Locus 4724

Sequence ID 3R_DroMel_CAF1
Location 12,404,363 – 12,404,519
Length 156
Max. P 0.997771
window7758 window7759 window7760

overview

Window 8

Location 12,404,363 – 12,404,456
Length 93
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 75.41
Mean single sequence MFE -31.65
Consensus MFE -15.65
Energy contribution -17.35
Covariance contribution 1.70
Combinations/Pair 1.06
Mean z-score -3.29
Structure conservation index 0.49
SVM decision value 2.93
SVM RNA-class probability 0.997771
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12404363 93 - 27905053
ACCAUAU-----GUGCUGUGAAAAACAACGCGUAUACGUAAUGUG---GUCCUAUUGCAUCGCGUAUACGUA---------AGUGCUUGAAAUCCACUUAAAUACGUGGA
..((...-----(..((((.....))...(((((((((..(((..---((...))..)))..))))))))).---------))..).))...(((((........))))) ( -29.40)
>DroSec_CAF1 3502 92 - 1
ACCAUAU-----GUGCUGUGAA-AACAGCGCGUAUACGUAAUGUG---GUACUCUUGCAUCGCAUAUACGUA---------AGUGCUCGAAAUCCACUUAAAUACGUGGA
....(((-----(((((((...-.))))))))))(((((((((((---((.(....).))))))).))))))---------...........(((((........))))) ( -33.50)
>DroSim_CAF1 3105 92 - 1
ACCAUAU-----GUGCUGUGAA-AACAGCGCGUAUACGUAAUGUG---GUACUCUUGCAUCGCGUAUACGUA---------AGUGCUCGAAAUCCACUUAAAUACGUGGA
.((((..-----(((((((...-.)))))))(((((((..(((..---(.....)..)))..))))))).((---------((((.........)))))).....)))). ( -35.80)
>DroEre_CAF1 3696 100 - 1
GCCAUAUCGUAUGUGCUGUGAA-AACAGCGCGUAUACGUAAUGUGAUGGUUCUCCUGCAUCGCGUAUACGUA---------AGUGCUCGAAAUCCACUUAAAUACGUCGA
.......((((((((((((...-.)))))))(((((((..((((...((....)).))))..))))))).((---------((((.........)))))).))))).... ( -35.50)
>DroYak_CAF1 3635 100 - 1
ACCAUAUGUGCUGUGCUGUGAA-AACAGCGCGUAUACGUAAUGUGGUGGCUCUCCUGCAUCGCGUAUACGUA---------AGUGCUCGAAAUCCACUUAAAUACGUCGA
.....(((((..(((((((...-.)))))))(((((((..(((..(........)..)))..))))))).((---------((((.........))))))..)))))... ( -34.20)
>DroPer_CAF1 11306 101 - 1
UGCAGAUUUGGCAAGCCGACAA-GACAAGAC-AAGACGGCAGGCA---GUCC----UCGUUGCGUAUACGUAAUAUGACCCAAAACAUGAAUUCCAUUUGAAUGCGCCAA
.......(((((..((((....-........-....))))..(((---(((.----..((((((....))))))..))).(((...(((.....))))))..)))))))) ( -21.49)
>consensus
ACCAUAU_____GUGCUGUGAA_AACAGCGCGUAUACGUAAUGUG___GUACUCUUGCAUCGCGUAUACGUA_________AGUGCUCGAAAUCCACUUAAAUACGUCGA
..............(((((.....)))))(((((((((..((((............))))..)))))))))....................................... (-15.65 = -17.35 +   1.70)

alignment

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secondary structure

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Window 9

Location 12,404,392 – 12,404,494
Length 102
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 72.45
Mean single sequence MFE -32.13
Consensus MFE -15.65
Energy contribution -17.35
Covariance contribution 1.70
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.49
SVM decision value 2.37
SVM RNA-class probability 0.993103
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12404392 102 - 27905053
CAGACAUAAGCGUGACGUUCACUUUCGAUUUAAGCA-CCACCAUAU-----GUGCUGUGAAAAACAACGCGUAUACGUAAUGUG---GUCCUAUUGCAUCGCGUAUACGUA-----
...((....((((....(((((..........((((-(........-----)))))))))).....))))(((((((..(((..---((...))..)))..))))))))).----- ( -31.50)
>DroSec_CAF1 3531 101 - 1
CAGACAUAAGCAUGACGAUCGCUUUCGAUUUAAGCA-CCACCAUAU-----GUGCUGUGAA-AACAGCGCGUAUACGUAAUGUG---GUACUCUUGCAUCGCAUAUACGUA-----
.........((.((((((......)))..))).)).-.....((((-----(((((((...-.)))))))))))((((((((((---((.(....).))))))).))))).----- ( -31.30)
>DroSim_CAF1 3134 101 - 1
CAGACAUAAGCAUGACGUUCGCUUUCGAUUUAAGCA-CCACCAUAU-----GUGCUGUGAA-AACAGCGCGUAUACGUAAUGUG---GUACUCUUGCAUCGCGUAUACGUA-----
...((((((((.....))).((((.......)))).-......)))-----))(((((...-.)))))(((((((((..(((..---(.....)..)))..))))))))).----- ( -33.50)
>DroEre_CAF1 3725 109 - 1
CAGUCAUGAUCAUGAGUUUCGCUUUCGGUUUAAGCA-CCGCCAUAUCGUAUGUGCUGUGAA-AACAGCGCGUAUACGUAAUGUGAUGGUUCUCCUGCAUCGCGUAUACGUA-----
.....(((((.(((.((...((((.......)))).-..))))))))))..(((((((...-.)))))))(((((((..((((...((....)).))))..)))))))...----- ( -37.00)
>DroYak_CAF1 3664 104 - 1
CAAUCAUGAUCAUGACG-----UUUCGGUUUAUACA-CCACCAUAUGUGCUGUGCUGUGAA-AACAGCGCGUAUACGUAAUGUGGUGGCUCUCCUGCAUCGCGUAUACGUA-----
...((((....))))..-----...........(((-.(((.....))).)))(((((...-.)))))(((((((((..(((..(........)..)))..))))))))).----- ( -33.80)
>DroPer_CAF1 11339 107 - 1
CAUAUAUUAGCAUGCCAUUCCGUUUCGCCGACAUCUUCUUGCAGAUUUGGCAAGCCGACAA-GACAAGAC-AAGACGGCAGGCA---GUCC----UCGUUGCGUAUACGUAAUAUG
.........((.((((..........(((((.((((......)))))))))..((((....-........-....)))).))))---))..----..((((((....))))))... ( -25.69)
>consensus
CAGACAUAAGCAUGACGUUCGCUUUCGAUUUAAGCA_CCACCAUAU_____GUGCUGUGAA_AACAGCGCGUAUACGUAAUGUG___GUACUCUUGCAUCGCGUAUACGUA_____
.....................................................(((((.....)))))(((((((((..((((............))))..)))))))))...... (-15.65 = -17.35 +   1.70)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,404,424 – 12,404,519
Length 95
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 74.05
Mean single sequence MFE -25.05
Consensus MFE -10.83
Energy contribution -14.30
Covariance contribution 3.47
Combinations/Pair 1.12
Mean z-score -2.48
Structure conservation index 0.43
SVM decision value 1.74
SVM RNA-class probability 0.974954
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12404424 95 - 27905053
UAUAAUAAAAUCGCAACGUGAAUGACAGACAUAAGCGUGACGUUCACUUUCGAUUUAAGCA-CCACCAUAU-----GUGCUGUGAAAAACAACGCGUAUAC
.......((((((.((.(((((((.((..(....)..)).))))))).)))))))).....-.....((((-----(((.(((.....))).))))))).. ( -21.60)
>DroSec_CAF1 3563 94 - 1
UAUAAUAAAAUCGUAACGUGAAUGACAGACAUAAGCAUGACGAUCGCUUUCGAUUUAAGCA-CCACCAUAU-----GUGCUGUGAA-AACAGCGCGUAUAC
.........(((((..((((.(((.....)))...))))))))).((((.......)))).-.....((((-----(((((((...-.))))))))))).. ( -26.00)
>DroSim_CAF1 3166 94 - 1
UAUAAUAAAAUCGUAACGUGAAUGACAGACAUAAGCAUGACGUUCGCUUUCGAUUUAAGCA-CCACCAUAU-----GUGCUGUGAA-AACAGCGCGUAUAC
.......((((((.((.(((((((.((..(....)..)).))))))).)))))))).....-.....((((-----(((((((...-.))))))))))).. ( -29.90)
>DroEre_CAF1 3760 99 - 1
UAUAAUAAAAUCGCAAAGUGAAUGACAGUCAUGAUCAUGAGUUUCGCUUUCGGUUUAAGCA-CCGCCAUAUCGUAUGUGCUGUGAA-AACAGCGCGUAUAC
.......((((((.((((((((....(.((((....)))).))))))))))))))).....-..........(((((((((((...-.))))))))))).. ( -31.30)
>DroYak_CAF1 3699 93 - 1
UGUAAUAAAAUCGCA-GGUGAAUGACAAUCAUGAUCAUGACG-----UUUCGGUUUAUACA-CCACCAUAUGUGCUGUGCUGUGAA-AACAGCGCGUAUAC
((((...((((((.(-..((.((((((....)).))))..))-----..))))))).))))-........(((((.(((((((...-.)))))))))))). ( -24.50)
>DroPer_CAF1 11372 99 - 1
UUUGGGACACUCAUAAUACGAAUGACAUAUAUUAGCAUGCCAUUCCGUUUCGCCGACAUCUUCUUGCAGAUUUGGCAAGCCGACAA-GACAAGAC-AAGAC
.((((..............(((((.(((........))).)))))......(((((.((((......)))))))))...))))...-........-..... ( -17.00)
>consensus
UAUAAUAAAAUCGCAACGUGAAUGACAGACAUAAGCAUGACGUUCGCUUUCGAUUUAAGCA_CCACCAUAU_____GUGCUGUGAA_AACAGCGCGUAUAC
.......((((((.((.(((((((.((..........)).))))))).))))))))....................(((((((.....)))))))...... (-10.83 = -14.30 +   3.47)

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 11:37:26 2006