Locus 1636

Sequence ID	2R_DroMel_CAF1
Location	6,170,731 – 6,170,835
Length	104
Max. P	0.721246

overview

Window 8

Location	6,170,731 – 6,170,835
Length	104
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	81.21
Mean single sequence MFE	-41.07
Consensus MFE	-21.34
Energy contribution	-21.28
Covariance contribution	-0.05
Combinations/Pair	1.06
Mean z-score	-2.55
Structure conservation index	0.52
SVM decision value	0.40
SVM RNA-class probability	0.721246
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6170731 104 + 20766785
UUGGUGGGAAACACAGCCGCAACUUUAGCGGC--GACAUUUCCUCAGGGCUUUGCCGCAAAUUAUGCGGUCGGG-GACGUCUUGCCAC-CAGAA--GGAACUCUGACAGG
(((((((((((....(((((.......)))))--....))))).((((((...((((((.....)))))).(..-..))))))).)))-)))..--.............. ( -38.70)
>DroPse_CAF1 7722 96 + 1
UUUGAG-GAAACACAGCCGCAACUUUAGCGGCGGGACAUUUCCUCUGGGCUUUGCUGCAAAUUAUGCGGUGGGGCCAUGUCUUGGGGCACGGAA--GGA-----------
...(((-((((..(.(((((.......))))).)....)))))))..(((((..(((((.....)))))..))))).((((....))))(....--)..----------- ( -40.90)
>DroEre_CAF1 12003 105 + 1
UUGGUG-GAAACACAGCCGCAACUUUAGCGGC--GACAUUUCCUCGGGGCUUUGCCGCAAAUUAUGCGGUCGGG-GGCGUCUUGCCUC-CAGACUGGGAACACCGCCUUG
..((((-(.......(((((.......)))))--.....((((.(((......((((((.....)))))).(((-(((.....)))))-)...)))))))..)))))... ( -45.00)
>DroYak_CAF1 8983 101 + 1
UUCGAG-GAAACACAGCCGCAACUUUAGCGGC--GACAUUUCCUCGGGGCUUUGCCGCAAAUUAUGCGGUCGGG-GACGUCUUGCCAC-CAGAA--GGA--ACUGCCUGG
.(((((-((((....(((((.......)))))--....)))))))))(((...((((((.....))))))((..-..))....))).(-(((..--...--.....)))) ( -41.70)
>DroAna_CAF1 12180 103 + 1
UUUGAG-GCAACACAGCCGCAACUUUAGCGGC--GACAUUUCCUCCGGGCAUUGCCGCAAAUUAUGCGGUCGGG-GAUGUCUUGCCAC-CAAAA--GGAGCUGUCUCCAG
((((.(-((((....(((((.......)))))--(((((..((.((.(((...)))(((.....)))))..)).-.))))))))))..-)))).--((((....)))).. ( -41.80)
>DroPer_CAF1 7744 96 + 1
UUUGAG-GAAACACAGCCGCAACUUUAGCGGCGGGACAUUUCCUCUGGGCUUUGCUGCAAAUUAUGCGGUGGGGCCAUGUCUUGGGGUACGGAA--GGA-----------
...(((-((((..(.(((((.......))))).)....)))))))..(((((..(((((.....)))))..))))).............(....--)..----------- ( -38.30)
>consensus
UUUGAG_GAAACACAGCCGCAACUUUAGCGGC__GACAUUUCCUCGGGGCUUUGCCGCAAAUUAUGCGGUCGGG_GACGUCUUGCCAC_CAGAA__GGA___CUG_C__G
...............(((((.......)))))..(((....((....))((..((((((.....))))))..))....)))............................. (-21.34 = -21.28 +  -0.05)

alignment

secondary structure

dotplot

Window 9

Location	6,170,731 – 6,170,835
Length	104
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.21
Mean single sequence MFE	-36.43
Consensus MFE	-19.88
Energy contribution	-20.72
Covariance contribution	0.83
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.55
SVM decision value	0.18
SVM RNA-class probability	0.623343
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6170731 104 - 20766785
CCUGUCAGAGUUCC--UUCUG-GUGGCAAGACGUC-CCCGACCGCAUAAUUUGCGGCAAAGCCCUGAGGAAAUGUC--GCCGCUAAAGUUGCGGCUGUGUUUCCCACCAA
....((((.(((..--....(-(.(((.....)))-.))(.(((((.....))))))..))).))))(((((..(.--(((((.......))))).)..)))))...... ( -36.00)
>DroPse_CAF1 7722 96 - 1
-----------UCC--UUCCGUGCCCCAAGACAUGGCCCCACCGCAUAAUUUGCAGCAAAGCCCAGAGGAAAUGUCCCGCCGCUAAAGUUGCGGCUGUGUUUC-CUCAAA
-----------...--..(((((........))))).......(((.....)))...........(((((((..(...(((((.......))))).)..))))-)))... ( -28.40)
>DroEre_CAF1 12003 105 - 1
CAAGGCGGUGUUCCCAGUCUG-GAGGCAAGACGCC-CCCGACCGCAUAAUUUGCGGCAAAGCCCCGAGGAAAUGUC--GCCGCUAAAGUUGCGGCUGUGUUUC-CACCAA
...(((..(((.....(((.(-(.(((.....)))-)).)))((((.....)))))))..)))....(((((..(.--(((((.......))))).)..))))-)..... ( -42.50)
>DroYak_CAF1 8983 101 - 1
CCAGGCAGU--UCC--UUCUG-GUGGCAAGACGUC-CCCGACCGCAUAAUUUGCGGCAAAGCCCCGAGGAAAUGUC--GCCGCUAAAGUUGCGGCUGUGUUUC-CUCGAA
...(((...--...--....(-(.(((.....)))-.))(.(((((.....))))))...))).((((((((..(.--(((((.......))))).)..))))-)))).. ( -43.10)
>DroAna_CAF1 12180 103 - 1
CUGGAGACAGCUCC--UUUUG-GUGGCAAGACAUC-CCCGACCGCAUAAUUUGCGGCAAUGCCCGGAGGAAAUGUC--GCCGCUAAAGUUGCGGCUGUGUUGC-CUCAAA
..((((....))))--.((((-(.(((((.(((((-((((...(((.....)))(((...)))))).)))......--(((((.......)))))))).))))-)))))) ( -41.60)
>DroPer_CAF1 7744 96 - 1
-----------UCC--UUCCGUACCCCAAGACAUGGCCCCACCGCAUAAUUUGCAGCAAAGCCCAGAGGAAAUGUCCCGCCGCUAAAGUUGCGGCUGUGUUUC-CUCAAA
-----------...--..................(((....(.(((.....))).)....)))..(((((((..(...(((((.......))))).)..))))-)))... ( -27.00)
>consensus
C__G_CAG___UCC__UUCUG_GUGGCAAGACAUC_CCCGACCGCAUAAUUUGCGGCAAAGCCCAGAGGAAAUGUC__GCCGCUAAAGUUGCGGCUGUGUUUC_CUCAAA
.........................................(((((.....))))).........(((((((..(...(((((.......))))).)..)))).)))... (-19.88 = -20.72 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:26 2006