Locus 4624

Sequence ID	3R_DroMel_CAF1
Location	12,165,948 – 12,166,089
Length	141
Max. P	0.680390

overview

Window 8

Location	12,165,948 – 12,166,053
Length	105
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	80.94
Mean single sequence MFE	-22.55
Consensus MFE	-15.29
Energy contribution	-15.02
Covariance contribution	-0.27
Combinations/Pair	1.35
Mean z-score	-1.59
Structure conservation index	0.68
SVM decision value	0.30
SVM RNA-class probability	0.680390
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12165948 105 + 27905053
GAGUUAUAAUAUAAUAU-GUAGGAAGCAGA--CUGAGCAAAGGCUCAAAAGAUAAUCAAAAGCAAAUCAAGGAAUGCCGAGUGC--UUUUGGCCAAAGAGAAUUCCUUGG
.................-.......((...--.(((((....)))))...(.....)....))....((((((((((((((...--.))))))........)))))))). ( -21.70)
>DroSec_CAF1 72543 104 + 1
GAUUUAUAAUAUAAUAU-GUAGGAAGCAGA--CUGAGCAAAGGCUCGAAAUAA-AACAAAAGCAAAUCAAGGAAUGCCGAGCGC--UUGUGGCCAAAGAGAAUUCCUUGG
..(((((.........(-((.....)))..--.(((((....)))))..))))-)............((((((((((((.....--...))))........)))))))). ( -18.10)
>DroSim_CAF1 73271 104 + 1
GAUUUAUAAUAUAAUAU-GUAGGAAGCAGA--CUGAGCAAAGGCUCAAAAUAA-AACAAAAGCAAAUCAAGGAAUGCCGAGCGC--UUGUGGCCAAAGAGAAUUCCUUGG
..(((((.........(-((.....)))..--.(((((....)))))..))))-)............((((((((((((.....--...))))........)))))))). ( -18.80)
>DroEre_CAF1 73648 104 + 1
GAUUUAUAAUAUUAUUU-GUAGUAUGCAGA--CUGAGCAAAGGCUCAAAAUAA-AACAAAAGUAAAUCAAGGAAUGCCGAGUGG--UUGUGGCCUAAGAAAAUUCCUUGG
(((((((.......(((-((.....)))))--.(((((....)))))......-.......)))))))(((((((.......((--(....))).......))))))).. ( -23.74)
>DroYak_CAF1 84964 104 + 1
GAUUUAUAAUAUAAUUU-GUAGUAUGCAGA--CUGAGCAAAGGCUCAAAAUAA-AACAAAAGCAAAUCAAGGAAUGCCGAGUGG--UUGUUGCCUAAGAAAAUUCCUUGG
..............(((-((..(((.....--.(((((....)))))..))).-.))))).......((((((((.......((--(....))).......)))))))). ( -22.24)
>DroAna_CAF1 73096 101 + 1
AGCUCGUUAAAUAAUUUAGCAUGAUGCAGAGGCUG-GCAAGGGUUAAAAAUAA-UCGAAAUGCGAAACAGGGAAUGCUACGUGGAAAUGUGGCU-------GCUCCCUGG
((((((((((.....)))))....(((........-))).)))))........-(((.....)))..((((((..(((((((....))))))).-------..)))))). ( -30.70)
>consensus
GAUUUAUAAUAUAAUAU_GUAGGAAGCAGA__CUGAGCAAAGGCUCAAAAUAA_AACAAAAGCAAAUCAAGGAAUGCCGAGUGC__UUGUGGCCAAAGAGAAUUCCUUGG
.................................(((((....)))))....................((((((((((((..........))))........)))))))). (-15.29 = -15.02 +  -0.27)

alignment

secondary structure

dotplot

Window 9

Location	12,165,948 – 12,166,053
Length	105
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	80.94
Mean single sequence MFE	-18.98
Consensus MFE	-11.75
Energy contribution	-12.50
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-1.62
Structure conservation index	0.62
SVM decision value	0.05
SVM RNA-class probability	0.557041
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12165948 105 - 27905053
CCAAGGAAUUCUCUUUGGCCAAAA--GCACUCGGCAUUCCUUGAUUUGCUUUUGAUUAUCUUUUGAGCCUUUGCUCAG--UCUGCUUCCUAC-AUAUUAUAUUAUAACUC
(((((((....))))))).(((((--(((.((((......))))..))))))))........((((((....))))))--............-................. ( -22.00)
>DroSec_CAF1 72543 104 - 1
CCAAGGAAUUCUCUUUGGCCACAA--GCGCUCGGCAUUCCUUGAUUUGCUUUUGUU-UUAUUUCGAGCCUUUGCUCAG--UCUGCUUCCUAC-AUAUUAUAUUAUAAAUC
(((((((....)))))))....((--(((((.((((...(((((...((....)).-.....)))))....)))).))--)..)))).....-................. ( -19.70)
>DroSim_CAF1 73271 104 - 1
CCAAGGAAUUCUCUUUGGCCACAA--GCGCUCGGCAUUCCUUGAUUUGCUUUUGUU-UUAUUUUGAGCCUUUGCUCAG--UCUGCUUCCUAC-AUAUUAUAUUAUAAAUC
(((((((....)))))))....((--(((..(((((..........))))......-......(((((....))))))--..))))).....-................. ( -18.70)
>DroEre_CAF1 73648 104 - 1
CCAAGGAAUUUUCUUAGGCCACAA--CCACUCGGCAUUCCUUGAUUUACUUUUGUU-UUAUUUUGAGCCUUUGCUCAG--UCUGCAUACUAC-AAAUAAUAUUAUAAAUC
.((((((((........(((....--......))))))))))).......(((((.-.(((.((((((....))))))--.....)))..))-))).............. ( -19.00)
>DroYak_CAF1 84964 104 - 1
CCAAGGAAUUUUCUUAGGCAACAA--CCACUCGGCAUUCCUUGAUUUGCUUUUGUU-UUAUUUUGAGCCUUUGCUCAG--UCUGCAUACUAC-AAAUUAUAUUAUAAAUC
.((((((((.......(....)..--((....)).))))))))(((((....(((.-.....((((((....))))))--...))).....)-))))............. ( -19.40)
>DroAna_CAF1 73096 101 - 1
CCAGGGAGC-------AGCCACAUUUCCACGUAGCAUUCCCUGUUUCGCAUUUCGA-UUAUUUUUAACCCUUGC-CAGCCUCUGCAUCAUGCUAAAUUAUUUAACGAGCU
.(((((((.-------.((.((........)).)).)))))))....((...(((.-(((..((((.(...(((-........)))....).)))).....)))))))). ( -15.10)
>consensus
CCAAGGAAUUCUCUUUGGCCACAA__CCACUCGGCAUUCCUUGAUUUGCUUUUGUU_UUAUUUUGAGCCUUUGCUCAG__UCUGCAUCCUAC_AAAUUAUAUUAUAAAUC
.((((((((........(((............)))))))))))....................(((((....)))))................................. (-11.75 = -12.50 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	12,165,982 – 12,166,089
Length	107
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	80.49
Mean single sequence MFE	-25.07
Consensus MFE	-13.19
Energy contribution	-14.05
Covariance contribution	0.86
Combinations/Pair	1.16
Mean z-score	-2.08
Structure conservation index	0.53
SVM decision value	0.06
SVM RNA-class probability	0.563506
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12165982 107 + 27905053
CAAAGGCUCAAAAGAUAAUCAAAAGCAAAUCAAGGAAUGCC----GAGUGCUUUUGGCCAAAGAGAAUUCCUUGGUUUACAGUUGUCAUUUUA-GAACUGUUUUUGUCAAAU
.............(((((........(((((((((((((((----(((....))))))........))))))))))))((((((.(......)-.))))))..))))).... ( -25.90)
>DroSec_CAF1 72577 106 + 1
CAAAGGCUCGAAAUAA-AACAAAAGCAAAUCAAGGAAUGCC----GAGCGCUUGUGGCCAAAGAGAAUUCCUUGGUUUACAGUUGUCAUUUUA-GGAGUGUUUUUGUCAAAU
(((((((.(....(((-(((((..(.(((((((((((((((----(........))))........)))))))))))).)..))))...))))-...).)))))))...... ( -24.50)
>DroSim_CAF1 73305 106 + 1
CAAAGGCUCAAAAUAA-AACAAAAGCAAAUCAAGGAAUGCC----GAGCGCUUGUGGCCAAAGAGAAUUCCUUGGUUUACAGUUGUCAUUUUA-GGAGUGUUUUUGUUAAAU
.(((.((((.......-.((((..(.(((((((((((((((----(........))))........)))))))))))).)..)))).......-.)))).)))......... ( -24.89)
>DroEre_CAF1 73682 106 + 1
CAAAGGCUCAAAAUAA-AACAAAAGUAAAUCAAGGAAUGCC----GAGUGGUUGUGGCCUAAGAAAAUUCCUUGGUUUACACUUGCCAUUUUU-GAACUGUUUUUGUCAAAU
(((((((((((((...-..(((..((((((((((((((...----....(((....))).......))))))))))))))..)))....))))-))...)))))))...... ( -29.84)
>DroYak_CAF1 84998 106 + 1
CAAAGGCUCAAAAUAA-AACAAAAGCAAAUCAAGGAAUGCC----GAGUGGUUGUUGCCUAAGAAAAUUCCUUGGUUUACACUUGCCAUUUUU-GAACUGUUUUUGUCAAAU
................-.(((((((((..(((((.((((.(----(((((......(((.(((.......))))))...)))))).)))))))-))..)))))))))..... ( -25.70)
>DroPer_CAF1 79527 104 + 1
CAGACAAUUAAAAUCG--------AUAAAACAAGGAAUACUUAACAAGUGAGGCUCGCCAAAAAUAGUUCCUUGAGUUACAAUUUUAGUUUUGCGAAAAGUUUUAGUCAAAU
..((((((((((((.(--------.(((..(((((((((((.....)))..((....)).......))))))))..)))).)))))))))..((.....))....))).... ( -19.60)
>consensus
CAAAGGCUCAAAAUAA_AACAAAAGCAAAUCAAGGAAUGCC____GAGUGCUUGUGGCCAAAGAGAAUUCCUUGGUUUACAGUUGUCAUUUUA_GAACUGUUUUUGUCAAAU
(((((((............(((..(.((((((((((((.........((.......))........)))))))))))).)..)))..............)))))))...... (-13.19 = -14.05 +   0.86)

alignment

secondary structure

dotplot

Window 1

Location	12,165,982 – 12,166,089
Length	107
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	80.49
Mean single sequence MFE	-23.98
Consensus MFE	-12.18
Energy contribution	-13.24
Covariance contribution	1.06
Combinations/Pair	1.19
Mean z-score	-2.26
Structure conservation index	0.51
SVM decision value	0.17
SVM RNA-class probability	0.618420
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12165982 107 - 27905053
AUUUGACAAAAACAGUUC-UAAAAUGACAACUGUAAACCAAGGAAUUCUCUUUGGCCAAAAGCACUC----GGCAUUCCUUGAUUUGCUUUUGAUUAUCUUUUGAGCCUUUG
......((((((((((((-......))..)))))...(((((((....))))))).((((((((.((----((......))))..))))))))......)))))........ ( -22.50)
>DroSec_CAF1 72577 106 - 1
AUUUGACAAAAACACUCC-UAAAAUGACAACUGUAAACCAAGGAAUUCUCUUUGGCCACAAGCGCUC----GGCAUUCCUUGAUUUGCUUUUGUU-UUAUUUCGAGCCUUUG
..............(((.-......(((((..(((((.((((((((.((....((((....).))).----)).)))))))).)))))..)))))-.......)))...... ( -22.34)
>DroSim_CAF1 73305 106 - 1
AUUUAACAAAAACACUCC-UAAAAUGACAACUGUAAACCAAGGAAUUCUCUUUGGCCACAAGCGCUC----GGCAUUCCUUGAUUUGCUUUUGUU-UUAUUUUGAGCCUUUG
..............(((.-......(((((..(((((.((((((((.((....((((....).))).----)).)))))))).)))))..)))))-.......)))...... ( -22.34)
>DroEre_CAF1 73682 106 - 1
AUUUGACAAAAACAGUUC-AAAAAUGGCAAGUGUAAACCAAGGAAUUUUCUUAGGCCACAACCACUC----GGCAUUCCUUGAUUUACUUUUGUU-UUAUUUUGAGCCUUUG
..............((((-((((..((((((.(((((.((((((((........(((..........----))))))))))).))))).))))))-...))))))))..... ( -27.30)
>DroYak_CAF1 84998 106 - 1
AUUUGACAAAAACAGUUC-AAAAAUGGCAAGUGUAAACCAAGGAAUUUUCUUAGGCAACAACCACUC----GGCAUUCCUUGAUUUGCUUUUGUU-UUAUUUUGAGCCUUUG
..............((((-((((..((((((.(((((.((((((((.......(....)..((....----)).)))))))).))))).))))))-...))))))))..... ( -27.40)
>DroPer_CAF1 79527 104 - 1
AUUUGACUAAAACUUUUCGCAAAACUAAAAUUGUAACUCAAGGAACUAUUUUUGGCGAGCCUCACUUGUUAAGUAUUCCUUGUUUUAU--------CGAUUUUAAUUGUCUG
..................((((...(((((((((((..(((((((.(((..((((((((.....))))))))))))))))))..))).--------)))))))).))))... ( -22.00)
>consensus
AUUUGACAAAAACAGUUC_UAAAAUGACAACUGUAAACCAAGGAAUUCUCUUUGGCCACAAGCACUC____GGCAUUCCUUGAUUUGCUUUUGUU_UUAUUUUGAGCCUUUG
.........................(((((..(((((.((((((((........(((..............))))))))))).)))))..)))))................. (-12.18 = -13.24 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:56 2006