Locus 758

Sequence ID	3L_DroMel_CAF1
Location	2,257,247 – 2,257,391
Length	144
Max. P	0.781486

overview

Window 0

Location	2,257,247 – 2,257,358
Length	111
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	81.24
Mean single sequence MFE	-35.21
Consensus MFE	-28.53
Energy contribution	-28.53
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.20
Structure conservation index	0.81
SVM decision value	0.05
SVM RNA-class probability	0.558925
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2257247 111 - 23771897
AAUGUA-GUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCGACUUGAAAAUGG-CGA-ACUCAGAGCGCC
..((((-((((.(((((...(((((.......)))))((.(..(((((.....)))))..).))..)))))))))))))................((-((.-........)))) ( -37.10)
>DroVir_CAF1 7285 111 - 1
AAAGUGAAUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCC-AUAUAAAAAACU-UAC-AGUUAGAGCUGU
.((((........(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))-.........)))-)((-(((....))))) ( -33.33)
>DroGri_CAF1 7010 110 - 1
AAUCAA-AUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCC-CAAUGAAAUAUA-CGC-AGUUAGAGCUGC
..((((-((.((.(((....)))))))))))...((((.....(((((.....)))))..((((.......))))......)))-)...........-.((-(((....))))) ( -34.80)
>DroMoj_CAF1 6629 111 - 1
AAUAUG-AUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCAAUAUGAAAAAAC-GAG-AUUGGUAGCUAU
......-....((((((...(((((.......)))))((.(..(((((.....)))))..).))..))))))(((((.....(((((.((......)-)..-)))))))))).. ( -33.10)
>DroAna_CAF1 7697 111 - 1
AAAGUU-ACCAAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCGACUUGGUGUUGA-AGC-UCUGGGAGUGCC
......-.......((((..(((((.......)))))..))))(((((.....)))))..((.((.(((..((((((((((........)))))...-)))-)).))))).)). ( -39.40)
>DroPer_CAF1 6225 112 - 1
GUUGUG-UUCCAAGGGGGCACCCGGAUUUGAACCGGGGGCCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCAACUUGAAAACAGGCGCCACUGAGA-UGUA
......-...(((((((((.(((((.......))))).)))))(((((.....)))))..((((.......))))...........))))....(((......)))...-.... ( -33.50)
>consensus
AAUGUG_AUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCC_ACAUGAAAAAAA_CGC_ACUGAGAGCGCC
.............(((((..(((((.......)))))......(((((.....)))))..((((.......))))....))))).............................. (-28.53 = -28.53 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	2,257,285 – 2,257,391
Length	106
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	80.54
Mean single sequence MFE	-30.83
Consensus MFE	-26.82
Energy contribution	-27.15
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	0.87
SVM decision value	0.26
SVM RNA-class probability	0.657168
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2257285 106 + 23771897
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUGGAAC-UACAUUUUUUGCCAUAUUUUUUUUUGU-UGGCUGCUC-AAG
.(((((((....(((......))).((((....))))(((((.......)))))...)))))))...-..........((((.............-)))).....-... ( -32.22)
>DroVir_CAF1 7322 103 + 1
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUGGAAUUCACUUUUAU--UUAUUUUUU--AUUUUCCACAUUCUC-AA-
....((((((..(((......))).((((....))))(((((.......))))))))))).(((((...........--.........--...))))).......-..- ( -28.40)
>DroEre_CAF1 8132 104 + 1
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUGGAAC-CACAUUUUUGGUCAUGUUUU--UUUGC-UGGCUACUC-AAG
.....((((((((((...((..(((((((((((((..(((((.......)))))..))...((....-))...)))))))).)))..)--).)))-)..))))))-... ( -33.80)
>DroYak_CAF1 7817 105 + 1
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUGGAAC-CACAUUUUUGAUCAUAUUUU--UUUGU-GGCCUGCUCUAAG
....(((((((.(((......))).((((((((((..(((((.......)))))..))...((....-))...)))))))).......--.....-...)))))))... ( -32.80)
>DroMoj_CAF1 6667 97 + 1
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUGGAAU-CAUAUUUUU--UUAU-------AUUACUUCCAUUCCA-GC-
....((((((..(((......))).((((....))))(((((.......)))))))))))(((((((-.........--....-------.........))))))-).- ( -31.25)
>DroAna_CAF1 7735 97 + 1
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUUGGU-AACUUUUU----AAUACUUUUUUAUGC-GAACGCC------
....((((((..(((......))).((((....))))(((((.......))))))))))).......-........----.............((-....)).------ ( -26.50)
>consensus
CUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUGGAAC_CACAUUUUU__UCAUAUUUU__UUUGC_UGCCUGCUC_AA_
.(((((((....(((......))).((((....))))(((((.......)))))...)))))))............................................. (-26.82 = -27.15 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	2,257,285 – 2,257,391
Length	106
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	80.54
Mean single sequence MFE	-30.75
Consensus MFE	-25.87
Energy contribution	-26.03
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.84
SVM decision value	0.56
SVM RNA-class probability	0.781486
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2257285 106 - 23771897
CUU-GAGCAGCCA-ACAAAAAAAAAUAUGGCAAAAAAUGUA-GUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
...-(((((((((-.............))))......((((-(.((.(((((...(((((.......)))))..))))).)).)))))......))))).......... ( -36.42)
>DroVir_CAF1 7322 103 - 1
-UU-GAGAAUGUGGAAAAU--AAAAAAUAA--AUAAAAGUGAAUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
-..-...............--.........--..............((((((...(((((.......)))))((.(..(((((.....)))))..).))..)))))).. ( -26.70)
>DroEre_CAF1 8132 104 - 1
CUU-GAGUAGCCA-GCAAA--AAAACAUGACCAAAAAUGUG-GUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
...-.........-.....--.......(((((......))-))).((((((...(((((.......)))))((.(..(((((.....)))))..).))..)))))).. ( -30.30)
>DroYak_CAF1 7817 105 - 1
CUUAGAGCAGGCC-ACAAA--AAAAUAUGAUCAAAAAUGUG-GUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
..(((((((((((-(((..--................))))-)))....((((..(((((.......)))))..))))(((((.....))))).)))))))........ ( -34.97)
>DroMoj_CAF1 6667 97 - 1
-GC-UGGAAUGGAAGUAAU-------AUAA--AAAAAUAUG-AUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
-..-.....(((((...((-------((..--....)))).-.)))))(((((..(((((.......)))))((.(..(((((.....)))))..).))..)))))... ( -29.20)
>DroAna_CAF1 7735 97 - 1
------GGCGUUC-GCAUAAAAAAGUAUU----AAAAAGUU-ACCAAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
------(((((((-((........(((..----.......)-))....(((((..(((((.......)))))..))))).........).))))))))........... ( -26.90)
>consensus
_UU_GAGAAGGCA_ACAAA__AAAAUAUGA__AAAAAUGUG_AUUCCAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAG
..............................................((((((...(((((.......)))))((.(..(((((.....)))))..).))..)))))).. (-25.87 = -26.03 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:33 2006