Multiple sequence alignment - TraesCS7B01G083400

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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 TraesCS7B01G083400 chr7B 100.000 3495 0 0 1 3495 94187315 94183821 0.000000e+00 6455.0
1 TraesCS7B01G083400 chr7B 99.234 1044 8 0 1437 2480 94143107 94142064 0.000000e+00 1884.0
2 TraesCS7B01G083400 chr7B 92.770 1314 48 26 926 2207 94118445 94117147 0.000000e+00 1857.0
3 TraesCS7B01G083400 chr7B 89.926 1221 67 22 796 1972 93571301 93572509 0.000000e+00 1522.0
4 TraesCS7B01G083400 chr7B 89.983 1188 80 20 1036 2207 157808504 157809668 0.000000e+00 1498.0
5 TraesCS7B01G083400 chr7B 91.132 1060 47 18 926 1972 93650573 93651598 0.000000e+00 1393.0
6 TraesCS7B01G083400 chr7B 85.166 782 59 21 1769 2532 94049536 94048794 0.000000e+00 749.0
7 TraesCS7B01G083400 chr7B 81.266 758 114 20 2751 3495 94141734 94140992 3.890000e-164 588.0
8 TraesCS7B01G083400 chr7B 79.134 762 110 29 2750 3495 94115108 94114380 6.780000e-132 481.0
9 TraesCS7B01G083400 chr7B 84.409 372 28 17 440 810 94143685 94143343 4.320000e-89 339.0
10 TraesCS7B01G083400 chr7B 89.922 258 14 3 1 258 94143922 94143677 4.350000e-84 322.0
11 TraesCS7B01G083400 chr7B 93.085 188 10 2 256 442 606591267 606591082 4.450000e-69 272.0
12 TraesCS7B01G083400 chr7B 95.070 142 7 0 2211 2352 93572787 93572928 1.260000e-54 224.0
13 TraesCS7B01G083400 chr7B 95.070 142 7 0 2211 2352 93651940 93652081 1.260000e-54 224.0
14 TraesCS7B01G083400 chr7B 77.805 401 58 19 1980 2378 157809507 157809878 5.870000e-53 219.0
15 TraesCS7B01G083400 chr7B 80.903 288 36 11 2386 2670 93652080 93652351 3.530000e-50 209.0
16 TraesCS7B01G083400 chr7B 77.089 371 71 9 3128 3495 28509673 28510032 5.920000e-48 202.0
17 TraesCS7B01G083400 chr7B 93.077 130 9 0 2360 2489 94115388 94115259 1.280000e-44 191.0
18 TraesCS7B01G083400 chr7B 81.778 225 13 11 796 992 94143325 94143101 2.790000e-36 163.0
19 TraesCS7B01G083400 chr7B 93.878 98 4 2 2572 2668 94115216 94115120 2.810000e-31 147.0
20 TraesCS7B01G083400 chr7B 85.321 109 16 0 150 258 93570942 93571050 2.850000e-21 113.0
21 TraesCS7B01G083400 chr7D 90.193 1448 91 32 796 2211 132831070 132829642 0.000000e+00 1840.0
22 TraesCS7B01G083400 chr7D 87.782 1596 103 37 926 2505 132157077 132158596 0.000000e+00 1783.0
23 TraesCS7B01G083400 chr7D 88.691 1459 93 38 796 2207 132764749 132763316 0.000000e+00 1714.0
24 TraesCS7B01G083400 chr7D 88.274 1501 68 46 938 2401 132741110 132742539 0.000000e+00 1698.0
25 TraesCS7B01G083400 chr7D 86.618 1517 104 47 926 2379 132135597 132137077 0.000000e+00 1585.0
26 TraesCS7B01G083400 chr7D 89.231 1300 95 23 926 2207 194129343 194130615 0.000000e+00 1583.0
27 TraesCS7B01G083400 chr7D 88.677 1051 43 37 932 1939 132197303 132198320 0.000000e+00 1212.0
28 TraesCS7B01G083400 chr7D 79.305 691 70 40 1984 2669 132829804 132829182 1.940000e-112 416.0
29 TraesCS7B01G083400 chr7D 78.745 701 70 43 1983 2678 132763475 132762849 2.530000e-106 396.0
30 TraesCS7B01G083400 chr7D 85.498 331 48 0 440 770 132765155 132764825 2.580000e-91 346.0
31 TraesCS7B01G083400 chr7D 83.657 361 39 14 1852 2207 133194576 133194921 4.350000e-84 322.0
32 TraesCS7B01G083400 chr7D 81.963 377 57 9 3125 3495 540722117 540722488 3.390000e-80 309.0
33 TraesCS7B01G083400 chr7D 82.493 377 23 18 2306 2678 132158398 132158735 1.230000e-74 291.0
34 TraesCS7B01G083400 chr7D 92.982 171 11 1 88 258 132832446 132832277 7.490000e-62 248.0
35 TraesCS7B01G083400 chr7D 84.314 255 31 7 796 1042 132831879 132831626 1.250000e-59 241.0
36 TraesCS7B01G083400 chr7D 83.402 241 29 8 1855 2091 131822462 131822229 2.730000e-51 213.0
37 TraesCS7B01G083400 chr7D 90.780 141 12 1 448 588 132747581 132747720 1.660000e-43 187.0
38 TraesCS7B01G083400 chr7D 84.800 125 16 2 132 256 132739635 132739756 4.740000e-24 122.0
39 TraesCS7B01G083400 chr7D 91.209 91 5 2 1 91 132832590 132832503 1.700000e-23 121.0
40 TraesCS7B01G083400 chr7D 87.000 100 12 1 118 216 132135053 132135152 1.030000e-20 111.0
41 TraesCS7B01G083400 chr7A 86.168 1793 127 56 456 2194 131122002 131120277 0.000000e+00 1825.0
42 TraesCS7B01G083400 chr7A 85.887 1736 124 57 513 2194 130781990 130783658 0.000000e+00 1736.0
43 TraesCS7B01G083400 chr7A 88.191 1448 130 23 804 2211 131187739 131186293 0.000000e+00 1688.0
44 TraesCS7B01G083400 chr7A 89.550 1110 63 18 1113 2207 131109279 131108208 0.000000e+00 1358.0
45 TraesCS7B01G083400 chr7A 88.217 314 19 12 1896 2207 130893837 130894134 3.320000e-95 359.0
46 TraesCS7B01G083400 chr7A 87.220 313 26 7 2078 2379 130784691 130785000 9.290000e-91 344.0
47 TraesCS7B01G083400 chr7A 87.220 313 26 7 2078 2379 131119244 131118935 9.290000e-91 344.0
48 TraesCS7B01G083400 chr7A 78.804 552 64 27 1984 2532 210253325 210253826 4.350000e-84 322.0
49 TraesCS7B01G083400 chr7A 76.487 706 73 45 1983 2678 131108367 131107745 7.330000e-77 298.0
50 TraesCS7B01G083400 chr7A 88.983 236 23 3 23 258 131126787 131126555 4.410000e-74 289.0
51 TraesCS7B01G083400 chr7A 78.302 424 62 18 1980 2401 203697937 203698332 2.690000e-61 246.0
52 TraesCS7B01G083400 chr7A 87.234 141 17 1 118 258 130781551 130781690 3.610000e-35 159.0
53 TraesCS7B01G083400 chr7A 90.805 87 8 0 840 926 131126209 131126123 2.200000e-22 117.0
54 TraesCS7B01G083400 chr7A 91.045 67 4 2 2605 2669 131186032 131185966 4.800000e-14 89.8
55 TraesCS7B01G083400 chr5D 78.999 819 114 29 2720 3495 181631225 181630422 1.120000e-139 507.0
56 TraesCS7B01G083400 chr5D 92.228 193 12 3 256 448 348748657 348748468 1.600000e-68 270.0
57 TraesCS7B01G083400 chr5D 76.042 192 35 9 2699 2883 249494383 249494570 4.800000e-14 89.8
58 TraesCS7B01G083400 chr6D 78.117 818 116 39 2720 3489 285501905 285502707 8.840000e-126 460.0
59 TraesCS7B01G083400 chr6D 81.673 251 37 7 3251 3495 60128572 60128325 2.130000e-47 200.0
60 TraesCS7B01G083400 chr6D 80.503 159 22 9 3332 3489 364498394 364498244 2.850000e-21 113.0
61 TraesCS7B01G083400 chr4A 76.970 825 134 36 2706 3489 663454352 663455161 1.500000e-113 420.0
62 TraesCS7B01G083400 chr4A 76.848 825 137 33 2706 3489 663435647 663436458 1.940000e-112 416.0
63 TraesCS7B01G083400 chr4A 75.971 824 144 33 2706 3489 663420743 663421552 3.290000e-100 375.0
64 TraesCS7B01G083400 chr3B 79.406 471 74 17 3040 3495 444677189 444676727 9.420000e-81 311.0
65 TraesCS7B01G083400 chr3D 92.647 204 12 3 246 447 506177119 506177321 1.230000e-74 291.0
66 TraesCS7B01G083400 chr3D 93.085 188 11 2 256 441 486691452 486691639 1.240000e-69 274.0
67 TraesCS7B01G083400 chr3D 90.863 197 17 1 245 440 25293925 25294121 2.680000e-66 263.0
68 TraesCS7B01G083400 chr3D 76.738 374 66 12 3125 3493 205383268 205382911 4.610000e-44 189.0
69 TraesCS7B01G083400 chr2B 95.055 182 7 2 260 440 771215316 771215136 5.710000e-73 285.0
70 TraesCS7B01G083400 chr2B 82.576 132 18 5 2765 2893 541383769 541383640 1.030000e-20 111.0
71 TraesCS7B01G083400 chr6A 80.159 378 64 9 3125 3495 76623008 76622635 4.450000e-69 272.0
72 TraesCS7B01G083400 chr6A 76.744 430 73 21 3079 3495 608098249 608097834 7.600000e-52 215.0
73 TraesCS7B01G083400 chr2D 92.553 188 13 1 252 439 537187725 537187911 5.750000e-68 268.0
74 TraesCS7B01G083400 chr2D 76.699 206 39 8 2720 2920 515816437 515816236 4.770000e-19 106.0
75 TraesCS7B01G083400 chr2D 88.406 69 4 3 2931 2996 54881180 54881247 2.890000e-11 80.5
76 TraesCS7B01G083400 chr5A 90.594 202 17 2 249 448 35660093 35659892 2.070000e-67 267.0
77 TraesCS7B01G083400 chr5A 77.132 258 42 13 2720 2975 170860295 170860053 2.190000e-27 134.0
78 TraesCS7B01G083400 chr1D 90.547 201 17 2 249 449 375012104 375011906 7.440000e-67 265.0
79 TraesCS7B01G083400 chr3A 75.806 434 80 19 3068 3493 599995399 599994983 2.750000e-46 196.0
80 TraesCS7B01G083400 chr3A 75.155 322 62 11 3172 3489 25534974 25534667 6.090000e-28 135.0
81 TraesCS7B01G083400 chr3A 77.540 187 37 4 2711 2893 463124964 463124779 1.330000e-19 108.0
82 TraesCS7B01G083400 chr5B 81.373 204 34 3 2720 2920 163283291 163283089 2.790000e-36 163.0
83 TraesCS7B01G083400 chr5B 97.297 37 0 1 2934 2970 163283052 163283017 1.050000e-05 62.1
84 TraesCS7B01G083400 chr6B 81.761 159 22 7 3331 3489 549653806 549653655 3.660000e-25 126.0
85 TraesCS7B01G083400 chr1A 100.000 28 0 0 2951 2978 133990615 133990588 6.000000e-03 52.8


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 TraesCS7B01G083400 chr7B 94183821 94187315 3494 True 6455.000000 6455 100.000000 1 3495 1 chr7B.!!$R2 3494
1 TraesCS7B01G083400 chr7B 157808504 157809878 1374 False 858.500000 1498 83.894000 1036 2378 2 chr7B.!!$F4 1342
2 TraesCS7B01G083400 chr7B 94048794 94049536 742 True 749.000000 749 85.166000 1769 2532 1 chr7B.!!$R1 763
3 TraesCS7B01G083400 chr7B 94114380 94118445 4065 True 669.000000 1857 89.714750 926 3495 4 chr7B.!!$R4 2569
4 TraesCS7B01G083400 chr7B 94140992 94143922 2930 True 659.200000 1884 87.321800 1 3495 5 chr7B.!!$R5 3494
5 TraesCS7B01G083400 chr7B 93570942 93572928 1986 False 619.666667 1522 90.105667 150 2352 3 chr7B.!!$F2 2202
6 TraesCS7B01G083400 chr7B 93650573 93652351 1778 False 608.666667 1393 89.035000 926 2670 3 chr7B.!!$F3 1744
7 TraesCS7B01G083400 chr7D 194129343 194130615 1272 False 1583.000000 1583 89.231000 926 2207 1 chr7D.!!$F4 1281
8 TraesCS7B01G083400 chr7D 132197303 132198320 1017 False 1212.000000 1212 88.677000 932 1939 1 chr7D.!!$F1 1007
9 TraesCS7B01G083400 chr7D 132157077 132158735 1658 False 1037.000000 1783 85.137500 926 2678 2 chr7D.!!$F7 1752
10 TraesCS7B01G083400 chr7D 132739635 132742539 2904 False 910.000000 1698 86.537000 132 2401 2 chr7D.!!$F8 2269
11 TraesCS7B01G083400 chr7D 132135053 132137077 2024 False 848.000000 1585 86.809000 118 2379 2 chr7D.!!$F6 2261
12 TraesCS7B01G083400 chr7D 132762849 132765155 2306 True 818.666667 1714 84.311333 440 2678 3 chr7D.!!$R2 2238
13 TraesCS7B01G083400 chr7D 132829182 132832590 3408 True 573.200000 1840 87.600600 1 2669 5 chr7D.!!$R3 2668
14 TraesCS7B01G083400 chr7A 131118935 131122002 3067 True 1084.500000 1825 86.694000 456 2379 2 chr7A.!!$R2 1923
15 TraesCS7B01G083400 chr7A 131185966 131187739 1773 True 888.900000 1688 89.618000 804 2669 2 chr7A.!!$R4 1865
16 TraesCS7B01G083400 chr7A 131107745 131109279 1534 True 828.000000 1358 83.018500 1113 2678 2 chr7A.!!$R1 1565
17 TraesCS7B01G083400 chr7A 130781551 130785000 3449 False 746.333333 1736 86.780333 118 2379 3 chr7A.!!$F4 2261
18 TraesCS7B01G083400 chr7A 210253325 210253826 501 False 322.000000 322 78.804000 1984 2532 1 chr7A.!!$F3 548
19 TraesCS7B01G083400 chr7A 131126123 131126787 664 True 203.000000 289 89.894000 23 926 2 chr7A.!!$R3 903
20 TraesCS7B01G083400 chr5D 181630422 181631225 803 True 507.000000 507 78.999000 2720 3495 1 chr5D.!!$R1 775
21 TraesCS7B01G083400 chr6D 285501905 285502707 802 False 460.000000 460 78.117000 2720 3489 1 chr6D.!!$F1 769
22 TraesCS7B01G083400 chr4A 663454352 663455161 809 False 420.000000 420 76.970000 2706 3489 1 chr4A.!!$F3 783
23 TraesCS7B01G083400 chr4A 663435647 663436458 811 False 416.000000 416 76.848000 2706 3489 1 chr4A.!!$F2 783
24 TraesCS7B01G083400 chr4A 663420743 663421552 809 False 375.000000 375 75.971000 2706 3489 1 chr4A.!!$F1 783

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
666 1845 0.236187 GCACCGTGATTGTAAACGCA 59.764 50.0 1.65 0.0 38.46 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2562 6881 1.757682 TCAACGAAGCACAAAACCCT 58.242 45.0 0.0 0.0 0.0 4.34 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
33 34 3.655777 TCTGGTCCCATTAACCAAAGAGT 59.344 43.478 0.00 0.00 45.86 3.24
58 59 1.227118 GTTGCTCCTAGCTCGCTCC 60.227 63.158 0.00 0.00 42.97 4.70
101 162 9.841880 AACACAGTATATACATAGACGCTATTG 57.158 33.333 15.18 2.79 30.24 1.90
143 204 5.925506 TGAGTAATGAGTCCACCGAAATA 57.074 39.130 0.00 0.00 0.00 1.40
247 311 9.027202 ACCGGAATTTGTATTAAATAACAACCT 57.973 29.630 9.46 0.00 35.43 3.50
277 341 9.705290 AAATAAATGGTTTGTTTAGGACACATC 57.295 29.630 0.00 0.00 38.18 3.06
278 342 6.976934 AAATGGTTTGTTTAGGACACATCT 57.023 33.333 0.00 0.00 38.18 2.90
279 343 9.747898 ATAAATGGTTTGTTTAGGACACATCTA 57.252 29.630 0.00 0.00 38.18 1.98
280 344 7.687941 AATGGTTTGTTTAGGACACATCTAG 57.312 36.000 0.00 0.00 38.18 2.43
281 345 6.428083 TGGTTTGTTTAGGACACATCTAGA 57.572 37.500 0.00 0.00 38.18 2.43
282 346 7.016153 TGGTTTGTTTAGGACACATCTAGAT 57.984 36.000 0.00 0.00 38.18 1.98
283 347 6.878923 TGGTTTGTTTAGGACACATCTAGATG 59.121 38.462 27.63 27.63 44.15 2.90
325 389 8.498054 CATCTAAACTGATGTCCACTGTATTT 57.502 34.615 0.00 0.00 39.05 1.40
326 390 7.905604 TCTAAACTGATGTCCACTGTATTTG 57.094 36.000 0.00 0.00 0.00 2.32
327 391 7.450074 TCTAAACTGATGTCCACTGTATTTGT 58.550 34.615 0.00 0.00 0.00 2.83
328 392 5.947228 AACTGATGTCCACTGTATTTGTG 57.053 39.130 0.00 0.00 35.39 3.33
385 449 9.800433 TCTTGTTGTTGCATTATATATTTGTGG 57.200 29.630 0.00 0.00 0.00 4.17
386 450 8.939201 TTGTTGTTGCATTATATATTTGTGGG 57.061 30.769 0.00 0.00 0.00 4.61
387 451 8.298729 TGTTGTTGCATTATATATTTGTGGGA 57.701 30.769 0.00 0.00 0.00 4.37
388 452 8.412456 TGTTGTTGCATTATATATTTGTGGGAG 58.588 33.333 0.00 0.00 0.00 4.30
389 453 6.980593 TGTTGCATTATATATTTGTGGGAGC 58.019 36.000 0.00 0.00 0.00 4.70
390 454 6.777091 TGTTGCATTATATATTTGTGGGAGCT 59.223 34.615 0.00 0.00 0.00 4.09
391 455 7.287466 TGTTGCATTATATATTTGTGGGAGCTT 59.713 33.333 0.00 0.00 0.00 3.74
392 456 8.792633 GTTGCATTATATATTTGTGGGAGCTTA 58.207 33.333 0.00 0.00 0.00 3.09
393 457 8.565896 TGCATTATATATTTGTGGGAGCTTAG 57.434 34.615 0.00 0.00 0.00 2.18
394 458 8.382405 TGCATTATATATTTGTGGGAGCTTAGA 58.618 33.333 0.00 0.00 0.00 2.10
395 459 9.401058 GCATTATATATTTGTGGGAGCTTAGAT 57.599 33.333 0.00 0.00 0.00 1.98
398 462 9.725019 TTATATATTTGTGGGAGCTTAGATGTG 57.275 33.333 0.00 0.00 0.00 3.21
399 463 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
400 464 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
401 465 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
402 466 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
403 467 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
404 468 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
405 469 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
406 470 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
407 471 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
408 472 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
409 473 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
410 474 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
411 475 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
467 531 1.915614 GCCCTGCATGTCTTGACGTG 61.916 60.000 16.18 16.18 0.00 4.49
500 564 5.486735 TGGTTGATTGCCTGAATTTTCAT 57.513 34.783 0.00 0.00 36.46 2.57
545 615 6.928979 TTCGTTCTCAAGAAAATGGTGTTA 57.071 33.333 0.00 0.00 35.58 2.41
601 1562 1.757118 TGATAGGTCTGAAGGCCGAAG 59.243 52.381 0.00 0.00 0.00 3.79
647 1608 6.912591 GCTCAAAGGATATTTTGGACGTTATG 59.087 38.462 0.00 0.00 38.33 1.90
666 1845 0.236187 GCACCGTGATTGTAAACGCA 59.764 50.000 1.65 0.00 38.46 5.24
676 1855 6.241385 GTGATTGTAAACGCAGATTGAGTAC 58.759 40.000 0.00 0.00 28.03 2.73
712 1912 7.397892 TTTAGAAGAAAACAATGGTGTGTGA 57.602 32.000 0.00 0.00 38.27 3.58
764 1964 3.003480 ACACTAGAGAAAGCAAATCGCC 58.997 45.455 0.00 0.00 44.04 5.54
1007 3121 1.452108 CATTTCGCACCCCCTCTCC 60.452 63.158 0.00 0.00 0.00 3.71
1365 3612 3.920412 TCTCAACATCGTGAGTCAAATCG 59.080 43.478 0.00 0.00 44.56 3.34
1962 4257 1.390463 GCTTCGTTGATCGTCTTGGAC 59.610 52.381 0.00 0.00 40.80 4.02
2352 5053 2.949644 GTGAACTGGCAGTTACAGGTTT 59.050 45.455 31.24 8.47 38.80 3.27
2470 6783 7.284489 TGTGTGCTTATCCTTGAGTTTAACTTT 59.716 33.333 0.00 0.00 0.00 2.66
2539 6858 2.094675 GAACAGTCACATGGGAATGGG 58.905 52.381 27.46 5.78 37.20 4.00
2550 6869 5.046735 CACATGGGAATGGGATTTGTTTGTA 60.047 40.000 0.00 0.00 0.00 2.41
2551 6870 5.187576 ACATGGGAATGGGATTTGTTTGTAG 59.812 40.000 0.00 0.00 0.00 2.74
2556 6875 6.209788 GGGAATGGGATTTGTTTGTAGTTGTA 59.790 38.462 0.00 0.00 0.00 2.41
2560 6879 7.033530 TGGGATTTGTTTGTAGTTGTAGTTG 57.966 36.000 0.00 0.00 0.00 3.16
2562 6881 7.774157 TGGGATTTGTTTGTAGTTGTAGTTGTA 59.226 33.333 0.00 0.00 0.00 2.41
2563 6882 8.287503 GGGATTTGTTTGTAGTTGTAGTTGTAG 58.712 37.037 0.00 0.00 0.00 2.74
2564 6883 8.287503 GGATTTGTTTGTAGTTGTAGTTGTAGG 58.712 37.037 0.00 0.00 0.00 3.18
2565 6884 7.556733 TTTGTTTGTAGTTGTAGTTGTAGGG 57.443 36.000 0.00 0.00 0.00 3.53
2566 6885 6.237887 TGTTTGTAGTTGTAGTTGTAGGGT 57.762 37.500 0.00 0.00 0.00 4.34
2567 6886 6.652053 TGTTTGTAGTTGTAGTTGTAGGGTT 58.348 36.000 0.00 0.00 0.00 4.11
2568 6887 7.111466 TGTTTGTAGTTGTAGTTGTAGGGTTT 58.889 34.615 0.00 0.00 0.00 3.27
2569 6888 7.611079 TGTTTGTAGTTGTAGTTGTAGGGTTTT 59.389 33.333 0.00 0.00 0.00 2.43
2570 6889 7.556733 TTGTAGTTGTAGTTGTAGGGTTTTG 57.443 36.000 0.00 0.00 0.00 2.44
2571 6890 6.652053 TGTAGTTGTAGTTGTAGGGTTTTGT 58.348 36.000 0.00 0.00 0.00 2.83
2572 6891 6.539464 TGTAGTTGTAGTTGTAGGGTTTTGTG 59.461 38.462 0.00 0.00 0.00 3.33
2593 6912 3.673338 TGCTTCGTTGATTTACTCGAGTG 59.327 43.478 28.12 8.61 33.98 3.51
2603 6922 9.297586 GTTGATTTACTCGAGTGTAATGTGATA 57.702 33.333 28.12 0.23 33.16 2.15
2697 7068 3.283684 CGGGAAGGTGTTGCGCAA 61.284 61.111 21.02 21.02 0.00 4.85
2700 7071 1.212751 GGAAGGTGTTGCGCAATCC 59.787 57.895 27.79 27.96 0.00 3.01
2701 7072 1.523154 GGAAGGTGTTGCGCAATCCA 61.523 55.000 32.82 23.57 31.02 3.41
2704 7075 2.126346 GTGTTGCGCAATCCAGGC 60.126 61.111 27.79 12.73 0.00 4.85
2709 7080 2.517875 GCGCAATCCAGGCCATCT 60.518 61.111 5.01 0.00 0.00 2.90
2717 7122 0.482446 TCCAGGCCATCTGTTTGGTT 59.518 50.000 5.01 0.00 41.83 3.67
2723 7128 5.363939 CAGGCCATCTGTTTGGTTTTAAAA 58.636 37.500 5.01 0.00 39.11 1.52
2739 7144 4.657436 TTAAAAGGACACAAAATGCGGT 57.343 36.364 0.00 0.00 0.00 5.68
2790 7218 1.770294 TTTTTGTCCCGCTTTCCACT 58.230 45.000 0.00 0.00 0.00 4.00
2899 7598 0.098025 CGTTGGTGACACAAACGCTT 59.902 50.000 29.66 0.00 42.67 4.68
2900 7599 1.544686 GTTGGTGACACAAACGCTTG 58.455 50.000 10.06 0.00 42.67 4.01
2932 7631 2.284112 TTCCCTTCGCCCCTACGT 60.284 61.111 0.00 0.00 0.00 3.57
2934 7633 4.203076 CCCTTCGCCCCTACGTCG 62.203 72.222 0.00 0.00 0.00 5.12
2935 7634 4.867599 CCTTCGCCCCTACGTCGC 62.868 72.222 0.00 0.00 0.00 5.19
3001 7729 1.307647 CCAAACCCCTGCCATAGCT 59.692 57.895 0.00 0.00 40.80 3.32
3003 7731 0.323725 CAAACCCCTGCCATAGCTGT 60.324 55.000 0.00 0.00 40.80 4.40
3026 7757 1.683011 CCATTTTCTCGGCCACCTCAT 60.683 52.381 2.24 0.00 0.00 2.90
3031 7762 0.904865 TCTCGGCCACCTCATTGTCT 60.905 55.000 2.24 0.00 0.00 3.41
3053 7791 2.125673 CGACCGCCGGATTTGAGT 60.126 61.111 11.71 0.00 33.91 3.41
3056 7794 3.508840 CCGCCGGATTTGAGTGCC 61.509 66.667 5.05 0.00 0.00 5.01
3088 7827 3.211963 GCTACGCCTTGCCATGGG 61.212 66.667 15.13 0.00 0.00 4.00
3091 7830 0.107410 CTACGCCTTGCCATGGGTTA 60.107 55.000 15.13 0.00 0.00 2.85
3160 7907 4.815108 TCCGCCTCTAGCCGCTCA 62.815 66.667 0.00 0.00 38.78 4.26
3165 7912 1.459455 GCCTCTAGCCGCTCAGATCA 61.459 60.000 0.00 0.00 34.35 2.92
3166 7913 1.255882 CCTCTAGCCGCTCAGATCAT 58.744 55.000 0.00 0.00 0.00 2.45
3168 7915 2.822561 CCTCTAGCCGCTCAGATCATTA 59.177 50.000 0.00 0.00 0.00 1.90
3193 7999 1.379527 GGAGGTTCACCGGCAAATAG 58.620 55.000 0.00 0.00 42.08 1.73
3204 8010 2.900337 CAAATAGACGCCCGGCCC 60.900 66.667 3.10 0.00 0.00 5.80
3216 8022 3.072468 CGGCCCTTGTCCGGACTA 61.072 66.667 33.39 25.77 42.99 2.59
3228 8034 2.689034 GGACTAGGTGCTGGCCCT 60.689 66.667 0.00 7.52 36.04 5.19
3262 8068 2.811431 CTCACCGTTGCCACTCATAAAA 59.189 45.455 0.00 0.00 0.00 1.52
3276 8084 1.066002 CATAAAATGCGGACTGCCCAG 59.934 52.381 3.22 0.00 45.60 4.45
3344 8152 5.923204 TGGGTGTTTATCAAGTGCAAAAAT 58.077 33.333 0.00 0.00 0.00 1.82
3355 8169 5.954752 TCAAGTGCAAAAATGATGGGGTATA 59.045 36.000 0.00 0.00 0.00 1.47
3358 8172 5.898972 AGTGCAAAAATGATGGGGTATATGT 59.101 36.000 0.00 0.00 0.00 2.29
3389 8203 1.156736 CGGTTGTGCTTTCGGATTCT 58.843 50.000 0.00 0.00 0.00 2.40
3409 8223 3.052745 CTGCGCATTTTCGATAGCTCTA 58.947 45.455 12.24 0.00 0.00 2.43
3448 8262 5.372343 TTGTATGTAGGATGGATGCAAGT 57.628 39.130 0.00 0.00 0.00 3.16
3464 8278 5.359194 TGCAAGTTTTTGGTATTGGGAAA 57.641 34.783 0.00 0.00 34.79 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.764890 AGCTAGGAGCAACCACACAA 59.235 50.000 0.64 0.00 45.56 3.33
251 315 9.705290 GATGTGTCCTAAACAAACCATTTATTT 57.295 29.630 0.00 0.00 40.31 1.40
252 316 9.088987 AGATGTGTCCTAAACAAACCATTTATT 57.911 29.630 0.00 0.00 40.31 1.40
253 317 8.650143 AGATGTGTCCTAAACAAACCATTTAT 57.350 30.769 0.00 0.00 40.31 1.40
254 318 9.226606 CTAGATGTGTCCTAAACAAACCATTTA 57.773 33.333 0.00 0.00 40.31 1.40
255 319 6.976934 AGATGTGTCCTAAACAAACCATTT 57.023 33.333 0.00 0.00 40.31 2.32
256 320 7.458397 TCTAGATGTGTCCTAAACAAACCATT 58.542 34.615 0.00 0.00 40.31 3.16
257 321 7.016153 TCTAGATGTGTCCTAAACAAACCAT 57.984 36.000 0.00 0.00 40.31 3.55
258 322 6.428083 TCTAGATGTGTCCTAAACAAACCA 57.572 37.500 0.00 0.00 40.31 3.67
259 323 7.308782 CATCTAGATGTGTCCTAAACAAACC 57.691 40.000 22.42 0.00 40.31 3.27
301 365 8.103305 ACAAATACAGTGGACATCAGTTTAGAT 58.897 33.333 0.00 0.00 0.00 1.98
302 366 7.387673 CACAAATACAGTGGACATCAGTTTAGA 59.612 37.037 0.00 0.00 33.43 2.10
303 367 7.521529 CACAAATACAGTGGACATCAGTTTAG 58.478 38.462 0.00 0.00 33.43 1.85
304 368 7.433708 CACAAATACAGTGGACATCAGTTTA 57.566 36.000 0.00 0.00 33.43 2.01
305 369 6.317789 CACAAATACAGTGGACATCAGTTT 57.682 37.500 0.00 0.00 33.43 2.66
306 370 5.947228 CACAAATACAGTGGACATCAGTT 57.053 39.130 0.00 0.00 33.43 3.16
359 423 9.800433 CCACAAATATATAATGCAACAACAAGA 57.200 29.630 0.00 0.00 0.00 3.02
360 424 9.033481 CCCACAAATATATAATGCAACAACAAG 57.967 33.333 0.00 0.00 0.00 3.16
361 425 8.753133 TCCCACAAATATATAATGCAACAACAA 58.247 29.630 0.00 0.00 0.00 2.83
362 426 8.298729 TCCCACAAATATATAATGCAACAACA 57.701 30.769 0.00 0.00 0.00 3.33
363 427 7.382218 GCTCCCACAAATATATAATGCAACAAC 59.618 37.037 0.00 0.00 0.00 3.32
364 428 7.287466 AGCTCCCACAAATATATAATGCAACAA 59.713 33.333 0.00 0.00 0.00 2.83
365 429 6.777091 AGCTCCCACAAATATATAATGCAACA 59.223 34.615 0.00 0.00 0.00 3.33
366 430 7.219484 AGCTCCCACAAATATATAATGCAAC 57.781 36.000 0.00 0.00 0.00 4.17
367 431 7.838079 AAGCTCCCACAAATATATAATGCAA 57.162 32.000 0.00 0.00 0.00 4.08
368 432 8.382405 TCTAAGCTCCCACAAATATATAATGCA 58.618 33.333 0.00 0.00 0.00 3.96
369 433 8.792830 TCTAAGCTCCCACAAATATATAATGC 57.207 34.615 0.00 0.00 0.00 3.56
372 436 9.725019 CACATCTAAGCTCCCACAAATATATAA 57.275 33.333 0.00 0.00 0.00 0.98
373 437 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
374 438 7.880195 GTCACATCTAAGCTCCCACAAATATAT 59.120 37.037 0.00 0.00 0.00 0.86
375 439 7.147567 TGTCACATCTAAGCTCCCACAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
376 440 6.058183 GTCACATCTAAGCTCCCACAAATAT 58.942 40.000 0.00 0.00 0.00 1.28
377 441 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
378 442 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
379 443 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
380 444 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
381 445 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
382 446 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
383 447 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
384 448 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
385 449 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
386 450 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
427 491 9.444600 CAGGGCTTTATTTAACAGTTAGTCTAA 57.555 33.333 0.00 0.00 0.00 2.10
428 492 7.551617 GCAGGGCTTTATTTAACAGTTAGTCTA 59.448 37.037 0.00 0.00 0.00 2.59
429 493 6.374613 GCAGGGCTTTATTTAACAGTTAGTCT 59.625 38.462 0.00 0.00 0.00 3.24
430 494 6.150474 TGCAGGGCTTTATTTAACAGTTAGTC 59.850 38.462 0.00 0.00 0.00 2.59
431 495 6.007703 TGCAGGGCTTTATTTAACAGTTAGT 58.992 36.000 0.00 0.00 0.00 2.24
432 496 6.509418 TGCAGGGCTTTATTTAACAGTTAG 57.491 37.500 0.00 0.00 0.00 2.34
433 497 6.435904 ACATGCAGGGCTTTATTTAACAGTTA 59.564 34.615 2.31 0.00 0.00 2.24
434 498 5.245977 ACATGCAGGGCTTTATTTAACAGTT 59.754 36.000 2.31 0.00 0.00 3.16
435 499 4.772100 ACATGCAGGGCTTTATTTAACAGT 59.228 37.500 2.31 0.00 0.00 3.55
436 500 5.126061 AGACATGCAGGGCTTTATTTAACAG 59.874 40.000 0.00 0.00 0.00 3.16
437 501 5.016173 AGACATGCAGGGCTTTATTTAACA 58.984 37.500 0.00 0.00 0.00 2.41
438 502 5.582689 AGACATGCAGGGCTTTATTTAAC 57.417 39.130 0.00 0.00 0.00 2.01
451 515 1.991264 CTCTCACGTCAAGACATGCAG 59.009 52.381 0.00 0.00 0.00 4.41
467 531 3.248266 GCAATCAACCAAACATGCTCTC 58.752 45.455 0.00 0.00 0.00 3.20
601 1562 1.102978 AAATCCAAGCCATACCGCAC 58.897 50.000 0.00 0.00 0.00 5.34
647 1608 0.236187 TGCGTTTACAATCACGGTGC 59.764 50.000 2.51 0.00 36.88 5.01
700 1899 3.676172 GCAATCAACATCACACACCATTG 59.324 43.478 0.00 0.00 0.00 2.82
712 1912 4.761975 CTGGGCAATAAAGCAATCAACAT 58.238 39.130 0.00 0.00 35.83 2.71
764 1964 6.018180 GCAAGGAATAAACTACTCGGTTATGG 60.018 42.308 0.00 0.00 0.00 2.74
820 2079 6.301486 TGGATGAAGATAATTGTGGATCTGG 58.699 40.000 0.00 0.00 32.66 3.86
1007 3121 1.305219 TTTGGATTCTTGCGGCGAGG 61.305 55.000 12.98 0.00 0.00 4.63
1014 3128 4.565564 GCTGTGATGATTTTGGATTCTTGC 59.434 41.667 0.00 0.00 0.00 4.01
1195 3407 2.428187 CTGGGTGTTGTACGGGCA 59.572 61.111 0.00 0.00 0.00 5.36
1365 3612 1.135575 CCAAAAGCAGATCAGAACGCC 60.136 52.381 0.00 0.00 0.00 5.68
1962 4257 2.526888 TCAGACCACTACCTACTGGG 57.473 55.000 0.00 0.00 41.89 4.45
2352 5053 4.751098 GGAACAGCAAGCAAAAATCATCAA 59.249 37.500 0.00 0.00 0.00 2.57
2480 6793 8.232913 ACAACTACAAACTGGAACAATTACAT 57.767 30.769 0.00 0.00 38.70 2.29
2535 6854 7.286775 ACAACTACAACTACAAACAAATCCCAT 59.713 33.333 0.00 0.00 0.00 4.00
2536 6855 6.603997 ACAACTACAACTACAAACAAATCCCA 59.396 34.615 0.00 0.00 0.00 4.37
2539 6858 8.287503 CCCTACAACTACAACTACAAACAAATC 58.712 37.037 0.00 0.00 0.00 2.17
2550 6869 4.337274 GCACAAAACCCTACAACTACAACT 59.663 41.667 0.00 0.00 0.00 3.16
2551 6870 4.337274 AGCACAAAACCCTACAACTACAAC 59.663 41.667 0.00 0.00 0.00 3.32
2556 6875 2.616842 CGAAGCACAAAACCCTACAACT 59.383 45.455 0.00 0.00 0.00 3.16
2560 6879 2.614983 TCAACGAAGCACAAAACCCTAC 59.385 45.455 0.00 0.00 0.00 3.18
2562 6881 1.757682 TCAACGAAGCACAAAACCCT 58.242 45.000 0.00 0.00 0.00 4.34
2563 6882 2.793278 ATCAACGAAGCACAAAACCC 57.207 45.000 0.00 0.00 0.00 4.11
2564 6883 5.278604 AGTAAATCAACGAAGCACAAAACC 58.721 37.500 0.00 0.00 0.00 3.27
2565 6884 5.113529 CGAGTAAATCAACGAAGCACAAAAC 59.886 40.000 0.00 0.00 0.00 2.43
2566 6885 5.006844 TCGAGTAAATCAACGAAGCACAAAA 59.993 36.000 0.00 0.00 0.00 2.44
2567 6886 4.508492 TCGAGTAAATCAACGAAGCACAAA 59.492 37.500 0.00 0.00 0.00 2.83
2568 6887 4.052608 TCGAGTAAATCAACGAAGCACAA 58.947 39.130 0.00 0.00 0.00 3.33
2569 6888 3.644823 TCGAGTAAATCAACGAAGCACA 58.355 40.909 0.00 0.00 0.00 4.57
2570 6889 3.673809 ACTCGAGTAAATCAACGAAGCAC 59.326 43.478 18.46 0.00 34.50 4.40
2571 6890 3.673338 CACTCGAGTAAATCAACGAAGCA 59.327 43.478 19.57 0.00 34.50 3.91
2572 6891 3.673809 ACACTCGAGTAAATCAACGAAGC 59.326 43.478 19.57 0.00 34.50 3.86
2593 6912 7.277981 ACGACCAAATCAGTTCTATCACATTAC 59.722 37.037 0.00 0.00 0.00 1.89
2603 6922 2.372172 AGGGAACGACCAAATCAGTTCT 59.628 45.455 7.05 0.00 39.13 3.01
2680 7050 2.527547 GATTGCGCAACACCTTCCCG 62.528 60.000 27.64 0.00 0.00 5.14
2700 7071 4.599047 TTAAAACCAAACAGATGGCCTG 57.401 40.909 3.32 0.00 44.75 4.85
2701 7072 5.454613 CCTTTTAAAACCAAACAGATGGCCT 60.455 40.000 3.32 0.00 44.75 5.19
2704 7075 6.478673 GTGTCCTTTTAAAACCAAACAGATGG 59.521 38.462 0.00 0.00 46.38 3.51
2709 7080 8.507249 CATTTTGTGTCCTTTTAAAACCAAACA 58.493 29.630 0.00 0.00 0.00 2.83
2717 7122 5.012328 ACCGCATTTTGTGTCCTTTTAAA 57.988 34.783 0.00 0.00 0.00 1.52
2723 7128 0.179004 TGGACCGCATTTTGTGTCCT 60.179 50.000 14.89 0.00 32.84 3.85
2739 7144 2.442212 TCATTTACTCGCGTGTTGGA 57.558 45.000 19.81 9.09 0.00 3.53
2790 7218 3.761897 ACCCAAATTTGACCGAGAATGA 58.238 40.909 19.86 0.00 0.00 2.57
2883 7544 1.169577 AACAAGCGTTTGTGTCACCA 58.830 45.000 18.70 0.00 46.54 4.17
2886 7547 4.167554 AGAAAAACAAGCGTTTGTGTCA 57.832 36.364 18.70 0.00 46.54 3.58
2899 7598 5.330233 GAAGGGAAGGGGAATAGAAAAACA 58.670 41.667 0.00 0.00 0.00 2.83
2900 7599 4.398358 CGAAGGGAAGGGGAATAGAAAAAC 59.602 45.833 0.00 0.00 0.00 2.43
2932 7631 2.395360 CCGAGAAAAATGGCGGCGA 61.395 57.895 12.98 0.00 37.08 5.54
2940 7639 1.305930 GCGAGGTGGCCGAGAAAAAT 61.306 55.000 0.00 0.00 0.00 1.82
2981 7709 1.076044 CTATGGCAGGGGTTTGGGG 60.076 63.158 0.00 0.00 0.00 4.96
2985 7713 0.034089 GACAGCTATGGCAGGGGTTT 60.034 55.000 3.10 0.00 41.70 3.27
3026 7757 3.766691 GGCGGTCGGGCTAGACAA 61.767 66.667 0.00 0.00 42.62 3.18
3074 7813 1.378514 CTAACCCATGGCAAGGCGT 60.379 57.895 6.09 0.00 0.00 5.68
3160 7907 3.889538 TGAACCTCCGACGATAATGATCT 59.110 43.478 0.00 0.00 0.00 2.75
3165 7912 2.884894 GGTGAACCTCCGACGATAAT 57.115 50.000 0.00 0.00 0.00 1.28
3204 8010 0.108615 CAGCACCTAGTCCGGACAAG 60.109 60.000 35.00 24.10 0.00 3.16
3228 8034 4.400109 GTGAGTCGACGAGCCGCA 62.400 66.667 10.46 0.00 0.00 5.69
3281 8089 1.792118 TAGATACGCGGCGCATGACT 61.792 55.000 32.61 24.39 0.00 3.41
3329 8137 4.776837 ACCCCATCATTTTTGCACTTGATA 59.223 37.500 0.00 0.00 0.00 2.15
3344 8152 5.719085 AGCAAAACAAACATATACCCCATCA 59.281 36.000 0.00 0.00 0.00 3.07
3355 8169 3.616379 CACAACCGAAGCAAAACAAACAT 59.384 39.130 0.00 0.00 0.00 2.71
3358 8172 1.996191 GCACAACCGAAGCAAAACAAA 59.004 42.857 0.00 0.00 0.00 2.83
3389 8203 1.939974 AGAGCTATCGAAAATGCGCA 58.060 45.000 14.96 14.96 0.00 6.09
3418 8232 9.463443 GCATCCATCCTACATACAAATTTTTAC 57.537 33.333 0.00 0.00 0.00 2.01
3420 8234 8.076910 TGCATCCATCCTACATACAAATTTTT 57.923 30.769 0.00 0.00 0.00 1.94
3421 8235 7.658525 TGCATCCATCCTACATACAAATTTT 57.341 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.