Locus 1531

Sequence ID 3L_DroMel_CAF1
Location 4,424,850 – 4,424,984
Length 134
Max. P 0.886888
window2381 window2382 window2383

overview

Window 1

Location 4,424,850 – 4,424,950
Length 100
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 82.27
Mean single sequence MFE -21.90
Consensus MFE -12.96
Energy contribution -13.68
Covariance contribution 0.73
Combinations/Pair 1.24
Mean z-score -2.20
Structure conservation index 0.59
SVM decision value 0.14
SVM RNA-class probability 0.602102
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4424850 100 + 23771897
CAUCAUCAUCCACGCCAUGUGCCGCAUGGAAAUAAUC-AUUCGAAGCCGAAAA-A---AAGAACCGCA-AAACGGGUUCUUCUAAUAGCCAUUAAGCUAUCGUCUC
..............(((((.....)))))........-.((((....))))..-.---(((((((...-.....)))))))...(((((......)))))...... ( -19.80)
>DroPse_CAF1 8375 104 + 1
CAAGAUAAUCAUCGUCAU-UAUCGUUUUGCCAAAAUCCAAAUAAAACCAACAAAAAAAAAAAACCAAAUAAACAGGUUCCCUUAAUGGCCAUUAGGC-AGAGAUUC
...((((((.......))-)))).(((((((..............................((((.........)))).((.....))......)))-)))).... ( -13.80)
>DroSec_CAF1 6837 101 + 1
CAUCAUCAUCCACGCCAUGUGCCGCAUGGAGAUAAUC-AUUCGAAACCGAAAAAA---AAGAACCCCA-AAACGGGUUCUUCUAAUAGCCAUUAAGCUAUCGUCUC
..............(((((.....)))))((((....-.((((....))))....---((((((((..-....))))))))...(((((......))))).)))). ( -24.00)
>DroSim_CAF1 4209 101 + 1
CAUCAUCAUCCACGCCAUGUGCCGCAUGGAGAUAAUC-AUUCGAAACCGAAAAAA---AAGAACCCCA-AAACGGGUUCUUCUAAUAGCCAUUAAGCUAUCGUCUC
..............(((((.....)))))((((....-.((((....))))....---((((((((..-....))))))))...(((((......))))).)))). ( -24.00)
>DroEre_CAF1 6954 100 + 1
CAUCAUUAUCCACGUCAUGUGCCGCAUGGAGGUAAUC-AUGCGAAGCCGAAAAA----AAGAACACCA-AAACGGGUUCUUCUAAUGGCCAUUAAGCCAUCGUCUC
...........(((..(((.(((((((((......))-)))))..((((.....----((((((.((.-....))))))))....))))......))))))))... ( -24.10)
>DroYak_CAF1 7909 101 + 1
CAUCAUCAUCCACGCCAUGUGCCGCCUGGAGAUAAUC-AUACGAAGCUGAAAAAU---AAGAACCCCA-AAACGGGUUCUUCUAAUGGCCAUUAAGCCAUCGUCUC
....(((.((((.((........)).)))))))....-..((((...........---((((((((..-....))))))))....((((......))))))))... ( -25.70)
>consensus
CAUCAUCAUCCACGCCAUGUGCCGCAUGGAGAUAAUC_AUUCGAAACCGAAAAAA___AAGAACCCCA_AAACGGGUUCUUCUAAUAGCCAUUAAGCUAUCGUCUC
........((((.((........)).))))...........(((..............((((((((.......))))))))....((((......))))))).... (-12.96 = -13.68 +   0.73)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,424,850 – 4,424,950
Length 100
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 82.27
Mean single sequence MFE -33.17
Consensus MFE -22.96
Energy contribution -24.22
Covariance contribution 1.26
Combinations/Pair 1.31
Mean z-score -2.86
Structure conservation index 0.69
SVM decision value 0.94
SVM RNA-class probability 0.886888
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4424850 100 - 23771897
GAGACGAUAGCUUAAUGGCUAUUAGAAGAACCCGUUU-UGCGGUUCUU---U-UUUUCGGCUUCGAAU-GAUUAUUUCCAUGCGGCACAUGGCGUGGAUGAUGAUG
((((.(((((((....)))))))(((((((((.....-...)))))))---)-)))))..........-.(((((((((((((........))))))).)))))). ( -30.60)
>DroPse_CAF1 8375 104 - 1
GAAUCUCU-GCCUAAUGGCCAUUAAGGGAACCUGUUUAUUUGGUUUUUUUUUUUUGUUGGUUUUAUUUGGAUUUUGGCAAAACGAUA-AUGACGAUGAUUAUCUUG
.((((((.-(((....)))(((((((((((((.........))))))))..((((((..(..((.....))..)..))))))...))-)))..)).))))...... ( -20.20)
>DroSec_CAF1 6837 101 - 1
GAGACGAUAGCUUAAUGGCUAUUAGAAGAACCCGUUU-UGGGGUUCUU---UUUUUUCGGUUUCGAAU-GAUUAUCUCCAUGCGGCACAUGGCGUGGAUGAUGAUG
((((((((((((....)))))))((((((((((....-..))))))))---))......)))))....-.(((((((((((((........))))))).)))))). ( -41.10)
>DroSim_CAF1 4209 101 - 1
GAGACGAUAGCUUAAUGGCUAUUAGAAGAACCCGUUU-UGGGGUUCUU---UUUUUUCGGUUUCGAAU-GAUUAUCUCCAUGCGGCACAUGGCGUGGAUGAUGAUG
((((((((((((....)))))))((((((((((....-..))))))))---))......)))))....-.(((((((((((((........))))))).)))))). ( -41.10)
>DroEre_CAF1 6954 100 - 1
GAGACGAUGGCUUAAUGGCCAUUAGAAGAACCCGUUU-UGGUGUUCUU----UUUUUCGGCUUCGCAU-GAUUACCUCCAUGCGGCACAUGACGUGGAUAAUGAUG
((((.(((((((....)))))))((((((((((....-.)).))))))----))))))....((((((-(........)))))))(((.....))).......... ( -29.50)
>DroYak_CAF1 7909 101 - 1
GAGACGAUGGCUUAAUGGCCAUUAGAAGAACCCGUUU-UGGGGUUCUU---AUUUUUCAGCUUCGUAU-GAUUAUCUCCAGGCGGCACAUGGCGUGGAUGAUGAUG
((((.(((((((....)))))))..((((((((....-..))))))))---...))))..........-.((((((((((.((........)).)))).)))))). ( -36.50)
>consensus
GAGACGAUAGCUUAAUGGCCAUUAGAAGAACCCGUUU_UGGGGUUCUU___UUUUUUCGGCUUCGAAU_GAUUAUCUCCAUGCGGCACAUGGCGUGGAUGAUGAUG
(((.((((((((....)))))))..((((((((.......))))))))...........).)))......(((((((((((((........))))))).)))))). (-22.96 = -24.22 +   1.26)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,424,889 – 4,424,984
Length 95
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 81.85
Mean single sequence MFE -28.63
Consensus MFE -16.91
Energy contribution -19.05
Covariance contribution 2.14
Combinations/Pair 1.26
Mean z-score -2.96
Structure conservation index 0.59
SVM decision value 0.88
SVM RNA-class probability 0.872227
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4424889 95 - 23771897
GCAAAUGCUGAUUAUUAUGAUCGUAUUUGAGAGUGAGACGAUAGCUUAAUGGCUAUUAGAAGAACCCGUUUUGCGGUUCUUU-UUUUCGGCUUCGA
.(((((((.((((.....))))))))))).((((((((.(((((((....)))))))(((((((((........))))))))-))))).))))... ( -27.20)
>DroSec_CAF1 6876 96 - 1
GCAAAUUCUGAUUAUUAUGGUCGCAUUUGAGAGUGAGACGAUAGCUUAAUGGCUAUUAGAAGAACCCGUUUUGGGGUUCUUUUUUUUCGGUUUCGA
.........((((.....))))....((((((.(((((.(((((((....)))))))((((((((((......)))))))))).))))).)))))) ( -29.30)
>DroSim_CAF1 4248 96 - 1
GCAAAUGCUGAUUAUUAUGGUCGCAUUUGAGAGUGAGACGAUAGCUUAAUGGCUAUUAGAAGAACCCGUUUUGGGGUUCUUUUUUUUCGGUUUCGA
.(((((((.((((.....)))))))))))....(((((((((((((....)))))))((((((((((......))))))))))......)))))). ( -35.10)
>DroEre_CAF1 6993 95 - 1
GCAAAUGCUGAUUAUUAUGGUCGUAUUUGAGAGCGAGACGAUGGCUUAAUGGCCAUUAGAAGAACCCGUUUUGGUGUUCUU-UUUUUCGGCUUCGC
.(((((((.((((.....)))))))))))...(((((.((((((((....)))))..((((((((((.....)).))))))-))..)))..))))) ( -30.70)
>DroYak_CAF1 7948 96 - 1
GCAAAUGCUGAUUAUUAUAGUCGUAUUUGAGAGUGAGACGAUGGCUUAAUGGCCAUUAGAAGAACCCGUUUUGGGGUUCUUAUUUUUCAGCUUCGU
.(((((((.(((((...)))))))))))).((((((((.(((((((....)))))))..((((((((......))))))))...))))).)))... ( -32.50)
>DroAna_CAF1 7247 74 - 1
GCUAAUGCUGAUUAUUAUGGUCUUAGAA------GAGGCUUUAG-UUAAUGGCCAUUAGAAAAACCCGUUUGA------------UUUGGC---CG
((....))((((((....((((((....------)))))).)))-)))..((((((((((........)))))------------..))))---). ( -17.00)
>consensus
GCAAAUGCUGAUUAUUAUGGUCGUAUUUGAGAGUGAGACGAUAGCUUAAUGGCCAUUAGAAGAACCCGUUUUGGGGUUCUUUUUUUUCGGCUUCGA
.(((((((.((((.....)))))))))))....(((((.(((((((....)))))))..((((((((......))))))))...)))))....... (-16.91 = -19.05 +   2.14)

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 10:10:00 2006