Origin IGS: gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatggtaatcattttgttatacgccttcaaaggtatgcaataattaacaataatattaaagaaaatcgcccgcattgccaggcatgcccgccaaaacgagcagggacgtatttacggcatcacgtttatctcggacgaagccggtatcgctgccaatggctcgcgc Mask Tandem Repeat Region ================================================ gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Find is-nt database================================================ Query_seq: TF0880:TF0881|TF0880:TF0881:conserved hypothetical protein:conserved hypothetical protein:->->:934432..934598 167 gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0880:TF0881|TF0880:TF0881:conserved hypothetical protein:conserved hypothetical protein:->->:934432..934598 167 gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0880:TF0881|TF0880:TF0881:conserved hypothetical protein:conserved hypothetical protein:->->:934432..934598 167 gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 10 End: 108 ......... M G S D T G F V R D K R D A V N T S L L V L A G M P G N A G D F L ........................................................... Protein_Len: 37 Strand: + Start: 56 End: 166 ....................................................... M R P C S F W R A C L A M R A I F F N I I V N Y C I P L K A Y N K M I T I . Protein_Len: 30 Strand: - Start: 3 End: 92 .. R A M P L S V P K T R S L R S A T F V D R S T K A P M G P M ........................................................................... Protein_Len: 49 Strand: - Start: 2 End: 148 . A L W Q C R Y R S R G L Y V H H R L Y T G A R K P P C A Q C H P R N E K I N N N I I A Y R Q L R M ................... Protein_Len: 39 Strand: - Start: 1 End: 117 R S G N A A I G A E D S I F T I G Y I R G Q E N Q R A H R A I R A I K K L I M .................................................. gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc 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================================================ gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -2.5 Tail_Score: -4.99568 Start: 64 End: 101 Full_Region: GCCGTAAATACGTCC CTGCTCGTTTTGGCGGG CATG CCTGGCAATGCGGGCGA TTTTCTTTAATATTA ...............................................................CTGCTCGTTTTGGCGGGCATGCCTGGCAATGCGGGCGA.................................................................. Find igs database================================================ Query_seq: TF0880:TF0881|TF0880:TF0881:conserved hypothetical protein:conserved hypothetical protein:->->:934432..934598 167 gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: tfor_TF0880_TF0881|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[934432,934598]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc gcgcgagccattggcagcgataccggcttcgtccgagataaacgtgatgccgtaaatacgtccctgctcgttttggcgggcatgcctggcaatgcgggcgattttctttaatattattgttaattattgcatacctttgaaggcgtataacaaaatgattaccattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGCGAGCCAUUGGCAGCGAUACCGGCUUCGUCCGAGAUAAACGUGAUGCCGUAAAUACGUCCCUGCUCGUUUUGGCGGGCAUGCCUGGCAAUGCGGGCGAUUUUCUUUAAUAUUAUUGUUAAUUAUUGCAUACCUUUGAAGGCGUAUAACAAAAUGAUUACCAUUC .(((..(((...))).)))....((((...(((((.......)).)))))))...(((((((..(((((((.(((.((((....)))).))).))))))).......((((((....))))))..................)))))))................... (-44.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUGGUAAUCAUUUUGUUAUACGCCUUCAAAGGUAUGCAAUAAUUAACAAUAAUAUUAAAGAAAAUCGCCCGCAUUGCCAGGCAUGCCCGCCAAAACGAGCAGGGACGUAUUUACGGCAUCACGUUUAUCUCGGACGAAGCCGGUAUCGCUGCCAAUGGCUCGCGC ...((((((((...(((((.((..(((....)))..)).))))).................(.....)....).)))))))(((......)))....(((((..((..((.....((((....(((((.....)))))..)))).....))..))....)))))... (-35.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 102 64 57 8 tfor:TF1479|5end_ABC_transporter,_permease_component_1572241..1572471_POSITIVE 458 100 59 159 117 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 445 90 44 220 163 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 442 101 64 229 181 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 435 100 62 36 3 tfor:TF2264|5end_transfer_region-related_protein,_TraO_2432890..2433120_POSITIVE 434 100 51 66 4 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 433 100 59 231 181 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 424 90 42 190 146 tfor:TF2530|5end_conserved_hypothetical_protein_2711416..2711646_POSITIVE 418 100 59 225 176 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 417 102 62 68 24 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 416 100 51 223 164 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 414 100 62 148 91 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 413 50 1 196 148 tfor:TF2535|5end_histidyl-tRNA_synthetase_2717740..2717970_POSITIVE 412 88 42 206 153 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 410 90 43 230 189 tfor:TF3160|5end_conserved_hypothetical_protein_3395531..3395761_POSITIVE 410 100 59 74 24 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 410 100 59 229 179 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 407 99 57 67 23 tfor:TF2263|5end_transfer_region-related_protein,_TraN_2431901..2432131_POSITIVE 407 70 24 60 18 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 407 70 24 53 11 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 445 90 44 143 86 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 439 100 59 52 5 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 417 102 62 68 24 tfor:TF0593|3end_membrane-associated_phospholipid_phosphatase_627051..627201_POSITIVE 414 100 62 148 91 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 403 106 63 61 18 tfor:TF1403|3end_hypothetical_protein_1478025..1478175_POSITIVE 399 102 73 32 1 tfor:TF1478|3end_membrane_fusion_efflux_protein_1572296..1572446_POSITIVE 395 109 64 52 5 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE 391 100 59 54 1 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 384 100 59 47 6 tfor:TF2895|3end_hypothetical_protein_3084192..3084342_POSITIVE 383 99 56 60 12 tfor:TF2248|3end_transfer_region-related_protein,_TraB_2423068..2423218_POSITIVE 382 50 4 142 92 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 377 99 59 112 71 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 376 99 59 63 8 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 372 35 1 44 5 tfor:TF2118|3end_conserved_hypothetical_protein_2291693..2291843_POSITIVE 369 50 1 86 41 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 369 50 1 141 91 tfor:TF1663|3end_ABC_transporter,_permease_component_1778755..1778905_POSITIVE 368 99 60 129 80 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 367 90 44 81 20 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 366 102 63 151 105 tfor:TF2550|3end_translation_elongation_factor_G_2734492..2734642_POSITIVE 365 49 3 139 93 tfor:TF1105|3end_arylsulfatase_regulator;_Fe-S_oxidoreductase_1174178..1174328_POSITIVE