Origin IGS: acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct .........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 agaacaaggagtgtcttttcgtccgccgagaaaacgaagccttatatccgaatggtgaaaaccggaggcggggaaacccgaaaagacgaccgaaccttaaccttactatctgataccgaagggttccccgtcctcctttttccatggcggatacaaatgtattgaattataaacctgaaatccaatcgt Mask Tandem Repeat Region ================================================ acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Find is-nt database================================================ Query_seq: PG1483:PG1484|PG1483:PG1484:conjugative transposon protein TraE:hypothetical protein:<-<-:1559176..1559364 189 acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1483:PG1484|PG1483:PG1484:conjugative transposon protein TraE:hypothetical protein:<-<-:1559176..1559364 189 acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1483:PG1484|PG1483:PG1484:conjugative transposon protein TraE:hypothetical protein:<-<-:1559176..1559364 189 acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 5 End: 145 .... M D F R F I I Q Y I C I R H G K R R T G N P S V S D S K V K V R S S F R V S P P P V F T I R I ............................................ Protein_Len: 48 Strand: + Start: 45 End: 188 ............................................ M E K G G R G T L R Y Q I V R L R F G R L F G F P R L R F S P F G Y K A S F S R R T K R H S L F . Protein_Len: 39 Strand: - Start: 28 End: 144 ........................... Y M Q I R W P F L L V P F G E T D S L L T L T R D D K R T E G G G T K V M R M ............................................. acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct 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================================================ acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1483:PG1484|PG1483:PG1484:conjugative transposon protein TraE:hypothetical protein:<-<-:1559176..1559364 189 acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_002950_PG1483_PG1484|conjugative transposon protein TraE:hypothetical protein|NEGATIVE:NEGATIVE|[1559176,1559364]|189 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct acgattggatttcaggtttataattcaatacatttgtatccgccatggaaaaaggaggacggggaacccttcggtatcagatagtaaggttaaggttcggtcgtcttttcgggtttccccgcctccggttttcaccattcggatataaggcttcgttttctcggcggacgaaaagacactccttgttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAUUGGAUUUCAGGUUUAUAAUUCAAUACAUUUGUAUCCGCCAUGGAAAAAGGAGGACGGGGAACCCUUCGGUAUCAGAUAGUAAGGUUAAGGUUCGGUCGUCUUUUCGGGUUUCCCCGCCUCCGGUUUUCACCAUUCGGAUAUAAGGCUUCGUUUUCUCGGCGGACGAAAAGACACUCCUUGUUCU ...((((((((..........))))))))...((((((((((...((((((..(((((.((((((((((...((.(((..((..((....))..))..)))...))....))).))))))))))))..)))))).....)))))))))).....(((((.(((.....))).)))))............ (-56.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAACAAGGAGUGUCUUUUCGUCCGCCGAGAAAACGAAGCCUUAUAUCCGAAUGGUGAAAACCGGAGGCGGGGAAACCCGAAAAGACGACCGAACCUUAACCUUACUAUCUGAUACCGAAGGGUUCCCCGUCCUCCUUUUUCCAUGGCGGAUACAAAUGUAUUGAAUUAUAAACCUGAAAUCCAAUCGU .....((((..(((.((((((.....)))))).)))...)))).((((((.((((.(((((..((((((((((((.(((.........................................)))))))))).))))))))))))))..))))))...(((.((((.(((.((....)).))).))))))) (-50.98) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1013 140 91 231 182 NC_002950:PG1483|5end_conjugative_transposon_protein_TraE_1559085..1559315_NEGATIVE 428 167 121 142 94 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 416 142 104 224 173 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 407 142 102 141 96 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 386 128 81 165 90 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 370 127 94 141 96 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 369 160 111 176 113 NC_002950:PG1954|5end_NAD_dependent_epimerase/reductase-related_protein_2044513..2044743_POSITIVE 369 133 98 111 78 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 366 140 94 67 17 NC_002950:PG0144|5end_hypothetical_protein_167668..167898_NEGATIVE 365 169 121 217 163 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 358 105 61 205 156 NC_002950:PG0053|5end_hypothetical_protein_65086..65316_NEGATIVE 357 170 123 231 191 NC_002950:PG0064|5end_heavy_metal_efflux_pump,_CzcA_family_80193..80423_NEGATIVE 354 130 94 195 155 NC_002950:PG1943|5end_hypothetical_protein_2030260..2030490_NEGATIVE 354 135 93 223 178 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 351 129 87 104 55 NC_002950:PG0209|5end_formate/nitrite_transporter_243231..243461_POSITIVE 349 160 111 54 3 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 347 143 101 188 129 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 346 168 122 204 151 NC_002950:PG1352|5end_hypothetical_protein_1433150..1433380_NEGATIVE 345 120 71 196 143 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 343 129 87 197 147 NC_002950:PG0929|5end_hypothetical_protein_987149..987379_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 150 104 131 72 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 428 167 121 145 97 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 386 128 81 137 62 NC_002950:PG1487|3end_hypothetical_protein_1561799..1561949_POSITIVE 383 136 96 144 106 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 370 127 94 127 82 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 346 176 133 118 74 NC_002950:PG0106|3end_glycosyl_transferase,_group_4_family_protein_129934..130084_POSITIVE 344 154 111 151 102 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 343 127 83 55 3 NC_002950:PG2206|3end_ABC_transporter,_ATP-binding_protein_2317250..2317400_NEGATIVE 336 170 127 35 2 NC_002950:PG0098|3end_hypothetical_protein_115745..115895_NEGATIVE 331 79 41 45 11 NC_002950:PG2144|3end_hypothetical_protein_2253290..2253440_POSITIVE 328 162 121 88 44 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 326 166 121 121 76 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 324 78 34 132 86 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 324 136 94 83 44 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 322 167 125 149 107 NC_002950:PG1750|3end_alpha-1,3/4-fucosidase,_putative_1837223..1837373_POSITIVE 322 129 85 69 17 NC_002950:PG0471|3end_hypothetical_protein_513432..513582_POSITIVE 319 124 88 106 73 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 319 159 111 123 74 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 317 128 88 141 89 NC_002950:PG1521|3end_O-succinylbenzoic_acid--CoA_ligase_1598054..1598204_NEGATIVE 316 103 63 76 36 NC_002950:PG1948|3end_lipoprotein,_putative_2037940..2038090_POSITIVE