Origin IGS: gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 catgaagaaggaggtgtgtcaataatcatggcgcacctcctttgcattaatatgggacggtcgggtacaccgctattccgagactcctaaggagtccctaccgagacccctaaggagtctccaccaagacccctaaggagtctccaccgagatccctaaggagtccctaccaagacccctaaggggtcccaacagagactccttaggggttcctcaatgctttacttcaggaggggttcgtgcggtcttataatccattcgaatggagacatcgggagcagtgaccggcgaaaggaagccgaagc Mask Tandem Repeat Region ================================================ gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Find is-nt database================================================ Query_seq: PG0685:PG0686|PG0685:PG0686:ABC transporter, ATP-binding protein:hypothetical protein:-><-:740916..741220 305 gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0685:PG0686|PG0685:PG0686:ABC transporter, ATP-binding protein:hypothetical protein:-><-:740916..741220 305 gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0685:PG0686|PG0685:PG0686:ABC transporter, ATP-binding protein:hypothetical protein:-><-:740916..741220 305 gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 56 End: 154 ....................................................... L V A R V G G S T F C Q P V G L S D R N P G R L P R P L S E K P M ....................................................................................................................................................... gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg 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================================================ gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -14.9 Tail_Score: -3.1505 Start: 95 End: 132 Full_Region: AGTAAAGCATTGAGG AACCCCTAAGGAGTCTC TGTT GGGACCCCTTAGGGGTC TTGGTAGGGACTCCT ..............................................................................................AACCCCTAAGGAGTCTCTGTTGGGACCCCTTAGGGGTC............................................................................................................................................................................. TransTerm Strand: + Conf: 89 HP_score: -17.5 Tail_Score: -3.1372 Start: 97 End: 130 Full_Region: TAAAGCATTGAGGAA CCCCTAAGGAGTCTC TGTT GGGACCCCTTAGGGG TCTTGGTAGGGACTC ................................................................................................CCCCTAAGGAGTCTCTGTTGGGACCCCTTAGGGG............................................................................................................................................................................... TransTerm Strand: - Conf: 89 HP_score: -17.5 Tail_Score: -3.2115 Start: 97 End: 130 Full_Region: gagtccctaccaaga cccctaaggggtccc aaca gagactccttagggg ttcctcaatgcttta ................................................................................................cccctaaggggtcccaacagagactccttagggg............................................................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -12.3 Tail_Score: -2.72991 Start: 107 End: 143 Full_Region: AGGAACCCCTAAGGA GTCTCTGTTGGGACCCC TTA GGGGTCTTGGTAGGGAC TCCTTAGGGATCTCG ..........................................................................................................GTCTCTGTTGGGACCCCTTAGGGGTCTTGGTAGGGAC.................................................................................................................................................................. TransTerm Strand: + Conf: 71 HP_score: -11.3 Tail_Score: -3.1505 Start: 141 End: 178 Full_Region: AGGGGTCTTGGTAGG GACTCCTTAGGGATCTC GGTG GAGACTCCTTAGGGGTC TTGGTGGAGACTCCT ............................................................................................................................................GACTCCTTAGGGATCTCGGTGGAGACTCCTTAGGGGTC............................................................................................................................... Find igs database================================================ Query_seq: PG0685:PG0686|PG0685:PG0686:ABC transporter, ATP-binding protein:hypothetical protein:-><-:740916..741220 305 gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Intra-Species Hit: Count: 1 Min: 1 Max: 305 Len: 305 Subject: NC_002950_PG0685_PG0686|ABC transporter, ATP-binding protein:hypothetical protein|POSITIVE:NEGATIVE|[740916,741220]|305 HSP 1 e-value: 1.0E-172 bit: 605.0 Len: 305 Query Start:1 Query End:305 Subject Strand: POSITIVE Subject Start: 1 Subject End: 305 gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg gcttcggcttcctttcgccggtcactgctcccgatgtctccattcgaatggattataagaccgcacgaacccctcctgaagtaaagcattgaggaacccctaaggagtctctgttgggaccccttaggggtcttggtagggactccttagggatctcggtggagactccttaggggtcttggtggagactccttaggggtctcggtagggactccttaggagtctcggaatagcggtgtacccgaccgtcccatattaatgcaaaggaggtgcgccatgattattgacacacctccttcttcatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUCGGCUUCCUUUCGCCGGUCACUGCUCCCGAUGUCUCCAUUCGAAUGGAUUAUAAGACCGCACGAACCCCUCCUGAAGUAAAGCAUUGAGGAACCCCUAAGGAGUCUCUGUUGGGACCCCUUAGGGGUCUUGGUAGGGACUCCUUAGGGAUCUCGGUGGAGACUCCUUAGGGGUCUUGGUGGAGACUCCUUAGGGGUCUCGGUAGGGACUCCUUAGGAGUCUCGGAAUAGCGGUGUACCCGACCGUCCCAUAUUAAUGCAAAGGAGGUGCGCCAUGAUUAUUGACACACCUCCUUCUUCAUG (((((((......((((.(((((...((.......)).(((((....)))))......)))))..))))......)))))))...(((((((...((((((((((((((((..((((((.((((.(((((((((....))))))))).)))).))))))..))))))))))))))))..(((..(((((((((.(((((((((....))))))))).)))))))))......(((((.......))))).)))..))))))).(((((((((.(.((.......)).).)))))))))....... (-147.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGAAGAAGGAGGUGUGUCAAUAAUCAUGGCGCACCUCCUUUGCAUUAAUAUGGGACGGUCGGGUACACCGCUAUUCCGAGACUCCUAAGGAGUCCCUACCGAGACCCCUAAGGAGUCUCCACCAAGACCCCUAAGGAGUCUCCACCGAGAUCCCUAAGGAGUCCCUACCAAGACCCCUAAGGGGUCCCAACAGAGACUCCUUAGGGGUUCCUCAAUGCUUUACUUCAGGAGGGGUUCGUGCGGUCUUAUAAUCCAUUCGAAUGGAGACAUCGGGAGCAGUGACCGGCGAAAGGAAGCCGAAGC ......(((((((((((((((.......)))))))))))))))(((((.....((((..(.(((.....))))..))))(((((((((.(((.(((.(....).))).))).)))))))))......(((((((((((((((((....(.(((((((.(((.(((........))).))).))))))).)....)))))))))))))))))....)))))....((((.((.....(((((.(((((......(((...(((.((....)))))))).....))))))))))......)))))). (-139.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 149 102 71 21 NC_002950:PG1546|5end_hypothetical_protein_1624087..1624317_POSITIVE 435 46 5 85 37 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 410 47 5 187 148 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 409 205 162 76 38 NC_002950:PG0844|5end_hypothetical_protein_905289..905519_POSITIVE 404 148 103 175 125 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 398 45 1 55 6 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 398 45 1 213 164 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 396 49 1 80 19 NC_002950:PG0488|5end_Holliday_junction_DNA_helicase_RuvB_528169..528399_POSITIVE 395 41 1 62 18 NC_002950:PG1771|5end_phenylalanyl-tRNA_synthetase_alpha_subunit_1858038..1858268_POSITIVE 393 169 121 220 155 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 393 216 173 213 161 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 391 247 207 41 2 NC_002950:PG2037|5end_hypothetical_protein_2137812..2138042_NEGATIVE 389 240 191 85 24 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 388 45 1 173 123 NC_002950:PG0315|5end_50S_ribosomal_protein_L27_348080..348310_POSITIVE 387 43 6 88 47 NC_002950:PG1472|5end_hypothetical_protein_1549033..1549263_POSITIVE 384 137 97 219 170 NC_002950:PG1696|5end_type_II_DNA_modification_methyltransferase,_putative_1779973..1780203_POSITIVE 381 229 182 218 162 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 381 48 2 189 138 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 376 47 1 100 48 NC_002950:PG0376|5end_30S_ribosomal_protein_S9_406399..406629_POSITIVE 375 48 1 65 18 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 149 102 59 9 NC_002950:PG1545|3end_superoxide_dismutase,_Fe-Mn_1624155..1624305_POSITIVE 443 200 156 143 103 NC_002950:PG1956|3end_4-hydroxybutyrate_CoA-transferase_2046215..2046365_NEGATIVE 442 247 203 44 1 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE 402 48 1 142 100 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 389 228 181 106 65 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 388 45 1 145 95 NC_002950:PG0314|3end_ribosomal_protein_L21_348132..348282_POSITIVE 387 43 6 53 12 NC_002950:PG1471|3end_hypothetical_protein_1549078..1549228_POSITIVE 376 47 1 90 38 NC_002950:PG0375|3end_50S_ribosomal_protein_L13_406469..406619_POSITIVE 370 238 195 136 79 NC_002950:PG0671|3end_iron_compound_ABC_transporter,_permease_protein_723038..723188_POSITIVE 364 257 213 67 15 NC_002950:PG0027|3end_hypothetical_protein_33936..34086_POSITIVE 363 228 189 59 15 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 361 249 205 99 36 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 361 107 61 97 41 NC_002950:PG1587|3end_PAP2_superfamily_protein_1665779..1665929_POSITIVE 360 297 265 84 53 NC_002950:PG1283|3end_hypothetical_protein_1362795..1362945_POSITIVE 359 250 203 83 24 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 359 160 111 78 27 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 356 50 3 100 45 NC_002950:PG0484|3end_hypothetical_protein_523851..524001_NEGATIVE 355 212 172 125 73 NC_002950:PG0740|3end_NLP/P60_family_protein_788485..788635_POSITIVE 355 277 233 70 9 NC_002950:PG0604|3end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_661211..661361_POSITIVE 354 47 5 80 37 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE