Locus 1253

Sequence ID 3R_DroMel_CAF1
Location 3,761,253 – 3,761,422
Length 169
Max. P 0.936246
window2038 window2039 window2040 window2041

overview

Window 8

Location 3,761,253 – 3,761,355
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.30
Mean single sequence MFE -28.91
Consensus MFE -24.39
Energy contribution -24.59
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.84
SVM decision value 1.25
SVM RNA-class probability 0.936246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3761253 102 - 27905053
UACUCCCGUCAACAUAAUUUGAAUAUCUAUGACGGGGGUGAGCUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUUC-AUUAACU-----AGAGUAACGAAUA------------C
(((((((((((..................))))))))))).((((((........))))))...((.(((((.......))-))).)).-----.............------------. ( -29.87)
>DroPse_CAF1 16019 102 - 1
UACUCCCGUCAGCAUAAUUUGAAUAUCUAUGACGGGGGUGAGCUACGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUUC-AUUAAUU-----GAAGUAACGAAUA------------U
(((((((((((..(((.......)))...))))))))))).(((.(((........))).((((...(((((.......))-))).)))-----).)))........------------. ( -27.10)
>DroGri_CAF1 17913 102 - 1
UACUCCCGUCAACACAAUUUGAAUAUCUAUGACGGGGGUGAGUUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUUAUACUAAUU-----AAAUUGCC-AACA------------A
(((((((((((..................))))))))))).((((((........)))((((((.(((((((......)))).)))...-----..))))))-))).------------. ( -30.27)
>DroEre_CAF1 14603 102 - 1
UACUCCCGUCAGCAUAAUUUGAAUAUCUAUGACGGGGGUGAGCUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUUC-AUUAACU-----AGAGUAACAUGUA------------C
(((((((((((..(((.......)))...))))))))))).((((((........))))))...((.(((((.......))-))).)).-----.............------------. ( -30.90)
>DroMoj_CAF1 16303 100 - 1
UACUCCCGUCAAAACAAUUUAAAUAUUUAUGACGGGGGUGAGCUACGUAACACAACGCGGCAAUGUGGAUGAUAAUUGUUCUAUUAAUC-----AAUUUG---AAUA------------U
(((((((((((..................))))))))))).((..(((......)))..))....(((.(((((.......))))).))-----).....---....------------. ( -24.27)
>DroAna_CAF1 13738 119 - 1
UACUCCCGUCAGCACAAUUUGAAUAUCUAUGACGGGGGUGAGCUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUUC-AUGAACUAAACUAAAGUAACGAUAAUUGCGAUAAUCCU
(((((((((((..................))))))))))).((((((........)))))).....((((((.......))-...............((((......))))....)))). ( -31.07)
>consensus
UACUCCCGUCAACACAAUUUGAAUAUCUAUGACGGGGGUGAGCUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUUC_AUUAACU_____AAAGUAACGAAUA____________U
(((((((((((..................))))))))))).((((((........))))))........................................................... (-24.39 = -24.59 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,761,275 – 3,761,394
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.09
Mean single sequence MFE -33.59
Consensus MFE -26.41
Energy contribution -26.05
Covariance contribution -0.36
Combinations/Pair 1.08
Mean z-score -2.26
Structure conservation index 0.79
SVM decision value 0.09
SVM RNA-class probability 0.579603
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3761275 119 - 27905053
UCGAUCUGAUCUA-AACCAGGCCAAUACGUUGUGAAUGAGUACUCCCGUCAACAUAAUUUGAAUAUCUAUGACGGGGGUGAGCUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUU
...(((..(((((-......(((....(((((((......(((((((((((..................))))))))))).((...))..))))))).)))....))))))))....... ( -33.47)
>DroVir_CAF1 16389 120 - 1
UCGAUCUGAUCAAUCAUUAGGCCAGUAUGUUGUCAAUGAAUACUCCCGUCAAAACAAUUUAAAUAUCUAUGACGGGGGUGAGCUACGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUU
........((((.((((...(((.((.((((((....(..(((((((((((..................)))))))))))..)...))))))..))..)))...)))).))))....... ( -35.37)
>DroGri_CAF1 17935 120 - 1
UUGAUUUGAUCAAUUACCAGGCCAAUAUGUUGUGAAUGAAUACUCCCGUCAACACAAUUUGAAUAUCUAUGACGGGGGUGAGUUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUU
........((((.((((...(((....((((((((((...(((((((((((..................))))))))))).))).)))))))......)))...)))).))))....... ( -34.57)
>DroWil_CAF1 19480 108 - 1
UCGAU------------CAGGCCAAUAUGUUGUAAAUGAAUACUCCCGUCAACAUAAUUUGAAUAUGUAUGACGGGGGUGAGCUACGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUU
...((------------((..(((....(((((.......((((((((((((((((.......))))).))))))))))).....(((........)))))))).))).))))....... ( -34.50)
>DroMoj_CAF1 16323 113 - 1
UCGAUCUGG-------AUAGGCCAAUAUGUUGUCAAUGAAUACUCCCGUCAAAACAAUUUAAAUAUUUAUGACGGGGGUGAGCUACGUAACACAACGCGGCAAUGUGGAUGAUAAUUGUU
......(((-------.....)))...(((..((......(((((((((((..................))))))))))).((..(((......)))..))......))..)))...... ( -29.37)
>DroAna_CAF1 13777 119 - 1
UCGAUCUGAUUCA-AACCAGGCCAAUACGUUGUGAAUGAAUACUCCCGUCAGCACAAUUUGAAUAUCUAUGACGGGGGUGAGCUGCGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUU
..(..(((.....-...)))..)..((((((.........(((((((((((..................))))))))))).((((((........))))))))))))............. ( -34.27)
>consensus
UCGAUCUGAUC_A__ACCAGGCCAAUAUGUUGUGAAUGAAUACUCCCGUCAACACAAUUUGAAUAUCUAUGACGGGGGUGAGCUACGCAACACAACGCGGCAAUGUGGAUGAUAAUUUUU
......................((.((((((((.......(((((((((((..................))))))))))).....(((........)))))))))))..))......... (-26.41 = -26.05 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,761,315 – 3,761,422
Length 107
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.59
Mean single sequence MFE -25.50
Consensus MFE -18.07
Energy contribution -17.78
Covariance contribution -0.29
Combinations/Pair 1.15
Mean z-score -1.54
Structure conservation index 0.71
SVM decision value 0.75
SVM RNA-class probability 0.841986
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3761315 107 + 27905053
CACCCCCGUCAUAGAUAUUCAAAUUAUGUUGACGGGAGUACUCAUUCACAACGUAUUGGCCUGGUU-UAGAUCAGAUCGAGAGACAUUCG----GCAUUUUAUUAUACAAUU
.((.(((((((.(.(((.......))).)))))))).)).............((.(((..(((((.-...)))))..)))...)).....----.................. ( -21.80)
>DroPse_CAF1 16081 105 + 1
CACCCCCGUCAUAGAUAUUCAAAUUAUGCUGACGGGAGUACUCAUUCACAACGUACUGGCCUGGUU-UGGAUCAGAUCGGAAGAUAUUGG----GAG-UUUAUUAUACGU-U
.((.(((((((...(((.......)))..))))))).))..........((((((((((((.....-.)).))))(((....))).....----...-.......)))))-) ( -26.10)
>DroGri_CAF1 17975 110 + 1
CACCCCCGUCAUAGAUAUUCAAAUUGUGUUGACGGGAGUAUUCAUUCACAACAUAUUGGCCUGGUAAUUGAUCAAAUCAAAACAUAUAUUUAUGGGUAUAUAUAGCA--AAC
....(((((((.(.(((.......))).)))))))).((((((((..........((((..((((.....))))..))))...........))))))))........--... ( -19.60)
>DroMoj_CAF1 16363 100 + 1
CACCCCCGUCAUAAAUAUUUAAAUUGUUUUGACGGGAGUAUUCAUUGACAACAUAUUGGCCUAU-------CCAGAUCGAAAGAUAUGUA---GGUAAUAUGUUAUA--GUU
.((.(((((((.(((((.......)))))))))))).))..........(((((((((.(((((-------....(((....)))..)))---)))))))))))...--... ( -32.30)
>DroAna_CAF1 13817 104 + 1
CACCCCCGUCAUAGAUAUUCAAAUUGUGCUGACGGGAGUAUUCAUUCACAACGUAUUGGCCUGGUU-UGAAUCAGAUCGAAAGACAUUCG----CCAUUUAAU---ACGAGU
.((.(((((((..(((......)))....))))))).))............((((((((((((((.-...))))).((....)).....)----)))....))---)))... ( -27.10)
>DroPer_CAF1 16529 105 + 1
CACCCCCGUCAUAGAUAUUCAAAUUAUGCUGACGGGAGUACUCAUUCACAACGUACUGGCCUGGUU-UGGAUCAGAUCGGAAGAUAUUGG----GAA-UUUAUUAUACGU-U
.((.(((((((...(((.......)))..))))))).))..........((((((((((((.....-.)).))))(((....))).....----...-.......)))))-) ( -26.10)
>consensus
CACCCCCGUCAUAGAUAUUCAAAUUAUGCUGACGGGAGUACUCAUUCACAACGUAUUGGCCUGGUU_UGGAUCAGAUCGAAAGAUAUUCG____GAA_UUUAUUAUACGA_U
.((.(((((((...(((.......)))..))))))).))................(((..(((((.....)))))..)))................................ (-18.07 = -17.78 +  -0.29)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,761,315 – 3,761,422
Length 107
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -24.48
Consensus MFE -18.08
Energy contribution -17.80
Covariance contribution -0.28
Combinations/Pair 1.13
Mean z-score -1.33
Structure conservation index 0.74
SVM decision value 0.57
SVM RNA-class probability 0.784525
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3761315 107 - 27905053
AAUUGUAUAAUAAAAUGC----CGAAUGUCUCUCGAUCUGAUCUA-AACCAGGCCAAUACGUUGUGAAUGAGUACUCCCGUCAACAUAAUUUGAAUAUCUAUGACGGGGGUG
....((((..........----.((.......))(..(((.....-...)))..).))))............(((((((((((..................))))))))))) ( -20.27)
>DroPse_CAF1 16081 105 - 1
A-ACGUAUAAUAAA-CUC----CCAAUAUCUUCCGAUCUGAUCCA-AACCAGGCCAGUACGUUGUGAAUGAGUACUCCCGUCAGCAUAAUUUGAAUAUCUAUGACGGGGGUG
(-((((((......-...----.....(((....)))(((.....-...)))....))))))).........(((((((((((..(((.......)))...))))))))))) ( -23.50)
>DroGri_CAF1 17975 110 - 1
GUU--UGCUAUAUAUACCCAUAAAUAUAUGUUUUGAUUUGAUCAAUUACCAGGCCAAUAUGUUGUGAAUGAAUACUCCCGUCAACACAAUUUGAAUAUCUAUGACGGGGGUG
(((--..(.((((((.((((((....))))..(((((...)))))......))...)))))).)..)))...(((((((((((..................))))))))))) ( -23.67)
>DroMoj_CAF1 16363 100 - 1
AAC--UAUAACAUAUUACC---UACAUAUCUUUCGAUCUGG-------AUAGGCCAAUAUGUUGUCAAUGAAUACUCCCGUCAAAACAAUUUAAAUAUUUAUGACGGGGGUG
...--.((((((((((.((---((((.(((....))).)).-------.))))..)))))))))).......(((((((((((..................))))))))))) ( -27.87)
>DroAna_CAF1 13817 104 - 1
ACUCGU---AUUAAAUGG----CGAAUGUCUUUCGAUCUGAUUCA-AACCAGGCCAAUACGUUGUGAAUGAAUACUCCCGUCAGCACAAUUUGAAUAUCUAUGACGGGGGUG
((.(((---((....(((----((((.....)))...(((.....-...))))))))))))..)).......(((((((((((..................))))))))))) ( -28.07)
>DroPer_CAF1 16529 105 - 1
A-ACGUAUAAUAAA-UUC----CCAAUAUCUUCCGAUCUGAUCCA-AACCAGGCCAGUACGUUGUGAAUGAGUACUCCCGUCAGCAUAAUUUGAAUAUCUAUGACGGGGGUG
(-((((((......-...----.....(((....)))(((.....-...)))....))))))).........(((((((((((..(((.......)))...))))))))))) ( -23.50)
>consensus
A_UCGUAUAAUAAA_UGC____CAAAUAUCUUUCGAUCUGAUCCA_AACCAGGCCAAUACGUUGUGAAUGAAUACUCCCGUCAACACAAUUUGAAUAUCUAUGACGGGGGUG
..................................(..(((.........)))..).................(((((((((((..................))))))))))) (-18.08 = -17.80 +  -0.28)

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 10:04:42 2006