Locus 1721

Sequence ID 2L_DroMel_CAF1
Location 4,730,225 – 4,730,350
Length 125
Max. P 0.987011
window2757 window2758 window2759

overview

Window 7

Location 4,730,225 – 4,730,327
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.12
Mean single sequence MFE -23.05
Consensus MFE -16.08
Energy contribution -15.92
Covariance contribution -0.17
Combinations/Pair 1.06
Mean z-score -1.23
Structure conservation index 0.70
SVM decision value 0.20
SVM RNA-class probability 0.631528
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4730225 102 + 22407834
---UUUUGC--UGGACGGACUUGGCUC-C--GCAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAA-AACAUUCAGCA---ACAGC------AAG
---..((((--(((.((((......))-)--))..((.(((........)))........(((((((.((........)).)))))))...-........)).---.))))------)). ( -29.60)
>DroPse_CAF1 186698 99 + 1
----------------GUUCUCUGUUCCC--CAAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA---ACAGCGGCAGCAAG
----------------((((((((((...--....((.(((........))).)).....(((((((.((........)).)))))))..............)---)))).)).)))... ( -21.30)
>DroWil_CAF1 165363 92 + 1
---UU---------------UUGGGUC-CUGGCAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUUAACA---AUAGC------AAA
---..---------------.......-...((..((.(((........))).)).....(((((((.((........)).)))))))...............---...))------... ( -17.90)
>DroYak_CAF1 165206 105 + 1
---UUUUGG--CGGACGGACUUGGCUC-C--ACAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAA-AACAUUCAGCAGCAAGAGC------AAG
---.((((.--....))))((((.(((-.--....((.(((........)))........(((((((.((........)).)))))))...-........)).....))))------))) ( -23.90)
>DroAna_CAF1 177667 107 + 1
GGCUUUCACUAUAGAACGACUUCGUUC-C--GCAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA---ACAGC------A-G
(..((((......(((((....)))))-(--((((.............))))).......(((((((.((........)).)))))))))))..)........---.....------.-. ( -24.32)
>DroPer_CAF1 184125 99 + 1
----------------GUUCUCUGUUCCC--CAAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA---ACAGCGGCAGCAAG
----------------((((((((((...--....((.(((........))).)).....(((((((.((........)).)))))))..............)---)))).)).)))... ( -21.30)
>consensus
___UU___________GGACUUGGUUC_C__GCAGGCAGCAUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA___ACAGC______AAG
.......................(((.........((.(((........))).)).....(((((((.((........)).)))))))...........))).................. (-16.08 = -15.92 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,730,257 – 4,730,350
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.42
Mean single sequence MFE -22.05
Consensus MFE -12.67
Energy contribution -12.53
Covariance contribution -0.14
Combinations/Pair 1.07
Mean z-score -2.35
Structure conservation index 0.57
SVM decision value 2.06
SVM RNA-class probability 0.987011
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4730257 93 + 22407834
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAA-AACAUUCAGCA---ACAGC------AAGUGAAAC-------CAGCAGAAAAUGG-GCAA---------
........(((((((.....(((((((.((........)).)))))))...-..((((..((.---...))------.))))..))-------).)))).......-....--------- ( -20.60)
>DroPse_CAF1 186720 112 + 1
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA---ACAGCGGCAGCAAGAGCAACACGGACUCAGCUCACAAG-----AGGGCCGGCAA
........((((........(((((((.((........)).)))))))...............---....((((.....((((......).)))..(((....)-----)).)))))))) ( -26.70)
>DroWil_CAF1 165384 82 + 1
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUUAACA---AUAGC------AAAAGCAAC-------UAGCC----------------------
..........(((((.....(((((((.((........)).)))))))...............---...((------....)).))-------).)).---------------------- ( -15.00)
>DroYak_CAF1 165238 97 + 1
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAA-AACAUUCAGCAGCAAGAGC------AAGUGAAAC-------CAGCAGAAAAUGGGGAAA---------
........(((((((.....(((((((.((........)).)))))))...-....((((...((....))------...))))))-------).))))............--------- ( -21.10)
>DroAna_CAF1 177704 102 + 1
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA---ACAGC------A-GCGGCAG-------CAACAAGAACCAG-GCAGUACCCGCAA
........((((((..(((.(((((((.((........)).)))))))...............---...((------.-..((...-------(.....)..))..-)))))..)))))) ( -22.20)
>DroPer_CAF1 184147 112 + 1
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA---ACAGCGGCAGCAAGAGCAACACGGACUCAGCUCACAAG-----AGGGCCGGCAA
........((((........(((((((.((........)).)))))))...............---....((((.....((((......).)))..(((....)-----)).)))))))) ( -26.70)
>consensus
AUAAUUAAUUGCGGUAAUUAGUGUGUUGGCAACAAACAGCAAACACACGAAAAACAUUCAACA___ACAGC______AAGAGCAAC_______CAGCACAAAAG_____AG_________
..........((........(((((((.((........)).)))))))(((.....)))..........))................................................. (-12.67 = -12.53 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,730,257 – 4,730,350
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.42
Mean single sequence MFE -22.42
Consensus MFE -13.20
Energy contribution -13.37
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.59
SVM decision value -0.01
SVM RNA-class probability 0.528374
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4730257 93 - 22407834
---------UUGC-CCAUUUUCUGCUG-------GUUUCACUU------GCUGU---UGCUGAAUGUU-UUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
---------((((-.(((((...((.(-------((.......------)))..---.)).)))))..-...(((((((.((........)).)))))))........))))........ ( -19.40)
>DroPse_CAF1 186720 112 - 1
UUGCCGGCCCU-----CUUGUGAGCUGAGUCCGUGUUGCUCUUGCUGCCGCUGU---UGUUGAAUGUUUUUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
((((((((.(.-----.....)(((.((((.......))))..)))))))....---........((..((.(((((((.((........)).))))))).))..)).))))........ ( -25.40)
>DroWil_CAF1 165384 82 - 1
----------------------GGCUA-------GUUGCUUUU------GCUAU---UGUUAAAUGUUUUUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
----------------------...((-------((((((((.------((...---.)).))).((..((.(((((((.((........)).))))))).))..)).)))))))..... ( -18.60)
>DroYak_CAF1 165238 97 - 1
---------UUUCCCCAUUUUCUGCUG-------GUUUCACUU------GCUCUUGCUGCUGAAUGUU-UUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
---------.............(((.(-------((((((...------((....))...))))....-...(((((((.((........)).))))))).....))))))......... ( -20.60)
>DroAna_CAF1 177704 102 - 1
UUGCGGGUACUGC-CUGGUUCUUGUUG-------CUGCCGC-U------GCUGU---UGUUGAAUGUUUUUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
((((((.......-...((((.....(-------(.((...-.------)).))---....)))).......(((((((.((........)).)))))))......))))))........ ( -25.10)
>DroPer_CAF1 184147 112 - 1
UUGCCGGCCCU-----CUUGUGAGCUGAGUCCGUGUUGCUCUUGCUGCCGCUGU---UGUUGAAUGUUUUUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
((((((((.(.-----.....)(((.((((.......))))..)))))))....---........((..((.(((((((.((........)).))))))).))..)).))))........ ( -25.40)
>consensus
_________CU_____AUUUUCUGCUG_______GUUGCUCUU______GCUGU___UGUUGAAUGUUUUUCGUGUGUUUGCUGUUUGUUGCCAACACACUAAUUACCGCAAUUAAUUAU
.................................................((..........(((.....)))(((((((.((........)).)))))))........)).......... (-13.20 = -13.37 +   0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:23 2006