Locus 5679

Sequence ID 3L_DroMel_CAF1
Location 15,562,873 – 15,563,132
Length 259
Max. P 0.999076
window8977 window8978 window8979 window8980 window8981 window8982

overview

Window 7

Location 15,562,873 – 15,562,979
Length 106
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 80.30
Mean single sequence MFE -13.50
Consensus MFE -7.47
Energy contribution -7.51
Covariance contribution 0.04
Combinations/Pair 1.07
Mean z-score -1.93
Structure conservation index 0.55
SVM decision value 0.18
SVM RNA-class probability 0.622880
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15562873 106 + 23771897
AAAUGGUCCGAUAUAUUUCAUUUUUAUGAAUGAAAAAAAAAAA---------AAGAAAAAACCAGCAAAGCAAGCAGCCAACGGCAUGGCAAAUAAACAAAGUUAACAAUAAAUG
...............((((((((....))))))))........---------............((.......)).((((......))))......................... ( -11.90)
>DroSec_CAF1 25314 97 + 1
AAAAUCUCCGACAUUUUUCAUUUUUAUGAAUGAAAAAAA-AAA---------AAGGAAAAACCAGCAAAGCAC--------AGGCAGGGCAAAUAAACAAAGUUAACAAUAAAUG
......(((....((((((((((....))))))))))..-...---------..))).......((...((..--------..))...))......................... ( -12.60)
>DroSim_CAF1 25791 95 + 1
AAAAUCUCCGACAUUUUUCAUUUUUAUGAAUGAAAAAAA-AAA---------GAGAAAAAACCAGCAAAGC----------AAGCAGGGCAAAUAAACAAAGUUAACAAUAAAUG
....((((.....((((((((((....))))))))))..-...---------)))).....((.((.....----------..)).))........................... ( -13.90)
>DroEre_CAF1 25631 91 + 1
AAAUUGUCCGACAUAUUUCAUUUUUAUGAAUGAAAAAAA--------------------AGCCAGCGAAGC----AGCCAACAGCAGGGCAAAAAAACAAAGUUAACAAUAAAUG
..(((((..(((...((((((((....))))))))....--------------------.(((.((...))----.((.....))..)))...........))).)))))..... ( -15.80)
>DroYak_CAF1 45828 110 + 1
AAAUUGUCCGACAUAUUUCAUUUUUAUGAAUGAAAAAAA-AAAAAAAACGAAAAGAAACAGCCAGCGAAGC----AGUCAACAGCAGGGUAAAUAAACAAAGUUAACAAUAAAUG
..(((((..(((...((((((((....))))))))....-....................(((.((.....----........))..)))...........))).)))))..... ( -13.32)
>consensus
AAAUUGUCCGACAUAUUUCAUUUUUAUGAAUGAAAAAAA_AAA_________AAGAAAAAACCAGCAAAGC____AG_CAACAGCAGGGCAAAUAAACAAAGUUAACAAUAAAUG
.........(((...((((((((....))))))))..........................((.((.................)).)).............)))........... ( -7.47 =  -7.51 +   0.04)

alignment

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secondary structure

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Window 8

Location 15,562,939 – 15,563,056
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 90.70
Mean single sequence MFE -21.22
Consensus MFE -15.28
Energy contribution -14.72
Covariance contribution -0.56
Combinations/Pair 1.21
Mean z-score -1.79
Structure conservation index 0.72
SVM decision value -0.02
SVM RNA-class probability 0.522197
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15562939 117 + 23771897
AGCCAACGGCAUGGCAAAUAAACAAAGUUAACAAUAAAUGAAAAUGAUUCAUCUGAAUAAAAUGACGAGUUUGCCGGAUUGUCAAUGAACAAUACGCAGAAGCUACGUUUGCCAAAU
.(((...))).((((((((.......((((.......((....)).((((....))))....))))(..(((((...(((((......)))))..)))))..)...))))))))... ( -24.60)
>DroSec_CAF1 25377 110 + 1
------AGGCAGGGCAAAUAAACAAAGUUAACAAUAAAUGAAAAUGAUUCAUCUAAAUAAAAUGACGAGU-UGUCCGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCCGCCAAAU
------.(((.((((...........(((.....((.(((((.....))))).)).......((((((..-.......))))))...))).....((....))...))))))).... ( -22.50)
>DroSim_CAF1 25852 111 + 1
------AAGCAGGGCAAAUAAACAAAGUUAACAAUAAAUGAAGAUGAUUCAUCUAAAUAAAAUGACGAGUUUGUCCGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCCAAAU
------..(((((............................(((((...)))))...........(((((((.(.(((((((......))))).)).).))))).)))))))..... ( -20.70)
>DroEre_CAF1 25682 116 + 1
AGCCAACAGCAGGGCAAAAAAACAAAGUUAACAAUAAAUGAAAAUGAUUCAUCUAAAUAAAAUGACGAGU-UUUCUGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCCAAAU
........(((((.(...........(((.(((((....((((((...((((.........))))...))-))))..))))).))).........((....))...))))))..... ( -18.80)
>DroYak_CAF1 45898 116 + 1
AGUCAACAGCAGGGUAAAUAAACAAAGUUAACAAUAAAUGAAAAUGAUUCAUCUAAAUAAAAUGACGAGU-UGUCUGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCGAAAU
........((((((((..........(((.....((.(((((.....))))).)).......((((((..-.......))))))...))).....((....))))).)))))..... ( -19.50)
>consensus
AG_CAACAGCAGGGCAAAUAAACAAAGUUAACAAUAAAUGAAAAUGAUUCAUCUAAAUAAAAUGACGAGU_UGUCCGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCCAAAU
........((.((((...........(((.....((.(((((.....))))).)).......((((((..........))))))...))).....((....))...))))))..... (-15.28 = -14.72 +  -0.56)

alignment

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secondary structure

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Window 9

Location 15,562,939 – 15,563,056
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 90.70
Mean single sequence MFE -26.02
Consensus MFE -23.04
Energy contribution -23.40
Covariance contribution 0.36
Combinations/Pair 1.14
Mean z-score -2.44
Structure conservation index 0.89
SVM decision value 3.36
SVM RNA-class probability 0.999076
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15562939 117 - 23771897
AUUUGGCAAACGUAGCUUCUGCGUAUUGUUCAUUGACAAUCCGGCAAACUCGUCAUUUUAUUCAGAUGAAUCAUUUUCAUUUAUUGUUAACUUUGUUUAUUUGCCAUGCCGUUGGCU
...((((((((((((...))))))........((((((((..(((......))).........(((((((.....)))))))))))))))..........)))))).(((...))). ( -26.70)
>DroSec_CAF1 25377 110 - 1
AUUUGGCGGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCGGACA-ACUCGUCAUUUUAUUUAGAUGAAUCAUUUUCAUUUAUUGUUAACUUUGUUUAUUUGCCCUGCCU------
....(((((((((((...))))..........(((((((...(((.-....)))........((((((((.....)))))))))))))))............)))).))).------ ( -27.70)
>DroSim_CAF1 25852 111 - 1
AUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCGGACAAACUCGUCAUUUUAUUUAGAUGAAUCAUCUUCAUUUAUUGUUAACUUUGUUUAUUUGCCCUGCUU------
....((((((.(((((....))..........(((((((...(((......)))........((((((((.....)))))))))))))))...........))))))))).------ ( -25.00)
>DroEre_CAF1 25682 116 - 1
AUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCAGAAA-ACUCGUCAUUUUAUUUAGAUGAAUCAUUUUCAUUUAUUGUUAACUUUGUUUUUUUGCCCUGCUGUUGGCU
....((((((.(((((....))..........((((((((..((((-(....((((((.....))))))....)))))....))))))))...........)))))))))....... ( -25.30)
>DroYak_CAF1 45898 116 - 1
AUUUCGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCAGACA-ACUCGUCAUUUUAUUUAGAUGAAUCAUUUUCAUUUAUUGUUAACUUUGUUUAUUUACCCUGCUGUUGACU
.....(((((.(((((....))..........(((((((...(((.-....)))........((((((((.....)))))))))))))))...........))))))))........ ( -25.40)
>consensus
AUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCAGACA_ACUCGUCAUUUUAUUUAGAUGAAUCAUUUUCAUUUAUUGUUAACUUUGUUUAUUUGCCCUGCUGUUG_CU
....((((((.(((((....))..........(((((((...(((......)))........((((((((.....)))))))))))))))...........)))))))))....... (-23.04 = -23.40 +   0.36)

alignment

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secondary structure

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Window 0

Location 15,562,979 – 15,563,094
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 94.25
Mean single sequence MFE -22.94
Consensus MFE -20.98
Energy contribution -20.82
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.63
Structure conservation index 0.91
SVM decision value 1.84
SVM RNA-class probability 0.979468
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15562979 115 + 23771897
AAAAUGAUUCAUCUGAAUAAAAUGACGAGUUUGCCGGAUUGUCAAUGAACAAUACGCAGAAGCUACGUUUGCCAAAUGCUAAAUAUUUUCAAUAUCGGAAACUAUUUAGCACUGA
.(((((((((....))))........(..(((((...(((((......)))))..)))))..)..)))))......((((((((((((((......))))).))))))))).... ( -23.30)
>DroSec_CAF1 25411 114 + 1
AAAAUGAUUCAUCUAAAUAAAAUGACGAGU-UGUCCGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCCGCCAAAUGCUAAAUAUUUUCAAUAUCGGAAACUAUUUAGCACUGA
...(..((((.((..........)).))))-..).(((((((......))))).))(((..((.......))....((((((((((((((......))))).)))))))))))). ( -20.20)
>DroSim_CAF1 25886 115 + 1
AAGAUGAUUCAUCUAAAUAAAAUGACGAGUUUGUCCGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCCAAAUGCUAAAUAUUUUCAAUAUCGGAAACUAUUUAGCACUGA
.(((((...)))))...........(((((((.(.(((((((......))))).)).).))))).)).........((((((((((((((......))))).))))))))).... ( -23.30)
>DroEre_CAF1 25722 114 + 1
AAAAUGAUUCAUCUAAAUAAAAUGACGAGU-UUUCUGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCCAAAUGCUAAAUAUUUUCAAAUUCGGAAACUAUUUAGCACUGG
.........................(((((-((.((((((((......)))))...)))))))).))....(((..((((((((((((((......))))).))))))))).))) ( -21.10)
>DroYak_CAF1 45938 114 + 1
AAAAUGAUUCAUCUAAAUAAAAUGACGAGU-UGUCUGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCGAAAUGCUAAAUAUUUCCAAAAUCGGAAACUAUUUAGCACUGG
....((.(((((..........((((((..-.......)))))))))))))...(((((.........)))))...((((((((((((((......))))).))))))))).... ( -26.80)
>consensus
AAAAUGAUUCAUCUAAAUAAAAUGACGAGU_UGUCCGAUUGUCAAUGAACAAUACGCAGAAGCUACGCCUGCCAAAUGCUAAAUAUUUUCAAUAUCGGAAACUAUUUAGCACUGA
....((.(((((..........((((((..........))))))))))))).....(((..((.......))....((((((((((((((......))))).)))))))))))). (-20.98 = -20.82 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,562,979 – 15,563,094
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 94.25
Mean single sequence MFE -26.79
Consensus MFE -23.45
Energy contribution -22.85
Covariance contribution -0.60
Combinations/Pair 1.15
Mean z-score -1.88
Structure conservation index 0.88
SVM decision value 2.06
SVM RNA-class probability 0.986947
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15562979 115 - 23771897
UCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCAAACGUAGCUUCUGCGUAUUGUUCAUUGACAAUCCGGCAAACUCGUCAUUUUAUUCAGAUGAAUCAUUUU
...((((((((((.((((.......)))).))))))))))(((.(..((((((...))))))((((((....))))))..).)))..(((((..........)))))........ ( -24.60)
>DroSec_CAF1 25411 114 - 1
UCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCGGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCGGACA-ACUCGUCAUUUUAUUUAGAUGAAUCAUUUU
(((((((((((((.((((.......)))).)))))))))).((((((((((((...)))))..((((((..........)))))-))))))))...........)))........ ( -27.70)
>DroSim_CAF1 25886 115 - 1
UCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCGGACAAACUCGUCAUUUUAUUUAGAUGAAUCAUCUU
..(((((((((((.((((.......)))).)))))))))))((((((((((((...)))))).((((((..........)))))).)).))))........(((((...))))). ( -27.20)
>DroEre_CAF1 25722 114 - 1
CCAGUGCUAAAUAGUUUCCGAAUUUGAAAAUAUUUAGCAUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCAGAAA-ACUCGUCAUUUUAUUUAGAUGAAUCAUUUU
(((((((((((((.((((.......)))).))))))))).))))..((((....(((((...((((((....))))))))))).-...))))....................... ( -26.30)
>DroYak_CAF1 45938 114 - 1
CCAGUGCUAAAUAGUUUCCGAUUUUGGAAAUAUUUAGCAUUUCGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCAGACA-ACUCGUCAUUUUAUUUAGAUGAAUCAUUUU
..(((((((((((.((((((....))))))))))))))))).((((((.......))))))....(((((((........(((.-....)))..........)))))))...... ( -28.17)
>consensus
UCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGACAAUCAGACA_ACUCGUCAUUUUAUUUAGAUGAAUCAUUUU
..(((((((((((.((((.......)))).)))))))))))..((((((((((...)))))).))))(((((........(((......)))..........)))))........ (-23.45 = -22.85 +  -0.60)

alignment

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secondary structure

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Window 2

Location 15,563,019 – 15,563,132
Length 113
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 92.40
Mean single sequence MFE -26.42
Consensus MFE -20.80
Energy contribution -20.24
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.68
Structure conservation index 0.79
SVM decision value 0.46
SVM RNA-class probability 0.745465
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15563019 113 - 23771897
ACACGGCCAAAACAUUAGCAUAAAAC--UAUUUCCACGAAUCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCAAACGUAGCUUCUGCGUAUUGUUCAUUGAC
.....((((((.............((--(..(((...)))..)))((((((((.((((.......)))).)))))))).))))))..((((((...))))))............. ( -24.10)
>DroSec_CAF1 25450 115 - 1
AACCGGCCAAAACAUUAGCAUACAGCCAUAUUUCCACGAAUCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCGGGCGUAGCUUCUGCGUAUUGUUCAUUGAC
..(((.(((((......((.....))..................(((((((((.((((.......)))).)))))))))))))))))((((((...))))))............. ( -26.80)
>DroSim_CAF1 25926 115 - 1
AACCGGCCAAAACAUUAGCAUACACCCAUAUUUCCACGAAUCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGAC
.....((((((........................((......))((((((((.((((.......)))).)))))))).))))))..((((((...))))))............. ( -23.30)
>DroEre_CAF1 25761 113 - 1
AACCGCCAAAAGCAUUAGCAUACACU--UAUUUCCACGAACCAGUGCUAAAUAGUUUCCGAAUUUGAAAAUAUUUAGCAUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGAC
....((((((.((....)).......--................(((((((((.((((.......)))).)))))))))))))))..((((((...))))))............. ( -26.00)
>DroYak_CAF1 45977 113 - 1
AACCGGCAAAAGCAUUAGCAUACACC--UAUUUCCACGAACCAGUGCUAAAUAGUUUCCGAUUUUGGAAAUAUUUAGCAUUUCGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGAC
....(((((..(((..(((.(((.((--(.......((((...((((((((((.((((((....)))))))))))))))))))).))).))))))..)))...)))))....... ( -31.90)
>consensus
AACCGGCCAAAACAUUAGCAUACACC__UAUUUCCACGAAUCAGUGCUAAAUAGUUUCCGAUAUUGAAAAUAUUUAGCAUUUGGCAGGCGUAGCUUCUGCGUAUUGUUCAUUGAC
.....................................((((.(((((((((((.((((.......)))).)))))))))))......((((((...))))))...))))...... (-20.80 = -20.24 +  -0.56)

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 11:56:26 2006