Locus 334

Sequence ID	2R_DroMel_CAF1
Location	2,172,225 – 2,172,335
Length	110
Max. P	0.995882

overview

Window 5

Location	2,172,225 – 2,172,335
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.63
Mean single sequence MFE	-30.46
Consensus MFE	-14.07
Energy contribution	-14.74
Covariance contribution	0.67
Combinations/Pair	1.50
Mean z-score	-2.94
Structure conservation index	0.46
SVM decision value	2.63
SVM RNA-class probability	0.995882
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2172225 110 + 20766785
----UAAUCGUC-UACCAAAAUGGGCUUACGCCGCAUCAGAUAUUUUUUGGCGGCGUA-GCCUG-AACUACGCUUU-UCGGCUUCGCAUAACAUAUCAGAGAUUAGUUAAACUUAC--AA
----(((((.((-(........(((((.(((((((..((((.....))))))))))))-)))).-......(((..-..)))...............))))))))...........--.. ( -28.80)
>DroPse_CAF1 28901 115 + 1
----AAAAUGUAACAUUACACUCGGCUCGCACCUUCCCAGAUAUUUGGGGGUGGUGUGUUGCUGGAACUACGCUUU-UUGGCUUCGCAUAACAUAUCAAAAACUGGUUAGUCCUAUUUAA
----.(((((..((.......(((((.(((((((((((((....))))))).))))))..)))))(((((.(.(((-((((..............))))))))))))).))..))))).. ( -29.24)
>DroSec_CAF1 6756 109 + 1
----UAAUCGUC-UACCAAAAUGGGCAUACGCCGC--CAGAUAUUUUUUGGCGGCGUA-GCCUAAAACUACGCUUU-UUAGCUUCGCAUAACAUAUCAGAGAUUAGUUAAACUUAC--AA
----(((((.((-(.......(((((.((((((((--((((.....))))))))))))-))))).......(((..-..)))...............))))))))...........--.. ( -36.80)
>DroSim_CAF1 6813 111 + 1
----UAAUCGUC-UACCAAAAUGGGCAUACGCCGCAUCAGAUAUUUUUUGGCGGCGUA-GCCUAAAACUACGCUUU-UUAGCUUCGCAUAACAUAUCAGAGAUUAGUUAAACUUAC--AA
----(((((.((-(.......(((((.((((((((..((((.....))))))))))))-))))).......(((..-..)))...............))))))))...........--.. ( -30.70)
>DroYak_CAF1 7045 108 + 1
-------UCGUC-UACCAAAAUUGUCUUACGCCGCAACAAAUAUUUUGUGACGGCGUA-GCCUU-AACUACGCUUUUUUGGCUUUGCACAACAUAUCAGAAAUUAGUUAAACUUAC--AA
-------.....-........((((.((((((((..((((.....))))..)))))))-)..((-(((((....(((((((...((.....))..))))))).)))))))....))--)) ( -22.00)
>DroAna_CAF1 6882 112 + 1
AACUCAACCA---UACCAAAUGGGGCUCCCGCCAC--CAUUUGUUAUGGUGCGCGGGA-UCCUUGAACUACGCUUUUUUGGCUUUGCAUAACAUAUCAGAAACUAGCUAAUCGUAU--GA
........((---(((.....((((.(((((((((--(((.....)))))).))))))-.)))).......((((((((((...((.....))..)))))))..))).....))))--). ( -35.20)
>consensus
____UAAUCGUC_UACCAAAAUGGGCUUACGCCGCA_CAGAUAUUUUGUGGCGGCGUA_GCCUA_AACUACGCUUU_UUGGCUUCGCAUAACAUAUCAGAAAUUAGUUAAACUUAC__AA
.....................(((((.((((((((...............)))))))).))))).......(((.....)))...................................... (-14.07 = -14.74 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	2,172,225 – 2,172,335
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.63
Mean single sequence MFE	-28.83
Consensus MFE	-16.27
Energy contribution	-16.86
Covariance contribution	0.59
Combinations/Pair	1.41
Mean z-score	-1.48
Structure conservation index	0.56
SVM decision value	0.09
SVM RNA-class probability	0.580416
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2172225 110 - 20766785
UU--GUAAGUUUAACUAAUCUCUGAUAUGUUAUGCGAAGCCGA-AAAGCGUAGUU-CAGGC-UACGCCGCCAAAAAAUAUCUGAUGCGGCGUAAGCCCAUUUUGGUA-GACGAUUA----
..--....(((((.((((.....(((((.....(((.......-...(((((((.-...))-))))))))......))))).((((.(((....)))))))))))))-))).....---- ( -28.70)
>DroPse_CAF1 28901 115 - 1
UUAAAUAGGACUAACCAGUUUUUGAUAUGUUAUGCGAAGCCAA-AAAGCGUAGUUCCAGCAACACACCACCCCCAAAUAUCUGGGAAGGUGCGAGCCGAGUGUAAUGUUACAUUUU----
.......((((((....((((((.....(((......)))..)-))))).))))))..((..(.((((...((((......))))..)))).).)).(((((((....))))))).---- ( -23.20)
>DroSec_CAF1 6756 109 - 1
UU--GUAAGUUUAACUAAUCUCUGAUAUGUUAUGCGAAGCUAA-AAAGCGUAGUUUUAGGC-UACGCCGCCAAAAAAUAUCUG--GCGGCGUAUGCCCAUUUUGGUA-GACGAUUA----
..--....(((((.((((...........((((((........-...)))))).....(((-((((((((((.........))--)))))))).)))....))))))-))).....---- ( -33.30)
>DroSim_CAF1 6813 111 - 1
UU--GUAAGUUUAACUAAUCUCUGAUAUGUUAUGCGAAGCUAA-AAAGCGUAGUUUUAGGC-UACGCCGCCAAAAAAUAUCUGAUGCGGCGUAUGCCCAUUUUGGUA-GACGAUUA----
..--....(((((.((((...........((((((........-...)))))).....(((-((((((((...............)))))))).)))....))))))-))).....---- ( -27.66)
>DroYak_CAF1 7045 108 - 1
UU--GUAAGUUUAACUAAUUUCUGAUAUGUUGUGCAAAGCCAAAAAAGCGUAGUU-AAGGC-UACGCCGUCACAAAAUAUUUGUUGCGGCGUAAGACAAUUUUGGUA-GACGA-------
((--((..((.((((.............)))).))...(((((((....(((((.-...))-)))(((((.((((.....)))).))))).........))))))).-.))))------- ( -26.42)
>DroAna_CAF1 6882 112 - 1
UC--AUACGAUUAGCUAGUUUCUGAUAUGUUAUGCAAAGCCAAAAAAGCGUAGUUCAAGGA-UCCCGCGCACCAUAACAAAUG--GUGGCGGGAGCCCCAUUUGGUA---UGGUUGAGUU
..--......(((((((....(..(.(((((((((............)))))).....((.-((((((.((((((.....)))--))))))))).)).))))..)..---)))))))... ( -33.70)
>consensus
UU__GUAAGUUUAACUAAUCUCUGAUAUGUUAUGCGAAGCCAA_AAAGCGUAGUU_AAGGC_UACGCCGCCAAAAAAUAUCUG_UGCGGCGUAAGCCCAUUUUGGUA_GACGAUUA____
.............(((((...........((((((............)))))).....(((.((((((((...............)))))))).)))....))))).............. (-16.27 = -16.86 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:49 2006