Origin IGS: acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacgggagacgcttttgcatctcatccgtttccgaacataccgcggagaggccggacacaaaaatcatttggagacagcctctctttttcgtttccccaaaaacgttttcctttgtttttcaaatattcgacgt Mask Tandem Repeat Region ================================================ acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Find is-nt database================================================ Query_seq: TF2886:TF2887|TF2886:TF2887:RNA methylase SpoU family:phosphomannomutase/phosphoglucomutase:->->:3076331..3076466 136 acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2886:TF2887|TF2886:TF2887:RNA methylase SpoU family:phosphomannomutase/phosphoglucomutase:->->:3076331..3076466 136 acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2886:TF2887|TF2886:TF2887:RNA methylase SpoU family:phosphomannomutase/phosphoglucomutase:->->:3076331..3076466 136 acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 12 End: 110 ........... M K N K G K R F W G N E K E R L S P N D F C V R P L R G M F G N G .......................... Protein_Len: 38 Strand: - Start: 3 End: 116 .. D F I Q F V F S F T K P S V F F L P Q R W I I K T D P R E A T H E S V S S M .................... Protein_Len: 32 Strand: - Start: 2 End: 97 . T S Y K F F L P F R K Q P F S F S L S D G F S K Q T R G R R P M ....................................... Protein_Len: 40 Strand: - Start: 1 End: 120 R R I N S F C L F V N K P F R F L S A T E L H N K H G A E G R Y T R F R I L H M ................ acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta 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================================================ acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -3.4 Tail_Score: -4.98531 Start: 51 End: 63 Full_Region: cacaaaaatcatttg gaga cagcc tctc tttttcgtttcccca ..................................................gagacagcctctc......................................................................... Find igs database================================================ Query_seq: TF2886:TF2887|TF2886:TF2887:RNA methylase SpoU family:phosphomannomutase/phosphoglucomutase:->->:3076331..3076466 136 acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: tfor_TF2886_TF2887|RNA methylase SpoU family:phosphomannomutase/phosphoglucomutase|POSITIVE:PO SITIVE|[3076331,3076466]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta acgtcgaatatttgaaaaacaaaggaaaacgtttttggggaaacgaaaaagagaggctgtctccaaatgatttttgtgtccggcctctccgcggtatgttcggaaacggatgagatgcaaaagcgtctcccgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUCGAAUAUUUGAAAAACAAAGGAAAACGUUUUUGGGGAAACGAAAAAGAGAGGCUGUCUCCAAAUGAUUUUUGUGUCCGGCCUCUCCGCGGUAUGUUCGGAAACGGAUGAGAUGCAAAAGCGUCUCCCGUUUA ....((((((((((...............((((((....)))))).....(((((((((..(.((((.....)))).)..)))))))))..))).))))))).((((((..(((((((....))))))))))))). (-45.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACGGGAGACGCUUUUGCAUCUCAUCCGUUUCCGAACAUACCGCGGAGAGGCCGGACACAAAAAUCAUUUGGAGACAGCCUCUCUUUUUCGUUUCCCCAAAAACGUUUUCCUUUGUUUUUCAAAUAUUCGACGU .((((((((((.((....)).))))..)))))).((((........((((((((.(....((((.....))))....).)))))))).............(((((((........)))))))......)))).... (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 98 51 209 149 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 396 94 53 196 147 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 395 129 81 77 22 tfor:TF2705|5end_conserved_hypothetical_protein;_possible_SufE_Fe/S-cluster-related_protein_2876850..2877080_POSITIVE 385 117 72 231 180 tfor:TF0304|5end_peptidyl-prolyl_cis-trans_isomerase_329567..329797_POSITIVE 378 118 77 52 4 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 377 108 62 72 19 tfor:TF1298|5end_possible_membrane_protein_1380107..1380337_POSITIVE 375 130 81 88 32 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 364 129 81 161 120 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 363 98 51 65 10 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 359 116 77 64 6 tfor:TF2912|5end_hypothetical_protein_3106508..3106738_POSITIVE 359 113 72 75 30 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 356 109 76 187 156 tfor:TF1352|5end_polysaccharide_deacetylase-like_protein_1432006..1432236_POSITIVE 355 119 71 194 147 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 354 127 83 189 148 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 351 130 81 184 129 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 351 127 81 209 155 tfor:TF0975|5end_hypothetical_protein_1023994..1024224_POSITIVE 351 126 81 91 34 tfor:TF0249|5end_3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl_carrier_protein)_dehydratase_278808..279038_POSITIVE 350 129 81 180 144 tfor:TF2782|5end_conserved_hypothetical_protein_2966455..2966685_POSITIVE 350 118 80 199 158 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 349 97 52 218 172 tfor:TF2936|5end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_3138522..3138752_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 451 98 51 120 60 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 395 129 81 68 13 tfor:TF2704|3end_ribonuclease_HII_2876921..2877071_POSITIVE 378 129 82 89 41 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 378 118 77 52 4 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 375 130 81 61 5 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 363 90 41 78 24 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 359 116 77 116 58 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 358 129 81 77 17 tfor:TF0883|3end_hypothetical_protein_937472..937622_POSITIVE 356 109 76 151 120 tfor:TF1351|3end_conserved_hypothetical_protein_1432050..1432200_POSITIVE 355 130 81 100 38 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE 354 127 83 86 45 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 351 126 81 98 41 tfor:TF0248|3end_hypothetical_protein_278895..279045_POSITIVE 350 113 77 149 114 tfor:TF0983|3end_nitroreductase_family_protein,__possible_NADH_dehydrogenase/NAD(P)H_nitroreductase_1040034..1040184_POSITIVE 340 109 61 147 100 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE 334 90 48 53 15 tfor:TF0196|3end_conserved_hypothetical_protein_221037..221187_POSITIVE 332 130 81 70 12 tfor:TF0062|3end_conserved_hypothetical_protein_66180..66330_POSITIVE 329 95 53 143 93 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 328 108 62 130 79 tfor:TF2487|3end_transposase_2663956..2664106_POSITIVE 327 118 73 98 42 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 326 119 71 142 81 tfor:TF2855|3end_ATPase,_AAA_family_3042011..3042161_POSITIVE