Multiple sequence alignment - TraesCS3B01G047000

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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 TraesCS3B01G047000 chr3B 100.000 3744 0 0 1 3744 23946627 23942884 0.000000e+00 6914.0
1 TraesCS3B01G047000 chr3B 85.477 661 90 4 2097 2755 23915038 23915694 0.000000e+00 684.0
2 TraesCS3B01G047000 chr3B 83.978 181 29 0 3564 3744 31356114 31356294 1.380000e-39 174.0
3 TraesCS3B01G047000 chr3B 95.604 91 3 1 1636 1725 497104973 497104883 1.080000e-30 145.0
4 TraesCS3B01G047000 chr3B 80.769 182 30 5 3564 3744 437917793 437917970 1.810000e-28 137.0
5 TraesCS3B01G047000 chr3D 85.754 1790 180 30 1786 3526 16502451 16500688 0.000000e+00 1823.0
6 TraesCS3B01G047000 chr3D 92.140 827 44 16 1 813 16507616 16506797 0.000000e+00 1147.0
7 TraesCS3B01G047000 chr3D 92.453 795 32 9 813 1595 16503438 16502660 0.000000e+00 1110.0
8 TraesCS3B01G047000 chr3D 90.137 659 60 3 2100 2754 16496322 16495665 0.000000e+00 852.0
9 TraesCS3B01G047000 chr3D 86.767 665 75 9 2100 2753 16378895 16378233 0.000000e+00 728.0
10 TraesCS3B01G047000 chr3D 89.459 370 28 6 1225 1587 16497276 16496911 1.230000e-124 457.0
11 TraesCS3B01G047000 chr3D 87.179 390 39 7 1205 1587 16379512 16379127 2.070000e-117 433.0
12 TraesCS3B01G047000 chr3D 83.887 391 55 7 2364 2749 16376775 16376388 2.120000e-97 366.0
13 TraesCS3B01G047000 chr3D 84.502 271 33 6 1330 1594 16364519 16364252 3.710000e-65 259.0
14 TraesCS3B01G047000 chr3D 84.191 272 37 5 1817 2084 549901799 549902068 3.710000e-65 259.0
15 TraesCS3B01G047000 chr3D 83.392 283 40 6 1802 2080 600540003 600539724 4.800000e-64 255.0
16 TraesCS3B01G047000 chr3D 88.835 206 17 4 2841 3041 292726309 292726105 8.030000e-62 248.0
17 TraesCS3B01G047000 chr3D 87.821 156 17 2 1636 1789 16502665 16502510 8.260000e-42 182.0
18 TraesCS3B01G047000 chr3D 90.909 110 8 2 1637 1744 16496907 16496798 3.010000e-31 147.0
19 TraesCS3B01G047000 chr3D 96.552 87 2 1 1639 1725 381634266 381634181 3.900000e-30 143.0
20 TraesCS3B01G047000 chr3D 93.548 93 4 2 1636 1726 546330125 546330217 1.810000e-28 137.0
21 TraesCS3B01G047000 chr3D 97.436 78 2 0 1652 1729 16379108 16379031 2.350000e-27 134.0
22 TraesCS3B01G047000 chr3A 91.031 1115 91 8 2151 3259 20039021 20040132 0.000000e+00 1496.0
23 TraesCS3B01G047000 chr3A 90.065 765 62 9 1 756 20037045 20037804 0.000000e+00 979.0
24 TraesCS3B01G047000 chr3A 85.693 657 87 7 2097 2748 20098734 20099388 0.000000e+00 686.0
25 TraesCS3B01G047000 chr3A 87.179 390 39 5 1205 1587 20098225 20098610 2.070000e-117 433.0
26 TraesCS3B01G047000 chr3A 87.606 355 24 8 856 1197 20038658 20039005 9.750000e-106 394.0
27 TraesCS3B01G047000 chr3A 82.766 470 33 11 3322 3744 20040661 20041129 3.530000e-100 375.0
28 TraesCS3B01G047000 chr3A 85.199 277 38 3 1312 1585 20101460 20101736 7.920000e-72 281.0
29 TraesCS3B01G047000 chr3A 92.079 101 5 3 1632 1729 683068192 683068292 5.040000e-29 139.0
30 TraesCS3B01G047000 chr3A 80.874 183 28 7 3564 3744 97901907 97902084 1.810000e-28 137.0
31 TraesCS3B01G047000 chr4A 77.846 975 143 35 2837 3744 173724389 173723421 1.530000e-148 536.0
32 TraesCS3B01G047000 chr4A 98.734 79 1 0 1651 1729 34769690 34769768 1.400000e-29 141.0
33 TraesCS3B01G047000 chr4A 94.382 89 2 3 1638 1726 34766610 34766695 2.350000e-27 134.0
34 TraesCS3B01G047000 chr2B 84.615 351 41 10 2842 3184 355381832 355381487 1.670000e-88 337.0
35 TraesCS3B01G047000 chr2B 84.083 289 34 12 1802 2082 643677063 643676779 6.160000e-68 268.0
36 TraesCS3B01G047000 chr2B 77.126 341 44 20 3432 3744 679964726 679965060 2.310000e-37 167.0
37 TraesCS3B01G047000 chr2B 79.558 181 34 3 3564 3742 620002495 620002674 3.930000e-25 126.0
38 TraesCS3B01G047000 chr2B 76.503 183 35 7 1337 1515 793646905 793646727 3.980000e-15 93.5
39 TraesCS3B01G047000 chr4D 80.097 412 51 21 2842 3233 233169569 233169169 1.020000e-70 278.0
40 TraesCS3B01G047000 chr4D 81.373 306 49 8 1789 2090 80988971 80989272 3.740000e-60 243.0
41 TraesCS3B01G047000 chr4D 76.488 336 50 17 3432 3744 290737969 290738298 5.010000e-34 156.0
42 TraesCS3B01G047000 chr4D 95.402 87 3 1 1639 1725 429556588 429556503 1.810000e-28 137.0
43 TraesCS3B01G047000 chr4D 96.341 82 2 1 1641 1722 433370737 433370817 2.350000e-27 134.0
44 TraesCS3B01G047000 chr4D 80.337 178 30 5 3569 3744 102745568 102745394 3.030000e-26 130.0
45 TraesCS3B01G047000 chr4D 93.103 87 4 2 1637 1722 433374591 433374676 3.930000e-25 126.0
46 TraesCS3B01G047000 chr5A 89.320 206 18 2 2842 3043 372092302 372092097 4.800000e-64 255.0
47 TraesCS3B01G047000 chr5A 82.432 296 43 8 1799 2089 7375491 7375782 2.230000e-62 250.0
48 TraesCS3B01G047000 chr5A 85.083 181 27 0 3564 3744 123835178 123835358 6.390000e-43 185.0
49 TraesCS3B01G047000 chr5A 82.514 183 29 3 3564 3744 320567961 320567780 1.390000e-34 158.0
50 TraesCS3B01G047000 chr5A 92.079 101 3 5 1639 1736 402024048 402024146 1.810000e-28 137.0
51 TraesCS3B01G047000 chrUn 82.818 291 42 8 1799 2084 392320958 392320671 1.730000e-63 254.0
52 TraesCS3B01G047000 chr1B 82.759 290 42 8 1799 2083 532396873 532396587 6.210000e-63 252.0
53 TraesCS3B01G047000 chr1B 76.106 339 51 16 3432 3744 280816442 280816776 2.330000e-32 150.0
54 TraesCS3B01G047000 chr1A 83.045 289 38 10 1799 2081 529440628 529440911 6.210000e-63 252.0
55 TraesCS3B01G047000 chr1A 98.734 79 1 0 1651 1729 531015376 531015298 1.400000e-29 141.0
56 TraesCS3B01G047000 chr1A 98.734 79 1 0 1651 1729 531051520 531051442 1.400000e-29 141.0
57 TraesCS3B01G047000 chr2A 88.780 205 19 4 2841 3043 61512053 61511851 8.030000e-62 248.0
58 TraesCS3B01G047000 chr2A 76.696 339 45 22 3432 3744 497533332 497533002 1.390000e-34 158.0
59 TraesCS3B01G047000 chr7D 80.000 350 57 10 2870 3211 460808263 460808607 2.890000e-61 246.0
60 TraesCS3B01G047000 chr7D 76.440 382 72 17 2971 3345 375979026 375979396 1.370000e-44 191.0
61 TraesCS3B01G047000 chr7D 94.565 92 1 4 1640 1730 458941703 458941791 5.040000e-29 139.0
62 TraesCS3B01G047000 chr7D 94.444 90 5 0 1639 1728 586760912 586761001 5.040000e-29 139.0
63 TraesCS3B01G047000 chr7D 93.548 93 4 2 1641 1733 586806878 586806788 1.810000e-28 137.0
64 TraesCS3B01G047000 chr5B 81.908 304 43 10 1796 2088 680235536 680235838 2.890000e-61 246.0
65 TraesCS3B01G047000 chr5B 76.946 334 47 24 3432 3744 118727438 118727114 2.990000e-36 163.0
66 TraesCS3B01G047000 chr5D 80.935 278 46 6 2914 3188 368847065 368846792 2.930000e-51 213.0
67 TraesCS3B01G047000 chr5D 83.105 219 33 3 2970 3187 219460433 219460648 2.950000e-46 196.0
68 TraesCS3B01G047000 chr5D 76.627 338 48 18 3432 3744 331247489 331247158 1.390000e-34 158.0
69 TraesCS3B01G047000 chr5D 97.333 75 2 0 1652 1726 377373972 377373898 1.090000e-25 128.0
70 TraesCS3B01G047000 chr7A 80.623 289 43 10 2970 3252 269940218 269940499 1.050000e-50 211.0
71 TraesCS3B01G047000 chr7A 95.699 93 3 1 1636 1728 677846261 677846352 8.380000e-32 148.0
72 TraesCS3B01G047000 chr4B 82.727 220 34 3 2970 3188 169814026 169813810 3.820000e-45 193.0
73 TraesCS3B01G047000 chr4B 96.386 83 2 1 1640 1722 531488243 531488324 6.520000e-28 135.0
74 TraesCS3B01G047000 chr4B 94.318 88 3 2 1639 1726 531570511 531570596 2.350000e-27 134.0
75 TraesCS3B01G047000 chr6D 76.331 338 48 20 3432 3744 178226157 178226487 6.480000e-33 152.0
76 TraesCS3B01G047000 chr6D 76.435 331 47 16 3432 3735 220607053 220606727 2.330000e-32 150.0
77 TraesCS3B01G047000 chr6D 83.333 168 21 7 3579 3744 392889979 392889817 8.380000e-32 148.0
78 TraesCS3B01G047000 chr6D 98.649 74 1 0 1652 1725 306134926 306134853 8.440000e-27 132.0
79 TraesCS3B01G047000 chr7B 96.591 88 1 2 1641 1728 657623470 657623385 1.080000e-30 145.0
80 TraesCS3B01G047000 chr7B 95.506 89 4 0 1638 1726 657534512 657534424 3.900000e-30 143.0
81 TraesCS3B01G047000 chr6B 94.681 94 3 2 1638 1729 473060907 473060814 1.080000e-30 145.0
82 TraesCS3B01G047000 chr2D 75.882 340 49 19 3432 3744 256737768 256738101 3.900000e-30 143.0
83 TraesCS3B01G047000 chr2D 93.548 93 4 2 1638 1728 476338455 476338547 1.810000e-28 137.0
84 TraesCS3B01G047000 chr6A 93.617 94 4 2 1638 1729 441496866 441496773 5.040000e-29 139.0
85 TraesCS3B01G047000 chr1D 98.718 78 1 0 1652 1729 432400469 432400392 5.040000e-29 139.0
86 TraesCS3B01G047000 chr1D 93.103 87 5 1 1641 1727 432706742 432706657 3.930000e-25 126.0


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 TraesCS3B01G047000 chr3B 23942884 23946627 3743 True 6914.000000 6914 100.000000 1 3744 1 chr3B.!!$R1 3743
1 TraesCS3B01G047000 chr3B 23915038 23915694 656 False 684.000000 684 85.477000 2097 2755 1 chr3B.!!$F1 658
2 TraesCS3B01G047000 chr3D 16495665 16507616 11951 True 816.857143 1823 89.810429 1 3526 7 chr3D.!!$R6 3525
3 TraesCS3B01G047000 chr3D 16376388 16379512 3124 True 415.250000 728 88.817250 1205 2753 4 chr3D.!!$R5 1548
4 TraesCS3B01G047000 chr3A 20037045 20041129 4084 False 811.000000 1496 87.867000 1 3744 4 chr3A.!!$F3 3743
5 TraesCS3B01G047000 chr3A 20098225 20101736 3511 False 466.666667 686 86.023667 1205 2748 3 chr3A.!!$F4 1543
6 TraesCS3B01G047000 chr4A 173723421 173724389 968 True 536.000000 536 77.846000 2837 3744 1 chr4A.!!$R1 907

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
737 757 0.250901 AGGTCCATGTGCAGGTGAAC 60.251 55.0 0.0 0.0 0.0 3.18 F
1599 5249 0.036765 AGGTAACCAGCGAAATGCGA 60.037 50.0 0.0 0.0 45.1 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 5267 0.316114 GTGTGTGTGTGTGTGCATCG 60.316 55.0 0.0 0.0 0.0 3.84 R
3368 8294 0.392193 CAGAACAGAGGATTGCGGCT 60.392 55.0 0.0 0.0 0.0 5.52 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
155 156 5.904080 CGTGAGTGTGAGAAGAAAATCAAAC 59.096 40.000 0.00 0.00 34.44 2.93
197 198 1.002430 CACCTAGGCTGCTCTGTTGAA 59.998 52.381 9.30 0.00 0.00 2.69
200 201 3.519510 ACCTAGGCTGCTCTGTTGAATTA 59.480 43.478 9.30 0.00 0.00 1.40
207 208 4.427312 CTGCTCTGTTGAATTATTTGGCC 58.573 43.478 0.00 0.00 0.00 5.36
316 321 2.910688 TCGAGAAGCCCCATTGATAC 57.089 50.000 0.00 0.00 0.00 2.24
450 455 3.918220 CTCGTCATCGCGGCAAGC 61.918 66.667 6.13 0.00 43.95 4.01
492 497 1.373497 GATCGCGTATGCCCTCAGG 60.373 63.158 5.77 0.00 38.08 3.86
549 554 1.759459 GACCCGGTCATCCCCATCTC 61.759 65.000 13.05 0.00 32.09 2.75
550 555 1.460305 CCCGGTCATCCCCATCTCT 60.460 63.158 0.00 0.00 0.00 3.10
562 567 1.300481 CCATCTCTGAGTGCATGCAG 58.700 55.000 23.41 9.73 0.00 4.41
564 570 0.910338 ATCTCTGAGTGCATGCAGGT 59.090 50.000 23.41 11.94 33.05 4.00
568 574 1.632948 CTGAGTGCATGCAGGTGTCG 61.633 60.000 23.41 3.90 0.00 4.35
587 593 4.976224 TCGTAAGATCCGAGATTGTTCA 57.024 40.909 0.00 0.00 45.01 3.18
588 594 5.515797 TCGTAAGATCCGAGATTGTTCAT 57.484 39.130 0.00 0.00 45.01 2.57
589 595 5.281727 TCGTAAGATCCGAGATTGTTCATG 58.718 41.667 0.00 0.00 45.01 3.07
590 596 5.067283 TCGTAAGATCCGAGATTGTTCATGA 59.933 40.000 0.00 0.00 45.01 3.07
596 611 3.996363 TCCGAGATTGTTCATGAACTGTG 59.004 43.478 32.57 18.54 41.67 3.66
604 619 2.455674 TCATGAACTGTGAACTCCCG 57.544 50.000 0.00 0.00 0.00 5.14
698 718 1.692519 ACGTTGTGTTCCTCCTAAGCT 59.307 47.619 0.00 0.00 0.00 3.74
737 757 0.250901 AGGTCCATGTGCAGGTGAAC 60.251 55.000 0.00 0.00 0.00 3.18
804 824 8.438676 TCTAATCTAAAATAGAAACCTGCTGC 57.561 34.615 0.00 0.00 38.50 5.25
940 4562 4.208686 CCTCCCCGACGTAGCTGC 62.209 72.222 0.00 0.00 0.00 5.25
965 4596 7.682741 GCGGTCCAGTGTGTATAAGTAATAAGA 60.683 40.741 0.00 0.00 0.00 2.10
966 4597 7.861372 CGGTCCAGTGTGTATAAGTAATAAGAG 59.139 40.741 0.00 0.00 0.00 2.85
967 4598 8.693625 GGTCCAGTGTGTATAAGTAATAAGAGT 58.306 37.037 0.00 0.00 0.00 3.24
979 4610 4.714308 AGTAATAAGAGTCCAAGAGCTGCT 59.286 41.667 0.00 0.00 0.00 4.24
981 4612 2.470983 AAGAGTCCAAGAGCTGCTTC 57.529 50.000 2.53 0.00 33.60 3.86
1008 4646 2.184322 CGACGTAGCATGGCCAGT 59.816 61.111 13.05 1.14 0.00 4.00
1155 4799 0.692419 AGGAATCCCATCTCACGCCT 60.692 55.000 0.00 0.00 33.88 5.52
1183 4827 1.439644 CCGCTGCCTTCTCTCCTAC 59.560 63.158 0.00 0.00 0.00 3.18
1184 4828 1.064946 CGCTGCCTTCTCTCCTACG 59.935 63.158 0.00 0.00 0.00 3.51
1185 4829 1.439644 GCTGCCTTCTCTCCTACGG 59.560 63.158 0.00 0.00 0.00 4.02
1186 4830 1.324005 GCTGCCTTCTCTCCTACGGT 61.324 60.000 0.00 0.00 0.00 4.83
1187 4831 0.741915 CTGCCTTCTCTCCTACGGTC 59.258 60.000 0.00 0.00 0.00 4.79
1188 4832 1.030488 TGCCTTCTCTCCTACGGTCG 61.030 60.000 0.00 0.00 0.00 4.79
1189 4833 1.031029 GCCTTCTCTCCTACGGTCGT 61.031 60.000 0.69 0.69 0.00 4.34
1190 4834 1.015868 CCTTCTCTCCTACGGTCGTC 58.984 60.000 0.00 0.00 0.00 4.20
1191 4835 0.651551 CTTCTCTCCTACGGTCGTCG 59.348 60.000 0.00 0.00 45.88 5.12
1192 4836 1.364626 TTCTCTCCTACGGTCGTCGC 61.365 60.000 0.00 0.00 43.89 5.19
1193 4837 2.821366 TCTCCTACGGTCGTCGCC 60.821 66.667 0.00 0.00 43.89 5.54
1223 4867 2.267961 GCCAACTCCGGTGGTAGG 59.732 66.667 10.99 8.25 0.00 3.18
1591 5241 2.040544 CCAAGCCAGGTAACCAGCG 61.041 63.158 0.00 0.00 31.64 5.18
1595 5245 0.328258 AGCCAGGTAACCAGCGAAAT 59.672 50.000 0.00 0.00 31.64 2.17
1596 5246 0.451783 GCCAGGTAACCAGCGAAATG 59.548 55.000 0.00 0.00 37.17 2.32
1597 5247 0.451783 CCAGGTAACCAGCGAAATGC 59.548 55.000 0.00 0.00 41.05 3.56
1598 5248 0.096976 CAGGTAACCAGCGAAATGCG 59.903 55.000 0.00 0.00 45.10 4.73
1599 5249 0.036765 AGGTAACCAGCGAAATGCGA 60.037 50.000 0.00 0.00 45.10 5.10
1600 5250 1.609580 AGGTAACCAGCGAAATGCGAA 60.610 47.619 0.00 0.00 45.10 4.70
1601 5251 3.131456 AGGTAACCAGCGAAATGCGAAA 61.131 45.455 0.00 0.00 45.10 3.46
1602 5252 4.426879 AGGTAACCAGCGAAATGCGAAAT 61.427 43.478 0.00 0.00 45.10 2.17
1603 5253 5.874199 AGGTAACCAGCGAAATGCGAAATT 61.874 41.667 0.00 0.00 45.10 1.82
1622 5272 9.183620 GCGAAATTAAAATAAGAAAAACGATGC 57.816 29.630 0.00 0.00 0.00 3.91
1627 5277 8.858003 TTAAAATAAGAAAAACGATGCACACA 57.142 26.923 0.00 0.00 0.00 3.72
1628 5278 6.747659 AAATAAGAAAAACGATGCACACAC 57.252 33.333 0.00 0.00 0.00 3.82
1629 5279 3.773860 AAGAAAAACGATGCACACACA 57.226 38.095 0.00 0.00 0.00 3.72
1630 5280 3.065019 AGAAAAACGATGCACACACAC 57.935 42.857 0.00 0.00 0.00 3.82
1631 5281 2.421775 AGAAAAACGATGCACACACACA 59.578 40.909 0.00 0.00 0.00 3.72
1632 5282 2.187351 AAAACGATGCACACACACAC 57.813 45.000 0.00 0.00 0.00 3.82
1633 5283 1.090728 AAACGATGCACACACACACA 58.909 45.000 0.00 0.00 0.00 3.72
1634 5284 0.376852 AACGATGCACACACACACAC 59.623 50.000 0.00 0.00 0.00 3.82
1635 5285 0.742635 ACGATGCACACACACACACA 60.743 50.000 0.00 0.00 0.00 3.72
1636 5286 0.316114 CGATGCACACACACACACAC 60.316 55.000 0.00 0.00 0.00 3.82
1637 5287 0.731994 GATGCACACACACACACACA 59.268 50.000 0.00 0.00 0.00 3.72
1638 5288 1.132073 GATGCACACACACACACACAA 59.868 47.619 0.00 0.00 0.00 3.33
1639 5289 0.954452 TGCACACACACACACACAAA 59.046 45.000 0.00 0.00 0.00 2.83
1640 5290 1.338020 TGCACACACACACACACAAAA 59.662 42.857 0.00 0.00 0.00 2.44
1641 5291 2.223805 TGCACACACACACACACAAAAA 60.224 40.909 0.00 0.00 0.00 1.94
1722 5372 0.044092 TCCCAACTGAGCTATCCCCA 59.956 55.000 0.00 0.00 0.00 4.96
1730 5443 0.464554 GAGCTATCCCCACTTGTGCC 60.465 60.000 0.00 0.00 0.00 5.01
1732 5445 0.323360 GCTATCCCCACTTGTGCCAA 60.323 55.000 0.00 0.00 0.00 4.52
1748 5461 9.855021 ACTTGTGCCAATTTACTTGATAATAAC 57.145 29.630 0.00 0.00 36.97 1.89
1766 5480 6.530019 AATAACCTTTATTTCCAGGTGCTG 57.470 37.500 0.00 0.00 43.05 4.41
1779 5493 2.163010 CAGGTGCTGTTTTGGCTCATAG 59.837 50.000 0.00 0.00 0.00 2.23
1782 5496 2.095059 GTGCTGTTTTGGCTCATAGGTG 60.095 50.000 0.00 0.00 0.00 4.00
1791 5505 8.052748 TGTTTTGGCTCATAGGTGTAGATAATT 58.947 33.333 0.00 0.00 0.00 1.40
1792 5506 8.903820 GTTTTGGCTCATAGGTGTAGATAATTT 58.096 33.333 0.00 0.00 0.00 1.82
1793 5507 8.677148 TTTGGCTCATAGGTGTAGATAATTTC 57.323 34.615 0.00 0.00 0.00 2.17
1795 5509 7.217200 TGGCTCATAGGTGTAGATAATTTCAC 58.783 38.462 0.00 0.00 0.00 3.18
1796 5510 6.366332 GGCTCATAGGTGTAGATAATTTCACG 59.634 42.308 0.00 0.00 0.00 4.35
1797 5511 6.366332 GCTCATAGGTGTAGATAATTTCACGG 59.634 42.308 0.00 0.00 0.00 4.94
1798 5512 6.755206 TCATAGGTGTAGATAATTTCACGGG 58.245 40.000 0.00 0.00 0.00 5.28
1801 5515 3.311596 GGTGTAGATAATTTCACGGGTGC 59.688 47.826 0.00 0.00 0.00 5.01
1804 5518 4.814234 TGTAGATAATTTCACGGGTGCATC 59.186 41.667 0.00 0.00 0.00 3.91
1805 5519 3.884895 AGATAATTTCACGGGTGCATCA 58.115 40.909 0.00 0.00 0.00 3.07
1814 5590 1.097547 CGGGTGCATCAGGACATTCC 61.098 60.000 0.00 0.00 37.91 3.01
1826 5602 1.069227 GGACATTCCTTGTTCGCACAC 60.069 52.381 0.00 0.00 39.18 3.82
1914 5691 7.795734 GTGAATAACTGTAATCATGCATCGAAG 59.204 37.037 0.00 0.00 0.00 3.79
1916 5693 8.613060 AATAACTGTAATCATGCATCGAAGAT 57.387 30.769 0.00 0.00 45.12 2.40
1918 5695 9.710900 ATAACTGTAATCATGCATCGAAGATTA 57.289 29.630 11.29 11.29 45.12 1.75
1970 5748 4.511617 TTTCACTGAAACTTTGTGCACA 57.488 36.364 17.42 17.42 0.00 4.57
1971 5749 4.511617 TTCACTGAAACTTTGTGCACAA 57.488 36.364 27.96 27.96 0.00 3.33
1973 5751 5.070770 TCACTGAAACTTTGTGCACAAAT 57.929 34.783 37.51 26.57 43.92 2.32
1985 5763 8.965819 ACTTTGTGCACAAATATATAATGTCCA 58.034 29.630 37.51 16.18 43.92 4.02
1986 5764 9.454585 CTTTGTGCACAAATATATAATGTCCAG 57.545 33.333 37.51 20.87 43.92 3.86
1997 5775 2.760634 AATGTCCAGATGTACACGCA 57.239 45.000 0.00 0.00 0.00 5.24
1999 5777 1.253100 TGTCCAGATGTACACGCAGA 58.747 50.000 0.00 0.00 0.00 4.26
2000 5778 1.616374 TGTCCAGATGTACACGCAGAA 59.384 47.619 0.00 0.00 0.00 3.02
2059 5838 5.887214 ACTAGACAATGGGTGCATATACA 57.113 39.130 0.00 0.00 0.00 2.29
2081 5860 5.183904 ACACCTATGAGCCAAAGTGAATTTC 59.816 40.000 0.00 0.00 0.00 2.17
2082 5861 4.706962 ACCTATGAGCCAAAGTGAATTTCC 59.293 41.667 0.00 0.00 0.00 3.13
2090 5869 4.915667 GCCAAAGTGAATTTCCGACTTTAC 59.084 41.667 12.11 6.65 37.74 2.01
2257 6036 2.711922 CGCCTACGCCTTCCTCACT 61.712 63.158 0.00 0.00 0.00 3.41
2258 6037 1.381928 CGCCTACGCCTTCCTCACTA 61.382 60.000 0.00 0.00 0.00 2.74
2298 6077 4.659172 CAGCTTCCCCACCCGCAA 62.659 66.667 0.00 0.00 0.00 4.85
2527 6306 4.717313 GCCAACCGGACCCTCACC 62.717 72.222 9.46 0.00 0.00 4.02
2757 6545 5.798434 GGTTCGGCTGAAATTTTGTATGTAC 59.202 40.000 10.18 0.00 35.46 2.90
2760 6548 6.607689 TCGGCTGAAATTTTGTATGTACAAG 58.392 36.000 0.00 0.00 45.77 3.16
2765 6553 8.289618 GCTGAAATTTTGTATGTACAAGAGTCA 58.710 33.333 0.00 8.31 45.77 3.41
2781 6569 3.043586 GAGTCACTAGTTCGTGTGTGTG 58.956 50.000 0.00 0.00 36.33 3.82
2787 6575 4.328983 CACTAGTTCGTGTGTGTGTTTTCT 59.671 41.667 0.00 0.00 0.00 2.52
2829 6620 4.881057 TTTTTCGGAAGGCCACGA 57.119 50.000 5.01 9.58 37.33 4.35
2839 6774 2.273557 GAAGGCCACGACGCTTTATTA 58.726 47.619 5.01 0.00 0.00 0.98
2984 6996 0.833287 ATGCTGATACGCCTCCAACT 59.167 50.000 0.00 0.00 0.00 3.16
3099 7532 2.964740 TCTAGTGCACAGCATGAGTTC 58.035 47.619 21.04 0.00 41.91 3.01
3102 7535 0.520404 GTGCACAGCATGAGTTCCTG 59.480 55.000 13.17 0.00 41.91 3.86
3276 7746 0.458543 CGCGCTACCTGATCTTGTGT 60.459 55.000 5.56 0.00 0.00 3.72
3281 7751 2.234908 GCTACCTGATCTTGTGTGTCCT 59.765 50.000 0.00 0.00 0.00 3.85
3284 7754 1.625315 CCTGATCTTGTGTGTCCTCCA 59.375 52.381 0.00 0.00 0.00 3.86
3312 7782 0.874390 CCTGGTGTGATTCCAACACG 59.126 55.000 1.02 0.00 40.61 4.49
3341 8266 9.967559 AAAATCCTATAAATTCATAAACCCCCT 57.032 29.630 0.00 0.00 0.00 4.79
3368 8294 7.603180 AGTTGACCTATATGAGTTATCTGCA 57.397 36.000 0.00 0.00 0.00 4.41
3408 8334 2.284754 AGCGATCTCATCTAGAGCCA 57.715 50.000 0.00 0.00 44.35 4.75
3424 8350 4.040755 AGAGCCATATTCTAACACCCTGT 58.959 43.478 0.00 0.00 0.00 4.00
3425 8351 4.475016 AGAGCCATATTCTAACACCCTGTT 59.525 41.667 0.00 0.00 43.88 3.16
3427 8353 4.227300 AGCCATATTCTAACACCCTGTTGA 59.773 41.667 0.00 0.00 41.30 3.18
3430 8380 5.590259 CCATATTCTAACACCCTGTTGAAGG 59.410 44.000 0.00 0.00 46.94 3.46
3441 8391 3.618351 CCTGTTGAAGGCTTCATCATCT 58.382 45.455 30.74 0.00 39.93 2.90
3447 8397 1.709578 AGGCTTCATCATCTCCGCTA 58.290 50.000 0.00 0.00 0.00 4.26
3513 8463 5.800941 GCTATGTACCAGTAGATATGCGTTC 59.199 44.000 0.00 0.00 0.00 3.95
3521 8511 5.351740 CCAGTAGATATGCGTTCGATCTCTA 59.648 44.000 0.00 0.00 32.27 2.43
3531 8521 4.979197 GCGTTCGATCTCTATCTCATGTTT 59.021 41.667 0.00 0.00 0.00 2.83
3575 8587 9.461312 ACCATAAGCTTTGTTATGATGTTCTTA 57.539 29.630 3.20 0.00 41.22 2.10
3665 9024 5.616488 TTGAATTTAAGACCACCTAACGC 57.384 39.130 0.00 0.00 0.00 4.84
3666 9025 3.680937 TGAATTTAAGACCACCTAACGCG 59.319 43.478 3.53 3.53 0.00 6.01
3673 9040 0.961019 ACCACCTAACGCGTGTCTTA 59.039 50.000 14.98 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
316 321 7.485913 GTCCTGCATAAATTGAGTAACATGTTG 59.514 37.037 21.42 1.32 0.00 3.33
492 497 1.941999 GCTGGTTGCCATTGCTCCTC 61.942 60.000 5.52 0.00 38.71 3.71
538 543 0.835276 TGCACTCAGAGATGGGGATG 59.165 55.000 3.79 0.00 0.00 3.51
549 554 1.632948 CGACACCTGCATGCACTCAG 61.633 60.000 18.46 7.02 0.00 3.35
550 555 1.668793 CGACACCTGCATGCACTCA 60.669 57.895 18.46 0.00 0.00 3.41
562 567 3.181489 ACAATCTCGGATCTTACGACACC 60.181 47.826 0.00 0.00 36.25 4.16
564 570 4.157105 TGAACAATCTCGGATCTTACGACA 59.843 41.667 0.00 0.00 36.25 4.35
568 574 6.758886 AGTTCATGAACAATCTCGGATCTTAC 59.241 38.462 33.92 7.62 43.47 2.34
576 582 5.596268 TTCACAGTTCATGAACAATCTCG 57.404 39.130 33.92 19.11 43.47 4.04
585 591 1.967779 TCGGGAGTTCACAGTTCATGA 59.032 47.619 0.00 0.00 0.00 3.07
586 592 2.029020 TCTCGGGAGTTCACAGTTCATG 60.029 50.000 0.00 0.00 0.00 3.07
587 593 2.248248 TCTCGGGAGTTCACAGTTCAT 58.752 47.619 0.00 0.00 0.00 2.57
588 594 1.699730 TCTCGGGAGTTCACAGTTCA 58.300 50.000 0.00 0.00 0.00 3.18
589 595 2.996621 CAATCTCGGGAGTTCACAGTTC 59.003 50.000 0.00 0.00 0.00 3.01
590 596 2.872038 GCAATCTCGGGAGTTCACAGTT 60.872 50.000 0.00 0.00 0.00 3.16
596 611 2.159043 TCATGAGCAATCTCGGGAGTTC 60.159 50.000 0.00 0.00 42.26 3.01
604 619 7.114953 CACAAATATGCAATCATGAGCAATCTC 59.885 37.037 13.02 0.00 44.88 2.75
698 718 4.015084 CCTCTAGGTCGAAAGTTCCTGTA 58.985 47.826 1.91 0.00 37.58 2.74
737 757 4.245660 TCAGCAAAAGTCTCTGTATTCGG 58.754 43.478 0.00 0.00 0.00 4.30
804 824 1.689273 CTCCCTCTTAACCCCAGATCG 59.311 57.143 0.00 0.00 0.00 3.69
866 4488 5.862924 TTCTACTACATGCAAAAGTCAGC 57.137 39.130 0.00 0.00 0.00 4.26
923 4545 4.208686 GCAGCTACGTCGGGGAGG 62.209 72.222 0.00 0.00 0.00 4.30
940 4562 7.709947 TCTTATTACTTATACACACTGGACCG 58.290 38.462 0.00 0.00 0.00 4.79
965 4596 1.643310 AGAGAAGCAGCTCTTGGACT 58.357 50.000 0.00 0.00 42.41 3.85
979 4610 2.164827 TGCTACGTCGGCATAAAGAGAA 59.835 45.455 11.30 0.00 34.56 2.87
981 4612 2.203800 TGCTACGTCGGCATAAAGAG 57.796 50.000 11.30 0.00 34.56 2.85
1201 4845 2.264480 CACCGGAGTTGGCGATGA 59.736 61.111 9.46 0.00 0.00 2.92
1327 4977 2.173382 GTCGGTCATGTTGTGCGC 59.827 61.111 0.00 0.00 0.00 6.09
1328 4978 1.944699 CTCGTCGGTCATGTTGTGCG 61.945 60.000 0.00 0.00 0.00 5.34
1596 5246 9.183620 GCATCGTTTTTCTTATTTTAATTTCGC 57.816 29.630 0.00 0.00 0.00 4.70
1601 5251 9.469807 TGTGTGCATCGTTTTTCTTATTTTAAT 57.530 25.926 0.00 0.00 0.00 1.40
1602 5252 8.747666 GTGTGTGCATCGTTTTTCTTATTTTAA 58.252 29.630 0.00 0.00 0.00 1.52
1603 5253 7.915923 TGTGTGTGCATCGTTTTTCTTATTTTA 59.084 29.630 0.00 0.00 0.00 1.52
1608 5258 4.095036 TGTGTGTGTGCATCGTTTTTCTTA 59.905 37.500 0.00 0.00 0.00 2.10
1611 5261 2.529894 GTGTGTGTGTGCATCGTTTTTC 59.470 45.455 0.00 0.00 0.00 2.29
1617 5267 0.316114 GTGTGTGTGTGTGTGCATCG 60.316 55.000 0.00 0.00 0.00 3.84
1619 5269 1.172175 TTGTGTGTGTGTGTGTGCAT 58.828 45.000 0.00 0.00 0.00 3.96
1621 5271 2.057503 TTTTGTGTGTGTGTGTGTGC 57.942 45.000 0.00 0.00 0.00 4.57
1639 5289 2.030274 GCTCACCGCAACCACTATTTTT 60.030 45.455 0.00 0.00 38.92 1.94
1640 5290 1.539827 GCTCACCGCAACCACTATTTT 59.460 47.619 0.00 0.00 38.92 1.82
1641 5291 1.165270 GCTCACCGCAACCACTATTT 58.835 50.000 0.00 0.00 38.92 1.40
1642 5292 1.019278 CGCTCACCGCAACCACTATT 61.019 55.000 0.00 0.00 39.08 1.73
1643 5293 1.447838 CGCTCACCGCAACCACTAT 60.448 57.895 0.00 0.00 39.08 2.12
1644 5294 2.048597 CGCTCACCGCAACCACTA 60.049 61.111 0.00 0.00 39.08 2.74
1645 5295 4.235762 ACGCTCACCGCAACCACT 62.236 61.111 0.00 0.00 41.76 4.00
1646 5296 4.012895 CACGCTCACCGCAACCAC 62.013 66.667 0.00 0.00 41.76 4.16
1648 5298 4.980805 TCCACGCTCACCGCAACC 62.981 66.667 0.00 0.00 41.76 3.77
1748 5461 4.871933 AAACAGCACCTGGAAATAAAGG 57.128 40.909 0.00 0.00 39.65 3.11
1761 5475 2.095059 CACCTATGAGCCAAAACAGCAC 60.095 50.000 0.00 0.00 0.00 4.40
1766 5480 8.451908 AATTATCTACACCTATGAGCCAAAAC 57.548 34.615 0.00 0.00 0.00 2.43
1779 5493 3.311596 GCACCCGTGAAATTATCTACACC 59.688 47.826 0.00 0.00 0.00 4.16
1782 5496 4.814234 TGATGCACCCGTGAAATTATCTAC 59.186 41.667 0.00 0.00 0.00 2.59
1791 5505 1.003839 GTCCTGATGCACCCGTGAA 60.004 57.895 0.00 0.00 0.00 3.18
1792 5506 1.552799 ATGTCCTGATGCACCCGTGA 61.553 55.000 0.00 0.00 0.00 4.35
1793 5507 0.677731 AATGTCCTGATGCACCCGTG 60.678 55.000 0.00 0.00 0.00 4.94
1795 5509 1.097547 GGAATGTCCTGATGCACCCG 61.098 60.000 0.00 0.00 32.53 5.28
1796 5510 2.799176 GGAATGTCCTGATGCACCC 58.201 57.895 0.00 0.00 32.53 4.61
1814 5590 2.525891 CGAAAGTTTGTGTGCGAACAAG 59.474 45.455 0.00 0.00 40.93 3.16
1815 5591 2.510874 CGAAAGTTTGTGTGCGAACAA 58.489 42.857 0.00 0.00 40.59 2.83
1882 5659 9.612066 TGCATGATTACAGTTATTCACAAGATA 57.388 29.630 0.00 0.00 0.00 1.98
1883 5660 8.510243 TGCATGATTACAGTTATTCACAAGAT 57.490 30.769 0.00 0.00 0.00 2.40
1884 5661 7.920160 TGCATGATTACAGTTATTCACAAGA 57.080 32.000 0.00 0.00 0.00 3.02
1885 5662 7.585210 CGATGCATGATTACAGTTATTCACAAG 59.415 37.037 2.46 0.00 0.00 3.16
1886 5663 7.279758 TCGATGCATGATTACAGTTATTCACAA 59.720 33.333 2.46 0.00 0.00 3.33
1887 5664 6.760770 TCGATGCATGATTACAGTTATTCACA 59.239 34.615 2.46 0.00 0.00 3.58
1888 5665 7.177498 TCGATGCATGATTACAGTTATTCAC 57.823 36.000 2.46 0.00 0.00 3.18
1889 5666 7.710475 TCTTCGATGCATGATTACAGTTATTCA 59.290 33.333 2.46 0.00 0.00 2.57
1890 5667 8.076714 TCTTCGATGCATGATTACAGTTATTC 57.923 34.615 2.46 0.00 0.00 1.75
1895 5672 8.093307 AGATAATCTTCGATGCATGATTACAGT 58.907 33.333 15.58 4.79 35.22 3.55
1944 5722 6.311200 GTGCACAAAGTTTCAGTGAAAAAGAT 59.689 34.615 19.63 4.51 33.14 2.40
1948 5726 4.876125 TGTGCACAAAGTTTCAGTGAAAA 58.124 34.783 19.28 2.01 33.14 2.29
1950 5728 4.511617 TTGTGCACAAAGTTTCAGTGAA 57.488 36.364 29.36 0.08 35.33 3.18
1951 5729 4.511617 TTTGTGCACAAAGTTTCAGTGA 57.488 36.364 35.10 14.21 40.55 3.41
1964 5742 8.786898 ACATCTGGACATTATATATTTGTGCAC 58.213 33.333 10.75 10.75 36.89 4.57
1970 5748 9.151471 GCGTGTACATCTGGACATTATATATTT 57.849 33.333 0.00 0.00 0.00 1.40
1971 5749 8.311109 TGCGTGTACATCTGGACATTATATATT 58.689 33.333 0.00 0.00 0.00 1.28
1973 5751 7.175990 TCTGCGTGTACATCTGGACATTATATA 59.824 37.037 0.00 0.00 0.00 0.86
2029 5807 4.504858 CACCCATTGTCTAGTACACCTTC 58.495 47.826 0.00 0.00 38.00 3.46
2032 5810 2.027561 TGCACCCATTGTCTAGTACACC 60.028 50.000 0.00 0.00 38.00 4.16
2059 5838 4.706962 GGAAATTCACTTTGGCTCATAGGT 59.293 41.667 0.00 0.00 0.00 3.08
2308 6087 2.033602 CGGCGGAGGAAAAAGGGT 59.966 61.111 0.00 0.00 0.00 4.34
2527 6306 2.044555 TCTCGGCCAGTCGGTGTAG 61.045 63.158 2.24 0.00 33.28 2.74
2642 6430 2.147387 AGAACTCAACCGCCCCACT 61.147 57.895 0.00 0.00 0.00 4.00
2644 6432 2.429930 CAGAACTCAACCGCCCCA 59.570 61.111 0.00 0.00 0.00 4.96
2700 6488 0.533755 AGCGAGCTCAAGCAACTTGT 60.534 50.000 15.40 0.00 45.16 3.16
2757 6545 3.731216 CACACACGAACTAGTGACTCTTG 59.269 47.826 0.00 0.00 44.43 3.02
2760 6548 3.043586 CACACACACGAACTAGTGACTC 58.956 50.000 0.00 0.00 44.43 3.36
2765 6553 4.328983 CAGAAAACACACACACGAACTAGT 59.671 41.667 0.00 0.00 0.00 2.57
2829 6620 9.502091 TTCCTAGCATCATAATTAATAAAGCGT 57.498 29.630 0.00 0.00 0.00 5.07
2839 6774 9.412460 TCAATCAGTTTTCCTAGCATCATAATT 57.588 29.630 0.00 0.00 0.00 1.40
2936 6947 1.550130 AATTCCTGCTCGTCCCCGAA 61.550 55.000 0.00 0.00 43.69 4.30
2940 6951 1.134371 AGCTTAATTCCTGCTCGTCCC 60.134 52.381 0.00 0.00 30.41 4.46
3071 7475 8.588472 ACTCATGCTGTGCACTAGATTAATATA 58.412 33.333 19.41 0.00 43.04 0.86
3137 7571 7.504924 TCAAGTTTGGACTTCGTTTGATATT 57.495 32.000 0.00 0.00 44.14 1.28
3141 7575 6.928979 TTATCAAGTTTGGACTTCGTTTGA 57.071 33.333 0.00 0.00 44.14 2.69
3269 7739 1.416401 GTTCCTGGAGGACACACAAGA 59.584 52.381 0.00 0.00 45.39 3.02
3276 7746 2.773458 GGAAGGTTCCTGGAGGACA 58.227 57.895 1.16 0.00 45.39 4.02
3341 8266 9.982651 GCAGATAACTCATATAGGTCAACTTTA 57.017 33.333 0.00 0.00 0.00 1.85
3368 8294 0.392193 CAGAACAGAGGATTGCGGCT 60.392 55.000 0.00 0.00 0.00 5.52
3376 8302 2.425312 GAGATCGCTTCAGAACAGAGGA 59.575 50.000 0.00 0.00 0.00 3.71
3408 8334 5.193679 GCCTTCAACAGGGTGTTAGAATAT 58.806 41.667 0.00 0.00 44.16 1.28
3424 8350 2.910199 CGGAGATGATGAAGCCTTCAA 58.090 47.619 11.81 0.00 43.95 2.69
3425 8351 1.473965 GCGGAGATGATGAAGCCTTCA 60.474 52.381 10.01 10.01 45.01 3.02
3427 8353 0.835941 AGCGGAGATGATGAAGCCTT 59.164 50.000 0.00 0.00 0.00 4.35
3430 8380 1.342819 AGGTAGCGGAGATGATGAAGC 59.657 52.381 0.00 0.00 0.00 3.86
3441 8391 1.077285 TCGTCATGGAGGTAGCGGA 60.077 57.895 0.00 0.00 0.00 5.54
3554 8550 9.289782 AGAAGTAAGAACATCATAACAAAGCTT 57.710 29.630 0.00 0.00 0.00 3.74
3646 8902 3.434299 CACGCGTTAGGTGGTCTTAAATT 59.566 43.478 10.22 0.00 0.00 1.82
3651 9010 0.319297 GACACGCGTTAGGTGGTCTT 60.319 55.000 10.22 0.00 39.69 3.01
3659 9018 2.407361 CCACAAGTAAGACACGCGTTAG 59.593 50.000 10.22 0.71 0.00 2.34
3665 9024 3.572584 GAGTACCCACAAGTAAGACACG 58.427 50.000 0.00 0.00 0.00 4.49
3666 9025 3.005155 ACGAGTACCCACAAGTAAGACAC 59.995 47.826 0.00 0.00 0.00 3.67
3673 9040 0.391597 CACCACGAGTACCCACAAGT 59.608 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.