Locus 1726

Sequence ID 3L_DroMel_CAF1
Location 5,001,752 – 5,002,004
Length 252
Max. P 0.955039
window2658 window2659 window2660 window2661 window2662

overview

Window 8

Location 5,001,752 – 5,001,864
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.27
Mean single sequence MFE -33.96
Consensus MFE -31.06
Energy contribution -31.45
Covariance contribution 0.39
Combinations/Pair 1.07
Mean z-score -1.29
Structure conservation index 0.91
SVM decision value 0.75
SVM RNA-class probability 0.841250
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5001752 112 + 23771897
CAAGUGUU--------UCGGUUAGUGCAGCUGGAGUCUGCUUAGCAUCUUUUUUUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUU
.(((((((--------((((((.....)))))))).).))))((((.........(((((((.(..((((((((((........)))))))))).....)))))))).........)))) ( -32.87)
>DroSec_CAF1 222363 111 + 1
CGAGUGUU--------UCGGUUAGUGCAGCUGGAGUCUGCUUAGCAUCUUUU-CUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUU
((((...)--------)))(((((.(((((....).))))))))).......-..(((((((.(..((((((((((........)))))))))).....))))))))............. ( -33.20)
>DroSim_CAF1 242139 111 + 1
CGAGUGUU--------UCGGUUAGUGCAGCUGGAGUCUGCUUAGCAUCUUUU-UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUU
((((...)--------)))(((((.(((((....).))))))))).......-..(((((((.(..((((((((((........)))))))))).....))))))))............. ( -33.20)
>DroEre_CAF1 225498 110 + 1
CGAGUGUU--------UCGGUUAGUGCAGCUGGAGUCUGCUUAGCAUCUUU--UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUU
((((...)--------)))(((((.(((((....).)))))))))......--..(((((((.(..((((((((((........)))))))))).....))))))))............. ( -33.20)
>DroYak_CAF1 230468 111 + 1
CGAGUGUU--------UCGGUUAGUGCAGCUGGAGUCUGCUUAGCAUCUUUU-UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUU
((((...)--------)))(((((.(((((....).))))))))).......-..(((((((.(..((((((((((........)))))))))).....))))))))............. ( -33.20)
>DroAna_CAF1 232501 118 + 1
CGAGUGUUUUCGGUGUUCGGUGAGUGCAGCUGGAGUCUGUGCAGCAUCUUU--UUUGGCGCCGCGUCGAGCUGCAAUUUCCAAUUUGCAAUUUGCCCGAGGGCGCCAUAAUUAUUUUGUU
.(((....)))(((((((((..(((((((.(((((....((((((......--.((((((...))))))))))))..)))))..)))).)))..))...))))))).............. ( -38.11)
>consensus
CGAGUGUU________UCGGUUAGUGCAGCUGGAGUCUGCUUAGCAUCUUUU_UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUU
...................(((((.(((((....).)))))))))..........(((((((.(..((((((((((........)))))))))).....))))))))............. (-31.06 = -31.45 +   0.39)

alignment

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secondary structure

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Window 9

Location 5,001,752 – 5,001,864
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -27.25
Consensus MFE -24.11
Energy contribution -24.00
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -1.48
Structure conservation index 0.88
SVM decision value 0.62
SVM RNA-class probability 0.803415
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5001752 112 - 23771897
AACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAAAAAAAGAUGCUAAGCAGACUCCAGCUGCACUAACCGA--------AACACUUG
.............(((((((((.(((....(((((....(....))))))))).).).)))))))...............((((.(....))))).........--------........ ( -26.20)
>DroSec_CAF1 222363 111 - 1
AACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAG-AAAAGAUGCUAAGCAGACUCCAGCUGCACUAACCGA--------AACACUCG
.............(((((((((.(((....(((((....(....))))))))).).).)))))))..-............((((.(....))))).........--------........ ( -26.20)
>DroSim_CAF1 242139 111 - 1
AACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA-AAAAGAUGCUAAGCAGACUCCAGCUGCACUAACCGA--------AACACUCG
.............(((((((((.(((....(((((....(....))))))))).).).)))))))..-............((((.(....))))).........--------........ ( -26.20)
>DroEre_CAF1 225498 110 - 1
AACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA--AAAGAUGCUAAGCAGACUCCAGCUGCACUAACCGA--------AACACUCG
.............(((((((((.(((....(((((....(....))))))))).).).)))))))..--...........((((.(....))))).........--------........ ( -26.20)
>DroYak_CAF1 230468 111 - 1
AACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA-AAAAGAUGCUAAGCAGACUCCAGCUGCACUAACCGA--------AACACUCG
.............(((((((((.(((....(((((....(....))))))))).).).)))))))..-............((((.(....))))).........--------........ ( -26.20)
>DroAna_CAF1 232501 118 - 1
AACAAAAUAAUUAUGGCGCCCUCGGGCAAAUUGCAAAUUGGAAAUUGCAGCUCGACGCGGCGCCAAA--AAAGAUGCUGCACAGACUCCAGCUGCACUCACCGAACACCGAAAACACUCG
.............((((((((((((((....(((((........))))))))))).).)))))))..--...(((((.((..........)).))).)).........(((......))) ( -32.50)
>consensus
AACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA_AAAAGAUGCUAAGCAGACUCCAGCUGCACUAACCGA________AACACUCG
.............(((((((((.(((....(((((....(....))))))))).).).)))))))...............((((.(....)))))......................... (-24.11 = -24.00 +  -0.11)

alignment

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secondary structure

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Window 0

Location 5,001,784 – 5,001,895
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.53
Mean single sequence MFE -30.95
Consensus MFE -27.40
Energy contribution -27.29
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.89
SVM decision value 1.45
SVM RNA-class probability 0.955039
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5001784 111 + 23771897
UUAGCAUCUUUUUUUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAAG-----GAA----
.........(((((((((((..(.((((((((((((........))))))...(((....)))((.((((.....)))).))..........)))))).)))))))))-----)))---- ( -30.90)
>DroSec_CAF1 222395 110 + 1
UUAGCAUCUUUU-CUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAAG-----GAA----
.........((.-.((((((..(.((((((((((((........))))))...(((....)))((.((((.....)))).))..........)))))).)))))))..-----)).---- ( -29.00)
>DroSim_CAF1 242171 110 + 1
UUAGCAUCUUUU-UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAAG-----GAA----
.........(((-(((((((..(.((((((((((((........))))))...(((....)))((.((((.....)))).))..........)))))).)))))))))-----)).---- ( -30.80)
>DroEre_CAF1 225530 109 + 1
UUAGCAUCUUU--UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAAG-----GAA----
........(((--(((((((..(.((((((((((((........))))))...(((....)))((.((((.....)))).))..........)))))).)))))))))-----)).---- ( -30.70)
>DroYak_CAF1 230500 110 + 1
UUAGCAUCUUUU-UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAAG-----GAA----
.........(((-(((((((..(.((((((((((((........))))))...(((....)))((.((((.....)))).))..........)))))).)))))))))-----)).---- ( -30.80)
>DroAna_CAF1 232541 118 + 1
GCAGCAUCUUU--UUUGGCGCCGCGUCGAGCUGCAAUUUCCAAUUUGCAAUUUGCCCGAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAUGCGAAAGAAAAGC
((((((.....--..(((((((.(.(((.(((((((........)))))....)).))))))))))).........)))))).........((((.....(((....))).))))..... ( -33.49)
>consensus
UUAGCAUCUUUU_UUUGGCGCCGCGUCGAGUUGCAGUUUCCAAUUUGCAAUUUGCCCCAGGGCGCCAUAAUUAUUUUGUUGCAAUUAAAAGUCUUGACACUGCCAAAG_____GAA____
.(((((.........(((((((.(..((((((((((........)))))))))).....)))))))).........)))))....................................... (-27.40 = -27.29 +  -0.11)

alignment

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secondary structure

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Window 1

Location 5,001,784 – 5,001,895
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.53
Mean single sequence MFE -28.87
Consensus MFE -25.94
Energy contribution -25.67
Covariance contribution -0.28
Combinations/Pair 1.07
Mean z-score -1.46
Structure conservation index 0.90
SVM decision value 0.87
SVM RNA-class probability 0.871028
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5001784 111 - 23771897
----UUC-----CUUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAAAAAAAGAUGCUAA
----...-----.......((((((........((((((........))))))(((((((((.(((....(((((....(....))))))))).).).))))))).......)))))).. ( -26.90)
>DroSec_CAF1 222395 110 - 1
----UUC-----CUUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAG-AAAAGAUGCUAA
----...-----..((((((...((........((((((........))))))(((((((((.(((....(((((....(....))))))))).).).))))))).)-).....)))))) ( -27.40)
>DroSim_CAF1 242171 110 - 1
----UUC-----CUUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA-AAAAGAUGCUAA
----...-----.......((((((........((((((........))))))(((((((((.(((....(((((....(....))))))))).).).)))))))..-....)))))).. ( -26.90)
>DroEre_CAF1 225530 109 - 1
----UUC-----CUUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA--AAAGAUGCUAA
----...-----.......((((((........((((((........))))))(((((((((.(((....(((((....(....))))))))).).).)))))))..--...)))))).. ( -26.90)
>DroYak_CAF1 230500 110 - 1
----UUC-----CUUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA-AAAAGAUGCUAA
----...-----.......((((((........((((((........))))))(((((((((.(((....(((((....(....))))))))).).).)))))))..-....)))))).. ( -26.90)
>DroAna_CAF1 232541 118 - 1
GCUUUUCUUUCGCAUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUCGGGCAAAUUGCAAAUUGGAAAUUGCAGCUCGACGCGGCGCCAAA--AAAGAUGCUGC
((.........))....((((((((........((((((........))))))((((((((((((((....(((((........))))))))))).).)))))))..--...)))))))) ( -38.20)
>consensus
____UUC_____CUUUGGCAGUGUCAAGACUUUUAAUUGCAACAAAAUAAUUAUGGCGCCCUGGGGCAAAUUGCAAAUUGGAAACUGCAACUCGACGCGGCGCCAAA_AAAAGAUGCUAA
...................((((((........((((((........))))))(((((((((.(((....(((((....(....))))))))).).).))))))).......)))))).. (-25.94 = -25.67 +  -0.28)

alignment

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secondary structure

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Window 2

Location 5,001,895 – 5,002,004
Length 109
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 95.52
Mean single sequence MFE -31.58
Consensus MFE -28.70
Energy contribution -28.94
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.91
SVM decision value 1.25
SVM RNA-class probability 0.936344
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5001895 109 - 23771897
AAAAGUUUGCCCUAGAAUCGCAAUUGCUUGGGCGGCGUAAUUGUUCUUUCGCAGCAUUUUC-CCUCCUGGCAAACAAACCGUAAAGGCUGGGGCAUAAAUUGGGCAAAUU
...(((((((((..(((..((((((((.........))))))))...)))...........-..(((..((..((.....))....))..)))........))))))))) ( -28.50)
>DroSec_CAF1 222505 110 - 1
AAAAGUUUGCCCUCGAAUUGCAAUUGCUUGGGCGGCGUAAUUGUUCUUUCGCAGCUUUUUCCCCUCUUGGCAAACAAACCGUAGAAGCUGGGGCAUAAAUUGGGCAAAUU
...(((((((((.((((..((((((((.........))))))))...))))((((((((.......(((.....))).....))))))))...........))))))))) ( -31.60)
>DroSim_CAF1 242281 109 - 1
AAAAGUUUGCCCUCGAAUUGCAAUUGCUUGGGCGGCGUAAUUGUUCUUUCGCAGCUUUUUC-CCUCUUGGCAAACAAACCGUAGAAGCUGGGGCAUAAAUUGGGCAAAUU
...(((((((((.((((..((((((((.........))))))))...))))((((((((..-....(((.....))).....))))))))...........))))))))) ( -32.20)
>DroEre_CAF1 225639 108 - 1
AAAAGUUUGCCCUCGAAUUGCAAUUGCUUGGGCGGCGUAAUUGUUCUUUCGCAGCUUUUUC--CUCUUGGCAAACAAACCGUAAAAGCUGGGGCAUAAAUUGGGCAAAUU
...(((((((((.((((..((((((((.........))))))))...))))((((((((..--...(((.....))).....))))))))...........))))))))) ( -32.70)
>DroYak_CAF1 230610 109 - 1
AAAAGUUUGCCCUCGAAUUGCAAUUGCUUGGGCGGCGUAAUUGUUCUUUCGCAGCUUCUUC-UCACUUGGCAAGCAAACCGUAAAAGCUGGGGCAUAAAUUGGGCAAAUU
...(((((((((......(((....((((..((((......(((......)))((((((..-......)).))))...))))..))))....)))......))))))))) ( -32.90)
>consensus
AAAAGUUUGCCCUCGAAUUGCAAUUGCUUGGGCGGCGUAAUUGUUCUUUCGCAGCUUUUUC_CCUCUUGGCAAACAAACCGUAAAAGCUGGGGCAUAAAUUGGGCAAAUU
...(((((((((......(((....((((..((((......(((......)))(((............))).......))))..))))....)))......))))))))) (-28.70 = -28.94 +   0.24)

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 10:14:38 2006