Locus 7271

Sequence ID	2L_DroMel_CAF1
Location	20,357,298 – 20,357,466
Length	168
Max. P	0.703446

overview

Window 4

Location	20,357,298 – 20,357,405
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.62
Mean single sequence MFE	-30.03
Consensus MFE	-21.19
Energy contribution	-21.13
Covariance contribution	-0.05
Combinations/Pair	1.18
Mean z-score	-1.96
Structure conservation index	0.71
SVM decision value	0.36
SVM RNA-class probability	0.703446
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20357298 107 - 22407834
CCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGCUUUGUUGCUU-UCCU------------CGUCGGAUUUCUAUAAACCAUAAACCAGGCUAUACGU
((......))((...((((.........(((((((((((.....)).)))))))))(((((.....-(((.------------....))).....)))))..........))))..)).. ( -31.50)
>DroSec_CAF1 14176 104 - 1
CCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGUUUUGUUGCUU-UCCUCACU--------CGCCGGAUUUCUAUAA-------ACCAGCCUAUACAU
......(((((((.((............(((((((((((.....)).)))))))))(((((.....-(((.....--------....))).....))))-------)))))))))).... ( -29.10)
>DroSim_CAF1 13220 104 - 1
CCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGCUUUGCUGCUU-UCCUCACU--------CGCCGGAUUUCUAUAA-------ACCAGGCUAUACAU
........((((..(((...........(((((((((((.....)).)))))))))..........-)))..)))--------)(((((.((.....))-------.)).)))....... ( -30.10)
>DroEre_CAF1 14941 104 - 1
CCUUAAAUGGGUUCGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGCCUUGCUGCUU-UCCUCACU--------CGUUGGAUUUCUGUAA-------GCCAGGCUAUACAU
.((((((((((((((((((...........)))))))....)))))))))))..((((.(((((..-(((.....--------....))).....)).)-------)).))))....... ( -36.20)
>DroYak_CAF1 14056 104 - 1
UCUUAAAUGGGUUCGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGUCGCUUUGUUGCUU-UCCUCACU--------CGUUGGAUUUCUAUAC-------AGCAGGCUAUACAU
...((((((((((((((((...........)))))))....)))))))))(((((((.(((.....-(((.....--------....))).....))).-------))).))))...... ( -31.00)
>DroAna_CAF1 14396 104 - 1
CCUUAAAUGGGUUUGGGCCAUUAAAUCUGCUGCCUGAUGAAACUCAUUUGGGCUGCUUUGUUACCUUUCCGCCCUGUGGACUCCCCCCGAUUUCUUGAA-------ACU---------AU
.......((((...(((...........((.(((..(((.....)).)..))).))...........(((((...)))))..)))))))..........-------...---------.. ( -22.30)
>consensus
CCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGCUUUGUUGCUU_UCCUCACU________CGCCGGAUUUCUAUAA_______ACCAGGCUAUACAU
........(((...((((...((((...(((((((((((.....)).)))))))))))))..)))).))).................................................. (-21.19 = -21.13 +  -0.05)

alignment

secondary structure

dotplot

Window 5

Location	20,357,335 – 20,357,437
Length	102
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.89
Mean single sequence MFE	-35.00
Consensus MFE	-23.40
Energy contribution	-22.82
Covariance contribution	-0.58
Combinations/Pair	1.29
Mean z-score	-1.65
Structure conservation index	0.67
SVM decision value	0.16
SVM RNA-class probability	0.610625
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20357335 102 - 22407834
AAUUGGGCGCAGGGCGAAAGUGUAGU------AAGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGCUUUGUUGCUU-UCCU---------
....((((((((((((...(((....------....)))((((((((((((((((((...........)))))))....))))))))))).))))))).)))))-....--------- ( -35.90)
>DroPse_CAF1 14458 111 - 1
AAUUGGGCUCAGGGCGAAAGUGUAGUACGAGUAUGCCGCCUUAAAUGGGUCUGGGCCAUUAAAUUGUUUGGCUGAUGAAUCUCAUUUGAGAC-UUUUGUAGUUU-UUCGGACU-----
.....(((((((((((.(..((.....))..).))))((((.....)))))))))))........(((((((((..((.((((....)))).-))...))))..-..))))).----- ( -30.40)
>DroSec_CAF1 14206 106 - 1
AAUUGGGCGCAGGGCGAAAGUGUAGU------AAGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGUUUUGUUGCUU-UCCUCACU-----
....((((((((((((...(((....------....)))((((((((((((((((((...........)))))))....))))))))))).))))))).)))))-........----- ( -33.40)
>DroYak_CAF1 14086 106 - 1
AAUUGGGCGCAGGGCGAAAGUGUAGU------AAGCCAUCUUAAAUGGGUUCGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGUCGCUUUGUUGCUU-UCCUCACU-----
...........(((.(((((((....------((((...((((((((((((((((((...........)))))))....)))))))))))..))))...)))))-)))))...----- ( -38.40)
>DroAna_CAF1 14420 112 - 1
AAUUGGGCGCAGGGCGAAAGUGUAGU------GUGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCUGCCUGAUGAAACUCAUUUGGGCUGCUUUGUUACCUUUCCGCCCUGUGGA
.......(((((((((((((.(((((------(.(((((((.....))))...)))))).......((.(((..(((.....)).)..))).)).....))))))).))))))))).. ( -42.40)
>DroPer_CAF1 14389 111 - 1
AAUUGGGCUCAGGGCGAAAGUGUAGUACGAGUAUGCCGCCUUAAAUGGGUCUGGGCCAUUAAAUUGUUUGGCUGAUGAAUCUCAUUUGGGAC-UUUUGUAGUUU-UUCGGACU-----
.....(((((((((((.(..((.....))..).))))((((.....)))))))))))........(((((((((..((.((((....)))).-))...))))..-..))))).----- ( -29.50)
>consensus
AAUUGGGCGCAGGGCGAAAGUGUAGU______AAGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGAAACUCAUUUGGGCCGCUUUGUUGCUU_UCCGCACU_____
....((((((((((((...(((..((........)))))(((((((((((((((((.............))))))....))))))))))).))))))).))))).............. (-23.40 = -22.82 +  -0.58)

alignment

secondary structure

dotplot

Window 6

Location	20,357,365 – 20,357,466
Length	101
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-28.33
Consensus MFE	-19.22
Energy contribution	-19.72
Covariance contribution	0.50
Combinations/Pair	1.19
Mean z-score	-1.76
Structure conservation index	0.68
SVM decision value	0.21
SVM RNA-class probability	0.634730
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20357365 101 - 22407834
UGC--GAAAAAGCAGCUAAGAAAA--U-AAACGGAAUUGGGCGCAGGGCGAAAGUGUAGU------AAGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGA
(((--......)))..........--.-.......((((((((((((((....)).....------..(((((((.....))))...))).......))))).))))))).. ( -30.10)
>DroPse_CAF1 14491 107 - 1
UGCUCGCAAAAGU---AAAGAAAA--CAAAACGGAAUUGGGCUCAGGGCGAAAGUGUAGUACGAGUAUGCCGCCUUAAAUGGGUCUGGGCCAUUAAAUUGUUUGGCUGAUGA
......((..(((---.....(((--(((....((....(((((((((((.(..((.....))..).))))((((.....))))))))))).))...)))))).)))..)). ( -25.30)
>DroSec_CAF1 14240 101 - 1
UGC--GAAAAAGCAGGUAACAAAA--U-AAACGGAAUUGGGCGCAGGGCGAAAGUGUAGU------AAGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGA
(((--......)))..........--.-.......((((((((((((((....)).....------..(((((((.....))))...))).......))))).))))))).. ( -30.10)
>DroYak_CAF1 14120 101 - 1
GGC--AAAAAAGCUGCUAAGAAAA--U-AAACGGAAUUGGGCGCAGGGCGAAAGUGUAGU------AAGCCAUCUUAAAUGGGUUCGGGCCAUUAAAUCUGCGGCCCGAUGA
(((--(.......)))).......--.-.......((((((((((((((....)).....------..(((((((.....))))...))).......))))).))))))).. ( -27.30)
>DroAna_CAF1 14460 102 - 1
UGC--GAAAAAA-AGUAAAGAAACCUA-AAACGGAAUUGGGCGCAGGGCGAAAGUGUAGU------GUGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCUGCCUGAUGA
(((--.......-.)))......((..-....)).((..((((((((((....)).((((------(.(((((((.....))))...))))))))..))))).)))..)).. ( -30.70)
>DroPer_CAF1 14422 107 - 1
UGCUGGCAAAAGU---AAAGAAAA--CAAAACGGAAUUGGGCUCAGGGCGAAAGUGUAGUACGAGUAUGCCGCCUUAAAUGGGUCUGGGCCAUUAAAUUGUUUGGCUGAUGA
.((..((((....---........--(((.......)))(((((((((((.(..((.....))..).))))((((.....)))))))))))......))).)..))...... ( -26.50)
>consensus
UGC__GAAAAAGCAG_AAAGAAAA__U_AAACGGAAUUGGGCGCAGGGCGAAAGUGUAGU______AAGCCACCUUAAAUGGGUUUGGGCCAUUAAAUCUGCGGCCCGAUGA
...................................((((((((((((((....)).............(((((((.....))))...))).......))))).))))))).. (-19.22 = -19.72 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:00 2006