Multiple sequence alignment - TraesCS1B01G325900

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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 TraesCS1B01G325900 chr1B 100.000 2792 0 0 1 2792 551240019 551237228 0.000000e+00 5156
1 TraesCS1B01G325900 chr1B 92.683 205 13 2 1816 2018 109484336 109484540 7.560000e-76 294
2 TraesCS1B01G325900 chr7A 94.794 1556 60 6 1 1536 542716445 542717999 0.000000e+00 2405
3 TraesCS1B01G325900 chr7A 93.115 1438 69 4 1 1421 660573919 660575343 0.000000e+00 2080
4 TraesCS1B01G325900 chr7A 92.308 208 12 2 1816 2019 195283659 195283452 2.720000e-75 292
5 TraesCS1B01G325900 chr7A 94.857 175 9 0 1537 1711 542718051 542718225 9.850000e-70 274
6 TraesCS1B01G325900 chr7A 93.333 105 7 0 1710 1814 16001670 16001566 3.720000e-34 156
7 TraesCS1B01G325900 chr1A 94.666 1556 62 6 1 1536 564158135 564156581 0.000000e+00 2394
8 TraesCS1B01G325900 chr1A 94.944 178 9 0 1537 1714 564156529 564156352 2.120000e-71 279
9 TraesCS1B01G325900 chr3A 94.473 1556 64 5 1 1536 144699561 144701114 0.000000e+00 2377
10 TraesCS1B01G325900 chr3A 94.101 1085 47 7 1 1071 352472157 352473238 0.000000e+00 1633
11 TraesCS1B01G325900 chr3A 96.000 175 7 0 1537 1711 126054764 126054938 4.550000e-73 285
12 TraesCS1B01G325900 chr4B 94.462 1553 65 6 2 1534 167376856 167375305 0.000000e+00 2372
13 TraesCS1B01G325900 chr4B 89.498 1076 77 15 1 1051 595722813 595721749 0.000000e+00 1328
14 TraesCS1B01G325900 chr4B 95.429 175 8 0 1537 1711 273961028 273961202 2.120000e-71 279
15 TraesCS1B01G325900 chr3B 94.344 1556 66 7 1 1536 228016664 228018217 0.000000e+00 2366
16 TraesCS1B01G325900 chr3B 90.205 439 32 7 2360 2792 18501082 18501515 1.880000e-156 562
17 TraesCS1B01G325900 chr3B 90.367 436 31 7 2363 2792 558498485 558498055 1.880000e-156 562
18 TraesCS1B01G325900 chr3B 88.988 336 31 6 2015 2348 18500702 18501033 7.200000e-111 411
19 TraesCS1B01G325900 chr3B 88.690 336 32 6 2015 2348 558498868 558498537 3.350000e-109 405
20 TraesCS1B01G325900 chr3B 91.589 214 14 2 1809 2018 140996265 140996478 2.720000e-75 292
21 TraesCS1B01G325900 chr4A 94.280 1556 68 6 1 1536 147534094 147532540 0.000000e+00 2361
22 TraesCS1B01G325900 chr4A 94.944 178 9 0 1537 1714 410957949 410957772 2.120000e-71 279
23 TraesCS1B01G325900 chr4A 94.382 178 10 0 1537 1714 147532488 147532311 9.850000e-70 274
24 TraesCS1B01G325900 chr4A 93.396 106 6 1 1710 1814 625546315 625546210 3.720000e-34 156
25 TraesCS1B01G325900 chr4A 93.333 105 6 1 1711 1814 636654177 636654281 1.340000e-33 154
26 TraesCS1B01G325900 chr4A 91.071 112 9 1 1704 1814 465894289 465894400 1.730000e-32 150
27 TraesCS1B01G325900 chr6B 94.023 1556 72 7 1 1536 18467373 18468927 0.000000e+00 2338
28 TraesCS1B01G325900 chr6B 94.199 1086 49 2 1 1073 18462004 18460920 0.000000e+00 1644
29 TraesCS1B01G325900 chr6B 91.514 436 30 4 2360 2792 289527430 289527861 6.660000e-166 593
30 TraesCS1B01G325900 chr6B 91.748 206 14 2 1816 2018 622747812 622748017 1.640000e-72 283
31 TraesCS1B01G325900 chr6B 91.667 204 15 2 1816 2017 41421867 41421664 5.890000e-72 281
32 TraesCS1B01G325900 chr2B 94.023 1556 72 6 1 1536 311908795 311907241 0.000000e+00 2338
33 TraesCS1B01G325900 chr2B 90.160 437 31 7 2363 2792 648357693 648357262 2.430000e-155 558
34 TraesCS1B01G325900 chr2B 88.988 336 31 6 2015 2348 648358076 648357745 7.200000e-111 411
35 TraesCS1B01G325900 chr7B 93.830 1556 74 7 1 1536 660103653 660105206 0.000000e+00 2322
36 TraesCS1B01G325900 chr5D 91.908 1557 95 11 1 1536 34212321 34213867 0.000000e+00 2148
37 TraesCS1B01G325900 chr5D 90.575 435 35 6 2360 2792 72926824 72927254 3.120000e-159 571
38 TraesCS1B01G325900 chr5D 89.759 332 30 4 2015 2345 72926445 72926773 3.320000e-114 422
39 TraesCS1B01G325900 chr6A 93.324 1438 66 6 1 1421 435088487 435087063 0.000000e+00 2097
40 TraesCS1B01G325900 chr6A 94.502 873 35 3 1 860 603907598 603908470 0.000000e+00 1334
41 TraesCS1B01G325900 chr6A 87.265 1115 96 19 18 1098 367764473 367763371 0.000000e+00 1230
42 TraesCS1B01G325900 chr6A 94.857 175 9 0 1537 1711 603926365 603926539 9.850000e-70 274
43 TraesCS1B01G325900 chr6A 93.396 106 6 1 1710 1814 576393141 576393246 3.720000e-34 156
44 TraesCS1B01G325900 chr6A 92.453 106 7 1 1710 1814 576195614 576195719 1.730000e-32 150
45 TraesCS1B01G325900 chr6D 93.789 1272 58 4 285 1536 39064109 39062839 0.000000e+00 1892
46 TraesCS1B01G325900 chr6D 94.382 178 10 0 1537 1714 39062787 39062610 9.850000e-70 274
47 TraesCS1B01G325900 chr5A 88.428 1132 84 21 1 1098 115995543 115994425 0.000000e+00 1321
48 TraesCS1B01G325900 chr5A 84.486 535 57 18 2015 2539 685589421 685589939 3.210000e-139 505
49 TraesCS1B01G325900 chr5A 92.308 208 12 2 1816 2019 314674244 314674037 2.720000e-75 292
50 TraesCS1B01G325900 chr5A 92.453 106 7 1 1710 1814 664849491 664849596 1.730000e-32 150
51 TraesCS1B01G325900 chr3D 88.428 1132 83 18 1 1098 376076276 376075159 0.000000e+00 1321
52 TraesCS1B01G325900 chrUn 96.401 778 25 3 2016 2792 51237365 51236590 0.000000e+00 1279
53 TraesCS1B01G325900 chrUn 96.620 503 14 3 2016 2517 51191503 51191003 0.000000e+00 832
54 TraesCS1B01G325900 chrUn 96.620 503 14 3 2016 2517 51330257 51330757 0.000000e+00 832
55 TraesCS1B01G325900 chrUn 95.673 208 8 1 1812 2018 51192065 51191858 1.600000e-87 333
56 TraesCS1B01G325900 chrUn 95.673 208 8 1 1812 2018 51237927 51237720 1.600000e-87 333
57 TraesCS1B01G325900 chrUn 95.673 208 8 1 1812 2018 51329695 51329902 1.600000e-87 333
58 TraesCS1B01G325900 chrUn 91.632 239 12 6 2558 2792 87714807 87714573 9.650000e-85 324
59 TraesCS1B01G325900 chr4D 80.030 1332 192 44 1 1288 410307762 410309063 0.000000e+00 918
60 TraesCS1B01G325900 chr4D 87.271 817 55 31 2015 2792 456043156 456043962 0.000000e+00 887
61 TraesCS1B01G325900 chr4D 79.328 1340 193 43 1 1288 132437082 132435775 0.000000e+00 863
62 TraesCS1B01G325900 chr4D 79.558 181 21 13 2174 2345 31653302 31653475 6.320000e-22 115
63 TraesCS1B01G325900 chr1D 81.356 1062 152 21 4 1023 432577233 432578290 0.000000e+00 822
64 TraesCS1B01G325900 chr2D 90.152 528 39 4 1 515 13520535 13520008 0.000000e+00 675
65 TraesCS1B01G325900 chr2D 91.475 434 26 9 2363 2792 354381530 354381104 1.110000e-163 586
66 TraesCS1B01G325900 chr2D 95.280 339 16 0 1 339 618322678 618322340 3.160000e-149 538
67 TraesCS1B01G325900 chr2D 94.944 178 9 0 1537 1714 618321307 618321130 2.120000e-71 279
68 TraesCS1B01G325900 chr2D 93.396 106 6 1 1710 1814 516440355 516440250 3.720000e-34 156
69 TraesCS1B01G325900 chr2A 94.175 103 5 1 1713 1814 448553074 448553176 3.720000e-34 156


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 TraesCS1B01G325900 chr1B 551237228 551240019 2791 True 5156.0 5156 100.0000 1 2792 1 chr1B.!!$R1 2791
1 TraesCS1B01G325900 chr7A 660573919 660575343 1424 False 2080.0 2080 93.1150 1 1421 1 chr7A.!!$F1 1420
2 TraesCS1B01G325900 chr7A 542716445 542718225 1780 False 1339.5 2405 94.8255 1 1711 2 chr7A.!!$F2 1710
3 TraesCS1B01G325900 chr1A 564156352 564158135 1783 True 1336.5 2394 94.8050 1 1714 2 chr1A.!!$R1 1713
4 TraesCS1B01G325900 chr3A 144699561 144701114 1553 False 2377.0 2377 94.4730 1 1536 1 chr3A.!!$F2 1535
5 TraesCS1B01G325900 chr3A 352472157 352473238 1081 False 1633.0 1633 94.1010 1 1071 1 chr3A.!!$F3 1070
6 TraesCS1B01G325900 chr4B 167375305 167376856 1551 True 2372.0 2372 94.4620 2 1534 1 chr4B.!!$R1 1532
7 TraesCS1B01G325900 chr4B 595721749 595722813 1064 True 1328.0 1328 89.4980 1 1051 1 chr4B.!!$R2 1050
8 TraesCS1B01G325900 chr3B 228016664 228018217 1553 False 2366.0 2366 94.3440 1 1536 1 chr3B.!!$F2 1535
9 TraesCS1B01G325900 chr3B 18500702 18501515 813 False 486.5 562 89.5965 2015 2792 2 chr3B.!!$F3 777
10 TraesCS1B01G325900 chr3B 558498055 558498868 813 True 483.5 562 89.5285 2015 2792 2 chr3B.!!$R1 777
11 TraesCS1B01G325900 chr4A 147532311 147534094 1783 True 1317.5 2361 94.3310 1 1714 2 chr4A.!!$R3 1713
12 TraesCS1B01G325900 chr6B 18467373 18468927 1554 False 2338.0 2338 94.0230 1 1536 1 chr6B.!!$F1 1535
13 TraesCS1B01G325900 chr6B 18460920 18462004 1084 True 1644.0 1644 94.1990 1 1073 1 chr6B.!!$R1 1072
14 TraesCS1B01G325900 chr2B 311907241 311908795 1554 True 2338.0 2338 94.0230 1 1536 1 chr2B.!!$R1 1535
15 TraesCS1B01G325900 chr2B 648357262 648358076 814 True 484.5 558 89.5740 2015 2792 2 chr2B.!!$R2 777
16 TraesCS1B01G325900 chr7B 660103653 660105206 1553 False 2322.0 2322 93.8300 1 1536 1 chr7B.!!$F1 1535
17 TraesCS1B01G325900 chr5D 34212321 34213867 1546 False 2148.0 2148 91.9080 1 1536 1 chr5D.!!$F1 1535
18 TraesCS1B01G325900 chr5D 72926445 72927254 809 False 496.5 571 90.1670 2015 2792 2 chr5D.!!$F2 777
19 TraesCS1B01G325900 chr6A 435087063 435088487 1424 True 2097.0 2097 93.3240 1 1421 1 chr6A.!!$R2 1420
20 TraesCS1B01G325900 chr6A 603907598 603908470 872 False 1334.0 1334 94.5020 1 860 1 chr6A.!!$F3 859
21 TraesCS1B01G325900 chr6A 367763371 367764473 1102 True 1230.0 1230 87.2650 18 1098 1 chr6A.!!$R1 1080
22 TraesCS1B01G325900 chr6D 39062610 39064109 1499 True 1083.0 1892 94.0855 285 1714 2 chr6D.!!$R1 1429
23 TraesCS1B01G325900 chr5A 115994425 115995543 1118 True 1321.0 1321 88.4280 1 1098 1 chr5A.!!$R1 1097
24 TraesCS1B01G325900 chr5A 685589421 685589939 518 False 505.0 505 84.4860 2015 2539 1 chr5A.!!$F2 524
25 TraesCS1B01G325900 chr3D 376075159 376076276 1117 True 1321.0 1321 88.4280 1 1098 1 chr3D.!!$R1 1097
26 TraesCS1B01G325900 chrUn 51236590 51237927 1337 True 806.0 1279 96.0370 1812 2792 2 chrUn.!!$R3 980
27 TraesCS1B01G325900 chrUn 51191003 51192065 1062 True 582.5 832 96.1465 1812 2517 2 chrUn.!!$R2 705
28 TraesCS1B01G325900 chrUn 51329695 51330757 1062 False 582.5 832 96.1465 1812 2517 2 chrUn.!!$F1 705
29 TraesCS1B01G325900 chr4D 410307762 410309063 1301 False 918.0 918 80.0300 1 1288 1 chr4D.!!$F2 1287
30 TraesCS1B01G325900 chr4D 456043156 456043962 806 False 887.0 887 87.2710 2015 2792 1 chr4D.!!$F3 777
31 TraesCS1B01G325900 chr4D 132435775 132437082 1307 True 863.0 863 79.3280 1 1288 1 chr4D.!!$R1 1287
32 TraesCS1B01G325900 chr1D 432577233 432578290 1057 False 822.0 822 81.3560 4 1023 1 chr1D.!!$F1 1019
33 TraesCS1B01G325900 chr2D 13520008 13520535 527 True 675.0 675 90.1520 1 515 1 chr2D.!!$R1 514
34 TraesCS1B01G325900 chr2D 618321130 618322678 1548 True 408.5 538 95.1120 1 1714 2 chr2D.!!$R4 1713

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
116 118 2.16141 CAGCGGCAACTGCATAACTTAA 59.839 45.455 1.45 0.0 44.36 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2001 0.249398 ACCGGGATTTCGACTTGAGG 59.751 55.0 6.32 0.0 0.0 3.86 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
35 36 4.275781 CCACCTTTGGGTTGCTGT 57.724 55.556 0.00 0.00 44.73 4.40
111 113 3.589579 CCAGCGGCAACTGCATAA 58.410 55.556 1.45 0.00 44.36 1.90
116 118 2.161410 CAGCGGCAACTGCATAACTTAA 59.839 45.455 1.45 0.00 44.36 1.85
168 170 6.015940 GGAGTCAGTTCTCAACAATTTCCAAT 60.016 38.462 0.00 0.00 36.30 3.16
198 200 9.855021 GATTATGTTACAAACAACTTGGCTAAT 57.145 29.630 0.00 0.00 45.86 1.73
259 261 8.156820 TGAACTTGGATGACTTCTTTGATAAGA 58.843 33.333 0.00 0.00 38.61 2.10
343 345 5.163416 GGGTTGATTCTTCCCCACATAATTG 60.163 44.000 5.74 0.00 37.09 2.32
367 369 7.164122 TGAGAAGTTGAATGCAAAGACTAGAT 58.836 34.615 0.00 0.00 35.42 1.98
406 408 4.588951 TGGTAGAAAGCTCAGAAGAAGTCA 59.411 41.667 0.00 0.00 0.00 3.41
437 452 3.767131 ACAACAGCTTTAGGTTTGTGGTT 59.233 39.130 0.00 0.00 31.17 3.67
447 462 7.642082 TTTAGGTTTGTGGTTAACTTGCTTA 57.358 32.000 5.42 0.00 0.00 3.09
494 509 3.149981 GCAAGTTTCTAGCCTTCCTTGT 58.850 45.455 0.00 0.00 33.57 3.16
502 517 5.755409 TCTAGCCTTCCTTGTAAACATGA 57.245 39.130 0.00 0.00 0.00 3.07
703 720 3.744530 GCGGGTAGGCATAAAACTGAGAT 60.745 47.826 0.00 0.00 0.00 2.75
829 846 7.037438 CCAAATGACATTGCTGCTATTTTAGT 58.963 34.615 0.34 0.00 0.00 2.24
936 985 3.763897 GCTCATGTAAAGGACCACCAAAT 59.236 43.478 0.00 0.00 38.94 2.32
992 1050 3.133014 CGAGGATGATGCTCCGGT 58.867 61.111 8.41 0.00 40.46 5.28
1041 1099 1.394917 GCCACTTTACACTCATGCTCG 59.605 52.381 0.00 0.00 0.00 5.03
1108 1185 4.228912 CAAAGCTTGGAACCTACAACTG 57.771 45.455 0.00 0.00 0.00 3.16
1110 1187 1.142870 AGCTTGGAACCTACAACTGCA 59.857 47.619 0.00 0.00 0.00 4.41
1310 1395 4.455877 CCAGAGTAGCAAAAAGGTAACCTG 59.544 45.833 0.00 0.00 32.13 4.00
1312 1397 5.531287 CAGAGTAGCAAAAAGGTAACCTGTT 59.469 40.000 0.00 0.00 31.31 3.16
1333 1418 8.755018 CCTGTTGTTGTTTCTGAATTTTATGTC 58.245 33.333 0.00 0.00 0.00 3.06
1556 1695 0.944386 GCACACGAAGCAAAAGGAGA 59.056 50.000 0.00 0.00 0.00 3.71
1619 1758 6.706295 TGGTTCATTTTGGAAACTTTTGAGT 58.294 32.000 0.00 0.00 35.50 3.41
1658 1797 3.291584 TGTGAACATGGGCTTTTGTACA 58.708 40.909 0.00 0.00 0.00 2.90
1667 1806 7.230747 ACATGGGCTTTTGTACATGCTATATA 58.769 34.615 13.23 0.00 43.28 0.86
1683 1822 9.657419 CATGCTATATATGACCTTCATGTGTTA 57.343 33.333 0.00 0.00 37.70 2.41
1711 1850 4.184629 GACATGATGTGAACCTGGACTAC 58.815 47.826 1.23 0.00 0.00 2.73
1714 1853 5.105310 ACATGATGTGAACCTGGACTACTAC 60.105 44.000 0.00 0.00 0.00 2.73
1715 1854 4.673968 TGATGTGAACCTGGACTACTACT 58.326 43.478 0.00 0.00 0.00 2.57
1716 1855 4.705507 TGATGTGAACCTGGACTACTACTC 59.294 45.833 0.00 0.00 0.00 2.59
1717 1856 3.428532 TGTGAACCTGGACTACTACTCC 58.571 50.000 0.00 0.00 0.00 3.85
1718 1857 2.759535 GTGAACCTGGACTACTACTCCC 59.240 54.545 0.00 0.00 0.00 4.30
1719 1858 2.653366 TGAACCTGGACTACTACTCCCT 59.347 50.000 0.00 0.00 0.00 4.20
1720 1859 3.289836 GAACCTGGACTACTACTCCCTC 58.710 54.545 0.00 0.00 0.00 4.30
1721 1860 1.570024 ACCTGGACTACTACTCCCTCC 59.430 57.143 0.00 0.00 0.00 4.30
1722 1861 1.477195 CCTGGACTACTACTCCCTCCG 60.477 61.905 0.00 0.00 0.00 4.63
1723 1862 1.212441 CTGGACTACTACTCCCTCCGT 59.788 57.143 0.00 0.00 0.00 4.69
1724 1863 1.211457 TGGACTACTACTCCCTCCGTC 59.789 57.143 0.00 0.00 0.00 4.79
1725 1864 1.476652 GGACTACTACTCCCTCCGTCC 60.477 61.905 0.00 0.00 33.53 4.79
1726 1865 0.550432 ACTACTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
1727 1866 0.534652 CTACTACTCCCTCCGTCCCG 60.535 65.000 0.00 0.00 0.00 5.14
1728 1867 0.982852 TACTACTCCCTCCGTCCCGA 60.983 60.000 0.00 0.00 0.00 5.14
1729 1868 1.077212 CTACTCCCTCCGTCCCGAA 60.077 63.158 0.00 0.00 0.00 4.30
1730 1869 0.467659 CTACTCCCTCCGTCCCGAAT 60.468 60.000 0.00 0.00 0.00 3.34
1731 1870 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.000 0.00 0.00 0.00 2.17
1732 1871 0.032813 ACTCCCTCCGTCCCGAATTA 60.033 55.000 0.00 0.00 0.00 1.40
1733 1872 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
1734 1873 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.000 0.00 0.00 0.00 2.24
1735 1874 0.828677 CCCTCCGTCCCGAATTACTT 59.171 55.000 0.00 0.00 0.00 2.24
1736 1875 1.472728 CCCTCCGTCCCGAATTACTTG 60.473 57.143 0.00 0.00 0.00 3.16
1737 1876 1.206371 CCTCCGTCCCGAATTACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
1738 1877 2.537401 CTCCGTCCCGAATTACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
1739 1878 1.135315 TCCGTCCCGAATTACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
1740 1879 0.643820 CGTCCCGAATTACTTGTCGC 59.356 55.000 0.00 0.00 35.93 5.19
1741 1880 1.717194 GTCCCGAATTACTTGTCGCA 58.283 50.000 0.00 0.00 35.93 5.10
1742 1881 2.277084 GTCCCGAATTACTTGTCGCAT 58.723 47.619 0.00 0.00 35.93 4.73
1743 1882 2.030457 GTCCCGAATTACTTGTCGCATG 59.970 50.000 0.00 0.00 35.93 4.06
1744 1883 2.006888 CCCGAATTACTTGTCGCATGT 58.993 47.619 0.00 4.39 35.93 3.21
1745 1884 3.119065 TCCCGAATTACTTGTCGCATGTA 60.119 43.478 0.00 2.87 35.93 2.29
1746 1885 3.807622 CCCGAATTACTTGTCGCATGTAT 59.192 43.478 0.00 0.00 35.93 2.29
1747 1886 4.318760 CCCGAATTACTTGTCGCATGTATG 60.319 45.833 0.00 0.00 35.93 2.39
1748 1887 4.318760 CCGAATTACTTGTCGCATGTATGG 60.319 45.833 0.00 4.42 35.93 2.74
1749 1888 4.506288 CGAATTACTTGTCGCATGTATGGA 59.494 41.667 0.00 0.00 0.00 3.41
1750 1889 5.177511 CGAATTACTTGTCGCATGTATGGAT 59.822 40.000 0.00 0.00 0.00 3.41
1751 1890 5.929697 ATTACTTGTCGCATGTATGGATG 57.070 39.130 0.00 0.00 0.00 3.51
1752 1891 3.266510 ACTTGTCGCATGTATGGATGT 57.733 42.857 0.00 0.00 0.00 3.06
1753 1892 4.400529 ACTTGTCGCATGTATGGATGTA 57.599 40.909 0.00 0.00 0.00 2.29
1754 1893 4.960938 ACTTGTCGCATGTATGGATGTAT 58.039 39.130 0.00 0.00 0.00 2.29
1755 1894 4.991056 ACTTGTCGCATGTATGGATGTATC 59.009 41.667 0.00 0.00 0.00 2.24
1756 1895 4.871933 TGTCGCATGTATGGATGTATCT 57.128 40.909 0.00 0.00 0.00 1.98
1757 1896 5.975693 TGTCGCATGTATGGATGTATCTA 57.024 39.130 0.00 0.00 0.00 1.98
1758 1897 6.339587 TGTCGCATGTATGGATGTATCTAA 57.660 37.500 0.00 0.00 0.00 2.10
1759 1898 6.754193 TGTCGCATGTATGGATGTATCTAAA 58.246 36.000 0.00 0.00 0.00 1.85
1760 1899 7.386059 TGTCGCATGTATGGATGTATCTAAAT 58.614 34.615 0.00 0.00 0.00 1.40
1761 1900 7.331687 TGTCGCATGTATGGATGTATCTAAATG 59.668 37.037 0.00 0.00 0.00 2.32
1762 1901 7.331934 GTCGCATGTATGGATGTATCTAAATGT 59.668 37.037 0.00 0.00 0.00 2.71
1763 1902 8.527810 TCGCATGTATGGATGTATCTAAATGTA 58.472 33.333 0.00 0.00 0.00 2.29
1764 1903 9.317936 CGCATGTATGGATGTATCTAAATGTAT 57.682 33.333 0.00 0.00 0.00 2.29
1789 1928 9.927081 ATTTTAGTTCCAGATACATCCATTTCT 57.073 29.630 0.00 0.00 0.00 2.52
1793 1932 8.324191 AGTTCCAGATACATCCATTTCTAAGA 57.676 34.615 0.00 0.00 0.00 2.10
1794 1933 8.207545 AGTTCCAGATACATCCATTTCTAAGAC 58.792 37.037 0.00 0.00 0.00 3.01
1795 1934 6.749139 TCCAGATACATCCATTTCTAAGACG 58.251 40.000 0.00 0.00 0.00 4.18
1796 1935 6.549736 TCCAGATACATCCATTTCTAAGACGA 59.450 38.462 0.00 0.00 0.00 4.20
1797 1936 6.865726 CCAGATACATCCATTTCTAAGACGAG 59.134 42.308 0.00 0.00 0.00 4.18
1798 1937 7.429633 CAGATACATCCATTTCTAAGACGAGT 58.570 38.462 0.00 0.00 0.00 4.18
1799 1938 8.568794 CAGATACATCCATTTCTAAGACGAGTA 58.431 37.037 0.00 0.00 0.00 2.59
1800 1939 9.132923 AGATACATCCATTTCTAAGACGAGTAA 57.867 33.333 0.00 0.00 0.00 2.24
1801 1940 9.915629 GATACATCCATTTCTAAGACGAGTAAT 57.084 33.333 0.00 0.00 0.00 1.89
1804 1943 8.883731 ACATCCATTTCTAAGACGAGTAATTTG 58.116 33.333 0.00 0.00 0.00 2.32
1805 1944 7.843490 TCCATTTCTAAGACGAGTAATTTGG 57.157 36.000 0.00 0.00 0.00 3.28
1806 1945 7.617225 TCCATTTCTAAGACGAGTAATTTGGA 58.383 34.615 0.00 0.00 0.00 3.53
1807 1946 8.098286 TCCATTTCTAAGACGAGTAATTTGGAA 58.902 33.333 0.00 0.00 0.00 3.53
1808 1947 8.893727 CCATTTCTAAGACGAGTAATTTGGAAT 58.106 33.333 0.00 0.00 0.00 3.01
1809 1948 9.708222 CATTTCTAAGACGAGTAATTTGGAATG 57.292 33.333 0.00 0.00 0.00 2.67
1810 1949 7.843490 TTCTAAGACGAGTAATTTGGAATGG 57.157 36.000 0.00 0.00 0.00 3.16
1811 1950 6.346096 TCTAAGACGAGTAATTTGGAATGGG 58.654 40.000 0.00 0.00 0.00 4.00
1812 1951 3.886123 AGACGAGTAATTTGGAATGGGG 58.114 45.455 0.00 0.00 0.00 4.96
1813 1952 2.949644 GACGAGTAATTTGGAATGGGGG 59.050 50.000 0.00 0.00 0.00 5.40
1814 1953 1.681264 CGAGTAATTTGGAATGGGGGC 59.319 52.381 0.00 0.00 0.00 5.80
1815 1954 2.745968 GAGTAATTTGGAATGGGGGCA 58.254 47.619 0.00 0.00 0.00 5.36
1816 1955 3.103742 GAGTAATTTGGAATGGGGGCAA 58.896 45.455 0.00 0.00 0.00 4.52
1817 1956 3.517500 GAGTAATTTGGAATGGGGGCAAA 59.482 43.478 0.00 0.00 0.00 3.68
1834 1973 4.314961 GGCAAAGTCCATTTTAAACCCTG 58.685 43.478 0.00 0.00 0.00 4.45
1835 1974 4.039852 GGCAAAGTCCATTTTAAACCCTGA 59.960 41.667 0.00 0.00 0.00 3.86
1846 1985 2.719426 AAACCCTGAACTCGTAGACG 57.281 50.000 0.00 0.00 41.45 4.18
2148 2644 7.438459 ACACAGCGAATACTTTTCTGATATACC 59.562 37.037 0.00 0.00 0.00 2.73
2269 2766 6.503524 ACTGACACACCATTTTTGTGATTAC 58.496 36.000 9.38 0.00 46.18 1.89
2287 2786 8.285776 GTGATTACTCACTGAAAAATTTGTGG 57.714 34.615 5.99 1.80 46.84 4.17
2321 2820 8.368668 TGAAAAACCATTTAAATACCCGTTGAT 58.631 29.630 0.00 0.00 0.00 2.57
2603 3147 3.061469 CCGTGCGCTCTTTTAACAAAAAC 60.061 43.478 9.73 0.00 0.00 2.43
2619 3163 2.394930 AAACAAAACAAAAGCGGGCT 57.605 40.000 0.00 0.00 0.00 5.19
2751 3297 1.499007 AGTAATCCCGGCCATCCAAAT 59.501 47.619 2.24 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 113 2.567615 CCTAGTGTGCCACCTCTTAAGT 59.432 50.000 1.63 0.00 34.49 2.24
116 118 0.687354 CAACCTAGTGTGCCACCTCT 59.313 55.000 0.00 0.00 34.49 3.69
168 170 7.429633 CCAAGTTGTTTGTAACATAATCCACA 58.570 34.615 1.45 0.00 41.79 4.17
198 200 7.041107 GGTGCTTAATCCAATTATTGAAGCAA 58.959 34.615 23.71 12.01 36.91 3.91
343 345 7.608308 ATCTAGTCTTTGCATTCAACTTCTC 57.392 36.000 0.00 0.00 30.75 2.87
367 369 7.392393 GCTTTCTACCACCTCCAAGTTTAATTA 59.608 37.037 0.00 0.00 0.00 1.40
406 408 4.130118 CCTAAAGCTGTTGTCACTTCAGT 58.870 43.478 0.00 0.00 0.00 3.41
447 462 6.205464 CATTGTCTACAAGAACATGTCCTGTT 59.795 38.462 0.00 0.00 43.12 3.16
703 720 3.965379 TCTCACCGCAACCTTTATACA 57.035 42.857 0.00 0.00 0.00 2.29
923 972 2.291605 GCCCTCTTATTTGGTGGTCCTT 60.292 50.000 0.00 0.00 34.23 3.36
936 985 1.440618 TGGTGGTCTTTGCCCTCTTA 58.559 50.000 0.00 0.00 0.00 2.10
992 1050 2.890808 CGGAAAGCACATAGAGGCTA 57.109 50.000 0.00 0.00 40.01 3.93
1141 1218 7.398024 ACTAGTTATCACCTTTTTGATGCTCT 58.602 34.615 0.00 0.00 36.84 4.09
1312 1397 9.814899 AACATGACATAAAATTCAGAAACAACA 57.185 25.926 0.00 0.00 0.00 3.33
1644 1783 8.108999 TCATATATAGCATGTACAAAAGCCCAT 58.891 33.333 0.00 4.32 0.00 4.00
1667 1806 8.806429 TGTCAAATATAACACATGAAGGTCAT 57.194 30.769 0.00 0.00 37.65 3.06
1683 1822 6.319658 GTCCAGGTTCACATCATGTCAAATAT 59.680 38.462 0.00 0.00 0.00 1.28
1722 1861 1.717194 TGCGACAAGTAATTCGGGAC 58.283 50.000 0.00 0.00 35.73 4.46
1723 1862 2.276201 CATGCGACAAGTAATTCGGGA 58.724 47.619 0.00 0.00 35.73 5.14
1724 1863 2.006888 ACATGCGACAAGTAATTCGGG 58.993 47.619 0.00 0.00 35.73 5.14
1725 1864 4.318760 CCATACATGCGACAAGTAATTCGG 60.319 45.833 0.00 0.00 35.73 4.30
1726 1865 4.506288 TCCATACATGCGACAAGTAATTCG 59.494 41.667 0.00 0.00 38.31 3.34
1727 1866 5.984233 TCCATACATGCGACAAGTAATTC 57.016 39.130 0.00 0.00 0.00 2.17
1728 1867 5.822519 ACATCCATACATGCGACAAGTAATT 59.177 36.000 0.00 0.00 0.00 1.40
1729 1868 5.368145 ACATCCATACATGCGACAAGTAAT 58.632 37.500 0.00 0.00 0.00 1.89
1730 1869 4.765273 ACATCCATACATGCGACAAGTAA 58.235 39.130 0.00 0.00 0.00 2.24
1731 1870 4.400529 ACATCCATACATGCGACAAGTA 57.599 40.909 0.00 0.00 0.00 2.24
1732 1871 3.266510 ACATCCATACATGCGACAAGT 57.733 42.857 0.00 0.00 0.00 3.16
1733 1872 5.233225 AGATACATCCATACATGCGACAAG 58.767 41.667 0.00 0.00 0.00 3.16
1734 1873 5.213891 AGATACATCCATACATGCGACAA 57.786 39.130 0.00 0.00 0.00 3.18
1735 1874 4.871933 AGATACATCCATACATGCGACA 57.128 40.909 0.00 0.00 0.00 4.35
1736 1875 7.331934 ACATTTAGATACATCCATACATGCGAC 59.668 37.037 0.00 0.00 0.00 5.19
1737 1876 7.386059 ACATTTAGATACATCCATACATGCGA 58.614 34.615 0.00 0.00 0.00 5.10
1738 1877 7.601073 ACATTTAGATACATCCATACATGCG 57.399 36.000 0.00 0.00 0.00 4.73
1763 1902 9.927081 AGAAATGGATGTATCTGGAACTAAAAT 57.073 29.630 0.00 0.00 0.00 1.82
1767 1906 9.434275 TCTTAGAAATGGATGTATCTGGAACTA 57.566 33.333 0.00 0.00 0.00 2.24
1768 1907 8.207545 GTCTTAGAAATGGATGTATCTGGAACT 58.792 37.037 0.00 0.00 0.00 3.01
1769 1908 7.169982 CGTCTTAGAAATGGATGTATCTGGAAC 59.830 40.741 0.00 0.00 0.00 3.62
1770 1909 7.069455 TCGTCTTAGAAATGGATGTATCTGGAA 59.931 37.037 0.00 0.00 0.00 3.53
1771 1910 6.549736 TCGTCTTAGAAATGGATGTATCTGGA 59.450 38.462 0.00 0.00 0.00 3.86
1772 1911 6.749139 TCGTCTTAGAAATGGATGTATCTGG 58.251 40.000 0.00 0.00 0.00 3.86
1773 1912 7.429633 ACTCGTCTTAGAAATGGATGTATCTG 58.570 38.462 0.00 0.00 0.00 2.90
1774 1913 7.589958 ACTCGTCTTAGAAATGGATGTATCT 57.410 36.000 0.00 0.00 0.00 1.98
1775 1914 9.915629 ATTACTCGTCTTAGAAATGGATGTATC 57.084 33.333 0.00 0.00 0.00 2.24
1778 1917 8.883731 CAAATTACTCGTCTTAGAAATGGATGT 58.116 33.333 0.00 0.00 0.00 3.06
1779 1918 8.338259 CCAAATTACTCGTCTTAGAAATGGATG 58.662 37.037 0.00 0.00 0.00 3.51
1780 1919 8.265055 TCCAAATTACTCGTCTTAGAAATGGAT 58.735 33.333 0.00 0.00 0.00 3.41
1781 1920 7.617225 TCCAAATTACTCGTCTTAGAAATGGA 58.383 34.615 0.00 0.00 0.00 3.41
1782 1921 7.843490 TCCAAATTACTCGTCTTAGAAATGG 57.157 36.000 0.00 0.00 0.00 3.16
1783 1922 9.708222 CATTCCAAATTACTCGTCTTAGAAATG 57.292 33.333 0.00 0.00 0.00 2.32
1784 1923 8.893727 CCATTCCAAATTACTCGTCTTAGAAAT 58.106 33.333 0.00 0.00 0.00 2.17
1785 1924 7.335924 CCCATTCCAAATTACTCGTCTTAGAAA 59.664 37.037 0.00 0.00 0.00 2.52
1786 1925 6.821665 CCCATTCCAAATTACTCGTCTTAGAA 59.178 38.462 0.00 0.00 0.00 2.10
1787 1926 6.346096 CCCATTCCAAATTACTCGTCTTAGA 58.654 40.000 0.00 0.00 0.00 2.10
1788 1927 5.527582 CCCCATTCCAAATTACTCGTCTTAG 59.472 44.000 0.00 0.00 0.00 2.18
1789 1928 5.433526 CCCCATTCCAAATTACTCGTCTTA 58.566 41.667 0.00 0.00 0.00 2.10
1790 1929 4.270008 CCCCATTCCAAATTACTCGTCTT 58.730 43.478 0.00 0.00 0.00 3.01
1791 1930 3.371595 CCCCCATTCCAAATTACTCGTCT 60.372 47.826 0.00 0.00 0.00 4.18
1792 1931 2.949644 CCCCCATTCCAAATTACTCGTC 59.050 50.000 0.00 0.00 0.00 4.20
1793 1932 2.948600 GCCCCCATTCCAAATTACTCGT 60.949 50.000 0.00 0.00 0.00 4.18
1794 1933 1.681264 GCCCCCATTCCAAATTACTCG 59.319 52.381 0.00 0.00 0.00 4.18
1795 1934 2.745968 TGCCCCCATTCCAAATTACTC 58.254 47.619 0.00 0.00 0.00 2.59
1796 1935 2.938428 TGCCCCCATTCCAAATTACT 57.062 45.000 0.00 0.00 0.00 2.24
1797 1936 3.263170 ACTTTGCCCCCATTCCAAATTAC 59.737 43.478 0.00 0.00 0.00 1.89
1798 1937 3.517500 GACTTTGCCCCCATTCCAAATTA 59.482 43.478 0.00 0.00 0.00 1.40
1799 1938 2.305635 GACTTTGCCCCCATTCCAAATT 59.694 45.455 0.00 0.00 0.00 1.82
1800 1939 1.908619 GACTTTGCCCCCATTCCAAAT 59.091 47.619 0.00 0.00 0.00 2.32
1801 1940 1.347062 GACTTTGCCCCCATTCCAAA 58.653 50.000 0.00 0.00 0.00 3.28
1802 1941 0.544120 GGACTTTGCCCCCATTCCAA 60.544 55.000 0.00 0.00 0.00 3.53
1803 1942 1.078347 GGACTTTGCCCCCATTCCA 59.922 57.895 0.00 0.00 0.00 3.53
1804 1943 0.325577 ATGGACTTTGCCCCCATTCC 60.326 55.000 0.00 0.00 37.39 3.01
1805 1944 1.571955 AATGGACTTTGCCCCCATTC 58.428 50.000 0.00 0.00 44.77 2.67
1806 1945 3.813611 AATGGACTTTGCCCCCATT 57.186 47.368 0.00 0.00 43.62 3.16
1807 1946 2.043307 AAAATGGACTTTGCCCCCAT 57.957 45.000 0.00 0.00 42.08 4.00
1808 1947 2.704190 TAAAATGGACTTTGCCCCCA 57.296 45.000 0.00 0.00 0.00 4.96
1809 1948 3.558321 GGTTTAAAATGGACTTTGCCCCC 60.558 47.826 0.00 0.00 0.00 5.40
1810 1949 3.558321 GGGTTTAAAATGGACTTTGCCCC 60.558 47.826 0.00 0.00 0.00 5.80
1811 1950 3.326588 AGGGTTTAAAATGGACTTTGCCC 59.673 43.478 0.00 0.00 0.00 5.36
1812 1951 4.039852 TCAGGGTTTAAAATGGACTTTGCC 59.960 41.667 0.00 0.00 0.00 4.52
1813 1952 5.208463 TCAGGGTTTAAAATGGACTTTGC 57.792 39.130 0.00 0.00 0.00 3.68
1814 1953 6.816136 AGTTCAGGGTTTAAAATGGACTTTG 58.184 36.000 5.00 0.00 26.44 2.77
1815 1954 6.238925 CGAGTTCAGGGTTTAAAATGGACTTT 60.239 38.462 10.18 0.00 31.56 2.66
1816 1955 5.240844 CGAGTTCAGGGTTTAAAATGGACTT 59.759 40.000 10.18 0.00 31.56 3.01
1817 1956 4.760204 CGAGTTCAGGGTTTAAAATGGACT 59.240 41.667 9.08 9.08 34.14 3.85
1834 1973 1.125021 TCGTCGAACGTCTACGAGTTC 59.875 52.381 9.86 2.88 39.20 3.01
1835 1974 1.139989 TCGTCGAACGTCTACGAGTT 58.860 50.000 9.86 0.00 39.20 3.01
1857 1996 2.000447 GGATTTCGACTTGAGGGTTCG 59.000 52.381 0.00 0.00 0.00 3.95
1862 2001 0.249398 ACCGGGATTTCGACTTGAGG 59.751 55.000 6.32 0.00 0.00 3.86
1944 2083 1.078143 GGCCCACCAGCTAGACAAG 60.078 63.158 0.00 0.00 35.26 3.16
2252 2748 6.969366 TCAGTGAGTAATCACAAAAATGGTG 58.031 36.000 23.89 11.44 42.68 4.17
2269 2766 5.343058 CGCATACCACAAATTTTTCAGTGAG 59.657 40.000 7.71 2.23 33.99 3.51
2280 2779 3.932545 TTTTCAGCGCATACCACAAAT 57.067 38.095 11.47 0.00 0.00 2.32
2287 2786 6.698359 TTTAAATGGTTTTTCAGCGCATAC 57.302 33.333 11.47 0.00 0.00 2.39
2552 3096 2.668212 CATGCGACCCCGTGTTGT 60.668 61.111 0.00 0.00 38.24 3.32
2555 3099 2.358247 GAACATGCGACCCCGTGT 60.358 61.111 0.00 0.00 38.24 4.49
2603 3147 1.498043 GCCAGCCCGCTTTTGTTTTG 61.498 55.000 0.00 0.00 0.00 2.44
2751 3297 5.235516 GGTCTAAATCAAACCTTCGAGTCA 58.764 41.667 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.