Locus 1482

Sequence ID	3L_DroMel_CAF1
Location	4,323,433 – 4,323,602
Length	169
Max. P	0.948616

overview

Window 5

Location	4,323,433 – 4,323,527
Length	94
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	78.90
Mean single sequence MFE	-26.47
Consensus MFE	-19.90
Energy contribution	-21.10
Covariance contribution	1.20
Combinations/Pair	1.12
Mean z-score	-1.98
Structure conservation index	0.75
SVM decision value	1.38
SVM RNA-class probability	0.948616
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4323433 94 - 23771897
CACCCCUGGCCAUAUAUCUAUAUACAUUUAUGUUUCUUUUAUAAUAUAUGUAUAUGUAGGUAGGUAGAGCAGUCGAAGC-----------------AAUUUCCCGCCGGCG
.....(((((....((((((((((.((.((((((........)))))).)).))))))))))((.(((((.......))-----------------..))).))))))).. ( -21.00)
>DroSec_CAF1 10117 105 - 1
CACCCCUGGCCAUAUAUAUAUAUA------UGUUUUUCUUUUUAUAUAUAUGUAUGUAGGUAGGUAGAGCAGCCGAAGCAGAUCAAUUGGAAAAACAAUUUCCCGCCGGCG
....((((.(((((((((((((((------((..........))))))))))))))).)))))).......((((..((.((..(((((......)))))))..)))))). ( -29.20)
>DroSim_CAF1 8738 103 - 1
CACCCCUGGCCAUAUAUAUGUAUA------UGCUUUUCUU--UAUAUAUAUGUAUGUAGGUAGGUAGAGCAGCCGAAGCAGAUCAAUUGGAAAAACAAUUUCCCGCCGGCG
....((((.(((((((((((((((------((........--))))))))))))))).)))))).......((((..((.((..(((((......)))))))..)))))). ( -29.20)
>consensus
CACCCCUGGCCAUAUAUAUAUAUA______UGUUUUUCUU_UUAUAUAUAUGUAUGUAGGUAGGUAGAGCAGCCGAAGCAGAUCAAUUGGAAAAACAAUUUCCCGCCGGCG
.(((((((..((((((((((((((..................))))))))))))))))))..)))......((((..((.....(((((......)))))....)))))). (-19.90 = -21.10 +   1.20)

alignment

secondary structure

dotplot

Window 6

Location	4,323,451 – 4,323,567
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.55
Mean single sequence MFE	-26.78
Consensus MFE	-17.49
Energy contribution	-19.93
Covariance contribution	2.44
Combinations/Pair	1.18
Mean z-score	-1.97
Structure conservation index	0.65
SVM decision value	0.36
SVM RNA-class probability	0.702563
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4323451 116 - 23771897
AUUCCAUUUAAUCAAACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUCUAUAUACAUUUAUGUUUCUUUUAUAAUAUAUGUAUAUGUAGGUAGGUAGAGCAGUCGA----
.((((((((.........)))))))).(((((((....)))....(((.((...((((((((((.((.((((((........)))))).)).)))))))))))))))..))))...---- ( -25.40)
>DroSec_CAF1 10152 110 - 1
AUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUAUAUAUA------UGUUUUUCUUUUUAUAUAUAUGUAUGUAGGUAGGUAGAGCAGCCGA----
.((((((((.........))))))))...((((.....(((.(..((.((((((((((((((((------((..........))))))))))))))).))).))..).))))))).---- ( -31.10)
>DroSim_CAF1 8773 108 - 1
AUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUAUGUAUA------UGCUUUUCUU--UAUAUAUAUGUAUGUAGGUAGGUAGAGCAGCCGA----
.((((((((.........))))))))...((((..((.(((...((((..((((((((((((((------..........--))))))))))))))))))...)))..)).)))).---- ( -31.10)
>DroEre_CAF1 10016 105 - 1
AUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCUCCCCUGGCCAUGUA----UA--------UGUAUUUCUU--UAUAUAUGU-UAUGUAGGUAGGUAGAGCAGUCGAUUGG
.((((((((.........))))))))........((..(((((..((.((((((((----((--------(((((.....--.))))))).-))))).))).))..)))))..))..... ( -26.90)
>DroYak_CAF1 9028 95 - 1
AUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUACACCCCUGGCCAUAAAUAUGUA--------UGUAUUUCUU--UAUAUAU----AUGUAGGUAGGUAGAG-----------
.((((((((.........))))))))..................((((.((....(((((((--------((((......--)))))))----)))).)))))).....----------- ( -19.40)
>consensus
AUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUAUAUAUA______UGUUUUUCUU__UAUAUAUAU_UAUGUAGGUAGGUAGAGCAGCCGA____
.((((((((.........))))))))....(((..((.(((...((((..(((((((((((((....................)))))))))))))))))...)))..)).)))...... (-17.49 = -19.93 +   2.44)

alignment

secondary structure

dotplot

Window 7

Location	4,323,487 – 4,323,602
Length	115
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	88.83
Mean single sequence MFE	-25.84
Consensus MFE	-21.10
Energy contribution	-21.14
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.57
Structure conservation index	0.82
SVM decision value	0.44
SVM RNA-class probability	0.736237
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4323487 115 - 23771897
ACUUUCCUGACCCA-ACGAGAGGCGGGCAAUUUGCCAUUCCAUUUAAUCAAACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUCUAUAUACAUUUAUGUUUCUUUU
..............-..((((((((((((...(((((((((((((.........))))))))...)))))....))).)).......((((....))))........))))))).. ( -23.10)
>DroSec_CAF1 10188 109 - 1
ACUUUCCUGCCCCA-ACAAGCGGCGGGCAAUUUGCCAUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUAUAUAUA------UGUUUUUCUU
......(((((.(.-....).)))))(((...(((((((((((((.........))))))))...)))))....))).........((((((....))))------))........ ( -25.30)
>DroSim_CAF1 8807 109 - 1
ACUUUCCUGCCCCA-ACGAGCGGCGGGCAAUUUGCCAUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUAUGUAUA------UGCUUUUCUU
......(((((.(.-....).)))))(((...(((((((((((((.........))))))))...)))))....)))......(((.(((((....))))------))))...... ( -26.20)
>DroEre_CAF1 10053 104 - 1
ACUUUCCUGCCCCAAACAAGCGGCAGGCGAUUUGCCAUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCUCCCCUGGCCAUGUA----UA--------UGUAUUUCUU
.....((((((.(......).)))))).....(((((((((((((.........))))))))...))))).(((((((.....)).))))).----..--------.......... ( -27.40)
>DroYak_CAF1 9051 108 - 1
ACUUUCCUGCCCCAAACAAGCGGCGGGCAAUUUGCCAUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUACACCCCUGGCCAUAAAUAUGUA--------UGUAUUUCUU
.....((((((.(......).)))))).....(((((((((((((.........))))))))...))))).(((((((................))))--------)))....... ( -27.19)
>consensus
ACUUUCCUGCCCCA_ACAAGCGGCGGGCAAUUUGCCAUUCCAUUUAAUCAGACAAGAUGGAAAACUGGCACGCAUGCACCCCUGGCCAUAUAUAUAUAUA______UGUUUUUCUU
.....((((((.(......).)))))).....(((((((((((((.........))))))))...))))).............................................. (-21.10 = -21.14 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:48 2006