Locus 2040

Sequence ID 2R_DroMel_CAF1
Location 7,686,031 – 7,686,172
Length 141
Max. P 0.966708
window3376 window3377 window3378 window3379

overview

Window 6

Location 7,686,031 – 7,686,134
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -20.86
Consensus MFE -16.46
Energy contribution -16.46
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.19
Structure conservation index 0.79
SVM decision value 0.12
SVM RNA-class probability 0.594021
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7686031 103 + 20766785
UUCAUUCGAUC-------U-UAUA---AUCGUCGCCUUUCGAAUGUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCGGU----CU-U-AACUUGACUGUCGACGGAUAGCUCU
..(((((((..-------.-....---...........)))))))..........(((((...(((.(((((((............----..-.-......)))))))..)))..))))) ( -21.97)
>DroVir_CAF1 6101 100 + 1
U-------GUA-----UAUGUAUAAA-GUCGUCGCUUUUCGAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCUGU----A--U-AGCUUGACUGUCGACGGAUAGCUCU
.-------...-----..(((((((.-.(((........)))...)))))))...(((((...(((.(((((((..(((.....))----)--.-......)))))))..)))..))))) ( -25.50)
>DroGri_CAF1 6744 100 + 1
U-------AUA-------U-UAUAAAUAUCGUCGCUUUUCGAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCGGU----AUAU-AACUUGACUGUCGACGGAUAGCUCU
.-------...-------.-(((((...(((........)))...))))).....(((((...(((.(((((((..(((.....))----)...-......)))))))..)))..))))) ( -18.90)
>DroWil_CAF1 1588 101 + 1
G-------UUA-------G-UAAA---ACCGUCGAUUUUCGAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUUCGGAUGUAU-UAAACUGGACUGUCGACGGAUAGCUCU
.-------...-------(-((..---....(((.....)))......)))....(((((...(((.(((((((..((((.......)))).-........)))))))..)))..))))) ( -21.20)
>DroMoj_CAF1 253 106 + 1
U-------AUAGUUUAUACAUAUAU--AUCGUCGAUUUUCGAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUAAAAUAUGU----AUAU-AACUUGACUGUCGACGGAUAGCUCU
.-------..............(((--(...(((.....)))....)))).....(((((...(((.(((((((......(((...----.)))-......)))))))..)))..))))) ( -19.80)
>DroAna_CAF1 7428 89 + 1
---------------------------AUCGUCGCCUUUCGAAUGUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCCGU--GUUU-U-AACUUGACUGUCGACGGAUAGCUCU
---------------------------.(((........))).............(((((...(((.(((((((..(((.....))--)...-.-......)))))))..)))..))))) ( -17.80)
>consensus
U_______AUA_______U_UAUA___AUCGUCGCUUUUCGAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCCGU____AU_U_AACUUGACUGUCGACGGAUAGCUCU
...............................(((.....))).............(((((...(((.(((((((...........................)))))))..)))..))))) (-16.46 = -16.46 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 7,686,031 – 7,686,134
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.69
Mean single sequence MFE -24.97
Consensus MFE -18.50
Energy contribution -18.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.54
Structure conservation index 0.74
SVM decision value 1.26
SVM RNA-class probability 0.937211
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7686031 103 - 20766785
AGAGCUAUCCGUCGACAGUCAAGUU-A-AG----ACCGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAACAUUCGAAAGGCGACGAU---UAUA-A-------GAUCGAAUGAA
(((((..(((((.((((((..((((-.-..----...)))).....)))))))))))...)))))..........(((((....(....)(((---(...-.-------))))))))).. ( -26.70)
>DroVir_CAF1 6101 100 - 1
AGAGCUAUCCGUCGACAGUCAAGCU-A--U----ACAGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUCGAAAAGCGACGAC-UUUAUACAUA-----UAC-------A
(((((..(((((.(((((((((.((-.--.----..)).)))....)))))))))))...)))))...(((((((...(((........))).-.)))))))..-----...-------. ( -26.20)
>DroGri_CAF1 6744 100 - 1
AGAGCUAUCCGUCGACAGUCAAGUU-AUAU----ACCGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUCGAAAAGCGACGAUAUUUAUA-A-------UAU-------A
(((((..(((((.((((((...(((-(((.----......)))))))))))))))))...))))).....(((((...(((........)))...)))))-.-------...-------. ( -25.50)
>DroWil_CAF1 1588 101 - 1
AGAGCUAUCCGUCGACAGUCCAGUUUA-AUACAUCCGAAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUCGAAAAUCGACGGU---UUUA-C-------UAA-------C
(((((..(((((.((((((.((((((.-........))))))....)))))))))))...)))))....(((.(((..(((.....)))..))---).))-)-------...-------. ( -25.70)
>DroMoj_CAF1 253 106 - 1
AGAGCUAUCCGUCGACAGUCAAGUU-AUAU----ACAUAUUUUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUCGAAAAUCGACGAU--AUAUAUGUAUAAACUAU-------A
(((((..(((((.((((((...(((-(...----........)))))))))))))))...))))).(((((((((((((((........))).--)))).))))))))....-------. ( -25.00)
>DroAna_CAF1 7428 89 - 1
AGAGCUAUCCGUCGACAGUCAAGUU-A-AAAC--ACGGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAACAUUCGAAAGGCGACGAU---------------------------
(((((..(((((.((((((..((((-.-....--...)))).....)))))))))))...))))).............((....)).......--------------------------- ( -20.70)
>consensus
AGAGCUAUCCGUCGACAGUCAAGUU_A_AU____ACAGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUCGAAAAGCGACGAU___UAUA_A_______UAU_______A
(((((..(((((.((((((...........................)))))))))))...))))).............(((.....)))............................... (-18.50 = -18.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 7,686,060 – 7,686,172
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.43
Mean single sequence MFE -27.27
Consensus MFE -23.43
Energy contribution -23.49
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.15
Structure conservation index 0.86
SVM decision value 1.40
SVM RNA-class probability 0.950366
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7686060 112 + 20766785
GAAUGUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCGGU----CU-U-AACUUGACUGUCGACGGAUAGCUCUCUUCAUUUCACAAUUCGCGGA-GGAUCUG-AAAGCGGAAA
...(((......((((((((...(((.(((((((............----..-.-......)))))))..)))..))))))))......))).(((((...-.......-...))))).. ( -26.92)
>DroVir_CAF1 6128 110 + 1
GAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCUGU----A--U-AGCUUGACUGUCGACGGAUAGCUCUCUUCAUUUCGCUAUUCGCAAGUU--UGGU-UAGCUUGAAA
(((((.......((((((((...(((.(((((((..(((.....))----)--.-......)))))))..)))..))))))))........))))).((((((--....-.))))))... ( -30.66)
>DroGri_CAF1 6769 114 + 1
GAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCGGU----AUAU-AACUUGACUGUCGACGGAUAGCUCUCUUCAUUUCGCUAUUCGUAAUUUGUUGUG-AAACUUAAAA
............((((((((...(((.(((((((..(((.....))----)...-......)))))))..)))..))))))))..((((((....((.....))..)))-)))....... ( -25.90)
>DroWil_CAF1 1610 112 + 1
GAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUUCGGAUGUAU-UAAACUGGACUGUCGACGGAUAGCUCUCUUCAUUUCGCUAUUCGGAUG-CAAUUUUGU--GCA----
(((((.......((((((((...(((.(((((((..((((.......)))).-........)))))))..)))..))))))))........)))))...((-((......)--)))---- ( -27.86)
>DroMoj_CAF1 284 95 + 1
GAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUAAAAUAUGU----AUAU-AACUUGACUGUCGACGGAUAGCUCUCUUCAUUUCGCUAUUCGCAG--------------------
(((((.......((((((((...(((.(((((((......(((...----.)))-......)))))))..)))..))))))))........)))))....-------------------- ( -24.86)
>DroAna_CAF1 7441 108 + 1
GAAUGUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCCGU--GUUU-U-AACUUGACUGUCGACGGAUAGCUCUCUUCAUUUCACUAUUCGUGGA-GUAUCCU-U--GCG----
....((.((((.((((((((...(((.(((((((..(((.....))--)...-.-......)))))))..)))..))))))))...(((((.....)))))-))))...-.--)).---- ( -27.40)
>consensus
GAAUAUUAUACAAAGAGAGCAAUUCCAUGACAGUAUUACAAUCCGU____AU_U_AACUUGACUGUCGACGGAUAGCUCUCUUCAUUUCGCUAUUCGCAGA_G_AUCUU_U__GCG____
(((((.......((((((((...(((.(((((((...........................)))))))..)))..))))))))........)))))........................ (-23.43 = -23.49 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,686,060 – 7,686,172
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.43
Mean single sequence MFE -32.30
Consensus MFE -27.80
Energy contribution -28.13
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.88
Structure conservation index 0.86
SVM decision value 1.60
SVM RNA-class probability 0.966708
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7686060 112 - 20766785
UUUCCGCUUU-CAGAUCC-UCCGCGAAUUGUGAAAUGAAGAGAGCUAUCCGUCGACAGUCAAGUU-A-AG----ACCGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAACAUUC
....(((...-.......-...)))...(((...(..((((((((..(((((.((((((..((((-.-..----...)))).....)))))))))))...))))))))..)...)))... ( -31.72)
>DroVir_CAF1 6128 110 - 1
UUUCAAGCUA-ACCA--AACUUGCGAAUAGCGAAAUGAAGAGAGCUAUCCGUCGACAGUCAAGCU-A--U----ACAGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUC
..........-....--...((((.....)))).(..((((((((..(((((.(((((((((.((-.--.----..)).)))....)))))))))))...))))))))..)......... ( -31.60)
>DroGri_CAF1 6769 114 - 1
UUUUAAGUUU-CACAACAAAUUACGAAUAGCGAAAUGAAGAGAGCUAUCCGUCGACAGUCAAGUU-AUAU----ACCGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUC
..........-.............(((((...(.(..((((((((..(((((.((((((...(((-(((.----......)))))))))))))))))...))))))))..).)..))))) ( -33.20)
>DroWil_CAF1 1610 112 - 1
----UGC--ACAAAAUUG-CAUCCGAAUAGCGAAAUGAAGAGAGCUAUCCGUCGACAGUCCAGUUUA-AUACAUCCGAAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUC
----(((--(......))-))...(((((...(.(..((((((((..(((((.((((((.((((((.-........))))))....)))))))))))...))))))))..).)..))))) ( -34.90)
>DroMoj_CAF1 284 95 - 1
--------------------CUGCGAAUAGCGAAAUGAAGAGAGCUAUCCGUCGACAGUCAAGUU-AUAU----ACAUAUUUUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUC
--------------------....(((((...(.(..((((((((..(((((.((((((...(((-(...----........)))))))))))))))...))))))))..).)..))))) ( -30.10)
>DroAna_CAF1 7441 108 - 1
----CGC--A-AGGAUAC-UCCACGAAUAGUGAAAUGAAGAGAGCUAUCCGUCGACAGUCAAGUU-A-AAAC--ACGGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAACAUUC
----...--.-.((....-.))..((((.((...(..((((((((..(((((.((((((..((((-.-....--...)))).....)))))))))))...))))))))..)...)))))) ( -32.30)
>consensus
____AGC__A_AACAU_A_CCUGCGAAUAGCGAAAUGAAGAGAGCUAUCCGUCGACAGUCAAGUU_A_AU____ACAGAUUGUAAUACUGUCAUGGAAUUGCUCUCUUUGUAUAAUAUUC
........................(((((...(.(..((((((((..(((((.((((((...........................)))))))))))...))))))))..).)..))))) (-27.80 = -28.13 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:39 2006