Locus 4847

Sequence ID 2L_DroMel_CAF1
Location 13,772,902 – 13,773,003
Length 101
Max. P 0.882337
window7693 window7694

overview

Window 3

Location 13,772,902 – 13,773,003
Length 101
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -23.05
Consensus MFE -18.94
Energy contribution -18.80
Covariance contribution -0.14
Combinations/Pair 1.22
Mean z-score -1.81
Structure conservation index 0.82
SVM decision value 0.92
SVM RNA-class probability 0.882337
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13772902 101 + 22407834
U--AAUCAAACCU----UCCAUGCGCAUUUU--UCCAGCACUCUGAUGGCGGGCAUCUUGCCCUUUGGCGCCGUCUUCAUUGAACUCUUCUUUGUGUUCACGGCCAUCU
.--..........----....(((.......--....)))....((((((((((.....)))).................(((((.(......).)))))..)))))). ( -24.40)
>DroGri_CAF1 1565 105 + 1
UAUACUCAACUC-GCUCUAAUC---UUUCUGUCCACAGCACUCUGAUGGCUGGCAUUUUGCCCUUUGGCGCCGUUUUUAUAGAGCUCUUCUUUGUCUUUACGGCCAUUU
............-(((......---.....(.((((((....))).)))).(((.....)))....)))(((((....((((((.....))))))....)))))..... ( -20.80)
>DroSim_CAF1 1567 100 + 1
U--AAUCAAACU-----UUCACGCGCAUUUU--UGCAGCACUCUGAUGGCGGGCAUCUUGCCCUUUGGCGCCGUCUUCAUUGAACUCUUCUUUGUGUUCACGGCCAUCU
.--.........-----.....(((((....--))).)).....((((((((((.....)))).................(((((.(......).)))))..)))))). ( -28.00)
>DroEre_CAF1 1776 99 + 1
U--UAUCAAACU-----CAUAC-CGAAUUUU--UGCAGCACUCUGAUGGCUGGCAUCUUGCCCUUUGGCGCCGUCUUCAUUGAACUCUUCUUUGUGUUCACGGCCAUCU
.--.........-----.....-........--...........((((((((.......(((....)))...........(((((.(......).))))))))))))). ( -22.50)
>DroYak_CAF1 1564 99 + 1
U--AAUCAAACC-----UCCAC-CGCUUUUU--UCCAGCACUCUGAUGGCGGGUAUCUUGCCCUUUGGCGCCGUCUUCAUUGAACUCUUCUUUGUGUUCACGGCCAUCU
.--.........-----.....-.(((....--...))).....((((((((((.....)))).................(((((.(......).)))))..)))))). ( -22.50)
>DroAna_CAF1 1544 90 + 1
U--AAU---------------UGCAUAUCUU--UUUAGCACUUUGAUGGCUGGCAUUUUGCCGUUUGGCGCCGUCUUCAUUGAGCUCUUCUUUGUAUUCACGGCCAUCU
.--...---------------(((.((....--..)))))....((((((((.......(((....)))((((.......)).))...............)))))))). ( -20.10)
>consensus
U__AAUCAAACC_____UACAC_CGCAUUUU__UCCAGCACUCUGAUGGCGGGCAUCUUGCCCUUUGGCGCCGUCUUCAUUGAACUCUUCUUUGUGUUCACGGCCAUCU
............................................((((((.(((.....(((....))))))........(((((.(......).)))))..)))))). (-18.94 = -18.80 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,772,902 – 13,773,003
Length 101
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -24.02
Consensus MFE -16.53
Energy contribution -17.58
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -1.39
Structure conservation index 0.69
SVM decision value 0.20
SVM RNA-class probability 0.632686
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13772902 101 - 22407834
AGAUGGCCGUGAACACAAAGAAGAGUUCAAUGAAGACGGCGCCAAAGGGCAAGAUGCCCGCCAUCAGAGUGCUGGA--AAAAUGCGCAUGGA----AGGUUUGAUU--A
.((((((..(((((.(......).))))).................((((.....))))))))))...((((....--.....)))).....----..........--. ( -27.40)
>DroGri_CAF1 1565 105 - 1
AAAUGGCCGUAAAGACAAAGAAGAGCUCUAUAAAAACGGCGCCAAAGGGCAAAAUGCCAGCCAUCAGAGUGCUGUGGACAGAAA---GAUUAGAGC-GAGUUGAGUAUA
...((((...........(((.....)))........((((((....))).....))).))))((((..((((.(((.(.....---).))).)))-)..))))..... ( -21.70)
>DroSim_CAF1 1567 100 - 1
AGAUGGCCGUGAACACAAAGAAGAGUUCAAUGAAGACGGCGCCAAAGGGCAAGAUGCCCGCCAUCAGAGUGCUGCA--AAAAUGCGCGUGAA-----AGUUUGAUU--A
.((((((..(((((.(......).))))).................((((.....))))))))))...((((....--.....)))).....-----.........--. ( -27.40)
>DroEre_CAF1 1776 99 - 1
AGAUGGCCGUGAACACAAAGAAGAGUUCAAUGAAGACGGCGCCAAAGGGCAAGAUGCCAGCCAUCAGAGUGCUGCA--AAAAUUCG-GUAUG-----AGUUUGAUA--A
.((((((..(((((.(......).)))))........((((((....))).....))).))))))...((((((..--......))-)))).-----.........--. ( -25.40)
>DroYak_CAF1 1564 99 - 1
AGAUGGCCGUGAACACAAAGAAGAGUUCAAUGAAGACGGCGCCAAAGGGCAAGAUACCCGCCAUCAGAGUGCUGGA--AAAAAGCG-GUGGA-----GGUUUGAUU--A
.....(((((((((.(......).)))).......)))))(((....))).((((..(((((((....))(((...--....))))-)))).-----.))))....--. ( -23.71)
>DroAna_CAF1 1544 90 - 1
AGAUGGCCGUGAAUACAAAGAAGAGCUCAAUGAAGACGGCGCCAAACGGCAAAAUGCCAGCCAUCAAAGUGCUAAA--AAGAUAUGCA---------------AUU--A
.((((((............((.....)).........((((((....))).....))).))))))....(((....--.......)))---------------...--. ( -18.50)
>consensus
AGAUGGCCGUGAACACAAAGAAGAGUUCAAUGAAGACGGCGCCAAAGGGCAAGAUGCCAGCCAUCAGAGUGCUGCA__AAAAUGCG_GUGGA_____GGUUUGAUU__A
.((((((..(((((.(......).)))))........((((((....))).....))).))))))............................................ (-16.53 = -17.58 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:17 2006