Origin IGS: gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccccccatcgccggccctttcctattctgcttttcgacagaaggcaaggagaaaaaacaagaagagagcgttgcacgaccgttagcggtgcaacgctctcttttcatttcatctttttttgctcggttgccgcagatgttatttgctccggaggtctttctc Mask Tandem Repeat Region ================================================ gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Find is-nt database================================================ Query_seq: PG0129:PG0130|PG0129:PG0130:mannosyltransferase:phosphoglyceromutase:-><-:151850..152011 162 gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0129:PG0130|PG0129:PG0130:mannosyltransferase:phosphoglyceromutase:-><-:151850..152011 162 gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0129:PG0130|PG0129:PG0130:mannosyltransferase:phosphoglyceromutase:-><-:151850..152011 162 gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 26 End: 160 ......................... M C G N R A K K D E M K R E R C T A N G R A T L S S C F F S L P S V E K Q N R K G P A M G .. Protein_Len: 46 Strand: - Start: 2 End: 139 . S L G G S C I V D A A V S C F F I F H F S L T A G S V T T C R E R R T K E G Q R R D F L L M ....................... Protein_Len: 52 Strand: - Start: 1 End: 156 L F V E P A F L M Q P L R A F F S S I F L S R Q V A L P R A V S E E Q K K E K G E T S F C F L F P G A M ...... gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg 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================================================ gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.7 Tail_Score: -5.37345 Start: 57 End: 105 Full_Region: CAAAAAAAGATGAAA TGAAAAGAGAGCGTTGCACCGCT AAC GGTCGTGCAACGCTCTCTTCTTG TTTTTTCTCCTTGCC ........................................................TGAAAAGAGAGCGTTGCACCGCTAACGGTCGTGCAACGCTCTCTTCTTG......................................................... TransTerm Strand: + Conf: 100 HP_score: -16.4 Tail_Score: -4.75967 Start: 60 End: 102 Full_Region: AAAAAGATGAAATGA AAAGAGAGCGTTGCACCGCT AAC GGTCGTGCAACGCTCTCTTC TTGTTTTTTCTCCTT ...........................................................AAAGAGAGCGTTGCACCGCTAACGGTCGTGCAACGCTCTCTTC............................................................ TransTerm Strand: + Conf: 100 HP_score: -18.1 Tail_Score: -4.44307 Start: 63 End: 99 Full_Region: AAGATGAAATGAAAA GAGAGCGTTGCACCGCT AAC GGTCGTGCAACGCTCTC TTCTTGTTTTTTCTC ..............................................................GAGAGCGTTGCACCGCTAACGGTCGTGCAACGCTCTC............................................................... TransTerm Strand: - Conf: 100 HP_score: -15.2 Tail_Score: -4.61284 Start: 63 End: 99 Full_Region: gagaaaaaacaagaa gagagcgttgcacgac cgtta gcggtgcaacgctctc ttttcatttcatctt ..............................................................gagagcgttgcacgaccgttagcggtgcaacgctctc............................................................... Find igs database================================================ Query_seq: PG0129:PG0130|PG0129:PG0130:mannosyltransferase:phosphoglyceromutase:-><-:151850..152011 162 gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_002950_PG0129_PG0130|mannosyltransferase:phosphoglyceromutase|PO SITIVE:NEGATIVE|[151850,152011]|162 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 gagaaagacctccggagcaaataacatctgcggcaaccgagcnnnnnnngatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg gagaaagacctccggagcaaataacatctgcggcaaccgagcaaaaaaagatgaaatgaaaagagagcgttgcaccgctaacggtcgtgcaacgctctcttcttgttttttctccttgccttctgtcgaaaagcagaataggaaagggccggcgatgggggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAAGACCUCCGGAGCAAAUAACAUCUGCGGCAACCGAGCAAAAAAAGAUGAAAUGAAAAGAGAGCGUUGCACCGCUAACGGUCGUGCAACGCUCUCUUCUUGUUUUUUCUCCUUGCCUUCUGUCGAAAAGCAGAAUAGGAAAGGGCCGGCGAUGGGGGG ........((((((..((............((((..............(((.((((..(.(((((((((((((((.((.....)).))))))))))))))).)..)))).)))((((.((((((((......)))))..))).))))))))))..)))))). (-63.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCCCCAUCGCCGGCCCUUUCCUAUUCUGCUUUUCGACAGAAGGCAAGGAGAAAAAACAAGAAGAGAGCGUUGCACGACCGUUAGCGGUGCAACGCUCUCUUUUCAUUUCAUCUUUUUUUGCUCGGUUGCCGCAGAUGUUAUUUGCUCCGGAGGUCUUUCUC ......(((.((((..(........(((((....((((....((((((((((..(((..(((((((((((((((...((((....)))))))))))))))))))..)))..))))..))))))..))))..)))))........)..)))).)))....... (-55.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 158 111 54 19 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 382 100 63 168 127 NC_002950:PG0191|5end_outer_membrane_protein,_putative_226858..227088_POSITIVE 381 106 62 122 75 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 381 128 81 165 105 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 360 158 113 203 152 NC_002950:PG2047|5end_helicase,_putative_2148043..2148273_NEGATIVE 358 160 118 228 177 NC_002950:PG0568|5end_elongation_factor_P_624565..624795_NEGATIVE 357 159 112 57 5 NC_002950:PG0027|5end_hypothetical_protein_32681..32911_POSITIVE 352 107 62 84 31 NC_002950:PG1928|5end_50S_ribosomal_protein_L14_2019945..2020175_NEGATIVE 351 101 64 131 95 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 350 159 111 192 151 NC_002950:PG1852|5end_exonuclease_1951973..1952203_NEGATIVE 347 155 111 133 82 NC_002950:PG1307|5end_glucose-inhibited_division_protein_B_1387849..1388079_NEGATIVE 347 128 81 225 183 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 346 160 111 88 21 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 339 160 116 52 12 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 338 102 63 191 146 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 333 160 111 231 193 NC_002950:PG2110|5end_thiamine_biosynthesis_protein_ThiC_2221212..2221442_NEGATIVE 333 129 82 196 143 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 332 160 114 79 15 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 330 155 113 65 22 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 327 159 115 33 1 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 120 72 59 1 NC_002950:PG0129|3end_mannosyltransferase_151789..151939_POSITIVE 382 100 63 150 109 NC_002950:PG0190|3end_undecaprenyl_diphosphate_synthase_226920..227070_POSITIVE 382 130 83 73 21 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 381 106 62 108 61 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 377 110 61 84 33 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 368 119 75 139 95 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE 366 149 101 150 96 NC_002950:PG1706|3end_hypothetical_protein_1793849..1793999_NEGATIVE 360 158 113 112 61 NC_002950:PG2048|3end_hypothetical_protein_2148134..2148284_NEGATIVE 358 158 111 137 88 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 358 160 118 96 45 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 352 107 62 82 29 NC_002950:PG1929|3end_ribosomal_protein_S17_2019947..2020097_NEGATIVE 347 155 111 99 48 NC_002950:PG1308|3end_hypothetical_protein_1387883..1388033_NEGATIVE 334 124 82 108 53 NC_002950:PG0995|3end_hypothetical_protein_1055469..1055619_NEGATIVE 333 159 111 63 5 NC_002950:PG1608|3end_methylmalonyl-CoA_decarboxylase,_beta_subunit_1688685..1688835_NEGATIVE 333 110 62 73 15 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 332 120 74 54 5 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 332 160 114 72 8 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 330 130 82 82 33 NC_002950:PG0431|3end_hypothetical_protein_469174..469324_POSITIVE 327 159 116 58 22 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 327 160 114 77 37 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE