Locus 5900

Sequence ID 2L_DroMel_CAF1
Location 16,676,323 – 16,676,467
Length 144
Max. P 0.998652
window9359 window9360 window9361 window9362

overview

Window 9

Location 16,676,323 – 16,676,431
Length 108
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 76.87
Mean single sequence MFE -26.35
Consensus MFE -11.84
Energy contribution -13.07
Covariance contribution 1.23
Combinations/Pair 1.35
Mean z-score -2.54
Structure conservation index 0.45
SVM decision value 1.29
SVM RNA-class probability 0.938187
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16676323 108 + 22407834
GUUUAACUUUUUGGCGCAAUAUUAUUCACCUUGACCACGCACCGGUGUGCAAAAGAUUCACCGCA---CACCGGUGCACUUAAAUUCACCACAGCCUUAAUAAUUCUUACG
............(((..........((.....))....((((((((((((............)))---)))))))))................)))............... ( -29.50)
>DroSec_CAF1 131062 108 + 1
GUUUAACUUUUUGGCGCAAUAUUAUUCACCUUGACCACGCACCGGUGUGCAAAAGAUUAACCGCA---CAUCGGUGCAUUUAAAUUCACCACAGCCGUAAUAAUUCCUACG
............(((..........((.....))....((((((((((((............)))---)))))))))................)))(((........))). ( -27.80)
>DroSim_CAF1 122918 108 + 1
GUUUAACUUUUUGGCGCAAUAUUAUUCACCUUGACCACGCACCGGUGUGCAAAAGAUUCACCGCA---CAUCGGUGCAUUUAAAUUCACCACAGCCCUAAUAAUUCCUACG
((........((((.((........((.....))....((((((((((((............)))---)))))))))................)).))))........)). ( -26.79)
>DroEre_CAF1 131403 108 + 1
GUUUGACUUUUUGGCGCAAUAAUAUUCACCUUGACCAUACACCGGUGUGCAAAAAAUUCACCGCA---CGCCGGUGCAUACAAAUUCACCACCGCCGUAAUGAUUCUUACG
((..((.((..(((((.........((.....)).....(((((((((((............)))---))))))))................)))))....)).))..)). ( -28.60)
>DroYak_CAF1 130401 106 + 1
GUUUGACUUUUUGGCGCAAUAUUAUUCACCUUGACCACACACCGGUGUGCAAA-AAUUCACCGCA---CACCGGUAUAUUGAAAUUCACCACAGUCCUAAUGAUUC-UAUG
....((((...(((.(((((((...((.....))......((((((((((...-........)))---))))))))))))).....).))).))))..........-.... ( -24.30)
>DroPer_CAF1 150315 89 + 1
GUUUGACUUUUUGGCGCAAAAUAAUCUACC--------ACACCGGUGAGAGA---ACUCCCCACAGCAUGGUGGCCCAA-----UGCGC-----AAUUU-UUGCCCAAACG
.........(((((.((((((.........--------.....((.(((...---.))).))...((((((....)).)-----)))..-----...))-))))))))).. ( -21.10)
>consensus
GUUUAACUUUUUGGCGCAAUAUUAUUCACCUUGACCACACACCGGUGUGCAAAAGAUUCACCGCA___CACCGGUGCAUUUAAAUUCACCACAGCCCUAAUAAUUCCUACG
............(((..........((.....))....((((((((((((............)))...)))))))))................)))............... (-11.84 = -13.07 +   1.23)

alignment

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secondary structure

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Window 0

Location 16,676,323 – 16,676,431
Length 108
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.87
Mean single sequence MFE -34.20
Consensus MFE -16.92
Energy contribution -17.90
Covariance contribution 0.98
Combinations/Pair 1.44
Mean z-score -2.75
Structure conservation index 0.49
SVM decision value 1.92
SVM RNA-class probability 0.982555
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16676323 108 - 22407834
CGUAAGAAUUAUUAAGGCUGUGGUGAAUUUAAGUGCACCGGUG---UGCGGUGAAUCUUUUGCACACCGGUGCGUGGUCAAGGUGAAUAAUAUUGCGCCAAAAAGUUAAAC
...............((((.(((((.........(((((((((---(((((........))))))))))))))....((.....)).........)))))...)))).... ( -36.60)
>DroSec_CAF1 131062 108 - 1
CGUAGGAAUUAUUACGGCUGUGGUGAAUUUAAAUGCACCGAUG---UGCGGUUAAUCUUUUGCACACCGGUGCGUGGUCAAGGUGAAUAAUAUUGCGCCAAAAAGUUAAAC
(((((......)))))(((.(((((.......((((((((.((---(((((........))))))).))))))))..((.....)).........)))))...)))..... ( -33.90)
>DroSim_CAF1 122918 108 - 1
CGUAGGAAUUAUUAGGGCUGUGGUGAAUUUAAAUGCACCGAUG---UGCGGUGAAUCUUUUGCACACCGGUGCGUGGUCAAGGUGAAUAAUAUUGCGCCAAAAAGUUAAAC
(((((..((((((...(((....(((......((((((((.((---(((((........))))))).))))))))..))).))).)))))).))))).............. ( -32.10)
>DroEre_CAF1 131403 108 - 1
CGUAAGAAUCAUUACGGCGGUGGUGAAUUUGUAUGCACCGGCG---UGCGGUGAAUUUUUUGCACACCGGUGUAUGGUCAAGGUGAAUAUUAUUGCGCCAAAAAGUCAAAC
.((((......))))(((.(..((((.....((((((((((.(---(((((........)))))).)))))))))).((.....))...))))..))))............ ( -37.00)
>DroYak_CAF1 130401 106 - 1
CAUA-GAAUCAUUAGGACUGUGGUGAAUUUCAAUAUACCGGUG---UGCGGUGAAUU-UUUGCACACCGGUGUGUGGUCAAGGUGAAUAAUAUUGCGCCAAAAAGUCAAAC
....-..........((((.(((((.......(((((((((((---(((((......-.))))))))))))))))..((.....)).........)))))...)))).... ( -37.20)
>DroPer_CAF1 150315 89 - 1
CGUUUGGGCAA-AAAUU-----GCGCA-----UUGGGCCACCAUGCUGUGGGGAGU---UCUCUCACCGGUGU--------GGUAGAUUAUUUUGCGCCAAAAAGUCAAAC
..(((((((((-((...-----(.((.-----....)))(((((((((..((((..---..))))..))))))--------)))......)))))).)))))......... ( -28.40)
>consensus
CGUAAGAAUUAUUAAGGCUGUGGUGAAUUUAAAUGCACCGGUG___UGCGGUGAAUCUUUUGCACACCGGUGCGUGGUCAAGGUGAAUAAUAUUGCGCCAAAAAGUCAAAC
...............((((.((((........((((((((.((...(((((........))))))).)))))))).......((((......))))))))...)))).... (-16.92 = -17.90 +   0.98)

alignment

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secondary structure

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Window 1

Location 16,676,356 – 16,676,467
Length 111
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 69.30
Mean single sequence MFE -34.54
Consensus MFE -14.23
Energy contribution -15.15
Covariance contribution 0.92
Combinations/Pair 1.48
Mean z-score -3.08
Structure conservation index 0.41
SVM decision value 3.17
SVM RNA-class probability 0.998652
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16676356 111 + 22407834
ACCACGCACCGGUGUGCAAAAGAUUCACCGCA---CACCGGUGCACUUAAAUUCACCACAGCCUUAAUAAUUCUUACGGC-AUUUCCGUGCUCAAUGGUGAAUGGUCGCACUGAA
(((..((((((((((((............)))---)))))))))......((((((((.(((.............((((.-....)))))))...)))))))))))......... ( -40.81)
>DroSec_CAF1 131095 111 + 1
ACCACGCACCGGUGUGCAAAAGAUUAACCGCA---CAUCGGUGCAUUUAAAUUCACCACAGCCGUAAUAAUUCCUACGGC-AUUUCUGUGCUCAAUGGUGAAAGGUCGCACUGAA
(((..((((((((((((............)))---))))))))).......(((((((..((((((........))))))-.....((....)).))))))).)))......... ( -42.40)
>DroSim_CAF1 122951 111 + 1
ACCACGCACCGGUGUGCAAAAGAUUCACCGCA---CAUCGGUGCAUUUAAAUUCACCACAGCCCUAAUAAUUCCUACGGC-AUUUCUGUGCUCAAUGGUGAAAGGUCGCACUGAA
(((..((((((((((((............)))---))))))))).......(((((((..(((.((........)).)))-.....((....)).))))))).)))......... ( -36.70)
>DroEre_CAF1 131436 111 + 1
ACCAUACACCGGUGUGCAAAAAAUUCACCGCA---CGCCGGUGCAUACAAAUUCACCACCGCCGUAAUGAUUCUUACGCG-AUUUUUGUACUUAAUGGCGACUGGUCACACUGAG
......(((((((((((............)))---))))))))...........((((.((((((((......))))(((-(...)))).......))))..))))......... ( -32.10)
>DroYak_CAF1 130434 109 + 1
ACCACACACCGGUGUGCAAA-AAUUCACCGCA---CACCGGUAUAUUGAAAUUCACCACAGUCCUAAUGAUUC-UAUGAG-GUUUUUGUGCUUAAUGGCGACUGGCCACACUGAG
.......((((((((((...-........)))---)))))))..........(((.(((((.(((.(((....-))).))-)...))))).....((((.....))))...))). ( -30.60)
>DroPer_CAF1 150345 91 + 1
-----ACACCGGUGAGAGA---ACUCCCCACAGCAUGGUGGCCCAA-----UGCGC-----AAUUU-UUGCCCAAACGCGU-GUUCUCCUUCCG-CGGCGUGCGGCAACUCU---
-----.....((.(((...---.))).))...((((((....)).)-----)))..-----.....-(((((((..((((.-(........)))-))...)).)))))....--- ( -24.60)
>consensus
ACCACACACCGGUGUGCAAAAGAUUCACCGCA___CACCGGUGCAUUUAAAUUCACCACAGCCCUAAUAAUUCCUACGGC_AUUUCUGUGCUCAAUGGCGAAUGGUCACACUGAA
.((..((((((((((((............)))...)))))))))........((((((................(((((......))))).....))))))..)).......... (-14.23 = -15.15 +   0.92)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,676,356 – 16,676,467
Length 111
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 69.30
Mean single sequence MFE -39.06
Consensus MFE -16.82
Energy contribution -17.87
Covariance contribution 1.05
Combinations/Pair 1.40
Mean z-score -2.62
Structure conservation index 0.43
SVM decision value 2.57
SVM RNA-class probability 0.995393
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16676356 111 - 22407834
UUCAGUGCGACCAUUCACCAUUGAGCACGGAAAU-GCCGUAAGAAUUAUUAAGGCUGUGGUGAAUUUAAGUGCACCGGUG---UGCGGUGAAUCUUUUGCACACCGGUGCGUGGU
.........((((((((((((..(((((((....-.))))((......))...))))))))))........(((((((((---(((((........))))))))))))))))))) ( -45.90)
>DroSec_CAF1 131095 111 - 1
UUCAGUGCGACCUUUCACCAUUGAGCACAGAAAU-GCCGUAGGAAUUAUUACGGCUGUGGUGAAUUUAAAUGCACCGAUG---UGCGGUUAAUCUUUUGCACACCGGUGCGUGGU
.........(((.((((((((.............-(((((((......))))))).)))))))).....((((((((.((---(((((........))))))).))))))))))) ( -43.04)
>DroSim_CAF1 122951 111 - 1
UUCAGUGCGACCUUUCACCAUUGAGCACAGAAAU-GCCGUAGGAAUUAUUAGGGCUGUGGUGAAUUUAAAUGCACCGAUG---UGCGGUGAAUCUUUUGCACACCGGUGCGUGGU
.........(((.((((((((.............-(((.(((......))).))).)))))))).....((((((((.((---(((((........))))))).))))))))))) ( -39.44)
>DroEre_CAF1 131436 111 - 1
CUCAGUGUGACCAGUCGCCAUUAAGUACAAAAAU-CGCGUAAGAAUCAUUACGGCGGUGGUGAAUUUGUAUGCACCGGCG---UGCGGUGAAUUUUUUGCACACCGGUGUAUGGU
..(((..(.((((.(((((.....((........-.))((((......))))))))))))).)..)))((((((((((.(---(((((........)))))).)))))))))).. ( -40.10)
>DroYak_CAF1 130434 109 - 1
CUCAGUGUGGCCAGUCGCCAUUAAGCACAAAAAC-CUCAUA-GAAUCAUUAGGACUGUGGUGAAUUUCAAUAUACCGGUG---UGCGGUGAAUU-UUUGCACACCGGUGUGUGGU
....(((((((.....))).....))))....((-(.....-(((((((((......))))))..))).(((((((((((---(((((......-.))))))))))))))))))) ( -37.30)
>DroPer_CAF1 150345 91 - 1
---AGAGUUGCCGCACGCCG-CGGAAGGAGAAC-ACGCGUUUGGGCAA-AAAUU-----GCGCA-----UUGGGCCACCAUGCUGUGGGGAGU---UCUCUCACCGGUGU-----
---...........((((((-.(...(((((((-.(.((..((.(((.-....)-----)).))-----.)).)((.((((...)))))).))---)))))..)))))))----- ( -28.60)
>consensus
UUCAGUGCGACCAUUCACCAUUGAGCACAGAAAU_CCCGUAAGAAUUAUUAAGGCUGUGGUGAAUUUAAAUGCACCGGUG___UGCGGUGAAUCUUUUGCACACCGGUGCGUGGU
.........(((..(((((((...................................)))))))......((((((((.((...(((((........))))))).))))))))))) (-16.82 = -17.87 +   1.05)

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 11:55:49 2006