Origin IGS: ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc .........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 gagatttttaagatttgtttaagataggtcgggtatactatagacagttacaagaagacctcctaacttgttgtaacaaatatcctaaacttttctttttcataataatctccctataaagtcaccgcattcggtggctttttttgtcttgggattcatgatataataataaaatcgataagtaggaaaagagaaacgg Mask Tandem Repeat Region ================================================ ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Find is-nt database================================================ Query_seq: SMT_1674:SMT_1675|SMT_1674:SMT_1675:hypothetical protein predicted by Glimmer/Critica:adenylosuccinate synthetase:<-<-:1660592..1660790 199 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1674:SMT_1675|SMT_1674:SMT_1675:hypothetical protein predicted by Glimmer/Critica:adenylosuccinate synthetase:<-<-:1660592..1660790 199 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1674:SMT_1675|SMT_1674:SMT_1675:hypothetical protein predicted by Glimmer/Critica:adenylosuccinate synthetase:<-<-:1660592..1660790 199 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 84 End: 185 ................................................................................... L S I I I F F F L K P Y K N C C T L L D E Q L Q R Y Y V R G I K F M .............. ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc 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================================================ ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -6.9 Tail_Score: -3.86822 Start: 62 End: 79 Full_Region: CCCAAGACAAAAAAA GCCACCG AATG CGGTGAC TTTATAGGGAGATTA .............................................................GCCACCGAATGCGGTGAC........................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -5.80817 Start: 62 End: 79 Full_Region: taatctccctataaa gtcaccg catt cggtggc tttttttgtcttggg .............................................................gtcaccgcattcggtggc........................................................................................................................ TransTerm Strand: + Conf: 43 HP_score: -2.7 Tail_Score: -3.04269 Start: 123 End: 153 Full_Region: AAGTTTAGGATATTT GTTACAACAAG TTAGGAGGT CTTCTTGTAAC TGTCTATAGTATACC ..........................................................................................................................GTTACAACAAGTTAGGAGGTCTTCTTGTAAC.............................................. Find igs database================================================ Query_seq: SMT_1674:SMT_1675|SMT_1674:SMT_1675:hypothetical protein predicted by Glimmer/Critica:adenylosuccinate synthetase:<-<-:1660592..1660790 199 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Intra-Species Hit: Count: 2 Min: 1 Max: 199 Len: 199 Subject: smit_SMT_1836_SMT_1837|cytidine/deoxycytidylate deaminase family protein:adenylosuccinate synthetase|NEGATIVE:NEGATIVE|[1804589,1804787]|199 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacnnnnnnngccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Subject: smit_SMT_1674_SMT_1675|hypothetical protein predicted by Glimmer/Critica:adenylosuccinate synthetase|NEGATIVE:NEGATIVE|[1660592,1660790]|199 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacnnnnnnngccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc ccgtttctcttttcctacttatcgattttattattatatcatgaatcccaagacaaaaaaagccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Inter-species Hit: Count: 3 Min: 4 Max: 199 Len: 196 Subject: NC_008533_SPD_0024_SPD_0025|adenylosuccinate synthetase:cytidine/deoxycytidylate deaminase family protein|POSITIVE:POSITIVE|[23922,24121]|200 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 196 Query Start:4 Query End:199 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 196 ...tttctcttttcctacttatcgattttattattatatcatgaatcccaagacnnnnnnngccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc ...tttctcttttcctacttatcgattttattattatatcatgaatcccaacacaaaaaaagccaccgaatgcggtgactctatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaaccgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Subject: NC_003098_spr0021_spr0022|adenylosuccinate synthetase:hypothetical protein|POSITIVE:POSITIVE|[23922,24121]|200 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 196 Query Start:4 Query End:199 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 196 ...tttctcttttcctacttatcgattttattattatatcatgaatcccaagacnnnnnnngccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc ...tttctcttttcctacttatcgattttattattatatcatgaatcccaacacaaaaaaagccaccgaatgcggtgactctatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaaccgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Subject: NC_003028_SP_0019_SP_0020|adenylosuccinate synthetase:cytidine/deoxycytidylate deaminase family protein|POSITIVE:POSITIVE|[24119,24318]|200 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 196 Query Start:4 Query End:199 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 196 ...tttctcttttcctacttatcgattttattattatatcatgaatcccaagacnnnnnnngccaccgaatgcggtgactttatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaactgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc ...tttctcttttcctacttatcgattttattattatatcatgaatcccaacacaaaaaaagccaccgaatgcggtgactctatagggagattattatgaaaaagaaaagtttaggatatttgttacaacaagttaggaggtcttcttgtaaccgtctatagtatacccgacctatcttaaacaaatcttaaaaatctc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCUUUUCCUACUUAUCGAUUUUAUUAUUAUAUCAUGAAUCCCAAGACAAAAAAAGCCACCGAAUGCGGUGACUUUAUAGGGAGAUUAUUAUGAAAAAGAAAAGUUUAGGAUAUUUGUUACAACAAGUUAGGAGGUCUUCUUGUAACUGUCUAUAGUAUACCCGACCUAUCUUAAACAAAUCUUAAAAAUCUC ....................((((((.........((((((.((((.........((((.(((((....))))).))))...)))).....))))))..((((...((((((((((...(((((((.(((.........))).))))))).(((............))).))))))))))...)))).)))))).. (-38.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUUUUUAAGAUUUGUUUAAGAUAGGUCGGGUAUACUAUAGACAGUUACAAGAAGACCUCCUAACUUGUUGUAACAAAUAUCCUAAACUUUUCUUUUUCAUAAUAAUCUCCCUAUAAAGUCACCGCAUUCGGUGGCUUUUUUUGUCUUGGGAUUCAUGAUAUAAUAAUAAAAUCGAUAAGUAGGAAAAGAGAAA ................(((((.((((.(((.((....))...))).(((((((.(((.........))).)))))))...)))).))))).((((((((((.........((((...((((((((((....)))))))))).........))))....((((...........)))).......)))))))))).. (-45.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 90 41 184 135 smit:SMT_1836|5end_cytidine/deoxycytidylate_deaminase_family_protein_1804498..1804728_NEGATIVE 897 90 41 184 135 smit:SMT_1674|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1660501..1660731_NEGATIVE 515 140 91 176 128 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 436 100 55 181 136 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 436 100 55 181 136 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 436 100 55 181 136 smit:SMT_201|5end_phosphoglycerate_mutase_131329..131559_POSITIVE 378 77 31 149 99 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 378 77 31 149 99 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 294 50 3 148 91 smit:SMT_1056|5end_K07738_ATP-cone_domain_protein_994842..995072_POSITIVE 292 90 47 102 51 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 292 90 47 102 51 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 291 76 31 197 149 smit:SMT_486|5end_hypothetical_protein_422305..422535_NEGATIVE 279 79 43 187 149 smit:SMT_835|5end_polypeptide_deformylase_777549..777779_NEGATIVE 275 144 102 181 135 smit:SMT_2107|5end_tyrosine_recombinase_1998537..1998767_NEGATIVE 261 170 125 217 158 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 258 167 121 63 16 smit:SMT_1073|5end_L-asparaginase_1011209..1011439_POSITIVE 256 58 11 147 100 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 255 93 58 44 11 smit:SMT_1161|5end_K05837_rod_shape_determining_protein_RodA_1106408..1106638_NEGATIVE 249 46 7 144 94 smit:SMT_254|5end_K02025_multiple_sugar_transport_system_permease_protein_190796..191026_POSITIVE 248 79 53 226 202 smit:SMT_836|5end_cell_surface_protein_precursor_779832..780062_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 170 121 64 15 smit:SMT_1837|3end_adenylosuccinate_synthetase_1804698..1804848_NEGATIVE 856 180 131 74 25 smit:SMT_103|3end_adenylosuccinate_synthetase_42174..42324_POSITIVE 331 171 131 60 17 smit:SMT_2063|3end_hypothetical_protein_1971670..1971820_NEGATIVE 331 171 131 60 17 smit:SMT_1996|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1920995..1921145_NEGATIVE 331 171 131 60 17 smit:SMT_200|3end_hypothetical_protein_131164..131314_POSITIVE 292 114 82 29 1 smit:SMT_217|3end_hypothetical_protein_149888..150038_POSITIVE 286 180 131 66 18 smit:SMT_210|3end_acetyltransferase,_GNAT_family_143876..144026_POSITIVE 279 79 43 72 34 smit:SMT_836|3end_cell_surface_protein_precursor_777664..777814_NEGATIVE 261 170 125 130 71 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 256 58 11 58 11 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 248 79 53 87 63 smit:SMT_837|3end_cation_transport_ATPase_779971..780121_NEGATIVE 247 42 3 71 35 smit:SMT_549|3end_hypothetical_cytosolic_protein_467367..467517_POSITIVE 242 70 22 135 93 smit:SMT_980|3end_hypothetical_protein_928227..928377_POSITIVE 238 176 135 64 15 smit:SMT_2060|3end_hypothetical_protein_1970083..1970233_POSITIVE 237 90 59 60 30 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 236 98 53 87 46 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 233 87 59 68 39 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 224 170 129 145 111 smit:SMT_1454|3end_cytidine_deaminase_1437497..1437647_NEGATIVE 222 177 136 118 59 smit:SMT_1139|3end_rRNA_(guanine-N1-)-methyltransferase_1080683..1080833_POSITIVE 221 177 134 57 15 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE