Locus 287

Sequence ID	2R_DroMel_CAF1
Location	1,697,485 – 1,697,616
Length	131
Max. P	0.986936

overview

Window 8

Location	1,697,485 – 1,697,590
Length	105
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	82.46
Mean single sequence MFE	-30.10
Consensus MFE	-29.60
Energy contribution	-29.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.98
SVM decision value	1.69
SVM RNA-class probability	0.972498
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1697485 105 + 20766785
AAAUGUAUAGAGG-----AUAAAAAAAUGUGUUUGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGC
............(-----(((((........))))))(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) ( -32.60)
>DroGri_CAF1 9999 103 + 1
A-A-----GAAGCAUAACAUGAA-AAAAAUUAUUGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGC
.-.-----...............-.............(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) ( -29.60)
>DroSec_CAF1 83237 89 + 1
---------------------AAAAAAAGUAUUUGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGC
---------------------................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) ( -29.60)
>DroWil_CAF1 13069 98 + 1
AAA-----CCC-------AAUAAAAAAAUCAUUUUGCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGC
...-----...-------...................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) ( -29.60)
>DroYak_CAF1 8782 96 + 1
-AAAGU------------GUUAAA-AAAGUGUUUGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGC
-.....------------......-............(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) ( -29.60)
>DroMoj_CAF1 8578 96 + 1
--U-----AGCGAAC------AA-AAAAAUUAUAUCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGC
--.-----.......------..-.............(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) ( -29.60)
>consensus
__A_______________AU_AAAAAAAGUAUUUGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGC
.....................................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))) (-29.60 = -29.60 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	1,697,485 – 1,697,590
Length	105
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	82.46
Mean single sequence MFE	-37.65
Consensus MFE	-36.90
Energy contribution	-36.90
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.34
Structure conservation index	0.98
SVM decision value	2.06
SVM RNA-class probability	0.986936
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1697485 105 - 20766785
GCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACAAACACAUUUUUUUAU-----CCUCUAUACAUUU
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))...................-----............. ( -36.90)
>DroGri_CAF1 9999 103 - 1
GCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACAAUAAUUUUU-UUCAUGUUAUGCUUC-----U-U
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))((..(((((....-.....)))))...))-----.-. ( -37.30)
>DroSec_CAF1 83237 89 - 1
GCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACAAAUACUUUUUUU---------------------
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))................--------------------- ( -36.90)
>DroWil_CAF1 13069 98 - 1
GCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGCAAAAUGAUUUUUUUAUU-------GGG-----UUU
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))((..(((((.....)))))-------..)-----).. ( -39.10)
>DroYak_CAF1 8782 96 - 1
GCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACAAACACUUU-UUUAAC------------ACUUU-
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))............-......------------.....- ( -36.90)
>DroMoj_CAF1 8578 96 - 1
GCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGAUAUAAUUUUU-UU------GUUCGCU-----A--
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))(((((........-.)------))))...-----.-- ( -38.80)
>consensus
GCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACAAAAACUUUUUUU_AU_______________U__
(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))..................................... (-36.90 = -36.90 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	1,697,513 – 1,697,616
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.33
Mean single sequence MFE	-34.15
Consensus MFE	-30.62
Energy contribution	-30.62
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.90
SVM decision value	1.12
SVM RNA-class probability	0.918438
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1697513 103 + 20766785
--UGU-CGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCAUGUAAGG-------CGGAAAAAAAAUUU------UCU-
--.((-((((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).......))-------)((((((....)))------)))- ( -32.11)
>DroVir_CAF1 17990 103 + 1
UGAGU-CGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCCAUGUUUGC-------CGGG--UGAAUUUU------UAU-
....(-(((((((((((((.......))))).....((((((.....)))))).((((.........))))..))).(((.......))-------))))--))).....------...- ( -37.70)
>DroGri_CAF1 10025 98 + 1
--UGU-CGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUGUU-------------GUA--CACCAGCUGUCUAA----
--...-.(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).(((-------------(..--...)))).......---- ( -32.60)
>DroWil_CAF1 13090 103 + 1
--UUG-CGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCGAUGUCUAC-------UCCCG-AAAAAUUU------GUAA
--...-((((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))))........-------.....-........------.... ( -33.00)
>DroYak_CAF1 8801 101 + 1
--UGU-CGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGUGGAAAC-------UUCG--AAAAAUGU------UCU-
--...-.(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))((.(....)-------..))--........------...- ( -32.80)
>DroAna_CAF1 9579 109 + 1
--AAUCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAAAAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCCACGGAGACGCUCGAGCAGCAAAAAAAUU--------CA-
--..((((((....))))))(((((.((.((.....((((((.....)))))).((((.........))))...)).))...((....)).))))).............--------..- ( -36.70)
>consensus
__UGU_CGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCAUGUAAAC_______CGGA__AAAAAUUU______UCU_
.......(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))........................................ (-30.62 = -30.62 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	1,697,513 – 1,697,616
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.33
Mean single sequence MFE	-37.78
Consensus MFE	-36.47
Energy contribution	-36.47
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.02
Structure conservation index	0.97
SVM decision value	0.22
SVM RNA-class probability	0.639490
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1697513 103 - 20766785
-AGA------AAAUUUUUUUUCCG-------CCUUACAUGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCG-ACA--
-.((------(((....)))))..-------.........(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).-...-- ( -38.50)
>DroVir_CAF1 17990 103 - 1
-AUA------AAAAUUCA--CCCG-------GCAAACAUGGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCG-ACUCA
-...------........--....-------.........(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).-..... ( -36.90)
>DroGri_CAF1 10025 98 - 1
----UUAGACAGCUGGUG--UAC-------------AACAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCG-ACA--
----..............--...-------------....(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).-...-- ( -37.10)
>DroWil_CAF1 13090 103 - 1
UUAC------AAAUUUUU-CGGGA-------GUAGACAUCGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCG-CAA--
....------........-.....-------........((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))))-...-- ( -38.10)
>DroYak_CAF1 8801 101 - 1
-AGA------ACAUUUUU--CGAA-------GUUUCCACGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCG-ACA--
-...------........--....-------.........(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).-...-- ( -36.90)
>DroAna_CAF1 9579 109 - 1
-UG--------AAUUUUUUUGCUGCUCGAGCGUCUCCGUGGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUUUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGAUU--
-..--------..........((((((..((((..((((((((.....))).))..)))...))))..((((....(((((....)))))((((.......))))))))))))))...-- ( -39.20)
>consensus
_AGA______AAAUUUUU__CCCG_______GUAUACAUGGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCG_ACA__
........................................(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))....... (-36.47 = -36.47 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:36 2006