Locus 295

Sequence ID	2L_DroMel_CAF1
Location	842,113 – 842,280
Length	167
Max. P	0.947414

overview

Window 7

Location	842,113 – 842,208
Length	95
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	85.91
Mean single sequence MFE	-24.86
Consensus MFE	-18.06
Energy contribution	-17.62
Covariance contribution	-0.44
Combinations/Pair	1.19
Mean z-score	-2.18
Structure conservation index	0.73
SVM decision value	0.85
SVM RNA-class probability	0.866757
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 842113 95 - 22407834
AAAUUAGCUCCGUGGAGUGGUCAUAACUAACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCAUUCUUCUGCAUCUCCCCGA--GAUCAUCACCACAC
......(((..((((((..(..((.((.....)).))..)..)))))).)))..(((((......))))).(((((...))--)))........... ( -24.00)
>DroSec_CAF1 7473 97 - 1
AAAUUAGCUGUGUGGAGUGGUCAUAACUAACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCAUUCUUCUGCAUCUCCCCGAGAGAUCAUCUCCACAC
.........(((((((((((((.........((((..((..((((...((....))))))....))..))))((((...))))))))).)))))))) ( -26.40)
>DroSim_CAF1 8148 97 - 1
AAAUUAGCUGUGUGGAGUGGUCAUAACUAACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCAUUCUGCUGCAUCUCCCCGAGAGAUCAUCUCCACAC
.........(((((((((((((................((.((.....((((......))))....)).)).((((...))))))))).)))))))) ( -28.40)
>DroEre_CAF1 7086 92 - 1
AAAUUAGCUCUUUGGAGUGGUCAUAACUAACUGUAAUAACUGCUCCACUGGCCCCGGAGCCAUUCCUCUCCAGCUCUGCGAGAUCU-----CUCCUC
......((.(..(((((..((.((.((.....)).)).))..)))))..)))..((((((............)))))).(((....-----)))... ( -24.30)
>DroYak_CAF1 6299 92 - 1
AAAUUAGCUCUUUGGAGUGGUCAUAACUAACUGUAAUAACUGCUCCAGUGGCCCCAGAGUCAUUCUUCUCCAUCUCGUCGAGAUCU-----CUCCUC
......(((..((((((..((.((.((.....)).)).))..)))))).)))...((((....((((..(......)..)))).))-----)).... ( -21.20)
>consensus
AAAUUAGCUCUGUGGAGUGGUCAUAACUAACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCAUUCUUCUGCAUCUCCCCGAGAGAUCAUC_CCACAC
...........((((((..((.((.((.....)).)).))..))))))((((......))))................................... (-18.06 = -17.62 +  -0.44)

alignment

secondary structure

dotplot

Window 8

Location	842,146 – 842,248
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.21
Mean single sequence MFE	-26.87
Consensus MFE	-13.30
Energy contribution	-13.44
Covariance contribution	0.14
Combinations/Pair	1.20
Mean z-score	-2.08
Structure conservation index	0.49
SVM decision value	0.35
SVM RNA-class probability	0.699327
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 842146 102 + 22407834
-----UGACUCUGGGGCCAGUGGAGCAGCUAUUACAGUU-------------AGUUAUGACCACUCCACGGAGCUAAUUUGAUUUUUAGAGCCUCACUCUUUAGGCCAACAAACACUUUC
-----.........((((.((((((..(.(((.((....-------------.)).))).)..))))))((..((((........))))..))..........))))............. ( -25.20)
>DroSec_CAF1 7508 102 + 1
-----UGACUCUGGGGCCAGUGGAGCAGCUAUUACAGUU-------------AGUUAUGACCACUCCACACAGCUAAUUUAAUUUUUAGAGCCCCACUCUUUGGGCCAACAAACACUUUC
-----......((((((..((((((..(.(((.((....-------------.)).))).)..))))))....((((........)))).))))))...((((......))))....... ( -24.30)
>DroSim_CAF1 8183 90 + 1
-----UGACUCUGGGGCCAGUGGAGCAGCUAUUACAGUU-------------AGUUAUGACCACUCCACACAGCUAAUUUAAUUUUUAGAGCCC------------CAACAAACACUUUC
-----......((((((..((((((..(.(((.((....-------------.)).))).)..))))))....((((........)))).))))------------))............ ( -23.60)
>DroEre_CAF1 7116 99 + 1
-----UGGCUCCGGGGCCAGUGGAGCAGUUAUUACAGUU-------------AGUUAUGACCACUCCAAAGAGCUAAUUUAAUUUUUAGAGCCCCCCGCUUUGAGCC---AAACUCUUUC
-----(((((((((((....(((((..(((((.((....-------------.)).)))))..)))))..(..((((........))))..).)))))....)))))---)......... ( -31.80)
>DroYak_CAF1 6329 99 + 1
-----UGACUCUGGGGCCACUGGAGCAGUUAUUACAGUU-------------AGUUAUGACCACUCCAAAGAGCUAAUUUAAUUUUUAGAGCCCCACUCUUUAGGCC---AAGCACUUUC
-----......((((((...(((((..(((((.((....-------------.)).)))))..))))).....((((........)))).))))))...........---.......... ( -24.20)
>DroAna_CAF1 5976 115 + 1
ACCACUGAGGCUGGGGCCAUUGGAACAGCCAUUACAGUUAUUCCAGCCAGCCAGUUAGGGCCACUCCU-AGUGUUAAUUUCAUU-UUAGUGCCCUACUCUCUCAACA---CAACACUUUC
.....((((((((((((...(((((.(((.......))).))))))))..)))))((((((.(((...-((((.......))))-..)))))))))....))))...---.......... ( -32.10)
>consensus
_____UGACUCUGGGGCCAGUGGAGCAGCUAUUACAGUU_____________AGUUAUGACCACUCCACAGAGCUAAUUUAAUUUUUAGAGCCCCACUCUUUAGGCC___AAACACUUUC
............(((((...(((((..(.(((.((..................)).))).)..))))).....((((........)))).)))))......................... (-13.30 = -13.44 +   0.14)

alignment

secondary structure

dotplot

Window 9

Location	842,146 – 842,248
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.21
Mean single sequence MFE	-30.12
Consensus MFE	-19.52
Energy contribution	-20.35
Covariance contribution	0.83
Combinations/Pair	1.18
Mean z-score	-1.80
Structure conservation index	0.65
SVM decision value	0.90
SVM RNA-class probability	0.877813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 842146 102 - 22407834
GAAAGUGUUUGUUGGCCUAAAGAGUGAGGCUCUAAAAAUCAAAUUAGCUCCGUGGAGUGGUCAUAACU-------------AACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCA-----
.......((((..((((...((((.....))))..................((((((..(..((.((.-------------....)).))..)..)))))).)))).))))....----- ( -29.60)
>DroSec_CAF1 7508 102 - 1
GAAAGUGUUUGUUGGCCCAAAGAGUGGGGCUCUAAAAAUUAAAUUAGCUGUGUGGAGUGGUCAUAACU-------------AACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCA-----
.....(.((((......)))).).(((((((((((........))))....((((((..(..((.((.-------------....)).))..)..)))))).)))))))......----- ( -29.80)
>DroSim_CAF1 8183 90 - 1
GAAAGUGUUUGUUG------------GGGCUCUAAAAAUUAAAUUAGCUGUGUGGAGUGGUCAUAACU-------------AACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCA-----
...........(((------------(((((((((........))))....((((((..(..((.((.-------------....)).))..)..)))))).)))))))).....----- ( -30.00)
>DroEre_CAF1 7116 99 - 1
GAAAGAGUUU---GGCUCAAAGCGGGGGGCUCUAAAAAUUAAAUUAGCUCUUUGGAGUGGUCAUAACU-------------AACUGUAAUAACUGCUCCACUGGCCCCGGAGCCA-----
.........(---(((((....(((((((((..............))))(..(((((..((.((.((.-------------....)).)).))..)))))..).)))))))))))----- ( -32.64)
>DroYak_CAF1 6329 99 - 1
GAAAGUGCUU---GGCCUAAAGAGUGGGGCUCUAAAAAUUAAAUUAGCUCUUUGGAGUGGUCAUAACU-------------AACUGUAAUAACUGCUCCAGUGGCCCCAGAGUCA-----
......((((---........))))((((((((((........))))....((((((..((.((.((.-------------....)).)).))..)))))).)))))).......----- ( -27.00)
>DroAna_CAF1 5976 115 - 1
GAAAGUGUUG---UGUUGAGAGAGUAGGGCACUAA-AAUGAAAUUAACACU-AGGAGUGGCCCUAACUGGCUGGCUGGAAUAACUGUAAUGGCUGUUCCAAUGGCCCCAGCCUCAGUGGU
...((((((.---((((....)).)).))))))..-...........((((-(((..(((........(((((..(((((((.((.....)).))))))).)))))))).))).)))).. ( -31.70)
>consensus
GAAAGUGUUU___GGCCCAAAGAGUGGGGCUCUAAAAAUUAAAUUAGCUCUGUGGAGUGGUCAUAACU_____________AACUGUAAUAGCUGCUCCACUGGCCCCAGAGUCA_____
.........................((((((((((........))))....((((((..((.((.((..................)).)).))..)))))).))))))............ (-19.52 = -20.35 +   0.83)

alignment

secondary structure

dotplot

Window 0

Location	842,180 – 842,280
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.09
Mean single sequence MFE	-29.37
Consensus MFE	-15.98
Energy contribution	-16.48
Covariance contribution	0.50
Combinations/Pair	1.40
Mean z-score	-1.93
Structure conservation index	0.54
SVM decision value	1.37
SVM RNA-class probability	0.947414
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 842180 100 - 22407834
--------CGAAACUGGACCACGCCACAUUGGCGUAGCUAGAAAGUGUUUGUUGGCCUAAAGAGUGAGGCUCUAAAAAUCAAAUUAGCUCCGUGGAGUGGUCAUAACU------------
--------........((((((.((((...((...((((((......(((...(((((........)))))...)))......)))))))))))).))))))......------------ ( -29.90)
>DroSec_CAF1 7542 99 - 1
--------CGAAACUGGACCACGCCGCAUUG-UGCAGCUAGAAAGUGUUUGUUGGCCCAAAGAGUGGGGCUCUAAAAAUUAAAUUAGCUGUGUGGAGUGGUCAUAACU------------
--------........((((((.((((....-.((((((((.....((((...(((((........)))))....))))....)))))))))))).))))))......------------ ( -35.30)
>DroSim_CAF1 8217 87 - 1
--------CGAAACUGGACCACGCCGCAUUG-UGCAGCUAGAAAGUGUUUGUUG------------GGGCUCUAAAAAUUAAAUUAGCUGUGUGGAGUGGUCAUAACU------------
--------........((((((.((((....-.((((((((.....((((.(((------------(....))))))))....)))))))))))).))))))......------------ ( -27.10)
>DroEre_CAF1 7150 103 - 1
-UUCGUUAGAAAACUGGACCACGCCACAAUG-UGAAGCUAGAAAGAGUUU---GGCUCAAAGCGGGGGGCUCUAAAAAUUAAAUUAGCUCUUUGGAGUGGUCAUAACU------------
-...((((........((((((.((......-(((.((((((.....)))---))))))....((((((((..............)))))))))).)))))).)))).------------ ( -26.94)
>DroYak_CAF1 6363 104 - 1
CAUCGUUGGGAAACUGGACCACGCCACAUUG-UGAAGCUAGAAAGUGCUU---GGCCUAAAGAGUGGGGCUCUAAAAAUUAAAUUAGCUCUUUGGAGUGGUCAUAACU------------
....(((((....)).((((((........(-(.((((........))))---.))(((((((((.....................))))))))).))))))..))).------------ ( -29.30)
>DroAna_CAF1 6016 105 - 1
--------GCAAACUGGUCCAGAUAG-UGAG-UGACCUUAGAAAGUGUUG---UGUUGAGAGAGUAGGGCACUAA-AAUGAAAUUAACACU-AGGAGUGGCCCUAACUGGCUGGCUGGAA
--------.....(..(.((((.(((-(..(-(.(((((((..((((((.---((((....)).)).))))))..-..((.......))))-))).)).))....)))).)))))..).. ( -27.70)
>consensus
________CGAAACUGGACCACGCCACAUUG_UGAAGCUAGAAAGUGUUU___GGCCCAAAGAGUGGGGCUCUAAAAAUUAAAUUAGCUCUGUGGAGUGGUCAUAACU____________
................((((((.(((.........((((((............(((((........)))))............))))))...))).)))))).................. (-15.98 = -16.48 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:18 2006