Locus 4824

Sequence ID	3R_DroMel_CAF1
Location	12,607,278 – 12,607,376
Length	98
Max. P	0.735356

overview

Window 5

Location	12,607,278 – 12,607,376
Length	98
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	81.97
Mean single sequence MFE	-25.86
Consensus MFE	-21.65
Energy contribution	-21.52
Covariance contribution	-0.13
Combinations/Pair	1.21
Mean z-score	-1.45
Structure conservation index	0.84
SVM decision value	0.29
SVM RNA-class probability	0.669996
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12607278 98 + 27905053
AAAAGAGGCGGUUUCUGACCG------AAGAGUAUGGGACGCACAUUUGGCCAAAUAUCAUUUUCUUGGCCAAGUUUCCGCCAUAAAUUUACAUGUCCAGAGC---A
......(((((.((((.....------.))))............((((((((((...........))))))))))..))))).....................---. ( -23.60)
>DroVir_CAF1 98239 99 + 1
GAGAG-GCCGGAUUCUGUCCGUAACAGCACA--AUUUACC----ACUUUGCCAAAAAUC-UUUUCUUAGCCAAGUUCUUGGCAUAAGCUCAAGUGUCGAGUGUUCAA
(((((-(.(((((...))))).....(((..--.......----....))).......)-)))))...(((((....)))))....((((.......))))...... ( -18.52)
>DroSec_CAF1 89795 94 + 1
AAAAGAGGCGGUUUCUGACCG------AAGAGGAUGGGAC----ACUUGGCCAAAUAUCAUUUUCUUGGCCAAGUUUCCGCCAUAAAUUUACAUGUCCAGAGC---A
......(((((((...)))).------.........(((.----((((((((((...........)))))))))).)))))).....................---. ( -28.50)
>DroSim_CAF1 90085 94 + 1
AAAAGAGGCGGUUUCUGACCG------AAGAGGAUGGGAU----ACUUGGCCAAAUAUCAUUUUCUUGGCCAAGUUUCCGCCAUAAAUUUACAUGUCCAGAGC---A
......(((((((...)))).------.........(((.----((((((((((...........)))))))))).)))))).....................---. ( -28.70)
>DroEre_CAF1 88445 94 + 1
AAAAGAGGCGGUAUCUGACCG------AAGAGGAUGGGAC----ACUUGGCCAAAUAUCAUUUUCUUGGCCAAGUUUCCGCCAUAAAUUUACUAGUCCGGAGC---A
......((((((.....))).------.........(((.----((((((((((...........)))))))))).)))))).....................---. ( -28.40)
>DroYak_CAF1 89072 94 + 1
GAAAGAGGCGGUUUUUGACCG------AAGAGGAUGGGAC----ACUUGGCCAAAUAUCAUUUUCCUGGCCAAGUUUCCGCCAUAAAUUUACUAGUCCAGAGC---A
......(((((((...)))).------.........(((.----(((((((((.............))))))))).)))))).....................---. ( -27.42)
>consensus
AAAAGAGGCGGUUUCUGACCG______AAGAGGAUGGGAC____ACUUGGCCAAAUAUCAUUUUCUUGGCCAAGUUUCCGCCAUAAAUUUACAUGUCCAGAGC___A
......((((((.....)))................(((.....((((((((((...........)))))))))).))))))......................... (-21.65 = -21.52 +  -0.13)

alignment

secondary structure

dotplot

Window 6

Location	12,607,278 – 12,607,376
Length	98
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	81.97
Mean single sequence MFE	-25.42
Consensus MFE	-21.59
Energy contribution	-21.15
Covariance contribution	-0.44
Combinations/Pair	1.25
Mean z-score	-1.55
Structure conservation index	0.85
SVM decision value	0.44
SVM RNA-class probability	0.735356
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12607278 98 - 27905053
U---GCUCUGGACAUGUAAAUUUAUGGCGGAAACUUGGCCAAGAAAAUGAUAUUUGGCCAAAUGUGCGUCCCAUACUCUU------CGGUCAGAAACCGCCUCUUUU
.---.....................(((((....(((((((((.........)))))))))......(.((.(......)------.)).).....)))))...... ( -21.60)
>DroVir_CAF1 98239 99 - 1
UUGAACACUCGACACUUGAGCUUAUGCCAAGAACUUGGCUAAGAAAA-GAUUUUUGGCAAAGU----GGUAAAU--UGUGCUGUUACGGACAGAAUCCGGC-CUCUC
..............(((...((((.(((((....)))))))))..))-)......(((..((.----.(((...--..)))..)).((((.....))))))-).... ( -23.50)
>DroSec_CAF1 89795 94 - 1
U---GCUCUGGACAUGUAAAUUUAUGGCGGAAACUUGGCCAAGAAAAUGAUAUUUGGCCAAGU----GUCCCAUCCUCUU------CGGUCAGAAACCGCCUCUUUU
.---((...(((((((......))))(.(((.(((((((((((.........)))))))))))----.)))).)))....------.(((.....)))))....... ( -27.00)
>DroSim_CAF1 90085 94 - 1
U---GCUCUGGACAUGUAAAUUUAUGGCGGAAACUUGGCCAAGAAAAUGAUAUUUGGCCAAGU----AUCCCAUCCUCUU------CGGUCAGAAACCGCCUCUUUU
.---((...(((((((......))))(.(((.(((((((((((.........)))))))))))----.)))).)))....------.(((.....)))))....... ( -27.00)
>DroEre_CAF1 88445 94 - 1
U---GCUCCGGACUAGUAAAUUUAUGGCGGAAACUUGGCCAAGAAAAUGAUAUUUGGCCAAGU----GUCCCAUCCUCUU------CGGUCAGAUACCGCCUCUUUU
.---.....................(((((..(((((((((((.........)))))))))))----.....(((..(..------..)...))).)))))...... ( -27.00)
>DroYak_CAF1 89072 94 - 1
U---GCUCUGGACUAGUAAAUUUAUGGCGGAAACUUGGCCAGGAAAAUGAUAUUUGGCCAAGU----GUCCCAUCCUCUU------CGGUCAAAAACCGCCUCUUUC
.---.....................((((((.(((((((((((.........)))))))))))----.))).........------.(((.....))))))...... ( -26.40)
>consensus
U___GCUCUGGACAUGUAAAUUUAUGGCGGAAACUUGGCCAAGAAAAUGAUAUUUGGCCAAGU____GUCCCAUCCUCUU______CGGUCAGAAACCGCCUCUUUU
.........................((((((.(((((((((((.........))))))))))).....)))................(((.....))))))...... (-21.59 = -21.15 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:44 2006