Multiple sequence alignment - TraesCS6B01G458200

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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 TraesCS6B01G458200 chr6B 100.000 6239 0 0 1 6239 713457676 713463914 0.000000e+00 11522.0
1 TraesCS6B01G458200 chr6B 96.404 4560 129 16 891 5439 713943762 713948297 0.000000e+00 7480.0
2 TraesCS6B01G458200 chr6B 92.010 3179 231 12 2305 5478 713907795 713910955 0.000000e+00 4442.0
3 TraesCS6B01G458200 chr6B 84.009 3258 405 63 2321 5528 713498067 713501258 0.000000e+00 3024.0
4 TraesCS6B01G458200 chr6B 87.712 2238 225 27 3252 5478 713679823 713682021 0.000000e+00 2564.0
5 TraesCS6B01G458200 chr6B 89.286 2016 190 9 3380 5393 713771105 713773096 0.000000e+00 2503.0
6 TraesCS6B01G458200 chr6B 92.674 1720 121 3 3759 5477 713358642 713360357 0.000000e+00 2473.0
7 TraesCS6B01G458200 chr6B 90.198 1816 163 9 3662 5464 713825978 713827791 0.000000e+00 2353.0
8 TraesCS6B01G458200 chr6B 86.068 1615 168 29 734 2303 713905767 713907369 0.000000e+00 1683.0
9 TraesCS6B01G458200 chr6B 83.217 1436 217 21 2335 3761 713345516 713346936 0.000000e+00 1295.0
10 TraesCS6B01G458200 chr6B 94.467 723 14 6 5522 6239 713502016 713502717 0.000000e+00 1090.0
11 TraesCS6B01G458200 chr6B 84.046 1122 162 9 991 2103 713755381 713756494 0.000000e+00 1064.0
12 TraesCS6B01G458200 chr6B 83.408 1121 162 14 991 2103 713669096 713670200 0.000000e+00 1018.0
13 TraesCS6B01G458200 chr6B 82.696 1098 165 11 1006 2094 713822645 713823726 0.000000e+00 952.0
14 TraesCS6B01G458200 chr6B 78.982 1356 230 34 977 2301 713768014 713769345 0.000000e+00 874.0
15 TraesCS6B01G458200 chr6B 78.613 1384 238 38 2321 3689 713824633 713825973 0.000000e+00 863.0
16 TraesCS6B01G458200 chr6B 81.668 1091 139 32 2322 3395 713770043 713771089 0.000000e+00 850.0
17 TraesCS6B01G458200 chr6B 83.927 871 121 10 1241 2099 713496458 713497321 0.000000e+00 815.0
18 TraesCS6B01G458200 chr6B 77.371 928 159 23 2325 3220 713677437 713678345 2.600000e-138 503.0
19 TraesCS6B01G458200 chr6B 79.293 594 108 13 2568 3155 713871830 713872414 9.740000e-108 401.0
20 TraesCS6B01G458200 chr6B 86.071 280 39 0 1020 1299 713496182 713496461 1.020000e-77 302.0
21 TraesCS6B01G458200 chr6B 90.526 95 8 1 525 618 713943590 713943684 2.360000e-24 124.0
22 TraesCS6B01G458200 chr6B 78.109 201 34 4 5514 5705 713920022 713920221 1.100000e-22 119.0
23 TraesCS6B01G458200 chr6B 85.870 92 13 0 527 618 713495907 713495998 1.430000e-16 99.0
24 TraesCS6B01G458200 chr6B 83.158 95 15 1 525 618 713905674 713905768 1.110000e-12 86.1
25 TraesCS6B01G458200 chr6B 82.609 92 16 0 525 616 713668761 713668852 1.440000e-11 82.4
26 TraesCS6B01G458200 chr6B 94.118 51 3 0 525 575 713822274 713822324 1.860000e-10 78.7
27 TraesCS6B01G458200 chr6B 94.286 35 2 0 5910 5944 713834194 713834228 3.000000e-03 54.7
28 TraesCS6B01G458200 chr6D 85.560 3892 448 57 2325 6161 467858004 467861836 0.000000e+00 3969.0
29 TraesCS6B01G458200 chr6D 88.126 1398 155 8 3754 5144 263266707 263265314 0.000000e+00 1652.0
30 TraesCS6B01G458200 chr6D 80.076 1581 227 50 764 2303 467855760 467857293 0.000000e+00 1094.0
31 TraesCS6B01G458200 chr6D 81.869 1070 184 7 3986 5051 1509268 1508205 0.000000e+00 893.0
32 TraesCS6B01G458200 chr6D 79.308 1271 243 17 3782 5043 751615 752874 0.000000e+00 872.0
33 TraesCS6B01G458200 chr6D 95.455 44 2 0 5943 5986 20407163 20407120 3.120000e-08 71.3
34 TraesCS6B01G458200 chr6D 93.478 46 3 0 5944 5989 335991173 335991128 1.120000e-07 69.4
35 TraesCS6B01G458200 chr6D 93.023 43 3 0 5944 5986 27789761 27789719 5.220000e-06 63.9
36 TraesCS6B01G458200 chr6D 96.970 33 1 0 5943 5975 63799609 63799641 8.740000e-04 56.5
37 TraesCS6B01G458200 chr6A 92.576 2034 130 12 3709 5733 613974728 613976749 0.000000e+00 2900.0
38 TraesCS6B01G458200 chr6A 93.256 1379 86 5 2335 3713 613973143 613974514 0.000000e+00 2025.0
39 TraesCS6B01G458200 chr6A 86.333 1617 167 27 734 2303 613969240 613970849 0.000000e+00 1712.0
40 TraesCS6B01G458200 chr6A 81.538 1040 170 14 4006 5043 108892 109911 0.000000e+00 837.0
41 TraesCS6B01G458200 chr6A 80.984 1057 197 4 3997 5051 3352806 3351752 0.000000e+00 835.0
42 TraesCS6B01G458200 chr6A 96.543 376 13 0 149 524 435591806 435592181 1.910000e-174 623.0
43 TraesCS6B01G458200 chr6A 91.579 95 7 1 525 618 613969147 613969241 5.080000e-26 130.0
44 TraesCS6B01G458200 chr3B 98.102 527 8 2 1 526 52652046 52652571 0.000000e+00 917.0
45 TraesCS6B01G458200 chr3B 95.703 512 20 2 14 525 815309762 815310271 0.000000e+00 822.0
46 TraesCS6B01G458200 chr3B 92.308 117 6 3 609 724 797464005 797463891 5.000000e-36 163.0
47 TraesCS6B01G458200 chr3B 90.244 123 9 3 603 724 115549503 115549623 2.330000e-34 158.0
48 TraesCS6B01G458200 chr4D 78.912 1323 263 13 3785 5098 19810194 19808879 0.000000e+00 883.0
49 TraesCS6B01G458200 chr4D 95.349 43 1 1 5944 5986 433366209 433366250 4.040000e-07 67.6
50 TraesCS6B01G458200 chr7A 96.762 525 16 1 1 524 642102070 642102594 0.000000e+00 874.0
51 TraesCS6B01G458200 chr7A 94.545 110 4 2 616 724 672155141 672155033 1.080000e-37 169.0
52 TraesCS6B01G458200 chr7A 97.500 40 1 0 5944 5983 67464858 67464897 1.120000e-07 69.4
53 TraesCS6B01G458200 chr4A 95.890 511 20 1 14 524 648782090 648781581 0.000000e+00 826.0
54 TraesCS6B01G458200 chr4A 95.703 512 21 1 14 525 730989724 730989214 0.000000e+00 822.0
55 TraesCS6B01G458200 chr4A 93.878 49 3 0 5942 5990 563405309 563405357 2.410000e-09 75.0
56 TraesCS6B01G458200 chr1B 91.978 536 30 9 1 525 612223106 612222573 0.000000e+00 739.0
57 TraesCS6B01G458200 chr1B 95.918 147 6 0 1 147 325297746 325297600 8.080000e-59 239.0
58 TraesCS6B01G458200 chr1B 90.244 123 10 2 603 724 175418439 175418560 6.470000e-35 159.0
59 TraesCS6B01G458200 chr5B 91.776 535 31 9 1 524 96016798 96017330 0.000000e+00 732.0
60 TraesCS6B01G458200 chr5B 92.308 117 6 3 609 724 358816907 358817021 5.000000e-36 163.0
61 TraesCS6B01G458200 chr5B 91.597 119 6 4 608 724 563340499 563340615 1.800000e-35 161.0
62 TraesCS6B01G458200 chr3A 96.809 376 12 0 149 524 49472925 49472550 4.110000e-176 628.0
63 TraesCS6B01G458200 chr3A 95.455 44 2 0 5943 5986 94204065 94204108 3.120000e-08 71.3
64 TraesCS6B01G458200 chr2B 96.809 376 12 0 149 524 573128487 573128862 4.110000e-176 628.0
65 TraesCS6B01G458200 chr2B 91.597 119 7 3 607 724 547962622 547962506 1.800000e-35 161.0
66 TraesCS6B01G458200 chr2B 97.561 41 1 0 5943 5983 69041375 69041415 3.120000e-08 71.3
67 TraesCS6B01G458200 chr7B 93.634 377 16 3 149 524 713752084 713752453 1.960000e-154 556.0
68 TraesCS6B01G458200 chr7B 93.694 111 6 1 614 724 635493278 635493387 1.390000e-36 165.0
69 TraesCS6B01G458200 chr7B 91.489 47 4 0 5943 5989 245077526 245077480 1.450000e-06 65.8
70 TraesCS6B01G458200 chr1A 81.056 549 74 20 1 525 97804792 97805334 1.620000e-110 411.0
71 TraesCS6B01G458200 chr1D 98.639 147 2 0 1 147 225432195 225432049 1.730000e-65 261.0
72 TraesCS6B01G458200 chr1D 95.455 44 2 0 5943 5986 462898701 462898744 3.120000e-08 71.3
73 TraesCS6B01G458200 chr4B 94.495 109 5 1 616 724 548610792 548610685 3.870000e-37 167.0
74 TraesCS6B01G458200 chr4B 97.368 38 1 0 5949 5986 639479790 639479753 1.450000e-06 65.8
75 TraesCS6B01G458200 chrUn 87.013 77 10 0 1223 1299 30238334 30238410 3.100000e-13 87.9
76 TraesCS6B01G458200 chr5D 95.349 43 2 0 5944 5986 97073871 97073829 1.120000e-07 69.4
77 TraesCS6B01G458200 chr5D 93.478 46 3 0 5941 5986 544773739 544773784 1.120000e-07 69.4
78 TraesCS6B01G458200 chr7D 91.304 46 4 0 5944 5989 601485699 601485654 5.220000e-06 63.9


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 TraesCS6B01G458200 chr6B 713457676 713463914 6238 False 11522.000000 11522 100.000000 1 6239 1 chr6B.!!$F3 6238
1 TraesCS6B01G458200 chr6B 713943590 713948297 4707 False 3802.000000 7480 93.465000 525 5439 2 chr6B.!!$F14 4914
2 TraesCS6B01G458200 chr6B 713358642 713360357 1715 False 2473.000000 2473 92.674000 3759 5477 1 chr6B.!!$F2 1718
3 TraesCS6B01G458200 chr6B 713905674 713910955 5281 False 2070.366667 4442 87.078667 525 5478 3 chr6B.!!$F13 4953
4 TraesCS6B01G458200 chr6B 713677437 713682021 4584 False 1533.500000 2564 82.541500 2325 5478 2 chr6B.!!$F10 3153
5 TraesCS6B01G458200 chr6B 713768014 713773096 5082 False 1409.000000 2503 83.312000 977 5393 3 chr6B.!!$F11 4416
6 TraesCS6B01G458200 chr6B 713345516 713346936 1420 False 1295.000000 1295 83.217000 2335 3761 1 chr6B.!!$F1 1426
7 TraesCS6B01G458200 chr6B 713495907 713502717 6810 False 1066.000000 3024 86.868800 527 6239 5 chr6B.!!$F8 5712
8 TraesCS6B01G458200 chr6B 713755381 713756494 1113 False 1064.000000 1064 84.046000 991 2103 1 chr6B.!!$F4 1112
9 TraesCS6B01G458200 chr6B 713822274 713827791 5517 False 1061.675000 2353 86.406250 525 5464 4 chr6B.!!$F12 4939
10 TraesCS6B01G458200 chr6B 713668761 713670200 1439 False 550.200000 1018 83.008500 525 2103 2 chr6B.!!$F9 1578
11 TraesCS6B01G458200 chr6B 713871830 713872414 584 False 401.000000 401 79.293000 2568 3155 1 chr6B.!!$F6 587
12 TraesCS6B01G458200 chr6D 467855760 467861836 6076 False 2531.500000 3969 82.818000 764 6161 2 chr6D.!!$F3 5397
13 TraesCS6B01G458200 chr6D 263265314 263266707 1393 True 1652.000000 1652 88.126000 3754 5144 1 chr6D.!!$R4 1390
14 TraesCS6B01G458200 chr6D 1508205 1509268 1063 True 893.000000 893 81.869000 3986 5051 1 chr6D.!!$R1 1065
15 TraesCS6B01G458200 chr6D 751615 752874 1259 False 872.000000 872 79.308000 3782 5043 1 chr6D.!!$F1 1261
16 TraesCS6B01G458200 chr6A 613969147 613976749 7602 False 1691.750000 2900 90.936000 525 5733 4 chr6A.!!$F3 5208
17 TraesCS6B01G458200 chr6A 108892 109911 1019 False 837.000000 837 81.538000 4006 5043 1 chr6A.!!$F1 1037
18 TraesCS6B01G458200 chr6A 3351752 3352806 1054 True 835.000000 835 80.984000 3997 5051 1 chr6A.!!$R1 1054
19 TraesCS6B01G458200 chr3B 52652046 52652571 525 False 917.000000 917 98.102000 1 526 1 chr3B.!!$F1 525
20 TraesCS6B01G458200 chr3B 815309762 815310271 509 False 822.000000 822 95.703000 14 525 1 chr3B.!!$F3 511
21 TraesCS6B01G458200 chr4D 19808879 19810194 1315 True 883.000000 883 78.912000 3785 5098 1 chr4D.!!$R1 1313
22 TraesCS6B01G458200 chr7A 642102070 642102594 524 False 874.000000 874 96.762000 1 524 1 chr7A.!!$F2 523
23 TraesCS6B01G458200 chr4A 648781581 648782090 509 True 826.000000 826 95.890000 14 524 1 chr4A.!!$R1 510
24 TraesCS6B01G458200 chr4A 730989214 730989724 510 True 822.000000 822 95.703000 14 525 1 chr4A.!!$R2 511
25 TraesCS6B01G458200 chr1B 612222573 612223106 533 True 739.000000 739 91.978000 1 525 1 chr1B.!!$R2 524
26 TraesCS6B01G458200 chr5B 96016798 96017330 532 False 732.000000 732 91.776000 1 524 1 chr5B.!!$F1 523
27 TraesCS6B01G458200 chr1A 97804792 97805334 542 False 411.000000 411 81.056000 1 525 1 chr1A.!!$F1 524

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
600 636 0.178992 TTGCAAGGCCTAGTGTTGCT 60.179 50.000 23.33 0.0 45.56 3.91 F
1280 1411 0.685097 ACCTGCGACAACACCACTAT 59.315 50.000 0.00 0.0 0.00 2.12 F
1285 1416 3.064207 TGCGACAACACCACTATTTCTC 58.936 45.455 0.00 0.0 0.00 2.87 F
2986 6278 1.083489 CGCGCTCCAACTTCCATTAA 58.917 50.000 5.56 0.0 0.00 1.40 F
3676 8519 2.308570 TGTGTTGGATGAATGGTAGGCT 59.691 45.455 0.00 0.0 0.00 4.58 F
4327 9400 3.409026 AGTCTAAGTTGGTGGAGCAAG 57.591 47.619 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2678 5961 3.060602 GCTCCCATCGCTTGTATAACTC 58.939 50.000 0.00 0.00 0.00 3.01 R
2966 6256 0.248012 TAATGGAAGTTGGAGCGCGA 59.752 50.000 12.10 0.00 0.00 5.87 R
3276 8044 3.244112 GCCAAACTCTAGTACTGGTGTGT 60.244 47.826 13.76 6.52 35.02 3.72 R
4644 9717 2.158957 TGAAGCACCGAAGTCAGAAACT 60.159 45.455 0.00 0.00 41.10 2.66 R
4752 9825 2.868899 TCACTCTTCTCACTCAGCTCA 58.131 47.619 0.00 0.00 0.00 4.26 R
5859 11723 0.979187 GTGGGTCGGAGGGGAATACA 60.979 60.000 0.00 0.00 0.00 2.29 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
488 522 2.480845 AGTGGTAGTTTTCTGTCACGC 58.519 47.619 0.00 0.00 38.33 5.34
580 615 5.287035 CAGACGTACCTTGACCGTATAAAAC 59.713 44.000 0.00 0.00 34.51 2.43
590 625 2.490509 ACCGTATAAAACTTGCAAGGCC 59.509 45.455 29.18 0.00 0.00 5.19
600 636 0.178992 TTGCAAGGCCTAGTGTTGCT 60.179 50.000 23.33 0.00 45.56 3.91
616 652 4.809426 GTGTTGCTAAACGGCTACTATCAT 59.191 41.667 0.00 0.00 39.30 2.45
617 653 5.981315 GTGTTGCTAAACGGCTACTATCATA 59.019 40.000 0.00 0.00 39.30 2.15
618 654 5.981315 TGTTGCTAAACGGCTACTATCATAC 59.019 40.000 0.00 0.00 39.30 2.39
619 655 6.183360 TGTTGCTAAACGGCTACTATCATACT 60.183 38.462 0.00 0.00 39.30 2.12
620 656 6.010294 TGCTAAACGGCTACTATCATACTC 57.990 41.667 0.00 0.00 0.00 2.59
621 657 5.048224 TGCTAAACGGCTACTATCATACTCC 60.048 44.000 0.00 0.00 0.00 3.85
622 658 4.868314 AAACGGCTACTATCATACTCCC 57.132 45.455 0.00 0.00 0.00 4.30
623 659 3.810721 ACGGCTACTATCATACTCCCT 57.189 47.619 0.00 0.00 0.00 4.20
624 660 3.688235 ACGGCTACTATCATACTCCCTC 58.312 50.000 0.00 0.00 0.00 4.30
625 661 3.018149 CGGCTACTATCATACTCCCTCC 58.982 54.545 0.00 0.00 0.00 4.30
626 662 3.018149 GGCTACTATCATACTCCCTCCG 58.982 54.545 0.00 0.00 0.00 4.63
627 663 3.561744 GGCTACTATCATACTCCCTCCGT 60.562 52.174 0.00 0.00 0.00 4.69
628 664 3.690628 GCTACTATCATACTCCCTCCGTC 59.309 52.174 0.00 0.00 0.00 4.79
629 665 4.566070 GCTACTATCATACTCCCTCCGTCT 60.566 50.000 0.00 0.00 0.00 4.18
630 666 3.757270 ACTATCATACTCCCTCCGTCTG 58.243 50.000 0.00 0.00 0.00 3.51
631 667 3.394940 ACTATCATACTCCCTCCGTCTGA 59.605 47.826 0.00 0.00 0.00 3.27
632 668 2.820728 TCATACTCCCTCCGTCTGAA 57.179 50.000 0.00 0.00 0.00 3.02
633 669 3.095912 TCATACTCCCTCCGTCTGAAA 57.904 47.619 0.00 0.00 0.00 2.69
634 670 3.437213 TCATACTCCCTCCGTCTGAAAA 58.563 45.455 0.00 0.00 0.00 2.29
635 671 4.030913 TCATACTCCCTCCGTCTGAAAAT 58.969 43.478 0.00 0.00 0.00 1.82
636 672 5.205821 TCATACTCCCTCCGTCTGAAAATA 58.794 41.667 0.00 0.00 0.00 1.40
637 673 3.889520 ACTCCCTCCGTCTGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
638 674 3.442076 ACTCCCTCCGTCTGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
639 675 3.838903 ACTCCCTCCGTCTGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
640 676 4.286291 ACTCCCTCCGTCTGAAAATACTTT 59.714 41.667 0.00 0.00 0.00 2.66
641 677 5.221864 ACTCCCTCCGTCTGAAAATACTTTT 60.222 40.000 0.00 0.00 35.12 2.27
718 754 6.477053 TCCTTTTTGTCCATTTTGATGACA 57.523 33.333 0.00 0.00 0.00 3.58
719 755 6.882656 TCCTTTTTGTCCATTTTGATGACAA 58.117 32.000 0.00 0.00 34.47 3.18
720 756 7.507829 TCCTTTTTGTCCATTTTGATGACAAT 58.492 30.769 5.27 0.00 35.96 2.71
721 757 7.441760 TCCTTTTTGTCCATTTTGATGACAATG 59.558 33.333 5.27 0.00 35.96 2.82
722 758 7.227116 CCTTTTTGTCCATTTTGATGACAATGT 59.773 33.333 5.27 0.00 35.96 2.71
723 759 9.258826 CTTTTTGTCCATTTTGATGACAATGTA 57.741 29.630 5.27 0.00 35.96 2.29
724 760 8.815141 TTTTGTCCATTTTGATGACAATGTAG 57.185 30.769 5.27 0.00 35.96 2.74
725 761 7.757941 TTGTCCATTTTGATGACAATGTAGA 57.242 32.000 0.00 0.00 35.85 2.59
726 762 7.381766 TGTCCATTTTGATGACAATGTAGAG 57.618 36.000 0.00 0.00 35.85 2.43
727 763 7.167535 TGTCCATTTTGATGACAATGTAGAGA 58.832 34.615 0.00 0.00 35.85 3.10
728 764 7.335171 TGTCCATTTTGATGACAATGTAGAGAG 59.665 37.037 0.00 0.00 35.85 3.20
729 765 6.825213 TCCATTTTGATGACAATGTAGAGAGG 59.175 38.462 0.00 0.00 35.85 3.69
730 766 6.039047 CCATTTTGATGACAATGTAGAGAGGG 59.961 42.308 0.00 0.00 35.85 4.30
731 767 6.373005 TTTTGATGACAATGTAGAGAGGGA 57.627 37.500 0.00 0.00 35.85 4.20
732 768 5.604758 TTGATGACAATGTAGAGAGGGAG 57.395 43.478 0.00 0.00 0.00 4.30
737 773 4.822350 TGACAATGTAGAGAGGGAGTATCG 59.178 45.833 0.00 0.00 34.37 2.92
823 864 3.135994 CGCAAGTACTGGTGGTAACTTT 58.864 45.455 2.58 0.00 37.61 2.66
854 919 7.743116 AAAAATAAAATAACTTCCCCCGGAT 57.257 32.000 0.73 0.00 0.00 4.18
855 920 7.743116 AAAATAAAATAACTTCCCCCGGATT 57.257 32.000 0.73 0.00 0.00 3.01
856 921 7.743116 AAATAAAATAACTTCCCCCGGATTT 57.257 32.000 0.73 0.00 0.00 2.17
857 922 7.743116 AATAAAATAACTTCCCCCGGATTTT 57.257 32.000 0.73 7.24 0.00 1.82
858 923 7.743116 ATAAAATAACTTCCCCCGGATTTTT 57.257 32.000 0.73 0.00 0.00 1.94
938 1023 4.298332 CTTTTTAATACGCCATCCATGCC 58.702 43.478 0.00 0.00 0.00 4.40
964 1049 1.021390 GGCAGCACGCATACACTCTT 61.021 55.000 0.00 0.00 45.17 2.85
1028 1159 2.061509 AACCAACCACCAACACCTAC 57.938 50.000 0.00 0.00 0.00 3.18
1037 1168 3.066203 CCACCAACACCTACAACAAACTC 59.934 47.826 0.00 0.00 0.00 3.01
1217 1348 4.280929 CGGGGATGTAGACATTCACTATCA 59.719 45.833 1.76 0.00 32.99 2.15
1280 1411 0.685097 ACCTGCGACAACACCACTAT 59.315 50.000 0.00 0.00 0.00 2.12
1285 1416 3.064207 TGCGACAACACCACTATTTCTC 58.936 45.455 0.00 0.00 0.00 2.87
2303 2532 8.755696 TTTGTAGAATATTTGACACATTTGGC 57.244 30.769 3.54 0.00 0.00 4.52
2318 2547 8.292444 ACACATTTGGCTGCTATAATAAAAGA 57.708 30.769 0.00 0.00 0.00 2.52
2678 5961 3.785486 TGATGAAGATCTTGCGGTAGTG 58.215 45.455 14.00 0.00 0.00 2.74
2966 6256 1.409241 CCAGATGGCTGCACAGGTAAT 60.409 52.381 0.50 0.00 40.91 1.89
2986 6278 1.083489 CGCGCTCCAACTTCCATTAA 58.917 50.000 5.56 0.00 0.00 1.40
3106 6407 8.291032 GCAATTCTTCTATCATCTTGATCCAAG 58.709 37.037 0.51 0.51 42.25 3.61
3276 8044 5.018539 ACATTACGCTAAATGACTAGGCA 57.981 39.130 0.00 0.00 38.84 4.75
3676 8519 2.308570 TGTGTTGGATGAATGGTAGGCT 59.691 45.455 0.00 0.00 0.00 4.58
4212 9283 6.238484 CCTTGGAGGAATTAGATAAAGCAACG 60.238 42.308 0.00 0.00 37.67 4.10
4327 9400 3.409026 AGTCTAAGTTGGTGGAGCAAG 57.591 47.619 0.00 0.00 0.00 4.01
4515 9588 7.396055 AGTGCTAAATGCTTACTTTTATGGGAA 59.604 33.333 0.00 0.00 43.37 3.97
4644 9717 6.013206 TCCTAGATGGCAACTTTACTACCAAA 60.013 38.462 1.54 0.00 33.30 3.28
5059 10133 9.436957 TGCAACTCCTAAAAACTAGAAGATTAG 57.563 33.333 0.00 0.06 0.00 1.73
5859 11723 0.037232 GCGGCAACTCCTAGAACACT 60.037 55.000 0.00 0.00 0.00 3.55
5956 11821 4.695606 TGTAGAACCTACTCCCTCCATTT 58.304 43.478 5.82 0.00 0.00 2.32
6145 12015 2.820037 GCGAGAAAAGGCTCCCGG 60.820 66.667 0.00 0.00 0.00 5.73
6167 12037 4.753107 GGCAATGGCTCAATGATAAATTGG 59.247 41.667 0.00 0.00 40.87 3.16
6189 12059 3.710326 TCTTGTTATCCTCCGTGATCG 57.290 47.619 0.00 0.00 0.00 3.69
6233 12103 3.472652 TGGGTCTGTTGAACATGTGTAC 58.527 45.455 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 4.022242 GTCGTCCCTAGATAAGCAAGCATA 60.022 45.833 0.00 0.00 0.00 3.14
320 353 2.165437 GCTAAAAATGCAATCGGGTCCA 59.835 45.455 0.00 0.00 0.00 4.02
488 522 6.198216 CCAAAAACTACCACAATTCACGAAAG 59.802 38.462 0.00 0.00 0.00 2.62
533 567 0.401738 TTGTGGCCAAGGAGAAGGAG 59.598 55.000 7.24 0.00 0.00 3.69
580 615 0.242017 GCAACACTAGGCCTTGCAAG 59.758 55.000 19.93 19.93 40.09 4.01
590 625 3.846360 AGTAGCCGTTTAGCAACACTAG 58.154 45.455 0.00 0.00 32.54 2.57
600 636 5.638133 AGGGAGTATGATAGTAGCCGTTTA 58.362 41.667 0.00 0.00 0.00 2.01
616 652 4.607239 AGTATTTTCAGACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
617 653 3.442076 AGTATTTTCAGACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
618 654 4.473477 AAGTATTTTCAGACGGAGGGAG 57.527 45.455 0.00 0.00 0.00 4.30
619 655 4.903045 AAAGTATTTTCAGACGGAGGGA 57.097 40.909 0.00 0.00 31.62 4.20
692 728 8.814931 TGTCATCAAAATGGACAAAAAGGATAT 58.185 29.630 0.00 0.00 33.42 1.63
693 729 8.187913 TGTCATCAAAATGGACAAAAAGGATA 57.812 30.769 0.00 0.00 33.42 2.59
694 730 7.065120 TGTCATCAAAATGGACAAAAAGGAT 57.935 32.000 0.00 0.00 33.42 3.24
695 731 6.477053 TGTCATCAAAATGGACAAAAAGGA 57.523 33.333 0.00 0.00 33.42 3.36
696 732 7.227116 ACATTGTCATCAAAATGGACAAAAAGG 59.773 33.333 10.06 4.32 36.93 3.11
697 733 8.145316 ACATTGTCATCAAAATGGACAAAAAG 57.855 30.769 10.06 6.60 36.93 2.27
698 734 9.258826 CTACATTGTCATCAAAATGGACAAAAA 57.741 29.630 10.06 0.02 36.93 1.94
699 735 8.637099 TCTACATTGTCATCAAAATGGACAAAA 58.363 29.630 10.06 0.31 36.93 2.44
700 736 8.175925 TCTACATTGTCATCAAAATGGACAAA 57.824 30.769 10.06 0.00 36.93 2.83
701 737 7.665145 TCTCTACATTGTCATCAAAATGGACAA 59.335 33.333 8.64 8.64 37.96 3.18
702 738 7.167535 TCTCTACATTGTCATCAAAATGGACA 58.832 34.615 0.00 0.00 37.96 4.02
703 739 7.201679 CCTCTCTACATTGTCATCAAAATGGAC 60.202 40.741 0.00 0.00 37.96 4.02
704 740 6.825213 CCTCTCTACATTGTCATCAAAATGGA 59.175 38.462 0.00 0.00 37.96 3.41
705 741 6.039047 CCCTCTCTACATTGTCATCAAAATGG 59.961 42.308 0.00 0.00 37.96 3.16
706 742 6.825213 TCCCTCTCTACATTGTCATCAAAATG 59.175 38.462 0.00 0.00 39.26 2.32
707 743 6.962182 TCCCTCTCTACATTGTCATCAAAAT 58.038 36.000 0.00 0.00 37.11 1.82
708 744 6.013379 ACTCCCTCTCTACATTGTCATCAAAA 60.013 38.462 0.00 0.00 37.11 2.44
709 745 5.485353 ACTCCCTCTCTACATTGTCATCAAA 59.515 40.000 0.00 0.00 37.11 2.69
710 746 5.026121 ACTCCCTCTCTACATTGTCATCAA 58.974 41.667 0.00 0.00 37.98 2.57
711 747 4.614475 ACTCCCTCTCTACATTGTCATCA 58.386 43.478 0.00 0.00 0.00 3.07
712 748 6.348950 CGATACTCCCTCTCTACATTGTCATC 60.349 46.154 0.00 0.00 0.00 2.92
713 749 5.475220 CGATACTCCCTCTCTACATTGTCAT 59.525 44.000 0.00 0.00 0.00 3.06
714 750 4.822350 CGATACTCCCTCTCTACATTGTCA 59.178 45.833 0.00 0.00 0.00 3.58
715 751 4.216687 CCGATACTCCCTCTCTACATTGTC 59.783 50.000 0.00 0.00 0.00 3.18
716 752 4.145807 CCGATACTCCCTCTCTACATTGT 58.854 47.826 0.00 0.00 0.00 2.71
717 753 3.057174 GCCGATACTCCCTCTCTACATTG 60.057 52.174 0.00 0.00 0.00 2.82
718 754 3.158676 GCCGATACTCCCTCTCTACATT 58.841 50.000 0.00 0.00 0.00 2.71
719 755 2.377193 AGCCGATACTCCCTCTCTACAT 59.623 50.000 0.00 0.00 0.00 2.29
720 756 1.775459 AGCCGATACTCCCTCTCTACA 59.225 52.381 0.00 0.00 0.00 2.74
721 757 2.156098 CAGCCGATACTCCCTCTCTAC 58.844 57.143 0.00 0.00 0.00 2.59
722 758 1.074084 CCAGCCGATACTCCCTCTCTA 59.926 57.143 0.00 0.00 0.00 2.43
723 759 0.178975 CCAGCCGATACTCCCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
724 760 1.811645 GCCAGCCGATACTCCCTCTC 61.812 65.000 0.00 0.00 0.00 3.20
725 761 1.834822 GCCAGCCGATACTCCCTCT 60.835 63.158 0.00 0.00 0.00 3.69
726 762 2.737830 GCCAGCCGATACTCCCTC 59.262 66.667 0.00 0.00 0.00 4.30
727 763 2.844839 GGCCAGCCGATACTCCCT 60.845 66.667 0.00 0.00 0.00 4.20
728 764 2.666596 CTTGGCCAGCCGATACTCCC 62.667 65.000 5.11 0.00 39.42 4.30
729 765 1.227674 CTTGGCCAGCCGATACTCC 60.228 63.158 5.11 0.00 39.42 3.85
730 766 1.889573 GCTTGGCCAGCCGATACTC 60.890 63.158 5.11 0.00 43.65 2.59
731 767 2.190578 GCTTGGCCAGCCGATACT 59.809 61.111 5.11 0.00 43.65 2.12
752 788 3.588057 TTGTCGCTGCATGCCGAGA 62.588 57.895 17.63 14.63 38.78 4.04
801 838 0.794473 GTTACCACCAGTACTTGCGC 59.206 55.000 0.00 0.00 0.00 6.09
938 1023 2.061773 GTATGCGTGCTGCCTATGTAG 58.938 52.381 0.00 0.00 45.60 2.74
952 1037 7.171848 AGACAGATACTACTAAGAGTGTATGCG 59.828 40.741 0.00 0.00 34.27 4.73
1028 1159 4.383602 CGGCGGGCGAGTTTGTTG 62.384 66.667 20.10 0.00 0.00 3.33
1280 1411 3.444388 GTCTAGAAAGAGCCTCGGAGAAA 59.556 47.826 6.58 0.00 29.46 2.52
1285 1416 2.231478 TGTTGTCTAGAAAGAGCCTCGG 59.769 50.000 0.00 0.00 30.45 4.63
2678 5961 3.060602 GCTCCCATCGCTTGTATAACTC 58.939 50.000 0.00 0.00 0.00 3.01
2856 6143 2.048127 GTGACGGGTGACAGGAGC 60.048 66.667 0.00 0.00 0.00 4.70
2857 6144 1.544825 ATGGTGACGGGTGACAGGAG 61.545 60.000 0.00 0.00 0.00 3.69
2966 6256 0.248012 TAATGGAAGTTGGAGCGCGA 59.752 50.000 12.10 0.00 0.00 5.87
2986 6278 3.678529 GCATACGGTTGGATGGCAATTTT 60.679 43.478 0.00 0.00 0.00 1.82
3276 8044 3.244112 GCCAAACTCTAGTACTGGTGTGT 60.244 47.826 13.76 6.52 35.02 3.72
3480 8280 4.637483 TTCATTTCCATGAGGCGAATTC 57.363 40.909 0.00 0.00 40.66 2.17
3558 8367 9.715121 ATCTTAGTAAACGACCAAATTCTACAA 57.285 29.630 0.00 0.00 0.00 2.41
3560 8369 9.148104 ACATCTTAGTAAACGACCAAATTCTAC 57.852 33.333 0.00 0.00 0.00 2.59
3676 8519 2.627933 ACCAAAGCTAGGTCACCCTTA 58.372 47.619 4.99 0.00 42.66 2.69
4212 9283 4.795970 ACGACTGACATCAAAGTTGTTC 57.204 40.909 0.00 0.00 37.70 3.18
4327 9400 5.446473 CGTTGATAAACTGGTCAATCTCAGC 60.446 44.000 0.00 0.00 36.79 4.26
4515 9588 5.847304 TCTACTGCAATTCTAATGCGATCT 58.153 37.500 0.00 0.00 46.76 2.75
4644 9717 2.158957 TGAAGCACCGAAGTCAGAAACT 60.159 45.455 0.00 0.00 41.10 2.66
4656 9729 3.125316 GTGATAAAGACCTTGAAGCACCG 59.875 47.826 0.00 0.00 0.00 4.94
4752 9825 2.868899 TCACTCTTCTCACTCAGCTCA 58.131 47.619 0.00 0.00 0.00 4.26
5428 10514 8.398665 CCTTTATTCACCACTGTAGCTTAATTC 58.601 37.037 0.00 0.00 0.00 2.17
5556 11407 6.151817 CGAAAGGGGAAGAGAAAAGATTTCAT 59.848 38.462 5.71 0.00 0.00 2.57
5859 11723 0.979187 GTGGGTCGGAGGGGAATACA 60.979 60.000 0.00 0.00 0.00 2.29
6145 12015 5.603596 TCCAATTTATCATTGAGCCATTGC 58.396 37.500 8.14 0.00 37.95 3.56
6167 12037 4.230657 CGATCACGGAGGATAACAAGATC 58.769 47.826 0.00 0.00 35.72 2.75


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

AutoCloner maintained by Alex Coulton.