Locus 1028

Sequence ID	2L_DroMel_CAF1
Location	2,913,130 – 2,913,310
Length	180
Max. P	0.940207

overview

Window 0

Location	2,913,130 – 2,913,233
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.92
Mean single sequence MFE	-34.26
Consensus MFE	-24.67
Energy contribution	-24.63
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.72
SVM decision value	0.03
SVM RNA-class probability	0.547924
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2913130 103 + 22407834
GUUCAAAUGUCAUCGC---------------CGUCGUAGCUAGCCAA-AUUGCCGGGCAUGCCCACAAAAUACCUUCAUGGAACCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG-CU
..............((---------------(((((((((.......-......(((....)))............(((((.......)))))))))))))...((....))...))-). ( -30.30)
>DroSec_CAF1 31633 103 + 1
GUUCAAAUGUCAUCGG---------------CGUCGUAGCUAGCCAA-AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAAGCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG-CU
.......((((.((((---------------.((((((((((.....-.((((.(((....)))........((.....))..))))....))))))))))....)))).))))...-.. ( -35.40)
>DroSim_CAF1 32238 103 + 1
GUUCAAAUGUCAUCGG---------------CGUCGUAGCUAGCCAA-AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAAGCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG-AU
..((...((((.((((---------------.((((((((((.....-.((((.(((....)))........((.....))..))))....))))))))))....)))).))))..)-). ( -35.90)
>DroEre_CAF1 32464 119 + 1
GUUCAAAUGUCAUCGUAGUCGUAGUCGUAGUCGUCGUAGCCAGCCAAAAUGGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAACCAAGCCAUGGCUACGGAAUUUCCGAGGACACGG-CU
......(((.(......).)))((((((.(((.((((((((((((.....))).((((((.........))))))....((.......)).)))))))((.....)))).)))))))-)) ( -39.40)
>DroYak_CAF1 32617 101 + 1
GUUCAAAUGUCAUCGUG------------------GUAGCCAACCAA-AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAACCAAGCCAUGGCUACGGAAUUUCCGAGGACACGGACU
((((...((((.((...------------------(((((((.....-.(((..((((((.........)))))).)))((.......)).)))))))((.....)))).)))).)))). ( -30.30)
>consensus
GUUCAAAUGUCAUCGG_______________CGUCGUAGCUAGCCAA_AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAACCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG_CU
.......((((.((.....................(((((((..........((((((((.........))))))....))..........)))))))((.....)))).))))...... (-24.67 = -24.63 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	2,913,155 – 2,913,273
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.17
Mean single sequence MFE	-36.42
Consensus MFE	-22.36
Energy contribution	-22.36
Covariance contribution	-0.00
Combinations/Pair	1.07
Mean z-score	-2.09
Structure conservation index	0.61
SVM decision value	0.68
SVM RNA-class probability	0.820359
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2913155 118 + 22407834
UAGCCAA-AUUGCCGGGCAUGCCCACAAAAUACCUUCAUGGAACCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG-CUUGCUUCGCUUCGCUUUGGUUUUGGUUUGCUUCGGUUUGGU
..(((((-...((((((....)))................(((.(((((((..((((.(((.....(((((.((...-..)))))))....))).))))..))))))).))))))))))) ( -38.00)
>DroSec_CAF1 31658 102 + 1
UAGCCAA-AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAAGCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG-CUUGCUUCGCUUUGGUUUG----------------GUUUGGU
..(((((-((((((((((((.........))))))..(((((((((((((.((.((.(((.....))).)).)).))-)))))))).))).)))..)----------------))))))) ( -42.60)
>DroSim_CAF1 32263 113 + 1
UAGCCAA-AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAAGCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG-AUUGCUUCGCUUUGGUUUGGUUCAG-----UUUUGGUUUGGU
..(((((-...(((((((((.........)))))).....(((.(((((((.(((...((((..((((......)))-).))))..))).))))))).)))..-----....)))))))) ( -41.20)
>DroEre_CAF1 32504 93 + 1
CAGCCAAAAUGGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAACCAAGCCAUGGCUACGGAAUUUCCGAGGACACGG-CUUGCUUUG--------------------------CUUUGGU
..(((.....))).((((((.........))))))((((((...((((((.((.((.(((.....))).)).)).))-)))).....--------------------------)))))). ( -31.70)
>DroYak_CAF1 32639 93 + 1
CAACCAA-AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAACCAAGCCAUGGCUACGGAAUUUCCGAGGACACGGACUUGCUUUG--------------------------GUUUGGU
..(((((-((....((((((.........)))))).(((((...((((((.((.((.(((.....))).)).)).)).)))))))))--------------------------))))))) ( -28.60)
>consensus
UAGCCAA_AUUGCCGGGCAUGCCCACAAAAUGCCUUCAAGGAACCAAGCCAUGGCUACGGCAUUUCCGAGGACACGG_CUUGCUUCGCUU_G_UUUG________________GUUUGGU
..(((((.......((((((.........)))))).....(((.((((((.((.((.(((.....))).)).)).)).)))).))).............................))))) (-22.36 = -22.36 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	2,913,155 – 2,913,273
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.17
Mean single sequence MFE	-36.00
Consensus MFE	-25.24
Energy contribution	-25.72
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.22
Structure conservation index	0.70
SVM decision value	1.28
SVM RNA-class probability	0.940207
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2913155 118 - 22407834
ACCAAACCGAAGCAAACCAAAACCAAAGCGAAGCGAAGCAAG-CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGGUUCCAUGAAGGUAUUUUGUGGGCAUGCCCGGCAAU-UUGGCUA
.((((((((..(((..(((..(((...((...))(((.((((-(((((.(..(((.....)))..).))))))))).)))......)))......)))...))).)))...)-))))... ( -37.90)
>DroSec_CAF1 31658 102 - 1
ACCAAAC----------------CAAACCAAAGCGAAGCAAG-CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGCUUCCUUGAAGGCAUUUUGUGGGCAUGCCCGGCAAU-UUGGCUA
.......----------------.......(((.((((((((-(((((.(..(((.....)))..).))))))))))))))))..((.((..(((((((....))).)))).-.)).)). ( -42.40)
>DroSim_CAF1 32263 113 - 1
ACCAAACCAAAA-----CUGAACCAAACCAAAGCGAAGCAAU-CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGCUUCCUUGAAGGCAUUUUGUGGGCAUGCCCGGCAAU-UUGGCUA
............-----.............(((.(((((((.-(((((.(..(((.....)))..).))))).))))))))))..((.((..(((((((....))).)))).-.)).)). ( -35.80)
>DroEre_CAF1 32504 93 - 1
ACCAAAG--------------------------CAAAGCAAG-CCGUGUCCUCGGAAAUUCCGUAGCCAUGGCUUGGUUCCUUGAAGGCAUUUUGUGGGCAUGCCCGGCCAUUUUGGCUG
......(--------------------------(((((((((-(((((.(..(((.....)))..).)))))))))...((.....))..))))))(((....)))((((.....)))). ( -33.90)
>DroYak_CAF1 32639 93 - 1
ACCAAAC--------------------------CAAAGCAAGUCCGUGUCCUCGGAAAUUCCGUAGCCAUGGCUUGGUUCCUUGAAGGCAUUUUGUGGGCAUGCCCGGCAAU-UUGGUUG
....(((--------------------------((((.((((.(((((.(..(((.....)))..).)))))))))................(((((((....))).)))))-)))))). ( -30.00)
>consensus
ACCAAAC________________CAAA_C_AAGCGAAGCAAG_CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGGUUCCUUGAAGGCAUUUUGUGGGCAUGCCCGGCAAU_UUGGCUA
..................................(((.((((.(((((.(..(((.....)))..).))))))))).))).....((.((..(((((((....))).))))...)).)). (-25.24 = -25.72 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	2,913,194 – 2,913,310
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.42
Mean single sequence MFE	-26.33
Consensus MFE	-17.50
Energy contribution	-18.10
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.66
SVM decision value	-0.02
SVM RNA-class probability	0.524699
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2913194 116 - 22407834
UUUAUUUUAGCCC---CUGUGCUAAUUCCUGGUCUAAGUAACCAAACCGAAGCAAACCAAAACCAAAGCGAAGCGAAGCAAG-CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGGUUC
......(((((..---....)))))(((.((((.......)))).......((..............)))))..(((.((((-(((((.(..(((.....)))..).))))))))).))) ( -28.54)
>DroSec_CAF1 31697 100 - 1
UUUAUUUUAGCCC---CUGUGCUAAUUCCUGGUCUAAGUAACCAAAC----------------CAAACCAAAGCGAAGCAAG-CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGCUUC
......(((((..---....)))))....((((.......))))...----------------...........((((((((-(((((.(..(((.....)))..).))))))))))))) ( -32.70)
>DroSim_CAF1 32302 111 - 1
UUUAUUUUAGUCC---CUGUGCUAAUUCCUGGUCUAAGUAACCAAACCAAAA-----CUGAACCAAACCAAAGCGAAGCAAU-CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGCUUC
.............---....(((......((((...(((............)-----))..))))......)))(((((((.-(((((.(..(((.....)))..).))))).))))))) ( -26.60)
>DroEre_CAF1 32544 90 - 1
UUGAUUAUGCCCC---CUGUGCUAAUUCCUGGUCUAAGUAACCAAAG--------------------------CAAAGCAAG-CCGUGUCCUCGGAAAUUCCGUAGCCAUGGCUUGGUUC
.............---((.((((......((((.......)))).))--------------------------)).))((((-(((((.(..(((.....)))..).))))))))).... ( -24.70)
>DroYak_CAF1 32678 94 - 1
UUUAUAAUUCCCCCUCCUGUGCUAAUUCCUGGUCUAAGUAACCAAAC--------------------------CAAAGCAAGUCCGUGUCCUCGGAAAUUCCGUAGCCAUGGCUUGGUUC
............((......(((......((((.......))))...--------------------------...)))(((.(((((.(..(((.....)))..).))))))))))... ( -19.10)
>consensus
UUUAUUUUAGCCC___CUGUGCUAAUUCCUGGUCUAAGUAACCAAAC________________CAAA_C_AAGCGAAGCAAG_CCGUGUCCUCGGAAAUGCCGUAGCCAUGGCUUGGUUC
.............................((((.......))))..............................(((.((((.(((((.(..(((.....)))..).))))))))).))) (-17.50 = -18.10 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:29 2006