Locus 6512

Sequence ID	3R_DroMel_CAF1
Location	17,165,271 – 17,165,391
Length	120
Max. P	0.996982

overview

Window 3

Location	17,165,271 – 17,165,364
Length	93
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	78.56
Mean single sequence MFE	-27.77
Consensus MFE	-20.28
Energy contribution	-20.45
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.05
Structure conservation index	0.73
SVM decision value	0.12
SVM RNA-class probability	0.595274
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17165271 93 + 27905053
CAUGCGCAGGAUCAGCGC------AGCGCUCUGAACUCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACUAAAGUCGA----ACAUAUAUAUCUGGCUA
..(((((.......))))------)..((((........)))).(((.((((((....)))))).....((((....)))).----...........)))... ( -28.20)
>DroPse_CAF1 73082 83 + 1
CAUGCGCAGGAUCAGCGCAGGAGCAGCGCUCUGAACUCUGAGCCCCGACUGAGCCGCAGCUCAGACCUCGA--------------------GACCUCUGGCCG
..(((((.......)))))((..(((.(.(((((..(((((((..((.......))..)))))))..)).)--------------------)).).))).)). ( -29.40)
>DroSec_CAF1 74530 77 + 1
CAUGCGCAGGAUCAGCGC------AGCGCUCUGAACUCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACU--------------------AUCUGGCUA
...((((.......))))------(((((((........)))).....((((((....))))))..........--------------------.....))). ( -23.90)
>DroEre_CAF1 65627 93 + 1
CAUGCGCAGGAUCAGCGC------AGCGCUCUGAACUCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACUAAAGUCGA----ACAUAUAUAUCUGGCCA
..(((((.......))))------)..((((........)))).(((.((((((....)))))).....((((....)))).----...........)))... ( -28.20)
>DroYak_CAF1 93139 97 + 1
CAUGCGCAGGAUCAGCGC------AGCCCUCUGAACUCUGAGCCCCAACUGAGCCGCUGCUCAGAGCUCUGACUAAAGUCGAACGAACAUAUAUAUCUGGCUA
...((((.......))))------((((....((.((((((((..(.........)..)))))))).))((((....)))).................)))). ( -27.50)
>DroPer_CAF1 84968 83 + 1
CAUGCGCAGGAUCAGCGCAGGAGCAGCGCUCUGAACUCUGAGCCCCGACUGAGCCGCAGCUCAGACCUCGA--------------------GACCUCUGGCCG
..(((((.......)))))((..(((.(.(((((..(((((((..((.......))..)))))))..)).)--------------------)).).))).)). ( -29.40)
>consensus
CAUGCGCAGGAUCAGCGC______AGCGCUCUGAACUCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACU_________________UAUAUCUGGCCA
...((((.......)))).......((((((........)))).....((((((....))))))...................................)).. (-20.28 = -20.45 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	17,165,271 – 17,165,364
Length	93
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	78.56
Mean single sequence MFE	-36.15
Consensus MFE	-31.04
Energy contribution	-30.98
Covariance contribution	-0.06
Combinations/Pair	1.04
Mean z-score	-1.71
Structure conservation index	0.86
SVM decision value	1.16
SVM RNA-class probability	0.923648
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17165271 93 - 27905053
UAGCCAGAUAUAUAUGU----UCGACUUUAGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGAGUUCAGAGCGCU------GCGCUGAUCCUGCGCAUG
..(((((.........(----(((((....))))))((((...((((((.(((.....((((.....)))).)))))))------))...))))))).))... ( -33.50)
>DroPse_CAF1 73082 83 - 1
CGGCCAGAGGUC--------------------UCGAGGUCUGAGCUGCGGCUCAGUCGGGGCUCAGAGUUCAGAGCGCUGCUCCUGCGCUGAUCCUGCGCAUG
..(((((.((((--------------------..(((.((((((((.((((...)))).)))))))).)))..(((((.......)))))))))))).))... ( -41.90)
>DroSec_CAF1 74530 77 - 1
UAGCCAGAU--------------------AGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGAGUUCAGAGCGCU------GCGCUGAUCCUGCGCAUG
..(((((..--------------------.(((.(((.(((((((..((((...))))..))))))).)))..((((..------.))))))).))).))... ( -27.60)
>DroEre_CAF1 65627 93 - 1
UGGCCAGAUAUAUAUGU----UCGACUUUAGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGAGUUCAGAGCGCU------GCGCUGAUCCUGCGCAUG
..(((((.........(----(((((....))))))((((...((((((.(((.....((((.....)))).)))))))------))...))))))).))... ( -33.30)
>DroYak_CAF1 93139 97 - 1
UAGCCAGAUAUAUAUGUUCGUUCGACUUUAGUCAGAGCUCUGAGCAGCGGCUCAGUUGGGGCUCAGAGUUCAGAGGGCU------GCGCUGAUCCUGCGCAUG
.((((..................(((....))).(((((((((((..((((...))))..)))))))))))....))))------((((.......))))... ( -38.70)
>DroPer_CAF1 84968 83 - 1
CGGCCAGAGGUC--------------------UCGAGGUCUGAGCUGCGGCUCAGUCGGGGCUCAGAGUUCAGAGCGCUGCUCCUGCGCUGAUCCUGCGCAUG
..(((((.((((--------------------..(((.((((((((.((((...)))).)))))))).)))..(((((.......)))))))))))).))... ( -41.90)
>consensus
UAGCCAGAUAUA_________________AGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGAGUUCAGAGCGCU______GCGCUGAUCCUGCGCAUG
..(((((...........................(((.(((((((..((((...))))..))))))).)))..(((((.......)))))....))).))... (-31.04 = -30.98 +  -0.06)

alignment

secondary structure

dotplot

Window 5

Location	17,165,301 – 17,165,391
Length	90
Sequences	4
Columns	96
Reading direction	forward
Mean pairwise identity	82.92
Mean single sequence MFE	-22.20
Consensus MFE	-15.80
Energy contribution	-17.68
Covariance contribution	1.87
Combinations/Pair	1.05
Mean z-score	-3.37
Structure conservation index	0.71
SVM decision value	2.78
SVM RNA-class probability	0.996982
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17165301 90 + 27905053
UCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACUAAAGUCGA----ACAUAUAUAUCUGGCUAUAGCCAG--UCAUACACUUACACAAUAUA
..((((......((((((....)))))).....((((....)))).----.....(((..(((((....)))))--..)))..))))......... ( -22.40)
>DroSec_CAF1 74560 70 + 1
UCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACU--------------------AUCUGGCUAUAGCC------AUACACUUACACAAUAUA
..((((......((((((....))))))..........--------------------...((((....)))------)....))))......... ( -14.80)
>DroEre_CAF1 65657 92 + 1
UCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACUAAAGUCGA----ACAUAUAUAUCUGGCCACAGCCAGAGCUAUACACUUACACAAUAUA
....(((.....((((((....)))))).....((((....)))).----.........((((((....))))))))).................. ( -24.80)
>DroYak_CAF1 93169 96 + 1
UCUGAGCCCCAACUGAGCCGCUGCUCAGAGCUCUGACUAAAGUCGAACGAACAUAUAUAUCUGGCUAUAGCCAGAGCUAUACACUUACACAAUAUA
..((((......((((((....))))))(((((((.(((.(((((................))))).))).))))))).....))))......... ( -26.79)
>consensus
UCUGAGCCCCAACUGAGCCGCUGCUCAGACCUCCGACUAAAGUCGA____ACAUAUAUAUCUGGCUAUAGCCAG__CUAUACACUUACACAAUAUA
..((((......((((((....)))))).....((((....))))..............((((((....))))))........))))......... (-15.80 = -17.68 +   1.87)

alignment

secondary structure

dotplot

Window 6

Location	17,165,301 – 17,165,391
Length	90
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	82.92
Mean single sequence MFE	-29.77
Consensus MFE	-20.70
Energy contribution	-21.20
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.73
Structure conservation index	0.70
SVM decision value	1.93
SVM RNA-class probability	0.983100
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17165301 90 - 27905053
UAUAUUGUGUAAGUGUAUGA--CUGGCUAUAGCCAGAUAUAUAUGU----UCGACUUUAGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGA
............(((((((.--(((((....))))).))))))).(----(((((....))))))..(((((((..((((...))))..))))))) ( -32.90)
>DroSec_CAF1 74560 70 - 1
UAUAUUGUGUAAGUGUAU------GGCUAUAGCCAGAU--------------------AGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGA
((((((.....))))))(------((((((......))--------------------)))))....(((((((..((((...))))..))))))) ( -20.20)
>DroEre_CAF1 65657 92 - 1
UAUAUUGUGUAAGUGUAUAGCUCUGGCUGUGGCCAGAUAUAUAUGU----UCGACUUUAGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGA
............(((((((..((((((....))))))))))))).(----(((((....))))))..(((((((..((((...))))..))))))) ( -33.00)
>DroYak_CAF1 93169 96 - 1
UAUAUUGUGUAAGUGUAUAGCUCUGGCUAUAGCCAGAUAUAUAUGUUCGUUCGACUUUAGUCAGAGCUCUGAGCAGCGGCUCAGUUGGGGCUCAGA
........(...(((((((..((((((....)))))))))))))...)(((((((....))).))))(((((((..((((...))))..))))))) ( -33.00)
>consensus
UAUAUUGUGUAAGUGUAUAG__CUGGCUAUAGCCAGAUAUAUAUGU____UCGACUUUAGUCGGAGGUCUGAGCAGCGGCUCAGUUGGGGCUCAGA
((((((.....)))))).....(((((....)))))...............................(((((((..((((...))))..))))))) (-20.70 = -21.20 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:11 2006