Locus 9427

Sequence ID	3R_DroMel_CAF1
Location	24,975,253 – 24,975,489
Length	236
Max. P	0.929671

overview

Window 0

Location	24,975,253 – 24,975,345
Length	92
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	77.33
Mean single sequence MFE	-20.27
Consensus MFE	-14.81
Energy contribution	-14.53
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-1.66
Structure conservation index	0.73
SVM decision value	1.20
SVM RNA-class probability	0.929671
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24975253 92 + 27905053
UCAUAUCAUCUUUUUAC-----CAUA--UCCUUGUCCAA-UCCAGACCUUUCUGAGGACGCCAUCAUGGCCCUAAAUCUGCCCACGGGCAUUCCGUUCGU
.................-----....--.....((((..-..((((....)))).))))(((.....)))........((((....)))).......... ( -17.80)
>DroVir_CAF1 1965 96 + 1
----AUUAUUCCAUAAGAAUUGAAUCUACUCUCAACCCAUUACAGAUCUGUCCGAGGAUGCCAUCAUGGCGCUGAACUUGCCCACCGGCAUACCGUUUGU
----...............((((........))))......(((((((.....))(((((((....(((.((.......)))))..))))).)).))))) ( -15.40)
>DroSec_CAF1 2350 92 + 1
ACAUAUCAUCAUUUUAC-----CAUG--UCCUUGUCCUA-UCCAGACCUCUCUGAGGACGCCAUCAUGGCCCUGAACCUGCCCACGGGCAUUCCGUUCGU
................(-----((((--....((((((.-..((((....))))))))))....)))))....((((.((((....))))....)))).. ( -25.40)
>DroEre_CAF1 2478 92 + 1
GCAUAUCAUCCUUUUAC-----CAUA--ACCUCGUCCUA-UCCAGACCUCUCUGAGGACGCCAUCAUGGCCCUGAACCUGCCCACGGGCAUUCCGUUCGU
................(-----(((.--....((((((.-..((((....)))))))))).....))))....((((.((((....))))....)))).. ( -23.40)
>DroYak_CAF1 2456 92 + 1
GCGUAUCAUCCUUUUAC-----CAUA--AUCUUGUCCUA-UCCAGACCUCUCUGAGGACGCCAUCAUGGCCCUGAACCUGCCCACGGGCAUUCCGUUCGU
................(-----(((.--((..((((((.-..((((....))))))))))..)).))))....((((.((((....))))....)))).. ( -22.50)
>DroMoj_CAF1 1965 89 + 1
---GAUCAUUUUUAAAG-----UAUCCACU--UCAUCCA-UACAGAUCUGUCUGAGGAUGCCAUCAUGGCCCUGAACUUGCCCACUGGCAUACCGUUUGU
---..............-----........--.((..(.-..((((....)))).((((((((....(((.........)))...)))))).)))..)). ( -17.10)
>consensus
_CAUAUCAUCCUUUUAC_____CAUA__ACCUUGUCCUA_UCCAGACCUCUCUGAGGACGCCAUCAUGGCCCUGAACCUGCCCACGGGCAUUCCGUUCGU
..........................................((((....)))).(((((((.....)))........((((....))))....)))).. (-14.81 = -14.53 +  -0.28)

alignment

secondary structure

dotplot

Window 1

Location	24,975,253 – 24,975,345
Length	92
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	77.33
Mean single sequence MFE	-26.67
Consensus MFE	-17.44
Energy contribution	-18.17
Covariance contribution	0.72
Combinations/Pair	1.20
Mean z-score	-1.50
Structure conservation index	0.65
SVM decision value	0.60
SVM RNA-class probability	0.796280
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24975253 92 - 27905053
ACGAACGGAAUGCCCGUGGGCAGAUUUAGGGCCAUGAUGGCGUCCUCAGAAAGGUCUGGA-UUGGACAAGGA--UAUG-----GUAAAAAGAUGAUAUGA
...........((((((((.(........).)))))..)))(((((((((....))))).-..))))....(--(((.-----((......)).)))).. ( -21.80)
>DroVir_CAF1 1965 96 - 1
ACAAACGGUAUGCCGGUGGGCAAGUUCAGCGCCAUGAUGGCAUCCUCGGACAGAUCUGUAAUGGGUUGAGAGUAGAUUCAAUUCUUAUGGAAUAAU----
......((.((((((((((((.......)).))))..)))))))).........(((((((.((((((((......))))))))))))))).....---- ( -26.70)
>DroSec_CAF1 2350 92 - 1
ACGAACGGAAUGCCCGUGGGCAGGUUCAGGGCCAUGAUGGCGUCCUCAGAGAGGUCUGGA-UAGGACAAGGA--CAUG-----GUAAAAUGAUGAUAUGU
..((((....((((....)))).))))...((((((.....(((((((((....))))..-.))))).....--))))-----))............... ( -27.40)
>DroEre_CAF1 2478 92 - 1
ACGAACGGAAUGCCCGUGGGCAGGUUCAGGGCCAUGAUGGCGUCCUCAGAGAGGUCUGGA-UAGGACGAGGU--UAUG-----GUAAAAGGAUGAUAUGC
..((((....((((....)))).))))...((((((((..((((((((((....))))..-.))))))..))--))))-----))............... ( -33.80)
>DroYak_CAF1 2456 92 - 1
ACGAACGGAAUGCCCGUGGGCAGGUUCAGGGCCAUGAUGGCGUCCUCAGAGAGGUCUGGA-UAGGACAAGAU--UAUG-----GUAAAAGGAUGAUACGC
..((((....((((....)))).))))...((((((((...(((((((((....))))..-.)))))...))--))))-----))............... ( -28.50)
>DroMoj_CAF1 1965 89 - 1
ACAAACGGUAUGCCAGUGGGCAAGUUCAGGGCCAUGAUGGCAUCCUCAGACAGAUCUGUA-UGGAUGA--AGUGGAUA-----CUUUAAAAAUGAUC---
......(((((.((.((((.(........).)))).((..(((((.((((....))))..-.))))).--.)))))))-----))............--- ( -21.80)
>consensus
ACGAACGGAAUGCCCGUGGGCAGGUUCAGGGCCAUGAUGGCGUCCUCAGAGAGGUCUGGA_UAGGACAAGAA__UAUG_____GUAAAAGGAUGAUAUG_
..((((....((((....)))).))))...(((.....)))(((((((((....))))....)))))................................. (-17.44 = -18.17 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	24,975,274 – 24,975,382
Length	108
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	74.37
Mean single sequence MFE	-31.31
Consensus MFE	-23.01
Energy contribution	-23.18
Covariance contribution	0.17
Combinations/Pair	1.28
Mean z-score	-1.24
Structure conservation index	0.74
SVM decision value	1.01
SVM RNA-class probability	0.899032
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24975274 108 + 27905053
--------UCCUUGUCCAA-UCCAGACCUUUCUGAGGACGCCAUCAUGGCCCUAAAUCUGCCCACGGGCAUUCCGUUCGUCUACGAGCUGGACGAGAACUUCAAGCCGGUGGUGUCC
--------...........-..((((....)))).((((((((((..(((........((((....)))).((((((((....))))).)))............))))))))))))) ( -38.20)
>DroVir_CAF1 1987 111 + 1
---UA---CUCUCAACCCAUUACAGAUCUGUCCGAGGAUGCCAUCAUGGCGCUGAACUUGCCCACCGGCAUACCGUUUGUAUACGAGCUGGAUGAGAACUUCAAGCCCGUUGUAUCC
---..---....((((.......((.((((((((.(((((((....(((.((.......)))))..))))).))(((((....)))))))))).))).))........))))..... ( -26.76)
>DroGri_CAF1 697 114 + 1
---UAUUGUUGUUAACCUCGCACAGAUCUCUCGGAGGAUGCCAUCAUGAAUCUGAACUUGCCAACUGGCAUUCCUUUUGUCUAUGAACUCGAUGAAAACUUCAAGCCAGUUGUCUCC
---................((((((((.((...((((...)).))..)))))))....)))((((((((.....(((..((.........))..))).......))))))))..... ( -21.80)
>DroWil_CAF1 1917 116 + 1
GACAAUUGGCUUUUAACUU-UCUAGAUCUCUCUGAGGAUGCUAUUAUGGCUCUGAAUCUGCCCACUGGUAUCCCAUUCGUUUAUGAGUUGGAUGAAAACUUCAAGCCUGUGGUGUCC
((((...(((((.......-............((.((((((((....(((.........)))...))))))))))((((((((.....))))))))......))))).....)))). ( -29.40)
>DroMoj_CAF1 1983 108 + 1
---CA---CU--UCAUCCA-UACAGAUCUGUCUGAGGAUGCCAUCAUGGCCCUGAACUUGCCCACUGGCAUACCGUUUGUCUACGAGCUGGACGAGAACUUCAAGCCCGUGGUAUCC
---..---..--.......-..((((....)))).(((((((((...(((..((((..((((....)))).....((((((((.....))))))))...)))).))).))))))))) ( -32.60)
>DroAna_CAF1 2309 98 + 1
------------------U-UUUAGAUCUCUCUGAGGACGCCAUCAUGGCUCUGAACCUGCCCACGGGCAUCCCGUUCGUUUACGAGCUGGACGAGAACUUCAAGCCCGUGGUGUCG
------------------.-((((((....))))))((((((((...((((.((((..((((....))))(((.(((((....))))).))).......)))))))).)))))))). ( -39.10)
>consensus
____A___CU_UUAACCCA_UACAGAUCUCUCUGAGGAUGCCAUCAUGGCUCUGAACCUGCCCACUGGCAUACCGUUCGUCUACGAGCUGGACGAGAACUUCAAGCCCGUGGUGUCC
......................((((....)))).(((((((((...(((..((((..((((....)))).....((((((((.....))))))))...)))).))).))))))))) (-23.01 = -23.18 +   0.17)

alignment

secondary structure

dotplot

Window 3

Location	24,975,382 – 24,975,489
Length	107
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	75.32
Mean single sequence MFE	-36.45
Consensus MFE	-28.57
Energy contribution	-27.98
Covariance contribution	-0.58
Combinations/Pair	1.15
Mean z-score	-1.26
Structure conservation index	0.78
SVM decision value	1.13
SVM RNA-class probability	0.919263
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24975382 107 + 27905053
AUGCAGUUCCUCGGCGACGAGGAGACCGUGAAGAAGGCCAUCGAGGCUGUGGCCGCCCAGGGCAAGGCCAAGUAAGCA--CGCAGGCCAC------ACCUCAUG-AGAAUCC---ACUC
......(((((((....)))))))..(((((.(..((((..((..(((.((((((((...)))..)))))....))).--))..))))..------.).)))))-.......---.... ( -40.10)
>DroGri_CAF1 811 87 + 1
AUGCAGUUCCUCGGCGACGAGGAGACCGUGAAGAAGGCCAUCGAAGCUGUCGCUGCCCAGGGCAAGGCCAAGUAAAUC--CA---UCUA-------AUC--------------------
.(((..(((((((....)))))))...........((((.....(((....)))(((...)))..))))..)))....--..---....-------...-------------------- ( -27.10)
>DroEre_CAF1 2607 110 + 1
AUGCAGUUCCUCGGCGACGAGGAGACUGUGAAGAAGGCCAUCGAGGCUGUGGCUGCCCAGGGCAAGGCCAAGUAAGCA--GGCAGGCUAGCG----CCCUCAUGGAGAAUUC---ACCC
..(((((((((((....)))))).)))))...(((..((((.((((((.((((((((...)))..)))))....))).--(((........)----)))))))))....)))---.... ( -44.20)
>DroYak_CAF1 2585 108 + 1
AUGCAGUUCCUCGGCGACGAGGAGACUGUGAAGAAGGCCAUCGAGGCGGUGGCUGCCCAGGGCAAGGCCAAGUAAGCA--CGCUGGCCAG------ACCGCAUGGAGAAUCC---ACUC
..(((((((((((....)))))).))))).............((((((((...((((...)))).(((((.((.....--.)))))))..------))))).(((.....))---)))) ( -43.70)
>DroMoj_CAF1 2091 88 + 1
AUGCAGUUCCUUGGCGACGAGGAGACAGUCAAGAAGGCCAUCGAAGCUGUUGCUGCCCAGGGCAAGGCCAAGUAAACGCUAA-UCUCUA------------------------------
..((..((.(((((((((..(....).)))......(((.....(((....)))......)))...)))))).))..))...-......------------------------------ ( -26.30)
>DroAna_CAF1 2407 115 + 1
AUGCAGUUCCUCGGCGACGAGGAGACCGUGAAGAAGGCCAUUGAGGCUGUCGCCGCCCAGGGCAAGGCCAAGUAAGCU--AG-AGGCUAUCUACAUAUAUCAAU-GGAAUCCAACAUCC
......(((((((....)))))))...((...((...(((((((((((...(((......)))..))))..((((((.--..-..)))...))).....)))))-))..))..)).... ( -37.30)
>consensus
AUGCAGUUCCUCGGCGACGAGGAGACCGUGAAGAAGGCCAUCGAGGCUGUGGCUGCCCAGGGCAAGGCCAAGUAAGCA__CG_AGGCUA_______ACCUCAUG_AGAAUCC___AC_C
.(((..(((((((....)))))))...........((((.....(((....)))(((...)))..))))..)))............................................. (-28.57 = -27.98 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:28 2006