Locus 4516

Sequence ID	2R_DroMel_CAF1
Location	14,812,562 – 14,812,716
Length	154
Max. P	0.998697

overview

Window 5

Location	14,812,562 – 14,812,679
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	83.29
Mean single sequence MFE	-24.63
Consensus MFE	-25.53
Energy contribution	-24.87
Covariance contribution	-0.66
Combinations/Pair	1.11
Mean z-score	-1.54
Structure conservation index	1.04
SVM decision value	3.19
SVM RNA-class probability	0.998697
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812562 117 + 20766785
GCUUCUUGUUGUUGUUGC---CUUUUUUCGAAUAUUUCAUUCAAUUUUCUUAGCUUCGUAGUGUUGGUGUGAAAAACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAG
...(((((.....(((((---(((((((.((((.....))))..................((((.(((((.....))))).))))................))))))).)))))))))). ( -25.60)
>DroEre_CAF1 7257 116 + 1
GCU--UUCUUGUUGUUGCUGCGCUUUUUCGAAUAUUUCAUUCAAUUUUCUUAGCUUCGCAGUGUUGGUGUGA--AACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAG
...--.(((((.....(((((.((((((.((((.....))))..................((((.((((...--..)))).)))).................)))))).)))))))))). ( -26.20)
>DroYak_CAF1 8536 97 + 1
---------------------UAUUUUUCGAAUAUUUCAUUCAAUUUUCUUGGCUUUGUAGUGUUGGUGUGA--AACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAG
---------------------........((((.....)))).....((((((((.....((((.((((...--..)))).)))).....(((((....))))).......)))))))). ( -22.10)
>consensus
GCU__UU_UUGUUGUUGC___CAUUUUUCGAAUAUUUCAUUCAAUUUUCUUAGCUUCGUAGUGUUGGUGUGA__AACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAG
.............................((((.....)))).....(((((((..(((.((((.(((((.....))))).)))).....(((((....))))).....)))))))))). (-25.53 = -24.87 +  -0.66)

alignment

secondary structure

dotplot

Window 6

Location	14,812,562 – 14,812,679
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.29
Mean single sequence MFE	-21.50
Consensus MFE	-20.33
Energy contribution	-20.67
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.95
SVM decision value	1.86
SVM RNA-class probability	0.980214
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812562 117 - 20766785
CUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUUUUUCACACCAACACUACGAAGCUAAGAAAAUUGAAUGAAAUAUUCGAAAAAAG---GCAACAACAACAAGAAGC
.(((((((........(((((....))))).....((((.(((((.....))))).))))......)))))))...(((((((...))))))).....(---....)............. ( -23.00)
>DroEre_CAF1 7257 116 - 1
CUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUU--UCACACCAACACUGCGAAGCUAAGAAAAUUGAAUGAAAUAUUCGAAAAAGCGCAGCAACAACAAGAA--AGC
.((((((((((.....(((((....))))).....((((.((((..--...)))).)))).)))..)))))))...(((((((...)))))))......................--... ( -24.60)
>DroYak_CAF1 8536 97 - 1
CUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUU--UCACACCAACACUACAAAGCCAAGAAAAUUGAAUGAAAUAUUCGAAAAAUA---------------------
.((((.((........(((((....))))).....((((.((((..--...)))).))))......)).))))...(((((((...)))))))......--------------------- ( -16.90)
>consensus
CUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUU__UCACACCAACACUACGAAGCUAAGAAAAUUGAAUGAAAUAUUCGAAAAAAA___GCAACAACAA_AA__AGC
.(((((((........(((((....))))).....((((.(((((.....))))).))))......)))))))...(((((((...)))))))........................... (-20.33 = -20.67 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	14,812,599 – 14,812,716
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.28
Mean single sequence MFE	-27.10
Consensus MFE	-25.22
Energy contribution	-25.14
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.79
Structure conservation index	0.93
SVM decision value	2.54
SVM RNA-class probability	0.995101
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812599 117 + 20766785
UCAAUUUUCUUAGCUUCGUAGUGUUGGUGUGAAAAACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAGAAAGAUCCAAAUUUCUG---UUACAAAGUGGUAUUGGUGU
....(((((((((((.(...((((.(((((.....))))).)))).....(((((....))))).....).)))))))))))....((((((..((.---......))..)).))))... ( -29.80)
>DroSec_CAF1 14424 120 + 1
UCAAUUUUCUUAGCUUCGUAGUAUUGGUUUGAAAAACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAGAAAGAUCCAAAUUUCUGUUGUUACAAAGUGGUAUUGGUGU
....(((((((((((.(...((...(((((....)).)))...)).....(((((....))))).....).)))))))))))....((((....(..((.......))..)..))))... ( -19.30)
>DroSim_CAF1 8684 120 + 1
UCAAUUUUCUUAGCUUCGUAGUGUUGGUGUGAAAAACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAGAAAGAUCCAAAUUUCUGUUGUUACAAAGUGGUAUUGGUGU
....(((((((((((.(...((((.(((((.....))))).)))).....(((((....))))).....).)))))))))))....((((....(..((.......))..)..))))... ( -30.00)
>DroEre_CAF1 7295 115 + 1
UCAAUUUUCUUAGCUUCGCAGUGUUGGUGUGA--AACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAGAAAGAUACAAAUUUCUU---UUACAAAGUGGUAUUAGUGU
....((((((((((..(((.((((.((((...--..)))).)))).....(((((....))))).....))))))))))))).(((((...(((...---....)))...)))))..... ( -29.00)
>DroYak_CAF1 8555 115 + 1
UCAAUUUUCUUGGCUUUGUAGUGUUGGUGUGA--AACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAGAAAGAUCGAAAUUUCUU---UUACAAAGUGGUAUUGGUGU
(((((.....(.((((((((((((.((((...--..)))).)))).................(((((((.(((((.......)).)))...))))))---))))))))).).)))))... ( -27.40)
>consensus
UCAAUUUUCUUAGCUUCGUAGUGUUGGUGUGAAAAACACCCACACAAAAAUUUAUUUUUAUAAAAGAGAGCGGCUAAGAGAAAGAUCCAAAUUUCUG___UUACAAAGUGGUAUUGGUGU
....((((((((((..(((.((((.(((((.....))))).)))).....(((((....))))).....)))))))))))))(((........)))........................ (-25.22 = -25.14 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	14,812,599 – 14,812,716
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.28
Mean single sequence MFE	-21.50
Consensus MFE	-18.58
Energy contribution	-18.66
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.69
Structure conservation index	0.86
SVM decision value	1.39
SVM RNA-class probability	0.948894
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812599 117 - 20766785
ACACCAAUACCACUUUGUAA---CAGAAAUUUGGAUCUUUCUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUUUUUCACACCAACACUACGAAGCUAAGAAAAUUGA
....((((.(((..((....---....))..))).......(((((((........(((((....))))).....((((.(((((.....))))).))))......)))))))..)))). ( -23.00)
>DroSec_CAF1 14424 120 - 1
ACACCAAUACCACUUUGUAACAACAGAAAUUUGGAUCUUUCUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUUUUUCAAACCAAUACUACGAAGCUAAGAAAAUUGA
....((((.(((.(((((....)))))....))).......((((((((((((.....((((((((....)))))))).)))))...(((.............))))))))))..)))). ( -19.12)
>DroSim_CAF1 8684 120 - 1
ACACCAAUACCACUUUGUAACAACAGAAAUUUGGAUCUUUCUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUUUUUCACACCAACACUACGAAGCUAAGAAAAUUGA
....((((.(((.(((((....)))))....))).......(((((((........(((((....))))).....((((.(((((.....))))).))))......)))))))..)))). ( -24.10)
>DroEre_CAF1 7295 115 - 1
ACACUAAUACCACUUUGUAA---AAGAAAUUUGUAUCUUUCUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUU--UCACACCAACACUGCGAAGCUAAGAAAAUUGA
...................(---((((........))))).((((((((((.....(((((....))))).....((((.((((..--...)))).)))).)))..)))))))....... ( -23.00)
>DroYak_CAF1 8555 115 - 1
ACACCAAUACCACUUUGUAA---AAGAAAUUUCGAUCUUUCUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUU--UCACACCAACACUACAAAGCCAAGAAAAUUGA
....((((.....(((((((---((((.....((..((.......)).))...))))))))))).......(((((((((((((..--...))))..))).))))))........)))). ( -18.30)
>consensus
ACACCAAUACCACUUUGUAA___CAGAAAUUUGGAUCUUUCUCUUAGCCGCUCUCUUUUAUAAAAAUAAAUUUUUGUGUGGGUGUUUUUCACACCAACACUACGAAGCUAAGAAAAUUGA
....((((.................((((........))))(((((((........(((((....))))).....((((.(((((.....))))).))))......)))))))..)))). (-18.58 = -18.66 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:56 2006