Locus 5571

Sequence ID	2L_DroMel_CAF1
Location	15,841,432 – 15,841,643
Length	211
Max. P	0.998510

overview

Window 2

Location	15,841,432 – 15,841,543
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.35
Mean single sequence MFE	-14.94
Consensus MFE	-9.07
Energy contribution	-10.07
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.61
SVM decision value	0.01
SVM RNA-class probability	0.538671
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15841432 111 - 22407834
CAGUA---AAAAAAAAACGACAAUAAU--ACAUAGCACAAAAAAUGAG----AAAAUUGUCUACAAAAUGGUUGACAGGCAAUUUGCCUACACACAUUUUUCCACCCAAAUGUUUCGUCA
.....---..........(((...(((--(.........(((((((..----......(((.((......)).)))((((.....)))).....))))))).........))))..))). ( -15.77)
>DroSec_CAF1 13613 109 - 1
CAGUA---AAA--AAAACGACAAUAAU--ACAUAGCACAAAAAAUGAG----AAAAUUGUCUACAAAAUGGUUGACAGGCAAUUUGCCUACACACAUUUUUCCACCCAAAUGUUUCGUCA
.....---...--.....(((...(((--(.........(((((((..----......(((.((......)).)))((((.....)))).....))))))).........))))..))). ( -15.77)
>DroSim_CAF1 13924 109 - 1
CAGUA---AAA--AAAACGACAAUAAU--ACAUAGCACAAAAAAUGAG----AAAAUUGUCUACAAAAUGGUUGACAGGCAAUUUGCCUACACACAUUUUUCCACCCAAAUGUUUCGUCA
.....---...--.....(((...(((--(.........(((((((..----......(((.((......)).)))((((.....)))).....))))))).........))))..))). ( -15.77)
>DroPer_CAF1 25992 102 - 1
AAAUACACAAA--AAAGCAAUAAUAACAGACAAAGCAAAAAAAAAAAAAAAAGGAAUUGUCUACAAA-UUUUUGACAGGCAAUUUGCCUACACACAUAUUUGCCC---------------
...........--...((((.......((((((..(.................)..)))))).....-........((((.....))))..........))))..--------------- ( -12.43)
>consensus
CAGUA___AAA__AAAACGACAAUAAU__ACAUAGCACAAAAAAUGAG____AAAAUUGUCUACAAAAUGGUUGACAGGCAAUUUGCCUACACACAUUUUUCCACCCAAAUGUUUCGUCA
.......................................(((((((............(((.((......)).)))((((.....)))).....)))))))................... ( -9.07 = -10.07 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	15,841,472 – 15,841,583
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.10
Mean single sequence MFE	-24.56
Consensus MFE	-17.76
Energy contribution	-17.52
Covariance contribution	-0.25
Combinations/Pair	1.22
Mean z-score	-2.94
Structure conservation index	0.72
SVM decision value	2.55
SVM RNA-class probability	0.995191
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15841472 111 + 22407834
GCCUGUCAACCAUUUUGUAGACAAUUUU----CUCAUUUUUUGUGCUAUGU--AUUAUUGUCGUUUUUUUUU---UACUGAUGUACAAUGCCUGAUGCUUAUCAAAAAUGGUUGACACAA
...(((((((((((((((((((((....----........)))).))))((--((((((((((((.......---....)))).)))))....)))))......)))))))))))))... ( -26.20)
>DroSec_CAF1 13653 109 + 1
GCCUGUCAACCAUUUUGUAGACAAUUUU----CUCAUUUUUUGUGCUAUGU--AUUAUUGUCGUUUU--UUU---UACUGACGUACAUUGCCUGAUGCUUAUCAAAAAUGGUUGACACAA
...(((((((((((((((((((((....----........)))).))))((--((((.(((((((..--...---....)))).))).....))))))......)))))))))))))... ( -27.10)
>DroSim_CAF1 13964 109 + 1
GCCUGUCAACCAUUUUGUAGACAAUUUU----CUCAUUUUUUGUGCUAUGU--AUUAUUGUCGUUUU--UUU---UACUGACGUACAUUGCCUGAUGCUUAUCAAAAAUGGUUGACACAA
...(((((((((((((((((((((....----........)))).))))((--((((.(((((((..--...---....)))).))).....))))))......)))))))))))))... ( -27.10)
>DroPer_CAF1 26017 111 + 1
GCCUGUCAAAAA-UUUGUAGACAAUUCCUUUUUUUUUUUUUUUUGCUUUGUCUGUUAUUAUUGCUUU--UUUGUGUAUUUCUGU------UCUGAUGUUUAUCAGAAAUGUUUGACGCAA
....(.(((.((-(...(((((((.......................)))))))..))).))))...--.((((((.......(------((((((....))))))).......)))))) ( -17.84)
>consensus
GCCUGUCAACCAUUUUGUAGACAAUUUU____CUCAUUUUUUGUGCUAUGU__AUUAUUGUCGUUUU__UUU___UACUGACGUACAUUGCCUGAUGCUUAUCAAAAAUGGUUGACACAA
...(((((((((((((...((((((..(......(((.....)))........)..))))))..............................((((....)))))))))))))))))... (-17.76 = -17.52 +  -0.25)

alignment

secondary structure

dotplot

Window 4

Location	15,841,472 – 15,841,583
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.10
Mean single sequence MFE	-23.56
Consensus MFE	-16.35
Energy contribution	-16.36
Covariance contribution	0.00
Combinations/Pair	1.14
Mean z-score	-3.61
Structure conservation index	0.69
SVM decision value	3.12
SVM RNA-class probability	0.998510
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15841472 111 - 22407834
UUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAUUGUACAUCAGUA---AAAAAAAAACGACAAUAAU--ACAUAGCACAAAAAAUGAG----AAAAUUGUCUACAAAAUGGUUGACAGGC
.(.(((((((((((((((((..(((........)))..))))...---..........((((((...--.(((..........)))..----...))))))...))))))))))))).). ( -24.20)
>DroSec_CAF1 13653 109 - 1
UUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAAUGUACGUCAGUA---AAA--AAAACGACAAUAAU--ACAUAGCACAAAAAAUGAG----AAAAUUGUCUACAAAAUGGUUGACAGGC
.(.(((((((((((((.(((((...(((.((.(((((.(((.((.---...--...))))).....)--)))).))........))).----....)))))...))))))))))))).). ( -27.10)
>DroSim_CAF1 13964 109 - 1
UUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAAUGUACGUCAGUA---AAA--AAAACGACAAUAAU--ACAUAGCACAAAAAAUGAG----AAAAUUGUCUACAAAAUGGUUGACAGGC
.(.(((((((((((((.(((((...(((.((.(((((.(((.((.---...--...))))).....)--)))).))........))).----....)))))...))))))))))))).). ( -27.10)
>DroPer_CAF1 26017 111 - 1
UUGCGUCAAACAUUUCUGAUAAACAUCAGA------ACAGAAAUACACAAA--AAAGCAAUAAUAACAGACAAAGCAAAAAAAAAAAAAAAAGGAAUUGUCUACAAA-UUUUUGACAGGC
....((((((...(((((((....))))))------)..............--..............((((((..(.................)..)))))).....-..)))))).... ( -15.83)
>consensus
UUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAAUGUACAUCAGUA___AAA__AAAACGACAAUAAU__ACAUAGCACAAAAAAUGAG____AAAAUUGUCUACAAAAUGGUUGACAGGC
....((((((((((((((((....))))).............................((((((...............................))))))....))))))))))).... (-16.35 = -16.36 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	15,841,543 – 15,841,643
Length	100
Sequences	3
Columns	100
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-18.60
Consensus MFE	-17.91
Energy contribution	-17.80
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.96
SVM decision value	0.76
SVM RNA-class probability	0.842535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15841543 100 - 22407834
ACUGUCGCAUUGUACACAACCUAUUGCAAAUAAACACAUCAUACGUUUUUAUGACGAAAAUUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAUUGUACAU
..........((((((...(((..(((...........(((((......)))))(((((((.((....)).)))))))....)))..)))...)))))). ( -21.00)
>DroSec_CAF1 13722 100 - 1
ACUAUCGCAUUGUACACAACUUAUUGCAAAUAAACACAUCAUACGUUUUUAUUACGAAAAUUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAAUGUACGU
......(((((((......(((((((.((((..(((((.....(((.......))).....))))).....)))).)))))))......))))))).... ( -17.50)
>DroSim_CAF1 14033 100 - 1
ACUAUCGAAUUGUACACAACUUAUUGCAAAUAAACACAUCAUACGUUUUUAUUACGAAAAUUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAAUGUACGU
...........(((((...(((..(((.((((((.((.......)).)))))).(((((((.((....)).)))))))....)))..)))...))))).. ( -17.30)
>consensus
ACUAUCGCAUUGUACACAACUUAUUGCAAAUAAACACAUCAUACGUUUUUAUUACGAAAAUUGUGUCAACCAUUUUUGAUAAGCAUCAGGCAAUGUACGU
..........((((((...(((..(((.((((((.((.......)).)))))).(((((((.((....)).)))))))....)))..)))...)))))). (-17.91 = -17.80 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:32 2006