Locus 2092

Sequence ID X_DroMel_CAF1
Location 5,696,945 – 5,697,193
Length 248
Max. P 0.990250
window3401 window3402 window3403

overview

Window 1

Location 5,696,945 – 5,697,062
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.37
Mean single sequence MFE -18.96
Consensus MFE -14.12
Energy contribution -14.52
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.74
SVM decision value 0.43
SVM RNA-class probability 0.731690
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5696945 117 - 22224390
GCGCUUCGCUUGUGUUUAUGCAAAUAUUUGUAUUCCAUUUGCAUUUCAAUAAUUGAAA--UUUUUAUUUUUUCUGCCUUUGCGCUCUUGUUUUUC-UCGCACCCGCGCCCGCGCCAUUCC
((((...((..(((...((((((....))))))..)))..))((((((.....)))))--)...................((((...(((.....-..)))...))))..))))...... ( -23.20)
>DroSec_CAF1 17894 111 - 1
GCGCUUCGCUUGUGUUUAUGCAAAUAUUUGUAUUCCAUUUGCAUUUCAAUAAUUGAAA--UUUUUUUUUUUUCUGCCUUUGCGCUCUUGUUUUUC-CCGCACCC------CCGCCAUUCC
((((...((..(((...((((((....))))))..)))..))((((((.....)))))--)...................))))...........-..((....------..))...... ( -18.20)
>DroSim_CAF1 21168 111 - 1
GCGCUUCGCUUGUGUUUAUGCAAAUAUUUGUAUUCCAUUUGCAUUUCAAUAAUUGAAA--UUUUUAUUUUUUCUGCCUUUGCGCUCUUGUUCUUC-CCGCACCC------CCGCCAUUCC
((((...((..(((...((((((....))))))..)))..))((((((.....)))))--)...................))))...........-..((....------..))...... ( -18.20)
>DroEre_CAF1 17104 113 - 1
-CGCUUCGCUUGUGUUUAUGCAAAUAUUUGUAUUCCAUUUGCAUUUCAAUAAUUGAAAAUUUUUUGUUUUUUCCGCCCUUGCGCUCUUGUUUUUCGCCGACC------CGUCGCCAUUCC
-(((...((..(((...((((((....))))))..)))..)).(((((.....)))))......................)))............(.(((..------..))).)..... ( -15.30)
>DroYak_CAF1 20805 115 - 1
-CGCUUCGCUUGUGUUUAUGCAAAUAUUUGUAUUCCAUUUGCAUUUCAAUAAUUGAAA---UUUUAUUUUUUCUGCCUUGGCGCUCUUGUUUUUU-CCGCUCCCUCGCCAUUGCCAUUCC
-......((..(((...((((((....))))))..)))..))((((((.....)))))---)............((..(((((.....((.....-..)).....)))))..))...... ( -19.90)
>consensus
GCGCUUCGCUUGUGUUUAUGCAAAUAUUUGUAUUCCAUUUGCAUUUCAAUAAUUGAAA__UUUUUAUUUUUUCUGCCUUUGCGCUCUUGUUUUUC_CCGCACCC____C_CCGCCAUUCC
((((...((..(((...((((((....))))))..)))..)).(((((.....)))))......................)))).................................... (-14.12 = -14.52 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,697,062 – 5,697,180
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 84.68
Mean single sequence MFE -34.45
Consensus MFE -27.63
Energy contribution -27.63
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -1.85
Structure conservation index 0.80
SVM decision value 0.32
SVM RNA-class probability 0.687000
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5697062 118 - 22224390
GCUCGAAAAAAAUGAAUAUAUAUACUGUGUGGCCAUAUCAGAGGUGAAGCCCUCUAGAAAAGUGGGCGUGGCCAGGCGGUGUGUCUCUCUCUCUCUUUUUUUUUUUUUGUUCGUAUUU
(..(((((((((.(((...(((((((((.(((((((.(((....))).((((.((.....)).))))))))))).)))))))))............))).)))))))))..)...... ( -37.16)
>DroSec_CAF1 18005 102 - 1
GCUUGAAAAAAAUG--UAUAUAUGCAGUGUGGCCAUAUCAGAGGUGAAGCCCCCUGGAAAAGUGGGCAUGGCCAGGCGGGGUGUCUCUCU--------UUUUU------UUGGUGUGU
(((.(((((((..(--...((((.(.((.(((((((.(((....))).((((.((.....)).))))))))))).)).).))))..)..)--------)))))------).))).... ( -33.10)
>DroSim_CAF1 21279 110 - 1
GCUUGAAAAAAAUG--UAUAUAUGCAGUGUGGCCAUAUCAGAGGUGAAGCCCCCUGGAAAAGUGGGCGUGGCCAGGCGGGGUGUCUCUCUCUCUUUUUUUUUU------UUGGUGUGU
(((.((((((((((--((....))))((.(((((((.(((....))).((((.((.....)).))))))))))).))((((.(.....).))))..)))))))------).))).... ( -33.10)
>consensus
GCUUGAAAAAAAUG__UAUAUAUGCAGUGUGGCCAUAUCAGAGGUGAAGCCCCCUGGAAAAGUGGGCGUGGCCAGGCGGGGUGUCUCUCUCUCU_UUUUUUUU______UUGGUGUGU
...................((((((.((.(((((((.(((....))).((((.((.....)).))))))))))).))((((.....))))......................)))))) (-27.63 = -27.63 +   0.01)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,697,102 – 5,697,193
Length 91
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 80.11
Mean single sequence MFE -34.97
Consensus MFE -26.45
Energy contribution -28.23
Covariance contribution 1.78
Combinations/Pair 1.04
Mean z-score -2.58
Structure conservation index 0.76
SVM decision value 2.20
SVM RNA-class probability 0.990250
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5697102 91 - 22224390
C---------------------------GAGAAGAUUUGAGCUCGAAAAAAAUGAAUAUAUAUACUGUGUGGCCAUAUCAGAGGUGAAGCCCUCUAGAAAAGUGGGCGUGGCCAGGCG
(---------------------------(((..........)))).....................((.(((((((.(((....))).((((.((.....)).))))))))))).)). ( -27.80)
>DroSec_CAF1 18031 116 - 1
CAUUUCCGCUGCGUAGAGUGUAGAGUUCGAGAAGAUUUGAGCUUGAAAAAAAUG--UAUAUAUGCAGUGUGGCCAUAUCAGAGGUGAAGCCCCCUGGAAAAGUGGGCAUGGCCAGGCG
......(((((((((..((...(((((((((....))))))))).......)).--....)))))))))(((((((.(((....))).((((.((.....)).))))))))))).... ( -38.40)
>DroSim_CAF1 21313 116 - 1
CAUUUCCGCUGCGUAGAGUGUAGAGUUCGAGAAGAUUUGAGCUUGAAAAAAAUG--UAUAUAUGCAGUGUGGCCAUAUCAGAGGUGAAGCCCCCUGGAAAAGUGGGCGUGGCCAGGCG
......(((((((((..((...(((((((((....))))))))).......)).--....)))))))))(((((((.(((....))).((((.((.....)).))))))))))).... ( -38.70)
>consensus
CAUUUCCGCUGCGUAGAGUGUAGAGUUCGAGAAGAUUUGAGCUUGAAAAAAAUG__UAUAUAUGCAGUGUGGCCAUAUCAGAGGUGAAGCCCCCUGGAAAAGUGGGCGUGGCCAGGCG
......................(((((((((....)))))))))......................((.(((((((.(((....))).((((.((.....)).))))))))))).)). (-26.45 = -28.23 +   1.78)

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 10:26:04 2006