Locus 4474

Sequence ID	2L_DroMel_CAF1
Location	12,816,562 – 12,816,675
Length	113
Max. P	0.597861

overview

Window 8

Location	12,816,562 – 12,816,675
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.84
Mean single sequence MFE	-27.75
Consensus MFE	-18.44
Energy contribution	-19.50
Covariance contribution	1.06
Combinations/Pair	1.19
Mean z-score	-1.87
Structure conservation index	0.66
SVM decision value	0.13
SVM RNA-class probability	0.597861
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12816562 113 + 22407834
-------GUUCCAUUAUUAUUCCUUGACUCAGUUUUAAGCUUCUGAGGGUAUUCCAUAUGCCUCGUUCACGGACAUGAUUUUGGCCUCCCCCGAUUAGCCAUAUCGAUUCAAGCCACACU
-------...(((..((((((((.((((((((..........)))))(((((.....)))))....))).))).)))))..))).......((((.......)))).............. ( -23.40)
>DroSec_CAF1 82501 113 + 1
-------GUGUCAUUAUUAUGUCUUGGCUCAGUUUUAAGCUCCUUAGGGCAUUCCAUAUGCCCCGUUCACGGACAUGAUUUUGGCCUCCCCCGAUUAGCCAUAUCGAUUCAAGCCACACU
-------((((....(((((((((.((((........)))).....((((((.....)))))).......)))))))))...(((......((((.......))))......))))))). ( -29.30)
>DroSim_CAF1 85821 113 + 1
-------GUGCCAUUAUUAUGCCUUCGCUCAGUUUUAAGCUCCUUAGGGCAUUCCAUAUGCCCCGUUCACGGACAUGAUUUUGGCCUCCCCCGAUUAGCCAUAUCGAUUCAAGCCACACU
-------..((((..((((((((...(((........)))......((((((.....)))))).......)).))))))..))))......((((.......)))).............. ( -28.40)
>DroYak_CAF1 86342 120 + 1
UUUCUAUGCCCCAUUGUUAUACCUUGGCUCAGUGGUAAGCUCCAAGGGGUAUUCCAUAUGCCCCAUUCACGGGCAUGAUUUUUGCCUCCCCCGAUUAGCCAUAUCGAUUCAAGCCACACU
......((..(((..(.....)..)))..))(((((.........((((((.....(((((((.......))))))).....))))))...((((.......))))......)))))... ( -29.90)
>consensus
_______GUGCCAUUAUUAUGCCUUGGCUCAGUUUUAAGCUCCUUAGGGCAUUCCAUAUGCCCCGUUCACGGACAUGAUUUUGGCCUCCCCCGAUUAGCCAUAUCGAUUCAAGCCACACU
.........((((..(((((((((..(((........)))......((((((.....)))))).......)))))))))..))))......((((.......)))).............. (-18.44 = -19.50 +   1.06)

alignment

secondary structure

dotplot

Window 9

Location	12,816,562 – 12,816,675
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.84
Mean single sequence MFE	-32.00
Consensus MFE	-26.61
Energy contribution	-26.67
Covariance contribution	0.06
Combinations/Pair	1.13
Mean z-score	-1.40
Structure conservation index	0.83
SVM decision value	0.04
SVM RNA-class probability	0.553539
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12816562 113 - 22407834
AGUGUGGCUUGAAUCGAUAUGGCUAAUCGGGGGAGGCCAAAAUCAUGUCCGUGAACGAGGCAUAUGGAAUACCCUCAGAAGCUUAAAACUGAGUCAAGGAAUAAUAAUGGAAC-------
..(((..(((((.(((....((((..((((((((..(((.....(((((((....)).))))).)))..).))))).))))))......))).)))))..)))..........------- ( -28.60)
>DroSec_CAF1 82501 113 - 1
AGUGUGGCUUGAAUCGAUAUGGCUAAUCGGGGGAGGCCAAAAUCAUGUCCGUGAACGGGGCAUAUGGAAUGCCCUAAGGAGCUUAAAACUGAGCCAAGACAUAAUAAUGACAC-------
.(((((((((...(((((.......)))))...)))))......(((((((....))((((((.....))))))....(.(((((....))))))..))))).......))))------- ( -32.80)
>DroSim_CAF1 85821 113 - 1
AGUGUGGCUUGAAUCGAUAUGGCUAAUCGGGGGAGGCCAAAAUCAUGUCCGUGAACGGGGCAUAUGGAAUGCCCUAAGGAGCUUAAAACUGAGCGAAGGCAUAAUAAUGGCAC-------
.(((((((((...(((((.......)))))...)))))......(((((((....))((((((.....))))))......(((((....)))))...))))).......))))------- ( -33.20)
>DroYak_CAF1 86342 120 - 1
AGUGUGGCUUGAAUCGAUAUGGCUAAUCGGGGGAGGCAAAAAUCAUGCCCGUGAAUGGGGCAUAUGGAAUACCCCUUGGAGCUUACCACUGAGCCAAGGUAUAACAAUGGGGCAUAGAAA
..((((.(((...((.(((((.((..(((.(((.((......))...))).)))...)).))))).)).((..((((((..(........)..))))))..)).....))).)))).... ( -33.40)
>consensus
AGUGUGGCUUGAAUCGAUAUGGCUAAUCGGGGGAGGCCAAAAUCAUGUCCGUGAACGGGGCAUAUGGAAUACCCUAAGGAGCUUAAAACUGAGCCAAGGCAUAAUAAUGGCAC_______
..((((.((((..(((....((((....((((.(..(((.....(((((((....)).))))).)))..).))))....))))......)))..)))).))))................. (-26.61 = -26.67 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:41 2006