Locus 1207

Sequence ID	3L_DroMel_CAF1
Location	3,436,260 – 3,436,368
Length	108
Max. P	0.995601

overview

Window 9

Location	3,436,260 – 3,436,368
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.43
Mean single sequence MFE	-28.09
Consensus MFE	-5.94
Energy contribution	-6.70
Covariance contribution	0.76
Combinations/Pair	1.11
Mean z-score	-2.28
Structure conservation index	0.21
SVM decision value	1.93
SVM RNA-class probability	0.982870
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3436260 108 + 23771897
CAGUGAUGGGAACCAAAUGGA-AGGUGUU--G-UA-CCAAAAAGAUGGGUACAUUUCU--UUGAAUUGAAAAUAUCUACAC-AAGCUUGAGAAAGUGCUUAAGAAUAAGCGUU---GG-A
..((((((.....(((.(.((-(((...(--(-((-((.........))))))..)))--)).).)))....)))).)).(-((((((....))))(((((....))))).))---).-. ( -22.30)
>DroSec_CAF1 51566 116 + 1
CAGUGAUGGGUACCAAAUGGAAAGGUGUACCCCUACCCAGAAUGAUGGGUACAUUUUUAAGCGAAUUAA-A--AUCUACACGAAGCUUGAGAACGUGCUUAUGAUUUCGGAGGGGGGA-G
((....))..((((.........))))..(((((..((..(((.((((((((.(((((((((.......-.--...........))))))))).)))))))).)))..))..))))).-. ( -37.01)
>DroSim_CAF1 40769 109 + 1
CAGUGAUGGGUACCAAAUGGA-AGGUGUACCC-UA-CCAGAAAGAUGGGUACAUU-UUACGCGAAUUAAAA--AUGUACAC-AAGCUUGAGAAAGUGCUUAAGAAUUCGCGUU---GG-A
((....))....((((....(-((((((((((-..-..........)))))))))-)).((((((((....--.((....)-)..((((((......))))))))))))))))---))-. ( -32.10)
>DroEre_CAF1 53409 92 + 1
CAGUGAUGGGUA-CAAAUGGA-AGGUGUACCC-UU-CUAUAAAGAUGGGUACUUU-UUAAGUGAAUUUAAA--AUGCACAC-AAGCCUGA-GAA----------------AUU---UGUA
((....))..((-(((((...-((((((((((-.(-((....))).))))))...-....(((........--...)))..-..))))..-...----------------)))---)))) ( -22.60)
>DroYak_CAF1 50835 109 + 1
CAGCGAUGGGUAAUAAAUGGA-AGGAGUACCC-UA-CUAGAAAGAUGGGUACUUU-UUAAAUUCAUAAAAA--AUGCACAC-AAGUCGGG-AAAGUGCUUAAGAAUUCGCGUU---GGUA
(((((.(((((....(((..(-((((((((((-..-((....))..)))))))))-))..)))........--..((((..-........-...))))......)))))))))---)... ( -26.42)
>consensus
CAGUGAUGGGUACCAAAUGGA_AGGUGUACCC_UA_CCAGAAAGAUGGGUACAUU_UUAAGUGAAUUAAAA__AUGUACAC_AAGCUUGAGAAAGUGCUUAAGAAUUCGCGUU___GG_A
.......................(((((((((..............)))))))))................................................................. ( -5.94 =  -6.70 +   0.76)

alignment

secondary structure

dotplot

Window 0

Location	3,436,260 – 3,436,368
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.43
Mean single sequence MFE	-22.49
Consensus MFE	-5.22
Energy contribution	-5.98
Covariance contribution	0.76
Combinations/Pair	1.14
Mean z-score	-2.55
Structure conservation index	0.23
SVM decision value	2.59
SVM RNA-class probability	0.995601
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3436260 108 - 23771897
U-CC---AACGCUUAUUCUUAAGCACUUUCUCAAGCUU-GUGUAGAUAUUUUCAAUUCAA--AGAAAUGUACCCAUCUUUUUGG-UA-C--AACACCU-UCCAUUUGGUUCCCAUCACUG
.-((---((.(((((....)))))..............-((((......((((.......--.))))((((((.........))-))-)--)))))..-.....))))............ ( -17.50)
>DroSec_CAF1 51566 116 - 1
C-UCCCCCCUCCGAAAUCAUAAGCACGUUCUCAAGCUUCGUGUAGAU--U-UUAAUUCGCUUAAAAAUGUACCCAUCAUUCUGGGUAGGGGUACACCUUUCCAUUUGGUACCCAUCACUG
.-...((((...((((((....(((((...........))))).)))--)-))................((((((......))))))))))...(((.........)))........... ( -24.00)
>DroSim_CAF1 40769 109 - 1
U-CC---AACGCGAAUUCUUAAGCACUUUCUCAAGCUU-GUGUACAU--UUUUAAUUCGCGUAA-AAUGUACCCAUCUUUCUGG-UA-GGGUACACCU-UCCAUUUGGUACCCAUCACUG
.-((---((((((((((.....((((............-))))....--....)))))))))..-..((((((((((.....))-).-)))))))...-......)))............ ( -26.92)
>DroEre_CAF1 53409 92 - 1
UACA---AAU----------------UUC-UCAGGCUU-GUGUGCAU--UUUAAAUUCACUUAA-AAAGUACCCAUCUUUAUAG-AA-GGGUACACCU-UCCAUUUG-UACCCAUCACUG
....---...----------------...-.(((...(-(.((((((--(((((......))))-)).((((((.(((....))-).-))))))....-......))-))).))...))) ( -21.90)
>DroYak_CAF1 50835 109 - 1
UACC---AACGCGAAUUCUUAAGCACUUU-CCCGACUU-GUGUGCAU--UUUUUAUGAAUUUAA-AAAGUACCCAUCUUUCUAG-UA-GGGUACUCCU-UCCAUUUAUUACCCAUCGCUG
....---...((((........((((...-........-..))))..--.....((((((..((-..(((((((..((....))-..-)))))))..)-)..))))))......)))).. ( -22.12)
>consensus
U_CC___AACGCGAAUUCUUAAGCACUUUCUCAAGCUU_GUGUACAU__UUUUAAUUCACUUAA_AAUGUACCCAUCUUUCUGG_UA_GGGUACACCU_UCCAUUUGGUACCCAUCACUG
...................................................................(((((((..............)))))))......................... ( -5.22 =  -5.98 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:10 2006