Locus 5961

Sequence ID	2L_DroMel_CAF1
Location	16,780,877 – 16,781,157
Length	280
Max. P	0.939668

overview

Window 2

Location	16,780,877 – 16,780,997
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	91.78
Mean single sequence MFE	-42.87
Consensus MFE	-36.92
Energy contribution	-36.40
Covariance contribution	-0.52
Combinations/Pair	1.24
Mean z-score	-1.49
Structure conservation index	0.86
SVM decision value	0.13
SVM RNA-class probability	0.595770
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16780877 120 - 22407834
ACUCGUACUUGCUGCGCCACACCUGGGCCUCAGCGUUGGCCUUGCUCAGCUGGCGCUGCAGAUCGGCCUUGCCCUCAGCCUCCUCCUCAACCUGCUCGCGCAGAUUGUCCAGGUCGUGCU
.............((((...((((((((((((((((..((........))..)))))).))...(((..........)))...........((((....))))...)))))))).)))). ( -42.30)
>DroVir_CAF1 1155 120 - 1
ACUCGUACUUGCUGCGCCAGACCUGGGCCUCAGCGUUAGCCUUGCUGAGUUGACGCUGCAAAUCAGCCUUGCCCUCAGCCUCCUCCUCAACCUGCUCGCGCAAGUUGUCGAGGUCGUGCU
....((((..((((.((.((..((((....(((((((((((.....).))))))))))....)))).)).))...))))..((((..((((.(((....))).))))..))))..)))). ( -43.30)
>DroPse_CAF1 3975 120 - 1
ACUCGUACUUGCUGCGCCAGAUCUGGGACUCGGCGUUGGCCUUGCUCAAUUGACGUUGCAGAUCAGCCUUGCCCUCGGCCUCCUCCUCAACCUGUUCGCGCAGGUUGUCGAGGUCGUGCU
....((((..((...((..((((((.((((((..((((((...)).))))))).))).)))))).))...))....((((((.....((((((((....))))))))..)))))))))). ( -43.30)
>DroGri_CAF1 1263 120 - 1
AUUCGUACUUGCUGCGCCAGACCUGAGCCUCAGCGUUAGCCUUGCUGAGUUGACGCUGCAGAUCAGCCUUGCCCUCAGCCUCCUCCUCAACCUGUUCGCGCAGGUUGUCCAGGUCGUGCU
....((((..((((.((.((..((((..(((((((((((((.....).)))))))))).)).)))).)).))...))))..(((...((((((((....))))))))...)))..)))). ( -45.20)
>DroWil_CAF1 571 120 - 1
AUUCGUACUUGCUACGCCAGACCUGGGCUUCGGCGUUGGCCUUGCUCAAUUGACGCUGCAAAUCAGCCUUACCCUCAGCCUCCUCCUCAACCUGUUCGCGCAGGUUGUCGAGGUCGUGCU
....((((..(((..((.((.((.(.((....)).).)).)).)).....(((.((((.....)))).))).....)))..((((..((((((((....))))))))..))))..)))). ( -39.80)
>DroPer_CAF1 3847 120 - 1
ACUCGUACUUGCUGCGCCAGAUCUGGGACUCGGCGUUGGCCUUGCUCAAUUGACGUUGCAGAUCAGCCUUGCCCUCGGCCUCCUCCUCAACCUGUUCGCGCAGGUUGUCGAGGUCGUGCU
....((((..((...((..((((((.((((((..((((((...)).))))))).))).)))))).))...))....((((((.....((((((((....))))))))..)))))))))). ( -43.30)
>consensus
ACUCGUACUUGCUGCGCCAGACCUGGGCCUCAGCGUUGGCCUUGCUCAAUUGACGCUGCAGAUCAGCCUUGCCCUCAGCCUCCUCCUCAACCUGUUCGCGCAGGUUGUCGAGGUCGUGCU
....((((..((((.((.((..((((....(((((((((..........)))))))))....)))).)).))...))))..((((..((((((((....))))))))..))))..)))). (-36.92 = -36.40 +  -0.52)

alignment

secondary structure

dotplot

Window 3

Location	16,780,917 – 16,781,037
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-49.30
Consensus MFE	-46.21
Energy contribution	-45.97
Covariance contribution	-0.24
Combinations/Pair	1.32
Mean z-score	-1.45
Structure conservation index	0.94
SVM decision value	1.15
SVM RNA-class probability	0.922737
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16780917 120 + 22407834
GGCUGAGGGCAAGGCCGAUCUGCAGCGCCAGCUGAGCAAGGCCAACGCUGAGGCCCAGGUGUGGCGCAGCAAGUACGAGUCCGAUGGCGUUGCCCGCUCUGAGGAGCUGGAGGAAGCCAA
((((..((((((.((((...(((.((((((.(((.((..(((....)))...)).)))...)))))).)))....((....)).)))).))))))((((....)))).......)))).. ( -55.20)
>DroVir_CAF1 1195 120 + 1
GGCUGAGGGCAAGGCUGAUUUGCAGCGUCAACUCAGCAAGGCUAACGCUGAGGCCCAGGUCUGGCGCAGCAAGUACGAGUCCGAUGGUGUUGCCCGCUCUGAGGAGCUGGAGGAGGCCAA
((((..((((((.(((.((((((.((((((.((((((.........))))))((....)).)))))).)))))).((....))..))).))))))((((....)))).......)))).. ( -52.00)
>DroPse_CAF1 4015 120 + 1
GGCCGAGGGCAAGGCUGAUCUGCAACGUCAAUUGAGCAAGGCCAACGCCGAGUCCCAGAUCUGGCGCAGCAAGUACGAGUCCGAUGGUGUUGCCCGCUCUGAGGAGCUGGAGGAGGCCAA
((((..((((((.(((....(((..((((((((..((..(((....)))..))....))).)))))..)))....((....))..))).))))))((((....)))).......)))).. ( -43.90)
>DroGri_CAF1 1303 120 + 1
GGCUGAGGGCAAGGCUGAUCUGCAGCGUCAACUCAGCAAGGCUAACGCUGAGGCUCAGGUCUGGCGCAGCAAGUACGAAUCCGAUGGCGUUGCCCGCUCCGAGGAGCUAGAGGAGGCCAA
((((..((((((.(((....(((.((((((.((.(((..(((....)))...))).))...)))))).)))....((....))..))).))))))((((....)))).......)))).. ( -53.00)
>DroWil_CAF1 611 120 + 1
GGCUGAGGGUAAGGCUGAUUUGCAGCGUCAAUUGAGCAAGGCCAACGCCGAAGCCCAGGUCUGGCGUAGCAAGUACGAAUCGGACGGUGUUGCCCGUUCCGAGGAGUUGGAGGAAGCCAA
((((..((((((.((((((((((.((((((.(((.((..(((....)))...)).)))...)))))).)))))).((...))..)))).)))))).((((((....))))))..)))).. ( -47.80)
>DroPer_CAF1 3887 120 + 1
GGCCGAGGGCAAGGCUGAUCUGCAACGUCAAUUGAGCAAGGCCAACGCCGAGUCCCAGAUCUGGCGCAGCAAGUACGAGUCCGAUGGUGUUGCCCGCUCUGAGGAGCUGGAGGAGGCCAA
((((..((((((.(((....(((..((((((((..((..(((....)))..))....))).)))))..)))....((....))..))).))))))((((....)))).......)))).. ( -43.90)
>consensus
GGCUGAGGGCAAGGCUGAUCUGCAGCGUCAACUGAGCAAGGCCAACGCCGAGGCCCAGGUCUGGCGCAGCAAGUACGAGUCCGAUGGUGUUGCCCGCUCUGAGGAGCUGGAGGAGGCCAA
((((..((((((.((((...(((.((((((.(((.((..(((....)))...)).)))...)))))).)))....((....)).)))).))))))((((....)))).......)))).. (-46.21 = -45.97 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	16,781,037 – 16,781,157
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.83
Mean single sequence MFE	-50.50
Consensus MFE	-42.30
Energy contribution	-42.97
Covariance contribution	0.67
Combinations/Pair	1.15
Mean z-score	-2.60
Structure conservation index	0.84
SVM decision value	1.30
SVM RNA-class probability	0.939668
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16781037 120 - 22407834
AGCUGCAGAUCCUCCACCUCGGUGGACAGACGCUGCUUGGUCUUCUCCAGGCCAAUGCACUUCUGGUUGAGGGACUCGAUGGUCUCCUCGGCCUCGGCCAAACGGGCCUGCAGCUUCCUC
((((((((..(((((((....)))))((((.(.((((((((((.....))))))).)))).))))(((((((((((....)))).))))(((....))).)))))..))))))))..... ( -58.90)
>DroVir_CAF1 1315 120 - 1
AGCUGCAAGUCCUCGACUUCGGUGGACAGGCGCUGCUUGGUCUUCUCCAGGCCGAUGCACUUCUGGUUGAGCGACUCGAUGGUCUCCUCAGCCUCGGCAAGGCGGGCCUGCAGCUUCCUC
((((((..(((((((....))).))))((((.(((((((((((.....)))))..(((......(((((((.((((....))))..)))))))...)))))))))))))))))))..... ( -54.40)
>DroPse_CAF1 4135 120 - 1
AGCUGGAGAUCCUCGACUUCGGUGGACAGACGCUGCUUGGUCUUCUCCAGGCCAAUGCACUUCUGGUUAAGGGACUCGAUGGUCUCCUCAGCCUCGGCGAGACGGGCCUGCAGCUUGCGC
(((((.((..((((.((....)).))....(((((((((((((.....))))))).))......((((.(((((((....)))).))).))))..))))....))..)).)))))..... ( -46.70)
>DroWil_CAF1 731 120 - 1
AAUUGCAGAUCCUCCACUUCAGUGGACAGACGCUGCUUGGUCUUCUCCAGACCAAUGCACUUCUGGUUGAGGGACUCAAUGGUCUCUUCAGCCUCAGCCAAACGGGCCUGCAACUUCCUC
..((((((..(((((((....))))).....((((((((((((.....))))))).))......((((((((((((....)))).))))))))..))).....))..))))))....... ( -47.70)
>DroMoj_CAF1 1298 120 - 1
AGCUGCAAGUCCUCCACUUCGGUGGACAGGCGCUGCUUGGUCUUCUCCAGGCCGAUGCACUUCUGGUUGAGCGACUCAAUGGUCUCCUCAGCCUCGGCAAGGCGGGCCUGCAACUUCCUC
((.((((.(((((((((....))))).....(((((((((......))))))...(((......(((((((.((((....))))..)))))))...))).))))))).)))).))..... ( -48.60)
>DroPer_CAF1 4007 120 - 1
AGCUGGAGAUCCUCGACUUCGGUGGACAGACGCUGCUUGGUCUUCUCCAGGCCAAUGCACUUCUGGUUAAGGGACUCGAUGGUCUCCUCAGCCUCGGCGAGACGGGCCUGCAGCUUGCGC
(((((.((..((((.((....)).))....(((((((((((((.....))))))).))......((((.(((((((....)))).))).))))..))))....))..)).)))))..... ( -46.70)
>consensus
AGCUGCAGAUCCUCCACUUCGGUGGACAGACGCUGCUUGGUCUUCUCCAGGCCAAUGCACUUCUGGUUGAGGGACUCGAUGGUCUCCUCAGCCUCGGCAAGACGGGCCUGCAGCUUCCUC
((((((((.(((((.((....)).)).....((((((((((((.....))))))).))......((((((((((((....)))).))))))))..))).....))).))))))))..... (-42.30 = -42.97 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:37 2006