Locus 692

Sequence ID	2L_DroMel_CAF1
Location	2,010,824 – 2,010,948
Length	124
Max. P	0.987801

overview

Window 1

Location	2,010,824 – 2,010,922
Length	98
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	72.85
Mean single sequence MFE	-19.83
Consensus MFE	-15.30
Energy contribution	-15.63
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.77
SVM decision value	2.05
SVM RNA-class probability	0.986684
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2010824 98 + 22407834
----AAAAUC-UAAGUUUACU----UAAAAAAAA-------AG-AACAAAAAAUGUAG--UAUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
----......-((((....))----)).......-------..-...........(((--(((........(((((.......)))))....((((((.....)))))).)))))). ( -20.30)
>DroVir_CAF1 20281 96 + 1
----AAAAGAAGUAA----------AAAUAAAAU-------AGAAAAAUAAACUUUAAUAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
----......((((.----------.........-------.((......(((((........)))))...(((((.......))))).)).((((((.....))))))..)))).. ( -17.10)
>DroPse_CAF1 33756 114 + 1
AUAUAAAAAC-AGAAUUCAUCGUAUUAACAGAAAUAUUAUUAAAAAACAAAAUUUCAC--UUCAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
..........-............................................(((--(.((((((((.((..((((((....))))))...))....)))).)))))))).... ( -19.20)
>DroGri_CAF1 47716 95 + 1
----AUAA-AAUUGU----------AUUGAAAAU-------ACAAAAAUAAUCGAGAUAAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
----....-..((((----------((.....))-------))))......(((((.((((((.((.....))..))))))..))))).....((.((((((....)))))).)).. ( -21.70)
>DroEre_CAF1 25481 99 + 1
----AGA-ACACUAGUUUACC----UAAAUAAAA-------AAGAAAAAAAAAGUCCG--UAUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
----...-.((((((...(((----((.......-------.................--..))))).)).(((((.......)))))....((((((.....)))))))))).... ( -19.67)
>DroYak_CAF1 29826 97 + 1
----AAAAAAAUUAG-CAACC----AAA--AAAA-------AUGAAAAAAAAACUUAG--UAUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
----.......((((-((...----...--....-------..((......((((((.--..))))))...(((((.......))))).)).((((((.....))))))..)))))) ( -21.00)
>consensus
____AAAAAAAUUAG_U_ACC____AAAAAAAAA_______AAAAAAAAAAAAUUUAG__UACAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAA
................................................................(((.((.(((((.......)))))....((((((.....)))))))).))).. (-15.30 = -15.63 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	2,010,824 – 2,010,922
Length	98
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	72.85
Mean single sequence MFE	-17.56
Consensus MFE	-12.20
Energy contribution	-12.20
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-0.84
Structure conservation index	0.69
SVM decision value	-0.02
SVM RNA-class probability	0.523911
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2010824 98 - 22407834
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA--CUACAUUUUUUGUU-CU-------UUUUUUUUA----AGUAAACUUA-GAUUUU----
......(.(((((.......))))).)..(((((.......))))).(((((.....--...........)))-))-------.....((((----((....))))-))....---- ( -16.19)
>DroVir_CAF1 20281 96 - 1
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAUUAUUAAAGUUUAUUUUUCU-------AUUUUAUUU----------UUACUUCUUUU----
......(.(((((.......))))).)..(((((.......)))))(((((...((((.....)))).....))))-------)........----------...........---- ( -13.10)
>DroPse_CAF1 33756 114 - 1
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUGAA--GUGAAAUUUUGUUUUUUAAUAAUAUUUCUGUUAAUACGAUGAAUUCU-GUUUUUAUAU
((((((((((((..((((.(((....)))(((((.......))))))))).)))).)--))(((((.(((((....))))).))))).)))))....(((((....-...))))).. ( -21.50)
>DroGri_CAF1 47716 95 - 1
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAUUUAUCUCGAUUAUUUUUGU-------AUUUUCAAU----------ACAAUU-UUAU----
......(.(((((.......))))).)...((((...(((((..((.....)).)))))..)))).......((((-------((.....))----------))))..-....---- ( -17.50)
>DroEre_CAF1 25481 99 - 1
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA--CGGACUUUUUUUUUCUU-------UUUUAUUUA----GGUAAACUAGUGU-UCU----
..((((((.((.((.((((((....(...(((((.......)))))..)..((....--.))..............-------....)))))----)))...)))))))-)..---- ( -18.30)
>DroYak_CAF1 29826 97 - 1
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA--CUAAGUUUUUUUUUCAU-------UUUU--UUU----GGUUG-CUAAUUUUUUU----
((((((..((((((((.((.((....)))).))))))....((..(((.......))--)..))............-------....--..)----)..))-)))).......---- ( -18.80)
>consensus
UUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAAA__CUAAAUUUUUUUUUUCU_______UUUUUUUUA____GGU_A_CUAAUGUUUUU____
......(.(((((.......))))).)..(((((.......)))))....................................................................... (-12.20 = -12.20 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	2,010,849 – 2,010,948
Length	99
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	84.49
Mean single sequence MFE	-28.10
Consensus MFE	-26.00
Energy contribution	-25.50
Covariance contribution	-0.50
Combinations/Pair	1.05
Mean z-score	-2.60
Structure conservation index	0.93
SVM decision value	2.09
SVM RNA-class probability	0.987801
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2010849 99 + 22407834
AG-AACAAAAAAUGUAG----UAUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUAGAACCUCUAUGGG
..-.........(((((----(...((((...(((((.......))))).....((.((((((....)))))).))))))))))))((((((.....)))))). ( -29.10)
>DroVir_CAF1 20301 102 + 1
AGAAAAAUAAACUUUAAUA--AUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGUUGAGAA
...................--....((((((((((((.......))))).....((.((((((....)))))).)).............)))))))........ ( -26.90)
>DroGri_CAF1 47735 102 + 1
ACAAAAAUAAUCGAGAUAA--AUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCCGGUGAU
.........((((.((...--.)).((((((((((((.......))))).....((.((((((....)))))).)).............))))))).))))... ( -27.60)
>DroEre_CAF1 25506 100 + 1
AAGAAAAAAAAAGUCCG----UAUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUAGAACCUCUAUGAG
...............((----((.(((((((((((((.......))))).....((.((((((....)))))).)).............)))))))).)))).. ( -28.90)
>DroYak_CAF1 29849 100 + 1
AUGAAAAAAAAACUUAG----UAUAGGUUCUACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUAGAACCUCUAUGAG
............((((.----...(((((((((((((.......))))).....((.((((((....)))))).)).............))))))))...)))) ( -27.00)
>DroMoj_CAF1 19288 104 + 1
AAAAAAAAAAAAGGUCACACCGACAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCACUGCGUC
.............(((.....))).((((((((((((.......))))).....((.((((((....)))))).)).............)))))))........ ( -29.10)
>consensus
AAAAAAAAAAAAGUUAG____UACAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUAGAACCUCUAUGAG
.........................((((((((((((.......))))).....((.((((((....)))))).)).............)))))))........ (-26.00 = -25.50 +  -0.50)

alignment

secondary structure

dotplot

Window 4

Location	2,010,849 – 2,010,948
Length	99
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	84.49
Mean single sequence MFE	-26.23
Consensus MFE	-25.08
Energy contribution	-24.83
Covariance contribution	-0.25
Combinations/Pair	1.09
Mean z-score	-1.25
Structure conservation index	0.96
SVM decision value	0.19
SVM RNA-class probability	0.626303
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2010849 99 - 22407834
CCCAUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA----CUACAUUUUUUGUU-CU
.......((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))...----..............-.. ( -24.90)
>DroVir_CAF1 20301 102 - 1
UUCUCAACGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAU--UAUUAAAGUUUAUUUUUCU
........(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))....--................... ( -25.70)
>DroGri_CAF1 47735 102 - 1
AUCACCGGGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGAU--UUAUCUCGAUUAUUUUUGU
.(((((((((((...((((((........)))).))((((((.((.((....)))).)))))).)))))))))))........--................... ( -27.10)
>DroEre_CAF1 25506 100 - 1
CUCAUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA----CGGACUUUUUUUUUCUU
.((....((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))...----..))............. ( -25.40)
>DroYak_CAF1 29849 100 - 1
CUCAUAGAGGUUCUAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA----CUAAGUUUUUUUUUCAU
.......((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))...----................. ( -24.90)
>DroMoj_CAF1 19288 104 - 1
GACGCAGUGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUGUCGGUGUGACCUUUUUUUUUUUU
.((((...(((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))).....))))................ ( -29.40)
>consensus
CUCACAGAGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUAGAACCUAUA____CUAACUUUUUUUUUUCU
.......((((((((.(((((........)))))(((((.......)))))....(((((.......)))))))))))))........................ (-25.08 = -24.83 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:04 2006