Locus 5403

Sequence ID	2R_DroMel_CAF1
Location	17,447,652 – 17,447,772
Length	120
Max. P	0.820753

overview

Window 8

Location	17,447,652 – 17,447,772
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.74
Mean single sequence MFE	-35.05
Consensus MFE	-26.12
Energy contribution	-26.88
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.75
SVM decision value	0.19
SVM RNA-class probability	0.627013
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17447652 120 + 20766785
AUGUCGCGGGCAAUGAAAAUGCGCCAGGAAAAUGGCCAAGUGUCUGGGCCAUAAAUGUCAUCAUGUGAUGUACGAGGUUAAUUAGCUCUCCACACAUUUUCAUUUUCCGUGCAUUUGCGU
(((.((((((.((((((((((.(...(((..((((((.((...)).))))))....((((((....)))).))(((.(.....).)))))).).)))))))))).)))))))))...... ( -38.50)
>DroSim_CAF1 167232 120 + 1
AUGUCGCGGGCAAUGAAAAUACGCCAGGAAAAUGGCCAAGUGUCUGGGCCAUAAAUGUCAUCAUGUGAUGUACGAGGUUAAUUAGCUCUCCACACAUUUUCAUUUUCCGUGCAUUUGCGU
(((.((((((.(((((((((..((((......))))...((((..((((..(((.(((((((....)))).)))...)))....))))...))))))))))))).)))))))))...... ( -36.20)
>DroEre_CAF1 161237 114 + 1
AUGUCGCGGGCAAUGAAAACACGCCAGGAAAAUGGCCAAGUGUCUGGGCCAUAAAUGCCAUCAUGUGAUGUACGAGCUUAAUUAGCUCUCCACACAUU------UUCCCUGCAUUUGUGC
..(((.((((((.((....)).((((......))))....)))))))))(((((((((....(((((.((...(((((.....)))))..))))))).------......))))))))). ( -33.00)
>DroYak_CAF1 147551 114 + 1
AUGUCGCGGGCAAUGAAAAUACGCCAGGAAAAUGGCCAAGUGUUUGGGCCAUAAAUGCCAUCAAAUGAUGUACGAGCUUAAUUAGCUCUCCACACAUU------UUCCGUGCAUUUGCAU
(((.((((((.((((.((((((((((......))))...))))))(((..........((((....))))...(((((.....))))))))...))))------.)))))))))...... ( -32.50)
>consensus
AUGUCGCGGGCAAUGAAAAUACGCCAGGAAAAUGGCCAAGUGUCUGGGCCAUAAAUGCCAUCAUGUGAUGUACGAGCUUAAUUAGCUCUCCACACAUU______UUCCGUGCAUUUGCGU
(((.((((((............((((......))))..(((((.((((..........((((....))))...(((((.....))))))))).))))).......)))))))))...... (-26.12 = -26.88 +   0.75)

alignment

secondary structure

dotplot

Window 9

Location	17,447,652 – 17,447,772
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.74
Mean single sequence MFE	-36.12
Consensus MFE	-27.17
Energy contribution	-27.55
Covariance contribution	0.38
Combinations/Pair	1.09
Mean z-score	-2.52
Structure conservation index	0.75
SVM decision value	0.68
SVM RNA-class probability	0.820753
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17447652 120 - 20766785
ACGCAAAUGCACGGAAAAUGAAAAUGUGUGGAGAGCUAAUUAACCUCGUACAUCACAUGAUGACAUUUAUGGCCCAGACACUUGGCCAUUUUCCUGGCGCAUUUUCAUUGCCCGCGACAU
......((((.(((..((((((((((((((((((.............((.((((....))))))....((((((.((...)).)))))))))))..)))))))))))))..))).).))) ( -39.80)
>DroSim_CAF1 167232 120 - 1
ACGCAAAUGCACGGAAAAUGAAAAUGUGUGGAGAGCUAAUUAACCUCGUACAUCACAUGAUGACAUUUAUGGCCCAGACACUUGGCCAUUUUCCUGGCGUAUUUUCAUUGCCCGCGACAU
......((((.(((..((((((((((((((((((.............((.((((....))))))....((((((.((...)).)))))))))))..)))))))))))))..))).).))) ( -34.90)
>DroEre_CAF1 161237 114 - 1
GCACAAAUGCAGGGAA------AAUGUGUGGAGAGCUAAUUAAGCUCGUACAUCACAUGAUGGCAUUUAUGGCCCAGACACUUGGCCAUUUUCCUGGCGUGUUUUCAUUGCCCGCGACAU
.........(((((((------((((((((..(((((.....)))))...)).)))))...........(((((.((...)).)))))))))))))(((.((.......)).)))..... ( -35.10)
>DroYak_CAF1 147551 114 - 1
AUGCAAAUGCACGGAA------AAUGUGUGGAGAGCUAAUUAAGCUCGUACAUCAUUUGAUGGCAUUUAUGGCCCAAACACUUGGCCAUUUUCCUGGCGUAUUUUCAUUGCCCGCGACAU
.(((((((((.((..(------((((((((..(((((.....))))).)))).)))))..))))))))((((((.........))))))......((((.........)))).))).... ( -34.70)
>consensus
ACGCAAAUGCACGGAA______AAUGUGUGGAGAGCUAAUUAACCUCGUACAUCACAUGAUGACAUUUAUGGCCCAGACACUUGGCCAUUUUCCUGGCGUAUUUUCAUUGCCCGCGACAU
.......(((..((((.....((((((.....(((((.....)))))...((((....))))))))))((((((.........)))))).)))).((.(((.......)))))))).... (-27.17 = -27.55 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:55 2006