Locus 5029

Sequence ID	3R_DroMel_CAF1
Location	13,249,640 – 13,249,740
Length	100
Max. P	0.917050

overview

Window 5

Location	13,249,640 – 13,249,740
Length	100
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	80.61
Mean single sequence MFE	-23.15
Consensus MFE	-13.46
Energy contribution	-13.32
Covariance contribution	-0.14
Combinations/Pair	1.14
Mean z-score	-2.76
Structure conservation index	0.58
SVM decision value	1.11
SVM RNA-class probability	0.917050
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13249640 100 + 27905053
AAUUGGUAAACUAAUACCGGCGACAUGCUAAUGUUUUGCUCUACAUUGAGACUGUGCGUAAACAAAAAUGUCACACGCCAUUAAA-----------------AAU-UACUAGCAUGUU
..((((((......)))))).(((((((((..(((((.(((......)))..((.((((..(((....)))...))))))...))-----------------)))-...))))))))) ( -23.80)
>DroVir_CAF1 1389 99 + 1
AAAUAAGAAACUAAUAU-GCAAACAUGCUAAUGUUUUGCUCUACAUUUAGGCGGUGCGUAAACAAAAAUGUCACACGCCAUUAAA-----------------AUU-UAAUGGCAUGUU
.................-...(((((((((((((........))))...((((((((((........))).))).))))......-----------------...-...))))))))) ( -23.30)
>DroGri_CAF1 6402 99 + 1
AAAUAAGUAACUAAUAU-GCCAACAUGCUAAUGUUUUGCUCUACAUUGACGCUGUGCGUAAACAAAAAUGUCACACGACAUUAAA-----------------AUU-UAAUGGCAUGUU
............(((((-(((((((.((((((((........))))))..)))))...........((((((....))))))...-----------------...-...))))))))) ( -21.80)
>DroSec_CAF1 2113 96 + 1
AAUUGGUA-ACUAAUACCG-CGACAUGCUA-UG-UUUGCUCUACAUUGA-GCUGUGCGUAAACAAAAAUGUCACACGCCAUUAAA-----------------AAUUUAAUAGCAUGUU
....((((-.....)))).-.(((((((((-(.-...((((......))-))((.((((..(((....)))...)))))).....-----------------......)))))))))) ( -26.40)
>DroWil_CAF1 8771 114 + 1
AUAUUGAAAACUAAUGC---CGACAUGCUAAUGUUUUGCUCUACAUUGAAGCCAUGCGUUAACAAAAAUGUCACACGACAUUAAAAAAAGAUAAAAACAAAAAAU-UAAUAGCAUGUU
.................---.(((((((((((((...((((......).)))...)))))).....((((((....)))))).......................-.....))))))) ( -20.50)
>DroMoj_CAF1 1359 99 + 1
GAAUGAGCAACUAAUAU-GCGACCAUGUUAAUGUUUUGCUCUACAUUGAAGCUGUGCGUAAACAAAAAUGUCACACGCCAUUAAA-----------------AUC-UAAUGGCAUGUU
....((((((.((((((-(....))))))).....)))))).((((....(.(((((((........))).)))))(((((((..-----------------...-))))))))))). ( -23.10)
>consensus
AAAUGAGAAACUAAUAC_GCCAACAUGCUAAUGUUUUGCUCUACAUUGAAGCUGUGCGUAAACAAAAAUGUCACACGCCAUUAAA_________________AAU_UAAUAGCAUGUU
.....................(((((((((.((((((((................))).)))))..((((........))))...........................))))))))) (-13.46 = -13.32 +  -0.14)

alignment

secondary structure

dotplot

Window 6

Location	13,249,640 – 13,249,740
Length	100
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	80.61
Mean single sequence MFE	-25.30
Consensus MFE	-13.43
Energy contribution	-13.93
Covariance contribution	0.50
Combinations/Pair	1.07
Mean z-score	-2.62
Structure conservation index	0.53
SVM decision value	0.75
SVM RNA-class probability	0.840248
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13249640 100 - 27905053
AACAUGCUAGUA-AUU-----------------UUUAAUGGCGUGUGACAUUUUUGUUUACGCACAGUCUCAAUGUAGAGCAAAACAUUAGCAUGUCGCCGGUAUUAGUUUACCAAUU
.((((((((((.-...-----------------.....(((((((.((((....))))))))).))(.(((......)))).....))))))))))....((((......)))).... ( -27.70)
>DroVir_CAF1 1389 99 - 1
AACAUGCCAUUA-AAU-----------------UUUAAUGGCGUGUGACAUUUUUGUUUACGCACCGCCUAAAUGUAGAGCAAAACAUUAGCAUGUUUGC-AUAUUAGUUUCUUAUUU
.(((((((((((-...-----------------..)))))))))))((((....))))...((...(((((....))).)).((((((....))))))))-................. ( -23.00)
>DroGri_CAF1 6402 99 - 1
AACAUGCCAUUA-AAU-----------------UUUAAUGUCGUGUGACAUUUUUGUUUACGCACAGCGUCAAUGUAGAGCAAAACAUUAGCAUGUUGGC-AUAUUAGUUACUUAUUU
...((((((...-.((-----------------.(((((((..(((.(((((..((((.......))))..)))))...)))..))))))).))..))))-))............... ( -22.40)
>DroSec_CAF1 2113 96 - 1
AACAUGCUAUUAAAUU-----------------UUUAAUGGCGUGUGACAUUUUUGUUUACGCACAGC-UCAAUGUAGAGCAAA-CA-UAGCAUGUCG-CGGUAUUAGU-UACCAAUU
.(((((((((......-----------------.....(((((((.((((....))))))))).))((-((......))))...-.)-))))))))..-.((((.....-)))).... ( -29.80)
>DroWil_CAF1 8771 114 - 1
AACAUGCUAUUA-AUUUUUUGUUUUUAUCUUUUUUUAAUGUCGUGUGACAUUUUUGUUAACGCAUGGCUUCAAUGUAGAGCAAAACAUUAGCAUGUCG---GCAUUAGUUUUCAAUAU
.((((((((...-......((((((..(((.........(((((((((((....)))...))))))))........)))..)))))).))))))))..---................. ( -23.73)
>DroMoj_CAF1 1359 99 - 1
AACAUGCCAUUA-GAU-----------------UUUAAUGGCGUGUGACAUUUUUGUUUACGCACAGCUUCAAUGUAGAGCAAAACAUUAACAUGGUCGC-AUAUUAGUUGCUCAUUC
.(((((((((((-(..-----------------.))))))))((((((((....)).)))))).........)))).(((((....(((((.(((....)-)).)))))))))).... ( -25.20)
>consensus
AACAUGCCAUUA_AAU_________________UUUAAUGGCGUGUGACAUUUUUGUUUACGCACAGCCUCAAUGUAGAGCAAAACAUUAGCAUGUCGGC_AUAUUAGUUUCCCAUUU
.(((((((((((.......................)))))))))))(((((((((((((..(((.........))).)))))))).......)))))..................... (-13.43 = -13.93 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:38 2006