Multiple sequence alignment - TraesCS5A01G104200

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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 TraesCS5A01G104200 chr5A 100.000 4946 0 0 1 4946 168239945 168235000 0.000000e+00 9134.0
1 TraesCS5A01G104200 chr5A 82.459 724 97 15 2856 3574 168130162 168129464 1.520000e-169 606.0
2 TraesCS5A01G104200 chr5A 88.095 420 45 5 3160 3574 30400927 30401346 1.240000e-135 494.0
3 TraesCS5A01G104200 chr5A 83.333 258 40 3 2416 2672 168130590 168130335 8.280000e-58 235.0
4 TraesCS5A01G104200 chr5D 95.196 4413 158 24 1 4362 136942922 136947331 0.000000e+00 6926.0
5 TraesCS5A01G104200 chr5D 86.364 418 54 3 3160 3574 42011143 42011560 2.100000e-123 453.0
6 TraesCS5A01G104200 chr5D 76.988 591 87 30 2455 3030 42057245 42056689 4.840000e-75 292.0
7 TraesCS5A01G104200 chr5D 88.889 198 18 2 3624 3817 42055955 42055758 1.780000e-59 241.0
8 TraesCS5A01G104200 chr5D 88.442 199 17 4 3624 3817 42011778 42011975 8.280000e-58 235.0
9 TraesCS5A01G104200 chr5D 82.609 184 24 6 2853 3030 42010875 42011056 6.630000e-34 156.0
10 TraesCS5A01G104200 chr5D 82.143 112 10 4 4354 4455 482166741 482166630 2.450000e-13 87.9
11 TraesCS5A01G104200 chr5D 73.529 238 37 17 4359 4573 460073369 460073603 3.200000e-07 67.6
12 TraesCS5A01G104200 chr5B 94.443 2897 139 14 236 3124 185506589 185509471 0.000000e+00 4438.0
13 TraesCS5A01G104200 chr5B 94.202 1121 46 10 3111 4219 185510761 185511874 0.000000e+00 1692.0
14 TraesCS5A01G104200 chr5B 87.952 415 49 1 3157 3571 185535144 185535557 5.750000e-134 488.0
15 TraesCS5A01G104200 chr5B 88.175 389 46 0 3186 3574 36775292 36774904 9.700000e-127 464.0
16 TraesCS5A01G104200 chr5B 87.786 393 47 1 3182 3574 36695535 36695926 4.510000e-125 459.0
17 TraesCS5A01G104200 chr5B 87.940 199 18 4 3624 3817 36696149 36696346 3.850000e-56 230.0
18 TraesCS5A01G104200 chr5B 87.940 199 18 4 3624 3817 36815896 36815699 3.850000e-56 230.0
19 TraesCS5A01G104200 chr5B 85.802 162 20 3 2513 2673 185534557 185534716 8.510000e-38 169.0
20 TraesCS5A01G104200 chr5B 83.735 166 4 5 1 162 185506109 185506255 8.640000e-28 135.0
21 TraesCS5A01G104200 chr5B 86.275 102 12 2 2930 3030 36775510 36775410 5.230000e-20 110.0
22 TraesCS5A01G104200 chr3D 87.566 571 55 8 4387 4945 188352500 188353066 0.000000e+00 647.0
23 TraesCS5A01G104200 chr3D 87.478 559 53 11 4399 4945 575931067 575931620 3.250000e-176 628.0
24 TraesCS5A01G104200 chr3D 75.902 610 103 28 4359 4945 524952250 524951662 6.310000e-69 272.0
25 TraesCS5A01G104200 chr6D 86.319 614 58 16 4357 4945 414471535 414470923 0.000000e+00 645.0
26 TraesCS5A01G104200 chr7A 86.207 609 61 10 4359 4945 183645459 183646066 5.400000e-179 638.0
27 TraesCS5A01G104200 chr2A 86.842 570 63 6 4387 4945 699603311 699603879 1.170000e-175 627.0
28 TraesCS5A01G104200 chr2A 81.961 571 87 9 4387 4945 652523583 652523017 2.080000e-128 470.0
29 TraesCS5A01G104200 chr2A 79.091 110 11 4 4351 4448 44239491 44239600 1.150000e-06 65.8
30 TraesCS5A01G104200 chr4B 85.762 604 64 6 4359 4940 94105078 94105681 1.960000e-173 619.0
31 TraesCS5A01G104200 chr2D 88.867 503 53 3 4446 4945 146726111 146726613 2.530000e-172 616.0
32 TraesCS5A01G104200 chr2D 85.893 560 75 4 4387 4942 527541420 527541979 1.190000e-165 593.0
33 TraesCS5A01G104200 chr2D 83.599 628 57 13 4350 4945 419368959 419369572 9.360000e-152 547.0
34 TraesCS5A01G104200 chr7D 85.067 596 77 6 4359 4945 630693245 630693837 9.160000e-167 597.0
35 TraesCS5A01G104200 chrUn 88.175 389 46 0 3186 3574 65844322 65844710 9.700000e-127 464.0
36 TraesCS5A01G104200 chrUn 87.940 199 18 4 3624 3817 340277500 340277697 3.850000e-56 230.0
37 TraesCS5A01G104200 chrUn 87.940 199 18 4 3624 3817 340336028 340336225 3.850000e-56 230.0
38 TraesCS5A01G104200 chrUn 86.275 102 12 2 2930 3030 65844104 65844204 5.230000e-20 110.0
39 TraesCS5A01G104200 chr2B 76.998 613 94 20 4359 4945 493718234 493718825 1.730000e-79 307.0
40 TraesCS5A01G104200 chr6B 75.973 437 69 18 4359 4774 624229738 624230159 5.050000e-45 193.0
41 TraesCS5A01G104200 chr6A 98.592 71 1 0 1395 1465 111403088 111403018 5.200000e-25 126.0
42 TraesCS5A01G104200 chr6A 100.000 33 0 0 1024 1056 111403117 111403085 1.490000e-05 62.1
43 TraesCS5A01G104200 chr7B 76.126 222 48 5 1463 1681 647752211 647752430 1.460000e-20 111.0
44 TraesCS5A01G104200 chr4A 80.952 105 18 2 4359 4462 34291634 34291737 1.140000e-11 82.4


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 TraesCS5A01G104200 chr5A 168235000 168239945 4945 True 9134.000000 9134 100.000000 1 4946 1 chr5A.!!$R1 4945
1 TraesCS5A01G104200 chr5A 168129464 168130590 1126 True 420.500000 606 82.896000 2416 3574 2 chr5A.!!$R2 1158
2 TraesCS5A01G104200 chr5D 136942922 136947331 4409 False 6926.000000 6926 95.196000 1 4362 1 chr5D.!!$F1 4361
3 TraesCS5A01G104200 chr5D 42010875 42011975 1100 False 281.333333 453 85.805000 2853 3817 3 chr5D.!!$F3 964
4 TraesCS5A01G104200 chr5D 42055758 42057245 1487 True 266.500000 292 82.938500 2455 3817 2 chr5D.!!$R2 1362
5 TraesCS5A01G104200 chr5B 185506109 185511874 5765 False 2088.333333 4438 90.793333 1 4219 3 chr5B.!!$F2 4218
6 TraesCS5A01G104200 chr5B 36695535 36696346 811 False 344.500000 459 87.863000 3182 3817 2 chr5B.!!$F1 635
7 TraesCS5A01G104200 chr5B 185534557 185535557 1000 False 328.500000 488 86.877000 2513 3571 2 chr5B.!!$F3 1058
8 TraesCS5A01G104200 chr5B 36774904 36775510 606 True 287.000000 464 87.225000 2930 3574 2 chr5B.!!$R2 644
9 TraesCS5A01G104200 chr3D 188352500 188353066 566 False 647.000000 647 87.566000 4387 4945 1 chr3D.!!$F1 558
10 TraesCS5A01G104200 chr3D 575931067 575931620 553 False 628.000000 628 87.478000 4399 4945 1 chr3D.!!$F2 546
11 TraesCS5A01G104200 chr3D 524951662 524952250 588 True 272.000000 272 75.902000 4359 4945 1 chr3D.!!$R1 586
12 TraesCS5A01G104200 chr6D 414470923 414471535 612 True 645.000000 645 86.319000 4357 4945 1 chr6D.!!$R1 588
13 TraesCS5A01G104200 chr7A 183645459 183646066 607 False 638.000000 638 86.207000 4359 4945 1 chr7A.!!$F1 586
14 TraesCS5A01G104200 chr2A 699603311 699603879 568 False 627.000000 627 86.842000 4387 4945 1 chr2A.!!$F2 558
15 TraesCS5A01G104200 chr2A 652523017 652523583 566 True 470.000000 470 81.961000 4387 4945 1 chr2A.!!$R1 558
16 TraesCS5A01G104200 chr4B 94105078 94105681 603 False 619.000000 619 85.762000 4359 4940 1 chr4B.!!$F1 581
17 TraesCS5A01G104200 chr2D 146726111 146726613 502 False 616.000000 616 88.867000 4446 4945 1 chr2D.!!$F1 499
18 TraesCS5A01G104200 chr2D 527541420 527541979 559 False 593.000000 593 85.893000 4387 4942 1 chr2D.!!$F3 555
19 TraesCS5A01G104200 chr2D 419368959 419369572 613 False 547.000000 547 83.599000 4350 4945 1 chr2D.!!$F2 595
20 TraesCS5A01G104200 chr7D 630693245 630693837 592 False 597.000000 597 85.067000 4359 4945 1 chr7D.!!$F1 586
21 TraesCS5A01G104200 chrUn 65844104 65844710 606 False 287.000000 464 87.225000 2930 3574 2 chrUn.!!$F3 644
22 TraesCS5A01G104200 chr2B 493718234 493718825 591 False 307.000000 307 76.998000 4359 4945 1 chr2B.!!$F1 586

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
887 1159 0.174845 CTCCGTATGGAAAGACGCCA 59.825 55.000 4.92 0.0 45.87 5.69 F
1115 1387 1.450531 GGCTCGGATTTGGGCTCATG 61.451 60.000 0.00 0.0 0.00 3.07 F
1701 1973 1.484240 AGTCAGGTGAGCTATCTTGGC 59.516 52.381 0.00 0.0 0.00 4.52 F
2881 3183 1.321474 ACTGGCACTGTTGATGTTGG 58.679 50.000 0.00 0.0 37.12 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 2675 0.104671 CGGCCCATAATTTGCCTTGG 59.895 55.0 0.0 0.0 43.12 3.61 R
2499 2775 0.321346 TCTCTGCCTTGTTGATGCGA 59.679 50.0 0.0 0.0 0.00 5.10 R
3447 5095 0.329261 TGCCTTCCCAGTCATTCAGG 59.671 55.0 0.0 0.0 0.00 3.86 R
4347 6208 0.039074 AGTTGCTCTCACTTCGTCCG 60.039 55.0 0.0 0.0 0.00 4.79 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
100 101 4.065088 CACAGCTGTGCTCCTACTTAAAA 58.935 43.478 32.39 0.00 36.40 1.52
124 125 9.822185 AAAAATGGAGTGCCTGATTAATTAATC 57.178 29.630 25.14 25.14 41.81 1.75
200 220 0.792640 CCGCTGATCTGAACACACAC 59.207 55.000 3.42 0.00 0.00 3.82
226 248 2.732412 ATCAACACAGAGAGGACACG 57.268 50.000 0.00 0.00 0.00 4.49
227 249 1.399714 TCAACACAGAGAGGACACGT 58.600 50.000 0.00 0.00 0.00 4.49
229 251 2.167693 TCAACACAGAGAGGACACGTTT 59.832 45.455 0.00 0.00 0.00 3.60
322 587 5.798125 TCTTATCCTGCTCCTCTTACATG 57.202 43.478 0.00 0.00 0.00 3.21
371 638 5.439721 TGGACTGCAAATATGTTGCTATCT 58.560 37.500 17.58 4.29 45.13 1.98
401 668 2.038387 ACTGTTGTGCGGTTCTCTTT 57.962 45.000 0.00 0.00 31.36 2.52
421 688 2.959507 ATTTTGGCAAGGTATTCGCC 57.040 45.000 0.00 0.00 46.43 5.54
424 691 2.513897 GGCAAGGTATTCGCCGCT 60.514 61.111 0.00 0.00 35.79 5.52
430 697 1.299541 AGGTATTCGCCGCTGAATTG 58.700 50.000 13.21 0.00 39.27 2.32
478 745 1.343465 TCGGGTCTCACTTTTCTCCAC 59.657 52.381 0.00 0.00 0.00 4.02
481 748 1.149148 GTCTCACTTTTCTCCACCGC 58.851 55.000 0.00 0.00 0.00 5.68
486 753 0.661020 ACTTTTCTCCACCGCGTTTG 59.339 50.000 4.92 0.95 0.00 2.93
531 802 2.070783 GTTCATACTCGCGGGACAAAA 58.929 47.619 15.95 0.00 0.00 2.44
664 935 0.321919 TCTCTGGCCAATGAGTGTGC 60.322 55.000 18.71 0.00 0.00 4.57
711 982 4.672862 TCAACATTTTACGCAAATCACACG 59.327 37.500 0.00 0.00 32.24 4.49
721 992 3.171277 GCAAATCACACGCATAGGTTTC 58.829 45.455 0.00 0.00 0.00 2.78
729 1000 4.616802 CACACGCATAGGTTTCATTTTCAC 59.383 41.667 0.00 0.00 0.00 3.18
741 1012 9.410556 AGGTTTCATTTTCACGATTTGATTTAG 57.589 29.630 0.00 0.00 32.84 1.85
823 1094 3.308401 GTCCATTTCTTGGCCCCATTAT 58.692 45.455 0.00 0.00 46.01 1.28
854 1126 0.993509 TCCTCCCCATAAAGCCCCAG 60.994 60.000 0.00 0.00 0.00 4.45
887 1159 0.174845 CTCCGTATGGAAAGACGCCA 59.825 55.000 4.92 0.00 45.87 5.69
959 1231 7.309990 GGACTTTGATTGAAAAGATCCCATTCA 60.310 37.037 3.82 2.31 39.12 2.57
1003 1275 7.401060 TGTATCACTATAAAATCCCCCATGT 57.599 36.000 0.00 0.00 0.00 3.21
1115 1387 1.450531 GGCTCGGATTTGGGCTCATG 61.451 60.000 0.00 0.00 0.00 3.07
1136 1408 8.553459 TCATGTAGTCATCTTTTCTTTCCTTC 57.447 34.615 0.00 0.00 31.15 3.46
1145 1417 7.499232 TCATCTTTTCTTTCCTTCTTCGTTCTT 59.501 33.333 0.00 0.00 0.00 2.52
1226 1498 7.014038 GGTTCTCAATGATTGGATGCTCTAATT 59.986 37.037 5.20 0.00 27.21 1.40
1366 1638 7.552687 TGGTTTCATTATCCACATCAGTAACTC 59.447 37.037 0.00 0.00 0.00 3.01
1385 1657 5.475273 ACTCGAAATATCTGACGAACGTA 57.525 39.130 0.00 0.00 34.50 3.57
1464 1736 4.883585 GGCCTCAACATGTTCATCATAGAA 59.116 41.667 8.48 0.00 34.67 2.10
1617 1889 2.499205 CTTGCGGCCGTCCTCATA 59.501 61.111 28.70 6.16 0.00 2.15
1701 1973 1.484240 AGTCAGGTGAGCTATCTTGGC 59.516 52.381 0.00 0.00 0.00 4.52
1914 2186 7.472543 CATGGTTGTTGTTATAGGTAAAGCTC 58.527 38.462 0.00 0.00 0.00 4.09
1958 2230 8.002984 AGTGCAATGAATACATTTGATGATGA 57.997 30.769 0.00 0.00 43.17 2.92
2073 2345 4.698583 ACACTAGTTATCTGACACGTCC 57.301 45.455 0.00 0.00 0.00 4.79
2162 2434 6.040166 AGCAAATTGGGCTATCAATCTTAGTG 59.960 38.462 3.21 0.00 40.47 2.74
2360 2636 4.801891 TCAGTAGCTACACCAAACTAACG 58.198 43.478 25.28 0.00 0.00 3.18
2368 2644 2.218603 CACCAAACTAACGGTTGCTCT 58.781 47.619 3.07 0.00 38.29 4.09
2369 2645 2.032030 CACCAAACTAACGGTTGCTCTG 60.032 50.000 3.07 0.00 38.29 3.35
2386 2662 6.425210 TGCTCTGCTATTATCCTATGTGTT 57.575 37.500 0.00 0.00 0.00 3.32
2493 2769 5.186409 AGGCACGACACTAAATTACTTCCTA 59.814 40.000 0.00 0.00 0.00 2.94
2499 2775 8.529476 ACGACACTAAATTACTTCCTAGACAAT 58.471 33.333 0.00 0.00 0.00 2.71
2510 2786 4.200838 TCCTAGACAATCGCATCAACAA 57.799 40.909 0.00 0.00 0.00 2.83
2645 2921 8.581578 CACAAATACCTACAAACTTGGGTAAAT 58.418 33.333 0.00 0.00 37.77 1.40
2646 2922 8.799367 ACAAATACCTACAAACTTGGGTAAATC 58.201 33.333 0.00 0.00 37.77 2.17
2666 2942 2.031120 CCTTCCCACTTTCTTGCACAA 58.969 47.619 0.00 0.00 0.00 3.33
2700 2980 6.128634 GGTCTAACTGAAACATCTTAACCACG 60.129 42.308 0.00 0.00 0.00 4.94
2881 3183 1.321474 ACTGGCACTGTTGATGTTGG 58.679 50.000 0.00 0.00 37.12 3.77
3054 3371 6.420903 ACTGTAATTCCGTCATACAATCATCG 59.579 38.462 0.00 0.00 0.00 3.84
3100 3438 4.989279 TGATCTTTGCCCTAAATCTTGC 57.011 40.909 0.00 0.00 0.00 4.01
3101 3439 4.343231 TGATCTTTGCCCTAAATCTTGCA 58.657 39.130 0.00 0.00 0.00 4.08
3173 4814 2.301296 AGACCACTGAACTGATCTGGTG 59.699 50.000 5.35 3.18 36.88 4.17
3447 5095 3.636153 AAGTCATCCTTCAAGGCCTAC 57.364 47.619 5.16 0.00 34.61 3.18
3593 5426 7.363443 GGTTTGTCCAATTAATGCTTAGCCTTA 60.363 37.037 0.29 0.00 35.97 2.69
3595 5428 7.710676 TGTCCAATTAATGCTTAGCCTTAAA 57.289 32.000 16.16 0.72 33.79 1.52
3811 5655 1.679139 CAGGTCACAGGAGCACAAAA 58.321 50.000 0.00 0.00 43.97 2.44
3819 5663 3.504906 CACAGGAGCACAAAATGATCTGT 59.495 43.478 0.00 0.00 43.64 3.41
3821 5665 4.586001 ACAGGAGCACAAAATGATCTGTTT 59.414 37.500 0.00 0.00 43.64 2.83
3847 5691 6.712547 CCCCATCCTTTCATCAGTTATTCTAC 59.287 42.308 0.00 0.00 0.00 2.59
3848 5692 6.712547 CCCATCCTTTCATCAGTTATTCTACC 59.287 42.308 0.00 0.00 0.00 3.18
3854 5698 7.201679 CCTTTCATCAGTTATTCTACCTTGCAG 60.202 40.741 0.00 0.00 0.00 4.41
3860 5704 5.645497 CAGTTATTCTACCTTGCAGCTCTTT 59.355 40.000 0.00 0.00 0.00 2.52
4002 5846 5.777802 TGTACATAACCACAAAAATGGCAG 58.222 37.500 0.00 0.00 44.33 4.85
4066 5921 5.576447 AAAAGGATGTGTTGTTCGTTCTT 57.424 34.783 0.00 0.00 0.00 2.52
4136 5991 7.701078 TGCTACGAAAGATCACTATGAAGTTAC 59.299 37.037 0.00 0.00 31.97 2.50
4233 6094 7.524912 TGTTGCTACTAAGTAAACTACTCGAG 58.475 38.462 11.84 11.84 38.26 4.04
4275 6136 6.375174 TCTCATTTGTGAACAGGATAACATGG 59.625 38.462 0.00 0.00 31.68 3.66
4298 6159 6.619852 TGGTATATTTTCCTTTCCTCCTAGCT 59.380 38.462 0.00 0.00 0.00 3.32
4299 6160 7.162761 GGTATATTTTCCTTTCCTCCTAGCTC 58.837 42.308 0.00 0.00 0.00 4.09
4300 6161 4.511786 ATTTTCCTTTCCTCCTAGCTCC 57.488 45.455 0.00 0.00 0.00 4.70
4301 6162 1.880941 TTCCTTTCCTCCTAGCTCCC 58.119 55.000 0.00 0.00 0.00 4.30
4302 6163 0.397254 TCCTTTCCTCCTAGCTCCCG 60.397 60.000 0.00 0.00 0.00 5.14
4303 6164 0.688087 CCTTTCCTCCTAGCTCCCGT 60.688 60.000 0.00 0.00 0.00 5.28
4304 6165 0.461961 CTTTCCTCCTAGCTCCCGTG 59.538 60.000 0.00 0.00 0.00 4.94
4305 6166 0.976073 TTTCCTCCTAGCTCCCGTGG 60.976 60.000 0.00 0.00 0.00 4.94
4306 6167 1.870941 TTCCTCCTAGCTCCCGTGGA 61.871 60.000 0.00 0.00 0.00 4.02
4307 6168 1.381327 CCTCCTAGCTCCCGTGGAA 60.381 63.158 0.00 0.00 0.00 3.53
4308 6169 1.677637 CCTCCTAGCTCCCGTGGAAC 61.678 65.000 0.00 0.00 0.00 3.62
4309 6170 0.684805 CTCCTAGCTCCCGTGGAACT 60.685 60.000 0.00 2.16 32.45 3.01
4310 6171 0.683504 TCCTAGCTCCCGTGGAACTC 60.684 60.000 0.00 0.00 30.18 3.01
4311 6172 1.677637 CCTAGCTCCCGTGGAACTCC 61.678 65.000 0.00 0.00 30.18 3.85
4312 6173 1.677637 CTAGCTCCCGTGGAACTCCC 61.678 65.000 0.00 0.00 30.18 4.30
4313 6174 2.164332 TAGCTCCCGTGGAACTCCCT 62.164 60.000 0.00 0.00 30.18 4.20
4314 6175 3.020237 GCTCCCGTGGAACTCCCTC 62.020 68.421 0.00 0.00 35.38 4.30
4315 6176 2.284405 TCCCGTGGAACTCCCTCC 60.284 66.667 0.00 0.00 35.38 4.30
4316 6177 3.400054 CCCGTGGAACTCCCTCCC 61.400 72.222 0.00 0.00 34.22 4.30
4317 6178 3.400054 CCGTGGAACTCCCTCCCC 61.400 72.222 0.00 0.00 34.22 4.81
4318 6179 3.400054 CGTGGAACTCCCTCCCCC 61.400 72.222 0.00 0.00 34.22 5.40
4319 6180 2.125225 GTGGAACTCCCTCCCCCT 59.875 66.667 0.00 0.00 34.22 4.79
4320 6181 1.541620 GTGGAACTCCCTCCCCCTT 60.542 63.158 0.00 0.00 34.22 3.95
4321 6182 1.229853 TGGAACTCCCTCCCCCTTC 60.230 63.158 0.00 0.00 34.22 3.46
4322 6183 2.001838 GGAACTCCCTCCCCCTTCC 61.002 68.421 0.00 0.00 0.00 3.46
4323 6184 2.001838 GAACTCCCTCCCCCTTCCC 61.002 68.421 0.00 0.00 0.00 3.97
4324 6185 3.598173 AACTCCCTCCCCCTTCCCC 62.598 68.421 0.00 0.00 0.00 4.81
4325 6186 4.845307 CTCCCTCCCCCTTCCCCC 62.845 77.778 0.00 0.00 0.00 5.40
4339 6200 4.778143 CCCCACCGCCTCCGAAAG 62.778 72.222 0.00 0.00 36.29 2.62
4450 6343 2.379634 GCCAAAACCCAAATCGCGC 61.380 57.895 0.00 0.00 0.00 6.86
4484 6381 1.528292 TTACGGCCCAAATTTGCGCT 61.528 50.000 23.21 10.41 32.76 5.92
4511 6409 3.060020 ATCGACGCGGACACGGAAT 62.060 57.895 12.47 0.00 41.36 3.01
4753 6680 2.659063 CCACCACAGCGAGATGGGA 61.659 63.158 0.00 0.00 40.59 4.37
4764 6692 1.747552 CGAGATGGGACTCTTCTCCGA 60.748 57.143 11.58 0.00 41.17 4.55
4835 6763 1.609794 GAGTTCCTCCCACCTCCGT 60.610 63.158 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 8.537728 TGATTAATTAATCAGGCACTCCATTT 57.462 30.769 28.93 0.00 45.03 2.32
120 121 7.436933 AGCTGATGATACACGAGAATTGATTA 58.563 34.615 0.00 0.00 0.00 1.75
124 125 5.045872 TGAGCTGATGATACACGAGAATTG 58.954 41.667 0.00 0.00 0.00 2.32
200 220 7.752686 CGTGTCCTCTCTGTGTTGATATATATG 59.247 40.741 0.00 0.00 0.00 1.78
212 234 2.509052 TGAAACGTGTCCTCTCTGTG 57.491 50.000 2.58 0.00 0.00 3.66
226 248 7.707104 TCTTCCTTGAAAGAACTCAATGAAAC 58.293 34.615 5.83 0.00 38.58 2.78
227 249 7.775093 TCTCTTCCTTGAAAGAACTCAATGAAA 59.225 33.333 5.83 0.00 38.58 2.69
229 251 6.830912 TCTCTTCCTTGAAAGAACTCAATGA 58.169 36.000 0.00 0.00 34.95 2.57
371 638 2.289274 CGCACAACAGTTTGTCCATGTA 59.711 45.455 0.00 0.00 44.57 2.29
391 658 4.022329 ACCTTGCCAAAATAAAGAGAACCG 60.022 41.667 0.00 0.00 0.00 4.44
421 688 2.424601 ACATGGATCCAACAATTCAGCG 59.575 45.455 20.67 0.06 0.00 5.18
424 691 3.444742 GCTCACATGGATCCAACAATTCA 59.555 43.478 20.67 0.00 0.00 2.57
430 697 2.408271 TGAGCTCACATGGATCCAAC 57.592 50.000 20.67 4.41 0.00 3.77
478 745 2.323939 TTATTGCTTCACAAACGCGG 57.676 45.000 12.47 0.00 42.86 6.46
522 789 3.568007 TGAATCTTGTCCTTTTTGTCCCG 59.432 43.478 0.00 0.00 0.00 5.14
531 802 1.425066 TGGGCACTGAATCTTGTCCTT 59.575 47.619 7.42 0.00 38.41 3.36
664 935 6.952773 ATGTAAGCAGGAGAAGTAGAGTAG 57.047 41.667 0.00 0.00 0.00 2.57
711 982 6.806249 TCAAATCGTGAAAATGAAACCTATGC 59.194 34.615 0.00 0.00 31.51 3.14
721 992 7.375781 GCGAACTAAATCAAATCGTGAAAATG 58.624 34.615 0.00 0.00 40.50 2.32
729 1000 3.061563 TCCACGCGAACTAAATCAAATCG 59.938 43.478 15.93 0.00 36.64 3.34
741 1012 0.949105 ACAATGACCTCCACGCGAAC 60.949 55.000 15.93 0.00 0.00 3.95
854 1126 0.179000 ACGGAGATCACCAATGGAGC 59.821 55.000 6.16 0.00 0.00 4.70
887 1159 5.536161 ACTCACACAGCTATTGGAAATTTGT 59.464 36.000 0.00 0.00 0.00 2.83
1003 1275 1.917495 CCAGAGCATGGTCCATGGA 59.083 57.895 29.17 11.44 44.91 3.41
1115 1387 7.385478 ACGAAGAAGGAAAGAAAAGATGACTAC 59.615 37.037 0.00 0.00 0.00 2.73
1136 1408 7.493971 ACAGATGAGATTATCCAAAGAACGAAG 59.506 37.037 0.00 0.00 0.00 3.79
1145 1417 7.720957 CCAATTACCACAGATGAGATTATCCAA 59.279 37.037 0.00 0.00 0.00 3.53
1242 1514 4.827284 CAGGGCAGAAAAGAAGGAAAACTA 59.173 41.667 0.00 0.00 0.00 2.24
1355 1627 7.132863 TCGTCAGATATTTCGAGTTACTGATG 58.867 38.462 16.92 16.92 39.63 3.07
1366 1638 7.377832 AGAATTACGTTCGTCAGATATTTCG 57.622 36.000 0.00 0.00 41.84 3.46
1385 1657 3.565307 TCTTCAACCACCTGCAAGAATT 58.435 40.909 0.00 0.00 34.07 2.17
1464 1736 3.224007 AATGGCGCCCCCTTTGTCT 62.224 57.895 26.77 0.00 30.34 3.41
1701 1973 1.256812 ATCCCCAAGTTTTTCCTGCG 58.743 50.000 0.00 0.00 0.00 5.18
1914 2186 7.101652 TGCACTTTAAGTAGTAGAGGAGATG 57.898 40.000 0.00 0.00 0.00 2.90
1958 2230 8.297426 CACATGCATCATCAGAAGCTAAATAAT 58.703 33.333 0.00 0.00 39.15 1.28
1965 2237 3.206964 CTCACATGCATCATCAGAAGCT 58.793 45.455 0.00 0.00 39.15 3.74
2013 2285 7.770897 CCCCTCCAGTAATGCTTATATATGAAC 59.229 40.741 0.00 0.00 0.00 3.18
2032 2304 4.953579 GTGTTAAATAATTGAGCCCCTCCA 59.046 41.667 0.00 0.00 0.00 3.86
2162 2434 5.679734 TTTGAATCTTGTGAAGTGAGCTC 57.320 39.130 6.82 6.82 0.00 4.09
2246 2520 6.017687 CAGACTGCGATGGAATTCAATGAATA 60.018 38.462 9.09 0.00 31.46 1.75
2284 2560 6.601613 AGTTTGTTGTCCTCTTATTGTGAACA 59.398 34.615 0.00 0.00 0.00 3.18
2360 2636 5.641209 CACATAGGATAATAGCAGAGCAACC 59.359 44.000 0.00 0.00 0.00 3.77
2368 2644 9.020731 TCGATTAGAACACATAGGATAATAGCA 57.979 33.333 0.00 0.00 0.00 3.49
2369 2645 9.856488 TTCGATTAGAACACATAGGATAATAGC 57.144 33.333 0.00 0.00 33.14 2.97
2386 2662 3.973206 TGCCTTGGTTCTTCGATTAGA 57.027 42.857 0.00 0.00 0.00 2.10
2399 2675 0.104671 CGGCCCATAATTTGCCTTGG 59.895 55.000 0.00 0.00 43.12 3.61
2401 2677 0.687427 AGCGGCCCATAATTTGCCTT 60.687 50.000 0.00 0.00 43.12 4.35
2402 2678 0.687427 AAGCGGCCCATAATTTGCCT 60.687 50.000 0.00 0.00 43.12 4.75
2493 2769 1.470098 GCCTTGTTGATGCGATTGTCT 59.530 47.619 0.00 0.00 0.00 3.41
2499 2775 0.321346 TCTCTGCCTTGTTGATGCGA 59.679 50.000 0.00 0.00 0.00 5.10
2510 2786 3.328931 TCCAGTGAAAAGAATCTCTGCCT 59.671 43.478 0.00 0.00 38.81 4.75
2645 2921 1.214175 TGTGCAAGAAAGTGGGAAGGA 59.786 47.619 0.00 0.00 0.00 3.36
2646 2922 1.691196 TGTGCAAGAAAGTGGGAAGG 58.309 50.000 0.00 0.00 0.00 3.46
2672 2948 3.678056 AGATGTTTCAGTTAGACCGCA 57.322 42.857 0.00 0.00 0.00 5.69
2673 2949 5.163884 GGTTAAGATGTTTCAGTTAGACCGC 60.164 44.000 0.00 0.00 0.00 5.68
2674 2950 5.929992 TGGTTAAGATGTTTCAGTTAGACCG 59.070 40.000 0.00 0.00 0.00 4.79
2700 2980 5.449304 CACCGAACAGATCCAAGTTAAAAC 58.551 41.667 0.00 0.00 0.00 2.43
2711 2991 1.200020 CCCAAAAGCACCGAACAGATC 59.800 52.381 0.00 0.00 0.00 2.75
2719 2999 1.595093 GATGGACCCCAAAAGCACCG 61.595 60.000 0.00 0.00 36.95 4.94
2843 3143 6.260714 TGCCAGTAGTTCATACAATTATGCAG 59.739 38.462 0.00 0.00 35.86 4.41
3095 3433 4.338964 TGCTTCTCTGTTTTGAATGCAAGA 59.661 37.500 0.00 0.00 35.04 3.02
3100 3438 8.752766 ACAATTATGCTTCTCTGTTTTGAATG 57.247 30.769 0.00 0.00 0.00 2.67
3101 3439 8.579006 TGACAATTATGCTTCTCTGTTTTGAAT 58.421 29.630 0.00 0.00 0.00 2.57
3173 4814 9.678941 CAAATACCTGGAAAAGTAAGAAGTTTC 57.321 33.333 0.00 0.00 0.00 2.78
3447 5095 0.329261 TGCCTTCCCAGTCATTCAGG 59.671 55.000 0.00 0.00 0.00 3.86
3677 5521 3.891366 CCAAATAGCAGGATACCCCAAAG 59.109 47.826 0.00 0.00 37.41 2.77
3811 5655 4.017222 TGAAAGGATGGGGAAACAGATCAT 60.017 41.667 0.00 0.00 0.00 2.45
3819 5663 4.402616 AACTGATGAAAGGATGGGGAAA 57.597 40.909 0.00 0.00 0.00 3.13
3821 5665 5.433051 AGAATAACTGATGAAAGGATGGGGA 59.567 40.000 0.00 0.00 0.00 4.81
3897 5741 1.059584 TGGTCAAGGGCTCAAGTCCA 61.060 55.000 3.04 0.00 43.78 4.02
4002 5846 9.229784 CACTAACTTGAAATATGCATCAACATC 57.770 33.333 0.19 0.00 32.46 3.06
4136 5991 7.221452 GCTAAACTGCATCCAAATCAAACATAG 59.779 37.037 0.00 0.00 0.00 2.23
4233 6094 4.754372 TGAGATGTCAATTTGTGCAGAC 57.246 40.909 0.00 0.00 0.00 3.51
4275 6136 7.162761 GGAGCTAGGAGGAAAGGAAAATATAC 58.837 42.308 0.00 0.00 0.00 1.47
4298 6159 2.284405 GGAGGGAGTTCCACGGGA 60.284 66.667 0.00 0.00 37.20 5.14
4299 6160 3.400054 GGGAGGGAGTTCCACGGG 61.400 72.222 0.00 0.00 39.09 5.28
4300 6161 3.400054 GGGGAGGGAGTTCCACGG 61.400 72.222 0.00 0.00 39.09 4.94
4301 6162 3.400054 GGGGGAGGGAGTTCCACG 61.400 72.222 0.00 0.00 41.84 4.94
4302 6163 1.541620 AAGGGGGAGGGAGTTCCAC 60.542 63.158 0.00 0.00 40.09 4.02
4303 6164 1.229853 GAAGGGGGAGGGAGTTCCA 60.230 63.158 0.00 0.00 39.09 3.53
4304 6165 2.001838 GGAAGGGGGAGGGAGTTCC 61.002 68.421 0.00 0.00 36.46 3.62
4305 6166 2.001838 GGGAAGGGGGAGGGAGTTC 61.002 68.421 0.00 0.00 0.00 3.01
4306 6167 2.127528 GGGAAGGGGGAGGGAGTT 59.872 66.667 0.00 0.00 0.00 3.01
4307 6168 4.040198 GGGGAAGGGGGAGGGAGT 62.040 72.222 0.00 0.00 0.00 3.85
4308 6169 4.845307 GGGGGAAGGGGGAGGGAG 62.845 77.778 0.00 0.00 0.00 4.30
4322 6183 4.778143 CTTTCGGAGGCGGTGGGG 62.778 72.222 0.00 0.00 0.00 4.96
4323 6184 4.778143 CCTTTCGGAGGCGGTGGG 62.778 72.222 0.00 0.00 39.09 4.61
4343 6204 3.685214 CTCTCACTTCGTCCGGCGG 62.685 68.421 22.51 22.51 41.72 6.13
4344 6205 2.202492 CTCTCACTTCGTCCGGCG 60.202 66.667 11.37 11.37 43.01 6.46
4345 6206 2.507324 GCTCTCACTTCGTCCGGC 60.507 66.667 0.00 0.00 0.00 6.13
4346 6207 1.009389 GTTGCTCTCACTTCGTCCGG 61.009 60.000 0.00 0.00 0.00 5.14
4347 6208 0.039074 AGTTGCTCTCACTTCGTCCG 60.039 55.000 0.00 0.00 0.00 4.79
4348 6209 2.062519 GAAGTTGCTCTCACTTCGTCC 58.937 52.381 0.00 0.00 31.96 4.79
4349 6210 2.743938 TGAAGTTGCTCTCACTTCGTC 58.256 47.619 8.00 0.00 41.81 4.20
4350 6211 2.890808 TGAAGTTGCTCTCACTTCGT 57.109 45.000 8.00 0.00 41.81 3.85
4351 6212 3.120408 CCATTGAAGTTGCTCTCACTTCG 60.120 47.826 8.00 0.00 41.81 3.79
4352 6213 3.190118 CCCATTGAAGTTGCTCTCACTTC 59.810 47.826 5.96 5.96 39.99 3.01
4353 6214 3.152341 CCCATTGAAGTTGCTCTCACTT 58.848 45.455 0.00 0.00 0.00 3.16
4354 6215 2.553904 CCCCATTGAAGTTGCTCTCACT 60.554 50.000 0.00 0.00 0.00 3.41
4355 6216 1.815003 CCCCATTGAAGTTGCTCTCAC 59.185 52.381 0.00 0.00 0.00 3.51
4432 6303 2.379634 GCGCGATTTGGGTTTTGGC 61.380 57.895 12.10 0.00 0.00 4.52
4435 6306 2.654289 GGGCGCGATTTGGGTTTT 59.346 55.556 12.10 0.00 0.00 2.43
4450 6343 2.202824 TAAATGCGTCGGAGCGGG 60.203 61.111 0.00 0.00 40.67 6.13
4484 6381 2.460275 CCGCGTCGATGCATTTGGA 61.460 57.895 27.92 0.00 34.15 3.53
4639 6548 2.736682 CCGCACGGTCGGCTTAAAG 61.737 63.158 0.00 0.00 43.18 1.85
4660 6569 1.811558 CGATTTGGATGAGGACGGCAT 60.812 52.381 0.00 0.00 0.00 4.40
4661 6570 0.461870 CGATTTGGATGAGGACGGCA 60.462 55.000 0.00 0.00 0.00 5.69
4710 6627 3.599285 CTAGGGTTTGCCGGCGACA 62.599 63.158 27.40 13.29 34.97 4.35
4753 6680 2.995872 GCTGGCGTCGGAGAAGAGT 61.996 63.158 0.00 0.00 38.59 3.24
4798 6726 2.776536 CTCTGATGGGAAAGGGATGACT 59.223 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.