Locus 2224

Sequence ID	3R_DroMel_CAF1
Location	6,338,384 – 6,338,521
Length	137
Max. P	0.747398

overview

Window 2

Location	6,338,384 – 6,338,484
Length	100
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	77.68
Mean single sequence MFE	-24.26
Consensus MFE	-14.57
Energy contribution	-14.60
Covariance contribution	0.03
Combinations/Pair	1.25
Mean z-score	-1.66
Structure conservation index	0.60
SVM decision value	0.47
SVM RNA-class probability	0.747398
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6338384 100 + 27905053
--------UUUGACUUUUCAAUUUGCAGUUCAGUUCGUUUGCGAUCUGCCCCUGAUUUUUG-CUCAUUUUGGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
--------.((((....)))).......(((((..((((.((((((((((((.........-........)))))))).....))))))))..)))))........... ( -27.33)
>DroVir_CAF1 109191 92 + 1
UA-----UUUUUUUUUUUCAAUUUGCAGUUCAUUUCUGCUGC----------UGG-CUUUG-CUCAUUUUGAGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
..-----........(((((....(((((........)))))----------.((-(.(((-(.((.(((.......))).))..)))).))).))))).......... ( -18.00)
>DroPse_CAF1 100247 99 + 1
--UUGGACUUGGACUUUUCAAUUUGCUGUUGAUUUCUGCUGUGUUC-------GAGCUCUG-CUCAUUUUAGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
--..((((.(((.....(((((.....)))))......))).))))-------((((...)-)))(((((((((((.............)))))))))))......... ( -26.82)
>DroGri_CAF1 130418 94 + 1
CUU---GAUUUUUUUUUUCAAUUUGCAGUUCAUUUCUGUUGC----------UGG-CUGUG-CUCAUUUUGAGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
..(---(((......(((((..((((((...((((((((.((----------...-..)).-(((.....)))))))))))..)))))).....)))))......)))) ( -17.40)
>DroAna_CAF1 105388 105 + 1
-CU---UUUUUGACUUUUCAAUUUGCAGUUCGUUUGGACUGUCCGGUGGCCCCAAUUGCUGCCUCAUUUUGGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
-..---.....(((.(((((....(((((((....)))))))..((((((..(((((.(((((((.....))))))).)))))..))..)))).)))))..)))..... ( -31.00)
>DroPer_CAF1 106581 93 + 1
--------UUGGACUUUUCAAUUUGCUGUUGAUUUCUGCUGUGUUC-------GAGCUCUG-CUCAUUUUAGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
--------.(((((.(((((..((((...(((((((((((.((...-------((((...)-)))....)).)))))))))))..)))).....)))))..)))))... ( -25.00)
>consensus
________UUUGACUUUUCAAUUUGCAGUUCAUUUCUGCUGCG_UC______UGA_CUCUG_CUCAUUUUGGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCA
........................(((((........))))).......................(((((((((((.............)))))))))))......... (-14.57 = -14.60 +   0.03)

alignment

secondary structure

dotplot

Window 3

Location	6,338,415 – 6,338,521
Length	106
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	81.49
Mean single sequence MFE	-26.21
Consensus MFE	-21.41
Energy contribution	-21.52
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.19
Structure conservation index	0.82
SVM decision value	0.00
SVM RNA-class probability	0.534966
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6338415 106 + 27905053
UGCGAUCUGCCCCUGAUUUUUG-CUCAUUUUGGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUUGAGUUCCGUUCUGCCAUA--U
(((((((((((((.........-........)))))))).....)))))...........((((((....))))))((.((((((((...)))))))).)).....--. ( -28.43)
>DroVir_CAF1 109225 88 + 1
UGC----------UGG-CUUUG-CUCAUUUUGAGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUUGAGUUCCGUUGC---------
...----------.((-(.(((-(.((.(((.......))).))..)))).)))......((((((....))))))...((((((((...))))))))..--------- ( -19.10)
>DroPse_CAF1 100284 93 + 1
UGUGUUC-------GAGCUCUG-CUCAUUUUAGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUUGAGUUCCGUU--GCC------
.......-------((((...)-))).((((((((((.............))))))))))((((((....))))))...((((((((...))))))))--...------ ( -28.82)
>DroGri_CAF1 130454 88 + 1
UGC----------UGG-CUGUG-CUCAUUUUGAGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUUGAGUUCCGUUGC---------
...----------...-((((.-(((.....)))))))........(((((.........((((((....))))))......(((((...))))))))))--------- ( -19.20)
>DroAna_CAF1 105423 109 + 1
UGUCCGGUGGCCCCAAUUGCUGCCUCAUUUUGGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUCGAGUUCCGUUCCACCAUGCCC
.....((((((..(((((.(((((((.....))))))).)))))..))............((((((....))))))...((((((((...)))))))).))))...... ( -32.90)
>DroPer_CAF1 106612 93 + 1
UGUGUUC-------GAGCUCUG-CUCAUUUUAGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUUGAGUUCCGUU--GCC------
.......-------((((...)-))).((((((((((.............))))))))))((((((....))))))...((((((((...))))))))--...------ ( -28.82)
>consensus
UGCG_UC______UGA_CUCUG_CUCAUUUUGGGGCGGAAAUUGUUGCAACGCCCUGAAAUCGUUUAUCAAAACGACAAAAUGGAAUUGAGUUCCGUU_CGCC______
...........................((((((((((.............))))))))))((((((....))))))...((((((((...))))))))........... (-21.41 = -21.52 +   0.11)

alignment

secondary structure

dotplot

Window 4

Location	6,338,415 – 6,338,521
Length	106
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	81.49
Mean single sequence MFE	-24.62
Consensus MFE	-16.94
Energy contribution	-16.50
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-1.30
Structure conservation index	0.69
SVM decision value	-0.04
SVM RNA-class probability	0.514670
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6338415 106 - 27905053
A--UAUGGCAGAACGGAACUCAAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCCCAAAAUGAG-CAAAAAUCAGGGGCAGAUCGCA
.--.(((((((((.((((.....)))).))))))))).........((((((..(((.((((...)))).)))(((((....(((.-......)))))))))))))).. ( -30.10)
>DroVir_CAF1 109225 88 - 1
---------GCAACGGAACUCAAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCUCAAAAUGAG-CAAAG-CCA----------GCA
---------((...((((.....)))).((((((((((((((.....(....)..((((..(.......)..))))))))))))).-)))))-...----------)). ( -19.80)
>DroPse_CAF1 100284 93 - 1
------GGC--AACGGAACUCAAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCCUAAAAUGAG-CAGAGCUC-------GAACACA
------(..--..)((((.....)))).....(((((((....)))))))(((((((((..(.......)..)))))).....(((-(...))))-------))).... ( -23.40)
>DroGri_CAF1 130454 88 - 1
---------GCAACGGAACUCAAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCUCAAAAUGAG-CACAG-CCA----------GCA
---------((..(((((..((((.((.....(((((((....))))))).....)).)))).......))))).(((.....)))-.....-...----------)). ( -18.70)
>DroAna_CAF1 105423 109 - 1
GGGCAUGGUGGAACGGAACUCGAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCCCAAAAUGAGGCAGCAAUUGGGGCCACCGGACA
..(..((((((..(((((..((((.((.....(((((((....))))))).....)).)))).......)))))((((((..((......)).))))))))))))..). ( -32.30)
>DroPer_CAF1 106612 93 - 1
------GGC--AACGGAACUCAAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCCUAAAAUGAG-CAGAGCUC-------GAACACA
------(..--..)((((.....)))).....(((((((....)))))))(((((((((..(.......)..)))))).....(((-(...))))-------))).... ( -23.40)
>consensus
______GGCG_AACGGAACUCAAUUCCAUUUUGUCGUUUUGAUAAACGAUUUCAGGGCGUUGCAACAAUUUCCGCCCCAAAAUGAG_CAGAG_UCA______GA_CACA
..............((((.....))))((((((((((((....)))))).....(((((..(.......)..))))))))))).......................... (-16.94 = -16.50 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:18 2006