Multiple sequence alignment - TraesCS3B01G341600

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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 TraesCS3B01G341600 chr3B 100.000 8175 0 0 1 8175 548376828 548368654 0.000000e+00 15097.0
1 TraesCS3B01G341600 chr3B 95.427 4330 136 22 7 4308 548557315 548553020 0.000000e+00 6842.0
2 TraesCS3B01G341600 chr3B 95.975 3801 104 20 4 3774 548850721 548846940 0.000000e+00 6126.0
3 TraesCS3B01G341600 chr3B 97.815 1510 32 1 3773 5281 548846846 548845337 0.000000e+00 2604.0
4 TraesCS3B01G341600 chr3B 98.936 1128 11 1 4593 5719 548084278 548083151 0.000000e+00 2015.0
5 TraesCS3B01G341600 chr3B 93.988 1314 50 6 4411 5719 548553022 548551733 0.000000e+00 1962.0
6 TraesCS3B01G341600 chr3B 97.313 1005 22 3 6578 7581 548841219 548840219 0.000000e+00 1701.0
7 TraesCS3B01G341600 chr3B 96.612 1033 21 6 4688 5719 548843165 548842146 0.000000e+00 1701.0
8 TraesCS3B01G341600 chr3B 96.915 1005 25 4 6578 7581 548550667 548549668 0.000000e+00 1679.0
9 TraesCS3B01G341600 chr3B 96.583 995 26 3 5717 6708 548842114 548841125 0.000000e+00 1642.0
10 TraesCS3B01G341600 chr3B 95.792 998 33 5 6578 7574 548082015 548081026 0.000000e+00 1602.0
11 TraesCS3B01G341600 chr3B 95.734 586 19 2 6126 6708 548551155 548550573 0.000000e+00 939.0
12 TraesCS3B01G341600 chr3B 98.008 502 6 2 4108 4607 548084963 548084464 0.000000e+00 869.0
13 TraesCS3B01G341600 chr3B 95.437 526 18 2 6186 6708 548082443 548081921 0.000000e+00 833.0
14 TraesCS3B01G341600 chr3B 95.703 512 19 2 7664 8175 548836045 548835537 0.000000e+00 821.0
15 TraesCS3B01G341600 chr3B 93.750 544 19 8 7642 8175 548549682 548549144 0.000000e+00 802.0
16 TraesCS3B01G341600 chr3B 98.438 320 3 1 5717 6036 548083119 548082802 5.540000e-156 562.0
17 TraesCS3B01G341600 chr3B 96.875 320 5 2 5717 6036 548551701 548551387 1.560000e-146 531.0
18 TraesCS3B01G341600 chr3B 84.010 419 38 14 7655 8068 548080734 548080340 7.750000e-100 375.0
19 TraesCS3B01G341600 chr3B 98.101 158 3 0 6031 6188 548082760 548082603 8.080000e-70 276.0
20 TraesCS3B01G341600 chr3B 90.840 131 10 2 4285 4413 733436532 733436402 3.030000e-39 174.0
21 TraesCS3B01G341600 chr3B 96.939 98 3 0 6031 6128 548551345 548551248 1.830000e-36 165.0
22 TraesCS3B01G341600 chr3B 96.970 66 1 1 7576 7641 756263150 756263214 8.670000e-20 110.0
23 TraesCS3B01G341600 chr3B 93.243 74 3 2 7568 7641 529807260 529807189 3.120000e-19 108.0
24 TraesCS3B01G341600 chr3B 100.000 39 0 0 2480 2518 548554976 548554938 1.140000e-08 73.1
25 TraesCS3B01G341600 chr3B 100.000 39 0 0 2480 2518 548848368 548848330 1.140000e-08 73.1
26 TraesCS3B01G341600 chr3B 97.436 39 1 0 2352 2390 548374349 548374311 5.300000e-07 67.6
27 TraesCS3B01G341600 chr3B 97.436 39 1 0 2480 2518 548374477 548374439 5.300000e-07 67.6
28 TraesCS3B01G341600 chr3B 97.436 39 1 0 2352 2390 548554848 548554810 5.300000e-07 67.6
29 TraesCS3B01G341600 chr3B 97.436 39 1 0 2352 2390 548848240 548848202 5.300000e-07 67.6
30 TraesCS3B01G341600 chr3B 96.875 32 1 0 7642 7673 548840233 548840202 4.000000e-03 54.7
31 TraesCS3B01G341600 chr3A 92.837 3616 169 46 1 3587 529611279 529614833 0.000000e+00 5160.0
32 TraesCS3B01G341600 chr3A 95.837 1129 39 3 4593 5719 529616335 529617457 0.000000e+00 1818.0
33 TraesCS3B01G341600 chr3A 93.793 1015 48 6 6575 7581 529618424 529619431 0.000000e+00 1511.0
34 TraesCS3B01G341600 chr3A 94.453 685 28 5 6031 6711 529617847 529618525 0.000000e+00 1046.0
35 TraesCS3B01G341600 chr3A 89.646 792 40 20 3816 4607 529615396 529616145 0.000000e+00 970.0
36 TraesCS3B01G341600 chr3A 95.000 320 12 2 5717 6036 529617489 529617804 4.410000e-137 499.0
37 TraesCS3B01G341600 chr3A 80.000 480 77 11 2655 3118 741827297 741826821 3.660000e-88 337.0
38 TraesCS3B01G341600 chr3A 96.257 187 4 2 3633 3817 529615087 529615272 3.710000e-78 303.0
39 TraesCS3B01G341600 chr3A 84.190 253 31 7 7924 8172 529619710 529619957 3.810000e-58 237.0
40 TraesCS3B01G341600 chr3A 92.638 163 9 2 7642 7803 529619417 529619577 1.770000e-56 231.0
41 TraesCS3B01G341600 chr3A 76.347 334 55 15 2085 2404 732731861 732732184 3.050000e-34 158.0
42 TraesCS3B01G341600 chr3A 100.000 63 0 0 3586 3648 529614937 529614999 5.180000e-22 117.0
43 TraesCS3B01G341600 chr3A 80.952 105 17 3 3134 3238 741863530 741863429 6.800000e-11 80.5
44 TraesCS3B01G341600 chr3A 77.444 133 26 4 6384 6514 529618521 529618651 8.800000e-10 76.8
45 TraesCS3B01G341600 chr3A 97.674 43 1 0 2348 2390 529613723 529613765 3.160000e-09 75.0
46 TraesCS3B01G341600 chr3D 92.417 2400 120 23 4 2389 421378012 421375661 0.000000e+00 3367.0
47 TraesCS3B01G341600 chr3D 97.842 1112 23 1 2476 3587 421375702 421374592 0.000000e+00 1919.0
48 TraesCS3B01G341600 chr3D 93.459 1009 54 7 6578 7581 421371107 421370106 0.000000e+00 1487.0
49 TraesCS3B01G341600 chr3D 95.580 724 23 4 3586 4308 421374433 421373718 0.000000e+00 1151.0
50 TraesCS3B01G341600 chr3D 93.632 691 22 9 5036 5719 421372743 421372068 0.000000e+00 1013.0
51 TraesCS3B01G341600 chr3D 92.952 681 32 7 6031 6708 421371680 421371013 0.000000e+00 977.0
52 TraesCS3B01G341600 chr3D 94.877 527 26 1 4669 5194 421373267 421372741 0.000000e+00 822.0
53 TraesCS3B01G341600 chr3D 87.361 538 32 10 7642 8175 421370120 421369615 1.180000e-162 584.0
54 TraesCS3B01G341600 chr3D 95.639 321 7 4 5717 6036 421372036 421371722 7.320000e-140 508.0
55 TraesCS3B01G341600 chr3D 93.116 276 18 1 4411 4685 421373720 421373445 3.550000e-108 403.0
56 TraesCS3B01G341600 chr3D 94.872 117 6 0 4298 4414 42634833 42634717 5.040000e-42 183.0
57 TraesCS3B01G341600 chr3D 94.286 70 2 2 7572 7641 500634280 500634213 1.120000e-18 106.0
58 TraesCS3B01G341600 chr3D 77.692 130 25 4 6390 6517 421371007 421370880 8.800000e-10 76.8
59 TraesCS3B01G341600 chr3D 92.000 50 3 1 3457 3505 42889281 42889232 1.470000e-07 69.4
60 TraesCS3B01G341600 chr3D 100.000 32 0 0 8132 8163 581422336 581422367 8.860000e-05 60.2
61 TraesCS3B01G341600 chr7B 97.414 116 3 0 4306 4421 695049288 695049403 1.800000e-46 198.0
62 TraesCS3B01G341600 chr7B 95.690 116 3 2 4307 4421 730205114 730205228 1.400000e-42 185.0
63 TraesCS3B01G341600 chrUn 96.552 116 4 0 4306 4421 347838518 347838633 8.370000e-45 193.0
64 TraesCS3B01G341600 chrUn 96.552 116 4 0 4306 4421 441816837 441816722 8.370000e-45 193.0
65 TraesCS3B01G341600 chrUn 93.421 76 3 2 7566 7641 12510656 12510583 2.410000e-20 111.0
66 TraesCS3B01G341600 chrUn 79.114 158 28 5 8023 8175 29675255 29675412 4.040000e-18 104.0
67 TraesCS3B01G341600 chr7D 94.915 118 4 2 4297 4413 382742653 382742537 5.040000e-42 183.0
68 TraesCS3B01G341600 chr7D 94.366 71 1 3 7571 7641 53612253 53612320 1.120000e-18 106.0
69 TraesCS3B01G341600 chr2B 84.685 111 15 2 8067 8175 601211779 601211669 8.670000e-20 110.0
70 TraesCS3B01G341600 chr1D 95.588 68 2 1 7574 7641 101106494 101106428 3.120000e-19 108.0
71 TraesCS3B01G341600 chr1D 89.024 82 5 3 7561 7641 202541830 202541908 1.880000e-16 99.0
72 TraesCS3B01G341600 chr6A 89.535 86 5 4 7557 7641 4545081 4545163 1.120000e-18 106.0
73 TraesCS3B01G341600 chr1A 93.151 73 3 2 7571 7641 84790755 84790827 1.120000e-18 106.0
74 TraesCS3B01G341600 chr2A 95.238 42 2 0 7744 7785 54010900 54010859 5.300000e-07 67.6


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 TraesCS3B01G341600 chr3B 548368654 548376828 8174 True 5077.400000 15097 98.290667 1 8175 3 chr3B.!!$R5 8174
1 TraesCS3B01G341600 chr3B 548840202 548850721 10519 True 1746.175000 6126 97.326125 4 7673 8 chr3B.!!$R7 7669
2 TraesCS3B01G341600 chr3B 548549144 548557315 8171 True 1451.188889 6842 96.340444 7 8175 9 chr3B.!!$R6 8168
3 TraesCS3B01G341600 chr3B 548080340 548084963 4623 True 933.142857 2015 95.531714 4108 8068 7 chr3B.!!$R4 3960
4 TraesCS3B01G341600 chr3B 548835537 548836045 508 True 821.000000 821 95.703000 7664 8175 1 chr3B.!!$R2 511
5 TraesCS3B01G341600 chr3A 529611279 529619957 8678 False 1003.650000 5160 92.480750 1 8172 12 chr3A.!!$F2 8171
6 TraesCS3B01G341600 chr3D 421369615 421378012 8397 True 1118.890909 3367 92.233364 4 8175 11 chr3D.!!$R4 8171

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
508 532 0.175073 ACATACTCCCTCCGTTTCGC 59.825 55.000 0.00 0.0 0.00 4.70 F
1499 1543 0.755079 GGGTACATCCGGGTCCTTAC 59.245 60.000 0.00 0.0 37.00 2.34 F
1500 1544 1.690527 GGGTACATCCGGGTCCTTACT 60.691 57.143 0.00 0.0 37.00 2.24 F
1501 1545 2.113807 GGTACATCCGGGTCCTTACTT 58.886 52.381 0.00 0.0 0.00 2.24 F
1529 1573 2.139917 CACTTCGTGGTCGGATTTTGA 58.860 47.619 0.00 0.0 37.69 2.69 F
2384 2570 2.500098 TGCGCTGTAGTTTATCCCTCTT 59.500 45.455 9.73 0.0 0.00 2.85 F
2732 2918 4.212214 CCTACAAGTCTCAGTTGCAAGTTC 59.788 45.833 3.38 0.0 31.85 3.01 F
4153 4825 4.246458 GGTGGTGTGTCAGATTAGAGAAC 58.754 47.826 0.00 0.0 0.00 3.01 F
4424 5096 4.966805 ACGGAGGGAGTAGGATTTAAATGA 59.033 41.667 5.17 0.0 0.00 2.57 F
6772 11183 1.818674 GCCACCAACCAATACTTCCAG 59.181 52.381 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2119 0.788391 GCGTCACCAAACTTCTACCG 59.212 55.000 0.00 0.0 0.00 4.02 R
2468 2654 6.351456 GCAATATGGGGTTTAAGTGCCTTTAA 60.351 38.462 0.00 0.0 0.00 1.52 R
2732 2918 7.789273 AATCTTTATGTCTCTTCTGAGCATG 57.211 36.000 10.73 0.0 40.03 4.06 R
3951 4623 5.298777 CAGTTGATTTGGAGATGGAGGAATC 59.701 44.000 0.00 0.0 0.00 2.52 R
3977 4649 2.038387 AACTTTCGCCTTGAGTGTGT 57.962 45.000 0.00 0.0 0.00 3.72 R
4018 4690 5.473504 ACCGTCATCTGTTTTTGCTTCTTAT 59.526 36.000 0.00 0.0 0.00 1.73 R
4866 5938 2.584835 TTTTGATAGCTGGTGTGGCT 57.415 45.000 0.00 0.0 43.02 4.75 R
5178 6408 2.629051 CCGTTGATTGAGGGAGGTTAC 58.371 52.381 0.00 0.0 0.00 2.50 R
6781 11192 0.752743 AGGCACTGCAGTTGCTTTCA 60.753 50.000 28.26 0.0 42.66 2.69 R
7628 12049 0.108138 AGAAGTGAGTGGCCGTATGC 60.108 55.000 0.00 0.0 40.16 3.14 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
53 57 2.691252 GAACCCCACCCCCGAGAT 60.691 66.667 0.00 0.00 0.00 2.75
155 159 1.071542 TGCATGAAGAGTTGAACGGGA 59.928 47.619 0.00 0.00 0.00 5.14
244 248 2.111932 TTTTAGCACTGCACGCGTGG 62.112 55.000 37.47 25.17 33.10 4.94
280 284 4.159377 CTCGAGAGCTTGCTAGATTAGG 57.841 50.000 6.58 0.00 0.00 2.69
387 394 9.214957 TGAAATGAAATAAAGTAGTGACGATGT 57.785 29.630 0.00 0.00 0.00 3.06
422 429 5.279685 AGGAATGTCCATTCTCTCTCTCTT 58.720 41.667 17.06 0.00 44.90 2.85
450 473 1.276421 CAGACGGTCACATCCCTTTCT 59.724 52.381 11.27 0.00 0.00 2.52
508 532 0.175073 ACATACTCCCTCCGTTTCGC 59.825 55.000 0.00 0.00 0.00 4.70
516 540 2.562298 TCCCTCCGTTTCGCTTTACTTA 59.438 45.455 0.00 0.00 0.00 2.24
518 542 3.308866 CCCTCCGTTTCGCTTTACTTATG 59.691 47.826 0.00 0.00 0.00 1.90
531 555 5.751990 GCTTTACTTATGGTACGTGCAGTAT 59.248 40.000 5.86 0.00 37.69 2.12
534 558 5.192327 ACTTATGGTACGTGCAGTATACC 57.808 43.478 5.86 12.20 39.12 2.73
551 577 9.971744 GCAGTATACCAAATATTTTGCAAAAAG 57.028 29.630 27.10 14.48 34.20 2.27
552 578 9.971744 CAGTATACCAAATATTTTGCAAAAAGC 57.028 29.630 27.10 6.89 45.96 3.51
553 579 9.161629 AGTATACCAAATATTTTGCAAAAAGCC 57.838 29.630 27.10 4.58 44.83 4.35
582 608 7.022384 CGTACTTTCAAACACCTAACAAAACA 58.978 34.615 0.00 0.00 0.00 2.83
583 609 7.698970 CGTACTTTCAAACACCTAACAAAACAT 59.301 33.333 0.00 0.00 0.00 2.71
584 610 9.361315 GTACTTTCAAACACCTAACAAAACATT 57.639 29.630 0.00 0.00 0.00 2.71
587 613 6.783708 TCAAACACCTAACAAAACATTCCT 57.216 33.333 0.00 0.00 0.00 3.36
601 627 4.453480 ACATTCCTGTTTCCTTCCTTCA 57.547 40.909 0.00 0.00 28.70 3.02
608 634 1.073923 GTTTCCTTCCTTCAGCCTCCA 59.926 52.381 0.00 0.00 0.00 3.86
634 660 2.034066 CCATGTGTCGCCTGGGTT 59.966 61.111 0.00 0.00 30.38 4.11
721 748 2.363925 ACCGCCCACCTAGTCTCC 60.364 66.667 0.00 0.00 0.00 3.71
758 785 2.125326 CGGGACATAGCTCCACGGA 61.125 63.158 0.00 0.00 30.97 4.69
759 786 1.742768 GGGACATAGCTCCACGGAG 59.257 63.158 8.84 8.84 44.56 4.63
760 787 1.742768 GGACATAGCTCCACGGAGG 59.257 63.158 14.86 0.71 42.19 4.30
761 788 1.068250 GACATAGCTCCACGGAGGC 59.932 63.158 14.86 7.23 42.19 4.70
762 789 2.028190 CATAGCTCCACGGAGGCG 59.972 66.667 14.86 0.00 42.19 5.52
1052 1082 2.954611 GAACCCACAAAGGAGCGC 59.045 61.111 0.00 0.00 41.22 5.92
1498 1542 0.756442 CGGGTACATCCGGGTCCTTA 60.756 60.000 0.00 0.00 45.78 2.69
1499 1543 0.755079 GGGTACATCCGGGTCCTTAC 59.245 60.000 0.00 0.00 37.00 2.34
1500 1544 1.690527 GGGTACATCCGGGTCCTTACT 60.691 57.143 0.00 0.00 37.00 2.24
1501 1545 2.113807 GGTACATCCGGGTCCTTACTT 58.886 52.381 0.00 0.00 0.00 2.24
1529 1573 2.139917 CACTTCGTGGTCGGATTTTGA 58.860 47.619 0.00 0.00 37.69 2.69
1683 1729 7.274447 AGGTGCATTTTCTTTTCTTTTCATCA 58.726 30.769 0.00 0.00 0.00 3.07
1774 1821 8.888579 ATTCTAGTAGAAATGGATGGTTTACG 57.111 34.615 16.37 0.00 37.82 3.18
1775 1822 7.649533 TCTAGTAGAAATGGATGGTTTACGA 57.350 36.000 0.00 0.00 0.00 3.43
1776 1823 7.713750 TCTAGTAGAAATGGATGGTTTACGAG 58.286 38.462 0.00 0.00 0.00 4.18
2063 2119 7.849804 TTTGGTAGCTATCTGATTCTGAAAC 57.150 36.000 5.42 0.00 0.00 2.78
2384 2570 2.500098 TGCGCTGTAGTTTATCCCTCTT 59.500 45.455 9.73 0.00 0.00 2.85
2432 2618 6.073222 CCTTATGACGAGTAAAAAGTTGCACT 60.073 38.462 0.00 0.00 0.00 4.40
2448 2634 7.190920 AGTTGCACTTCTGTTGATACTTTAC 57.809 36.000 0.00 0.00 0.00 2.01
2468 2654 8.796475 ACTTTACTTTCTGCATACATTGAACAT 58.204 29.630 0.00 0.00 0.00 2.71
2732 2918 4.212214 CCTACAAGTCTCAGTTGCAAGTTC 59.788 45.833 3.38 0.00 31.85 3.01
3977 4649 4.782691 TCCTCCATCTCCAAATCAACTGTA 59.217 41.667 0.00 0.00 0.00 2.74
4153 4825 4.246458 GGTGGTGTGTCAGATTAGAGAAC 58.754 47.826 0.00 0.00 0.00 3.01
4424 5096 4.966805 ACGGAGGGAGTAGGATTTAAATGA 59.033 41.667 5.17 0.00 0.00 2.57
4626 5504 7.630242 AACTAACATGTCTGAATGGTAATGG 57.370 36.000 0.00 0.00 29.46 3.16
4819 5891 7.523709 GCATACCATCCTGGGTACAATTTATTG 60.524 40.741 0.00 1.03 45.72 1.90
4866 5938 8.939201 TTGCAAAGAGTTTGTCAAAATCATAA 57.061 26.923 23.48 10.61 42.56 1.90
5178 6408 9.090692 CCAGCATTATTTCATTAAGGTCAAAAG 57.909 33.333 0.00 0.00 0.00 2.27
5322 9305 4.625742 CGTTGACAGTAGTACTTCCCAATG 59.374 45.833 0.00 6.92 0.00 2.82
5765 9789 4.826274 TGCTAGTGAGTTTTCTGCCTAT 57.174 40.909 0.00 0.00 0.00 2.57
5778 9802 8.332487 AGTTTTCTGCCTATCTTCCTATCTTTT 58.668 33.333 0.00 0.00 0.00 2.27
5779 9803 8.961634 GTTTTCTGCCTATCTTCCTATCTTTTT 58.038 33.333 0.00 0.00 0.00 1.94
5886 9911 4.081862 TCTGGTCCACGTTCCTGTTTATAG 60.082 45.833 0.00 0.00 0.00 1.31
6049 10170 3.270877 ACAGTTTGGACAGTTCACTGAC 58.729 45.455 14.00 7.39 46.59 3.51
6542 10920 6.542821 ACAATCTCCTGTTGAAACTATCCAA 58.457 36.000 0.00 0.00 0.00 3.53
6720 11131 6.591834 CGAGGATGAAGTAATGAACTCAACTT 59.408 38.462 0.00 0.00 37.50 2.66
6772 11183 1.818674 GCCACCAACCAATACTTCCAG 59.181 52.381 0.00 0.00 0.00 3.86
6781 11192 0.328258 AATACTTCCAGCCTTGCGGT 59.672 50.000 0.00 0.00 0.00 5.68
7513 11931 2.496070 AGCGCTGTGTGGTCTATTCTAA 59.504 45.455 10.39 0.00 0.00 2.10
7575 11996 2.762535 TAACTGGCCACACTTCTAGC 57.237 50.000 0.00 0.00 0.00 3.42
7577 11998 1.938585 ACTGGCCACACTTCTAGCTA 58.061 50.000 0.00 0.00 0.00 3.32
7578 11999 1.827969 ACTGGCCACACTTCTAGCTAG 59.172 52.381 15.01 15.01 39.48 3.42
7579 12000 1.827969 CTGGCCACACTTCTAGCTAGT 59.172 52.381 20.10 0.63 0.00 2.57
7580 12001 2.234908 CTGGCCACACTTCTAGCTAGTT 59.765 50.000 20.10 3.74 0.00 2.24
7581 12002 2.637872 TGGCCACACTTCTAGCTAGTTT 59.362 45.455 20.10 3.39 0.00 2.66
7583 12004 4.072839 GGCCACACTTCTAGCTAGTTTTT 58.927 43.478 20.10 1.28 0.00 1.94
7608 12029 0.331616 AAAAAGGAGGATGACCCCCG 59.668 55.000 0.00 0.00 36.73 5.73
7609 12030 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
7615 12036 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
7621 12042 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
7622 12043 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
7623 12044 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
7626 12047 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
7627 12048 2.827423 CCTCTGCATCTGGGCGAT 59.173 61.111 0.00 0.00 36.28 4.58
7634 12055 2.156542 CATCTGGGCGATGCATACG 58.843 57.895 0.00 6.68 42.75 3.06
7635 12056 1.004560 ATCTGGGCGATGCATACGG 60.005 57.895 16.56 6.65 0.00 4.02
7640 12061 2.588877 GCGATGCATACGGCCACT 60.589 61.111 16.56 0.00 43.89 4.00
7641 12062 2.598632 GCGATGCATACGGCCACTC 61.599 63.158 16.56 0.00 43.89 3.51
7690 12348 0.400594 TGAGACACTCCGGAGTCTGA 59.599 55.000 34.28 20.53 41.97 3.27
7699 12357 3.082548 CTCCGGAGTCTGACTGTTCTTA 58.917 50.000 24.04 0.00 0.00 2.10
7732 12390 5.179533 ACTTTGCCGTTTGTATTTTGGTTT 58.820 33.333 0.00 0.00 0.00 3.27
7733 12391 6.338937 ACTTTGCCGTTTGTATTTTGGTTTA 58.661 32.000 0.00 0.00 0.00 2.01
8046 12783 1.826327 CAAAAGAGCACGTGTGTTGG 58.174 50.000 18.38 0.28 0.00 3.77
8105 12845 5.549228 TGATCATGAGTCAAGGCCCTAATAT 59.451 40.000 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.105960 GAAATGATTCTCCGCCGCCG 62.106 60.000 0.00 0.00 32.57 6.46
53 57 2.161855 GGCCATGTTTGAGTGTCATCA 58.838 47.619 0.00 0.00 0.00 3.07
155 159 3.650281 TGTCATCACATGGGTGCTAAT 57.350 42.857 0.00 0.00 44.87 1.73
244 248 2.278271 GAGCCACGCGACTAGCTC 60.278 66.667 15.93 19.65 44.36 4.09
280 284 5.293569 CCACAACTTCGGGTGATAATCTTAC 59.706 44.000 0.00 0.00 37.18 2.34
433 456 0.324943 CCAGAAAGGGATGTGACCGT 59.675 55.000 0.00 0.00 0.00 4.83
508 532 7.380602 GGTATACTGCACGTACCATAAGTAAAG 59.619 40.741 2.25 0.00 38.18 1.85
516 540 4.475051 TTTGGTATACTGCACGTACCAT 57.525 40.909 16.58 0.25 45.18 3.55
518 542 7.486802 AAATATTTGGTATACTGCACGTACC 57.513 36.000 0.00 9.45 38.65 3.34
531 555 5.707764 GGGGCTTTTTGCAAAATATTTGGTA 59.292 36.000 24.39 6.94 45.15 3.25
534 558 5.390779 CGAGGGGCTTTTTGCAAAATATTTG 60.391 40.000 24.39 13.25 45.15 2.32
536 560 4.252878 CGAGGGGCTTTTTGCAAAATATT 58.747 39.130 24.39 8.21 45.15 1.28
551 577 1.534163 GTGTTTGAAAGTACGAGGGGC 59.466 52.381 0.00 0.00 0.00 5.80
552 578 2.148768 GGTGTTTGAAAGTACGAGGGG 58.851 52.381 0.00 0.00 0.00 4.79
553 579 3.121738 AGGTGTTTGAAAGTACGAGGG 57.878 47.619 0.00 0.00 0.00 4.30
582 608 3.425659 GCTGAAGGAAGGAAACAGGAAT 58.574 45.455 0.00 0.00 0.00 3.01
583 609 2.489073 GGCTGAAGGAAGGAAACAGGAA 60.489 50.000 0.00 0.00 0.00 3.36
584 610 1.073923 GGCTGAAGGAAGGAAACAGGA 59.926 52.381 0.00 0.00 0.00 3.86
587 613 1.073923 GGAGGCTGAAGGAAGGAAACA 59.926 52.381 0.00 0.00 0.00 2.83
590 616 0.693049 GTGGAGGCTGAAGGAAGGAA 59.307 55.000 0.00 0.00 0.00 3.36
608 634 2.351276 GACACATGGGCGAAGGGT 59.649 61.111 0.00 0.00 0.00 4.34
634 660 1.813859 CGGAATCTGACGGTGCCTA 59.186 57.895 0.00 0.00 0.00 3.93
690 717 1.742768 GCGGTGAGGGAATCGAGAT 59.257 57.895 0.00 0.00 0.00 2.75
747 774 2.829003 CTCGCCTCCGTGGAGCTA 60.829 66.667 10.53 0.00 40.69 3.32
760 787 4.443266 AAGACCAGCTCGCCTCGC 62.443 66.667 0.00 0.00 0.00 5.03
761 788 2.290122 ATCAAGACCAGCTCGCCTCG 62.290 60.000 0.00 0.00 0.00 4.63
762 789 0.107945 AATCAAGACCAGCTCGCCTC 60.108 55.000 0.00 0.00 0.00 4.70
1052 1082 0.942962 GCTGGATTGATGCTCCTTCG 59.057 55.000 0.00 0.00 33.69 3.79
1349 1379 4.657824 CCGTGCTGAACCCGTCGT 62.658 66.667 0.00 0.00 0.00 4.34
1498 1542 2.928361 CGAAGTGTTCGCGCAAGT 59.072 55.556 8.75 0.00 46.97 3.16
1529 1573 2.890945 CCTGAAACCGAAAGTTGGGAAT 59.109 45.455 0.00 0.00 39.19 3.01
1683 1729 1.153756 CCCAGTTTGTTCAGGCCCT 59.846 57.895 0.00 0.00 0.00 5.19
1734 1781 5.480642 ACTAGAATCTCAATCGCCATCAT 57.519 39.130 0.00 0.00 0.00 2.45
1739 1786 6.367422 CCATTTCTACTAGAATCTCAATCGCC 59.633 42.308 0.00 0.00 33.67 5.54
1774 1821 9.456147 TCTACTAGAATCTCAATATAGCCACTC 57.544 37.037 0.00 0.00 0.00 3.51
1775 1822 9.815306 TTCTACTAGAATCTCAATATAGCCACT 57.185 33.333 0.00 0.00 0.00 4.00
2063 2119 0.788391 GCGTCACCAAACTTCTACCG 59.212 55.000 0.00 0.00 0.00 4.02
2384 2570 8.302515 AGGAAATAACTTCGTATCTAGTTCCA 57.697 34.615 14.27 0.00 39.71 3.53
2432 2618 8.621532 ATGCAGAAAGTAAAGTATCAACAGAA 57.378 30.769 0.00 0.00 0.00 3.02
2448 2634 9.079833 CCTTTAATGTTCAATGTATGCAGAAAG 57.920 33.333 0.00 0.00 0.00 2.62
2468 2654 6.351456 GCAATATGGGGTTTAAGTGCCTTTAA 60.351 38.462 0.00 0.00 0.00 1.52
2631 2817 8.682936 ACAAGTGTGAAAGAATATCAAGAACT 57.317 30.769 0.00 0.00 0.00 3.01
2732 2918 7.789273 AATCTTTATGTCTCTTCTGAGCATG 57.211 36.000 10.73 0.00 40.03 4.06
3951 4623 5.298777 CAGTTGATTTGGAGATGGAGGAATC 59.701 44.000 0.00 0.00 0.00 2.52
3977 4649 2.038387 AACTTTCGCCTTGAGTGTGT 57.962 45.000 0.00 0.00 0.00 3.72
4018 4690 5.473504 ACCGTCATCTGTTTTTGCTTCTTAT 59.526 36.000 0.00 0.00 0.00 1.73
4153 4825 5.619132 ATCATTTGGGGGCATCTTAAAAG 57.381 39.130 0.00 0.00 0.00 2.27
4399 5071 5.767277 TTTAAATCCTACTCCCTCCGTTT 57.233 39.130 0.00 0.00 0.00 3.60
4424 5096 8.593945 ACATGTCCATCCTACATAACAATTTT 57.406 30.769 0.00 0.00 35.82 1.82
4626 5504 7.665559 TGAGGGCATGAATAAACCATAGTAATC 59.334 37.037 0.00 0.00 0.00 1.75
4819 5891 6.257630 GCAAGAGATTAGAGATGTGTTCCTTC 59.742 42.308 0.00 0.00 0.00 3.46
4866 5938 2.584835 TTTTGATAGCTGGTGTGGCT 57.415 45.000 0.00 0.00 43.02 4.75
4989 6061 4.999950 GGTCTGAATCGATGCATCCTATTT 59.000 41.667 20.87 9.12 0.00 1.40
4990 6062 4.040829 TGGTCTGAATCGATGCATCCTATT 59.959 41.667 20.87 18.93 0.00 1.73
5178 6408 2.629051 CCGTTGATTGAGGGAGGTTAC 58.371 52.381 0.00 0.00 0.00 2.50
5299 9282 3.928727 TGGGAAGTACTACTGTCAACG 57.071 47.619 0.00 0.00 0.00 4.10
5322 9305 3.721087 TTCTGTTTCAGGGGAAGGATC 57.279 47.619 0.00 0.00 33.82 3.36
5886 9911 5.412526 TGTGTTTCTTACGGAAATCACAC 57.587 39.130 15.27 8.15 44.46 3.82
6049 10170 5.490139 AAACAAGATCTACGATTGCATGG 57.510 39.130 0.00 0.00 0.00 3.66
6542 10920 7.093771 GGTTTATCATTTTCCATCTTGACAGGT 60.094 37.037 0.00 0.00 0.00 4.00
6720 11131 1.902508 GGGGAGAGATGTGTGTTCTGA 59.097 52.381 0.00 0.00 0.00 3.27
6781 11192 0.752743 AGGCACTGCAGTTGCTTTCA 60.753 50.000 28.26 0.00 42.66 2.69
7513 11931 3.684788 GGTATTCAGCAATGACGTGTCTT 59.315 43.478 0.00 0.00 0.00 3.01
7604 12025 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
7605 12026 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
7609 12030 3.472943 ATCGCCCAGATGCAGAGGC 62.473 63.158 8.59 8.59 42.18 4.70
7610 12031 2.827423 ATCGCCCAGATGCAGAGG 59.173 61.111 0.00 0.00 38.36 3.69
7617 12038 1.004560 CCGTATGCATCGCCCAGAT 60.005 57.895 0.19 0.00 41.01 2.90
7618 12039 2.421314 CCGTATGCATCGCCCAGA 59.579 61.111 0.19 0.00 0.00 3.86
7619 12040 3.349006 GCCGTATGCATCGCCCAG 61.349 66.667 0.19 0.00 40.77 4.45
7620 12041 4.927782 GGCCGTATGCATCGCCCA 62.928 66.667 17.54 0.00 43.89 5.36
7621 12042 4.927782 TGGCCGTATGCATCGCCC 62.928 66.667 22.75 16.75 43.89 6.13
7622 12043 3.649986 GTGGCCGTATGCATCGCC 61.650 66.667 20.23 20.23 43.89 5.54
7623 12044 2.588877 AGTGGCCGTATGCATCGC 60.589 61.111 0.19 3.34 43.89 4.58
7624 12045 1.227234 TGAGTGGCCGTATGCATCG 60.227 57.895 0.19 7.03 43.89 3.84
7625 12046 0.179073 AGTGAGTGGCCGTATGCATC 60.179 55.000 0.19 0.00 43.89 3.91
7626 12047 0.253044 AAGTGAGTGGCCGTATGCAT 59.747 50.000 3.79 3.79 43.89 3.96
7627 12048 0.391130 GAAGTGAGTGGCCGTATGCA 60.391 55.000 0.00 0.00 43.89 3.96
7628 12049 0.108138 AGAAGTGAGTGGCCGTATGC 60.108 55.000 0.00 0.00 40.16 3.14
7629 12050 2.799917 GCTAGAAGTGAGTGGCCGTATG 60.800 54.545 0.00 0.00 0.00 2.39
7630 12051 1.409427 GCTAGAAGTGAGTGGCCGTAT 59.591 52.381 0.00 0.00 0.00 3.06
7631 12052 0.815734 GCTAGAAGTGAGTGGCCGTA 59.184 55.000 0.00 0.00 0.00 4.02
7632 12053 0.900647 AGCTAGAAGTGAGTGGCCGT 60.901 55.000 0.00 0.00 0.00 5.68
7633 12054 1.066303 CTAGCTAGAAGTGAGTGGCCG 59.934 57.143 16.15 0.00 0.00 6.13
7634 12055 2.104170 ACTAGCTAGAAGTGAGTGGCC 58.896 52.381 27.45 0.00 0.00 5.36
7635 12056 3.878160 AACTAGCTAGAAGTGAGTGGC 57.122 47.619 27.45 0.00 0.00 5.01
7636 12057 5.883673 AGACTAACTAGCTAGAAGTGAGTGG 59.116 44.000 27.45 5.21 38.55 4.00
7637 12058 6.995511 AGACTAACTAGCTAGAAGTGAGTG 57.004 41.667 27.45 9.88 38.55 3.51
7638 12059 7.169591 TCAAGACTAACTAGCTAGAAGTGAGT 58.830 38.462 27.45 15.81 40.71 3.41
7639 12060 7.335924 ACTCAAGACTAACTAGCTAGAAGTGAG 59.664 40.741 27.45 25.75 33.93 3.51
7640 12061 7.169591 ACTCAAGACTAACTAGCTAGAAGTGA 58.830 38.462 27.45 18.53 0.00 3.41
7641 12062 7.385778 ACTCAAGACTAACTAGCTAGAAGTG 57.614 40.000 27.45 16.86 0.00 3.16
7690 12348 7.817641 GCAAAGTTAAGCCTAATAAGAACAGT 58.182 34.615 0.00 0.00 0.00 3.55
7883 12613 7.631717 AAAGAAAAACAGTGCTCTACTTTCT 57.368 32.000 10.69 10.69 37.60 2.52
8011 12746 6.040391 TGCTCTTTTGCTAGTACCAAAATTGT 59.960 34.615 8.38 0.00 40.26 2.71
8036 12773 1.364901 CTCCCGTACCAACACACGT 59.635 57.895 0.00 0.00 36.44 4.49
8070 12810 4.721274 TGACTCATGATCATTGGGTTAGGA 59.279 41.667 5.16 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.