Multiple sequence alignment - TraesCS4D01G055200

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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 TraesCS4D01G055200 chr4D 100.000 4168 0 0 1 4168 30419297 30423464 0.000000e+00 7697.0
1 TraesCS4D01G055200 chr4D 84.733 1048 121 28 2172 3204 30413050 30414073 0.000000e+00 1013.0
2 TraesCS4D01G055200 chr4D 91.486 599 36 8 3571 4168 175863498 175862914 0.000000e+00 809.0
3 TraesCS4D01G055200 chr4D 80.233 774 110 26 1992 2759 30503474 30504210 3.670000e-150 542.0
4 TraesCS4D01G055200 chr4D 87.432 366 46 0 2842 3207 30504317 30504682 4.980000e-114 422.0
5 TraesCS4D01G055200 chr4D 86.575 365 49 0 2842 3206 30510234 30510598 1.800000e-108 403.0
6 TraesCS4D01G055200 chr4D 80.753 478 75 13 2287 2759 30509666 30510131 1.420000e-94 357.0
7 TraesCS4D01G055200 chr4D 94.737 57 3 0 3234 3290 30504764 30504820 5.740000e-14 89.8
8 TraesCS4D01G055200 chr4A 94.711 1645 69 9 1566 3208 572551533 572549905 0.000000e+00 2540.0
9 TraesCS4D01G055200 chr4A 87.562 1214 78 35 1 1179 572552882 572551707 0.000000e+00 1338.0
10 TraesCS4D01G055200 chr4A 90.833 600 48 3 3571 4168 308947897 308948491 0.000000e+00 797.0
11 TraesCS4D01G055200 chr4A 78.935 1239 193 46 1998 3206 572536320 572535120 0.000000e+00 780.0
12 TraesCS4D01G055200 chr4A 92.941 340 19 3 3234 3573 572549821 572549487 1.350000e-134 490.0
13 TraesCS4D01G055200 chr4A 87.603 363 45 0 2845 3207 572542046 572541684 4.980000e-114 422.0
14 TraesCS4D01G055200 chr4A 82.875 473 63 14 2300 2759 572542638 572542171 3.880000e-110 409.0
15 TraesCS4D01G055200 chr4A 95.429 175 8 0 1320 1494 572551706 572551532 3.170000e-71 279.0
16 TraesCS4D01G055200 chr4A 88.550 131 15 0 3234 3364 572541598 572541468 4.310000e-35 159.0
17 TraesCS4D01G055200 chr4B 90.090 1675 110 27 1567 3208 43751178 43752829 0.000000e+00 2122.0
18 TraesCS4D01G055200 chr4B 88.742 1288 99 29 93 1361 43749818 43751078 0.000000e+00 1533.0
19 TraesCS4D01G055200 chr4B 91.062 593 46 3 3571 4163 330738210 330738795 0.000000e+00 795.0
20 TraesCS4D01G055200 chr4B 91.931 347 15 4 3234 3573 43752909 43753249 1.360000e-129 473.0
21 TraesCS4D01G055200 chr4B 87.819 353 43 0 2854 3206 43767684 43768036 8.340000e-112 414.0
22 TraesCS4D01G055200 chr4B 87.847 288 35 0 2485 2772 43758337 43758624 5.160000e-89 339.0
23 TraesCS4D01G055200 chr4B 80.342 468 74 12 2297 2759 43767008 43767462 5.160000e-89 339.0
24 TraesCS4D01G055200 chr4B 92.453 106 6 2 1 106 43749696 43749799 2.600000e-32 150.0
25 TraesCS4D01G055200 chr4B 91.139 79 3 3 1492 1566 601766406 601766484 2.050000e-18 104.0
26 TraesCS4D01G055200 chr4B 94.737 57 3 0 3234 3290 43759179 43759235 5.740000e-14 89.8
27 TraesCS4D01G055200 chr6A 87.145 599 74 3 3571 4167 448054035 448054632 0.000000e+00 676.0
28 TraesCS4D01G055200 chr7A 86.833 600 74 5 3571 4167 378185401 378184804 0.000000e+00 665.0
29 TraesCS4D01G055200 chr7B 86.226 363 50 0 2845 3207 104259085 104258723 1.090000e-105 394.0
30 TraesCS4D01G055200 chr7B 82.529 435 61 11 2300 2730 104260315 104259892 6.580000e-98 368.0
31 TraesCS4D01G055200 chr5A 87.793 213 25 1 3956 4167 375054902 375054690 8.950000e-62 248.0
32 TraesCS4D01G055200 chr5A 94.805 77 2 1 1493 1567 552280817 552280741 7.320000e-23 119.0
33 TraesCS4D01G055200 chr5A 93.590 78 3 1 1493 1568 552280741 552280818 9.470000e-22 115.0
34 TraesCS4D01G055200 chr5B 95.062 81 3 1 1489 1568 51150096 51150176 4.370000e-25 126.0
35 TraesCS4D01G055200 chr5B 86.916 107 6 4 1474 1573 517796855 517796960 3.410000e-21 113.0
36 TraesCS4D01G055200 chr5B 91.026 78 6 1 1492 1569 334662317 334662393 2.050000e-18 104.0
37 TraesCS4D01G055200 chr1D 92.105 76 3 1 1492 1567 118886170 118886242 2.050000e-18 104.0
38 TraesCS4D01G055200 chr3B 88.372 86 7 2 1491 1574 450143555 450143471 2.650000e-17 100.0
39 TraesCS4D01G055200 chr2A 91.781 73 2 4 262 330 172556596 172556524 9.540000e-17 99.0
40 TraesCS4D01G055200 chr2A 91.781 73 2 4 262 330 646837850 646837778 9.540000e-17 99.0
41 TraesCS4D01G055200 chr6B 91.667 72 2 4 263 330 401410815 401410886 3.430000e-16 97.1
42 TraesCS4D01G055200 chr6B 98.148 54 0 1 262 314 533998683 533998736 4.440000e-15 93.5
43 TraesCS4D01G055200 chr5D 87.356 87 8 2 1487 1570 405847477 405847563 3.430000e-16 97.1


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 TraesCS4D01G055200 chr4D 30419297 30423464 4167 False 7697.000000 7697 100.000000 1 4168 1 chr4D.!!$F2 4167
1 TraesCS4D01G055200 chr4D 30413050 30414073 1023 False 1013.000000 1013 84.733000 2172 3204 1 chr4D.!!$F1 1032
2 TraesCS4D01G055200 chr4D 175862914 175863498 584 True 809.000000 809 91.486000 3571 4168 1 chr4D.!!$R1 597
3 TraesCS4D01G055200 chr4D 30509666 30510598 932 False 380.000000 403 83.664000 2287 3206 2 chr4D.!!$F4 919
4 TraesCS4D01G055200 chr4D 30503474 30504820 1346 False 351.266667 542 87.467333 1992 3290 3 chr4D.!!$F3 1298
5 TraesCS4D01G055200 chr4A 572549487 572552882 3395 True 1161.750000 2540 92.660750 1 3573 4 chr4A.!!$R3 3572
6 TraesCS4D01G055200 chr4A 308947897 308948491 594 False 797.000000 797 90.833000 3571 4168 1 chr4A.!!$F1 597
7 TraesCS4D01G055200 chr4A 572535120 572536320 1200 True 780.000000 780 78.935000 1998 3206 1 chr4A.!!$R1 1208
8 TraesCS4D01G055200 chr4A 572541468 572542638 1170 True 330.000000 422 86.342667 2300 3364 3 chr4A.!!$R2 1064
9 TraesCS4D01G055200 chr4B 43749696 43753249 3553 False 1069.500000 2122 90.804000 1 3573 4 chr4B.!!$F3 3572
10 TraesCS4D01G055200 chr4B 330738210 330738795 585 False 795.000000 795 91.062000 3571 4163 1 chr4B.!!$F1 592
11 TraesCS4D01G055200 chr4B 43767008 43768036 1028 False 376.500000 414 84.080500 2297 3206 2 chr4B.!!$F5 909
12 TraesCS4D01G055200 chr4B 43758337 43759235 898 False 214.400000 339 91.292000 2485 3290 2 chr4B.!!$F4 805
13 TraesCS4D01G055200 chr6A 448054035 448054632 597 False 676.000000 676 87.145000 3571 4167 1 chr6A.!!$F1 596
14 TraesCS4D01G055200 chr7A 378184804 378185401 597 True 665.000000 665 86.833000 3571 4167 1 chr7A.!!$R1 596
15 TraesCS4D01G055200 chr7B 104258723 104260315 1592 True 381.000000 394 84.377500 2300 3207 2 chr7B.!!$R1 907

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
315 350 0.183492 AGCTTTGCTTGTCCACAGGA 59.817 50.0 0.0 0.0 33.89 3.86 F
1505 1594 0.106116 ATCACCTACTCCCTCCGTCC 60.106 60.0 0.0 0.0 0.00 4.79 F
2188 2308 0.398318 AAGTCTCAAGTGGAGGGCAC 59.602 55.0 0.0 0.0 44.19 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2010 0.036671 GCTTACGGGCTTACACTGGT 60.037 55.000 0.0 0.0 0.00 4.00 R
2550 2738 1.004044 AGAACTGCATTCTCCAGGGTG 59.996 52.381 5.8 0.0 44.99 4.61 R
4045 5124 0.396417 AGAGTGGATCTCCCTGACGG 60.396 60.000 0.0 0.0 43.71 4.79 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
34 35 4.024302 CGTTAGAAGTCAAAAGTTGGGGTC 60.024 45.833 0.00 0.00 0.00 4.46
61 62 5.929697 TTAACAAGTCAGAGTTGCATCAG 57.070 39.130 16.75 0.00 31.85 2.90
216 249 0.675633 GTGGCAGCATGTGAAACCTT 59.324 50.000 0.00 0.00 39.31 3.50
219 252 1.885887 GGCAGCATGTGAAACCTTACA 59.114 47.619 0.00 0.00 39.31 2.41
229 262 6.767524 TGTGAAACCTTACACACATTTTCT 57.232 33.333 0.00 0.00 41.19 2.52
310 345 1.202592 TGTCGTAGCTTTGCTTGTCCA 60.203 47.619 0.00 0.00 40.44 4.02
312 347 1.202592 TCGTAGCTTTGCTTGTCCACA 60.203 47.619 0.00 0.00 40.44 4.17
314 349 1.537202 GTAGCTTTGCTTGTCCACAGG 59.463 52.381 0.00 0.00 40.44 4.00
315 350 0.183492 AGCTTTGCTTGTCCACAGGA 59.817 50.000 0.00 0.00 33.89 3.86
327 370 4.009675 TGTCCACAGGATAATGCAACTTC 58.990 43.478 0.00 0.00 32.73 3.01
374 417 2.607187 GATGGAGTACGGTCACTTGTG 58.393 52.381 0.00 0.00 0.00 3.33
387 430 0.817013 ACTTGTGGTTGCCTGTTGTG 59.183 50.000 0.00 0.00 0.00 3.33
443 486 5.957842 TGTAGGCTTAACACATTTTCTGG 57.042 39.130 0.00 0.00 0.00 3.86
514 557 2.910688 TTTGGGTGACAGAGACAGTC 57.089 50.000 0.00 0.00 36.55 3.51
542 585 5.359009 AGAGCAAATGCACTTATGTATGCTT 59.641 36.000 8.28 0.00 45.16 3.91
543 586 5.969423 AGCAAATGCACTTATGTATGCTTT 58.031 33.333 8.28 0.00 45.16 3.51
544 587 5.808540 AGCAAATGCACTTATGTATGCTTTG 59.191 36.000 8.28 12.60 45.16 2.77
545 588 5.501252 GCAAATGCACTTATGTATGCTTTGC 60.501 40.000 19.88 19.88 46.20 3.68
546 589 5.587388 AATGCACTTATGTATGCTTTGCT 57.413 34.783 0.00 0.00 42.55 3.91
554 602 3.564235 TGTATGCTTTGCTTGCTGAAG 57.436 42.857 0.00 0.30 0.00 3.02
568 616 0.890683 CTGAAGTGGGTCCAAATGCC 59.109 55.000 0.00 0.00 0.00 4.40
618 666 6.275692 TCAGGATGGTAAGACCTCATAGTA 57.724 41.667 0.00 0.00 39.58 1.82
619 667 6.307776 TCAGGATGGTAAGACCTCATAGTAG 58.692 44.000 0.00 0.00 39.58 2.57
633 681 5.992217 CCTCATAGTAGGGTAATCTTTGCAC 59.008 44.000 0.00 0.00 32.55 4.57
733 785 8.109634 ACATTATGGTCATCTTAGTCCAACTTT 58.890 33.333 0.00 0.00 33.55 2.66
734 786 7.921786 TTATGGTCATCTTAGTCCAACTTTG 57.078 36.000 0.00 0.00 33.55 2.77
749 829 8.474025 AGTCCAACTTTGATTGTCATTTTGTAA 58.526 29.630 0.00 0.00 0.00 2.41
885 967 9.424659 TCAAAAGTAACGACGAACTTATTTTTC 57.575 29.630 16.65 0.00 34.91 2.29
888 970 8.982925 AAGTAACGACGAACTTATTTTTCAAG 57.017 30.769 15.37 0.00 34.23 3.02
1076 1158 7.305474 CGACAAGCAAAGGTACTAATTGAAAT 58.695 34.615 9.11 0.00 38.49 2.17
1246 1331 7.604927 TGTTACTGCAATATTAATACGATCCCC 59.395 37.037 0.00 0.00 0.00 4.81
1295 1382 7.726216 AGATGGGAAAGGTAAAGAAAAACTTG 58.274 34.615 0.00 0.00 38.98 3.16
1296 1383 6.228616 TGGGAAAGGTAAAGAAAAACTTGG 57.771 37.500 0.00 0.00 38.98 3.61
1317 1406 6.522625 TGGAAGTTTCAGTTTGACAATCAA 57.477 33.333 0.00 0.00 34.03 2.57
1402 1491 9.421399 AGGATATCTAAACAAGTTAAAATGGGG 57.579 33.333 2.05 0.00 0.00 4.96
1435 1524 5.941555 ACCTGAATATAGCATAGTAGCCC 57.058 43.478 0.00 0.00 34.23 5.19
1457 1546 5.221048 CCCGAATGGTTCTGGCTTAATAAAG 60.221 44.000 0.00 0.00 35.68 1.85
1469 1558 7.942341 TCTGGCTTAATAAAGGAAGAACAAAGA 59.058 33.333 0.00 0.00 32.98 2.52
1500 1589 6.980416 ATGTAAGTTATCACCTACTCCCTC 57.020 41.667 0.00 0.00 0.00 4.30
1501 1590 5.206587 TGTAAGTTATCACCTACTCCCTCC 58.793 45.833 0.00 0.00 0.00 4.30
1502 1591 2.946785 AGTTATCACCTACTCCCTCCG 58.053 52.381 0.00 0.00 0.00 4.63
1503 1592 2.244252 AGTTATCACCTACTCCCTCCGT 59.756 50.000 0.00 0.00 0.00 4.69
1504 1593 2.622470 GTTATCACCTACTCCCTCCGTC 59.378 54.545 0.00 0.00 0.00 4.79
1505 1594 0.106116 ATCACCTACTCCCTCCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
1506 1595 1.757340 CACCTACTCCCTCCGTCCC 60.757 68.421 0.00 0.00 0.00 4.46
1507 1596 2.243888 ACCTACTCCCTCCGTCCCA 61.244 63.158 0.00 0.00 0.00 4.37
1508 1597 1.001248 CCTACTCCCTCCGTCCCAA 59.999 63.158 0.00 0.00 0.00 4.12
1509 1598 0.616679 CCTACTCCCTCCGTCCCAAA 60.617 60.000 0.00 0.00 0.00 3.28
1510 1599 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
1511 1600 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
1512 1601 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1513 1602 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
1514 1603 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
1515 1604 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
1516 1605 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
1517 1606 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
1518 1607 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
1519 1608 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
1520 1609 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
1521 1610 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
1522 1611 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
1523 1612 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
1524 1613 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
1525 1614 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
1553 1642 9.458374 AGTGTCAAAAACGTTCTTATATTTTGG 57.542 29.630 15.53 0.00 39.94 3.28
1554 1643 8.696175 GTGTCAAAAACGTTCTTATATTTTGGG 58.304 33.333 15.53 0.00 39.94 4.12
1555 1644 8.630917 TGTCAAAAACGTTCTTATATTTTGGGA 58.369 29.630 15.53 4.35 39.94 4.37
1556 1645 9.634163 GTCAAAAACGTTCTTATATTTTGGGAT 57.366 29.630 15.53 0.00 39.94 3.85
1557 1646 9.632807 TCAAAAACGTTCTTATATTTTGGGATG 57.367 29.630 15.53 0.00 39.94 3.51
1558 1647 8.868916 CAAAAACGTTCTTATATTTTGGGATGG 58.131 33.333 0.00 0.00 37.34 3.51
1559 1648 7.948034 AAACGTTCTTATATTTTGGGATGGA 57.052 32.000 0.00 0.00 0.00 3.41
1560 1649 7.568199 AACGTTCTTATATTTTGGGATGGAG 57.432 36.000 0.00 0.00 0.00 3.86
1561 1650 6.062095 ACGTTCTTATATTTTGGGATGGAGG 58.938 40.000 0.00 0.00 0.00 4.30
1562 1651 5.473504 CGTTCTTATATTTTGGGATGGAGGG 59.526 44.000 0.00 0.00 0.00 4.30
1563 1652 6.610830 GTTCTTATATTTTGGGATGGAGGGA 58.389 40.000 0.00 0.00 0.00 4.20
1564 1653 6.454223 TCTTATATTTTGGGATGGAGGGAG 57.546 41.667 0.00 0.00 0.00 4.30
1565 1654 5.917087 TCTTATATTTTGGGATGGAGGGAGT 59.083 40.000 0.00 0.00 0.00 3.85
1666 1755 5.106948 CGGGAATGATACTGTGACAATATGC 60.107 44.000 0.00 0.00 0.00 3.14
1744 1838 1.726248 CTGTTTTGCATAAAAGCCCGC 59.274 47.619 0.00 0.00 36.51 6.13
1762 1856 4.743493 CCCGCAATGTAGCATTTTTACTT 58.257 39.130 0.00 0.00 0.00 2.24
1787 1889 7.561021 TTTAAGAGTGAAATGTACACAAGCA 57.439 32.000 0.00 0.00 40.25 3.91
1855 1965 3.134081 ACAACATAGTCCCCTTCCGTATG 59.866 47.826 0.00 0.00 0.00 2.39
1900 2011 7.872113 ATGAATCCTTTAGATGTTTCCAGAC 57.128 36.000 0.00 0.00 34.56 3.51
1906 2017 4.974645 TTAGATGTTTCCAGACCAGTGT 57.025 40.909 0.00 0.00 0.00 3.55
1924 2035 4.024893 CAGTGTAAGCCCGTAAGCAATATG 60.025 45.833 0.00 0.00 34.23 1.78
1956 2072 7.555306 ACTAGTTCTTGTCAAAGAGAAAACC 57.445 36.000 0.00 0.00 43.27 3.27
2030 2150 8.950210 GTCCATTTCTCATGAAACAATCTTCTA 58.050 33.333 0.00 0.00 43.90 2.10
2031 2151 8.950210 TCCATTTCTCATGAAACAATCTTCTAC 58.050 33.333 0.00 0.00 43.90 2.59
2142 2262 1.244019 AAGCCCGCAACTGGAATGTC 61.244 55.000 0.00 0.00 0.00 3.06
2188 2308 0.398318 AAGTCTCAAGTGGAGGGCAC 59.602 55.000 0.00 0.00 44.19 5.01
2239 2369 7.147742 GGGTAAATATGCATTTTCCTTCCTTGA 60.148 37.037 3.54 0.00 39.98 3.02
2254 2384 6.947733 TCCTTCCTTGAAATAAATGCTCAAGA 59.052 34.615 11.60 0.00 45.86 3.02
2279 2409 7.795047 AGATTTCTTTCCAAAAACTTGACCAT 58.205 30.769 0.00 0.00 0.00 3.55
2482 2663 4.019174 CCTAACCTTGAATTCACCTGCAT 58.981 43.478 7.89 0.00 0.00 3.96
2483 2664 5.192927 CCTAACCTTGAATTCACCTGCATA 58.807 41.667 7.89 0.00 0.00 3.14
2529 2717 4.447054 CAGAATACATCGTCTCATGAAGGC 59.553 45.833 0.00 0.00 0.00 4.35
2550 2738 4.868734 GGCCAGTTGCGGTATCTTATATAC 59.131 45.833 0.00 0.00 42.61 1.47
3140 4139 0.103208 CTCAGGTCATACCGCAGTCC 59.897 60.000 0.00 0.00 44.90 3.85
3208 4209 7.148018 CCATCTCACCTGTTATTGCAAAAGTAT 60.148 37.037 1.71 0.00 0.00 2.12
3349 4420 3.701205 ATTCCCTTGGCCAACAATTTC 57.299 42.857 16.05 0.00 38.65 2.17
3356 4427 2.911484 TGGCCAACAATTTCAAACACC 58.089 42.857 0.61 0.00 0.00 4.16
3507 4582 6.086011 TCCATATATATCCCCCGCAAAAAT 57.914 37.500 0.00 0.00 0.00 1.82
3521 4600 8.215050 CCCCCGCAAAAATACTCCATATATATA 58.785 37.037 0.00 0.00 0.00 0.86
3522 4601 9.793259 CCCCGCAAAAATACTCCATATATATAT 57.207 33.333 0.00 0.00 0.00 0.86
3564 4643 7.673641 AGAGAAACCTCATGTCTATGATCTT 57.326 36.000 0.00 0.00 42.19 2.40
3718 4797 0.321653 AGATCGCCGGAAAACTGCTT 60.322 50.000 5.05 0.00 0.00 3.91
3721 4800 0.534203 TCGCCGGAAAACTGCTTTCT 60.534 50.000 5.05 0.00 42.73 2.52
3736 4815 1.279025 TTTCTATCCGCTTGGCCCCT 61.279 55.000 0.00 0.00 0.00 4.79
3746 4825 0.631212 CTTGGCCCCTTTCCTACCAT 59.369 55.000 0.00 0.00 0.00 3.55
3845 4924 1.736645 CGTAGCCTCCACCAACACG 60.737 63.158 0.00 0.00 0.00 4.49
3925 5004 3.416156 GTCCTTTGTGATGGAGCTCTTT 58.584 45.455 14.64 0.61 32.36 2.52
4045 5124 2.044946 ATCCACCGCAAAGGCCTC 60.045 61.111 5.23 0.00 46.52 4.70
4079 5158 2.035704 CCACTCTCTCCCATGATCTTCG 59.964 54.545 0.00 0.00 0.00 3.79
4163 5243 2.819984 GATTCGCTTGCCACCCTCCA 62.820 60.000 0.00 0.00 0.00 3.86
4164 5244 2.826777 ATTCGCTTGCCACCCTCCAG 62.827 60.000 0.00 0.00 0.00 3.86
4166 5246 4.357279 GCTTGCCACCCTCCAGCT 62.357 66.667 0.00 0.00 0.00 4.24
4167 5247 2.971598 GCTTGCCACCCTCCAGCTA 61.972 63.158 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.820131 TGCAACTCTGACTTGTTAATTGTG 58.180 37.500 0.00 0.00 0.00 3.33
61 62 1.600916 CGGCCTTAATAGCAGCCCC 60.601 63.158 0.00 0.00 42.66 5.80
153 186 2.990479 GGTGCGTGGAGGAATCCT 59.010 61.111 0.00 0.00 36.03 3.24
216 249 4.869215 CACATGGCAAGAAAATGTGTGTA 58.131 39.130 8.18 0.00 43.92 2.90
229 262 6.209192 ACATCTGTTTTCTAATCACATGGCAA 59.791 34.615 0.00 0.00 0.00 4.52
310 345 7.187824 TCTAGAAGAAGTTGCATTATCCTGT 57.812 36.000 0.00 0.00 0.00 4.00
312 347 6.385467 ACCTCTAGAAGAAGTTGCATTATCCT 59.615 38.462 0.00 0.00 0.00 3.24
314 349 7.496747 AGACCTCTAGAAGAAGTTGCATTATC 58.503 38.462 0.00 0.00 0.00 1.75
315 350 7.430760 AGACCTCTAGAAGAAGTTGCATTAT 57.569 36.000 0.00 0.00 0.00 1.28
327 370 5.011125 TGAACAAGTCCAAGACCTCTAGAAG 59.989 44.000 0.00 0.00 32.18 2.85
374 417 2.032981 CAGACCACAACAGGCAACC 58.967 57.895 0.00 0.00 37.17 3.77
387 430 0.326264 ATCAACTGTCCCAGCAGACC 59.674 55.000 0.00 0.00 39.62 3.85
443 486 3.063997 CGTCACACATCAATTAAGAGGGC 59.936 47.826 0.00 0.00 0.00 5.19
498 541 1.179814 ACCGACTGTCTCTGTCACCC 61.180 60.000 6.21 0.00 33.00 4.61
501 544 2.701107 CTCTACCGACTGTCTCTGTCA 58.299 52.381 6.21 0.00 33.00 3.58
514 557 3.623060 ACATAAGTGCATTTGCTCTACCG 59.377 43.478 4.47 2.63 43.19 4.02
542 585 0.823356 GGACCCACTTCAGCAAGCAA 60.823 55.000 0.00 0.00 32.09 3.91
543 586 1.228245 GGACCCACTTCAGCAAGCA 60.228 57.895 0.00 0.00 32.09 3.91
544 587 0.823356 TTGGACCCACTTCAGCAAGC 60.823 55.000 0.00 0.00 32.09 4.01
545 588 1.691196 TTTGGACCCACTTCAGCAAG 58.309 50.000 0.00 0.00 35.50 4.01
546 589 1.962807 CATTTGGACCCACTTCAGCAA 59.037 47.619 0.00 0.00 0.00 3.91
554 602 1.535204 CCACAGGCATTTGGACCCAC 61.535 60.000 0.00 0.00 34.46 4.61
568 616 4.569966 GTCTGAATGAAGCATAGACCACAG 59.430 45.833 0.00 0.00 33.44 3.66
612 660 5.760253 CCAGTGCAAAGATTACCCTACTATG 59.240 44.000 0.00 0.00 0.00 2.23
618 666 1.075374 TGCCAGTGCAAAGATTACCCT 59.925 47.619 0.00 0.00 46.66 4.34
619 667 1.544724 TGCCAGTGCAAAGATTACCC 58.455 50.000 0.00 0.00 46.66 3.69
633 681 1.002033 GTCAGCTCTTTTGTGTGCCAG 60.002 52.381 0.00 0.00 0.00 4.85
705 757 8.768397 AGTTGGACTAAGATGACCATAATGTAA 58.232 33.333 0.00 0.00 32.45 2.41
706 758 8.319057 AGTTGGACTAAGATGACCATAATGTA 57.681 34.615 0.00 0.00 32.45 2.29
707 759 7.200434 AGTTGGACTAAGATGACCATAATGT 57.800 36.000 0.00 0.00 32.45 2.71
708 760 8.400947 CAAAGTTGGACTAAGATGACCATAATG 58.599 37.037 0.00 0.00 32.45 1.90
720 772 8.971321 CAAAATGACAATCAAAGTTGGACTAAG 58.029 33.333 0.00 0.00 33.40 2.18
723 775 6.877236 ACAAAATGACAATCAAAGTTGGACT 58.123 32.000 0.00 0.00 33.40 3.85
749 829 8.988934 CCTATTACAACAGTTCGCATATAACAT 58.011 33.333 0.00 0.00 0.00 2.71
756 836 5.730550 TCTTCCTATTACAACAGTTCGCAT 58.269 37.500 0.00 0.00 0.00 4.73
823 904 2.449031 ATCTGACCAAGTTGGCGCGA 62.449 55.000 22.25 14.82 42.67 5.87
824 905 1.577328 AATCTGACCAAGTTGGCGCG 61.577 55.000 22.25 0.00 42.67 6.86
944 1026 9.689976 TCAAATGTGAAATGACGACAAATTAAT 57.310 25.926 0.00 0.00 0.00 1.40
1076 1158 2.645802 ACAGCGTAACCAAAACCTGAA 58.354 42.857 0.00 0.00 0.00 3.02
1182 1267 6.875948 ATTACTGGCGCATATGTTATCAAA 57.124 33.333 10.83 0.00 0.00 2.69
1197 1282 8.943909 ACAACTACATTAAGAGTATTACTGGC 57.056 34.615 0.00 0.00 0.00 4.85
1263 1350 7.525158 TCTTTACCTTTCCCATCTTAATCCT 57.475 36.000 0.00 0.00 0.00 3.24
1264 1351 8.589701 TTTCTTTACCTTTCCCATCTTAATCC 57.410 34.615 0.00 0.00 0.00 3.01
1271 1358 6.929049 CCAAGTTTTTCTTTACCTTTCCCATC 59.071 38.462 0.00 0.00 33.63 3.51
1295 1382 6.564328 AGTTGATTGTCAAACTGAAACTTCC 58.436 36.000 0.00 0.00 38.22 3.46
1296 1383 8.466086 AAAGTTGATTGTCAAACTGAAACTTC 57.534 30.769 9.01 0.00 38.22 3.01
1307 1394 9.248291 GAAGCTTGATAAAAAGTTGATTGTCAA 57.752 29.630 2.10 11.04 35.27 3.18
1435 1524 5.588648 TCCTTTATTAAGCCAGAACCATTCG 59.411 40.000 0.00 0.00 34.02 3.34
1493 1582 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
1494 1583 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
1495 1584 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
1496 1585 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
1497 1586 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
1498 1587 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
1499 1588 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
1500 1589 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
1527 1616 9.458374 CCAAAATATAAGAACGTTTTTGACACT 57.542 29.630 13.87 0.00 38.79 3.55
1528 1617 8.696175 CCCAAAATATAAGAACGTTTTTGACAC 58.304 33.333 13.87 0.00 38.79 3.67
1529 1618 8.630917 TCCCAAAATATAAGAACGTTTTTGACA 58.369 29.630 13.87 0.01 38.79 3.58
1530 1619 9.634163 ATCCCAAAATATAAGAACGTTTTTGAC 57.366 29.630 13.87 0.00 38.79 3.18
1531 1620 9.632807 CATCCCAAAATATAAGAACGTTTTTGA 57.367 29.630 13.87 2.81 38.79 2.69
1532 1621 8.868916 CCATCCCAAAATATAAGAACGTTTTTG 58.131 33.333 13.87 12.16 37.14 2.44
1533 1622 8.808092 TCCATCCCAAAATATAAGAACGTTTTT 58.192 29.630 9.22 9.22 0.00 1.94
1534 1623 8.356000 TCCATCCCAAAATATAAGAACGTTTT 57.644 30.769 0.46 0.00 0.00 2.43
1535 1624 7.068226 CCTCCATCCCAAAATATAAGAACGTTT 59.932 37.037 0.46 0.00 0.00 3.60
1536 1625 6.546034 CCTCCATCCCAAAATATAAGAACGTT 59.454 38.462 0.00 0.00 0.00 3.99
1537 1626 6.062095 CCTCCATCCCAAAATATAAGAACGT 58.938 40.000 0.00 0.00 0.00 3.99
1538 1627 5.473504 CCCTCCATCCCAAAATATAAGAACG 59.526 44.000 0.00 0.00 0.00 3.95
1539 1628 6.610830 TCCCTCCATCCCAAAATATAAGAAC 58.389 40.000 0.00 0.00 0.00 3.01
1540 1629 6.392842 ACTCCCTCCATCCCAAAATATAAGAA 59.607 38.462 0.00 0.00 0.00 2.52
1541 1630 5.917087 ACTCCCTCCATCCCAAAATATAAGA 59.083 40.000 0.00 0.00 0.00 2.10
1542 1631 6.206180 ACTCCCTCCATCCCAAAATATAAG 57.794 41.667 0.00 0.00 0.00 1.73
1543 1632 7.905144 ATACTCCCTCCATCCCAAAATATAA 57.095 36.000 0.00 0.00 0.00 0.98
1545 1634 9.764776 ATATATACTCCCTCCATCCCAAAATAT 57.235 33.333 0.00 0.00 0.00 1.28
1546 1635 9.588432 AATATATACTCCCTCCATCCCAAAATA 57.412 33.333 0.00 0.00 0.00 1.40
1547 1636 8.482378 AATATATACTCCCTCCATCCCAAAAT 57.518 34.615 0.00 0.00 0.00 1.82
1548 1637 7.905144 AATATATACTCCCTCCATCCCAAAA 57.095 36.000 0.00 0.00 0.00 2.44
1549 1638 9.588432 AATAATATATACTCCCTCCATCCCAAA 57.412 33.333 0.00 0.00 0.00 3.28
1550 1639 9.588432 AAATAATATATACTCCCTCCATCCCAA 57.412 33.333 0.00 0.00 0.00 4.12
1666 1755 4.389687 GCCACACAAAATTATGCAAAGAGG 59.610 41.667 0.00 0.00 0.00 3.69
1683 1777 3.664107 TGTAAGATCTGAACTGCCACAC 58.336 45.455 0.00 0.00 0.00 3.82
1762 1856 7.990917 TGCTTGTGTACATTTCACTCTTAAAA 58.009 30.769 0.00 0.00 36.83 1.52
1787 1889 9.013229 TGTATCAAAAGAAGCACATGTAGAAAT 57.987 29.630 0.00 0.00 0.00 2.17
1842 1952 1.764854 GGCTCCATACGGAAGGGGA 60.765 63.158 0.00 0.00 42.21 4.81
1899 2010 0.036671 GCTTACGGGCTTACACTGGT 60.037 55.000 0.00 0.00 0.00 4.00
1900 2011 0.036765 TGCTTACGGGCTTACACTGG 60.037 55.000 0.00 0.00 0.00 4.00
1906 2017 4.323417 CATCCATATTGCTTACGGGCTTA 58.677 43.478 0.00 0.00 0.00 3.09
1924 2035 6.818644 TCTTTGACAAGAACTAGTATGCATCC 59.181 38.462 0.19 0.00 35.99 3.51
1956 2072 4.848357 ACCAAGATGAAGATACCAAGGTG 58.152 43.478 1.07 0.00 0.00 4.00
2030 2150 1.269723 TCAGTTCGTTGATCTGCTCGT 59.730 47.619 0.00 0.00 31.62 4.18
2031 2151 1.916651 CTCAGTTCGTTGATCTGCTCG 59.083 52.381 0.00 0.00 31.62 5.03
2142 2262 4.994852 TCCAACATTTTCCTAGACTTGTCG 59.005 41.667 0.00 0.00 0.00 4.35
2188 2308 3.616076 CGAATATCCTCAGGCCTGCTAAG 60.616 52.174 28.91 19.67 0.00 2.18
2239 2369 9.866798 GGAAAGAAATCTCTTGAGCATTTATTT 57.133 29.630 17.34 17.34 41.23 1.40
2243 2373 6.906157 TGGAAAGAAATCTCTTGAGCATTT 57.094 33.333 0.00 7.34 41.23 2.32
2254 2384 7.181569 TGGTCAAGTTTTTGGAAAGAAATCT 57.818 32.000 0.00 0.00 34.97 2.40
2279 2409 9.442047 AAACAATCAAAAGAATGTTTGGTTACA 57.558 25.926 9.98 0.00 39.29 2.41
2529 2717 5.867716 GGTGTATATAAGATACCGCAACTGG 59.132 44.000 0.00 0.00 0.00 4.00
2550 2738 1.004044 AGAACTGCATTCTCCAGGGTG 59.996 52.381 5.80 0.00 44.99 4.61
3236 4307 9.952188 GCGAGATATTCTGCAGTTACATATATA 57.048 33.333 14.67 1.26 0.00 0.86
3240 4311 6.332735 AGCGAGATATTCTGCAGTTACATA 57.667 37.500 14.67 6.84 0.00 2.29
3349 4420 9.927668 AATAGGTGAATTATTCTTTGGTGTTTG 57.072 29.630 6.50 0.00 0.00 2.93
3465 4536 3.917629 TGGAGTTACTTGGGGAAATGGTA 59.082 43.478 0.00 0.00 0.00 3.25
3466 4537 2.719705 TGGAGTTACTTGGGGAAATGGT 59.280 45.455 0.00 0.00 0.00 3.55
3521 4600 9.118300 GTTTCTCTATGACCATCATCTTTTCAT 57.882 33.333 0.00 0.00 38.26 2.57
3522 4601 7.554118 GGTTTCTCTATGACCATCATCTTTTCA 59.446 37.037 0.00 0.00 38.26 2.69
3718 4797 1.279025 AAGGGGCCAAGCGGATAGAA 61.279 55.000 4.39 0.00 0.00 2.10
3721 4800 1.226262 GAAAGGGGCCAAGCGGATA 59.774 57.895 4.39 0.00 0.00 2.59
3736 4815 3.269381 AGGGAATCAGCAATGGTAGGAAA 59.731 43.478 0.00 0.00 0.00 3.13
3746 4825 0.549902 TGGGAGGAGGGAATCAGCAA 60.550 55.000 0.00 0.00 0.00 3.91
3845 4924 4.154347 CAGCAGAGCCGGGTCCTC 62.154 72.222 29.33 20.48 0.00 3.71
4045 5124 0.396417 AGAGTGGATCTCCCTGACGG 60.396 60.000 0.00 0.00 43.71 4.79
4079 5158 3.320830 TGGGGCAATTGCAAGGGC 61.321 61.111 30.32 16.26 44.36 5.19


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

AutoCloner maintained by Alex Coulton.