Origin IGS: acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt .........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 aaggttttattttattacgaaaatcagttttattcaagacagtgcattacctcaccaattatactttatcaattaatcgaattcgtctttattcccccgcactttatggagctatgcctccctgctgtgcggagcactccctccatacggtcgggagctatgcctccgtgttgtgtggagttatccttccatactgtcgggagctatgcctccctgctacagggagggttaatttccgtttttttagcgt Mask Tandem Repeat Region ================================================ acgctaaaaaaacggaaattaaccctccctgtagcagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Find is-nt database================================================ Query_seq: TDE1247:TDE1248|TDE1247:TDE1248:hypothetical protein:hypothetical protein:->->:1282486..1282735 250 acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1247:TDE1248|TDE1247:TDE1248:hypothetical protein:hypothetical protein:->->:1282486..1282735 250 acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1247:TDE1248|TDE1247:TDE1248:hypothetical protein:hypothetical protein:->->:1282486..1282735 250 acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 90 End: 179 ......................................................................................... M A P D R M E G V L R T A G R H S S I K C G G I K T N S I N ....................................................................... Protein_Len: 36 Strand: - Start: 22 End: 129 ..................... G E R Y C P P M A G S L I S P Y S W V V R L C L E R G Y P P L A G C L M ......................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 242 .. L I V G C L V S A Y S G V T H L S H E A C C P P M A G Y L A P S Y L R I R N I S L T Y N T L Y H V T K F L V S K R L L M ........ Protein_Len: 60 Strand: - Start: 2 End: 205 . G Q L L S A Y S G V T H F S L E V C C P P M A G S R I S P T S R V A P L C L E M F H P P I F V F E I L Q Y L I I P S T M ............................................. acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 213 End: 242 ....................................................................................................................................................................................................................CTTGAATAAAACTGATTTTCGTAATAAAAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -11.1 Tail_Score: -3.61803 Start: 23 End: 43 Full_Region: actgtcgggagctat gcctccctg cta cagggaggg ttaatttccgttttt ......................gcctccctgctacagggaggg............................................................................................................................................................................................................... TransTerm Strand: - Conf: 90 HP_score: -14.6 Tail_Score: -2.75455 Start: 24 End: 42 Full_Region: ctgtcgggagctatg cctccctg cta cagggagg gttaatttccgtttt .......................cctccctgctacagggagg................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE1247:TDE1248|TDE1247:TDE1248:hypothetical protein:hypothetical protein:->->:1282486..1282735 250 acgctaaaaaaacggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Intra-Species Hit: Count: 1 Min: 13 Max: 250 Len: 238 Subject: NC_002967_TDE1247_TDE1248|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1282486,1282735]|250 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 238 Query Start:13 Query End:250 Subject Strand: POSITIVE Subject Start: 13 Subject End: 250 ............cggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt ............cggaaattaaccctccctgtagcagggaggcatagctcccgacagtatggaaggataactccacacaacacggaggcatagctcccgaccgtatggagggagtgctccgcacagcagggaggcatagctccataaagtgcgggggaataaagacgaattcgattaattgataaagtataattggtgaggtaatgcactgtcttgaataaaactgattttcgtaataaaataaaacctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGAAAUUAACCCUCCCUGUAGCAGGGAGGCAUAGCUCCCGACAGUAUGGAAGGAUAACUCCACACAACACGGAGGCAUAGCUCCCGACCGUAUGGAGGGAGUGCUCCGCACAGCAGGGAGGCAUAGCUCCAUAAAGUGCGGGGGAAUAAAGACGAAUUCGAUUAAUUGAUAAAGUAUAAUUGGUGAGGUAAUGCACUGUCUUGAAUAAAACUGAUUUUCGUAAUAAAAUAAAACCUU (((((((((..((((((((...))))))))....((((((..((.(((((..(((....)))........(((..((...))..))).)))))))..)))))).((((((((.....((((......)))).....)))))))).....(((((.....(((((((((.....))).))))))(((........))).))))).........)))))))))................. (-75.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUUUUAUUUUAUUACGAAAAUCAGUUUUAUUCAAGACAGUGCAUUACCUCACCAAUUAUACUUUAUCAAUUAAUCGAAUUCGUCUUUAUUCCCCCGCACUUUAUGGAGCUAUGCCUCCCUGCUGUGCGGAGCACUCCCUCCAUACGGUCGGGAGCUAUGCCUCCGUGUUGUGUGGAGUUAUCCUUCCAUACUGUCGGGAGCUAUGCCUCCCUGCUACAGGGAGGGUUAAUUUCCG ..((((((...........))))))............(((((((..................................((((........))))..((((((..(((((((.((((.(((((.((((((.((((......)))).)))))).))))).)))).)))))))..)))))).............)))))))(((((.((..((((((((...))))))))..)).))))). (-75.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 128 81 129 76 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 404 149 106 88 48 NC_002967:TDE1451|5end_hypothetical_protein_1498968..1499198_NEGATIVE 379 120 76 215 165 NC_002967:TDE2386|5end_hypothetical_protein_2415411..2415641_POSITIVE 368 130 81 219 166 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 366 131 95 155 113 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 363 118 71 125 67 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 358 119 71 70 28 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 355 130 95 47 5 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 355 120 71 57 2 NC_002967:TDE1223|5end_zinc_ABC_transporter,_permease_protein_1257835..1258065_NEGATIVE 353 119 71 59 7 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 352 115 78 225 184 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 344 130 84 117 76 NC_002967:TDE2526|5end_hypothetical_protein_2555034..2555264_NEGATIVE 343 130 81 169 118 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 340 124 85 65 22 NC_002967:TDE0882|5end_hypothetical_protein_901449..901679_POSITIVE 334 59 13 225 165 NC_002967:TDE2438|5end_hypothetical_protein_2469257..2469487_NEGATIVE 333 140 92 86 28 NC_002967:TDE1622|5end_hypothetical_protein_1670981..1671211_NEGATIVE 329 111 73 50 10 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 328 140 95 55 3 NC_002967:TDE2684|5end_hypothetical_protein_2724848..2725078_NEGATIVE 328 131 94 79 32 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 326 149 105 182 128 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 128 89 55 10 NC_002967:TDE2087|3end_translation_initiation_factor_IF-1_2115468..2115618_NEGATIVE 408 128 81 104 51 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 380 129 81 60 4 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 376 119 73 140 69 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 358 119 71 65 23 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 355 130 95 139 97 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 352 120 71 68 4 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 347 106 68 147 107 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 336 120 72 80 31 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 334 47 15 36 1 NC_002967:TDE2118|3end_DNA_topoisomerase_IV_subunit_A_2149154..2149304_NEGATIVE 333 120 71 118 65 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 332 113 76 142 109 NC_002967:TDE0341|3end_ribonucleotide-diphosphate_reductase_alpha_subunit_379589..379739_NEGATIVE 331 117 74 149 93 NC_002967:TDE0256|3end_hypothetical_protein_290742..290892_NEGATIVE 330 122 83 67 24 NC_002967:TDE1247|3end_hypothetical_protein_1282425..1282575_POSITIVE 324 146 105 47 11 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 324 116 71 84 27 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 323 118 72 83 28 NC_002967:TDE2610|3end_hypothetical_protein_2651854..2652004_NEGATIVE 321 112 74 131 93 NC_002967:TDE2272|3end_hypothetical_protein_2308980..2309130_NEGATIVE 319 116 71 84 26 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 318 110 65 76 36 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE