Locus 3060

Sequence ID	2L_DroMel_CAF1
Location	8,751,991 – 8,752,127
Length	136
Max. P	0.624882

overview

Window 8

Location	8,751,991 – 8,752,087
Length	96
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	84.11
Mean single sequence MFE	-29.87
Consensus MFE	-19.70
Energy contribution	-22.65
Covariance contribution	2.95
Combinations/Pair	1.25
Mean z-score	-2.67
Structure conservation index	0.66
SVM decision value	0.19
SVM RNA-class probability	0.624882
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8751991 96 + 22407834
UUUCUCGGGCUUCGGCUCUCUGAUUUCAUUU-UUUGUUUUCUUCUC-CGAAAGAGGA-------UGAGAGGGCCUCAAUUUGAUGGCCCAAAAACGAUGAAGAAU
......((((....)))).....(((((((.-(((..((((.((..-(....)..))-------.))))(((((((.....)).)))))..))).)))))))... ( -32.10)
>DroSec_CAF1 56230 96 + 1
UUUCUCGGGCUUCGGCUCUCUGAUUUCAUUU-UUUGUUUUCUUCUC-CGAAAGAGGA-------UGAGUGGGCCUCAAAUUGAUGGCCCAAAAACGAUGAAGAAU
......((((....)))).....(((((((.-(((...(((.((..-(....)..))-------.)))((((((((.....)).)))))).))).)))))))... ( -31.30)
>DroSim_CAF1 59288 96 + 1
UUUCUCGGGCUUCGGCUCUCUGAUUUCAUUU-UUUGUUUUCUUCUC-CGAAAGAGGA-------UGAGUGGGCCUCAAAUUGAUGGCCCAAAAACGAUGAAGAAU
......((((....)))).....(((((((.-(((...(((.((..-(....)..))-------.)))((((((((.....)).)))))).))).)))))))... ( -31.30)
>DroEre_CAF1 60119 95 + 1
CUUCACGGGCUUCGGCUCCCUGAUUUCAUUU-UUUGUUUUCUUCUC-CGAAGCAGGA-------UGAGUGGGCCUCAAAUUGAUGGCCCAA-AACGAUGAAGAAU
..(((.((((....)).)).)))(((((((.-(((.....(((.((-(......)))-------.)))((((((((.....)).)))))))-)).)))))))... ( -31.80)
>DroYak_CAF1 58643 103 + 1
CUUCUCGGGCUUCGGCUCUCUGAUUUCAUUU-UUUGUUUUCUUCUC-CAAUGGAGGAUUGAGGCUGAGUGGGCCUCAAAUUGAUGGCCCAAAAACGAUGAGGAAU
(((((((...((((((.(((.((...((...-..))...))(((((-(...))))))..)))))))))((((((((.....)).))))))....))).))))... ( -35.00)
>DroAna_CAF1 55690 92 + 1
UUUUUUUGGCUUCAGCUCCCUGUUUCCAUUUUUUUGUUUUCCUCUCUCCAAGGAGGC-------UCAAUCGACCUCUAUUCGAUGGACCGAAAAUGAGG------
......(((...(((....)))...)))............((((.......(((((.-------((....))))))).((((......))))...))))------ ( -17.70)
>consensus
UUUCUCGGGCUUCGGCUCUCUGAUUUCAUUU_UUUGUUUUCUUCUC_CGAAAGAGGA_______UGAGUGGGCCUCAAAUUGAUGGCCCAAAAACGAUGAAGAAU
((((..((((....))))...............((((((((((((......)))))............((((((((.....)).))))))))))))).))))... (-19.70 = -22.65 +   2.95)

alignment

secondary structure

dotplot

Window 9

Location	8,752,028 – 8,752,127
Length	99
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.70
Mean single sequence MFE	-31.83
Consensus MFE	-22.71
Energy contribution	-24.38
Covariance contribution	1.67
Combinations/Pair	1.14
Mean z-score	-1.47
Structure conservation index	0.71
SVM decision value	0.17
SVM RNA-class probability	0.617000
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8752028 99 + 22407834
UUCUUCUCCGAAAGAGGA-------UGAGAGGGCCUCAAUUUGAUGGCCCAAAA------------ACGAUGAAGAAU-AAGCCCUCAAGAGGUGUGGCAGAGUCGGCACUUUUGCGGC
(((((((((......)))-------.....(((((((.....)).)))))....------------.....)))))).-..(((....((((((((.(......).))))))))..))) ( -32.00)
>DroSec_CAF1 56267 99 + 1
UUCUUCUCCGAAAGAGGA-------UGAGUGGGCCUCAAAUUGAUGGCCCAAAA------------ACGAUGAAGAAU-AAGCCCUCAAGAGGUGUGGCAGAGUCGGCACUUUUGCGGC
(((((((((......)))-------....((((((((.....)).))))))...------------.....)))))).-..(((....((((((((.(......).))))))))..))) ( -32.70)
>DroSim_CAF1 59325 99 + 1
UUCUUCUCCGAAAGAGGA-------UGAGUGGGCCUCAAAUUGAUGGCCCAAAA------------ACGAUGAAGAAU-AAGCCCUCAAGAGGUGUGGCAGAGUCGGCACUUUUGCGGC
(((((((((......)))-------....((((((((.....)).))))))...------------.....)))))).-..(((....((((((((.(......).))))))))..))) ( -32.70)
>DroEre_CAF1 60156 98 + 1
UUCUUCUCCGAAGCAGGA-------UGAGUGGGCCUCAAAUUGAUGGCCCAA-A------------ACGAUGAAGAAU-AAGCCCUCAAGAGGUGUGGCAGAGUCGGCACUUUUGCGGC
(((((((((......)))-------....((((((((.....)).)))))).-.------------.....)))))).-..(((....((((((((.(......).))))))))..))) ( -32.70)
>DroYak_CAF1 58680 106 + 1
UUCUUCUCCAAUGGAGGAUUGAGGCUGAGUGGGCCUCAAAUUGAUGGCCCAAAA------------ACGAUGAGGAAU-AAGUCCUCAGGAGGUGUGGCAGAGUCGGCACUUUUGCGGC
...((((((...)))))).....((((..((((((((.....)).))))))...------------....((((((..-...))))))((((((((.(......).)))))))).)))) ( -36.60)
>DroPer_CAF1 71446 99 + 1
U-C------------GGC-------UCAGUCGGCCUCAAUUUGAUUUCCAAAAAAAAUGGCAAAAGAAGAUGAAGAAUCGAGCGGUCUUGAGGUGUGGCACAGUCGGCACUUUUGUGGU
(-(------------(((-------(..(((((((((((((((.....))))......(((....(..(((.....)))...).)))))))))).))))..))))))(((....))).. ( -24.30)
>consensus
UUCUUCUCCGAAAGAGGA_______UGAGUGGGCCUCAAAUUGAUGGCCCAAAA____________ACGAUGAAGAAU_AAGCCCUCAAGAGGUGUGGCAGAGUCGGCACUUUUGCGGC
(((((((((......)))...........((((((((.....)).))))))....................))))))....(((....((((((((.(......).))))))))..))) (-22.71 = -24.38 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:21 2006