Origin IGS: tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca .........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 tgaaagtcggtgtccgatattgtctttatatataataaggtgtaaagctattgaaaacccaaaaagaaacaaaaatatcactattttgcaaaaaagttgctcaaaaatttggagattaatgaattaatacatacttttgcagtgtactacataaataatacagcataacaagaaatgataatttaaacaaaaatacagctatgattgaagtcaaaaacttagtattcaactatcccggcaacaagaaaaaggtgttcgacgga Mask Tandem Repeat Region ================================================ tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Find is-nt database================================================ Query_seq: PI0066:PI0067|PI0066:PI0067:ABC transport system, ATP-binding component:hypothetical protein:->->:66150..66412 263 tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0066:PI0067|PI0066:PI0067:ABC transport system, ATP-binding component:hypothetical protein:->->:66150..66412 263 tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0066:PI0067|PI0066:PI0067:ABC transport system, ATP-binding component:hypothetical protein:->->:66150..66412 263 tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 35 End: 145 .................................. M N T K F L T S I I A V F L F K L S F L V M L Y Y L C S T L Q K Y V L I H ...................................................................................................................... Protein_Len: 40 Strand: + Start: 144 End: 263 ............................................................................................................................................... M N L Q I F E Q L F C K I V I F L F L F G F S I A L H L I I Y K D N I G H R L S Protein_Len: 36 Strand: - Start: 140 End: 247 ........................................................................................................................................... N M L R W I K S C S K Q L I T I N K N R K P N E I A K C R I I Y L S L M ................ Protein_Len: 33 Strand: - Start: 1 End: 99 G D F V K K K N G P Y N F V L N K V E I M A T N K N L N D N R T M .................................................................................................................................................................... tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca 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================================================ tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0066:PI0067|PI0066:PI0067:ABC transport system, ATP-binding component:hypothetical protein:->->:66150..66412 263 tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaatttttgagcaacttttttgcaaaatagtgatatttttgtttctttttgggttttcaatagctttacaccttattatatataaagacaatatcggacaccgactttca Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: pint_PI0066_PI0067|ABC transport system, ATP-binding component:hypothetical protein|POSITIVE:POSITIVE|[66150,66412]|263 HSP 1 e-value: 3.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaa........................................................................................................... tccgtcgaacacctttttcttgttgccgggatagttgaatactaagtttttgacttcaatcatagctgtatttttgtttaaattatcatttcttgttatgctgtattatttatgtagtacactgcaaaagtatgtattaattcattaatctccaaa........................................................................................................... HSP 2 e-value: 7.0E-16 bit: 85.7 Len: 43 Query Start:221 Query End:263 Subject Strand: POSITIVE Subject Start: 221 Subject End: 263 ............................................................................................................................................................................................................................acaccttattatatataaagacaatatcggacaccgactttca ............................................................................................................................................................................................................................acaccttattatatataaagacaatatcggacaccgactttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGUCGAACACCUUUUUCUUGUUGCCGGGAUAGUUGAAUACUAAGUUUUUGACUUCAAUCAUAGCUGUAUUUUUGUUUAAAUUAUCAUUUCUUGUUAUGCUGUAUUAUUUAUGUAGUACACUGCAAAAGUAUGUAUUAAUUCAUUAAUCUCCAAAUUUUUGAGCAACUUUUUUGCAAAAUAGUGAUAUUUUUGUUUCUUUUUGGGUUUUCAAUAGCUUUACACCUUAUUAUAUAUAAAGACAAUAUCGGACACCGACUUUCA ...((((....((......(((((.....(((((((((((((..((((..(((......))).)))))))))).......)))))))......(((...(((((..(((((.(((((....))))).)))))..................((((((.....((((((.....(..(......)..).....))))))...))))))......)))))...)))................)))))....))....))))..... (-39.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGUCGGUGUCCGAUAUUGUCUUUAUAUAUAAUAAGGUGUAAAGCUAUUGAAAACCCAAAAAGAAACAAAAAUAUCACUAUUUUGCAAAAAAGUUGCUCAAAAAUUUGGAGAUUAAUGAAUUAAUACAUACUUUUGCAGUGUACUACAUAAAUAAUACAGCAUAACAAGAAAUGAUAAUUUAAACAAAAAUACAGCUAUGAUUGAAGUCAAAAACUUAGUAUUCAACUAUCCCGGCAACAAGAAAAAGGUGUUCGACGGA .....(((((...))))).....((((((((........))))))))(..(((((.(((............((((((....))))))........((((((.......(((((.((((((((.(((((.((((((..(((.((((............)))).))).......((((....))))............)).)))))))))..))).....))))).))))).......))))))........))).)))))..). (-35.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 50 3 67 19 pint:PI0844|5end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_777793..778023_POSITIVE 279 37 3 179 142 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 271 43 1 87 50 pint:PI1747|5end_membrane-bound_lytic_murein_transglycosylase_D_1667483..1667713_POSITIVE 265 47 2 184 148 pint:PI0353|5end_hypothetical_protein_324610..324840_POSITIVE 263 203 166 198 162 pint:PI1424|5end_probable_peptidase_family_M48_1343149..1343379_POSITIVE 254 48 1 102 56 pint:PI0342|5end_hypothetical_protein_317556..317786_POSITIVE 254 48 1 51 5 pint:PI0343|5end_hypothetical_protein_317505..317735_POSITIVE 250 229 182 187 140 pint:PI2018|5end_50S_ribosomal_protein_L34_1975757..1975987_POSITIVE 249 34 2 83 52 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 247 46 1 56 11 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 246 52 11 165 124 pint:PI1746|5end_hypothetical_protein_1667356..1667586_POSITIVE 245 37 2 86 56 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 244 237 203 141 105 pint:PI1236|5end_10_kDa_chaperonin,_cpn10,_GroES_1158934..1159164_POSITIVE 241 218 171 145 106 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 240 170 121 163 115 pint:PI1177|5end_hypothtical_protein_1098856..1099086_POSITIVE 238 41 1 89 50 pint:PI1559|5end_hypothetical_protein_1476506..1476736_POSITIVE 238 253 211 152 110 pint:PI0591|5end_adenylosuccinate_lyase_538595..538825_POSITIVE 236 31 2 78 42 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 234 37 2 187 140 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 233 208 164 210 158 pint:PI1467|5end_conserved_hypothetical_protein_1393503..1393733_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 50 3 56 8 pint:PI0843|3end_carboxyl-terminal_protease_777862..778012_POSITIVE 271 43 1 130 93 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 254 48 1 81 35 pint:PI0341|3end_conserved_hypothetical_protein_317615..317765_POSITIVE 250 229 182 68 21 pint:PI2017|3end_conserved_hypothetical_protein_1975718..1975868_POSITIVE 249 34 2 75 44 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 247 46 1 56 11 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 246 52 11 146 105 pint:PI1745|3end_conserved_hypothetical_protein_1667417..1667567_POSITIVE 231 78 33 124 85 pint:PI0487|3end_50S_ribosomal_protein_L17_446703..446853_POSITIVE 226 50 3 72 32 pint:PI0114|3end_hypothetical_protein_108527..108677_POSITIVE 223 218 173 38 1 pint:PI1759|3end_hypothetical_protein_1684386..1684536_POSITIVE 220 37 1 149 121 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 220 88 43 58 6 pint:PI1249|3end_conserved_hypothetical_protein_1174147..1174297_POSITIVE 219 49 3 151 102 pint:PI2102|3end_DNA_topoisomerase_IV,_subunit_B_2057729..2057879_POSITIVE 219 38 7 125 97 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 219 43 3 46 11 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 218 53 20 61 22 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 217 209 161 139 92 pint:PI1917|3end_uracil-DNA_glycosylase_1861596..1861746_POSITIVE 216 68 22 101 65 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 216 126 82 46 9 pint:PI1492|3end_triosephosphate_isomerase_1412310..1412460_POSITIVE 216 79 33 79 24 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE