Origin IGS: taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctacacttaggaaaaatatttacatattttttagaaattctttcaccttctcaataagggacattaccattattccaaatagtgcaaacaaaaatatgatgcaaacaaaaagggctcgcaagcgatgcttgcgagcccttttaagttgtataaagttcatttgtttta Mask Tandem Repeat Region ================================================ taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Find is-nt database================================================ Query_seq: PI0447:PI0448|PI0447:PI0448:DNA-directed RNA polymerase, beta' subunit:hypothetical protein:->->:421816..421983 168 taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0447:PI0448|PI0447:PI0448:DNA-directed RNA polymerase, beta' subunit:hypothetical protein:->->:421816..421983 168 taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0447:PI0448|PI0447:PI0448:DNA-directed RNA polymerase, beta' subunit:hypothetical protein:->->:421816..421983 168 taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 9 End: 146 ........ M N F I Q L K R A R K H R L R A L F V C I I F L F A L F G I M V M S L I E K V K E F L K N M ...................... Protein_Len: 50 Strand: - Start: 2 End: 151 . F C I F K I C S L L A R L C R K R A R K T Q M M N K N A S N P I I T I D R I S F T F S N R F F I Y M ................. taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag 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================================================ taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -17.5 Tail_Score: -4.27026 Start: 16 End: 72 Full_Region: TAAAACAAATGAACT TTATACAACTTAAAAGGGCTCGCAAGC ATC GCTTGCGAGCCCTTTTTGTTTGCATCA TATTTTTGTTTGCAC ...............TTATACAACTTAAAAGGGCTCGCAAGCATCGCTTGCGAGCCCTTTTTGTTTGCATCA................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -9.89999 Tail_Score: -5.28942 Start: 16 End: 74 Full_Region: TAAAACAAATGAACT TTATACAACTTAAAAGGGCTCGCAAGC ATC GCTTGCGAGCCCTTTTTGTTTGCATCATA TTTTTGTTTGCACTA ...............TTATACAACTTAAAAGGGCTCGCAAGCATCGCTTGCGAGCCCTTTTTGTTTGCATCATA.............................................................................................. TransTerm Strand: + Conf: 100 HP_score: -21.2 Tail_Score: -3.73281 Start: 25 End: 63 Full_Region: TGAACTTTATACAAC TTAAAAGGGCTCGCAAGC ATC GCTTGCGAGCCCTTTTTG TTTGCATCATATTTT ........................TTAAAAGGGCTCGCAAGCATCGCTTGCGAGCCCTTTTTG......................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -22.4 Tail_Score: -4.34267 Start: 31 End: 57 Full_Region: tgatgcaaacaaaaa gggctcgcaagc gat gcttgcgagccc ttttaagttgtataa ..............................gggctcgcaagcgatgcttgcgagccc............................................................................................................... Find igs database================================================ Query_seq: PI0447:PI0448|PI0447:PI0448:DNA-directed RNA polymerase, beta' subunit:hypothetical protein:->->:421816..421983 168 taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: pint_PI0447_PI0448|DNA-directed RNA polymerase, beta' subunit:hypothetical protein|POSITIVE:POSITIVE|[421816,421983]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag taaaacaaatgaactttatacaacttaaaagggctcgcaagcatcgcttgcgagccctttttgtttgcatcatatttttgtttgcactatttggaataatggtaatgtcccttattgagaaggtgaaagaatttctaaaaaatatgtaaatatttttcctaagtgtag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACAAAUGAACUUUAUACAACUUAAAAGGGCUCGCAAGCAUCGCUUGCGAGCCCUUUUUGUUUGCAUCAUAUUUUUGUUUGCACUAUUUGGAAUAAUGGUAAUGUCCCUUAUUGAGAAGGUGAAAGAAUUUCUAAAAAAUAUGUAAAUAUUUUUCCUAAGUGUAG ................(((((.....((((((((((((((((...))))))))))))))))(((((((((.((.((((.((((.((((.(((..(((((.((......)).)))))..)))))))...))))....)))).)))))))))))..........))))). (-47.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUACACUUAGGAAAAAUAUUUACAUAUUUUUUAGAAAUUCUUUCACCUUCUCAAUAAGGGACAUUACCAUUAUUCCAAAUAGUGCAAACAAAAAUAUGAUGCAAACAAAAAGGGCUCGCAAGCGAUGCUUGCGAGCCCUUUUAAGUUGUAUAAAGUUCAUUUGUUUUA ...((((..((((.(((................(((.....))).((((......)))).........))).))))....)))).(((((((...((.((((((...((((((((((((((((...))))))))))))))))...))))))...))...))))))).. (-46.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 67 32 189 164 pint:PI1386|5end_sugar_phosphate_isomerase_1307004..1307234_POSITIVE 337 68 22 112 66 pint:PI1825|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1764996..1765226_POSITIVE 326 88 41 178 133 pint:PI1670|5end_hypothetical_protein_1583725..1583955_POSITIVE 325 67 30 192 165 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 320 69 30 184 119 pint:PI0546|5end_hypothetical_protein_497799..498029_POSITIVE 318 69 33 125 81 pint:PI1854|5end_possible_glycosyl_transferase_1800925..1801155_POSITIVE 307 69 26 211 171 pint:PI1437|5end_hypothetical_protein_1356088..1356318_POSITIVE 307 69 26 84 44 pint:PI1436|5end_hypothetical_protein_1355961..1356191_POSITIVE 303 77 33 95 50 pint:PI0729|5end_integrase_661428..661658_POSITIVE 302 74 33 85 41 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 301 88 44 105 59 pint:PI2157|5end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2103736..2103966_POSITIVE 298 80 31 74 23 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 295 80 34 62 10 pint:PI1848|5end_hypothetical_protein_1793799..1794029_POSITIVE 293 56 14 60 1 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 292 66 28 89 28 pint:PI1679|5end_hypothetical_protein_1594744..1594974_POSITIVE 289 130 88 172 129 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 285 69 31 172 135 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 285 79 33 162 107 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 285 73 33 52 12 pint:PI0602|5end_conserved_hypothetical_protein_549099..549329_POSITIVE 283 84 42 222 177 pint:PI0085|5end_RNase_P_protein_component_84440..84670_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 591 61 27 64 30 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 338 68 21 74 28 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 334 68 31 41 3 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 325 67 30 123 96 pint:PI0735|3end_ABC_transporter,_ATP-binding_/_permease_670591..670741_POSITIVE 305 68 28 116 79 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 303 77 33 95 50 pint:PI0728|3end_integrase_661508..661658_POSITIVE 302 74 33 72 28 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 298 80 31 71 20 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 289 130 88 59 16 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 282 59 18 52 11 pint:PI0623|3end_hypothetical_protein_573080..573230_POSITIVE 282 79 35 88 40 pint:PI0472|3end_50S_ribosomal_protein_L5_438705..438855_POSITIVE 279 59 15 53 12 pint:PI0622|3end_hypothetical_protein_572087..572237_POSITIVE 275 80 32 146 93 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 275 72 33 77 25 pint:PI0307|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290667..290817_POSITIVE 274 85 50 46 8 pint:PI1244|3end_hypothetical_protein_1169176..1169326_POSITIVE 274 78 35 81 33 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 273 93 52 110 64 pint:PI1711|3end_ABC_transporter,_ATP-binding_protein_1628429..1628579_POSITIVE 273 67 23 67 11 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 270 88 41 145 95 pint:PI1157|3end_hypothetical_protein_1082725..1082875_POSITIVE 269 79 31 115 51 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE