Locus 840

Sequence ID	X_DroMel_CAF1
Location	2,356,704 – 2,356,805
Length	101
Max. P	0.683187

overview

Window 5

Location	2,356,704 – 2,356,805
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.88
Mean single sequence MFE	-28.48
Consensus MFE	-21.86
Energy contribution	-21.08
Covariance contribution	-0.78
Combinations/Pair	1.26
Mean z-score	-1.01
Structure conservation index	0.77
SVM decision value	-0.02
SVM RNA-class probability	0.523398
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2356704 101 + 22224390
----CGUAUUU---------------UACUCACCCUCGCAGUAGCGCUCAUCGGAAAUGUCCUCGGGACAAUCGAUGUUGCCAUUGCAGAGUAGUUCCUUAGCUAUACAGGUGCCGUCGU
----.......---------------....((((((((((((.(((..((((((...(((((...))))).)))))).))).))))).)))((((......))))....))))....... ( -28.70)
>DroPse_CAF1 1570 109 + 1
----UGUUUUU----UC---UACAGAUACUCACCCUCGCAGUAGCGCUCAUCGGAUAUGUCCUCGGGACAAUCGAUGUUGCCAUUGCAGAGCAGCUCCUUGGCAAUGCAGGUACCAUCAU
----.......----..---....(((....(((...(((((.(((..((((((...(((((...))))).)))))).))).)))))...((((((....)))..))).)))...))).. ( -28.00)
>DroGri_CAF1 1752 112 + 1
GAUACACA-UC----GA---UACACACACUCACCAUCGCAAUAGCGCUCAUCGGAUAUAUCCUCGGGGCAAUCGAUGUUGCCAUUGCAGAGCAGCUCCUUGGCAAUGCAAGUGCCAUCAU
(((.((((-((----((---(................((....))((((...(((....)))...)))).))))))(((((((..((......))....)))))))....)))..))).. ( -30.70)
>DroWil_CAF1 2754 110 + 1
----CUAAUUA------AUUGAUCUACACUCACCAUCGCAAUAGCGUUCAUCGGAUAUGUCCUCGGGACAAUCAAUGUUGCCAUUGCAUAACAAUUCCUUGGCAAUGCAAGUGCCAUCAU
----.......------..(((...............(((((.(((..(((..(((.(((((...)))))))).))).))).)))))............(((((.......)))))))). ( -23.10)
>DroAna_CAF1 1412 116 + 1
----UAUUUUUUUUUUGGGGGAUAACUACUCACCAUCGCAAUAGCGUUCAUCGGAUAUGUCCUCGGGACAAUCGAUGUUGCCGUUGCAGAGCAGUUCCUUGGCAAUACAAGUGCCAUCGU
----.............(((((..(((.(((......((((..(((..((((((...(((((...))))).)))))).)))..)))).))).))))))))((((.......))))..... ( -32.40)
>DroPer_CAF1 1560 109 + 1
----UGUUUUU----UC---UACAGAUACUCACCCUCGCAGUAGCGCUCAUCGGAUAUGUCCUCGGGACAAUCGAUGUUGCCAUUGCACAGCAGCUCCUUGGCAAUGCAGGUACCAUCAU
----.......----..---....(((....(((...(((((.(((..((((((...(((((...))))).)))))).))).)))))...((((((....)))..))).)))...))).. ( -28.00)
>consensus
____CGUAUUU____U____UACAGAUACUCACCAUCGCAAUAGCGCUCAUCGGAUAUGUCCUCGGGACAAUCGAUGUUGCCAUUGCAGAGCAGCUCCUUGGCAAUGCAAGUGCCAUCAU
..........................((((.......(((((.(((..((((((...(((((...))))).)))))).))).)))))...(((...(....)...))).))))....... (-21.86 = -21.08 +  -0.78)

alignment

secondary structure

dotplot

Window 6

Location	2,356,704 – 2,356,805
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.88
Mean single sequence MFE	-32.67
Consensus MFE	-23.45
Energy contribution	-22.53
Covariance contribution	-0.91
Combinations/Pair	1.27
Mean z-score	-1.33
Structure conservation index	0.72
SVM decision value	0.31
SVM RNA-class probability	0.683187
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2356704 101 - 22224390
ACGACGGCACCUGUAUAGCUAAGGAACUACUCUGCAAUGGCAACAUCGAUUGUCCCGAGGACAUUUCCGAUGAGCGCUACUGCGAGGGUGAGUA---------------AAAUACG----
...((..((((....(((........)))(((.(((.((((..(((((..(((((...)))))....)))))...)))).)))))))))).)).---------------.......---- ( -28.00)
>DroPse_CAF1 1570 109 - 1
AUGAUGGUACCUGCAUUGCCAAGGAGCUGCUCUGCAAUGGCAACAUCGAUUGUCCCGAGGACAUAUCCGAUGAGCGCUACUGCGAGGGUGAGUAUCUGUA---GA----AAAAACA----
..((((.(((((((.((((((.((((...))))....))))))(((((..(((((...)))))....))))).))((....))..)))))..))))....---..----.......---- ( -32.40)
>DroGri_CAF1 1752 112 - 1
AUGAUGGCACUUGCAUUGCCAAGGAGCUGCUCUGCAAUGGCAACAUCGAUUGCCCCGAGGAUAUAUCCGAUGAGCGCUAUUGCGAUGGUGAGUGUGUGUA---UC----GA-UGUGUAUC
.((((((((((..((((((.((..(((.((((......(((((......)))))....(((....)))...))))))).))))))).)..)))))...))---))----).-........ ( -34.00)
>DroWil_CAF1 2754 110 - 1
AUGAUGGCACUUGCAUUGCCAAGGAAUUGUUAUGCAAUGGCAACAUUGAUUGUCCCGAGGACAUAUCCGAUGAACGCUAUUGCGAUGGUGAGUGUAGAUCAAU------UAAUUAG----
.((((.(((((..(.....(((....)))...(((((((((..(((((..(((((...)))))....)))))...)))))))))...)..)))))..))))..------.......---- ( -34.10)
>DroAna_CAF1 1412 116 - 1
ACGAUGGCACUUGUAUUGCCAAGGAACUGCUCUGCAACGGCAACAUCGAUUGUCCCGAGGACAUAUCCGAUGAACGCUAUUGCGAUGGUGAGUAGUUAUCCCCCAAAAAAAAAAUA----
....(((((.......))))).(((((((((((((((..((..(((((..(((((...)))))....)))))...))..))))).....)))))))..)))...............---- ( -35.60)
>DroPer_CAF1 1560 109 - 1
AUGAUGGUACCUGCAUUGCCAAGGAGCUGCUGUGCAAUGGCAACAUCGAUUGUCCCGAGGACAUAUCCGAUGAGCGCUACUGCGAGGGUGAGUAUCUGUA---GA----AAAAACA----
..((((.(((((((.((((((..(.((....)).)..))))))(((((..(((((...)))))....))))).))((....))..)))))..))))....---..----.......---- ( -31.90)
>consensus
AUGAUGGCACCUGCAUUGCCAAGGAACUGCUCUGCAAUGGCAACAUCGAUUGUCCCGAGGACAUAUCCGAUGAGCGCUACUGCGAGGGUGAGUAUCUGUA____A____AAAAACA____
.......((((.(((...(....)...)))..((((.((((..(((((..(((((...)))))....)))))...)))).))))..)))).............................. (-23.45 = -22.53 +  -0.91)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:02 2006