Locus 2099

Sequence ID	X_DroMel_CAF1
Location	5,707,435 – 5,707,591
Length	156
Max. P	0.996724

overview

Window 5

Location	5,707,435 – 5,707,551
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.88
Mean single sequence MFE	-30.58
Consensus MFE	-16.78
Energy contribution	-18.82
Covariance contribution	2.04
Combinations/Pair	1.12
Mean z-score	-2.74
Structure conservation index	0.55
SVM decision value	2.74
SVM RNA-class probability	0.996724
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5707435 116 + 22224390
---UUAAUGAAAUCAGAAAUAAGAACUAGA-UUUCUUGCCAUACACAAAUACAUGGCUCGAAUCGAUAUCUUGGCCCAAAGGCCAUCGAUCUUGGUCCGGGCCCCCCCCCAGUUCGAUUU
---......((((((....)..(((((.((-(((...(((((..........)))))..)))))........(((((...(((((.......))))).))))).......)))))))))) ( -31.00)
>DroSec_CAF1 35642 115 + 1
UUGUUAAUAUAAUCAGAAAUAAGAACUGGA-UUUCUGGCCAUACAUAAAUACAUGGCUCGAAUCGAUUCCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG----CCCCCCAGUUCGAUUU
......................(((((((.-.(((.((((((..........)))))).)))..........((((....(((((.......))))).))----))..)))))))..... ( -34.80)
>DroSim_CAF1 33240 97 + 1
UUGUUAAUAUAAUCAGAAAUAAGAACUGGA-UUUCUG------------------GCUCGAAUCGAUUCCUUGGCCCACAGGCCAUCGAUCUUGGCCCGG----CCCCCCAGUUCGAUUU
......................(((((((.-...(((------------------(..((((((((.....(((((....)))))))))).)))..))))----....)))))))..... ( -30.50)
>DroEre_CAF1 26411 113 + 1
UUAUUAAUAAAACCAGAACCAAUUUCUGGACUUUCUGGCCAUACAUAAA-AGAUGGCC-AAAUCGAUUUCAUGGCCCAAACACCAUCGAUCUUGGCCUGC-----CACCCAGUUCGAUUU
............((((((.....))))))......(((((((.(.....-.)))))))-)((((((.....((((((((............))))...))-----))......)))))). ( -28.40)
>DroYak_CAF1 27785 113 + 1
UUACUAAUAAAUUCAGAACUAGGAACUGCACUUUCUGGCCGUACAUAA--ACAUGGCCGGAAUCGAUUUCGUGGCCCAAGAACCAUCGAUCUUGGCCUGG-----CCCCCCAUUCGAUUU
................................((((((((((......--..))))))))))((((......((((.((((........))))))))(((-----....))).))))... ( -28.20)
>consensus
UUAUUAAUAAAAUCAGAAAUAAGAACUGGA_UUUCUGGCCAUACAUAAA_ACAUGGCUCGAAUCGAUUUCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG____CCCCCCAGUUCGAUUU
......................(((((((.........................((((.(.(((((.....(((((....)))))))))).).)))).((......)))))))))..... (-16.78 = -18.82 +   2.04)

alignment

secondary structure

dotplot

Window 6

Location	5,707,435 – 5,707,551
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.88
Mean single sequence MFE	-34.80
Consensus MFE	-21.34
Energy contribution	-21.94
Covariance contribution	0.60
Combinations/Pair	1.22
Mean z-score	-2.09
Structure conservation index	0.61
SVM decision value	1.37
SVM RNA-class probability	0.947578
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5707435 116 - 22224390
AAAUCGAACUGGGGGGGGGCCCGGACCAAGAUCGAUGGCCUUUGGGCCAAGAUAUCGAUUCGAGCCAUGUAUUUGUGUAUGGCAAGAAA-UCUAGUUCUUAUUUCUGAUUUCAUUAA---
.((((((.(((((......)))))......(((..(((((....))))).))).))))))...((((((........))))))..((((-((.((.........)))))))).....--- ( -36.10)
>DroSec_CAF1 35642 115 - 1
AAAUCGAACUGGGGGG----CCGGGCCAAGAUCGAUGGCCUUUGGGCCAAGGAAUCGAUUCGAGCCAUGUAUUUAUGUAUGGCCAGAAA-UCCAGUUCUUAUUUCUGAUUAUAUUAACAA
.....((((((((.((----((.(((...(((((((((((....))))).....))))))...)))..((((....)))))))).....-))))))))...................... ( -38.90)
>DroSim_CAF1 33240 97 - 1
AAAUCGAACUGGGGGG----CCGGGCCAAGAUCGAUGGCCUGUGGGCCAAGGAAUCGAUUCGAGC------------------CAGAAA-UCCAGUUCUUAUUUCUGAUUAUAUUAACAA
.....((((((((...----...(((...(((((((((((....))))).....))))))...))------------------).....-))))))))...................... ( -31.30)
>DroEre_CAF1 26411 113 - 1
AAAUCGAACUGGGUG-----GCAGGCCAAGAUCGAUGGUGUUUGGGCCAUGAAAUCGAUUU-GGCCAUCU-UUUAUGUAUGGCCAGAAAGUCCAGAAAUUGGUUCUGGUUUUAUUAAUAA
.(((.((((..(.((-----(....))).(((((((....(((((((..((....)).(((-(((((((.-.....).)))))))))..))))))).))))))))..)))).)))..... ( -33.50)
>DroYak_CAF1 27785 113 - 1
AAAUCGAAUGGGGGG-----CCAGGCCAAGAUCGAUGGUUCUUGGGCCACGAAAUCGAUUCCGGCCAUGU--UUAUGUACGGCCAGAAAGUGCAGUUCCUAGUUCUGAAUUUAUUAGUAA
...((((((.(((((-----(..((((..(((((((((((....))))).....))))))..))))....--...(((((.........))))))))))).)))).))............ ( -34.20)
>consensus
AAAUCGAACUGGGGGG____CCGGGCCAAGAUCGAUGGCCUUUGGGCCAAGAAAUCGAUUCGAGCCAUGU_UUUAUGUAUGGCCAGAAA_UCCAGUUCUUAUUUCUGAUUUUAUUAACAA
.....(((((((((......)).(((...(((((((((((....))))).....))))))...))).........................)))))))...................... (-21.34 = -21.94 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	5,707,471 – 5,707,591
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.95
Mean single sequence MFE	-31.63
Consensus MFE	-21.60
Energy contribution	-22.24
Covariance contribution	0.64
Combinations/Pair	1.10
Mean z-score	-1.65
Structure conservation index	0.68
SVM decision value	-0.00
SVM RNA-class probability	0.532814
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5707471 120 + 22224390
AUACACAAAUACAUGGCUCGAAUCGAUAUCUUGGCCCAAAGGCCAUCGAUCUUGGUCCGGGCCCCCCCCCAGUUCGAUUUAUAUUCCUAGCCCAGUUGGCGAUGCUAAUCGAUGUGCAUU
...((((.......((((((.(((((.(((.(((((....)))))..))).))))).))))))..........((((((..((((.(((((...))))).))))..)))))))))).... ( -38.70)
>DroSec_CAF1 35681 116 + 1
AUACAUAAAUACAUGGCUCGAAUCGAUUCCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG----CCCCCCAGUUCGAUUUAUAUUCCUAGUCCAGUUGGCGAUGCUAAUCGAUGUGCAUU
.(((((..((...(((((((((((((......((((....(((((.......))))).))----)).......))))))).........(((.....))))).))))))..))))).... ( -29.72)
>DroSim_CAF1 33276 101 + 1
---------------GCUCGAAUCGAUUCCUUGGCCCACAGGCCAUCGAUCUUGGCCCGG----CCCCCCAGUUCGAUUUAUAUUCCUAGCCCAGUUGGCGAUGCUAAUCGAUGUGCAUU
---------------((..(((((((......((((....(((((.......))))).))----)).......)))))))(((((....(((.....)))(((....))))))))))... ( -29.02)
>DroEre_CAF1 26451 113 + 1
AUACAUAAA-AGAUGGCC-AAAUCGAUUUCAUGGCCCAAACACCAUCGAUCUUGGCCUGC-----CACCCAGUUCGAUUUAUAUUCCUCGCCCAGUUGGCGAUGCUAAUCGAUGUGCAUU
.........-....((((-(((((((.....(((........)))))))).))))))(((-----.((.....((((((..((....(((((.....)))))))..)))))).))))).. ( -28.30)
>DroYak_CAF1 27825 113 + 1
GUACAUAA--ACAUGGCCGGAAUCGAUUUCGUGGCCCAAGAACCAUCGAUCUUGGCCUGG-----CCCCCCAUUCGAUUUAUAUUCCUAGCCCAUUUGGCGAUGCUAAUCGAUGUGCAUU
(((((...--....((((((..((((..((((((........))).)))..)))).))))-----))......((((((..((((....(((.....)))))))..)))))))))))... ( -32.40)
>consensus
AUACAUAAA_ACAUGGCUCGAAUCGAUUUCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG____CCCCCCAGUUCGAUUUAUAUUCCUAGCCCAGUUGGCGAUGCUAAUCGAUGUGCAUU
..............((((.(.(((((.....(((((....)))))))))).).))))................((((((..((((.((((.....)))).))))..))))))........ (-21.60 = -22.24 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:16 2006