Locus 5938

Sequence ID	2R_DroMel_CAF1
Location	18,734,677 – 18,734,778
Length	101
Max. P	0.975088

overview

Window 4

Location	18,734,677 – 18,734,778
Length	101
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	74.61
Mean single sequence MFE	-17.02
Consensus MFE	-3.58
Energy contribution	-3.30
Covariance contribution	-0.28
Combinations/Pair	1.43
Mean z-score	-2.20
Structure conservation index	0.21
SVM decision value	1.74
SVM RNA-class probability	0.975088
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18734677 101 + 20766785
-CCUUU-CCCACAUAUGCAAAUA--UG--------U--AUACGUGGAGUAGAGA-UUUUUUCCACACAAAGAA--AAAUAUAAUUUUGGAACAAUCAUUUUCUCUGCCCCUUCACUAA
-.....-.((((.((((((....--))--------)--))).)))).(((((((-.((((((........)))--)))..........((....))....)))))))........... ( -20.30)
>DroSec_CAF1 97457 111 + 1
-CCUUU-CCCACAUAUUCAUACAUACGUAUAUGCAUACAUACGUUGGGUA-UGA-UUUUUUCCACACAAAUAA--CAA-AUAAUUUGUGAACAAUCAUUUUCUCUGCCCUUUCGCUAA
-.....-.........((((((..((((((........))))))...)))-)))-.........(((((((..--...-...)))))))................((......))... ( -18.00)
>DroSim_CAF1 98263 101 + 1
-CCUUU-UCAACAUAUGCAAAUA--UG--------UAUAUACGUGGAGAA-UGA-UUUUUUCCACACAAAUAA--CAA-AUAAUUUGUGAACAAUCAUUUUCUCUGCCCUUUCGCUAA
-.....-.....(((((((....--))--------)))))..(..(((((-(((-((.((....(((((((..--...-...))))))))).))))))..))))..)........... ( -19.80)
>DroEre_CAF1 98659 106 + 1
UUAUUUGCAAAUAUAUGCAUAUC--UA--------CAUAUAUGUAGAAUA-CGAUACGAUCCCACACAAAUAGCACGA-AUAAUUUGCGAACAAUGAUUUUCUCCGCCCUUUUACUAA
...(((((((((...(((...((--((--------((....))))))...-.(((...)))...........)))...-...)))))))))........................... ( -13.60)
>DroYak_CAF1 99707 98 + 1
GUAUUU-CACACAUAUGCAAAUU--U------------GUAUGUAGAAUA-UGA-AUUUUUCCACACAAGUAA--CAA-AUAAUUUGUGAACAAUGAUUUUCUCUGCCCUUUUACUAA
(((...-.......(((((....--)------------))))(((((...-.((-(((......(((((((..--...-...)))))))......)))))..))))).....)))... ( -13.40)
>consensus
_CCUUU_CCCACAUAUGCAAAUA__UG________UA_AUACGUAGAGUA_UGA_UUUUUUCCACACAAAUAA__CAA_AUAAUUUGUGAACAAUCAUUUUCUCUGCCCUUUCACUAA
..........................................((((((....(........)..(((((((...........)))))))....................))))))... ( -3.58 =  -3.30 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	18,734,677 – 18,734,778
Length	101
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	74.61
Mean single sequence MFE	-22.72
Consensus MFE	-7.62
Energy contribution	-7.46
Covariance contribution	-0.16
Combinations/Pair	1.32
Mean z-score	-1.72
Structure conservation index	0.34
SVM decision value	0.01
SVM RNA-class probability	0.539326
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18734677 101 - 20766785
UUAGUGAAGGGGCAGAGAAAAUGAUUGUUCCAAAAUUAUAUUU--UUCUUUGUGUGGAAAAAA-UCUCUACUCCACGUAU--A--------CA--UAUUUGCAUAUGUGGG-AAAGG-
...........(((((((((((((((.......))))))...)--))))))))(((((.....-..)))))(((((((((--.--------((--....)).)))))))))-.....- ( -24.80)
>DroSec_CAF1 97457 111 - 1
UUAGCGAAAGGGCAGAGAAAAUGAUUGUUCACAAAUUAU-UUG--UUAUUUGUGUGGAAAAAA-UCA-UACCCAACGUAUGUAUGCAUAUACGUAUGUAUGAAUAUGUGGG-AAAGG-
...((......)).......((((((.((((((...((.-...--.))....))))))...))-)))-).((((.(((((.((((((((....)))))))).)))))))))-.....- ( -28.70)
>DroSim_CAF1 98263 101 - 1
UUAGCGAAAGGGCAGAGAAAAUGAUUGUUCACAAAUUAU-UUG--UUAUUUGUGUGGAAAAAA-UCA-UUCUCCACGUAUAUA--------CA--UAUUUGCAUAUGUUGA-AAAGG-
((((((.....(((((((.(((((((.((((((...((.-...--.))....))))))...))-)))-)).))...((....)--------).--..)))))...))))))-.....- ( -18.70)
>DroEre_CAF1 98659 106 - 1
UUAGUAAAAGGGCGGAGAAAAUCAUUGUUCGCAAAUUAU-UCGUGCUAUUUGUGUGGGAUCGUAUCG-UAUUCUACAUAUAUG--------UA--GAUAUGCAUAUAUUUGCAAAUAA
.........((((((.(.....).))))))(((((((((-.((((((((.((((((((((((...))-.))))))))))...)--------))--).)))).))).))))))...... ( -26.10)
>DroYak_CAF1 99707 98 - 1
UUAGUAAAAGGGCAGAGAAAAUCAUUGUUCACAAAUUAU-UUG--UUACUUGUGUGGAAAAAU-UCA-UAUUCUACAUAC------------A--AAUUUGCAUAUGUGUG-AAAUAC
..((((...((((((.(.....).))))))((((.....-)))--)))))(((((((((....-...-..))))))))).------------.--..((..((....))..-)).... ( -15.30)
>consensus
UUAGUGAAAGGGCAGAGAAAAUGAUUGUUCACAAAUUAU_UUG__UUAUUUGUGUGGAAAAAA_UCA_UACUCCACGUAU_UA________CA__UAUUUGCAUAUGUGGG_AAAGG_
...(((((.((((((.........))))))....................((((((((.............))))))))..................)))))................ ( -7.62 =  -7.46 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:31 2006