Multiple sequence alignment - TraesCS3D01G488200

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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 TraesCS3D01G488200 chr3D 100.000 2829 0 0 1 2829 583027805 583024977 0.000000e+00 5225.0
1 TraesCS3D01G488200 chr3D 90.229 1269 108 7 676 1930 583162300 583161034 0.000000e+00 1642.0
2 TraesCS3D01G488200 chr3D 86.832 1496 143 35 675 2136 583179398 583177923 0.000000e+00 1622.0
3 TraesCS3D01G488200 chr3D 86.275 204 18 4 675 868 583276138 583275935 2.210000e-51 213.0
4 TraesCS3D01G488200 chr3D 79.710 345 27 11 2487 2829 583160637 583160334 2.860000e-50 209.0
5 TraesCS3D01G488200 chr3D 87.730 163 16 2 518 676 583223286 583223124 1.340000e-43 187.0
6 TraesCS3D01G488200 chr3D 88.000 150 15 1 531 677 583179582 583179433 1.040000e-39 174.0
7 TraesCS3D01G488200 chrUn 93.660 1940 86 11 1 1930 41698269 41700181 0.000000e+00 2867.0
8 TraesCS3D01G488200 chrUn 84.713 1655 168 47 575 2180 101984429 101982811 0.000000e+00 1576.0
9 TraesCS3D01G488200 chrUn 86.453 1469 123 35 755 2180 101987586 101986151 0.000000e+00 1541.0
10 TraesCS3D01G488200 chrUn 89.127 1122 99 17 825 1930 352585814 352586928 0.000000e+00 1375.0
11 TraesCS3D01G488200 chrUn 88.235 459 25 7 2383 2829 41700619 41701060 3.230000e-144 521.0
12 TraesCS3D01G488200 chr6B 87.171 1481 114 34 743 2180 62688932 62687485 0.000000e+00 1613.0
13 TraesCS3D01G488200 chr6B 77.723 404 61 20 2428 2812 62632271 62631878 1.320000e-53 220.0
14 TraesCS3D01G488200 chr6B 84.921 126 17 2 556 680 62691238 62691114 2.960000e-25 126.0
15 TraesCS3D01G488200 chr6B 86.667 105 12 2 556 659 62634423 62634320 6.400000e-22 115.0
16 TraesCS3D01G488200 chr6B 87.342 79 8 2 2735 2812 62614824 62614747 3.880000e-14 89.8
17 TraesCS3D01G488200 chr6A 89.176 1275 97 23 743 1986 34273361 34272097 0.000000e+00 1552.0
18 TraesCS3D01G488200 chr6A 90.133 1206 94 14 743 1930 34278163 34276965 0.000000e+00 1544.0
19 TraesCS3D01G488200 chr6A 86.483 1450 122 33 743 2156 34390733 34389322 0.000000e+00 1524.0
20 TraesCS3D01G488200 chr6A 78.431 408 57 19 2428 2812 34388899 34388500 1.310000e-58 237.0
21 TraesCS3D01G488200 chr6A 77.696 408 60 19 2428 2812 34271504 34271105 1.320000e-53 220.0
22 TraesCS3D01G488200 chr6A 87.037 108 12 2 556 662 34280505 34280399 1.380000e-23 121.0
23 TraesCS3D01G488200 chr6A 87.037 108 12 2 556 662 34282483 34282377 1.380000e-23 121.0
24 TraesCS3D01G488200 chr6A 84.158 101 14 2 563 662 34393072 34392973 2.320000e-16 97.1
25 TraesCS3D01G488200 chr3B 91.614 1109 79 7 801 1900 780295721 780294618 0.000000e+00 1520.0
26 TraesCS3D01G488200 chr3B 88.184 1261 119 20 692 1930 780324134 780322882 0.000000e+00 1476.0
27 TraesCS3D01G488200 chr3B 88.025 1261 122 19 692 1930 780314155 780312902 0.000000e+00 1465.0
28 TraesCS3D01G488200 chr3B 86.869 396 35 7 2441 2829 780085267 780084882 7.240000e-116 427.0
29 TraesCS3D01G488200 chr3B 83.526 346 28 8 2487 2829 780293337 780293018 2.130000e-76 296.0
30 TraesCS3D01G488200 chr3B 86.831 243 23 4 1690 1930 780317743 780317508 2.160000e-66 263.0
31 TraesCS3D01G488200 chr3B 90.184 163 13 1 517 676 780339342 780339180 2.860000e-50 209.0
32 TraesCS3D01G488200 chr3B 85.714 161 11 5 2036 2186 780294478 780294320 2.920000e-35 159.0
33 TraesCS3D01G488200 chr3B 87.050 139 12 4 2184 2321 780293619 780293486 4.880000e-33 152.0
34 TraesCS3D01G488200 chr4A 80.352 341 31 18 2431 2764 645762185 645761874 2.840000e-55 226.0
35 TraesCS3D01G488200 chr7A 83.770 191 21 4 2641 2829 54604184 54604002 3.750000e-39 172.0
36 TraesCS3D01G488200 chr5D 85.235 149 11 8 2044 2190 527377200 527377061 2.940000e-30 143.0


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 TraesCS3D01G488200 chr3D 583024977 583027805 2828 True 5225.000000 5225 100.0000 1 2829 1 chr3D.!!$R1 2828
1 TraesCS3D01G488200 chr3D 583160334 583162300 1966 True 925.500000 1642 84.9695 676 2829 2 chr3D.!!$R4 2153
2 TraesCS3D01G488200 chr3D 583177923 583179582 1659 True 898.000000 1622 87.4160 531 2136 2 chr3D.!!$R5 1605
3 TraesCS3D01G488200 chrUn 41698269 41701060 2791 False 1694.000000 2867 90.9475 1 2829 2 chrUn.!!$F2 2828
4 TraesCS3D01G488200 chrUn 101982811 101987586 4775 True 1558.500000 1576 85.5830 575 2180 2 chrUn.!!$R1 1605
5 TraesCS3D01G488200 chrUn 352585814 352586928 1114 False 1375.000000 1375 89.1270 825 1930 1 chrUn.!!$F1 1105
6 TraesCS3D01G488200 chr6B 62687485 62691238 3753 True 869.500000 1613 86.0460 556 2180 2 chr6B.!!$R3 1624
7 TraesCS3D01G488200 chr6A 34271105 34282483 11378 True 711.600000 1552 86.2158 556 2812 5 chr6A.!!$R1 2256
8 TraesCS3D01G488200 chr6A 34388500 34393072 4572 True 619.366667 1524 83.0240 563 2812 3 chr6A.!!$R2 2249
9 TraesCS3D01G488200 chr3B 780322882 780324134 1252 True 1476.000000 1476 88.1840 692 1930 1 chr3B.!!$R2 1238
10 TraesCS3D01G488200 chr3B 780312902 780317743 4841 True 864.000000 1465 87.4280 692 1930 2 chr3B.!!$R5 1238
11 TraesCS3D01G488200 chr3B 780293018 780295721 2703 True 531.750000 1520 86.9760 801 2829 4 chr3B.!!$R4 2028

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
79 80 0.768221 ACTCTCCACCACCACCACAT 60.768 55.0 0.0 0.00 0.0 3.21 F
1324 10409 0.035725 CATCCAAGAGCTGCAGGTGA 60.036 55.0 25.6 14.68 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 10423 0.305009 CTTGAGCAGCTGCATCATCG 59.695 55.0 38.24 24.42 45.16 3.84 R
2356 17388 0.040067 CGCTGGCCTGTTTCAGTTTC 60.040 55.0 11.69 0.00 33.81 2.78 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
79 80 0.768221 ACTCTCCACCACCACCACAT 60.768 55.000 0.00 0.00 0.00 3.21
245 249 5.270083 CACAACTTTTTGCATGTTCTACGA 58.730 37.500 0.00 0.00 36.00 3.43
257 261 6.816140 TGCATGTTCTACGAGATCAACAATAA 59.184 34.615 0.00 0.00 32.66 1.40
262 266 8.466798 TGTTCTACGAGATCAACAATAATCTGA 58.533 33.333 0.00 0.00 32.43 3.27
302 306 3.163630 TGCCAGTGCTCAAAGTTTTTC 57.836 42.857 0.00 0.00 38.71 2.29
330 334 9.199645 TGCTTCCCATCTAATGATTCATAAAAA 57.800 29.630 0.00 0.00 0.00 1.94
372 376 9.374960 CGCTTTATATGCTTATTTCAGACTTTC 57.625 33.333 0.00 0.00 0.00 2.62
377 381 5.947228 TGCTTATTTCAGACTTTCACCAG 57.053 39.130 0.00 0.00 0.00 4.00
426 430 4.393062 TCGGTTAGTACGACAAAGAGGTAG 59.607 45.833 0.00 0.00 35.12 3.18
479 483 3.932009 CCCACGGGCATGCATAAA 58.068 55.556 21.36 0.00 0.00 1.40
481 485 1.614996 CCCACGGGCATGCATAAATA 58.385 50.000 21.36 0.00 0.00 1.40
482 486 1.959985 CCCACGGGCATGCATAAATAA 59.040 47.619 21.36 0.00 0.00 1.40
483 487 2.562298 CCCACGGGCATGCATAAATAAT 59.438 45.455 21.36 0.00 0.00 1.28
524 528 2.034124 GCTACTTACACGGTGGGGATA 58.966 52.381 13.48 0.00 0.00 2.59
553 560 2.711311 CGCCATGGATCTTGTGCG 59.289 61.111 18.40 4.98 35.81 5.34
597 604 1.376424 CATGCCAGCTCCGACAGTT 60.376 57.895 0.00 0.00 0.00 3.16
752 3650 4.646945 TGGCTCATCTAAAGGACAGTAGAG 59.353 45.833 0.00 0.00 30.11 2.43
914 5809 6.936900 GCATTTCTGTATAAATAGGCCTCAGA 59.063 38.462 9.68 11.68 0.00 3.27
1020 5927 2.673775 TGGCTTTCCACCAAAGATCA 57.326 45.000 0.00 0.00 44.02 2.92
1072 5979 1.001406 AGACCGAAGTTGAGCAAGAGG 59.999 52.381 0.00 0.00 0.00 3.69
1202 10287 0.465287 CCAAGCCACCAAGTTTGCTT 59.535 50.000 0.00 0.00 44.40 3.91
1263 10348 4.902443 CTCCGTTGAGCTGTTAGATCTA 57.098 45.455 0.00 0.00 30.68 1.98
1324 10409 0.035725 CATCCAAGAGCTGCAGGTGA 60.036 55.000 25.60 14.68 0.00 4.02
1338 10423 2.744741 GCAGGTGACTCTAAGAAAAGGC 59.255 50.000 0.00 0.00 40.21 4.35
1582 10673 0.383949 GAAGAAGGCCGTTGTTTGCA 59.616 50.000 0.00 0.00 0.00 4.08
1872 16062 9.794685 TTGTGATATCGATATTAATCTCTCTGC 57.205 33.333 18.69 2.89 0.00 4.26
1876 16066 4.727475 TCGATATTAATCTCTCTGCAGCG 58.273 43.478 9.47 2.08 0.00 5.18
1907 16110 9.321562 GATGAATATGCATGACAAAAGGAAATT 57.678 29.630 10.16 0.00 0.00 1.82
1930 16133 8.827177 ATTTGTATGATTTCAATCCATCATGC 57.173 30.769 5.13 4.52 39.87 4.06
1932 16135 7.349412 TGTATGATTTCAATCCATCATGCAA 57.651 32.000 9.59 0.00 44.57 4.08
1941 16144 2.830293 TCCATCATGCAATTTTGGGGA 58.170 42.857 0.00 0.00 0.00 4.81
1958 16181 6.844097 TTGGGGATACAGGTTACATTTTTC 57.156 37.500 0.00 0.00 39.74 2.29
1959 16182 4.944930 TGGGGATACAGGTTACATTTTTCG 59.055 41.667 0.00 0.00 39.74 3.46
2003 16283 6.710295 TGATGTTATACCAACATGCAGGTATC 59.290 38.462 24.92 16.51 45.56 2.24
2004 16284 6.247229 TGTTATACCAACATGCAGGTATCT 57.753 37.500 24.92 12.07 45.56 1.98
2005 16285 6.658849 TGTTATACCAACATGCAGGTATCTT 58.341 36.000 24.92 11.52 45.56 2.40
2006 16286 7.116075 TGTTATACCAACATGCAGGTATCTTT 58.884 34.615 24.92 11.25 45.56 2.52
2007 16287 7.282224 TGTTATACCAACATGCAGGTATCTTTC 59.718 37.037 24.92 16.54 45.56 2.62
2008 16288 4.032960 ACCAACATGCAGGTATCTTTCA 57.967 40.909 3.57 0.00 36.07 2.69
2009 16289 4.603131 ACCAACATGCAGGTATCTTTCAT 58.397 39.130 3.57 0.00 36.07 2.57
2010 16290 5.754782 ACCAACATGCAGGTATCTTTCATA 58.245 37.500 3.57 0.00 36.07 2.15
2011 16291 6.186957 ACCAACATGCAGGTATCTTTCATAA 58.813 36.000 3.57 0.00 36.07 1.90
2013 16293 6.319658 CCAACATGCAGGTATCTTTCATAAGT 59.680 38.462 3.57 0.00 32.98 2.24
2014 16294 7.498900 CCAACATGCAGGTATCTTTCATAAGTA 59.501 37.037 3.57 0.00 32.98 2.24
2015 16295 8.892723 CAACATGCAGGTATCTTTCATAAGTAA 58.107 33.333 3.57 0.00 32.98 2.24
2016 16296 9.461312 AACATGCAGGTATCTTTCATAAGTAAA 57.539 29.630 3.57 0.00 32.98 2.01
2017 16297 8.893727 ACATGCAGGTATCTTTCATAAGTAAAC 58.106 33.333 0.06 0.00 32.98 2.01
2018 16298 8.892723 CATGCAGGTATCTTTCATAAGTAAACA 58.107 33.333 0.00 0.00 32.98 2.83
2019 16299 9.632638 ATGCAGGTATCTTTCATAAGTAAACAT 57.367 29.630 0.00 0.00 32.98 2.71
2020 16300 9.461312 TGCAGGTATCTTTCATAAGTAAACATT 57.539 29.630 0.00 0.00 32.98 2.71
2065 16367 5.511545 CCACACCTACCATAAGATTAGCCTC 60.512 48.000 0.00 0.00 0.00 4.70
2071 16373 7.939588 ACCTACCATAAGATTAGCCTCATTTTC 59.060 37.037 0.00 0.00 0.00 2.29
2072 16374 7.939039 CCTACCATAAGATTAGCCTCATTTTCA 59.061 37.037 0.00 0.00 0.00 2.69
2080 16382 3.191078 AGCCTCATTTTCAGGATCTCG 57.809 47.619 0.00 0.00 31.91 4.04
2154 16469 8.038351 TGTACTTAGCACATAAATCAACTAGCA 58.962 33.333 0.00 0.00 0.00 3.49
2155 16470 7.545362 ACTTAGCACATAAATCAACTAGCAG 57.455 36.000 0.00 0.00 0.00 4.24
2156 16471 4.889832 AGCACATAAATCAACTAGCAGC 57.110 40.909 0.00 0.00 0.00 5.25
2157 16472 4.264253 AGCACATAAATCAACTAGCAGCA 58.736 39.130 0.00 0.00 0.00 4.41
2158 16473 4.334759 AGCACATAAATCAACTAGCAGCAG 59.665 41.667 0.00 0.00 0.00 4.24
2159 16474 4.497006 GCACATAAATCAACTAGCAGCAGG 60.497 45.833 0.00 0.00 0.00 4.85
2180 16495 3.381590 GGGATTCCCTTCATAGTTGCAAC 59.618 47.826 22.17 22.17 41.34 4.17
2184 16499 5.452078 TTCCCTTCATAGTTGCAACTTTG 57.548 39.130 35.20 33.43 40.37 2.77
2186 16501 3.573967 CCCTTCATAGTTGCAACTTTGGT 59.426 43.478 34.74 19.86 40.37 3.67
2190 16505 4.211125 TCATAGTTGCAACTTTGGTCCAA 58.789 39.130 34.74 20.88 40.37 3.53
2191 16506 4.646945 TCATAGTTGCAACTTTGGTCCAAA 59.353 37.500 34.74 20.33 40.37 3.28
2193 16508 4.058721 AGTTGCAACTTTGGTCCAAATC 57.941 40.909 26.36 7.99 35.21 2.17
2194 16509 3.706086 AGTTGCAACTTTGGTCCAAATCT 59.294 39.130 26.36 5.11 35.21 2.40
2206 17233 3.006752 GGTCCAAATCTCAAAACCATGCA 59.993 43.478 0.00 0.00 0.00 3.96
2212 17239 5.471556 AATCTCAAAACCATGCATGTTCA 57.528 34.783 24.58 0.00 0.00 3.18
2221 17248 7.466746 AAACCATGCATGTTCAACTATAACT 57.533 32.000 24.58 0.00 0.00 2.24
2235 17262 8.902540 TCAACTATAACTTTGTCACTCAATGT 57.097 30.769 0.00 0.00 43.21 2.71
2237 17264 8.773645 CAACTATAACTTTGTCACTCAATGTCA 58.226 33.333 0.00 0.00 41.44 3.58
2241 17268 2.524569 TTGTCACTCAATGTCAGCGA 57.475 45.000 0.00 0.00 0.00 4.93
2242 17269 1.783284 TGTCACTCAATGTCAGCGAC 58.217 50.000 0.00 2.32 0.00 5.19
2243 17270 1.068434 TGTCACTCAATGTCAGCGACA 59.932 47.619 12.53 12.53 46.90 4.35
2317 17349 1.470805 GGTTTGTGCACTTGAACACCC 60.471 52.381 19.41 4.79 32.21 4.61
2319 17351 1.774110 TTGTGCACTTGAACACCCAT 58.226 45.000 19.41 0.00 32.21 4.00
2320 17352 2.647683 TGTGCACTTGAACACCCATA 57.352 45.000 19.41 0.00 35.90 2.74
2321 17353 3.153369 TGTGCACTTGAACACCCATAT 57.847 42.857 19.41 0.00 35.90 1.78
2322 17354 4.293662 TGTGCACTTGAACACCCATATA 57.706 40.909 19.41 0.00 35.90 0.86
2324 17356 5.260424 TGTGCACTTGAACACCCATATATT 58.740 37.500 19.41 0.00 35.90 1.28
2325 17357 5.714333 TGTGCACTTGAACACCCATATATTT 59.286 36.000 19.41 0.00 35.90 1.40
2326 17358 6.887002 TGTGCACTTGAACACCCATATATTTA 59.113 34.615 19.41 0.00 35.90 1.40
2327 17359 7.559533 TGTGCACTTGAACACCCATATATTTAT 59.440 33.333 19.41 0.00 35.90 1.40
2328 17360 8.413229 GTGCACTTGAACACCCATATATTTATT 58.587 33.333 10.32 0.00 0.00 1.40
2332 17364 9.860650 ACTTGAACACCCATATATTTATTAGCA 57.139 29.630 0.00 0.00 0.00 3.49
2353 17385 6.342111 AGCACTACTAGAGGAATTTGTAAGC 58.658 40.000 0.00 0.00 0.00 3.09
2355 17387 6.763610 GCACTACTAGAGGAATTTGTAAGCAT 59.236 38.462 0.00 0.00 0.00 3.79
2356 17388 7.254590 GCACTACTAGAGGAATTTGTAAGCATG 60.255 40.741 0.00 0.00 0.00 4.06
2357 17389 7.981789 CACTACTAGAGGAATTTGTAAGCATGA 59.018 37.037 0.00 0.00 0.00 3.07
2360 17392 8.045176 ACTAGAGGAATTTGTAAGCATGAAAC 57.955 34.615 0.00 0.00 0.00 2.78
2361 17393 7.885399 ACTAGAGGAATTTGTAAGCATGAAACT 59.115 33.333 0.00 0.00 0.00 2.66
2362 17394 6.917533 AGAGGAATTTGTAAGCATGAAACTG 58.082 36.000 0.00 0.00 0.00 3.16
2364 17396 7.231317 AGAGGAATTTGTAAGCATGAAACTGAA 59.769 33.333 0.00 0.00 0.00 3.02
2366 17398 7.653311 AGGAATTTGTAAGCATGAAACTGAAAC 59.347 33.333 0.00 0.00 0.00 2.78
2368 17400 7.935338 ATTTGTAAGCATGAAACTGAAACAG 57.065 32.000 0.00 0.00 37.52 3.16
2369 17401 5.437289 TGTAAGCATGAAACTGAAACAGG 57.563 39.130 0.00 0.00 35.51 4.00
2370 17402 3.375782 AAGCATGAAACTGAAACAGGC 57.624 42.857 0.00 0.00 40.75 4.85
2372 17404 1.340889 GCATGAAACTGAAACAGGCCA 59.659 47.619 5.01 0.00 35.73 5.36
2374 17406 1.032014 TGAAACTGAAACAGGCCAGC 58.968 50.000 5.01 0.00 35.51 4.85
2375 17407 0.040067 GAAACTGAAACAGGCCAGCG 60.040 55.000 5.01 0.00 35.51 5.18
2376 17408 0.465460 AAACTGAAACAGGCCAGCGA 60.465 50.000 5.01 0.00 35.51 4.93
2377 17409 0.250901 AACTGAAACAGGCCAGCGAT 60.251 50.000 5.01 0.00 35.51 4.58
2378 17410 0.957395 ACTGAAACAGGCCAGCGATG 60.957 55.000 5.01 0.00 35.51 3.84
2380 17412 0.537143 TGAAACAGGCCAGCGATGTT 60.537 50.000 5.01 2.97 38.76 2.71
2381 17413 0.109597 GAAACAGGCCAGCGATGTTG 60.110 55.000 5.01 0.00 37.24 3.33
2382 17414 0.823356 AAACAGGCCAGCGATGTTGT 60.823 50.000 5.01 0.00 37.24 3.32
2383 17415 1.518056 AACAGGCCAGCGATGTTGTG 61.518 55.000 5.01 0.00 35.89 3.33
2384 17416 1.672030 CAGGCCAGCGATGTTGTGA 60.672 57.895 5.01 0.00 0.00 3.58
2391 17423 1.136141 CAGCGATGTTGTGAAGAGTGC 60.136 52.381 0.00 0.00 0.00 4.40
2398 17430 4.979943 TGTTGTGAAGAGTGCAAAATGA 57.020 36.364 0.00 0.00 0.00 2.57
2401 17433 5.067544 TGTTGTGAAGAGTGCAAAATGATCA 59.932 36.000 0.00 0.00 0.00 2.92
2414 17446 4.978083 AAATGATCATGTGAGGTTGAGC 57.022 40.909 9.46 0.00 0.00 4.26
2415 17447 2.014335 TGATCATGTGAGGTTGAGCG 57.986 50.000 0.00 0.00 31.03 5.03
2416 17448 0.654683 GATCATGTGAGGTTGAGCGC 59.345 55.000 0.00 0.00 0.00 5.92
2417 17449 0.745845 ATCATGTGAGGTTGAGCGCC 60.746 55.000 2.29 0.00 0.00 6.53
2418 17450 1.672030 CATGTGAGGTTGAGCGCCA 60.672 57.895 2.29 0.00 0.00 5.69
2446 17482 3.084786 GGACAAAGGCTGTTAGCAGAAT 58.915 45.455 11.20 0.00 44.75 2.40
2448 17484 3.084786 ACAAAGGCTGTTAGCAGAATCC 58.915 45.455 11.20 2.21 44.75 3.01
2493 17539 2.936919 TGAAGTCAATGACACCAGCT 57.063 45.000 16.38 0.00 34.60 4.24
2569 17620 1.485895 TGTACATAGCATGCCAGCAGA 59.514 47.619 15.66 0.00 36.85 4.26
2706 17796 3.006859 TGACAGGCCCATATACTCATTCG 59.993 47.826 0.00 0.00 0.00 3.34
2711 17801 4.707448 AGGCCCATATACTCATTCGTAGAG 59.293 45.833 0.00 0.00 38.43 2.43
2783 17874 3.051081 AGTGGCAAACTCTCATGACTC 57.949 47.619 0.00 0.00 31.64 3.36
2801 17892 4.838423 TGACTCAACTGACCAAGATTCCTA 59.162 41.667 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.286248 GGTGGTGGAGAGTATGGGTT 58.714 55.000 0.00 0.00 0.00 4.11
108 112 7.789273 TGGACTTAGTCGTATGAAACAAAAA 57.211 32.000 6.27 0.00 32.65 1.94
218 222 4.869861 AGAACATGCAAAAAGTTGTGGTTC 59.130 37.500 0.00 0.00 39.17 3.62
245 249 9.003658 ACGTTTTTCTCAGATTATTGTTGATCT 57.996 29.630 0.00 0.00 33.01 2.75
257 261 7.745620 AGTTTGGATTACGTTTTTCTCAGAT 57.254 32.000 0.00 0.00 0.00 2.90
262 266 5.163499 TGGCAAGTTTGGATTACGTTTTTCT 60.163 36.000 0.00 0.00 0.00 2.52
302 306 6.896021 ATGAATCATTAGATGGGAAGCAAG 57.104 37.500 0.00 0.00 33.90 4.01
330 334 1.375551 AGCGTCGGTTGTTCTTTGTT 58.624 45.000 0.00 0.00 0.00 2.83
372 376 5.969423 ACATTGGCATCTTATTTTCTGGTG 58.031 37.500 0.00 0.00 0.00 4.17
373 377 5.127682 GGACATTGGCATCTTATTTTCTGGT 59.872 40.000 0.00 0.00 0.00 4.00
375 379 5.066375 TCGGACATTGGCATCTTATTTTCTG 59.934 40.000 0.00 0.00 0.00 3.02
377 381 5.296780 TCTCGGACATTGGCATCTTATTTTC 59.703 40.000 0.00 0.00 0.00 2.29
414 418 5.932303 TGTGCAATCTTACTACCTCTTTGTC 59.068 40.000 0.00 0.00 0.00 3.18
417 421 7.817418 TTTTGTGCAATCTTACTACCTCTTT 57.183 32.000 0.00 0.00 0.00 2.52
426 430 7.475771 TTCCAATGTTTTTGTGCAATCTTAC 57.524 32.000 0.00 0.00 0.00 2.34
462 466 1.614996 TATTTATGCATGCCCGTGGG 58.385 50.000 16.68 0.00 38.57 4.61
524 528 1.597797 CCATGGCGGTTCAGCATGTT 61.598 55.000 0.00 0.00 39.27 2.71
597 604 5.924356 TGTGAATCACAGGTTAAAGTCTCA 58.076 37.500 12.63 0.00 39.62 3.27
752 3650 9.901724 CTCGTGATTAGTACATAATTTTGTGTC 57.098 33.333 11.30 5.23 34.10 3.67
914 5809 6.174720 TGGTTTGATGTGTCTACTTCTCTT 57.825 37.500 0.00 0.00 33.44 2.85
958 5860 5.724328 TCTCTGTATTGTGGTTGATGAGAC 58.276 41.667 0.00 0.00 0.00 3.36
1072 5979 1.731720 CTTGCTTCTAGGCTGTGGAC 58.268 55.000 0.00 0.00 0.00 4.02
1123 10208 1.064946 GAGTCCTGAGACCATCGCG 59.935 63.158 0.00 0.00 44.72 5.87
1324 10409 3.873952 GCATCATCGCCTTTTCTTAGAGT 59.126 43.478 0.00 0.00 0.00 3.24
1338 10423 0.305009 CTTGAGCAGCTGCATCATCG 59.695 55.000 38.24 24.42 45.16 3.84
1582 10673 0.700564 TCCTGCAATTGCTCCTCCTT 59.299 50.000 29.37 0.00 42.66 3.36
1753 15934 4.142600 GCAAAACTGTATCAAGATCGGCTT 60.143 41.667 0.00 0.00 37.29 4.35
1872 16062 4.212636 TCATGCATATTCATCAGAACGCTG 59.787 41.667 0.00 0.00 43.67 5.18
1876 16066 7.434307 CCTTTTGTCATGCATATTCATCAGAAC 59.566 37.037 0.00 0.00 36.39 3.01
1907 16110 7.349412 TGCATGATGGATTGAAATCATACAA 57.651 32.000 0.00 0.00 40.68 2.41
1930 16133 6.790232 ATGTAACCTGTATCCCCAAAATTG 57.210 37.500 0.00 0.00 0.00 2.32
1932 16135 7.806680 AAAATGTAACCTGTATCCCCAAAAT 57.193 32.000 0.00 0.00 0.00 1.82
1941 16144 7.999450 TTTACCCGAAAAATGTAACCTGTAT 57.001 32.000 0.00 0.00 0.00 2.29
1958 16181 7.479980 ACATCATTGTTGTTATCATTTACCCG 58.520 34.615 0.00 0.00 29.55 5.28
1986 16237 5.172687 TGAAAGATACCTGCATGTTGGTA 57.827 39.130 17.13 17.13 42.23 3.25
2014 16294 9.567848 CGCAACAAATAGAACCTAATAATGTTT 57.432 29.630 0.00 0.00 0.00 2.83
2015 16295 7.700656 GCGCAACAAATAGAACCTAATAATGTT 59.299 33.333 0.30 0.00 0.00 2.71
2016 16296 7.193595 GCGCAACAAATAGAACCTAATAATGT 58.806 34.615 0.30 0.00 0.00 2.71
2017 16297 6.636850 GGCGCAACAAATAGAACCTAATAATG 59.363 38.462 10.83 0.00 0.00 1.90
2018 16298 6.320164 TGGCGCAACAAATAGAACCTAATAAT 59.680 34.615 10.83 0.00 0.00 1.28
2019 16299 5.648526 TGGCGCAACAAATAGAACCTAATAA 59.351 36.000 10.83 0.00 0.00 1.40
2020 16300 5.065474 GTGGCGCAACAAATAGAACCTAATA 59.935 40.000 10.88 0.00 0.00 0.98
2021 16301 4.013728 TGGCGCAACAAATAGAACCTAAT 58.986 39.130 10.83 0.00 0.00 1.73
2022 16302 3.189702 GTGGCGCAACAAATAGAACCTAA 59.810 43.478 10.88 0.00 0.00 2.69
2023 16303 2.745281 GTGGCGCAACAAATAGAACCTA 59.255 45.455 10.88 0.00 0.00 3.08
2024 16304 1.539827 GTGGCGCAACAAATAGAACCT 59.460 47.619 10.88 0.00 0.00 3.50
2025 16305 1.268352 TGTGGCGCAACAAATAGAACC 59.732 47.619 17.09 0.00 0.00 3.62
2026 16306 2.315901 GTGTGGCGCAACAAATAGAAC 58.684 47.619 21.54 0.71 0.00 3.01
2027 16307 1.268352 GGTGTGGCGCAACAAATAGAA 59.732 47.619 21.54 0.00 34.21 2.10
2028 16308 0.878416 GGTGTGGCGCAACAAATAGA 59.122 50.000 21.54 0.00 34.21 1.98
2029 16309 0.881118 AGGTGTGGCGCAACAAATAG 59.119 50.000 21.54 0.00 37.23 1.73
2033 16313 1.894756 GGTAGGTGTGGCGCAACAA 60.895 57.895 21.54 0.23 37.23 2.83
2065 16367 6.600350 CATGATAAGCGAGATCCTGAAAATG 58.400 40.000 0.00 0.00 0.00 2.32
2071 16373 3.036075 TGCATGATAAGCGAGATCCTG 57.964 47.619 0.00 0.00 33.85 3.86
2072 16374 3.597255 CATGCATGATAAGCGAGATCCT 58.403 45.455 22.59 0.00 33.85 3.24
2080 16382 1.265095 CGTGTCCCATGCATGATAAGC 59.735 52.381 28.31 13.21 0.00 3.09
2156 16471 8.995826 AGTTGCAACTATGAAGGGAATCCCTG 62.996 46.154 30.25 11.44 45.57 4.45
2158 16473 3.297134 TGCAACTATGAAGGGAATCCC 57.703 47.619 11.16 11.16 45.90 3.85
2159 16474 4.273318 AGTTGCAACTATGAAGGGAATCC 58.727 43.478 30.25 0.00 37.52 3.01
2180 16495 5.275067 TGGTTTTGAGATTTGGACCAAAG 57.725 39.130 23.45 0.00 36.76 2.77
2184 16499 3.006752 TGCATGGTTTTGAGATTTGGACC 59.993 43.478 0.00 0.00 0.00 4.46
2186 16501 4.283978 ACATGCATGGTTTTGAGATTTGGA 59.716 37.500 29.41 0.00 0.00 3.53
2190 16505 5.471556 TGAACATGCATGGTTTTGAGATT 57.528 34.783 29.41 11.93 0.00 2.40
2191 16506 5.011329 AGTTGAACATGCATGGTTTTGAGAT 59.989 36.000 29.41 3.16 0.00 2.75
2193 16508 4.624015 AGTTGAACATGCATGGTTTTGAG 58.376 39.130 29.41 3.17 0.00 3.02
2194 16509 4.669206 AGTTGAACATGCATGGTTTTGA 57.331 36.364 29.41 7.58 0.00 2.69
2206 17233 8.902540 TGAGTGACAAAGTTATAGTTGAACAT 57.097 30.769 0.00 0.00 0.00 2.71
2212 17239 8.902540 TGACATTGAGTGACAAAGTTATAGTT 57.097 30.769 0.00 0.00 39.90 2.24
2221 17248 2.543848 GTCGCTGACATTGAGTGACAAA 59.456 45.455 11.95 0.00 46.04 2.83
2250 17277 8.810427 ACATTTTCTGCAAATTGATATTAAGCG 58.190 29.630 0.00 0.00 32.24 4.68
2277 17304 2.038295 CCTTTGTGGCCCAAAAATGCTA 59.962 45.455 16.87 0.00 42.31 3.49
2327 17359 7.980099 GCTTACAAATTCCTCTAGTAGTGCTAA 59.020 37.037 0.00 0.00 0.00 3.09
2328 17360 7.123697 TGCTTACAAATTCCTCTAGTAGTGCTA 59.876 37.037 0.00 0.00 0.00 3.49
2330 17362 6.106673 TGCTTACAAATTCCTCTAGTAGTGC 58.893 40.000 0.00 0.00 0.00 4.40
2331 17363 7.981789 TCATGCTTACAAATTCCTCTAGTAGTG 59.018 37.037 0.00 0.00 0.00 2.74
2332 17364 8.079211 TCATGCTTACAAATTCCTCTAGTAGT 57.921 34.615 0.00 0.00 0.00 2.73
2333 17365 8.948631 TTCATGCTTACAAATTCCTCTAGTAG 57.051 34.615 0.00 0.00 0.00 2.57
2335 17367 7.885399 AGTTTCATGCTTACAAATTCCTCTAGT 59.115 33.333 0.00 0.00 0.00 2.57
2336 17368 8.180267 CAGTTTCATGCTTACAAATTCCTCTAG 58.820 37.037 0.00 0.00 0.00 2.43
2338 17370 6.716628 TCAGTTTCATGCTTACAAATTCCTCT 59.283 34.615 0.00 0.00 0.00 3.69
2340 17372 6.899393 TCAGTTTCATGCTTACAAATTCCT 57.101 33.333 0.00 0.00 0.00 3.36
2342 17374 8.351495 TGTTTCAGTTTCATGCTTACAAATTC 57.649 30.769 0.00 0.00 0.00 2.17
2344 17376 6.925165 CCTGTTTCAGTTTCATGCTTACAAAT 59.075 34.615 0.00 0.00 0.00 2.32
2345 17377 6.272318 CCTGTTTCAGTTTCATGCTTACAAA 58.728 36.000 0.00 0.00 0.00 2.83
2346 17378 5.735922 GCCTGTTTCAGTTTCATGCTTACAA 60.736 40.000 0.00 0.00 0.00 2.41
2348 17380 4.229876 GCCTGTTTCAGTTTCATGCTTAC 58.770 43.478 0.00 0.00 0.00 2.34
2349 17381 3.255642 GGCCTGTTTCAGTTTCATGCTTA 59.744 43.478 0.00 0.00 0.00 3.09
2350 17382 2.036346 GGCCTGTTTCAGTTTCATGCTT 59.964 45.455 0.00 0.00 0.00 3.91
2352 17384 1.340889 TGGCCTGTTTCAGTTTCATGC 59.659 47.619 3.32 0.00 0.00 4.06
2353 17385 2.608752 GCTGGCCTGTTTCAGTTTCATG 60.609 50.000 11.69 0.00 33.81 3.07
2355 17387 1.032014 GCTGGCCTGTTTCAGTTTCA 58.968 50.000 11.69 0.00 33.81 2.69
2356 17388 0.040067 CGCTGGCCTGTTTCAGTTTC 60.040 55.000 11.69 0.00 33.81 2.78
2357 17389 0.465460 TCGCTGGCCTGTTTCAGTTT 60.465 50.000 11.69 0.00 33.81 2.66
2360 17392 0.957395 ACATCGCTGGCCTGTTTCAG 60.957 55.000 11.69 0.00 0.00 3.02
2361 17393 0.537143 AACATCGCTGGCCTGTTTCA 60.537 50.000 11.69 0.00 29.06 2.69
2362 17394 0.109597 CAACATCGCTGGCCTGTTTC 60.110 55.000 11.69 0.00 30.99 2.78
2364 17396 1.228245 ACAACATCGCTGGCCTGTT 60.228 52.632 11.69 6.49 33.55 3.16
2366 17398 1.236616 TTCACAACATCGCTGGCCTG 61.237 55.000 3.32 4.26 0.00 4.85
2368 17400 0.955428 TCTTCACAACATCGCTGGCC 60.955 55.000 0.00 0.00 0.00 5.36
2369 17401 0.445436 CTCTTCACAACATCGCTGGC 59.555 55.000 0.00 0.00 0.00 4.85
2370 17402 1.462283 CACTCTTCACAACATCGCTGG 59.538 52.381 0.00 0.00 0.00 4.85
2372 17404 1.151668 GCACTCTTCACAACATCGCT 58.848 50.000 0.00 0.00 0.00 4.93
2374 17406 3.607422 TTTGCACTCTTCACAACATCG 57.393 42.857 0.00 0.00 0.00 3.84
2375 17407 5.522456 TCATTTTGCACTCTTCACAACATC 58.478 37.500 0.00 0.00 0.00 3.06
2376 17408 5.518848 TCATTTTGCACTCTTCACAACAT 57.481 34.783 0.00 0.00 0.00 2.71
2377 17409 4.979943 TCATTTTGCACTCTTCACAACA 57.020 36.364 0.00 0.00 0.00 3.33
2378 17410 5.522456 TGATCATTTTGCACTCTTCACAAC 58.478 37.500 0.00 0.00 0.00 3.32
2380 17412 5.242171 ACATGATCATTTTGCACTCTTCACA 59.758 36.000 5.16 0.00 0.00 3.58
2381 17413 5.571741 CACATGATCATTTTGCACTCTTCAC 59.428 40.000 5.16 0.00 0.00 3.18
2382 17414 5.474189 TCACATGATCATTTTGCACTCTTCA 59.526 36.000 5.16 0.00 0.00 3.02
2383 17415 5.946298 TCACATGATCATTTTGCACTCTTC 58.054 37.500 5.16 0.00 0.00 2.87
2384 17416 5.105877 CCTCACATGATCATTTTGCACTCTT 60.106 40.000 5.16 0.00 0.00 2.85
2391 17423 5.100259 GCTCAACCTCACATGATCATTTTG 58.900 41.667 5.16 6.60 0.00 2.44
2398 17430 0.745845 GGCGCTCAACCTCACATGAT 60.746 55.000 7.64 0.00 0.00 2.45
2401 17433 1.376424 CTGGCGCTCAACCTCACAT 60.376 57.895 7.64 0.00 0.00 3.21
2414 17446 1.213537 CTTTGTCCATTGGCTGGCG 59.786 57.895 0.00 0.00 45.52 5.69
2415 17447 1.593265 CCTTTGTCCATTGGCTGGC 59.407 57.895 0.00 0.00 45.52 4.85
2446 17482 1.066430 GTTCCAGGTTGTGCTATCGGA 60.066 52.381 0.00 0.00 0.00 4.55
2448 17484 2.093306 TGTTCCAGGTTGTGCTATCG 57.907 50.000 0.00 0.00 0.00 2.92
2493 17539 1.758592 GAGGGTGTGGTTGGTGCTA 59.241 57.895 0.00 0.00 0.00 3.49
2569 17620 2.488153 GACTAACCCGCTTCATGCTTTT 59.512 45.455 0.00 0.00 40.11 2.27
2628 17714 8.251026 ACGAGGATCAGTTTTTCTTTTCTTTTT 58.749 29.630 0.00 0.00 33.17 1.94
2629 17715 7.702348 CACGAGGATCAGTTTTTCTTTTCTTTT 59.298 33.333 0.00 0.00 33.17 2.27
2630 17716 7.148069 ACACGAGGATCAGTTTTTCTTTTCTTT 60.148 33.333 0.00 0.00 33.17 2.52
2631 17717 6.318900 ACACGAGGATCAGTTTTTCTTTTCTT 59.681 34.615 0.00 0.00 33.17 2.52
2632 17718 5.823045 ACACGAGGATCAGTTTTTCTTTTCT 59.177 36.000 0.00 0.00 33.17 2.52
2633 17719 5.909610 CACACGAGGATCAGTTTTTCTTTTC 59.090 40.000 0.00 0.00 33.17 2.29
2634 17720 5.357032 ACACACGAGGATCAGTTTTTCTTTT 59.643 36.000 0.00 0.00 33.17 2.27
2635 17721 4.881850 ACACACGAGGATCAGTTTTTCTTT 59.118 37.500 0.00 0.00 33.17 2.52
2636 17722 4.273480 CACACACGAGGATCAGTTTTTCTT 59.727 41.667 0.00 0.00 33.17 2.52
2637 17723 3.809832 CACACACGAGGATCAGTTTTTCT 59.190 43.478 0.00 0.00 33.17 2.52
2638 17724 3.807622 TCACACACGAGGATCAGTTTTTC 59.192 43.478 0.00 0.00 33.17 2.29
2639 17725 3.804036 TCACACACGAGGATCAGTTTTT 58.196 40.909 0.00 0.00 33.17 1.94
2711 17801 8.144478 TCTGCTGTCATCTTATAGTTTCATACC 58.856 37.037 0.00 0.00 0.00 2.73
2778 17869 3.648067 AGGAATCTTGGTCAGTTGAGTCA 59.352 43.478 0.00 0.00 0.00 3.41
2783 17874 6.093219 CAGACAATAGGAATCTTGGTCAGTTG 59.907 42.308 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.