Origin IGS: cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtcgtattatctatgaattagaaatatcaggagcggactctgccactcctaatcattatccggagcaaaatggccaatcgggagaacgaagggcgaataacatatccgtccgccataatccgagattaaagccactcctgtctctcttaccacg Mask Tandem Repeat Region ================================================ cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Find is-nt database================================================ Query_seq: PG0793:PG0794|PG0793:PG0794:fructose-1,6-bisphosphatase:penicillin-binding protein 1A, putative:->->:846396..846550 155 cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0793:PG0794|PG0793:PG0794:fructose-1,6-bisphosphatase:penicillin-binding protein 1A, putative:->->:846396..846550 155 cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0793:PG0794|PG0793:PG0794:fructose-1,6-bisphosphatase:penicillin-binding protein 1A, putative:->->:846396..846550 155 cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 2 End: 103 . M V R E T G V A L I S D Y G G R I C Y S P F V L P I G H F A P D N D .................................................... Protein_Len: 30 Strand: + Start: 36 End: 125 ................................... M M A D G Y V I R P S F S R L A I L L R I M I R S G R V R S .............................. Protein_Len: 49 Strand: - Start: 3 End: 149 .. P L L S L L P K L R P N H R V S I N N A R R E G S Q G N Q E P Y H N P T A S D A G S I E L E Y I M ...... cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg 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================================================ cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 63 HP_score: -5.0 Tail_Score: -4.08144 Start: 101 End: 130 Full_Region: TTTGCTCCGGATAAT GATTAGGAGTGG CAGAGT CCGCTCCTGATA TTTCTAATTCATAGA ....................................................................................................GATTAGGAGTGGCAGAGTCCGCTCCTGATA......................... TransTerm Strand: + Conf: 64 HP_score: -7.6 Tail_Score: -3.63241 Start: 103 End: 128 Full_Region: TGCTCCGGATAATGA TTAGGAGTGG CAGAGT CCGCTCCTGA TATTTCTAATTCATA ......................................................................................................TTAGGAGTGGCAGAGTCCGCTCCTGA........................... Find igs database================================================ Query_seq: PG0793:PG0794|PG0793:PG0794:fructose-1,6-bisphosphatase:penicillin-binding protein 1A, putative:->->:846396..846550 155 cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: NC_002950_PG0793_PG0794|fructose-1, 6-bisphosphatase:penicillin-binding protein 1A, putative|POSITIVE:POSITIVE|[846396,846550]|155 HSP 1 e-value: 6.0E-83 bit: 307.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg cgtggtaagagagacaggagtggctttaatctcggattatggcggacggatatgttattcgcccttcgttctcccgattggccattttgctccggataatgattaggagtggcagagtccgctcctgatatttctaattcatagataatacgacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGGUAAGAGAGACAGGAGUGGCUUUAAUCUCGGAUUAUGGCGGACGGAUAUGUUAUUCGCCCUUCGUUCUCCCGAUUGGCCAUUUUGCUCCGGAUAAUGAUUAGGAGUGGCAGAGUCCGCUCCUGAUAUUUCUAAUUCAUAGAUAAUACGACG (((.(((...(((...(((((((((..((((..(((..((((.((.((((((...)))))).)).))))..))).))))))))))))).))).(((.....(((((((((((......)))))))))))...))).............))).))) (-51.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCGUAUUAUCUAUGAAUUAGAAAUAUCAGGAGCGGACUCUGCCACUCCUAAUCAUUAUCCGGAGCAAAAUGGCCAAUCGGGAGAACGAAGGGCGAAUAACAUAUCCGUCCGCCAUAAUCCGAGAUUAAAGCCACUCCUGUCUCUCUUACCACG (((.(((...((((.....)))).....((((((.((.((..((((((((............)))).....)))).((((.(((.......(((((.(((...))).))))).......)))..))))..)))).)))))).......))).))) (-38.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 50 1 231 174 NC_002950:PG1018|5end_hypothetical_protein_1078894..1079124_POSITIVE 390 98 54 175 127 NC_002950:PG1995|5end_hypothetical_protein_2085584..2085814_POSITIVE 390 90 42 181 119 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 383 123 81 152 109 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 372 78 31 58 2 NC_002950:PG0368|5end_DNA_topoisomerase_IV_subunit_B_401245..401475_POSITIVE 372 80 34 75 29 NC_002950:PG0045|5end_heat_shock_protein_90_54059..54289_POSITIVE 364 70 25 159 121 NC_002950:PG2078|5end_hypothetical_protein_2178600..2178830_NEGATIVE 363 90 42 211 147 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 353 88 41 182 131 NC_002950:PG1396|5end_cell_shape-determining_protein_MreB_1478726..1478956_NEGATIVE 351 126 82 188 139 NC_002950:PG1184|5end_alginate_O-acetyltransferase,_putative_1266870..1267100_NEGATIVE 351 90 41 121 69 NC_002950:PG0659|5end_hypothetical_protein_709148..709378_NEGATIVE 350 49 2 191 142 NC_002950:PG0731|5end_hypothetical_protein_782676..782906_NEGATIVE 350 77 33 172 127 NC_002950:PG0648|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_701285..701515_NEGATIVE 349 77 34 165 125 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 348 126 81 174 129 NC_002950:PG1696|5end_type_II_DNA_modification_methyltransferase,_putative_1779973..1780203_POSITIVE 345 84 43 173 131 NC_002950:PG0329|5end_formiminotransferase-cyclodeaminase-related_protein_364429..364659_NEGATIVE 344 109 61 203 155 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 343 136 92 184 141 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 342 95 53 72 19 NC_002950:PG1561|5end_dTDP-4-dehydrorhamnose_reductase_1640995..1641225_NEGATIVE 340 120 75 191 136 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 121 81 146 101 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 383 123 81 74 31 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 374 80 31 110 62 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 364 120 74 146 97 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 360 50 1 104 55 NC_002950:PG0897|3end_alpha-amylase_family_protein_960868..961018_NEGATIVE 353 88 41 79 28 NC_002950:PG1397|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1478829..1478979_NEGATIVE 351 90 41 128 76 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 345 84 43 124 82 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 342 95 53 75 22 NC_002950:PG1562|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_1640992..1641142_NEGATIVE 338 48 4 148 105 NC_002950:PG2108|3end_thiazole_synthase_2216671..2216821_NEGATIVE 337 91 57 151 114 NC_002950:PG0953|3end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_1013238..1013388_POSITIVE 336 122 81 53 10 NC_002950:PG0664|3end_oxidoreductase,_Gfo/Idh/MocA_family_711860..712010_POSITIVE 336 128 81 82 39 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 335 127 81 106 47 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 332 70 22 75 32 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 331 49 1 121 78 NC_002950:PG0223|3end_exonuclease_257119..257269_NEGATIVE 328 78 32 88 45 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 327 127 81 106 53 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 326 53 12 137 98 NC_002950:PG0279|3end_NADP-dependent_malic_enzyme_310675..310825_NEGATIVE 325 83 41 111 56 NC_002950:PG2114|3end_hypothetical_protein_2223982..2224132_NEGATIVE