Locus 6078

Sequence ID	2R_DroMel_CAF1
Location	19,130,669 – 19,130,760
Length	91
Max. P	0.996336

overview

Window 1

Location	19,130,669 – 19,130,760
Length	91
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	76.97
Mean single sequence MFE	-26.06
Consensus MFE	-14.28
Energy contribution	-14.50
Covariance contribution	0.22
Combinations/Pair	1.14
Mean z-score	-3.45
Structure conservation index	0.55
SVM decision value	2.68
SVM RNA-class probability	0.996336
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19130669 91 + 20766785
AAAUGCGGCAAGGAAUCACAGCCACGCCACUACAAGCUGUAAACUUGUUGCAGAUCAAAAACGGCU-GCAC----CCUGGAACAGGGUAGCAGUAC
...(((((((((.....(((((.............)))))...)))))))))...........(((-((((----((((...)))))).))))).. ( -33.02)
>DroPse_CAF1 23394 82 + 1
AAGUGCAGCGCAAAAUCACAGCCAAAGCGCAACAAGCUGUAAACUUGUUGCAGAUCAAAAAAAAA--------------GAACGAGAUAUUCGCAC
.......(((.((.(((...((....))((((((((.......))))))))..............--------------......))).))))).. ( -17.90)
>DroEre_CAF1 19493 91 + 1
AAAUGCGGCAAGAAAUCACAGCCACGGCACUACAAGCUGUAAACUUGUUGCAGAUCAAAAACGGCU-GCAC----CCUGGAACGGGGUAGCAGCAC
...(((((((((.....(((((...(......)..)))))...)))))))))...........(((-((((----((((...)))))).))))).. ( -33.70)
>DroYak_CAF1 20442 91 + 1
AAAUGCGGCAAGAAAUCACAGCCACGGCACUACAAGCUGUAAACUUGUUGCAGAUCAAAAACGGCU-GCAC----CCUGGAACAGGGUAGCAGCAC
...(((((((((.....(((((...(......)..)))))...)))))))))...........(((-((((----((((...)))))).))))).. ( -34.40)
>DroAna_CAF1 22615 95 + 1
AAAUGCGGCAAGAAAUCACAGCCAAGGCGCAACAAGCUGUAAACUUGUUGCAGAUAAAAAAAAAUUUGAAAGAUAUUCGCAAAAGGGUA-UGGUAC
...(((((.......(((..((....))((((((((.......))))))))...............))).......)))))........-...... ( -19.34)
>DroPer_CAF1 23412 82 + 1
AAGUGCAGCGCAAAAUCACAGCCAAAGCGCAACAAGCUGUAAACUUGUUGCAGAUCAAAAAAAAA--------------GAAGGAGAUAUUCGCAC
..((((........(((...((....))((((((((.......)))))))).)))..........--------------(((.......))))))) ( -18.00)
>consensus
AAAUGCGGCAAGAAAUCACAGCCAAGGCACAACAAGCUGUAAACUUGUUGCAGAUCAAAAAAAACU_GCAC____CCUGGAACAGGGUAGCAGCAC
...(((((((((.....(((((.............)))))...)))))))))............................................ (-14.28 = -14.50 +   0.22)

alignment

secondary structure

dotplot

Window 2

Location	19,130,669 – 19,130,760
Length	91
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	76.97
Mean single sequence MFE	-27.07
Consensus MFE	-13.19
Energy contribution	-12.83
Covariance contribution	-0.36
Combinations/Pair	1.20
Mean z-score	-2.83
Structure conservation index	0.49
SVM decision value	1.97
SVM RNA-class probability	0.984206
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19130669 91 - 20766785
GUACUGCUACCCUGUUCCAGG----GUGC-AGCCGUUUUUGAUCUGCAACAAGUUUACAGCUUGUAGUGGCGUGGCUGUGAUUCCUUGCCGCAUUU
...((((.((((((...))))----))))-))...........(..(.((((((.....)))))).)..).(((((...........))))).... ( -30.70)
>DroPse_CAF1 23394 82 - 1
GUGCGAAUAUCUCGUUC--------------UUUUUUUUUGAUCUGCAACAAGUUUACAGCUUGUUGCGCUUUGGCUGUGAUUUUGCGCUGCACUU
(((((((.(((.(....--------------..............(((((((((.....)))))))))((....)).).))))))))))....... ( -24.10)
>DroEre_CAF1 19493 91 - 1
GUGCUGCUACCCCGUUCCAGG----GUGC-AGCCGUUUUUGAUCUGCAACAAGUUUACAGCUUGUAGUGCCGUGGCUGUGAUUUCUUGCCGCAUUU
(.(((((.((((.......))----))))-))))..........(((..((((.((((((((...........))))))))...))))..)))... ( -30.10)
>DroYak_CAF1 20442 91 - 1
GUGCUGCUACCCUGUUCCAGG----GUGC-AGCCGUUUUUGAUCUGCAACAAGUUUACAGCUUGUAGUGCCGUGGCUGUGAUUUCUUGCCGCAUUU
(.(((((.((((((...))))----))))-))))..........(((..((((.((((((((...........))))))))...))))..)))... ( -33.50)
>DroAna_CAF1 22615 95 - 1
GUACCA-UACCCUUUUGCGAAUAUCUUUCAAAUUUUUUUUUAUCUGCAACAAGUUUACAGCUUGUUGCGCCUUGGCUGUGAUUUCUUGCCGCAUUU
......-........((((........(((...............(((((((((.....)))))))))((....))..)))........))))... ( -20.69)
>DroPer_CAF1 23412 82 - 1
GUGCGAAUAUCUCCUUC--------------UUUUUUUUUGAUCUGCAACAAGUUUACAGCUUGUUGCGCUUUGGCUGUGAUUUUGCGCUGCACUU
(((((((.(((......--------------..............(((((((((.....)))))))))((....))...))))))))))....... ( -23.30)
>consensus
GUGCUACUACCCCGUUCCAGG____GUGC_AGCCGUUUUUGAUCUGCAACAAGUUUACAGCUUGUAGCGCCGUGGCUGUGAUUUCUUGCCGCAUUU
((((.........................................((.((((((.....)))))).)).....(((...........))))))).. (-13.19 = -12.83 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:17 2006