Locus 6799

Sequence ID 3R_DroMel_CAF1
Location 17,961,615 – 17,961,740
Length 125
Max. P 0.829745
window11035 window11036 window11037 window11038

overview

Window 5

Location 17,961,615 – 17,961,713
Length 98
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 83.60
Mean single sequence MFE -30.08
Consensus MFE -19.83
Energy contribution -19.25
Covariance contribution -0.58
Combinations/Pair 1.21
Mean z-score -2.06
Structure conservation index 0.66
SVM decision value 0.00
SVM RNA-class probability 0.533878
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17961615 98 + 27905053
CAUGGUUCCUGCUGC----------CACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AGAGGAGCACUCUUCACAGCUCCACA
.....((((((((((----------(((....((....)).....))))))))....(((((..........))))).)).)-)).(((((..........)))))... ( -27.60)
>DroSec_CAF1 5072 99 + 1
CAUGGUUCCUGCUGC----------CACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCGGAGAGUAGCACUCUUCACAGCUCUACA
....(((...(((((----------(((....((....)).....)))))))).)))...(((.........((.....))((((((.....))))))..)))...... ( -27.90)
>DroSim_CAF1 6025 99 + 1
CAUGGUUCCUGCUGC----------CACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCGGAGAGUAGCACUCUUCACAGCUCCACA
.........((((((----------..(....)..))))))....((((.(((....(((((..........)))))..(.((((((.....)))))).).))))))). ( -29.30)
>DroEre_CAF1 5196 96 + 1
--UGGUUCCUGCUGC----------CACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AGGGGAGUACUCUUCGCAGCUCCACA
--.......((((((----------..(....)..))))))....((((.(((....(((((..........)))))..(((-(((((....)))))))).))))))). ( -33.20)
>DroYak_CAF1 5462 87 + 1
CAUGGUUGCUGCUGC----------CACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AGAGGAACACUCUUC-----------
..((((.((.(((((----------(((....((....)).....)))))))).......)).)))).....((.....))(-((((.....))))).----------- ( -26.70)
>DroAna_CAF1 5040 97 + 1
AAGGGCUGUGGCUGCGCUGAGGCAGCACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AUGCGAGGAGCCUCC-----------
...((((((.(((..((((.(((.........))).))))....))).))))))..(((((((...............))))-))).(((....))).----------- ( -35.76)
>consensus
CAUGGUUCCUGCUGC__________CACAGAAGCCGCAGCAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG_AGAGGAGCACUCUUCACAGCUCCACA
...((((.(((.((...........))))).))))(((.......(((((((......)))))))......))).......(.((((.....)))).)........... (-19.83 = -19.25 +  -0.58)

alignment

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secondary structure

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Window 6

Location 17,961,615 – 17,961,713
Length 98
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 83.60
Mean single sequence MFE -36.58
Consensus MFE -23.60
Energy contribution -24.97
Covariance contribution 1.36
Combinations/Pair 1.19
Mean z-score -2.71
Structure conservation index 0.65
SVM decision value 0.31
SVM RNA-class probability 0.682296
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17961615 98 - 27905053
UGUGGAGCUGUGAAGAGUGCUCCUCU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUG----------GCAGCAGGAACCAUG
.((((...(((((.(((((.......-))))).)))))....(((((((.......))))))).((((((((((.((....)).----------)))))))))))))). ( -39.10)
>DroSec_CAF1 5072 99 - 1
UGUAGAGCUGUGAAGAGUGCUACUCUCCGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUG----------GCAGCAGGAACCAUG
(((.((...(((.((((.....)))).)))...)))))....(((((((.......))))))).((((((((((.((....)).----------))))))))))..... ( -36.00)
>DroSim_CAF1 6025 99 - 1
UGUGGAGCUGUGAAGAGUGCUACUCUCCGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUG----------GCAGCAGGAACCAUG
.((((...(((((.(((((........))))).)))))....(((((((.......))))))).((((((((((.((....)).----------)))))))))))))). ( -39.60)
>DroEre_CAF1 5196 96 - 1
UGUGGAGCUGCGAAGAGUACUCCCCU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUG----------GCAGCAGGAACCA--
..(((...(((((.((((........-.)))).)))))....(((((((.......))))))).((((((((((.((....)).----------)))))))))))))-- ( -36.80)
>DroYak_CAF1 5462 87 - 1
-----------GAAGAGUGUUCCUCU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUG----------GCAGCAGCAACCAUG
-----------((.(((((.......-))))).))((.....(((((((.......))))))).....((((((.((....)).----------))))))))....... ( -31.60)
>DroAna_CAF1 5040 97 - 1
-----------GGAGGCUCCUCGCAU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUGCUGCCUCAGCGCAGCCACAGCCCUU
-----------((.(((..((.((((-.(((.((((......))))))).)))).))..))).......((((.((((...((((((...)))))))))).)))))).. ( -36.40)
>consensus
UGUGGAGCUGUGAAGAGUGCUCCUCU_CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUGCUGCGGCUUCUGUG__________GCAGCAGGAACCAUG
........(((((.(((((........))))).)))))....(((((((.......))))))).((((((((((....................))))))))))..... (-23.60 = -24.97 +   1.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,961,644 – 17,961,740
Length 96
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 80.18
Mean single sequence MFE -23.83
Consensus MFE -16.15
Energy contribution -15.48
Covariance contribution -0.66
Combinations/Pair 1.25
Mean z-score -1.84
Structure conservation index 0.68
SVM decision value 0.71
SVM RNA-class probability 0.829745
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17961644 96 + 27905053
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AGAGGAGCACUCUUCACAGCUCCACAGACUCACAGCUGAUGCUAUUUC-------ACCUU
......(((((((......))))))).......((.....))(-((((((((..........)))))..........(((....))).))))-------..... ( -21.60)
>DroSec_CAF1 5101 96 + 1
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCGGAGAGUAGCACUCUUCACAGCUCUACAGACUCACAGCUGAUGCUAUUUC-------ACCU-
....((((((((((....(((((..........)))))..))((((((.....)))))).(((((............))))).)))))))).-------....- ( -23.70)
>DroSim_CAF1 6054 96 + 1
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCGGAGAGUAGCACUCUUCACAGCUCCACAGACUCACAGCUGAUGCUAUUUC-------ACCU-
....((((((((((....(((((..........)))))..))((((((.....)))))).(((((............))))).)))))))).-------....- ( -23.70)
>DroEre_CAF1 5223 95 + 1
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AGGGGAGUACUCUUCGCAGCUCCACAGCUCCACAGCUGAUGCCAUUCC-------ACCU-
.....(((((((((....(((((..........)))))..(((-(((((....)))))))).))....(((((....))))).)))))))..-------....- ( -30.90)
>DroYak_CAF1 5491 79 + 1
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AGAGGAACACUCUUC----------------ACAGCUGAUGCUAUUUU-------ACCU-
...(((((((((......(((((..........))))).(((.-.(((((....)))))----------------...)))..)))))))))-------....- ( -19.30)
>DroAna_CAF1 5079 86 + 1
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG-AUGCGAGGAGCCUCC----------------GCAGCUGAUGCCACUUCUGAACGCGGCC-
....((((((((......(((((..........))))).(((.-.((((((....)).)----------------))))))..))))))))............- ( -23.80)
>consensus
CAAAAAGUGGCAGCCAACAUUGCUACCAAUUAUGCGAUAAGCG_AGAGGAGCACUCUUCACAGCUCCACAGACUCACAGCUGAUGCUAUUUC_______ACCU_
....((((((((((....(((((..........)))))..))(.((((.....)))).)........................))))))))............. (-16.15 = -15.48 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,961,644 – 17,961,740
Length 96
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 80.18
Mean single sequence MFE -27.90
Consensus MFE -18.98
Energy contribution -19.62
Covariance contribution 0.64
Combinations/Pair 1.23
Mean z-score -1.21
Structure conservation index 0.68
SVM decision value -0.02
SVM RNA-class probability 0.521185
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17961644 96 - 27905053
AAGGU-------GAAAUAGCAUCAGCUGUGAGUCUGUGGAGCUGUGAAGAGUGCUCCUCU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
..(((-------(......)))).((.((((((..(.(((((..........))))).).-.)))))).)).....(((((((.......)))))))....... ( -31.20)
>DroSec_CAF1 5101 96 - 1
-AGGU-------GAAAUAGCAUCAGCUGUGAGUCUGUAGAGCUGUGAAGAGUGCUACUCUCCGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
-..((-------((...(((..(((((.((......)).))))).(.((((.....)))).))))..)))).....(((((((.......)))))))....... ( -28.20)
>DroSim_CAF1 6054 96 - 1
-AGGU-------GAAAUAGCAUCAGCUGUGAGUCUGUGGAGCUGUGAAGAGUGCUACUCUCCGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
-.(((-------(......))))...(((((....((((((..(((........))).))))))...)))))....(((((((.......)))))))....... ( -28.20)
>DroEre_CAF1 5223 95 - 1
-AGGU-------GGAAUGGCAUCAGCUGUGGAGCUGUGGAGCUGCGAAGAGUACUCCCCU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
-..((-------((...(((..(((((....))))).((((.(((.....)))))))...-.)))..)))).....(((((((.......)))))))....... ( -29.70)
>DroYak_CAF1 5491 79 - 1
-AGGU-------AAAAUAGCAUCAGCUGU----------------GAAGAGUGUUCCUCU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
-....-------.....(((....)))((----------------((.(((((.......-))))).)))).....(((((((.......)))))))....... ( -21.10)
>DroAna_CAF1 5079 86 - 1
-GGCCGCGUUCAGAAGUGGCAUCAGCUGC----------------GGAGGCUCCUCGCAU-CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
-..........((((((((((((((((((----------------(.((....)))))).-.(((.((((......)))))))...))))).)))))))))).. ( -29.00)
>consensus
_AGGU_______GAAAUAGCAUCAGCUGUGAGUCUGUGGAGCUGUGAAGAGUGCUCCUCU_CGCUUAUCGCAUAAUUGGUAGCAAUGUUGGCUGCCACUUUUUG
...............(((((....))))).............(((((.(((((........))))).)))))....(((((((.......)))))))....... (-18.98 = -19.62 +   0.64)

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 12:30:14 2006