Locus 5797

Sequence ID	2R_DroMel_CAF1
Location	18,353,470 – 18,353,590
Length	120
Max. P	0.972615

overview

Window 3

Location	18,353,470 – 18,353,590
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-39.13
Consensus MFE	-35.83
Energy contribution	-35.89
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-2.24
Structure conservation index	0.92
SVM decision value	1.67
SVM RNA-class probability	0.971413
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18353470 120 + 20766785
UUUCGGAGGAGCCUGUUUGACGAUUUGGCUUGUAAACUAGUUUCGCAGCACAAUUUUGUUGAAGCUGCUUAUUAGCUGGCAUUGCCAAUUUUUUGAACAUGCAGUUCGGUGACUUGAGGU
((((((((..((.((((..(.((.(((((.(((...(((((...(((((.((((...))))..)))))..)))))...)))..))))).)).)..)))).))..)))(....).))))). ( -35.10)
>DroSim_CAF1 3631 118 + 1
UUUCGGAGGAGCCUGUUUGACGAUUUGGCUU-UAAACUAGUUUCGCAGCACAGUUUGGUCACAGCUGCUUAUUAGCUGGCAUUGCCAAUUU-UUAAACAGGCAGUUCGGUGACUUGAGGU
((((((((..((((((((((.((.(((((..-....((((((..(((((..............))))).....))))))....))))).))-))))))))))..)))(....).))))). ( -36.84)
>DroEre_CAF1 3475 119 + 1
UUUCGGAGGAGCCUGUUUGACGAUUUGGCUUGUAAACUAGUUUCGCAGCACAGUUUGGUUACAGCUGCUUAUUAGCUAGCAUCGCCAAUUU-UCGAACAGGCAGUUCGGUGACUUGAGGU
((((((((..((((((((((.((.(((((.(((...(((((...(((((...((......)).)))))..)))))...)))..))))).))-))))))))))..)))(....).))))). ( -39.70)
>DroYak_CAF1 3686 119 + 1
UUUCGGAGGAGCCUGUUUGACGAUUUGGCUUGUAAACUAGUUUCGCAGCACAGUUUGGUUACAGCUGCUUAUUAGCUUGCAACGCCAAUUU-UCGAACAGGCAGUUCGGUGACUGGAGGU
((((((((..((((((((((.((.(((((((((((.(((((...(((((...((......)).)))))..))))).)))))).))))).))-))))))))))..)))(....)))))).. ( -44.90)
>consensus
UUUCGGAGGAGCCUGUUUGACGAUUUGGCUUGUAAACUAGUUUCGCAGCACAGUUUGGUUACAGCUGCUUAUUAGCUGGCAUCGCCAAUUU_UCGAACAGGCAGUUCGGUGACUUGAGGU
..(((((...((((((((((.((.(((((.(((...(((((...(((((..............)))))..)))))...)))..))))).)).))))))))))..)))))........... (-35.83 = -35.89 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	18,353,470 – 18,353,590
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-31.20
Consensus MFE	-27.17
Energy contribution	-27.92
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.87
SVM decision value	1.70
SVM RNA-class probability	0.972615
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18353470 120 - 20766785
ACCUCAAGUCACCGAACUGCAUGUUCAAAAAAUUGGCAAUGCCAGCUAAUAAGCAGCUUCAACAAAAUUGUGCUGCGAAACUAGUUUACAAGCCAAAUCGUCAAACAGGCUCCUCCGAAA
......((((...((((.....))))......(((((..((..(((((....(((((..(((.....))).))))).....)))))..)).)))))...........))))......... ( -25.80)
>DroSim_CAF1 3631 118 - 1
ACCUCAAGUCACCGAACUGCCUGUUUAA-AAAUUGGCAAUGCCAGCUAAUAAGCAGCUGUGACCAAACUGUGCUGCGAAACUAGUUUA-AAGCCAAAUCGUCAAACAGGCUCCUCCGAAA
............((....((((((((..-...(((((......(((((....(((((.((......))...))))).....)))))..-..)))))......)))))))).....))... ( -29.40)
>DroEre_CAF1 3475 119 - 1
ACCUCAAGUCACCGAACUGCCUGUUCGA-AAAUUGGCGAUGCUAGCUAAUAAGCAGCUGUAACCAAACUGUGCUGCGAAACUAGUUUACAAGCCAAAUCGUCAAACAGGCUCCUCCGAAA
............((....(((((((.((-...(((((..((..(((((....(((((.((......))...))))).....)))))..)).)))))....)).))))))).....))... ( -33.90)
>DroYak_CAF1 3686 119 - 1
ACCUCCAGUCACCGAACUGCCUGUUCGA-AAAUUGGCGUUGCAAGCUAAUAAGCAGCUGUAACCAAACUGUGCUGCGAAACUAGUUUACAAGCCAAAUCGUCAAACAGGCUCCUCCGAAA
............((....(((((((.((-...(((((.(((.((((((....(((((.((......))...))))).....)))))).))))))))....)).))))))).....))... ( -35.70)
>consensus
ACCUCAAGUCACCGAACUGCCUGUUCAA_AAAUUGGCAAUGCCAGCUAAUAAGCAGCUGUAACCAAACUGUGCUGCGAAACUAGUUUACAAGCCAAAUCGUCAAACAGGCUCCUCCGAAA
............((....(((((((.((....(((((......(((((....(((((..............))))).....))))).....)))))....)).))))))).....))... (-27.17 = -27.92 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:37 2006