Locus 4385

Sequence ID	X_DroMel_CAF1
Location	11,537,319 – 11,537,409
Length	90
Max. P	0.991318

overview

Window 3

Location	11,537,319 – 11,537,409
Length	90
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	88.76
Mean single sequence MFE	-25.47
Consensus MFE	-22.75
Energy contribution	-22.75
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.89
SVM decision value	2.26
SVM RNA-class probability	0.991318
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11537319 90 + 22224390
CGAUAAUAAAAUCAAGCAAUCGGGCCGGCAGACCCAACUCAUGACCAUAU------GC-AACCCUGCCGGCCCAGCAUUCGUGUGUCUGUUUUCCGU-
.(((......)))(((((...((((((((((........((((....)))------).-....)))))))))).((((....)))).))))).....- ( -26.22)
>DroSec_CAF1 3112 90 + 1
CGAUAAUAAAAUCAAACAAUCGGGCCGGCAGACCCAACUAAUGACCAUAU------GC-AACCCUGCCGGCCCAGCAUUCGUGUGUCUGUGUUUCGU-
.(((......)))(((((...((((((((((...................------..-....)))))))))).((((....))))...)))))...- ( -26.21)
>DroSim_CAF1 3147 90 + 1
CGAUAAUAAAAUCAAACUAUCGGGCCGGCAGACCCAACUCAUGACCAUAU------GC-AACCCUGCCGGCCCAGCAUUCGUGUGUCUGUGUUUCGU-
(((.((((.............((((((((((........((((....)))------).-....)))))))))).((((....))))...))))))).- ( -25.52)
>DroEre_CAF1 3237 84 + 1
CGAUA-----AUCAAACAAUCGGGCCGGCAGACCCAACUCAUGACCAUAU------GC-AACCCUGCCGGCCCAGCAUUCGUG--UCUUUGUUCCGUU
.....-----....(((((..((((((((((........((((....)))------).-....)))))))))).(((....))--)..)))))..... ( -23.92)
>DroYak_CAF1 3153 90 + 1
CGAUA-----AUCAAACAAUCGGGCCGGCAGACCCAACUCAUGACCAUAUAUGUAUGCAAAACCUGCCGGCCCAGCAUUCGUG--UCUGUGUUCCGU-
.....-----...........((((((((((...((.....))..((((....))))......))))))))))(((((.....--...)))))....- ( -25.50)
>consensus
CGAUAAUAAAAUCAAACAAUCGGGCCGGCAGACCCAACUCAUGACCAUAU______GC_AACCCUGCCGGCCCAGCAUUCGUGUGUCUGUGUUCCGU_
.(((......)))........((((((((((................................))))))))))......................... (-22.75 = -22.75 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	11,537,319 – 11,537,409
Length	90
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	88.76
Mean single sequence MFE	-28.88
Consensus MFE	-26.41
Energy contribution	-26.61
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.91
SVM decision value	-0.00
SVM RNA-class probability	0.531144
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11537319 90 - 22224390
-ACGGAAAACAGACACACGAAUGCUGGGCCGGCAGGGUU-GC------AUAUGGUCAUGAGUUGGGUCUGCCGGCCCGAUUGCUUGAUUUUAUUAUCG
-.....................((((((((((((((.((-.(------((......)))....)).))))))))))))...))..(((......))). ( -27.10)
>DroSec_CAF1 3112 90 - 1
-ACGAAACACAGACACACGAAUGCUGGGCCGGCAGGGUU-GC------AUAUGGUCAUUAGUUGGGUCUGCCGGCCCGAUUGUUUGAUUUUAUUAUCG
-........((((((((....)).((((((((((((.((-..------.((.......))...)).))))))))))))..))))))............ ( -28.00)
>DroSim_CAF1 3147 90 - 1
-ACGAAACACAGACACACGAAUGCUGGGCCGGCAGGGUU-GC------AUAUGGUCAUGAGUUGGGUCUGCCGGCCCGAUAGUUUGAUUUUAUUAUCG
-........................(((((((((((.((-.(------((......)))....)).)))))))))))((((((........)))))). ( -29.90)
>DroEre_CAF1 3237 84 - 1
AACGGAACAAAGA--CACGAAUGCUGGGCCGGCAGGGUU-GC------AUAUGGUCAUGAGUUGGGUCUGCCGGCCCGAUUGUUUGAU-----UAUCG
....((((((((.--((....))))(((((((((((.((-.(------((......)))....)).)))))))))))..))))))...-----..... ( -28.70)
>DroYak_CAF1 3153 90 - 1
-ACGGAACACAGA--CACGAAUGCUGGGCCGGCAGGUUUUGCAUACAUAUAUGGUCAUGAGUUGGGUCUGCCGGCCCGAUUGUUUGAU-----UAUCG
-........((((--((.......((((((((((((..(..(((((.......)).)))....)..))))))))))))..))))))..-----..... ( -30.70)
>consensus
_ACGGAACACAGACACACGAAUGCUGGGCCGGCAGGGUU_GC______AUAUGGUCAUGAGUUGGGUCUGCCGGCCCGAUUGUUUGAUUUUAUUAUCG
.................(((((..((((((((((((.((.((..................)).)).))))))))))))...)))))............ (-26.41 = -26.61 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:43 2006