Locus 3778

Sequence ID	3R_DroMel_CAF1
Location	10,245,356 – 10,245,479
Length	123
Max. P	0.918604

overview

Window 3

Location	10,245,356 – 10,245,450
Length	94
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	74.46
Mean single sequence MFE	-21.88
Consensus MFE	-9.50
Energy contribution	-9.37
Covariance contribution	-0.14
Combinations/Pair	1.27
Mean z-score	-2.13
Structure conservation index	0.43
SVM decision value	0.79
SVM RNA-class probability	0.850165
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10245356 94 + 27905053
AGG-CUCUGC-CAAAAAAUAAAAAGGUUAAC------CUUCUCGAGAGAGGGGCUACAAAUCGUCGACAAUUUGGCUGUCGACUGGGAACACGCAAAACCAA
.((-(...))-)............((((..(------(((((....))))))((........(((((((.......)))))))((....)).))..)))).. ( -27.30)
>DroGri_CAF1 107754 86 + 1
AUG-CUUUAAUCGCAAUGU-GAAAAGUUAA----------C----AAUAUGAGCAACAAAUCGUCGACAAUUUGGCUGUCGACCAAAAACACGCAAAACCAA
.((-(.......))).(((-(.........----------.----.....((........))(((((((.......)))))))........))))....... ( -14.20)
>DroEre_CAF1 103994 90 + 1
AGG-CUCCGC-CGAA------AAAGGUUAACCCAAACCCAC----GAGAGGGGCUACAAAUCGUCGACAAUUUGGCUGUCGACUGGGAACACGCAAAACCAA
..(-(...((-(...------...)))...((((..(((.(----....)))).........(((((((.......))))))))))).....))........ ( -26.00)
>DroYak_CAF1 109672 87 + 1
AGG-CUCUGC-CAAAAA---AAAAGGUUAAC------CCAC----GAGAGGGGCUACAAAUCGUCGACAAUUUGGCUGUCGACUGGGAACACGCAAAACCAA
.((-(...))-).....---....((((..(------((..----....)))((........(((((((.......)))))))((....)).))..)))).. ( -23.90)
>DroMoj_CAF1 112186 87 + 1
AGGUUUUUAAUCGCAAUGC-CAAAAGUCAA----------C----AAUAAGAGCAACAAAUCGUCGACAAUUUGGCUGUCGGCCGAAAACACGCAAAACCAA
.((((((.....((..(((-(.........----------.----.....).))).....(((((((((.......)))))).)))......)))))))).. ( -15.86)
>DroAna_CAF1 93333 85 + 1
-GA-GUGUGU-A-AAAA---AUAAGGUUAAC------ACAG----GAGAGCGGCAACAAAUCGUCGACAAUUUGGCUGUCGCUCGGGAACACGCAAAACCAA
-..-((((((-.-....---....(.....)------....----..((((((((.(((((.(....).)))))..))))))))....))))))........ ( -24.00)
>consensus
AGG_CUCUGC_CGAAAA___AAAAGGUUAAC______CCAC____GAGAGGGGCAACAAAUCGUCGACAAUUUGGCUGUCGACCGGGAACACGCAAAACCAA
....................................................((......(((((((((.......))))))).))......))........ ( -9.50 =  -9.37 +  -0.14)

alignment

secondary structure

dotplot

Window 4

Location	10,245,356 – 10,245,450
Length	94
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	74.46
Mean single sequence MFE	-25.98
Consensus MFE	-10.32
Energy contribution	-10.60
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.36
Structure conservation index	0.40
SVM decision value	1.12
SVM RNA-class probability	0.918604
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10245356 94 - 27905053
UUGGUUUUGCGUGUUCCCAGUCGACAGCCAAAUUGUCGACGAUUUGUAGCCCCUCUCUCGAGAAG------GUUAACCUUUUUAUUUUUUG-GCAGAG-CCU
..((((((((.........((((((((.....))))))))...................((((((------(....)))))))........-))))))-)). ( -29.10)
>DroGri_CAF1 107754 86 - 1
UUGGUUUUGCGUGUUUUUGGUCGACAGCCAAAUUGUCGACGAUUUGUUGCUCAUAUU----G----------UUAACUUUUC-ACAUUGCGAUUAAAG-CAU
...((((((..(((...((((((((((.....))))))))((...(((((.......----)----------.))))...))-.))..)))..)))))-).. ( -18.80)
>DroEre_CAF1 103994 90 - 1
UUGGUUUUGCGUGUUCCCAGUCGACAGCCAAAUUGUCGACGAUUUGUAGCCCCUCUC----GUGGGUUUGGGUUAACCUUU------UUCG-GCGGAG-CCU
..((((((((((...((((((((((((.....)))))))).......((((((....----).)))))))))...))(...------...)-))))))-)). ( -31.40)
>DroYak_CAF1 109672 87 - 1
UUGGUUUUGCGUGUUCCCAGUCGACAGCCAAAUUGUCGACGAUUUGUAGCCCCUCUC----GUGG------GUUAACCUUUU---UUUUUG-GCAGAG-CCU
..((((((((.........((((((((.....))))))))......(((((((....----).))------)))).......---......-))))))-)). ( -29.60)
>DroMoj_CAF1 112186 87 - 1
UUGGUUUUGCGUGUUUUCGGCCGACAGCCAAAUUGUCGACGAUUUGUUGCUCUUAUU----G----------UUGACUUUUG-GCAUUGCGAUUAAAAACCU
..((((((.((((((.......))).((((((..(((((((((..(.....)..)))----)----------))))).))))-))...)))....)))))). ( -27.10)
>DroAna_CAF1 93333 85 - 1
UUGGUUUUGCGUGUUCCCGAGCGACAGCCAAAUUGUCGACGAUUUGUUGCCGCUCUC----CUGU------GUUAACCUUAU---UUUU-U-ACACAC-UC-
..........((((....(((((.((((.((((((....)))))))))).)))))..----..((------(..((......---))..-)-))))))-..- ( -19.90)
>consensus
UUGGUUUUGCGUGUUCCCAGUCGACAGCCAAAUUGUCGACGAUUUGUAGCCCCUCUC____GUGG______GUUAACCUUUU___UUUUCG_GCAGAG_CCU
..(((...(((.(((....((((((((.....))))))))))).))).)))................................................... (-10.32 = -10.60 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	10,245,385 – 10,245,479
Length	94
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	81.61
Mean single sequence MFE	-22.78
Consensus MFE	-15.72
Energy contribution	-15.75
Covariance contribution	0.03
Combinations/Pair	1.12
Mean z-score	-2.35
Structure conservation index	0.69
SVM decision value	0.82
SVM RNA-class probability	0.860090
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10245385 94 + 27905053
CUUCUCGAGAGAGGGGCUACAAAUCGUCGACAAUUUGGCUGUCGACUGGGAACACGCAAAACCAAUUAAUGGGCGUGAAAAAAUCAGUAC------CG----AC
..((((....))))((.(((.....(((((((.......)))))))......(((((....(((.....)))))))).........))))------).----.. ( -27.30)
>DroVir_CAF1 119619 86 + 1
---C----AAUAAGAGCAACAAAUUGUCGACAAUUUGGCUGUCAGCCAAAAACACGCAAAACCAAUUAAUGGGCGUGAAAAAAUCAGUUC-------G----UC
---.----.....((((................((((((.....))))))..(((((....(((.....)))))))).........))))-------.----.. ( -20.20)
>DroPse_CAF1 111213 94 + 1
CAAC----AGAAACAGCAACAAAUCGUCGACAAUUUGGCUGUCGGCCAGAAACACGCAAAACCAAUUAAUGGGCGUGAAAAAAUCAGUAG------AGUAAAAC
....----.((..............(((((((.......)))))))......(((((....(((.....))))))))......)).....------........ ( -17.30)
>DroGri_CAF1 107782 86 + 1
---C----AAUAUGAGCAACAAAUCGUCGACAAUUUGGCUGUCGACCAAAAACACGCAAAACCAAUUAAUGGGCGUGAAAAAAUCAGUUC-------G----AC
---.----....(((((........(((((((.......)))))))......(((((....(((.....)))))))).........))))-------)----.. ( -22.40)
>DroMoj_CAF1 112215 86 + 1
---C----AAUAAGAGCAACAAAUCGUCGACAAUUUGGCUGUCGGCCGAAAACACGCAAAACCAAUUAAUGGGCGUGAAAAAAUCAGUGC-------G----AC
---.----.......(((.....(((((((((.......)))))).)))...(((((....(((.....))))))))..........)))-------.----.. ( -20.80)
>DroAna_CAF1 93357 96 + 1
ACAG----GAGAGCGGCAACAAAUCGUCGACAAUUUGGCUGUCGCUCGGGAACACGCAAAACCAAUUAAUGGGCGUGAAAAAGUCAGUACGAGCUCCG----AC
...(----((((((((((.(((((.(....).)))))..)))))))).....(((((....(((.....)))))))).................))).----.. ( -28.70)
>consensus
___C____AAUAAGAGCAACAAAUCGUCGACAAUUUGGCUGUCGGCCAAAAACACGCAAAACCAAUUAAUGGGCGUGAAAAAAUCAGUAC_______G____AC
...............((........(((((((.......)))))))......(((((....(((.....)))))))).........))................ (-15.72 = -15.75 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:50 2006