Locus 4728

Sequence ID	2R_DroMel_CAF1
Location	15,510,723 – 15,510,863
Length	140
Max. P	0.916866

overview

Window 6

Location	15,510,723 – 15,510,838
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.96
Mean single sequence MFE	-27.63
Consensus MFE	-24.03
Energy contribution	-24.20
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.87
SVM decision value	0.46
SVM RNA-class probability	0.743645
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15510723 115 + 20766785
AAC-U-UAAUGCAAUUUCGGUCUGGCAGAUUUCAUUUGUGUGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAC-
...-(-(((((....(((((((..((...(..((((((.....))))))..).))..)))).(((.....)))...--.....)))..)))))).......(((((.......))))).- ( -28.30)
>DroVir_CAF1 414654 119 + 1
AACUU-UAAUGCAAUUUCGCUCUAGCAGAUUUCAUUUGUGUGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAUAUAAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCACA
(((((-(((((....((((((...((...(..((((((.....))))))..).))..)))..(((.....)))..........)))..)))).))))))..(((((.......))))).. ( -26.40)
>DroPse_CAF1 343307 115 + 1
AAC-U-UAAUGCAAUUUCGCUCCAGCAGAUUUCAUUUGUGUGACAAAUGGUGGGCGUGGCCAUGCAAAUCGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAACUUUGGCAC-
...-.-...(((......((.(((.((....((((....))))....)).)))))(((((..(((.....)))...--.....(((((.......)))))..)))))........))).- ( -27.30)
>DroWil_CAF1 574318 116 + 1
AAC-UUUAAUGCAAUUUCGCUCAACCAGAUUUCAUUUGUGUGACAAAUGGGGGGCGUGGCCAUGCAAAUUGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAC-
...-.....((((((((.((....((((.(..((((((.....))))))..)..).)))....))))))))))...--.....(((((.......))))).(((((.......))))).- ( -28.30)
>DroMoj_CAF1 467601 119 + 1
AACUU-UAAUGCAAUUUCGCUCUAGCAGAUUUCAUUUGUGUGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAUAUAAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAUA
(((((-(((((....((((((...((...(..((((((.....))))))..).))..)))..(((.....)))..........)))..)))).))))))(((((((.......))))))) ( -28.20)
>DroPer_CAF1 306937 115 + 1
AAC-U-UAAUGCAAUUUCGCUCCAGCAGAUUUCAUUUGUGUGACAAAUGGUGGGCGUGGCCAUGCAAAUCGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAACUUUGGCAC-
...-.-...(((......((.(((.((....((((....))))....)).)))))(((((..(((.....)))...--.....(((((.......)))))..)))))........))).- ( -27.30)
>consensus
AAC_U_UAAUGCAAUUUCGCUCUAGCAGAUUUCAUUUGUGUGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAU__AAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAC_
.........(((............((...(..((((((.....))))))..).))(((((..(((.....)))..........(((((.......)))))..)))))........))).. (-24.03 = -24.20 +   0.17)

alignment

secondary structure

dotplot

Window 7

Location	15,510,723 – 15,510,838
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.96
Mean single sequence MFE	-26.68
Consensus MFE	-24.71
Energy contribution	-24.60
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-1.33
Structure conservation index	0.93
SVM decision value	1.11
SVM RNA-class probability	0.916866
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15510723 115 - 20766785
-GUGCCAAACUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUU--AUUUGCGAUUUGCAUGGCCACGCCCCCCAUUUGUCACACAAAUGAAAUCUGCCAGACCGAAAUUGCAUUA-A-GUU
-((((((.......)))))).(((((.....)))))...(((--(..(((((((((..((((.........((((((.....))))))......))))...).)))))))).))-)-).. ( -24.16)
>DroVir_CAF1 414654 119 - 1
UGUGCCAAACUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUUAUAUUUGCGAUUUGCAUGGCCACGCCCCCCAUUUGUCACACAAAUGAAAUCUGCUAGAGCGAAAUUGCAUUA-AAGUU
(((((((.......)))))))(((((.....)))))..(((((....((((((((((..(((...)))...((((((.....))))))............)).)))))))).))-))).. ( -27.00)
>DroPse_CAF1 343307 115 - 1
-GUGCCAAAGUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUU--AUUUGCGAUUUGCAUGGCCACGCCCACCAUUUGUCACACAAAUGAAAUCUGCUGGAGCGAAAUUGCAUUA-A-GUU
-((((((.......)))))).(((((.....)))))...(((--(..((((((((((....(((.((....((((((.....))))))......))))).)).)))))))).))-)-).. ( -26.50)
>DroWil_CAF1 574318 116 - 1
-GUGCCAAACUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUU--AUUUGCAAUUUGCAUGGCCACGCCCCCCAUUUGUCACACAAAUGAAAUCUGGUUGAGCGAAAUUGCAUUAAA-GUU
-((((((.......)))))).(((((.....)))))..((((--(..((((((((((.((((((.......((((((.....)))))).....)))))).)).)))))))).))))-).. ( -28.90)
>DroMoj_CAF1 467601 119 - 1
UAUGCCAAACUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUUAUAUUUGCGAUUUGCAUGGCCACGCCCCCCAUUUGUCACACAAAUGAAAUCUGCUAGAGCGAAAUUGCAUUA-AAGUU
(((((((.......)))))))(((((.....)))))..(((((....((((((((((..(((...)))...((((((.....))))))............)).)))))))).))-))).. ( -27.00)
>DroPer_CAF1 306937 115 - 1
-GUGCCAAAGUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUU--AUUUGCGAUUUGCAUGGCCACGCCCACCAUUUGUCACACAAAUGAAAUCUGCUGGAGCGAAAUUGCAUUA-A-GUU
-((((((.......)))))).(((((.....)))))...(((--(..((((((((((....(((.((....((((((.....))))))......))))).)).)))))))).))-)-).. ( -26.50)
>consensus
_GUGCCAAACUUUGUGGCAUAAACUUUUAAUGAGUUCUUUUU__AUUUGCGAUUUGCAUGGCCACGCCCCCCAUUUGUCACACAAAUGAAAUCUGCUAGAGCGAAAUUGCAUUA_A_GUU
.((((((.......)))))).(((((.....)))))...........((((((((((..(((...)))...((((((.....))))))............)).))))))))......... (-24.71 = -24.60 +  -0.11)

alignment

secondary structure

dotplot

Window 8

Location	15,510,761 – 15,510,863
Length	102
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	79.58
Mean single sequence MFE	-26.51
Consensus MFE	-17.70
Energy contribution	-18.23
Covariance contribution	0.53
Combinations/Pair	1.14
Mean z-score	-2.04
Structure conservation index	0.67
SVM decision value	1.01
SVM RNA-class probability	0.898897
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15510761 102 + 20766785
UGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAC---CCGACCCGAUGCCACGCCCCUAUCC--------
.........(((((((((((..(((.....)))...--.....(((((.......))))).(((((.......))))).---..........)))))))))))....-------- ( -34.00)
>DroVir_CAF1 414693 101 + 1
UGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAUAUAAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCACAACCCUCUCCUCC--------CCUCUCC------AG
........((((((.(((((..(((.....)))..........(((((.......)))))..))))).......((......))....))))--------)).....------.. ( -23.10)
>DroPse_CAF1 343345 105 + 1
UGACAAAUGGUGGGCGUGGCCAUGCAAAUCGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAACUUUGGCAC---CCUACCCCCUGCCAAAGACCUGAACC---CA--
..........((((.(((((..(((.....)))...--.....(((((.......)))))..)))))...((((((((.---.........)))))))).......))---))-- ( -27.30)
>DroWil_CAF1 574357 104 + 1
UGACAAAUGGGGGGCGUGGCCAUGCAAAUUGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAC---CCGACCCUCUACCACUC---UACCC---CCUUG
........(((((..(((((..(((.....)))...--.....(((((.......)))))..)))))..((..(((...---...........)))..)---).)))---))... ( -25.84)
>DroMoj_CAF1 467640 98 + 1
UGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAUAUAAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAUAGUCCUAUCCUCC--------C---UCU------CG
........((((((...((.(.(((.....)))..........................(((((((.......)))))))).))...)))))--------)---...------.. ( -23.70)
>DroAna_CAF1 282457 107 + 1
UGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAU--AAAAAGAACUCAUUAAAAGUUUAUGCCACAAACUUUGCCAC---CCGACCCCGGCC--CACCGCAAUCCAAU-UCGG
.......(((((((((((((..(((.....)))...--...............(((((((.......))))))))))))---.((....)))))--).)).)).......-.... ( -25.10)
>consensus
UGACAAAUGGGGGGCGUGGCCAUGCAAAUCGCAAAU__AAAAAGAACUCAUUAAAAGUUUAUGCCACAAAGUUUGGCAC___CCGACCCUCU_C__C_C_CCUAUCC_______G
........((((((.(((((..(((.....)))..........(((((.......)))))..))))).......((......))..))))))....................... (-17.70 = -18.23 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:54 2006