Origin IGS: aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt .........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 aaacgtggcgcgggaactttttcgttttggttcgggaaagaaaaaattcccgcgcgagaacgaaaaaattcccacgccacttcctttcagcttttggttcgcagttcgggcgactttcggctcgtatttttccctgatcgactgaatgactctgcgccttgatgccgtttttcttctatttgtatcggttgttcttgccataggcatggcattgaactttaatcattattttcgcaccggactttgattacagtgtaatt Mask Tandem Repeat Region ================================================ aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Find is-nt database================================================ Query_seq: PG0130:PG0132|PG0130:PG0132:phosphoglyceromutase:hypothetical protein:<-->:152759..153018 260 aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0130:PG0132|PG0130:PG0132:phosphoglyceromutase:hypothetical protein:<-->:152759..153018 260 aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0130:PG0132|PG0130:PG0132:phosphoglyceromutase:hypothetical protein:<-->:152759..153018 260 aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 49 End: 171 ................................................ M P C L W Q E Q P I Q I E E K R H Q G A E S F S R S G K N T S R K S P E L R T K S ......................................................................................... Protein_Len: 54 Strand: + Start: 98 End: 259 ................................................................................................. M K A Q S H S V D Q G K I R A E S R P N C E P K A E R K W R G N F F V L A R E F F L S R T K T K K F P R H V . Protein_Len: 60 Strand: + Start: 54 End: 260 ..................................................... M P M A R T T D T N R R K T A S R R R V I Q S I R E K Y E P K V A R T A N Q K L K G S G V G I F S F S R G N F F F P E P Protein_Len: 36 Strand: - Start: 127 End: 234 .............................................................................................................................. P F I R A S L R G F Q S G F A S L F H R P F K K T R A R S N K R E R V M .......................... Protein_Len: 46 Strand: - Start: 119 End: 256 ...................................................................................................................... D I L S F Y S G F T A R V A F W F S F P L P T P I K E N E R P F K K K G S G F R F L E R A M .... Protein_Len: 38 Strand: - Start: 102 End: 215 ..................................................................................................... P A S D N L R D P F F V L R F D G S S R V L L Q F S T A H S N K R E R A P M ............................................. Protein_Len: 33 Strand: - Start: 17 End: 115 ................ L G T R F Y H N F N L A M G I A L V V S V F L L F V A D L R L T M ................................................................................................................................................. aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt 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================================================ aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -3.1 Tail_Score: -5.63517 Start: 201 End: 214 Full_Region: GTGGGAATTTTTTCG TTCTC GCGC GGGAA TTTTTTCTTTCCCGA ........................................................................................................................................................................................................TTCTCGCGCGGGAA.............................................. Find igs database================================================ Query_seq: PG0130:PG0132|PG0130:PG0132:phosphoglyceromutase:hypothetical protein:<-->:152759..153018 260 aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Intra-Species Hit: Count: 1 Min: 1 Max: 260 Len: 260 Subject: NC_002950_PG0130_PG0132|phosphoglyceromutase:hypothetical protein|NEGATIVE:POSITIVE|[152759,153018]|260 HSP 1 e-value: 1.0E-145 bit: 515.0 Len: 260 Query Start:1 Query End:260 Subject Strand: POSITIVE Subject Start: 1 Subject End: 260 aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt aattacactgtaatcaaagtccggtgcgaaaataatgattaaagttcaatgccatgcctatggcaagaacaaccgatacaaatagaagaaaaacggcatcaaggcgcagagtcattcagtcgatcagggaaaaatacgagccgaaagtcgcccgaactgcgaaccaaaagctgaaaggaagtggcgtgggaattttttcgttctcgcgcgggaattttttctttcccgaaccaaaacgaaaaagttcccgcgccacgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACACUGUAAUCAAAGUCCGGUGCGAAAAUAAUGAUUAAAGUUCAAUGCCAUGCCUAUGGCAAGAACAACCGAUACAAAUAGAAGAAAAACGGCAUCAAGGCGCAGAGUCAUUCAGUCGAUCAGGGAAAAAUACGAGCCGAAAGUCGCCCGAACUGCGAACCAAAAGCUGAAAGGAAGUGGCGUGGGAAUUUUUUCGUUCUCGCGCGGGAAUUUUUUCUUUCCCGAACCAAAACGAAAAAGUUCCCGCGCCACGUUU .............((..(((.(((.((((..............((((..((((((....)))))).)))).......................((((.((..(((.....)))..((....))..............))))))....))))))).)))..))........((....))..((((((((((((((((((((((......((((((........))))))......)))))))))))))))))))))).... (-83.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACGUGGCGCGGGAACUUUUUCGUUUUGGUUCGGGAAAGAAAAAAUUCCCGCGCGAGAACGAAAAAAUUCCCACGCCACUUCCUUUCAGCUUUUGGUUCGCAGUUCGGGCGACUUUCGGCUCGUAUUUUUCCCUGAUCGACUGAAUGACUCUGCGCCUUGAUGCCGUUUUUCUUCUAUUUGUAUCGGUUGUUCUUGCCAUAGGCAUGGCAUUGAACUUUAAUCAUUAUUUUCGCACCGGACUUUGAUUACAGUGUAAUU ....((((((.(((((.(((((((((((.((.((((((........)))))).)).))))))))))).))))).)))))).........((..(((..(((.(((((((((((..(((((.(((.(((.......))))))))))).((......(((..(((((................)))))))).((((.((((((....))))))..)))).....)).......)))).))))))).)))...))).)).... (-88.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 967 140 91 231 182 NC_002950:PG0130|5end_phosphoglyceromutase_152668..152898_NEGATIVE 741 260 211 117 67 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 636 230 181 180 131 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 633 260 211 81 26 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 617 260 211 95 45 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 605 240 193 97 50 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 544 260 211 83 28 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 460 229 181 108 60 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 396 214 176 142 103 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 386 189 141 211 152 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 380 219 176 231 188 NC_002950:PG0470|5end_hypothetical_protein_511883..512113_NEGATIVE 358 260 215 113 69 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 351 160 113 210 158 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 342 68 21 229 179 NC_002950:PG2121|5end_L-asparaginase_2229624..2229854_NEGATIVE 339 228 183 57 4 NC_002950:PG2078|5end_hypothetical_protein_2178600..2178830_NEGATIVE 339 138 93 200 145 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 332 186 141 100 46 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 332 186 141 100 46 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 332 186 141 100 46 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 332 190 142 81 22 NC_002950:PG1106|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,_6-diaminopimelate--D-alanyl-D-alanyl_ligase_1178429..1178659_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 236 196 36 1 NC_002950:PG1626|3end_hypothetical_protein_1710486..1710636_POSITIVE 377 256 222 51 19 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 344 211 176 60 16 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 331 149 103 51 12 NC_002950:PG1953|3end_YitT_family_protein_2044589..2044739_POSITIVE 327 190 142 76 21 NC_002950:PG1152|3end_hypothetical_protein_1234674..1234824_NEGATIVE 326 210 164 60 9 NC_002950:PG0381|3end_cell_volume_regulation_protein_CvrA_411185..411335_NEGATIVE 322 209 170 115 67 NC_002950:PG0843|3end_hypothetical_protein_904871..905021_NEGATIVE 321 127 85 79 35 NC_002950:PG0977|3end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1040116..1040266_POSITIVE 320 165 122 83 42 NC_002950:PG0408|3end_hypothetical_protein_440952..441102_NEGATIVE 320 189 141 127 72 NC_002950:PG0245|3end_universal_stress_protein_family_279773..279923_NEGATIVE 317 130 93 49 6 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE 316 189 141 61 13 NC_002950:PG2213|3end_nitrite_reductase-related_protein_2324848..2324998_NEGATIVE 316 216 176 116 68 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 315 229 181 149 106 NC_002950:PG0628|3end_ABC_transporter,_ATP-binding_protein_681684..681834_NEGATIVE 311 64 21 65 25 NC_002950:PG1493|3end_hypothetical_protein_1569538..1569688_POSITIVE 311 209 173 124 73 NC_002950:PG0874|3end_mobilizable_transposon,_int_protein_936910..937060_NEGATIVE 309 260 227 90 57 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 309 190 149 40 1 NC_002950:PG0723|3end_hypothetical_protein_775355..775505_POSITIVE 306 154 111 101 63 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 306 159 113 122 70 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE