Multiple sequence alignment - TraesCS6D01G185500

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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 TraesCS6D01G185500 chr6D 100.000 8878 0 0 1 8878 239051298 239042421 0.000000e+00 16395.0
1 TraesCS6D01G185500 chr6D 91.533 437 34 3 8443 8876 238991849 238991413 4.590000e-167 599.0
2 TraesCS6D01G185500 chr6D 90.800 250 22 1 75 323 325821258 325821009 5.140000e-87 333.0
3 TraesCS6D01G185500 chr6D 89.256 242 26 0 386 627 325820896 325820655 4.030000e-78 303.0
4 TraesCS6D01G185500 chr6B 97.086 4050 71 13 820 4853 376301637 376297619 0.000000e+00 6782.0
5 TraesCS6D01G185500 chr6B 96.694 1603 41 6 6367 7964 376294120 376292525 0.000000e+00 2656.0
6 TraesCS6D01G185500 chr6B 93.750 896 37 13 7925 8807 376292531 376291642 0.000000e+00 1327.0
7 TraesCS6D01G185500 chr6B 96.467 736 25 1 4853 5588 376296602 376295868 0.000000e+00 1214.0
8 TraesCS6D01G185500 chr6B 94.307 527 20 2 5581 6107 376295839 376295323 0.000000e+00 798.0
9 TraesCS6D01G185500 chr6B 90.414 459 10 2 5817 6275 376294564 376294140 2.780000e-159 573.0
10 TraesCS6D01G185500 chr6B 93.059 389 11 2 6331 6715 376294940 376294564 1.010000e-153 555.0
11 TraesCS6D01G185500 chr6B 91.200 250 21 1 75 323 496986726 496986975 1.100000e-88 339.0
12 TraesCS6D01G185500 chr6B 83.590 195 22 8 8255 8444 76773723 76773912 3.290000e-39 174.0
13 TraesCS6D01G185500 chr6B 97.727 88 2 0 6189 6276 376295323 376295236 1.540000e-32 152.0
14 TraesCS6D01G185500 chr6A 97.768 3270 52 10 826 4074 319209018 319205749 0.000000e+00 5614.0
15 TraesCS6D01G185500 chr6A 96.213 2852 60 9 5579 8424 319203621 319200812 0.000000e+00 4625.0
16 TraesCS6D01G185500 chr6A 95.455 836 20 6 4753 5588 319204465 319203648 0.000000e+00 1317.0
17 TraesCS6D01G185500 chr6A 97.869 610 6 3 4060 4666 319205613 319205008 0.000000e+00 1048.0
18 TraesCS6D01G185500 chr6A 96.703 364 12 0 8348 8711 319200814 319200451 2.740000e-169 606.0
19 TraesCS6D01G185500 chr6A 93.966 348 21 0 8443 8790 319163383 319163036 2.200000e-145 527.0
20 TraesCS6D01G185500 chr6A 90.000 250 24 1 75 323 464690804 464690555 1.110000e-83 322.0
21 TraesCS6D01G185500 chr6A 89.256 242 26 0 386 627 464690442 464690201 4.030000e-78 303.0
22 TraesCS6D01G185500 chr6A 98.077 104 2 0 4667 4770 319204750 319204647 1.970000e-41 182.0
23 TraesCS6D01G185500 chr7B 97.768 1299 29 0 2616 3914 530662812 530664110 0.000000e+00 2239.0
24 TraesCS6D01G185500 chr7B 96.275 349 13 0 2272 2620 530652509 530652857 2.780000e-159 573.0
25 TraesCS6D01G185500 chr7B 89.024 164 18 0 3452 3615 78318808 78318645 4.200000e-48 204.0
26 TraesCS6D01G185500 chr3B 89.571 700 64 5 3047 3741 312485401 312486096 0.000000e+00 880.0
27 TraesCS6D01G185500 chr3B 92.391 276 20 1 8443 8717 257324588 257324313 8.360000e-105 392.0
28 TraesCS6D01G185500 chr3B 86.520 319 40 3 8431 8747 338470066 338470383 1.830000e-91 348.0
29 TraesCS6D01G185500 chr2D 79.656 1047 179 25 2549 3571 398464498 398465534 0.000000e+00 723.0
30 TraesCS6D01G185500 chr2D 74.812 532 99 20 7078 7599 398467154 398467660 3.250000e-49 207.0
31 TraesCS6D01G185500 chr2D 91.870 123 9 1 8323 8444 572056382 572056260 4.260000e-38 171.0
32 TraesCS6D01G185500 chr2D 91.870 123 9 1 8323 8444 641085759 641085881 4.260000e-38 171.0
33 TraesCS6D01G185500 chr2D 100.000 35 0 0 3707 3741 607128257 607128223 2.070000e-06 65.8
34 TraesCS6D01G185500 chr2B 79.274 1047 182 26 2549 3571 471444986 471443951 0.000000e+00 699.0
35 TraesCS6D01G185500 chr2B 90.196 306 29 1 8443 8747 237468136 237468441 1.800000e-106 398.0
36 TraesCS6D01G185500 chr2B 76.306 536 100 19 7078 7598 471442182 471441659 2.460000e-65 261.0
37 TraesCS6D01G185500 chr2B 100.000 35 0 0 3707 3741 622490599 622490633 2.070000e-06 65.8
38 TraesCS6D01G185500 chr2A 78.797 1047 188 25 2549 3571 535712408 535713444 0.000000e+00 673.0
39 TraesCS6D01G185500 chr2A 87.574 507 44 11 323 813 535217798 535217295 3.600000e-158 569.0
40 TraesCS6D01G185500 chr2A 88.372 301 33 2 8443 8742 623683583 623683882 2.360000e-95 361.0
41 TraesCS6D01G185500 chr2A 75.763 557 117 9 7051 7598 535715362 535715909 1.900000e-66 265.0
42 TraesCS6D01G185500 chr3A 85.979 485 53 12 324 800 648104504 648104981 1.030000e-138 505.0
43 TraesCS6D01G185500 chr3A 93.519 324 20 1 1 323 648104137 648104460 1.730000e-131 481.0
44 TraesCS6D01G185500 chr1B 84.961 512 47 14 323 809 193289066 193289572 8.010000e-135 492.0
45 TraesCS6D01G185500 chr1A 84.533 375 56 2 8434 8807 75748335 75748708 3.920000e-98 370.0
46 TraesCS6D01G185500 chr5B 84.167 240 38 0 388 627 579515149 579515388 5.360000e-57 233.0
47 TraesCS6D01G185500 chr5B 80.282 142 10 7 323 448 690230857 690230996 3.410000e-14 91.6
48 TraesCS6D01G185500 chr4A 92.063 126 9 1 8310 8434 49222386 49222511 9.160000e-40 176.0
49 TraesCS6D01G185500 chr3D 91.870 123 9 1 8323 8444 346965719 346965841 4.260000e-38 171.0
50 TraesCS6D01G185500 chr1D 91.870 123 9 1 8323 8444 166626050 166626172 4.260000e-38 171.0


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 TraesCS6D01G185500 chr6D 239042421 239051298 8877 True 16395.000 16395 100.000000 1 8878 1 chr6D.!!$R2 8877
1 TraesCS6D01G185500 chr6D 325820655 325821258 603 True 318.000 333 90.028000 75 627 2 chr6D.!!$R3 552
2 TraesCS6D01G185500 chr6B 376291642 376301637 9995 True 1757.125 6782 94.938000 820 8807 8 chr6B.!!$R1 7987
3 TraesCS6D01G185500 chr6A 319200451 319209018 8567 True 2232.000 5614 97.014167 826 8711 6 chr6A.!!$R2 7885
4 TraesCS6D01G185500 chr6A 464690201 464690804 603 True 312.500 322 89.628000 75 627 2 chr6A.!!$R3 552
5 TraesCS6D01G185500 chr7B 530662812 530664110 1298 False 2239.000 2239 97.768000 2616 3914 1 chr7B.!!$F2 1298
6 TraesCS6D01G185500 chr3B 312485401 312486096 695 False 880.000 880 89.571000 3047 3741 1 chr3B.!!$F1 694
7 TraesCS6D01G185500 chr2D 398464498 398467660 3162 False 465.000 723 77.234000 2549 7599 2 chr2D.!!$F2 5050
8 TraesCS6D01G185500 chr2B 471441659 471444986 3327 True 480.000 699 77.790000 2549 7598 2 chr2B.!!$R1 5049
9 TraesCS6D01G185500 chr2A 535217295 535217798 503 True 569.000 569 87.574000 323 813 1 chr2A.!!$R1 490
10 TraesCS6D01G185500 chr2A 535712408 535715909 3501 False 469.000 673 77.280000 2549 7598 2 chr2A.!!$F2 5049
11 TraesCS6D01G185500 chr3A 648104137 648104981 844 False 493.000 505 89.749000 1 800 2 chr3A.!!$F1 799
12 TraesCS6D01G185500 chr1B 193289066 193289572 506 False 492.000 492 84.961000 323 809 1 chr1B.!!$F1 486

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
527 595 0.184451 GGCCACATCCCAGTCATCAT 59.816 55.000 0.00 0.00 0.00 2.45 F
573 641 0.324943 AGGCCTACAACATCAACGCT 59.675 50.000 1.29 0.00 0.00 5.07 F
802 881 0.840722 CACTTAGTCCCACCCCCACT 60.841 60.000 0.00 0.00 0.00 4.00 F
2120 2238 0.868406 GCTACAGTTGTGGTGTCTGC 59.132 55.000 0.00 0.00 33.12 4.26 F
2415 2533 1.065854 CCAAGTTGGGTCCTGCTAGAG 60.066 57.143 14.64 0.00 32.67 2.43 F
3748 4621 1.474478 AGTGTATCACTCAGACTGGCG 59.526 52.381 1.81 0.00 41.21 5.69 F
5496 8160 0.749818 AACAACGGTGTGCATGGACA 60.750 50.000 16.89 16.89 38.27 4.02 F
5757 8457 1.133325 AGGCACTCTAGGATCATCGGT 60.133 52.381 0.00 0.00 0.00 4.69 F
7052 11019 1.251251 ATCTGGCAGCAAGAAACACC 58.749 50.000 10.34 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1661 2.420022 CCAAGTTCCAATCCTACGCTTG 59.580 50.000 0.00 0.00 33.70 4.01 R
1547 1665 2.629051 GGTCCAAGTTCCAATCCTACG 58.371 52.381 0.00 0.00 0.00 3.51 R
2357 2475 3.046390 CTCTTCGCTTACCTATTCGCAG 58.954 50.000 0.00 0.00 0.00 5.18 R
3748 4621 1.753956 GGTGAACATGTTGAACACGC 58.246 50.000 17.58 7.51 31.94 5.34 R
4032 5054 5.682943 ACGCAAAATGTTTAGAGCTAACA 57.317 34.783 3.12 3.12 0.00 2.41 R
5613 8313 0.108662 CTAGTCCACGCACATGCTCA 60.109 55.000 1.82 0.00 39.32 4.26 R
7430 11409 1.279271 GAAGGTGACTGCATGTAGGGT 59.721 52.381 15.65 0.00 42.68 4.34 R
7484 11466 4.660938 ACGGCTTTCCCAGGTGGC 62.661 66.667 0.00 0.00 0.00 5.01 R
8810 12914 0.036010 ACAGCCGTTCATCCTGAAGG 60.036 55.000 3.26 3.26 40.71 3.46 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
25 26 1.059692 CAACAGCTACATTGCGTCTCG 59.940 52.381 0.00 0.00 38.13 4.04
98 99 4.374702 CGTGGTGCTGAACTGCGC 62.375 66.667 0.00 0.00 42.15 6.09
154 155 1.583054 GTTCAAGAGCAAGACGGTGT 58.417 50.000 0.00 0.00 0.00 4.16
167 168 0.746063 ACGGTGTTGGTGAAGTACGA 59.254 50.000 0.00 0.00 0.00 3.43
357 409 4.159321 TCAGCAAGGTCAACATCAACAAAA 59.841 37.500 0.00 0.00 0.00 2.44
375 427 1.603236 AAGCAGCTCGTCTCCCTCAG 61.603 60.000 0.00 0.00 0.00 3.35
378 430 2.183046 GCTCGTCTCCCTCAGCAC 59.817 66.667 0.00 0.00 0.00 4.40
379 431 2.347322 GCTCGTCTCCCTCAGCACT 61.347 63.158 0.00 0.00 0.00 4.40
380 432 1.032657 GCTCGTCTCCCTCAGCACTA 61.033 60.000 0.00 0.00 0.00 2.74
381 433 1.021202 CTCGTCTCCCTCAGCACTAG 58.979 60.000 0.00 0.00 0.00 2.57
405 473 2.031012 CTCTGTGGCAAGGACGCA 59.969 61.111 0.00 0.00 0.00 5.24
526 594 1.609239 GGCCACATCCCAGTCATCA 59.391 57.895 0.00 0.00 0.00 3.07
527 595 0.184451 GGCCACATCCCAGTCATCAT 59.816 55.000 0.00 0.00 0.00 2.45
573 641 0.324943 AGGCCTACAACATCAACGCT 59.675 50.000 1.29 0.00 0.00 5.07
581 649 2.942376 ACAACATCAACGCTGAAACTGA 59.058 40.909 0.00 0.00 34.49 3.41
585 653 1.882912 TCAACGCTGAAACTGATGCT 58.117 45.000 0.00 0.00 0.00 3.79
601 669 2.185350 CTGTGGAGATCGCGGCTT 59.815 61.111 6.13 0.00 0.00 4.35
644 714 7.079182 TGTTGCTTTCTTTTTAGAAGACGAA 57.921 32.000 0.00 0.00 0.00 3.85
773 852 5.738619 AAACAATTTAAGTGGGATGGGAC 57.261 39.130 0.00 0.00 0.00 4.46
796 875 2.158798 GCTAATCCCACTTAGTCCCACC 60.159 54.545 0.00 0.00 32.39 4.61
802 881 0.840722 CACTTAGTCCCACCCCCACT 60.841 60.000 0.00 0.00 0.00 4.00
809 888 4.290622 CCACCCCCACTTGCAGCT 62.291 66.667 0.00 0.00 0.00 4.24
813 892 2.270986 CCCCCACTTGCAGCTTGAC 61.271 63.158 0.00 0.00 0.00 3.18
814 893 1.529010 CCCCACTTGCAGCTTGACA 60.529 57.895 0.00 0.00 0.00 3.58
815 894 0.896940 CCCCACTTGCAGCTTGACAT 60.897 55.000 0.00 0.00 0.00 3.06
816 895 1.614051 CCCCACTTGCAGCTTGACATA 60.614 52.381 0.00 0.00 0.00 2.29
817 896 1.470098 CCCACTTGCAGCTTGACATAC 59.530 52.381 0.00 0.00 0.00 2.39
818 897 1.129251 CCACTTGCAGCTTGACATACG 59.871 52.381 0.00 0.00 0.00 3.06
982 1065 2.976509 CACACTAATAGCGCAGATCTCG 59.023 50.000 11.47 9.37 0.00 4.04
1394 1507 1.071071 GTTTGGGTTTGGGGTTTAGGC 59.929 52.381 0.00 0.00 0.00 3.93
1455 1568 3.262420 CTTACCTCCATTCGGTTGAGTG 58.738 50.000 0.00 0.00 35.98 3.51
1543 1661 7.040686 TCCTTGTTTTAGTTGAATCAGTTAGGC 60.041 37.037 0.00 0.00 0.00 3.93
1547 1665 5.880054 TTAGTTGAATCAGTTAGGCAAGC 57.120 39.130 0.00 0.00 0.00 4.01
1987 2105 6.152932 TGGTTTAGATAGGGTCGATTACAC 57.847 41.667 0.00 0.00 0.00 2.90
2120 2238 0.868406 GCTACAGTTGTGGTGTCTGC 59.132 55.000 0.00 0.00 33.12 4.26
2178 2296 5.754406 TGTCTGCAACATTCTGAAATTTTGG 59.246 36.000 0.00 0.00 34.52 3.28
2415 2533 1.065854 CCAAGTTGGGTCCTGCTAGAG 60.066 57.143 14.64 0.00 32.67 2.43
2976 3094 2.596851 GGCTCAGGGTTGCCTCTGA 61.597 63.158 0.00 0.00 45.26 3.27
2999 3117 7.581476 TGATTTTTCTGAAGGTATTCGTGTTC 58.419 34.615 0.00 0.00 38.34 3.18
3013 3131 2.125633 GTTCGGGAGGCGAAGACC 60.126 66.667 0.00 0.00 31.70 3.85
3299 3424 6.152323 AGAGGTTGCGAAGTGTAAGTTCTATA 59.848 38.462 0.00 0.00 44.11 1.31
3748 4621 1.474478 AGTGTATCACTCAGACTGGCG 59.526 52.381 1.81 0.00 41.21 5.69
3865 4885 7.567250 TCAATGGATACCAAATAGACCAGTAGA 59.433 37.037 0.00 0.00 36.95 2.59
4667 6115 8.203681 TGATAGTCTGCTCAGGTAGTAGTATA 57.796 38.462 0.00 0.00 38.90 1.47
4668 6116 8.827758 TGATAGTCTGCTCAGGTAGTAGTATAT 58.172 37.037 0.00 0.00 38.90 0.86
4792 6439 1.991965 GGTGTTAATGCCACATTTGCG 59.008 47.619 0.00 0.00 34.46 4.85
4879 7543 4.396166 AGGGTGTCTCAAATGCTTAATTCG 59.604 41.667 0.00 0.00 0.00 3.34
5014 7678 1.651987 AATACACCGATTGAGCACCG 58.348 50.000 0.00 0.00 0.00 4.94
5055 7719 6.169557 ACAATACGGTGCTTAATCTATCCA 57.830 37.500 0.00 0.00 0.00 3.41
5145 7809 7.109501 TCTCTATCTCTCTCACTATGGCATAC 58.890 42.308 2.32 0.00 0.00 2.39
5196 7860 3.713826 ATAGGAACGGAAAAAGGAGCA 57.286 42.857 0.00 0.00 0.00 4.26
5232 7896 1.376086 CAGGACCTCATGTGCCACA 59.624 57.895 0.00 0.00 35.58 4.17
5462 8126 3.661648 GGGAGTGGTGGGCATGGT 61.662 66.667 0.00 0.00 0.00 3.55
5496 8160 0.749818 AACAACGGTGTGCATGGACA 60.750 50.000 16.89 16.89 38.27 4.02
5757 8457 1.133325 AGGCACTCTAGGATCATCGGT 60.133 52.381 0.00 0.00 0.00 4.69
5932 8632 4.101448 GCTGGGAGTGCCACGGAT 62.101 66.667 0.00 0.00 35.15 4.18
6324 10285 8.531982 GCAATAAGTTCCCTAAATCCTCTTTTT 58.468 33.333 0.00 0.00 0.00 1.94
6477 10438 4.101448 GCCCAGGACCGACTGCAT 62.101 66.667 0.00 0.00 37.16 3.96
6486 10447 1.447838 CCGACTGCATGTACCGCTT 60.448 57.895 6.01 0.00 0.00 4.68
6888 10850 7.284820 CACATCATGGATGCCCTTATATATGA 58.715 38.462 6.15 0.00 43.15 2.15
6889 10851 7.942894 CACATCATGGATGCCCTTATATATGAT 59.057 37.037 6.15 0.00 43.15 2.45
6890 10852 8.336801 CATCATGGATGCCCTTATATATGATG 57.663 38.462 0.00 0.00 42.06 3.07
6928 10891 3.452264 TGCTGCTTCTGGTATAGATGTGT 59.548 43.478 0.00 0.00 34.80 3.72
7052 11019 1.251251 ATCTGGCAGCAAGAAACACC 58.749 50.000 10.34 0.00 0.00 4.16
7430 11409 3.765381 TGATGATGGCTTCACTTTTCCA 58.235 40.909 5.09 0.00 37.11 3.53
7734 11716 2.450609 TGGACGAACTCCTGTTTAGC 57.549 50.000 0.00 0.00 40.26 3.09
8038 12052 8.302438 TGTTTTTCCTTTTGAATTGCATGTTTT 58.698 25.926 0.00 0.00 31.67 2.43
8054 12068 6.017852 TGCATGTTTTGTTATGTAAGACACGA 60.018 34.615 0.00 0.00 0.00 4.35
8121 12135 1.135024 CCGGGCCAACAAATGAATGAG 60.135 52.381 4.39 0.00 0.00 2.90
8127 12144 5.408299 GGGCCAACAAATGAATGAGTTTAAC 59.592 40.000 4.39 0.00 0.00 2.01
8172 12189 3.820557 AGTGAGCCACAACATAAACACT 58.179 40.909 7.86 0.00 36.74 3.55
8205 12222 1.134551 CACCCCTCTAGCTGCTCTTTC 60.135 57.143 4.91 0.00 0.00 2.62
8244 12261 6.871044 TTCATCGTCTTCTCTTTTCATACG 57.129 37.500 0.00 0.00 0.00 3.06
8505 12609 1.705873 AACCGAGGTGAACTCACTCT 58.294 50.000 9.60 5.39 46.98 3.24
8517 12621 6.761714 GGTGAACTCACTCTTACTTGAGAAAA 59.238 38.462 9.60 0.00 45.73 2.29
8540 12644 5.651612 ATATGGACATGAATGGGACTTGA 57.348 39.130 0.00 0.00 0.00 3.02
8587 12691 6.560003 ATGTGTCATTAGGTATGAAGACCA 57.440 37.500 0.00 0.00 44.62 4.02
8693 12797 3.640407 GACTGCACCTCCCAGGCA 61.640 66.667 0.00 0.00 39.63 4.75
8749 12853 1.768077 GGCTACCCAGGGAGCTGAT 60.768 63.158 20.28 0.22 38.79 2.90
8796 12900 2.874664 TACCGTGCACACAGGACCC 61.875 63.158 18.64 0.00 34.68 4.46
8797 12901 3.941188 CCGTGCACACAGGACCCT 61.941 66.667 18.64 0.00 34.68 4.34
8798 12902 2.357517 CGTGCACACAGGACCCTC 60.358 66.667 18.64 0.00 34.68 4.30
8800 12904 2.842462 TGCACACAGGACCCTCGT 60.842 61.111 0.00 0.00 0.00 4.18
8803 12907 3.991051 ACACAGGACCCTCGTGCG 61.991 66.667 14.31 0.00 35.83 5.34
8816 12920 3.414700 GTGCGCACGACCCTTCAG 61.415 66.667 26.77 0.00 0.00 3.02
8817 12921 4.680237 TGCGCACGACCCTTCAGG 62.680 66.667 5.66 0.00 43.78 3.86
8818 12922 4.373116 GCGCACGACCCTTCAGGA 62.373 66.667 0.30 0.00 39.89 3.86
8819 12923 2.579201 CGCACGACCCTTCAGGAT 59.421 61.111 0.00 0.00 39.89 3.24
8820 12924 1.811266 CGCACGACCCTTCAGGATG 60.811 63.158 0.00 0.00 39.89 3.51
8831 12935 2.361189 TCAGGATGAACGGCTGTGA 58.639 52.632 0.00 0.00 45.97 3.58
8832 12936 0.247460 TCAGGATGAACGGCTGTGAG 59.753 55.000 0.00 0.00 45.97 3.51
8833 12937 1.078848 AGGATGAACGGCTGTGAGC 60.079 57.895 0.00 0.00 41.46 4.26
8834 12938 1.078848 GGATGAACGGCTGTGAGCT 60.079 57.895 0.00 0.00 41.99 4.09
8840 12944 2.667536 CGGCTGTGAGCTGCTGTT 60.668 61.111 7.01 0.00 41.20 3.16
8841 12945 2.952245 GGCTGTGAGCTGCTGTTG 59.048 61.111 7.01 0.00 41.99 3.33
8842 12946 2.623915 GGCTGTGAGCTGCTGTTGG 61.624 63.158 7.01 0.00 41.99 3.77
8843 12947 2.623915 GCTGTGAGCTGCTGTTGGG 61.624 63.158 7.01 0.00 38.45 4.12
8844 12948 1.228063 CTGTGAGCTGCTGTTGGGT 60.228 57.895 7.01 0.00 0.00 4.51
8845 12949 1.227943 TGTGAGCTGCTGTTGGGTC 60.228 57.895 7.01 0.00 0.00 4.46
8846 12950 1.072159 GTGAGCTGCTGTTGGGTCT 59.928 57.895 7.01 0.00 0.00 3.85
8847 12951 0.952984 GTGAGCTGCTGTTGGGTCTC 60.953 60.000 7.01 0.00 0.00 3.36
8848 12952 1.376553 GAGCTGCTGTTGGGTCTCC 60.377 63.158 7.01 0.00 0.00 3.71
8849 12953 2.116983 GAGCTGCTGTTGGGTCTCCA 62.117 60.000 7.01 0.00 42.25 3.86
8850 12954 1.968540 GCTGCTGTTGGGTCTCCAC 60.969 63.158 0.00 0.00 43.94 4.02
8851 12955 1.757306 CTGCTGTTGGGTCTCCACT 59.243 57.895 0.00 0.00 43.94 4.00
8852 12956 0.109342 CTGCTGTTGGGTCTCCACTT 59.891 55.000 0.00 0.00 43.94 3.16
8853 12957 0.108585 TGCTGTTGGGTCTCCACTTC 59.891 55.000 0.00 0.00 43.94 3.01
8854 12958 0.951040 GCTGTTGGGTCTCCACTTCG 60.951 60.000 0.00 0.00 43.94 3.79
8855 12959 0.951040 CTGTTGGGTCTCCACTTCGC 60.951 60.000 0.00 0.00 43.94 4.70
8856 12960 1.671379 GTTGGGTCTCCACTTCGCC 60.671 63.158 0.00 0.00 43.94 5.54
8857 12961 2.890766 TTGGGTCTCCACTTCGCCC 61.891 63.158 0.00 0.00 43.94 6.13
8858 12962 4.097361 GGGTCTCCACTTCGCCCC 62.097 72.222 0.00 0.00 33.40 5.80
8859 12963 4.097361 GGTCTCCACTTCGCCCCC 62.097 72.222 0.00 0.00 0.00 5.40
8873 12977 4.485530 CCCCCGCCCACCTACCTA 62.486 72.222 0.00 0.00 0.00 3.08
8874 12978 2.122547 CCCCGCCCACCTACCTAT 60.123 66.667 0.00 0.00 0.00 2.57
8875 12979 1.156803 CCCCGCCCACCTACCTATA 59.843 63.158 0.00 0.00 0.00 1.31
8876 12980 0.472352 CCCCGCCCACCTACCTATAA 60.472 60.000 0.00 0.00 0.00 0.98
8877 12981 1.426751 CCCGCCCACCTACCTATAAA 58.573 55.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.878406 AGACGCAATGTAGCTGTTGTTT 59.122 40.909 0.00 0.00 0.00 2.83
154 155 1.372004 CGCCGTCGTACTTCACCAA 60.372 57.895 0.00 0.00 0.00 3.67
204 205 0.734889 GGACAAGGTTGCGGATCATG 59.265 55.000 0.00 0.00 0.00 3.07
288 290 3.422303 GACGCCGATGTGCTGCAA 61.422 61.111 2.77 0.00 0.00 4.08
311 313 1.237285 GCACCATCTTGCGGAACTGT 61.237 55.000 0.00 0.00 31.51 3.55
357 409 2.036414 TGAGGGAGACGAGCTGCT 59.964 61.111 0.00 0.00 34.97 4.24
375 427 2.105930 CAGAGGCCTCGCTAGTGC 59.894 66.667 26.95 0.79 34.09 4.40
378 430 2.811101 CCACAGAGGCCTCGCTAG 59.189 66.667 26.95 19.33 34.09 3.42
470 538 0.818296 GAGCACGGAGAGGTGTACAT 59.182 55.000 0.00 0.00 40.08 2.29
471 539 1.248785 GGAGCACGGAGAGGTGTACA 61.249 60.000 0.00 0.00 40.08 2.90
573 641 3.603532 GATCTCCACAGCATCAGTTTCA 58.396 45.455 0.00 0.00 0.00 2.69
581 649 2.107750 CCGCGATCTCCACAGCAT 59.892 61.111 8.23 0.00 0.00 3.79
585 653 2.184322 GAAGCCGCGATCTCCACA 59.816 61.111 8.23 0.00 0.00 4.17
601 669 2.045045 CTTCTGGGCGCCAATGGA 60.045 61.111 30.85 16.70 30.80 3.41
644 714 1.268899 GCAGTGATCAGCAACAGCTTT 59.731 47.619 0.00 0.00 36.19 3.51
725 802 1.547675 GGCTCCCATTGGACAAGACAA 60.548 52.381 3.62 0.00 35.03 3.18
727 804 0.681243 GGGCTCCCATTGGACAAGAC 60.681 60.000 3.62 0.60 35.03 3.01
751 828 4.219725 CGTCCCATCCCACTTAAATTGTTT 59.780 41.667 0.00 0.00 0.00 2.83
756 833 1.409661 GCCGTCCCATCCCACTTAAAT 60.410 52.381 0.00 0.00 0.00 1.40
773 852 1.070289 GGGACTAAGTGGGATTAGCCG 59.930 57.143 0.00 0.00 36.42 5.52
796 875 0.896940 ATGTCAAGCTGCAAGTGGGG 60.897 55.000 1.02 0.00 35.30 4.96
802 881 1.078709 GCTCGTATGTCAAGCTGCAA 58.921 50.000 1.02 0.00 33.23 4.08
809 888 0.738975 CCTCCGAGCTCGTATGTCAA 59.261 55.000 32.41 9.44 37.74 3.18
813 892 0.589223 GTCTCCTCCGAGCTCGTATG 59.411 60.000 32.41 21.06 35.94 2.39
814 893 0.535553 GGTCTCCTCCGAGCTCGTAT 60.536 60.000 32.41 0.00 35.94 3.06
815 894 1.153208 GGTCTCCTCCGAGCTCGTA 60.153 63.158 32.41 18.61 35.94 3.43
816 895 2.438795 GGTCTCCTCCGAGCTCGT 60.439 66.667 32.41 0.00 35.94 4.18
873 953 9.298774 CCTTGTCTTTACGACTTTTATACTAGG 57.701 37.037 0.00 0.00 43.25 3.02
895 975 1.142748 CTCTCTACCGCCTGCCTTG 59.857 63.158 0.00 0.00 0.00 3.61
1028 1111 1.728426 GAAGCGCGCGATACCGTAT 60.728 57.895 37.18 11.66 38.24 3.06
1168 1278 1.207329 CCAAAACTCTAGCCCTAGCGT 59.793 52.381 0.00 0.00 46.67 5.07
1394 1507 3.531538 TCCTAATTAAAGCAGCCGACAG 58.468 45.455 0.00 0.00 0.00 3.51
1455 1568 7.270579 GGAAGCTTAACAACAACATTACGAATC 59.729 37.037 0.00 0.00 0.00 2.52
1543 1661 2.420022 CCAAGTTCCAATCCTACGCTTG 59.580 50.000 0.00 0.00 33.70 4.01
1547 1665 2.629051 GGTCCAAGTTCCAATCCTACG 58.371 52.381 0.00 0.00 0.00 3.51
2120 2238 7.380870 TCACCGTTGTATTCAATTTGAAATGTG 59.619 33.333 15.34 13.25 40.12 3.21
2357 2475 3.046390 CTCTTCGCTTACCTATTCGCAG 58.954 50.000 0.00 0.00 0.00 5.18
2415 2533 8.451748 GTTTATGATCTTGTACCTTCCTTCAAC 58.548 37.037 0.00 0.00 0.00 3.18
2554 2672 5.398467 GCCTTCTATTCTTTTGGGAGAGGAT 60.398 44.000 0.00 0.00 0.00 3.24
2976 3094 6.348213 CCGAACACGAATACCTTCAGAAAAAT 60.348 38.462 0.00 0.00 0.00 1.82
2999 3117 3.701604 CTTCGGTCTTCGCCTCCCG 62.702 68.421 0.00 0.00 41.75 5.14
3013 3131 6.721571 TGATCCTTAACAGTAAAAGCTTCG 57.278 37.500 0.00 0.00 0.00 3.79
3748 4621 1.753956 GGTGAACATGTTGAACACGC 58.246 50.000 17.58 7.51 31.94 5.34
4032 5054 5.682943 ACGCAAAATGTTTAGAGCTAACA 57.317 34.783 3.12 3.12 0.00 2.41
4568 5757 8.621286 CCTATAGAAATAACAATGGTGGACAAC 58.379 37.037 0.00 0.00 0.00 3.32
4792 6439 2.050985 GCAGTTTGCAGCCACGAC 60.051 61.111 0.00 0.00 44.26 4.34
4996 7660 0.821517 TCGGTGCTCAATCGGTGTAT 59.178 50.000 0.00 0.00 0.00 2.29
5011 7675 3.492011 GTCACGTTTAGTCATGTTTCGGT 59.508 43.478 0.00 0.00 0.00 4.69
5014 7678 6.730619 CGTATTGTCACGTTTAGTCATGTTTC 59.269 38.462 0.00 0.00 37.16 2.78
5081 7745 2.113139 CAAACAGGGCCCACTCGT 59.887 61.111 27.56 12.74 0.00 4.18
5196 7860 1.964373 GTGTTTGATGCCCCGACGT 60.964 57.895 0.00 0.00 0.00 4.34
5232 7896 1.066215 TGTATTGGCTGACTCGTGCAT 60.066 47.619 0.00 0.00 0.00 3.96
5462 8126 1.143329 TTGTTGGCCCCACCCTCATA 61.143 55.000 0.00 0.00 37.83 2.15
5613 8313 0.108662 CTAGTCCACGCACATGCTCA 60.109 55.000 1.82 0.00 39.32 4.26
5736 8436 1.967066 CCGATGATCCTAGAGTGCCTT 59.033 52.381 0.00 0.00 0.00 4.35
5932 8632 3.083349 ATGCTGGCCTCCTACGCA 61.083 61.111 3.32 3.56 34.83 5.24
6151 9882 4.394729 TGGAGTCAAATAAACTGGTGGTC 58.605 43.478 0.00 0.00 0.00 4.02
6477 10438 4.028490 CCCAGGCCAAGCGGTACA 62.028 66.667 5.01 0.00 33.28 2.90
6560 10521 6.291648 AGAAGATGATGAGTAGCACTTGAA 57.708 37.500 0.00 0.00 0.00 2.69
6888 10850 4.380233 GCAGCAGTCAGTTTCTTTATGCAT 60.380 41.667 3.79 3.79 34.71 3.96
6889 10851 3.058016 GCAGCAGTCAGTTTCTTTATGCA 60.058 43.478 0.00 0.00 34.71 3.96
6890 10852 3.190118 AGCAGCAGTCAGTTTCTTTATGC 59.810 43.478 0.00 0.00 0.00 3.14
6928 10891 6.805016 AAATTACAAATATCATGTGGCCCA 57.195 33.333 0.00 0.00 32.27 5.36
7052 11019 1.929836 GCAGCGTTATTCTGAGGACTG 59.070 52.381 0.00 0.00 33.54 3.51
7430 11409 1.279271 GAAGGTGACTGCATGTAGGGT 59.721 52.381 15.65 0.00 42.68 4.34
7484 11466 4.660938 ACGGCTTTCCCAGGTGGC 62.661 66.667 0.00 0.00 0.00 5.01
7898 11880 8.990163 TGTTTTTCTTAACCAAAGGAGATACT 57.010 30.769 0.00 0.00 35.75 2.12
8038 12052 4.862574 GCTGTCATCGTGTCTTACATAACA 59.137 41.667 0.00 0.00 0.00 2.41
8054 12068 6.426587 AGTCTATGGTAAATTTGGCTGTCAT 58.573 36.000 0.00 0.00 0.00 3.06
8121 12135 7.073342 AGGAGTAAAATGAGCATCGTTAAAC 57.927 36.000 0.00 0.00 45.15 2.01
8127 12144 5.052481 TCATGAGGAGTAAAATGAGCATCG 58.948 41.667 0.00 0.00 38.61 3.84
8172 12189 3.928754 AGAGGGGTGCATGAAGATACTA 58.071 45.455 0.00 0.00 0.00 1.82
8205 12222 5.751680 ACGATGAATGACAAGTTCAACAAG 58.248 37.500 0.00 0.00 38.89 3.16
8322 12352 9.927668 TGCATTATATCTCTTCATTCGTTGATA 57.072 29.630 0.00 0.00 33.34 2.15
8517 12621 6.017211 TCAAGTCCCATTCATGTCCATATT 57.983 37.500 0.00 0.00 0.00 1.28
8540 12644 3.056607 GCATGTTTTGGTGAGGTAGCAAT 60.057 43.478 0.00 0.00 45.35 3.56
8587 12691 3.289834 CAGCTGCTTGGTGGCGTT 61.290 61.111 0.00 0.00 40.23 4.84
8800 12904 4.680237 CCTGAAGGGTCGTGCGCA 62.680 66.667 5.66 5.66 0.00 6.09
8803 12907 0.036388 TTCATCCTGAAGGGTCGTGC 60.036 55.000 0.00 0.00 31.83 5.34
8805 12909 0.246635 CGTTCATCCTGAAGGGTCGT 59.753 55.000 0.00 0.00 37.00 4.34
8806 12910 3.050703 CGTTCATCCTGAAGGGTCG 57.949 57.895 0.00 0.00 37.00 4.79
8810 12914 0.036010 ACAGCCGTTCATCCTGAAGG 60.036 55.000 3.26 3.26 40.71 3.46
8811 12915 1.081892 CACAGCCGTTCATCCTGAAG 58.918 55.000 0.00 0.00 37.00 3.02
8812 12916 0.684535 TCACAGCCGTTCATCCTGAA 59.315 50.000 0.00 0.00 33.32 3.02
8813 12917 0.247460 CTCACAGCCGTTCATCCTGA 59.753 55.000 0.00 0.00 0.00 3.86
8814 12918 1.364626 GCTCACAGCCGTTCATCCTG 61.365 60.000 0.00 0.00 34.48 3.86
8815 12919 1.078848 GCTCACAGCCGTTCATCCT 60.079 57.895 0.00 0.00 34.48 3.24
8816 12920 1.078848 AGCTCACAGCCGTTCATCC 60.079 57.895 0.00 0.00 43.77 3.51
8817 12921 1.975363 GCAGCTCACAGCCGTTCATC 61.975 60.000 0.00 0.00 43.77 2.92
8818 12922 2.037136 GCAGCTCACAGCCGTTCAT 61.037 57.895 0.00 0.00 43.77 2.57
8819 12923 2.666190 GCAGCTCACAGCCGTTCA 60.666 61.111 0.00 0.00 43.77 3.18
8820 12924 2.358003 AGCAGCTCACAGCCGTTC 60.358 61.111 0.00 0.00 43.77 3.95
8821 12925 2.667536 CAGCAGCTCACAGCCGTT 60.668 61.111 0.00 0.00 43.77 4.44
8822 12926 3.466791 AACAGCAGCTCACAGCCGT 62.467 57.895 0.00 0.00 43.77 5.68
8823 12927 2.667536 AACAGCAGCTCACAGCCG 60.668 61.111 0.00 0.00 43.77 5.52
8824 12928 2.623915 CCAACAGCAGCTCACAGCC 61.624 63.158 0.00 0.00 43.77 4.85
8825 12929 2.623915 CCCAACAGCAGCTCACAGC 61.624 63.158 0.00 0.00 42.84 4.40
8826 12930 1.228063 ACCCAACAGCAGCTCACAG 60.228 57.895 0.00 0.00 0.00 3.66
8827 12931 1.227943 GACCCAACAGCAGCTCACA 60.228 57.895 0.00 0.00 0.00 3.58
8828 12932 0.952984 GAGACCCAACAGCAGCTCAC 60.953 60.000 0.00 0.00 0.00 3.51
8829 12933 1.372683 GAGACCCAACAGCAGCTCA 59.627 57.895 0.00 0.00 0.00 4.26
8830 12934 1.376553 GGAGACCCAACAGCAGCTC 60.377 63.158 0.00 0.00 0.00 4.09
8831 12935 2.149383 TGGAGACCCAACAGCAGCT 61.149 57.895 0.00 0.00 40.09 4.24
8832 12936 1.968540 GTGGAGACCCAACAGCAGC 60.969 63.158 0.00 0.00 45.59 5.25
8833 12937 0.109342 AAGTGGAGACCCAACAGCAG 59.891 55.000 0.00 0.00 45.59 4.24
8834 12938 0.108585 GAAGTGGAGACCCAACAGCA 59.891 55.000 0.00 0.00 45.59 4.41
8835 12939 0.951040 CGAAGTGGAGACCCAACAGC 60.951 60.000 0.00 0.00 45.59 4.40
8836 12940 0.951040 GCGAAGTGGAGACCCAACAG 60.951 60.000 0.00 0.00 45.59 3.16
8837 12941 1.070786 GCGAAGTGGAGACCCAACA 59.929 57.895 0.00 0.00 45.59 3.33
8838 12942 1.671379 GGCGAAGTGGAGACCCAAC 60.671 63.158 0.00 0.00 45.59 3.77
8839 12943 2.747686 GGCGAAGTGGAGACCCAA 59.252 61.111 0.00 0.00 45.59 4.12
8840 12944 3.319198 GGGCGAAGTGGAGACCCA 61.319 66.667 0.00 0.00 40.52 4.51
8842 12946 4.097361 GGGGGCGAAGTGGAGACC 62.097 72.222 0.00 0.00 33.88 3.85
8856 12960 2.390777 TATAGGTAGGTGGGCGGGGG 62.391 65.000 0.00 0.00 0.00 5.40
8857 12961 0.472352 TTATAGGTAGGTGGGCGGGG 60.472 60.000 0.00 0.00 0.00 5.73
8858 12962 1.426751 TTTATAGGTAGGTGGGCGGG 58.573 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.