Locus 8320

Sequence ID 3R_DroMel_CAF1
Location 22,220,401 – 22,220,536
Length 135
Max. P 0.940599
window13412 window13413 window13414

overview

Window 2

Location 22,220,401 – 22,220,501
Length 100
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.06
Mean single sequence MFE -35.37
Consensus MFE -20.26
Energy contribution -22.35
Covariance contribution 2.09
Combinations/Pair 1.07
Mean z-score -1.97
Structure conservation index 0.57
SVM decision value 0.56
SVM RNA-class probability 0.780436
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22220401 100 - 27905053
GUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG--GGGCCCG------CCUUUCUCCAUUCGCUGCCAAUCCCUGGCCAUAUUUUCUU--
(.((((((((((((....)))))))))........((((((((...((..(((--(((....------....)))))).))...))))))))..))))..........-- ( -34.60)
>DroSec_CAF1 55798 100 - 1
GUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG--GGGCACG------CCUUUCCCCUUUCACUGCCAAUCCCCGGCCAUAUUUUCUU--
(.((((((((((((....)))))))))......(.((((((((...((...((--(((....------....)))))..))...)))))))).)))))..........-- ( -35.30)
>DroSim_CAF1 54733 100 - 1
GUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG--GGGCACG------CCUUUCCCCUUUCGCUGCCAAUCCCCGGCCAUAUUUUCUU--
(.((((((((((((....)))))))))......(.((((((((...((...((--(((....------....)))))..))...)))))))).)))))..........-- ( -36.40)
>DroEre_CAF1 69969 101 - 1
GUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGCUCAGACUUGU--GGGCCCG------CCUUUACCCUCUCGCUGCCAAUCCUGG-CCAUAUUUUUUUUU
(.(((..........((((((((((((.((..((.((((.((((((......)--))))).)------))).))....)).))))))))))))))-))............ ( -37.80)
>DroYak_CAF1 63020 101 - 1
GUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG--GGUCCCG------CCUUUCCCCUUUCGCUGCCAAUCCCUG-GUUCAAUUUUUUUA
((((.(((((((((....)))))))))..))))..((((((((...((...((--((.....------.....))))..))...))))))))...-.............. ( -34.10)
>DroMoj_CAF1 80177 91 - 1
GUGCUGCUGUCAAUGAGGAUUGGCAGGCAGCAUGCGGGCUGAGCAGGACUGGGCU-----CGGAUCAGCUUUUGGCUUUUGG------------GGCUUUCAUUUCUU--
((((((((((((((....))))))).))))))).((((((.((.....)).))))-----))((..((((((........))------------)))).)).......-- ( -34.00)
>consensus
GUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG__GGGCCCG______CCUUUCCCCUUUCGCUGCCAAUCCCCGGCCAUAUUUUCUU__
((((.(((((((((....)))))))).).))))..((((((((...((...((..(((..........)))....))..))...)))))))).................. (-20.26 = -22.35 +   2.09)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,220,434 – 22,220,536
Length 102
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 79.84
Mean single sequence MFE -30.89
Consensus MFE -20.77
Energy contribution -20.77
Covariance contribution 0.00
Combinations/Pair 1.05
Mean z-score -1.54
Structure conservation index 0.67
SVM decision value 0.41
SVM RNA-class probability 0.726013
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22220434 102 + 27905053
AGAAAGG------CGGGCCC----CCAAGUCUGAACCAACCCGCAUGCUGACUGCCAAUCCUUAUUGACAGCGGCACUUCCGCUUUGGCAGCCAAAAUAGCUGCGAGCCCCA
.(.((((------((((...----...............))))).(((((.(((.((((....)))).))))))))))).)((((..(((((.......))))))))).... ( -30.97)
>DroVir_CAF1 89151 112 + 1
CCAAAAGCUGAGCCGUGAACUCAGCCCAGACCAGCUCAGCCCGCAUGCUGCCUGCCAAUCCUUAUUGACAGCAGCACUUCCGCUUUGGCAGCCAAAAUAGCUGCGAGCGCCA
......((((((.......))))))........(((((((.....((((((.((.((((....)))).)))))))).....)))...(((((.......))))))))).... ( -37.10)
>DroEre_CAF1 70003 102 + 1
GUAAAGG------CGGGCCC----ACAAGUCUGAGCCAACCCGCAUGCUGACUGCCAAUCCUUAUUGACAGCGGCACUUCCGCCUUGGCAGCCAAAAUAGCUGCGAGCCCCA
...((((------(((((.(----(......)).)))........(((((.(((.((((....)))).))))))))....)))))).(((((.......)))))........ ( -33.60)
>DroYak_CAF1 63054 102 + 1
GGAAAGG------CGGGACC----CCAAGUCUGAACCAACCCGCAUGCUGACUGCCAAUCCUUAUUGACAGCGGCACUUCCGCUUUGGCAGCCAAAAUAGCUGCGAGCCCCA
((((..(------((((...----...............))))).(((((.(((.((((....)))).)))))))).))))((((..(((((.......))))))))).... ( -34.07)
>DroMoj_CAF1 80198 105 + 1
CCAAAAGCUGAUCCG-------AGCCCAGUCCUGCUCAGCCCGCAUGCUGCCUGCCAAUCCUCAUUGACAGCAGCACUUCCGCUUUGGCAGCCAAAAUAGCUGCGAGCGCCA
......(((((.(.(-------..(...)..).).)))))..((.((((((.((.((((....)))).)))))))).....((((..(((((.......))))))))))).. ( -31.30)
>DroAna_CAF1 88923 85 + 1
---------------------------AGCCUGAACUAACCCGCAUGCUGACUGCCAAUCCUUAUUGACAGCCGCACUUCCGCAUUGGCAGCCAAAAUAGCUGCGAGCCCCA
---------------------------..............((((.((((.((((((((.(.....)......((......))))))))))......))))))))....... ( -18.30)
>consensus
CCAAAGG______CGGG_CC____CCAAGUCUGAACCAACCCGCAUGCUGACUGCCAAUCCUUAUUGACAGCGGCACUUCCGCUUUGGCAGCCAAAAUAGCUGCGAGCCCCA
..........................................((.(((((.(((.((((....)))).))))))))...........(((((.......)))))..)).... (-20.77 = -20.77 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,220,434 – 22,220,536
Length 102
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 79.84
Mean single sequence MFE -43.00
Consensus MFE -31.73
Energy contribution -30.98
Covariance contribution -0.74
Combinations/Pair 1.27
Mean z-score -2.31
Structure conservation index 0.74
SVM decision value 1.31
SVM RNA-class probability 0.940599
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22220434 102 - 27905053
UGGGGCUCGCAGCUAUUUUGGCUGCCAAAGCGGAAGUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG----GGGCCCG------CCUUUCU
..((((((.(.((.((.((((((((((((((((.....))))).((......))))))))))))).))))(((((......)))))).----)))))).------....... ( -41.80)
>DroVir_CAF1 89151 112 - 1
UGGCGCUCGCAGCUAUUUUGGCUGCCAAAGCGGAAGUGCUGCUGUCAAUAAGGAUUGGCAGGCAGCAUGCGGGCUGAGCUGGUCUGGGCUGAGUUCACGGCUCAGCUUUUGG
..(((((.((((((.....))))))...)))....((((((((((((((....))))))).)))))))))(((((((((((...(((((...)))))))))))))))).... ( -51.50)
>DroEre_CAF1 70003 102 - 1
UGGGGCUCGCAGCUAUUUUGGCUGCCAAGGCGGAAGUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGCUCAGACUUGU----GGGCCCG------CCUUUAC
..(((((((((((.((.((((((((((((((((.....))))).((......))))))))))))).))))(((....))).....)))----)))))).------....... ( -45.10)
>DroYak_CAF1 63054 102 - 1
UGGGGCUCGCAGCUAUUUUGGCUGCCAAAGCGGAAGUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG----GGUCCCG------CCUUUCC
.(((((((((((((.....((((((((((((((.....))))).((......)))))))))))))).)))(((((......))))).)----)))))).------....... ( -41.80)
>DroMoj_CAF1 80198 105 - 1
UGGCGCUCGCAGCUAUUUUGGCUGCCAAAGCGGAAGUGCUGCUGUCAAUGAGGAUUGGCAGGCAGCAUGCGGGCUGAGCAGGACUGGGCU-------CGGAUCAGCUUUUGG
...((((.((((((.....))))))...))))(((((((((((((((((....))))))).)))))((.((((((.((.....)).))))-------)).))..)))))... ( -44.50)
>DroAna_CAF1 88923 85 - 1
UGGGGCUCGCAGCUAUUUUGGCUGCCAAUGCGGAAGUGCGGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUAGUUCAGGCU---------------------------
..(((((.((((((.....)))))).(((.((...((((((((((((((....)))))))))).)))).)).)))))))).....--------------------------- ( -33.30)
>consensus
UGGGGCUCGCAGCUAUUUUGGCUGCCAAAGCGGAAGUGCCGCUGUCAAUAAGGAUUGGCAGUCAGCAUGCGGGUUGGUUCAGACUUGG____GG_CCCG______CCUUUCC
((((((((((((((.....((((((((((((((.....))))).((......)))))))))))))).)))))))...))))............................... (-31.73 = -30.98 +  -0.74)

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 13:08:46 2006