Locus 186

Sequence ID	2R_DroMel_CAF1
Location	1,443,098 – 1,443,251
Length	153
Max. P	0.914737

overview

Window 2

Location	1,443,098 – 1,443,214
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.06
Mean single sequence MFE	-33.74
Consensus MFE	-26.22
Energy contribution	-26.78
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.08
Structure conservation index	0.78
SVM decision value	1.10
SVM RNA-class probability	0.914737
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1443098 116 + 20766785
AUGUUGUUA----GGGGCUGCGGUUGCGCUUAAAUGCGCCAUUAAAGCCACGGUCAGCAAAAACAAUGCCAGAAAUCUGGCAUUCAGGGGCAGGGAAAGGAGCGAAUAGAUUUGGGCGUA
.(((((...----(.((((..(((.((((......)))).)))..)))).)...))))).....((((((((....)))))))).................(((..((....))..))). ( -33.50)
>DroSec_CAF1 61088 109 + 1
AUGUUGUUA----GGGGCUGCGGUUGCGCUUAAAUGCGCCAUUAAAGCCACGGUCAGCAAAAACAAUGCCAGAAAUCUGGCAUUCAG-------GAAAGGAGCGAGUAGAUUUGGCCAUA
.(((((...----(.((((..(((.((((......)))).)))..)))).)...))))).....((((((((....))))))))...-------....((..((((....)))).))... ( -34.80)
>DroSim_CAF1 59839 109 + 1
AUGUUGUUA----GGGGCUGCGGUUGCGCUUAAAUGCGCCAUUAAAGCCACGGUCAGCAAAAACAAUGCCAGAAAUCUGGCAUUCAG-------GAAAGGAGCGAAUAGAUUUGGCCAUA
.(((((...----(.((((..(((.((((......)))).)))..)))).)...))))).....((((((((....))))))))...-------....((..((((....)))).))... ( -35.10)
>DroEre_CAF1 70264 108 + 1
AUGUUGUUA----GGGGCUGCGGUUGCGCUUAAAUGCGCCAUUAAAGCCACGGUCAGCAAGAACAAUGCCAGAAAUCUGU-GUUAGG-------GAAAAAGGAGAACAGAUUUGGGCAUA
.(((((...----(.((((..(((.((((......)))).)))..)))).)...)))))......(((((..((((((((-......-------...........)))))))).))))). ( -35.83)
>DroYak_CAF1 65954 111 + 1
AUGUUGUUAGGUAGGGGCUGCGGUUGCGCUUAAAUGCGCCAUUAAAGCCACGGUCAGCAAAAACAAUCCCAGAAAUCUGU-GUUAGG--------AAAAGAGAGAAUAGAUUUGGGCAUA
..((((((..((...(((((.((((((((......))))......)))).))))).))...))))))((((..(((((((-......--------..........))))))))))).... ( -29.49)
>consensus
AUGUUGUUA____GGGGCUGCGGUUGCGCUUAAAUGCGCCAUUAAAGCCACGGUCAGCAAAAACAAUGCCAGAAAUCUGGCAUUCAG_______GAAAGGAGCGAAUAGAUUUGGGCAUA
.(((((.........((((..(((.((((......)))).)))..)))).....))))).....((((((((....)))))))).................................... (-26.22 = -26.78 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	1,443,134 – 1,443,251
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.77
Mean single sequence MFE	-26.92
Consensus MFE	-18.04
Energy contribution	-19.08
Covariance contribution	1.04
Combinations/Pair	1.06
Mean z-score	-1.64
Structure conservation index	0.67
SVM decision value	0.05
SVM RNA-class probability	0.558049
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1443134 117 - 20766785
CAAUGUGUGGGCAUCUCCUUUUUUGCCAGGUCU---CUGCUACGCCCAAAUCUAUUCGCUCCUUUCCCUGCCCCUGAAUGCCAGAUUUCUGGCAUUGUUUUUGCUGACCGUGGCUUUAAU
........(((....)))......((((((((.---..((.((..............((..........)).....((((((((....))))))))))....)).)))).))))...... ( -27.70)
>DroSec_CAF1 61124 112 - 1
CAAUGUGUGGGUAUCUCCUU-UUGGCCAGGUCCCCCCUGCUAUGGCCAAAUCUACUCGCUCCUUUC-------CUGAAUGCCAGAUUUCUGGCAUUGUUUUUGCUGACCGUGGCUUUAAU
......(((((((......(-((((((((((.......))).))))))))..))))))).......-------...((((((((....))))))))......(((......)))...... ( -32.80)
>DroSim_CAF1 59875 113 - 1
CAAUGUGUGGGCAUCUCCUUUUUUGCCAGGUCCCCCCUGCUAUGGCCAAAUCUAUUCGCUCCUUUC-------CUGAAUGCCAGAUUUCUGGCAUUGUUUUUGCUGACCGUGGCUUUAAU
.........((((..........))))(((.....)))(((((((.((..................-------...((((((((....))))))))((....)))).)))))))...... ( -28.70)
>DroEre_CAF1 70300 108 - 1
CACUGUGUGGGCAUCACCUU-UUUGCCAGGUUCCU---CCUAUGCCCAAAUCUGUUCUCCUUUUUC-------CCUAAC-ACAGAUUUCUGGCAUUGUUCUUGCUGACCGUGGCUUUAAU
(((.(.((.((((.......-......(((.....---)))(((((.((((((((...........-------......-))))))))..)))))......)))).))))))........ ( -22.83)
>DroYak_CAF1 65994 104 - 1
CAAU-----GGCAUCUCCUG-GUCGCCAGGUCCCAAA-UCUAUGCCCAAAUCUAUUCUCUCUUUU--------CCUAAC-ACAGAUUUCUGGGAUUGUUUUUGCUGACCGUGGCUUUAAU
....-----(((........-)))((((((((.((((-......(((((((((............--------......-..)))))..))))......))))..)))).))))...... ( -22.55)
>consensus
CAAUGUGUGGGCAUCUCCUU_UUUGCCAGGUCCCC_CUGCUAUGCCCAAAUCUAUUCGCUCCUUUC_______CUGAAUGCCAGAUUUCUGGCAUUGUUUUUGCUGACCGUGGCUUUAAU
........................((((((((............................................((((((((....))))))))((....)).)))).))))...... (-18.04 = -19.08 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:39 2006