Locus 4775

Sequence ID	3L_DroMel_CAF1
Location	13,391,423 – 13,391,541
Length	118
Max. P	0.918708

overview

Window 6

Location	13,391,423 – 13,391,541
Length	118
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	74.59
Mean single sequence MFE	-49.95
Consensus MFE	-21.58
Energy contribution	-22.81
Covariance contribution	1.23
Combinations/Pair	1.32
Mean z-score	-2.27
Structure conservation index	0.43
SVM decision value	1.12
SVM RNA-class probability	0.918708
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13391423 118 + 23771897
UGAUGCUCGGUGGCGCUUCGUGUGCCAAGUCUAGCGAUGGUUGACCAGAAGCUGGCG-AGGAUUCGGCCACUGCUACGGCUGCUGCAGCAGCAGCCAUCUGAAAUUGAUUGGGCAGGAA
.(((.((((.((((((.....))))))...(((((..(((....)))...)))))))-)).)))......(((((..((((((((...))))))))(((.......)))..)))))... ( -48.40)
>DroGri_CAF1 4369 109 + 1
UCAAGGACACGGGCGCUUCGUGCGCCAAAUCCAA----GGCUGGU-----GCUGUGU-UUGACUCGGCAACGGCAACAGCAGCCGCAGCGGCAGCCAACUGAAACUGAUUGGGUAGAAA
(((((((....(((((.....)))))...)))..----(((((.(-----((((((.-(((.((.(....)(....)))))).))))))).)))))............))))....... ( -42.90)
>DroEre_CAF1 4518 118 + 1
UAAUGCCCGGUGGCGCCUCAUGGGCCAAGUCCAGCGAUGGCUGGCCAGAAGCUGGCG-AGGAUUCGGCCACAGCUACGGCUGCUGCAGCAGCCGCCAUCUGAAAUUGAUUGGGCAGGAA
...(((((((((((((..((..((((.((((((((....))).(((((...))))).-.))))).)))).((((....)))).))..)).))))))(((.......))).))))).... ( -55.50)
>DroWil_CAF1 6706 115 + 1
UGAUCAUCUGCGUCGUUUCAUGGGCCAAAUCCAA----GGCUGGCGCUGUGCUGGCAUUGGUCUCGGCCACUGCUGCAGCAGCUGCAGCUGCAGCCAAUUGAAACUGAUUGGGUAGAAA
......((((((((((((((..((((....((((----.((..((.....))..)).))))....))))...((((((((.......))))))))....)))))).)))...))))).. ( -48.30)
>DroYak_CAF1 4038 118 + 1
UAAUGGCGGGUGGCGCCUCAUGUGCCAAGUCCAGCGAUGGCUGGCCAGAAGCUGGCG-AGGAUUCGGCCACUGCUACGGCUGCUGCAGCAGCCGCCAUCUGAAAUUGAUUGGGCAGGAA
...((((.((((((((.....)))))).(.(((((..(((....)))...)))))).-.....)).))))((((..(((((((....)))))))(((((.......)).)))))))... ( -52.30)
>DroAna_CAF1 12573 115 + 1
UGAUGUCCAGUGGCGCCUCAUGGCCCAGGUCCAGGGACGCC---CCUGAGGCUGGCG-AGGAUUCGGCCACCGCCACAGCAGCCGCGGCUGCAGCCAUAUGAAACUGGUUCGGCAGGAA
.....(((.(((((.((((...(((..(((((((((....)---)))).))))))))-))).....))))).(((...(((((....)))))(((((........))))).))).))). ( -52.30)
>consensus
UGAUGCCCGGUGGCGCCUCAUGGGCCAAGUCCAGCGAUGGCUGGCCAGAAGCUGGCG_AGGAUUCGGCCACUGCUACAGCAGCUGCAGCAGCAGCCAUCUGAAACUGAUUGGGCAGGAA
.........((((((.....((.(((.(((((.....((((.........)))).....))))).))))).)))))).(((((....))))).(((...............)))..... (-21.58 = -22.81 +   1.23)

alignment

secondary structure

dotplot

Window 7

Location	13,391,423 – 13,391,541
Length	118
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	74.59
Mean single sequence MFE	-44.97
Consensus MFE	-21.06
Energy contribution	-21.57
Covariance contribution	0.50
Combinations/Pair	1.33
Mean z-score	-1.95
Structure conservation index	0.47
SVM decision value	0.55
SVM RNA-class probability	0.777433
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13391423 118 - 23771897
UUCCUGCCCAAUCAAUUUCAGAUGGCUGCUGCUGCAGCAGCCGUAGCAGUGGCCGAAUCCU-CGCCAGCUUCUGGUCAACCAUCGCUAGACUUGGCACACGAAGCGCCACCGAGCAUCA
....(((.(............((((((((((...))))))))))....((((((((....)-))...((((((((((((...((....)).))))).)).)))))))))).).)))... ( -40.40)
>DroGri_CAF1 4369 109 - 1
UUUCUACCCAAUCAGUUUCAGUUGGCUGCCGCUGCGGCUGCUGUUGCCGUUGCCGAGUCAA-ACACAGC-----ACCAGCC----UUGGAUUUGGCGCACGAAGCGCCCGUGUCCUUGA
............((((..(((....)))..)))).(((((.(((((...(((......)))-...))))-----).)))))----..((((..(((((.....)))))...)))).... ( -35.60)
>DroEre_CAF1 4518 118 - 1
UUCCUGCCCAAUCAAUUUCAGAUGGCGGCUGCUGCAGCAGCCGUAGCUGUGGCCGAAUCCU-CGCCAGCUUCUGGCCAGCCAUCGCUGGACUUGGCCCAUGAGGCGCCACCGGGCAUUA
....(((((..........((...((((((((....))))))))..))((((((((....)-))...(((((.(((((((((....))).).)))))...)))))))))).)))))... ( -54.00)
>DroWil_CAF1 6706 115 - 1
UUUCUACCCAAUCAGUUUCAAUUGGCUGCAGCUGCAGCUGCUGCAGCAGUGGCCGAGACCAAUGCCAGCACAGCGCCAGCC----UUGGAUUUGGCCCAUGAAACGACGCAGAUGAUCA
..............((((((....((((((((.......)))))))).(.(((((((.((((.((..((.....))..)).----)))).)))))))).)))))).............. ( -43.20)
>DroYak_CAF1 4038 118 - 1
UUCCUGCCCAAUCAAUUUCAGAUGGCGGCUGCUGCAGCAGCCGUAGCAGUGGCCGAAUCCU-CGCCAGCUUCUGGCCAGCCAUCGCUGGACUUGGCACAUGAGGCGCCACCCGCCAUUA
....................((((((((((((....))))))......((((((((....)-))...(((((((((((((((....))).).)))).)).))))))))))..)))))). ( -47.50)
>DroAna_CAF1 12573 115 - 1
UUCCUGCCGAACCAGUUUCAUAUGGCUGCAGCCGCGGCUGCUGUGGCGGUGGCCGAAUCCU-CGCCAGCCUCAGG---GGCGUCCCUGGACCUGGGCCAUGAGGCGCCACUGGACAUCA
.(((.((((..(((........)))..(((((....)))))..))))(((((((((....)-))((((..(((((---(....))))))..))))(((....))))))))))))..... ( -49.10)
>consensus
UUCCUGCCCAAUCAAUUUCAGAUGGCUGCUGCUGCAGCAGCCGUAGCAGUGGCCGAAUCCU_CGCCAGCUUCUGGCCAGCCAUCGCUGGACUUGGCCCAUGAAGCGCCACCGGCCAUCA
...............((((...((((..(.(((((.......))))).)..))))........(((((.......(((((....)))))..)))))....))))............... (-21.06 = -21.57 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:54 2006