Multiple sequence alignment - TraesCS6D01G147800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G147800 chr6D 100.000 4545 0 0 1 4545 120671246 120666702 0.000000e+00 8394
1 TraesCS6D01G147800 chr6B 91.753 2983 160 35 700 3623 212417892 212420847 0.000000e+00 4067
2 TraesCS6D01G147800 chr6B 94.312 545 28 3 1 543 212417201 212417744 0.000000e+00 832
3 TraesCS6D01G147800 chr6A 89.065 1829 136 36 699 2481 158943375 158941565 0.000000e+00 2211
4 TraesCS6D01G147800 chr6A 95.771 1135 42 4 2507 3637 158941505 158940373 0.000000e+00 1825
5 TraesCS6D01G147800 chr6A 87.537 682 38 21 1 670 158944018 158943372 0.000000e+00 745
6 TraesCS6D01G147800 chr2D 93.859 863 43 5 3638 4497 598854708 598853853 0.000000e+00 1291
7 TraesCS6D01G147800 chr2D 100.000 60 0 0 4486 4545 598853843 598853784 1.340000e-20 111
8 TraesCS6D01G147800 chr4B 93.048 863 49 6 3638 4497 664526678 664525824 0.000000e+00 1251
9 TraesCS6D01G147800 chr4B 92.326 417 27 5 4081 4494 83306326 83305912 5.070000e-164 588
10 TraesCS6D01G147800 chrUn 92.627 868 50 8 3637 4497 234087904 234087044 0.000000e+00 1236
11 TraesCS6D01G147800 chrUn 92.512 868 52 8 3637 4497 408354561 408353700 0.000000e+00 1230
12 TraesCS6D01G147800 chrUn 92.166 868 55 8 3637 4497 215573296 215572435 0.000000e+00 1214
13 TraesCS6D01G147800 chrUn 92.254 865 54 8 3637 4494 374770230 374771088 0.000000e+00 1214
14 TraesCS6D01G147800 chrUn 91.132 857 64 10 3638 4490 305638507 305639355 0.000000e+00 1151
15 TraesCS6D01G147800 chr2B 92.343 862 54 6 3637 4494 432931324 432932177 0.000000e+00 1216
16 TraesCS6D01G147800 chr3B 91.744 860 62 5 3638 4494 762509350 762510203 0.000000e+00 1186
17 TraesCS6D01G147800 chr1A 91.866 418 28 6 4081 4494 65898792 65898377 3.050000e-161 579
18 TraesCS6D01G147800 chr1B 88.798 491 27 6 4081 4545 377838979 377839467 1.100000e-160 577
19 TraesCS6D01G147800 chr7D 92.562 242 16 1 4255 4494 430098340 430098099 3.370000e-91 346
20 TraesCS6D01G147800 chr7D 87.066 317 18 2 4252 4545 145240371 145240687 2.030000e-88 337
21 TraesCS6D01G147800 chr7D 98.571 140 2 0 4353 4492 16901782 16901643 9.760000e-62 248
22 TraesCS6D01G147800 chr3D 85.449 323 18 2 4252 4545 39043025 39043347 4.420000e-80 309
23 TraesCS6D01G147800 chr3D 79.481 424 52 10 4147 4545 446117990 446118403 7.490000e-68 268


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G147800 chr6D 120666702 120671246 4544 True 8394.000000 8394 100.0000 1 4545 1 chr6D.!!$R1 4544
1 TraesCS6D01G147800 chr6B 212417201 212420847 3646 False 2449.500000 4067 93.0325 1 3623 2 chr6B.!!$F1 3622
2 TraesCS6D01G147800 chr6A 158940373 158944018 3645 True 1593.666667 2211 90.7910 1 3637 3 chr6A.!!$R1 3636
3 TraesCS6D01G147800 chr2D 598853784 598854708 924 True 701.000000 1291 96.9295 3638 4545 2 chr2D.!!$R1 907
4 TraesCS6D01G147800 chr4B 664525824 664526678 854 True 1251.000000 1251 93.0480 3638 4497 1 chr4B.!!$R2 859
5 TraesCS6D01G147800 chrUn 234087044 234087904 860 True 1236.000000 1236 92.6270 3637 4497 1 chrUn.!!$R2 860
6 TraesCS6D01G147800 chrUn 408353700 408354561 861 True 1230.000000 1230 92.5120 3637 4497 1 chrUn.!!$R3 860
7 TraesCS6D01G147800 chrUn 215572435 215573296 861 True 1214.000000 1214 92.1660 3637 4497 1 chrUn.!!$R1 860
8 TraesCS6D01G147800 chrUn 374770230 374771088 858 False 1214.000000 1214 92.2540 3637 4494 1 chrUn.!!$F2 857
9 TraesCS6D01G147800 chrUn 305638507 305639355 848 False 1151.000000 1151 91.1320 3638 4490 1 chrUn.!!$F1 852
10 TraesCS6D01G147800 chr2B 432931324 432932177 853 False 1216.000000 1216 92.3430 3637 4494 1 chr2B.!!$F1 857
11 TraesCS6D01G147800 chr3B 762509350 762510203 853 False 1186.000000 1186 91.7440 3638 4494 1 chr3B.!!$F1 856

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
95 96 0.179936 ATGCAGCCCTTCAGCTACTC 59.820 55.0 0.0 0.0 42.61 2.59 F
552 565 0.904649 CTGGTGGGTACAGATGAGCA 59.095 55.0 0.0 0.0 38.20 4.26 F
1190 1301 0.108233 GCTCTGCTTCTCCCAGTGAG 60.108 60.0 0.0 0.0 42.90 3.51 F
2238 2363 0.252103 ACCCGTGTGGACTGTAGGAT 60.252 55.0 0.0 0.0 37.49 3.24 F
2434 2559 0.319211 TCAACGTCTACGGCAAGGTG 60.319 55.0 7.5 0.0 44.95 4.00 F
2448 2574 0.320160 AAGGTGCGTCCGGTAACTTC 60.320 55.0 0.0 0.0 32.25 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1175 0.322277 AGAACACAGGCCAGATGCAG 60.322 55.000 5.01 0.0 43.89 4.41 R
2434 2559 0.165295 GCAAAGAAGTTACCGGACGC 59.835 55.000 9.46 0.0 0.00 5.19 R
2499 2625 0.463295 CTGCTTCGACTGCCATCCAT 60.463 55.000 7.07 0.0 0.00 3.41 R
3345 3514 0.324738 TCGAAGATCTCCAGGCACCT 60.325 55.000 0.00 0.0 0.00 4.00 R
3458 3627 1.524621 CATGGACCTGACGATGGCC 60.525 63.158 0.00 0.0 0.00 5.36 R
4013 4195 1.876714 CAGCAAGCATCAATGGCGC 60.877 57.895 0.00 0.0 36.08 6.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 8.960591 CAATTACCCTACTGACTTTTGAATCAT 58.039 33.333 0.00 0.00 0.00 2.45
95 96 0.179936 ATGCAGCCCTTCAGCTACTC 59.820 55.000 0.00 0.00 42.61 2.59
152 153 3.869246 CCGAATGACCATGTACTTACACC 59.131 47.826 0.00 0.00 39.30 4.16
289 294 8.752766 AATGTATCAGAAAGAAATGTTTGCAG 57.247 30.769 0.00 0.00 0.00 4.41
337 342 2.955660 CTGCCAGTTGTACTTGGGAAAA 59.044 45.455 11.76 0.00 0.00 2.29
338 343 2.691011 TGCCAGTTGTACTTGGGAAAAC 59.309 45.455 11.76 0.00 0.00 2.43
394 400 4.757149 GCAAGACTTCCAACAAGACATACT 59.243 41.667 0.00 0.00 0.00 2.12
459 465 1.302949 CGCAATCCTGGGGGAGAAA 59.697 57.895 0.00 0.00 45.86 2.52
469 475 2.756760 CTGGGGGAGAAAATGTGATGTG 59.243 50.000 0.00 0.00 0.00 3.21
470 476 2.102578 GGGGGAGAAAATGTGATGTGG 58.897 52.381 0.00 0.00 0.00 4.17
471 477 1.478105 GGGGAGAAAATGTGATGTGGC 59.522 52.381 0.00 0.00 0.00 5.01
514 522 1.344763 ACGACTGGTTTCTTCCTCCTG 59.655 52.381 0.00 0.00 0.00 3.86
516 524 2.224305 CGACTGGTTTCTTCCTCCTGTT 60.224 50.000 0.00 0.00 34.48 3.16
552 565 0.904649 CTGGTGGGTACAGATGAGCA 59.095 55.000 0.00 0.00 38.20 4.26
594 646 4.337274 CGTGGATTTACCTCCAATAAACCC 59.663 45.833 0.00 0.00 46.66 4.11
674 726 9.798994 AGAAAAGCTTCTGCAGATATTTATTTG 57.201 29.630 19.04 1.18 40.54 2.32
675 727 8.937634 AAAAGCTTCTGCAGATATTTATTTGG 57.062 30.769 19.04 0.00 42.74 3.28
676 728 7.651027 AAGCTTCTGCAGATATTTATTTGGT 57.349 32.000 19.04 2.71 42.74 3.67
677 729 7.651027 AGCTTCTGCAGATATTTATTTGGTT 57.349 32.000 19.04 0.00 42.74 3.67
678 730 8.752005 AGCTTCTGCAGATATTTATTTGGTTA 57.248 30.769 19.04 0.00 42.74 2.85
679 731 8.844244 AGCTTCTGCAGATATTTATTTGGTTAG 58.156 33.333 19.04 7.57 42.74 2.34
680 732 8.624776 GCTTCTGCAGATATTTATTTGGTTAGT 58.375 33.333 19.04 0.00 39.41 2.24
682 734 9.905713 TTCTGCAGATATTTATTTGGTTAGTCT 57.094 29.630 19.04 0.00 0.00 3.24
683 735 9.547753 TCTGCAGATATTTATTTGGTTAGTCTC 57.452 33.333 13.74 0.00 0.00 3.36
684 736 9.553064 CTGCAGATATTTATTTGGTTAGTCTCT 57.447 33.333 8.42 0.00 0.00 3.10
685 737 9.905713 TGCAGATATTTATTTGGTTAGTCTCTT 57.094 29.630 0.00 0.00 0.00 2.85
805 858 4.248859 CAACACGGATGGATGATAGATCC 58.751 47.826 0.00 0.00 38.66 3.36
844 897 4.735822 GCACGCTAGAACTAGATACAACAG 59.264 45.833 12.33 0.00 35.21 3.16
937 1024 2.357517 AAGCGACCACAAGCTCGG 60.358 61.111 0.00 0.00 43.78 4.63
1007 1094 1.709147 CCTGCGCTCACCATGTAAGC 61.709 60.000 9.73 0.00 0.00 3.09
1052 1139 8.909423 AATTCTTCCTAAATTTGTATCCCCAA 57.091 30.769 0.00 0.00 0.00 4.12
1060 1147 3.495434 TTTGTATCCCCAAGTTCACGT 57.505 42.857 0.00 0.00 0.00 4.49
1126 1213 3.132629 CTGCATGACAGTTCATTCAGC 57.867 47.619 0.00 0.00 43.59 4.26
1128 1215 2.486592 TGCATGACAGTTCATTCAGCAG 59.513 45.455 0.00 0.00 40.79 4.24
1130 1217 3.686241 GCATGACAGTTCATTCAGCAGTA 59.314 43.478 0.00 0.00 40.79 2.74
1131 1218 4.154737 GCATGACAGTTCATTCAGCAGTAA 59.845 41.667 0.00 0.00 40.79 2.24
1132 1219 5.625251 CATGACAGTTCATTCAGCAGTAAC 58.375 41.667 0.00 0.00 40.79 2.50
1133 1220 4.065088 TGACAGTTCATTCAGCAGTAACC 58.935 43.478 0.00 0.00 0.00 2.85
1135 1222 4.655963 ACAGTTCATTCAGCAGTAACCAT 58.344 39.130 0.00 0.00 0.00 3.55
1136 1223 5.072741 ACAGTTCATTCAGCAGTAACCATT 58.927 37.500 0.00 0.00 0.00 3.16
1137 1224 5.182001 ACAGTTCATTCAGCAGTAACCATTC 59.818 40.000 0.00 0.00 0.00 2.67
1138 1225 5.181811 CAGTTCATTCAGCAGTAACCATTCA 59.818 40.000 0.00 0.00 0.00 2.57
1139 1226 5.769662 AGTTCATTCAGCAGTAACCATTCAA 59.230 36.000 0.00 0.00 0.00 2.69
1140 1227 6.265196 AGTTCATTCAGCAGTAACCATTCAAA 59.735 34.615 0.00 0.00 0.00 2.69
1148 1255 5.697633 AGCAGTAACCATTCAAATGCAAAAG 59.302 36.000 0.00 0.00 35.08 2.27
1152 1259 6.705825 AGTAACCATTCAAATGCAAAAGTTCC 59.294 34.615 0.00 0.00 35.08 3.62
1155 1262 4.453136 CCATTCAAATGCAAAAGTTCCCAG 59.547 41.667 0.00 0.00 35.08 4.45
1190 1301 0.108233 GCTCTGCTTCTCCCAGTGAG 60.108 60.000 0.00 0.00 42.90 3.51
1238 1355 3.521937 TCCTCCTCCACCGTATGAATTTT 59.478 43.478 0.00 0.00 0.00 1.82
1421 1541 2.223340 CGCCTACATTGACAAAGATGGC 60.223 50.000 15.79 15.79 34.00 4.40
1580 1700 1.068474 CGTCACCATTTCCTGTCGTC 58.932 55.000 0.00 0.00 0.00 4.20
1733 1853 1.812686 CGTTCAGAAGGGGACGGACA 61.813 60.000 0.00 0.00 32.29 4.02
1909 2034 1.066573 AGTTGAAGCTCTGATGGACGG 60.067 52.381 0.00 0.00 0.00 4.79
2222 2347 1.756430 GAGCCTCTCCATTTCAACCC 58.244 55.000 0.00 0.00 0.00 4.11
2224 2349 0.322546 GCCTCTCCATTTCAACCCGT 60.323 55.000 0.00 0.00 0.00 5.28
2225 2350 1.453155 CCTCTCCATTTCAACCCGTG 58.547 55.000 0.00 0.00 0.00 4.94
2226 2351 1.271379 CCTCTCCATTTCAACCCGTGT 60.271 52.381 0.00 0.00 0.00 4.49
2227 2352 1.806542 CTCTCCATTTCAACCCGTGTG 59.193 52.381 0.00 0.00 0.00 3.82
2228 2353 0.881118 CTCCATTTCAACCCGTGTGG 59.119 55.000 0.00 0.00 41.37 4.17
2229 2354 0.474614 TCCATTTCAACCCGTGTGGA 59.525 50.000 0.00 0.00 37.49 4.02
2231 2356 1.604604 CATTTCAACCCGTGTGGACT 58.395 50.000 0.00 0.00 37.49 3.85
2232 2357 1.266718 CATTTCAACCCGTGTGGACTG 59.733 52.381 0.00 0.00 37.49 3.51
2233 2358 0.253610 TTTCAACCCGTGTGGACTGT 59.746 50.000 0.00 0.00 37.49 3.55
2234 2359 1.121378 TTCAACCCGTGTGGACTGTA 58.879 50.000 0.00 0.00 37.49 2.74
2235 2360 0.677288 TCAACCCGTGTGGACTGTAG 59.323 55.000 0.00 0.00 37.49 2.74
2236 2361 0.320421 CAACCCGTGTGGACTGTAGG 60.320 60.000 0.00 0.00 37.49 3.18
2237 2362 0.470456 AACCCGTGTGGACTGTAGGA 60.470 55.000 0.00 0.00 37.49 2.94
2238 2363 0.252103 ACCCGTGTGGACTGTAGGAT 60.252 55.000 0.00 0.00 37.49 3.24
2239 2364 1.006281 ACCCGTGTGGACTGTAGGATA 59.994 52.381 0.00 0.00 37.49 2.59
2240 2365 1.681793 CCCGTGTGGACTGTAGGATAG 59.318 57.143 0.00 0.00 37.49 2.08
2241 2366 2.376109 CCGTGTGGACTGTAGGATAGT 58.624 52.381 0.00 0.00 37.49 2.12
2248 2373 4.017126 TGGACTGTAGGATAGTGTCACTG 58.983 47.826 16.03 0.00 0.00 3.66
2259 2384 3.667448 TGTCACTGACACTGACAGC 57.333 52.632 7.84 0.00 42.47 4.40
2260 2385 1.114627 TGTCACTGACACTGACAGCT 58.885 50.000 7.84 0.00 42.47 4.24
2261 2386 1.482182 TGTCACTGACACTGACAGCTT 59.518 47.619 7.84 0.00 42.47 3.74
2275 2400 5.172687 TGACAGCTTGATTAATGGTGGTA 57.827 39.130 0.00 0.00 34.02 3.25
2278 2403 6.663093 TGACAGCTTGATTAATGGTGGTATTT 59.337 34.615 0.00 0.00 34.02 1.40
2293 2418 1.659098 GTATTTTCTCCAGGTGCGACG 59.341 52.381 0.00 0.00 0.00 5.12
2302 2427 0.669318 CAGGTGCGACGGTGTACAAT 60.669 55.000 0.00 0.00 0.00 2.71
2305 2430 2.030401 TGCGACGGTGTACAATGCC 61.030 57.895 0.00 0.00 0.00 4.40
2323 2448 3.417275 CTACCTCGACGGGCTGCTG 62.417 68.421 0.00 0.00 36.97 4.41
2374 2499 1.476891 GTGTACCAGAGGATGAAGCGA 59.523 52.381 0.00 0.00 0.00 4.93
2434 2559 0.319211 TCAACGTCTACGGCAAGGTG 60.319 55.000 7.50 0.00 44.95 4.00
2448 2574 0.320160 AAGGTGCGTCCGGTAACTTC 60.320 55.000 0.00 0.00 32.25 3.01
2451 2577 1.505425 GTGCGTCCGGTAACTTCTTT 58.495 50.000 0.00 0.00 0.00 2.52
2455 2581 1.459592 CGTCCGGTAACTTCTTTGCTG 59.540 52.381 0.00 0.00 0.00 4.41
2464 2590 3.845781 ACTTCTTTGCTGTGGAGAAGA 57.154 42.857 16.60 0.00 45.79 2.87
2465 2591 3.737850 ACTTCTTTGCTGTGGAGAAGAG 58.262 45.455 16.60 0.00 45.79 2.85
2467 2593 4.345257 ACTTCTTTGCTGTGGAGAAGAGTA 59.655 41.667 16.60 0.00 45.79 2.59
2468 2594 5.012561 ACTTCTTTGCTGTGGAGAAGAGTAT 59.987 40.000 16.60 0.00 45.79 2.12
2469 2595 5.078411 TCTTTGCTGTGGAGAAGAGTATC 57.922 43.478 0.00 0.00 0.00 2.24
2470 2596 4.528206 TCTTTGCTGTGGAGAAGAGTATCA 59.472 41.667 0.00 0.00 37.82 2.15
2471 2597 5.188555 TCTTTGCTGTGGAGAAGAGTATCAT 59.811 40.000 0.00 0.00 37.82 2.45
2472 2598 4.662468 TGCTGTGGAGAAGAGTATCATC 57.338 45.455 0.00 0.00 37.82 2.92
2473 2599 4.026052 TGCTGTGGAGAAGAGTATCATCA 58.974 43.478 0.00 0.00 34.77 3.07
2474 2600 4.142071 TGCTGTGGAGAAGAGTATCATCAC 60.142 45.833 0.00 0.00 34.77 3.06
2475 2601 4.739137 GCTGTGGAGAAGAGTATCATCACC 60.739 50.000 0.00 0.00 42.66 4.02
2476 2602 4.614475 TGTGGAGAAGAGTATCATCACCT 58.386 43.478 1.34 0.00 42.76 4.00
2477 2603 4.403752 TGTGGAGAAGAGTATCATCACCTG 59.596 45.833 1.34 0.00 42.76 4.00
2478 2604 4.646945 GTGGAGAAGAGTATCATCACCTGA 59.353 45.833 1.34 0.00 42.76 3.86
2479 2605 4.646945 TGGAGAAGAGTATCATCACCTGAC 59.353 45.833 1.34 0.00 42.76 3.51
2480 2606 4.892934 GGAGAAGAGTATCATCACCTGACT 59.107 45.833 0.00 0.00 39.87 3.41
2825 2991 2.125961 GTGGACGCCTACGGGAGAT 61.126 63.158 0.00 0.00 46.04 2.75
2850 3016 2.100991 CCACCGAGGTACGTACGC 59.899 66.667 16.72 12.50 40.78 4.42
3152 3321 2.583593 GACGACATGGAGCGGCTC 60.584 66.667 21.57 21.57 31.57 4.70
3345 3514 1.618888 CCAGGAAGAAGGAGTACCGGA 60.619 57.143 9.46 0.00 41.83 5.14
3458 3627 2.047844 CAGGTGGAGCAGGTCACG 60.048 66.667 1.20 0.00 34.93 4.35
3491 3660 1.186917 CCATGCACAAGGAGGCCAAA 61.187 55.000 5.01 0.00 0.00 3.28
3522 3692 7.119699 TGTTCACCATATGACAAAGATGAAGAC 59.880 37.037 3.65 0.00 36.92 3.01
3533 3703 6.211515 ACAAAGATGAAGACAAATCTTGTGC 58.788 36.000 0.00 0.00 45.60 4.57
3547 3717 8.237267 ACAAATCTTGTGCTAATTAGTTAGTGC 58.763 33.333 13.91 0.02 43.48 4.40
3555 3725 7.544566 TGTGCTAATTAGTTAGTGCAGACTTAC 59.455 37.037 13.91 0.00 39.60 2.34
3686 3859 2.333701 AAAGTTTCGGCCGGTCCAGT 62.334 55.000 27.83 6.81 34.01 4.00
3729 3903 2.361104 GGCCGTTGGATCCAAGCA 60.361 61.111 29.61 10.33 36.52 3.91
3730 3904 1.976474 GGCCGTTGGATCCAAGCAA 60.976 57.895 29.61 9.99 36.52 3.91
3731 3905 1.531739 GGCCGTTGGATCCAAGCAAA 61.532 55.000 29.61 9.63 36.52 3.68
3732 3906 0.316841 GCCGTTGGATCCAAGCAAAA 59.683 50.000 27.73 1.83 36.52 2.44
3773 3948 1.468985 CAGCTCTCTTCTTCCTCGGA 58.531 55.000 0.00 0.00 0.00 4.55
3790 3965 0.613777 GGAGAGTTGGTTGGATCCGT 59.386 55.000 7.39 0.00 0.00 4.69
3798 3973 0.834612 GGTTGGATCCGTATGTCCCA 59.165 55.000 7.39 0.00 33.45 4.37
4073 4255 1.877637 CCGTCAGTCAATCAACACCA 58.122 50.000 0.00 0.00 0.00 4.17
4096 4278 7.884354 ACCATTTTGAATGGATGTAGCAAAAAT 59.116 29.630 22.74 0.00 40.47 1.82
4173 4355 0.732880 CGTCTTTCGTGAGGTCGCAT 60.733 55.000 0.00 0.00 34.52 4.73
4257 4439 3.443037 CAGCAAAAATCAAACACCGTCA 58.557 40.909 0.00 0.00 0.00 4.35
4301 4483 1.202639 CCGCCTTACATGGATGTAGCA 60.203 52.381 0.00 0.00 43.44 3.49
4451 4635 1.903404 CGGTTGCAGCTTCCCCTTT 60.903 57.895 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.599047 GAGTAGCTGAAGGGCTGCA 59.401 57.895 0.50 0.00 45.12 4.41
95 96 3.691049 TTTTTGCTTGACAGAGAACCG 57.309 42.857 0.00 0.00 0.00 4.44
135 136 2.892215 TGTCGGTGTAAGTACATGGTCA 59.108 45.455 0.00 0.00 38.63 4.02
152 153 3.016736 AGGGCCTTGAAATGTATTGTCG 58.983 45.455 0.00 0.00 0.00 4.35
214 215 2.214347 TCTCATTCGAGCTCTACTCCG 58.786 52.381 12.85 0.00 43.01 4.63
283 288 2.224426 ACGATACAACACCCTCTGCAAA 60.224 45.455 0.00 0.00 0.00 3.68
289 294 3.173668 TGCATACGATACAACACCCTC 57.826 47.619 0.00 0.00 0.00 4.30
337 342 9.153721 CATGATTAACAAAATTGGCAGTTATGT 57.846 29.630 0.00 0.00 0.00 2.29
338 343 8.605746 CCATGATTAACAAAATTGGCAGTTATG 58.394 33.333 0.00 0.00 0.00 1.90
394 400 2.355197 CAAGTTCCACGGCACATCATA 58.645 47.619 0.00 0.00 0.00 2.15
459 465 0.038166 AAGGACGGCCACATCACATT 59.962 50.000 11.69 0.00 36.29 2.71
469 475 3.508402 TGAAATAAAAAGGAAGGACGGCC 59.492 43.478 0.00 0.00 0.00 6.13
470 476 4.733850 CTGAAATAAAAAGGAAGGACGGC 58.266 43.478 0.00 0.00 0.00 5.68
471 477 4.217550 TGCTGAAATAAAAAGGAAGGACGG 59.782 41.667 0.00 0.00 0.00 4.79
514 522 6.142817 CACCAGCTTAGTTTCATACAACAAC 58.857 40.000 0.00 0.00 0.00 3.32
516 524 4.759693 CCACCAGCTTAGTTTCATACAACA 59.240 41.667 0.00 0.00 0.00 3.33
552 565 1.665679 CGGTTATCTCGTGCATTTGCT 59.334 47.619 3.94 0.00 42.66 3.91
561 574 3.703052 AGGTAAATCCACGGTTATCTCGT 59.297 43.478 0.00 0.00 41.93 4.18
623 675 5.390885 GCTGCGTTTCTGAATTCTGATACAA 60.391 40.000 24.68 16.07 0.00 2.41
687 739 5.598830 TGGACTAACCAAATGCCACTAAAAA 59.401 36.000 0.00 0.00 46.75 1.94
688 740 5.141182 TGGACTAACCAAATGCCACTAAAA 58.859 37.500 0.00 0.00 46.75 1.52
689 741 4.730966 TGGACTAACCAAATGCCACTAAA 58.269 39.130 0.00 0.00 46.75 1.85
690 742 4.374689 TGGACTAACCAAATGCCACTAA 57.625 40.909 0.00 0.00 46.75 2.24
692 744 2.969821 TGGACTAACCAAATGCCACT 57.030 45.000 0.00 0.00 46.75 4.00
699 751 9.985474 CAGTGCTCTGTTACTGGACTAACCAAA 62.985 44.444 7.63 0.00 41.15 3.28
700 752 8.628620 CAGTGCTCTGTTACTGGACTAACCAA 62.629 46.154 7.63 0.00 41.15 3.67
701 753 7.243479 CAGTGCTCTGTTACTGGACTAACCA 62.243 48.000 7.63 0.00 40.38 3.67
757 809 7.122799 GTCTTATCCAGAAGGCAAATAAAACCT 59.877 37.037 0.00 0.00 31.28 3.50
805 858 1.597854 TGCCGTTTGAGCCTCACAG 60.598 57.895 0.00 0.00 0.00 3.66
825 878 4.099573 TGGGCTGTTGTATCTAGTTCTAGC 59.900 45.833 2.31 0.00 0.00 3.42
839 892 4.026052 AGATATTTCCCTTTGGGCTGTTG 58.974 43.478 0.00 0.00 43.94 3.33
844 897 2.103094 GCCAAGATATTTCCCTTTGGGC 59.897 50.000 0.00 0.00 43.94 5.36
937 1024 1.001406 CTCCCAAGGGACAGATATCGC 59.999 57.143 3.04 0.00 39.76 4.58
1007 1094 8.103948 AGAATTCATGAAGGTAGAAAGTGTTG 57.896 34.615 14.54 0.00 0.00 3.33
1043 1130 3.881937 ACTACGTGAACTTGGGGATAC 57.118 47.619 0.00 0.00 0.00 2.24
1047 1134 2.287368 GCAAAACTACGTGAACTTGGGG 60.287 50.000 0.00 0.00 0.00 4.96
1052 1139 1.202557 TCGGGCAAAACTACGTGAACT 60.203 47.619 0.00 0.00 0.00 3.01
1088 1175 0.322277 AGAACACAGGCCAGATGCAG 60.322 55.000 5.01 0.00 43.89 4.41
1094 1181 0.607217 TCATGCAGAACACAGGCCAG 60.607 55.000 5.01 0.00 0.00 4.85
1116 1203 5.627499 TGAATGGTTACTGCTGAATGAAC 57.373 39.130 0.00 0.00 0.00 3.18
1121 1208 4.280425 TGCATTTGAATGGTTACTGCTGAA 59.720 37.500 5.91 0.00 36.90 3.02
1123 1210 4.177165 TGCATTTGAATGGTTACTGCTG 57.823 40.909 5.91 0.00 36.90 4.41
1124 1211 4.870123 TTGCATTTGAATGGTTACTGCT 57.130 36.364 5.91 0.00 36.90 4.24
1125 1212 5.466393 ACTTTTGCATTTGAATGGTTACTGC 59.534 36.000 5.91 0.00 36.90 4.40
1126 1213 7.307337 GGAACTTTTGCATTTGAATGGTTACTG 60.307 37.037 5.91 0.00 36.90 2.74
1128 1215 6.073276 GGGAACTTTTGCATTTGAATGGTTAC 60.073 38.462 5.91 2.30 36.90 2.50
1130 1217 4.821260 GGGAACTTTTGCATTTGAATGGTT 59.179 37.500 5.91 1.50 36.90 3.67
1131 1218 4.141528 TGGGAACTTTTGCATTTGAATGGT 60.142 37.500 5.91 0.00 36.90 3.55
1132 1219 4.387598 TGGGAACTTTTGCATTTGAATGG 58.612 39.130 5.91 0.00 36.90 3.16
1133 1220 5.178067 GTCTGGGAACTTTTGCATTTGAATG 59.822 40.000 0.00 0.00 39.40 2.67
1135 1222 4.161189 TGTCTGGGAACTTTTGCATTTGAA 59.839 37.500 0.00 0.00 0.00 2.69
1136 1223 3.703556 TGTCTGGGAACTTTTGCATTTGA 59.296 39.130 0.00 0.00 0.00 2.69
1137 1224 4.057406 TGTCTGGGAACTTTTGCATTTG 57.943 40.909 0.00 0.00 0.00 2.32
1138 1225 4.081198 TGTTGTCTGGGAACTTTTGCATTT 60.081 37.500 0.00 0.00 0.00 2.32
1139 1226 3.450457 TGTTGTCTGGGAACTTTTGCATT 59.550 39.130 0.00 0.00 0.00 3.56
1140 1227 3.030291 TGTTGTCTGGGAACTTTTGCAT 58.970 40.909 0.00 0.00 0.00 3.96
1148 1255 2.143925 GCTAGTGTGTTGTCTGGGAAC 58.856 52.381 0.00 0.00 0.00 3.62
1152 1259 1.702886 CGAGCTAGTGTGTTGTCTGG 58.297 55.000 0.00 0.00 0.00 3.86
1155 1262 1.068194 AGAGCGAGCTAGTGTGTTGTC 60.068 52.381 0.00 0.00 0.00 3.18
1215 1327 2.241281 TTCATACGGTGGAGGAGGAA 57.759 50.000 0.00 0.00 0.00 3.36
1238 1355 2.679082 GGAGCCTGTATCCTCAACCTA 58.321 52.381 0.00 0.00 33.77 3.08
1354 1471 2.483106 TCGCCGTATCTAGAGGAATTCG 59.517 50.000 0.00 0.00 0.00 3.34
1421 1541 4.771356 TCGAAGGTCCGCGCTTCG 62.771 66.667 29.41 29.41 41.88 3.79
1580 1700 5.519722 ACTTGAAGCTGTAAAACCATTTCG 58.480 37.500 0.00 0.00 0.00 3.46
1624 1744 2.892425 CAACCGCGGCCTCTCATC 60.892 66.667 28.58 0.00 0.00 2.92
1639 1759 2.652095 CCCGGAGCCGTACTTCCAA 61.652 63.158 0.73 0.00 37.81 3.53
1748 1868 3.642755 GACGTTGTCCAGTGCCTG 58.357 61.111 0.00 0.00 0.00 4.85
1880 2002 3.070018 CAGAGCTTCAACTGAAACCGAT 58.930 45.455 0.00 0.00 36.38 4.18
1909 2034 1.202031 GGAATCACACCGTCGAAATGC 60.202 52.381 0.00 0.00 0.00 3.56
2205 2330 0.322546 ACGGGTTGAAATGGAGAGGC 60.323 55.000 0.00 0.00 0.00 4.70
2206 2331 1.271379 ACACGGGTTGAAATGGAGAGG 60.271 52.381 0.00 0.00 0.00 3.69
2207 2332 1.806542 CACACGGGTTGAAATGGAGAG 59.193 52.381 0.00 0.00 0.00 3.20
2212 2337 1.266718 CAGTCCACACGGGTTGAAATG 59.733 52.381 0.00 0.00 38.11 2.32
2213 2338 1.133915 ACAGTCCACACGGGTTGAAAT 60.134 47.619 0.00 0.00 38.11 2.17
2215 2340 1.069513 CTACAGTCCACACGGGTTGAA 59.930 52.381 0.00 0.00 38.11 2.69
2216 2341 0.677288 CTACAGTCCACACGGGTTGA 59.323 55.000 0.00 0.00 38.11 3.18
2217 2342 0.320421 CCTACAGTCCACACGGGTTG 60.320 60.000 0.00 0.00 38.11 3.77
2218 2343 0.470456 TCCTACAGTCCACACGGGTT 60.470 55.000 0.00 0.00 38.11 4.11
2219 2344 0.252103 ATCCTACAGTCCACACGGGT 60.252 55.000 0.00 0.00 38.11 5.28
2221 2346 2.099263 CACTATCCTACAGTCCACACGG 59.901 54.545 0.00 0.00 0.00 4.94
2222 2347 2.753452 ACACTATCCTACAGTCCACACG 59.247 50.000 0.00 0.00 0.00 4.49
2224 2349 3.762288 GTGACACTATCCTACAGTCCACA 59.238 47.826 0.00 0.00 31.76 4.17
2225 2350 4.017808 AGTGACACTATCCTACAGTCCAC 58.982 47.826 6.24 0.00 31.65 4.02
2226 2351 4.017126 CAGTGACACTATCCTACAGTCCA 58.983 47.826 8.02 0.00 0.00 4.02
2227 2352 4.096682 GTCAGTGACACTATCCTACAGTCC 59.903 50.000 18.54 0.00 32.09 3.85
2228 2353 4.700692 TGTCAGTGACACTATCCTACAGTC 59.299 45.833 22.06 0.00 37.67 3.51
2229 2354 4.663334 TGTCAGTGACACTATCCTACAGT 58.337 43.478 22.06 0.00 37.67 3.55
2248 2373 4.697352 ACCATTAATCAAGCTGTCAGTGTC 59.303 41.667 0.93 0.00 0.00 3.67
2253 2378 4.032960 ACCACCATTAATCAAGCTGTCA 57.967 40.909 0.00 0.00 0.00 3.58
2259 2384 8.292444 TGGAGAAAATACCACCATTAATCAAG 57.708 34.615 0.00 0.00 0.00 3.02
2260 2385 7.341769 CCTGGAGAAAATACCACCATTAATCAA 59.658 37.037 0.00 0.00 32.44 2.57
2261 2386 6.833416 CCTGGAGAAAATACCACCATTAATCA 59.167 38.462 0.00 0.00 32.44 2.57
2275 2400 0.673644 CCGTCGCACCTGGAGAAAAT 60.674 55.000 0.00 0.00 0.00 1.82
2278 2403 2.915659 ACCGTCGCACCTGGAGAA 60.916 61.111 0.00 0.00 0.00 2.87
2293 2418 1.479323 TCGAGGTAGGCATTGTACACC 59.521 52.381 0.00 0.00 0.00 4.16
2305 2430 3.141488 AGCAGCCCGTCGAGGTAG 61.141 66.667 4.18 0.00 38.74 3.18
2434 2559 0.165295 GCAAAGAAGTTACCGGACGC 59.835 55.000 9.46 0.00 0.00 5.19
2442 2567 5.163301 ACTCTTCTCCACAGCAAAGAAGTTA 60.163 40.000 10.24 0.00 44.09 2.24
2448 2574 4.825422 TGATACTCTTCTCCACAGCAAAG 58.175 43.478 0.00 0.00 0.00 2.77
2451 2577 4.026052 TGATGATACTCTTCTCCACAGCA 58.974 43.478 0.00 0.00 0.00 4.41
2455 2581 4.646945 TCAGGTGATGATACTCTTCTCCAC 59.353 45.833 11.40 0.00 36.94 4.02
2464 2590 4.644234 CAGTCAGAGTCAGGTGATGATACT 59.356 45.833 0.00 0.00 40.92 2.12
2465 2591 4.642437 TCAGTCAGAGTCAGGTGATGATAC 59.358 45.833 0.00 0.00 40.92 2.24
2467 2593 3.706183 TCAGTCAGAGTCAGGTGATGAT 58.294 45.455 0.00 0.00 40.92 2.45
2468 2594 3.160679 TCAGTCAGAGTCAGGTGATGA 57.839 47.619 0.00 0.00 34.79 2.92
2469 2595 3.949842 TTCAGTCAGAGTCAGGTGATG 57.050 47.619 0.00 0.00 0.00 3.07
2470 2596 4.963318 TTTTCAGTCAGAGTCAGGTGAT 57.037 40.909 0.00 0.00 0.00 3.06
2471 2597 4.753516 TTTTTCAGTCAGAGTCAGGTGA 57.246 40.909 0.00 0.00 0.00 4.02
2495 2621 2.205074 CTTCGACTGCCATCCATACAC 58.795 52.381 0.00 0.00 0.00 2.90
2496 2622 1.473257 GCTTCGACTGCCATCCATACA 60.473 52.381 0.00 0.00 0.00 2.29
2497 2623 1.221414 GCTTCGACTGCCATCCATAC 58.779 55.000 0.00 0.00 0.00 2.39
2498 2624 0.829990 TGCTTCGACTGCCATCCATA 59.170 50.000 7.07 0.00 0.00 2.74
2499 2625 0.463295 CTGCTTCGACTGCCATCCAT 60.463 55.000 7.07 0.00 0.00 3.41
2502 2628 3.096791 GCTGCTTCGACTGCCATC 58.903 61.111 7.07 0.00 0.00 3.51
2668 2834 3.129502 TAGACGTCGGGCTCGTGG 61.130 66.667 5.57 0.89 41.64 4.94
2850 3016 2.555199 GTTCGAGGAGTCCATGATTGG 58.445 52.381 12.86 0.00 45.15 3.16
3324 3493 1.618888 CCGGTACTCCTTCTTCCTGGA 60.619 57.143 0.00 0.00 0.00 3.86
3345 3514 0.324738 TCGAAGATCTCCAGGCACCT 60.325 55.000 0.00 0.00 0.00 4.00
3458 3627 1.524621 CATGGACCTGACGATGGCC 60.525 63.158 0.00 0.00 0.00 5.36
3491 3660 6.068010 TCTTTGTCATATGGTGAACAAGGTT 58.932 36.000 13.38 0.00 38.90 3.50
3522 3692 8.236586 TGCACTAACTAATTAGCACAAGATTTG 58.763 33.333 12.54 1.84 41.48 2.32
3624 3797 8.630037 GCCTATAAGCGCCCATAATTTTTATAT 58.370 33.333 2.29 0.00 0.00 0.86
3625 3798 7.992008 GCCTATAAGCGCCCATAATTTTTATA 58.008 34.615 2.29 1.83 0.00 0.98
3626 3799 6.863275 GCCTATAAGCGCCCATAATTTTTAT 58.137 36.000 2.29 0.56 0.00 1.40
3627 3800 6.262193 GCCTATAAGCGCCCATAATTTTTA 57.738 37.500 2.29 0.00 0.00 1.52
3686 3859 2.435234 CAAATCGAACGGCCCGGA 60.435 61.111 8.57 0.00 0.00 5.14
3689 3862 2.761195 GGCTCAAATCGAACGGCCC 61.761 63.158 0.00 0.00 34.19 5.80
3773 3948 2.838202 ACATACGGATCCAACCAACTCT 59.162 45.455 13.41 0.00 0.00 3.24
3923 4102 4.681978 GCGACAAGGACAGCCGGT 62.682 66.667 1.90 0.00 39.96 5.28
4013 4195 1.876714 CAGCAAGCATCAATGGCGC 60.877 57.895 0.00 0.00 36.08 6.53
4073 4255 9.729281 AAGATTTTTGCTACATCCATTCAAAAT 57.271 25.926 0.00 0.00 36.77 1.82
4096 4278 4.339872 TTTTTGCTACTACGGGTGAAGA 57.660 40.909 0.00 0.00 0.00 2.87
4231 4413 3.622612 GGTGTTTGATTTTTGCTGCAACT 59.377 39.130 15.72 2.66 0.00 3.16
4257 4439 2.257676 GACCTCGCGAAAGACGGT 59.742 61.111 15.98 15.98 42.83 4.83
4338 4521 3.701241 ACAACGACGATTTTTGTTGCAT 58.299 36.364 0.00 0.00 42.53 3.96
4451 4635 2.694628 AGCTTCAATGGAACTGCACAAA 59.305 40.909 0.00 0.00 0.00 2.83


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.