Locus 3459

Sequence ID 2R_DroMel_CAF1
Location 11,620,846 – 11,620,953
Length 107
Max. P 0.736121
window5643 window5644

overview

Window 3

Location 11,620,846 – 11,620,953
Length 107
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.19
Mean single sequence MFE -21.27
Consensus MFE -13.88
Energy contribution -14.38
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.65
SVM decision value 0.44
SVM RNA-class probability 0.736121
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11620846 107 + 20766785
UCGAGACGGCAACUAGGGCCGCGCUGCAAGUCAAAAAGAGGAAGAAGACCAGAUGCCUUUUGCUCUAAAAGAGCAAAU--CAACA-ACAU---GAA-AAUC-UUUA-CCACAC-ACA--
....((((((.......)))((...))..))).......((..(((((..........(((((((.....)))))))(--((...-...)---)).-..))-))).-))....-...-- ( -20.30)
>DroGri_CAF1 2232 105 + 1
UCGAGACAGCAACCAGGGCUGCACUGCAAGUUAAAAAGCGGAAGAAGCCCAAAUGCCUUUUGCUCUAAAAGAGCAAAU---AACA-AAAA-A-AAGAAUUC-UAUA-C-AUAC-A----
...(((..(((....(((((...((((..........))))....)))))...)))..(((((((.....))))))).---....-....-.-......))-)...-.-....-.---- ( -23.70)
>DroWil_CAF1 9322 109 + 1
UUGAAACGGCAACCCGAGCUGCACUGCAAGUUAAAAAGAGGAAGAAGACCAGAUGCCUUUUGCUCUAAAAGAGCAAAAUACAAAA-ACACAAAGCA-AAUCGUUUA-ACAAA-------
...((((((((......((......))............((.......))...))))((((((((.....)))))))).......-..........-....)))).-.....------- ( -19.60)
>DroMoj_CAF1 1805 98 + 1
UCGAGACAGCAACCAGGGCUGCACUGCAAGUUAAAAAACGGAAGAAGCCCAAAUGCCUUUUGCUCUAAAAGAGCAAAU---AACA-AA---------AUUC-UAUA-C-AAAC-A----
...(((..(((....(((((...((....(((....)))...)).)))))...)))..(((((((.....))))))).---....-..---------..))-)...-.-....-.---- ( -20.70)
>DroAna_CAF1 2045 103 + 1
UUGAGACGGCAACCCGGGCCGCGCUGCAAGUCAAAAAGAGGAAGAAGACCAGAUGCCUUUUGCUCUAAAAGAGCAAAU--CAACAAACAU---GAA-AAUC-UUUA-CCAC--------
....((((((.......)))((...))..))).......((..(((((..........(((((((.....)))))))(--((.......)---)).-..))-))).-))..-------- ( -19.80)
>DroPer_CAF1 4221 109 + 1
UUGAGACGGCAACCAGGGCUGCGUUGCAGGUUAAAAAGAGGAAGAAGACCAGAUGCCUUUUGCUCUAAAAGAGCAACU---AACA-A-AU---GAA-AAUC-UUUAACCAUAAUACAAC
........(((((((....)).))))).(((((((((((((..............))))))((((.....))))....---....-.-..---...-....-))))))).......... ( -23.54)
>consensus
UCGAGACGGCAACCAGGGCUGCACUGCAAGUUAAAAAGAGGAAGAAGACCAGAUGCCUUUUGCUCUAAAAGAGCAAAU___AACA_ACAU___GAA_AAUC_UUUA_CCAAAC_A____
.......((((......((......))............((.......))...)))).(((((((.....))))))).......................................... (-13.88 = -14.38 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,620,846 – 11,620,953
Length 107
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.19
Mean single sequence MFE -25.92
Consensus MFE -17.61
Energy contribution -17.42
Covariance contribution -0.19
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.68
SVM decision value 0.37
SVM RNA-class probability 0.709871
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11620846 107 - 20766785
--UGU-GUGUGG-UAAA-GAUU-UUC---AUGU-UGUUG--AUUUGCUCUUUUAGAGCAAAAGGCAUCUGGUCUUCUUCCUCUUUUUGACUUGCAGCGCGGCCCUAGUUGCCGUCUCGA
--...-..(.((-..((-((((-...---((((-(....--.(((((((.....))))))).)))))..))))))...)).).....(((..(((((.........))))).))).... ( -24.60)
>DroGri_CAF1 2232 105 - 1
----U-GUAU-G-UAUA-GAAUUCUU-U-UUUU-UGUU---AUUUGCUCUUUUAGAGCAAAAGGCAUUUGGGCUUCUUCCGCUUUUUAACUUGCAGUGCAGCCCUGGUUGCUGUCUCGA
----(-(((.-(-(.((-(((..(..-.-....-(((.---.(((((((.....)))))))..)))...(((.....))))..))))))).))))..(((((....)))))........ ( -24.30)
>DroWil_CAF1 9322 109 - 1
-------UUUGU-UAAACGAUU-UGCUUUGUGU-UUUUGUAUUUUGCUCUUUUAGAGCAAAAGGCAUCUGGUCUUCUUCCUCUUUUUAACUUGCAGUGCAGCUCGGGUUGCCGUUUCAA
-------.....-.(((((..(-(((...((..-...(((.((((((((.....)))))))).)))...((.......))........))..)))).(((((....))))))))))... ( -24.30)
>DroMoj_CAF1 1805 98 - 1
----U-GUUU-G-UAUA-GAAU---------UU-UGUU---AUUUGCUCUUUUAGAGCAAAAGGCAUUUGGGCUUCUUCCGUUUUUUAACUUGCAGUGCAGCCCUGGUUGCUGUCUCGA
----(-((..-(-(.((-(((.---------..-(((.---.(((((((.....)))))))..)))...(((.....)))...)))))))..)))..(((((....)))))........ ( -23.70)
>DroAna_CAF1 2045 103 - 1
--------GUGG-UAAA-GAUU-UUC---AUGUUUGUUG--AUUUGCUCUUUUAGAGCAAAAGGCAUCUGGUCUUCUUCCUCUUUUUGACUUGCAGCGCGGCCCGGGUUGCCGUCUCAA
--------(.((-..((-((((-...---((((((....--.(((((((.....)))))))))))))..))))))...)).).....(((..(((((.((...)).))))).))).... ( -27.10)
>DroPer_CAF1 4221 109 - 1
GUUGUAUUAUGGUUAAA-GAUU-UUC---AU-U-UGUU---AGUUGCUCUUUUAGAGCAAAAGGCAUCUGGUCUUCUUCCUCUUUUUAACCUGCAACGCAGCCCUGGUUGCCGUCUCAA
((((((....(((((((-((..-.((---(.-.-((((---..((((((.....))))))..))))..)))...)))........))))))))))))(((((....)))))........ ( -31.50)
>consensus
____U_GUAUGG_UAAA_GAUU_UUC___AUGU_UGUU___AUUUGCUCUUUUAGAGCAAAAGGCAUCUGGUCUUCUUCCUCUUUUUAACUUGCAGCGCAGCCCUGGUUGCCGUCUCAA
..........................................(((((((.....)))))))((((....((.......)).................(((((....))))).))))... (-17.61 = -17.42 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:03 2006