Multiple sequence alignment - TraesCS5B01G355500

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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 TraesCS5B01G355500 chr5B 100.000 9214 0 0 1 9214 535105106 535095893 0.000000e+00 17016.0
1 TraesCS5B01G355500 chr5B 96.367 6056 169 20 1198 7239 52315853 52321871 0.000000e+00 9917.0
2 TraesCS5B01G355500 chr5B 96.961 1053 26 3 7238 8288 52322603 52323651 0.000000e+00 1762.0
3 TraesCS5B01G355500 chr5B 98.285 933 14 2 8283 9214 579009626 579010557 0.000000e+00 1633.0
4 TraesCS5B01G355500 chr5B 98.071 933 16 2 8283 9214 557765305 557766236 0.000000e+00 1622.0
5 TraesCS5B01G355500 chr5B 97.966 934 17 2 8283 9214 606593485 606592552 0.000000e+00 1618.0
6 TraesCS5B01G355500 chr5B 97.222 720 17 2 1 718 557764601 557765319 0.000000e+00 1216.0
7 TraesCS5B01G355500 chr5B 97.222 720 17 2 1 718 606594189 606593471 0.000000e+00 1216.0
8 TraesCS5B01G355500 chr5B 95.052 485 14 3 711 1186 430202247 430202730 0.000000e+00 754.0
9 TraesCS5B01G355500 chr5B 95.052 485 14 3 711 1186 430205185 430205668 0.000000e+00 754.0
10 TraesCS5B01G355500 chr5B 95.052 485 14 3 711 1186 430217915 430218398 0.000000e+00 754.0
11 TraesCS5B01G355500 chr5B 94.639 485 16 3 711 1186 430108897 430109380 0.000000e+00 743.0
12 TraesCS5B01G355500 chr5B 93.613 501 22 3 711 1201 345507695 345508195 0.000000e+00 739.0
13 TraesCS5B01G355500 chr5A 96.667 4831 131 18 2007 6812 32955199 32950374 0.000000e+00 8002.0
14 TraesCS5B01G355500 chr5A 97.343 1054 22 3 7238 8290 32947493 32946445 0.000000e+00 1786.0
15 TraesCS5B01G355500 chr5A 88.402 707 50 13 4839 5523 10046590 10045894 0.000000e+00 822.0
16 TraesCS5B01G355500 chr5A 96.296 432 14 2 6808 7239 32948663 32948234 0.000000e+00 708.0
17 TraesCS5B01G355500 chr5A 93.939 99 4 2 4439 4536 696955264 696955361 2.070000e-31 148.0
18 TraesCS5B01G355500 chr2B 98.848 3733 37 4 983 4711 657485389 657481659 0.000000e+00 6650.0
19 TraesCS5B01G355500 chr2B 97.456 3499 73 5 4799 8290 657481660 657478171 0.000000e+00 5954.0
20 TraesCS5B01G355500 chr2B 98.071 933 17 1 8283 9214 732358475 732359407 0.000000e+00 1622.0
21 TraesCS5B01G355500 chr2B 95.296 829 33 3 7452 8279 145373651 145372828 0.000000e+00 1310.0
22 TraesCS5B01G355500 chr2B 97.500 720 15 2 1 718 6926171 6925453 0.000000e+00 1227.0
23 TraesCS5B01G355500 chr6B 98.553 3731 44 5 983 4711 151881136 151884858 0.000000e+00 6582.0
24 TraesCS5B01G355500 chr6B 97.894 3467 64 3 4831 8290 151884866 151888330 0.000000e+00 5989.0
25 TraesCS5B01G355500 chr6B 98.204 3118 45 6 2131 5242 80798629 80801741 0.000000e+00 5437.0
26 TraesCS5B01G355500 chr6B 98.121 1437 25 2 709 2143 80788659 80790095 0.000000e+00 2503.0
27 TraesCS5B01G355500 chr6B 97.964 933 18 1 8283 9214 49692292 49691360 0.000000e+00 1616.0
28 TraesCS5B01G355500 chr6B 98.370 736 9 2 6890 7625 80801745 80802477 0.000000e+00 1290.0
29 TraesCS5B01G355500 chr6B 96.797 718 19 3 1 718 194745005 194745718 0.000000e+00 1195.0
30 TraesCS5B01G355500 chr6B 96.797 718 18 2 1 718 672341241 672340529 0.000000e+00 1194.0
31 TraesCS5B01G355500 chr6B 96.797 718 13 4 1 718 17430004 17430711 0.000000e+00 1190.0
32 TraesCS5B01G355500 chr6B 86.441 59 7 1 5520 5578 560784978 560785035 7.720000e-06 63.9
33 TraesCS5B01G355500 chr2A 98.280 3720 58 4 983 4700 441100497 441104212 0.000000e+00 6510.0
34 TraesCS5B01G355500 chr2A 97.949 3462 63 2 4837 8291 441104212 441107672 0.000000e+00 5993.0
35 TraesCS5B01G355500 chr2A 96.671 721 16 4 1 718 625940442 625941157 0.000000e+00 1192.0
36 TraesCS5B01G355500 chr3A 97.016 3787 96 10 3035 6811 336007343 336003564 0.000000e+00 6351.0
37 TraesCS5B01G355500 chr3A 95.389 1800 73 7 2639 4435 58067626 58069418 0.000000e+00 2856.0
38 TraesCS5B01G355500 chr3A 95.924 1055 31 4 7238 8291 335997890 335996847 0.000000e+00 1700.0
39 TraesCS5B01G355500 chr3A 94.419 430 15 3 1198 1627 587984749 587985169 0.000000e+00 652.0
40 TraesCS5B01G355500 chr3A 90.762 433 12 5 6807 7239 335999026 335998622 3.760000e-153 553.0
41 TraesCS5B01G355500 chrUn 95.937 3618 121 9 3630 7239 73440559 73444158 0.000000e+00 5843.0
42 TraesCS5B01G355500 chrUn 96.184 1153 32 4 1198 2350 73439422 73440562 0.000000e+00 1875.0
43 TraesCS5B01G355500 chrUn 96.869 1054 27 3 7238 8290 73444893 73445941 0.000000e+00 1759.0
44 TraesCS5B01G355500 chrUn 96.537 722 20 2 1 718 275376375 275375655 0.000000e+00 1190.0
45 TraesCS5B01G355500 chrUn 94.467 488 18 2 708 1186 254615467 254615954 0.000000e+00 743.0
46 TraesCS5B01G355500 chrUn 94.639 485 16 3 711 1186 387538635 387538152 0.000000e+00 743.0
47 TraesCS5B01G355500 chrUn 94.639 485 17 2 711 1186 407200618 407201102 0.000000e+00 743.0
48 TraesCS5B01G355500 chr7A 94.947 1781 79 11 2661 4435 107709781 107711556 0.000000e+00 2780.0
49 TraesCS5B01G355500 chr7A 96.538 1011 22 6 1623 2631 107677929 107678928 0.000000e+00 1661.0
50 TraesCS5B01G355500 chr7B 97.725 1011 18 4 1623 2631 472920178 472919171 0.000000e+00 1735.0
51 TraesCS5B01G355500 chr7B 97.725 1011 18 3 1623 2631 606364579 606365586 0.000000e+00 1735.0
52 TraesCS5B01G355500 chr7B 97.964 933 18 1 8283 9214 110264872 110263940 0.000000e+00 1616.0
53 TraesCS5B01G355500 chr7B 88.529 401 35 8 5062 5453 702500884 702501282 8.370000e-130 475.0
54 TraesCS5B01G355500 chr3B 98.071 933 17 1 8283 9214 821991429 821990497 0.000000e+00 1622.0
55 TraesCS5B01G355500 chr3B 98.069 932 16 2 8283 9213 7461662 7460732 0.000000e+00 1620.0
56 TraesCS5B01G355500 chr3B 97.970 936 14 3 8283 9214 145243769 145244703 0.000000e+00 1618.0
57 TraesCS5B01G355500 chr3B 90.169 295 27 2 7999 8291 729975426 729975720 5.220000e-102 383.0
58 TraesCS5B01G355500 chr1D 95.556 765 27 4 7240 8003 2455611 2456369 0.000000e+00 1218.0
59 TraesCS5B01G355500 chr1D 88.136 59 6 1 5520 5578 480634553 480634610 1.660000e-07 69.4
60 TraesCS5B01G355500 chr1B 96.797 718 18 2 1 718 514680655 514681367 0.000000e+00 1194.0
61 TraesCS5B01G355500 chr7D 87.937 829 64 13 4715 5523 287708659 287707847 0.000000e+00 944.0
62 TraesCS5B01G355500 chr7D 94.651 430 14 1 1198 1627 105872204 105872624 0.000000e+00 658.0
63 TraesCS5B01G355500 chr7D 88.520 392 35 6 5070 5453 205653562 205653173 5.040000e-127 466.0
64 TraesCS5B01G355500 chr7D 86.239 327 43 2 4537 4862 376561540 376561215 4.090000e-93 353.0
65 TraesCS5B01G355500 chr1A 87.866 717 56 13 4828 5523 308348172 308348878 0.000000e+00 813.0
66 TraesCS5B01G355500 chr1A 89.046 283 18 4 4937 5207 292891989 292891708 1.150000e-88 339.0
67 TraesCS5B01G355500 chr1A 89.427 227 17 4 4715 4938 292892293 292892071 7.050000e-71 279.0
68 TraesCS5B01G355500 chr1A 88.136 59 6 1 5520 5578 577183227 577183284 1.660000e-07 69.4
69 TraesCS5B01G355500 chr1A 88.136 59 6 1 5520 5578 577204756 577204813 1.660000e-07 69.4
70 TraesCS5B01G355500 chr4A 87.815 714 55 14 4832 5523 216809780 216810483 0.000000e+00 808.0
71 TraesCS5B01G355500 chr4A 88.060 402 36 8 5062 5453 663304768 663304369 5.040000e-127 466.0
72 TraesCS5B01G355500 chr4A 89.286 56 1 5 5523 5578 593756800 593756750 2.150000e-06 65.8
73 TraesCS5B01G355500 chr6D 95.116 430 14 2 1198 1627 232760672 232760250 0.000000e+00 671.0
74 TraesCS5B01G355500 chr4B 87.980 391 37 6 5070 5453 610799853 610800240 3.920000e-123 453.0
75 TraesCS5B01G355500 chr4B 79.304 517 82 15 6426 6927 247571894 247571388 1.150000e-88 339.0
76 TraesCS5B01G355500 chr5D 89.017 173 18 1 5129 5300 25316225 25316397 7.250000e-51 213.0


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 TraesCS5B01G355500 chr5B 535095893 535105106 9213 True 17016.000000 17016 100.000000 1 9214 1 chr5B.!!$R1 9213
1 TraesCS5B01G355500 chr5B 52315853 52323651 7798 False 5839.500000 9917 96.664000 1198 8288 2 chr5B.!!$F5 7090
2 TraesCS5B01G355500 chr5B 579009626 579010557 931 False 1633.000000 1633 98.285000 8283 9214 1 chr5B.!!$F4 931
3 TraesCS5B01G355500 chr5B 557764601 557766236 1635 False 1419.000000 1622 97.646500 1 9214 2 chr5B.!!$F7 9213
4 TraesCS5B01G355500 chr5B 606592552 606594189 1637 True 1417.000000 1618 97.594000 1 9214 2 chr5B.!!$R2 9213
5 TraesCS5B01G355500 chr5B 430202247 430205668 3421 False 754.000000 754 95.052000 711 1186 2 chr5B.!!$F6 475
6 TraesCS5B01G355500 chr5B 345507695 345508195 500 False 739.000000 739 93.613000 711 1201 1 chr5B.!!$F1 490
7 TraesCS5B01G355500 chr5A 32946445 32955199 8754 True 3498.666667 8002 96.768667 2007 8290 3 chr5A.!!$R2 6283
8 TraesCS5B01G355500 chr5A 10045894 10046590 696 True 822.000000 822 88.402000 4839 5523 1 chr5A.!!$R1 684
9 TraesCS5B01G355500 chr2B 657478171 657485389 7218 True 6302.000000 6650 98.152000 983 8290 2 chr2B.!!$R3 7307
10 TraesCS5B01G355500 chr2B 732358475 732359407 932 False 1622.000000 1622 98.071000 8283 9214 1 chr2B.!!$F1 931
11 TraesCS5B01G355500 chr2B 145372828 145373651 823 True 1310.000000 1310 95.296000 7452 8279 1 chr2B.!!$R2 827
12 TraesCS5B01G355500 chr2B 6925453 6926171 718 True 1227.000000 1227 97.500000 1 718 1 chr2B.!!$R1 717
13 TraesCS5B01G355500 chr6B 151881136 151888330 7194 False 6285.500000 6582 98.223500 983 8290 2 chr6B.!!$F6 7307
14 TraesCS5B01G355500 chr6B 80798629 80802477 3848 False 3363.500000 5437 98.287000 2131 7625 2 chr6B.!!$F5 5494
15 TraesCS5B01G355500 chr6B 80788659 80790095 1436 False 2503.000000 2503 98.121000 709 2143 1 chr6B.!!$F2 1434
16 TraesCS5B01G355500 chr6B 49691360 49692292 932 True 1616.000000 1616 97.964000 8283 9214 1 chr6B.!!$R1 931
17 TraesCS5B01G355500 chr6B 194745005 194745718 713 False 1195.000000 1195 96.797000 1 718 1 chr6B.!!$F3 717
18 TraesCS5B01G355500 chr6B 672340529 672341241 712 True 1194.000000 1194 96.797000 1 718 1 chr6B.!!$R2 717
19 TraesCS5B01G355500 chr6B 17430004 17430711 707 False 1190.000000 1190 96.797000 1 718 1 chr6B.!!$F1 717
20 TraesCS5B01G355500 chr2A 441100497 441107672 7175 False 6251.500000 6510 98.114500 983 8291 2 chr2A.!!$F2 7308
21 TraesCS5B01G355500 chr2A 625940442 625941157 715 False 1192.000000 1192 96.671000 1 718 1 chr2A.!!$F1 717
22 TraesCS5B01G355500 chr3A 336003564 336007343 3779 True 6351.000000 6351 97.016000 3035 6811 1 chr3A.!!$R1 3776
23 TraesCS5B01G355500 chr3A 58067626 58069418 1792 False 2856.000000 2856 95.389000 2639 4435 1 chr3A.!!$F1 1796
24 TraesCS5B01G355500 chr3A 335996847 335999026 2179 True 1126.500000 1700 93.343000 6807 8291 2 chr3A.!!$R2 1484
25 TraesCS5B01G355500 chrUn 73439422 73445941 6519 False 3159.000000 5843 96.330000 1198 8290 3 chrUn.!!$F3 7092
26 TraesCS5B01G355500 chrUn 275375655 275376375 720 True 1190.000000 1190 96.537000 1 718 1 chrUn.!!$R1 717
27 TraesCS5B01G355500 chr7A 107709781 107711556 1775 False 2780.000000 2780 94.947000 2661 4435 1 chr7A.!!$F2 1774
28 TraesCS5B01G355500 chr7A 107677929 107678928 999 False 1661.000000 1661 96.538000 1623 2631 1 chr7A.!!$F1 1008
29 TraesCS5B01G355500 chr7B 472919171 472920178 1007 True 1735.000000 1735 97.725000 1623 2631 1 chr7B.!!$R2 1008
30 TraesCS5B01G355500 chr7B 606364579 606365586 1007 False 1735.000000 1735 97.725000 1623 2631 1 chr7B.!!$F1 1008
31 TraesCS5B01G355500 chr7B 110263940 110264872 932 True 1616.000000 1616 97.964000 8283 9214 1 chr7B.!!$R1 931
32 TraesCS5B01G355500 chr3B 821990497 821991429 932 True 1622.000000 1622 98.071000 8283 9214 1 chr3B.!!$R2 931
33 TraesCS5B01G355500 chr3B 7460732 7461662 930 True 1620.000000 1620 98.069000 8283 9213 1 chr3B.!!$R1 930
34 TraesCS5B01G355500 chr3B 145243769 145244703 934 False 1618.000000 1618 97.970000 8283 9214 1 chr3B.!!$F1 931
35 TraesCS5B01G355500 chr1D 2455611 2456369 758 False 1218.000000 1218 95.556000 7240 8003 1 chr1D.!!$F1 763
36 TraesCS5B01G355500 chr1B 514680655 514681367 712 False 1194.000000 1194 96.797000 1 718 1 chr1B.!!$F1 717
37 TraesCS5B01G355500 chr7D 287707847 287708659 812 True 944.000000 944 87.937000 4715 5523 1 chr7D.!!$R2 808
38 TraesCS5B01G355500 chr1A 308348172 308348878 706 False 813.000000 813 87.866000 4828 5523 1 chr1A.!!$F1 695
39 TraesCS5B01G355500 chr1A 292891708 292892293 585 True 309.000000 339 89.236500 4715 5207 2 chr1A.!!$R1 492
40 TraesCS5B01G355500 chr4A 216809780 216810483 703 False 808.000000 808 87.815000 4832 5523 1 chr4A.!!$F1 691
41 TraesCS5B01G355500 chr4B 247571388 247571894 506 True 339.000000 339 79.304000 6426 6927 1 chr4B.!!$R1 501

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
782 800 1.003718 CCACCTCACCCGGTCTTTC 60.004 63.158 0.00 0.00 34.29 2.62 F
1081 4047 1.150992 ACCGCTAGATCCCTACGCT 59.849 57.895 0.00 0.00 0.00 5.07 F
2907 5883 1.134371 GGGAGTACTACGACTACCGGT 60.134 57.143 13.98 13.98 40.71 5.28 F
4273 7269 0.845337 TAACCCCGTCCTGGTTGTTT 59.155 50.000 4.98 0.00 45.50 2.83 F
5255 8356 1.046472 ACAGTCCAGGTTGACCGTCA 61.046 55.000 0.00 0.00 42.08 4.35 F
5658 8763 2.297597 ACTGTGTAACTCTGGAGTGAGC 59.702 50.000 3.88 0.00 41.58 4.26 F
6695 9809 1.063942 TCCCACGATCAGCTCTAAGGA 60.064 52.381 0.00 0.00 0.00 3.36 F
7009 11853 1.138671 GCACGGCAAACACACAAGT 59.861 52.632 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 5359 0.823460 ACAAACACAAGGCCAACAGG 59.177 50.000 5.01 0.0 0.00 4.00 R
3281 6258 9.822727 TTAACAGAGGAAAGGGAGATTTTTATT 57.177 29.630 0.00 0.0 0.00 1.40 R
4643 7641 3.247948 TGTTGTACACTCTAGGGGACA 57.752 47.619 0.00 0.0 0.00 4.02 R
5303 8404 1.938585 ACTGGTCTGATTTCTCCCGA 58.061 50.000 0.00 0.0 0.00 5.14 R
6655 9769 0.445436 GAAGCTGTCACGCATCTTGG 59.555 55.000 0.00 0.0 34.11 3.61 R
7009 11853 4.785511 TTTTTCCTTTGTTTGACGACCA 57.214 36.364 0.00 0.0 0.00 4.02 R
7996 13587 0.671251 TTCATTCCCACGGTGTTTGC 59.329 50.000 7.45 0.0 0.00 3.68 R
8825 14418 2.035632 GGTTCATTGACCCAAACACCA 58.964 47.619 0.00 0.0 33.41 4.17 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
302 320 5.163457 ACGATGACAATTGGAAGTGGTTTTT 60.163 36.000 10.83 0.00 0.00 1.94
431 449 1.228894 TTCTCCCGCACCTCTCTGT 60.229 57.895 0.00 0.00 0.00 3.41
572 590 1.368345 CTTTCGGACGCCATCATGCA 61.368 55.000 0.00 0.00 0.00 3.96
782 800 1.003718 CCACCTCACCCGGTCTTTC 60.004 63.158 0.00 0.00 34.29 2.62
823 3787 2.746277 CCCACCTCCCGCGAAAAG 60.746 66.667 8.23 0.86 0.00 2.27
839 3803 3.494223 CGAAAAGCCAAGAAAAACCCCAT 60.494 43.478 0.00 0.00 0.00 4.00
927 3892 3.133183 ACAAACCAGCAAAATAAACCGGT 59.867 39.130 0.00 0.00 0.00 5.28
971 3937 1.456705 ACAAACCAACCACCCGCAT 60.457 52.632 0.00 0.00 0.00 4.73
1081 4047 1.150992 ACCGCTAGATCCCTACGCT 59.849 57.895 0.00 0.00 0.00 5.07
1224 4190 3.352338 GAAGGATGGCGACGACGGT 62.352 63.158 9.67 0.00 40.15 4.83
2388 5359 3.766051 AGGAGCATTGGTTCAGATTTTCC 59.234 43.478 0.00 0.00 0.00 3.13
2907 5883 1.134371 GGGAGTACTACGACTACCGGT 60.134 57.143 13.98 13.98 40.71 5.28
3281 6258 7.766738 TGTTTCTCCATGCATAACGAATTACTA 59.233 33.333 0.00 0.00 0.00 1.82
3594 6571 1.235281 GGTTGAGGCGGTTCAGGTTC 61.235 60.000 0.00 0.00 0.00 3.62
3609 6586 4.138290 TCAGGTTCGTCTCTATCATCCTC 58.862 47.826 0.00 0.00 0.00 3.71
4273 7269 0.845337 TAACCCCGTCCTGGTTGTTT 59.155 50.000 4.98 0.00 45.50 2.83
4367 7363 2.464459 GCTCGACCATTTGCTCCGG 61.464 63.158 0.00 0.00 0.00 5.14
4901 7901 1.463444 CTAAAGCCGAAAAGGTGGTCG 59.537 52.381 0.00 0.00 43.70 4.79
5139 8237 5.964958 TCACAAGCCCAATAAGAGAAAAG 57.035 39.130 0.00 0.00 0.00 2.27
5255 8356 1.046472 ACAGTCCAGGTTGACCGTCA 61.046 55.000 0.00 0.00 42.08 4.35
5303 8404 3.097614 ACACCCGAAAGCAGAGTATACT 58.902 45.455 4.68 4.68 0.00 2.12
5324 8425 2.758979 TCGGGAGAAATCAGACCAGTAC 59.241 50.000 0.00 0.00 34.75 2.73
5335 8436 2.692557 CAGACCAGTACATAGCTCTGCT 59.307 50.000 0.00 0.00 43.41 4.24
5536 8641 5.951747 AGCCTGATAGCCAGTTTCAAATAAA 59.048 36.000 0.00 0.00 41.33 1.40
5658 8763 2.297597 ACTGTGTAACTCTGGAGTGAGC 59.702 50.000 3.88 0.00 41.58 4.26
6126 9233 9.801873 ACAACATTTATTAATAGTTCACCATGC 57.198 29.630 0.00 0.00 0.00 4.06
6444 9558 5.875224 TGTCAGAATATGGAAACTCACCAA 58.125 37.500 0.00 0.00 40.93 3.67
6695 9809 1.063942 TCCCACGATCAGCTCTAAGGA 60.064 52.381 0.00 0.00 0.00 3.36
6719 9833 2.485966 AGTGCCACCTAGATCCAGAT 57.514 50.000 0.00 0.00 0.00 2.90
7009 11853 1.138671 GCACGGCAAACACACAAGT 59.861 52.632 0.00 0.00 0.00 3.16
7652 13243 1.612950 TGCTTCATCCATTTTGCACGT 59.387 42.857 0.00 0.00 0.00 4.49
7750 13341 6.148811 CGTGTGGGATAGTTACAATCTTTGTT 59.851 38.462 0.00 0.00 42.22 2.83
7843 13434 7.435488 AGCGTGTCAAAGTAGATATGTTACATC 59.565 37.037 0.00 0.00 0.00 3.06
7996 13587 1.586422 CCGCTTGGATGTATGAGTGG 58.414 55.000 0.00 0.00 33.91 4.00
8683 14276 7.883311 AGCTAGTAGGCAAAAACAGAGAATTTA 59.117 33.333 0.00 0.00 34.17 1.40
8825 14418 7.994425 TTATCCGCCATGTGTATTCATTAAT 57.006 32.000 0.00 0.00 0.00 1.40
9058 14654 7.041712 TGCGTCTTGATTGTATAACTGAAACAA 60.042 33.333 0.00 0.00 37.51 2.83
9136 14732 2.505407 TCACCATGAGGGACAATCGATT 59.495 45.455 4.39 4.39 41.15 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 449 8.704668 TGCATATTGATCTCCTTCTTAACAGTA 58.295 33.333 0.00 0.00 0.00 2.74
505 523 4.689345 GGTACGCTTGTCAGAACACTATTT 59.311 41.667 0.00 0.00 34.35 1.40
782 800 5.866207 AGGAAGTACCAAAGAAGTACCAAG 58.134 41.667 0.00 0.00 40.83 3.61
823 3787 2.417243 CGATCATGGGGTTTTTCTTGGC 60.417 50.000 0.00 0.00 0.00 4.52
839 3803 3.708210 GGGTGTGGGACTCGATCA 58.292 61.111 0.00 0.00 0.00 2.92
1174 4140 2.616765 CCGAGAGTGAGAGAGAAGGTGA 60.617 54.545 0.00 0.00 0.00 4.02
1431 4397 1.200948 GCTTGATCTGCTCCGCTTTTT 59.799 47.619 0.00 0.00 0.00 1.94
2388 5359 0.823460 ACAAACACAAGGCCAACAGG 59.177 50.000 5.01 0.00 0.00 4.00
3281 6258 9.822727 TTAACAGAGGAAAGGGAGATTTTTATT 57.177 29.630 0.00 0.00 0.00 1.40
3370 6347 5.394883 CCCATACTTTTCGCCTACTGTTCTA 60.395 44.000 0.00 0.00 0.00 2.10
3594 6571 1.551452 GGGGGAGGATGATAGAGACG 58.449 60.000 0.00 0.00 0.00 4.18
4367 7363 4.020128 TCCTTCTGAGCTAAAAACTCCCTC 60.020 45.833 0.00 0.00 32.98 4.30
4643 7641 3.247948 TGTTGTACACTCTAGGGGACA 57.752 47.619 0.00 0.00 0.00 4.02
5139 8237 2.231964 TGCATTCTTCAGGATGTTTGCC 59.768 45.455 0.00 0.00 37.40 4.52
5255 8356 9.850628 CTGATTTGATGACAAGAATATTGTGTT 57.149 29.630 0.00 0.00 37.32 3.32
5303 8404 1.938585 ACTGGTCTGATTTCTCCCGA 58.061 50.000 0.00 0.00 0.00 5.14
5305 8406 4.762289 ATGTACTGGTCTGATTTCTCCC 57.238 45.455 0.00 0.00 0.00 4.30
5324 8425 3.320256 TGACAGTATGGAGCAGAGCTATG 59.680 47.826 3.34 3.34 43.62 2.23
5335 8436 3.719268 ATGGTTGCTTGACAGTATGGA 57.281 42.857 0.00 0.00 43.62 3.41
5536 8641 2.425312 CTGGAGCACTGAGATCTTACGT 59.575 50.000 0.00 0.00 31.91 3.57
5796 8901 5.565592 TGTTCCATGTAATGTGAATCTGC 57.434 39.130 0.00 0.00 44.81 4.26
5863 8970 2.272471 GCCCTAGAGCAACCACCC 59.728 66.667 0.00 0.00 0.00 4.61
6126 9233 6.873605 TGTAGTACCAAATCAACTGAGTGATG 59.126 38.462 0.00 0.00 38.28 3.07
6262 9376 4.334552 TGAAAATTCAGGCTACATGAGCA 58.665 39.130 15.83 0.31 41.99 4.26
6655 9769 0.445436 GAAGCTGTCACGCATCTTGG 59.555 55.000 0.00 0.00 34.11 3.61
7009 11853 4.785511 TTTTTCCTTTGTTTGACGACCA 57.214 36.364 0.00 0.00 0.00 4.02
7620 13211 9.866655 AAAATGGATGAAGCAATTAGGTAGATA 57.133 29.630 0.00 0.00 0.00 1.98
7936 13527 2.584835 TCTAACCATGCAACCAGCTT 57.415 45.000 0.00 0.00 45.94 3.74
7996 13587 0.671251 TTCATTCCCACGGTGTTTGC 59.329 50.000 7.45 0.00 0.00 3.68
8382 13975 6.389906 CCTTTATTCATTTTCTTTGTCGGCT 58.610 36.000 0.00 0.00 0.00 5.52
8512 14105 9.095065 GACTCACTACTCAAAGTTAAAACTGAA 57.905 33.333 0.00 0.00 39.66 3.02
8683 14276 6.015027 GTGAGTCACACTGTCTTGTACTAT 57.985 41.667 18.54 0.00 45.13 2.12
8825 14418 2.035632 GGTTCATTGACCCAAACACCA 58.964 47.619 0.00 0.00 33.41 4.17
9058 14654 5.655488 CTCTGTCCGTTGAGTATTCTGAAT 58.345 41.667 8.14 8.14 0.00 2.57
9136 14732 8.519526 GGTACATGAACATTACCAAGATTTCAA 58.480 33.333 0.00 0.00 36.12 2.69


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

AutoCloner maintained by Alex Coulton.