Multiple sequence alignment - TraesCS1B01G184000

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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 TraesCS1B01G184000 chr1B 100.000 2465 0 0 1 2465 330626774 330624310 0.000000e+00 4553.0
1 TraesCS1B01G184000 chr1B 80.966 352 59 6 67 411 543536870 543537220 3.120000e-69 272.0
2 TraesCS1B01G184000 chr1A 95.253 653 22 8 838 1485 300396264 300395616 0.000000e+00 1026.0
3 TraesCS1B01G184000 chr1A 86.137 743 76 12 1 732 300398564 300397838 0.000000e+00 776.0
4 TraesCS1B01G184000 chr1A 84.071 339 44 8 52 382 99143556 99143220 3.960000e-83 318.0
5 TraesCS1B01G184000 chr1A 88.519 270 22 3 1485 1754 300395561 300395301 3.960000e-83 318.0
6 TraesCS1B01G184000 chr1A 79.310 406 66 15 64 460 12030556 12030160 4.040000e-68 268.0
7 TraesCS1B01G184000 chr1D 96.683 603 14 6 886 1485 247241206 247241805 0.000000e+00 998.0
8 TraesCS1B01G184000 chr1D 90.922 705 53 10 138 837 247240494 247241192 0.000000e+00 937.0
9 TraesCS1B01G184000 chr1D 89.744 273 20 2 1491 1763 247241939 247242203 2.350000e-90 342.0
10 TraesCS1B01G184000 chr1D 81.180 356 53 11 88 433 315636606 315636255 8.680000e-70 274.0
11 TraesCS1B01G184000 chr4A 86.571 834 75 23 647 1471 29079541 29080346 0.000000e+00 885.0
12 TraesCS1B01G184000 chr4A 82.353 204 22 5 1557 1758 29080361 29080552 5.450000e-37 165.0
13 TraesCS1B01G184000 chr4B 89.756 615 37 13 863 1471 544602788 544603382 0.000000e+00 763.0
14 TraesCS1B01G184000 chr4D 89.916 595 36 14 863 1440 439784643 439785230 0.000000e+00 745.0
15 TraesCS1B01G184000 chr6A 89.057 530 47 3 1943 2462 186507692 186508220 0.000000e+00 647.0
16 TraesCS1B01G184000 chr7A 88.825 519 44 8 1953 2460 653023055 653022540 2.080000e-175 625.0
17 TraesCS1B01G184000 chr5B 87.048 525 57 6 1943 2457 186149550 186149027 1.270000e-162 582.0
18 TraesCS1B01G184000 chr3A 89.293 467 38 3 2008 2462 199698113 199698579 2.130000e-160 575.0
19 TraesCS1B01G184000 chr2D 83.019 530 78 4 1943 2460 166172256 166172785 1.030000e-128 470.0
20 TraesCS1B01G184000 chr2D 79.851 402 70 10 67 463 557168235 557167840 1.440000e-72 283.0
21 TraesCS1B01G184000 chr2D 79.839 372 64 8 93 455 467885687 467886056 6.760000e-66 261.0
22 TraesCS1B01G184000 chr6D 84.225 355 42 13 62 411 395697395 395697740 1.410000e-87 333.0
23 TraesCS1B01G184000 chr7D 81.250 368 57 11 64 422 72934837 72935201 1.120000e-73 287.0
24 TraesCS1B01G184000 chr7D 100.000 29 0 0 2183 2211 469902656 469902684 1.000000e-03 54.7


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 TraesCS1B01G184000 chr1B 330624310 330626774 2464 True 4553.000000 4553 100.000000 1 2465 1 chr1B.!!$R1 2464
1 TraesCS1B01G184000 chr1A 300395301 300398564 3263 True 706.666667 1026 89.969667 1 1754 3 chr1A.!!$R3 1753
2 TraesCS1B01G184000 chr1D 247240494 247242203 1709 False 759.000000 998 92.449667 138 1763 3 chr1D.!!$F1 1625
3 TraesCS1B01G184000 chr4A 29079541 29080552 1011 False 525.000000 885 84.462000 647 1758 2 chr4A.!!$F1 1111
4 TraesCS1B01G184000 chr4B 544602788 544603382 594 False 763.000000 763 89.756000 863 1471 1 chr4B.!!$F1 608
5 TraesCS1B01G184000 chr4D 439784643 439785230 587 False 745.000000 745 89.916000 863 1440 1 chr4D.!!$F1 577
6 TraesCS1B01G184000 chr6A 186507692 186508220 528 False 647.000000 647 89.057000 1943 2462 1 chr6A.!!$F1 519
7 TraesCS1B01G184000 chr7A 653022540 653023055 515 True 625.000000 625 88.825000 1953 2460 1 chr7A.!!$R1 507
8 TraesCS1B01G184000 chr5B 186149027 186149550 523 True 582.000000 582 87.048000 1943 2457 1 chr5B.!!$R1 514
9 TraesCS1B01G184000 chr2D 166172256 166172785 529 False 470.000000 470 83.019000 1943 2460 1 chr2D.!!$F1 517

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
99 100 0.466124 GACCACCCTCAGCTACATCC 59.534 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 3450 0.24912 CGCTGGTCATAGTGGGAACA 59.751 55.0 0.0 0.0 38.7 3.18 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
62 63 8.420374 TTTGAGAGTGTAGTTACTTTCTTGTG 57.580 34.615 0.00 0.00 34.06 3.33
79 80 3.885724 TGTGCGATAATCCACTTCTCA 57.114 42.857 0.00 0.00 33.26 3.27
85 86 4.363999 CGATAATCCACTTCTCAGACCAC 58.636 47.826 0.00 0.00 0.00 4.16
86 87 4.698575 GATAATCCACTTCTCAGACCACC 58.301 47.826 0.00 0.00 0.00 4.61
99 100 0.466124 GACCACCCTCAGCTACATCC 59.534 60.000 0.00 0.00 0.00 3.51
103 104 2.659897 CCTCAGCTACATCCGCGC 60.660 66.667 0.00 0.00 0.00 6.86
177 181 5.996219 TGTGTGGTATATAATTTGATGCGC 58.004 37.500 0.00 0.00 0.00 6.09
207 211 6.823182 TCCGCTCTAATTTTCAAATCATCTGA 59.177 34.615 0.00 0.00 0.00 3.27
284 293 3.187227 ACTGTTCACGCAATGTTCTGATC 59.813 43.478 0.00 0.00 0.00 2.92
288 297 1.061131 CACGCAATGTTCTGATCCGAC 59.939 52.381 0.00 0.00 0.00 4.79
319 329 1.269988 TGCCGAGAGCTATTCAGATGC 60.270 52.381 0.00 0.00 44.23 3.91
350 361 2.290896 TGAAAATTGGAGCGGACCTCAT 60.291 45.455 0.00 0.00 42.62 2.90
351 362 3.054728 TGAAAATTGGAGCGGACCTCATA 60.055 43.478 0.00 0.00 42.62 2.15
352 363 3.864789 AAATTGGAGCGGACCTCATAT 57.135 42.857 0.00 0.00 42.62 1.78
438 452 2.124983 CTCACCAGGTGCGGATGG 60.125 66.667 15.64 0.00 42.60 3.51
440 454 4.033776 CACCAGGTGCGGATGGGT 62.034 66.667 6.67 0.00 41.13 4.51
448 462 4.820744 GCGGATGGGTGTGGCCAT 62.821 66.667 9.72 0.00 39.65 4.40
455 469 1.602323 GGGTGTGGCCATCGAAACA 60.602 57.895 9.72 0.00 39.65 2.83
474 488 3.347216 ACACTGCACTTCTTTCTTGTGT 58.653 40.909 0.00 0.00 34.52 3.72
475 489 4.513442 ACACTGCACTTCTTTCTTGTGTA 58.487 39.130 0.00 0.00 35.94 2.90
476 490 4.572389 ACACTGCACTTCTTTCTTGTGTAG 59.428 41.667 8.44 8.44 45.39 2.74
477 491 4.770795 ACTGCACTTCTTTCTTGTGTAGT 58.229 39.130 9.56 9.56 46.91 2.73
848 2370 8.996651 ACAAAATACTCCCCCTCTTATATTTG 57.003 34.615 0.00 0.00 0.00 2.32
854 2376 7.150447 ACTCCCCCTCTTATATTTGTTTAGG 57.850 40.000 0.00 0.00 0.00 2.69
856 2378 6.221850 TCCCCCTCTTATATTTGTTTAGGGA 58.778 40.000 6.07 0.00 44.18 4.20
985 2519 4.466015 TCAAACCCAAAGAAAGCAAGAACT 59.534 37.500 0.00 0.00 0.00 3.01
1027 2561 1.002242 CTACCCCCTCCTCCTCCTCT 61.002 65.000 0.00 0.00 0.00 3.69
1030 2564 1.456705 CCCCTCCTCCTCCTCTTCG 60.457 68.421 0.00 0.00 0.00 3.79
1031 2565 2.131067 CCCTCCTCCTCCTCTTCGC 61.131 68.421 0.00 0.00 0.00 4.70
1553 3225 4.448210 TGGAAAACTCTATTGATACGGCC 58.552 43.478 0.00 0.00 0.00 6.13
1558 3230 5.552870 AACTCTATTGATACGGCCTGATT 57.447 39.130 0.00 0.00 0.00 2.57
1572 3244 4.662145 GGCCTGATTATTTGAACAAGACG 58.338 43.478 0.00 0.00 0.00 4.18
1577 3249 6.066054 TGATTATTTGAACAAGACGCACAA 57.934 33.333 0.00 0.00 0.00 3.33
1605 3277 8.137437 AGTCATTGTTTCAATTAACCTTCTGTG 58.863 33.333 0.00 0.00 0.00 3.66
1610 3282 2.811431 TCAATTAACCTTCTGTGCCGTG 59.189 45.455 0.00 0.00 0.00 4.94
1611 3283 1.821216 ATTAACCTTCTGTGCCGTGG 58.179 50.000 0.00 0.00 0.00 4.94
1612 3284 0.470766 TTAACCTTCTGTGCCGTGGT 59.529 50.000 0.00 0.00 0.00 4.16
1613 3285 0.250124 TAACCTTCTGTGCCGTGGTG 60.250 55.000 0.00 0.00 0.00 4.17
1614 3286 2.669569 CCTTCTGTGCCGTGGTGG 60.670 66.667 0.00 0.00 42.50 4.61
1615 3287 2.111043 CTTCTGTGCCGTGGTGGT 59.889 61.111 0.00 0.00 41.21 4.16
1657 3329 5.536916 AGCTCTATACGATTCCAGTTTAGCT 59.463 40.000 0.00 0.00 0.00 3.32
1763 3437 9.391006 TCACAGATTAGTTTATGGTAATTGTCC 57.609 33.333 0.00 0.00 0.00 4.02
1764 3438 8.335356 CACAGATTAGTTTATGGTAATTGTCCG 58.665 37.037 0.00 0.00 0.00 4.79
1765 3439 7.497909 ACAGATTAGTTTATGGTAATTGTCCGG 59.502 37.037 0.00 0.00 0.00 5.14
1766 3440 7.713507 CAGATTAGTTTATGGTAATTGTCCGGA 59.286 37.037 0.00 0.00 0.00 5.14
1767 3441 7.931948 AGATTAGTTTATGGTAATTGTCCGGAG 59.068 37.037 3.06 0.00 0.00 4.63
1768 3442 5.687166 AGTTTATGGTAATTGTCCGGAGA 57.313 39.130 3.06 0.00 0.00 3.71
1769 3443 5.425630 AGTTTATGGTAATTGTCCGGAGAC 58.574 41.667 3.06 0.00 43.83 3.36
1782 3456 4.566987 GTCCGGAGACATAATATGTTCCC 58.433 47.826 3.06 16.04 45.03 3.97
1783 3457 4.039973 GTCCGGAGACATAATATGTTCCCA 59.960 45.833 3.06 10.27 45.03 4.37
1784 3458 4.039973 TCCGGAGACATAATATGTTCCCAC 59.960 45.833 19.36 5.45 45.03 4.61
1785 3459 4.040461 CCGGAGACATAATATGTTCCCACT 59.960 45.833 19.36 9.08 45.03 4.00
1786 3460 5.245301 CCGGAGACATAATATGTTCCCACTA 59.755 44.000 19.36 0.00 45.03 2.74
1787 3461 6.070767 CCGGAGACATAATATGTTCCCACTAT 60.071 42.308 19.36 0.00 45.03 2.12
1788 3462 6.813649 CGGAGACATAATATGTTCCCACTATG 59.186 42.308 19.36 8.45 45.03 2.23
1789 3463 7.309805 CGGAGACATAATATGTTCCCACTATGA 60.310 40.741 19.36 0.00 45.03 2.15
1790 3464 7.819900 GGAGACATAATATGTTCCCACTATGAC 59.180 40.741 7.39 0.00 45.03 3.06
1791 3465 7.680730 AGACATAATATGTTCCCACTATGACC 58.319 38.462 7.39 0.00 45.03 4.02
1792 3466 7.292356 AGACATAATATGTTCCCACTATGACCA 59.708 37.037 7.39 0.00 45.03 4.02
1793 3467 7.453393 ACATAATATGTTCCCACTATGACCAG 58.547 38.462 0.00 0.00 41.63 4.00
1794 3468 2.717639 ATGTTCCCACTATGACCAGC 57.282 50.000 0.00 0.00 0.00 4.85
1795 3469 0.249120 TGTTCCCACTATGACCAGCG 59.751 55.000 0.00 0.00 0.00 5.18
1796 3470 0.249398 GTTCCCACTATGACCAGCGT 59.751 55.000 0.00 0.00 0.00 5.07
1797 3471 0.981183 TTCCCACTATGACCAGCGTT 59.019 50.000 0.00 0.00 0.00 4.84
1798 3472 0.981183 TCCCACTATGACCAGCGTTT 59.019 50.000 0.00 0.00 0.00 3.60
1799 3473 1.086696 CCCACTATGACCAGCGTTTG 58.913 55.000 0.00 0.00 0.00 2.93
1800 3474 1.338674 CCCACTATGACCAGCGTTTGA 60.339 52.381 0.00 0.00 0.00 2.69
1801 3475 2.422597 CCACTATGACCAGCGTTTGAA 58.577 47.619 0.00 0.00 0.00 2.69
1802 3476 2.416547 CCACTATGACCAGCGTTTGAAG 59.583 50.000 0.00 0.00 0.00 3.02
1803 3477 3.067106 CACTATGACCAGCGTTTGAAGT 58.933 45.455 0.00 0.00 0.00 3.01
1804 3478 4.242475 CACTATGACCAGCGTTTGAAGTA 58.758 43.478 0.00 0.00 0.00 2.24
1805 3479 4.688879 CACTATGACCAGCGTTTGAAGTAA 59.311 41.667 0.00 0.00 0.00 2.24
1806 3480 4.929808 ACTATGACCAGCGTTTGAAGTAAG 59.070 41.667 0.00 0.00 0.00 2.34
1807 3481 3.188159 TGACCAGCGTTTGAAGTAAGT 57.812 42.857 0.00 0.00 0.00 2.24
1808 3482 3.537580 TGACCAGCGTTTGAAGTAAGTT 58.462 40.909 0.00 0.00 0.00 2.66
1809 3483 4.695396 TGACCAGCGTTTGAAGTAAGTTA 58.305 39.130 0.00 0.00 0.00 2.24
1810 3484 5.302360 TGACCAGCGTTTGAAGTAAGTTAT 58.698 37.500 0.00 0.00 0.00 1.89
1811 3485 5.407387 TGACCAGCGTTTGAAGTAAGTTATC 59.593 40.000 0.00 0.00 0.00 1.75
1812 3486 5.302360 ACCAGCGTTTGAAGTAAGTTATCA 58.698 37.500 0.00 0.00 0.00 2.15
1813 3487 5.938125 ACCAGCGTTTGAAGTAAGTTATCAT 59.062 36.000 0.00 0.00 0.00 2.45
1814 3488 6.092259 ACCAGCGTTTGAAGTAAGTTATCATC 59.908 38.462 0.00 0.00 0.00 2.92
1815 3489 6.178507 CAGCGTTTGAAGTAAGTTATCATCG 58.821 40.000 0.00 0.00 0.00 3.84
1816 3490 4.956184 GCGTTTGAAGTAAGTTATCATCGC 59.044 41.667 14.58 14.58 38.49 4.58
1817 3491 5.445407 GCGTTTGAAGTAAGTTATCATCGCA 60.445 40.000 19.65 1.75 41.59 5.10
1818 3492 6.705782 CGTTTGAAGTAAGTTATCATCGCAT 58.294 36.000 0.00 0.00 0.00 4.73
1819 3493 7.516155 GCGTTTGAAGTAAGTTATCATCGCATA 60.516 37.037 19.65 0.00 41.59 3.14
1820 3494 7.998767 CGTTTGAAGTAAGTTATCATCGCATAG 59.001 37.037 0.00 0.00 0.00 2.23
1821 3495 7.408132 TTGAAGTAAGTTATCATCGCATAGC 57.592 36.000 0.00 0.00 0.00 2.97
1822 3496 6.512297 TGAAGTAAGTTATCATCGCATAGCA 58.488 36.000 0.00 0.00 0.00 3.49
1823 3497 7.154656 TGAAGTAAGTTATCATCGCATAGCAT 58.845 34.615 0.00 0.00 0.00 3.79
1824 3498 7.657354 TGAAGTAAGTTATCATCGCATAGCATT 59.343 33.333 0.00 0.00 0.00 3.56
1825 3499 7.969536 AGTAAGTTATCATCGCATAGCATTT 57.030 32.000 0.00 0.00 0.00 2.32
1826 3500 8.023050 AGTAAGTTATCATCGCATAGCATTTC 57.977 34.615 0.00 0.00 0.00 2.17
1827 3501 5.869753 AGTTATCATCGCATAGCATTTCC 57.130 39.130 0.00 0.00 0.00 3.13
1828 3502 4.697352 AGTTATCATCGCATAGCATTTCCC 59.303 41.667 0.00 0.00 0.00 3.97
1829 3503 2.636647 TCATCGCATAGCATTTCCCA 57.363 45.000 0.00 0.00 0.00 4.37
1830 3504 2.929641 TCATCGCATAGCATTTCCCAA 58.070 42.857 0.00 0.00 0.00 4.12
1831 3505 2.880268 TCATCGCATAGCATTTCCCAAG 59.120 45.455 0.00 0.00 0.00 3.61
1832 3506 2.708216 TCGCATAGCATTTCCCAAGA 57.292 45.000 0.00 0.00 0.00 3.02
1833 3507 2.288666 TCGCATAGCATTTCCCAAGAC 58.711 47.619 0.00 0.00 0.00 3.01
1834 3508 2.016318 CGCATAGCATTTCCCAAGACA 58.984 47.619 0.00 0.00 0.00 3.41
1835 3509 2.423185 CGCATAGCATTTCCCAAGACAA 59.577 45.455 0.00 0.00 0.00 3.18
1836 3510 3.119531 CGCATAGCATTTCCCAAGACAAA 60.120 43.478 0.00 0.00 0.00 2.83
1837 3511 4.617995 CGCATAGCATTTCCCAAGACAAAA 60.618 41.667 0.00 0.00 0.00 2.44
1838 3512 5.422145 GCATAGCATTTCCCAAGACAAAAT 58.578 37.500 0.00 0.00 0.00 1.82
1839 3513 5.292589 GCATAGCATTTCCCAAGACAAAATG 59.707 40.000 0.00 0.00 41.26 2.32
1840 3514 6.632909 CATAGCATTTCCCAAGACAAAATGA 58.367 36.000 10.35 0.00 40.97 2.57
1841 3515 5.143376 AGCATTTCCCAAGACAAAATGAG 57.857 39.130 10.35 0.00 40.97 2.90
1842 3516 4.590222 AGCATTTCCCAAGACAAAATGAGT 59.410 37.500 10.35 0.00 40.97 3.41
1843 3517 4.925646 GCATTTCCCAAGACAAAATGAGTC 59.074 41.667 10.35 0.00 40.97 3.36
1844 3518 5.509501 GCATTTCCCAAGACAAAATGAGTCA 60.510 40.000 10.35 0.00 40.97 3.41
1845 3519 6.514947 CATTTCCCAAGACAAAATGAGTCAA 58.485 36.000 0.00 0.00 40.97 3.18
1846 3520 6.537453 TTTCCCAAGACAAAATGAGTCAAA 57.463 33.333 0.00 0.00 38.46 2.69
1847 3521 6.537453 TTCCCAAGACAAAATGAGTCAAAA 57.463 33.333 0.00 0.00 38.46 2.44
1848 3522 6.537453 TCCCAAGACAAAATGAGTCAAAAA 57.463 33.333 0.00 0.00 38.46 1.94
1849 3523 7.123355 TCCCAAGACAAAATGAGTCAAAAAT 57.877 32.000 0.00 0.00 38.46 1.82
1850 3524 7.563906 TCCCAAGACAAAATGAGTCAAAAATT 58.436 30.769 0.00 0.00 38.46 1.82
1851 3525 7.710475 TCCCAAGACAAAATGAGTCAAAAATTC 59.290 33.333 0.00 0.00 38.46 2.17
1852 3526 7.306749 CCCAAGACAAAATGAGTCAAAAATTCG 60.307 37.037 0.00 0.00 38.46 3.34
1853 3527 7.434897 CCAAGACAAAATGAGTCAAAAATTCGA 59.565 33.333 0.00 0.00 38.46 3.71
1854 3528 8.474577 CAAGACAAAATGAGTCAAAAATTCGAG 58.525 33.333 0.00 0.00 38.46 4.04
1855 3529 7.930217 AGACAAAATGAGTCAAAAATTCGAGA 58.070 30.769 0.00 0.00 38.46 4.04
1856 3530 8.405531 AGACAAAATGAGTCAAAAATTCGAGAA 58.594 29.630 0.00 0.00 38.46 2.87
1857 3531 8.925161 ACAAAATGAGTCAAAAATTCGAGAAA 57.075 26.923 0.00 0.00 0.00 2.52
1858 3532 9.364989 ACAAAATGAGTCAAAAATTCGAGAAAA 57.635 25.926 0.00 0.00 0.00 2.29
1920 3594 9.760926 ACCACATATGACACTATATCTATGAGT 57.239 33.333 10.38 0.00 0.00 3.41
2028 3703 2.629050 CTACGCCACCATCCACCTCG 62.629 65.000 0.00 0.00 0.00 4.63
2149 3825 3.989698 CTCGCTCGCAATCCGGTGT 62.990 63.158 0.00 0.00 37.59 4.16
2175 3851 1.290324 GCTGAAGGCTGACTGTCGA 59.710 57.895 2.98 0.00 38.06 4.20
2214 3900 1.067295 TCCAAAGCTCCCACATGACT 58.933 50.000 0.00 0.00 0.00 3.41
2228 3914 0.543749 ATGACTAGAAGGCACAGGGC 59.456 55.000 0.00 0.00 35.04 5.19
2245 3931 2.105128 CCTGCATCGTCCTCGTCC 59.895 66.667 0.00 0.00 38.33 4.79
2350 4036 1.004277 TGAACACCTTGGCCCATACTC 59.996 52.381 0.00 0.00 0.00 2.59
2364 4050 1.065418 CATACTCCCCTCGCCAAAACT 60.065 52.381 0.00 0.00 0.00 2.66
2406 4092 0.446616 TCGTCTCCTCGTGTTGATCG 59.553 55.000 0.00 0.00 0.00 3.69
2415 4102 0.443869 CGTGTTGATCGCAGAAAGGG 59.556 55.000 0.00 0.00 43.58 3.95
2421 4108 1.303561 ATCGCAGAAAGGGCAAGCA 60.304 52.632 0.00 0.00 43.58 3.91
2424 4111 1.310933 CGCAGAAAGGGCAAGCATCT 61.311 55.000 0.00 0.00 0.00 2.90
2449 4136 1.313812 CGGTAGTCCTCTCCGTGCTT 61.314 60.000 0.00 0.00 39.51 3.91
2462 4149 1.514087 GTGCTTACCGGTCCGATGA 59.486 57.895 12.40 0.00 0.00 2.92
2463 4150 0.804933 GTGCTTACCGGTCCGATGAC 60.805 60.000 12.40 0.00 40.98 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.940463 TCGCACAAGAAAGTAACTACACT 58.060 39.130 0.00 0.00 0.00 3.55
59 60 3.447229 TCTGAGAAGTGGATTATCGCACA 59.553 43.478 13.42 0.00 31.46 4.57
62 63 3.181475 TGGTCTGAGAAGTGGATTATCGC 60.181 47.826 0.00 0.00 31.46 4.58
79 80 1.490574 GATGTAGCTGAGGGTGGTCT 58.509 55.000 0.00 0.00 0.00 3.85
85 86 2.028190 CGCGGATGTAGCTGAGGG 59.972 66.667 0.00 0.00 0.00 4.30
86 87 2.659897 GCGCGGATGTAGCTGAGG 60.660 66.667 8.83 0.00 0.00 3.86
177 181 2.888594 TGAAAATTAGAGCGGACCTCG 58.111 47.619 0.00 0.00 45.54 4.63
274 283 4.543590 AAGACAAGTCGGATCAGAACAT 57.456 40.909 0.00 0.00 34.09 2.71
319 329 5.278169 CCGCTCCAATTTTCAGATCATTAGG 60.278 44.000 0.00 0.00 0.00 2.69
423 437 4.033776 ACCCATCCGCACCTGGTG 62.034 66.667 22.46 22.46 36.51 4.17
427 441 4.033776 CCACACCCATCCGCACCT 62.034 66.667 0.00 0.00 0.00 4.00
438 452 0.889186 AGTGTTTCGATGGCCACACC 60.889 55.000 8.16 0.00 40.42 4.16
440 454 1.514678 GCAGTGTTTCGATGGCCACA 61.515 55.000 8.16 0.00 0.00 4.17
445 459 2.146342 AGAAGTGCAGTGTTTCGATGG 58.854 47.619 0.00 0.00 0.00 3.51
448 462 3.531538 AGAAAGAAGTGCAGTGTTTCGA 58.468 40.909 17.67 0.00 34.39 3.71
455 469 4.770795 ACTACACAAGAAAGAAGTGCAGT 58.229 39.130 0.00 0.00 35.60 4.40
489 503 6.038161 CCCCTCCATTTGTTTTCTTTGTTTTC 59.962 38.462 0.00 0.00 0.00 2.29
594 608 1.137614 GAGTGCACGCGATCTCTGA 59.862 57.895 15.93 0.00 0.00 3.27
848 2370 2.570302 TGCTTGTACTCCCTCCCTAAAC 59.430 50.000 0.00 0.00 0.00 2.01
854 2376 1.623811 TCACTTGCTTGTACTCCCTCC 59.376 52.381 0.00 0.00 0.00 4.30
856 2378 1.002544 GCTCACTTGCTTGTACTCCCT 59.997 52.381 0.00 0.00 0.00 4.20
859 2381 2.675348 GGATGCTCACTTGCTTGTACTC 59.325 50.000 0.00 0.00 0.00 2.59
985 2519 4.418328 CATGGACGGCCGGGGAAA 62.418 66.667 31.76 10.55 36.79 3.13
1553 3225 5.688823 TGTGCGTCTTGTTCAAATAATCAG 58.311 37.500 0.00 0.00 0.00 2.90
1558 3230 4.814234 ACTCTTGTGCGTCTTGTTCAAATA 59.186 37.500 0.00 0.00 0.00 1.40
1572 3244 7.096065 GGTTAATTGAAACAATGACTCTTGTGC 60.096 37.037 0.00 0.00 39.25 4.57
1577 3249 8.571336 CAGAAGGTTAATTGAAACAATGACTCT 58.429 33.333 0.00 0.00 0.00 3.24
1605 3277 2.510064 TATCCACGAACCACCACGGC 62.510 60.000 0.00 0.00 39.03 5.68
1763 3437 5.215252 AGTGGGAACATATTATGTCTCCG 57.785 43.478 20.08 0.00 44.07 4.63
1764 3438 7.819900 GTCATAGTGGGAACATATTATGTCTCC 59.180 40.741 19.36 19.36 44.07 3.71
1765 3439 7.819900 GGTCATAGTGGGAACATATTATGTCTC 59.180 40.741 9.68 9.25 44.07 3.36
1766 3440 7.292356 TGGTCATAGTGGGAACATATTATGTCT 59.708 37.037 9.68 5.25 44.07 3.41
1767 3441 7.450074 TGGTCATAGTGGGAACATATTATGTC 58.550 38.462 9.68 4.27 44.07 3.06
1769 3443 6.372659 GCTGGTCATAGTGGGAACATATTATG 59.627 42.308 2.03 2.03 46.14 1.90
1770 3444 6.476378 GCTGGTCATAGTGGGAACATATTAT 58.524 40.000 0.00 0.00 46.14 1.28
1771 3445 5.510690 CGCTGGTCATAGTGGGAACATATTA 60.511 44.000 0.00 0.00 46.14 0.98
1772 3446 4.718961 GCTGGTCATAGTGGGAACATATT 58.281 43.478 0.00 0.00 46.14 1.28
1773 3447 3.244215 CGCTGGTCATAGTGGGAACATAT 60.244 47.826 0.00 0.00 46.14 1.78
1774 3448 2.102420 CGCTGGTCATAGTGGGAACATA 59.898 50.000 0.00 0.00 46.14 2.29
1775 3449 1.134401 CGCTGGTCATAGTGGGAACAT 60.134 52.381 0.00 0.00 46.14 2.71
1776 3450 0.249120 CGCTGGTCATAGTGGGAACA 59.751 55.000 0.00 0.00 38.70 3.18
1777 3451 0.249398 ACGCTGGTCATAGTGGGAAC 59.751 55.000 0.00 0.00 32.56 3.62
1778 3452 0.981183 AACGCTGGTCATAGTGGGAA 59.019 50.000 0.00 0.00 32.56 3.97
1779 3453 0.981183 AAACGCTGGTCATAGTGGGA 59.019 50.000 0.00 0.00 32.56 4.37
1780 3454 1.086696 CAAACGCTGGTCATAGTGGG 58.913 55.000 0.00 0.00 32.56 4.61
1781 3455 2.093306 TCAAACGCTGGTCATAGTGG 57.907 50.000 0.00 0.00 32.56 4.00
1782 3456 3.067106 ACTTCAAACGCTGGTCATAGTG 58.933 45.455 0.00 0.00 0.00 2.74
1783 3457 3.402628 ACTTCAAACGCTGGTCATAGT 57.597 42.857 0.00 0.00 0.00 2.12
1784 3458 4.929808 ACTTACTTCAAACGCTGGTCATAG 59.070 41.667 0.00 0.00 0.00 2.23
1785 3459 4.890088 ACTTACTTCAAACGCTGGTCATA 58.110 39.130 0.00 0.00 0.00 2.15
1786 3460 3.740115 ACTTACTTCAAACGCTGGTCAT 58.260 40.909 0.00 0.00 0.00 3.06
1787 3461 3.188159 ACTTACTTCAAACGCTGGTCA 57.812 42.857 0.00 0.00 0.00 4.02
1788 3462 5.407387 TGATAACTTACTTCAAACGCTGGTC 59.593 40.000 0.00 0.00 0.00 4.02
1789 3463 5.302360 TGATAACTTACTTCAAACGCTGGT 58.698 37.500 0.00 0.00 0.00 4.00
1790 3464 5.856126 TGATAACTTACTTCAAACGCTGG 57.144 39.130 0.00 0.00 0.00 4.85
1791 3465 6.178507 CGATGATAACTTACTTCAAACGCTG 58.821 40.000 0.00 0.00 0.00 5.18
1792 3466 5.220416 GCGATGATAACTTACTTCAAACGCT 60.220 40.000 0.00 0.00 41.38 5.07
1793 3467 4.956184 GCGATGATAACTTACTTCAAACGC 59.044 41.667 0.00 0.00 39.70 4.84
1794 3468 6.089920 TGCGATGATAACTTACTTCAAACG 57.910 37.500 0.00 0.00 0.00 3.60
1795 3469 7.794349 GCTATGCGATGATAACTTACTTCAAAC 59.206 37.037 0.00 0.00 0.00 2.93
1796 3470 7.494298 TGCTATGCGATGATAACTTACTTCAAA 59.506 33.333 0.00 0.00 0.00 2.69
1797 3471 6.983890 TGCTATGCGATGATAACTTACTTCAA 59.016 34.615 0.00 0.00 0.00 2.69
1798 3472 6.512297 TGCTATGCGATGATAACTTACTTCA 58.488 36.000 0.00 0.00 0.00 3.02
1799 3473 7.588143 ATGCTATGCGATGATAACTTACTTC 57.412 36.000 0.00 0.00 0.00 3.01
1800 3474 7.969536 AATGCTATGCGATGATAACTTACTT 57.030 32.000 0.00 0.00 0.00 2.24
1801 3475 7.118390 GGAAATGCTATGCGATGATAACTTACT 59.882 37.037 0.00 0.00 0.00 2.24
1802 3476 7.237173 GGAAATGCTATGCGATGATAACTTAC 58.763 38.462 0.00 0.00 0.00 2.34
1803 3477 6.371548 GGGAAATGCTATGCGATGATAACTTA 59.628 38.462 0.00 0.00 0.00 2.24
1804 3478 5.182001 GGGAAATGCTATGCGATGATAACTT 59.818 40.000 0.00 0.00 0.00 2.66
1805 3479 4.697352 GGGAAATGCTATGCGATGATAACT 59.303 41.667 0.00 0.00 0.00 2.24
1806 3480 4.455533 TGGGAAATGCTATGCGATGATAAC 59.544 41.667 0.00 0.00 0.00 1.89
1807 3481 4.650734 TGGGAAATGCTATGCGATGATAA 58.349 39.130 0.00 0.00 0.00 1.75
1808 3482 4.284829 TGGGAAATGCTATGCGATGATA 57.715 40.909 0.00 0.00 0.00 2.15
1809 3483 3.144657 TGGGAAATGCTATGCGATGAT 57.855 42.857 0.00 0.00 0.00 2.45
1810 3484 2.636647 TGGGAAATGCTATGCGATGA 57.363 45.000 0.00 0.00 0.00 2.92
1811 3485 2.880268 TCTTGGGAAATGCTATGCGATG 59.120 45.455 0.00 0.00 0.00 3.84
1812 3486 2.880890 GTCTTGGGAAATGCTATGCGAT 59.119 45.455 0.00 0.00 0.00 4.58
1813 3487 2.288666 GTCTTGGGAAATGCTATGCGA 58.711 47.619 0.00 0.00 0.00 5.10
1814 3488 2.016318 TGTCTTGGGAAATGCTATGCG 58.984 47.619 0.00 0.00 0.00 4.73
1815 3489 4.454728 TTTGTCTTGGGAAATGCTATGC 57.545 40.909 0.00 0.00 0.00 3.14
1816 3490 6.632909 TCATTTTGTCTTGGGAAATGCTATG 58.367 36.000 0.00 0.00 39.44 2.23
1817 3491 6.438425 ACTCATTTTGTCTTGGGAAATGCTAT 59.562 34.615 0.00 0.00 39.44 2.97
1818 3492 5.774690 ACTCATTTTGTCTTGGGAAATGCTA 59.225 36.000 0.00 0.00 39.44 3.49
1819 3493 4.590222 ACTCATTTTGTCTTGGGAAATGCT 59.410 37.500 0.00 0.00 39.44 3.79
1820 3494 4.886579 ACTCATTTTGTCTTGGGAAATGC 58.113 39.130 0.00 0.00 39.44 3.56
1821 3495 6.088016 TGACTCATTTTGTCTTGGGAAATG 57.912 37.500 0.00 0.00 40.41 2.32
1822 3496 6.729690 TTGACTCATTTTGTCTTGGGAAAT 57.270 33.333 0.00 0.00 35.63 2.17
1823 3497 6.537453 TTTGACTCATTTTGTCTTGGGAAA 57.463 33.333 0.00 0.00 35.63 3.13
1824 3498 6.537453 TTTTGACTCATTTTGTCTTGGGAA 57.463 33.333 0.00 0.00 35.63 3.97
1825 3499 6.537453 TTTTTGACTCATTTTGTCTTGGGA 57.463 33.333 0.00 0.00 35.63 4.37
1826 3500 7.306749 CGAATTTTTGACTCATTTTGTCTTGGG 60.307 37.037 0.00 0.00 35.63 4.12
1827 3501 7.434897 TCGAATTTTTGACTCATTTTGTCTTGG 59.565 33.333 0.00 0.00 35.63 3.61
1828 3502 8.338985 TCGAATTTTTGACTCATTTTGTCTTG 57.661 30.769 0.00 0.00 35.63 3.02
1829 3503 8.405531 TCTCGAATTTTTGACTCATTTTGTCTT 58.594 29.630 0.00 0.00 35.63 3.01
1830 3504 7.930217 TCTCGAATTTTTGACTCATTTTGTCT 58.070 30.769 0.00 0.00 35.63 3.41
1831 3505 8.560576 TTCTCGAATTTTTGACTCATTTTGTC 57.439 30.769 0.00 0.00 35.21 3.18
1832 3506 8.925161 TTTCTCGAATTTTTGACTCATTTTGT 57.075 26.923 0.00 0.00 0.00 2.83
1894 3568 9.760926 ACTCATAGATATAGTGTCATATGTGGT 57.239 33.333 1.90 0.00 0.00 4.16
2175 3851 2.183409 GCACCAGAATGCCATCGTT 58.817 52.632 0.00 0.00 39.86 3.85
2228 3914 2.105128 GGACGAGGACGATGCAGG 59.895 66.667 0.00 0.00 42.66 4.85
2251 3937 3.151710 CCGGCAGGATACCCACGA 61.152 66.667 0.00 0.00 41.02 4.35
2315 4001 1.963855 TTCACGACCATGGGCGTTG 60.964 57.895 42.57 33.34 34.45 4.10
2350 4036 0.955919 GAGTGAGTTTTGGCGAGGGG 60.956 60.000 0.00 0.00 0.00 4.79
2364 4050 0.321919 GCCACCTGCTCATTGAGTGA 60.322 55.000 14.90 1.99 36.87 3.41
2406 4092 0.893447 AAGATGCTTGCCCTTTCTGC 59.107 50.000 0.00 0.00 0.00 4.26
2415 4102 1.305219 TACCGCACCAAGATGCTTGC 61.305 55.000 1.73 0.00 43.80 4.01
2421 4108 0.824759 GAGGACTACCGCACCAAGAT 59.175 55.000 0.00 0.00 41.83 2.40
2424 4111 1.255667 GGAGAGGACTACCGCACCAA 61.256 60.000 0.00 0.00 43.53 3.67


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

AutoCloner maintained by Alex Coulton.