Locus 5726

Sequence ID 3L_DroMel_CAF1
Location 15,603,609 – 15,603,747
Length 138
Max. P 0.965930
window9067 window9068 window9069

overview

Window 7

Location 15,603,609 – 15,603,707
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.11
Mean single sequence MFE -15.32
Consensus MFE -13.32
Energy contribution -13.04
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -2.05
Structure conservation index 0.87
SVM decision value 1.59
SVM RNA-class probability 0.965930
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15603609 98 + 23771897
AUCUUUUAUCCAAACACAACAAGCCUCAU------UCUUAACC----------------UCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGAGAUAUCUCCC
......((((...................------........----------------........(((((((((.((....)).)))))))))(((........))).))))...... ( -13.40)
>DroSec_CAF1 26744 94 + 1
AUCUUUUAUCCAAACACAACAAGCCUCAU------UCUCAACC----------------UCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGGGAUAUC----
......(((((..................------........----------------........(((((((((.((....)).)))))))))(((........))))))))..---- ( -17.60)
>DroSim_CAF1 26652 100 + 1
AUCUUUUAUCCAAACACAACAAGCCUCAUUCUCAUUCUCAAUC----------------UCCGACCCUUCGACCAAAUGCCGUCAGUUGUUCGAACACUCCUCCUUGUGGGAUAUC----
......(((((....(((((.......................----------------...((....))(((........))).))))).....(((........))))))))..---- ( -13.50)
>DroEre_CAF1 26709 92 + 1
AUCUUUUAUCCAAACACAACAAGCCUCAA------UCUCAACC----------------UCCGACCCUUCGAGCAAAUGCCGUCAGUUGCUCGAACACUCCUCUUUGUGAGAUA------
............................(------(((((...----------------...((...(((((((((.((....)).)))))))))...)).......)))))).------ ( -18.62)
>DroYak_CAF1 28734 110 + 1
AUCUUUUAUCCAAACACAACAAGCCUCAU------UCUCAACCUCAGUACCUCAGACCCUCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGAGAUAUC----
......((((....(((((..((......------................((.(.....).))...(((((((((.((....)).))))))))).....))..))))).))))..---- ( -13.50)
>consensus
AUCUUUUAUCCAAACACAACAAGCCUCAU______UCUCAACC________________UCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGAGAUAUC____
((((...............................................................(((((((((.((....)).)))))))))(((........)))))))....... (-13.32 = -13.04 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,603,609 – 15,603,707
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.11
Mean single sequence MFE -25.14
Consensus MFE -21.86
Energy contribution -21.58
Covariance contribution -0.28
Combinations/Pair 1.07
Mean z-score -1.47
Structure conservation index 0.87
SVM decision value 0.16
SVM RNA-class probability 0.613416
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15603609 98 - 23771897
GGGAGAUAUCUCACAAAGAGGAGUGUUCGAACAACUGACGGCAUUUGUUCGAAGGGUCGGA----------------GGUUAAGA------AUGAGGCUUGUUGUGUUUGGAUAAAAGAU
......((((((((((....((.(.(((((((((.((....)).))))))))).).))..(----------------((((....------....))))).)))))...)))))...... ( -23.40)
>DroSec_CAF1 26744 94 - 1
----GAUAUCCCACAAAGAGGAGUGUUCGAACAACUGACGGCAUUUGUUCGAAGGGUCGGA----------------GGUUGAGA------AUGAGGCUUGUUGUGUUUGGAUAAAAGAU
----..((((((((((.(((...(((((...(((((..((((.(((....)))..))))..----------------))))).))------)))...))).)))))...)))))...... ( -26.90)
>DroSim_CAF1 26652 100 - 1
----GAUAUCCCACAAGGAGGAGUGUUCGAACAACUGACGGCAUUUGGUCGAAGGGUCGGA----------------GAUUGAGAAUGAGAAUGAGGCUUGUUGUGUUUGGAUAAAAGAU
----..((((((((((.(((.(((.(((((....((..((((.....))))..)).)))))----------------.)))....((....))....))).)))))...)))))...... ( -22.90)
>DroEre_CAF1 26709 92 - 1
------UAUCUCACAAAGAGGAGUGUUCGAGCAACUGACGGCAUUUGCUCGAAGGGUCGGA----------------GGUUGAGA------UUGAGGCUUGUUGUGUUUGGAUAAAAGAU
------((((((((((....((.(.(((((((((.((....)).))))))))).).))..(----------------((((....------....))))).)))))...)))))...... ( -25.80)
>DroYak_CAF1 28734 110 - 1
----GAUAUCUCACAAAGAGGAGUGUUCGAACAACUGACGGCAUUUGUUCGAAGGGUCGGAGGGUCUGAGGUACUGAGGUUGAGA------AUGAGGCUUGUUGUGUUUGGAUAAAAGAU
----..((((((((((....((.(.(((((((((.((....)).))))))))).).))...((((((.(...((....)).....------.).)))))).)))))...)))))...... ( -26.70)
>consensus
____GAUAUCUCACAAAGAGGAGUGUUCGAACAACUGACGGCAUUUGUUCGAAGGGUCGGA________________GGUUGAGA______AUGAGGCUUGUUGUGUUUGGAUAAAAGAU
......((((((((((.(((((.(.(((((((((.((....)).))))))))).).)).....................((............))..))).)))))...)))))...... (-21.86 = -21.58 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,603,643 – 15,603,747
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.01
Mean single sequence MFE -19.88
Consensus MFE -15.71
Energy contribution -16.27
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.41
Structure conservation index 0.79
SVM decision value 0.15
SVM RNA-class probability 0.608616
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15603643 104 + 23771897
ACC----------------UCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGAGAUAUCUCCCUAUCUCCCGAUGUUCUCGGUUCCCGAUUCCCCGUUUUGCC
...----------------.((((...(((((((((.((....)).))))))))).........(((.((((((......)))))).))).....))))..................... ( -20.60)
>DroSec_CAF1 26778 86 + 1
ACC----------------UCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGGGAUAUC--------UCCCGAUGUUCCCGGUCCCCGAUUCC----------
...----------------...((((.(((((((((.((....)).)))))))))...........(.((((((((--------....))))))))))))).........---------- ( -24.10)
>DroSim_CAF1 26692 86 + 1
AUC----------------UCCGACCCUUCGACCAAAUGCCGUCAGUUGUUCGAACACUCCUCCUUGUGGGAUAUC--------UCCCGAUGUUCCCGGUCCCCGAUUCC----------
...----------------...((((.(((((.(((.((....)).))).)))))...........(.((((((((--------....))))))))))))).........---------- ( -19.90)
>DroYak_CAF1 28768 109 + 1
ACCUCAGUACCUCAGACCCUCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGAGAUAUC--------UCCCCAUGUUCCCGGCCCCCGAUCCCCCGAUAU---
....................(((....(((((((((.((....)).)))))))))(((........))).......--------............)))..................--- ( -14.90)
>consensus
ACC________________UCCGACCCUUCGAACAAAUGCCGUCAGUUGUUCGAACACUCCUCUUUGUGAGAUAUC________UCCCGAUGUUCCCGGUCCCCGAUUCC__________
......................((((.(((((((((.((....)).))))))))).............((((((((............)))).))))))))................... (-15.71 = -16.27 +   0.56)

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 11:57:53 2006