Locus 4663

Sequence ID	X_DroMel_CAF1
Location	12,183,040 – 12,183,199
Length	159
Max. P	0.997327

overview

Window 0

Location	12,183,040 – 12,183,159
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-19.08
Consensus MFE	-18.15
Energy contribution	-17.96
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.57
Structure conservation index	0.95
SVM decision value	0.68
SVM RNA-class probability	0.820025
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12183040 119 + 22224390
CCAUUU-UAUCCCUGCCUUCUUUACGUUUUUGUUGUUCAUUUUUUUUCGUAUUUUGGCCAACGCGUAAAAUAUGCUUAAAUAUUUUAAAUUUAAUCACACGCUUCGCUGGCCUCGGCAAA
......-......((((.....((((.....................))))....(((((..(((.......((.((((((.......)))))).)).......))))))))..)))).. ( -20.14)
>DroSec_CAF1 9643 115 + 1
CCAUUUUUUUCCCUGCCUUCUUUACGUUUUUGUUGCUCUUU---UUU--UAUUUUGGCCAACGCGUAAAAUAUGCUUAAAUAUUUUAAAUUUAAUCACACGCUUCGCUGGCCUCGGCAAA
.............((((......(((....)))........---...--......(((((..(((.......((.((((((.......)))))).)).......))))))))..)))).. ( -18.64)
>DroSim_CAF1 12359 118 + 1
CCAUUUUUUUCCCUGCCUUCUUUACGUUUUUGUUGCUCUUUUUUUUU--UAUUUUGGCCAACGCGUAAAAUAUGCUUAAAUAUUUUAAAUUUAAUCACACGCUUCGCUGGCCUCGGCAAA
.............((((......(((....)))..............--......(((((..(((.......((.((((((.......)))))).)).......))))))))..)))).. ( -18.64)
>DroEre_CAF1 9789 113 + 1
CCAUUU-UUUCCCAGCCUUCUUUGCGUUUUUGUUGUUCUUUUUGU------UUUUGGCCAACGCGUAAAAUAUGCUUAAAUAUUUUAAAUUUAAUCACACGCUUCGCUGGCCUCGGCAAA
......-....(((((.......((((....((((..(.......------....)..))))...((((((((......))))))))...........))))...))))).......... ( -18.90)
>consensus
CCAUUU_UUUCCCUGCCUUCUUUACGUUUUUGUUGCUCUUUUUUUUU__UAUUUUGGCCAACGCGUAAAAUAUGCUUAAAUAUUUUAAAUUUAAUCACACGCUUCGCUGGCCUCGGCAAA
..............(((......(((....)))......................(((((..(((.......((.((((((.......)))))).)).......))))))))..)))... (-18.15 = -17.96 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	12,183,040 – 12,183,159
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.13
Mean single sequence MFE	-27.30
Consensus MFE	-25.98
Energy contribution	-26.23
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-3.42
Structure conservation index	0.95
SVM decision value	2.84
SVM RNA-class probability	0.997327
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12183040 119 - 22224390
UUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUACGAAAAAAAAUGAACAACAAAAACGUAAAGAAGGCAGGGAUA-AAAUGG
((((((..((((((((....(((((.((((((.......)))))).)))))......))))))))....((((.....................)))).....))))))....-...... ( -29.00)
>DroSec_CAF1 9643 115 - 1
UUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUA--AAA---AAAGAGCAACAAAAACGUAAAGAAGGCAGGGAAAAAAAUGG
((((((..((((((((....(((((.((((((.......)))))).)))))......))))))))......--...---........((......))......))))))........... ( -27.50)
>DroSim_CAF1 12359 118 - 1
UUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUA--AAAAAAAAAGAGCAACAAAAACGUAAAGAAGGCAGGGAAAAAAAUGG
((((((..((((((((....(((((.((((((.......)))))).)))))......))))))))......--..............((......))......))))))........... ( -27.50)
>DroEre_CAF1 9789 113 - 1
UUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAA------ACAAAAAGAACAACAAAAACGCAAAGAAGGCUGGGAAA-AAAUGG
(((.(((.((((((((....(((((.((((((.......)))))).)))))......))))))))....------....................((.......))))).)))-...... ( -25.20)
>consensus
UUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUA__AAAAAAAAAGAACAACAAAAACGUAAAGAAGGCAGGGAAA_AAAUGG
((((((..((((((((....(((((.((((((.......)))))).)))))......)))))))).............................(.....)..))))))........... (-25.98 = -26.23 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	12,183,079 – 12,183,199
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.52
Mean single sequence MFE	-29.55
Consensus MFE	-27.10
Energy contribution	-27.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.92
SVM decision value	1.56
SVM RNA-class probability	0.963787
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12183079 120 - 22224390
AAGCAGCUUCACAUCAUUUGUUUGCAUAUGCAUUGACGUAUUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUACGAAAAAAA
..(((((...(((.....)))..))...))).....(((((((.....((((((((....(((((.((((((.......)))))).)))))......)))))))).)))))))....... ( -30.70)
>DroSec_CAF1 9683 115 - 1
AAGCAGCUUCACAUCAUUUGUUCGCAUAUGCAUUGACGUAUUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUA--AAA---A
................((((((.(((.((((......)))).)))...((((((((....(((((.((((((.......)))))).)))))......))))))))..))))--)).---. ( -28.00)
>DroSim_CAF1 12399 118 - 1
AAGCAGCUUCACAUCAUUUGUUUGCAUAUGCAUUGACGUAUUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUA--AAAAAAA
................((((((((((.((((......)))).)))...((((((((....(((((.((((((.......)))))).)))))......)))))))).)))))--))..... ( -29.20)
>DroEre_CAF1 9828 114 - 1
AAGCAGCUUCACAUCAUUUGUUUGCAUAUGCAUUGACGUAUUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAA------ACAAA
................((((((((((.((((......)))).)))...((((((((....(((((.((((((.......)))))).)))))......))))))))..))------))))) ( -30.30)
>consensus
AAGCAGCUUCACAUCAUUUGUUUGCAUAUGCAUUGACGUAUUUGCCGAGGCCAGCGAAGCGUGUGAUUAAAUUUAAAAUAUUUAAGCAUAUUUUACGCGUUGGCCAAAAUA__AAAAAAA
..(((((.(((...(((.((....)).)))...))).))...)))...((((((((....(((((.((((((.......)))))).)))))......))))))))............... (-27.10 = -27.10 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:25 2006