Origin IGS: cactaacggcacaccttttaactctggagcgtctctttgttccacagaagcaaagaaggcgtccatatctatatggattattttacgcaatactgaaatttttctggtgcaaagatactcaaaaacaaaagtatttaagaaaaatatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca .........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 tgtctactcggttcttattactgtcttgtttaaagtctttctgaatgcctgacctatgggctgaacatcagaaagtggacggctattgcatagtgcccacttgtatataaactccattttctgaaatttgttgcaaagataatatatttttcttaaatacttttgtttttgagtatctttgcaccagaaaaatttcagtattgcgtaaaataatccatatagatatggacgccttctttgcttctgtggaacaaagagacgctccagagttaaaaggtgtgccgttagtg Mask Tandem Repeat Region ================================================ cactaacggcacaccttttaactctggagcgtctctttgttccacagaagcaaagaaggcgtccatatctatatggattattttacgcaatactgaaatttttctggtgcaaagatactcaaaaacaaaagtatttaagaaaaatatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Find is-nt database================================================ Query_seq: PI1347:PI1348|PI1347:PI1348:DNA damage-inducible protein:glycosyltransferase:->->:1262239..1262528 290 cactaacggcacaccttttaactctggagcgtctctttgttccacagaagcaaagaaggcgtccatatctatatggattattttacgcaatactgaaatttttctggtgcaaagatactcaaaaacaaaagtatttaagaaaaatatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1347:PI1348|PI1347:PI1348:DNA damage-inducible protein:glycosyltransferase:->->:1262239..1262528 290 cactaacggcacaccttttaactctggagcgtctctttgttccacagaagcaaagaaggcgtccatatctatatggattattttacgcaatactgaaatttttctggtgcaaagatactcaaaaacaaaagtatttaagaaaaatatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1347:PI1348|PI1347:PI1348:DNA damage-inducible protein:glycosyltransferase:->->:1262239..1262528 290 cactaacggcacaccttttaactctggagcgtctctttgttccacagaagcaaagaaggcgtccatatctatatggattattttacgcaatactgaaatttttctggtgcaaagatactcaaaaacaaaagtatttaagaaaaatatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 4 Max: 144 Len: 141 Subject: UniRef90_Q89W32 Cluster: DNA-damage-inducible protein; n=1; Bradyrhizobium japonicum|Rep: DNA-damage-inducible protein - Bradyrhizobium japonicum HSP 1 e-value: 2.0E-6 bit: 53.5 Len: 105 Query Start:4 Query End:108 Subject Strand: null Subject Start: 8 Subject End: 42 ... T R K I S V L R K I I H I D M D A F F A S V E Q R D A P E L K G V P L ...................................................................................................................................................................................... ... T G E T S P V R K I I H I D M D A F Y A S V E Q R D N P E L R G K P V ...................................................................................................................................................................................... Subject: UniRef90_Q2G4Y1 Cluster: DNA-directed DNA polymerase; n=1; Novosphingobium aromaticivorans DSM 12444|Rep: DNA-directed DNA polymerase - Novosphingobium aromaticivorans (strain DSM 12444) HSP 1 e-value: 4.0E-6 bit: 52.8 Len: 102 Query Start:4 Query End:105 Subject Strand: null Subject Start: 12 Subject End: 45 ... R K I S V L R K I I H I D M D A F F A S V E Q R D A P E L K G V P L ......................................................................................................................................................................................... ... R S A T G L R K V I H V D M D A F F A S V E Q R D N P D L R G K P V ......................................................................................................................................................................................... Subject: UniRef90_A0IXU5 Cluster: UMUC-like DNA-repair protein; n=1; Shewanella woodyi ATCC 51908|Rep: UMUC-like DNA-repair protein - Shewanella woodyi ATCC 51908 HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 141 Query Start:4 Query End:144 Subject Strand: null Subject Start: 15 Subject End: 68 ... F F L N T - F V F E Y L C T R K I - - - - - - S V L R K I I H I D M D A F F A S V E Q R D A P E L K G V P L .................................................................................................................................................. ... F L L D T V F I Y S I V C G S H L F R R V L K N I L R K I I H I D M D C Y F A A V E M R D F P E L R G K P I .................................................................................................................................................. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 65 End: 205 ................................................................ M S I W I I L R N T E I F L V Q R Y S K T K V F K K N I L S L Q Q I S E N G V Y I Q V G T M Q ..................................................................................... Protein_Len: 60 Strand: + Start: 24 End: 284 ....................... M E R L F V P Q K Q R R R P Y L Y G L F Y A I L K F F W C K D T Q K Q K Y L R K I Y Y L C N K F Q K M E F I Y K W A L C ...... Protein_Len: 55 Strand: - Start: 1 End: 165 V L P V G K L E P A D R Q E V S A F F A D M D I H I I K R L V S I K R T C L Y E F V F T N L F F I N D K C C M ............................................................................................................................. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca 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================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1347:PI1348|PI1347:PI1348:DNA damage-inducible protein:glycosyltransferase:->->:1262239..1262528 290 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Intra-Species Hit: Count: 1 Min: 145 Max: 290 Len: 146 Subject: pint_PI1347_PI1348|DNA damage-inducible protein:glycosyltransferase|POSITIVE:POSITIVE|[1262239, 1262528]|290 HSP 1 e-value: 3.0E-77 bit: 289.0 Len: 146 Query Start:145 Query End:290 Subject Strand: POSITIVE Subject Start: 145 Subject End: 290 ................................................................................................................................................tatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca ................................................................................................................................................tatattatctttgcaacaaatttcagaaaatggagtttatatacaagtgggcactatgcaatagccgtccactttctgatgttcagcccataggtcaggcattcagaaagactttaaacaagacagtaataagaaccgagtagaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUAUCUUUGCAACAAAUUUCAGAAAAUGGAGUUUAUAUACAAGUGGGCACUAUGCAAUAGCCGUCCACUUUCUGAUGUUCAGCCCAUAGGUCAGGCAUUCAGAAAGACUUUAAACAAGACAGUAAUAAGAACCGAGUAGACA .........(((((...((((((((.....))))))))...(((.(((((((.((((...))))..)))))))((((((((((..(((....)))..)))).)))))).................)))...........))))).. (-30.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUACUCGGUUCUUAUUACUGUCUUGUUUAAAGUCUUUCUGAAUGCCUGACCUAUGGGCUGAACAUCAGAAAGUGGACGGCUAUUGCAUAGUGCCCACUUGUAUAUAAACUCCAUUUUCUGAAAUUUGUUGCAAAGAUAAUAUA (((((..(((((((........(((..((....((.....))....))..)))....)))))))...((((((((((((.(..(((((((.(((....))))))).)))..)))))))))))))............)))))..... (-34.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 73 37 78 38 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 346 100 64 99 55 pint:PI2106|5end_hypothetical_protein_2059221..2059451_POSITIVE 322 100 57 87 48 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 318 100 51 226 165 pint:PI0965|5end_hypothetical_protein_894154..894384_POSITIVE 315 70 31 75 37 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 305 99 51 178 117 pint:PI0345|5end_conserved_hypothetical_protein_319485..319715_POSITIVE 302 100 60 81 37 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 288 94 64 231 191 pint:PI2105|5end_hypothetical_protein_2059357..2059587_POSITIVE 285 87 44 67 19 pint:PI1327|5end_conserved_hypothetical_protein_1245563..1245793_POSITIVE 284 101 64 42 5 pint:PI1777|5end_conserved_hypothetical_protein_1709402..1709632_POSITIVE 284 84 49 230 185 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 283 82 44 228 198 pint:PI0289|5end_hypothetical_protein_272424..272654_POSITIVE 283 82 44 76 46 pint:PI0288|5end_hypothetical_protein_(possible_ISPg3-related_transposase)_272272..272502_POSITIVE 282 100 51 225 158 pint:PI0080|5end_hypothetical_protein_79047..79277_POSITIVE 281 89 47 172 130 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 280 100 51 190 149 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 280 89 44 97 50 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 279 85 46 96 56 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 279 99 63 109 69 pint:PI0917|5end_phosphoglycolate_phosphatase_846371..846601_POSITIVE 275 100 54 197 141 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 77 31 88 35 pint:PI0301|3end_probable_transposase_285982..286132_POSITIVE 350 73 39 39 1 pint:PI0170|3end_hypothetical_protein_163891..164041_POSITIVE 293 87 44 72 12 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 283 82 44 76 46 pint:PI0287|3end_ISPg3-related_transposase_272352..272502_POSITIVE 281 89 47 133 91 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 280 89 44 58 11 pint:PI0276|3end_anti-restriction_protein_265021..265171_POSITIVE 277 99 53 55 3 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 276 109 63 67 10 pint:PI1879|3end_uracil_phosphoribosyltransferase_1821245..1821395_POSITIVE 276 119 71 93 43 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 268 100 51 87 44 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 266 99 55 52 1 pint:PI0344|3end_conserved_hypothetical_protein_319439..319589_POSITIVE 263 95 51 59 6 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE 263 76 31 149 92 pint:PI0964|3end_conserved_hypothetical_protein_894187..894337_POSITIVE 261 88 44 45 5 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 258 75 32 114 69 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 257 87 45 136 80 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 257 100 51 88 28 pint:PI0398|3end_hypothetical_protein_363541..363691_POSITIVE 252 78 31 138 92 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 251 99 51 60 19 pint:PI0097|3end_aspartate_aminotransferase_94682..94832_POSITIVE 245 113 78 43 2 pint:PI0228|3end_outer_membrane_cobalamin_receptor_protein_228204..228354_POSITIVE