Locus 4317

Sequence ID	2R_DroMel_CAF1
Location	14,185,643 – 14,185,748
Length	105
Max. P	0.799413

overview

Window 4

Location	14,185,643 – 14,185,748
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.22
Mean single sequence MFE	-20.35
Consensus MFE	-18.58
Energy contribution	-18.75
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.91
SVM decision value	0.57
SVM RNA-class probability	0.786271
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14185643 105 + 20766785
UA---A------UACAAAAAAAAAAAAAAAAUCGUAAUUUGAAGUUCGUAAAAAUGACGCGUUUCCUGUCAUU-UGGCGAGCACUUUAAGUGCGUAAUUUG-CUAUCCGCCAAAUA----
..---.------....................((((.((((((((((((..((((((((.......)))))))-).))))..))))))))))))..(((((-(.....).))))).---- ( -19.70)
>DroVir_CAF1 6864 91 + 1
U----------------------A----AAAUCGUAAUUUGAAGUUCGUAAAAAUGACGCGUUUCCUGUCAUU-UGGCGAGCACUUUAAGUGCGUAAUUUG-CUCCCCAC-ACACACUGA
.----------------------.----....((((.((((((((((((..((((((((.......)))))))-).))))..)))))))))))).......-........-......... ( -18.80)
>DroPse_CAF1 9739 90 + 1
U----------------------A--AAAAAUCGUAAUUUGAAGUUCGUAAAAAUGACGCGUUUCCUGUCAUUUUGGCGAGCACUUUAAGUGCGUAAUUUG-CUAUCCAC-AAAUA----
.----------------------.--......((((.((((((((((((.(((((((((.......))))))))).))))..))))))))))))..(((((-.......)-)))).---- ( -21.90)
>DroGri_CAF1 3388 91 + 1
U----------------------A----AAAUCGUAAUUUGAAGUUCGAAAAAAUGACGCGUUUCCUGUCAUU-UGGCGAGCACUUUAAGUGCGUAAUUUG-CUCCCCAC-ACACACACA
.----------------------.----....((((.(((((((((((...((((((((.......)))))))-)..)))..)))))))))))).......-........-......... ( -18.70)
>DroWil_CAF1 4562 118 + 1
UCGAAAUAUACCUACAGAUACAAAACAAAUCUCGUAAUUUGAAGUUCGUAAAAAUGACGCGUUUCCUGUCAUU-UGGCGAGCACUUUAAGUGCGUAAUUUGGCUCCCCAC-AAAAACACA
.........................(((((..((((.((((((((((((..((((((((.......)))))))-).))))..))))))))))))..))))).........-......... ( -24.20)
>DroMoj_CAF1 7156 84 + 1
U----------------------A----AAAUCGUAAUUUGAAGUUCGUAAAAAUGACGCGUUUCCUGUCAUU-UGGCGAGCACUUUAAGUGCGUAAUUUG-CUCCCCAC-AC-------
.----------------------.----....((((.((((((((((((..((((((((.......)))))))-).))))..)))))))))))).......-........-..------- ( -18.80)
>consensus
U______________________A____AAAUCGUAAUUUGAAGUUCGUAAAAAUGACGCGUUUCCUGUCAUU_UGGCGAGCACUUUAAGUGCGUAAUUUG_CUCCCCAC_AAACA____
................................((((.((((((((((((...(((((((.......)))))))...))))..)))))))))))).......................... (-18.58 = -18.75 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	14,185,643 – 14,185,748
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.22
Mean single sequence MFE	-23.02
Consensus MFE	-17.75
Energy contribution	-18.03
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.53
Structure conservation index	0.77
SVM decision value	0.61
SVM RNA-class probability	0.799413
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14185643 105 - 20766785
----UAUUUGGCGGAUAG-CAAAUUACGCACUUAAAGUGCUCGCCA-AAUGACAGGAAACGCGUCAUUUUUACGAACUUCAAAUUACGAUUUUUUUUUUUUUUUUGUA------U---UA
----.(((((((((((..-...)))..((((.....)))).)))))-)))(((.(....)..)))...................(((((..............)))))------.---.. ( -20.74)
>DroVir_CAF1 6864 91 - 1
UCAGUGUGU-GUGGGGAG-CAAAUUACGCACUUAAAGUGCUCGCCA-AAUGACAGGAAACGCGUCAUUUUUACGAACUUCAAAUUACGAUUU----U----------------------A
..(((.(((-(.((.(((-((..(((......)))..))))).))(-((((((.(....)..))))))).)))).)))..............----.----------------------. ( -23.70)
>DroPse_CAF1 9739 90 - 1
----UAUUU-GUGGAUAG-CAAAUUACGCACUUAAAGUGCUCGCCAAAAUGACAGGAAACGCGUCAUUUUUACGAACUUCAAAUUACGAUUUUU--U----------------------A
----.((((-(.((....-........((((.....))))(((..((((((((.(....)..))))))))..))).)).)))))..........--.----------------------. ( -21.10)
>DroGri_CAF1 3388 91 - 1
UGUGUGUGU-GUGGGGAG-CAAAUUACGCACUUAAAGUGCUCGCCA-AAUGACAGGAAACGCGUCAUUUUUUCGAACUUCAAAUUACGAUUU----U----------------------A
.(((..((.-((((.(((-((..(((......)))..))))).))(-((((((.(....)..)))))))......))..))...))).....----.----------------------. ( -22.90)
>DroWil_CAF1 4562 118 - 1
UGUGUUUUU-GUGGGGAGCCAAAUUACGCACUUAAAGUGCUCGCCA-AAUGACAGGAAACGCGUCAUUUUUACGAACUUCAAAUUACGAGAUUUGUUUUGUAUCUGUAGGUAUAUUUCGA
(((((....-.(((....)))....)))))......(((((..(.(-((((((.(....)..))))))).((((((...((((((....)))))).))))))...)..)))))....... ( -28.20)
>DroMoj_CAF1 7156 84 - 1
-------GU-GUGGGGAG-CAAAUUACGCACUUAAAGUGCUCGCCA-AAUGACAGGAAACGCGUCAUUUUUACGAACUUCAAAUUACGAUUU----U----------------------A
-------((-(.((.(((-((..(((......)))..))))).))(-((((((.(....)..))))))).)))...................----.----------------------. ( -21.50)
>consensus
____UAUGU_GUGGGGAG_CAAAUUACGCACUUAAAGUGCUCGCCA_AAUGACAGGAAACGCGUCAUUUUUACGAACUUCAAAUUACGAUUU____U______________________A
...........(((((...........((((.....))))(((....((((((.(....)..))))))....))).)))))....................................... (-17.75 = -18.03 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:55 2006