Multiple sequence alignment - TraesCS1A01G366500

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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 TraesCS1A01G366500 chr1A 100.000 3530 0 0 1 3530 545419703 545416174 0.000000e+00 6519.0
1 TraesCS1A01G366500 chr1A 98.897 272 3 0 3259 3530 545350821 545350550 1.470000e-133 486.0
2 TraesCS1A01G366500 chr1D 94.444 2052 83 13 745 2777 450144140 450142101 0.000000e+00 3129.0
3 TraesCS1A01G366500 chr1D 85.851 523 61 10 1 518 450145727 450145213 8.620000e-151 544.0
4 TraesCS1A01G366500 chr1D 91.667 180 13 2 515 693 450145161 450144983 7.570000e-62 248.0
5 TraesCS1A01G366500 chr1D 93.182 44 2 1 686 728 450144169 450144126 2.940000e-06 63.9
6 TraesCS1A01G366500 chr1B 92.992 2012 96 23 745 2731 616771474 616769483 0.000000e+00 2892.0
7 TraesCS1A01G366500 chr1B 82.846 752 97 19 2798 3529 610000651 609999912 0.000000e+00 645.0
8 TraesCS1A01G366500 chr6D 83.442 1534 220 21 1009 2530 157452134 157450623 0.000000e+00 1395.0
9 TraesCS1A01G366500 chr6D 78.974 780 108 34 2777 3530 350126636 350125887 6.850000e-132 481.0
10 TraesCS1A01G366500 chr6D 76.923 442 74 15 48 469 80713809 80714242 3.550000e-55 226.0
11 TraesCS1A01G366500 chr6D 74.286 490 99 11 16 486 271613112 271613593 7.780000e-42 182.0
12 TraesCS1A01G366500 chr2B 81.307 1423 246 13 1119 2535 105895518 105896926 0.000000e+00 1136.0
13 TraesCS1A01G366500 chr2A 81.036 1429 226 23 1115 2535 69313560 69314951 0.000000e+00 1096.0
14 TraesCS1A01G366500 chr2A 76.798 431 76 9 1 412 502630575 502630150 1.650000e-53 220.0
15 TraesCS1A01G366500 chr2D 82.268 970 159 6 1570 2535 69275274 69276234 0.000000e+00 826.0
16 TraesCS1A01G366500 chr7B 77.921 1395 259 29 1123 2506 246387256 246385900 0.000000e+00 824.0
17 TraesCS1A01G366500 chr7B 74.891 458 86 19 49 484 650574853 650575303 7.780000e-42 182.0
18 TraesCS1A01G366500 chr7B 74.672 458 87 19 49 484 650563031 650563481 3.620000e-40 176.0
19 TraesCS1A01G366500 chr7B 74.454 458 88 19 49 484 650585812 650586262 1.680000e-38 171.0
20 TraesCS1A01G366500 chr7D 77.825 1407 259 30 1120 2507 266207362 266208734 0.000000e+00 821.0
21 TraesCS1A01G366500 chr7D 78.600 757 113 29 2775 3506 596367613 596368345 4.150000e-124 455.0
22 TraesCS1A01G366500 chr7D 78.613 346 50 11 49 375 582062671 582062331 1.280000e-49 207.0
23 TraesCS1A01G366500 chr7A 78.122 1129 200 26 1395 2507 291659831 291660928 0.000000e+00 673.0
24 TraesCS1A01G366500 chr7A 81.618 680 93 23 2872 3530 674013936 674013268 5.190000e-148 534.0
25 TraesCS1A01G366500 chr5D 87.158 584 69 6 2912 3491 503959690 503960271 0.000000e+00 658.0
26 TraesCS1A01G366500 chr5D 79.970 659 99 23 2887 3530 551758959 551758319 4.150000e-124 455.0
27 TraesCS1A01G366500 chr5A 83.237 692 89 10 2844 3530 631715363 631716032 8.380000e-171 610.0
28 TraesCS1A01G366500 chr5A 73.611 504 99 18 4 487 13092008 13092497 2.820000e-36 163.0
29 TraesCS1A01G366500 chr3D 81.686 759 109 21 2777 3530 459090070 459089337 3.900000e-169 604.0
30 TraesCS1A01G366500 chr3D 79.692 778 116 31 2775 3530 594143550 594142793 1.120000e-144 523.0
31 TraesCS1A01G366500 chr3D 76.285 506 94 18 1 487 275908558 275909056 2.720000e-61 246.0
32 TraesCS1A01G366500 chr3D 77.317 410 76 14 1 401 475439158 475438757 3.550000e-55 226.0
33 TraesCS1A01G366500 chr6B 84.952 525 74 3 2010 2530 280999281 280998758 8.680000e-146 527.0
34 TraesCS1A01G366500 chr6B 78.776 245 45 4 11 250 615603232 615603474 1.310000e-34 158.0
35 TraesCS1A01G366500 chr5B 81.489 524 79 16 3005 3527 27802918 27802412 7.050000e-112 414.0
36 TraesCS1A01G366500 chr3B 74.217 543 106 21 2 518 55113684 55113150 2.780000e-46 196.0
37 TraesCS1A01G366500 chr3B 80.822 146 26 2 343 487 686489986 686490130 2.880000e-21 113.0
38 TraesCS1A01G366500 chr3A 75.053 473 80 23 14 468 364449635 364449183 6.020000e-43 185.0
39 TraesCS1A01G366500 chr6A 75.000 452 82 14 62 490 536762365 536762808 2.800000e-41 180.0
40 TraesCS1A01G366500 chr4A 76.884 199 41 4 290 486 713733824 713733629 1.340000e-19 108.0
41 TraesCS1A01G366500 chr4B 78.142 183 29 6 2777 2951 580857498 580857677 4.820000e-19 106.0


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 TraesCS1A01G366500 chr1A 545416174 545419703 3529 True 6519.000 6519 100.000 1 3530 1 chr1A.!!$R2 3529
1 TraesCS1A01G366500 chr1D 450142101 450145727 3626 True 996.225 3129 91.286 1 2777 4 chr1D.!!$R1 2776
2 TraesCS1A01G366500 chr1B 616769483 616771474 1991 True 2892.000 2892 92.992 745 2731 1 chr1B.!!$R2 1986
3 TraesCS1A01G366500 chr1B 609999912 610000651 739 True 645.000 645 82.846 2798 3529 1 chr1B.!!$R1 731
4 TraesCS1A01G366500 chr6D 157450623 157452134 1511 True 1395.000 1395 83.442 1009 2530 1 chr6D.!!$R1 1521
5 TraesCS1A01G366500 chr6D 350125887 350126636 749 True 481.000 481 78.974 2777 3530 1 chr6D.!!$R2 753
6 TraesCS1A01G366500 chr2B 105895518 105896926 1408 False 1136.000 1136 81.307 1119 2535 1 chr2B.!!$F1 1416
7 TraesCS1A01G366500 chr2A 69313560 69314951 1391 False 1096.000 1096 81.036 1115 2535 1 chr2A.!!$F1 1420
8 TraesCS1A01G366500 chr2D 69275274 69276234 960 False 826.000 826 82.268 1570 2535 1 chr2D.!!$F1 965
9 TraesCS1A01G366500 chr7B 246385900 246387256 1356 True 824.000 824 77.921 1123 2506 1 chr7B.!!$R1 1383
10 TraesCS1A01G366500 chr7D 266207362 266208734 1372 False 821.000 821 77.825 1120 2507 1 chr7D.!!$F1 1387
11 TraesCS1A01G366500 chr7D 596367613 596368345 732 False 455.000 455 78.600 2775 3506 1 chr7D.!!$F2 731
12 TraesCS1A01G366500 chr7A 291659831 291660928 1097 False 673.000 673 78.122 1395 2507 1 chr7A.!!$F1 1112
13 TraesCS1A01G366500 chr7A 674013268 674013936 668 True 534.000 534 81.618 2872 3530 1 chr7A.!!$R1 658
14 TraesCS1A01G366500 chr5D 503959690 503960271 581 False 658.000 658 87.158 2912 3491 1 chr5D.!!$F1 579
15 TraesCS1A01G366500 chr5D 551758319 551758959 640 True 455.000 455 79.970 2887 3530 1 chr5D.!!$R1 643
16 TraesCS1A01G366500 chr5A 631715363 631716032 669 False 610.000 610 83.237 2844 3530 1 chr5A.!!$F2 686
17 TraesCS1A01G366500 chr3D 459089337 459090070 733 True 604.000 604 81.686 2777 3530 1 chr3D.!!$R1 753
18 TraesCS1A01G366500 chr3D 594142793 594143550 757 True 523.000 523 79.692 2775 3530 1 chr3D.!!$R3 755
19 TraesCS1A01G366500 chr6B 280998758 280999281 523 True 527.000 527 84.952 2010 2530 1 chr6B.!!$R1 520
20 TraesCS1A01G366500 chr5B 27802412 27802918 506 True 414.000 414 81.489 3005 3527 1 chr5B.!!$R1 522

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
129 130 0.107017 CATGTGCCCCTAAGGACCAG 60.107 60.0 0.00 0.00 38.24 4.00 F
448 449 0.250510 GGCATCGGGGAGAAGAATCC 60.251 60.0 0.00 0.00 38.76 3.01 F
574 635 0.521867 CATGTGAAACGCGCTCCATG 60.522 55.0 5.73 14.29 42.39 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1960 0.744057 GCTGAGCAAGAAGAGGAGCC 60.744 60.000 0.0 0.0 0.00 4.70 R
1953 2864 2.126307 CACTCCAGCGAGGTCACG 60.126 66.667 0.0 0.0 40.77 4.35 R
2539 3482 1.827344 TGAGCAGAATGGATGAGACGT 59.173 47.619 0.0 0.0 35.86 4.34 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
23 24 1.135402 CCAAAAGACCACTATTGCCGC 60.135 52.381 0.00 0.00 0.00 6.53
46 47 3.671262 ACGAACCGTCAATGTGTCA 57.329 47.368 0.00 0.00 33.69 3.58
52 53 2.844946 ACCGTCAATGTGTCATTGTCA 58.155 42.857 17.93 2.25 0.00 3.58
65 66 0.824759 ATTGTCACCGCTCCTCTACC 59.175 55.000 0.00 0.00 0.00 3.18
85 86 0.678048 GGAGCCGGCTTGATCTTGTT 60.678 55.000 33.34 3.09 0.00 2.83
90 91 2.358957 CCGGCTTGATCTTGTTGATGA 58.641 47.619 0.00 0.00 35.14 2.92
97 98 3.588955 TGATCTTGTTGATGACAGACGG 58.411 45.455 0.00 0.00 39.94 4.79
129 130 0.107017 CATGTGCCCCTAAGGACCAG 60.107 60.000 0.00 0.00 38.24 4.00
131 132 2.204074 TGCCCCTAAGGACCAGCA 60.204 61.111 0.00 0.00 38.24 4.41
134 135 1.635817 GCCCCTAAGGACCAGCATCA 61.636 60.000 0.00 0.00 38.24 3.07
145 146 1.659622 CCAGCATCATGAAGCCGCAA 61.660 55.000 18.76 0.00 0.00 4.85
148 149 1.066605 AGCATCATGAAGCCGCAATTC 59.933 47.619 18.76 0.00 0.00 2.17
152 153 0.729116 CATGAAGCCGCAATTCTCGT 59.271 50.000 0.00 0.00 0.00 4.18
157 158 1.359848 AGCCGCAATTCTCGTTGTAG 58.640 50.000 0.00 0.00 0.00 2.74
166 167 2.450609 TCTCGTTGTAGAACCCTTGC 57.549 50.000 0.00 0.00 0.00 4.01
170 171 4.020928 TCTCGTTGTAGAACCCTTGCATAA 60.021 41.667 0.00 0.00 0.00 1.90
184 185 7.122715 ACCCTTGCATAAATATGAAACACCTA 58.877 34.615 4.63 0.00 35.75 3.08
198 199 4.946784 AACACCTAACATCAAATCTCGC 57.053 40.909 0.00 0.00 0.00 5.03
214 215 2.093306 TCGCCACATGACGAGAAAAT 57.907 45.000 0.00 0.00 33.69 1.82
216 217 2.002586 CGCCACATGACGAGAAAATCT 58.997 47.619 0.00 0.00 0.00 2.40
217 218 3.119280 TCGCCACATGACGAGAAAATCTA 60.119 43.478 0.00 0.00 33.69 1.98
225 226 6.369065 ACATGACGAGAAAATCTAACTTCACC 59.631 38.462 0.00 0.00 0.00 4.02
231 232 0.988832 AATCTAACTTCACCGCCCCA 59.011 50.000 0.00 0.00 0.00 4.96
232 233 0.988832 ATCTAACTTCACCGCCCCAA 59.011 50.000 0.00 0.00 0.00 4.12
236 237 2.002018 AACTTCACCGCCCCAAGGAA 62.002 55.000 0.00 0.00 33.47 3.36
243 244 2.325082 CGCCCCAAGGAAACGACAG 61.325 63.158 0.00 0.00 33.47 3.51
251 252 4.184629 CCAAGGAAACGACAGGAATCTAG 58.815 47.826 0.00 0.00 0.00 2.43
253 254 3.442076 AGGAAACGACAGGAATCTAGGT 58.558 45.455 0.00 0.00 0.00 3.08
262 263 2.035321 CAGGAATCTAGGTCGAAGCTCC 59.965 54.545 0.00 0.00 0.00 4.70
271 272 2.084844 TCGAAGCTCCGTCGACTAC 58.915 57.895 14.70 0.00 42.31 2.73
309 310 6.777526 ATTCAGAAGACAAACTCGAAGAAG 57.222 37.500 0.00 0.00 34.09 2.85
315 316 1.527311 ACAAACTCGAAGAAGAAGCGC 59.473 47.619 0.00 0.00 34.09 5.92
318 319 2.126071 TCGAAGAAGAAGCGCCGG 60.126 61.111 2.29 0.00 0.00 6.13
323 324 3.577313 GAAGAAGCGCCGGCATCC 61.577 66.667 28.98 14.13 43.41 3.51
353 354 2.664851 CACGCCTGCGAGGACAAA 60.665 61.111 19.52 0.00 42.83 2.83
382 383 5.654209 CCTAACCTAAACTACTAACCGGAGT 59.346 44.000 9.46 4.33 0.00 3.85
403 404 2.235891 GGAAACACCAAGATTCCCGTT 58.764 47.619 0.00 0.00 41.87 4.44
435 436 4.598894 CCGGAGAGGCAGGCATCG 62.599 72.222 0.00 0.00 0.00 3.84
448 449 0.250510 GGCATCGGGGAGAAGAATCC 60.251 60.000 0.00 0.00 38.76 3.01
453 454 2.604118 GGGGAGAAGAATCCACGGA 58.396 57.895 0.00 0.00 41.52 4.69
456 457 1.137282 GGGAGAAGAATCCACGGACTC 59.863 57.143 0.00 0.00 41.52 3.36
458 459 1.743958 GAGAAGAATCCACGGACTCGA 59.256 52.381 0.00 0.00 40.11 4.04
459 460 2.359531 GAGAAGAATCCACGGACTCGAT 59.640 50.000 0.00 0.00 40.11 3.59
485 486 5.408909 GTGAAGTCTAAAGGGTAGAGTTTGC 59.591 44.000 5.23 0.00 37.34 3.68
488 489 4.597940 AGTCTAAAGGGTAGAGTTTGCCTT 59.402 41.667 0.00 0.00 0.00 4.35
491 492 7.037514 AGTCTAAAGGGTAGAGTTTGCCTTAAT 60.038 37.037 0.00 0.00 0.00 1.40
492 493 7.280428 GTCTAAAGGGTAGAGTTTGCCTTAATC 59.720 40.741 0.00 0.00 0.00 1.75
493 494 5.514500 AAGGGTAGAGTTTGCCTTAATCA 57.486 39.130 0.00 0.00 0.00 2.57
495 496 6.824958 AGGGTAGAGTTTGCCTTAATCATA 57.175 37.500 0.00 0.00 0.00 2.15
521 582 2.239654 TCAGGGGATGAACCAAGATGTC 59.760 50.000 0.00 0.00 41.20 3.06
574 635 0.521867 CATGTGAAACGCGCTCCATG 60.522 55.000 5.73 14.29 42.39 3.66
584 645 3.038946 CGCTCCATGTGCATTTTGG 57.961 52.632 8.35 6.26 0.00 3.28
585 646 1.079875 CGCTCCATGTGCATTTTGGC 61.080 55.000 7.46 0.34 0.00 4.52
586 647 1.079875 GCTCCATGTGCATTTTGGCG 61.080 55.000 7.46 3.60 36.28 5.69
624 686 5.734720 TGGAGTTGCTCTTATAGTTGGAAG 58.265 41.667 0.00 0.00 0.00 3.46
631 693 5.208463 CTCTTATAGTTGGAAGAGCCTCC 57.792 47.826 0.00 0.00 41.55 4.30
635 697 2.035442 GTTGGAAGAGCCTCCGCAC 61.035 63.158 0.00 0.00 38.44 5.34
636 698 2.217038 TTGGAAGAGCCTCCGCACT 61.217 57.895 0.00 0.00 38.44 4.40
638 700 2.659610 GAAGAGCCTCCGCACTGT 59.340 61.111 0.00 0.00 35.94 3.55
690 752 1.869132 GCACGCCACATCATTTCGC 60.869 57.895 0.00 0.00 0.00 4.70
714 1597 6.127842 GCAATTAAGGTCAATTCTTTCCCGTA 60.128 38.462 0.00 0.00 0.00 4.02
715 1598 7.472543 CAATTAAGGTCAATTCTTTCCCGTAG 58.527 38.462 0.00 0.00 0.00 3.51
716 1599 4.903045 AAGGTCAATTCTTTCCCGTAGA 57.097 40.909 0.00 0.00 0.00 2.59
717 1600 5.437191 AAGGTCAATTCTTTCCCGTAGAT 57.563 39.130 0.00 0.00 0.00 1.98
718 1601 5.024785 AGGTCAATTCTTTCCCGTAGATC 57.975 43.478 0.00 0.00 0.00 2.75
719 1602 4.717280 AGGTCAATTCTTTCCCGTAGATCT 59.283 41.667 0.00 0.00 0.00 2.75
720 1603 5.897824 AGGTCAATTCTTTCCCGTAGATCTA 59.102 40.000 0.00 0.00 0.00 1.98
721 1604 6.041069 AGGTCAATTCTTTCCCGTAGATCTAG 59.959 42.308 1.64 0.00 0.00 2.43
722 1605 5.692654 GTCAATTCTTTCCCGTAGATCTAGC 59.307 44.000 1.64 0.00 0.00 3.42
723 1606 5.362717 TCAATTCTTTCCCGTAGATCTAGCA 59.637 40.000 1.64 0.00 0.00 3.49
724 1607 6.042093 TCAATTCTTTCCCGTAGATCTAGCAT 59.958 38.462 1.64 0.00 0.00 3.79
725 1608 7.232737 TCAATTCTTTCCCGTAGATCTAGCATA 59.767 37.037 1.64 0.00 0.00 3.14
726 1609 7.726033 ATTCTTTCCCGTAGATCTAGCATAT 57.274 36.000 1.64 0.00 0.00 1.78
727 1610 7.540474 TTCTTTCCCGTAGATCTAGCATATT 57.460 36.000 1.64 0.00 0.00 1.28
728 1611 7.159322 TCTTTCCCGTAGATCTAGCATATTC 57.841 40.000 1.64 0.00 0.00 1.75
729 1612 6.948886 TCTTTCCCGTAGATCTAGCATATTCT 59.051 38.462 1.64 0.00 0.00 2.40
730 1613 6.516739 TTCCCGTAGATCTAGCATATTCTG 57.483 41.667 1.64 0.00 0.00 3.02
731 1614 5.816682 TCCCGTAGATCTAGCATATTCTGA 58.183 41.667 1.64 0.00 0.00 3.27
732 1615 6.246163 TCCCGTAGATCTAGCATATTCTGAA 58.754 40.000 1.64 0.00 0.00 3.02
733 1616 6.719829 TCCCGTAGATCTAGCATATTCTGAAA 59.280 38.462 1.64 0.00 0.00 2.69
734 1617 7.232737 TCCCGTAGATCTAGCATATTCTGAAAA 59.767 37.037 1.64 0.00 0.00 2.29
735 1618 8.037758 CCCGTAGATCTAGCATATTCTGAAAAT 58.962 37.037 1.64 0.00 0.00 1.82
783 1666 2.048503 CCGTGACCTCGGGTTGTC 60.049 66.667 2.85 0.00 45.88 3.18
795 1678 4.181578 CTCGGGTTGTCGATGAGTTTATT 58.818 43.478 0.00 0.00 38.55 1.40
796 1679 4.571919 TCGGGTTGTCGATGAGTTTATTT 58.428 39.130 0.00 0.00 33.92 1.40
797 1680 5.722263 TCGGGTTGTCGATGAGTTTATTTA 58.278 37.500 0.00 0.00 33.92 1.40
870 1753 6.384258 TTCTCTTCCAGATATCGACAAGAG 57.616 41.667 22.34 22.34 38.72 2.85
900 1783 1.559814 CAATGCGAGTATGCGACGG 59.440 57.895 0.00 0.00 37.81 4.79
937 1826 4.434520 GCCAGCACTAGGAAAGTAGTTAG 58.565 47.826 0.00 0.00 35.76 2.34
974 1863 4.785511 TGGAACAGTACAGTAGAAGCTC 57.214 45.455 0.00 0.00 0.00 4.09
976 1865 3.427773 GGAACAGTACAGTAGAAGCTCGG 60.428 52.174 0.00 0.00 0.00 4.63
1064 1960 2.126149 ACTCTCGCTCGCAGCTTG 60.126 61.111 6.58 0.63 39.60 4.01
1158 2054 2.726351 GGCGCTAGTCTTCCTGGCT 61.726 63.158 7.64 0.00 44.95 4.75
1783 2685 1.384989 GGACGAGATCTTGCTCCCGA 61.385 60.000 10.09 0.00 0.00 5.14
1795 2697 1.218230 GCTCCCGATGATCGAAGCAC 61.218 60.000 26.15 7.80 43.74 4.40
2103 3022 2.043248 GTGGTCCTCGAGGGGCTA 60.043 66.667 30.80 18.58 40.18 3.93
2148 3067 4.457496 CTCCCTCACGGCGTGCAT 62.457 66.667 33.59 0.00 32.98 3.96
2172 3094 2.597805 ACGGAGATCGGCGGCTAT 60.598 61.111 7.21 0.09 44.45 2.97
2367 3310 2.069776 CAGGATGTGCCCGGGATAT 58.930 57.895 29.31 14.97 37.37 1.63
2535 3478 3.274288 CATCCCAAGGACTTGAAGCTAC 58.726 50.000 13.35 0.00 42.93 3.58
2536 3479 2.334977 TCCCAAGGACTTGAAGCTACA 58.665 47.619 13.35 0.00 42.93 2.74
2537 3480 2.303022 TCCCAAGGACTTGAAGCTACAG 59.697 50.000 13.35 0.00 42.93 2.74
2538 3481 2.039084 CCCAAGGACTTGAAGCTACAGT 59.961 50.000 13.35 0.00 42.93 3.55
2539 3482 3.260884 CCCAAGGACTTGAAGCTACAGTA 59.739 47.826 13.35 0.00 42.93 2.74
2566 3509 0.538584 TCCATTCTGCTCAGCGTCAT 59.461 50.000 0.00 0.00 0.00 3.06
2623 3568 0.107993 AGTCCATGATGCGGTGTCTG 60.108 55.000 0.00 0.00 0.00 3.51
2640 3585 7.346695 CGGTGTCTGTAGTTAAATTCGAAAAA 58.653 34.615 0.00 0.00 0.00 1.94
2660 3612 9.360514 CGAAAAATATATTGTACGCAACGTATT 57.639 29.630 2.90 0.00 44.12 1.89
2672 3624 8.489559 TGTACGCAACGTATTTATAATGGATTC 58.510 33.333 2.90 0.00 44.12 2.52
2681 3633 9.093970 CGTATTTATAATGGATTCGCTATTCCA 57.906 33.333 4.52 4.52 45.69 3.53
2718 3672 4.462133 TGGTCATTTTTAACACGGGAAGA 58.538 39.130 0.00 0.00 0.00 2.87
2733 3688 2.235155 GGGAAGAGACCAGAAAGTCCTC 59.765 54.545 0.00 0.00 37.49 3.71
2737 3692 2.559231 AGAGACCAGAAAGTCCTCGAAC 59.441 50.000 0.00 0.00 37.49 3.95
2758 3713 7.012515 TCGAACCTGCTTCATAAAACAAAAGTA 59.987 33.333 0.00 0.00 0.00 2.24
2761 3716 7.951591 ACCTGCTTCATAAAACAAAAGTATGT 58.048 30.769 0.00 0.00 34.24 2.29
2762 3717 7.867403 ACCTGCTTCATAAAACAAAAGTATGTG 59.133 33.333 0.00 0.00 32.81 3.21
2763 3718 7.329226 CCTGCTTCATAAAACAAAAGTATGTGG 59.671 37.037 0.00 0.00 32.81 4.17
2764 3719 7.151308 TGCTTCATAAAACAAAAGTATGTGGG 58.849 34.615 0.00 0.00 32.81 4.61
2765 3720 7.014711 TGCTTCATAAAACAAAAGTATGTGGGA 59.985 33.333 0.00 0.00 32.81 4.37
2766 3721 7.870445 GCTTCATAAAACAAAAGTATGTGGGAA 59.130 33.333 0.00 0.00 32.81 3.97
2767 3722 9.410556 CTTCATAAAACAAAAGTATGTGGGAAG 57.589 33.333 0.00 0.00 32.81 3.46
2768 3723 7.375053 TCATAAAACAAAAGTATGTGGGAAGC 58.625 34.615 0.00 0.00 32.81 3.86
2769 3724 3.915437 AACAAAAGTATGTGGGAAGCG 57.085 42.857 0.00 0.00 32.81 4.68
2770 3725 2.858745 ACAAAAGTATGTGGGAAGCGT 58.141 42.857 0.00 0.00 30.82 5.07
2771 3726 3.219281 ACAAAAGTATGTGGGAAGCGTT 58.781 40.909 0.00 0.00 30.82 4.84
2772 3727 3.634910 ACAAAAGTATGTGGGAAGCGTTT 59.365 39.130 0.00 0.00 30.82 3.60
2773 3728 4.822896 ACAAAAGTATGTGGGAAGCGTTTA 59.177 37.500 0.00 0.00 30.82 2.01
2850 3808 4.461992 GCCGAAATAGCGTATTTTAGCA 57.538 40.909 13.92 0.00 38.42 3.49
2854 3812 5.173673 CCGAAATAGCGTATTTTAGCACGTA 59.826 40.000 0.00 0.00 38.42 3.57
2857 3816 7.305590 CGAAATAGCGTATTTTAGCACGTAAGA 60.306 37.037 0.00 0.00 38.42 2.10
2865 3824 8.589629 CGTATTTTAGCACGTAAGAGTGTTTAT 58.410 33.333 0.00 0.00 43.61 1.40
2930 3891 0.179174 GCCGCTGTAAAATCCAACGG 60.179 55.000 0.00 0.00 42.83 4.44
3019 4068 6.440328 ACATAGTTTAAATTCAAGCCCCACAT 59.560 34.615 0.00 0.00 0.00 3.21
3042 4091 2.054363 CAAGCTAGTCCATACGATGCG 58.946 52.381 0.00 0.00 0.00 4.73
3048 4097 5.103000 GCTAGTCCATACGATGCGAATAAT 58.897 41.667 0.00 0.00 0.00 1.28
3049 4098 5.004821 GCTAGTCCATACGATGCGAATAATG 59.995 44.000 0.00 0.00 0.00 1.90
3110 4183 5.950965 AAATGCGTCGACAACTAGATAAG 57.049 39.130 17.16 0.00 0.00 1.73
3204 4287 3.371063 GTCGACGCAGGTCCCAGA 61.371 66.667 0.00 0.00 40.17 3.86
3238 4321 2.435586 CCAGTGCCTTCCGCTCAG 60.436 66.667 0.00 0.00 38.78 3.35
3248 4331 2.435586 CCGCTCAGGCTTGTCCAG 60.436 66.667 0.00 0.00 37.29 3.86
3249 4332 2.345244 CGCTCAGGCTTGTCCAGT 59.655 61.111 0.00 0.00 37.29 4.00
3279 4362 3.073735 CGCTCTGCCCTCCTCTGT 61.074 66.667 0.00 0.00 0.00 3.41
3297 4380 2.490115 CTGTGCCTAGAACTCGTTCTCT 59.510 50.000 14.99 0.00 46.13 3.10
3374 4457 3.838271 GGCGATGAGGAGGCGACA 61.838 66.667 0.00 0.00 32.27 4.35
3448 4532 2.579201 GAGTTCCTGCGCCTGCTA 59.421 61.111 4.18 0.00 43.34 3.49
3450 4534 2.232298 GAGTTCCTGCGCCTGCTAGT 62.232 60.000 4.18 0.00 43.34 2.57
3481 4568 3.759418 CGTTAGAGAAGTTCATCTGCGA 58.241 45.455 5.50 0.00 31.46 5.10
3483 4570 4.673061 CGTTAGAGAAGTTCATCTGCGACT 60.673 45.833 5.50 0.00 31.46 4.18
3494 4581 3.241530 TGCGACTGTGGCCTTCCT 61.242 61.111 12.30 0.00 0.00 3.36
3506 4593 2.660064 CCTTCCTAGGCACCACGCT 61.660 63.158 2.96 0.00 41.91 5.07
3508 4595 2.172483 CTTCCTAGGCACCACGCTGT 62.172 60.000 2.96 0.00 41.91 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.221840 CTGGCGGCAATAGTGGTCT 59.778 57.895 14.48 0.00 0.00 3.85
36 37 1.535028 GCGGTGACAATGACACATTGA 59.465 47.619 24.67 6.62 39.65 2.57
42 43 0.037326 GAGGAGCGGTGACAATGACA 60.037 55.000 0.00 0.00 0.00 3.58
46 47 0.824759 GGTAGAGGAGCGGTGACAAT 59.175 55.000 0.00 0.00 0.00 2.71
65 66 2.176273 CAAGATCAAGCCGGCTCCG 61.176 63.158 32.93 24.15 39.44 4.63
71 72 2.743664 TGTCATCAACAAGATCAAGCCG 59.256 45.455 0.00 0.00 33.72 5.52
97 98 1.129437 GGCACATGCTCGAAGACTTTC 59.871 52.381 3.48 0.00 41.70 2.62
129 130 1.066605 AGAATTGCGGCTTCATGATGC 59.933 47.619 22.04 22.04 0.00 3.91
131 132 1.600957 CGAGAATTGCGGCTTCATGAT 59.399 47.619 0.00 0.00 0.00 2.45
134 135 1.131126 CAACGAGAATTGCGGCTTCAT 59.869 47.619 0.00 0.00 0.00 2.57
145 146 3.244422 TGCAAGGGTTCTACAACGAGAAT 60.244 43.478 0.00 0.00 37.75 2.40
148 149 2.163818 TGCAAGGGTTCTACAACGAG 57.836 50.000 0.00 0.00 32.68 4.18
152 153 8.815565 TTCATATTTATGCAAGGGTTCTACAA 57.184 30.769 0.00 0.00 33.76 2.41
157 158 6.756542 GGTGTTTCATATTTATGCAAGGGTTC 59.243 38.462 0.00 0.00 33.76 3.62
184 185 3.127548 GTCATGTGGCGAGATTTGATGTT 59.872 43.478 0.00 0.00 0.00 2.71
198 199 6.368791 TGAAGTTAGATTTTCTCGTCATGTGG 59.631 38.462 0.00 0.00 0.00 4.17
214 215 0.323629 CTTGGGGCGGTGAAGTTAGA 59.676 55.000 0.00 0.00 0.00 2.10
216 217 1.128809 TCCTTGGGGCGGTGAAGTTA 61.129 55.000 0.00 0.00 0.00 2.24
217 218 2.002018 TTCCTTGGGGCGGTGAAGTT 62.002 55.000 0.00 0.00 0.00 2.66
225 226 2.281208 TGTCGTTTCCTTGGGGCG 60.281 61.111 0.00 0.00 0.00 6.13
231 232 3.838903 ACCTAGATTCCTGTCGTTTCCTT 59.161 43.478 0.00 0.00 0.00 3.36
232 233 3.442076 ACCTAGATTCCTGTCGTTTCCT 58.558 45.455 0.00 0.00 0.00 3.36
243 244 1.001158 CGGAGCTTCGACCTAGATTCC 60.001 57.143 9.41 0.00 0.00 3.01
253 254 2.084844 GTAGTCGACGGAGCTTCGA 58.915 57.895 24.16 13.69 43.07 3.71
287 288 5.902681 TCTTCTTCGAGTTTGTCTTCTGAA 58.097 37.500 0.00 0.00 0.00 3.02
289 290 5.332959 GCTTCTTCTTCGAGTTTGTCTTCTG 60.333 44.000 0.00 0.00 0.00 3.02
290 291 4.747605 GCTTCTTCTTCGAGTTTGTCTTCT 59.252 41.667 0.00 0.00 0.00 2.85
338 339 3.339731 TTTTTGTCCTCGCAGGCG 58.660 55.556 7.46 7.46 34.61 5.52
353 354 7.661437 CCGGTTAGTAGTTTAGGTTAGGTTTTT 59.339 37.037 0.00 0.00 0.00 1.94
374 375 1.916738 TGGTGTTTCCACTCCGGTT 59.083 52.632 0.00 0.00 41.93 4.44
382 383 1.144093 ACGGGAATCTTGGTGTTTCCA 59.856 47.619 3.59 0.00 43.14 3.53
424 425 4.804420 TCTCCCCGATGCCTGCCT 62.804 66.667 0.00 0.00 0.00 4.75
429 430 0.250510 GGATTCTTCTCCCCGATGCC 60.251 60.000 0.00 0.00 0.00 4.40
430 431 0.469917 TGGATTCTTCTCCCCGATGC 59.530 55.000 0.00 0.00 34.12 3.91
435 436 0.178301 GTCCGTGGATTCTTCTCCCC 59.822 60.000 0.00 0.00 34.12 4.81
448 449 0.243907 ACTTCACCATCGAGTCCGTG 59.756 55.000 0.00 0.00 37.05 4.94
453 454 3.195825 CCCTTTAGACTTCACCATCGAGT 59.804 47.826 0.00 0.00 0.00 4.18
456 457 3.611766 ACCCTTTAGACTTCACCATCG 57.388 47.619 0.00 0.00 0.00 3.84
458 459 5.342866 ACTCTACCCTTTAGACTTCACCAT 58.657 41.667 0.00 0.00 0.00 3.55
459 460 4.748701 ACTCTACCCTTTAGACTTCACCA 58.251 43.478 0.00 0.00 0.00 4.17
488 489 4.838403 TCATCCCCTGACCCTTATGATTA 58.162 43.478 0.00 0.00 0.00 1.75
491 492 2.777692 GTTCATCCCCTGACCCTTATGA 59.222 50.000 0.00 0.00 32.17 2.15
492 493 2.158608 GGTTCATCCCCTGACCCTTATG 60.159 54.545 0.00 0.00 33.73 1.90
493 494 2.136026 GGTTCATCCCCTGACCCTTAT 58.864 52.381 0.00 0.00 33.73 1.73
495 496 0.477597 TGGTTCATCCCCTGACCCTT 60.478 55.000 0.00 0.00 37.34 3.95
501 507 2.240667 AGACATCTTGGTTCATCCCCTG 59.759 50.000 0.00 0.00 34.77 4.45
546 607 1.069906 GCGTTTCACATGGACACAGAC 60.070 52.381 0.00 0.00 0.00 3.51
574 635 3.679262 GCGATCGCCAAAATGCAC 58.321 55.556 29.48 0.00 34.56 4.57
601 662 5.483937 TCTTCCAACTATAAGAGCAACTCCA 59.516 40.000 0.00 0.00 0.00 3.86
624 686 3.426568 GCAACAGTGCGGAGGCTC 61.427 66.667 5.78 5.78 41.93 4.70
635 697 4.947645 TGGAGAAATTTTTGGAGCAACAG 58.052 39.130 0.00 0.00 0.00 3.16
636 698 4.740334 GCTGGAGAAATTTTTGGAGCAACA 60.740 41.667 0.00 0.00 0.00 3.33
638 700 3.387374 TGCTGGAGAAATTTTTGGAGCAA 59.613 39.130 11.34 0.00 32.47 3.91
678 740 5.639757 TGACCTTAATTGCGAAATGATGTG 58.360 37.500 0.00 0.00 0.00 3.21
690 752 6.267496 ACGGGAAAGAATTGACCTTAATTG 57.733 37.500 0.00 0.00 30.78 2.32
737 1620 9.971922 GTGCCAATAATGCTAGATCTTATTTTT 57.028 29.630 0.00 0.00 0.00 1.94
738 1621 8.292448 CGTGCCAATAATGCTAGATCTTATTTT 58.708 33.333 0.00 0.00 0.00 1.82
739 1622 7.573843 GCGTGCCAATAATGCTAGATCTTATTT 60.574 37.037 0.00 0.00 0.00 1.40
740 1623 6.128172 GCGTGCCAATAATGCTAGATCTTATT 60.128 38.462 0.00 2.81 0.00 1.40
741 1624 5.352569 GCGTGCCAATAATGCTAGATCTTAT 59.647 40.000 0.00 0.00 0.00 1.73
742 1625 4.690748 GCGTGCCAATAATGCTAGATCTTA 59.309 41.667 0.00 0.00 0.00 2.10
743 1626 3.499918 GCGTGCCAATAATGCTAGATCTT 59.500 43.478 0.00 0.00 0.00 2.40
783 1666 8.018677 ACTGCGGAATATAAATAAACTCATCG 57.981 34.615 0.00 0.00 0.00 3.84
870 1753 1.584483 CGCATTGGACGCATTCAGC 60.584 57.895 0.00 0.00 40.87 4.26
900 1783 2.417097 GGCGTATGGGCATTTGGC 59.583 61.111 0.00 0.00 41.77 4.52
937 1826 1.014044 TCCAGTGCAATCGTTCGAGC 61.014 55.000 0.00 0.72 0.00 5.03
966 1855 3.556999 AGCTATTCTGACCGAGCTTCTA 58.443 45.455 0.00 0.00 42.59 2.10
967 1856 2.383855 AGCTATTCTGACCGAGCTTCT 58.616 47.619 0.00 0.00 42.59 2.85
968 1857 2.880963 AGCTATTCTGACCGAGCTTC 57.119 50.000 0.00 0.00 42.59 3.86
972 1861 2.468831 GCTCAAGCTATTCTGACCGAG 58.531 52.381 0.00 0.00 38.21 4.63
973 1862 2.586258 GCTCAAGCTATTCTGACCGA 57.414 50.000 0.00 0.00 38.21 4.69
1064 1960 0.744057 GCTGAGCAAGAAGAGGAGCC 60.744 60.000 0.00 0.00 0.00 4.70
1146 2042 2.909217 AGGAACTTAGCCAGGAAGACT 58.091 47.619 0.00 0.00 27.25 3.24
1147 2043 3.431068 GCTAGGAACTTAGCCAGGAAGAC 60.431 52.174 4.91 0.00 41.75 3.01
1158 2054 2.012902 GCCGGAGCGCTAGGAACTTA 62.013 60.000 29.08 0.00 41.75 2.24
1624 2526 3.994587 CTGCATCTCGTCGAGCAG 58.005 61.111 17.61 17.43 46.98 4.24
1783 2685 3.264897 GCGCCGTGCTTCGATCAT 61.265 61.111 0.00 0.00 42.86 2.45
1953 2864 2.126307 CACTCCAGCGAGGTCACG 60.126 66.667 0.00 0.00 40.77 4.35
2148 3067 2.831366 GCCGATCTCCGTGTCGCTA 61.831 63.158 0.00 0.00 36.57 4.26
2223 3166 3.681835 GCCCACACCGTCTCGTCT 61.682 66.667 0.00 0.00 0.00 4.18
2367 3310 4.449568 TGCAGCATGGCGAGCGTA 62.450 61.111 0.00 0.00 37.29 4.42
2535 3478 3.119291 GCAGAATGGATGAGACGTACTG 58.881 50.000 0.00 0.00 35.86 2.74
2536 3479 3.027412 AGCAGAATGGATGAGACGTACT 58.973 45.455 0.00 0.00 35.86 2.73
2537 3480 3.181486 TGAGCAGAATGGATGAGACGTAC 60.181 47.826 0.00 0.00 35.86 3.67
2538 3481 3.023832 TGAGCAGAATGGATGAGACGTA 58.976 45.455 0.00 0.00 35.86 3.57
2539 3482 1.827344 TGAGCAGAATGGATGAGACGT 59.173 47.619 0.00 0.00 35.86 4.34
2566 3509 6.961360 TTCTTCAGAGTTCAGAGTTGACTA 57.039 37.500 0.00 0.00 31.71 2.59
2672 3624 7.594758 CCATTTGGTTGTTTATATGGAATAGCG 59.405 37.037 0.00 0.00 35.63 4.26
2700 3652 4.517453 TGGTCTCTTCCCGTGTTAAAAATG 59.483 41.667 0.00 0.00 0.00 2.32
2701 3653 4.721132 TGGTCTCTTCCCGTGTTAAAAAT 58.279 39.130 0.00 0.00 0.00 1.82
2711 3665 1.066787 GGACTTTCTGGTCTCTTCCCG 60.067 57.143 0.00 0.00 36.55 5.14
2718 3672 1.619332 GGTTCGAGGACTTTCTGGTCT 59.381 52.381 0.00 0.00 36.55 3.85
2733 3688 5.977129 ACTTTTGTTTTATGAAGCAGGTTCG 59.023 36.000 7.83 0.00 38.09 3.95
2737 3692 7.329226 CCACATACTTTTGTTTTATGAAGCAGG 59.671 37.037 0.00 0.00 0.00 4.85
2758 3713 3.877508 GCTCTAATAAACGCTTCCCACAT 59.122 43.478 0.00 0.00 0.00 3.21
2761 3716 3.620427 TGCTCTAATAAACGCTTCCCA 57.380 42.857 0.00 0.00 0.00 4.37
2762 3717 4.381411 AGATGCTCTAATAAACGCTTCCC 58.619 43.478 0.00 0.00 0.00 3.97
2763 3718 5.050490 TGAGATGCTCTAATAAACGCTTCC 58.950 41.667 0.00 0.00 0.00 3.46
2764 3719 6.414890 GTTGAGATGCTCTAATAAACGCTTC 58.585 40.000 0.00 0.00 0.00 3.86
2765 3720 5.294552 GGTTGAGATGCTCTAATAAACGCTT 59.705 40.000 0.00 0.00 0.00 4.68
2766 3721 4.811557 GGTTGAGATGCTCTAATAAACGCT 59.188 41.667 0.00 0.00 0.00 5.07
2767 3722 4.570772 TGGTTGAGATGCTCTAATAAACGC 59.429 41.667 0.00 0.00 0.00 4.84
2768 3723 6.019479 GTCTGGTTGAGATGCTCTAATAAACG 60.019 42.308 0.00 0.00 31.63 3.60
2769 3724 6.258947 GGTCTGGTTGAGATGCTCTAATAAAC 59.741 42.308 0.00 0.00 31.63 2.01
2770 3725 6.349300 GGTCTGGTTGAGATGCTCTAATAAA 58.651 40.000 0.00 0.00 31.63 1.40
2771 3726 5.451937 CGGTCTGGTTGAGATGCTCTAATAA 60.452 44.000 0.00 0.00 31.63 1.40
2772 3727 4.038042 CGGTCTGGTTGAGATGCTCTAATA 59.962 45.833 0.00 0.00 31.63 0.98
2773 3728 3.181471 CGGTCTGGTTGAGATGCTCTAAT 60.181 47.826 0.00 0.00 31.63 1.73
2802 3757 1.303091 AAAAATTAGGACGCCGCGCT 61.303 50.000 13.88 5.35 0.00 5.92
2850 3808 6.148315 GCCTGGTAAAATAAACACTCTTACGT 59.852 38.462 0.00 0.00 0.00 3.57
2854 3812 6.016276 CAGTGCCTGGTAAAATAAACACTCTT 60.016 38.462 0.00 0.00 35.06 2.85
2857 3816 4.022329 GCAGTGCCTGGTAAAATAAACACT 60.022 41.667 2.85 0.00 37.60 3.55
2865 3824 3.895232 TTTTTGCAGTGCCTGGTAAAA 57.105 38.095 13.72 9.32 31.21 1.52
2951 3938 6.746104 TCGTATGTGTTGCTTCAATTTTTG 57.254 33.333 0.00 0.00 0.00 2.44
3002 4015 3.772387 TGTGATGTGGGGCTTGAATTTA 58.228 40.909 0.00 0.00 0.00 1.40
3019 4068 3.490933 GCATCGTATGGACTAGCTTGTGA 60.491 47.826 5.27 0.00 0.00 3.58
3048 4097 7.307396 GCATCTTAGCATCGTTTTTATCTAGCA 60.307 37.037 0.00 0.00 0.00 3.49
3049 4098 7.012358 GCATCTTAGCATCGTTTTTATCTAGC 58.988 38.462 0.00 0.00 0.00 3.42
3091 4156 2.422479 AGCTTATCTAGTTGTCGACGCA 59.578 45.455 11.62 0.00 0.00 5.24
3110 4183 0.589223 CGAGGAGGATGACGAGTAGC 59.411 60.000 0.00 0.00 0.00 3.58
3238 4321 3.112709 GCGTCGACTGGACAAGCC 61.113 66.667 14.70 0.00 46.42 4.35


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

AutoCloner maintained by Alex Coulton.