Locus 1346

Sequence ID	2L_DroMel_CAF1
Location	3,571,857 – 3,572,009
Length	152
Max. P	0.831917

overview

Window 6

Location	3,571,857 – 3,571,948
Length	91
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	80.93
Mean single sequence MFE	-31.97
Consensus MFE	-22.83
Energy contribution	-23.28
Covariance contribution	0.46
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.71
SVM decision value	0.50
SVM RNA-class probability	0.760132
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3571857 91 + 22407834
UGGAGAUGGGCACUUUAAAGUGCCCCGU-AAACUGUCAACGGCAGCCCGAAGGGAACCGAAAACGGUUGUCGGGGUUACCGG------UACCAGACUU
..(((..(((((((....)))))))...-...(((....(((.(((((...((.(((((....))))).)).))))).))).------...))).))) ( -35.70)
>DroSec_CAF1 39754 91 + 1
UCGAGAUGGGCACUUUAAAGUGCCCCGU-GAACUGUCAACGGCAGCCCGAAGGGAUCCGAAAACGGUUGUCGGGGUUACCGG------UACCGGACUU
(((.((((((((((....)))))))...-...((((.....)))).((....))))))))...(((.(..(((.....))).------.))))..... ( -33.10)
>DroSim_CAF1 40618 91 + 1
UCAAGAUGGGCACUUUAAAGUGCCCCGU-GAACUGUCAACGGCAGCCCGAAGGGAUCCGAAAACGGUUGUCGGGGUUACCGG------UACCGGACUU
(((....(((((((....)))))))..)-))...(((..(((...(((...)))..)))....(((.(..(((.....))).------.))))))).. ( -33.80)
>DroEre_CAF1 41312 83 + 1
UCGAGAUGGGCACUUUAAAGUGCCCCGU-GAACUGUCAACGGCAGCCCGAAGGGAUCCGAAAACGGUGGUCGGGAU--------------CCGGAUUC
(((.((((((((((....)))))))...-...((((.....))))(((((......(((....)))...)))))))--------------)))).... ( -29.50)
>DroYak_CAF1 41923 97 + 1
UCGAGAUGGGCACUUUAAAGUGCCCCGU-GAACUGUCAACGGCAGCCCGAGGGGAUCCGAAAACGGUUGUCGGGGUUACCGGUACUGGUACCGGAAUU
(((....(((((((....)))))))..)-)).((((.....))))(((((.((...(((....))))).)))))....((((((....)))))).... ( -37.60)
>DroAna_CAF1 44234 73 + 1
------UGAGCACUUUAAACUGCCCCGCAGAACUGUCAACGGCAGCCCGAAAGGGA-------------UCGGGGUUAUGGA------UUCCGGAUUU
------.............(((((..(((....)))....)))))(((....))).-------------((((((((...))------)))))).... ( -22.10)
>consensus
UCGAGAUGGGCACUUUAAAGUGCCCCGU_GAACUGUCAACGGCAGCCCGAAGGGAUCCGAAAACGGUUGUCGGGGUUACCGG______UACCGGACUU
.......(((((((....))))))).......((((.....))))(((((......(((....)))...)))))........................ (-22.83 = -23.28 +   0.46)

alignment

secondary structure

dotplot

Window 7

Location	3,571,857 – 3,571,948
Length	91
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	80.93
Mean single sequence MFE	-29.75
Consensus MFE	-21.85
Energy contribution	-22.53
Covariance contribution	0.68
Combinations/Pair	1.21
Mean z-score	-1.85
Structure conservation index	0.73
SVM decision value	0.72
SVM RNA-class probability	0.831917
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3571857 91 - 22407834
AAGUCUGGUA------CCGGUAACCCCGACAACCGUUUUCGGUUCCCUUCGGGCUGCCGUUGACAGUUU-ACGGGGCACUUUAAAGUGCCCAUCUCCA
....(((.((------.(((((..(((((.(((((....)))))....))))).))))).)).)))...-...(((((((....)))))))....... ( -34.10)
>DroSec_CAF1 39754 91 - 1
AAGUCCGGUA------CCGGUAACCCCGACAACCGUUUUCGGAUCCCUUCGGGCUGCCGUUGACAGUUC-ACGGGGCACUUUAAAGUGCCCAUCUCGA
....(((...------.)))......(((.(((.(((..(((...((....))...)))..))).))).-...(((((((....)))))))...))). ( -31.30)
>DroSim_CAF1 40618 91 - 1
AAGUCCGGUA------CCGGUAACCCCGACAACCGUUUUCGGAUCCCUUCGGGCUGCCGUUGACAGUUC-ACGGGGCACUUUAAAGUGCCCAUCUUGA
....(((...------.)))......((..(((.(((..(((...((....))...)))..))).))).-.))(((((((....)))))))....... ( -31.00)
>DroEre_CAF1 41312 83 - 1
GAAUCCGG--------------AUCCCGACCACCGUUUUCGGAUCCCUUCGGGCUGCCGUUGACAGUUC-ACGGGGCACUUUAAAGUGCCCAUCUCGA
.....(((--------------((..((...((.(((..(((...((....))...)))..))).))..-.))(((((((....)))))))))).)). ( -28.50)
>DroYak_CAF1 41923 97 - 1
AAUUCCGGUACCAGUACCGGUAACCCCGACAACCGUUUUCGGAUCCCCUCGGGCUGCCGUUGACAGUUC-ACGGGGCACUUUAAAGUGCCCAUCUCGA
....((((((....))))))......(((.(((.(((..(((..(((...)))...)))..))).))).-...(((((((....)))))))...))). ( -34.80)
>DroAna_CAF1 44234 73 - 1
AAAUCCGGAA------UCCAUAACCCCGA-------------UCCCUUUCGGGCUGCCGUUGACAGUUCUGCGGGGCAGUUUAAAGUGCUCA------
....((((((------(...(((((((((-------------......))))).....))))...)))))).)(((((.(....).))))).------ ( -18.80)
>consensus
AAGUCCGGUA______CCGGUAACCCCGACAACCGUUUUCGGAUCCCUUCGGGCUGCCGUUGACAGUUC_ACGGGGCACUUUAAAGUGCCCAUCUCGA
....((((........))))....(((((...(((....)))......)))))....(((.((....)).)))(((((((....)))))))....... (-21.85 = -22.53 +   0.68)

alignment

secondary structure

dotplot

Window 8

Location	3,571,915 – 3,572,009
Length	94
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.65
Mean single sequence MFE	-27.68
Consensus MFE	-14.69
Energy contribution	-16.42
Covariance contribution	1.72
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.53
SVM decision value	0.42
SVM RNA-class probability	0.731019
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3571915 94 + 22407834
AAAACGGUUGUCGGGGUUACCGG------UACCAGACUUCGGAAUCCGGAAUCCGGGU---UAUA---------UAUUUGGUUAUAUGCUUCGUUGAUCUUUGA-------ACGCAAAA
.....(((((.((((((......------.(((((((....)(((((((...))))))---)...---------..)))))).....)))))).))))).....-------........ ( -23.30)
>DroSec_CAF1 39812 94 + 1
AAAACGGUUGUCGGGGUUACCGG------UACCGGACUUCGGAAUCCGGAAUCCGGGU---UAUA---------UAUUUAGUUAUAUGCUUCGUUGAUCUUUGA-------ACGCAAAA
.....(((((.((((((..((((------..((((((....)..)))))...))))..---.(((---------((......))))))))))).))))).....-------........ ( -25.90)
>DroSim_CAF1 40676 94 + 1
AAAACGGUUGUCGGGGUUACCGG------UACCGGACUUCGGAAUCCGGAAUCCGGGU---UAUA---------UAUUUGGUUAUAUGCUUCGUUGAUCUUUAA-------ACGCAAAA
.....(((((.((((((..((((------..((((((....)..)))))...))))..---.(((---------((......))))))))))).))))).....-------........ ( -25.90)
>DroEre_CAF1 41370 86 + 1
AAAACGGUGGUCGGGAU--------------CCGGAUUCCGGAUUCCGGAAUCCGGGA---CAUA---------UAUUCGGUUAUAUGCUUCGUUGAUCUUUGA-------ACGCAAAA
......(((.(((((((--------------(((((((((((...))))))))))(((---((((---------((......)))))).)))...)))).))))-------.))).... ( -32.10)
>DroYak_CAF1 41981 109 + 1
AAAACGGUUGUCGGGGUUACCGGUACUGGUACCGGAAUUCAGAGUCCGGAAUCCGGGA---UAUACAUACAUAUUAUUUGGUUAUAUGCUUCGUUGAUCUUUGA-------ACGCAAAA
.....(((((.((((((.(((((..((((..(((((........)))))...))))((---(((......)))))..))))).....)))))).))))).....-------........ ( -25.80)
>DroAna_CAF1 44284 93 + 1
----------UCGGGGUUAUGGA------UUCCGGAUUUCGGAUUCCGUAUUCCGGGUGGAUAUA---------UAUUU-UUUAUAUGCAUCGUUGAUCUUUCAAUGGUUAACAAAAAA
----------.((((((.(((((------.((((.....)))).)))))))))))((((.(((((---------.....-..))))).))))(((((((.......)))))))...... ( -33.10)
>consensus
AAAACGGUUGUCGGGGUUACCGG______UACCGGACUUCGGAAUCCGGAAUCCGGGU___UAUA_________UAUUUGGUUAUAUGCUUCGUUGAUCUUUGA_______ACGCAAAA
.....(((((.((((((..............(((((.(((((...))))).)))))..................(((......))).)))))).))))).................... (-14.69 = -16.42 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:12 2006