Origin IGS: tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta .........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 tagttaaaagtgaataatgaagaacgaaaagtgaaaagtttttcgggtgtttaactgttgagttgtttgacggttgaatggaacaatgacgaatgacgtgaataaccgcaaatgaaaacttgcgaaccttgcggaatcctttgtgaatcttgcggtttattttaccgcaaagcacgcaatggaaaccgcaaagggcgcgaaggttgttatcacgggcgaacacagaggttcgctcctacgcggcataccgaacgctgtgtcctggcctgaaaactgatggctgaccgctgaatgcacagtcgctatttgcta Mask Tandem Repeat Region ================================================ tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Find is-nt database================================================ Query_seq: TF1165:TF1166|TF1165:TF1166:conserved hypothetical protein:ABC transporter, permease component:->->:1245982..1246293 312 tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1165:TF1166|TF1165:TF1166:conserved hypothetical protein:ABC transporter, permease component:->->:1245982..1246293 312 tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1165:TF1166|TF1165:TF1166:conserved hypothetical protein:ABC transporter, permease component:->->:1245982..1246293 312 tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 7 End: 153 ...... M A T V H S A V S H Q F S G Q D T A F G M P R R S E P L C S P V I T T F A P F A V S I A C F A V K ............................................................................................................................................................... Protein_Len: 35 Strand: + Start: 202 End: 306 ......................................................................................................................................................................................................... M R L F T S F V I V P F N R Q T T Q Q L N T R K T F H F S F F I I H F ...... Protein_Len: 60 Strand: + Start: 90 End: 311 ......................................................................................... M F A R D N N L R A L C G F H C V L C G K I N R K I H K G F R K V R K F S F A V I H V I R H C S I Q P S N N S T V K H P . Protein_Len: 52 Strand: - Start: 46 End: 201 ............................................. A L V C R E T H R T P A F R Q T R G H Y C G E R G K R N G N R A K R Y F L G C S E C L I G C P E C T K M ............................................................................................................... Protein_Len: 44 Strand: - Start: 39 End: 170 ...................................... N E P W S V A N P I G R L L S G R H E G T I V V K A G K A T E M A H K A T F Y V A L N M .............................................................................................................................................. Protein_Len: 45 Strand: - Start: 32 End: 166 ............................... G D T K L G P C L T R Y A A Y S R V E T N A R S L L R R A R Q P K W Q T S Q P L I F R L M .................................................................................................................................................. tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta 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================================================ tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1165:TF1166|TF1165:TF1166:conserved hypothetical protein:ABC transporter, permease component:->->:1245982..1246293 312 tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: tfor_TF1165_TF1166|conserved hypothetical protein:ABC transporter, permease component|POSITIVE:POSITIVE|[1245982,1246293]|312 HSP 1 e-value: 1.0E-176 bit: 618.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta tagcaaatagcgactgtgcattcagcggtcagccatcagttttcaggccaggacacagcgttcggtatgccgcgtaggagcgaacctctgtgttcgcccgtgataacaaccttcgcgccctttgcggtttccattgcgtgctttgcggtaaaataaaccgcaagattcacaaaggattccgcaaggttcgcaagttttcatttgcggttattcacgtcattcgtcattgttccattcaaccgtcaaacaactcaacagttaaacacccgaaaaacttttcacttttcgttcttcattattcacttttaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAAAUAGCGACUGUGCAUUCAGCGGUCAGCCAUCAGUUUUCAGGCCAGGACACAGCGUUCGGUAUGCCGCGUAGGAGCGAACCUCUGUGUUCGCCCGUGAUAACAACCUUCGCGCCCUUUGCGGUUUCCAUUGCGUGCUUUGCGGUAAAAUAAACCGCAAGAUUCACAAAGGAUUCCGCAAGGUUCGCAAGUUUUCAUUUGCGGUUAUUCACGUCAUUCGUCAUUGUUCCAUUCAACCGUCAAACAACUCAACAGUUAAACACCCGAAAAACUUUUCACUUUUCGUUCUUCAUUAUUCACUUUUAACUA .........((((((((.......)))))).))....((((....(((..((((((((.(((((.....((.....))..)))))..))))))))))).((((((((...(((.(((..((((((((..(((.(((.(...((((((((.......))))))))...).))).)))..))))))))..))))))......(((((((((........((........))........))))).))))..........))))......((((((.........))))))...........))))....)))). (-83.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAAAAGUGAAUAAUGAAGAACGAAAAGUGAAAAGUUUUUCGGGUGUUUAACUGUUGAGUUGUUUGACGGUUGAAUGGAACAAUGACGAAUGACGUGAAUAACCGCAAAUGAAAACUUGCGAACCUUGCGGAAUCCUUUGUGAAUCUUGCGGUUUAUUUUACCGCAAAGCACGCAAUGGAAACCGCAAAGGGCGCGAAGGUUGUUAUCACGGGCGAACACAGAGGUUCGCUCCUACGCGGCAUACCGAACGCUGUGUCCUGGCCUGAAAACUGAUGGCUGACCGCUGAAUGCACAGUCGCUAUUUGCUA ........((..((((.(((.........(((.(..((((((.(((((((((((((((..((...))..))))))))))(((...(((((((....((((......(((((.(....).)))))..((((((((..(((.(((((....(((((((.......)))))))....))))).)))..)))).)))).))))....)))))))...((((((((......))))))))...((((((.........)))))))))..)))))))))))..).)))....((.....))....))).))))..)). (-100.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 712 98 51 231 184 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 520 99 66 226 194 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 515 120 74 120 62 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 515 120 74 120 62 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 515 120 74 120 62 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 514 120 74 126 68 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 514 120 74 120 62 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 514 120 74 120 62 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 514 120 74 120 62 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 486 100 59 63 17 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 479 99 51 139 78 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 467 100 57 176 135 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 460 106 74 231 199 tfor:TF1169|5end_lipoprotein_ABC_transporter,_permease_component_1249136..1249366_POSITIVE 457 120 74 111 62 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 449 129 81 99 43 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 449 129 81 92 36 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 428 87 41 55 8 tfor:TF0665|5end_conserved_hypothetical_protein_709497..709727_POSITIVE 424 100 56 196 151 tfor:TF1850|5end_Na+/H+-exchanging_protein_1998542..1998772_POSITIVE 424 218 179 214 176 tfor:TF0535|5end_surface_antigen_BspA_559804..560034_POSITIVE 407 100 51 72 10 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 645 96 51 151 106 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 635 98 56 100 57 tfor:TF1716|3end_hypothetical_protein_1837710..1837860_POSITIVE 551 120 77 55 1 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 514 120 74 134 75 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 482 117 71 144 97 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 479 99 51 146 85 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 474 99 56 110 61 tfor:TF2346|3end_hypothetical_protein_2509973..2510123_POSITIVE 428 87 41 48 1 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 424 218 179 98 60 tfor:TF0534|3end_hypothetical_protein_559768..559918_POSITIVE 412 87 45 149 90 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE 406 300 252 109 63 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 406 300 252 126 80 tfor:TF1817|3end_hypothetical_protein_1957991..1958141_POSITIVE 405 89 47 75 30 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 400 53 15 39 1 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 400 149 110 139 93 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 398 294 252 53 11 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 388 68 21 58 13 tfor:TF1715|3end_thermolysin;_zinc_metalloprotease_1837202..1837352_POSITIVE 388 66 25 99 63 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 387 103 64 46 3 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 386 83 43 83 31 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE