Locus 2750

Sequence ID	3R_DroMel_CAF1
Location	7,362,143 – 7,362,233
Length	90
Max. P	0.982271

overview

Window 9

Location	7,362,143 – 7,362,233
Length	90
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.33
Mean single sequence MFE	-19.64
Consensus MFE	-11.03
Energy contribution	-11.68
Covariance contribution	0.64
Combinations/Pair	1.24
Mean z-score	-2.66
Structure conservation index	0.56
SVM decision value	1.91
SVM RNA-class probability	0.982271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7362143 90 + 27905053
UAUUUUUCAAUUGUACAACUGUGCUGGUUUU--------------CGUAAACAAAAAAUUAAUUCAAUCUA-------ACUUUUGUUGCCACUUGGCACCAGCAAA-AAGUU
................((((.(((((((...--------------....(((((((...............-------..)))))))(((....))))))))))..-.)))) ( -20.03)
>DroGri_CAF1 37120 106 + 1
----UUUCGAAUGUGUAAUUGUACUAAGCUUAUAGCUUAAGCUGAAGUAAGGCAACAGCAAAUUUGAUAUGGAAAAACCCUUUUUUUGC-AAAUGCUGCCAGAAAU-AAUUU
----((((.............((((.((((((.....))))))..)))).((((.(((((((...((...((......)).)).)))))-...)).)))).)))).-..... ( -21.80)
>DroSec_CAF1 38041 90 + 1
UAUUUUUCAAUUGUACAACUGUGCUGGUUUU--------------CGUAAACAAAAAAUUAAUUCAAUCUA-------ACUUUUGUUGCCACUUGGCACCAGCAAA-AAGUU
................((((.(((((((...--------------....(((((((...............-------..)))))))(((....))))))))))..-.)))) ( -20.03)
>DroSim_CAF1 43561 90 + 1
UAUUUUUCAAUUGUACAACUGUGCUGGUUUU--------------CGUAAACAAAAAAUUAAUUCAAUCUA-------ACUUUUGUUGCCACUUGGCACCAGCAAA-AAGUU
................((((.(((((((...--------------....(((((((...............-------..)))))))(((....))))))))))..-.)))) ( -20.03)
>DroEre_CAF1 41726 90 + 1
UAUUUUUCAAUUGUAUAUAU-UGUUGGUUUU--------------CAUAAACAAAAAAUUAAUUCAAUCUA-------ACUUUUGUUGCCACUUGGCACCAGCAAAAAAGUU
...................(-(((((((...--------------....(((((((...............-------..)))))))(((....)))))))))))....... ( -16.03)
>DroYak_CAF1 42997 89 + 1
UAUUUUUCAAUUGUAUAACUGUGCUGGUUUU--------------CA-AAACAAAAAAUUAAUUCAAUCUA-------ACUUUUGUUGCCACUUGGCACCAGCAAA-AAGUU
................((((.(((((((...--------------..-.(((((((...............-------..)))))))(((....))))))))))..-.)))) ( -19.93)
>consensus
UAUUUUUCAAUUGUACAACUGUGCUGGUUUU______________CGUAAACAAAAAAUUAAUUCAAUCUA_______ACUUUUGUUGCCACUUGGCACCAGCAAA_AAGUU
.....................(((((((.....................(((((((........................)))))))(((....))))))))))........ (-11.03 = -11.68 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	7,362,143 – 7,362,233
Length	90
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	77.33
Mean single sequence MFE	-19.99
Consensus MFE	-10.51
Energy contribution	-11.90
Covariance contribution	1.39
Combinations/Pair	1.11
Mean z-score	-2.28
Structure conservation index	0.53
SVM decision value	1.16
SVM RNA-class probability	0.923533
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7362143 90 - 27905053
AACUU-UUUGCUGGUGCCAAGUGGCAACAAAAGU-------UAGAUUGAAUUAAUUUUUUGUUUACG--------------AAAACCAGCACAGUUGUACAAUUGAAAAAUA
.....-..((((((((((....)))(((((((((-------(((......)))).))))))))....--------------...)))))))(((((....)))))....... ( -21.30)
>DroGri_CAF1 37120 106 - 1
AAAUU-AUUUCUGGCAGCAUUU-GCAAAAAAAGGGUUUUUCCAUAUCAAAUUUGCUGUUGCCUUACUUCAGCUUAAGCUAUAAGCUUAGUACAAUUACACAUUCGAAA----
.....-.((((.(((((((...-(((((.....((.....))........)))))))))))).((((..((((((.....)))))).)))).............))))---- ( -22.12)
>DroSec_CAF1 38041 90 - 1
AACUU-UUUGCUGGUGCCAAGUGGCAACAAAAGU-------UAGAUUGAAUUAAUUUUUUGUUUACG--------------AAAACCAGCACAGUUGUACAAUUGAAAAAUA
.....-..((((((((((....)))(((((((((-------(((......)))).))))))))....--------------...)))))))(((((....)))))....... ( -21.30)
>DroSim_CAF1 43561 90 - 1
AACUU-UUUGCUGGUGCCAAGUGGCAACAAAAGU-------UAGAUUGAAUUAAUUUUUUGUUUACG--------------AAAACCAGCACAGUUGUACAAUUGAAAAAUA
.....-..((((((((((....)))(((((((((-------(((......)))).))))))))....--------------...)))))))(((((....)))))....... ( -21.30)
>DroEre_CAF1 41726 90 - 1
AACUUUUUUGCUGGUGCCAAGUGGCAACAAAAGU-------UAGAUUGAAUUAAUUUUUUGUUUAUG--------------AAAACCAACA-AUAUAUACAAUUGAAAAAUA
.......(((.(((((((....)))(((((((((-------(((......)))).))))))))....--------------...)))).))-)................... ( -13.50)
>DroYak_CAF1 42997 89 - 1
AACUU-UUUGCUGGUGCCAAGUGGCAACAAAAGU-------UAGAUUGAAUUAAUUUUUUGUUU-UG--------------AAAACCAGCACAGUUAUACAAUUGAAAAAUA
.....-..((((((((((....)))(((((((((-------(((......)))).)))))))).-..--------------...)))))))(((((....)))))....... ( -20.40)
>consensus
AACUU_UUUGCUGGUGCCAAGUGGCAACAAAAGU_______UAGAUUGAAUUAAUUUUUUGUUUACG______________AAAACCAGCACAGUUAUACAAUUGAAAAAUA
........((((((((((....)))((((((((......................)))))))).....................)))))))..................... (-10.51 = -11.90 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:59 2006