Locus 2557

Sequence ID	3R_DroMel_CAF1
Location	6,932,465 – 6,932,687
Length	222
Max. P	0.995013

overview

Window 0

Location	6,932,465 – 6,932,585
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.21
Mean single sequence MFE	-42.82
Consensus MFE	-32.52
Energy contribution	-32.48
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.92
Structure conservation index	0.76
SVM decision value	0.01
SVM RNA-class probability	0.539191
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6932465 120 - 27905053
GUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUGCCAUGGGCGCAGCUUCAAGGGGGCAGCUAGCUCACUGGCGGGGCUCUACAUUGAUUUCGCAUUCAUUGGCUGAUGAAGAG
....((((((((.(((((..((((((((.....))))(((((...)))))..))))...(((((.(((((....)))))...)))))))))).)))).))))(((((....))))).... ( -39.20)
>DroSec_CAF1 81109 115 - 1
GUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUGCCAGGGGCGCAGCUUCUAGGGGGCAG----CUCACUGGCG-GGCUCUACAUUGAUUUCGCAUUCAUUGGCUGAUGAAGAG
......((.(((((..((((((((..((.(((...((.((((((((((...((((.....)))).)----))).))))))-.)).))).))...))))))))))))).)).......... ( -41.10)
>DroSim_CAF1 82400 115 - 1
GUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUGCCAGGGGCGCAGCUUGAAGGGGGCAG----CUCACUGGCG-GGCUCUACAUUGAUUUCGCAUUCAUUGGCUGAUGAAGAG
......((.(((((..((((((((..((.(((...((.((((((((((((..((....))..)).)----))).))))))-.)).))).))...))))))))))))).)).......... ( -39.70)
>DroEre_CAF1 83010 115 - 1
GUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCCUGCCAGGGGCGCUGCUUCAAGGGGGCAG----CUCUCUGGCA-GGCUCUACAUUGAUUUCGCAUUCAUUGGCUGAUGAAGAG
......((.(((((..((((((((..((.(((...((((((((((((.(((((((.....))))))----))))))))))-))).))).))...))))))))))))).)).......... ( -52.30)
>DroYak_CAF1 83126 115 - 1
GUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUGCCAGGGGCGUAGCUUCAAGGGGGCAG----CUCUCUGGCA-GGCUCUACAUUGAUUUCGCAUUCAUUGGCUGAUGAAGAG
......((.(((((..((((((((..((.(((...((.((((((((((...((((.....)))).)----).))))))))-.)).))).))...))))))))))))).)).......... ( -41.80)
>consensus
GUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUGCCAGGGGCGCAGCUUCAAGGGGGCAG____CUCACUGGCG_GGCUCUACAUUGAUUUCGCAUUCAUUGGCUGAUGAAGAG
....((((((((.((((((.(((.((((.....)))).(((((((((....((((.....))))......))).))))))...))))))))).)))).))))(((((....))))).... (-32.52 = -32.48 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	6,932,545 – 6,932,661
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	98.10
Mean single sequence MFE	-43.46
Consensus MFE	-42.92
Energy contribution	-43.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.99
SVM decision value	2.53
SVM RNA-class probability	0.995013
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6932545 116 - 27905053
GCGGGCCAGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGUGUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUG
((((((...))))...(((((..((((.((((..((((((((.....(((....))).........))))))))..))))(..((......))..)..))))..)))))..))... ( -44.64)
>DroSec_CAF1 81184 116 - 1
GCGGGCCUGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGUGUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUG
((((((...))))...(((((..((((.((((..((((((((.....(((....))).........))))))))..))))(..((......))..)..))))..)))))..))... ( -44.64)
>DroSim_CAF1 82475 116 - 1
GCGGGCCAGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGUGUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUG
((((((...))))...(((((..((((.((((..((((((((.....(((....))).........))))))))..))))(..((......))..)..))))..)))))..))... ( -44.64)
>DroEre_CAF1 83085 116 - 1
GCGGACCAUGCCCGAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGUGUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCCUG
.(((.......)))..(((((..((((.((((..((((((((.....(((....))).........))))))))..))))(..((......))..)..))))..)))))....... ( -38.74)
>DroYak_CAF1 83201 116 - 1
GCGGGCCAUGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGUGUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUG
((((((...))))...(((((..((((.((((..((((((((.....(((....))).........))))))))..))))(..((......))..)..))))..)))))..))... ( -44.64)
>consensus
GCGGGCCAGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGUGUAGGUGCAAAUGGAUGUGCGAGGGUAUUUGGUAUGCGUG
((((((...))))...(((((..((((.((((..((((((((.....(((....))).........))))))))..))))(..((......))..)..))))..)))))..))... (-42.92 = -43.12 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	6,932,585 – 6,932,687
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	98.24
Mean single sequence MFE	-37.66
Consensus MFE	-33.86
Energy contribution	-33.90
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.90
SVM decision value	-0.00
SVM RNA-class probability	0.533073
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6932585 102 + 27905053
ACGAUCCUGCUUAUUUAGUGGCCAUGGCCGAUGGACAGGACCUGGUAGUGGGUCGUUGGUUUUGGGCCUGGCCCGCUUUGUUUGCUCAUCGCCACAGACAGU
.((((...((..((..((((((((.((((.(....((((((((......))))).)))....).))))))).)))))..))..))..))))........... ( -36.60)
>DroSec_CAF1 81224 102 + 1
ACGAUCCUGCUUAUUUAGUGGCCAUGGCCGAUGGACAGGACCUGGUAGUGGGUCGUUGGUUUUGGGCCAGGCCCGCUUUGUUUGCUCAUCGCCACAGACAGU
.((((...((..((..(((((((.(((((.(....((((((((......))))).)))....).))))))).)))))..))..))..))))........... ( -36.60)
>DroSim_CAF1 82515 102 + 1
ACGAUCCUGCUUAUUUAGUGGCCAUGGCCGAUGGACAGGACCUGGUAGUGGGUCGUUGGUUUUGGGCCUGGCCCGCUUUGUUUGCUCAUCGCCACAGACAGU
.((((...((..((..((((((((.((((.(....((((((((......))))).)))....).))))))).)))))..))..))..))))........... ( -36.60)
>DroEre_CAF1 83125 102 + 1
ACGAUCCUGCUUAUUUAGUGGCCAUGGCCGAUGGACAGGACCUGGUAGUGGGUCGUUGGUUUCGGGCAUGGUCCGCUUUGUUUGCUCAUCGCCACAGACAGU
.((((...((..((..((((((((((.((((....((((((((......))))).)))...)))).))))).)))))..))..))..))))........... ( -40.30)
>DroYak_CAF1 83241 102 + 1
ACGAUCCUGCUUAUUUAGUGGCCAUGGCCGAUGGACAGGACCUGGUAGUGGGUCGUUGGUUUUGGGCAUGGCCCGCUUUGUUUGCUCAUCGCCACAGACAGU
.((((...((..((..((((((((((.((((....((((((((......))))).)))...)))).))))).)))))..))..))..))))........... ( -38.20)
>consensus
ACGAUCCUGCUUAUUUAGUGGCCAUGGCCGAUGGACAGGACCUGGUAGUGGGUCGUUGGUUUUGGGCCUGGCCCGCUUUGUUUGCUCAUCGCCACAGACAGU
.((((...((..((..((((((((.(.((((....((((((((......))))).)))...)))).).))).)))))..))..))..))))........... (-33.86 = -33.90 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	6,932,585 – 6,932,687
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	98.24
Mean single sequence MFE	-30.41
Consensus MFE	-28.66
Energy contribution	-28.86
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.94
SVM decision value	0.74
SVM RNA-class probability	0.837889
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6932585 102 - 27905053
ACUGUCUGUGGCGAUGAGCAAACAAAGCGGGCCAGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGU
((.((((...((((((..((........((((...)))).........((((........)))).))..))))(((....))).........)).)))).)) ( -30.20)
>DroSec_CAF1 81224 102 - 1
ACUGUCUGUGGCGAUGAGCAAACAAAGCGGGCCUGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGU
.((((..(((((.(((.((.......((((((((((.....................))))).)))))......))))).))))).......))))...... ( -32.32)
>DroSim_CAF1 82515 102 - 1
ACUGUCUGUGGCGAUGAGCAAACAAAGCGGGCCAGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGU
((.((((...((((((..((........((((...)))).........((((........)))).))..))))(((....))).........)).)))).)) ( -30.20)
>DroEre_CAF1 83125 102 - 1
ACUGUCUGUGGCGAUGAGCAAACAAAGCGGACCAUGCCCGAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGU
.(((..(((.((.....))......((.((.(((((.((((.......((((........)))).......)))).))))))).))..)))..)))...... ( -29.14)
>DroYak_CAF1 83241 102 - 1
ACUGUCUGUGGCGAUGAGCAAACAAAGCGGGCCAUGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGU
((.((((...((((((..((........((((...)))).........((((........)))).))..))))(((....))).........)).)))).)) ( -30.20)
>consensus
ACUGUCUGUGGCGAUGAGCAAACAAAGCGGGCCAGGCCCAAAACCAACGACCCACUACCAGGUCCUGUCCAUCGGCCAUGGCCACUAAAUAAGCAGGAUCGU
((.((((...((((((..((........((((...)))).........((((........)))).))..))))(((....))).........)).)))).)) (-28.66 = -28.86 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:14 2006