Locus 2

Sequence ID	pao.3275
Location	6,183,520 – 6,183,693
Length	173
Max. P	0.768746

overview

Window 5

Location	6,183,520 – 6,183,636
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.10
Mean single sequence MFE	-42.37
Consensus MFE	-26.74
Energy contribution	-25.47
Covariance contribution	-1.28
Combinations/Pair	1.29
Mean z-score	-2.81
Structure conservation index	0.63
SVM decision value	0.14
SVM RNA-class probability	0.604698
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3275 6183520 116 + 6264404
AUUCCAGGC-AAAAAAAACCCCGAGCUUCGUAUGGGGAGGGGGAAGUUC-GGGGUUCAAG-UCCGGACCGCUAGGGCGGGGUCCAG-GAAUCUGCCAACACUAAACACUGCAAAGGAGCA
.((((.(((-(.....(((((((((((((.(.........).)))))))-))))))....-((((((((.(......).))))).)-))...))))..((........))....)))).. ( -43.10)
>pau.3414 6456433 114 + 6537648
--UCCAGGC-AAAAAAAACCCCGAGCUUCGUAUGGGGAGGGGGAAGUUC-GGGGUUCAAG-UCCGGACCGCUAGGGCGGGGUCCAG-GAAUCUGCCAACACUAAACACUGCAAAGGAGCA
--....(((-(.....(((((((((((((.(.........).)))))))-))))))....-((((((((.(......).))))).)-))...)))).............((......)). ( -42.80)
>pst.213 373001 114 + 6397126
----CAGGCAAAAAAAGACCCCGGACUUCACAUGGGGA-GGGGAAGUACCGGGGCUUAAGGUCCGGACC-UUAGGGUGGGGUCCGGAAUAACUGCCAACACUUAACACAACUUAAGAGCA
----..((((....(((.(((((((((((.(.......-.).))))).)))))))))....((((((((-((.....)))))))))).....))))....(((((......))))).... ( -45.70)
>psp.161 299555 112 + 5928787
----CAGGC-AAAAAAGACCCCGGACUUCGCAUGGGGAGGGGGAAGUUCCGGGGCUUAAGGUCCAGACC-UUAGGGUGGGAUCUGG-AUAACUGCCAACACUUAACACAAC-UAGGAGCA
----..(((-(...(((.(((((((((((.(.........).)))).))))))))))...(((((((((-(......))).)))))-))...))))....((((.......-)))).... ( -41.80)
>pfo.30 60766 114 + 6438405
----CAGGC-AAAAAAAGCCCCGGACUUCAUAUGGGGAGGGAGAAGUUCCGGGGUUUAAGUUCCGAACCGCUAGGGCGGGGUUCAG-AUAUCUGCCAACACUUAACACAACAUAGGAGCA
----.....-.....((((((((((((((.............)))).))))))))))..(((((...((((....))))((..(((-....)))))..................))))). ( -39.02)
>pss.175 287452 112 + 6093698
----CAGGC-AAAAAAGACCCCGGACUUCGCAUGGGGAGGGGGAAGUUCCGGGGCUUAAGGUCCAGACC-UUAGGGUGGGAUCUGG-AUAACUGCCAACACUUAACACAAC-UAGGAGCA
----..(((-(...(((.(((((((((((.(.........).)))).))))))))))...(((((((((-(......))).)))))-))...))))....((((.......-)))).... ( -41.80)
>consensus
____CAGGC_AAAAAAAACCCCGGACUUCGCAUGGGGAGGGGGAAGUUCCGGGGCUUAAGGUCCGGACC_CUAGGGCGGGGUCCAG_AUAACUGCCAACACUUAACACAACAUAGGAGCA
......(((.....(((.(((((((((((.(.........).))))))).))))))).......(((((.(......).))))).........)))........................ (-26.74 = -25.47 +  -1.28)

alignment

secondary structure

dotplot

Window 6

Location	6,183,520 – 6,183,636
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.10
Mean single sequence MFE	-37.98
Consensus MFE	-30.00
Energy contribution	-28.54
Covariance contribution	-1.47
Combinations/Pair	1.29
Mean z-score	-2.14
Structure conservation index	0.79
SVM decision value	0.52
SVM RNA-class probability	0.768746
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3275 6183520 116 - 6264404
UGCUCCUUUGCAGUGUUUAGUGUUGGCAGAUUC-CUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCC-GAACUUCCCCCUCCCCAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAAU
(((......)))............((((((...-(((((((.(......).))))))).-...(((((((-((.((((.............)))).)))))))))..)))-)))...... ( -39.72)
>pau.3414 6456433 114 - 6537648
UGCUCCUUUGCAGUGUUUAGUGUUGGCAGAUUC-CUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCC-GAACUUCCCCCUCCCCAUACGAAGCUCGGGGUUUUUUUU-GCCUGGA--
(((......)))............((((((...-(((((((.(......).))))))).-...(((((((-((.((((.............)))).)))))))))..)))-)))....-- ( -39.72)
>pst.213 373001 114 - 6397126
UGCUCUUAAGUUGUGUUAAGUGUUGGCAGUUAUUCCGGACCCCACCCUAA-GGUCCGGACCUUAAGCCCCGGUACUUCCCC-UCCCCAUGUGAAGUCCGGGGUCUUUUUUUGCCUG----
.((.(((((......))))).)).(((((....((((((((.........-))))))))......(((((((.(((((.(.-.......).))))))))))))......)))))..---- ( -41.90)
>psp.161 299555 112 - 5928787
UGCUCCUA-GUUGUGUUAAGUGUUGGCAGUUAU-CCAGAUCCCACCCUAA-GGUCUGGACCUUAAGCCCCGGAACUUCCCCCUCCCCAUGCGAAGUCCGGGGUCUUUUUU-GCCUG----
........-...............(((((...(-(((((((.........-))))))))......((((((((.((((.............)))))))))))).....))-)))..---- ( -34.72)
>pfo.30 60766 114 - 6438405
UGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUAU-CUGAACCCCGCCCUAGCGGUUCGGAACUUAAACCCCGGAACUUCUCCCUCCCCAUAUGAAGUCCGGGGCUUUUUUU-GCCUG----
........................((((((..(-(((((((.(......).)))))))).......(((((((.((((.............))))))))))).....)))-)))..---- ( -37.12)
>pss.175 287452 112 - 6093698
UGCUCCUA-GUUGUGUUAAGUGUUGGCAGUUAU-CCAGAUCCCACCCUAA-GGUCUGGACCUUAAGCCCCGGAACUUCCCCCUCCCCAUGCGAAGUCCGGGGUCUUUUUU-GCCUG----
........-...............(((((...(-(((((((.........-))))))))......((((((((.((((.............)))))))))))).....))-)))..---- ( -34.72)
>consensus
UGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUAU_CCGGACCCCACCCUAA_GGUCCGGACCUUAAACCCCGGAACUUCCCCCUCCCCAUACGAAGUCCGGGGUCUUUUUU_GCCUG____
........................(((.......(((((((..........))))))).....(((((((((.(((((.............))))))))))).))).....)))...... (-30.00 = -28.54 +  -1.47)

alignment

secondary structure

dotplot

Window 7

Location	6,183,575 – 6,183,693
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.42
Mean single sequence MFE	-38.43
Consensus MFE	-23.16
Energy contribution	-21.50
Covariance contribution	-1.66
Combinations/Pair	1.39
Mean z-score	-1.40
Structure conservation index	0.60
SVM decision value	0.10
SVM RNA-class probability	0.584280
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3275 6183575 118 - 6264404
GAACUUUCCCGUUUUGCCGACAGUCAGAACACACGAAUGGCUUCUUGAGCCCUUCGAUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAUUC-CUGGACCCCGCCCUAGCGGUCCGGA-CUU
............((((((((((.(..((((((.((((.(((((...))))).)))).(((......)))))))))).))))))))))...-(((((((.(......).))))))).-... ( -45.80)
>pau.3414 6456486 118 - 6537648
GAACUUUCCCGUUUUGCCGACAGUCAGAACACACGAAUGGCUUCUUGAGCCCUUCGAUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAUUC-CUGGACCCCGCCCUAGCGGUCCGGA-CUU
............((((((((((.(..((((((.((((.(((((...))))).)))).(((......)))))))))).))))))))))...-(((((((.(......).))))))).-... ( -45.80)
>pst.213 373053 117 - 6397126
GAACUUAACCGUUUGGACAGGAGUCAGAGGUUCCGAUUGAUUGA-AAAAUCCAUCG-UGCUCUUAAGUUGUGUUAAGUGUUGGCAGUUAUUCCGGACCCCACCCUAA-GGUCCGGACCUU
..(((((((((....(((....)))((((....((((.((((..-..)))).))))-..)))).....)).)))))))............((((((((.........-)))))))).... ( -33.00)
>psp.161 299607 115 - 5928787
GAACUUAACCGUUUGGAUAGGAGUCAGAGGUCUCGAUUGGUUGA-AAAAUCGAUCG-UGCUCCUA-GUUGUGUUAAGUGUUGGCAGUUAU-CCAGAUCCCACCCUAA-GGUCUGGACCUU
..(((((((((......(((((((..((....))((((((((..-..)))))))).-.)))))))-..)).)))))))...........(-(((((((.........-)))))))).... ( -35.30)
>ppk.74 6051361 118 + 6181863
GAACUAAACCGGUGAAGCGGAACUCAGAGUAACUGAAUGGCUGGUGAAGCCCUUCGAUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUAU-CUGGACCCCGCCCUAGCGGUCCGGA-CUU
........(((..(.((((.(((...(((((..((((.((((.....)))).)))).)))))....))).))))...)..)))......(-(((((((.(......).))))))))-... ( -35.00)
>pel.46 5814211 118 + 5888780
GAACUAAAUCGGUGAAGCGCUACUCAGAGGUACUGAAUGGCUGGUGAAGCCUUUCGAUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUAU-CUGGACCCCGCCCUAGCGGUCCGGA-CUU
.......(((.((..((((((((..((..(((.((((.((((.....)))).)))).)))..))..)).......)))))).)).))).(-(((((((.(......).))))))))-... ( -35.71)
>consensus
GAACUUAACCGUUUAGACGGCAGUCAGAGGACCCGAAUGGCUGAUAAAGCCCUUCGAUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUAU_CUGGACCCCGCCCUAGCGGUCCGGA_CUU
......................(((((......((((.((((.....)))).))))..((......))...........))))).......(((((((.(......).)))))))..... (-23.16 = -21.50 +  -1.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:03:20 2007