Origin IGS: gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc .........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 gcaggcgtacgtcttctcactacgccttgtggacgtttgtatatgcctttttcctatcactattttattggataaatagttggccgaatcacattgtctttatctatttcgggagctattacattcctgtcctcaaagattatatcggatgtcattaaatgatgcgagggcaatggttttttattttctttgcgtagatatcaatctcaatacacactaaaaacaatcgatc Mask Tandem Repeat Region ================================================ gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Find is-nt database================================================ Query_seq: PG1340:PG1341|PG1340:PG1341:L-lactate permease:hypothetical protein:<-->:1421939..1422170 232 gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1340:PG1341|PG1340:PG1341:L-lactate permease:hypothetical protein:<-->:1421939..1422170 232 gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1340:PG1341|PG1340:PG1341:L-lactate permease:hypothetical protein:<-->:1421939..1422170 232 gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 60 End: 170 ........................................................... M P S H H L M T S D I I F E D R N V I A P E I D K D N V I R P T I Y P I K .............................................................. Protein_Len: 43 Strand: - Start: 78 End: 206 ............................................................................. H C G I Y D K L V P I Y Y S G F Y I F V I H N P W S N I W Y F L S L F F A Y V F T W M .......................... Protein_Len: 46 Strand: - Start: 16 End: 153 ............... H T N L N I D V C L F Y F V M A R A D N L S M R Y L R Q P C S H L L E R F L Y L C H S E A M ............................................................................... gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc 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================================================ gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1340:PG1341|PG1340:PG1341:L-lactate permease:hypothetical protein:<-->:1421939..1422170 232 gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_002950_PG1340_PG1341|L-lactate permease:hypothetical protein|NEGATIVE:POSITIVE|[1421939,1422170]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc gatcgattgtttttagtgtgtattgagattgatatctacgcaaagaaaataaaaaaccattgccctcgcatcatttaatgacatccgatataatctttgaggacaggaatgtaatagctcccgaaatagataaagacaatgtgattcggccaactatttatccaataaaatagtgataggaaaaaggcatatacaaacgtccacaaggcgtagtgagaagacgtacgcctgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCGAUUGUUUUUAGUGUGUAUUGAGAUUGAUAUCUACGCAAAGAAAAUAAAAAACCAUUGCCCUCGCAUCAUUUAAUGACAUCCGAUAUAAUCUUUGAGGACAGGAAUGUAAUAGCUCCCGAAAUAGAUAAAGACAAUGUGAUUCGGCCAACUAUUUAUCCAAUAAAAUAGUGAUAGGAAAAAGGCAUAUACAAACGUCCACAAGGCGUAGUGAGAAGACGUACGCCUGC .((((.((((((((..(((((....((((....)))))))))..))))))))........(((....)))...............))))...........((((.(...((((...(((.(((((.((.((.......)).)).)))))((.(((((((........)))))))....)).....)))...))))..)))))...(((((((((......)).))))))).. (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGGCGUACGUCUUCUCACUACGCCUUGUGGACGUUUGUAUAUGCCUUUUUCCUAUCACUAUUUUAUUGGAUAAAUAGUUGGCCGAAUCACAUUGUCUUUAUCUAUUUCGGGAGCUAUUACAUUCCUGUCCUCAAAGAUUAUAUCGGAUGUCAUUAAAUGAUGCGAGGGCAAUGGUUUUUUAUUUUCUUUGCGUAGAUAUCAAUCUCAAUACACACUAAAAACAAUCGAUC ..(((((((.((......)))))))))((.(((((..((((...((............(((((((........)))))))...(((((...................)))))..))...))))....))))).)).((((((((((....(((((...)))))(((((((.(((((....))))).)))))))...))))).)))))......................... (-46.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 890 110 61 201 152 NC_002950:PG1340|5end_L-lactate_permease_1421848..1422078_NEGATIVE 346 230 188 71 37 NC_002950:PG0094|5end_outer_membrane_efflux_protein,_putative_111193..111423_NEGATIVE 298 229 186 53 2 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 293 230 185 204 159 NC_002950:PG0290|5end_hypothetical_protein_323904..324134_POSITIVE 290 149 101 65 11 NC_002950:PG0794|5end_penicillin-binding_protein_1A,_putative_846411..846641_POSITIVE 287 90 50 150 101 NC_002950:PG1372|5end_hypothetical_protein_1454722..1454952_NEGATIVE 281 230 186 228 178 NC_002950:PG1968|5end_hypothetical_protein_2058564..2058794_NEGATIVE 281 160 111 87 28 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 270 136 95 210 172 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 269 152 111 42 2 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 264 230 198 68 43 NC_002950:PG0466|5end_hypothetical_protein_510244..510474_NEGATIVE 264 229 197 47 23 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 262 41 1 182 145 NC_002950:PG1634|5end_hypothetical_protein_1715148..1715378_NEGATIVE 258 189 147 51 12 NC_002950:PG0190|5end_undecaprenyl_diphosphate_synthase_226076..226306_POSITIVE 257 108 62 136 100 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 256 154 113 63 18 NC_002950:PG0357|5end_aspartate_carbamoyltransferase_catalytic_subunit_391440..391670_POSITIVE 255 88 57 221 193 NC_002950:PG1588|5end_hypothetical_protein_1666532..1666762_NEGATIVE 255 68 23 192 136 NC_002950:PG0721|5end_NLP/P60_family_protein_773847..774077_POSITIVE 254 230 185 54 6 NC_002950:PG0575|5end_penicillin-binding_protein_2,_putative_629501..629731_POSITIVE 253 228 196 72 39 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 229 194 46 4 NC_002950:PG0702|3end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_758217..758367_POSITIVE 281 160 111 83 24 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 276 169 121 85 34 NC_002950:PG0441|3end_hypothetical_protein_481447..481597_POSITIVE 271 122 82 36 3 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 270 136 95 51 13 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 270 224 181 81 39 NC_002950:PG0194|3end_ISPg3,_transposase_231910..232060_POSITIVE 262 41 1 116 79 NC_002950:PG1635|3end_hypothetical_protein_1715214..1715364_NEGATIVE 262 124 83 125 77 NC_002950:PG1022|3end_hypothetical_protein_1085098..1085248_POSITIVE 260 103 61 83 45 NC_002950:PG0062|3end_TPR_domain_protein_75810..75960_POSITIVE 258 89 57 74 42 NC_002950:PG1402|3end_AP_endonuclease_domain_protein_1485031..1485181_NEGATIVE 255 212 178 98 64 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 252 149 101 69 25 NC_002950:PG0877|3end_hypothetical_protein_940838..940988_NEGATIVE 251 229 186 79 19 NC_002950:PG1696|3end_type_II_DNA_modification_methyltransferase,_putative_1781090..1781240_POSITIVE 250 110 61 131 71 NC_002950:PG1609|3end_methylmalonyl-CoA_decarboxylase,_gamma_subunit_1689841..1689991_NEGATIVE 250 150 101 141 88 NC_002950:PG0949|3end_hypothetical_protein_1009773..1009923_POSITIVE 240 122 84 118 84 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE 240 119 77 70 17 NC_002950:PG0872|3end_mobilizable_transposon,_xis_protein_934846..934996_NEGATIVE 239 210 173 57 17 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 239 230 181 67 33 NC_002950:PG1430|3end_TPR_domain_protein_1515114..1515264_NEGATIVE 239 214 179 74 45 NC_002950:PG0323|3end_hypothetical_protein_357059..357209_NEGATIVE