Locus 5703

Sequence ID	3L_DroMel_CAF1
Location	15,590,372 – 15,590,647
Length	275
Max. P	0.997413

overview

Window 7

Location	15,590,372 – 15,590,488
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.94
Mean single sequence MFE	-31.77
Consensus MFE	-25.16
Energy contribution	-25.17
Covariance contribution	0.00
Combinations/Pair	1.08
Mean z-score	-2.17
Structure conservation index	0.79
SVM decision value	0.19
SVM RNA-class probability	0.624693
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15590372 116 + 23771897
AUAAGGGAAAGCAAAAAGACAGUCAACGUGACACACAACACAUAGUCACACAAACACAC----ACAUGUGCACGGGAGUUGUGCAUGUUGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUG
.....................(((.....)))..............(((((..((((((----(((((..(((....).))..)))))..))))))(((......))).......))))) ( -28.60)
>DroSec_CAF1 13624 118 + 1
AUAAGGGAAAGCAAGAAGACAGUCAACGUGACACACAACACAUAGGCACACAAACACAC--ACACGUGUGCACGGGAGUUGUGCAUGCUGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUG
.....................(((.....)))..............(((((..((((((--.((.(((((((((.....)))))))))))))))))(((......))).......))))) ( -30.10)
>DroYak_CAF1 14912 116 + 1
GUAAGGGAAAGCCAAAAGAUAGUCGACGUGACACACAACACAUAGGCACA----CACACACACGCAUGUGCACGGGAGUUGUGCAUGUGGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUG
..........(((....(.....)...(((........)))...))).((----(((((((((.((((((((((.....)))))))))).))))))(((......))).......))))) ( -36.60)
>consensus
AUAAGGGAAAGCAAAAAGACAGUCAACGUGACACACAACACAUAGGCACACAAACACAC__ACACAUGUGCACGGGAGUUGUGCAUGUUGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUG
.....................(((.....))).....((((.............(((((....(((((..(((....).))..)))))..)))))((((......))))......)))). (-25.16 = -25.17 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	15,590,372 – 15,590,488
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.94
Mean single sequence MFE	-33.11
Consensus MFE	-22.23
Energy contribution	-23.57
Covariance contribution	1.34
Combinations/Pair	1.06
Mean z-score	-3.19
Structure conservation index	0.67
SVM decision value	0.29
SVM RNA-class probability	0.671442
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15590372 116 - 23771897
CACACUUAAUUUGCAUAUUUUCGCACACACCAACAUGCACAACUCCCGUGCACAUGU----GUGUGUUUGUGUGACUAUGUGUUGUGUGUCACGUUGACUGUCUUUUUGCUUUCCCUUAU
.(((.(((((.(((((((...(((((((((.((((((((((.............)))----))))))).)))))....))))..))))).)).))))).))).................. ( -29.52)
>DroSec_CAF1 13624 118 - 1
CACACUUAAUUUGCAUAUUUUCGCACACACCAGCAUGCACAACUCCCGUGCACACGUGU--GUGUGUUUGUGUGCCUAUGUGUUGUGUGUCACGUUGACUGUCUUCUUGCUUUCCCUUAU
(((((...((..((((((...(((((((((.....(((((.......)))))...))))--)))))...))))))..)).....)))))............................... ( -33.10)
>DroYak_CAF1 14912 116 - 1
CACACUUAAUUUGCAUAUUUUCGCACACACCCACAUGCACAACUCCCGUGCACAUGCGUGUGUGUG----UGUGCCUAUGUGUUGUGUGUCACGUCGACUAUCUUUUGGCUUUCCCUUAC
(((((.......((((((....((((((((.((((((((..((....)).....)))))))).)))----)))))..)))))).)))))....(((((.......))))).......... ( -36.70)
>consensus
CACACUUAAUUUGCAUAUUUUCGCACACACCAACAUGCACAACUCCCGUGCACAUGUGU__GUGUGUUUGUGUGCCUAUGUGUUGUGUGUCACGUUGACUGUCUUUUUGCUUUCCCUUAU
.(((.(((((.(((((((...(((((((((.(((..((((.......))))((((......))))))).)))))....))))..))))).)).))))).))).................. (-22.23 = -23.57 +   1.34)

alignment

secondary structure

dotplot

Window 9

Location	15,590,412 – 15,590,528
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	91.62
Mean single sequence MFE	-41.07
Consensus MFE	-34.60
Energy contribution	-35.27
Covariance contribution	0.67
Combinations/Pair	1.06
Mean z-score	-3.07
Structure conservation index	0.84
SVM decision value	1.22
SVM RNA-class probability	0.932791
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15590412 116 + 23771897
CAUAGUCACACAAACACAC----ACAUGUGCACGGGAGUUGUGCAUGUUGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUGGCGACUUUUGUUCUCGCCGUUUUUUGGUGUAGAAAGCGUA
....(((((((..((((((----(((((..(((....).))..)))))..))))))(((......))).......)))))))........(((((((((.....))))).))))...... ( -40.30)
>DroSec_CAF1 13664 118 + 1
CAUAGGCACACAAACACAC--ACACGUGUGCACGGGAGUUGUGCAUGCUGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUGGCGACUUUUGUUUUCGCCGUUUUUUGGUAUAGAAAGCGUA
....(.(((((..((((((--.((.(((((((((.....)))))))))))))))))(((......))).......))))).).......((((((((((.....))))...))))))... ( -39.20)
>DroYak_CAF1 14952 116 + 1
CAUAGGCACA----CACACACACGCAUGUGCACGGGAGUUGUGCAUGUGGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUGGCGACUUUUGUUCUCGCCGUUUUUUGGUGUAGAAAGCGUA
......((((----(((((((.((((((..(((....).))..)))))).))))))(((......))).......)))))(((.(((((.....(((((.....)))))..)))))))). ( -43.70)
>consensus
CAUAGGCACACAAACACAC__ACACAUGUGCACGGGAGUUGUGCAUGUUGGUGUGUGCGAAAAUAUGCAAAUUAAGUGUGGCGACUUUUGUUCUCGCCGUUUUUUGGUGUAGAAAGCGUA
......(((((...(((((....(((((..(((....).))..)))))..)))))((((......))))......)))))(((.(((((.....(((((.....)))))..)))))))). (-34.60 = -35.27 +   0.67)

alignment

secondary structure

dotplot

Window 0

Location	15,590,412 – 15,590,528
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	91.62
Mean single sequence MFE	-32.03
Consensus MFE	-22.67
Energy contribution	-23.34
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	0.71
SVM decision value	0.21
SVM RNA-class probability	0.636554
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15590412 116 - 23771897
UACGCUUUCUACACCAAAAAACGGCGAGAACAAAAGUCGCCACACUUAAUUUGCAUAUUUUCGCACACACCAACAUGCACAACUCCCGUGCACAUGU----GUGUGUUUGUGUGACUAUG
...........((((((.....(((((.........))))).....................((((((((.....(((((.......)))))...))----))))))))).)))...... ( -28.30)
>DroSec_CAF1 13664 118 - 1
UACGCUUUCUAUACCAAAAAACGGCGAAAACAAAAGUCGCCACACUUAAUUUGCAUAUUUUCGCACACACCAGCAUGCACAACUCCCGUGCACACGUGU--GUGUGUUUGUGUGCCUAUG
......................(((((.........)))))...........((((((...(((((((((.....(((((.......)))))...))))--)))))...))))))..... ( -34.40)
>DroYak_CAF1 14952 116 - 1
UACGCUUUCUACACCAAAAAACGGCGAGAACAAAAGUCGCCACACUUAAUUUGCAUAUUUUCGCACACACCCACAUGCACAACUCCCGUGCACAUGCGUGUGUGUG----UGUGCCUAUG
......................(((((.........)))))...........(((((....(((((((((.((..(((((.......)))))..)).)))))))))----)))))..... ( -33.40)
>consensus
UACGCUUUCUACACCAAAAAACGGCGAGAACAAAAGUCGCCACACUUAAUUUGCAUAUUUUCGCACACACCAACAUGCACAACUCCCGUGCACAUGUGU__GUGUGUUUGUGUGCCUAUG
......................(((((.........)))))...........((((((...(((((.........(((((.......))))).........)))))...))))))..... (-22.67 = -23.34 +   0.67)

alignment

secondary structure

dotplot

Window 1

Location	15,590,528 – 15,590,647
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.39
Mean single sequence MFE	-33.67
Consensus MFE	-29.88
Energy contribution	-31.24
Covariance contribution	1.36
Combinations/Pair	1.08
Mean z-score	-2.14
Structure conservation index	0.89
SVM decision value	2.85
SVM RNA-class probability	0.997413
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15590528 119 + 23771897
AAAAGCAAGCAAAAACUGUACGUAUACACAUUAUUUGGGCUGGCGAUUGUGGAAAGCAAAGCGCCGAAA-AAAACGAGUAUACGCCCCGUUGUACAGUCAGUCAGUCCGCAAUAUGUGUG
....((..(((.....)))..)).(((((((.((((((((((((((((((((...((...)).))....-..((((.((....))..))))..)))))).))))))))).)))))))))) ( -31.30)
>DroSec_CAF1 13782 119 + 1
AAAAGCGAGCAAAAACUGUACGUAUACACAUUAUUUGGGCUGGCGAUUGUGGAAAGCAAAGCGCCGAAA-AAAACGAUAAUACGCCCCGUUGUACAGUCAGUCAGUCCGCAAUAUGUGUA
....(((.(((.....))).))).(((((((.(((((((((((((((((((.((......(((......-............)))....)).))))))).))))))))).)))))))))) ( -34.77)
>DroSim_CAF1 13745 119 + 1
AAAAGCGAGCAAAAACUGUACGUAUACACAUUAUUUGGGCUGGCGAUUGUGGAAAGCAAAGCGCCGAAA-AAAACGAGUAUACGCCCCGUUGUACAGUCAGUCAGCCCGCAAUAUGUGUG
....(((.(((.....))).))).(((((((.((((((((((((((((((((...((...)).))....-..((((.((....))..))))..)))))).))))))))).)))))))))) ( -37.70)
>DroEre_CAF1 13748 110 + 1
AAAAGCGAGCAAAAACUGUACGUAUACACAUUAUUUGGGCUGGCGAUUGUGGAAAGCAAAGCGCCGAAAAAAAACGAGUAUACGCCCCGUUG---------UCAGUCCGCAGUAUGUGU-
....(((.(((.....))).)))..((((((.(((((((((((((((.(.((...((...))((((........)).)).....))).))))---------)))))))).)))))))))- ( -29.60)
>DroYak_CAF1 15068 119 + 1
AAAAGCGAGCAAAAACUGUACGUAUACACAUUAUUUGGGCUGGCGAUUGUGGAAAGCAAAGCGCCGAAA-AAAACGAGUAUACGCCCCGUUGUACAGUCAGUCAGUCCGCAAUAUGUGUG
....(((.(((.....))).))).(((((((.((((((((((((((((((((...((...)).))....-..((((.((....))..))))..)))))).))))))))).)))))))))) ( -35.00)
>consensus
AAAAGCGAGCAAAAACUGUACGUAUACACAUUAUUUGGGCUGGCGAUUGUGGAAAGCAAAGCGCCGAAA_AAAACGAGUAUACGCCCCGUUGUACAGUCAGUCAGUCCGCAAUAUGUGUG
....(((.(((.....))).))).(((((((.((((((((((((((((((((...((...)).)).......((((...........))))..)))))).))))))))).)))))))))) (-29.88 = -31.24 +   1.36)

alignment

secondary structure

dotplot

Window 2

Location	15,590,528 – 15,590,647
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.39
Mean single sequence MFE	-30.94
Consensus MFE	-24.65
Energy contribution	-26.09
Covariance contribution	1.44
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.80
SVM decision value	0.17
SVM RNA-class probability	0.618841
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15590528 119 - 23771897
CACACAUAUUGCGGACUGACUGACUGUACAACGGGGCGUAUACUCGUUUU-UUUCGGCGCUUUGCUUUCCACAAUCGCCAGCCCAAAUAAUGUGUAUACGUACAGUUUUUGCUUGCUUUU
..........(((((..(((((.(((.....))).((((((((.((((.(-((..((((..(((.......))).)))).....))).)))).)))))))).))))))))))........ ( -29.00)
>DroSec_CAF1 13782 119 - 1
UACACAUAUUGCGGACUGACUGACUGUACAACGGGGCGUAUUAUCGUUUU-UUUCGGCGCUUUGCUUUCCACAAUCGCCAGCCCAAAUAAUGUGUAUACGUACAGUUUUUGCUCGCUUUU
..........(((..(.(((((((((((((...(((((......).....-....((((..(((.......))).)))).))))........)))))).)).)))))...)..))).... ( -30.30)
>DroSim_CAF1 13745 119 - 1
CACACAUAUUGCGGGCUGACUGACUGUACAACGGGGCGUAUACUCGUUUU-UUUCGGCGCUUUGCUUUCCACAAUCGCCAGCCCAAAUAAUGUGUAUACGUACAGUUUUUGCUCGCUUUU
..........((((((.(((((.(((.....))).((((((((.((((.(-((..((((..(((.......))).)))).....))).)))).)))))))).)))))...)))))).... ( -37.00)
>DroEre_CAF1 13748 110 - 1
-ACACAUACUGCGGACUGA---------CAACGGGGCGUAUACUCGUUUUUUUUCGGCGCUUUGCUUUCCACAAUCGCCAGCCCAAAUAAUGUGUAUACGUACAGUUUUUGCUCGCUUUU
-.........(((..(.((---------.(((...((((((((.((((.(((...((((..(((.......))).)))).....))).)))).))))))))...))))).)..))).... ( -26.90)
>DroYak_CAF1 15068 119 - 1
CACACAUAUUGCGGACUGACUGACUGUACAACGGGGCGUAUACUCGUUUU-UUUCGGCGCUUUGCUUUCCACAAUCGCCAGCCCAAAUAAUGUGUAUACGUACAGUUUUUGCUCGCUUUU
..........(((..(.(((((.(((.....))).((((((((.((((.(-((..((((..(((.......))).)))).....))).)))).)))))))).)))))...)..))).... ( -31.50)
>consensus
CACACAUAUUGCGGACUGACUGACUGUACAACGGGGCGUAUACUCGUUUU_UUUCGGCGCUUUGCUUUCCACAAUCGCCAGCCCAAAUAAUGUGUAUACGUACAGUUUUUGCUCGCUUUU
..........(((..(.(((((.(((.....))).((((((((.((((.......((((..(((.......))).)))).........)))).)))))))).)))))...)..))).... (-24.65 = -26.09 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:06 2006