Locus 135

Sequence ID	pao.1628
Location	3,106,792 – 3,106,920
Length	128
Max. P	0.923423

overview

Window 8

Location	3,106,792 – 3,106,892
Length	100
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.20
Mean single sequence MFE	-37.15
Consensus MFE	-25.90
Energy contribution	-25.52
Covariance contribution	-0.38
Combinations/Pair	1.35
Mean z-score	-1.51
Structure conservation index	0.70
SVM decision value	1.15
SVM RNA-class probability	0.923423
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1628 3106792 100 - 6264404
UCUCCGUCCGCGCGCUUCGG-CGCAGGGGU-GCCGCAAGGCGCCUGCCACUGUGAGGCAGGCCG-------------GCC--CGGCGGGCGACGCUUACUGGCACAUCCCAACCCAC
....(((((((((((....)-)))..((((-(((....)))(((((((.......)))))))..-------------)))--).)))))))..(((....))).............. ( -56.20)
>pst.1443 3769800 88 + 6397126
UCU----------GGUCCGG-UUCAAGGUUGGCCCCAAGGCUCCUGCCACUGUGAGGCAGGCAU-------------ACU---ACCGGAUCACG--UACUGGCUCAUCCCAACCCAC
..(----------(((((((-(.....((..(((.((.(((....)))....)).)))..))..-------------...---)))))))))..--...(((......)))...... ( -29.60)
>psp.1295 3437666 88 + 5928787
UCU----------GGUCCGG-UUCAAGGUUGGCCCCAAGGCUCCUGCCACUGUGAGGCAGGCAU-------------ACC---ACCGGAUCACG--UACUGGCUCAUCCCAACCCAC
..(----------(((((((-(....((((((((....))).((((((.......)))))))).-------------)))---)))))))))..--...(((......)))...... ( -30.90)
>pfo.1115 4237985 105 + 6438405
UCU----------GGUUCGGUUUUCCGGUUGGCCGCAAGGCUCCUGCCGCUGUAAGGCAGGCGUUCGUCAUUGAAUGGCCUGGAUCGGAUCUUG--UACUGGCUCAUCCCAACCCAC
...----------((((.((....(((((.(((((..((((.((((((.......))))))((((((....))))))))))....))).))...--.))))).....)).))))... ( -37.80)
>pf5.1270 4744026 104 + 7074893
UCU----------GGUUCGGUUUUUCGGUUGGCCGCAAGGCUCUUGCCACUGUGAGGCAGGCGUUCGUAGCAGAACGGCC-GGACUGAAUCGCG--UACUGGCUCAUCCCAACCCAC
...----------(((((((((...((((.((((....))))((((((.......))))))(((((......))))))))-))))))))))((.--.....)).............. ( -37.50)
>pss.1326 3578004 88 + 6093698
UCU----------GGUCCGG-UUCAAGGUUGGCCCCAAGGCUCCUGCCACUGUGAGGCAGGCAU-------------ACC---ACCGGAUCACG--UACUGGCUCAUCCCAACCCAC
..(----------(((((((-(....((((((((....))).((((((.......)))))))).-------------)))---)))))))))..--...(((......)))...... ( -30.90)
>consensus
UCU__________GGUCCGG_UUCAAGGUUGGCCCCAAGGCUCCUGCCACUGUGAGGCAGGCAU_____________ACC___ACCGGAUCACG__UACUGGCUCAUCCCAACCCAC
.............(((((((......(((.((((....))))((((((.......))))))................)))....)))))))........(((......)))...... (-25.90 = -25.52 +  -0.38)

alignment

secondary structure

dotplot

Window 9

Location	3,106,821 – 3,106,920
Length	99
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	66.32
Mean single sequence MFE	-31.78
Consensus MFE	-17.36
Energy contribution	-17.75
Covariance contribution	0.39
Combinations/Pair	1.14
Mean z-score	-1.29
Structure conservation index	0.55
SVM decision value	0.16
SVM RNA-class probability	0.612492
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1628 3106821 99 + 6264404
CCGCCG--GGC-------------CGGCCUGCCUCACAGUGGCAGGCGCCUUGCGGC-ACCCCUGCG-CCGAAGCGCGCGGACGGAGA-UCACUGGGAAUGGAUACUGACGAAAAAC
((((.(--(((-------------..(((((((.......))))))))))).)))).-.((((((((-(......))))))..((...-...))))).................... ( -40.40)
>pst.1443 3769827 82 - 6397126
CCGGU---AGU-------------AUGCCUGCCUCACAGUGGCAGGAGCCUUGGGGCCAACCUUGAA-CCGGACC----------AGA-UGACUGGAA-UGUACG------AAAACC
(((((---...-------------...((((((.......))))))....(..(((....)))..))-)))).((----------((.-...))))..-......------...... ( -28.60)
>psp.1295 3437693 82 - 5928787
CCGGU---GGU-------------AUGCCUGCCUCACAGUGGCAGGAGCCUUGGGGCCAACCUUGAA-CCGGACC----------AGA-UGACUGGAA-UGUACG------AAAAAC
(((((---(((-------------...((((((.......)))))).)))(..(((....)))..))-)))).((----------((.-...))))..-......------...... ( -32.00)
>pfo.1115 4238012 94 - 6438405
CCGAUCCAGGCCAUUCAAUGACGAACGCCUGCCUUACAGCGGCAGGAGCCUUGCGGCCAACCGGAAAACCGAACC----------AGAGUGACUGGGA-UUCAAA------------
....(((((..(((((...........((((((.......)))))).(((....)))....(((....)))....----------.))))).))))).-......------------ ( -29.50)
>pf5.1270 4744053 93 - 7074893
UCAGUCC-GGCCGUUCUGCUACGAACGCCUGCCUCACAGUGGCAAGAGCCUUGCGGCCAACCGAAAAACCGAACC----------AGAGUGACUGGGG-UUCACA------------
.......-(((.((((......)))))))((((.......)))).(((((...(((....)))..........((----------((.....))))))-)))...------------ ( -28.20)
>pss.1326 3578031 76 - 6093698
CCGGU---GGU-------------AUGCCUGCCUCACAGUGGCAGGAGCCUUGGGGCCAACCUUGAA-CCGGACC----------AGA-UGACUGGAA-UGUACG------------
(((((---(((-------------...((((((.......)))))).)))(..(((....)))..))-)))).((----------((.-...))))..-......------------ ( -32.00)
>consensus
CCGGU___GGC_____________AUGCCUGCCUCACAGUGGCAGGAGCCUUGCGGCCAACCUUGAA_CCGAACC__________AGA_UGACUGGAA_UGUACA____________
(((((......................((((((.......)))))).(((....)))..................................)))))..................... (-17.36 = -17.75 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:14:26 2007