Multiple sequence alignment - TraesCS5B01G281700

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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 TraesCS5B01G281700 chr5B 100.000 4953 0 0 1 4953 466782665 466777713 0.000000e+00 9147.0
1 TraesCS5B01G281700 chr5B 84.375 416 50 5 591 1003 466968706 466968303 1.290000e-105 394.0
2 TraesCS5B01G281700 chr5B 100.000 86 0 0 2820 2905 466779761 466779846 5.130000e-35 159.0
3 TraesCS5B01G281700 chr5A 93.024 2007 83 13 2269 4262 491294899 491292937 0.000000e+00 2878.0
4 TraesCS5B01G281700 chr5A 87.603 1823 108 61 490 2273 491296721 491294978 0.000000e+00 2006.0
5 TraesCS5B01G281700 chr5A 90.946 497 34 5 4 498 491298476 491297989 0.000000e+00 658.0
6 TraesCS5B01G281700 chr5A 94.131 426 20 2 4530 4953 491291227 491290805 1.160000e-180 643.0
7 TraesCS5B01G281700 chr5A 90.566 318 12 9 4188 4501 491292967 491292664 5.970000e-109 405.0
8 TraesCS5B01G281700 chr5A 83.649 422 60 4 591 1012 491313743 491313331 6.010000e-104 388.0
9 TraesCS5B01G281700 chr5D 93.179 1818 79 30 490 2279 388104817 388103017 0.000000e+00 2628.0
10 TraesCS5B01G281700 chr5D 95.962 1486 55 4 2894 4378 388102479 388100998 0.000000e+00 2407.0
11 TraesCS5B01G281700 chr5D 94.872 546 27 1 2300 2845 388103024 388102480 0.000000e+00 852.0
12 TraesCS5B01G281700 chr5D 91.434 502 32 5 1 500 388106170 388105678 0.000000e+00 678.0
13 TraesCS5B01G281700 chr5D 88.414 561 22 16 4403 4953 388100999 388100472 1.940000e-178 636.0
14 TraesCS5B01G281700 chr5D 83.577 274 41 1 591 864 388426469 388426200 2.290000e-63 254.0
15 TraesCS5B01G281700 chr5D 86.486 148 19 1 860 1006 388424243 388424096 1.430000e-35 161.0
16 TraesCS5B01G281700 chr1B 88.690 672 41 18 1277 1922 507473736 507473074 0.000000e+00 787.0
17 TraesCS5B01G281700 chr1B 86.441 413 47 3 591 1003 507472340 507472743 1.270000e-120 444.0
18 TraesCS5B01G281700 chr1D 87.059 680 44 18 1277 1922 378870074 378869405 0.000000e+00 728.0
19 TraesCS5B01G281700 chr1D 85.714 413 48 5 592 1003 378868672 378869074 4.580000e-115 425.0
20 TraesCS5B01G281700 chr1D 93.333 90 4 2 2823 2911 433188084 433187996 1.120000e-26 132.0
21 TraesCS5B01G281700 chr1D 96.250 80 3 0 2823 2902 433188005 433188084 1.120000e-26 132.0
22 TraesCS5B01G281700 chr1D 91.463 82 3 1 1145 1226 378871137 378871060 5.240000e-20 110.0
23 TraesCS5B01G281700 chr1A 83.149 451 27 11 1494 1922 479711731 479711308 2.820000e-97 366.0
24 TraesCS5B01G281700 chr1A 82.132 319 45 5 688 1003 479710673 479710982 3.800000e-66 263.0
25 TraesCS5B01G281700 chr1A 90.000 50 4 1 3501 3550 77098083 77098131 4.140000e-06 63.9
26 TraesCS5B01G281700 chr6D 78.862 492 65 21 512 1001 106953547 106953093 3.750000e-76 296.0
27 TraesCS5B01G281700 chr4B 97.590 83 2 0 2821 2903 25847393 25847311 5.170000e-30 143.0
28 TraesCS5B01G281700 chr4B 97.590 83 2 0 2822 2904 25847311 25847393 5.170000e-30 143.0
29 TraesCS5B01G281700 chr4B 85.484 62 7 2 3492 3552 517959146 517959086 4.140000e-06 63.9
30 TraesCS5B01G281700 chr2A 96.471 85 2 1 2819 2902 667018367 667018451 6.690000e-29 139.0
31 TraesCS5B01G281700 chr2A 96.429 84 2 1 2823 2905 667018451 667018368 2.400000e-28 137.0
32 TraesCS5B01G281700 chr3D 94.382 89 3 2 2818 2905 442362882 442362795 8.650000e-28 135.0
33 TraesCS5B01G281700 chr3D 94.318 88 4 1 2816 2903 442362792 442362878 3.110000e-27 134.0
34 TraesCS5B01G281700 chr3D 89.610 77 7 1 3500 3575 119114417 119114493 4.080000e-16 97.1
35 TraesCS5B01G281700 chr6A 89.744 78 5 3 3499 3575 168004063 168004138 4.080000e-16 97.1
36 TraesCS5B01G281700 chr6A 82.558 86 7 5 3501 3580 55751749 55751832 8.900000e-08 69.4
37 TraesCS5B01G281700 chr6B 83.529 85 9 5 3501 3581 658546029 658546112 1.910000e-09 75.0
38 TraesCS5B01G281700 chr6B 100.000 34 0 0 3542 3575 123378624 123378657 4.140000e-06 63.9
39 TraesCS5B01G281700 chr2B 93.478 46 2 1 3499 3544 198447640 198447684 3.200000e-07 67.6
40 TraesCS5B01G281700 chr2B 97.059 34 1 0 3542 3575 798677698 798677665 1.930000e-04 58.4
41 TraesCS5B01G281700 chr3A 93.182 44 3 0 3534 3577 13089652 13089695 1.150000e-06 65.8


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 TraesCS5B01G281700 chr5B 466777713 466782665 4952 True 9147.0 9147 100.0000 1 4953 1 chr5B.!!$R1 4952
1 TraesCS5B01G281700 chr5A 491290805 491298476 7671 True 1318.0 2878 91.2540 4 4953 5 chr5A.!!$R2 4949
2 TraesCS5B01G281700 chr5D 388100472 388106170 5698 True 1440.2 2628 92.7722 1 4953 5 chr5D.!!$R1 4952
3 TraesCS5B01G281700 chr5D 388424096 388426469 2373 True 207.5 254 85.0315 591 1006 2 chr5D.!!$R2 415
4 TraesCS5B01G281700 chr1B 507473074 507473736 662 True 787.0 787 88.6900 1277 1922 1 chr1B.!!$R1 645
5 TraesCS5B01G281700 chr1D 378869405 378871137 1732 True 419.0 728 89.2610 1145 1922 2 chr1D.!!$R2 777

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
500 503 0.107945 GCATGAGGACTCCAGGACAC 60.108 60.0 0.00 0.0 0.00 3.67 F
1403 5642 0.103026 GATTTCCGCTGGATTTGCCC 59.897 55.0 0.00 0.0 34.97 5.36 F
2101 6384 0.108992 GCCGTCGTGGAGTATCAACA 60.109 55.0 0.51 0.0 39.73 3.33 F
2403 6769 0.889186 TTTTGCAGAGGAGGAACCGC 60.889 55.0 0.00 0.0 44.74 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 6769 0.177604 CAGGCTGCCTCCTAGTTCTG 59.822 60.0 20.49 0.7 33.95 3.02 R
3221 7587 0.179004 ACGAACAAAGGGGTGCATCA 60.179 50.0 0.00 0.0 0.00 3.07 R
3659 8039 1.725641 TAGCACAAATCACGAGGCAG 58.274 50.0 0.00 0.0 0.00 4.85 R
4193 8573 1.325476 CCCCATTTCAGGCAGAAGGC 61.325 60.0 0.00 0.0 43.74 4.35 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
24 25 5.822519 TGTAACCCATCTATGTGCATTTCTC 59.177 40.000 0.00 0.00 0.00 2.87
25 26 3.825328 ACCCATCTATGTGCATTTCTCC 58.175 45.455 0.00 0.00 0.00 3.71
29 30 2.826428 TCTATGTGCATTTCTCCGAGC 58.174 47.619 0.00 0.00 0.00 5.03
44 45 0.447406 CGAGCAATTTCGTGATGCCA 59.553 50.000 0.00 0.00 40.93 4.92
56 57 2.035469 ATGCCATTGCGGACACCA 59.965 55.556 0.00 0.00 41.78 4.17
58 59 0.971959 ATGCCATTGCGGACACCATT 60.972 50.000 0.00 0.00 41.78 3.16
71 72 4.016444 GGACACCATTGGCTCTATTGAAA 58.984 43.478 1.54 0.00 0.00 2.69
94 95 0.613260 TGGTCAGTGTCAGGCATACC 59.387 55.000 0.00 0.00 0.00 2.73
98 99 0.179100 CAGTGTCAGGCATACCCTCG 60.179 60.000 0.00 0.00 44.09 4.63
126 127 1.880027 CAGTGGTTTCACAAGTAGGGC 59.120 52.381 0.00 0.00 45.91 5.19
200 201 4.523083 ACTTCAAGTGTTTGTAAGCCTGA 58.477 39.130 0.00 0.00 35.73 3.86
270 271 8.715998 CATAGATTTCTTCCATTCCTATTGTCG 58.284 37.037 0.00 0.00 0.00 4.35
327 328 3.230134 TCTGCCAAAAACCTGCATAGTT 58.770 40.909 0.00 0.00 33.97 2.24
360 361 1.205064 CGCCTCAACTTGCAAGTCG 59.795 57.895 31.20 24.48 38.57 4.18
363 364 1.333619 GCCTCAACTTGCAAGTCGAAA 59.666 47.619 31.20 15.83 38.57 3.46
369 370 7.526608 CCTCAACTTGCAAGTCGAAATATTTA 58.473 34.615 31.20 5.07 38.57 1.40
401 402 2.038426 CCATGCCATGCAATTCATCCAT 59.962 45.455 0.00 0.00 43.62 3.41
405 406 3.128349 GCCATGCAATTCATCCATTGAC 58.872 45.455 0.00 0.00 36.39 3.18
406 407 3.181469 GCCATGCAATTCATCCATTGACT 60.181 43.478 0.00 0.00 36.39 3.41
407 408 4.617959 CCATGCAATTCATCCATTGACTC 58.382 43.478 0.00 0.00 36.39 3.36
408 409 4.341235 CCATGCAATTCATCCATTGACTCT 59.659 41.667 0.00 0.00 36.39 3.24
409 410 5.507482 CCATGCAATTCATCCATTGACTCTC 60.507 44.000 0.00 0.00 36.39 3.20
410 411 4.851843 TGCAATTCATCCATTGACTCTCT 58.148 39.130 0.00 0.00 36.39 3.10
411 412 4.638865 TGCAATTCATCCATTGACTCTCTG 59.361 41.667 0.00 0.00 36.39 3.35
412 413 4.880120 GCAATTCATCCATTGACTCTCTGA 59.120 41.667 0.00 0.00 36.39 3.27
424 425 3.380320 TGACTCTCTGAACGTTTGAGTGA 59.620 43.478 26.13 18.99 38.00 3.41
429 431 5.164233 TCTCTGAACGTTTGAGTGATGATC 58.836 41.667 22.64 1.39 0.00 2.92
430 432 4.881920 TCTGAACGTTTGAGTGATGATCA 58.118 39.130 0.46 0.00 0.00 2.92
434 436 5.469760 TGAACGTTTGAGTGATGATCATGTT 59.530 36.000 14.30 7.42 0.00 2.71
447 449 7.712639 GTGATGATCATGTTATTAGTCCACACT 59.287 37.037 14.30 0.00 36.55 3.55
450 452 6.818142 TGATCATGTTATTAGTCCACACTGTG 59.182 38.462 6.19 6.19 33.62 3.66
500 503 0.107945 GCATGAGGACTCCAGGACAC 60.108 60.000 0.00 0.00 0.00 3.67
501 504 0.174389 CATGAGGACTCCAGGACACG 59.826 60.000 0.00 0.00 0.00 4.49
504 507 1.939769 GAGGACTCCAGGACACGCTC 61.940 65.000 0.00 0.00 0.00 5.03
506 509 1.214062 GACTCCAGGACACGCTCTG 59.786 63.158 0.00 0.00 0.00 3.35
507 510 2.125753 CTCCAGGACACGCTCTGC 60.126 66.667 0.00 0.00 0.00 4.26
508 511 2.917227 TCCAGGACACGCTCTGCA 60.917 61.111 0.00 0.00 0.00 4.41
525 1812 6.264088 GCTCTGCATTTTCTTAGATGAAAGG 58.736 40.000 0.00 0.00 37.27 3.11
659 1947 2.950309 TCCTCGACATTGTAGTAGAGCC 59.050 50.000 0.00 0.00 39.15 4.70
777 2065 0.814010 ACGTTCCTGCTCCACAACAC 60.814 55.000 0.00 0.00 0.00 3.32
805 2093 1.747206 GCAACCCGCTGAACTATCCAT 60.747 52.381 0.00 0.00 37.77 3.41
809 2097 3.305720 ACCCGCTGAACTATCCATAAGA 58.694 45.455 0.00 0.00 0.00 2.10
816 2126 5.282055 TGAACTATCCATAAGAGCACCAG 57.718 43.478 0.00 0.00 0.00 4.00
821 2131 1.908619 TCCATAAGAGCACCAGCAGAA 59.091 47.619 0.00 0.00 45.49 3.02
822 2132 2.093288 TCCATAAGAGCACCAGCAGAAG 60.093 50.000 0.00 0.00 45.49 2.85
823 2133 2.355513 CCATAAGAGCACCAGCAGAAGT 60.356 50.000 0.00 0.00 45.49 3.01
825 2135 2.758736 AAGAGCACCAGCAGAAGTAG 57.241 50.000 0.00 0.00 45.49 2.57
828 2138 0.397941 AGCACCAGCAGAAGTAGCAA 59.602 50.000 0.00 0.00 45.49 3.91
830 2140 1.068954 GCACCAGCAGAAGTAGCAAAC 60.069 52.381 0.00 0.00 41.58 2.93
831 2141 2.221169 CACCAGCAGAAGTAGCAAACA 58.779 47.619 0.00 0.00 0.00 2.83
842 3543 2.028112 AGTAGCAAACAGATCCGCAAGA 60.028 45.455 0.00 0.00 43.02 3.02
873 4131 1.613925 CACCTGAACTGGACTCTCGAA 59.386 52.381 4.82 0.00 0.00 3.71
1142 4428 0.680061 GGGGAAGAGACAGACGTGTT 59.320 55.000 0.00 0.00 36.88 3.32
1143 4429 1.336980 GGGGAAGAGACAGACGTGTTC 60.337 57.143 0.00 0.00 36.88 3.18
1403 5642 0.103026 GATTTCCGCTGGATTTGCCC 59.897 55.000 0.00 0.00 34.97 5.36
1405 5644 2.721803 TTTCCGCTGGATTTGCCCCA 62.722 55.000 0.00 0.00 34.97 4.96
1568 5812 0.536006 CGGGAAATCAGGGGCATCTC 60.536 60.000 0.00 0.00 0.00 2.75
1668 5941 1.197721 GTGGGATTCAGCAAGTCGTTG 59.802 52.381 0.00 0.00 36.67 4.10
1786 6059 4.125703 GTTGGATTTTGCATTGTTGGTCA 58.874 39.130 0.00 0.00 0.00 4.02
1847 6127 5.371526 AGCATCGATGTCCTTGATTTATGT 58.628 37.500 25.47 0.00 0.00 2.29
1848 6128 6.524734 AGCATCGATGTCCTTGATTTATGTA 58.475 36.000 25.47 0.00 0.00 2.29
2044 6327 5.163581 GCAATCACAAGATGCTGATAAGGTT 60.164 40.000 0.00 0.00 33.90 3.50
2098 6381 1.807226 CAGCCGTCGTGGAGTATCA 59.193 57.895 0.51 0.00 42.00 2.15
2101 6384 0.108992 GCCGTCGTGGAGTATCAACA 60.109 55.000 0.51 0.00 39.73 3.33
2219 6502 2.164827 TCGCGAGGCAGTAAGTTCATAA 59.835 45.455 3.71 0.00 0.00 1.90
2332 6698 6.934645 TGAGGAAGAGTATTACAAGTTGGTTG 59.065 38.462 7.96 0.00 42.48 3.77
2376 6742 8.750515 TCATTTCTGGCATTTATATTGAGTCA 57.249 30.769 0.00 0.00 0.00 3.41
2403 6769 0.889186 TTTTGCAGAGGAGGAACCGC 60.889 55.000 0.00 0.00 44.74 5.68
2407 6773 1.975327 CAGAGGAGGAACCGCAGAA 59.025 57.895 0.00 0.00 44.74 3.02
2439 6805 4.158579 CAGCCTGTGACTGTAGTTGATCTA 59.841 45.833 0.00 0.00 0.00 1.98
2497 6863 9.803315 CTACTTAGTCTTACTATGTTGCATTCA 57.197 33.333 9.91 0.00 39.10 2.57
2589 6955 5.882557 TCTGCCTAATCAATTCTTCTGGAAC 59.117 40.000 0.00 0.00 36.70 3.62
2653 7019 4.940463 TGACCGTAAGTGCTGATTATACC 58.060 43.478 0.00 0.00 0.00 2.73
2684 7050 9.668497 GACATAAGTTTACTTTCTAGTGGGAAT 57.332 33.333 0.00 0.00 37.40 3.01
2745 7111 5.406477 GCTTTCTTTTGTGGCTAATTTCCTG 59.594 40.000 0.00 0.00 0.00 3.86
2831 7197 6.697641 TGGAAGTTGTAAAATACTCCCTCT 57.302 37.500 0.00 0.00 0.00 3.69
2845 7211 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
2852 7218 5.935945 TCTGTCCCAAAATAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
2853 7219 5.763204 TCTGTCCCAAAATAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
2854 7220 5.690865 TGTCCCAAAATAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
2855 7221 6.126409 TGTCCCAAAATAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
2856 7222 6.605594 TGTCCCAAAATAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
2857 7223 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2858 7224 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2859 7225 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2860 7226 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2861 7227 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2867 7233 7.578310 AGTGACTCAACTTTGTACTAGTACA 57.422 36.000 27.99 27.99 43.61 2.90
2938 7304 7.081349 GCTGTCTGACTATATATCACTGTCAC 58.919 42.308 9.51 0.00 34.51 3.67
2950 7316 2.300152 TCACTGTCACTTAAGCCTCCTG 59.700 50.000 1.29 0.00 0.00 3.86
3065 7431 5.538877 TCCCCTGTAATAAACATCTCTCCT 58.461 41.667 0.00 0.00 37.50 3.69
3101 7467 5.252164 AGGGTCCAGCTTACAGGTATTTAAA 59.748 40.000 0.00 0.00 0.00 1.52
3221 7587 5.815233 ATAACAGCTGGTATCTAGTGCAT 57.185 39.130 18.83 0.00 0.00 3.96
3301 7667 7.494952 GGACTAAGGGTGTAACTATGTTTGATC 59.505 40.741 0.00 0.00 36.74 2.92
3411 7777 2.549349 GGCCAACGGTTAAGACTCTTGA 60.549 50.000 0.00 0.00 0.00 3.02
3428 7794 6.585416 ACTCTTGATTGGCACTGAAAATTTT 58.415 32.000 2.28 2.28 0.00 1.82
3529 7895 3.007635 CCGTCCCAAAATAAGTGTCTCC 58.992 50.000 0.00 0.00 0.00 3.71
3540 7906 3.470645 AAGTGTCTCCGCTTTGTACTT 57.529 42.857 0.00 0.00 38.22 2.24
3566 7945 5.638234 AGTTGAGACACTTATTTTAGGACGC 59.362 40.000 0.00 0.00 0.00 5.19
3629 8009 7.796054 TCCTAAGAAAGCTGCTCTATACATTT 58.204 34.615 1.00 0.00 0.00 2.32
3659 8039 2.799917 CGTCCAGTTCCTACTAGCATGC 60.800 54.545 10.51 10.51 31.96 4.06
3694 8074 2.028020 GTGCTAAACTCTGGCTACCTGT 60.028 50.000 0.00 0.00 0.00 4.00
3702 8082 1.771854 TCTGGCTACCTGTGTTTCCAA 59.228 47.619 0.00 0.00 0.00 3.53
3704 8084 3.157087 CTGGCTACCTGTGTTTCCAATT 58.843 45.455 0.00 0.00 0.00 2.32
3705 8085 3.571590 TGGCTACCTGTGTTTCCAATTT 58.428 40.909 0.00 0.00 0.00 1.82
3844 8224 1.376424 CGGCCACATCTTCTGCACT 60.376 57.895 2.24 0.00 0.00 4.40
3959 8339 3.470393 ACCTCCCGTTAAGGTGAGT 57.530 52.632 6.85 0.00 45.50 3.41
3998 8378 3.063180 CGCCTTAATCTGTTGAGCTTCAG 59.937 47.826 7.79 7.79 0.00 3.02
4041 8421 6.128499 CCGTTCGATGTGTTAAAATGAACCTA 60.128 38.462 0.00 0.00 32.69 3.08
4043 8423 7.634817 CGTTCGATGTGTTAAAATGAACCTATC 59.365 37.037 0.00 0.00 32.69 2.08
4134 8514 3.065786 GCATTGTGTACCATCATCACCTG 59.934 47.826 0.00 0.00 0.00 4.00
4193 8573 1.615883 CCTGATGACCGGACTGGATAG 59.384 57.143 9.46 0.00 42.00 2.08
4216 8639 2.806945 TCTGCCTGAAATGGGGTTAG 57.193 50.000 0.00 0.00 0.00 2.34
4223 8646 2.954318 CTGAAATGGGGTTAGCCTGATG 59.046 50.000 0.00 0.00 34.45 3.07
4376 8802 1.796459 GTTGGTCGATGTAACTGCGTT 59.204 47.619 0.00 0.02 0.00 4.84
4381 8807 2.984471 GTCGATGTAACTGCGTTTGAGA 59.016 45.455 0.00 0.00 0.00 3.27
4383 8809 4.796830 GTCGATGTAACTGCGTTTGAGATA 59.203 41.667 0.00 0.00 0.00 1.98
4384 8810 5.287752 GTCGATGTAACTGCGTTTGAGATAA 59.712 40.000 0.00 0.00 0.00 1.75
4385 8811 6.019801 GTCGATGTAACTGCGTTTGAGATAAT 60.020 38.462 0.00 0.00 0.00 1.28
4386 8812 6.019881 TCGATGTAACTGCGTTTGAGATAATG 60.020 38.462 0.00 0.00 0.00 1.90
4388 8814 3.389687 AACTGCGTTTGAGATAATGCG 57.610 42.857 0.00 0.00 41.78 4.73
4389 8815 2.616960 ACTGCGTTTGAGATAATGCGA 58.383 42.857 0.00 0.00 41.78 5.10
4390 8816 2.604914 ACTGCGTTTGAGATAATGCGAG 59.395 45.455 0.00 0.00 41.78 5.03
4391 8817 1.933181 TGCGTTTGAGATAATGCGAGG 59.067 47.619 0.00 0.00 41.78 4.63
4392 8818 1.261619 GCGTTTGAGATAATGCGAGGG 59.738 52.381 0.00 0.00 31.10 4.30
4393 8819 2.550978 CGTTTGAGATAATGCGAGGGT 58.449 47.619 0.00 0.00 0.00 4.34
4394 8820 2.936498 CGTTTGAGATAATGCGAGGGTT 59.064 45.455 0.00 0.00 0.00 4.11
4395 8821 3.374058 CGTTTGAGATAATGCGAGGGTTT 59.626 43.478 0.00 0.00 0.00 3.27
4396 8822 4.142687 CGTTTGAGATAATGCGAGGGTTTT 60.143 41.667 0.00 0.00 0.00 2.43
4397 8823 4.963276 TTGAGATAATGCGAGGGTTTTG 57.037 40.909 0.00 0.00 0.00 2.44
4398 8824 2.682856 TGAGATAATGCGAGGGTTTTGC 59.317 45.455 0.00 0.00 36.67 3.68
4422 8848 4.827284 ACCTTTGGTATTTCTGTTCAGTGG 59.173 41.667 0.00 0.00 32.11 4.00
4423 8849 4.827284 CCTTTGGTATTTCTGTTCAGTGGT 59.173 41.667 0.00 0.00 0.00 4.16
4624 10475 2.860735 GACTACTACAAGCGCATCCAAG 59.139 50.000 11.47 2.42 0.00 3.61
4682 10537 1.268896 GCATCACAATTGATCCGCTGG 60.269 52.381 13.59 0.00 40.79 4.85
4695 10550 0.729116 CCGCTGGTCACTTGCAATAG 59.271 55.000 0.00 0.00 0.00 1.73
4766 10621 2.424601 TGCTGGCAGCTTGTTCATTATC 59.575 45.455 36.50 6.99 42.97 1.75
4784 10639 0.457853 TCGGGCTGATCTTTTCGTCG 60.458 55.000 0.00 0.00 0.00 5.12
4835 10690 5.579564 AGGTTTCGTAGAAGTCCAGTATC 57.420 43.478 8.09 0.00 45.90 2.24
4872 10727 2.455557 TCACCTGGGTATTGCAAATGG 58.544 47.619 1.71 2.35 0.00 3.16
4915 10779 2.735259 TATGAGGGGGAAGGGGTATC 57.265 55.000 0.00 0.00 0.00 2.24
4942 10806 3.761657 ACATGCGCTTACAATGTTCATG 58.238 40.909 9.73 1.27 36.75 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.248215 GGCATCACGAAATTGCTCGG 60.248 55.000 4.68 0.00 43.22 4.63
25 26 0.447406 TGGCATCACGAAATTGCTCG 59.553 50.000 0.00 0.00 44.50 5.03
29 30 1.584761 CGCAATGGCATCACGAAATTG 59.415 47.619 14.76 2.91 41.24 2.32
44 45 1.304381 AGCCAATGGTGTCCGCAAT 60.304 52.632 0.00 0.00 0.00 3.56
56 57 5.184892 ACCAGAGTTTCAATAGAGCCAAT 57.815 39.130 0.00 0.00 0.00 3.16
58 59 3.582647 TGACCAGAGTTTCAATAGAGCCA 59.417 43.478 0.00 0.00 0.00 4.75
71 72 0.760567 TGCCTGACACTGACCAGAGT 60.761 55.000 3.76 1.69 34.98 3.24
94 95 0.905357 AACCACTGATTCCCTCGAGG 59.095 55.000 25.36 25.36 0.00 4.63
98 99 3.140325 TGTGAAACCACTGATTCCCTC 57.860 47.619 0.00 0.00 35.63 4.30
126 127 2.173356 TCCCCTGGACAATGAAGCATAG 59.827 50.000 0.00 0.00 0.00 2.23
161 162 5.818136 TGAAGTTGCTTGGCTACATTATC 57.182 39.130 6.83 1.49 36.81 1.75
200 201 1.000396 GTGCTCCTGGGATGCCTTT 60.000 57.895 4.35 0.00 0.00 3.11
270 271 2.315925 TTTCTCGATGATGAGGGTGC 57.684 50.000 0.00 0.00 36.61 5.01
360 361 9.340695 GGCATGGCTTTTGTTTTTAAATATTTC 57.659 29.630 12.86 0.00 0.00 2.17
363 364 7.992754 TGGCATGGCTTTTGTTTTTAAATAT 57.007 28.000 21.08 0.00 0.00 1.28
369 370 2.293955 GCATGGCATGGCTTTTGTTTTT 59.706 40.909 27.48 0.00 0.00 1.94
380 381 1.414550 TGGATGAATTGCATGGCATGG 59.585 47.619 27.48 10.64 38.76 3.66
401 402 4.112634 CACTCAAACGTTCAGAGAGTCAA 58.887 43.478 27.47 0.00 37.45 3.18
405 406 4.550422 TCATCACTCAAACGTTCAGAGAG 58.450 43.478 27.47 21.94 33.69 3.20
406 407 4.584327 TCATCACTCAAACGTTCAGAGA 57.416 40.909 27.47 18.62 33.69 3.10
407 408 4.925646 TGATCATCACTCAAACGTTCAGAG 59.074 41.667 22.08 22.08 35.56 3.35
408 409 4.881920 TGATCATCACTCAAACGTTCAGA 58.118 39.130 12.85 8.37 0.00 3.27
409 410 5.121298 ACATGATCATCACTCAAACGTTCAG 59.879 40.000 4.86 3.24 0.00 3.02
410 411 4.996758 ACATGATCATCACTCAAACGTTCA 59.003 37.500 4.86 0.00 0.00 3.18
411 412 5.536554 ACATGATCATCACTCAAACGTTC 57.463 39.130 4.86 0.00 0.00 3.95
412 413 5.947228 AACATGATCATCACTCAAACGTT 57.053 34.783 4.86 0.00 0.00 3.99
424 425 7.496920 CACAGTGTGGACTAATAACATGATCAT 59.503 37.037 15.86 1.18 0.00 2.45
447 449 2.719531 TTGTGCTTGTCTAACCCACA 57.280 45.000 0.00 0.00 34.90 4.17
450 452 6.318648 TCAATATGATTGTGCTTGTCTAACCC 59.681 38.462 0.00 0.00 0.00 4.11
453 455 9.176460 TGAATCAATATGATTGTGCTTGTCTAA 57.824 29.630 10.12 0.00 46.20 2.10
455 457 7.634671 TGAATCAATATGATTGTGCTTGTCT 57.365 32.000 10.12 0.00 46.20 3.41
456 458 7.043590 GCTTGAATCAATATGATTGTGCTTGTC 60.044 37.037 10.12 0.00 46.20 3.18
500 503 5.475273 TTCATCTAAGAAAATGCAGAGCG 57.525 39.130 0.00 0.00 0.00 5.03
501 504 6.264088 CCTTTCATCTAAGAAAATGCAGAGC 58.736 40.000 0.00 0.00 37.09 4.09
504 507 5.032863 CGCCTTTCATCTAAGAAAATGCAG 58.967 41.667 0.00 0.00 37.09 4.41
506 509 4.986622 ACGCCTTTCATCTAAGAAAATGC 58.013 39.130 0.00 0.00 37.09 3.56
507 510 6.182039 TGACGCCTTTCATCTAAGAAAATG 57.818 37.500 0.00 0.00 37.09 2.32
508 511 6.678900 GCATGACGCCTTTCATCTAAGAAAAT 60.679 38.462 0.00 0.00 37.09 1.82
525 1812 1.441515 CAAGCTGTGTGCATGACGC 60.442 57.895 0.00 0.00 42.37 5.19
538 1825 2.728007 GTTGGGGCTTCTTATCAAGCT 58.272 47.619 5.24 0.00 46.89 3.74
805 2093 2.093973 GCTACTTCTGCTGGTGCTCTTA 60.094 50.000 0.00 0.00 40.48 2.10
809 2097 0.397941 TTGCTACTTCTGCTGGTGCT 59.602 50.000 0.00 0.00 40.48 4.40
816 2126 2.349886 CGGATCTGTTTGCTACTTCTGC 59.650 50.000 0.00 0.00 0.00 4.26
821 2131 2.028112 TCTTGCGGATCTGTTTGCTACT 60.028 45.455 2.89 0.00 0.00 2.57
822 2132 2.346803 TCTTGCGGATCTGTTTGCTAC 58.653 47.619 2.89 0.00 0.00 3.58
823 2133 2.621338 CTCTTGCGGATCTGTTTGCTA 58.379 47.619 2.89 0.00 0.00 3.49
825 2135 0.449388 CCTCTTGCGGATCTGTTTGC 59.551 55.000 2.89 0.00 0.00 3.68
828 2138 1.480137 CTCTCCTCTTGCGGATCTGTT 59.520 52.381 2.89 0.00 31.43 3.16
830 2140 0.249405 GCTCTCCTCTTGCGGATCTG 60.249 60.000 0.00 0.00 31.43 2.90
831 2141 0.685785 TGCTCTCCTCTTGCGGATCT 60.686 55.000 0.00 0.00 31.43 2.75
842 3543 2.210013 TTCAGGTGCGTGCTCTCCT 61.210 57.895 0.00 0.00 0.00 3.69
1079 4358 1.523938 GCTATCTTGGCCCACGTCC 60.524 63.158 0.00 0.00 0.00 4.79
1130 4416 0.104304 AAAGGCGAACACGTCTGTCT 59.896 50.000 0.00 0.00 41.16 3.41
1131 4417 0.935196 AAAAGGCGAACACGTCTGTC 59.065 50.000 0.00 0.00 41.16 3.51
1132 4418 1.375551 AAAAAGGCGAACACGTCTGT 58.624 45.000 0.00 0.00 41.16 3.41
1133 4419 3.720920 CGATAAAAAGGCGAACACGTCTG 60.721 47.826 0.00 0.00 41.16 3.51
1169 4455 1.926426 AAGGATGCGAAAGGGGGAGG 61.926 60.000 0.00 0.00 0.00 4.30
1294 5533 4.200283 GGACGAGCAGAGGAGGCG 62.200 72.222 0.00 0.00 36.08 5.52
1403 5642 2.047844 CTGGATCGGCGCCTATGG 60.048 66.667 26.68 9.07 0.00 2.74
1503 5746 1.006805 CGGCGAATCTGGCTAGGAG 60.007 63.158 0.00 0.00 0.00 3.69
1505 5748 1.300233 GACGGCGAATCTGGCTAGG 60.300 63.158 16.62 0.00 0.00 3.02
1541 5784 2.224548 CCCCTGATTTCCCGATTCCTAC 60.225 54.545 0.00 0.00 0.00 3.18
1549 5792 0.536006 GAGATGCCCCTGATTTCCCG 60.536 60.000 0.00 0.00 0.00 5.14
1553 5796 0.465097 CGCAGAGATGCCCCTGATTT 60.465 55.000 0.00 0.00 32.37 2.17
1786 6059 1.202154 CGTCTCGACAAAGCTACCGAT 60.202 52.381 0.00 0.00 0.00 4.18
1847 6127 6.464322 CCCTGTGACCATCTTTGCAGTATATA 60.464 42.308 0.00 0.00 0.00 0.86
1848 6128 5.371526 CCTGTGACCATCTTTGCAGTATAT 58.628 41.667 0.00 0.00 0.00 0.86
2044 6327 2.546778 GTTGAGACCAAGTTCACGACA 58.453 47.619 0.00 0.00 32.06 4.35
2098 6381 3.486263 GCGCCAGCGTTAGATGTT 58.514 55.556 14.22 0.00 42.09 2.71
2219 6502 4.934356 ACACCATGGTCCTTAAACATCAT 58.066 39.130 16.53 0.00 0.00 2.45
2325 6691 5.345741 GCATCACATTCATGTAACAACCAAC 59.654 40.000 0.00 0.00 39.39 3.77
2332 6698 7.919091 AGAAATGATGCATCACATTCATGTAAC 59.081 33.333 35.17 20.60 39.84 2.50
2403 6769 0.177604 CAGGCTGCCTCCTAGTTCTG 59.822 60.000 20.49 0.70 33.95 3.02
2407 6773 1.079256 TCACAGGCTGCCTCCTAGT 59.921 57.895 20.49 11.14 33.95 2.57
2427 6793 7.588497 AGCATGTACATCTAGATCAACTACA 57.412 36.000 5.07 6.86 0.00 2.74
2439 6805 0.393077 GCCGGGTAGCATGTACATCT 59.607 55.000 5.07 8.94 0.00 2.90
2497 6863 6.354130 TGTTAGAAGCCAAAACAACTCTACT 58.646 36.000 0.00 0.00 30.54 2.57
2548 6914 9.848710 ATTAGGCAGATCATAATAGAATGATGG 57.151 33.333 4.16 0.00 44.69 3.51
2563 6929 6.294473 TCCAGAAGAATTGATTAGGCAGATC 58.706 40.000 0.00 0.00 0.00 2.75
2602 6968 6.978338 AGCAGCATGATATAGGTGATTTTTG 58.022 36.000 0.00 0.00 39.69 2.44
2695 7061 3.067320 GGGTCCAATTTTCAGCATAGCTC 59.933 47.826 0.00 0.00 36.40 4.09
2745 7111 6.959311 CACGTTGCAACAGGAAGTTATTATAC 59.041 38.462 28.01 0.00 38.74 1.47
2795 7161 1.675552 ACTTCCAGTTGTGGTTTCCG 58.324 50.000 0.00 0.00 45.28 4.30
2831 7197 5.690865 AGTTGAGTCACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
2856 7222 7.578310 AGTGACTCAACTTTGTACTAGTACA 57.422 36.000 27.99 27.99 43.61 2.90
2862 7228 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2863 7229 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2864 7230 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2865 7231 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2866 7232 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2867 7233 6.605594 TGTCCCAAAATAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
2868 7234 6.126409 TGTCCCAAAATAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
2869 7235 5.690865 TGTCCCAAAATAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
2870 7236 5.763204 TCTGTCCCAAAATAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
2871 7237 5.935945 TCTGTCCCAAAATAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
2872 7238 5.513094 CCTCTGTCCCAAAATAAGTGACTCA 60.513 44.000 0.00 0.00 0.00 3.41
2873 7239 4.938226 CCTCTGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
2874 7240 4.263506 CCCTCTGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 0.00 3.41
2875 7241 4.010349 CCCTCTGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
2876 7242 3.913799 TCCCTCTGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
2877 7243 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
2938 7304 1.767681 AGGCAGATCAGGAGGCTTAAG 59.232 52.381 0.00 0.00 34.14 1.85
2950 7316 7.709947 TGATTGAATAAACAATGAGGCAGATC 58.290 34.615 0.00 0.00 40.03 2.75
3065 7431 1.699634 CTGGACCCTTCTCCTGTTTCA 59.300 52.381 0.00 0.00 0.00 2.69
3168 7534 9.930693 ATAAAGGACAAAGTAGAGAACAACTAG 57.069 33.333 0.00 0.00 0.00 2.57
3221 7587 0.179004 ACGAACAAAGGGGTGCATCA 60.179 50.000 0.00 0.00 0.00 3.07
3301 7667 8.895845 CATACAACGAGAAATTCTTTCAACTTG 58.104 33.333 0.00 0.00 42.10 3.16
3411 7777 6.183360 ACAATTGCAAAATTTTCAGTGCCAAT 60.183 30.769 1.71 7.07 36.12 3.16
3428 7794 7.783090 TGCTTCTTGAAATTTAACAATTGCA 57.217 28.000 5.05 1.43 36.28 4.08
3529 7895 5.462398 AGTGTCTCAACTTAAGTACAAAGCG 59.538 40.000 8.92 0.00 0.00 4.68
3540 7906 7.330208 GCGTCCTAAAATAAGTGTCTCAACTTA 59.670 37.037 0.00 0.00 44.52 2.24
3604 7983 6.985653 ATGTATAGAGCAGCTTTCTTAGGA 57.014 37.500 0.00 0.00 0.00 2.94
3659 8039 1.725641 TAGCACAAATCACGAGGCAG 58.274 50.000 0.00 0.00 0.00 4.85
3959 8339 5.416271 AAGGCGTATAGAAACTGAAAGGA 57.584 39.130 0.00 0.00 39.30 3.36
3998 8378 4.124851 ACGGACCTGTATCTGATGAAAC 57.875 45.455 0.00 0.00 0.00 2.78
4041 8421 6.051717 CCCTGACGATAGATTTCAAAGTGAT 58.948 40.000 0.00 0.00 41.38 3.06
4043 8423 5.178797 ACCCTGACGATAGATTTCAAAGTG 58.821 41.667 0.00 0.00 41.38 3.16
4134 8514 4.082125 GACCCATTCCCATACATTCATCC 58.918 47.826 0.00 0.00 0.00 3.51
4193 8573 1.325476 CCCCATTTCAGGCAGAAGGC 61.325 60.000 0.00 0.00 43.74 4.35
4216 8639 2.706339 ATCCACTCTGTTCATCAGGC 57.294 50.000 0.00 0.00 43.76 4.85
4223 8646 3.620821 GCAGAAAGCTATCCACTCTGTTC 59.379 47.826 0.00 0.00 41.15 3.18
4376 8802 3.128589 GCAAAACCCTCGCATTATCTCAA 59.871 43.478 0.00 0.00 0.00 3.02
4381 8807 1.476488 GGTGCAAAACCCTCGCATTAT 59.524 47.619 0.00 0.00 44.02 1.28
4383 8809 1.665442 GGTGCAAAACCCTCGCATT 59.335 52.632 0.00 0.00 44.02 3.56
4384 8810 3.365535 GGTGCAAAACCCTCGCAT 58.634 55.556 0.00 0.00 44.02 4.73
4392 8818 5.356426 ACAGAAATACCAAAGGTGCAAAAC 58.644 37.500 0.00 0.00 36.19 2.43
4393 8819 5.606348 ACAGAAATACCAAAGGTGCAAAA 57.394 34.783 0.00 0.00 36.19 2.44
4394 8820 5.127845 TGAACAGAAATACCAAAGGTGCAAA 59.872 36.000 0.00 0.00 36.19 3.68
4395 8821 4.646945 TGAACAGAAATACCAAAGGTGCAA 59.353 37.500 0.00 0.00 36.19 4.08
4396 8822 4.211125 TGAACAGAAATACCAAAGGTGCA 58.789 39.130 0.00 0.00 36.19 4.57
4397 8823 4.278419 ACTGAACAGAAATACCAAAGGTGC 59.722 41.667 8.87 0.00 36.19 5.01
4398 8824 5.278463 CCACTGAACAGAAATACCAAAGGTG 60.278 44.000 8.87 0.00 36.19 4.00
4399 8825 4.827284 CCACTGAACAGAAATACCAAAGGT 59.173 41.667 8.87 0.00 40.16 3.50
4400 8826 4.827284 ACCACTGAACAGAAATACCAAAGG 59.173 41.667 8.87 0.00 0.00 3.11
4401 8827 5.299279 ACACCACTGAACAGAAATACCAAAG 59.701 40.000 8.87 0.00 0.00 2.77
4422 8848 4.151335 CAGTCACTTCAGAACATAGCACAC 59.849 45.833 0.00 0.00 0.00 3.82
4423 8849 4.309933 CAGTCACTTCAGAACATAGCACA 58.690 43.478 0.00 0.00 0.00 4.57
4578 10429 9.098355 TCTGTGATACTTGACATTTATAACTGC 57.902 33.333 2.90 0.00 0.00 4.40
4608 10459 1.939974 TAGCTTGGATGCGCTTGTAG 58.060 50.000 9.73 0.64 37.68 2.74
4682 10537 6.864342 TCTTAGACCTACTATTGCAAGTGAC 58.136 40.000 4.94 0.00 0.00 3.67
4766 10621 1.421410 CCGACGAAAAGATCAGCCCG 61.421 60.000 0.00 0.00 0.00 6.13
4835 10690 6.040166 CCCAGGTGAAGAATATTTCAATGGAG 59.960 42.308 16.95 8.79 42.85 3.86
4872 10727 4.013267 ACCCATCCAATTGATCGAGATC 57.987 45.455 7.12 6.16 38.29 2.75
4915 10779 2.414058 TTGTAAGCGCATGTTTGTGG 57.586 45.000 11.47 0.00 33.82 4.17


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

AutoCloner maintained by Alex Coulton.