Locus 5331

Sequence ID	X_DroMel_CAF1
Location	13,920,900 – 13,921,060
Length	160
Max. P	0.999879

overview

Window 3

Location	13,920,900 – 13,921,020
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-40.48
Consensus MFE	-39.54
Energy contribution	-39.74
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.98
SVM decision value	1.26
SVM RNA-class probability	0.937403
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13920900 120 + 22224390
AAUGACAUGGGAGGAAGCUACCAACUUAGCGCCCUUGGGCCAAGCAAUCUGAGCCACGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUU
.((((..(((.((....)).))).....(.((((.((((((((((...........((....))(((((........)))))........))))))).)))...)))))....))))... ( -39.60)
>DroSec_CAF1 1154 120 + 1
AAUGACACGGGAGGAAGCUACCAACUUAGCGCCCUUGGGCCAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUU
.((((((.(((.....((((......)))).))).))((((.........(((((((((.((..(((((........)))))....))..)))))))))......))))....))))... ( -40.56)
>DroSim_CAF1 3139 120 + 1
AAUGACAUGGGAGGAAGCUACCAACUUAGCGCCCUUGGGCCAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUU
.((((((.(((.....((((......)))).))).))((((.........(((((((((.((..(((((........)))))....))..)))))))))......))))....))))... ( -40.56)
>DroEre_CAF1 2651 119 + 1
AAUGACAUGGGAGGAAGCUACCAACUUAGCGCCCUUGGGCC-AGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUU
.((((((.(((.....((((......)))).))).))((((-........(((((((((.((..(((((........)))))....))..)))))))))......))))....))))... ( -41.14)
>DroYak_CAF1 2585 120 + 1
AAUGACAUGGGAGGAAGCUACCAACUUAGCGCCCUUGGGCCAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUA
.((((((.(((.....((((......)))).))).))((((.........(((((((((.((..(((((........)))))....))..)))))))))......))))....))))... ( -40.56)
>consensus
AAUGACAUGGGAGGAAGCUACCAACUUAGCGCCCUUGGGCCAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUU
.((((((.(((.....((((......)))).))).))((((.........(((((((((.((..(((((........)))))....))..)))))))))......))))....))))... (-39.54 = -39.74 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	13,920,900 – 13,921,020
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-50.60
Consensus MFE	-49.38
Energy contribution	-49.62
Covariance contribution	0.24
Combinations/Pair	1.02
Mean z-score	-3.20
Structure conservation index	0.98
SVM decision value	4.36
SVM RNA-class probability	0.999879
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13920900 120 - 22224390
AAGAUGAUGUUGGCCCGAAUGGAGCCAAGCGAGAAAAUGGAGCUGCAGUUGGCCCCCGUCAACGUGGCUCAGAUUGCUUGGCCCAAGGGCGCUAAGUUGGUAGCUUCCUCCCAUGUCAUU
..((((((((.(((((...(((.(((((((((.......((((..(.((((((....)))))))..))))...)))))))))))).))))((((......))))......).)))))))) ( -52.90)
>DroSec_CAF1 1154 120 - 1
AAGAUGAUGUUGGCCCGAAUGGAGCCAAGCGAGAAAAUGGAGCUGCAGUUGGCCCCCGUCAACUUGGCUCAGAUUGCUUGGCCCAAGGGCGCUAAGUUGGUAGCUUCCUCCCGUGUCAUU
..(((((..(.(((((...(((.(((((((((.......((((((.(((((((....)))))))))))))...)))))))))))).))))((((......))))......).)..))))) ( -50.90)
>DroSim_CAF1 3139 120 - 1
AAGAUGAUGUUGGCCCGAAUGGAGCCAAGCGAGAAAAUGGAGCUGCAGUUGGCCCCCGUCAACUUGGCUCAGAUUGCUUGGCCCAAGGGCGCUAAGUUGGUAGCUUCCUCCCAUGUCAUU
..((((((((.(((((...(((.(((((((((.......((((((.(((((((....)))))))))))))...)))))))))))).))))((((......))))......).)))))))) ( -51.30)
>DroEre_CAF1 2651 119 - 1
AAGAUGAUGUUGGCCCGAAUGGAGCCAAGCGAGAAAAUGGAGCUGCAGUUGGCCCCCGUCAACUUGGCUCAGAUUGCU-GGCCCAAGGGCGCUAAGUUGGUAGCUUCCUCCCAUGUCAUU
..((((((((.(((((...(((.((((.((((.......((((((.(((((((....)))))))))))))...)))))-)))))).))))((((......))))......).)))))))) ( -46.60)
>DroYak_CAF1 2585 120 - 1
UAGAUGAUGUUGGCCCGAAUGGAGCCAAGCGAGAAAAUGGAGCUGCAGUUGGCCCCCGUCAACUUGGCUCAGAUUGCUUGGCCCAAGGGCGCUAAGUUGGUAGCUUCCUCCCAUGUCAUU
..((((((((.(((((...(((.(((((((((.......((((((.(((((((....)))))))))))))...)))))))))))).))))((((......))))......).)))))))) ( -51.30)
>consensus
AAGAUGAUGUUGGCCCGAAUGGAGCCAAGCGAGAAAAUGGAGCUGCAGUUGGCCCCCGUCAACUUGGCUCAGAUUGCUUGGCCCAAGGGCGCUAAGUUGGUAGCUUCCUCCCAUGUCAUU
..(((((..(.(((((...(((.(((((((((.......((((((.(((((((....)))))))))))))...)))))))))))).))))((((......))))......).)..))))) (-49.38 = -49.62 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	13,920,940 – 13,921,060
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-38.59
Consensus MFE	-34.13
Energy contribution	-34.57
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.74
Structure conservation index	0.88
SVM decision value	1.48
SVM RNA-class probability	0.957789
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13920940 120 + 22224390
CAAGCAAUCUGAGCCACGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUUCUUCACUUCGUCUUCGCGUUUUGGCCUCAAGUCGGUUGGC
(((.(.(..((((((((((.(((((((((........)))))........(.(((((((.....))))))))................))))...))))...)).))))..).).))).. ( -34.40)
>DroSec_CAF1 1194 120 + 1
CAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUUCUUCUCUUCGCCUUCGCGUUUUGGCCUCAAGUCGGUUGGC
....(((((.(((((((((.((..(((((........)))))....))..))))))))).....(((((((.................(((....)))..)))))))......))))).. ( -36.81)
>DroSim_CAF1 3179 120 + 1
CAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUUCUUCUCUUCGCCUUCGCGUUUUGGCCUCAAGUCGGUUGGC
....(((((.(((((((((.((..(((((........)))))....))..))))))))).....(((((((.................(((....)))..)))))))......))))).. ( -36.81)
>DroEre_CAF1 2691 119 + 1
C-AGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUUCUUCUCUUCGCCUUCGCGUUUUGGCCUGAAGUCGGUUGCG
.-.((((((.(((((((((.((..(((((........)))))....))..)))))))))..((((((((((.................(((....)))..))))))))))...)))))). ( -46.01)
>DroYak_CAF1 2625 120 + 1
CAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUACUUCUCUUAGCCUUCGCGUUUUGGCCUCAAGUCGCUUGGC
(((((.(..(((((((((.((.(((((((.......(((...........)))((((((.....))))))...................))))))))).))))).))))..).))))).. ( -38.90)
>consensus
CAAGCAAUCUGAGCCAAGUUGACGGGGGCCAACUGCAGCUCCAUUUUCUCGCUUGGCUCCAUUCGGGCCAACAUCAUCUUCUUCUCUUCGCCUUCGCGUUUUGGCCUCAAGUCGGUUGGC
....(((((.(((((((((.((..(((((........)))))....))..))))))))).....(((((((.................(((....)))..)))))))......))))).. (-34.13 = -34.57 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:10 2006