Origin IGS: tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttttggagggtatccgctcggaaaagacagaggcagtgtccaaatactaaagacactgcctccgtcttttttcctccatggaagtgaggagagagagaagagaatgctgcaagtgcgtcggccttatgaccggatttacagaggctctctcgaatttacaatcgacactctcaacaagaaaaagcga Mask Tandem Repeat Region ================================================ tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Find is-nt database================================================ Query_seq: PG0530:PG0531|PG0530:PG0531:carbamoyl-phosphate synthase, large subunit:NAD(+) synthetase:-><-:579097..579285 189 tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0530:PG0531|PG0530:PG0531:carbamoyl-phosphate synthase, large subunit:NAD(+) synthetase:-><-:579097..579285 189 tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0530:PG0531|PG0530:PG0531:carbamoyl-phosphate synthase, large subunit:NAD(+) synthetase:-><-:579097..579285 189 tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 83 End: 187 .................................................................................. M L F S L S S L P W R K K D G G S V F S I W T L P L S F P S G Y P P K .. Protein_Len: 52 Strand: + Start: 33 End: 188 ................................ M R E S L C K S G H K A D A L A A F S S L S P H F H G G K K T E A V S L V F G H C L C L F R A D T L Q K . Protein_Len: 36 Strand: - Start: 3 End: 110 .. S K R T S L T S Q L N S L A E T F G T M L G V C K C C E R R E R R V E M ............................................................................... Protein_Len: 48 Strand: - Start: 1 End: 144 R K K K N L T D I T F E L S G R Y I R D Y P R R V Q L M R K E R E E S G H L F F S P P L T K L M ............................................. tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.6 Tail_Score: -4.07885 Start: 122 End: 162 Full_Region: CCATGGAGGAAAAAA GACGGAGGCAGTGTCT TTAGTATTT GGACACTGCCTCTGTC TTTTCCGAGCGGATA .........................................................................................................................GACGGAGGCAGTGTCTTTAGTATTTGGACACTGCCTCTGTC........................... TransTerm Strand: - Conf: 100 HP_score: -12.7 Tail_Score: -5.1675 Start: 122 End: 162 Full_Region: tatccgctcggaaaa gacagaggcagtgtc caaatactaaa gacactgcctccgtc ttttttcctccatgg .........................................................................................................................gacagaggcagtgtccaaatactaaagacactgcctccgtc........................... Find igs database================================================ Query_seq: PG0530:PG0531|PG0530:PG0531:carbamoyl-phosphate synthase, large subunit:NAD(+) synthetase:-><-:579097..579285 189 tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcattctcttctctctctcctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_002950_PG0530_PG0531|carbamoyl-phosphate synthase, large subunit:NAD(+) synthetase|POSITIVE:NEGATIVE|[579097,579285]|189 HSP 1 e-value: 4.0E-44 bit: 178.0 Len: 90 Query Start:100 Query End:189 Subject Strand: POSITIVE Subject Start: 100 Subject End: 189 ...................................................................................................ctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga ...................................................................................................ctcacttccatggaggaaaaaagacggaggcagtgtctttagtatttggacactgcctctgtcttttccgagcggataccctccaaaaga HSP 2 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcat......................................................................................................... tcgctttttcttgttgagagtgtcgattgtaaattcgagagagcctctgtaaatccggtcataaggccgacgcacttgcagcat......................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGCUUUUUCUUGUUGAGAGUGUCGAUUGUAAAUUCGAGAGAGCCUCUGUAAAUCCGGUCAUAAGGCCGACGCACUUGCAGCAUUCUCUUCUCUCUCUCCUCACUUCCAUGGAGGAAAAAAGACGGAGGCAGUGUCUUUAGUAUUUGGACACUGCCUCUGUCUUUUCCGAGCGGAUACCCUCCAAAAGA ........((((...(((.(((((............(((((((...((((((...(((((....)))))......))))))..)))))))..(((..(((((.(......)))))).((((((((((((((((((((.........))))))))))))))))))))..)))..))))).)))...)))) (-71.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUGGAGGGUAUCCGCUCGGAAAAGACAGAGGCAGUGUCCAAAUACUAAAGACACUGCCUCCGUCUUUUUUCCUCCAUGGAAGUGAGGAGAGAGAGAAGAGAAUGCUGCAAGUGCGUCGGCCUUAUGACCGGAUUUACAGAGGCUCUCUCGAAUUUACAAUCGACACUCUCAACAAGAAAAAGCGA ((((...((((((.((..(((.((((((((.(((((((((((...........))))))))))).))))))))((((((......).)))))))).((((.(((....(((.((((.(((((......))).)).)))).)))...)))))))............)).))))))...))))........ (-66.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 180 132 172 122 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 354 45 1 126 61 NC_002950:PG1963|5end_Sua5/YciO/YrdC/YwlC_family_protein_2052338..2052568_POSITIVE 340 80 37 223 180 NC_002950:PG0413|5end_hypothetical_protein_451781..452011_NEGATIVE 339 110 64 190 144 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 339 180 132 230 174 NC_002950:PG0771|5end_hypothetical_protein_824524..824754_POSITIVE 336 85 43 173 124 NC_002950:PG1132|5end_valyl-tRNA_synthetase_1210912..1211142_POSITIVE 335 60 13 42 3 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 334 100 51 226 168 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 332 156 111 64 13 NC_002950:PG0568|5end_elongation_factor_P_624565..624795_NEGATIVE 332 100 55 58 5 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 331 136 92 114 67 NC_002950:PG1494|5end_hypothetical_protein_1569841..1570071_POSITIVE 330 70 24 61 11 NC_002950:PG2034|5end_oxidoreductase,_FAD-binding,_putative_2135701..2135931_NEGATIVE 328 86 44 210 171 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 327 70 21 69 19 NC_002950:PG1848|5end_RNA_methyltransferase,_TrmH_family_1947382..1947612_NEGATIVE 327 99 54 169 113 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 327 88 41 146 86 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 326 79 45 73 30 NC_002950:PG0094|5end_outer_membrane_efflux_protein,_putative_111193..111423_NEGATIVE 325 136 91 74 32 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 325 87 41 83 18 NC_002950:PG1755|5end_fructose-bisphosphate_aldolase_1843278..1843508_NEGATIVE 324 179 141 211 173 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 80 35 145 104 NC_002950:PG1080|3end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1148291..1148441_POSITIVE 359 169 124 119 79 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 354 83 43 68 32 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 348 100 54 102 48 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 329 108 63 87 38 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 329 170 121 147 98 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 327 70 21 72 22 NC_002950:PG1849|3end_DNA_repair_protein_RecN_1947379..1947529_NEGATIVE 327 88 41 126 66 NC_002950:PG1056|3end_hypothetical_protein_1123479..1123629_POSITIVE 325 136 91 87 45 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 324 60 11 141 91 NC_002950:PG0957|3end_riboflavin_biosynthesis_protein_RibF_1018131..1018281_POSITIVE 320 106 66 102 51 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 317 108 67 57 13 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 315 158 112 54 6 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 315 110 66 57 9 NC_002950:PG1634|3end_hypothetical_protein_1714723..1714873_NEGATIVE 314 108 66 118 69 NC_002950:PG0366|3end_hypothetical_protein_400255..400405_NEGATIVE 313 67 21 67 12 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 310 108 61 142 76 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE 309 99 53 54 3 NC_002950:PG1836|3end_nucleoside_permease_NupG_1929858..1930008_POSITIVE 309 79 36 61 9 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 308 100 53 142 93 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE