Locus 2747

Sequence ID	3R_DroMel_CAF1
Location	7,355,596 – 7,355,692
Length	96
Max. P	0.989643

overview

Window 4

Location	7,355,596 – 7,355,692
Length	96
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-28.41
Consensus MFE	-22.66
Energy contribution	-23.22
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.80
SVM decision value	2.17
SVM RNA-class probability	0.989643
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7355596 96 + 27905053
ACCCGCCCAC---UUUAAGGUAAACAAAUAUUUGAUUGGCCCCAAAAAGAUGGGGGCCCGUGCUCCAGCAUCUUUUGUUUACCUGAGCACAACGAUAAA
...((.....---....(((((((((((.........((((((.........)))))).((((....))))..)))))))))))........))..... ( -28.43)
>DroSec_CAF1 31616 96 + 1
AACCGCCCAC---UUUAAGCUAAACAAAUAUUUGAUUGGGCCCAAAAAGAUGGGGGCCCGUGCUCCAGCAUCUUUUGUUUACCUGGGCACAUCGAUAAA
....(((((.---.....(.((((((((.........((((((..........))))))((((....))))..)))))))).))))))........... ( -29.10)
>DroSim_CAF1 37081 96 + 1
AACCGCCCAC---UUUAAGCUAAACAAAUAUUUGAUUGGGCCCAAAAAGAUGGGGGCCCGUGCUCCAGCAUCUUUUGUUUACCUGGGCACAUCGAUAAA
....(((((.---.....(.((((((((.........((((((..........))))))((((....))))..)))))))).))))))........... ( -29.10)
>DroEre_CAF1 35388 92 + 1
---UGCCCCC---UUCGAGCUAAACAAAUAUUUGAUUGGGCCCAA-AAGAUGGGGGCCUGUGCUCCACCAUCUUUUGUUUACCUGGGCACAUCGAUAAA
---(((((((---.(((((.((......)))))))..))...(((-(((((((((((....)).)).)))))))))).......))))).......... ( -28.30)
>DroYak_CAF1 36421 95 + 1
---CGCCCCCCUUUUCAAGCUAAACAAAUAUUUGAUUGGGCCCAA-AAGAUGGGGGCCUGCGCUUCAGCAUCUUUUGUUUACCUGGGCACAUCGAUAAA
---.(((((((...(((((.((......)))))))..)))..(((-(((((((((((....)))))..))))))))).......))))........... ( -27.10)
>consensus
A_CCGCCCAC___UUUAAGCUAAACAAAUAUUUGAUUGGGCCCAAAAAGAUGGGGGCCCGUGCUCCAGCAUCUUUUGUUUACCUGGGCACAUCGAUAAA
....((((.........((.((((((((.........((((((..........))))))((((....))))..)))))))).))))))........... (-22.66 = -23.22 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	7,355,596 – 7,355,692
Length	96
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	90.50
Mean single sequence MFE	-30.80
Consensus MFE	-23.42
Energy contribution	-23.74
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-2.24
Structure conservation index	0.76
SVM decision value	1.08
SVM RNA-class probability	0.911592
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7355596 96 - 27905053
UUUAUCGUUGUGCUCAGGUAAACAAAAGAUGCUGGAGCACGGGCCCCCAUCUUUUUGGGGCCAAUCAAAUAUUUGUUUACCUUAAA---GUGGGCGGGU
....(((((.((((.(((((((((((...(((....)))..((((((.........)))))).........)))))))))))...)---)))))))).. ( -31.80)
>DroSec_CAF1 31616 96 - 1
UUUAUCGAUGUGCCCAGGUAAACAAAAGAUGCUGGAGCACGGGCCCCCAUCUUUUUGGGCCCAAUCAAAUAUUUGUUUAGCUUAAA---GUGGGCGGUU
..........(((((((.((((((((...(((....))).((((((..........)))))).........)))))))).).....---.))))))... ( -30.10)
>DroSim_CAF1 37081 96 - 1
UUUAUCGAUGUGCCCAGGUAAACAAAAGAUGCUGGAGCACGGGCCCCCAUCUUUUUGGGCCCAAUCAAAUAUUUGUUUAGCUUAAA---GUGGGCGGUU
..........(((((((.((((((((...(((....))).((((((..........)))))).........)))))))).).....---.))))))... ( -30.10)
>DroEre_CAF1 35388 92 - 1
UUUAUCGAUGUGCCCAGGUAAACAAAAGAUGGUGGAGCACAGGCCCCCAUCUU-UUGGGCCCAAUCAAAUAUUUGUUUAGCUCGAA---GGGGGCA---
........(((.(((.(((...((((((((((.((.((....)))))))))))-))).)))..........((((.......))))---))).)))--- ( -32.00)
>DroYak_CAF1 36421 95 - 1
UUUAUCGAUGUGCCCAGGUAAACAAAAGAUGCUGAAGCGCAGGCCCCCAUCUU-UUGGGCCCAAUCAAAUAUUUGUUUAGCUUGAAAAGGGGGGCG---
........(((((...((((.........))))...))))).((((((...((-(..(((.....(((....)))....)))..)))..)))))).--- ( -30.00)
>consensus
UUUAUCGAUGUGCCCAGGUAAACAAAAGAUGCUGGAGCACGGGCCCCCAUCUUUUUGGGCCCAAUCAAAUAUUUGUUUAGCUUAAA___GUGGGCGG_U
..........(((((((.((((((((.(.(((....))))((((((..........)))))).........)))))))).)).........)))))... (-23.42 = -23.74 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:55 2006