Locus 4532

Sequence ID 3R_DroMel_CAF1
Location 12,025,497 – 12,025,649
Length 152
Max. P 0.977162
window7398 window7399 window7400

overview

Window 8

Location 12,025,497 – 12,025,617
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -40.78
Consensus MFE -24.04
Energy contribution -23.43
Covariance contribution -0.61
Combinations/Pair 1.44
Mean z-score -1.66
Structure conservation index 0.59
SVM decision value 0.05
SVM RNA-class probability 0.556433
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12025497 120 - 27905053
GGGGAGUUUGGAAAGUACCAGUUCCUGCAGUUCUUCCUGCAGGUGCUCUCCGGCCUGACCGCUGGCAUGCACAUGCUAUCGCUGGUCACGGUGGCCGCCGUGCCUGAGCAUCGCUGCUUC
(((((((((((......))))..(((((((......))))))).))))))).((((((((((((((((....))))))..)).))))).)))(((.((.((((....)))).)).))).. ( -52.40)
>DroVir_CAF1 14003 120 - 1
GGUGAAUUUGGUAAAUAUCAAUUUGCCCAAUUCUUUCUGCAAGUGCUGUCCGCUCUCACGGCGGGUAUGCACAUGCUCUCGCUGGUGACUGUUGCUGCUGUGCCCGAGCAUCGCUGCUUU
...(((((.(((((((....))))))).))))).....(((.(((((..(((((.....)))))..).)))).)))....((.(....).)).((.((.((((....)))).)).))... ( -40.10)
>DroPse_CAF1 12122 120 - 1
GGGGAAUUUGGUAAAUACCAAUUCUUGCAGUUCUUCCUGCAAGUCCUCUCCGCUUUGACCGCAGGCAUGCAUAUGCUCUCCCUGGUUACGGUAUCCGCAGUGCCAGAGCAUCGCUGCUUU
(((((..(((((....)))))..(((((((......)))))))...)))))((.......))(((((.((..(((((((....(((..(((...)))....)))))))))).))))))). ( -39.10)
>DroGri_CAF1 4253 120 - 1
GGUGAAUUUGGCAAAUAUCAAUUUGCCCAAUUCUUUUUGCAAGUGCUCUCGGCACUGACGGCGGGAAUGCAUAUGCUGUCUCUGGUAACUGUGGCUGCUGUUCCGGAGCAUCGGUGCUUU
...(((((.(((((((....))))))).))))).....(((.((((((.(((....((((((((...((((..((((......))))..)))).)))))))))))))))))...)))... ( -41.90)
>DroWil_CAF1 3659 120 - 1
GGGGAAUUUGGUAAAUACCAAUUCCUUCAAUUCUUCCUGCAAGUAUUAUCCGCCUUGACUGCUGGUCUGCAUAUGCUCUCACUGGUCACAGUUGCCGCUGUGCCCGAGCAUCGUUGUUUC
((((((((.(((....)))))))))))...........((((.........((...(((.....))).))..((((((.....((.((((((....)))))).))))))))..))))... ( -30.20)
>DroMoj_CAF1 12540 120 - 1
GGUGAAUUCGGCAAAUACCAAUUCGCCCAAUUUUUCCUGCAAGUGUUGUCCGCAUUGACAGCGGGCAUGCACAUGCUGUCCCUGGUGACUGUUGCAUCAGUGCCCGAGCAUCGCUGCUUU
((((((((.((......))))))))))...........(((.(((((((((((.......))))))).))))((((((..(((((((.(....))))))).)..).)))))...)))... ( -41.00)
>consensus
GGGGAAUUUGGUAAAUACCAAUUCGCCCAAUUCUUCCUGCAAGUGCUCUCCGCACUGACCGCGGGCAUGCACAUGCUCUCCCUGGUCACUGUUGCCGCUGUGCCCGAGCAUCGCUGCUUU
((((((((.((......))))))))))...........(((.((((...((((.......)).))...)))).))).......((.((((((....)))))))).(((((....))))). (-24.04 = -23.43 +  -0.61)

alignment

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secondary structure

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Window 9

Location 12,025,537 – 12,025,649
Length 112
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 75.77
Mean single sequence MFE -29.07
Consensus MFE -18.13
Energy contribution -17.68
Covariance contribution -0.44
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.62
SVM decision value 1.07
SVM RNA-class probability 0.910464
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12025537 112 + 27905053
GAUAGCAUGUGCAUGCCAGCGGUCAGGCCGGAGAGCACCUGCAGGAAGAACUGCAGGAACUGGUACUUUCCAAACUCCCCUGCAAUUGGAUAGAAAAAAAUAGAAAGACAUU
....((....))...((((..(.((((..((((....(((((((......)))))))...(((......)))..)))))))))..))))....................... ( -32.70)
>DroPse_CAF1 12162 101 + 1
GAGAGCAUAUGCAUGCCUGCGGUCAAAGCGGAGAGGACUUGCAGGAAGAACUGCAAGAAUUGGUAUUUACCAAAUUCCCCUGUA---GGA------AAAAGAG--CGACGAA
....((....)).(((((....((...((((.(.((((((((((......)))))))..(((((....)))))..)))))))).---.))------...)).)--))..... ( -28.70)
>DroEre_CAF1 3838 106 + 1
GAUAGCAUGUGCAUGCCAGCGGUCAGGCCGGAAAGCACCUGCAGGAAGAACUGCAGGAACUGGUACUUUCCAAACUCCCCUGGAAUGGGU------AAGAUAGAGAGUCAUA
....((....)).(((((((((.....))).......(((((((......)))))))..))))))(((((.......(((......))).------......)))))..... ( -34.44)
>DroWil_CAF1 3699 96 + 1
GAGAGCAUAUGCAGACCAGCAGUCAAGGCGGAUAAUACUUGCAGGAAGAAUUGAAGGAAUUGGUAUUUACCAAAUUCCCCUAAAAUGAUC------AAG----------GAA
..((.(((.(((......)))....(((.(((.....(((.(((......))))))...(((((....)))))..))))))...))).))------...----------... ( -16.90)
>DroYak_CAF1 3804 92 + 1
GAUAGCAUGUGCAUGCCAGCGGUCAGGCCGGAAAGCACCUGCAGGAAGAACUGCAGGAACUGGUACUUUCCAAACUCCCCUGGAAUUGGA------A--------------A
....((....)).(((((((((.....))).......(((((((......)))))))..))))))..((((((..(((...))).)))))------)--------------. ( -33.00)
>DroPer_CAF1 12128 101 + 1
GAGAGCAUAUGCAUGCCUGCGGUCAAAGCGGAGAGGACUUGCAGGAAGAACUGCAAGAAUUGGUAUUUACCAAAUUCCCCUGUA---GGA------AAAAGAG--CGACGAA
....((....)).(((((....((...((((.(.((((((((((......)))))))..(((((....)))))..)))))))).---.))------...)).)--))..... ( -28.70)
>consensus
GAGAGCAUAUGCAUGCCAGCGGUCAAGCCGGAGAGCACCUGCAGGAAGAACUGCAGGAACUGGUACUUACCAAACUCCCCUGGAAU_GGA______AAAA_AG___GACGAA
((..((............))..)).....(((.....(((((((......)))))))...(((......)))...))).................................. (-18.13 = -17.68 +  -0.44)

alignment

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secondary structure

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Window 0

Location 12,025,537 – 12,025,649
Length 112
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 75.77
Mean single sequence MFE -28.17
Consensus MFE -20.99
Energy contribution -21.35
Covariance contribution 0.36
Combinations/Pair 1.26
Mean z-score -1.94
Structure conservation index 0.75
SVM decision value 1.79
SVM RNA-class probability 0.977162
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12025537 112 - 27905053
AAUGUCUUUCUAUUUUUUUCUAUCCAAUUGCAGGGGAGUUUGGAAAGUACCAGUUCCUGCAGUUCUUCCUGCAGGUGCUCUCCGGCCUGACCGCUGGCAUGCACAUGCUAUC
...(((((((((..(((..((..........))..)))..))))))).)).(((..((((((......))))))((((...(((((......)))))...))))..)))... ( -34.80)
>DroPse_CAF1 12162 101 - 1
UUCGUCG--CUCUUUU------UCC---UACAGGGGAAUUUGGUAAAUACCAAUUCUUGCAGUUCUUCCUGCAAGUCCUCUCCGCUUUGACCGCAGGCAUGCAUAUGCUCUC
...(((.--.......------...---...((((((..(((((....)))))..(((((((......)))))))))))))..((.......)).)))..((....)).... ( -24.90)
>DroEre_CAF1 3838 106 - 1
UAUGACUCUCUAUCUU------ACCCAUUCCAGGGGAGUUUGGAAAGUACCAGUUCCUGCAGUUCUUCCUGCAGGUGCUUUCCGGCCUGACCGCUGGCAUGCACAUGCUAUC
...((((((((.....------..........)))))))).((((((((((......(((((......)))))))))))))))((.....))..((((((....)))))).. ( -34.06)
>DroWil_CAF1 3699 96 - 1
UUC----------CUU------GAUCAUUUUAGGGGAAUUUGGUAAAUACCAAUUCCUUCAAUUCUUCCUGCAAGUAUUAUCCGCCUUGACUGCUGGUCUGCAUAUGCUCUC
...----------(((------(......((..(((((((.(((....))))))))))..)).........))))........((...(((.....))).)).......... ( -17.16)
>DroYak_CAF1 3804 92 - 1
U--------------U------UCCAAUUCCAGGGGAGUUUGGAAAGUACCAGUUCCUGCAGUUCUUCCUGCAGGUGCUUUCCGGCCUGACCGCUGGCAUGCACAUGCUAUC
.--------------.------..........((..((..(((((((((((......(((((......))))))))))))))))..))..))..((((((....)))))).. ( -33.20)
>DroPer_CAF1 12128 101 - 1
UUCGUCG--CUCUUUU------UCC---UACAGGGGAAUUUGGUAAAUACCAAUUCUUGCAGUUCUUCCUGCAAGUCCUCUCCGCUUUGACCGCAGGCAUGCAUAUGCUCUC
...(((.--.......------...---...((((((..(((((....)))))..(((((((......)))))))))))))..((.......)).)))..((....)).... ( -24.90)
>consensus
UUCGUC___CU_UUUU______UCC_AUUACAGGGGAAUUUGGAAAAUACCAAUUCCUGCAGUUCUUCCUGCAAGUGCUCUCCGCCCUGACCGCUGGCAUGCACAUGCUAUC
................................(((((((((((......))))..(((((((......))))))).)))))))............(((((....)))))... (-20.99 = -21.35 +   0.36)

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 11:31:36 2006