Locus 4579

Sequence ID 2L_DroMel_CAF1
Location 13,127,966 – 13,128,219
Length 253
Max. P 0.993694
window7219 window7220 window7221

overview

Window 9

Location 13,127,966 – 13,128,073
Length 107
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 84.18
Mean single sequence MFE -27.21
Consensus MFE -23.05
Energy contribution -22.30
Covariance contribution -0.75
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.85
SVM decision value 0.66
SVM RNA-class probability 0.814256
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13127966 107 - 22407834
CCCUUUGUUCGACUGGUUAGUUGAA-AACGCAAAUACAUUCGUACAUCCGAAACUAACCGAAACUUGGUUGGAUGCAUGAUUAAUGUCCGCAUUGAGUCAUGUCCGAG
...(((((((((((....)))))).-...)))))....((((......)))).((((((((...))))))))..((((((((((((....)))))).))))))..... ( -25.80)
>DroSec_CAF1 20934 87 - 1
CCCUUUGUUCGACUGGUUAGUUGAA-AACACA--------------------ACUAACCGAAACUUGGUUGGAUGCAUGAUUAAUGUCCGCAUUGAGUCAUGUCCGAG
......(((((((((((((((((..-....))--------------------))))))).......))))))))((((((((((((....)))))).))))))..... ( -27.51)
>DroSim_CAF1 22018 87 - 1
CCCUUUGUUCGACUGGUUAGUUGAA-AACACA--------------------ACUAACCGAAACUUGGUUGGAUGCAUGAUUAAUGUCCGCAUUGAGUCAUGUCCGAG
......(((((((((((((((((..-....))--------------------))))))).......))))))))((((((((((((....)))))).))))))..... ( -27.51)
>DroYak_CAF1 21367 102 - 1
CCCUUUGUUUGGCUGGUUAGUUGGAAAACGCACAUACAUCUGUACG------ACUAACCGAAACUCGGUUGGAUGCAUGAUUAAUGUCCGCAUUGAGUCAUGUCCGAG
.((.......)).((((((((((.....................))------))))))))...(((((......((((((((((((....)))))).))))))))))) ( -28.00)
>consensus
CCCUUUGUUCGACUGGUUAGUUGAA_AACACA____________________ACUAACCGAAACUUGGUUGGAUGCAUGAUUAAUGUCCGCAUUGAGUCAUGUCCGAG
.......(((((((....)))))))............................((((((((...))))))))..((((((((((((....)))))).))))))..... (-23.05 = -22.30 +  -0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 13,128,003 – 13,128,113
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.64
Mean single sequence MFE -28.32
Consensus MFE -19.65
Energy contribution -19.17
Covariance contribution -0.48
Combinations/Pair 1.24
Mean z-score -2.41
Structure conservation index 0.69
SVM decision value 2.42
SVM RNA-class probability 0.993694
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13128003 110 + 22407834
--------CAACCAAGUUUCGGUUAGUUUCGGAUGUACGAAUGUAUUUGCGU-U-UUCAACUAACCAGUCGAACAAAGGGUGUUAGAAUGCUUUUUGUUUCAGCAUCGCUGAGCAGAGAU
--------.......(((((((((((((..(((((((..........)))))-)-)..)))))))).((..((((((((((((....))))))))))))(((((...))))))).))))) ( -29.70)
>DroSec_CAF1 20971 90 + 1
--------CAACCAAGUUUCGGUUAGU--------------------UGUGU-U-UUCAACUAACCAGUCGAACAAAGGGUGUUAGAAUGCUUUUUGUUUCAGCAUCGCUGAGCAGAGAU
--------.......((((((((((((--------------------((...-.-..))))))))).((..((((((((((((....))))))))))))(((((...))))))).))))) ( -28.90)
>DroSim_CAF1 22055 90 + 1
--------CAACCAAGUUUCGGUUAGU--------------------UGUGU-U-UUCAACUAACCAGUCGAACAAAGGGUGUUAGAAUGCUUUUUGUUUCAGCAUCGCUGAGCAGAGAU
--------.......((((((((((((--------------------((...-.-..))))))))).((..((((((((((((....))))))))))))(((((...))))))).))))) ( -28.90)
>DroYak_CAF1 21404 105 + 1
--------CAACCGAGUUUCGGUUAGU------CGUACAGAUGUAUGUGCGU-UUUCCAACUAACCAGCCAAACAAAGGGUGUUAGAAUGCUUUUUGUUUCAGCAUCGCUGAGCAGAGAU
--------.......((((((((((((------((((((......)))))).-......))))))).((..((((((((((((....))))))))))))(((((...))))))).))))) ( -32.51)
>DroAna_CAF1 28092 101 + 1
AGACCACACAACAAAGUCUUGAAUAUA------------------UAUGGAUAU-UUGAAAAAGCUAAACGAACAAAGAGUGUUAGAAUACUUUUUGUUUCAGCAUCGUUGAGCAGAGAU
...............(((((((((((.------------------.....))))-))......(((.((((((((((((((((....))))))))))).......))))).))).))))) ( -21.61)
>consensus
________CAACCAAGUUUCGGUUAGU__________________U_UGCGU_U_UUCAACUAACCAGUCGAACAAAGGGUGUUAGAAUGCUUUUUGUUUCAGCAUCGCUGAGCAGAGAU
...............((((((((((((................................))))))).....((((((((((((....))))))))))))(((((...)))))...))))) (-19.65 = -19.17 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,128,113 – 13,128,219
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.20
Mean single sequence MFE -22.08
Consensus MFE -13.57
Energy contribution -14.57
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.61
SVM decision value 0.19
SVM RNA-class probability 0.628082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13128113 106 - 22407834
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGUUUCUUUAUUGUUGUUUUGCGGUUGCUUUUUUU-C-C---ACCGACUCCCCUG---------CCCCAAAAGCGACUCUUAA
...((((((((........(((((....))))).(((((..........((......))(((.(........-)-.---)))..........---------..))))).))))))))... ( -21.00)
>DroSec_CAF1 21061 95 - 1
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGUUUCUUUAUUGUUGUUUUGCGGUUGCUUUUUUUUC-C---AC---------UG------------CAAAAGCGACUCUUAA
...((((((((((((((..(((((....)))))..))))))............(((((((((............-.---))---------))------------)))))))))))))... ( -24.42)
>DroSim_CAF1 22145 95 - 1
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGUUUCUUUAUUGUUGUUUUGCGGUUGCUUUUUUUUC-C---AC---------UG------------CAAAAGCGACUCUUAA
...((((((((((((((..(((((....)))))..))))))............(((((((((............-.---))---------))------------)))))))))))))... ( -24.42)
>DroEre_CAF1 22480 100 - 1
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGUUUCUUUAUUGUUGUUUUGCGGUUUGCUUUUUUCCGC---ACCC-----------------CCCCCAAAACCGACUCUUAA
...(((((((.((((((..(((((....)))))..))))))...........((((((.((..(((........))---)..)-----------------)...)))))))))))))... ( -21.20)
>DroYak_CAF1 21509 119 - 1
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGUUUCUUUAUUGUUGUUUUGCGGUUGCUUUUUUUUCGCCUCACCCA-UCCCCUGACAGCCUCCACCAAAAAGCGACUCUUAA
...((((((((........(((((....))))).((((((.........((((((.((.(((.((.........))...)))))-......))))))....))))))..))))))))... ( -26.12)
>DroAna_CAF1 28193 87 - 1
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGCUUCUUUAUUGUUGUUUUGCGGUUGCUGGUUAUUU-C---GU---------UC--------------------UCUCUCAA
.((((((..((((.(((((((.((((............)))).))))))).....))))..)).))))......-.---..---------..--------------------........ ( -15.30)
>consensus
UCCAGAGUUGCAAUUAGUAGAAAAGUAAUUUUCGUUUGGUUUCUUUAUUGUUGUUUUGCGGUUGCUUUUUUUUC_C___AC_________UG____________CAAAAGCGACUCUUAA
...((((((((((((((..(((((....)))))..)))))).....(((((......)))))...............................................))))))))... (-13.57 = -14.57 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:35 2006