Locus 4710

Sequence ID	2R_DroMel_CAF1
Location	15,426,278 – 15,426,408
Length	130
Max. P	0.795530

overview

Window 9

Location	15,426,278 – 15,426,379
Length	101
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	81.42
Mean single sequence MFE	-31.20
Consensus MFE	-20.91
Energy contribution	-21.97
Covariance contribution	1.06
Combinations/Pair	1.15
Mean z-score	-1.37
Structure conservation index	0.67
SVM decision value	-0.03
SVM RNA-class probability	0.518207
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15426278 101 + 20766785
U-U-UAUAGAUAUAUGUAGAGAGUAGUGCGGAG-GCGG------CUGG--UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCUAG
.-.-............(((..(((((..((.((-((..------...)--))).))((((((((((.(((((..(((....))).))))).)))))))))))))))..))). ( -31.00)
>DroPse_CAF1 270375 99 + 1
G-C------AGCUCUGGCGGCAGCGGUGCGGAGUGCGG------CUCGAUUCUGCGAGUAACAAAAUUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCGGG
(-(------(.(.(((....))).).)))((((((.((------((((......))).((((((((((((((..(((....))).))))))))))))))))))))))).... ( -33.30)
>DroSim_CAF1 210370 102 + 1
U-UAUAUAGAUAUAUGUAGAGAGUAGUGCGGAG-GCGG------GUGG--UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCCAG
.-((((((....))))))(..(((((..((.((-((..------...)--))).))((((((((((.(((((..(((....))).))))).)))))))))))))))..)... ( -30.20)
>DroEre_CAF1 218756 103 + 1
UUUACAUAGAUAUAUAUGGUGAGUGGUGCGGAG-GCGG------GUGG--CAUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCUGG
....((((......))))(..((((..(((...-((..------...)--).)))(((((((((((.(((((..(((....))).))))).)))))))))))))))..)... ( -29.00)
>DroYak_CAF1 226046 109 + 1
UUUAUAAAGAUAUAUAUAGAUAGUAGUGUGGAG-GCGGGUGCGGGUGG--UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCUGG
((((((........)))))).........((((-(.....((((....--.))))(((((((((((.(((((..(((....))).))))).)))))))))))..)))))... ( -29.60)
>DroPer_CAF1 231079 99 + 1
G-C------AGCUCUGUCGGCAGCGGUGCGGAGUGCGG------CUCGAUUCUGCGAGUAACAAAAUUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCGGG
(-(------(.(.(((....))).).)))((((((.((------((((......))).((((((((((((((..(((....))).))))))))))))))))))))))).... ( -34.10)
>consensus
U_U_UAUAGAUAUAUGUAGAGAGUAGUGCGGAG_GCGG______CUGG__UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCUGG
................(((..((((..(((((...((........))...)))))(((((((((((.(((((..(((....))).))))).)))))))))))))))..))). (-20.91 = -21.97 +   1.06)

alignment

secondary structure

dotplot

Window 0

Location	15,426,278 – 15,426,379
Length	101
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	81.42
Mean single sequence MFE	-23.55
Consensus MFE	-17.30
Energy contribution	-17.13
Covariance contribution	-0.17
Combinations/Pair	1.19
Mean z-score	-1.83
Structure conservation index	0.73
SVM decision value	0.60
SVM RNA-class probability	0.795530
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15426278 101 - 20766785
CUAGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA--CCAG------CCGC-CUCCGCACUACUCUCUACAUAUAUCUAUA-A-A
.(((..(((((((((((((((.((.(((((......)).))).)).)))))))))))((.((--....------....-.)).))..))))..)))............-.-. ( -24.10)
>DroPse_CAF1 270375 99 - 1
CCCGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAAAUUUUGUUACUCGCAGAAUCGAG------CCGCACUCCGCACCGCUGCCGCCAGAGCU------G-C
...(((.((.((((((((((((((.(((((......)).))).))))))))))).(((......))))------))..)))))(((.(.(((....))).).)------)-) ( -24.70)
>DroSim_CAF1 210370 102 - 1
CUGGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA--CCAC------CCGC-CUCCGCACUACUCUCUACAUAUAUCUAUAUA-A
.(((..(((((((((((((((.((.(((((......)).))).)).)))))))))))((.((--....------....-.)).))..))))..)))..............-. ( -23.80)
>DroEre_CAF1 218756 103 - 1
CCAGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAUG--CCAC------CCGC-CUCCGCACCACUCACCAUAUAUAUCUAUGUAAA
...((.....(((((((((((.((.(((((......)).))).)).))))))))))).....--))..------..((-....)).........((((......)))).... ( -20.90)
>DroYak_CAF1 226046 109 - 1
CCAGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA--CCACCCGCACCCGC-CUCCACACUACUAUCUAUAUAUAUCUUUAUAAA
...(((.((.(((((((((((.((.(((((......)).))).)).)))))))))))((.(.--....).))....))-.)))............................. ( -22.70)
>DroPer_CAF1 231079 99 - 1
CCCGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAAAUUUUGUUACUCGCAGAAUCGAG------CCGCACUCCGCACCGCUGCCGACAGAGCU------G-C
...(((.((.((((((((((((((.(((((......)).))).))))))))))).(((......))))------))..)))))(((.(.(((....))).).)------)-) ( -25.10)
>consensus
CCAGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA__CCAC______CCGC_CUCCGCACCACUCUCUACAUAUAUCUAUA_A_A
..(((.(((.(((((((((((.((.(((((......)).))).)).)))))))))))...................((.....))...))).)))................. (-17.30 = -17.13 +  -0.17)

alignment

secondary structure

dotplot

Window 1

Location	15,426,311 – 15,426,408
Length	97
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	80.14
Mean single sequence MFE	-31.82
Consensus MFE	-17.49
Energy contribution	-17.68
Covariance contribution	0.20
Combinations/Pair	1.12
Mean z-score	-2.23
Structure conservation index	0.55
SVM decision value	0.51
SVM RNA-class probability	0.765745
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15426311 97 + 20766785
G-G------CUGG--UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCUAGCGAAAUUGCUUACAGGCAAUGCGCAG-------GCA----
.-.------...(--((((((((((((((((.(((((..(((....))).))))).))))))))))).........((...((((((....))))))))))))-------)).---- ( -36.00)
>DroPse_CAF1 270404 99 + 1
G-G------CUCGAUUCUGCGAGUAACAAAAUUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCGGGCCAAAUUGCUUACAGACAAUGCACAG-------GCG----
(-(------((((...(((((....(((.....))).)))))...(((((((.......))))))).......)))))).....((((.((.....))...))-------)).---- ( -27.00)
>DroGri_CAF1 277819 106 + 1
GGGC-------UGCGAGUGUGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUUUGGCCAAAAUUGCUUACAGACAAUGCACAGAAGCAAUGCG----
.(((-------((.(((((.(((((((((((.(((((..(((....))).))))).)))))))))))))))).)))))...(((((((.((.....)).....)))))))...---- ( -36.00)
>DroWil_CAF1 454651 94 + 1
G-----------G--GUUGUGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUUUAGGAGAAAUUGCUUAC---CAUGGCCCAU-------GCAAGAG
(-----------(--((..((((((((((((.(((((..(((....))).))))).)))))))))((((....))))............)---))..))))..-------....... ( -29.10)
>DroYak_CAF1 226081 103 + 1
G-GGUGCGGGUGG--UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCUGGCGAAAUUGCUUACAGGCAAUGCGCAG-------GCA----
.-..........(--((((((((((((((((.(((((..(((....))).))))).))))))))))).........((...((((((....))))))))))))-------)).---- ( -35.80)
>DroPer_CAF1 231108 99 + 1
G-G------CUCGAUUCUGCGAGUAACAAAAUUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCGGGCCAAAUUGCUUACAGACAAUGCACAG-------GCG----
(-(------((((...(((((....(((.....))).)))))...(((((((.......))))))).......)))))).....((((.((.....))...))-------)).---- ( -27.00)
>consensus
G_G______CUCG__UCUGCGGCUAACAAAAGUUGUGCGCAGUCAGUUGACAUAAAUUUUGUUAGCCUACUUCCGGGCGAAAUUGCUUACAGACAAUGCACAG_______GCA____
.................((((((((((((((.(((((..(((....))).))))).)))))))))))................(((...........)))..........))).... (-17.49 = -17.68 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	15,426,311 – 15,426,408
Length	97
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	80.14
Mean single sequence MFE	-25.43
Consensus MFE	-17.45
Energy contribution	-18.12
Covariance contribution	0.67
Combinations/Pair	1.15
Mean z-score	-1.39
Structure conservation index	0.69
SVM decision value	0.24
SVM RNA-class probability	0.648784
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15426311 97 - 20766785
----UGC-------CUGCGCAUUGCCUGUAAGCAAUUUCGCUAGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA--CCAG------C-C
----..(-------(((((.(((((......)))))..))).))).....(((((((((((.((.(((((......)).))).)).)))))))))))((...--...)------)-. ( -28.40)
>DroPse_CAF1 270404 99 - 1
----CGC-------CUGUGCAUUGUCUGUAAGCAAUUUGGCCCGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAAAUUUUGUUACUCGCAGAAUCGAG------C-C
----...-------....((.(((((((..((......(((((....)..))))((((((((((.(((((......)).))).)))))))))).))..))))..))))------)-. ( -23.40)
>DroGri_CAF1 277819 106 - 1
----CGCAUUGCUUCUGUGCAUUGUCUGUAAGCAAUUUUGGCCAAAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCACACUCGCA-------GCCC
----.((..(((((.((.(((((((......)))))....)))).)))))(((((((((((.((.(((((......)).))).)).)))))))))))......)).-------.... ( -27.30)
>DroWil_CAF1 454651 94 - 1
CUCUUGC-------AUGGGCCAUG---GUAAGCAAUUUCUCCUAAAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCACAAC--C-----------C
...((((-------....((....---))..))))............((.(((((((((((.((.(((((......)).))).)).)))))))))))))...--.-----------. ( -21.20)
>DroYak_CAF1 226081 103 - 1
----UGC-------CUGCGCAUUGCCUGUAAGCAAUUUCGCCAGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA--CCACCCGCACC-C
----..(-------(((.(((((((......)))))...)))))).....(((((((((((.((.(((((......)).))).)).)))))))))))((.(.--....).))...-. ( -28.90)
>DroPer_CAF1 231108 99 - 1
----CGC-------CUGUGCAUUGUCUGUAAGCAAUUUGGCCCGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAAAUUUUGUUACUCGCAGAAUCGAG------C-C
----...-------....((.(((((((..((......(((((....)..))))((((((((((.(((((......)).))).)))))))))).))..))))..))))------)-. ( -23.40)
>consensus
____CGC_______CUGUGCAUUGUCUGUAAGCAAUUUCGCCCGGAAGUAGGCUAACAAAAUUUAUGUCAACUGACUGCGCACAACUUUUGUUAGCCGCAGA__CCAG______C_C
..............((((..(((((......)))))..............(((((((((((.((.(((((......)).))).)).)))))))))))))))................ (-17.45 = -18.12 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:25 2006