Locus 6224

Sequence ID	X_DroMel_CAF1
Location	15,826,361 – 15,826,677
Length	316
Max. P	0.994655

overview

Window 6

Location	15,826,361 – 15,826,481
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-20.63
Consensus MFE	-18.90
Energy contribution	-19.57
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.92
SVM decision value	0.14
SVM RNA-class probability	0.603072
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826361 120 + 22224390
UUAUGGAAUACUUAUCGAUAUUCUUACAGUACUGGAAAACUUUUUCAUAUCGAUUUAUUUUUCUGCGUAUACAGAACGUACUUUCGUUUCAUUGUUGUCCAAAAAAGAUAAUAAUAUUAU
..(((((((((..((((((((.....((....))((((....))))))))))))......(((((......))))).))).))))))...(((((((((.......)))))))))..... ( -20.10)
>DroSec_CAF1 5229 120 + 1
UUAUGGAAUACUUAUCGAUAUUCUUAUAGUACUGGAAAACUUUUUCAUAUCGAUUUAUUUUUCUGCGUAUACAGAACGUACUUUCCUUUCAUUGUAUUCCAAAAAAGAUAAUAUUAUUAU
...((((((((..((((((((......(((........))).....))))))))......(((((......))))).................))))))))................... ( -20.90)
>DroSim_CAF1 5018 120 + 1
UUAUGGAAUACUUAUCGAUAUUCUUAUAGUACUGGAAAACUUUUUCAUAUCGAUUUAUUUUUCUGCGUAUACAGAACGUACUUUCCUUUCAUUGUAUUCCAAAAAAGAUAAUAUUAUUAU
...((((((((..((((((((......(((........))).....))))))))......(((((......))))).................))))))))................... ( -20.90)
>consensus
UUAUGGAAUACUUAUCGAUAUUCUUAUAGUACUGGAAAACUUUUUCAUAUCGAUUUAUUUUUCUGCGUAUACAGAACGUACUUUCCUUUCAUUGUAUUCCAAAAAAGAUAAUAUUAUUAU
...((((((((..((((((((......(((........))).....))))))))......(((((......))))).................))))))))................... (-18.90 = -19.57 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	15,826,361 – 15,826,481
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-23.37
Consensus MFE	-23.10
Energy contribution	-23.77
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.99
SVM decision value	1.66
SVM RNA-class probability	0.970795
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826361 120 - 22224390
AUAAUAUUAUUAUCUUUUUUGGACAACAAUGAAACGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAAGUUUUCCAGUACUGUAAGAAUAUCGAUAAGUAUUCCAUAA
...................((((..((......((....))...((((((....))))))......((((((((.....(((........)))......))))))))..))..))))... ( -21.10)
>DroSec_CAF1 5229 120 - 1
AUAAUAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAAGUUUUCCAGUACUAUAAGAAUAUCGAUAAGUAUUCCAUAA
...................((((((((.................((((((....))))))......((((((((.....(((........)))......))))))))..))))))))... ( -24.50)
>DroSim_CAF1 5018 120 - 1
AUAAUAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAAGUUUUCCAGUACUAUAAGAAUAUCGAUAAGUAUUCCAUAA
...................((((((((.................((((((....))))))......((((((((.....(((........)))......))))))))..))))))))... ( -24.50)
>consensus
AUAAUAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAAGUUUUCCAGUACUAUAAGAAUAUCGAUAAGUAUUCCAUAA
...................((((((((.................((((((....))))))......((((((((.....(((........)))......))))))))..))))))))... (-23.10 = -23.77 +   0.67)

alignment

secondary structure

dotplot

Window 8

Location	15,826,401 – 15,826,521
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.83
Mean single sequence MFE	-20.32
Consensus MFE	-19.76
Energy contribution	-19.48
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-1.23
Structure conservation index	0.97
SVM decision value	0.66
SVM RNA-class probability	0.814751
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826401 120 - 22224390
UAGUGACACAUUACUUGCAGUUGUAAAUAACCGCAAGUAUAUAAUAUUAUUAUCUUUUUUGGACAACAAUGAAACGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAA
(((((......(((((((.((((....)))).))))))).....))))).(((((((.(((.....))).)))((....))...((((((....)))))).........))))....... ( -20.80)
>DroSec_CAF1 5269 120 - 1
UAGUGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAUAUAAUAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAA
...........(((((((.((((....)))).)))))))........((((.(((((((((.....))..))))))).))))..((((((....)))))).................... ( -18.80)
>DroSim_CAF1 5058 120 - 1
UAGUGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAUAUAAUAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAA
...........(((((((.((((....)))).)))))))........((((.(((((((((.....))..))))))).))))..((((((....)))))).................... ( -18.80)
>DroEre_CAF1 5775 120 - 1
UAGCGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAUAUAAAAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAA
...(((.....(((((((.((((....)))).)))))))........((((.(((((((((.....))..))))))).))))..((((((....)))))).......))).......... ( -20.20)
>DroYak_CAF1 5071 120 - 1
UAGCGACACAUUACUUGCAGUUGUAAAUAACCGCAAGUAUACAAAAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAA
..(((......(((((((.((((....)))).)))))))((((((..((((.(((((((((.....))..))))))).))))..)).))))..)))........................ ( -23.00)
>consensus
UAGUGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAUAUAAUAAUAUUAUCUUUUUUGGAAUACAAUGAAAGGAAAGUACGUUCUGUAUACGCAGAAAAAUAAAUCGAUAUGAAAAA
...(((.....(((((((.((((....)))).)))))))........((((.(((((((((.....))..))))))).))))..((((((....)))))).......))).......... (-19.76 = -19.48 +  -0.28)

alignment

secondary structure

dotplot

Window 9

Location	15,826,481 – 15,826,601
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.17
Mean single sequence MFE	-24.08
Consensus MFE	-18.83
Energy contribution	-18.39
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-2.02
Structure conservation index	0.78
SVM decision value	0.77
SVM RNA-class probability	0.845812
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826481 120 + 22224390
AUACUUGCGGUUAUUUACAACUGCAAGUAAUGUGUCACUAAUUUUUAGUGAAAAUAACACAAAAUACGACUUGUACGGCAAAUAAGUAUACGAGGCAAUCACGAUAAAUAAAAAACCGUG
.(((((((((((......))))))))))).((((((((((.....))))))......))))........((((((..((......)).)))))).....((((.............)))) ( -28.12)
>DroSec_CAF1 5349 120 + 1
AUACUUGCGGUUAUUUACAACUGCAAAUAAUGUGUCACUAAUUUUUAGUGAAAAUAGCACAAAAUACGACUUGCACGGCAAAUAAGUAUACGAGGCAAUCACGAUAAAUAAAAAACCGUG
....((((((((......))))))))....((((((((((.....)))))).....((.....((((...((((...))))....)))).....))...))))................. ( -22.20)
>DroSim_CAF1 5138 120 + 1
AUACUUGCGGUUAUUUACAACUGCAAAUAAUGUGUCACUAAUUUUUAGUGAAAAUAGCACGAAAUACGACUUGCACGGCAAAUAAGUAUACGAGGCAAUCACGAUAAAUAAAAAACCGUG
....((((((((......))))))))....((((((((((.....)))))).....((.((..((((...((((...))))....)))).))..))...))))................. ( -22.40)
>DroEre_CAF1 5855 119 + 1
AUACUUGCGGUUAUUUACAACUGCAAAUAAUGUGUCGCUAAUUUGUAGUGAAAAUAACCCAAAAUACGACUUGCACGGCAUAUAAAUAUAAGAGGC-AUCACUAUAAAUAAAAAACCGUG
....(((.((((((((...(((((((((...(.....)..)))))))))..)))))))))))...........(((((..............((..-....))............))))) ( -23.17)
>DroYak_CAF1 5151 120 + 1
AUACUUGCGGUUAUUUACAACUGCAAGUAAUGUGUCGCUAAACUUUAGUGAAAAUAACAGAAAAUACGACUUGCACGGCAAAUAAAUAUAAGAGGCAAUCACGAUAAAUAAAAAACCGUG
.(((((((((((......))))))))))).(((.((((((.....)))))).....)))..............(((((........(((..((.....))...))).........))))) ( -24.53)
>consensus
AUACUUGCGGUUAUUUACAACUGCAAAUAAUGUGUCACUAAUUUUUAGUGAAAAUAACACAAAAUACGACUUGCACGGCAAAUAAGUAUACGAGGCAAUCACGAUAAAUAAAAAACCGUG
....((((((((......))))))))....(((.((((((.....)))))).....)))..............(((((........(((..((.....))...))).........))))) (-18.83 = -18.39 +  -0.44)

alignment

secondary structure

dotplot

Window 0

Location	15,826,481 – 15,826,601
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-26.16
Consensus MFE	-20.44
Energy contribution	-20.76
Covariance contribution	0.32
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.78
SVM decision value	0.54
SVM RNA-class probability	0.776521
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826481 120 - 22224390
CACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUUUGCCGUACAAGUCGUAUUUUGUGUUAUUUUCACUAAAAAUUAGUGACACAUUACUUGCAGUUGUAAAUAACCGCAAGUAU
.(((((....((..(((((.(.....).)).)))..))...))))).............(((((((((.............))))))))).(((((((.((((....)))).))))))). ( -25.62)
>DroSec_CAF1 5349 120 - 1
CACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUUUGCCGUGCAAGUCGUAUUUUGUGCUAUUUUCACUAAAAAUUAGUGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAU
((((((.........))))))...............(((((((.(..((((......))))..).....((((((.....))))))....((((((((....))))))))..))))))). ( -27.00)
>DroSim_CAF1 5138 120 - 1
CACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUUUGCCGUGCAAGUCGUAUUUCGUGCUAUUUUCACUAAAAAUUAGUGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAU
((((((.........))))))...((..((.((((..((((((...)))))).))))..)).)).....((((((.....)))))).....(((((((.((((....)))).))))))). ( -26.60)
>DroEre_CAF1 5855 119 - 1
CACGGUUUUUUAUUUAUAGUGAU-GCCUCUUAUAUUUAUAUGCCGUGCAAGUCGUAUUUUGGGUUAUUUUCACUACAAAUUAGCGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAU
((((((....((..(((((.((.-...)))))))..))...))))))...(((((..(((((((.......))).))))...)))))....(((((((.((((....)))).))))))). ( -27.50)
>DroYak_CAF1 5151 120 - 1
CACGGUUUUUUAUUUAUCGUGAUUGCCUCUUAUAUUUAUUUGCCGUGCAAGUCGUAUUUUCUGUUAUUUUCACUAAAGUUUAGCGACACAUUACUUGCAGUUGUAAAUAACCGCAAGUAU
((((((....((..(((...((.....))..)))..))...))))))...((((((((((..((.......)).)))))...)))))....(((((((.((((....)))).))))))). ( -24.10)
>consensus
CACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUUUGCCGUGCAAGUCGUAUUUUGUGUUAUUUUCACUAAAAAUUAGUGACACAUUAUUUGCAGUUGUAAAUAACCGCAAGUAU
((((((....((..(((((.(.....).)).)))..))...))))))......................((((((.....)))))).....(((((((.((((....)))).))))))). (-20.44 = -20.76 +   0.32)

alignment

secondary structure

dotplot

Window 1

Location	15,826,561 – 15,826,677
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.09
Mean single sequence MFE	-26.48
Consensus MFE	-23.84
Energy contribution	-23.56
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-2.00
Structure conservation index	0.90
SVM decision value	2.50
SVM RNA-class probability	0.994655
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826561 116 - 22224390
AAGGUGUAUGUACAUAUCCACACAUCGAUAU----AUGUGCAUGUAAGUAUUGAGAAGCGUCCACUUGAAAUUCCAUACUCACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUU
......(((((((((((............))----)))))))))(((((((((((..(((..(((.(((((..((........))..)))))......)))..))))))).))))))).. ( -25.90)
>DroSec_CAF1 5429 116 - 1
AAGGUGUAUGUACAUAUCCACACAUCGAUAU----AUGUGCAUGUAAGUAUUGAGAAGCGUCCACUUGAAAUUCCAUACUCACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUU
......(((((((((((............))----)))))))))(((((((((((..(((..(((.(((((..((........))..)))))......)))..))))))).))))))).. ( -25.90)
>DroSim_CAF1 5218 116 - 1
AAGGUGUAUGUACAUAUCCACACAUCGAUAU----AUGUGCAUGUAAGUAUUGAGAAGCGUCCACUUGAAAUUCCAUACUCACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUU
......(((((((((((............))----)))))))))(((((((((((..(((..(((.(((((..((........))..)))))......)))..))))))).))))))).. ( -25.90)
>DroEre_CAF1 5935 119 - 1
AAGGUGUAUGUACAUAUCCACACAUCGAUAUACAUAUAUGCAUGUAAGUAUUGAGAAGCGUCCACUUGAAAUUCCAUACUCACGGUUUUUUAUUUAUAGUGAU-GCCUCUUAUAUUUAUA
...(((((((((.(((((........)))))...)))))))))((((((((.((((.(((((.((((((((..((........))..))))).....))))))-)).)))))))))))). ( -29.30)
>DroYak_CAF1 5231 116 - 1
AAGGUGUAUGUACAUAUCCACACAUCGAUAU----AUAUGCAUGUAAGUAUUGAGAAGCGUCCACUUGAAAUUCCAUACUCACGGUUUUUUAUUUAUCGUGAUUGCCUCUUAUAUUUAUU
...(((((((((..((((........)))))----))))))))((((((((.((((.(((..(((.(((((..((........))..)))))......)))..))).)))))))))))). ( -25.40)
>consensus
AAGGUGUAUGUACAUAUCCACACAUCGAUAU____AUGUGCAUGUAAGUAUUGAGAAGCGUCCACUUGAAAUUCCAUACUCACGGUUUUUUAUUUAUCGUGAUUGCCUCGUAUACUUAUU
...((((((((..(((((........)))))....))))))))((((((((...((.(((..(((.(((((..((........))..)))))......)))..))).))..)))))))). (-23.84 = -23.56 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:42 2006