Multiple sequence alignment - TraesCS3D01G000800

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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 TraesCS3D01G000800 chr3D 100.000 4105 0 0 1 4105 493225 497329 0.000000e+00 7581.0
1 TraesCS3D01G000800 chr3D 91.667 72 5 1 69 140 23157484 23157554 9.390000e-17 99.0
2 TraesCS3D01G000800 chr3D 89.744 78 6 2 63 140 558703581 558703656 9.390000e-17 99.0
3 TraesCS3D01G000800 chr3A 90.997 2066 105 28 589 2602 9067110 9065074 0.000000e+00 2710.0
4 TraesCS3D01G000800 chr3A 92.892 816 54 3 3290 4103 719473748 719472935 0.000000e+00 1182.0
5 TraesCS3D01G000800 chr3A 87.890 545 33 17 56 596 9068493 9067978 9.760000e-171 610.0
6 TraesCS3D01G000800 chr3A 96.960 329 10 0 2719 3047 9064990 9064662 1.670000e-153 553.0
7 TraesCS3D01G000800 chr3A 87.843 255 20 3 3034 3288 9063700 9063457 5.190000e-74 289.0
8 TraesCS3D01G000800 chr3A 100.000 38 0 0 2 39 9068530 9068493 2.050000e-08 71.3
9 TraesCS3D01G000800 chrUn 95.130 965 37 4 966 1925 35559529 35560488 0.000000e+00 1513.0
10 TraesCS3D01G000800 chrUn 95.787 451 15 3 2137 2583 35560552 35561002 0.000000e+00 725.0
11 TraesCS3D01G000800 chrUn 92.733 344 20 1 2709 3047 35561019 35561362 3.690000e-135 492.0
12 TraesCS3D01G000800 chrUn 87.379 309 20 7 655 952 35559172 35559472 1.830000e-88 337.0
13 TraesCS3D01G000800 chrUn 81.818 330 52 5 2234 2556 28786152 28785824 1.880000e-68 270.0
14 TraesCS3D01G000800 chrUn 83.468 248 37 3 1655 1900 78169397 78169152 1.150000e-55 228.0
15 TraesCS3D01G000800 chr3B 95.130 965 37 4 966 1925 6098232 6097273 0.000000e+00 1513.0
16 TraesCS3D01G000800 chr3B 90.615 618 52 6 1 616 5838405 5839018 0.000000e+00 815.0
17 TraesCS3D01G000800 chr3B 95.595 454 16 3 2137 2586 6097209 6096756 0.000000e+00 725.0
18 TraesCS3D01G000800 chr3B 92.733 344 20 1 2709 3047 6096742 6096399 3.690000e-135 492.0
19 TraesCS3D01G000800 chr3B 87.379 309 20 7 655 952 6098589 6098289 1.830000e-88 337.0
20 TraesCS3D01G000800 chr6D 98.544 824 11 1 3282 4105 460242445 460243267 0.000000e+00 1454.0
21 TraesCS3D01G000800 chr6D 98.291 819 14 0 3287 4105 158852690 158853508 0.000000e+00 1435.0
22 TraesCS3D01G000800 chr6D 82.609 552 68 20 1038 1581 76050519 76051050 2.890000e-126 462.0
23 TraesCS3D01G000800 chr6D 86.598 388 47 3 1037 1420 110165857 110166243 1.360000e-114 424.0
24 TraesCS3D01G000800 chr6D 84.211 247 37 2 1655 1900 76051048 76051293 5.300000e-59 239.0
25 TraesCS3D01G000800 chr7D 98.293 820 14 0 3286 4105 47982897 47982078 0.000000e+00 1437.0
26 TraesCS3D01G000800 chr7D 88.889 81 5 3 64 140 3252205 3252125 3.380000e-16 97.1
27 TraesCS3D01G000800 chr2D 98.293 820 14 0 3286 4105 621695864 621696683 0.000000e+00 1437.0
28 TraesCS3D01G000800 chr2D 91.781 73 4 2 69 140 403383418 403383347 2.610000e-17 100.0
29 TraesCS3D01G000800 chr2D 88.889 72 6 2 3211 3281 563149203 563149133 2.030000e-13 87.9
30 TraesCS3D01G000800 chr4B 93.228 945 50 6 979 1918 544646454 544645519 0.000000e+00 1378.0
31 TraesCS3D01G000800 chr4B 91.481 493 42 0 3287 3779 398528714 398529206 0.000000e+00 678.0
32 TraesCS3D01G000800 chr4B 91.080 426 38 0 2140 2565 544645481 544645056 9.890000e-161 577.0
33 TraesCS3D01G000800 chr4B 90.826 327 22 5 3782 4103 398529334 398529657 8.150000e-117 431.0
34 TraesCS3D01G000800 chr4B 83.696 184 30 0 2777 2960 544644932 544644749 1.520000e-39 174.0
35 TraesCS3D01G000800 chr4A 93.888 818 31 3 3286 4103 646601160 646600362 0.000000e+00 1216.0
36 TraesCS3D01G000800 chr4A 92.224 643 39 6 1260 1902 29082920 29082289 0.000000e+00 900.0
37 TraesCS3D01G000800 chr4A 87.126 435 35 3 2137 2565 29082237 29081818 1.340000e-129 473.0
38 TraesCS3D01G000800 chr4A 83.217 143 17 2 2725 2860 29081772 29081630 1.550000e-24 124.0
39 TraesCS3D01G000800 chr4A 85.714 84 5 4 2029 2108 4845452 4845532 9.460000e-12 82.4
40 TraesCS3D01G000800 chr4D 94.295 631 32 2 979 1609 439820635 439820009 0.000000e+00 963.0
41 TraesCS3D01G000800 chr4D 89.461 427 44 1 2140 2565 439819623 439819197 4.670000e-149 538.0
42 TraesCS3D01G000800 chr4D 91.930 285 17 4 1634 1918 439819932 439819654 1.070000e-105 394.0
43 TraesCS3D01G000800 chr4D 85.641 195 27 1 2777 2971 439819097 439818904 1.930000e-48 204.0
44 TraesCS3D01G000800 chr4D 94.030 67 4 0 2594 2660 315809153 315809087 7.260000e-18 102.0
45 TraesCS3D01G000800 chr4D 85.882 85 10 2 58 140 50796160 50796244 5.650000e-14 89.8
46 TraesCS3D01G000800 chr6B 87.468 391 47 2 1038 1427 149730384 149730773 2.250000e-122 449.0
47 TraesCS3D01G000800 chr6A 86.632 389 45 5 1037 1420 134682028 134682414 1.360000e-114 424.0
48 TraesCS3D01G000800 chr6A 75.290 777 145 28 3281 4023 30486632 30487395 1.100000e-85 327.0
49 TraesCS3D01G000800 chr6A 86.111 252 32 3 1656 1905 134682541 134682791 6.760000e-68 268.0
50 TraesCS3D01G000800 chr6A 92.754 69 4 1 72 140 468343014 468343081 9.390000e-17 99.0
51 TraesCS3D01G000800 chr5A 85.846 325 46 0 2234 2558 391754641 391754317 3.040000e-91 346.0
52 TraesCS3D01G000800 chr5A 92.958 71 4 1 2592 2661 589321003 589320933 7.260000e-18 102.0
53 TraesCS3D01G000800 chr5A 88.750 80 5 3 2029 2107 656708491 656708415 1.210000e-15 95.3
54 TraesCS3D01G000800 chr5A 87.719 57 6 1 2655 2710 566087667 566087611 9.520000e-07 65.8
55 TraesCS3D01G000800 chr5B 85.030 334 50 0 2225 2558 351148071 351148404 1.410000e-89 340.0
56 TraesCS3D01G000800 chr5B 90.000 70 6 1 2029 2097 669443323 669443392 5.650000e-14 89.8
57 TraesCS3D01G000800 chr1A 78.935 432 84 5 3287 3713 424436412 424435983 1.870000e-73 287.0
58 TraesCS3D01G000800 chr1A 96.721 61 2 0 2594 2654 309178223 309178283 7.260000e-18 102.0
59 TraesCS3D01G000800 chr1A 96.721 61 2 0 2594 2654 454517223 454517283 7.260000e-18 102.0
60 TraesCS3D01G000800 chr1A 94.118 68 3 1 2594 2661 494886892 494886958 7.260000e-18 102.0
61 TraesCS3D01G000800 chr2A 95.522 67 3 0 2594 2660 38649961 38649895 1.560000e-19 108.0
62 TraesCS3D01G000800 chr2A 94.286 70 3 1 2588 2657 680509973 680510041 5.610000e-19 106.0
63 TraesCS3D01G000800 chr2A 92.000 75 6 0 2583 2657 694587391 694587465 5.610000e-19 106.0
64 TraesCS3D01G000800 chr2A 90.566 53 5 0 2658 2710 735856037 735856089 2.050000e-08 71.3
65 TraesCS3D01G000800 chr1B 96.721 61 2 0 2594 2654 476872738 476872798 7.260000e-18 102.0
66 TraesCS3D01G000800 chr7B 91.549 71 5 1 70 140 143261155 143261086 3.380000e-16 97.1


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 TraesCS3D01G000800 chr3D 493225 497329 4104 False 7581.000000 7581 100.000000 1 4105 1 chr3D.!!$F1 4104
1 TraesCS3D01G000800 chr3A 719472935 719473748 813 True 1182.000000 1182 92.892000 3290 4103 1 chr3A.!!$R1 813
2 TraesCS3D01G000800 chr3A 9063457 9068530 5073 True 846.660000 2710 92.738000 2 3288 5 chr3A.!!$R2 3286
3 TraesCS3D01G000800 chrUn 35559172 35561362 2190 False 766.750000 1513 92.757250 655 3047 4 chrUn.!!$F1 2392
4 TraesCS3D01G000800 chr3B 5838405 5839018 613 False 815.000000 815 90.615000 1 616 1 chr3B.!!$F1 615
5 TraesCS3D01G000800 chr3B 6096399 6098589 2190 True 766.750000 1513 92.709250 655 3047 4 chr3B.!!$R1 2392
6 TraesCS3D01G000800 chr6D 460242445 460243267 822 False 1454.000000 1454 98.544000 3282 4105 1 chr6D.!!$F3 823
7 TraesCS3D01G000800 chr6D 158852690 158853508 818 False 1435.000000 1435 98.291000 3287 4105 1 chr6D.!!$F2 818
8 TraesCS3D01G000800 chr6D 76050519 76051293 774 False 350.500000 462 83.410000 1038 1900 2 chr6D.!!$F4 862
9 TraesCS3D01G000800 chr7D 47982078 47982897 819 True 1437.000000 1437 98.293000 3286 4105 1 chr7D.!!$R2 819
10 TraesCS3D01G000800 chr2D 621695864 621696683 819 False 1437.000000 1437 98.293000 3286 4105 1 chr2D.!!$F1 819
11 TraesCS3D01G000800 chr4B 544644749 544646454 1705 True 709.666667 1378 89.334667 979 2960 3 chr4B.!!$R1 1981
12 TraesCS3D01G000800 chr4B 398528714 398529657 943 False 554.500000 678 91.153500 3287 4103 2 chr4B.!!$F1 816
13 TraesCS3D01G000800 chr4A 646600362 646601160 798 True 1216.000000 1216 93.888000 3286 4103 1 chr4A.!!$R1 817
14 TraesCS3D01G000800 chr4A 29081630 29082920 1290 True 499.000000 900 87.522333 1260 2860 3 chr4A.!!$R2 1600
15 TraesCS3D01G000800 chr4D 439818904 439820635 1731 True 524.750000 963 90.331750 979 2971 4 chr4D.!!$R2 1992
16 TraesCS3D01G000800 chr6A 134682028 134682791 763 False 346.000000 424 86.371500 1037 1905 2 chr6A.!!$F3 868
17 TraesCS3D01G000800 chr6A 30486632 30487395 763 False 327.000000 327 75.290000 3281 4023 1 chr6A.!!$F1 742

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
475 476 0.107654 GATTAGCGCCCAGTTCTGGT 60.108 55.0 16.33 2.17 0.00 4.00 F
599 1479 0.759346 ATGATCCCTAGCGGTTCACC 59.241 55.0 11.14 0.00 42.05 4.02 F
1708 2813 0.108774 GCCACTCTTATAGGGTGCCC 59.891 60.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 2448 1.153978 TCGACATACGCGTCCAACC 60.154 57.895 18.63 1.32 42.26 3.77 R
2201 3351 2.046314 CCACCGCCGTCCTTGAAT 60.046 61.111 0.00 0.00 0.00 2.57 R
3242 5433 0.036577 ACTGCGCTGCTTCATCTTCT 60.037 50.000 14.80 0.00 0.00 2.85 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
64 65 6.554784 TGCATATCCCATCCATATTTTGTCT 58.445 36.000 0.00 0.00 0.00 3.41
98 99 2.059756 TGAAAAGGAGGATGACCCCT 57.940 50.000 0.00 0.00 38.08 4.79
130 131 2.191513 GGACGATGCATGCAGCCAT 61.192 57.895 28.76 18.07 44.83 4.40
168 169 3.933332 CCCTTCCTATCAGACGAAAACAC 59.067 47.826 0.00 0.00 0.00 3.32
208 209 1.472480 CGATTTGTGTTCCATCCCACC 59.528 52.381 0.00 0.00 0.00 4.61
222 223 1.517832 CCACCGTCCTCATCTCCAC 59.482 63.158 0.00 0.00 0.00 4.02
236 237 1.354368 TCTCCACAGAAACCCCATTCC 59.646 52.381 0.00 0.00 0.00 3.01
243 244 0.898326 GAAACCCCATTCCAACCGCT 60.898 55.000 0.00 0.00 0.00 5.52
281 282 2.311688 CTGCCCCGTATCTGTCACCC 62.312 65.000 0.00 0.00 0.00 4.61
342 343 4.544689 CGCCTCCGAGCTCACGAG 62.545 72.222 15.40 16.49 36.29 4.18
403 404 9.626045 CCCAAAATTGACTAGACTTATTTGTTC 57.374 33.333 0.00 0.00 0.00 3.18
429 430 9.066892 CCCGAAAAATCAGGAGATATTAAATCA 57.933 33.333 0.00 0.00 33.08 2.57
433 434 9.425248 AAAAATCAGGAGATATTAAATCAGCCA 57.575 29.630 0.00 0.00 33.08 4.75
475 476 0.107654 GATTAGCGCCCAGTTCTGGT 60.108 55.000 16.33 2.17 0.00 4.00
524 526 3.835378 TCGTACTTATCAACGACTGCA 57.165 42.857 0.00 0.00 42.74 4.41
565 569 6.056236 GGACAGGAAATGGTCTTATAGGAAC 58.944 44.000 0.00 0.00 34.49 3.62
580 584 7.510685 TCTTATAGGAACCTAGGACGAGTAGTA 59.489 40.741 17.98 0.00 31.45 1.82
599 1479 0.759346 ATGATCCCTAGCGGTTCACC 59.241 55.000 11.14 0.00 42.05 4.02
653 1533 0.853530 AGGAAAAGGGGCACTCTGTT 59.146 50.000 0.00 0.00 0.00 3.16
670 1550 1.205893 TGTTGGGAAAATAATGCGGCC 59.794 47.619 0.00 0.00 0.00 6.13
954 1854 6.238293 GGTTACTTAAAGGACGTGAATATGCC 60.238 42.308 0.00 0.00 0.00 4.40
955 1855 4.839121 ACTTAAAGGACGTGAATATGCCA 58.161 39.130 0.00 0.00 0.00 4.92
958 1858 2.024176 AGGACGTGAATATGCCACAC 57.976 50.000 0.00 0.00 34.36 3.82
976 1919 1.618343 CACAAAATTCACACCTCCCCC 59.382 52.381 0.00 0.00 0.00 5.40
1281 2230 2.747686 GGCTTCACCGACTTCCCA 59.252 61.111 0.00 0.00 0.00 4.37
1493 2448 3.583882 ATGGTGCCAACGGGAAGGG 62.584 63.158 0.00 0.00 35.59 3.95
1506 2461 1.219935 GAAGGGGTTGGACGCGTAT 59.780 57.895 13.97 0.00 31.02 3.06
1571 2526 0.966875 TCGCAGCCAAGATTGCCAAT 60.967 50.000 0.00 0.00 37.00 3.16
1632 2668 5.065859 TGCATGTTCCCATAATCGTTTACTG 59.934 40.000 0.00 0.00 0.00 2.74
1696 2801 1.376942 GCAGATGCACAGCCACTCT 60.377 57.895 0.00 0.00 41.59 3.24
1708 2813 0.108774 GCCACTCTTATAGGGTGCCC 59.891 60.000 0.00 0.00 0.00 5.36
1807 2912 0.327924 TGGCCAAGGAGGTGTACATG 59.672 55.000 0.61 0.00 40.61 3.21
1956 3095 6.432162 ACACGTAGAAGAGAACCAATAGTACA 59.568 38.462 0.00 0.00 0.00 2.90
1991 3133 5.220381 TGCTAAGTCTTTGTTACGTCTCAG 58.780 41.667 0.00 0.00 0.00 3.35
1994 3136 5.517322 AAGTCTTTGTTACGTCTCAGTCT 57.483 39.130 0.00 0.00 0.00 3.24
2002 3144 7.797038 TTGTTACGTCTCAGTCTATGCTATA 57.203 36.000 0.00 0.00 0.00 1.31
2003 3145 7.981102 TGTTACGTCTCAGTCTATGCTATAT 57.019 36.000 0.00 0.00 0.00 0.86
2004 3146 9.498176 TTGTTACGTCTCAGTCTATGCTATATA 57.502 33.333 0.00 0.00 0.00 0.86
2005 3147 9.668497 TGTTACGTCTCAGTCTATGCTATATAT 57.332 33.333 0.00 0.00 0.00 0.86
2009 3151 9.456147 ACGTCTCAGTCTATGCTATATATCTTT 57.544 33.333 0.00 0.00 0.00 2.52
2010 3152 9.929722 CGTCTCAGTCTATGCTATATATCTTTC 57.070 37.037 0.00 0.00 0.00 2.62
2027 3169 8.752766 ATATCTTTCTTTGATTTTGCACACAG 57.247 30.769 0.00 0.00 0.00 3.66
2028 3170 5.964758 TCTTTCTTTGATTTTGCACACAGT 58.035 33.333 0.00 0.00 0.00 3.55
2047 3189 6.477688 ACACAGTCTTTCTTTGATTTTGCATG 59.522 34.615 0.00 0.00 0.00 4.06
2048 3190 5.987347 ACAGTCTTTCTTTGATTTTGCATGG 59.013 36.000 0.00 0.00 0.00 3.66
2183 3333 1.306642 CGTAGGTGGAGCGTCTCTGT 61.307 60.000 6.78 0.00 0.00 3.41
2216 3372 2.746277 GCATTCAAGGACGGCGGT 60.746 61.111 13.24 0.00 0.00 5.68
2267 3423 2.362397 CGTCATCTACTGCACAGGGTAT 59.638 50.000 2.21 0.00 0.00 2.73
2602 3758 9.962759 CTCGGTATGTGTTACACTTTTATTAAC 57.037 33.333 16.79 4.45 35.11 2.01
2604 3760 9.749490 CGGTATGTGTTACACTTTTATTAACAG 57.251 33.333 16.79 2.07 36.60 3.16
2625 3781 7.801716 ACAGTTTTGTTAAAGCACATCTAGA 57.198 32.000 0.00 0.00 32.28 2.43
2626 3782 8.396272 ACAGTTTTGTTAAAGCACATCTAGAT 57.604 30.769 0.00 0.00 32.28 1.98
2627 3783 8.292448 ACAGTTTTGTTAAAGCACATCTAGATG 58.708 33.333 27.63 27.63 38.39 2.90
2642 3798 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
2643 3799 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
2651 3807 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
2652 3808 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
2653 3809 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
2654 3810 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41
2655 3811 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
2656 3812 9.710900 CCATAAGTATTGCACATCTAAGTCATA 57.289 33.333 0.00 0.00 0.00 2.15
2658 3814 9.935241 ATAAGTATTGCACATCTAAGTCATAGG 57.065 33.333 0.00 0.00 32.09 2.57
2659 3815 7.366847 AGTATTGCACATCTAAGTCATAGGT 57.633 36.000 0.00 0.00 32.09 3.08
2660 3816 7.796054 AGTATTGCACATCTAAGTCATAGGTT 58.204 34.615 0.00 0.00 32.09 3.50
2661 3817 6.932356 ATTGCACATCTAAGTCATAGGTTG 57.068 37.500 0.00 0.00 32.09 3.77
2662 3818 4.191544 TGCACATCTAAGTCATAGGTTGC 58.808 43.478 0.00 0.00 33.26 4.17
2663 3819 4.191544 GCACATCTAAGTCATAGGTTGCA 58.808 43.478 0.00 0.00 33.07 4.08
2664 3820 4.818546 GCACATCTAAGTCATAGGTTGCAT 59.181 41.667 0.00 0.00 33.07 3.96
2665 3821 5.277683 GCACATCTAAGTCATAGGTTGCATG 60.278 44.000 0.00 0.00 33.07 4.06
2666 3822 4.818546 ACATCTAAGTCATAGGTTGCATGC 59.181 41.667 11.82 11.82 32.09 4.06
2667 3823 4.486125 TCTAAGTCATAGGTTGCATGCA 57.514 40.909 18.46 18.46 32.09 3.96
2668 3824 5.039920 TCTAAGTCATAGGTTGCATGCAT 57.960 39.130 23.37 9.62 32.09 3.96
2669 3825 4.818005 TCTAAGTCATAGGTTGCATGCATG 59.182 41.667 23.37 22.70 32.09 4.06
2670 3826 2.304092 AGTCATAGGTTGCATGCATGG 58.696 47.619 27.34 10.03 0.00 3.66
2671 3827 2.092267 AGTCATAGGTTGCATGCATGGA 60.092 45.455 27.34 22.97 0.00 3.41
2672 3828 2.889045 GTCATAGGTTGCATGCATGGAT 59.111 45.455 27.34 13.03 0.00 3.41
2673 3829 3.319972 GTCATAGGTTGCATGCATGGATT 59.680 43.478 27.34 15.45 0.00 3.01
2674 3830 3.319689 TCATAGGTTGCATGCATGGATTG 59.680 43.478 27.34 16.28 0.00 2.67
2675 3831 1.855295 AGGTTGCATGCATGGATTGA 58.145 45.000 27.34 7.93 0.00 2.57
2676 3832 1.479323 AGGTTGCATGCATGGATTGAC 59.521 47.619 27.34 19.03 0.00 3.18
2687 3843 1.243342 TGGATTGACGCAAAGGCCAG 61.243 55.000 5.01 0.00 36.38 4.85
2699 3855 2.037367 GGCCAGGGGTTTTCCTCC 59.963 66.667 0.00 0.00 42.67 4.30
2707 3863 3.709141 CAGGGGTTTTCCTCCTTTTCAAA 59.291 43.478 0.00 0.00 42.67 2.69
2710 3866 4.879545 GGGGTTTTCCTCCTTTTCAAAAAC 59.120 41.667 0.00 0.00 38.48 2.43
2711 3867 5.338871 GGGGTTTTCCTCCTTTTCAAAAACT 60.339 40.000 8.40 0.00 38.94 2.66
2892 4108 2.036387 TGGACAAGTTCGAGACCTTCA 58.964 47.619 0.00 0.00 0.00 3.02
2900 4116 0.034380 TCGAGACCTTCAGGGACGAT 60.034 55.000 0.00 0.00 40.27 3.73
2913 4129 0.535335 GGACGATTACCAGGACAGCA 59.465 55.000 0.00 0.00 0.00 4.41
2971 4187 1.079543 GTCTGCACAGCTCGTCCAT 60.080 57.895 0.00 0.00 0.00 3.41
2991 4207 2.033194 GCCGGTTCTGAGGTTTCGG 61.033 63.158 1.90 0.00 40.33 4.30
3012 4228 2.813908 CCGGGGCGAAACGAGAAG 60.814 66.667 0.00 0.00 0.00 2.85
3082 5273 0.593128 ACATCAGTTTCAGCGGCAAC 59.407 50.000 1.45 0.00 0.00 4.17
3083 5274 0.592637 CATCAGTTTCAGCGGCAACA 59.407 50.000 1.45 0.00 0.00 3.33
3094 5285 2.358582 CAGCGGCAACAAATATGGATCA 59.641 45.455 1.45 0.00 0.00 2.92
3097 5288 4.081752 AGCGGCAACAAATATGGATCAAAA 60.082 37.500 1.45 0.00 0.00 2.44
3180 5371 1.860950 CCGTAAATCCATCTGCACTCG 59.139 52.381 0.00 0.00 0.00 4.18
3185 5376 4.946784 AAATCCATCTGCACTCGTTTAC 57.053 40.909 0.00 0.00 0.00 2.01
3190 5381 3.120546 CCATCTGCACTCGTTTACAACAG 60.121 47.826 0.00 0.00 0.00 3.16
3203 5394 7.439381 TCGTTTACAACAGTATCCTCTTCTTT 58.561 34.615 0.00 0.00 0.00 2.52
3208 5399 7.736447 ACAACAGTATCCTCTTCTTTTCTTG 57.264 36.000 0.00 0.00 0.00 3.02
3216 5407 5.380043 TCCTCTTCTTTTCTTGTCATTGCT 58.620 37.500 0.00 0.00 0.00 3.91
3217 5408 5.240183 TCCTCTTCTTTTCTTGTCATTGCTG 59.760 40.000 0.00 0.00 0.00 4.41
3237 5428 1.926561 TGCTAGTAGCGATGCACAAG 58.073 50.000 17.16 0.00 46.26 3.16
3238 5429 1.476488 TGCTAGTAGCGATGCACAAGA 59.524 47.619 17.16 0.00 46.26 3.02
3239 5430 2.123342 GCTAGTAGCGATGCACAAGAG 58.877 52.381 6.36 0.00 0.00 2.85
3240 5431 2.736978 CTAGTAGCGATGCACAAGAGG 58.263 52.381 0.00 0.00 0.00 3.69
3241 5432 1.186200 AGTAGCGATGCACAAGAGGA 58.814 50.000 0.00 0.00 0.00 3.71
3242 5433 1.550524 AGTAGCGATGCACAAGAGGAA 59.449 47.619 0.00 0.00 0.00 3.36
3243 5434 1.929836 GTAGCGATGCACAAGAGGAAG 59.070 52.381 0.00 0.00 0.00 3.46
3244 5435 0.610174 AGCGATGCACAAGAGGAAGA 59.390 50.000 0.00 0.00 0.00 2.87
3254 5445 4.321718 CACAAGAGGAAGAAGATGAAGCA 58.678 43.478 0.00 0.00 0.00 3.91
3255 5446 4.392445 CACAAGAGGAAGAAGATGAAGCAG 59.608 45.833 0.00 0.00 0.00 4.24
3256 5447 3.264998 AGAGGAAGAAGATGAAGCAGC 57.735 47.619 0.00 0.00 0.00 5.25
3272 5463 2.051345 GCGCAGTTCCGTGTTTGG 60.051 61.111 0.30 0.00 0.00 3.28
3401 5592 2.920645 ATCTCCCGTCGGCTATGCG 61.921 63.158 5.50 0.00 0.00 4.73
3439 5630 6.039717 ACATTAATAGCCGACGGTACTCTTAA 59.960 38.462 16.73 13.51 0.00 1.85
3475 5666 3.746900 GGTATTAAGCCGACGGTGT 57.253 52.632 16.73 6.21 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.215942 TCGTCCAGATGAAGAGGTCA 57.784 50.000 0.00 0.00 41.67 4.02
158 159 3.066203 ACAATTGGTCTGGTGTTTTCGTC 59.934 43.478 10.83 0.00 0.00 4.20
168 169 0.667993 ACAACGCACAATTGGTCTGG 59.332 50.000 10.83 0.00 0.00 3.86
208 209 2.611518 GTTTCTGTGGAGATGAGGACG 58.388 52.381 0.00 0.00 0.00 4.79
222 223 0.887933 CGGTTGGAATGGGGTTTCTG 59.112 55.000 0.00 0.00 0.00 3.02
281 282 1.002857 ATTTGGGGGAGGAGGAACAG 58.997 55.000 0.00 0.00 0.00 3.16
403 404 9.066892 TGATTTAATATCTCCTGATTTTTCGGG 57.933 33.333 0.00 0.00 37.50 5.14
429 430 4.412199 TGGGATTGCTATTAACTACTGGCT 59.588 41.667 0.00 0.00 0.00 4.75
433 434 7.195374 TCAAGTGGGATTGCTATTAACTACT 57.805 36.000 0.00 0.00 0.00 2.57
475 476 1.818674 TGCATCTCTCGTGAGCTGTTA 59.181 47.619 16.88 6.72 38.35 2.41
543 545 5.731678 AGGTTCCTATAAGACCATTTCCTGT 59.268 40.000 0.00 0.00 35.89 4.00
565 569 4.019141 AGGGATCATACTACTCGTCCTAGG 60.019 50.000 0.82 0.82 0.00 3.02
580 584 0.759346 GGTGAACCGCTAGGGATCAT 59.241 55.000 8.65 0.00 43.47 2.45
634 1514 0.853530 AACAGAGTGCCCCTTTTCCT 59.146 50.000 0.00 0.00 0.00 3.36
635 1515 0.961753 CAACAGAGTGCCCCTTTTCC 59.038 55.000 0.00 0.00 0.00 3.13
653 1533 1.388065 CGGGCCGCATTATTTTCCCA 61.388 55.000 15.42 0.00 33.43 4.37
723 1605 0.041312 GTTGGCTGTAGCAACACACG 60.041 55.000 6.18 0.00 44.36 4.49
954 1854 2.035832 GGGGAGGTGTGAATTTTGTGTG 59.964 50.000 0.00 0.00 0.00 3.82
955 1855 2.316108 GGGGAGGTGTGAATTTTGTGT 58.684 47.619 0.00 0.00 0.00 3.72
958 1858 0.887933 CGGGGGAGGTGTGAATTTTG 59.112 55.000 0.00 0.00 0.00 2.44
976 1919 3.777925 CGGCAAGAAGTCACGGCG 61.778 66.667 4.80 4.80 41.08 6.46
1026 1969 1.738099 CACCTTCTTCGACTGCGGG 60.738 63.158 0.00 0.00 38.28 6.13
1281 2230 2.273449 CCGCTCTTGGGGCAGAAT 59.727 61.111 0.00 0.00 39.46 2.40
1493 2448 1.153978 TCGACATACGCGTCCAACC 60.154 57.895 18.63 1.32 42.26 3.77
1571 2526 6.208402 TGCATTGCTTTACTTACCTTTGATGA 59.792 34.615 10.49 0.00 0.00 2.92
1632 2668 6.253083 GCCTGTACGTACATCTTCTTCTTTAC 59.747 42.308 27.50 0.00 35.36 2.01
1972 3111 5.517322 AGACTGAGACGTAACAAAGACTT 57.483 39.130 0.00 0.00 0.00 3.01
2002 3144 8.362639 ACTGTGTGCAAAATCAAAGAAAGATAT 58.637 29.630 0.00 0.00 0.00 1.63
2003 3145 7.715657 ACTGTGTGCAAAATCAAAGAAAGATA 58.284 30.769 0.00 0.00 0.00 1.98
2004 3146 6.576185 ACTGTGTGCAAAATCAAAGAAAGAT 58.424 32.000 0.00 0.00 0.00 2.40
2005 3147 5.964758 ACTGTGTGCAAAATCAAAGAAAGA 58.035 33.333 0.00 0.00 0.00 2.52
2006 3148 6.038356 AGACTGTGTGCAAAATCAAAGAAAG 58.962 36.000 0.00 0.00 0.00 2.62
2007 3149 5.964758 AGACTGTGTGCAAAATCAAAGAAA 58.035 33.333 0.00 0.00 0.00 2.52
2008 3150 5.581126 AGACTGTGTGCAAAATCAAAGAA 57.419 34.783 0.00 0.00 0.00 2.52
2009 3151 5.581126 AAGACTGTGTGCAAAATCAAAGA 57.419 34.783 0.00 0.00 0.00 2.52
2010 3152 6.038356 AGAAAGACTGTGTGCAAAATCAAAG 58.962 36.000 0.00 0.00 0.00 2.77
2011 3153 5.964758 AGAAAGACTGTGTGCAAAATCAAA 58.035 33.333 0.00 0.00 0.00 2.69
2012 3154 5.581126 AGAAAGACTGTGTGCAAAATCAA 57.419 34.783 0.00 0.00 0.00 2.57
2013 3155 5.581126 AAGAAAGACTGTGTGCAAAATCA 57.419 34.783 0.00 0.00 0.00 2.57
2014 3156 6.035843 TCAAAGAAAGACTGTGTGCAAAATC 58.964 36.000 0.00 0.00 35.48 2.17
2015 3157 5.964758 TCAAAGAAAGACTGTGTGCAAAAT 58.035 33.333 0.00 0.00 35.48 1.82
2016 3158 5.384063 TCAAAGAAAGACTGTGTGCAAAA 57.616 34.783 0.00 0.00 35.48 2.44
2017 3159 5.581126 ATCAAAGAAAGACTGTGTGCAAA 57.419 34.783 0.00 0.00 35.48 3.68
2018 3160 5.581126 AATCAAAGAAAGACTGTGTGCAA 57.419 34.783 0.00 0.00 35.48 4.08
2019 3161 5.581126 AAATCAAAGAAAGACTGTGTGCA 57.419 34.783 0.00 0.00 35.48 4.57
2020 3162 5.276536 GCAAAATCAAAGAAAGACTGTGTGC 60.277 40.000 0.00 0.00 35.48 4.57
2021 3163 5.806502 TGCAAAATCAAAGAAAGACTGTGTG 59.193 36.000 0.00 0.00 35.48 3.82
2022 3164 5.964758 TGCAAAATCAAAGAAAGACTGTGT 58.035 33.333 0.00 0.00 35.48 3.72
2023 3165 6.073980 CCATGCAAAATCAAAGAAAGACTGTG 60.074 38.462 0.00 0.00 35.29 3.66
2024 3166 5.987347 CCATGCAAAATCAAAGAAAGACTGT 59.013 36.000 0.00 0.00 0.00 3.55
2025 3167 6.218019 TCCATGCAAAATCAAAGAAAGACTG 58.782 36.000 0.00 0.00 0.00 3.51
2026 3168 6.266103 TCTCCATGCAAAATCAAAGAAAGACT 59.734 34.615 0.00 0.00 0.00 3.24
2027 3169 6.449698 TCTCCATGCAAAATCAAAGAAAGAC 58.550 36.000 0.00 0.00 0.00 3.01
2028 3170 6.653526 TCTCCATGCAAAATCAAAGAAAGA 57.346 33.333 0.00 0.00 0.00 2.52
2201 3351 2.046314 CCACCGCCGTCCTTGAAT 60.046 61.111 0.00 0.00 0.00 2.57
2216 3372 3.013327 ATGCTGGAGCTGGAGCCA 61.013 61.111 10.38 1.69 43.38 4.75
2510 3666 3.501458 GATCTCCCTGGCGCGGTAC 62.501 68.421 8.83 0.00 0.00 3.34
2602 3758 8.665175 CATCTAGATGTGCTTTAACAAAACTG 57.335 34.615 22.42 0.00 34.23 3.16
2628 3784 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
2629 3785 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
2630 3786 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
2632 3788 9.935241 CCTATGACTTAGATGTGCAATACTTAT 57.065 33.333 0.00 0.00 0.00 1.73
2633 3789 8.924303 ACCTATGACTTAGATGTGCAATACTTA 58.076 33.333 0.00 0.00 0.00 2.24
2634 3790 7.796054 ACCTATGACTTAGATGTGCAATACTT 58.204 34.615 0.00 0.00 0.00 2.24
2635 3791 7.366847 ACCTATGACTTAGATGTGCAATACT 57.633 36.000 0.00 0.00 0.00 2.12
2636 3792 7.519008 GCAACCTATGACTTAGATGTGCAATAC 60.519 40.741 0.00 0.00 32.99 1.89
2637 3793 6.483307 GCAACCTATGACTTAGATGTGCAATA 59.517 38.462 0.00 0.00 32.99 1.90
2638 3794 5.297776 GCAACCTATGACTTAGATGTGCAAT 59.702 40.000 0.00 0.00 32.99 3.56
2639 3795 4.635765 GCAACCTATGACTTAGATGTGCAA 59.364 41.667 0.00 0.00 32.99 4.08
2640 3796 4.191544 GCAACCTATGACTTAGATGTGCA 58.808 43.478 10.40 0.00 32.99 4.57
2641 3797 4.191544 TGCAACCTATGACTTAGATGTGC 58.808 43.478 0.00 4.61 33.18 4.57
2642 3798 5.277683 GCATGCAACCTATGACTTAGATGTG 60.278 44.000 14.21 0.00 0.00 3.21
2643 3799 4.818546 GCATGCAACCTATGACTTAGATGT 59.181 41.667 14.21 0.00 0.00 3.06
2644 3800 4.818005 TGCATGCAACCTATGACTTAGATG 59.182 41.667 20.30 0.00 0.00 2.90
2645 3801 5.039920 TGCATGCAACCTATGACTTAGAT 57.960 39.130 20.30 0.00 0.00 1.98
2646 3802 4.486125 TGCATGCAACCTATGACTTAGA 57.514 40.909 20.30 0.00 0.00 2.10
2647 3803 4.023450 CCATGCATGCAACCTATGACTTAG 60.023 45.833 26.68 0.86 0.00 2.18
2648 3804 3.884693 CCATGCATGCAACCTATGACTTA 59.115 43.478 26.68 0.00 0.00 2.24
2649 3805 2.691526 CCATGCATGCAACCTATGACTT 59.308 45.455 26.68 0.00 0.00 3.01
2650 3806 2.092267 TCCATGCATGCAACCTATGACT 60.092 45.455 26.68 0.80 0.00 3.41
2651 3807 2.300433 TCCATGCATGCAACCTATGAC 58.700 47.619 26.68 0.00 0.00 3.06
2652 3808 2.732844 TCCATGCATGCAACCTATGA 57.267 45.000 26.68 11.75 0.00 2.15
2653 3809 3.319689 TCAATCCATGCATGCAACCTATG 59.680 43.478 26.68 19.96 0.00 2.23
2654 3810 3.319972 GTCAATCCATGCATGCAACCTAT 59.680 43.478 26.68 12.96 0.00 2.57
2655 3811 2.689471 GTCAATCCATGCATGCAACCTA 59.311 45.455 26.68 11.09 0.00 3.08
2656 3812 1.479323 GTCAATCCATGCATGCAACCT 59.521 47.619 26.68 5.25 0.00 3.50
2657 3813 1.799917 CGTCAATCCATGCATGCAACC 60.800 52.381 26.68 5.44 0.00 3.77
2658 3814 1.552226 CGTCAATCCATGCATGCAAC 58.448 50.000 26.68 15.19 0.00 4.17
2659 3815 0.179132 GCGTCAATCCATGCATGCAA 60.179 50.000 26.68 9.06 0.00 4.08
2660 3816 1.313812 TGCGTCAATCCATGCATGCA 61.314 50.000 25.04 25.04 33.18 3.96
2661 3817 0.179132 TTGCGTCAATCCATGCATGC 60.179 50.000 21.69 11.82 38.12 4.06
2662 3818 2.190161 CTTTGCGTCAATCCATGCATG 58.810 47.619 20.19 20.19 38.12 4.06
2663 3819 1.135527 CCTTTGCGTCAATCCATGCAT 59.864 47.619 0.00 0.00 38.12 3.96
2664 3820 0.527113 CCTTTGCGTCAATCCATGCA 59.473 50.000 0.00 0.00 36.47 3.96
2665 3821 0.803380 GCCTTTGCGTCAATCCATGC 60.803 55.000 0.00 0.00 0.00 4.06
2666 3822 0.179129 GGCCTTTGCGTCAATCCATG 60.179 55.000 0.00 0.00 38.85 3.66
2667 3823 0.611618 TGGCCTTTGCGTCAATCCAT 60.612 50.000 3.32 0.00 38.85 3.41
2668 3824 1.228398 TGGCCTTTGCGTCAATCCA 60.228 52.632 3.32 0.00 38.85 3.41
2669 3825 1.508088 CTGGCCTTTGCGTCAATCC 59.492 57.895 3.32 0.00 38.85 3.01
2670 3826 1.508088 CCTGGCCTTTGCGTCAATC 59.492 57.895 3.32 0.00 38.85 2.67
2671 3827 1.978617 CCCTGGCCTTTGCGTCAAT 60.979 57.895 3.32 0.00 38.85 2.57
2672 3828 2.597217 CCCTGGCCTTTGCGTCAA 60.597 61.111 3.32 0.00 38.85 3.18
2673 3829 4.659172 CCCCTGGCCTTTGCGTCA 62.659 66.667 3.32 0.00 38.85 4.35
2674 3830 4.660938 ACCCCTGGCCTTTGCGTC 62.661 66.667 3.32 0.00 38.85 5.19
2675 3831 3.749284 AAACCCCTGGCCTTTGCGT 62.749 57.895 3.32 0.00 38.85 5.24
2676 3832 2.434658 GAAAACCCCTGGCCTTTGCG 62.435 60.000 3.32 0.00 38.85 4.85
2687 3843 4.764050 TTTTGAAAAGGAGGAAAACCCC 57.236 40.909 0.00 0.00 34.66 4.95
2699 3855 4.679654 GGCGTGGTCATAGTTTTTGAAAAG 59.320 41.667 0.00 0.00 0.00 2.27
2707 3863 1.743995 GGCGGCGTGGTCATAGTTT 60.744 57.895 9.37 0.00 0.00 2.66
2710 3866 1.743623 TTTGGCGGCGTGGTCATAG 60.744 57.895 9.37 0.00 0.00 2.23
2711 3867 2.036006 GTTTGGCGGCGTGGTCATA 61.036 57.895 9.37 0.00 0.00 2.15
2892 4108 1.486211 CTGTCCTGGTAATCGTCCCT 58.514 55.000 0.00 0.00 0.00 4.20
2900 4116 1.429930 TGGAGTTGCTGTCCTGGTAA 58.570 50.000 0.00 0.00 34.86 2.85
2913 4129 1.377725 CAGCCTTGCCGATGGAGTT 60.378 57.895 0.00 0.00 0.00 3.01
2971 4187 1.072505 GAAACCTCAGAACCGGCCA 59.927 57.895 0.00 0.00 0.00 5.36
3012 4228 2.596904 TCGTATTTAGAGGCACCAGC 57.403 50.000 0.00 0.00 41.10 4.85
3067 5258 2.138596 ATTTGTTGCCGCTGAAACTG 57.861 45.000 0.31 0.00 0.00 3.16
3068 5259 3.367292 CCATATTTGTTGCCGCTGAAACT 60.367 43.478 0.31 0.00 0.00 2.66
3082 5273 8.408601 CCCACTACTCTTTTTGATCCATATTTG 58.591 37.037 0.00 0.00 0.00 2.32
3083 5274 8.336235 TCCCACTACTCTTTTTGATCCATATTT 58.664 33.333 0.00 0.00 0.00 1.40
3155 5346 4.067896 GTGCAGATGGATTTACGGATCAT 58.932 43.478 0.00 0.00 0.00 2.45
3190 5381 7.120432 AGCAATGACAAGAAAAGAAGAGGATAC 59.880 37.037 0.00 0.00 0.00 2.24
3203 5394 3.743521 ACTAGCACAGCAATGACAAGAA 58.256 40.909 0.00 0.00 0.00 2.52
3208 5399 1.590238 CGCTACTAGCACAGCAATGAC 59.410 52.381 8.78 0.00 42.58 3.06
3234 5425 3.374678 GCTGCTTCATCTTCTTCCTCTTG 59.625 47.826 0.00 0.00 0.00 3.02
3235 5426 3.608796 GCTGCTTCATCTTCTTCCTCTT 58.391 45.455 0.00 0.00 0.00 2.85
3236 5427 2.418471 CGCTGCTTCATCTTCTTCCTCT 60.418 50.000 0.00 0.00 0.00 3.69
3237 5428 1.932511 CGCTGCTTCATCTTCTTCCTC 59.067 52.381 0.00 0.00 0.00 3.71
3238 5429 2.011046 GCGCTGCTTCATCTTCTTCCT 61.011 52.381 0.00 0.00 0.00 3.36
3239 5430 0.376502 GCGCTGCTTCATCTTCTTCC 59.623 55.000 0.00 0.00 0.00 3.46
3240 5431 1.062294 CTGCGCTGCTTCATCTTCTTC 59.938 52.381 9.73 0.00 0.00 2.87
3241 5432 1.085091 CTGCGCTGCTTCATCTTCTT 58.915 50.000 9.73 0.00 0.00 2.52
3242 5433 0.036577 ACTGCGCTGCTTCATCTTCT 60.037 50.000 14.80 0.00 0.00 2.85
3243 5434 0.801251 AACTGCGCTGCTTCATCTTC 59.199 50.000 14.80 0.00 0.00 2.87
3244 5435 0.801251 GAACTGCGCTGCTTCATCTT 59.199 50.000 14.80 0.00 0.00 2.40
3254 5445 2.542907 CCAAACACGGAACTGCGCT 61.543 57.895 9.73 0.00 0.00 5.92
3255 5446 2.051345 CCAAACACGGAACTGCGC 60.051 61.111 0.00 0.00 0.00 6.09
3256 5447 2.051345 GCCAAACACGGAACTGCG 60.051 61.111 0.00 0.00 0.00 5.18
3272 5463 4.827835 TCTAGTAGTGGATGTACTCATGGC 59.172 45.833 0.00 0.00 34.06 4.40
3401 5592 4.143179 GCTATTAATGTAATGGCCGACGAC 60.143 45.833 0.00 0.00 44.05 4.34
3439 5630 9.774413 CTTAATACCGTGGGAAAAGATATTAGT 57.226 33.333 0.00 0.00 0.00 2.24
3475 5666 1.539496 GCCTAAACATATCCGACGGCA 60.539 52.381 9.66 0.00 36.37 5.69


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

AutoCloner maintained by Alex Coulton.