Locus 2093

Sequence ID	2R_DroMel_CAF1
Location	7,850,068 – 7,850,244
Length	176
Max. P	0.993996

overview

Window 1

Location	7,850,068 – 7,850,167
Length	99
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	70.72
Mean single sequence MFE	-18.28
Consensus MFE	-16.58
Energy contribution	-16.20
Covariance contribution	-0.38
Combinations/Pair	1.06
Mean z-score	-1.05
Structure conservation index	0.91
SVM decision value	2.08
SVM RNA-class probability	0.987343
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850068 99 + 20766785
UAAUCUUAAAUUGUUGAAAGGUUUAAAAAAUAAAAAAAAACCCCGACUCCGUGACAAUGCAUAUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGU
............((((...(((((.............))))).))))((((.(.((((((........))))))))).))(((((.......))))).. ( -21.22)
>DroPse_CAF1 7711 89 + 1
GAAUUAUAAAUUAUUCUG---------AC-AAAAAGAAAGACCAAACUCCGUGACAAUGCAUAUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGU
.............((((.---------..-....)))).........((((.(.((((((........))))))))).))(((((.......))))).. ( -18.30)
>DroSim_CAF1 8115 99 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAACCGACUCCGUGACAAUGUUUGUUUCAACAUUGCCGUGACCAGGAUUCGAACCUGGGU
...............................................((((.(.(((((((......)))))))))).))(((((.......))))).. ( -15.30)
>DroPer_CAF1 7712 89 + 1
GAAUUAUAAAUUAUUCUG---------AC-AAAAAGAAAGACCAAACUCCGUGACAAUGCAUAUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGU
.............((((.---------..-....)))).........((((.(.((((((........))))))))).))(((((.......))))).. ( -18.30)
>consensus
GAAUUAUAAAUUAUUCUG_________AC_AAAAAAAAAAACCAAACUCCGUGACAAUGCAUAUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGU
...............................................((((.(.((((((........))))))))).))(((((.......))))).. (-16.58 = -16.20 +  -0.38)

alignment

secondary structure

dotplot

Window 2

Location	7,850,068 – 7,850,167
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	70.72
Mean single sequence MFE	-21.57
Consensus MFE	-18.95
Energy contribution	-18.57
Covariance contribution	-0.38
Combinations/Pair	1.08
Mean z-score	-1.51
Structure conservation index	0.88
SVM decision value	2.44
SVM RNA-class probability	0.993996
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850068 99 - 20766785
ACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAUAUGCAUUGUCACGGAGUCGGGGUUUUUUUUUAUUUUUUAAACCUUUCAACAAUUUAAGAUUA
....(((((.(((((((((((..((((((((........))))))))...)).)))))))))..............))))).................. ( -23.26)
>DroPse_CAF1 7711 89 - 1
ACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAUAUGCAUUGUCACGGAGUUUGGUCUUUCUUUUU-GU---------CAGAAUAAUUUAUAAUUC
..(((((.......)))))....((((((((........))))))))...(((((.(((..((((....-..---------.))))..)))...))))) ( -22.20)
>DroSim_CAF1 8115 99 - 1
ACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUGAAACAAACAUUGUCACGGAGUCGGUUUUUUUUUUNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
..(((((.......)))))....(((((((((......))))))))).................................................... ( -18.60)
>DroPer_CAF1 7712 89 - 1
ACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAUAUGCAUUGUCACGGAGUUUGGUCUUUCUUUUU-GU---------CAGAAUAAUUUAUAAUUC
..(((((.......)))))....((((((((........))))))))...(((((.(((..((((....-..---------.))))..)))...))))) ( -22.20)
>consensus
ACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAUAUGCAUUGUCACGGAGUCGGGUCUUUCUUUUU_GU_________CAGAAUAAUUUAUAAUUC
..(((((.......)))))....((((((((........)))))))).................................................... (-18.95 = -18.57 +  -0.38)

alignment

secondary structure

dotplot

Window 3

Location	7,850,100 – 7,850,207
Length	107
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	87.31
Mean single sequence MFE	-31.58
Consensus MFE	-29.58
Energy contribution	-29.08
Covariance contribution	-0.50
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.94
SVM decision value	1.50
SVM RNA-class probability	0.959211
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850100 107 + 20766785
AAAAAA----------AACCCCGACUCCGUGACAAUGCAUAU-UGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
......----------.((((((.....(((..(((((....-....)))))((((((.(((((.......))))).....)))))))))....)))))).................. ( -33.20)
>DroVir_CAF1 35074 108 + 1
AAAAAA----------CAAUCCGAUUCCGUGACAAUGCAGGUUUACAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
......----------.....((.....(((..(((((.(.....).)))))((((((.(((((.......))))).....)))))))))...((((........))))....))... ( -30.80)
>DroGri_CAF1 24936 115 + 1
AAAAAUU--UAAAAUUCAACCAGAUUCCGUGACAAUGU-GCUUCGAAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
.......--.............((((..(((..(((((-........)))))((((((.(((((.......))))).....)))))))))...((((........)))).....)))) ( -29.20)
>DroSim_CAF1 8147 107 + 1
AAAAAA----------AAAACCGACUCCGUGACAAUGUUUGU-UUCAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
......----------......(((((((((..((((((...-...))))))((((((.(((((.......))))).....)))))).....)))))))))................. ( -30.80)
>DroWil_CAF1 15841 107 + 1
AAAAAU----------UAACCUAACUCCGUGACAAUGCAUCU-UGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
......----------....(((.....(((..(((((....-....)))))((((((.(((((.......))))).....)))))))))...((((........)))))))...... ( -30.80)
>DroMoj_CAF1 19660 113 + 1
AAAGAUUGUUC-----AAAUUCGACUCCGUGACAAUGCCUCUUAAUAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
...((((((..-----......(((((((((..(((((.........)))))((((((.(((((.......))))).....)))))).....)))))))))(((.....))))))))) ( -34.70)
>consensus
AAAAAA__________AAACCCGACUCCGUGACAAUGCAUCU_UGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUC
......................(((((((((..(((((.........)))))((((((.(((((.......))))).....)))))).....)))))))))................. (-29.58 = -29.08 +  -0.50)

alignment

secondary structure

dotplot

Window 4

Location	7,850,128 – 7,850,244
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.39
Mean single sequence MFE	-39.08
Consensus MFE	-31.70
Energy contribution	-31.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.81
SVM decision value	0.47
SVM RNA-class probability	0.749324
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850128 116 + 20766785
AUAU-UGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACAUCGGGU-GAU-GUUUGACUGCUG-CCAAAUU
....-.((((((..((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))))).(((((....-)))-)).....)))))-)...... ( -44.30)
>DroVir_CAF1 35102 117 + 1
AGGUUUACAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACAUCGGUU-AU--GUUGCCCGACCGACUAAAGU
.((((..((((((.((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..)))))))..........-))--))))...))))......... ( -39.70)
>DroGri_CAF1 24972 116 + 1
-GCUUCGAAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUAUACCAGUU-GUUCGUGAA--UGUUGCCCAAAUU
-.......((((((((((((.(((((.......))))).....))))))(((...((((........)))).....((..((((((.....))))-)))))))))--))))......... ( -34.00)
>DroWil_CAF1 15869 117 + 1
AUCU-UGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUAUGUGAGGUUGUU-GAAUCUGGUUUG-CCAAAUG
((((-..((.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..)))))))..))..))))....-.....(((....-))).... ( -40.90)
>DroMoj_CAF1 19693 117 + 1
CUCUUAAUAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACGUCGAAU-CU--GUAAAGCCUUUGUCUAAAUC
..............((((((.(((((.......))))).....))))))......((((........))))(((((((....(((((((......-.)--))..)))).))))))).... ( -34.00)
>DroAna_CAF1 7742 117 + 1
UUAU-UUCAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACGUUGGGUUGUU-GAAUGUAGCCGG-CCAAAUG
....-.....((((((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))(((((((((.(.....)-.)))))))))))-)..)))) ( -41.60)
>consensus
AUCU_UGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACAUCGGGU_GUU_GUAUAUCGGCUG_CCAAAUU
..............((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..)))))))................................... (-31.70 = -31.70 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:00 2006