Origin IGS: taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagaaaagctgcttgtagttacttcaaataaaaaaggaattcatctccccccccgcaagaaaacaaaaaagaggcgcaccctgcgtagggaacgcctcttatatataataatgtaatactgaatta Mask Tandem Repeat Region ================================================ taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Find is-nt database================================================ Query_seq: PI0814:PI0815|PI0814:PI0815:conserved hypothetical protein:hypothetical protein:->->:754487..754614 128 taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0814:PI0815|PI0814:PI0815:conserved hypothetical protein:hypothetical protein:->->:754487..754614 128 taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0814:PI0815|PI0814:PI0815:conserved hypothetical protein:hypothetical protein:->->:754487..754614 128 taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 10 End: 105 ......... M T L L Y I R G V P Y A G C A S F L F S C G G G D E F L F Y L K ....................... Protein_Len: 35 Strand: - Start: 14 End: 118 ............. M I I Y L L R E R R L T R R K K T K K R P P L H I G K K N S T V V L M .......... taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta 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================================================ taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -8.7 Tail_Score: -4.63218 Start: 22 End: 63 Full_Region: AGTATTACATTATTA TATATAAGAGGCGTTCCCT ACGC AGGGTGCGCCTCTTTTTTG TTTTCTTGCGGGGGG .....................TATATAAGAGGCGTTCCCTACGCAGGGTGCGCCTCTTTTTTG................................................................. TransTerm Strand: - Conf: 83 HP_score: -11.2 Tail_Score: -3.62616 Start: 29 End: 56 Full_Region: caagaaaacaaaaaa gaggcgcaccct gcgt agggaacgcctc ttatatataataatg ............................gaggcgcaccctgcgtagggaacgcctc........................................................................ Find igs database================================================ Query_seq: PI0814:PI0815|PI0814:PI0815:conserved hypothetical protein:hypothetical protein:->->:754487..754614 128 taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: pint_PI0814_PI0815|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[754487,754614]|128 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcnnnnnnnnagatgaattccttttttatttgaagtaactacaagcagcttttcttta taattcagtattacattattatatataagaggcgttccctacgcagggtgcgcctcttttttgttttcttgcggggggggagatgaattccttttttatttgaagtaactacaagcagcttttcttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCAGUAUUACAUUAUUAUAUAUAAGAGGCGUUCCCUACGCAGGGUGCGCCUCUUUUUUGUUUUCUUGCGGGGGGGGAGAUGAAUUCCUUUUUUAUUUGAAGUAACUACAAGCAGCUUUUCUUUA .......(((((((......(((...(((((((((.((((....)))).)))))))))...))).(((..(..(((((((((.....)))))))))..)..))))))).)))................ (-33.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAAAAGCUGCUUGUAGUUACUUCAAAUAAAAAAGGAAUUCAUCUCCCCCCCCGCAAGAAAACAAAAAAGAGGCGCACCCUGCGUAGGGAACGCCUCUUAUAUAUAAUAAUGUAAUACUGAAUUA ....(((.(((((....)))))..)))............((((((..........(....).........((((((((..((((....))))..))))))))...................)))))). (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 80 31 53 5 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 366 70 28 107 57 pint:PI0943|5end_conserved_hypothetical_protein_875153..875383_POSITIVE 365 69 28 177 129 pint:PI0177|5end_2-oxoglutarate_synthase,_subunit_korB_168499..168729_POSITIVE 353 82 43 50 12 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 345 79 31 227 183 pint:PI1508|5end_undecaprenol_kinase_1427288..1427518_POSITIVE 342 77 33 103 54 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 336 119 72 64 28 pint:PI2027|5end_arginine_decarboxylase_1980161..1980391_POSITIVE 331 86 42 182 134 pint:PI0247|5end_conjugative_transposon_protein,_TraA_245373..245603_POSITIVE 325 86 41 63 20 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 318 77 31 61 18 pint:PI0658|5end_conserved_hypothetical_protein_602187..602417_POSITIVE 314 78 32 54 1 pint:PI1782|5end_possible_LPS_biosynthesis_protein_1714482..1714712_POSITIVE 314 64 21 170 117 pint:PI1405|5end_conserved_hypothetical_protein_1326035..1326265_POSITIVE 314 56 30 204 178 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 314 70 21 169 111 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 313 85 47 179 138 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 311 79 33 154 113 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 311 82 41 74 29 pint:PI0611|5end_hypothetical_protein_559387..559617_POSITIVE 307 63 25 68 25 pint:PI0754|5end_possible_outer_membrane_receptor_683771..684001_POSITIVE 307 86 45 211 170 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 305 58 15 221 171 pint:PI1005|5end_hypothetical_protein_926201..926431_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 80 31 53 5 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 402 58 27 64 33 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 366 70 28 123 73 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 354 54 28 119 90 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 342 77 33 142 93 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 325 86 41 58 15 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 321 85 42 91 47 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 321 84 43 90 58 pint:PI0925|3end_ribosomal_protein_L11_methyltransferase_856638..856788_POSITIVE 314 64 21 54 1 pint:PI1404|3end_hypothetical_protein_1325999..1326149_POSITIVE 308 78 31 49 6 pint:PI0927|3end_transglutaminase-related_protein_859696..859846_POSITIVE 307 63 25 68 25 pint:PI0753|3end_hypothetical_protein_683851..684001_POSITIVE 303 87 41 95 43 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 302 73 33 141 101 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 301 73 32 150 96 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 299 87 45 40 1 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 296 76 31 101 55 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 295 80 32 76 6 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 293 106 61 94 43 pint:PI1688|3end_possible_GTPase_1603903..1604053_POSITIVE 292 85 49 73 28 pint:PI1916|3end_conserved_hypothetical_protein_1860740..1860890_POSITIVE 289 80 32 81 19 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE