Locus 118

Sequence ID	2R_DroMel_CAF1
Location	1,374,402 – 1,374,522
Length	120
Max. P	0.825096

overview

Window 3

Location	1,374,402 – 1,374,522
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.46
Mean single sequence MFE	-39.54
Consensus MFE	-28.52
Energy contribution	-29.32
Covariance contribution	0.80
Combinations/Pair	1.07
Mean z-score	-2.56
Structure conservation index	0.72
SVM decision value	0.69
SVM RNA-class probability	0.825096
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1374402 120 + 20766785
UGCCACAUGCAAGGGGUUCCUCCUUAAGGUUCUCCUACGUAAUCAAAUAUGUAAAAGCCCCUACUUCCCGCAGCCCGUGUGGAUGCAUACGUACUGAUACACGCUGCUGCAGUGGCGUUU
.(((((.((((((((((((((.....)))......((((((......))))))..))))))).......(((((..(((((....)))))(((....)))..)))))))))))))).... ( -42.40)
>DroSec_CAF1 6678 119 + 1
UGCCACAUGCAAGGGGUUCCUCCUUAAGGUUCUCCUACGUAAUCAAAUAUGUAAAAGCC-CUACUCCCCGCCGCCCGUGUGGAUGCAUACGUACUGAUACACGCUGCUGCAGUGGCGUUU
.(((((..((..((((..(((.....)))..))))((((((......))))))...)).-.........((.((.((((((..(((....)))....))))))..)).)).))))).... ( -35.40)
>DroSim_CAF1 11364 118 + 1
UGCCACAUGCAAGGGGUU-CUCCUUAAGGUUCUCCUACGUAAUCAAAUAUGUAAAAGCC-CUACUCCCCGCAGCCCGUGUGGAUGCAUACGUACUGAUACACGCUGCUGCAGUGGCGUUU
.(((((.((((.((((..-.......(((..((..((((((......))))))..)).)-))...))))(((((..(((((....)))))(((....)))..)))))))))))))).... ( -39.60)
>DroEre_CAF1 4703 117 + 1
UGCCACAUGCAAGGGGUU---CCUUAAGGUUCUCCUACGUAAUCAAAUAUGUAAAAGCCCCUACUCCCCGCAGCCCUUGUGGAUGCAUACGUACUGAUACACGUUGGUGCAGUGGCGUUU
.(((((((((((((((((---......((....))((((((......))))))..))))))).....((((((...)))))).)))))..((((..((....))..)))).))))).... ( -42.00)
>DroYak_CAF1 3137 117 + 1
AGCCACAUGCAAGGGGUU---GCUUAAGGUUCUCAUACGUAAUCAAAUAUGUGAAAAACCCAACCUCCAGCAGACCGUGUGGAUGCAUACGUACUGAUAAACGUUGGUACCGUGGCGUUU
.(((((.(((..((((((---(.....((((.(((((..(......)..)))))..)))))))))))..)))....(((((....)))))((((..((....))..)))).))))).... ( -38.30)
>consensus
UGCCACAUGCAAGGGGUU_CUCCUUAAGGUUCUCCUACGUAAUCAAAUAUGUAAAAGCCCCUACUCCCCGCAGCCCGUGUGGAUGCAUACGUACUGAUACACGCUGCUGCAGUGGCGUUU
.(((((.((((.((((...........((....))((((((......))))))............)))).(((..((((((....))))))..)))...........))))))))).... (-28.52 = -29.32 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	1,374,402 – 1,374,522
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.46
Mean single sequence MFE	-40.68
Consensus MFE	-29.30
Energy contribution	-30.82
Covariance contribution	1.52
Combinations/Pair	1.11
Mean z-score	-2.20
Structure conservation index	0.72
SVM decision value	0.32
SVM RNA-class probability	0.689389
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1374402 120 - 20766785
AAACGCCACUGCAGCAGCGUGUAUCAGUACGUAUGCAUCCACACGGGCUGCGGGAAGUAGGGGCUUUUACAUAUUUGAUUACGUAGGAGAACCUUAAGGAGGAACCCCUUGCAUGUGGCA
....(((((((((((..(((((....(((....)))....))))).)))))))...((((((((((((((.((......)).)))))))..((((...))))...)))))))...)))). ( -43.90)
>DroSec_CAF1 6678 119 - 1
AAACGCCACUGCAGCAGCGUGUAUCAGUACGUAUGCAUCCACACGGGCGGCGGGGAGUAG-GGCUUUUACAUAUUUGAUUACGUAGGAGAACCUUAAGGAGGAACCCCUUGCAUGUGGCA
....(((((((((((.((((((((......))))))..((....)))).))((((.....-..(((((((.((......)).)))))))..((((...))))..)))).)))).))))). ( -39.50)
>DroSim_CAF1 11364 118 - 1
AAACGCCACUGCAGCAGCGUGUAUCAGUACGUAUGCAUCCACACGGGCUGCGGGGAGUAG-GGCUUUUACAUAUUUGAUUACGUAGGAGAACCUUAAGGAG-AACCCCUUGCAUGUGGCA
....((((((((((((((((((((......))))))..((....)))))))((((..(((-(((((((((.((......)).)))))))..))))).....-..)))).)))).))))). ( -43.70)
>DroEre_CAF1 4703 117 - 1
AAACGCCACUGCACCAACGUGUAUCAGUACGUAUGCAUCCACAAGGGCUGCGGGGAGUAGGGGCUUUUACAUAUUUGAUUACGUAGGAGAACCUUAAGG---AACCCCUUGCAUGUGGCA
....(((((((((...(((((......)))))..((((((....))).)))((((...(((..(((((((.((......)).)))))))..))).....---..)))).)))).))))). ( -41.00)
>DroYak_CAF1 3137 117 - 1
AAACGCCACGGUACCAACGUUUAUCAGUACGUAUGCAUCCACACGGUCUGCUGGAGGUUGGGUUUUUCACAUAUUUGAUUACGUAUGAGAACCUUAAGC---AACCCCUUGCAUGUGGCU
....((((((((.(((((.((((.(((..(((.((....)).)))..))).)))).))))).....((.(((((........))))).)))))....((---((....))))..))))). ( -35.30)
>consensus
AAACGCCACUGCAGCAGCGUGUAUCAGUACGUAUGCAUCCACACGGGCUGCGGGGAGUAGGGGCUUUUACAUAUUUGAUUACGUAGGAGAACCUUAAGGAG_AACCCCUUGCAUGUGGCA
....(((((((((((.(((((......)))))......((....)))))))))...((((((((((((((.((......)).)))))))..((....))......)))))))...)))). (-29.30 = -30.82 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:52 2006