Locus 4100

Sequence ID	2R_DroMel_CAF1
Location	13,493,639 – 13,493,771
Length	132
Max. P	0.562690

overview

Window 7

Location	13,493,639 – 13,493,740
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.57
Mean single sequence MFE	-32.16
Consensus MFE	-24.42
Energy contribution	-24.75
Covariance contribution	0.34
Combinations/Pair	1.24
Mean z-score	-0.86
Structure conservation index	0.76
SVM decision value	0.04
SVM RNA-class probability	0.552854
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13493639 101 + 20766785
---------------CC----UCUACUUACCGACGACACUCAGGUGCAGGAAAAUCGAGGUGGGCGGAUGGGUGGACACCUGGCACUCGUAGACGCCGGCGUCACGUAACUGCACGAAUU
---------------..----......................((((((.......((.((.((((.(((((((..(....).)))))))...)))).)).))......))))))..... ( -32.32)
>DroVir_CAF1 3891 113 + 1
UCGACUGACU---UCUU----UUUACUUACCGACUACGCUCAAAUGUAGAAAUAUGGAUGUGGGCGGAUGUGUGGAUACUUGACACUCGUACACGCCGGCGUCACGUAGCUGCACAAAUU
..........---....----.......................(((((...(((((((((.((((.(((.(((.........))).)))...)))).))))).)))).)))))...... ( -30.40)
>DroGri_CAF1 4144 117 + 1
UCAACUAACU---UCUUGCUGUCCACUUACCGACAACACUCAAGUGCAAAAAUAUAGAUGUGGGUGGAUGCGUGGAAACUUGACACUCGUAGACGCCCGCAUCACGCAGCUGCACAAAUU
..........---...((.((((........)))).)).....(((((........((((((((((..((((.(...........).))))..)))))))))).......)))))..... ( -33.86)
>DroWil_CAF1 4133 101 + 1
---------------UC----GUUACUCACCGACAACACUCAGAUGCAAGAAUAUCGAUGUGGGCGGAUGUGUGGACACUUGACACUCAUAGACACCAGCAUCACGUUGUUGCACAAAUU
---------------..----.........(((((((.....((((......))))(((((.((.(.(((.(((.........))).)))...).)).)))))..)))))))........ ( -24.60)
>DroMoj_CAF1 4355 116 + 1
UCGGUUGCCCCCGUCGC----UCUACUUACCGACUACACUCAAGUGCAAGAAUAUGGAUGUGGGCGGAUGUGUGGACACUUGGCACUCGUAGACGCCGGCAUCACGUAGCUGCACAAAUU
(((((.((.......))----.......)))))..........(((((....(((((((((.((((.(((.(((..(....).))).)))...)))).))))).))))..)))))..... ( -35.90)
>DroPer_CAF1 47777 101 + 1
---------------CC----UCUACUUACCGACGACACUCAGGUGCAGGAAUAUCGAUGUGGGCGGAUGAGUGGACACCUGGCACUCGUAGACGCCUGCAUCACGUAGCUGCACGAAUU
---------------..----......................((((((...(((.((((..((((.(((((((..(....).)))))))...))))..))))..))).))))))..... ( -35.90)
>consensus
_______________UC____UCUACUUACCGACAACACUCAAGUGCAAGAAUAUCGAUGUGGGCGGAUGUGUGGACACUUGACACUCGUAGACGCCGGCAUCACGUAGCUGCACAAAUU
...........................................((((((.......(((((.((((.(((.(((.........))).)))...)))).)))))......))))))..... (-24.42 = -24.75 +   0.34)

alignment

secondary structure

dotplot

Window 8

Location	13,493,660 – 13,493,771
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.35
Mean single sequence MFE	-36.02
Consensus MFE	-24.51
Energy contribution	-23.73
Covariance contribution	-0.77
Combinations/Pair	1.30
Mean z-score	-1.59
Structure conservation index	0.68
SVM decision value	0.06
SVM RNA-class probability	0.562690
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13493660 111 + 20766785
CAGGUGCAGGAAAAUCGAGGUGGGCGGAUGGGUGGACACCUGGCACUCGUAGACGCCGGCGUCACGUAACUGCACGAAUUUGAUUUGCAGUGUCCAGUCCUG-UAGGC----G--AAA--
...((((((.......((.((.((((.(((((((..(....).)))))))...)))).)).))......))))))...((((.(((((((.(......))))-)))))----)--)).-- ( -39.62)
>DroVir_CAF1 3924 114 + 1
CAAAUGUAGAAAUAUGGAUGUGGGCGGAUGUGUGGAUACUUGACACUCGUACACGCCGGCGUCACGUAGCUGCACAAAUUUGAUUUGCAAUGUCCAAUCCUG-UACAA----AAGAAAA-
(((((((((...(((((((((.((((.(((.(((.........))).)))...)))).))))).)))).)))))....))))........(((.((....))-.))).----.......- ( -31.30)
>DroGri_CAF1 4181 114 + 1
CAAGUGCAAAAAUAUAGAUGUGGGUGGAUGCGUGGAAACUUGACACUCGUAGACGCCCGCAUCACGCAGCUGCACAAAUUUAAUUUGCAAUGUCCAAUCCUG-UUGAA----GACGAAA-
....((((((......((((((((((..((((.(...........).))))..))))))))))..((....))..........)))))).((((((((...)-)))..----))))...- ( -34.50)
>DroWil_CAF1 4154 113 + 1
CAGAUGCAAGAAUAUCGAUGUGGGCGGAUGUGUGGACACUUGACACUCAUAGACACCAGCAUCACGUUGUUGCACAAAUUUGAUUUGCAAUGUCCAAUCCUGGCAGAC----A--AAUA-
....(((((.(((...(((((.((.(.(((.(((.........))).)))...).)).)))))..))).)))))...(((((.(((((...(......)...))))))----)--))).- ( -28.30)
>DroMoj_CAF1 4391 118 + 1
CAAGUGCAAGAAUAUGGAUGUGGGCGGAUGUGUGGACACUUGGCACUCGUAGACGCCGGCAUCACGUAGCUGCACAAAUUUGAUUUGCAAUGUCCAAUCCUG-CAGAGCGAGUGGAAAA-
...(((((....(((((((((.((((.(((.(((..(....).))).)))...)))).))))).))))..)))))...(((.((((((..(((........)-))..)))))).)))..- ( -41.30)
>DroPer_CAF1 47798 113 + 1
CAGGUGCAGGAAUAUCGAUGUGGGCGGAUGAGUGGACACCUGGCACUCGUAGACGCCUGCAUCACGUAGCUGCACGAAUUUGAUUUGCAAUGUCCAAUCCUG-CGGGC----G--AGAAC
...((((((...(((.((((..((((.(((((((..(....).)))))))...))))..))))..))).))))))...............(((((.......-.))))----)--..... ( -41.10)
>consensus
CAAGUGCAAGAAUAUCGAUGUGGGCGGAUGUGUGGACACUUGACACUCGUAGACGCCGGCAUCACGUAGCUGCACAAAUUUGAUUUGCAAUGUCCAAUCCUG_CAGAC____G__AAAA_
....((((((......(((((.((((.(((.(((.........))).)))...)))).)))))..((....))..........))))))............................... (-24.51 = -23.73 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:51 2006