Locus 2785

Sequence ID	3L_DroMel_CAF1
Location	7,903,943 – 7,904,076
Length	133
Max. P	0.822955

overview

Window 5

Location	7,903,943 – 7,904,048
Length	105
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	81.20
Mean single sequence MFE	-46.82
Consensus MFE	-38.05
Energy contribution	-38.38
Covariance contribution	0.34
Combinations/Pair	1.16
Mean z-score	-1.51
Structure conservation index	0.81
SVM decision value	0.45
SVM RNA-class probability	0.742436
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7903943 105 + 23771897
UGUGGGCAGGGCUUCCUCCGCCGGUGUGACGAAACAUCGGCCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGUUGGAGGGGCUG-----UCCAU--AUA--G---AAAG
(((((((((..........((((((((......)))))))).(((((((..(((((.((.(((((.....))))))))))))))))))))))-----)))))--)..--.---.... ( -55.80)
>DroVir_CAF1 5661 103 + 1
UGUGGGCAGGGCUUCCUCCGCCUGUGUGACGAAACAUCGGCCCCCCUCCAAGCCCGUCGGCGCCGCGCUCCGACGAACGAUUGGAGUGGCUG-----UUCGGU--AA--G-----UA
.(..(((.(((....))).)))..)....((((....(((((...((((((...((((((.((...)).)))))).....)))))).)))))-----))))..--..--.-----.. ( -37.70)
>DroGri_CAF1 5269 108 + 1
UGUGGGCAGGGCUUCCUCCGCCUGUGUGACGAAACAUAGGCCCCCCUCCAAGGCCGUCAGCGACGCGUUCCGUCGGACGAUUGGAGGGGCUGCAAAUUUUUUA--UA--G-----CA
.....((((..........((((((((......)))))))).(((((((((...((((..(((((.....))))))))).)))))))))))))..........--..--.-----.. ( -46.60)
>DroMoj_CAF1 5440 103 + 1
UGUGGGCAGGACUUCCUCCGCCUGUGUGACGAAACAUCGGCCCCCCUCCAAGACCGUCAGCGACGCGUUCCGUCGGACGGUUGGAGGGGCUG-----UUGUGA--GA--G-----UA
.(..(((.(((.....))))))..)...((...(((.(((((((..((((..((((((..(((((.....))))))))))))))))))))))-----.)))..--..--)-----). ( -45.70)
>DroAna_CAF1 3080 102 + 1
UGUGGGCAGGGCUUCCUCCGCCGGUGUGACGAAACAUCGGCCCCCCUCCGAGACCGUCCGCGACGCGUUCCGUCGGGCGGUUGGAGGGGCUG-----UUUGGA----------AGAA
...........(((((...((((((((......)))))))).(((((((..(((((((((((........)).))))))))))))))))...-----...)))----------)).. ( -51.90)
>DroPer_CAF1 3547 112 + 1
UGUGGGCAGGACUUCCUCCCCCGGUAUUACGAAACAUCGGCCCCCCUCCCAGCCCGUCGGCGAUGCGUUCCGUCGGGCGAUUGGAGGGGCUG-----UCACGAAACAGAGUAGAGAC
...(((.(((....))))))(((((.((....)).)))))..(((((((..(((((.(((.........))).)))))....)))))))(((-----(......))))......... ( -43.20)
>consensus
UGUGGGCAGGGCUUCCUCCGCCGGUGUGACGAAACAUCGGCCCCCCUCCAAGACCGUCAGCGACGCGUUCCGUCGGACGAUUGGAGGGGCUG_____UUCGGA__UA__G_____AA
....((.(((....)))))((((((((......)))))))).(((((((((...((((..(((((.....))))))))).)))))))))............................ (-38.05 = -38.38 +   0.34)

alignment

secondary structure

dotplot

Window 6

Location	7,903,943 – 7,904,048
Length	105
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	81.20
Mean single sequence MFE	-45.35
Consensus MFE	-32.19
Energy contribution	-31.92
Covariance contribution	-0.27
Combinations/Pair	1.19
Mean z-score	-1.81
Structure conservation index	0.71
SVM decision value	0.57
SVM RNA-class probability	0.785744
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7903943 105 - 23771897
CUUU---C--UAU--AUGGA-----CAGCCCCUCCAACCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGGCCGAUGUUUCGUCACACCGGCGGAGGAAGCCCUGCCCACA
....---.--...--.(((.-----((((((((((.(((((((((((.....))))).)).))))...)))))))(((...(.(((((((.....))))))).).)))))).))).. ( -45.30)
>DroVir_CAF1 5661 103 - 1
UA-----C--UU--ACCGAA-----CAGCCACUCCAAUCGUUCGUCGGAGCGCGGCGCCGACGGGCUUGGAGGGGGGCCGAUGUUUCGUCACACAGGCGGAGGAAGCCCUGCCCACA
..-----.--..--......-----...((.((((((..(((((((((.((...)).)))))))))))))))))((((.(..(((((.((.(......))).))))).).))))... ( -41.30)
>DroGri_CAF1 5269 108 - 1
UG-----C--UA--UAAAAAAUUUGCAGCCCCUCCAAUCGUCCGACGGAACGCGUCGCUGACGGCCUUGGAGGGGGGCCUAUGUUUCGUCACACAGGCGGAGGAAGCCCUGCCCACA
..-----.--..--..........(((((((((((((((((((((((.....)))))..)))))..)))))))))(((...(.(((((((.....))))))).).)))))))..... ( -44.00)
>DroMoj_CAF1 5440 103 - 1
UA-----C--UC--UCACAA-----CAGCCCCUCCAACCGUCCGACGGAACGCGUCGCUGACGGUCUUGGAGGGGGGCCGAUGUUUCGUCACACAGGCGGAGGAAGUCCUGCCCACA
..-----.--..--......-----....((((((((((((((((((.....)))))..))))))..)))))))((((.(((.(((((((.....)))))))...)))..))))... ( -45.20)
>DroAna_CAF1 3080 102 - 1
UUCU----------UCCAAA-----CAGCCCCUCCAACCGCCCGACGGAACGCGUCGCGGACGGUCUCGGAGGGGGGCCGAUGUUUCGUCACACCGGCGGAGGAAGCCCUGCCCACA
((((----------(((...-----...(((((((.(((((((((((.....))))).)).))))...))))))).((((.(((......))).)))))))))))............ ( -49.40)
>DroPer_CAF1 3547 112 - 1
GUCUCUACUCUGUUUCGUGA-----CAGCCCCUCCAAUCGCCCGACGGAACGCAUCGCCGACGGGCUGGGAGGGGGGCCGAUGUUUCGUAAUACCGGGGGAGGAAGUCCUGCCCACA
(((......(((((....))-----)))(((((((....(((((.(((.........))).)))))..))))))))))((.((((....)))).))(((.(((....))).)))... ( -46.90)
>consensus
UU_____C__UA__UCAAAA_____CAGCCCCUCCAACCGCCCGACGGAACGCGUCGCCGACGGUCUUGGAGGGGGGCCGAUGUUUCGUCACACAGGCGGAGGAAGCCCUGCCCACA
............................(((((((..(((..(((((.....)))))....)))....))))))).((((.(((......))).))))(((((....))).)).... (-32.19 = -31.92 +  -0.27)

alignment

secondary structure

dotplot

Window 7

Location	7,903,983 – 7,904,076
Length	93
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	82.28
Mean single sequence MFE	-35.03
Consensus MFE	-27.96
Energy contribution	-28.02
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-1.51
Structure conservation index	0.80
SVM decision value	0.25
SVM RNA-class probability	0.654952
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7903983 93 + 23771897
CCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGUUGGAGGGGCUGUCCAU-AUAG-AAAGGUUAACAAGUUAAUA-UAGGGCAUUCUG-G
..(((((((..(((((.((.(((((.....))))))))))))))))))).(((((((-((.(-(...(....)...)).)))-).))))).....-. ( -36.20)
>DroSec_CAF1 3272 94 + 1
CCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGUUGGAGGGGCUGUCAGGGGGUG-AAAGGUUAACAAGUUAAUA-UAGGGCAUUCUG-G
..(((((((..(((((.((.(((((.....))))))))))))))))))).......((((((-....(((((....))))).-.....)))))).-. ( -36.00)
>DroSim_CAF1 3284 94 + 1
CCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGUUGGAGGGGCUGUCAGGGGGUG-AAAGGUUAACAAGUUAAUA-UACGGCAUUCUG-G
..(((((((..(((((.((.(((((.....))))))))))))))))))).......((((((-....(((((....))))).-.....)))))).-. ( -36.00)
>DroEre_CAF1 3529 93 + 1
CCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGCUGGAGGAGCUGUUCAU-AUAG-AGCGGUAAAUAUGUUAAUA-AAGGGCAUUCAG-A
.((((((((.((.(((.((.(((((.....))))))))))))))))).(((((((..-...)-)))))).............-..))).......-. ( -34.90)
>DroYak_CAF1 3302 95 + 1
CCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGUUGGAGGGGCUGUCCAU-AUAGAAGCGGUUAACAUGUUAAUACAAAAGUUUUCUA-A
..(((((((..(((((.((.(((((.....)))))))))))))))))))........-.(((((((.(((((....)))))......).))))))-. ( -33.20)
>DroAna_CAF1 3120 91 + 1
CCCCCCUCCGAGACCGUCCGCGACGCGUUCCGUCGGGCGGUUGGAGGGGCUGUUUGGA-----AGAAGUUCAAAAGUUAAUU-GUCUGCAUGGUAAG
(((((((((..(((((((((((........)).))))))))))))))))...((((((-----.....))))))........-........)).... ( -33.90)
>consensus
CCCCCCUCCGAGACCGUCCGCAACGCGUUCCGUUGGGCGGUUGGAGGGGCUGUCCAG_AUAG_AAAGGUUAACAAGUUAAUA_UAGGGCAUUCUG_G
..(((((((..(((((.((.(((((.....)))))))))))))))))))................................................ (-27.96 = -28.02 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	7,903,983 – 7,904,076
Length	93
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	82.28
Mean single sequence MFE	-31.39
Consensus MFE	-29.90
Energy contribution	-29.35
Covariance contribution	-0.55
Combinations/Pair	1.17
Mean z-score	-1.52
Structure conservation index	0.95
SVM decision value	0.69
SVM RNA-class probability	0.822955
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7903983 93 - 23771897
C-CAGAAUGCCCUA-UAUUAACUUGUUAACCUUU-CUAU-AUGGACAGCCCCUCCAACCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGG
(-(....((((.((-((((((....)))).....-.)))-).)).)).(((((((.(((((((((((.....))))).)).))))...))))))))) ( -31.70)
>DroSec_CAF1 3272 94 - 1
C-CAGAAUGCCCUA-UAUUAACUUGUUAACCUUU-CACCCCCUGACAGCCCCUCCAACCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGG
(-(...........-.......((((((......-.......))))))(((((((.(((((((((((.....))))).)).))))...))))))))) ( -30.92)
>DroSim_CAF1 3284 94 - 1
C-CAGAAUGCCGUA-UAUUAACUUGUUAACCUUU-CACCCCCUGACAGCCCCUCCAACCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGG
.-.......((...-.......((((((......-.......))))))(((((((.(((((((((((.....))))).)).))))...))))))))) ( -31.12)
>DroEre_CAF1 3529 93 - 1
U-CUGAAUGCCCUU-UAUUAACAUAUUUACCGCU-CUAU-AUGAACAGCUCCUCCAGCCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGG
.-.......(((..-......(((((........-..))-))).......(((((((((((((((((.....))))).)).))).)).)))))))). ( -30.20)
>DroYak_CAF1 3302 95 - 1
U-UAGAAAACUUUUGUAUUAACAUGUUAACCGCUUCUAU-AUGGACAGCCCCUCCAACCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGG
.-.....(((...(((....))).)))..((((((((..-..))).)))((((((.(((((((((((.....))))).)).))))...)))))))). ( -32.40)
>DroAna_CAF1 3120 91 - 1
CUUACCAUGCAGAC-AAUUAACUUUUGAACUUCU-----UCCAAACAGCCCCUCCAACCGCCCGACGGAACGCGUCGCGGACGGUCUCGGAGGGGGG
....((.......(-((.......))).......-----.........(((((((.(((((((((((.....))))).)).))))...))))))))) ( -32.00)
>consensus
C_CAGAAUGCCCUA_UAUUAACUUGUUAACCUCU_CUAU_ACGGACAGCCCCUCCAACCGCCCAACGGAACGCGUUGCGGACGGUCUCGGAGGGGGG
................................................(((((((.(((((((((((.....))))).)).))))...))))))).. (-29.90 = -29.35 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:36 2006