Multiple sequence alignment - TraesCS2D01G472700

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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 TraesCS2D01G472700 chr2D 100.000 5101 0 0 1 5101 576278443 576283543 0.000000e+00 9420.0
1 TraesCS2D01G472700 chr2D 86.608 799 58 22 3003 3784 617726913 617726147 0.000000e+00 837.0
2 TraesCS2D01G472700 chr2D 90.323 62 6 0 1273 1334 405062407 405062468 1.180000e-11 82.4
3 TraesCS2D01G472700 chr2D 96.875 32 1 0 4759 4790 503453800 503453831 3.000000e-03 54.7
4 TraesCS2D01G472700 chr2A 94.446 3961 129 41 862 4784 714328236 714332143 0.000000e+00 6011.0
5 TraesCS2D01G472700 chr2A 90.377 239 19 3 162 399 714326905 714327140 1.380000e-80 311.0
6 TraesCS2D01G472700 chr2A 90.968 155 12 2 4808 4960 714332510 714332664 1.860000e-49 207.0
7 TraesCS2D01G472700 chr2A 84.524 84 13 0 1273 1356 543120707 543120790 3.270000e-12 84.2
8 TraesCS2D01G472700 chr2B 91.895 3282 129 58 1483 4696 692460847 692464059 0.000000e+00 4460.0
9 TraesCS2D01G472700 chr2B 89.501 1343 60 32 400 1715 692459561 692460849 0.000000e+00 1624.0
10 TraesCS2D01G472700 chr2B 85.354 396 37 13 4712 5101 692464188 692464568 1.720000e-104 390.0
11 TraesCS2D01G472700 chr2B 88.623 167 19 0 1 167 692457326 692457492 2.410000e-48 204.0
12 TraesCS2D01G472700 chr2B 83.333 84 14 0 1273 1356 479852662 479852745 1.520000e-10 78.7
13 TraesCS2D01G472700 chr5B 88.272 324 17 8 3132 3454 302833789 302834092 8.070000e-98 368.0
14 TraesCS2D01G472700 chr5B 88.424 311 27 6 3478 3784 381076388 381076693 2.900000e-97 366.0
15 TraesCS2D01G472700 chr5B 87.963 324 18 7 3132 3454 35495523 35495826 3.750000e-96 363.0
16 TraesCS2D01G472700 chr5B 90.588 255 23 1 400 653 465987752 465987498 2.280000e-88 337.0
17 TraesCS2D01G472700 chr5B 89.024 246 24 2 3539 3784 302834091 302834333 8.300000e-78 302.0
18 TraesCS2D01G472700 chr5B 86.853 251 25 4 3539 3784 35495825 35496072 1.810000e-69 274.0
19 TraesCS2D01G472700 chr5B 89.172 157 13 2 1 156 566131982 566131829 5.210000e-45 193.0
20 TraesCS2D01G472700 chr3B 88.037 326 15 10 3132 3454 512426198 512426502 1.040000e-96 364.0
21 TraesCS2D01G472700 chr6B 87.379 309 26 9 3480 3784 526021370 526021669 4.890000e-90 342.0
22 TraesCS2D01G472700 chr6B 93.301 209 12 2 452 659 713167358 713167151 1.780000e-79 307.0
23 TraesCS2D01G472700 chr6B 89.172 157 16 1 1 156 692558908 692558752 1.450000e-45 195.0
24 TraesCS2D01G472700 chr6B 74.946 463 88 21 3223 3672 124477271 124476824 2.420000e-43 187.0
25 TraesCS2D01G472700 chr6B 87.671 73 9 0 1262 1334 357125682 357125610 9.100000e-13 86.1
26 TraesCS2D01G472700 chr6B 88.136 59 7 0 2691 2749 185669397 185669339 2.550000e-08 71.3
27 TraesCS2D01G472700 chr1B 90.421 261 22 3 400 659 655132968 655133226 1.760000e-89 340.0
28 TraesCS2D01G472700 chr1B 89.024 246 24 2 3539 3784 30436430 30436188 8.300000e-78 302.0
29 TraesCS2D01G472700 chr1B 83.333 324 13 16 3132 3454 30436712 30436429 1.410000e-65 261.0
30 TraesCS2D01G472700 chr1B 93.220 59 4 0 2691 2749 629772933 629772991 2.530000e-13 87.9
31 TraesCS2D01G472700 chr4B 86.084 309 33 6 3479 3784 564128329 564128028 1.770000e-84 324.0
32 TraesCS2D01G472700 chr4B 94.737 38 2 0 2723 2760 413832116 413832153 5.520000e-05 60.2
33 TraesCS2D01G472700 chr4A 85.606 264 32 3 400 658 705429414 705429676 6.510000e-69 272.0
34 TraesCS2D01G472700 chr4A 84.906 265 34 3 400 659 62312891 62313154 3.920000e-66 263.0
35 TraesCS2D01G472700 chr7B 89.904 208 19 2 452 658 1358831 1358625 3.030000e-67 267.0
36 TraesCS2D01G472700 chr7B 84.211 266 36 3 400 660 10206482 10206218 2.360000e-63 254.0
37 TraesCS2D01G472700 chr7B 89.172 157 13 2 1 156 630663664 630663511 5.210000e-45 193.0
38 TraesCS2D01G472700 chr7B 89.172 157 13 2 1 156 708841269 708841116 5.210000e-45 193.0
39 TraesCS2D01G472700 chr7D 85.714 252 31 2 414 660 471323070 471323321 1.410000e-65 261.0
40 TraesCS2D01G472700 chr4D 91.083 157 13 1 1 156 99207434 99207590 1.440000e-50 211.0
41 TraesCS2D01G472700 chr6A 89.809 157 15 1 1 156 540151571 540151727 3.110000e-47 200.0
42 TraesCS2D01G472700 chr6A 77.545 334 61 10 3340 3672 68512261 68511941 6.740000e-44 189.0
43 TraesCS2D01G472700 chr6A 81.905 105 17 2 1262 1364 356209865 356209761 2.530000e-13 87.9
44 TraesCS2D01G472700 chr7A 89.172 157 16 1 1 156 10222289 10222133 1.450000e-45 195.0
45 TraesCS2D01G472700 chr7A 77.545 334 60 8 3340 3672 387175727 387176046 2.420000e-43 187.0
46 TraesCS2D01G472700 chr1D 89.172 157 16 1 1 156 276770247 276770091 1.450000e-45 195.0
47 TraesCS2D01G472700 chr6D 75.053 469 89 21 3217 3672 47260557 47261010 5.210000e-45 193.0
48 TraesCS2D01G472700 chr6D 87.671 73 9 0 1262 1334 234427641 234427569 9.100000e-13 86.1
49 TraesCS2D01G472700 chr6D 86.441 59 8 0 2691 2749 101241949 101241891 1.190000e-06 65.8


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 TraesCS2D01G472700 chr2D 576278443 576283543 5100 False 9420.000000 9420 100.000000 1 5101 1 chr2D.!!$F3 5100
1 TraesCS2D01G472700 chr2D 617726147 617726913 766 True 837.000000 837 86.608000 3003 3784 1 chr2D.!!$R1 781
2 TraesCS2D01G472700 chr2A 714326905 714332664 5759 False 2176.333333 6011 91.930333 162 4960 3 chr2A.!!$F2 4798
3 TraesCS2D01G472700 chr2B 692457326 692464568 7242 False 1669.500000 4460 88.843250 1 5101 4 chr2B.!!$F2 5100
4 TraesCS2D01G472700 chr5B 302833789 302834333 544 False 335.000000 368 88.648000 3132 3784 2 chr5B.!!$F3 652
5 TraesCS2D01G472700 chr5B 35495523 35496072 549 False 318.500000 363 87.408000 3132 3784 2 chr5B.!!$F2 652
6 TraesCS2D01G472700 chr1B 30436188 30436712 524 True 281.500000 302 86.178500 3132 3784 2 chr1B.!!$R1 652

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
802 2886 0.037232 GACACCAGTTCTCTTCCGGG 60.037 60.0 0.00 0.0 0.00 5.73 F
1335 3850 0.534412 ACATCTACAGCTGCTTCGCT 59.466 50.0 15.27 0.0 41.90 4.93 F
1370 3885 0.741326 CGTGTCCCGATCTGTCTGAT 59.259 55.0 0.00 0.0 39.56 2.90 F
3778 6569 0.250901 TTTCAGCCTCAGGAAGCCAC 60.251 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2721 5460 0.599558 CCGTCCCGAAGTAAGTGTCA 59.400 55.000 0.00 0.0 0.00 3.58 R
2882 5622 3.838244 ACTGCTAAACTCTGGTGAACA 57.162 42.857 0.00 0.0 0.00 3.18 R
3962 6753 3.306780 CGATAGGGAACTTCACCTGTTGT 60.307 47.826 8.38 0.0 43.67 3.32 R
5001 8294 0.099968 CCACGGAGATTTAGACGCGA 59.900 55.000 15.93 0.0 0.00 5.87 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
20 21 2.597217 CAAGTTTGCCCGGCTCCA 60.597 61.111 11.61 0.00 0.00 3.86
39 40 3.391382 CGAGGGAGGGGTGGTGAC 61.391 72.222 0.00 0.00 0.00 3.67
89 90 1.624336 TGTAGTCGTTGCTAGGTGGT 58.376 50.000 0.00 0.00 0.00 4.16
98 99 3.675228 CGTTGCTAGGTGGTCTACGAATT 60.675 47.826 0.00 0.00 0.00 2.17
143 144 8.940768 TTCTGATATTCGTTGTATTGTCATGA 57.059 30.769 0.00 0.00 0.00 3.07
147 148 8.558700 TGATATTCGTTGTATTGTCATGATTGG 58.441 33.333 0.00 0.00 0.00 3.16
200 2044 0.450583 CGCAGTTGCTCGACCTACTA 59.549 55.000 2.29 0.00 39.32 1.82
242 2086 6.131264 TGCTCATGATGGGAAAACTGAATAT 58.869 36.000 0.00 0.00 0.00 1.28
251 2095 4.214332 GGGAAAACTGAATATCGATGGCTC 59.786 45.833 8.54 2.29 0.00 4.70
261 2105 0.108804 TCGATGGCTCAGTTTCCGAC 60.109 55.000 0.00 0.00 0.00 4.79
272 2116 1.906824 TTTCCGACGAGGGCTCTGT 60.907 57.895 0.00 0.00 41.52 3.41
273 2117 1.469335 TTTCCGACGAGGGCTCTGTT 61.469 55.000 0.00 0.00 41.52 3.16
275 2119 2.125912 CGACGAGGGCTCTGTTGG 60.126 66.667 0.00 0.00 0.00 3.77
299 2143 0.618458 GGTATGGTGCTCAGGGACAA 59.382 55.000 0.00 0.00 35.41 3.18
306 2150 1.133181 TGCTCAGGGACAACATGGGA 61.133 55.000 0.00 0.00 0.00 4.37
307 2151 0.678048 GCTCAGGGACAACATGGGAC 60.678 60.000 0.00 0.00 0.00 4.46
326 2170 5.070981 TGGGACAATATTGTTTTCTTGGCAA 59.929 36.000 21.63 0.00 42.43 4.52
358 2202 4.486090 TGTTTTCACGTAGAGATGCTCTC 58.514 43.478 0.00 5.36 43.70 3.20
423 2325 7.596494 TCTTATTCAAGCCAAAGAAGTTGATG 58.404 34.615 0.00 0.00 39.87 3.07
442 2344 4.040461 TGATGGATCGGTTTATCCTTCTCC 59.960 45.833 15.64 0.00 44.66 3.71
443 2345 2.364324 TGGATCGGTTTATCCTTCTCCG 59.636 50.000 4.63 0.00 44.98 4.63
451 2353 4.081254 GGTTTATCCTTCTCCGGTTACAGT 60.081 45.833 0.00 0.00 0.00 3.55
453 2355 6.271566 GTTTATCCTTCTCCGGTTACAGTAG 58.728 44.000 0.00 0.00 0.00 2.57
454 2356 3.726557 TCCTTCTCCGGTTACAGTAGA 57.273 47.619 0.00 0.00 0.00 2.59
455 2357 3.350833 TCCTTCTCCGGTTACAGTAGAC 58.649 50.000 0.00 0.00 0.00 2.59
486 2392 7.348080 TGAGTCCTCGTGAATCTTGTATTAT 57.652 36.000 6.69 0.00 38.86 1.28
705 2779 6.349300 AGGAAAGCTTCTCTATATTTCGCAA 58.651 36.000 0.00 0.00 32.03 4.85
706 2780 6.823689 AGGAAAGCTTCTCTATATTTCGCAAA 59.176 34.615 0.00 0.00 32.03 3.68
710 2784 7.240414 AGCTTCTCTATATTTCGCAAAAGAC 57.760 36.000 0.00 0.00 0.00 3.01
713 2787 8.125448 GCTTCTCTATATTTCGCAAAAGACAAT 58.875 33.333 0.00 0.00 0.00 2.71
767 2841 9.901172 AAAAAGAGAGTACTCCTACTTTGAAAA 57.099 29.630 26.12 0.00 43.53 2.29
768 2842 8.890124 AAAGAGAGTACTCCTACTTTGAAAAC 57.110 34.615 25.43 1.38 43.53 2.43
769 2843 7.598759 AGAGAGTACTCCTACTTTGAAAACA 57.401 36.000 19.38 0.00 43.53 2.83
780 2864 3.610677 ACTTTGAAAACAAAAAGCGGACG 59.389 39.130 0.00 0.00 36.97 4.79
791 2875 3.681835 GCGGACGAGGACACCAGT 61.682 66.667 0.00 0.00 0.00 4.00
793 2877 1.080705 CGGACGAGGACACCAGTTC 60.081 63.158 0.00 0.00 0.00 3.01
802 2886 0.037232 GACACCAGTTCTCTTCCGGG 60.037 60.000 0.00 0.00 0.00 5.73
803 2887 1.296715 CACCAGTTCTCTTCCGGGG 59.703 63.158 0.00 0.00 0.00 5.73
804 2888 1.918800 ACCAGTTCTCTTCCGGGGG 60.919 63.158 0.00 0.00 0.00 5.40
1335 3850 0.534412 ACATCTACAGCTGCTTCGCT 59.466 50.000 15.27 0.00 41.90 4.93
1367 3882 1.093159 GTACGTGTCCCGATCTGTCT 58.907 55.000 0.00 0.00 40.70 3.41
1370 3885 0.741326 CGTGTCCCGATCTGTCTGAT 59.259 55.000 0.00 0.00 39.56 2.90
1449 3966 3.617538 GGATGTACGCGTCGCTGC 61.618 66.667 18.63 2.29 0.00 5.25
1460 3977 1.922444 GCGTCGCTGCTCTAGATGTAC 60.922 57.143 10.68 0.00 0.00 2.90
1462 3979 2.031595 CGTCGCTGCTCTAGATGTACAT 60.032 50.000 8.43 8.43 0.00 2.29
1485 4004 6.381498 TGGTTAGGGATTTAGTTGTGATGA 57.619 37.500 0.00 0.00 0.00 2.92
1499 4018 6.108687 AGTTGTGATGATAGAATTGCGAGAA 58.891 36.000 0.00 0.00 0.00 2.87
1505 4024 6.478016 TGATGATAGAATTGCGAGAAGAGTTG 59.522 38.462 0.00 0.00 0.00 3.16
1652 4171 2.942376 TGTCAACTGCGTCTTGTGAAAT 59.058 40.909 0.00 0.00 0.00 2.17
1654 4173 3.725740 GTCAACTGCGTCTTGTGAAATTG 59.274 43.478 0.00 0.00 0.00 2.32
1679 4198 9.658799 TGAAAATTCTCTAGTTAACTGATGGAG 57.341 33.333 18.56 17.24 0.00 3.86
1686 4205 9.256228 TCTCTAGTTAACTGATGGAGTATTTGT 57.744 33.333 18.56 0.00 33.09 2.83
1687 4206 9.877178 CTCTAGTTAACTGATGGAGTATTTGTT 57.123 33.333 18.56 0.00 33.09 2.83
1762 4492 9.503427 GCAGTATATTTGTAAAGTTGCTAAAGG 57.497 33.333 0.00 0.00 0.00 3.11
1763 4493 9.503427 CAGTATATTTGTAAAGTTGCTAAAGGC 57.497 33.333 0.00 0.00 42.22 4.35
1767 4497 5.699097 TTGTAAAGTTGCTAAAGGCGATT 57.301 34.783 0.00 0.00 45.43 3.34
1769 4499 5.695818 TGTAAAGTTGCTAAAGGCGATTTC 58.304 37.500 0.00 0.00 45.43 2.17
1773 4503 4.798574 AGTTGCTAAAGGCGATTTCTTTG 58.201 39.130 0.00 0.00 45.43 2.77
1780 4510 6.087687 GCTAAAGGCGATTTCTTTGTGTTAAC 59.912 38.462 0.00 0.00 36.12 2.01
1792 4522 4.630894 TTGTGTTAACTTGCAGTTCCAG 57.369 40.909 7.22 0.00 39.51 3.86
2047 4777 4.422057 TGTTACAGGAGACATTCAGGGTA 58.578 43.478 0.00 0.00 0.00 3.69
2080 4810 0.955905 TAAAGGGCGCAAAGGTTGTC 59.044 50.000 10.83 0.00 0.00 3.18
2206 4936 1.650912 CAGACCTATGCGCATTGGC 59.349 57.895 39.17 31.75 37.23 4.52
2221 4951 0.971959 TTGGCCCAGCAGCAAATAGG 60.972 55.000 0.00 0.00 0.00 2.57
2304 5040 9.755064 GGCTTTTTGCTATTACATGTATATACG 57.245 33.333 6.36 0.00 42.39 3.06
2438 5177 5.910637 TTTTTGCATGCAAGAAGACATTC 57.089 34.783 30.25 0.00 37.24 2.67
2854 5594 8.400186 TCAATCAGAATATACACATGCAAAGTG 58.600 33.333 17.96 17.96 42.56 3.16
2882 5622 5.645929 TGGTATATTGTGTCGTGATTGCTTT 59.354 36.000 0.00 0.00 0.00 3.51
3696 6487 8.854312 GTTTAATTCTTGCATGCTAAACTTCTC 58.146 33.333 20.33 0.00 0.00 2.87
3698 6489 5.618056 TTCTTGCATGCTAAACTTCTCTG 57.382 39.130 20.33 0.00 0.00 3.35
3699 6490 4.645535 TCTTGCATGCTAAACTTCTCTGT 58.354 39.130 20.33 0.00 0.00 3.41
3700 6491 4.692625 TCTTGCATGCTAAACTTCTCTGTC 59.307 41.667 20.33 0.00 0.00 3.51
3701 6492 3.338249 TGCATGCTAAACTTCTCTGTCC 58.662 45.455 20.33 0.00 0.00 4.02
3702 6493 3.008375 TGCATGCTAAACTTCTCTGTCCT 59.992 43.478 20.33 0.00 0.00 3.85
3703 6494 3.620821 GCATGCTAAACTTCTCTGTCCTC 59.379 47.826 11.37 0.00 0.00 3.71
3778 6569 0.250901 TTTCAGCCTCAGGAAGCCAC 60.251 55.000 0.00 0.00 0.00 5.01
4044 6837 2.420628 AAATGTTGCACCGACATGTG 57.579 45.000 1.15 0.00 38.36 3.21
4047 6840 1.383523 TGTTGCACCGACATGTGAAA 58.616 45.000 1.15 0.00 38.55 2.69
4054 6847 0.240945 CCGACATGTGAAAACCAGCC 59.759 55.000 1.15 0.00 0.00 4.85
4075 6868 2.354821 CGCCTGGCTAATCCAAAACTAC 59.645 50.000 17.92 0.00 46.01 2.73
4090 6883 5.154222 CAAAACTACGCCATCTTTTCCTTC 58.846 41.667 0.00 0.00 0.00 3.46
4103 6896 1.346062 TTCCTTCTCTGCAGTGAGCT 58.654 50.000 17.24 0.00 45.94 4.09
4112 6905 1.181741 TGCAGTGAGCTCTCCTCGTT 61.182 55.000 16.19 0.00 43.82 3.85
4115 6908 1.216710 GTGAGCTCTCCTCGTTGGG 59.783 63.158 16.19 0.00 43.82 4.12
4283 7079 1.480212 ATCAGCTGTTGTCCGTCCCA 61.480 55.000 14.67 0.00 0.00 4.37
4432 7229 4.510711 TGCTGCATTTGTTTATGTTGTTGG 59.489 37.500 0.00 0.00 0.00 3.77
4471 7275 8.263640 TGGATTCTCCTTTTTATCAGAGAAGAG 58.736 37.037 7.32 0.00 45.67 2.85
4506 7315 1.367346 TTGGTCTGGTGGCCTGATTA 58.633 50.000 3.32 0.00 34.19 1.75
4612 7429 8.916654 CATACTACTAGAATGGTTTGATTAGCG 58.083 37.037 0.00 0.00 0.00 4.26
4625 7457 0.532862 ATTAGCGCCTGTGGATTCGG 60.533 55.000 2.29 0.00 0.00 4.30
4632 7464 1.748493 GCCTGTGGATTCGGCAATTAA 59.252 47.619 0.00 0.00 43.25 1.40
4644 7477 7.201785 GGATTCGGCAATTAATTTGAGGTCTTA 60.202 37.037 0.00 0.00 37.53 2.10
4677 7510 6.382859 AGTTGTAATCTCCCTTTTGTTTGGTT 59.617 34.615 0.00 0.00 0.00 3.67
4696 7529 9.626045 GTTTGGTTTCATTTTGGTTCTATCTAG 57.374 33.333 0.00 0.00 0.00 2.43
4706 7539 7.962964 TTTGGTTCTATCTAGTGTTCTGTTG 57.037 36.000 0.00 0.00 0.00 3.33
4710 7656 7.178451 TGGTTCTATCTAGTGTTCTGTTGATCA 59.822 37.037 0.00 0.00 0.00 2.92
4723 7669 8.239314 TGTTCTGTTGATCAAATAATTGCTCTC 58.761 33.333 10.35 0.00 36.45 3.20
4726 7672 9.322773 TCTGTTGATCAAATAATTGCTCTCTAG 57.677 33.333 10.35 0.00 36.45 2.43
4728 7674 9.322773 TGTTGATCAAATAATTGCTCTCTAGAG 57.677 33.333 13.98 13.98 44.75 2.43
4730 7676 9.539825 TTGATCAAATAATTGCTCTCTAGAGAC 57.460 33.333 18.76 15.11 43.67 3.36
4784 7731 6.186234 TGGTTCTACTTTCTACTACTCCCTC 58.814 44.000 0.00 0.00 0.00 4.30
4785 7732 5.593909 GGTTCTACTTTCTACTACTCCCTCC 59.406 48.000 0.00 0.00 0.00 4.30
4790 7737 1.890552 TCTACTACTCCCTCCGTCCT 58.109 55.000 0.00 0.00 0.00 3.85
4791 7738 1.489649 TCTACTACTCCCTCCGTCCTG 59.510 57.143 0.00 0.00 0.00 3.86
4982 8275 6.701841 TGATGAATCTAAAGATAAGCACGGTC 59.298 38.462 0.00 0.00 33.73 4.79
4983 8276 5.972935 TGAATCTAAAGATAAGCACGGTCA 58.027 37.500 0.00 0.00 33.73 4.02
4986 8279 7.552687 TGAATCTAAAGATAAGCACGGTCAATT 59.447 33.333 0.00 0.00 33.73 2.32
4987 8280 6.903883 TCTAAAGATAAGCACGGTCAATTC 57.096 37.500 0.00 0.00 0.00 2.17
4988 8281 6.640518 TCTAAAGATAAGCACGGTCAATTCT 58.359 36.000 0.00 0.00 0.00 2.40
4990 8283 8.255206 TCTAAAGATAAGCACGGTCAATTCTAA 58.745 33.333 0.00 0.00 0.00 2.10
4991 8284 7.681939 AAAGATAAGCACGGTCAATTCTAAA 57.318 32.000 0.00 0.00 0.00 1.85
4992 8285 7.865706 AAGATAAGCACGGTCAATTCTAAAT 57.134 32.000 0.00 0.00 0.00 1.40
4993 8286 7.251704 AGATAAGCACGGTCAATTCTAAATG 57.748 36.000 0.00 0.00 0.00 2.32
4997 8290 4.088648 GCACGGTCAATTCTAAATGTTCG 58.911 43.478 0.00 0.00 0.00 3.95
4998 8291 4.378046 GCACGGTCAATTCTAAATGTTCGT 60.378 41.667 0.00 0.00 0.00 3.85
4999 8292 5.079406 CACGGTCAATTCTAAATGTTCGTG 58.921 41.667 0.00 0.00 37.52 4.35
5000 8293 4.992319 ACGGTCAATTCTAAATGTTCGTGA 59.008 37.500 0.00 0.00 0.00 4.35
5001 8294 5.642063 ACGGTCAATTCTAAATGTTCGTGAT 59.358 36.000 0.00 0.00 0.00 3.06
5002 8295 6.183360 ACGGTCAATTCTAAATGTTCGTGATC 60.183 38.462 0.00 0.00 0.00 2.92
5003 8296 6.185399 GGTCAATTCTAAATGTTCGTGATCG 58.815 40.000 0.00 0.00 38.55 3.69
5004 8297 5.672856 GTCAATTCTAAATGTTCGTGATCGC 59.327 40.000 0.00 0.00 36.96 4.58
5005 8298 3.899835 TTCTAAATGTTCGTGATCGCG 57.100 42.857 22.36 22.36 36.96 5.87
5006 8299 2.871133 TCTAAATGTTCGTGATCGCGT 58.129 42.857 26.40 10.20 36.96 6.01
5007 8300 2.850060 TCTAAATGTTCGTGATCGCGTC 59.150 45.455 26.40 20.12 36.96 5.19
5008 8301 1.710013 AAATGTTCGTGATCGCGTCT 58.290 45.000 26.40 8.56 36.96 4.18
5013 8306 2.850060 TGTTCGTGATCGCGTCTAAATC 59.150 45.455 26.40 8.22 36.96 2.17
5029 8322 0.246635 AATCTCCGTGGACAAGGACG 59.753 55.000 2.77 1.18 35.20 4.79
5035 8328 1.068474 CGTGGACAAGGACGAATGTC 58.932 55.000 0.00 0.00 44.07 3.06
5065 8358 7.079451 TCTAGAAATGGTTTGAAGGAGTTCT 57.921 36.000 0.00 0.00 33.38 3.01
5084 8377 3.001406 ACTCCCTGGTGTACGGCC 61.001 66.667 0.00 0.00 0.00 6.13
5089 8382 2.589157 CCTGGTGTACGGCCTTGGA 61.589 63.158 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.597217 TGGAGCCGGGCAAACTTG 60.597 61.111 23.09 0.00 0.00 3.16
55 56 2.338500 ACTACAAGCACTAAAGCGAGC 58.662 47.619 0.00 0.00 40.15 5.03
60 61 3.741344 AGCAACGACTACAAGCACTAAAG 59.259 43.478 0.00 0.00 0.00 1.85
120 121 9.590088 CAATCATGACAATACAACGAATATCAG 57.410 33.333 0.00 0.00 0.00 2.90
122 123 8.773645 TCCAATCATGACAATACAACGAATATC 58.226 33.333 0.00 0.00 0.00 1.63
135 136 6.664384 TCCAAATTCATCTCCAATCATGACAA 59.336 34.615 0.00 0.00 0.00 3.18
242 2086 0.108804 GTCGGAAACTGAGCCATCGA 60.109 55.000 0.00 0.00 0.00 3.59
251 2095 1.446272 GAGCCCTCGTCGGAAACTG 60.446 63.158 0.00 0.00 33.16 3.16
272 2116 2.252072 GAGCACCATACCCGCTCCAA 62.252 60.000 0.00 0.00 45.14 3.53
273 2117 2.687200 AGCACCATACCCGCTCCA 60.687 61.111 0.00 0.00 0.00 3.86
299 2143 6.700352 CCAAGAAAACAATATTGTCCCATGT 58.300 36.000 21.02 0.88 41.31 3.21
306 2150 7.378181 CCTACTTGCCAAGAAAACAATATTGT 58.622 34.615 15.47 15.47 44.72 2.71
307 2151 6.813152 CCCTACTTGCCAAGAAAACAATATTG 59.187 38.462 12.25 14.01 0.00 1.90
308 2152 6.723977 TCCCTACTTGCCAAGAAAACAATATT 59.276 34.615 12.25 0.00 0.00 1.28
321 2165 4.038642 GTGAAAACAATTCCCTACTTGCCA 59.961 41.667 0.00 0.00 0.00 4.92
326 2170 6.014840 TCTCTACGTGAAAACAATTCCCTACT 60.015 38.462 0.00 0.00 0.00 2.57
358 2202 1.004610 CATGCATACAACTCCGCTTCG 60.005 52.381 0.00 0.00 0.00 3.79
399 2244 6.810182 CCATCAACTTCTTTGGCTTGAATAAG 59.190 38.462 0.00 0.00 35.69 1.73
423 2325 2.288886 CCGGAGAAGGATAAACCGATCC 60.289 54.545 0.00 0.00 45.31 3.36
442 2344 6.157211 ACTCAAAAGATGTCTACTGTAACCG 58.843 40.000 0.00 0.00 0.00 4.44
443 2345 6.590677 GGACTCAAAAGATGTCTACTGTAACC 59.409 42.308 0.00 0.00 0.00 2.85
451 2353 4.765339 TCACGAGGACTCAAAAGATGTCTA 59.235 41.667 0.00 0.00 0.00 2.59
453 2355 3.914312 TCACGAGGACTCAAAAGATGTC 58.086 45.455 0.00 0.00 0.00 3.06
454 2356 4.336889 TTCACGAGGACTCAAAAGATGT 57.663 40.909 0.00 0.00 0.00 3.06
455 2357 5.174395 AGATTCACGAGGACTCAAAAGATG 58.826 41.667 0.00 0.00 0.00 2.90
498 2404 7.690256 ACTGTCACTAACCCTATTTTGAGATT 58.310 34.615 0.00 0.00 0.00 2.40
502 2408 7.389607 GCTAAACTGTCACTAACCCTATTTTGA 59.610 37.037 0.00 0.00 0.00 2.69
596 2506 5.752892 AGAATTACAATCATCAGCAGCTG 57.247 39.130 17.10 17.10 0.00 4.24
682 2756 6.604735 TTGCGAAATATAGAGAAGCTTTCC 57.395 37.500 0.00 0.00 0.00 3.13
761 2835 3.430931 CTCGTCCGCTTTTTGTTTTCAA 58.569 40.909 0.00 0.00 38.10 2.69
763 2837 2.032426 TCCTCGTCCGCTTTTTGTTTTC 59.968 45.455 0.00 0.00 0.00 2.29
764 2838 2.018515 TCCTCGTCCGCTTTTTGTTTT 58.981 42.857 0.00 0.00 0.00 2.43
765 2839 1.332686 GTCCTCGTCCGCTTTTTGTTT 59.667 47.619 0.00 0.00 0.00 2.83
766 2840 0.942252 GTCCTCGTCCGCTTTTTGTT 59.058 50.000 0.00 0.00 0.00 2.83
767 2841 0.179067 TGTCCTCGTCCGCTTTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
768 2842 0.234884 GTGTCCTCGTCCGCTTTTTG 59.765 55.000 0.00 0.00 0.00 2.44
769 2843 0.883370 GGTGTCCTCGTCCGCTTTTT 60.883 55.000 0.00 0.00 0.00 1.94
780 2864 1.067495 CGGAAGAGAACTGGTGTCCTC 60.067 57.143 0.00 0.00 0.00 3.71
1367 3882 1.089481 GCCGAACGAATCTGGCATCA 61.089 55.000 16.71 0.00 43.09 3.07
1370 3885 2.435938 GGCCGAACGAATCTGGCA 60.436 61.111 20.17 0.00 44.42 4.92
1449 3966 7.546250 AATCCCTAACCATGTACATCTAGAG 57.454 40.000 5.07 1.66 0.00 2.43
1460 3977 6.828273 TCATCACAACTAAATCCCTAACCATG 59.172 38.462 0.00 0.00 0.00 3.66
1462 3979 6.381498 TCATCACAACTAAATCCCTAACCA 57.619 37.500 0.00 0.00 0.00 3.67
1485 4004 4.764172 AGCAACTCTTCTCGCAATTCTAT 58.236 39.130 0.00 0.00 0.00 1.98
1491 4010 1.002468 GCAAAGCAACTCTTCTCGCAA 60.002 47.619 0.00 0.00 32.88 4.85
1499 4018 4.319766 CGTAATTCACAGCAAAGCAACTCT 60.320 41.667 0.00 0.00 0.00 3.24
1505 4024 1.200020 AGGCGTAATTCACAGCAAAGC 59.800 47.619 0.00 0.00 0.00 3.51
1557 4076 3.937706 CTCCAGAACCACAGCTAAATCAG 59.062 47.826 0.00 0.00 0.00 2.90
1558 4077 3.869912 GCTCCAGAACCACAGCTAAATCA 60.870 47.826 0.00 0.00 0.00 2.57
1559 4078 2.680339 GCTCCAGAACCACAGCTAAATC 59.320 50.000 0.00 0.00 0.00 2.17
1560 4079 2.040278 TGCTCCAGAACCACAGCTAAAT 59.960 45.455 0.00 0.00 32.76 1.40
1654 4173 9.660180 ACTCCATCAGTTAACTAGAGAATTTTC 57.340 33.333 21.58 0.00 26.56 2.29
1683 4202 9.418045 GCAAAAGGTATATAAGCAGAAAAACAA 57.582 29.630 0.00 0.00 0.00 2.83
1684 4203 8.580720 TGCAAAAGGTATATAAGCAGAAAAACA 58.419 29.630 0.00 0.00 0.00 2.83
1685 4204 8.860128 GTGCAAAAGGTATATAAGCAGAAAAAC 58.140 33.333 0.00 0.00 0.00 2.43
1686 4205 8.580720 TGTGCAAAAGGTATATAAGCAGAAAAA 58.419 29.630 0.00 0.00 0.00 1.94
1687 4206 8.116651 TGTGCAAAAGGTATATAAGCAGAAAA 57.883 30.769 0.00 0.00 0.00 2.29
1706 4225 3.796165 GCAGAACATTCACACATGTGCAA 60.796 43.478 25.68 18.17 45.25 4.08
1737 4467 9.503427 GCCTTTAGCAACTTTACAAATATACTG 57.497 33.333 0.00 0.00 42.97 2.74
1745 4475 5.699097 AATCGCCTTTAGCAACTTTACAA 57.301 34.783 0.00 0.00 44.04 2.41
1746 4476 5.472137 AGAAATCGCCTTTAGCAACTTTACA 59.528 36.000 0.00 0.00 44.04 2.41
1762 4492 4.737765 TGCAAGTTAACACAAAGAAATCGC 59.262 37.500 8.61 0.00 0.00 4.58
1763 4493 6.424557 CTGCAAGTTAACACAAAGAAATCG 57.575 37.500 8.61 0.00 0.00 3.34
1780 4510 2.245159 TGACAGACTGGAACTGCAAG 57.755 50.000 7.51 0.00 38.74 4.01
1792 4522 2.924290 GTCACGGATAAGCTTGACAGAC 59.076 50.000 9.86 6.08 38.60 3.51
1870 4600 1.067915 GTCTGAAGAACTCGCTCAGCT 60.068 52.381 0.00 0.00 0.00 4.24
2062 4792 1.040339 TGACAACCTTTGCGCCCTTT 61.040 50.000 4.18 0.00 0.00 3.11
2080 4810 2.481568 ACGCATTGTCATCTTGTCAGTG 59.518 45.455 0.00 0.00 0.00 3.66
2206 4936 2.019984 GTCTTCCTATTTGCTGCTGGG 58.980 52.381 0.00 0.00 0.00 4.45
2221 4951 1.420138 TCCTGAACCCCTGTTGTCTTC 59.580 52.381 0.00 0.00 33.97 2.87
2297 5033 9.850628 GGTATGCATGAGAAGTAAACGTATATA 57.149 33.333 10.16 0.00 0.00 0.86
2298 5034 8.585881 AGGTATGCATGAGAAGTAAACGTATAT 58.414 33.333 10.16 0.00 0.00 0.86
2299 5035 7.948357 AGGTATGCATGAGAAGTAAACGTATA 58.052 34.615 10.16 0.00 0.00 1.47
2300 5036 6.817184 AGGTATGCATGAGAAGTAAACGTAT 58.183 36.000 10.16 0.00 0.00 3.06
2301 5037 6.216801 AGGTATGCATGAGAAGTAAACGTA 57.783 37.500 10.16 0.00 0.00 3.57
2302 5038 5.086104 AGGTATGCATGAGAAGTAAACGT 57.914 39.130 10.16 0.00 0.00 3.99
2303 5039 7.715265 ATTAGGTATGCATGAGAAGTAAACG 57.285 36.000 10.16 0.00 0.00 3.60
2304 5040 7.857885 GCAATTAGGTATGCATGAGAAGTAAAC 59.142 37.037 10.16 0.00 42.12 2.01
2446 5185 6.985645 GCAAATCCATGCTGAAACCATTATAA 59.014 34.615 0.00 0.00 43.06 0.98
2603 5342 1.355720 AGGACAGCAAACTTAGGGCAT 59.644 47.619 0.00 0.00 0.00 4.40
2604 5343 0.771127 AGGACAGCAAACTTAGGGCA 59.229 50.000 0.00 0.00 0.00 5.36
2608 5347 6.619801 ACAAACTTAGGACAGCAAACTTAG 57.380 37.500 0.00 0.00 0.00 2.18
2721 5460 0.599558 CCGTCCCGAAGTAAGTGTCA 59.400 55.000 0.00 0.00 0.00 3.58
2854 5594 6.705782 CAATCACGACACAATATACCAGTTC 58.294 40.000 0.00 0.00 0.00 3.01
2882 5622 3.838244 ACTGCTAAACTCTGGTGAACA 57.162 42.857 0.00 0.00 0.00 3.18
3962 6753 3.306780 CGATAGGGAACTTCACCTGTTGT 60.307 47.826 8.38 0.00 43.67 3.32
4022 6813 3.913763 CACATGTCGGTGCAACATTTAAG 59.086 43.478 0.98 0.00 39.98 1.85
4024 6815 3.142174 TCACATGTCGGTGCAACATTTA 58.858 40.909 0.98 0.00 39.98 1.40
4025 6816 1.952990 TCACATGTCGGTGCAACATTT 59.047 42.857 0.98 0.00 39.98 2.32
4036 6829 0.110238 CGGCTGGTTTTCACATGTCG 60.110 55.000 0.00 0.00 0.00 4.35
4067 6860 4.766404 AGGAAAAGATGGCGTAGTTTTG 57.234 40.909 4.45 0.00 0.00 2.44
4075 6868 1.399791 GCAGAGAAGGAAAAGATGGCG 59.600 52.381 0.00 0.00 0.00 5.69
4090 6883 0.457035 GAGGAGAGCTCACTGCAGAG 59.543 60.000 23.35 13.75 45.94 3.35
4103 6896 1.975407 GGACGACCCAACGAGGAGA 60.975 63.158 0.00 0.00 41.22 3.71
4112 6905 0.251608 TCATCTGTCTGGACGACCCA 60.252 55.000 0.34 1.16 42.13 4.51
4115 6908 2.416162 GGTTCTCATCTGTCTGGACGAC 60.416 54.545 0.00 0.00 43.14 4.34
4283 7079 5.769835 ACATATCCAAAGGATCACCACAAT 58.230 37.500 1.05 0.00 42.11 2.71
4432 7229 3.642705 GAGAATCCAAACCACAAAGCAC 58.357 45.455 0.00 0.00 0.00 4.40
4471 7275 2.492088 GACCAAAGCTGTTGGGTTATCC 59.508 50.000 23.11 8.46 40.50 2.59
4516 7325 0.687427 TGCCCTGTGATCTGATCGGA 60.687 55.000 6.72 6.72 0.00 4.55
4518 7327 1.509703 CATGCCCTGTGATCTGATCG 58.490 55.000 12.65 0.00 0.00 3.69
4625 7457 8.827677 ACGACTATAAGACCTCAAATTAATTGC 58.172 33.333 0.39 0.00 38.98 3.56
4632 7464 8.064336 ACAACTACGACTATAAGACCTCAAAT 57.936 34.615 0.00 0.00 0.00 2.32
4644 7477 7.657023 AAAGGGAGATTACAACTACGACTAT 57.343 36.000 0.00 0.00 0.00 2.12
4677 7510 9.219603 CAGAACACTAGATAGAACCAAAATGAA 57.780 33.333 0.00 0.00 0.00 2.57
4696 7529 8.166367 GAGCAATTATTTGATCAACAGAACAC 57.834 34.615 7.89 0.00 45.46 3.32
4706 7539 9.709495 ATGTCTCTAGAGAGCAATTATTTGATC 57.291 33.333 22.95 6.50 46.28 2.92
4710 7656 7.721402 ACGATGTCTCTAGAGAGCAATTATTT 58.279 34.615 22.95 7.85 41.80 1.40
4723 7669 6.586463 TCTTGCAGTAAAAACGATGTCTCTAG 59.414 38.462 0.00 0.00 0.00 2.43
4726 7672 5.591643 TCTTGCAGTAAAAACGATGTCTC 57.408 39.130 0.00 0.00 0.00 3.36
4728 7674 4.151798 GCTCTTGCAGTAAAAACGATGTC 58.848 43.478 0.00 0.00 39.41 3.06
4730 7676 4.145876 TGCTCTTGCAGTAAAAACGATG 57.854 40.909 0.00 0.00 45.31 3.84
4784 7731 1.336517 TGAAACGCTCTTACAGGACGG 60.337 52.381 0.00 0.00 0.00 4.79
4785 7732 1.719780 GTGAAACGCTCTTACAGGACG 59.280 52.381 0.00 0.00 0.00 4.79
4790 7737 4.579454 ACACTAGTGAAACGCTCTTACA 57.421 40.909 29.30 0.00 45.86 2.41
4791 7738 6.998258 TTTACACTAGTGAAACGCTCTTAC 57.002 37.500 29.30 0.00 45.86 2.34
4818 8109 9.288576 CTCACTTCATCCCATTATATAAAAGCA 57.711 33.333 0.00 0.00 0.00 3.91
4829 8120 9.561069 GTATTGTATTACTCACTTCATCCCATT 57.439 33.333 0.00 0.00 0.00 3.16
4960 8253 5.972935 TGACCGTGCTTATCTTTAGATTCA 58.027 37.500 0.00 0.00 36.05 2.57
4971 8264 7.391148 AACATTTAGAATTGACCGTGCTTAT 57.609 32.000 0.00 0.00 0.00 1.73
4977 8270 4.992319 TCACGAACATTTAGAATTGACCGT 59.008 37.500 0.00 0.00 0.00 4.83
4978 8271 5.524511 TCACGAACATTTAGAATTGACCG 57.475 39.130 0.00 0.00 0.00 4.79
4982 8275 4.661776 CGCGATCACGAACATTTAGAATTG 59.338 41.667 0.00 0.00 42.66 2.32
4983 8276 4.328983 ACGCGATCACGAACATTTAGAATT 59.671 37.500 15.93 0.00 42.66 2.17
4986 8279 2.850060 GACGCGATCACGAACATTTAGA 59.150 45.455 15.93 0.00 42.66 2.10
4987 8280 2.852413 AGACGCGATCACGAACATTTAG 59.148 45.455 15.93 0.00 42.66 1.85
4988 8281 2.871133 AGACGCGATCACGAACATTTA 58.129 42.857 15.93 0.00 42.66 1.40
4990 8283 2.554806 TAGACGCGATCACGAACATT 57.445 45.000 15.93 0.00 42.66 2.71
4991 8284 2.554806 TTAGACGCGATCACGAACAT 57.445 45.000 15.93 0.00 42.66 2.71
4992 8285 2.334971 TTTAGACGCGATCACGAACA 57.665 45.000 15.93 0.00 42.66 3.18
4993 8286 3.106672 AGATTTAGACGCGATCACGAAC 58.893 45.455 15.93 3.77 42.66 3.95
4997 8290 2.044860 CGGAGATTTAGACGCGATCAC 58.955 52.381 15.93 3.09 0.00 3.06
4998 8291 1.674441 ACGGAGATTTAGACGCGATCA 59.326 47.619 15.93 0.00 0.00 2.92
4999 8292 2.044860 CACGGAGATTTAGACGCGATC 58.955 52.381 15.93 4.58 0.00 3.69
5000 8293 1.269102 CCACGGAGATTTAGACGCGAT 60.269 52.381 15.93 2.85 0.00 4.58
5001 8294 0.099968 CCACGGAGATTTAGACGCGA 59.900 55.000 15.93 0.00 0.00 5.87
5002 8295 0.099968 TCCACGGAGATTTAGACGCG 59.900 55.000 3.53 3.53 0.00 6.01
5003 8296 1.135199 TGTCCACGGAGATTTAGACGC 60.135 52.381 0.00 0.00 0.00 5.19
5004 8297 2.933495 TGTCCACGGAGATTTAGACG 57.067 50.000 0.00 0.00 0.00 4.18
5005 8298 3.194968 TCCTTGTCCACGGAGATTTAGAC 59.805 47.826 0.00 0.00 0.00 2.59
5006 8299 3.194968 GTCCTTGTCCACGGAGATTTAGA 59.805 47.826 0.00 0.00 28.60 2.10
5007 8300 3.522553 GTCCTTGTCCACGGAGATTTAG 58.477 50.000 0.00 0.00 28.60 1.85
5008 8301 2.094390 CGTCCTTGTCCACGGAGATTTA 60.094 50.000 0.00 0.00 32.19 1.40
5013 8306 0.246635 ATTCGTCCTTGTCCACGGAG 59.753 55.000 0.00 0.00 36.64 4.63
5029 8322 9.143631 CAAACCATTTCTAGATTTTGGACATTC 57.856 33.333 18.15 0.00 0.00 2.67
5035 8328 7.895759 TCCTTCAAACCATTTCTAGATTTTGG 58.104 34.615 12.31 12.31 0.00 3.28
5036 8329 8.579863 ACTCCTTCAAACCATTTCTAGATTTTG 58.420 33.333 0.00 0.00 0.00 2.44
5037 8330 8.712228 ACTCCTTCAAACCATTTCTAGATTTT 57.288 30.769 0.00 0.00 0.00 1.82
5065 8358 2.280552 GCCGTACACCAGGGAGTGA 61.281 63.158 0.00 0.00 40.34 3.41


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

AutoCloner maintained by Alex Coulton.