Locus 4336

Sequence ID	2L_DroMel_CAF1
Location	12,416,136 – 12,416,244
Length	108
Max. P	0.971287

overview

Window 1

Location	12,416,136 – 12,416,244
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.40
Mean single sequence MFE	-28.88
Consensus MFE	-22.18
Energy contribution	-22.18
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.77
SVM decision value	1.67
SVM RNA-class probability	0.971287
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12416136 108 + 22407834
UCUUUCCCUCGGG-AAU-----------UUUCUCCCGAUCCCGAAAUGUGACAAUCGUGUCACGUACUCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
........(((((-(..-----------....)))))).....(((((((((((.((((..((((..(((((.((....)).))))))))))))).)))))))))))............. ( -33.00)
>DroVir_CAF1 315272 81 + 1
--------------------------------------UG-CCAAAUGUGACAAUCGUGUCACGUACGCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
--------------------------------------..-..(((((((((((.((((..((((...((((.((....)).)))).)))))))).)))))))))))............. ( -22.90)
>DroPse_CAF1 328634 118 + 1
UCUCUCUCUCUGG-GAUCCCUCCCCUUUUUGGUGGCGCUG-CCAAAUGUGACAAUCGUGUCACGUACUCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
.......(((.((-((....))))......(((......)-))(((((((((((.((((..((((..(((((.((....)).))))))))))))).))))))))))).....)))..... ( -32.50)
>DroMoj_CAF1 321259 97 + 1
----------------------UUGCUGUUGUUGGCAAUG-CCAAAUGUGACAAUCGUGUCACGUACGCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
----------------------(((((......)))))..-..(((((((((((.((((..((((...((((.((....)).)))).)))))))).)))))))))))............. ( -26.80)
>DroAna_CAF1 226735 107 + 1
UUUGGGC--CGAAAAUU-----------UCUCUCCCAUUCGCCAAAUGUGACAAUCGUGUCACGUACCCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
...(((.--.((.....-----------..)).)))(((((..(((((((((((.((((..((((...((((.((....)).)))).)))))))).)))))))))))....))))).... ( -25.70)
>DroPer_CAF1 331355 116 + 1
UCUC--UCUCUGG-GACCCCUCCCCUUUUUGGUGGCGCUG-CCAAAUGUGACAAUCGUGUCACGUACUCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
....--.(((.((-((....))))......(((......)-))(((((((((((.((((..((((..(((((.((....)).))))))))))))).))))))))))).....)))..... ( -32.40)
>consensus
UCU______C_GG__AU___________UUGCUGGCGAUG_CCAAAUGUGACAAUCGUGUCACGUACUCAAUGUUCUGGAAGAUUGAACGUUACGUUUGUCGCGUUUAAAAUGAGUUUUU
...........................................(((((((((((.((((..((((...((((.((....)).)))).)))))))).)))))))))))............. (-22.18 = -22.18 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	12,416,136 – 12,416,244
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.40
Mean single sequence MFE	-25.07
Consensus MFE	-14.20
Energy contribution	-14.45
Covariance contribution	0.25
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.57
SVM decision value	0.93
SVM RNA-class probability	0.885106
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12416136 108 - 22407834
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGAGUACGUGACACGAUUGUCACAUUUCGGGAUCGGGAGAAA-----------AUU-CCCGAGGGAAAGA
....(((((........(((.....)))...((((.........))))..)))))..((((((....)))))).((((((((((....))..-----------..)-)))))))...... ( -27.50)
>DroVir_CAF1 315272 81 - 1
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGCGUACGUGACACGAUUGUCACAUUUGG-CA--------------------------------------
.................((.....((((((.((((.........)))).))))))..((((((....)))))).....)-).-------------------------------------- ( -19.10)
>DroPse_CAF1 328634 118 - 1
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGAGUACGUGACACGAUUGUCACAUUUGG-CAGCGCCACCAAAAAGGGGAGGGAUC-CCAGAGAGAGAGA
.....(((.((((....(.(((((.(((.(((((((((.((....)).)))))..))))...))).))))).)...(((-(...))))........((((....))-)).)))))))... ( -27.40)
>DroMoj_CAF1 321259 97 - 1
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGCGUACGUGACACGAUUGUCACAUUUGG-CAUUGCCAACAACAGCAA----------------------
.................((.....((((((.((((.........)))).))))))..((((((....))))))..((((-(...))))).....))..---------------------- ( -23.10)
>DroAna_CAF1 226735 107 - 1
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGGGUACGUGACACGAUUGUCACAUUUGGCGAAUGGGAGAGA-----------AAUUUUCG--GCCCAAA
................(((.....((.(((.((((.........)))).))).))..((((((....)))))).....)))..((((.((((-----------...)))).--.)))).. ( -24.20)
>DroPer_CAF1 331355 116 - 1
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGAGUACGUGACACGAUUGUCACAUUUGG-CAGCGCCACCAAAAAGGGGAGGGGUC-CCAGAGA--GAGA
.....(((.........(.(((((.(((.(((((((((.((....)).)))))..))))...))).))))).).(((((-..((.((.((......))..)).)).-)))))))--)... ( -29.10)
>consensus
AAAAACUCAUUUUAAACGCGACAAACGUAACGUUCAAUCUUCCAGAACAUUGAGUACGUGACACGAUUGUCACAUUUGG_CAGCGCCACCAA___________AU__CC_G______AGA
....(((((........(((.....)))...((((.........))))..)))))..((((((....))))))............................................... (-14.20 = -14.45 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:21 2006