Locus 2160

Sequence ID	X_DroMel_CAF1
Location	5,857,302 – 5,857,403
Length	101
Max. P	0.638239

overview

Window 1

Location	5,857,302 – 5,857,403
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.99
Mean single sequence MFE	-37.97
Consensus MFE	-25.95
Energy contribution	-26.20
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-1.49
Structure conservation index	0.68
SVM decision value	0.22
SVM RNA-class probability	0.638239
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5857302 101 + 22224390
-------------------CAACUCACCUUGCAGCAGCCGGUUUUCGGCGUCGGUGAAGCUGAGCACCCAGGCGUCGCCCUCCAUGGCGGAGUUCUUGCCCUGCAGUGCGAUGCACUCCU
-------------------...((((.(((.((.(.((((.....))))...).))))).)))).......(((((((.((.((.(((((.....))))).)).)).)))))))...... ( -35.30)
>DroVir_CAF1 85442 109 + 1
-----------ACCGGGAAGAACUCACCUUGCAACAGACGAUUCUCGGCGUCUGUAAAGCUGAGCACCCAGGCAUCGCCCUCCAUGGCGGAGUUCUUGCCCUGGAGCGCGAUGCACUCCU
-----------...(((.....((((.(((...(((((((........))))))).))).))))..)))..(((((((.(((((.(((((.....))))).))))).)))))))...... ( -47.80)
>DroGri_CAF1 84896 120 + 1
AUAGAUGUGUGAAUGGGGUCAACUCACCUUGCAAAAGACGAUUCUCGGCGUCCGUAAAGCUGAGCACCCAGGCAUCGCCCUCCAUGGCGGAGUUCUUGCCCUGGAGUGCGAUGCACUCCU
...............((((...((((.(((......((((........))))....))).)))).))))..(((((((.(((((.(((((.....))))).))))).)))))))...... ( -43.50)
>DroWil_CAF1 68761 101 + 1
-------------------ACACUUACCUUGAAGCAAACGAUUCUCGGCAUCGGUGAAGCUGAGCACCCAGGCAUCACCUUCCAUGGCCGAAUUUUUGCCCUGCAGUGCUAUGCACUCUU
-------------------..............(((((.(((..(((((....(.((((.(((((......)).))).)))))...))))))))))))).....(((((...)))))... ( -24.70)
>DroMoj_CAF1 80341 109 + 1
-----------GCAGUUGAGCACUCACCUUGCAAUAGCCGAUUCUCGGCGUCCGUAAAGCUGAGCACCCAGGCAUCGCCCUCCAUGGCGGAGUUCUUGCCCUGGAGUGCGAUGCACUCCU
-----------......(((..(((((.((((....((((.....))))....)))).).)))).......(((((((.(((((.(((((.....))))).))))).))))))).))).. ( -43.50)
>DroAna_CAF1 65992 107 + 1
-------------AUUCAAAAACUCACCUUGCAGCAAUCGAUUCUCGGCGUCGGUGAAGCUCAGGACCCAGGCAUCGCCCUCCAUGGCGGAGUUCUUGCCCUGCAGAGCGAUGCACUCCU
-------------..............((((.(((.((((((.......))))))...)))))))......(((((((.((.((.(((((.....))))).)).)).)))))))...... ( -33.00)
>consensus
______________G___AAAACUCACCUUGCAACAGACGAUUCUCGGCGUCGGUAAAGCUGAGCACCCAGGCAUCGCCCUCCAUGGCGGAGUUCUUGCCCUGCAGUGCGAUGCACUCCU
...........................................((((((.........)))))).......(((((((.((.((.(((((.....))))).)).)).)))))))...... (-25.95 = -26.20 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	5,857,302 – 5,857,403
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.99
Mean single sequence MFE	-42.55
Consensus MFE	-25.83
Energy contribution	-25.55
Covariance contribution	-0.27
Combinations/Pair	1.21
Mean z-score	-1.69
Structure conservation index	0.61
SVM decision value	0.04
SVM RNA-class probability	0.555141
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5857302 101 - 22224390
AGGAGUGCAUCGCACUGCAGGGCAAGAACUCCGCCAUGGAGGGCGACGCCUGGGUGCUCAGCUUCACCGACGCCGAAAACCGGCUGCUGCAAGGUGAGUUG-------------------
.(.(((((...))))).).((((..(..((((.....))))..)...))))....(((((.(((((.((..((((.....)))))).)).))).)))))..------------------- ( -35.90)
>DroVir_CAF1 85442 109 - 1
AGGAGUGCAUCGCGCUCCAGGGCAAGAACUCCGCCAUGGAGGGCGAUGCCUGGGUGCUCAGCUUUACAGACGCCGAGAAUCGUCUGUUGCAAGGUGAGUUCUUCCCGGU-----------
......(((((((.(((((.(((.........))).))))).)))))))(((((.(((((.(((.(((((((........)))))))...))).)))))....))))).----------- ( -54.30)
>DroGri_CAF1 84896 120 - 1
AGGAGUGCAUCGCACUCCAGGGCAAGAACUCCGCCAUGGAGGGCGAUGCCUGGGUGCUCAGCUUUACGGACGCCGAGAAUCGUCUUUUGCAAGGUGAGUUGACCCCAUUCACACAUCUAU
..(((((((((((.(((((.(((.........))).))))).)))))))..(((((((((.(((...(((((........))))).....))).)))))..)))).)))).......... ( -46.00)
>DroWil_CAF1 68761 101 - 1
AAGAGUGCAUAGCACUGCAGGGCAAAAAUUCGGCCAUGGAAGGUGAUGCCUGGGUGCUCAGCUUCACCGAUGCCGAGAAUCGUUUGCUUCAAGGUAAGUGU-------------------
...........(((((((.(((((((..((((((.......(((((.((.(((....))))).)))))...)))))).....)))))))....)).)))))------------------- ( -29.80)
>DroMoj_CAF1 80341 109 - 1
AGGAGUGCAUCGCACUCCAGGGCAAGAACUCCGCCAUGGAGGGCGAUGCCUGGGUGCUCAGCUUUACGGACGCCGAGAAUCGGCUAUUGCAAGGUGAGUGCUCAACUGC-----------
.(.((((((((((.(((((.(((.........))).))))).))))))).((((..((((.((((.(((..((((.....))))..))).))))))))..))))))).)----------- ( -50.50)
>DroAna_CAF1 65992 107 - 1
AGGAGUGCAUCGCUCUGCAGGGCAAGAACUCCGCCAUGGAGGGCGAUGCCUGGGUCCUGAGCUUCACCGACGCCGAGAAUCGAUUGCUGCAAGGUGAGUUUUUGAAU-------------
((((.(((((((((((.((.(((.........))).)).))))))))))...).))))(((((.((((...(((((.......)))..))..)))))))))......------------- ( -38.80)
>consensus
AGGAGUGCAUCGCACUCCAGGGCAAGAACUCCGCCAUGGAGGGCGAUGCCUGGGUGCUCAGCUUCACCGACGCCGAGAAUCGUCUGCUGCAAGGUGAGUUCU___C______________
.(((((.....(((((...(((((.(..((((.....))))..)..))))).)))))...))))).....((((..................))))........................ (-25.83 = -25.55 +  -0.27)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:35 2006