Locus 3583

Sequence ID	2R_DroMel_CAF1
Location	11,928,354 – 11,928,493
Length	139
Max. P	0.981449

overview

Window 7

Location	11,928,354 – 11,928,459
Length	105
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.64
Mean single sequence MFE	-33.33
Consensus MFE	-22.67
Energy contribution	-22.75
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.68
SVM decision value	1.21
SVM RNA-class probability	0.930957
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11928354 105 + 20766785
AAAGCAACAGAGGCCG------------AGCUGAGUAGACUUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCCACCCAACUUCUGGCCUCGGCU
..(((....(((((((------------((.(((((((((......))))))).(((((((((((.(((((....)))))..)))))...))))))...)).)))..)))))).))) ( -39.30)
>DroPse_CAF1 35239 114 + 1
GCAGCAACAGAAGCUGUAACCGAAGCAAGUCUGAGUAGAAUUUUGUGUUUAUUGAGGCUACUUAUCGACUGUACACAGUCAAGUGAGCUUUGGCCU--UUGACCACAGGCC-CUCCU
(((((.......)))))....(((((.(((((.((((((........)))))).))))).......(((((....)))))......)))))(((((--........)))))-..... ( -34.90)
>DroSec_CAF1 29942 90 + 1
AAAGCAACAGAGGCCG------------AGCUGAGUAGACUUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC--CCAAC-------------U
...........(((((------------((((.(((((((......))))))).))(((((((...(((((....))))))))).)))))))))).--.....-------------. ( -27.80)
>DroYak_CAF1 28664 103 + 1
AAAGCAACAGAGGCCG------------AGCUGAGUAGACUUUUGUGAUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC--CCAACUUGUGGCCUCGGCU
..(((....(((((((------------....((((..((....)).......((((((((((((.(((((....)))))..)))))...))))))--)..)))).))))))).))) ( -37.70)
>DroAna_CAF1 54024 93 + 1
AAAGCAACAGAGGCCAA----------AAGCUGAGUAGACUUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC--CC------------CAACU
...........((((((----------(..((.(((((((......))))))).))(((((((...(((((....))))))))).)))))))))).--..------------..... ( -28.70)
>DroPer_CAF1 35695 114 + 1
GCAGCAACAGAAGCCGUAACCGAAGCAAGUCUGAGUAGAAUUUUGUGUUUAUUGAGGCUACUUAUCGACUGUACACAGUCAAGUGAGCUUUGGCUU--UUGACCACAGGCC-CUCCU
.......((((((((......(((((.(((((.((((((........)))))).))))).......(((((....)))))......))))))))))--))).....(((..-..))) ( -31.60)
>consensus
AAAGCAACAGAGGCCG____________AGCUGAGUAGACUUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC__CCAAC__C_GGCC_CGCCU
...........((((...............((.(((((((......))))))).))(((((((...(((((....))))))))).)))...))))...................... (-22.67 = -22.75 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	11,928,382 – 11,928,493
Length	111
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.41
Mean single sequence MFE	-37.99
Consensus MFE	-19.92
Energy contribution	-19.45
Covariance contribution	-0.47
Combinations/Pair	1.15
Mean z-score	-2.98
Structure conservation index	0.52
SVM decision value	1.55
SVM RNA-class probability	0.962902
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11928382 111 + 20766785
UUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCCACCCAACUUCUGGCCUCGGCUUUGACCCAUUUGG--GGCUUAGUC----UUGGCCAGAUAG
......(((.....(((((((((((.(((((....)))))..)))))...))))))....))).(((((((..((((..(.(((....))--).)..))))----..)))))))... ( -42.80)
>DroPse_CAF1 35279 108 + 1
UUUUGUGUUUAUUGAGGCUACUUAUCGACUGUACACAGUCAAGUGAGCUUUGGCCU--UUGACCACAGGCC-CUCCUCUGGCCUAUUUAA--GGCUUAGGC----UUGGCCAGAUUG
...((((.(((..((((((((((((.(((((....)))))..)))))...))))))--)))).))))((((-..(((..(((((.....)--)))).))).----..))))...... ( -39.60)
>DroSec_CAF1 29970 96 + 1
UUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC--CCAAC-------------UUUGACCCAUUUGG--GUCCUAGUC----UUGGCCAGAUAG
.((((.(((....((((((((((((.(((((....)))))..)))))...))))))--)..((-------------(..(((((....))--)))..))).----..)))))))... ( -32.90)
>DroYak_CAF1 28692 113 + 1
UUUUGUGAUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC--CCAACUUGUGGCCUCGGCUUUGACUCAUUUGG--AGCUUAGACUUACUUGGCCAGAUAG
.............((((((((((((.(((((....)))))..)))))...))))))--).....(.(((((..(((((..(.....)..)--))))...........))))).)... ( -33.92)
>DroAna_CAF1 54054 99 + 1
UUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC--CC------------CAACUUUGACCCAUUUGGGGGGCCAAGUC----UCGGCCAAAUGG
.........((((..((((.......(((((....)))))....(((.((((((((--((------------(((...........))))))))))))).)----)))))).)))). ( -41.80)
>DroPer_CAF1 35735 108 + 1
UUUUGUGUUUAUUGAGGCUACUUAUCGACUGUACACAGUCAAGUGAGCUUUGGCUU--UUGACCACAGGCC-CUCCUCUGGCCUAUUUAA--GGCUUAGGC----UUGGCCAGAUUG
...((((.(((..((((((((((((.(((((....)))))..)))))...))))))--)))).))))((((-..(((..(((((.....)--)))).))).----..))))...... ( -36.90)
>consensus
UUUUGUGUUUAUUGGGGCUACUUAUCGACUGAGCACAGUCAAGUGAGCUUUGGCCC__CCAAC__C_GGCC_CGCCUUUGACCCAUUUGG__GGCUUAGUC____UUGGCCAGAUAG
..............(((((((((((.(((((....)))))..)))))...))))))....................................((((...........))))...... (-19.92 = -19.45 +  -0.47)

alignment

secondary structure

dotplot

Window 9

Location	11,928,382 – 11,928,493
Length	111
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.41
Mean single sequence MFE	-35.23
Consensus MFE	-17.83
Energy contribution	-17.49
Covariance contribution	-0.33
Combinations/Pair	1.11
Mean z-score	-3.41
Structure conservation index	0.51
SVM decision value	1.89
SVM RNA-class probability	0.981449
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11928382 111 - 20766785
CUAUCUGGCCAA----GACUAAGCC--CCAAAUGGGUCAAAGCCGAGGCCAGAAGUUGGGUGGGCCAAAGCUCACUUGACUGUGCUCAGUCGAUAAGUAGCCCCAAUAAACACAAAA
...(((((((..----(.((..(((--(.....))))...)).)..))))))).(((((((((((....))))))(((((((....))))))).........))))).......... ( -39.90)
>DroPse_CAF1 35279 108 - 1
CAAUCUGGCCAA----GCCUAAGCC--UUAAAUAGGCCAGAGGAG-GGCCUGUGGUCAA--AGGCCAAAGCUCACUUGACUGUGUACAGUCGAUAAGUAGCCUCAAUAAACACAAAA
......((((..----.(((..(((--(.....))))...)))..-))))((((.....--((((....(((...(((((((....)))))))..))).)))).......))))... ( -35.60)
>DroSec_CAF1 29970 96 - 1
CUAUCUGGCCAA----GACUAGGAC--CCAAAUGGGUCAAA-------------GUUGG--GGGCCAAAGCUCACUUGACUGUGCUCAGUCGAUAAGUAGCCCCAAUAAACACAAAA
.....(((((..----((((..(((--((....)))))..)-------------)))..--.)))))..(((.(((((((((....)))))...)))))))................ ( -33.90)
>DroYak_CAF1 28692 113 - 1
CUAUCUGGCCAAGUAAGUCUAAGCU--CCAAAUGAGUCAAAGCCGAGGCCACAAGUUGG--GGGCCAAAGCUCACUUGACUGUGCUCAGUCGAUAAGUAGCCCCAAUAAUCACAAAA
.....(((((.((.....))..(((--(.....)))).........))))).......(--((((....(((...(((((((....)))))))..))).)))))............. ( -29.40)
>DroAna_CAF1 54054 99 - 1
CCAUUUGGCCGA----GACUUGGCCCCCCAAAUGGGUCAAAGUUG------------GG--GGGCCAAAGCUCACUUGACUGUGCUCAGUCGAUAAGUAGCCCCAAUAAACACAAAA
......(((.((----(..((((((((((((.(.......).)))------------))--)))))))..)))..(((((((....)))))))......)))............... ( -40.40)
>DroPer_CAF1 35735 108 - 1
CAAUCUGGCCAA----GCCUAAGCC--UUAAAUAGGCCAGAGGAG-GGCCUGUGGUCAA--AAGCCAAAGCUCACUUGACUGUGUACAGUCGAUAAGUAGCCUCAAUAAACACAAAA
......((((..----.(((..(((--(.....))))...)))..-))))..((((...--..))))..(((.(((((((((....)))))...)))))))................ ( -32.20)
>consensus
CUAUCUGGCCAA____GACUAAGCC__CCAAAUGGGUCAAAGCAG_GGCC_G__GUUGG__GGGCCAAAGCUCACUUGACUGUGCUCAGUCGAUAAGUAGCCCCAAUAAACACAAAA
.....(((((........................)))))......................((((....(((...(((((((....)))))))..))).)))).............. (-17.83 = -17.49 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:11 2006