Locus 4302

Sequence ID	2R_DroMel_CAF1
Location	14,145,466 – 14,145,573
Length	107
Max. P	0.670592

overview

Window 2

Location	14,145,466 – 14,145,573
Length	107
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	78.55
Mean single sequence MFE	-34.83
Consensus MFE	-19.60
Energy contribution	-21.08
Covariance contribution	1.48
Combinations/Pair	1.34
Mean z-score	-1.70
Structure conservation index	0.56
SVM decision value	0.10
SVM RNA-class probability	0.585378
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14145466 107 + 20766785
CGAUGGUUCU--GAGCCAA-CAACUUACUCUUCCUUUGCGAUACAAGGCUUUGGAGUUAUUUGGCUGGCACCGCAGCACAUGCUCCACGGACUGCAGAGCUGCGUCAUAA
.((((((.((--.((((((-......(((((..(((((.....)))))....)))))...)))))))).)))(((((...(((((....))..)))..)))))))).... ( -34.30)
>DroVir_CAF1 430 102 + 1
----CGUGUU--UAACUAGC--ACUCACUCUGCCCUUGCGGUAUAAAGCCUUUGGAUUAUUUGGCUGACAACGCAAUACAUUCUCCACGGACUGUAAUGCGGCAUCAUAU
----.(((((--.....)))--))......((((.(((((......((((............)))).....)))))((((.(((....))).))))....))))...... ( -24.60)
>DroGri_CAF1 400 104 + 1
----CGUGAUAACAGCUCGC--ACUCACCCUUCCCUUGCGGUACAAUGCCUUGGGAUUAUUCGGCUGGCAUCGCAGCACAUGCUCCACGGACUGCAGUGCGGCGUCAUAG
----.(((((....(((.((--.........((((..(((......)))...)))).......)).)))...((.((((.(((((....))..))))))).))))))).. ( -31.09)
>DroSec_CAF1 414 107 + 1
CUAUGGUUUU--GGGCCAA-CAACUUACUCUGCCUUUGCGGUACAAGGCUUUGGAGUUAUUUGGCUGGCACCGCAGCACAUGCUCCACGGACUGCAGAGCUGCGUCAUAA
.(((((....--((((((.-(((...((((((((((........)))))...)))))...)))..)))).))(((((...(((((....))..)))..))))).))))). ( -36.60)
>DroEre_CAF1 403 107 + 1
AUUUGGUGCU--GAGCUAG-CCACUUACUCUGCCCUUGCGGUACAAGGCUUUGGAGUUGUUUGGCUGGCAUCGCAGCACAUGCUCUACAGACUGUAGAGCUGCGUCAAAA
.(((((((((--(.(((((-(((...((((((.(((((.....)))))...))))))....))))))))....))))))..(((((((.....))))))).....)))). ( -46.60)
>DroYak_CAF1 403 107 + 1
CUCUGCUGCA--GAGCCAA-CAACUUACUCUGCCUUUGCGGUACAAGGCUUUGGAGUUAUUUGGCUGGCACCGCAGCACAUGCUCUACAGACUGCAGAGCUGCGUCAAAG
...((((((.--(.((((.-(((...((((((((((........)))))...)))))...)))..)))).).))))))((.(((((.(.....).)))))))........ ( -35.80)
>consensus
CU_UGGUGCU__GAGCCAA_CAACUUACUCUGCCCUUGCGGUACAAGGCUUUGGAGUUAUUUGGCUGGCACCGCAGCACAUGCUCCACGGACUGCAGAGCUGCGUCAUAA
....((((((...((((((...((((.....(((.(((.....))))))....))))...))))))))))))(((((...(((((....))..)))..)))))....... (-19.60 = -21.08 +   1.48)

alignment

secondary structure

dotplot

Window 3

Location	14,145,466 – 14,145,573
Length	107
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.55
Mean single sequence MFE	-36.87
Consensus MFE	-18.45
Energy contribution	-17.98
Covariance contribution	-0.47
Combinations/Pair	1.42
Mean z-score	-2.07
Structure conservation index	0.50
SVM decision value	0.29
SVM RNA-class probability	0.670592
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14145466 107 - 20766785
UUAUGACGCAGCUCUGCAGUCCGUGGAGCAUGUGCUGCGGUGCCAGCCAAAUAACUCCAAAGCCUUGUAUCGCAAAGGAAGAGUAAGUUG-UUGGCUC--AGAACCAUCG
.......(((((.((((..((....))))).).)))))(((...((((((.(((((......((((........)))).......)))))-)))))).--...))).... ( -32.82)
>DroVir_CAF1 430 102 - 1
AUAUGAUGCCGCAUUACAGUCCGUGGAGAAUGUAUUGCGUUGUCAGCCAAAUAAUCCAAAGGCUUUAUACCGCAAGGGCAGAGUGAGU--GCUAGUUA--AACACG----
...((((...(((((.((.((.((.((.((((.....)))).))((((............)))).....((....)))).)).)))))--))..))))--......---- ( -24.10)
>DroGri_CAF1 400 104 - 1
CUAUGACGCCGCACUGCAGUCCGUGGAGCAUGUGCUGCGAUGCCAGCCGAAUAAUCCCAAGGCAUUGUACCGCAAGGGAAGGGUGAGU--GCGAGCUGUUAUCACG----
..(((((((((((((((((..((((...))))..))))...(((.(((............)))......((....))....))).)))--))).)).)))))....---- ( -37.60)
>DroSec_CAF1 414 107 - 1
UUAUGACGCAGCUCUGCAGUCCGUGGAGCAUGUGCUGCGGUGCCAGCCAAAUAACUCCAAAGCCUUGUACCGCAAAGGCAGAGUAAGUUG-UUGGCCC--AAAACCAUAG
.((((..(((((.((((..((....))))).).)))))((.((((((.((...((((....(((((........))))).))))...)))-)))))))--.....)))). ( -37.80)
>DroEre_CAF1 403 107 - 1
UUUUGACGCAGCUCUACAGUCUGUAGAGCAUGUGCUGCGAUGCCAGCCAAACAACUCCAAAGCCUUGUACCGCAAGGGCAGAGUAAGUGG-CUAGCUC--AGCACCAAAU
.((((.....(((((((.....)))))))..((((((....((.(((((....((((....(((((........))))).))))...)))-)).)).)--))))))))). ( -41.50)
>DroYak_CAF1 403 107 - 1
CUUUGACGCAGCUCUGCAGUCUGUAGAGCAUGUGCUGCGGUGCCAGCCAAAUAACUCCAAAGCCUUGUACCGCAAAGGCAGAGUAAGUUG-UUGGCUC--UGCAGCAGAG
(((((.(((((((((((.....))))))).))))((((((.((((((.((...((((....(((((........))))).))))...)))-))))).)--)))))))))) ( -47.40)
>consensus
UUAUGACGCAGCUCUGCAGUCCGUGGAGCAUGUGCUGCGGUGCCAGCCAAAUAACUCCAAAGCCUUGUACCGCAAAGGCAGAGUAAGUUG_CUAGCUC__AGCACCA_AG
.......((.(((((((.....))))))).((.((((......))))))....((((....(((((........))))).))))..........)).............. (-18.45 = -17.98 +  -0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:34 2006