Locus 4159

Sequence ID	3R_DroMel_CAF1
Location	11,325,168 – 11,325,407
Length	239
Max. P	0.999895

overview

Window 6

Location	11,325,168 – 11,325,287
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.49
Mean single sequence MFE	-30.16
Consensus MFE	-29.36
Energy contribution	-29.32
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.21
Structure conservation index	0.97
SVM decision value	0.23
SVM RNA-class probability	0.642329
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11325168 119 - 27905053
UUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCCU-UUCCGCUCAACUUUUCGCAUUCGGCGCUUGGCAAAUUA
..((((...((((....))))..))))............((((((.(.((((((...........(((...(((...))).-..)))..........))))))).))))))......... ( -28.30)
>DroSec_CAF1 64377 119 - 1
UUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCCU-UUCCGCUCAACUUUUCGCAUUCCGCGUUUGGCAAAUUA
..((((...((((....))))..))))............((((((((.((((((...........(((...(((...))).-..)))..........))))))))))))))......... ( -30.20)
>DroSim_CAF1 60660 119 - 1
UUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCCU-UUCCGCUCAACUUUUCGCAUUCCGCGUUUGGCAAAUUA
..((((...((((....))))..))))............((((((((.((((((...........(((...(((...))).-..)))..........))))))))))))))......... ( -30.20)
>DroEre_CAF1 59720 120 - 1
UUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCCUCUUCCGCUCAACUUUUCGCAUUCCGCGCUUGGCAAAUUA
..((((...((((....))))..))))............((((((((.((((((...........(((...(((...)))....)))..........))))))))))))))......... ( -31.90)
>DroYak_CAF1 61447 119 - 1
UUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUAUGCAAUUUUUGGUCUGGGCUUCCCU-UUCCGCUCAACUUUUCGCAUUCCGCGUUUGGCAAAUUA
..((((...((((....))))..))))............((((((((.((((((...........(((...(((...))).-..)))..........))))))))))))))......... ( -30.20)
>consensus
UUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCCU_UUCCGCUCAACUUUUCGCAUUCCGCGUUUGGCAAAUUA
..((((...((((....))))..))))............((((((((.((((((...........(((...(((...)))....)))..........))))))))))))))......... (-29.36 = -29.32 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	11,325,207 – 11,325,327
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-37.58
Consensus MFE	-37.20
Energy contribution	-37.04
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.39
Structure conservation index	0.99
SVM decision value	3.47
SVM RNA-class probability	0.999268
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11325207 120 - 27905053
UUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCC
...............(((((((((((((....(((((((....(((....)))....)))))))..))))))(((((((.((((((....)))).)).)))))))...)))))))..... ( -37.50)
>DroSec_CAF1 64416 120 - 1
UUGGCCAACUAUUUCGCCUAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCC
..(((((((((((((.....)))))))))...(((((((....(((....)))....))))))).((.....(((((((.((((((....)))).)).))))))).....)))))).... ( -37.90)
>DroSim_CAF1 60699 120 - 1
UUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCC
...............(((((((((((((....(((((((....(((....)))....)))))))..))))))(((((((.((((((....)))).)).)))))))...)))))))..... ( -37.50)
>DroEre_CAF1 59760 120 - 1
UUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCC
...............(((((((((((((....(((((((....(((....)))....)))))))..))))))(((((((.((((((....)))).)).)))))))...)))))))..... ( -37.50)
>DroYak_CAF1 61486 120 - 1
UUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUAUGCAAUUUUUGGUCUGGGCUUCCC
...............(((((((((((((....(((((((....(((....)))....)))))))..))))))(((((((..(((((....)))))...)))))))...)))))))..... ( -37.50)
>consensus
UUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGAAGCGCGGUAAUGUGUCUGCAAUUUUUGGUCUGGGCUUCCC
...............(((((((((((((....(((((((....(((....)))....)))))))..))))))(((((((..(((((....)))))...)))))))...)))))))..... (-37.20 = -37.04 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	11,325,247 – 11,325,367
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-33.84
Consensus MFE	-33.12
Energy contribution	-33.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.02
Structure conservation index	0.98
SVM decision value	4.30
SVM RNA-class probability	0.999864
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11325247 120 + 27905053
UCAAUUUCAAUAAUGUGGAACACUCGAGUGUGAACACAAACGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAU
...(((((.....((((..((((....))))...)))).....((((.((((....)))).)))))))))....((((((((....)))))))).....(((.........)))...... ( -33.90)
>DroSec_CAF1 64456 120 + 1
UCAAUUUCAAUAAUGUGGAACACUCGAGUGUGAACACAAACGUGCUCCGAAAACUAUUUCUAGGCGAAAUAGUUGGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAU
....((((.....((((..((((....))))...))))....((((..((.(((((((((.....))))))))).(((((((....))))))).))...))))...)))).......... ( -32.80)
>DroSim_CAF1 60739 120 + 1
UCAAUUUCAAUAAUGUGGAACACUCGAGUGUGAACACAAACGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAU
...(((((.....((((..((((....))))...)))).....((((.((((....)))).)))))))))....((((((((....)))))))).....(((.........)))...... ( -33.90)
>DroEre_CAF1 59800 119 + 1
UCAAUUUCAAUAAUGUGGAACACUCGAGUGUGAACACAAACGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAG-AGAAAGGCCAAAAAU
....((((.....((((..((((....))))...))))......(((((.((((((((((.....))))))))))(((((((....))))))).....))).))-.)))).......... ( -34.70)
>DroYak_CAF1 61526 120 + 1
UCAAUUUCAAUAAUGUGGAACACUCGAGUGUGAACACAAACGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAU
...(((((.....((((..((((....))))...)))).....((((.((((....)))).)))))))))....((((((((....)))))))).....(((.........)))...... ( -33.90)
>consensus
UCAAUUUCAAUAAUGUGGAACACUCGAGUGUGAACACAAACGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAU
....((((.....((((..((((....))))...))))....((((..((((((((((((.....))))))))))(((((((....))))))).))...))))...)))).......... (-33.12 = -33.32 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	11,325,247 – 11,325,367
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-42.00
Consensus MFE	-41.56
Energy contribution	-41.76
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-4.33
Structure conservation index	0.99
SVM decision value	4.01
SVM RNA-class probability	0.999757
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11325247 120 - 27905053
AUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGA
(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..(((((((....(((....)))....)))))))................ ( -42.20)
>DroSec_CAF1 64456 120 - 1
AUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCCAACUAUUUCGCCUAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGA
(((((((((.........)))))))))(((((((....))))))).(((((((((.....)))))))))...(((((((....(((....)))....)))))))................ ( -40.40)
>DroSim_CAF1 60739 120 - 1
AUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGA
(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..(((((((....(((....)))....)))))))................ ( -42.20)
>DroEre_CAF1 59800 119 - 1
AUUUUUGGCCUUUCU-CUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGA
(((((((((......-..)))))))))(((((((....)))))))((((((((((.....))))))))))..(((((((....(((....)))....)))))))................ ( -43.00)
>DroYak_CAF1 61526 120 - 1
AUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGA
(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..(((((((....(((....)))....)))))))................ ( -42.20)
>consensus
AUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACGUUUGUGUUCACACUCGAGUGUUCCACAUUAUUGAAAUUGA
(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..(((((((....(((....)))....)))))))................ (-41.56 = -41.76 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	11,325,287 – 11,325,407
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-35.48
Consensus MFE	-34.22
Energy contribution	-34.46
Covariance contribution	0.24
Combinations/Pair	1.02
Mean z-score	-3.29
Structure conservation index	0.96
SVM decision value	4.42
SVM RNA-class probability	0.999895
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11325287 120 + 27905053
CGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAUUGGUAUUAUUGAACAGCAAUAAAUUUGACUAGGAACACAG
.(((.(((((((((((((((.....))))))))))(((((((....))))))).))...((((((......((((.....)))).((((((.....)))))).)))).)).))).))).. ( -35.30)
>DroSec_CAF1 64496 120 + 1
CGUGCUCCGAAAACUAUUUCUAGGCGAAAUAGUUGGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAUUGGUAUUAUUGAACAGCAAUAAAUUUGACUAGGAACACAG
.(((.(((((.(((((((((.....))))))))).(((((((....))))))).))...((((((......((((.....)))).((((((.....)))))).)))).)).))).))).. ( -34.40)
>DroSim_CAF1 60779 120 + 1
CGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAUUGGUAUUAUUGAACAGCAAUAAAUUUGACUAGGAACACAG
.(((.(((((((((((((((.....))))))))))(((((((....))))))).))...((((((......((((.....)))).((((((.....)))))).)))).)).))).))).. ( -35.30)
>DroEre_CAF1 59840 119 + 1
CGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAG-AGAAAGGCCAAAAAUUGGUAUUAUUGAACAGCAAUAAAUUUGACUAGGAACACAG
.(((.(((((((((((((((.....))))))))))(((((((....))))))).))...(((((-(.....((((.....)))).((((((.....)))))).)))).)).))).))).. ( -35.40)
>DroYak_CAF1 61566 120 + 1
CGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAUUGGUAUUAUUGAACAGCAAUAAAUUUGACUAGGAACACGG
((((.(((((((((((((((.....))))))))))(((((((....))))))).))...((((((......((((.....)))).((((((.....)))))).)))).)).))).)))). ( -37.00)
>consensus
CGUGCUCCGAAAACUAUUUCUGGGCGAAAUAGUUUGCCAACACAUCUGUUGGCAUCUCCGGCAAAAGAAAGGCCAAAAAUUGGUAUUAUUGAACAGCAAUAAAUUUGACUAGGAACACAG
.(((.(((((((((((((((.....))))))))))(((((((....))))))).))...((((((......((((.....)))).((((((.....)))))).)))).)).))).))).. (-34.22 = -34.46 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	11,325,287 – 11,325,407
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-39.76
Consensus MFE	-39.12
Energy contribution	-39.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-4.23
Structure conservation index	0.98
SVM decision value	4.22
SVM RNA-class probability	0.999840
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11325287 120 - 27905053
CUGUGUUCCUAGUCAAAUUUAUUGCUGUUCAAUAAUACCAAUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACG
..(((((((.........((((((.....)))))).....(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..))))))). ( -39.70)
>DroSec_CAF1 64496 120 - 1
CUGUGUUCCUAGUCAAAUUUAUUGCUGUUCAAUAAUACCAAUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCCAACUAUUUCGCCUAGAAAUAGUUUUCGGAGCACG
..(((((((.........((((((.....)))))).....(((((((((.........)))))))))(((((((....))))))).(((((((((.....)))))))))...))))))). ( -37.90)
>DroSim_CAF1 60779 120 - 1
CUGUGUUCCUAGUCAAAUUUAUUGCUGUUCAAUAAUACCAAUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACG
..(((((((.........((((((.....)))))).....(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..))))))). ( -39.70)
>DroEre_CAF1 59840 119 - 1
CUGUGUUCCUAGUCAAAUUUAUUGCUGUUCAAUAAUACCAAUUUUUGGCCUUUCU-CUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACG
..(((((((..((((((...((((.((((....)))).)))).))))))...(((-(.....))))((((((((....))))))))(((((((((.....)))))))))...))))))). ( -40.80)
>DroYak_CAF1 61566 120 - 1
CCGUGUUCCUAGUCAAAUUUAUUGCUGUUCAAUAAUACCAAUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACG
.((((((((.........((((((.....)))))).....(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..)))))))) ( -40.70)
>consensus
CUGUGUUCCUAGUCAAAUUUAUUGCUGUUCAAUAAUACCAAUUUUUGGCCUUUCUUUUGCCGGAGAUGCCAACAGAUGUGUUGGCAAACUAUUUCGCCCAGAAAUAGUUUUCGGAGCACG
..(((((((.........((((((.....)))))).....(((((((((.........)))))))))(((((((....)))))))((((((((((.....))))))))))..))))))). (-39.12 = -39.32 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:50 2006