Origin IGS: gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa .........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 tttcttcttctgagtaattggggacaaaggtagtaaaacgggctgtttttcggaatggatatccaagtgttcggattctgcacattccatctgcaagagcgttgcatttgcaggcaaaaaaagacgccgacgaaagtgctctcatcggcgtcaataggattccaagatatctcttgatagagtttttcagctgacgatatccgtc Mask Tandem Repeat Region ================================================ gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Find is-nt database================================================ Query_seq: PG0614:PG0615|PG0614:PG0615:hypothetical protein:GTP-binding protein TypA:->->:666968..667172 205 gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0614:PG0615|PG0614:PG0615:hypothetical protein:GTP-binding protein TypA:->->:666968..667172 205 gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0614:PG0615|PG0614:PG0615:hypothetical protein:GTP-binding protein TypA:->->:666968..667172 205 gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 6 End: 203 ..... M S S A E K L Y Q E I S W N P I D A D E S T F V G V F F C L Q M Q R S C R W N V Q N P N T W I S I P K N S P F Y Y L C P .. Protein_Len: 60 Strand: + Start: 16 End: 204 ............... M K N S I K R Y L G I L L T P M R A L S S A S F F A C K C N A L A D G M C R I R T L G Y P F R K T A R F T T F V P N Y S . Protein_Len: 39 Strand: + Start: 89 End: 205 ........................................................................................ M P A N A T L L Q M E C A E S E H L D I H S E K Q P V L L P L S P I T Q K K K Protein_Len: 46 Strand: - Start: 52 End: 189 ................................................... Q R R H S C K R R R R K K G A F A V S K C I S H A S D S C K S I W E S F C G T K S G K D G M ................ Protein_Len: 44 Strand: - Start: 32 End: 163 ............................... S I D Q F G I S A S S L V K T P T K K Q R C I C R E Q L H F T C F G F V Q I D M G F F M .......................................... Protein_Len: 58 Strand: - Start: 15 End: 188 .............. S F F E I L L Y R P I R N V G I L A S E D A D K K A Q L H L A R A S P I H L I R V S P Y G N R F V A R K V V K T G M ................. gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa 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================================================ gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -4.4 Tail_Score: -4.62069 Start: 24 End: 35 Full_Region: aggattccaagatat ctct tgat agag tttttcagctgacga .......................ctcttgatagag.......................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -15.1 Tail_Score: -5.47218 Start: 54 End: 83 Full_Region: TCTTGGAATCCTATT GACGCCGATGAGA GCAC TTTCGTCGGCGTC TTTTTTTGCCTGCAA .....................................................GACGCCGATGAGAGCACTTTCGTCGGCGTC.......................................................................................................................... TransTerm Strand: - Conf: 54 HP_score: -4.3 Tail_Score: -3.53012 Start: 100 End: 114 Full_Region: tctgcacattccatc tgcaa gagcg ttgca tttgcaggcaaaaaa ...................................................................................................tgcaagagcgttgca........................................................................................... Find igs database================================================ Query_seq: PG0614:PG0615|PG0614:PG0615:hypothetical protein:GTP-binding protein TypA:->->:666968..667172 205 gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_002950_PG0614_PG0615|hypothetical protein:GTP-binding protein TypA|POSITIVE:POSITIVE|[666968,667172]|205 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtcnnnnnnngcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa gacggatatcgtcagctgaaaaactctatcaagagatatcttggaatcctattgacgccgatgagagcactttcgtcggcgtctttttttgcctgcaaatgcaacgctcttgcagatggaatgtgcagaatccgaacacttggatatccattccgaaaaacagcccgttttactacctttgtccccaattactcagaagaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGGAUAUCGUCAGCUGAAAAACUCUAUCAAGAGAUAUCUUGGAAUCCUAUUGACGCCGAUGAGAGCACUUUCGUCGGCGUCUUUUUUUGCCUGCAAAUGCAACGCUCUUGCAGAUGGAAUGUGCAGAAUCCGAACACUUGGAUAUCCAUUCCGAAAAACAGCCCGUUUUACUACCUUUGUCCCCAAUUACUCAGAAGAAGAAA ((((.....))))..((((....((((....)))).....((((.........(((((((((((((....))))))))))))).........((((((..((...))..))))))..((((((....((((((((....)))))).))))))))..(((((.....))))).............))))....))))......... (-57.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUCUUCUGAGUAAUUGGGGACAAAGGUAGUAAAACGGGCUGUUUUUCGGAAUGGAUAUCCAAGUGUUCGGAUUCUGCACAUUCCAUCUGCAAGAGCGUUGCAUUUGCAGGCAAAAAAAGACGCCGACGAAAGUGCUCUCAUCGGCGUCAAUAGGAUUCCAAGAUAUCUCUUGAUAGAGUUUUUCAGCUGACGAUAUCCGUC .......(((((((...(((....)))...((((.......))))...))))))).(((((((..(((....((((((((.....(((.((((((((.((...)).))))))))........((((((((.((........)).))))))))....)))...(((((....))))).))))))))....)))...)))))))... (-60.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 118 76 103 65 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 363 95 56 175 142 NC_002950:PG1612|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1693065..1693295_NEGATIVE 362 96 56 177 142 NC_002950:PG1248|5end_hypothetical_protein_1326532..1326762_NEGATIVE 362 118 71 62 8 NC_002950:PG1119|5end_flavodoxin,_putative_1194843..1195073_POSITIVE 351 95 51 197 147 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 349 109 61 227 161 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 344 129 81 228 171 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 344 118 72 213 159 NC_002950:PG0412|5end_DNA_mismatch_repair_protein_MutL_451440..451670_NEGATIVE 344 93 56 176 136 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 341 95 57 73 26 NC_002950:PG0133|5end_hypothetical_protein_155764..155994_NEGATIVE 336 150 102 195 149 NC_002950:PG2181|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_2289769..2289999_NEGATIVE 336 118 72 206 161 NC_002950:PG1720|5end_hypothetical_protein_1808615..1808845_POSITIVE 331 96 55 37 2 NC_002950:PG1848|5end_RNA_methyltransferase,_TrmH_family_1947382..1947612_NEGATIVE 331 97 52 90 44 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 330 97 51 75 41 NC_002950:PG0620|5end_ATP-dependent_protease_La_672963..673193_POSITIVE 327 96 57 180 143 NC_002950:PG1994|5end_D-tyrosyl-tRNA_deacylase_2085127..2085357_POSITIVE 327 128 83 111 67 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 326 85 50 60 25 NC_002950:PG0975|5end_PhoH_family_protein_1037284..1037514_POSITIVE 325 143 101 185 138 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 325 129 86 197 149 NC_002950:PG0720|5end_DNA-binding_response_regulator_773665..773895_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 494 83 54 37 8 NC_002950:PG0614|3end_hypothetical_protein_666907..667057_POSITIVE 363 95 56 76 43 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 356 95 52 140 99 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 351 79 31 140 81 NC_002950:PG1375|3end_hypothetical_protein_1456743..1456893_POSITIVE 349 97 51 112 61 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 349 109 61 138 72 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 342 186 141 85 22 NC_002950:PG0753|3end_protease_800288..800438_POSITIVE 341 119 78 59 5 NC_002950:PG0425|3end_esterase,_putative_463219..463369_NEGATIVE 341 95 57 54 7 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 331 96 55 40 5 NC_002950:PG1849|3end_DNA_repair_protein_RecN_1947379..1947529_NEGATIVE 323 95 53 50 5 NC_002950:PG1751|3end_aminotransferase,_class_V_1838490..1838640_POSITIVE 323 80 32 146 85 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 323 85 43 57 22 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 316 79 32 89 46 NC_002950:PG0838|3end_integrase_896855..897005_POSITIVE 314 118 71 148 94 NC_002950:PG0900|3end_cytochrome_d_ubiquinol_oxidase,_subunit_I_964706..964856_NEGATIVE 313 80 34 140 96 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 310 134 92 116 75 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 310 120 71 140 77 NC_002950:PG0442|3end_hypothetical_protein_481514..481664_NEGATIVE 306 119 75 42 5 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE 305 116 74 86 40 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE