Locus 2494

Sequence ID 3R_DroMel_CAF1
Location 6,826,302 – 6,826,471
Length 169
Max. P 0.959558
window4084 window4085 window4086

overview

Window 4

Location 6,826,302 – 6,826,392
Length 90
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 86.99
Mean single sequence MFE -18.92
Consensus MFE -13.36
Energy contribution -14.08
Covariance contribution 0.72
Combinations/Pair 1.11
Mean z-score -3.48
Structure conservation index 0.71
SVM decision value 0.33
SVM RNA-class probability 0.692055
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6826302 90 + 27905053
UGUAAGCAGCCGGAAAAAAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUGAGCGGCCGAAGCACAA-------AAAAAAAAAUCAAAGAAGA-A
(((...(.(((((((((((.(((((......)))))...))))))))..((....))))).)..)))...-------...................-. ( -19.30)
>DroSec_CAF1 85396 86 + 1
UGUAAGCAGCCGGAAA-AAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUCAGCGGCCCAAGCACAA-------AA---AAAAUCAAAGAAGA-A
.....((.((((((((-((((((((......)))))...))))))))..((....)))))....))....-------..---..............-. ( -18.90)
>DroSim_CAF1 91311 90 + 1
UGUAAGCAGCCGGAAAAAAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUCAGCGGCCCAAGCACAA-------AAAAAAAAAUCAAAGAAGA-A
.....((.(((((((((((.(((((......)))))...))))))))..((....)))))....))....-------...................-. ( -19.00)
>DroEre_CAF1 70317 96 + 1
UGUAAGCAGCCGGAAAAAAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUCAGCGGGCCGG-CAAAAAAAAAAAGAAAAAAAAUCAAAGAAGA-A
........(((((((((((.(((((......)))))...))))))))..((((....)))).))-)..............................-. ( -22.50)
>DroYak_CAF1 83638 87 + 1
UGUAAGCAGCCGGAAAAGAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUCAGCGGCCCAGGCAACA----------AAAAAAUCAAAGAAGA-A
........(((((((((((.(((((......)))))...))))))))..(((.....)))...)))....----------................-. ( -21.70)
>DroAna_CAF1 41909 86 + 1
UGUAAGCAACCGA-GAAAAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUGAGCAGCCAAA-CAAAA----------AAAAAUUGAAAGAAGAAA
(((..((....((-(((((.(((((......)))))...)))))))..(((....)))))...)-))...----------.................. ( -12.10)
>consensus
UGUAAGCAGCCGGAAAAAAAACACAUUAAAUUGUGUAAAUUUUUUCCAUGCCUCAGCGGCCCAAGCAAAA_______AA_AAAAAAUCAAAGAAGA_A
........(((((((((((.(((((......)))))...))))))))..((....)))))...................................... (-13.36 = -14.08 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,826,302 – 6,826,392
Length 90
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 86.99
Mean single sequence MFE -20.03
Consensus MFE -17.17
Energy contribution -17.62
Covariance contribution 0.45
Combinations/Pair 1.16
Mean z-score -2.65
Structure conservation index 0.86
SVM decision value 1.50
SVM RNA-class probability 0.959558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6826302 90 - 27905053
U-UCUUCUUUGAUUUUUUUUU-------UUGUGCUUCGGCCGCUCAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUUUUUUCCGGCUGCUUACA
.-...................-------.((((...(((((((....))..((((((((...(((((......))))).)))))))))))))..)))) ( -23.90)
>DroSec_CAF1 85396 86 - 1
U-UCUUCUUUGAUUUU---UU-------UUGUGCUUGGGCCGCUGAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUU-UUUCCGGCUGCUUACA
.-..............---..-------....((...((((((....))..((((((((...(((((......))))))))-)))))))))))..... ( -19.90)
>DroSim_CAF1 91311 90 - 1
U-UCUUCUUUGAUUUUUUUUU-------UUGUGCUUGGGCCGCUGAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUUUUUUCCGGCUGCUUACA
.-...................-------....((...((((((....))..((((((((...(((((......))))).))))))))))))))..... ( -21.40)
>DroEre_CAF1 70317 96 - 1
U-UCUUCUUUGAUUUUUUUUCUUUUUUUUUUUG-CCGGCCCGCUGAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUUUUUUCCGGCUGCUUACA
.-..............................(-((.(((......)))..((((((((...(((((......))))).)))))))))))........ ( -22.00)
>DroYak_CAF1 83638 87 - 1
U-UCUUCUUUGAUUUUUU----------UGUUGCCUGGGCCGCUGAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUCUUUUCCGGCUGCUUACA
.-................----------.((.(((...(((.....)))..((((((.....(((((......)))))...))))))))).))..... ( -20.80)
>DroAna_CAF1 41909 86 - 1
UUUCUUCUUUCAAUUUUU----------UUUUG-UUUGGCUGCUCAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUUUUC-UCGGUUGCUUACA
...........(((((((----------(((((-(((((....))))))).)))))))))).(((((......)))))......-............. ( -12.20)
>consensus
U_UCUUCUUUGAUUUUUU_UU_______UUGUGCUUGGGCCGCUGAGGCAUGGAAAAAAUUUACACAAUUUAAUGUGUUUUUUUUCCGGCUGCUUACA
.....................................((((((....))..((((((((...(((((......))))).))))))))))))....... (-17.17 = -17.62 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 6,826,368 – 6,826,471
Length 103
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 86.62
Mean single sequence MFE -20.42
Consensus MFE -15.54
Energy contribution -16.23
Covariance contribution 0.70
Combinations/Pair 1.05
Mean z-score -2.21
Structure conservation index 0.76
SVM decision value -0.03
SVM RNA-class probability 0.518508
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6826368 103 + 27905053
ACAA-------AAAAAAAAAUCAAAGAAGA-ACCAAAAAUACUAAGCAUCUUAGGCAUUUUCCUGCUGGCCUUUUAAAGAUGUU-UGGGCUUCCCUCACUAGUCCUUCUUCG
....-------..............(((((-(...........(((((((((((((............))))....))))))))-)(((((.........))))))))))). ( -23.00)
>DroSec_CAF1 85461 100 + 1
ACAA-------AA---AAAAUCAAAGAAGA-ACCAAAAAUACUAAGCAUCUUAGGCAUUUUCCUGCUGGCCUUUUAAAGAUGUU-CGGGCUUCCCUUACUAGUCCUUCUUUG
....-------..---.....((((((((.-((...........((((((((((((............))))....))))))))-.(((...)))......)).)))))))) ( -21.90)
>DroSim_CAF1 91377 104 + 1
ACAA-------AAAAAAAAAUCAAAGAAGA-ACCAAAAAUACUAAGCAUCUUAGGCAUUUUCCUGCUGGCCUUUUAAAGAUGUUUUGGGCUUCCCUCACUAGUCCUUCUUUG
....-------..........((((((((.-((..........(((((((((((((............))))....))))))))).(((...)))......)).)))))))) ( -22.40)
>DroEre_CAF1 70382 110 + 1
AAAAAAAAAAAGAAAAAAAAUCAAAGAAGA-ACCAAAAAUACUAAGCAUCUUAGGCAUUUUCCUGCUGGCCUUUUAAAGAUGUU-UGGGCUUCCCUUACUAGUCCUCCUUUA
.........................((((.-............(((((((((((((............))))....))))))))-)(((((.........)))))..)))). ( -18.50)
>DroYak_CAF1 83704 100 + 1
AACA----------AAAAAAUCAAAGAAGA-ACCAAAAAUACUAAGCAUCUUAGGCAUUUUCCAGCUGGCCUUUUAAAGAUGUU-UGGGCUUCCCUUACUAGUCCUUCUUUA
....----------........(((((((.-..........(((((((((((((((............))))....))))))))-)))(((.........))).))))))). ( -22.00)
>DroAna_CAF1 41973 96 + 1
AAAA----------AAAAAUUGAAAGAAGAAACCAAAAAUACUAAGCAUCUUAGGUAUUUCUUUGCCGGCCUUUUAAAGAUGUU-CAGGCUUCCCGUACU-----UUCUAUA
....----------.......(((((...............((.((((((((.((((......)))).........))))))))-.))((.....)).))-----))).... ( -14.70)
>consensus
AAAA_______AA_AAAAAAUCAAAGAAGA_ACCAAAAAUACUAAGCAUCUUAGGCAUUUUCCUGCUGGCCUUUUAAAGAUGUU_UGGGCUUCCCUUACUAGUCCUUCUUUA
......................(((((((...............((((((((((((............))))....))))))))..(((...))).........))))))). (-15.54 = -16.23 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:49 2006