Locus 2296

Sequence ID	2R_DroMel_CAF1
Location	8,465,378 – 8,465,585
Length	207
Max. P	0.988384

overview

Window 6

Location	8,465,378 – 8,465,477
Length	99
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	76.74
Mean single sequence MFE	-41.70
Consensus MFE	-26.26
Energy contribution	-26.97
Covariance contribution	0.70
Combinations/Pair	1.41
Mean z-score	-2.63
Structure conservation index	0.63
SVM decision value	2.12
SVM RNA-class probability	0.988384
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8465378 99 + 20766785
GUGUGUAGGCCGGAGGCCUGUCA------GGAAAUGGCAUCGCAGCCAAAUCCGGAUAUGGAUAUGGUUUGGCCGGCAGUGGCGGCGCCAUUGCCGGUGGAGAAG
.((((.(((((...)))))((((------.....))))..))))((((.(((((....))))).))))((.((((((((((((...)))))))))))).)).... ( -46.60)
>DroSec_CAF1 8945 99 + 1
GUGUGUAGGCCGGAGGCCUGUCA------GGAAAUGGCAUGGCAGCCAAAUCCGGAUAGGGAUAUGGUUUGGCCGGCAGUGGCGGCGCCAUGGCCAGUGGCGAAG
........((((..((((.((((------.....))))((((((((((.((((......)))).)))))..((((.(...).)))))))))))))..)))).... ( -43.10)
>DroEre_CAF1 10418 99 + 1
GUGUGUAAGCCGGAGGCCUGUCA------GGAAAUGGCAUGGCAGCCAAAUUCGGAUAGGGAUAUGGCUUGGCUGACAGUGGCGGCGCCAUUGCCGGUGGAGAAG
.....(((((((....((((((.------(((..((((......))))..))).))))))....)))))))((((.(((((((...))))))).))))....... ( -38.80)
>DroYak_CAF1 9533 99 + 1
GUGUGUAAGCCGGAGGCCUGUCA------GGAAAUGGCAUAGCAGCCAAGUGCGGAUAGGGGUAUGGUUUGGCUGGCAGUGGCGGCGCCAUUGCCGGUGGAGAUG
.....(((((((....((((((.------(.(..((((......))))..).).))))))....)))))))((((((((((((...))))))))))))....... ( -43.00)
>DroAna_CAF1 9739 105 + 1
GCGUAUAAGCCGGCGGUCUGUCCUUGAUUGGAAAAGGCAUAGCAGCUAGGUCCGGAUAGGGAUAGGGCUUGAGGGCCACCGGAGGAGCGGGUGGUGGUGGCGAGG
........((((.((.((((((((((.(((((...(((......)))...))))).)))))))))).)......((((((.(.....).))))))).)))).... ( -42.30)
>DroPer_CAF1 8997 105 + 1
GCGUAUAAGCUGGUGGCCUGUCGGUCAUUGGGAACGGCAUUGCGGCCAGAUGCGGAUACUUAUACGGCUUCUCAACCACAGGCGGAGCGGGUGUAGGUGGAGACG
.(((((...(((((.((.(((((.((.....)).)))))..)).))))))))))...((((((((.(((((.(........).)))))..))))))))(....). ( -36.40)
>consensus
GUGUGUAAGCCGGAGGCCUGUCA______GGAAAUGGCAUAGCAGCCAAAUCCGGAUAGGGAUAUGGCUUGGCCGGCAGUGGCGGCGCCAUUGCCGGUGGAGAAG
.....(((((((....((((((.......(((..((((......))))..))).))))))....)))))))...(((((((((...))))))))).......... (-26.26 = -26.97 +   0.70)

alignment

secondary structure

dotplot

Window 7

Location	8,465,378 – 8,465,477
Length	99
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.74
Mean single sequence MFE	-28.45
Consensus MFE	-13.41
Energy contribution	-14.38
Covariance contribution	0.97
Combinations/Pair	1.31
Mean z-score	-1.96
Structure conservation index	0.47
SVM decision value	0.20
SVM RNA-class probability	0.628568
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8465378 99 - 20766785
CUUCUCCACCGGCAAUGGCGCCGCCACUGCCGGCCAAACCAUAUCCAUAUCCGGAUUUGGCUGCGAUGCCAUUUCC------UGACAGGCCUCCGGCCUACACAC
........((((((.((((...)))).))))))................((.(((..((((......))))..)))------.)).(((((...)))))...... ( -36.50)
>DroSec_CAF1 8945 99 - 1
CUUCGCCACUGGCCAUGGCGCCGCCACUGCCGGCCAAACCAUAUCCCUAUCCGGAUUUGGCUGCCAUGCCAUUUCC------UGACAGGCCUCCGGCCUACACAC
....(((.(((((..((((...))))..)))))............(((.((.(((..((((......))))..)))------.)).))).....)))........ ( -34.50)
>DroEre_CAF1 10418 99 - 1
CUUCUCCACCGGCAAUGGCGCCGCCACUGUCAGCCAAGCCAUAUCCCUAUCCGAAUUUGGCUGCCAUGCCAUUUCC------UGACAGGCCUCCGGCUUACACAC
..........((((.((((...)))).))))....(((((.....(((.((.(((..((((......)))).))).------.)).))).....)))))...... ( -27.10)
>DroYak_CAF1 9533 99 - 1
CAUCUCCACCGGCAAUGGCGCCGCCACUGCCAGCCAAACCAUACCCCUAUCCGCACUUGGCUGCUAUGCCAUUUCC------UGACAGGCCUCCGGCUUACACAC
..........((((.((((...)))).))))((((..........(((.((.(....((((......))))....)------.)).))).....))))....... ( -24.26)
>DroAna_CAF1 9739 105 - 1
CCUCGCCACCACCACCCGCUCCUCCGGUGGCCCUCAAGCCCUAUCCCUAUCCGGACCUAGCUGCUAUGCCUUUUCCAAUCAAGGACAGACCGCCGGCUUAUACGC
....((((((...............))))))....(((((...(((......)))....((.(((...((((........))))..)).).)).)))))...... ( -22.76)
>DroPer_CAF1 8997 105 - 1
CGUCUCCACCUACACCCGCUCCGCCUGUGGUUGAGAAGCCGUAUAAGUAUCCGCAUCUGGCCGCAAUGCCGUUCCCAAUGACCGACAGGCCACCAGCUUAUACGC
..((((.(((.(((..((...))..)))))).))))...(((((((((..........(((......)))........((.((....)).))...))))))))). ( -25.60)
>consensus
CUUCUCCACCGGCAAUGGCGCCGCCACUGCCAGCCAAACCAUAUCCCUAUCCGGAUUUGGCUGCCAUGCCAUUUCC______UGACAGGCCUCCGGCUUACACAC
..........((((.((((...)))).))))..........................((((......))))...............((((.....))))...... (-13.41 = -14.38 +   0.97)

alignment

secondary structure

dotplot

Window 8

Location	8,465,412 – 8,465,511
Length	99
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.62
Mean single sequence MFE	-41.95
Consensus MFE	-27.33
Energy contribution	-27.75
Covariance contribution	0.42
Combinations/Pair	1.47
Mean z-score	-1.50
Structure conservation index	0.65
SVM decision value	0.54
SVM RNA-class probability	0.775320
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8465412 99 + 20766785
CGCAGCCAAAUCC---GGAUAUGGAUAUGGUUUGGCCGGCAGUGGCGGC---GCCAUUGCCGGUGGAGAAGGUGGUGGCGGCGGCGAUAGUGGACACUUUUCCGG
((.(((((.((((---(....))))).)))))))((((((((((((...---))))))))))))(((((((((.((.((....)).)).....)).))))))).. ( -44.70)
>DroSec_CAF1 8979 99 + 1
GGCAGCCAAAUCC---GGAUAGGGAUAUGGUUUGGCCGGCAGUGGCGGC---GCCAUGGCCAGUGGCGAAGGUGGUGGCGGCGGCGUUAGUGGACACUUUUCCGG
(((.((((.((((---......)))).))))...)))..((.(((((.(---(((...((((.(.((....)).))))))))).))))).))............. ( -41.50)
>DroEre_CAF1 10452 99 + 1
GGCAGCCAAAUUC---GGAUAGGGAUAUGGCUUGGCUGACAGUGGCGGC---GCCAUUGCCGGUGGAGAAGGUGGUGGCGGCGGCGAGAGCGGACACUUUUCCGG
((((((((.((((---......)))).)))))..)))...((((.((.(---(((((..((.........))..)))))).))((....))...))))....... ( -40.50)
>DroYak_CAF1 9567 99 + 1
AGCAGCCAAGUGC---GGAUAGGGGUAUGGUUUGGCUGGCAGUGGCGGC---GCCAUUGCCGGUGGAGAUGGGGGUGGCGGCGGUGUGAGCGGACACUUUUCCGG
.((.((((.((((---........))))..(((.((((((((((((...---)))))))))))).))).......)))).))........((((......)))). ( -38.10)
>DroMoj_CAF1 14050 105 + 1
CGUAUCAAAGUCCGGCGGAUAGGGAUACGGCUUGCGUGCCACUGGCGGCUUAGCCAGCACCGCUGGUGGCGGUGGCGGUGGCGGUGUCGGUGGACACUUCUCGGC
((((((...((((...))))...))))))......((((((((((((.(...((((.(.((((((....)))))).).))))).))))))))).)))........ ( -46.90)
>DroAna_CAF1 9779 99 + 1
AGCAGCUAGGUCC---GGAUAGGGAUAGGGCUUGAGGGCCACCGGAGGA---GCGGGUGGUGGUGGCGAGGGAGGUGGCGGCGGGGUGAGUGGGCACUUCUCCGG
.((((((..((((---......))))..)))).....((((((.(....---.).))))))....))(.((((((((.(.((.......)).).))))))))).. ( -40.00)
>consensus
AGCAGCCAAAUCC___GGAUAGGGAUAUGGCUUGGCUGGCAGUGGCGGC___GCCAUUGCCGGUGGAGAAGGUGGUGGCGGCGGCGUGAGUGGACACUUUUCCGG
...(((((.((((.........)))).)))))..((((((((((((......))))))))))))......((.((((.(.((.......)).).))))...)).. (-27.33 = -27.75 +   0.42)

alignment

secondary structure

dotplot

Window 9

Location	8,465,443 – 8,465,548
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.80
Mean single sequence MFE	-52.13
Consensus MFE	-31.53
Energy contribution	-32.53
Covariance contribution	1.00
Combinations/Pair	1.34
Mean z-score	-2.03
Structure conservation index	0.60
SVM decision value	1.09
SVM RNA-class probability	0.913603
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8465443 105 + 20766785
GCCGGCAGUGGCGGC---GCCAUUGCCGGUGGAGAAGGUGGUGGCGGCGGCGAUAGUGGACACUUUUCCGGCUCCUCUAGUGGAGGAGGUGGUGGCGGCAGCUGCCAG
((((((((((((...---))))))))))))......((..((.((.((.((.((..((((......)))).((((((.....)))))))).)).)).)).))..)).. ( -55.80)
>DroSec_CAF1 9010 105 + 1
GCCGGCAGUGGCGGC---GCCAUGGCCAGUGGCGAAGGUGGUGGCGGCGGCGUUAGUGGACACUUUUCCGGCUCCUCUAGUGGAGGAGGUGGUGGCGGCAGCUGCCAG
((((.((.(((((.(---(((...((((.(.((....)).))))))))).))))).)).........(((.((((((.....)))))).)))))))(((....))).. ( -51.70)
>DroEre_CAF1 10483 105 + 1
GCUGACAGUGGCGGC---GCCAUUGCCGGUGGAGAAGGUGGUGGCGGCGGCGAGAGCGGACACUUUUCCGGCUGCUCUAGUGGAGGAGGUGGUGGUGGCAGCUGCCAG
........(((((((---(((((..((.........))..))))).((.((....))...((((...(((.((.(((.....))).)).))).)))))).))))))). ( -50.30)
>DroYak_CAF1 9598 102 + 1
GCUGGCAGUGGCGGC---GCCAUUGCCGGUGGAGAUGGGGGUGGCGGCGGUGUGAGCGGACACUUUUCCGGCUCCUCCAGUGGAGGAGGUG---GUGGCAGUUGCCAG
((((((((((((...---)))))))))))).........((..((.(((((((......)))))...(((.(((((((...))))))).))---)..)).))..)).. ( -51.70)
>DroMoj_CAF1 14084 108 + 1
CGUGCCACUGGCGGCUUAGCCAGCACCGCUGGUGGCGGUGGCGGUGGCGGUGUCGGUGGACACUUCUCGGCCAACUCCAAUGCAUCCGGUGGUGGGGGCAGCUGCCAG
.......(((((((((..(((..(((((((((..(((.(((.(.((((((((((....)))))).....)))).).))).)))..)))))))))..)))))))))))) ( -59.90)
>DroPer_CAF1 9068 102 + 1
UCAACCACAGGCGGA---GCGGGUGUAGGUGGAGACGGGGGCGGCGGCGGUGUUAGUGGACACUUCUCCAGCUCCUCCGGCGGCGG---CGGCGGUGGCAGCUGCCAG
.........(.((((---(.((((......(....)((((((....))((((((....)))))).)))).))))))))).)(((((---(.((....)).)))))).. ( -43.40)
>consensus
GCUGGCAGUGGCGGC___GCCAUUGCCGGUGGAGAAGGUGGUGGCGGCGGCGUUAGUGGACACUUUUCCGGCUCCUCCAGUGGAGGAGGUGGUGGUGGCAGCUGCCAG
((((.(((((((......))))))).)))).........((((((.((.((.....((((......)))).(((((((...)))))))......)).)).)))))).. (-31.53 = -32.53 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	8,465,477 – 8,465,585
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	82.01
Mean single sequence MFE	-49.12
Consensus MFE	-32.03
Energy contribution	-34.95
Covariance contribution	2.92
Combinations/Pair	1.15
Mean z-score	-1.50
Structure conservation index	0.65
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8465477 108 + 20766785
GUGGUGGCGGCGGCGAUAGUGGACACUUUUCCGGCUCCUCUAGUGGAGGAGGUGGUGGCGGCAGCUGCCAGCCAGGAACCACUCUGCGCUCCUCCACCAAAAUCUCAU
.((((((.((.((((..(((((........(((.((((((.....)))))).)))(((((((....))).))))....)))))...)))))).))))))......... ( -52.90)
>DroSec_CAF1 9044 108 + 1
GUGGUGGCGGCGGCGUUAGUGGACACUUUUCCGGCUCCUCUAGUGGAGGAGGUGGUGGCGGCAGCUGCCAGCCAGGAACCACUCUGCGCUCCUCCACCAAAAUUUCGU
.((((((.((.(((((.(((((........(((.((((((.....)))))).)))(((((((....))).))))....)))))..))))))).))))))......... ( -54.50)
>DroEre_CAF1 10517 108 + 1
GUGGUGGCGGCGGCGAGAGCGGACACUUUUCCGGCUGCUCUAGUGGAGGAGGUGGUGGUGGCAGCUGCCAGCCAGGUACCACUCGACGCUCCUCCACCAAUAUCUCGU
.((((((.((.(((.(((((((.(........).))))))).((.(((..((((.(((((((....)))).)))..)))).))).))))))).))))))......... ( -47.40)
>DroYak_CAF1 9632 105 + 1
GGGGUGGCGGCGGUGUGAGCGGACACUUUUCCGGCUCCUCCAGUGGAGGAGGUG---GUGGCAGUUGCCAGCCGGGCACCACUCUGCGCUCCUCCACCAAAAUCUCGU
..(((((.((.((((((((.((..((((..(((.(((((((...))))))).))---)..).)))((((.....)))))).))).))))))).))))).......... ( -46.90)
>DroAna_CAF1 9844 105 + 1
GAGGUGGCGGCGGGGUGAGUGGGCACUUCUCCGGCUCCUCUAGAGGCG---GCGGCGGUGGCAGACUCCAUCCGGCAACCACACGUCGCUCCUCCACCAGAAUCUCAU
((((.(.(((.((((((......)))))).))).).))))..((((.(---((((((((((..(.((......)))..)))).))))))))))).............. ( -44.60)
>DroPer_CAF1 9102 105 + 1
GGGGCGGCGGCGGUGUUAGUGGACACUUCUCCAGCUCCUCCGGCGGCGG---CGGCGGUGGCAGCUGCCAGCCGGGCACAACCCUCCUCUCCUCCACGAGGAUCUCGU
(((((((.((.((((((....)))))).)))).)))))(((((((((((---(.((....)).)))))).))))))........(((((........)))))...... ( -48.40)
>consensus
GUGGUGGCGGCGGCGUGAGUGGACACUUUUCCGGCUCCUCUAGUGGAGGAGGUGGUGGUGGCAGCUGCCAGCCAGGAACCACUCUGCGCUCCUCCACCAAAAUCUCGU
..(((((.((.((((..(((((........(((.(((((((...))))))).)))(((((((....))).))))....)))))...)))))).))))).......... (-32.03 = -34.95 +   2.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:06 2006