Locus 6681

Sequence ID	3L_DroMel_CAF1
Location	17,760,203 – 17,760,363
Length	160
Max. P	0.986064

overview

Window 2

Location	17,760,203 – 17,760,323
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.17
Mean single sequence MFE	-26.20
Consensus MFE	-20.18
Energy contribution	-21.86
Covariance contribution	1.68
Combinations/Pair	1.06
Mean z-score	-1.64
Structure conservation index	0.77
SVM decision value	0.29
SVM RNA-class probability	0.669204
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17760203 120 + 23771897
AUCUCUUUUCUCAGCACCCCCCGAUUGGCGAGAAUUGAGGUCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCACUGAGCUUAAGCUGAAUCCCCGAACACCCAAAAUGUUCAU
..........(((((...........((((((.((....)).)).))))...((((((((((...(((.....))).))).)))))))..)))))......(((((.......))))).. ( -27.60)
>DroSec_CAF1 7657 120 + 1
AUCUCGUUUCUCAGCACCUCCCGAGUGGCGAGUAUUGAGGUCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCACUGAGCUUAAACUGAAUCCCCGAACACCUAAAGUGUUCAU
..(((((..(((..........)))..)))))...((.(((.....))).))((((((((((...(((.....))).))).))))))).............((((((.....)))))).. ( -29.50)
>DroSim_CAF1 11734 120 + 1
AUCUCGUUUCUCAGCACCUCCCGAGUGGCGAGUAUUGAGGUCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCGCUGAGCUUAAACUGAAUCCCCGAACACCUAAAGUGUUCAU
.....((((((((((.((........)).((((.(((.(((.....))).))).)))).....................))))))...)))).........((((((.....)))))).. ( -29.40)
>DroEre_CAF1 7691 120 + 1
AUCUCUUUUCUCAGCACCUCCCAUUUUGCGCGUAUUUAGGUCCUCCGCUCCCAAGGUCAUGAAAAUCUCCUCCAGACUCACUGAGCUUAUGCUGAAACCCCGCACACCCAACGUGUUCAU
..........((((((......................((....))((((....((((..((........))..))))....))))...))))))......(.((((.....)))).).. ( -20.50)
>DroYak_CAF1 25253 120 + 1
AUCUCUUUUGUCAGCACCUCCCGUUUUGCGAGUAUCGGCGUCCUCCGCCCCAAAGCUCAUGAAAAUCUCCUCCAGGCUCACUGAGCUCAUGCUGAAACCCCGAACACCCAAAGUAUUCAU
..........((((((.......((((..((((...((((.....)))).....))))..))))..........(((((...)))))..))))))......(((.((.....)).))).. ( -24.00)
>consensus
AUCUCUUUUCUCAGCACCUCCCGAUUGGCGAGUAUUGAGGUCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCACUGAGCUUAAGCUGAAUCCCCGAACACCCAAAGUGUUCAU
..........(((((...........((((((.((....)).)).))))...((((((((((...(((.....))).))).)))))))..)))))......((((((.....)))))).. (-20.18 = -21.86 +   1.68)

alignment

secondary structure

dotplot

Window 3

Location	17,760,203 – 17,760,323
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.17
Mean single sequence MFE	-38.10
Consensus MFE	-28.96
Energy contribution	-29.32
Covariance contribution	0.36
Combinations/Pair	1.18
Mean z-score	-1.58
Structure conservation index	0.76
SVM decision value	0.12
SVM RNA-class probability	0.592210
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17760203 120 - 23771897
AUGAACAUUUUGGGUGUUCGGGGAUUCAGCUUAAGCUCAGUGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGACCUCAAUUCUCGCCAAUCGGGGGGUGCUGAGAAAAGAGAU
..((((((.....))))))((((.(((.(((((((((((..((((((.....))))))...)))))))..)))).)))..))))...((((.....((((......)))).....)))). ( -39.70)
>DroSec_CAF1 7657 120 - 1
AUGAACACUUUAGGUGUUCGGGGAUUCAGUUUAAGCUCAGUGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGACCUCAAUACUCGCCACUCGGGAGGUGCUGAGAAACGAGAU
..((((((.....))))))((((.(((.(((((((((((..((((((.....))))))...)))))))..)))).)))..))))....((((...(((((......)))))...)))).. ( -41.60)
>DroSim_CAF1 11734 120 - 1
AUGAACACUUUAGGUGUUCGGGGAUUCAGUUUAAGCUCAGCGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGACCUCAAUACUCGCCACUCGGGAGGUGCUGAGAAACGAGAU
..((((((.....))))))((((.(((.(((((((((((..((((((.....))))))...)))))))..)))).)))..))))....((((...(((((......)))))...)))).. ( -40.90)
>DroEre_CAF1 7691 120 - 1
AUGAACACGUUGGGUGUGCGGGGUUUCAGCAUAAGCUCAGUGAGUCUGGAGGAGAUUUUCAUGACCUUGGGAGCGGAGGACCUAAAUACGCGCAAAAUGGGAGGUGCUGAGAAAAGAGAU
.((.((((.....)))).))...(((((((((...((((.((..(((.((((............)))).)))(((.............))).))...))))..)))))))))........ ( -30.92)
>DroYak_CAF1 25253 120 - 1
AUGAAUACUUUGGGUGUUCGGGGUUUCAGCAUGAGCUCAGUGAGCCUGGAGGAGAUUUUCAUGAGCUUUGGGGCGGAGGACGCCGAUACUCGCAAAACGGGAGGUGCUGACAAAAGAGAU
.(((((((.....))))))).....((((((((((((((.((((((....)).....)))))))))))...((((.....))))....(((.(.....).)))))))))).......... ( -37.40)
>consensus
AUGAACACUUUGGGUGUUCGGGGAUUCAGCUUAAGCUCAGUGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGACCUCAAUACUCGCCAAUCGGGAGGUGCUGAGAAAAGAGAU
..((((((.....))))))(((..(((.((..(((((((..((((((.....))))))...)))))))....)).)))..))).....(((.....((((......)))).....))).. (-28.96 = -29.32 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	17,760,243 – 17,760,363
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-31.16
Consensus MFE	-25.48
Energy contribution	-25.84
Covariance contribution	0.36
Combinations/Pair	1.14
Mean z-score	-1.59
Structure conservation index	0.82
SVM decision value	0.59
SVM RNA-class probability	0.793122
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17760243 120 + 23771897
UCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCACUGAGCUUAAGCUGAAUCCCCGAACACCCAAAAUGUUCAUUUGGCUCUCCAAGUCACGGAAGAGCGAGGAAAAGUACUUU
(((((.((......))..........(((((((.((((....(((....(((..(((....(((((.......))))))))..))))))..))))..))))))).))))).......... ( -31.10)
>DroSec_CAF1 7697 120 + 1
UCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCACUGAGCUUAAACUGAAUCCCCGAACACCUAAAGUGUUCAUUUGGCUCUCCAAGUCACGGAAGAGCGAGGAAAAGGAAUUU
(((((.((......))..........(((((((.((((....(((((.((...(......)((((((.....)))))).)).)))))....))))..))))))).))))).......... ( -33.60)
>DroSim_CAF1 11774 120 + 1
UCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCGCUGAGCUUAAACUGAAUCCCCGAACACCUAAAGUGUUCAUUUGGCUCUCCAAGUCACGAAAGAGCGAGGAAAAGGAAUGU
(((((((((...((((((((((...(((.....))).))).))))))).............((((((.....))))))....)))...........(....).).))))).......... ( -29.90)
>DroEre_CAF1 7731 120 + 1
UCCUCCGCUCCCAAGGUCAUGAAAAUCUCCUCCAGACUCACUGAGCUUAUGCUGAAACCCCGCACACCCAACGUGUUCAUCUGGCGCUCCAAGUCGCGGAAGAGCGGGGAAUAGGAAUUG
...(((((((....((((..((........))..))))....))))...........((((((((((.....))))...(((..(((........)))..)))))))))....))).... ( -34.20)
>DroYak_CAF1 25293 120 + 1
UCCUCCGCCCCAAAGCUCAUGAAAAUCUCCUCCAGGCUCACUGAGCUCAUGCUGAAACCCCGAACACCCAAAGUAUUCAUUUGGCGCUCCAAGUCGCGGAAGAGCGAGGAAAAGGAAUUU
...(((((......))...........((((((((.....))).((((.............(((.((.....)).))).(((.((((.....).))).))))))))))))...))).... ( -27.00)
>consensus
UCCUCCGCCCCAAAGCUCAUGAAAAUCUCUUCCAGACUCACUGAGCUUAAGCUGAAUCCCCGAACACCCAAAGUGUUCAUUUGGCUCUCCAAGUCACGGAAGAGCGAGGAAAAGGAAUUU
(((((((((...((((((((((...(((.....))).))).))))))).............((((((.....))))))....)))...........(....).).))))).......... (-25.48 = -25.84 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	17,760,243 – 17,760,363
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.50
Mean single sequence MFE	-42.40
Consensus MFE	-36.86
Energy contribution	-36.90
Covariance contribution	0.04
Combinations/Pair	1.15
Mean z-score	-1.96
Structure conservation index	0.87
SVM decision value	2.03
SVM RNA-class probability	0.986064
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17760243 120 - 23771897
AAAGUACUUUUCCUCGCUCUUCCGUGACUUGGAGAGCCAAAUGAACAUUUUGGGUGUUCGGGGAUUCAGCUUAAGCUCAGUGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGA
..........((((((((((.(((.....)))))))).....((((((.....)))))))))))(((.(((((((((((..((((((.....))))))...)))))))..)))).))).. ( -42.00)
>DroSec_CAF1 7697 120 - 1
AAAUUCCUUUUCCUCGCUCUUCCGUGACUUGGAGAGCCAAAUGAACACUUUAGGUGUUCGGGGAUUCAGUUUAAGCUCAGUGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGA
....((((((((((((((((.(((.....)))))))).....((((((.....)))))))))))....(((((((((((..((((((.....))))))...)))))))..)))))))))) ( -44.80)
>DroSim_CAF1 11774 120 - 1
ACAUUCCUUUUCCUCGCUCUUUCGUGACUUGGAGAGCCAAAUGAACACUUUAGGUGUUCGGGGAUUCAGUUUAAGCUCAGCGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGA
....((((((((((((((((((........))))))).....((((((.....)))))))))))....(((((((((((..((((((.....))))))...)))))))..)))))))))) ( -41.50)
>DroEre_CAF1 7731 120 - 1
CAAUUCCUAUUCCCCGCUCUUCCGCGACUUGGAGCGCCAGAUGAACACGUUGGGUGUGCGGGGUUUCAGCAUAAGCUCAGUGAGUCUGGAGGAGAUUUUCAUGACCUUGGGAGCGGAGGA
..........((((((((((((((.(((((.(((((((.((((....)))).)))((((.........))))..))))...))))))))))))...(..((......))..))))).))) ( -42.30)
>DroYak_CAF1 25293 120 - 1
AAAUUCCUUUUCCUCGCUCUUCCGCGACUUGGAGCGCCAAAUGAAUACUUUGGGUGUUCGGGGUUUCAGCAUGAGCUCAGUGAGCCUGGAGGAGAUUUUCAUGAGCUUUGGGGCGGAGGA
....(((((..((((.((((((((((((((.(((((((.((........)).))))))).)))))...))....((((...))))..))))))).(((....)))....))))..))))) ( -41.40)
>consensus
AAAUUCCUUUUCCUCGCUCUUCCGUGACUUGGAGAGCCAAAUGAACACUUUGGGUGUUCGGGGAUUCAGCUUAAGCUCAGUGAGUCUGGAAGAGAUUUUCAUGAGCUUUGGGGCGGAGGA
..........((((((((((((((.....))))(((((...(((((((.....))))))).)).))).....(((((((..((((((.....))))))...))))))).))))))).))) (-36.86 = -36.90 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:28 2006