Locus 2690

Sequence ID	3R_DroMel_CAF1
Location	7,236,542 – 7,236,689
Length	147
Max. P	0.980941

overview

Window 7

Location	7,236,542 – 7,236,650
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	76.92
Mean single sequence MFE	-28.97
Consensus MFE	-23.31
Energy contribution	-23.28
Covariance contribution	-0.02
Combinations/Pair	1.18
Mean z-score	-2.42
Structure conservation index	0.80
SVM decision value	1.87
SVM RNA-class probability	0.980941
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7236542 108 + 27905053
-UAAGUCUGCUAUUCAUUUCUUAUGGG-UUUUAAUGUGCGAAGUCUGUUCCCCUGUUUGGCGUUCAAUUUUCGCCUGA-AAGGUUUUAAGACUUCGUAGAUCAAAUAUAAG
-...((((((.((((((.....)))))-)..........(((((((.....(((....((((.........))))...-.))).....))))))))))))).......... ( -28.20)
>DroSec_CAF1 686 109 + 1
-UCUGUCUAUUAUUCAUUUCUUAGGGU-UUUCAAUGUGCGAAGUCUGUUCCCCUGUUUGGCGUUCAAUUUUCGCCUAAAAAGGUUUUAAGACUUCGCAGAUGAAAUAUGAG
-..................((((....-(((((.(.((((((((((.....(((.(((((((.........)))).))).))).....)))))))))).))))))..)))) ( -31.80)
>DroSim_CAF1 693 108 + 1
-UCUGUCUGUUAUUCAUUUCGUAGGGU-UUUCAAUGUGCGAAGUCUGUUCCCCUGUUUGGCGUUCAAUUUUCGCCUGA-AAGGUUUUAAGACUUCGCAGAUCAAAUAUGAG
-.................(((((.(((-(.......((((((((((.....(((....((((.........))))...-.))).....))))))))))))))...))))). ( -30.71)
>DroEre_CAF1 691 108 + 1
UACAAUUUUUCAGUAAUUUCUUAAGGU-UUUCAAUAUGCGAAGUC-GUUCCCCUCAUUGGCGUUCAAUUUUCGCCUGU-AAGGUUUUAAGACUCCGCAGAACAAUUAUAAG
...................((((..((-((((....((((.((((-.....(((.((.((((.........)))).))-.)))......)))).))))))).)))..)))) ( -21.70)
>DroYak_CAF1 698 109 + 1
UUUAAUUUUUGAGUAAUUUCUUAGGUU-UUUUAAUGUGCGAAAUCUGUUCCCCUCGUUGGCGUUCAAUUUUCGCCUGU-AAGGUUUUAAGAUUUCGCAGAUCAAAUAUAAG
.......((((((......))))))..-.(((.((.((((((((((.....(((..(.((((.........)))).).-.))).....)))))))))).)).)))...... ( -28.00)
>DroPer_CAF1 1041 99 + 1
UAUAGU-----AGA----ACGUAUGUAUAUUU--UAUGCGAAGUCUGUUCCCCUCCGUGGCGUCCAGAGAUCGCCUUG-GAGGUUUAAGUACUUCGCAGAGCAACUGUAGC
((((((-----...----((....))......--..((((((((((.....((((((.((((((....)).)))).))-))))....)).)))))))).....)))))).. ( -33.40)
>consensus
_UCAGUCUGUUAGUCAUUUCUUAGGGU_UUUCAAUGUGCGAAGUCUGUUCCCCUCUUUGGCGUUCAAUUUUCGCCUGA_AAGGUUUUAAGACUUCGCAGAUCAAAUAUAAG
....................................((((((((((.....(((....((((.........)))).....))).....))))))))))............. (-23.31 = -23.28 +  -0.02)

alignment

secondary structure

dotplot

Window 8

Location	7,236,542 – 7,236,650
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	76.92
Mean single sequence MFE	-28.01
Consensus MFE	-22.78
Energy contribution	-23.62
Covariance contribution	0.84
Combinations/Pair	1.13
Mean z-score	-3.52
Structure conservation index	0.81
SVM decision value	1.76
SVM RNA-class probability	0.976104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7236542 108 - 27905053
CUUAUAUUUGAUCUACGAAGUCUUAAAACCUU-UCAGGCGAAAAUUGAACGCCAAACAGGGGAACAGACUUCGCACAUUAAAA-CCCAUAAGAAAUGAAUAGCAGACUUA-
(((((.((((((...((((((((.....(((.-...((((.........))))....))).....))))))))...)))))).-...)))))..................- ( -22.90)
>DroSec_CAF1 686 109 - 1
CUCAUAUUUCAUCUGCGAAGUCUUAAAACCUUUUUAGGCGAAAAUUGAACGCCAAACAGGGGAACAGACUUCGCACAUUGAAA-ACCCUAAGAAAUGAAUAAUAGACAGA-
......(((((..((((((((((.....(((.(((.((((.........))))))).))).....))))))))))...)))))-..........................- ( -29.40)
>DroSim_CAF1 693 108 - 1
CUCAUAUUUGAUCUGCGAAGUCUUAAAACCUU-UCAGGCGAAAAUUGAACGCCAAACAGGGGAACAGACUUCGCACAUUGAAA-ACCCUACGAAAUGAAUAACAGACAGA-
......((..((.((((((((((.....(((.-...((((.........))))....))).....)))))))))).))..)).-..........................- ( -27.90)
>DroEre_CAF1 691 108 - 1
CUUAUAAUUGUUCUGCGGAGUCUUAAAACCUU-ACAGGCGAAAAUUGAACGCCAAUGAGGGGAAC-GACUUCGCAUAUUGAAA-ACCUUAAGAAAUUACUGAAAAAUUGUA
..(((((((.((((((((((((......((((-(..((((.........))))..))))).....-)))))))))........-....(((....)))..))).))))))) ( -29.70)
>DroYak_CAF1 698 109 - 1
CUUAUAUUUGAUCUGCGAAAUCUUAAAACCUU-ACAGGCGAAAAUUGAACGCCAACGAGGGGAACAGAUUUCGCACAUUAAAA-AACCUAAGAAAUUACUCAAAAAUUAAA
......((((((.((((((((((.....((((-...((((.........))))...)))).....)))))))))).)))))).-........................... ( -27.50)
>DroPer_CAF1 1041 99 - 1
GCUACAGUUGCUCUGCGAAGUACUUAAACCUC-CAAGGCGAUCUCUGGACGCCACGGAGGGGAACAGACUUCGCAUA--AAAUAUACAUACGU----UCU-----ACUAUA
((.......))..((((((((.......((((-(..((((.((....))))))..))))).......))))))))..--..............----...-----...... ( -30.64)
>consensus
CUUAUAUUUGAUCUGCGAAGUCUUAAAACCUU_UCAGGCGAAAAUUGAACGCCAAACAGGGGAACAGACUUCGCACAUUAAAA_ACCCUAAGAAAUGAAUAAAAGACUGA_
.......(((((.((((((((((.....((((....((((.........))))....))))....)))))))))).))))).............................. (-22.78 = -23.62 +   0.84)

alignment

secondary structure

dotplot

Window 9

Location	7,236,574 – 7,236,689
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.54
Mean single sequence MFE	-32.14
Consensus MFE	-25.15
Energy contribution	-24.65
Covariance contribution	-0.50
Combinations/Pair	1.20
Mean z-score	-1.72
Structure conservation index	0.78
SVM decision value	0.58
SVM RNA-class probability	0.788893
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7236574 115 + 27905053
UGUGCGAAGUCUGUUCCCCUGUUUGGCGUUCAAUUUUCGCCUGA-AAGGUUUUAAGACUUCGUAGAUCAAAUAUA---AGCAA-UCAUUCACCCGCAUCCAAGUGAAGCUCAAUUGGUUC
..((((((((((.....(((....((((.........))))...-.))).....))))))))))((((((.....---(((..-...(((((..........))))))))...)))))). ( -30.30)
>DroSec_CAF1 718 116 + 1
UGUGCGAAGUCUGUUCCCCUGUUUGGCGUUCAAUUUUCGCCUAAAAAGGUUUUAAGACUUCGCAGAUGAAAUAUG---AGCAA-UCAUUCACCCGCAUCCAAGUGAAGCUCAAUUGGUUC
..((((((((((.....(((.(((((((.........)))).))).))).....)))))))))).........((---(((..-...(((((..........))))))))))........ ( -34.60)
>DroEre_CAF1 724 114 + 1
UAUGCGAAGUC-GUUCCCCUCAUUGGCGUUCAAUUUUCGCCUGU-AAGGUUUUAAGACUCCGCAGAACAAUUAUA---AGCAA-UCAUUCACCCGCGUCCAAGUGAAGCUCAAUUGGUUC
..((((.((((-.....(((.((.((((.........)))).))-.)))......)))).))))((((.......---(((..-...(((((..........))))))))......)))) ( -26.22)
>DroWil_CAF1 1264 118 + 1
UGUGCGAAACCUGUUCCCCUUGCUGGCGUGCAGUGAUAGCCUUC-AAGGUUUUAAGGUUUCGCAAAUCAAAUGUACAGAGCAA-AAAUUCACCCGCCUCCAAGUGAAGCACUAUUGGUCA
..((((((((((.....(((((..(((...........)))..)-)))).....)))))))))).............((.(((-...(((((..........)))))......))).)). ( -34.70)
>DroYak_CAF1 731 115 + 1
UGUGCGAAAUCUGUUCCCCUCGUUGGCGUUCAAUUUUCGCCUGU-AAGGUUUUAAGAUUUCGCAGAUCAAAUAUA---AGCAA-UCAUUCACCCGCGUCCAAGUGAAGCACAAUUGGUUC
..((((((((((.....(((..(.((((.........)))).).-.))).....))))))))))..........(---(.(((-(..(((((..........))))).....)))).)). ( -28.60)
>DroMoj_CAF1 74633 114 + 1
-AUGCGACAUUUGUUCCCCUUGCUGGCGUGCAGCUGUAGCCAGA-AAGGUUUCAAGAUGUCGCAGAGCAAACA-G---AGCAACUGUUUCACCCGCAUCCAACUGAAGUACUAUUGGGUU
-.((((((((((.....((((.(((((.(((....)))))))).-)))).....))))))))))..(((((((-(---.....)))))).....))((((((..(.....)..)))))). ( -38.40)
>consensus
UGUGCGAAAUCUGUUCCCCUCGUUGGCGUUCAAUUUUCGCCUGA_AAGGUUUUAAGACUUCGCAGAUCAAAUAUA___AGCAA_UCAUUCACCCGCAUCCAAGUGAAGCACAAUUGGUUC
..((((((((((.....(((....((((.........)))).....))).....))))))))))................(((....(((((..........)))))......))).... (-25.15 = -24.65 +  -0.50)

alignment

secondary structure

dotplot

Window 0

Location	7,236,574 – 7,236,689
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.54
Mean single sequence MFE	-37.05
Consensus MFE	-28.44
Energy contribution	-28.25
Covariance contribution	-0.19
Combinations/Pair	1.15
Mean z-score	-2.70
Structure conservation index	0.77
SVM decision value	1.22
SVM RNA-class probability	0.931835
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7236574 115 - 27905053
GAACCAAUUGAGCUUCACUUGGAUGCGGGUGAAUGA-UUGCU---UAUAUUUGAUCUACGAAGUCUUAAAACCUU-UCAGGCGAAAAUUGAACGCCAAACAGGGGAACAGACUUCGCACA
....(((.(((((((((((((....))))))))...-..)))---))...))).....((((((((.....(((.-...((((.........))))....))).....)))))))).... ( -31.90)
>DroSec_CAF1 718 116 - 1
GAACCAAUUGAGCUUCACUUGGAUGCGGGUGAAUGA-UUGCU---CAUAUUUCAUCUGCGAAGUCUUAAAACCUUUUUAGGCGAAAAUUGAACGCCAAACAGGGGAACAGACUUCGCACA
(((.....(((((((((((((....))))))))...-..)))---))...)))...((((((((((.....(((.(((.((((.........))))))).))).....)))))))))).. ( -39.50)
>DroEre_CAF1 724 114 - 1
GAACCAAUUGAGCUUCACUUGGACGCGGGUGAAUGA-UUGCU---UAUAAUUGUUCUGCGGAGUCUUAAAACCUU-ACAGGCGAAAAUUGAACGCCAAUGAGGGGAAC-GACUUCGCAUA
((((....(((((((((((((....))))))))...-..)))---)).....))))(((((((((......((((-(..((((.........))))..))))).....-))))))))).. ( -39.80)
>DroWil_CAF1 1264 118 - 1
UGACCAAUAGUGCUUCACUUGGAGGCGGGUGAAUUU-UUGCUCUGUACAUUUGAUUUGCGAAACCUUAAAACCUU-GAAGGCUAUCACUGCACGCCAGCAAGGGGAACAGGUUUCGCACA
......((((.((((((((((....))))))))...-..)).))))..........((((((((((.....((((-(..(((...........)))..))))).....)))))))))).. ( -38.90)
>DroYak_CAF1 731 115 - 1
GAACCAAUUGUGCUUCACUUGGACGCGGGUGAAUGA-UUGCU---UAUAUUUGAUCUGCGAAAUCUUAAAACCUU-ACAGGCGAAAAUUGAACGCCAACGAGGGGAACAGAUUUCGCACA
....((((..(...(((((((....))))))))..)-)))..---...........((((((((((.....((((-...((((.........))))...)))).....)))))))))).. ( -33.10)
>DroMoj_CAF1 74633 114 - 1
AACCCAAUAGUACUUCAGUUGGAUGCGGGUGAAACAGUUGCU---C-UGUUUGCUCUGCGACAUCUUGAAACCUU-UCUGGCUACAGCUGCACGCCAGCAAGGGGAACAAAUGUCGCAU-
...(((((.(.....).)))))....((((.((((((.....---)-)))))))))((((((((.(((...((((-((((((...........))))).)))))...))))))))))).- ( -39.10)
>consensus
GAACCAAUUGAGCUUCACUUGGAUGCGGGUGAAUGA_UUGCU___UAUAUUUGAUCUGCGAAAUCUUAAAACCUU_UCAGGCGAAAAUUGAACGCCAACAAGGGGAACAGACUUCGCACA
.............((((((((....)))))))).......................((((((((((.....((((....((((.........))))....))))....)))))))))).. (-28.44 = -28.25 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:22 2006