Locus 1074

Sequence ID 2L_DroMel_CAF1
Location 2,963,842 – 2,963,985
Length 143
Max. P 0.827928
window1732 window1733 window1734

overview

Window 2

Location 2,963,842 – 2,963,956
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.86
Mean single sequence MFE -32.00
Consensus MFE -21.25
Energy contribution -21.03
Covariance contribution -0.22
Combinations/Pair 1.29
Mean z-score -1.74
Structure conservation index 0.66
SVM decision value 0.41
SVM RNA-class probability 0.727294
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2963842 114 + 22407834
ACGAAAUUUAUUUACAACAAGCCCCAGAACCAAUACGAGUUGUUGCAGCAGCAGCUGCAGCUGCAGCAGGAGUUCGCCCAGUUUUUGACCAAUGUGGCCAACAGCG------CCGCAACG
........................(((((.(....((((((((((((((.((....)).))))))))))...))))....).))))).....(((((((....).)------)))))... ( -30.20)
>DroVir_CAF1 22624 114 + 1
ACGAAAUUCAUAUACAAUAAGCCACAAAAUCAUUUCGAGCUACUGCAACAGCAGCUGCAGCUGCAGCAGGAAUUUGCCCAGUUCCUCACAAAUGUGGCAAACAGUG------CAGCUGGG
...((((((..........((((.............).))).((((....(((((....))))).)))))))))).(((((((...(((....)))(((.....))------)))))))) ( -30.52)
>DroGri_CAF1 20215 114 + 1
ACGAAAUUCAUUUACAAUAAGCCACAAAAUCAUUUCGAGCUGCUGCAACAGCAGCUGCAACUGCAGCAGGAAUUUGCACAGUUCCUUACGAAUGUGGCCAAUAGUG------CAACUGGG
............(((.((..((((((...((.....((((((.(((((...(.(((((....)))))..)...))))))))))).....)).))))))..)).)))------........ ( -31.00)
>DroMoj_CAF1 23091 114 + 1
ACGAAAUUCAUCUACAAUAAGCCGCAGAAUCAUUUCGAAUUGCUACAACAGCAGCUGCAGCUGCAGCAGGAGUUUGCUCAGUUCCUUACCAAUGUGGCUAAUAGUG------CAGCUGGA
......((((.((.((...((((((((((....)))((((((........(((((....)))))(((((....)))))))))))........))))))).....))------.)).)))) ( -30.50)
>DroAna_CAF1 17169 120 + 1
ACGAAAUUUGUAUACAACAAGCCCCAAAAUCACUUUGAGUUGUUGCAGCAGCAACUGCAGCUGCAGCAGGAGUUCGCCCAGUUCUUAACUAACGUGGCCAACAGCGCUGCUGCCGCAGCU
......(((((.....)))))...((((.....))))((((((.((((((((..((((.......))))..(((.(((..(((.......)))..))).)))...)))))))).)))))) ( -37.30)
>DroPer_CAF1 124948 114 + 1
ACAAAAUUCAUUUACAACAAGCCACAAAAUCAAUUUGAGUUGCUCCAGCAACAGCUGCAACUGCAGCAGGAAUUCGCCCAGUUCCUGACAAACGUGGCCAGCAGUG------CAGUAGGA
..........(((((.....(((((.............(((((....))))).(((((....)))))(((((((.....))))))).......)))))..((...)------).))))). ( -32.50)
>consensus
ACGAAAUUCAUUUACAACAAGCCACAAAAUCAUUUCGAGUUGCUGCAACAGCAGCUGCAGCUGCAGCAGGAAUUCGCCCAGUUCCUGACAAAUGUGGCCAACAGUG______CAGCAGGG
....................(((((.............((((......)))).(((((....)))))(((((((.....))))))).......)))))...................... (-21.25 = -21.03 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,963,842 – 2,963,956
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.86
Mean single sequence MFE -38.12
Consensus MFE -22.09
Energy contribution -20.85
Covariance contribution -1.24
Combinations/Pair 1.54
Mean z-score -1.98
Structure conservation index 0.58
SVM decision value 0.22
SVM RNA-class probability 0.640713
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2963842 114 - 22407834
CGUUGCGG------CGCUGUUGGCCACAUUGGUCAAAAACUGGGCGAACUCCUGCUGCAGCUGCAGCUGCUGCUGCAACAACUCGUAUUGGUUCUGGGGCUUGUUGUAAAUAAAUUUCGU
.(((((((------((..(((.(((.((.(........).))))).)))...)))))))))((((((....))))))(((((.......((((....)))).)))))............. ( -37.00)
>DroVir_CAF1 22624 114 - 1
CCCAGCUG------CACUGUUUGCCACAUUUGUGAGGAACUGGGCAAAUUCCUGCUGCAGCUGCAGCUGCUGUUGCAGUAGCUCGAAAUGAUUUUGUGGCUUAUUGUAUAUGAAUUUCGU
..((((((------(((.(((((((.((.((......)).)))))))))....).)))))))).((((((((...))))))))((((((.....((..(....)..)).....)))))). ( -35.70)
>DroGri_CAF1 20215 114 - 1
CCCAGUUG------CACUAUUGGCCACAUUCGUAAGGAACUGUGCAAAUUCCUGCUGCAGUUGCAGCUGCUGUUGCAGCAGCUCGAAAUGAUUUUGUGGCUUAUUGUAAAUGAAUUUCGU
..((.(((------((.....(((((((.((((..(.(((((((((......))).)))))).)((((((((...))))))))....))))...)))))))...))))).))........ ( -40.30)
>DroMoj_CAF1 23091 114 - 1
UCCAGCUG------CACUAUUAGCCACAUUGGUAAGGAACUGAGCAAACUCCUGCUGCAGCUGCAGCUGCUGUUGUAGCAAUUCGAAAUGAUUCUGCGGCUUAUUGUAGAUGAAUUUCGU
..((((((------(.......(((.....))).........((((......)))))))))))..(((((....)))))....((((((...(((((((....)))))))...)))))). ( -37.30)
>DroAna_CAF1 17169 120 - 1
AGCUGCGGCAGCAGCGCUGUUGGCCACGUUAGUUAAGAACUGGGCGAACUCCUGCUGCAGCUGCAGUUGCUGCUGCAACAACUCAAAGUGAUUUUGGGGCUUGUUGUAUACAAAUUUCGU
(((((((((.((((((..(((.(((..(((.......)))..))).)))...)))))).))))))))).....(((((((.(((((((...)))))))...)))))))............ ( -44.70)
>DroPer_CAF1 124948 114 - 1
UCCUACUG------CACUGCUGGCCACGUUUGUCAGGAACUGGGCGAAUUCCUGCUGCAGUUGCAGCUGUUGCUGGAGCAACUCAAAUUGAUUUUGUGGCUUGUUGUAAAUGAAUUUUGU
......((------((..((.(((((((...(((((....((((....((((.((.(((((....))))).)).))))...))))..)))))..))))))).))))))............ ( -33.70)
>consensus
CCCAGCUG______CACUGUUGGCCACAUUGGUAAGGAACUGGGCAAACUCCUGCUGCAGCUGCAGCUGCUGCUGCAGCAACUCGAAAUGAUUUUGUGGCUUAUUGUAAAUGAAUUUCGU
...............((.((.((((.((...(((........))).......(((((((((.((....)).)))))))))..............)).)))).)).))............. (-22.09 = -20.85 +  -1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 2,963,882 – 2,963,985
Length 103
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 77.61
Mean single sequence MFE -36.55
Consensus MFE -19.25
Energy contribution -19.17
Covariance contribution -0.08
Combinations/Pair 1.24
Mean z-score -2.07
Structure conservation index 0.53
SVM decision value 0.70
SVM RNA-class probability 0.827928
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2963882 103 + 22407834
UGUUGCAGCAGCAGCUGCAGCUGCAGCAGGAGUUCGCCCAGUUUUUGACCAAUGUGGCCAACAGCG------CCGCAACG---CCAUCCAGCAACGGCUCGGCCAACUCGAC-
(((((((((.((....)).))))))))).(((((.(((.(((..((......(((((((....).)------)))))..(---(......))))..))).))).)))))...- ( -41.30)
>DroPse_CAF1 123286 104 + 1
UGCUCCAGCAACAGCUGCAACUGCAGCAGGAAUUCGCCCAGUUCCUUACAAACGUAGCCAGCAGUG------CAGUAGGAUCAGGAUCCAGCAGU---GCAGCCAACACAUCA
(((....)))...((((((.((((.(((((((((.....))))))((((....)))).......))------)....((((....)))).)))))---))))).......... ( -31.50)
>DroEre_CAF1 16395 103 + 1
UGUUGCAGCAGCAGCUGCAGCUGCAGCAGGAGUUCGCCCAGUUCUUGACCAAUGUGGCCAACAGCG------CCGCAACU---CCAUCCAGCAACGGCUCGGCCAACACGGC-
.(((((.((.(((((....))))).)).((((((.((...(((.(((.((.....)).))).))).------..))))))---)).....)))))(((...)))........- ( -39.00)
>DroYak_CAF1 16577 103 + 1
UGUUGCAACAGCAGCUGCAGCUGCAGCAGGAGUUUGCCCAGUUCUUGACCAAUGUGGCCAACAGCG------CCGCAACU---CCAUCCAGCAACGGCUCGGCUAACUCGAC-
...(((....)))(((((....)))))..(((((.(((.(((..(((.....(((((((....).)------))))).((---......)))))..))).))).)))))...- ( -34.80)
>DroAna_CAF1 17209 109 + 1
UGUUGCAGCAGCAACUGCAGCUGCAGCAGGAGUUCGCCCAGUUCUUAACUAACGUGGCCAACAGCGCUGCUGCCGCAGCU---ACACCCAGCAACAGCUCAACUAGCUCAAU-
((((((.((((...))))((((((.((((.((..(((...(((....((....))....))).))))).)))).))))))---.......))))))(((.....))).....- ( -38.10)
>DroPer_CAF1 124988 104 + 1
UGCUCCAGCAACAGCUGCAACUGCAGCAGGAAUUCGCCCAGUUCCUGACAAACGUGGCCAGCAGUG------CAGUAGGAUCAGGAUCCAGCAGU---GCAGCCAACACAUCA
(((....)))...(((((....)))))(((((((.....)))))))((......((((..(((.((------(....((((....)))).))).)---)).)))).....)). ( -34.60)
>consensus
UGUUGCAGCAGCAGCUGCAGCUGCAGCAGGAGUUCGCCCAGUUCUUGACCAACGUGGCCAACAGCG______CCGCAACU___CCAUCCAGCAACGGCUCAGCCAACACAAC_
.(((((.......(((((....))))).((((((.(((..(((.......)))..))).))).(((.......)))..........))).))))).................. (-19.25 = -19.17 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:47 2006