Locus 4289

Sequence ID	3R_DroMel_CAF1
Location	11,413,768 – 11,413,878
Length	110
Max. P	0.988701

overview

Window 7

Location	11,413,768 – 11,413,878
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-41.80
Consensus MFE	-35.36
Energy contribution	-35.52
Covariance contribution	0.16
Combinations/Pair	1.10
Mean z-score	-1.50
Structure conservation index	0.85
SVM decision value	0.69
SVM RNA-class probability	0.823155
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11413768 110 + 27905053
AAUAAAAGGACC----------CAAGGCGAACGGAAGACAUGGCUACCUGGCCAGGACAAAGCCAGCUCCCUGUCCAUGGCGAAUCGCUGGCAGGAUGUGAGGUCCUGCCCUCGGCAGAU
......((((((----------(..(((...(....)...(((((....))))).......))).((..((((((...((((...))))))))))..))).))))))(((...))).... ( -39.30)
>DroSec_CAF1 161424 110 + 1
AAUAAAAGGACC----------CAAGGCGAGCGGAUGACAUGGCUACCUGGCCAGGACAAAGCCAGCUCCCUGUCCAUGGCGAAUCGCUGACAGGAUGUGAGGUCCUGCCCUCGGCAGAU
......((((((----------((....((((((.((...(((((....)))))...))...)).))))((((((...((((...))))))))))...)).))))))(((...))).... ( -40.90)
>DroSim_CAF1 152865 110 + 1
AAUAAAAGGACC----------CAAGGCGAGCGGAUGACAUGGCUACCUGGCCAGGACAAAGCCAGCUCCCUGUCCAUGGCGAAUCGCUGGCAGGAUGUGAGGUCCUGCCCUCGGCAGAU
.......((((.----------..(((.((((((.((...(((((....)))))...))...)).))))))))))).((.(((......((((((((.....)))))))).))).))... ( -41.70)
>DroEre_CAF1 149200 110 + 1
AAUAAAGGGACC----------CAAGGCGAGCGGAGGACAUGGCUACCUGGCCGGGACAAAGCCAGCUCCCUGUCCAUGGCGAAUCGCUGGCAAGAUGUGAGGUCCUGCCCUUGGCAGAU
......((((((----------((.(((((((.(.(((((.((((....))))(((((.......).))))))))).).))...))))).........)).))))))(((...))).... ( -38.80)
>DroYak_CAF1 153250 120 + 1
AAUAAAAGGACCAAGGACCGACCAAGGCGAGCGGAAGACAGGGCUACCUGGCCAGGACAAAGCCAGCUCCCUGUCCAUGGCGAAUCGCUGGCAGGAUGUGAGGUCCUGCCCUUGGCAGAU
.......((.(....).))(.(((((((((((.(..(((((((....(((((.........)))))..)))))))..).))...)))).((((((((.....)))))))))))))).... ( -48.30)
>consensus
AAUAAAAGGACC__________CAAGGCGAGCGGAAGACAUGGCUACCUGGCCAGGACAAAGCCAGCUCCCUGUCCAUGGCGAAUCGCUGGCAGGAUGUGAGGUCCUGCCCUCGGCAGAU
......((((((................((((((......(((((....)))))........)).))))((((((...((((...))))))))))......))))))(((...))).... (-35.36 = -35.52 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	11,413,768 – 11,413,878
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.16
Mean single sequence MFE	-44.28
Consensus MFE	-37.94
Energy contribution	-37.54
Covariance contribution	-0.40
Combinations/Pair	1.16
Mean z-score	-2.01
Structure conservation index	0.86
SVM decision value	2.13
SVM RNA-class probability	0.988701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11413768 110 - 27905053
AUCUGCCGAGGGCAGGACCUCACAUCCUGCCAGCGAUUCGCCAUGGACAGGGAGCUGGCUUUGUCCUGGCCAGGUAGCCAUGUCUUCCGUUCGCCUUG----------GGUCCUUUUAUU
.....((((((((((((.......))))))).((((..((....(((((((.(.((((((.......)))))).)..)).)))))..)).))))))))----------)........... ( -43.40)
>DroSec_CAF1 161424 110 - 1
AUCUGCCGAGGGCAGGACCUCACAUCCUGUCAGCGAUUCGCCAUGGACAGGGAGCUGGCUUUGUCCUGGCCAGGUAGCCAUGUCAUCCGCUCGCCUUG----------GGUCCUUUUAUU
.....((((((((((((.......))))))).((((...((....((((((.(.((((((.......)))))).)..)).))))....))))))))))----------)........... ( -39.70)
>DroSim_CAF1 152865 110 - 1
AUCUGCCGAGGGCAGGACCUCACAUCCUGCCAGCGAUUCGCCAUGGACAGGGAGCUGGCUUUGUCCUGGCCAGGUAGCCAUGUCAUCCGCUCGCCUUG----------GGUCCUUUUAUU
.....((((((((((((.......))))))).((((...((....((((((.(.((((((.......)))))).)..)).))))....))))))))))----------)........... ( -42.40)
>DroEre_CAF1 149200 110 - 1
AUCUGCCAAGGGCAGGACCUCACAUCUUGCCAGCGAUUCGCCAUGGACAGGGAGCUGGCUUUGUCCCGGCCAGGUAGCCAUGUCCUCCGCUCGCCUUG----------GGUCCCUUUAUU
.....((((((((((((.......))))))).((((...((...(((((((.(.((((((.......)))))).)..)).)))))...))))))))))----------)........... ( -42.50)
>DroYak_CAF1 153250 120 - 1
AUCUGCCAAGGGCAGGACCUCACAUCCUGCCAGCGAUUCGCCAUGGACAGGGAGCUGGCUUUGUCCUGGCCAGGUAGCCCUGUCUUCCGCUCGCCUUGGUCGGUCCUUGGUCCUUUUAUU
....(((((((((((((.......))))))).((((...((...((((((((..((((((.......))))))....))))))))...)))))))))))).((.(....).))....... ( -53.40)
>consensus
AUCUGCCGAGGGCAGGACCUCACAUCCUGCCAGCGAUUCGCCAUGGACAGGGAGCUGGCUUUGUCCUGGCCAGGUAGCCAUGUCAUCCGCUCGCCUUG__________GGUCCUUUUAUU
......(((((((((((.......))))))).((((...((...(((((((.(.((((((.......)))))).)..)).)))))...))))))))))...................... (-37.94 = -37.54 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:49 2006