Origin IGS: taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc .........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 ggcatatcgtattaagtgtatatattttgttttttactgtctcttctttttttcatcggtttgcaggttgtttccggcatcgcgatgttagtcagctttccagtggtcagcaaacaattcaacagctcaacaactaccccctgcaaggctgaaaaaacgaaaagagagccgcctccttttgagacagctctcttatttccgacacttccaaaaatctttta Mask Tandem Repeat Region ================================================ taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Find is-nt database================================================ Query_seq: TF2349:TF2350|TF2349:TF2350:conserved hypothetical protein:hypothetical protein:->->:2514982..2515202 221 taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2349:TF2350|TF2349:TF2350:conserved hypothetical protein:hypothetical protein:->->:2514982..2515202 221 taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2349:TF2350|TF2349:TF2350:conserved hypothetical protein:hypothetical protein:->->:2514982..2515202 221 taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 7 End: 207 ...... M F G S V G N K R A V S K G G G S L F V F S A L Q G V V V E L L N C L L T T G K L T N I A M P E T T C K P M K K R R D S .............. Protein_Len: 48 Strand: - Start: 73 End: 216 ........................................................................ G Q L P Y N N L Q Q I T Q Q G S S L Q S V D R H R F C G A F R H F F S S V T F F L I Y V S L V M ..... Protein_Len: 60 Strand: - Start: 3 End: 206 .. L L A T E F P P P E R K T K E A K C P T T T S S N F Q K S V V P F S V L M A I G S V V Q L G I F F L L S L L F C F I Y M ............... taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc 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================================================ taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -5.4 Tail_Score: -5.055 Start: 24 End: 64 Full_Region: TTTTGGAAGTGTCGG AAATAAGAGAGCTGTCTC AAAAG GAGGCGGCTCTCTTTTCG TTTTTTCAGCCTTGC .......................AAATAAGAGAGCTGTCTCAAAAGGAGGCGGCTCTCTTTTCG............................................................................................................................................................. TransTerm Strand: + Conf: 75 HP_score: -8.9 Tail_Score: -3.62577 Start: 25 End: 63 Full_Region: TTTGGAAGTGTCGGA AATAAGAGAGCTGTCTC AAAAG GAGGCGGCTCTCTTTTC GTTTTTTCAGCCTTG ........................AATAAGAGAGCTGTCTCAAAAGGAGGCGGCTCTCTTTTC.............................................................................................................................................................. TransTerm Strand: - Conf: 80 HP_score: -8.8 Tail_Score: -3.91488 Start: 30 End: 58 Full_Region: ctgaaaaaacgaaaa gagagccgcctc ctttt gagacagctctc ttatttccgacactt .............................gagagccgcctccttttgagacagctctc................................................................................................................................................................... Find igs database================================================ Query_seq: TF2349:TF2350|TF2349:TF2350:conserved hypothetical protein:hypothetical protein:->->:2514982..2515202 221 taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Intra-Species Hit: Count: 1 Min: 1 Max: 221 Len: 221 Subject: tfor_TF2349_TF2350|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2514982,2515202]|221 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 221 Query Start:1 Query End:221 Subject Strand: POSITIVE Subject Start: 1 Subject End: 221 taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgnnnnnnngaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc taaaagatttttggaagtgtcggaaataagagagctgtctcaaaaggaggcggctctcttttcgttttttcagccttgcagggggtagttgttgagctgttgaattgtttgctgaccactggaaagctgactaacatcgcgatgccggaaacaacctgcaaaccgatgaaaaaaagaagagacagtaaaaaacaaaatatatacacttaatacgatatgcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAUUUUUGGAAGUGUCGGAAAUAAGAGAGCUGUCUCAAAAGGAGGCGGCUCUCUUUUCGUUUUUUCAGCCUUGCAGGGGGUAGUUGUUGAGCUGUUGAAUUGUUUGCUGACCACUGGAAAGCUGACUAACAUCGCGAUGCCGGAAACAACCUGCAAACCGAUGAAAAAAAGAAGAGACAGUAAAAAACAAAAUAUAUACACUUAAUACGAUAUGCC ............((..((((((....((((.((((((((((.....))))))))))(((((((.((((((((...(((((((.((((.((((.((..(((((....(((.(((..((...))..))).))))))))))))))))))(....)..))))))).....)))))))).))))))).......................))))...)))))).)) (-62.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAUAUCGUAUUAAGUGUAUAUAUUUUGUUUUUUACUGUCUCUUCUUUUUUUCAUCGGUUUGCAGGUUGUUUCCGGCAUCGCGAUGUUAGUCAGCUUUCCAGUGGUCAGCAAACAAUUCAACAGCUCAACAACUACCCCCUGCAAGGCUGAAAAAACGAAAAGAGAGCCGCCUCCUUUUGAGACAGCUCUCUUAUUUCCGACACUUCCAAAAAUCUUUUA .............((((((......(((((((((...................(((((...(((.((......)).)))...)))))....((((((((.(((.((..((.......................))..)).))).)))))))))))))))))((((((((.(.(((.....))).).)))))))).......)))))).............. (-49.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 130 81 172 115 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 457 130 83 164 113 tfor:TF1175|5end_membrane-fusion_protein_1258140..1258370_POSITIVE 440 86 50 67 29 tfor:TF0584|5end_phosphopantetheinyl_transferase_613755..613985_POSITIVE 401 130 83 175 133 tfor:TF0359|5end_conserved_hypothetical_protein_376943..377173_POSITIVE 398 62 23 200 163 tfor:TF2925|5end_beta-N-acetylglucosaminidase_3125700..3125930_POSITIVE 392 60 11 133 75 tfor:TF0570|5end_possible_transcriptional_regulator_602483..602713_POSITIVE 384 130 81 169 111 tfor:TF0367|5end_eukaryotic-like__metalloproteinase_384007..384237_POSITIVE 384 130 81 169 111 tfor:TF0364|5end_ysyl_endopeptidase_380395..380625_POSITIVE 371 149 102 196 132 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 370 129 81 212 159 tfor:TF1528|5end_malate_dehydrogenase_1633287..1633517_POSITIVE 369 86 44 124 78 tfor:TF2912|5end_hypothetical_protein_3106508..3106738_POSITIVE 368 130 81 199 140 tfor:TF0347|5end_possible_serine_protease_367542..367772_POSITIVE 365 100 51 52 7 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 365 130 90 147 104 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 364 130 83 58 2 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 361 63 22 89 48 tfor:TF2788|5end_hypothetical_protein_2972201..2972431_POSITIVE 359 147 104 61 19 tfor:TF1137|5end_asparaginyl-tRNA_synthetase_(asparagine--tRNA_ligase)_1212443..1212673_POSITIVE 358 90 46 189 146 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 358 90 46 183 140 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 355 115 71 73 28 tfor:TF2747|5end_heat_shock_protein,_HSP90_family_2928279..2928509_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 483 64 21 70 27 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 440 86 50 61 23 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 438 130 84 64 17 tfor:TF1172|3end_ABC_transporter,_permease_component_1255213..1255363_POSITIVE 403 90 45 71 31 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 398 62 23 38 1 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 383 60 11 139 91 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE 367 90 46 84 33 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 366 79 31 91 35 tfor:TF0305|3end_peptidyl-prolyl_cis-trans_isomerase_331112..331262_POSITIVE 363 85 46 100 52 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 361 63 22 66 25 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE 358 90 46 79 36 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 354 130 82 108 55 tfor:TF1170|3end_conserved_hypothetical_protein_1252799..1252949_POSITIVE 342 57 13 148 117 tfor:TF2334|3end_dihydropicolinate_reductase_2494794..2494944_POSITIVE 339 61 29 32 1 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 339 129 81 150 105 tfor:TF0692|3end_conserved_hypothetical_protein_736992..737142_POSITIVE 339 63 28 53 18 tfor:TF0196|3end_conserved_hypothetical_protein_221037..221187_POSITIVE 337 70 29 72 22 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 336 72 31 55 3 tfor:TF2886|3end_RNA_methylase_SpoU_family_3076270..3076420_POSITIVE 334 90 47 77 22 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 333 116 71 64 8 tfor:TF2444|3end_regulatory_protein_RecX_2621549..2621699_POSITIVE