Locus 1436

Sequence ID	3L_DroMel_CAF1
Location	4,153,828 – 4,153,965
Length	137
Max. P	0.999424

overview

Window 7

Location	4,153,828 – 4,153,925
Length	97
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	70.97
Mean single sequence MFE	-29.93
Consensus MFE	-23.12
Energy contribution	-23.46
Covariance contribution	0.34
Combinations/Pair	1.17
Mean z-score	-1.88
Structure conservation index	0.77
SVM decision value	3.59
SVM RNA-class probability	0.999424
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153828 97 + 23771897
-UAAUG-------GGAAAUAU---UGGCCAUUUGAAAAGCACCUGCUGUGCUGAGUGACCGCACUUCG---------CUCGUCAAGUGUGGUAUUUUUUAGUACGUUUCGGCGCUUA
-.((((-------(.......---...)))))....((((.((.((.((((((((..(((((((((..---------......)))))))))....))))))))))...)).)))). ( -30.40)
>DroSim_CAF1 3415 108 + 1
UAAAUUUAAGCAUGUAAGCACUUGUUACUUUUUGAAAAGCACCCGCUGUGCUGAGUGACCGCACUUUG---------CUCGGCAAGUGUGGUAUUUUUUAGUACUUUUCGGCGCUUA
....((((((...((((.(....)))))..))))))((((.((....((((((((..(((((((((.(---------(...)))))))))))....)))))))).....)).)))). ( -31.20)
>DroYak_CAF1 3585 114 + 1
---AUUGAAAUAUUUACACACUUGUUCCUAUUUGAAAAGCACCUGCUGUACUGAGUGACCGCAUUCCGUAAUGCUACCUCGCAAGACGUGGUAUUUUUUAGUACAUUUCGGCGCUCG
---.((.(((((...(((....)))...))))).)).(((.((...(((((((((((....)))))...((((((((.((....)).))))))))....))))))....)).))).. ( -28.20)
>consensus
__AAUU_AA__AUGUAAACACUUGUUACUAUUUGAAAAGCACCUGCUGUGCUGAGUGACCGCACUUCG_________CUCGCCAAGUGUGGUAUUUUUUAGUACAUUUCGGCGCUUA
....................................((((.((...(((((((((..(((((((((.................)))))))))....)))))))))....)).)))). (-23.12 = -23.46 +   0.34)

alignment

secondary structure

dotplot

Window 8

Location	4,153,828 – 4,153,925
Length	97
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	70.97
Mean single sequence MFE	-26.27
Consensus MFE	-16.25
Energy contribution	-15.26
Covariance contribution	-0.99
Combinations/Pair	1.29
Mean z-score	-1.71
Structure conservation index	0.62
SVM decision value	1.56
SVM RNA-class probability	0.963714
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153828 97 - 23771897
UAAGCGCCGAAACGUACUAAAAAAUACCACACUUGACGAG---------CGAAGUGCGGUCACUCAGCACAGCAGGUGCUUUUCAAAUGGCCA---AUAUUUCC-------CAUUA-
.(((((((.................(((.(((((......---------..))))).)))......((...)).)))))))....(((((...---.......)-------)))).- ( -20.50)
>DroSim_CAF1 3415 108 - 1
UAAGCGCCGAAAAGUACUAAAAAAUACCACACUUGCCGAG---------CAAAGUGCGGUCACUCAGCACAGCGGGUGCUUUUCAAAAAGUAACAAGUGCUUACAUGCUUAAAUUUA
((((((..((((((((((.......(((.(((((((...)---------).))))).)))......((...)).))))))))))...(((((.....)))))...))))))...... ( -28.40)
>DroYak_CAF1 3585 114 - 1
CGAGCGCCGAAAUGUACUAAAAAAUACCACGUCUUGCGAGGUAGCAUUACGGAAUGCGGUCACUCAGUACAGCAGGUGCUUUUCAAAUAGGAACAAGUGUGUAAAUAUUUCAAU---
.(((((((....((((((......((((.((.....)).))))(((((....)))))........))))))...))))))).............((((((....))))))....--- ( -29.90)
>consensus
UAAGCGCCGAAAAGUACUAAAAAAUACCACACUUGACGAG_________CGAAGUGCGGUCACUCAGCACAGCAGGUGCUUUUCAAAUAGCAACAAGUGUUUACAU__UU_AAUU__
.(((((((.................(((.(((((.................))))).)))......((...)).))))))).................................... (-16.25 = -15.26 +  -0.99)

alignment

secondary structure

dotplot

Window 9

Location	4,153,854 – 4,153,965
Length	111
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.75
Mean single sequence MFE	-42.53
Consensus MFE	-32.95
Energy contribution	-33.73
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-2.74
Structure conservation index	0.77
SVM decision value	1.14
SVM RNA-class probability	0.921795
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153854 111 + 23771897
AGCACCUGCUGUGCUGAGUGACCGCACUUCG---------CUCGUCAAGUGUGGUAUUUUUUAGUACGUUUCGGCGCUUAGCGCGUGCGGUCACACAAACGCCAGGUACGUGUCCAAAAU
.(.(((((.(((..((.((((((((((..((---------(((((((((((((.((.....)).))))))).))))...)))).)))))))))).)).))).))))).)........... ( -43.60)
>DroSim_CAF1 3452 111 + 1
AGCACCCGCUGUGCUGAGUGACCGCACUUUG---------CUCGGCAAGUGUGGUAUUUUUUAGUACUUUUCGGCGCUUAGCGCGUGCGGUCACACAAACGCCAAGUACGUGUCCAAAAU
.((((.((((((((((((..(((((((((.(---------(...)))))))))))..............))))))))..)))).))))((.(((....((.....))..))).))..... ( -39.99)
>DroYak_CAF1 3619 120 + 1
AGCACCUGCUGUACUGAGUGACCGCAUUCCGUAAUGCUACCUCGCAAGACGUGGUAUUUUUUAGUACAUUUCGGCGCUCGGCGCCUGCGGUCACACAAACGCCAAGUACGUGUCCAAAAU
.((((.((((....((.(((((((((......((((((((.((....)).))))))))..............(((((...)))))))))))))).)).......)))).))))....... ( -44.00)
>consensus
AGCACCUGCUGUGCUGAGUGACCGCACUUCG_________CUCGCCAAGUGUGGUAUUUUUUAGUACAUUUCGGCGCUUAGCGCGUGCGGUCACACAAACGCCAAGUACGUGUCCAAAAU
.((((.(((((((.((.((((((((((..........................(((((....)))))......((((...)))))))))))))).))..)))..)))).))))....... (-32.95 = -33.73 +   0.78)

alignment

secondary structure

dotplot

Window 0

Location	4,153,854 – 4,153,965
Length	111
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	85.75
Mean single sequence MFE	-41.83
Consensus MFE	-35.57
Energy contribution	-35.47
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-2.56
Structure conservation index	0.85
SVM decision value	1.34
SVM RNA-class probability	0.943850
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153854 111 - 23771897
AUUUUGGACACGUACCUGGCGUUUGUGUGACCGCACGCGCUAAGCGCCGAAACGUACUAAAAAAUACCACACUUGACGAG---------CGAAGUGCGGUCACUCAGCACAGCAGGUGCU
...........(((((((..(((((.((((((((((((((...))))((...(((.(.................))))..---------))..)))))))))).))).))..))))))). ( -40.93)
>DroSim_CAF1 3452 111 - 1
AUUUUGGACACGUACUUGGCGUUUGUGUGACCGCACGCGCUAAGCGCCGAAAAGUACUAAAAAAUACCACACUUGCCGAG---------CAAAGUGCGGUCACUCAGCACAGCGGGUGCU
...........(((((((..(((((.((((((((((((.....))((((..((((...............))))..)).)---------)...)))))))))).))).))..))))))). ( -39.16)
>DroYak_CAF1 3619 120 - 1
AUUUUGGACACGUACUUGGCGUUUGUGUGACCGCAGGCGCCGAGCGCCGAAAUGUACUAAAAAAUACCACGUCUUGCGAGGUAGCAUUACGGAAUGCGGUCACUCAGUACAGCAGGUGCU
...........(((((((..(((((.((((((((((((((...))))).....................(((..(((......)))..)))...))))))))).))).))..))))))). ( -45.40)
>consensus
AUUUUGGACACGUACUUGGCGUUUGUGUGACCGCACGCGCUAAGCGCCGAAAAGUACUAAAAAAUACCACACUUGACGAG_________CGAAGUGCGGUCACUCAGCACAGCAGGUGCU
...........(((((((..(((((.((((((((((((((...))))......(((........)))..........................)))))))))).))).))..))))))). (-35.57 = -35.47 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:37 2006