Multiple sequence alignment - TraesCS1B01G285900

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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 TraesCS1B01G285900 chr1B 100.000 3736 0 0 1 3736 497272363 497276098 0.000000e+00 6900.0
1 TraesCS1B01G285900 chr1B 92.308 65 3 2 3631 3694 497276056 497275993 1.430000e-14 91.6
2 TraesCS1B01G285900 chr1D 93.849 1951 67 29 1721 3635 372360106 372362039 0.000000e+00 2889.0
3 TraesCS1B01G285900 chr1D 89.711 1798 92 26 1 1752 372358354 372360104 0.000000e+00 2209.0
4 TraesCS1B01G285900 chr1D 88.921 343 35 2 3263 3602 435925057 435924715 1.600000e-113 420.0
5 TraesCS1B01G285900 chr1D 97.333 75 2 0 3662 3736 372362037 372362111 1.090000e-25 128.0
6 TraesCS1B01G285900 chr1A 94.209 1226 55 12 2049 3263 471729898 471731118 0.000000e+00 1857.0
7 TraesCS1B01G285900 chr1A 90.464 1185 79 15 897 2052 471728640 471729819 0.000000e+00 1531.0
8 TraesCS1B01G285900 chr1A 92.998 457 26 5 1 451 471727989 471728445 0.000000e+00 662.0
9 TraesCS1B01G285900 chr1A 93.237 207 9 5 466 668 471728430 471728635 2.180000e-77 300.0
10 TraesCS1B01G285900 chr1A 92.754 69 5 0 3598 3666 471731130 471731198 2.370000e-17 100.0
11 TraesCS1B01G285900 chr1A 100.000 30 0 0 3664 3693 516780612 516780641 5.210000e-04 56.5
12 TraesCS1B01G285900 chr1A 100.000 29 0 0 3666 3694 19300060 19300088 2.000000e-03 54.7
13 TraesCS1B01G285900 chr3A 89.216 408 21 6 2201 2608 621893438 621893054 4.340000e-134 488.0
14 TraesCS1B01G285900 chr3B 89.024 410 22 6 2199 2608 638357252 638356866 1.560000e-133 486.0
15 TraesCS1B01G285900 chr3B 100.000 35 0 0 3632 3666 752800486 752800520 8.660000e-07 65.8
16 TraesCS1B01G285900 chr3D 87.413 429 33 4 2199 2627 478653364 478652957 1.210000e-129 473.0
17 TraesCS1B01G285900 chr6B 90.909 341 27 4 3263 3602 454503198 454502861 4.400000e-124 455.0
18 TraesCS1B01G285900 chr4D 90.746 335 25 5 3263 3594 505256989 505256658 3.420000e-120 442.0
19 TraesCS1B01G285900 chr4D 100.000 33 0 0 3628 3660 312868381 312868349 1.120000e-05 62.1
20 TraesCS1B01G285900 chr7B 90.029 341 29 5 3263 3602 167716777 167717113 1.590000e-118 436.0
21 TraesCS1B01G285900 chr7D 89.213 343 34 3 3257 3597 617491700 617491359 3.450000e-115 425.0
22 TraesCS1B01G285900 chr7D 97.297 37 0 1 3627 3663 416626635 416626600 1.120000e-05 62.1
23 TraesCS1B01G285900 chr4A 88.571 350 35 4 3257 3602 533455245 533455593 1.600000e-113 420.0
24 TraesCS1B01G285900 chr2D 89.150 341 31 5 3263 3602 334578747 334578412 1.600000e-113 420.0
25 TraesCS1B01G285900 chr2A 88.921 343 35 2 3262 3602 482532794 482533135 1.600000e-113 420.0
26 TraesCS1B01G285900 chr5D 85.788 387 47 7 2200 2582 285839916 285839534 1.620000e-108 403.0
27 TraesCS1B01G285900 chr5D 97.143 35 1 0 3630 3664 476613862 476613828 4.030000e-05 60.2
28 TraesCS1B01G285900 chr5D 94.444 36 1 1 3660 3694 473360339 473360374 2.000000e-03 54.7
29 TraesCS1B01G285900 chr5A 85.751 386 49 6 2200 2582 378272191 378271809 1.620000e-108 403.0
30 TraesCS1B01G285900 chr5A 85.714 70 2 3 3632 3693 462150465 462150534 2.410000e-07 67.6
31 TraesCS1B01G285900 chr5A 85.294 68 4 4 3632 3693 681084469 681084536 8.660000e-07 65.8
32 TraesCS1B01G285900 chr5A 94.595 37 2 0 3624 3660 536890402 536890438 1.450000e-04 58.4
33 TraesCS1B01G285900 chr5A 94.444 36 0 2 3666 3700 552064868 552064834 2.000000e-03 54.7
34 TraesCS1B01G285900 chr5B 85.492 386 48 8 2201 2582 324248816 324248435 2.700000e-106 396.0
35 TraesCS1B01G285900 chr5B 85.067 375 35 11 2199 2573 446996504 446996857 2.740000e-96 363.0
36 TraesCS1B01G285900 chrUn 100.000 29 0 0 3666 3694 252717039 252717067 2.000000e-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 TraesCS1B01G285900 chr1B 497272363 497276098 3735 False 6900 6900 100.0000 1 3736 1 chr1B.!!$F1 3735
1 TraesCS1B01G285900 chr1D 372358354 372362111 3757 False 1742 2889 93.6310 1 3736 3 chr1D.!!$F1 3735
2 TraesCS1B01G285900 chr1A 471727989 471731198 3209 False 890 1857 92.7324 1 3666 5 chr1A.!!$F3 3665

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
535 557 0.034756 CCCCACCATCGATATTCGCA 59.965 55.0 0.00 0.00 40.21 5.10 F
671 699 0.108207 GTCATGCTAGCTCCAGGCAT 59.892 55.0 17.23 9.54 45.91 4.40 F
1558 1620 0.105194 TCAGTTGAGGGGTCAGACCA 60.105 55.0 21.75 0.00 41.02 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1606 0.040646 ATACGTGGTCTGACCCCTCA 59.959 55.000 23.42 7.48 37.50 3.86 R
2368 2571 1.006102 CGTGCGGAAGTCCTTGAGT 60.006 57.895 0.00 0.00 0.00 3.41 R
3173 3390 3.526931 AGAGACCATAATGTCCGTGTG 57.473 47.619 0.00 0.00 35.83 3.82 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
32 33 2.375766 GCACGTGTCTGAAGCCGAG 61.376 63.158 18.38 0.00 0.00 4.63
110 112 9.734620 CATATCTAGCTAGAGAACAAGATATGC 57.265 37.037 26.64 0.00 42.68 3.14
116 118 3.397482 AGAGAACAAGATATGCGATGGC 58.603 45.455 0.00 0.00 40.52 4.40
132 134 7.324354 TGCGATGGCGTAGAGTATATAATAA 57.676 36.000 0.00 0.00 44.10 1.40
182 184 5.798125 ACTCCCTGTCATATGACTACATG 57.202 43.478 30.67 20.94 44.99 3.21
297 301 2.650163 GCGACGTAGCTACCTGTTG 58.350 57.895 18.16 14.86 0.00 3.33
374 382 3.572632 AGCTACCACAATCAGCATCAT 57.427 42.857 0.00 0.00 37.78 2.45
429 438 7.607250 AGTGATAGAATAATACTGGTAGCAGC 58.393 38.462 21.58 3.71 0.00 5.25
430 439 7.453126 AGTGATAGAATAATACTGGTAGCAGCT 59.547 37.037 21.58 10.90 0.00 4.24
431 440 7.543868 GTGATAGAATAATACTGGTAGCAGCTG 59.456 40.741 21.58 10.11 0.00 4.24
432 441 5.878406 AGAATAATACTGGTAGCAGCTGT 57.122 39.130 21.58 9.17 0.00 4.40
433 442 6.978674 AGAATAATACTGGTAGCAGCTGTA 57.021 37.500 21.58 11.01 35.18 2.74
436 445 3.802948 ATACTGGTAGCAGCTGTACAC 57.197 47.619 21.58 10.46 33.90 2.90
437 446 0.243907 ACTGGTAGCAGCTGTACACG 59.756 55.000 21.58 12.25 0.00 4.49
439 448 0.677288 TGGTAGCAGCTGTACACGTT 59.323 50.000 16.64 0.00 0.00 3.99
440 449 1.069513 TGGTAGCAGCTGTACACGTTT 59.930 47.619 16.64 0.00 0.00 3.60
441 450 2.140717 GGTAGCAGCTGTACACGTTTT 58.859 47.619 16.64 0.00 0.00 2.43
442 451 2.546789 GGTAGCAGCTGTACACGTTTTT 59.453 45.455 16.64 0.00 0.00 1.94
493 503 1.273327 TGACATCCCATGATCGATCGG 59.727 52.381 20.03 15.36 0.00 4.18
494 504 0.036952 ACATCCCATGATCGATCGGC 60.037 55.000 20.03 8.58 0.00 5.54
495 505 1.080435 CATCCCATGATCGATCGGCG 61.080 60.000 20.03 0.00 42.69 6.46
522 544 1.564483 TACCCGAATTGACCCCCACC 61.564 60.000 0.00 0.00 0.00 4.61
535 557 0.034756 CCCCACCATCGATATTCGCA 59.965 55.000 0.00 0.00 40.21 5.10
598 620 2.299297 GGCAATAGTATCTGTACCCGCT 59.701 50.000 0.00 0.00 0.00 5.52
608 631 4.392166 TACCCGCTGCCCCAGAGA 62.392 66.667 0.00 0.00 33.20 3.10
671 699 0.108207 GTCATGCTAGCTCCAGGCAT 59.892 55.000 17.23 9.54 45.91 4.40
677 705 1.270041 GCTAGCTCCAGGCATCAGTAC 60.270 57.143 7.70 0.00 44.79 2.73
710 738 2.717639 ATACAGCTCGCCCTTTTCAT 57.282 45.000 0.00 0.00 0.00 2.57
751 779 0.474184 GCCCCCAGCTTAATCTGCTA 59.526 55.000 0.59 0.00 38.92 3.49
752 780 1.074566 GCCCCCAGCTTAATCTGCTAT 59.925 52.381 0.59 0.00 38.92 2.97
753 781 2.489802 GCCCCCAGCTTAATCTGCTATT 60.490 50.000 0.59 0.00 38.92 1.73
754 782 3.416156 CCCCCAGCTTAATCTGCTATTC 58.584 50.000 0.59 0.00 38.92 1.75
755 783 3.073650 CCCCCAGCTTAATCTGCTATTCT 59.926 47.826 0.59 0.00 38.92 2.40
756 784 4.070716 CCCCAGCTTAATCTGCTATTCTG 58.929 47.826 0.59 0.00 38.92 3.02
757 785 3.501445 CCCAGCTTAATCTGCTATTCTGC 59.499 47.826 0.59 0.00 38.92 4.26
758 786 4.387598 CCAGCTTAATCTGCTATTCTGCT 58.612 43.478 0.59 0.00 38.92 4.24
769 797 3.194755 TGCTATTCTGCTTACCTCACGAA 59.805 43.478 0.00 0.00 0.00 3.85
773 801 1.199327 TCTGCTTACCTCACGAACTCG 59.801 52.381 0.00 0.00 46.33 4.18
774 802 0.388134 TGCTTACCTCACGAACTCGC 60.388 55.000 0.00 0.00 44.43 5.03
776 804 0.797249 CTTACCTCACGAACTCGCGG 60.797 60.000 6.13 0.00 44.43 6.46
793 821 2.034687 GCAGCCTTCCAAGCTCCA 59.965 61.111 0.00 0.00 38.95 3.86
863 903 3.334054 GCACCAGCTTCCCTCCCT 61.334 66.667 0.00 0.00 37.91 4.20
888 928 1.376812 CCTTCCCCGTTTCTTCCCG 60.377 63.158 0.00 0.00 0.00 5.14
928 968 0.907704 ACATAGACGACCCCTGCCAA 60.908 55.000 0.00 0.00 0.00 4.52
958 998 1.231641 CAGAACCCAACCCAACCCA 59.768 57.895 0.00 0.00 0.00 4.51
959 999 0.397816 CAGAACCCAACCCAACCCAA 60.398 55.000 0.00 0.00 0.00 4.12
960 1000 0.397957 AGAACCCAACCCAACCCAAC 60.398 55.000 0.00 0.00 0.00 3.77
962 1002 2.525629 CCCAACCCAACCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
964 1004 2.915137 CAACCCAACCCAACCCCG 60.915 66.667 0.00 0.00 0.00 5.73
965 1005 3.104568 AACCCAACCCAACCCCGA 61.105 61.111 0.00 0.00 0.00 5.14
966 1006 2.475172 AACCCAACCCAACCCCGAT 61.475 57.895 0.00 0.00 0.00 4.18
967 1007 1.141410 AACCCAACCCAACCCCGATA 61.141 55.000 0.00 0.00 0.00 2.92
968 1008 0.922243 ACCCAACCCAACCCCGATAT 60.922 55.000 0.00 0.00 0.00 1.63
1010 1050 2.068519 TGCGATATATTGCAAGCGAGG 58.931 47.619 22.86 0.00 43.84 4.63
1011 1051 2.069273 GCGATATATTGCAAGCGAGGT 58.931 47.619 18.49 0.00 37.15 3.85
1023 1063 4.303853 CGAGGTACGCCGATCTTG 57.696 61.111 0.00 0.00 40.50 3.02
1024 1064 1.944676 CGAGGTACGCCGATCTTGC 60.945 63.158 0.00 0.00 40.50 4.01
1043 1083 2.105993 TGCGAGCTACATAGAGGAGGTA 59.894 50.000 0.00 0.00 0.00 3.08
1056 1112 8.847816 ACATAGAGGAGGTACTATATATGGTGT 58.152 37.037 11.70 3.14 41.55 4.16
1069 1125 2.543777 ATGGTGTTGAGTGCTTACGT 57.456 45.000 0.00 0.00 0.00 3.57
1117 1173 1.002544 GTACTTTGAGTGGCTCAGGCT 59.997 52.381 0.00 0.00 41.75 4.58
1148 1204 2.663188 GCATCCTCGCCGTCATCC 60.663 66.667 0.00 0.00 0.00 3.51
1236 1292 2.917227 TGTGTCTGCCGCTCCTCA 60.917 61.111 0.00 0.00 0.00 3.86
1282 1338 4.874977 GAGCGGCGGTACCTCTGC 62.875 72.222 25.32 25.32 46.83 4.26
1286 1342 3.391382 GGCGGTACCTCTGCTGGT 61.391 66.667 10.90 2.55 46.74 4.00
1436 1492 0.395862 TGGACGAGGATGAGGAGGAC 60.396 60.000 0.00 0.00 0.00 3.85
1484 1546 0.896226 AGGAGAAGCCAAGGTACGAC 59.104 55.000 0.00 0.00 40.02 4.34
1485 1547 0.458025 GGAGAAGCCAAGGTACGACG 60.458 60.000 0.00 0.00 36.34 5.12
1497 1559 3.869473 TACGACGGGTGCAAGGTGC 62.869 63.158 0.00 0.00 45.29 5.01
1534 1596 2.221169 TGAACACAGTGAGATGTTGGC 58.779 47.619 7.81 0.00 39.13 4.52
1550 1612 2.266055 GCGGAGTCAGTTGAGGGG 59.734 66.667 0.00 0.00 0.00 4.79
1558 1620 0.105194 TCAGTTGAGGGGTCAGACCA 60.105 55.000 21.75 0.00 41.02 4.02
1718 1780 2.797278 GGTGACCGATCGATGCCCT 61.797 63.158 18.66 0.00 0.00 5.19
1719 1781 1.144057 GTGACCGATCGATGCCCTT 59.856 57.895 18.66 0.00 0.00 3.95
1771 1868 3.366985 GCCGAATCCAAGTTTTCCGATTT 60.367 43.478 0.00 0.00 0.00 2.17
1780 1877 9.681062 ATCCAAGTTTTCCGATTTATCTTCTAA 57.319 29.630 0.00 0.00 0.00 2.10
1822 1919 8.460428 ACGACCTAGTTGTGTTTTGAATTTAAA 58.540 29.630 0.00 0.00 0.00 1.52
1823 1920 9.291664 CGACCTAGTTGTGTTTTGAATTTAAAA 57.708 29.630 4.15 4.15 0.00 1.52
1846 1943 7.585286 AATTTTCACATATGAACACATGCAC 57.415 32.000 10.38 0.00 44.66 4.57
1925 2026 4.237724 CAATACTGCGAGTGAGACAAGAA 58.762 43.478 0.00 0.00 0.00 2.52
1934 2035 7.264947 TGCGAGTGAGACAAGAATTATATTCA 58.735 34.615 2.60 0.00 0.00 2.57
2082 2272 5.104485 GGAAATGGAACTAGACCACCATAGT 60.104 44.000 13.60 6.75 41.47 2.12
2141 2332 6.898041 TCACACATGCATTTTTCTACAGTAC 58.102 36.000 0.00 0.00 0.00 2.73
2196 2399 1.302752 GACTGACATGCTGGTGCCA 60.303 57.895 0.00 0.00 38.71 4.92
2670 2876 2.552585 ATACGGTTCGACCAGTGCCG 62.553 60.000 0.00 3.43 46.83 5.69
3033 3243 8.637281 TGCATGATTTCAAATTGTATGTGATC 57.363 30.769 0.00 0.00 0.00 2.92
3060 3270 9.911788 AATGAGATGGACTATCAGTTGTTAAAT 57.088 29.630 1.30 0.00 38.31 1.40
3090 3307 8.774586 AGTTGATAATTATTTAGTGATGGCGTC 58.225 33.333 0.00 0.00 0.00 5.19
3133 3350 1.271762 ACACATTCCTCATGCAGCTGT 60.272 47.619 16.64 0.00 36.14 4.40
3173 3390 9.262472 CTCAGTTTTGTTGTTAATATACGAAGC 57.738 33.333 0.00 0.00 0.00 3.86
3177 3394 8.624028 GTTTTGTTGTTAATATACGAAGCACAC 58.376 33.333 0.00 0.00 0.00 3.82
3179 3396 5.062433 TGTTGTTAATATACGAAGCACACGG 59.938 40.000 0.00 0.00 34.93 4.94
3180 3397 4.996344 TGTTAATATACGAAGCACACGGA 58.004 39.130 0.00 0.00 34.93 4.69
3305 3523 7.472543 CAAAATAAGTTATTCTTCACCCGAGG 58.527 38.462 8.56 0.00 37.56 4.63
3311 3529 5.661759 AGTTATTCTTCACCCGAGGTAATCT 59.338 40.000 0.00 0.00 32.11 2.40
3397 3616 6.926272 ACTGCGTAAAATTTGGCATAAGAAAA 59.074 30.769 10.94 0.00 34.49 2.29
3581 3804 8.933807 CACAAAATTATGGTGCATTGATGTTAA 58.066 29.630 0.00 0.00 0.00 2.01
3594 3817 6.098266 GCATTGATGTTAAAATAGAAGGGGGT 59.902 38.462 0.00 0.00 0.00 4.95
3599 3822 8.561769 TGATGTTAAAATAGAAGGGGGTGAATA 58.438 33.333 0.00 0.00 0.00 1.75
3618 3841 7.647715 GGTGAATAATGGATTTAAACATGTCCG 59.352 37.037 0.00 0.00 33.39 4.79
3632 3855 7.857734 AAACATGTCCGTGTGAATTATGATA 57.142 32.000 0.00 0.00 31.49 2.15
3633 3856 6.844696 ACATGTCCGTGTGAATTATGATAC 57.155 37.500 0.00 0.00 0.00 2.24
3634 3857 6.582636 ACATGTCCGTGTGAATTATGATACT 58.417 36.000 0.00 0.00 0.00 2.12
3635 3858 6.701841 ACATGTCCGTGTGAATTATGATACTC 59.298 38.462 0.00 0.00 0.00 2.59
3636 3859 5.597806 TGTCCGTGTGAATTATGATACTCC 58.402 41.667 0.00 0.00 0.00 3.85
3637 3860 4.989168 GTCCGTGTGAATTATGATACTCCC 59.011 45.833 0.00 0.00 0.00 4.30
3638 3861 4.899457 TCCGTGTGAATTATGATACTCCCT 59.101 41.667 0.00 0.00 0.00 4.20
3639 3862 5.010719 TCCGTGTGAATTATGATACTCCCTC 59.989 44.000 0.00 0.00 0.00 4.30
3640 3863 5.230942 CGTGTGAATTATGATACTCCCTCC 58.769 45.833 0.00 0.00 0.00 4.30
3641 3864 5.221441 CGTGTGAATTATGATACTCCCTCCA 60.221 44.000 0.00 0.00 0.00 3.86
3642 3865 6.591935 GTGTGAATTATGATACTCCCTCCAA 58.408 40.000 0.00 0.00 0.00 3.53
3643 3866 7.227156 GTGTGAATTATGATACTCCCTCCAAT 58.773 38.462 0.00 0.00 0.00 3.16
3644 3867 7.389053 GTGTGAATTATGATACTCCCTCCAATC 59.611 40.741 0.00 0.00 0.00 2.67
3645 3868 6.881602 GTGAATTATGATACTCCCTCCAATCC 59.118 42.308 0.00 0.00 0.00 3.01
3646 3869 6.562223 TGAATTATGATACTCCCTCCAATCCA 59.438 38.462 0.00 0.00 0.00 3.41
3647 3870 7.073598 TGAATTATGATACTCCCTCCAATCCAA 59.926 37.037 0.00 0.00 0.00 3.53
3648 3871 6.840090 TTATGATACTCCCTCCAATCCAAA 57.160 37.500 0.00 0.00 0.00 3.28
3649 3872 5.937492 ATGATACTCCCTCCAATCCAAAT 57.063 39.130 0.00 0.00 0.00 2.32
3650 3873 5.732331 TGATACTCCCTCCAATCCAAATT 57.268 39.130 0.00 0.00 0.00 1.82
3651 3874 6.840090 TGATACTCCCTCCAATCCAAATTA 57.160 37.500 0.00 0.00 0.00 1.40
3652 3875 7.219601 TGATACTCCCTCCAATCCAAATTAA 57.780 36.000 0.00 0.00 0.00 1.40
3653 3876 7.825709 TGATACTCCCTCCAATCCAAATTAAT 58.174 34.615 0.00 0.00 0.00 1.40
3654 3877 8.288812 TGATACTCCCTCCAATCCAAATTAATT 58.711 33.333 0.00 0.00 0.00 1.40
3655 3878 6.796785 ACTCCCTCCAATCCAAATTAATTG 57.203 37.500 0.39 0.00 38.84 2.32
3656 3879 6.502138 ACTCCCTCCAATCCAAATTAATTGA 58.498 36.000 0.39 0.00 41.85 2.57
3657 3880 6.381133 ACTCCCTCCAATCCAAATTAATTGAC 59.619 38.462 0.39 0.00 41.85 3.18
3658 3881 5.359576 TCCCTCCAATCCAAATTAATTGACG 59.640 40.000 0.39 0.00 41.85 4.35
3659 3882 5.043248 CCTCCAATCCAAATTAATTGACGC 58.957 41.667 0.39 0.00 41.85 5.19
3660 3883 5.394005 CCTCCAATCCAAATTAATTGACGCA 60.394 40.000 0.39 0.00 41.85 5.24
3726 3949 5.673337 TCATTTATTGCGCAGAGTTATCC 57.327 39.130 11.31 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.061711 GCTTCAGACACGTGCATGATC 59.938 52.381 20.17 9.73 0.00 2.92
32 33 3.781079 TGCAGGTTTGTGCTATATTGC 57.219 42.857 1.87 1.87 44.32 3.56
110 112 8.565416 TGGATTATTATATACTCTACGCCATCG 58.435 37.037 0.00 0.00 42.43 3.84
132 134 0.749649 CGCTGCTTACCTCTCTGGAT 59.250 55.000 0.00 0.00 39.71 3.41
291 295 9.608617 CTAGAATACGTATGTATGTACAACAGG 57.391 37.037 9.24 3.14 40.42 4.00
297 301 9.836076 TGATTGCTAGAATACGTATGTATGTAC 57.164 33.333 9.24 4.25 40.42 2.90
374 382 4.848841 CGCACGTATTTAATTTGCTGTTGA 59.151 37.500 0.00 0.00 0.00 3.18
461 470 6.987386 TCATGGGATGTCAAAATACGTTTTT 58.013 32.000 0.00 0.00 35.41 1.94
462 471 6.582677 TCATGGGATGTCAAAATACGTTTT 57.417 33.333 0.00 0.00 38.03 2.43
463 472 6.458206 CGATCATGGGATGTCAAAATACGTTT 60.458 38.462 0.00 0.00 32.67 3.60
464 473 5.007626 CGATCATGGGATGTCAAAATACGTT 59.992 40.000 0.00 0.00 32.67 3.99
469 478 4.453478 CGATCGATCATGGGATGTCAAAAT 59.547 41.667 24.40 0.00 32.67 1.82
522 544 4.027724 CGATCTCTCTGCGAATATCGATG 58.972 47.826 8.54 0.00 43.74 3.84
535 557 3.593442 AGGTTCTCCATCGATCTCTCT 57.407 47.619 0.00 0.00 35.89 3.10
608 631 4.085204 TTACATTCCCGCCGCCGT 62.085 61.111 0.00 0.00 0.00 5.68
671 699 1.496060 AATCCGGGCATCTGTACTGA 58.504 50.000 0.00 4.80 0.00 3.41
677 705 2.027745 AGCTGTATAATCCGGGCATCTG 60.028 50.000 0.00 0.00 0.00 2.90
738 766 5.994668 GGTAAGCAGAATAGCAGATTAAGCT 59.005 40.000 0.00 0.00 45.77 3.74
751 779 3.673594 CGAGTTCGTGAGGTAAGCAGAAT 60.674 47.826 0.00 0.00 34.11 2.40
752 780 2.351447 CGAGTTCGTGAGGTAAGCAGAA 60.351 50.000 0.00 0.00 34.11 3.02
753 781 1.199327 CGAGTTCGTGAGGTAAGCAGA 59.801 52.381 0.00 0.00 34.11 4.26
754 782 1.618861 CGAGTTCGTGAGGTAAGCAG 58.381 55.000 0.00 0.00 34.11 4.24
755 783 0.388134 GCGAGTTCGTGAGGTAAGCA 60.388 55.000 3.27 0.00 42.22 3.91
756 784 2.360794 GCGAGTTCGTGAGGTAAGC 58.639 57.895 3.27 0.00 42.22 3.09
774 802 3.130160 GAGCTTGGAAGGCTGCCG 61.130 66.667 13.96 0.00 40.40 5.69
776 804 2.034687 TGGAGCTTGGAAGGCTGC 59.965 61.111 0.00 0.00 45.98 5.25
863 903 1.982958 AGAAACGGGGAAGGAAAGCTA 59.017 47.619 0.00 0.00 0.00 3.32
928 968 0.621862 GGGTTCTGGGTGGAGAGGAT 60.622 60.000 0.00 0.00 0.00 3.24
958 998 5.286267 CCGGCTTTATATATATCGGGGTT 57.714 43.478 10.52 0.00 33.27 4.11
959 999 4.950205 CCGGCTTTATATATATCGGGGT 57.050 45.455 10.52 0.00 33.27 4.95
962 1002 3.556423 GGCCCCGGCTTTATATATATCGG 60.556 52.174 5.55 11.15 41.60 4.18
964 1004 4.642429 CAGGCCCCGGCTTTATATATATC 58.358 47.826 0.00 0.00 41.60 1.63
965 1005 3.181443 GCAGGCCCCGGCTTTATATATAT 60.181 47.826 0.00 0.00 41.60 0.86
966 1006 2.171870 GCAGGCCCCGGCTTTATATATA 59.828 50.000 0.00 0.00 41.60 0.86
967 1007 1.064685 GCAGGCCCCGGCTTTATATAT 60.065 52.381 0.00 0.00 41.60 0.86
968 1008 0.326927 GCAGGCCCCGGCTTTATATA 59.673 55.000 0.00 0.00 41.60 0.86
1023 1063 1.611519 ACCTCCTCTATGTAGCTCGC 58.388 55.000 0.00 0.00 0.00 5.03
1024 1064 4.010667 AGTACCTCCTCTATGTAGCTCG 57.989 50.000 0.00 0.00 0.00 5.03
1043 1083 7.145985 CGTAAGCACTCAACACCATATATAGT 58.854 38.462 0.00 0.00 0.00 2.12
1056 1112 2.560981 TCTCCATCACGTAAGCACTCAA 59.439 45.455 0.00 0.00 45.62 3.02
1085 1141 3.927163 AAAGTACCGCACGCCGAGG 62.927 63.158 0.00 0.00 41.15 4.63
1148 1204 1.664017 CGAGAGCGAGGATGGCATG 60.664 63.158 3.81 0.00 44.88 4.06
1282 1338 3.730761 GGCTTGTCTGCGCACCAG 61.731 66.667 5.66 0.00 43.17 4.00
1286 1342 1.153369 GATAGGGCTTGTCTGCGCA 60.153 57.895 10.98 10.98 46.41 6.09
1368 1424 1.776662 TCAGAACTATAGCCGCCACT 58.223 50.000 0.00 0.00 0.00 4.00
1436 1492 1.136984 CGTTTCGACCTCCTCCTCG 59.863 63.158 0.00 0.00 0.00 4.63
1497 1559 3.582120 AACGTGCACGCCTGGTTG 61.582 61.111 37.35 10.87 44.43 3.77
1500 1562 3.276091 TTCAACGTGCACGCCTGG 61.276 61.111 37.35 23.49 44.43 4.45
1534 1596 1.185618 TGACCCCTCAACTGACTCCG 61.186 60.000 0.00 0.00 0.00 4.63
1544 1606 0.040646 ATACGTGGTCTGACCCCTCA 59.959 55.000 23.42 7.48 37.50 3.86
1570 1632 4.521062 CGCTGCTCTCTTCCCCGG 62.521 72.222 0.00 0.00 0.00 5.73
1780 1877 8.221965 ACTAGGTCGTTTGAAAAAGAGAAAAT 57.778 30.769 0.00 0.00 0.00 1.82
1822 1919 7.153315 TGTGCATGTGTTCATATGTGAAAATT 58.847 30.769 6.45 0.00 45.38 1.82
1823 1920 6.689554 TGTGCATGTGTTCATATGTGAAAAT 58.310 32.000 6.45 0.00 45.38 1.82
1846 1943 3.689161 TCATCCATTAAGCTCCAACGTTG 59.311 43.478 21.47 21.47 0.00 4.10
1925 2026 8.970020 TGGAGACACAAGCAAAATGAATATAAT 58.030 29.630 0.00 0.00 33.40 1.28
2141 2332 6.482308 ACGGAAGAGAAACGAATATATTTGGG 59.518 38.462 15.70 4.58 0.00 4.12
2365 2568 1.118965 TGCGGAAGTCCTTGAGTGGA 61.119 55.000 0.00 0.00 0.00 4.02
2368 2571 1.006102 CGTGCGGAAGTCCTTGAGT 60.006 57.895 0.00 0.00 0.00 3.41
2734 2940 5.569413 GCATGTACGCAAAACTAGCTAATT 58.431 37.500 0.00 0.00 0.00 1.40
2831 3037 9.944376 GGCAAACCTCTATGATCTTATTGTATA 57.056 33.333 0.00 0.00 0.00 1.47
2998 3204 7.946655 ATTTGAAATCATGCATGCTTGATAG 57.053 32.000 35.72 14.02 39.07 2.08
2999 3205 7.766738 ACAATTTGAAATCATGCATGCTTGATA 59.233 29.630 35.72 25.24 39.07 2.15
3000 3206 6.597672 ACAATTTGAAATCATGCATGCTTGAT 59.402 30.769 32.42 32.42 40.88 2.57
3001 3207 5.935206 ACAATTTGAAATCATGCATGCTTGA 59.065 32.000 31.21 31.21 35.17 3.02
3033 3243 8.722480 TTAACAACTGATAGTCCATCTCATTG 57.278 34.615 0.00 0.00 34.46 2.82
3090 3307 8.330302 GTGTTCATGAAAAACAAGAAAATGGAG 58.670 33.333 10.35 0.00 37.82 3.86
3160 3377 4.996344 TGTCCGTGTGCTTCGTATATTAA 58.004 39.130 0.00 0.00 0.00 1.40
3173 3390 3.526931 AGAGACCATAATGTCCGTGTG 57.473 47.619 0.00 0.00 35.83 3.82
3253 3471 8.344939 ACCCCGGGTGATGAATATATATAATT 57.655 34.615 21.85 0.00 32.98 1.40
3274 3492 6.811665 GTGAAGAATAACTTATTTTGCACCCC 59.188 38.462 10.34 0.00 39.13 4.95
3352 3570 9.494271 ACGCAGTGAATCAATATGAATATAACT 57.506 29.630 0.00 0.00 42.51 2.24
3373 3592 6.942886 TTTCTTATGCCAAATTTTACGCAG 57.057 33.333 9.48 0.00 34.15 5.18
3515 3738 9.794653 GTCTTATTTCAGACGTAAAAAGAGAAC 57.205 33.333 0.00 0.00 34.12 3.01
3548 3771 6.073327 TGCACCATAATTTTGTGTTTCGTA 57.927 33.333 0.00 0.00 32.62 3.43
3550 3773 6.145209 TCAATGCACCATAATTTTGTGTTTCG 59.855 34.615 0.00 0.00 32.62 3.46
3581 3804 6.606241 TCCATTATTCACCCCCTTCTATTT 57.394 37.500 0.00 0.00 0.00 1.40
3594 3817 8.187480 CACGGACATGTTTAAATCCATTATTCA 58.813 33.333 0.00 0.00 0.00 2.57
3599 3822 5.475220 TCACACGGACATGTTTAAATCCATT 59.525 36.000 0.00 0.00 0.00 3.16
3618 3841 6.174720 TGGAGGGAGTATCATAATTCACAC 57.825 41.667 0.00 0.00 36.25 3.82
3632 3855 6.381133 GTCAATTAATTTGGATTGGAGGGAGT 59.619 38.462 0.00 0.00 35.92 3.85
3633 3856 6.460123 CGTCAATTAATTTGGATTGGAGGGAG 60.460 42.308 0.00 0.00 35.92 4.30
3634 3857 5.359576 CGTCAATTAATTTGGATTGGAGGGA 59.640 40.000 0.00 0.00 35.92 4.20
3635 3858 5.591099 CGTCAATTAATTTGGATTGGAGGG 58.409 41.667 0.00 0.00 35.92 4.30
3636 3859 5.043248 GCGTCAATTAATTTGGATTGGAGG 58.957 41.667 0.00 0.00 35.92 4.30
3637 3860 5.649557 TGCGTCAATTAATTTGGATTGGAG 58.350 37.500 0.00 5.39 35.92 3.86
3638 3861 5.651387 TGCGTCAATTAATTTGGATTGGA 57.349 34.783 0.00 0.00 35.92 3.53
3639 3862 5.868801 AGTTGCGTCAATTAATTTGGATTGG 59.131 36.000 0.00 0.00 35.92 3.16
3640 3863 6.949578 AGTTGCGTCAATTAATTTGGATTG 57.050 33.333 0.00 0.00 35.92 2.67
3641 3864 7.440856 ACAAAGTTGCGTCAATTAATTTGGATT 59.559 29.630 0.00 0.00 35.92 3.01
3642 3865 6.928492 ACAAAGTTGCGTCAATTAATTTGGAT 59.072 30.769 0.00 0.00 35.92 3.41
3643 3866 6.276847 ACAAAGTTGCGTCAATTAATTTGGA 58.723 32.000 0.00 0.00 35.92 3.53
3644 3867 6.199908 TGACAAAGTTGCGTCAATTAATTTGG 59.800 34.615 0.00 0.00 39.14 3.28
3645 3868 7.159437 TGACAAAGTTGCGTCAATTAATTTG 57.841 32.000 0.00 0.00 39.14 2.32
3646 3869 7.763172 TTGACAAAGTTGCGTCAATTAATTT 57.237 28.000 14.17 0.00 44.88 1.82
3654 3877 6.199908 CCAAATTAATTGACAAAGTTGCGTCA 59.800 34.615 0.39 4.65 41.85 4.35
3655 3878 6.419413 TCCAAATTAATTGACAAAGTTGCGTC 59.581 34.615 0.39 0.00 41.85 5.19
3656 3879 6.276847 TCCAAATTAATTGACAAAGTTGCGT 58.723 32.000 0.39 0.00 41.85 5.24
3657 3880 6.761731 TCCAAATTAATTGACAAAGTTGCG 57.238 33.333 0.39 0.00 41.85 4.85
3658 3881 8.016801 CCAATCCAAATTAATTGACAAAGTTGC 58.983 33.333 0.39 0.00 41.85 4.17
3659 3882 9.270640 TCCAATCCAAATTAATTGACAAAGTTG 57.729 29.630 0.39 2.20 41.85 3.16
3660 3883 9.492973 CTCCAATCCAAATTAATTGACAAAGTT 57.507 29.630 0.39 0.00 41.85 2.66


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

AutoCloner maintained by Alex Coulton.