Locus 1786

Sequence ID	2L_DroMel_CAF1
Location	4,880,787 – 4,880,877
Length	90
Max. P	0.998826

overview

Window 8

Location	4,880,787 – 4,880,877
Length	90
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	72.81
Mean single sequence MFE	-32.30
Consensus MFE	-12.26
Energy contribution	-12.93
Covariance contribution	0.67
Combinations/Pair	1.43
Mean z-score	-2.28
Structure conservation index	0.38
SVM decision value	1.14
SVM RNA-class probability	0.920562
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4880787 90 + 22407834
UAUUGGGGUUAGUUCGGCGAUCACGCCGCCCCAGUCGCAAAGGAAGACCCACAAAAAAC----UACGUGGGUAUCCCCCCCUUUGAGCUAGAGC
.(((((((......(((((....))))))))))))..((((((...((((((.......----...)))))).......))))))......... ( -31.00)
>DroSec_CAF1 30325 77 + 1
UAUUGGGGUUAACUCGGCGAUCACGCCGCCCCAGACGCAAAGGGAGUCCC-------------UUUGAGGGAGUC----CCUUUGAGCUGGAGC
....(((.....)))((((....))))((.((((...((((((((.((((-------------.....)))).))----))))))..)))).)) ( -40.00)
>DroSim_CAF1 31463 77 + 1
UAUUGGGGUUAGCUCGGCGAUCACGCCGCCCCAGACGCAGAGGGAGUCCC-------------UUUGAGGGUGUC----CCUUUGAGCUGGAGC
.....(((....)))((((....))))((.((((...((((((((..(((-------------.....)))..))----))))))..)))).)) ( -35.70)
>DroEre_CAF1 31945 83 + 1
UAUUGGGGUUAGCUCGGCGAUCACGCAGCCCCAAACGCAAAGGGAGCCCCACA-AACAG----AACGU--GGUUC----CCUUUGAGCUGGAGC
..((((((((.((...........))))))))))...(((((((((((.(...-.....----...).--)))))----))))))......... ( -30.20)
>DroYak_CAF1 31899 84 + 1
UAUUGGGGUUAGCUCGGCGAUCACGCCGCACCAGAAGCAAAGGGAGUCCCACAAAACAG----AACGU--GUUUC----CCUUUGAGCUGGAGC
.....(((....)))((((....))))((.((((...(((((((((...(((.......----...))--).)))----))))))..)))).)) ( -31.40)
>DroAna_CAF1 35807 88 + 1
UAUUAGGGUUAGCUGGGCGAUCUUGCGGUAACGCGCUCAUUCAGAGUCCCACACAUGACUAAUAGUGU--GGUUC----CGUACGAGCUGAAGC
........((((((.((((.....(((....)))((((.....)))).((((((((.....)).))))--))...----))).).))))))... ( -25.50)
>consensus
UAUUGGGGUUAGCUCGGCGAUCACGCCGCCCCAGACGCAAAGGGAGUCCCACA_AA_A_____AACGU__GUUUC____CCUUUGAGCUGGAGC
.....(((....)))((((....))))((.((((...((((((((.((......................)).))....))))))..)))).)) (-12.26 = -12.93 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	4,880,787 – 4,880,877
Length	90
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	72.81
Mean single sequence MFE	-34.63
Consensus MFE	-14.29
Energy contribution	-15.27
Covariance contribution	0.98
Combinations/Pair	1.33
Mean z-score	-3.32
Structure conservation index	0.41
SVM decision value	3.24
SVM RNA-class probability	0.998826
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4880787 90 - 22407834
GCUCUAGCUCAAAGGGGGGGAUACCCACGUA----GUUUUUUGUGGGUCUUCCUUUGCGACUGGGGCGGCGUGAUCGCCGAACUAACCCCAAUA
((((((((.(((((((((....(((((((..----......)))))))))))))))).).)))))))((((....))))............... ( -39.80)
>DroSec_CAF1 30325 77 - 1
GCUCCAGCUCAAAGG----GACUCCCUCAAA-------------GGGACUCCCUUUGCGUCUGGGGCGGCGUGAUCGCCGAGUUAACCCCAAUA
((((((((.((((((----((.((((.....-------------)))).)))))))).).)))))))((((....))))............... ( -41.20)
>DroSim_CAF1 31463 77 - 1
GCUCCAGCUCAAAGG----GACACCCUCAAA-------------GGGACUCCCUCUGCGUCUGGGGCGGCGUGAUCGCCGAGCUAACCCCAAUA
((((((((.((.(((----((..(((.....-------------)))..))))).)).).)))))))((((....))))............... ( -34.60)
>DroEre_CAF1 31945 83 - 1
GCUCCAGCUCAAAGG----GAACC--ACGUU----CUGUU-UGUGGGGCUCCCUUUGCGUUUGGGGCUGCGUGAUCGCCGAGCUAACCCCAAUA
((((((((.((((((----((.((--(((..----.....-)))))...)))))))).).))))))).(((....)))................ ( -32.30)
>DroYak_CAF1 31899 84 - 1
GCUCCAGCUCAAAGG----GAAAC--ACGUU----CUGUUUUGUGGGACUCCCUUUGCUUCUGGUGCGGCGUGAUCGCCGAGCUAACCCCAAUA
((.((((..((((((----((..(--(((..----......))))....))))))))...)))).))((((....))))............... ( -31.20)
>DroAna_CAF1 35807 88 - 1
GCUUCAGCUCGUACG----GAACC--ACACUAUUAGUCAUGUGUGGGACUCUGAAUGAGCGCGUUACCGCAAGAUCGCCCAGCUAACCCUAAUA
(((...((((((.((----((.((--((((..........))))))...)))).))))))(((....(....)..)))..)))........... ( -28.70)
>consensus
GCUCCAGCUCAAAGG____GAAAC__ACAUA_____U_UU_UGUGGGACUCCCUUUGCGUCUGGGGCGGCGUGAUCGCCGAGCUAACCCCAAUA
((((((((.((((((....................................)))))).).)))))))((((....))))............... (-14.29 = -15.27 +   0.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:17 2006