Locus 2124

Sequence ID 2R_DroMel_CAF1
Location 7,949,620 – 7,949,750
Length 130
Max. P 0.985802
window3521 window3522 window3523 window3524

overview

Window 1

Location 7,949,620 – 7,949,735
Length 115
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 76.77
Mean single sequence MFE -39.58
Consensus MFE -21.22
Energy contribution -22.03
Covariance contribution 0.81
Combinations/Pair 1.28
Mean z-score -2.22
Structure conservation index 0.54
SVM decision value 1.24
SVM RNA-class probability 0.935125
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7949620 115 + 20766785
CGUUAGUUCGUAGCGCAGCGAGUGAUGCAUCAGGGCAAUCUGCUGCUGCACUUUCAUGAGCAGCACUGAAUUGCACUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAAAUGGAA
......(((((...((((((((((.....(((((((.....)))(((((.(......).))))).))))....))))))...((((((.....))))))....))))..))))). ( -41.20)
>DroVir_CAF1 1311 114 + 1
CGUCAGCUCGUAACGCAUCGAAUGAUGCAUCAACGCGAUCUGCUGCUGCACCUUCUGCAACAACAUCGAACCGCUCUCGAUGAGCAGGAUUUGCCGCACAAAGCUGCGGGGG-AG
..((..((((((..(((((....)))))......((....((.(((.(((..((((((.....((((((.......)))))).))))))..))).)))))..)))))))).)-). ( -36.50)
>DroPse_CAF1 1285 115 + 1
UGUCAGCUCACACCGCAUCGAGUGGUGCAUAAGGGCAAUCUGUUGCUGCACCUUCAGCAGCAGCAAAGAAUCGCUCUGGACCAGCAGUAUCUGGCGGCUGAAACUGAGAGAGAAA
..((((((..((((((.....))))))....(((((..(((((((((((.......))))))))..)))...))))).(.((((......))))))))))).............. ( -39.30)
>DroGri_CAF1 1342 109 + 1
CGUCAGCUCGUAACGCAUCGAAUGAUGCAUCAACGCAAUCUGCUGCUGCACCUUCAGCAGCAGCAACGAGCCGCUCUCAAUCAGUAGAAUCUGACGCACAAAACUGCAA------
.((((((((((...(((((....)))))............(((((((((.......)))))))))))))))...((((.....).)))...))))(((......)))..------ ( -38.80)
>DroMoj_CAF1 1830 114 + 1
CGUCAGCUCGUAGCGCAGCGAGUGGUGCAUCAAUGCCAACUGCUGCUGCACCUUCAGCAGCAACAAGGAGCCGCUCUCAAUAAGCAGGAUUUGACGCACGAAGCUGCAGGGG-AA
(.((.((.....))(((((...(.((((.((((..((...((((((((......))))))))..........(((.......))).))..)))).)))).).))))).)).)-.. ( -40.80)
>DroPer_CAF1 1285 115 + 1
UGUCAGCUCACACCGCAUCGAGUGGUGCAUAAGGGCAAUCUGUUGCUGCACCUUCAGCAGCAGCAAAGAAUCGCUCUGGACCAGCAGUAUCUGGCGGCUGAAACUGAGAGGGAAA
..((((((..((((((.....))))))....(((((..(((((((((((.......))))))))..)))...))))).(.((((......)))))))))))..((....)).... ( -40.90)
>consensus
CGUCAGCUCGUAACGCAUCGAGUGAUGCAUCAAGGCAAUCUGCUGCUGCACCUUCAGCAGCAGCAAAGAACCGCUCUCGAUCAGCAGGAUCUGACGCACAAAACUGCAAGGG_AA
((((((.((.....(((((....)))))............(((((((((.......)))))))))..))...(((.......))).....))))))................... (-21.22 = -22.03 +   0.81)

alignment

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secondary structure

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Window 2

Location 7,949,620 – 7,949,735
Length 115
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 76.77
Mean single sequence MFE -41.90
Consensus MFE -25.68
Energy contribution -25.88
Covariance contribution 0.20
Combinations/Pair 1.33
Mean z-score -2.22
Structure conservation index 0.61
SVM decision value 1.60
SVM RNA-class probability 0.966924
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7949620 115 - 20766785
UUCCAUUUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAGUGCAAUUCAGUGCUGCUCAUGAAAGUGCAGCAGCAGAUUGCCCUGAUGCAUCACUCGCUGCGCUACGAACUAACG
........(((((...((((((.....))))))....(((((....((((((((((((((....))).))))))).......)))).....)))))))))).............. ( -38.71)
>DroVir_CAF1 1311 114 - 1
CU-CCCCCGCAGCUUUGUGCGGCAAAUCCUGCUCAUCGAGAGCGGUUCGAUGUUGUUGCAGAAGGUGCAGCAGCAGAUCGCGUUGAUGCAUCAUUCGAUGCGUUACGAGCUGACG
..-....((((((((...(((((.....((((((.....)))))).....((((((((((.....))))))))))).))))((.((((((((....)))))))))))))))).)) ( -45.40)
>DroPse_CAF1 1285 115 - 1
UUUCUCUCUCAGUUUCAGCCGCCAGAUACUGCUGGUCCAGAGCGAUUCUUUGCUGCUGCUGAAGGUGCAGCAACAGAUUGCCCUUAUGCACCACUCGAUGCGGUGUGAGCUGACA
..............(((((((((((......)))))..((.((((((..(((((((.((.....)))))))))..)))))).))...(((((.(.....).)))))).))))).. ( -38.00)
>DroGri_CAF1 1342 109 - 1
------UUGCAGUUUUGUGCGUCAGAUUCUACUGAUUGAGAGCGGCUCGUUGCUGCUGCUGAAGGUGCAGCAGCAGAUUGCGUUGAUGCAUCAUUCGAUGCGUUACGAGCUGACG
------..(((......)))(((((......))))).....((((((((((((((((((.......)))))))))).......(((((((((....)))))))))))))))).). ( -45.50)
>DroMoj_CAF1 1830 114 - 1
UU-CCCCUGCAGCUUCGUGCGUCAAAUCCUGCUUAUUGAGAGCGGCUCCUUGUUGCUGCUGAAGGUGCAGCAGCAGUUGGCAUUGAUGCACCACUCGCUGCGCUACGAGCUGACG
..-.....(((((...(((((((((....(((((.....)))))(((..((((((((((.......))))))))))..))).))))))))).....)))))((.....))..... ( -45.80)
>DroPer_CAF1 1285 115 - 1
UUUCCCUCUCAGUUUCAGCCGCCAGAUACUGCUGGUCCAGAGCGAUUCUUUGCUGCUGCUGAAGGUGCAGCAACAGAUUGCCCUUAUGCACCACUCGAUGCGGUGUGAGCUGACA
..............(((((((((((......)))))..((.((((((..(((((((.((.....)))))))))..)))))).))...(((((.(.....).)))))).))))).. ( -38.00)
>consensus
UU_CCCUCGCAGUUUCAGCCGCCAAAUCCUGCUGAUCGAGAGCGAUUCGUUGCUGCUGCUGAAGGUGCAGCAGCAGAUUGCCCUGAUGCACCACUCGAUGCGCUACGAGCUGACG
.........((((((...((.....................((((((...(((((((((.......)))))))))))))))......(((.(....).)))))...))))))... (-25.68 = -25.88 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,949,660 – 7,949,750
Length 90
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 77.58
Mean single sequence MFE -28.37
Consensus MFE -15.35
Energy contribution -16.35
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.54
SVM decision value 1.03
SVM RNA-class probability 0.902733
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7949660 90 + 20766785
UGCUGCUGCACUUUCAUGAGCAGCACUGAAUUGCACUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAAAUGGAAAAUGAG--UAUAUGUAG-----------
(((((((.((......)))))))))(((...((.(((((...((((((.....))))))....((......))....))))--).))..)))----------- ( -23.90)
>DroSec_CAF1 1409 101 + 1
UGCUGCUGCACUUUCAUGAGCAGCACUGAAUUGCCUUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAAAUGGAAUAGGAG--UAUAUGUAGUUUGUUAUUGU
(((((((.((......)))))))))............(((((((((((.....)))))).((((((((.(((.........--))).))))))))..))))). ( -28.00)
>DroSim_CAF1 1412 101 + 1
UGCUGCUGCACUUUCAUGAGCAGCACUGAAUUGCCUUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAAAUGGAAAAGGAG--UAUAUGUAGUUUGUUAUUGU
(((((((.((......)))))))))............(((((((((((.....)))))).((((((((.(((.........--))).))))))))..))))). ( -28.00)
>DroEre_CAF1 1434 97 + 1
UGCUGCUGCACUUUCAUAAGCAGCACUGAAUUGCACUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAUAAGGAAAAGUGG--U----GUAGUUAGUUAUUGU
.((((((...........))))))(((((.(((((((.....((((((.....))))))....((.....)).......))--)----)))))))))...... ( -28.30)
>DroYak_CAF1 1398 97 + 1
UGCUGCUGCAUUUUCAUGAGCAGCACUGAACUGCACUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAAAAGGAAAAUGGG--U----GCAGUUAGUUAUUAU
.((((((.(((....)))))))))(((((.(((((((((...((((((.....))))))....((.....)).....))))--)----)))))))))...... ( -37.80)
>DroMoj_CAF1 1870 91 + 1
UGCUGCUGCACCUUCAGCAGCAACAAGGAGCCGCUCUCAAUAAGCAGGAUUUGACGCACGAAGCUGCAGGGG-AAGAGGAGAUUAAA-G----------ACAG
((((((((......))))))))........((.(((((.....((((..((((.....)))).))))..)))-.)).))........-.----------.... ( -24.20)
>consensus
UGCUGCUGCACUUUCAUGAGCAGCACUGAAUUGCACUCGAUAAGCAGGAUUUGCCUGCUAAAACUGCAAAUGGAAAAGGAG__UAUA_GUAGUU_GUUAUUGU
(((((((((..........)))))).................((((((.....))))))......)))................................... (-15.35 = -16.35 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,949,660 – 7,949,750
Length 90
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 77.58
Mean single sequence MFE -27.67
Consensus MFE -20.33
Energy contribution -20.56
Covariance contribution 0.23
Combinations/Pair 1.35
Mean z-score -3.22
Structure conservation index 0.73
SVM decision value 2.02
SVM RNA-class probability 0.985802
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7949660 90 - 20766785
-----------CUACAUAUA--CUCAUUUUCCAUUUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAGUGCAAUUCAGUGCUGCUCAUGAAAGUGCAGCAGCA
-----------.........--............(((((.((..((((((.....))))))....)).))))).....((((((((((....))).))))))) ( -28.90)
>DroSec_CAF1 1409 101 - 1
ACAAUAACAAACUACAUAUA--CUCCUAUUCCAUUUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAAGGCAAUUCAGUGCUGCUCAUGAAAGUGCAGCAGCA
....................--............((((..((..((((((.....))))))....))..)))).....((((((((((....))).))))))) ( -26.60)
>DroSim_CAF1 1412 101 - 1
ACAAUAACAAACUACAUAUA--CUCCUUUUCCAUUUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAAGGCAAUUCAGUGCUGCUCAUGAAAGUGCAGCAGCA
....................--............((((..((..((((((.....))))))....))..)))).....((((((((((....))).))))))) ( -26.60)
>DroEre_CAF1 1434 97 - 1
ACAAUAACUAACUAC----A--CCACUUUUCCUUAUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAGUGCAAUUCAGUGCUGCUUAUGAAAGUGCAGCAGCA
...............----.--.............((((.((..((((((.....))))))....)).))))......((((((((((....))).))))))) ( -26.10)
>DroYak_CAF1 1398 97 - 1
AUAAUAACUAACUGC----A--CCCAUUUUCCUUUUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAGUGCAGUUCAGUGCUGCUCAUGAAAAUGCAGCAGCA
......(((((((((----(--(.(......((.....))....((((((.....))))))....).)))))))).)))(((((((((....))).)))))). ( -33.50)
>DroMoj_CAF1 1870 91 - 1
CUGU----------C-UUUAAUCUCCUCUU-CCCCUGCAGCUUCGUGCGUCAAAUCCUGCUUAUUGAGAGCGGCUCCUUGUUGCUGCUGAAGGUGCAGCAGCA
....----------.-..............-...(((((.(((((.(((.(((...((((((.....)))))).......))).)))))))).)))))..... ( -24.30)
>consensus
ACAAUAAC_AACUAC_UAUA__CUCCUUUUCCAUUUGCAGUUUUAGCAGGCAAAUCCUGCUUAUCGAGUGCAAUUCAGUGCUGCUCAUGAAAGUGCAGCAGCA
..................................((((......((((((.....))))))........)))).....((((((((((....))).))))))) (-20.33 = -20.56 +   0.23)

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 10:22:00 2006