Locus 2113

Sequence ID	3L_DroMel_CAF1
Location	5,794,682 – 5,794,775
Length	93
Max. P	0.972788

overview

Window 0

Location	5,794,682 – 5,794,775
Length	93
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	78.30
Mean single sequence MFE	-25.39
Consensus MFE	-13.34
Energy contribution	-13.23
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-2.80
Structure conservation index	0.53
SVM decision value	1.70
SVM RNA-class probability	0.972788
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5794682 93 + 23771897
UUUGUU-------UUU--UU-UUUGCA-----UUUCAUUUCGGG---G----CCGACGCGCUUUUCCUCUCGAGCGCAACGCCGCCGCCAAUGAUUCAUGCAAAUCCAUCAAGAA
((((..-------...--..-((((((-----(.(((((.((((---(----(.(..((((((........))))))..)))).)))..)))))...))))))).....)))).. ( -28.50)
>DroVir_CAF1 4764 83 + 1
UUUU-------GCUCG--UUUUUUGCA-----ACUCAUUUCUG-------------GGCGCUUUUCCU-UCGAGCGUGACGCC----UCAAUGAUUCAUGCAAAUCCAUCAAAAA
((((-------(....--...((((((-----..(((((...(-------------(((((((.....-..))))))....))----..)))))....)))))).....))))). ( -15.70)
>DroPse_CAF1 3398 106 + 1
UCUUCUUGUAUU-UUU--UU-UUUGCA-----UUUCAUUUCAGUUGUGCCCCGCGACGCGCUUUUCUUCUCGAGCGUGACGCGGCCGCCAAUGAUUCAUGCAAAUCCAUCAACGA
.....((((...-...--..-((((((-----(......(((.(((.((.(((((.(((((((........))))))).)))))..))))))))...))))))).......)))) ( -29.76)
>DroSec_CAF1 2810 85 + 1
U-----------------UU-UUUGCA-----UUUCAUUUCGGG---G----CCGACGCGCUUUUCCUCUCGAGCGUAACGCCGCCGCCAAUGAUUCAUGCAAAUCCAUCAAGAA
.-----------------..-((((((-----(.(((((.((((---(----(....((((((........))))))...))).)))..)))))...)))))))........... ( -25.60)
>DroEre_CAF1 2702 100 + 1
UUUUUU-------CCUUUUU-UUUGCAUUUCAUUUCAUUUCGGG---G----CCGACGCGCUUUUCUUCUCGAGCGUAACGCCGCCGCCAAUGAUUCAUGCAAAUCCAUCAAGAA
......-------.......-(((((((......(((((.((((---(----(....((((((........))))))...))).)))..)))))...)))))))........... ( -24.40)
>DroYak_CAF1 2937 93 + 1
UUUUUU-------UGC--UU-UUUGCA-----UUUCAUUUCGGG---G----CCGACGCGCUUUUCCUCUCGAGCGUAACGCCGCCGCUAAUGAUUCAUGCAAAUCCAUCAAGAA
..((((-------((.--..-((((((-----(.(((((.((((---(----(....((((((........))))))...))).)))..)))))...))))))).....)))))) ( -28.40)
>consensus
UUUUUU_______UCU__UU_UUUGCA_____UUUCAUUUCGGG___G____CCGACGCGCUUUUCCUCUCGAGCGUAACGCCGCCGCCAAUGAUUCAUGCAAAUCCAUCAAGAA
.....................((((((.......(((((..................((((((........))))))...((....)).)))))....))))))........... (-13.34 = -13.23 +  -0.11)

alignment

secondary structure

dotplot

Window 1

Location	5,794,682 – 5,794,775
Length	93
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	78.30
Mean single sequence MFE	-25.75
Consensus MFE	-12.28
Energy contribution	-13.38
Covariance contribution	1.10
Combinations/Pair	1.04
Mean z-score	-2.02
Structure conservation index	0.48
SVM decision value	0.04
SVM RNA-class probability	0.555506
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5794682 93 - 23771897
UUCUUGAUGGAUUUGCAUGAAUCAUUGGCGGCGGCGUUGCGCUCGAGAGGAAAAGCGCGUCGG----C---CCCGAAAUGAAA-----UGCAAA-AA--AAA-------AACAAA
...........(((((((...(((((..(((.(((..(((((((....)....))))))...)----)---)))).))))).)-----))))))-..--...-------...... ( -30.20)
>DroVir_CAF1 4764 83 - 1
UUUUUGAUGGAUUUGCAUGAAUCAUUGA----GGCGUCACGCUCGA-AGGAAAAGCGCC-------------CAGAAAUGAGU-----UGCAAAAAA--CGAGC-------AAAA
.(((((.((..((((((....(((((..----(((((.....((..-..))...)))))-------------....)))))..-----))))))...--))..)-------)))) ( -20.10)
>DroPse_CAF1 3398 106 - 1
UCGUUGAUGGAUUUGCAUGAAUCAUUGGCGGCCGCGUCACGCUCGAGAAGAAAAGCGCGUCGCGGGGCACAACUGAAAUGAAA-----UGCAAA-AA--AAA-AAUACAAGAAGA
...........(((((((...(((((....(((.(((.((((.(..........).)))).))).)))........))))).)-----))))))-..--...-............ ( -26.70)
>DroSec_CAF1 2810 85 - 1
UUCUUGAUGGAUUUGCAUGAAUCAUUGGCGGCGGCGUUACGCUCGAGAGGAAAAGCGCGUCGG----C---CCCGAAAUGAAA-----UGCAAA-AA-----------------A
...........(((((((...(((((..(((.(((...((((.(..........).))))..)----)---)))).))))).)-----))))))-..-----------------. ( -26.00)
>DroEre_CAF1 2702 100 - 1
UUCUUGAUGGAUUUGCAUGAAUCAUUGGCGGCGGCGUUACGCUCGAGAAGAAAAGCGCGUCGG----C---CCCGAAAUGAAAUGAAAUGCAAA-AAAAAGG-------AAAAAA
(((((......(((((((...(((((..(((.(((...((((.(..........).))))..)----)---)))).)))))......)))))))-....)))-------)).... ( -26.70)
>DroYak_CAF1 2937 93 - 1
UUCUUGAUGGAUUUGCAUGAAUCAUUAGCGGCGGCGUUACGCUCGAGAGGAAAAGCGCGUCGG----C---CCCGAAAUGAAA-----UGCAAA-AA--GCA-------AAAAAA
...........(((((((...(((((..(((.(((...((((.(..........).))))..)----)---)))).))))).)-----))))))-..--...-------...... ( -24.80)
>consensus
UUCUUGAUGGAUUUGCAUGAAUCAUUGGCGGCGGCGUUACGCUCGAGAGGAAAAGCGCGUCGG____C___CCCGAAAUGAAA_____UGCAAA_AA__AAA_______AAAAAA
...........((((((....(((((..((((((((...((((..........)))))))))..........))).))))).......))))))..................... (-12.28 = -13.38 +   1.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:43 2006