Locus 4401

Sequence ID	3R_DroMel_CAF1
Location	11,634,615 – 11,634,839
Length	224
Max. P	0.691700

overview

Window 6

Location	11,634,615 – 11,634,731
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.54
Mean single sequence MFE	-28.10
Consensus MFE	-21.31
Energy contribution	-21.87
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-2.90
Structure conservation index	0.76
SVM decision value	0.33
SVM RNA-class probability	0.691700
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11634615 116 + 27905053
AGUUCGCAGACCAA----UGCCAAAGUAAAGAUUUCCACGUUGUGGCUGUAACGGAACCAAAAUGGGUUCGCCAAUAGCCAAAGACGUUCAAGAACUUUACAACAAAUAAAGAAAAAUAU
..((((((......----)))....((((((.(((..(((((.(((((((....(((((......)))))....)))))))..)))))...))).))))))..........)))...... ( -29.80)
>DroSec_CAF1 15765 115 + 1
AGUUCGUAGACCAA----UGCCAAAGUAAAGAUUUCCACGUUGUGGCUGUAAAGGAACCAAAAUGGGUUCGCCAAUAGCCAAAGACGUUCAAGAACUUUACAACAAAUAAAGAA-AAUAU
..((((((......----)))....((((((.(((..(((((.(((((((....(((((......)))))....)))))))..)))))...))).))))))..........)))-..... ( -27.80)
>DroSim_CAF1 13063 115 + 1
AGUUCGCAGACCAA----UGCCCAAGUAAAGAUUUCCACGUUGUGGCUGUAAAGGAACCGAAAUGGGUUCGCCAAUAGCCAAAAACGUUCAAGAACUUUACAACAAAUAAAGAA-AAUAU
..((((((......----)))....((((((.(((..(((((.(((((((....(((((......)))))....)))))))..)))))...))).))))))..........)))-..... ( -29.60)
>DroEre_CAF1 13674 113 + 1
AGUUCGCAGAUUAA----UGCCAAAGUAAAGAUUUCCACGUUGUGGCAGUAAAGGAACCAAAAUGGCUUCGCCAAUAGCCAAAGACGUUCAAGAACUUUACAACAAAU--AAAG-AAUAU
.(((((((......----)))....((((((.(((..(((((.((((......(....)....((((...))))...))))..)))))...))).)))))).......--...)-))).. ( -25.10)
>DroYak_CAF1 16146 115 + 1
AGUUCGCAGACUAA----UGCCGAAGUAAAGAUUUCCACGUUGUGGCUGUAAAGGAACCGAAAUGGGUUCGCCAGUAGCCAAAGACGUUCAAGAACUUUACAACAAAUUAAAAA-AAUAU
..((((((......----)).))))((((((.(((..(((((.((((((.....(((((......))))).....))))))..)))))...))).)))))).............-..... ( -28.60)
>DroAna_CAF1 14852 119 + 1
AGUUCGCAGAUUAAGAGAUUUCGAAGUAAAGAUUUCCACGUUGUGGCUGCAAGGAACAUAAAAUUAGUUCGCCAAAAGCCAACAACGUUCAAGAACUUUACAACAAUAUUACAU-UUUCU
..((((.(((((....)))))))))((((((.(((..(((((((((((....(((((.........)))).)....)))).)))))))...))).)))))).............-..... ( -27.70)
>consensus
AGUUCGCAGACCAA____UGCCAAAGUAAAGAUUUCCACGUUGUGGCUGUAAAGGAACCAAAAUGGGUUCGCCAAUAGCCAAAGACGUUCAAGAACUUUACAACAAAUAAAGAA_AAUAU
.........................((((((.(((..(((((.(((((((....(((((......)))))....)))))))..)))))...))).))))))................... (-21.31 = -21.87 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	11,634,731 – 11,634,839
Length	108
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	77.06
Mean single sequence MFE	-14.91
Consensus MFE	-1.36
Energy contribution	-1.24
Covariance contribution	-0.12
Combinations/Pair	1.33
Mean z-score	-1.42
Structure conservation index	0.09
SVM decision value	0.05
SVM RNA-class probability	0.560716
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11634731 108 - 27905053
UUUGCUUUUUUGAGGUAUUCCUUUCA----ACUACUUUCACAGCUCCUUA--AAAAUUCAUUUG--UGCUGU-UCA-UUUCCACUAUCUUUUAUGAGAUUUUAGUUUGUACAUACAUA
..((..(((((((((...........----...............)))))--))))..))..((--((.(((-.((-........(((((....))))).......)).))))))).. ( -14.03)
>DroSec_CAF1 15880 105 - 1
UUUGC-UUUUUAAGGUGUUCCUUUUA----ACCACUUUCACAGCUCCUUA--AAAAUUCAUUUGUGUGCAGU-UCA-UUUCCACUAUCUUUUAUGGCAUUUCAGUUUGCAC----AUA
.....-(((((((((.(((.......----...........))).)))))--))))......(((((((((.-...-...(((.((.....))))).........))))))----))) ( -17.86)
>DroSim_CAF1 13178 106 - 1
UUUGCCUUUUUAAGGUGUUCCUUUUA----ACCACUUUCACAGCUCUUUA--AAAAUUCAUUUGUGUGCCGU-UCA-UUUCCACUAUCUUUUAUGGCAUUUCAGUUUGCAC----AUA
..(((.(((((((((.(((.......----...........))).)))))--)))).....(((.(((((((-...-...............)))))))..)))...))).----... ( -14.64)
>DroEre_CAF1 13787 108 - 1
UUUGCCUUUAUAAGCUGUUCUUUUCA----ACCACUUUCACAGCUCCUAAAAAAAGUUAUUUUGUGUGCAGC-UCG-UUUACACCUUCUUUUAUAGCACUUCAGUUUGCAC----AUA
......((((..((((((........----.........))))))..))))...........((((((((((-(..-.................)))((....)).)))))----))) ( -14.74)
>DroYak_CAF1 16261 103 - 1
---------UUAAAAUGUUAUUUGCAACCAACCACUUACACAACUACUUA--AAAGUUAUUUCAUGUGCACUAUUGUGUUCCACUAUCUUUUAUGGCAUUUCAGUUUGCAC----AUA
---------......(((.....)))...............((((.....--..)))).....(((((((..((((.((.(((.((.....))))).))..)))).)))))----)). ( -13.30)
>consensus
UUUGC_UUUUUAAGGUGUUCCUUUCA____ACCACUUUCACAGCUCCUUA__AAAAUUCAUUUGUGUGCAGU_UCA_UUUCCACUAUCUUUUAUGGCAUUUCAGUUUGCAC____AUA
...............................................................................................(((........)))......... ( -1.36 =  -1.24 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:11 2006