Locus 9029

Sequence ID	3R_DroMel_CAF1
Location	24,179,416 – 24,179,527
Length	111
Max. P	0.783385

overview

Window 3

Location	24,179,416 – 24,179,527
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.22
Mean single sequence MFE	-37.59
Consensus MFE	-24.86
Energy contribution	-25.00
Covariance contribution	0.14
Combinations/Pair	1.17
Mean z-score	-2.90
Structure conservation index	0.66
SVM decision value	-0.01
SVM RNA-class probability	0.526618
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24179416 111 + 27905053
UUAAGCCGGUGUUGUUACAGCCAGUUGGCUAAUUAAGCCAUGUUAAUGGCAAUAACUGCUAUGGAAAACCAGUGCCUGCGCCUGUUAAUGCCUUUUGCAUUAUUGGCCUUG---------
....((.(((((((((..((((....))))......(((((....))))))))))).....(((....)))..))).))(((...((((((.....))))))..)))....--------- ( -34.80)
>DroPse_CAF1 1572 120 + 1
UUAAGCUGGUGCGGUUUAAGCCACUUGGCUAAUUAAGCCUUGUUAAUGGCAAUAACUGCGUUGAAAAAUCAGUGCCGGGGUCUGUUAAUGCCUUUUGCAUUAUUGGCCCAGACGCUCGUU
...(((((((((((((...(((((..((((.....))))..))....)))...)))))).((((....)))).))))(((((...((((((.....))))))..)))))....))).... ( -39.10)
>DroSim_CAF1 1485 111 + 1
UUAAGCCGGUGUUGUUACAGCCAGUUUGCUAAUUAAGCCAUGUUAAUGGCAAUAACUGCUAUGGAAAACCAGUGCCUGCGCCUGUUAAUGCCUUUUGCAUUAUUGGCCUUG---------
....((.((..(((......(((....((.......(((((....))))).......))..))).....)))..)).))(((...((((((.....))))))..)))....--------- ( -33.04)
>DroYak_CAF1 2889 111 + 1
UUAAGCCGGUGUUGUUACAGCCAGUUGGCUAAUUAAGCCAUGUUAAUGGCAAUAACUGCUAUGGAAAACCAGUGCCCGGGCCUGUUAAUGCCUUUUGCAUUAUUGGCCUUG---------
......(((.((((((..((((....))))......(((((....))))))))))).((..(((....)))..)))))((((...((((((.....))))))..))))...--------- ( -37.10)
>DroAna_CAF1 1411 110 + 1
UUAAGCCAGCGUUGUUACAACGAGUUGGCUAAUUAAGCCAUGUUAAUGGCAAUAACUGCUCUGGAAAACCAGUGCUU-CGCCAUUUAAUGCCUUUUGCAUUAUUGGCCUUG---------
...(((((((.((((....)))))))))))......(((((....))))).......((.((((....)))).))..-.((((..((((((.....)))))).))))....--------- ( -39.10)
>DroPer_CAF1 1593 120 + 1
UUAAGCUGGCGCGGUUUAAGCCACUUGGCUAAUUAAGCCUUGUUAAUGGCAAUAACUGCGUUGAAAAAUCAGUUCCGGGGCCUGUUAAUGCCUUUUGCAUUAUUGGCCCAGUCGCUCGUU
...(((.(((((((((...(((((..((((.....))))..))....)))...)))))))))...............(((((...((((((.....))))))..)))))....))).... ( -42.40)
>consensus
UUAAGCCGGUGUUGUUACAGCCAGUUGGCUAAUUAAGCCAUGUUAAUGGCAAUAACUGCUAUGGAAAACCAGUGCCUGCGCCUGUUAAUGCCUUUUGCAUUAUUGGCCUUG_________
.......(((((.((((.((((....))))......(((((....)))))..)))).))..(((....)))..)))...(((...((((((.....))))))..)))............. (-24.86 = -25.00 +   0.14)

alignment

secondary structure

dotplot

Window 4

Location	24,179,416 – 24,179,527
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	85.22
Mean single sequence MFE	-36.08
Consensus MFE	-24.36
Energy contribution	-25.42
Covariance contribution	1.06
Combinations/Pair	1.12
Mean z-score	-3.60
Structure conservation index	0.68
SVM decision value	0.56
SVM RNA-class probability	0.783385
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24179416 111 - 27905053
---------CAAGGCCAAUAAUGCAAAAGGCAUUAACAGGCGCAGGCACUGGUUUUCCAUAGCAGUUAUUGCCAUUAACAUGGCUUAAUUAGCCAACUGGCUGUAACAACACCGGCUUAA
---------..(((((..((((((.....))))))...((.(...((..(((....)))..)).(((((.((((......(((((.....)))))..)))).)))))..).))))))).. ( -34.30)
>DroPse_CAF1 1572 120 - 1
AACGAGCGUCUGGGCCAAUAAUGCAAAAGGCAUUAACAGACCCCGGCACUGAUUUUUCAACGCAGUUAUUGCCAUUAACAAGGCUUAAUUAGCCAAGUGGCUUAAACCGCACCAGCUUAA
...(((((((.((((...((((((.....))))))...).))).)))..............((.(((...((((((.....((((.....)))).))))))...))).))....)))).. ( -34.50)
>DroSim_CAF1 1485 111 - 1
---------CAAGGCCAAUAAUGCAAAAGGCAUUAACAGGCGCAGGCACUGGUUUUCCAUAGCAGUUAUUGCCAUUAACAUGGCUUAAUUAGCAAACUGGCUGUAACAACACCGGCUUAA
---------..(((((..((((((.....))))))...(..((((.((.(((....)))..(((((((..(((((....))))).))))).))....)).))))..)......))))).. ( -32.40)
>DroYak_CAF1 2889 111 - 1
---------CAAGGCCAAUAAUGCAAAAGGCAUUAACAGGCCCGGGCACUGGUUUUCCAUAGCAGUUAUUGCCAUUAACAUGGCUUAAUUAGCCAACUGGCUGUAACAACACCGGCUUAA
---------...((((..((((((.....))))))...))))(((((..(((....)))..)).(((((.((((......(((((.....)))))..)))).)))))....)))...... ( -37.00)
>DroAna_CAF1 1411 110 - 1
---------CAAGGCCAAUAAUGCAAAAGGCAUUAAAUGGCG-AAGCACUGGUUUUCCAGAGCAGUUAUUGCCAUUAACAUGGCUUAAUUAGCCAACUCGUUGUAACAACGCUGGCUUAA
---------..((((((.((((((.....))))))(((((((-(.((.((((....)))).)).....))))))))....))))))....(((((...(((((...))))).)))))... ( -38.10)
>DroPer_CAF1 1593 120 - 1
AACGAGCGACUGGGCCAAUAAUGCAAAAGGCAUUAACAGGCCCCGGAACUGAUUUUUCAACGCAGUUAUUGCCAUUAACAAGGCUUAAUUAGCCAAGUGGCUUAAACCGCGCCAGCUUAA
...((((....(((((..((((((.....))))))...))))).((...(((....))).(((.(((...((((((.....((((.....)))).))))))...))).))))).)))).. ( -40.20)
>consensus
_________CAAGGCCAAUAAUGCAAAAGGCAUUAACAGGCCCAGGCACUGGUUUUCCAUAGCAGUUAUUGCCAUUAACAUGGCUUAAUUAGCCAACUGGCUGUAACAACACCGGCUUAA
...........(((((..((((((.....))))))...((.....((..(((....)))..)).(((((.((((......(((((.....)))))..)))).)))))....))))))).. (-24.36 = -25.42 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:25:07 2006