Origin IGS: ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatggacagggtagcttctgtcggtgtggtaacgggagtattgacggtagcaagggagtcgataggagtccccgccgactgaacgggaatttgcagaaagggaatgcttggaatattcattggattatcaatgtgattgttactgtttcgattttat Mask Tandem Repeat Region ================================================ ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Find is-nt database================================================ Query_seq: PG0630:PG0631|PG0630:PG0631:pyridoxal phosphate biosynthetic protein:MotA/TolQ/ExbB proton channel family protein:->->:684249..684405 157 ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0630:PG0631|PG0630:PG0631:pyridoxal phosphate biosynthetic protein:MotA/TolQ/ExbB proton channel family protein:->->:684249..684405 157 ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0630:PG0631|PG0630:PG0631:pyridoxal phosphate biosynthetic protein:MotA/TolQ/ExbB proton channel family protein:->->:684249..684405 157 ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 42 End: 155 ......................................... M F Q A F P F C K F P F S R R G L L S T P L L P S I L P L P H R Q K L P C P .. Protein_Len: 44 Strand: + Start: 26 End: 157 ......................... M D N P M N I P S I P F L Q I P V Q S A G T P I D S L A T V N T P V T T P T E A T L S I Protein_Len: 39 Strand: - Start: 2 End: 118 . L I S V T V I V N I I W H I N W A N G K Q L N G N L R R P S R D V G K S G D M ....................................... ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt 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================================================ ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0630:PG0631|PG0630:PG0631:pyridoxal phosphate biosynthetic protein:MotA/TolQ/ExbB proton channel family protein:->->:684249..684405 157 ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_002950_PG0630_PG0631|pyridoxal phosphate biosynthetic protein:MotA/TolQ/ExbB proton channel family protein|POSITIVE:POSITIVE|[684249,684405]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt ataaaatcgaaacagtaacaatcacattgataatccaatgaatattccaagcattccctttctgcaaattcccgttcagtcggcggggactcctatcgactcccttgctaccgtcaatactcccgttaccacaccgacagaagctaccctgtccatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUCGAAACAGUAACAAUCACAUUGAUAAUCCAAUGAAUAUUCCAAGCAUUCCCUUUCUGCAAAUUCCCGUUCAGUCGGCGGGGACUCCUAUCGACUCCCUUGCUACCGUCAAUACUCCCGUUACCACACCGACAGAAGCUACCCUGUCCAUU ..............(((((.....(((((......))))).........((((..................(((......))).(((((.((.....)).)))))))))...............)))))......(((((........))))).... (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGACAGGGUAGCUUCUGUCGGUGUGGUAACGGGAGUAUUGACGGUAGCAAGGGAGUCGAUAGGAGUCCCCGCCGACUGAACGGGAAUUUGCAGAAAGGGAAUGCUUGGAAUAUUCAUUGGAUUAUCAAUGUGAUUGUUACUGUUUCGAUUUUAU .((.(((((((....))))))).)).........(((((...(((((((((((((((.((.....)).))))..((((.((((((((.((((.(.....).)))).)))).....)))))))).............)))))))))))...))))).. (-40.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 108 70 213 166 NC_002950:PG0384|5end_MutS2_family_protein_416095..416325_POSITIVE 366 99 54 205 146 NC_002950:PG1676|5end_phosphoenolpyruvate_carboxykinase_1762096..1762326_NEGATIVE 364 114 71 226 185 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 356 130 84 61 10 NC_002950:PG0160|5end_hypothetical_protein_184085..184315_NEGATIVE 354 120 71 91 34 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 353 103 69 229 177 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 350 118 72 214 162 NC_002950:PG1601|5end_biotin--acetyl-CoA-carboxylase_ligase_1681792..1682022_NEGATIVE 350 114 71 110 53 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 350 110 64 104 51 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 350 125 81 46 1 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 348 115 72 133 72 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 347 98 51 171 125 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 345 110 62 71 20 NC_002950:PG0302|5end_hypothetical_protein_338219..338449_POSITIVE 344 124 81 213 171 NC_002950:PG1803|5end_V-type_ATP_synthase_subunit_A_1896488..1896718_POSITIVE 341 104 61 154 108 NC_002950:PG0463|5end_folylpolyglutamate_synthase_507606..507836_NEGATIVE 340 120 71 68 30 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 339 139 97 71 30 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 338 99 60 204 158 NC_002950:PG1982|5end_CRISPR-associated_protein_Cas1_2072620..2072850_NEGATIVE 336 96 57 186 143 NC_002950:PG1595|5end_ribulose-phosphate_3-epimerase_1674250..1674480_NEGATIVE 334 116 71 51 7 NC_002950:PG1063|5end_transcriptional_regulator,_putative_1131056..1131286_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 103 64 59 10 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 372 89 49 145 99 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 370 120 72 134 69 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 366 114 71 122 70 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 365 109 64 57 9 NC_002950:PG0568|3end_elongation_factor_P_623999..624149_NEGATIVE 362 120 73 136 87 NC_002950:PG2205|3end_2-dehydropantoate_2-reductase_2317145..2317295_POSITIVE 350 114 71 129 72 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 350 110 64 67 14 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 349 114 73 149 95 NC_002950:PG0750|3end_glycosyl_transferase,_group_2_family_protein_795946..796096_NEGATIVE 349 116 71 84 33 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 343 115 71 129 84 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 342 112 71 46 4 NC_002950:PG1875|3end_hemolysin_1969647..1969797_NEGATIVE 340 120 71 71 33 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 339 139 97 58 17 NC_002950:PG1474|3end_conjugative_transposon_protein_TraO_1550238..1550388_NEGATIVE 338 99 60 143 97 NC_002950:PG1983|3end_CRISPR-associated_TM1791_family_protein_2072681..2072831_NEGATIVE 337 115 73 147 89 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 336 115 78 114 81 NC_002950:PG0030|3end_cytidine_deaminase_36402..36552_POSITIVE 325 97 57 103 56 NC_002950:PG1775|3end_grpE_protein_1865508..1865658_POSITIVE 324 115 72 129 75 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 324 115 72 129 75 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE