Origin IGS: taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca .........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 tgaccttacaacccatcagacgtacggacctcccgtattccgacgggagcggtaagctcttacctcaccttttcacccttacctcgccttacggcgcggcggttcttttctgctacgttactctgccctcgcagacagcttcccgttaggaaggatggcgccctgtgttgcccggactttcctctcatccccaaaagaataagcgacagaccggtctgctgccaagagacaaagatagtggaaataatcgattcaacgcatttgggggcgctaaaaaacgtgcgccataagcgtgtttgttcgtgcggaagattgcctctta Mask Tandem Repeat Region ================================================ taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Find is-nt database================================================ Query_seq: TF0815:TF0816|TF0815:TF0816:conserved hypothetical protein:hypothetical protein:->->:874035..874356 322 taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0815:TF0816|TF0815:TF0816:conserved hypothetical protein:hypothetical protein:->->:874035..874356 322 taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0815:TF0816|TF0815:TF0816:conserved hypothetical protein:hypothetical protein:->->:874035..874356 322 taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 10 End: 135 ......... M F R T N K H A Y G A R F L A P P N A L N R L F P L S L S L G S R P V C R L F F W G ........................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 71 End: 202 ...................................................................... M D Y F H Y L C L L A A D R S V A Y S F G D E R K V R A T Q G A I L P N G K L S A R A E ........................................................................................................................ Protein_Len: 60 Strand: + Start: 75 End: 260 .......................................................................... M I S T I F V S W Q Q T G L S L I L L G M R G K S G Q H R A P S F L T G S C L R G Q S N V A E K N R R A V R R G K G E K .............................................................. Protein_Len: 44 Strand: - Start: 177 End: 308 ................................................................................................................................................................................ R S A T Q S P L T V Y C F L V A A G Y P S T L T F L H P L L K G S G D S Y P L D T R R M .............. Protein_Len: 30 Strand: - Start: 124 End: 213 ........................................................................................................................... E K P S S L F T R A V C P A M R G L P F S D A L A S Y R L M ............................................................................................................. Protein_Len: 41 Strand: - Start: 36 End: 158 ................................... P A R K K A G G F A N F R N N G S D K D R P L L G T Q R K N K Q P H S S L G P L M .................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 2 End: 286 . V P R D S I R K P I L P F D P C C L A G D K R V P L Q R R P C L L T A S F F R R A T L R P L P S F T L Y S S V A G T P M .................................... taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca 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================================================ taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0815:TF0816|TF0815:TF0816:conserved hypothetical protein:hypothetical protein:->->:874035..874356 322 taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Intra-Species Hit: Count: 1 Min: 1 Max: 322 Len: 322 Subject: tfor_TF0815_TF0816|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[874035,874356]|322 HSP 1 e-value: 0.0 bit: 638.0 Len: 322 Query Start:1 Query End:322 Subject Strand: POSITIVE Subject Start: 1 Subject End: 322 taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca taagaggcaatcttccgcacgaacaaacacgcttatggcgcacgttttttagcgcccccaaatgcgttgaatcgattatttccactatctttgtctcttggcagcagaccggtctgtcgcttattcttttggggatgagaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgtaaggcgaggtaagggtgaaaaggtgaggtaagagcttaccgctcccgtcggaatacgggaggtccgtacgtctgatgggttgtaaggtca Inter-species Hit: Count: 1 Min: 139 Max: 272 Len: 134 Subject: NC_004663_BT_1314_BT_1315|dipeptidyl-peptidase VI:ribonuclease BN|NEGATIVE:POSITIVE|[1639905,1640398]|494 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 134 Query Start:139 Query End:272 Subject Strand: POSITIVE Subject Start: 136 Subject End: 271 ..........................................................................................................................................gaggaaagtccgggcaacacagggcgccatccttcctaacgggaagctgtctgcgagggcagagtaacgtagcagaaaagaaccgccgcgccgt--aaggcgaggtaagggtgaaaaggtgaggtaagagcttacc.................................................. ..........................................................................................................................................gaggaaagtccgggcaacacagagcatcctacttcctaacagaaagctgtccgcgagggtagagtaacgtagaagaaaataaccgccgctcctttcggggagaggtaagggtgagaaggtggggtaagagcctacc.................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGAAAGUCCGGGCAACACAGGGCGCCAUCCUUCCUAACGGGAAGCUGUCUGCGAGGGCAGAGUAACGUAGCAGAAAAGAACCGCCGCGCCGUAAGGCGAGGUAAGGGUGAAAAGGUGAGGUAAGAGCUUACC .......((((.(....)...))))..(((((((....(((..(..((((((....))))))..)..)))..............(((.((((....)))).))))))))))....((((((.......)))))) (-46.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAAGCUCUUACCUCACCUUUUCACCCUUACCUCGCCUUACGGCGCGGCGGUUCUUUUCUGCUACGUUACUCUGCCCUCGCAGACAGCUUCCCGUUAGGAAGGAUGGCGCCCUGUGUUGCCCGGACUUUCCUC ((.(((((................(((....((.((((....)))).)).)))..................(((((....))))).))))).))...(((((((.(((.((........)))))..))))))). (-35.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 98 51 62 7 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 431 89 41 159 103 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 429 59 11 54 12 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 421 69 24 44 4 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 420 90 46 69 12 tfor:TF2616|5end_outer_membrane_protein,_TonB_dependent_receptor_2791470..2791700_POSITIVE 418 60 11 85 37 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 402 69 23 51 9 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 402 59 13 126 77 tfor:TF2435|5end_DNA_repair_protein_radC_2614352..2614582_POSITIVE 400 60 12 74 33 tfor:TF0687|5end_hypothetical_protein_732226..732456_POSITIVE 400 60 12 47 6 tfor:TF0686|5end_hypothetical_protein_732199..732429_POSITIVE 399 70 21 127 67 tfor:TF1312|5end_hypothetical_protein_1388465..1388695_POSITIVE 399 70 21 127 67 tfor:TF1311|5end_hypothetical_protein_1388242..1388472_POSITIVE 399 46 3 218 169 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 388 80 31 222 161 tfor:TF0474|5end_outer_membrane_efflux_protein_492104..492334_POSITIVE 387 56 11 198 143 tfor:TF1350|5end_possible_transcriptional_regulator_1429639..1429869_POSITIVE 386 123 82 51 5 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 386 123 82 161 115 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 386 116 74 105 68 tfor:TF0797|5end_conserved_hypothetical_protein_853296..853526_POSITIVE 385 100 51 83 28 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 385 50 1 206 153 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 98 51 56 1 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 423 60 11 117 52 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 402 69 23 51 9 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 402 59 13 57 8 tfor:TF2434|3end_conserved_hypothetical_protein_2614363..2614513_POSITIVE 399 46 3 54 5 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 399 70 21 140 80 tfor:TF1311|3end_hypothetical_protein_1388558..1388708_POSITIVE 399 70 21 140 80 tfor:TF1310|3end_hypothetical_protein_1388335..1388485_POSITIVE 396 100 52 83 21 tfor:TF0362|3end_hypothetical_protein_380199..380349_POSITIVE 395 59 12 42 1 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 387 70 21 142 96 tfor:TF3141|3end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3376267..3376417_POSITIVE 385 50 1 115 62 tfor:TF1719|3end_ribonuclease_R_1843668..1843818_POSITIVE 385 67 24 50 9 tfor:TF0020|3end_possible_glycoprotein_endopeptidase_16029..16179_POSITIVE 384 49 9 52 8 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 379 68 24 87 30 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 373 100 52 83 21 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 370 70 21 140 80 tfor:TF1312|3end_hypothetical_protein_1388781..1388931_POSITIVE 368 37 3 66 22 tfor:TF2662|3end_hypothetical_protein_2837131..2837281_POSITIVE 367 75 31 58 13 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 365 59 11 103 47 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 365 55 12 55 10 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE