Locus 5871

Sequence ID 2R_DroMel_CAF1
Location 18,560,824 – 18,560,987
Length 163
Max. P 0.990963
window9424 window9425 window9426 window9427 window9428

overview

Window 4

Location 18,560,824 – 18,560,916
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 77.25
Mean single sequence MFE -23.77
Consensus MFE -13.98
Energy contribution -15.57
Covariance contribution 1.59
Combinations/Pair 1.19
Mean z-score -1.47
Structure conservation index 0.59
SVM decision value 0.04
SVM RNA-class probability 0.552277
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18560824 92 + 20766785
AC------UAACCCAUCCAAUAUACCCU-UUACAAAUGGUUGGGUGGCGAAAAAUAAUGCAUGCCACCGCUGAUGGAUACGAGCAUCGAUGUCGAUGCU
..------....(((((........((.-........))...(((((((............)))))))...))))).....(((((((....))))))) ( -26.70)
>DroSec_CAF1 40634 92 + 1
AC------UAACCCAUCCUAUAUACCCU-UUAUAAAUGGUUGGGUGGCGAAAAAUGAUGCAUGCCACCGCUGAUGGAUACGAGCAUCGAUGUCGAUGCU
..------....(((((........((.-........))...(((((((............)))))))...))))).....(((((((....))))))) ( -26.70)
>DroSim_CAF1 36525 92 + 1
AC------UAACCCAUCCUAUAUACCCU-UUAUAAAUGGAUGGGUGGCGAAAAAUGAUGCAUGCCACCGCUGAUGGAUACGAGCAUCGAUGUCGAUGCU
.(------((((((((((..((((....-.))))...))))))))((((....(((...))).....))))..))).....(((((((....))))))) ( -28.10)
>DroEre_CAF1 42601 98 + 1
UUUAAUCAAUCCAUAAUCAAUAUACCCG-UAAUAAACGGUUCAGUGGCGAAAAAUGAUGCAUGCCACCGCUGAUGGAUACGAACAUCGAUGUCGAUGCU
........(((((............(((-(.....)))).(((((((.(....(((...)))..).)))))))))))).....(((((....))))).. ( -23.70)
>DroYak_CAF1 42308 98 + 1
UAGGAUGAAAACCUUUCCAGUAUACCCG-CAAUAAAUGGUUGGGUGGCGAAAAAUGAUGCAUGCCACCGCUGAUGGAUACGAACAUCGAUGUCGAUGCU
..(((..........))).((((.((..-((((.....))))(((((((............)))))))......))))))...(((((....))))).. ( -23.60)
>DroAna_CAF1 38607 94 + 1
UUU-----GAAACCUUCGUAUAUACCCCACAAGAUGUGAAACAUAGGCGAAUAAUUAUUUAUUCCACUGUUGAUGGAUACAAACAUCACUGUCGAUCUA
...-----.......................((((.(((...((((..((((((....))))))..))))(((((........)))))...))))))). ( -13.80)
>consensus
AC______UAACCCAUCCAAUAUACCCU_UAAUAAAUGGUUGGGUGGCGAAAAAUGAUGCAUGCCACCGCUGAUGGAUACGAACAUCGAUGUCGAUGCU
............(((((........((..........))...(((((((............)))))))...))))).....(((((((....))))))) (-13.98 = -15.57 +   1.59)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,560,824 – 18,560,916
Length 92
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -27.53
Consensus MFE -17.15
Energy contribution -18.46
Covariance contribution 1.31
Combinations/Pair 1.27
Mean z-score -2.27
Structure conservation index 0.62
SVM decision value 1.62
SVM RNA-class probability 0.968002
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18560824 92 - 20766785
AGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUUAUUUUUCGCCACCCAACCAUUUGUAA-AGGGUAUAUUGGAUGGGUUA------GU
(((((((....)))))))...(((((((.(.((((((..............))))))).(((........-..)))......)))))))..------.. ( -29.54)
>DroSec_CAF1 40634 92 - 1
AGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAACCAUUUAUAA-AGGGUAUAUAGGAUGGGUUA------GU
(((((((....)))))))...(((((((.(.((((((..............))))))).(((........-..)))......)))))))..------.. ( -29.54)
>DroSim_CAF1 36525 92 - 1
AGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAUCCAUUUAUAA-AGGGUAUAUAGGAUGGGUUA------GU
(((((((....))))))).((((((((.....)))).)))).............((((((((...((((.-....))))..))))))))..------.. ( -31.40)
>DroEre_CAF1 42601 98 - 1
AGCAUCGACAUCGAUGUUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACUGAACCGUUUAUUA-CGGGUAUAUUGAUUAUGGAUUGAUUAAA
.((((((....))))))(((.((((((((((((((((..............)))))))..((((.....)-))).....))))...))))))))..... ( -29.34)
>DroYak_CAF1 42308 98 - 1
AGCAUCGACAUCGAUGUUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAACCAUUUAUUG-CGGGUAUACUGGAAAGGUUUUCAUCCUA
(((((((....))))))).((((((....(.((((((..............)))))))...((.....))-.)))))).......(((.......))). ( -24.14)
>DroAna_CAF1 38607 94 - 1
UAGAUCGACAGUGAUGUUUGUAUCCAUCAACAGUGGAAUAAAUAAUUAUUCGCCUAUGUUUCACAUCUUGUGGGGUAUAUACGAAGGUUUC-----AAA
.(((((........(((((((.(((((.....))))))))))))....((((..((((..((((.....))))..))))..))))))))).-----... ( -21.20)
>consensus
AGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAACCAUUUAUAA_AGGGUAUAUAGGAUGGGUUA______GA
(((((((....)))))))...(((((((...((((((..............))))))...((..........))........))))))).......... (-17.15 = -18.46 +   1.31)

alignment

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secondary structure

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Window 6

Location 18,560,852 – 18,560,949
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 90.24
Mean single sequence MFE -27.58
Consensus MFE -25.42
Energy contribution -25.42
Covariance contribution 0.00
Combinations/Pair 1.15
Mean z-score -1.15
Structure conservation index 0.92
SVM decision value 0.15
SVM RNA-class probability 0.607065
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18560852 97 - 20766785
CGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUUAUUUUUCGCCACCCAACCAU
.(((.....)))(((((((((........)))))((((((....))))))..((((((((.....)))).)))).........)))).......... ( -29.70)
>DroSec_CAF1 40662 97 - 1
CGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAACCAU
.(((.....)))(((((((((........)))))((((((....))))))..((((((((.....)))).)))).........)))).......... ( -29.70)
>DroSim_CAF1 36553 97 - 1
CGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAUCCAU
.(((.....)))(((((((((........)))))((((((....))))))..((((((((.....)))).)))).........)))).......... ( -29.70)
>DroEre_CAF1 42635 97 - 1
CGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGUUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACUGAACCGU
.(((.....)))(((((((((........)))))((((((....))))))..((((((((.....)))).)))).........)))).......... ( -27.30)
>DroYak_CAF1 42342 97 - 1
CGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGUUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAACCAU
.(((.....)))(((((((((........)))))((((((....))))))..((((((((.....)))).)))).........)))).......... ( -27.30)
>DroAna_CAF1 38637 97 - 1
CGUGAAAAGCGCGGCGUGGAAAACUCUUGCUCCUAGAUCGACAGUGAUGUUUGUAUCCAUCAACAGUGGAAUAAAUAAUUAUUCGCCUAUGUUUCAC
.((((((.....(((((.((....(((.......))))).))((((((((((((.(((((.....))))))))))).)))))).)))....)))))) ( -21.80)
>consensus
CGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAGCGGUGGCAUGCAUCAUUUUUCGCCACCCAACCAU
.(((.....)))(((((((((........)))))((((((....))))))..((((((((.....)))).)))).........)))).......... (-25.42 = -25.42 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,560,886 – 18,560,987
Length 101
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 85.61
Mean single sequence MFE -33.05
Consensus MFE -27.09
Energy contribution -27.65
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -1.58
Structure conservation index 0.82
SVM decision value -0.04
SVM RNA-class probability 0.512214
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18560886 101 + 20766785
CUGAUGGAUACGAGCAUCGAUGUCGAUGCUGGAACGAGAGUUUUCCACGCCGCGCUUUUCACGGCCGCAUCCAUCAAAUCCAUGAAAUGCGCAGAGCGCGG
.((((((((.(((((((((....)))))))(((((....))..)))..((((.(.....).)))))).))))))))...........(((((...))))). ( -38.60)
>DroSec_CAF1 40696 94 + 1
CUGAUGGAUACGAGCAUCGAUGUCGAUGCUGGAACGAGAGUUUUCCACGCCGCGCUUUUCACGGCCGCAUCCAUCAAAUCCAUGAAAUGCGCA-------G
.((((((((.(((((((((....)))))))(((((....))..)))..((((.(.....).)))))).)))))))).................-------. ( -33.10)
>DroSim_CAF1 36587 101 + 1
CUGAUGGAUACGAGCAUCGAUGUCGAUGCUGGAACGAGAGUUUUCCACGCCGCGCUUUUCACGGCCGCAUCCAUCAAAUCCAUGAAAUGCGCAGAGCGCGG
.((((((((.(((((((((....)))))))(((((....))..)))..((((.(.....).)))))).))))))))...........(((((...))))). ( -38.60)
>DroEre_CAF1 42669 92 + 1
CUGAUGGAUACGAACAUCGAUGUCGAUGCUGGAACGAGAGUUUUCCACGCCGCGCUUUUCACGGCCGCAUCCAUCAAAUCC---------GCAGAGCGCGG
.((((((((.((..(((((....))))).((((((....))..)))).((((.(.....).)))))).))))))))...((---------((.....)))) ( -33.50)
>DroYak_CAF1 42376 92 + 1
CUGAUGGAUACGAACAUCGAUGUCGAUGCUGGAACGAGAGUUUUCCACGCCGCGCUUUUCACGGCCGCAUCCAUCAAAUCC---------GCAGAGCGCGG
.((((((((.((..(((((....))))).((((((....))..)))).((((.(.....).)))))).))))))))...((---------((.....)))) ( -33.50)
>DroAna_CAF1 38671 95 + 1
UUGAUGGAUACAAACAUCACUGUCGAUCUAGGAGCAAGAGUUUUCCACGCCGCGCUUUUCACGGUCGCAUCCAUCAA-UCCGCCGUAGCCGUA-----GGG
((((((((((((........)))(((((.((((((..(.((.......)))..))))))...))))).)))))))))-.((..((....))..-----)). ( -21.00)
>consensus
CUGAUGGAUACGAACAUCGAUGUCGAUGCUGGAACGAGAGUUUUCCACGCCGCGCUUUUCACGGCCGCAUCCAUCAAAUCCAUGAAAUGCGCAGAGCGCGG
.((((((((.(((((((((....)))))))(((((....))..)))..((((.(.....).)))))).))))))))......................... (-27.09 = -27.65 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,560,886 – 18,560,987
Length 101
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 85.61
Mean single sequence MFE -42.15
Consensus MFE -36.48
Energy contribution -36.48
Covariance contribution 0.00
Combinations/Pair 1.14
Mean z-score -3.79
Structure conservation index 0.87
SVM decision value 2.24
SVM RNA-class probability 0.990963
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18560886 101 - 20766785
CCGCGCUCUGCGCAUUUCAUGGAUUUGAUGGAUGCGGCCGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAG
..((((...))))............(((((((((((((((((.....)))))).(((((........)))))((((((....)))))).))))))))))). ( -46.40)
>DroSec_CAF1 40696 94 - 1
C-------UGCGCAUUUCAUGGAUUUGAUGGAUGCGGCCGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAG
.-------.................(((((((((((((((((.....)))))).(((((........)))))((((((....)))))).))))))))))). ( -40.90)
>DroSim_CAF1 36587 101 - 1
CCGCGCUCUGCGCAUUUCAUGGAUUUGAUGGAUGCGGCCGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAG
..((((...))))............(((((((((((((((((.....)))))).(((((........)))))((((((....)))))).))))))))))). ( -46.40)
>DroEre_CAF1 42669 92 - 1
CCGCGCUCUGC---------GGAUUUGAUGGAUGCGGCCGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGUUCGUAUCCAUCAG
((((.....))---------))...(((((((((((((((((.....)))))).(((((........)))))((((((....)))))).))))))))))). ( -44.20)
>DroYak_CAF1 42376 92 - 1
CCGCGCUCUGC---------GGAUUUGAUGGAUGCGGCCGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGUUCGUAUCCAUCAG
((((.....))---------))...(((((((((((((((((.....)))))).(((((........)))))((((((....)))))).))))))))))). ( -44.20)
>DroAna_CAF1 38671 95 - 1
CCC-----UACGGCUACGGCGGA-UUGAUGGAUGCGACCGUGAAAAGCGCGGCGUGGAAAACUCUUGCUCCUAGAUCGACAGUGAUGUUUGUAUCCAUCAA
...-----..(.((....)).).-((((((((((((.(((((.....))))))..(((..........)))......((((....)))).))))))))))) ( -30.80)
>consensus
CCGCGCUCUGCGCAUUUCAUGGAUUUGAUGGAUGCGGCCGUGAAAAGCGCGGCGUGGAAAACUCUCGUUCCAGCAUCGACAUCGAUGCUCGUAUCCAUCAG
.........................(((((((((((((((((.....)))))).(((((........)))))((((((....)))))).))))))))))). (-36.48 = -36.48 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:56 2006