Locus 4517

Sequence ID 2R_DroMel_CAF1
Location 14,812,756 – 14,812,913
Length 157
Max. P 0.918946
window7239 window7240 window7241

overview

Window 9

Location 14,812,756 – 14,812,873
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.70
Mean single sequence MFE -20.60
Consensus MFE -11.80
Energy contribution -11.64
Covariance contribution -0.16
Combinations/Pair 1.27
Mean z-score -2.49
Structure conservation index 0.57
SVM decision value 0.57
SVM RNA-class probability 0.785456
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812756 117 + 20766785
CUAUUAUUUUUCUCACAUUUAUUGCGAAUUUCCCAGCGUAACAACCUACUUGUUCCACAUUGCGUAUGCUUGAUAUGCGCCAUU--UUAUUCAAGUAUUCCCAUUGUGAACUUCACAAA-
............(((((....(((((..........))))).....((((((.........(((((((.....)))))))....--.....)))))).......)))))..........- ( -19.07)
>DroSec_CAF1 14584 113 + 1
CUAUUAUUUUUCUCACAUUUAUUUUGAAUUUCCCAGGAUG-UUACCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACAAUU--U---UCAAGUGUUCACAUUGUGAACUUCACAAA-
............(((((..(((((((.......)))))))-.....((((((........(((((((.....))))))).....--.---.)))))).......)))))..........- ( -18.96)
>DroSim_CAF1 8844 113 + 1
CUAUUAUUUUUCUCACAUUUAUUUUGAAUUUCCCAGGAUG-UUACCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACAAUU--U---UCAAGUGUUCACAUUGUGAAGUUCACAAA-
........................((((((((..(.((((-(....((((((........(((((((.....))))))).....--.---.))))))...))))).)))))))))....- ( -21.96)
>DroEre_CAF1 7450 115 + 1
CUAUUAUAUUUCUCACAUUUAUUUUGAACUACCCAGCGUAAUAUCCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACCACA--U---UCAAGUGCUCACAUUGUGAACUUUAGGAAA
..................((((.(((.......))).))))..(((((...((((((...(((((((.....))))))).(((.--.---....))).......)).))))..))))).. ( -18.50)
>DroYak_CAF1 8710 117 + 1
CUAUUAUUUUUCUCACAUUUAUUUUAAACUACCAAGCGUAAUAUCCUACUUGUUCCACGUUGCGUAUGCUUGAUAUCCACUUUGAUA---UCAAGUAUUCACAUUGUGUACUUUAGAAAA
.....................(((((((.(((((((((((((................)))))))((((((((((((......))))---)))))))).....))).))).))))))).. ( -24.49)
>consensus
CUAUUAUUUUUCUCACAUUUAUUUUGAAUUUCCCAGCGUAAUAACCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACAAUU__U___UCAAGUGUUCACAUUGUGAACUUCACAAA_
.....................(((((((.(((.(((..........((((((........(((((((.....)))))))............))))))......))).))).))))))).. (-11.80 = -11.64 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,812,796 – 14,812,913
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.44
Mean single sequence MFE -20.98
Consensus MFE -10.43
Energy contribution -10.23
Covariance contribution -0.20
Combinations/Pair 1.22
Mean z-score -1.98
Structure conservation index 0.50
SVM decision value 0.80
SVM RNA-class probability 0.854276
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812796 117 + 20766785
ACAACCUACUUGUUCCACAUUGCGUAUGCUUGAUAUGCGCCAUU--UUAUUCAAGUAUUCCCAUUGUGAACUUCACAAA-CUUCGCAACGGAAUGUUUUGUUUUUUAUUGUGUGUUUAUU
...........((((.(((.((.(.((((((((...........--....)))))))).).)).))))))).....(((-(..(((((..(((.........)))..))))).))))... ( -22.26)
>DroSec_CAF1 14624 99 + 1
-UUACCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACAAUU--U---UCAAGUGUUCACAUUGUGAACUUCACAAA-CUUCGCAACGCAAUGUUUUGUUUUUC--------------
-.....((((((........(((((((.....))))))).....--.---.))))))...((((((((...........-........))))))))..........-------------- ( -17.67)
>DroSim_CAF1 8884 99 + 1
-UUACCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACAAUU--U---UCAAGUGUUCACAUUGUGAAGUUCACAAA-CUUCGCAACGCAAUGUUUUGUUUUUC--------------
-.....((((((........(((((((.....))))))).....--.---.))))))......((((((((((....))-)))))))).((((....)))).....-------------- ( -22.76)
>DroEre_CAF1 7490 111 + 1
AUAUCCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACCACA--U---UCAAGUGCUCACAUUGUGAACUUUAGGAAACAUCG--ACGAAAUGUUUUGCUUUUCA--GUAUCUUUAUU
...(((((...((((((...(((((((.....))))))).(((.--.---....))).......)).))))..))))).......--..((((.(.....).)))).--........... ( -19.70)
>DroYak_CAF1 8750 113 + 1
AUAUCCUACUUGUUCCACGUUGCGUAUGCUUGAUAUCCACUUUGAUA---UCAAGUAUUCACAUUGUGUACUUUAGAAAAAAUGU--ACGAAUUGUUUUGCUUCUCA--GUAUCUUUAUU
...............((((.((.(.((((((((((((......))))---)))))))).).)).))))((((..((((((((((.--......))))))..)))).)--)))........ ( -22.50)
>consensus
AUAACCUACUUGUUCCACUAUGCGUAUGCUUAAUAUGCACAAUU__U___UCAAGUGUUCACAUUGUGAACUUCACAAA_CUUCGCAACGAAAUGUUUUGUUUUUCA__GU_U_UUUAUU
......((((((........(((((((.....)))))))............))))))......(((((.....))))).......................................... (-10.43 = -10.23 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 14,812,796 – 14,812,913
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.44
Mean single sequence MFE -23.17
Consensus MFE -8.11
Energy contribution -8.67
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 0.35
SVM decision value 1.12
SVM RNA-class probability 0.918946
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14812796 117 - 20766785
AAUAAACACACAAUAAAAAACAAAACAUUCCGUUGCGAAG-UUUGUGAAGUUCACAAUGGGAAUACUUGAAUAA--AAUGGCGCAUAUCAAGCAUACGCAAUGUGGAACAAGUAGGUUGU
.........(((((.............((((((((.(((.-((....)).))).)))))))).((((((.....--....(((.((.......)).))).........)))))).))))) ( -22.17)
>DroSec_CAF1 14624 99 - 1
--------------GAAAAACAAAACAUUGCGUUGCGAAG-UUUGUGAAGUUCACAAUGUGAACACUUGA---A--AAUUGUGCAUAUUAAGCAUACGCAUAGUGGAACAAGUAGGUAA-
--------------.....(((((...((((...))))..-)))))...((((((...))))))(((((.---.--.(((((((.(((.....))).)))))))....)))))......- ( -21.60)
>DroSim_CAF1 8884 99 - 1
--------------GAAAAACAAAACAUUGCGUUGCGAAG-UUUGUGAACUUCACAAUGUGAACACUUGA---A--AAUUGUGCAUAUUAAGCAUACGCAUAGUGGAACAAGUAGGUAA-
--------------.............(..(((((.((((-((....)))))).)))))..)..(((((.---.--.(((((((.(((.....))).)))))))....)))))......- ( -25.30)
>DroEre_CAF1 7490 111 - 1
AAUAAAGAUAC--UGAAAAGCAAAACAUUUCGU--CGAUGUUUCCUAAAGUUCACAAUGUGAGCACUUGA---A--UGUGGUGCAUAUUAAGCAUACGCAUAGUGGAACAAGUAGGAUAU
..........(--(....))...((((((....--.))))))(((((...(((((.(((((..(((....---.--.)))((((.......)))).))))).))))).....)))))... ( -24.80)
>DroYak_CAF1 8750 113 - 1
AAUAAAGAUAC--UGAGAAGCAAAACAAUUCGU--ACAUUUUUUCUAAAGUACACAAUGUGAAUACUUGA---UAUCAAAGUGGAUAUCAAGCAUACGCAACGUGGAACAAGUAGGAUAU
........(((--(((((((....((.....))--....))))))....((.(((..((((.((.(((((---((((......))))))))).)).))))..)))..)).))))...... ( -22.00)
>consensus
AAUAAA_A_AC__UGAAAAACAAAACAUUGCGUUGCGAAG_UUUGUGAAGUUCACAAUGUGAACACUUGA___A__AAUGGUGCAUAUUAAGCAUACGCAUAGUGGAACAAGUAGGUUAU
..................................................(((((.(((((....(((((.................)))))....))))).)))))............. ( -8.11 =  -8.67 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:59 2006