Multiple sequence alignment - TraesCS2D01G278700

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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 TraesCS2D01G278700 chr2D 100.000 8508 0 0 1 8508 349928673 349920166 0.000000e+00 15712.0
1 TraesCS2D01G278700 chr2D 90.097 4726 427 32 3799 8508 500581256 500576556 0.000000e+00 6096.0
2 TraesCS2D01G278700 chr2D 89.662 4730 441 41 3800 8508 91977773 91973071 0.000000e+00 5982.0
3 TraesCS2D01G278700 chr2D 91.899 1864 109 24 1960 3799 565870598 565868753 0.000000e+00 2567.0
4 TraesCS2D01G278700 chr2D 86.912 489 46 15 46 530 579140387 579140861 4.520000e-147 532.0
5 TraesCS2D01G278700 chr3D 93.067 4731 294 31 3795 8508 188788435 188793148 0.000000e+00 6889.0
6 TraesCS2D01G278700 chr3D 91.257 1853 134 17 1960 3799 88492709 88494546 0.000000e+00 2499.0
7 TraesCS2D01G278700 chr3D 87.935 1467 128 25 534 1962 540910907 540912362 0.000000e+00 1683.0
8 TraesCS2D01G278700 chr3D 88.889 171 15 4 136 306 140056409 140056243 3.110000e-49 207.0
9 TraesCS2D01G278700 chr7D 90.815 4725 400 30 3799 8508 261497552 261502257 0.000000e+00 6290.0
10 TraesCS2D01G278700 chr7D 89.738 4726 455 28 3797 8507 463188132 463183422 0.000000e+00 6013.0
11 TraesCS2D01G278700 chr7D 88.793 4729 493 35 3800 8507 243393184 243397896 0.000000e+00 5762.0
12 TraesCS2D01G278700 chr7D 91.729 1862 130 11 1960 3799 356095348 356097207 0.000000e+00 2564.0
13 TraesCS2D01G278700 chr7D 88.117 1498 118 27 513 1958 298427627 298429116 0.000000e+00 1725.0
14 TraesCS2D01G278700 chr7D 88.005 1484 117 30 534 1962 209966495 209965018 0.000000e+00 1698.0
15 TraesCS2D01G278700 chr7D 86.739 1478 141 27 534 1962 638024798 638023327 0.000000e+00 1592.0
16 TraesCS2D01G278700 chr6D 90.097 4736 423 43 3798 8508 76741687 76736973 0.000000e+00 6106.0
17 TraesCS2D01G278700 chr6D 89.738 4726 451 31 3800 8507 394052672 394057381 0.000000e+00 6010.0
18 TraesCS2D01G278700 chr6D 89.407 4739 449 43 3793 8507 435524081 435519372 0.000000e+00 5921.0
19 TraesCS2D01G278700 chr6D 91.806 1855 127 15 1960 3799 320812779 320814623 0.000000e+00 2560.0
20 TraesCS2D01G278700 chr6D 91.541 1856 121 24 1960 3799 355945878 355944043 0.000000e+00 2525.0
21 TraesCS2D01G278700 chr6D 91.239 1872 121 19 1960 3799 143245425 143247285 0.000000e+00 2508.0
22 TraesCS2D01G278700 chr6D 91.183 1860 134 20 1960 3799 166125569 166123720 0.000000e+00 2499.0
23 TraesCS2D01G278700 chr6D 84.483 58 9 0 472 529 472014459 472014402 3.320000e-04 58.4
24 TraesCS2D01G278700 chr4D 89.311 4715 462 34 3800 8498 66162517 66157829 0.000000e+00 5877.0
25 TraesCS2D01G278700 chr4D 92.237 1855 105 24 1964 3799 122834191 122836025 0.000000e+00 2591.0
26 TraesCS2D01G278700 chr4D 91.510 1861 128 18 1960 3799 298592233 298594084 0.000000e+00 2534.0
27 TraesCS2D01G278700 chr4D 77.889 398 57 16 137 531 273981243 273981612 1.440000e-52 219.0
28 TraesCS2D01G278700 chr3A 87.340 1485 127 31 534 1962 358555714 358554235 0.000000e+00 1644.0
29 TraesCS2D01G278700 chr3A 87.273 1485 119 35 534 1962 551086806 551088276 0.000000e+00 1631.0
30 TraesCS2D01G278700 chr3A 84.574 739 70 20 534 1234 668348217 668347485 0.000000e+00 693.0
31 TraesCS2D01G278700 chr4A 87.142 1501 118 43 513 1957 235944095 235945576 0.000000e+00 1633.0
32 TraesCS2D01G278700 chr4A 78.195 399 47 23 140 531 728221282 728220917 1.440000e-52 219.0
33 TraesCS2D01G278700 chr2B 86.748 1479 139 31 534 1962 216332530 216331059 0.000000e+00 1592.0
34 TraesCS2D01G278700 chr2B 81.769 373 59 8 157 525 38441229 38441596 3.860000e-78 303.0
35 TraesCS2D01G278700 chr3B 86.735 1470 145 28 534 1957 612455161 612453696 0.000000e+00 1589.0
36 TraesCS2D01G278700 chr3B 89.780 1184 104 9 788 1957 598803332 598802152 0.000000e+00 1500.0
37 TraesCS2D01G278700 chr5B 90.764 1191 90 12 788 1962 316038502 316039688 0.000000e+00 1572.0
38 TraesCS2D01G278700 chr5B 84.344 709 79 21 534 1231 441400019 441400706 0.000000e+00 665.0
39 TraesCS2D01G278700 chr5B 86.402 478 41 4 75 530 483521207 483520732 1.270000e-137 501.0
40 TraesCS2D01G278700 chr5B 87.634 186 21 2 140 325 649446681 649446864 1.860000e-51 215.0
41 TraesCS2D01G278700 chr4B 90.236 1188 100 12 788 1962 499888152 499889336 0.000000e+00 1537.0
42 TraesCS2D01G278700 chr4B 89.899 1188 103 10 788 1962 13186691 13187874 0.000000e+00 1513.0
43 TraesCS2D01G278700 chr4B 79.202 351 49 13 157 504 211591274 211591603 1.110000e-53 222.0
44 TraesCS2D01G278700 chr6B 89.815 1188 99 13 788 1962 580348368 580347190 0.000000e+00 1504.0
45 TraesCS2D01G278700 chr7A 84.144 1274 124 38 534 1752 393553640 393552390 0.000000e+00 1162.0
46 TraesCS2D01G278700 chr7A 85.536 1044 92 23 534 1523 443628955 443627917 0.000000e+00 1037.0
47 TraesCS2D01G278700 chr7A 84.386 570 49 24 534 1068 273789689 273789125 2.720000e-144 523.0
48 TraesCS2D01G278700 chr7A 84.872 509 61 12 513 1012 305235808 305236309 4.590000e-137 499.0
49 TraesCS2D01G278700 chr7A 81.159 138 25 1 382 519 115784316 115784452 9.030000e-20 110.0
50 TraesCS2D01G278700 chr5A 83.178 856 81 30 534 1331 562346220 562345370 0.000000e+00 725.0
51 TraesCS2D01G278700 chr5A 85.572 603 47 13 534 1100 238770816 238770218 5.690000e-166 595.0
52 TraesCS2D01G278700 chr2A 83.515 825 75 24 536 1311 403710974 403711786 0.000000e+00 713.0
53 TraesCS2D01G278700 chr1D 87.230 556 38 14 1 530 36393724 36394272 3.400000e-168 603.0
54 TraesCS2D01G278700 chr1D 90.698 172 10 3 136 306 76949332 76949498 3.090000e-54 224.0
55 TraesCS2D01G278700 chr1B 83.022 536 56 25 3 530 601175546 601176054 3.620000e-123 453.0


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 TraesCS2D01G278700 chr2D 349920166 349928673 8507 True 15712 15712 100.000 1 8508 1 chr2D.!!$R2 8507
1 TraesCS2D01G278700 chr2D 500576556 500581256 4700 True 6096 6096 90.097 3799 8508 1 chr2D.!!$R3 4709
2 TraesCS2D01G278700 chr2D 91973071 91977773 4702 True 5982 5982 89.662 3800 8508 1 chr2D.!!$R1 4708
3 TraesCS2D01G278700 chr2D 565868753 565870598 1845 True 2567 2567 91.899 1960 3799 1 chr2D.!!$R4 1839
4 TraesCS2D01G278700 chr3D 188788435 188793148 4713 False 6889 6889 93.067 3795 8508 1 chr3D.!!$F2 4713
5 TraesCS2D01G278700 chr3D 88492709 88494546 1837 False 2499 2499 91.257 1960 3799 1 chr3D.!!$F1 1839
6 TraesCS2D01G278700 chr3D 540910907 540912362 1455 False 1683 1683 87.935 534 1962 1 chr3D.!!$F3 1428
7 TraesCS2D01G278700 chr7D 261497552 261502257 4705 False 6290 6290 90.815 3799 8508 1 chr7D.!!$F2 4709
8 TraesCS2D01G278700 chr7D 463183422 463188132 4710 True 6013 6013 89.738 3797 8507 1 chr7D.!!$R2 4710
9 TraesCS2D01G278700 chr7D 243393184 243397896 4712 False 5762 5762 88.793 3800 8507 1 chr7D.!!$F1 4707
10 TraesCS2D01G278700 chr7D 356095348 356097207 1859 False 2564 2564 91.729 1960 3799 1 chr7D.!!$F4 1839
11 TraesCS2D01G278700 chr7D 298427627 298429116 1489 False 1725 1725 88.117 513 1958 1 chr7D.!!$F3 1445
12 TraesCS2D01G278700 chr7D 209965018 209966495 1477 True 1698 1698 88.005 534 1962 1 chr7D.!!$R1 1428
13 TraesCS2D01G278700 chr7D 638023327 638024798 1471 True 1592 1592 86.739 534 1962 1 chr7D.!!$R3 1428
14 TraesCS2D01G278700 chr6D 76736973 76741687 4714 True 6106 6106 90.097 3798 8508 1 chr6D.!!$R1 4710
15 TraesCS2D01G278700 chr6D 394052672 394057381 4709 False 6010 6010 89.738 3800 8507 1 chr6D.!!$F3 4707
16 TraesCS2D01G278700 chr6D 435519372 435524081 4709 True 5921 5921 89.407 3793 8507 1 chr6D.!!$R4 4714
17 TraesCS2D01G278700 chr6D 320812779 320814623 1844 False 2560 2560 91.806 1960 3799 1 chr6D.!!$F2 1839
18 TraesCS2D01G278700 chr6D 355944043 355945878 1835 True 2525 2525 91.541 1960 3799 1 chr6D.!!$R3 1839
19 TraesCS2D01G278700 chr6D 143245425 143247285 1860 False 2508 2508 91.239 1960 3799 1 chr6D.!!$F1 1839
20 TraesCS2D01G278700 chr6D 166123720 166125569 1849 True 2499 2499 91.183 1960 3799 1 chr6D.!!$R2 1839
21 TraesCS2D01G278700 chr4D 66157829 66162517 4688 True 5877 5877 89.311 3800 8498 1 chr4D.!!$R1 4698
22 TraesCS2D01G278700 chr4D 122834191 122836025 1834 False 2591 2591 92.237 1964 3799 1 chr4D.!!$F1 1835
23 TraesCS2D01G278700 chr4D 298592233 298594084 1851 False 2534 2534 91.510 1960 3799 1 chr4D.!!$F3 1839
24 TraesCS2D01G278700 chr3A 358554235 358555714 1479 True 1644 1644 87.340 534 1962 1 chr3A.!!$R1 1428
25 TraesCS2D01G278700 chr3A 551086806 551088276 1470 False 1631 1631 87.273 534 1962 1 chr3A.!!$F1 1428
26 TraesCS2D01G278700 chr3A 668347485 668348217 732 True 693 693 84.574 534 1234 1 chr3A.!!$R2 700
27 TraesCS2D01G278700 chr4A 235944095 235945576 1481 False 1633 1633 87.142 513 1957 1 chr4A.!!$F1 1444
28 TraesCS2D01G278700 chr2B 216331059 216332530 1471 True 1592 1592 86.748 534 1962 1 chr2B.!!$R1 1428
29 TraesCS2D01G278700 chr3B 612453696 612455161 1465 True 1589 1589 86.735 534 1957 1 chr3B.!!$R2 1423
30 TraesCS2D01G278700 chr3B 598802152 598803332 1180 True 1500 1500 89.780 788 1957 1 chr3B.!!$R1 1169
31 TraesCS2D01G278700 chr5B 316038502 316039688 1186 False 1572 1572 90.764 788 1962 1 chr5B.!!$F1 1174
32 TraesCS2D01G278700 chr5B 441400019 441400706 687 False 665 665 84.344 534 1231 1 chr5B.!!$F2 697
33 TraesCS2D01G278700 chr4B 499888152 499889336 1184 False 1537 1537 90.236 788 1962 1 chr4B.!!$F3 1174
34 TraesCS2D01G278700 chr4B 13186691 13187874 1183 False 1513 1513 89.899 788 1962 1 chr4B.!!$F1 1174
35 TraesCS2D01G278700 chr6B 580347190 580348368 1178 True 1504 1504 89.815 788 1962 1 chr6B.!!$R1 1174
36 TraesCS2D01G278700 chr7A 393552390 393553640 1250 True 1162 1162 84.144 534 1752 1 chr7A.!!$R2 1218
37 TraesCS2D01G278700 chr7A 443627917 443628955 1038 True 1037 1037 85.536 534 1523 1 chr7A.!!$R3 989
38 TraesCS2D01G278700 chr7A 273789125 273789689 564 True 523 523 84.386 534 1068 1 chr7A.!!$R1 534
39 TraesCS2D01G278700 chr7A 305235808 305236309 501 False 499 499 84.872 513 1012 1 chr7A.!!$F2 499
40 TraesCS2D01G278700 chr5A 562345370 562346220 850 True 725 725 83.178 534 1331 1 chr5A.!!$R2 797
41 TraesCS2D01G278700 chr5A 238770218 238770816 598 True 595 595 85.572 534 1100 1 chr5A.!!$R1 566
42 TraesCS2D01G278700 chr2A 403710974 403711786 812 False 713 713 83.515 536 1311 1 chr2A.!!$F1 775
43 TraesCS2D01G278700 chr1D 36393724 36394272 548 False 603 603 87.230 1 530 1 chr1D.!!$F1 529
44 TraesCS2D01G278700 chr1B 601175546 601176054 508 False 453 453 83.022 3 530 1 chr1B.!!$F1 527

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
483 535 0.257039 CATGGGAGGTGGGAGGAAAG 59.743 60.000 0.00 0.0 0.00 2.62 F
1082 1178 2.158755 CCCGGTAGGCATCTCATCTTTT 60.159 50.000 0.00 0.0 35.76 2.27 F
1648 1789 0.892755 CAACATGTGATGCTTGCCCT 59.107 50.000 0.00 0.0 0.00 5.19 F
3361 3579 1.741770 CGAGGAAGGTCAAAGGCGG 60.742 63.158 0.00 0.0 0.00 6.13 F
3925 4173 0.544833 TACTGGTTCGGCCCCTTACA 60.545 55.000 0.00 0.0 36.04 2.41 F
4589 4847 0.248012 TTCTCGCGCCCACTTATGAA 59.752 50.000 0.00 0.0 0.00 2.57 F
5990 6290 0.537371 CTGGAACCAACACACCCTCC 60.537 60.000 0.00 0.0 0.00 4.30 F
6646 6951 0.107654 GATACCGGAGCAAGCAACCT 60.108 55.000 9.46 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1778 0.822164 GCAAAGATGAGGGCAAGCAT 59.178 50.000 0.00 0.00 0.00 3.79 R
2986 3193 0.379669 CGCCATGGCAGAGATTTGAC 59.620 55.000 34.93 2.44 42.06 3.18 R
3389 3607 0.179137 CACGCTGGAGCTTATCGACA 60.179 55.000 0.00 0.00 39.32 4.35 R
4396 4653 0.032952 TCACGCCGGGTTATAGCATC 59.967 55.000 2.18 0.00 0.00 3.91 R
4923 5215 0.388520 GAAATGAGTGCCAAACCGCC 60.389 55.000 0.00 0.00 0.00 6.13 R
6271 6571 0.107459 GTCTTGCAGAAGGGGGCTAG 60.107 60.000 0.00 0.00 34.80 3.42 R
7397 7705 1.069204 GCTCAGATTGGCATAGTCGGA 59.931 52.381 0.00 0.00 0.00 4.55 R
8095 8406 0.035152 AAGTCGCTGGCAATGATGGA 60.035 50.000 0.00 0.00 0.00 3.41 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
72 74 3.157252 TCCTCGCCAGGATCAGCC 61.157 66.667 0.00 0.00 44.75 4.85
106 131 3.390521 TTCAGCGCCGGATCCTGT 61.391 61.111 5.05 0.00 0.00 4.00
253 298 1.812922 GGAGACCTCGCTCGTACGA 60.813 63.158 18.41 18.41 40.36 3.43
273 318 2.418976 GAGCGGTCAATTGGTTTAGGTC 59.581 50.000 10.30 4.96 0.00 3.85
367 417 1.259142 TGGGTGCGATCGGAGGTTAA 61.259 55.000 18.30 0.00 0.00 2.01
380 430 1.378646 GGTTAAGCCCTGGAGTGCC 60.379 63.158 0.00 0.00 0.00 5.01
382 432 0.678048 GTTAAGCCCTGGAGTGCCTG 60.678 60.000 0.00 0.00 34.31 4.85
411 461 1.686800 GGGGCCTCGGTACAAGGTA 60.687 63.158 0.84 0.00 0.00 3.08
417 467 3.376234 GGCCTCGGTACAAGGTATTTTTC 59.624 47.826 13.40 0.00 0.00 2.29
423 473 4.692155 CGGTACAAGGTATTTTTCGGTTCT 59.308 41.667 0.00 0.00 0.00 3.01
432 482 1.770294 TTTTCGGTTCTTGGTGGCTT 58.230 45.000 0.00 0.00 0.00 4.35
478 530 0.409484 AAAACCATGGGAGGTGGGAG 59.591 55.000 18.09 0.00 42.25 4.30
483 535 0.257039 CATGGGAGGTGGGAGGAAAG 59.743 60.000 0.00 0.00 0.00 2.62
492 544 2.239400 GTGGGAGGAAAGAAAACCTGG 58.761 52.381 0.00 0.00 36.57 4.45
508 560 3.034635 ACCTGGAAGCGAGACTATCAAT 58.965 45.455 0.00 0.00 0.00 2.57
520 575 6.347240 GCGAGACTATCAATTGCTTCATTAGG 60.347 42.308 0.00 0.00 0.00 2.69
530 585 9.147732 TCAATTGCTTCATTAGGAGTAGAGATA 57.852 33.333 0.00 0.00 0.00 1.98
563 618 4.520492 GCCATGCTTACCTTGCAAGTATAT 59.480 41.667 24.35 9.88 44.01 0.86
616 671 4.488879 GTTGCTGCAAAAATTCCCTAGAG 58.511 43.478 17.80 0.00 0.00 2.43
663 719 8.435430 GTTGGAACTTTTTGCATAATAAGCTTC 58.565 33.333 0.00 0.00 32.39 3.86
1082 1178 2.158755 CCCGGTAGGCATCTCATCTTTT 60.159 50.000 0.00 0.00 35.76 2.27
1120 1216 4.036027 TCGTTTAGTATCGGTTGAGCCTAG 59.964 45.833 0.00 0.00 34.25 3.02
1134 1232 4.655963 TGAGCCTAGTTTTGCTTCTTCAT 58.344 39.130 0.00 0.00 38.11 2.57
1382 1520 9.786105 CATATCATGTCTAGTAGTAGCTTCATG 57.214 37.037 19.48 19.48 34.55 3.07
1423 1561 6.600882 AATCTTTTGAGGCTTGACAATCAT 57.399 33.333 0.00 0.00 0.00 2.45
1436 1575 7.010738 GGCTTGACAATCATAATTTTGGTCATG 59.989 37.037 7.09 9.50 0.00 3.07
1480 1619 9.804758 ATTAGTATAAGGAAGAGAACTTTCACG 57.195 33.333 0.00 0.00 36.39 4.35
1527 1666 4.853468 TTTGTGATTGTGAGCCCCTATA 57.147 40.909 0.00 0.00 0.00 1.31
1565 1705 6.348213 GCTATAATTGTTGACGTTGGACAAGT 60.348 38.462 14.60 14.28 36.80 3.16
1638 1778 6.298441 TGTCATAGATCCTTCAACATGTGA 57.702 37.500 0.00 0.00 0.00 3.58
1648 1789 0.892755 CAACATGTGATGCTTGCCCT 59.107 50.000 0.00 0.00 0.00 5.19
1661 1803 2.943199 GCTTGCCCTCATCTTTGCTAGT 60.943 50.000 0.00 0.00 0.00 2.57
1811 1955 7.548097 TCGGTGCAATAAGGCAATAAAAATTA 58.452 30.769 0.00 0.00 46.93 1.40
1845 2005 8.934507 AGTGTTAGATCATTTAGTGTAAGAGC 57.065 34.615 0.00 0.00 0.00 4.09
1874 2034 4.689071 AGTGTTGTACGAACTTGTGATGA 58.311 39.130 0.00 0.00 0.00 2.92
1958 2119 2.158726 ACGTTCTTTTGCACTAAGGGGA 60.159 45.455 7.66 0.00 0.00 4.81
2014 2175 7.346751 AGCCATTTAATGACCGTAATTCAAT 57.653 32.000 6.50 0.00 0.00 2.57
2088 2251 3.439895 TTGTGTACTTGTGTGCGAGTA 57.560 42.857 0.00 0.00 39.85 2.59
2094 2257 5.050634 GTGTACTTGTGTGCGAGTAAATTCA 60.051 40.000 0.00 0.00 41.75 2.57
2258 2428 5.337491 GCCACCAAGATGATGTGGTAAAAAT 60.337 40.000 9.42 0.00 46.61 1.82
2516 2691 7.925993 TCTAGCCATTTAATGACCGTAATTTG 58.074 34.615 6.50 0.00 0.00 2.32
2669 2852 4.660938 GGCAAGACAACCGGCCCT 62.661 66.667 0.00 0.00 40.55 5.19
2770 2957 4.839121 TGGAAACCGTCAGCTATTATGTT 58.161 39.130 0.00 0.00 0.00 2.71
2817 3004 7.148306 GGGAATCGTGTGTAATTCAAACTACAT 60.148 37.037 0.00 0.00 34.28 2.29
2869 3056 7.040617 TGTGTACTATTCCCGTCAATCTAGATC 60.041 40.741 5.51 0.00 0.00 2.75
2931 3118 4.746089 GCCTGCATTCTCATCTACATCCTT 60.746 45.833 0.00 0.00 0.00 3.36
2970 3169 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
2982 3189 5.982356 TCTCTCTCTCTTTCTCTCTCTCTG 58.018 45.833 0.00 0.00 0.00 3.35
2986 3193 5.491070 TCTCTCTTTCTCTCTCTCTGTCTG 58.509 45.833 0.00 0.00 0.00 3.51
3086 3303 1.828660 CAGCGACGAGGACCCCTAT 60.829 63.158 0.00 0.00 31.76 2.57
3218 3436 1.945819 GCGTTCAAGAAGGAGATGGCA 60.946 52.381 6.68 0.00 0.00 4.92
3297 3515 4.148825 CGACGGAGCTTGGGGAGG 62.149 72.222 0.00 0.00 0.00 4.30
3361 3579 1.741770 CGAGGAAGGTCAAAGGCGG 60.742 63.158 0.00 0.00 0.00 6.13
3389 3607 4.664677 GTCGCTGCGTGGAGGTGT 62.665 66.667 22.48 0.00 0.00 4.16
3391 3609 4.969196 CGCTGCGTGGAGGTGTGT 62.969 66.667 14.93 0.00 0.00 3.72
3448 3666 2.740438 GGCGCCCAACAAAATGGT 59.260 55.556 18.11 0.00 38.91 3.55
3904 4152 1.476291 GGACAAGGAACACGAGGGTTT 60.476 52.381 0.00 0.00 0.00 3.27
3925 4173 0.544833 TACTGGTTCGGCCCCTTACA 60.545 55.000 0.00 0.00 36.04 2.41
3947 4195 5.013183 ACAGTGAAGGTAAAAGCCTACATCT 59.987 40.000 0.00 0.00 38.03 2.90
3957 4207 6.869206 AAAAGCCTACATCTAGTTGAGGTA 57.131 37.500 7.81 0.00 40.45 3.08
4010 4260 0.622665 AACTGCTATGCCTGGCTCTT 59.377 50.000 21.03 7.38 0.00 2.85
4216 4468 1.475213 CCGGGTCTTAAGCCCATCTTC 60.475 57.143 25.33 1.76 46.40 2.87
4275 4527 4.742440 GCGATGACCATTATGAGTAACCCA 60.742 45.833 0.00 0.00 0.00 4.51
4377 4634 8.084590 TCTTTAACTCTTTCGACAGAAAATCC 57.915 34.615 2.42 0.00 44.77 3.01
4396 4653 0.591170 CCCGGCTTATAATTGCGTGG 59.409 55.000 0.00 0.00 0.00 4.94
4398 4655 2.151202 CCGGCTTATAATTGCGTGGAT 58.849 47.619 0.00 0.00 0.00 3.41
4401 4658 2.554032 GGCTTATAATTGCGTGGATGCT 59.446 45.455 0.00 0.00 35.36 3.79
4515 4773 2.288030 ACGGATCTTATCTTTACCGCCG 60.288 50.000 0.00 0.00 43.36 6.46
4589 4847 0.248012 TTCTCGCGCCCACTTATGAA 59.752 50.000 0.00 0.00 0.00 2.57
4615 4873 1.353022 CCTTATAAATAGCCCGGCCCA 59.647 52.381 5.55 0.00 0.00 5.36
4625 4886 2.460853 CCCGGCCCATTACCTCCAT 61.461 63.158 0.00 0.00 0.00 3.41
4659 4920 2.484651 TCTTCGTCTTCTTCCTCTGTCG 59.515 50.000 0.00 0.00 0.00 4.35
4719 5005 1.597027 CTTCGTCAACCTTGGCCGT 60.597 57.895 0.00 0.00 0.00 5.68
4771 5059 3.432588 CGACCTCCGCGACTCACT 61.433 66.667 8.23 0.00 0.00 3.41
4843 5134 3.203716 GTCCTGTTCTTCCGTGTTCTTT 58.796 45.455 0.00 0.00 0.00 2.52
4875 5167 4.151867 CCACGAGCTCTTGGTAGTTTTTAC 59.848 45.833 27.01 0.00 31.32 2.01
4923 5215 1.009675 GCATAGAACCAATGCGGCG 60.010 57.895 0.51 0.51 40.27 6.46
4953 5245 3.430895 GGCACTCATTTCAAATGCAAGTG 59.569 43.478 20.35 20.35 38.05 3.16
5126 5419 3.134127 GCCCCCGTTGAGTCATGC 61.134 66.667 0.00 0.00 0.00 4.06
5179 5472 2.579878 CGTAGGACCTTCTGGCTCA 58.420 57.895 0.00 0.00 36.63 4.26
5280 5575 4.409574 TCCAACGGCTTAGATAACCCAATA 59.590 41.667 0.00 0.00 0.00 1.90
5318 5614 3.489513 GGCCCCTCCATAAGCCGT 61.490 66.667 0.00 0.00 35.30 5.68
5643 5943 5.482908 GGCTCAAAGTTCTTCAGAGATGTA 58.517 41.667 14.62 0.00 0.00 2.29
5832 6132 1.067295 TGGAACTTGGTGGCATCTCT 58.933 50.000 0.00 0.00 0.00 3.10
5990 6290 0.537371 CTGGAACCAACACACCCTCC 60.537 60.000 0.00 0.00 0.00 4.30
6087 6387 2.105821 TGGTCTCAACGGAATTGACCTT 59.894 45.455 11.07 0.00 42.62 3.50
6088 6388 3.325425 TGGTCTCAACGGAATTGACCTTA 59.675 43.478 11.07 0.00 42.62 2.69
6330 6630 4.558538 AAGCCGCTGATATGAACATTTC 57.441 40.909 0.00 0.00 0.00 2.17
6355 6655 9.823647 TCATCTTCCTTTGTAGATATTCTTCAC 57.176 33.333 0.00 0.00 28.62 3.18
6592 6896 9.175060 GCTTTTGTTGTGTTTGTTGTTTATTTT 57.825 25.926 0.00 0.00 0.00 1.82
6612 6917 9.616156 TTATTTTTGTCCGCCTTATCAATACTA 57.384 29.630 0.00 0.00 0.00 1.82
6641 6946 0.394565 AGGATGATACCGGAGCAAGC 59.605 55.000 9.46 0.00 34.73 4.01
6646 6951 0.107654 GATACCGGAGCAAGCAACCT 60.108 55.000 9.46 0.00 0.00 3.50
6673 6978 7.393515 GGTGGTTGAAGAGGTAATGATACTTTT 59.606 37.037 0.00 0.00 32.36 2.27
6798 7104 0.687354 ACAGACTCATGAAAGCCGGT 59.313 50.000 1.90 0.00 0.00 5.28
6984 7290 1.339610 CCTCTTCTGGCGACTCTATGG 59.660 57.143 0.00 0.00 0.00 2.74
7422 7730 2.366590 ACTATGCCAATCTGAGCATCGA 59.633 45.455 6.19 0.00 46.58 3.59
7506 7814 3.405831 TGAACCAGATTCAGCAGAAGTG 58.594 45.455 0.00 0.00 42.62 3.16
7507 7815 3.071457 TGAACCAGATTCAGCAGAAGTGA 59.929 43.478 0.00 0.00 42.62 3.41
7529 7837 4.941713 AGAGGTATCACTCTTCTGTCCTT 58.058 43.478 0.00 0.00 45.21 3.36
7536 7844 7.878644 GGTATCACTCTTCTGTCCTTTTACTTT 59.121 37.037 0.00 0.00 0.00 2.66
7719 8027 1.981256 TGGAAAGTGCTTGGGACTTC 58.019 50.000 5.03 0.55 32.33 3.01
7757 8065 9.498176 AATAATTGTTCATACTATAACCCGGAC 57.502 33.333 0.73 0.00 0.00 4.79
7859 8168 2.001872 CGGAAAGCCAATGCCAAATTC 58.998 47.619 0.00 0.00 38.69 2.17
8079 8388 3.063045 CCGGCTTTCGTCCAGTTTATAAC 59.937 47.826 0.00 0.00 37.11 1.89
8189 8500 0.392998 CCAAGCTGAAGGCCGTGTAT 60.393 55.000 0.00 0.00 43.05 2.29
8279 8590 1.374758 GACTCACCTGGCGGAAGTG 60.375 63.158 0.00 0.00 32.56 3.16
8399 8710 2.376109 CTTCTAGAGTTAGACCCGGCA 58.624 52.381 0.00 0.00 35.67 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 2.573609 GAACACGTCCAGGATCCGGG 62.574 65.000 23.93 23.93 0.00 5.73
106 131 2.420568 GCCCTCCATCGGACACGTA 61.421 63.158 0.00 0.00 41.85 3.57
128 153 1.267806 CACATCAAAGGCGCTTCACTT 59.732 47.619 7.64 0.00 0.00 3.16
159 184 4.918201 CCGCTCCATCCCTTCGCC 62.918 72.222 0.00 0.00 0.00 5.54
185 210 0.595310 GACTATCTGCCCTCGTTCGC 60.595 60.000 0.00 0.00 0.00 4.70
190 215 1.299468 GCACGACTATCTGCCCTCG 60.299 63.158 0.00 0.00 0.00 4.63
253 298 2.039879 AGACCTAAACCAATTGACCGCT 59.960 45.455 7.12 0.00 0.00 5.52
339 388 0.669318 GATCGCACCCAAGACGAACA 60.669 55.000 0.00 0.00 39.56 3.18
343 392 2.885644 CCGATCGCACCCAAGACG 60.886 66.667 10.32 0.00 0.00 4.18
406 456 4.279922 CCACCAAGAACCGAAAAATACCTT 59.720 41.667 0.00 0.00 0.00 3.50
411 461 2.316108 AGCCACCAAGAACCGAAAAAT 58.684 42.857 0.00 0.00 0.00 1.82
417 467 1.156736 CACTAAGCCACCAAGAACCG 58.843 55.000 0.00 0.00 0.00 4.44
423 473 1.136828 ACCTCACACTAAGCCACCAA 58.863 50.000 0.00 0.00 0.00 3.67
432 482 0.041238 CCTCCTCCCACCTCACACTA 59.959 60.000 0.00 0.00 0.00 2.74
478 530 2.226674 CTCGCTTCCAGGTTTTCTTTCC 59.773 50.000 0.00 0.00 0.00 3.13
483 535 2.171341 AGTCTCGCTTCCAGGTTTTC 57.829 50.000 0.00 0.00 0.00 2.29
492 544 5.076911 GAAGCAATTGATAGTCTCGCTTC 57.923 43.478 10.34 7.57 44.72 3.86
508 560 9.823647 CTTTTATCTCTACTCCTAATGAAGCAA 57.176 33.333 0.00 0.00 0.00 3.91
520 575 5.186198 TGGCAAAGGCTTTTATCTCTACTC 58.814 41.667 10.36 0.00 40.87 2.59
530 585 2.289631 GGTAAGCATGGCAAAGGCTTTT 60.290 45.455 23.21 8.54 44.93 2.27
598 653 6.581171 AACTTCTCTAGGGAATTTTTGCAG 57.419 37.500 5.27 0.00 0.00 4.41
641 696 8.620533 ATCGAAGCTTATTATGCAAAAAGTTC 57.379 30.769 0.00 0.00 0.00 3.01
893 983 8.139350 TCAACAAGAACTCGTGAGATAAGTTAA 58.861 33.333 3.44 0.00 40.84 2.01
1100 1196 5.927281 AACTAGGCTCAACCGATACTAAA 57.073 39.130 0.00 0.00 46.52 1.85
1120 1216 6.034256 GCACACATCATATGAAGAAGCAAAAC 59.966 38.462 14.59 0.00 0.00 2.43
1134 1232 5.830799 ATCCAAGGATAGCACACATCATA 57.169 39.130 0.00 0.00 32.36 2.15
1365 1503 5.269991 ACCCAACATGAAGCTACTACTAGA 58.730 41.667 0.00 0.00 0.00 2.43
1371 1509 5.499004 TCTAAACCCAACATGAAGCTACT 57.501 39.130 0.00 0.00 0.00 2.57
1382 1520 8.817100 CAAAAGATTTCACTTTCTAAACCCAAC 58.183 33.333 0.00 0.00 38.86 3.77
1423 1561 6.228995 TGAATTGCTTGCATGACCAAAATTA 58.771 32.000 3.33 0.00 0.00 1.40
1480 1619 6.543831 AGATTTCCAGGATAGTGTATTTGCAC 59.456 38.462 0.00 0.00 39.51 4.57
1542 1681 8.604640 TTACTTGTCCAACGTCAACAATTATA 57.395 30.769 9.80 3.21 32.85 0.98
1544 1683 6.762187 TCTTACTTGTCCAACGTCAACAATTA 59.238 34.615 9.80 7.04 32.85 1.40
1638 1778 0.822164 GCAAAGATGAGGGCAAGCAT 59.178 50.000 0.00 0.00 0.00 3.79
1648 1789 6.582295 GCGAAATTTTTGACTAGCAAAGATGA 59.418 34.615 12.85 4.37 46.38 2.92
1661 1803 5.529430 TCTCTACTTGGTGCGAAATTTTTGA 59.471 36.000 0.31 0.00 0.00 2.69
1697 1839 5.554437 TTGGGTTTAAGGGTTTTTGGATC 57.446 39.130 0.00 0.00 0.00 3.36
1845 2005 6.194508 CACAAGTTCGTACAACACTCAATTTG 59.805 38.462 9.74 0.00 0.00 2.32
1874 2034 6.318648 TGCAGTCTGTCACTTTTATTCTTTGT 59.681 34.615 0.93 0.00 30.26 2.83
2014 2175 7.523219 CCGTTGCATGTAGATGTAGTTTAAAA 58.477 34.615 1.37 0.00 31.50 1.52
2018 2179 3.374058 GCCGTTGCATGTAGATGTAGTTT 59.626 43.478 1.37 0.00 37.47 2.66
2114 2277 7.598493 CCGTGAGACCAATATGTTTGAAAATTT 59.402 33.333 0.00 0.00 0.00 1.82
2258 2428 3.482436 ACTTTCGTCAAACAGGCCAATA 58.518 40.909 5.01 0.00 0.00 1.90
2304 2474 3.305403 CGAACCTTCTAGTGAGTTGCTCA 60.305 47.826 0.00 0.00 38.25 4.26
2516 2691 9.210426 CGTTGCATGTAGATGTAGTTTAAATTC 57.790 33.333 1.37 0.00 31.50 2.17
2522 2697 3.374058 GCCGTTGCATGTAGATGTAGTTT 59.626 43.478 1.37 0.00 37.47 2.66
2571 2748 5.545658 ACTCACACACAAGTACACAAAAG 57.454 39.130 0.00 0.00 0.00 2.27
2606 2784 5.746721 TGAACACCAGATATTTACATCGTCG 59.253 40.000 0.00 0.00 0.00 5.12
2669 2852 2.760650 AGATAGAGTGCCAATCGTGTGA 59.239 45.455 0.00 0.00 0.00 3.58
2770 2957 1.268999 GCAGCAAAATCCGTGTGTGAA 60.269 47.619 0.00 0.00 0.00 3.18
2817 3004 3.514645 GGTCGCCAGAATTTACGAGTAA 58.485 45.455 0.00 0.00 34.83 2.24
2869 3056 0.536460 AGTATTTATTGGCGGCCGGG 60.536 55.000 29.38 0.00 0.00 5.73
2970 3169 6.009589 AGATTTGACAGACAGAGAGAGAGAA 58.990 40.000 0.00 0.00 0.00 2.87
2982 3189 2.681848 CCATGGCAGAGATTTGACAGAC 59.318 50.000 0.00 0.00 39.98 3.51
2986 3193 0.379669 CGCCATGGCAGAGATTTGAC 59.620 55.000 34.93 2.44 42.06 3.18
3143 3361 6.480320 GCGACTTCCATAGACAAAGATTGTAT 59.520 38.462 0.00 0.00 45.52 2.29
3218 3436 0.325765 GGTACCTGGCTTCCTCCTCT 60.326 60.000 4.06 0.00 0.00 3.69
3389 3607 0.179137 CACGCTGGAGCTTATCGACA 60.179 55.000 0.00 0.00 39.32 4.35
3391 3609 1.226974 GCACGCTGGAGCTTATCGA 60.227 57.895 0.00 0.00 39.32 3.59
3842 4086 4.592192 CGGCGATGGCTCCACGAT 62.592 66.667 0.00 0.00 39.81 3.73
3904 4152 2.041701 GTAAGGGGCCGAACCAGTATA 58.958 52.381 0.00 0.00 42.05 1.47
3925 4173 5.763876 AGATGTAGGCTTTTACCTTCACT 57.236 39.130 0.00 0.00 39.58 3.41
3947 4195 6.200114 ACCCTAAGCAATACTACCTCAACTA 58.800 40.000 0.00 0.00 0.00 2.24
3957 4207 5.116882 GTCATCGAAACCCTAAGCAATACT 58.883 41.667 0.00 0.00 0.00 2.12
3964 4214 2.420129 CCCTGGTCATCGAAACCCTAAG 60.420 54.545 15.52 8.05 35.84 2.18
4025 4275 2.736682 CGGCAGCGGTTTAGGAACG 61.737 63.158 0.00 0.00 36.61 3.95
4028 4278 4.090588 CCCGGCAGCGGTTTAGGA 62.091 66.667 0.00 0.00 0.00 2.94
4247 4499 3.244009 ACTCATAATGGTCATCGCCAGAG 60.244 47.826 0.00 0.00 42.47 3.35
4377 4634 0.591170 CCACGCAATTATAAGCCGGG 59.409 55.000 2.18 0.00 0.00 5.73
4396 4653 0.032952 TCACGCCGGGTTATAGCATC 59.967 55.000 2.18 0.00 0.00 3.91
4398 4655 1.142314 GTCACGCCGGGTTATAGCA 59.858 57.895 2.18 0.00 0.00 3.49
4401 4658 1.311651 TGACGTCACGCCGGGTTATA 61.312 55.000 15.76 0.00 0.00 0.98
4515 4773 2.810012 GCGCCTCGATTTTCGGGAC 61.810 63.158 0.00 0.00 44.60 4.46
4615 4873 4.889780 AGAGAGGAGTGAATGGAGGTAAT 58.110 43.478 0.00 0.00 0.00 1.89
4625 4886 3.757270 AGACGAAGAAGAGAGGAGTGAA 58.243 45.455 0.00 0.00 0.00 3.18
4719 5005 0.327924 ACCGATTCAGGGTGATGCAA 59.672 50.000 0.00 0.00 36.14 4.08
4771 5059 0.902531 GCCAGGACTTACAGGTGCTA 59.097 55.000 0.00 0.00 36.16 3.49
4875 5167 8.553459 TTAAGATCAAGAAGAGGCAGTAAAAG 57.447 34.615 0.00 0.00 0.00 2.27
4923 5215 0.388520 GAAATGAGTGCCAAACCGCC 60.389 55.000 0.00 0.00 0.00 6.13
4926 5218 3.187022 GCATTTGAAATGAGTGCCAAACC 59.813 43.478 21.14 0.00 32.26 3.27
4953 5245 4.156739 CCTTTATGCAGTCAAAAGAGGTCC 59.843 45.833 12.59 0.00 33.05 4.46
5173 5466 0.612732 CATGGCCTCCTTTTGAGCCA 60.613 55.000 3.32 4.86 45.27 4.75
5318 5614 9.997482 GAAATTTACAGTTCAGTGTTAAAGTGA 57.003 29.630 5.20 0.00 36.40 3.41
5618 5918 2.628178 TCTCTGAAGAACTTTGAGCCGA 59.372 45.455 10.96 0.00 0.00 5.54
5643 5943 2.069273 CGCAGGTCGAAGAAATTCAGT 58.931 47.619 0.00 0.00 39.69 3.41
5832 6132 1.826921 GTCCCTCCGTCGCTGGATA 60.827 63.158 3.72 0.00 37.41 2.59
5904 6204 3.009723 CGTGTCTTGGCAATAGAACCAT 58.990 45.455 0.00 0.00 35.42 3.55
5990 6290 2.410053 GCTTGAGTTAGCTTGTCTGACG 59.590 50.000 2.98 0.00 36.51 4.35
6097 6397 4.873129 CACCCGCCACGAGATCCG 62.873 72.222 0.00 2.55 45.44 4.18
6171 6471 2.997315 CGGCTGTGTCTCAGGGGA 60.997 66.667 4.18 0.00 43.78 4.81
6271 6571 0.107459 GTCTTGCAGAAGGGGGCTAG 60.107 60.000 0.00 0.00 34.80 3.42
6330 6630 9.050601 GGTGAAGAATATCTACAAAGGAAGATG 57.949 37.037 0.00 0.00 34.36 2.90
6337 6637 9.829507 AGATTCAGGTGAAGAATATCTACAAAG 57.170 33.333 0.00 0.00 37.48 2.77
6348 6648 9.573166 TGATTTCTTAAAGATTCAGGTGAAGAA 57.427 29.630 0.00 0.00 37.48 2.52
6349 6649 9.745018 ATGATTTCTTAAAGATTCAGGTGAAGA 57.255 29.630 0.00 0.00 37.48 2.87
6450 6752 2.203480 TTGGCGGCTTTCTTGGCT 60.203 55.556 11.43 0.00 0.00 4.75
6592 6896 6.822442 TGAATAGTATTGATAAGGCGGACAA 58.178 36.000 0.00 0.00 0.00 3.18
6646 6951 4.927267 ATCATTACCTCTTCAACCACCA 57.073 40.909 0.00 0.00 0.00 4.17
6798 7104 4.572571 GTTGGTCCGGGTGTGCCA 62.573 66.667 0.00 0.00 36.17 4.92
6984 7290 3.591254 AAGCCGGCAGGTTCGACTC 62.591 63.158 31.54 0.00 40.50 3.36
7396 7704 2.748605 CTCAGATTGGCATAGTCGGAC 58.251 52.381 0.00 0.00 0.00 4.79
7397 7705 1.069204 GCTCAGATTGGCATAGTCGGA 59.931 52.381 0.00 0.00 0.00 4.55
7506 7814 4.532834 AGGACAGAAGAGTGATACCTCTC 58.467 47.826 0.00 0.00 40.93 3.20
7507 7815 4.601406 AGGACAGAAGAGTGATACCTCT 57.399 45.455 0.00 0.00 43.65 3.69
8079 8388 8.242053 GCAATGATGGATTATGAGACATAAAGG 58.758 37.037 8.00 0.00 0.00 3.11
8095 8406 0.035152 AAGTCGCTGGCAATGATGGA 60.035 50.000 0.00 0.00 0.00 3.41
8189 8500 0.178903 AGAGTTGCTCCACCAGGGTA 60.179 55.000 0.00 0.00 38.11 3.69
8234 8545 0.468029 CATTGGATAGGGCCACCACC 60.468 60.000 14.83 8.89 37.75 4.61
8383 8694 1.005097 TGTCTGCCGGGTCTAACTCTA 59.995 52.381 2.18 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.