Locus 260

Sequence ID 3R_DroMel_CAF1
Location 1,020,714 – 1,020,926
Length 212
Max. P 0.968558
window451 window452 window453 window454

overview

Window 1

Location 1,020,714 – 1,020,809
Length 95
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 74.00
Mean single sequence MFE -28.65
Consensus MFE -22.62
Energy contribution -22.32
Covariance contribution -0.30
Combinations/Pair 1.26
Mean z-score -1.30
Structure conservation index 0.79
SVM decision value 1.39
SVM RNA-class probability 0.949268
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1020714 95 + 27905053
----------AGUUCUACAUGCAUUCAAGAGGCGGCUCCCUGUAAAGUAAAGGAGCC-U-GGUCCAAAAAUUCCGAACUCCAAUCGCG-AACGAUCGGCGAGCGGGGG-----
----------.(..(((...((.........))((((((.(........).))))))-)-))..).....(((((..(.((.((((..-..)))).)).)..))))).----- ( -23.80)
>DroGri_CAF1 80317 104 + 1
--------UUAGUUUUCAAUGUAUACAAUAGACGACCCCCUAUAAAGUAAGGGGGCC-UUUUUCCAAAAAUUCCGAAAGCUAAUCACGAGAUGAUCAGCAAACGGGGGCUGAU
--------(((((((((..((....))......(.((((((........)))))).)-................)))))))))..........((((((........)))))) ( -26.20)
>DroEre_CAF1 68394 96 + 1
---------UAGUUUUAUAUGCAUUUAAGAGGCGGCGCCCUGUAAAGUAAGGGCGCC-U-GGUCCAAAAAUUCCGAACUCCAAUCGCG-AACGAUCGGCGAGCGGGGG-----
---------..(((((.((......)).)))))((((((((........))))))))-.-..........(((((..(.((.((((..-..)))).)).)..))))).----- ( -32.40)
>DroYak_CAF1 70171 105 + 1
UUCAACAUCUAGUUUUAUAUGCAUUAAAGAGGCGGCUCCCUGUAAAGUAAGGAAGCC-U-AGUCCAAAAAUUCCGAACUCCAAUCGCG-AACGAUCGACGAGCGGGGG-----
(((........(((((............)))))((((.(((........))).))))-.-..............)))((((..(((((-(....))).)))..)))).----- ( -23.20)
>DroMoj_CAF1 65459 98 + 1
--------GUGAAUGUAAAUGUAUUAUAUAGACGACUCCCUAUGAAGUAAGGGAGUC-U-UUUCCAAAAAUUCCGAACGCUAAUCGCA-G-AGAUCAGCGAGCGGGGGUU---
--------((..((((((.....))))))..))((((((((........))))))))-.-..........(((((..((((.(((...-.-.))).))))..)))))...--- ( -30.90)
>DroAna_CAF1 65709 100 + 1
UU------AUAAUAUCAAAUGUAUUUAUGAGACGGCCCCCUGUUAAGUAAGGGGGCCUU-GGUCCAAAAAUUCCGAACCCUGAUCGCA-GGCGACCAGUGAGCGGGGG-----
..------..............((((.((.(((((((((((........))))))))..-.))))).))))......(((((.((((.-((...)).)))).))))).----- ( -35.40)
>consensus
_________UAGUUUUAAAUGCAUUAAAGAGACGGCUCCCUGUAAAGUAAGGGAGCC_U_GGUCCAAAAAUUCCGAACUCCAAUCGCG_AACGAUCAGCGAGCGGGGG_____
..............................(((((((((((........))))))))....)))......(((((..(.((.((((.....)))).)).)..)))))...... (-22.62 = -22.32 +  -0.30) 

alignment

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secondary structure

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dotplot

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Window 2

Location 1,020,714 – 1,020,809
Length 95
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 74.00
Mean single sequence MFE -33.48
Consensus MFE -30.03
Energy contribution -27.98
Covariance contribution -2.05
Combinations/Pair 1.58
Mean z-score -3.27
Structure conservation index 0.90
SVM decision value 1.63
SVM RNA-class probability 0.968558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1020714 95 - 27905053
-----CCCCCGCUCGCCGAUCGUU-CGCGAUUGGAGUUCGGAAUUUUUGGACC-A-GGCUCCUUUACUUUACAGGGAGCCGCCUCUUGAAUGCAUGUAGAACU----------
-----...(((..(.(((((((..-..))))))).)..))).((((..(((..-.-((((((((........))))))))...))).))))............---------- ( -31.10)
>DroGri_CAF1 80317 104 - 1
AUCAGCCCCCGUUUGCUGAUCAUCUCGUGAUUAGCUUUCGGAAUUUUUGGAAAAA-GGCCCCCUUACUUUAUAGGGGGUCGUCUAUUGUAUACAUUGAAAACUAA--------
.((((...(((...(((((((((...)))))))))...)))......((((....-((((((((........)))))))).)))).........)))).......-------- ( -35.00)
>DroEre_CAF1 68394 96 - 1
-----CCCCCGCUCGCCGAUCGUU-CGCGAUUGGAGUUCGGAAUUUUUGGACC-A-GGCGCCCUUACUUUACAGGGCGCCGCCUCUUAAAUGCAUAUAAAACUA---------
-----...(((..(.(((((((..-..))))))).)..))).((((..(((..-.-((((((((........))))))))...))).)))).............--------- ( -34.70)
>DroYak_CAF1 70171 105 - 1
-----CCCCCGCUCGUCGAUCGUU-CGCGAUUGGAGUUCGGAAUUUUUGGACU-A-GGCUUCCUUACUUUACAGGGAGCCGCCUCUUUAAUGCAUAUAAAACUAGAUGUUGAA
-----...(((..(..((((((..-..))))))..)..)))(((.(((((...-.-((((((((........))))))))((.........))........))))).)))... ( -29.70)
>DroMoj_CAF1 65459 98 - 1
---AACCCCCGCUCGCUGAUCU-C-UGCGAUUAGCGUUCGGAAUUUUUGGAAA-A-GACUCCCUUACUUCAUAGGGAGUCGUCUAUAUAAUACAUUUACAUUCAC--------
---.....(((..((((((((.-.-...))))))))..)))......((((..-.-((((((((........)))))))).))))....................-------- ( -33.90)
>DroAna_CAF1 65709 100 - 1
-----CCCCCGCUCACUGGUCGCC-UGCGAUCAGGGUUCGGAAUUUUUGGACC-AAGGCCCCCUUACUUAACAGGGGGCCGUCUCAUAAAUACAUUUGAUAUUAU------AA
-----...(((..(.(((((((..-..))))))).)..))).((((.(((((.-..((((((((........))))))))))).)).))))..............------.. ( -36.50)
>consensus
_____CCCCCGCUCGCCGAUCGUC_CGCGAUUAGAGUUCGGAAUUUUUGGACC_A_GGCUCCCUUACUUUACAGGGAGCCGCCUCUUAAAUACAUUUAAAACUA_________
........(((..(.(((((((.....))))))).)..)))...............((((((((........))))))))................................. (-30.03 = -27.98 +  -2.05) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,020,744 – 1,020,847
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.11
Mean single sequence MFE -30.85
Consensus MFE -17.17
Energy contribution -16.98
Covariance contribution -0.19
Combinations/Pair 1.35
Mean z-score -1.97
Structure conservation index 0.56
SVM decision value 1.00
SVM RNA-class probability 0.897038
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1020744 103 - 27905053
GUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUGACA-------CCCCCGCUCGCCGAUCGUU-CGCGAUUGGAG-------UUCGGAAUUUUUGGACC-A-GGCUCCUUUACUUUACA
((..(((((((.(((((.((....)).)))))......-------...(((..(.(((((((..-..))))))).)-------..)))............-.-.....)))))))..)). ( -28.10)
>DroVir_CAF1 73521 108 - 1
GUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUAACAAAAAACCCCCGUUCGCUGAUC----UUCGAUCGGCG-------CUCGGAAUUUUUGGAAAUA-GACUCCCUUACUUUAUA
((..(((((((.(((((.((....)).)))))......((((((....(((..((((((((----...))))))))-------..)))..))))))......-.....)))))))..)). ( -31.80)
>DroGri_CAF1 80349 112 - 1
GUAUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUUAACAUCAGCCCCCGUUUGCUGAUCAUCUCGUGAUUAGCU-------UUCGGAAUUUUUGGAAAAA-GGCCCCCUUACUUUAUA
(((.(((((((.(((((.((....)).)))))............(((.(((...(((((((((...))))))))).-------..)))....(((....)))-)))..))))))).))). ( -33.30)
>DroWil_CAF1 74570 110 - 1
GUAUAGUGAGGACAUUGCUGCUGACACCAAAGAUAUAA-------AUCUAAGCCCCCGUUCGUU-GGUUAUUGAAGCCAAAUGAUCGGAAUUUUUGGAAA-A-GGCUCCCUUACUUUAUA
(((.(((((((.....(((.......((((((((....-------))))......(((.(((((-((((.....)))).))))).))).....))))...-.-)))..))))))).))). ( -27.20)
>DroMoj_CAF1 65491 105 - 1
GUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUAAU----AACCCCCGCUCGCUGAUCU-C-UGCGAUUAGCG-------UUCGGAAUUUUUGGAAA-A-GACUCCCUUACUUCAUA
....(((((((.(((((.((....)).))))).......----.....(((..((((((((.-.-...))))))))-------..)))............-.-.....)))))))..... ( -29.20)
>DroAna_CAF1 65743 104 - 1
GUCUAGUGAGGGCAUUGCUGCUGACACCAAAGAUAUUA-------CCCCCGCUCACUGGUCGCC-UGCGAUCAGGG-------UUCGGAAUUUUUGGACC-AAGGCCCCCUUACUUAACA
((..((((((((....(((..((...((((((((....-------...(((..(.(((((((..-..))))))).)-------..))).))))))))..)-).))).))))))))..)). ( -35.50)
>consensus
GUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUAA_______CCCCCGCUCGCUGAUCGUC_UGCGAUUAGCG_______UUCGGAAUUUUUGGAAA_A_GGCUCCCUUACUUUAUA
((..(((((((.(((((.((....)).))))).......................(((((((.....)))))))..................................)))))))..)). (-17.17 = -16.98 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,020,809 – 1,020,926
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.51
Mean single sequence MFE -35.72
Consensus MFE -22.49
Energy contribution -21.97
Covariance contribution -0.53
Combinations/Pair 1.13
Mean z-score -1.56
Structure conservation index 0.63
SVM decision value 0.25
SVM RNA-class probability 0.652087
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1020809 117 - 27905053
UGGCCACUUUUGCUUGAGGUGAG-CGCGCAUUCCAACACUCUACCUUCCUUGUCUUGGGGAGCAGAAAUGUUCAAUGAACGUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUGACA--
(((.((((((.....))))))((-((.(((.(((..((((..((...(((......)))(((((....))))).......))..)))).)))...)))))))....))).........-- ( -29.90)
>DroVir_CAF1 73589 119 - 1
UGGCUGCGGCCGCAUAAGGUUGC-GCAAACUGCCAUAACUCGAUCUUCCUUGUCUUGGGGAGCAGAAAUGUCCAAUGAACGUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUAACA
(((((((((((......))))))-)......))))...............(((((((((.(((((.(((((((.....((.....))..))))))).)))))..).)))).))))..... ( -37.00)
>DroGri_CAF1 80421 119 - 1
AAGCGACGGCUGCUUGAGUUGCC-GCAACUUGCCAGCAAUCGACCUUCCUUGUCUUGGGGAGCAGAAAUGUCCAAUGAACGUAUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUUAAC
...(((..((((...((((((..-.))))))..))))..)))........(((((((((.(((((.(((((((.....((.....))..))))))).)))))..).)))).))))..... ( -36.50)
>DroWil_CAF1 74642 117 - 1
UAGCAUUUUUUGCUUAAGGUUCG-GCUGCAUUCCAUCACUCUAUCUUCCUUGUCUUGGGGAGCAGAAAUGUUCAAUGAACGUAUAGUGAGGACAUUGCUGCUGACACCAAAGAUAUAA--
.((((.....))))...((((((-((.(((.(((.(((((((..((((((......)))))).))).((((((...))))))...)))))))...))).))))).)))..........-- ( -36.60)
>DroMoj_CAF1 65557 119 - 1
UGACUGUCGGCGCUUAAGGUCUCUGGCAUUUGCCAACGAUCGUCCUUCCUUGUCUUGGGGAGCAGAAAUGUUCAAUGAACGUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUAAU-
....(((((((((....((((..((((....))))..))))(((((..(((((.(((..(((((....)))))..))))))...))..)))))...)).))))))).............- ( -40.40)
>DroAna_CAF1 65809 117 - 1
AAGCGAAAUUUUCAUGAGGUUGG-CUGAAAUGCCGAUACUCUACCUUCCUUGUCUUGGGGAGCAGAAAUGUCCAAUGAACGUCUAGUGAGGGCAUUGCUGCUGACACCAAAGAUAUUA--
...............((((((((-(......)))))).))).........(((((((((.(((((.(((((((.....((.....))..))))))).)))))..).)).))))))...-- ( -33.90)
>consensus
UAGCGACGGUUGCUUAAGGUUCC_GCAACAUGCCAACACUCGACCUUCCUUGUCUUGGGGAGCAGAAAUGUCCAAUGAACGUCUAGUGAGGACAUUGCUGCUGACACCAAUGAUAUAA__
..................................................(((((((((.(((((.(((((((.....((.....))..))))))).)))))..).)))).))))..... (-22.49 = -21.97 +  -0.53) 

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 09:38:55 2006