Locus 4609

Sequence ID	3L_DroMel_CAF1
Location	13,143,259 – 13,143,488
Length	229
Max. P	0.999912

overview

Window 7

Location	13,143,259 – 13,143,375
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.41
Mean single sequence MFE	-29.33
Consensus MFE	-24.82
Energy contribution	-25.02
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.84
Structure conservation index	0.85
SVM decision value	3.04
SVM RNA-class probability	0.998216
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143259 116 - 23771897
UGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCGCAGGGAGGAGGA----AACCGAUAAAUCUGUGGCAGAGCA
..(((((((((((((((....))))))............................(((((.....((((......))))..........(..----..)))))).....).)))))))). ( -27.70)
>DroSec_CAF1 130955 116 - 1
UGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCGCUGGGAGGAGGA----AACCGAUAAAUCUGUGGCAGAGCA
..(((((((((((((((....))))))............................(((((.....((((......))))..........(..----..)))))).....).)))))))). ( -27.70)
>DroSim_CAF1 130856 116 - 1
UGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCGUUGGGAGGAGGA----AACCGAUAAAUCUGUGGCAGAGCA
..(((((((((((((((....))))))............................(((((..(((((((......))))))).......(..----..)))))).....).)))))))). ( -30.20)
>DroEre_CAF1 127810 116 - 1
UGGUUUUGCCCACAAACGAAAGUUUGUUAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAGAGGUCGCAGGGAGGAGGA----AACCGAUAAAUCUGCGGCAGAGCA
..((((((((.((((((....))))))((((((((...........................))))))))(((((.((((.........(..----..)))))...))))))))))))). ( -31.13)
>DroYak_CAF1 132296 120 - 1
UGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAGAGUUCGCUGGCAGGAGGAGGAGGACCGAUAAAUCUGCGGCAGAGCA
....((((((.((((((....)))))).(((((((.........)))))))..................))))))((((((((.((((....((....))......)))))))).)))). ( -29.90)
>consensus
UGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCGCUGGGAGGAGGA____AACCGAUAAAUCUGUGGCAGAGCA
..(((((((((((((((....)))))).(((((((...............((......((((..((.....))...)))).......))((.......)))))))))..).)))))))). (-24.82 = -25.02 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	13,143,295 – 13,143,415
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-24.60
Consensus MFE	-23.94
Energy contribution	-24.14
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.97
SVM decision value	2.30
SVM RNA-class probability	0.992043
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143295 120 + 23771897
CGAACUAUGCCAUUCAUUUUCGAUAUUUGAUUUAUUUUAAUUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCUACCUU
((((..(((.....))).))))......((((((((.........))))))))((((((....))))))(((((((......)))((((((.........)))))))))).......... ( -25.10)
>DroSec_CAF1 130991 120 + 1
CGAACUAUGCCAUUCAUUUUCGAUAUUUGAUUUAUUUUAAUUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCUAAGCUAUGGCCACGCCCUCGCCACCUU
((((..(((.....))).))))......((((((((.........))))))))((((((....))))))(((((((......)))((((((.........)))))))))).......... ( -25.10)
>DroSim_CAF1 130892 120 + 1
CGAACUAUGCCAUUCAUUUUCGAUAUUUGAUUUAUUUUAAUUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUU
((((..(((.....))).))))......((((((((.........))))))))((((((....))))))(((((((......)))((((((.........)))))))))).......... ( -25.10)
>DroEre_CAF1 127846 120 + 1
CGACCUCUGCCAUUCAUUUUCGAUAUUUGAUUUAUUUUAAUUUGUAAUAAAUAACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUU
(((....((((..................(((((((.........))))))).((((((....)))))).))))...........((((((.........))))))....)))....... ( -23.20)
>DroYak_CAF1 132336 120 + 1
CGAACUCUGCCAUUCAUUUUCGAUAUUUGAUUUAUUUUAAUUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUU
(((....((((.................((((((((.........))))))))((((((....)))))).))))...........((((((.........))))))....)))....... ( -24.50)
>consensus
CGAACUAUGCCAUUCAUUUUCGAUAUUUGAUUUAUUUUAAUUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUU
(((....((((.................((((((((.........))))))))((((((....)))))).))))...........((((((.........))))))....)))....... (-23.94 = -24.14 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	13,143,295 – 13,143,415
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-31.88
Consensus MFE	-30.94
Energy contribution	-31.18
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.65
Structure conservation index	0.97
SVM decision value	4.09
SVM RNA-class probability	0.999790
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143295 120 - 23771897
AAGGUAGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCG
..((((..(((((((..((((((..((((.....))))))))))..)))))((((((....)))))).......................))...))))......((((......)))). ( -32.60)
>DroSec_CAF1 130991 120 - 1
AAGGUGGCGAGGGCGUGGCCAUAGCUUAGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCG
..((((..((((((((((((.........))))))(((......)))))))((((((....)))))).......................))...))))......((((......)))). ( -30.80)
>DroSim_CAF1 130892 120 - 1
AAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCG
..((((..(((((((..((((((..((((.....))))))))))..)))))((((((....)))))).......................))...))))......((((......)))). ( -32.30)
>DroEre_CAF1 127846 120 - 1
AAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUUAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAGAGGUCG
..((((..(((((((..((((((..((((.....))))))))))..)))))((((((....)))))).......................))...))))..........(((....))). ( -31.40)
>DroYak_CAF1 132336 120 - 1
AAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAGAGUUCG
..((((..(((((((..((((((..((((.....))))))))))..)))))((((((....)))))).......................))...))))......((((......)))). ( -32.30)
>consensus
AAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAAUUAAAAUAAAUCAAAUAUCGAAAAUGAAUGGCAUAGUUCG
..((((..(((((((..((((((..((((.....))))))))))..)))))((((((....)))))).......................))...))))......((((......)))). (-30.94 = -31.18 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	13,143,335 – 13,143,455
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-35.34
Consensus MFE	-33.84
Energy contribution	-33.68
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.06
Structure conservation index	0.96
SVM decision value	2.89
SVM RNA-class probability	0.997586
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143335 120 + 23771897
UUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCUACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCGGGCGGC
(((((((....)))))))........(((((......)))))...((((((.........))))))((((((((((((.....)))((((..((((....))))..)))))))))).))) ( -37.90)
>DroSec_CAF1 131031 120 + 1
UUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCUAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCUGGCGGC
.............((((((....))))))(((((((......)))((((((.........))))))))))((((((((.....))(((((..((((....))))..)))))..)))))). ( -34.50)
>DroSim_CAF1 130932 120 + 1
UUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCUGGCGGC
.............((((((....))))))(((((((......)))((((((.........))))))))))((((((((.....))(((((..((((....))))..)))))..)))))). ( -34.50)
>DroEre_CAF1 127886 120 + 1
UUUGUAAUAAAUAACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCGGGCGGC
........(((((((((((....))))))((......)).)))))((((((.........))))))((((((((.(((.....)))((((..((((....))))..)))).))))).))) ( -35.50)
>DroYak_CAF1 132376 120 + 1
UUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGUAGGCGGC
.............((((((....))))))(((((((......)))((((((.........))))))))))((((((((.....)))((((..((((....))))..))))....))))). ( -34.30)
>consensus
UUUGUAAUAAAUUACAAACUUUCGUUUGUGGGCAAAACCAUAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCGGGCGGC
.............((((((....))))))(((((((......)))((((((.........))))))))))((((((((.....)))((((..((((....))))..))))....))))). (-33.84 = -33.68 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	13,143,335 – 13,143,455
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-41.28
Consensus MFE	-39.88
Energy contribution	-40.48
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-3.82
Structure conservation index	0.97
SVM decision value	4.51
SVM RNA-class probability	0.999912
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143335 120 - 23771897
GCCGCCCGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUAGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAA
((..((.(((.............)))..(((....)))....))..))..(((((..((((((..((((.....))))))))))..)))))((((((....))))))............. ( -37.62)
>DroSec_CAF1 131031 120 - 1
GCCGCCAGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUAGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAA
((((((.(((.............)))..(((....)))....))))))..((((((((((.........))))))(((......)))))))((((((....))))))............. ( -42.22)
>DroSim_CAF1 130932 120 - 1
GCCGCCAGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAA
((((((.(((.............)))..(((....)))....))))))..(((((..((((((..((((.....))))))))))..)))))((((((....))))))............. ( -43.72)
>DroEre_CAF1 127886 120 - 1
GCCGCCCGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUUAUUUAUUACAAA
((((((.(((.............)))..(((....)))....))))))..(((((..((((((..((((.....))))))))))..)))))((((((....))))))............. ( -42.32)
>DroYak_CAF1 132376 120 - 1
GCCGCCUACUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAA
(((((((..((((((..............))))))......)))))))..(((((..((((((..((((.....))))))))))..)))))((((((....))))))............. ( -40.54)
>consensus
GCCGCCAGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUAUGGUUUUGCCCACAAACGAAAGUUUGUAAUUUAUUACAAA
((((((.(((.............)))..(((....)))....))))))..(((((..((((((..((((.....))))))))))..)))))((((((....))))))............. (-39.88 = -40.48 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	13,143,375 – 13,143,488
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.30
Mean single sequence MFE	-34.50
Consensus MFE	-29.01
Energy contribution	-29.21
Covariance contribution	0.20
Combinations/Pair	1.10
Mean z-score	-1.32
Structure conservation index	0.84
SVM decision value	0.09
SVM RNA-class probability	0.578762
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143375 113 + 23771897
UAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCUACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCGGGCGGCAAAAAGCGAAAGAAAAGUGAGAGUCU-------CUCGGCA
.....((((((.........))))))((((((((((((.....)))((((..((((....))))..)))))))))).)))......(....)....(((((.....-------))).)). ( -35.40)
>DroSec_CAF1 131071 113 + 1
UAUUUGUGGCCCUAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCUGGCGGCAAAAAGCGAAAGAAAAGUGAGAGUCU-------AUCGGCA
.....((((((.........))))))(((((((((.((.....(.(((((..((((....))))..))))).).)).)))......(....)........)))...-------...))). ( -32.40)
>DroSim_CAF1 130972 113 + 1
UAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCUGGCGGCAAAAAGCGAAAGAAAAGUGAGAGUCU-------AUCGGCA
.....((((((.........))))))(((((((((.((.....(.(((((..((((....))))..))))).).)).)))......(....)........)))...-------...))). ( -32.40)
>DroEre_CAF1 127926 113 + 1
UAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCGGGCGGCAAAAGGCGAAAGAAAAGUGAGAGUCU-------CUCCGCA
.....((((((.........))))))((((((((.(((.....)))((((..((((....))))..)))).))))).)))......(....)....(((.(((...-------)))))). ( -35.00)
>DroYak_CAF1 132416 120 + 1
UAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGUAGGCGGCAAAAAGCGAACGAAAAGUGAGAGUCUCUCGUCUCUCGGCA
.....((((((.........))))))(((...(((.(((....(.(((((..((((....))))..))))).)))).)))..................(((((.(....).)))))))). ( -37.30)
>consensus
UAUUUGUGGCCCAAAGCUAUGGCCACGCCCUCGCCACCUUAAUGGUUUUCCAAUGCUAAUGUGUGAGAAAAGCGGGCGGCAAAAAGCGAAAGAAAAGUGAGAGUCU_______CUCGGCA
.....((((((.........))))))(((((((((.(((....(.(((((..((((....))))..))))).)))).)))......(....)........))).............))). (-29.01 = -29.21 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	13,143,375 – 13,143,488
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.30
Mean single sequence MFE	-36.54
Consensus MFE	-30.42
Energy contribution	-30.66
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.83
SVM decision value	1.89
SVM RNA-class probability	0.981531
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143375 113 - 23771897
UGCCGAG-------AGACUCUCACUUUUCUUUCGCUUUUUGCCGCCCGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUAGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUA
.((((((-------(((..........))))))....(((((..((.(((.............)))..(((....)))....))..))))))))((((((.........))))))..... ( -32.82)
>DroSec_CAF1 131071 113 - 1
UGCCGAU-------AGACUCUCACUUUUCUUUCGCUUUUUGCCGCCAGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUAGGGCCACAAAUA
.(((((.-------(((..........))).))....(((((((((.(((.............)))..(((....)))....))))))))))))((((((.........))))))..... ( -35.52)
>DroSim_CAF1 130972 113 - 1
UGCCGAU-------AGACUCUCACUUUUCUUUCGCUUUUUGCCGCCAGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUA
.(((((.-------(((..........))).))....(((((((((.(((.............)))..(((....)))....))))))))))))((((((.........))))))..... ( -35.52)
>DroEre_CAF1 127926 113 - 1
UGCGGAG-------AGACUCUCACUUUUCUUUCGCCUUUUGCCGCCCGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUA
....(((-------(((..........))))))((((((.((((((.(((.............)))..(((....)))....))))))))))))((((((.........))))))..... ( -38.82)
>DroYak_CAF1 132416 120 - 1
UGCCGAGAGACGAGAGACUCUCACUUUUCGUUCGCUUUUUGCCGCCUACUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUA
.((((((((.(....).)))))...............((((((((((..((((((..............))))))......)))))))))))))((((((.........))))))..... ( -40.04)
>consensus
UGCCGAG_______AGACUCUCACUUUUCUUUCGCUUUUUGCCGCCAGCUUUUCUCACACAUUAGCAUUGGAAAACCAUUAAGGUGGCGAGGGCGUGGCCAUAGCUUUGGGCCACAAAUA
.................................((((((.((((((.(((.............)))..(((....)))....))))))))))))((((((.........))))))..... (-30.42 = -30.66 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:24 2006