Locus 59

Sequence ID	pao_1
Location	4,785,689 – 4,785,808
Length	119
Max. P	0.841875

overview

Window 7

Location	4,785,689 – 4,785,808
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	93.22
Mean single sequence MFE	-42.30
Consensus MFE	-37.28
Energy contribution	-37.28
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.88
SVM decision value	0.51
SVM RNA-class probability	0.765140
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4785689 119 + 1
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUGAACUAUACCCGCGGAGCCCGAAGCUCACGCUUUUAAACU-GGUGGAGGGAGAAGGAUU
....((((((((((((.......)))))....((((((.....))))))(((((.......))))).))))))).....((....(((.((((........-))))..)))....))... ( -43.40)
>pel_1 1 117 + 1
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUAAACUAUACCCGCGGAGCUUGCGGCUCUCGCUG--AAACU-GGUGGAGGGAGAAGGAUU
....((((((((((((.......)))))....((((((.....))))))((.....)).........)))))))(((((.....)))))((((.--.....-)))).............. ( -40.90)
>pfo_1 1 118 + 1
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUAAACUAUACCCGCGGAGCUUGCAGCUCACGCUA--AAAUCUGGUGGAGGGAGAAGGAUU
....((((((((((((.......)))))....((((((.....))))))((.....)).........))))))).((((.....)))).(((((--.....))))).............. ( -41.50)
>pfs_1 1 116 + 1
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUAAACUAUACCCGCGGAGCUUGCAGCUCACGCUA--AAAU--GGUGGAGGGGGAAGGAUU
((..((((((..((.....)).))))))..))((((((.....))))))((((((.((.((..(((((....(((((((.....)))).)))..--..))--)))..))..)).)))))) ( -43.10)
>pss_1 1 117 + 1
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUAAACUAUACCCGCACAACUUGCAGCUCGCGCUA--AAUCU-GGUGGAGGGGGAAGGAUU
....((((((((((((.......)))))....((((((.....))))))((.....)).........)))))))....(((.(..(((.(((((--....)-)))))))..).))).... ( -43.80)
>pst_1 1 117 + 1
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUAAACUAUACCCGCGCAAUUUGCAGCUCGCGCUA--AAUCU-GGUGGAGGGGGAAGGAUU
....((((((((((((.......)))))....((((((.....))))))((.....)).........)))))))((.....))..(((.(((((--....)-)))))))........... ( -41.10)
>consensus
UGGAGCGGGUAGCGGGAAUCGAACCCGCAUCAUCAGCUUGGAAGGCUGAGGUUCUACCACUAAACUAUACCCGCGGAGCUUGCAGCUCACGCUA__AAACU_GGUGGAGGGAGAAGGAUU
....((((((((((((.......)))))....((((((.....))))))((.....)).........)))))))...........(((.((((.........)))))))........... (-37.28 = -37.28 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	4,785,689 – 4,785,808
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.22
Mean single sequence MFE	-35.60
Consensus MFE	-33.94
Energy contribution	-33.88
Covariance contribution	-0.05
Combinations/Pair	1.07
Mean z-score	-1.08
Structure conservation index	0.95
SVM decision value	0.75
SVM RNA-class probability	0.841875
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4785689 119 - 1
AAUCCUUCUCCCUCCACC-AGUUUAAAAGCGUGAGCUUCGGGCUCCGCGGGUAUAGUUCAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
..................-(((((..((((....)))).)))))..(((((((..((((.......)))).(((((.......)))))....(((((.......)))))))))))).... ( -36.90)
>pel_1 1 117 - 1
AAUCCUUCUCCCUCCACC-AGUUU--CAGCGAGAGCCGCAAGCUCCGCGGGUAUAGUUUAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
..................-(((((--(.((....)).).)))))..(((((((((((((.(.(((.(.....).)))..).)))))).....(((((.......)))))))))))).... ( -35.00)
>pfo_1 1 118 - 1
AAUCCUUCUCCCUCCACCAGAUUU--UAGCGUGAGCUGCAAGCUCCGCGGGUAUAGUUUAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
.....((((....((((.(((((.--..(((.((((.....)))))))......))))).)))).))))..(((((.......)))))((..((((((.((.....))..))))))..)) ( -36.80)
>pfs_1 1 116 - 1
AAUCCUUCCCCCUCCACC--AUUU--UAGCGUGAGCUGCAAGCUCCGCGGGUAUAGUUUAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
..................--....--((((....))))........(((((((((((((.(.(((.(.....).)))..).)))))).....(((((.......)))))))))))).... ( -35.10)
>pss_1 1 117 - 1
AAUCCUUCCCCCUCCACC-AGAUU--UAGCGCGAGCUGCAAGUUGUGCGGGUAUAGUUUAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
.................(-((...--((((....))))....))).(((((((((((((.(.(((.(.....).)))..).)))))).....(((((.......)))))))))))).... ( -34.70)
>pst_1 1 117 - 1
AAUCCUUCCCCCUCCACC-AGAUU--UAGCGCGAGCUGCAAAUUGCGCGGGUAUAGUUUAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
..................-.....--.(((....)))((.....))(((((((((((((.(.(((.(.....).)))..).)))))).....(((((.......)))))))))))).... ( -35.10)
>consensus
AAUCCUUCCCCCUCCACC_AGUUU__UAGCGUGAGCUGCAAGCUCCGCGGGUAUAGUUUAGUGGUAGAACCUCAGCCUUCCAAGCUGAUGAUGCGGGUUCGAUUCCCGCUACCCGCUCCA
..........................((((....))))........(((((((((((((.(.(((.(.....).)))..).)))))).....(((((.......)))))))))))).... (-33.94 = -33.88 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:48:55 2007