Locus 4668

Sequence ID	2R_DroMel_CAF1
Location	15,242,839 – 15,242,939
Length	100
Max. P	0.895929

overview

Window 6

Location	15,242,839 – 15,242,939
Length	100
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.69
Mean single sequence MFE	-28.37
Consensus MFE	-25.28
Energy contribution	-25.28
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.89
SVM decision value	0.71
SVM RNA-class probability	0.828466
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15242839 100 + 20766785
------UUG-CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGACACAUACCUAUUUAGUCA-AUCUCC-----
------.((-..((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))..))..............-......----- ( -26.20)
>DroPse_CAF1 109498 106 + 1
------GUA-CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUAGUCAUCAUUGGUCCAAAACUGCAUUU
------(((-.(((((.....)))))........(((((.(((((.(....))))))(((((((..............)))))))...........))))).....))).... ( -27.84)
>DroEre_CAF1 66660 109 + 1
AAAAGAUACCUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUACACCAUCUUUUAGUCA-AAACACCA---
(((((((.....((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))......))))))).....-........--- ( -30.10)
>DroWil_CAF1 166992 106 + 1
------AUA-CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUAUUUGUUCUGGGCACAAUUUGCCAGUU
------(((-..((((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))))..)))........((((.....)))).... ( -31.10)
>DroYak_CAF1 69729 100 + 1
------UUC-CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUCCAAGAUUCUGGUCA-AAACAC-----
------(((-.(((((.....)))))..)))....((((.(((.(((....))).(((((((((..............)))))))))..)))....)))).-......----- ( -27.84)
>DroPer_CAF1 67537 106 + 1
------UUA-CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUACUUGUCUUUGGUCCAAAACUGCAUUU
------...-.(((((.....)))))........(((((.(((((.(....))))))(((((((..............)))))))...........)))))............ ( -27.14)
>consensus
______UUA_CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGGAUAUACUAGUUUUUGGUCA_AAACACCA___
............((((((((((((.......)))))....(((((.......)))))....((((...))))....))))))).............................. (-25.28 = -25.28 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	15,242,839 – 15,242,939
Length	100
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.69
Mean single sequence MFE	-35.00
Consensus MFE	-29.58
Energy contribution	-29.58
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.85
SVM decision value	0.99
SVM RNA-class probability	0.895929
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15242839 100 - 20766785
-----GGAGAU-UGACUAAAUAGGUAUGUGUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG-CAA------
-----......-..............(((.((((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))).)-)).------ ( -32.50)
>DroPse_CAF1 109498 106 - 1
AAAUGCAGUUUUGGACCAAUGAUGACUAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG-UAC------
...(((....(((((((..........((((((....(((((....)))))))))))(.(((((((.....))))))).))))))))(((((.....))))))-)).------ ( -33.50)
>DroEre_CAF1 66660 109 - 1
---UGGUGUUU-UGACUAAAAGAUGGUGUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAAGGUAUCUUUU
---((((....-..))))(((((((.(...((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))..).))))))). ( -36.00)
>DroWil_CAF1 166992 106 - 1
AACUGGCAAAUUGUGCCCAGAACAAAUAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG-UAU------
..((((((.....)).)))).....((((.((((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))).)-)))------ ( -36.40)
>DroYak_CAF1 69729 100 - 1
-----GUGUUU-UGACCAGAAUCUUGGAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG-GAA------
-----......-...((.((((((.((((((((....(((((....)))))))))))))(((((((.....))))))).))))))..(((((.....))))))-)..------ ( -36.60)
>DroPer_CAF1 67537 106 - 1
AAAUGCAGUUUUGGACCAAAGACAAGUAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG-UAA------
...(((....(((((((.......((.((((((....(((((....)))))))))))))(((((((.....)))))))..)))))))(((((.....))))))-)).------ ( -35.00)
>consensus
___UGGAGUUU_GGACCAAAAACAAGUAUAUCCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG_UAA______
..............................((((((((((((....)))).........(((((((.....)))))))((((.......))))))))))))............ (-29.58 = -29.58 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:12 2006