Locus 2256

Sequence ID	3L_DroMel_CAF1
Location	6,258,688 – 6,258,860
Length	172
Max. P	0.997311

overview

Window 6

Location	6,258,688 – 6,258,781
Length	93
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-20.46
Consensus MFE	-13.00
Energy contribution	-13.80
Covariance contribution	0.80
Combinations/Pair	1.09
Mean z-score	-1.94
Structure conservation index	0.64
SVM decision value	0.63
SVM RNA-class probability	0.805691
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6258688 93 + 23771897
ACACAAAAAAAA--AGUAAAAAAUGUCGGGAGGUGUGGCCAAUUGUAAAGGCUUGCAAAGC--------AUUUGACACAUUGGAAACAUGUGGUAACAUGCAA
............--.((((...((..(....)..)).(((.........)))))))...((--------(((((.(((((.(....)))))).))).)))).. ( -19.30)
>DroSec_CAF1 25406 81 + 1
ACAAA--------------AAAAUGUCGGGAGGUGUGGCCAAUUGUAAAGGCUGGCAAAGC--------AUUUGACACAUUGGCAACAUGUGGCAACAUGCAA
.....--------------....(((......((((.(((((((((....(((.....)))--------.....))).)))))).))))(((....)))))). ( -20.90)
>DroSim_CAF1 26005 73 + 1
ACAAAAA------------AAAAUGUCGGGAGGUGUGGCCAAUUGUAAAGGCUUGCAAAGC--------AUUUGACACAUUGGCA----------ACAUGCAA
.......------------.............((((.(((((((((....(((.....)))--------.....))).)))))).----------)))).... ( -16.20)
>DroEre_CAF1 25751 99 + 1
ACAAAAAGAAAC----AGAAAAAUGUCGGGAGGUGUGGUCAUUUGUAAAGGCUGGCAAAGCGCAGCCACAUUUGACACAUUGGCAACAUGUGGCAACAUGCAA
............----.......(((((....(((((.(((..(((...(((((((...)).))))))))..))))))))))))).(((((....)))))... ( -26.50)
>DroYak_CAF1 29149 95 + 1
ACAAAAAGAAAACGAGAAAAAAAUGUCAGGAGGUGUGGUCAAUUGUAGAGGCUGGCAAAGC--------AUUUGACACAUUGGCAACAUGUGGCAACAUGCAA
.......................((((((....((..(....)..))....))))))..((--------(((((.(((((.(....)))))).))).)))).. ( -19.40)
>consensus
ACAAAAA_AAA_______AAAAAUGUCGGGAGGUGUGGCCAAUUGUAAAGGCUGGCAAAGC________AUUUGACACAUUGGCAACAUGUGGCAACAUGCAA
.......................((((((...((((((((.........))))..((((...........)))))))).)))))).(((((....)))))... (-13.00 = -13.80 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	6,258,722 – 6,258,821
Length	99
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	75.85
Mean single sequence MFE	-25.92
Consensus MFE	-8.91
Energy contribution	-9.49
Covariance contribution	0.59
Combinations/Pair	1.21
Mean z-score	-2.74
Structure conservation index	0.34
SVM decision value	1.20
SVM RNA-class probability	0.929236
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6258722 99 + 23771897
GGCCAAUUGUAAAGGCUUGCAAAGC--------AUUUGACACAUUGGAAACAUGU----GGUAACAUGCAAAUGUUGCAACGAUACCAUACCACAUUACGAUUGCUAAAUU
(((.((((((((.((((.....)))--------..(((.(((((.(....)))))----)(((((((....)))))))..)))..........).)))))))))))..... ( -25.80)
>DroSec_CAF1 25428 94 + 1
GGCCAAUUGUAAAGGCUGGCAAAGC--------AUUUGACACAUUGGCAACAUGU----GGCAACAUGCAAAUGUUGCAA-----CCAUACCACAUUACGAUUGCUAAAUU
(((.((((((((.((((.....)))--------......(((((.(....)))))----)(((((((....)))))))..-----........).)))))))))))..... ( -28.00)
>DroSim_CAF1 26029 84 + 1
GGCCAAUUGUAAAGGCUUGCAAAGC--------AUUUGACACAUUGGCA--------------ACAUGCAAAUGUUGCAA-----CCAUACCACAUUACGAUUGCUAAAUU
(((.((((((((.((.(((((..((--------(((((.((...((...--------------.))))))))))))))))-----))........)))))))))))..... ( -21.90)
>DroEre_CAF1 25783 101 + 1
GGUCAUUUGUAAAGGCUGGCAAAGCGCAGCCACAUUUGACACAUUGGCAACAUGU----GGCAACAUGCAAAUGUUGCAA-----CCAUGCCACAUUACGUUUGCUAAAU-
.((((..(((...(((((((...)).))))))))..))))...((((((((((((----((((...((((.....)))).-----...))))))))...).)))))))..- ( -36.70)
>DroYak_CAF1 29185 94 + 1
GGUCAAUUGUAGAGGCUGGCAAAGC--------AUUUGACACAUUGGCAACAUGU----GGCAACAUGCAAAUGUUGCAA-----CCUUACCACAUUACGUUGGAUAAAUA
.(((...(((((.((((.....)))--------......(((((.(....)))))----)(((((((....)))))))..-----........).)))))...)))..... ( -23.90)
>DroAna_CAF1 25064 82 + 1
-----------AACGCCGGCAACAC--------AUUUAACAAAUUGGCAACAUGUCGCUGGCAACAUGCAAAUGUUGCAA-----CGGGUUCAGAUCG-----AGUAAAUG
-----------......(....).(--------(((((........(((((((...((((....)).))..)))))))..-----(((.......)))-----..)))))) ( -19.20)
>consensus
GGCCAAUUGUAAAGGCUGGCAAAGC________AUUUGACACAUUGGCAACAUGU____GGCAACAUGCAAAUGUUGCAA_____CCAUACCACAUUACGAUUGCUAAAUU
.......(((((.((((.....)))...................(((.............(((((((....)))))))............)))).)))))........... ( -8.91 =  -9.49 +   0.59)

alignment

secondary structure

dotplot

Window 8

Location	6,258,747 – 6,258,860
Length	113
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	68.39
Mean single sequence MFE	-26.05
Consensus MFE	-7.96
Energy contribution	-8.21
Covariance contribution	0.25
Combinations/Pair	1.20
Mean z-score	-3.27
Structure conservation index	0.31
SVM decision value	2.84
SVM RNA-class probability	0.997311
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6258747 113 + 23771897
AUUUGACACAUUGGAAACAUGU----GGUAACAUGCAAAUGUUGCAACGAUACCAUACCACAUUACGAUUGCUAAAUUAAAAAUGUGGUACA-UUAUGGUACAAUGCCAAUGACUACG
........((((((.....(((----.(((((((....))))))).))).((((((((((((((..((((....))))...)))))))))..-...))))).....))))))...... ( -31.30)
>DroSec_CAF1 25453 108 + 1
AUUUGACACAUUGGCAACAUGU----GGCAACAUGCAAAUGUUGCAA-----CCAUACCACAUUACGAUUGCUAAAUUAAAAAUGUGGUACA-UUAUGGUACAAUGCCAAUGACUGCG
........((((((((...(((----.(((((((....))))))).(-----((((((((((((..((((....))))...)))))))))..-...))))))).))))))))...... ( -35.60)
>DroSim_CAF1 26054 98 + 1
AUUUGACACAUUGGCA--------------ACAUGCAAAUGUUGCAA-----CCAUACCACAUUACGAUUGCUAAAUUAAAAAUGUGGUACA-UUAUGGUACAAUGCCAAUGAGUACG
.....((.((((((((--------------...((((.....))))(-----((((((((((((..((((....))))...)))))))))..-...))))....)))))))).))... ( -30.00)
>DroEre_CAF1 25816 88 + 1
AUUUGACACAUUGGCAACAUGU----GGCAACAUGCAAAUGUUGCAA-----CCAUGCCACAUUACGUUUGCUAAAU-GACUACGAA-CAUAGAUAUUU-------------------
........((((((((((((((----((((...((((.....)))).-----...))))))))...).))))).)))-)........-...........------------------- ( -20.60)
>DroYak_CAF1 29210 100 + 1
AUUUGACACAUUGGCAACAUGU----GGCAACAUGCAAAUGUUGCAA-----CCUUACCACAUUACGUUGGAUAAAUAGAAUAUGAA-AAUA-AUACUUAACAAUACCUA-------G
(((..((((((.(....)))))----.(((((((....)))))))..-----..............))..)))........(((...-.)))-.................-------. ( -18.20)
>DroAna_CAF1 25078 93 + 1
AUUUAACAAAUUGGCAACAUGUCGCUGGCAACAUGCAAAUGUUGCAA-----CGGGUUCAGAUCG-----AGUAAAUGGAAUAUUU-------AUUCUUU-UAAUAUCUU-------G
.............(((((((...((((....)).))..)))))))..-----.((((...((..(-----((((((((...)))))-------))))..)-)...)))).-------. ( -20.60)
>consensus
AUUUGACACAUUGGCAACAUGU____GGCAACAUGCAAAUGUUGCAA_____CCAUACCACAUUACGAUUGCUAAAUUAAAAAUGUG_UACA_AUAUGGUACAAUGCCAA_______G
...........(((.............(((((((....)))))))............))).......................................................... ( -7.96 =  -8.21 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	6,258,747 – 6,258,860
Length	113
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	68.39
Mean single sequence MFE	-24.34
Consensus MFE	-6.85
Energy contribution	-8.10
Covariance contribution	1.25
Combinations/Pair	1.08
Mean z-score	-2.12
Structure conservation index	0.28
SVM decision value	0.50
SVM RNA-class probability	0.760558
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6258747 113 - 23771897
CGUAGUCAUUGGCAUUGUACCAUAA-UGUACCACAUUUUUAAUUUAGCAAUCGUAAUGUGGUAUGGUAUCGUUGCAACAUUUGCAUGUUACC----ACAUGUUUCCAAUGUGUCAAAU
........(((((((.........(-(((((((((((.................)))))))))(((((.(((.(((.....)))))).))))----)))).........))))))).. ( -26.80)
>DroSec_CAF1 25453 108 - 1
CGCAGUCAUUGGCAUUGUACCAUAA-UGUACCACAUUUUUAAUUUAGCAAUCGUAAUGUGGUAUGG-----UUGCAACAUUUGCAUGUUGCC----ACAUGUUGCCAAUGUGUCAAAU
.(((..((((((((.(((((((...-..(((((((((.................))))))))))))-----).(((((((....))))))).----)))...)))))))))))..... ( -32.13)
>DroSim_CAF1 26054 98 - 1
CGUACUCAUUGGCAUUGUACCAUAA-UGUACCACAUUUUUAAUUUAGCAAUCGUAAUGUGGUAUGG-----UUGCAACAUUUGCAUGU--------------UGCCAAUGUGUCAAAU
.(.((.((((((((....((((...-..(((((((((.................))))))))))))-----)((((.....))))...--------------)))))))).))).... ( -27.73)
>DroEre_CAF1 25816 88 - 1
-------------------AAAUAUCUAUG-UUCGUAGUC-AUUUAGCAAACGUAAUGUGGCAUGG-----UUGCAACAUUUGCAUGUUGCC----ACAUGUUGCCAAUGUGUCAAAU
-------------------((((..((((.-...))))..-)))).((((.....((((((((...-----.((((.....))))...))))----)))).))))............. ( -22.50)
>DroYak_CAF1 29210 100 - 1
C-------UAGGUAUUGUUAAGUAU-UAUU-UUCAUAUUCUAUUUAUCCAACGUAAUGUGGUAAGG-----UUGCAACAUUUGCAUGUUGCC----ACAUGUUGCCAAUGUGUCAAAU
.-------..(((((((.((((((.-.((.-.....))..))))))..)))....(((((((((.(-----(.(((.....))))).)))))----))))..))))............ ( -21.60)
>DroAna_CAF1 25078 93 - 1
C-------AAGAUAUUA-AAAGAAU-------AAAUAUUCCAUUUACU-----CGAUCUGAACCCG-----UUGCAACAUUUGCAUGUUGCCAGCGACAUGUUGCCAAUUUGUUAAAU
.-------.((((..((-((.((((-------....))))..))))..-----..)))).(((..(-----(((((((((((((.((....)))))).)))))).))))..))).... ( -15.30)
>consensus
C_______UUGGCAUUGUAAAAUAA_UGUA_CACAUAUUCAAUUUAGCAAUCGUAAUGUGGUAUGG_____UUGCAACAUUUGCAUGUUGCC____ACAUGUUGCCAAUGUGUCAAAU
..........................................................(((((..........(((((((....)))))))...........)))))........... ( -6.85 =  -8.10 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:58 2006