Multiple sequence alignment - TraesCS7A01G153300

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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 TraesCS7A01G153300 chr7A 100.000 3391 0 0 1 3391 106677644 106681034 0.000000e+00 6263.0
1 TraesCS7A01G153300 chr7A 98.701 77 1 0 3311 3387 106680880 106680956 1.640000e-28 137.0
2 TraesCS7A01G153300 chr7A 98.701 77 1 0 3237 3313 106680954 106681030 1.640000e-28 137.0
3 TraesCS7A01G153300 chr7A 87.755 49 3 3 2548 2595 547332574 547332528 2.000000e-03 54.7
4 TraesCS7A01G153300 chr7D 94.845 1940 61 14 1402 3313 102538032 102539960 0.000000e+00 2992.0
5 TraesCS7A01G153300 chr7D 97.183 710 19 1 1 709 49766574 49765865 0.000000e+00 1199.0
6 TraesCS7A01G153300 chr7D 95.000 640 17 5 708 1336 102537400 102538035 0.000000e+00 990.0
7 TraesCS7A01G153300 chr7D 95.979 373 15 0 337 709 87772481 87772853 1.040000e-169 606.0
8 TraesCS7A01G153300 chr7D 93.506 77 5 0 3311 3387 102539884 102539960 7.690000e-22 115.0
9 TraesCS7A01G153300 chr7B 96.267 1152 36 5 1402 2552 59742825 59743970 0.000000e+00 1882.0
10 TraesCS7A01G153300 chr7B 94.010 601 25 3 708 1298 59742173 59742772 0.000000e+00 900.0
11 TraesCS7A01G153300 chr4A 98.307 709 12 0 1 709 681232147 681232855 0.000000e+00 1243.0
12 TraesCS7A01G153300 chr6A 97.475 713 18 0 1 713 35134031 35133319 0.000000e+00 1218.0
13 TraesCS7A01G153300 chr6A 94.118 51 3 0 1365 1415 600459430 600459380 1.010000e-10 78.7
14 TraesCS7A01G153300 chr3D 97.461 709 18 0 1 709 544787521 544786813 0.000000e+00 1210.0
15 TraesCS7A01G153300 chr3D 96.053 380 14 1 337 716 141465366 141465744 4.810000e-173 617.0
16 TraesCS7A01G153300 chr3D 87.129 101 11 2 2453 2551 401881894 401881794 2.770000e-21 113.0
17 TraesCS7A01G153300 chr2A 97.179 709 19 1 1 709 314587255 314587962 0.000000e+00 1197.0
18 TraesCS7A01G153300 chr6D 97.174 637 17 1 75 710 54497339 54497975 0.000000e+00 1075.0
19 TraesCS7A01G153300 chr6D 76.296 405 64 17 2442 2821 144066035 144066432 1.610000e-43 187.0
20 TraesCS7A01G153300 chr5D 97.360 606 16 0 105 710 57096501 57095896 0.000000e+00 1031.0
21 TraesCS7A01G153300 chr5D 77.099 393 56 22 2442 2811 195652954 195652573 2.670000e-46 196.0
22 TraesCS7A01G153300 chr5D 100.000 44 0 0 1365 1408 310766871 310766828 7.800000e-12 82.4
23 TraesCS7A01G153300 chr5B 98.035 509 9 1 1 509 502446263 502445756 0.000000e+00 883.0
24 TraesCS7A01G153300 chr5B 89.855 69 7 0 1335 1403 314316407 314316475 4.660000e-14 89.8
25 TraesCS7A01G153300 chr4B 86.319 614 54 18 1858 2443 659052288 659052899 2.850000e-180 641.0
26 TraesCS7A01G153300 chr4B 88.889 441 31 15 1402 1832 659051860 659052292 8.330000e-146 527.0
27 TraesCS7A01G153300 chr4B 90.833 120 10 1 735 853 659004125 659004244 3.500000e-35 159.0
28 TraesCS7A01G153300 chr4B 88.732 71 8 0 1335 1405 381378241 381378311 1.680000e-13 87.9
29 TraesCS7A01G153300 chr1B 89.157 498 41 10 1915 2402 594492620 594492126 2.890000e-170 608.0
30 TraesCS7A01G153300 chr1B 84.096 415 47 12 1479 1883 594493027 594492622 1.910000e-102 383.0
31 TraesCS7A01G153300 chr1B 83.688 141 16 3 761 896 594493541 594493403 3.550000e-25 126.0
32 TraesCS7A01G153300 chr1B 90.244 82 7 1 1335 1415 344044838 344044757 4.630000e-19 106.0
33 TraesCS7A01G153300 chr1B 88.732 71 4 2 1335 1405 17391555 17391621 2.170000e-12 84.2
34 TraesCS7A01G153300 chr1A 87.945 506 40 10 1915 2402 535078980 535078478 8.160000e-161 577.0
35 TraesCS7A01G153300 chr1A 98.382 309 5 0 5 313 25476266 25475958 8.280000e-151 544.0
36 TraesCS7A01G153300 chr1A 85.222 406 48 8 1487 1883 535079384 535078982 1.130000e-109 407.0
37 TraesCS7A01G153300 chr1A 76.794 418 56 23 2442 2836 38740170 38740569 2.670000e-46 196.0
38 TraesCS7A01G153300 chr1A 94.366 71 3 1 1335 1405 552161737 552161668 1.290000e-19 108.0
39 TraesCS7A01G153300 chr1A 97.872 47 0 1 1366 1412 99872661 99872706 2.800000e-11 80.5
40 TraesCS7A01G153300 chr1D 87.352 506 43 10 1915 2402 438582157 438581655 8.220000e-156 560.0
41 TraesCS7A01G153300 chr1D 83.716 479 56 15 1418 1883 438582628 438582159 1.870000e-117 433.0
42 TraesCS7A01G153300 chr1D 85.938 128 12 2 761 883 438583383 438583257 7.630000e-27 132.0
43 TraesCS7A01G153300 chr1D 77.340 203 30 9 2616 2811 113878424 113878617 4.630000e-19 106.0
44 TraesCS7A01G153300 chr2B 81.203 399 44 20 2441 2815 383373965 383374356 3.310000e-75 292.0
45 TraesCS7A01G153300 chr2B 79.688 320 40 10 2442 2739 652599957 652600273 1.230000e-49 207.0
46 TraesCS7A01G153300 chr4D 82.222 270 20 13 835 1089 508644308 508644564 1.230000e-49 207.0
47 TraesCS7A01G153300 chr4D 82.759 203 31 3 1584 1782 508643172 508642970 9.670000e-41 178.0
48 TraesCS7A01G153300 chr4D 74.005 377 68 21 1970 2327 508585862 508586227 3.550000e-25 126.0
49 TraesCS7A01G153300 chr5A 85.714 189 23 4 1596 1781 30215277 30215090 2.670000e-46 196.0
50 TraesCS7A01G153300 chr5A 77.215 395 53 19 2442 2811 232836605 232836223 2.670000e-46 196.0
51 TraesCS7A01G153300 chr5A 81.757 148 23 4 2675 2820 608443311 608443166 1.650000e-23 121.0
52 TraesCS7A01G153300 chr5A 88.235 68 4 4 1365 1429 505504798 505504732 1.010000e-10 78.7
53 TraesCS7A01G153300 chr6B 75.123 406 67 23 2442 2821 88890786 88891183 3.500000e-35 159.0


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 TraesCS7A01G153300 chr7A 106677644 106681034 3390 False 2179.000000 6263 99.134000 1 3391 3 chr7A.!!$F1 3390
1 TraesCS7A01G153300 chr7D 102537400 102539960 2560 False 1365.666667 2992 94.450333 708 3387 3 chr7D.!!$F2 2679
2 TraesCS7A01G153300 chr7D 49765865 49766574 709 True 1199.000000 1199 97.183000 1 709 1 chr7D.!!$R1 708
3 TraesCS7A01G153300 chr7B 59742173 59743970 1797 False 1391.000000 1882 95.138500 708 2552 2 chr7B.!!$F1 1844
4 TraesCS7A01G153300 chr4A 681232147 681232855 708 False 1243.000000 1243 98.307000 1 709 1 chr4A.!!$F1 708
5 TraesCS7A01G153300 chr6A 35133319 35134031 712 True 1218.000000 1218 97.475000 1 713 1 chr6A.!!$R1 712
6 TraesCS7A01G153300 chr3D 544786813 544787521 708 True 1210.000000 1210 97.461000 1 709 1 chr3D.!!$R2 708
7 TraesCS7A01G153300 chr2A 314587255 314587962 707 False 1197.000000 1197 97.179000 1 709 1 chr2A.!!$F1 708
8 TraesCS7A01G153300 chr6D 54497339 54497975 636 False 1075.000000 1075 97.174000 75 710 1 chr6D.!!$F1 635
9 TraesCS7A01G153300 chr5D 57095896 57096501 605 True 1031.000000 1031 97.360000 105 710 1 chr5D.!!$R1 605
10 TraesCS7A01G153300 chr5B 502445756 502446263 507 True 883.000000 883 98.035000 1 509 1 chr5B.!!$R1 508
11 TraesCS7A01G153300 chr4B 659051860 659052899 1039 False 584.000000 641 87.604000 1402 2443 2 chr4B.!!$F3 1041
12 TraesCS7A01G153300 chr1B 594492126 594493541 1415 True 372.333333 608 85.647000 761 2402 3 chr1B.!!$R2 1641
13 TraesCS7A01G153300 chr1A 535078478 535079384 906 True 492.000000 577 86.583500 1487 2402 2 chr1A.!!$R3 915
14 TraesCS7A01G153300 chr1D 438581655 438583383 1728 True 375.000000 560 85.668667 761 2402 3 chr1D.!!$R1 1641

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
288 290 1.962807 CCTCCTCTACCTCAGCATCTG 59.037 57.143 0.00 0.0 0.00 2.90 F
649 652 1.985159 ACAAATGTGCCTAGAGGGTGA 59.015 47.619 0.00 0.0 37.43 4.02 F
1814 2124 2.567985 ACCACCTTAAGTTGTGTTCGG 58.432 47.619 9.97 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 1368 1.318576 CACCCCCTATCCGAAAATGC 58.681 55.0 0.0 0.0 0.00 3.56 R
1994 2323 2.820787 TCCTCTCTTTCTCTTCCACGAC 59.179 50.0 0.0 0.0 0.00 4.34 R
2821 3188 0.254178 ACGGGAAATGCATGAGAGCT 59.746 50.0 0.0 0.0 34.99 4.09 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
99 100 3.404224 TGGTGTTGCGAATGTACCTTA 57.596 42.857 0.00 0.00 32.68 2.69
288 290 1.962807 CCTCCTCTACCTCAGCATCTG 59.037 57.143 0.00 0.00 0.00 2.90
390 393 2.838202 GTGTGGGAAGAGGAGGAACATA 59.162 50.000 0.00 0.00 0.00 2.29
547 550 3.320256 TGTTGTGGTGCATGCAGATTTAA 59.680 39.130 23.41 10.25 0.00 1.52
589 592 3.625649 AAGAGGAGTGGATCAGCTTTC 57.374 47.619 0.00 0.00 0.00 2.62
649 652 1.985159 ACAAATGTGCCTAGAGGGTGA 59.015 47.619 0.00 0.00 37.43 4.02
725 728 4.041815 GGGAGTAGATAAGACCAAATCCCC 59.958 50.000 0.00 0.00 38.33 4.81
1047 1069 8.522830 TCTTGTGTTTATGGAGAAATTTGGATC 58.477 33.333 0.00 0.00 0.00 3.36
1240 1368 6.921307 ACGTTTTTCCAACTAAATAAGCCTTG 59.079 34.615 0.00 0.00 0.00 3.61
1251 1379 5.343307 AAATAAGCCTTGCATTTTCGGAT 57.657 34.783 0.00 0.00 0.00 4.18
1298 1426 9.824534 TGCACTGCATATTTTATTCATTATACG 57.175 29.630 0.00 0.00 31.71 3.06
1299 1427 9.825972 GCACTGCATATTTTATTCATTATACGT 57.174 29.630 0.00 0.00 0.00 3.57
1336 1632 5.178809 CAGCCAGTTTGGTAAAGTGTAGTAC 59.821 44.000 7.97 0.00 40.46 2.73
1337 1633 5.071384 AGCCAGTTTGGTAAAGTGTAGTACT 59.929 40.000 0.00 0.00 40.46 2.73
1338 1634 5.407691 GCCAGTTTGGTAAAGTGTAGTACTC 59.592 44.000 0.00 0.00 40.46 2.59
1339 1635 5.930569 CCAGTTTGGTAAAGTGTAGTACTCC 59.069 44.000 0.00 0.00 39.62 3.85
1340 1636 5.930569 CAGTTTGGTAAAGTGTAGTACTCCC 59.069 44.000 0.00 0.00 39.18 4.30
1341 1637 5.842874 AGTTTGGTAAAGTGTAGTACTCCCT 59.157 40.000 0.00 0.00 39.18 4.20
1342 1638 5.990120 TTGGTAAAGTGTAGTACTCCCTC 57.010 43.478 0.00 0.00 39.18 4.30
1343 1639 4.347607 TGGTAAAGTGTAGTACTCCCTCC 58.652 47.826 0.00 0.43 39.18 4.30
1344 1640 4.202706 TGGTAAAGTGTAGTACTCCCTCCA 60.203 45.833 0.00 2.77 39.18 3.86
1345 1641 4.961099 GGTAAAGTGTAGTACTCCCTCCAT 59.039 45.833 0.00 0.00 39.18 3.41
1346 1642 5.068855 GGTAAAGTGTAGTACTCCCTCCATC 59.931 48.000 0.00 0.00 39.18 3.51
1347 1643 3.315880 AGTGTAGTACTCCCTCCATCC 57.684 52.381 0.00 0.00 33.17 3.51
1348 1644 2.585900 AGTGTAGTACTCCCTCCATCCA 59.414 50.000 0.00 0.00 33.17 3.41
1349 1645 3.012502 AGTGTAGTACTCCCTCCATCCAA 59.987 47.826 0.00 0.00 33.17 3.53
1350 1646 3.773119 GTGTAGTACTCCCTCCATCCAAA 59.227 47.826 0.00 0.00 0.00 3.28
1351 1647 4.224370 GTGTAGTACTCCCTCCATCCAAAA 59.776 45.833 0.00 0.00 0.00 2.44
1352 1648 4.847512 TGTAGTACTCCCTCCATCCAAAAA 59.152 41.667 0.00 0.00 0.00 1.94
1353 1649 5.491078 TGTAGTACTCCCTCCATCCAAAAAT 59.509 40.000 0.00 0.00 0.00 1.82
1354 1650 6.674861 TGTAGTACTCCCTCCATCCAAAAATA 59.325 38.462 0.00 0.00 0.00 1.40
1355 1651 6.848562 AGTACTCCCTCCATCCAAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
1356 1652 7.947782 AGTACTCCCTCCATCCAAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
1357 1653 8.344939 AGTACTCCCTCCATCCAAAAATATAA 57.655 34.615 0.00 0.00 0.00 0.98
1358 1654 8.440771 AGTACTCCCTCCATCCAAAAATATAAG 58.559 37.037 0.00 0.00 0.00 1.73
1359 1655 7.465900 ACTCCCTCCATCCAAAAATATAAGA 57.534 36.000 0.00 0.00 0.00 2.10
1360 1656 7.882755 ACTCCCTCCATCCAAAAATATAAGAA 58.117 34.615 0.00 0.00 0.00 2.52
1361 1657 7.780271 ACTCCCTCCATCCAAAAATATAAGAAC 59.220 37.037 0.00 0.00 0.00 3.01
1362 1658 6.770785 TCCCTCCATCCAAAAATATAAGAACG 59.229 38.462 0.00 0.00 0.00 3.95
1363 1659 6.546034 CCCTCCATCCAAAAATATAAGAACGT 59.454 38.462 0.00 0.00 0.00 3.99
1364 1660 7.068226 CCCTCCATCCAAAAATATAAGAACGTT 59.932 37.037 0.00 0.00 0.00 3.99
1365 1661 9.116067 CCTCCATCCAAAAATATAAGAACGTTA 57.884 33.333 0.00 0.00 0.00 3.18
1367 1663 9.675464 TCCATCCAAAAATATAAGAACGTTAGT 57.325 29.630 0.00 0.00 0.00 2.24
1368 1664 9.716507 CCATCCAAAAATATAAGAACGTTAGTG 57.283 33.333 0.00 0.00 0.00 2.74
1371 1667 9.491675 TCCAAAAATATAAGAACGTTAGTGTCA 57.508 29.630 0.00 0.00 0.00 3.58
1387 1683 9.801714 CGTTAGTGTCAAAAACGTTCTTATATT 57.198 29.630 0.00 0.00 40.69 1.28
1391 1687 8.504005 AGTGTCAAAAACGTTCTTATATTCTGG 58.496 33.333 0.00 0.00 0.00 3.86
1392 1688 7.749126 GTGTCAAAAACGTTCTTATATTCTGGG 59.251 37.037 0.00 0.00 0.00 4.45
1393 1689 7.662258 TGTCAAAAACGTTCTTATATTCTGGGA 59.338 33.333 0.00 0.00 0.00 4.37
1394 1690 7.961283 GTCAAAAACGTTCTTATATTCTGGGAC 59.039 37.037 0.00 0.00 0.00 4.46
1395 1691 7.662258 TCAAAAACGTTCTTATATTCTGGGACA 59.338 33.333 0.00 0.00 0.00 4.02
1413 1709 7.947782 TGGGACAGAGGGAGTAATATAAAAT 57.052 36.000 0.00 0.00 0.00 1.82
1415 1711 8.877195 TGGGACAGAGGGAGTAATATAAAATAC 58.123 37.037 0.00 0.00 0.00 1.89
1416 1712 9.102453 GGGACAGAGGGAGTAATATAAAATACT 57.898 37.037 0.00 0.00 35.13 2.12
1491 1791 3.558505 CTCAACTGCATTGTGCTTACAC 58.441 45.455 3.41 0.00 45.31 2.90
1667 1968 3.465403 CCCCTGAGGAGCTGACGG 61.465 72.222 0.00 0.00 38.24 4.79
1814 2124 2.567985 ACCACCTTAAGTTGTGTTCGG 58.432 47.619 9.97 0.00 0.00 4.30
1911 2222 6.088173 CCTAATTAAGTGTTTTGCGGGTTAC 58.912 40.000 0.00 0.00 0.00 2.50
2032 2361 2.496470 GAGGAACCAAGTCTATGGACGT 59.504 50.000 3.29 0.00 46.29 4.34
2494 2842 9.399797 CACACACCCCTATACGAATATAGTATA 57.600 37.037 0.00 9.35 39.06 1.47
2577 2943 2.971598 CGTGAGGAATGGGTGCCCT 61.972 63.158 8.91 0.00 36.94 5.19
2587 2953 1.080638 TGGGTGCCCTTGGTATTCTT 58.919 50.000 8.91 0.00 36.94 2.52
2696 3063 0.179009 CACGGGCATCCATTCCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
2705 3072 5.221126 GGCATCCATTCCTCATGAAACTAAC 60.221 44.000 0.00 0.00 36.33 2.34
2709 3076 4.701651 CCATTCCTCATGAAACTAACTGCA 59.298 41.667 0.00 0.00 36.33 4.41
2716 3083 4.042311 TCATGAAACTAACTGCAGGGGTAA 59.958 41.667 19.93 4.01 0.00 2.85
2748 3115 7.321908 CAACCATGTTTGATATCACCAAATCA 58.678 34.615 4.48 0.00 36.14 2.57
2811 3178 4.534647 TTCATATAGGGGTTTGTGGCAT 57.465 40.909 0.00 0.00 0.00 4.40
2821 3188 2.355108 GGTTTGTGGCATCTGAGAGCTA 60.355 50.000 0.00 0.00 0.00 3.32
2822 3189 2.935201 GTTTGTGGCATCTGAGAGCTAG 59.065 50.000 0.00 0.00 0.00 3.42
2823 3190 0.463204 TGTGGCATCTGAGAGCTAGC 59.537 55.000 6.62 6.62 0.00 3.42
2824 3191 0.752054 GTGGCATCTGAGAGCTAGCT 59.248 55.000 19.45 19.45 0.00 3.32
2825 3192 1.039068 TGGCATCTGAGAGCTAGCTC 58.961 55.000 33.21 33.21 43.03 4.09
2846 3213 1.543802 TCATGCATTTCCCGTTTGGTC 59.456 47.619 0.00 0.00 34.77 4.02
2879 3246 0.908910 TGGTTCAGGTGTATGGCGAT 59.091 50.000 0.00 0.00 0.00 4.58
2931 3298 1.950015 GCATGTGACATGCAGGGTGTA 60.950 52.381 37.33 0.00 44.00 2.90
2932 3299 2.435422 CATGTGACATGCAGGGTGTAA 58.565 47.619 13.15 0.00 0.00 2.41
3112 3482 2.208872 ACTTGGTGGCCATATTCTCCT 58.791 47.619 9.72 0.00 31.53 3.69
3145 3515 2.100584 GTGCGACCATGAAGAGAGAGAT 59.899 50.000 0.00 0.00 0.00 2.75
3147 3517 3.954258 TGCGACCATGAAGAGAGAGATAA 59.046 43.478 0.00 0.00 0.00 1.75
3148 3518 4.202060 TGCGACCATGAAGAGAGAGATAAC 60.202 45.833 0.00 0.00 0.00 1.89
3149 3519 4.202060 GCGACCATGAAGAGAGAGATAACA 60.202 45.833 0.00 0.00 0.00 2.41
3150 3520 5.508825 GCGACCATGAAGAGAGAGATAACAT 60.509 44.000 0.00 0.00 0.00 2.71
3151 3521 5.919707 CGACCATGAAGAGAGAGATAACATG 59.080 44.000 0.00 0.00 35.11 3.21
3195 3569 9.131791 GTAGGGATTATAGCCATTCAAGAAAAA 57.868 33.333 0.00 0.00 0.00 1.94
3220 3594 3.924114 TTGTAGGGCTTAATGCTGCTA 57.076 42.857 0.00 0.00 42.39 3.49
3224 3598 3.303351 AGGGCTTAATGCTGCTACATT 57.697 42.857 0.00 9.28 42.73 2.71
3235 3609 7.642071 AATGCTGCTACATTTTTGTAAGTTG 57.358 32.000 0.00 0.00 36.91 3.16
3254 3628 0.788391 GTAACGCTTGACGGTCTTGG 59.212 55.000 9.88 0.97 36.55 3.61
3297 3671 7.534085 TTGTAATTTGTGTATCATCTCGTCC 57.466 36.000 0.00 0.00 0.00 4.79
3299 3673 6.533723 TGTAATTTGTGTATCATCTCGTCCAC 59.466 38.462 0.00 0.00 0.00 4.02
3313 3687 3.521560 TCGTCCACTGCAAACATCTATC 58.478 45.455 0.00 0.00 0.00 2.08
3314 3688 2.282555 CGTCCACTGCAAACATCTATCG 59.717 50.000 0.00 0.00 0.00 2.92
3315 3689 2.030946 GTCCACTGCAAACATCTATCGC 59.969 50.000 0.00 0.00 0.00 4.58
3316 3690 2.093500 TCCACTGCAAACATCTATCGCT 60.093 45.455 0.00 0.00 0.00 4.93
3317 3691 2.679837 CCACTGCAAACATCTATCGCTT 59.320 45.455 0.00 0.00 0.00 4.68
3318 3692 3.486375 CCACTGCAAACATCTATCGCTTG 60.486 47.826 0.00 0.00 0.00 4.01
3319 3693 3.371898 CACTGCAAACATCTATCGCTTGA 59.628 43.478 0.00 0.00 0.00 3.02
3320 3694 3.372206 ACTGCAAACATCTATCGCTTGAC 59.628 43.478 0.00 0.00 0.00 3.18
3321 3695 2.348362 TGCAAACATCTATCGCTTGACG 59.652 45.455 0.00 0.00 45.62 4.35
3322 3696 2.285834 GCAAACATCTATCGCTTGACGG 60.286 50.000 0.00 0.00 43.89 4.79
3323 3697 2.930040 CAAACATCTATCGCTTGACGGT 59.070 45.455 0.00 0.00 43.89 4.83
3324 3698 2.493713 ACATCTATCGCTTGACGGTC 57.506 50.000 0.00 0.00 43.89 4.79
3325 3699 2.025155 ACATCTATCGCTTGACGGTCT 58.975 47.619 9.88 0.00 43.89 3.85
3326 3700 2.427453 ACATCTATCGCTTGACGGTCTT 59.573 45.455 9.88 0.00 43.89 3.01
3327 3701 2.561733 TCTATCGCTTGACGGTCTTG 57.438 50.000 9.88 3.38 43.89 3.02
3328 3702 1.134367 TCTATCGCTTGACGGTCTTGG 59.866 52.381 9.88 0.97 43.89 3.61
3329 3703 0.174845 TATCGCTTGACGGTCTTGGG 59.825 55.000 9.88 10.01 43.89 4.12
3330 3704 1.827399 ATCGCTTGACGGTCTTGGGT 61.827 55.000 9.88 0.23 43.89 4.51
3331 3705 1.597027 CGCTTGACGGTCTTGGGTT 60.597 57.895 9.88 0.00 38.44 4.11
3332 3706 1.566018 CGCTTGACGGTCTTGGGTTC 61.566 60.000 9.88 0.00 38.44 3.62
3333 3707 0.534203 GCTTGACGGTCTTGGGTTCA 60.534 55.000 9.88 0.00 0.00 3.18
3334 3708 1.961793 CTTGACGGTCTTGGGTTCAA 58.038 50.000 9.88 0.00 0.00 2.69
3345 3719 4.431661 CTTGGGTTCAAGCATCTCTTTC 57.568 45.455 0.00 0.00 43.10 2.62
3346 3720 3.795688 TGGGTTCAAGCATCTCTTTCT 57.204 42.857 0.00 0.00 31.27 2.52
3347 3721 4.104383 TGGGTTCAAGCATCTCTTTCTT 57.896 40.909 0.00 0.00 31.27 2.52
3348 3722 4.473444 TGGGTTCAAGCATCTCTTTCTTT 58.527 39.130 0.00 0.00 31.27 2.52
3349 3723 4.279169 TGGGTTCAAGCATCTCTTTCTTTG 59.721 41.667 0.00 0.00 31.27 2.77
3350 3724 4.279420 GGGTTCAAGCATCTCTTTCTTTGT 59.721 41.667 0.00 0.00 31.27 2.83
3351 3725 5.473504 GGGTTCAAGCATCTCTTTCTTTGTA 59.526 40.000 0.00 0.00 31.27 2.41
3352 3726 6.016276 GGGTTCAAGCATCTCTTTCTTTGTAA 60.016 38.462 0.00 0.00 31.27 2.41
3353 3727 7.309438 GGGTTCAAGCATCTCTTTCTTTGTAAT 60.309 37.037 0.00 0.00 31.27 1.89
3354 3728 8.084684 GGTTCAAGCATCTCTTTCTTTGTAATT 58.915 33.333 0.00 0.00 31.27 1.40
3355 3729 9.468532 GTTCAAGCATCTCTTTCTTTGTAATTT 57.531 29.630 0.00 0.00 31.27 1.82
3356 3730 9.467258 TTCAAGCATCTCTTTCTTTGTAATTTG 57.533 29.630 0.00 0.00 31.27 2.32
3357 3731 8.632679 TCAAGCATCTCTTTCTTTGTAATTTGT 58.367 29.630 0.00 0.00 31.27 2.83
3358 3732 8.697067 CAAGCATCTCTTTCTTTGTAATTTGTG 58.303 33.333 0.00 0.00 31.27 3.33
3359 3733 7.945134 AGCATCTCTTTCTTTGTAATTTGTGT 58.055 30.769 0.00 0.00 0.00 3.72
3360 3734 9.066892 AGCATCTCTTTCTTTGTAATTTGTGTA 57.933 29.630 0.00 0.00 0.00 2.90
3361 3735 9.846248 GCATCTCTTTCTTTGTAATTTGTGTAT 57.154 29.630 0.00 0.00 0.00 2.29
3369 3743 8.771920 TCTTTGTAATTTGTGTATCATCTCGT 57.228 30.769 0.00 0.00 0.00 4.18
3370 3744 8.869897 TCTTTGTAATTTGTGTATCATCTCGTC 58.130 33.333 0.00 0.00 0.00 4.20
3371 3745 7.534085 TTGTAATTTGTGTATCATCTCGTCC 57.466 36.000 0.00 0.00 0.00 4.79
3372 3746 6.635755 TGTAATTTGTGTATCATCTCGTCCA 58.364 36.000 0.00 0.00 0.00 4.02
3373 3747 6.533723 TGTAATTTGTGTATCATCTCGTCCAC 59.466 38.462 0.00 0.00 0.00 4.02
3374 3748 4.801330 TTTGTGTATCATCTCGTCCACT 57.199 40.909 0.00 0.00 0.00 4.00
3375 3749 3.782889 TGTGTATCATCTCGTCCACTG 57.217 47.619 0.00 0.00 0.00 3.66
3376 3750 2.159240 TGTGTATCATCTCGTCCACTGC 60.159 50.000 0.00 0.00 0.00 4.40
3377 3751 2.099405 TGTATCATCTCGTCCACTGCA 58.901 47.619 0.00 0.00 0.00 4.41
3378 3752 2.495669 TGTATCATCTCGTCCACTGCAA 59.504 45.455 0.00 0.00 0.00 4.08
3379 3753 2.768253 ATCATCTCGTCCACTGCAAA 57.232 45.000 0.00 0.00 0.00 3.68
3380 3754 1.795768 TCATCTCGTCCACTGCAAAC 58.204 50.000 0.00 0.00 0.00 2.93
3381 3755 1.069978 TCATCTCGTCCACTGCAAACA 59.930 47.619 0.00 0.00 0.00 2.83
3382 3756 2.079158 CATCTCGTCCACTGCAAACAT 58.921 47.619 0.00 0.00 0.00 2.71
3383 3757 1.795768 TCTCGTCCACTGCAAACATC 58.204 50.000 0.00 0.00 0.00 3.06
3384 3758 1.344438 TCTCGTCCACTGCAAACATCT 59.656 47.619 0.00 0.00 0.00 2.90
3385 3759 2.560981 TCTCGTCCACTGCAAACATCTA 59.439 45.455 0.00 0.00 0.00 1.98
3386 3760 3.195610 TCTCGTCCACTGCAAACATCTAT 59.804 43.478 0.00 0.00 0.00 1.98
3387 3761 3.935203 CTCGTCCACTGCAAACATCTATT 59.065 43.478 0.00 0.00 0.00 1.73
3388 3762 4.323417 TCGTCCACTGCAAACATCTATTT 58.677 39.130 0.00 0.00 0.00 1.40
3389 3763 5.483811 TCGTCCACTGCAAACATCTATTTA 58.516 37.500 0.00 0.00 0.00 1.40
3390 3764 6.112734 TCGTCCACTGCAAACATCTATTTAT 58.887 36.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 0.252103 TCAAGGTTCTCGGCTAGGGT 60.252 55.000 0.00 0.00 0.00 4.34
390 393 5.854338 CGAAACTTGTATAAAATGGCAACGT 59.146 36.000 0.00 0.00 42.51 3.99
483 486 3.510753 TGCATGCACCACAATTCTAATGT 59.489 39.130 18.46 0.00 0.00 2.71
589 592 1.921887 GTCCATCAATGTTTGCATGCG 59.078 47.619 14.09 0.00 35.15 4.73
649 652 9.898152 TCAAAAACTATTTGTCCCAAAATCTTT 57.102 25.926 1.35 0.00 32.16 2.52
675 678 1.270550 CCAGTTCGCAAGGCAAAATCT 59.729 47.619 0.00 0.00 38.47 2.40
855 868 0.530744 CGGTTGAATCAGAGGGACGA 59.469 55.000 0.00 0.00 0.00 4.20
964 986 1.047596 ACCGCTCCTGCATCAGATCT 61.048 55.000 0.00 0.00 39.64 2.75
1047 1069 6.530181 TGAACAAATAGTGTCTGCATACGTAG 59.470 38.462 0.08 0.00 40.60 3.51
1176 1304 3.359033 CTGGGAGAGCATGGAAAAATCA 58.641 45.455 0.00 0.00 0.00 2.57
1240 1368 1.318576 CACCCCCTATCCGAAAATGC 58.681 55.000 0.00 0.00 0.00 3.56
1298 1426 8.085909 ACCAAACTGGCTGTTATAATGTAAAAC 58.914 33.333 10.29 0.00 42.67 2.43
1299 1427 8.184304 ACCAAACTGGCTGTTATAATGTAAAA 57.816 30.769 10.29 0.00 42.67 1.52
1300 1428 7.768807 ACCAAACTGGCTGTTATAATGTAAA 57.231 32.000 10.29 0.00 42.67 2.01
1336 1632 7.041098 CGTTCTTATATTTTTGGATGGAGGGAG 60.041 40.741 0.00 0.00 0.00 4.30
1337 1633 6.770785 CGTTCTTATATTTTTGGATGGAGGGA 59.229 38.462 0.00 0.00 0.00 4.20
1338 1634 6.546034 ACGTTCTTATATTTTTGGATGGAGGG 59.454 38.462 0.00 0.00 0.00 4.30
1339 1635 7.568199 ACGTTCTTATATTTTTGGATGGAGG 57.432 36.000 0.00 0.00 0.00 4.30
1341 1637 9.675464 ACTAACGTTCTTATATTTTTGGATGGA 57.325 29.630 2.82 0.00 0.00 3.41
1342 1638 9.716507 CACTAACGTTCTTATATTTTTGGATGG 57.283 33.333 2.82 0.00 0.00 3.51
1345 1641 9.491675 TGACACTAACGTTCTTATATTTTTGGA 57.508 29.630 2.82 0.00 0.00 3.53
1351 1647 9.801714 CGTTTTTGACACTAACGTTCTTATATT 57.198 29.630 2.82 0.00 39.64 1.28
1365 1661 8.504005 CCAGAATATAAGAACGTTTTTGACACT 58.496 33.333 13.87 4.79 0.00 3.55
1366 1662 7.749126 CCCAGAATATAAGAACGTTTTTGACAC 59.251 37.037 13.87 2.84 0.00 3.67
1367 1663 7.662258 TCCCAGAATATAAGAACGTTTTTGACA 59.338 33.333 13.87 0.01 0.00 3.58
1368 1664 7.961283 GTCCCAGAATATAAGAACGTTTTTGAC 59.039 37.037 13.87 5.89 0.00 3.18
1369 1665 7.662258 TGTCCCAGAATATAAGAACGTTTTTGA 59.338 33.333 13.87 2.81 0.00 2.69
1370 1666 7.812648 TGTCCCAGAATATAAGAACGTTTTTG 58.187 34.615 13.87 0.00 0.00 2.44
1371 1667 7.881232 TCTGTCCCAGAATATAAGAACGTTTTT 59.119 33.333 9.22 9.22 37.57 1.94
1372 1668 7.391620 TCTGTCCCAGAATATAAGAACGTTTT 58.608 34.615 0.46 0.00 37.57 2.43
1373 1669 6.942976 TCTGTCCCAGAATATAAGAACGTTT 58.057 36.000 0.46 0.00 37.57 3.60
1374 1670 6.407074 CCTCTGTCCCAGAATATAAGAACGTT 60.407 42.308 0.00 0.00 40.18 3.99
1375 1671 5.069251 CCTCTGTCCCAGAATATAAGAACGT 59.931 44.000 0.00 0.00 40.18 3.99
1376 1672 5.509840 CCCTCTGTCCCAGAATATAAGAACG 60.510 48.000 0.00 0.00 40.18 3.95
1377 1673 5.602978 TCCCTCTGTCCCAGAATATAAGAAC 59.397 44.000 0.00 0.00 40.18 3.01
1378 1674 5.788430 TCCCTCTGTCCCAGAATATAAGAA 58.212 41.667 0.00 0.00 40.18 2.52
1379 1675 5.103043 ACTCCCTCTGTCCCAGAATATAAGA 60.103 44.000 0.00 0.00 40.18 2.10
1380 1676 5.151454 ACTCCCTCTGTCCCAGAATATAAG 58.849 45.833 0.00 0.00 40.18 1.73
1381 1677 5.157770 ACTCCCTCTGTCCCAGAATATAA 57.842 43.478 0.00 0.00 40.18 0.98
1382 1678 4.834406 ACTCCCTCTGTCCCAGAATATA 57.166 45.455 0.00 0.00 40.18 0.86
1383 1679 3.715648 ACTCCCTCTGTCCCAGAATAT 57.284 47.619 0.00 0.00 40.18 1.28
1384 1680 4.620086 TTACTCCCTCTGTCCCAGAATA 57.380 45.455 0.00 0.00 40.18 1.75
1385 1681 3.491766 TTACTCCCTCTGTCCCAGAAT 57.508 47.619 0.00 0.00 40.18 2.40
1386 1682 3.491766 ATTACTCCCTCTGTCCCAGAA 57.508 47.619 0.00 0.00 40.18 3.02
1387 1683 4.834406 ATATTACTCCCTCTGTCCCAGA 57.166 45.455 0.00 0.00 38.25 3.86
1388 1684 6.996180 TTTATATTACTCCCTCTGTCCCAG 57.004 41.667 0.00 0.00 0.00 4.45
1389 1685 7.947782 ATTTTATATTACTCCCTCTGTCCCA 57.052 36.000 0.00 0.00 0.00 4.37
1390 1686 9.102453 AGTATTTTATATTACTCCCTCTGTCCC 57.898 37.037 0.00 0.00 0.00 4.46
1425 1721 9.877178 AAGGTATATGACGATTAAGAATGATCC 57.123 33.333 0.00 0.00 0.00 3.36
1491 1791 6.293845 GCATGCATGGAGTAGAGAAATTAAGG 60.294 42.308 27.34 0.00 0.00 2.69
1814 2124 7.443272 ACAGCCGTTTAGTTCCATATAATAACC 59.557 37.037 0.00 0.00 0.00 2.85
1994 2323 2.820787 TCCTCTCTTTCTCTTCCACGAC 59.179 50.000 0.00 0.00 0.00 4.34
2696 3063 4.440826 TTTACCCCTGCAGTTAGTTTCA 57.559 40.909 13.81 0.00 0.00 2.69
2705 3072 0.614415 TGCCCATTTTACCCCTGCAG 60.614 55.000 6.78 6.78 0.00 4.41
2709 3076 0.489567 TGGTTGCCCATTTTACCCCT 59.510 50.000 0.00 0.00 35.17 4.79
2787 3154 6.212840 TGCCACAAACCCCTATATGAATAT 57.787 37.500 0.00 0.00 0.00 1.28
2821 3188 0.254178 ACGGGAAATGCATGAGAGCT 59.746 50.000 0.00 0.00 34.99 4.09
2822 3189 1.098050 AACGGGAAATGCATGAGAGC 58.902 50.000 0.00 0.00 0.00 4.09
2823 3190 2.159338 CCAAACGGGAAATGCATGAGAG 60.159 50.000 0.00 0.00 40.01 3.20
2824 3191 1.818060 CCAAACGGGAAATGCATGAGA 59.182 47.619 0.00 0.00 40.01 3.27
2825 3192 1.545582 ACCAAACGGGAAATGCATGAG 59.454 47.619 0.00 0.00 41.15 2.90
2826 3193 1.543802 GACCAAACGGGAAATGCATGA 59.456 47.619 0.00 0.00 41.15 3.07
2846 3213 7.556844 ACACCTGAACCATATAGTAGACAAAG 58.443 38.462 0.00 0.00 0.00 2.77
2879 3246 7.051623 TCTTGCCACACTCTAAAAAGAACTTA 58.948 34.615 0.00 0.00 0.00 2.24
2931 3298 2.586648 ATGCTTCGGTTCCTTCCTTT 57.413 45.000 0.00 0.00 0.00 3.11
2932 3299 3.054361 ACATATGCTTCGGTTCCTTCCTT 60.054 43.478 1.58 0.00 0.00 3.36
3055 3424 3.626930 GCAAGTCCCAACCCATGTATAA 58.373 45.455 0.00 0.00 0.00 0.98
3147 3517 7.939039 CCTACCAAGTTGATAATATGTCCATGT 59.061 37.037 3.87 0.00 0.00 3.21
3148 3518 7.391554 CCCTACCAAGTTGATAATATGTCCATG 59.608 40.741 3.87 0.00 0.00 3.66
3149 3519 7.294720 TCCCTACCAAGTTGATAATATGTCCAT 59.705 37.037 3.87 0.00 0.00 3.41
3150 3520 6.617784 TCCCTACCAAGTTGATAATATGTCCA 59.382 38.462 3.87 0.00 0.00 4.02
3151 3521 7.074653 TCCCTACCAAGTTGATAATATGTCC 57.925 40.000 3.87 0.00 0.00 4.02
3201 3575 2.503765 TGTAGCAGCATTAAGCCCTACA 59.496 45.455 15.65 15.65 46.96 2.74
3208 3582 8.970691 ACTTACAAAAATGTAGCAGCATTAAG 57.029 30.769 6.25 8.05 38.03 1.85
3220 3594 7.219344 GTCAAGCGTTACAACTTACAAAAATGT 59.781 33.333 0.00 0.00 0.00 2.71
3224 3598 5.257108 CGTCAAGCGTTACAACTTACAAAA 58.743 37.500 0.00 0.00 35.54 2.44
3235 3609 0.788391 CCAAGACCGTCAAGCGTTAC 59.212 55.000 0.40 0.00 39.32 2.50
3254 3628 5.444663 ACAAAGAAAGAGATGCTTGAACC 57.555 39.130 0.00 0.00 36.80 3.62
3293 3667 2.282555 CGATAGATGTTTGCAGTGGACG 59.717 50.000 0.00 0.00 39.76 4.79
3297 3671 3.371898 TCAAGCGATAGATGTTTGCAGTG 59.628 43.478 0.00 0.00 39.76 3.66
3299 3673 3.542875 CGTCAAGCGATAGATGTTTGCAG 60.543 47.826 0.00 0.00 44.77 4.41
3313 3687 1.566018 GAACCCAAGACCGTCAAGCG 61.566 60.000 0.40 0.00 40.95 4.68
3314 3688 0.534203 TGAACCCAAGACCGTCAAGC 60.534 55.000 0.40 0.00 0.00 4.01
3315 3689 1.961793 TTGAACCCAAGACCGTCAAG 58.038 50.000 0.40 0.00 0.00 3.02
3325 3699 4.104383 AGAAAGAGATGCTTGAACCCAA 57.896 40.909 0.00 0.00 36.80 4.12
3326 3700 3.795688 AGAAAGAGATGCTTGAACCCA 57.204 42.857 0.00 0.00 36.80 4.51
3327 3701 4.279420 ACAAAGAAAGAGATGCTTGAACCC 59.721 41.667 0.00 0.00 36.80 4.11
3328 3702 5.444663 ACAAAGAAAGAGATGCTTGAACC 57.555 39.130 0.00 0.00 36.80 3.62
3329 3703 9.468532 AAATTACAAAGAAAGAGATGCTTGAAC 57.531 29.630 0.00 0.00 36.80 3.18
3330 3704 9.467258 CAAATTACAAAGAAAGAGATGCTTGAA 57.533 29.630 0.00 0.00 36.80 2.69
3331 3705 8.632679 ACAAATTACAAAGAAAGAGATGCTTGA 58.367 29.630 0.00 0.00 36.80 3.02
3332 3706 8.697067 CACAAATTACAAAGAAAGAGATGCTTG 58.303 33.333 0.00 0.00 36.80 4.01
3333 3707 8.416329 ACACAAATTACAAAGAAAGAGATGCTT 58.584 29.630 0.00 0.00 38.88 3.91
3334 3708 7.945134 ACACAAATTACAAAGAAAGAGATGCT 58.055 30.769 0.00 0.00 0.00 3.79
3335 3709 9.846248 ATACACAAATTACAAAGAAAGAGATGC 57.154 29.630 0.00 0.00 0.00 3.91
3343 3717 9.214957 ACGAGATGATACACAAATTACAAAGAA 57.785 29.630 0.00 0.00 0.00 2.52
3344 3718 8.771920 ACGAGATGATACACAAATTACAAAGA 57.228 30.769 0.00 0.00 0.00 2.52
3345 3719 8.116753 GGACGAGATGATACACAAATTACAAAG 58.883 37.037 0.00 0.00 0.00 2.77
3346 3720 7.604545 TGGACGAGATGATACACAAATTACAAA 59.395 33.333 0.00 0.00 0.00 2.83
3347 3721 7.064134 GTGGACGAGATGATACACAAATTACAA 59.936 37.037 0.00 0.00 0.00 2.41
3348 3722 6.533723 GTGGACGAGATGATACACAAATTACA 59.466 38.462 0.00 0.00 0.00 2.41
3349 3723 6.757010 AGTGGACGAGATGATACACAAATTAC 59.243 38.462 0.00 0.00 0.00 1.89
3350 3724 6.756542 CAGTGGACGAGATGATACACAAATTA 59.243 38.462 0.00 0.00 0.00 1.40
3351 3725 5.582269 CAGTGGACGAGATGATACACAAATT 59.418 40.000 0.00 0.00 0.00 1.82
3352 3726 5.111989 CAGTGGACGAGATGATACACAAAT 58.888 41.667 0.00 0.00 0.00 2.32
3353 3727 4.494484 CAGTGGACGAGATGATACACAAA 58.506 43.478 0.00 0.00 0.00 2.83
3354 3728 3.676049 GCAGTGGACGAGATGATACACAA 60.676 47.826 0.00 0.00 0.00 3.33
3355 3729 2.159240 GCAGTGGACGAGATGATACACA 60.159 50.000 0.00 0.00 0.00 3.72
3356 3730 2.159240 TGCAGTGGACGAGATGATACAC 60.159 50.000 0.00 0.00 0.00 2.90
3357 3731 2.099405 TGCAGTGGACGAGATGATACA 58.901 47.619 0.00 0.00 0.00 2.29
3358 3732 2.871182 TGCAGTGGACGAGATGATAC 57.129 50.000 0.00 0.00 0.00 2.24
3359 3733 3.056179 TGTTTGCAGTGGACGAGATGATA 60.056 43.478 0.00 0.00 0.00 2.15
3360 3734 2.289631 TGTTTGCAGTGGACGAGATGAT 60.290 45.455 0.00 0.00 0.00 2.45
3361 3735 1.069978 TGTTTGCAGTGGACGAGATGA 59.930 47.619 0.00 0.00 0.00 2.92
3362 3736 1.511850 TGTTTGCAGTGGACGAGATG 58.488 50.000 0.00 0.00 0.00 2.90
3363 3737 2.027745 AGATGTTTGCAGTGGACGAGAT 60.028 45.455 0.00 0.00 0.00 2.75
3364 3738 1.344438 AGATGTTTGCAGTGGACGAGA 59.656 47.619 0.00 0.00 0.00 4.04
3365 3739 1.800805 AGATGTTTGCAGTGGACGAG 58.199 50.000 0.00 0.00 0.00 4.18
3366 3740 3.610040 ATAGATGTTTGCAGTGGACGA 57.390 42.857 0.00 0.00 0.00 4.20
3367 3741 4.685169 AAATAGATGTTTGCAGTGGACG 57.315 40.909 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.