Origin IGS: cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc .........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 gattcgaaaaaatgtttagttgttgaattgtttactgaccgctgtaaaagccctgaaagggcgcattaattcagtccaatgcgaagcgttggggaaaaaagcatcgcatctcagcggagggctgaaagcctgaatgaatatggatttagatatccctttgtcattccgaacgtagtgaggaatctcgcctcgaacgccctcggcgttcgtccctcaggcctcgggcg Mask Tandem Repeat Region ================================================ cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Find is-nt database================================================ Query_seq: TF2640:TF2641|TF2640:TF2641:hypothetical protein:riboflavin kinase/FAD synthase:->->:2809594..2809820 227 cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2640:TF2641|TF2640:TF2641:hypothetical protein:riboflavin kinase/FAD synthase:->->:2809594..2809820 227 cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2640:TF2641|TF2640:TF2641:hypothetical protein:riboflavin kinase/FAD synthase:->->:2809594..2809820 227 cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 45 End: 209 ............................................ M P H Y V R N D K G I S K S I F I Q A F S P P L R C D A F F P N A S H W T E L M R P F R A F T A V S K Q F N N .................. Protein_Len: 37 Strand: - Start: 98 End: 208 ................................................................................................. A K L G G S L H S A K K G L A E C Q V S N I R G K L A K V A T L L C N L M ................... Protein_Len: 49 Strand: - Start: 3 End: 149 .. G L G S P R V G L A N S A L N R V V N P I V F P Y R F G Y E N L S E A R R Q S A I S K E G V S R M .............................................................................. cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc 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================================================ cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -9.1 Tail_Score: -4.08767 Start: 166 End: 178 Full_Region: GGACTGAATTAATGC GCCCT TTC AGGGC TTTTACAGCGGTCAG .....................................................................................................................................................................GCCCTTTCAGGGC................................................. Find igs database================================================ Query_seq: TF2640:TF2641|TF2640:TF2641:hypothetical protein:riboflavin kinase/FAD synthase:->->:2809594..2809820 227 cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Intra-Species Hit: Count: 8 Min: 1 Max: 227 Len: 227 Subject: tfor_TF2640_TF2641|hypothetical protein:riboflavin kinase/FAD synthase|POSITIVE:POSITIVE|[2809594,2809820]|227 HSP 1 e-value: 1.0E-126 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc cgcccgaggcctgagggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattttttcgaatc Subject: tfor_TF1181_TF1183|methylated-DNA--[protein]-cysteine S-methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[1268052,1268530]|479 HSP 1 e-value: 3.0E-42 bit: 172.0 Len: 115 Query Start:104 Query End:218 Subject Strand: NEGATIVE Subject Start: 343 Subject End: 457 .......................................................................................................cagccctccgctgagatgcgatgcttttttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaacattt......... .......................................................................................................cagcccttcgccgagatgcgatgcctttttccccaacgcttcgcattgggctgaattaatgcgccctttcagggcttttacagtggtcagtaaacagatcaacaactaaacattt......... Subject: tfor_TF0685_TF0686|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[731193,732338]|1146 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 121 Query Start:95 Query End:215 Subject Strand: POSITIVE Subject Start: 770 Subject End: 900 ..............................................................................................tcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgc----------attggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaaca............ ..............................................................................................tcaggcttacagccctccgccgagatgcgatgccttttttcccaacgcttcgctgcgctccacattgggctgaattaatgcgccctttcagggctgttacaacggtcagcaaacaaatcaacaactcaaca............ Subject: tfor_TF2914_TF2915|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3109704,3110561]|858 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 60 Query Start:15 Query End:74 Subject Strand: POSITIVE Subject Start: 522 Subject End: 581 ..............gggacgaacgccgagggcgttcgaggcgagattcctcactacgttcggaatgacaaaggg......................................................................................................................................................... ..............gggacgaacgccgagggcgttcgaggcgagattccttacttcgttcggaatgacaaaggg......................................................................................................................................................... HSP 2 e-value: 6.0E-13 bit: 75.8 Len: 105 Query Start:95 Query End:199 Subject Strand: POSITIVE Subject Start: 358 Subject End: 466 ..............................................................................................tcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgc-----attggactgaattaatgcgccctttcagggcttttacagcggtcagtaaaca............................ ..............................................................................................tcaggctttcagccctccgccgagggggg-tgcctgttttcccaacgcttcgctgcacattgggctgaattaacgtgccctttcagggcttttacagcggtcagcaaaca............................ HSP 3 e-value: 1.0E-7 bit: 58.0 Len: 41 Query Start:34 Query End:74 Subject Strand: POSITIVE Subject Start: 253 Subject End: 293 .................................ttcgaggcgagattcctcactacgttcggaatgacaaaggg......................................................................................................................................................... .................................ttcgaggcgagattcctcacggtgttcggaatgacaaaggg......................................................................................................................................................... Subject: tfor_TF1588_TF1589|hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[1702621,1703328]|708 HSP 1 e-value: 4.0E-20 bit: 99.6 Len: 85 Query Start:34 Query End:118 Subject Strand: POSITIVE Subject Start: 234 Subject End: 319 .................................ttcgaggcgagattcctcactacgttcggaatgacaaagggatatctaaatccat-attcattcaggctttcagccctccgctgag............................................................................................................. .................................ttcggggcgggattcctcactgcgttcggaatgacaaagggacatccaaatcaatcattcattcaggcttccagccctccgctgag............................................................................................................. HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 63 Query Start:131 Query End:193 Subject Strand: POSITIVE Subject Start: 331 Subject End: 393 ..................................................................................................................................tttccccaacgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcag.................................. ..................................................................................................................................tttccccaacgctgcgcattgggctgaattaacacgccctttcagggctcttacagcagtcag.................................. HSP 3 e-value: 5.0E-7 bit: 56.0 Len: 32 Query Start:41 Query End:72 Subject Strand: POSITIVE Subject Start: 527 Subject End: 558 ........................................cgagattcctcactacgttcggaatgacaaag........................................................................................................................................................... ........................................cgagattcctcactgcgttcggaatgacaaag........................................................................................................................................................... Subject: tfor_TF2920_TF2921|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3117231,3118637]|1407 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 77 Query Start:42 Query End:118 Subject Strand: POSITIVE Subject Start: 775 Subject End: 853 .........................................gagattcctcactacgttcggaatgacaaagggat--atctaaatccatattcattcaggctttcagccctccgctgag............................................................................................................. .........................................gagattcctcactgcgttcggaatgacaaagggcagcatccaaatcattattcattcaggctttcagccctccgctgag............................................................................................................. HSP 2 e-value: 2.0E-16 bit: 87.7 Len: 76 Query Start:140 Query End:215 Subject Strand: POSITIVE Subject Start: 888 Subject End: 963 ...........................................................................................................................................cgcttcgcattggactgaattaatgcgccctttcagggcttttacagcggtcagtaaacaattcaacaactaaaca............ ...........................................................................................................................................cgctgcgcattgggctgaattaatacgccctttcagggctcttacaacggtcagcaaacagatcaacaactaaaca............ HSP 3 e-value: 6.0E-13 bit: 75.8 Len: 71 Query Start:44 Query End:114 Subject Strand: POSITIVE Subject Start: 458 Subject End: 530 ...........................................gattcctcactacgttcggaatgacaaaggg--atatctaaatccatattcattcaggctttcagccctccgc................................................................................................................. ...........................................gattcctcactgcgttcggaatgacaaagggcagcatccaaatcattattcattcaggctttcagccctccgc................................................................................................................. HSP 4 e-value: 2.0E-9 bit: 63.9 Len: 40 Query Start:147 Query End:186 Subject Strand: POSITIVE Subject Start: 572 Subject End: 611 ..................................................................................................................................................cattggactgaattaatgcgccctttcagggcttttacag......................................... ..................................................................................................................................................cattggactgaattaacgcgccctttcagggctgttacag......................................... Subject: tfor_TF2823_TF2824|TPR-containing protein:nucleoside-transporting protein nupG|POSITIVE:POSITIVE|[3014398,3014840]|443 HSP 1 e-value: 4.0E-14 bit: 79.8 Len: 63 Query Start:131 Query End:193 Subject Strand: NEGATIVE Subject Start: 331 Subject End: 394 ..................................................................................................................................tttccccaacgcttcgcattggactgaattaatgc-gccctttcagggcttttacagcggtcag.................................. ..................................................................................................................................tttccccaacgcttcgcattgggctgaattaacacagccctttcagggctgttacagcggtcag.................................. HSP 2 e-value: 9.0E-9 bit: 61.9 Len: 35 Query Start:40 Query End:74 Subject Strand: NEGATIVE Subject Start: 101 Subject End: 135 .......................................gcgagattcctcactacgttcggaatgacaaaggg......................................................................................................................................................... .......................................gcgagattcctcactgcgttcggaatgacaaaggg......................................................................................................................................................... Subject: tfor_TF2922_TF2923|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[3121599,3122307]|709 HSP 1 e-value: 9.0E-12 bit: 71.9 Len: 72 Query Start:76 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 72 ...........................................................................tatctaaatccatattcattcaggctttcagccctccgctgagatgcgatgcttttttccccaacgcttcgc................................................................................ ...........................................................................tatccaaatccatattcattcaggctttcagccctccgccgaggggggcgccctttttccccaacgcttcgc................................................................................ HSP 2 e-value: 9.0E-9 bit: 61.9 Len: 31 Query Start:44 Query End:74 Subject Strand: POSITIVE Subject Start: 468 Subject End: 498 ...........................................gattcctcactacgttcggaatgacaaaggg......................................................................................................................................................... ...........................................gattcctcactacgttcggaatgacaaaggg......................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCCCGAGGCCUGAGGGACGAACGCCGAGGGCGUUCGAGGCGAGAUUCCUCACUACGUUCGGAAUGACAAAGGGAUAUCUAAAUCCAUAUUCAUUCAGGCUUUCAGCCCUCCGCUGAGAUGCGAUGCUUUUUUCCCCAACGCUUCGCAUUGGACUGAAUUAAUGCGCCCUUUCAGGGCUUUUACAGCGGUCAGUAAACAAUUCAACAACUAAACAUUUUUUCGAAUC .((..((((((.((((((((((((((...))))))))........))))))..........((((((.....((((......))))....)))))).))))))..))...((((((.(((((((.((.............)).)))))))...............((((.....)))).....))))))...................................... (-66.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUCGAAAAAAUGUUUAGUUGUUGAAUUGUUUACUGACCGCUGUAAAAGCCCUGAAAGGGCGCAUUAAUUCAGUCCAAUGCGAAGCGUUGGGGAAAAAAGCAUCGCAUCUCAGCGGAGGGCUGAAAGCCUGAAUGAAUAUGGAUUUAGAUAUCCCUUUGUCAUUCCGAACGUAGUGAGGAAUCUCGCCUCGAACGCCCUCGGCGUUCGUCCCUCAGGCCUCGGGCG (((((((...(((.....))).))))))).........((((((.....((((.....)))).......(((...(((((((...))))))).)))...............))))))..(.((((..((((((.......((((....((((......))))..))))......(((((....)))))..((((((((...))))))))....)))))).)))).). (-69.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1111 50 1 55 6 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 1064 50 1 55 7 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 1064 50 1 165 117 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 946 70 21 60 11 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 937 180 131 190 141 tfor:TF1183|5end_hypothetical_protein_1268391..1268621_POSITIVE 933 70 26 45 1 tfor:TF1844|5end_hypothetical_protein_1996389..1996619_POSITIVE 899 150 104 164 118 tfor:TF1186|5end_hypothetical_protein_1269568..1269798_POSITIVE 899 150 104 49 4 tfor:TF0821|5end_hypothetical_protein_879879..880109_POSITIVE 873 190 141 187 138 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 860 147 104 65 22 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 858 180 131 200 151 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 823 179 131 190 141 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 823 150 104 187 141 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 819 179 131 116 68 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 819 179 131 78 30 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 771 179 135 219 170 tfor:TF2478|5end_hypothetical_protein_2655375..2655605_POSITIVE 767 180 131 124 65 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 767 180 131 117 58 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 740 90 41 213 163 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 663 74 34 185 145 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 943 150 104 117 71 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 899 150 104 79 33 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 860 147 104 134 91 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 814 160 112 51 3 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 752 179 135 61 17 tfor:TF0820|3end_hypothetical_protein_879942..880092_POSITIVE 733 90 41 94 45 tfor:TF0369|3end_hypothetical_protein_386186..386336_POSITIVE 723 36 1 151 117 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 663 74 34 45 5 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 625 179 131 82 25 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 551 190 141 64 10 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 530 73 34 84 45 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 523 147 101 141 94 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 497 137 95 128 80 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 495 138 93 132 86 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 461 49 2 119 64 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 455 45 2 144 93 tfor:TF2076|3end_lipopolysaccharide_biosynthesis_protein_2243381..2243531_POSITIVE 442 42 1 117 65 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE 437 45 1 73 25 tfor:TF2749|3end_possible_hemolysin_2934518..2934668_POSITIVE 434 50 4 65 22 tfor:TF2994|3end_hypothetical_protein_3210849..3210999_POSITIVE 423 43 2 149 115 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE