Locus 1061

Sequence ID	2R_DroMel_CAF1
Location	4,327,985 – 4,328,159
Length	174
Max. P	0.955470

overview

Window 3

Location	4,327,985 – 4,328,089
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.30
Mean single sequence MFE	-37.13
Consensus MFE	-19.87
Energy contribution	-20.23
Covariance contribution	0.36
Combinations/Pair	1.13
Mean z-score	-2.58
Structure conservation index	0.54
SVM decision value	0.14
SVM RNA-class probability	0.604481
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4327985 104 - 20766785
UCCAAG---------------GAGCUCGGGGCUGACUUUAAGGUCAGCCGCCUCACAUAACAAAUGUCGGGCGAUAUUUCC-CAGGAAUGCCGGCAGAUGAAAACUUUCCUCAUUUGCAC
(((..(---------------(((.((..((((((((....))))))))((((.((((.....)))).))))))...))))-..)))......((((((((.........)))))))).. ( -39.30)
>DroPse_CAF1 26630 114 - 1
CCCAAGACGGCUGCGUCCGUGGAG--UG-GACUGGCUUUAAGGUCAG---CUUCACAUAACAAAUGCCGGGCGAUAUUUCUUCGGGAAAGCUGAGAGAUGAAAACUUUCCUCAUUUGCAC
.(((.((((....))))..))).(--((-((((((((....))))))---.)))))....((((((...(((....((((....)))).)))(((((.(....))))))..))))))... ( -32.80)
>DroSec_CAF1 7232 104 - 1
CCCAAG---------------GAGCUCAGGGCUGACUUUAAGGUCAGCCGCCUCACAUAACAAAUGUCGGGCGAUAUUUCC-CGGGAAUGCCGGCAGAUGAAAACUUUCCUCAUUUGCAC
(((..(---------------(((.((..((((((((....))))))))((((.((((.....)))).))))))...))))-.))).......((((((((.........)))))))).. ( -39.90)
>DroPer_CAF1 26469 114 - 1
CCCAAGACGGCUGGGUCCGUGGAG--UG-GACUGGCUUUAAGGUCAG---CUUCACAUAACAAAUGCCGGGCGAUAUUUCUUGGGGAAAGCUGAGAGAUGAAAACUUUCCUCAUUUGCAC
(((((((((.((((.((....))(--((-((((((((....))))))---.)))))..........)))).)).....)))))))....((((((.((.........))))))...)).. ( -36.80)
>DroEre_CAF1 6503 100 - 1
CCCAAG---------------GAGCUCG-GGCUGACUUUAAGGUCAG---CCUCACAUAACAAAUGUGGGGCGAUAUUUCC-CGGGAAUGCCGGCAGAUGAAAACUUUCCUCAUUUGCAC
.....(---------------(..((((-((.(((((....)))))(---((((((((.....))))))))).......))-))))....)).((((((((.........)))))))).. ( -40.50)
>DroYak_CAF1 7358 100 - 1
CCCUUG---------------GAGCUCG-GGCUGACUUUAAGGUCAG---CCUCACAUAACAAAUGUCGGGCGAUAUUUCC-CGGGAAUGCCGGCAGAUAAAAACUUUCCUCAUUUGCAC
.....(---------------(((((((-((((((((....))))))---))..((((.....)))))))))..(((((.(-(((.....)))).))))).......))).......... ( -33.50)
>consensus
CCCAAG_______________GAGCUCG_GGCUGACUUUAAGGUCAG___CCUCACAUAACAAAUGUCGGGCGAUAUUUCC_CGGGAAUGCCGGCAGAUGAAAACUUUCCUCAUUUGCAC
(((..................(((.......((((((....))))))....))).(((.....)))..)))((.((((((....)))))).))((((((((.........)))))))).. (-19.87 = -20.23 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	4,328,064 – 4,328,159
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	70.14
Mean single sequence MFE	-33.18
Consensus MFE	-13.21
Energy contribution	-16.61
Covariance contribution	3.40
Combinations/Pair	1.12
Mean z-score	-2.11
Structure conservation index	0.40
SVM decision value	1.45
SVM RNA-class probability	0.955470
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4328064 95 + 20766785
UAAAGUCAGCCCCGAGCUC---------------CUUGGA--UCGCACUCCUCGUGUGACCGGGCUC-CUGAUGGCUCAACUUACAUCACAGCAAGCCAUCCGGCCAGCUCCC-------
...(((..(((..((((((---------------...((.--((((((.....))))))))))))))-..(((((((...((........))..))))))).)))..)))...------- ( -32.50)
>DroPse_CAF1 26707 115 + 1
UAAAGCCAGUC-CA--CUCCACGGACGCAGCCGUCUUGGGGCCCGCACUUCGGGUGUGACUGUGUCCCGCAAUGGCUCAAGCAGCAUU--GGCUAGCCACCCGCCCUUCCGCCACCCGCC
...((((((((-(.--......))))((((((((..((((((((((((.....)))))...).))))))..))))))...)).....)--)))).((.....((......)).....)). ( -37.50)
>DroSec_CAF1 7311 95 + 1
UAAAGUCAGCCCUGAGCUC---------------CUUGGG--UCGCACUCCUCGUGUGACCGGGCUC-CUGAUGGCUCAACUUACAUCACAGCCAGCCAUCCGGCCAGCUCCC-------
...(((..(((..((((((---------------....((--((((((.....))))))))))))))-..(((((((...((........))..))))))).)))..)))...------- ( -35.60)
>DroEre_CAF1 6579 81 + 1
UAAAGUCAGCC-CGAGCUC---------------CUUGGG--UCGCACUCCUCGUGUGACCGGACUC-CCGAUGGCUCAACUUACAUC-------------CGACCAGCUCCC-------
...........-.(((((.---------------.(((((--((((((.....))))))))((....-))((((..........))))-------------)))..)))))..------- ( -25.30)
>DroYak_CAF1 7434 94 + 1
UAAAGUCAGCC-CGAGCUC---------------CAAGGG--UCGCACUCCUCGUGUGACCAGGCUC-CUGAUGGCUCAACUUACAUCACAGGCAGCCAUUCGGCCAGCUCCC-------
...........-.((((((---------------(...((--((((((.....)))))))).(((((-((((((..........))))..))).))))....))..)))))..------- ( -35.00)
>consensus
UAAAGUCAGCC_CGAGCUC_______________CUUGGG__UCGCACUCCUCGUGUGACCGGGCUC_CUGAUGGCUCAACUUACAUCACAGCCAGCCAUCCGGCCAGCUCCC_______
.............(((((...................((...((((((.....)))))))).((((....(((((((.................))))))).)))))))))......... (-13.21 = -16.61 +   3.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:25 2006