Locus 7640

Sequence ID	3R_DroMel_CAF1
Location	20,465,348 – 20,465,498
Length	150
Max. P	0.628077

overview

Window 4

Location	20,465,348 – 20,465,440
Length	92
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	76.29
Mean single sequence MFE	-25.42
Consensus MFE	-19.56
Energy contribution	-18.95
Covariance contribution	-0.61
Combinations/Pair	1.28
Mean z-score	-0.83
Structure conservation index	0.77
SVM decision value	0.19
SVM RNA-class probability	0.628077
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20465348 92 + 27905053
UAU-GAGAUCAUUCAAUAUUCC--AAACAAUUUACCGAUAACUGUGCGGAUUGAGGGCCAGCAGCUUGUGUUGCGAGUGGGCGCGGAAGUUGGCC
...-........(((((.((((--...(((((..(((.....)).)..))))).(.(((.(((((....))))).....))).)))))))))).. ( -24.10)
>DroVir_CAF1 16830 85 + 1
UCAUCA--GUAAAGC------U--GCAGCAUUUACCGAUAACUGUGCGGAUUGAGAGCCAACAACUUAUGUUGUGAGUGAGCGCGGAAGUUGGCA
..(((.--(((((((------.--...)).))))).)))..((((((((........)).(((((....)))))......))))))......... ( -21.70)
>DroSec_CAF1 12220 92 + 1
UAA-GAGAUCAUUCAAUAUUUC--AAAUAGUUUACCGAUAACUGUGAGGAUUGAGGGCCAGCAGCUUGUGUUGCGAGUGGGCGCGGAAGUUGGCC
...-.......((((((.((((--(..(((((.......))))))))))))))))(((((((.(((((.....)))))..))((....))))))) ( -26.10)
>DroSim_CAF1 12366 92 + 1
UAA-GAGAUCAUUCAGUAUUCC--AAAUAGUUUACCGAUAACUGUGAGGAUUGAGGGCCAGCAGCUUGUGUUGCGAGUGGGCGCGGAAGUUGGCC
...-.......(((((...(((--..((((((.......))))))..))))))))(((((((.(((((.....)))))..))((....))))))) ( -27.30)
>DroYak_CAF1 12414 85 + 1
UUA-UAGAUCA---------UCACAUAUUACUUACCGAUAACUGUGUGGAUUGAGGGCCAGCAGCUUGUGUUGCGAGUGGGCGCGGAAGUUGGCC
...-....(((---------((((((((((........))).)))))))..))).(((((((.(((((.....)))))..))((....))))))) ( -23.60)
>DroMoj_CAF1 18150 90 + 1
AAA-GA--CAAUAGCUAA--CUGAACAGCAAUUACCGGUAGCUGUGCGGGUUGAGAGCCAACAGCUUGUGCUGUGAGUGGGCGCGGAAGUUGGCG
...-..--.....(((((--((.....((....(((.(((....))).))).....(((.(((((....))))).....)))))...))))))). ( -29.70)
>consensus
UAA_GAGAUCAUUCA_UA__CC__AAAUAAUUUACCGAUAACUGUGCGGAUUGAGGGCCAGCAGCUUGUGUUGCGAGUGGGCGCGGAAGUUGGCC
..................................(((((..((((((((........)).(((((....)))))......))))))..))))).. (-19.56 = -18.95 +  -0.61)

alignment

secondary structure

dotplot

Window 5

Location	20,465,400 – 20,465,498
Length	98
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	82.11
Mean single sequence MFE	-36.87
Consensus MFE	-26.69
Energy contribution	-26.38
Covariance contribution	-0.30
Combinations/Pair	1.32
Mean z-score	-1.27
Structure conservation index	0.72
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20465400 98 + 27905053
GGCCAGCAGCUUGUGUUGCGAGUGGGCGCGGAAGUUGGCCCGGAAUGGCUGGGAGGGUACCAGUGCCACCAGCAGAAAGGCGGCAGCUGU---AAUAAAAC--
.....((((((...(((((...(((((((....))..))))).....(((((...((((....)))).)))))......)))))))))))---........-- ( -39.40)
>DroVir_CAF1 16875 100 + 1
AGCCAACAACUUAUGUUGUGAGUGAGCGCGGAAGUUGGCACGAAACGGCUGGGAGGGCACCAGCGCCACCAGCAGGCAGGCAGCGGCUAC---AAUAUGAAUA
.(((.(((((....)))))..(((...((....))...)))......(((((...(((......))).))))).))).(((....)))..---.......... ( -33.20)
>DroPse_CAF1 14992 100 + 1
GGCCAACAGCUUGUGCUGCGAGUGCGCCCGAAAGUUGGCGCGGAAGGGCUGCGAGGGUACCAGAGCCACCAGCAGGAAGGCGGCAGCUAG---AACAUGUGUA
..((..((((....)))).....((((((....)..)))))))...(((((((..(((......)))..).((......)).))))))..---.......... ( -33.90)
>DroGri_CAF1 20727 103 + 1
GGCCAACAACUUGUGCUGCGAGUGGGCGCGAAAGUUGGCCCGAAACGGUUGCGAGGGCACCAACGCCACCAGCAGACAGGCAGCGGCUACAACAAUAUGAAUA
((((.....(((((.((((...(((((((....))..)))))....(((.(((..(....)..))).))).)))))))))....))))............... ( -36.80)
>DroMoj_CAF1 18200 100 + 1
AGCCAACAGCUUGUGCUGUGAGUGGGCGCGGAAGUUGGCGCGGAACGGCUGCGACGGCACCAGCGCCACUAGCAGACAGGCAGCGGCUAU---AAUGUAAAUA
((((....((((((.((((.(((((.(((((..((((.(((((.....))))).)))).)).)))))))).))))))))))...))))..---.......... ( -44.00)
>DroPer_CAF1 15759 100 + 1
GGCCAACAGCUUGUGCUGCGAGUGCGCCCGAAAGUUGGCGCGGAAGGGCUGCGAGGGUACCAGAGCCACCAGCAGGAAGGCGGCAGCUAG---AACAUGUGUA
..((..((((....)))).....((((((....)..)))))))...(((((((..(((......)))..).((......)).))))))..---.......... ( -33.90)
>consensus
GGCCAACAGCUUGUGCUGCGAGUGGGCGCGAAAGUUGGCGCGGAACGGCUGCGAGGGCACCAGCGCCACCAGCAGAAAGGCAGCAGCUAC___AAUAUGAAUA
.((((((...(((((((.......)))))))..)))))).......(((((((..(((......)))..).((......)).))))))............... (-26.69 = -26.38 +  -0.30)

alignment

secondary structure

dotplot

Window 6

Location	20,465,400 – 20,465,498
Length	98
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	82.11
Mean single sequence MFE	-33.77
Consensus MFE	-24.70
Energy contribution	-24.32
Covariance contribution	-0.38
Combinations/Pair	1.39
Mean z-score	-1.48
Structure conservation index	0.73
SVM decision value	0.15
SVM RNA-class probability	0.606329
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20465400 98 - 27905053
--GUUUUAUU---ACAGCUGCCGCCUUUCUGCUGGUGGCACUGGUACCCUCCCAGCCAUUCCGGGCCAACUUCCGCGCCCACUCGCAACACAAGCUGCUGGCC
--........---.(((.(((((((........))))))))))........(((((......(((((.......).))))....((.......)).))))).. ( -32.20)
>DroVir_CAF1 16875 100 - 1
UAUUCAUAUU---GUAGCCGCUGCCUGCCUGCUGGUGGCGCUGGUGCCCUCCCAGCCGUUUCGUGCCAACUUCCGCGCUCACUCACAACAUAAGUUGUUGGCU
..........---..((((((..((........))..))(((((.......)))))......((((........))))......(((((....))))).)))) ( -28.70)
>DroPse_CAF1 14992 100 - 1
UACACAUGUU---CUAGCUGCCGCCUUCCUGCUGGUGGCUCUGGUACCCUCGCAGCCCUUCCGCGCCAACUUUCGGGCGCACUCGCAGCACAAGCUGUUGGCC
.......((.---((((..((((((........)))))).)))).)).......(((.....(((((........)))))....(((((....))))).))). ( -36.00)
>DroGri_CAF1 20727 103 - 1
UAUUCAUAUUGUUGUAGCCGCUGCCUGUCUGCUGGUGGCGUUGGUGCCCUCGCAACCGUUUCGGGCCAACUUUCGCGCCCACUCGCAGCACAAGUUGUUGGCC
................(((((.((.(((((((.((((((((.(((((((..((....))...))))..)))...))).))))).)))).))).)).).)))). ( -34.70)
>DroMoj_CAF1 18200 100 - 1
UAUUUACAUU---AUAGCCGCUGCCUGUCUGCUAGUGGCGCUGGUGCCGUCGCAGCCGUUCCGCGCCAACUUCCGCGCCCACUCACAGCACAAGCUGUUGGCU
..........---..((((((.((.((((((..((((((((((((((.(..((....))..)))))))......))).)))))..))).))).)).).))))) ( -35.00)
>DroPer_CAF1 15759 100 - 1
UACACAUGUU---CUAGCUGCCGCCUUCCUGCUGGUGGCUCUGGUACCCUCGCAGCCCUUCCGCGCCAACUUUCGGGCGCACUCGCAGCACAAGCUGUUGGCC
.......((.---((((..((((((........)))))).)))).)).......(((.....(((((........)))))....(((((....))))).))). ( -36.00)
>consensus
UAUUCAUAUU___AUAGCCGCCGCCUGCCUGCUGGUGGCGCUGGUACCCUCGCAGCCGUUCCGCGCCAACUUCCGCGCCCACUCGCAGCACAAGCUGUUGGCC
..............(((.(((((((........))))))))))...........(((.....(((((.......).))))....(((((....))))).))). (-24.70 = -24.32 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:58 2006