Locus 1042

Sequence ID	3L_DroMel_CAF1
Location	3,079,485 – 3,079,627
Length	142
Max. P	0.926672

overview

Window 1

Location	3,079,485 – 3,079,599
Length	114
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	79.20
Mean single sequence MFE	-40.25
Consensus MFE	-29.80
Energy contribution	-29.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.02
Structure conservation index	0.74
SVM decision value	0.03
SVM RNA-class probability	0.549397
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079485 114 + 23771897
GCUCAUGGAAC----CUUUGUUGGAGCACGCAGCCACACUUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUA
((((....(((----....))).))))..........((((((((.....((((.......))))....(((....((((....))))(((((.......))))).))))))))))). ( -37.80)
>DroVir_CAF1 29421 112 + 1
GGG-AUUGUAGCUCCAUUGGUUGGAGCUGC-----AAGUGUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUA
...-.(((((((((((.....)))))))))-----))....(((((((..((((.......))))...........((((....))))(((((.......))))))))))))...... ( -47.80)
>DroPse_CAF1 15026 114 + 1
CUUCAUUACCG----CUCAUUUGGACGGGUGAAACACACGUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUGAGAU
.(((((..(((----..(....)..)))))))).....((.(((((((..((((.......))))...........((((....))))(((((.......)))))))))))))).... ( -37.20)
>DroGri_CAF1 24351 112 + 1
GCG-ACUGUAGCUCCAUGUGGUGGAGAUCA-----CAUAAUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUA
.((-(((((((((((((...(((.....))-----)...)))))).....((((.......))))......)))))).)))((.((.((((((.......))))).).)).))..... ( -40.10)
>DroAna_CAF1 11842 114 + 1
GCUCUUGGGAG----CUCCGUUGGAGCCCGCACCAACACAUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUAAUC
((((....)))----)...(((((.(....).)))))....(((((((..((((.......))))...........((((....))))(((((.......))))))))))))...... ( -42.00)
>DroPer_CAF1 15198 114 + 1
CUUCAUUAGCG----CUCAUUUGGACGGGUGAAACACGCGUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAAGAU
........(((----(((((((....)))))).....))))(((((((..((((.......))))...........((((....))))(((((.......))))))))))))...... ( -36.60)
>consensus
GCUCAUUGGAG____CUCAGUUGGAGCGCG_A__CACACGUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAAGUA
.........................................(((((((..((((.......))))...........((((....))))(((((.......))))))))))))...... (-29.80 = -29.80 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	3,079,485 – 3,079,599
Length	114
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	79.20
Mean single sequence MFE	-38.38
Consensus MFE	-28.90
Energy contribution	-28.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.75
SVM decision value	0.89
SVM RNA-class probability	0.875350
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079485 114 - 23771897
UACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAAGUGUGGCUGCGUGCUCCAACAAAG----GUUCCAUGAGC
.((((.(((....)))))))..((((((((((....(((((.....)))))..((((.......))))....)))))...((..((.....))..)).....)----))))....... ( -38.10)
>DroVir_CAF1 29421 112 - 1
UACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCACACUU-----GCAGCUCCAACCAAUGGAGCUACAAU-CCC
......(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))....((-----(.(((((((.....))))))).))).-... ( -41.10)
>DroPse_CAF1 15026 114 - 1
AUCUCAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCACGUGUGUUUCACCCGUCCAAAUGAG----CGGUAAUGAAG
...(((.(..((((.(((((....)))(((((....(((((.....)))))..((((.......))))....))))).)).))))..)..(((..(....)..----)))...))).. ( -37.20)
>DroGri_CAF1 24351 112 - 1
UACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAUUAUG-----UGAUCUCCACCACAUGGAGCUACAGU-CGC
......(((((..(((((.......)))))......(((((.....)))))..((((.......))))....))))).....(-----(((((((((.....))))).....))-))) ( -36.50)
>DroAna_CAF1 11842 114 - 1
GAUUAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAUGUGUUGGUGCGGGCUCCAACGGAG----CUCCCAAGAGC
(((..(((((...(((((.......)))))..)))))..))).(((.......((((.......)))).......(((.....))))))(((((((...))))----)))........ ( -42.10)
>DroPer_CAF1 15198 114 - 1
AUCUUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCACGCGUGUUUCACCCGUCCAAAUGAG----CGCUAAUGAAG
.(((((((..((((.(((((....)))(((((....(((((.....)))))..((((.......))))....))))).)).))))..)...((..(....)..----)))))).)).. ( -35.30)
>consensus
UACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCACGUGUG__U_ACAGCUCCAACAGAG____CUACAAUGAGC
......(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))......................................... (-28.90 = -28.90 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	3,079,519 – 3,079,627
Length	108
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	81.15
Mean single sequence MFE	-33.69
Consensus MFE	-29.80
Energy contribution	-29.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.88
SVM decision value	0.47
SVM RNA-class probability	0.750252
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079519 108 + 23771897
CUUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUU-UUC----CCAUCUGCCU-----AAUAUUAU
...(((((((..((((.......))))...........((((....))))(((((.......))))))))))))((((((.......-...----.....)))))-----)....... ( -33.96)
>DroVir_CAF1 29453 112 + 1
UGUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACUUUU-UGU----GUUGCCUUUUGCUUUAAUUUUU-
...(((((((..((((.......))))...........((((....))))(((((.......))))))))))))..(((((((....-.))----.)))))................- ( -34.40)
>DroPse_CAF1 15060 111 + 1
CGUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUGAGAUUACUUUUUUUGUUUUUCAUCUGUAA-----AGGAUU--
...(((((((..((((.......))))...........((((....))))(((((.......))))))))))))(((((..((.......)).)))))(((....-----.)))..-- ( -32.10)
>DroGri_CAF1 24383 102 + 1
AAUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACCUUU-UUG----A-U---------GUCAAUAUUC-
...(((((((..((((.......))))...........((((....))))(((((.......)))))))))))).(((....)))..-...----.-.---------..........- ( -31.30)
>DroMoj_CAF1 25722 112 + 1
CAUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACUUUU-UUG----CCAGCUUCCCCCAUUAAUUUUU-
.((((((....((((....(((((((((......)))..((((((.((.((((((.......))))).).)).)))))).......)-)))----))))))..))))))........- ( -39.30)
>DroAna_CAF1 11876 106 + 1
CAUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUAAUCA-CUUUU-UUG----UUUCAUAC-A-----AGUUUUAA
...(((((((..((((.......))))...........((((....))))(((((.......)))))))))))).......-....(-(((----(.....))-)-----))...... ( -31.10)
>consensus
CAUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACUUUU_UUG____CCAGCUGC_A_____AAUAUUA_
...(((((((..((((.......))))...........((((....))))(((((.......))))))))))))............................................ (-29.80 = -29.80 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	3,079,519 – 3,079,627
Length	108
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.15
Mean single sequence MFE	-32.02
Consensus MFE	-28.90
Energy contribution	-28.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.90
SVM decision value	1.18
SVM RNA-class probability	0.926672
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079519 108 - 23771897
AUAAUAUU-----AGGCAGAUGG----GAA-AAAAGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAAG
.......(-----(((.((((..----...-....)))).))))(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))... ( -32.70)
>DroVir_CAF1 29453 112 - 1
-AAAAAUUAAAGCAAAAGGCAAC----ACA-AAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCACA
-................(....)----...-.............(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))... ( -30.10)
>DroPse_CAF1 15060 111 - 1
--AAUCCU-----UUACAGAUGAAAAACAAAAAAAGUAAUCUCAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCACG
--......-----...............................(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))... ( -28.90)
>DroGri_CAF1 24383 102 - 1
-GAAUAUUGAC---------A-U----CAA-AAAGGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAUU
-.....(((..---------.-.----)))-...(((((((((.(((....)))))))..)))))(((((....(((((.....)))))..((((.......))))....)))))... ( -33.30)
>DroMoj_CAF1 25722 112 - 1
-AAAAAUUAAUGGGGGAAGCUGG----CAA-AAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAUG
-........((((((((((((..----...-...))))).....((((...(((((.......)))))..))))(((((.....)))))..((((.......))))....))))))). ( -37.50)
>DroAna_CAF1 11876 106 - 1
UUAAAACU-----U-GUAUGAAA----CAA-AAAAG-UGAUUAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAUG
((((.(((-----(-........----...-..)))-)..))))(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))... ( -29.62)
>consensus
_AAAAAUU_____A_GAAGAAGA____CAA_AAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAUG
............................................(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))... (-28.90 = -28.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:36 2006