Locus 1412

Sequence ID 3R_DroMel_CAF1
Location 4,097,374 – 4,097,562
Length 188
Max. P 0.999849
window2343 window2344 window2345 window2346 window2347

overview

Window 3

Location 4,097,374 – 4,097,494
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.41
Mean single sequence MFE -33.32
Consensus MFE -25.44
Energy contribution -25.84
Covariance contribution 0.40
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.76
SVM decision value 0.43
SVM RNA-class probability 0.731902
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4097374 120 - 27905053
UUCAACCGCAAAGGUCACUUAUAGUUAGCUGAAGUGACCACACAGAGACUGGAAGGAUGAAUCUGGUCAGGUAGCUGAGGACAUUGCCUAAGAAGGGGAAAAUUCCCAGCAAAUUAGCAG
....(((.....((((((((.(((....))))))))))).......(((..((........))..))).))).((((.(((..((.(((.....))).))...))))))).......... ( -38.60)
>DroSec_CAF1 9313 119 - 1
UACAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCACACAGAGGCUGAAACGAAGAAUCUGGUCAGGUAGCUGA-GACAUUGCCUAAGAAUGGGAAAAUUCCCAGCAAAUUAGCAG
....(((......(((((((.(((....))))))))))....((((..((.......))..))))....))).(((((-....((((.......(((((....))))))))).))))).. ( -32.91)
>DroSim_CAF1 9344 120 - 1
UUCAACCGCAAAUGUCACUUAUAUUUAGCUGAAGUGACCACACAGAGGCUGAAACGAAAAAUCUGGUCAGGUAGCUGAGGACAUUGCCUAAGAAGGGGAAAAUUCCCAGCAAAUUAGCAG
(((....((((.((((.((((..(((((((...(((....)))...))))))).......((((....))))...))))))))))))....))).((((....)))).((......)).. ( -28.70)
>DroEre_CAF1 9360 118 - 1
UUCAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCACACAGCGGCUGGAAGGG--AAUCUGGUCAGGUAGCAAAGAACAUUGCCUAAGAGGGGGAAAAUUCCCAGCAAUUUAGCAG
((((.((((....(((((((.(((....))))))))))......)))).)))).(((--(((((..((((((((.........))))))..))..))....)))))).((......)).. ( -32.00)
>DroYak_CAF1 9317 119 - 1
UUCAACCGCAAAUGUCACUUAAAGUUAGCUGAAGUGACCACACAGCGACUAGAAGGG-CAAUUUGGUCUGGUAGCGGGGGACAUUGCCGAAGGGAGGGAACAUUCCCAGCAAAUUAGCAG
.((..((((....(((((((..((....)).)))))))........(((((((....-...))))))).....))))..)).....((....)).((((....)))).((......)).. ( -34.40)
>consensus
UUCAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCACACAGAGGCUGGAAGGA_GAAUCUGGUCAGGUAGCUGAGGACAUUGCCUAAGAAGGGGAAAAUUCCCAGCAAAUUAGCAG
....(((......(((((((.(((....))))))))))........(((((((........))))))).))).(((((.....((((........((((....)))).)))).))))).. (-25.44 = -25.84 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,097,414 – 4,097,534
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.33
Mean single sequence MFE -29.46
Consensus MFE -27.39
Energy contribution -27.99
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.93
SVM decision value 4.25
SVM RNA-class probability 0.999849
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4097414 120 + 27905053
CCUCAGCUACCUGACCAGAUUCAUCCUUCCAGUCUCUGUGUGGUCACUUCAGCUAACUAUAAGUGACCUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCC
....((((...((((((.((.................)).))))))....))))..(((...(((((..(((((..(((((((....))))))).....)))))..)))))..))).... ( -29.23)
>DroSec_CAF1 9353 119 + 1
C-UCAGCUACCUGACCAGAUUCUUCGUUUCAGCCUCUGUGUGGUCACUUCAGCUAACUAUAAGUGACAUUUGCGGUUGUAAAUAUCAAUUUCCAUAAAAUGCAAUUGUCACCUUAGCGCC
.-..((((...((((((.((.....((....))....)).))))))....))))..(((...((((((.(((((..((.((((....)))).)).....))))).))))))..))).... ( -27.60)
>DroSim_CAF1 9384 120 + 1
CCUCAGCUACCUGACCAGAUUUUUCGUUUCAGCCUCUGUGUGGUCACUUCAGCUAAAUAUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUCCAUAAAAUGCAAUUGUCACCUUAGCGCC
.....((....((((((.((.....((....))....)).)))))).....(((((......((((((.((((((((((.....)))))..........))))).)))))).))))))). ( -27.30)
>DroEre_CAF1 9400 118 + 1
UCUUUGCUACCUGACCAGAUU--CCCUUCCAGCCGCUGUGUGGUCACUUCAGCUAACUAUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCC
.....((....((((((.((.--..............)).)))))).....(((((......((((((.(((((..(((((((....))))))).....))))).)))))).))))))). ( -30.66)
>DroYak_CAF1 9357 119 + 1
CCCCCGCUACCAGACCAAAUUG-CCCUUCUAGUCGCUGUGUGGUCACUUCAGCUAACUUUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCC
....(((((...(((((....(-(..........))....))))).................((((((.(((((..(((((((....))))))).....))))).))))))..))))).. ( -32.50)
>consensus
CCUCAGCUACCUGACCAGAUUC_UCCUUCCAGCCUCUGUGUGGUCACUUCAGCUAACUAUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCC
.....((.....(((((.((.................)).)))))......(((((......((((((.(((((..(((((((....))))))).....))))).)))))).))))))). (-27.39 = -27.99 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,097,414 – 4,097,534
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.33
Mean single sequence MFE -33.88
Consensus MFE -28.72
Energy contribution -29.00
Covariance contribution 0.28
Combinations/Pair 1.17
Mean z-score -1.99
Structure conservation index 0.85
SVM decision value 1.91
SVM RNA-class probability 0.982113
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4097414 120 - 27905053
GGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAGGUCACUUAUAGUUAGCUGAAGUGACCACACAGAGACUGGAAGGAUGAAUCUGGUCAGGUAGCUGAGG
(((((...(....)....))......(((((((....)))))))(((.....((((((((.(((....))))))))))).......(((..((........))..))).))).))).... ( -35.30)
>DroSec_CAF1 9353 119 - 1
GGCGCUAAGGUGACAAUUGCAUUUUAUGGAAAUUGAUAUUUACAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCACACAGAGGCUGAAACGAAGAAUCUGGUCAGGUAGCUGA-G
...((((((((((((.((((......((.((((....)))).))...)))).)))))))).))))((((((...((((((....((..((.......))..))))))))..)))))).-. ( -31.80)
>DroSim_CAF1 9384 120 - 1
GGCGCUAAGGUGACAAUUGCAUUUUAUGGAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAUAUUUAGCUGAAGUGACCACACAGAGGCUGAAACGAAAAAUCUGGUCAGGUAGCUGAGG
.......((((((((.((((......(((((((....)))))))...)))).))))))))...((((((((...((((((..(((...)))....((....))))))))..)))))))). ( -33.10)
>DroEre_CAF1 9400 118 - 1
GGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCACACAGCGGCUGGAAGGG--AAUCUGGUCAGGUAGCAAAGA
.((((((((((((((.((((......(((((((....)))))))...)))).)))))))).))))..((((..((....)).))))(((..((....--..))..))).....))..... ( -34.70)
>DroYak_CAF1 9357 119 - 1
GGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAAAGUUAGCUGAAGUGACCACACAGCGACUAGAAGGG-CAAUUUGGUCUGGUAGCGGGGG
..(((((((((((((.((((......(((((((....)))))))...)))).)))))))).......((((..((....)).))))(((((((....-...)))))))...))))).... ( -34.50)
>consensus
GGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCACACAGAGGCUGGAAGGA_GAAUCUGGUCAGGUAGCUGAGG
.......((((((((.((((......(((((((....)))))))...)))).))))))))....(((((((..(((....)))...(((((((........)))))))...))))))).. (-28.72 = -29.00 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,097,454 – 4,097,562
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -28.02
Consensus MFE -24.77
Energy contribution -25.57
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.88
SVM decision value 2.12
SVM RNA-class probability 0.988350
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4097454 108 + 27905053
UGGUCACUUCAGCUAACUAUAAGUGACCUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCCGAGACCUCCCCCAAU------------GUCAGCGCGCCAA
((((...............((((((((..(((((..(((((((....))))))).....)))))..)))).))))((((...(((..........------------))).)))))))). ( -27.50)
>DroSec_CAF1 9392 120 + 1
UGGUCACUUCAGCUAACUAUAAGUGACAUUUGCGGUUGUAAAUAUCAAUUUCCAUAAAAUGCAAUUGUCACCUUAGCGCCGAGACCUCCCCCAAUGAUCAAGAAACUGUCAGCGCGCCAA
((((...............(((((((((.(((((..((.((((....)))).)).....))))).))))).))))((((.((....))......(((.((......))))))))))))). ( -25.00)
>DroSim_CAF1 9424 120 + 1
UGGUCACUUCAGCUAAAUAUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUCCAUAAAAUGCAAUUGUCACCUUAGCGCCGAGACCUCCCCCAAUGAUCAAGAAACUGUCAGCGCGCCAA
((((...............(((((((((.((((((((((.....)))))..........))))).))))).))))((((.((....))......(((.((......))))))))))))). ( -25.10)
>DroEre_CAF1 9438 120 + 1
UGGUCACUUCAGCUAACUAUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCCGAGACCUCCCCCAAUGAUCAAGAAACUGUCAGCGGGCCAA
.((((.(....(((((......((((((.(((((..(((((((....))))))).....))))).)))))).)))))...).))))...(((..(((.((......)))))..))).... ( -33.20)
>DroYak_CAF1 9396 120 + 1
UGGUCACUUCAGCUAACUUUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCCGAGACCUCCCCCAAUGAUCAAGAAACUGUCAGCGCGCCAA
((((..................((((((.(((((..(((((((....))))))).....))))).))))))....((((.((....))......(((.((......))))))))))))). ( -29.30)
>consensus
UGGUCACUUCAGCUAACUAUAAGUGACAUUUGCGGUUGAAAAUAUCAAUUUUCAUAAAAUGCAAUUGUCACCUUAGCGCCGAGACCUCCCCCAAUGAUCAAGAAACUGUCAGCGCGCCAA
((((...............(((((((((.(((((..(((((((....))))))).....))))).))))).))))((((...(((......................))).)))))))). (-24.77 = -25.57 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,097,454 – 4,097,562
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -37.92
Consensus MFE -32.72
Energy contribution -34.80
Covariance contribution 2.08
Combinations/Pair 1.03
Mean z-score -2.60
Structure conservation index 0.86
SVM decision value 3.33
SVM RNA-class probability 0.999011
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4097454 108 - 27905053
UUGGCGCGCUGAC------------AUUGGGGGAGGUCUCGGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAGGUCACUUAUAGUUAGCUGAAGUGACCA
...(((((((((.------------(((......))).)))))))(((((((.(....))))))))(((((((....)))))))...))...((((((((.(((....))))))))))). ( -35.50)
>DroSec_CAF1 9392 120 - 1
UUGGCGCGCUGACAGUUUCUUGAUCAUUGGGGGAGGUCUCGGCGCUAAGGUGACAAUUGCAUUUUAUGGAAAUUGAUAUUUACAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCA
(..(((((((((.(.((((((.(....).)))))).).)))))))..((((((((.((((......((.((((....)))).))...)))).)))))))).......))..)........ ( -35.10)
>DroSim_CAF1 9424 120 - 1
UUGGCGCGCUGACAGUUUCUUGAUCAUUGGGGGAGGUCUCGGCGCUAAGGUGACAAUUGCAUUUUAUGGAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAUAUUUAGCUGAAGUGACCA
(..(((((((((.(.((((((.(....).)))))).).)))))))..((((((((.((((......(((((((....)))))))...)))).)))))))).......))..)........ ( -39.00)
>DroEre_CAF1 9438 120 - 1
UUGGCCCGCUGACAGUUUCUUGAUCAUUGGGGGAGGUCUCGGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCA
....((((.((((((....))).))).))))...(((((((((((((((((((((.((((......(((((((....)))))))...)))).)))))))).))))..)))))...)))). ( -40.50)
>DroYak_CAF1 9396 120 - 1
UUGGCGCGCUGACAGUUUCUUGAUCAUUGGGGGAGGUCUCGGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAAAGUUAGCUGAAGUGACCA
(..(((((((((.(.((((((.(....).)))))).).)))))))..((((((((.((((......(((((((....)))))))...)))).)))))))).......))..)........ ( -39.50)
>consensus
UUGGCGCGCUGACAGUUUCUUGAUCAUUGGGGGAGGUCUCGGCGCUAAGGUGACAAUUGCAUUUUAUGAAAAUUGAUAUUUUCAACCGCAAAUGUCACUUAUAGUUAGCUGAAGUGACCA
(..(((((((((.(.((((((.(....).)))))).).)))))))..((((((((.((((......(((((((....)))))))...)))).)))))))).......))..)........ (-32.72 = -34.80 +   2.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:47 2006