Locus 4064

Sequence ID	3L_DroMel_CAF1
Location	11,843,914 – 11,844,013
Length	99
Max. P	0.860403

overview

Window 9

Location	11,843,914 – 11,844,013
Length	99
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	74.79
Mean single sequence MFE	-27.09
Consensus MFE	-16.12
Energy contribution	-15.95
Covariance contribution	-0.17
Combinations/Pair	1.22
Mean z-score	-1.60
Structure conservation index	0.59
SVM decision value	0.65
SVM RNA-class probability	0.811025
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11843914 99 + 23771897
CUACGUCGAGGACUUACGGCUCGAGUGUCU----CCCUGG------UCCUUGAUGCCAUUCACCC----AGAAUUCCGCCCAGAAUCUGCUCCUUCGCAGUCACCC-CGCAAAA
...(((((((((((...(((......))).----....))------)))))))))..((((....----.))))...((.......((((......))))......-.)).... ( -25.24)
>DroPse_CAF1 18689 89 + 1
CCUCGUCGAGAGCUUACGGCUCGAGUGUCUGUUUCUCCGG------CCCUCGAUGCCAUUCACUC------------------UAUCUGCUCUUUCGCAGUCCCCC-AGCCCCA
........((((.....((((((((.(((.(.....).))------).))))).))).....)))------------------)..((((......))))......-....... ( -22.30)
>DroEre_CAF1 19541 98 + 1
CCACGUCGAGGGCUUACGGCUCGAGUGUCU----CUCUGG------UCCUCGAUGCCAUUCACCC----AGAAUUCCGCCCAGAAUCUGCUCUUUCGCAGUCCCUC-C-CCACA
.........((((....((((((((..((.----....))------..))))).)))((((....----.))))...)))).....((((......))))......-.-..... ( -28.00)
>DroYak_CAF1 20618 105 + 1
CCACGUCGAGGGCUUACGGCUCGAGUGUCU----CUCUGGUCCUGGUCCUCGAUGCCAUUCACCC----AGAAUUCCGCCCACAAUCUGCUCUUUCGCAGUCUCCCGC-CCCCA
...(((((((((((...((((.(((.....----))).))))..)))))))))))..((((....----.))))...((.......((((......))))......))-..... ( -31.22)
>DroAna_CAF1 18678 88 + 1
CCUCGUCGAGGGCUUACGACUCGAGUGUCU----UUCGGG------CCCUCGAUGCCAUUCAGCCCGGAAGAAUG------GGUAUCUGCUCUUUCGCAGUCCC----------
...((((((((((((..(((......))).----...)))------))))))))).......(((((......))------)))..((((......))))....---------- ( -33.50)
>DroPer_CAF1 18697 89 + 1
CCUCGUCGAGAGCUUACGGCUCGAGUGUCUGUUUCUCCGG------CCCUCGAUGCCAUUCACUC------------------UAUCUGCUCUUUCGCAGUCCCCC-AGCCCCA
........((((.....((((((((.(((.(.....).))------).))))).))).....)))------------------)..((((......))))......-....... ( -22.30)
>consensus
CCACGUCGAGGGCUUACGGCUCGAGUGUCU____CUCUGG______CCCUCGAUGCCAUUCACCC____AGAAUU______AGAAUCUGCUCUUUCGCAGUCCCCC_C_CCCCA
...(((((((((.......((.(((.........))).))......)))))))))...............................((((......)))).............. (-16.12 = -15.95 +  -0.17)

alignment

secondary structure

dotplot

Window 0

Location	11,843,914 – 11,844,013
Length	99
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	74.79
Mean single sequence MFE	-32.17
Consensus MFE	-23.21
Energy contribution	-22.85
Covariance contribution	-0.36
Combinations/Pair	1.17
Mean z-score	-1.21
Structure conservation index	0.72
SVM decision value	0.83
SVM RNA-class probability	0.860403
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11843914 99 - 23771897
UUUUGCG-GGGUGACUGCGAAGGAGCAGAUUCUGGGCGGAAUUCU----GGGUGAAUGGCAUCAAGGA------CCAGGG----AGACACUCGAGCCGUAAGUCCUCGACGUAG
...((((-(((((.((((......)))).((((((.(((....))----)((((.....)))).....------))))))----...)))))(((.(....)..)))..)))). ( -30.60)
>DroPse_CAF1 18689 89 - 1
UGGGGCU-GGGGGACUGCGAAAGAGCAGAUA------------------GAGUGAAUGGCAUCGAGGG------CCGGAGAAACAGACACUCGAGCCGUAAGCUCUCGACGAGG
.....((-.(..((((((......))))...------------------((((..(((((.(((((..------(.(......).)...))))))))))..))))))..).)). ( -29.70)
>DroEre_CAF1 19541 98 - 1
UGUGG-G-GAGGGACUGCGAAAGAGCAGAUUCUGGGCGGAAUUCU----GGGUGAAUGGCAUCGAGGA------CCAGAG----AGACACUCGAGCCGUAAGCCCUCGACGUGG
...(.-.-(((((.((((......))))......(((((..((((----.((((.....)))).))))------)).(((----.....)))..))).....)))))..).... ( -32.60)
>DroYak_CAF1 20618 105 - 1
UGGGG-GCGGGAGACUGCGAAAGAGCAGAUUGUGGGCGGAAUUCU----GGGUGAAUGGCAUCGAGGACCAGGACCAGAG----AGACACUCGAGCCGUAAGCCCUCGACGUGG
.((((-((......((((......))))......(((((..((((----((.(((......)))....)))))))).(((----.....)))..)))....))))))....... ( -35.40)
>DroAna_CAF1 18678 88 - 1
----------GGGACUGCGAAAGAGCAGAUACC------CAUUCUUCCGGGCUGAAUGGCAUCGAGGG------CCCGAA----AGACACUCGAGUCGUAAGCCCUCGACGAGG
----------(((.((((......))))...))------).(((.((.(((((..(((((.(((((..------..(...----.)...)))))))))).)))))..)).))). ( -35.00)
>DroPer_CAF1 18697 89 - 1
UGGGGCU-GGGGGACUGCGAAAGAGCAGAUA------------------GAGUGAAUGGCAUCGAGGG------CCGGAGAAACAGACACUCGAGCCGUAAGCUCUCGACGAGG
.....((-.(..((((((......))))...------------------((((..(((((.(((((..------(.(......).)...))))))))))..))))))..).)). ( -29.70)
>consensus
UGGGG_G_GGGGGACUGCGAAAGAGCAGAUACU______AAUUCU____GGGUGAAUGGCAUCGAGGA______CCAGAG____AGACACUCGAGCCGUAAGCCCUCGACGAGG
..............((((......)))).....................((((..(((((.(((((.......................))))))))))..))))......... (-23.21 = -22.85 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:41 2006