Multiple sequence alignment - TraesCS7A01G201600

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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 TraesCS7A01G201600 chr7A 100.000 2411 0 0 1 2411 163371612 163374022 0.000000e+00 4453.0
1 TraesCS7A01G201600 chr7A 95.981 622 18 2 1712 2327 671189471 671188851 0.000000e+00 1003.0
2 TraesCS7A01G201600 chr7A 88.226 654 35 15 811 1422 163364435 163365088 0.000000e+00 743.0
3 TraesCS7A01G201600 chr7A 82.413 688 69 28 787 1429 163360778 163361458 9.740000e-154 553.0
4 TraesCS7A01G201600 chr7A 79.647 850 90 39 662 1444 163234729 163235562 3.530000e-148 534.0
5 TraesCS7A01G201600 chr7A 79.849 794 69 49 690 1444 163299463 163300204 1.660000e-136 496.0
6 TraesCS7A01G201600 chr7A 80.798 677 69 33 788 1444 163353021 163353656 7.800000e-130 473.0
7 TraesCS7A01G201600 chr7A 80.228 263 21 6 553 797 163364025 163364274 4.120000e-38 169.0
8 TraesCS7A01G201600 chr7D 87.222 1213 74 23 510 1649 162628675 162629879 0.000000e+00 1306.0
9 TraesCS7A01G201600 chr7D 85.965 798 54 25 673 1427 162219034 162219816 0.000000e+00 800.0
10 TraesCS7A01G201600 chr7D 83.309 683 76 22 788 1444 162201183 162201853 1.600000e-166 595.0
11 TraesCS7A01G201600 chr7D 82.551 682 65 32 788 1444 162214427 162215079 3.500000e-153 551.0
12 TraesCS7A01G201600 chr7D 93.803 355 20 2 1969 2323 28382845 28383197 1.270000e-147 532.0
13 TraesCS7A01G201600 chr7D 78.523 880 105 41 612 1444 162129966 162130808 3.580000e-138 501.0
14 TraesCS7A01G201600 chr7D 80.355 733 81 42 754 1443 162114907 162115619 4.630000e-137 497.0
15 TraesCS7A01G201600 chr7D 96.887 257 8 0 1712 1968 28368911 28369167 4.760000e-117 431.0
16 TraesCS7A01G201600 chr7D 81.905 210 25 9 690 891 162190784 162190988 5.330000e-37 165.0
17 TraesCS7A01G201600 chr1A 96.135 621 18 1 1712 2326 549415334 549414714 0.000000e+00 1009.0
18 TraesCS7A01G201600 chr6A 96.123 619 20 1 1712 2326 88095900 88095282 0.000000e+00 1007.0
19 TraesCS7A01G201600 chr6A 94.516 620 24 2 1712 2331 479404527 479403918 0.000000e+00 948.0
20 TraesCS7A01G201600 chr6A 92.473 93 4 2 2239 2328 479403939 479403847 1.950000e-26 130.0
21 TraesCS7A01G201600 chr5B 96.460 565 14 1 1712 2270 522907590 522908154 0.000000e+00 928.0
22 TraesCS7A01G201600 chr5B 82.101 514 85 6 5 513 660692549 660693060 1.320000e-117 433.0
23 TraesCS7A01G201600 chr7B 88.131 733 43 14 728 1419 124548554 124549283 0.000000e+00 832.0
24 TraesCS7A01G201600 chr7B 78.748 1054 128 58 598 1578 124257011 124258041 3.410000e-173 617.0
25 TraesCS7A01G201600 chr7B 80.930 839 99 35 601 1409 124531207 124532014 7.370000e-170 606.0
26 TraesCS7A01G201600 chr7B 81.600 750 83 26 726 1437 124536333 124537065 9.670000e-159 569.0
27 TraesCS7A01G201600 chr7B 80.024 836 99 40 651 1444 124140998 124141807 7.530000e-155 556.0
28 TraesCS7A01G201600 chr7B 83.628 623 57 27 846 1444 124360198 124360799 5.860000e-151 544.0
29 TraesCS7A01G201600 chr7B 79.554 807 90 48 690 1444 124236121 124236904 7.690000e-140 507.0
30 TraesCS7A01G201600 chr7B 84.457 534 46 20 936 1444 124129381 124129902 2.150000e-135 492.0
31 TraesCS7A01G201600 chr7B 75.812 277 48 13 612 887 124137410 124137668 3.260000e-24 122.0
32 TraesCS7A01G201600 chr7B 87.342 79 10 0 617 695 124548477 124548555 9.180000e-15 91.6
33 TraesCS7A01G201600 chr4A 82.685 514 82 6 5 513 684949653 684950164 1.310000e-122 449.0
34 TraesCS7A01G201600 chr4A 82.330 515 82 8 5 513 597728857 597729368 2.850000e-119 438.0
35 TraesCS7A01G201600 chr3A 82.490 514 83 6 5 513 87795638 87795127 6.120000e-121 444.0
36 TraesCS7A01G201600 chr4B 82.296 514 84 6 5 513 612337422 612336911 2.850000e-119 438.0
37 TraesCS7A01G201600 chr5A 82.101 514 84 7 5 513 10296700 10296190 1.320000e-117 433.0
38 TraesCS7A01G201600 chr5D 81.907 514 86 6 5 513 15726329 15725818 6.160000e-116 427.0
39 TraesCS7A01G201600 chr5D 81.942 515 84 8 5 513 477879214 477878703 6.160000e-116 427.0
40 TraesCS7A01G201600 chr1B 81.907 514 86 6 5 513 59521278 59521789 6.160000e-116 427.0


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 TraesCS7A01G201600 chr7A 163371612 163374022 2410 False 4453.000000 4453 100.000000 1 2411 1 chr7A.!!$F4 2410
1 TraesCS7A01G201600 chr7A 671188851 671189471 620 True 1003.000000 1003 95.981000 1712 2327 1 chr7A.!!$R1 615
2 TraesCS7A01G201600 chr7A 163234729 163235562 833 False 534.000000 534 79.647000 662 1444 1 chr7A.!!$F1 782
3 TraesCS7A01G201600 chr7A 163299463 163300204 741 False 496.000000 496 79.849000 690 1444 1 chr7A.!!$F2 754
4 TraesCS7A01G201600 chr7A 163360778 163365088 4310 False 488.333333 743 83.622333 553 1429 3 chr7A.!!$F5 876
5 TraesCS7A01G201600 chr7A 163353021 163353656 635 False 473.000000 473 80.798000 788 1444 1 chr7A.!!$F3 656
6 TraesCS7A01G201600 chr7D 162628675 162629879 1204 False 1306.000000 1306 87.222000 510 1649 1 chr7D.!!$F7 1139
7 TraesCS7A01G201600 chr7D 162214427 162219816 5389 False 675.500000 800 84.258000 673 1444 2 chr7D.!!$F8 771
8 TraesCS7A01G201600 chr7D 162201183 162201853 670 False 595.000000 595 83.309000 788 1444 1 chr7D.!!$F6 656
9 TraesCS7A01G201600 chr7D 162129966 162130808 842 False 501.000000 501 78.523000 612 1444 1 chr7D.!!$F4 832
10 TraesCS7A01G201600 chr7D 162114907 162115619 712 False 497.000000 497 80.355000 754 1443 1 chr7D.!!$F3 689
11 TraesCS7A01G201600 chr1A 549414714 549415334 620 True 1009.000000 1009 96.135000 1712 2326 1 chr1A.!!$R1 614
12 TraesCS7A01G201600 chr6A 88095282 88095900 618 True 1007.000000 1007 96.123000 1712 2326 1 chr6A.!!$R1 614
13 TraesCS7A01G201600 chr6A 479403847 479404527 680 True 539.000000 948 93.494500 1712 2331 2 chr6A.!!$R2 619
14 TraesCS7A01G201600 chr5B 522907590 522908154 564 False 928.000000 928 96.460000 1712 2270 1 chr5B.!!$F1 558
15 TraesCS7A01G201600 chr5B 660692549 660693060 511 False 433.000000 433 82.101000 5 513 1 chr5B.!!$F2 508
16 TraesCS7A01G201600 chr7B 124257011 124258041 1030 False 617.000000 617 78.748000 598 1578 1 chr7B.!!$F3 980
17 TraesCS7A01G201600 chr7B 124531207 124532014 807 False 606.000000 606 80.930000 601 1409 1 chr7B.!!$F5 808
18 TraesCS7A01G201600 chr7B 124536333 124537065 732 False 569.000000 569 81.600000 726 1437 1 chr7B.!!$F6 711
19 TraesCS7A01G201600 chr7B 124360198 124360799 601 False 544.000000 544 83.628000 846 1444 1 chr7B.!!$F4 598
20 TraesCS7A01G201600 chr7B 124236121 124236904 783 False 507.000000 507 79.554000 690 1444 1 chr7B.!!$F2 754
21 TraesCS7A01G201600 chr7B 124129381 124129902 521 False 492.000000 492 84.457000 936 1444 1 chr7B.!!$F1 508
22 TraesCS7A01G201600 chr7B 124548477 124549283 806 False 461.800000 832 87.736500 617 1419 2 chr7B.!!$F8 802
23 TraesCS7A01G201600 chr7B 124137410 124141807 4397 False 339.000000 556 77.918000 612 1444 2 chr7B.!!$F7 832
24 TraesCS7A01G201600 chr4A 684949653 684950164 511 False 449.000000 449 82.685000 5 513 1 chr4A.!!$F2 508
25 TraesCS7A01G201600 chr4A 597728857 597729368 511 False 438.000000 438 82.330000 5 513 1 chr4A.!!$F1 508
26 TraesCS7A01G201600 chr3A 87795127 87795638 511 True 444.000000 444 82.490000 5 513 1 chr3A.!!$R1 508
27 TraesCS7A01G201600 chr4B 612336911 612337422 511 True 438.000000 438 82.296000 5 513 1 chr4B.!!$R1 508
28 TraesCS7A01G201600 chr5A 10296190 10296700 510 True 433.000000 433 82.101000 5 513 1 chr5A.!!$R1 508
29 TraesCS7A01G201600 chr5D 15725818 15726329 511 True 427.000000 427 81.907000 5 513 1 chr5D.!!$R1 508
30 TraesCS7A01G201600 chr5D 477878703 477879214 511 True 427.000000 427 81.942000 5 513 1 chr5D.!!$R2 508
31 TraesCS7A01G201600 chr1B 59521278 59521789 511 False 427.000000 427 81.907000 5 513 1 chr1B.!!$F1 508

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
232 235 0.110486 ACCGCCTCAACCACAGATTT 59.89 50.0 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 9551 0.377203 CGAGCTTGTTATTTCCCGGC 59.623 55.0 0.0 0.0 0.0 6.13 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
24 25 0.251354 CTTGGCTAGCAAGGAGAGCA 59.749 55.000 18.24 0.00 37.98 4.26
42 43 7.039714 AGGAGAGCATGGTTAAAAACTTTAAGG 60.040 37.037 0.00 0.00 0.00 2.69
43 44 6.993079 AGAGCATGGTTAAAAACTTTAAGGG 58.007 36.000 0.00 0.00 0.00 3.95
55 56 3.421844 ACTTTAAGGGCTTTGAATCGCT 58.578 40.909 0.00 0.00 0.00 4.93
56 57 3.440522 ACTTTAAGGGCTTTGAATCGCTC 59.559 43.478 0.00 0.00 0.00 5.03
63 64 1.945819 GCTTTGAATCGCTCACCTCCA 60.946 52.381 0.00 0.00 32.21 3.86
66 67 0.904649 TGAATCGCTCACCTCCATGT 59.095 50.000 0.00 0.00 0.00 3.21
67 68 1.278985 TGAATCGCTCACCTCCATGTT 59.721 47.619 0.00 0.00 0.00 2.71
96 98 5.581085 CGACCTGTAATTTTCTCCCAACTAG 59.419 44.000 0.00 0.00 0.00 2.57
99 101 5.581085 CCTGTAATTTTCTCCCAACTAGACG 59.419 44.000 0.00 0.00 0.00 4.18
101 103 6.395629 TGTAATTTTCTCCCAACTAGACGAG 58.604 40.000 0.00 0.00 0.00 4.18
108 110 4.141228 TCTCCCAACTAGACGAGTGGATAT 60.141 45.833 0.00 0.00 38.87 1.63
114 116 2.054232 AGACGAGTGGATATGTCGGT 57.946 50.000 0.00 0.00 38.03 4.69
134 136 4.263025 CGGTGATCATTATCATCTCCCCAA 60.263 45.833 0.00 0.00 43.87 4.12
140 142 6.773976 TCATTATCATCTCCCCAACAAAAC 57.226 37.500 0.00 0.00 0.00 2.43
155 157 5.240183 CCAACAAAACTCTCTGATCATGTGT 59.760 40.000 0.00 0.00 0.00 3.72
206 208 8.116136 GGAAACTTAAAAACACTCATTGCAAAG 58.884 33.333 1.71 0.00 0.00 2.77
210 212 4.734398 AAAACACTCATTGCAAAGGTGA 57.266 36.364 25.55 15.78 32.09 4.02
214 216 2.227388 CACTCATTGCAAAGGTGAGGAC 59.773 50.000 24.97 0.00 42.75 3.85
227 229 2.847234 AGGACCGCCTCAACCACA 60.847 61.111 0.00 0.00 42.19 4.17
232 235 0.110486 ACCGCCTCAACCACAGATTT 59.890 50.000 0.00 0.00 0.00 2.17
236 239 3.443681 CCGCCTCAACCACAGATTTATTT 59.556 43.478 0.00 0.00 0.00 1.40
238 241 4.675146 CGCCTCAACCACAGATTTATTTGG 60.675 45.833 0.00 0.00 35.06 3.28
239 242 4.220602 GCCTCAACCACAGATTTATTTGGT 59.779 41.667 0.00 0.00 44.52 3.67
247 250 6.209391 ACCACAGATTTATTTGGTTCTCCTTG 59.791 38.462 0.00 0.00 39.41 3.61
255 258 0.620556 TGGTTCTCCTTGGCTCCATC 59.379 55.000 0.00 0.00 34.23 3.51
298 301 7.336176 CAGTTCAATCATTCATTCTCTTCCTCA 59.664 37.037 0.00 0.00 0.00 3.86
305 308 9.917887 ATCATTCATTCTCTTCCTCACTTTATT 57.082 29.630 0.00 0.00 0.00 1.40
310 313 9.354673 TCATTCTCTTCCTCACTTTATTTTTGT 57.645 29.630 0.00 0.00 0.00 2.83
313 318 7.940850 TCTCTTCCTCACTTTATTTTTGTTGG 58.059 34.615 0.00 0.00 0.00 3.77
327 332 9.549078 TTATTTTTGTTGGTTGAATTTACCCTC 57.451 29.630 7.88 3.17 34.66 4.30
334 339 5.505780 TGGTTGAATTTACCCTCTACCATG 58.494 41.667 7.88 0.00 40.85 3.66
348 354 1.496060 ACCATGCGTCCTCTGGAATA 58.504 50.000 0.00 0.00 31.38 1.75
374 380 7.530863 GGCAAACCTAGTTATTTCTCTTCAAG 58.469 38.462 0.00 0.00 0.00 3.02
376 382 8.231161 GCAAACCTAGTTATTTCTCTTCAAGAC 58.769 37.037 0.00 0.00 32.27 3.01
396 402 5.484173 GACTCACAGTCACAACATTCAAA 57.516 39.130 0.00 0.00 44.45 2.69
398 404 6.266168 ACTCACAGTCACAACATTCAAAAA 57.734 33.333 0.00 0.00 0.00 1.94
453 459 3.576078 TTGTTTCCAAGGAGCAGAGAA 57.424 42.857 0.00 0.00 0.00 2.87
477 483 4.747108 CGTTTAGATGGACTGATTAGCTGG 59.253 45.833 0.00 0.00 0.00 4.85
496 502 1.520342 CCAGTGGCTCGCTCTTAGC 60.520 63.158 0.00 0.00 39.33 3.09
519 525 2.408271 TCAGGATGTGCTTGATCACC 57.592 50.000 0.00 0.00 37.40 4.02
520 526 1.629861 TCAGGATGTGCTTGATCACCA 59.370 47.619 0.00 0.00 37.40 4.17
539 545 7.473735 TCACCATTTGCTTTATTTATGTCCA 57.526 32.000 0.00 0.00 0.00 4.02
556 562 5.538849 TGTCCATGTACTGTAGTTTGACA 57.461 39.130 0.00 6.24 0.00 3.58
610 616 2.948720 GCCTCGGCCTCTTGTGTCT 61.949 63.158 0.00 0.00 34.56 3.41
644 4200 0.678048 GGAGTCGGCAGCAGGAAAAT 60.678 55.000 0.00 0.00 0.00 1.82
649 4205 1.065199 TCGGCAGCAGGAAAATGATCT 60.065 47.619 0.00 0.00 0.00 2.75
705 4664 4.150980 CCGAATTAACAACTCAACGTGCTA 59.849 41.667 0.00 0.00 0.00 3.49
717 4677 3.696084 GTGCTACACGAGGGGAGT 58.304 61.111 0.00 0.00 0.00 3.85
733 4701 1.270147 GGAGTATACCATCCACCACGC 60.270 57.143 6.34 0.00 35.54 5.34
1029 5153 4.243008 GGGAGCGCTAAGGGCCTC 62.243 72.222 11.50 0.00 42.59 4.70
1257 9016 4.724602 GAGCTGCTCCGTGTCGCA 62.725 66.667 18.80 0.00 34.54 5.10
1324 9110 0.391661 GCAGCGGTTCATGGAGAAGA 60.392 55.000 0.00 0.00 36.78 2.87
1332 9126 1.207791 TCATGGAGAAGAGGAAGGGC 58.792 55.000 0.00 0.00 0.00 5.19
1387 9187 4.373116 ACGGCGATGCGTCCTGTT 62.373 61.111 16.62 0.00 0.00 3.16
1422 9225 3.299340 ACGCTCTAGTTCGTGTTCAAT 57.701 42.857 10.30 0.00 37.55 2.57
1445 9259 4.589798 TCGTACTCTAGAGTAGCCTGAGAT 59.410 45.833 29.00 5.26 43.84 2.75
1446 9260 4.688879 CGTACTCTAGAGTAGCCTGAGATG 59.311 50.000 29.00 11.88 43.84 2.90
1449 9263 4.080015 ACTCTAGAGTAGCCTGAGATGTGT 60.080 45.833 24.04 0.00 40.43 3.72
1480 9325 1.461127 GTCGATGTGTGTCTTTGCTCC 59.539 52.381 0.00 0.00 0.00 4.70
1481 9326 0.798776 CGATGTGTGTCTTTGCTCCC 59.201 55.000 0.00 0.00 0.00 4.30
1494 9339 6.095860 TGTCTTTGCTCCCAATTATGATCAAG 59.904 38.462 0.00 0.00 0.00 3.02
1498 9343 6.889301 TGCTCCCAATTATGATCAAGATTC 57.111 37.500 0.00 0.00 0.00 2.52
1514 9359 7.563888 TCAAGATTCTTGCTCTGAATTATGG 57.436 36.000 19.53 0.00 34.67 2.74
1550 9395 4.327087 GCTGTTCTTGTTTTGACAAACTGG 59.673 41.667 0.00 0.00 42.61 4.00
1564 9409 1.909700 AACTGGTCATGGCGAATTGT 58.090 45.000 0.00 0.00 0.00 2.71
1565 9410 1.909700 ACTGGTCATGGCGAATTGTT 58.090 45.000 0.00 0.00 0.00 2.83
1586 9431 5.351189 TGTTGAGGTGTCAAATCATACATCG 59.649 40.000 0.00 0.00 44.44 3.84
1591 9436 4.201812 GGTGTCAAATCATACATCGTGTGG 60.202 45.833 1.58 0.00 0.00 4.17
1621 9466 1.742768 CCGGGAATCTCTTCGAGGG 59.257 63.158 0.00 0.00 31.75 4.30
1662 9507 3.429141 CTGCCCGCAGTGCTTGAG 61.429 66.667 14.33 0.00 39.10 3.02
1689 9534 3.490759 CTGTGCGCGTCCATCCAC 61.491 66.667 8.43 6.66 0.00 4.02
1694 9539 4.530857 CGCGTCCATCCACCCCTC 62.531 72.222 0.00 0.00 0.00 4.30
1695 9540 4.530857 GCGTCCATCCACCCCTCG 62.531 72.222 0.00 0.00 0.00 4.63
1696 9541 3.075005 CGTCCATCCACCCCTCGT 61.075 66.667 0.00 0.00 0.00 4.18
1697 9542 2.901042 GTCCATCCACCCCTCGTC 59.099 66.667 0.00 0.00 0.00 4.20
1698 9543 1.686110 GTCCATCCACCCCTCGTCT 60.686 63.158 0.00 0.00 0.00 4.18
1699 9544 1.080354 TCCATCCACCCCTCGTCTT 59.920 57.895 0.00 0.00 0.00 3.01
1700 9545 0.976073 TCCATCCACCCCTCGTCTTC 60.976 60.000 0.00 0.00 0.00 2.87
1701 9546 1.522569 CATCCACCCCTCGTCTTCC 59.477 63.158 0.00 0.00 0.00 3.46
1702 9547 1.689582 ATCCACCCCTCGTCTTCCC 60.690 63.158 0.00 0.00 0.00 3.97
1703 9548 3.771160 CCACCCCTCGTCTTCCCG 61.771 72.222 0.00 0.00 0.00 5.14
1704 9549 2.995574 CACCCCTCGTCTTCCCGT 60.996 66.667 0.00 0.00 0.00 5.28
1705 9550 2.203743 ACCCCTCGTCTTCCCGTT 60.204 61.111 0.00 0.00 0.00 4.44
1706 9551 2.264794 CCCCTCGTCTTCCCGTTG 59.735 66.667 0.00 0.00 0.00 4.10
1707 9552 2.434359 CCCTCGTCTTCCCGTTGC 60.434 66.667 0.00 0.00 0.00 4.17
1708 9553 2.434359 CCTCGTCTTCCCGTTGCC 60.434 66.667 0.00 0.00 0.00 4.52
1709 9554 2.809601 CTCGTCTTCCCGTTGCCG 60.810 66.667 0.00 0.00 0.00 5.69
1892 9737 3.012518 CCTTGTTGCTGGACTTCCTATG 58.987 50.000 0.00 0.00 36.82 2.23
2079 9924 4.447724 GCGATGTGTCTTGTGAGAAGTTAA 59.552 41.667 0.00 0.00 32.66 2.01
2083 9928 3.184581 GTGTCTTGTGAGAAGTTAAGCGG 59.815 47.826 0.00 0.00 32.66 5.52
2150 10001 2.302587 TTTCCCGCCAGGATTCTTTT 57.697 45.000 0.00 0.00 46.94 2.27
2195 10046 7.661847 GGAAACTTTCCTGTGAAATAGAGAAGA 59.338 37.037 12.69 0.00 46.57 2.87
2197 10048 7.546250 ACTTTCCTGTGAAATAGAGAAGAGA 57.454 36.000 0.00 0.00 39.65 3.10
2203 10054 9.442047 TCCTGTGAAATAGAGAAGAGAAAAATC 57.558 33.333 0.00 0.00 0.00 2.17
2257 10182 6.816640 CCTGTAAATCAAACGATTACCAGAGA 59.183 38.462 12.20 0.00 35.12 3.10
2328 10253 6.260493 CCATGAATCAAAGGAGCTCTAAGAAG 59.740 42.308 14.64 0.00 0.00 2.85
2329 10254 6.611613 TGAATCAAAGGAGCTCTAAGAAGA 57.388 37.500 14.64 5.24 0.00 2.87
2338 10263 1.475403 CTCTAAGAAGAGCCCGTCCA 58.525 55.000 0.00 0.00 42.79 4.02
2339 10264 1.135333 CTCTAAGAAGAGCCCGTCCAC 59.865 57.143 0.00 0.00 42.79 4.02
2340 10265 0.175989 CTAAGAAGAGCCCGTCCACC 59.824 60.000 0.00 0.00 0.00 4.61
2341 10266 1.601419 TAAGAAGAGCCCGTCCACCG 61.601 60.000 0.00 0.00 0.00 4.94
2342 10267 3.379445 GAAGAGCCCGTCCACCGA 61.379 66.667 0.00 0.00 39.56 4.69
2343 10268 2.683933 AAGAGCCCGTCCACCGAT 60.684 61.111 0.00 0.00 39.56 4.18
2344 10269 2.907897 GAAGAGCCCGTCCACCGATG 62.908 65.000 0.00 0.00 39.56 3.84
2348 10273 4.530857 CCCGTCCACCGATGCCTC 62.531 72.222 0.00 0.00 39.56 4.70
2349 10274 4.530857 CCGTCCACCGATGCCTCC 62.531 72.222 0.00 0.00 39.56 4.30
2350 10275 4.873129 CGTCCACCGATGCCTCCG 62.873 72.222 0.00 0.00 39.56 4.63
2351 10276 3.458163 GTCCACCGATGCCTCCGA 61.458 66.667 0.00 0.00 0.00 4.55
2352 10277 3.147595 TCCACCGATGCCTCCGAG 61.148 66.667 0.00 0.00 0.00 4.63
2353 10278 3.147595 CCACCGATGCCTCCGAGA 61.148 66.667 0.00 0.00 0.00 4.04
2354 10279 2.721167 CCACCGATGCCTCCGAGAA 61.721 63.158 0.00 0.00 0.00 2.87
2355 10280 1.519455 CACCGATGCCTCCGAGAAC 60.519 63.158 0.00 0.00 0.00 3.01
2356 10281 1.682684 ACCGATGCCTCCGAGAACT 60.683 57.895 0.00 0.00 0.00 3.01
2357 10282 1.227089 CCGATGCCTCCGAGAACTG 60.227 63.158 0.00 0.00 0.00 3.16
2358 10283 1.880340 CGATGCCTCCGAGAACTGC 60.880 63.158 0.00 0.00 0.00 4.40
2359 10284 1.519719 GATGCCTCCGAGAACTGCT 59.480 57.895 0.00 0.00 0.00 4.24
2360 10285 0.529555 GATGCCTCCGAGAACTGCTC 60.530 60.000 0.00 0.00 40.38 4.26
2361 10286 0.975040 ATGCCTCCGAGAACTGCTCT 60.975 55.000 0.00 0.00 41.66 4.09
2362 10287 1.188219 TGCCTCCGAGAACTGCTCTT 61.188 55.000 0.00 0.00 41.66 2.85
2363 10288 0.739112 GCCTCCGAGAACTGCTCTTG 60.739 60.000 0.00 0.00 41.66 3.02
2364 10289 0.739112 CCTCCGAGAACTGCTCTTGC 60.739 60.000 0.00 0.00 41.66 4.01
2365 10290 1.075425 CTCCGAGAACTGCTCTTGCG 61.075 60.000 0.00 0.00 41.66 4.85
2372 10297 2.866028 CTGCTCTTGCGGTCTTGC 59.134 61.111 0.00 0.00 43.34 4.01
2373 10298 2.669569 TGCTCTTGCGGTCTTGCC 60.670 61.111 0.00 0.00 43.34 4.52
2399 10324 4.680237 CACCGACGAGCCTGCCAA 62.680 66.667 0.00 0.00 0.00 4.52
2400 10325 4.681978 ACCGACGAGCCTGCCAAC 62.682 66.667 0.00 0.00 0.00 3.77
2401 10326 4.379243 CCGACGAGCCTGCCAACT 62.379 66.667 0.00 0.00 0.00 3.16
2402 10327 2.357517 CGACGAGCCTGCCAACTT 60.358 61.111 0.00 0.00 0.00 2.66
2403 10328 1.961277 CGACGAGCCTGCCAACTTT 60.961 57.895 0.00 0.00 0.00 2.66
2404 10329 1.576421 GACGAGCCTGCCAACTTTG 59.424 57.895 0.00 0.00 0.00 2.77
2405 10330 0.884704 GACGAGCCTGCCAACTTTGA 60.885 55.000 0.00 0.00 0.00 2.69
2406 10331 1.166531 ACGAGCCTGCCAACTTTGAC 61.167 55.000 0.00 0.00 0.00 3.18
2407 10332 1.576421 GAGCCTGCCAACTTTGACG 59.424 57.895 0.00 0.00 0.00 4.35
2408 10333 2.050077 GCCTGCCAACTTTGACGC 60.050 61.111 0.00 0.00 0.00 5.19
2409 10334 2.252260 CCTGCCAACTTTGACGCG 59.748 61.111 3.53 3.53 0.00 6.01
2410 10335 2.427410 CTGCCAACTTTGACGCGC 60.427 61.111 5.73 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.179936 ACCATGCTCTCCTTGCTAGC 59.820 55.000 8.10 8.10 36.77 3.42
15 16 6.731292 AAAGTTTTTAACCATGCTCTCCTT 57.269 33.333 0.00 0.00 0.00 3.36
24 25 7.797062 TCAAAGCCCTTAAAGTTTTTAACCAT 58.203 30.769 0.00 0.00 0.00 3.55
42 43 0.729690 GAGGTGAGCGATTCAAAGCC 59.270 55.000 0.00 0.00 37.61 4.35
43 44 0.729690 GGAGGTGAGCGATTCAAAGC 59.270 55.000 0.00 0.00 37.61 3.51
67 68 5.828859 TGGGAGAAAATTACAGGTCGAAAAA 59.171 36.000 0.00 0.00 0.00 1.94
72 73 4.324267 AGTTGGGAGAAAATTACAGGTCG 58.676 43.478 0.00 0.00 0.00 4.79
73 74 6.594547 GTCTAGTTGGGAGAAAATTACAGGTC 59.405 42.308 0.00 0.00 0.00 3.85
74 75 6.473758 GTCTAGTTGGGAGAAAATTACAGGT 58.526 40.000 0.00 0.00 0.00 4.00
82 84 3.006537 CCACTCGTCTAGTTGGGAGAAAA 59.993 47.826 8.38 0.00 35.76 2.29
96 98 1.674441 TCACCGACATATCCACTCGTC 59.326 52.381 0.00 0.00 0.00 4.20
99 101 4.527509 ATGATCACCGACATATCCACTC 57.472 45.455 0.00 0.00 0.00 3.51
101 103 6.398095 TGATAATGATCACCGACATATCCAC 58.602 40.000 0.00 0.00 37.15 4.02
108 110 4.021104 GGGAGATGATAATGATCACCGACA 60.021 45.833 0.00 0.00 44.90 4.35
114 116 5.910355 TGTTGGGGAGATGATAATGATCA 57.090 39.130 0.00 0.00 46.13 2.92
134 136 7.389232 TCATACACATGATCAGAGAGTTTTGT 58.611 34.615 0.00 0.00 36.22 2.83
140 142 5.456548 AGCTCATACACATGATCAGAGAG 57.543 43.478 0.00 0.69 40.40 3.20
155 157 4.836825 CAACCCTTTCTGAGAAGCTCATA 58.163 43.478 0.00 0.00 39.92 2.15
163 165 1.434188 TCCAGCAACCCTTTCTGAGA 58.566 50.000 0.00 0.00 0.00 3.27
214 216 2.107950 TAAATCTGTGGTTGAGGCGG 57.892 50.000 0.00 0.00 0.00 6.13
222 224 5.892348 AGGAGAACCAAATAAATCTGTGGT 58.108 37.500 0.00 0.00 46.38 4.16
227 229 5.583932 AGCCAAGGAGAACCAAATAAATCT 58.416 37.500 0.00 0.00 38.94 2.40
232 235 2.647299 TGGAGCCAAGGAGAACCAAATA 59.353 45.455 0.00 0.00 38.94 1.40
236 239 0.620556 GATGGAGCCAAGGAGAACCA 59.379 55.000 0.00 0.00 38.94 3.67
238 241 0.537188 TCGATGGAGCCAAGGAGAAC 59.463 55.000 0.00 0.00 0.00 3.01
239 242 1.275666 TTCGATGGAGCCAAGGAGAA 58.724 50.000 0.00 0.00 0.00 2.87
273 276 7.336427 GTGAGGAAGAGAATGAATGATTGAACT 59.664 37.037 0.00 0.00 0.00 3.01
276 279 6.955364 AGTGAGGAAGAGAATGAATGATTGA 58.045 36.000 0.00 0.00 0.00 2.57
291 294 7.978975 TCAACCAACAAAAATAAAGTGAGGAAG 59.021 33.333 0.00 0.00 0.00 3.46
305 308 6.800072 AGAGGGTAAATTCAACCAACAAAA 57.200 33.333 11.04 0.00 38.87 2.44
310 313 5.586155 TGGTAGAGGGTAAATTCAACCAA 57.414 39.130 11.04 0.00 38.87 3.67
313 318 4.035208 CGCATGGTAGAGGGTAAATTCAAC 59.965 45.833 0.00 0.00 0.00 3.18
322 327 1.001760 AGGACGCATGGTAGAGGGT 59.998 57.895 0.00 0.00 0.00 4.34
325 330 0.387202 CCAGAGGACGCATGGTAGAG 59.613 60.000 0.00 0.00 0.00 2.43
327 332 0.824109 TTCCAGAGGACGCATGGTAG 59.176 55.000 0.00 0.00 35.51 3.18
334 339 0.178068 TTGCCTATTCCAGAGGACGC 59.822 55.000 0.00 0.00 35.99 5.19
360 366 7.653713 GTGACTGTGAGTCTTGAAGAGAAATAA 59.346 37.037 0.00 0.00 45.27 1.40
369 375 4.200838 TGTTGTGACTGTGAGTCTTGAA 57.799 40.909 5.39 0.00 45.27 2.69
374 380 5.484173 TTTGAATGTTGTGACTGTGAGTC 57.516 39.130 0.00 0.00 45.26 3.36
395 401 9.547279 AGGATGGACAGGAAGTAATAAATTTTT 57.453 29.630 0.00 0.00 0.00 1.94
396 402 9.190317 GAGGATGGACAGGAAGTAATAAATTTT 57.810 33.333 0.00 0.00 0.00 1.82
398 404 8.107196 AGAGGATGGACAGGAAGTAATAAATT 57.893 34.615 0.00 0.00 0.00 1.82
420 426 4.572985 TGGAAACAAATGCTCACAAGAG 57.427 40.909 0.00 0.00 40.70 2.85
453 459 5.352284 CAGCTAATCAGTCCATCTAAACGT 58.648 41.667 0.00 0.00 0.00 3.99
492 498 3.076621 CAAGCACATCCTGAACAGCTAA 58.923 45.455 0.00 0.00 0.00 3.09
496 502 3.126514 GTGATCAAGCACATCCTGAACAG 59.873 47.826 0.00 0.00 38.63 3.16
577 583 0.393132 GAGGCCCCTCTGCTAACAAC 60.393 60.000 0.00 0.00 39.80 3.32
578 584 1.899437 CGAGGCCCCTCTGCTAACAA 61.899 60.000 12.21 0.00 40.69 2.83
579 585 2.359169 CGAGGCCCCTCTGCTAACA 61.359 63.158 12.21 0.00 40.69 2.41
610 616 1.363807 CTCCGGTGCAGCGATCATA 59.636 57.895 37.48 16.52 0.00 2.15
649 4205 9.102757 GCAGACAGATTAGAAATTGATGAAGTA 57.897 33.333 0.00 0.00 0.00 2.24
705 4664 2.595238 GATGGTATACTCCCCTCGTGT 58.405 52.381 2.25 0.00 0.00 4.49
717 4677 1.783071 TCAGCGTGGTGGATGGTATA 58.217 50.000 0.00 0.00 0.00 1.47
733 4701 2.554032 AGGGACAGCACGAAAATTTCAG 59.446 45.455 6.53 1.82 0.00 3.02
837 4838 2.333926 TGATTTATAGGAATCGCGCGG 58.666 47.619 31.69 11.75 38.57 6.46
988 5108 4.781959 CGCCATTGCTTGCCGGTG 62.782 66.667 1.90 0.00 34.43 4.94
1101 5234 3.866582 GGCATGAGGGGGAGGACG 61.867 72.222 0.00 0.00 0.00 4.79
1205 5344 3.063084 GGACCTCGTCGAGCACCT 61.063 66.667 17.02 0.00 32.65 4.00
1422 9225 3.959449 TCTCAGGCTACTCTAGAGTACGA 59.041 47.826 25.58 17.91 42.54 3.43
1445 9259 4.386350 CACATCGACCGTAAATTACACACA 59.614 41.667 3.91 0.00 0.00 3.72
1446 9260 4.386652 ACACATCGACCGTAAATTACACAC 59.613 41.667 3.91 0.00 0.00 3.82
1449 9263 4.558178 ACACACATCGACCGTAAATTACA 58.442 39.130 3.91 0.00 0.00 2.41
1480 9325 8.076781 CAGAGCAAGAATCTTGATCATAATTGG 58.923 37.037 33.59 15.43 37.30 3.16
1481 9326 8.837389 TCAGAGCAAGAATCTTGATCATAATTG 58.163 33.333 33.59 24.65 37.30 2.32
1494 9339 6.765036 TCTGACCATAATTCAGAGCAAGAATC 59.235 38.462 0.00 0.00 43.69 2.52
1514 9359 4.276926 ACAAGAACAGCAGGAATTTCTGAC 59.723 41.667 18.45 8.81 36.93 3.51
1550 9395 1.812571 ACCTCAACAATTCGCCATGAC 59.187 47.619 0.00 0.00 0.00 3.06
1564 9409 5.351189 CACGATGTATGATTTGACACCTCAA 59.649 40.000 0.00 0.00 34.39 3.02
1565 9410 4.869861 CACGATGTATGATTTGACACCTCA 59.130 41.667 0.00 0.00 0.00 3.86
1672 9517 3.490759 GTGGATGGACGCGCACAG 61.491 66.667 5.73 0.00 0.00 3.66
1677 9522 4.530857 GAGGGGTGGATGGACGCG 62.531 72.222 3.53 3.53 0.00 6.01
1678 9523 4.530857 CGAGGGGTGGATGGACGC 62.531 72.222 0.00 0.00 0.00 5.19
1679 9524 3.075005 ACGAGGGGTGGATGGACG 61.075 66.667 0.00 0.00 0.00 4.79
1680 9525 1.265454 AAGACGAGGGGTGGATGGAC 61.265 60.000 0.00 0.00 0.00 4.02
1681 9526 0.976073 GAAGACGAGGGGTGGATGGA 60.976 60.000 0.00 0.00 0.00 3.41
1682 9527 1.522569 GAAGACGAGGGGTGGATGG 59.477 63.158 0.00 0.00 0.00 3.51
1683 9528 1.522569 GGAAGACGAGGGGTGGATG 59.477 63.158 0.00 0.00 0.00 3.51
1684 9529 1.689582 GGGAAGACGAGGGGTGGAT 60.690 63.158 0.00 0.00 0.00 3.41
1685 9530 2.284405 GGGAAGACGAGGGGTGGA 60.284 66.667 0.00 0.00 0.00 4.02
1686 9531 3.771160 CGGGAAGACGAGGGGTGG 61.771 72.222 0.00 0.00 35.47 4.61
1687 9532 2.580601 AACGGGAAGACGAGGGGTG 61.581 63.158 0.00 0.00 37.61 4.61
1688 9533 2.203743 AACGGGAAGACGAGGGGT 60.204 61.111 0.00 0.00 37.61 4.95
1689 9534 2.264794 CAACGGGAAGACGAGGGG 59.735 66.667 0.00 0.00 37.61 4.79
1690 9535 2.434359 GCAACGGGAAGACGAGGG 60.434 66.667 0.00 0.00 37.61 4.30
1691 9536 2.434359 GGCAACGGGAAGACGAGG 60.434 66.667 0.00 0.00 37.61 4.63
1703 9548 1.544246 AGCTTGTTATTTCCCGGCAAC 59.456 47.619 0.00 0.00 0.00 4.17
1704 9549 1.816224 GAGCTTGTTATTTCCCGGCAA 59.184 47.619 0.00 0.00 0.00 4.52
1705 9550 1.459450 GAGCTTGTTATTTCCCGGCA 58.541 50.000 0.00 0.00 0.00 5.69
1706 9551 0.377203 CGAGCTTGTTATTTCCCGGC 59.623 55.000 0.00 0.00 0.00 6.13
1707 9552 2.018542 TCGAGCTTGTTATTTCCCGG 57.981 50.000 0.00 0.00 0.00 5.73
1708 9553 3.458189 AGATCGAGCTTGTTATTTCCCG 58.542 45.455 0.00 0.00 0.00 5.14
1709 9554 6.920569 TTTAGATCGAGCTTGTTATTTCCC 57.079 37.500 9.21 0.00 0.00 3.97
1818 9663 3.516700 CCTCCTTTGCTTCCCATGATTTT 59.483 43.478 0.00 0.00 0.00 1.82
1892 9737 1.139058 TCCTTGCTTCTATTCCTCCGC 59.861 52.381 0.00 0.00 0.00 5.54
2079 9924 2.386272 CGGTAAATAAACGCCCGCT 58.614 52.632 0.00 0.00 0.00 5.52
2227 10079 9.451002 TGGTAATCGTTTGATTTACAGGAATAA 57.549 29.630 0.00 0.00 42.14 1.40
2331 10256 4.530857 GAGGCATCGGTGGACGGG 62.531 72.222 0.00 0.00 44.45 5.28
2332 10257 4.530857 GGAGGCATCGGTGGACGG 62.531 72.222 0.00 0.00 44.45 4.79
2333 10258 4.873129 CGGAGGCATCGGTGGACG 62.873 72.222 0.00 0.00 46.11 4.79
2334 10259 3.432051 CTCGGAGGCATCGGTGGAC 62.432 68.421 5.81 0.00 0.00 4.02
2335 10260 3.147595 CTCGGAGGCATCGGTGGA 61.148 66.667 5.81 0.00 0.00 4.02
2336 10261 2.721167 TTCTCGGAGGCATCGGTGG 61.721 63.158 4.96 1.38 0.00 4.61
2337 10262 1.519455 GTTCTCGGAGGCATCGGTG 60.519 63.158 4.96 3.85 0.00 4.94
2338 10263 1.682684 AGTTCTCGGAGGCATCGGT 60.683 57.895 4.96 0.00 0.00 4.69
2339 10264 1.227089 CAGTTCTCGGAGGCATCGG 60.227 63.158 4.96 0.00 0.00 4.18
2340 10265 1.880340 GCAGTTCTCGGAGGCATCG 60.880 63.158 4.96 0.00 0.00 3.84
2341 10266 0.529555 GAGCAGTTCTCGGAGGCATC 60.530 60.000 4.96 0.00 31.20 3.91
2342 10267 0.975040 AGAGCAGTTCTCGGAGGCAT 60.975 55.000 4.96 0.00 46.44 4.40
2343 10268 1.188219 AAGAGCAGTTCTCGGAGGCA 61.188 55.000 4.96 0.00 46.44 4.75
2344 10269 0.739112 CAAGAGCAGTTCTCGGAGGC 60.739 60.000 4.96 0.37 46.44 4.70
2345 10270 0.739112 GCAAGAGCAGTTCTCGGAGG 60.739 60.000 4.96 0.00 46.44 4.30
2346 10271 1.075425 CGCAAGAGCAGTTCTCGGAG 61.075 60.000 0.00 0.00 46.44 4.63
2347 10272 1.080501 CGCAAGAGCAGTTCTCGGA 60.081 57.895 0.00 0.00 46.44 4.55
2348 10273 2.097038 CCGCAAGAGCAGTTCTCGG 61.097 63.158 0.79 0.79 46.44 4.63
2349 10274 1.347817 GACCGCAAGAGCAGTTCTCG 61.348 60.000 0.00 0.00 46.44 4.04
2350 10275 0.037790 AGACCGCAAGAGCAGTTCTC 60.038 55.000 0.00 0.00 42.27 2.87
2351 10276 0.394565 AAGACCGCAAGAGCAGTTCT 59.605 50.000 0.00 0.00 42.27 3.01
2352 10277 0.514691 CAAGACCGCAAGAGCAGTTC 59.485 55.000 0.00 0.00 42.27 3.01
2353 10278 1.510480 GCAAGACCGCAAGAGCAGTT 61.510 55.000 0.00 0.00 42.27 3.16
2354 10279 1.963338 GCAAGACCGCAAGAGCAGT 60.963 57.895 0.00 0.00 42.27 4.40
2355 10280 2.684843 GGCAAGACCGCAAGAGCAG 61.685 63.158 0.00 0.00 42.27 4.24
2356 10281 2.669569 GGCAAGACCGCAAGAGCA 60.670 61.111 0.00 0.00 42.27 4.26
2382 10307 4.680237 TTGGCAGGCTCGTCGGTG 62.680 66.667 0.00 0.00 0.00 4.94
2383 10308 4.681978 GTTGGCAGGCTCGTCGGT 62.682 66.667 0.00 0.00 0.00 4.69
2384 10309 3.883744 AAGTTGGCAGGCTCGTCGG 62.884 63.158 0.00 0.00 0.00 4.79
2385 10310 1.961277 AAAGTTGGCAGGCTCGTCG 60.961 57.895 0.00 0.00 0.00 5.12
2386 10311 0.884704 TCAAAGTTGGCAGGCTCGTC 60.885 55.000 0.00 0.00 0.00 4.20
2387 10312 1.148273 TCAAAGTTGGCAGGCTCGT 59.852 52.632 0.00 0.00 0.00 4.18
2388 10313 1.576421 GTCAAAGTTGGCAGGCTCG 59.424 57.895 0.00 0.00 31.86 5.03
2389 10314 1.576421 CGTCAAAGTTGGCAGGCTC 59.424 57.895 0.00 0.00 31.86 4.70
2390 10315 2.555547 GCGTCAAAGTTGGCAGGCT 61.556 57.895 0.00 0.00 31.86 4.58
2391 10316 2.050077 GCGTCAAAGTTGGCAGGC 60.050 61.111 0.00 0.00 31.86 4.85
2392 10317 2.252260 CGCGTCAAAGTTGGCAGG 59.748 61.111 0.00 0.00 31.86 4.85
2393 10318 2.427410 GCGCGTCAAAGTTGGCAG 60.427 61.111 8.43 0.00 31.86 4.85


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

AutoCloner maintained by Alex Coulton.