Locus 1342

Sequence ID	3R_DroMel_CAF1
Location	3,965,231 – 3,965,364
Length	133
Max. P	0.973338

overview

Window 5

Location	3,965,231 – 3,965,334
Length	103
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	82.93
Mean single sequence MFE	-36.22
Consensus MFE	-30.92
Energy contribution	-30.92
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.15
Structure conservation index	0.85
SVM decision value	1.66
SVM RNA-class probability	0.970324
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3965231 103 + 27905053
---------GU-AUUCAAAAUAUAUACUUAAGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCA----UUGAU
---------((-((.........)))).......(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).----..... ( -31.50)
>DroPse_CAF1 13522 104 + 1
---------UUUCGGCAAA----AGAUUUGAGCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGAUAUGGAG
---------..(((((...----.(.(((((((((((....))))).)))))).).((.....((((((.....)))))).((((.........))))...))..)))))....... ( -40.10)
>DroSim_CAF1 13390 112 + 1
AAUACUUAAGU-AUUCAAAAUAAAUACUUAAGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCA----UUGAU
...((((((((-(((.......))))))))))).(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).----..... ( -40.40)
>DroYak_CAF1 12360 103 + 1
---------CA-AUUCAAAAAAGAUACUUCAGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCA----UUGAU
---------..-................(((((.(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))))----)))). ( -34.40)
>DroAna_CAF1 13223 99 + 1
----------U-AUAAAAAAAAAG----UAAUCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCUC---AUGAU
----------.-............----......(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))..---..... ( -30.80)
>DroPer_CAF1 14884 104 + 1
---------UUUCGGCAAA----AGAUUUGAGCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGAUAUGGAA
---------..(((((...----.(.(((((((((((....))))).)))))).).((.....((((((.....)))))).((((.........))))...))..)))))....... ( -40.10)
>consensus
_________GU_AUUCAAAA_A_AUACUUAAGCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCA____UUGAU
..................................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).......... (-30.92 = -30.92 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	3,965,231 – 3,965,334
Length	103
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	82.93
Mean single sequence MFE	-40.80
Consensus MFE	-36.93
Energy contribution	-36.93
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.91
SVM decision value	1.71
SVM RNA-class probability	0.973338
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3965231 103 - 27905053
AUCAA----UGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACUUAAGUAUAUAUUUUGAAU-AC---------
.((((----((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))((....)).......))))..-..--------- ( -37.80)
>DroPse_CAF1 13522 104 - 1
CUCCAUAUCGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGCUCAAAUCU----UUUGCCGAAA---------
.......((.(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))(((........----...)))))..--------- ( -41.40)
>DroSim_CAF1 13390 112 - 1
AUCAA----UGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACUUAAGUAUUUAUUUUGAAU-ACUUAAGUAUU
.....----((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))((((((((((((.....))))-))))))))... ( -49.00)
>DroYak_CAF1 12360 103 - 1
AUCAA----UGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACUGAAGUAUCUUUUUUGAAU-UG---------
.(((.----((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))..)))................-..--------- ( -38.00)
>DroAna_CAF1 13223 99 - 1
AUCAU---GAGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGAUUA----CUUUUUUUUUAU-A----------
(((..---..(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).)))..----............-.---------- ( -37.20)
>DroPer_CAF1 14884 104 - 1
UUCCAUAUCGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGCUCAAAUCU----UUUGCCGAAA---------
.......((.(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))(((........----...)))))..--------- ( -41.40)
>consensus
AUCAA____UGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACUUAAGUAU_U_UUUUGAAU_AA_________
..........(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).................................. (-36.93 = -36.93 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	3,965,258 – 3,965,364
Length	106
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.50
Mean single sequence MFE	-31.27
Consensus MFE	-24.30
Energy contribution	-24.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.31
Structure conservation index	0.78
SVM decision value	0.48
SVM RNA-class probability	0.752257
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3965258 106 + 27905053
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCA-UUGAUCAACAUGAGACAAA--AUAGCUACU-UGAACAC-------
.((((((((.......))))).....((((((.....)))))).((((.........))))..))).((((-((..((.....)).....)--)).)))...-.......------- ( -26.30)
>DroVir_CAF1 15274 106 + 1
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCAGUUAAUGUCCAGAGGGCAAA--UUAUAAACU-UUAC-AC-------
(((...(((((...(((..((..((.((((((.....)))))).((((.........))))...)).))..)))...)))))..)))....--.........-....-..------- ( -29.90)
>DroGri_CAF1 13636 115 + 1
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCAGUUAGUCACCCACCGGCAAU--AUAUGAAACAUAAUGCCCGUUACU
...(((((.(((.(..((.((.....((((((.....)))))).((((.........))))...)).))...).))))))))((.((((.(--((.......))).)))).)).... ( -34.00)
>DroWil_CAF1 18247 105 + 1
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCACUUGUCCUCCCAGUGACUAAUACUAGUUAA--UGAA----------
...(((.((((..(..((.((.....((((((.....)))))).((((.........))))...)).))..)..)))).)))..((((((....)))))).--....---------- ( -34.60)
>DroMoj_CAF1 16560 108 + 1
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCAGCUGAUCUCAUGCUGGCAGA--AUAUCAAAUAUUAGGCC-------
.((((((((.......))))).....((((((.....)))))).((((.........))))..))).(.((((((....)).)))).)...--.................------- ( -32.80)
>DroAna_CAF1 13245 103 + 1
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCUCAUGAUCAGGUCGCGCCAAA--CUCAAUACU-UAA-----------
....(((((.......))))).....((((((.....)))))).((((..((((((((.(((.....))).))..))).))).))))....--.........-...----------- ( -30.00)
>consensus
CCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCAGUUGAUCACCAAGCGGCAAA__AUAUAAAAU_UAAA__C_______
.((((((((.......))))).....((((((.....)))))).((((.........))))..)))................................................... (-24.30 = -24.30 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	3,965,258 – 3,965,364
Length	106
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.50
Mean single sequence MFE	-37.92
Consensus MFE	-27.20
Energy contribution	-27.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.04
Structure conservation index	0.72
SVM decision value	-0.04
SVM RNA-class probability	0.513176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3965258 106 - 27905053
-------GUGUUCA-AGUAGCUAU--UUUGUCUCAUGUUGAUCAA-UGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
-------(((..((-((.......--))))...)))(((((((((-((((.....)))...))))))))))(..((((((..((((((....))))))..).)))))..)....... ( -32.80)
>DroVir_CAF1 15274 106 - 1
-------GU-GUAA-AGUUUAUAA--UUUGCCCUCUGGACAUUAACUGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
-------..-....-.........--....(((..(((((...(((..((.(((.....)..(((((((((((.....)).)))))))))..))..))..)))...)))))...))) ( -34.10)
>DroGri_CAF1 13636 115 - 1
AGUAACGGGCAUUAUGUUUCAUAU--AUUGCCGGUGGGUGACUAACUGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
.....((((((.(((((...))))--).))))((((((((.(((((((((.....)))......))))))))).((((((..((((((....))))))..).))))).))))))).. ( -46.40)
>DroWil_CAF1 18247 105 - 1
----------UUCA--UUAACUAGUAUUAGUCACUGGGAGGACAAGUGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
----------....--.................(((((.((((..(((((.....)))))...............(((((..((((((....))))))..).)))))))).))))). ( -41.70)
>DroMoj_CAF1 16560 108 - 1
-------GGCCUAAUAUUUGAUAU--UCUGCCAGCAUGAGAUCAGCUGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
-------((......((((((...--.(..(((((.........((.(((.....)))))..(((((((((((.....)).)))))))))...)))))..).))))))....))... ( -36.50)
>DroAna_CAF1 13245 103 - 1
-----------UUA-AGUAUUGAG--UUUGGCGCGACCUGAUCAUGAGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
-----------...-.......((--(..((((((..(((((..((.(((.....))).)))))))....))))))..)))...((((....))))(((((.......))))).... ( -36.00)
>consensus
_______G__UUAA_AGUAGAUAU__UUUGCCACCAGGAGAUCAACUGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGG
................................................(((..(((((((.........)))).((((((..((((((....))))))..).)))))..)))..))) (-27.20 = -27.20 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:16 2006