Locus 4058

Sequence ID 2R_DroMel_CAF1
Location 13,388,725 – 13,388,852
Length 127
Max. P 0.858160
window6537 window6538 window6539

overview

Window 7

Location 13,388,725 – 13,388,831
Length 106
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 73.49
Mean single sequence MFE -31.27
Consensus MFE -16.08
Energy contribution -15.80
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -1.86
Structure conservation index 0.51
SVM decision value 0.82
SVM RNA-class probability 0.858160
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13388725 106 + 20766785
CGGG--AAAAAAGAGAUGCUGCGACGUCGACAGAGGCGAAAAGCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGGCUUCGAAAGUCGGA
...(--(.....(((.((((((..((((......))))....))))))(((((..((((......)))).....((((((...)))))).)))))))).....))... ( -33.50)
>DroVir_CAF1 9080 88 + 1
CCAC--GA-UUUAAGAUGCUGCAAC-----------------GCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGA
((.(--((-(((....((((((...-----------------)))))).....)))))).(((((((((((...((((((...)))))).)))))...)))))).)). ( -26.70)
>DroGri_CAF1 7831 90 + 1
CUGUGCUG-CUAAAGAUGCAGCAUC-----------------GUGGCAGCCACAAGUUGCUUUCUCGACGUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGA
.(((((((-(((..((((...))))-----------------.)))))).))))..(((((((.((((.(....((((((...)))))).....).))))))))))). ( -30.00)
>DroYak_CAF1 6382 105 + 1
CGGG--AA-AAAGAGAUGCUGCGACGUCGACAGAGGCGAAAGGCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGGCUUCGAAAGUCGGA
...(--(.-.....((.((..(...(((((.((((((((..(((....))).....))))))))))))).....((((((...)))))).)..)).)).....))... ( -35.10)
>DroMoj_CAF1 7269 80 + 1
CUUU--CG-CUGAAGAUG-------------------------CAGCAGCCACAAGUUGCCUUUUCGAUAUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGA
..((--((-((((((((.-------------------------(((((((.((..(((((.............))))).)).)))))))...))))))....)))))) ( -27.32)
>DroAna_CAF1 6696 101 + 1
CGGC--AA---ACGGAUGCUGCGA-GUUGGCAGACAC-AGCAGCAGCAGCCACAAGUUGCCUUUGCCACAUUUGCAACAGUUGCUGUUGAGUGACUUCGAAAGGCGGA
.(((--((---..((.((((((..-((((.......)-))).)))))).)).....)))))((((((...((((....(((..((....))..))).)))).)))))) ( -35.00)
>consensus
CGGC__AA_AUAAAGAUGCUGCGAC_________________GCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGA
...........................................(((((((.((..(((((.............))))).)).)))))))......((((.....)))) (-16.08 = -15.80 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,388,725 – 13,388,831
Length 106
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 73.49
Mean single sequence MFE -26.94
Consensus MFE -16.19
Energy contribution -16.90
Covariance contribution 0.71
Combinations/Pair 1.17
Mean z-score -1.48
Structure conservation index 0.60
SVM decision value 0.55
SVM RNA-class probability 0.778155
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13388725 106 - 20766785
UCCGACUUUCGAAGCCACUCAACAGCAACUGUUGCAAAUGUCGAAAAGGCAACUUGUGGCUGCUGCUUUUCGCCUCUGUCGACGUCGCAGCAUCUCUUUUUU--CCCG
..((.....)).((((((.((((((...))))))....((((.....))))....))))))(((((...((((....).)))....)))))...........--.... ( -26.90)
>DroVir_CAF1 9080 88 - 1
UCCGCUUUUCGAAGACACUCAACAGCAACUGUUGCAAAUGUCGAAAAGGCAACUUGUGGCUGCUGC-----------------GUUGCAGCAUCUUAAA-UC--GUGG
.((((..(((((.......((((((...))))))......)))))(((....)))...(((((...-----------------...)))))........-..--)))) ( -25.32)
>DroGri_CAF1 7831 90 - 1
UCCGCUUUUCGAAGACACUCAACAGCAACUGUUGCAAACGUCGAGAAAGCAACUUGUGGCUGCCAC-----------------GAUGCUGCAUCUUUAG-CAGCACAG
...(((((((((.......((((((...))))))......))))).))))...((((((...))))-----------------))((((((.......)-)))))... ( -28.32)
>DroYak_CAF1 6382 105 - 1
UCCGACUUUCGAAGCCACUCAACAGCAACUGUUGCAAAUGUCGAAAAGGCAACUUGUGGCUGCUGCCUUUCGCCUCUGUCGACGUCGCAGCAUCUCUUU-UU--CCCG
..((.....)).((((((.((((((...))))))....((((.....))))....))))))(((((...((((....).)))....)))))........-..--.... ( -26.90)
>DroMoj_CAF1 7269 80 - 1
UCCGCUUUUCGAAGACACUCAACAGCAACUGUUGCAAAUAUCGAAAAGGCAACUUGUGGCUGCUG-------------------------CAUCUUCAG-CG--AAAG
..((((....(((((....((.((((.((.(((((.............)))))..)).)))).))-------------------------..)))))))-))--.... ( -21.02)
>DroAna_CAF1 6696 101 - 1
UCCGCCUUUCGAAGUCACUCAACAGCAACUGUUGCAAAUGUGGCAAAGGCAACUUGUGGCUGCUGCUGCU-GUGUCUGCCAAC-UCGCAGCAUCCGU---UU--GCCG
...((((((....(((((.((((((...)))))).....))))))))))).......(((.((.(.((((-(((.........-.))))))).).))---..--))). ( -33.20)
>consensus
UCCGCCUUUCGAAGACACUCAACAGCAACUGUUGCAAAUGUCGAAAAGGCAACUUGUGGCUGCUGC_________________GUCGCAGCAUCUUUAG_UU__ACCG
...(((((((((.......((((((...))))))......))).)))))).......((.((((((....................)))))).))............. (-16.19 = -16.90 +   0.71)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,388,754 – 13,388,852
Length 98
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 79.37
Mean single sequence MFE -31.10
Consensus MFE -21.22
Energy contribution -22.05
Covariance contribution 0.83
Combinations/Pair 1.05
Mean z-score -1.41
Structure conservation index 0.68
SVM decision value 0.35
SVM RNA-class probability 0.701377
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13388754 98 + 20766785
AGAGGCGAAAAGCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGGCUUCGAAAGUCGGACGUGGCGA----AAGGUAU------AGCGCA
....(((....((....(((((.....(((..(((((((...(((.....)))))))))).)))((((.....)))).)))))..----...))..------..))). ( -30.00)
>DroVir_CAF1 9102 97 + 1
-----------GCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGACGUGGCAAAUCAAAGGUAGCGGAACAGCGCG
-----------...((.(((((...((((.((((((((((...((((((...)))))).)))))...)))))))))..)))))............((......)))). ( -30.80)
>DroGri_CAF1 7855 97 + 1
-----------GUGGCAGCCACAAGUUGCUUUCUCGACGUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGACGUGGCAAAUUAAAGGUAACGCAGCACCGCG
-----------...((.(((((...(((((((.((((.(....((((((...)))))).....).)))))))))))..)))))........(((........))))). ( -30.60)
>DroYak_CAF1 6410 98 + 1
AGAGGCGAAAGGCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGGCUUCGAAAGUCGGACGUGGCGA----AAGGUAU------AGCGCA
....(((.((((((((........))))))))((((((.((((....(((..((....))..))).)))).)))))).(((.(..----..).)))------..))). ( -32.20)
>DroMoj_CAF1 7284 96 + 1
------------CAGCAGCCACAAGUUGCCUUUUCGAUAUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGACGUGGCAAAUCAAAGGUAGCGGACGAACGCG
------------.....(((((...((((.(((((((......((((((...)))))).......)))))))))))..)))))............(((......))). ( -30.72)
>DroAna_CAF1 6721 98 + 1
AGACAC-AGCAGCAGCAGCCACAAGUUGCCUUUGCCACAUUUGCAACAGUUGCUGUUGAGUGACUUCGAAAGGCGGACGUGGCAAA---AAGGUAU------AGCGGA
......-.((.(((((........))))).((((((((.(((((...(((..((....))..))).(....)))))).))))))))---.......------.))... ( -32.30)
>consensus
___________GCAGCAGCCACAAGUUGCCUUUUCGACAUUUGCAACAGUUGCUGUUGAGUGUCUUCGAAAAGCGGACGUGGCAAA___AAGGUAU______AGCGCA
.................(((((...((((((((.(((......((((((...)))))).......)))))))))))..)))))......................... (-21.22 = -22.05 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:46 2006