Locus 4196

Sequence ID	2R_DroMel_CAF1
Location	13,804,666 – 13,804,761
Length	95
Max. P	0.823723

overview

Window 8

Location	13,804,666 – 13,804,761
Length	95
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	74.42
Mean single sequence MFE	-22.98
Consensus MFE	-13.88
Energy contribution	-13.88
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.60
SVM decision value	0.69
SVM RNA-class probability	0.823723
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13804666 95 + 20766785
GGAGACACAGGGCCUCGGCCCUCGGGCCAAAUGGUUCAUUUUCAAAACUGCAAG--AUAGAG----CAGAGCGAACGAUUGAUUAGUU----GU--UGCAAUGCAAU
(((((...(((((....))))).(((((....))))).)))))....((((...--.....)----))).((.((((((......)))----))--)))........ ( -28.50)
>DroPse_CAF1 102469 98 + 1
GGAGACGCAGGGCCUCGGCCCUCGGGCCAAACUGUUCAUUUUCAAAACUGCAAA---GAGAG--CGGAGAAACAAAAA----UUAAUAUGGAAUAUAAGAAUAUAAU
((...((.(((((....)))))))..))...((((((.((((((....)).)))---).)))--)))...........----......................... ( -22.80)
>DroWil_CAF1 128676 90 + 1
AGAGACACAGGGCCUCGGCCCUCGGGCCAAACUGUUCAUUUUCAAAACUGCAAA--AGCAAA----AAGAAAACAAAA----AUAGUC----AA---GAAAUUAAAU
...(((..(((((....))))).((((......)))).(((((.....(((...--.)))..----..))))).....----...)))----..---.......... ( -17.80)
>DroYak_CAF1 109948 92 + 1
GGAGACACAGGGCCUCGGCCCUCGGGCCAAAUGGUUCAUUUUCAAAACUGCAAG--AUAGAGAACGUAGUAGG---GA----UUAGUU----GU--UGCAAUGCAAU
(((((...(((((....))))).(((((....))))).))))).....((((..--...((.(((.((((...---.)----))))))----.)--)....)))).. ( -23.60)
>DroAna_CAF1 113882 91 + 1
UGAGACACAGGGCCUCGGCCCUCGGGCCAAAUGGUUCAUUUUCAAAACUGCAAUUAUUCGAG----AGGAGAAUAAGA----UUCG------AU--UAAUAUGCAAU
(((((...(((((....))))).(((((....)))))..)))))....((((((((.(((((----............----))))------).--)))).)))).. ( -25.70)
>DroPer_CAF1 103447 96 + 1
GGAGACGCAGGGCCUCGGCCCUCGGGCCAAACUGUUCAUUUUCAAAACUGCAAA---GAGAG--CGAAGAAACAAAAA----UUAAUAUGGAAU--AACAAUAUAAU
((...((.(((((....)))))))..))....(((((.((((((....)).)))---).)))--))............----............--........... ( -19.50)
>consensus
GGAGACACAGGGCCUCGGCCCUCGGGCCAAACGGUUCAUUUUCAAAACUGCAAA__AGAGAG____AAGAAAAAAAAA____UUAGUA____AU__UACAAUGCAAU
.((((...(((((....))))).((((......))))..))))................................................................ (-13.88 = -13.88 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	13,804,666 – 13,804,761
Length	95
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	74.42
Mean single sequence MFE	-20.52
Consensus MFE	-14.80
Energy contribution	-14.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-0.89
Structure conservation index	0.72
SVM decision value	0.22
SVM RNA-class probability	0.641173
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13804666 95 - 20766785
AUUGCAUUGCA--AC----AACUAAUCAAUCGUUCGCUCUG----CUCUAU--CUUGCAGUUUUGAAAAUGAACCAUUUGGCCCGAGGGCCGAGGCCCUGUGUCUCC
...(((..((.--..----..........(((((..(.(((----(.....--...))))....)..)))))....(((((((....)))))))))..)))...... ( -23.40)
>DroPse_CAF1 102469 98 - 1
AUUAUAUUCUUAUAUUCCAUAUUAA----UUUUUGUUUCUCCG--CUCUC---UUUGCAGUUUUGAAAAUGAACAGUUUGGCCCGAGGGCCGAGGCCCUGCGUCUCC
.........................----.............(--(....---...)).((((.......)))).....((((....))))(((((.....))))). ( -16.60)
>DroWil_CAF1 128676 90 - 1
AUUUAAUUUC---UU----GACUAU----UUUUGUUUUCUU----UUUGCU--UUUGCAGUUUUGAAAAUGAACAGUUUGGCCCGAGGGCCGAGGCCCUGUGUCUCU
..........---..----(((...----..(..(((((..----.((((.--...))))....)))))..)(((((((((((....)))))))...)))))))... ( -24.80)
>DroYak_CAF1 109948 92 - 1
AUUGCAUUGCA--AC----AACUAA----UC---CCUACUACGUUCUCUAU--CUUGCAGUUUUGAAAAUGAACCAUUUGGCCCGAGGGCCGAGGCCCUGUGUCUCC
...(((..((.--..----......----..---........((((....(--(..........))....))))..(((((((....)))))))))..)))...... ( -17.10)
>DroAna_CAF1 113882 91 - 1
AUUGCAUAUUA--AU------CGAA----UCUUAUUCUCCU----CUCGAAUAAUUGCAGUUUUGAAAAUGAACCAUUUGGCCCGAGGGCCGAGGCCCUGUGUCUCA
((((((.((((--.(------(((.----............----.)))).))))))))))..................((((....))))(((((.....))))). ( -23.44)
>DroPer_CAF1 103447 96 - 1
AUUAUAUUGUU--AUUCCAUAUUAA----UUUUUGUUUCUUCG--CUCUC---UUUGCAGUUUUGAAAAUGAACAGUUUGGCCCGAGGGCCGAGGCCCUGCGUCUCC
.....((((((--...........(----((((((...((..(--(....---...))))...))))))).))))))..((((....))))(((((.....))))). ( -17.80)
>consensus
AUUGCAUUGCA__AU____AACUAA____UCUUUCUUUCUU____CUCUAU__UUUGCAGUUUUGAAAAUGAACAAUUUGGCCCGAGGGCCGAGGCCCUGUGUCUCC
...........................................................((((.......)))).....((((....))))(((((.....))))). (-14.80 = -14.80 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:06 2006