Locus 1404

Sequence ID	2R_DroMel_CAF1
Location	5,429,725 – 5,429,823
Length	98
Max. P	0.757415

overview

Window 7

Location	5,429,725 – 5,429,823
Length	98
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-31.10
Consensus MFE	-20.07
Energy contribution	-20.23
Covariance contribution	0.17
Combinations/Pair	1.27
Mean z-score	-1.14
Structure conservation index	0.65
SVM decision value	0.03
SVM RNA-class probability	0.547274
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5429725 98 + 20766785
--------AAAGGUGCGAGAAUC-AAAUGCAUACCUGGAGUGGGUGUGAUGUGGCCCGUGGACGAGGGACGCGAGUUGGGCAUGCCCAGGUGAUGUUGCUGCGCGUG
--------....((((.((.(((-(....(((((((.....))))))).((((.(((........))).))))..(((((....))))).))))....))))))... ( -32.50)
>DroVir_CAF1 35199 95 + 1
-------GUAAUAGUUGAAUUU--GUGGACAUACCUGGAGUCGGUGUUAUGUGGCCGGUGGACGAGGGCCGCGAAUUGGACAUGACCAGAUG---CUGUUGCGAAUG
-------((((((((.....(.--.((..((((((.......)))))..(((((((..........)))))))....)..))..)......)---)))))))..... ( -27.90)
>DroGri_CAF1 33935 102 + 1
UUUUGGCGAAAUAUUUGAGAAA--UUGGACAUACCUGGUGUGGGUGUUAUAUGGCCGGUGGAUGAGGGCCGUGAAUUGGGCAUGACCAGGUG---CUGUUGCGAAUG
..((.((((....((..(....--)..))(((((((((((((...(((.(((((((..........))))))))))....))).))))))))---.)))))).)).. ( -29.90)
>DroSec_CAF1 18463 98 + 1
--------AAAGGUUCGAGAAUC-AAAAGCAUACCUGGAGUGGGUGUGAUGUGGCCCGUGGACGAGGGCCGCGAGUUGGACAUGACCAGGUGAUGUUGCUGCGCGUG
--------...((((....))))-...(((((((((((.(((..((...((((((((........))))))))...))..)))..)))))))....))))....... ( -33.30)
>DroYak_CAF1 19406 98 + 1
--------AAAGGUGCAGGAAUC-AAAACCAUACCUGGAGUGGGUGUGAUGUGGCCCGUGGAUGAGGGUCGCGAGUUGGGCAUGACCAGGUGGUGCUGCUGCGCGUG
--------....((((((....(-((...(((((((.....))))))).((((((((........))))))))..)))(((((.((...)).))))).))))))... ( -38.60)
>DroMoj_CAF1 25082 95 + 1
-------A-AAUAA-AGAAUUUCGCUGGACAUACCUGGUGUCGGUGUUAUGUGACCUGUUGAGGAGGGCCGCGAAUUGGGCAUGACCAGAUG---CUGUUGCGAAUG
-------.-.....-.....(((((.((.....)).((((((.(.(((((((..((..(((.((....)).)))...)))))))))).))))---))...))))).. ( -24.40)
>consensus
________AAAGAUUCGAGAAUC_AAAGACAUACCUGGAGUGGGUGUGAUGUGGCCCGUGGACGAGGGCCGCGAAUUGGGCAUGACCAGGUG___CUGCUGCGAAUG
...........................(((((((((((.....((.(..((((((((........))))))))....).))....)))))))....))))....... (-20.07 = -20.23 +   0.17)

alignment

secondary structure

dotplot

Window 8

Location	5,429,725 – 5,429,823
Length	98
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	75.00
Mean single sequence MFE	-20.11
Consensus MFE	-12.51
Energy contribution	-12.53
Covariance contribution	0.03
Combinations/Pair	1.25
Mean z-score	-1.44
Structure conservation index	0.62
SVM decision value	0.49
SVM RNA-class probability	0.757415
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5429725 98 - 20766785
CACGCGCAGCAACAUCACCUGGGCAUGCCCAACUCGCGUCCCUCGUCCACGGGCCACAUCACACCCACUCCAGGUAUGCAUUU-GAUUCUCGCACCUUU--------
...(((.((....((((..((((....))))....((((.(((.(.....(((..........)))...).))).))))...)-))).)))))......-------- ( -21.60)
>DroVir_CAF1 35199 95 - 1
CAUUCGCAACAG---CAUCUGGUCAUGUCCAAUUCGCGGCCCUCGUCCACCGGCCACAUAACACCGACUCCAGGUAUGUCCAC--AAAUUCAACUAUUAC-------
........(((.---.((((((....(((......(.((((..........)))).)........))).)))))).)))....--...............------- ( -16.14)
>DroGri_CAF1 33935 102 - 1
CAUUCGCAACAG---CACCUGGUCAUGCCCAAUUCACGGCCCUCAUCCACCGGCCAUAUAACACCCACACCAGGUAUGUCCAA--UUUCUCAAAUAUUUCGCCAAAA
........(((.---.(((((((..............((((..........)))).............))))))).)))....--...................... ( -16.93)
>DroSec_CAF1 18463 98 - 1
CACGCGCAGCAACAUCACCUGGUCAUGUCCAACUCGCGGCCCUCGUCCACGGGCCACAUCACACCCACUCCAGGUAUGCUUUU-GAUUCUCGAACCUUU--------
..((.(...((((((.((((((...((........(.(((((........))))).)........))..)))))))))...))-)...).)).......-------- ( -22.39)
>DroYak_CAF1 19406 98 - 1
CACGCGCAGCAGCACCACCUGGUCAUGCCCAACUCGCGACCCUCAUCCACGGGCCACAUCACACCCACUCCAGGUAUGGUUUU-GAUUCCUGCACCUUU--------
.....(((((((.(((((((((....((.......))(.(((........))).)..............))))))..))).))-)....))))......-------- ( -22.40)
>DroMoj_CAF1 25082 95 - 1
CAUUCGCAACAG---CAUCUGGUCAUGCCCAAUUCGCGGCCCUCCUCAACAGGUCACAUAACACCGACACCAGGUAUGUCCAGCGAAAUUCU-UUAUU-U-------
..(((((.(((.---.(((((((...((((.....).)))...........(((........)))...))))))).)))...))))).....-.....-.------- ( -21.20)
>consensus
CACGCGCAACAG___CACCUGGUCAUGCCCAACUCGCGGCCCUCGUCCACGGGCCACAUAACACCCACUCCAGGUAUGUCCAU_GAUUCUCGAACAUUU________
................((((((....((.......))((((..........))))..............))))))................................ (-12.51 = -12.53 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:02 2006