Locus 3154

Sequence ID	3R_DroMel_CAF1
Location	8,356,697 – 8,356,816
Length	119
Max. P	0.878123

overview

Window 8

Location	8,356,697 – 8,356,788
Length	91
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	81.15
Mean single sequence MFE	-14.67
Consensus MFE	-8.53
Energy contribution	-9.45
Covariance contribution	0.92
Combinations/Pair	1.08
Mean z-score	-2.07
Structure conservation index	0.58
SVM decision value	0.27
SVM RNA-class probability	0.662855
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8356697 91 - 27905053
CACACAAUACCAGGGCACAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAACGCACACAAGCACACACACAAAGCCAAUUUGAAGCCCUUUU
...........(((((..................(((..((((((......)).))))))).......((((.....))))..)))))... ( -18.80)
>DroPse_CAF1 20547 72 - 1
CU--GAGUGCC-GGGCACACGAAUAAUCUUGCACGCUCCUGUGGCU----C------------UCACACAAAGCCGACUCGAAGCCUUUUU
.(--((((((.-((((...(((......)))...)).)).))((((----.------------........)))).))))).......... ( -13.30)
>DroSec_CAF1 18936 79 - 1
CACACAAUACCAACGCACAUAAAUAAUCUGGCCCGCUUUUGUGGCCAAAAC------------ACACACAAAGCCAAUUUGAAGCCCUUUU
..............((............(((((.((....)))))))....------------.....((((.....))))..))...... ( -11.80)
>DroSim_CAF1 15860 79 - 1
CACACAAUACCAACGCACAUAAAUAAUCUGGCCCGCUUUUGUGGCCAAAAC------------ACACACAAAGCCAAUUUGAAGCCCUUUU
..............((............(((((.((....)))))))....------------.....((((.....))))..))...... ( -11.80)
>DroEre_CAF1 20309 83 - 1
CACACAAUACCUGGGCUCAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAACACAC--------UCACACAAAGCCAAUUUGAAGCCCUUUU
............(((((...........(((.((((....)))).))).......--------.....((((.....)))).))))).... ( -16.20)
>DroYak_CAF1 19145 87 - 1
CACACAAUACUUGGGCACAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAACACACAC----ACACACACAAAGCCAAUUUGAAGCCCUUUU
............((((............(((.((((....)))).))).........----.......((((.....))))..)))).... ( -16.10)
>consensus
CACACAAUACCAGGGCACAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAAC____________ACACACAAAGCCAAUUUGAAGCCCUUUU
............((((..............((.(((....))))).......................((((.....))))..)))).... ( -8.53 =  -9.45 +   0.92)

alignment

secondary structure

dotplot

Window 9

Location	8,356,721 – 8,356,816
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	79.99
Mean single sequence MFE	-15.90
Consensus MFE	-8.66
Energy contribution	-9.58
Covariance contribution	0.92
Combinations/Pair	1.09
Mean z-score	-2.51
Structure conservation index	0.54
SVM decision value	0.90
SVM RNA-class probability	0.878123
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8356721 95 - 27905053
UACUCAAAAACAUCAAAGUGCCCCCAAACACACAAUACCAGGGCACAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAACGCACACAAGCACACAC
.................((((...................(((((............)))))....(((((((......)).))))))))).... ( -19.70)
>DroSec_CAF1 18960 83 - 1
UACUCAAAAACAUCAAAGUGCCCGCAAACACACAAUACCAACGCACAUAAAUAAUCUGGCCCGCUUUUGUGGCCAAAAC------------ACAC
.................((((.....................))))..........(((((.((....)))))))....------------.... ( -12.20)
>DroSim_CAF1 15884 83 - 1
UACUCAAAAACAUCAAAGUGCCCGCAAACACACAAUACCAACGCACAUAAAUAAUCUGGCCCGCUUUUGUGGCCAAAAC------------ACAC
.................((((.....................))))..........(((((.((....)))))))....------------.... ( -12.20)
>DroEre_CAF1 20333 87 - 1
UACUCGAAAACAUCAAAGUGCCUGCAAACACACAAUACCUGGGCUCAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAACACAC--------UCAC
................((((..........(((((....(((((..............)))))...))))).........)))--------)... ( -14.15)
>DroYak_CAF1 19169 91 - 1
UACUCAAGAACAUCAAAGUGCCCGCAAACACACAAUACUUGGGCACAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAACACACAC----ACACAC
....(((((........(((((((...............)))))))........))))).((((....)))).............----...... ( -17.55)
>DroPer_CAF1 19529 73 - 1
GACUCG---ACAUCAAAGUGGCCGCAAACG--GAGUGCC-GGGCACACGAAUAAUCUUGCACGCUCCUGUGGCU----C------------UCAC
......---..........(((((((...(--(((((..-..(((...((....)).))).)))))))))))))----.------------.... ( -19.60)
>consensus
UACUCAAAAACAUCAAAGUGCCCGCAAACACACAAUACCAGGGCACAUAAAUAAUCUUGCCCGCUUUUGUGGCCAAAAC____________ACAC
.................((((((.................))))))............((.(((....)))))...................... ( -8.66 =  -9.58 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:21 2006