Multiple sequence alignment - TraesCS2A01G080500

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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 TraesCS2A01G080500 chr2A 100.000 3374 0 0 1 3374 36393626 36390253 0.000000e+00 6231.0
1 TraesCS2A01G080500 chr2A 87.184 1225 103 28 814 2027 36411934 36410753 0.000000e+00 1343.0
2 TraesCS2A01G080500 chr2A 87.018 1194 100 26 889 2063 36400210 36399053 0.000000e+00 1295.0
3 TraesCS2A01G080500 chr2A 83.790 839 84 20 2408 3196 36398853 36398017 0.000000e+00 749.0
4 TraesCS2A01G080500 chr2A 83.170 814 84 27 820 1603 79342308 79343098 0.000000e+00 695.0
5 TraesCS2A01G080500 chr2A 83.738 535 55 17 2608 3114 36410240 36409710 8.470000e-131 477.0
6 TraesCS2A01G080500 chr2A 89.024 164 17 1 3162 3324 36409507 36409670 5.710000e-48 202.0
7 TraesCS2A01G080500 chr2A 93.182 88 5 1 1 88 752852552 752852638 9.830000e-26 128.0
8 TraesCS2A01G080500 chr2B 86.687 1630 103 52 816 2411 55210420 55208871 0.000000e+00 1703.0
9 TraesCS2A01G080500 chr2B 90.583 1253 42 18 2145 3374 55202409 55201210 0.000000e+00 1591.0
10 TraesCS2A01G080500 chr2B 84.384 1396 122 52 816 2187 55227659 55226336 0.000000e+00 1282.0
11 TraesCS2A01G080500 chr2B 86.204 1138 93 31 889 1997 55855927 55854825 0.000000e+00 1173.0
12 TraesCS2A01G080500 chr2B 90.186 805 58 11 2408 3196 55208830 55208031 0.000000e+00 1029.0
13 TraesCS2A01G080500 chr2B 84.449 1061 86 36 1392 2409 55514206 55513182 0.000000e+00 972.0
14 TraesCS2A01G080500 chr2B 87.105 822 71 10 2408 3196 55513139 55512320 0.000000e+00 898.0
15 TraesCS2A01G080500 chr2B 87.664 762 55 16 858 1614 55699399 55698672 0.000000e+00 850.0
16 TraesCS2A01G080500 chr2B 80.851 846 88 48 815 1614 122926378 122927195 6.230000e-167 597.0
17 TraesCS2A01G080500 chr2B 95.380 368 11 2 1654 2015 55202831 55202464 6.280000e-162 580.0
18 TraesCS2A01G080500 chr2B 80.549 838 94 42 819 1613 122992187 122992998 6.280000e-162 580.0
19 TraesCS2A01G080500 chr2B 91.932 409 30 3 2165 2572 693564077 693564483 1.360000e-158 569.0
20 TraesCS2A01G080500 chr2B 85.252 556 65 8 850 1397 55537037 55536491 1.060000e-154 556.0
21 TraesCS2A01G080500 chr2B 85.273 550 61 12 2664 3196 55697529 55696983 1.770000e-152 549.0
22 TraesCS2A01G080500 chr2B 88.732 355 26 6 1664 2012 55698651 55698305 4.030000e-114 422.0
23 TraesCS2A01G080500 chr2B 87.500 240 30 0 162 401 63045059 63045298 9.220000e-71 278.0
24 TraesCS2A01G080500 chr2B 93.478 138 7 2 811 946 55537323 55537186 1.590000e-48 204.0
25 TraesCS2A01G080500 chr2B 87.879 165 17 3 3162 3324 55206585 55206422 1.240000e-44 191.0
26 TraesCS2A01G080500 chr2B 93.258 89 5 1 1 89 441855763 441855850 2.730000e-26 130.0
27 TraesCS2A01G080500 chr2B 93.258 89 5 1 1 89 704738233 704738320 2.730000e-26 130.0
28 TraesCS2A01G080500 chr2B 86.364 88 8 4 2083 2168 55207669 55207584 3.580000e-15 93.5
29 TraesCS2A01G080500 chr2D 84.660 1734 150 46 889 2584 33242152 33240497 0.000000e+00 1622.0
30 TraesCS2A01G080500 chr2D 88.940 1311 65 37 2093 3374 33314232 33312973 0.000000e+00 1544.0
31 TraesCS2A01G080500 chr2D 90.215 838 30 14 816 1622 33315540 33314724 0.000000e+00 1046.0
32 TraesCS2A01G080500 chr2D 89.219 807 54 16 1207 2012 33373920 33373146 0.000000e+00 977.0
33 TraesCS2A01G080500 chr2D 88.705 726 52 13 889 1614 33581160 33580465 0.000000e+00 859.0
34 TraesCS2A01G080500 chr2D 95.494 466 13 4 1614 2073 33314686 33314223 0.000000e+00 737.0
35 TraesCS2A01G080500 chr2D 81.463 793 84 38 827 1571 79084882 79085659 2.900000e-165 592.0
36 TraesCS2A01G080500 chr2D 80.316 696 132 5 119 811 566166416 566165723 3.860000e-144 521.0
37 TraesCS2A01G080500 chr2D 88.605 430 40 6 2772 3193 33579247 33578819 6.460000e-142 514.0
38 TraesCS2A01G080500 chr2D 83.848 551 58 16 2608 3129 33372557 33372009 2.340000e-136 496.0
39 TraesCS2A01G080500 chr2D 88.378 370 28 6 1664 2027 33580444 33580084 6.690000e-117 431.0
40 TraesCS2A01G080500 chr2D 90.000 110 7 3 2063 2168 33371910 33371801 4.540000e-29 139.0
41 TraesCS2A01G080500 chr2D 85.385 130 10 2 2039 2168 33373150 33373030 3.530000e-25 126.0
42 TraesCS2A01G080500 chr1B 89.146 691 74 1 121 811 514369443 514370132 0.000000e+00 859.0
43 TraesCS2A01G080500 chr1B 88.020 409 29 8 2165 2572 76377296 76377685 1.830000e-127 466.0
44 TraesCS2A01G080500 chr1B 92.473 93 5 2 1 93 1850879 1850789 7.600000e-27 132.0
45 TraesCS2A01G080500 chr3B 87.027 555 65 6 120 671 284359592 284359042 1.330000e-173 619.0
46 TraesCS2A01G080500 chr3B 92.308 91 7 0 1 91 788714087 788714177 2.730000e-26 130.0
47 TraesCS2A01G080500 chr3B 92.222 90 6 1 1 90 390218330 390218242 3.530000e-25 126.0
48 TraesCS2A01G080500 chr6B 82.251 693 117 5 122 811 176298301 176298990 8.060000e-166 593.0
49 TraesCS2A01G080500 chr6B 91.925 161 11 2 2165 2324 464575445 464575286 1.220000e-54 224.0
50 TraesCS2A01G080500 chr4B 91.443 409 32 3 2165 2572 217280516 217280922 2.940000e-155 558.0
51 TraesCS2A01G080500 chr4B 92.638 163 8 3 2165 2324 97763517 97763356 7.280000e-57 231.0
52 TraesCS2A01G080500 chr4B 92.391 92 6 1 1 92 659612174 659612264 2.730000e-26 130.0
53 TraesCS2A01G080500 chr4B 95.000 40 1 1 2560 2598 661708832 661708793 1.010000e-05 62.1
54 TraesCS2A01G080500 chr4A 89.563 412 40 3 2165 2575 723917725 723917316 1.390000e-143 520.0
55 TraesCS2A01G080500 chr4A 85.100 349 45 7 119 463 741094838 741094493 1.930000e-92 350.0
56 TraesCS2A01G080500 chr4A 83.843 229 31 2 1654 1876 723918011 723917783 2.640000e-51 213.0
57 TraesCS2A01G080500 chr4A 97.222 36 1 0 1614 1649 723918032 723917997 1.010000e-05 62.1
58 TraesCS2A01G080500 chr7B 79.577 568 110 5 247 811 554196765 554196201 5.240000e-108 401.0
59 TraesCS2A01G080500 chr1D 81.881 436 75 4 119 553 254789748 254789316 6.880000e-97 364.0
60 TraesCS2A01G080500 chr5B 94.340 159 6 3 2165 2321 61757451 61757608 1.210000e-59 241.0
61 TraesCS2A01G080500 chr5D 81.185 287 50 4 121 404 348516388 348516103 9.420000e-56 228.0
62 TraesCS2A01G080500 chr5D 83.125 160 27 0 638 797 509288588 509288747 2.710000e-31 147.0
63 TraesCS2A01G080500 chr5A 92.222 90 6 1 1 90 423145897 423145985 3.530000e-25 126.0
64 TraesCS2A01G080500 chr1A 87.850 107 9 3 1 103 546803934 546804040 4.570000e-24 122.0


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 TraesCS2A01G080500 chr2A 36390253 36393626 3373 True 6231.000000 6231 100.000000 1 3374 1 chr2A.!!$R1 3373
1 TraesCS2A01G080500 chr2A 36398017 36400210 2193 True 1022.000000 1295 85.404000 889 3196 2 chr2A.!!$R2 2307
2 TraesCS2A01G080500 chr2A 36409710 36411934 2224 True 910.000000 1343 85.461000 814 3114 2 chr2A.!!$R3 2300
3 TraesCS2A01G080500 chr2A 79342308 79343098 790 False 695.000000 695 83.170000 820 1603 1 chr2A.!!$F2 783
4 TraesCS2A01G080500 chr2B 55226336 55227659 1323 True 1282.000000 1282 84.384000 816 2187 1 chr2B.!!$R1 1371
5 TraesCS2A01G080500 chr2B 55854825 55855927 1102 True 1173.000000 1173 86.204000 889 1997 1 chr2B.!!$R2 1108
6 TraesCS2A01G080500 chr2B 55512320 55514206 1886 True 935.000000 972 85.777000 1392 3196 2 chr2B.!!$R4 1804
7 TraesCS2A01G080500 chr2B 55201210 55210420 9210 True 864.583333 1703 89.513167 816 3374 6 chr2B.!!$R3 2558
8 TraesCS2A01G080500 chr2B 55696983 55699399 2416 True 607.000000 850 87.223000 858 3196 3 chr2B.!!$R6 2338
9 TraesCS2A01G080500 chr2B 122926378 122927195 817 False 597.000000 597 80.851000 815 1614 1 chr2B.!!$F2 799
10 TraesCS2A01G080500 chr2B 122992187 122992998 811 False 580.000000 580 80.549000 819 1613 1 chr2B.!!$F3 794
11 TraesCS2A01G080500 chr2B 55536491 55537323 832 True 380.000000 556 89.365000 811 1397 2 chr2B.!!$R5 586
12 TraesCS2A01G080500 chr2D 33240497 33242152 1655 True 1622.000000 1622 84.660000 889 2584 1 chr2D.!!$R1 1695
13 TraesCS2A01G080500 chr2D 33312973 33315540 2567 True 1109.000000 1544 91.549667 816 3374 3 chr2D.!!$R3 2558
14 TraesCS2A01G080500 chr2D 33578819 33581160 2341 True 601.333333 859 88.562667 889 3193 3 chr2D.!!$R5 2304
15 TraesCS2A01G080500 chr2D 79084882 79085659 777 False 592.000000 592 81.463000 827 1571 1 chr2D.!!$F1 744
16 TraesCS2A01G080500 chr2D 566165723 566166416 693 True 521.000000 521 80.316000 119 811 1 chr2D.!!$R2 692
17 TraesCS2A01G080500 chr2D 33371801 33373920 2119 True 434.500000 977 87.113000 1207 3129 4 chr2D.!!$R4 1922
18 TraesCS2A01G080500 chr1B 514369443 514370132 689 False 859.000000 859 89.146000 121 811 1 chr1B.!!$F2 690
19 TraesCS2A01G080500 chr3B 284359042 284359592 550 True 619.000000 619 87.027000 120 671 1 chr3B.!!$R1 551
20 TraesCS2A01G080500 chr6B 176298301 176298990 689 False 593.000000 593 82.251000 122 811 1 chr6B.!!$F1 689
21 TraesCS2A01G080500 chr4A 723917316 723918032 716 True 265.033333 520 90.209333 1614 2575 3 chr4A.!!$R2 961
22 TraesCS2A01G080500 chr7B 554196201 554196765 564 True 401.000000 401 79.577000 247 811 1 chr7B.!!$R1 564

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
73 74 0.036732 TGCTTGATGACGCCTTCCTT 59.963 50.0 0.0 0.0 0.0 3.36 F
80 81 0.179234 TGACGCCTTCCTTGTGTTCA 59.821 50.0 0.0 0.0 0.0 3.18 F
1435 8503 0.252558 GTACCTCCCCTGGAACTCCA 60.253 60.0 0.0 0.0 45.3 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1195 1508 0.542232 AGGAGCAGGTACGGACAGTT 60.542 55.000 0.00 0.0 0.00 3.16 R
1474 8542 0.745845 GGCTCGACGACCCAGTAGTA 60.746 60.000 4.26 0.0 0.00 1.82 R
2985 10755 2.320587 GGCGTCCAGTTCTGCTGTG 61.321 63.158 0.00 0.0 43.55 3.66 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
45 46 9.671279 ATTGTACATTGTCTATGAGTTGAATGA 57.329 29.630 0.00 0.00 37.69 2.57
46 47 9.500785 TTGTACATTGTCTATGAGTTGAATGAA 57.499 29.630 0.00 0.00 37.69 2.57
47 48 9.500785 TGTACATTGTCTATGAGTTGAATGAAA 57.499 29.630 1.04 0.00 37.69 2.69
53 54 8.722480 TGTCTATGAGTTGAATGAAATAGTGG 57.278 34.615 0.00 0.00 0.00 4.00
54 55 8.321353 TGTCTATGAGTTGAATGAAATAGTGGT 58.679 33.333 0.00 0.00 0.00 4.16
55 56 8.607459 GTCTATGAGTTGAATGAAATAGTGGTG 58.393 37.037 0.00 0.00 0.00 4.17
56 57 5.627499 TGAGTTGAATGAAATAGTGGTGC 57.373 39.130 0.00 0.00 0.00 5.01
57 58 5.316167 TGAGTTGAATGAAATAGTGGTGCT 58.684 37.500 0.00 0.00 0.00 4.40
58 59 5.769662 TGAGTTGAATGAAATAGTGGTGCTT 59.230 36.000 0.00 0.00 0.00 3.91
59 60 6.017400 AGTTGAATGAAATAGTGGTGCTTG 57.983 37.500 0.00 0.00 0.00 4.01
60 61 5.769662 AGTTGAATGAAATAGTGGTGCTTGA 59.230 36.000 0.00 0.00 0.00 3.02
61 62 6.435277 AGTTGAATGAAATAGTGGTGCTTGAT 59.565 34.615 0.00 0.00 0.00 2.57
62 63 6.198650 TGAATGAAATAGTGGTGCTTGATG 57.801 37.500 0.00 0.00 0.00 3.07
63 64 5.945191 TGAATGAAATAGTGGTGCTTGATGA 59.055 36.000 0.00 0.00 0.00 2.92
64 65 5.824904 ATGAAATAGTGGTGCTTGATGAC 57.175 39.130 0.00 0.00 0.00 3.06
65 66 3.684305 TGAAATAGTGGTGCTTGATGACG 59.316 43.478 0.00 0.00 0.00 4.35
66 67 1.656652 ATAGTGGTGCTTGATGACGC 58.343 50.000 0.00 0.00 0.00 5.19
67 68 0.391130 TAGTGGTGCTTGATGACGCC 60.391 55.000 0.00 0.00 36.96 5.68
68 69 1.672356 GTGGTGCTTGATGACGCCT 60.672 57.895 0.00 0.00 37.35 5.52
69 70 1.073025 TGGTGCTTGATGACGCCTT 59.927 52.632 0.00 0.00 37.35 4.35
70 71 0.955428 TGGTGCTTGATGACGCCTTC 60.955 55.000 0.00 0.00 37.35 3.46
71 72 1.648467 GGTGCTTGATGACGCCTTCC 61.648 60.000 0.00 0.00 33.53 3.46
72 73 0.674895 GTGCTTGATGACGCCTTCCT 60.675 55.000 0.00 0.00 0.00 3.36
73 74 0.036732 TGCTTGATGACGCCTTCCTT 59.963 50.000 0.00 0.00 0.00 3.36
74 75 0.449388 GCTTGATGACGCCTTCCTTG 59.551 55.000 0.00 0.00 0.00 3.61
75 76 1.813513 CTTGATGACGCCTTCCTTGT 58.186 50.000 0.00 0.00 0.00 3.16
76 77 1.466167 CTTGATGACGCCTTCCTTGTG 59.534 52.381 0.00 0.00 0.00 3.33
77 78 0.396435 TGATGACGCCTTCCTTGTGT 59.604 50.000 0.00 0.00 0.00 3.72
78 79 1.202758 TGATGACGCCTTCCTTGTGTT 60.203 47.619 0.00 0.00 0.00 3.32
79 80 1.464997 GATGACGCCTTCCTTGTGTTC 59.535 52.381 0.00 0.00 0.00 3.18
80 81 0.179234 TGACGCCTTCCTTGTGTTCA 59.821 50.000 0.00 0.00 0.00 3.18
81 82 1.305201 GACGCCTTCCTTGTGTTCAA 58.695 50.000 0.00 0.00 0.00 2.69
82 83 1.673920 GACGCCTTCCTTGTGTTCAAA 59.326 47.619 0.00 0.00 32.87 2.69
83 84 1.404035 ACGCCTTCCTTGTGTTCAAAC 59.596 47.619 0.00 0.00 32.87 2.93
84 85 1.403679 CGCCTTCCTTGTGTTCAAACA 59.596 47.619 0.00 0.00 36.38 2.83
85 86 2.159310 CGCCTTCCTTGTGTTCAAACAA 60.159 45.455 0.00 0.00 41.21 2.83
86 87 3.674682 CGCCTTCCTTGTGTTCAAACAAA 60.675 43.478 0.00 0.00 41.21 2.83
87 88 4.249661 GCCTTCCTTGTGTTCAAACAAAA 58.750 39.130 0.00 0.00 41.21 2.44
88 89 4.693095 GCCTTCCTTGTGTTCAAACAAAAA 59.307 37.500 0.00 0.00 41.21 1.94
111 112 6.780457 AAAGGTACATCATTTCTTCATGGG 57.220 37.500 0.00 0.00 0.00 4.00
112 113 5.715439 AGGTACATCATTTCTTCATGGGA 57.285 39.130 0.00 0.00 0.00 4.37
113 114 5.440610 AGGTACATCATTTCTTCATGGGAC 58.559 41.667 0.00 0.00 0.00 4.46
114 115 5.192522 AGGTACATCATTTCTTCATGGGACT 59.807 40.000 0.00 0.00 0.00 3.85
115 116 5.888161 GGTACATCATTTCTTCATGGGACTT 59.112 40.000 0.00 0.00 0.00 3.01
116 117 5.909621 ACATCATTTCTTCATGGGACTTG 57.090 39.130 0.00 0.00 0.00 3.16
117 118 4.708421 ACATCATTTCTTCATGGGACTTGG 59.292 41.667 0.00 0.00 0.00 3.61
118 119 4.387026 TCATTTCTTCATGGGACTTGGT 57.613 40.909 0.00 0.00 0.00 3.67
190 191 0.734889 CAATCAATGTCTGGCGGGTC 59.265 55.000 0.00 0.00 0.00 4.46
202 203 3.290776 GCGGGTCTATAAGCCACAG 57.709 57.895 0.00 0.00 46.52 3.66
332 334 9.039870 GTTGTCTCATTGATCTCCTTAACTATG 57.960 37.037 0.00 0.00 0.00 2.23
357 359 2.866762 GCATACATTCCTCCTGTTCGAC 59.133 50.000 0.00 0.00 0.00 4.20
426 428 4.923415 TCTAGACAACTGGAGATCTGTCA 58.077 43.478 0.00 0.00 40.53 3.58
427 429 5.514169 TCTAGACAACTGGAGATCTGTCAT 58.486 41.667 0.00 0.00 40.53 3.06
428 430 4.468765 AGACAACTGGAGATCTGTCATG 57.531 45.455 0.00 0.00 40.53 3.07
486 488 1.450312 GCTGGATCGGTCAACCCAG 60.450 63.158 0.00 0.00 46.67 4.45
503 505 3.054139 ACCCAGTGTACTTCATGCATGAT 60.054 43.478 29.13 18.10 36.56 2.45
526 528 1.272258 ACCCAAAAACATACCCTCCGG 60.272 52.381 0.00 0.00 0.00 5.14
538 540 1.002134 CCTCCGGGTTTCTGCACAT 60.002 57.895 0.00 0.00 0.00 3.21
554 556 2.745281 GCACATAACGCTAAAAGACCCA 59.255 45.455 0.00 0.00 0.00 4.51
562 564 3.941483 ACGCTAAAAGACCCATCATTCAG 59.059 43.478 0.00 0.00 0.00 3.02
597 600 6.068010 ACCACACCATCAACTCTCAATTTTA 58.932 36.000 0.00 0.00 0.00 1.52
607 610 5.825593 ACTCTCAATTTTACCACTCCAGA 57.174 39.130 0.00 0.00 0.00 3.86
621 624 3.470888 CAGACGCCGGGGGAATCT 61.471 66.667 23.83 13.64 0.00 2.40
633 636 1.134491 GGGGAATCTACCGTGTTCTGG 60.134 57.143 0.00 0.00 0.00 3.86
683 686 2.671619 GGCTGCGGTGGCTTACAA 60.672 61.111 0.00 0.00 40.82 2.41
749 752 6.488683 TCGACATAGGACTTTGGAAAATGTTT 59.511 34.615 0.00 0.00 0.00 2.83
787 790 2.734723 CGCATACCAGATCGCCCG 60.735 66.667 0.00 0.00 0.00 6.13
811 814 2.156343 GTCACCAGAACCTGAGTGAC 57.844 55.000 21.21 21.21 45.37 3.67
812 815 1.788229 TCACCAGAACCTGAGTGACA 58.212 50.000 11.49 0.00 37.04 3.58
1160 1473 2.512515 GCTCCACGCCTCCATGAC 60.513 66.667 0.00 0.00 0.00 3.06
1195 1508 1.011968 GCACATCTACAACGGCGACA 61.012 55.000 16.62 0.00 0.00 4.35
1198 1511 1.000506 ACATCTACAACGGCGACAACT 59.999 47.619 16.62 0.00 0.00 3.16
1200 1543 0.386476 TCTACAACGGCGACAACTGT 59.614 50.000 16.62 10.88 0.00 3.55
1347 1690 2.048023 CATGTGGCAAGCCGTGGAT 61.048 57.895 6.60 0.00 39.42 3.41
1435 8503 0.252558 GTACCTCCCCTGGAACTCCA 60.253 60.000 0.00 0.00 45.30 3.86
1474 8542 1.028330 CAACGCCAGCTCCATGATGT 61.028 55.000 0.00 0.00 0.00 3.06
1475 8543 0.541392 AACGCCAGCTCCATGATGTA 59.459 50.000 0.00 0.00 0.00 2.29
1476 8544 0.179073 ACGCCAGCTCCATGATGTAC 60.179 55.000 0.00 0.00 0.00 2.90
1518 8597 2.993008 GCCAGAGAGGACATGCCA 59.007 61.111 8.58 0.00 41.22 4.92
1681 8842 3.753815 TGTGATTCAACTGCAGAATCCA 58.246 40.909 23.35 15.17 46.78 3.41
1705 8884 1.460305 CCTCCTCGGGGTCATCCAT 60.460 63.158 0.00 0.00 37.22 3.41
1706 8885 1.750930 CTCCTCGGGGTCATCCATG 59.249 63.158 0.00 0.00 37.22 3.66
1814 8993 2.204090 GGTTCAGGGGGAGGTCCA 60.204 66.667 0.00 0.00 37.91 4.02
2083 9282 2.185004 ACCGATGGTCTTTGGTTGAG 57.815 50.000 0.00 0.00 28.17 3.02
2250 9492 8.397906 TCACTGAAATTGTTGTAGTCTGAAAAG 58.602 33.333 0.00 0.00 0.00 2.27
2285 9527 3.206150 TCTGTTGAAGTCTGAAACTGCC 58.794 45.455 0.98 0.00 38.58 4.85
2287 9529 3.351740 TGTTGAAGTCTGAAACTGCCAA 58.648 40.909 0.98 0.00 38.58 4.52
2328 9570 5.106157 GCAACTGCTGTAATCTTGTTGGTAT 60.106 40.000 0.00 0.00 36.35 2.73
2412 9736 4.717991 TGATTCGTTTGATTTAGCCAACG 58.282 39.130 0.00 0.00 0.00 4.10
2545 10195 8.871686 AAAAAGGATATTATGATTCGTTTGGC 57.128 30.769 0.00 0.00 30.46 4.52
2564 10254 3.826157 TGGCTATGACTTGGAAAAAGGTG 59.174 43.478 0.00 0.00 0.00 4.00
2934 10702 1.025812 ACGCGGAGTAGAGGAAGATG 58.974 55.000 12.47 0.00 0.00 2.90
2985 10755 4.736896 AGTTTCGCCGCCTCGACC 62.737 66.667 0.00 0.00 38.30 4.79
3119 10895 1.068055 GTGTTGCTTCCAATGGCTGAG 60.068 52.381 0.00 0.00 32.75 3.35
3233 11019 4.218417 GGGTTTATTGCAGTGAGTTGACAT 59.782 41.667 0.00 0.00 0.00 3.06
3336 11122 7.447374 TTCATTTTAGACAAATGGATCGTGT 57.553 32.000 7.31 0.00 38.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.671279 TCATTCAACTCATAGACAATGTACAAT 57.329 29.630 0.00 0.00 36.89 2.71
20 21 9.500785 TTCATTCAACTCATAGACAATGTACAA 57.499 29.630 0.00 0.00 36.89 2.41
21 22 9.500785 TTTCATTCAACTCATAGACAATGTACA 57.499 29.630 0.00 0.00 36.89 2.90
27 28 9.166173 CCACTATTTCATTCAACTCATAGACAA 57.834 33.333 0.00 0.00 0.00 3.18
28 29 8.321353 ACCACTATTTCATTCAACTCATAGACA 58.679 33.333 0.00 0.00 0.00 3.41
29 30 8.607459 CACCACTATTTCATTCAACTCATAGAC 58.393 37.037 0.00 0.00 0.00 2.59
30 31 7.280876 GCACCACTATTTCATTCAACTCATAGA 59.719 37.037 0.00 0.00 0.00 1.98
31 32 7.281774 AGCACCACTATTTCATTCAACTCATAG 59.718 37.037 0.00 0.00 0.00 2.23
32 33 7.112122 AGCACCACTATTTCATTCAACTCATA 58.888 34.615 0.00 0.00 0.00 2.15
33 34 5.948162 AGCACCACTATTTCATTCAACTCAT 59.052 36.000 0.00 0.00 0.00 2.90
34 35 5.316167 AGCACCACTATTTCATTCAACTCA 58.684 37.500 0.00 0.00 0.00 3.41
35 36 5.886960 AGCACCACTATTTCATTCAACTC 57.113 39.130 0.00 0.00 0.00 3.01
36 37 5.769662 TCAAGCACCACTATTTCATTCAACT 59.230 36.000 0.00 0.00 0.00 3.16
37 38 6.012658 TCAAGCACCACTATTTCATTCAAC 57.987 37.500 0.00 0.00 0.00 3.18
38 39 6.433716 TCATCAAGCACCACTATTTCATTCAA 59.566 34.615 0.00 0.00 0.00 2.69
39 40 5.945191 TCATCAAGCACCACTATTTCATTCA 59.055 36.000 0.00 0.00 0.00 2.57
40 41 6.261118 GTCATCAAGCACCACTATTTCATTC 58.739 40.000 0.00 0.00 0.00 2.67
41 42 5.163723 CGTCATCAAGCACCACTATTTCATT 60.164 40.000 0.00 0.00 0.00 2.57
42 43 4.333649 CGTCATCAAGCACCACTATTTCAT 59.666 41.667 0.00 0.00 0.00 2.57
43 44 3.684305 CGTCATCAAGCACCACTATTTCA 59.316 43.478 0.00 0.00 0.00 2.69
44 45 3.485877 GCGTCATCAAGCACCACTATTTC 60.486 47.826 0.00 0.00 0.00 2.17
45 46 2.420022 GCGTCATCAAGCACCACTATTT 59.580 45.455 0.00 0.00 0.00 1.40
46 47 2.009774 GCGTCATCAAGCACCACTATT 58.990 47.619 0.00 0.00 0.00 1.73
47 48 1.656652 GCGTCATCAAGCACCACTAT 58.343 50.000 0.00 0.00 0.00 2.12
48 49 0.391130 GGCGTCATCAAGCACCACTA 60.391 55.000 0.00 0.00 34.54 2.74
49 50 1.672356 GGCGTCATCAAGCACCACT 60.672 57.895 0.00 0.00 34.54 4.00
50 51 1.237285 AAGGCGTCATCAAGCACCAC 61.237 55.000 0.00 0.00 34.54 4.16
51 52 0.955428 GAAGGCGTCATCAAGCACCA 60.955 55.000 0.00 0.00 34.54 4.17
52 53 1.648467 GGAAGGCGTCATCAAGCACC 61.648 60.000 2.23 0.00 34.54 5.01
53 54 0.674895 AGGAAGGCGTCATCAAGCAC 60.675 55.000 2.23 0.00 34.54 4.40
54 55 0.036732 AAGGAAGGCGTCATCAAGCA 59.963 50.000 2.23 0.00 34.54 3.91
55 56 0.449388 CAAGGAAGGCGTCATCAAGC 59.551 55.000 2.23 0.00 0.00 4.01
56 57 1.466167 CACAAGGAAGGCGTCATCAAG 59.534 52.381 2.23 0.00 0.00 3.02
57 58 1.202758 ACACAAGGAAGGCGTCATCAA 60.203 47.619 2.23 0.00 0.00 2.57
58 59 0.396435 ACACAAGGAAGGCGTCATCA 59.604 50.000 2.23 0.00 0.00 3.07
59 60 1.464997 GAACACAAGGAAGGCGTCATC 59.535 52.381 2.23 0.00 0.00 2.92
60 61 1.202758 TGAACACAAGGAAGGCGTCAT 60.203 47.619 2.23 0.00 0.00 3.06
61 62 0.179234 TGAACACAAGGAAGGCGTCA 59.821 50.000 2.23 0.00 0.00 4.35
62 63 1.305201 TTGAACACAAGGAAGGCGTC 58.695 50.000 0.00 0.00 0.00 5.19
63 64 1.404035 GTTTGAACACAAGGAAGGCGT 59.596 47.619 0.00 0.00 0.00 5.68
64 65 1.403679 TGTTTGAACACAAGGAAGGCG 59.596 47.619 0.00 0.00 33.17 5.52
65 66 3.518634 TTGTTTGAACACAAGGAAGGC 57.481 42.857 0.00 0.00 38.92 4.35
86 87 7.454380 TCCCATGAAGAAATGATGTACCTTTTT 59.546 33.333 0.00 0.00 0.00 1.94
87 88 6.953520 TCCCATGAAGAAATGATGTACCTTTT 59.046 34.615 0.00 0.00 0.00 2.27
88 89 6.378280 GTCCCATGAAGAAATGATGTACCTTT 59.622 38.462 0.00 0.00 0.00 3.11
89 90 5.888161 GTCCCATGAAGAAATGATGTACCTT 59.112 40.000 0.00 0.00 0.00 3.50
90 91 5.192522 AGTCCCATGAAGAAATGATGTACCT 59.807 40.000 0.00 0.00 0.00 3.08
91 92 5.440610 AGTCCCATGAAGAAATGATGTACC 58.559 41.667 0.00 0.00 0.00 3.34
92 93 6.183360 CCAAGTCCCATGAAGAAATGATGTAC 60.183 42.308 0.00 0.00 0.00 2.90
93 94 5.887598 CCAAGTCCCATGAAGAAATGATGTA 59.112 40.000 0.00 0.00 0.00 2.29
94 95 4.708421 CCAAGTCCCATGAAGAAATGATGT 59.292 41.667 0.00 0.00 0.00 3.06
95 96 4.708421 ACCAAGTCCCATGAAGAAATGATG 59.292 41.667 0.00 0.00 0.00 3.07
96 97 4.939255 ACCAAGTCCCATGAAGAAATGAT 58.061 39.130 0.00 0.00 0.00 2.45
97 98 4.387026 ACCAAGTCCCATGAAGAAATGA 57.613 40.909 0.00 0.00 0.00 2.57
98 99 5.473066 AAACCAAGTCCCATGAAGAAATG 57.527 39.130 0.00 0.00 0.00 2.32
99 100 6.499106 AAAAACCAAGTCCCATGAAGAAAT 57.501 33.333 0.00 0.00 0.00 2.17
100 101 5.948742 AAAAACCAAGTCCCATGAAGAAA 57.051 34.783 0.00 0.00 0.00 2.52
218 219 4.320023 TCGCTAAACATGCTTTTGGTCTA 58.680 39.130 0.00 0.00 0.00 2.59
292 294 5.723672 TGAGACAACTACCTACTTTCAGG 57.276 43.478 0.00 0.00 41.87 3.86
332 334 1.212935 ACAGGAGGAATGTATGCACCC 59.787 52.381 0.00 0.00 30.14 4.61
357 359 5.300752 AGGCGTAGTTTGAGATATTCATGG 58.699 41.667 0.00 0.00 35.27 3.66
424 426 1.205655 GTGAGGCACTAGCACTCATGA 59.794 52.381 12.84 0.00 44.28 3.07
426 428 0.174389 CGTGAGGCACTAGCACTCAT 59.826 55.000 12.84 0.00 44.28 2.90
427 429 1.586541 CGTGAGGCACTAGCACTCA 59.413 57.895 7.34 7.34 41.55 3.41
428 430 4.485554 CGTGAGGCACTAGCACTC 57.514 61.111 0.00 0.00 41.55 3.51
503 505 2.243810 GAGGGTATGTTTTTGGGTGCA 58.756 47.619 0.00 0.00 0.00 4.57
526 528 4.413495 TTTAGCGTTATGTGCAGAAACC 57.587 40.909 0.00 0.00 33.85 3.27
538 540 5.492895 TGAATGATGGGTCTTTTAGCGTTA 58.507 37.500 0.00 0.00 0.00 3.18
554 556 5.045359 TGTGGTTTCCAGAGATCTGAATGAT 60.045 40.000 11.44 0.00 46.59 2.45
562 564 2.859165 TGGTGTGGTTTCCAGAGATC 57.141 50.000 0.00 0.00 32.34 2.75
607 610 3.159347 GGTAGATTCCCCCGGCGT 61.159 66.667 6.01 0.00 0.00 5.68
621 624 0.599558 CCTCGAACCAGAACACGGTA 59.400 55.000 0.00 0.00 34.99 4.02
633 636 1.374758 CAGCAGTCCCACCTCGAAC 60.375 63.158 0.00 0.00 0.00 3.95
683 686 5.590530 AGTATCTTCGTGAGCTGAAAGAT 57.409 39.130 5.59 5.59 34.07 2.40
749 752 1.486310 AGACGCCAAGCTATCCATGAA 59.514 47.619 0.00 0.00 0.00 2.57
787 790 4.058817 CACTCAGGTTCTGGTGACTTTAC 58.941 47.826 9.39 0.00 35.92 2.01
811 814 0.593518 CACACTATCGAGCTCCGCTG 60.594 60.000 8.47 0.00 39.88 5.18
812 815 1.729470 CCACACTATCGAGCTCCGCT 61.729 60.000 8.47 0.00 43.88 5.52
935 949 1.966451 CCGGCGAGGAAAGCTGTTT 60.966 57.895 9.30 0.00 45.00 2.83
1048 1347 1.525077 GGTGCCTGTCGTGGAACAA 60.525 57.895 5.61 0.00 44.16 2.83
1049 1348 2.110213 GGTGCCTGTCGTGGAACA 59.890 61.111 5.61 0.00 37.38 3.18
1166 1479 2.588201 TAGATGTGCACCGCCCACA 61.588 57.895 15.69 3.99 46.10 4.17
1195 1508 0.542232 AGGAGCAGGTACGGACAGTT 60.542 55.000 0.00 0.00 0.00 3.16
1198 1511 1.681327 GGAGGAGCAGGTACGGACA 60.681 63.158 0.00 0.00 0.00 4.02
1200 1543 1.681327 GTGGAGGAGCAGGTACGGA 60.681 63.158 0.00 0.00 0.00 4.69
1317 1660 1.379916 CCACATGAAGGCCTCCACA 59.620 57.895 5.23 7.80 0.00 4.17
1474 8542 0.745845 GGCTCGACGACCCAGTAGTA 60.746 60.000 4.26 0.00 0.00 1.82
1475 8543 2.045131 GGCTCGACGACCCAGTAGT 61.045 63.158 4.26 0.00 0.00 2.73
1476 8544 2.772691 GGGCTCGACGACCCAGTAG 61.773 68.421 22.78 2.80 46.22 2.57
1681 8842 1.075450 GACCCCGAGGAGGTATGGT 60.075 63.158 0.00 0.00 37.88 3.55
1814 8993 2.342648 GTCCCTCAGGCGAAACGT 59.657 61.111 0.00 0.00 0.00 3.99
2083 9282 5.885881 TGTGTACCACAATCTGAACAAAAC 58.114 37.500 0.00 0.00 41.69 2.43
2250 9492 9.646427 AGACTTCAACAGATTCAGTTAACTATC 57.354 33.333 8.04 8.92 0.00 2.08
2285 9527 2.361757 TGCAGACAATTCCCAACACTTG 59.638 45.455 0.00 0.00 0.00 3.16
2287 9529 2.362077 GTTGCAGACAATTCCCAACACT 59.638 45.455 0.00 0.00 38.27 3.55
2412 9736 9.851043 GTGCAGAAACGAGATTTATTTAGTATC 57.149 33.333 0.00 0.00 0.00 2.24
2543 10193 4.079253 TCACCTTTTTCCAAGTCATAGCC 58.921 43.478 0.00 0.00 0.00 3.93
2545 10195 7.277174 ACTTTCACCTTTTTCCAAGTCATAG 57.723 36.000 0.00 0.00 0.00 2.23
2683 10416 7.442062 AGGTAAAATGAACTTGATTTGGCTTTG 59.558 33.333 0.00 0.00 0.00 2.77
2817 10581 9.903682 ACAATCAATAACAACATCAAGAAGAAG 57.096 29.630 0.00 0.00 0.00 2.85
2985 10755 2.320587 GGCGTCCAGTTCTGCTGTG 61.321 63.158 0.00 0.00 43.55 3.66
3094 10870 4.036027 CAGCCATTGGAAGCAACACTATAG 59.964 45.833 6.95 0.00 0.00 1.31
3119 10895 2.697431 TGCAACGACCTACAAATTGC 57.303 45.000 0.00 0.00 44.66 3.56
3233 11019 8.750515 TGTATGATCTCAAAATATTGCAGGAA 57.249 30.769 0.00 0.00 36.45 3.36
3336 11122 4.141251 AGCTCTCAGGAAAAACCCACTAAA 60.141 41.667 0.00 0.00 40.05 1.85


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

AutoCloner maintained by Alex Coulton.