Origin IGS: tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcaaagagtcaaataaaacggcttctgtgaatgtttcacggaagccgtttctcttttctttaaacgtatttacacccaaatattgttgctctgtaaagctgcaaaaacaacacacagataaattatttacgtgtaaataattctttttcta Mask Tandem Repeat Region ================================================ tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Find is-nt database================================================ Query_seq: PI2105:PI2108|PI2105:PI2108:hypothetical protein:cell surface protein; possible cell surface antigen BspA:->->:2059647..2059800 154 tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2105:PI2108|PI2105:PI2108:hypothetical protein:cell surface protein; possible cell surface antigen BspA:->->:2059647..2059800 154 tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2105:PI2108|PI2105:PI2108:hypothetical protein:cell surface protein; possible cell surface antigen BspA:->->:2059647..2059800 154 tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 37 End: 153 .................................... M C C F C S F T E Q Q Y L G V N T F K E K R N G F R E T F T E A V L F D S L L . Protein_Len: 37 Strand: - Start: 15 End: 125 .............. K C T F L K D T H Q K Q L K V S C C Y K P T F V N L S F L F P K R S V N M ............................. tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta 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================================================ tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.1 Tail_Score: -4.93288 Start: 105 End: 133 Full_Region: TAAAGAAAAGAGAAA CGGCTTCCGTGAA ACA TTCACAGAAGCCG TTTTATTTGACTCTT ........................................................................................................CGGCTTCCGTGAAACATTCACAGAAGCCG..................... Find igs database================================================ Query_seq: PI2105:PI2108|PI2105:PI2108:hypothetical protein:cell surface protein; possible cell surface antigen BspA:->->:2059647..2059800 154 tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: pint_PI2105_PI2108|hypothetical protein:cell surface protein; possible cell surface antigen BspA|POSITIVE:POSITIVE|[2059647,2059800]|154 HSP 1 e-value: 2.0E-82 bit: 305.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta tagaaaaagaattatttacacgtaaataatttatctgtgtgttgtttttgcagctttacagagcaacaatatttgggtgtaaatacgtttaaagaaaagagaaacggcttccgtgaaacattcacagaagccgttttatttgactctttgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAAGAAUUAUUUACACGUAAAUAAUUUAUCUGUGUGUUGUUUUUGCAGCUUUACAGAGCAACAAUAUUUGGGUGUAAAUACGUUUAAAGAAAAGAGAAACGGCUUCCGUGAAACAUUCACAGAAGCCGUUUUAUUUGACUCUUUGCUUA ........(((((((((((((.((((((.....((((((.(((((....)))))..)))))).......)))))).))))))))).)))).(((.((((((((((((((((.((((.....)))).)))))))))).......)))))).))). (-50.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAAAGAGUCAAAUAAAACGGCUUCUGUGAAUGUUUCACGGAAGCCGUUUCUCUUUUCUUUAAACGUAUUUACACCCAAAUAUUGUUGCUCUGUAAAGCUGCAAAAACAACACACAGAUAAAUUAUUUACGUGUAAAUAAUUCUUUUUCUA .(((.((((((.......(((((((((((((((.....))))))))))))))))))))).)))......(((((((((..(((((...(((.(((((...(.((......)).)..))))))))..)))))..)))))))))............ (-43.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 136 92 187 136 pint:PI2107|5end_hypothetical_protein_2059704..2059934_POSITIVE 299 44 7 205 164 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 299 44 7 191 150 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 299 44 7 156 115 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 290 89 41 74 31 pint:PI1382|5end_hypothetical_protein_1303608..1303838_POSITIVE 282 134 94 214 167 pint:PI1886|5end_cell_division_protein_1827633..1827863_POSITIVE 275 87 41 88 42 pint:PI0014|5end_hypothetical_protein_17256..17486_POSITIVE 271 87 41 65 20 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 270 50 1 183 136 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 255 85 48 43 4 pint:PI1917|5end_uracil-DNA_glycosylase_1860797..1861027_POSITIVE 255 90 41 174 122 pint:PI1244|5end_hypothetical_protein_1168803..1169033_POSITIVE 255 67 21 189 131 pint:PI0002|5end_conserved_hypothetical_protein_2972..3202_POSITIVE 254 80 33 181 132 pint:PI0520|5end_hypothetical_protein_478755..478985_POSITIVE 253 90 41 217 172 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 253 90 41 71 26 pint:PI1294|5end_hypothetical_protein_1208490..1208720_POSITIVE 253 76 34 74 32 pint:PI0799|5end_alpha-amylase_family_protein_737083..737313_POSITIVE 251 87 50 203 172 pint:PI1083|5end_TPR-repeat-containing_protein_1001975..1002205_POSITIVE 247 66 34 164 130 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 247 116 73 123 80 pint:PI1525|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1446758..1446988_POSITIVE 242 88 41 75 19 pint:PI2145|5end_hypothetical_protein_2092213..2092443_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 41 1 139 99 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 290 89 41 62 19 pint:PI1381|3end_conserved_hypothetical_protein_1303676..1303826_POSITIVE 283 49 1 99 44 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 283 52 12 35 1 pint:PI0491|3end_hypothetical_protein_451227..451377_POSITIVE 282 134 94 140 93 pint:PI1885|3end_cell_division_protein_1827639..1827789_POSITIVE 276 80 34 53 1 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 273 75 36 51 1 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 271 69 36 135 108 pint:PI1586|3end_possible_HesA/MoeB/ThiF_family_protein_1515183..1515333_POSITIVE 271 87 41 75 30 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 264 52 11 95 54 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE 259 39 1 54 16 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 258 65 34 78 44 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 253 100 53 61 7 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE 251 87 50 70 39 pint:PI1082|3end_polypeptide_deformylase_1001922..1002072_POSITIVE 247 66 34 147 113 pint:PI1830|3end_conserved_hypothetical_protein_1770361..1770511_POSITIVE 247 79 36 149 101 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 242 88 41 82 26 pint:PI2144|3end_hypothetical_protein_2092300..2092450_POSITIVE 241 140 98 76 35 pint:PI2123|3end_adenine_phosphoribosyltransferase_2072324..2072474_POSITIVE 240 100 52 97 47 pint:PI1279|3end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195891..1196041_POSITIVE 235 84 43 62 26 pint:PI1324|3end_conserved_hypothetical_protein_1243025..1243175_POSITIVE