Multiple sequence alignment - TraesCS1B01G382800

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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 TraesCS1B01G382800 chr1B 100.000 3852 0 0 1 3852 614966975 614970826 0.000000e+00 7114
1 TraesCS1B01G382800 chr1B 90.625 128 12 0 1025 1152 614942630 614942757 1.840000e-38 171
2 TraesCS1B01G382800 chr1D 89.450 2455 142 46 624 3042 449309408 449311781 0.000000e+00 2990
3 TraesCS1B01G382800 chr1D 91.646 790 35 12 3073 3852 449312421 449313189 0.000000e+00 1064
4 TraesCS1B01G382800 chr1D 90.625 128 12 0 1025 1152 449281827 449281954 1.840000e-38 171
5 TraesCS1B01G382800 chr1A 91.554 1622 84 24 1440 3042 544493290 544494877 0.000000e+00 2187
6 TraesCS1B01G382800 chr1A 92.221 797 46 8 3067 3852 544495135 544495926 0.000000e+00 1114
7 TraesCS1B01G382800 chr1A 87.925 853 60 17 526 1356 544492403 544493234 0.000000e+00 965
8 TraesCS1B01G382800 chr1A 89.062 128 14 0 1025 1152 544487035 544487162 3.980000e-35 159
9 TraesCS1B01G382800 chr3B 83.935 1052 117 35 1000 2036 8686911 8685897 0.000000e+00 959
10 TraesCS1B01G382800 chr3B 92.966 526 33 3 1 525 803482128 803481606 0.000000e+00 763
11 TraesCS1B01G382800 chr3B 92.776 526 34 3 1 525 545798267 545798789 0.000000e+00 758
12 TraesCS1B01G382800 chr3B 93.010 515 33 2 1 514 179581439 179580927 0.000000e+00 749
13 TraesCS1B01G382800 chr3B 92.803 264 17 2 2517 2780 8685319 8685058 7.810000e-102 381
14 TraesCS1B01G382800 chr3B 77.162 451 62 25 2064 2489 8685817 8685383 1.390000e-54 224
15 TraesCS1B01G382800 chr2B 93.064 519 34 1 1 519 335463449 335462933 0.000000e+00 758
16 TraesCS1B01G382800 chr7B 93.191 514 32 2 1 514 147157804 147158314 0.000000e+00 752
17 TraesCS1B01G382800 chr7B 92.843 517 32 4 1 514 693284426 693284940 0.000000e+00 745
18 TraesCS1B01G382800 chr4B 92.678 519 36 1 1 519 446199496 446200012 0.000000e+00 747
19 TraesCS1B01G382800 chr5B 92.829 516 33 3 1 514 703477700 703477187 0.000000e+00 745
20 TraesCS1B01G382800 chr5B 91.932 533 35 7 1 528 416104886 416104357 0.000000e+00 739
21 TraesCS1B01G382800 chr3A 86.842 608 65 7 1435 2040 13189253 13189847 0.000000e+00 665
22 TraesCS1B01G382800 chr3A 79.454 769 68 42 644 1356 13188155 13188889 2.710000e-126 462
23 TraesCS1B01G382800 chr3A 93.182 264 16 2 2517 2780 13190414 13190675 1.680000e-103 387
24 TraesCS1B01G382800 chr3A 83.815 173 19 5 2064 2227 13189915 13190087 5.150000e-34 156
25 TraesCS1B01G382800 chr3D 86.230 610 65 13 1435 2040 7123911 7123317 0.000000e+00 643
26 TraesCS1B01G382800 chr3D 80.724 773 77 41 624 1356 7124976 7124236 1.570000e-148 536
27 TraesCS1B01G382800 chr3D 93.561 264 15 2 2517 2780 7122765 7122504 3.610000e-105 392
28 TraesCS1B01G382800 chr3D 86.527 334 36 7 3519 3852 141484648 141484324 3.660000e-95 359
29 TraesCS1B01G382800 chr3D 86.280 328 36 5 3519 3846 301332255 301332573 7.920000e-92 348
30 TraesCS1B01G382800 chr3D 85.671 328 32 6 3519 3846 53783131 53783443 7.980000e-87 331
31 TraesCS1B01G382800 chr7D 87.385 325 33 5 3522 3846 53741739 53741423 2.190000e-97 366
32 TraesCS1B01G382800 chr7D 86.826 334 35 5 3519 3852 221986253 221985929 7.860000e-97 364
33 TraesCS1B01G382800 chr7D 85.976 328 37 4 3519 3846 488105884 488106202 3.690000e-90 342
34 TraesCS1B01G382800 chrUn 85.976 328 35 7 3519 3846 79581125 79581441 1.330000e-89 340


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 TraesCS1B01G382800 chr1B 614966975 614970826 3851 False 7114.000000 7114 100.000000 1 3852 1 chr1B.!!$F2 3851
1 TraesCS1B01G382800 chr1D 449309408 449313189 3781 False 2027.000000 2990 90.548000 624 3852 2 chr1D.!!$F2 3228
2 TraesCS1B01G382800 chr1A 544492403 544495926 3523 False 1422.000000 2187 90.566667 526 3852 3 chr1A.!!$F2 3326
3 TraesCS1B01G382800 chr3B 803481606 803482128 522 True 763.000000 763 92.966000 1 525 1 chr3B.!!$R2 524
4 TraesCS1B01G382800 chr3B 545798267 545798789 522 False 758.000000 758 92.776000 1 525 1 chr3B.!!$F1 524
5 TraesCS1B01G382800 chr3B 179580927 179581439 512 True 749.000000 749 93.010000 1 514 1 chr3B.!!$R1 513
6 TraesCS1B01G382800 chr3B 8685058 8686911 1853 True 521.333333 959 84.633333 1000 2780 3 chr3B.!!$R3 1780
7 TraesCS1B01G382800 chr2B 335462933 335463449 516 True 758.000000 758 93.064000 1 519 1 chr2B.!!$R1 518
8 TraesCS1B01G382800 chr7B 147157804 147158314 510 False 752.000000 752 93.191000 1 514 1 chr7B.!!$F1 513
9 TraesCS1B01G382800 chr7B 693284426 693284940 514 False 745.000000 745 92.843000 1 514 1 chr7B.!!$F2 513
10 TraesCS1B01G382800 chr4B 446199496 446200012 516 False 747.000000 747 92.678000 1 519 1 chr4B.!!$F1 518
11 TraesCS1B01G382800 chr5B 703477187 703477700 513 True 745.000000 745 92.829000 1 514 1 chr5B.!!$R2 513
12 TraesCS1B01G382800 chr5B 416104357 416104886 529 True 739.000000 739 91.932000 1 528 1 chr5B.!!$R1 527
13 TraesCS1B01G382800 chr3A 13188155 13190675 2520 False 417.500000 665 85.823250 644 2780 4 chr3A.!!$F1 2136
14 TraesCS1B01G382800 chr3D 7122504 7124976 2472 True 523.666667 643 86.838333 624 2780 3 chr3D.!!$R2 2156

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
784 800 0.039617 CATCGGCGAGAGATGAGACC 60.040 60.0 17.22 0.0 46.09 3.85 F
1439 1548 0.031178 GCTCACAGTGCACTTTTGGG 59.969 55.0 18.94 18.1 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2368 0.523072 CAGTCGCCACCTGAAAATGG 59.477 55.0 0.0 0.0 39.16 3.16 R
3204 4402 0.751277 TCTGGTGTGTGGCTTTGGTG 60.751 55.0 0.0 0.0 0.00 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
247 248 6.620733 GCAACTGCACTTAAACGAACATAGAT 60.621 38.462 0.00 0.00 41.59 1.98
255 256 6.154706 ACTTAAACGAACATAGATGAGGGTCT 59.845 38.462 0.00 0.00 0.00 3.85
351 352 2.437002 GGGCGTGTGGGCGAAATA 60.437 61.111 0.00 0.00 43.46 1.40
352 353 2.469516 GGGCGTGTGGGCGAAATAG 61.470 63.158 0.00 0.00 43.46 1.73
355 356 1.539496 GGCGTGTGGGCGAAATAGATA 60.539 52.381 0.00 0.00 0.00 1.98
356 357 2.206750 GCGTGTGGGCGAAATAGATAA 58.793 47.619 0.00 0.00 0.00 1.75
366 368 3.191669 CGAAATAGATAACGCCCACACA 58.808 45.455 0.00 0.00 0.00 3.72
388 390 1.168407 CGCGTATAAGAGGGACCGGA 61.168 60.000 9.46 0.00 0.00 5.14
425 430 1.524008 GGGCGCTAGTTGTTTTGCCT 61.524 55.000 7.64 0.00 42.11 4.75
459 464 1.063183 GGGCTGATCCTCTTAGGCAT 58.937 55.000 6.00 0.00 38.60 4.40
468 473 2.497675 TCCTCTTAGGCATCACACAGAC 59.502 50.000 0.00 0.00 34.61 3.51
562 567 7.615757 AGAAAGATCAAATCTCGGGGTAAAAAT 59.384 33.333 0.00 0.00 39.08 1.82
622 628 0.766752 TCGTGGATCATGATGCCCAT 59.233 50.000 22.72 0.00 35.44 4.00
649 659 6.121590 TGAGTATCCAGCTGCAAATTAATGA 58.878 36.000 8.66 0.00 0.00 2.57
767 783 3.814268 GCAACATCGCCGGTGCAT 61.814 61.111 11.05 1.88 37.32 3.96
784 800 0.039617 CATCGGCGAGAGATGAGACC 60.040 60.000 17.22 0.00 46.09 3.85
785 801 1.175983 ATCGGCGAGAGATGAGACCC 61.176 60.000 17.22 0.00 0.00 4.46
786 802 2.851071 CGGCGAGAGATGAGACCCC 61.851 68.421 0.00 0.00 0.00 4.95
787 803 1.456705 GGCGAGAGATGAGACCCCT 60.457 63.158 0.00 0.00 0.00 4.79
791 816 0.825840 GAGAGATGAGACCCCTCCGG 60.826 65.000 0.00 0.00 38.66 5.14
890 919 3.912907 CCCGCGCGTCCTTATCCT 61.913 66.667 29.95 0.00 0.00 3.24
891 920 2.354773 CCGCGCGTCCTTATCCTC 60.355 66.667 29.95 0.00 0.00 3.71
892 921 2.354773 CGCGCGTCCTTATCCTCC 60.355 66.667 24.19 0.00 0.00 4.30
893 922 2.812499 GCGCGTCCTTATCCTCCA 59.188 61.111 8.43 0.00 0.00 3.86
894 923 1.591863 GCGCGTCCTTATCCTCCAC 60.592 63.158 8.43 0.00 0.00 4.02
895 924 1.067582 CGCGTCCTTATCCTCCACC 59.932 63.158 0.00 0.00 0.00 4.61
896 925 1.446366 GCGTCCTTATCCTCCACCC 59.554 63.158 0.00 0.00 0.00 4.61
897 926 2.041206 GCGTCCTTATCCTCCACCCC 62.041 65.000 0.00 0.00 0.00 4.95
898 927 1.408453 CGTCCTTATCCTCCACCCCC 61.408 65.000 0.00 0.00 0.00 5.40
899 928 1.074775 TCCTTATCCTCCACCCCCG 60.075 63.158 0.00 0.00 0.00 5.73
956 1006 2.935238 GCCAAATCAGCTTCCGTCACTA 60.935 50.000 0.00 0.00 0.00 2.74
957 1007 2.932614 CCAAATCAGCTTCCGTCACTAG 59.067 50.000 0.00 0.00 0.00 2.57
985 1046 2.083522 GCGTGACTGAGCTCGTGAC 61.084 63.158 14.47 14.58 0.00 3.67
1162 1243 2.039974 CAGGTACGCAGCAATGGCA 61.040 57.895 0.00 0.00 44.61 4.92
1206 1295 3.110178 GCGTTCCGTTGACCCTCG 61.110 66.667 0.00 0.00 0.00 4.63
1351 1447 2.964389 GCGGCGAGATCAAGCTCC 60.964 66.667 12.98 0.00 0.00 4.70
1356 1452 0.107945 GCGAGATCAAGCTCCTGGTT 60.108 55.000 0.00 0.00 0.00 3.67
1358 1454 1.800655 CGAGATCAAGCTCCTGGTTCG 60.801 57.143 0.00 0.00 0.00 3.95
1362 1458 0.606604 TCAAGCTCCTGGTTCGTACC 59.393 55.000 3.92 3.92 45.26 3.34
1363 1459 0.391263 CAAGCTCCTGGTTCGTACCC 60.391 60.000 8.91 0.00 44.35 3.69
1364 1460 1.885163 AAGCTCCTGGTTCGTACCCG 61.885 60.000 8.91 1.96 44.35 5.28
1365 1461 2.183555 CTCCTGGTTCGTACCCGC 59.816 66.667 8.91 0.00 44.35 6.13
1366 1462 2.601067 TCCTGGTTCGTACCCGCA 60.601 61.111 8.91 0.00 44.35 5.69
1367 1463 2.433664 CCTGGTTCGTACCCGCAC 60.434 66.667 8.91 0.00 44.35 5.34
1370 1466 2.433664 GGTTCGTACCCGCACCTG 60.434 66.667 0.00 0.00 45.40 4.00
1371 1467 2.341176 GTTCGTACCCGCACCTGT 59.659 61.111 0.00 0.00 0.00 4.00
1372 1468 2.025418 GTTCGTACCCGCACCTGTG 61.025 63.158 0.00 0.00 0.00 3.66
1373 1469 3.229156 TTCGTACCCGCACCTGTGG 62.229 63.158 0.00 0.00 45.02 4.17
1375 1471 4.323477 GTACCCGCACCTGTGGCA 62.323 66.667 0.00 0.00 44.11 4.92
1376 1472 4.015406 TACCCGCACCTGTGGCAG 62.015 66.667 0.00 0.00 44.11 4.85
1381 1477 2.987547 GCACCTGTGGCAGCACAT 60.988 61.111 0.00 0.00 34.25 3.21
1382 1478 2.567497 GCACCTGTGGCAGCACATT 61.567 57.895 0.00 0.00 34.25 2.71
1383 1479 1.582968 CACCTGTGGCAGCACATTC 59.417 57.895 0.00 0.00 34.25 2.67
1384 1480 0.892358 CACCTGTGGCAGCACATTCT 60.892 55.000 0.00 0.00 34.25 2.40
1385 1481 0.892358 ACCTGTGGCAGCACATTCTG 60.892 55.000 0.00 0.00 34.25 3.02
1386 1482 0.892358 CCTGTGGCAGCACATTCTGT 60.892 55.000 0.00 0.00 36.49 3.41
1387 1483 0.520404 CTGTGGCAGCACATTCTGTC 59.480 55.000 0.00 0.00 39.06 3.51
1389 1485 0.801251 GTGGCAGCACATTCTGTCTC 59.199 55.000 0.00 0.00 39.33 3.36
1391 1487 0.321919 GGCAGCACATTCTGTCTCCA 60.322 55.000 0.00 0.00 35.88 3.86
1397 1494 2.815589 GCACATTCTGTCTCCACCCTTT 60.816 50.000 0.00 0.00 0.00 3.11
1401 1498 4.597507 ACATTCTGTCTCCACCCTTTTCTA 59.402 41.667 0.00 0.00 0.00 2.10
1405 1502 3.519510 CTGTCTCCACCCTTTTCTATCCA 59.480 47.826 0.00 0.00 0.00 3.41
1407 1504 3.263425 GTCTCCACCCTTTTCTATCCACA 59.737 47.826 0.00 0.00 0.00 4.17
1410 1507 2.009774 CACCCTTTTCTATCCACAGCG 58.990 52.381 0.00 0.00 0.00 5.18
1411 1508 1.065418 ACCCTTTTCTATCCACAGCGG 60.065 52.381 0.00 0.00 0.00 5.52
1418 1515 3.693382 TATCCACAGCGGCGTCACG 62.693 63.158 9.37 0.00 33.14 4.35
1429 1538 2.932083 GCGTCACGTGCTCACAGTG 61.932 63.158 11.67 14.29 37.26 3.66
1438 1547 0.740149 TGCTCACAGTGCACTTTTGG 59.260 50.000 18.94 8.65 35.31 3.28
1439 1548 0.031178 GCTCACAGTGCACTTTTGGG 59.969 55.000 18.94 18.10 0.00 4.12
1456 1883 3.202706 GCCCGTCAGATTTCCGGC 61.203 66.667 0.00 0.00 40.38 6.13
1463 1890 1.062587 GTCAGATTTCCGGCAACATCG 59.937 52.381 0.00 0.00 0.00 3.84
1838 2265 0.943673 CACCAACGTGCACATCAAGA 59.056 50.000 18.64 0.00 32.04 3.02
1898 2325 8.997323 TCTGAATCTGAACTGAAATTTTCTCTC 58.003 33.333 10.33 5.13 0.00 3.20
1924 2352 3.429085 GCGAATTCTGCTGGTGTTTATG 58.571 45.455 12.90 0.00 0.00 1.90
1926 2354 4.094294 GCGAATTCTGCTGGTGTTTATGTA 59.906 41.667 12.90 0.00 0.00 2.29
1928 2356 6.194463 CGAATTCTGCTGGTGTTTATGTATG 58.806 40.000 3.52 0.00 0.00 2.39
1932 2360 6.892658 TCTGCTGGTGTTTATGTATGTTTT 57.107 33.333 0.00 0.00 0.00 2.43
1933 2361 6.908825 TCTGCTGGTGTTTATGTATGTTTTC 58.091 36.000 0.00 0.00 0.00 2.29
1935 2363 6.676950 TGCTGGTGTTTATGTATGTTTTCTG 58.323 36.000 0.00 0.00 0.00 3.02
1936 2364 6.264292 TGCTGGTGTTTATGTATGTTTTCTGT 59.736 34.615 0.00 0.00 0.00 3.41
1938 2366 7.308589 GCTGGTGTTTATGTATGTTTTCTGTCT 60.309 37.037 0.00 0.00 0.00 3.41
1939 2367 7.870826 TGGTGTTTATGTATGTTTTCTGTCTG 58.129 34.615 0.00 0.00 0.00 3.51
1940 2368 6.801862 GGTGTTTATGTATGTTTTCTGTCTGC 59.198 38.462 0.00 0.00 0.00 4.26
2036 2469 1.523938 GGCCTCGGCATCAGGTAAC 60.524 63.158 10.51 0.00 44.11 2.50
2056 2495 4.151258 ACGTGTCATCTCTTTGCAAATG 57.849 40.909 13.23 8.25 0.00 2.32
2057 2496 3.058016 ACGTGTCATCTCTTTGCAAATGG 60.058 43.478 13.23 8.62 0.00 3.16
2058 2497 3.189080 CGTGTCATCTCTTTGCAAATGGA 59.811 43.478 13.23 13.64 0.00 3.41
2059 2498 4.670992 CGTGTCATCTCTTTGCAAATGGAG 60.671 45.833 13.23 16.13 0.00 3.86
2096 2583 7.085746 TCAAATGTTAAGCTGAATGTGTCATG 58.914 34.615 0.00 0.00 35.07 3.07
2143 2639 0.895530 TTGGGCGAGAACCAGAGTAG 59.104 55.000 0.00 0.00 39.57 2.57
2242 2738 7.256756 ACGAGGTAGTACAATATGTAGTGAC 57.743 40.000 2.06 1.99 37.13 3.67
2249 2745 9.245962 GTAGTACAATATGTAGTGACCATGAAC 57.754 37.037 7.87 0.00 37.13 3.18
2250 2746 8.079211 AGTACAATATGTAGTGACCATGAACT 57.921 34.615 0.00 0.00 35.34 3.01
2267 2763 8.954350 ACCATGAACTAAAATTCTCATCTGAAG 58.046 33.333 0.00 0.00 0.00 3.02
2268 2764 9.170734 CCATGAACTAAAATTCTCATCTGAAGA 57.829 33.333 0.00 0.00 0.00 2.87
2507 3034 3.558931 ATCCGATGGTGCATTTCACTA 57.441 42.857 0.00 0.00 44.98 2.74
2508 3035 2.905075 TCCGATGGTGCATTTCACTAG 58.095 47.619 0.00 0.00 44.98 2.57
2510 3037 2.009051 CGATGGTGCATTTCACTAGCA 58.991 47.619 0.00 0.00 41.82 3.49
2511 3038 2.031314 CGATGGTGCATTTCACTAGCAG 59.969 50.000 0.00 0.00 41.82 4.24
2514 3041 2.539346 GTGCATTTCACTAGCAGCAG 57.461 50.000 0.00 0.00 42.38 4.24
2515 3042 1.808945 GTGCATTTCACTAGCAGCAGT 59.191 47.619 0.00 0.00 42.38 4.40
2540 3104 6.260936 TGTCTCTGAATTTGTTTGGAACTCTC 59.739 38.462 0.00 0.00 0.00 3.20
2690 3257 2.732658 GGGTGAACCTGACGACGT 59.267 61.111 0.00 0.00 35.85 4.34
2876 3443 6.749923 ACTGTTCCTAGAATTTGATCTTGC 57.250 37.500 0.00 0.00 0.00 4.01
2879 3446 5.124457 TGTTCCTAGAATTTGATCTTGCAGC 59.876 40.000 0.00 0.00 0.00 5.25
2880 3447 5.108187 TCCTAGAATTTGATCTTGCAGCT 57.892 39.130 0.00 0.00 0.00 4.24
2973 3541 1.614903 TGAACATGCCTTCAAAGCCAG 59.385 47.619 0.00 0.00 0.00 4.85
2990 3558 2.223572 GCCAGGCATAATTTCCAAGACG 60.224 50.000 6.55 0.00 0.00 4.18
2992 3560 3.065371 CCAGGCATAATTTCCAAGACGAC 59.935 47.826 0.00 0.00 0.00 4.34
2993 3561 2.936498 AGGCATAATTTCCAAGACGACG 59.064 45.455 0.00 0.00 0.00 5.12
3011 3579 8.534333 AGACGACGCAACAATATGATAATATT 57.466 30.769 0.00 0.00 0.00 1.28
3013 3581 8.534333 ACGACGCAACAATATGATAATATTCT 57.466 30.769 0.00 0.00 0.00 2.40
3037 3605 3.000727 GAGTTGTCCAATTGTCCTACCG 58.999 50.000 4.43 0.00 0.00 4.02
3091 4289 6.817765 TTATCATGGTTTCACTGAAGAACC 57.182 37.500 5.88 5.88 0.00 3.62
3094 4292 2.930950 TGGTTTCACTGAAGAACCCAG 58.069 47.619 9.31 0.00 35.47 4.45
3150 4348 2.670934 AGCAGCGAGGCAAACAGG 60.671 61.111 1.57 0.00 35.83 4.00
3236 4438 2.756760 CACACCAGATTCAGATTTGGGG 59.243 50.000 0.00 0.00 44.52 4.96
3237 4439 1.753073 CACCAGATTCAGATTTGGGGC 59.247 52.381 1.71 0.00 40.87 5.80
3296 4504 2.048601 AGATGAGATCTGCTTGAGGGG 58.951 52.381 0.00 0.00 38.44 4.79
3335 4546 1.027255 AGATTGAGCAGCAGCAGCAG 61.027 55.000 12.92 0.00 45.49 4.24
3421 4632 1.134848 ACGCTCTCCTTCATCAAGCTC 60.135 52.381 0.00 0.00 0.00 4.09
3422 4633 1.134877 CGCTCTCCTTCATCAAGCTCA 60.135 52.381 0.00 0.00 0.00 4.26
3759 4979 3.304721 CCACCGGACCACGTACCA 61.305 66.667 9.46 0.00 42.24 3.25
3760 4980 2.260434 CACCGGACCACGTACCAG 59.740 66.667 9.46 0.00 42.24 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.449131 TGCAGTTGCCATGATTTCAAAAA 58.551 34.783 1.06 0.00 41.18 1.94
129 130 4.103153 TCTCAGGTCAAAGTTCCAGATTGT 59.897 41.667 0.00 0.00 0.00 2.71
169 170 2.479566 ACTACAGTTGCCATGTCTGG 57.520 50.000 0.00 0.00 46.17 3.86
347 348 3.687698 GTGTGTGTGGGCGTTATCTATTT 59.312 43.478 0.00 0.00 0.00 1.40
348 349 3.267483 GTGTGTGTGGGCGTTATCTATT 58.733 45.455 0.00 0.00 0.00 1.73
351 352 0.669318 CGTGTGTGTGGGCGTTATCT 60.669 55.000 0.00 0.00 0.00 1.98
352 353 1.785321 CGTGTGTGTGGGCGTTATC 59.215 57.895 0.00 0.00 0.00 1.75
366 368 0.743097 GGTCCCTCTTATACGCGTGT 59.257 55.000 24.59 19.31 0.00 4.49
446 451 3.133721 GTCTGTGTGATGCCTAAGAGGAT 59.866 47.826 0.00 0.00 37.67 3.24
491 496 2.091588 CGATAACTGTAACACGTGTGCC 59.908 50.000 24.16 15.99 0.00 5.01
492 497 2.091588 CCGATAACTGTAACACGTGTGC 59.908 50.000 24.16 18.31 0.00 4.57
502 507 3.316071 TTTTGGACGCCGATAACTGTA 57.684 42.857 0.00 0.00 0.00 2.74
503 508 2.172851 TTTTGGACGCCGATAACTGT 57.827 45.000 0.00 0.00 0.00 3.55
534 539 3.209410 CCCCGAGATTTGATCTTTCTGG 58.791 50.000 0.00 0.00 40.38 3.86
537 542 6.753107 TTTTACCCCGAGATTTGATCTTTC 57.247 37.500 0.00 0.00 40.38 2.62
622 628 2.857186 TTGCAGCTGGATACTCAACA 57.143 45.000 17.12 0.00 37.61 3.33
667 677 0.721718 CCGGCGATCTGTTTGACTTC 59.278 55.000 9.30 0.00 0.00 3.01
699 710 2.660802 CTGGTACACGGTCACCCC 59.339 66.667 6.09 0.00 33.61 4.95
750 766 3.739782 GATGCACCGGCGATGTTGC 62.740 63.158 9.30 12.03 45.35 4.17
751 767 2.404789 GATGCACCGGCGATGTTG 59.595 61.111 9.30 0.40 45.35 3.33
752 768 3.195002 CGATGCACCGGCGATGTT 61.195 61.111 9.30 0.00 45.35 2.71
760 776 3.490793 ATCTCTCGCCGATGCACCG 62.491 63.158 0.00 0.00 37.32 4.94
767 783 1.824329 GGGTCTCATCTCTCGCCGA 60.824 63.158 0.00 0.00 0.00 5.54
791 816 3.166489 ACGAAACAAGATCCGGATCTC 57.834 47.619 40.06 27.78 46.75 2.75
873 902 3.843117 GAGGATAAGGACGCGCGGG 62.843 68.421 35.22 22.69 0.00 6.13
874 903 2.354773 GAGGATAAGGACGCGCGG 60.355 66.667 35.22 16.31 0.00 6.46
878 907 1.446366 GGGTGGAGGATAAGGACGC 59.554 63.158 0.00 0.00 0.00 5.19
882 911 2.819284 GCGGGGGTGGAGGATAAGG 61.819 68.421 0.00 0.00 0.00 2.69
884 913 2.070039 CAGCGGGGGTGGAGGATAA 61.070 63.158 0.00 0.00 0.00 1.75
885 914 2.445845 CAGCGGGGGTGGAGGATA 60.446 66.667 0.00 0.00 0.00 2.59
915 961 1.569479 GCGAGTTGAGTTGGGTGAGC 61.569 60.000 0.00 0.00 0.00 4.26
1206 1295 3.320626 GAATGCCTGGAGAAAACAAAGC 58.679 45.455 0.00 0.00 0.00 3.51
1356 1452 3.687102 CCACAGGTGCGGGTACGA 61.687 66.667 0.00 0.00 44.60 3.43
1358 1454 4.323477 TGCCACAGGTGCGGGTAC 62.323 66.667 0.00 0.00 0.00 3.34
1379 1475 4.026356 AGAAAAGGGTGGAGACAGAATG 57.974 45.455 0.00 0.00 44.46 2.67
1380 1476 5.104318 GGATAGAAAAGGGTGGAGACAGAAT 60.104 44.000 0.00 0.00 44.46 2.40
1381 1477 4.225267 GGATAGAAAAGGGTGGAGACAGAA 59.775 45.833 0.00 0.00 44.46 3.02
1382 1478 3.775316 GGATAGAAAAGGGTGGAGACAGA 59.225 47.826 0.00 0.00 44.46 3.41
1383 1479 3.519510 TGGATAGAAAAGGGTGGAGACAG 59.480 47.826 0.00 0.00 44.46 3.51
1384 1480 3.263425 GTGGATAGAAAAGGGTGGAGACA 59.737 47.826 0.00 0.00 38.70 3.41
1385 1481 3.263425 TGTGGATAGAAAAGGGTGGAGAC 59.737 47.826 0.00 0.00 0.00 3.36
1386 1482 3.519510 CTGTGGATAGAAAAGGGTGGAGA 59.480 47.826 0.00 0.00 0.00 3.71
1387 1483 3.878778 CTGTGGATAGAAAAGGGTGGAG 58.121 50.000 0.00 0.00 0.00 3.86
1389 1485 2.369394 GCTGTGGATAGAAAAGGGTGG 58.631 52.381 0.00 0.00 0.00 4.61
1391 1487 1.065418 CCGCTGTGGATAGAAAAGGGT 60.065 52.381 0.00 0.00 42.00 4.34
1397 1494 1.141019 GACGCCGCTGTGGATAGAA 59.859 57.895 12.29 0.00 42.00 2.10
1410 1507 3.406361 CTGTGAGCACGTGACGCC 61.406 66.667 22.23 0.35 0.00 5.68
1411 1508 2.658593 ACTGTGAGCACGTGACGC 60.659 61.111 22.23 18.34 0.00 5.19
1419 1516 0.740149 CCAAAAGTGCACTGTGAGCA 59.260 50.000 22.49 0.00 40.19 4.26
1420 1517 0.031178 CCCAAAAGTGCACTGTGAGC 59.969 55.000 22.49 2.93 0.00 4.26
1429 1538 2.909965 TGACGGGCCCAAAAGTGC 60.910 61.111 24.92 6.34 0.00 4.40
1434 1543 0.610785 GGAAATCTGACGGGCCCAAA 60.611 55.000 24.92 5.06 0.00 3.28
1438 1547 2.513897 CCGGAAATCTGACGGGCC 60.514 66.667 0.00 0.00 43.69 5.80
1838 2265 0.818296 CCGACGGAGAAGAGGTCATT 59.182 55.000 8.64 0.00 0.00 2.57
1864 2291 4.344968 TCAGTTCAGATTCAGAACCAGTGA 59.655 41.667 15.81 11.45 44.91 3.41
1924 2352 6.446318 TGAAAATGGCAGACAGAAAACATAC 58.554 36.000 0.00 0.00 0.00 2.39
1926 2354 5.510179 CCTGAAAATGGCAGACAGAAAACAT 60.510 40.000 12.24 0.00 35.39 2.71
1928 2356 4.202151 ACCTGAAAATGGCAGACAGAAAAC 60.202 41.667 12.24 0.00 35.39 2.43
1932 2360 2.507484 CACCTGAAAATGGCAGACAGA 58.493 47.619 12.24 0.00 35.39 3.41
1933 2361 1.542915 CCACCTGAAAATGGCAGACAG 59.457 52.381 0.00 0.00 35.39 3.51
1940 2368 0.523072 CAGTCGCCACCTGAAAATGG 59.477 55.000 0.00 0.00 39.16 3.16
2036 2469 3.189080 TCCATTTGCAAAGAGATGACACG 59.811 43.478 18.19 0.00 0.00 4.49
2077 2564 6.246420 AGAACATGACACATTCAGCTTAAC 57.754 37.500 0.00 0.00 37.77 2.01
2096 2583 4.436584 CCAATGCTGACGATGAAGAAGAAC 60.437 45.833 0.00 0.00 0.00 3.01
2143 2639 6.690957 CGTCTTGATCTTCTCTATCTTGTGAC 59.309 42.308 0.00 0.00 0.00 3.67
2233 2729 9.167311 GAGAATTTTAGTTCATGGTCACTACAT 57.833 33.333 0.00 0.00 0.00 2.29
2235 2731 8.547967 TGAGAATTTTAGTTCATGGTCACTAC 57.452 34.615 0.00 0.00 0.00 2.73
2238 2734 8.180267 CAGATGAGAATTTTAGTTCATGGTCAC 58.820 37.037 0.00 0.00 30.85 3.67
2242 2738 9.170734 TCTTCAGATGAGAATTTTAGTTCATGG 57.829 33.333 0.00 0.00 30.85 3.66
2267 2763 1.234821 TGTCACACGGCCATTCTTTC 58.765 50.000 2.24 0.00 0.00 2.62
2268 2764 1.541147 CATGTCACACGGCCATTCTTT 59.459 47.619 2.24 0.00 0.00 2.52
2474 2990 2.159240 CCATCGGATTCAGACAAGACGA 60.159 50.000 0.00 0.00 0.00 4.20
2507 3034 2.812591 CAAATTCAGAGACACTGCTGCT 59.187 45.455 0.00 0.00 45.38 4.24
2508 3035 2.551459 ACAAATTCAGAGACACTGCTGC 59.449 45.455 0.00 0.00 45.38 5.25
2510 3037 4.037208 CCAAACAAATTCAGAGACACTGCT 59.963 41.667 0.00 0.00 45.38 4.24
2511 3038 4.036734 TCCAAACAAATTCAGAGACACTGC 59.963 41.667 0.00 0.00 45.38 4.40
2513 3040 5.888161 AGTTCCAAACAAATTCAGAGACACT 59.112 36.000 0.00 0.00 0.00 3.55
2514 3041 6.038714 AGAGTTCCAAACAAATTCAGAGACAC 59.961 38.462 0.00 0.00 0.00 3.67
2515 3042 6.122277 AGAGTTCCAAACAAATTCAGAGACA 58.878 36.000 0.00 0.00 0.00 3.41
2827 3394 2.277969 CAATCAGCAGCATCTTCGTCT 58.722 47.619 0.00 0.00 0.00 4.18
2830 3397 1.063616 CACCAATCAGCAGCATCTTCG 59.936 52.381 0.00 0.00 0.00 3.79
2879 3446 1.657594 CACACTGCATACAAGCTCGAG 59.342 52.381 8.45 8.45 34.99 4.04
2880 3447 1.000843 ACACACTGCATACAAGCTCGA 59.999 47.619 0.00 0.00 34.99 4.04
2944 3512 8.139989 GCTTTGAAGGCATGTTCATTTATATCT 58.860 33.333 0.00 0.00 36.34 1.98
2973 3541 2.538939 GCGTCGTCTTGGAAATTATGCC 60.539 50.000 0.00 0.00 0.00 4.40
2990 3558 9.887189 CGTAGAATATTATCATATTGTTGCGTC 57.113 33.333 0.00 0.00 35.96 5.19
3011 3579 3.576982 AGGACAATTGGACAACTCGTAGA 59.423 43.478 10.83 0.00 0.00 2.59
3013 3581 4.322198 GGTAGGACAATTGGACAACTCGTA 60.322 45.833 10.83 0.52 0.00 3.43
3037 3605 8.970691 TGTTGTAGTACGTACTAATTTCCTTC 57.029 34.615 31.52 18.98 40.20 3.46
3091 4289 2.113774 TGGTTGAGGTGCTGCTGG 59.886 61.111 0.00 0.00 0.00 4.85
3094 4292 1.968540 GAGGTGGTTGAGGTGCTGC 60.969 63.158 0.00 0.00 0.00 5.25
3150 4348 4.098416 GGATTGACTTTATTTCGTGCTGC 58.902 43.478 0.00 0.00 0.00 5.25
3155 4353 4.014406 GGTGGGGATTGACTTTATTTCGT 58.986 43.478 0.00 0.00 0.00 3.85
3204 4402 0.751277 TCTGGTGTGTGGCTTTGGTG 60.751 55.000 0.00 0.00 0.00 4.17
3236 4438 9.351570 CTTCTTCTTTTCTGAGAAATATTTGGC 57.648 33.333 8.64 0.00 35.38 4.52
3296 4504 2.360801 CTCTTCTCGATCTGGTCTTCCC 59.639 54.545 0.00 0.00 0.00 3.97
3335 4546 2.751259 TCATCATCTTGTTCCTTGCTGC 59.249 45.455 0.00 0.00 0.00 5.25
3336 4547 4.398358 ACATCATCATCTTGTTCCTTGCTG 59.602 41.667 0.00 0.00 0.00 4.41
3338 4549 4.495349 CGACATCATCATCTTGTTCCTTGC 60.495 45.833 0.00 0.00 0.00 4.01
3339 4550 4.495349 GCGACATCATCATCTTGTTCCTTG 60.495 45.833 0.00 0.00 0.00 3.61
3340 4551 3.624861 GCGACATCATCATCTTGTTCCTT 59.375 43.478 0.00 0.00 0.00 3.36
3341 4552 3.201290 GCGACATCATCATCTTGTTCCT 58.799 45.455 0.00 0.00 0.00 3.36
3342 4553 2.289002 GGCGACATCATCATCTTGTTCC 59.711 50.000 0.00 0.00 0.00 3.62
3343 4554 2.033407 CGGCGACATCATCATCTTGTTC 60.033 50.000 0.00 0.00 0.00 3.18
3421 4632 1.222936 GGAGTGGGTGAGGAGCATG 59.777 63.158 0.00 0.00 0.00 4.06
3422 4633 2.362369 CGGAGTGGGTGAGGAGCAT 61.362 63.158 0.00 0.00 0.00 3.79
3515 4732 2.508663 GTTGAGGCCGTCCGTAGC 60.509 66.667 0.00 0.00 37.47 3.58
3516 4733 2.202570 CGTTGAGGCCGTCCGTAG 60.203 66.667 0.00 0.00 37.47 3.51
3517 4734 4.424566 GCGTTGAGGCCGTCCGTA 62.425 66.667 0.00 0.00 37.47 4.02
3749 4969 2.993264 CGGGTCCTGGTACGTGGT 60.993 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.