Locus 3249

Sequence ID 3R_DroMel_CAF1
Location 8,663,667 – 8,663,851
Length 184
Max. P 0.999921
window5251 window5252 window5253 window5254

overview

Window 1

Location 8,663,667 – 8,663,779
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.68
Mean single sequence MFE -31.38
Consensus MFE -24.68
Energy contribution -24.65
Covariance contribution -0.03
Combinations/Pair 1.07
Mean z-score -2.57
Structure conservation index 0.79
SVM decision value 0.61
SVM RNA-class probability 0.798384
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8663667 112 - 27905053
AGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGCU----CGCACAUGGUGCAAACGAAAA-GGCAAAGGCAU---UGGC
((((((((((........))))))))))..((((((((..........(((((....))))).(((....)))..)----)))))))(((((...(.....-)......))))---)... ( -29.50)
>DroVir_CAF1 110809 110 - 1
AGGAAGCGAUAAAAUCAAAUUGUUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGAGG----CGCACAUGGUCUCAACA--UU-GGCAUCGGCAU---UGGC
((((((((((........))))))))))(((((((..((((((..........))))))..)))))))...(((((----(.......)))))).((--..-.((....))..---)).. ( -30.00)
>DroWil_CAF1 112661 120 - 1
AGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGGAUGGAAGCACAUGGUGCAAGGGGAGAUGGUACAUACAUAUAUGGG
((((((((((........))))))))))..(((((((...........(....).(((((((.((((.......))))...((((...))))...)))))))....)))))))....... ( -32.90)
>DroYak_CAF1 96492 111 - 1
AGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGCU----CGCACAUGGUGCAAACGAAAA--GCAAAGGCAU---UGGC
((((((((((........))))))))))(((((((..((((((..........))))))..))))))).....(((----.((((...)))).........--((....))..---.))) ( -29.40)
>DroMoj_CAF1 141265 110 - 1
AGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGAGG----CGCACAUGGUCUCAACA--GC-GGCAGAGACUU---GGGC
((((((((((........))))))))))(((((((..((((((..........))))))..))))))).......(----(.((...((((((....--..-....)))))))---).)) ( -32.80)
>DroAna_CAF1 84675 112 - 1
AGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGCC----CGCACAUGGUGCAAAAGGCAA-CUCAAAGGCAU---UGCC
((((((((((........))))))))))(((((((..((((((..........))))))..))))))).....(((----.((((...))))...((....-))....)))..---.... ( -33.70)
>consensus
AGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGCG____CGCACAUGGUGCAAACG_AAA_GGCAAAGGCAU___UGGC
((((((((((........))))))))))(((((((..((((((..........))))))..))))))).............((((...))))............................ (-24.68 = -24.65 +  -0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,663,703 – 8,663,819
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.15
Mean single sequence MFE -22.33
Consensus MFE -20.13
Energy contribution -20.30
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.90
SVM decision value 0.57
SVM RNA-class probability 0.783688
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8663703 116 + 27905053
----AGCCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAGCAAUUCGAUUUUAUCGCUUCCUCAUGACUAUACGUUCAAUUAUUGAAGAGUUUACGUUUUGC
----.........((((((..((((((..........))))))..)))))).(((((((.((........)).)))))))((.(((((.((.((((.....))))..)).)).))).)). ( -22.60)
>DroVir_CAF1 110843 115 + 1
----CCUCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAACAAUUUGAUUUUAUCGCUUCCUCAUGACUUCACGUUCAAUUAUUGAAGAGUUUACGUU-UGC
----.(((......(((.(((((((((((((((...................))))))))))))(((...)))...))).))).........((((.....)))))))........-... ( -20.31)
>DroGri_CAF1 90099 115 + 1
----CCUCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAGCAAUUUGAUUUUAUCGCUUCCUCAUGACUUCACGUUCAAUUAUUGAAGAGUUUACGUU-UGC
----..((((...((((((..((((((..........))))))..)))))).(((((((.((........)).))))))).))))(((((...........)))))..........-... ( -23.70)
>DroWil_CAF1 112701 119 + 1
UCCAUCCCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAGCAAUUCGAUUUUAUCGCUUCCUCAUGACUACACGUUCAAUUAUUGAAGAGUUUACGUU-UGC
.............((((((..((((((..........))))))..)))))).(((((((.((........)).)))))))...(((((.((.((((.....))))..)).)).)))-... ( -21.30)
>DroMoj_CAF1 141299 115 + 1
----CCUCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAGCAAUUUGAUUUUAUCGCUUCCUCAUGACUUCACGUUCAAUUAUUGAAGAGUUUACGUU-UGC
----..((((...((((((..((((((..........))))))..)))))).(((((((.((........)).))))))).))))(((((...........)))))..........-... ( -23.70)
>DroAna_CAF1 84711 116 + 1
----GGCCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAGCAAUUCGAUUUUAUCGCUUCCUCAUGACUACACGUUCAAUUAUUGAAGAGUUUACGUUUUGC
----.........((((((..((((((..........))))))..)))))).(((((((.((........)).)))))))((.(((((.((.((((.....))))..)).)).))).)). ( -22.40)
>consensus
____CCCCAUAACAAUGUGGAAAAUUGUUUCCUGUAUCAAUUUCACACAUUAAGGAAGCAAUUCGAUUUUAUCGCUUCCUCAUGACUACACGUUCAAUUAUUGAAGAGUUUACGUU_UGC
.............((((((..((((((..........))))))..)))))).(((((((.((........)).)))))))((.(((...((.((((.....))))..))....))).)). (-20.13 = -20.30 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 8,663,703 – 8,663,819
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.15
Mean single sequence MFE -29.75
Consensus MFE -27.95
Energy contribution -27.56
Covariance contribution -0.39
Combinations/Pair 1.06
Mean z-score -2.97
Structure conservation index 0.94
SVM decision value 4.57
SVM RNA-class probability 0.999921
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8663703 116 - 27905053
GCAAAACGUAAACUCUUCAAUAAUUGAACGUAUAGUCAUGAGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGCU----
.....((((.......(((.....)))))))..(((((((((((((((((........))))))))).(((((((..((((((..........))))))..)))))))))))))))---- ( -31.41)
>DroVir_CAF1 110843 115 - 1
GCA-AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGUUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGAGG----
...-..........(((((.........((((....))))((((((((((........))))))))))(((((((..((((((..........))))))..)))))))...)))))---- ( -27.50)
>DroGri_CAF1 90099 115 - 1
GCA-AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGAGG----
...-..........(((((.........((((....))))((((((((((........))))))))))(((((((..((((((..........))))))..)))))))...)))))---- ( -29.90)
>DroWil_CAF1 112701 119 - 1
GCA-AACGUAAACUCUUCAAUAAUUGAACGUGUAGUCAUGAGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGGAUGGA
...-..(((((.................((((....))))((((((((((........))))))))))(((((((..((((((..........))))))..))))))))))))....... ( -28.70)
>DroMoj_CAF1 141299 115 - 1
GCA-AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGAGG----
...-..........(((((.........((((....))))((((((((((........))))))))))(((((((..((((((..........))))))..)))))))...)))))---- ( -29.90)
>DroAna_CAF1 84711 116 - 1
GCAAAACGUAAACUCUUCAAUAAUUGAACGUGUAGUCAUGAGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGGCC----
...........((.(((((.....)))).).)).((((((((((((((((........))))))))).(((((((..((((((..........))))))..)))))))))))))).---- ( -31.10)
>consensus
GCA_AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAAUUGAUACAGGAAACAAUUUUCCACAUUGUUAUGAGG____
.....((((.......(((.....)))))))....(((((((((((((((........))))))))).(((((((..((((((..........))))))..)))))))))))))...... (-27.95 = -27.56 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 8,663,739 – 8,663,851
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.07
Mean single sequence MFE -28.06
Consensus MFE -19.10
Energy contribution -19.18
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -2.40
Structure conservation index 0.68
SVM decision value 1.70
SVM RNA-class probability 0.972634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8663739 112 - 27905053
AGUGCUGGAAUUUCGGAAAG-------GGAACGCCGCCGGCAAAACGUAAACUCUUCAAUAAUUGAACGUAUAGUCAUGAGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAA
..((((((.....(((...(-------....).)))))))))..((((......((((.....))))..........((((((((((((........))))))))))))))))...... ( -29.70)
>DroVir_CAF1 110879 112 - 1
AGUGGCGGACGGUGGCAAAA------GGAGGCGCAGACAGCA-AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGUUUCCUUAAUGUGUGAAA
.((.((.....)).))....------....((((((((....-.((((.......(((.....)))))))...))).((((((((((((........)))))))))))).))))).... ( -25.81)
>DroGri_CAF1 90135 106 - 1
------------UGGGAAACGGAGUCGAAGGCGUAGACAGCA-AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAA
------------..(....)(((((((...((.......)).-..))...)))))(((...(((((.((((....)))).(((((((((........))))))))))))))...))).. ( -26.80)
>DroWil_CAF1 112741 97 - 1
AUCA-----A--------CA-------UCAACG-CAACGGCA-AACGUAAACUCUUCAAUAAUUGAACGUGUAGUCAUGAGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAA
....-----.--------..-------(((.((-((..(((.-.((((.......(((.....)))))))...))).((((((((((((........)))))))))))).))))))).. ( -25.81)
>DroMoj_CAF1 141335 101 - 1
CGUGGU-----GCG------------GCAGGCGCAGACAGCA-AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAA
.((..(-----(((------------....((.......)).-..)))).))..((((...(((((.((((....)))).(((((((((........))))))))))))))...)))). ( -26.80)
>DroAna_CAF1 84747 112 - 1
AUCGCAGGAAUUUCAGGCCA-------ACAAGGCCGACGGCAAAACGUAAACUCUUCAAUAAUUGAACGUGUAGUCAUGAGGAAGCGAUAAAAUCGAAUUGCUUCCUUAAUGUGUGAAA
.(((((.(.......((((.-------....))))...(((...((((.......(((.....)))))))...))).((((((((((((........)))))))))))).).))))).. ( -33.41)
>consensus
AGUG_____A__UGGGAAAA_______AAAACGCAGACAGCA_AACGUAAACUCUUCAAUAAUUGAACGUGAAGUCAUGAGGAAGCGAUAAAAUCAAAUUGCUUCCUUAAUGUGUGAAA
................................((.....)).............((((...(((((.((((....)))).(((((((((........))))))))))))))...)))). (-19.10 = -19.18 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:41 2006