Origin IGS: aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttaaataatttttacctagatatataacatactcataggacaaaaagtctttaaaatcagaaaacgcataatatcaagtgttaaaaatccttgatattatgcgttttattgttagaaaatttgctttattttctcctctaattgagtttttgcccagcctcaaaacaccaacttcattttacctaccaagcacagtcattcgtcatttattttttccaatattatctacgaactttgataaaaagagaggtaccatagctataaaaacttgccctctttctccccatgcaaataaaacgactgcaagaacagctgaaaagattgctaaacatatagatattagacgacatattttcttattattcatagcactgctcct Mask Tandem Repeat Region ================================================ aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Find is-nt database================================================ Query_seq: SMT_1052:SMT_1053|SMT_1052:SMT_1053:hypothetical protein predicted by Glimmer/Critica:ABC transporter permease protein:-><-:992615..992996 382 aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1052:SMT_1053|SMT_1052:SMT_1053:hypothetical protein predicted by Glimmer/Critica:ABC transporter permease protein:-><-:992615..992996 382 aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1052:SMT_1053|SMT_1052:SMT_1053:hypothetical protein predicted by Glimmer/Critica:ABC transporter permease protein:-><-:992615..992996 382 aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 30 End: 155 ............................. M S S N I Y M F S N L F S C S C S R F I C M G R K R A S F Y S Y G T S L F I K V R R ................................................................................................................................................................................................................................... Protein_Len: 54 Strand: + Start: 13 End: 174 ............ M N N K K I C R L I S I C L A I F S A V L A V V L F A W G E R G Q V F I A M V P L F L S K F V D N I G K N K ................................................................................................................................................................................................................ Protein_Len: 38 Strand: - Start: 125 End: 238 ............................................................................................................................ P V E R K I L T R L Y Y Q F F Y I V F S Q A Q Y T F H L Q H K S A P C F S M ................................................................................................................................................ Protein_Len: 60 Strand: - Start: 3 End: 302 .. I T G R K K D F N T S L I P F F L H R I V T S P L Y F S T P T K L S P L F E I L P S F L A F K R V I F R M I D L I K L M ................................................................................ aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa 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================================================ aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.7 Tail_Score: -3.64283 Start: 272 End: 320 Full_Region: aagtctttaaaatca gaaaacgcataatatcaagtgtt aaa aatccttgatattatgcgtttta ttgttagaaaatttg ...............................................................................................................................................................................................................................................................................gaaaacgcataatatcaagtgttaaaaatccttgatattatgcgtttta.............................................................. TransTerm Strand: - Conf: 100 HP_score: -15.6 Tail_Score: -4.89477 Start: 277 End: 315 Full_Region: tttaaaatcagaaaa cgcataatatcaagtgtt aaa aatccttgatattatgcg ttttattgttagaaa ....................................................................................................................................................................................................................................................................................cgcataatatcaagtgttaaaaatccttgatattatgcg................................................................... Find igs database================================================ Query_seq: SMT_1052:SMT_1053|SMT_1052:SMT_1053:hypothetical protein predicted by Glimmer/Critica:ABC transporter permease protein:-><-:992615..992996 382 aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 382 Len: 382 Subject: smit_SMT_1052_SMT_1053|hypothetical protein predicted by Glimmer/Critica:ABC transporter permease protein|POSITIVE:NEGATIVE|[992615,992996]|382 HSP 1 e-value: 0.0 bit: 757.0 Len: 382 Query Start:1 Query End:382 Subject Strand: POSITIVE Subject Start: 1 Subject End: 382 aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa aggagcagtgctatgaataataagaaaatatgtcgtctaatatctatatgtttagcaatcttttcagctgttcttgcagtcgttttatttgcatggggagaaagagggcaagtttttatagctatggtacctctctttttatcaaagttcgtagataatattggaaaaaataaatgacgaatgactgtgcttggtaggtaaaatgaagttggtgttttgaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcgttttctgattttaaagactttttgtcctatgagtatgttatatatctaggtaaaaattatttaaaaa Inter-species Hit: Count: 6 Min: 219 Max: 338 Len: 120 Subject: NC_003028_SP_2168_SP_2169|fucose operon repressor, putative:zinc ABC transporter, zinc-binding lipoprotein|POSITIVE:NEGATIVE|[2085658,2086816]|1159 HSP 1 e-value: 6.0E-14 bit: 79.8 Len: 119 Query Start:219 Query End:337 Subject Strand: POSITIVE Subject Start: 235 Subject End: 353 ..........................................................................................................................................................................................................................gaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcg-ttttctgattttaaagactttt............................................. ..........................................................................................................................................................................................................................gaggctggacaaaaactcaatttcaggagaaaatggagtaaaccttcccacaataaaacgcatagtatcaa-gtttttgcacacctgatattatgcgtttttctgattttaaagattttt............................................. Subject: NC_008533_SPD_1996_SPD_1997|fucose operon repressor, putative:zinc ABC transporter, zinc-binding lipoprotein|POSITIVE:NEGATIVE|[1972472,1973599]|1128 HSP 1 e-value: 3.0E-13 bit: 77.8 Len: 118 Query Start:219 Query End:336 Subject Strand: POSITIVE Subject Start: 194 Subject End: 311 ..........................................................................................................................................................................................................................gaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcg-ttttctgattttaaagacttt.............................................. ..........................................................................................................................................................................................................................gaggctggacaaaaactcaatttcaggagaaaatggagtaaaccttcccacaataaaacgcatagtatcaa-gtttttgcacacctgatattatgcgtttttttgattttaaagacttt.............................................. Subject: NC_003098_spr1974_spr1975|Regulator of fucose operon:ABC transporter substrate-binding protein - Zinc (Zn2+) transport|POSITIVE:NEGATIVE|[1964970,1966097]|1128 HSP 1 e-value: 3.0E-13 bit: 77.8 Len: 118 Query Start:219 Query End:336 Subject Strand: POSITIVE Subject Start: 194 Subject End: 311 ..........................................................................................................................................................................................................................gaggctgggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcg-ttttctgattttaaagacttt.............................................. ..........................................................................................................................................................................................................................gaggctggacaaaaactcaatttcaggagaaaatggagtaaaccttcccacaataaaacgcatagtatcaa-gtttttgcacacctgatattatgcgtttttttgattttaaagacttt.............................................. Subject: NC_008533_SPD_1137_SPD_1138|ABC transporter, ATP-binding protein:heat shock protein HtpX|POSITIVE:NEGATIVE|[1172029,1172176]|148 HSP 1 e-value: 4.0E-12 bit: 73.8 Len: 114 Query Start:225 Query End:338 Subject Strand: POSITIVE Subject Start: 24 Subject End: 135 ................................................................................................................................................................................................................................gggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcg-ttttctgattttaaagacttttt............................................ ................................................................................................................................................................................................................................gggcaaaaacacaattttaggagaaaaagaagtaaatcttcccatagtaaaacgcataatatcaag---ttttcacacctgatattatgcgtttttcagattttaaagacttttt............................................ Subject: NC_003098_spr1161_spr1162|ABC transporter ATP-binding protein - unknown substrate:heat shock protein HtpX|POSITIVE:NEGATIVE|[1164498,1164645]|148 HSP 1 e-value: 4.0E-12 bit: 73.8 Len: 114 Query Start:225 Query End:338 Subject Strand: POSITIVE Subject Start: 24 Subject End: 135 ................................................................................................................................................................................................................................gggcaaaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcg-ttttctgattttaaagacttttt............................................ ................................................................................................................................................................................................................................gggcaaaaacacaattttaggagaaaaagaagtaaatcttcccatagtaaaacgcataatatcaag---ttttcacacctgatattatgcgtttttcagattttaaagacttttt............................................ Subject: NC_003028_SP_1427_SP_1428|peptidase, U32 family:hypothetical protein|NEGATIVE:NEGATIVE|[1346713,1346960]|248 HSP 1 e-value: 2.0E-10 bit: 67.9 Len: 109 Query Start:230 Query End:338 Subject Strand: NEGATIVE Subject Start: 113 Subject End: 222 .....................................................................................................................................................................................................................................aaaactcaattagaggagaaaataaagcaaattttctaacaataaaacgcataatatcaaggatttttaacacttgatattatgcg-ttttctgattttaaagacttttt............................................ .....................................................................................................................................................................................................................................aaaactcaatttcaagagaaaatgaagtaaatcttcccacaataaaacgcataatatcaagattgttcaatacctgatactatgcgtttttaagattttaaagacttttt............................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGCUGGGCAAAAACUCAAUUAGAGGAGAAAAUAAAGCAAAUUUUCUAACAAUAAAACGCAUAAUAUCAAGGAUUUUUAACACUUGAUAUUAUGCGUUUUCUGAUUUUAAAGACUUUUU (((..(......)..))).((((((..(((((((.......))))))).......(((((((((((((((((...........))))))))))))))))))))))).............. (-30.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGUCUUUAAAAUCAGAAAACGCAUAAUAUCAAGUGUUAAAAAUCCUUGAUAUUAUGCGUUUUAUUGUUAGAAAAUUUGCUUUAUUUUCUCCUCUAAUUGAGUUUUUGCCCAGCCUC (((((.((........(((((((((((((((((((((.(........))))))))))))))))))).)))..(((((((.......))))))).........)).))))).......... (-29.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 47 1 222 176 smit:SMT_733|5end_hypothetical_protein_639798..640028_NEGATIVE 340 120 72 48 1 smit:SMT_1018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_954564..954794_POSITIVE 242 103 84 173 154 smit:SMT_734|5end_hypothetical_protein_639967..640197_POSITIVE 219 49 1 182 149 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 210 85 43 161 112 smit:SMT_1033|5end_K07485_transposase_969792..970022_POSITIVE 207 109 65 225 181 smit:SMT_1833|5end_tagatose_1,6-diphosphate_aldolase_1801369..1801599_POSITIVE 206 30 5 36 5 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 205 49 1 105 60 smit:SMT_380|5end_hypothetical_protein_316376..316606_POSITIVE 205 49 1 105 60 smit:SMT_371|5end_hypothetical_protein_305248..305478_POSITIVE 198 112 84 65 38 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 198 112 84 65 38 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 195 48 5 214 162 smit:SMT_1222|5end_pneumococcal_surface_protein_A_1187008..1187238_NEGATIVE 194 115 72 114 66 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 194 108 67 142 96 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 190 39 1 31 1 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 189 115 71 89 41 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 186 115 72 190 141 smit:SMT_1686|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1670175..1670405_POSITIVE 185 41 3 58 19 smit:SMT_1276|5end_rod_shape-determining_protein_MreD_1239412..1239642_POSITIVE 184 107 79 66 31 smit:SMT_187|5end_30S_ribosomal_protein_S5_122997..123227_POSITIVE 180 106 67 145 116 smit:SMT_784|5end_hypothetical_protein_696298..696528_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 505 100 51 58 11 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 489 97 52 55 10 smit:SMT_1308|3end_hypothetical_protein_1273854..1274004_POSITIVE 404 100 52 72 24 smit:SMT_130|3end_capsular_polysaccharide_biosynthesis_protein_82925..83075_POSITIVE 359 120 71 143 94 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE 314 100 55 70 25 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 309 100 53 58 12 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 309 100 51 77 31 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 293 100 55 64 21 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 266 106 68 74 36 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 259 100 55 73 38 smit:SMT_972|3end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_919256..919406_NEGATIVE 247 119 90 32 1 smit:SMT_736|3end_hypothetical_protein_641500..641650_NEGATIVE 236 109 65 74 33 smit:SMT_637|3end_lactose_phosphotransferase_system_repressor_543105..543255_POSITIVE 223 107 68 78 36 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 216 100 52 53 5 smit:SMT_638|3end_hypothetical_protein_543180..543330_NEGATIVE 205 120 74 60 8 smit:SMT_2027|3end_competence-specific_global_transcription_modulator_1943025..1943175_NEGATIVE 205 120 74 60 8 smit:SMT_1091|3end_competence-specific_global_transcription_modulator_1032561..1032711_NEGATIVE 205 120 74 91 39 smit:SMT_1039|3end_tRNA_(uracil-5-)_-methyltransferase_981343..981493_NEGATIVE 205 27 1 140 109 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 205 49 1 105 60 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 205 49 1 105 60 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE