CACCAGCACCACACCUCGCCAGUGUCCACAAGCAUGACCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACCGAAUCCGGCGCCAUAUUUAGUU
...............(((((.(((..((......))..)))..(((((.....)))))....)))))..(((....)))..((((.((((..........))))))))......... ( -30.20)
>consensus
CACC_AC____GCC_UC___GCAGUCCACAAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACCAAAUCCGGCGCCAUAUUUAGUU
..............................((((((((((....)))))))...........((((...(((....)))..((((....))))((......)))))).......))) (-21.69 = -22.25 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,373,990 – 12,374,107
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.35
Mean single sequence MFE -44.05
Consensus MFE -36.20
Energy contribution -36.20
Covariance contribution 0.00
Combinations/Pair 1.15
Mean z-score -2.55
Structure conservation index 0.82
SVM decision value 1.33
SVM RNA-class probability 0.942375
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12373990 117 - 22407834
AACUAAAUAUGGCGCCGGAUUCGGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGACGGCUGGAGUGGGUG
.(((.........((((....))))(((....)))..(((...((((((....(((..(((((...(((((((....)))))))..)))))....)))..))))))....)))))). ( -43.20)
>DroVir_CAF1 246009 114 - 1
AACUAAAUAUGGCGCCGGAUUUGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGGCUGC---UGCUGCUGAAGUUGGUG
............((((((.((..(..(((((((((....(((..(((.......)))..)))....(((((((....))))))).......))))))---)))..)..)).)))))) ( -50.90)
>DroGri_CAF1 252910 97 - 1
AACUAAAUAUGGCGCCGGAUUUGGUGGCGGUAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACUGU--------------------
...((((((((((.((((....((((((((((((......)))))))))))).)))).(((((.((.....)).)))))))))))))))........-------------------- ( -38.00)
>DroWil_CAF1 254973 113 - 1
AACUAAAUAUGGCGCCGGAUUCGGUGGGGGUAGCCAAUAGGUCGCUGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGCGGACAUCGAUGAGGGC----GUCGGAG
.........((((((((.(((((((((.((..(((....)))..))....))))))))).)..((.(((((((....)))))(((((....)))))..)).)))))----))))... ( -38.90)
>DroMoj_CAF1 250797 97 - 1
AACUAAAUAUGGCGCCGGAUUUGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUAGUGGGCUGC--------------------
..........(((.((((....((((((((((((......)))))))))))).))))...(.(((((((((((....))))))..))))).))))..-------------------- ( -42.60)
>DroAna_CAF1 185452 117 - 1
AACUAAAUAUGGCGCCGGAUUCGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGUCAUGCUUGUGGACACUGGCGAGGUGUGGUGCUGGUG
..........(((((((.((((((((((((((((......))))))))))))(((((.(((((...(((((((....)))))))..)))))....))))))).)).))))))).... ( -50.70)
>consensus
AACUAAAUAUGGCGCCGGAUUCGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAGC___GA_GGC____GU_GGUG
...((((((((((.((((...(((((((((((((......))))))))))))))))).(((((.((.....)).)))))))))))))))............................ (-36.20 = -36.20 +   0.00)

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 11:15:03 2006