Locus 575

Sequence ID	2R_DroMel_CAF1
Location	2,959,238 – 2,959,378
Length	140
Max. P	0.989442

overview

Window 0

Location	2,959,238 – 2,959,345
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	79.20
Mean single sequence MFE	-28.28
Consensus MFE	-18.59
Energy contribution	-19.15
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.54
Structure conservation index	0.66
SVM decision value	-0.02
SVM RNA-class probability	0.521705
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2959238 107 + 20766785
CCCAUAAACCGUUAGUUGGCUCGAAUGUGGCCAGCCGCGGGUCAGCACCGAACCGAUAUAUAAUGUUAUCGGGCAUCGAUGAGCAGGUACAAUCACAAGCAGCUGGU
........((((..(((((((.......))))))).)))).(((((..(((.((((((........))))))...)))....((..((......))..)).))))). ( -33.50)
>DroSec_CAF1 2351 85 + 1
CAAAUUAACCG-------------------CCAGUCGCG---CAUCACCGAACCGAUACACAAUGUUAUCGGGCAUCGAUGAGCAGGUACAAUCACAAGCAGCUGGU
..........(-------------------(((((.(((---(.(((.(((.((((((........))))))...))).)))))..((......))..)).)))))) ( -25.40)
>DroSim_CAF1 1035 85 + 1
CACAUAAACCG-------------------CCAGCCGCG---CAUCACCGAACCGAUAGACAAUGUUAUCGGGCAUCGAUGAGCAGGUACAAUCACAAGCAGCUGGU
..........(-------------------(((((.(((---(.(((.(((.(((((((......)))))))...))).)))))..((......))..)).)))))) ( -27.90)
>DroEre_CAF1 970 107 + 1
UCCAUAAACCGUUAAUUCAAUAUGGUGUGGCCAGUCGCAAGGCAGCACCGAACCGAUACUCAAUGUUAUCGAGCAUCGAUGAGCAGGUACAAUCACAAGCAGCUGGU
.((((..(((((.........)))))))))(((((.((..((.....))(.(((....(((((((((....)))))...))))..))).)........)).))))). ( -25.50)
>DroYak_CAF1 940 107 + 1
CCCAUAAACCGUUAAUUCAACAUGGUGUGGCCAGCCGCAAGGCAGCACCGAACCGAUAUAUACUGUUAUCGAGCAUCGAUGAGCAGGUACAAUCACAAGCAGCUGGU
.((((..(((((.........)))))))))(((((.((..((.....)).....(((.....(((((((((.....)))))).))).....)))....)).))))). ( -29.10)
>consensus
CCCAUAAACCGUUA_UU________UGUGGCCAGCCGCG_G_CAGCACCGAACCGAUACACAAUGUUAUCGGGCAUCGAUGAGCAGGUACAAUCACAAGCAGCUGGU
.............................((((((.((........(((...((((((........))))))((........)).)))..........)).)))))) (-18.59 = -19.15 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	2,959,238 – 2,959,345
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	79.20
Mean single sequence MFE	-32.06
Consensus MFE	-23.78
Energy contribution	-23.94
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.74
SVM decision value	0.43
SVM RNA-class probability	0.734189
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2959238 107 - 20766785
ACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUAUAUAUCGGUUCGGUGCUGACCCGCGGCUGGCCACAUUCGAGCCAACUAACGGUUUAUGGG
.((((((((..((.(..(((((.((........))((((((........))))))...)))))).))..))))))))((.(((..(((((.......)))))))))) ( -34.90)
>DroSec_CAF1 2351 85 - 1
ACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUGUGUAUCGGUUCGGUGAUG---CGCGACUGG-------------------CGGUUAAUUUG
...(((((((...(.((((....(((((((((...((((((........)))))).))))))).)---)))))).))-------------------)))))...... ( -26.50)
>DroSim_CAF1 1035 85 - 1
ACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUGUCUAUCGGUUCGGUGAUG---CGCGGCUGG-------------------CGGUUUAUGUG
.((((((((..(((....)))..(((((((((...((((((........)))))).))))))).)---)))))))))-------------------........... ( -32.60)
>DroEre_CAF1 970 107 - 1
ACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCUCGAUAACAUUGAGUAUCGGUUCGGUGCUGCCUUGCGACUGGCCACACCAUAUUGAAUUAACGGUUUAUGGA
.((((.(((..(.(...(((((.....(((((((((((((...)))))))))))))..)))))..))..))).)))).....(((((..............))))). ( -34.14)
>DroYak_CAF1 940 107 - 1
ACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCUCGAUAACAGUAUAUAUCGGUUCGGUGCUGCCUUGCGGCUGGCCACACCAUGUUGAAUUAACGGUUUAUGGG
.((((((((..(.(...(((((.((........))((((((........))))))...)))))..))..)))))))).....(((((..............))))). ( -32.14)
>consensus
ACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUGUAUAUCGGUUCGGUGCUG_C_CGCGGCUGGCCACA________AA_UAACGGUUUAUGGG
.((((((((..(((....))).....((((((...((((((........)))))).)))))).......)))))))).............................. (-23.78 = -23.94 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	2,959,278 – 2,959,378
Length	100
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	92.81
Mean single sequence MFE	-30.16
Consensus MFE	-26.10
Energy contribution	-25.54
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-1.97
Structure conservation index	0.87
SVM decision value	2.16
SVM RNA-class probability	0.989442
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2959278 100 - 20766785
GAAGUAA-GGCACAGGUUCAAAUGACAAUUUUGAACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUAUAUAUCGGUUCGGUGCUGAC
..((((.-((.(((((((((((.......)))))))).((.....))...))).))))))((((((...((((((........)))))).))))))..... ( -28.20)
>DroSec_CAF1 2371 98 - 1
GAAGUAA-GGCACAGGUUUAAAUGACAAUUUUGAACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUGUGUAUCGGUUCGGUGAUG--
...(((.-((.(((((((((((.......)))))))).((.....))...))).)))))(((((((...((((((........)))))).)))))))..-- ( -27.50)
>DroSim_CAF1 1055 98 - 1
GAAGUAA-GGCACAGGUUCAAAUGACAAUUUUGAACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUGUCUAUCGGUUCGGUGAUG--
...(((.-((.(((((((((((.......)))))))).((.....))...))).)))))(((((((...((((((........)))))).)))))))..-- ( -29.90)
>DroEre_CAF1 1010 100 - 1
AAAGUAA-GGGGCAGGUUCAAAUGACAAUUUUGAACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCUCGAUAACAUUGAGUAUCGGUUCGGUGCUGCC
....(((-(.(((.((((((((.......)))))))).))).)))).....(((((.....(((((((((((((...)))))))))))))..))))).... ( -37.80)
>DroYak_CAF1 980 101 - 1
AAAGUAAAGGGACAGGUUCAAAUGACAAUUUUGAACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCUCGAUAACAGUAUAUAUCGGUUCGGUGCUGCC
.......(((.(((((((((((.......)))))))).((.....))...))).)))((.((((((.((.(((((........)))))))))))))..)). ( -27.40)
>consensus
GAAGUAA_GGCACAGGUUCAAAUGACAAUUUUGAACCAGCUGCUUGUGAUUGUACCUGCUCAUCGAUGCCCGAUAACAUUGUAUAUCGGUUCGGUGCUG_C
..((((..((.(((((((((((.......)))))))).((.....))...))).))))))((((((...((((((........)))))).))))))..... (-26.10 = -25.54 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:00 2006