Origin IGS: gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attctcaaaaaatgtttctaactttgtagtatcatcaaaaacgcaaggctatggaaataacaaccgacactccacccgacaatttgatgcgcctcgcaaactgcaacggaggcgcagcgtaaaagaaatatccggaacgcggaaaacaagtataaacgtttaaaaacagaaaaac Mask Tandem Repeat Region ================================================ gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Find is-nt database================================================ Query_seq: TF2176:TF2177|TF2176:TF2177:hypothetical protein:hypothetical protein:->->:2349246..2349420 175 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2176:TF2177|TF2176:TF2177:hypothetical protein:hypothetical protein:->->:2349246..2349420 175 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2176:TF2177|TF2176:TF2177:hypothetical protein:hypothetical protein:->->:2349246..2349420 175 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 23 End: 124 ...................... M L V F R V P D I S F T L R L R C S L R G A S N C R V E C R L L F P ................................................... Protein_Len: 44 Strand: + Start: 7 End: 138 ...... M F L N V Y T C F P R S G Y F F Y A A P P L Q F A R R I K L S G G V S V V I S I A L R F ..................................... Protein_Len: 43 Strand: + Start: 27 End: 155 .......................... M F S A F R I F L L R C A S V A V C E A H Q I V G W S V G C Y F H S L A F L M I L Q S .................... gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat 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================================================ gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2176:TF2177|TF2176:TF2177:hypothetical protein:hypothetical protein:->->:2349246..2349420 175 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Intra-Species Hit: Count: 4 Min: 1 Max: 175 Len: 175 Subject: tfor_TF2176_TF2177|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2349246,2349420]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat Subject: tfor_TF1713_TF1714|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1833777,1834264]|488 HSP 1 e-value: 7.0E-55 bit: 214.0 Len: 171 Query Start:5 Query End:175 Subject Strand: NEGATIVE Subject Start: 315 Subject End: 485 ....ttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcg-tttttgatgatactacaaagttagaaacattttttgagaat ....ttcttttttttaaggtttataattactttccgcgttccggatatttcttttacgctgcgcctccggtgcggtctgtgaggcgcatcgaattgtcgggtggagtgtcggtcgtt-tttccatagccttgcgttttttgatgatactacaaagttagaaacattttttgagaat Subject: tfor_TF0358_TF0359|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[376365,377082]|718 HSP 1 e-value: 4.0E-53 bit: 208.0 Len: 164 Query Start:12 Query End:175 Subject Strand: POSITIVE Subject Start: 18 Subject End: 179 ...........tttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat ...........tttaaacgtttatacttgttttccgcgttccggatagttgtt--acgctgcgcctccggtgcggcctgtgaggcgcagcgaattgtcgggtggagtgtcggtcgttatttccatagccttgcgttttttatgatactacaaagttaaaaacattttttgagaat Subject: tfor_TF0365_TF0366|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[383213,383703]|491 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 gtttttctgtttttaaacgtttatacttgttttccgcgttccggatatttcttttacgctgcgcctccgttgcagtttgcgaggcgcatcaaattgtcgggtggagtgtcggttgttatttccatagccttgcgtttttgatgatactacaaagttagaaacattttttgagaat gtttttctgtttttaaacgtttatacttgttt-ccgcgttccagatagttgtcat--gctgcgcctccggtgcggtttgcgaggcgcatcgaattgtcgggtggagtgtcggttgttatttccatagccttgcatttttgatgatactacaaagttataaacgatttctgagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUCUGUUUUUAAACGUUUAUACUUGUUUUCCGCGUUCCGGAUAUUUCUUUUACGCUGCGCCUCCGUUGCAGUUUGCGAGGCGCAUCAAAUUGUCGGGUGGAGUGUCGGUUGUUAUUUCCAUAGCCUUGCGUUUUUGAUGAUACUACAAAGUUAGAAACAUUUUUUGAGAAU ........(((((((((.((((..((((.......((((...(((....)))...)))).(((((((((........)).))))))).(((((.(((.((((((((((........))))))....)))).)))..)))))..........))))...))))....))))))))) (-39.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUCAAAAAAUGUUUCUAACUUUGUAGUAUCAUCAAAAACGCAAGGCUAUGGAAAUAACAACCGACACUCCACCCGACAAUUUGAUGCGCCUCGCAAACUGCAACGGAGGCGCAGCGUAAAAGAAAUAUCCGGAACGCGGAAAACAAGUAUAAACGUUUAAAAACAGAAAAAC .((((....((((((((...((((.((.............((((..((...((((...............)))).))..........((((((((((.....))....))))))))))))..........((((.....))))..))))))..))))))))......)))).... (-35.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 882 130 81 219 171 tfor:TF1714|5end_hypothetical_protein_1834125..1834355_POSITIVE 464 89 41 222 167 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 449 118 72 181 131 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 433 110 63 153 99 tfor:TF1302|5end_conserved_hypothetical_protein;_possible_tetracycline_resistance_element_1383256..1383486_POSITIVE 422 105 61 57 5 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 417 110 63 59 11 tfor:TF1297|5end_hypothetical_protein_1379024..1379254_POSITIVE 415 89 41 130 76 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 413 99 59 47 2 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 408 99 55 130 72 tfor:TF0595|5end_hypothetical_protein_627820..628050_POSITIVE 402 80 33 227 157 tfor:TF0032|5end_sugar_phosphate_permease,_major_facilitator_superfamily_27911..28141_POSITIVE 400 116 72 208 164 tfor:TF1300|5end_conserved_hypothetical_protein_1382389..1382619_POSITIVE 398 112 71 65 21 tfor:TF0611|5end_lysine_decarboxylase_642750..642980_POSITIVE 397 86 43 223 165 tfor:TF1628|5end_conserved_hypothetical_protein_1740627..1740857_POSITIVE 395 88 41 58 6 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 393 134 101 41 9 tfor:TF0532|5end_hypothetical_protein_557509..557739_POSITIVE 391 69 28 231 191 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 391 88 57 32 1 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 390 100 51 195 147 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 389 108 62 230 172 tfor:TF2250|5end_transfer_region-related_protein,_TraD_2423380..2423610_POSITIVE 388 76 37 151 110 tfor:TF1217|5end_hypothetical_protein_1303825..1304055_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 112 72 147 102 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 424 109 61 68 7 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 422 105 61 57 5 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 415 89 41 130 76 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 398 112 71 48 4 tfor:TF0609|3end_conserved_hypothetical_protein_642813..642963_POSITIVE 393 139 98 85 43 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 391 88 57 32 1 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 388 76 37 148 107 tfor:TF1216|3end_possible_ECF-family_RNA_polymerase_sigma_factor_1303902..1304052_POSITIVE 387 86 41 59 17 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 383 108 64 98 53 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 370 87 41 52 7 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 370 110 61 69 5 tfor:TF0368|3end_hypothetical_protein_385834..385984_POSITIVE 369 98 51 150 107 tfor:TF2426|3end_conserved_hypothetical_protein;_possible_TonB_receptor_2605931..2606081_POSITIVE 368 86 41 63 22 tfor:TF0686|3end_hypothetical_protein_732950..733100_POSITIVE 364 109 62 62 1 tfor:TF0358|3end_hypothetical_protein_376304..376454_POSITIVE 363 134 93 131 90 tfor:TF2328|3end_conserved_hypothetical_protein_2488349..2488499_POSITIVE 361 109 61 68 4 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 358 98 52 113 64 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 354 108 61 147 88 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 352 108 63 86 42 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE