Locus 971

Sequence ID	3R_DroMel_CAF1
Location	3,157,809 – 3,158,049
Length	240
Max. P	0.974026

overview

Window 5

Location	3,157,809 – 3,157,929
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.81
Mean single sequence MFE	-36.45
Consensus MFE	-34.31
Energy contribution	-34.88
Covariance contribution	0.56
Combinations/Pair	1.14
Mean z-score	-1.80
Structure conservation index	0.94
SVM decision value	1.21
SVM RNA-class probability	0.931417
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3157809 120 - 27905053
CUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACCCCCGAUCCUUGAACCUAUUUGAUCUGUGCUUACACUGGUAAAAACUGAGAUACCGCUGA
(((((.......(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..))))).....(((.(((.(((....))).))).))).))))).......... ( -39.20)
>DroSec_CAF1 5663 120 - 1
CUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACUCCCGAUCCUUGAACCUAUGUGAUCUGUGCUUACACUGGUAAAAAAUGAGACACCGCCGA
((((........(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))(((..(((((.......)))))..)))......)))).......... ( -36.20)
>DroSim_CAF1 7837 120 - 1
CUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACUCCCGAUCCUUGAACCUAUGUGAUCUGUGCCUACACUGGUAAAAACCAAGAUACCGUUAA
............(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))....(((..(((((((....)))((((....))))))))..)))... ( -33.50)
>DroYak_CAF1 5367 120 - 1
CUCGGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAGGACCACCGAUUCUUGAGCCUAUGUGAUCUGUGUUUGCACUGGUGAAAACUGAGAUACAGUUGA
(((((..(((..(((((..(.((((.(((((((..(.((((...)))).).))))))).)).)).)..)))))(((..((..(.......)..))..))))))..))))).......... ( -36.90)
>consensus
CUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACCCCCGAUCCUUGAACCUAUGUGAUCUGUGCUUACACUGGUAAAAACUGAGAUACCGCUGA
(((((.......(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))(((..(((((.......)))))..))).....))))).......... (-34.31 = -34.88 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	3,157,849 – 3,157,969
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-33.23
Consensus MFE	-30.59
Energy contribution	-30.90
Covariance contribution	0.31
Combinations/Pair	1.06
Mean z-score	-2.16
Structure conservation index	0.92
SVM decision value	1.17
SVM RNA-class probability	0.925039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3157849 120 - 27905053
AUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACCCCCGAUCCUUGAACCUAUU
...................(((((((....).))))))..............(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))....... ( -35.70)
>DroSec_CAF1 5703 120 - 1
AUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACUCCCGAUCCUUGAACCUAUG
...................(((((((....).))))))..............(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))....... ( -32.70)
>DroSim_CAF1 7877 120 - 1
AUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACUCCCGAUCCUUGAACCUAUG
...................(((((((....).))))))..............(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))....... ( -32.70)
>DroYak_CAF1 5407 120 - 1
AUCUAAUAAAUUAUCAUUUGAACUGCAAUCGUCAGCGUCCCUCGGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAGGACCACCGAUUCUUGAGCCUAUG
....................(((.(((.(.(((((.(.(((((((((((.....))))))))))).).))))).)..))).)))(((.(((((((.(.....)))))...)))))).... ( -31.80)
>consensus
AUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGCCGUUGGCAUCAAUCGAAGACCCCCGAUCCUUGAACCUAUG
...................(((((((....).))))))..............(((((.(((((((.(((((((..(.((((...)))).).))))))).)))))))..)))))....... (-30.59 = -30.90 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	3,157,889 – 3,158,009
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-39.70
Consensus MFE	-35.67
Energy contribution	-36.30
Covariance contribution	0.63
Combinations/Pair	1.05
Mean z-score	-2.79
Structure conservation index	0.90
SVM decision value	1.72
SVM RNA-class probability	0.974026
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3157889 120 + 27905053
GCAGCUGAUCAAAGGCCCCCAAACUUGAUUGAAGUCUGAGGGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGCCAGUCGCGGA
((.(((......(((((((((.((((.....)))).)).))......((.(((((((((.(.(((((....))))).)))))))))))).)))))((((((....))))))))).))... ( -40.80)
>DroSec_CAF1 5743 120 + 1
GCAGCUGAUCAAAGGCCCCCAAACUUGAUUGAAGUCUGAGGGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGUCAGUCGCGAA
((.(((......(((((((((.((((.....)))).)).))......((.(((((((((.(.(((((....))))).)))))))))))).)))))((((((....))))))))).))... ( -38.10)
>DroSim_CAF1 7917 120 + 1
GCAGCUGAUCAAAGGCCCCCAAACUUGAUUGAAGUCUGAGGGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGCCAGUCGCGAA
((.(((......(((((((((.((((.....)))).)).))......((.(((((((((.(.(((((....))))).)))))))))))).)))))((((((....))))))))).))... ( -40.80)
>DroYak_CAF1 5447 116 + 1
GCAGCUGAUCAAAGGCCCCCAAACUUGAUUGAAGUCCGAGGGACGCUGACGAUUGCAGUUCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCAUGGCACAAAAAUGUGC----CGUGAA
.((((.((((((.(.........)))))))...((((...))))))))..((((((((((..(((((....))))).)))))))))).....(((((((((....)))))----)))).. ( -39.10)
>consensus
GCAGCUGAUCAAAGGCCCCCAAACUUGAUUGAAGUCUGAGGGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGCCAGUCGCGAA
((.(((..(((....(((.((.((((.....)))).)).)))....))).(((((((((.(.(((((....))))).))))))))))...)))((((((((....))))))))..))... (-35.67 = -36.30 +   0.63)

alignment

secondary structure

dotplot

Window 8

Location	3,157,889 – 3,158,009
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.42
Mean single sequence MFE	-38.60
Consensus MFE	-33.76
Energy contribution	-35.07
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-3.05
Structure conservation index	0.87
SVM decision value	1.54
SVM RNA-class probability	0.962507
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3157889 120 - 27905053
UCCGCGACUGGCACAUUUUUGUGCCAGGCCAGAGAUCGCAAUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGC
...((..((((((((....))))))))......((((......................(((((((....).))))))(((((((((((.....))))))))))).....)))).))... ( -42.40)
>DroSec_CAF1 5743 120 - 1
UUCGCGACUGACACAUUUUUGUGCCAGGCCAGAGAUCGCAAUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGC
...((..(((.((((....)))).)))......((((......................(((((((....).))))))(((((((((((.....))))))))))).....)))).))... ( -35.30)
>DroSim_CAF1 7917 120 - 1
UUCGCGACUGGCACAUUUUUGUGCCAGGCCAGAGAUCGCAAUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGC
...((..((((((((....))))))))......((((......................(((((((....).))))))(((((((((((.....))))))))))).....)))).))... ( -42.40)
>DroYak_CAF1 5447 116 - 1
UUCACG----GCACAUUUUUGUGCCAUGCCAGAGAUCGCAAUCUAAUAAAUUAUCAUUUGAACUGCAAUCGUCAGCGUCCCUCGGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGC
.....(----(((((....))))))....(((.(((.(((.((.(((........))).))..))).)))(((((.(.(((((((((((.....))))))))))).).)))))...))). ( -34.30)
>consensus
UUCGCGACUGGCACAUUUUUGUGCCAGGCCAGAGAUCGCAAUCUAAUAAAUUAUCAUUUGCACUGCAAUCGUCAGUGUCCCUCAGACUUCAAUCAAGUUUGGGGGCCUUUGAUCAGCUGC
.......((((((((....))))))))..(((.((((......................(((((((....).))))))(((((((((((.....))))))))))).....))))..))). (-33.76 = -35.07 +   1.31)

alignment

secondary structure

dotplot

Window 9

Location	3,157,929 – 3,158,049
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-35.38
Consensus MFE	-29.80
Energy contribution	-30.42
Covariance contribution	0.63
Combinations/Pair	1.05
Mean z-score	-2.18
Structure conservation index	0.84
SVM decision value	0.73
SVM RNA-class probability	0.835935
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3157929 120 + 27905053
GGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGCCAGUCGCGGAUAGAAGAUCGGGGCUCCUUUGGCAUUUUUAUUGAAUUAAU
(((..((((((((((((((.(.(((((....))))).))))))))))(((((.((((((((....)))))))).).)))).....).))))...)))....................... ( -36.30)
>DroSec_CAF1 5783 120 + 1
GGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGUCAGUCGCGAAUAGAAGAUCGGGGCUCCUUUGGCAUUUUUAUUGAAUUAAU
.(.(((((.......))))))......(((((((.((((.(((((((((((((((((((((....))))))))..))...))).)))))((....))....)))..)))).))))))).. ( -32.50)
>DroSim_CAF1 7957 120 + 1
GGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGCCAGUCGCGAAUAGAAGAUCGGGGCUCCUUUGGCAUUUUUAUUGAAUUAAU
.(.(((((.......))))))......(((((((.((((.(((((((((((((((((((((....))))))))..))...))).)))))((....))....)))..)))).))))))).. ( -35.20)
>DroYak_CAF1 5487 116 + 1
GGACGCUGACGAUUGCAGUUCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCAUGGCACAAAAAUGUGC----CGUGAAUAGAAGCUCCGGGCUCCUUUGGCAUUUUUAUUGAAUUAAU
(((.(((...((((((((((..(((((....))))).))))))))))((((.(((((((((....)))))----))))..))))))))))..(((.....)))................. ( -37.50)
>consensus
GGACACUGACGAUUGCAGUGCAAAUGAUAAUUUAUUAGAUUGCGAUCUCUGGCCUGGCACAAAAAUGUGCCAGUCGCGAAUAGAAGAUCGGGGCUCCUUUGGCAUUUUUAUUGAAUUAAU
((((.((((((((((((((.(.(((((....))))).))))))))))((((((((((((((....))))))))..))...)))).).)))).).)))....................... (-29.80 = -30.42 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:01 2006