Locus 5592

Sequence ID	3R_DroMel_CAF1
Location	14,775,429 – 14,775,602
Length	173
Max. P	0.861361

overview

Window 4

Location	14,775,429 – 14,775,538
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	85.24
Mean single sequence MFE	-39.84
Consensus MFE	-25.80
Energy contribution	-27.60
Covariance contribution	1.80
Combinations/Pair	1.10
Mean z-score	-2.32
Structure conservation index	0.65
SVM decision value	0.54
SVM RNA-class probability	0.776164
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14775429 109 + 27905053
CCUGUCAGCUUUGGCACCACCUGAUGGCCUGGCACCUGGAAACCUUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGUUUUGGCUUU
...(((((((..(((.(((((.((((((.(((((..(((.....((((((.....)))))).....)))..)))))))))))..).))))..)))..)))..))))... ( -42.00)
>DroSec_CAF1 34178 109 + 1
GCUGUCAGCUUUGGCGCCACCUGAUGGCCUGGCACCUGGAAACCUUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGCUUUGCCUUU
((....((((..(((((((((.((((((.(((((..(((.....((((((.....)))))).....)))..)))))))))))..).))))).)))..))))..)).... ( -46.30)
>DroSim_CAF1 35920 109 + 1
GCUGUCAGCUUUGGCGCCACCUGAUGUCCUGGCACCUGGAAACCCUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGCUUUGCCUUU
((....((((..((((((((.(((....((((((..(((......(((((.....)))))......)))..)))))).....))).))))).)))..))))..)).... ( -41.30)
>DroEre_CAF1 34436 103 + 1
CCUGUCAGCUUUUGCUCCUCCUGAUGGCCUGCCACCUGGAAACCUUCAGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGAUUUGGC------UUU
...(((((..(((((..(((..((((((.((.((..(((.....((((((.....)))))).....)))..)).))))))))..)))..))))).)))))------... ( -36.50)
>DroYak_CAF1 43365 90 + 1
CCUGUCAGCUUUGGGUCCUCCUGAUGGCCUGCCACCUGGCGG-------------CCUGGAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGAUUUGGC------UUU
......(((((..((....))..).((((.(((....)))))-------------))..(((((((((((.((..........)).))))))))))))))------).. ( -33.10)
>consensus
CCUGUCAGCUUUGGCGCCACCUGAUGGCCUGGCACCUGGAAACCUUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGCUUUG_CUUU
...((((((....))(((.((.((((((.(((((..(((.....((((((.....)))))).....)))..)))))))))))......)).)))..))))......... (-25.80 = -27.60 +   1.80)

alignment

secondary structure

dotplot

Window 5

Location	14,775,469 – 14,775,576
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	88.16
Mean single sequence MFE	-39.14
Consensus MFE	-29.58
Energy contribution	-30.90
Covariance contribution	1.32
Combinations/Pair	1.08
Mean z-score	-2.05
Structure conservation index	0.76
SVM decision value	0.83
SVM RNA-class probability	0.861361
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14775469 107 + 27905053
AACCUUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGUUUUGGCUUUGGAUGGGCGAUUAAAGCGCUCGUCGGCCACUCGAACAA
......((((((((....))))))))............(((.(((((((((((((........))))...((((((((.......)))))))).)))))))))))). ( -40.90)
>DroSec_CAF1 34218 107 + 1
AACCUUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGCUUUGCCUUUGGAUGGGCGAUUAAAGCGCUCGUCGGCCACUCGAACAA
......((((((((....))))))))............(((.((((((((((((.........)))....((((((((.......)))))))).)))))))))))). ( -42.00)
>DroSim_CAF1 35960 107 + 1
AACCCUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGCUUUGCCUUUGGAUGGGCGAUUAAAGCGCUCGUCGGCCACUCGAACAA
......((((((((....))))))))............(((.((((((((((((.........)))....((((((((.......)))))))).)))))))))))). ( -42.00)
>DroEre_CAF1 34476 101 + 1
AACCUUCAGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGAUUUGGC------UUUGGAUGGGCGAUUAAAGCGCUCGUCGGCCCCUCGAACAA
....((((((.....))))))....(((....((((.(((((......)))))...))))------....((((((((.......)))))))))))........... ( -35.90)
>DroYak_CAF1 43405 88 + 1
GG-------------CCUGGAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGAUUUGGC------UUUGGAUGGACGAUUAAAGCGCUCGUCGGCCACUCGAACAA
((-------------(.(((......)))...)))...(((.(((((((((.(((..(((------(((((........))))))).)..))).)))))))))))). ( -34.90)
>consensus
AACCUUCGGGUUUCACCUGAAAUCUGCCACCUGCCAGCUGUCUCGAGUGGCGGCUUUGGCUUUG_CUUUGGAUGGGCGAUUAAAGCGCUCGUCGGCCACUCGAACAA
.....(((((.....))))).....(((....((((((((((......))))))..))))..........((((((((.......)))))))))))........... (-29.58 = -30.90 +   1.32)

alignment

secondary structure

dotplot

Window 6

Location	14,775,505 – 14,775,602
Length	97
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	83.10
Mean single sequence MFE	-38.98
Consensus MFE	-25.67
Energy contribution	-26.75
Covariance contribution	1.08
Combinations/Pair	1.12
Mean z-score	-2.53
Structure conservation index	0.66
SVM decision value	0.41
SVM RNA-class probability	0.724324
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14775505 97 + 27905053
GC-UGUCUCGAGUGGCGGCUUUGGUUUUGGCUUUGGAUGGGCGAUUAAAGCGCUCGU--CGGCCACUCGAACAAACAGAAUCGACGGCUCAUUGAGCCGC---------
.(-(((.(((((((((((((........))))...((((((((.......)))))))--).)))))))))....))))......((((((...)))))).--------- ( -43.60)
>DroSec_CAF1 34254 97 + 1
GC-UGUCUCGAGUGGCGGCUUUGGCUUUGCCUUUGGAUGGGCGAUUAAAGCGCUCGU--CGGCCACUCGAACAAACAGAAUCGACGGCUCAUUGAGCCGC---------
.(-(((.((((((((((((.........)))....((((((((.......)))))))--).)))))))))....))))......((((((...)))))).--------- ( -44.70)
>DroSim_CAF1 35996 97 + 1
GC-UGUCUCGAGUGGCGGCUUUGGCUUUGCCUUUGGAUGGGCGAUUAAAGCGCUCGU--CGGCCACUCGAACAAACAGAAUCGACGGCUCAUUGAGCCGC---------
.(-(((.((((((((((((.........)))....((((((((.......)))))))--).)))))))))....))))......((((((...)))))).--------- ( -44.70)
>DroEre_CAF1 34512 91 + 1
GC-UGUCUCGAGUGGCGGAUUUGGC------UUUGGAUGGGCGAUUAAAGCGCUCGU--CGGCCCCUCGAACAAACAGAAUCGACGGCUCAUUGAGCCGC---------
.(-(((.(((((.(((((......)------)...((((((((.......)))))))--).))).)))))....))))......((((((...)))))).--------- ( -34.00)
>DroYak_CAF1 43428 91 + 1
GC-UGUCUCGAGUGGCGGAUUUGGC------UUUGGAUGGACGAUUAAAGCGCUCGU--CGGCCACUCGAACAAACAGAAUCGACGGCUCAUUGAGCCGC---------
.(-(((.(((((((((.(((..(((------(((((........))))))).)..))--).)))))))))....))))......((((((...)))))).--------- ( -38.60)
>DroPer_CAF1 32981 97 + 1
CGGGGUGUCAAGUGGAGGCUUU-----------UUGGCGAGCGAUUAAAGCGG-CGUCCUGGCCACUCGAACAAAUAAAAUCAACGACUCAUUGAGCCACAGCACUUCA
.(((((((...((((.((((..-----------..((((.((.......))..-))))..)))).(((((.....................))))))))).))))))). ( -28.30)
>consensus
GC_UGUCUCGAGUGGCGGCUUUGGC______UUUGGAUGGGCGAUUAAAGCGCUCGU__CGGCCACUCGAACAAACAGAAUCGACGGCUCAUUGAGCCGC_________
...(((.(((((((((.(..................(((((((.......)))))))..).))))))))))))...........((((((...)))))).......... (-25.67 = -26.75 +   1.08)

alignment

secondary structure

dotplot

Window 7

Location	14,775,505 – 14,775,602
Length	97
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	83.10
Mean single sequence MFE	-32.53
Consensus MFE	-22.34
Energy contribution	-22.32
Covariance contribution	-0.03
Combinations/Pair	1.18
Mean z-score	-1.62
Structure conservation index	0.69
SVM decision value	-0.04
SVM RNA-class probability	0.512488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14775505 97 - 27905053
---------GCGGCUCAAUGAGCCGUCGAUUCUGUUUGUUCGAGUGGCCG--ACGAGCGCUUUAAUCGCCCAUCCAAAGCCAAAACCAAAGCCGCCACUCGAGACA-GC
---------(((((((...))))))).....(((((...(((((((((.(--(.(.(((.......))).).))....((..........)).)))))))))))))-). ( -32.20)
>DroSec_CAF1 34254 97 - 1
---------GCGGCUCAAUGAGCCGUCGAUUCUGUUUGUUCGAGUGGCCG--ACGAGCGCUUUAAUCGCCCAUCCAAAGGCAAAGCCAAAGCCGCCACUCGAGACA-GC
---------(((((((...))))))).....(((((...(((((((((.(--.(....(((((....(((........))))))))....)).)))))))))))))-). ( -37.60)
>DroSim_CAF1 35996 97 - 1
---------GCGGCUCAAUGAGCCGUCGAUUCUGUUUGUUCGAGUGGCCG--ACGAGCGCUUUAAUCGCCCAUCCAAAGGCAAAGCCAAAGCCGCCACUCGAGACA-GC
---------(((((((...))))))).....(((((...(((((((((.(--.(....(((((....(((........))))))))....)).)))))))))))))-). ( -37.60)
>DroEre_CAF1 34512 91 - 1
---------GCGGCUCAAUGAGCCGUCGAUUCUGUUUGUUCGAGGGGCCG--ACGAGCGCUUUAAUCGCCCAUCCAAA------GCCAAAUCCGCCACUCGAGACA-GC
---------(((((((...))))))).....(((((...(((((.(((.(--(...(.(((((............)))------)))...)).))).)))))))))-). ( -29.30)
>DroYak_CAF1 43428 91 - 1
---------GCGGCUCAAUGAGCCGUCGAUUCUGUUUGUUCGAGUGGCCG--ACGAGCGCUUUAAUCGUCCAUCCAAA------GCCAAAUCCGCCACUCGAGACA-GC
---------(((((((...))))))).....(((((...(((((((((.(--(...(.(((((............)))------)))...)).)))))))))))))-). ( -34.00)
>DroPer_CAF1 32981 97 - 1
UGAAGUGCUGUGGCUCAAUGAGUCGUUGAUUUUAUUUGUUCGAGUGGCCAGGACG-CCGCUUUAAUCGCUCGCCAA-----------AAAGCCUCCACUUGACACCCCG
((.((.(((.((((((((((...))))))........(((.(((((((......)-)))))).))).....)))).-----------..))))).))............ ( -24.50)
>consensus
_________GCGGCUCAAUGAGCCGUCGAUUCUGUUUGUUCGAGUGGCCG__ACGAGCGCUUUAAUCGCCCAUCCAAA______GCCAAAGCCGCCACUCGAGACA_GC
.........(((((((...)))))))...........((((((((((((.....).(((.......)))........................))))))))).)).... (-22.34 = -22.32 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:55 2006