Locus 6775

Sequence ID	X_DroMel_CAF1
Location	16,848,856 – 16,848,956
Length	100
Max. P	0.637175

overview

Window 5

Location	16,848,856 – 16,848,956
Length	100
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	84.23
Mean single sequence MFE	-30.15
Consensus MFE	-22.10
Energy contribution	-22.38
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.15
Structure conservation index	0.73
SVM decision value	0.21
SVM RNA-class probability	0.637175
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16848856 100 + 22224390
AUAAUUACCUCCAUUUGGGAGCCCUUCUUGCCCAUGGAAC---CACCGCCACCCGUGUGGCCGCCGCUCUGUGCGGCAUUCAUACUGGCU--UUU-CUUCUUGUAU
.........((((..((((...........))))))))..---....((((...((((((..(((((.....)))))..)))))))))).--...-.......... ( -29.40)
>DroVir_CAF1 4542 85 + 1
AUAAUUACCUCCAUUUGGGAGCCCUUCUUGCCCAUGGAAC------CGCCACCCGUGUGGCCGCCGCUCUGUGCGGCAUUCAUCGU---------------UGUAU
.........((((..((((...........))))))))..------.(((((....))))).(((((.....))))).........---------------..... ( -26.00)
>DroEre_CAF1 33233 100 + 1
AUAAUUACCUCCAUUUGGGAGCCCUUCUUGCCCAUGGAGC---CACCGCCACCCGUGUGGCCGCCGCUCUGUGCGGCAUUCAUACUGGUU--UUU-CUUCUGGUAU
........((((.....)))).......((((((((((((---..(.(((((....))))).)..)))))))).))))...((((..(..--...-...)..)))) ( -35.10)
>DroWil_CAF1 33134 100 + 1
AUAAUUACCUCCAUUUGAGAUCCCUUCUUGCCCAUUGAGCCACCACCGCCUCCGGUGUGGCCGCCGCUUUGUGCGGCAUUCAUG---GCU--UCUGCUUCU-GAUG
................((((.....))))(((...((((((((.((((....))))))))).(((((.....)))))..))).)---)).--.........-.... ( -31.50)
>DroYak_CAF1 32243 102 + 1
AUAAUUACCUCCAUUUGGGAGCCCUUCUUGCCCAUGGAGC---CACCGCCACCCGUGUGGCCGCCGCUCUGUGCGGCAUUCAUACUGGUUGUUUU-CUUCUUGUAU
(((((((.((((.....)))).......((((((((((((---..(.(((((....))))).)..)))))))).)))).......)))))))...-.......... ( -31.90)
>DroAna_CAF1 50589 99 + 1
AUAAUUACCUCCAUUUGGGAGCCCUUCUUGCCCAUCGAAC---CGCCGCCGCCCGUGUGGCCGCCGCUCUGUGCGGCAUUCAUUUUG-CU--AUU-GUAUUUGUAU
((((.(((((((.....)))).......(((((((.((.(---.((.(((((....))))).)).).)).))).)))).........-..--...-))).)))).. ( -27.00)
>consensus
AUAAUUACCUCCAUUUGGGAGCCCUUCUUGCCCAUGGAAC___CACCGCCACCCGUGUGGCCGCCGCUCUGUGCGGCAUUCAUACUGGCU__UUU_CUUCUUGUAU
........((((.....))))........((((((((...............))))).))).(((((.....)))))............................. (-22.10 = -22.38 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	16,848,856 – 16,848,956
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	84.23
Mean single sequence MFE	-33.02
Consensus MFE	-23.88
Energy contribution	-24.47
Covariance contribution	0.59
Combinations/Pair	1.17
Mean z-score	-2.18
Structure conservation index	0.72
SVM decision value	0.18
SVM RNA-class probability	0.623761
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16848856 100 - 22224390
AUACAAGAAG-AAA--AGCCAGUAUGAAUGCCGCACAGAGCGGCGGCCACACGGGUGGCGGUG---GUUCCAUGGGCAAGAAGGGCUCCCAAAUGGAGGUAAUUAU
.(((......-...--((((..(.....((((.((..((((.((.(((((....))))).)).---))))..))))))..)..)))).((....))..)))..... ( -32.90)
>DroVir_CAF1 4542 85 - 1
AUACA---------------ACGAUGAAUGCCGCACAGAGCGGCGGCCACACGGGUGGCG------GUUCCAUGGGCAAGAAGGGCUCCCAAAUGGAGGUAAUUAU
.(((.---------------........((((((.....))))))(((((....))))).------.((((((((((.......))))....)))))))))..... ( -28.10)
>DroEre_CAF1 33233 100 - 1
AUACCAGAAG-AAA--AACCAGUAUGAAUGCCGCACAGAGCGGCGGCCACACGGGUGGCGGUG---GCUCCAUGGGCAAGAAGGGCUCCCAAAUGGAGGUAAUUAU
.((((.....-...--............((((.((..((((.((.(((((....))))).)).---))))..))))))....((....)).......))))..... ( -36.10)
>DroWil_CAF1 33134 100 - 1
CAUC-AGAAGCAGA--AGC---CAUGAAUGCCGCACAAAGCGGCGGCCACACCGGAGGCGGUGGUGGCUCAAUGGGCAAGAAGGGAUCUCAAAUGGAGGUAAUUAU
....-.........--.((---(.(((.((((((.....))))))(((((((((....)))).))))))))...)))........(((((.....)))))...... ( -35.00)
>DroYak_CAF1 32243 102 - 1
AUACAAGAAG-AAAACAACCAGUAUGAAUGCCGCACAGAGCGGCGGCCACACGGGUGGCGGUG---GCUCCAUGGGCAAGAAGGGCUCCCAAAUGGAGGUAAUUAU
..........-...((..(((.......((((.((..((((.((.(((((....))))).)).---))))..))))))....((....))...)))..))...... ( -35.50)
>DroAna_CAF1 50589 99 - 1
AUACAAAUAC-AAU--AG-CAAAAUGAAUGCCGCACAGAGCGGCGGCCACACGGGCGGCGGCG---GUUCGAUGGGCAAGAAGGGCUCCCAAAUGGAGGUAAUUAU
.......(((-...--..-.........((((.((..((((.((.(((.(....).))).)).---))))..)))))).......((((.....)))))))..... ( -30.50)
>consensus
AUACAAGAAG_AAA__AGCCAGUAUGAAUGCCGCACAGAGCGGCGGCCACACGGGUGGCGGUG___GCUCCAUGGGCAAGAAGGGCUCCCAAAUGGAGGUAAUUAU
.................(((........((((((.....))))))(((((....)))))))).....(((((((((...........))))..)))))........ (-23.88 = -24.47 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:39 2006