Origin IGS: tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaagaagagatacccctgtcatgatctcctgaaaaatcgtagcgtaatgttttcctatcttccgtcgcaacgggaaagcacagctcaatgcaagaatccttccggccatggccggaaagattcataccggtatatttgaactgtgtttcgggacgaaacaggctgcta Mask Tandem Repeat Region ================================================ tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Find is-nt database================================================ Query_seq: TF0308:TF0309|TF0308:TF0309:hypothetical protein:conserved hypothetical protein:->->:334143..334313 171 tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0308:TF0309|TF0308:TF0309:hypothetical protein:conserved hypothetical protein:->->:334143..334313 171 tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0308:TF0309|TF0308:TF0309:hypothetical protein:conserved hypothetical protein:->->:334143..334313 171 tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 8 End: 169 ....... M F R P E T Q F K Y T G M N L S G H G R K D S C I E L C F P V A T E D R K T L R Y D F S G D H D R G I S S F .. Protein_Len: 41 Strand: + Start: 48 End: 170 ............................................... M F P A M A G R I L A L S C A F P L R R K I G K H Y A T I F Q E I M T G V S L L F . Protein_Len: 36 Strand: - Start: 33 End: 140 ................................ I Y R Y S D K R G H G S P N K C Q A T S E R Q S P L Y S F M V S R N K M ............................... Protein_Len: 37 Strand: - Start: 2 End: 112 . A A Q K T G F C L E F I G T H I K G A M A P L I R A N L Q A K G N R R F M ........................................................... tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta 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================================================ tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -17.3 Tail_Score: -3.1875 Start: 46 End: 75 Full_Region: CAAATATACCGGTAT GAATCTTTCCGGC CATG GCCGGAAGGATTC TTGCATTGAGCTGTG .............................................GAATCTTTCCGGCCATGGCCGGAAGGATTC................................................................................................ TransTerm Strand: + Conf: 93 HP_score: -13.2 Tail_Score: -3.73336 Start: 49 End: 72 Full_Region: ATATACCGGTATGAA TCTTTCCGGC CATG GCCGGAAGGA TTCTTGCATTGAGCT ................................................TCTTTCCGGCCATGGCCGGAAGGA................................................................................................... Find igs database================================================ Query_seq: TF0308:TF0309|TF0308:TF0309:hypothetical protein:conserved hypothetical protein:->->:334143..334313 171 tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: tfor_TF0308_TF0309|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[334143,334313]|171 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta tagcagcctgtttcgtcccgaaacacagttcaaatataccggtatgaatctttccggccatggccggaaggattcttgcattgagctgtgctttcccgttgcgacggaagataggaaaacattacgctacgatttttcaggagatcatgacaggggtatctcttcttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAGCCUGUUUCGUCCCGAAACACAGUUCAAAUAUACCGGUAUGAAUCUUUCCGGCCAUGGCCGGAAGGAUUCUUGCAUUGAGCUGUGCUUUCCCGUUGCGACGGAAGAUAGGAAAACAUUACGCUACGAUUUUUCAGGAGAUCAUGACAGGGGUAUCUCUUCUUUUUA ..((..((((((..(((((((((((((((((((........(((.(((((((((((((....))))))))))))).))).)))))))))).)))).(((.(((.(....)...(.....)....))).)))........)).)))...)))))).)).............. (-59.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGAAGAGAUACCCCUGUCAUGAUCUCCUGAAAAAUCGUAGCGUAAUGUUUUCCUAUCUUCCGUCGCAACGGGAAAGCACAGCUCAAUGCAAGAAUCCUUCCGGCCAUGGCCGGAAAGAUUCAUACCGGUAUAUUUGAACUGUGUUUCGGGACGAAACAGGCUGCUA .........(((((............)))))..........(((((....(((((((((...((((((....))))))((((((((.(((((((..(((((.(((((((....))))))).)))))......))))...))).)))))))).))))..))))).))))).. (-52.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 423 107 61 72 6 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 418 80 35 190 138 tfor:TF1066|5end_hypothetical_protein_1136545..1136775_POSITIVE 416 96 52 60 4 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 404 108 64 47 1 tfor:TF2499|5end_possible_thioesterase_family_protein_2673903..2674133_POSITIVE 397 110 63 184 137 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 391 103 63 170 113 tfor:TF2877|5end_regulatory_protein_3065601..3065831_POSITIVE 389 106 61 182 124 tfor:TF1853|5end_homoserine_O-succinyltransferase_2006470..2006700_POSITIVE 387 107 62 229 175 tfor:TF0032|5end_sugar_phosphate_permease,_major_facilitator_superfamily_27911..28141_POSITIVE 385 106 61 105 59 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 384 100 54 51 9 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 381 99 54 55 3 tfor:TF0093|5end_outer_membrane_protein,_TonB_dependent_receptor_100497..100727_POSITIVE 378 98 54 207 143 tfor:TF1475|5end_glucose-6-phosphate_1-dehydrogenase_1568034..1568264_POSITIVE 374 100 54 74 16 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 362 79 40 160 116 tfor:TF2788|5end_hypothetical_protein_2972201..2972431_POSITIVE 361 100 55 56 1 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 357 99 51 52 4 tfor:TF2184|5end_conserved_hypothetical_protein_2355578..2355808_POSITIVE 353 78 36 227 179 tfor:TF0425|5end_outer_membrane_protein_443069..443299_POSITIVE 352 79 39 176 139 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 352 66 24 52 7 tfor:TF0119|5end_gluconate_aldolase_130577..130807_POSITIVE 351 97 52 52 7 tfor:TF2412|5end_outer_membrane_protein_2587017..2587247_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 664 90 42 67 12 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 416 96 52 60 4 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 388 89 41 75 29 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 375 95 55 132 92 tfor:TF2876|3end_cytosine_deaminase_3065664..3065814_POSITIVE 363 110 61 151 92 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 362 79 40 137 93 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE 357 79 38 146 96 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 352 79 39 141 104 tfor:TF2257|3end_transfer_region-related_protein,_TraJ_2429622..2429772_POSITIVE 345 88 49 105 67 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 342 68 29 145 106 tfor:TF2571|3end_30S_ribosomal_protein_S5_2743140..2743290_POSITIVE 338 98 55 59 7 tfor:TF2113|3end_phosphoribosylaminoimidazole_carboxylase_2283086..2283236_POSITIVE 338 106 61 115 70 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 338 106 61 105 60 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 338 79 38 44 6 tfor:TF0336|3end_Xaa-Pro_aminopeptidase_361868..362018_POSITIVE 336 90 51 82 38 tfor:TF1479|3end_ABC_transporter,_permease_component_1573592..1573742_POSITIVE 333 107 64 121 75 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 331 99 52 59 5 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 331 106 65 115 73 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 330 99 55 69 15 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 329 88 41 82 34 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE