Multiple sequence alignment - TraesCS3D01G151000

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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 TraesCS3D01G151000 chr3D 100.000 4326 0 0 1 4326 116018538 116022863 0.000000e+00 7989
1 TraesCS3D01G151000 chr3D 90.091 767 48 20 63 827 231171501 231170761 0.000000e+00 970
2 TraesCS3D01G151000 chr3D 89.714 768 52 13 62 827 231187141 231186399 0.000000e+00 955
3 TraesCS3D01G151000 chr3D 87.856 527 59 5 3803 4325 116011110 116011635 7.950000e-172 614
4 TraesCS3D01G151000 chr3B 95.198 1895 86 2 827 2718 169429561 169431453 0.000000e+00 2990
5 TraesCS3D01G151000 chr3B 94.824 1449 47 8 2880 4326 169431452 169432874 0.000000e+00 2235
6 TraesCS3D01G151000 chr3B 87.205 508 62 3 3821 4325 169424777 169425284 3.750000e-160 575
7 TraesCS3D01G151000 chr3B 97.619 168 4 0 2714 2881 571752692 571752525 5.470000e-74 289
8 TraesCS3D01G151000 chr3A 92.069 1450 99 10 831 2266 112925821 112927268 0.000000e+00 2026
9 TraesCS3D01G151000 chr3A 91.871 775 35 12 3566 4326 112936450 112937210 0.000000e+00 1057
10 TraesCS3D01G151000 chr3A 85.340 839 78 36 1 827 562235666 562236471 0.000000e+00 826
11 TraesCS3D01G151000 chr3A 88.068 528 57 5 3802 4325 112917991 112918516 4.750000e-174 621
12 TraesCS3D01G151000 chr3A 91.250 320 25 3 3050 3367 112935973 112936291 2.390000e-117 433
13 TraesCS3D01G151000 chr3A 86.486 296 31 7 2426 2718 112933748 112934037 2.510000e-82 316
14 TraesCS3D01G151000 chr3A 89.011 182 18 2 2263 2443 112931844 112932024 1.570000e-54 224
15 TraesCS3D01G151000 chr3A 90.141 142 9 3 3434 3570 112936281 112936422 3.440000e-41 180
16 TraesCS3D01G151000 chr6B 84.117 1574 211 22 842 2390 179659692 179658133 0.000000e+00 1485
17 TraesCS3D01G151000 chr6B 80.330 727 65 39 116 827 29216898 29216235 3.030000e-131 479
18 TraesCS3D01G151000 chr6D 84.088 1546 203 24 862 2378 93433970 93435501 0.000000e+00 1452
19 TraesCS3D01G151000 chr6D 83.333 1494 181 34 838 2295 96643939 96642478 0.000000e+00 1317
20 TraesCS3D01G151000 chr6D 82.019 1585 213 41 835 2378 96650679 96649126 0.000000e+00 1282
21 TraesCS3D01G151000 chr6D 78.415 366 53 20 3193 3553 93436005 93436349 9.420000e-52 215
22 TraesCS3D01G151000 chr6D 91.270 126 11 0 702 827 264165464 264165589 5.750000e-39 172
23 TraesCS3D01G151000 chr6A 83.086 1484 169 32 849 2283 115347861 115346411 0.000000e+00 1275
24 TraesCS3D01G151000 chr6A 84.211 969 132 15 1433 2390 115341643 115340685 0.000000e+00 922
25 TraesCS3D01G151000 chr6A 79.953 429 47 28 422 827 68621649 68621237 3.290000e-71 279
26 TraesCS3D01G151000 chr6A 84.672 137 16 5 1149 1281 115341769 115341634 9.760000e-27 132
27 TraesCS3D01G151000 chr6A 81.522 92 15 2 3462 3553 115339232 115339143 1.670000e-09 75
28 TraesCS3D01G151000 chr2A 89.062 768 57 20 62 827 511264535 511263793 0.000000e+00 928
29 TraesCS3D01G151000 chr2A 88.684 760 60 20 62 819 511248044 511247309 0.000000e+00 904
30 TraesCS3D01G151000 chr7D 86.831 729 67 20 62 788 309304675 309303974 0.000000e+00 787
31 TraesCS3D01G151000 chr7D 92.252 413 27 5 190 601 309318162 309317754 8.060000e-162 580
32 TraesCS3D01G151000 chr7D 95.480 177 7 1 2705 2881 149093800 149093625 9.160000e-72 281
33 TraesCS3D01G151000 chr7D 90.551 127 10 2 702 828 386549755 386549879 2.680000e-37 167
34 TraesCS3D01G151000 chr1B 84.665 776 83 27 62 837 313276083 313276822 0.000000e+00 741
35 TraesCS3D01G151000 chr7B 80.958 814 96 41 42 827 355723897 355724679 1.340000e-164 590
36 TraesCS3D01G151000 chr5A 79.531 811 92 49 32 827 95517984 95518735 1.070000e-140 510
37 TraesCS3D01G151000 chr5A 83.429 350 30 19 482 828 580538935 580539259 2.530000e-77 300
38 TraesCS3D01G151000 chr5A 95.000 180 8 1 2705 2884 640948268 640948090 9.160000e-72 281
39 TraesCS3D01G151000 chr4A 79.663 772 92 39 64 827 175480915 175480201 3.000000e-136 496
40 TraesCS3D01G151000 chr4A 82.105 190 22 11 639 828 142465684 142465861 7.490000e-33 152
41 TraesCS3D01G151000 chr1A 97.619 168 4 0 2715 2882 393948620 393948453 5.470000e-74 289
42 TraesCS3D01G151000 chr7A 94.149 188 8 3 2707 2893 6316657 6316842 2.550000e-72 283
43 TraesCS3D01G151000 chr7A 93.514 185 8 4 2711 2893 604387336 604387518 5.510000e-69 272
44 TraesCS3D01G151000 chr7A 77.366 486 62 28 377 827 529292230 529291758 1.200000e-60 244
45 TraesCS3D01G151000 chr2D 95.480 177 6 2 2708 2883 516708485 516708310 9.160000e-72 281
46 TraesCS3D01G151000 chr2D 95.954 173 7 0 2714 2886 560959482 560959654 9.160000e-72 281
47 TraesCS3D01G151000 chr2D 92.973 185 12 1 2707 2891 316333938 316334121 7.130000e-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 TraesCS3D01G151000 chr3D 116018538 116022863 4325 False 7989.000000 7989 100.000000 1 4326 1 chr3D.!!$F2 4325
1 TraesCS3D01G151000 chr3D 231170761 231171501 740 True 970.000000 970 90.091000 63 827 1 chr3D.!!$R1 764
2 TraesCS3D01G151000 chr3D 231186399 231187141 742 True 955.000000 955 89.714000 62 827 1 chr3D.!!$R2 765
3 TraesCS3D01G151000 chr3D 116011110 116011635 525 False 614.000000 614 87.856000 3803 4325 1 chr3D.!!$F1 522
4 TraesCS3D01G151000 chr3B 169429561 169432874 3313 False 2612.500000 2990 95.011000 827 4326 2 chr3B.!!$F2 3499
5 TraesCS3D01G151000 chr3B 169424777 169425284 507 False 575.000000 575 87.205000 3821 4325 1 chr3B.!!$F1 504
6 TraesCS3D01G151000 chr3A 112925821 112927268 1447 False 2026.000000 2026 92.069000 831 2266 1 chr3A.!!$F2 1435
7 TraesCS3D01G151000 chr3A 562235666 562236471 805 False 826.000000 826 85.340000 1 827 1 chr3A.!!$F3 826
8 TraesCS3D01G151000 chr3A 112917991 112918516 525 False 621.000000 621 88.068000 3802 4325 1 chr3A.!!$F1 523
9 TraesCS3D01G151000 chr3A 112931844 112937210 5366 False 442.000000 1057 89.751800 2263 4326 5 chr3A.!!$F4 2063
10 TraesCS3D01G151000 chr6B 179658133 179659692 1559 True 1485.000000 1485 84.117000 842 2390 1 chr6B.!!$R2 1548
11 TraesCS3D01G151000 chr6B 29216235 29216898 663 True 479.000000 479 80.330000 116 827 1 chr6B.!!$R1 711
12 TraesCS3D01G151000 chr6D 96642478 96643939 1461 True 1317.000000 1317 83.333000 838 2295 1 chr6D.!!$R1 1457
13 TraesCS3D01G151000 chr6D 96649126 96650679 1553 True 1282.000000 1282 82.019000 835 2378 1 chr6D.!!$R2 1543
14 TraesCS3D01G151000 chr6D 93433970 93436349 2379 False 833.500000 1452 81.251500 862 3553 2 chr6D.!!$F2 2691
15 TraesCS3D01G151000 chr6A 115346411 115347861 1450 True 1275.000000 1275 83.086000 849 2283 1 chr6A.!!$R2 1434
16 TraesCS3D01G151000 chr6A 115339143 115341769 2626 True 376.333333 922 83.468333 1149 3553 3 chr6A.!!$R3 2404
17 TraesCS3D01G151000 chr2A 511263793 511264535 742 True 928.000000 928 89.062000 62 827 1 chr2A.!!$R2 765
18 TraesCS3D01G151000 chr2A 511247309 511248044 735 True 904.000000 904 88.684000 62 819 1 chr2A.!!$R1 757
19 TraesCS3D01G151000 chr7D 309303974 309304675 701 True 787.000000 787 86.831000 62 788 1 chr7D.!!$R2 726
20 TraesCS3D01G151000 chr1B 313276083 313276822 739 False 741.000000 741 84.665000 62 837 1 chr1B.!!$F1 775
21 TraesCS3D01G151000 chr7B 355723897 355724679 782 False 590.000000 590 80.958000 42 827 1 chr7B.!!$F1 785
22 TraesCS3D01G151000 chr5A 95517984 95518735 751 False 510.000000 510 79.531000 32 827 1 chr5A.!!$F1 795
23 TraesCS3D01G151000 chr4A 175480201 175480915 714 True 496.000000 496 79.663000 64 827 1 chr4A.!!$R1 763

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
133 140 1.135344 GCTCCTACGTTCAGACTCCAC 60.135 57.143 0.0 0.0 0.00 4.02 F
1075 1194 0.944311 GTTGCGTCACATCCTCGTGT 60.944 55.000 0.0 0.0 38.12 4.49 F
2153 2293 0.036022 AGCACCTTCACTTCTGAGGC 59.964 55.000 0.0 0.0 0.00 4.70 F
2424 2750 1.080569 GTTTTGGCACCCGCAGATG 60.081 57.895 0.0 0.0 41.24 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1280 0.250467 CAGGGTGACAGGACTTGTGG 60.250 60.000 0.0 0.0 41.05 4.17 R
2869 4959 2.761208 CCTGTCAATCTACTTCCTCCGT 59.239 50.000 0.0 0.0 0.00 4.69 R
3188 7486 0.874390 GGCACGCATCAGAACTTCAA 59.126 50.000 0.0 0.0 0.00 2.69 R
3929 8282 1.005394 GCGGTCCACCTCGAAGAAA 60.005 57.895 0.0 0.0 34.09 2.52 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
29 30 4.852134 TGAATGTGCTACTGTGCAAAAT 57.148 36.364 6.51 2.63 45.12 1.82
133 140 1.135344 GCTCCTACGTTCAGACTCCAC 60.135 57.143 0.00 0.00 0.00 4.02
259 268 2.465813 AGAGAGATGAAGACAGTGGGG 58.534 52.381 0.00 0.00 0.00 4.96
347 360 3.661944 TGCTCTGCTCTCTCTTCTTTTG 58.338 45.455 0.00 0.00 0.00 2.44
679 701 4.159693 CAGCTGTACTGTTGGAGGTGTATA 59.840 45.833 5.25 0.00 41.86 1.47
680 702 4.962995 AGCTGTACTGTTGGAGGTGTATAT 59.037 41.667 1.46 0.00 0.00 0.86
763 811 9.890352 GAAATCTGAGATGGATTTGCTTAATAC 57.110 33.333 0.00 0.00 41.59 1.89
805 853 6.659824 AGTTAAGGGTGGAATTACTATGTGG 58.340 40.000 0.00 0.00 0.00 4.17
833 881 4.565531 GGGTCGTTACACGTGAGG 57.434 61.111 25.01 6.58 43.14 3.86
949 1026 5.576447 TCGACTGATTACTGAGCAACATA 57.424 39.130 0.00 0.00 0.00 2.29
1057 1176 2.037136 GCGCTGCCTGAAGACATGT 61.037 57.895 0.00 0.00 0.00 3.21
1075 1194 0.944311 GTTGCGTCACATCCTCGTGT 60.944 55.000 0.00 0.00 38.12 4.49
1161 1280 3.793144 CCGCTCTTCGTTGCAGCC 61.793 66.667 0.00 0.00 36.19 4.85
1171 1290 1.529244 GTTGCAGCCCACAAGTCCT 60.529 57.895 0.00 0.00 0.00 3.85
1182 1301 0.694444 ACAAGTCCTGTCACCCTGGT 60.694 55.000 0.00 0.00 29.87 4.00
1234 1356 4.892934 TGTTTGAAAGAGGCACCATTAACT 59.107 37.500 0.00 0.00 0.00 2.24
1236 1358 6.547880 TGTTTGAAAGAGGCACCATTAACTTA 59.452 34.615 0.00 0.00 0.00 2.24
1237 1359 7.232534 TGTTTGAAAGAGGCACCATTAACTTAT 59.767 33.333 0.00 0.00 0.00 1.73
1377 1508 2.189521 CCTGCCACGGGTGATACC 59.810 66.667 0.00 0.00 37.60 2.73
1440 1571 3.244976 GCAACATTTCTTCCCACAATCG 58.755 45.455 0.00 0.00 0.00 3.34
1581 1712 1.925120 CCATGCAAGATGGAGGGGA 59.075 57.895 0.00 0.00 41.64 4.81
1616 1747 0.109723 GCCCCTGTCACAAGTAACCA 59.890 55.000 0.00 0.00 0.00 3.67
1644 1775 7.450074 ACAGAAGTATTGTTGTCAATGGAGTA 58.550 34.615 4.06 0.00 43.17 2.59
1799 1936 2.351157 GCAGCTTTGTTAAGGACAGCAG 60.351 50.000 0.00 0.00 39.94 4.24
1829 1966 6.039159 AGGTGCGGTTACTTTAGTCTATACTC 59.961 42.308 0.00 0.00 37.15 2.59
1833 1970 6.072783 GCGGTTACTTTAGTCTATACTCGGAT 60.073 42.308 0.00 0.00 37.15 4.18
1844 1981 5.065474 GTCTATACTCGGATCTATCACTGGC 59.935 48.000 0.00 0.00 0.00 4.85
2097 2237 4.589647 TGGGATGAGAAATTCCACATCA 57.410 40.909 22.21 8.47 40.26 3.07
2153 2293 0.036022 AGCACCTTCACTTCTGAGGC 59.964 55.000 0.00 0.00 0.00 4.70
2169 2309 2.748605 GAGGCGAGTGTTATCCTCATG 58.251 52.381 2.53 0.00 43.42 3.07
2176 2325 4.256920 GAGTGTTATCCTCATGTGCTTGT 58.743 43.478 0.00 0.00 0.00 3.16
2314 2474 9.606631 TGCATTTTTAGGAAAAGTAATTGTTGT 57.393 25.926 0.00 0.00 38.09 3.32
2424 2750 1.080569 GTTTTGGCACCCGCAGATG 60.081 57.895 0.00 0.00 41.24 2.90
2676 4766 5.944007 AGACTTGTCCAGTTTACTTTTGTGT 59.056 36.000 0.00 0.00 35.01 3.72
2680 4770 5.250200 TGTCCAGTTTACTTTTGTGTCTGT 58.750 37.500 0.00 0.00 0.00 3.41
2695 4785 5.428253 TGTGTCTGTTCATCCTATTTAGGC 58.572 41.667 0.00 0.00 43.31 3.93
2725 4815 9.448587 ACTGGTTAATTATGTTATACTCCCTCT 57.551 33.333 0.00 0.00 0.00 3.69
2726 4816 9.712305 CTGGTTAATTATGTTATACTCCCTCTG 57.288 37.037 0.00 0.00 0.00 3.35
2727 4817 9.220906 TGGTTAATTATGTTATACTCCCTCTGT 57.779 33.333 0.00 0.00 0.00 3.41
2731 4821 8.568617 AATTATGTTATACTCCCTCTGTTCCT 57.431 34.615 0.00 0.00 0.00 3.36
2732 4822 9.670442 AATTATGTTATACTCCCTCTGTTCCTA 57.330 33.333 0.00 0.00 0.00 2.94
2733 4823 9.670442 ATTATGTTATACTCCCTCTGTTCCTAA 57.330 33.333 0.00 0.00 0.00 2.69
2734 4824 7.989947 ATGTTATACTCCCTCTGTTCCTAAA 57.010 36.000 0.00 0.00 0.00 1.85
2735 4825 7.989947 TGTTATACTCCCTCTGTTCCTAAAT 57.010 36.000 0.00 0.00 0.00 1.40
2736 4826 9.670442 ATGTTATACTCCCTCTGTTCCTAAATA 57.330 33.333 0.00 0.00 0.00 1.40
2737 4827 9.670442 TGTTATACTCCCTCTGTTCCTAAATAT 57.330 33.333 0.00 0.00 0.00 1.28
2742 4832 8.809468 ACTCCCTCTGTTCCTAAATATTTTTC 57.191 34.615 5.91 0.00 0.00 2.29
2743 4833 8.615705 ACTCCCTCTGTTCCTAAATATTTTTCT 58.384 33.333 5.91 0.00 0.00 2.52
2744 4834 9.467796 CTCCCTCTGTTCCTAAATATTTTTCTT 57.532 33.333 5.91 0.00 0.00 2.52
2745 4835 9.822727 TCCCTCTGTTCCTAAATATTTTTCTTT 57.177 29.630 5.91 0.00 0.00 2.52
2822 4912 6.578023 AGTGTAGATTCACTCATTTAGCTCC 58.422 40.000 0.00 0.00 44.07 4.70
2823 4913 5.460419 GTGTAGATTCACTCATTTAGCTCCG 59.540 44.000 0.00 0.00 35.68 4.63
2824 4914 4.744795 AGATTCACTCATTTAGCTCCGT 57.255 40.909 0.00 0.00 0.00 4.69
2825 4915 5.854010 AGATTCACTCATTTAGCTCCGTA 57.146 39.130 0.00 0.00 0.00 4.02
2826 4916 6.412362 AGATTCACTCATTTAGCTCCGTAT 57.588 37.500 0.00 0.00 0.00 3.06
2827 4917 6.219473 AGATTCACTCATTTAGCTCCGTATG 58.781 40.000 0.00 0.00 0.00 2.39
2828 4918 5.339008 TTCACTCATTTAGCTCCGTATGT 57.661 39.130 0.00 0.00 0.00 2.29
2829 4919 6.459670 TTCACTCATTTAGCTCCGTATGTA 57.540 37.500 0.00 0.00 0.00 2.29
2830 4920 6.073327 TCACTCATTTAGCTCCGTATGTAG 57.927 41.667 0.00 0.00 0.00 2.74
2831 4921 5.593095 TCACTCATTTAGCTCCGTATGTAGT 59.407 40.000 0.00 0.00 0.00 2.73
2832 4922 5.915758 CACTCATTTAGCTCCGTATGTAGTC 59.084 44.000 0.00 0.00 0.00 2.59
2833 4923 5.593095 ACTCATTTAGCTCCGTATGTAGTCA 59.407 40.000 0.00 0.00 0.00 3.41
2834 4924 5.828747 TCATTTAGCTCCGTATGTAGTCAC 58.171 41.667 0.00 0.00 0.00 3.67
2835 4925 5.593095 TCATTTAGCTCCGTATGTAGTCACT 59.407 40.000 0.00 0.00 0.00 3.41
2836 4926 5.909621 TTTAGCTCCGTATGTAGTCACTT 57.090 39.130 0.00 0.00 0.00 3.16
2837 4927 3.784701 AGCTCCGTATGTAGTCACTTG 57.215 47.619 0.00 0.00 0.00 3.16
2838 4928 3.090037 AGCTCCGTATGTAGTCACTTGT 58.910 45.455 0.00 0.00 0.00 3.16
2839 4929 3.510360 AGCTCCGTATGTAGTCACTTGTT 59.490 43.478 0.00 0.00 0.00 2.83
2840 4930 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2841 4931 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2842 4932 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2843 4933 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2844 4934 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2845 4935 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2846 4936 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2847 4937 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2848 4938 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2849 4939 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2850 4940 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2851 4941 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2852 4942 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2853 4943 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2854 4944 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2855 4945 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2856 4946 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2857 4947 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2858 4948 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2859 4949 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2872 4962 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2873 4963 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2874 4964 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2875 4965 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2876 4966 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
2877 4967 6.954232 AGACAAATATTTAGGAACGGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
2878 4968 7.048512 AGACAAATATTTAGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
2879 4969 6.718294 ACAAATATTTAGGAACGGAGGAAGT 58.282 36.000 0.00 0.00 0.00 3.01
2916 5006 8.538039 GTTACCTACATTTTATGTTCGTCTAGC 58.462 37.037 0.00 0.00 41.63 3.42
3016 5531 8.620116 ATTAAAATAAACTGCCAGCAATGTTT 57.380 26.923 12.72 12.72 36.69 2.83
3151 7429 3.750371 TCCAAATCTGTAGTTGTGTGGG 58.250 45.455 0.00 0.00 0.00 4.61
3188 7486 8.614814 ACTGGCAGTATATATATTGGGTTTGAT 58.385 33.333 20.61 0.00 0.00 2.57
3378 7676 5.525745 CCGTATTGGCTTTATGTGTATGTGA 59.474 40.000 0.00 0.00 0.00 3.58
3542 7842 4.623595 GTCTTAGAGAACACTGTTGCTAGC 59.376 45.833 8.10 8.10 0.00 3.42
3613 7948 4.638865 TGATCTTGTGATTTCCTGATGCAG 59.361 41.667 0.00 0.00 32.19 4.41
3652 7987 0.883833 CTGACATGTGGGCCTGAAAC 59.116 55.000 1.15 0.00 0.00 2.78
3653 7988 0.478072 TGACATGTGGGCCTGAAACT 59.522 50.000 1.15 0.00 0.00 2.66
3694 8029 1.656818 GACATGTGGGCCCAATCGTG 61.657 60.000 30.64 27.62 0.00 4.35
3712 8060 2.418746 CGTGAGAAGGGGTAGATTGGTG 60.419 54.545 0.00 0.00 0.00 4.17
3723 8071 3.381590 GGTAGATTGGTGGATTTTGGCTC 59.618 47.826 0.00 0.00 0.00 4.70
3724 8072 3.173953 AGATTGGTGGATTTTGGCTCA 57.826 42.857 0.00 0.00 0.00 4.26
3726 8074 3.259123 AGATTGGTGGATTTTGGCTCAAC 59.741 43.478 0.00 0.00 0.00 3.18
3734 8082 3.068024 GGATTTTGGCTCAACAGTGTTGA 59.932 43.478 31.33 31.33 0.00 3.18
3839 8192 2.607750 TTCCTCCTGGCGCTCCTT 60.608 61.111 7.64 0.00 0.00 3.36
3929 8282 4.954118 TCGGAGCCACCCACCACT 62.954 66.667 0.00 0.00 34.64 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.513806 TGCACAGTAGCACATTCAATATTT 57.486 33.333 0.00 0.00 40.11 1.40
10 11 5.846203 AGAAATTTTGCACAGTAGCACATT 58.154 33.333 0.00 0.00 45.61 2.71
11 12 5.458041 AGAAATTTTGCACAGTAGCACAT 57.542 34.783 0.00 0.00 45.61 3.21
133 140 2.802719 CTAGAAGCTAGCCTAGAGGGG 58.197 57.143 18.25 0.00 35.55 4.79
259 268 0.538287 AACCAGCAGCTTGTCTTCCC 60.538 55.000 0.00 0.00 0.00 3.97
347 360 6.238869 GCCAAGGAAGATGGTTTTCTGATATC 60.239 42.308 0.00 0.00 40.23 1.63
566 585 2.719531 TGCCACACCAAACTTAGACA 57.280 45.000 0.00 0.00 0.00 3.41
719 741 8.456471 TCAGATTTCTTCAACAAGCATAATCAG 58.544 33.333 0.00 0.00 31.16 2.90
833 881 6.985188 TTCTACTATTCACCAATCTTGTGC 57.015 37.500 0.00 0.00 0.00 4.57
949 1026 1.139058 CAGCAGGGGAGTACGCTTATT 59.861 52.381 0.00 0.00 40.92 1.40
1057 1176 1.365999 ACACGAGGATGTGACGCAA 59.634 52.632 0.24 0.00 42.55 4.85
1161 1280 0.250467 CAGGGTGACAGGACTTGTGG 60.250 60.000 0.00 0.00 41.05 4.17
1171 1290 1.906574 GATTAGTGGACCAGGGTGACA 59.093 52.381 0.00 0.00 0.00 3.58
1182 1301 5.047590 ACAGTTACATGTGACGATTAGTGGA 60.048 40.000 14.39 0.00 30.46 4.02
1234 1356 3.245229 ACATGGCCAGACAAGTCCAATAA 60.245 43.478 13.05 0.00 31.66 1.40
1236 1358 1.076024 ACATGGCCAGACAAGTCCAAT 59.924 47.619 13.05 0.00 31.66 3.16
1237 1359 0.478072 ACATGGCCAGACAAGTCCAA 59.522 50.000 13.05 0.00 31.66 3.53
1371 1502 2.101783 CTGGGCAATGCAAAGGTATCA 58.898 47.619 7.79 0.00 0.00 2.15
1377 1508 1.444895 GCGACTGGGCAATGCAAAG 60.445 57.895 7.79 6.20 0.00 2.77
1440 1571 4.028852 GACAACCTGTCCAAAGTCAAAC 57.971 45.455 0.00 0.00 41.37 2.93
1500 1631 5.568423 GCTGGACTCATGATCGGAATTATCT 60.568 44.000 0.00 0.00 0.00 1.98
1616 1747 8.862325 TCCATTGACAACAATACTTCTGTTAT 57.138 30.769 0.00 0.00 43.76 1.89
1799 1936 1.170290 AAAGTAACCGCACCTGCCAC 61.170 55.000 0.00 0.00 37.91 5.01
1829 1966 4.261322 CCAAATTTGCCAGTGATAGATCCG 60.261 45.833 12.92 0.00 0.00 4.18
1833 1970 4.646040 CCATCCAAATTTGCCAGTGATAGA 59.354 41.667 12.92 1.86 0.00 1.98
2097 2237 4.900054 AGACTTCCAGTGTAAGTACCAACT 59.100 41.667 0.46 0.00 37.31 3.16
2153 2293 3.170791 AGCACATGAGGATAACACTCG 57.829 47.619 0.00 0.00 37.79 4.18
2230 2387 6.412362 ACATCGCCTAGAAACTTATCTCAT 57.588 37.500 0.00 0.00 0.00 2.90
2239 2397 4.501071 TGTTCCTTACATCGCCTAGAAAC 58.499 43.478 0.00 0.00 0.00 2.78
2285 2445 9.435688 ACAATTACTTTTCCTAAAAATGCATCC 57.564 29.630 0.00 0.00 34.00 3.51
2314 2474 4.123497 GTGCATCACACCTATGACACTA 57.877 45.455 0.00 0.00 44.02 2.74
2424 2750 6.183360 CCATTCTCAAAAAGGAAGGGATCATC 60.183 42.308 0.00 0.00 43.45 2.92
2481 4553 8.245195 ACCTTTGAATAAAACCTAAGAAAGCA 57.755 30.769 0.00 0.00 0.00 3.91
2676 4766 7.987458 CAGTAAAGCCTAAATAGGATGAACAGA 59.013 37.037 10.71 0.00 46.63 3.41
2680 4770 7.208064 ACCAGTAAAGCCTAAATAGGATGAA 57.792 36.000 10.71 0.00 46.63 2.57
2717 4807 8.615705 AGAAAAATATTTAGGAACAGAGGGAGT 58.384 33.333 0.01 0.00 0.00 3.85
2718 4808 9.467796 AAGAAAAATATTTAGGAACAGAGGGAG 57.532 33.333 0.01 0.00 0.00 4.30
2719 4809 9.822727 AAAGAAAAATATTTAGGAACAGAGGGA 57.177 29.630 0.01 0.00 0.00 4.20
2743 4833 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2744 4834 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2745 4835 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2746 4836 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2747 4837 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2748 4838 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2749 4839 8.562892 CATATGTGGTAGTCCATTTGAAATCTC 58.437 37.037 0.00 0.00 46.20 2.75
2750 4840 7.503566 CCATATGTGGTAGTCCATTTGAAATCT 59.496 37.037 0.00 0.00 46.20 2.40
2751 4841 7.502226 TCCATATGTGGTAGTCCATTTGAAATC 59.498 37.037 8.51 0.00 46.20 2.17
2752 4842 7.353525 TCCATATGTGGTAGTCCATTTGAAAT 58.646 34.615 8.51 0.00 46.20 2.17
2753 4843 6.726379 TCCATATGTGGTAGTCCATTTGAAA 58.274 36.000 8.51 0.00 46.20 2.69
2754 4844 6.320434 TCCATATGTGGTAGTCCATTTGAA 57.680 37.500 8.51 0.00 46.20 2.69
2755 4845 5.966853 TCCATATGTGGTAGTCCATTTGA 57.033 39.130 8.51 0.00 46.20 2.69
2756 4846 6.064060 ACATCCATATGTGGTAGTCCATTTG 58.936 40.000 8.51 0.00 44.79 2.32
2757 4847 6.266131 ACATCCATATGTGGTAGTCCATTT 57.734 37.500 8.51 0.00 44.79 2.32
2758 4848 5.912149 ACATCCATATGTGGTAGTCCATT 57.088 39.130 8.51 0.00 44.79 3.16
2759 4849 8.860517 ATATACATCCATATGTGGTAGTCCAT 57.139 34.615 8.51 3.29 45.99 3.41
2760 4850 9.421399 CTATATACATCCATATGTGGTAGTCCA 57.579 37.037 8.51 1.36 45.99 4.02
2761 4851 9.642343 TCTATATACATCCATATGTGGTAGTCC 57.358 37.037 8.51 0.00 45.99 3.85
2763 4853 9.990868 TGTCTATATACATCCATATGTGGTAGT 57.009 33.333 8.51 10.44 45.99 2.73
2799 4889 5.460419 CGGAGCTAAATGAGTGAATCTACAC 59.540 44.000 0.00 0.00 40.60 2.90
2800 4890 5.127194 ACGGAGCTAAATGAGTGAATCTACA 59.873 40.000 0.00 0.00 0.00 2.74
2801 4891 5.593010 ACGGAGCTAAATGAGTGAATCTAC 58.407 41.667 0.00 0.00 0.00 2.59
2802 4892 5.854010 ACGGAGCTAAATGAGTGAATCTA 57.146 39.130 0.00 0.00 0.00 1.98
2803 4893 4.744795 ACGGAGCTAAATGAGTGAATCT 57.255 40.909 0.00 0.00 0.00 2.40
2804 4894 5.986135 ACATACGGAGCTAAATGAGTGAATC 59.014 40.000 0.00 0.00 0.00 2.52
2805 4895 5.918608 ACATACGGAGCTAAATGAGTGAAT 58.081 37.500 0.00 0.00 0.00 2.57
2806 4896 5.339008 ACATACGGAGCTAAATGAGTGAA 57.661 39.130 0.00 0.00 0.00 3.18
2807 4897 5.593095 ACTACATACGGAGCTAAATGAGTGA 59.407 40.000 0.00 0.00 0.00 3.41
2808 4898 5.833082 ACTACATACGGAGCTAAATGAGTG 58.167 41.667 0.00 0.00 0.00 3.51
2809 4899 5.593095 TGACTACATACGGAGCTAAATGAGT 59.407 40.000 0.00 0.00 0.00 3.41
2810 4900 5.915758 GTGACTACATACGGAGCTAAATGAG 59.084 44.000 0.00 0.00 0.00 2.90
2811 4901 5.593095 AGTGACTACATACGGAGCTAAATGA 59.407 40.000 0.00 0.00 0.00 2.57
2812 4902 5.833082 AGTGACTACATACGGAGCTAAATG 58.167 41.667 0.00 0.00 0.00 2.32
2813 4903 6.127423 ACAAGTGACTACATACGGAGCTAAAT 60.127 38.462 0.00 0.00 0.00 1.40
2814 4904 5.184479 ACAAGTGACTACATACGGAGCTAAA 59.816 40.000 0.00 0.00 0.00 1.85
2815 4905 4.703575 ACAAGTGACTACATACGGAGCTAA 59.296 41.667 0.00 0.00 0.00 3.09
2816 4906 4.267536 ACAAGTGACTACATACGGAGCTA 58.732 43.478 0.00 0.00 0.00 3.32
2817 4907 3.090037 ACAAGTGACTACATACGGAGCT 58.910 45.455 0.00 0.00 0.00 4.09
2818 4908 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2819 4909 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2820 4910 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2821 4911 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2822 4912 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2823 4913 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2825 4915 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2826 4916 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2827 4917 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2828 4918 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2829 4919 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2830 4920 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2831 4921 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2832 4922 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2833 4923 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2846 4936 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2847 4937 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2848 4938 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2849 4939 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2850 4940 7.551617 TCCTCCGTTCCTAAATATTTGTCTTTC 59.448 37.037 11.05 0.00 0.00 2.62
2851 4941 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
2852 4942 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
2853 4943 6.555463 TCCTCCGTTCCTAAATATTTGTCT 57.445 37.500 11.05 0.00 0.00 3.41
2854 4944 6.822170 ACTTCCTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2855 4945 6.718294 ACTTCCTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2856 4946 8.202137 TCTACTTCCTCCGTTCCTAAATATTTG 58.798 37.037 11.05 1.40 0.00 2.32
2857 4947 8.315220 TCTACTTCCTCCGTTCCTAAATATTT 57.685 34.615 5.89 5.89 0.00 1.40
2858 4948 7.909485 TCTACTTCCTCCGTTCCTAAATATT 57.091 36.000 0.00 0.00 0.00 1.28
2859 4949 8.368668 CAATCTACTTCCTCCGTTCCTAAATAT 58.631 37.037 0.00 0.00 0.00 1.28
2860 4950 7.562454 TCAATCTACTTCCTCCGTTCCTAAATA 59.438 37.037 0.00 0.00 0.00 1.40
2861 4951 6.383147 TCAATCTACTTCCTCCGTTCCTAAAT 59.617 38.462 0.00 0.00 0.00 1.40
2862 4952 5.718130 TCAATCTACTTCCTCCGTTCCTAAA 59.282 40.000 0.00 0.00 0.00 1.85
2863 4953 5.126707 GTCAATCTACTTCCTCCGTTCCTAA 59.873 44.000 0.00 0.00 0.00 2.69
2864 4954 4.643784 GTCAATCTACTTCCTCCGTTCCTA 59.356 45.833 0.00 0.00 0.00 2.94
2865 4955 3.447944 GTCAATCTACTTCCTCCGTTCCT 59.552 47.826 0.00 0.00 0.00 3.36
2866 4956 3.194968 TGTCAATCTACTTCCTCCGTTCC 59.805 47.826 0.00 0.00 0.00 3.62
2867 4957 4.425520 CTGTCAATCTACTTCCTCCGTTC 58.574 47.826 0.00 0.00 0.00 3.95
2868 4958 3.195825 CCTGTCAATCTACTTCCTCCGTT 59.804 47.826 0.00 0.00 0.00 4.44
2869 4959 2.761208 CCTGTCAATCTACTTCCTCCGT 59.239 50.000 0.00 0.00 0.00 4.69
2870 4960 2.761208 ACCTGTCAATCTACTTCCTCCG 59.239 50.000 0.00 0.00 0.00 4.63
2871 4961 4.828072 AACCTGTCAATCTACTTCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
2872 4962 5.422650 AGGTAACCTGTCAATCTACTTCCTC 59.577 44.000 0.00 0.00 29.57 3.71
2873 4963 5.342866 AGGTAACCTGTCAATCTACTTCCT 58.657 41.667 0.00 0.00 29.57 3.36
2874 4964 5.678955 AGGTAACCTGTCAATCTACTTCC 57.321 43.478 0.00 0.00 29.57 3.46
2875 4965 7.166691 TGTAGGTAACCTGTCAATCTACTTC 57.833 40.000 0.00 0.00 34.61 3.01
2876 4966 7.735326 ATGTAGGTAACCTGTCAATCTACTT 57.265 36.000 0.00 0.00 34.61 2.24
2877 4967 7.735326 AATGTAGGTAACCTGTCAATCTACT 57.265 36.000 0.00 0.00 34.61 2.57
2878 4968 8.788325 AAAATGTAGGTAACCTGTCAATCTAC 57.212 34.615 0.00 0.00 34.61 2.59
2994 5509 6.054295 TCAAACATTGCTGGCAGTTTATTTT 58.946 32.000 17.16 7.89 33.30 1.82
3045 5560 6.541278 ACCAATCTACATGTGACATGAAGATG 59.459 38.462 30.26 19.63 35.49 2.90
3048 5563 7.848223 TTACCAATCTACATGTGACATGAAG 57.152 36.000 30.26 12.84 0.00 3.02
3136 7414 2.097110 ACCTCCCACACAACTACAGA 57.903 50.000 0.00 0.00 0.00 3.41
3151 7429 2.841442 ACTGCCAGTGAGTTAACCTC 57.159 50.000 0.00 0.27 40.89 3.85
3188 7486 0.874390 GGCACGCATCAGAACTTCAA 59.126 50.000 0.00 0.00 0.00 2.69
3194 7492 1.266718 GAACAAAGGCACGCATCAGAA 59.733 47.619 0.00 0.00 0.00 3.02
3428 7726 3.737559 TGGTGAAAGCCTAATGGATGT 57.262 42.857 0.00 0.00 34.57 3.06
3502 7802 3.116096 AGACCCAACTAGGCTGACATA 57.884 47.619 0.00 0.00 35.39 2.29
3613 7948 1.897560 GCCCTAGGCCATATTGACAC 58.102 55.000 5.01 0.00 44.06 3.67
3652 7987 1.338136 CCCCTAGGTGGTGCCACTAG 61.338 65.000 19.37 16.75 45.52 2.57
3653 7988 1.306654 CCCCTAGGTGGTGCCACTA 60.307 63.158 19.37 9.84 45.52 2.74
3694 8029 2.478292 TCCACCAATCTACCCCTTCTC 58.522 52.381 0.00 0.00 0.00 2.87
3712 8060 3.068024 TCAACACTGTTGAGCCAAAATCC 59.932 43.478 18.83 0.00 0.00 3.01
3723 8071 7.116948 TGGTTTAAACAATTGTCAACACTGTTG 59.883 33.333 19.57 14.79 0.00 3.33
3724 8072 7.155328 TGGTTTAAACAATTGTCAACACTGTT 58.845 30.769 19.57 2.35 0.00 3.16
3726 8074 6.237808 GCTGGTTTAAACAATTGTCAACACTG 60.238 38.462 19.57 12.54 0.00 3.66
3734 8082 4.649218 AGTGGAGCTGGTTTAAACAATTGT 59.351 37.500 19.57 4.92 0.00 2.71
3929 8282 1.005394 GCGGTCCACCTCGAAGAAA 60.005 57.895 0.00 0.00 34.09 2.52
3989 8342 1.077357 GGAGTCGGAGAGGAGCAGA 60.077 63.158 0.00 0.00 36.95 4.26
4215 8568 2.105128 CGACCAGAGGATGCCGTC 59.895 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.