Locus 1292

Sequence ID	3L_DroMel_CAF1
Location	3,747,551 – 3,747,686
Length	135
Max. P	0.999781

overview

Window 1

Location	3,747,551 – 3,747,660
Length	109
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	77.98
Mean single sequence MFE	-21.02
Consensus MFE	-15.44
Energy contribution	-15.52
Covariance contribution	0.08
Combinations/Pair	1.13
Mean z-score	-1.60
Structure conservation index	0.73
SVM decision value	0.65
SVM RNA-class probability	0.810890
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3747551 109 - 23771897
UGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCUCUGUUUUUUUUUUAGUUUUUAUUAAA-GAUAAGCAAAGA--UAAAAAAAAAUGUGGGUGAAAAAAACGAG
....((((..(((((.(((((((((....))))......(((.(((((..((((((((....))))))-)).))))).)))--.........))))).)))))..))))... ( -22.40)
>DroSec_CAF1 142108 90 - 1
UGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCCUUCAG-UUUUUCUAGUUUUUAUUAAAGGAUAUGCAAACG--AGAAUAAAAU-------------------
..............(((((((((((((((((((((.((((.....))-)).)))).))))))))....)))))))))....--..........------------------- ( -18.30)
>DroSim_CAF1 139658 90 - 1
UGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCCCUCAG-UUUUUCUAGUUUUUCUUAAAGGAUAUGCAAAAG--UAAAGAAAAA-------------------
.........((((.(((((((((..(((((.((((.....)))).((-.....))....)))))....))))))))).)))--).........------------------- ( -19.60)
>DroEre_CAF1 137673 101 - 1
UGCAGUUUAAUUUAUGCAUGUCUGUGAAAACAGGGUGAUUCCCUCAG-UUUUUCCAGUUUUUAAUUAAGGAUAUGCAAAAAAAAAAAUGAAAA-ACUGCUG---------AG
.(((((((..(((((((((((((.(((((((((((.....))))..(-......).))))))).....)))))))))..........))))))-)))))..---------.. ( -25.20)
>DroYak_CAF1 127558 97 - 1
UGCAGUUUAAUUUAUGCAUGUCUGUGAAAACAGGGUGAUUCCCUCAG-CUUUUCUAACUUUUAAUUAAGGAUAUGCAAAG---AAAAUGAAAA-GUGGGUG---------A-
.((..((((.(((.(((((((((((....))((((.....))))...-....................)))))))))...---))).))))..-)).....---------.- ( -19.60)
>consensus
UGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCCCUCAG_UUUUUCUAGUUUUUAUUAAAGGAUAUGCAAAAA__AAAAUAAAAA____G_UG_________A_
..............(((((((((((....))((((.....))))........................)))))))))................................... (-15.44 = -15.52 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	3,747,586 – 3,747,686
Length	100
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	91.72
Mean single sequence MFE	-27.15
Consensus MFE	-23.81
Energy contribution	-23.81
Covariance contribution	0.00
Combinations/Pair	1.08
Mean z-score	-2.91
Structure conservation index	0.88
SVM decision value	4.06
SVM RNA-class probability	0.999781
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3747586 100 + 23771897
CUUAUC-UUUAAUAAAAACUAAAAAAAAAACAGAGAAUCACCCUGUUUCCACAGACAUGCAUAAAUUAAACUGCAUGUUUGGUCAGGGAAAAGUGGGCG-GA
......-..............................((.(((..(((((.((((((((((..........)))))))))).....)))))...))).)-). ( -24.40)
>DroSec_CAF1 142124 101 + 1
CAUAUCCUUUAAUAAAAACUAGAAAAA-CUGAAGGAAUCACCCUGUUUCCACAGACAUGCAUAAAUUAAACUGCAUGUUUGGUCAGGGAAAAGUGGGCGGGA
....(((((((................-.))))))).((.(((..(((((.((((((((((..........)))))))))).....)))))...))).)).. ( -29.43)
>DroSim_CAF1 139674 101 + 1
CAUAUCCUUUAAGAAAAACUAGAAAAA-CUGAGGGAAUCACCCUGUUUCCACAGACAUGCAUAAAUUAAACUGCAUGUUUGGUCAGGGAAAAGUGGGCGGGA
....(((((((................-.))))))).((.(((..(((((.((((((((((..........)))))))))).....)))))...))).)).. ( -29.13)
>DroEre_CAF1 137700 101 + 1
CAUAUCCUUAAUUAAAAACUGGAAAAA-CUGAGGGAAUCACCCUGUUUUCACAGACAUGCAUAAAUUAAACUGCAUGUUUGGCCAGGGAAAAGUGGGCGGGA
....((((..(((.....((((.((((-(..((((.....)))))))))..((((((((((..........)))))))))).)))).....)))....)))) ( -26.70)
>DroYak_CAF1 127581 101 + 1
CAUAUCCUUAAUUAAAAGUUAGAAAAG-CUGAGGGAAUCACCCUGUUUUCACAGACAUGCAUAAAUUAAACUGCAUGUUUGGCCAGGGAAAAGUGGGCGGGA
....(((((.......((((.....))-)).))))).((.(((..(((((.((((((((((..........)))))))))).....)))))...))).)).. ( -26.10)
>consensus
CAUAUCCUUUAAUAAAAACUAGAAAAA_CUGAGGGAAUCACCCUGUUUCCACAGACAUGCAUAAAUUAAACUGCAUGUUUGGUCAGGGAAAAGUGGGCGGGA
....(((((......................))))).((.(((..(((((.((((((((((..........)))))))))).....)))))...))).)).. (-23.81 = -23.81 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	3,747,586 – 3,747,686
Length	100
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	91.72
Mean single sequence MFE	-22.42
Consensus MFE	-18.72
Energy contribution	-18.72
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.83
SVM decision value	0.90
SVM RNA-class probability	0.877502
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3747586 100 - 23771897
UC-CGCCCACUUUUCCCUGACCAAACAUGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCUCUGUUUUUUUUUUAGUUUUUAUUAAA-GAUAAG
..-(((((.............((.(((((((..........))))))).))((....))))))).............((((((((....))))))-)).... ( -23.00)
>DroSec_CAF1 142124 101 - 1
UCCCGCCCACUUUUCCCUGACCAAACAUGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCCUUCAG-UUUUUCUAGUUUUUAUUAAAGGAUAUG
...(((((.............((.(((((((..........))))))).))((....)))))))..(((((.((-(.............))).))))).... ( -23.82)
>DroSim_CAF1 139674 101 - 1
UCCCGCCCACUUUUCCCUGACCAAACAUGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCCCUCAG-UUUUUCUAGUUUUUCUUAAAGGAUAUG
...(((((.............((.(((((((..........))))))).))((....))))))).........(-(((((..((.....))..))))))... ( -22.20)
>DroEre_CAF1 137700 101 - 1
UCCCGCCCACUUUUCCCUGGCCAAACAUGCAGUUUAAUUUAUGCAUGUCUGUGAAAACAGGGUGAUUCCCUCAG-UUUUUCCAGUUUUUAAUUAAGGAUAUG
(((.(((...........)))...(((((((..........)))))))(((..(((((((((.....))))..)-))))..)))...........))).... ( -23.30)
>DroYak_CAF1 127581 101 - 1
UCCCGCCCACUUUUCCCUGGCCAAACAUGCAGUUUAAUUUAUGCAUGUCUGUGAAAACAGGGUGAUUCCCUCAG-CUUUUCUAACUUUUAAUUAAGGAUAUG
(((...........(((((.(((.(((((((..........))))))).)).)....)))))(((.....))).-....................))).... ( -19.80)
>consensus
UCCCGCCCACUUUUCCCUGACCAAACAUGCAGUUUAAUUUAUGCAUGUCUGUGGAAACAGGGUGAUUCCCUCAG_UUUUUCUAGUUUUUAUUAAAGGAUAUG
...(((((.............((.(((((((..........))))))).))((....)))))))...................................... (-18.72 = -18.72 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:05 2006