Locus 7905

Sequence ID	3R_DroMel_CAF1
Location	21,214,165 – 21,214,305
Length	140
Max. P	0.962425

overview

Window 1

Location	21,214,165 – 21,214,279
Length	114
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.15
Mean single sequence MFE	-42.17
Consensus MFE	-23.90
Energy contribution	-25.93
Covariance contribution	2.03
Combinations/Pair	1.11
Mean z-score	-2.77
Structure conservation index	0.57
SVM decision value	1.54
SVM RNA-class probability	0.962425
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21214165 114 + 27905053
ACUUUGAAGCCGCUGCCGAUGGUGAAGCUAUAGCAAAAGCUAUGGCCAAAGCUAAGGCUCAAGCCCAUGC--UGAUGUGGCCAUGAACGAGGGCUGGAUCGUUCGACGGAAGUGGU
........((((((.((((((((...((((((((....))))))))((.(((...(((....)))...))--)....)))))))((((((........))))))..))).)))))) ( -45.80)
>DroSec_CAF1 40846 102 + 1
ACUUUGAAGCCGCUGCCGAUGGUGAAGC------------UAUGGCCAGAGCUAAGGCUCAAGCCCAUGC--UGAUGUGGCCAUGAACGAGGGCUGCAUCGGUCGACGGAAGUGGA
.........(((((.((((((((((.((------------(.((((....)))).))))))...))))((--(((((..(((.........)))..)))))))...))).))))). ( -41.60)
>DroSim_CAF1 42732 114 + 1
ACUUUGAAGCCGCUGCCGAUGGUGAAGCUAUAGCAAAAGCUAUGGCCAGAGCUAAGGCUCAAGCCCAUGA--UGAUGUGGCCAUGAACGAGGGCUGCAUCGGUCGACGGCAGAGGA
.........((.((((((((((....((((((((....))))))))..((((....))))....))))((--(((((..(((.........)))..)))).)))..)))))).)). ( -50.50)
>DroEre_CAF1 42310 106 + 1
ACUUUGAAGCCGCUGCCGAUGGUUAAGCUAUAGCAAAAGCUAUGGCCAGAACUAAGGCUCAAGUCCAUGC--UGAUGUGGCCAUGAACGAGGGCUGCAUCGA--------AAGGGG
.((((..(((.((((((..(((((..((((((((....))))))))...))))).)))...)))....))--)((((..(((.........)))..)))).)--------)))... ( -37.50)
>DroYak_CAF1 42878 106 + 1
ACUUUGAAGCCGCUGCCGAUGGUAAAGCUAUAGCAAAAGCUAUGGCCAAAGCUAAGGCUCAAGCCCAUGC--UUAUGUGGCCAUGAACGAGGGCUGCAUCGC--------AGGCGG
.........(((((..(((((....(((((((((....)))))(((((((((...(((....)))...))--))...))))).........)))).))))).--------.))))) ( -40.00)
>DroAna_CAF1 39907 106 + 1
ACUUUGAAGCCGAUGCUGAUGCUGAUGCUGAUGCUGAUG------CUGAUGCUAAGGCCCUUGGCAAAGCCAUGAUGUGGCCAUGAACGAGGGCUGCAUCGACCGA----AAGGCA
.......(((....((....((....))....))....)------))(((((...((((((((.((..(((((...)))))..))..)))))))))))))(.((..----..))). ( -37.60)
>consensus
ACUUUGAAGCCGCUGCCGAUGGUGAAGCUAUAGCAAAAGCUAUGGCCAAAGCUAAGGCUCAAGCCCAUGC__UGAUGUGGCCAUGAACGAGGGCUGCAUCGAUCGA____AGGGGA
........((....(((..((((...((((((((....))))))))....)))).)))....))........((((((((((.........))))))))))............... (-23.90 = -25.93 +   2.03)

alignment

secondary structure

dotplot

Window 2

Location	21,214,165 – 21,214,279
Length	114
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.15
Mean single sequence MFE	-35.40
Consensus MFE	-19.58
Energy contribution	-21.63
Covariance contribution	2.06
Combinations/Pair	1.11
Mean z-score	-2.14
Structure conservation index	0.55
SVM decision value	0.66
SVM RNA-class probability	0.815555
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21214165 114 - 27905053
ACCACUUCCGUCGAACGAUCCAGCCCUCGUUCAUGGCCACAUCA--GCAUGGGCUUGAGCCUUAGCUUUGGCCAUAGCUUUUGCUAUAGCUUCACCAUCGGCAGCGGCUUCAAAGU
.((.((.(((..((((((........))))))..(((((....(--((..((((....))))..))).)))))(((((....)))))...........))).)).))......... ( -36.10)
>DroSec_CAF1 40846 102 - 1
UCCACUUCCGUCGACCGAUGCAGCCCUCGUUCAUGGCCACAUCA--GCAUGGGCUUGAGCCUUAGCUCUGGCCAUA------------GCUUCACCAUCGGCAGCGGCUUCAAAGU
.......((((.(.((((((........(((.(((((((....(--((..((((....))))..))).))))))))------------)).....))))))).))))......... ( -33.62)
>DroSim_CAF1 42732 114 - 1
UCCUCUGCCGUCGACCGAUGCAGCCCUCGUUCAUGGCCACAUCA--UCAUGGGCUUGAGCCUUAGCUCUGGCCAUAGCUUUUGCUAUAGCUUCACCAUCGGCAGCGGCUUCAAAGU
......(((((.(.((((((.(((....(((((.((((.(((..--..))))))))))))....)))..(((.(((((....))))).)))....))))))).)))))........ ( -40.70)
>DroEre_CAF1 42310 106 - 1
CCCCUU--------UCGAUGCAGCCCUCGUUCAUGGCCACAUCA--GCAUGGACUUGAGCCUUAGUUCUGGCCAUAGCUUUUGCUAUAGCUUAACCAUCGGCAGCGGCUUCAAAGU
.((((.--------((((((........(((((((.........--.)))))))((((((..((((...(((....)))...))))..)))))).)))))).)).))......... ( -29.00)
>DroYak_CAF1 42878 106 - 1
CCGCCU--------GCGAUGCAGCCCUCGUUCAUGGCCACAUAA--GCAUGGGCUUGAGCCUUAGCUUUGGCCAUAGCUUUUGCUAUAGCUUUACCAUCGGCAGCGGCUUCAAAGU
((((.(--------((((((.(((..........(((((...((--((..((((....))))..)))))))))(((((....))))).)))....)))).)))))))......... ( -38.90)
>DroAna_CAF1 39907 106 - 1
UGCCUU----UCGGUCGAUGCAGCCCUCGUUCAUGGCCACAUCAUGGCUUUGCCAAGGGCCUUAGCAUCAG------CAUCAGCAUCAGCAUCAGCAUCAGCAUCGGCUUCAAAGU
...(((----(.(((((((((.(((((.(..((.(((((.....))))).)).).)))))....((....(------(....))....))..........)))))))))..)))). ( -34.10)
>consensus
UCCCCU____UCGACCGAUGCAGCCCUCGUUCAUGGCCACAUCA__GCAUGGGCUUGAGCCUUAGCUCUGGCCAUAGCUUUUGCUAUAGCUUCACCAUCGGCAGCGGCUUCAAAGU
..................((.((((((.(((.((((...............((((.((((....)))).))))(((((....))))).......)))).))))).)))).)).... (-19.58 = -21.63 +   2.06)

alignment

secondary structure

dotplot

Window 3

Location	21,214,201 – 21,214,305
Length	104
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	72.74
Mean single sequence MFE	-34.83
Consensus MFE	-20.10
Energy contribution	-20.52
Covariance contribution	0.42
Combinations/Pair	1.16
Mean z-score	-1.63
Structure conservation index	0.58
SVM decision value	0.80
SVM RNA-class probability	0.853679
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21214201 104 + 27905053
AAGCUAUGGCCAAAGCUAAGGCUCAAGCCCAUGC--UGAUGUGGCCAUGAACGAGGGCUGGAUCGUUCGACGGAAGUGGUGGCGUUGAGAUGGUGGGGAUUCAUGG--------
.((((.((((....)))).))))....(((((.(--((((((.(((.(((((((........)))))))((....))))).))))).))...))))).........-------- ( -36.40)
>DroSec_CAF1 40874 100 + 1
----UAUGGCCAGAGCUAAGGCUCAAGCCCAUGC--UGAUGUGGCCAUGAACGAGGGCUGCAUCGGUCGACGGAAGUGGAGUCGGUGAGAUGGUGGGGAUUCAUGG--------
----(((((...((((....))))...(((((.(--(((((..(((.........)))..))))))((.((....)).))(((.....))).)))))...))))).-------- ( -37.40)
>DroSim_CAF1 42768 112 + 1
AAGCUAUGGCCAGAGCUAAGGCUCAAGCCCAUGA--UGAUGUGGCCAUGAACGAGGGCUGCAUCGGUCGACGGCAGAGGAGGCGGUGAGAUGGUGGGGAUUCAUGGAGGGGAUU
...((((((...((((....))))...(((((.(--(((((..(((.........)))..)))).(((..(......)..)))......)).)))))...))))))........ ( -37.40)
>DroEre_CAF1 42346 96 + 1
AAGCUAUGGCCAGAACUAAGGCUCAAGUCCAUGC--UGAUGUGGCCAUGAACGAGGGCUGCAUCGA--------AAGGGGGGCGGCGGGUUGGUGGGGUUUCAUGG--------
...((((((((...((((..((((..((((.(..--(((((..(((.........)))..))))).--------.)...))))...))))))))..)))..)))))-------- ( -32.20)
>DroYak_CAF1 42914 90 + 1
AAGCUAUGGCCAAAGCUAAGGCUCAAGCCCAUGC--UUAUGUGGCCAUGAACGAGGGCUGCAUCGC--------AGGCGGG------GAUUGGUGGGGAUUCGUGG--------
....((((((((((((...(((....)))...))--))...)))))))).(((((..((.(((((.--------.......------...))))).)).)))))..-------- ( -30.40)
>DroAna_CAF1 39943 87 + 1
AUG------CUGAUGCUAAGGCCCUUGGCAAAGCCAUGAUGUGGCCAUGAACGAGGGCUGCAUCGACCGA----AAGGCAGACGGA-AGCUGGUGAGG----------------
...------.((((((...((((((((.((..(((((...)))))..))..)))))))))))))).((..----..))(((.(...-.))))......---------------- ( -35.20)
>consensus
AAGCUAUGGCCAAAGCUAAGGCUCAAGCCCAUGC__UGAUGUGGCCAUGAACGAGGGCUGCAUCGAUCGA____AGGGGAGGCGGUGAGAUGGUGGGGAUUCAUGG________
...((((((((...((((.(((....))).......((((((((((.........)))))))))).........................))))..))..))))))........ (-20.10 = -20.52 +   0.42)

alignment

secondary structure

dotplot

Window 4

Location	21,214,201 – 21,214,305
Length	104
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	72.74
Mean single sequence MFE	-25.40
Consensus MFE	-13.29
Energy contribution	-14.07
Covariance contribution	0.78
Combinations/Pair	1.13
Mean z-score	-1.66
Structure conservation index	0.52
SVM decision value	0.42
SVM RNA-class probability	0.730432
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21214201 104 - 27905053
--------CCAUGAAUCCCCACCAUCUCAACGCCACCACUUCCGUCGAACGAUCCAGCCCUCGUUCAUGGCCACAUCA--GCAUGGGCUUGAGCCUUAGCUUUGGCCAUAGCUU
--------.......................((.............((((((........))))))(((((((....(--((..((((....))))..))).))))))).)).. ( -27.60)
>DroSec_CAF1 40874 100 - 1
--------CCAUGAAUCCCCACCAUCUCACCGACUCCACUUCCGUCGACCGAUGCAGCCCUCGUUCAUGGCCACAUCA--GCAUGGGCUUGAGCCUUAGCUCUGGCCAUA----
--------.((((.................((((.........))))...((((..(((.........)))..)))).--.))))((((.((((....)))).))))...---- ( -27.40)
>DroSim_CAF1 42768 112 - 1
AAUCCCCUCCAUGAAUCCCCACCAUCUCACCGCCUCCUCUGCCGUCGACCGAUGCAGCCCUCGUUCAUGGCCACAUCA--UCAUGGGCUUGAGCCUUAGCUCUGGCCAUAGCUU
.........(((((............((((.((.......)).)).))..((((..(((.........)))..)))).--)))))((((.((((....)))).))))....... ( -26.60)
>DroEre_CAF1 42346 96 - 1
--------CCAUGAAACCCCACCAACCCGCCGCCCCCCUU--------UCGAUGCAGCCCUCGUUCAUGGCCACAUCA--GCAUGGACUUGAGCCUUAGUUCUGGCCAUAGCUU
--------................................--------..((((..(((.........)))..))))(--((((((.((.((((....)))).)))))).))). ( -19.40)
>DroYak_CAF1 42914 90 - 1
--------CCACGAAUCCCCACCAAUC------CCCGCCU--------GCGAUGCAGCCCUCGUUCAUGGCCACAUAA--GCAUGGGCUUGAGCCUUAGCUUUGGCCAUAGCUU
--------...................------.....((--------((...)))).....(((.(((((((...((--((..((((....))))..)))))))))))))).. ( -24.90)
>DroAna_CAF1 39943 87 - 1
----------------CCUCACCAGCU-UCCGUCUGCCUU----UCGGUCGAUGCAGCCCUCGUUCAUGGCCACAUCAUGGCUUUGCCAAGGGCCUUAGCAUCAG------CAU
----------------........(((-.(((........----.)))..(((((.(((((.(..((.(((((.....))))).)).).)))))....)))))))------).. ( -26.50)
>consensus
________CCAUGAAUCCCCACCAUCUCACCGCCUCCCCU____UCGACCGAUGCAGCCCUCGUUCAUGGCCACAUCA__GCAUGGGCUUGAGCCUUAGCUCUGGCCAUAGCUU
..................................................((((..(((.........)))..))))........((((.((((....)))).))))....... (-13.29 = -14.07 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:43 2006