Locus 4329

Sequence ID	2R_DroMel_CAF1
Location	14,228,293 – 14,228,460
Length	167
Max. P	0.644171

overview

Window 0

Location	14,228,293 – 14,228,388
Length	95
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	78.92
Mean single sequence MFE	-27.67
Consensus MFE	-13.18
Energy contribution	-13.52
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.48
SVM decision value	0.23
SVM RNA-class probability	0.644171
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14228293 95 + 20766785
CCAU-GGU---UUUUAACCACGACUUUAAGUGCGACGAUAAGGUUGUCAAGUGCGGACAGUUUUAUCAGGCCGCACAG-CAAAUGCAAUUUAAAUGCAUU
...(-(((---.....)))).........(((((.((((((..(((((.......)))))..))))).)..)))))..-..((((((.......)))))) ( -26.00)
>DroSim_CAF1 9246 95 + 1
CCAU-GGU---UUUUAACCACGAGUUUAAGUGCGGCGAUAAGGUUGUCAAGUGCGGACAGUUUUAUCAGGCCGUACGG-CAAAUGCAAUUUAAAUGCAUU
((.(-(((---.....)))).........((((((((((((..(((((.......)))))..)))))..)))))))))-..((((((.......)))))) ( -31.00)
>DroEre_CAF1 8011 95 + 1
GCAU-GGU---UUUUAACCACGAGCUUAAGUGCGGCGAUAAGGUUGUCAAGUGCGGACAGUUUUAUCAGCCCGCACAG-CAAAUGCAAUUUAAAUGCAUU
((.(-(((---.....)))).........((((((((((((..(((((.......)))))..))))).).)))))).)-).((((((.......)))))) ( -31.90)
>DroYak_CAF1 7705 87 + 1
GCAU-GGU---UUUUUACCACGGGUUUAAGUGCGCCGAUAAGGUUGUCAAGUGCGGACAGUUUUAUCAGC---------CAAAUGCAAUUUAAAUGCAUU
...(-(((---.....)))).(.((((((((((((.(((((..(((((.......)))))..))))).))---------.....)).)))))))).)... ( -23.80)
>DroAna_CAF1 13533 90 + 1
GAAU-GGU---UUUUU-CC---ACUUUGGGCGUUGCGAUAAGGUUGUCAAGUGCCGACAGGUUUAUCUU-CCGCCAAA-GAAACGCAAUUUAAAUGCAUU
...(-((.---.....-))---)((((((.((..(.((((((.(((((.......))))).))))))).-.)))))))-)....(((.......)))... ( -24.50)
>DroPer_CAF1 10962 97 + 1
CCAUUGGUGUGCUUGGAGC---ACUUUAAAGUCGGCGAUAAUAUUGUCAAGUGUCGACAGUUUUAUCAGCUGCCAGAGCCAAAUGCAAUUUAAGUGCACU
.....((((..((((((..---........(.(((((((((.((((((.......)))))).))))).)))).)...((.....))..))))))..)))) ( -28.80)
>consensus
CCAU_GGU___UUUUAACCACGACUUUAAGUGCGGCGAUAAGGUUGUCAAGUGCGGACAGUUUUAUCAGCCCGCACAG_CAAAUGCAAUUUAAAUGCAUU
....................................(((((..(((((.......)))))..)))))..............((((((.......)))))) (-13.18 = -13.52 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	14,228,293 – 14,228,388
Length	95
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	78.92
Mean single sequence MFE	-24.40
Consensus MFE	-10.19
Energy contribution	-9.92
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-2.33
Structure conservation index	0.42
SVM decision value	0.01
SVM RNA-class probability	0.537381
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14228293 95 - 20766785
AAUGCAUUUAAAUUGCAUUUG-CUGUGCGGCCUGAUAAAACUGUCCGCACUUGACAACCUUAUCGUCGCACUUAAAGUCGUGGUUAAAA---ACC-AUGG
((((((.......))))))..-..(((((((..(((((...((((.......))))...)))))))))))).......((((((.....---)))-))). ( -27.30)
>DroSim_CAF1 9246 95 - 1
AAUGCAUUUAAAUUGCAUUUG-CCGUACGGCCUGAUAAAACUGUCCGCACUUGACAACCUUAUCGCCGCACUUAAACUCGUGGUUAAAA---ACC-AUGG
((((((.......))))))..-..((.((((..(((((...((((.......))))...))))))))).)).......((((((.....---)))-))). ( -23.70)
>DroEre_CAF1 8011 95 - 1
AAUGCAUUUAAAUUGCAUUUG-CUGUGCGGGCUGAUAAAACUGUCCGCACUUGACAACCUUAUCGCCGCACUUAAGCUCGUGGUUAAAA---ACC-AUGC
((((((.......)))))).(-((((((((.(.(((((...((((.......))))...))))))))))))...))).((((((.....---)))-))). ( -28.50)
>DroYak_CAF1 7705 87 - 1
AAUGCAUUUAAAUUGCAUUUG---------GCUGAUAAAACUGUCCGCACUUGACAACCUUAUCGGCGCACUUAAACCCGUGGUAAAAA---ACC-AUGC
((((((.......))))))((---------((((((((...((((.......))))...)))))))).))........((((((.....---)))-))). ( -23.00)
>DroAna_CAF1 13533 90 - 1
AAUGCAUUUAAAUUGCGUUUC-UUUGGCGG-AAGAUAAACCUGUCGGCACUUGACAACCUUAUCGCAACGCCCAAAGU---GG-AAAAA---ACC-AUUC
((((((.......)))))).(-(((((((.-..(((((...(((((.....)))))...)))))....)).))))))(---((-.....---.))-)... ( -21.70)
>DroPer_CAF1 10962 97 - 1
AGUGCACUUAAAUUGCAUUUGGCUCUGGCAGCUGAUAAAACUGUCGACACUUGACAAUAUUAUCGCCGACUUUAAAGU---GCUCCAAGCACACCAAUGG
.(((((.......)))))((((...((((....(((((.(.((((((...)))))).).)))))))))........((---((.....)))).))))... ( -22.20)
>consensus
AAUGCAUUUAAAUUGCAUUUG_CUGUGCGGGCUGAUAAAACUGUCCGCACUUGACAACCUUAUCGCCGCACUUAAACUCGUGGUUAAAA___ACC_AUGC
((((((.......))))))..............(((((...((((.......))))...))))).................................... (-10.19 =  -9.92 +  -0.28)

alignment

secondary structure

dotplot

Window 2

Location	14,228,351 – 14,228,460
Length	109
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	83.87
Mean single sequence MFE	-30.36
Consensus MFE	-18.10
Energy contribution	-18.18
Covariance contribution	0.08
Combinations/Pair	1.25
Mean z-score	-1.92
Structure conservation index	0.60
SVM decision value	-0.06
SVM RNA-class probability	0.505303
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14228351 109 - 20766785
CCACAUGCGUGUGCUUCGU----UUUAUGGGCACACAUCCUUCGGCUUUCCACGCUCCCC---UGCAUUUUUAUUUU-CGAAUGCAUUUAAAUUGCAUUUGCUGUGCGGCCUGAUAA
........((((((((...----.....)))))))).......((((...(((((.....---.))...........-((((((((.......))))))))..))).))))...... ( -29.30)
>DroSec_CAF1 7731 109 - 1
CCACAUGCGUGUGCUUCGU----UUUAUGGGCACACAUCCUUCGGUUUUCCACGCUCCCC---UGCAUUUUUAUUUU-CGAAUGCAUUUAAAUUGCAUUUGCUGUGCGGCCUGAUAA
......((((((((((...----.....)))))))).......((....))..))....(---(((((.........-((((((((.......))))))))..))))))........ ( -27.20)
>DroSim_CAF1 9304 109 - 1
CCACAUGCGUGUGCUUCGU----GUUAUGGGCACACAUCCUUCGGUUUUCCACGCUCCCC---UGCAUUUUUAUUUU-CGAAUGCAUUUAAAUUGCAUUUGCCGUACGGCCUGAUAA
...((.((((((((((...----.....))))))))......((((.......((.....---.))...........-.(((((((.......)))))))))))....)).)).... ( -26.80)
>DroEre_CAF1 8069 109 - 1
CCACAUGCGUGUGCUUCGU----UUUAUGGGCACACAUCCUUCGGUUUUCCACGCUCCCC---UGCGCUUUUAUUUU-CGAAUGCAUUUAAAUUGCAUUUGCUGUGCGGGCUGAUAA
......((((((((((...----.....)))))))).......((....))..))...((---(((((.........-((((((((.......))))))))..)))))))....... ( -31.60)
>DroAna_CAF1 13587 114 - 1
--GGGUGUGGGGGCUCCGGUGUGUUUAUGGCCACACAUCCUUUGGCUUACCGCGCCGCGGAGUGGUGCUUUUAUUUUGUGAAUGCAUUUAAAUUGCGUUUCUUUGGCGG-AAGAUAA
--(((((((..((((...(((....))))))).))))))).....(((.((((..((((((((((.....))))))))))((((((.......))))))......))))-))).... ( -36.90)
>consensus
CCACAUGCGUGUGCUUCGU____UUUAUGGGCACACAUCCUUCGGUUUUCCACGCUCCCC___UGCAUUUUUAUUUU_CGAAUGCAUUUAAAUUGCAUUUGCUGUGCGGCCUGAUAA
....((((((((((.((((.......)))))))))).......((....)).............))))..........((((((((.......))))))))................ (-18.10 = -18.18 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:11 2006