Multiple sequence alignment - TraesCS1D01G165800

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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 TraesCS1D01G165800 chr1D 100.000 3698 0 0 1 3698 236855399 236859096 0.000000e+00 6830.0
1 TraesCS1D01G165800 chr1D 98.851 87 0 1 3612 3698 266781774 266781689 1.780000e-33 154.0
2 TraesCS1D01G165800 chr1D 94.898 98 1 4 3604 3698 417732390 417732294 2.300000e-32 150.0
3 TraesCS1D01G165800 chr1D 94.845 97 1 3 3604 3698 281176352 281176446 8.270000e-32 148.0
4 TraesCS1D01G165800 chr1B 93.844 2453 88 29 469 2892 342321951 342324369 0.000000e+00 3635.0
5 TraesCS1D01G165800 chr1B 88.692 451 37 5 1 440 342319243 342319690 4.200000e-149 538.0
6 TraesCS1D01G165800 chr1B 93.575 358 14 8 3262 3617 342327728 342328078 3.270000e-145 525.0
7 TraesCS1D01G165800 chr1B 97.110 173 5 0 3094 3266 342327356 342327528 3.610000e-75 292.0
8 TraesCS1D01G165800 chr1B 85.507 276 12 13 2776 3051 342326759 342327006 2.830000e-66 263.0
9 TraesCS1D01G165800 chr1B 95.556 45 2 0 3055 3099 637372706 637372662 5.120000e-09 73.1
10 TraesCS1D01G165800 chr1A 93.700 2365 78 29 648 2998 308806907 308804600 0.000000e+00 3476.0
11 TraesCS1D01G165800 chr1A 85.569 492 41 18 129 604 308807851 308807374 4.290000e-134 488.0
12 TraesCS1D01G165800 chr1A 93.594 281 13 4 3338 3617 308790516 308790240 7.390000e-112 414.0
13 TraesCS1D01G165800 chr1A 94.872 78 4 0 3202 3279 308790594 308790517 5.020000e-24 122.0
14 TraesCS1D01G165800 chr1A 92.683 82 3 1 585 666 308806989 308806911 8.390000e-22 115.0
15 TraesCS1D01G165800 chr1A 100.000 29 0 0 3022 3050 308804594 308804566 2.000000e-03 54.7
16 TraesCS1D01G165800 chr3D 82.803 849 122 16 1109 1951 131241572 131242402 0.000000e+00 737.0
17 TraesCS1D01G165800 chr3D 80.351 626 103 11 2073 2693 131242464 131243074 1.210000e-124 457.0
18 TraesCS1D01G165800 chr3D 82.629 426 64 9 2116 2533 130999005 130999428 5.830000e-98 368.0
19 TraesCS1D01G165800 chr3A 81.647 850 133 17 1109 1952 143533245 143534077 0.000000e+00 684.0
20 TraesCS1D01G165800 chr3A 79.233 626 107 10 2073 2693 143534140 143534747 7.390000e-112 414.0
21 TraesCS1D01G165800 chr3A 78.615 491 94 10 2116 2598 143022848 143023335 7.710000e-82 315.0
22 TraesCS1D01G165800 chr3B 81.199 851 137 14 1109 1951 187575800 187576635 0.000000e+00 664.0
23 TraesCS1D01G165800 chr2A 85.797 345 37 8 3270 3612 703980583 703980917 4.540000e-94 355.0
24 TraesCS1D01G165800 chr6B 84.463 354 37 16 3265 3612 17804397 17804738 2.130000e-87 333.0
25 TraesCS1D01G165800 chr7A 84.545 330 31 6 3261 3582 39068136 39068453 3.590000e-80 309.0
26 TraesCS1D01G165800 chr7D 86.347 271 24 4 3261 3530 39093968 39094226 2.170000e-72 283.0
27 TraesCS1D01G165800 chr7D 91.667 108 4 5 3592 3698 291731604 291731707 1.070000e-30 145.0
28 TraesCS1D01G165800 chr7D 86.000 100 8 6 3431 3527 510388793 510388697 6.530000e-18 102.0
29 TraesCS1D01G165800 chr7D 93.846 65 3 1 3049 3113 548948862 548948925 3.040000e-16 97.1
30 TraesCS1D01G165800 chr4A 83.077 325 39 10 3261 3571 644035934 644036256 7.820000e-72 281.0
31 TraesCS1D01G165800 chr2B 84.452 283 36 8 3273 3552 772822579 772822302 4.710000e-69 272.0
32 TraesCS1D01G165800 chr4D 80.592 304 52 6 3265 3565 386158118 386158417 1.030000e-55 228.0
33 TraesCS1D01G165800 chr4D 85.787 197 20 4 3271 3467 322220297 322220109 6.260000e-48 202.0
34 TraesCS1D01G165800 chr4D 98.851 87 0 1 3612 3698 415632949 415633034 1.780000e-33 154.0
35 TraesCS1D01G165800 chr4D 91.346 104 7 2 3595 3698 444355891 444355790 1.380000e-29 141.0
36 TraesCS1D01G165800 chr5B 100.000 85 0 0 3614 3698 463388581 463388497 1.370000e-34 158.0
37 TraesCS1D01G165800 chr5B 94.845 97 2 2 3604 3698 4002518 4002423 8.270000e-32 148.0
38 TraesCS1D01G165800 chr4B 95.745 94 2 2 3605 3698 33579114 33579023 2.300000e-32 150.0
39 TraesCS1D01G165800 chrUn 95.522 67 3 0 3049 3115 150141217 150141283 1.400000e-19 108.0
40 TraesCS1D01G165800 chrUn 98.361 61 1 0 3055 3115 172386894 172386834 1.400000e-19 108.0
41 TraesCS1D01G165800 chrUn 95.522 67 3 0 3049 3115 321413915 321413981 1.400000e-19 108.0
42 TraesCS1D01G165800 chr5D 76.744 172 31 7 2338 2503 74419926 74420094 1.830000e-13 87.9
43 TraesCS1D01G165800 chr5A 76.744 172 31 7 2338 2503 69546454 69546622 1.830000e-13 87.9


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 TraesCS1D01G165800 chr1D 236855399 236859096 3697 False 6830.000 6830 100.0000 1 3698 1 chr1D.!!$F1 3697
1 TraesCS1D01G165800 chr1B 342319243 342328078 8835 False 1050.600 3635 91.7456 1 3617 5 chr1B.!!$F1 3616
2 TraesCS1D01G165800 chr1A 308804566 308807851 3285 True 1033.425 3476 92.9880 129 3050 4 chr1A.!!$R2 2921
3 TraesCS1D01G165800 chr3D 131241572 131243074 1502 False 597.000 737 81.5770 1109 2693 2 chr3D.!!$F2 1584
4 TraesCS1D01G165800 chr3A 143533245 143534747 1502 False 549.000 684 80.4400 1109 2693 2 chr3A.!!$F2 1584
5 TraesCS1D01G165800 chr3B 187575800 187576635 835 False 664.000 664 81.1990 1109 1951 1 chr3B.!!$F1 842

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
81 82 0.597568 TTTGTCCCGCTGATTGCTTG 59.402 50.0 0.00 0.0 40.11 4.01 F
84 85 0.598065 GTCCCGCTGATTGCTTGTTT 59.402 50.0 0.00 0.0 40.11 2.83 F
1557 4271 0.109597 CCTACGCCAACTACGTCGTT 60.110 55.0 1.78 0.0 43.88 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 3734 0.180406 CGACCAAGGTGGGGATAAGG 59.820 60.0 0.00 0.00 43.37 2.69 R
2006 4727 0.319211 GCGCACGCCTACCATATACA 60.319 55.0 0.30 0.00 34.56 2.29 R
2702 5426 0.460109 TAACGATGAGCGCTGCATGT 60.460 50.0 18.48 14.85 46.04 3.21 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
26 27 1.375523 GCGGGTTTCTGTGGACGAT 60.376 57.895 0.00 0.00 0.00 3.73
81 82 0.597568 TTTGTCCCGCTGATTGCTTG 59.402 50.000 0.00 0.00 40.11 4.01
84 85 0.598065 GTCCCGCTGATTGCTTGTTT 59.402 50.000 0.00 0.00 40.11 2.83
88 89 3.319405 TCCCGCTGATTGCTTGTTTAAAA 59.681 39.130 0.00 0.00 40.11 1.52
89 90 4.021544 TCCCGCTGATTGCTTGTTTAAAAT 60.022 37.500 0.00 0.00 40.11 1.82
90 91 4.091800 CCCGCTGATTGCTTGTTTAAAATG 59.908 41.667 0.00 0.00 40.11 2.32
171 175 8.454106 GTTGATGTGCTGATTAACAAGATTAGT 58.546 33.333 0.00 0.00 0.00 2.24
176 180 5.887598 TGCTGATTAACAAGATTAGTGCCAT 59.112 36.000 0.00 0.00 0.00 4.40
181 185 3.004752 ACAAGATTAGTGCCATCACCC 57.995 47.619 0.00 0.00 44.16 4.61
185 189 1.145738 GATTAGTGCCATCACCCCCAT 59.854 52.381 0.00 0.00 44.16 4.00
235 239 4.162320 CCATGCCTTAGTCTTAGTCCTTGA 59.838 45.833 0.00 0.00 0.00 3.02
260 264 9.485206 GACCTTTGTTGTCTTAGTGTTTATCTA 57.515 33.333 0.00 0.00 0.00 1.98
304 311 1.304134 GGGCCGGGTTTGAGTCATT 60.304 57.895 2.18 0.00 0.00 2.57
305 312 0.898326 GGGCCGGGTTTGAGTCATTT 60.898 55.000 2.18 0.00 0.00 2.32
312 319 3.365364 CGGGTTTGAGTCATTTTGCTCTC 60.365 47.826 0.00 0.00 33.22 3.20
348 355 8.671384 TGTTTGAGCTATTTTGTAGTACTTGT 57.329 30.769 0.00 0.00 0.00 3.16
349 356 9.767228 TGTTTGAGCTATTTTGTAGTACTTGTA 57.233 29.630 0.00 0.00 0.00 2.41
374 388 4.250464 TCCATTCGAGCGTCAACTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
387 401 2.181975 ACTAATTTCGGACGGAGGGAA 58.818 47.619 0.00 0.00 0.00 3.97
399 413 4.282703 GGACGGAGGGAATATTAACTAGCA 59.717 45.833 0.00 0.00 0.00 3.49
416 430 9.893634 TTAACTAGCATACTTGGCTGTTATTTA 57.106 29.630 0.00 0.00 42.62 1.40
418 432 8.980481 ACTAGCATACTTGGCTGTTATTTAAT 57.020 30.769 0.00 0.00 42.62 1.40
424 438 9.964303 CATACTTGGCTGTTATTTAATATTGCA 57.036 29.630 0.00 0.00 0.00 4.08
459 803 9.722056 CTTTATTTATAAAGTCTGACATGGTGC 57.278 33.333 10.88 0.00 42.53 5.01
502 2748 3.294371 CGCAACATTGTTGTTCGAATACG 59.706 43.478 25.88 16.16 44.24 3.06
515 2761 4.320667 TCGAATACGCTGTTGTTCAATG 57.679 40.909 0.00 0.00 39.58 2.82
516 2762 2.840176 CGAATACGCTGTTGTTCAATGC 59.160 45.455 0.00 0.00 0.00 3.56
517 2763 3.424829 CGAATACGCTGTTGTTCAATGCT 60.425 43.478 10.01 3.40 0.00 3.79
518 2764 4.201676 CGAATACGCTGTTGTTCAATGCTA 60.202 41.667 10.01 4.79 0.00 3.49
519 2765 5.621197 AATACGCTGTTGTTCAATGCTAA 57.379 34.783 10.01 2.11 0.00 3.09
520 2766 3.542712 ACGCTGTTGTTCAATGCTAAG 57.457 42.857 10.01 0.00 0.00 2.18
522 2768 2.245096 GCTGTTGTTCAATGCTAAGCG 58.755 47.619 0.00 0.00 0.00 4.68
523 2769 2.095768 GCTGTTGTTCAATGCTAAGCGA 60.096 45.455 0.00 0.00 0.00 4.93
524 2770 3.482786 CTGTTGTTCAATGCTAAGCGAC 58.517 45.455 0.00 0.00 0.00 5.19
525 2771 2.875317 TGTTGTTCAATGCTAAGCGACA 59.125 40.909 0.00 0.00 0.00 4.35
526 2772 3.058983 TGTTGTTCAATGCTAAGCGACAG 60.059 43.478 0.00 0.00 0.00 3.51
529 2775 3.812609 TGTTCAATGCTAAGCGACAGAAA 59.187 39.130 0.00 0.00 0.00 2.52
530 2776 4.083855 TGTTCAATGCTAAGCGACAGAAAG 60.084 41.667 0.00 0.00 0.00 2.62
532 2778 3.928992 TCAATGCTAAGCGACAGAAAGAG 59.071 43.478 0.00 0.00 0.00 2.85
533 2779 3.601443 ATGCTAAGCGACAGAAAGAGT 57.399 42.857 0.00 0.00 0.00 3.24
534 2780 2.947852 TGCTAAGCGACAGAAAGAGTC 58.052 47.619 0.00 0.00 0.00 3.36
614 3273 5.050091 GCGGCTTATGCGATGCTATATTAAT 60.050 40.000 0.00 0.00 40.82 1.40
615 3274 6.145534 GCGGCTTATGCGATGCTATATTAATA 59.854 38.462 0.00 0.00 40.82 0.98
616 3275 7.307160 GCGGCTTATGCGATGCTATATTAATAA 60.307 37.037 0.00 0.00 40.82 1.40
674 3355 0.819259 GCTCCACACTTGCTGGTGAA 60.819 55.000 14.56 2.04 40.13 3.18
730 3412 1.944676 CGCATAGCCGTCCGTTCTC 60.945 63.158 0.00 0.00 0.00 2.87
769 3455 4.299586 TCAAATAGATGGTGACCTGCAA 57.700 40.909 2.11 0.00 0.00 4.08
797 3502 5.463286 TCTGATCAAATGTGTACGTACGTT 58.537 37.500 27.92 10.83 0.00 3.99
862 3567 3.931907 AACATGGAATCCTCGGATGAA 57.068 42.857 0.00 0.00 34.70 2.57
1010 3715 2.048023 CAGCATCCATGGCGGTGTT 61.048 57.895 19.46 9.25 36.08 3.32
1013 3718 2.035469 ATCCATGGCGGTGTTGCA 59.965 55.556 6.96 0.00 36.28 4.08
1029 3734 2.892425 CATGCCGCGGTCCTCTTC 60.892 66.667 28.70 8.52 0.00 2.87
1032 3737 4.083862 GCCGCGGTCCTCTTCCTT 62.084 66.667 28.70 0.00 0.00 3.36
1100 3808 2.501492 GCATCAGCAATGGGAAGCT 58.499 52.632 1.83 0.00 42.94 3.74
1283 3991 1.303309 GCGGAGGAGGTGATGAAATG 58.697 55.000 0.00 0.00 0.00 2.32
1557 4271 0.109597 CCTACGCCAACTACGTCGTT 60.110 55.000 1.78 0.00 43.88 3.85
1971 4692 3.924918 AGACGTTATGCTCATATCGCT 57.075 42.857 15.98 12.37 39.04 4.93
1974 4695 4.695928 AGACGTTATGCTCATATCGCTCTA 59.304 41.667 15.98 0.00 39.04 2.43
1990 4711 6.812879 TCGCTCTAATCTATACCGATCAAA 57.187 37.500 0.00 0.00 0.00 2.69
1991 4712 6.843208 TCGCTCTAATCTATACCGATCAAAG 58.157 40.000 0.00 0.00 0.00 2.77
1992 4713 6.430308 TCGCTCTAATCTATACCGATCAAAGT 59.570 38.462 0.00 0.00 0.00 2.66
2006 4727 8.839310 ACCGATCAAAGTATATAGTACGTACT 57.161 34.615 29.62 29.62 40.24 2.73
2007 4728 8.715998 ACCGATCAAAGTATATAGTACGTACTG 58.284 37.037 33.23 16.84 37.10 2.74
2034 4755 0.311477 TAGGCGTGCGCGTGATATAA 59.689 50.000 22.18 0.00 43.06 0.98
2035 4756 0.528901 AGGCGTGCGCGTGATATAAA 60.529 50.000 22.18 0.00 43.06 1.40
2036 4757 0.382636 GGCGTGCGCGTGATATAAAC 60.383 55.000 22.18 0.23 43.06 2.01
2059 4780 5.356751 ACTGTTGTTGTTGTTGATAAGCTGA 59.643 36.000 0.00 0.00 0.00 4.26
2063 4784 6.000891 TGTTGTTGTTGATAAGCTGACATC 57.999 37.500 0.00 0.00 0.00 3.06
2064 4785 4.926860 TGTTGTTGATAAGCTGACATCG 57.073 40.909 0.00 0.00 0.00 3.84
2586 5310 1.679680 CTGCATCGCTTTGATTGGGAT 59.320 47.619 0.00 0.00 34.13 3.85
2701 5425 2.386661 AGCGTGGTTTCCATAGACAG 57.613 50.000 0.00 0.00 35.28 3.51
2702 5426 1.899814 AGCGTGGTTTCCATAGACAGA 59.100 47.619 0.00 0.00 35.28 3.41
2703 5427 2.000447 GCGTGGTTTCCATAGACAGAC 59.000 52.381 0.00 0.00 35.28 3.51
2705 5429 3.861840 CGTGGTTTCCATAGACAGACAT 58.138 45.455 0.00 0.00 35.28 3.06
2706 5430 3.618594 CGTGGTTTCCATAGACAGACATG 59.381 47.826 0.00 0.00 35.28 3.21
2707 5431 3.375299 GTGGTTTCCATAGACAGACATGC 59.625 47.826 0.00 0.00 35.28 4.06
2708 5432 3.008923 TGGTTTCCATAGACAGACATGCA 59.991 43.478 0.00 0.00 0.00 3.96
2709 5433 3.624861 GGTTTCCATAGACAGACATGCAG 59.375 47.826 0.00 0.00 0.00 4.41
2712 5436 0.580578 CATAGACAGACATGCAGCGC 59.419 55.000 0.00 0.00 0.00 5.92
2714 5438 0.179127 TAGACAGACATGCAGCGCTC 60.179 55.000 7.13 2.98 0.00 5.03
2715 5439 1.739196 GACAGACATGCAGCGCTCA 60.739 57.895 7.13 9.72 0.00 4.26
2717 5441 1.088340 ACAGACATGCAGCGCTCATC 61.088 55.000 7.13 4.73 0.00 2.92
2718 5442 1.881709 AGACATGCAGCGCTCATCG 60.882 57.895 7.13 11.26 42.12 3.84
2719 5443 2.125391 ACATGCAGCGCTCATCGT 60.125 55.556 7.13 11.83 41.07 3.73
2720 5444 1.699656 GACATGCAGCGCTCATCGTT 61.700 55.000 7.13 1.20 41.07 3.85
2721 5445 0.460109 ACATGCAGCGCTCATCGTTA 60.460 50.000 7.13 0.00 41.07 3.18
2726 5450 2.292292 TGCAGCGCTCATCGTTATACTA 59.708 45.455 7.13 0.00 41.07 1.82
2735 5459 6.401260 CGCTCATCGTTATACTATCTTCGTCT 60.401 42.308 0.00 0.00 0.00 4.18
2936 8143 1.271054 ACTCTTTGGCGCATTCTCACT 60.271 47.619 10.83 0.00 0.00 3.41
3082 8612 9.691362 TTTTTATTTTACTGTTCATGAGGAAGC 57.309 29.630 0.00 0.00 35.82 3.86
3083 8613 7.994425 TTATTTTACTGTTCATGAGGAAGCA 57.006 32.000 0.00 0.00 35.82 3.91
3084 8614 8.579850 TTATTTTACTGTTCATGAGGAAGCAT 57.420 30.769 0.00 0.00 35.82 3.79
3085 8615 6.899393 TTTTACTGTTCATGAGGAAGCATT 57.101 33.333 0.00 0.00 35.82 3.56
3086 8616 6.899393 TTTACTGTTCATGAGGAAGCATTT 57.101 33.333 0.00 0.00 35.82 2.32
3087 8617 4.778534 ACTGTTCATGAGGAAGCATTTG 57.221 40.909 0.00 0.00 35.82 2.32
3088 8618 4.401022 ACTGTTCATGAGGAAGCATTTGA 58.599 39.130 0.00 0.00 35.82 2.69
3089 8619 4.458295 ACTGTTCATGAGGAAGCATTTGAG 59.542 41.667 0.00 0.00 35.82 3.02
3090 8620 3.192001 TGTTCATGAGGAAGCATTTGAGC 59.808 43.478 0.00 0.00 35.82 4.26
3092 8622 3.276857 TCATGAGGAAGCATTTGAGCTC 58.723 45.455 6.82 6.82 45.89 4.09
3093 8623 1.730501 TGAGGAAGCATTTGAGCTCG 58.269 50.000 9.64 0.00 45.89 5.03
3094 8624 1.012841 GAGGAAGCATTTGAGCTCGG 58.987 55.000 9.64 0.00 45.89 4.63
3166 8696 0.725117 CAATTTCGTCTACCGTGGCC 59.275 55.000 0.00 0.00 37.94 5.36
3204 8734 7.684317 TGGGAGTGGACAAGATATTGTTATA 57.316 36.000 7.23 0.00 34.90 0.98
3236 8766 5.299279 TCTCAAAGGTAAAGCAGAAACAAGG 59.701 40.000 0.00 0.00 0.00 3.61
3339 9073 9.632807 TGTATAATTTACATCACCAAAAAGTGC 57.367 29.630 0.00 0.00 37.68 4.40
3340 9074 9.855021 GTATAATTTACATCACCAAAAAGTGCT 57.145 29.630 0.00 0.00 37.68 4.40
3412 9146 8.777865 TTGATGATGTAAAACTTCTACTCCAG 57.222 34.615 0.00 0.00 0.00 3.86
3466 9200 9.337396 AGTTCAACTACTACATCATTTCAAACA 57.663 29.630 0.00 0.00 0.00 2.83
3488 9223 7.851822 ACACAATTTAAAATAGCACGTTCAG 57.148 32.000 0.00 0.00 0.00 3.02
3555 9290 6.525578 TCAAACTAGTACATCCATCGAACT 57.474 37.500 0.00 0.00 0.00 3.01
3568 9303 8.646004 ACATCCATCGAACTACTACTACTACTA 58.354 37.037 0.00 0.00 0.00 1.82
3570 9305 8.243961 TCCATCGAACTACTACTACTACTACT 57.756 38.462 0.00 0.00 0.00 2.57
3571 9306 8.700051 TCCATCGAACTACTACTACTACTACTT 58.300 37.037 0.00 0.00 0.00 2.24
3572 9307 8.977505 CCATCGAACTACTACTACTACTACTTC 58.022 40.741 0.00 0.00 0.00 3.01
3573 9308 9.748708 CATCGAACTACTACTACTACTACTTCT 57.251 37.037 0.00 0.00 0.00 2.85
3585 9320 8.621286 ACTACTACTACTTCTAGTCTACTCGTC 58.379 40.741 0.00 0.00 34.79 4.20
3607 9342 1.153667 GCTCTCGAACTGCTCCCAG 60.154 63.158 0.00 0.00 44.80 4.45
3617 9352 0.397941 CTGCTCCCAGAACTTGTCCA 59.602 55.000 0.00 0.00 41.77 4.02
3618 9353 1.004044 CTGCTCCCAGAACTTGTCCAT 59.996 52.381 0.00 0.00 41.77 3.41
3619 9354 1.003580 TGCTCCCAGAACTTGTCCATC 59.996 52.381 0.00 0.00 0.00 3.51
3620 9355 1.003580 GCTCCCAGAACTTGTCCATCA 59.996 52.381 0.00 0.00 0.00 3.07
3621 9356 2.704572 CTCCCAGAACTTGTCCATCAC 58.295 52.381 0.00 0.00 0.00 3.06
3622 9357 2.304180 CTCCCAGAACTTGTCCATCACT 59.696 50.000 0.00 0.00 0.00 3.41
3623 9358 3.515502 CTCCCAGAACTTGTCCATCACTA 59.484 47.826 0.00 0.00 0.00 2.74
3624 9359 3.260884 TCCCAGAACTTGTCCATCACTAC 59.739 47.826 0.00 0.00 0.00 2.73
3625 9360 3.007940 CCCAGAACTTGTCCATCACTACA 59.992 47.826 0.00 0.00 0.00 2.74
3626 9361 4.504864 CCCAGAACTTGTCCATCACTACAA 60.505 45.833 0.00 0.00 34.57 2.41
3627 9362 5.063204 CCAGAACTTGTCCATCACTACAAA 58.937 41.667 0.00 0.00 35.32 2.83
3628 9363 5.530915 CCAGAACTTGTCCATCACTACAAAA 59.469 40.000 0.00 0.00 35.32 2.44
3629 9364 6.039270 CCAGAACTTGTCCATCACTACAAAAA 59.961 38.462 0.00 0.00 35.32 1.94
3652 9387 6.583912 AAAATACACTTCCGTGATGATACG 57.416 37.500 0.00 0.00 43.97 3.06
3653 9388 4.913335 ATACACTTCCGTGATGATACGT 57.087 40.909 0.00 0.00 43.97 3.57
3654 9389 2.876091 ACACTTCCGTGATGATACGTG 58.124 47.619 0.00 0.00 43.97 4.49
3655 9390 2.230508 ACACTTCCGTGATGATACGTGT 59.769 45.455 0.00 0.00 43.97 4.49
3656 9391 3.250744 CACTTCCGTGATGATACGTGTT 58.749 45.455 0.00 0.00 43.97 3.32
3657 9392 3.678072 CACTTCCGTGATGATACGTGTTT 59.322 43.478 0.00 0.00 43.97 2.83
3658 9393 3.678072 ACTTCCGTGATGATACGTGTTTG 59.322 43.478 0.00 0.00 42.24 2.93
3659 9394 3.306917 TCCGTGATGATACGTGTTTGT 57.693 42.857 0.00 0.00 42.24 2.83
3660 9395 3.247442 TCCGTGATGATACGTGTTTGTC 58.753 45.455 0.00 0.00 42.24 3.18
3661 9396 2.990514 CCGTGATGATACGTGTTTGTCA 59.009 45.455 0.00 0.00 42.24 3.58
3662 9397 3.181534 CCGTGATGATACGTGTTTGTCAC 60.182 47.826 0.00 6.93 42.24 3.67
3663 9398 3.427193 CGTGATGATACGTGTTTGTCACA 59.573 43.478 18.33 0.60 46.44 3.58
3664 9399 4.432892 CGTGATGATACGTGTTTGTCACAG 60.433 45.833 18.33 11.29 46.44 3.66
3665 9400 4.447724 GTGATGATACGTGTTTGTCACAGT 59.552 41.667 15.50 0.00 46.44 3.55
3666 9401 5.631929 GTGATGATACGTGTTTGTCACAGTA 59.368 40.000 15.50 0.00 46.44 2.74
3667 9402 5.861787 TGATGATACGTGTTTGTCACAGTAG 59.138 40.000 0.00 0.00 46.44 2.57
3668 9403 4.552355 TGATACGTGTTTGTCACAGTAGG 58.448 43.478 0.00 0.00 46.44 3.18
3669 9404 2.973694 ACGTGTTTGTCACAGTAGGT 57.026 45.000 0.00 0.00 46.44 3.08
3670 9405 2.817901 ACGTGTTTGTCACAGTAGGTC 58.182 47.619 0.00 0.00 46.44 3.85
3671 9406 1.784856 CGTGTTTGTCACAGTAGGTCG 59.215 52.381 0.00 0.00 46.44 4.79
3672 9407 1.525619 GTGTTTGTCACAGTAGGTCGC 59.474 52.381 0.00 0.00 45.51 5.19
3673 9408 0.782384 GTTTGTCACAGTAGGTCGCG 59.218 55.000 0.00 0.00 0.00 5.87
3674 9409 0.386476 TTTGTCACAGTAGGTCGCGT 59.614 50.000 5.77 0.00 0.00 6.01
3675 9410 0.386476 TTGTCACAGTAGGTCGCGTT 59.614 50.000 5.77 0.00 0.00 4.84
3676 9411 0.386476 TGTCACAGTAGGTCGCGTTT 59.614 50.000 5.77 0.00 0.00 3.60
3677 9412 1.202440 TGTCACAGTAGGTCGCGTTTT 60.202 47.619 5.77 0.00 0.00 2.43
3678 9413 1.862827 GTCACAGTAGGTCGCGTTTTT 59.137 47.619 5.77 0.00 0.00 1.94
3697 9432 5.718724 TTTTTGTCATGCATGTACATCCA 57.281 34.783 25.43 2.99 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.816074 GTCCACAGAAACCCGCATTA 58.184 50.000 0.00 0.00 0.00 1.90
6 7 1.671054 CGTCCACAGAAACCCGCAT 60.671 57.895 0.00 0.00 0.00 4.73
10 11 0.323629 TGGATCGTCCACAGAAACCC 59.676 55.000 3.02 0.00 42.67 4.11
56 57 3.128589 GCAATCAGCGGGACAAATAAGAA 59.871 43.478 0.00 0.00 0.00 2.52
81 82 3.371898 GCAGGCAGGCAATCATTTTAAAC 59.628 43.478 0.00 0.00 0.00 2.01
84 85 2.177734 TGCAGGCAGGCAATCATTTTA 58.822 42.857 1.11 0.00 41.65 1.52
105 109 7.136203 AGATCTTAGGGAGAGGTTTTCATAGT 58.864 38.462 0.00 0.00 37.93 2.12
171 175 1.307309 CAAGATGGGGGTGATGGCA 59.693 57.895 0.00 0.00 0.00 4.92
176 180 0.407918 GGGAAACAAGATGGGGGTGA 59.592 55.000 0.00 0.00 0.00 4.02
181 185 4.342092 GTGATATTGGGGAAACAAGATGGG 59.658 45.833 0.00 0.00 32.88 4.00
185 189 3.596046 AGGGTGATATTGGGGAAACAAGA 59.404 43.478 0.00 0.00 33.23 3.02
260 264 0.109342 CCGCCCATAGGAAGAGCAAT 59.891 55.000 0.00 0.00 33.47 3.56
291 296 3.365364 CGAGAGCAAAATGACTCAAACCC 60.365 47.826 0.00 0.00 35.28 4.11
304 311 2.224281 ACAATCACCAGTCGAGAGCAAA 60.224 45.455 0.00 0.00 0.00 3.68
305 312 1.344438 ACAATCACCAGTCGAGAGCAA 59.656 47.619 0.00 0.00 0.00 3.91
312 319 2.146342 AGCTCAAACAATCACCAGTCG 58.854 47.619 0.00 0.00 0.00 4.18
347 354 4.547532 AGTTGACGCTCGAATGGATATAC 58.452 43.478 0.00 0.00 0.00 1.47
348 355 4.848562 AGTTGACGCTCGAATGGATATA 57.151 40.909 0.00 0.00 0.00 0.86
349 356 3.735237 AGTTGACGCTCGAATGGATAT 57.265 42.857 0.00 0.00 0.00 1.63
350 357 4.642445 TTAGTTGACGCTCGAATGGATA 57.358 40.909 0.00 0.00 0.00 2.59
351 358 3.520290 TTAGTTGACGCTCGAATGGAT 57.480 42.857 0.00 0.00 0.00 3.41
355 369 3.306166 CCGAAATTAGTTGACGCTCGAAT 59.694 43.478 0.00 0.00 0.00 3.34
374 388 3.569491 AGTTAATATTCCCTCCGTCCGA 58.431 45.455 0.00 0.00 0.00 4.55
448 792 1.002888 AGAGACAAGGCACCATGTCAG 59.997 52.381 22.90 0.00 44.74 3.51
459 803 5.147162 GCGTGAAACATTTTAGAGACAAGG 58.853 41.667 0.00 0.00 35.74 3.61
502 2748 2.095768 TCGCTTAGCATTGAACAACAGC 60.096 45.455 4.70 0.00 0.00 4.40
515 2761 2.947852 TGACTCTTTCTGTCGCTTAGC 58.052 47.619 0.00 0.00 37.26 3.09
516 2762 5.907197 TTTTGACTCTTTCTGTCGCTTAG 57.093 39.130 0.00 0.00 37.26 2.18
517 2763 6.861065 AATTTTGACTCTTTCTGTCGCTTA 57.139 33.333 0.00 0.00 37.26 3.09
518 2764 5.757850 AATTTTGACTCTTTCTGTCGCTT 57.242 34.783 0.00 0.00 37.26 4.68
519 2765 7.173218 TCAATAATTTTGACTCTTTCTGTCGCT 59.827 33.333 0.00 0.00 37.26 4.93
520 2766 7.298122 TCAATAATTTTGACTCTTTCTGTCGC 58.702 34.615 0.00 0.00 37.26 5.19
529 2775 9.250624 GCGTACTAGATCAATAATTTTGACTCT 57.749 33.333 0.00 10.25 0.00 3.24
530 2776 8.488764 GGCGTACTAGATCAATAATTTTGACTC 58.511 37.037 0.00 5.58 0.00 3.36
532 2778 7.281484 CGGCGTACTAGATCAATAATTTTGAC 58.719 38.462 0.00 2.31 0.00 3.18
533 2779 6.073980 GCGGCGTACTAGATCAATAATTTTGA 60.074 38.462 9.37 5.81 0.00 2.69
534 2780 6.071463 GCGGCGTACTAGATCAATAATTTTG 58.929 40.000 9.37 0.00 0.00 2.44
674 3355 2.381911 CAGGGCACTTGGATAATTGCT 58.618 47.619 0.00 0.00 40.93 3.91
677 3358 2.582636 AGTCCAGGGCACTTGGATAATT 59.417 45.455 9.89 0.00 33.91 1.40
730 3412 9.231297 TCTATTTGATCAGAACCCTTAAGTTTG 57.769 33.333 0.97 0.00 0.00 2.93
769 3455 5.297547 ACGTACACATTTGATCAGAACAGT 58.702 37.500 0.00 0.00 0.00 3.55
797 3502 0.960364 GGCCCAACTCATCGCTTGAA 60.960 55.000 0.00 0.00 32.78 2.69
1013 3718 4.162690 GGAAGAGGACCGCGGCAT 62.163 66.667 28.58 16.46 0.00 4.40
1027 3732 1.920351 GACCAAGGTGGGGATAAGGAA 59.080 52.381 0.00 0.00 43.37 3.36
1029 3734 0.180406 CGACCAAGGTGGGGATAAGG 59.820 60.000 0.00 0.00 43.37 2.69
1032 3737 2.090943 AGATACGACCAAGGTGGGGATA 60.091 50.000 6.22 0.00 43.37 2.59
1082 3790 2.501492 AGCTTCCCATTGCTGATGC 58.499 52.632 0.00 0.00 38.21 3.91
1263 3971 0.911769 ATTTCATCACCTCCTCCGCA 59.088 50.000 0.00 0.00 0.00 5.69
1920 4634 5.041191 AGATAATGGCCTTGATTTCGACT 57.959 39.130 3.32 0.00 0.00 4.18
1981 4702 8.715998 CAGTACGTACTATATACTTTGATCGGT 58.284 37.037 26.95 0.00 34.13 4.69
1982 4703 8.715998 ACAGTACGTACTATATACTTTGATCGG 58.284 37.037 26.95 11.64 34.13 4.18
2002 4723 3.572584 GCACGCCTACCATATACAGTAC 58.427 50.000 0.00 0.00 0.00 2.73
2003 4724 2.227149 CGCACGCCTACCATATACAGTA 59.773 50.000 0.00 0.00 0.00 2.74
2004 4725 1.000607 CGCACGCCTACCATATACAGT 60.001 52.381 0.00 0.00 0.00 3.55
2005 4726 1.698165 CGCACGCCTACCATATACAG 58.302 55.000 0.00 0.00 0.00 2.74
2006 4727 0.319211 GCGCACGCCTACCATATACA 60.319 55.000 0.30 0.00 34.56 2.29
2007 4728 1.342082 CGCGCACGCCTACCATATAC 61.342 60.000 8.75 0.00 37.98 1.47
2013 4734 3.652733 TATATCACGCGCACGCCTACC 62.653 57.143 5.73 0.00 45.53 3.18
2016 4737 0.528901 TTTATATCACGCGCACGCCT 60.529 50.000 5.73 0.00 45.53 5.52
2034 4755 6.035843 CAGCTTATCAACAACAACAACAGTT 58.964 36.000 0.00 0.00 0.00 3.16
2035 4756 5.356751 TCAGCTTATCAACAACAACAACAGT 59.643 36.000 0.00 0.00 0.00 3.55
2036 4757 5.682862 GTCAGCTTATCAACAACAACAACAG 59.317 40.000 0.00 0.00 0.00 3.16
2064 4785 1.333931 TCCTGCTCGATCGTGATACAC 59.666 52.381 20.54 3.37 0.00 2.90
2701 5425 1.699656 AACGATGAGCGCTGCATGTC 61.700 55.000 18.48 7.46 46.04 3.06
2702 5426 0.460109 TAACGATGAGCGCTGCATGT 60.460 50.000 18.48 14.85 46.04 3.21
2703 5427 0.863799 ATAACGATGAGCGCTGCATG 59.136 50.000 18.48 14.28 46.04 4.06
2705 5429 1.067060 AGTATAACGATGAGCGCTGCA 59.933 47.619 18.48 13.78 46.04 4.41
2706 5430 1.772182 AGTATAACGATGAGCGCTGC 58.228 50.000 18.48 7.36 46.04 5.25
2707 5431 4.975788 AGATAGTATAACGATGAGCGCTG 58.024 43.478 18.48 1.67 46.04 5.18
2708 5432 5.630661 AAGATAGTATAACGATGAGCGCT 57.369 39.130 11.27 11.27 46.04 5.92
2709 5433 4.492645 CGAAGATAGTATAACGATGAGCGC 59.507 45.833 0.00 0.00 46.04 5.92
2712 5436 8.019769 TGAGACGAAGATAGTATAACGATGAG 57.980 38.462 0.00 0.00 0.00 2.90
2714 5438 9.447040 TTTTGAGACGAAGATAGTATAACGATG 57.553 33.333 0.00 0.00 0.00 3.84
2726 5450 8.237267 GGTCAACATTTATTTTGAGACGAAGAT 58.763 33.333 0.00 0.00 32.40 2.40
3059 8589 7.994425 TGCTTCCTCATGAACAGTAAAATAA 57.006 32.000 0.00 0.00 0.00 1.40
3060 8590 8.579850 AATGCTTCCTCATGAACAGTAAAATA 57.420 30.769 0.00 0.00 0.00 1.40
3072 8602 2.031807 CGAGCTCAAATGCTTCCTCATG 59.968 50.000 15.40 0.00 44.17 3.07
3075 8605 1.012841 CCGAGCTCAAATGCTTCCTC 58.987 55.000 15.40 0.00 44.17 3.71
3079 8609 3.165606 CTCCCGAGCTCAAATGCTT 57.834 52.632 15.40 0.00 44.17 3.91
3090 8620 1.698506 AGTCCTATTCAGCTCCCGAG 58.301 55.000 0.00 0.00 0.00 4.63
3091 8621 2.160721 AAGTCCTATTCAGCTCCCGA 57.839 50.000 0.00 0.00 0.00 5.14
3092 8622 2.168521 TGAAAGTCCTATTCAGCTCCCG 59.831 50.000 0.00 0.00 33.15 5.14
3093 8623 3.198853 AGTGAAAGTCCTATTCAGCTCCC 59.801 47.826 0.00 0.00 37.46 4.30
3094 8624 4.479786 AGTGAAAGTCCTATTCAGCTCC 57.520 45.455 0.00 0.00 37.46 4.70
3166 8696 3.133362 CCACTCCCAATCCCATTTTGATG 59.867 47.826 0.00 0.00 0.00 3.07
3177 8707 5.440610 ACAATATCTTGTCCACTCCCAATC 58.559 41.667 0.00 0.00 41.86 2.67
3204 8734 9.905713 TTCTGCTTTACCTTTGAGAACATATAT 57.094 29.630 0.00 0.00 0.00 0.86
3236 8766 7.498239 AGTTCTTTTTCTACTTTACCTCACACC 59.502 37.037 0.00 0.00 0.00 4.16
3358 9092 5.305128 ACATCATGTGTTGGAGTTGGAAATT 59.695 36.000 0.00 0.00 38.01 1.82
3360 9094 4.214310 ACATCATGTGTTGGAGTTGGAAA 58.786 39.130 0.00 0.00 38.01 3.13
3363 9097 7.572523 AATATACATCATGTGTTGGAGTTGG 57.427 36.000 0.00 0.00 42.29 3.77
3412 9146 9.443283 GTTTACATCTTCAAATACATCATCTGC 57.557 33.333 0.00 0.00 0.00 4.26
3466 9200 9.953697 TTAACTGAACGTGCTATTTTAAATTGT 57.046 25.926 0.00 0.00 0.00 2.71
3482 9217 6.857964 AGAATGATGTTTGCTTTAACTGAACG 59.142 34.615 0.00 0.00 0.00 3.95
3532 9267 6.525578 AGTTCGATGGATGTACTAGTTTGA 57.474 37.500 0.00 0.00 0.00 2.69
3540 9275 7.727331 AGTAGTAGTAGTTCGATGGATGTAC 57.273 40.000 0.00 0.00 0.00 2.90
3568 9303 3.178267 CGACGACGAGTAGACTAGAAGT 58.822 50.000 0.00 0.00 42.66 3.01
3570 9305 1.923204 GCGACGACGAGTAGACTAGAA 59.077 52.381 12.29 0.00 42.66 2.10
3571 9306 1.133982 AGCGACGACGAGTAGACTAGA 59.866 52.381 12.29 0.00 42.66 2.43
3572 9307 1.518102 GAGCGACGACGAGTAGACTAG 59.482 57.143 12.29 0.00 42.66 2.57
3573 9308 1.133982 AGAGCGACGACGAGTAGACTA 59.866 52.381 12.29 0.00 42.66 2.59
3637 9372 3.678072 ACAAACACGTATCATCACGGAAG 59.322 43.478 0.00 0.00 46.12 3.46
3638 9373 3.655486 ACAAACACGTATCATCACGGAA 58.345 40.909 0.00 0.00 46.12 4.30
3639 9374 3.247442 GACAAACACGTATCATCACGGA 58.753 45.455 0.00 0.00 46.12 4.69
3640 9375 2.990514 TGACAAACACGTATCATCACGG 59.009 45.455 0.00 0.00 46.12 4.94
3653 9388 1.860676 GCGACCTACTGTGACAAACA 58.139 50.000 0.00 0.00 37.22 2.83
3654 9389 0.782384 CGCGACCTACTGTGACAAAC 59.218 55.000 0.00 0.00 0.00 2.93
3655 9390 0.386476 ACGCGACCTACTGTGACAAA 59.614 50.000 15.93 0.00 0.00 2.83
3656 9391 0.386476 AACGCGACCTACTGTGACAA 59.614 50.000 15.93 0.00 0.00 3.18
3657 9392 0.386476 AAACGCGACCTACTGTGACA 59.614 50.000 15.93 0.00 0.00 3.58
3658 9393 1.494824 AAAACGCGACCTACTGTGAC 58.505 50.000 15.93 0.00 0.00 3.67
3659 9394 2.228138 AAAAACGCGACCTACTGTGA 57.772 45.000 15.93 0.00 0.00 3.58
3675 9410 5.718724 TGGATGTACATGCATGACAAAAA 57.281 34.783 32.75 16.53 34.14 1.94


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

AutoCloner maintained by Alex Coulton.