Multiple sequence alignment - TraesCS5D01G140900

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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 TraesCS5D01G140900 chr5D 100.000 3512 0 0 1 3512 224762756 224759245 0.000000e+00 6486.0
1 TraesCS5D01G140900 chr5D 72.126 348 85 9 2672 3014 371515149 371514809 1.040000e-15 95.3
2 TraesCS5D01G140900 chr5A 95.117 2089 77 13 529 2615 299255053 299252988 0.000000e+00 3269.0
3 TraesCS5D01G140900 chr5A 86.936 842 103 6 2672 3508 70858583 70857744 0.000000e+00 939.0
4 TraesCS5D01G140900 chr5A 90.283 494 33 8 3 491 20815412 20815895 1.780000e-177 632.0
5 TraesCS5D01G140900 chr5A 80.764 811 149 7 2672 3477 432434960 432434152 8.280000e-176 627.0
6 TraesCS5D01G140900 chr5B 95.784 1589 51 5 687 2275 246951135 246952707 0.000000e+00 2549.0
7 TraesCS5D01G140900 chr5B 82.641 818 138 4 2663 3477 106404080 106404896 0.000000e+00 721.0
8 TraesCS5D01G140900 chr5B 80.796 854 158 6 2663 3512 394692462 394693313 0.000000e+00 664.0
9 TraesCS5D01G140900 chr5B 95.165 393 11 4 2271 2660 246958161 246958548 6.440000e-172 614.0
10 TraesCS5D01G140900 chr5B 78.268 612 124 9 2868 3475 223919124 223919730 5.500000e-103 385.0
11 TraesCS5D01G140900 chr5B 80.916 131 21 4 2101 2229 609844596 609844468 2.230000e-17 100.0
12 TraesCS5D01G140900 chr2D 83.109 1409 225 10 1047 2450 584897209 584898609 0.000000e+00 1271.0
13 TraesCS5D01G140900 chr2B 82.202 1444 242 12 1047 2481 705530102 705531539 0.000000e+00 1229.0
14 TraesCS5D01G140900 chr2B 81.959 1419 239 13 1047 2458 705328130 705326722 0.000000e+00 1186.0
15 TraesCS5D01G140900 chr2B 83.749 843 129 7 2672 3510 656598549 656597711 0.000000e+00 791.0
16 TraesCS5D01G140900 chr2B 90.669 493 40 6 1 491 654321560 654322048 0.000000e+00 651.0
17 TraesCS5D01G140900 chr2B 83.740 123 19 1 410 531 746717517 746717639 7.970000e-22 115.0
18 TraesCS5D01G140900 chr2A 81.696 1415 240 14 1047 2450 719204617 719206023 0.000000e+00 1160.0
19 TraesCS5D01G140900 chr2A 90.726 496 36 8 1 490 14234283 14233792 0.000000e+00 652.0
20 TraesCS5D01G140900 chr6A 89.252 856 82 7 2661 3511 180382934 180382084 0.000000e+00 1062.0
21 TraesCS5D01G140900 chr6A 74.814 806 164 20 2663 3460 604853945 604854719 9.400000e-86 327.0
22 TraesCS5D01G140900 chr4B 89.085 852 89 3 2663 3511 473871178 473872028 0.000000e+00 1055.0
23 TraesCS5D01G140900 chr4B 91.423 548 33 8 1 535 621844168 621843622 0.000000e+00 739.0
24 TraesCS5D01G140900 chr4B 78.960 808 160 9 2671 3474 148210430 148209629 3.080000e-150 542.0
25 TraesCS5D01G140900 chr7B 88.759 854 90 5 2663 3512 271958805 271959656 0.000000e+00 1040.0
26 TraesCS5D01G140900 chr7B 85.053 843 120 5 2672 3512 59337781 59336943 0.000000e+00 854.0
27 TraesCS5D01G140900 chr7B 87.006 708 86 5 2718 3424 594695986 594695284 0.000000e+00 793.0
28 TraesCS5D01G140900 chr3D 93.233 532 32 4 1 529 429311650 429311120 0.000000e+00 780.0
29 TraesCS5D01G140900 chr3D 76.055 806 176 15 2663 3460 355747388 355748184 1.520000e-108 403.0
30 TraesCS5D01G140900 chr3D 72.489 687 165 20 2672 3346 369478241 369477567 2.140000e-47 200.0
31 TraesCS5D01G140900 chr3D 74.041 339 70 16 1866 2195 75962965 75963294 4.760000e-24 122.0
32 TraesCS5D01G140900 chr6D 83.655 777 123 4 2672 3445 119473658 119472883 0.000000e+00 728.0
33 TraesCS5D01G140900 chr6D 71.839 696 173 20 2663 3346 22673010 22673694 1.000000e-40 178.0
34 TraesCS5D01G140900 chr6D 72.545 499 120 15 2856 3346 22357558 22358047 2.820000e-31 147.0
35 TraesCS5D01G140900 chr6D 72.941 255 58 8 2663 2911 22451225 22451474 1.050000e-10 78.7
36 TraesCS5D01G140900 chr7A 93.402 485 24 6 1 483 732614715 732615193 0.000000e+00 712.0
37 TraesCS5D01G140900 chr7A 90.000 60 6 0 1868 1927 182385313 182385372 1.050000e-10 78.7
38 TraesCS5D01G140900 chr6B 81.712 853 150 6 2663 3512 677143295 677144144 0.000000e+00 706.0
39 TraesCS5D01G140900 chr6B 92.137 496 25 9 1 491 122972510 122972024 0.000000e+00 688.0
40 TraesCS5D01G140900 chrUn 92.089 493 36 3 1 491 462207781 462207290 0.000000e+00 691.0
41 TraesCS5D01G140900 chr1B 90.486 494 39 6 1 491 643809895 643809407 0.000000e+00 645.0
42 TraesCS5D01G140900 chr1A 76.971 799 174 9 2663 3457 30643777 30644569 6.920000e-122 448.0
43 TraesCS5D01G140900 chr1D 70.929 743 189 22 2672 3403 204998974 204998248 2.180000e-32 150.0
44 TraesCS5D01G140900 chr1D 71.809 376 96 9 2874 3244 321706013 321705643 8.020000e-17 99.0
45 TraesCS5D01G140900 chr3A 84.328 134 19 2 2071 2203 90365157 90365289 2.850000e-26 130.0
46 TraesCS5D01G140900 chr3A 86.207 116 14 2 2071 2185 90294363 90294477 1.320000e-24 124.0
47 TraesCS5D01G140900 chr4D 73.820 233 57 3 3095 3325 507766316 507766086 4.830000e-14 89.8
48 TraesCS5D01G140900 chr7D 87.143 70 8 1 1858 1927 178292520 178292588 1.050000e-10 78.7


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 TraesCS5D01G140900 chr5D 224759245 224762756 3511 True 6486 6486 100.000 1 3512 1 chr5D.!!$R1 3511
1 TraesCS5D01G140900 chr5A 299252988 299255053 2065 True 3269 3269 95.117 529 2615 1 chr5A.!!$R2 2086
2 TraesCS5D01G140900 chr5A 70857744 70858583 839 True 939 939 86.936 2672 3508 1 chr5A.!!$R1 836
3 TraesCS5D01G140900 chr5A 432434152 432434960 808 True 627 627 80.764 2672 3477 1 chr5A.!!$R3 805
4 TraesCS5D01G140900 chr5B 246951135 246952707 1572 False 2549 2549 95.784 687 2275 1 chr5B.!!$F3 1588
5 TraesCS5D01G140900 chr5B 106404080 106404896 816 False 721 721 82.641 2663 3477 1 chr5B.!!$F1 814
6 TraesCS5D01G140900 chr5B 394692462 394693313 851 False 664 664 80.796 2663 3512 1 chr5B.!!$F5 849
7 TraesCS5D01G140900 chr5B 223919124 223919730 606 False 385 385 78.268 2868 3475 1 chr5B.!!$F2 607
8 TraesCS5D01G140900 chr2D 584897209 584898609 1400 False 1271 1271 83.109 1047 2450 1 chr2D.!!$F1 1403
9 TraesCS5D01G140900 chr2B 705530102 705531539 1437 False 1229 1229 82.202 1047 2481 1 chr2B.!!$F2 1434
10 TraesCS5D01G140900 chr2B 705326722 705328130 1408 True 1186 1186 81.959 1047 2458 1 chr2B.!!$R2 1411
11 TraesCS5D01G140900 chr2B 656597711 656598549 838 True 791 791 83.749 2672 3510 1 chr2B.!!$R1 838
12 TraesCS5D01G140900 chr2A 719204617 719206023 1406 False 1160 1160 81.696 1047 2450 1 chr2A.!!$F1 1403
13 TraesCS5D01G140900 chr6A 180382084 180382934 850 True 1062 1062 89.252 2661 3511 1 chr6A.!!$R1 850
14 TraesCS5D01G140900 chr6A 604853945 604854719 774 False 327 327 74.814 2663 3460 1 chr6A.!!$F1 797
15 TraesCS5D01G140900 chr4B 473871178 473872028 850 False 1055 1055 89.085 2663 3511 1 chr4B.!!$F1 848
16 TraesCS5D01G140900 chr4B 621843622 621844168 546 True 739 739 91.423 1 535 1 chr4B.!!$R2 534
17 TraesCS5D01G140900 chr4B 148209629 148210430 801 True 542 542 78.960 2671 3474 1 chr4B.!!$R1 803
18 TraesCS5D01G140900 chr7B 271958805 271959656 851 False 1040 1040 88.759 2663 3512 1 chr7B.!!$F1 849
19 TraesCS5D01G140900 chr7B 59336943 59337781 838 True 854 854 85.053 2672 3512 1 chr7B.!!$R1 840
20 TraesCS5D01G140900 chr7B 594695284 594695986 702 True 793 793 87.006 2718 3424 1 chr7B.!!$R2 706
21 TraesCS5D01G140900 chr3D 429311120 429311650 530 True 780 780 93.233 1 529 1 chr3D.!!$R2 528
22 TraesCS5D01G140900 chr3D 355747388 355748184 796 False 403 403 76.055 2663 3460 1 chr3D.!!$F2 797
23 TraesCS5D01G140900 chr6D 119472883 119473658 775 True 728 728 83.655 2672 3445 1 chr6D.!!$R1 773
24 TraesCS5D01G140900 chr6B 677143295 677144144 849 False 706 706 81.712 2663 3512 1 chr6B.!!$F1 849
25 TraesCS5D01G140900 chr1A 30643777 30644569 792 False 448 448 76.971 2663 3457 1 chr1A.!!$F1 794

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
459 462 0.033228 CAAATGCAAAACTGGGCGGA 59.967 50.0 0.00 0.0 0.00 5.54 F
460 463 0.033366 AAATGCAAAACTGGGCGGAC 59.967 50.0 0.00 0.0 0.00 4.79 F
747 751 0.179189 GTCCGCTCAATTTTCGGCTG 60.179 55.0 5.23 0.0 42.65 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1848 0.874175 TAAACAGATGGATCCGCGCG 60.874 55.000 25.67 25.67 0.00 6.86 R
2207 2234 3.884581 TTCGTCGGCTGGTCGAACG 62.885 63.158 17.59 9.27 41.05 3.95 R
2622 2649 0.108615 ACAGTATCCACTCACTGCGC 60.109 55.000 0.00 0.00 44.89 6.09 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
135 137 1.078848 AGGCCGACATGCTCAAGTC 60.079 57.895 0.00 0.00 0.00 3.01
232 234 1.003718 CGAACTCAAGTCCCACCCC 60.004 63.158 0.00 0.00 0.00 4.95
306 309 6.998074 TGAACTGTGGTGATATTTTCTGAAGT 59.002 34.615 0.00 0.00 0.00 3.01
384 387 2.748647 GCCGCGGGCCTTCTTTAA 60.749 61.111 29.38 0.00 44.06 1.52
385 388 2.337246 GCCGCGGGCCTTCTTTAAA 61.337 57.895 29.38 0.00 44.06 1.52
453 456 1.782044 CCGACCCAAATGCAAAACTG 58.218 50.000 0.00 0.00 0.00 3.16
454 457 1.605202 CCGACCCAAATGCAAAACTGG 60.605 52.381 0.00 0.00 0.00 4.00
456 459 2.931246 CCCAAATGCAAAACTGGGC 58.069 52.632 11.50 0.00 42.10 5.36
457 460 0.950071 CCCAAATGCAAAACTGGGCG 60.950 55.000 11.50 0.00 42.10 6.13
458 461 0.950071 CCAAATGCAAAACTGGGCGG 60.950 55.000 0.00 0.00 0.00 6.13
459 462 0.033228 CAAATGCAAAACTGGGCGGA 59.967 50.000 0.00 0.00 0.00 5.54
460 463 0.033366 AAATGCAAAACTGGGCGGAC 59.967 50.000 0.00 0.00 0.00 4.79
461 464 2.141122 AATGCAAAACTGGGCGGACG 62.141 55.000 0.00 0.00 0.00 4.79
462 465 4.700365 GCAAAACTGGGCGGACGC 62.700 66.667 8.39 8.39 41.06 5.19
494 497 2.497304 CGACCAAACGGACAAATACG 57.503 50.000 0.00 0.00 38.54 3.06
495 498 1.462869 CGACCAAACGGACAAATACGC 60.463 52.381 0.00 0.00 34.47 4.42
496 499 0.876399 ACCAAACGGACAAATACGCC 59.124 50.000 0.00 0.00 34.47 5.68
500 503 4.489249 CGGACAAATACGCCGTCT 57.511 55.556 0.00 0.00 40.17 4.18
501 504 1.995991 CGGACAAATACGCCGTCTG 59.004 57.895 0.00 0.00 40.17 3.51
502 505 0.734942 CGGACAAATACGCCGTCTGT 60.735 55.000 0.00 0.00 40.17 3.41
503 506 1.435577 GGACAAATACGCCGTCTGTT 58.564 50.000 0.00 0.00 0.00 3.16
504 507 1.392510 GGACAAATACGCCGTCTGTTC 59.607 52.381 0.00 0.00 0.00 3.18
505 508 1.058695 GACAAATACGCCGTCTGTTCG 59.941 52.381 0.00 0.00 0.00 3.95
522 525 4.324991 GGGTCCGCCCGTTGAAGT 62.325 66.667 0.00 0.00 46.51 3.01
523 526 2.281276 GGTCCGCCCGTTGAAGTT 60.281 61.111 0.00 0.00 0.00 2.66
524 527 2.613506 GGTCCGCCCGTTGAAGTTG 61.614 63.158 0.00 0.00 0.00 3.16
525 528 2.975799 TCCGCCCGTTGAAGTTGC 60.976 61.111 0.00 0.00 0.00 4.17
526 529 2.978010 CCGCCCGTTGAAGTTGCT 60.978 61.111 0.00 0.00 0.00 3.91
527 530 2.556287 CGCCCGTTGAAGTTGCTC 59.444 61.111 0.00 0.00 0.00 4.26
531 534 2.084546 GCCCGTTGAAGTTGCTCTTAT 58.915 47.619 0.00 0.00 36.40 1.73
535 538 4.466828 CCGTTGAAGTTGCTCTTATTGTG 58.533 43.478 0.00 0.00 36.40 3.33
543 546 5.858381 AGTTGCTCTTATTGTGTGAGAGAA 58.142 37.500 3.93 0.00 41.77 2.87
544 547 5.931146 AGTTGCTCTTATTGTGTGAGAGAAG 59.069 40.000 3.93 0.00 41.77 2.85
579 582 5.473504 GGTCTGCCATATTAGGGTTACATTG 59.526 44.000 0.00 0.00 34.09 2.82
580 583 6.062095 GTCTGCCATATTAGGGTTACATTGT 58.938 40.000 0.00 0.00 0.00 2.71
584 587 5.009610 GCCATATTAGGGTTACATTGTGGTG 59.990 44.000 0.00 0.00 0.00 4.17
632 635 0.312102 GGTTGGTGAGCTGCTGAAAC 59.688 55.000 7.01 0.39 0.00 2.78
634 637 0.823356 TTGGTGAGCTGCTGAAACCC 60.823 55.000 7.01 0.00 0.00 4.11
636 639 1.239968 GGTGAGCTGCTGAAACCCTG 61.240 60.000 7.01 0.00 0.00 4.45
637 640 1.601759 TGAGCTGCTGAAACCCTGC 60.602 57.895 7.01 0.00 39.79 4.85
657 660 5.928264 CCTGCATTTCTTAAACAAGGGAAAG 59.072 40.000 0.00 0.00 32.41 2.62
662 665 7.686859 GCATTTCTTAAACAAGGGAAAGGTTCT 60.687 37.037 0.00 0.00 33.75 3.01
743 747 1.423845 CCGGTCCGCTCAATTTTCG 59.576 57.895 5.50 0.00 0.00 3.46
744 748 1.423845 CGGTCCGCTCAATTTTCGG 59.576 57.895 0.00 4.00 44.16 4.30
747 751 0.179189 GTCCGCTCAATTTTCGGCTG 60.179 55.000 5.23 0.00 42.65 4.85
750 754 2.154569 GCTCAATTTTCGGCTGCGC 61.155 57.895 0.00 0.00 0.00 6.09
762 767 2.895680 CTGCGCCTTCTCCTGCTA 59.104 61.111 4.18 0.00 0.00 3.49
763 768 1.227205 CTGCGCCTTCTCCTGCTAG 60.227 63.158 4.18 0.00 0.00 3.42
764 769 2.587473 GCGCCTTCTCCTGCTAGC 60.587 66.667 8.10 8.10 0.00 3.42
772 777 2.284754 TCTCCTGCTAGCAGATCGAT 57.715 50.000 40.03 0.00 46.30 3.59
782 787 0.528466 GCAGATCGATTGCTCGGACA 60.528 55.000 19.01 0.00 45.10 4.02
933 951 1.803334 CTCGACGATTTTCCCAACCA 58.197 50.000 0.00 0.00 0.00 3.67
945 963 2.802719 TCCCAACCATTTAAGAGCCAC 58.197 47.619 0.00 0.00 0.00 5.01
946 964 2.109128 TCCCAACCATTTAAGAGCCACA 59.891 45.455 0.00 0.00 0.00 4.17
947 965 2.493278 CCCAACCATTTAAGAGCCACAG 59.507 50.000 0.00 0.00 0.00 3.66
948 966 3.157087 CCAACCATTTAAGAGCCACAGT 58.843 45.455 0.00 0.00 0.00 3.55
949 967 3.191371 CCAACCATTTAAGAGCCACAGTC 59.809 47.826 0.00 0.00 0.00 3.51
950 968 3.073274 ACCATTTAAGAGCCACAGTCC 57.927 47.619 0.00 0.00 0.00 3.85
951 969 2.375174 ACCATTTAAGAGCCACAGTCCA 59.625 45.455 0.00 0.00 0.00 4.02
952 970 2.749621 CCATTTAAGAGCCACAGTCCAC 59.250 50.000 0.00 0.00 0.00 4.02
953 971 3.411446 CATTTAAGAGCCACAGTCCACA 58.589 45.455 0.00 0.00 0.00 4.17
954 972 2.839486 TTAAGAGCCACAGTCCACAG 57.161 50.000 0.00 0.00 0.00 3.66
955 973 2.009681 TAAGAGCCACAGTCCACAGA 57.990 50.000 0.00 0.00 0.00 3.41
1205 1223 3.061848 CCGCCGCATGTTCCCTTT 61.062 61.111 0.00 0.00 0.00 3.11
1259 1280 1.142748 CAGACGGTGCCATCTCCTC 59.857 63.158 0.00 0.00 0.00 3.71
1261 1282 3.083997 ACGGTGCCATCTCCTCCC 61.084 66.667 0.00 0.00 0.00 4.30
1355 1376 2.573869 CGCCGAGAGCCTCTTTGA 59.426 61.111 0.00 0.00 38.78 2.69
1521 1542 2.299326 ACTACCACTACTTCCACGGT 57.701 50.000 0.00 0.00 0.00 4.83
1821 1848 4.790861 GTCGGGTCTTCGGCCGAC 62.791 72.222 31.19 17.94 45.70 4.79
1839 1866 2.173669 CGCGCGGATCCATCTGTTT 61.174 57.895 24.84 0.00 35.60 2.83
2163 2190 2.126031 GGGTGGAACTCGACGCTC 60.126 66.667 2.33 0.00 36.74 5.03
2504 2531 5.013704 AGGATACAAACACCATAAGTCCACA 59.986 40.000 0.00 0.00 41.41 4.17
2533 2560 3.181510 ACGAAATCGATGCCAAACTTAGC 60.182 43.478 10.16 0.00 43.02 3.09
2552 2579 2.959030 AGCCTATAGATTCGCACAGTCA 59.041 45.455 0.00 0.00 0.00 3.41
2553 2580 3.576118 AGCCTATAGATTCGCACAGTCAT 59.424 43.478 0.00 0.00 0.00 3.06
2588 2615 8.823818 CAACTCGGGATTTAAATACTCGTTTAT 58.176 33.333 10.27 0.26 0.00 1.40
2589 2616 8.953368 ACTCGGGATTTAAATACTCGTTTATT 57.047 30.769 10.27 0.00 0.00 1.40
2615 2642 6.205853 AGGATTTGCACGTGTATGTTTTAAGA 59.794 34.615 18.38 0.00 0.00 2.10
2616 2643 7.027161 GGATTTGCACGTGTATGTTTTAAGAT 58.973 34.615 18.38 0.00 0.00 2.40
2617 2644 7.008266 GGATTTGCACGTGTATGTTTTAAGATG 59.992 37.037 18.38 0.00 0.00 2.90
2618 2645 5.289917 TGCACGTGTATGTTTTAAGATGG 57.710 39.130 18.38 0.00 0.00 3.51
2619 2646 4.155099 TGCACGTGTATGTTTTAAGATGGG 59.845 41.667 18.38 0.00 0.00 4.00
2620 2647 4.658071 CACGTGTATGTTTTAAGATGGGC 58.342 43.478 7.58 0.00 0.00 5.36
2621 2648 4.155099 CACGTGTATGTTTTAAGATGGGCA 59.845 41.667 7.58 0.00 0.00 5.36
2622 2649 4.394920 ACGTGTATGTTTTAAGATGGGCAG 59.605 41.667 0.00 0.00 0.00 4.85
2623 2650 4.672409 GTGTATGTTTTAAGATGGGCAGC 58.328 43.478 0.00 0.00 0.00 5.25
2624 2651 3.376859 TGTATGTTTTAAGATGGGCAGCG 59.623 43.478 0.00 0.00 0.00 5.18
2625 2652 0.525761 TGTTTTAAGATGGGCAGCGC 59.474 50.000 0.00 0.00 0.00 5.92
2626 2653 0.525761 GTTTTAAGATGGGCAGCGCA 59.474 50.000 15.49 15.49 0.00 6.09
2627 2654 0.810648 TTTTAAGATGGGCAGCGCAG 59.189 50.000 18.16 1.31 0.00 5.18
2628 2655 0.322456 TTTAAGATGGGCAGCGCAGT 60.322 50.000 18.16 8.14 0.00 4.40
2629 2656 1.026182 TTAAGATGGGCAGCGCAGTG 61.026 55.000 18.16 0.00 0.00 3.66
2630 2657 1.898330 TAAGATGGGCAGCGCAGTGA 61.898 55.000 18.16 0.00 0.00 3.41
2631 2658 3.200593 GATGGGCAGCGCAGTGAG 61.201 66.667 18.16 0.00 0.00 3.51
2632 2659 3.965539 GATGGGCAGCGCAGTGAGT 62.966 63.158 18.16 0.00 0.00 3.41
2633 2660 4.994471 TGGGCAGCGCAGTGAGTG 62.994 66.667 11.47 0.00 0.00 3.51
2635 2662 4.687215 GGCAGCGCAGTGAGTGGA 62.687 66.667 11.47 0.00 0.00 4.02
2636 2663 2.435586 GCAGCGCAGTGAGTGGAT 60.436 61.111 11.47 0.00 0.00 3.41
2637 2664 1.153568 GCAGCGCAGTGAGTGGATA 60.154 57.895 11.47 0.00 0.00 2.59
2638 2665 1.424493 GCAGCGCAGTGAGTGGATAC 61.424 60.000 11.47 0.00 0.00 2.24
2639 2666 0.174389 CAGCGCAGTGAGTGGATACT 59.826 55.000 11.47 0.00 40.66 2.12
2640 2667 0.174389 AGCGCAGTGAGTGGATACTG 59.826 55.000 11.47 0.00 45.40 2.74
2641 2668 0.108615 GCGCAGTGAGTGGATACTGT 60.109 55.000 0.30 0.00 44.66 3.55
2642 2669 1.914634 CGCAGTGAGTGGATACTGTC 58.085 55.000 0.00 0.00 44.66 3.51
2659 2686 2.211375 TCCCGACAGATGGACATGG 58.789 57.895 0.00 0.00 0.00 3.66
2660 2687 0.325203 TCCCGACAGATGGACATGGA 60.325 55.000 0.00 0.00 0.00 3.41
2661 2688 0.761187 CCCGACAGATGGACATGGAT 59.239 55.000 0.00 0.00 0.00 3.41
2667 2694 5.127682 CCGACAGATGGACATGGATCATATA 59.872 44.000 0.00 0.00 0.00 0.86
2668 2695 6.038985 CGACAGATGGACATGGATCATATAC 58.961 44.000 0.00 0.00 0.00 1.47
2703 2731 4.407296 AGATAAGGTAAAGAGTGCCTCCAG 59.593 45.833 0.00 0.00 42.45 3.86
2740 2773 7.238514 AGGGTTATCAATACATGCTAATCCTCT 59.761 37.037 0.00 0.00 44.31 3.69
2744 2777 6.692849 TCAATACATGCTAATCCTCTCCAT 57.307 37.500 0.00 0.00 0.00 3.41
2749 2782 4.411540 ACATGCTAATCCTCTCCATTCACT 59.588 41.667 0.00 0.00 0.00 3.41
2753 2786 4.100808 GCTAATCCTCTCCATTCACTCACT 59.899 45.833 0.00 0.00 0.00 3.41
2798 2831 5.710567 GGAGTTGCATTCCCTTTTAGTAACT 59.289 40.000 6.52 0.00 37.74 2.24
2802 2835 4.020039 TGCATTCCCTTTTAGTAACTCGGA 60.020 41.667 0.00 0.00 0.00 4.55
2848 2882 8.845227 TCATAACAAATCTTTTGTAGCAACTGA 58.155 29.630 6.09 2.23 31.50 3.41
2850 2884 7.992180 AACAAATCTTTTGTAGCAACTGAAG 57.008 32.000 6.09 0.00 31.50 3.02
2915 2950 0.601841 CCACAACTCCCACCACGTAC 60.602 60.000 0.00 0.00 0.00 3.67
2976 3011 1.359848 GATCCACGCTTGTCAATCGT 58.640 50.000 8.58 8.58 36.84 3.73
3026 3061 1.303309 GATCCAAGCTGGTGAATCCG 58.697 55.000 0.00 0.00 39.03 4.18
3040 3075 1.131504 GAATCCGGCGCAACACAAATA 59.868 47.619 10.83 0.00 0.00 1.40
3229 3287 1.941812 CAAAGGAGCACGCGACTTT 59.058 52.632 15.93 11.93 33.76 2.66
3244 3303 2.417719 GACTTTCATGTCAAGTCCGCT 58.582 47.619 20.91 0.42 43.01 5.52
3369 3428 1.195442 TCGGATGCCACCCAAGTACA 61.195 55.000 0.00 0.00 0.00 2.90
3493 3556 1.204704 CGTCCTGCATGTTCTAGGTGA 59.795 52.381 0.00 0.00 33.30 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 137 2.669670 GCCATAGATCACTCGTCATCGG 60.670 54.545 0.00 0.00 37.69 4.18
232 234 1.862201 CACATGCCAGCACACAAAAAG 59.138 47.619 0.00 0.00 0.00 2.27
335 338 2.124570 GCCATGTCTCATGCCGGT 60.125 61.111 1.90 0.00 0.00 5.28
391 394 3.181473 CCCATTTCATGTCCGCATTCAAT 60.181 43.478 0.00 0.00 31.99 2.57
475 478 1.462869 GCGTATTTGTCCGTTTGGTCG 60.463 52.381 0.00 0.00 36.30 4.79
476 479 1.135888 GGCGTATTTGTCCGTTTGGTC 60.136 52.381 0.00 0.00 36.30 4.02
477 480 0.876399 GGCGTATTTGTCCGTTTGGT 59.124 50.000 0.00 0.00 36.30 3.67
478 481 0.179210 CGGCGTATTTGTCCGTTTGG 60.179 55.000 0.00 0.00 38.47 3.28
479 482 3.283712 CGGCGTATTTGTCCGTTTG 57.716 52.632 0.00 0.00 38.47 2.93
484 487 1.392510 GAACAGACGGCGTATTTGTCC 59.607 52.381 14.74 1.97 33.09 4.02
485 488 1.058695 CGAACAGACGGCGTATTTGTC 59.941 52.381 14.74 5.70 0.00 3.18
486 489 1.065358 CGAACAGACGGCGTATTTGT 58.935 50.000 14.74 15.33 0.00 2.83
487 490 0.368907 CCGAACAGACGGCGTATTTG 59.631 55.000 14.74 14.62 46.20 2.32
488 491 2.745728 CCGAACAGACGGCGTATTT 58.254 52.632 14.74 6.20 46.20 1.40
489 492 4.489249 CCGAACAGACGGCGTATT 57.511 55.556 14.74 8.08 46.20 1.89
506 509 2.281276 AACTTCAACGGGCGGACC 60.281 61.111 0.00 0.00 0.00 4.46
507 510 2.943653 CAACTTCAACGGGCGGAC 59.056 61.111 0.00 0.00 0.00 4.79
508 511 2.975799 GCAACTTCAACGGGCGGA 60.976 61.111 0.00 0.00 0.00 5.54
509 512 2.966309 GAGCAACTTCAACGGGCGG 61.966 63.158 0.00 0.00 0.00 6.13
510 513 1.507141 AAGAGCAACTTCAACGGGCG 61.507 55.000 0.00 0.00 32.91 6.13
511 514 1.519408 TAAGAGCAACTTCAACGGGC 58.481 50.000 0.00 0.00 39.72 6.13
512 515 3.502211 ACAATAAGAGCAACTTCAACGGG 59.498 43.478 0.00 0.00 39.72 5.28
513 516 4.024048 ACACAATAAGAGCAACTTCAACGG 60.024 41.667 0.00 0.00 39.72 4.44
514 517 4.905866 CACACAATAAGAGCAACTTCAACG 59.094 41.667 0.00 0.00 39.72 4.10
515 518 6.017934 TCTCACACAATAAGAGCAACTTCAAC 60.018 38.462 0.00 0.00 39.72 3.18
516 519 6.054941 TCTCACACAATAAGAGCAACTTCAA 58.945 36.000 0.00 0.00 39.72 2.69
517 520 5.610398 TCTCACACAATAAGAGCAACTTCA 58.390 37.500 0.00 0.00 39.72 3.02
518 521 5.928839 TCTCTCACACAATAAGAGCAACTTC 59.071 40.000 0.00 0.00 39.72 3.01
519 522 5.858381 TCTCTCACACAATAAGAGCAACTT 58.142 37.500 2.10 2.10 42.04 2.66
520 523 5.474578 TCTCTCACACAATAAGAGCAACT 57.525 39.130 0.00 0.00 37.14 3.16
521 524 5.928839 TCTTCTCTCACACAATAAGAGCAAC 59.071 40.000 0.00 0.00 37.14 4.17
522 525 6.015095 TCTCTTCTCTCACACAATAAGAGCAA 60.015 38.462 0.00 0.00 39.69 3.91
523 526 5.478332 TCTCTTCTCTCACACAATAAGAGCA 59.522 40.000 0.00 0.00 39.69 4.26
524 527 5.960113 TCTCTTCTCTCACACAATAAGAGC 58.040 41.667 0.00 0.00 39.69 4.09
525 528 7.336679 TCTCTCTCTTCTCTCACACAATAAGAG 59.663 40.741 0.00 0.00 40.69 2.85
526 529 7.171653 TCTCTCTCTTCTCTCACACAATAAGA 58.828 38.462 0.00 0.00 0.00 2.10
527 530 7.389803 TCTCTCTCTTCTCTCACACAATAAG 57.610 40.000 0.00 0.00 0.00 1.73
531 534 5.047448 CCATTCTCTCTCTTCTCTCACACAA 60.047 44.000 0.00 0.00 0.00 3.33
535 538 4.023291 ACCCATTCTCTCTCTTCTCTCAC 58.977 47.826 0.00 0.00 0.00 3.51
543 546 1.273495 TGGCAGACCCATTCTCTCTCT 60.273 52.381 0.00 0.00 39.18 3.10
544 547 1.198713 TGGCAGACCCATTCTCTCTC 58.801 55.000 0.00 0.00 39.18 3.20
616 619 1.228245 GGGTTTCAGCAGCTCACCA 60.228 57.895 14.48 0.00 0.00 4.17
619 622 1.601759 GCAGGGTTTCAGCAGCTCA 60.602 57.895 0.00 0.00 0.00 4.26
620 623 0.964358 ATGCAGGGTTTCAGCAGCTC 60.964 55.000 0.00 0.00 42.14 4.09
632 635 3.831911 TCCCTTGTTTAAGAAATGCAGGG 59.168 43.478 0.00 0.00 35.92 4.45
634 637 5.928264 CCTTTCCCTTGTTTAAGAAATGCAG 59.072 40.000 0.00 0.00 35.92 4.41
636 639 5.853936 ACCTTTCCCTTGTTTAAGAAATGC 58.146 37.500 0.00 0.00 35.92 3.56
637 640 7.726216 AGAACCTTTCCCTTGTTTAAGAAATG 58.274 34.615 0.00 0.00 35.92 2.32
747 751 2.587473 GCTAGCAGGAGAAGGCGC 60.587 66.667 10.63 0.00 34.54 6.53
750 754 1.000385 CGATCTGCTAGCAGGAGAAGG 60.000 57.143 37.60 20.28 45.79 3.46
763 768 0.528466 TGTCCGAGCAATCGATCTGC 60.528 55.000 18.79 18.79 40.24 4.26
764 769 1.791204 CATGTCCGAGCAATCGATCTG 59.209 52.381 0.00 0.67 34.64 2.90
772 777 1.375908 GGCTGACATGTCCGAGCAA 60.376 57.895 29.08 10.04 32.25 3.91
933 951 3.327757 TCTGTGGACTGTGGCTCTTAAAT 59.672 43.478 0.00 0.00 0.00 1.40
945 963 1.290203 GTGTGTGTGTCTGTGGACTG 58.710 55.000 0.00 0.00 42.54 3.51
946 964 0.179111 CGTGTGTGTGTCTGTGGACT 60.179 55.000 0.00 0.00 42.54 3.85
947 965 1.762222 GCGTGTGTGTGTCTGTGGAC 61.762 60.000 0.00 0.00 42.42 4.02
948 966 1.520564 GCGTGTGTGTGTCTGTGGA 60.521 57.895 0.00 0.00 0.00 4.02
949 967 2.870341 CGCGTGTGTGTGTCTGTGG 61.870 63.158 0.00 0.00 0.00 4.17
950 968 2.620459 CGCGTGTGTGTGTCTGTG 59.380 61.111 0.00 0.00 0.00 3.66
951 969 2.584970 CCGCGTGTGTGTGTCTGT 60.585 61.111 4.92 0.00 0.00 3.41
952 970 4.000557 GCCGCGTGTGTGTGTCTG 62.001 66.667 4.92 0.00 0.00 3.51
953 971 4.522689 TGCCGCGTGTGTGTGTCT 62.523 61.111 4.92 0.00 0.00 3.41
954 972 4.293626 GTGCCGCGTGTGTGTGTC 62.294 66.667 4.92 0.00 0.00 3.67
1257 1278 1.668101 CGTCGGAGAAGGGAAGGGAG 61.668 65.000 0.00 0.00 39.69 4.30
1259 1280 2.893398 CGTCGGAGAAGGGAAGGG 59.107 66.667 0.00 0.00 39.69 3.95
1588 1609 1.760086 CACGGATCCTGAGAGGCCT 60.760 63.158 3.86 3.86 34.61 5.19
1821 1848 0.874175 TAAACAGATGGATCCGCGCG 60.874 55.000 25.67 25.67 0.00 6.86
2207 2234 3.884581 TTCGTCGGCTGGTCGAACG 62.885 63.158 17.59 9.27 41.05 3.95
2504 2531 1.670811 GGCATCGATTTCGTCATGGTT 59.329 47.619 0.00 0.00 40.80 3.67
2533 2560 7.542890 AGAATATGACTGTGCGAATCTATAGG 58.457 38.462 0.00 0.00 0.00 2.57
2588 2615 5.950758 AAACATACACGTGCAAATCCTAA 57.049 34.783 17.22 0.00 0.00 2.69
2589 2616 5.950758 AAAACATACACGTGCAAATCCTA 57.049 34.783 17.22 0.00 0.00 2.94
2590 2617 4.846779 AAAACATACACGTGCAAATCCT 57.153 36.364 17.22 0.00 0.00 3.24
2600 2627 4.730613 GCTGCCCATCTTAAAACATACACG 60.731 45.833 0.00 0.00 0.00 4.49
2615 2642 4.025858 ACTCACTGCGCTGCCCAT 62.026 61.111 14.80 0.00 0.00 4.00
2616 2643 4.994471 CACTCACTGCGCTGCCCA 62.994 66.667 14.80 0.00 0.00 5.36
2618 2645 2.578163 TATCCACTCACTGCGCTGCC 62.578 60.000 14.80 0.00 0.00 4.85
2619 2646 1.153568 TATCCACTCACTGCGCTGC 60.154 57.895 14.80 0.00 0.00 5.25
2620 2647 0.174389 AGTATCCACTCACTGCGCTG 59.826 55.000 13.23 13.23 0.00 5.18
2621 2648 0.174389 CAGTATCCACTCACTGCGCT 59.826 55.000 9.73 0.00 36.09 5.92
2622 2649 0.108615 ACAGTATCCACTCACTGCGC 60.109 55.000 0.00 0.00 44.89 6.09
2623 2650 1.914634 GACAGTATCCACTCACTGCG 58.085 55.000 1.78 0.00 44.89 5.18
2641 2668 0.325203 TCCATGTCCATCTGTCGGGA 60.325 55.000 0.00 0.00 0.00 5.14
2642 2669 0.761187 ATCCATGTCCATCTGTCGGG 59.239 55.000 0.00 0.00 0.00 5.14
2643 2670 1.413812 TGATCCATGTCCATCTGTCGG 59.586 52.381 0.00 0.00 0.00 4.79
2644 2671 2.896745 TGATCCATGTCCATCTGTCG 57.103 50.000 0.00 0.00 0.00 4.35
2645 2672 7.040494 CAGTATATGATCCATGTCCATCTGTC 58.960 42.308 0.00 0.00 0.00 3.51
2646 2673 6.499699 ACAGTATATGATCCATGTCCATCTGT 59.500 38.462 0.00 0.00 0.00 3.41
2647 2674 6.944096 ACAGTATATGATCCATGTCCATCTG 58.056 40.000 0.00 0.00 0.00 2.90
2648 2675 8.851106 ATACAGTATATGATCCATGTCCATCT 57.149 34.615 0.00 0.00 0.00 2.90
2703 2731 6.757947 TGTATTGATAACCCTGTAAACTACGC 59.242 38.462 0.00 0.00 0.00 4.42
2740 2773 3.769844 GGGTAGAGAAGTGAGTGAATGGA 59.230 47.826 0.00 0.00 0.00 3.41
2744 2777 5.258216 AGTAGGGTAGAGAAGTGAGTGAA 57.742 43.478 0.00 0.00 0.00 3.18
2749 2782 6.890814 CCTTCTTTAGTAGGGTAGAGAAGTGA 59.109 42.308 9.31 0.00 38.62 3.41
2780 2813 4.510571 TCCGAGTTACTAAAAGGGAATGC 58.489 43.478 0.00 0.00 0.00 3.56
2798 2831 2.427812 GTTTGGTTTGGTCCTTTTCCGA 59.572 45.455 0.00 0.00 0.00 4.55
2802 2835 2.769663 GAGGGTTTGGTTTGGTCCTTTT 59.230 45.455 0.00 0.00 0.00 2.27
2848 2882 2.746277 GCACGGCCATCGGTTCTT 60.746 61.111 2.24 0.00 44.45 2.52
2850 2884 3.799755 GTGCACGGCCATCGGTTC 61.800 66.667 2.24 0.00 44.45 3.62
2915 2950 1.878524 CTGCGCACCATTTTTGCACG 61.879 55.000 5.66 0.00 40.20 5.34
3026 3061 1.514014 CGGCTATTTGTGTTGCGCC 60.514 57.895 4.18 0.00 0.00 6.53
3040 3075 0.179000 CTAGAACAATCTGGGCGGCT 59.821 55.000 9.56 0.00 37.10 5.52
3229 3287 1.511850 CAACAGCGGACTTGACATGA 58.488 50.000 0.00 0.00 0.00 3.07
3310 3369 2.162338 TTAAGTGGTCGTGGGAGGCG 62.162 60.000 0.00 0.00 0.00 5.52
3369 3428 1.152963 ACGCTCTGGCAAGTGGTTT 60.153 52.632 12.54 0.00 38.60 3.27


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

AutoCloner maintained by Alex Coulton.