Locus 4611

Sequence ID 2L_DroMel_CAF1
Location 13,191,508 – 13,191,743
Length 235
Max. P 0.942218
window7280 window7281 window7282 window7283

overview

Window 0

Location 13,191,508 – 13,191,625
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.85
Mean single sequence MFE -31.58
Consensus MFE -19.88
Energy contribution -19.50
Covariance contribution -0.38
Combinations/Pair 1.21
Mean z-score -1.67
Structure conservation index 0.63
SVM decision value -0.05
SVM RNA-class probability 0.508462
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13191508 117 + 22407834
UUUUCGCCUCCUUUUUACCUUGGAAAAACUCAUCUCAAGUGAGUGUGUGCGUGUGUGAGCACAUAUGUACAUA-CAUA--UGCAUGUAAUGUGCAAGGUGCUGCAGCUUAAGAUGUUGCC
....(((((.....((((.(((((........)).)))))))((((((((((((((....)))))))))))))-)...--(((((.....))))))))))..(((((.......))))). ( -37.20)
>DroSec_CAF1 11910 118 + 1
UUUUCGCCUCCUUUUUACCUUGGAAAAACUCAUCUGAAGUGAGUGUGUGCGUAUGUGAGCAUAUACAUAUGUAAAAUA--UGUAUGUAAUGCGCAAGGUGUUGCAGCUUAAGAUGUUACC
........(((..........)))...((((((.....))))))(((.((((...(((((..((((((((.....)))--)))))(((((((.....))))))).)))))..))))))). ( -28.60)
>DroSim_CAF1 11852 118 + 1
UUUUCGCCUCCUUUUUACCUUGGAAAAACUCAUCUCAAGUGAGUGUGUGCGUAUGUGAGCAUAUACAUAUGUAAAAUA--UGUAUGUAUUGCGCAAGGUGUUGCAGCUUAAGAUGUUACC
........(((..........)))...((((((.....))))))(((.((((...(((((((((((((((.....)))--))))))).....((((....)))).)))))..))))))). ( -28.40)
>DroYak_CAF1 12062 105 + 1
UUUUCGCCUCCUUUUUACCUUGGGAAAACUCAUCUCAAGUGAGUGUGUG--UGUGUGAGUACAUAUGUACGUA-CAUACGUGCAUGUAG------------UGCAGCUGAAGAUGUUGCC
..............(((((((((((.......)))))))...(((..((--((((((.((((....)))).))-))))))..)))))))------------.(((((.......))))). ( -32.10)
>consensus
UUUUCGCCUCCUUUUUACCUUGGAAAAACUCAUCUCAAGUGAGUGUGUGCGUAUGUGAGCACAUACAUACGUA_AAUA__UGCAUGUAAUGCGCAAGGUGUUGCAGCUUAAGAUGUUACC
........(((..........)))......(((((.((((..((((((((........))))))))..................((((..((((...)))))))))))).)))))..... (-19.88 = -19.50 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,191,548 – 13,191,665
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.24
Mean single sequence MFE -36.15
Consensus MFE -19.24
Energy contribution -19.55
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.72
Structure conservation index 0.53
SVM decision value 1.32
SVM RNA-class probability 0.942218
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13191548 117 + 22407834
GAGUGUGUGCGUGUGUGAGCACAUAUGUACAUA-CAUA--UGCAUGUAAUGUGCAAGGUGCUGCAGCUUAAGAUGUUGCCAAGGGCAACGAUUCGCGGCUCGGAUUCGGAUGUAAAUCGA
..((((((((((((((....)))))))))))))-)...--(((((.....)))))..((.(((((((.......)))))..)).))..(((((..((..(((....))).))..))))). ( -41.50)
>DroSec_CAF1 11950 118 + 1
GAGUGUGUGCGUAUGUGAGCAUAUACAUAUGUAAAAUA--UGUAUGUAAUGCGCAAGGUGUUGCAGCUUAAGAUGUUACCAAGGGCAACGAUUUGAGGCUCUGAUUCGGAUUUAAAUCGA
...((.((((((...(((((..((((((((.....)))--)))))(((((((.....))))))).)))))..))).))))).......(((((((((..((((...))))))))))))). ( -31.10)
>DroSim_CAF1 11892 112 + 1
GAGUGUGUGCGUAUGUGAGCAUAUACAUAUGUAAAAUA--UGUAUGUAUUGCGCAAGGUGUUGCAGCUUAAGAUGUUACCAAGGGCAACGAUUUGCGGCUCUGA------UGUAAAUCGA
((.....(((((....((((((((((((((.....)))--)))))))....((((((.((((((..(((...........))).)))))).))))))))))..)------))))..)).. ( -34.60)
>DroYak_CAF1 12102 105 + 1
GAGUGUGUG--UGUGUGAGUACAUAUGUACGUA-CAUACGUGCAUGUAG------------UGCAGCUGAAGAUGUUGCCAAGGGCAACAAUUUGAGGCUCUGAUUCGGAUGCUGAUCGG
..(((..((--((((((.((((....)))).))-))))))..)))....------------...((((..((((((((((...)))))).))))..))))(((((.(((...)))))))) ( -37.40)
>consensus
GAGUGUGUGCGUAUGUGAGCACAUACAUACGUA_AAUA__UGCAUGUAAUGCGCAAGGUGUUGCAGCUUAAGAUGUUACCAAGGGCAACGAUUUGAGGCUCUGAUUCGGAUGUAAAUCGA
..((((((((........))))))))..................((((..((((...))))))))(((..((((((((((...)))))).))))..)))..................... (-19.24 = -19.55 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,191,548 – 13,191,665
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.24
Mean single sequence MFE -24.82
Consensus MFE -11.71
Energy contribution -12.40
Covariance contribution 0.69
Combinations/Pair 1.14
Mean z-score -2.72
Structure conservation index 0.47
SVM decision value 0.51
SVM RNA-class probability 0.763484
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13191548 117 - 22407834
UCGAUUUACAUCCGAAUCCGAGCCGCGAAUCGUUGCCCUUGGCAACAUCUUAAGCUGCAGCACCUUGCACAUUACAUGCA--UAUG-UAUGUACAUAUGUGCUCACACACGCACACACUC
(((((((......)))).)))...(((....((((((...)))))).......((....)).....(((((((((((((.--...)-))))))...)))))).......)))........ ( -30.20)
>DroSec_CAF1 11950 118 - 1
UCGAUUUAAAUCCGAAUCAGAGCCUCAAAUCGUUGCCCUUGGUAACAUCUUAAGCUGCAACACCUUGCGCAUUACAUACA--UAUUUUACAUAUGUAUAUGCUCACAUACGCACACACUC
..(((((......))))).((((........((((((...)))))).......((.((((....)))))).....(((((--(((.....))))))))..))))................ ( -24.50)
>DroSim_CAF1 11892 112 - 1
UCGAUUUACA------UCAGAGCCGCAAAUCGUUGCCCUUGGUAACAUCUUAAGCUGCAACACCUUGCGCAAUACAUACA--UAUUUUACAUAUGUAUAUGCUCACAUACGCACACACUC
..........------...(((((((((...(((((.(((((.......)))))..)))))...)))))......(((((--(((.....))))))))..))))................ ( -23.30)
>DroYak_CAF1 12102 105 - 1
CCGAUCAGCAUCCGAAUCAGAGCCUCAAAUUGUUGCCCUUGGCAACAUCUUCAGCUGCA------------CUACAUGCACGUAUG-UACGUACAUAUGUACUCACACA--CACACACUC
.......((((......(((...((.((..(((((((...)))))))..)).)))))..------------....))))(((((((-(....)))))))).........--......... ( -21.30)
>consensus
UCGAUUUACAUCCGAAUCAGAGCCGCAAAUCGUUGCCCUUGGCAACAUCUUAAGCUGCAACACCUUGCGCAUUACAUACA__UAUG_UACAUACAUAUAUGCUCACACACGCACACACUC
...................((((........((((((...))))))..........((((....))))................................))))................ (-11.71 = -12.40 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,191,625 – 13,191,743
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.70
Mean single sequence MFE -27.93
Consensus MFE -18.58
Energy contribution -20.64
Covariance contribution 2.06
Combinations/Pair 1.08
Mean z-score -1.58
Structure conservation index 0.67
SVM decision value -0.04
SVM RNA-class probability 0.512792
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13191625 118 - 22407834
ACAAAGGGUGAAAAAAAUGCGAAACCAGAAGUUUCGGUGGCUUC-AUAAUUACCUGGAAUGAGAUA-CUCCCGUUAUUUCUCGAUUUACAUCCGAAUCCGAGCCGCGAAUCGUUGCCCUU
...(((((..(........((((((.....))))))(((((((.-...............((((.(-(....))....))))(((((......))))).)))))))......)..))))) ( -30.90)
>DroSec_CAF1 12028 109 - 1
ACAAAGGGUGAAA-AAAUGCGAAACCAGAAGUUUCGGUUAUUUCCGUUAU-UUCUCGAUU---------UCCGUUAUUUCUCGAUUUAAAUCCGAAUCAGAGCCUCAAAUCGUUGCCCUU
...((((((((((-.((((.(((((.((((((..(((......)))..))-)))).).))---------)))))).))))..(((((......)))))................)))))) ( -27.60)
>DroSim_CAF1 11970 110 - 1
ACAAAGGGUGAAA-AAGUGCGAAACCAGAAGUUUCGGUGGCUUC-AUAAU-ACCUGGAAUUAGAUA-CUCCCGUUAUUUCUCGAUUUACA------UCAGAGCCGCAAAUCGUUGCCCUU
...(((((..(..-...((((.....((((((..(((..(..((-.((((-.......))))))..-)..)))..)))))).(((....)------)).....)))).....)..))))) ( -28.40)
>DroYak_CAF1 12167 118 - 1
ACAAAGGGUGAAAAAAAAGCGAAACCAGAAGUUUCGGUGGCUUC-AUAAU-ACCAAGAACUAGAUAACCCCUGUUAUUACCCGAUCAGCAUCCGAAUCAGAGCCUCAAAUUGUUGCCCUU
...(((((..(........((((((.....))))))(.(((((.-.....-...........((((((....))))))....(((..(....)..))).))))).)......)..))))) ( -24.80)
>consensus
ACAAAGGGUGAAA_AAAUGCGAAACCAGAAGUUUCGGUGGCUUC_AUAAU_ACCUGGAAUUAGAUA_CUCCCGUUAUUUCUCGAUUUACAUCCGAAUCAGAGCCGCAAAUCGUUGCCCUU
...(((((..(........((((((.....))))))(((((((............((.............))..........(((((......))))).)))))))......)..))))) (-18.58 = -20.64 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:35 2006