Origin IGS: tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag .........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 ctgtttttctgtgtcgttataggtatgaatacctcagctcctctatgacttgtgcgacacgctctacgggtgaaaacgataccgaaaagatacttcttgattttgcaaaggtctctttttgacttgatacagattgcctcgcaattcaataggaagttgaatttatcgtgaaacgaaaagtatactctatgccgtaaggaagagaaacaaaaacggccatggcgatccgaatacgatcacacacggcctctttctttcaaaaaaaacagttgggagatttcctttctaagggaagatgta Mask Tandem Repeat Region ================================================ tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Find is-nt database================================================ Query_seq: PG0264:PG0265|PG0264:PG0265:glycosyl transferase, group 2 family protein:hypothetical protein:-><-:298183..298482 300 tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0264:PG0265|PG0264:PG0265:glycosyl transferase, group 2 family protein:hypothetical protein:-><-:298183..298482 300 tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0264:PG0265|PG0264:PG0265:glycosyl transferase, group 2 family protein:hypothetical protein:-><-:298183..298482 300 tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 57 End: 152 ........................................................ M C D R I R I A M A V F V S L P Y G I E Y T F R F T I N S T S Y .................................................................................................................................................... Protein_Len: 32 Strand: + Start: 139 End: 234 .......................................................................................................................................... M Q L P I E L R G N L Y Q V K K R P L Q N Q E V S F R Y R F H P .................................................................. Protein_Len: 42 Strand: + Start: 156 End: 281 ........................................................................................................................................................... M A R Q S V S S Q K E T F A K S R S I F S V S F S P V E R V A Q V I E E L R Y S Y L ................... Protein_Len: 49 Strand: + Start: 152 End: 298 ....................................................................................................................................................... M N C E A I C I K S K R D L C K I K K Y L F G I V F T R R A C R T S H R G A E V F I P I T T Q K N .. Protein_Len: 37 Strand: - Start: 182 End: 292 ..................................................................................................................................................................................... F S V K A F D L L I K E T D N E G T S R T A C T M S S S L Y E Y R Y R C M ........ Protein_Len: 39 Strand: - Start: 133 End: 249 .................................................................................................................................... S L N L K R N F Q S A I Q I L D F L S R Q L I L F Y R K P I T K V R L A H R M ................................................... Protein_Len: 42 Strand: - Start: 15 End: 140 .............. F P F R G V T K K S L F L G H T I T N P D G H G N K N R K R V A Y L I S K T E R Y M ................................................................................................................................................................ tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag 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================================================ tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -4.0 Tail_Score: -5.4659 Start: 52 End: 87 Full_Region: TTTTTTGAAAGAAAG AGGCCGTGTGTGATC GTATTCG GATCGCCATGGCCG TTTTTGTTTCTCTTC ...................................................AGGCCGTGTGTGATCGTATTCGGATCGCCATGGCCG..................................................................................................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -7.5 Tail_Score: -3.85514 Start: 53 End: 86 Full_Region: TTTTTGAAAGAAAGA GGCCGTGTGTGATC GTATTCG GATCGCCATGGCC GTTTTTGTTTCTCTT ....................................................GGCCGTGTGTGATCGTATTCGGATCGCCATGGCC...................................................................................................................................................................................................................... TransTerm Strand: - Conf: 54 HP_score: -3.1 Tail_Score: -3.81557 Start: 53 End: 86 Full_Region: aagagaaacaaaaac ggccatggcgatc cgaatac gatcacacacggcc tctttctttcaaaaa ....................................................ggccatggcgatccgaatacgatcacacacggcc...................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG0264:PG0265|PG0264:PG0265:glycosyl transferase, group 2 family protein:hypothetical protein:-><-:298183..298482 300 tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Intra-Species Hit: Count: 2 Min: 1 Max: 300 Len: 300 Subject: NC_002950_PG0264_PG0265|glycosyl transferase, group 2 family protein:hypothetical protein|POSITIVE:NEGATIVE|[298183,298482]|300 HSP 1 e-value: 1.0E-155 bit: 547.0 Len: 300 Query Start:1 Query End:300 Subject Strand: POSITIVE Subject Start: 1 Subject End: 300 tacatcttcccttagaaaggaaatctcccaactgnnnnnnnngaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag tacatcttcccttagaaaggaaatctcccaactgttttttttgaaagaaagaggccgtgtgtgatcgtattcggatcgccatggccgtttttgtttctcttccttacggcatagagtatacttttcgtttcacgataaattcaacttcctattgaattgcgaggcaatctgtatcaagtcaaaaagagacctttgcaaaatcaagaagtatcttttcggtatcgttttcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag Subject: NC_002950_PG0088_PG0090|peptidase, M16 family:Dps family protein|POSITIVE:POSITIVE|[104633,105663]|1031 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 101 Query Start:200 Query End:300 Subject Strand: POSITIVE Subject Start: 195 Subject End: 298 .......................................................................................................................................................................................................atcaagaagtatcttttcggtatcgttt----tcacccgtagagcgtgtcgcacaagtcatagaggagctgaggtattcatacctataacgacacagaaaaacag .......................................................................................................................................................................................................atcaagaagtatcttttcggtatcgtttttgctcacctatagagcgtgtcgcacaagtcatggaggag-agaggtattcatatctataacgacactgaaaaacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAUCUUCCCUUAGAAAGGAAAUCUCCCAACUGUUUUUUUUGAAAGAAAGAGGCCGUGUGUGAUCGUAUUCGGAUCGCCAUGGCCGUUUUUGUUUCUCUUCCUUACGGCAUAGAGUAUACUUUUCGUUUCACGAUAAAUUCAACUUCCUAUUGAAUUGCGAGGCAAUCUGUAUCAAGUCAAAAAGAGACCUUUGCAAAAUCAAGAAGUAUCUUUUCGGUAUCGUUUUCACCCGUAGAGCGUGUCGCACAAGUCAUAGAGGAGCUGAGGUAUUCAUACCUAUAACGACACAGAAAAACAG ......((((........)))).........((((((((((.((((.((((((((((((.((((((.......))))))))))))).))))).)))).........((..((((.((((.....(((.....)))....((((.((((((((.((..(((((.((..((((..........((((((...((((..........))))..)))))).(((.........)))..))))..)).)))))....)))))).)))).))))......))))))))..))....)))))))))) (-76.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUUUUCUGUGUCGUUAUAGGUAUGAAUACCUCAGCUCCUCUAUGACUUGUGCGACACGCUCUACGGGUGAAAACGAUACCGAAAAGAUACUUCUUGAUUUUGCAAAGGUCUCUUUUUGACUUGAUACAGAUUGCCUCGCAAUUCAAUAGGAAGUUGAAUUUAUCGUGAAACGAAAAGUAUACUCUAUGCCGUAAGGAAGAGAAACAAAAACGGCCAUGGCGAUCCGAAUACGAUCACACACGGCCUCUUUCUUUCAAAAAAAACAGUUGGGAGAUUUCCUUUCUAAGGGAAGAUGUA .(((((((((...((.((((.(((((((((((.(((((((((...(((....(((((..((.(((....((....)).....((((((((.((((.(((......))))))).)))))))).........))).))..)))))..)))..))).)))))).....(((.....)))...))))..)).))))))))).))))))))))).....((((.(((.((((.......)))).).)).))))....(((..(((.........)))..))).((((((....))))))...... (-75.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 756 250 201 110 57 NC_002950:PG0492|5end_hypothetical_protein_534668..534898_NEGATIVE 403 87 47 172 133 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 386 116 74 204 159 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 386 116 74 204 159 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 386 116 74 204 159 NC_002950:PG0101|5end_hypothetical_protein_119198..119428_POSITIVE 370 270 230 70 31 NC_002950:PG1770|5end_hypothetical_protein_1857284..1857514_POSITIVE 368 87 50 185 141 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 367 110 64 197 141 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 365 97 51 110 57 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 359 100 53 153 95 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 357 110 62 217 167 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 357 98 53 181 134 NC_002950:PG2040|5end_DNA-binding_protein,_histone-like_family_2138874..2139104_NEGATIVE 355 90 45 65 15 NC_002950:PG0002|5end_hexapeptide_transferase_family_protein_1295..1525_POSITIVE 350 99 53 206 141 NC_002950:PG1536|5end_cell_division_protein_FtsX,_putative_1616362..1616592_POSITIVE 350 90 46 76 32 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 350 99 52 148 96 NC_002950:PG0854|5end_hypothetical_protein_914870..915100_POSITIVE 349 85 41 178 130 NC_002950:PG2001|5end_signal_peptidase_I_2090855..2091085_NEGATIVE 348 117 71 196 142 NC_002950:PG0539|5end_efflux_transporter,_MFP_component,_RND_family_590574..590804_POSITIVE 344 268 229 229 193 NC_002950:PG0351|5end_hypothetical_protein_386774..387004_POSITIVE 343 260 211 47 3 NC_002950:PG2174|5end_hypothetical_protein_2282578..2282808_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 290 241 79 27 NC_002950:PG0493|3end_hypothetical_protein_534742..534892_NEGATIVE 621 290 241 79 26 NC_002950:PG1426|3end_hypothetical_protein_1511152..1511302_NEGATIVE 388 97 53 48 5 NC_002950:PG0264|3end_glycosyl_transferase,_group_2_family_protein_298122..298272_POSITIVE 369 89 46 74 31 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 359 100 53 133 75 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 357 108 61 90 29 NC_002950:PG0793|3end_fructose-1,6-bisphosphatase_846335..846485_POSITIVE 355 90 45 52 2 NC_002950:PG0001|3end_chromosomal_replication_initiation_protein_1362..1512_POSITIVE 350 99 52 147 95 NC_002950:PG2152|3end_DNA-binding_protein,_histone-like_family_2260315..2260465_POSITIVE 350 90 46 69 25 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 350 99 52 147 95 NC_002950:PG0853|3end_DNA-binding_protein,_histone-like_family_914949..915099_POSITIVE 341 248 211 144 102 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 338 269 225 68 4 NC_002950:PG1702|3end_DNA_gyrase,_B_subunit_1787946..1788096_NEGATIVE 338 100 54 82 34 NC_002950:PG0126|3end_type_I_phosphodiesterase/nucleotide_pyrophosphatase_family_protein_146783..146933_NEGATIVE 337 100 53 149 107 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 334 87 46 106 75 NC_002950:PG1604|3end_immunoreactive_84_kDa_antigen_PG93_1685147..1685297_POSITIVE 333 88 50 137 95 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 332 86 44 56 14 NC_002950:PG0599|3end_3,4-dihydroxy-2-butanone_4-phosphate_synthase/GTP_cyclohydrolase_II_657732..657882_POSITIVE 332 116 71 151 98 NC_002950:PG0538|3end_outer_membrane_efflux_protein_590610..590760_POSITIVE 332 95 51 135 94 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 328 98 52 109 42 NC_002950:PG2110|3end_thiamine_biosynthesis_protein_ThiC_2219449..2219599_NEGATIVE