Multiple sequence alignment - TraesCS2B01G082300

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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 TraesCS2B01G082300 chr2B 100.000 5029 0 0 1 5029 45693712 45698740 0.000000e+00 9287.0
1 TraesCS2B01G082300 chr2B 88.884 2474 239 18 1802 4262 44903379 44905829 0.000000e+00 3013.0
2 TraesCS2B01G082300 chr2B 80.530 755 109 17 656 1389 44902448 44903185 3.420000e-151 545.0
3 TraesCS2B01G082300 chr2B 88.063 444 24 15 149 581 44901119 44901544 2.700000e-137 499.0
4 TraesCS2B01G082300 chr2B 88.690 336 31 3 3934 4262 44897335 44897670 2.180000e-108 403.0
5 TraesCS2B01G082300 chr2B 100.000 207 0 0 4056 4262 45621571 45621777 2.840000e-102 383.0
6 TraesCS2B01G082300 chr2B 96.903 226 7 0 3657 3882 44897115 44897340 3.670000e-101 379.0
7 TraesCS2B01G082300 chr2B 100.000 29 0 0 580 608 44901555 44901583 3.000000e-03 54.7
8 TraesCS2B01G082300 chr2A 94.112 2904 157 8 1369 4262 30276654 30273755 0.000000e+00 4403.0
9 TraesCS2B01G082300 chr2A 87.933 2627 266 23 1443 4061 30307805 30305222 0.000000e+00 3048.0
10 TraesCS2B01G082300 chr2A 93.400 1394 86 4 1612 3004 30198141 30196753 0.000000e+00 2060.0
11 TraesCS2B01G082300 chr2A 91.600 750 42 7 655 1389 30199497 30198754 0.000000e+00 1016.0
12 TraesCS2B01G082300 chr2A 89.007 755 58 6 655 1389 30277455 30276706 0.000000e+00 911.0
13 TraesCS2B01G082300 chr2A 87.859 453 52 3 938 1389 30308664 30308214 3.450000e-146 529.0
14 TraesCS2B01G082300 chr2A 84.828 435 38 15 149 581 30278353 30277945 3.620000e-111 412.0
15 TraesCS2B01G082300 chr2A 95.600 250 9 2 1369 1617 30198702 30198454 2.820000e-107 399.0
16 TraesCS2B01G082300 chr2A 88.830 188 19 2 1382 1568 30308008 30307822 3.920000e-56 230.0
17 TraesCS2B01G082300 chr2D 93.843 2696 159 7 1369 4061 28084452 28081761 0.000000e+00 4052.0
18 TraesCS2B01G082300 chr2D 88.107 2800 298 16 1443 4231 28071813 28069038 0.000000e+00 3293.0
19 TraesCS2B01G082300 chr2D 88.367 2682 282 23 1598 4262 28423625 28420957 0.000000e+00 3197.0
20 TraesCS2B01G082300 chr2D 89.369 1411 137 9 2634 4042 28079402 28078003 0.000000e+00 1762.0
21 TraesCS2B01G082300 chr2D 90.280 751 51 12 655 1389 28085248 28084504 0.000000e+00 963.0
22 TraesCS2B01G082300 chr2D 83.046 755 92 20 655 1389 28072888 28072150 0.000000e+00 652.0
23 TraesCS2B01G082300 chr2D 90.663 407 38 0 983 1389 28424399 28423993 4.430000e-150 542.0
24 TraesCS2B01G082300 chr2D 83.624 458 40 12 149 581 28073771 28073324 1.010000e-106 398.0
25 TraesCS2B01G082300 chr2D 82.237 456 36 13 149 581 28086167 28085734 8.010000e-93 351.0
26 TraesCS2B01G082300 chr2D 75.923 623 143 7 2998 3616 27933261 27932642 3.780000e-81 313.0
27 TraesCS2B01G082300 chr2D 75.283 619 144 9 2998 3611 27979948 27979334 2.290000e-73 287.0
28 TraesCS2B01G082300 chr2D 86.590 261 20 8 695 942 28090472 28090214 1.780000e-69 274.0
29 TraesCS2B01G082300 chr2D 91.358 162 12 2 1382 1542 28423787 28423627 2.360000e-53 220.0
30 TraesCS2B01G082300 chr2D 96.226 106 4 0 46 151 28091168 28091063 1.860000e-39 174.0
31 TraesCS2B01G082300 chr2D 89.888 89 2 5 4131 4215 28077943 28077858 1.910000e-19 108.0
32 TraesCS2B01G082300 chr2D 100.000 29 0 0 580 608 28073313 28073285 3.000000e-03 54.7
33 TraesCS2B01G082300 chr3B 96.329 681 15 2 4359 5029 428092909 428092229 0.000000e+00 1110.0
34 TraesCS2B01G082300 chr3D 94.404 679 32 3 4353 5029 434955754 434955080 0.000000e+00 1038.0
35 TraesCS2B01G082300 chr3A 93.548 682 38 3 4354 5029 47265798 47266479 0.000000e+00 1011.0
36 TraesCS2B01G082300 chr3A 92.560 672 48 2 4356 5027 739915744 739915075 0.000000e+00 963.0
37 TraesCS2B01G082300 chr3A 92.208 77 2 3 4131 4206 329751792 329751865 6.890000e-19 106.0
38 TraesCS2B01G082300 chr3A 92.982 57 3 1 1 56 678317403 678317347 1.160000e-11 82.4
39 TraesCS2B01G082300 chr7D 93.324 689 35 8 4349 5027 555056548 555055861 0.000000e+00 1007.0
40 TraesCS2B01G082300 chr7D 94.231 52 3 0 1 52 598598552 598598603 4.170000e-11 80.5
41 TraesCS2B01G082300 chr6B 93.109 682 39 5 4355 5029 611658032 611658712 0.000000e+00 992.0
42 TraesCS2B01G082300 chr5B 92.826 683 42 3 4354 5029 460760891 460761573 0.000000e+00 983.0
43 TraesCS2B01G082300 chr5B 91.942 695 43 4 4348 5029 232634788 232634094 0.000000e+00 961.0
44 TraesCS2B01G082300 chr5B 86.111 72 5 5 1 69 263801614 263801683 6.980000e-09 73.1
45 TraesCS2B01G082300 chr5A 92.690 684 42 3 4354 5029 59642448 59641765 0.000000e+00 979.0
46 TraesCS2B01G082300 chr5A 87.879 66 7 1 1 66 675668250 675668314 5.400000e-10 76.8
47 TraesCS2B01G082300 chr4B 92.375 682 44 3 4356 5029 646236237 646236918 0.000000e+00 965.0
48 TraesCS2B01G082300 chr4B 88.235 68 3 3 1 65 529207604 529207539 5.400000e-10 76.8
49 TraesCS2B01G082300 chr1B 92.208 77 2 3 4131 4206 197864584 197864511 6.890000e-19 106.0
50 TraesCS2B01G082300 chr1B 87.692 65 5 3 1 64 683748003 683747941 6.980000e-09 73.1
51 TraesCS2B01G082300 chr7A 89.706 68 5 1 1 68 619099746 619099681 8.970000e-13 86.1
52 TraesCS2B01G082300 chr7A 96.078 51 1 1 1 51 511953952 511953903 1.160000e-11 82.4
53 TraesCS2B01G082300 chr4A 94.340 53 1 2 1 52 680328411 680328360 4.170000e-11 80.5


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 TraesCS2B01G082300 chr2B 45693712 45698740 5028 False 9287.000000 9287 100.000000 1 5029 1 chr2B.!!$F2 5028
1 TraesCS2B01G082300 chr2B 44897115 44905829 8714 False 815.616667 3013 90.511667 149 4262 6 chr2B.!!$F3 4113
2 TraesCS2B01G082300 chr2A 30273755 30278353 4598 True 1908.666667 4403 89.315667 149 4262 3 chr2A.!!$R2 4113
3 TraesCS2B01G082300 chr2A 30305222 30308664 3442 True 1269.000000 3048 88.207333 938 4061 3 chr2A.!!$R3 3123
4 TraesCS2B01G082300 chr2A 30196753 30199497 2744 True 1158.333333 2060 93.533333 655 3004 3 chr2A.!!$R1 2349
5 TraesCS2B01G082300 chr2D 28077858 28086167 8309 True 1447.200000 4052 89.123400 149 4215 5 chr2D.!!$R4 4066
6 TraesCS2B01G082300 chr2D 28420957 28424399 3442 True 1319.666667 3197 90.129333 983 4262 3 chr2D.!!$R6 3279
7 TraesCS2B01G082300 chr2D 28069038 28073771 4733 True 1099.425000 3293 88.694250 149 4231 4 chr2D.!!$R3 4082
8 TraesCS2B01G082300 chr2D 27932642 27933261 619 True 313.000000 313 75.923000 2998 3616 1 chr2D.!!$R1 618
9 TraesCS2B01G082300 chr2D 27979334 27979948 614 True 287.000000 287 75.283000 2998 3611 1 chr2D.!!$R2 613
10 TraesCS2B01G082300 chr2D 28090214 28091168 954 True 224.000000 274 91.408000 46 942 2 chr2D.!!$R5 896
11 TraesCS2B01G082300 chr3B 428092229 428092909 680 True 1110.000000 1110 96.329000 4359 5029 1 chr3B.!!$R1 670
12 TraesCS2B01G082300 chr3D 434955080 434955754 674 True 1038.000000 1038 94.404000 4353 5029 1 chr3D.!!$R1 676
13 TraesCS2B01G082300 chr3A 47265798 47266479 681 False 1011.000000 1011 93.548000 4354 5029 1 chr3A.!!$F1 675
14 TraesCS2B01G082300 chr3A 739915075 739915744 669 True 963.000000 963 92.560000 4356 5027 1 chr3A.!!$R2 671
15 TraesCS2B01G082300 chr7D 555055861 555056548 687 True 1007.000000 1007 93.324000 4349 5027 1 chr7D.!!$R1 678
16 TraesCS2B01G082300 chr6B 611658032 611658712 680 False 992.000000 992 93.109000 4355 5029 1 chr6B.!!$F1 674
17 TraesCS2B01G082300 chr5B 460760891 460761573 682 False 983.000000 983 92.826000 4354 5029 1 chr5B.!!$F2 675
18 TraesCS2B01G082300 chr5B 232634094 232634788 694 True 961.000000 961 91.942000 4348 5029 1 chr5B.!!$R1 681
19 TraesCS2B01G082300 chr5A 59641765 59642448 683 True 979.000000 979 92.690000 4354 5029 1 chr5A.!!$R1 675
20 TraesCS2B01G082300 chr4B 646236237 646236918 681 False 965.000000 965 92.375000 4356 5029 1 chr4B.!!$F1 673

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
618 4523 0.035739 ATTCACCGTAAACGTGGCCT 59.964 50.0 3.32 0.0 37.74 5.19 F
682 5027 0.252197 AAACGTGTATCAGGCCCTCC 59.748 55.0 0.00 0.0 0.00 4.30 F
2108 7788 0.802494 GTCGGCACAATACCAGTTGG 59.198 55.0 0.00 0.0 42.17 3.77 F
3183 8866 1.002250 CGCGTGACAGCTTCGTTACT 61.002 55.0 0.00 0.0 34.40 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 8074 1.261619 GTTGTGCCACTGAAGAGTTCG 59.738 52.381 0.00 0.00 0.00 3.95 R
2651 8331 3.893753 TTCCAACAAGGGAATTCTGGA 57.106 42.857 5.23 6.58 41.92 3.86 R
3437 9121 1.115467 AATCGCAGTGGACTAGAGGG 58.885 55.000 0.00 0.00 0.00 4.30 R
4266 13698 0.094046 GACAACGTGAATTACCGCGG 59.906 55.000 26.86 26.86 43.55 6.46 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 9.231297 CACTAATCTAAGACAAGAATTTTGGGA 57.769 33.333 5.68 0.00 0.00 4.37
33 34 9.232473 ACTAATCTAAGACAAGAATTTTGGGAC 57.768 33.333 5.68 0.00 0.00 4.46
34 35 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
35 36 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
36 37 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
37 38 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
38 39 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
39 40 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
40 41 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
41 42 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
42 43 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
43 44 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
44 45 1.732117 TTTTGGGACGGAGGGAGTAA 58.268 50.000 0.00 0.00 0.00 2.24
88 89 9.480053 CATAAAGGTGTTTTTGAATGAACTGAT 57.520 29.630 0.00 0.00 28.84 2.90
165 4026 1.153549 CTGAACTAGCGGCAGGGAC 60.154 63.158 1.45 0.00 0.00 4.46
207 4068 2.048222 CGTCTCTGGCTTTCCGCA 60.048 61.111 0.00 0.00 41.67 5.69
232 4098 2.815589 GCTTTCTGCCCCTCTTTCTTCA 60.816 50.000 0.00 0.00 35.15 3.02
243 4109 2.558795 CTCTTTCTTCAGTCGGTCCAGA 59.441 50.000 0.00 0.00 0.00 3.86
322 4208 1.078426 CCGTCTCCTTCGCCCATTT 60.078 57.895 0.00 0.00 0.00 2.32
412 4298 2.627699 TCAACAAAGGGCCTGCTTAAAG 59.372 45.455 6.92 0.00 0.00 1.85
530 4423 2.046023 CACGGCTGCCCTGAATCA 60.046 61.111 14.12 0.00 0.00 2.57
608 4513 3.810941 GTCTCAACCAAACATTCACCGTA 59.189 43.478 0.00 0.00 0.00 4.02
609 4514 4.273969 GTCTCAACCAAACATTCACCGTAA 59.726 41.667 0.00 0.00 0.00 3.18
610 4515 4.882427 TCTCAACCAAACATTCACCGTAAA 59.118 37.500 0.00 0.00 0.00 2.01
611 4516 4.922719 TCAACCAAACATTCACCGTAAAC 58.077 39.130 0.00 0.00 0.00 2.01
612 4517 3.612472 ACCAAACATTCACCGTAAACG 57.388 42.857 0.00 0.00 39.44 3.60
617 4522 0.167251 CATTCACCGTAAACGTGGCC 59.833 55.000 0.00 0.00 37.74 5.36
618 4523 0.035739 ATTCACCGTAAACGTGGCCT 59.964 50.000 3.32 0.00 37.74 5.19
619 4524 0.600782 TTCACCGTAAACGTGGCCTC 60.601 55.000 3.32 0.00 37.74 4.70
620 4525 2.030958 CACCGTAAACGTGGCCTCC 61.031 63.158 3.32 0.00 37.74 4.30
621 4526 2.212110 ACCGTAAACGTGGCCTCCT 61.212 57.895 3.32 0.00 37.74 3.69
629 4955 1.192146 ACGTGGCCTCCTCTAAAGCA 61.192 55.000 3.32 0.00 0.00 3.91
644 4970 7.575414 CTCTAAAGCATTCAGTAGAGGAGTA 57.425 40.000 0.00 0.00 37.16 2.59
645 4971 7.956328 TCTAAAGCATTCAGTAGAGGAGTAA 57.044 36.000 0.00 0.00 0.00 2.24
646 4972 7.773149 TCTAAAGCATTCAGTAGAGGAGTAAC 58.227 38.462 0.00 0.00 0.00 2.50
647 4973 5.346181 AAGCATTCAGTAGAGGAGTAACC 57.654 43.478 0.00 0.00 39.35 2.85
682 5027 0.252197 AAACGTGTATCAGGCCCTCC 59.748 55.000 0.00 0.00 0.00 4.30
734 5081 2.847327 AGCGCATCATAACCTAGCAT 57.153 45.000 11.47 0.00 0.00 3.79
750 5097 3.252974 AGCATAGTACCAAGTGCTGAC 57.747 47.619 10.05 0.00 45.44 3.51
769 5130 1.801913 GTACCAGTCTCTGCACGCG 60.802 63.158 3.53 3.53 0.00 6.01
821 5596 4.331168 CCGTCTCATTTCTCATCCACTTTC 59.669 45.833 0.00 0.00 0.00 2.62
822 5597 5.174395 CGTCTCATTTCTCATCCACTTTCT 58.826 41.667 0.00 0.00 0.00 2.52
823 5598 5.063186 CGTCTCATTTCTCATCCACTTTCTG 59.937 44.000 0.00 0.00 0.00 3.02
861 5641 2.733593 GGTCTGTGACGCGTGACC 60.734 66.667 25.72 25.30 41.52 4.02
877 5659 2.749621 GTGACCAAGATTACAGGCAAGG 59.250 50.000 0.00 0.00 0.00 3.61
970 5752 8.090788 ACTTAGGGAGACACATATAACACAAT 57.909 34.615 0.00 0.00 0.00 2.71
981 5764 7.148255 ACACATATAACACAATGAATTCGCACT 60.148 33.333 0.04 0.00 0.00 4.40
1090 5879 2.631160 ATTGTTCTCGTCCAACACCA 57.369 45.000 0.00 0.00 33.42 4.17
1266 6058 1.270094 CCAACTCGTGTGGTCTTGCTA 60.270 52.381 0.00 0.00 0.00 3.49
1625 7299 7.987458 CCTTATTCAGAACCTTAGTATGCTCAA 59.013 37.037 0.00 0.00 0.00 3.02
1654 7328 1.839747 AACTACCTGTCGGGGCACA 60.840 57.895 1.89 0.00 40.03 4.57
2108 7788 0.802494 GTCGGCACAATACCAGTTGG 59.198 55.000 0.00 0.00 42.17 3.77
2176 7856 1.100510 GCTTTCCGGTGTTATTCCCC 58.899 55.000 0.00 0.00 0.00 4.81
2394 8074 2.755103 CCTTGAAGGACCAATACCAAGC 59.245 50.000 4.95 0.00 37.67 4.01
2500 8180 1.964223 TGCTTCAACTTCTCCGACTCT 59.036 47.619 0.00 0.00 0.00 3.24
2515 8195 6.040616 TCTCCGACTCTATATTTCCTTCAACC 59.959 42.308 0.00 0.00 0.00 3.77
2780 8460 5.587844 GTGGCATCTTTCAGAATCATAGTGT 59.412 40.000 0.00 0.00 0.00 3.55
2787 8467 4.307443 TCAGAATCATAGTGTGGTAGCG 57.693 45.455 0.00 0.00 0.00 4.26
2873 8556 2.932663 CAACGTCAGCTGTTGGGAT 58.067 52.632 14.67 0.00 42.27 3.85
2913 8596 9.907229 CTCTTATTGGTAAAAGTAATTCCTCCT 57.093 33.333 0.00 0.00 0.00 3.69
2963 8646 2.545946 GCTTTGTGGTCACTCTTCTGAC 59.454 50.000 2.66 0.00 40.02 3.51
3093 8776 1.005394 AAGTCGCACCGGTTCGATT 60.005 52.632 30.91 24.56 37.06 3.34
3129 8812 2.285977 GAGTTTGACACGGACTTGGTT 58.714 47.619 0.00 0.00 0.00 3.67
3183 8866 1.002250 CGCGTGACAGCTTCGTTACT 61.002 55.000 0.00 0.00 34.40 2.24
3365 9049 1.077993 AGCCCCAAGAGAGTACTGAGT 59.922 52.381 0.00 0.00 0.00 3.41
3408 9092 1.852067 GATGGACGTTGCGTTGGCTT 61.852 55.000 0.00 0.00 41.37 4.35
3437 9121 3.030652 CACAACCAGTTGACGCCC 58.969 61.111 17.06 0.00 42.93 6.13
3496 9180 1.250328 TTGGACTACGACATGACCGT 58.750 50.000 18.29 18.29 43.26 4.83
3617 9301 4.157656 CCTGGTGAGTTCAACTTTGTTTCA 59.842 41.667 0.00 0.00 33.92 2.69
3718 9402 2.700371 TCTCGCCAGGATGTGATGTATT 59.300 45.455 0.00 0.00 0.00 1.89
4033 9717 6.621596 GCGTTCTTTGAGTTCTGCTGATTAAT 60.622 38.462 0.00 0.00 0.00 1.40
4054 9738 9.624373 ATTAATCTGCAGATCTACATGTTCTTT 57.376 29.630 28.83 12.05 32.75 2.52
4262 13694 5.008415 GCTGAGTTCATGTGATCCCAATTAG 59.992 44.000 0.00 0.00 0.00 1.73
4263 13695 5.439721 TGAGTTCATGTGATCCCAATTAGG 58.560 41.667 0.00 0.00 37.03 2.69
4264 13696 5.191522 TGAGTTCATGTGATCCCAATTAGGA 59.808 40.000 0.00 0.00 41.22 2.94
4265 13697 5.688807 AGTTCATGTGATCCCAATTAGGAG 58.311 41.667 0.00 0.00 39.95 3.69
4266 13698 4.090761 TCATGTGATCCCAATTAGGAGC 57.909 45.455 0.77 0.77 42.89 4.70
4267 13699 3.152341 CATGTGATCCCAATTAGGAGCC 58.848 50.000 5.70 0.00 41.84 4.70
4268 13700 1.140852 TGTGATCCCAATTAGGAGCCG 59.859 52.381 5.70 0.00 41.84 5.52
4269 13701 0.108585 TGATCCCAATTAGGAGCCGC 59.891 55.000 5.70 0.00 41.84 6.53
4270 13702 0.951040 GATCCCAATTAGGAGCCGCG 60.951 60.000 0.00 0.00 39.95 6.46
4271 13703 2.397413 ATCCCAATTAGGAGCCGCGG 62.397 60.000 24.05 24.05 39.95 6.46
4272 13704 2.189521 CCAATTAGGAGCCGCGGT 59.810 61.111 28.70 13.92 41.22 5.68
4273 13705 1.444250 CCAATTAGGAGCCGCGGTA 59.556 57.895 28.70 8.24 41.22 4.02
4274 13706 0.179067 CCAATTAGGAGCCGCGGTAA 60.179 55.000 28.70 17.50 41.22 2.85
4275 13707 1.542547 CCAATTAGGAGCCGCGGTAAT 60.543 52.381 28.70 19.02 41.22 1.89
4276 13708 2.218603 CAATTAGGAGCCGCGGTAATT 58.781 47.619 28.70 23.42 0.00 1.40
4277 13709 2.165319 ATTAGGAGCCGCGGTAATTC 57.835 50.000 28.70 18.30 0.00 2.17
4278 13710 0.825410 TTAGGAGCCGCGGTAATTCA 59.175 50.000 28.70 4.38 0.00 2.57
4279 13711 0.103572 TAGGAGCCGCGGTAATTCAC 59.896 55.000 28.70 7.91 0.00 3.18
4280 13712 2.522638 GGAGCCGCGGTAATTCACG 61.523 63.158 28.70 0.00 0.00 4.35
4281 13713 1.808390 GAGCCGCGGTAATTCACGT 60.808 57.895 28.70 0.00 0.00 4.49
4282 13714 1.356527 GAGCCGCGGTAATTCACGTT 61.357 55.000 28.70 0.00 0.00 3.99
4283 13715 1.225908 GCCGCGGTAATTCACGTTG 60.226 57.895 28.70 0.00 0.00 4.10
4284 13716 1.903783 GCCGCGGTAATTCACGTTGT 61.904 55.000 28.70 0.00 0.00 3.32
4285 13717 0.094046 CCGCGGTAATTCACGTTGTC 59.906 55.000 19.50 0.00 0.00 3.18
4286 13718 1.065358 CGCGGTAATTCACGTTGTCT 58.935 50.000 0.00 0.00 0.00 3.41
4287 13719 1.201769 CGCGGTAATTCACGTTGTCTG 60.202 52.381 0.00 0.00 0.00 3.51
4288 13720 2.063266 GCGGTAATTCACGTTGTCTGA 58.937 47.619 0.00 0.00 0.00 3.27
4289 13721 2.092211 GCGGTAATTCACGTTGTCTGAG 59.908 50.000 0.00 0.00 0.00 3.35
4290 13722 2.092211 CGGTAATTCACGTTGTCTGAGC 59.908 50.000 0.00 0.00 0.00 4.26
4291 13723 3.326747 GGTAATTCACGTTGTCTGAGCT 58.673 45.455 0.00 0.00 0.00 4.09
4292 13724 3.368236 GGTAATTCACGTTGTCTGAGCTC 59.632 47.826 6.82 6.82 0.00 4.09
4293 13725 2.820059 ATTCACGTTGTCTGAGCTCA 57.180 45.000 17.19 17.19 0.00 4.26
4294 13726 2.820059 TTCACGTTGTCTGAGCTCAT 57.180 45.000 18.63 0.00 0.00 2.90
4295 13727 2.070262 TCACGTTGTCTGAGCTCATG 57.930 50.000 18.63 10.90 0.00 3.07
4296 13728 0.441533 CACGTTGTCTGAGCTCATGC 59.558 55.000 18.63 13.38 40.05 4.06
4307 13739 2.526545 GCTCATGCTCATCTACGCC 58.473 57.895 0.00 0.00 36.03 5.68
4308 13740 0.948141 GCTCATGCTCATCTACGCCC 60.948 60.000 0.00 0.00 36.03 6.13
4309 13741 0.665670 CTCATGCTCATCTACGCCCG 60.666 60.000 0.00 0.00 0.00 6.13
4310 13742 1.068083 CATGCTCATCTACGCCCGT 59.932 57.895 0.00 0.00 0.00 5.28
4311 13743 0.530650 CATGCTCATCTACGCCCGTT 60.531 55.000 0.00 0.00 0.00 4.44
4312 13744 0.530650 ATGCTCATCTACGCCCGTTG 60.531 55.000 0.00 0.00 0.00 4.10
4313 13745 1.141019 GCTCATCTACGCCCGTTGA 59.859 57.895 7.35 7.35 34.75 3.18
4314 13746 0.459585 GCTCATCTACGCCCGTTGAA 60.460 55.000 8.81 0.00 34.05 2.69
4315 13747 2.004583 CTCATCTACGCCCGTTGAAA 57.995 50.000 8.81 1.13 34.05 2.69
4316 13748 1.659098 CTCATCTACGCCCGTTGAAAC 59.341 52.381 8.81 0.00 34.05 2.78
4317 13749 1.274167 TCATCTACGCCCGTTGAAACT 59.726 47.619 8.81 0.00 34.05 2.66
4318 13750 2.492881 TCATCTACGCCCGTTGAAACTA 59.507 45.455 8.81 0.00 34.05 2.24
4319 13751 3.056678 TCATCTACGCCCGTTGAAACTAA 60.057 43.478 8.81 0.00 34.05 2.24
4320 13752 3.383620 TCTACGCCCGTTGAAACTAAA 57.616 42.857 0.00 0.00 0.00 1.85
4321 13753 3.929094 TCTACGCCCGTTGAAACTAAAT 58.071 40.909 0.00 0.00 0.00 1.40
4322 13754 4.317488 TCTACGCCCGTTGAAACTAAATT 58.683 39.130 0.00 0.00 0.00 1.82
4323 13755 3.994204 ACGCCCGTTGAAACTAAATTT 57.006 38.095 0.00 0.00 0.00 1.82
4324 13756 5.931146 TCTACGCCCGTTGAAACTAAATTTA 59.069 36.000 0.00 0.00 0.00 1.40
4325 13757 5.435820 ACGCCCGTTGAAACTAAATTTAA 57.564 34.783 0.00 0.00 0.00 1.52
4326 13758 5.829829 ACGCCCGTTGAAACTAAATTTAAA 58.170 33.333 0.00 0.00 0.00 1.52
4327 13759 6.271566 ACGCCCGTTGAAACTAAATTTAAAA 58.728 32.000 0.00 0.00 0.00 1.52
4328 13760 6.755607 ACGCCCGTTGAAACTAAATTTAAAAA 59.244 30.769 0.00 0.00 0.00 1.94
4329 13761 7.438757 ACGCCCGTTGAAACTAAATTTAAAAAT 59.561 29.630 0.00 0.00 0.00 1.82
4330 13762 8.913656 CGCCCGTTGAAACTAAATTTAAAAATA 58.086 29.630 0.00 0.00 0.00 1.40
4400 13834 6.042143 ACTTTGCGTTTCATTTCATTGAACT 58.958 32.000 0.00 0.00 35.42 3.01
4412 13846 4.535526 TCATTGAACTGGAAGACATCGA 57.464 40.909 0.00 0.00 37.43 3.59
4450 13888 0.107410 GGAGGGACACACACACACAA 60.107 55.000 0.00 0.00 0.00 3.33
4729 14187 1.118838 GATCTGCTCCCTGTGTAGCT 58.881 55.000 0.00 0.00 39.53 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.014297 CCCAAAATTCTTGTCTTAGATTAGTGT 57.986 33.333 0.00 0.00 0.00 3.55
6 7 9.231297 TCCCAAAATTCTTGTCTTAGATTAGTG 57.769 33.333 0.00 0.00 0.00 2.74
10 11 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
13 14 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
15 16 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
17 18 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
19 20 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
21 22 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
22 23 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
24 25 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
25 26 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
26 27 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
28 29 1.557832 CAAATTACTCCCTCCGTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
29 30 1.558294 ACAAATTACTCCCTCCGTCCC 59.442 52.381 0.00 0.00 0.00 4.46
32 33 5.646360 CACATTTACAAATTACTCCCTCCGT 59.354 40.000 0.00 0.00 0.00 4.69
33 34 5.646360 ACACATTTACAAATTACTCCCTCCG 59.354 40.000 0.00 0.00 0.00 4.63
34 35 6.183360 CGACACATTTACAAATTACTCCCTCC 60.183 42.308 0.00 0.00 0.00 4.30
35 36 6.370718 ACGACACATTTACAAATTACTCCCTC 59.629 38.462 0.00 0.00 0.00 4.30
36 37 6.235664 ACGACACATTTACAAATTACTCCCT 58.764 36.000 0.00 0.00 0.00 4.20
37 38 6.490566 ACGACACATTTACAAATTACTCCC 57.509 37.500 0.00 0.00 0.00 4.30
38 39 8.020861 TGTACGACACATTTACAAATTACTCC 57.979 34.615 0.00 0.00 30.04 3.85
43 44 9.834628 CCTTTATGTACGACACATTTACAAATT 57.165 29.630 11.57 0.00 46.01 1.82
44 45 9.005777 ACCTTTATGTACGACACATTTACAAAT 57.994 29.630 11.57 0.00 46.01 2.32
96 97 9.396022 CACCTGTGACCAGATTTATTAGTAAAT 57.604 33.333 3.09 3.09 41.90 1.40
165 4026 1.075600 GAGGGGAGGGACAGAGAGG 60.076 68.421 0.00 0.00 0.00 3.69
213 4074 2.443255 ACTGAAGAAAGAGGGGCAGAAA 59.557 45.455 0.00 0.00 0.00 2.52
214 4075 2.039084 GACTGAAGAAAGAGGGGCAGAA 59.961 50.000 0.00 0.00 0.00 3.02
215 4076 1.625818 GACTGAAGAAAGAGGGGCAGA 59.374 52.381 0.00 0.00 0.00 4.26
216 4077 1.674221 CGACTGAAGAAAGAGGGGCAG 60.674 57.143 0.00 0.00 0.00 4.85
217 4078 0.321671 CGACTGAAGAAAGAGGGGCA 59.678 55.000 0.00 0.00 0.00 5.36
218 4079 0.391793 CCGACTGAAGAAAGAGGGGC 60.392 60.000 0.00 0.00 0.00 5.80
219 4080 0.977395 ACCGACTGAAGAAAGAGGGG 59.023 55.000 0.00 0.00 0.00 4.79
220 4081 1.066787 GGACCGACTGAAGAAAGAGGG 60.067 57.143 0.00 0.00 0.00 4.30
223 4084 2.594131 TCTGGACCGACTGAAGAAAGA 58.406 47.619 0.00 0.00 0.00 2.52
225 4086 3.830178 TGTATCTGGACCGACTGAAGAAA 59.170 43.478 0.00 0.00 0.00 2.52
261 4147 1.881973 GTTTGCTTGAGATGTGCTGGA 59.118 47.619 0.00 0.00 0.00 3.86
265 4151 2.029649 ACATGGTTTGCTTGAGATGTGC 60.030 45.455 0.00 0.00 0.00 4.57
322 4208 1.548357 GCACCAGCTTCCTCCTCAGA 61.548 60.000 0.00 0.00 37.91 3.27
412 4298 4.273724 AGGAAAAGAGAAAAGTGACGAAGC 59.726 41.667 0.00 0.00 0.00 3.86
464 4352 3.699894 CAGGCGTGCACCTCCTCT 61.700 66.667 19.23 4.66 38.26 3.69
501 4389 2.742372 GCCGTGTTCAGGCGTCAT 60.742 61.111 0.00 0.00 45.58 3.06
530 4423 3.263681 GCCAGGGAGTAAAAGTAGACCTT 59.736 47.826 0.00 0.00 33.79 3.50
608 4513 1.610886 GCTTTAGAGGAGGCCACGTTT 60.611 52.381 5.01 0.00 0.00 3.60
609 4514 0.036294 GCTTTAGAGGAGGCCACGTT 60.036 55.000 5.01 0.00 0.00 3.99
610 4515 1.192146 TGCTTTAGAGGAGGCCACGT 61.192 55.000 5.01 0.00 0.00 4.49
611 4516 0.179000 ATGCTTTAGAGGAGGCCACG 59.821 55.000 5.01 0.00 0.00 4.94
612 4517 2.293170 GAATGCTTTAGAGGAGGCCAC 58.707 52.381 5.01 0.00 0.00 5.01
620 4525 6.463995 ACTCCTCTACTGAATGCTTTAGAG 57.536 41.667 3.85 3.85 38.10 2.43
621 4526 7.147880 GGTTACTCCTCTACTGAATGCTTTAGA 60.148 40.741 0.00 0.00 0.00 2.10
629 4955 4.949121 ACCAGGTTACTCCTCTACTGAAT 58.051 43.478 0.00 0.00 46.24 2.57
640 4966 5.793030 ACTGCAGATATACCAGGTTACTC 57.207 43.478 23.35 0.00 0.00 2.59
641 4967 7.498443 GTTTACTGCAGATATACCAGGTTACT 58.502 38.462 23.35 0.00 0.00 2.24
644 4970 5.105064 ACGTTTACTGCAGATATACCAGGTT 60.105 40.000 23.35 0.00 0.00 3.50
645 4971 4.404715 ACGTTTACTGCAGATATACCAGGT 59.595 41.667 23.35 0.00 0.00 4.00
646 4972 4.745125 CACGTTTACTGCAGATATACCAGG 59.255 45.833 23.35 5.03 0.00 4.45
647 4973 5.348986 ACACGTTTACTGCAGATATACCAG 58.651 41.667 23.35 6.26 0.00 4.00
648 4974 5.333299 ACACGTTTACTGCAGATATACCA 57.667 39.130 23.35 0.00 0.00 3.25
649 4975 7.143340 TGATACACGTTTACTGCAGATATACC 58.857 38.462 23.35 1.81 0.00 2.73
651 4977 7.368059 CCTGATACACGTTTACTGCAGATATA 58.632 38.462 23.35 0.00 0.00 0.86
652 4978 6.216569 CCTGATACACGTTTACTGCAGATAT 58.783 40.000 23.35 0.00 0.00 1.63
682 5027 2.287915 CAGACCAGTTTTCGGTTCAGTG 59.712 50.000 0.00 0.00 36.69 3.66
734 5081 2.489329 GGTACGTCAGCACTTGGTACTA 59.511 50.000 0.00 0.00 35.13 1.82
750 5097 1.801913 GCGTGCAGAGACTGGTACG 60.802 63.158 9.15 9.15 44.26 3.67
769 5130 4.666618 CGACGAAAAAGCAGAGAGAAAAAC 59.333 41.667 0.00 0.00 0.00 2.43
821 5596 0.683973 ACTCCTCAGTGGCAGAACAG 59.316 55.000 0.00 0.00 35.26 3.16
822 5597 0.394192 CACTCCTCAGTGGCAGAACA 59.606 55.000 0.00 0.00 45.75 3.18
823 5598 3.223661 CACTCCTCAGTGGCAGAAC 57.776 57.895 0.00 0.00 45.75 3.01
861 5641 2.557924 TGTTGCCTTGCCTGTAATCTTG 59.442 45.455 0.00 0.00 0.00 3.02
877 5659 3.380320 ACCTTTACTTGACTTGGTGTTGC 59.620 43.478 0.00 0.00 0.00 4.17
981 5764 5.059161 GCCATGTCTAATTCAGTGCATCTA 58.941 41.667 0.00 0.00 0.00 1.98
992 5781 2.493278 GTTGCAGGTGCCATGTCTAATT 59.507 45.455 0.00 0.00 41.18 1.40
1090 5879 1.402968 GTTGCTGATGGATTGTGCGAT 59.597 47.619 0.00 0.00 0.00 4.58
1266 6058 2.615912 GAGCTGTGCAGAGTTCAAGTTT 59.384 45.455 20.64 0.00 0.00 2.66
1625 7299 6.168389 CCCGACAGGTAGTTGTTACTTAAAT 58.832 40.000 0.00 0.00 33.44 1.40
1654 7328 4.974645 TGTTACAGAGTTTGGTGGAGAT 57.025 40.909 0.00 0.00 0.00 2.75
2108 7788 5.242171 TGGAGGTTTCGAAGGTTAAAAATCC 59.758 40.000 0.00 0.00 0.00 3.01
2176 7856 3.652869 TGGCCTAGATTCCCAATAAGAGG 59.347 47.826 3.32 0.00 0.00 3.69
2292 7972 3.882888 TGTTCCCACTCAACTCATTGTTC 59.117 43.478 0.00 0.00 36.63 3.18
2394 8074 1.261619 GTTGTGCCACTGAAGAGTTCG 59.738 52.381 0.00 0.00 0.00 3.95
2500 8180 8.292444 CCAGACAATTGGTTGAAGGAAATATA 57.708 34.615 10.83 0.00 38.71 0.86
2515 8195 4.228912 GTGGAACTTGACCAGACAATTG 57.771 45.455 3.24 3.24 38.14 2.32
2651 8331 3.893753 TTCCAACAAGGGAATTCTGGA 57.106 42.857 5.23 6.58 41.92 3.86
2780 8460 0.034574 ATTGCCATCCAACGCTACCA 60.035 50.000 0.00 0.00 35.99 3.25
2787 8467 2.097825 AGCTCTTCATTGCCATCCAAC 58.902 47.619 0.00 0.00 35.99 3.77
2811 8491 2.489275 GGTGGTGGTTGCACCTGTG 61.489 63.158 0.00 0.00 45.21 3.66
2815 8495 2.500392 TATAAGGTGGTGGTTGCACC 57.500 50.000 0.00 0.00 45.20 5.01
2873 8556 6.240894 ACCAATAAGAGTGCATTCTTCTTGA 58.759 36.000 33.03 18.38 40.72 3.02
2963 8646 3.557595 AGTTGTTTCTGCTTGACTTCTCG 59.442 43.478 0.00 0.00 0.00 4.04
2970 8653 4.136796 AGCATGTAGTTGTTTCTGCTTGA 58.863 39.130 0.00 0.00 36.62 3.02
3093 8776 6.378564 TGTCAAACTCAAACCTTCCAATGTAA 59.621 34.615 0.00 0.00 0.00 2.41
3129 8812 4.079844 TGGAGATGGAATAACTTGATGGCA 60.080 41.667 0.00 0.00 0.00 4.92
3183 8866 2.026945 TTCGCAGCACCTCACACTCA 62.027 55.000 0.00 0.00 0.00 3.41
3365 9049 3.825908 ATTCTTAACCTCTGGCCCAAA 57.174 42.857 0.00 0.00 0.00 3.28
3408 9092 5.948758 TCAACTGGTTGTGCATATAATCCAA 59.051 36.000 12.34 0.00 41.16 3.53
3437 9121 1.115467 AATCGCAGTGGACTAGAGGG 58.885 55.000 0.00 0.00 0.00 4.30
3496 9180 3.117701 TGACCCAAAATCACCAACTCTCA 60.118 43.478 0.00 0.00 0.00 3.27
3718 9402 6.484288 TCTAGAATGAGGATTCCAAAAGCAA 58.516 36.000 5.29 0.00 39.14 3.91
4010 9694 7.961827 CAGATTAATCAGCAGAACTCAAAGAAC 59.038 37.037 17.56 0.00 0.00 3.01
4033 9717 5.798132 ACAAAGAACATGTAGATCTGCAGA 58.202 37.500 20.79 20.79 28.74 4.26
4054 9738 8.046708 ACAGCAAAGATATTCACACCTTATACA 58.953 33.333 0.00 0.00 0.00 2.29
4262 13694 2.522638 CGTGAATTACCGCGGCTCC 61.523 63.158 28.58 10.90 36.51 4.70
4263 13695 1.356527 AACGTGAATTACCGCGGCTC 61.357 55.000 28.58 17.21 43.55 4.70
4264 13696 1.375013 AACGTGAATTACCGCGGCT 60.375 52.632 28.58 15.49 43.55 5.52
4265 13697 1.225908 CAACGTGAATTACCGCGGC 60.226 57.895 28.58 9.24 43.55 6.53
4266 13698 0.094046 GACAACGTGAATTACCGCGG 59.906 55.000 26.86 26.86 43.55 6.46
4267 13699 1.065358 AGACAACGTGAATTACCGCG 58.935 50.000 0.00 0.00 44.66 6.46
4268 13700 2.063266 TCAGACAACGTGAATTACCGC 58.937 47.619 0.00 0.00 0.00 5.68
4269 13701 2.092211 GCTCAGACAACGTGAATTACCG 59.908 50.000 0.00 0.00 0.00 4.02
4270 13702 3.326747 AGCTCAGACAACGTGAATTACC 58.673 45.455 0.00 0.00 0.00 2.85
4271 13703 3.987868 TGAGCTCAGACAACGTGAATTAC 59.012 43.478 13.74 0.00 0.00 1.89
4272 13704 4.251543 TGAGCTCAGACAACGTGAATTA 57.748 40.909 13.74 0.00 0.00 1.40
4273 13705 3.111853 TGAGCTCAGACAACGTGAATT 57.888 42.857 13.74 0.00 0.00 2.17
4274 13706 2.820059 TGAGCTCAGACAACGTGAAT 57.180 45.000 13.74 0.00 0.00 2.57
4275 13707 2.407090 CATGAGCTCAGACAACGTGAA 58.593 47.619 22.96 0.00 0.00 3.18
4276 13708 1.936656 GCATGAGCTCAGACAACGTGA 60.937 52.381 22.96 0.00 37.91 4.35
4277 13709 0.441533 GCATGAGCTCAGACAACGTG 59.558 55.000 22.96 14.18 37.91 4.49
4278 13710 2.832931 GCATGAGCTCAGACAACGT 58.167 52.632 22.96 0.00 37.91 3.99
4289 13721 0.948141 GGGCGTAGATGAGCATGAGC 60.948 60.000 0.00 0.00 42.56 4.26
4290 13722 0.665670 CGGGCGTAGATGAGCATGAG 60.666 60.000 0.00 0.00 34.54 2.90
4291 13723 1.363807 CGGGCGTAGATGAGCATGA 59.636 57.895 0.00 0.00 34.54 3.07
4292 13724 0.530650 AACGGGCGTAGATGAGCATG 60.531 55.000 0.00 0.00 34.54 4.06
4293 13725 0.530650 CAACGGGCGTAGATGAGCAT 60.531 55.000 0.00 0.00 34.54 3.79
4294 13726 1.153647 CAACGGGCGTAGATGAGCA 60.154 57.895 0.00 0.00 34.54 4.26
4295 13727 0.459585 TTCAACGGGCGTAGATGAGC 60.460 55.000 0.00 0.00 0.00 4.26
4296 13728 1.659098 GTTTCAACGGGCGTAGATGAG 59.341 52.381 0.00 0.00 0.00 2.90
4297 13729 1.274167 AGTTTCAACGGGCGTAGATGA 59.726 47.619 0.00 0.00 0.00 2.92
4298 13730 1.722011 AGTTTCAACGGGCGTAGATG 58.278 50.000 0.00 0.00 0.00 2.90
4299 13731 3.598019 TTAGTTTCAACGGGCGTAGAT 57.402 42.857 0.00 0.00 0.00 1.98
4300 13732 3.383620 TTTAGTTTCAACGGGCGTAGA 57.616 42.857 0.00 0.00 0.00 2.59
4301 13733 4.673534 AATTTAGTTTCAACGGGCGTAG 57.326 40.909 0.00 0.00 0.00 3.51
4302 13734 6.551385 TTAAATTTAGTTTCAACGGGCGTA 57.449 33.333 0.00 0.00 0.00 4.42
4303 13735 3.994204 AAATTTAGTTTCAACGGGCGT 57.006 38.095 0.00 0.00 0.00 5.68
4304 13736 6.750775 TTTTAAATTTAGTTTCAACGGGCG 57.249 33.333 0.00 0.00 0.00 6.13
4400 13834 2.225382 TGTACCCTCGATGTCTTCCA 57.775 50.000 0.00 0.00 0.00 3.53
4412 13846 1.985895 CCTTTCTGGAGGTTGTACCCT 59.014 52.381 0.00 0.00 39.75 4.34
4450 13888 1.678598 TTGGTGAGGACGGTCGTGTT 61.679 55.000 8.23 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.