Locus 5939

Sequence ID	2L_DroMel_CAF1
Location	16,764,720 – 16,764,834
Length	114
Max. P	0.623380

overview

Window 8

Location	16,764,720 – 16,764,834
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.71
Mean single sequence MFE	-40.28
Consensus MFE	-31.88
Energy contribution	-31.60
Covariance contribution	-0.27
Combinations/Pair	1.21
Mean z-score	-1.29
Structure conservation index	0.79
SVM decision value	0.08
SVM RNA-class probability	0.574836
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16764720 114 + 22407834
UGCUGGAUCCCCGACGAGAAGGAGGGUUAUCUCCUUGGUGAGAUCAAGGCCACCAAGGGCGAUAUCGUCUCCGUUGGUCUGCAGGGUGGAGAGGUAAAGU-CAU-CGUCUACACG----A
(((.(((...((((((.((..((.(((.((((((((((((..........))))))))).)))))).))))))))))))))))..(((((..(((.....-.))-).)))))...----. ( -37.10)
>DroVir_CAF1 35033 115 + 1
UGUUGGGUGCCCGAUGAGAAGGAGGGUUAUCUUCUUGGUGAGAUCAAGGCCACCAAGGGCGAUAUCGUCUCCGUCGGUCUGCCUGGUGGAGAGGUAAAUG-CACCAGAGUCCCAAU----
.((((((.((((((((.((..((.(((.((((((((((((..........))))))))).)))))).)))))))))).....((((((.(........).-)))))).))))))))---- ( -42.70)
>DroPse_CAF1 33052 118 + 1
UGCUGGGUGCCCGACGAGAAGGAGGGCUAUCUCCUUGGUGAGAUCAAGGCCACCAAGGGCGAUAUCGUCUCCGUCGGCUUGCCUGGAGGAGAGGUAAUGA-AAU-CAUAUCCAAAAAAAA
..(..(((..((((((.((..((.((.(((((((((((((..........))))))))).)))))).))))))))))...)))..).(((..(((.....-.))-)...)))........ ( -41.40)
>DroGri_CAF1 32586 114 + 1
UGCUGGGUUCCCGACGAGAAGGAGGGUUUCCUCAUUGGUGAUAUCAAGGCCACCAAGGGAGAUAUCGUCUCCGUCGGUCUGCCUGGUGGAGAGGUAA-UG-CAGCGAUGCUCAAAC----
.((..(((..(((((((((..((..(((((((..((((((..........))))))))))))).)).))).))))))...)))..))..........-.(-((....)))......---- ( -40.40)
>DroWil_CAF1 45467 118 + 1
UGCUGGGUGCCCGAUGAGAAGGAGGGUUAUCUCCUUGGUGAAAUCAAGGCCACCAAGGGUGAUAUCGUCUCCGUUGGCUUGCCUGGUGGAGAGGUAAUGA-UAU-AAAGUACCAAAACAA
.....(((((...(((....((((((.(((((((((((((..........))))))))).)))).).)))))((((.((..((....))..)).))))..-)))-...)))))....... ( -38.20)
>DroMoj_CAF1 34852 113 + 1
UGUUGGGUGCCCGAUGAGAAGGAGGGCUAUCUCCUUGGUGAGAUCAAGGCCACCAAGGGCGAUAUCGUCUCUGUCGGUCUGCCUGGUGGAGAGGUAAAUAAUGCCGGA---CCAAU----
.(((.(((((((......(((((((....)))))))((((..........))))..))))..((((.((((..((((.....))))..))))))))......))).))---)....---- ( -41.90)
>consensus
UGCUGGGUGCCCGACGAGAAGGAGGGUUAUCUCCUUGGUGAGAUCAAGGCCACCAAGGGCGAUAUCGUCUCCGUCGGUCUGCCUGGUGGAGAGGUAAAGA_CAU_AAAGUACAAAA____
.......(((((......(((((((....)))))))((((..........))))..))))).((((.(((((..(((.....)))..)))))))))........................ (-31.88 = -31.60 +  -0.27)

alignment

secondary structure

dotplot

Window 9

Location	16,764,720 – 16,764,834
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.71
Mean single sequence MFE	-33.82
Consensus MFE	-23.00
Energy contribution	-23.83
Covariance contribution	0.83
Combinations/Pair	1.04
Mean z-score	-1.60
Structure conservation index	0.68
SVM decision value	0.18
SVM RNA-class probability	0.623380
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16764720 114 - 22407834
U----CGUGUAGACG-AUG-ACUUUACCUCUCCACCCUGCAGACCAACGGAGACGAUAUCGCCCUUGGUGGCCUUGAUCUCACCAAGGAGAUAACCCUCCUUCUCGUCGGGGAUCCAGCA
(----(((....)))-)..-..............(((((((((....((....)).((((..(((((((((........))))))))).))))........))).).)))))........ ( -32.60)
>DroVir_CAF1 35033 115 - 1
----AUUGGGACUCUGGUG-CAUUUACCUCUCCACCAGGCAGACCGACGGAGACGAUAUCGCCCUUGGUGGCCUUGAUCUCACCAAGAAGAUAACCCUCCUUCUCAUCGGGCACCCAACA
----.(((((..(((((((-............)))))))....((((((....)).((((...((((((((........))))))))..)))).............))))...))))).. ( -36.70)
>DroPse_CAF1 33052 118 - 1
UUUUUUUUGGAUAUG-AUU-UCAUUACCUCUCCUCCAGGCAAGCCGACGGAGACGAUAUCGCCCUUGGUGGCCUUGAUCUCACCAAGGAGAUAGCCCUCCUUCUCGUCGGGCACCCAGCA
......((((.....-...-......(.(((((....((....))...))))).).((((..(((((((((........))))))))).))))((((..(.....)..))))..)))).. ( -36.20)
>DroGri_CAF1 32586 114 - 1
----GUUUGAGCAUCGCUG-CA-UUACCUCUCCACCAGGCAGACCGACGGAGACGAUAUCUCCCUUGGUGGCCUUGAUAUCACCAAUGAGGAAACCCUCCUUCUCGUCGGGAACCCAGCA
----...........((((-..-...........(.((((..(((((.(((((.....))))).))))).)))).)...((.((.(((((((........))))))).))))...)))). ( -34.90)
>DroWil_CAF1 45467 118 - 1
UUGUUUUGGUACUUU-AUA-UCAUUACCUCUCCACCAGGCAAGCCAACGGAGACGAUAUCACCCUUGGUGGCCUUGAUUUCACCAAGGAGAUAACCCUCCUUCUCAUCGGGCACCCAGCA
.((((..(((.....-.((-((....(.(((((....((....))...))))).).......(((((((((........))))))))).)))).(((...........))).))).)))) ( -29.90)
>DroMoj_CAF1 34852 113 - 1
----AUUGG---UCCGGCAUUAUUUACCUCUCCACCAGGCAGACCGACAGAGACGAUAUCGCCCUUGGUGGCCUUGAUCUCACCAAGGAGAUAGCCCUCCUUCUCAUCGGGCACCCAACA
----.((((---....((..........(((((....)).)))((((..((((.((((((..(((((((((........))))))))).))))....))..)))).))))))..)))).. ( -32.60)
>consensus
____AUUGGGACACC_AUG_UAUUUACCUCUCCACCAGGCAGACCGACGGAGACGAUAUCGCCCUUGGUGGCCUUGAUCUCACCAAGGAGAUAACCCUCCUUCUCAUCGGGCACCCAGCA
..........................(.(((((....((....))...))))).).....(((((((((((........)))))))((((......))))........))))........ (-23.00 = -23.83 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:02 2006