Locus 1938

Sequence ID	2L_DroMel_CAF1
Location	5,249,367 – 5,249,630
Length	263
Max. P	0.716885

overview

Window 0

Location	5,249,367 – 5,249,460
Length	93
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	89.23
Mean single sequence MFE	-33.88
Consensus MFE	-27.41
Energy contribution	-28.77
Covariance contribution	1.36
Combinations/Pair	1.04
Mean z-score	-2.30
Structure conservation index	0.81
SVM decision value	0.39
SVM RNA-class probability	0.716885
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5249367 93 - 22407834
CUCCGUGGCCCCGCUGCCAUAACCAUGUUUUCCUCGGAAAACCCUGCUCGUUUAUCAGGCGGCAGGCAUCGGGCAA-AAGAGCUC------AGGCCGCAA
....(((((((((.((((........((((((....))))))..(((.((((.....))))))))))).)))((..-....))..------.)))))).. ( -36.50)
>DroSec_CAF1 26215 93 - 1
CUCCAUGGCCCCGCUGCCAUAACCAUGUUUUCCUCGGAAAACCCUGCUCGUUUAUCAGGCGGCAGGCAUCGGGCAA-AAGAGCUC------AGGCCGCAA
......(((((((.((((........((((((....))))))..(((.((((.....))))))))))).)))((..-....))..------.)))).... ( -32.30)
>DroSim_CAF1 27371 93 - 1
CUCCGUGGCCCCGCUGCCAUAACCAUGUUUUCCUCGGAAAACCCUGCUCGUUUAUCAGGCGGCAGGCAUCGGGCAA-AAGAGCUC------AGGCCGCAA
....(((((((((.((((........((((((....))))))..(((.((((.....))))))))))).)))((..-....))..------.)))))).. ( -36.50)
>DroEre_CAF1 19048 93 - 1
CUCCGUGGCCCCGCUGCCAUAACCAUGUUUUCCUCGGAAAACCCUGCUCGUUUAUCAGGCGGCAGGCAUCAGGCAA-AGGAGCUC------AGGCCGCAA
....((((((((..((((........((((((....))))))(((((.((((.....))))))))).....)))).-.)).....------.)))))).. ( -36.90)
>DroYak_CAF1 28370 93 - 1
CUCCGUGGCCCCGCUGCCAUAACCAUGUUUUCCUCGGAAAACCCUGCUCGUUUAUCAGGCGGCAGGCAUCGGGCAC-CAGAGCUC------AGGCCGCAA
....(((((((((.((((........((((((....))))))..(((.((((.....))))))))))).)))((..-....))..------.)))))).. ( -36.50)
>DroAna_CAF1 7416 93 - 1
------GGACCCGCAACCAUAACCAUGUUUUCCACAGAAAACUCUGUCGGUUUAUCAGGCGGCAGGCAUCGGCCAACAACAGCUCCCAGCCAGGCCGAA-
------......((............((((((....)))))).((((((.(......).)))))))).((((((.......((.....))..)))))).- ( -24.60)
>consensus
CUCCGUGGCCCCGCUGCCAUAACCAUGUUUUCCUCGGAAAACCCUGCUCGUUUAUCAGGCGGCAGGCAUCGGGCAA_AAGAGCUC______AGGCCGCAA
....(((((((((.((((........((((((....))))))..(((.((((.....))))))))))).)))((.......)).........)))))).. (-27.41 = -28.77 +   1.36)

alignment

secondary structure

dotplot

Window 1

Location	5,249,395 – 5,249,498
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.09
Mean single sequence MFE	-40.10
Consensus MFE	-23.64
Energy contribution	-24.78
Covariance contribution	1.14
Combinations/Pair	1.18
Mean z-score	-1.40
Structure conservation index	0.59
SVM decision value	0.10
SVM RNA-class probability	0.583616
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5249395 103 + 22407834
CUGCCGCCUGAUAAACGAG---------------CAGGGUUUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGG
((.((((((.(((..((((---------------(...((((((....))))))...))).))...((..((((.....)))).))))).--))))))...))..((((......)))). ( -36.70)
>DroPse_CAF1 23717 118 + 1
CCGCCGCCUGAUAGCGGGGGACGCCGUGGCAUGGCCCGACUUUCCGAGGAAAACAUGGUUAUGGCCUGGGGGCCACAGAGGCCAGCUAUGAGAGGUGGA-AGGUGGCAUAUCACAGUGG-
((.((((......)))).)).(((.(((..(((.((..((((((((.......((((((..((((((..(.....)..)))))))))))).....))))-)))))))))..))).))).- ( -49.00)
>DroSec_CAF1 26243 103 + 1
CUGCCGCCUGAUAAACGAG---------------CAGGGUUUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCAUGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGG
((.((((((.(((..((((---------------(...((((((....))))))...))).))...((..((((.....)))).))))).--))))))...))..((((......)))). ( -36.70)
>DroYak_CAF1 28398 103 + 1
CUGCCGCCUGAUAAACGAG---------------CAGGGUUUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGG
((.((((((.(((..((((---------------(...((((((....))))))...))).))...((..((((.....)))).))))).--))))))...))..((((......)))). ( -36.70)
>DroAna_CAF1 7450 95 + 1
CUGCCGCCUGAUAAACCGA---------------CAGAGUUUUCUGUGGAAAACAUGGUUAUGGUUGCGGGUCC-------CCAGGUGGA--AGGUGGU-AGGUGCCACAAAGCAGCGGG
((((((((((.....(((.---------------(((......(((((.....)))))......))))))....-------.))))))..--..(((((-....)))))......)))). ( -31.40)
>DroPer_CAF1 23808 118 + 1
CCGCCGCCUGAUAGCGGGGGACGCCGUGGCAUGGCCCGACUUUCCGAGGAAAACAUGGUUAUGGCCUGGGGGCCACAGAGGCCAGCUAUGGGAGGUGGA-AGGUGGCAUAUCACAGUGG-
..(((((((..((.(.(....).(((((((.((((((...((((....)))).........(((((....)))))..).))))))))))))..).))..-)))))))............- ( -50.10)
>consensus
CUGCCGCCUGAUAAACGAG_______________CAGGGUUUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG__AGGUGGA_AGGUGCCACAAAGCAGUGGG
((.((((((.............................((((((....)))))).....((((((.....((((.....)))).))))))..))))))...))..((((......)))). (-23.64 = -24.78 +   1.14)

alignment

secondary structure

dotplot

Window 2

Location	5,249,420 – 5,249,528
Length	108
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	82.37
Mean single sequence MFE	-34.75
Consensus MFE	-24.71
Energy contribution	-24.97
Covariance contribution	0.25
Combinations/Pair	1.19
Mean z-score	-1.34
Structure conservation index	0.71
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5249420 108 + 22407834
UUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGGAGUGCGACUGG----UUGUGGGAGUCGUUGCCAC
((((....)))).........(((((((((..((.((.(..((.(((((.--..((((.......))))...))))).))..).))((...----..)).))..))))))))). ( -36.30)
>DroPse_CAF1 23757 97 + 1
UUUCCGAGGAAAACAUGGUUAUGGCCUGGGGGCCACAGAGGCCAGCUAUGAGAGGUGGA-AGGUGGCAUAUCACAGUGG----------------GUGUGGGAGUCAUGGUGAG
..(((.(((....(((....))).))).)))(((((.....(((.((.....)).))).-..)))))...((((.((((----------------.(.....).)))).)))). ( -30.20)
>DroSec_CAF1 26268 108 + 1
UUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCAUGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGGAGUGCGACUGG----UUGUGGGAGUCGUUGCCAC
((((....)))).........(((((((((((((.....))))..(((..--((((.(...(.(.((((......)))).).).).)))..----)..)))...))))))))). ( -35.90)
>DroEre_CAF1 19101 108 + 1
UUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGGAGUGCGACUGG----UUGUGGGAGUCGUUGCCUA
((((....))))..........((((((((..((.((.(..((.(((((.--..((((.......))))...))))).))..).))((...----..)).))..)))))))).. ( -35.10)
>DroYak_CAF1 28423 112 + 1
UUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG--AGGUGGAAAGGUGCCACAAAGUGGUGGGAGUGCGACUGGUUGGUUGUGGGAGUCGUUGCCAC
((((....)))).........(((((((((..((.((..((((((((...--.(((.(...(.(.((((......)))).).).).))))))))))).))))..))))))))). ( -40.00)
>DroPer_CAF1 23848 97 + 1
UUUCCGAGGAAAACAUGGUUAUGGCCUGGGGGCCACAGAGGCCAGCUAUGGGAGGUGGA-AGGUGGCAUAUCACAGUGG----------------GUGUGGGAGUCAUGGUGAG
((((((.......((((((..((((((..(.....)..)))))))))))).....))))-))(((((...(((((....----------------.)))))..)))))...... ( -31.00)
>consensus
UUUCCGAGGAAAACAUGGUUAUGGCAGCGGGGCCACGGAGGCCAGCUAUG__AGGUGGAAAGGUGCCACAAAGUGGUGGGAGUGCGACUGG____UUGUGGGAGUCGUUGCCAC
((((....)))).........(((((((((..(((((....(((.((.....)).))).......((((......)))).................)))))...))))))))). (-24.71 = -24.97 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	5,249,528 – 5,249,630
Length	102
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	84.82
Mean single sequence MFE	-33.92
Consensus MFE	-24.10
Energy contribution	-23.74
Covariance contribution	-0.36
Combinations/Pair	1.23
Mean z-score	-2.19
Structure conservation index	0.71
SVM decision value	-0.01
SVM RNA-class probability	0.527621
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5249528 102 + 22407834
AAUGUGGGCGUGCCGCACAACGCUUAGAUGUGGCCAACAAAAACGGGCAGCAAAAGCGCGUGGAGCGUGCCUCAUAAUUGGCAAC--GUGA---AUGGCCAAAGACG
.((.(((((((........))))))).)).((((((......(((.((.......)).)))...(((((((........))).))--))..---.))))))...... ( -34.90)
>DroPse_CAF1 23854 88 + 1
AAUGUGGGCGUGCUGCA-ACAUUU------UGGCCAGGAAA-----------GAGGCGCGUGGAGCGUGCCUCAUAAUUGGCAAAAAGUGG-AAGAGGCUGGCGACG
...((.(.((.(((...-.(((((------(.(((((....-----------((((((((.....))))))))....)))))..)))))).-....))))).).)). ( -35.80)
>DroSec_CAF1 26376 102 + 1
AAUGUGGGCGUGCCGCA-AACGCUUAGAUGUGGCCAACAAAAACGGGCAGCAAAAGCGCGUGGAGCGUGCCUCAUAAUUGGCAAC--GUGAA--ACGGCCAAAGACG
.((.(((((((......-.))))))).)).(((((.......(((.((.......)).)))...(((((((........))).))--))...--..)))))...... ( -33.90)
>DroSim_CAF1 27532 102 + 1
AAUGUGGGCGUGCCGCA-AACGCUUAGAUGUGGCCAACAAAAACGGGCAGCAAAAGCGCGUGGAGCGUGCCUCAUAAUUGGCAAC--GUGAA--ACGGCCAAAGACG
.((.(((((((......-.))))))).)).(((((.......(((.((.......)).)))...(((((((........))).))--))...--..)))))...... ( -33.90)
>DroEre_CAF1 19209 100 + 1
AAUGUGGGCGUGCCACA-ACCGCUUAGAUGUGGCCAACAA-AACGGGCAGCAAAAGCGCGUGGAGCGUGCCUCAUAAUUGGCAAC--GUGA---ACGGCCAAAGACG
..(((((((((((..((-..(((((...(((.(((.....-....))).))).)))))..))..))))))).)))).(((((..(--(...---.)))))))..... ( -35.00)
>DroYak_CAF1 28535 100 + 1
AAUGUGGGCGUGCCGCA-ACCGCUUAGAUGUGGCAAACAA-AACGGGCAGAAAAAGCGCGUGGAGCGUGCCUCAUAAUUGGCAAC--GUGA---AUGGCCAAAGACG
......(((.(((((((-.(......).)))))))..((.-.(((.((.......)).)))...(((((((........))).))--))..---.)))))....... ( -30.00)
>consensus
AAUGUGGGCGUGCCGCA_AACGCUUAGAUGUGGCCAACAAAAACGGGCAGCAAAAGCGCGUGGAGCGUGCCUCAUAAUUGGCAAC__GUGA___ACGGCCAAAGACG
..(((((((..((((((...........)))))).....................((((.....))))))).)))).(((((...............)))))..... (-24.10 = -23.74 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:24 2006