Locus 1059

Sequence ID	2R_DroMel_CAF1
Location	4,325,854 – 4,326,028
Length	174
Max. P	0.780961

overview

Window 8

Location	4,325,854 – 4,325,964
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	67.82
Mean single sequence MFE	-33.10
Consensus MFE	-9.64
Energy contribution	-12.02
Covariance contribution	2.38
Combinations/Pair	1.19
Mean z-score	-2.03
Structure conservation index	0.29
SVM decision value	0.35
SVM RNA-class probability	0.698200
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4325854 110 - 20766785
UCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUGCUGUUG---------CUGCUGUUG-UUUUGCAAAUUGCUGACAAUAAAUGUUGGCAGCGACAGAGACAGAGGCCUGCGUGGCAG
........((....)).((.((..(.(((((.((..((((((---------(((((((((-((..((.....)).)))))).......)))))))))))..)).))))))..)).))... ( -40.61)
>DroPse_CAF1 23794 92 - 1
UCG----UCUCGUCUCCUCCCGUGACGU------UG---------------UUGCUGUUGCUUUCGCAAAUUGCUGACAAUAAAUGCUGCUGGCAUCGCAGCCAGCAACA---GCCCCGU
..(----((.((........)).)))((------((---------------((((((((((....))))................(((((.......)))))))))))))---))..... ( -30.10)
>DroSec_CAF1 5120 93 - 1
UCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUG---------------CUGCUGUUG-UUUUGCAAAUUGCUGACAAUAAAUGUUGGCAGCGACAGAGACAGAGAC-----------
........((..(........)..))(((((.((((---------------(((((((((-((..((.....)).)))))).......))))))))).)))))......----------- ( -28.21)
>DroSim_CAF1 6158 101 - 1
UCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUG---------------CUGCUGUUG-UUUUGCAAAUUGCUGACAAUAAAUGUUGGCAGCGACAGAGACAGAGACG---GAGGCAG
(((((...((..(........)..))(((((.((((---------------(((((((((-((..((.....)).)))))).......))))))))).)))))....)))---))..... ( -34.81)
>DroPer_CAF1 23663 92 - 1
UCG----UCUCCUCUCCUCCCGUGCCGU------UG---------------UUGCUGUUGCUUUCGCAAAUUGCUGACAAUAAAUGCUGCUGGCAUCGCAGCCAGCAACA---GCGCCGA
...----.............((.((.((------((---------------((((((((((....))))................(((((.......)))))))))))))---)))))). ( -29.60)
>DroEre_CAF1 4521 104 - 1
UCCGUAAUGCUGUAGCUCCGCUUGGCGUUUCAGUUGCUGUUGCUUCUGUUGC---UGUUG-UUUUGCAAAUUGCUGACAAUAAAUGUUGGCAGCGACAGAGAC------------GGCUG
........((((.(((.((....)).))).)))).((((((...((((((((---(.(((-.....)))...((..(((.....)))..))))))))))))))------------))).. ( -35.30)
>consensus
UCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUG_______________CUGCUGUUG_UUUUGCAAAUUGCUGACAAUAAAUGUUGGCAGCGACAGAGACAGAGAC____G_GGCAG
........((((.(((.((....)).))).))))....................(((((....(((....((((((.((((....)))).))))))))).)))))............... ( -9.64 = -12.02 +   2.38)

alignment

secondary structure

dotplot

Window 9

Location	4,325,924 – 4,326,028
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.84
Mean single sequence MFE	-31.58
Consensus MFE	-19.66
Energy contribution	-21.55
Covariance contribution	1.89
Combinations/Pair	1.05
Mean z-score	-2.07
Structure conservation index	0.62
SVM decision value	0.56
SVM RNA-class probability	0.780961
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4325924 104 - 20766785
------CAGUGCUGGU------UUUCCGCCC----ACUUGGGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCAGCUCAGCUCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUGCUGU
------(((((((((.------...))((((----....)))).......)))....((((((((((.....((((((((........)))).)))).....)))))...))))))))). ( -35.80)
>DroPse_CAF1 23860 106 - 1
UCCGUACAGUUCUCGUCUUCCCUUUCCUCCUUGAUUCGUUAGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCCAUUCCUCUCG----UCUCGUCUCCUCCCGUGACGU------UG----
...(..(((((...(((...............)))......((((....))))....)))))..)................((----((.((........)).)))).------..---- ( -17.66)
>DroSec_CAF1 5177 100 - 1
------CACUGCUGGU------UUUCCGCCC----ACUUGGGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCAGCUCAGCUCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUG----
------...((((((.------...))((((----....)))).......))))...((((((((((.....((((((((........)))).)))).....)))))...))))).---- ( -33.50)
>DroSim_CAF1 6223 100 - 1
------CACUGCUGGU------UUUCCGCCC----ACUUGGGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCAGCUCAGCUCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUG----
------...((((((.------...))((((----....)))).......))))...((((((((((.....((((((((........)))).)))).....)))))...))))).---- ( -33.50)
>DroEre_CAF1 4585 104 - 1
------CACUCCUGGU------UUUCCGCCC----ACUUGGGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCAGCUCAGCUCCGUAAUGCUGUAGCUCCGCUUGGCGUUUCAGUUGCUGU
------...(((.((.------...))((((----....)))).....)))(((((.....(((((((....((((((((........)))).))))....)))))))....)))))... ( -35.70)
>DroYak_CAF1 5250 104 - 1
------CACUCCUGGU------UUUCCGCCC----ACUUGGGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCAGUUCAGCUCCGUAAUGCUGUAGCUCCGCUUGGCGUUUCAGUUGCUGU
------...(((.((.------...))((((----....)))).....)))(((((.....(((((((....((((((((........)))).))))....)))))))....)))))... ( -33.30)
>consensus
______CACUGCUGGU______UUUCCGCCC____ACUUGGGCUCCUUGGAGCAAUAAACUGCGCUAAAUUCAGCUCAGCUCCGUAAUGCUGUAGCUCCUCGUGGCGUUUCAGUUG____
.........................................((((....))))....((((((((((.....((((((((........)))).)))).....)))))...)))))..... (-19.66 = -21.55 +   1.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:21 2006