Origin IGS: actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggggtgtcccctttggcagcgcgagtacaaccagcggagcttcgaggtcaaaagagggggtcatagggggagggaaacaaccaccgctctgacttgaaaagcccgtaagggaacgggggttcctcccttcccctaaaaaggagagtagt Mask Tandem Repeat Region ================================================ actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Find is-nt database================================================ Query_seq: TDE2259:TDE2260|TDE2259:TDE2260:hypothetical protein:hypothetical protein:<-->:2297328..2297477 150 actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2259:TDE2260|TDE2259:TDE2260:hypothetical protein:hypothetical protein:<-->:2297328..2297477 150 actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2259:TDE2260|TDE2259:TDE2260:hypothetical protein:hypothetical protein:<-->:2297328..2297477 150 actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Predict ORF larger than 30AA ================================================ actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct 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================================================ actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2259:TDE2260|TDE2259:TDE2260:hypothetical protein:hypothetical protein:<-->:2297328..2297477 150 actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Intra-Species Hit: Count: 2 Min: 1 Max: 150 Len: 150 Subject: NC_002967_TDE2259_TDE2260|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2297328,2297477]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct actactctcctttttaggggaagggaggaacccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctcttttgacctcgaagctccgctggttgtactcgcgctgccaaaggggacacccct Subject: NC_002967_TDE0469_TDE0470|hypothetical protein:cell division protein FtsH|NEGATIVE:POSITIVE|[524078,524640]|563 HSP 1 e-value: 1.0E-28 bit: 127.0 Len: 110 Query Start:32 Query End:141 Subject Strand: POSITIVE Subject Start: 83 Subject End: 190 ...............................ccccgttcccttacgggcttttcaagtcagagcggtggttgtttccctccccctatgaccccctct-tttgacctcgaagctccgctggttgtactcgcgctgccaaaggg......... ...............................ccccgttcccttacgggcttttcaagtcagagcag-ggtt--ttctctccccctataaccccctctcttttacctcgaagctacgctggttgtactcgcgctgccaaaggg......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUACUCUCCUUUUUAGGGGAAGGGAGGAACCCCCGUUCCCUUACGGGCUUUUCAAGUCAGAGCGGUGGUUGUUUCCCUCCCCCUAUGACCCCCUCUUUUGACCUCGAAGCUCCGCUGGUUGUACUCGCGCUGCCAAAGGGGACACCCCU ..............((((((.(((((((((((.((((((.......((((.....)))).)))))).)))).))))))).))))))....(((((..((((....))))((..(((.((.....)).)))..))...)))))........ (-51.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGGUGUCCCCUUUGGCAGCGCGAGUACAACCAGCGGAGCUUCGAGGUCAAAAGAGGGGGUCAUAGGGGGAGGGAAACAACCACCGCUCUGACUUGAAAAGCCCGUAAGGGAACGGGGGUUCCUCCCUUCCCCUAAAAAGGAGAGUAGU ....((((((((((((((..((.((((.(........).))))))..))))...))))))).)))(((((((((((...((((.(((.((......))....(((....)))..))).))))..)))))))))))............... (-56.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1098 130 81 221 172 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 873 70 23 211 163 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 834 67 23 192 146 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 638 107 61 103 58 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 638 107 61 82 37 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 638 107 61 204 159 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 572 100 58 181 143 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 533 107 63 88 49 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 530 107 64 195 155 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 501 150 103 194 149 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 500 106 63 182 144 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 440 149 103 231 180 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 411 145 103 52 8 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 381 49 1 65 2 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 377 52 14 214 172 NC_002967:TDE1364|5end_valyl-tRNA_synthetase_1404763..1404993_POSITIVE 374 118 72 220 178 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 369 119 77 218 177 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 360 128 83 222 167 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 358 48 6 215 181 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 356 50 8 172 128 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 834 67 23 105 59 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 822 150 102 52 2 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 572 100 58 49 11 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 506 150 103 60 10 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 441 150 103 87 34 NC_002967:TDE2135|3end_hypothetical_protein_2165418..2165568_POSITIVE 419 47 16 146 116 NC_002967:TDE0402|3end_hypothetical_protein_454248..454398_NEGATIVE 412 149 104 148 101 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 367 142 103 149 95 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 364 144 103 143 109 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 362 54 12 77 34 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 360 128 83 145 90 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 359 118 71 102 62 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 358 65 21 81 32 NC_002967:TDE2614|3end_ApbE_family_protein_2656018..2656168_NEGATIVE 358 48 6 44 10 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 356 59 14 130 91 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 356 79 31 132 67 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 355 119 77 122 70 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 347 125 96 80 52 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 345 82 45 73 35 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 335 80 31 47 1 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE