Locus 1507

Sequence ID 3R_DroMel_CAF1
Location 4,320,045 – 4,320,361
Length 316
Max. P 0.964578
window2505 window2506 window2507 window2508 window2509 window2510

overview

Window 5

Location 4,320,045 – 4,320,163
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.21
Mean single sequence MFE -21.93
Consensus MFE -21.35
Energy contribution -21.47
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.91
Structure conservation index 0.97
SVM decision value 0.79
SVM RNA-class probability 0.851958
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4320045 118 + 27905053
UAUAAAAUAUUCAAUGGUCGGUAUAUUUUUUGCUCGGCUUGAUUUUAAUUCCAAAUUCAUUUCGUCUAUAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGCGCCCAAAACACACAA--C
..((((((.......((((((((.......))).)))))..)))))).......................(((((((((.....)))))))))...(((((.(.......).)))))--. ( -18.70)
>DroSec_CAF1 7412 118 + 1
UAUAAAAUAUUCAAUGGUCGGUAUAUUUUUUGCUCGGCUUGAUUUUAAUUCCAAAUUCAUUUCGUCUAUAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGUGCCCAAAACACACAA--C
..((((((.......((((((((.......))).)))))..)))))).......................(((((((((.....)))))))))...(((((((.......)))))))--. ( -22.60)
>DroEre_CAF1 7418 120 + 1
UAUAAAAUAUUCAAUGGUCGGUAUAUUUUUUGCUCGGCCUGAUUUUAAUUCCAAAUUCAUUUCGUCUACAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGUGCCCAAAACACACAACAC
..((((((.......((((((((.......))).)))))..)))))).......................(((((((((.....)))))))))...(((((((.......)))))))... ( -24.50)
>consensus
UAUAAAAUAUUCAAUGGUCGGUAUAUUUUUUGCUCGGCUUGAUUUUAAUUCCAAAUUCAUUUCGUCUAUAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGUGCCCAAAACACACAA__C
..((((((.......((((((((.......))).)))))..)))))).......................(((((((((.....)))))))))...(((((((.......)))))))... (-21.35 = -21.47 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,320,085 – 4,320,203
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.21
Mean single sequence MFE -23.80
Consensus MFE -23.00
Energy contribution -23.33
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.97
SVM decision value 1.57
SVM RNA-class probability 0.964578
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4320085 118 + 27905053
GAUUUUAAUUCCAAAUUCAUUUCGUCUAUAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGCGCCCAAAACACACAA--CAGCCAGACGGCAAAGCUGCAAAACCAAUGGCAAAUACCGA
..........(((.........(((((...(((((((((.....)))))))))...(((((.(.......).)))))--.....)))))(((....)))........))).......... ( -21.20)
>DroSec_CAF1 7452 118 + 1
GAUUUUAAUUCCAAAUUCAUUUCGUCUAUAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGUGCCCAAAACACACAA--CAGCCAGACGGCAAAGCUGCAAAACCAAUGGCAAAUACCAA
..........(((.........(((((...(((((((((.....)))))))))...(((((((.......)))))))--.....)))))(((....)))........))).......... ( -25.10)
>DroEre_CAF1 7458 120 + 1
GAUUUUAAUUCCAAAUUCAUUUCGUCUACAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGUGCCCAAAACACACAACACAGCCAGACGGCAAAGCUGCAAAACCAAUGGCAAAUACCGA
..........(((.........(((((...(((((((((.....)))))))))...(((((((.......))))))).......)))))(((....)))........))).......... ( -25.10)
>consensus
GAUUUUAAUUCCAAAUUCAUUUCGUCUAUAAAUGCAAUUUUCUAAAUUGCAUUGAUUUGUGUGCCCAAAACACACAA__CAGCCAGACGGCAAAGCUGCAAAACCAAUGGCAAAUACCGA
..........(((.........(((((...(((((((((.....)))))))))...(((((((.......))))))).......)))))(((....)))........))).......... (-23.00 = -23.33 +   0.33)

alignment

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secondary structure

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Window 7

Location 4,320,085 – 4,320,203
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.21
Mean single sequence MFE -30.37
Consensus MFE -30.22
Energy contribution -30.00
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.60
Structure conservation index 1.00
SVM decision value 0.43
SVM RNA-class probability 0.732774
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4320085 118 - 27905053
UCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUG--UUGUGUGUUUUGGGCGCACAAAUCAAUGCAAUUUAGAAAAUUGCAUUUAUAGACGAAAUGAAUUUGGAAUUAAAAUC
..(((....))).((((((((((......))((((((....--((((((((.....))))))))...(((((((((.....)))))))))..))))))..........)))))))).... ( -30.00)
>DroSec_CAF1 7452 118 - 1
UUGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUG--UUGUGUGUUUUGGGCACACAAAUCAAUGCAAUUUAGAAAAUUGCAUUUAUAGACGAAAUGAAUUUGGAAUUAAAAUC
.((((....))))((((((((((......))((((((....--((((((((.....))))))))...(((((((((.....)))))))))..))))))..........)))))))).... ( -30.80)
>DroEre_CAF1 7458 120 - 1
UCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUGUGUUGUGUGUUUUGGGCACACAAAUCAAUGCAAUUUAGAAAAUUGCAUUUGUAGACGAAAUGAAUUUGGAAUUAAAAUC
..(((....))).((((((((((......))((((((......((((((((.....))))))))...(((((((((.....)))))))))..))))))..........)))))))).... ( -30.30)
>consensus
UCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUG__UUGUGUGUUUUGGGCACACAAAUCAAUGCAAUUUAGAAAAUUGCAUUUAUAGACGAAAUGAAUUUGGAAUUAAAAUC
..(((....))).((((((((((......))((((((......((((((((.....))))))))...(((((((((.....)))))))))..))))))..........)))))))).... (-30.22 = -30.00 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,320,125 – 4,320,243
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.21
Mean single sequence MFE -33.27
Consensus MFE -31.51
Energy contribution -31.07
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.81
Structure conservation index 0.95
SVM decision value 0.42
SVM RNA-class probability 0.731152
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4320125 118 - 27905053
GCGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUG--UUGUGUGUUUUGGGCGCACAAAUCAAUGCAAUUUAGA
..((((...(((((..((((((..(.....)..)))))))))))...))))(((((((((.((((((.........)))))--).((((((.....)))))))))))))))......... ( -33.40)
>DroSec_CAF1 7492 118 - 1
GCGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUUGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUG--UUGUGUGUUUUGGGCACACAAAUCAAUGCAAUUUAGA
..(((..............(((((((....((((((((...((((....)))))))))))).......)))))))(((...--((((((((.....)))))))).))).)))........ ( -32.00)
>DroEre_CAF1 7498 120 - 1
ACGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUGUGUUGUGUGUUUUGGGCACACAAAUCAAUGCAAUUUAGA
..((((...(((((..((((((..(.....)..)))))))))))...))))(((((((((.((((((.........))))))...((((((.....)))))))))))))))......... ( -34.40)
>consensus
GCGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCUG__UUGUGUGUUUUGGGCACACAAAUCAAUGCAAUUUAGA
..((((...(((((..((((((..(.....)..)))))))))))...))))(((((((((..(((((.........)))))....((((((.....)))))))))))))))......... (-31.51 = -31.07 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,320,163 – 4,320,283
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -27.07
Consensus MFE -26.35
Energy contribution -26.80
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.97
SVM decision value 0.37
SVM RNA-class probability 0.709014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4320163 120 - 27905053
GGAAUUCCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAUGCGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCU
((((((........)))))).........(((..(..((((.((((...(((((..((((((..(.....)..)))))))))))...))))))))..)..)))......(((....))). ( -28.70)
>DroSec_CAF1 7530 120 - 1
GGAAUUUCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAUGCGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUUGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCU
(((((((......))))))).........(((..(..((((.((((...(((((..((((((..(.....)..)))))))))))...))))))))..)..)))......(((....))). ( -27.50)
>DroEre_CAF1 7538 120 - 1
GGAAUUUCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAUACGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCU
(((((((......))))))).........(((..(..(((..((((...(((((..((((((..(.....)..)))))))))))...)))).)))..)..)))......(((....))). ( -25.00)
>consensus
GGAAUUUCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAUGCGCAAUUUUCGAAUUAUUGAUGGCACACAGAAAUCAAUUUCGGUAUUUGCCAUUGGUUUUGCAGCUUUGCCGUCUGGCU
(((((((......))))))).........(((..(..((((.((((...(((((..((((((..(.....)..)))))))))))...))))))))..)..)))......(((....))). (-26.35 = -26.80 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,320,243 – 4,320,361
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.02
Mean single sequence MFE -28.17
Consensus MFE -23.89
Energy contribution -24.33
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.85
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4320243 118 - 27905053
UUUAUGCCUAAUCUCCGAUUCCC--CGGGGCUGUUUGCACUGCCCAUUUUAGCGGCAGAAAAUUUAAUAGGCCCGCCGAUGGAAUUCCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAU
...((((.((((.......((..--((((.(((((....((((((......).))))).......))))).))))..)).((((((........)))))).....))))))))....... ( -27.60)
>DroSec_CAF1 7610 120 - 1
UUUAUGCCUACUCUCCGAUCGCCCGCGGGGAUGUUUGCACUGCCCAUUUCAGCGGCAGAAAAUUUAAUAGGCCCGUCGAUGGAAUUUCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAU
.....(((((.((((((........))))))........((((((......).))))).........)))))..((..(((((((((......))))))).....))..))......... ( -28.00)
>DroEre_CAF1 7618 117 - 1
UUUAUGCCUAAUCUCCGAUC-CC--CGGGGCUGUUUGCACUGCCCAUUUCAGCGGCACAGAAUUUAAUAGGCCCGCUGAUGGAAUUUCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAU
.....(((((..(((((...-..--)))))...((((..((((........))))..))))......)))))..(((((((((((((......))))))).....))))))......... ( -28.90)
>consensus
UUUAUGCCUAAUCUCCGAUC_CC__CGGGGCUGUUUGCACUGCCCAUUUCAGCGGCAGAAAAUUUAAUAGGCCCGCCGAUGGAAUUUCAAAUUAAAUUCCCUUAAAUUAGCAUUAAAAAU
.....(((((..(((((........))))).........((((((......).))))).........)))))..((.((((((((((......))))))).....))).))......... (-23.89 = -24.33 +   0.45)

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 10:12:25 2006