Locus 3383

Sequence ID	2R_DroMel_CAF1
Location	11,444,096 – 11,444,244
Length	148
Max. P	0.665978

overview

Window 6

Location	11,444,096 – 11,444,214
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	87.97
Mean single sequence MFE	-31.28
Consensus MFE	-22.44
Energy contribution	-22.84
Covariance contribution	0.40
Combinations/Pair	1.23
Mean z-score	-1.88
Structure conservation index	0.72
SVM decision value	0.28
SVM RNA-class probability	0.665978
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11444096 118 + 20766785
GCAUGUGGAAAUGUUGUGUUCAAUCAAAAGCAGCACAUAGUUGCCAUAGAAACCGGCAAACCUAACUUGCAUAAGUUUAUGCAGUUUAUUAACUGUAUAACGGUUAUACAUCUAAGCA
((.(((((.(((..(((((((........).))))))..))).)))))..(((((((((.......))))......((((((((((....)))))))))))))))..........)). ( -32.30)
>DroSec_CAF1 63000 118 + 1
GCACGUGGAAAUGUUGUGUUUAAUCAAAAGCAGCACAUAGUUGCCAUAGAAACCGGCAAACUUAACUUGCAUAAGUUUAUGCAGUUUGUAAUCUGUAAAGCGGUUAUACAUCUAAGCA
((((((....)))).((((.(((((....(((((.....))))).(((((.....(((((((......(((((....))))))))))))..))))).....))))).))))....)). ( -28.40)
>DroSim_CAF1 53006 118 + 1
GCAUGUGGAACUGUUGUGUUUAUUCAAAAGCAGCACAUAGUUGCCAUAGAAACCGGCAAACUUAACUUGCAUAAGUUCAUGCAGUUUGUUAACUGUAUAACGGUUAUACAUCUAAGCA
((.(((((((((((.(((((...........))))))))))).)))))..(((((((((.......))))........((((((((....))))))))..)))))..........)). ( -33.00)
>DroEre_CAF1 59934 118 + 1
GCAUGUGGCAAUGUUGUGUUUAAUCAAAAGCAGCACAUAGUAGUCAUGGAAACCGGCGAGCUCAACUUGCAUAAUUUCGUGCAGUUUGUUAACUGUUUACCGGUAAUGCAUCUAAGGA
(((((((((.((..((((((...........))))))..)).)))))....(((((..(((.(((.((((((......)))))).)))......)))..))))).))))......... ( -31.20)
>DroYak_CAF1 58645 118 + 1
GCAUGUGGCAAUGUUGUGUUUAAUCAAAAGCGGCACACAGUAGUCAUGGCAACCGGCGAACUCAACUUGCAUAAGUUCGUGCAGUUUGUUUGCUGUUCAGCGGUUAUGCAUCUAAGCA
((.((((((....(((........))).....)).)))).(((.((((((..(((((((((..((((.((((......)))))))).))))))))....)..))))))...))).)). ( -31.50)
>consensus
GCAUGUGGAAAUGUUGUGUUUAAUCAAAAGCAGCACAUAGUUGCCAUAGAAACCGGCAAACUUAACUUGCAUAAGUUCAUGCAGUUUGUUAACUGUAUAACGGUUAUACAUCUAAGCA
((.(((((......((((((...........))))))......)))))..(((((((((.......))))........((((((((....))))))))..)))))..........)). (-22.44 = -22.84 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	11,444,134 – 11,444,244
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.71
Mean single sequence MFE	-24.84
Consensus MFE	-14.94
Energy contribution	-15.82
Covariance contribution	0.88
Combinations/Pair	1.24
Mean z-score	-1.62
Structure conservation index	0.60
SVM decision value	0.27
SVM RNA-class probability	0.660300
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11444134 110 + 20766785
AGUUGCCAUAGAAACCGGCAAACCUAACUUGCAUAAGUUUAUGCAGUUUAUUAACUGUAUAACGGUUAUACAUCUAAGCAAAC---------UUUUUU-AAUUUUAAGGAUUCUAUAAGA
..((((..(((((((((((((.......))))......((((((((((....))))))))))))))).....)))).))))..---------......-..................... ( -23.00)
>DroSec_CAF1 63038 110 + 1
AGUUGCCAUAGAAACCGGCAAACUUAACUUGCAUAAGUUUAUGCAGUUUGUAAUCUGUAAAGCGGUUAUACAUCUAAGCAAAC---------UUUUGU-GAUUUUAAGGAUUCUAUGAAA
......(((((((.((.(((((((......(((((....))))))))))))((((...((((..(((.........)))...)---------)))...-))))....)).)))))))... ( -22.60)
>DroSim_CAF1 53044 98 + 1
AGUUGCCAUAGAAACCGGCAAACUUAACUUGCAUAAGUUCAUGCAGUUUGUUAACUGUAUAACGGUUAUACAUCUAAGCAAAC---------UUUUGU-GAUUUUAAG------------
..(((((.........))))).(((((.(..((.(((((..(((....(((((((((.....)))))).))).....))))))---------)).)).-.)..)))))------------ ( -22.30)
>DroEre_CAF1 59972 117 + 1
AGUAGUCAUGGAAACCGGCGAGCUCAACUUGCAUAAUUUCGUGCAGUUUGUUAACUGUUUACCGGUAAUGCAUCUAAGGAAUCUAACUAAGGAAUGCAAGUAGAUAUGUA---UAUACAA
.(((..((((...(((((..(((.(((.((((((......)))))).)))......)))..)))))..(((((((.((........)).))..)))))......))))..---..))).. ( -27.20)
>DroYak_CAF1 58683 107 + 1
AGUAGUCAUGGCAACCGGCGAACUCAACUUGCAUAAGUUCGUGCAGUUUGUUUGCUGUUCAGCGGUUAUGCAUCUAAGCAAAC---------AUUGCU-GUUUUUAGAAA---UAUGAAA
.....(((((.(...((((((((..((((.((((......)))))))).))))))))..(((((((..(((......)))...---------))))))-)......)...---))))).. ( -29.10)
>consensus
AGUUGCCAUAGAAACCGGCAAACUUAACUUGCAUAAGUUCAUGCAGUUUGUUAACUGUAUAACGGUUAUACAUCUAAGCAAAC_________UUUUCU_GAUUUUAAGGA___UAUAAAA
..((((..(((((((((((((.......))))........((((((((....))))))))..))))).....)))).))))....................................... (-14.94 = -15.82 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	11,444,134 – 11,444,244
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.71
Mean single sequence MFE	-22.94
Consensus MFE	-12.06
Energy contribution	-11.90
Covariance contribution	-0.16
Combinations/Pair	1.29
Mean z-score	-1.69
Structure conservation index	0.53
SVM decision value	0.05
SVM RNA-class probability	0.560884
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11444134 110 - 20766785
UCUUAUAGAAUCCUUAAAAUU-AAAAAA---------GUUUGCUUAGAUGUAUAACCGUUAUACAGUUAAUAAACUGCAUAAACUUAUGCAAGUUAGGUUUGCCGGUUUCUAUGGCAACU
..((((((((.((........-.....(---------(((((.((((.((((((.....)))))).))))))))))(((((....)))))......((....)))).))))))))..... ( -23.30)
>DroSec_CAF1 63038 110 - 1
UUUCAUAGAAUCCUUAAAAUC-ACAAAA---------GUUUGCUUAGAUGUAUAACCGCUUUACAGAUUACAAACUGCAUAAACUUAUGCAAGUUAAGUUUGCCGGUUUCUAUGGCAACU
..((((((((.((........-.....(---------(((((...(..((((.........))))..)..))))))(((..((((((.......))))))))).)).))))))))..... ( -22.30)
>DroSim_CAF1 53044 98 - 1
------------CUUAAAAUC-ACAAAA---------GUUUGCUUAGAUGUAUAACCGUUAUACAGUUAACAAACUGCAUGAACUUAUGCAAGUUAAGUUUGCCGGUUUCUAUGGCAACU
------------(((((....-.....(---------(((((.((((.((((((.....)))))).))))))))))(((((....)))))...))))).((((((.......)))))).. ( -22.90)
>DroEre_CAF1 59972 117 - 1
UUGUAUA---UACAUAUCUACUUGCAUUCCUUAGUUAGAUUCCUUAGAUGCAUUACCGGUAAACAGUUAACAAACUGCACGAAAUUAUGCAAGUUGAGCUCGCCGGUUUCCAUGACUACU
.(((((.---.....(((((((..........)).))))).......)))))..((((((....((((....(((((((........))).)))).)))).))))))............. ( -20.82)
>DroYak_CAF1 58683 107 - 1
UUUCAUA---UUUCUAAAAAC-AGCAAU---------GUUUGCUUAGAUGCAUAACCGCUGAACAGCAAACAAACUGCACGAACUUAUGCAAGUUGAGUUCGCCGGUUGCCAUGACUACU
..((((.---...........-.....(---------(((((((.....((......)).....))))))))(((((..((((((((.......)))))))).)))))...))))..... ( -25.40)
>consensus
UUUCAUA___UCCUUAAAAUC_ACAAAA_________GUUUGCUUAGAUGUAUAACCGCUAUACAGUUAACAAACUGCAUGAACUUAUGCAAGUUAAGUUUGCCGGUUUCUAUGGCAACU
...............................................(((...(((((.....(((((....)))))..((((((((.......)))))))).)))))..)))....... (-12.06 = -11.90 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:12 2006