Locus 2564

Sequence ID	2R_DroMel_CAF1
Location	9,080,469 – 9,080,633
Length	164
Max. P	0.997002

overview

Window 3

Location	9,080,469 – 9,080,562
Length	93
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	77.11
Mean single sequence MFE	-22.75
Consensus MFE	-14.52
Energy contribution	-14.52
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.64
SVM decision value	0.01
SVM RNA-class probability	0.537594
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9080469 93 - 20766785
CAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCAAAAAUGGCCCGCGGCAAAGGAAACGCCCCUCGGCCGCACUCU-ACU------------------CUUCAUAU
....................((((........(((((........)))))(((((..(((.......)))..)))))..)))-)..------------------........ ( -25.20)
>DroSec_CAF1 45273 86 - 1
CAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCAAAGGAGACGCCCCUCGGCCGCAC------U------------------CUCCACAU
....................((((........(((((...--...)))))(((((..(((.......)))..)))))..------.------------------.))))... ( -27.70)
>DroSim_CAF1 47552 78 - 1
CAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCAAAGGAAACGCCCCC--------C------U------------------CUCCAUAU
....................((((........(((((...--...)))))..(((...(....))))...--------.------.------------------.))))... ( -17.30)
>DroEre_CAF1 52609 105 - 1
CAUCAGGCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCAAAGGAAACGCCCCUC---CGAACUCUCUCUCUCU--CACACUCGCUAACUCCAUAU
.....(((.((..........(((........(((((...--...)))))..(((...(....))))..))---)((......)).....--....)).))).......... ( -19.70)
>DroYak_CAF1 50420 106 - 1
CAUCAGGCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCCAAGGAAACGCCCCUC---CGCACUCUCACUCCCUUUGACAUACAUGGACG-GAUAU
.(((...(.......((((..(((........(((((...--...)))))((((....(....)......)---)))........)))..))))........)...-))).. ( -23.86)
>consensus
CAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA__AAUGGCCCGCGGCAAAGGAAACGCCCCUC___CGCACUCU__CU__________________CUCCAUAU
.....................((.........(((((........)))))..(((...(....))))))........................................... (-14.52 = -14.52 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	9,080,490 – 9,080,599
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	96.65
Mean single sequence MFE	-29.38
Consensus MFE	-29.38
Energy contribution	-29.22
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	1.00
SVM decision value	1.19
SVM RNA-class probability	0.928329
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9080490 109 - 20766785
CCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCAAAAAUGGCCCGCGGCAAAGGAAACGCCCCUCG
....(((((((((((.....))).(((.......(((.(((......))).)))...............(((((........)))))..)))..))).)))))...... ( -29.40)
>DroSec_CAF1 45289 107 - 1
CCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCAAAGGAGACGCCCCUCG
....(((((((((((.....))).(((.......(((.(((......))).)))...............(((((...--...)))))..)))..)))).))))...... ( -29.60)
>DroSim_CAF1 47562 105 - 1
CCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCAAAGGAAACGCCCCC--
....(((((((((((.....))).(((.......(((.(((......))).)))...............(((((...--...)))))..)))..))).)))))....-- ( -29.60)
>DroEre_CAF1 52645 106 - 1
CCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGGCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCAAAGGAAACGCCCCUC-
....(((((((((((.....))).(((.......(((.(((......))).)))...............(((((...--...)))))..)))..))).))))).....- ( -29.60)
>DroYak_CAF1 50457 106 - 1
CCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGGCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA--AAUGGCCCGCGGCCAAGGAAACGCCCCUC-
....(((((((((((.....))).(((.......(((.(((......))).)))...............(((((...--...)))))..)))..))).))))).....- ( -28.70)
>consensus
CCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUAGGGUCUCA__AAUGGCCCGCGGCAAAGGAAACGCCCCUC_
....(((((((((((.....))).(((.......(((.(((......))).)))...............(((((........)))))..)))..))))).)))...... (-29.38 = -29.22 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	9,080,530 – 9,080,633
Length	103
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	90.72
Mean single sequence MFE	-31.50
Consensus MFE	-26.32
Energy contribution	-26.32
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.84
SVM decision value	1.84
SVM RNA-class probability	0.979348
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9080530 103 + 20766785
UAUAAUUUUCCAGUUGAUAAUCUUGGCUGAUGAUCGCUAAUUGGCUGUCAAAGGGACAGGAACGCAGGGUAGCCUAGCAAGCAACUGGUUGAUG---AUUGGAGA---G
....(((..(((((((....(((((.((..((((.(((....))).))))..))..)))))..(((((....))).))...)))))))..))).---........---. ( -29.50)
>DroSec_CAF1 45327 100 + 1
UAUAAUUUUCCAGUUGAUAAUCUUGGCUGAUGAUCGCUAAUUGGCUGUCAAAGGGACAGGAACGCAGGGUAGCCUAGCAAGCAACUGGUUG------AUUGCAGA---G
..(((((..(((((((....(((((.((..((((.(((....))).))))..))..)))))..(((((....))).))...)))))))..)------))))....---. ( -31.20)
>DroSim_CAF1 47598 100 + 1
UAUAAUUUUCCAGUUGAUAAUCUUGGCUGAUGAUCGCUAAUUGGCUGUCAAAGGGACAGGAACGCAGGGUAGCCUAGCAAGCAACUGGUUG------AUUGGAGA---G
..(((((..(((((((....(((((.((..((((.(((....))).))))..))..)))))..(((((....))).))...)))))))..)------))))....---. ( -31.50)
>DroEre_CAF1 52682 101 + 1
UAUAAUUUUCCAGUUGAUAAUCUUGCCUGAUGAUCGCUAAUUGGCUGUCAAAGGGACAGGAACGCAGGGUAGCCUAGCAAGCAACUGGUGA--------UGGGCAACAA
....(((..(((((((....((((((((..((((.(((....))).))))..))).)))))..(((((....))).))...))))))).))--------).(....).. ( -32.50)
>DroYak_CAF1 50494 105 + 1
UAUAAUUUUCCAGUUGAUAAUCUUGCCUGAUGAUCGCUAAUUGGCUGUCAAAGGGACAGGAACGCAGGGUCGCCUAGCAAGCAACUGGUGGAUCGAACUUGGGCA----
....(((..(((((((....((((((((..((((.(((....))).))))..))).)))))..(((((....))).))...)))))))..)))............---- ( -32.80)
>consensus
UAUAAUUUUCCAGUUGAUAAUCUUGGCUGAUGAUCGCUAAUUGGCUGUCAAAGGGACAGGAACGCAGGGUAGCCUAGCAAGCAACUGGUUG______AUUGGAGA___G
.........(((((((....(((((.((..((((.(((....))).))))..))..)))))..(((((....))).))...)))))))..................... (-26.32 = -26.32 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	9,080,530 – 9,080,633
Length	103
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	90.72
Mean single sequence MFE	-24.24
Consensus MFE	-22.82
Energy contribution	-22.82
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.94
SVM decision value	2.78
SVM RNA-class probability	0.997002
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9080530 103 - 20766785
C---UCUCCAAU---CAUCAACCAGUUGCUUGCUAGGCUACCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUA
.---........---......(((((((....((.((((......((((.(((((.....)))))......))))......)))).)).....)))))))......... ( -24.10)
>DroSec_CAF1 45327 100 - 1
C---UCUGCAAU------CAACCAGUUGCUUGCUAGGCUACCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUA
.---........------...(((((((....((.((((......((((.(((((.....)))))......))))......)))).)).....)))))))......... ( -24.10)
>DroSim_CAF1 47598 100 - 1
C---UCUCCAAU------CAACCAGUUGCUUGCUAGGCUACCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUA
.---........------...(((((((....((.((((......((((.(((((.....)))))......))))......)))).)).....)))))))......... ( -24.10)
>DroEre_CAF1 52682 101 - 1
UUGUUGCCCA--------UCACCAGUUGCUUGCUAGGCUACCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGGCAAGAUUAUCAACUGGAAAAUUAUA
..........--------...((((((((((((((((....)))((....(((((.....))))).......))........)))))).....)))))))......... ( -23.80)
>DroYak_CAF1 50494 105 - 1
----UGCCCAAGUUCGAUCCACCAGUUGCUUGCUAGGCGACCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGGCAAGAUUAUCAACUGGAAAAUUAUA
----.................(((((((((((((.(..((.((((.....(((((.....))))).....))).).))..).)))))).....)))))))......... ( -25.10)
>consensus
C___UCUCCAAU______CAACCAGUUGCUUGCUAGGCUACCCUGCGUUCCUGUCCCUUUGACAGCCAAUUAGCGAUCAUCAGCCAAGAUUAUCAACUGGAAAAUUAUA
.....................((((((....(((((((......))....(((((.....)))))....)))))(((.(((......))).)))))))))......... (-22.82 = -22.82 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:14 2006