Multiple sequence alignment - TraesCS6B01G400600

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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 TraesCS6B01G400600 chr6B 100.000 2558 0 0 1 2558 676046282 676048839 0.000000e+00 4724.0
1 TraesCS6B01G400600 chr6B 84.228 894 81 21 730 1594 676036087 676036949 0.000000e+00 815.0
2 TraesCS6B01G400600 chr6B 78.360 1012 115 41 673 1652 675702915 675701976 6.180000e-156 560.0
3 TraesCS6B01G400600 chr6B 82.549 510 38 20 2069 2558 676037531 676038009 3.960000e-108 401.0
4 TraesCS6B01G400600 chr6B 84.638 345 31 8 1740 2072 675672767 675672433 8.830000e-85 324.0
5 TraesCS6B01G400600 chr6B 81.871 342 34 17 1053 1387 676136344 676136664 1.950000e-66 263.0
6 TraesCS6B01G400600 chr6B 85.535 159 16 5 1200 1356 678357134 678357287 2.630000e-35 159.0
7 TraesCS6B01G400600 chr6B 91.667 72 5 1 336 407 22733739 22733669 5.820000e-17 99.0
8 TraesCS6B01G400600 chr6D 86.131 1370 106 38 769 2072 446881996 446883347 0.000000e+00 1400.0
9 TraesCS6B01G400600 chr6D 92.355 327 18 5 14 335 446881263 446881587 2.320000e-125 459.0
10 TraesCS6B01G400600 chr6D 86.429 420 39 10 1659 2072 446727426 446727019 6.490000e-121 444.0
11 TraesCS6B01G400600 chr6D 81.229 602 65 18 1088 1659 446728045 446727462 2.340000e-120 442.0
12 TraesCS6B01G400600 chr6D 85.117 383 45 11 410 784 446881606 446881984 5.160000e-102 381.0
13 TraesCS6B01G400600 chr6D 81.988 322 44 7 1088 1399 446934808 446935125 7.020000e-66 261.0
14 TraesCS6B01G400600 chr6D 82.432 296 20 10 1073 1367 446948436 446948700 1.980000e-56 230.0
15 TraesCS6B01G400600 chr6D 79.787 282 28 16 2066 2342 446883461 446883718 7.270000e-41 178.0
16 TraesCS6B01G400600 chr6D 81.385 231 22 13 2137 2363 446726824 446726611 4.380000e-38 169.0
17 TraesCS6B01G400600 chr6D 78.676 272 41 11 410 667 24580920 24581188 5.660000e-37 165.0
18 TraesCS6B01G400600 chr6A 81.591 1320 148 44 802 2072 593732570 593733843 0.000000e+00 1003.0
19 TraesCS6B01G400600 chr6A 81.453 647 73 21 1034 1659 593562365 593561745 1.060000e-133 486.0
20 TraesCS6B01G400600 chr6A 87.440 414 40 7 1659 2072 593561709 593561308 1.390000e-127 466.0
21 TraesCS6B01G400600 chr6A 82.267 344 46 10 1065 1399 593785693 593786030 1.500000e-72 283.0
22 TraesCS6B01G400600 chr6A 93.056 72 4 1 336 407 235083788 235083858 1.250000e-18 104.0
23 TraesCS6B01G400600 chr6A 95.161 62 3 0 2426 2487 593560619 593560558 5.820000e-17 99.0
24 TraesCS6B01G400600 chr6A 88.060 67 3 2 1776 1841 593575780 593575842 9.820000e-10 75.0
25 TraesCS6B01G400600 chr3A 83.200 250 32 6 410 650 65362122 65361874 1.190000e-53 220.0
26 TraesCS6B01G400600 chr7A 95.890 73 3 0 336 408 206709842 206709770 4.470000e-23 119.0
27 TraesCS6B01G400600 chr2B 94.521 73 3 1 336 407 659067321 659067249 7.480000e-21 111.0
28 TraesCS6B01G400600 chr2B 91.667 72 4 1 336 407 159968512 159968443 5.820000e-17 99.0
29 TraesCS6B01G400600 chr2D 94.444 72 3 1 336 407 637442006 637442076 2.690000e-20 110.0
30 TraesCS6B01G400600 chr4A 93.056 72 4 1 336 407 236541805 236541735 1.250000e-18 104.0
31 TraesCS6B01G400600 chr7B 91.781 73 5 1 336 408 589938043 589938114 1.620000e-17 100.0
32 TraesCS6B01G400600 chr5B 86.517 89 5 7 324 407 27509394 27509480 9.750000e-15 91.6


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 TraesCS6B01G400600 chr6B 676046282 676048839 2557 False 4724.000000 4724 100.000000 1 2558 1 chr6B.!!$F1 2557
1 TraesCS6B01G400600 chr6B 676036087 676038009 1922 False 608.000000 815 83.388500 730 2558 2 chr6B.!!$F4 1828
2 TraesCS6B01G400600 chr6B 675701976 675702915 939 True 560.000000 560 78.360000 673 1652 1 chr6B.!!$R3 979
3 TraesCS6B01G400600 chr6D 446881263 446883718 2455 False 604.500000 1400 85.847500 14 2342 4 chr6D.!!$F4 2328
4 TraesCS6B01G400600 chr6D 446726611 446728045 1434 True 351.666667 444 83.014333 1088 2363 3 chr6D.!!$R1 1275
5 TraesCS6B01G400600 chr6A 593732570 593733843 1273 False 1003.000000 1003 81.591000 802 2072 1 chr6A.!!$F3 1270
6 TraesCS6B01G400600 chr6A 593560558 593562365 1807 True 350.333333 486 88.018000 1034 2487 3 chr6A.!!$R1 1453

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
791 833 0.597568 TTCAAAGCGAGTTGGCATGG 59.402 50.0 0.0 0.0 34.64 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2641 0.392863 CCAACGCATCCACCATCTGA 60.393 55.0 0.0 0.0 0.0 3.27 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
19 20 1.758514 TTTGCCCCGGTTTTGCTCA 60.759 52.632 0.00 0.00 0.00 4.26
25 26 2.718731 CGGTTTTGCTCAACGGCA 59.281 55.556 0.00 0.00 40.74 5.69
46 47 4.386652 GCAACATGCAAATGTCGAAGAAAT 59.613 37.500 0.00 0.00 44.26 2.17
76 77 1.198759 TCCTACTCCTGGCACAACCC 61.199 60.000 0.00 0.00 38.70 4.11
113 114 0.886490 GGATTCGGATCGGCATTGCT 60.886 55.000 8.82 0.00 32.84 3.91
137 138 1.949465 AGTCCGAACACGCTTTTTCT 58.051 45.000 0.00 0.00 0.00 2.52
138 139 1.865340 AGTCCGAACACGCTTTTTCTC 59.135 47.619 0.00 0.00 0.00 2.87
143 146 3.535860 CGAACACGCTTTTTCTCAAGAG 58.464 45.455 0.00 0.00 0.00 2.85
150 153 4.444720 ACGCTTTTTCTCAAGAGACTTACG 59.555 41.667 0.00 3.71 37.14 3.18
159 162 3.255888 TCAAGAGACTTACGCATCAGTGT 59.744 43.478 0.00 0.00 42.14 3.55
176 179 1.530236 GTGTTGTTCACACGGAAACCG 60.530 52.381 8.67 8.67 46.51 4.44
335 341 7.394923 TGAAATAAACCCGACCTTTCATTGTAT 59.605 33.333 0.00 0.00 32.52 2.29
336 342 6.937436 ATAAACCCGACCTTTCATTGTATC 57.063 37.500 0.00 0.00 0.00 2.24
337 343 3.277142 ACCCGACCTTTCATTGTATCC 57.723 47.619 0.00 0.00 0.00 2.59
338 344 2.092592 ACCCGACCTTTCATTGTATCCC 60.093 50.000 0.00 0.00 0.00 3.85
340 346 3.467803 CCGACCTTTCATTGTATCCCTC 58.532 50.000 0.00 0.00 0.00 4.30
341 347 3.467803 CGACCTTTCATTGTATCCCTCC 58.532 50.000 0.00 0.00 0.00 4.30
343 349 2.844348 ACCTTTCATTGTATCCCTCCGT 59.156 45.455 0.00 0.00 0.00 4.69
344 350 3.265995 ACCTTTCATTGTATCCCTCCGTT 59.734 43.478 0.00 0.00 0.00 4.44
345 351 3.877508 CCTTTCATTGTATCCCTCCGTTC 59.122 47.826 0.00 0.00 0.00 3.95
346 352 3.553828 TTCATTGTATCCCTCCGTTCC 57.446 47.619 0.00 0.00 0.00 3.62
347 353 2.473070 TCATTGTATCCCTCCGTTCCA 58.527 47.619 0.00 0.00 0.00 3.53
348 354 2.841266 TCATTGTATCCCTCCGTTCCAA 59.159 45.455 0.00 0.00 0.00 3.53
349 355 3.264706 TCATTGTATCCCTCCGTTCCAAA 59.735 43.478 0.00 0.00 0.00 3.28
350 356 3.791953 TTGTATCCCTCCGTTCCAAAA 57.208 42.857 0.00 0.00 0.00 2.44
351 357 4.310022 TTGTATCCCTCCGTTCCAAAAT 57.690 40.909 0.00 0.00 0.00 1.82
353 359 5.031066 TGTATCCCTCCGTTCCAAAATAG 57.969 43.478 0.00 0.00 0.00 1.73
355 361 5.368523 TGTATCCCTCCGTTCCAAAATAGAT 59.631 40.000 0.00 0.00 0.00 1.98
356 362 4.150897 TCCCTCCGTTCCAAAATAGATG 57.849 45.455 0.00 0.00 0.00 2.90
357 363 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
358 364 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
359 365 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
360 366 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
361 367 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
362 368 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
363 369 6.234920 TCCGTTCCAAAATAGATGACTCAAA 58.765 36.000 0.00 0.00 0.00 2.69
364 370 6.371548 TCCGTTCCAAAATAGATGACTCAAAG 59.628 38.462 0.00 0.00 0.00 2.77
365 371 6.149474 CCGTTCCAAAATAGATGACTCAAAGT 59.851 38.462 0.00 0.00 0.00 2.66
366 372 7.308589 CCGTTCCAAAATAGATGACTCAAAGTT 60.309 37.037 0.00 0.00 0.00 2.66
367 373 8.717821 CGTTCCAAAATAGATGACTCAAAGTTA 58.282 33.333 0.00 0.00 0.00 2.24
369 375 9.793259 TTCCAAAATAGATGACTCAAAGTTAGT 57.207 29.630 0.00 0.00 0.00 2.24
381 387 9.841295 TGACTCAAAGTTAGTACAAAATTAGGT 57.159 29.630 0.00 0.00 0.00 3.08
383 389 9.841295 ACTCAAAGTTAGTACAAAATTAGGTCA 57.159 29.630 0.00 0.00 0.00 4.02
398 404 8.996024 AAATTAGGTCATTTATTTTGGAACGG 57.004 30.769 0.00 0.00 0.00 4.44
399 405 7.948034 ATTAGGTCATTTATTTTGGAACGGA 57.052 32.000 0.00 0.00 0.00 4.69
400 406 5.897377 AGGTCATTTATTTTGGAACGGAG 57.103 39.130 0.00 0.00 0.00 4.63
401 407 4.705023 AGGTCATTTATTTTGGAACGGAGG 59.295 41.667 0.00 0.00 0.00 4.30
402 408 4.142249 GGTCATTTATTTTGGAACGGAGGG 60.142 45.833 0.00 0.00 0.00 4.30
403 409 4.703093 GTCATTTATTTTGGAACGGAGGGA 59.297 41.667 0.00 0.00 0.00 4.20
404 410 4.947388 TCATTTATTTTGGAACGGAGGGAG 59.053 41.667 0.00 0.00 0.00 4.30
405 411 4.376225 TTTATTTTGGAACGGAGGGAGT 57.624 40.909 0.00 0.00 0.00 3.85
406 412 5.502089 TTTATTTTGGAACGGAGGGAGTA 57.498 39.130 0.00 0.00 0.00 2.59
407 413 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
408 414 0.978907 TTTGGAACGGAGGGAGTACC 59.021 55.000 0.00 0.00 40.67 3.34
483 489 8.756864 GCTAAAATAGTGTGAATAGTGAGCTAC 58.243 37.037 0.00 0.00 0.00 3.58
513 519 8.631797 AGCAAATAATTTTTGTCATTTTTGCCT 58.368 25.926 11.98 0.28 45.28 4.75
520 526 7.446001 TTTTTGTCATTTTTGCCTTCAAGTT 57.554 28.000 0.00 0.00 33.12 2.66
530 536 3.018149 TGCCTTCAAGTTAACGTTGGTT 58.982 40.909 11.99 0.00 40.20 3.67
576 583 3.694566 AGTGCGAAAGGAAGTCAAGTTTT 59.305 39.130 0.00 0.00 0.00 2.43
646 658 8.917414 ATCCTCATACAGGGTGTATATACAAT 57.083 34.615 17.07 3.61 41.28 2.71
651 663 7.733047 TCATACAGGGTGTATATACAATCAGGT 59.267 37.037 17.07 13.36 41.28 4.00
653 665 7.208064 ACAGGGTGTATATACAATCAGGTTT 57.792 36.000 17.07 0.00 38.04 3.27
660 672 9.095065 GTGTATATACAATCAGGTTTCGAAGTT 57.905 33.333 17.07 0.00 38.04 2.66
668 680 5.600908 TCAGGTTTCGAAGTTTATTTCCG 57.399 39.130 0.00 0.00 0.00 4.30
669 681 5.058490 TCAGGTTTCGAAGTTTATTTCCGT 58.942 37.500 0.00 0.00 0.00 4.69
670 682 6.222389 TCAGGTTTCGAAGTTTATTTCCGTA 58.778 36.000 0.00 0.00 0.00 4.02
671 683 6.875195 TCAGGTTTCGAAGTTTATTTCCGTAT 59.125 34.615 0.00 0.00 0.00 3.06
700 712 7.361127 GCGAGATGCTACTAATCAAAGTACTA 58.639 38.462 0.00 0.00 41.73 1.82
791 833 0.597568 TTCAAAGCGAGTTGGCATGG 59.402 50.000 0.00 0.00 34.64 3.66
880 930 3.941188 CCGGACCCACAGCACAGT 61.941 66.667 0.00 0.00 0.00 3.55
903 953 1.065600 CACAACGCCCACTGGTTTG 59.934 57.895 0.00 0.00 34.59 2.93
907 957 3.726517 CGCCCACTGGTTTGAGCG 61.727 66.667 1.90 1.90 37.39 5.03
958 1008 2.583441 CCCACCCACTGAAGCTCGA 61.583 63.158 0.00 0.00 0.00 4.04
975 1025 8.470805 TGAAGCTCGAAGTTCTCTATAAATTCT 58.529 33.333 0.56 0.00 32.68 2.40
1027 1077 1.372997 CCCGACTCAAGTGACACCG 60.373 63.158 0.84 0.00 0.00 4.94
1230 1298 1.581954 CAAGTCCGTCAGCGTCTCT 59.418 57.895 0.00 0.00 36.15 3.10
1236 1304 2.636412 CGTCAGCGTCTCTTCCCCA 61.636 63.158 0.00 0.00 0.00 4.96
1253 1321 3.470888 ATCTTCCTCCACCGGCGG 61.471 66.667 27.06 27.06 0.00 6.13
1305 1376 2.993264 TCCTCGACGAACCACCCC 60.993 66.667 0.00 0.00 0.00 4.95
1326 1397 3.883744 CTCGTTCCGGTGCAGCCTT 62.884 63.158 10.90 0.00 34.25 4.35
1389 1463 2.190578 GCTTCCCCTCCGTCCATG 59.809 66.667 0.00 0.00 0.00 3.66
1425 1499 1.143183 GGGCTCGAAGCGTATGGAA 59.857 57.895 0.00 0.00 43.62 3.53
1431 1505 0.804544 CGAAGCGTATGGAAAGCGGA 60.805 55.000 0.00 0.00 37.69 5.54
1434 1508 0.178068 AGCGTATGGAAAGCGGACAT 59.822 50.000 0.00 0.00 37.69 3.06
1437 1511 1.330521 CGTATGGAAAGCGGACATTGG 59.669 52.381 0.00 0.00 0.00 3.16
1442 1516 1.523154 GAAAGCGGACATTGGGCACA 61.523 55.000 0.00 0.00 0.00 4.57
1448 1522 0.962356 GGACATTGGGCACACAGGAG 60.962 60.000 0.00 0.00 0.00 3.69
1450 1524 1.679977 CATTGGGCACACAGGAGGG 60.680 63.158 0.00 0.00 0.00 4.30
1451 1525 2.922704 ATTGGGCACACAGGAGGGG 61.923 63.158 0.00 0.00 0.00 4.79
1452 1526 4.590553 TGGGCACACAGGAGGGGA 62.591 66.667 0.00 0.00 0.00 4.81
1453 1527 3.256960 GGGCACACAGGAGGGGAA 61.257 66.667 0.00 0.00 0.00 3.97
1454 1528 2.352805 GGCACACAGGAGGGGAAG 59.647 66.667 0.00 0.00 0.00 3.46
1455 1529 2.360475 GCACACAGGAGGGGAAGC 60.360 66.667 0.00 0.00 0.00 3.86
1457 1531 3.322466 ACACAGGAGGGGAAGCCG 61.322 66.667 0.00 0.00 0.00 5.52
1561 1674 3.628487 TCCCAACGACAACCAGTAAAAAG 59.372 43.478 0.00 0.00 0.00 2.27
1563 1676 4.096682 CCCAACGACAACCAGTAAAAAGAA 59.903 41.667 0.00 0.00 0.00 2.52
1577 1690 2.148916 AAAGAACAGCGTCGACATGA 57.851 45.000 21.00 0.00 0.00 3.07
1597 1717 9.144747 GACATGACATAGCAATATGTAGTTAGG 57.855 37.037 0.00 0.00 40.45 2.69
1598 1718 8.870116 ACATGACATAGCAATATGTAGTTAGGA 58.130 33.333 0.00 0.00 40.45 2.94
1605 1751 7.793927 AGCAATATGTAGTTAGGAGCTTTTC 57.206 36.000 0.00 0.00 0.00 2.29
1618 1764 1.681264 AGCTTTTCCGTTTTGACCCAG 59.319 47.619 0.00 0.00 0.00 4.45
1626 1772 2.292292 CCGTTTTGACCCAGTTCGATTT 59.708 45.455 0.00 0.00 0.00 2.17
1628 1774 3.250040 CGTTTTGACCCAGTTCGATTTCT 59.750 43.478 0.00 0.00 0.00 2.52
1629 1775 4.261031 CGTTTTGACCCAGTTCGATTTCTT 60.261 41.667 0.00 0.00 0.00 2.52
1646 1792 7.225538 TCGATTTCTTCCTGATCAATTTAGCTC 59.774 37.037 0.00 0.00 0.00 4.09
1663 1845 2.202623 CGCCCGTAGCTGTCTGTC 60.203 66.667 0.00 0.00 40.39 3.51
1670 1852 2.688446 CCGTAGCTGTCTGTCCATAGAA 59.312 50.000 0.00 0.00 0.00 2.10
1736 1921 9.184523 CCTTGGTTTTGGATATAACTACATGAA 57.815 33.333 0.00 0.00 0.00 2.57
1738 1923 9.747898 TTGGTTTTGGATATAACTACATGAACT 57.252 29.630 0.00 0.00 0.00 3.01
1754 1939 4.916983 TGAACTTGAGTGACAAATTGGG 57.083 40.909 0.00 0.00 38.08 4.12
1815 2001 1.048601 GGAGGCTTATCCGTCCATGA 58.951 55.000 0.00 0.00 40.77 3.07
1846 2050 1.481819 GCCGCAACAACTTTGTGCTG 61.482 55.000 11.90 8.30 41.31 4.41
1882 2086 1.194781 AGTGTGGATTGGTCTCGCCT 61.195 55.000 0.00 0.00 38.35 5.52
1914 2118 2.893637 TCGGATAAGCTCTGCAAAGAC 58.106 47.619 0.00 0.00 0.00 3.01
1923 2127 2.775890 CTCTGCAAAGACATCAGTGGT 58.224 47.619 0.00 0.00 0.00 4.16
1935 2139 2.910479 AGTGGTGTCTCGCCGTCA 60.910 61.111 0.00 0.00 36.72 4.35
2056 2261 7.114882 ACTTTCATGATCGAATCGATGAATC 57.885 36.000 23.67 9.91 47.00 2.52
2173 2535 7.974501 TCTCTCTATCAAATACGGTGTTTCTTC 59.025 37.037 0.00 0.00 0.00 2.87
2187 2549 4.691216 GTGTTTCTTCTGCTTAACGATCCT 59.309 41.667 0.00 0.00 0.00 3.24
2188 2550 4.690748 TGTTTCTTCTGCTTAACGATCCTG 59.309 41.667 0.00 0.00 0.00 3.86
2205 2567 8.759481 ACGATCCTGATACTGATCATACATAT 57.241 34.615 0.00 0.00 41.33 1.78
2206 2568 9.853177 ACGATCCTGATACTGATCATACATATA 57.147 33.333 0.00 0.00 41.33 0.86
2252 2615 1.000607 TCAGAACCGCTGTCTGTGTAC 60.001 52.381 7.71 0.00 45.14 2.90
2335 2723 0.819582 GGGTTGCTGATGGTGGAATG 59.180 55.000 0.00 0.00 0.00 2.67
2389 2777 8.912787 TTCTTTAACTGAATATCTGACGAGTC 57.087 34.615 0.00 0.00 0.00 3.36
2415 3056 6.072230 GGTAGTACTCCGTTCTAACAAACTCT 60.072 42.308 0.00 0.00 0.00 3.24
2416 3057 5.770417 AGTACTCCGTTCTAACAAACTCTG 58.230 41.667 0.00 0.00 0.00 3.35
2417 3058 4.667519 ACTCCGTTCTAACAAACTCTGT 57.332 40.909 0.00 0.00 41.27 3.41
2421 3062 7.043565 ACTCCGTTCTAACAAACTCTGTAAAA 58.956 34.615 0.00 0.00 37.23 1.52
2422 3063 7.713942 ACTCCGTTCTAACAAACTCTGTAAAAT 59.286 33.333 0.00 0.00 37.23 1.82
2423 3064 9.199982 CTCCGTTCTAACAAACTCTGTAAAATA 57.800 33.333 0.00 0.00 37.23 1.40
2424 3065 9.199982 TCCGTTCTAACAAACTCTGTAAAATAG 57.800 33.333 0.00 0.00 37.23 1.73
2510 3157 3.722295 ACAAATGCCACGGACGCG 61.722 61.111 3.53 3.53 0.00 6.01
2517 3164 4.717629 CCACGGACGCGAGCAGAA 62.718 66.667 15.93 0.00 0.00 3.02
2522 3169 1.782181 GGACGCGAGCAGAAGAAAC 59.218 57.895 15.93 0.00 0.00 2.78
2532 3179 2.371510 AGCAGAAGAAACTCTCTTGCCT 59.628 45.455 8.07 0.00 44.82 4.75
2537 3184 1.227943 AAACTCTCTTGCCTGCGCA 60.228 52.632 10.98 10.98 45.49 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.300620 GAGCAAAACCGGGGCAAAC 60.301 57.895 6.32 0.00 0.00 2.93
1 2 1.330655 TTGAGCAAAACCGGGGCAAA 61.331 50.000 6.32 0.33 0.00 3.68
2 3 1.758514 TTGAGCAAAACCGGGGCAA 60.759 52.632 6.32 0.00 0.00 4.52
3 4 2.123683 TTGAGCAAAACCGGGGCA 60.124 55.556 6.32 0.00 0.00 5.36
4 5 2.338620 GTTGAGCAAAACCGGGGC 59.661 61.111 6.32 3.68 0.00 5.80
5 6 2.642700 CGTTGAGCAAAACCGGGG 59.357 61.111 6.32 0.00 0.00 5.73
6 7 2.642700 CCGTTGAGCAAAACCGGG 59.357 61.111 6.32 0.00 0.00 5.73
7 8 2.050442 GCCGTTGAGCAAAACCGG 60.050 61.111 0.00 0.00 0.00 5.28
8 9 2.718731 TGCCGTTGAGCAAAACCG 59.281 55.556 0.00 0.00 40.56 4.44
19 20 1.782044 GACATTTGCATGTTGCCGTT 58.218 45.000 0.00 0.00 44.22 4.44
25 26 6.753279 CCATATTTCTTCGACATTTGCATGTT 59.247 34.615 0.00 0.00 44.22 2.71
113 114 2.029964 GCGTGTTCGGACTTGGGA 59.970 61.111 0.00 0.00 37.56 4.37
137 138 3.255888 ACACTGATGCGTAAGTCTCTTGA 59.744 43.478 0.00 0.00 41.68 3.02
138 139 3.579709 ACACTGATGCGTAAGTCTCTTG 58.420 45.455 0.00 0.00 41.68 3.02
143 146 3.493129 TGAACAACACTGATGCGTAAGTC 59.507 43.478 0.00 0.00 41.68 3.01
202 205 5.048852 GTCCGTGTCCCTCACTATATACTTC 60.049 48.000 0.00 0.00 44.16 3.01
210 213 0.538057 AACGTCCGTGTCCCTCACTA 60.538 55.000 0.00 0.00 44.16 2.74
211 214 1.397390 AAACGTCCGTGTCCCTCACT 61.397 55.000 0.00 0.00 44.16 3.41
212 215 1.068585 AAACGTCCGTGTCCCTCAC 59.931 57.895 0.00 0.00 43.03 3.51
213 216 1.068417 CAAACGTCCGTGTCCCTCA 59.932 57.895 0.00 0.00 0.00 3.86
224 227 1.385528 ACACCAAGGAACCAAACGTC 58.614 50.000 0.00 0.00 0.00 4.34
320 326 3.467803 GGAGGGATACAATGAAAGGTCG 58.532 50.000 0.00 0.00 39.74 4.79
335 341 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
336 342 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
337 343 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
338 344 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
340 346 6.149474 ACTTTGAGTCATCTATTTTGGAACGG 59.851 38.462 0.00 0.00 0.00 4.44
341 347 7.133891 ACTTTGAGTCATCTATTTTGGAACG 57.866 36.000 0.00 0.00 0.00 3.95
343 349 9.793259 ACTAACTTTGAGTCATCTATTTTGGAA 57.207 29.630 0.00 0.00 0.00 3.53
355 361 9.841295 ACCTAATTTTGTACTAACTTTGAGTCA 57.159 29.630 0.00 0.00 0.00 3.41
357 363 9.841295 TGACCTAATTTTGTACTAACTTTGAGT 57.159 29.630 0.00 0.00 0.00 3.41
372 378 9.430623 CCGTTCCAAAATAAATGACCTAATTTT 57.569 29.630 0.00 0.00 33.07 1.82
373 379 8.808092 TCCGTTCCAAAATAAATGACCTAATTT 58.192 29.630 0.00 0.00 34.24 1.82
374 380 8.356000 TCCGTTCCAAAATAAATGACCTAATT 57.644 30.769 0.00 0.00 0.00 1.40
375 381 7.068226 CCTCCGTTCCAAAATAAATGACCTAAT 59.932 37.037 0.00 0.00 0.00 1.73
376 382 6.376018 CCTCCGTTCCAAAATAAATGACCTAA 59.624 38.462 0.00 0.00 0.00 2.69
377 383 5.883673 CCTCCGTTCCAAAATAAATGACCTA 59.116 40.000 0.00 0.00 0.00 3.08
378 384 4.705023 CCTCCGTTCCAAAATAAATGACCT 59.295 41.667 0.00 0.00 0.00 3.85
379 385 4.142249 CCCTCCGTTCCAAAATAAATGACC 60.142 45.833 0.00 0.00 0.00 4.02
380 386 4.703093 TCCCTCCGTTCCAAAATAAATGAC 59.297 41.667 0.00 0.00 0.00 3.06
381 387 4.924625 TCCCTCCGTTCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
382 388 4.705023 ACTCCCTCCGTTCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
383 389 4.930696 ACTCCCTCCGTTCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
384 390 4.376225 ACTCCCTCCGTTCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
385 391 4.323715 GGTACTCCCTCCGTTCCAAAATAA 60.324 45.833 0.00 0.00 0.00 1.40
386 392 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
387 393 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
388 394 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
389 395 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
390 396 2.674958 GGTACTCCCTCCGTTCCAA 58.325 57.895 0.00 0.00 0.00 3.53
391 397 4.447734 GGTACTCCCTCCGTTCCA 57.552 61.111 0.00 0.00 0.00 3.53
414 420 8.040002 TGAAAATAAGTCAAAGGGGGATTTTT 57.960 30.769 0.00 0.00 0.00 1.94
419 425 7.439108 TTTTTGAAAATAAGTCAAAGGGGGA 57.561 32.000 0.00 0.00 43.76 4.81
465 471 6.307031 CTATCGTAGCTCACTATTCACACT 57.693 41.667 0.00 0.00 0.00 3.55
496 502 7.446001 AACTTGAAGGCAAAAATGACAAAAA 57.554 28.000 0.00 0.00 32.73 1.94
504 510 5.522097 CCAACGTTAACTTGAAGGCAAAAAT 59.478 36.000 0.00 0.00 32.73 1.82
552 559 3.279434 ACTTGACTTCCTTTCGCACTTT 58.721 40.909 0.00 0.00 0.00 2.66
553 560 2.919228 ACTTGACTTCCTTTCGCACTT 58.081 42.857 0.00 0.00 0.00 3.16
620 632 8.736097 TTGTATATACACCCTGTATGAGGATT 57.264 34.615 15.20 0.00 42.93 3.01
622 634 7.953493 TGATTGTATATACACCCTGTATGAGGA 59.047 37.037 15.20 0.00 42.93 3.71
623 635 8.134202 TGATTGTATATACACCCTGTATGAGG 57.866 38.462 15.20 0.00 42.93 3.86
626 638 7.907389 ACCTGATTGTATATACACCCTGTATG 58.093 38.462 15.20 2.92 42.93 2.39
633 645 7.709613 ACTTCGAAACCTGATTGTATATACACC 59.290 37.037 15.20 10.57 35.64 4.16
642 654 7.368059 GGAAATAAACTTCGAAACCTGATTGT 58.632 34.615 0.00 0.00 0.00 2.71
646 658 5.058490 ACGGAAATAAACTTCGAAACCTGA 58.942 37.500 0.00 0.00 0.00 3.86
651 663 8.693504 CGCTATATACGGAAATAAACTTCGAAA 58.306 33.333 0.00 0.00 0.00 3.46
653 665 7.584108 TCGCTATATACGGAAATAAACTTCGA 58.416 34.615 0.00 0.00 0.00 3.71
693 705 7.549147 TTTAGATGGACACAACCTAGTACTT 57.451 36.000 0.00 0.00 0.00 2.24
780 795 0.618458 TGTAGGACCCATGCCAACTC 59.382 55.000 0.00 0.00 0.00 3.01
791 833 5.152934 TCCCCAATATTCTACTGTAGGACC 58.847 45.833 14.47 0.00 0.00 4.46
867 917 2.510906 GGTGACTGTGCTGTGGGT 59.489 61.111 0.00 0.00 0.00 4.51
880 930 3.484806 AGTGGGCGTTGTGGGTGA 61.485 61.111 0.00 0.00 0.00 4.02
903 953 3.605749 TAACTGGGGCTGTGCGCTC 62.606 63.158 9.73 5.51 41.33 5.03
907 957 1.810755 GTTAACTAACTGGGGCTGTGC 59.189 52.381 0.00 0.00 33.52 4.57
958 1008 6.603599 GGTTGGGCAGAATTTATAGAGAACTT 59.396 38.462 0.00 0.00 0.00 2.66
975 1025 2.909965 GCTTCAACGGGTTGGGCA 60.910 61.111 18.13 3.52 40.78 5.36
1027 1077 1.344763 CGTGGAGGGGATGGAGATTAC 59.655 57.143 0.00 0.00 0.00 1.89
1135 1197 2.280865 GCGGTAGCTGGGTATGGC 60.281 66.667 0.00 0.00 41.01 4.40
1230 1298 1.271840 CGGTGGAGGAAGATGGGGAA 61.272 60.000 0.00 0.00 0.00 3.97
1236 1304 3.470888 CCGCCGGTGGAGGAAGAT 61.471 66.667 30.98 0.00 45.77 2.40
1269 1340 4.758251 CACATGCAGGACCGCCGA 62.758 66.667 4.84 0.00 39.96 5.54
1326 1397 1.962822 CTGCTTGCGCTCCTTGTGA 60.963 57.895 9.73 0.00 36.97 3.58
1419 1493 2.021723 GCCCAATGTCCGCTTTCCATA 61.022 52.381 0.00 0.00 0.00 2.74
1425 1499 2.115052 TGTGCCCAATGTCCGCTT 59.885 55.556 0.00 0.00 0.00 4.68
1431 1505 1.075482 CCTCCTGTGTGCCCAATGT 59.925 57.895 0.00 0.00 0.00 2.71
1434 1508 3.579302 CCCCTCCTGTGTGCCCAA 61.579 66.667 0.00 0.00 0.00 4.12
1437 1511 2.352805 CTTCCCCTCCTGTGTGCC 59.647 66.667 0.00 0.00 0.00 5.01
1450 1524 3.880846 CTGCGATTGCCGGCTTCC 61.881 66.667 29.70 17.11 41.78 3.46
1451 1525 4.543084 GCTGCGATTGCCGGCTTC 62.543 66.667 29.70 22.35 41.78 3.86
1546 1659 4.201881 ACGCTGTTCTTTTTACTGGTTGTC 60.202 41.667 0.00 0.00 0.00 3.18
1549 1662 3.001939 CGACGCTGTTCTTTTTACTGGTT 59.998 43.478 0.00 0.00 0.00 3.67
1586 1699 5.927281 ACGGAAAAGCTCCTAACTACATA 57.073 39.130 0.00 0.00 42.85 2.29
1597 1717 1.679153 TGGGTCAAAACGGAAAAGCTC 59.321 47.619 0.00 0.00 0.00 4.09
1598 1718 1.681264 CTGGGTCAAAACGGAAAAGCT 59.319 47.619 0.00 0.00 0.00 3.74
1605 1751 1.519408 ATCGAACTGGGTCAAAACGG 58.481 50.000 0.00 0.00 0.00 4.44
1606 1752 3.250040 AGAAATCGAACTGGGTCAAAACG 59.750 43.478 0.00 0.00 0.00 3.60
1618 1764 7.641802 GCTAAATTGATCAGGAAGAAATCGAAC 59.358 37.037 0.00 0.00 0.00 3.95
1626 1772 4.122776 GCGAGCTAAATTGATCAGGAAGA 58.877 43.478 0.00 0.00 0.00 2.87
1628 1774 3.206150 GGCGAGCTAAATTGATCAGGAA 58.794 45.455 0.00 0.00 0.00 3.36
1629 1775 2.485479 GGGCGAGCTAAATTGATCAGGA 60.485 50.000 0.00 0.00 0.00 3.86
1663 1845 2.890311 AGAGGACGAGCTCATTCTATGG 59.110 50.000 15.40 0.00 0.00 2.74
1670 1852 4.353325 AGCAGAGGACGAGCTCAT 57.647 55.556 15.40 0.00 32.05 2.90
1736 1921 3.222603 GTCCCCAATTTGTCACTCAAGT 58.777 45.455 0.00 0.00 37.35 3.16
1738 1923 2.955660 GTGTCCCCAATTTGTCACTCAA 59.044 45.455 0.00 0.00 0.00 3.02
1754 1939 6.707608 TCAGATTTAGATGCATGTATGTGTCC 59.292 38.462 2.46 0.00 0.00 4.02
1815 2001 1.068281 TGTTGCGGCACACAAATCATT 59.932 42.857 0.05 0.00 29.84 2.57
1846 2050 2.945668 ACACTCCAGAAACAGAAACAGC 59.054 45.455 0.00 0.00 0.00 4.40
1882 2086 2.997986 GCTTATCCGAAACCGAAACAGA 59.002 45.455 0.00 0.00 0.00 3.41
1914 2118 1.807165 CGGCGAGACACCACTGATG 60.807 63.158 0.00 0.00 0.00 3.07
1923 2127 2.355837 GCAAGTGACGGCGAGACA 60.356 61.111 16.62 8.06 0.00 3.41
1978 2182 2.359169 TTTCGCCTCGCCTGATCCT 61.359 57.895 0.00 0.00 0.00 3.24
2014 2218 5.694910 TGAAAGTTCTACACAAATCTCGTCC 59.305 40.000 0.00 0.00 0.00 4.79
2173 2535 5.188327 TCAGTATCAGGATCGTTAAGCAG 57.812 43.478 0.00 0.00 0.00 4.24
2213 2575 9.436957 GGTTCTGAACACAAGATCTTAATTAGA 57.563 33.333 21.01 5.14 37.28 2.10
2215 2577 7.148474 GCGGTTCTGAACACAAGATCTTAATTA 60.148 37.037 21.01 0.00 0.00 1.40
2216 2578 6.348540 GCGGTTCTGAACACAAGATCTTAATT 60.349 38.462 21.01 2.73 0.00 1.40
2217 2579 5.122396 GCGGTTCTGAACACAAGATCTTAAT 59.878 40.000 21.01 0.00 0.00 1.40
2218 2580 4.451096 GCGGTTCTGAACACAAGATCTTAA 59.549 41.667 21.01 0.00 0.00 1.85
2228 2590 0.861837 CAGACAGCGGTTCTGAACAC 59.138 55.000 21.01 12.70 45.72 3.32
2252 2615 2.814269 CATCCACCATCTGAGTGTACG 58.186 52.381 0.00 0.00 33.20 3.67
2259 2641 0.392863 CCAACGCATCCACCATCTGA 60.393 55.000 0.00 0.00 0.00 3.27
2260 2642 1.378882 CCCAACGCATCCACCATCTG 61.379 60.000 0.00 0.00 0.00 2.90
2261 2643 1.077501 CCCAACGCATCCACCATCT 60.078 57.895 0.00 0.00 0.00 2.90
2262 2644 2.774799 GCCCAACGCATCCACCATC 61.775 63.158 0.00 0.00 37.47 3.51
2263 2645 2.755469 GCCCAACGCATCCACCAT 60.755 61.111 0.00 0.00 37.47 3.55
2264 2646 4.277009 TGCCCAACGCATCCACCA 62.277 61.111 0.00 0.00 44.64 4.17
2314 2702 2.362889 CCACCATCAGCAACCCCC 60.363 66.667 0.00 0.00 0.00 5.40
2335 2723 4.669728 CGTCGGATATTCAACGAGTACTTC 59.330 45.833 0.00 0.00 37.30 3.01
2415 3056 9.733556 TCAGAATTTCTGGTTAGCTATTTTACA 57.266 29.630 22.86 0.00 44.39 2.41
2421 3062 6.879458 ACGTTTCAGAATTTCTGGTTAGCTAT 59.121 34.615 22.86 3.01 44.39 2.97
2422 3063 6.228258 ACGTTTCAGAATTTCTGGTTAGCTA 58.772 36.000 22.86 2.61 44.39 3.32
2423 3064 5.063880 ACGTTTCAGAATTTCTGGTTAGCT 58.936 37.500 22.86 0.00 44.39 3.32
2424 3065 5.049680 TGACGTTTCAGAATTTCTGGTTAGC 60.050 40.000 22.86 11.68 44.39 3.09
2501 3148 3.175240 CTTCTGCTCGCGTCCGTG 61.175 66.667 5.77 0.00 35.54 4.94
2510 3157 2.741517 GGCAAGAGAGTTTCTTCTGCTC 59.258 50.000 7.15 0.00 44.34 4.26
2517 3164 0.952984 GCGCAGGCAAGAGAGTTTCT 60.953 55.000 0.30 0.00 39.62 2.52
2537 3184 3.157217 GACTCGATCATGCCCCGCT 62.157 63.158 0.00 0.00 0.00 5.52
2540 3187 4.766970 CTGACTCGATCATGCCCC 57.233 61.111 0.00 0.00 36.48 5.80


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

AutoCloner maintained by Alex Coulton.