Locus 128

Sequence ID	2R_DroMel_CAF1
Location	1,389,267 – 1,389,395
Length	128
Max. P	0.711705

overview

Window 8

Location	1,389,267 – 1,389,364
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.63
Mean single sequence MFE	-32.20
Consensus MFE	-24.62
Energy contribution	-26.46
Covariance contribution	1.84
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.76
SVM decision value	0.08
SVM RNA-class probability	0.573402
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389267 97 + 20766785
UAACU-----------------GCGGCCCGAGCGACUUGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCU------UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
.....-----------------..((((....((((..(((((.....))))).....)))).....((((((------((((.....((....)))))).))))))..))))....... ( -32.00)
>DroSec_CAF1 16259 103 + 1
UAACU-----------------GAGGCCCAAGCGACUCGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCUUUGCUUUUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGUCCAUUUUCA
.....-----------------(((....((((((...(((((.....)))))...((((((....)))))).)))))))))(((((((((((((((....))).))))))))))))... ( -34.20)
>DroSim_CAF1 21007 103 + 1
UAACU-----------------GAGGCCCAAGCGACUUGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCUUUGCUUUUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
.....-----------------...((((((((((...(((((.....)))))...((((((....)))))).))))).......))))).......(((((((......)))))))... ( -33.41)
>DroEre_CAF1 14432 82 + 1
--------------------------CCCAAGUGACUUGCUGCCGACGGCAGCUUUGUGCCGAU------GCU------UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
--------------------------.(((..(((...((((((...)))))).....((....------)).------.)))..)))((....)).(((((((......)))))))... ( -27.30)
>DroYak_CAF1 12172 108 + 1
UAACUGUGCCCAAGCGUAGACUGAGGCCCAAGAGACUUGCUGCUGACGGCAGCUUUGUGCCGAU------GCU------UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
...((((((....)))))).....((((.((((.....(((((.....)))))....(((((..------(((------(((........))))))....)))))))))))))....... ( -34.10)
>consensus
UAACU_________________GAGGCCCAAGCGACUUGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCU______UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
.........................(((((........(((((.....)))))...((((((....)))))).............))))).......(((((((......)))))))... (-24.62 = -26.46 +   1.84)

alignment

secondary structure

dotplot

Window 9

Location	1,389,267 – 1,389,364
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.63
Mean single sequence MFE	-28.44
Consensus MFE	-19.56
Energy contribution	-21.44
Covariance contribution	1.88
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.69
SVM decision value	0.06
SVM RNA-class probability	0.565981
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389267 97 - 20766785
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCAAGUCGCUCGGGCCGC-----------------AGUUA
(((..(((((......))))))))(((((((......))))------))).(((....))).....((((((.(((.(.(((.....)))).))).))-----------------)))). ( -29.50)
>DroSec_CAF1 16259 103 - 1
UGAAAAUGGACAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCGAGUCGCUUGGGCCUC-----------------AGUUA
....(((((.(.....)))))).((((...(((((..(((...((......(((....)))......((((....)))).))...)))..)))))...-----------------)))). ( -26.20)
>DroSim_CAF1 21007 103 - 1
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCAAGUCGCUUGGGCCUC-----------------AGUUA
....((((((......)))))).((((...(((((..(((...........(((....)))......(((((.....)))))...)))..)))))...-----------------)))). ( -28.80)
>DroEre_CAF1 14432 82 - 1
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCGGCAGCAAGUCACUUGGG--------------------------
.........((((..((((.....(((((((......))))------)))------...))))....((((((...)))))).......)))).-------------------------- ( -25.80)
>DroYak_CAF1 12172 108 - 1
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCAGCAGCAAGUCUCUUGGGCCUCAGUCUACGCUUGGGCACAGUUA
.......((((....((((.....(((((((......))))------)))------...))))....(((((.....)))))..........))))...(((((....)))))....... ( -31.90)
>consensus
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA______AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCAAGUCGCUUGGGCCUC_________________AGUUA
(((..(((((......))))))))......(((((..(((...........(((....)))......(((((.....)))))...)))..)))))......................... (-19.56 = -21.44 +   1.88)

alignment

secondary structure

dotplot

Window 0

Location	1,389,290 – 1,389,395
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.78
Mean single sequence MFE	-37.24
Consensus MFE	-27.03
Energy contribution	-27.58
Covariance contribution	0.55
Combinations/Pair	1.07
Mean z-score	-1.80
Structure conservation index	0.73
SVM decision value	0.38
SVM RNA-class probability	0.711705
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389290 105 - 20766785
GAGUCGUCAGCGUCG---------UCAGCGCCGUCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
.........((..((---------.((((((..(((((((((((((((((......))))).....))))))))))..)).------.)).(((....)))......)))).))...)). ( -35.00)
>DroSec_CAF1 16282 111 - 1
GCGUCGUCAGCGUCG---------UCAGAGGCGUCGUGGGUGAAAAUGGACAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
((..((.((((...(---------((.((((((..((((((((((((((.(.....))))).....)))))))).((((.....))))))..)))).))))).....)))).))...)). ( -34.60)
>DroSim_CAF1 21030 111 - 1
GCGUCGUCAGCGUCG---------UCAGCGGCGUCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
((..((.((((((((---------....))))((((((((((((((((((......))))).....)))))))))((((.....))))..........)))).....)))).))...)). ( -39.20)
>DroEre_CAF1 14446 108 - 1
GCGUCGUCAGCGUCGUCAGCGUCGUCAGCGCCGCCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCGGCA
(((.(((..(((.((....)).)))..))).))).(((((((((((((((......))))).....)))))))))).....------.((------..(((((......)))))...)). ( -43.00)
>DroYak_CAF1 12212 90 - 1
GCGUCG------------------UCAGCGCGGCCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCAGCA
((..((------------------.((((...((((((((((((((((((......))))).....))))))))))..((.------...------.))))).....)))).))...)). ( -34.40)
>consensus
GCGUCGUCAGCGUCG_________UCAGCGCCGUCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA______AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
..((((...(((............((((.......(((((((((((((((......))))).....))))))))))))))............)))...)))).....((((....)))). (-27.03 = -27.58 +   0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:28:22 2006