Locus 2197

Sequence ID	3R_DroMel_CAF1
Location	6,273,463 – 6,273,631
Length	168
Max. P	0.994739

overview

Window 0

Location	6,273,463 – 6,273,554
Length	91
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	80.81
Mean single sequence MFE	-19.08
Consensus MFE	-15.37
Energy contribution	-15.23
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.50
Structure conservation index	0.81
SVM decision value	0.50
SVM RNA-class probability	0.759607
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6273463 91 - 27905053
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-CU------UGC------UGUCCC-----UGUCCCC-CAU
..............(((((.((((....))))))).))((((((((...))))))))((((((.....--.)-))------)))------......-----.......-... ( -19.70)
>DroVir_CAF1 40632 96 - 1
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-G--GC-ACUCCUCUGAAUGUCUC---------UCC-CAC
...................((((((..(((........((((((((...)))))))))))..))))))--..-(--((-(.((....)).))))..---------...-... ( -19.20)
>DroWil_CAF1 50443 103 - 1
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CCACCAGCAUGUCC------CCUCUCUCAAUUGUCCAC-CAU
...((((.((....(((((.((((....))))))).))((((((((...))))))))....(((((((--(.....))))))))------......)).)))).....-... ( -22.90)
>DroYak_CAF1 40508 92 - 1
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CCCCU------UGC------UGUCCC-----UGUCUCC-CUU
..............(((((.((((....))))))).))((((((((...))))))))((((((.....--..)))------)))------......-----.......-... ( -19.20)
>DroAna_CAF1 44793 86 - 1
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUGUGUGUC-CU------CUC------CGUCCC-----------A-CA-
.................((((((((..(((........((((((((...)))))))))))..))))))))..-..------...------......-----------.-..- ( -17.30)
>DroPer_CAF1 40396 98 - 1
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-CCGCCAAGUCC------UCUCCC-----UCUCCUGCCCU
........((....((...((((((..(((........((((((((...)))))))))))..))))))--..-.)).....)).------......-----........... ( -16.20)
>consensus
AUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG__CC_CU______UCC______UGUCCC_____UGUCCCC_CAU
...................((((((..(((........((((((((...)))))))))))..))))))............................................ (-15.37 = -15.23 +  -0.14)

alignment

secondary structure

dotplot

Window 1

Location	6,273,482 – 6,273,594
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.33
Mean single sequence MFE	-26.35
Consensus MFE	-24.57
Energy contribution	-24.43
Covariance contribution	-0.14
Combinations/Pair	1.03
Mean z-score	-1.87
Structure conservation index	0.93
SVM decision value	2.51
SVM RNA-class probability	0.994739
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6273482 112 - 27905053
GUAAAUGAAUAAAAUGGCUCGAGCCGCCGAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-CU-----
...(((((.......(((....))).........((((.......))))....))))).((((((..(((........((((((((...)))))))))))..))))))--..-..----- ( -24.90)
>DroPse_CAF1 35118 117 - 1
GUAAAUGAAUAAAAUGGCUCGAGCCGCCGAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-CCGCCAA
..............(((((((......)))..((((((...(((....))).)))))).((((((..(((........((((((((...)))))))))))..))))))--..-..)))). ( -27.50)
>DroWil_CAF1 50468 118 - 1
GUAAAUGAAUAAAAUGGCUCGAGCCGCCAAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CCACCAGCAU
...............(((....)))((.....((((((...(((....))).)))))).((((((..(((........((((((((...)))))))))))..))))))--......)).. ( -26.60)
>DroMoj_CAF1 60520 115 - 1
GUAAAUGAAUAAAAUGGCUCGAGCCGCCGAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-G--AAAA
...............(((....)))..((...((((((...(((....))).)))))).((((((..(((........((((((((...)))))))))))..))))))--.)-)--.... ( -25.40)
>DroAna_CAF1 44805 114 - 1
GUAAAUGAAUAAAAUGGCUCGAGCCGCCGAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUGUGUGUC-CU-----
...............(((....)))(((((..((((((...(((....))).))))))..((((....))))...)))((((((((...)))))))))).(((((....)))-))----- ( -26.20)
>DroPer_CAF1 40417 117 - 1
GUAAAUGAAUAAAAUGGCUCGAGCCGCCGAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG--CC-CCGCCAA
..............(((((((......)))..((((((...(((....))).)))))).((((((..(((........((((((((...)))))))))))..))))))--..-..)))). ( -27.50)
>consensus
GUAAAUGAAUAAAAUGGCUCGAGCCGCCGAAAAACGAUAAAUUCAAUCGAAAAUCGUUACAUGUCAAUGCAUUAAUCGGCCAUAAUCCCAUUAUGGCGCAAGGAUAUG__CC_CC__CAA
...(((((.......(((....))).........((((.......))))....))))).((((((..(((........((((((((...)))))))))))..))))))............ (-24.57 = -24.43 +  -0.14)

alignment

secondary structure

dotplot

Window 2

Location	6,273,514 – 6,273,631
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.23
Mean single sequence MFE	-26.58
Consensus MFE	-23.85
Energy contribution	-23.88
Covariance contribution	0.03
Combinations/Pair	1.03
Mean z-score	-1.51
Structure conservation index	0.90
SVM decision value	0.94
SVM RNA-class probability	0.886388
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6273514 117 + 27905053
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUCGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACGUACG---CUUCUGCAAUGAUAUUUGCACGCA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....)))............((((......)))).(---(...(((((......))))).)). ( -27.60)
>DroGri_CAF1 55341 111 + 1
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUCGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACGUA---------UGCAACGAUAUUUGCACACA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....))).......................((.---------(((((......))))).)). ( -25.40)
>DroWil_CAF1 50506 111 + 1
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUUGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACAUA---------UGCAAUAAUAUUUGCACUCA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....)))..........................---------(((((......))))).... ( -22.00)
>DroMoj_CAF1 60555 111 + 1
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUCGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACGUA---------UGCAACAAUAUUUGCACGCA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....))).......................(..---------(((((......)))))..). ( -26.20)
>DroAna_CAF1 44839 120 + 1
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUCGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACGUACAUGAGUUCUGCAAUGAUAUUUGCACGCA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....))).....((((((.((((......)))).))))))..(((((......))))).... ( -31.20)
>DroPer_CAF1 40454 111 + 1
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUCGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACGUA---------UGCAAUGAUAUUUGCACGCA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....))).......................(..---------(((((......)))))..). ( -27.10)
>consensus
GCCGAUUAAUGCAUUGACAUGUAACGAUUUUCGAUUGAAUUUAUCGUUUUUCGGCGGCUCGAGCCAUUUUAUUCAUUUACGCCCACACGUA_________UGCAAUGAUAUUUGCACGCA
(((((....(((((....)))))(((((.(((....)))...)))))...)))))(((....)))............((((......)))).........(((((......))))).... (-23.85 = -23.88 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:39 2006