Locus 1224

Sequence ID	2R_DroMel_CAF1
Location	4,836,375 – 4,836,491
Length	116
Max. P	0.992033

overview

Window 8

Location	4,836,375 – 4,836,491
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.61
Mean single sequence MFE	-28.35
Consensus MFE	-19.84
Energy contribution	-20.20
Covariance contribution	0.36
Combinations/Pair	1.17
Mean z-score	-2.49
Structure conservation index	0.70
SVM decision value	1.10
SVM RNA-class probability	0.915054
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4836375 116 + 20766785
GUUGGAAAAGCCCAAACAAGC-UGCACUUAGUGCGAGGCAGACA-AUUCCCUACUAGAAUUACCUGUCCGCUUGCAAUUUAUUUUCCAGUGCCAUAAAUUCAAGCUUUUCUUUUU--UUU
...((((((((.....(((((-.((((...))))(.(((((..(-((((.......)))))..))))))))))).(((((((...........)))))))...))))))))....--... ( -26.80)
>DroSec_CAF1 6949 104 + 1
GUUGGAAAAGCCCAAACAAGCCUGCACUUAGUGCGAGGCAGACA-AUUCCCUACUAGAAUUACCUGUCCGCUUGCCAUUUAUUUUCCAGUGCCAUAAAUUCAAGC---------------
.((((((((.......(((((..((((...))))(.(((((..(-((((.......)))))..))))))))))).......))))))))................--------------- ( -25.94)
>DroSim_CAF1 9790 119 + 1
GUUGGAAAAGCCCAAACAAGCCUGCACUUAGUGCGAGGCAGACA-AUUCCCUACUAGAAUUACCUGUCCGCUUGCCAUUUAUUUUCCAGUGCCAUAAAUUCAAGCUUUUCUUUUUUUUUU
...((((((((.....(((((..((((...))))(.(((((..(-((((.......)))))..))))))))))).((((........))))............))))))))......... ( -26.10)
>DroEre_CAF1 12097 116 + 1
GUCUGAAAAGCCCAAACAAGC-UGCACUUAGAGCCGGGCAGACAUAUUCCCUACCAGAAUUACCUGUCUGCUUGCCACUUAUUUUCCAGUGUCAUAAAUGCAAGCUUUUCCUUUU---UC
....((((((.......((((-((((.(((((..((((((((((.((((.......))))....)))))))))).((((........)))))).))).))).)))))...)))))---). ( -26.40)
>DroYak_CAF1 8081 117 + 1
AGUUGAAGAGCCCAAACAAGC-UGCACUUAGUGCAAGGCAGACAUAUUCCCUACCAGAAUUACCUGUCUGCCUGCAACUUAUUUUGCAGUGCCAUAAAAGCAUGCUUUUCUUUCU--UUU
....(((((((........((-((((...((((((.((((((((.((((.......))))....))))))))))).))).....))))))((.......))..))))))).....--... ( -36.50)
>consensus
GUUGGAAAAGCCCAAACAAGC_UGCACUUAGUGCGAGGCAGACA_AUUCCCUACUAGAAUUACCUGUCCGCUUGCCAUUUAUUUUCCAGUGCCAUAAAUUCAAGCUUUUCUUUUU__UUU
....(((((((............(((((.(((((.((((.((((.((((.......))))....)))).)))))).)))........)))))...........))))))).......... (-19.84 = -20.20 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	4,836,375 – 4,836,491
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.61
Mean single sequence MFE	-37.24
Consensus MFE	-26.79
Energy contribution	-28.75
Covariance contribution	1.96
Combinations/Pair	1.03
Mean z-score	-3.37
Structure conservation index	0.72
SVM decision value	2.30
SVM RNA-class probability	0.992033
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4836375 116 - 20766785
AAA--AAAAAGAAAAGCUUGAAUUUAUGGCACUGGAAAAUAAAUUGCAAGCGGACAGGUAAUUCUAGUAGGGAAU-UGUCUGCCUCGCACUAAGUGCA-GCUUGUUUGGGCUUUUCCAAC
...--.....((((((((..(((((((..(....)...)))))).((((((((.(((..((((((.....)))))-)..)))))..((((...)))).-)))))))..)))))))).... ( -38.00)
>DroSec_CAF1 6949 104 - 1
---------------GCUUGAAUUUAUGGCACUGGAAAAUAAAUGGCAAGCGGACAGGUAAUUCUAGUAGGGAAU-UGUCUGCCUCGCACUAAGUGCAGGCUUGUUUGGGCUUUUCCAAC
---------------(((.........)))..(((((((.....(((((((((.(((..((((((.....)))))-)..)))))..((((...))))..))))))).....))))))).. ( -35.10)
>DroSim_CAF1 9790 119 - 1
AAAAAAAAAAGAAAAGCUUGAAUUUAUGGCACUGGAAAAUAAAUGGCAAGCGGACAGGUAAUUCUAGUAGGGAAU-UGUCUGCCUCGCACUAAGUGCAGGCUUGUUUGGGCUUUUCCAAC
..........((((((((..(((((((..(....)...)))))).((((((((.(((..((((((.....)))))-)..)))))..((((...))))..)))))))..)))))))).... ( -38.60)
>DroEre_CAF1 12097 116 - 1
GA---AAAAGGAAAAGCUUGCAUUUAUGACACUGGAAAAUAAGUGGCAAGCAGACAGGUAAUUCUGGUAGGGAAUAUGUCUGCCCGGCUCUAAGUGCA-GCUUGUUUGGGCUUUUCAGAC
..---.....((((((((((((((((.((((((........))))((..(((((((....(((((.....))))).)))))))...))))))))))))-.........)))))))).... ( -35.90)
>DroYak_CAF1 8081 117 - 1
AAA--AGAAAGAAAAGCAUGCUUUUAUGGCACUGCAAAAUAAGUUGCAGGCAGACAGGUAAUUCUGGUAGGGAAUAUGUCUGCCUUGCACUAAGUGCA-GCUUGUUUGGGCUCUUCAACU
...--.....(((.(((.((((.....)))).....((((((((((((((((((((....(((((.....))))).))))))))).((.....)))))-))))))))..))).))).... ( -38.60)
>consensus
AAA__AAAAAGAAAAGCUUGAAUUUAUGGCACUGGAAAAUAAAUGGCAAGCGGACAGGUAAUUCUAGUAGGGAAU_UGUCUGCCUCGCACUAAGUGCA_GCUUGUUUGGGCUUUUCCAAC
..........(((((((((((((.....(((((............((..(((((((....(((((.....))))).)))))))...))....)))))......))))))))))))).... (-26.79 = -28.75 +   1.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:27 2006