Locus 375

Sequence ID	2R_DroMel_CAF1
Location	2,358,607 – 2,358,818
Length	211
Max. P	0.943254

overview

Window 4

Location	2,358,607 – 2,358,722
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.24
Mean single sequence MFE	-30.34
Consensus MFE	-23.40
Energy contribution	-24.08
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.77
SVM decision value	0.68
SVM RNA-class probability	0.820939
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2358607 115 + 20766785
AUAGGCAACAUUUGCCAUGAUAAUACGUAAUAUACAUAACAACCACAGUUAUGCGAGGCCGGGGGCGAUUCCGACCC-----UCAUGCAUAUUGAUGGUAUGCCGAAAAUAGUUCCUCAA
...((((.....))))..................((((((.......)))))).((((..(((((((....)).)))-----))..((((((.....))))))...........)))).. ( -30.40)
>DroSec_CAF1 8087 115 + 1
AUAGGAAACAUUUGCCAUGAUAAUACGUAAUAUACAUAACAACCACAGUUAUGCGAGGCCGGGGGCGAUACCGACCC-----CCAUGCAUAUUGAUGGUAUGCCGAAAAUAGUUCCUCAA
..(((((..((((((((((......)))......((((((.......))))))...))).(((((((....)).)))-----))..((((((.....))))))...))))..)))))... ( -31.50)
>DroSim_CAF1 8203 115 + 1
AUAGGCAACAUUUGCCAUGAUAAUACGUAAUAUACAUAACAACCACAGUUAUGCGAGGCCGGGGGCGAUACCGACCC-----CCAUGCAUAUUGAUGGUAUGCCGAAAAUAGUUCCUCAA
...((((.....))))..................((((((.......)))))).((((..(((((((....)).)))-----))..((((((.....))))))...........)))).. ( -33.40)
>DroEre_CAF1 8307 114 + 1
AUGGGCAACAUUUGCCAUGAUAAUACGUAAUACACAUAACAACCACAGUUAUGCCAGGCCGGAGGCGACUCCGACCCC------AUGCAUAUUGAUGGUAUGCCGAAAAUAGUUCCUCAA
...((((.....((((((..(((((.(((.....((((((.......))))))...((.(((((....))))).))..------.))).)))))))))))))))................ ( -30.90)
>DroYak_CAF1 7676 120 + 1
AAAGGCAACAUUUGCCAUGAUAAUACGUAAUAUACAUAACAAGCACAGUUAUGCGAGGCCGGAGGCAGCUCAAACCCCAUGCCCAUGCAUAUUGAUGGUAUGCCGAAAAUAGUUCCUCAA
...((((.....((((((..(((((.(((.....((((((.......)))))).(.(((.((.((.........))))..)))).))).)))))))))))))))................ ( -25.50)
>consensus
AUAGGCAACAUUUGCCAUGAUAAUACGUAAUAUACAUAACAACCACAGUUAUGCGAGGCCGGGGGCGAUUCCGACCC_____CCAUGCAUAUUGAUGGUAUGCCGAAAAUAGUUCCUCAA
...((((.....((((((..(((((.(((.....((((((.......))))))...((.(((((....))))).)).........))).)))))))))))))))................ (-23.40 = -24.08 +   0.68)

alignment

secondary structure

dotplot

Window 5

Location	2,358,607 – 2,358,722
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.24
Mean single sequence MFE	-34.90
Consensus MFE	-28.36
Energy contribution	-28.64
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-1.95
Structure conservation index	0.81
SVM decision value	1.33
SVM RNA-class probability	0.943254
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2358607 115 - 20766785
UUGAGGAACUAUUUUCGGCAUACCAUCAAUAUGCAUGA-----GGGUCGGAAUCGCCCCCGGCCUCGCAUAACUGUGGUUGUUAUGUAUAUUACGUAUUAUCAUGGCAAAUGUUGCCUAU
..(((((....)))))((((..((((...(((((....-----(((((((........))))))).)))))...))))((((((((.(((........)))))))))))....))))... ( -33.80)
>DroSec_CAF1 8087 115 - 1
UUGAGGAACUAUUUUCGGCAUACCAUCAAUAUGCAUGG-----GGGUCGGUAUCGCCCCCGGCCUCGCAUAACUGUGGUUGUUAUGUAUAUUACGUAUUAUCAUGGCAAAUGUUUCCUAU
...(((((.(((((.......(((((...(((((...(-----(((((((........)))))))))))))...))))).((((((.(((........)))))))))))))).))))).. ( -34.30)
>DroSim_CAF1 8203 115 - 1
UUGAGGAACUAUUUUCGGCAUACCAUCAAUAUGCAUGG-----GGGUCGGUAUCGCCCCCGGCCUCGCAUAACUGUGGUUGUUAUGUAUAUUACGUAUUAUCAUGGCAAAUGUUGCCUAU
..(((((....)))))((((..((((...(((((...(-----(((((((........)))))))))))))...))))((((((((.(((........)))))))))))....))))... ( -35.60)
>DroEre_CAF1 8307 114 - 1
UUGAGGAACUAUUUUCGGCAUACCAUCAAUAUGCAU------GGGGUCGGAGUCGCCUCCGGCCUGGCAUAACUGUGGUUGUUAUGUGUAUUACGUAUUAUCAUGGCAAAUGUUGCCCAU
..(((((....)))))((((..((((...(((((..------.(((((((((....))))))))).)))))...))))((((((((.(((........)))))))))))....))))... ( -38.50)
>DroYak_CAF1 7676 120 - 1
UUGAGGAACUAUUUUCGGCAUACCAUCAAUAUGCAUGGGCAUGGGGUUUGAGCUGCCUCCGGCCUCGCAUAACUGUGCUUGUUAUGUAUAUUACGUAUUAUCAUGGCAAAUGUUGCCUUU
..(((((....)))))((((..(((((.....).))))(((((((((..(((....)))..)))))((((....))))((((((((.(((........)))))))))))))))))))... ( -32.30)
>consensus
UUGAGGAACUAUUUUCGGCAUACCAUCAAUAUGCAUGG_____GGGUCGGAAUCGCCCCCGGCCUCGCAUAACUGUGGUUGUUAUGUAUAUUACGUAUUAUCAUGGCAAAUGUUGCCUAU
..(((((....)))))((((..((((...(((((.........(((((((........))))))).)))))...))))((((((((.(((........)))))))))))....))))... (-28.36 = -28.64 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	2,358,722 – 2,358,818
Length	96
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	84.58
Mean single sequence MFE	-33.65
Consensus MFE	-22.71
Energy contribution	-22.84
Covariance contribution	0.13
Combinations/Pair	1.16
Mean z-score	-1.64
Structure conservation index	0.67
SVM decision value	0.13
SVM RNA-class probability	0.598622
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2358722 96 + 20766785
AGAUAAUAAAUAGAUGCCAAACGCAGUGGCCAGCGCUAGCAGCUCUGCUUUCGGCCAACAUA---------GCGCACUAAACACAGCCAGCUGCU-------G-CUGCUGUUA
..........(((..((((.......))))..(((((((((....)))....(.....).))---------)))).)))...(((((.(((....-------)-))))))).. ( -26.70)
>DroSec_CAF1 8202 99 + 1
AGAUAAUAAAUAGAUGCCAAACGCAGUGGCCAGCGCCAGCAGCUCUGCUUUCGGCCAACAGA---------GCGCACUAAACACAGCCGGCUGCUGC----UG-CUGCUGUUA
...................(((((((..((.((((((.((.((((((...........))))---------))(.......)...)).))).)))))----..-)))).))). ( -32.70)
>DroSim_CAF1 8318 102 + 1
AGAUAAUAAAUAGAUGCCGAACGCAGUGGCCAGCGCCAGCAGCUCUGCUUUCGGCCAACAGA---------GCGCACUAAACACAGCCGGCUGCUGCUG-CUG-CUGCUGUUA
......................((((..((.((((.((((((((..(((((.(.....))))---------))((..........)).)))))))).))-)))-)..)))).. ( -34.80)
>DroEre_CAF1 8421 113 + 1
AGAUAAUAAAUAGCUGCCAAACGCAGUGGCCAGCGCCAUCAGCUCUGGAUUUGGCCAGCGGAGAGCGCUGUGCGCACUAAACACAGCCGGCCGCUGUUAACUGUCCACUGUUA
.((((.(.((((((.(((...(((..(((((((..(((.......)))..))))))))))....(.((((((.........)))))))))).)))))).).))))........ ( -40.40)
>consensus
AGAUAAUAAAUAGAUGCCAAACGCAGUGGCCAGCGCCAGCAGCUCUGCUUUCGGCCAACAGA_________GCGCACUAAACACAGCCGGCUGCUGC____UG_CUGCUGUUA
........(((((.........(((((((((.(((((((((....))))...)))................(.(.......).).)).)))))))))..........))))). (-22.71 = -22.84 +   0.13)

alignment

secondary structure

dotplot

Window 7

Location	2,358,722 – 2,358,818
Length	96
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	84.58
Mean single sequence MFE	-37.88
Consensus MFE	-28.38
Energy contribution	-28.00
Covariance contribution	-0.38
Combinations/Pair	1.17
Mean z-score	-1.76
Structure conservation index	0.75
SVM decision value	0.47
SVM RNA-class probability	0.749139
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2358722 96 - 20766785
UAACAGCAG-C-------AGCAGCUGGCUGUGUUUAGUGCGC---------UAUGUUGGCCGAAAGCAGAGCUGCUAGCGCUGGCCACUGCGUUUGGCAUCUAUUUAUUAUCU
...((((((-(-------(((.((..((.((((.....))))---------...))..))(....)....))))))...))))((((.......))))............... ( -31.90)
>DroSec_CAF1 8202 99 - 1
UAACAGCAG-CA----GCAGCAGCCGGCUGUGUUUAGUGCGC---------UCUGUUGGCCGAAAGCAGAGCUGCUGGCGCUGGCCACUGCGUUUGGCAUCUAUUUAUUAUCU
...((((..-((----(((((.((((((.((((.....))))---------...))))))(....)....)))))))..))))((((.......))))............... ( -38.00)
>DroSim_CAF1 8318 102 - 1
UAACAGCAG-CAG-CAGCAGCAGCCGGCUGUGUUUAGUGCGC---------UCUGUUGGCCGAAAGCAGAGCUGCUGGCGCUGGCCACUGCGUUCGGCAUCUAUUUAUUAUCU
...((((((-.((-(.(((((.....)))))((.....))))---------)))))))((((((.((((.(((((....)).)))..)))).))))))............... ( -39.30)
>DroEre_CAF1 8421 113 - 1
UAACAGUGGACAGUUAACAGCGGCCGGCUGUGUUUAGUGCGCACAGCGCUCUCCGCUGGCCAAAUCCAGAGCUGAUGGCGCUGGCCACUGCGUUUGGCAGCUAUUUAUUAUCU
....((((((.((((..((((((..((((((((.......))))))).)...))))))(((((((.(((......((((....))))))).))))))))))).)))))).... ( -42.30)
>consensus
UAACAGCAG_CA____GCAGCAGCCGGCUGUGUUUAGUGCGC_________UCUGUUGGCCGAAAGCAGAGCUGCUGGCGCUGGCCACUGCGUUUGGCAUCUAUUUAUUAUCU
...((((((..........((.((..((((....))))))))..........))))))((((((.((((.(((((....)).)))..)))).))))))............... (-28.38 = -28.00 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:49 2006