Multiple sequence alignment - TraesCS3D01G306800

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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 TraesCS3D01G306800 chr3D 100.000 6520 0 0 1 6520 420474429 420467910 0.000000e+00 12041.0
1 TraesCS3D01G306800 chr3D 98.206 4292 71 6 2233 6520 513874358 513878647 0.000000e+00 7494.0
2 TraesCS3D01G306800 chr3D 97.424 1669 42 1 568 2235 513860320 513861988 0.000000e+00 2843.0
3 TraesCS3D01G306800 chr3D 96.303 541 18 2 1 540 160537550 160538089 0.000000e+00 887.0
4 TraesCS3D01G306800 chr3D 84.937 239 12 9 568 806 500884459 500884245 3.060000e-53 220.0
5 TraesCS3D01G306800 chr3D 95.122 41 1 1 5295 5335 513877368 513877407 5.460000e-06 63.9
6 TraesCS3D01G306800 chr3D 95.000 40 1 1 5242 5280 420469135 420469096 1.960000e-05 62.1
7 TraesCS3D01G306800 chr3D 95.000 40 1 1 5242 5280 513877421 513877460 1.960000e-05 62.1
8 TraesCS3D01G306800 chr7B 94.809 1753 61 15 2912 4642 616811224 616812968 0.000000e+00 2706.0
9 TraesCS3D01G306800 chr7B 95.139 1152 39 7 1706 2846 616809966 616811111 0.000000e+00 1801.0
10 TraesCS3D01G306800 chr7B 89.144 1087 94 7 5160 6224 150927238 150928322 0.000000e+00 1332.0
11 TraesCS3D01G306800 chr7B 84.756 492 48 14 3058 3526 150884506 150884993 9.900000e-128 468.0
12 TraesCS3D01G306800 chr7B 82.857 420 54 11 568 977 611506428 611506839 1.730000e-95 361.0
13 TraesCS3D01G306800 chr7B 80.541 185 15 10 6356 6519 690935076 690934892 8.880000e-24 122.0
14 TraesCS3D01G306800 chr7B 95.833 72 3 0 3577 3648 150885877 150885948 4.130000e-22 117.0
15 TraesCS3D01G306800 chr7B 97.436 39 0 1 5242 5280 150927381 150927418 1.520000e-06 65.8
16 TraesCS3D01G306800 chr6A 94.544 1283 54 9 1576 2846 286423145 286424423 0.000000e+00 1967.0
17 TraesCS3D01G306800 chr6A 91.481 1303 83 5 3399 4699 286525372 286526648 0.000000e+00 1766.0
18 TraesCS3D01G306800 chr6A 92.913 1030 67 6 5160 6186 286526646 286527672 0.000000e+00 1493.0
19 TraesCS3D01G306800 chr6A 90.592 574 23 8 2835 3404 286428798 286429344 0.000000e+00 732.0
20 TraesCS3D01G306800 chr6A 85.103 584 62 14 5295 5863 559733902 559734475 2.040000e-159 573.0
21 TraesCS3D01G306800 chr6A 86.373 499 33 18 1869 2358 158945108 158944636 4.510000e-141 512.0
22 TraesCS3D01G306800 chr6A 86.818 440 47 5 1360 1789 158946787 158946349 1.270000e-131 481.0
23 TraesCS3D01G306800 chr6A 89.368 348 31 2 721 1062 103764012 103763665 3.610000e-117 433.0
24 TraesCS3D01G306800 chr6A 78.038 469 68 17 1908 2355 35146113 35146567 5.010000e-66 263.0
25 TraesCS3D01G306800 chr6A 95.122 41 1 1 5295 5335 286526728 286526767 5.460000e-06 63.9
26 TraesCS3D01G306800 chr7D 90.340 1087 81 6 5160 6224 182506501 182507585 0.000000e+00 1404.0
27 TraesCS3D01G306800 chr7D 96.303 541 19 1 1 541 302989048 302988509 0.000000e+00 887.0
28 TraesCS3D01G306800 chr7D 86.482 614 62 11 3054 3648 182503606 182504217 0.000000e+00 654.0
29 TraesCS3D01G306800 chr7D 90.753 465 38 3 4698 5162 14837993 14837534 3.340000e-172 616.0
30 TraesCS3D01G306800 chr7D 95.294 85 4 0 6357 6441 497009321 497009237 1.140000e-27 135.0
31 TraesCS3D01G306800 chr1D 86.246 887 81 14 5426 6297 298313339 298312479 0.000000e+00 924.0
32 TraesCS3D01G306800 chr1D 96.488 541 18 1 1 541 204827968 204827429 0.000000e+00 893.0
33 TraesCS3D01G306800 chr1D 95.294 85 4 0 6357 6441 159867830 159867746 1.140000e-27 135.0
34 TraesCS3D01G306800 chr1D 87.654 81 9 1 2357 2436 229408712 229408632 6.960000e-15 93.5
35 TraesCS3D01G306800 chr5D 96.673 541 17 1 1 541 352182451 352182990 0.000000e+00 898.0
36 TraesCS3D01G306800 chr5D 86.453 561 55 12 5295 5840 520297896 520298450 4.350000e-166 595.0
37 TraesCS3D01G306800 chr5D 89.453 256 21 3 6004 6253 355430112 355430367 1.050000e-82 318.0
38 TraesCS3D01G306800 chr5D 92.405 158 12 0 4479 4636 88351397 88351240 6.580000e-55 226.0
39 TraesCS3D01G306800 chr5D 91.765 85 6 1 6357 6441 480606110 480606027 4.130000e-22 117.0
40 TraesCS3D01G306800 chr6D 96.481 540 19 0 1 540 364401903 364401364 0.000000e+00 893.0
41 TraesCS3D01G306800 chr6D 89.509 448 38 6 1348 1789 120674001 120673557 5.710000e-155 558.0
42 TraesCS3D01G306800 chr6D 87.302 504 34 9 1868 2358 120672318 120671832 3.440000e-152 549.0
43 TraesCS3D01G306800 chr6D 88.571 350 32 4 721 1062 86147938 86147589 1.010000e-112 418.0
44 TraesCS3D01G306800 chr6D 95.349 43 1 1 2363 2404 471334054 471334012 4.220000e-07 67.6
45 TraesCS3D01G306800 chr2D 96.488 541 18 1 1 541 206162700 206162161 0.000000e+00 893.0
46 TraesCS3D01G306800 chr2D 96.303 541 19 1 1 541 139795660 139796199 0.000000e+00 887.0
47 TraesCS3D01G306800 chr2D 96.303 541 18 2 1 541 501029171 501029709 0.000000e+00 887.0
48 TraesCS3D01G306800 chr2D 85.500 400 34 12 3063 3441 630429135 630428739 4.740000e-106 396.0
49 TraesCS3D01G306800 chr2D 92.405 158 12 0 4479 4636 29300138 29299981 6.580000e-55 226.0
50 TraesCS3D01G306800 chr4D 96.303 541 19 1 1 541 155585559 155586098 0.000000e+00 887.0
51 TraesCS3D01G306800 chr4D 86.834 319 33 6 6017 6329 51860633 51860318 1.350000e-91 348.0
52 TraesCS3D01G306800 chr4D 82.576 264 25 8 598 844 24254496 24254237 5.120000e-51 213.0
53 TraesCS3D01G306800 chr1B 84.780 887 93 12 5426 6297 401194435 401193576 0.000000e+00 852.0
54 TraesCS3D01G306800 chr1B 86.473 584 54 14 5295 5863 667236318 667235745 9.290000e-173 617.0
55 TraesCS3D01G306800 chr1B 87.611 339 30 4 4727 5054 30523224 30523561 3.690000e-102 383.0
56 TraesCS3D01G306800 chr1A 85.097 718 67 14 5594 6297 371573859 371573168 0.000000e+00 697.0
57 TraesCS3D01G306800 chr1A 87.251 502 48 5 5594 6080 371773630 371773130 5.710000e-155 558.0
58 TraesCS3D01G306800 chr2B 85.026 581 57 9 5295 5860 90642722 90643287 1.230000e-156 564.0
59 TraesCS3D01G306800 chr2B 82.622 633 43 21 2835 3441 51930185 51929594 1.260000e-136 497.0
60 TraesCS3D01G306800 chr2B 83.090 479 63 13 4696 5160 317233325 317232851 2.810000e-113 420.0
61 TraesCS3D01G306800 chr2B 87.291 299 29 6 6004 6297 50042935 50043229 3.770000e-87 333.0
62 TraesCS3D01G306800 chr2B 89.423 208 18 2 6017 6224 546783241 546783038 6.490000e-65 259.0
63 TraesCS3D01G306800 chr2B 94.186 86 5 0 6356 6441 37318096 37318011 1.480000e-26 132.0
64 TraesCS3D01G306800 chr2B 94.805 77 4 0 688 764 798303098 798303174 3.190000e-23 121.0
65 TraesCS3D01G306800 chr6B 90.107 374 31 5 1421 1789 212414336 212414708 1.270000e-131 481.0
66 TraesCS3D01G306800 chr6B 87.772 368 36 5 721 1080 163235157 163234791 7.820000e-114 422.0
67 TraesCS3D01G306800 chr6B 87.549 257 15 4 2105 2358 212416347 212416589 1.380000e-71 281.0
68 TraesCS3D01G306800 chr6B 86.454 251 25 6 1869 2113 212415918 212416165 3.880000e-67 267.0
69 TraesCS3D01G306800 chr6B 92.500 80 4 1 1786 1863 212414887 212414966 5.340000e-21 113.0
70 TraesCS3D01G306800 chr6B 81.690 142 12 4 716 843 64305306 64305165 8.940000e-19 106.0
71 TraesCS3D01G306800 chr6B 83.784 111 17 1 568 678 64305416 64305307 3.220000e-18 104.0
72 TraesCS3D01G306800 chrUn 84.783 184 18 8 1869 2050 103113884 103114059 6.720000e-40 176.0
73 TraesCS3D01G306800 chrUn 84.615 182 21 3 1871 2050 103120682 103120858 2.420000e-39 174.0
74 TraesCS3D01G306800 chr3A 93.023 86 6 0 6356 6441 25010864 25010779 6.860000e-25 126.0
75 TraesCS3D01G306800 chr4B 79.459 185 17 9 6356 6519 577019974 577019790 1.920000e-20 111.0
76 TraesCS3D01G306800 chr5B 89.773 88 6 1 6356 6443 44702854 44702938 6.910000e-20 110.0
77 TraesCS3D01G306800 chr7A 100.000 31 0 0 3125 3155 310651036 310651006 2.540000e-04 58.4


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 TraesCS3D01G306800 chr3D 420467910 420474429 6519 True 12041.000000 12041 100.000000 1 6520 1 chr3D.!!$R1 6519
1 TraesCS3D01G306800 chr3D 513860320 513861988 1668 False 2843.000000 2843 97.424000 568 2235 1 chr3D.!!$F2 1667
2 TraesCS3D01G306800 chr3D 513874358 513878647 4289 False 2540.000000 7494 96.109333 2233 6520 3 chr3D.!!$F3 4287
3 TraesCS3D01G306800 chr3D 160537550 160538089 539 False 887.000000 887 96.303000 1 540 1 chr3D.!!$F1 539
4 TraesCS3D01G306800 chr7B 616809966 616812968 3002 False 2253.500000 2706 94.974000 1706 4642 2 chr7B.!!$F4 2936
5 TraesCS3D01G306800 chr7B 150927238 150928322 1084 False 698.900000 1332 93.290000 5160 6224 2 chr7B.!!$F3 1064
6 TraesCS3D01G306800 chr7B 150884506 150885948 1442 False 292.500000 468 90.294500 3058 3648 2 chr7B.!!$F2 590
7 TraesCS3D01G306800 chr6A 286423145 286424423 1278 False 1967.000000 1967 94.544000 1576 2846 1 chr6A.!!$F2 1270
8 TraesCS3D01G306800 chr6A 286525372 286527672 2300 False 1107.633333 1766 93.172000 3399 6186 3 chr6A.!!$F5 2787
9 TraesCS3D01G306800 chr6A 286428798 286429344 546 False 732.000000 732 90.592000 2835 3404 1 chr6A.!!$F3 569
10 TraesCS3D01G306800 chr6A 559733902 559734475 573 False 573.000000 573 85.103000 5295 5863 1 chr6A.!!$F4 568
11 TraesCS3D01G306800 chr6A 158944636 158946787 2151 True 496.500000 512 86.595500 1360 2358 2 chr6A.!!$R2 998
12 TraesCS3D01G306800 chr7D 182503606 182507585 3979 False 1029.000000 1404 88.411000 3054 6224 2 chr7D.!!$F1 3170
13 TraesCS3D01G306800 chr7D 302988509 302989048 539 True 887.000000 887 96.303000 1 541 1 chr7D.!!$R2 540
14 TraesCS3D01G306800 chr1D 298312479 298313339 860 True 924.000000 924 86.246000 5426 6297 1 chr1D.!!$R4 871
15 TraesCS3D01G306800 chr1D 204827429 204827968 539 True 893.000000 893 96.488000 1 541 1 chr1D.!!$R2 540
16 TraesCS3D01G306800 chr5D 352182451 352182990 539 False 898.000000 898 96.673000 1 541 1 chr5D.!!$F1 540
17 TraesCS3D01G306800 chr5D 520297896 520298450 554 False 595.000000 595 86.453000 5295 5840 1 chr5D.!!$F3 545
18 TraesCS3D01G306800 chr6D 364401364 364401903 539 True 893.000000 893 96.481000 1 540 1 chr6D.!!$R2 539
19 TraesCS3D01G306800 chr6D 120671832 120674001 2169 True 553.500000 558 88.405500 1348 2358 2 chr6D.!!$R4 1010
20 TraesCS3D01G306800 chr2D 206162161 206162700 539 True 893.000000 893 96.488000 1 541 1 chr2D.!!$R2 540
21 TraesCS3D01G306800 chr2D 139795660 139796199 539 False 887.000000 887 96.303000 1 541 1 chr2D.!!$F1 540
22 TraesCS3D01G306800 chr2D 501029171 501029709 538 False 887.000000 887 96.303000 1 541 1 chr2D.!!$F2 540
23 TraesCS3D01G306800 chr4D 155585559 155586098 539 False 887.000000 887 96.303000 1 541 1 chr4D.!!$F1 540
24 TraesCS3D01G306800 chr1B 401193576 401194435 859 True 852.000000 852 84.780000 5426 6297 1 chr1B.!!$R1 871
25 TraesCS3D01G306800 chr1B 667235745 667236318 573 True 617.000000 617 86.473000 5295 5863 1 chr1B.!!$R2 568
26 TraesCS3D01G306800 chr1A 371573168 371573859 691 True 697.000000 697 85.097000 5594 6297 1 chr1A.!!$R1 703
27 TraesCS3D01G306800 chr1A 371773130 371773630 500 True 558.000000 558 87.251000 5594 6080 1 chr1A.!!$R2 486
28 TraesCS3D01G306800 chr2B 90642722 90643287 565 False 564.000000 564 85.026000 5295 5860 1 chr2B.!!$F2 565
29 TraesCS3D01G306800 chr2B 51929594 51930185 591 True 497.000000 497 82.622000 2835 3441 1 chr2B.!!$R2 606
30 TraesCS3D01G306800 chr6B 212414336 212416589 2253 False 285.500000 481 89.152500 1421 2358 4 chr6B.!!$F1 937

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
959 961 0.251354 GCTGTCCTTGCAGATGGAGA 59.749 55.000 5.57 4.29 38.70 3.71 F
1140 1143 1.749258 GGTGCGTTTCAGATCCCCC 60.749 63.158 0.00 0.00 0.00 5.40 F
1255 1258 2.744202 CGATGCCACTTAGTTTCAAGCT 59.256 45.455 0.00 0.00 0.00 3.74 F
1497 1510 4.840716 TTCCATGCCCTTATGCAAATTT 57.159 36.364 0.00 0.00 45.84 1.82 F
3548 5040 3.055719 CGGTTGCGACCAAGCCAT 61.056 61.111 23.21 0.00 46.91 4.40 F
3672 6027 0.695347 CTGCCCTCTCTTGGTTTCCT 59.305 55.000 0.00 0.00 0.00 3.36 F
5036 9182 2.158986 CCTCTGGAATGAGCACTCGAAT 60.159 50.000 0.00 0.00 33.02 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 3244 1.005805 ACCAGAATGCCAGCAACCATA 59.994 47.619 0.00 0.00 31.97 2.74 R
2359 3747 4.387550 GCCTTATATTTTGGGAAGGAGGGT 60.388 45.833 3.71 0.00 40.88 4.34 R
3406 4897 6.259550 AGGAATCACTGCTTGTTAATGAAC 57.740 37.500 0.00 0.00 36.00 3.18 R
3566 5058 6.114187 TGAACTCATCATACCACTTTCTGT 57.886 37.500 0.00 0.00 31.50 3.41 R
4951 9097 0.657368 GGCAAAGCGACACAACTTCG 60.657 55.000 0.00 0.00 39.56 3.79 R
5147 9293 3.254060 CATGATATAAGGCTCCGTTCGG 58.746 50.000 4.74 4.74 0.00 4.30 R
6320 10550 0.675522 GCGCCTTAGCACAAGGGTTA 60.676 55.000 16.40 0.00 39.83 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
118 119 6.944234 ACCCATAAGCTTAAATAGTCTTGC 57.056 37.500 10.85 0.00 0.00 4.01
141 142 1.672356 GCGGGTGTGAGATTGCTGT 60.672 57.895 0.00 0.00 0.00 4.40
338 339 4.404394 GGGGTTGTCTTCTTTTCTTTTGGA 59.596 41.667 0.00 0.00 0.00 3.53
364 365 1.001633 AGTCGGACCAATGTGTGTACC 59.998 52.381 4.14 0.00 0.00 3.34
436 437 6.327386 AGCCAACTCTTTATCCCATTCTTA 57.673 37.500 0.00 0.00 0.00 2.10
491 493 3.254411 TCTTGCGACAAAACCATAATGCA 59.746 39.130 0.00 0.00 0.00 3.96
533 535 3.400255 CTCGACACGTGGGAGATATAGA 58.600 50.000 25.80 7.64 0.00 1.98
541 543 1.472878 TGGGAGATATAGACGCATCGC 59.527 52.381 0.00 0.00 0.00 4.58
542 544 1.746220 GGGAGATATAGACGCATCGCT 59.254 52.381 0.00 0.00 0.00 4.93
543 545 2.223386 GGGAGATATAGACGCATCGCTC 60.223 54.545 0.00 0.00 0.00 5.03
544 546 2.223386 GGAGATATAGACGCATCGCTCC 60.223 54.545 0.00 0.00 34.55 4.70
545 547 1.746220 AGATATAGACGCATCGCTCCC 59.254 52.381 0.00 0.00 0.00 4.30
546 548 1.746220 GATATAGACGCATCGCTCCCT 59.254 52.381 0.00 0.00 0.00 4.20
547 549 0.881796 TATAGACGCATCGCTCCCTG 59.118 55.000 0.00 0.00 0.00 4.45
548 550 2.427540 ATAGACGCATCGCTCCCTGC 62.428 60.000 0.00 0.00 38.57 4.85
549 551 4.819761 GACGCATCGCTCCCTGCA 62.820 66.667 0.00 0.00 43.06 4.41
550 552 4.827087 ACGCATCGCTCCCTGCAG 62.827 66.667 6.78 6.78 43.06 4.41
553 555 4.478371 CATCGCTCCCTGCAGCCA 62.478 66.667 8.66 0.00 43.06 4.75
554 556 3.486685 ATCGCTCCCTGCAGCCAT 61.487 61.111 8.66 0.00 43.06 4.40
555 557 3.472943 ATCGCTCCCTGCAGCCATC 62.473 63.158 8.66 0.00 43.06 3.51
584 586 2.364961 CCTCCCGTTCCTCTCCCT 59.635 66.667 0.00 0.00 0.00 4.20
588 590 0.614979 TCCCGTTCCTCTCCCTTCAG 60.615 60.000 0.00 0.00 0.00 3.02
619 621 2.895680 GTCGCTGCTCTCCCATCA 59.104 61.111 0.00 0.00 0.00 3.07
626 628 4.598894 CTCTCCCATCAGGCGCCG 62.599 72.222 23.20 16.49 34.51 6.46
663 665 1.377202 GCTGGCGTCTTGGGATTCA 60.377 57.895 0.00 0.00 0.00 2.57
671 673 0.679002 TCTTGGGATTCAGCAGCAGC 60.679 55.000 0.00 0.00 42.56 5.25
692 694 2.041265 AGGAGGGCCAACGGATCT 59.959 61.111 6.18 0.00 36.29 2.75
906 908 0.394565 GATTGAGAGGGGATGGACGG 59.605 60.000 0.00 0.00 0.00 4.79
959 961 0.251354 GCTGTCCTTGCAGATGGAGA 59.749 55.000 5.57 4.29 38.70 3.71
1071 1073 2.072298 GATACCTCGAGATGCCATTGC 58.928 52.381 15.71 0.00 38.26 3.56
1098 1101 2.451294 GCTCCCCTCCCCATCCAT 60.451 66.667 0.00 0.00 0.00 3.41
1140 1143 1.749258 GGTGCGTTTCAGATCCCCC 60.749 63.158 0.00 0.00 0.00 5.40
1255 1258 2.744202 CGATGCCACTTAGTTTCAAGCT 59.256 45.455 0.00 0.00 0.00 3.74
1388 1392 5.014123 ACCAAGAGAAGACAAACATATGGGA 59.986 40.000 7.80 0.00 0.00 4.37
1497 1510 4.840716 TTCCATGCCCTTATGCAAATTT 57.159 36.364 0.00 0.00 45.84 1.82
2359 3747 8.689061 TCTAGAATTCGCATAGTAAAAGGTACA 58.311 33.333 0.00 0.00 0.00 2.90
3406 4897 3.087031 CCCCATTATCTTGCTGGCTATG 58.913 50.000 0.00 0.00 0.00 2.23
3548 5040 3.055719 CGGTTGCGACCAAGCCAT 61.056 61.111 23.21 0.00 46.91 4.40
3672 6027 0.695347 CTGCCCTCTCTTGGTTTCCT 59.305 55.000 0.00 0.00 0.00 3.36
3675 6030 2.188817 GCCCTCTCTTGGTTTCCTCTA 58.811 52.381 0.00 0.00 0.00 2.43
3766 6121 3.119245 GCTCAACATGGTCTTCCTACGTA 60.119 47.826 0.00 0.00 34.23 3.57
4354 6811 3.262151 TCTGTTGGGTCCGAATCATGTAA 59.738 43.478 0.00 0.00 0.00 2.41
4705 8851 5.646360 GGTTATCAACTAACTTTAGGCTGCA 59.354 40.000 0.50 0.00 39.78 4.41
4732 8878 7.669427 TCGGTTTGTAGGTATAGAAAACTCAA 58.331 34.615 0.00 0.00 31.34 3.02
4756 8902 7.981102 AGACCAGAAAACTACAAAGGAATAC 57.019 36.000 0.00 0.00 0.00 1.89
4757 8903 7.514721 AGACCAGAAAACTACAAAGGAATACA 58.485 34.615 0.00 0.00 0.00 2.29
4818 8964 4.845580 AGAGAAGCATGCGGGGCG 62.846 66.667 13.01 0.00 36.08 6.13
5036 9182 2.158986 CCTCTGGAATGAGCACTCGAAT 60.159 50.000 0.00 0.00 33.02 3.34
5105 9251 4.922103 CGGTTCAGAGGTAGACAAAACTAC 59.078 45.833 0.00 0.00 41.13 2.73
5147 9293 4.385358 TTCCTTTGTTTTTCCTGCAGAC 57.615 40.909 17.39 5.30 0.00 3.51
5599 9806 1.338337 ACTACTGATCGGCGATTGGAG 59.662 52.381 24.81 24.68 0.00 3.86
6065 10294 6.560253 TTCTTGAGATGTTTCCTTTGTAGC 57.440 37.500 0.00 0.00 0.00 3.58
6205 10434 8.927675 ACTAAACTTGGTGTCAAATGGTTATA 57.072 30.769 0.00 0.00 31.77 0.98
6211 10440 7.602265 ACTTGGTGTCAAATGGTTATATTTTGC 59.398 33.333 0.00 0.00 31.77 3.68
6320 10550 1.324383 GACCAAAACATTGGGACCGT 58.676 50.000 11.92 0.00 46.23 4.83
6329 10559 1.069775 ATTGGGACCGTAACCCTTGT 58.930 50.000 0.00 0.00 46.82 3.16
6396 10626 8.547967 TCTTATGTGTTCTCACTTTTGGTATC 57.452 34.615 0.00 0.00 44.14 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 0.803768 CAATCTCACACCCGCGAGAG 60.804 60.000 8.23 6.91 41.39 3.20
491 493 2.159085 GGCACGACTTAGAGGCATAACT 60.159 50.000 0.00 0.00 0.00 2.24
560 562 4.410400 GGAACGGGAGGGCAGTGG 62.410 72.222 0.00 0.00 0.00 4.00
561 563 3.316573 GAGGAACGGGAGGGCAGTG 62.317 68.421 0.00 0.00 0.00 3.66
562 564 3.003763 GAGGAACGGGAGGGCAGT 61.004 66.667 0.00 0.00 0.00 4.40
563 565 2.685380 AGAGGAACGGGAGGGCAG 60.685 66.667 0.00 0.00 0.00 4.85
564 566 2.683933 GAGAGGAACGGGAGGGCA 60.684 66.667 0.00 0.00 0.00 5.36
565 567 3.471806 GGAGAGGAACGGGAGGGC 61.472 72.222 0.00 0.00 0.00 5.19
566 568 2.764547 GGGAGAGGAACGGGAGGG 60.765 72.222 0.00 0.00 0.00 4.30
644 646 2.436646 AATCCCAAGACGCCAGCG 60.437 61.111 11.05 11.05 46.03 5.18
663 665 3.400928 CCTCCTCCTGCTGCTGCT 61.401 66.667 17.00 0.00 40.48 4.24
671 673 4.101448 CCGTTGGCCCTCCTCCTG 62.101 72.222 0.00 0.00 0.00 3.86
747 749 2.537560 CCGCGCAATCTCCATCCAC 61.538 63.158 8.75 0.00 0.00 4.02
818 820 3.148279 ACCTGGATCGGCGAGGAC 61.148 66.667 17.22 8.54 44.66 3.85
856 858 1.328430 GGGCGCTAGTGGTAGGAACT 61.328 60.000 7.64 0.00 46.37 3.01
862 864 1.919308 TTTGGGGGCGCTAGTGGTA 60.919 57.895 7.64 0.00 0.00 3.25
892 894 3.083997 GTGCCGTCCATCCCCTCT 61.084 66.667 0.00 0.00 0.00 3.69
906 908 2.740981 CACCAGAGAATCAGTGAAGTGC 59.259 50.000 0.00 0.00 42.23 4.40
1081 1084 2.451294 ATGGATGGGGAGGGGAGC 60.451 66.667 0.00 0.00 0.00 4.70
1113 1116 2.281484 AAACGCACCTCGGCACAT 60.281 55.556 0.00 0.00 43.86 3.21
1114 1117 2.970324 GAAACGCACCTCGGCACA 60.970 61.111 0.00 0.00 43.86 4.57
1140 1143 1.406970 GAGAGCGCCGACGAGAAAAG 61.407 60.000 2.29 0.00 43.93 2.27
1255 1258 3.749226 TGTCATCACATTAACCAGCACA 58.251 40.909 0.00 0.00 0.00 4.57
1388 1392 9.942850 TGCAACACATAATGCATAGTAGTATAT 57.057 29.630 0.00 0.00 46.87 0.86
1497 1510 3.000819 AACGAGGGGGATGCGACA 61.001 61.111 0.00 0.00 0.00 4.35
1828 2027 4.177026 CCCTCAGAATCAGAAACACTACG 58.823 47.826 0.00 0.00 0.00 3.51
2057 3244 1.005805 ACCAGAATGCCAGCAACCATA 59.994 47.619 0.00 0.00 31.97 2.74
2318 3706 9.427127 GCGAATTCTAGATTTGATTACAGAAAC 57.573 33.333 4.64 0.00 0.00 2.78
2359 3747 4.387550 GCCTTATATTTTGGGAAGGAGGGT 60.388 45.833 3.71 0.00 40.88 4.34
3406 4897 6.259550 AGGAATCACTGCTTGTTAATGAAC 57.740 37.500 0.00 0.00 36.00 3.18
3564 5056 6.427853 TGAACTCATCATACCACTTTCTGTTG 59.572 38.462 0.00 0.00 31.50 3.33
3566 5058 6.114187 TGAACTCATCATACCACTTTCTGT 57.886 37.500 0.00 0.00 31.50 3.41
3766 6121 2.997897 GGTCCGTGGACTCAGCCT 60.998 66.667 17.99 0.00 44.04 4.58
3823 6178 2.609491 CGAACGAAGAGGACCACATCAA 60.609 50.000 0.00 0.00 0.00 2.57
4705 8851 8.316214 TGAGTTTTCTATACCTACAAACCGAAT 58.684 33.333 0.00 0.00 0.00 3.34
4732 8878 7.514721 TGTATTCCTTTGTAGTTTTCTGGTCT 58.485 34.615 0.00 0.00 0.00 3.85
4756 8902 4.943705 AGGCTGGTACTGTACAATCAATTG 59.056 41.667 18.79 0.00 43.26 2.32
4757 8903 5.179452 AGGCTGGTACTGTACAATCAATT 57.821 39.130 18.79 0.00 0.00 2.32
4791 8937 2.481952 GCATGCTTCTCTTCGTCTGTTT 59.518 45.455 11.37 0.00 0.00 2.83
4818 8964 1.774639 TTCACACCTACGCTTCGAAC 58.225 50.000 0.00 0.00 0.00 3.95
4826 8972 3.963383 ACAAAGCTTTTCACACCTACG 57.037 42.857 9.53 0.00 0.00 3.51
4951 9097 0.657368 GGCAAAGCGACACAACTTCG 60.657 55.000 0.00 0.00 39.56 3.79
5036 9182 3.966665 AGAAATTTGAAGGAAACCCTGCA 59.033 39.130 0.00 0.00 37.60 4.41
5147 9293 3.254060 CATGATATAAGGCTCCGTTCGG 58.746 50.000 4.74 4.74 0.00 4.30
6065 10294 9.900264 GCTAAATTTATACCAAAAGCAAATTCG 57.100 29.630 0.00 0.00 30.58 3.34
6095 10324 1.928868 AGCAAAGCAGCTACCCATTT 58.071 45.000 0.00 0.00 44.50 2.32
6205 10434 4.660789 AACAGAAGCAAGACAGCAAAAT 57.339 36.364 0.00 0.00 36.85 1.82
6211 10440 9.121517 CATTAATTTGTAACAGAAGCAAGACAG 57.878 33.333 0.00 0.00 0.00 3.51
6320 10550 0.675522 GCGCCTTAGCACAAGGGTTA 60.676 55.000 16.40 0.00 39.83 2.85
6329 10559 4.585526 CGGGATCGCGCCTTAGCA 62.586 66.667 19.68 0.00 39.83 3.49
6396 10626 5.290885 TGATAACCATTCGACATGAAGTTCG 59.709 40.000 0.00 0.00 40.65 3.95


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

AutoCloner maintained by Alex Coulton.