Locus 5087

Sequence ID	2R_DroMel_CAF1
Location	16,531,218 – 16,531,356
Length	138
Max. P	0.977369

overview

Window 1

Location	16,531,218 – 16,531,323
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.08
Mean single sequence MFE	-38.58
Consensus MFE	-28.43
Energy contribution	-28.74
Covariance contribution	0.31
Combinations/Pair	1.29
Mean z-score	-2.01
Structure conservation index	0.74
SVM decision value	1.79
SVM RNA-class probability	0.977369
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16531218 105 + 20766785
---------CGUAAAUAAUCGAAUAUUGGUGCAGGUACUCGGCAUGGAGUUAACAGCCAGUUGCGAGGGCGGCCACAAGUGGA---CUGGACGCCCUCCAACGCCUGUUUUCCGA---GC
---------................((((.((((((....(((.((.......))))).((((.(((((((.(((........---.))).)))))))))))))))))...))))---.. ( -40.90)
>DroVir_CAF1 23137 113 + 1
AUUAAAUUGUAUACAUACAUGGAU-GGGGUGCAGGUUCUUGGCAUGGAGGUAACAGCCAGUUGCGAGGGCGGUCAAAGAUGGA---CUGGACGCCCUCCAACGCCUGUCUUCCGC---GC
.......((((....))))..(.(-((((.((((((...((((.((.......))))))((((.(((((((..((........---.))..))))))))))))))))).))))))---.. ( -41.20)
>DroGri_CAF1 17024 103 + 1
---------UGUAC-UAUAUACAU-GUGGUGCAGGUUCUUGGCAUGGAGUUAACAACUAGUUGCGAGGGCGGUCAAAGAUGGA---CCGGAAGACCUCCAACGCCAGUUUAUCGC---AC
---------(((((-((((....)-))))))))(((..(((((....(((.....))).((((.((((.(((((.......))---))).....)))))))))))))...)))..---.. ( -33.80)
>DroWil_CAF1 34071 109 + 1
----------GUAAUAAAUCU-AGCUCGAUUUAGGUUUUGGGCAUGGAGUUAACAGCCAGUUGUGAGGGCGGCCAAAAAUGGAAUGCUGGACGCCCUCCAACUCCUGUUUUCCGAACAGC
----------...........-.((((((........)))))).(((((..(((((..(((((.(((((((.(((............))).)))))))))))).))))))))))...... ( -38.10)
>DroMoj_CAF1 17746 104 + 1
---------UGUAUAUACAUGUAU-GAGCUGCAGGUUCUUGGCAUGGAGCUAACAGCUAGUUGUGAGGGCGGUCAGAGGUGGA---CCGGACGCCCUCCAACACCUGUUUAUCGC---GC
---------.(((((.(((.((..-.(((((..((((((......))))))..))))).((((.(((((((.((...((....---)).))))))))))))))).))).))).))---.. ( -40.50)
>DroAna_CAF1 13536 105 + 1
---------AGUAAAUAAUUGCCUAUUGGUUCAGGUACUGGGCAUGGAGUUAACAGCCAGUUGCGAGGGUGGCCAAAAGUGGA---CUGGACGCCCUCCAACGCCUGUUUUCCGA---GC
---------.((((....))))...((((..(((((....(((.((.......))))).((((.(((((((.(((........---.))).))))))))))))))))....))))---.. ( -37.00)
>consensus
_________UGUAAAUAAAUGCAU_GUGGUGCAGGUUCUUGGCAUGGAGUUAACAGCCAGUUGCGAGGGCGGCCAAAAAUGGA___CUGGACGCCCUCCAACGCCUGUUUUCCGA___GC
.........................((((.((((((....(((.((.......))))).((((.(((((((.((..............)).)))))))))))))))))...))))..... (-28.43 = -28.74 +   0.31)

alignment

secondary structure

dotplot

Window 2

Location	16,531,218 – 16,531,323
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.08
Mean single sequence MFE	-33.32
Consensus MFE	-19.42
Energy contribution	-20.48
Covariance contribution	1.06
Combinations/Pair	1.22
Mean z-score	-1.73
Structure conservation index	0.58
SVM decision value	0.69
SVM RNA-class probability	0.824478
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16531218 105 - 20766785
GC---UCGGAAAACAGGCGUUGGAGGGCGUCCAG---UCCACUUGUGGCCGCCCUCGCAACUGGCUGUUAACUCCAUGCCGAGUACCUGCACCAAUAUUCGAUUAUUUACG---------
((---..(((.(((((.((((((((((((.(((.---........))).))))))).)))).).)))))...)))..))((((((..........))))))..........--------- ( -36.50)
>DroVir_CAF1 23137 113 - 1
GC---GCGGAAGACAGGCGUUGGAGGGCGUCCAG---UCCAUCUUUGACCGCCCUCGCAACUGGCUGUUACCUCCAUGCCAAGAACCUGCACCCC-AUCCAUGUAUGUAUACAAUUUAAU
((---(.(((.(((((.((((((((((((..(((---.......)))..))))))).)))).).)))))...))).))).....((.((((....-.....)))).))............ ( -34.90)
>DroGri_CAF1 17024 103 - 1
GU---GCGAUAAACUGGCGUUGGAGGUCUUCCGG---UCCAUCUUUGACCGCCCUCGCAACUAGUUGUUAACUCCAUGCCAAGAACCUGCACCAC-AUGUAUAUA-GUACA---------
((---(((......((((((.((((......(((---((.......))))).....((((....))))...))))))))))......)))))...-.(((((...-)))))--------- ( -28.50)
>DroWil_CAF1 34071 109 - 1
GCUGUUCGGAAAACAGGAGUUGGAGGGCGUCCAGCAUUCCAUUUUUGGCCGCCCUCACAACUGGCUGUUAACUCCAUGCCCAAAACCUAAAUCGAGCU-AGAUUUAUUAC----------
.((((((((.....(((((((((((((((.((((.(......).)))).))))))).)))))(((((.......)).))).....)))...)))))).-)).........---------- ( -35.70)
>DroMoj_CAF1 17746 104 - 1
GC---GCGAUAAACAGGUGUUGGAGGGCGUCCGG---UCCACCUCUGACCGCCCUCACAACUAGCUGUUAGCUCCAUGCCAAGAACCUGCAGCUC-AUACAUGUAUAUACA---------
((---(((...(((((.((((((((((((..(((---.......)))..))))))).)))).).))))).((.....))........))).))..-...............--------- ( -32.40)
>DroAna_CAF1 13536 105 - 1
GC---UCGGAAAACAGGCGUUGGAGGGCGUCCAG---UCCACUUUUGGCCACCCUCGCAACUGGCUGUUAACUCCAUGCCCAGUACCUGAACCAAUAGGCAAUUAUUUACU---------
..---..(((.(((((.((((((((((.(.((((---.......)))).).))))).)))).).)))))...))).((((.................))))..........--------- ( -31.93)
>consensus
GC___GCGGAAAACAGGCGUUGGAGGGCGUCCAG___UCCACCUUUGACCGCCCUCGCAACUGGCUGUUAACUCCAUGCCAAGAACCUGCACCAA_AUGCAAUUAUUUACA_________
.......(((.(((((.((((((((((((..(((..........)))..))))))).)))).).)))))...)))............................................. (-19.42 = -20.48 +   1.06)

alignment

secondary structure

dotplot

Window 3

Location	16,531,249 – 16,531,356
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.06
Mean single sequence MFE	-38.63
Consensus MFE	-26.13
Energy contribution	-26.19
Covariance contribution	0.06
Combinations/Pair	1.16
Mean z-score	-1.66
Structure conservation index	0.68
SVM decision value	1.17
SVM RNA-class probability	0.925898
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16531249 107 + 20766785
GGCAUGGAGUUAACAGCCAGUUGCGAGGGCGGCCACAAGUGGA---CUGGACGCCCUCCAACGCCUGUUUUCCGA---GCGCCAAGCGAACAUGUAAGUG--CCACUGACGCACA-----
(((((((((..(((((...((((.(((((((.(((........---.))).)))))))))))..)))))))))(.---.(((...)))..)......)))--))...........----- ( -40.50)
>DroVir_CAF1 23176 112 + 1
GGCAUGGAGGUAACAGCCAGUUGCGAGGGCGGUCAAAGAUGGA---CUGGACGCCCUCCAACGCCUGUCUUCCGC---GCAAAUAGUGAACAUGUAAGUG--CCUCCGCUGCACCUUAUU
.(((((((((((((((...((((.(((((((..((........---.))..)))))))))))..))))....(((---.......)))..........))--)))))).)))........ ( -42.70)
>DroGri_CAF1 17053 106 + 1
GGCAUGGAGUUAACAACUAGUUGCGAGGGCGGUCAAAGAUGGA---CCGGAAGACCUCCAACGCCAGUUUAUCGC---ACAAAUAGUGGAUAUGUAAGUGUGCCUUGACUAC--------
((((((((((.....))).((((.((((.(((((.......))---))).....)))))))).))....((((.(---((.....))))))).......)))))........-------- ( -30.60)
>DroWil_CAF1 34100 105 + 1
GGCAUGGAGUUAACAGCCAGUUGUGAGGGCGGCCAAAAAUGGAAUGCUGGACGCCCUCCAACUCCUGUUUUCCGAACAGCACAAAGCGAACAUGUAAGUG--UUGCC-------------
(((.(((((..(((((..(((((.(((((((.(((............))).)))))))))))).))))))))))....((.....)).(((((....)))--)))))------------- ( -38.00)
>DroYak_CAF1 13975 99 + 1
GGCAUGGAGUUAACAGCCAGUUGCGAGGGCGGCCACAAGUGGA---CUGGACGCCCUCCAACGCCUGUUUUCCGA---GCGCCAAGCGAACAUGUAAGCA--GCACU-------------
(((.(((((..(((((...((((.(((((((.(((........---.))).)))))))))))..)))))))))).---..)))..((..........)).--.....------------- ( -36.40)
>DroMoj_CAF1 17776 106 + 1
GGCAUGGAGCUAACAGCUAGUUGUGAGGGCGGUCAGAGGUGGA---CCGGACGCCCUCCAACACCUGUUUAUCGC---GCAUCCAGUGAACAUGUAAGUG--GCUCCGCUCCG------U
((..((((((((((((...((((.(((((((.((...((....---)).)))))))))))))..))))...((((---.......)))).........))--))))))..)).------. ( -43.60)
>consensus
GGCAUGGAGUUAACAGCCAGUUGCGAGGGCGGCCAAAAAUGGA___CUGGACGCCCUCCAACGCCUGUUUUCCGA___GCACAAAGCGAACAUGUAAGUG__CCUCCGCU_C________
.(((((.....(((((...((((.(((((((.((..............)).)))))))))))..))))).........((.....))...)))))......................... (-26.13 = -26.19 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	16,531,249 – 16,531,356
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.06
Mean single sequence MFE	-38.37
Consensus MFE	-20.26
Energy contribution	-21.35
Covariance contribution	1.09
Combinations/Pair	1.22
Mean z-score	-1.74
Structure conservation index	0.53
SVM decision value	0.25
SVM RNA-class probability	0.651684
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16531249 107 - 20766785
-----UGUGCGUCAGUGG--CACUUACAUGUUCGCUUGGCGC---UCGGAAAACAGGCGUUGGAGGGCGUCCAG---UCCACUUGUGGCCGCCCUCGCAACUGGCUGUUAACUCCAUGCC
-----.(.((((((((((--.((......)))))).))))))---.)(((.(((((.((((((((((((.(((.---........))).))))))).)))).).)))))...)))..... ( -45.90)
>DroVir_CAF1 23176 112 - 1
AAUAAGGUGCAGCGGAGG--CACUUACAUGUUCACUAUUUGC---GCGGAAGACAGGCGUUGGAGGGCGUCCAG---UCCAUCUUUGACCGCCCUCGCAACUGGCUGUUACCUCCAUGCC
........(((..(((((--..(((...(((.((.....)).---))).)))((((.((((((((((((..(((---.......)))..))))))).)))).).))))..))))).))). ( -41.10)
>DroGri_CAF1 17053 106 - 1
--------GUAGUCAAGGCACACUUACAUAUCCACUAUUUGU---GCGAUAAACUGGCGUUGGAGGUCUUCCGG---UCCAUCUUUGACCGCCCUCGCAACUAGUUGUUAACUCCAUGCC
--------........((((........(((((((.....))---).))))...(((.((((((((.....(((---((.......))))).))))((((....)))))))).))))))) ( -27.90)
>DroWil_CAF1 34100 105 - 1
-------------GGCAA--CACUUACAUGUUCGCUUUGUGCUGUUCGGAAAACAGGAGUUGGAGGGCGUCCAGCAUUCCAUUUUUGGCCGCCCUCACAACUGGCUGUUAACUCCAUGCC
-------------((((.--.............((.....)).....(((.(((((.((((((((((((.((((.(......).)))).))))))).)))))..)))))...))).)))) ( -37.30)
>DroYak_CAF1 13975 99 - 1
-------------AGUGC--UGCUUACAUGUUCGCUUGGCGC---UCGGAAAACAGGCGUUGGAGGGCGUCCAG---UCCACUUGUGGCCGCCCUCGCAACUGGCUGUUAACUCCAUGCC
-------------(((((--(((..........))..)))))---).(((.(((((.((((((((((((.(((.---........))).))))))).)))).).)))))...)))..... ( -38.10)
>DroMoj_CAF1 17776 106 - 1
A------CGGAGCGGAGC--CACUUACAUGUUCACUGGAUGC---GCGAUAAACAGGUGUUGGAGGGCGUCCGG---UCCACCUCUGACCGCCCUCACAACUAGCUGUUAGCUCCAUGCC
.------.(((((.((((--.........)))).........---......(((((.((((((((((((..(((---.......)))..))))))).)))).).))))).)))))..... ( -39.90)
>consensus
________G_AGCGGAGG__CACUUACAUGUUCACUUGGUGC___GCGGAAAACAGGCGUUGGAGGGCGUCCAG___UCCACCUUUGACCGCCCUCGCAACUGGCUGUUAACUCCAUGCC
...............................................(((.(((((.((((((((((((..(((..........)))..))))))).)))).).)))))...)))..... (-20.26 = -21.35 +   1.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:12 2006