Locus 4101

Sequence ID	3R_DroMel_CAF1
Location	11,200,387 – 11,200,484
Length	97
Max. P	0.958682

overview

Window 7

Location	11,200,387 – 11,200,484
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.58
Mean single sequence MFE	-31.44
Consensus MFE	-26.12
Energy contribution	-26.32
Covariance contribution	0.20
Combinations/Pair	1.20
Mean z-score	-2.68
Structure conservation index	0.83
SVM decision value	1.49
SVM RNA-class probability	0.958682
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11200387 97 + 27905053
-GGCAGUUGGGUAGAAAUCAGAGUGC--GCCA-----GCAGCGCGACCGAGAUGACCCACUUUUCGGUAUUCGCACUGAG---------ACCCAACUGCUACUACCCA------CAGAAA
-(((((((((((.....((((..(((--....-----)))(((..(((((((.........)))))))...))).)))).---------)))))))))))........------...... ( -39.60)
>DroVir_CAF1 2299 102 + 1
-GGCAGUUGGAUAGAAAUCAGAGUACAAACCAGCCGAGCAGCGCGACCGAGAUGACCCACUUUUCGGUUUUCGCAUUCAA---------AACUAACUGCUA-UACCAA------AUAA-A
-(((((((((...(....).((((........((...)).(((.((((((((.........))))))))..)))))))..---------..))))))))).-......------....-. ( -26.20)
>DroGri_CAF1 2760 104 + 1
AGGCAGUUGGAUAGAAAUCAGAGUACAAACCAGCCGAGCAGCGCGACCGAGAUGACCCACUUUUCGGUUUUCGCAUUCAA---------AUCCAACUGCUG-UACAAA------AUAAAA
.(((((((((((.(....).((((........((...)).(((.((((((((.........))))))))..)))))))..---------))))))))))).-......------...... ( -31.20)
>DroMoj_CAF1 2856 102 + 1
-GGCAGUUGGAUAGAAAUCAGAGUACAAACCAGCCGAGCAGCGCGACCGAGAUGACCCACUUUUCGGUUUUCGCAUUCAA---------AUCCAACUGCUA-UACAAA------AUAA-A
-(((((((((((.(....).((((........((...)).(((.((((((((.........))))))))..)))))))..---------))))))))))).-......------....-. ( -30.90)
>DroAna_CAF1 2618 106 + 1
----GGUUGGGCAGAAAUCAGAGUACAAACCAGCCGAGCAGCGCGACCGAGAUGACCCACUUUUCGGUUUUCGCACUGGA---------ACCCAACUGCU-CUACCAAACUAAAUUAAAU
----((((((...................))))))((((((.((((((((((.........))))))...))))..(((.---------..))).)))))-).................. ( -29.91)
>DroPer_CAF1 7443 110 + 1
-GGCAGUCGGGCAGAAAUCAGAGUACAAACCAGCCGAGCAGCGCGACCGAGAUGACCCACUUUUCGGUUUUCGCACCAACAGAACAAGAGCCCAACUGCU---AUCCG------AAAAAA
-((((((.((((....................((...)).(((.((((((((.........))))))))..)))...............)))).))))))---.....------...... ( -30.80)
>consensus
_GGCAGUUGGAUAGAAAUCAGAGUACAAACCAGCCGAGCAGCGCGACCGAGAUGACCCACUUUUCGGUUUUCGCACUCAA_________ACCCAACUGCUA_UACCAA______AUAAAA
.(((((((((((........(.((....))).........(((.((((((((.........))))))))..)))...............))))))))))).................... (-26.12 = -26.32 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	11,200,387 – 11,200,484
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.58
Mean single sequence MFE	-34.09
Consensus MFE	-26.41
Energy contribution	-27.44
Covariance contribution	1.03
Combinations/Pair	1.19
Mean z-score	-1.85
Structure conservation index	0.77
SVM decision value	0.87
SVM RNA-class probability	0.869915
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11200387 97 - 27905053
UUUCUG------UGGGUAGUAGCAGUUGGGU---------CUCAGUGCGAAUACCGAAAAGUGGGUCAUCUCGGUCGCGCUGC-----UGGC--GCACUCUGAUUUCUACCCAACUGCC-
......------(((((((...(((.((.((---------(.((((((((...((((.............)))))))))))).-----.)))--.))..)))....)))))))......- ( -36.72)
>DroVir_CAF1 2299 102 - 1
U-UUAU------UUGGUA-UAGCAGUUAGUU---------UUGAAUGCGAAAACCGAAAAGUGGGUCAUCUCGGUCGCGCUGCUCGGCUGGUUUGUACUCUGAUUUCUAUCCAACUGCC-
.-....------((((.(-(((.((((((..---------.....((((((..((((..(((((..(.....)..).))))..))))....))))))..)))))).)))))))).....- ( -26.50)
>DroGri_CAF1 2760 104 - 1
UUUUAU------UUUGUA-CAGCAGUUGGAU---------UUGAAUGCGAAAACCGAAAAGUGGGUCAUCUCGGUCGCGCUGCUCGGCUGGUUUGUACUCUGAUUUCUAUCCAACUGCCU
......------......-..((((((((((---------..((.((((((..((((..(((((..(.....)..).))))..))))....)))))).))........)))))))))).. ( -33.00)
>DroMoj_CAF1 2856 102 - 1
U-UUAU------UUUGUA-UAGCAGUUGGAU---------UUGAAUGCGAAAACCGAAAAGUGGGUCAUCUCGGUCGCGCUGCUCGGCUGGUUUGUACUCUGAUUUCUAUCCAACUGCC-
.-....------......-..((((((((((---------..((.((((((..((((..(((((..(.....)..).))))..))))....)))))).))........)))))))))).- ( -33.00)
>DroAna_CAF1 2618 106 - 1
AUUUAAUUUAGUUUGGUAG-AGCAGUUGGGU---------UCCAGUGCGAAAACCGAAAAGUGGGUCAUCUCGGUCGCGCUGCUCGGCUGGUUUGUACUCUGAUUUCUGCCCAACC----
..........(((.(((((-((((((((((.---------..((((((((...((((.............))))))))))))))))))))((....))......))))))).))).---- ( -34.02)
>DroPer_CAF1 7443 110 - 1
UUUUUU------CGGAU---AGCAGUUGGGCUCUUGUUCUGUUGGUGCGAAAACCGAAAAGUGGGUCAUCUCGGUCGCGCUGCUCGGCUGGUUUGUACUCUGAUUUCUGCCCGACUGCC-
......------.....---.((((((((((......((....((((((((..((((..(((((..(.....)..).))))..))))....))))))))..)).....)))))))))).- ( -41.30)
>consensus
UUUUAU______UUGGUA_UAGCAGUUGGGU_________UUGAAUGCGAAAACCGAAAAGUGGGUCAUCUCGGUCGCGCUGCUCGGCUGGUUUGUACUCUGAUUUCUACCCAACUGCC_
.....................((((((((((..............((((((..((((..(((((..(.....)..).))))..))))....))))))...........)))))))))).. (-26.41 = -27.44 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:09 2006