Locus 7374

Sequence ID 2L_DroMel_CAF1
Location 20,531,573 – 20,531,826
Length 253
Max. P 0.944767
window11846 window11847 window11848 window11849 window11850

overview

Window 6

Location 20,531,573 – 20,531,668
Length 95
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 77.52
Mean single sequence MFE -23.75
Consensus MFE -17.96
Energy contribution -18.52
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -1.26
Structure conservation index 0.76
SVM decision value 0.69
SVM RNA-class probability 0.823777
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20531573 95 - 22407834
CCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUGGCCCCAAAGCCC------CCCACAAG--------------
..((((.............((((..((((.(((..(((((..(.....)..)))))....)))))))))))((((....))))))))------........-------------- ( -26.00)
>DroSec_CAF1 52809 101 - 1
CCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUGGCCCCAAAGCCCCCCUCCCCCACAAG--------------
..((((.............((((..((((.(((..(((((..(.....)..)))))....)))))))))))((((....))))))))..............-------------- ( -26.00)
>DroSim_CAF1 54136 95 - 1
CCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUGGCCCCAAAGCCC------CCCACAAG--------------
..((((.............((((..((((.(((..(((((..(.....)..)))))....)))))))))))((((....))))))))------........-------------- ( -26.00)
>DroEre_CAF1 45943 98 - 1
CCCGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGCUGCCAUUUGGCCCCC-----------------ACAGCUCCAUUCCCCGC
...((((...(.....)...))))......(((..(((((..(.....)..)))))....)))(((((((....)))....-----------------..))))........... ( -21.70)
>DroYak_CAF1 48148 109 - 1
CCCGGCCUUUCAUCAAGUCUGGCCUAACUAGCACUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUGGCCCCAAAGCCC------CCCAAAAAGCCCAACACCCCGC
...(((.............((((..((((.(((..(((((..(.....)..)))))....)))))))))))...(((......))).------........)))........... ( -24.00)
>DroAna_CAF1 45440 75 - 1
CUGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAGUGUGUUUUGUUUAUUUUGGCGCCUUCUGCAGUGACCAUUUU----------------------------------------
.((((((...(.....)...))))))(((.((((.(((((..(.....)..)))))...))))))).........---------------------------------------- ( -18.80)
>consensus
CCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUGGCCCCAAAGCCC______CCCACAAG______________
...((((...(.....)...)))).((((.(((..(((((..(.....)..)))))....)))))))(((....)))...................................... (-17.96 = -18.52 +   0.56)

alignment

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secondary structure

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Window 7

Location 20,531,593 – 20,531,687
Length 94
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 89.16
Mean single sequence MFE -31.79
Consensus MFE -27.03
Energy contribution -27.50
Covariance contribution 0.47
Combinations/Pair 1.17
Mean z-score -2.17
Structure conservation index 0.85
SVM decision value 0.92
SVM RNA-class probability 0.881546
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20531593 94 + 22407834
CAAAUGGCAACUGCAGGAGGCGCCAAAAUAAACAAAGCGCAUUGCUAGUUAGGCCAGACUUGAUGAAAGGCCCGGGAAAGCUCCUGCCGGCCGG-----------------
(((.((((.(((((((...((((.............)))).)))).)))...))))...)))......(((((((((....)))))..))))..----------------- ( -31.72)
>DroSec_CAF1 52835 94 + 1
CAAAUGGCAACUGCAGGAGGCGCCAAAAUAAACAAAGCGCAUUGCUAGUUAGGCCAGACUUGAUGAAAGGCCCGGGAAAACUCCUGCCGGCCGG-----------------
(((.((((.(((((((...((((.............)))).)))).)))...))))...)))......(((((((((....)))))..))))..----------------- ( -31.72)
>DroSim_CAF1 54156 94 + 1
CAAAUGGCAACUGCAGGAGGCGCCAAAAUAAACAAAGCGCAUUGCUAGUUAGGCCAGACUUGAUGAAAGGCCCGGGAAAACUCCUGCCGGCCGG-----------------
(((.((((.(((((((...((((.............)))).)))).)))...))))...)))......(((((((((....)))))..))))..----------------- ( -31.72)
>DroEre_CAF1 45966 94 + 1
CAAAUGGCAGCUGCAGGAGGCGCCAAAAUAAACAAAGCGCAUUGCUAGUUAGGCCAGACUUGAUGAAAGGCCGGGGAAAACUCCUGCCGGCCGG-----------------
(((.((((.(((((((...((((.............)))).)))).)))...))))...)))......(((((((((....)))..))))))..----------------- ( -34.22)
>DroYak_CAF1 48182 94 + 1
CAAAUGGCAACUGCAGGAGGCGCCAAAAUAAACAAAGCGCAGUGCUAGUUAGGCCAGACUUGAUGAAAGGCCGGGGAAAACUCCUGCCGGCCGG-----------------
(((.((((.((((((....((((.............))))..))).)))...))))...)))......(((((((((....)))..))))))..----------------- ( -31.92)
>DroAna_CAF1 45440 111 + 1
AAAAUGGUCACUGCAGAAGGCGCCAAAAUAAACAAAACACACUGCUAGUUAGGCCAGACUUGAUGAAAGGCCCAGGAAAAGUCCUGCCGGGCAGAGAGAUCUGCGGAGCAG
....((((..((.....))..))))................(((((.....((((.............))))(((((....)))))((..(((((....)))))))))))) ( -29.42)
>consensus
CAAAUGGCAACUGCAGGAGGCGCCAAAAUAAACAAAGCGCAUUGCUAGUUAGGCCAGACUUGAUGAAAGGCCCGGGAAAACUCCUGCCGGCCGG_________________
....((((.(((((((...((((.............)))).)))).)))...))))............(((((((((....)))))..))))................... (-27.03 = -27.50 +   0.47)

alignment

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secondary structure

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Window 8

Location 20,531,593 – 20,531,687
Length 94
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 89.16
Mean single sequence MFE -32.55
Consensus MFE -28.36
Energy contribution -28.45
Covariance contribution 0.09
Combinations/Pair 1.14
Mean z-score -2.21
Structure conservation index 0.87
SVM decision value 1.35
SVM RNA-class probability 0.944767
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20531593 94 - 22407834
-----------------CCGGCCGGCAGGAGCUUUCCCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUG
-----------------..(((..(((((((((.....(((((...(.....)...)))))....)))...(((((..(.....)..))))).))))))....)))..... ( -33.60)
>DroSec_CAF1 52835 94 - 1
-----------------CCGGCCGGCAGGAGUUUUCCCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUG
-----------------..(((..(((((((.......(((((...(.....)...)))))..........(((((..(.....)..))))))))))))....)))..... ( -32.90)
>DroSim_CAF1 54156 94 - 1
-----------------CCGGCCGGCAGGAGUUUUCCCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUG
-----------------..(((..(((((((.......(((((...(.....)...)))))..........(((((..(.....)..))))))))))))....)))..... ( -32.90)
>DroEre_CAF1 45966 94 - 1
-----------------CCGGCCGGCAGGAGUUUUCCCCGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGCUGCCAUUUG
-----------------..(((..(((((((........((((...(.....)...))))...........(((((..(.....)..))))))))))))....)))..... ( -31.80)
>DroYak_CAF1 48182 94 - 1
-----------------CCGGCCGGCAGGAGUUUUCCCCGGCCUUUCAUCAAGUCUGGCCUAACUAGCACUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUG
-----------------..(((..(((((((........((((...(.....)...))))...........(((((..(.....)..))))))))))))....)))..... ( -31.80)
>DroAna_CAF1 45440 111 - 1
CUGCUCCGCAGAUCUCUCUGCCCGGCAGGACUUUUCCUGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAGUGUGUUUUGUUUAUUUUGGCGCCUUCUGCAGUGACCAUUUU
(((((..(((((....)))))..))))).........((((((...(.....)...))))))(((.((((.(((((..(.....)..)))))...)))))))......... ( -32.30)
>consensus
_________________CCGGCCGGCAGGAGUUUUCCCGGGCCUUUCAUCAAGUCUGGCCUAACUAGCAAUGCGCUUUGUUUAUUUUGGCGCCUCCUGCAGUUGCCAUUUG
...................(((..(((((((........((((...(.....)...))))...........(((((..(.....)..))))))))))))....)))..... (-28.36 = -28.45 +   0.09)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,531,687 – 20,531,795
Length 108
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 93.77
Mean single sequence MFE -31.68
Consensus MFE -24.77
Energy contribution -25.13
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -3.03
Structure conservation index 0.78
SVM decision value 0.57
SVM RNA-class probability 0.785735
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20531687 108 - 22407834
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAUCCAGUUUCGGCCGCCGCC---AAAUUUUCCC-------
...((((((.(((((....(((((((((((..(((....((.......))....)))..)))))).)))))((((.((.....))..)))).))))))---))))).....------- ( -31.60)
>DroSec_CAF1 52929 108 - 1
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAUCCAGUUUCGGCCGCCGCC---AAAUUUUCCC-------
...((((((.(((((....(((((((((((..(((....((.......))....)))..)))))).)))))((((.((.....))..)))).))))))---))))).....------- ( -31.60)
>DroSim_CAF1 54250 108 - 1
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAUCCAGUUUCGGCCGCCGCC---AAAUUUUCCC-------
...((((((.(((((....(((((((((((..(((....((.......))....)))..)))))).)))))((((.((.....))..)))).))))))---))))).....------- ( -31.60)
>DroEre_CAF1 46060 108 - 1
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAUCCAGUCUCGGCCGCCGCC---AAAUUUUCCC-------
...((((((.(((((..(((((((((((((..(((....((.......))....)))..))))))......(.....)......))))))).))))))---))))).....------- ( -33.10)
>DroYak_CAF1 48276 108 - 1
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAUCCAGUUUCGUCCGCCGCC---AAAUUUUCCC-------
...((((((.(((((....(((((((((((..(((....((.......))....)))..)))))).)))))(..((.......))..)....))))))---))))).....------- ( -31.20)
>DroAna_CAF1 45551 117 - 1
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGGAUCCAAC-UCGGUCUCCUCCCGAAAAUUGUCCUCUUUCCU
..........(..((.((..((((((((((..(((....((.......))....)))..))))))))))))))..)((((.....-((((.......)))).....))))........ ( -31.00)
>consensus
UAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAUCCAGUUUCGGCCGCCGCC___AAAUUUUCCC_______
......(((..(((((....((((((((((..(((....((.......))....)))..))))))))))....))).))..)))....(((....))).................... (-24.77 = -25.13 +   0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,531,715 – 20,531,826
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.72
Mean single sequence MFE -33.32
Consensus MFE -26.70
Energy contribution -26.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.80
SVM decision value 0.48
SVM RNA-class probability 0.751295
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20531715 111 - 22407834
UCAACUG-GG-------CGGAG-GCCCACGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAU
.((((((-((-------((...-.....))))((((((.(((.....)))...)))))).((((((((((..(((....((.......))....)))..))))))))))))))))..... ( -34.50)
>DroPse_CAF1 92320 110 - 1
NN--NNN-NN------NNNUGG-GCCCACGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGGAU
..--...-..------......-.....(((.((((((.(((.....)))...))))))(((((((((((..(((....((.......))....)))..)))))).)))))...)))... ( -27.20)
>DroSec_CAF1 52957 112 - 1
UCCACAG-GG-------CGGAGGGCCCGCGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAU
......(-((-------(.....))))((((.((((((.(((.....)))...))))))(((((((((((..(((....((.......))....)))..)))))).)))))...)))).. ( -38.70)
>DroEre_CAF1 46088 107 - 1
----CCG-GA-------CGGAG-GCCCACGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAU
----((.-..-------.))..-((.((.(((((((((.(((.....)))...)))))).((((((((((..(((....((.......))....)))..)))))))))).))))).)).. ( -27.70)
>DroAna_CAF1 45588 119 - 1
UUGGCCAGGACUCUCCUUGCAG-GCCCACGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGGAU
..(((((((.....)))....)-)))..(((.((((((.(((.....)))...))))))(((((((((((..(((....((.......))....)))..)))))).)))))...)))... ( -35.80)
>DroPer_CAF1 97269 110 - 1
UC--CAG-UG------CAGUGG-GCCCACGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGGAU
((--(((-((------((...(-((....)))...)))))).........(..((.((..((((((((((..(((....((.......))....)))..))))))))))))))..)))). ( -36.00)
>consensus
UC__CAG_GG_______CGGAG_GCCCACGCUAUAUGCAUUAUAAUUUGAGUGGCAUGUUGAGAGUGGCUUUUGUUUUGCUUUUAAUUAGAUUUACAUUGGCCACUUUUCAGUUGCGCAU
............................(((.((((((.(((.....)))...))))))(((((((((((..(((....((.......))....)))..)))))).)))))...)))... (-26.70 = -26.70 +  -0.00)

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 12:35:13 2006