Locus 5850

Sequence ID	2R_DroMel_CAF1
Location	18,507,032 – 18,507,163
Length	131
Max. P	0.743705

overview

Window 4

Location	18,507,032 – 18,507,130
Length	98
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	85.85
Mean single sequence MFE	-25.47
Consensus MFE	-21.14
Energy contribution	-21.20
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.96
Structure conservation index	0.83
SVM decision value	0.46
SVM RNA-class probability	0.743705
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18507032 98 + 20766785
--ACCGACG-CCCAGAUUUGUUUGCUAUAUGCCAAUUUGGCGGUGUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGAGAUUUCCAUUCACCG-
--..(..((-((..((((((.........((((.....))))..(((((((((.......)))))))))....)))))).))))..)..............- ( -26.30)
>DroPse_CAF1 3902 101 + 1
UUGCCUGAGUUUCUGUUCUGUUUGUUCUAUGCCAAUUUAGCGGCUUGUUUGCAUAUUUACUGUACACACUGUCUAAAUUAGGCGGAGAUUUCCUUUCAGCC-
....(((((.....................(((((((((((((..(((.((((.......)))).)))))).))))))).)))((......)).)))))..- ( -21.40)
>DroSim_CAF1 3517 98 + 1
--AACUCCG-CCCAGAUUUGUUUGCUAUAUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGAGAUUUCCAUUCACCG-
--..(((((-((...........((.....)).(((((((((((..(((((((.......))))))))))).))))))).)))))))..............- ( -31.20)
>DroEre_CAF1 9094 100 + 1
CCACCUCCG-CCCAGAUUUGUUUGCUAUAUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGAAGAUUUCCAUUCAGCG-
.........-.............(((....((((((((((((((..(((((((.......))))))))))).))))))).)))(((........)))))).- ( -25.80)
>DroYak_CAF1 11482 101 + 1
CCACCUCAG-CCCAGAUUUGUUUGCUAUAUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGCGCUUUCCAUUCACCGC
........(-((((((....))))......((((((((((((((..(((((((.......))))))))))).))))))).))))))................ ( -26.70)
>DroPer_CAF1 3812 101 + 1
UUGCCUGAGUUUCUGUUCUGUUUGUUCUAUGCCAAUUUAGCGGCUUGUUUGCAUAUUUACUGUACACACUGUCUAAAUUAGGCGGAGAUUUCCUUUCAGCC-
....(((((.....................(((((((((((((..(((.((((.......)))).)))))).))))))).)))((......)).)))))..- ( -21.40)
>consensus
__ACCUCAG_CCCAGAUUUGUUUGCUAUAUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGAGAUUUCCAUUCACCG_
..............................(((((((((((((..((((((((.......))))))))))).))))))).)))((......))......... (-21.14 = -21.20 +   0.06)

alignment

secondary structure

dotplot

Window 5

Location	18,507,057 – 18,507,163
Length	106
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	85.08
Mean single sequence MFE	-34.73
Consensus MFE	-23.92
Energy contribution	-24.42
Covariance contribution	0.50
Combinations/Pair	1.10
Mean z-score	-2.76
Structure conservation index	0.69
SVM decision value	0.11
SVM RNA-class probability	0.586545
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18507057 106 + 20766785
AUGCCAAUUUGGCGGUGUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGAGAUUUCCAUUCACCG---CCGUCCUUGA---GCU--AUUUGCCUAGGGGGCAUUCC
((((((((((((((((((..(((((.......))))))))))).))))))).(((((.((.......)).)))---))..(((((.---((.--....)).))))))))))... ( -41.20)
>DroPse_CAF1 3930 109 + 1
AUGCCAAUUUAGCGGCUUGUUUGCAUAUUUACUGUACACACUGUCUAAAUUAGGCGGAGAUUUCCUUUCAGCC---AUGUCCUUGGCACCUU--GUUUGUCCCUGGGAAAUACC
..(((((((((((((..(((.((((.......)))).)))))).))))))).)))((..(((((((....(((---(......))))..(..--....).....))))))).)) ( -27.30)
>DroSec_CAF1 6080 106 + 1
AUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGAGGUUUCCAUUCACCG---CCGUCCUUGA---GUU--GUUUGCGCAAGGGGCAUUCC
((((((((((((((((..(((((((.......))))))))))).))))))).(((((.((.......)).)))---))..(((((.---((.--....)).))))))))))... ( -40.10)
>DroEre_CAF1 9121 106 + 1
AUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGAAGAUUUCCAUUCAGCG---CCGUCCUUGA---GUU--AUUUGCCCAAGGGGAAUUCC
...(((((((((((((..(((((((.......))))))))))).))))))).((((..((.......))..))---))..(((((.---((.--....)).)))))))...... ( -32.40)
>DroYak_CAF1 11509 111 + 1
AUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGCGCUUUCCAUUCACCGCCGCCGUCCUUGA---GCUGAGUUUGCCCAAGGGGAAUUCC
...(((((((((((((..(((((((.......))))))))))).))))))).(((((((............)))))))..(((((.---((.......)).)))))))...... ( -40.10)
>DroPer_CAF1 3840 109 + 1
AUGCCAAUUUAGCGGCUUGUUUGCAUAUUUACUGUACACACUGUCUAAAUUAGGCGGAGAUUUCCUUUCAGCC---AUGUCCUUGGCACCUU--GUUUGUCCCUGGGAAAUACC
..(((((((((((((..(((.((((.......)))).)))))).))))))).)))((..(((((((....(((---(......))))..(..--....).....))))))).)) ( -27.30)
>consensus
AUGCCAAUUUGGCGGUCUGUUUGCAUAUUUACUGUAAACACUGUCCAAAUUAGGCGGAGAUUUCCAUUCACCG___CCGUCCUUGA___GUU__GUUUGCCCAAGGGGAAUUCC
..(((((((((((((..((((((((.......))))))))))).))))))).)))((......))..............((((((................))))))....... (-23.92 = -24.42 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:24 2006