Multiple sequence alignment - TraesCS2A01G251200

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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 TraesCS2A01G251200 chr2A 100.000 3100 0 0 1422 4521 379291528 379294627 0.000000e+00 5725.0
1 TraesCS2A01G251200 chr2A 100.000 1139 0 0 1 1139 379290107 379291245 0.000000e+00 2104.0
2 TraesCS2A01G251200 chr2A 74.560 1136 267 22 1724 2848 203270382 203271506 1.140000e-130 477.0
3 TraesCS2A01G251200 chr2A 72.232 551 133 17 1726 2270 595989794 595989258 7.830000e-33 152.0
4 TraesCS2A01G251200 chr2A 96.875 32 0 1 821 852 565081734 565081764 8.000000e-03 52.8
5 TraesCS2A01G251200 chr5D 91.367 1807 153 3 1724 3528 447220339 447218534 0.000000e+00 2470.0
6 TraesCS2A01G251200 chr5B 84.713 1812 262 14 1724 3528 364108612 364110415 0.000000e+00 1797.0
7 TraesCS2A01G251200 chr5B 85.548 1633 226 9 1782 3409 3875831 3874204 0.000000e+00 1700.0
8 TraesCS2A01G251200 chr5B 84.382 1415 203 15 2124 3531 603982815 603984218 0.000000e+00 1373.0
9 TraesCS2A01G251200 chr5B 84.906 106 16 0 1032 1137 554593621 554593726 1.720000e-19 108.0
10 TraesCS2A01G251200 chr2D 89.696 1184 66 15 1 1139 302303898 302305070 0.000000e+00 1459.0
11 TraesCS2A01G251200 chr2D 90.357 280 23 4 1427 1706 302305137 302305412 9.240000e-97 364.0
12 TraesCS2A01G251200 chr2D 94.083 169 10 0 3526 3694 302305396 302305564 1.610000e-64 257.0
13 TraesCS2A01G251200 chr3B 88.669 1112 122 3 2418 3528 445600217 445599109 0.000000e+00 1352.0
14 TraesCS2A01G251200 chr3B 86.510 467 55 7 3803 4266 640693282 640692821 1.450000e-139 507.0
15 TraesCS2A01G251200 chr3B 89.091 110 4 3 4412 4521 780813788 780813687 3.670000e-26 130.0
16 TraesCS2A01G251200 chr3B 87.387 111 13 1 1030 1139 3634536 3634426 4.750000e-25 126.0
17 TraesCS2A01G251200 chr3B 86.486 111 14 1 1030 1139 5202013 5202123 2.210000e-23 121.0
18 TraesCS2A01G251200 chr3B 85.455 110 12 3 1034 1139 594443202 594443093 1.330000e-20 111.0
19 TraesCS2A01G251200 chr2B 90.486 1009 55 15 170 1139 357955046 357956052 0.000000e+00 1293.0
20 TraesCS2A01G251200 chr2B 84.342 281 25 8 1426 1706 357956095 357956356 1.610000e-64 257.0
21 TraesCS2A01G251200 chr2B 90.533 169 16 0 3526 3694 357956340 357956508 1.640000e-54 224.0
22 TraesCS2A01G251200 chr2B 89.474 114 4 2 1 114 357954944 357955049 2.190000e-28 137.0
23 TraesCS2A01G251200 chr1D 93.506 847 40 7 3689 4521 458297209 458298054 0.000000e+00 1245.0
24 TraesCS2A01G251200 chr4A 90.586 478 37 6 3800 4270 521868703 521868227 1.070000e-175 627.0
25 TraesCS2A01G251200 chr4A 84.896 384 41 8 3896 4270 255307687 255307312 5.520000e-99 372.0
26 TraesCS2A01G251200 chr4A 87.379 103 11 2 3694 3794 521868844 521868742 2.860000e-22 117.0
27 TraesCS2A01G251200 chr6A 75.680 1139 259 18 1724 2853 524357987 524359116 1.840000e-153 553.0
28 TraesCS2A01G251200 chr5A 74.009 1135 262 24 1724 2848 520110829 520111940 8.980000e-117 431.0
29 TraesCS2A01G251200 chr4B 84.656 378 41 8 3896 4265 285533720 285533352 1.200000e-95 361.0
30 TraesCS2A01G251200 chr4B 88.073 109 10 3 1032 1139 615142866 615142760 4.750000e-25 126.0
31 TraesCS2A01G251200 chr4D 83.558 371 46 7 3900 4265 260719781 260719421 2.610000e-87 333.0
32 TraesCS2A01G251200 chr4D 87.368 95 12 0 1042 1136 487376513 487376607 4.780000e-20 110.0
33 TraesCS2A01G251200 chr3D 89.804 255 15 6 4270 4520 433782825 433783072 2.620000e-82 316.0
34 TraesCS2A01G251200 chr1A 85.455 110 16 0 1030 1139 570244469 570244360 1.030000e-21 115.0
35 TraesCS2A01G251200 chr7A 77.124 153 34 1 3006 3157 712468057 712467905 2.240000e-13 87.9
36 TraesCS2A01G251200 chr3A 85.714 70 7 3 3694 3760 35436113 35436044 2.260000e-08 71.3


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 TraesCS2A01G251200 chr2A 379290107 379294627 4520 False 3914.500000 5725 100.000000 1 4521 2 chr2A.!!$F3 4520
1 TraesCS2A01G251200 chr2A 203270382 203271506 1124 False 477.000000 477 74.560000 1724 2848 1 chr2A.!!$F1 1124
2 TraesCS2A01G251200 chr5D 447218534 447220339 1805 True 2470.000000 2470 91.367000 1724 3528 1 chr5D.!!$R1 1804
3 TraesCS2A01G251200 chr5B 364108612 364110415 1803 False 1797.000000 1797 84.713000 1724 3528 1 chr5B.!!$F1 1804
4 TraesCS2A01G251200 chr5B 3874204 3875831 1627 True 1700.000000 1700 85.548000 1782 3409 1 chr5B.!!$R1 1627
5 TraesCS2A01G251200 chr5B 603982815 603984218 1403 False 1373.000000 1373 84.382000 2124 3531 1 chr5B.!!$F3 1407
6 TraesCS2A01G251200 chr2D 302303898 302305564 1666 False 693.333333 1459 91.378667 1 3694 3 chr2D.!!$F1 3693
7 TraesCS2A01G251200 chr3B 445599109 445600217 1108 True 1352.000000 1352 88.669000 2418 3528 1 chr3B.!!$R2 1110
8 TraesCS2A01G251200 chr2B 357954944 357956508 1564 False 477.750000 1293 88.708750 1 3694 4 chr2B.!!$F1 3693
9 TraesCS2A01G251200 chr1D 458297209 458298054 845 False 1245.000000 1245 93.506000 3689 4521 1 chr1D.!!$F1 832
10 TraesCS2A01G251200 chr4A 521868227 521868844 617 True 372.000000 627 88.982500 3694 4270 2 chr4A.!!$R2 576
11 TraesCS2A01G251200 chr6A 524357987 524359116 1129 False 553.000000 553 75.680000 1724 2853 1 chr6A.!!$F1 1129
12 TraesCS2A01G251200 chr5A 520110829 520111940 1111 False 431.000000 431 74.009000 1724 2848 1 chr5A.!!$F1 1124

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
298 299 0.251832 AGAAGAGGCCACGAGAAGGA 60.252 55.0 5.01 0.0 0.00 3.36 F
935 970 0.326595 TGAACCATAAGCAGCCGGAA 59.673 50.0 5.05 0.0 0.00 4.30 F
1712 1761 0.843309 TCTTTGTCTTGGCAGTCCCA 59.157 50.0 0.00 0.0 43.51 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1760 1.073763 TGGGACATCACAGAACCCTTG 59.926 52.381 0.0 0.0 40.98 3.61 R
2353 2406 0.320374 TTTGAATCGAGACCGCCAGT 59.680 50.000 0.0 0.0 35.37 4.00 R
3565 3620 0.252197 ATAAACACCCTCGCACTCCC 59.748 55.000 0.0 0.0 0.00 4.30 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
78 79 7.849322 ATTTTACTAACACCCCATGAAAACT 57.151 32.000 0.00 0.00 0.00 2.66
79 80 8.943594 ATTTTACTAACACCCCATGAAAACTA 57.056 30.769 0.00 0.00 0.00 2.24
80 81 7.989416 TTTACTAACACCCCATGAAAACTAG 57.011 36.000 0.00 0.00 0.00 2.57
81 82 5.836024 ACTAACACCCCATGAAAACTAGA 57.164 39.130 0.00 0.00 0.00 2.43
82 83 6.388619 ACTAACACCCCATGAAAACTAGAT 57.611 37.500 0.00 0.00 0.00 1.98
146 147 1.224003 ATGGGGAAGGGGAACATGCT 61.224 55.000 0.00 0.00 0.00 3.79
167 168 0.667184 CCCTTGTGTTGCAAATCCGC 60.667 55.000 0.00 0.00 36.53 5.54
208 209 3.154710 CCGGCCTTTTATCCCTTAATCC 58.845 50.000 0.00 0.00 0.00 3.01
217 218 2.638480 TCCCTTAATCCATCGGCAAG 57.362 50.000 0.00 0.00 0.00 4.01
225 226 2.180017 CATCGGCAAGGCTTGTGC 59.820 61.111 26.71 15.48 41.45 4.57
295 296 1.546476 GAGAAGAAGAGGCCACGAGAA 59.454 52.381 5.01 0.00 0.00 2.87
298 299 0.251832 AGAAGAGGCCACGAGAAGGA 60.252 55.000 5.01 0.00 0.00 3.36
301 302 0.539051 AGAGGCCACGAGAAGGAATG 59.461 55.000 5.01 0.00 0.00 2.67
312 313 5.874810 CACGAGAAGGAATGAGGATTAAACA 59.125 40.000 0.00 0.00 0.00 2.83
351 352 5.118817 CCGCGCTTTATTTTAGATCCTAGAC 59.881 44.000 5.56 0.00 0.00 2.59
354 355 6.924060 GCGCTTTATTTTAGATCCTAGACAGA 59.076 38.462 0.00 0.00 0.00 3.41
393 394 7.994911 TGAGTGGCATGAAGAATAAGTAATCAT 59.005 33.333 0.00 0.00 0.00 2.45
398 399 7.014115 GCATGAAGAATAAGTAATCATCAGCG 58.986 38.462 0.00 0.00 28.18 5.18
423 424 1.811679 GCGCCTGGCTAACACTCTC 60.812 63.158 17.92 0.00 39.11 3.20
503 505 3.769201 AAGGTGCAGGAGCTTTGC 58.231 55.556 15.07 15.07 39.46 3.68
600 602 9.220767 ACTTGCTACTAGGAGTTCAAAAATAAG 57.779 33.333 3.31 0.00 0.00 1.73
628 645 9.393512 ACCACTCTAGTAGTACTAATACAACAG 57.606 37.037 11.15 0.00 35.76 3.16
724 741 7.277981 AGTTTATTTCTTGTATGTACCGAGCTG 59.722 37.037 0.00 0.00 0.00 4.24
786 803 5.701224 TGTTGAATTTTGTTACTCCCTCCT 58.299 37.500 0.00 0.00 0.00 3.69
793 810 2.037144 TGTTACTCCCTCCTATTCGCC 58.963 52.381 0.00 0.00 0.00 5.54
817 834 9.533983 GCCGATTTAGTACAAAGTTTTACTAAC 57.466 33.333 19.19 13.05 39.43 2.34
847 865 8.945195 TTAATATGGATCGAAGGGAGTACTAA 57.055 34.615 0.00 0.00 0.00 2.24
848 866 6.837471 ATATGGATCGAAGGGAGTACTAAC 57.163 41.667 0.00 0.00 0.00 2.34
849 867 3.972133 TGGATCGAAGGGAGTACTAACA 58.028 45.455 0.00 0.00 0.00 2.41
906 941 9.289303 CAATAACTCATGTTGGTAATTGCTTAC 57.711 33.333 0.00 0.00 37.59 2.34
931 966 5.582689 AAGTTTATGAACCATAAGCAGCC 57.417 39.130 13.35 0.00 39.08 4.85
934 969 0.546122 ATGAACCATAAGCAGCCGGA 59.454 50.000 5.05 0.00 0.00 5.14
935 970 0.326595 TGAACCATAAGCAGCCGGAA 59.673 50.000 5.05 0.00 0.00 4.30
965 1002 0.897621 GCAAAAGGGCCTTGTATGCT 59.102 50.000 29.86 11.37 30.84 3.79
1030 1070 7.623268 AAAAATCATTTTCTACAACGCAGAC 57.377 32.000 0.00 0.00 33.48 3.51
1049 1098 5.231991 GCAGACTTTTTGTAAACACACATGG 59.768 40.000 0.00 0.00 0.00 3.66
1071 1120 2.921121 ACATGTATATTATGTCCGCGCG 59.079 45.455 25.67 25.67 33.72 6.86
1449 1498 8.704234 GTTAAAGTTTCATAGATCCATAGCGAG 58.296 37.037 0.00 0.00 0.00 5.03
1456 1505 5.418840 TCATAGATCCATAGCGAGCACATAA 59.581 40.000 0.00 0.00 0.00 1.90
1467 1516 3.416277 CGAGCACATAAATGTTTCCACG 58.584 45.455 0.00 0.00 39.39 4.94
1473 1522 6.200097 AGCACATAAATGTTTCCACGAAAAAC 59.800 34.615 0.00 0.00 39.39 2.43
1568 1617 2.729194 ACTTCACTCTCCTCGTATGCT 58.271 47.619 0.00 0.00 0.00 3.79
1667 1716 5.095490 GCTGTTGCTTATTGTTGATGTACC 58.905 41.667 0.00 0.00 36.03 3.34
1706 1755 3.569701 GGATGAAAGTCTTTGTCTTGGCA 59.430 43.478 1.60 0.00 0.00 4.92
1707 1756 4.320788 GGATGAAAGTCTTTGTCTTGGCAG 60.321 45.833 1.60 0.00 0.00 4.85
1708 1757 3.620488 TGAAAGTCTTTGTCTTGGCAGT 58.380 40.909 1.60 0.00 0.00 4.40
1709 1758 3.627577 TGAAAGTCTTTGTCTTGGCAGTC 59.372 43.478 1.60 0.00 0.00 3.51
1710 1759 2.262423 AGTCTTTGTCTTGGCAGTCC 57.738 50.000 0.00 0.00 0.00 3.85
1711 1760 1.202818 AGTCTTTGTCTTGGCAGTCCC 60.203 52.381 0.00 0.00 0.00 4.46
1712 1761 0.843309 TCTTTGTCTTGGCAGTCCCA 59.157 50.000 0.00 0.00 43.51 4.37
1719 1768 2.843545 TGGCAGTCCCAAGGGTTC 59.156 61.111 4.80 0.28 41.82 3.62
1720 1769 1.774217 TGGCAGTCCCAAGGGTTCT 60.774 57.895 4.80 2.66 41.82 3.01
1721 1770 1.303643 GGCAGTCCCAAGGGTTCTG 60.304 63.158 20.19 20.19 39.32 3.02
1722 1771 1.456287 GCAGTCCCAAGGGTTCTGT 59.544 57.895 22.90 0.46 38.94 3.41
1816 1866 1.811965 CGGAAAGTGCATTGGATGTCA 59.188 47.619 0.00 0.00 0.00 3.58
1858 1909 2.042979 CAAAAGAGGGGGAGGAATTGGA 59.957 50.000 0.00 0.00 0.00 3.53
1865 1916 4.328394 AGGGGGAGGAATTGGATTTAGAT 58.672 43.478 0.00 0.00 0.00 1.98
1892 1943 4.892934 TGAAACTATTCAACCAAGCCTTGT 59.107 37.500 3.37 0.00 42.47 3.16
1918 1969 3.608316 AGACAAGCTTGGAGACTGATC 57.392 47.619 29.18 15.13 0.00 2.92
1966 2017 6.590292 CACGTGTTCTCAAATCCAAGTACTAT 59.410 38.462 7.58 0.00 0.00 2.12
1974 2025 4.955811 AATCCAAGTACTATCCGCATGA 57.044 40.909 0.00 0.00 0.00 3.07
1978 2029 4.404394 TCCAAGTACTATCCGCATGAAGAA 59.596 41.667 0.00 0.00 0.00 2.52
2119 2170 3.388024 TCCAAAGAGATAAGTGGATCCCG 59.612 47.826 9.90 0.00 35.22 5.14
2138 2189 1.003355 CGCAAGGAAGGGCTCAAGA 60.003 57.895 0.00 0.00 0.00 3.02
2158 2209 1.259316 CTGCAAACTTTATTCGGCGC 58.741 50.000 0.00 0.00 0.00 6.53
2227 2280 4.439968 GGTGGAATTCGGACCTAGTTAAG 58.560 47.826 15.03 0.00 0.00 1.85
2254 2307 1.250328 TCTACCCTTTCGACGCTGAA 58.750 50.000 0.00 0.00 0.00 3.02
2273 2326 5.381174 TGAAGAAATCTGCAACATCAAGG 57.619 39.130 0.00 0.00 0.00 3.61
2278 2331 2.093306 TCTGCAACATCAAGGTACCG 57.907 50.000 6.18 0.00 0.00 4.02
2326 2379 3.080300 TGGCACTATGAAAAATCCGGT 57.920 42.857 0.00 0.00 0.00 5.28
2353 2406 2.199117 GGTCAGGAGTGCATACCGA 58.801 57.895 0.00 0.00 0.00 4.69
2368 2421 2.490217 CGACTGGCGGTCTCGATT 59.510 61.111 23.18 0.00 42.44 3.34
2593 2646 2.672874 CGAGGAAGATGAATTTCACGCA 59.327 45.455 0.15 0.00 0.00 5.24
2608 2661 1.154413 CGCAGTCATTTCGTGCACC 60.154 57.895 12.15 0.00 37.01 5.01
2653 2706 0.540454 TGAGAGCAATCTGGGAGCTG 59.460 55.000 0.00 0.00 39.02 4.24
2747 2800 9.314321 CAGAGACTAGAACAAAAGTTTTACTGA 57.686 33.333 0.00 0.00 0.00 3.41
2750 2803 9.614792 AGACTAGAACAAAAGTTTTACTGATGT 57.385 29.630 0.00 0.00 31.67 3.06
2809 2862 0.621571 ATGCAGGGAAGGAGCTGGTA 60.622 55.000 0.00 0.00 0.00 3.25
2853 2906 3.633418 AGCAGTACGAGGAGGAACTAAT 58.367 45.455 0.00 0.00 41.55 1.73
2890 2943 5.369993 GGGAGAGGAAACTGATATAAAGGGT 59.630 44.000 0.00 0.00 44.43 4.34
2921 2974 3.697439 TTACAGGGCGGGCATGCTC 62.697 63.158 18.92 13.80 34.79 4.26
2959 3012 1.694150 CTGTTCCCTCTGTCAACAGGA 59.306 52.381 10.13 0.00 42.20 3.86
3054 3107 1.603802 CAAACTGAACACGGATGCAGT 59.396 47.619 0.00 0.00 42.91 4.40
3198 3252 4.577677 TTTGCTGACCGGGCTGCA 62.578 61.111 35.40 35.40 40.31 4.41
3210 3264 1.891919 GGCTGCAACACTTGTCCGA 60.892 57.895 0.50 0.00 0.00 4.55
3214 3268 0.531974 TGCAACACTTGTCCGACCTC 60.532 55.000 0.00 0.00 0.00 3.85
3216 3270 1.502231 CAACACTTGTCCGACCTCTG 58.498 55.000 0.00 0.00 0.00 3.35
3227 3281 2.040606 ACCTCTGTACGGGCCCAT 59.959 61.111 24.92 10.00 0.00 4.00
3258 3312 4.216257 GGAAACAGACTGTATGCACATTGT 59.784 41.667 8.91 0.00 33.14 2.71
3262 3316 4.214119 ACAGACTGTATGCACATTGTGAAC 59.786 41.667 20.77 14.00 33.73 3.18
3400 3454 3.285484 CAAAATGGCTCATCTACTGGCT 58.715 45.455 0.00 0.00 0.00 4.75
3475 3529 0.669318 TAAACGCTGCGCTAGTTGCT 60.669 50.000 23.51 0.00 40.11 3.91
3503 3558 5.738619 TGTGTTGGCTGAAGAGTAGATTA 57.261 39.130 0.00 0.00 0.00 1.75
3545 3600 4.590850 AAAAGTCTTTGTCTTGGCCATC 57.409 40.909 6.09 0.54 0.00 3.51
3546 3601 3.515602 AAGTCTTTGTCTTGGCCATCT 57.484 42.857 6.09 0.00 0.00 2.90
3547 3602 3.064900 AGTCTTTGTCTTGGCCATCTC 57.935 47.619 6.09 0.00 0.00 2.75
3548 3603 2.087646 GTCTTTGTCTTGGCCATCTCC 58.912 52.381 6.09 0.00 0.00 3.71
3549 3604 1.089920 CTTTGTCTTGGCCATCTCCG 58.910 55.000 6.09 0.00 0.00 4.63
3550 3605 0.690192 TTTGTCTTGGCCATCTCCGA 59.310 50.000 6.09 0.00 0.00 4.55
3551 3606 0.911769 TTGTCTTGGCCATCTCCGAT 59.088 50.000 6.09 0.00 0.00 4.18
3552 3607 0.465705 TGTCTTGGCCATCTCCGATC 59.534 55.000 6.09 0.00 0.00 3.69
3553 3608 0.598680 GTCTTGGCCATCTCCGATCG 60.599 60.000 6.09 8.51 0.00 3.69
3554 3609 1.301244 CTTGGCCATCTCCGATCGG 60.301 63.158 28.62 28.62 0.00 4.18
3555 3610 1.748329 CTTGGCCATCTCCGATCGGA 61.748 60.000 33.55 33.55 42.90 4.55
3556 3611 2.028125 TTGGCCATCTCCGATCGGAC 62.028 60.000 32.59 21.47 39.76 4.79
3557 3612 2.049985 GCCATCTCCGATCGGACG 60.050 66.667 32.59 25.67 39.76 4.79
3558 3613 2.846652 GCCATCTCCGATCGGACGT 61.847 63.158 32.59 20.36 39.76 4.34
3559 3614 1.008424 CCATCTCCGATCGGACGTG 60.008 63.158 32.59 28.68 39.76 4.49
3560 3615 1.008424 CATCTCCGATCGGACGTGG 60.008 63.158 32.59 22.23 39.76 4.94
3561 3616 2.846652 ATCTCCGATCGGACGTGGC 61.847 63.158 32.59 0.00 39.76 5.01
3562 3617 4.907034 CTCCGATCGGACGTGGCG 62.907 72.222 32.59 17.95 39.76 5.69
3630 3685 0.524862 GGAGTCGGCTTAGTCGTTGA 59.475 55.000 6.03 0.00 30.45 3.18
3657 3712 9.342308 TGTTTATTTCATATCTTGAGTGATCCC 57.658 33.333 0.00 0.00 35.27 3.85
3665 3720 3.833732 TCTTGAGTGATCCCGCTATAGT 58.166 45.455 0.84 0.00 32.40 2.12
3700 3755 5.651530 TGTACTCTGCTCATTAACTAGTGC 58.348 41.667 0.00 0.00 0.00 4.40
3760 3815 2.283101 GTGCCAGGTGGGAATGCA 60.283 61.111 0.00 0.00 40.01 3.96
3763 3818 1.683365 GCCAGGTGGGAATGCACAT 60.683 57.895 0.00 0.00 40.01 3.21
3783 3840 7.020010 GCACATCTTCTGATTAGTTTTGTGAG 58.980 38.462 12.85 0.00 0.00 3.51
3794 3851 7.817478 TGATTAGTTTTGTGAGATGTGTCGTAT 59.183 33.333 0.00 0.00 0.00 3.06
3796 3853 9.817809 ATTAGTTTTGTGAGATGTGTCGTATAT 57.182 29.630 0.00 0.00 0.00 0.86
3835 3925 5.142061 TGAAAGCAATGACAGATGCAAAT 57.858 34.783 15.88 4.14 44.95 2.32
3840 3930 6.028146 AGCAATGACAGATGCAAATGTAAA 57.972 33.333 15.88 0.65 44.95 2.01
3903 3994 6.964934 ACGCTTTGGACGAAATAATACAAATC 59.035 34.615 0.00 0.00 0.00 2.17
3904 3995 7.148306 ACGCTTTGGACGAAATAATACAAATCT 60.148 33.333 0.00 0.00 0.00 2.40
4073 4165 0.037697 TGTTGATCCCGTGACCTTCG 60.038 55.000 0.00 0.00 0.00 3.79
4124 4216 9.331282 AGATAGCACAAATTAGAATGTTACCTC 57.669 33.333 0.00 0.00 0.00 3.85
4171 4263 3.635591 ACTGGCCTAATGATTTCAAGGG 58.364 45.455 3.32 0.00 0.00 3.95
4262 4358 7.267857 CAAGATGTATGTAGTCATCAGGAACA 58.732 38.462 7.68 0.00 41.74 3.18
4305 4401 5.329035 GGAACATCCTACGTACAAACCTA 57.671 43.478 0.00 0.00 32.53 3.08
4320 4416 8.889717 CGTACAAACCTAAAGGAAACATGATAT 58.110 33.333 0.00 0.00 38.94 1.63
4352 4448 8.208718 ACAACCGAGTGTATTAACTACGTATA 57.791 34.615 0.00 0.00 32.61 1.47
4408 4504 9.268282 AGAGGACTGGAGAAAACATAATAGTTA 57.732 33.333 0.00 0.00 0.00 2.24
4433 4529 0.593128 AGGTTGCATTGTCGTTGCTC 59.407 50.000 0.00 0.00 40.77 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.028733 GTTTGCCCCAATGCTTGCG 61.029 57.895 0.00 0.00 0.00 4.85
64 65 8.352942 GCTAATTAATCTAGTTTTCATGGGGTG 58.647 37.037 0.00 0.00 0.00 4.61
105 106 7.495934 CCCATTAGAATTGACTAACACCTACAG 59.504 40.741 0.00 0.00 35.60 2.74
106 107 7.335627 CCCATTAGAATTGACTAACACCTACA 58.664 38.462 0.00 0.00 35.60 2.74
146 147 1.339610 CGGATTTGCAACACAAGGGAA 59.660 47.619 0.00 0.00 40.06 3.97
153 154 0.664166 CACCAGCGGATTTGCAACAC 60.664 55.000 0.00 0.00 37.31 3.32
167 168 3.007635 GGGGAAACGTCTAAATCACCAG 58.992 50.000 0.00 0.00 35.38 4.00
208 209 2.180017 GCACAAGCCTTGCCGATG 59.820 61.111 3.88 0.00 33.58 3.84
231 232 2.173569 CCCTCTTTTATCTCACAGGGGG 59.826 54.545 0.00 0.00 40.88 5.40
295 296 5.960202 AGCCATTTGTTTAATCCTCATTCCT 59.040 36.000 0.00 0.00 0.00 3.36
301 302 7.963981 GCTTTTAAGCCATTTGTTTAATCCTC 58.036 34.615 3.05 0.00 46.20 3.71
330 331 8.138712 AGTCTGTCTAGGATCTAAAATAAAGCG 58.861 37.037 0.00 0.00 0.00 4.68
351 352 2.347755 CACTCATGAATGCACGAGTCTG 59.652 50.000 0.00 0.00 43.46 3.51
411 412 5.561339 GCGATTAGACTAGAGAGTGTTAGCC 60.561 48.000 0.00 0.00 35.45 3.93
423 424 4.822896 ACAGAACTAGGGCGATTAGACTAG 59.177 45.833 0.00 0.00 39.00 2.57
495 497 0.179179 GCACGAATCCAGCAAAGCTC 60.179 55.000 0.00 0.00 36.40 4.09
503 505 0.798776 GACAAGTGGCACGAATCCAG 59.201 55.000 12.71 1.08 33.63 3.86
664 681 7.170151 GCTACTTAGGCATTTAGTTAAGAGAGC 59.830 40.741 0.00 0.00 33.29 4.09
786 803 7.599630 AAACTTTGTACTAAATCGGCGAATA 57.400 32.000 15.93 9.68 0.00 1.75
906 941 6.311200 GGCTGCTTATGGTTCATAAACTTTTG 59.689 38.462 0.00 0.00 36.14 2.44
919 954 1.917872 TTTTTCCGGCTGCTTATGGT 58.082 45.000 0.00 0.00 0.00 3.55
941 976 1.620822 ACAAGGCCCTTTTGCACTAG 58.379 50.000 0.00 0.00 0.00 2.57
1018 1057 6.193959 GTGTTTACAAAAAGTCTGCGTTGTAG 59.806 38.462 0.00 0.00 37.65 2.74
1027 1066 6.151985 TGTCCATGTGTGTTTACAAAAAGTCT 59.848 34.615 0.00 0.00 38.82 3.24
1030 1070 7.164226 CATGTCCATGTGTGTTTACAAAAAG 57.836 36.000 0.00 0.00 38.82 2.27
1068 1117 8.746328 AAAGTAAAATGTTTTGAAATTTCGCG 57.254 26.923 13.34 0.00 0.00 5.87
1421 1470 9.046296 CGCTATGGATCTATGAAACTTTAACTT 57.954 33.333 1.10 0.00 0.00 2.66
1422 1471 8.421784 TCGCTATGGATCTATGAAACTTTAACT 58.578 33.333 1.10 0.00 0.00 2.24
1423 1472 8.589335 TCGCTATGGATCTATGAAACTTTAAC 57.411 34.615 1.10 0.00 0.00 2.01
1424 1473 7.385205 GCTCGCTATGGATCTATGAAACTTTAA 59.615 37.037 1.10 0.00 0.00 1.52
1429 1478 4.387256 GTGCTCGCTATGGATCTATGAAAC 59.613 45.833 1.10 0.00 0.00 2.78
1446 1495 3.124466 TCGTGGAAACATTTATGTGCTCG 59.876 43.478 0.00 3.23 46.14 5.03
1449 1498 6.200097 AGTTTTTCGTGGAAACATTTATGTGC 59.800 34.615 11.45 0.00 46.14 4.57
1456 1505 8.934507 TCAAAATAGTTTTTCGTGGAAACATT 57.065 26.923 11.45 7.65 38.99 2.71
1593 1642 3.139397 AGACCCACCAATAAAGACCAACA 59.861 43.478 0.00 0.00 0.00 3.33
1594 1643 3.756963 GAGACCCACCAATAAAGACCAAC 59.243 47.826 0.00 0.00 0.00 3.77
1595 1644 3.396276 TGAGACCCACCAATAAAGACCAA 59.604 43.478 0.00 0.00 0.00 3.67
1642 1691 4.801891 ACATCAACAATAAGCAACAGCTG 58.198 39.130 13.48 13.48 38.93 4.24
1646 1695 4.155099 CCGGTACATCAACAATAAGCAACA 59.845 41.667 0.00 0.00 0.00 3.33
1667 1716 2.125912 CAGGTTGCCGAGACTCCG 60.126 66.667 0.00 0.00 0.00 4.63
1706 1755 1.352352 CATCACAGAACCCTTGGGACT 59.648 52.381 13.39 8.33 0.00 3.85
1707 1756 1.073923 ACATCACAGAACCCTTGGGAC 59.926 52.381 13.39 6.16 0.00 4.46
1708 1757 1.351017 GACATCACAGAACCCTTGGGA 59.649 52.381 13.39 0.00 0.00 4.37
1709 1758 1.614317 GGACATCACAGAACCCTTGGG 60.614 57.143 3.77 3.77 0.00 4.12
1710 1759 1.614317 GGGACATCACAGAACCCTTGG 60.614 57.143 0.00 0.00 37.75 3.61
1711 1760 1.073763 TGGGACATCACAGAACCCTTG 59.926 52.381 0.00 0.00 40.98 3.61
1712 1761 1.444933 TGGGACATCACAGAACCCTT 58.555 50.000 0.00 0.00 40.98 3.95
1713 1762 1.352352 CTTGGGACATCACAGAACCCT 59.648 52.381 0.00 0.00 39.30 4.34
1714 1763 1.614317 CCTTGGGACATCACAGAACCC 60.614 57.143 0.00 0.00 39.30 4.11
1715 1764 1.614317 CCCTTGGGACATCACAGAACC 60.614 57.143 0.00 0.00 39.30 3.62
1716 1765 1.073923 ACCCTTGGGACATCACAGAAC 59.926 52.381 13.39 0.00 39.30 3.01
1717 1766 1.444933 ACCCTTGGGACATCACAGAA 58.555 50.000 13.39 0.00 39.30 3.02
1718 1767 1.351017 GAACCCTTGGGACATCACAGA 59.649 52.381 13.39 0.00 39.30 3.41
1719 1768 1.352352 AGAACCCTTGGGACATCACAG 59.648 52.381 13.39 0.00 39.30 3.66
1720 1769 1.073763 CAGAACCCTTGGGACATCACA 59.926 52.381 13.39 0.00 39.30 3.58
1721 1770 1.073923 ACAGAACCCTTGGGACATCAC 59.926 52.381 13.39 0.00 39.30 3.06
1722 1771 1.073763 CACAGAACCCTTGGGACATCA 59.926 52.381 13.39 0.00 39.30 3.07
1816 1866 1.463674 GTTTGGTCATTCGCTCCCAT 58.536 50.000 0.00 0.00 0.00 4.00
1865 1916 8.902806 CAAGGCTTGGTTGAATAGTTTCATATA 58.097 33.333 19.55 0.00 41.38 0.86
1918 1969 2.482142 GCAAAGACTATCCGGTCTCTGG 60.482 54.545 0.00 0.00 44.67 3.86
1966 2017 3.002791 GTCAATCAGTTCTTCATGCGGA 58.997 45.455 0.00 0.00 0.00 5.54
1974 2025 5.339990 CAAAAACCGTGTCAATCAGTTCTT 58.660 37.500 0.00 0.00 0.00 2.52
1978 2029 2.540769 CGCAAAAACCGTGTCAATCAGT 60.541 45.455 0.00 0.00 0.00 3.41
2110 2161 3.969250 TTCCTTGCGCGGGATCCAC 62.969 63.158 19.97 3.79 32.41 4.02
2119 2170 2.672996 TTGAGCCCTTCCTTGCGC 60.673 61.111 0.00 0.00 0.00 6.09
2138 2189 1.401018 GCGCCGAATAAAGTTTGCAGT 60.401 47.619 0.00 0.00 0.00 4.40
2158 2209 4.524053 GGTTAACCCATCTTAACCTGGAG 58.476 47.826 14.16 0.00 46.78 3.86
2227 2280 2.479275 GTCGAAAGGGTAGAACAGTTGC 59.521 50.000 0.00 0.00 0.00 4.17
2254 2307 4.702131 GGTACCTTGATGTTGCAGATTTCT 59.298 41.667 4.06 0.00 0.00 2.52
2273 2326 4.468689 GCCACCTGCCCTCGGTAC 62.469 72.222 0.00 0.00 32.37 3.34
2326 2379 0.673985 CACTCCTGACCGAGAACACA 59.326 55.000 0.00 0.00 33.83 3.72
2353 2406 0.320374 TTTGAATCGAGACCGCCAGT 59.680 50.000 0.00 0.00 35.37 4.00
2368 2421 1.298667 GGCCCTAGCTCGGTTTTGA 59.701 57.895 3.23 0.00 39.73 2.69
2593 2646 2.146342 CTCTTGGTGCACGAAATGACT 58.854 47.619 15.42 0.00 0.00 3.41
2608 2661 5.724328 TCATGTCTTAGTGCCTTACTCTTG 58.276 41.667 0.00 0.00 40.89 3.02
2653 2706 6.375455 TGAATCTGAATTTTTCCTCACTAGGC 59.625 38.462 0.00 0.00 43.31 3.93
2676 2729 2.571202 TGTAGCCAATCATCACCTGTGA 59.429 45.455 1.93 1.93 44.59 3.58
2747 2800 1.327303 AACCAACATCGCCACAACAT 58.673 45.000 0.00 0.00 0.00 2.71
2750 2803 1.686355 AGAAACCAACATCGCCACAA 58.314 45.000 0.00 0.00 0.00 3.33
2809 2862 2.981859 AGAACATAACGGATCGGCTT 57.018 45.000 0.00 0.00 0.00 4.35
2853 2906 0.967887 CTCTCCCAAGACTCCGCAGA 60.968 60.000 0.00 0.00 0.00 4.26
2890 2943 1.066430 CCCTGTAACGCCTTCTGCTTA 60.066 52.381 0.00 0.00 38.05 3.09
2903 2956 3.697439 GAGCATGCCCGCCCTGTAA 62.697 63.158 15.66 0.00 0.00 2.41
2921 2974 0.543749 AGAGAAATCCCCTTCGCCAG 59.456 55.000 0.00 0.00 0.00 4.85
2959 3012 3.713764 CTCCCACCTCTTGTCCATCTATT 59.286 47.826 0.00 0.00 0.00 1.73
3029 3082 2.971660 TCCGTGTTCAGTTTGACAGA 57.028 45.000 0.00 0.00 0.00 3.41
3111 3164 2.292016 AGACAGCGAGAAGATGATACGG 59.708 50.000 0.00 0.00 38.85 4.02
3112 3165 3.002759 TCAGACAGCGAGAAGATGATACG 59.997 47.826 0.00 0.00 38.85 3.06
3113 3166 4.560136 TCAGACAGCGAGAAGATGATAC 57.440 45.455 0.00 0.00 38.85 2.24
3115 3168 3.194329 TGTTCAGACAGCGAGAAGATGAT 59.806 43.478 0.00 0.00 38.85 2.45
3180 3234 3.294493 GCAGCCCGGTCAGCAAAA 61.294 61.111 0.00 0.00 0.00 2.44
3181 3235 4.577677 TGCAGCCCGGTCAGCAAA 62.578 61.111 0.00 0.00 33.48 3.68
3198 3252 1.120530 ACAGAGGTCGGACAAGTGTT 58.879 50.000 10.76 0.00 0.00 3.32
3210 3264 1.615424 AATGGGCCCGTACAGAGGT 60.615 57.895 19.47 0.00 0.00 3.85
3214 3268 0.880278 CGATCAATGGGCCCGTACAG 60.880 60.000 19.47 10.87 0.00 2.74
3216 3270 2.251642 GCGATCAATGGGCCCGTAC 61.252 63.158 19.47 8.54 0.00 3.67
3227 3281 1.270094 ACAGTCTGTTTCCGCGATCAA 60.270 47.619 8.23 0.00 0.00 2.57
3258 3312 2.636412 CCCGACCTGAGCTCGTTCA 61.636 63.158 9.64 0.00 0.00 3.18
3278 3332 6.314784 GGTAACATGCAGACAAATTACTGAC 58.685 40.000 10.14 4.24 36.38 3.51
3279 3333 5.414454 GGGTAACATGCAGACAAATTACTGA 59.586 40.000 10.14 0.00 35.55 3.41
3345 3399 1.352017 TGACATGTTGGACCTGAGCAT 59.648 47.619 0.00 0.00 0.00 3.79
3400 3454 2.040884 ATTCTCCTAGCCCGGGCA 60.041 61.111 45.13 29.46 44.88 5.36
3414 3468 5.182001 GCTACCATGTACATTCCATCCATTC 59.818 44.000 5.37 0.00 0.00 2.67
3475 3529 1.211703 TCTTCAGCCAACACAAGGTCA 59.788 47.619 0.00 0.00 0.00 4.02
3528 3583 2.087646 GGAGATGGCCAAGACAAAGAC 58.912 52.381 10.96 0.00 0.00 3.01
3529 3584 1.339055 CGGAGATGGCCAAGACAAAGA 60.339 52.381 10.96 0.00 0.00 2.52
3530 3585 1.089920 CGGAGATGGCCAAGACAAAG 58.910 55.000 10.96 0.00 0.00 2.77
3531 3586 0.690192 TCGGAGATGGCCAAGACAAA 59.310 50.000 10.96 0.00 0.00 2.83
3532 3587 0.911769 ATCGGAGATGGCCAAGACAA 59.088 50.000 10.96 0.00 45.12 3.18
3533 3588 0.465705 GATCGGAGATGGCCAAGACA 59.534 55.000 10.96 0.00 45.12 3.41
3534 3589 0.598680 CGATCGGAGATGGCCAAGAC 60.599 60.000 10.96 4.46 45.12 3.01
3535 3590 1.742146 CGATCGGAGATGGCCAAGA 59.258 57.895 10.96 5.01 45.12 3.02
3536 3591 1.301244 CCGATCGGAGATGGCCAAG 60.301 63.158 30.62 0.00 45.12 3.61
3537 3592 1.760480 TCCGATCGGAGATGGCCAA 60.760 57.895 32.59 7.58 45.12 4.52
3538 3593 2.123468 TCCGATCGGAGATGGCCA 60.123 61.111 32.59 8.56 45.12 5.36
3539 3594 2.340443 GTCCGATCGGAGATGGCC 59.660 66.667 36.38 19.89 46.16 5.36
3540 3595 2.049985 CGTCCGATCGGAGATGGC 60.050 66.667 36.38 22.56 46.16 4.40
3541 3596 1.008424 CACGTCCGATCGGAGATGG 60.008 63.158 36.38 25.54 46.16 3.51
3542 3597 1.008424 CCACGTCCGATCGGAGATG 60.008 63.158 36.38 31.92 46.16 2.90
3543 3598 2.846652 GCCACGTCCGATCGGAGAT 61.847 63.158 36.38 24.07 46.16 2.75
3544 3599 3.515286 GCCACGTCCGATCGGAGA 61.515 66.667 36.38 14.84 46.16 3.71
3545 3600 4.907034 CGCCACGTCCGATCGGAG 62.907 72.222 36.38 28.75 46.16 4.63
3562 3617 4.436998 CACCCTCGCACTCCCGTC 62.437 72.222 0.00 0.00 0.00 4.79
3564 3619 2.162338 TAAACACCCTCGCACTCCCG 62.162 60.000 0.00 0.00 0.00 5.14
3565 3620 0.252197 ATAAACACCCTCGCACTCCC 59.748 55.000 0.00 0.00 0.00 4.30
3566 3621 2.007608 GAATAAACACCCTCGCACTCC 58.992 52.381 0.00 0.00 0.00 3.85
3567 3622 2.973945 AGAATAAACACCCTCGCACTC 58.026 47.619 0.00 0.00 0.00 3.51
3657 3712 2.533266 AGGCATGGACAACTATAGCG 57.467 50.000 0.00 0.00 0.00 4.26
3665 3720 2.875672 GCAGAGTACAAGGCATGGACAA 60.876 50.000 7.95 0.00 46.19 3.18
3700 3755 3.219198 GCAATAGCGGGCCCCAAG 61.219 66.667 18.66 2.81 0.00 3.61
3753 3808 6.690194 AACTAATCAGAAGATGTGCATTCC 57.310 37.500 0.00 0.00 33.90 3.01
3760 3815 8.944029 CATCTCACAAAACTAATCAGAAGATGT 58.056 33.333 0.00 0.00 33.90 3.06
3763 3818 7.933577 ACACATCTCACAAAACTAATCAGAAGA 59.066 33.333 0.00 0.00 0.00 2.87
3783 3840 9.244799 TCTGTATTTTGACATATACGACACATC 57.755 33.333 0.00 0.00 31.38 3.06
3824 3914 9.935682 CTATCGTATTTTTACATTTGCATCTGT 57.064 29.630 6.85 6.85 0.00 3.41
3845 3935 6.584954 GCACTACATTTGTATTGCTCTATCG 58.415 40.000 19.77 0.00 46.83 2.92
3864 3954 3.373748 CCAAAGCGTGATAATGTGCACTA 59.626 43.478 19.41 3.01 32.98 2.74
3903 3994 1.606668 TGCTGCTACGTTTTTCCCAAG 59.393 47.619 0.00 0.00 0.00 3.61
3904 3995 1.681538 TGCTGCTACGTTTTTCCCAA 58.318 45.000 0.00 0.00 0.00 4.12
3914 4005 6.089417 TCGTGAATCATATTTATGCTGCTACG 59.911 38.462 0.00 0.00 33.76 3.51
3994 4085 9.809096 TTTGTATTCTGTTGAAACTGCAAAATA 57.191 25.926 0.00 0.00 35.63 1.40
4124 4216 7.837202 ATAAAGGTTGCATTTCATCACATTG 57.163 32.000 0.00 0.00 0.00 2.82
4398 4494 9.935682 CAATGCAACCTACAAGTAACTATTATG 57.064 33.333 0.00 0.00 0.00 1.90
4408 4504 2.846193 ACGACAATGCAACCTACAAGT 58.154 42.857 0.00 0.00 0.00 3.16
4461 4564 5.250200 TCACAAAACAGTGTTGTTCTACCT 58.750 37.500 9.79 0.00 46.54 3.08
4462 4565 5.554822 TCACAAAACAGTGTTGTTCTACC 57.445 39.130 9.79 0.00 46.54 3.18


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

AutoCloner maintained by Alex Coulton.