Locus 4491

Sequence ID	2R_DroMel_CAF1
Location	14,762,106 – 14,762,299
Length	193
Max. P	0.994492

overview

Window 3

Location	14,762,106 – 14,762,219
Length	113
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.09
Mean single sequence MFE	-32.40
Consensus MFE	-31.30
Energy contribution	-31.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.47
Structure conservation index	0.97
SVM decision value	2.48
SVM RNA-class probability	0.994492
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14762106 113 + 20766785
CC--CCUCCG-CAGACCA----AACUCCAUCUAUUUUCUAUCCAAAUUGUCAGUUGGCCAGUUGGCUCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCU
..--.....(-(((((..----..........................))).(((((((....)))..))))..)))((((....))))..(((((((((((.....))))))))))).. ( -33.29)
>DroSim_CAF1 2534 114 + 1
CC--CCUCCCCCUCAACA----AACUCCAUCUAUUUUCUAUCCAAAUUGUCAGUUGGCCAGUUGGCUCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCU
..--..............----................(((((((..(((..(((((((....)))..))))...)))....)))).))).(((((((((((.....))))))))))).. ( -31.30)
>DroYak_CAF1 3855 120 + 1
CCAUCCAUCCCCACAACACAAGAACUCCAUCUAUUUUCUAUCCAAAUUGUCAGUUGGCCAGUUGGCCCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCU
..........(((..(((..(((......)))....................(((((((....))))..)))......)))..))).....(((((((((((.....))))))))))).. ( -32.60)
>consensus
CC__CCUCCCCCACAACA____AACUCCAUCUAUUUUCUAUCCAAAUUGUCAGUUGGCCAGUUGGCUCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCU
......................................(((((((..(((..(((((((....)))..))))...)))....)))).))).(((((((((((.....))))))))))).. (-31.30 = -31.30 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	14,762,106 – 14,762,219
Length	113
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.09
Mean single sequence MFE	-38.20
Consensus MFE	-32.43
Energy contribution	-32.43
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.85
SVM decision value	0.42
SVM RNA-class probability	0.731223
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14762106 113 - 20766785
AGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGAGCCAACUGGCCAACUGACAAUUUGGAUAGAAAAUAGAUGGAGUU----UGGUCUG-CGGAGG--GG
....(((((((((.....))))))))).((((.((((((.(((....(((..(.(((....)))...)..)))((((.......))))..)))...))----)))).))-))....--.. ( -38.60)
>DroSim_CAF1 2534 114 - 1
AGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGAGCCAACUGGCCAACUGACAAUUUGGAUAGAAAAUAGAUGGAGUU----UGUUGAGGGGGAGG--GG
.((((((((((((.....)))))))))..(((((......))))).........)))..((..((..((((((((..(..((.....))..)..)..)----)))).))..))..)--). ( -36.80)
>DroYak_CAF1 3855 120 - 1
AGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGGGCCAACUGGCCAACUGACAAUUUGGAUAGAAAAUAGAUGGAGUUCUUGUGUUGUGGGGAUGGAUGG
....(((((((((.....))))))))).(((.(.(((.(((((.((((((..(((((....))))..)..)))..)))..........(((......))).))))).))).))))..... ( -39.20)
>consensus
AGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGAGCCAACUGGCCAACUGACAAUUUGGAUAGAAAAUAGAUGGAGUU____UGUUGUGGGGGAGG__GG
.((((((((((((.....)))))))))..(((((......))))).........)))..(((.((((........)))).)))..................................... (-32.43 = -32.43 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	14,762,139 – 14,762,259
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	99.44
Mean single sequence MFE	-45.32
Consensus MFE	-45.14
Energy contribution	-44.92
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-3.94
Structure conservation index	1.00
SVM decision value	2.16
SVM RNA-class probability	0.989399
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14762139 120 + 20766785
UCCAAAUUGUCAGUUGGCCAGUUGGCUCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA
............(..((((.((((....)))).(..((.(((((((((((((((((((((((.....))))))))))).......))).))))).......))))))..)))))..)... ( -44.52)
>DroSim_CAF1 2568 120 + 1
UCCAAAUUGUCAGUUGGCCAGUUGGCUCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA
............(..((((.((((....)))).(..((.(((((((((((((((((((((((.....))))))))))).......))).))))).......))))))..)))))..)... ( -44.52)
>DroYak_CAF1 3895 120 + 1
UCCAAAUUGUCAGUUGGCCAGUUGGCCCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA
.............(((((.....((((((......(((.(((((((((((((((((((((((.....))))))))))).......))).))))).......)))))))))))))))))). ( -46.92)
>consensus
UCCAAAUUGUCAGUUGGCCAGUUGGCUCCAACAUUGCAUGUCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA
.............(((((.....((((((......(((.(((((((((((((((((((((((.....))))))))))).......))).))))).......)))))))))))))))))). (-45.14 = -44.92 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	14,762,139 – 14,762,259
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-44.97
Consensus MFE	-44.27
Energy contribution	-44.27
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.50
Structure conservation index	0.98
SVM decision value	2.14
SVM RNA-class probability	0.988948
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14762139 120 - 20766785
UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGAGCCAACUGGCCAACUGACAAUUUGGA
(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....))))))).....((((((..(.(((....)))...)..)))..))).. ( -43.90)
>DroSim_CAF1 2568 120 - 1
UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGAGCCAACUGGCCAACUGACAAUUUGGA
(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....))))))).....((((((..(.(((....)))...)..)))..))).. ( -43.90)
>DroYak_CAF1 3895 120 - 1
UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGGGCCAACUGGCCAACUGACAAUUUGGA
(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....))))))).....((((((..(((((....))))..)..)))..))).. ( -47.10)
>consensus
UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGACAUGCAAUGUUGGAGCCAACUGGCCAACUGACAAUUUGGA
(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....))))))).....((((((..(.(((....)))...)..)))..))).. (-44.27 = -44.27 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	14,762,179 – 14,762,299
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.38
Mean single sequence MFE	-42.44
Consensus MFE	-39.04
Energy contribution	-39.04
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-4.10
Structure conservation index	0.92
SVM decision value	1.71
SVM RNA-class probability	0.973231
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14762179 120 + 20766785
UCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAAAAAAUAAAGGUUGUCCUGAAAGCAGGAUUGUUAAUAGAUA
..((((((...(((((((((((.....)))))))))))............(((.((((.......)))).))))))))).............((((((....))))))............ ( -41.90)
>DroSim_CAF1 2608 119 + 1
UCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA-AAAUAAAGGUUGUCCUGAAAGCGGGAUUGUUAAUAGAUA
..((((((...(((((((((((.....)))))))))))............(((.((((.......)))).))))))))).-...........((((((....))))))............ ( -41.20)
>DroYak_CAF1 3935 119 + 1
UCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA-AAAUGGAGGUUGUCCUCAAAGCCUGAUUGUUAAUAGAUA
...(((((((((((((((((((.....))))))))))).......))).))))).((((((((.((.((((((.(((...-.......))).)))).)).)).))))))))......... ( -44.21)
>consensus
UCUUGGCAUACGUGGGCCAUGAAAAAUUCAUGGCCCGCCUUCAAUGUACUGCCACAUAAUUAGACUGUGGGGCUGCCAAA_AAAUAAAGGUUGUCCUGAAAGCAGGAUUGUUAAUAGAUA
...(((((((((((((((((((.....))))))))))).......))).))))).((((((...((..(((((.(((...........))).)))))...))...))))))......... (-39.04 = -39.04 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	14,762,179 – 14,762,299
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.38
Mean single sequence MFE	-39.43
Consensus MFE	-36.10
Energy contribution	-36.10
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-4.03
Structure conservation index	0.92
SVM decision value	1.69
SVM RNA-class probability	0.972365
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14762179 120 - 20766785
UAUCUAUUAACAAUCCUGCUUUCAGGACAACCUUUAUUUUUUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGA
.............(((((....)))))............((((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....)))))))) ( -41.00)
>DroSim_CAF1 2608 119 - 1
UAUCUAUUAACAAUCCCGCUUUCAGGACAACCUUUAUUU-UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGA
.............(((........)))...........(-(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....)))))))) ( -37.30)
>DroYak_CAF1 3935 119 - 1
UAUCUAUUAACAAUCAGGCUUUGAGGACAACCUCCAUUU-UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGA
......................((((....))))....(-(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....)))))))) ( -40.00)
>consensus
UAUCUAUUAACAAUCCCGCUUUCAGGACAACCUUUAUUU_UUUGGCAGCCCCACAGUCUAAUUAUGUGGCAGUACAUUGAAGGCGGGCCAUGAAUUUUUCAUGGCCCACGUAUGCCAAGA
.......................(((....))).......(((((((((((((((.........)))))(((....)))..)))(((((((((.....))))))))).....))))))). (-36.10 = -36.10 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:08 2006