Locus 412

Sequence ID 2R_DroMel_CAF1
Location 2,433,712 – 2,433,876
Length 164
Max. P 0.997974
window803 window804 window805 window806 window807

overview

Window 3

Location 2,433,712 – 2,433,803
Length 91
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 88.91
Mean single sequence MFE -27.62
Consensus MFE -19.08
Energy contribution -19.64
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.69
SVM decision value 0.40
SVM RNA-class probability 0.721345
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2433712 91 - 20766785
AGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGC-UGCAUUUUUCAGCUUGCACACAGUGCCACAC----ACACGUGUGUCUAGAUGU------A
..(((((...............(((((.(((((......((-((.......)))).))))).))))).(((((----....))))))))))....------. ( -26.80)
>DroSec_CAF1 89614 94 - 1
AGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGCAUGCAUUUUUCAGCUCGCACACAGUGCCACACA--CACACGUGUGUCUAGAUGU------A
..((((((((((.............)))))(((((((.(((..((........))..))).)))))))..((((--(....))))))))))....------. ( -27.22)
>DroSim_CAF1 47103 96 - 1
AGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGCAUGCAUUUUUCAGCUCGCACACAGUGCCACACACGCACACGUGUGUUUAGAUGU------A
..((((((((((.............)))))(((((((.(((..((........))..))).)))))))..((((((....)))))))))))....------. ( -26.52)
>DroYak_CAF1 45933 98 - 1
AGUUCGAAUCCAUUACUGCAAGCACUGUGUGCAUUGUUUGCAUUCAUUUUUCAGCUCGCACACAGUGCAAAAC----ACACGUGCGUCUAGAUGUACGAGUA
.............((((....(((((((((((...(((..............)))..))))))))))).....----...(((((((....))))))))))) ( -29.94)
>consensus
AGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGCAUGCAUUUUUCAGCUCGCACACAGUGCCACAC____ACACGUGUGUCUAGAUGU______A
((((((((........(((((.((.((....)).)).)))))......)))))))).((((((.(((...........)))))))))............... (-19.08 = -19.64 +   0.56)

alignment

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secondary structure

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Window 4

Location 2,433,733 – 2,433,841
Length 108
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 83.97
Mean single sequence MFE -35.10
Consensus MFE -25.30
Energy contribution -26.46
Covariance contribution 1.16
Combinations/Pair 1.04
Mean z-score -2.60
Structure conservation index 0.72
SVM decision value 1.61
SVM RNA-class probability 0.967145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2433733 108 + 20766785
GUGGCACUGUGUGCAAGCUGAAAAAUGCA-GCAAACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGUAAACACCUGGG--AAAUGUCAGAGGCGUCUGAAUG
...(((.(((.(((..((........)).-))).))).))).(((((((.((((((((.(((...)))..)))))))).)).)))))--.....(((((....)))))... ( -36.60)
>DroSec_CAF1 89637 109 + 1
GUGGCACUGUGUGCGAGCUGAAAAAUGCAUGCAAACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGCAAACACCUGGG--CAGGGUCAGAGGCGUCUGAAUG
...(((.(((.((((.((........)).)))).))).))).(((((((.((((((((.(((...)))..)))))))).)).)))))--.....(((((....)))))... ( -40.60)
>DroSim_CAF1 47128 109 + 1
GUGGCACUGUGUGCGAGCUGAAAAAUGCAUGCAAACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGCAAACACCUGGG--CAGGGUCAGAGGCGUCUGAAUG
...(((.(((.((((.((........)).)))).))).))).(((((((.((((((((.(((...)))..)))))))).)).)))))--.....(((((....)))))... ( -40.60)
>DroEre_CAF1 45343 100 + 1
-GUGCAC-GUGUGCGAGCUGAAAAAUGGAUGCAAACAAUGCACGCAGUGAUUGCAGUAAUGUA-------CACUGCAAACAACUGGG--AAGGGUCAGAGGCGACCGAGUG
-(((((.-((.((((..(........)..)))).))..)))))((((((..((((....))))-------))))))...........--...((((......))))..... ( -29.30)
>DroYak_CAF1 45960 102 + 1
UUUGCACUGUGUGCGAGCUGAAAAAUGAAUGCAAACAAUGCACACAGUGCUUGCAGUAAUGGAUUCGAACUACUGUAAACAACUGGGGAAAGGGUCAGAUAC---------
...((((((((((((.((............))......))))))))))))((((((((.(........).))))))))....((((........))))....--------- ( -28.40)
>consensus
GUGGCACUGUGUGCGAGCUGAAAAAUGCAUGCAAACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGCAAACACCUGGG__AAGGGUCAGAGGCGUCUGAAUG
...(((.(((.((((.((........)).)))).))).))).(((((((.((((((((............)))))))).)).)))))........................ (-25.30 = -26.46 +   1.16)

alignment

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secondary structure

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Window 5

Location 2,433,733 – 2,433,841
Length 108
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 83.97
Mean single sequence MFE -35.35
Consensus MFE -25.76
Energy contribution -28.48
Covariance contribution 2.72
Combinations/Pair 1.06
Mean z-score -3.78
Structure conservation index 0.73
SVM decision value 2.97
SVM RNA-class probability 0.997974
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2433733 108 - 20766785
CAUUCAGACGCCUCUGACAUUU--CCCAGGUGUUUACAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGC-UGCAUUUUUCAGCUUGCACACAGUGCCAC
...(((((....))))).....--(((((.((.((.((((((.(((...))))))))).)).))))))).(((((((.(((-.((........))..))).)))))))... ( -34.70)
>DroSec_CAF1 89637 109 - 1
CAUUCAGACGCCUCUGACCCUG--CCCAGGUGUUUGCAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGCAUGCAUUUUUCAGCUCGCACACAGUGCCAC
...(((((....)))))....(--(((((.((.(((((((((.(((...)))))))))))).))))))))(((((((.(((..((........))..))).)))))))... ( -43.90)
>DroSim_CAF1 47128 109 - 1
CAUUCAGACGCCUCUGACCCUG--CCCAGGUGUUUGCAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGCAUGCAUUUUUCAGCUCGCACACAGUGCCAC
...(((((....)))))....(--(((((.((.(((((((((.(((...)))))))))))).))))))))(((((((.(((..((........))..))).)))))))... ( -43.90)
>DroEre_CAF1 45343 100 - 1
CACUCGGUCGCCUCUGACCCUU--CCCAGUUGUUUGCAGUG-------UACAUUACUGCAAUCACUGCGUGCAUUGUUUGCAUCCAUUUUUCAGCUCGCACAC-GUGCAC-
.....(((((....)))))...--..((((.(.((((((((-------.....)))))))).))))).((((((.((.(((................))).))-))))))- ( -28.29)
>DroYak_CAF1 45960 102 - 1
---------GUAUCUGACCCUUUCCCCAGUUGUUUACAGUAGUUCGAAUCCAUUACUGCAAGCACUGUGUGCAUUGUUUGCAUUCAUUUUUCAGCUCGCACACAGUGCAAA
---------(((..((((..........))))..))).(((((...........)))))..(((((((((((...(((..............)))..)))))))))))... ( -25.94)
>consensus
CAUUCAGACGCCUCUGACCCUU__CCCAGGUGUUUGCAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUUUGCAUGCAUUUUUCAGCUCGCACACAGUGCCAC
...((((......)))).......(((((.((.(((((((((.((.....))))))))))).))))))).(((((((.(((..((........))..))).)))))))... (-25.76 = -28.48 +   2.72)

alignment

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secondary structure

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Window 6

Location 2,433,765 – 2,433,876
Length 111
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 79.98
Mean single sequence MFE -33.00
Consensus MFE -22.04
Energy contribution -23.40
Covariance contribution 1.36
Combinations/Pair 1.04
Mean z-score -2.69
Structure conservation index 0.67
SVM decision value 2.22
SVM RNA-class probability 0.990639
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2433765 111 + 20766785
AACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGUAAACACCUGGG--AAAUGUCAGAGGCGUCUGAAUGGCCC--CAAAAUAGUAUUGAGUAUUGUAUUCGUCCAU
.(((((((.(((((((.((((((((.(((...)))..)))))))).)).)))))--..........((.(((.....))).)--).............))))))).......... ( -34.20)
>DroSec_CAF1 89670 111 + 1
AACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGCAAACACCUGGG--CAGGGUCAGAGGCGUCUGAAUGCCCC--CAAAAUCGAAUUGAGUAUUGUAUUCGUCCAA
.(((((((.(((((((.((((((((.(((...)))..)))))))).)).)))))--..(((.....(((((....)))))))--).............))))))).......... ( -39.00)
>DroSim_CAF1 47161 111 + 1
AACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGCAAACACCUGGG--CAGGGUCAGAGGCGUCUGAAUGCCCC--CAAAAUAGUAUUGAGUAUUGUAUUCGUCCAU
.(((((((.(((((((.((((((((.(((...)))..)))))))).)).)))))--..(((.....(((((....)))))))--).............))))))).......... ( -39.00)
>DroEre_CAF1 45374 99 + 1
AACAAUGCACGCAGUGAUUGCAGUAAUGUA-------CACUGCAAACAACUGGG--AAGGGUCAGAGGCGACCGAGUGGCCCCCGAAAAUA-------GUAUUGUAUUCGUCCAU
.(((((((..((((((..((((....))))-------)))))).........((--..((((((..((...))...)))))))).......-------))))))).......... ( -31.40)
>DroYak_CAF1 45993 93 + 1
AACAAUGCACACAGUGCUUGCAGUAAUGGAUUCGAACUACUGUAAACAACUGGGGAAAGGGUCAGAUAC---------------CAAAAUA-------GUAUUGUAUUCGUCCAU
.(((((((...((((..((((((((.(........).))))))))...))))......((........)---------------)......-------))))))).......... ( -21.40)
>consensus
AACAAUGCACCCAGUGAUUGCAGUAAUGGAUUCCAGCUACUGCAAACACCUGGG__AAGGGUCAGAGGCGUCUGAAUGCCCC__CAAAAUAG_AUUGAGUAUUGUAUUCGUCCAU
.(((((((.(((((((.((((((((............)))))))).)).))))).......((((......)))).......................))))))).......... (-22.04 = -23.40 +   1.36)

alignment

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secondary structure

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Window 7

Location 2,433,765 – 2,433,876
Length 111
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 79.98
Mean single sequence MFE -30.44
Consensus MFE -16.66
Energy contribution -18.78
Covariance contribution 2.12
Combinations/Pair 1.07
Mean z-score -1.86
Structure conservation index 0.55
SVM decision value 0.06
SVM RNA-class probability 0.563110
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2433765 111 - 20766785
AUGGACGAAUACAAUACUCAAUACUAUUUUG--GGGCCAUUCAGACGCCUCUGACAUUU--CCCAGGUGUUUACAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUU
...(((((........(((((.......)))--))((...(((((....))))).....--(((((.((.((.((((((.(((...))))))))).)).))))))).)).))))) ( -27.20)
>DroSec_CAF1 89670 111 - 1
UUGGACGAAUACAAUACUCAAUUCGAUUUUG--GGGGCAUUCAGACGCCUCUGACCCUG--CCCAGGUGUUUGCAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUU
..((.(((((..........)))))...(..--(((((........)))))..).)).(--(((((.((.(((((((((.(((...)))))))))))).))))))))........ ( -38.80)
>DroSim_CAF1 47161 111 - 1
AUGGACGAAUACAAUACUCAAUACUAUUUUG--GGGGCAUUCAGACGCCUCUGACCCUG--CCCAGGUGUUUGCAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUU
...(((((....................(..--(((((........)))))..)....(--(((((.((.(((((((((.(((...)))))))))))).))))))))...))))) ( -37.20)
>DroEre_CAF1 45374 99 - 1
AUGGACGAAUACAAUAC-------UAUUUUCGGGGGCCACUCGGUCGCCUCUGACCCUU--CCCAGUUGUUUGCAGUG-------UACAUUACUGCAAUCACUGCGUGCAUUGUU
(((.(((..........-------.....((((((((.((...)).)))))))).....--..((((.(.((((((((-------.....)))))))).)))))))).))).... ( -30.60)
>DroYak_CAF1 45993 93 - 1
AUGGACGAAUACAAUAC-------UAUUUUG---------------GUAUCUGACCCUUUCCCCAGUUGUUUACAGUAGUUCGAAUCCAUUACUGCAAGCACUGUGUGCAUUGUU
(((.(((....((((((-------(.....)---------------)))).))..........((((.((((.(((((((........))))))).))))))))))).))).... ( -18.40)
>consensus
AUGGACGAAUACAAUACUCAAU_CUAUUUUG__GGGCCAUUCAGACGCCUCUGACCCUU__CCCAGGUGUUUGCAGUAGCUGGAAUCCAUUACUGCAAUCACUGGGUGCAUUGUU
...(((((................................((((......)))).......(((((.((.(((((((((.((.....))))))))))).)))))))....))))) (-16.66 = -18.78 +   2.12)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:59 2006