Locus 246

Sequence ID	2R_DroMel_CAF1
Location	1,630,951 – 1,631,088
Length	137
Max. P	0.940216

overview

Window 7

Location	1,630,951 – 1,631,064
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.70
Mean single sequence MFE	-43.87
Consensus MFE	-29.02
Energy contribution	-30.30
Covariance contribution	1.28
Combinations/Pair	1.26
Mean z-score	-1.99
Structure conservation index	0.66
SVM decision value	1.11
SVM RNA-class probability	0.917138
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1630951 113 + 20766785
CUGGCAGCCGAUAGUCGCCGUUUUGUGGCCGUUUUCCGUUCACU-UAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGU----C--UAUGUGGAGAAGAGCUAUCUCCUGGU
(..((.((((.((((((.((((..(((..((.....))..))).-.)))).))))))((((((((...)))))))))))).))..).----.--.....(((((.......))))).... ( -45.50)
>DroPse_CAF1 42527 115 + 1
UUGAUAGCCGACGGUCGCCGUUUUGUGGCCGUUAUCCUUACACGCUCUCUCUGGCUGGGGACAAGCGACUUGUCCCUGGCAAAAUGUUACAAAAAAAUUGAAGGAAAGGCUUGGC-----
.....(((((((((((((......))))))))).(((((..............((..((((((((...))))))))..)).........(((.....))))))))..))))....----- ( -43.40)
>DroSec_CAF1 16767 115 + 1
CUGGCAGCCGAUAGUCGCCGUUUUGUGGCCGUUUUCCGUUCACU-UAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGU----CAAUAUGUGGAGAAGAGCUAUCUCCUGGU
(..((.((((.((((((.((((..(((..((.....))..))).-.)))).))))))((((((((...)))))))))))).))..).----........(((((.......))))).... ( -45.50)
>DroSim_CAF1 15204 115 + 1
CUGGCAGCCGAUAGUCGCCGUUUUGUGGCCGUUUUCCGUUCACU-UAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGU----CAAUAUGUGGAGAAGAGCUAUCUCCUGGU
(..((.((((.((((((.((((..(((..((.....))..))).-.)))).))))))((((((((...)))))))))))).))..).----........(((((.......))))).... ( -45.50)
>DroEre_CAF1 19267 115 + 1
CUGGUAGCUAAUGGUCGCCGUUUUGGGGCCGUUUUCCGUUCACU-UAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGU----CAAUAUGUGGAGAAGAACUAUCUCCUGGU
..((.....(((((((.((.....)))))))))..))(((.(((-.(((....((..((((((((...))))))))..)).))))))----.)))....(((((.......))))).... ( -39.90)
>DroPer_CAF1 37083 115 + 1
UUGAUAGCCGACGGUCGCCGUUUUGUGGCCGUUAUCCUUACACGCUCUCUCUGGCUGGGGACAAGCGACUUGUCCCUGGCAAAAUGUUACAAAAAAAUUGAAGGAAAGGCUUGGC-----
.....(((((((((((((......))))))))).(((((..............((..((((((((...))))))))..)).........(((.....))))))))..))))....----- ( -43.40)
>consensus
CUGGCAGCCGAUAGUCGCCGUUUUGUGGCCGUUUUCCGUUCACU_UAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGU____CAAUAUGUGGAGAAGAGCUAUCUCCUGGU
(..((.((((.((((((.((((..(((..((.....))..)))...)))).))))))((((((((...)))))))))))).))..).............(((((.......))))).... (-29.02 = -30.30 +   1.28)

alignment

secondary structure

dotplot

Window 8

Location	1,630,951 – 1,631,064
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.70
Mean single sequence MFE	-37.03
Consensus MFE	-23.70
Energy contribution	-24.57
Covariance contribution	0.86
Combinations/Pair	1.15
Mean z-score	-2.23
Structure conservation index	0.64
SVM decision value	1.31
SVM RNA-class probability	0.940216
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1630951 113 - 20766785
ACCAGGAGAUAGCUCUUCUCCACAUA--G----ACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUA-AGUGAACGGAAAACGGCCACAAAACGGCGACUAUCGGCUGCCAG
....(((((.......))))).....--.----.....(((...((((((((...))))))))(((((((((((.-.(((..((.....))..))).....))))....))))))).))) ( -39.80)
>DroPse_CAF1 42527 115 - 1
-----GCCAAGCCUUUCCUUCAAUUUUUUUGUAACAUUUUGCCAGGGACAAGUCGCUUGUCCCCAGCCAGAGAGAGCGUGUAAGGAUAACGGCCACAAAACGGCGACCGUCGGCUAUCAA
-----(((..(((..(((((((.((((((((.........((..((((((((...))))))))..))))))))))...)).)))))....)))........(((....))))))...... ( -35.80)
>DroSec_CAF1 16767 115 - 1
ACCAGGAGAUAGCUCUUCUCCACAUAUUG----ACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUA-AGUGAACGGAAAACGGCCACAAAACGGCGACUAUCGGCUGCCAG
....(((((.......)))))........----.....(((...((((((((...))))))))(((((((((((.-.(((..((.....))..))).....))))....))))))).))) ( -39.80)
>DroSim_CAF1 15204 115 - 1
ACCAGGAGAUAGCUCUUCUCCACAUAUUG----ACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUA-AGUGAACGGAAAACGGCCACAAAACGGCGACUAUCGGCUGCCAG
....(((((.......)))))........----.....(((...((((((((...))))))))(((((((((((.-.(((..((.....))..))).....))))....))))))).))) ( -39.80)
>DroEre_CAF1 19267 115 - 1
ACCAGGAGAUAGUUCUUCUCCACAUAUUG----ACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUA-AGUGAACGGAAAACGGCCCCAAAACGGCGACCAUUAGCUACCAG
....(((((.......)))))........----.....(.((..((((((((...))))))))..)).)..((((-(.((..((.....))(((.......)))...)))))))...... ( -31.20)
>DroPer_CAF1 37083 115 - 1
-----GCCAAGCCUUUCCUUCAAUUUUUUUGUAACAUUUUGCCAGGGACAAGUCGCUUGUCCCCAGCCAGAGAGAGCGUGUAAGGAUAACGGCCACAAAACGGCGACCGUCGGCUAUCAA
-----(((..(((..(((((((.((((((((.........((..((((((((...))))))))..))))))))))...)).)))))....)))........(((....))))))...... ( -35.80)
>consensus
ACCAGGAGAUAGCUCUUCUCCACAUAUUG____ACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUA_AGUGAACGGAAAACGGCCACAAAACGGCGACCAUCGGCUACCAG
....(((((.......))))).................(((...((((((((...)))))))).((((((.......((.........)).(((.......))).....))))))..))) (-23.70 = -24.57 +   0.86)

alignment

secondary structure

dotplot

Window 9

Location	1,630,991 – 1,631,088
Length	97
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	95.96
Mean single sequence MFE	-36.58
Consensus MFE	-32.54
Energy contribution	-33.10
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.89
SVM decision value	0.87
SVM RNA-class probability	0.870674
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1630991 97 + 20766785
CACUUAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGUC--UAUGUGGAGAAGAGCUAUCUCCUGGUAAGAUCCUCUGUUGCUUUACGAAG
.....((((.(.((..((((((((...))))))))..))((..((((--(((..(((((.......)))))..)).)))))..))).))))........ ( -34.40)
>DroSec_CAF1 16807 99 + 1
CACUUAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGUCAAUAUGUGGAGAAGAGCUAUCUCCUGGUAAGAUCCUCUGUUGCUGUGUGAAU
(((.(((((.(.((..((((((((...))))))))..))((..((((..(((..(((((.......)))))..))).))))..))).))))).)))... ( -38.40)
>DroSim_CAF1 15244 99 + 1
CACUUAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGUCAAUAUGUGGAGAAGAGCUAUCUCCUGGUAAGAUCCUCUGUUGCAGUGCGAAG
((((((((....((..((((((((...))))))))..))((..((((..(((..(((((.......)))))..))).))))..)))))).))))..... ( -35.70)
>DroEre_CAF1 19307 99 + 1
CACUUAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGUCAAUAUGUGGAGAAGAACUAUCUCCUGGUAAGAUCCUCUGUUGCUGUGCGAAG
..(((.(((.((((.(((((((((...)))))))))(((((..((((..(((..(((((.......)))))..))).))))..)))))))))))).))) ( -37.80)
>consensus
CACUUAGCGUCGGCUGGGGACAAGGAGCUUGUCCCUGGCAGUUGGUCAAUAUGUGGAGAAGAGCUAUCUCCUGGUAAGAUCCUCUGUUGCUGUGCGAAG
......(((.((((.(((((((((...)))))))))(((((..((((..(((..(((((.......)))))..))).))))..)))))))))))).... (-32.54 = -33.10 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	1,630,991 – 1,631,088
Length	97
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	95.96
Mean single sequence MFE	-27.79
Consensus MFE	-25.84
Energy contribution	-25.72
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.81
Structure conservation index	0.93
SVM decision value	0.70
SVM RNA-class probability	0.826371
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1630991 97 - 20766785
CUUCGUAAAGCAACAGAGGAUCUUACCAGGAGAUAGCUCUUCUCCACAUA--GACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUAAGUG
........(((......((.(((.....(((((.......)))))....)--))))..(.((..((((((((...))))))))..)).)..)))..... ( -28.10)
>DroSec_CAF1 16807 99 - 1
AUUCACACAGCAACAGAGGAUCUUACCAGGAGAUAGCUCUUCUCCACAUAUUGACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUAAGUG
...(((..(((......((.((......(((((.......))))).......))))..(.((..((((((((...))))))))..)).)..)))..))) ( -28.22)
>DroSim_CAF1 15244 99 - 1
CUUCGCACUGCAACAGAGGAUCUUACCAGGAGAUAGCUCUUCUCCACAUAUUGACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUAAGUG
.....((((((......((.((......(((((.......))))).......))))..(.((..((((((((...))))))))..)).)..))..)))) ( -27.02)
>DroEre_CAF1 19307 99 - 1
CUUCGCACAGCAACAGAGGAUCUUACCAGGAGAUAGUUCUUCUCCACAUAUUGACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUAAGUG
...(((..(((......((.((......(((((.......))))).......))))..(.((..((((((((...))))))))..)).)..)))..))) ( -27.82)
>consensus
CUUCGCACAGCAACAGAGGAUCUUACCAGGAGAUAGCUCUUCUCCACAUAUUGACCAACUGCCAGGGACAAGCUCCUUGUCCCCAGCCGACGCUAAGUG
...(((..(((......((.((......(((((.......))))).......))))..(.((..((((((((...))))))))..)).)..)))..))) (-25.84 = -25.72 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:27 2006