Origin IGS: aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta .........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 taagccgaaaaggacataggacgatggccttgcttgttttcaggcgaatacgtctaagaccatggacgcttggctcggaggggctgccgaccagcttcagggacagatatcgagtgccaagataccgctaacttctccgaacgcatcgagcagaaaagttcattccctataaaatgattgcaggaacaaactggcagtgggtattttactatatcttcaaactcctcctctttgtcatcataggagtcttcaccgctcctttcacctgcttgtgggctgtctatagagttatcagggcttttcgataagaggtggtaattctccaactaatagttggagaattacgaatcaacattttatggacagaatgaaaaacttatagaaaaatt Mask Tandem Repeat Region ================================================ aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Find is-nt database================================================ Query_seq: TF1303:TF1304|TF1303:TF1304:conserved hypothetical protein:conserved hypothetical protein:->->:1384759..1385147 389 aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1303:TF1304|TF1303:TF1304:conserved hypothetical protein:conserved hypothetical protein:->->:1384759..1385147 389 aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1303:TF1304|TF1303:TF1304:conserved hypothetical protein:conserved hypothetical protein:->->:1384759..1385147 389 aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 64 End: 333 ............................................................... M E N Y H L L S K S P D N S I D S P Q A G E R S G E D S Y D D K E E E F E D I V K Y P L P V C S C N H F I G N E L F C S ........................................................ Protein_Len: 35 Strand: + Start: 284 End: 388 ........................................................................................................................................................................................................................................................................................... M S L K L V G S P S E P S V H G L R R I R L K T S K A I V L C P F R L . Protein_Len: 35 Strand: - Start: 262 End: 366 ..................................................................................................................................................................................................................................................................... R Y R P V R Y R D R F S T P L G E S G L T W P R L R I R R F V L L A M ....................... Protein_Len: 36 Strand: - Start: 221 End: 328 ............................................................................................................................................................................................................................ L S H V K R S S A N P S T L P I K A S S I Q G Q L Q D A A G G L W A D M ............................................................. Protein_Len: 35 Strand: - Start: 216 End: 320 ....................................................................................................................................................................................................................... K I P F S S K Q E I R E S F N A T D Q C E I D T G S A P R C G R R A M ..................................................................... Protein_Len: 31 Strand: - Start: 107 End: 199 .......................................................................................................... L C G V L L H F S R H L S R H H C L P P T Q L Y L L I G V A M .............................................................................................................................................................................................. Protein_Len: 48 Strand: - Start: 85 End: 228 .................................................................................... R F A R I V R Y V A W L C T F P A T F V G I I V F L L L K F I Y Y F V W Q W N T G A I M K Y P M ................................................................................................................................................................. aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta 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================================================ aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -9.7 Tail_Score: -3.28791 Start: 40 End: 81 Full_Region: TGTCCATAAAATGTT GATTCGTAATTCTCCAACT ATT AGTTGGAGAATTACCACCTC TTATCGAAAAGCCCT .......................................GATTCGTAATTCTCCAACTATTAGTTGGAGAATTACCACCTC.................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -12.5 Tail_Score: -2.52623 Start: 42 End: 78 Full_Region: TCCATAAAATGTTGA TTCGTAATTCTCCAACT ATT AGTTGGAGAATTACCAC CTCTTATCGAAAAGC .........................................TTCGTAATTCTCCAACTATTAGTTGGAGAATTACCAC....................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF1303:TF1304|TF1303:TF1304:conserved hypothetical protein:conserved hypothetical protein:->->:1384759..1385147 389 aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta Intra-Species Hit: Count: 1 Min: 1 Max: 389 Len: 389 Subject: tfor_TF1303_TF1304|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1384759,1385147]|389 HSP 1 e-value: 0.0 bit: 771.0 Len: 389 Query Start:1 Query End:389 Subject Strand: POSITIVE Subject Start: 1 Subject End: 389 aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta aatttttctataagtttttcattctgtccataaaatgttgattcgtaattctccaactattagttggagaattaccacctcttatcgaaaagccctgataactctatagacagcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttctgctcgatgcgttcggagaagttagcggtatcttggcactcgatatctgtccctgaagctggtcggcagcccctccgagccaagcgtccatggtcttagacgtattcgcctgaaaacaagcaaggccatcgtcctatgtccttttcggctta HSP 2 e-value: 4.0E-6 bit: 54.0 Len: 31 Query Start:45 Query End:75 Subject Strand: NEGATIVE Subject Start: 45 Subject End: 75 ............................................gtaattctccaactattagttggagaattac.......................................................................................................................................................................................................................................................................................................................... ............................................gtaattctccaactaatagttggagaattac.......................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 1 Min: 113 Max: 237 Len: 125 Subject: pint_PI0242_PI0243|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[240288,240645]|358 HSP 1 e-value: 5.0E-24 bit: 113.0 Len: 125 Query Start:113 Query End:237 Subject Strand: POSITIVE Subject Start: 134 Subject End: 257 ................................................................................................................gcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttc........................................................................................................................................................ ................................................................................................................gcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttata-ggaatgtacttttc........................................................................................................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCCACAAGCAGGUGAAAGGAGCGGUGAAGACUCCUAUGAUGACAAAGAGGAGGAGUUUGAAGAUAUAGUAAAAUACCCACUGCCAGUUUGUUCCUGCAAUCAUUUUAUAGGGAAUGAACUUUUC ........(((((.(((..(.((((((.((((((((....(.....)....)))))))).........(((...))).)))))))..)))...)))))..(((((((....)))))))....... (-30.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAGUUCAUUCCCUAUAAAAUGAUUGCAGGAACAAACUGGCAGUGGGUAUUUUACUAUAUCUUCAAACUCCUCCUCUUUGUCAUCAUAGGAGUCUUCACCGCUCCUUUCACCUGCUUGUGGGC .............(((((((.......(((((.(((((..((.((.((((..................))))))))..)))))......((((((.......))))))....)))))))))))). (-27.08) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 47 4 54 12 tfor:TF1402|5end_cation_efflux_system_protein_1477922..1478152_POSITIVE 311 49 1 186 124 tfor:TF2342|5end_glutathione_peroxidase_2505963..2506193_POSITIVE 308 70 24 72 14 tfor:TF1844|5end_hypothetical_protein_1996389..1996619_POSITIVE 308 48 1 187 125 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 307 49 2 103 39 tfor:TF2130|5end_conserved_hypothetical_protein;_possible_permease_2306486..2306716_POSITIVE 304 46 1 222 158 tfor:TF0922|5end_MATE_efflux_family_protein_959588..959818_POSITIVE 304 60 12 46 1 tfor:TF0634|5end_hypothetical_protein_668120..668350_POSITIVE 302 60 12 73 7 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 302 66 23 56 18 tfor:TF0663|5end_conserved_hypothetical_protein_708450..708680_POSITIVE 301 45 7 99 60 tfor:TF0142|5end_subtilisin-like_serine_proteinase_149740..149970_POSITIVE 296 50 1 161 119 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 292 65 22 75 29 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 291 43 6 228 190 tfor:TF2507|5end_ATP-dependent_DNA_helicase_2683928..2684158_POSITIVE 290 120 74 51 8 tfor:TF0762|5end_chromate_transport_protein_809124..809354_POSITIVE 289 38 2 58 10 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 284 60 11 104 43 tfor:TF2068|5end_N-acetylneuraminic_acid_synthetase_2234024..2234254_POSITIVE 282 27 2 231 202 tfor:TF0321|5end_glycosyltransferase_347438..347668_POSITIVE 280 66 22 215 168 tfor:TF2707|5end_glutamine_amidotransferase_2878305..2878535_POSITIVE 280 49 4 86 44 tfor:TF1675|5end_hypothetical_protein_1788602..1788832_POSITIVE 279 59 11 68 9 tfor:TF2521|5end_TPR-repeat-containing_protein_2699737..2699967_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 47 4 77 35 tfor:TF1403|3end_hypothetical_protein_1478025..1478175_POSITIVE 307 49 2 106 42 tfor:TF2129|3end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2306569..2306719_POSITIVE 302 66 23 80 42 tfor:TF0662|3end_hypothetical_protein_708554..708704_POSITIVE 301 45 7 109 70 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 292 68 22 113 66 tfor:TF1401|3end_Holliday_junction_DNA_helicase_1477610..1477760_POSITIVE 284 60 11 104 43 tfor:TF2067|3end_UDP-N-acetylglucosamine_2-epimerase_2234104..2234254_POSITIVE 281 29 1 144 105 tfor:TF1448|3end_possible_competence_protein_1533050..1533200_POSITIVE 280 49 4 99 57 tfor:TF1674|3end_ATP_synthase,_A_subunit_1788695..1788845_POSITIVE 279 59 11 75 16 tfor:TF2520|3end_conserved_hypothetical_protein_2699824..2699974_POSITIVE 275 50 1 70 17 tfor:TF2103|3end_transposase_2275417..2275567_POSITIVE 275 51 12 38 3 tfor:TF2036|3end_possible_pyruvate_formate-lyase_activating_enzyme_2196837..2196987_POSITIVE 275 50 1 70 17 tfor:TF0352|3end_transposase_element_371527..371677_POSITIVE 274 43 1 74 22 tfor:TF2370|3end_tRNA_delta-2_isopentenylpyrophosphate_transferase_2537044..2537194_POSITIVE 274 47 1 106 55 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 269 43 1 66 28 tfor:TF2693|3end_possible_aminotransferase_2869720..2869870_POSITIVE 266 39 3 133 97 tfor:TF2991|3end_conserved_hypothetical_protein_3209107..3209257_POSITIVE 264 116 77 140 94 tfor:TF2845|3end_hypothetical_protein_3034757..3034907_POSITIVE 264 48 1 97 54 tfor:TF0606|3end_signal_peptidase_II_637504..637654_POSITIVE 263 60 12 102 53 tfor:TF3155|3end_glycosyltransferase,_group_2_family_protein_3391444..3391594_POSITIVE 263 54 12 69 27 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE