Locus 2026

Sequence ID 3R_DroMel_CAF1
Location 5,745,671 – 5,745,804
Length 133
Max. P 0.940378
window3321 window3322 window3323

overview

Window 1

Location 5,745,671 – 5,745,778
Length 107
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 91.87
Mean single sequence MFE -39.56
Consensus MFE -34.72
Energy contribution -34.00
Covariance contribution -0.72
Combinations/Pair 1.17
Mean z-score -1.36
Structure conservation index 0.88
SVM decision value 0.55
SVM RNA-class probability 0.779637
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5745671 107 - 27905053
UAUGCCGUGUGGCAUGCGGCAUGUGGCAUGGGGCAACUGCCACUGGCGACUGGCAC----CACUGGCACUUGUUGGAAAUAGCUUAAAGCCGGGCUCGUGCAAACUAAAGU
((((((((((...))))))))))..(((((((((....))).(((((....(((..----..(..((....))..).....)))....)))))..)))))).......... ( -38.30)
>DroSec_CAF1 36965 107 - 1
UAUGCCGAGUGGCAUGCGGCAUGUGGCAUGGGGCAACUGCCGCUGGCGACUGGCAC----CACUGGCACUUGUUGGAAAUAGCUUAAAGCCGGGCUCGUGCAAACUAAAGU
..((((.(((.((..((((((.((.((.....)).))))))))..)).))))))).----..(((((....((((....)))).....)))))((....)).......... ( -38.70)
>DroSim_CAF1 38064 107 - 1
UAUGCCGAGUGACAUGCGGCAUGAGGCAUGGGGCAACUGCCGCUGGCGACUGGCAC----CACUGGCACUUGUUGGAAAUAGCUUAAAGCCGGGCUCGUGCAAACUAAAGU
..((((((((..(((((........))))).(((....))).(((((....(((..----..(..((....))..).....)))....)))))))))).)))......... ( -37.00)
>DroEre_CAF1 32838 110 - 1
UAUGCCGAGUGGCAUGCGGCAUUUGGCAUGGGGCAACUGCCACUGGCAGCUGGCACCA-CCACUGGCACUUGUUGGAAAUAACUUAAAGCCGGGCUCGUGGAAACUAAAGU
(((((((((((.(....).))))))))))).(.((.(((((...))))).)).).(((-(..(((((....((((....)))).....)))))....)))).......... ( -40.70)
>DroYak_CAF1 20930 111 - 1
UAUGCCGCGUGGCAUGCGGCAUUUGGCAUGGGGCAACUGCCACCGGCAACUGCCACUGGCAACUGGCACUUGUUGGAAAUAACUUAAAGCCGGGCUCGUGGAAACCAAAGU
....(((((.(((...((((...(((((...(....))))))(((((((.(((((..(....)))))).)))))))............)))).)))))))).......... ( -43.10)
>consensus
UAUGCCGAGUGGCAUGCGGCAUGUGGCAUGGGGCAACUGCCACUGGCGACUGGCAC____CACUGGCACUUGUUGGAAAUAGCUUAAAGCCGGGCUCGUGCAAACUAAAGU
..(((((.(((((((((........)))).((....))))))))))))....((((......(((((....((((....)))).....)))))....)))).......... (-34.72 = -34.00 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,745,711 – 5,745,804
Length 93
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 82.27
Mean single sequence MFE -39.02
Consensus MFE -24.27
Energy contribution -24.22
Covariance contribution -0.05
Combinations/Pair 1.23
Mean z-score -3.77
Structure conservation index 0.62
SVM decision value 1.31
SVM RNA-class probability 0.940378
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5745711 93 + 27905053
AAGUGCCAGUG----GUGCCAGUCG-CCAGUGGCAGUUGCCCCAUGCCACAUGCCGCAUGCCAC----A----CGGCAUAUCAUGGCAAAUGGGCAACAAUUUGAA
...(((((.((----(((.....))-))).)))))(((((((..(((((.((((((........----.----))))))....)))))...)))))))........ ( -43.30)
>DroSec_CAF1 37005 93 + 1
AAGUGCCAGUG----GUGCCAGUCG-CCAGCGGCAGUUGCCCCAUGCCACAUGCCGCAUGCCAC----U----CGGCAUAUCAUGGCAAAUGGGCAACAAUUUGAA
...((((..((----(((.....))-)))..))))(((((((..(((((.((((((........----.----))))))....)))))...)))))))........ ( -38.50)
>DroSim_CAF1 38104 93 + 1
AAGUGCCAGUG----GUGCCAGUCG-CCAGCGGCAGUUGCCCCAUGCCUCAUGCCGCAUGUCAC----U----CGGCAUAUCAUGGCAAAUGGGCAACAAUUUGAA
...((((..((----(((.....))-)))..))))(((((((..((((..((((((........----.----)))))).....))))...)))))))........ ( -37.40)
>DroEre_CAF1 32878 96 + 1
AAGUGCCAGUGG-UGGUGCCAGCUG-CCAGUGGCAGUUGCCCCAUGCCAAAUGCCGCAUGCCAC----U----CGGCAUAUCAUGGCAAAUGGGCAACAAUUUGAA
...(((((.(((-..((....))..-))).)))))(((((((..(((((.((((((........----.----))))))....)))))...)))))))........ ( -46.00)
>DroYak_CAF1 20970 97 + 1
AAGUGCCAGUUGCCAGUGGCAGUUG-CCGGUGGCAGUUGCCCCAUGCCAAAUGCCGCAUGCCAC----G----CGGCAUAUCAUGGCAAAUGGGCAACAAUUUGAA
..........(((((.((((....)-))).)))))(((((((..(((((.(((((((.......----)----))))))....)))))...)))))))........ ( -47.70)
>DroPer_CAF1 42665 96 + 1
AAGUGCCU--C----AUGCUCAUGCCCCAGCCCCAG----CCCAUGCCACAUGCCGCAUGGCCCCUACUCUACUGCCGUAUCAUAGCAAAUGGGCAGAAAUUUCAA
...(((((--.----.((((.((((..(((....((----.((((((........))))))...))......)))..))))...))))...))))).......... ( -21.20)
>consensus
AAGUGCCAGUG____GUGCCAGUCG_CCAGCGGCAGUUGCCCCAUGCCACAUGCCGCAUGCCAC____U____CGGCAUAUCAUGGCAAAUGGGCAACAAUUUGAA
...((((.........(((((........((((((...((.....))....))))))(((((............)))))....)))))....)))).......... (-24.27 = -24.22 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,745,711 – 5,745,804
Length 93
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 82.27
Mean single sequence MFE -40.18
Consensus MFE -23.82
Energy contribution -25.79
Covariance contribution 1.97
Combinations/Pair 1.11
Mean z-score -3.21
Structure conservation index 0.59
SVM decision value 0.92
SVM RNA-class probability 0.880942
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5745711 93 - 27905053
UUCAAAUUGUUGCCCAUUUGCCAUGAUAUGCCG----U----GUGGCAUGCGGCAUGUGGCAUGGGGCAACUGCCACUGG-CGACUGGCAC----CACUGGCACUU
........(((((((...((((((...((((((----(----((...)))))))))))))))..)))))))(((((.(((-.(.....).)----)).)))))... ( -43.80)
>DroSec_CAF1 37005 93 - 1
UUCAAAUUGUUGCCCAUUUGCCAUGAUAUGCCG----A----GUGGCAUGCGGCAUGUGGCAUGGGGCAACUGCCGCUGG-CGACUGGCAC----CACUGGCACUU
........(((((((...((((((...((((((----.----........))))))))))))..)))))))(((((.(((-.(.....).)----)).)))))... ( -40.60)
>DroSim_CAF1 38104 93 - 1
UUCAAAUUGUUGCCCAUUUGCCAUGAUAUGCCG----A----GUGACAUGCGGCAUGAGGCAUGGGGCAACUGCCGCUGG-CGACUGGCAC----CACUGGCACUU
........(((((((...((((....(((((((----.----........))))))).))))..)))))))(((((.(((-.(.....).)----)).)))))... ( -38.30)
>DroEre_CAF1 32878 96 - 1
UUCAAAUUGUUGCCCAUUUGCCAUGAUAUGCCG----A----GUGGCAUGCGGCAUUUGGCAUGGGGCAACUGCCACUGG-CAGCUGGCACCA-CCACUGGCACUU
........(((((((...(((((....((((((----.----........)))))).)))))..)))))))(((((.(((-....((....))-))).)))))... ( -40.00)
>DroYak_CAF1 20970 97 - 1
UUCAAAUUGUUGCCCAUUUGCCAUGAUAUGCCG----C----GUGGCAUGCGGCAUUUGGCAUGGGGCAACUGCCACCGG-CAACUGCCACUGGCAACUGGCACUU
........(((((((...(((((....((((((----(----((...))))))))).)))))..)))))))(((((..((-(....)))..))))).......... ( -47.20)
>DroPer_CAF1 42665 96 - 1
UUGAAAUUUCUGCCCAUUUGCUAUGAUACGGCAGUAGAGUAGGGGCCAUGCGGCAUGUGGCAUGGG----CUGGGGCUGGGGCAUGAGCAU----G--AGGCACUU
......(..(.((((.....((((..(((....)))..))))((.((((((.(....).)))))).----)).)))).)..).....((..----.--..)).... ( -31.20)
>consensus
UUCAAAUUGUUGCCCAUUUGCCAUGAUAUGCCG____A____GUGGCAUGCGGCAUGUGGCAUGGGGCAACUGCCACUGG_CGACUGGCAC____CACUGGCACUU
........(((((((...(((((((.(((((((..........)))))))...)))..))))..)))))))(((((.((................)).)))))... (-23.82 = -25.79 +   1.97)

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 10:25:36 2006