Origin IGS: cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtgacaaaaaaagactcttcgttgacgctctgaatgacaagggaagtgaaaagtgaaaaacgaaaagtgaagagtgagaaacgaatagtgaaaagtgaagcccttcggggtgtgagatgtttgtttgtttaattattgattggttaagttgggggtaggggtgaacctgtgtgttcgcccctacacggcatccgaatgccgaatgaccattaaccattaaatgacgctgaacgctgattagaatgacgaaatatgttttaactaaataatatacg Mask Tandem Repeat Region ================================================ cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Find is-nt database================================================ Query_seq: TF1587:TF1588|TF1587:TF1588:conserved hypothetical protein:hypothetical protein:->->:1702083..1702407 325 cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1587:TF1588|TF1587:TF1588:conserved hypothetical protein:hypothetical protein:->->:1702083..1702407 325 cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1587:TF1588|TF1587:TF1588:conserved hypothetical protein:hypothetical protein:->->:1702083..1702407 325 cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 32 End: 283 ............................... M L I S V Q R H L M V N G H S A F G C R V G A N T Q V H P Y P Q L N Q S I I K Q T N I S H P E G L H F S L F V S H S S L .......................................... Protein_Len: 35 Strand: + Start: 190 End: 294 ............................................................................................................................................................................................. M R F S L F T F R F S L F T S L V I Q S V N E E S F F V T F G L T Q K ............................... Protein_Len: 32 Strand: - Start: 147 End: 242 .................................................................................................................................................. V F L C R V G R L A E S K V I R K E S K V K R K E S K V E R T M ................................................................................... cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca 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================================================ cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1587:TF1588|TF1587:TF1588:conserved hypothetical protein:hypothetical protein:->->:1702083..1702407 325 cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaagggcttcacttttcactattcgtttctcactcttcacttttcgtttttcacttttcacttcccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Intra-Species Hit: Count: 1 Min: 1 Max: 325 Len: 325 Subject: tfor_TF1587_TF1588|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1702083,1702407]|325 HSP 1 e-value: 1.0E-94 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaaggg...................................................................................................................................................... cgtatattatttagttaaaacatatttcgtcattctaatcagcgttcagcgtcatttaatggttaatggtcattcggcattcggatgccgtgtaggggcgaacacacaggttcacccctacccccaacttaaccaatcaataattaaacaaacaaacatctcacaccccgaaggg...................................................................................................................................................... HSP 2 e-value: 2.0E-32 bit: 141.0 Len: 92 Query Start:234 Query End:325 Subject Strand: POSITIVE Subject Start: 234 Subject End: 325 .........................................................................................................................................................................................................................................ccttgtcattcagagcgtcaacgaagagtcnnnnnnngtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca .........................................................................................................................................................................................................................................ccttgtcattcagagcgtcaacgaagagtctttttttgtcacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUAUUAUUUAGUUAAAACAUAUUUCGUCAUUCUAAUCAGCGUUCAGCGUCAUUUAAUGGUUAAUGGUCAUUCGGCAUUCGGAUGCCGUGUAGGGGCGAACACACAGGUUCACCCCUACCCCCAACUUAACCAAUCAAUAAUUAAACAAACAAACAUCUCACACCCCGAAGGGCUUCACUUUUCACUAUUCGUUUCUCACUCUUCACUUUUCGUUUUUCACUUUUCACUUCCCUUGUCAUUCAGAGCGUCAACGAAGAGUCUUUUUUUGUCACUUUUGGCUUGACCCAAAAGUAACCCAAAGGUCAAGGCUUCGUGCGCUUCA (((((....((((((((........................((.....)).........((((((((((.....((((((....)))))).(((((((.((((......)))).)))))))..)))..))))))).....)))))))).......................(((.(((.((((((......................((((((((((...(.((((..((.......)).....)))).)..))))))))))........((.((((((((......)))))))).))..)))))).))).))).)))))..... (-71.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGCGCACGAAGCCUUGACCUUUGGGUUACUUUUGGGUCAAGCCAAAAGUGACAAAAAAAGACUCUUCGUUGACGCUCUGAAUGACAAGGGAAGUGAAAAGUGAAAAACGAAAAGUGAAGAGUGAGAAACGAAUAGUGAAAAGUGAAGCCCUUCGGGGUGUGAGAUGUUUGUUUGUUUAAUUAUUGAUUGGUUAAGUUGGGGGUAGGGGUGAACCUGUGUGUUCGCCCCUACACGGCAUCCGAAUGCCGAAUGACCAUUAACCAUUAAAUGACGCUGAACGCUGAUUAGAAUGACGAAAUAUGUUUUAACUAAAUAAUAUACG ...((((.....(((......((((..(((((((((((......)))))))))))....))))(((((((.((.((.((((........))))..)).))..((.....)).......)))))))...((((((((((...........((((....)))).........))))))))))..(((((...(((((((..(((..((((((((((((......)))))))))))).((((((....)))))).....))))))))))...))))).)))...))))..((((...((((.....))))....)))).......... (-94.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 320 274 209 163 tfor:TF1660|5end_hypothetical_protein_1775269..1775499_POSITIVE 868 320 271 180 131 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 862 320 271 188 139 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 849 320 271 85 35 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 849 320 274 227 181 tfor:TF1843|5end_surface_antigen_BspA_1992834..1993064_POSITIVE 822 320 274 208 162 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 822 320 274 102 56 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 686 320 274 102 56 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 595 230 181 150 101 tfor:TF1783|5end_conserved_hypothetical_protein_1923408..1923638_POSITIVE 547 100 51 167 116 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 518 121 85 230 195 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 518 103 61 219 173 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 502 140 96 68 19 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 443 100 60 51 4 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 424 268 229 151 115 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 419 250 205 220 177 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 413 113 71 58 15 tfor:TF2523|5end_NAD(P)H-flavin_oxidoreductase_2702114..2702344_POSITIVE 392 279 236 73 36 tfor:TF2816|5end_hypothetical_protein_3006925..3007155_POSITIVE 392 118 71 59 12 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 388 279 236 135 98 tfor:TF2777|5end_hypothetical_protein_2961595..2961825_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 320 274 69 23 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 891 320 271 136 87 tfor:TF2817|3end_hypothetical_protein_3007626..3007776_POSITIVE 868 320 271 51 2 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 862 320 271 95 46 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 862 320 271 69 20 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 862 320 272 85 37 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 849 320 274 113 67 tfor:TF1842|3end_hypothetical_protein_1992800..1992950_POSITIVE 822 320 274 95 49 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 822 320 274 85 39 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 822 320 274 95 49 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 822 320 274 69 23 tfor:TF1187|3end_hypothetical_protein_1269872..1270022_POSITIVE 724 320 274 95 49 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 706 320 280 41 1 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 686 320 274 95 49 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 650 290 241 146 97 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 617 230 181 91 35 tfor:TF1843|3end_surface_antigen_BspA_1996189..1996339_POSITIVE 595 230 181 67 18 tfor:TF1781|3end_imidazolonepropionase_1923384..1923534_POSITIVE 547 100 51 53 2 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 541 103 62 86 40 tfor:TF1716|3end_hypothetical_protein_1837710..1837860_POSITIVE 518 103 61 141 95 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE