Origin IGS: aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaaattgcacatttgcaagctttttgtctgcattcatagctatctaccctcttttagtcacacaaaaagctcttactcactccaaatatagcacttaatttggaattaaccacgctttttatgcaacaaaccatcaaaatattacccctcctcgaacactatatcgtcaacaataattcgaaataaaagctggggaaggaagaccgctttcgggtaacttgaaaattcaattgttgtttgtcgttatctaagactgtatcccccaaaaaaacgaaaacaaacaggggagactgtcaggaatttgtcctgacagtctctccctgtttgtttgtgcttcctgcgttt Mask Tandem Repeat Region ================================================ aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Find is-nt database================================================ Query_seq: PG0409:PG0410|PG0409:PG0410:hypothetical protein:hypothetical protein:->->:442411..442756 346 aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0409:PG0410|PG0409:PG0410:hypothetical protein:hypothetical protein:->->:442411..442756 346 aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0409:PG0410|PG0409:PG0410:hypothetical protein:hypothetical protein:->->:442411..442756 346 aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 62 End: 184 ............................................................. M F V F V F L G D T V L D N D K Q Q L N F Q V T R K R S S F P S F Y F E L L L T I .................................................................................................................................................................. Protein_Len: 32 Strand: - Start: 163 End: 258 .................................................................................................................................................................. K S N N N V I Y H E L L P L I K I T Q Q M F L T T L E L N L A M ........................................................................................ Protein_Len: 36 Strand: - Start: 1 End: 108 F A P L V F L C P S V T L V F E Q C D G R N T K T K K P S V T K S L S M .............................................................................................................................................................................................................................................. aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt 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================================================ aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.3 Tail_Score: -5.41143 Start: 16 End: 74 Full_Region: AAACGCAGGAAGCAC AAACAAACAGGGAGAGACTGTCAGGA CAAAT TCCTGACAGTCTCCCCTGTTTGTTTTCG TTTTTTTGGGGGATA ...............AAACAAACAGGGAGAGACTGTCAGGACAAATTCCTGACAGTCTCCCCTGTTTGTTTTCG................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -27.6 Tail_Score: -4.94243 Start: 19 End: 68 Full_Region: CGCAGGAAGCACAAA CAAACAGGGAGAGACTGTCAGGA CAAAT TCCTGACAGTCTCCCCTGTTTG TTTTCGTTTTTTTGG ..................CAAACAGGGAGAGACTGTCAGGACAAATTCCTGACAGTCTCCCCTGTTTG...................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -27.6 Tail_Score: -4.08144 Start: 19 End: 68 Full_Region: ccaaaaaaacgaaaa caaacaggggagactgtcagga atttg tcctgacagtctctccctgtttg tttgtgcttcctgcg ..................caaacaggggagactgtcaggaatttgtcctgacagtctctccctgtttg...................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -22.6 Tail_Score: -4.62622 Start: 23 End: 64 Full_Region: aaaaacgaaaacaaa caggggagactgtcagga atttg tcctgacagtctctccctg tttgtttgtgcttcc ......................caggggagactgtcaggaatttgtcctgacagtctctccctg.......................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG0409:PG0410|PG0409:PG0410:hypothetical protein:hypothetical protein:->->:442411..442756 346 aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Intra-Species Hit: Count: 1 Min: 1 Max: 346 Len: 346 Subject: NC_002950_PG0409_PG0410|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[442411,442756]|346 HSP 1 e-value: 0.0 bit: 644.0 Len: 346 Query Start:1 Query End:346 Subject Strand: POSITIVE Subject Start: 1 Subject End: 346 aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgnnnnnnngggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt aaacgcaggaagcacaaacaaacagggagagactgtcaggacaaattcctgacagtctcccctgtttgttttcgtttttttgggggatacagtcttagataacgacaaacaacaattgaattttcaagttacccgaaagcggtcttccttccccagcttttatttcgaattattgttgacgatatagtgttcgaggaggggtaatattttgatggtttgttgcataaaaagcgtggttaattccaaattaagtgctatatttggagtgagtaagagctttttgtgtgactaaaagagggtagatagctatgaatgcagacaaaaagcttgcaaatgtgcaatttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACGCAGGAAGCACAAACAAACAGGGAGAGACUGUCAGGACAAAUUCCUGACAGUCUCCCCUGUUUGUUUUCGUUUUUUUGGGGGAUACAGUCUUAGAUAACGACAAACAACAAUUGAAUUUUCAAGUUACCCGAAAGCGGUCUUCCUUCCCCAGCUUUUAUUUCGAAUUAUUGUUGACGAUAUAGUGUUCGAGGAGGGGUAAUAUUUUGAUGGUUUGUUGCAUAAAAAGCGUGGUUAAUUCCAAAUUAAGUGCUAUAUUUGGAGUGAGUAAGAGCUUUUUGUGUGACUAAAAGAGGGUAGAUAGCUAUGAAUGCAGACAAAAAGCUUGCAAAUGUGCAAUUUGU ....(((((..(((((.((((((((((.(((((((((((((.....))))))))))))))))))))))).(((((..(((((((.......(((.........))).........((((....))))....)))))))((.((((.(((((....((((((.(((((((((((((....)))))....))))))))))))))................((..((((((((((.((.(((.((((((((..........))))))))))).))...))))))))))..)).....))))).)))).)).)))))((((..(.....)..))))..)))))..))))) (-115.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAUUGCACAUUUGCAAGCUUUUUGUCUGCAUUCAUAGCUAUCUACCCUCUUUUAGUCACACAAAAAGCUCUUACUCACUCCAAAUAUAGCACUUAAUUUGGAAUUAACCACGCUUUUUAUGCAACAAACCAUCAAAAUAUUACCCCUCCUCGAACACUAUAUCGUCAACAAUAAUUCGAAAUAAAAGCUGGGGAAGGAAGACCGCUUUCGGGUAACUUGAAAAUUCAAUUGUUGUUUGUCGUUAUCUAAGACUGUAUCCCCCAAAAAAACGAAAACAAACAGGGGAGACUGUCAGGAAUUUGUCCUGACAGUCUCUCCCUGUUUGUUUGUGCUUCCUGCGUUU .......((((...((((..(.....)..))))......................(((((....(((((((..........(((((((..........))))))).........)))))))..((.((((((...(((....((((((.((((((.....(((.(((............))).))).....)))))).(((((....)))))))))))..(((....))).)))..)))))).)).......)))))..................(((((((((((((((((((((((((.....))))))))))))).))))))))))))))))........... (-91.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 69 22 129 88 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 368 176 133 78 32 NC_002950:PG2215|5end_mannose-1-phosphate_guanylyltransferase_2327695..2327925_NEGATIVE 328 67 23 178 132 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 327 87 47 169 130 NC_002950:PG1683|5end_hypothetical_protein_1769644..1769874_POSITIVE 327 68 24 166 118 NC_002950:PG0685|5end_ABC_transporter,_ATP-binding_protein_740116..740346_POSITIVE 314 74 31 68 20 NC_002950:PG1511|5end_hypothetical_protein_1587609..1587839_POSITIVE 304 200 159 191 138 NC_002950:PG0807|5end_NusB_family_protein_864724..864954_NEGATIVE 301 319 274 59 13 NC_002950:PG1600|5end_hypothetical_protein_1680984..1681214_NEGATIVE 300 180 138 223 175 NC_002950:PG0211|5end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_247810..248040_NEGATIVE 299 54 12 197 158 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 297 177 132 83 27 NC_002950:PG0130|5end_phosphoglyceromutase_152668..152898_NEGATIVE 296 300 258 199 149 NC_002950:PG0619|5end_alkyl_hydroperoxide_reductase,_F_subunit_671104..671334_POSITIVE 294 193 151 121 78 NC_002950:PG0097|5end_hypothetical_protein_115748..115978_NEGATIVE 292 180 132 108 57 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 292 46 5 220 178 NC_002950:PG0280|5end_ABC_transporter,_permease_protein,_putative_314625..314855_NEGATIVE 290 176 132 62 15 NC_002950:PG1528|5end_hypothetical_protein_1605783..1606013_POSITIVE 289 168 126 173 124 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 288 158 131 27 5 NC_002950:PG1525|5end_isochorismate_synthase,_putative_1603865..1604095_NEGATIVE 288 219 180 231 200 NC_002950:PG0269|5end_exodeoxyribonuclease_III_302028..302258_POSITIVE 287 200 151 191 157 NC_002950:PG1916|5end_translation_initiation_factor_IF-1_2013702..2013932_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 728 70 21 74 25 NC_002950:PG0409|3end_hypothetical_protein_442350..442500_POSITIVE 337 60 11 60 8 NC_002950:PG0322|3end_serine/threonine_transporter_356966..357116_POSITIVE 327 68 24 73 25 NC_002950:PG0684|3end_ABC_transporter,_permease_protein,_putative_740103..740253_POSITIVE 326 70 24 64 14 NC_002950:PG1332|3end_NAD(P)_transhydrogenase,_beta_subunit_1414110..1414260_POSITIVE 322 320 273 101 53 NC_002950:PG1896|3end_S-adenosylmethionine_synthetase_1995955..1996105_POSITIVE 321 99 55 126 77 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 305 239 192 137 85 NC_002950:PG1145|3end_long-chain-fatty-acid--CoA_ligase,_putative_1228482..1228632_NEGATIVE 302 200 154 68 17 NC_002950:PG1235|3end_epimerase/reductase,_putative_1310300..1310450_NEGATIVE 294 193 151 124 81 NC_002950:PG0098|3end_hypothetical_protein_115745..115895_NEGATIVE 292 180 132 111 60 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 291 89 43 151 71 NC_002950:PG1338|3end_umuC_protein_1419624..1419774_POSITIVE 287 99 51 79 41 NC_002950:PG1897|3end_thiamin_pyrophosphokinase_catalytic_domain_protein_1996053..1996203_NEGATIVE 284 339 295 99 57 NC_002950:PG1014|3end_TPR_domain_protein_1075855..1076005_POSITIVE 283 41 5 38 2 NC_002950:PG1404|3end_rhomboid_family_protein_1487071..1487221_NEGATIVE 282 318 275 63 16 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 280 119 82 82 45 NC_002950:PG1447|3end_transcriptional_regulator,_AraC_family_1531363..1531513_NEGATIVE 280 119 82 82 45 NC_002950:PG0826|3end_transcriptional_regulator,_AraC_family_884149..884299_POSITIVE 279 70 23 58 12 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 278 216 171 79 27 NC_002950:PG1126|3end_uracil_permease_1201746..1201896_NEGATIVE 278 86 42 112 64 NC_002950:PG0757|3end_hypothetical_protein_805723..805873_NEGATIVE