Locus 2132

Sequence ID 2L_DroMel_CAF1
Location 5,771,137 – 5,771,390
Length 253
Max. P 0.986106
window3444 window3445 window3446 window3447 window3448

overview

Window 4

Location 5,771,137 – 5,771,234
Length 97
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 80.31
Mean single sequence MFE -30.02
Consensus MFE -20.04
Energy contribution -20.48
Covariance contribution 0.44
Combinations/Pair 1.13
Mean z-score -2.37
Structure conservation index 0.67
SVM decision value 1.11
SVM RNA-class probability 0.917501
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5771137 97 + 22407834
AUGCUGCAGCGCAACAACCAAUUGCGGCGGGUGAACAUUUUCUGGCCCAGAGGCUCAAAACGCAUGUUGUAGCUGCA----AAAAAA--A-AUUAACAUUAAAA
....((((((((((((......((((..((((.(........).)))).(.....)....)))))))))).))))))----......--.-............. ( -25.40)
>DroVir_CAF1 10798 98 + 1
AUGCUGCAGCGCAACAGCCAAUUGCGGCGUGUAAACAUUUUCUGACCCAGCGGCUCAAAGCGCAUGUUGAAGCUGCA----AGCAGA--CAAUUGUUAAUUAAU
.(((((((((.((((((((......))).....................(((........))).)))))..))))).----))))((--(....)))....... ( -27.50)
>DroPse_CAF1 9912 93 + 1
AUGCUGCAGCGCAGCAGCCAAUUACGGCGCGAGAACAUUUUCUGGCCCAAAGGCUCAAAGCGCAUGUUGUAGCUGCA----AAGAAA--AUGCGGG-----AAA
....(((((((((((((((......)))(((((((....))))((((....)))).....))).)))))).))))))----......--.......-----... ( -30.70)
>DroEre_CAF1 8397 100 + 1
AUGCUGCAGCGCAGCAACCAGUUGCGGCGUGUGAACAUUUUCUGGCCCAGAGGCUCGAAACGCAUGUUGUAGCUAUA----AAAAAAAUAAGUUGGCAUUAACG
.((((((...))))))...((((((((((((((.....((((.((((....)))).))))))))))))))))))...----..........((((....)))). ( -33.60)
>DroYak_CAF1 8524 104 + 1
AUGCUGCAGCGCAGCAACCAGUUGCGGCGUGUGAACAUUUUCUGGCCCAGAGGCUCAAAACGCAUGUUGUAGCUGCAAAGAAAAAAAAAAACAUUGUAAUAACG
.((((((...))))))..(((((((((((((((.....(((..((((....))))..))))))))))))))))))............................. ( -32.20)
>DroPer_CAF1 9883 93 + 1
AUGCUGCAGCGCAGCAGCCAAUUACGGCGCGAGAACAUUUUCUGGCCCAAAGGCUCAAAGCGCAUGUUGUAGCUGCA----AAGAAA--AUGCGGG-----AAA
....(((((((((((((((......)))(((((((....))))((((....)))).....))).)))))).))))))----......--.......-----... ( -30.70)
>consensus
AUGCUGCAGCGCAGCAACCAAUUGCGGCGUGUGAACAUUUUCUGGCCCAGAGGCUCAAAACGCAUGUUGUAGCUGCA____AAAAAA__AAGUUGG_A_UAAAA
..((((((((((((.......)))).((((..(((....))).((((....))))....))))..))))))))............................... (-20.04 = -20.48 +   0.44)

alignment

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secondary structure

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Window 5

Location 5,771,137 – 5,771,234
Length 97
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 80.31
Mean single sequence MFE -27.03
Consensus MFE -22.29
Energy contribution -21.90
Covariance contribution -0.39
Combinations/Pair 1.17
Mean z-score -1.38
Structure conservation index 0.82
SVM decision value 0.45
SVM RNA-class probability 0.741241
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5771137 97 - 22407834
UUUUAAUGUUAAU-U--UUUUUU----UGCAGCUACAACAUGCGUUUUGAGCCUCUGGGCCAGAAAAUGUUCACCCGCCGCAAUUGGUUGUUGCGCUGCAGCAU
.............-.--.....(----((((((...(((((...(((((.(((....)))))))).)))))........(((((.....))))))))))))... ( -27.40)
>DroVir_CAF1 10798 98 - 1
AUUAAUUAACAAUUG--UCUGCU----UGCAGCUUCAACAUGCGCUUUGAGCCGCUGGGUCAGAAAAUGUUUACACGCCGCAAUUGGCUGUUGCGCUGCAGCAU
...............--..((((----.(((((..(((((.....(((((.((...)).)))))............((((....))))))))).))))))))). ( -27.40)
>DroPse_CAF1 9912 93 - 1
UUU-----CCCGCAU--UUUCUU----UGCAGCUACAACAUGCGCUUUGAGCCUUUGGGCCAGAAAAUGUUCUCGCGCCGUAAUUGGCUGCUGCGCUGCAGCAU
...-----...((((--((((..----.((.((........))))..((.(((....)))))))))))))......((((....))))((((((...)))))). ( -28.20)
>DroEre_CAF1 8397 100 - 1
CGUUAAUGCCAACUUAUUUUUUU----UAUAGCUACAACAUGCGUUUCGAGCCUCUGGGCCAGAAAAUGUUCACACGCCGCAACUGGUUGCUGCGCUGCAGCAU
.......................----....(((..(((((...((((..(((....)))..)))))))))..(((((.((((....)))).))).)).))).. ( -21.30)
>DroYak_CAF1 8524 104 - 1
CGUUAUUACAAUGUUUUUUUUUUUCUUUGCAGCUACAACAUGCGUUUUGAGCCUCUGGGCCAGAAAAUGUUCACACGCCGCAACUGGUUGCUGCGCUGCAGCAU
..........................(((((((...(((((...(((((.(((....)))))))).))))).....((.((((....)))).)))))))))... ( -29.70)
>DroPer_CAF1 9883 93 - 1
UUU-----CCCGCAU--UUUCUU----UGCAGCUACAACAUGCGCUUUGAGCCUUUGGGCCAGAAAAUGUUCUCGCGCCGUAAUUGGCUGCUGCGCUGCAGCAU
...-----...((((--((((..----.((.((........))))..((.(((....)))))))))))))......((((....))))((((((...)))))). ( -28.20)
>consensus
UUUUA_U_CCAACUU__UUUUUU____UGCAGCUACAACAUGCGCUUUGAGCCUCUGGGCCAGAAAAUGUUCACACGCCGCAAUUGGCUGCUGCGCUGCAGCAU
...........................((((((...(((((....((((.(((....)))))))..))))).....((.(((......))).)))))))).... (-22.29 = -21.90 +  -0.39)

alignment

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secondary structure

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Window 6

Location 5,771,234 – 5,771,351
Length 117
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 79.88
Mean single sequence MFE -24.18
Consensus MFE -15.52
Energy contribution -15.76
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -2.61
Structure conservation index 0.64
SVM decision value 2.03
SVM RNA-class probability 0.986106
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5771234 117 + 22407834
UAUAUGUUCAUUUGUAAAACAUGAUUU--GAAAAACAACAGAUGCGCGAAACUAAAAUCAUGUCCAUGCUAGCAUGUAGAUAUCCAUGUAGAAAACAUGUAGUUCUACAGCAGCGCCCU
..................(((((((((--.........................)))))))))....(((.((.((((((....(((((.....)))))....)))))))))))..... ( -24.01)
>DroSec_CAF1 8348 116 + 1
UAUAUGUCCAA-UGUAAAUCAUAAAUU--GAAUAACAACAGAUGCGCGAAACUAAAAUUAUGUCCAUGCUUGCAUGUAGAUAUCAAUGUAGAAAACAUGUAGUUCUACAGCAGCGCCAU
.....(((...-(((.(.(((.....)--)).).)))...)))((((..............((....)).(((.((((((.....((((.....)))).....)))))))))))))... ( -20.40)
>DroSim_CAF1 8547 116 + 1
UAUAUGUCCAU-UGUAAAUCAUAAUUU--GAAUAACAACAGACGCGCGAAACUAAAAUCAUUUCCAUGCUUGCAUGUAGAUAUCCAUGUAGAAAACAUGUAGUUCUACAGCAGCGCCCU
.....(((..(-(((.(.(((.....)--)).).))))..)))((((((........))...........(((.((((((....(((((.....)))))....)))))))))))))... ( -27.60)
>DroEre_CAF1 8497 105 + 1
UACA----------UAAACAA--AUCCUAGAAAAGCAUUAAAUGCGGGAAAAUAAAGUUAUUUACAUGCUAGCAUGUAGAUAUACAUGUACAAAACAUGUAGU-CUACAGCAGCGCCC-
....----------.......--...........((((...))))(((.(((((....)))))....(((.((.(((((((.(((((((.....)))))))))-)))))))))).)))- ( -26.70)
>DroYak_CAF1 8628 108 + 1
UAUU----------UAAACAAAAAUUUAAAAAAAACAACAAGUGCGGGAACCUAAAAUCAUUUACAUGCUAGCAUGUAGAUAUACAUGUACAAAACAUGUAGUUUUACAGCAGCGCCC-
..((----------((((......))))))...........((((.(((((........(((((((((....))))))))).(((((((.....))))))))))))......))))..- ( -22.20)
>consensus
UAUAUGU_CA__UGUAAACCAUAAUUU__GAAAAACAACAGAUGCGCGAAACUAAAAUCAUUUCCAUGCUAGCAUGUAGAUAUCCAUGUAGAAAACAUGUAGUUCUACAGCAGCGCCCU
...................................................................(((.((.((((((....(((((.....)))))....)))))))))))..... (-15.52 = -15.76 +   0.24)

alignment

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secondary structure

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Window 7

Location 5,771,234 – 5,771,351
Length 117
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 79.88
Mean single sequence MFE -27.30
Consensus MFE -17.01
Energy contribution -17.61
Covariance contribution 0.60
Combinations/Pair 1.26
Mean z-score -2.13
Structure conservation index 0.62
SVM decision value 1.00
SVM RNA-class probability 0.897041
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5771234 117 - 22407834
AGGGCGCUGCUGUAGAACUACAUGUUUUCUACAUGGAUAUCUACAUGCUAGCAUGGACAUGAUUUUAGUUUCGCGCAUCUGUUGUUUUUC--AAAUCAUGUUUUACAAAUGAACAUAUA
.(..((((((((((((....(((((.....)))))....)))))).)).)))..(((((((((((.((...((.((....))))...)).--))))))))))).......)..)..... ( -28.10)
>DroSec_CAF1 8348 116 - 1
AUGGCGCUGCUGUAGAACUACAUGUUUUCUACAUUGAUAUCUACAUGCAAGCAUGGACAUAAUUUUAGUUUCGCGCAUCUGUUGUUAUUC--AAUUUAUGAUUUACA-UUGGACAUAUA
(((((((.((((((((.....((((.....)))).....)))))).))((((.((((......)))))))).)))).(((..(((...((--(.....)))...)))-..))))))... ( -22.80)
>DroSim_CAF1 8547 116 - 1
AGGGCGCUGCUGUAGAACUACAUGUUUUCUACAUGGAUAUCUACAUGCAAGCAUGGAAAUGAUUUUAGUUUCGCGCGUCUGUUGUUAUUC--AAAUUAUGAUUUACA-AUGGACAUAUA
...(((((((((((((....(((((.....)))))....)))))).)))......(((((.......)))))))))(((((((((...((--(.....)))...)))-))))))..... ( -37.30)
>DroEre_CAF1 8497 105 - 1
-GGGCGCUGCUGUAG-ACUACAUGUUUUGUACAUGUAUAUCUACAUGCUAGCAUGUAAAUAACUUUAUUUUCCCGCAUUUAAUGCUUUUCUAGGAU--UUGUUUA----------UGUA
-(((.((((((((((-(.(((((((.....)))))))..)))))).)).)))..(((((....)))))...)))((((..(((.((.....)).))--).....)----------))). ( -25.80)
>DroYak_CAF1 8628 108 - 1
-GGGCGCUGCUGUAAAACUACAUGUUUUGUACAUGUAUAUCUACAUGCUAGCAUGUAAAUGAUUUUAGGUUCCCGCACUUGUUGUUUUUUUUAAAUUUUUGUUUA----------AAUA
-(((.(((..........(((((((.....)))))))(((.((((((....)))))).)))......))).)))...............(((((((....)))))----------)).. ( -22.50)
>consensus
AGGGCGCUGCUGUAGAACUACAUGUUUUCUACAUGGAUAUCUACAUGCUAGCAUGGAAAUGAUUUUAGUUUCGCGCAUCUGUUGUUUUUC__AAAUUAUGAUUUACA__UG_ACAUAUA
.....(((((((((((....(((((.....)))))....)))))).)).))).....((((((((.........(((.....))).......))))))))................... (-17.01 = -17.61 +   0.60)

alignment

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secondary structure

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Window 8

Location 5,771,271 – 5,771,390
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.28
Mean single sequence MFE -30.72
Consensus MFE -22.44
Energy contribution -23.36
Covariance contribution 0.92
Combinations/Pair 1.11
Mean z-score -1.72
Structure conservation index 0.73
SVM decision value 0.17
SVM RNA-class probability 0.619009
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5771271 119 - 22407834
GCCAUCUACCGUAAAGGGUGUUUCUUUUAA-AUCUGUGAGAGGGCGCUGCUGUAGAACUACAUGUUUUCUACAUGGAUAUCUACAUGCUAGCAUGGACAUGAUUUUAGUUUCGCGCAUCU
(((.(((((..(((((((....))))))).-....)).))).)))(.(((.(..(((((((((((((.(((((((........)))).)))...)))))))....))))))..)))).). ( -31.20)
>DroSec_CAF1 8384 119 - 1
GCCAUCUACCGUAAGGGGUGUUUCUUUUAA-AUCUAUGAGAUGGCGCUGCUGUAGAACUACAUGUUUUCUACAUUGAUAUCUACAUGCAAGCAUGGACAUAAUUUUAGUUUCGCGCAUCU
(((((((.((....))(((...........-)))....)))))))(((((((((((.....((((.....)))).....)))))).))).((..((((.........)))).)))).... ( -29.40)
>DroSim_CAF1 8583 119 - 1
GCCAUCUACCGUAAGGGGUGUUUCUUUUAA-AUCUAUGAGAGGGCGCUGCUGUAGAACUACAUGUUUUCUACAUGGAUAUCUACAUGCAAGCAUGGAAAUGAUUUUAGUUUCGCGCGUCU
..((((..((....))))))..(((((((.-.....)))))))(((((((((((((....(((((.....)))))....)))))).)))......(((((.......))))))))).... ( -33.30)
>DroEre_CAF1 8524 116 - 1
GCCAUCUACAGUACAA-GUGUUUCUUAUAAAAUCUCUGA--GGGCGCUGCUGUAG-ACUACAUGUUUUGUACAUGUAUAUCUACAUGCUAGCAUGUAAAUAACUUUAUUUUCCCGCAUUU
((..((((((((...(-(((((.((((.........)))--))))))))))))))-).(((((((.....)))))))(((.((((((....)))))).))).............)).... ( -30.30)
>DroYak_CAF1 8657 118 - 1
GCCAUCUACUGUACAGGGUGUUUCCCAUAAUAUCUCUGA--GGGCGCUGCUGUAAAACUACAUGUUUUGUACAUGUAUAUCUACAUGCUAGCAUGUAAAUGAUUUUAGGUUCCCGCACUU
((...........(((((((((......)))))).))).--(((.(((..........(((((((.....)))))))(((.((((((....)))))).)))......))).))))).... ( -29.40)
>consensus
GCCAUCUACCGUAAAGGGUGUUUCUUUUAA_AUCUAUGAGAGGGCGCUGCUGUAGAACUACAUGUUUUCUACAUGGAUAUCUACAUGCUAGCAUGGAAAUGAUUUUAGUUUCGCGCAUCU
(((.((.....(((((((....)))))))........))...)))(((((((((((....(((((.....)))))....)))))).)).)))............................ (-22.44 = -23.36 +   0.92)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:28 2006