Multiple sequence alignment - TraesCS5A01G085000

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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 TraesCS5A01G085000 chr5A 100.000 2919 0 0 985 3903 111588730 111591648 0.000000e+00 5391.0
1 TraesCS5A01G085000 chr5A 100.000 588 0 0 1 588 111587746 111588333 0.000000e+00 1086.0
2 TraesCS5A01G085000 chr5B 89.733 3000 171 54 986 3902 118452014 118454959 0.000000e+00 3707.0
3 TraesCS5A01G085000 chr5B 88.668 503 43 9 93 588 118451444 118451939 5.580000e-168 601.0
4 TraesCS5A01G085000 chr5D 87.804 2386 113 84 985 3265 108103449 108105761 0.000000e+00 2630.0
5 TraesCS5A01G085000 chr5D 88.367 490 35 12 109 588 108102896 108103373 1.570000e-158 569.0
6 TraesCS5A01G085000 chr5D 93.634 377 24 0 3426 3802 108105751 108106127 7.320000e-157 564.0
7 TraesCS5A01G085000 chr5D 95.181 83 4 0 3821 3903 108106120 108106202 8.800000e-27 132.0
8 TraesCS5A01G085000 chr6A 86.306 314 28 6 998 1302 504122129 504122436 1.050000e-85 327.0
9 TraesCS5A01G085000 chr6A 90.278 72 6 1 2513 2583 504122452 504122523 4.150000e-15 93.5
10 TraesCS5A01G085000 chr3D 79.773 440 69 13 989 1416 463230477 463230046 6.340000e-78 302.0
11 TraesCS5A01G085000 chr3D 79.545 440 66 12 988 1416 463199259 463198833 3.810000e-75 292.0
12 TraesCS5A01G085000 chr3A 79.398 432 71 14 998 1417 606446789 606446364 4.930000e-74 289.0
13 TraesCS5A01G085000 chr3A 81.734 323 42 12 1098 1416 606519063 606518754 1.800000e-63 254.0
14 TraesCS5A01G085000 chr3A 78.014 141 19 8 1524 1659 606446262 606446129 1.160000e-10 78.7
15 TraesCS5A01G085000 chr3B 79.215 433 62 20 998 1416 616426981 616426563 3.840000e-70 276.0
16 TraesCS5A01G085000 chr4D 84.848 264 27 5 1006 1266 404324365 404324112 1.800000e-63 254.0
17 TraesCS5A01G085000 chr7A 84.375 96 15 0 3335 3430 14301820 14301915 1.150000e-15 95.3
18 TraesCS5A01G085000 chr1A 90.909 44 4 0 3348 3391 126516081 126516038 4.210000e-05 60.2


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 TraesCS5A01G085000 chr5A 111587746 111591648 3902 False 3238.50 5391 100.0000 1 3903 2 chr5A.!!$F1 3902
1 TraesCS5A01G085000 chr5B 118451444 118454959 3515 False 2154.00 3707 89.2005 93 3902 2 chr5B.!!$F1 3809
2 TraesCS5A01G085000 chr5D 108102896 108106202 3306 False 973.75 2630 91.2465 109 3903 4 chr5D.!!$F1 3794

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
421 433 0.249447 GATCATGGCCACACGATCGA 60.249 55.0 24.34 0.00 36.7 3.59 F
422 434 0.530650 ATCATGGCCACACGATCGAC 60.531 55.0 24.34 5.26 0.0 4.20 F
1744 1794 0.664761 CGGTGTTGATCCATCCATGC 59.335 55.0 0.00 0.00 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1893 0.029035 GTGTCTCGTGTGACTCGTGT 59.971 55.0 6.94 0.00 37.79 4.49 R
1847 1897 0.306840 TGTCGTGTCTCGTGTGACTC 59.693 55.0 4.01 0.05 40.80 3.36 R
3442 3589 0.389391 AGACCGTAGCCGAATGGATG 59.611 55.0 0.00 0.00 37.49 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 5.856126 TTTATGTTAAGACTGCTGAACCG 57.144 39.130 0.00 0.00 34.99 4.44
61 62 2.902705 TGTTAAGACTGCTGAACCGT 57.097 45.000 0.00 0.00 34.99 4.83
62 63 2.479837 TGTTAAGACTGCTGAACCGTG 58.520 47.619 0.00 0.00 34.99 4.94
63 64 2.159014 TGTTAAGACTGCTGAACCGTGT 60.159 45.455 0.00 0.00 34.99 4.49
64 65 2.870411 GTTAAGACTGCTGAACCGTGTT 59.130 45.455 0.00 0.00 30.38 3.32
65 66 2.038387 AAGACTGCTGAACCGTGTTT 57.962 45.000 0.00 0.00 0.00 2.83
66 67 1.299541 AGACTGCTGAACCGTGTTTG 58.700 50.000 0.00 0.00 0.00 2.93
67 68 1.014352 GACTGCTGAACCGTGTTTGT 58.986 50.000 0.00 0.00 0.00 2.83
68 69 1.400494 GACTGCTGAACCGTGTTTGTT 59.600 47.619 0.00 0.00 0.00 2.83
69 70 1.816224 ACTGCTGAACCGTGTTTGTTT 59.184 42.857 0.00 0.00 0.00 2.83
70 71 2.184448 CTGCTGAACCGTGTTTGTTTG 58.816 47.619 0.00 0.00 0.00 2.93
71 72 1.135257 TGCTGAACCGTGTTTGTTTGG 60.135 47.619 0.00 0.00 0.00 3.28
72 73 1.801025 GCTGAACCGTGTTTGTTTGGG 60.801 52.381 0.00 0.00 0.00 4.12
73 74 1.474879 CTGAACCGTGTTTGTTTGGGT 59.525 47.619 0.00 0.00 0.00 4.51
74 75 1.473278 TGAACCGTGTTTGTTTGGGTC 59.527 47.619 0.00 0.00 38.72 4.46
75 76 1.746787 GAACCGTGTTTGTTTGGGTCT 59.253 47.619 0.00 0.00 35.29 3.85
76 77 1.842052 ACCGTGTTTGTTTGGGTCTT 58.158 45.000 0.00 0.00 0.00 3.01
77 78 1.474879 ACCGTGTTTGTTTGGGTCTTG 59.525 47.619 0.00 0.00 0.00 3.02
78 79 1.746220 CCGTGTTTGTTTGGGTCTTGA 59.254 47.619 0.00 0.00 0.00 3.02
79 80 2.360801 CCGTGTTTGTTTGGGTCTTGAT 59.639 45.455 0.00 0.00 0.00 2.57
80 81 3.181480 CCGTGTTTGTTTGGGTCTTGATT 60.181 43.478 0.00 0.00 0.00 2.57
81 82 4.041723 CGTGTTTGTTTGGGTCTTGATTC 58.958 43.478 0.00 0.00 0.00 2.52
82 83 4.439426 CGTGTTTGTTTGGGTCTTGATTCA 60.439 41.667 0.00 0.00 0.00 2.57
83 84 5.415221 GTGTTTGTTTGGGTCTTGATTCAA 58.585 37.500 0.00 0.00 0.00 2.69
84 85 6.048509 GTGTTTGTTTGGGTCTTGATTCAAT 58.951 36.000 0.00 0.00 0.00 2.57
85 86 7.206687 GTGTTTGTTTGGGTCTTGATTCAATA 58.793 34.615 0.00 0.00 0.00 1.90
86 87 7.708752 GTGTTTGTTTGGGTCTTGATTCAATAA 59.291 33.333 0.00 0.00 0.00 1.40
87 88 8.260818 TGTTTGTTTGGGTCTTGATTCAATAAA 58.739 29.630 0.00 0.00 0.00 1.40
88 89 9.103861 GTTTGTTTGGGTCTTGATTCAATAAAA 57.896 29.630 0.00 0.00 0.00 1.52
89 90 9.844257 TTTGTTTGGGTCTTGATTCAATAAAAT 57.156 25.926 0.00 0.00 0.00 1.82
90 91 9.844257 TTGTTTGGGTCTTGATTCAATAAAATT 57.156 25.926 0.00 0.00 0.00 1.82
91 92 9.270640 TGTTTGGGTCTTGATTCAATAAAATTG 57.729 29.630 0.00 0.00 0.00 2.32
97 98 9.927668 GGTCTTGATTCAATAAAATTGGAAAGA 57.072 29.630 0.00 0.00 0.00 2.52
251 255 1.668419 ACACCGCCAGAGCAAATATC 58.332 50.000 0.00 0.00 39.83 1.63
302 307 1.809619 CATGGTACCCACAGCGTCG 60.810 63.158 10.07 0.00 35.80 5.12
345 355 2.923655 CTCCACGTAGCACAACTGTATG 59.076 50.000 0.00 0.00 0.00 2.39
388 398 1.556564 CGGGTACGTTGCTATCTGTG 58.443 55.000 0.00 0.00 34.81 3.66
406 416 1.184970 TGGTGCCTCGTCACTGATCA 61.185 55.000 0.00 0.00 37.16 2.92
418 430 0.543277 ACTGATCATGGCCACACGAT 59.457 50.000 8.16 11.13 31.17 3.73
419 431 1.224075 CTGATCATGGCCACACGATC 58.776 55.000 24.83 24.83 44.36 3.69
420 432 0.530431 TGATCATGGCCACACGATCG 60.530 55.000 25.35 14.88 46.40 3.69
421 433 0.249447 GATCATGGCCACACGATCGA 60.249 55.000 24.34 0.00 36.70 3.59
422 434 0.530650 ATCATGGCCACACGATCGAC 60.531 55.000 24.34 5.26 0.00 4.20
458 470 4.687215 GCTGGCACACGAGGCTCA 62.687 66.667 15.95 0.00 34.73 4.26
468 480 3.325753 GAGGCTCACCACCCTGCT 61.326 66.667 10.25 0.00 39.06 4.24
469 481 3.322318 GAGGCTCACCACCCTGCTC 62.322 68.421 10.25 0.00 39.06 4.26
470 482 3.640407 GGCTCACCACCCTGCTCA 61.640 66.667 0.00 0.00 35.26 4.26
471 483 2.359230 GCTCACCACCCTGCTCAC 60.359 66.667 0.00 0.00 0.00 3.51
472 484 3.150949 CTCACCACCCTGCTCACA 58.849 61.111 0.00 0.00 0.00 3.58
473 485 1.004080 CTCACCACCCTGCTCACAG 60.004 63.158 0.00 0.00 44.05 3.66
474 486 2.670934 CACCACCCTGCTCACAGC 60.671 66.667 0.00 0.00 43.02 4.40
475 487 2.851102 ACCACCCTGCTCACAGCT 60.851 61.111 0.00 0.00 42.97 4.24
476 488 2.046507 CCACCCTGCTCACAGCTC 60.047 66.667 0.00 0.00 42.97 4.09
478 490 1.375652 CACCCTGCTCACAGCTCTG 60.376 63.158 0.00 0.00 42.97 3.35
583 596 2.821366 CACGCTCCCATGCACCTC 60.821 66.667 0.00 0.00 0.00 3.85
1144 1163 2.583441 CCGACCAAGGAGCAGGTGA 61.583 63.158 0.00 0.00 38.50 4.02
1284 1303 2.672996 CAGAACCACAAGGCCCGG 60.673 66.667 0.00 0.00 39.06 5.73
1480 1511 1.135972 CATGCAACAGACAAGGTACGC 60.136 52.381 0.00 0.00 0.00 4.42
1481 1512 1.218875 TGCAACAGACAAGGTACGCG 61.219 55.000 3.53 3.53 0.00 6.01
1482 1513 1.219522 GCAACAGACAAGGTACGCGT 61.220 55.000 19.17 19.17 0.00 6.01
1483 1514 1.931709 GCAACAGACAAGGTACGCGTA 60.932 52.381 16.41 16.41 0.00 4.42
1484 1515 1.717645 CAACAGACAAGGTACGCGTAC 59.282 52.381 35.42 35.42 35.40 3.67
1500 1540 1.841944 CGTACGTTACGTAGGCACATG 59.158 52.381 21.39 3.15 46.41 3.21
1501 1541 2.476018 CGTACGTTACGTAGGCACATGA 60.476 50.000 21.39 0.00 46.41 3.07
1510 1550 2.545526 CGTAGGCACATGAATCATCCAC 59.454 50.000 0.00 0.00 0.00 4.02
1511 1551 2.062971 AGGCACATGAATCATCCACC 57.937 50.000 0.00 0.00 0.00 4.61
1552 1592 1.544691 ACGTCTTGACTGATTAGCCGT 59.455 47.619 0.00 0.00 0.00 5.68
1554 1594 2.541556 GTCTTGACTGATTAGCCGTCC 58.458 52.381 0.00 0.00 0.00 4.79
1571 1611 4.481112 CATGGCCTGCGCGTTTCC 62.481 66.667 8.43 4.88 35.02 3.13
1612 1661 3.008485 GGGGTCTAGCTGGAAAGGATATG 59.992 52.174 0.00 0.00 0.00 1.78
1613 1662 3.008485 GGGTCTAGCTGGAAAGGATATGG 59.992 52.174 0.00 0.00 0.00 2.74
1614 1663 3.904339 GGTCTAGCTGGAAAGGATATGGA 59.096 47.826 0.00 0.00 0.00 3.41
1615 1664 4.534103 GGTCTAGCTGGAAAGGATATGGAT 59.466 45.833 0.00 0.00 0.00 3.41
1616 1665 5.013599 GGTCTAGCTGGAAAGGATATGGATT 59.986 44.000 0.00 0.00 0.00 3.01
1693 1742 4.012374 CAAAGCTGATCAATGTGGTAGGT 58.988 43.478 0.00 0.00 0.00 3.08
1694 1743 3.550437 AGCTGATCAATGTGGTAGGTC 57.450 47.619 0.00 0.00 0.00 3.85
1734 1784 3.558931 TGGATATGCTTCGGTGTTGAT 57.441 42.857 0.00 0.00 0.00 2.57
1740 1790 1.017387 GCTTCGGTGTTGATCCATCC 58.983 55.000 0.00 0.00 0.00 3.51
1741 1791 1.678728 GCTTCGGTGTTGATCCATCCA 60.679 52.381 0.00 0.00 0.00 3.41
1742 1792 2.923121 CTTCGGTGTTGATCCATCCAT 58.077 47.619 0.00 0.00 0.00 3.41
1743 1793 2.330440 TCGGTGTTGATCCATCCATG 57.670 50.000 0.00 0.00 0.00 3.66
1744 1794 0.664761 CGGTGTTGATCCATCCATGC 59.335 55.000 0.00 0.00 0.00 4.06
1745 1795 1.748244 CGGTGTTGATCCATCCATGCT 60.748 52.381 0.00 0.00 0.00 3.79
1746 1796 2.485302 CGGTGTTGATCCATCCATGCTA 60.485 50.000 0.00 0.00 0.00 3.49
1747 1797 3.759581 GGTGTTGATCCATCCATGCTAT 58.240 45.455 0.00 0.00 0.00 2.97
1748 1798 3.504906 GGTGTTGATCCATCCATGCTATG 59.495 47.826 0.00 0.00 0.00 2.23
1749 1799 3.057736 GTGTTGATCCATCCATGCTATGC 60.058 47.826 0.00 0.00 0.00 3.14
1774 1824 2.147749 GCACGCATGATGCAACACG 61.148 57.895 18.47 1.86 45.36 4.49
1832 1882 4.675510 TGTTCCTTGGTTCGTATCGTATC 58.324 43.478 0.00 0.00 0.00 2.24
1834 1884 2.945008 TCCTTGGTTCGTATCGTATCGT 59.055 45.455 0.00 0.00 0.00 3.73
1837 1887 4.849926 CCTTGGTTCGTATCGTATCGTATG 59.150 45.833 0.00 0.00 0.00 2.39
1838 1888 5.334337 CCTTGGTTCGTATCGTATCGTATGA 60.334 44.000 0.00 0.00 0.00 2.15
1841 1891 6.138088 TGGTTCGTATCGTATCGTATGAAAG 58.862 40.000 0.00 0.00 30.18 2.62
1843 1893 5.347012 TCGTATCGTATCGTATGAAAGCA 57.653 39.130 0.00 0.00 0.00 3.91
1844 1894 5.142265 TCGTATCGTATCGTATGAAAGCAC 58.858 41.667 0.00 0.00 0.00 4.40
1845 1895 4.907582 CGTATCGTATCGTATGAAAGCACA 59.092 41.667 0.00 0.00 0.00 4.57
1846 1896 5.164311 CGTATCGTATCGTATGAAAGCACAC 60.164 44.000 0.00 0.00 0.00 3.82
1847 1897 3.103007 TCGTATCGTATGAAAGCACACG 58.897 45.455 0.00 0.00 45.76 4.49
1982 2066 2.359230 GTGTCAGTGGAGCAGGGC 60.359 66.667 0.00 0.00 0.00 5.19
1983 2067 2.848679 TGTCAGTGGAGCAGGGCA 60.849 61.111 0.00 0.00 0.00 5.36
1984 2068 2.431683 GTCAGTGGAGCAGGGCAA 59.568 61.111 0.00 0.00 0.00 4.52
1985 2069 1.968540 GTCAGTGGAGCAGGGCAAC 60.969 63.158 0.00 0.00 0.00 4.17
2018 2102 2.413796 TCATGGTCACACGATTTAACGC 59.586 45.455 0.00 0.00 36.70 4.84
2103 2187 2.042979 AGCCCTTTTAATCTTCTGCCCA 59.957 45.455 0.00 0.00 0.00 5.36
2113 2197 1.171308 CTTCTGCCCACTGTTCATGG 58.829 55.000 0.00 0.00 36.94 3.66
2127 2213 3.906660 CATGGATCAATGCATGCCC 57.093 52.632 16.68 8.41 46.80 5.36
2128 2214 0.320374 CATGGATCAATGCATGCCCC 59.680 55.000 16.68 7.25 46.80 5.80
2129 2215 0.105401 ATGGATCAATGCATGCCCCA 60.105 50.000 16.68 12.56 37.46 4.96
2200 2297 1.002430 CGGCACCAGTCCTATATGCAT 59.998 52.381 3.79 3.79 38.05 3.96
2255 2353 2.232941 AGCAATGCTGATTTGTTCCCTG 59.767 45.455 7.07 0.00 37.57 4.45
2259 2357 2.715046 TGCTGATTTGTTCCCTGCTAG 58.285 47.619 0.00 0.00 0.00 3.42
2260 2358 2.040278 TGCTGATTTGTTCCCTGCTAGT 59.960 45.455 0.00 0.00 0.00 2.57
2261 2359 3.263170 TGCTGATTTGTTCCCTGCTAGTA 59.737 43.478 0.00 0.00 0.00 1.82
2262 2360 3.873952 GCTGATTTGTTCCCTGCTAGTAG 59.126 47.826 0.00 0.00 0.00 2.57
2282 2380 2.105821 AGTAACTAGTGCAAACTGGCCA 59.894 45.455 4.71 4.71 0.00 5.36
2283 2381 2.292828 AACTAGTGCAAACTGGCCAT 57.707 45.000 5.51 0.00 0.00 4.40
2284 2382 1.538047 ACTAGTGCAAACTGGCCATG 58.462 50.000 5.51 2.31 0.00 3.66
2285 2383 1.073763 ACTAGTGCAAACTGGCCATGA 59.926 47.619 5.51 0.00 0.00 3.07
2286 2384 2.161855 CTAGTGCAAACTGGCCATGAA 58.838 47.619 5.51 0.00 0.00 2.57
2287 2385 1.636148 AGTGCAAACTGGCCATGAAT 58.364 45.000 5.51 0.00 0.00 2.57
2288 2386 2.806434 AGTGCAAACTGGCCATGAATA 58.194 42.857 5.51 0.00 0.00 1.75
2374 2483 8.306680 TGTGTATTGAAGTAGTAGTTCTTTGC 57.693 34.615 16.79 9.37 0.00 3.68
2383 2492 9.425577 GAAGTAGTAGTTCTTTGCTCTAACATT 57.574 33.333 10.04 0.00 0.00 2.71
2406 2515 2.715749 TGCATTCGATCCATGTTCCT 57.284 45.000 0.00 0.00 0.00 3.36
2571 2680 3.134127 GGCGCATGACAAGGTCCC 61.134 66.667 10.83 0.00 0.00 4.46
2632 2741 1.805945 GAACAGCGCCGGTACTCAG 60.806 63.158 2.29 0.00 0.00 3.35
2889 2998 1.469251 GCCGCTGTATGACTTCTTCGA 60.469 52.381 0.00 0.00 0.00 3.71
2961 3073 1.815021 CGCATGCATTCCTATGGACCA 60.815 52.381 19.57 0.00 34.74 4.02
2997 3109 0.038526 AGTAAGCCGAACACCGACTG 60.039 55.000 0.00 0.00 41.76 3.51
3007 3119 0.468226 ACACCGACTGAAGGAGCAAA 59.532 50.000 0.00 0.00 0.00 3.68
3008 3120 1.151668 CACCGACTGAAGGAGCAAAG 58.848 55.000 0.00 0.00 0.00 2.77
3010 3122 1.968493 ACCGACTGAAGGAGCAAAGTA 59.032 47.619 0.00 0.00 0.00 2.24
3061 3173 3.777465 TTCGGTTCATCTTCTAGACGG 57.223 47.619 0.00 0.00 0.00 4.79
3074 3186 4.891727 GACGGGTGATGCGCCGAT 62.892 66.667 4.18 0.00 34.37 4.18
3158 3290 6.326323 ACAAGTCCCAAAAGATTTGTAATGGT 59.674 34.615 1.18 0.00 42.73 3.55
3220 3352 3.259374 ACCGATATGGCTATGGAGTTGAG 59.741 47.826 0.00 0.00 43.94 3.02
3226 3358 7.441157 CGATATGGCTATGGAGTTGAGTTTTTA 59.559 37.037 0.00 0.00 0.00 1.52
3237 3370 9.058174 TGGAGTTGAGTTTTTATTAAACGATCA 57.942 29.630 0.00 0.00 35.42 2.92
3276 3409 4.730966 TGTTAAAAGATGGGTGTGGCTAA 58.269 39.130 0.00 0.00 0.00 3.09
3282 3415 1.555075 GATGGGTGTGGCTAAGTCTCA 59.445 52.381 0.00 0.00 0.00 3.27
3287 3420 0.888619 TGTGGCTAAGTCTCAGTCGG 59.111 55.000 0.00 0.00 0.00 4.79
3290 3423 1.340697 TGGCTAAGTCTCAGTCGGCTA 60.341 52.381 0.00 0.00 0.00 3.93
3303 3436 5.553123 TCAGTCGGCTAAGATTTAACCAAA 58.447 37.500 0.00 0.00 0.00 3.28
3382 3529 5.784177 AGATTTCACGGATATAGCAACGAT 58.216 37.500 0.00 0.00 0.00 3.73
3391 3538 5.117745 CGGATATAGCAACGATTGAGACTTG 59.882 44.000 0.00 0.00 0.00 3.16
3393 3540 6.144724 GGATATAGCAACGATTGAGACTTGAC 59.855 42.308 0.00 0.00 0.00 3.18
3414 3561 3.932089 ACTAAGTCTTAGTCGACCGAGAC 59.068 47.826 28.26 28.26 42.62 3.36
3436 3583 7.454225 AGACTTAGCAAGACTGTTAAAGGATT 58.546 34.615 3.37 0.00 32.40 3.01
3437 3584 7.939588 AGACTTAGCAAGACTGTTAAAGGATTT 59.060 33.333 3.37 0.00 35.69 2.17
3442 3589 6.207614 AGCAAGACTGTTAAAGGATTTTCTCC 59.792 38.462 0.00 0.00 45.33 3.71
3454 3601 2.806945 TTTTCTCCATCCATTCGGCT 57.193 45.000 0.00 0.00 0.00 5.52
3459 3606 1.046472 TCCATCCATTCGGCTACGGT 61.046 55.000 0.00 0.00 41.39 4.83
3522 3669 1.962306 GGTTTTGCTACCGTCGGCA 60.962 57.895 12.28 0.01 36.62 5.69
3523 3670 1.303091 GGTTTTGCTACCGTCGGCAT 61.303 55.000 12.28 0.00 38.30 4.40
3650 3805 2.171840 GCTATCTCTCGATTAGGGGCA 58.828 52.381 0.00 0.00 0.00 5.36
3662 3817 4.115199 GGGGCAGATCAACCGGCT 62.115 66.667 0.00 0.00 0.00 5.52
3717 3872 7.968405 GCTTAATGATCTAAAATTTGTGACCGT 59.032 33.333 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.261381 ACGGTTCAGCAGTCTTAACATAAAAA 59.739 34.615 0.00 0.00 30.08 1.94
37 38 5.761234 ACGGTTCAGCAGTCTTAACATAAAA 59.239 36.000 0.00 0.00 30.08 1.52
38 39 5.178623 CACGGTTCAGCAGTCTTAACATAAA 59.821 40.000 0.00 0.00 30.08 1.40
39 40 4.688879 CACGGTTCAGCAGTCTTAACATAA 59.311 41.667 0.00 0.00 30.08 1.90
40 41 4.242475 CACGGTTCAGCAGTCTTAACATA 58.758 43.478 0.00 0.00 30.08 2.29
41 42 3.067106 CACGGTTCAGCAGTCTTAACAT 58.933 45.455 0.00 0.00 30.08 2.71
42 43 2.159014 ACACGGTTCAGCAGTCTTAACA 60.159 45.455 0.00 0.00 30.08 2.41
43 44 2.480845 ACACGGTTCAGCAGTCTTAAC 58.519 47.619 0.00 0.00 0.00 2.01
44 45 2.902705 ACACGGTTCAGCAGTCTTAA 57.097 45.000 0.00 0.00 0.00 1.85
45 46 2.869801 CAAACACGGTTCAGCAGTCTTA 59.130 45.455 0.00 0.00 0.00 2.10
46 47 1.670811 CAAACACGGTTCAGCAGTCTT 59.329 47.619 0.00 0.00 0.00 3.01
47 48 1.299541 CAAACACGGTTCAGCAGTCT 58.700 50.000 0.00 0.00 0.00 3.24
48 49 1.014352 ACAAACACGGTTCAGCAGTC 58.986 50.000 0.00 0.00 0.00 3.51
49 50 1.459450 AACAAACACGGTTCAGCAGT 58.541 45.000 0.00 0.00 0.00 4.40
50 51 2.184448 CAAACAAACACGGTTCAGCAG 58.816 47.619 0.00 0.00 0.00 4.24
51 52 1.135257 CCAAACAAACACGGTTCAGCA 60.135 47.619 0.00 0.00 0.00 4.41
52 53 1.555477 CCAAACAAACACGGTTCAGC 58.445 50.000 0.00 0.00 0.00 4.26
53 54 1.474879 ACCCAAACAAACACGGTTCAG 59.525 47.619 0.00 0.00 0.00 3.02
54 55 1.473278 GACCCAAACAAACACGGTTCA 59.527 47.619 0.00 0.00 0.00 3.18
55 56 1.746787 AGACCCAAACAAACACGGTTC 59.253 47.619 0.00 0.00 0.00 3.62
56 57 1.842052 AGACCCAAACAAACACGGTT 58.158 45.000 0.00 0.00 0.00 4.44
57 58 1.474879 CAAGACCCAAACAAACACGGT 59.525 47.619 0.00 0.00 0.00 4.83
58 59 1.746220 TCAAGACCCAAACAAACACGG 59.254 47.619 0.00 0.00 0.00 4.94
59 60 3.708563 ATCAAGACCCAAACAAACACG 57.291 42.857 0.00 0.00 0.00 4.49
60 61 5.004922 TGAATCAAGACCCAAACAAACAC 57.995 39.130 0.00 0.00 0.00 3.32
61 62 5.667539 TTGAATCAAGACCCAAACAAACA 57.332 34.783 0.00 0.00 0.00 2.83
62 63 8.655651 TTTATTGAATCAAGACCCAAACAAAC 57.344 30.769 1.10 0.00 0.00 2.93
63 64 9.844257 ATTTTATTGAATCAAGACCCAAACAAA 57.156 25.926 1.10 0.00 0.00 2.83
64 65 9.844257 AATTTTATTGAATCAAGACCCAAACAA 57.156 25.926 1.10 0.00 0.00 2.83
65 66 9.270640 CAATTTTATTGAATCAAGACCCAAACA 57.729 29.630 1.10 0.00 0.00 2.83
66 67 8.720562 CCAATTTTATTGAATCAAGACCCAAAC 58.279 33.333 1.10 0.00 0.00 2.93
67 68 8.654997 TCCAATTTTATTGAATCAAGACCCAAA 58.345 29.630 1.10 0.00 0.00 3.28
68 69 8.200024 TCCAATTTTATTGAATCAAGACCCAA 57.800 30.769 1.10 0.00 0.00 4.12
69 70 7.789202 TCCAATTTTATTGAATCAAGACCCA 57.211 32.000 1.10 0.00 0.00 4.51
70 71 9.154847 CTTTCCAATTTTATTGAATCAAGACCC 57.845 33.333 1.10 0.00 0.00 4.46
71 72 9.927668 TCTTTCCAATTTTATTGAATCAAGACC 57.072 29.630 1.10 0.00 0.00 3.85
171 175 1.670730 TGTGCACACAGCCATACGG 60.671 57.895 17.42 0.00 44.83 4.02
251 255 7.167468 GGAAATAAATTTGTGCCAAGTATAGCG 59.833 37.037 0.00 0.00 0.00 4.26
323 328 0.750850 ACAGTTGTGCTACGTGGAGT 59.249 50.000 1.81 0.00 0.00 3.85
345 355 3.746492 GTGTCCTTGTTGATCAGGTGTAC 59.254 47.826 0.00 0.00 0.00 2.90
388 398 0.176680 ATGATCAGTGACGAGGCACC 59.823 55.000 5.31 0.00 39.59 5.01
406 416 1.153568 CAGTCGATCGTGTGGCCAT 60.154 57.895 9.72 0.00 0.00 4.40
418 430 4.409218 GCCGTGTACCGCAGTCGA 62.409 66.667 0.00 0.00 38.10 4.20
419 431 4.710695 TGCCGTGTACCGCAGTCG 62.711 66.667 0.00 0.00 34.38 4.18
420 432 2.356553 TTGCCGTGTACCGCAGTC 60.357 61.111 0.00 0.00 34.38 3.51
421 433 2.357034 CTTGCCGTGTACCGCAGT 60.357 61.111 0.00 0.00 34.38 4.40
422 434 3.118454 CCTTGCCGTGTACCGCAG 61.118 66.667 0.00 0.00 34.38 5.18
458 470 2.851102 AGCTGTGAGCAGGGTGGT 60.851 61.111 0.00 0.00 45.56 4.16
468 480 2.580815 CGCCATCCAGAGCTGTGA 59.419 61.111 13.38 0.00 0.00 3.58
469 481 3.200593 GCGCCATCCAGAGCTGTG 61.201 66.667 3.32 3.32 0.00 3.66
470 482 4.827087 CGCGCCATCCAGAGCTGT 62.827 66.667 0.00 0.00 0.00 4.40
1481 1512 3.135414 TCATGTGCCTACGTAACGTAC 57.865 47.619 0.00 0.26 41.54 3.67
1482 1513 3.846423 TTCATGTGCCTACGTAACGTA 57.154 42.857 0.00 0.00 41.54 3.57
1483 1514 2.728690 TTCATGTGCCTACGTAACGT 57.271 45.000 0.00 0.00 44.35 3.99
1484 1515 3.183754 TGATTCATGTGCCTACGTAACG 58.816 45.455 0.00 0.00 0.00 3.18
1485 1516 4.211374 GGATGATTCATGTGCCTACGTAAC 59.789 45.833 3.32 0.00 0.00 2.50
1486 1517 4.141824 TGGATGATTCATGTGCCTACGTAA 60.142 41.667 3.32 0.00 0.00 3.18
1487 1518 3.386402 TGGATGATTCATGTGCCTACGTA 59.614 43.478 3.32 0.00 0.00 3.57
1488 1519 2.170397 TGGATGATTCATGTGCCTACGT 59.830 45.455 3.32 0.00 0.00 3.57
1491 1522 2.485302 CGGTGGATGATTCATGTGCCTA 60.485 50.000 3.32 0.00 0.00 3.93
1492 1523 1.748244 CGGTGGATGATTCATGTGCCT 60.748 52.381 3.32 0.00 0.00 4.75
1493 1524 0.664761 CGGTGGATGATTCATGTGCC 59.335 55.000 3.32 0.00 0.00 5.01
1495 1526 0.664761 GGCGGTGGATGATTCATGTG 59.335 55.000 3.32 0.00 0.00 3.21
1500 1540 3.640000 CGCGGCGGTGGATGATTC 61.640 66.667 15.84 0.00 0.00 2.52
1501 1541 3.969250 AACGCGGCGGTGGATGATT 62.969 57.895 27.37 6.04 0.00 2.57
1554 1594 4.481112 GGAAACGCGCAGGCCATG 62.481 66.667 5.73 0.97 35.02 3.66
1571 1611 2.673368 CCCAAGTGTAAAGCTAAGCGAG 59.327 50.000 0.00 0.00 0.00 5.03
1613 1662 5.741388 AATGGAAAGTCGTAGATGCAATC 57.259 39.130 0.00 0.00 46.04 2.67
1614 1663 5.677091 GCAAATGGAAAGTCGTAGATGCAAT 60.677 40.000 0.00 0.00 40.67 3.56
1615 1664 4.379394 GCAAATGGAAAGTCGTAGATGCAA 60.379 41.667 0.00 0.00 40.67 4.08
1616 1665 3.126858 GCAAATGGAAAGTCGTAGATGCA 59.873 43.478 0.00 0.00 40.67 3.96
1693 1742 0.179181 GCGTTATCGTCGTGTCCTGA 60.179 55.000 0.00 0.00 39.49 3.86
1694 1743 0.455464 TGCGTTATCGTCGTGTCCTG 60.455 55.000 0.00 0.00 39.49 3.86
1774 1824 1.806623 CGAATAGTACAGCCAGCCACC 60.807 57.143 0.00 0.00 0.00 4.61
1834 1884 3.057019 GTGTGACTCGTGTGCTTTCATA 58.943 45.455 0.00 0.00 0.00 2.15
1837 1887 0.229753 CGTGTGACTCGTGTGCTTTC 59.770 55.000 0.00 0.00 0.00 2.62
1838 1888 0.179121 TCGTGTGACTCGTGTGCTTT 60.179 50.000 6.94 0.00 0.00 3.51
1841 1891 1.008881 TCTCGTGTGACTCGTGTGC 60.009 57.895 6.94 0.00 0.00 4.57
1843 1893 0.029035 GTGTCTCGTGTGACTCGTGT 59.971 55.000 6.94 0.00 37.79 4.49
1844 1894 0.992263 CGTGTCTCGTGTGACTCGTG 60.992 60.000 14.65 4.93 44.05 4.35
1845 1895 1.156034 TCGTGTCTCGTGTGACTCGT 61.156 55.000 19.35 0.00 46.92 4.18
1846 1896 4.116834 CGTGTCTCGTGTGACTCG 57.883 61.111 10.70 10.70 43.78 4.18
1847 1897 0.306840 TGTCGTGTCTCGTGTGACTC 59.693 55.000 4.01 0.05 40.80 3.36
1848 1898 0.029035 GTGTCGTGTCTCGTGTGACT 59.971 55.000 4.01 0.00 40.80 3.41
1982 2066 2.289444 ACCATGACTACGAGGGTTGTTG 60.289 50.000 0.00 0.00 32.21 3.33
1983 2067 1.975680 ACCATGACTACGAGGGTTGTT 59.024 47.619 0.00 0.00 32.21 2.83
1984 2068 1.549170 GACCATGACTACGAGGGTTGT 59.451 52.381 0.00 0.00 34.79 3.32
1985 2069 1.548719 TGACCATGACTACGAGGGTTG 59.451 52.381 0.00 0.00 30.55 3.77
2103 2187 3.181479 GCATGCATTGATCCATGAACAGT 60.181 43.478 14.21 0.00 40.92 3.55
2113 2197 1.366366 GCTGGGGCATGCATTGATC 59.634 57.895 21.36 0.00 38.54 2.92
2126 2212 3.628646 CTTCGAACCTGGGGCTGGG 62.629 68.421 0.00 0.00 0.00 4.45
2127 2213 2.045926 CTTCGAACCTGGGGCTGG 60.046 66.667 0.00 0.00 0.00 4.85
2128 2214 2.045926 CCTTCGAACCTGGGGCTG 60.046 66.667 0.00 0.00 0.00 4.85
2129 2215 1.423794 TTTCCTTCGAACCTGGGGCT 61.424 55.000 0.00 0.00 0.00 5.19
2200 2297 1.642037 CTCGCTTCGGTCGTCCTACA 61.642 60.000 0.00 0.00 0.00 2.74
2259 2357 3.683340 GGCCAGTTTGCACTAGTTACTAC 59.317 47.826 0.00 0.00 0.00 2.73
2260 2358 3.325425 TGGCCAGTTTGCACTAGTTACTA 59.675 43.478 0.00 0.00 0.00 1.82
2261 2359 2.105821 TGGCCAGTTTGCACTAGTTACT 59.894 45.455 0.00 0.00 0.00 2.24
2262 2360 2.500229 TGGCCAGTTTGCACTAGTTAC 58.500 47.619 0.00 0.00 0.00 2.50
2272 2370 7.944061 TCTATTCATTATTCATGGCCAGTTTG 58.056 34.615 13.05 4.75 33.07 2.93
2276 2374 9.021807 AGAAATCTATTCATTATTCATGGCCAG 57.978 33.333 13.05 3.43 33.07 4.85
2282 2380 9.298250 AGCAGCAGAAATCTATTCATTATTCAT 57.702 29.630 0.00 0.00 0.00 2.57
2283 2381 8.687292 AGCAGCAGAAATCTATTCATTATTCA 57.313 30.769 0.00 0.00 0.00 2.57
2284 2382 9.609950 GAAGCAGCAGAAATCTATTCATTATTC 57.390 33.333 0.00 0.00 0.00 1.75
2285 2383 9.352191 AGAAGCAGCAGAAATCTATTCATTATT 57.648 29.630 0.00 0.00 0.00 1.40
2286 2384 8.784994 CAGAAGCAGCAGAAATCTATTCATTAT 58.215 33.333 0.00 0.00 0.00 1.28
2287 2385 7.772292 ACAGAAGCAGCAGAAATCTATTCATTA 59.228 33.333 0.00 0.00 0.00 1.90
2288 2386 6.602406 ACAGAAGCAGCAGAAATCTATTCATT 59.398 34.615 0.00 0.00 0.00 2.57
2374 2483 5.967674 GGATCGAATGCAAACAATGTTAGAG 59.032 40.000 0.00 0.00 0.00 2.43
2383 2492 3.119531 GGAACATGGATCGAATGCAAACA 60.120 43.478 0.00 0.00 33.18 2.83
2889 2998 1.141881 CATCTTCAGCGGCCTACGT 59.858 57.895 0.00 0.00 46.52 3.57
2997 3109 2.289694 TGTCTGCCTACTTTGCTCCTTC 60.290 50.000 0.00 0.00 0.00 3.46
3007 3119 8.919777 AACTAAAAATAGTTTGTCTGCCTACT 57.080 30.769 0.00 0.00 36.98 2.57
3008 3120 9.961265 AAAACTAAAAATAGTTTGTCTGCCTAC 57.039 29.630 13.09 0.00 46.18 3.18
3010 3122 7.926018 CCAAAACTAAAAATAGTTTGTCTGCCT 59.074 33.333 13.09 0.00 46.18 4.75
3039 3151 4.277672 CCCGTCTAGAAGATGAACCGAATA 59.722 45.833 7.30 0.00 33.07 1.75
3061 3173 1.003866 GTAAAAGATCGGCGCATCACC 60.004 52.381 10.83 0.00 0.00 4.02
3142 3254 8.397148 CAAAAACAGCACCATTACAAATCTTTT 58.603 29.630 0.00 0.00 0.00 2.27
3158 3290 6.132791 TGTATACGAAAACCAAAAACAGCA 57.867 33.333 0.00 0.00 0.00 4.41
3226 3358 7.605410 ACGTTAACTCCAATGATCGTTTAAT 57.395 32.000 3.71 0.00 0.00 1.40
3237 3370 8.460428 TCTTTTAACAACAACGTTAACTCCAAT 58.540 29.630 0.00 0.00 40.21 3.16
3276 3409 5.394333 GGTTAAATCTTAGCCGACTGAGACT 60.394 44.000 0.00 0.00 40.95 3.24
3282 3415 6.679327 GATTTGGTTAAATCTTAGCCGACT 57.321 37.500 5.70 0.00 45.57 4.18
3343 3490 7.854422 CCGTGAAATCTTACATTGAGATTCATG 59.146 37.037 0.36 0.00 41.66 3.07
3367 3514 4.799678 AGTCTCAATCGTTGCTATATCCG 58.200 43.478 0.00 0.00 0.00 4.18
3393 3540 4.183101 AGTCTCGGTCGACTAAGACTTAG 58.817 47.826 30.64 18.80 44.57 2.18
3414 3561 8.787852 AGAAAATCCTTTAACAGTCTTGCTAAG 58.212 33.333 0.00 0.00 0.00 2.18
3436 3583 2.483013 CGTAGCCGAATGGATGGAGAAA 60.483 50.000 0.00 0.00 37.49 2.52
3437 3584 1.068588 CGTAGCCGAATGGATGGAGAA 59.931 52.381 0.00 0.00 37.49 2.87
3442 3589 0.389391 AGACCGTAGCCGAATGGATG 59.611 55.000 0.00 0.00 37.49 3.51
3443 3590 0.389391 CAGACCGTAGCCGAATGGAT 59.611 55.000 0.00 0.00 37.49 3.41
3454 3601 2.164827 ACGTGAATGCATACAGACCGTA 59.835 45.455 0.00 0.00 0.00 4.02
3459 3606 4.808895 GGTATTCACGTGAATGCATACAGA 59.191 41.667 40.80 24.63 45.15 3.41
3522 3669 5.572211 CACGCACATTTTATGTTCTGCTAT 58.428 37.500 0.00 0.00 42.70 2.97
3523 3670 4.671508 GCACGCACATTTTATGTTCTGCTA 60.672 41.667 0.00 0.00 42.70 3.49
3596 3743 6.391227 AACGAATGTTGAAGTTGAATTCCT 57.609 33.333 2.27 0.00 36.81 3.36
3650 3805 1.078143 GCCAAGAGCCGGTTGATCT 60.078 57.895 1.90 0.00 34.35 2.75
3717 3872 4.128643 CGTGGTACCTTAACAAACCAAGA 58.871 43.478 14.36 0.00 43.34 3.02
3866 4022 0.100146 GCCTAGGGTTAGACGACGTG 59.900 60.000 11.72 0.00 0.00 4.49
3867 4023 1.372087 CGCCTAGGGTTAGACGACGT 61.372 60.000 11.72 0.00 35.11 4.34


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

AutoCloner maintained by Alex Coulton.