Locus 4326

Sequence ID 3L_DroMel_CAF1
Location 12,722,403 – 12,722,638
Length 235
Max. P 0.908420
window6696 window6697 window6698 window6699

overview

Window 6

Location 12,722,403 – 12,722,523
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.94
Mean single sequence MFE -30.94
Consensus MFE -20.15
Energy contribution -20.18
Covariance contribution 0.03
Combinations/Pair 1.40
Mean z-score -1.50
Structure conservation index 0.65
SVM decision value 0.10
SVM RNA-class probability 0.581800
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12722403 120 - 23771897
GUUUCGAUUAUGAACGGAAUCGCCGAGGUGCAGAAGGACAAUGAAAAGUCGGACAUGCUGCGAAAGAACAUCGAGAACAUCGAACUGGGCCUCAGCGAGGCCCAGGUGAUGAUGGCCCUG
.(((((((......(((.....)))...(((((...(((........))).......))))).......))))))).(((((..(((((((((...)))))))))....)))))...... ( -38.10)
>DroVir_CAF1 2876 120 - 1
GUUUCCAUAAUGAACGGUAUAUCAGAGGUGCAAAAAGAUAAUGAAAAAUCUGAUAUAUUACGAAAGAAUAUUGAAAACAUUGAACUUGGCUUGAGUGAAGCACAAGUCAUGAUGGCCCUA
....((((.((((..(((((((((((....((.........)).....))))))))))).(....)..................((((((((.....)))).)))))))).))))..... ( -25.60)
>DroGri_CAF1 3332 120 - 1
GUUUCCAUCAUAAACGGUAUAUCUGAGGUUCAGAAGGACAAUGAAAAAUCGGAUAUAUUGCGAAAGAAUAUUGAAAAUAUUGAGCUUGGCCUGAGUGAGGCCCAAGUGAUGAUGGCACUU
....(((((((...((((((((((((..((((.........))))...))))))))))))(....).................(((((((((.....))).)))))).)))))))..... ( -36.50)
>DroWil_CAF1 1565 120 - 1
AUUUCGAUUAUGAACGGCAUAGCUGAAGUUCAAAAGGACAAUGAGAAAUCGGAUAUGCUGAAAAAGAAUAUUGAAAAUAUUGAGCUUGGUCUGAGUGAAGCACAAGUUAUGAUGGCUCUA
.(((((((......(((((((.((...((((....))))...((....)))).))))))).........))))))).....(((((..((((((.(........).))).)))))))).. ( -24.86)
>DroMoj_CAF1 1715 120 - 1
GUUUCGAUUAUGAACGGAAUAUCCGAAGUUCAAAAAGAUAAUGAGAAAUCUGAUAUAUUACGAAAGAACAUAGAAAGCAUUGAACUUGGCUUGAGCGAGGCGCAGGUCAUGAUGGCCCUA
((((((.(((....(((.....)))((((((((...((((((.((....)).)).)))).(....).............))))))))....))).))))))...((((.....))))... ( -26.00)
>DroAna_CAF1 2995 120 - 1
GUCUCGAUUAUGAACGGCAUUUCUGAGGUGCAGAAGGACAACGAGAAGUCGGACAUGCUGCGGAAGAACAUUGAAAACAUCGAACUGGGUCUGAGCGAGGCCCAGGUGAUGAUGGCCCUC
((((((((......(((((((((((.....))))))(((........))).....)))))(....)...)))))...(((((..((((((((.....)))))))).)))))..))).... ( -34.60)
>consensus
GUUUCGAUUAUGAACGGAAUAUCUGAGGUGCAAAAGGACAAUGAAAAAUCGGAUAUACUGCGAAAGAACAUUGAAAACAUUGAACUUGGCCUGAGCGAGGCCCAAGUGAUGAUGGCCCUA
.((((.........((((((((((((......................))))))))))))(....)......)))).((((..(((((((((.....)))).)))))...))))...... (-20.15 = -20.18 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,722,443 – 12,722,563
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.78
Mean single sequence MFE -28.50
Consensus MFE -15.98
Energy contribution -14.48
Covariance contribution -1.50
Combinations/Pair 1.53
Mean z-score -2.35
Structure conservation index 0.56
SVM decision value 0.55
SVM RNA-class probability 0.777937
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12722443 120 + 23771897
AUGUUCUCGAUGUUCUUUCGCAGCAUGUCCGACUUUUCAUUGUCCUUCUGCACCUCGGCGAUUCCGUUCAUAAUCGAAACAUGCUCCACUCGCAAGGCUUCGAGGCCUUGAAGGACUGUU
...........((((((..(.(((((((..(((........)))..............(((((........)))))..))))))).).....(((((((....))))))))))))).... ( -28.60)
>DroVir_CAF1 2916 120 + 1
AUGUUUUCAAUAUUCUUUCGUAAUAUAUCAGAUUUUUCAUUAUCUUUUUGCACCUCUGAUAUACCGUUCAUUAUGGAAACAUGUUCGACCCGCAAGGCUUCCAAGCCUUGCAAAACAGUU
.((((((................(((((((((.....((.........))....)))))))))..(((...((((....))))...)))..((((((((....))))))))))))))... ( -29.70)
>DroGri_CAF1 3372 120 + 1
AUAUUUUCAAUAUUCUUUCGCAAUAUAUCCGAUUUUUCAUUGUCCUUCUGAACCUCAGAUAUACCGUUUAUGAUGGAAACAUGUUCAACGCGCAAAGCUUCCAAGCCCUGCAACACAGUU
...................((..((((((.((...((((.........))))..)).))))))..(((.(..(((....)))..).)))))(((..(((....)))..)))......... ( -18.20)
>DroWil_CAF1 1605 120 + 1
AUAUUUUCAAUAUUCUUUUUCAGCAUAUCCGAUUUCUCAUUGUCCUUUUGAACUUCAGCUAUGCCGUUCAUAAUCGAAAUAUGUUCGACACGCAGGGCCUCCAGGCCCUGCAGAACUGUU
......................(((((.(.((....(((.........)))...)).).))))).((((....(((((.....)))))...((((((((....)))))))).)))).... ( -32.00)
>DroMoj_CAF1 1755 120 + 1
AUGCUUUCUAUGUUCUUUCGUAAUAUAUCAGAUUUCUCAUUAUCUUUUUGAACUUCGGAUAUUCCGUUCAUAAUCGAAACAUGUUCAACGCGCAAGGCUUCCAAGCCUUGCAAAACAGUU
..((....((((......)))).......((((........))))..((((((..(((.....)))(((......)))....)))))).))((((((((....))))))))......... ( -25.00)
>DroAna_CAF1 3035 120 + 1
AUGUUUUCAAUGUUCUUCCGCAGCAUGUCCGACUUCUCGUUGUCCUUCUGCACCUCAGAAAUGCCGUUCAUAAUCGAGACAUGCUCCACUCGCAGGGCUUCCAGGCCCUGGAGCACUGUC
.......((.(((((....(.(((((((((((.........((..(((((.....)))))..)).........))).)))))))).).....(((((((....)))))))))))).)).. ( -37.47)
>consensus
AUGUUUUCAAUAUUCUUUCGCAACAUAUCCGAUUUCUCAUUGUCCUUCUGAACCUCAGAUAUACCGUUCAUAAUCGAAACAUGUUCAACGCGCAAGGCUUCCAAGCCCUGCAAAACAGUU
.....................(((((....(((........)))......................(((......)))..)))))......((((((((....))))))))......... (-15.98 = -14.48 +  -1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,722,443 – 12,722,563
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -34.29
Consensus MFE -21.71
Energy contribution -21.88
Covariance contribution 0.17
Combinations/Pair 1.39
Mean z-score -2.58
Structure conservation index 0.63
SVM decision value 1.06
SVM RNA-class probability 0.908420
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12722443 120 - 23771897
AACAGUCCUUCAAGGCCUCGAAGCCUUGCGAGUGGAGCAUGUUUCGAUUAUGAACGGAAUCGCCGAGGUGCAGAAGGACAAUGAAAAGUCGGACAUGCUGCGAAAGAACAUCGAGAACAU
....(((((((...((((((((((..(((.......))).)))))((((........))))...)))))...))))))).........(((...(((...(....)..))))))...... ( -32.90)
>DroVir_CAF1 2916 120 - 1
AACUGUUUUGCAAGGCUUGGAAGCCUUGCGGGUCGAACAUGUUUCCAUAAUGAACGGUAUAUCAGAGGUGCAAAAAGAUAAUGAAAAAUCUGAUAUAUUACGAAAGAAUAUUGAAAACAU
...((.(((((((((((....))))))))))).))...((((((.((........(((((((((((....((.........)).....))))))))))).(....).....)).)))))) ( -30.80)
>DroGri_CAF1 3372 120 - 1
AACUGUGUUGCAGGGCUUGGAAGCUUUGCGCGUUGAACAUGUUUCCAUCAUAAACGGUAUAUCUGAGGUUCAGAAGGACAAUGAAAAAUCGGAUAUAUUGCGAAAGAAUAUUGAAAAUAU
..(..(((.((((((((....)))))))))))..)...((((((.((.......((((((((((((..((((.........))))...))))))))))))(....).....)).)))))) ( -30.00)
>DroWil_CAF1 1605 120 - 1
AACAGUUCUGCAGGGCCUGGAGGCCCUGCGUGUCGAACAUAUUUCGAUUAUGAACGGCAUAGCUGAAGUUCAAAAGGACAAUGAGAAAUCGGAUAUGCUGAAAAAGAAUAUUGAAAAUAU
....(((((((((((((....))))))))..((((((.....))))))......(((((((.((...((((....))))...((....)))).)))))))....)))))........... ( -39.70)
>DroMoj_CAF1 1755 120 - 1
AACUGUUUUGCAAGGCUUGGAAGCCUUGCGCGUUGAACAUGUUUCGAUUAUGAACGGAAUAUCCGAAGUUCAAAAAGAUAAUGAGAAAUCUGAUAUAUUACGAAAGAACAUAGAAAGCAU
...((((((((((((((....))))))))...((((((((((((((........)))))))).....))))))...((((((.((....)).)).)))).(....).......)))))). ( -28.30)
>DroAna_CAF1 3035 120 - 1
GACAGUGCUCCAGGGCCUGGAAGCCCUGCGAGUGGAGCAUGUCUCGAUUAUGAACGGCAUUUCUGAGGUGCAGAAGGACAACGAGAAGUCGGACAUGCUGCGGAAGAACAUUGAAAACAU
..((((((((((((((......)))))).)))((.((((((((.(((((.......(..((((((.....))))))..).......))))))))))))).))......)))))....... ( -44.04)
>consensus
AACAGUUCUGCAAGGCCUGGAAGCCUUGCGAGUCGAACAUGUUUCGAUUAUGAACGGAAUAUCUGAGGUGCAAAAGGACAAUGAAAAAUCGGAUAUACUGCGAAAGAACAUUGAAAACAU
........((((((((......))))))))........(((((((.........((((((((((((......................))))))))))))(....)......))).)))) (-21.71 = -21.88 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,722,523 – 12,722,638
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.64
Mean single sequence MFE -28.87
Consensus MFE -17.45
Energy contribution -17.37
Covariance contribution -0.08
Combinations/Pair 1.19
Mean z-score -2.19
Structure conservation index 0.60
SVM decision value 0.10
SVM RNA-class probability 0.581355
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12722523 115 - 23771897
-----GUUUUGUAGACAGAAAAUUGAGAAAAUCGGCAAAAUGACGCAAAUGUCGCAGGACGAAAUCAUAACCAAUACGAAAACAGUCCUUCAAGGCCUCGAAGCCUUGCGAGUGGAGCAU
-----(((((((.((((......(((.....)))((........))...)))))))))))......................((.((...((((((......)))))).)).))...... ( -23.40)
>DroVir_CAF1 2996 112 - 1
--------CUGCAGACAGAAAAUUGAGCAAAUCGGCAGAAUGACGCAGAUGUCGCAAGACGAAAUUAUAAGCAAUACAAAAACUGUUUUGCAAGGCUUGGAAGCCUUGCGGGUCGAACAU
--------.....(((..........((..(((.((........)).)))(((....)))..........))...............((((((((((....)))))))))))))...... ( -29.40)
>DroPse_CAF1 5165 114 - 1
------UGUUCCAGACAGAAAAUUGAAAAAAUCGGCAAAAUGACUCAAAUGUCACAGGACGAAAUAAUAACCAAUACAAAAACAGUAUUGCAAGGCCUAGAGGCUUUGCGAGUGGAGCAU
------(((((((..................(((.(....((((......))))...).))).........................((((((((((....)))))))))).))))))). ( -30.20)
>DroGri_CAF1 3452 109 - 1
-----------CAGACAGAAAAUAGAGCAAAUCGGCAAAAUGACGCAAAUGUCGCAAGACGAAAUAAUAAGCAAUACAAAAACUGUGUUGCAGGGCUUGGAAGCUUUGCGCGUUGAACAU
-----------...............((......)).....(((((...((((....)))).........((((((((.....))))))))((((((....))))))..)))))...... ( -28.00)
>DroMoj_CAF1 1835 120 - 1
UUCUUUUUCUGCAGACAGAAAAUUGAGCAAAUCGGCAAAAUGACGCAGAUGUCGCAAGACGAAAUUAUAAGCAAUACAAAAACUGUUUUGCAAGGCUUGGAAGCCUUGCGCGUUGAACAU
.((.(((((((....)))))))..))((......)).....(((((...((((....))))............................((((((((....)))))))))))))...... ( -34.00)
>DroAna_CAF1 3115 115 - 1
-----UAUUUGCAGACAGAAAAUCGAAAAAAUCGGAAAAAUGACGCAAAUGUCGCAGGACGAAAUAAUAUCCAAUACGAAGACAGUGCUCCAGGGCCUGGAAGCCCUGCGAGUGGAGCAU
-----.((((((.(.((.....((((.....)))).....)).)))))))(((....))).........(((...((.......))((((((((((......)))))).))))))).... ( -28.20)
>consensus
______UUUUGCAGACAGAAAAUUGAGAAAAUCGGCAAAAUGACGCAAAUGUCGCAAGACGAAAUAAUAACCAAUACAAAAACAGUGUUGCAAGGCCUGGAAGCCUUGCGAGUGGAACAU
...............................((.((.............((((....))))...........................((((((((......)))))))).)).)).... (-17.45 = -17.37 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:43 2006