Origin IGS: agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaattgatactcttcgaaaatctcttcaaaccgtgtcaactctatctgcaacctccaaaccgtgttttgagcagcctgtggctagcttcctagtttgctctttgattttcagtgagtataaactcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa .........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 ttttctcctgtttctttttgagtctctttcattataccacaaactagccaccctgactagtttgttttacgctttcagggagggaatagacagcaaaaagaaccctgcttttctgcaaaagagagctccctactgagtttatactcactgaaaatcaaagagcaaactaggaagctagccacaggctgctcaaaacacggtttggaggttgcagatagagttgacacggtttgaagagattttcgaagagtatcaatttcatatttctgcctatccatttgtactaataaaagactgagacaccacatctcagcctttttct Mask Tandem Repeat Region ================================================ agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaattgatactcttcgaaaatctcttcaaaccgtgtcaactctatctgcaacctccaaaccgtgttttgagcagcctgtggctagcttcctagtttgctctttgattttcagtgagtataaactcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Find is-nt database================================================ Query_seq: SMT_1604:SMT_1605|SMT_1604:SMT_1605:K05833 putative ABC transport system ATP-binding protein:hypothetical protein:->->:1595224..1595545 322 agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaattgatactcttcgaaaatctcttcaaaccgtgtcaactctatctgcaacctccaaaccgtgttttgagcagcctgtggctagcttcctagtttgctctttgattttcagtgagtataaactcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1604:SMT_1605|SMT_1604:SMT_1605:K05833 putative ABC transport system ATP-binding protein:hypothetical protein:->->:1595224..1595545 322 agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaattgatactcttcgaaaatctcttcaaaccgtgtcaactctatctgcaacctccaaaccgtgttttgagcagcctgtggctagcttcctagtttgctctttgattttcagtgagtataaactcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1604:SMT_1605|SMT_1604:SMT_1605:K05833 putative ABC transport system ATP-binding protein:hypothetical protein:->->:1595224..1595545 322 agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaattgatactcttcgaaaatctcttcaaaccgtgtcaactctatctgcaacctccaaaccgtgttttgagcagcctgtggctagcttcctagtttgctctttgattttcagtgagtataaactcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 67 Max: 185 Len: 119 Subject: UniRef90_O05164 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 9.0E-7 bit: 48.1 Len: 78 Query Start:108 Query End:185 Subject Strand: null Subject Start: 20 Subject End: 45 ........................................................................................................... S A T S K P C F E Q P V A S F L V C S L I F S E Y K ......................................................................................................................................... ........................................................................................................... S T T S K Q C F E Q P A A S F L V C S L I F I E Y K ......................................................................................................................................... HSP 2 e-value: 9.0E-7 bit: 26.6 Len: 39 Query Start:67 Query End:105 Subject Strand: null Subject Start: 6 Subject End: 18 .................................................................. L I L F E N L F K P C Q L ......................................................................................................................................................................................................................... .................................................................. L I L F E N L F K P R Q L ......................................................................................................................................................................................................................... agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 49 End: 153 ................................................ M G R N M K L I L F E N L F K P C Q L Y L Q P P N R V L S S L W L A S ......................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 15 End: 245 .............. M W C L S L L L V Q M D R Q K Y E I D T L R K S L Q T V S T L S A T S K P C F E Q P V A S F L V C S L I F S E Y K L S R ............................................................................. Protein_Len: 34 Strand: + Start: 175 End: 276 .............................................................................................................................................................................. M S I N S V G S S L L Q K S R V L F A V Y S L P E S V K Q T S Q G G .............................................. Protein_Len: 42 Strand: - Start: 190 End: 315 ............................................................................................................................................................................................. Y P A R K Q L F A P N K K S D I G E R F A Y F L S T L T A L K H Y L S L S E F L F M ....... Protein_Len: 33 Strand: - Start: 92 End: 190 ........................................................................................... V T D V R D A V E L G H K S C G T A L K R T Q E K I K L S Y L S M .................................................................................................................................... agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 263 End: 292 ......................................................................................................................................................................................................................................................................CTAGTCAGGGTGGCTAGTTTGTGGTATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -4.0 Tail_Score: -4.87037 Start: 195 End: 223 Full_Region: TATAAACTCAGTAGG GAGCTCTCTTTT GCAG AAAAGCAGGGTTC TTTTTGCTGTCTATT ..................................................................................................................................................................................................GAGCTCTCTTTTGCAGAAAAGCAGGGTTC................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -12.3 Tail_Score: -2.66316 Start: 259 End: 283 Full_Region: CCTGAAAGCGTAAAA CAAACTAGTCA GGG TGGCTAGTTTG TGGTATAATGAAAGA ..................................................................................................................................................................................................................................................................CAAACTAGTCAGGGTGGCTAGTTTG....................................... TransTerm Strand: - Conf: 89 HP_score: -10.1 Tail_Score: -4.24002 Start: 259 End: 283 Full_Region: tctttcattatacca caaactagcca ccc tgactagtttg ttttacgctttcagg ..................................................................................................................................................................................................................................................................caaactagccaccctgactagtttg....................................... TransTerm Strand: - Conf: 74 HP_score: -5.1 Tail_Score: -4.69559 Start: 263 End: 279 Full_Region: tcattataccacaaa ctagcca ccc tgactag tttgttttacgcttt ......................................................................................................................................................................................................................................................................ctagccaccctgactag........................................... Find igs database================================================ Query_seq: SMT_1604:SMT_1605|SMT_1604:SMT_1605:K05833 putative ABC transport system ATP-binding protein:hypothetical protein:->->:1595224..1595545 322 agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 322 Len: 322 Subject: smit_SMT_1604_SMT_1605|K05833 putative ABC transport system ATP-binding protein:hypothetical protein|POSITIVE:POSITIVE|[1595224,1595545]|322 HSP 1 e-value: 7.0E-72 bit: 272.0 Len: 137 Query Start:186 Query End:322 Subject Strand: POSITIVE Subject Start: 186 Subject End: 322 .........................................................................................................................................................................................ctcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa .........................................................................................................................................................................................ctcagtagggagctctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa HSP 2 e-value: 2.0E-29 bit: 131.0 Len: 66 Query Start:1 Query End:66 Subject Strand: POSITIVE Subject Start: 1 Subject End: 66 agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaa................................................................................................................................................................................................................................................................ agaaaaaggctgagatgtggtgtctcagtcttttattagtacaaatggataggcagaaatatgaaa................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 2 Min: 200 Max: 322 Len: 123 Subject: NC_003028_SP_1882_SP_1883|hypothetical protein:dextran glucosidase DexS, putative|NEGATIVE:NEGATIVE|[1784624,1784878]|255 HSP 1 e-value: 3.0E-49 bit: 196.0 Len: 123 Query Start:200 Query End:322 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 126 .......................................................................................................................................................................................................ctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa .......................................................................................................................................................................................................ctctttttcagaaaagcagggttctttttgctgtctattccatccctgaaagtgtagaacaaactggtcagggtggctagtttgtggtataatgaaagggactcaaaaagaaacaggagaaaa Subject: NC_008533_SPD_1662_SPD_1663|hypothetical protein:alpha, alpha-phosphotrehalase|NEGATIVE:NEGATIVE|[1673680, 1673820]|141 HSP 1 e-value: 8.0E-47 bit: 188.0 Len: 123 Query Start:200 Query End:322 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 126 .......................................................................................................................................................................................................ctcttttgcagaaaagcagggttctttttgctgtctattccctccctgaaagcgtaaaacaaactagtcagggtggctagtttgtggtataatgaaagagactcaaaaagaaacaggagaaaa .......................................................................................................................................................................................................ctctttttcagaaaagcagggttctttttgctgtctattccatccttgaaagtgtagaacaaactggtcagggtggctagtttgtggtataatgaaagggactcaaaaagaaacaggagaaaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUUUGCAGAAAAGCAGGGUUCUUUUUGCUGUCUAUUCCCUCCCUGAAAGCGUAAAACAAACUAGUCAGGGUGGCUAGUUUGUGGUAUAAUGAAAGAGACUCAAAAAGAAACAGGAGAAAA (((((((((......))))..(((((((((..((((.(((.......)))...(((..(((((((((((.....)))))))))))..)))........)))).)))))))))..))))).... (-34.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUCCUGUUUCUUUUUGAGUCUCUUUCAUUAUACCACAAACUAGCCACCCUGACUAGUUUGUUUUACGCUUUCAGGGAGGGAAUAGACAGCAAAAAGAACCCUGCUUUUCUGCAAAAGAG ....(((....(((((((((.((((.((((........(((((((((.(.....).)))))))))....(.(.....).)..)))).))))..)))))))))...(((......)))...))) (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 87 41 163 96 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 284 87 42 144 98 smit:SMT_989|5end_hypothetical_protein_933548..933778_NEGATIVE 277 120 75 128 87 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 276 50 1 104 53 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 273 77 40 183 143 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 263 88 43 54 12 smit:SMT_271|5end_autoinducer-2_production_protein_211736..211966_NEGATIVE 263 88 42 74 28 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 259 42 16 62 37 smit:SMT_1669|5end_potassium_uptake_protein_KtrB_1658577..1658807_NEGATIVE 259 49 10 206 165 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 257 100 64 231 201 smit:SMT_319|5end_K02356_elongation_factor_EF-P_258864..259094_NEGATIVE 256 87 45 47 3 smit:SMT_935|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_887326..887556_POSITIVE 255 47 15 54 18 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 255 50 1 118 50 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 254 79 31 139 85 smit:SMT_1653|5end_hydrolase_1641328..1641558_POSITIVE 251 49 5 106 45 smit:SMT_1890|5end_hypothetical_protein_1843407..1843637_POSITIVE 251 80 34 195 154 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 250 95 51 54 10 smit:SMT_2085|5end_K01207_beta-N-acetylhexosaminidase_1983039..1983269_POSITIVE 250 70 24 90 36 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 250 41 8 58 9 smit:SMT_704|5end_Cof_family_protein_613662..613892_POSITIVE 249 103 66 206 162 smit:SMT_1424|5end_K02003_1409706..1409936_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 87 42 134 88 smit:SMT_990|3end_hypothetical_protein_933558..933708_NEGATIVE 282 107 66 68 32 smit:SMT_1277|3end_PcsB_protein_1241327..1241477_POSITIVE 276 50 1 95 44 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 263 88 42 72 26 smit:SMT_109|3end_beta-galactosidase_57523..57673_POSITIVE 262 86 64 146 126 smit:SMT_1303|3end_tRNA-dihydrouridine_synthase_1264676..1264826_NEGATIVE 255 50 1 121 53 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 254 79 31 139 85 smit:SMT_1652|3end_Cof_family_protein_1641408..1641558_POSITIVE 251 49 5 86 25 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 250 70 24 97 43 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 249 85 44 80 26 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 247 85 46 35 1 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 246 47 1 146 99 smit:SMT_1305|3end_glycerol_kinase_1269805..1269955_POSITIVE 245 59 14 65 9 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 244 55 15 69 27 smit:SMT_860|3end_homoserine_O-succinyltransferase_804067..804217_NEGATIVE 243 86 44 69 20 smit:SMT_1011|3end_xanthine_phosphoribosyltransferase_949234..949384_POSITIVE 241 85 44 81 51 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 239 54 23 73 27 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 237 43 15 31 8 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE 236 49 3 67 15 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 233 51 19 122 82 smit:SMT_1027|3end_K02026_multiple_sugar_transport_system_permease_protein_962641..962791_NEGATIVE