Locus 2471

Sequence ID	2R_DroMel_CAF1
Location	8,869,914 – 8,870,059
Length	145
Max. P	0.841530

overview

Window 1

Location	8,869,914 – 8,870,019
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	81.77
Mean single sequence MFE	-37.44
Consensus MFE	-28.38
Energy contribution	-28.18
Covariance contribution	-0.20
Combinations/Pair	1.24
Mean z-score	-1.78
Structure conservation index	0.76
SVM decision value	0.57
SVM RNA-class probability	0.784851
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8869914 105 + 20766785
AUAGUGCUACGAAAAGUUACCCAUGGAGCACUUACAUCGUGGAACUGCCUGGACACCUGGCCAUCCAUGUCCAGGCUGCUCCGACAGAUUGGGCAACGCUUGGCC
.....((((.(....(((.(((((((((((((........))....(((((((((..(((....)))))))))))))))))))......)))).))).).)))). ( -38.10)
>DroSec_CAF1 114764 94 + 1
CU-----------AAGUUGCCCAUGGAGCACUUACAUCGUGGAACUGCCUGGACACCCGGUCACCCAUGUCCAGGCUGCACCGACAGAUUGGGCAGCGCUUUGCC
..-----------..(((((((((((.(((((........))....(((((((((...((....)).)))))))))))).)))......))))))))........ ( -35.40)
>DroSim_CAF1 114588 94 + 1
CU-----------AAGUUGCCCAUGGAGCACUUACAUCGUGGAACUGCCUGGACACCCGGUCACCCAUGUCCAGGCUGCACCGACAGAUUGGGCAGCGCUUUGCC
..-----------..(((((((((((.(((((........))....(((((((((...((....)).)))))))))))).)))......))))))))........ ( -35.40)
>DroEre_CAF1 116259 96 + 1
CUAG---------AAGCUGCUCAUGGAGCACUUACAUAGUGCAACUGCCUGGACACCCGCUCCUCCAUGUCCAGGCGACGACGGCAGAUGGGGCAGCGCUUGGCC
((((---------..(((((((.((..(((((.....)))))...((((((((((............)))))))))).......))....)))))))..)))).. ( -38.00)
>DroYak_CAF1 119155 103 + 1
CUAGUGUU--UAAACGUUGCUCAUGGAGCACUUACAUCGCGCAACCGCCUGGGCACCUGGUCGUCCAUGUCCAGGCGGCGCCGGCAGAUGGGACAACGCUUGGCC
(.((((((--.......(((((...)))))....((((((((..(((((((((((..(((....)))))))))))))).))..)).))))....)))))).)... ( -40.30)
>consensus
CUAG_________AAGUUGCCCAUGGAGCACUUACAUCGUGGAACUGCCUGGACACCCGGUCAUCCAUGUCCAGGCUGCACCGACAGAUUGGGCAGCGCUUGGCC
...............((((((((((.........))).((((....(((((((((...((....)).)))))))))....)).)).....)))))))........ (-28.38 = -28.18 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	8,869,954 – 8,870,059
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	80.32
Mean single sequence MFE	-46.78
Consensus MFE	-30.64
Energy contribution	-31.03
Covariance contribution	0.39
Combinations/Pair	1.42
Mean z-score	-2.00
Structure conservation index	0.65
SVM decision value	0.75
SVM RNA-class probability	0.841530
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8869954 105 - 20766785
AAAGCUGUUUAGCACUGUACAGGGAAGCUCGCAACUGGGUGGCCAAGCGUUGCCCAAUCUGUCGGAGCAGCCUGGACAUGGAUGGCCAGGUGUCCAGGCAGUUCC
....((((.((....)).))))(((((((((((..((((..((.....))..))))...)))..)))).((((((((((((....)))..)))))))))..)))) ( -43.20)
>DroSec_CAF1 114793 105 - 1
AAAGCUGCUUAGCACUGUACAGGGAAGCCCGCAGCUGGGUGGCAAAGCGCUGCCCAAUCUGUCGGUGCAGCCUGGACAUGGGUGACCGGGUGUCCAGGCAGUUCC
..((((.....((((((.(((((..(((.....)))(((..((.....))..)))..))))))))))).((((((((((((....))..)))))))))))))).. ( -54.00)
>DroSim_CAF1 114617 105 - 1
AAAGCUGCUUAGCACUGUACAGGGAAGCCCGCAGCUGGGUGGCAAAGCGCUGCCCAAUCUGUCGGUGCAGCCUGGACAUGGGUGACCGGGUGUCCAGGCAGUUCC
..((((.....((((((.(((((..(((.....)))(((..((.....))..)))..))))))))))).((((((((((((....))..)))))))))))))).. ( -54.00)
>DroEre_CAF1 116290 105 - 1
AAAGCUGCUUGGCACUGUACAGGGAAGCCCGCAACUGGGUGGCCAAGCGCUGCCCCAUCUGCCGUCGUCGCCUGGACAUGGAGGAGCGGGUGUCCAGGCAGUUGC
..(((((((((((.((....))....((((((....(((..((.....))..)))..(((.((((.(((.....))))))).)))))))))).)))))))))).. ( -47.70)
>DroYak_CAF1 119193 105 - 1
AAAGCUGCUUAGCACUGUACAGGGAAGCCCGCAACUGGGUGGCCAAGCGUUGUCCCAUCUGCCGGCGCCGCCUGGACAUGGACGACCAGGUGCCCAGGCGGUUGC
..((((((((.(((((((.(((((..(((.(((..((((((((.....)))).))))..))).)))..).)))).)).(((....))))))))..)))))))).. ( -41.90)
>DroPer_CAF1 130310 99 - 1
AGGGCUGCUUGCAGAAAUACCGCGAGGCGCGCGGAUGGGUGGCCGAGCGCUGUCCGCUCUGCCGGCGCAGACUGGA------UGAUUAUGUGGCCCGGAACUGGA
.((((..(((((.........))))(((((.(((........))).)))))(((((.(((((....))))).))))------)......)..))))......... ( -39.90)
>consensus
AAAGCUGCUUAGCACUGUACAGGGAAGCCCGCAACUGGGUGGCCAAGCGCUGCCCAAUCUGCCGGCGCAGCCUGGACAUGGAUGACCAGGUGUCCAGGCAGUUCC
..(((((((..(((((((.((((...(((.(((..((((..((.....))..))))...))).)))....)))).)).(((....))))))))...))))))).. (-30.64 = -31.03 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:54 2006