Origin IGS: cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa .........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 ttgctcttgttattgatgctttatcaacagtcggcgcaaaaataataaatataatcgagaatgtagtttttttgtatctttgcaccccgaaaagcaaagataagcacgactttgagagagaaaaaacgaacagtttctccctttccgtgccacaatctctgccccggatttaaaaaaagaacaacgagaaaag Mask Tandem Repeat Region ================================================ cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Find is-nt database================================================ Query_seq: TF2655:TF2656|TF2655:TF2656:DNA topoisomerase I:valyl-tRNA synthetase:->->:2827023..2827215 193 cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2655:TF2656|TF2655:TF2656:DNA topoisomerase I:valyl-tRNA synthetase:->->:2827023..2827215 193 cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2655:TF2656|TF2655:TF2656:DNA topoisomerase I:valyl-tRNA synthetase:->->:2827023..2827215 193 cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 39 End: 167 ...................................... M W H G K G E T V R F F S L K V V L I F A F R G A K I Q K N Y I L D Y I Y Y F C A D C .......................... Protein_Len: 48 Strand: + Start: 38 End: 181 ..................................... M V A R K G R N C S F F L S Q S R A Y L C F S G C K D T K K L H S R L Y L L F L R R L L I K H Q ............ Protein_Len: 56 Strand: + Start: 25 End: 192 ........................ M R G R D C G T E R E K L F V F S L S K S C L S L L F G V Q R Y K K T T F S I I F I I F A P T V D K A S I T R A . Protein_Len: 53 Strand: - Start: 24 End: 182 ....................... I R P L S Q P V S L S F S N T K E R E F D H K D K S K P T C L Y L F V V N E I I N I I K A G V T S L A D M ........... Protein_Len: 39 Strand: - Start: 2 End: 118 . K R T T R K K F G P C L N H C P F P S V T R K K E R L T T S I K A K R P A F M ........................................................................... cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa 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================================================ cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.6 Tail_Score: -2.88861 Start: 54 End: 74 Full_Region: TTGTGGCACGGAAAG GGAGAAAC TGTTC GTTTTTTC TCTCTCAAAGTCGTG .....................................................GGAGAAACTGTTCGTTTTTTC....................................................................................................................... Find igs database================================================ Query_seq: TF2655:TF2656|TF2655:TF2656:DNA topoisomerase I:valyl-tRNA synthetase:->->:2827023..2827215 193 cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Intra-Species Hit: Count: 1 Min: 1 Max: 193 Len: 193 Subject: tfor_TF2655_TF2656|DNA topoisomerase I:valyl-tRNA synthetase|POSITIVE:POSITIVE|[2827023,2827215]|193 HSP 1 e-value: 2.0E-80 bit: 299.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 cttttctcgttgttcnnnnnnnaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacnnnnnnnctacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa cttttctcgttgttctttttttaaatccggggcagagattgtggcacggaaagggagaaactgttcgttttttctctctcaaagtcgtgcttatctttgcttttcggggtgcaaagatacaaaaaaactacattctcgattatatttattatttttgcgccgactgttgataaagcatcaataacaagagcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCUCGUUGUUCUUUUUUUAAAUCCGGGGCAGAGAUUGUGGCACGGAAAGGGAGAAACUGUUCGUUUUUUCUCUCUCAAAGUCGUGCUUAUCUUUGCUUUUCGGGGUGCAAAGAUACAAAAAAACUACAUUCUCGAUUAUAUUUAUUAUUUUUGCGCCGACUGUUGAUAAAGCAUCAAUAACAAGAGCAA .........((((((((.........(((((((((((((...(((((((..(((((((((..........))))))))).....))))))).)))))))))..))))((((((((((((..............................))))))))))))...(((((((.....)))))))..)))))))) (-56.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUCUUGUUAUUGAUGCUUUAUCAACAGUCGGCGCAAAAAUAAUAAAUAUAAUCGAGAAUGUAGUUUUUUUGUAUCUUUGCACCCCGAAAAGCAAAGAUAAGCACGACUUUGAGAGAGAAAAAACGAACAGUUUCUCCCUUUCCGUGCCACAAUCUCUGCCCCGGAUUUAAAAAAAGAACAACGAGAAAAG ....(((((((.((((((...))))))...((((.((....(((.....)))....((((.(((..........(((((((((..........))))))))).(((((.....(((.((((((..........)))))).)))..))))).))).)))).)).))))...............))))))).... (-42.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 80 32 79 32 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 395 48 6 135 87 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 369 88 41 149 84 tfor:TF0051|5end_hypothetical_protein_57327..57557_POSITIVE 364 66 26 209 175 tfor:TF1804|5end_hypothetical_protein_1947101..1947331_POSITIVE 346 49 5 162 129 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 344 65 25 136 102 tfor:TF2122|5end_NAD-specific_glutamate_dehydrogenase_2292734..2292964_POSITIVE 342 64 28 157 120 tfor:TF1619|5end_riboflavin_synthase,_beta_subunit_1733948..1734178_POSITIVE 341 114 74 64 23 tfor:TF1542|5end_transcriptional_regulator_1649105..1649335_POSITIVE 336 67 28 152 106 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 336 67 28 112 66 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 332 70 28 188 151 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 328 110 64 162 115 tfor:TF3094|5end_translation_elongation_factor_Ts_3326122..3326352_POSITIVE 325 108 61 115 58 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 325 112 73 59 12 tfor:TF0113|5end_4-deoxy-L-threo-5-hexosulose-uronate_ketol-isomerase_123149..123379_POSITIVE 324 68 26 91 41 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 324 70 26 137 99 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 323 67 27 193 143 tfor:TF1475|5end_glucose-6-phosphate_1-dehydrogenase_1568034..1568264_POSITIVE 323 49 2 226 171 tfor:TF1416|5end_outer_membrane_protein_1497576..1497806_POSITIVE 321 68 26 213 159 tfor:TF0997|5end_conserved_hypothetical_protein_1051475..1051705_POSITIVE 317 68 25 111 59 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 80 32 100 53 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 395 48 6 135 87 tfor:TF2788|3end_hypothetical_protein_2972511..2972661_POSITIVE 369 88 41 88 23 tfor:TF0049|3end_membrane-associated_HD_superfamily_hydrolase_57346..57496_POSITIVE 364 66 26 148 114 tfor:TF1803|3end_conserved_hypothetical_protein_1947120..1947270_POSITIVE 344 65 25 82 48 tfor:TF2120|3end_holliday_junction_endonuclease_2292760..2292910_POSITIVE 336 67 28 140 94 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 328 110 64 141 94 tfor:TF3093|3end_30S_ribosomal_protein_S2_3326181..3326331_POSITIVE 324 68 26 100 50 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 324 70 26 109 71 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 321 69 25 59 18 tfor:TF0007|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_3599..3749_POSITIVE 317 68 25 72 20 tfor:TF1462|3end_erythronate-4-phosphate_dehydrogenase_1553508..1553658_POSITIVE 315 120 71 140 87 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 311 111 74 45 7 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 310 116 75 59 19 tfor:TF3151|3end_glyoxalase_family_protein_3386705..3386855_POSITIVE 309 67 28 138 100 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 306 79 34 70 36 tfor:TF0860|3end_conserved_hypothetical_protein_913369..913519_POSITIVE 305 57 27 110 73 tfor:TF2272|3end_conserved_hypothetical_protein_2436514..2436664_POSITIVE 305 49 2 149 101 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 304 70 27 127 82 tfor:TF2734|3end_conserved_hypothetical_protein_2916738..2916888_POSITIVE 302 67 27 139 97 tfor:TF2103|3end_transposase_2275417..2275567_POSITIVE