Multiple sequence alignment - TraesCS7A01G089200

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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 TraesCS7A01G089200 chr7A 100.000 6296 0 0 1 6296 54194032 54187737 0.000000e+00 11627.0
1 TraesCS7A01G089200 chr7A 91.624 2961 160 34 2804 5745 436073257 436070366 0.000000e+00 4013.0
2 TraesCS7A01G089200 chr7A 97.440 1953 23 3 2531 4456 54150584 54148632 0.000000e+00 3304.0
3 TraesCS7A01G089200 chr7A 93.126 1542 65 7 4450 5989 54147590 54146088 0.000000e+00 2222.0
4 TraesCS7A01G089200 chr7A 98.369 981 16 0 1556 2536 54151720 54150740 0.000000e+00 1724.0
5 TraesCS7A01G089200 chr7A 87.810 968 53 25 403 1341 436076208 436075277 0.000000e+00 1074.0
6 TraesCS7A01G089200 chr7A 94.326 564 28 2 2178 2737 436073818 436073255 0.000000e+00 861.0
7 TraesCS7A01G089200 chr7A 81.936 847 55 23 1387 2176 436075047 436074242 1.490000e-175 627.0
8 TraesCS7A01G089200 chr7A 86.434 258 25 2 1 255 436095173 436094923 2.240000e-69 274.0
9 TraesCS7A01G089200 chr7A 88.462 78 5 2 2732 2805 250806268 250806345 2.420000e-14 91.6
10 TraesCS7A01G089200 chr7A 87.324 71 5 1 2733 2803 616747231 616747165 1.880000e-10 78.7
11 TraesCS7A01G089200 chr7B 92.362 3417 171 34 2175 5566 381511954 381508603 0.000000e+00 4782.0
12 TraesCS7A01G089200 chr7B 88.439 1358 101 22 1 1329 381514666 381513336 0.000000e+00 1587.0
13 TraesCS7A01G089200 chr7B 81.242 821 86 35 1393 2176 381513160 381512371 9.030000e-168 601.0
14 TraesCS7A01G089200 chr7B 88.312 77 5 1 2730 2802 372036731 372036655 8.690000e-14 89.8
15 TraesCS7A01G089200 chr7B 92.982 57 2 2 6008 6062 619060570 619060626 1.450000e-11 82.4
16 TraesCS7A01G089200 chr7D 92.891 3123 159 20 2804 5915 386662080 386659010 0.000000e+00 4479.0
17 TraesCS7A01G089200 chr7D 94.544 2456 107 14 298 2737 51689349 51686905 0.000000e+00 3768.0
18 TraesCS7A01G089200 chr7D 95.024 2090 64 13 3716 5779 51685914 51683839 0.000000e+00 3247.0
19 TraesCS7A01G089200 chr7D 88.467 1370 85 32 1 1341 386665346 386664021 0.000000e+00 1587.0
20 TraesCS7A01G089200 chr7D 94.559 919 36 6 2805 3717 51686906 51685996 0.000000e+00 1408.0
21 TraesCS7A01G089200 chr7D 95.187 561 26 1 2178 2737 386662638 386662078 0.000000e+00 885.0
22 TraesCS7A01G089200 chr7D 84.104 692 62 20 1522 2172 386663750 386663066 5.360000e-175 625.0
23 TraesCS7A01G089200 chr7D 92.177 294 23 0 1 294 51691916 51691623 3.510000e-112 416.0
24 TraesCS7A01G089200 chr7D 89.716 282 23 3 5765 6046 51683657 51683382 7.760000e-94 355.0
25 TraesCS7A01G089200 chr7D 92.478 226 17 0 6070 6295 51682584 51682359 2.190000e-84 324.0
26 TraesCS7A01G089200 chr4A 94.801 1308 45 8 2805 4098 666060626 666059328 0.000000e+00 2017.0
27 TraesCS7A01G089200 chr4A 89.439 1373 89 23 1 1341 666063516 666062168 0.000000e+00 1681.0
28 TraesCS7A01G089200 chr4A 94.318 1056 43 7 4359 5408 666058517 666057473 0.000000e+00 1602.0
29 TraesCS7A01G089200 chr4A 93.210 810 37 8 1376 2171 666062083 666061278 0.000000e+00 1175.0
30 TraesCS7A01G089200 chr4A 91.871 652 33 6 5394 6043 666057453 666056820 0.000000e+00 893.0
31 TraesCS7A01G089200 chr4A 94.322 546 29 2 2175 2719 666061197 666060653 0.000000e+00 835.0
32 TraesCS7A01G089200 chr4A 94.262 244 12 2 4124 4367 666059336 666059095 7.710000e-99 372.0
33 TraesCS7A01G089200 chrUn 85.489 317 36 3 4676 4989 26776026 26776335 7.870000e-84 322.0
34 TraesCS7A01G089200 chrUn 87.121 264 25 6 4371 4633 26775766 26776021 2.220000e-74 291.0
35 TraesCS7A01G089200 chrUn 89.333 75 5 1 2732 2803 215727632 215727706 2.420000e-14 91.6
36 TraesCS7A01G089200 chrUn 100.000 33 0 0 6032 6064 62939550 62939582 1.900000e-05 62.1
37 TraesCS7A01G089200 chr5A 86.567 268 29 4 4371 4638 493021962 493022222 7.990000e-74 289.0
38 TraesCS7A01G089200 chr5B 86.194 268 30 6 4371 4638 100047813 100048073 3.720000e-72 283.0
39 TraesCS7A01G089200 chr1D 87.742 155 17 2 6067 6221 41859460 41859612 5.010000e-41 180.0
40 TraesCS7A01G089200 chr3D 85.577 104 10 4 5744 5844 81716446 81716547 3.100000e-18 104.0
41 TraesCS7A01G089200 chr3D 85.507 69 9 1 5777 5844 285121527 285121459 3.150000e-08 71.3
42 TraesCS7A01G089200 chr2B 90.789 76 3 3 2735 2806 532093828 532093903 1.440000e-16 99.0
43 TraesCS7A01G089200 chr1A 93.939 66 3 1 2735 2799 38730066 38730001 1.440000e-16 99.0
44 TraesCS7A01G089200 chr2A 88.462 78 5 2 2732 2805 688574954 688574877 2.420000e-14 91.6
45 TraesCS7A01G089200 chr1B 88.462 78 6 2 2728 2803 634499481 634499557 2.420000e-14 91.6
46 TraesCS7A01G089200 chr3A 85.507 69 9 1 5777 5844 373346349 373346281 3.150000e-08 71.3
47 TraesCS7A01G089200 chr3B 84.722 72 7 3 5775 5844 127931573 127931642 1.130000e-07 69.4


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 TraesCS7A01G089200 chr7A 54187737 54194032 6295 True 11627.000000 11627 100.000000 1 6296 1 chr7A.!!$R1 6295
1 TraesCS7A01G089200 chr7A 54146088 54151720 5632 True 2416.666667 3304 96.311667 1556 5989 3 chr7A.!!$R4 4433
2 TraesCS7A01G089200 chr7A 436070366 436076208 5842 True 1643.750000 4013 88.924000 403 5745 4 chr7A.!!$R5 5342
3 TraesCS7A01G089200 chr7B 381508603 381514666 6063 True 2323.333333 4782 87.347667 1 5566 3 chr7B.!!$R2 5565
4 TraesCS7A01G089200 chr7D 386659010 386665346 6336 True 1894.000000 4479 90.162250 1 5915 4 chr7D.!!$R2 5914
5 TraesCS7A01G089200 chr7D 51682359 51691916 9557 True 1586.333333 3768 93.083000 1 6295 6 chr7D.!!$R1 6294
6 TraesCS7A01G089200 chr4A 666056820 666063516 6696 True 1225.000000 2017 93.174714 1 6043 7 chr4A.!!$R1 6042
7 TraesCS7A01G089200 chrUn 26775766 26776335 569 False 306.500000 322 86.305000 4371 4989 2 chrUn.!!$F3 618

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
545 2836 0.537828 GGGTAGGCCCGTGAAAACAA 60.538 55.000 0.00 0.0 46.51 2.83 F
546 2837 0.594602 GGTAGGCCCGTGAAAACAAC 59.405 55.000 0.00 0.0 0.00 3.32 F
648 2939 0.684153 ACAATTCATTCCAGCCCCCG 60.684 55.000 0.00 0.0 0.00 5.73 F
2022 4682 1.228063 CAGCAAGCACACTGAGGGT 60.228 57.895 0.00 0.0 35.90 4.34 F
2128 4788 1.441311 CTTTTGTGGTTGCCCGCTT 59.559 52.632 0.00 0.0 42.08 4.68 F
2373 5456 1.717032 TTCTACACTGTGAGCTGGGT 58.283 50.000 15.86 0.0 34.51 4.51 F
3942 7340 1.964223 TCGTGCTGATCTATCCCCTTC 59.036 52.381 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 5456 0.179059 TGTGCTGCGAAGGTCAGAAA 60.179 50.000 0.00 0.00 33.54 2.52 R
2632 5888 7.555965 AGCAGAAACACAACTTTTCCTAAAAT 58.444 30.769 0.00 0.00 34.07 1.82 R
2712 5968 4.397420 ACATGTTTTCACCATGCTAGACA 58.603 39.130 0.00 0.00 42.74 3.41 R
2899 6191 9.755064 ATGATTTGTAAGACGAAATAAGAAACG 57.245 29.630 0.00 0.00 0.00 3.60 R
4216 7625 2.961062 ACTCTGCAAGTTCAAGGCAAAT 59.039 40.909 0.00 0.00 37.06 2.32 R
4352 7761 4.278419 GCACAACCAGAACTAGTTTGGATT 59.722 41.667 28.55 20.14 35.89 3.01 R
5900 11203 0.103208 ATGAATCTCCCGCGACTGAC 59.897 55.000 8.23 0.00 0.00 3.51 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
65 66 1.068741 GGAAGGAGTACCGCGATTCAT 59.931 52.381 8.23 0.00 41.83 2.57
81 82 6.102663 GCGATTCATGTATCCTATGCTAACT 58.897 40.000 6.73 0.00 0.00 2.24
84 85 6.994421 TTCATGTATCCTATGCTAACTGGA 57.006 37.500 0.00 0.00 0.00 3.86
85 86 6.994421 TCATGTATCCTATGCTAACTGGAA 57.006 37.500 0.00 0.00 31.87 3.53
86 87 6.759272 TCATGTATCCTATGCTAACTGGAAC 58.241 40.000 0.00 0.00 31.87 3.62
95 96 6.761714 CCTATGCTAACTGGAACGATAACTTT 59.238 38.462 0.00 0.00 0.00 2.66
167 168 9.547279 AATCAATGAAGGTTTCTAGGGTAAATT 57.453 29.630 0.00 0.00 0.00 1.82
266 267 8.698210 AGCCATACACAAATCAATTATGTTGAT 58.302 29.630 3.17 3.17 40.57 2.57
503 2777 3.119849 GGGTTCATTCCACGAACATTCTG 60.120 47.826 5.50 0.00 43.70 3.02
543 2834 3.991999 GGGTAGGCCCGTGAAAAC 58.008 61.111 0.00 0.00 46.51 2.43
544 2835 1.073548 GGGTAGGCCCGTGAAAACA 59.926 57.895 0.00 0.00 46.51 2.83
545 2836 0.537828 GGGTAGGCCCGTGAAAACAA 60.538 55.000 0.00 0.00 46.51 2.83
546 2837 0.594602 GGTAGGCCCGTGAAAACAAC 59.405 55.000 0.00 0.00 0.00 3.32
547 2838 1.310904 GTAGGCCCGTGAAAACAACA 58.689 50.000 0.00 0.00 0.00 3.33
548 2839 1.265905 GTAGGCCCGTGAAAACAACAG 59.734 52.381 0.00 0.00 0.00 3.16
549 2840 1.106944 AGGCCCGTGAAAACAACAGG 61.107 55.000 0.00 0.00 0.00 4.00
550 2841 1.299850 GCCCGTGAAAACAACAGGC 60.300 57.895 0.00 0.00 0.00 4.85
551 2842 1.362355 CCCGTGAAAACAACAGGCC 59.638 57.895 0.00 0.00 0.00 5.19
552 2843 1.362355 CCGTGAAAACAACAGGCCC 59.638 57.895 0.00 0.00 0.00 5.80
573 2864 6.339730 GCCCATGAACACATATTTTGATCAA 58.660 36.000 3.38 3.38 0.00 2.57
642 2933 6.151648 ACACCAGAACATACAATTCATTCCAG 59.848 38.462 0.00 0.00 0.00 3.86
643 2934 5.126061 ACCAGAACATACAATTCATTCCAGC 59.874 40.000 0.00 0.00 0.00 4.85
644 2935 5.450965 CCAGAACATACAATTCATTCCAGCC 60.451 44.000 0.00 0.00 0.00 4.85
645 2936 4.646492 AGAACATACAATTCATTCCAGCCC 59.354 41.667 0.00 0.00 0.00 5.19
646 2937 3.299503 ACATACAATTCATTCCAGCCCC 58.700 45.455 0.00 0.00 0.00 5.80
647 2938 2.452600 TACAATTCATTCCAGCCCCC 57.547 50.000 0.00 0.00 0.00 5.40
648 2939 0.684153 ACAATTCATTCCAGCCCCCG 60.684 55.000 0.00 0.00 0.00 5.73
676 2970 1.293924 GCCATCGACATCCTTCACTG 58.706 55.000 0.00 0.00 0.00 3.66
695 2989 4.687948 CACTGCTGGTATCCATTATCTTCG 59.312 45.833 0.00 0.00 30.82 3.79
751 3045 1.947212 GCACCTTAACACTTACCCGGG 60.947 57.143 22.25 22.25 0.00 5.73
789 3083 7.709947 TGACATCTCATTGCCTTATTCAATTC 58.290 34.615 0.00 0.00 32.30 2.17
846 3140 1.760029 GGATCTGAGACTCCCCTGAAC 59.240 57.143 0.00 0.00 0.00 3.18
873 3167 1.412710 TCGGCGCTTTCTTCCATATCT 59.587 47.619 7.64 0.00 0.00 1.98
1040 3335 2.750237 GCCGTTGATGGGGTCCAC 60.750 66.667 0.00 0.00 35.80 4.02
1082 3404 7.148137 ACACGAAAAAGATTGTTACTCCAAACT 60.148 33.333 0.00 0.00 0.00 2.66
1275 3602 3.593442 TCCTCACAGTGGGAAATTTGT 57.407 42.857 0.33 0.00 0.00 2.83
1454 4008 6.588204 TGAGTTACAGTACAAATCCAGTTGT 58.412 36.000 0.00 0.00 43.95 3.32
1455 4009 7.728148 TGAGTTACAGTACAAATCCAGTTGTA 58.272 34.615 0.00 0.00 41.84 2.41
1456 4010 8.205512 TGAGTTACAGTACAAATCCAGTTGTAA 58.794 33.333 1.38 0.00 43.67 2.41
1457 4011 8.374327 AGTTACAGTACAAATCCAGTTGTAAC 57.626 34.615 15.66 15.66 43.67 2.50
1458 4012 7.443272 AGTTACAGTACAAATCCAGTTGTAACC 59.557 37.037 18.05 7.36 45.00 2.85
1459 4013 5.937111 ACAGTACAAATCCAGTTGTAACCT 58.063 37.500 1.38 0.00 43.67 3.50
1460 4014 5.763204 ACAGTACAAATCCAGTTGTAACCTG 59.237 40.000 12.43 12.43 43.67 4.00
1461 4015 5.763204 CAGTACAAATCCAGTTGTAACCTGT 59.237 40.000 1.38 0.00 43.67 4.00
1462 4016 5.763204 AGTACAAATCCAGTTGTAACCTGTG 59.237 40.000 1.38 0.00 43.67 3.66
1463 4017 4.532834 ACAAATCCAGTTGTAACCTGTGT 58.467 39.130 0.00 0.00 39.94 3.72
1464 4018 5.686753 ACAAATCCAGTTGTAACCTGTGTA 58.313 37.500 0.00 0.00 39.94 2.90
1465 4019 5.529800 ACAAATCCAGTTGTAACCTGTGTAC 59.470 40.000 0.00 0.00 39.94 2.90
1466 4020 3.374220 TCCAGTTGTAACCTGTGTACG 57.626 47.619 0.00 0.00 0.00 3.67
1467 4021 2.694628 TCCAGTTGTAACCTGTGTACGT 59.305 45.455 0.00 0.00 0.00 3.57
1468 4022 3.888323 TCCAGTTGTAACCTGTGTACGTA 59.112 43.478 0.00 0.00 0.00 3.57
1469 4023 4.523943 TCCAGTTGTAACCTGTGTACGTAT 59.476 41.667 0.00 0.00 0.00 3.06
1470 4024 5.709631 TCCAGTTGTAACCTGTGTACGTATA 59.290 40.000 0.00 0.00 0.00 1.47
1538 4134 8.977505 CAATTTGAAAACCCAATTACTGTACTG 58.022 33.333 0.00 0.00 0.00 2.74
1540 4136 4.214545 TGAAAACCCAATTACTGTACTGCG 59.785 41.667 0.00 0.00 0.00 5.18
1541 4137 3.412237 AACCCAATTACTGTACTGCGT 57.588 42.857 0.00 0.00 0.00 5.24
2022 4682 1.228063 CAGCAAGCACACTGAGGGT 60.228 57.895 0.00 0.00 35.90 4.34
2077 4737 2.747460 ACGCCCGCTACTACGACA 60.747 61.111 0.00 0.00 34.06 4.35
2128 4788 1.441311 CTTTTGTGGTTGCCCGCTT 59.559 52.632 0.00 0.00 42.08 4.68
2214 5297 4.468769 TACCGTGGCCTCCCCGAT 62.469 66.667 3.32 0.00 35.87 4.18
2363 5446 4.118410 GGATGCTCAGTCATTCTACACTG 58.882 47.826 0.00 0.00 41.32 3.66
2373 5456 1.717032 TTCTACACTGTGAGCTGGGT 58.283 50.000 15.86 0.00 34.51 4.51
2559 5814 6.069684 ACTATTCAGCTGCTTATTTGATGC 57.930 37.500 9.47 0.00 0.00 3.91
2632 5888 6.114767 TGTCATTCGAGATGATGATTTGGAA 58.885 36.000 11.63 0.00 0.00 3.53
2744 6011 3.244770 GGTGAAAACATGTACTCCCTCCA 60.245 47.826 0.00 0.00 0.00 3.86
2796 6088 7.653767 AAGTTGAGACACTTATTTTAGGACG 57.346 36.000 0.00 0.00 35.10 4.79
2899 6191 6.261118 ACTAATGATTACGAACGTGGAGTAC 58.739 40.000 10.14 0.00 0.00 2.73
3749 7147 4.541973 TTACTGCTGATCACTGACATGT 57.458 40.909 0.00 0.00 0.00 3.21
3942 7340 1.964223 TCGTGCTGATCTATCCCCTTC 59.036 52.381 0.00 0.00 0.00 3.46
4202 7611 9.540538 TGGTTTAATTATTTCCTGAAGGATGAA 57.459 29.630 0.00 0.00 44.98 2.57
4216 7625 6.714278 TGAAGGATGAAAACATCTGATCTGA 58.286 36.000 4.63 4.63 0.00 3.27
4589 9637 9.507329 AATTATTATCTGCGGACATATTTCTGT 57.493 29.630 0.00 0.00 0.00 3.41
4645 9695 1.754803 TGAGGATGGCCGTACTTGTAG 59.245 52.381 12.19 0.00 39.96 2.74
4690 9741 2.401583 AACATGCTCGTGGCTAATCA 57.598 45.000 0.00 0.00 42.39 2.57
4728 9779 1.886542 TCATCTACATCCACCCGATCG 59.113 52.381 8.51 8.51 0.00 3.69
4780 9831 2.485903 TGTGGTTAATCGTTTGCTCGT 58.514 42.857 0.00 0.00 0.00 4.18
4781 9832 3.651206 TGTGGTTAATCGTTTGCTCGTA 58.349 40.909 0.00 0.00 0.00 3.43
4782 9833 4.056740 TGTGGTTAATCGTTTGCTCGTAA 58.943 39.130 0.00 0.00 0.00 3.18
4783 9834 4.691685 TGTGGTTAATCGTTTGCTCGTAAT 59.308 37.500 0.00 0.00 0.00 1.89
5172 10243 3.691575 TGAAGTCTGGTTTTGGTGTTGA 58.308 40.909 0.00 0.00 0.00 3.18
5292 10363 2.726241 GGAACATGAAGCTGCGAAAAAC 59.274 45.455 0.00 0.00 0.00 2.43
5317 10388 1.452470 AACCGAAAACCACCGTGCT 60.452 52.632 0.00 0.00 0.00 4.40
5552 10657 4.868314 ACTTAAGTCCTCGTTGCTACTT 57.132 40.909 1.12 0.00 36.26 2.24
5569 10674 3.883830 ACTTGTTTGTTGTGCATTCCA 57.116 38.095 0.00 0.00 0.00 3.53
5576 10681 3.029320 TGTTGTGCATTCCAATTGAGC 57.971 42.857 7.12 6.14 0.00 4.26
5606 10715 1.154654 GCTGTTGCTCGCGTAACAC 60.155 57.895 17.49 12.63 40.16 3.32
5736 10845 2.873472 TGGAACGCGTGAATTTTACAGT 59.127 40.909 14.98 0.00 0.00 3.55
5756 10866 4.872691 CAGTAACTCTGCTTGGGATGTAAG 59.127 45.833 0.00 0.00 37.36 2.34
5764 10874 2.130821 TTGGGATGTAAGTGGCGCCA 62.131 55.000 29.03 29.03 0.00 5.69
5789 11092 2.035066 GGCCCGTTTAGTAGCTCGATAA 59.965 50.000 0.00 0.00 0.00 1.75
5852 11155 5.304101 CCAATAAGTGGGCTTATAAATGGCA 59.696 40.000 0.00 0.00 44.60 4.92
5946 11249 2.415224 GGTCTCTACCGGTTCTTCGTTC 60.415 54.545 15.04 0.00 35.62 3.95
5957 11260 3.247886 GGTTCTTCGTTCTGTTCCTCAAC 59.752 47.826 0.00 0.00 0.00 3.18
6010 11313 2.164338 GAAGTTGACCCGTCTCTCTCT 58.836 52.381 0.00 0.00 0.00 3.10
6011 11314 1.828979 AGTTGACCCGTCTCTCTCTC 58.171 55.000 0.00 0.00 0.00 3.20
6012 11315 0.812549 GTTGACCCGTCTCTCTCTCC 59.187 60.000 0.00 0.00 0.00 3.71
6067 11370 2.510918 GGAAACCCTAGCCGCGAC 60.511 66.667 8.23 0.00 0.00 5.19
6068 11371 2.884207 GAAACCCTAGCCGCGACG 60.884 66.667 8.23 0.00 0.00 5.12
6102 12179 2.281345 CCCATGGCTCGGATGCTC 60.281 66.667 6.09 0.00 0.00 4.26
6152 12229 1.679641 TGGCTGGTGATCGACGGTA 60.680 57.895 0.00 0.00 0.00 4.02
6166 12243 0.252375 ACGGTAGGTGGTGGTGGTAT 60.252 55.000 0.00 0.00 0.00 2.73
6170 12247 0.252974 TAGGTGGTGGTGGTATGGCT 60.253 55.000 0.00 0.00 0.00 4.75
6175 12252 1.303236 GTGGTGGTATGGCTGTGCA 60.303 57.895 0.00 0.00 0.00 4.57
6177 12254 1.303236 GGTGGTATGGCTGTGCACA 60.303 57.895 20.37 20.37 0.00 4.57
6183 12260 3.469008 GTATGGCTGTGCACATACCTA 57.531 47.619 29.15 19.91 42.11 3.08
6190 12267 2.872245 CTGTGCACATACCTATTTCGGG 59.128 50.000 22.00 0.00 0.00 5.14
6191 12268 1.602377 GTGCACATACCTATTTCGGGC 59.398 52.381 13.17 0.00 0.00 6.13
6205 12282 2.249535 CGGGCTTGGATCATGCGAG 61.250 63.158 0.00 0.00 35.73 5.03
6210 12287 1.153107 TTGGATCATGCGAGCTGGG 60.153 57.895 0.00 0.00 0.00 4.45
6287 12364 1.238625 GGCTACTCGATCCTCTCCGG 61.239 65.000 0.00 0.00 0.00 5.14
6295 12372 0.106419 GATCCTCTCCGGGACACTCT 60.106 60.000 0.00 0.00 38.30 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.451651 CCAAACAAAAAGCGCATCGAC 59.548 47.619 11.47 0.00 0.00 4.20
15 16 3.876320 TGGATTTCTGCCAAACAAAAAGC 59.124 39.130 0.00 0.00 31.13 3.51
65 66 4.891168 TCGTTCCAGTTAGCATAGGATACA 59.109 41.667 0.00 0.00 41.41 2.29
81 82 3.745799 TCCTGCAAAAGTTATCGTTCCA 58.254 40.909 0.00 0.00 0.00 3.53
84 85 5.790593 TCTACTCCTGCAAAAGTTATCGTT 58.209 37.500 6.01 0.00 0.00 3.85
85 86 5.401531 TCTACTCCTGCAAAAGTTATCGT 57.598 39.130 6.01 0.00 0.00 3.73
86 87 6.673316 GCTTTCTACTCCTGCAAAAGTTATCG 60.673 42.308 6.01 0.00 31.24 2.92
95 96 2.770164 GAGGCTTTCTACTCCTGCAA 57.230 50.000 0.00 0.00 0.00 4.08
167 168 5.367945 AAACTTCCAAGCCGGATATTCTA 57.632 39.130 5.05 0.00 45.80 2.10
340 2613 2.805671 TCGTTAAACTCTGGTGTGCATG 59.194 45.455 0.00 0.00 0.00 4.06
407 2681 3.719268 ACTCCCATTGATTGCACTACA 57.281 42.857 0.00 0.00 0.00 2.74
503 2777 1.376812 CTTGGGCCCGACACCTTAC 60.377 63.158 19.37 0.00 0.00 2.34
536 2827 1.686052 TCATGGGCCTGTTGTTTTCAC 59.314 47.619 4.53 0.00 0.00 3.18
537 2828 2.079170 TCATGGGCCTGTTGTTTTCA 57.921 45.000 4.53 0.00 0.00 2.69
538 2829 2.102252 TGTTCATGGGCCTGTTGTTTTC 59.898 45.455 4.53 0.00 0.00 2.29
539 2830 2.114616 TGTTCATGGGCCTGTTGTTTT 58.885 42.857 4.53 0.00 0.00 2.43
540 2831 1.412343 GTGTTCATGGGCCTGTTGTTT 59.588 47.619 4.53 0.00 0.00 2.83
541 2832 1.039856 GTGTTCATGGGCCTGTTGTT 58.960 50.000 4.53 0.00 0.00 2.83
542 2833 0.106268 TGTGTTCATGGGCCTGTTGT 60.106 50.000 4.53 0.00 0.00 3.32
543 2834 1.259609 ATGTGTTCATGGGCCTGTTG 58.740 50.000 4.53 0.00 32.51 3.33
544 2835 2.897271 TATGTGTTCATGGGCCTGTT 57.103 45.000 4.53 0.00 35.70 3.16
545 2836 3.386932 AATATGTGTTCATGGGCCTGT 57.613 42.857 4.53 0.00 35.70 4.00
546 2837 4.160065 TCAAAATATGTGTTCATGGGCCTG 59.840 41.667 4.53 0.24 35.70 4.85
547 2838 4.352009 TCAAAATATGTGTTCATGGGCCT 58.648 39.130 4.53 0.00 35.70 5.19
548 2839 4.734398 TCAAAATATGTGTTCATGGGCC 57.266 40.909 0.00 0.00 35.70 5.80
549 2840 5.904941 TGATCAAAATATGTGTTCATGGGC 58.095 37.500 0.00 0.00 35.70 5.36
550 2841 7.549839 AGTTGATCAAAATATGTGTTCATGGG 58.450 34.615 10.35 0.00 35.70 4.00
551 2842 9.726232 CTAGTTGATCAAAATATGTGTTCATGG 57.274 33.333 10.35 0.00 35.70 3.66
573 2864 9.197306 ACTGAAATTTAGGGTTTCAAAACTAGT 57.803 29.630 5.66 0.00 42.91 2.57
660 2951 1.134580 CCAGCAGTGAAGGATGTCGAT 60.135 52.381 0.00 0.00 0.00 3.59
663 2957 3.462021 GATACCAGCAGTGAAGGATGTC 58.538 50.000 8.14 0.72 0.00 3.06
676 2970 3.921021 CGACGAAGATAATGGATACCAGC 59.079 47.826 0.00 0.00 36.75 4.85
695 2989 1.614413 ACTGGAGAAGAGGAACACGAC 59.386 52.381 0.00 0.00 0.00 4.34
751 3045 5.784750 TGAGATGTCATTGTTCGATGAAC 57.215 39.130 4.53 2.80 42.26 3.18
789 3083 5.520376 AACCACAAAGAAAAGATGGTCAG 57.480 39.130 0.00 0.00 42.90 3.51
856 3150 1.265365 GCCAGATATGGAAGAAAGCGC 59.735 52.381 11.49 0.00 0.00 5.92
873 3167 3.573538 AGTATGTTTGACATGCTTTGCCA 59.426 39.130 5.94 0.00 46.95 4.92
1040 3335 2.066262 CGTGTACCACTTACTTGCCAG 58.934 52.381 0.00 0.00 31.34 4.85
1538 4134 4.601621 TTTTTGGCAAACCTTTAAACGC 57.398 36.364 13.10 0.00 36.63 4.84
1540 4136 6.685527 TCCATTTTTGGCAAACCTTTAAAC 57.314 33.333 13.10 0.00 36.63 2.01
1541 4137 7.112779 TCTTCCATTTTTGGCAAACCTTTAAA 58.887 30.769 13.10 3.47 36.63 1.52
2128 4788 1.547820 AGACAGAGCAAAGATCGAGCA 59.452 47.619 2.38 0.00 0.00 4.26
2214 5297 1.133945 TGCAGAACAGCCAAGTTACCA 60.134 47.619 0.00 0.00 0.00 3.25
2363 5446 2.934083 GGTCAGAAACCCAGCTCAC 58.066 57.895 0.00 0.00 42.85 3.51
2373 5456 0.179059 TGTGCTGCGAAGGTCAGAAA 60.179 50.000 0.00 0.00 33.54 2.52
2632 5888 7.555965 AGCAGAAACACAACTTTTCCTAAAAT 58.444 30.769 0.00 0.00 34.07 1.82
2712 5968 4.397420 ACATGTTTTCACCATGCTAGACA 58.603 39.130 0.00 0.00 42.74 3.41
2744 6011 7.839680 AAAGTTGAGACACTTATTTTGGGAT 57.160 32.000 0.00 0.00 35.87 3.85
2796 6088 4.530161 AGATCTGCTAGGTTGTATCCATCC 59.470 45.833 0.00 0.00 0.00 3.51
2899 6191 9.755064 ATGATTTGTAAGACGAAATAAGAAACG 57.245 29.630 0.00 0.00 0.00 3.60
4202 7611 5.713389 TCAAGGCAAATCAGATCAGATGTTT 59.287 36.000 0.79 0.00 0.00 2.83
4216 7625 2.961062 ACTCTGCAAGTTCAAGGCAAAT 59.039 40.909 0.00 0.00 37.06 2.32
4352 7761 4.278419 GCACAACCAGAACTAGTTTGGATT 59.722 41.667 28.55 20.14 35.89 3.01
4780 9831 4.216687 CCTTCACGGTTGCCTGTTTAATTA 59.783 41.667 0.00 0.00 0.00 1.40
4781 9832 3.005367 CCTTCACGGTTGCCTGTTTAATT 59.995 43.478 0.00 0.00 0.00 1.40
4782 9833 2.556622 CCTTCACGGTTGCCTGTTTAAT 59.443 45.455 0.00 0.00 0.00 1.40
4783 9834 1.950909 CCTTCACGGTTGCCTGTTTAA 59.049 47.619 0.00 0.00 0.00 1.52
5172 10243 4.065088 AGTGACACACAATTCTTATGCGT 58.935 39.130 8.59 0.00 36.74 5.24
5292 10363 1.269051 GGTGGTTTTCGGTTGCTTCAG 60.269 52.381 0.00 0.00 0.00 3.02
5552 10657 4.763073 TCAATTGGAATGCACAACAAACA 58.237 34.783 5.42 0.00 0.00 2.83
5576 10681 2.033757 AACAGCAGGCTCAGGCAG 59.966 61.111 0.00 0.00 40.87 4.85
5597 10702 1.083273 CGTTTGGGTGTGTTACGCG 60.083 57.895 3.53 3.53 44.60 6.01
5606 10715 3.224884 ACAAAGTGTTTCGTTTGGGTG 57.775 42.857 0.00 0.00 37.87 4.61
5736 10845 4.323485 CCACTTACATCCCAAGCAGAGTTA 60.323 45.833 0.00 0.00 0.00 2.24
5764 10874 0.981943 AGCTACTAAACGGGCCTTGT 59.018 50.000 0.84 0.00 0.00 3.16
5789 11092 6.428083 AAGGTTTTTACCGGGAAAATGAAT 57.572 33.333 25.04 9.79 34.28 2.57
5852 11155 0.541863 CCACGGAGCTTAGGGAATGT 59.458 55.000 0.00 0.00 0.00 2.71
5863 11166 2.552315 TCTTGACAAATTTCCACGGAGC 59.448 45.455 0.00 0.00 0.00 4.70
5900 11203 0.103208 ATGAATCTCCCGCGACTGAC 59.897 55.000 8.23 0.00 0.00 3.51
5940 11243 1.766496 AGGGTTGAGGAACAGAACGAA 59.234 47.619 0.00 0.00 33.27 3.85
5946 11249 4.402474 ACAAAAGAAAGGGTTGAGGAACAG 59.598 41.667 0.00 0.00 33.27 3.16
5957 11260 6.151144 CACTTATCAGGGTACAAAAGAAAGGG 59.849 42.308 0.00 0.00 0.00 3.95
6049 11352 3.777910 TCGCGGCTAGGGTTTCCC 61.778 66.667 6.13 0.00 45.90 3.97
6050 11353 2.510918 GTCGCGGCTAGGGTTTCC 60.511 66.667 1.90 0.00 0.00 3.13
6051 11354 2.884207 CGTCGCGGCTAGGGTTTC 60.884 66.667 9.90 0.00 0.00 2.78
6052 11355 4.446413 CCGTCGCGGCTAGGGTTT 62.446 66.667 9.90 0.00 41.17 3.27
6140 12217 0.179145 CACCACCTACCGTCGATCAC 60.179 60.000 0.00 0.00 0.00 3.06
6152 12229 1.541368 AGCCATACCACCACCACCT 60.541 57.895 0.00 0.00 0.00 4.00
6166 12243 3.278574 GAAATAGGTATGTGCACAGCCA 58.721 45.455 31.84 22.37 0.00 4.75
6170 12247 2.912771 CCCGAAATAGGTATGTGCACA 58.087 47.619 24.08 24.08 0.00 4.57
6175 12252 2.775384 TCCAAGCCCGAAATAGGTATGT 59.225 45.455 0.00 0.00 0.00 2.29
6177 12254 3.650942 TGATCCAAGCCCGAAATAGGTAT 59.349 43.478 0.00 0.00 0.00 2.73
6183 12260 1.035139 GCATGATCCAAGCCCGAAAT 58.965 50.000 0.00 0.00 0.00 2.17
6190 12267 1.647629 CAGCTCGCATGATCCAAGC 59.352 57.895 0.00 0.00 0.00 4.01
6191 12268 1.164662 CCCAGCTCGCATGATCCAAG 61.165 60.000 0.00 0.00 0.00 3.61
6210 12287 0.867746 GTCGTTACCGGGTTTTCACC 59.132 55.000 4.31 0.00 43.37 4.02
6263 12340 1.202830 AGAGGATCGAGTAGCCGTGAT 60.203 52.381 0.00 0.00 42.67 3.06
6266 12343 0.535553 GGAGAGGATCGAGTAGCCGT 60.536 60.000 0.00 0.00 42.67 5.68


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

AutoCloner maintained by Alex Coulton.