Locus 9339

Sequence ID 3R_DroMel_CAF1
Location 24,810,373 – 24,810,497
Length 124
Max. P 0.668532
window14944 window14945 window14946 window14947

overview

Window 4

Location 24,810,373 – 24,810,471
Length 98
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 78.92
Mean single sequence MFE -18.70
Consensus MFE -12.08
Energy contribution -12.42
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.65
SVM decision value 0.03
SVM RNA-class probability 0.549270
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24810373 98 + 27905053
CGAAG-------UCCUGGCAAAAUGGUGAAACAUUAAAUU-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUGGAAAAUGG
.....-------(((.(((..((((......)))).....-((((((((((........))))))))))....)))((....)).........----....)))...... ( -17.50)
>DroVir_CAF1 55574 82 + 1
-------------------AAAAUGGUGAAACAUUAAAUU-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGUCCAAAUACAUGCGAGU--------
-------------------....(((..............-((((((((((........))))))))))..((((.......))))))).............-------- ( -14.60)
>DroPse_CAF1 23028 90 + 1
AGACG-------UGGGCGAGAAAUGGUGAAACAUUAAAUU-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUG--------
.....-------((((((...((((......)))).....-((((((((((........))))))))))..............))))))....----.....-------- ( -21.80)
>DroGri_CAF1 56344 79 + 1
-------------------AAAAUGGUGAAACAUUAAAUUUUAUCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGUCCAAAUU----CGGCU--------
-------------------....((((((((.......))))))))......(((((....(((......)))((.......)))))))....----.....-------- ( -13.60)
>DroAna_CAF1 20337 98 + 1
AGAGGGGCCUGCGCCUGGCAAAAUGGUAAAACAUUAAAUU-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUGG-------
....((((..(((........((((......)))).....-((((((((((........))))))))))...))).((....)))))).....----......------- ( -22.90)
>DroPer_CAF1 23230 90 + 1
AGACG-------UGGGCGAGAAAUGGUGAAACAUUAAAUU-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUG--------
.....-------((((((...((((......)))).....-((((((((((........))))))))))..............))))))....----.....-------- ( -21.80)
>consensus
AGA_G_______U____G_AAAAUGGUGAAACAUUAAAUU_UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA____AAAUG________
.......................(((...............((((((((((........))))))))))...(((.......))).)))..................... (-12.08 = -12.42 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,810,373 – 24,810,471
Length 98
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 78.92
Mean single sequence MFE -17.66
Consensus MFE -11.97
Energy contribution -11.92
Covariance contribution -0.05
Combinations/Pair 1.07
Mean z-score -1.34
Structure conservation index 0.68
SVM decision value 0.29
SVM RNA-class probability 0.668532
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24810373 98 - 27905053
CCAUUUUCCAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-AAUUUAAUGUUUCACCAUUUUGCCAGGA-------CUUCG
......(((....----((..(((((((.((((((......)).))))...)))))))..))..((.((-((....(((......))))))).)))))-------..... ( -15.70)
>DroVir_CAF1 55574 82 - 1
--------ACUCGCAUGUAUUUGGACGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-AAUUUAAUGUUUCACCAUUUU-------------------
--------....(((.(((..(((((((.((((((......)).))))...)))))))..))).)))..-.....................------------------- ( -18.80)
>DroPse_CAF1 23028 90 - 1
--------CAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-AAUUUAAUGUUUCACCAUUUCUCGCCCA-------CGUCU
--------.....----....(((((((....))(((((((.......((((((......))))))...-....)))))))............)))))-------..... ( -18.14)
>DroGri_CAF1 56344 79 - 1
--------AGCCG----AAUUUGGACGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGAUAAAAUUUAAUGUUUCACCAUUUU-------------------
--------...((----(((.(((((((.((((((......)).))))...)))))))...))))).........................------------------- ( -15.20)
>DroAna_CAF1 20337 98 - 1
-------CCAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-AAUUUAAUGUUUUACCAUUUUGCCAGGCGCAGGCCCCUCU
-------......----.....((((((....)).((.....((((......)))).........(((.-.....((((......))))......)))))..)))).... ( -20.00)
>DroPer_CAF1 23230 90 - 1
--------CAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-AAUUUAAUGUUUCACCAUUUCUCGCCCA-------CGUCU
--------.....----....(((((((....))(((((((.......((((((......))))))...-....)))))))............)))))-------..... ( -18.14)
>consensus
________CAUUU____UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA_AAUUUAAUGUUUCACCAUUUU_C____A_______C_UCU
.................((..(((((((.((((((......)).))))...)))))))..))................................................ (-11.97 = -11.92 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,810,406 – 24,810,497
Length 91
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 80.16
Mean single sequence MFE -12.90
Consensus MFE -9.05
Energy contribution -9.55
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.12
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.510177
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24810406 91 + 27905053
-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUGGAAAAUGGA-AAAUGAAAAUGAAAAACC----AAAAAGG----
-((((((((((........))))))))))...(((.......))).(((....----...)))....(((.-..((....))......))----)......---- ( -13.20)
>DroVir_CAF1 55595 87 + 1
-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGUCCAAAUACAUGCGAGU--------A-AAAUAAAAAUGAAGGACC----AAAAAGG----
-((((((((((........))))))))))....((.......))((((...(((......))--------)-..((....))...)))).----.......---- ( -12.80)
>DroPse_CAF1 23061 87 + 1
-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUG--------A-AAAUGAAAAUGGAAAACC----AAAAAAGUAAA
-((((((((((........))))))))))...(((.......))).(((....----..((.--------.-..)).....)))......----........... ( -12.90)
>DroGri_CAF1 56365 88 + 1
UUAUCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGUCCAAAUU----CGGCU--------A-AAAUAUAAAUGAAGACCAACAAAAAAAGG----
...................(((((.(((...((((.......))))((.....----.))..--------.-.............))).))))).......---- ( -11.20)
>DroMoj_CAF1 54424 84 + 1
-UGCCAAAUAAAUGGACACUUGUUUGUCAUAACGCUACAAAUGCGUCCAAGAA----CGACU--------AAAAAUAAAAAUGAAAAACC----GAAAGGG----
-...........(((((....(((......)))((.......)))))))....----.....--------..................((----....)).---- ( -14.40)
>DroPer_CAF1 23263 87 + 1
-UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA----AAAUG--------A-AAAUGAAAAUGGAAAACC----AAAAACGUAAA
-((((((((((........))))))))))...(((.......))).(((....----..((.--------.-..)).....)))......----........... ( -12.90)
>consensus
_UGGCAAAUAAAUGGACACUUGUUUGUCAUAACGCUGCAAAUGCGCCCAAAUA____AAAUG________A_AAAUAAAAAUGAAAAACC____AAAAAGG____
.((((((((((........))))))))))...(((.......)))............................................................ ( -9.05 =  -9.55 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,810,406 – 24,810,497
Length 91
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 80.16
Mean single sequence MFE -14.88
Consensus MFE -11.85
Energy contribution -11.47
Covariance contribution -0.39
Combinations/Pair 1.15
Mean z-score -1.20
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.643210
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24810406 91 - 27905053
----CCUUUUU----GGUUUUUCAUUUUCAUUU-UCCAUUUUCCAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-
----((.....----))................-.........((...----((..(((((((.((((((......)).))))...)))))))..))..))...- ( -12.70)
>DroVir_CAF1 55595 87 - 1
----CCUUUUU----GGUCCUUCAUUUUUAUUU-U--------ACUCGCAUGUAUUUGGACGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-
----((.....----))................-.--------....(((.(((..(((((((.((((((......)).))))...)))))))..))).)))..- ( -19.10)
>DroPse_CAF1 23061 87 - 1
UUUACUUUUUU----GGUUUUCCAUUUUCAUUU-U--------CAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-
..........(----((....))).........-.--------.....----((..(((((((.((((((......)).))))...)))))))..)).......- ( -13.80)
>DroGri_CAF1 56365 88 - 1
----CCUUUUUUUGUUGGUCUUCAUUUAUAUUU-U--------AGCCG----AAUUUGGACGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGAUAA
----.............................-.--------...((----(((.(((((((.((((((......)).))))...)))))))...))))).... ( -15.20)
>DroMoj_CAF1 54424 84 - 1
----CCCUUUC----GGUUUUUCAUUUUUAUUUUU--------AGUCG----UUCUUGGACGCAUUUGUAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGGCA-
----.......----....................--------.((((----....(((((((.(((((.........)))))...)))))))......)))).- ( -14.60)
>DroPer_CAF1 23263 87 - 1
UUUACGUUUUU----GGUUUUCCAUUUUCAUUU-U--------CAUUU----UAUUUGGGCGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA-
.....(....(----((....)))....)....-.--------.....----((..(((((((.((((((......)).))))...)))))))..)).......- ( -13.90)
>consensus
____CCUUUUU____GGUUUUUCAUUUUCAUUU_U________AAUCG____UAUUUGGACGCAUUUGCAGCGUUAUGACAAACAAGUGUCCAUUUAUUUGCCA_
........................................................(((((((.((((((......)).))))...)))))))............ (-11.85 = -11.47 +  -0.39)

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 13:32:10 2006