Multiple sequence alignment - TraesCS6A01G207700

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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 TraesCS6A01G207700 chr6A 100.000 2472 0 0 1 2472 371239698 371242169 0.000000e+00 4566.0
1 TraesCS6A01G207700 chr7D 91.678 2175 111 23 1 2134 203038664 203036519 0.000000e+00 2950.0
2 TraesCS6A01G207700 chr7D 94.411 841 38 6 1 839 101006375 101007208 0.000000e+00 1284.0
3 TraesCS6A01G207700 chr7D 93.374 815 40 8 1 801 602281737 602282551 0.000000e+00 1194.0
4 TraesCS6A01G207700 chr7D 96.970 330 10 0 2143 2472 155239525 155239854 2.780000e-154 555.0
5 TraesCS6A01G207700 chr7D 86.770 514 41 5 1660 2148 173620896 173621407 4.650000e-152 547.0
6 TraesCS6A01G207700 chr7D 96.364 330 12 0 2143 2472 155237546 155237875 6.010000e-151 544.0
7 TraesCS6A01G207700 chr7D 92.593 297 19 2 1840 2134 550273792 550274087 8.170000e-115 424.0
8 TraesCS6A01G207700 chr2A 91.324 2190 144 18 1 2146 203391160 203388973 0.000000e+00 2950.0
9 TraesCS6A01G207700 chr1D 94.076 1857 90 13 1 1838 28017861 28019716 0.000000e+00 2802.0
10 TraesCS6A01G207700 chr1D 94.286 1750 84 12 1 1735 471280889 471282637 0.000000e+00 2663.0
11 TraesCS6A01G207700 chr1D 93.886 1750 91 12 1 1735 395974527 395976275 0.000000e+00 2625.0
12 TraesCS6A01G207700 chr1D 93.550 1752 92 13 1 1735 470557441 470555694 0.000000e+00 2590.0
13 TraesCS6A01G207700 chr1D 87.174 499 39 3 1660 2134 189395238 189395735 6.010000e-151 544.0
14 TraesCS6A01G207700 chr1D 87.298 496 36 5 1662 2133 395975996 395976488 2.160000e-150 542.0
15 TraesCS6A01G207700 chr1D 85.606 528 47 6 1660 2163 307836959 307837481 6.060000e-146 527.0
16 TraesCS6A01G207700 chr1A 92.195 1986 116 14 1 1949 6540869 6542852 0.000000e+00 2772.0
17 TraesCS6A01G207700 chr1A 92.195 1986 116 15 1 1949 6554444 6556427 0.000000e+00 2772.0
18 TraesCS6A01G207700 chr1A 90.694 591 49 5 1559 2146 331313139 331313726 0.000000e+00 782.0
19 TraesCS6A01G207700 chr7A 93.208 1855 109 12 1 1838 7721957 7723811 0.000000e+00 2712.0
20 TraesCS6A01G207700 chr3D 93.027 1850 103 13 4 1838 365508980 365507142 0.000000e+00 2678.0
21 TraesCS6A01G207700 chr3D 93.893 1752 90 10 1 1735 524198492 524200243 0.000000e+00 2627.0
22 TraesCS6A01G207700 chr3D 93.333 1755 79 15 1 1735 560124448 560126184 0.000000e+00 2558.0
23 TraesCS6A01G207700 chr3D 91.379 580 45 3 1557 2134 411638011 411637435 0.000000e+00 789.0
24 TraesCS6A01G207700 chr3D 89.106 615 42 3 1557 2147 365507526 365506913 0.000000e+00 741.0
25 TraesCS6A01G207700 chr3D 91.909 309 21 3 1840 2146 101854002 101854308 1.760000e-116 429.0
26 TraesCS6A01G207700 chr6D 94.486 1741 83 7 1 1735 413389107 413390840 0.000000e+00 2671.0
27 TraesCS6A01G207700 chr6D 87.375 499 36 5 1660 2134 427235365 427234870 4.650000e-152 547.0
28 TraesCS6A01G207700 chr6D 86.706 504 36 5 1660 2134 31860518 31861019 4.680000e-147 531.0
29 TraesCS6A01G207700 chr6D 91.582 297 23 1 1840 2134 97920264 97920560 2.290000e-110 409.0
30 TraesCS6A01G207700 chr6D 91.582 297 21 2 1840 2134 359437504 359437210 8.230000e-110 407.0
31 TraesCS6A01G207700 chr6D 92.014 288 20 2 1840 2125 11366511 11366797 3.830000e-108 401.0
32 TraesCS6A01G207700 chr5A 92.722 1855 116 14 1 1838 457875752 457873900 0.000000e+00 2660.0
33 TraesCS6A01G207700 chr5D 93.471 1746 93 12 3 1735 454209252 454210989 0.000000e+00 2573.0
34 TraesCS6A01G207700 chr5D 87.841 477 39 9 1660 2134 7009113 7008654 2.160000e-150 542.0
35 TraesCS6A01G207700 chr5D 85.938 512 41 5 1660 2146 454210713 454211218 3.640000e-143 518.0
36 TraesCS6A01G207700 chr5D 88.018 434 26 4 1737 2146 111595612 111595181 7.940000e-135 490.0
37 TraesCS6A01G207700 chr5D 91.613 310 22 3 1840 2146 304361115 304361423 2.270000e-115 425.0
38 TraesCS6A01G207700 chr4D 93.375 1283 69 12 571 1838 22538392 22537111 0.000000e+00 1884.0
39 TraesCS6A01G207700 chr4D 88.091 613 49 2 1558 2146 22537494 22536882 0.000000e+00 706.0
40 TraesCS6A01G207700 chr4D 87.135 513 37 6 1660 2147 488739023 488738515 2.780000e-154 555.0
41 TraesCS6A01G207700 chr4D 86.800 500 38 6 1660 2134 248321447 248320951 1.300000e-147 532.0
42 TraesCS6A01G207700 chr4D 85.658 509 48 8 1660 2145 6918741 6918235 1.700000e-141 512.0
43 TraesCS6A01G207700 chr4D 87.500 440 34 1 1661 2079 92078793 92078354 2.860000e-134 488.0
44 TraesCS6A01G207700 chr4D 86.946 406 28 4 1660 2043 484449151 484449553 1.360000e-117 433.0
45 TraesCS6A01G207700 chr4D 89.899 297 27 2 1840 2134 462136249 462135954 1.790000e-101 379.0
46 TraesCS6A01G207700 chrUn 91.392 790 45 7 1182 1949 364694801 364694013 0.000000e+00 1061.0
47 TraesCS6A01G207700 chrUn 90.909 308 26 2 1840 2145 89819484 89819177 1.770000e-111 412.0
48 TraesCS6A01G207700 chrUn 90.572 297 23 4 1840 2134 26612445 26612152 2.980000e-104 388.0
49 TraesCS6A01G207700 chrUn 93.367 196 13 0 1848 2043 349088933 349089128 8.650000e-75 291.0
50 TraesCS6A01G207700 chrUn 93.299 194 12 1 1851 2043 385119148 385118955 4.020000e-73 285.0
51 TraesCS6A01G207700 chrUn 92.347 196 15 0 1848 2043 35824447 35824252 1.870000e-71 279.0
52 TraesCS6A01G207700 chrUn 91.176 204 15 2 1840 2043 234296197 234295997 8.710000e-70 274.0
53 TraesCS6A01G207700 chrUn 91.848 184 14 1 1838 2020 47472744 47472561 3.150000e-64 255.0
54 TraesCS6A01G207700 chrUn 89.163 203 15 4 1934 2134 374223581 374223778 1.900000e-61 246.0
55 TraesCS6A01G207700 chrUn 86.730 211 7 5 1760 1949 410966372 410966162 5.350000e-52 215.0
56 TraesCS6A01G207700 chrUn 88.462 182 14 4 1955 2134 349408666 349408842 1.930000e-51 213.0
57 TraesCS6A01G207700 chrUn 88.172 93 8 2 2036 2125 349089058 349089150 9.350000e-20 108.0
58 TraesCS6A01G207700 chrUn 85.437 103 11 3 2036 2134 385119026 385118924 1.210000e-18 104.0
59 TraesCS6A01G207700 chrUn 90.541 74 5 2 2036 2108 26612312 26612240 2.020000e-16 97.1
60 TraesCS6A01G207700 chrUn 85.227 88 10 2 2049 2134 383611825 383611739 1.220000e-13 87.9
61 TraesCS6A01G207700 chrUn 87.838 74 6 3 2036 2108 349408684 349408755 1.580000e-12 84.2
62 TraesCS6A01G207700 chr2D 87.976 499 34 5 1660 2134 142521945 142521449 1.280000e-157 566.0
63 TraesCS6A01G207700 chr2D 91.167 317 23 4 1840 2152 60189497 60189182 2.270000e-115 425.0
64 TraesCS6A01G207700 chr6B 89.881 336 28 1 2143 2472 159098982 159098647 6.320000e-116 427.0
65 TraesCS6A01G207700 chr6B 94.475 181 10 0 2292 2472 339247223 339247043 1.870000e-71 279.0
66 TraesCS6A01G207700 chr6B 97.403 154 4 0 2143 2296 339260135 339259982 1.890000e-66 263.0
67 TraesCS6A01G207700 chr6B 92.424 132 7 3 2343 2472 159095791 159095661 4.200000e-43 185.0
68 TraesCS6A01G207700 chr4B 95.397 239 11 0 2234 2472 648174282 648174044 4.990000e-102 381.0
69 TraesCS6A01G207700 chr4B 97.368 114 3 0 2143 2256 648174284 648174397 6.980000e-46 195.0


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 TraesCS6A01G207700 chr6A 371239698 371242169 2471 False 4566.0 4566 100.0000 1 2472 1 chr6A.!!$F1 2471
1 TraesCS6A01G207700 chr7D 203036519 203038664 2145 True 2950.0 2950 91.6780 1 2134 1 chr7D.!!$R1 2133
2 TraesCS6A01G207700 chr7D 101006375 101007208 833 False 1284.0 1284 94.4110 1 839 1 chr7D.!!$F1 838
3 TraesCS6A01G207700 chr7D 602281737 602282551 814 False 1194.0 1194 93.3740 1 801 1 chr7D.!!$F4 800
4 TraesCS6A01G207700 chr7D 155237546 155239854 2308 False 549.5 555 96.6670 2143 2472 2 chr7D.!!$F5 329
5 TraesCS6A01G207700 chr7D 173620896 173621407 511 False 547.0 547 86.7700 1660 2148 1 chr7D.!!$F2 488
6 TraesCS6A01G207700 chr2A 203388973 203391160 2187 True 2950.0 2950 91.3240 1 2146 1 chr2A.!!$R1 2145
7 TraesCS6A01G207700 chr1D 28017861 28019716 1855 False 2802.0 2802 94.0760 1 1838 1 chr1D.!!$F1 1837
8 TraesCS6A01G207700 chr1D 471280889 471282637 1748 False 2663.0 2663 94.2860 1 1735 1 chr1D.!!$F4 1734
9 TraesCS6A01G207700 chr1D 470555694 470557441 1747 True 2590.0 2590 93.5500 1 1735 1 chr1D.!!$R1 1734
10 TraesCS6A01G207700 chr1D 395974527 395976488 1961 False 1583.5 2625 90.5920 1 2133 2 chr1D.!!$F5 2132
11 TraesCS6A01G207700 chr1D 307836959 307837481 522 False 527.0 527 85.6060 1660 2163 1 chr1D.!!$F3 503
12 TraesCS6A01G207700 chr1A 6540869 6542852 1983 False 2772.0 2772 92.1950 1 1949 1 chr1A.!!$F1 1948
13 TraesCS6A01G207700 chr1A 6554444 6556427 1983 False 2772.0 2772 92.1950 1 1949 1 chr1A.!!$F2 1948
14 TraesCS6A01G207700 chr1A 331313139 331313726 587 False 782.0 782 90.6940 1559 2146 1 chr1A.!!$F3 587
15 TraesCS6A01G207700 chr7A 7721957 7723811 1854 False 2712.0 2712 93.2080 1 1838 1 chr7A.!!$F1 1837
16 TraesCS6A01G207700 chr3D 524198492 524200243 1751 False 2627.0 2627 93.8930 1 1735 1 chr3D.!!$F2 1734
17 TraesCS6A01G207700 chr3D 560124448 560126184 1736 False 2558.0 2558 93.3330 1 1735 1 chr3D.!!$F3 1734
18 TraesCS6A01G207700 chr3D 365506913 365508980 2067 True 1709.5 2678 91.0665 4 2147 2 chr3D.!!$R2 2143
19 TraesCS6A01G207700 chr3D 411637435 411638011 576 True 789.0 789 91.3790 1557 2134 1 chr3D.!!$R1 577
20 TraesCS6A01G207700 chr6D 413389107 413390840 1733 False 2671.0 2671 94.4860 1 1735 1 chr6D.!!$F4 1734
21 TraesCS6A01G207700 chr6D 31860518 31861019 501 False 531.0 531 86.7060 1660 2134 1 chr6D.!!$F2 474
22 TraesCS6A01G207700 chr5A 457873900 457875752 1852 True 2660.0 2660 92.7220 1 1838 1 chr5A.!!$R1 1837
23 TraesCS6A01G207700 chr5D 454209252 454211218 1966 False 1545.5 2573 89.7045 3 2146 2 chr5D.!!$F2 2143
24 TraesCS6A01G207700 chr4D 22536882 22538392 1510 True 1295.0 1884 90.7330 571 2146 2 chr4D.!!$R6 1575
25 TraesCS6A01G207700 chr4D 488738515 488739023 508 True 555.0 555 87.1350 1660 2147 1 chr4D.!!$R5 487
26 TraesCS6A01G207700 chr4D 6918235 6918741 506 True 512.0 512 85.6580 1660 2145 1 chr4D.!!$R1 485
27 TraesCS6A01G207700 chrUn 364694013 364694801 788 True 1061.0 1061 91.3920 1182 1949 1 chrUn.!!$R5 767
28 TraesCS6A01G207700 chr6B 159095661 159098982 3321 True 306.0 427 91.1525 2143 2472 2 chr6B.!!$R3 329

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
506 516 0.178929 ACTCCTGTTTCCCCTCTCGT 60.179 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2824 1.080354 CCTCCCACCCTGGTCTACA 59.92 63.158 0.0 0.0 35.17 2.74 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
348 353 0.245266 TGCGCCAACGAGATCAAGTA 59.755 50.000 4.18 0.00 43.93 2.24
476 486 2.019249 CATTGACACCGCCATGATCTT 58.981 47.619 0.00 0.00 0.00 2.40
487 497 3.742327 CGCCATGATCTTCTCTTGCCTTA 60.742 47.826 0.00 0.00 0.00 2.69
500 510 0.696501 TGCCTTACTCCTGTTTCCCC 59.303 55.000 0.00 0.00 0.00 4.81
501 511 0.992695 GCCTTACTCCTGTTTCCCCT 59.007 55.000 0.00 0.00 0.00 4.79
502 512 1.065345 GCCTTACTCCTGTTTCCCCTC 60.065 57.143 0.00 0.00 0.00 4.30
503 513 2.552367 CCTTACTCCTGTTTCCCCTCT 58.448 52.381 0.00 0.00 0.00 3.69
504 514 2.502130 CCTTACTCCTGTTTCCCCTCTC 59.498 54.545 0.00 0.00 0.00 3.20
505 515 1.848652 TACTCCTGTTTCCCCTCTCG 58.151 55.000 0.00 0.00 0.00 4.04
506 516 0.178929 ACTCCTGTTTCCCCTCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
507 517 0.977395 CTCCTGTTTCCCCTCTCGTT 59.023 55.000 0.00 0.00 0.00 3.85
508 518 1.348036 CTCCTGTTTCCCCTCTCGTTT 59.652 52.381 0.00 0.00 0.00 3.60
509 519 1.772453 TCCTGTTTCCCCTCTCGTTTT 59.228 47.619 0.00 0.00 0.00 2.43
575 595 1.231068 CCATTGCAGGGGTAGCCAT 59.769 57.895 14.06 1.68 0.00 4.40
681 702 1.692042 CCACTCCCTCTCCATGCCT 60.692 63.158 0.00 0.00 0.00 4.75
682 703 1.525923 CACTCCCTCTCCATGCCTG 59.474 63.158 0.00 0.00 0.00 4.85
684 705 0.980231 ACTCCCTCTCCATGCCTGTC 60.980 60.000 0.00 0.00 0.00 3.51
685 706 0.690411 CTCCCTCTCCATGCCTGTCT 60.690 60.000 0.00 0.00 0.00 3.41
686 707 0.252881 TCCCTCTCCATGCCTGTCTT 60.253 55.000 0.00 0.00 0.00 3.01
687 708 1.008327 TCCCTCTCCATGCCTGTCTTA 59.992 52.381 0.00 0.00 0.00 2.10
690 711 3.495806 CCCTCTCCATGCCTGTCTTAATC 60.496 52.174 0.00 0.00 0.00 1.75
691 712 3.390639 CCTCTCCATGCCTGTCTTAATCT 59.609 47.826 0.00 0.00 0.00 2.40
693 714 4.774124 TCTCCATGCCTGTCTTAATCTTG 58.226 43.478 0.00 0.00 0.00 3.02
695 716 3.054139 TCCATGCCTGTCTTAATCTTGCT 60.054 43.478 0.00 0.00 0.00 3.91
700 721 3.620966 GCCTGTCTTAATCTTGCTCCACT 60.621 47.826 0.00 0.00 0.00 4.00
703 724 5.474876 CCTGTCTTAATCTTGCTCCACTTTT 59.525 40.000 0.00 0.00 0.00 2.27
704 725 6.317789 TGTCTTAATCTTGCTCCACTTTTG 57.682 37.500 0.00 0.00 0.00 2.44
705 726 5.157067 GTCTTAATCTTGCTCCACTTTTGC 58.843 41.667 0.00 0.00 0.00 3.68
706 727 5.048434 GTCTTAATCTTGCTCCACTTTTGCT 60.048 40.000 0.00 0.00 0.00 3.91
707 728 3.655276 AATCTTGCTCCACTTTTGCTG 57.345 42.857 0.00 0.00 0.00 4.41
708 729 2.057137 TCTTGCTCCACTTTTGCTGT 57.943 45.000 0.00 0.00 0.00 4.40
709 730 1.949525 TCTTGCTCCACTTTTGCTGTC 59.050 47.619 0.00 0.00 0.00 3.51
784 827 2.566529 CACGCCACACTCTCGCTA 59.433 61.111 0.00 0.00 0.00 4.26
787 830 2.573869 GCCACACTCTCGCTAGCA 59.426 61.111 16.45 0.92 0.00 3.49
821 864 1.487976 CTGCTGCTTCCTATCCCTTCA 59.512 52.381 0.00 0.00 0.00 3.02
848 891 3.771160 CTGTCGCGCCCCTACCTT 61.771 66.667 0.00 0.00 0.00 3.50
1089 1134 0.178921 AGAAGGTGTGGAGAGGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
1095 1140 1.194781 TGTGGAGAGGCAGAAGGTCC 61.195 60.000 0.00 0.00 0.00 4.46
1332 1405 9.525409 AAGTTGAGATTTTTGAACTGATTTCTG 57.475 29.630 0.00 0.00 34.97 3.02
1347 1420 3.467374 TTTCTGTGCAAATGGGGTTTC 57.533 42.857 0.00 0.00 0.00 2.78
1474 1547 9.281075 ACGTGTCTGTTATTTGTTTTCTAAAAC 57.719 29.630 10.66 10.66 46.40 2.43
1567 1640 7.945033 TGTTTCCTGAAAATCTGTTATTTGC 57.055 32.000 0.00 0.00 31.33 3.68
1570 1643 8.703336 GTTTCCTGAAAATCTGTTATTTGCTTC 58.297 33.333 0.00 0.00 31.33 3.86
1571 1644 6.924111 TCCTGAAAATCTGTTATTTGCTTCC 58.076 36.000 0.00 0.00 0.00 3.46
1573 1646 7.888021 TCCTGAAAATCTGTTATTTGCTTCCTA 59.112 33.333 0.00 0.00 0.00 2.94
1574 1647 8.522830 CCTGAAAATCTGTTATTTGCTTCCTAA 58.477 33.333 0.00 0.00 0.00 2.69
1575 1648 9.565213 CTGAAAATCTGTTATTTGCTTCCTAAG 57.435 33.333 0.00 0.00 0.00 2.18
1577 1650 9.561270 GAAAATCTGTTATTTGCTTCCTAAGAC 57.439 33.333 0.00 0.00 0.00 3.01
1580 1653 8.635765 ATCTGTTATTTGCTTCCTAAGACAAA 57.364 30.769 9.83 9.83 38.18 2.83
1581 1654 8.635765 TCTGTTATTTGCTTCCTAAGACAAAT 57.364 30.769 17.68 17.68 42.37 2.32
1582 1655 9.077885 TCTGTTATTTGCTTCCTAAGACAAATT 57.922 29.630 18.27 9.50 41.25 1.82
1583 1656 9.132521 CTGTTATTTGCTTCCTAAGACAAATTG 57.867 33.333 18.27 0.00 41.25 2.32
1586 1659 9.691362 TTATTTGCTTCCTAAGACAAATTGAAC 57.309 29.630 18.27 0.00 41.25 3.18
1587 1660 6.707440 TTGCTTCCTAAGACAAATTGAACA 57.293 33.333 0.00 0.00 0.00 3.18
1588 1661 6.707440 TGCTTCCTAAGACAAATTGAACAA 57.293 33.333 0.00 0.00 0.00 2.83
1590 1663 7.725251 TGCTTCCTAAGACAAATTGAACAAAT 58.275 30.769 0.00 0.00 0.00 2.32
1591 1664 8.855110 TGCTTCCTAAGACAAATTGAACAAATA 58.145 29.630 0.00 0.00 0.00 1.40
1592 1665 9.691362 GCTTCCTAAGACAAATTGAACAAATAA 57.309 29.630 0.00 0.00 0.00 1.40
1602 1675 9.757227 ACAAATTGAACAAATAAAAGGAATCGA 57.243 25.926 0.00 0.00 0.00 3.59
1611 1684 8.872845 ACAAATAAAAGGAATCGATTGATTTGC 58.127 29.630 16.96 0.00 44.79 3.68
1612 1685 8.871862 CAAATAAAAGGAATCGATTGATTTGCA 58.128 29.630 16.96 8.16 44.79 4.08
1617 1690 9.603921 AAAAGGAATCGATTGATTTGCATAATT 57.396 25.926 16.96 0.00 44.79 1.40
1693 1874 8.696410 TGTTTTCTAAGACAAATTGAACCAAC 57.304 30.769 0.00 0.00 0.00 3.77
1878 2653 9.137459 TGTTTCCTAAGACAAATTGAACCAATA 57.863 29.630 0.00 0.00 32.43 1.90
2207 2991 5.305902 TGAAGTTGTAGGACTGGTGTGAATA 59.694 40.000 0.00 0.00 0.00 1.75
2256 3046 2.356125 GCCTTGGCCTACTTCTTCATGA 60.356 50.000 3.32 0.00 0.00 3.07
2258 3048 4.335416 CCTTGGCCTACTTCTTCATGAAA 58.665 43.478 9.88 0.00 33.79 2.69
2315 3105 1.965643 ACTTGCATGCATGTGTTTCCT 59.034 42.857 31.59 10.82 33.85 3.36
2324 3114 2.483538 GCATGTGTTTCCTTTGGTTGCT 60.484 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 1.893808 CCATTCCCCTTCGATGCCG 60.894 63.158 0.00 0.00 37.07 5.69
348 353 3.321648 TCGATGCAGGGGTGCTGT 61.322 61.111 0.00 0.00 35.49 4.40
476 486 3.008049 GGAAACAGGAGTAAGGCAAGAGA 59.992 47.826 0.00 0.00 0.00 3.10
487 497 0.178929 ACGAGAGGGGAAACAGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
500 510 4.422546 ACCTAACGAGAGAAAACGAGAG 57.577 45.455 0.00 0.00 0.00 3.20
501 511 6.506500 AATACCTAACGAGAGAAAACGAGA 57.493 37.500 0.00 0.00 0.00 4.04
502 512 6.805271 TGAAATACCTAACGAGAGAAAACGAG 59.195 38.462 0.00 0.00 0.00 4.18
503 513 6.583806 GTGAAATACCTAACGAGAGAAAACGA 59.416 38.462 0.00 0.00 0.00 3.85
504 514 6.183360 GGTGAAATACCTAACGAGAGAAAACG 60.183 42.308 0.00 0.00 46.51 3.60
505 515 7.058298 GGTGAAATACCTAACGAGAGAAAAC 57.942 40.000 0.00 0.00 46.51 2.43
681 702 5.278463 GCAAAAGTGGAGCAAGATTAAGACA 60.278 40.000 0.00 0.00 0.00 3.41
682 703 5.048434 AGCAAAAGTGGAGCAAGATTAAGAC 60.048 40.000 0.00 0.00 0.00 3.01
684 705 5.159209 CAGCAAAAGTGGAGCAAGATTAAG 58.841 41.667 0.00 0.00 0.00 1.85
685 706 4.584325 ACAGCAAAAGTGGAGCAAGATTAA 59.416 37.500 0.00 0.00 0.00 1.40
686 707 4.144297 ACAGCAAAAGTGGAGCAAGATTA 58.856 39.130 0.00 0.00 0.00 1.75
687 708 2.961062 ACAGCAAAAGTGGAGCAAGATT 59.039 40.909 0.00 0.00 0.00 2.40
690 711 1.334419 CGACAGCAAAAGTGGAGCAAG 60.334 52.381 0.00 0.00 0.00 4.01
691 712 0.662619 CGACAGCAAAAGTGGAGCAA 59.337 50.000 0.00 0.00 0.00 3.91
693 714 0.235926 GACGACAGCAAAAGTGGAGC 59.764 55.000 0.00 0.00 0.00 4.70
695 716 1.495584 GCGACGACAGCAAAAGTGGA 61.496 55.000 0.00 0.00 34.19 4.02
700 721 2.938823 GAGCGCGACGACAGCAAAA 61.939 57.895 12.10 0.00 34.19 2.44
768 811 2.878429 CTAGCGAGAGTGTGGCGT 59.122 61.111 0.00 0.00 34.44 5.68
809 852 0.759436 GGGCGAGTGAAGGGATAGGA 60.759 60.000 0.00 0.00 0.00 2.94
977 1022 4.003788 AGCAGCGTACCAGCGGTT 62.004 61.111 5.57 0.00 40.81 4.44
1017 1062 0.680921 CCTCCGCCACATTTGTCCAT 60.681 55.000 0.00 0.00 0.00 3.41
1089 1134 3.782443 GACATCGCCCCGGACCTT 61.782 66.667 0.73 0.00 0.00 3.50
1102 1147 3.580084 ACCACAGCCAGGTGACAT 58.420 55.556 3.46 0.00 41.32 3.06
1219 1289 7.010160 GGAAATCACCCCTCCATTGATATTAA 58.990 38.462 0.00 0.00 29.64 1.40
1311 1384 6.919662 TGCACAGAAATCAGTTCAAAAATCTC 59.080 34.615 0.00 0.00 38.86 2.75
1312 1385 6.808829 TGCACAGAAATCAGTTCAAAAATCT 58.191 32.000 0.00 0.00 38.86 2.40
1332 1405 3.124578 ACAATGAAACCCCATTTGCAC 57.875 42.857 0.00 0.00 34.77 4.57
1347 1420 7.072177 ACTGATATCACGTTACCAAACAATG 57.928 36.000 0.00 0.00 35.16 2.82
1435 1508 2.936498 CAGACACGTCACAACTTTCCTT 59.064 45.455 0.00 0.00 0.00 3.36
1541 1614 8.825745 GCAAATAACAGATTTTCAGGAAACAAA 58.174 29.630 0.00 0.00 0.00 2.83
1542 1615 8.203485 AGCAAATAACAGATTTTCAGGAAACAA 58.797 29.630 0.00 0.00 0.00 2.83
1544 1617 8.593492 AAGCAAATAACAGATTTTCAGGAAAC 57.407 30.769 0.00 0.00 0.00 2.78
1545 1618 7.872483 GGAAGCAAATAACAGATTTTCAGGAAA 59.128 33.333 0.00 0.00 0.00 3.13
1548 1621 6.928520 AGGAAGCAAATAACAGATTTTCAGG 58.071 36.000 0.00 0.00 0.00 3.86
1549 1622 9.565213 CTTAGGAAGCAAATAACAGATTTTCAG 57.435 33.333 0.00 0.00 0.00 3.02
1551 1624 9.561270 GTCTTAGGAAGCAAATAACAGATTTTC 57.439 33.333 0.00 0.00 0.00 2.29
1552 1625 9.077885 TGTCTTAGGAAGCAAATAACAGATTTT 57.922 29.630 0.00 0.00 0.00 1.82
1553 1626 8.635765 TGTCTTAGGAAGCAAATAACAGATTT 57.364 30.769 0.00 0.00 0.00 2.17
1554 1627 8.635765 TTGTCTTAGGAAGCAAATAACAGATT 57.364 30.769 0.00 0.00 0.00 2.40
1555 1628 8.635765 TTTGTCTTAGGAAGCAAATAACAGAT 57.364 30.769 0.00 0.00 33.10 2.90
1556 1629 8.635765 ATTTGTCTTAGGAAGCAAATAACAGA 57.364 30.769 14.42 0.00 40.27 3.41
1557 1630 9.132521 CAATTTGTCTTAGGAAGCAAATAACAG 57.867 33.333 15.48 7.99 40.71 3.16
1558 1631 8.855110 TCAATTTGTCTTAGGAAGCAAATAACA 58.145 29.630 15.48 0.00 40.71 2.41
1559 1632 9.691362 TTCAATTTGTCTTAGGAAGCAAATAAC 57.309 29.630 15.48 0.00 40.71 1.89
1560 1633 9.691362 GTTCAATTTGTCTTAGGAAGCAAATAA 57.309 29.630 15.48 9.13 40.71 1.40
1562 1635 7.725251 TGTTCAATTTGTCTTAGGAAGCAAAT 58.275 30.769 12.06 12.06 41.98 2.32
1564 1637 6.707440 TGTTCAATTTGTCTTAGGAAGCAA 57.293 33.333 0.00 0.00 0.00 3.91
1566 1639 9.691362 TTATTTGTTCAATTTGTCTTAGGAAGC 57.309 29.630 0.00 0.00 0.00 3.86
1586 1659 8.871862 TGCAAATCAATCGATTCCTTTTATTTG 58.128 29.630 7.92 15.80 41.12 2.32
1587 1660 9.603921 ATGCAAATCAATCGATTCCTTTTATTT 57.396 25.926 7.92 5.26 41.12 1.40
1591 1664 9.603921 AATTATGCAAATCAATCGATTCCTTTT 57.396 25.926 7.92 5.75 41.12 2.27
1592 1665 9.603921 AAATTATGCAAATCAATCGATTCCTTT 57.396 25.926 7.92 8.03 41.12 3.11
1645 1718 9.883142 AACAAATAACAGATTTTCAGGAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
1693 1874 6.897259 ATGCAAATCAATCGATTCCTTTTG 57.103 33.333 21.42 21.42 41.12 2.44
1781 2328 8.987890 CGATTCCTTTTATTGGTTCAATTTGTT 58.012 29.630 0.00 0.00 35.54 2.83
1908 2683 9.530633 GTATAACAAATCACGGATCTAACTTCT 57.469 33.333 0.00 0.00 0.00 2.85
2032 2812 6.150474 CACCCTGGTCTACAATTTATTTTCGT 59.850 38.462 0.00 0.00 0.00 3.85
2044 2824 1.080354 CCTCCCACCCTGGTCTACA 59.920 63.158 0.00 0.00 35.17 2.74
2047 2827 4.354943 CCCCTCCCACCCTGGTCT 62.355 72.222 0.00 0.00 35.17 3.85
2091 2873 3.729462 CGTCTTCGGTTTGTTTTTGCTGA 60.729 43.478 0.00 0.00 0.00 4.26
2101 2883 2.139917 TGGTGAATCGTCTTCGGTTTG 58.860 47.619 0.00 0.00 40.67 2.93
2129 2913 9.646427 AACGGCAAGCAATCTTTATTTTTAATA 57.354 25.926 0.00 0.00 0.00 0.98
2140 2924 2.100584 TGTTCAAACGGCAAGCAATCTT 59.899 40.909 0.00 0.00 0.00 2.40
2207 2991 3.700038 ACGTTCGGTTAGATGGAGAAGAT 59.300 43.478 0.00 0.00 0.00 2.40
2256 3046 8.763601 AGATTTAGTAGAAGCTACATGGACTTT 58.236 33.333 7.29 0.00 0.00 2.66
2258 3048 7.906199 AGATTTAGTAGAAGCTACATGGACT 57.094 36.000 7.29 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.