Locus 8411

Sequence ID X_DroMel_CAF1
Location 20,883,219 – 20,883,494
Length 275
Max. P 0.788758
window13814 window13815 window13816 window13817 window13818

overview

Window 4

Location 20,883,219 – 20,883,339
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 73.96
Mean single sequence MFE -26.58
Consensus MFE -12.99
Energy contribution -17.43
Covariance contribution 4.44
Combinations/Pair 1.16
Mean z-score -2.17
Structure conservation index 0.49
SVM decision value 0.58
SVM RNA-class probability 0.788758
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20883219 120 + 22224390
UCCGGUAAACGGAAUCGUUGGAUUAUUCCUAUUGAUAAGUGAUCAAUUCAUUCAUUUAACUAACUUUCAAUUCAUCCUUAACCGUGUAAACUCAUUCAGGGCUUCAGGCCCAGUGAAUCC
..((((.((.(((.(((..(((....)))...)))(((((((.........)))))))................))))).)))).......(((((..((((.....))))))))).... ( -25.60)
>DroSec_CAF1 3318 104 + 1
UCCGGUAAACGAAAACGUUGGAUUGAUCCUUUUGUUAAGUGAUCAAUUGA----------------UCAAUUCAUCUUUUACCGAAUAAACUCAUUCAGGGCUUCAGGUCCAGUGAAUCC
..(((((((.((....(((((((((((((((.....))).))))))))..----------------.))))...)).))))))).......(((((..((((.....))))))))).... ( -26.40)
>DroSim_CAF1 3910 104 + 1
UCCGGUAAACGAAAACGUUGGAUUGAUCCUUUUGUUAAGUGAUCAAUUGA----------------UCAAUUCAUCUUUUACCGGAUAAACUUAUUCAGGGCUUCAGGCCCAGUGAAUCC
(((((((((.((....(((((((((((((((.....))).))))))))..----------------.))))...)).))))))))).......(((((((((.....))))..))))).. ( -32.90)
>DroYak_CAF1 4095 90 + 1
UUCGCUAAACGGAAACGCUGGC-------------CAAGUUAACAGUCCU----------------GCAAUGCAUCUUUAACCGGAUGAACUCAUUCAUGGCUUCAGGCCCAG-GAAACC
...((((..((....)).))))-------------...........((((----------------(................(((((....)))))..(((.....))))))-)).... ( -21.40)
>consensus
UCCGGUAAACGAAAACGUUGGAUUGAUCCUUUUGUUAAGUGAUCAAUUCA________________UCAAUUCAUCUUUAACCGGAUAAACUCAUUCAGGGCUUCAGGCCCAGUGAAUCC
((((((.((((....))))((((((((((((.....))).)))))))))...............................)))))).....(((((..((((.....))))))))).... (-12.99 = -17.43 +   4.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,883,299 – 20,883,416
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.84
Mean single sequence MFE -34.85
Consensus MFE -24.83
Energy contribution -25.57
Covariance contribution 0.75
Combinations/Pair 1.19
Mean z-score -1.92
Structure conservation index 0.71
SVM decision value 0.35
SVM RNA-class probability 0.700727
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20883299 117 + 22224390
ACCGUGUAAACUCAUUCAGGGCUUCAGGCCCAGUGAAUCCUUUUUGGCCAUUAAGAAGUCAAUUGAAUCUGCCUCGGGAAGCAACUGUUCCGAUCUCAUUCAGAGAUUGGCCAAAGU---
...........(((((..((((.....))))))))).....(((((((((...(((..((....)).)))...((((((........))))))((((.....)))).))))))))).--- ( -31.50)
>DroSec_CAF1 3382 113 + 1
ACCGAAUAAACUCAUUCAGGGCUUCAGGUCCAGUGAAUCCUUUUUGGCCAUUA----GUCAAUUGAAUCUACCUCGGGAGGCAACUGUUCCCAUCUCAUUCAGAGAUUGGCCAAAGU---
...........(((((..((((.....))))))))).....(((((((((...----..................(((((....)...))))(((((.....)))))))))))))).--- ( -30.10)
>DroSim_CAF1 3974 113 + 1
ACCGGAUAAACUUAUUCAGGGCUUCAGGCCCAGUGAAUCCUUUUUGGCCAUUA----GUCAAUUGAAUCUGCCUCGGGAGGCAACUGUUCCGAUCUCAUUCAGAGAUUGGCCAAAGU---
...((((..(((......((((.....)))))))..)))).((((((((....----.......((((.(((((....)))))...)))).((((((.....)))))))))))))).--- ( -37.70)
>DroYak_CAF1 4146 115 + 1
ACCGGAUGAACUCAUUCAUGGCUUCAGGCCCAG-GAAACCUUUUUGGCCAUUA----GUCAGUUGGAUCUGCCUCGAGAAGAAGCUGAUCCGAUCGCAUUCAGAGAUUGGCCAAAGUGGA
.(((((((....)))))..(((.....)))..)-)...((.(((((((((...----(((..(((((((.((.((.....)).)).)))))))((.......)))))))))))))).)). ( -40.10)
>consensus
ACCGGAUAAACUCAUUCAGGGCUUCAGGCCCAGUGAAUCCUUUUUGGCCAUUA____GUCAAUUGAAUCUGCCUCGGGAAGCAACUGUUCCGAUCUCAUUCAGAGAUUGGCCAAAGU___
...(((((....))))).((((.....))))..........((((((((..........((.(((..(((......)))..))).))....((((((.....)))))))))))))).... (-24.83 = -25.57 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,883,299 – 20,883,416
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.84
Mean single sequence MFE -34.83
Consensus MFE -27.89
Energy contribution -28.70
Covariance contribution 0.81
Combinations/Pair 1.15
Mean z-score -1.72
Structure conservation index 0.80
SVM decision value 0.49
SVM RNA-class probability 0.754820
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20883299 117 - 22224390
---ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGCUUCCCGAGGCAGAUUCAAUUGACUUCUUAAUGGCCAAAAAGGAUUCACUGGGCCUGAAGCCCUGAAUGAGUUUACACGGU
---..(((((((((((((.....)))))..(((...((((((....)))))).)))..............))))))))..(((((((..((((.....))))....)))))))....... ( -34.30)
>DroSec_CAF1 3382 113 - 1
---ACUUUGGCCAAUCUCUGAAUGAGAUGGGAACAGUUGCCUCCCGAGGUAGAUUCAAUUGAC----UAAUGGCCAAAAAGGAUUCACUGGACCUGAAGCCCUGAAUGAGUUUAUUCGGU
---..(((((((((((((.....)))))..(((...((((((....)))))).))).......----...))))))))..((.((((.......)))).))(((((((....))))))). ( -31.80)
>DroSim_CAF1 3974 113 - 1
---ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGCCUCCCGAGGCAGAUUCAAUUGAC----UAAUGGCCAAAAAGGAUUCACUGGGCCUGAAGCCCUGAAUAAGUUUAUCCGGU
---..(((((((((((((.....)))))..(((...((((((....)))))).))).......----...))))))))..((((..(((((((.....))))......)))..))))... ( -37.40)
>DroYak_CAF1 4146 115 - 1
UCCACUUUGGCCAAUCUCUGAAUGCGAUCGGAUCAGCUUCUUCUCGAGGCAGAUCCAACUGAC----UAAUGGCCAAAAAGGUUUC-CUGGGCCUGAAGCCAUGAAUGAGUUCAUCCGGU
.((..(((((((((((.(.....).))).(((((.(((((.....))))).))))).......----...))))))))..((((((-........))))))(((((....)))))..)). ( -35.80)
>consensus
___ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGCCUCCCGAGGCAGAUUCAAUUGAC____UAAUGGCCAAAAAGGAUUCACUGGGCCUGAAGCCCUGAAUGAGUUUAUCCGGU
.....(((((((((((((.....))))).(((....((((((....)))))).)))..............))))))))..(((((((..((((.....))))....)))))))....... (-27.89 = -28.70 +   0.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,883,339 – 20,883,454
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.63
Mean single sequence MFE -32.42
Consensus MFE -27.73
Energy contribution -27.48
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -1.47
Structure conservation index 0.86
SVM decision value 0.14
SVM RNA-class probability 0.603405
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20883339 115 - 22224390
GCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU-----ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGCUUCCCGAGGCAGAUUCAAUUGACUUCUUAAUGGCCAAAAA
((((((......(((((.(((..(((((((...(((..-----.....)))..)))))))..))))))))....)))))).......((((((.((....))..))).....)))..... ( -29.50)
>DroSec_CAF1 3422 111 - 1
GCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU-----ACUUUGGCCAAUCUCUGAAUGAGAUGGGAACAGUUGCCUCCCGAGGUAGAUUCAAUUGAC----UAAUGGCCAAAAA
.......((((....)))).(((((.((.((((..(((-----(((((((...(((((.....)))))(((........))).))))))))))....)))).)----)..)))))..... ( -32.00)
>DroSim_CAF1 4014 111 - 1
GCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU-----ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGCCUCCCGAGGCAGAUUCAAUUGAC----UAAUGGCCAAAAA
((.(((..(((.(((((.(((..(((((((...(((..-----.....)))..)))))))..))))))))(((...((((((....)))))).)))..)))..----.))).))...... ( -32.10)
>DroYak_CAF1 4185 116 - 1
GCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCUGCUCCACUUUGGCCAAUCUCUGAAUGCGAUCGGAUCAGCUUCUUCUCGAGGCAGAUCCAACUGAC----UAAUGGCCAAAAA
.......((((....)))).((.(((((......)))))..))..(((((((((((.(.....).))).(((((.(((((.....))))).))))).......----...)))))))).. ( -36.10)
>consensus
GCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU_____ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGCCUCCCGAGGCAGAUUCAAUUGAC____UAAUGGCCAAAAA
((.....))(..((.....))..)((((......)))).......(((((((((((((.....))))).(((....((((((....)))))).)))..............)))))))).. (-27.73 = -27.48 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,883,379 – 20,883,494
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -26.27
Consensus MFE -22.30
Energy contribution -22.12
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.54
Structure conservation index 0.85
SVM decision value 0.25
SVM RNA-class probability 0.652405
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20883379 115 - 22224390
AUAAAUAAAAAGUACACAUAAGUAUUAAAACCGAAACAGAGCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU-----ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGC
..........(((((......)))))..............((((((......(((((.(((..(((((((...(((..-----.....)))..)))))))..))))))))....)))))) ( -26.20)
>DroSec_CAF1 3458 108 - 1
-------AAAAGUACACAUAAGUAUUAAAACCGAAACGGAGCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU-----ACUUUGGCCAAUCUCUGAAUGAGAUGGGAACAGUUGC
-------...(((((......)))))....(((...))).((((((.((((....)))).((((((((.((......)-----))))))))).(((((.....)))))......)))))) ( -26.80)
>DroSim_CAF1 4050 108 - 1
-------AAAAGUACACAUAAGUAUUAAAACCGAAACAGAGCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU-----ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGC
-------...(((((......)))))..............((((((......(((((.(((..(((((((...(((..-----.....)))..)))))))..))))))))....)))))) ( -26.20)
>DroYak_CAF1 4221 113 - 1
-------AAAAGUACACAUAAGUAUUAAAACCAAAACAGAGCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCUGCUCCACUUUGGCCAAUCUCUGAAUGCGAUCGGAUCAGCUUC
-------...(((((......)))))..........((((....)))).((.(((((((.((((((((.....((...))....))))))))..((...))..)))))))..))...... ( -25.90)
>consensus
_______AAAAGUACACAUAAGUAUUAAAACCGAAACAGAGCAAUUUGCGAACGAUCGUCGGCCAGAGAUAAUGCUCU_____ACUUUGGCCAAUCUCUGAAUGAGAUCGGAACAGUUGC
..........(((((......)))))..........(((((......((((....)))).((((((((................))))))))...))))).................... (-22.30 = -22.12 +  -0.19)

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 13:03:21 2006