Locus 132

Sequence ID	pao.1768
Location	3,299,121 – 3,299,327
Length	206
Max. P	0.977424

overview

Window 3

Location	3,299,121 – 3,299,228
Length	107
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	69.70
Mean single sequence MFE	-46.25
Consensus MFE	-26.17
Energy contribution	-26.53
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-2.00
Structure conservation index	0.57
SVM decision value	1.79
SVM RNA-class probability	0.977424
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1768 3299121 107 + 6264404
CGCGCGCGUGCGCCGCA------GGCACCC-----CGUGCCGCGUAUUUCUUCGGGUAUUGGUUUAGCCACUCCGGCGCCUGAUACCCCAACGGCGCCCACGGUAUACGGGACGCCUA
.(((((((.....))).------(((((..-----.)))))))))........((((((..(....(((.....)))..)..))))))....((((.((.((.....)))).)))).. ( -45.30)
>ppk.1773 2715682 98 - 6181863
UUGCCGGCUGCGUGGCA------------------CCUGCCAGCUAUUACUUUGGGUAUUGGUUUAGCCACUAG-GCGCC-GAUACCCACCCGGCGUCCACCUUCGAGGGGCCGCCGA
.....((..((.((((.------------------...))))))........(((((((((((...(((....)-)))))-))))))))))(((((.((.((.....)))).))))). ( -44.20)
>pfo.1801 3510822 111 + 6438405
CGGCUGCCCGGGUGAAC------GGUGCCUCGGCUCCAGCAAGCUUUUAUUUUGGGUAUUGGUUUAGCCACUGGCGCGCCUGAUACCCAACCGGCGCCCAU-UUGAACGGGUCGCCUA
.(((.(((((..((((.------((((((..((((......))))......((((((((((((...(((...)))..))).)))))))))..))))))..)-)))..))))).))).. ( -49.90)
>pf5.2158 4113432 111 + 7074893
CGGCUGCCUGGGUCAAC------GGCACUCGGGCUCCGGCCAGCUUUUAUUUUGGGUAUUGGUUUAGCCACUGGCGCGCCUGAUACCCAACCGGCGCCCAC-UUCAACGGGUCGCCUA
.(((((((((((((...------.).))))))))...))))..........((((((((((((...(((...)))..))).)))))))))..(((((((..-......))).)))).. ( -48.40)
>pst.1799 3402093 117 + 6397126
CGGCUGUGCGGAUCGCAUCGGUGAGCACACGUCCGCAGCUCAACACUUAUUAUGGGUAUUGGUUUAGCCACUGGCGCGCCUGAUACCCAUCCGGCGCCCAC-UUCAAGGGGACGCCAA
.(((((((((..((((....)))).....)))..))))))...........((((((((((((...(((...)))..))).)))))))))..(((((((..-......))).)))).. ( -44.20)
>psp.1403 3226412 117 - 5928787
UGGCUGUGCGGGUUGCCUCGGUGAAUGCUCCUGUUCAGCUCAACUCUUAUUAUGGGUAUUGGUAUAGCCACUGGCGCGCCUGAUACCCAUCCGGCGCCCAC-UUCAAGGGGACGCCAA
.(((((.((((((..(....)..).....))))).)))))...........((((((((((((...(((...)))..))).)))))))))..(((((((..-......))).)))).. ( -45.50)
>consensus
CGGCUGCCCGGGUCGCA______GGCACCC__GCUCCGGCCAGCUAUUAUUUUGGGUAUUGGUUUAGCCACUGGCGCGCCUGAUACCCAACCGGCGCCCAC_UUCAACGGGACGCCUA
...................................................((((((((((((...((.....))..))).)))))))))..(((((((.........))).)))).. (-26.17 = -26.53 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	3,299,228 – 3,299,327
Length	99
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	68.12
Mean single sequence MFE	-35.02
Consensus MFE	-26.63
Energy contribution	-26.52
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-4.75
Structure conservation index	0.76
SVM decision value	1.19
SVM RNA-class probability	0.928764
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1768 3299228 99 + 6264404
CCCUGCACACGCAAACCCCCGGUCGGCUCCCCGACCGGGGGUUUUGU-UUUUCCGG--C-CCGUUUUUC--CGGCCCACAAGGCCACAACCACAGACCAACGCAC
...(((..(((.((((((((((((((....)))))))))))))))))-......((--.-(.((.....--.((((.....))))......)).).))...))). ( -41.00)
>ppk.1773 2715782 72 - 6181863
AUGAGAAUACUCAAACCCCCGGUCGGCUUCCCGACCGGGGGUUUUGU-UUUUCAGG--C-C--------------------UUUGACCAACA---------CCGA
.((((((.((..((((((((((((((....)))))))))))))).))-))))))((--.-.--------------------.....))....---------.... ( -33.40)
>pf5.2158 4113544 92 + 7074893
CAGAGAAAUCUCAA-CCCCCGGUCGGCCUCCCGACCGGGGGUUUUGUUUUUUCCGG--CACUGCAUUUU--CAACCACGACUUUCAGCGACA--------CACCG
..((((((.(..((-(((((((((((....)))))))))))))..).))))))(((--(.(((.....(--(......))....))).)...--------..))) ( -33.80)
>pfo.1801 3510934 81 + 6438405
CAGAGAUUUCUCAA-CCCCCGGUCGGCCUCCCGACCGGGGGUUUUGUUUUUUCAGG--C-CCGAACUUU------------UUUCAGCAAUA--------CACCA
..((((...(..((-(((((((((((....)))))))))))))..)...))))..(--(-..(((....------------.))).))....--------..... ( -32.40)
>psp.1403 3226530 89 - 5928787
CAGAGAAUUCUCUA-CCCCCGGUCGGCUUCCCGACCGGGGGUUUUGUUUUUUCAGGGCC-AGGUAUUUU--CAACC-----CUUCAUAAAUA-------UCACGC
..(((((..(...(-(((((((((((....))))))))))))...)..)))))((((..-.((.....)--)..))-----)).........-------...... ( -35.60)
>pst.1799 3402211 91 + 6397126
CAGAGAAUUCUCUA-CCCCCGGUCGGCUACCCGACCGGGGGUUUUGUUUUUUCAGGGCC-CUGUAUUUUUUCGACG-----CUUCAUAAAAA-------UCACGC
..(((((..(...(-(((((((((((....))))))))))))...)..)))))......-..((((((((..((..-----..))..)))))-------).)).. ( -33.90)
>consensus
CAGAGAAUUCUCAA_CCCCCGGUCGGCUUCCCGACCGGGGGUUUUGUUUUUUCAGG__C_CCGUAUUUU__C_ACC_____UUUCACAAACA________CACGC
..(((....)))...(((((((((((....)))))))))))................................................................ (-26.63 = -26.52 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	3,299,228 – 3,299,327
Length	99
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	68.12
Mean single sequence MFE	-41.52
Consensus MFE	-27.35
Energy contribution	-27.68
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-5.15
Structure conservation index	0.66
SVM decision value	1.47
SVM RNA-class probability	0.957078
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1768 3299228 99 - 6264404
GUGCGUUGGUCUGUGGUUGUGGCCUUGUGGGCCG--GAAAAACGG-G--CCGGAAAA-ACAAAACCCCCGGUCGGGGAGCCGACCGGGGGUUUGCGUGUGCAGGG
(..(.(((((((((..((.(((((.....)))))--.))..))))-)--))))....-((.((((((((((((((....))))))))))))))..)))..).... ( -59.30)
>ppk.1773 2715782 72 + 6181863
UCGG---------UGUUGGUCAAA--------------------G-G--CCUGAAAA-ACAAAACCCCCGGUCGGGAAGCCGACCGGGGGUUUGAGUAUUCUCAU
....---------((((..(((..--------------------.-.--..)))..)-)))((((((((((((((....))))))))))))))(((....))).. ( -37.90)
>pf5.2158 4113544 92 - 7074893
CGGUG--------UGUCGCUGAAAGUCGUGGUUG--AAAAUGCAGUG--CCGGAAAAAACAAAACCCCCGGUCGGGAGGCCGACCGGGGG-UUGAGAUUUCUCUG
((((.--------....((((....(((....))--).....)))))--)))..........(((((((((((((....)))))))))))-))(((....))).. ( -39.90)
>pfo.1801 3510934 81 - 6438405
UGGUG--------UAUUGCUGAAA------------AAAGUUCGG-G--CCUGAAAAAACAAAACCCCCGGUCGGGAGGCCGACCGGGGG-UUGAGAAAUCUCUG
.(((.--------(...(((....------------..)))..).-)--))...........(((((((((((((....)))))))))))-))(((....))).. ( -35.80)
>psp.1403 3226530 89 + 5928787
GCGUGA-------UAUUUAUGAAG-----GGUUG--AAAAUACCU-GGCCCUGAAAAAACAAAACCCCCGGUCGGGAAGCCGACCGGGGG-UAGAGAAUUCUCUG
.(((((-------...))))).((-----(((((--........)-))))))...........((((((((((((....)))))))))))-)((((....)))). ( -39.70)
>pst.1799 3402211 91 - 6397126
GCGUGA-------UUUUUAUGAAG-----CGUCGAAAAAAUACAG-GGCCCUGAAAAAACAAAACCCCCGGUCGGGUAGCCGACCGGGGG-UAGAGAAUUCUCUG
..((.(-------(((((.(((..-----..))).)))))).(((-....))).....))...((((((((((((....)))))))))))-)((((....)))). ( -36.50)
>consensus
GCGUG________UGUUGAUGAAA_____GGU_G__AAAAUACAG_G__CCUGAAAAAACAAAACCCCCGGUCGGGAAGCCGACCGGGGG_UUGAGAAUUCUCUG
................................................................(((((((((((....)))))))))))...(((....))).. (-27.35 = -27.68 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:14:11 2007