Locus 4571

Sequence ID	3R_DroMel_CAF1
Location	12,071,506 – 12,071,626
Length	120
Max. P	0.987554

overview

Window 6

Location	12,071,506 – 12,071,626
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.15
Mean single sequence MFE	-42.38
Consensus MFE	-39.76
Energy contribution	-40.56
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.94
SVM decision value	1.35
SVM RNA-class probability	0.945026
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12071506 120 + 27905053
UUGGCGCCGGACCGGCAUGGCACGGAUGUGUACAUGGAAUAUAGGAGGCGGCCGCCUUUGGUGAUGGUGAUUUCACUUUCAGAUACAUUAACACAAGUGCGCUGAAAUGCGCGCGCCUUU
..(((.(((..((.....))..))).(((((..(((.......((((((....))))))..(((.((((....)))).)))....)))..))))).((((((......)))))))))... ( -43.00)
>DroSec_CAF1 8035 120 + 1
UUGGCGCCGGACCGGCAUGGCACGGAUGUGUACAUGGAAUAUAGGAGGCGGCCGCCUUUGGUGAUUGUGAUUUCACUUUCAGAUACAUUAACACAAGUGCGCUGAAAUGCGCGCGCCUUU
..(((((((...)))).((.....(((((((...((((.....((((((....))))))(((((........))))))))).)))))))....)).((((((......)))))))))... ( -42.80)
>DroSim_CAF1 8471 120 + 1
UUGGCGCCGGACCGGCAUGGCACGGAUGUGUACAUGGAAUAUAGGAGGCGGCCGCCUUUGGUGAUGGUGAUUUCACUUUCAGAUACAUUAACACAAGUGCGCUGAAAUGCGCGCGCCUUU
..(((.(((..((.....))..))).(((((..(((.......((((((....))))))..(((.((((....)))).)))....)))..))))).((((((......)))))))))... ( -43.00)
>DroEre_CAF1 10046 114 + 1
UUGGCGCCGGACCGGCAUGGCACGGAUGUGUACAUGGAAUAUAGGAGGCGGCCGCCUUUGGU------GAUUUCACUUUCAGAUACAUUAACACAAGUGCGCUGAAAUGCGCGCGCCUUU
..(((((((...)))).((.....(((((((...((((.....((((((....))))))(((------(....)))))))).)))))))....)).((((((......)))))))))... ( -41.40)
>DroYak_CAF1 10248 114 + 1
UUGGCGCCGGACCGGCAUGGUACGGAUGUGUACAUGGAAUAUAGGAGGCGGCCGCCUUUGGU------GAUUUCACUUUCAGAUACAUUAACACAAGUGCGCUGAAUUGCGCGCGCCUUU
..(((((((...))))...((...(((((((...((((.....((((((....))))))(((------(....)))))))).)))))))...))..((((((......)))))))))... ( -41.70)
>consensus
UUGGCGCCGGACCGGCAUGGCACGGAUGUGUACAUGGAAUAUAGGAGGCGGCCGCCUUUGGUGAU_GUGAUUUCACUUUCAGAUACAUUAACACAAGUGCGCUGAAAUGCGCGCGCCUUU
..(((((((...)))).((.....(((((((...((((.....((((((....))))))(((((........))))))))).)))))))....)).((((((......)))))))))... (-39.76 = -40.56 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	12,071,506 – 12,071,626
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.15
Mean single sequence MFE	-36.94
Consensus MFE	-33.58
Energy contribution	-34.22
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.80
Structure conservation index	0.91
SVM decision value	2.08
SVM RNA-class probability	0.987554
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12071506 120 - 27905053
AAAGGCGCGCGCAUUUCAGCGCACUUGUGUUAAUGUAUCUGAAAGUGAAAUCACCAUCACCAAAGGCGGCCGCCUCCUAUAUUCCAUGUACACAUCCGUGCCAUGCCGGUCCGGCGCCAA
...(((((((((......))))...(((((..(((....(((..(((....)))..)))....((((....)))).........)))..)))))..((..((.....))..))))))).. ( -37.80)
>DroSec_CAF1 8035 120 - 1
AAAGGCGCGCGCAUUUCAGCGCACUUGUGUUAAUGUAUCUGAAAGUGAAAUCACAAUCACCAAAGGCGGCCGCCUCCUAUAUUCCAUGUACACAUCCGUGCCAUGCCGGUCCGGCGCCAA
...(((((((((......))))...(((((..(((....(((..(((....)))..)))....((((....)))).........)))..)))))..((..((.....))..))))))).. ( -37.70)
>DroSim_CAF1 8471 120 - 1
AAAGGCGCGCGCAUUUCAGCGCACUUGUGUUAAUGUAUCUGAAAGUGAAAUCACCAUCACCAAAGGCGGCCGCCUCCUAUAUUCCAUGUACACAUCCGUGCCAUGCCGGUCCGGCGCCAA
...(((((((((......))))...(((((..(((....(((..(((....)))..)))....((((....)))).........)))..)))))..((..((.....))..))))))).. ( -37.80)
>DroEre_CAF1 10046 114 - 1
AAAGGCGCGCGCAUUUCAGCGCACUUGUGUUAAUGUAUCUGAAAGUGAAAUC------ACCAAAGGCGGCCGCCUCCUAUAUUCCAUGUACACAUCCGUGCCAUGCCGGUCCGGCGCCAA
...(((((((((......))))...(((((..(((.........(((....)------))...((((....)))).........)))..)))))..((..((.....))..))))))).. ( -36.10)
>DroYak_CAF1 10248 114 - 1
AAAGGCGCGCGCAAUUCAGCGCACUUGUGUUAAUGUAUCUGAAAGUGAAAUC------ACCAAAGGCGGCCGCCUCCUAUAUUCCAUGUACACAUCCGUACCAUGCCGGUCCGGCGCCAA
...(((((((((......))))...(((((..(((.........(((....)------))...((((....)))).........)))..)))))..((.(((.....))).))))))).. ( -35.30)
>consensus
AAAGGCGCGCGCAUUUCAGCGCACUUGUGUUAAUGUAUCUGAAAGUGAAAUCAC_AUCACCAAAGGCGGCCGCCUCCUAUAUUCCAUGUACACAUCCGUGCCAUGCCGGUCCGGCGCCAA
...(((((((((......))))...(((((..(((.........((((........))))...((((....)))).........)))..)))))..((.(((.....))).))))))).. (-33.58 = -34.22 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:01 2006