Locus 7320

Sequence ID	X_DroMel_CAF1
Location	18,269,316 – 18,269,483
Length	167
Max. P	0.996316

overview

Window 5

Location	18,269,316 – 18,269,406
Length	90
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.47
Mean single sequence MFE	-23.70
Consensus MFE	-14.64
Energy contribution	-15.39
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.62
SVM decision value	0.28
SVM RNA-class probability	0.664446
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18269316 90 - 22224390
ACCAGAUUCAUCAUGGC---UAAUGAUGGGUCAUUCCUAAUCGGC---------------------------AACGCUCAUCUUUAACACGCCGCCGAGCUCACGUGCAAUAAAUGCAUU
....((((((((((...---..))))))))))........(((((---------------------------...((.............)).)))))......(((((.....))))). ( -23.32)
>DroSim_CAF1 12287 93 - 1
UUCAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAAUCGGC---------------------------ACCGCUCAUCUUCAACAAGCCGCCGAGCUCACGUGCAAUAAAUGCAUU
....(((((((((..........)))))))))........(((((---------------------------...(((...........))).)))))......(((((.....))))). ( -21.10)
>DroEre_CAF1 42214 99 - 1
GCCAGAUUCAUCAUAG---CUAAUGAUGGGUCAUUCCUGCUCGG------------------AAUGACUAUCUCCGCUCAUCUUCAACAAGUCGCCGUGCUCACGUGCAAUUAAUGCAUU
((..((((((((((..---...))))))(((((((((.....))------------------)))))))....................))))(((((....))).)).......))... ( -26.00)
>DroYak_CAF1 34234 117 - 1
UUCAGAUUCAUCAUUG---CUAAUGAUAGGUCAUGCCUAAUCGGCGUAUAAAUACUUAUGGCAGUGACUAUCUCCGUUCAUCUUCAACUAGCCGCCGUGCUCACGUGCAAUUAAUGCAUU
....(((..(((((..---...)))))..)))((((.....(((((((....)))....((((((.....................))).)))))))(((......)))......)))). ( -24.40)
>consensus
UCCAGAUUCAUCAUGG___CUAAUGAUGGGUCAUUCCUAAUCGGC___________________________ACCGCUCAUCUUCAACAAGCCGCCGAGCUCACGUGCAAUAAAUGCAUU
....((((((((((........)))))))))).........((((................................................)))).......(((((.....))))). (-14.64 = -15.39 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	18,269,356 – 18,269,446
Length	90
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	68.90
Mean single sequence MFE	-28.56
Consensus MFE	-16.68
Energy contribution	-16.52
Covariance contribution	-0.16
Combinations/Pair	1.26
Mean z-score	-1.61
Structure conservation index	0.58
SVM decision value	0.72
SVM RNA-class probability	0.833201
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18269356 90 + 22224390
UGAGCGUU---------------------------GCCGAUUAGGAAUGACCCAUCAUUA---GCCAUGAUGAAUCUGGUAAGUGGGGCCAGUUAACUGACCAGCUAGAUUCCACGGAGC
...((...---------------------------.(((((((((.((((....))))..---.)).))))(((((((((...(((...(((....))).))))))))))))..))).)) ( -24.00)
>DroSec_CAF1 37726 93 + 1
UGAGCGGU---------------------------GCCGAUUAGGAAUGACCCAUCAUUAUGAAUCGUGAUGAAUCUCAAAAGUGGGGCCAGUUAACUGGCCAGCUAGAUUCCACGGAAC
........---------------------------.((((((...(((((....)))))...))))(((..((((((....(((..((((((....)))))).))))))))))))))... ( -29.90)
>DroSim_CAF1 12327 93 + 1
UGAGCGGU---------------------------GCCGAUUAGGAAUGACCCAUCAUUAUGAAUCGUGAUGAAUCUGAAAAGUGGGGCCAGUUAACUGGGCAGCUAGAUUCCACGGAGC
...((...---------------------------.((((((...(((((....)))))...))))(((..((((((....(((..(.((((....)))).).)))))))))))))).)) ( -26.50)
>DroEre_CAF1 42254 92 + 1
UGAGCGGAGAUAGUCAUU------------------CCGAGCAGGAAUGACCCAUCAUUAG---CUAUGAUGAAUCUGGCAAAUGUGGCCAGUAAGCUGGUUAACUAGAUGCU-------
..(((.......((((((------------------((.....)))))))).((((((...---..)))))).((((((......(((((((....))))))).)))))))))------- ( -32.50)
>DroYak_CAF1 34274 117 + 1
UGAACGGAGAUAGUCACUGCCAUAAGUAUUUAUACGCCGAUUAGGCAUGACCUAUCAUUAG---CAAUGAUGAAUCUGAAUAAUGGGGCCAGUAAGCUGGUUAACUGGAUUCCAUCAAAC
.....((((.((((.....((((...((((((...(((.....)))........((((((.---...))))))...))))))))))((((((....)))))).))))..))))....... ( -29.90)
>consensus
UGAGCGGU___________________________GCCGAUUAGGAAUGACCCAUCAUUAG___CCAUGAUGAAUCUGAAAAGUGGGGCCAGUUAACUGGCCAGCUAGAUUCCACGGAAC
...........................................(((((((..((((((........))))))..))..........((((((....))))))......)))))....... (-16.68 = -16.52 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	18,269,356 – 18,269,446
Length	90
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	68.90
Mean single sequence MFE	-27.64
Consensus MFE	-14.92
Energy contribution	-15.92
Covariance contribution	1.00
Combinations/Pair	1.11
Mean z-score	-2.39
Structure conservation index	0.54
SVM decision value	2.68
SVM RNA-class probability	0.996316
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18269356 90 - 22224390
GCUCCGUGGAAUCUAGCUGGUCAGUUAACUGGCCCCACUUACCAGAUUCAUCAUGGC---UAAUGAUGGGUCAUUCCUAAUCGGC---------------------------AACGCUCA
((.(((.(((((......((((((....))))))..........((((((((((...---..)))))))))))))))....))).---------------------------...))... ( -29.00)
>DroSec_CAF1 37726 93 - 1
GUUCCGUGGAAUCUAGCUGGCCAGUUAACUGGCCCCACUUUUGAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAAUCGGC---------------------------ACCGCUCA
((.(((.(((((......((((((....))))))..........(((((((((..........))))))))))))))....))).---------------------------))...... ( -29.00)
>DroSim_CAF1 12327 93 - 1
GCUCCGUGGAAUCUAGCUGCCCAGUUAACUGGCCCCACUUUUCAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAAUCGGC---------------------------ACCGCUCA
((.(((.(((((........((((....))))............(((((((((..........))))))))))))))....))).---------------------------...))... ( -21.60)
>DroEre_CAF1 42254 92 - 1
-------AGCAUCUAGUUAACCAGCUUACUGGCCACAUUUGCCAGAUUCAUCAUAG---CUAAUGAUGGGUCAUUCCUGCUCGG------------------AAUGACUAUCUCCGCUCA
-------(((..................(((((.......)))))...((((((..---...))))))(((((((((.....))------------------)))))))......))).. ( -27.50)
>DroYak_CAF1 34274 117 - 1
GUUUGAUGGAAUCCAGUUAACCAGCUUACUGGCCCCAUUAUUCAGAUUCAUCAUUG---CUAAUGAUAGGUCAUGCCUAAUCGGCGUAUAAAUACUUAUGGCAGUGACUAUCUCCGUUCA
(..((((((...(((((..........)))))..))))))..)((((...((((((---(((((((....))))(((.....))).............)))))))))..))))....... ( -31.10)
>consensus
GCUCCGUGGAAUCUAGCUGACCAGUUAACUGGCCCCACUUUUCAGAUUCAUCAUGG___AUAAUGAUGGGUCAUUCCUAAUCGGC___________________________ACCGCUCA
.....((((...........((((....))))............((((((((((........)))))))))).........................................))))... (-14.92 = -15.92 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	18,269,369 – 18,269,483
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.25
Mean single sequence MFE	-34.95
Consensus MFE	-22.83
Energy contribution	-23.82
Covariance contribution	1.00
Combinations/Pair	1.24
Mean z-score	-1.74
Structure conservation index	0.65
SVM decision value	0.22
SVM RNA-class probability	0.640103
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18269369 114 + 22224390
UUAGGAAUGACCCAUCAUUA---GCCAUGAUGAAUCUGGUAAGUGGGGCCAGUUAACUGACCAGCUAGAUUCCACGGAGCACGUGCCGAUGGUU-UAUUAGUAAUGAAAUGCUGUUGG--
...((.((((....))))..---.)).....(((((((((...(((...(((....))).))))))))))))((((.....))))((((((((.-..(((....)))...))))))))-- ( -31.10)
>DroSec_CAF1 37739 117 + 1
UUAGGAAUGACCCAUCAUUAUGAAUCGUGAUGAAUCUCAAAAGUGGGGCCAGUUAACUGGCCAGCUAGAUUCCACGGAACACGUGCCGAUGGGU-UGUUGGUAAUGAAAUGCUGUUGG--
.....((..(((((((..((((..(((((..((((((....(((..((((((....)))))).))))))))))))))....))))..)))))))-..))((((......)))).....-- ( -40.90)
>DroSim_CAF1 12340 117 + 1
UUAGGAAUGACCCAUCAUUAUGAAUCGUGAUGAAUCUGAAAAGUGGGGCCAGUUAACUGGGCAGCUAGAUUCCACGGAGCACGUGCCGAUGGGU-UGUUGGUAAUGAAAUGCUGAUGG--
........((((((((........(((((..((((((....(((..(.((((....)))).).)))))))))))))).((....)).)))))))-)((..(((......)))..))..-- ( -37.40)
>DroYak_CAF1 34314 117 + 1
UUAGGCAUGACCUAUCAUUAG---CAAUGAUGAAUCUGAAUAAUGGGGCCAGUAAGCUGGUUAACUGGAUUCCAUCAAACACGUGCUGCUGAUUACACAAGUAAUGCUAUGCCGUAGGAU
...((((((.....(((.(((---((.((((((((((.........((((((....))))))....))))).)))))......))))).)))((((....))))...))))))....... ( -30.42)
>consensus
UUAGGAAUGACCCAUCAUUAU__ACCAUGAUGAAUCUGAAAAGUGGGGCCAGUUAACUGGCCAGCUAGAUUCCACGGAACACGUGCCGAUGGGU_UAUUAGUAAUGAAAUGCUGUUGG__
(((..(((((((((((...............((((((....(((..((((((....)))))).)))))))))((((.....))))..))))))).))))..)))................ (-22.83 = -23.82 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	18,269,369 – 18,269,483
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.25
Mean single sequence MFE	-29.70
Consensus MFE	-20.14
Energy contribution	-19.58
Covariance contribution	-0.56
Combinations/Pair	1.26
Mean z-score	-2.26
Structure conservation index	0.68
SVM decision value	1.47
SVM RNA-class probability	0.957060
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18269369 114 - 22224390
--CCAACAGCAUUUCAUUACUAAUA-AACCAUCGGCACGUGCUCCGUGGAAUCUAGCUGGUCAGUUAACUGGCCCCACUUACCAGAUUCAUCAUGGC---UAAUGAUGGGUCAUUCCUAA
--....(((((((........))).-..((((.(((....)).).))))......))))(((((....)))))...........((((((((((...---..))))))))))........ ( -28.40)
>DroSec_CAF1 37739 117 - 1
--CCAACAGCAUUUCAUUACCAACA-ACCCAUCGGCACGUGUUCCGUGGAAUCUAGCUGGCCAGUUAACUGGCCCCACUUUUGAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAA
--.......................-((((((((....(((...((((((((((((..((((((....))))))...))....))))))..))))...)))..))))))))......... ( -33.10)
>DroSim_CAF1 12340 117 - 1
--CCAUCAGCAUUUCAUUACCAACA-ACCCAUCGGCACGUGCUCCGUGGAAUCUAGCUGCCCAGUUAACUGGCCCCACUUUUCAGAUUCAUCACGAUUCAUAAUGAUGGGUCAUUCCUAA
--.......................-((((((((((....))).((((((((((((.((.((((....))))...))))....))))))..)))).........)))))))......... ( -26.30)
>DroYak_CAF1 34314 117 - 1
AUCCUACGGCAUAGCAUUACUUGUGUAAUCAGCAGCACGUGUUUGAUGGAAUCCAGUUAACCAGCUUACUGGCCCCAUUAUUCAGAUUCAUCAUUG---CUAAUGAUAGGUCAUGCCUAA
.......(((((.(((((((....)))))..))......((..((((((...(((((..........)))))..))))))..))(((..(((((..---...)))))..))))))))... ( -31.00)
>consensus
__CCAACAGCAUUUCAUUACCAACA_AACCAUCGGCACGUGCUCCGUGGAAUCUAGCUGGCCAGUUAACUGGCCCCACUUUUCAGAUUCAUCACGAU__AUAAUGAUGGGUCAUUCCUAA
.............((((((..............(((....))).((((((((((((..((((((....))))))...))....))))))..)))).....))))))((((.....)))). (-20.14 = -19.58 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:55 2006