Origin IGS: tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atagatgtattttacgaatcgttcagagagatgagaggagaagctgaaaatgtatctatgaactatacgtgcaaaaacgaaccgacgccgtagggcgattatggtgagcttttaaaagatgcattgtaaatagtcggagcaattggaggttgcgaaggatatatgagcgtagca Mask Tandem Repeat Region ================================================ tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Find is-nt database================================================ Query_seq: TDE0518:TDE0519|TDE0518:TDE0519:hypothetical protein:hypothetical protein:<-<-:565354..565527 174 tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0518:TDE0519|TDE0518:TDE0519:hypothetical protein:hypothetical protein:<-<-:565354..565527 174 tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0518:TDE0519|TDE0518:TDE0519:hypothetical protein:hypothetical protein:<-<-:565354..565527 174 tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 15 End: 116 .............. M L R N L Q L L R L F T M H L L K A H H N R P T A S V R F C T Y S S .......................................................... Protein_Len: 34 Strand: + Start: 73 End: 174 ........................................................................ M I A L R R R F V F A R I V H R Y I F S F S S H L S E R F V K Y I Y Protein_Len: 30 Strand: - Start: 85 End: 174 .................................................................................... P T P E N K C T Y N M S V N E A E G R M E R F S E Y F V D M tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat 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================================================ tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0518:TDE0519|TDE0518:TDE0519:hypothetical protein:hypothetical protein:<-<-:565354..565527 174 tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_002967_TDE0518_TDE0519|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[565354,565527]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat tgctacgctcatatatccttcgcaacctccaattgctccgactatttacaatgcatcttttaaaagctcaccataatcgccctacggcgtcggttcgtttttgcacgtatagttcatagatacattttcagcttctcctctcatctctctgaacgattcgtaaaatacatctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUACGCUCAUAUAUCCUUCGCAACCUCCAAUUGCUCCGACUAUUUACAAUGCAUCUUUUAAAAGCUCACCAUAAUCGCCCUACGGCGUCGGUUCGUUUUUGCACGUAUAGUUCAUAGAUACAUUUUCAGCUUCUCCUCUCAUCUCUCUGAACGAUUCGUAAAAUACAUCUAU ...((((.((...((((....((((.......))))...(((((..(((..((((.......(((((..(((.....((((....))))..)))..))))))))).))))))))....))))....(((((.................))))).))..))))............ (-22.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAUGUAUUUUACGAAUCGUUCAGAGAGAUGAGAGGAGAAGCUGAAAAUGUAUCUAUGAACUAUACGUGCAAAAACGAACCGACGCCGUAGGGCGAUUAUGGUGAGCUUUUAAAAGAUGCAUUGUAAAUAGUCGGAGCAAUUGGAGGUUGCGAAGGAUAUAUGAGCGUAGCA (((((((((((((.(...((.((((......))))..))...)...)))))))))))))......(((((.((........((((((((....)))..(((..(((..(((....)))...)))..)))...))))).(((((.....)))))..........)).)))))... (-40.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 968 110 61 201 152 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 369 107 76 83 41 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 353 115 77 62 4 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 349 119 71 93 38 NC_002967:TDE0035|5end_acetyltransferase,_GNAT_family_42020..42250_NEGATIVE 323 50 6 120 85 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 320 95 77 69 45 NC_002967:TDE1730|5end_glycosyl_hydrolase,_family_2_1785545..1785775_NEGATIVE 312 46 1 62 8 NC_002967:TDE1555|5end_hypothetical_protein_1598018..1598248_POSITIVE 309 109 61 92 44 NC_002967:TDE0761|5end_protease_complex-associated_polypeptide_799969..800199_POSITIVE 304 108 78 192 165 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 300 47 9 184 146 NC_002967:TDE0090|5end_hypothetical_protein_109206..109436_NEGATIVE 293 120 71 94 45 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 289 166 131 187 142 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 288 96 66 164 129 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 287 106 64 66 19 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 286 117 77 91 45 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 280 94 52 83 44 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 280 119 72 87 29 NC_002967:TDE1025|5end_ribosomal_protein_L32_1057101..1057331_POSITIVE 276 116 77 164 130 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 276 157 115 205 146 NC_002967:TDE1962|5end_hypothetical_protein_1975204..1975434_NEGATIVE 274 106 67 44 1 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 107 76 44 2 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 353 115 77 72 14 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 334 105 63 65 16 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 323 50 6 120 85 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 320 109 73 146 118 NC_002967:TDE2258|3end_surface_antigen_BspA,_putative_2295334..2295484_NEGATIVE 320 95 77 82 58 NC_002967:TDE1731|3end_hypothetical_protein_1785532..1785682_NEGATIVE 312 46 1 65 11 NC_002967:TDE1554|3end_hypothetical_protein_1598101..1598251_POSITIVE 309 109 61 56 8 NC_002967:TDE0760|3end_hypothetical_protein_800013..800163_POSITIVE 305 110 65 148 105 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 302 105 65 61 13 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 299 110 65 103 58 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 286 115 76 143 93 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 286 117 77 88 42 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 283 120 72 55 6 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 280 94 52 70 31 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 277 105 70 59 18 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 275 80 36 108 55 NC_002967:TDE0912|3end_hypothetical_protein_931528..931678_POSITIVE 274 105 66 59 14 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 274 58 16 100 58 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 273 105 65 56 9 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE