Locus 1725

Sequence ID	2R_DroMel_CAF1
Location	6,490,308 – 6,490,442
Length	134
Max. P	0.968088

overview

Window 4

Location	6,490,308 – 6,490,403
Length	95
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	87.53
Mean single sequence MFE	-30.15
Consensus MFE	-22.83
Energy contribution	-23.47
Covariance contribution	0.64
Combinations/Pair	1.08
Mean z-score	-2.75
Structure conservation index	0.76
SVM decision value	0.20
SVM RNA-class probability	0.630472
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6490308 95 - 20766785
C---UCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUGCCGAAAUUGCCUGCUC---ACUGCCAAUGGCAUCAGGCAGUGCAC-UGCAAUAUGAAACUUA
.---..((((((((.....((((....))))....))))))))..(((((..(..(---((((((..........)))))))..)-.))))).......... ( -30.00)
>DroSec_CAF1 58096 95 - 1
C---UCUGGUAUCGCUUACCAUACUUGUCUGAUUUCGAUACCGAAAUUGCCUGCUC---ACUGCCAAUGGCAUCAGGCAGUGCAC-UGCAAGAGGAAACUUA
.---..(((((.....)))))..(((((..(((((((....)))))))(((((((.---..((((...))))...))))).))..-.)))))((....)).. ( -30.20)
>DroSim_CAF1 45618 95 - 1
C---UCUGGUAUCGCUUACCAGACUUGUCUGAUUCCGAUGCCGAAAUUGCCUGCUC---ACUGCCAAUGGCAUCAGGCAGUGCAC-UGCAAUAUGCAACUUA
.---..((((((((.....((((....))))....))))))))....((((((((.---..((((...))))...))))).))).-(((.....)))..... ( -30.80)
>DroEre_CAF1 56602 98 - 1
C---UCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUACCGAAAUUGCCUGCUCUUUACUGCCAAUGGCAUCAGGCAGUGCAC-UGCAAUGUGCAACUUA
.---(((((((.....))))))).(((((((((((((....))))).((((.((........))....))))))))))))(((((-......)))))..... ( -34.40)
>DroYak_CAF1 61480 98 - 1
CUGCUCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUGCCGAAAUUGCCUGCUC---ACUGCCAAUGGCAUCAGGCAGUGCAC-UGCAAUGUGAAACUUU
.(((..((((((((.....((((....))))....))))))))....((((((((.---..((((...))))...))))).))).-.)))............ ( -31.20)
>DroAna_CAF1 57520 94 - 1
C---UAUGGUAUCGUUUACCAGACUUGUCUGAUUUCGAUGCCCGAAUUGCCCGUUC---ACUGCCAGUGGCGGCUGUGACUACACGUGAAAAAAAAAAC--A
.---...(((((((.....((((....))))....)))))))...........(((---((.(((......))).(((....)))))))).........--. ( -24.30)
>consensus
C___UCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUGCCGAAAUUGCCUGCUC___ACUGCCAAUGGCAUCAGGCAGUGCAC_UGCAAUAUGAAACUUA
.......(((((((.....((((....))))....)))))))...((((((((........((((...)))).))))))))((....))............. (-22.83 = -23.47 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	6,490,344 – 6,490,442
Length	98
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	90.70
Mean single sequence MFE	-35.07
Consensus MFE	-30.01
Energy contribution	-29.77
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-2.55
Structure conservation index	0.86
SVM decision value	1.62
SVM RNA-class probability	0.968088
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6490344 98 + 20766785
GGCAGU---GAGCAGGCAAUUUCGGCAUCGAAAUCAGACAAGUCUGGUAAGCGAUACCAGA---GUUCCAAUGGU-UUGGGGCAGCUGCCAAGCCGAAGCAUUUA
(((..(---(.((((.(......((.((((..((((((....))))))...)))).))...---(((((((....-))))))).))))))).))).......... ( -33.90)
>DroSec_CAF1 58132 98 + 1
GGCAGU---GAGCAGGCAAUUUCGGUAUCGAAAUCAGACAAGUAUGGUAAGCGAUACCAGA---GUCCCAAUGGC-UUGGGGCAACUGCCAAGCCGAAGCAUUUA
(((..(---(.((((........(((((((..((((........))))...)))))))...---(((((((....-)))))))..)))))).))).......... ( -35.90)
>DroSim_CAF1 45654 98 + 1
GGCAGU---GAGCAGGCAAUUUCGGCAUCGGAAUCAGACAAGUCUGGUAAGCGAUACCAGA---GUCCCAAUGGU-UUGGGGCAGCUGCCAAGCCGAAGCAUUUA
(((..(---(.((((.(......((.((((..((((((....))))))...)))).))...---(((((((....-))))))).))))))).))).......... ( -35.60)
>DroEre_CAF1 56638 101 + 1
GGCAGUAAAGAGCAGGCAAUUUCGGUAUCGAAAUCAGACAAGUCUGGUAAGCGAUACCAGA---GUCCCUUUGGU-UUGGGGCAGCUGCCAAGCCGAAGCAUUUA
((((((.................(((((((..((((((....))))))...)))))))...---(((((......-..))))).))))))..((....))..... ( -38.80)
>DroYak_CAF1 61516 101 + 1
GGCAGU---GAGCAGGCAAUUUCGGCAUCGAAAUCAGACAAGUCUGGUAAGCGAUACCAGAGCAGUCCCUUUGGU-UUGGGGCAGCUGCCAAGCCGAAGCAUUUA
.((..(---(.((.(((......((.((((..((((((....))))))...)))).))..(((.(((((......-..))))).))))))..))))..))..... ( -35.60)
>DroAna_CAF1 57555 99 + 1
GGCAGU---GAACGGGCAAUUCGGGCAUCGAAAUCAGACAAGUCUGGUAAACGAUACCAUA---GUCCUUAGGGUUUUGGGGCAGCUGCCAAACCCGAGCAUUUA
.((...---....((((......((.((((..((((((....))))))...)))).))...---))))...((((((...(((....)))))))))..))..... ( -30.60)
>consensus
GGCAGU___GAGCAGGCAAUUUCGGCAUCGAAAUCAGACAAGUCUGGUAAGCGAUACCAGA___GUCCCAAUGGU_UUGGGGCAGCUGCCAAGCCGAAGCAUUUA
((((((.................((.((((..((((((....))))))...)))).))......(((((.........))))).))))))............... (-30.01 = -29.77 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	6,490,344 – 6,490,442
Length	98
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	90.70
Mean single sequence MFE	-30.03
Consensus MFE	-25.51
Energy contribution	-26.10
Covariance contribution	0.59
Combinations/Pair	1.08
Mean z-score	-2.02
Structure conservation index	0.85
SVM decision value	0.76
SVM RNA-class probability	0.843296
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6490344 98 - 20766785
UAAAUGCUUCGGCUUGGCAGCUGCCCCAA-ACCAUUGGAAC---UCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUGCCGAAAUUGCCUGCUC---ACUGCC
.....((....))..(((((..((.((((-....))))...---..((((((((.....((((....))))....)))))))).........))..---.))))) ( -29.20)
>DroSec_CAF1 58132 98 - 1
UAAAUGCUUCGGCUUGGCAGUUGCCCCAA-GCCAUUGGGAC---UCUGGUAUCGCUUACCAUACUUGUCUGAUUUCGAUACCGAAAUUGCCUGCUC---ACUGCC
.....((....))..((((((.(((((((-....)))))..---..(((((.....))))).........(((((((....)))))))....))..---)))))) ( -30.00)
>DroSim_CAF1 45654 98 - 1
UAAAUGCUUCGGCUUGGCAGCUGCCCCAA-ACCAUUGGGAC---UCUGGUAUCGCUUACCAGACUUGUCUGAUUCCGAUGCCGAAAUUGCCUGCUC---ACUGCC
.....((....))..(((((..(((((((-....)))))..---..((((((((.....((((....))))....)))))))).........))..---.))))) ( -32.50)
>DroEre_CAF1 56638 101 - 1
UAAAUGCUUCGGCUUGGCAGCUGCCCCAA-ACCAAAGGGAC---UCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUACCGAAAUUGCCUGCUCUUUACUGCC
.....((....))..(((((....(((..-......)))..---..((((((((.....((((....))))....)))))))).................))))) ( -29.00)
>DroYak_CAF1 61516 101 - 1
UAAAUGCUUCGGCUUGGCAGCUGCCCCAA-ACCAAAGGGACUGCUCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUGCCGAAAUUGCCUGCUC---ACUGCC
.....((....))..(((((..((.....-.......((((...(((((((.....)))))))...))))(((((((....)))))))....))..---.))))) ( -32.20)
>DroAna_CAF1 57555 99 - 1
UAAAUGCUCGGGUUUGGCAGCUGCCCCAAAACCCUAAGGAC---UAUGGUAUCGUUUACCAGACUUGUCUGAUUUCGAUGCCCGAAUUGCCCGUUC---ACUGCC
.....((..(((((((((....)))...))))))...((((---...(((((((.....((((....))))....))))))).(.......)))))---...)). ( -27.30)
>consensus
UAAAUGCUUCGGCUUGGCAGCUGCCCCAA_ACCAUAGGGAC___UCUGGUAUCGCUUACCAGACUUGUCUGAUUUCGAUGCCGAAAUUGCCUGCUC___ACUGCC
.....((....))..(((((.................((((...(((((((.....)))))))...))))(((((((....)))))))............))))) (-25.51 = -26.10 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:48 2006