Locus 3897

Sequence ID	2R_DroMel_CAF1
Location	12,865,938 – 12,866,097
Length	159
Max. P	0.778227

overview

Window 2

Location	12,865,938 – 12,866,057
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.79
Mean single sequence MFE	-32.18
Consensus MFE	-29.23
Energy contribution	-29.84
Covariance contribution	0.61
Combinations/Pair	1.06
Mean z-score	-1.24
Structure conservation index	0.91
SVM decision value	0.37
SVM RNA-class probability	0.707664
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12865938 119 - 20766785
UUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGGUUUAUCACGAUUACAGCGGCCCUGCAAGUAAAUUCAA-GC
((((((((((((((........)))))........((((....))))..(((((((((((((((.((.........))..)))))).).)))))))))))))).)))..........-.. ( -33.80)
>DroSim_CAF1 221211 111 - 1
UUGAGGGCCAAAUGA-UGCGUCCAU-UAUC-AUAACUGAUCCUUCAGAUGCUGUG-UGGAUGAAAGUAU-UGCACGGCGGU-UAUCACGA-UACAGCGGCCCUGCAAGAAAA-UCAA-GU
(((((((((..((((-((.......-))))-))..((((....))))..((((((-(((((((..((..-......))..)-)))).).)-)))))))))))).))).....-....-.. ( -35.70)
>DroEre_CAF1 213330 119 - 1
UUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGGUUUAUCACGAUUACAGCGGCCCUGCAAGAAAAUUCAA-AG
((((((((((((((........)))))........((((....))))..(((((((((((((((.((.........))..)))))).).)))))))))))))).)))..........-.. ( -33.80)
>DroWil_CAF1 320797 120 - 1
UUUAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAAUUGAUCCUUCAAAUGCUGUGGUGGAUGAAAAUAUUUGCACGGCGGUUUAUCACGAUUACAGCGACCCUGCAAAAGUAAGAAAGAA
..(((((.((((((........)))))........((((....))))..((((((((.(.(((.((...((((...)))).)).)))).))))))))).)))))................ ( -23.80)
>DroYak_CAF1 219331 119 - 1
UUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGGUUUAUCACGAUUACAGCGGCCCUGCAAGAAAAUUCAA-AC
((((((((((((((........)))))........((((....))))..(((((((((((((((.((.........))..)))))).).)))))))))))))).)))..........-.. ( -33.80)
>consensus
UUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGGUUUAUCACGAUUACAGCGGCCCUGCAAGAAAAUUCAA_AC
((((((((((((((........)))))........((((....))))..((((((((.(.(((.((...((((...)))).)).)))).)))))))))))))).)))............. (-29.23 = -29.84 +   0.61)

alignment

secondary structure

dotplot

Window 3

Location	12,865,977 – 12,866,097
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.42
Mean single sequence MFE	-38.44
Consensus MFE	-35.26
Energy contribution	-35.30
Covariance contribution	0.04
Combinations/Pair	1.11
Mean z-score	-1.24
Structure conservation index	0.92
SVM decision value	0.55
SVM RNA-class probability	0.778227
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12865977 120 - 20766785
UUGGCCGGGCGCGAUGCCCAUCUGUUGCAUCAGUGCAUUCUUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGG
....(((((((((((((((.((...((((....)))).....))))))......)))))))))............((((....))))..(((((.(..((((....))))..)))))))) ( -40.00)
>DroSim_CAF1 221247 115 - 1
UUGGCCGGGCGCGAUGCCCAUCUGUUGCAUCAGUGCAUUCUUGAGGGCCAAAUGA-UGCGUCCAU-UAUC-AUAACUGAUCCUUCAGAUGCUGUG-UGGAUGAAAGUAU-UGCACGGCGG
((((((((((.....)))).((...((((....)))).....)).))))))((((-((.......-))))-))..((((....)))).(((((((-..(((....)).)-..))))))). ( -40.30)
>DroEre_CAF1 213369 120 - 1
CUGACCGGGCGCGAUGCCCAUCUGUUGCAUCAGUGCAUUCUUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGG
....(((((((((((((((.((...((((....)))).....))))))......)))))))))............((((....))))..(((((.(..((((....))))..)))))))) ( -40.30)
>DroWil_CAF1 320837 120 - 1
CUGACCGGGUGCUAUGCCCAUCUGUUGCAUCAAUGCGUUCUUUAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAAUUGAUCCUUCAAAUGCUGUGGUGGAUGAAAAUAUUUGCACGGCGG
....(((.((((...((((......((((....)))).......)))).(((((.((.((((((((...((.((.((((....)))).)).)).)))))))).)).)))))))))..))) ( -31.02)
>DroYak_CAF1 219370 120 - 1
CUGACCGGGCGCAAUGCCCAUCUGUUGCAUCAGUGCAUUCUUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGG
....(((((((((((((((.((...((((....)))).....))))))......)))))))))............((((....))))..(((((.(..((((....))))..)))))))) ( -40.60)
>consensus
CUGACCGGGCGCGAUGCCCAUCUGUUGCAUCAGUGCAUUCUUGAGGGCCAAAUGAUUGCGUCCAUUUAUCAAUAACUGAUCCUUCAGAUGCUGUGGUGGAUGAAAGUAUUUGCACGGCGG
....(((((((((((((((.((...((((....)))).....))))))......)))))))))............((((....))))..((((((.((((((....)))))))))))))) (-35.26 = -35.30 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:44 2006