Locus 4901

Sequence ID	2L_DroMel_CAF1
Location	14,010,548 – 14,010,669
Length	121
Max. P	0.896656

overview

Window 0

Location	14,010,548 – 14,010,639
Length	91
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	80.73
Mean single sequence MFE	-22.91
Consensus MFE	-22.10
Energy contribution	-22.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.96
SVM decision value	0.99
SVM RNA-class probability	0.896656
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14010548 91 + 22407834
-----------------AAAGCGAGUUCCUCAAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGG
-----------------.....(((...)))...((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... ( -22.90)
>DroVir_CAF1 178700 97 + 1
-----------AGAAAAAAAGAAAUUUCACUCAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCGGU
-----------.((((........))))......((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... ( -22.90)
>DroGri_CAF1 112875 93 + 1
------------UAAAAAAAGAAAAU-C--ACUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCGGU
------------..............-.--....((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... ( -22.10)
>DroWil_CAF1 142091 104 + 1
UUAAGAGUGAAGCAAAAAAA--UU-CC-ACCUUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGU
.((((.(((...........--..-.)-))))))((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... ( -25.34)
>DroMoj_CAF1 146794 96 + 1
-----------UGAAAAAAAGAAUCUUCG-ACUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCGGU
-----------..................-....((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... ( -22.10)
>DroPer_CAF1 120806 89 + 1
UUU--------GCAUCG-----------ACAUCAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGU
...--------......-----------......((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... ( -22.10)
>consensus
____________CAAAAAAAGAAA_UUCACACUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGU
..................................((((((((((((.......)))))..((((((((.....))))..))))...............)))))))... (-22.10 = -22.10 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	14,010,548 – 14,010,639
Length	91
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	80.73
Mean single sequence MFE	-26.27
Consensus MFE	-24.55
Energy contribution	-24.55
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.93
SVM decision value	0.96
SVM RNA-class probability	0.890301
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14010548 91 - 22407834
CCUGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUUGAGGAACUCGCUUU-----------------
((((((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))....)))..........----------------- ( -25.60)
>DroVir_CAF1 178700 97 - 1
ACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUGAGUGAAAUUUCUUUUUUUCU-----------
...(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))......((((........)))).----------- ( -25.60)
>DroGri_CAF1 112875 93 - 1
ACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAGU--G-AUUUUCUUUUUUUA------------
...(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))....--.-..............------------ ( -24.70)
>DroWil_CAF1 142091 104 - 1
ACUGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAAGGU-GG-AA--UUUUUUUGCUUCACUCUUAA
...(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))((((((-((-(.--.........))))).)))). ( -29.70)
>DroMoj_CAF1 146794 96 - 1
ACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAGU-CGAAGAUUCUUUUUUUCA-----------
...(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))....-.(((((......))))).----------- ( -27.60)
>DroPer_CAF1 120806 89 - 1
ACUGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGAUGU-----------CGAUGC--------AAA
...(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))......-----------......--------... ( -24.40)
>consensus
ACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAGUGUGAA_UUUCUUUUUUUC____________
...(((((((((((((........)))))((((((((.((.((....)))).))))))))......)))))))).................................. (-24.55 = -24.55 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	14,010,559 – 14,010,669
Length	110
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.29
Mean single sequence MFE	-28.72
Consensus MFE	-22.10
Energy contribution	-22.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.06
Structure conservation index	0.77
SVM decision value	0.31
SVM RNA-class probability	0.680916
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14010559 110 + 22407834
CUCAAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGGUGAAA-GUCCAACGAA-AAUUGGCACACUUGA--
......((((((((((((.......)))))..((((((((.....))))..))))...............)))))))(((((...-(.((((....-..))))).)))))..-- ( -27.50)
>DroVir_CAF1 178717 111 + 1
ACUCAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCGGUUGAUG-AAGGCAGCCU-AAUUG-GGGUAGUUAUA
.(((((((((((((((((.......)))))..((((((((.....))))..))))...............)))))))(((((...-....))))).-..)))-))......... ( -31.90)
>DroWil_CAF1 142115 111 + 1
ACCUUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGUUGUCA-GCACGGCGAACGAAUAACAUUCUGGA--
.((....((((..(((((.......))))).(((((((((.....))))...(((((.((.(((.............))).)).)-)))))))))..))))........)).-- ( -27.12)
>DroMoj_CAF1 146811 110 + 1
G-ACUAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCGGUUGAAU-GUGGCUGCGA-AAUUG-AAGAUGUUGUA
(-((.(..(((..(((((.......))))).(((((((((.....)))))....((((..((((..(((........)))..)))-))))).))))-....)-))..))))... ( -25.30)
>DroAna_CAF1 97032 111 + 1
UUUUCAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGGAUGAGUCCUUUAGGGAU-AAAUCGCAGGUUUUA--
......((((((((((((.......)))))....((((((.....))))))...................))))))).(((..((((.....))))-..)))..........-- ( -31.20)
>DroPer_CAF1 120815 110 + 1
ACAUCAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGUUGACU-GGCGCCCAGA-AAAUGGCCCAAAAGA--
......((((((((((((.......)))))..((((((((.....))))..))))...............))))))).......(-((.(((....-....)))))).....-- ( -29.30)
>consensus
ACAUAAGGUUCUACCGAGAUUUGAACUCGGAUCGCUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUAGAACCAGUUGAAU_GUCGCACGAA_AAAUGGCAGAAUUGA__
......((((((((((((.......)))))..((((((((.....))))..))))...............)))))))..................................... (-22.10 = -22.10 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	14,010,559 – 14,010,669
Length	110
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	78.29
Mean single sequence MFE	-29.46
Consensus MFE	-24.07
Energy contribution	-24.23
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.07
Structure conservation index	0.82
SVM decision value	0.37
SVM RNA-class probability	0.710314
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14010559 110 - 22407834
--UCAAGUGUGCCAAUU-UUCGUUGGAC-UUUCACCUGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUUGAG
--(((((.((..(....-.((((((((.-.((((...(((((...(((((........)))))..))))).)))))))))))).(((((.......)))))..).)).))))). ( -32.60)
>DroVir_CAF1 178717 111 - 1
UAUAACUACCC-CAAUU-AGGCUGCCUU-CAUCAACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUUGAGU
.....(((((.-.....-..((((((..-.....((((......)))).....)).))))..(((((((((.((.((....)))).)))))))))....))))).......... ( -27.60)
>DroWil_CAF1 142115 111 - 1
--UCCAGAAUGUUAUUCGUUCGCCGUGC-UGACAACUGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAAGGU
--.((.(((((.....)))))(((((((-((((.((((......))))......))))))))(((((((((.((.((....)))).)))))))))....))).........)). ( -31.60)
>DroMoj_CAF1 146811 110 - 1
UACAACAUCUU-CAAUU-UCGCAGCCAC-AUUCAACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAGU-C
...........-.....-..........-........(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))....-. ( -24.70)
>DroAna_CAF1 97032 111 - 1
--UAAAACCUGCGAUUU-AUCCCUAAAGGACUCAUCCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGAAAA
--.....(((.......-........))).....((.((((((((.(......((((.(.((((.((((.(((....))).).))))))).).)))).).)))))))).))... ( -26.46)
>DroPer_CAF1 120815 110 - 1
--UCUUUUGGGCCAUUU-UCUGGGCGCC-AGUCAACUGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGAUGU
--.....((((((....-....))).))-)((((...(((((((((((((........)))))((((((((.((.((....)))).))))))))......)))))))))))).. ( -33.80)
>consensus
__UAAAAUCUGCCAAUU_UUCCCGCCAC_AGUCAACCGGUUCUAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAAAGU
.....................................(((((((((((((........)))))((((((((.((.((....)))).))))))))......))))))))...... (-24.07 = -24.23 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:32 2006