Multiple sequence alignment - TraesCS2D01G142100

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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 TraesCS2D01G142100 chr2D 100.000 4438 0 0 1 4438 83825623 83821186 0.000000e+00 8196.0
1 TraesCS2D01G142100 chr2D 88.052 385 21 6 791 1169 83833640 83833275 2.450000e-117 433.0
2 TraesCS2D01G142100 chr2D 78.652 445 76 15 27 459 144999742 144999305 1.220000e-70 278.0
3 TraesCS2D01G142100 chr2D 94.167 120 7 0 4077 4196 84761326 84761445 2.730000e-42 183.0
4 TraesCS2D01G142100 chr2D 100.000 40 0 0 3662 3701 83821926 83821887 1.710000e-09 75.0
5 TraesCS2D01G142100 chr2D 100.000 40 0 0 3698 3737 83821962 83821923 1.710000e-09 75.0
6 TraesCS2D01G142100 chr2D 80.612 98 14 4 408 502 555310046 555309951 2.210000e-08 71.3
7 TraesCS2D01G142100 chr2D 100.000 30 0 0 4203 4232 84761492 84761521 6.200000e-04 56.5
8 TraesCS2D01G142100 chr2B 88.957 3894 276 68 20 3830 135695134 135691312 0.000000e+00 4667.0
9 TraesCS2D01G142100 chr2B 90.859 361 16 3 3877 4237 135691314 135690971 6.720000e-128 468.0
10 TraesCS2D01G142100 chr2B 90.498 221 7 3 4232 4438 135690200 135689980 3.380000e-71 279.0
11 TraesCS2D01G142100 chr2B 78.400 375 50 14 3856 4202 136620281 136620652 9.670000e-52 215.0
12 TraesCS2D01G142100 chr2B 100.000 30 0 0 4203 4232 136620692 136620721 6.200000e-04 56.5
13 TraesCS2D01G142100 chr2A 92.078 3219 167 40 1 3192 84555930 84552773 0.000000e+00 4451.0
14 TraesCS2D01G142100 chr2A 93.836 438 22 2 3229 3662 84552712 84552276 0.000000e+00 654.0
15 TraesCS2D01G142100 chr2A 94.041 386 17 4 3858 4237 84552044 84551659 8.270000e-162 580.0
16 TraesCS2D01G142100 chr2A 90.634 363 22 5 791 1146 84586877 84586520 5.200000e-129 472.0
17 TraesCS2D01G142100 chr2A 79.947 374 46 12 3856 4202 85596244 85596615 9.530000e-62 248.0
18 TraesCS2D01G142100 chr2A 93.293 164 11 0 3698 3861 84552265 84552102 4.430000e-60 243.0
19 TraesCS2D01G142100 chr2A 86.878 221 13 4 4232 4438 84550885 84550667 2.670000e-57 233.0
20 TraesCS2D01G142100 chr2A 81.457 151 16 6 518 660 752911152 752911006 3.630000e-21 113.0
21 TraesCS2D01G142100 chr2A 80.723 83 5 4 1260 1341 84586478 84586406 2.000000e-03 54.7
22 TraesCS2D01G142100 chr6B 85.411 1885 182 45 1678 3511 658295883 658297725 0.000000e+00 1871.0
23 TraesCS2D01G142100 chr6B 87.216 352 28 12 828 1168 658275962 658276307 6.960000e-103 385.0
24 TraesCS2D01G142100 chr6B 86.626 329 27 12 850 1171 658291323 658291641 9.140000e-92 348.0
25 TraesCS2D01G142100 chr6B 80.226 177 16 8 3541 3703 658297779 658297950 1.010000e-21 115.0
26 TraesCS2D01G142100 chr6B 83.333 84 13 1 420 502 43156281 43156364 4.760000e-10 76.8
27 TraesCS2D01G142100 chr6D 84.560 1250 130 32 2283 3511 435306986 435308193 0.000000e+00 1181.0
28 TraesCS2D01G142100 chr6D 87.337 766 76 11 1490 2244 435306166 435306921 0.000000e+00 857.0
29 TraesCS2D01G142100 chr6D 81.148 488 78 12 28 502 91040176 91039690 3.240000e-101 379.0
30 TraesCS2D01G142100 chr6D 87.021 339 24 13 842 1165 435300377 435300710 9.070000e-97 364.0
31 TraesCS2D01G142100 chr6D 80.451 133 11 4 3581 3702 435308273 435308401 2.200000e-13 87.9
32 TraesCS2D01G142100 chr6A 87.971 823 83 10 1658 2465 582252727 582253548 0.000000e+00 957.0
33 TraesCS2D01G142100 chr6A 84.043 1034 104 30 2507 3511 582253559 582254560 0.000000e+00 939.0
34 TraesCS2D01G142100 chr6A 86.626 329 24 13 850 1171 582248688 582249003 3.290000e-91 346.0
35 TraesCS2D01G142100 chr6A 81.538 130 9 4 3581 3699 582254640 582254765 4.730000e-15 93.5
36 TraesCS2D01G142100 chr1A 82.261 575 96 6 1674 2245 15345950 15345379 3.990000e-135 492.0
37 TraesCS2D01G142100 chr1A 86.486 296 31 5 846 1141 15348433 15348147 2.580000e-82 316.0
38 TraesCS2D01G142100 chr4D 82.082 413 61 7 26 427 507758719 507758309 1.530000e-89 340.0
39 TraesCS2D01G142100 chr7B 79.303 488 77 17 20 495 166965792 166965317 1.990000e-83 320.0
40 TraesCS2D01G142100 chr7B 76.360 478 89 14 27 497 289194712 289194252 7.420000e-58 235.0
41 TraesCS2D01G142100 chr3D 84.013 319 46 3 26 340 438630248 438629931 7.210000e-78 302.0
42 TraesCS2D01G142100 chr5D 79.333 450 76 12 37 474 394532043 394531599 2.590000e-77 300.0
43 TraesCS2D01G142100 chr5D 79.167 432 72 12 26 447 404474205 404473782 2.610000e-72 283.0
44 TraesCS2D01G142100 chr5D 87.273 55 5 2 506 559 133249340 133249393 1.330000e-05 62.1
45 TraesCS2D01G142100 chr5D 87.273 55 3 4 506 559 118272532 118272583 4.790000e-05 60.2
46 TraesCS2D01G142100 chr7A 76.220 164 33 5 343 502 79819792 79819953 1.020000e-11 82.4
47 TraesCS2D01G142100 chr7A 87.273 55 5 2 449 502 50423417 50423470 1.330000e-05 62.1
48 TraesCS2D01G142100 chr5A 85.135 74 6 2 615 684 76727947 76727875 2.210000e-08 71.3


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 TraesCS2D01G142100 chr2D 83821186 83825623 4437 True 2782.000000 8196 100.000000 1 4438 3 chr2D.!!$R4 4437
1 TraesCS2D01G142100 chr2B 135689980 135695134 5154 True 1804.666667 4667 90.104667 20 4438 3 chr2B.!!$R1 4418
2 TraesCS2D01G142100 chr2A 84550667 84555930 5263 True 1232.200000 4451 92.025200 1 4438 5 chr2A.!!$R2 4437
3 TraesCS2D01G142100 chr6B 658295883 658297950 2067 False 993.000000 1871 82.818500 1678 3703 2 chr6B.!!$F4 2025
4 TraesCS2D01G142100 chr6D 435306166 435308401 2235 False 708.633333 1181 84.116000 1490 3702 3 chr6D.!!$F2 2212
5 TraesCS2D01G142100 chr6A 582248688 582254765 6077 False 583.875000 957 85.044500 850 3699 4 chr6A.!!$F1 2849
6 TraesCS2D01G142100 chr1A 15345379 15348433 3054 True 404.000000 492 84.373500 846 2245 2 chr1A.!!$R1 1399

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
281 283 0.178873 AGTAAGGGGGAGAAGTGGCA 60.179 55.0 0.0 0.0 0.00 4.92 F
288 290 0.248843 GGGAGAAGTGGCAGAGTGAG 59.751 60.0 0.0 0.0 0.00 3.51 F
2109 6455 0.689623 CACCTTCTGGTTCTCCTGCT 59.310 55.0 0.0 0.0 46.05 4.24 F
3261 7707 0.107945 AGCAGCTCGAACTCCATTCC 60.108 55.0 0.0 0.0 33.26 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 6455 0.036164 ACGTACCCAAGCAGCATCAA 59.964 50.000 0.00 0.0 0.0 2.57 R
2192 6538 1.078848 GAGCTTGATCGTGGGCAGT 60.079 57.895 0.00 0.0 0.0 4.40 R
3414 7875 1.009829 GCGACATAGTTGGCCTTCTG 58.990 55.000 3.32 0.0 0.0 3.02 R
4344 9723 0.460284 AGATTGTGCGCCGAGTAAGG 60.460 55.000 4.18 0.0 0.0 2.69 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
60 61 8.461222 TCGAAAATAAGCTCAATGACATTTGAT 58.539 29.630 0.00 0.00 35.20 2.57
76 78 4.778143 ATCGAACACCTGCCGGCC 62.778 66.667 26.77 6.44 0.00 6.13
137 139 1.058284 TACCTGGGTACAAACGGCTT 58.942 50.000 0.00 0.00 0.00 4.35
200 202 0.608856 TGCTGGTTGCGAATGTCCAT 60.609 50.000 0.00 0.00 46.63 3.41
281 283 0.178873 AGTAAGGGGGAGAAGTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
288 290 0.248843 GGGAGAAGTGGCAGAGTGAG 59.751 60.000 0.00 0.00 0.00 3.51
301 303 3.124297 GCAGAGTGAGAGAAAATTGGACG 59.876 47.826 0.00 0.00 0.00 4.79
355 357 3.203716 GAGTCCAATTGTTATCCGGACC 58.796 50.000 6.12 0.00 46.00 4.46
359 361 1.064314 CAATTGTTATCCGGACCCCCA 60.064 52.381 6.12 0.00 0.00 4.96
383 385 1.302511 CACCCCCACTTTGTCTCCG 60.303 63.158 0.00 0.00 0.00 4.63
433 436 2.031314 CGAGCGAACCGATACAAGACTA 59.969 50.000 0.00 0.00 0.00 2.59
439 442 5.396484 CGAACCGATACAAGACTACTTTGA 58.604 41.667 0.00 0.00 33.70 2.69
454 457 1.613437 CTTTGAATGGCTTCCACGGTT 59.387 47.619 0.00 0.00 35.80 4.44
495 499 4.016706 CGGGCGGTTTGAGGGTCT 62.017 66.667 0.00 0.00 0.00 3.85
662 695 2.095059 ACAACAGAAAATGGAGATGCGC 60.095 45.455 0.00 0.00 0.00 6.09
678 711 1.596727 TGCGCAATTTTTGGAAAGCAC 59.403 42.857 8.16 0.00 0.00 4.40
759 826 4.227134 GCCGCTGCTAGCCTGCTA 62.227 66.667 21.86 0.00 38.18 3.49
760 827 2.279784 CCGCTGCTAGCCTGCTAC 60.280 66.667 21.86 2.86 38.18 3.58
761 828 2.279784 CGCTGCTAGCCTGCTACC 60.280 66.667 21.86 0.00 38.18 3.18
762 829 2.110006 GCTGCTAGCCTGCTACCC 59.890 66.667 13.29 0.00 34.48 3.69
763 830 2.419198 CTGCTAGCCTGCTACCCG 59.581 66.667 13.29 0.00 0.00 5.28
764 831 3.798954 CTGCTAGCCTGCTACCCGC 62.799 68.421 13.29 0.00 39.77 6.13
765 832 3.541713 GCTAGCCTGCTACCCGCT 61.542 66.667 2.29 0.00 40.11 5.52
766 833 2.419198 CTAGCCTGCTACCCGCTG 59.581 66.667 0.00 0.00 40.11 5.18
940 1025 4.764336 CGCTCGCCGTCGTGGTTA 62.764 66.667 0.00 0.00 41.21 2.85
941 1026 3.177249 GCTCGCCGTCGTGGTTAC 61.177 66.667 0.00 0.00 41.21 2.50
1236 1926 5.066593 TGATAATTTGCTACACCACACACA 58.933 37.500 0.00 0.00 0.00 3.72
1239 1929 1.948104 TTGCTACACCACACACACTC 58.052 50.000 0.00 0.00 0.00 3.51
1240 1930 1.119684 TGCTACACCACACACACTCT 58.880 50.000 0.00 0.00 0.00 3.24
1241 1931 1.484653 TGCTACACCACACACACTCTT 59.515 47.619 0.00 0.00 0.00 2.85
1242 1932 2.135933 GCTACACCACACACACTCTTC 58.864 52.381 0.00 0.00 0.00 2.87
1243 1933 2.394708 CTACACCACACACACTCTTCG 58.605 52.381 0.00 0.00 0.00 3.79
1245 1935 1.209128 CACCACACACACTCTTCGTC 58.791 55.000 0.00 0.00 0.00 4.20
1261 1951 3.663995 TCGTCGTTGGGTTAATCTTGA 57.336 42.857 0.00 0.00 0.00 3.02
1399 2090 0.833287 TGAGATGGAGTAAGCTGCCC 59.167 55.000 0.00 0.00 31.52 5.36
1414 2582 2.335712 GCCCGAAACTGAAGGCTGG 61.336 63.158 0.00 0.00 42.34 4.85
1551 5591 8.242053 ACAATGAAAGAAGATGACTTGCATTAG 58.758 33.333 11.82 9.68 45.95 1.73
1629 5702 4.346734 ACAGATGAACATTGTCGCATTC 57.653 40.909 6.57 0.00 0.00 2.67
1653 5730 5.163152 CCATCCTAACTCCTAAAATCCAGCT 60.163 44.000 0.00 0.00 0.00 4.24
1763 6109 2.612972 CCAACTATACCGCATGCTAGGG 60.613 54.545 17.13 12.37 0.00 3.53
1827 6173 1.447838 GTCATCGCCGTCATGTGGT 60.448 57.895 8.24 0.00 0.00 4.16
1997 6343 3.805307 CCGCTCGTCGTCTGCTCT 61.805 66.667 0.00 0.00 36.19 4.09
2109 6455 0.689623 CACCTTCTGGTTCTCCTGCT 59.310 55.000 0.00 0.00 46.05 4.24
2192 6538 0.452618 CCGACGCGTTCAACTACGTA 60.453 55.000 15.53 0.00 43.22 3.57
2198 6544 1.343506 CGTTCAACTACGTACTGCCC 58.656 55.000 0.00 0.00 36.80 5.36
2249 6595 4.879545 GTCATGGTTTGGTCGGTACATATT 59.120 41.667 0.00 0.00 0.00 1.28
2250 6596 6.050432 GTCATGGTTTGGTCGGTACATATTA 58.950 40.000 0.00 0.00 0.00 0.98
2251 6597 6.708949 GTCATGGTTTGGTCGGTACATATTAT 59.291 38.462 0.00 0.00 0.00 1.28
2252 6598 7.874016 GTCATGGTTTGGTCGGTACATATTATA 59.126 37.037 0.00 0.00 0.00 0.98
2253 6599 8.598916 TCATGGTTTGGTCGGTACATATTATAT 58.401 33.333 0.00 0.00 0.00 0.86
2311 6683 8.928733 CCATTATTGATTTTGAGTTTGTTGAGG 58.071 33.333 0.00 0.00 0.00 3.86
2356 6728 4.083271 GCGTTTGAGCTTCTGGTTCTTATT 60.083 41.667 0.00 0.00 0.00 1.40
2489 6872 2.233271 GTAGGCCATGACCCATGATTG 58.767 52.381 5.01 0.00 43.81 2.67
2491 6874 1.502039 AGGCCATGACCCATGATTGAT 59.498 47.619 5.01 0.00 43.81 2.57
2492 6875 2.090943 AGGCCATGACCCATGATTGATT 60.091 45.455 5.01 0.00 43.81 2.57
2493 6876 2.036733 GGCCATGACCCATGATTGATTG 59.963 50.000 0.00 0.00 43.81 2.67
2494 6877 2.036733 GCCATGACCCATGATTGATTGG 59.963 50.000 8.38 0.00 43.81 3.16
2538 6926 3.815569 CTCGAGCACGGAGGCGATC 62.816 68.421 0.00 0.00 40.21 3.69
2560 6948 2.288273 GCCTACATGATCACCTACGGAC 60.288 54.545 0.00 0.00 0.00 4.79
2568 6956 0.538746 TCACCTACGGACTCAGTGCA 60.539 55.000 0.00 0.00 0.00 4.57
2591 6979 3.310774 GCTGTAAGGTACGTACGATCTCA 59.689 47.826 24.41 12.60 45.96 3.27
2593 6981 5.505324 GCTGTAAGGTACGTACGATCTCAAT 60.505 44.000 24.41 0.00 45.96 2.57
2594 6982 6.441093 TGTAAGGTACGTACGATCTCAATT 57.559 37.500 24.41 9.26 45.96 2.32
2607 6995 7.736447 ACGATCTCAATTCTCAAGTTCTTTT 57.264 32.000 0.00 0.00 0.00 2.27
2633 7033 3.165498 CGTAAGCACGGCCTGTTC 58.835 61.111 0.00 0.00 44.59 3.18
2634 7034 1.374252 CGTAAGCACGGCCTGTTCT 60.374 57.895 0.00 0.00 44.59 3.01
2635 7035 0.949105 CGTAAGCACGGCCTGTTCTT 60.949 55.000 14.42 14.42 44.59 2.52
2636 7036 1.235724 GTAAGCACGGCCTGTTCTTT 58.764 50.000 14.98 5.94 35.59 2.52
2637 7037 1.197036 GTAAGCACGGCCTGTTCTTTC 59.803 52.381 14.98 8.67 35.59 2.62
2638 7038 0.179018 AAGCACGGCCTGTTCTTTCT 60.179 50.000 0.00 0.00 29.16 2.52
2639 7039 0.179018 AGCACGGCCTGTTCTTTCTT 60.179 50.000 0.00 0.00 0.00 2.52
2640 7040 1.071699 AGCACGGCCTGTTCTTTCTTA 59.928 47.619 0.00 0.00 0.00 2.10
2641 7041 2.084546 GCACGGCCTGTTCTTTCTTAT 58.915 47.619 0.00 0.00 0.00 1.73
2642 7042 2.096013 GCACGGCCTGTTCTTTCTTATC 59.904 50.000 0.00 0.00 0.00 1.75
2649 7053 6.457528 CGGCCTGTTCTTTCTTATCTTTCATC 60.458 42.308 0.00 0.00 0.00 2.92
2656 7060 6.534059 TCTTTCTTATCTTTCATCGTTTGCG 58.466 36.000 0.00 0.00 39.92 4.85
2694 7098 1.102978 TGTCGAATGAGATCGGAGCA 58.897 50.000 0.00 0.00 42.92 4.26
2708 7112 1.668151 GAGCAGGGAACGTGGACAC 60.668 63.158 0.00 0.00 45.29 3.67
2880 7284 0.817654 TGATGGTCTCGATCGTGCTT 59.182 50.000 15.94 0.00 0.00 3.91
2886 7290 1.131504 GTCTCGATCGTGCTTGACTCT 59.868 52.381 15.94 0.00 0.00 3.24
2913 7317 2.171448 GGGCATACTGTCAGGTGAGAAT 59.829 50.000 4.53 0.00 0.00 2.40
2922 7328 3.181472 TGTCAGGTGAGAATGATCCATCG 60.181 47.826 0.00 0.00 0.00 3.84
2926 7332 2.141517 GTGAGAATGATCCATCGGCTG 58.858 52.381 0.00 0.00 0.00 4.85
2986 7402 6.682113 GCACTGAACAGATAATTTCATGGCAT 60.682 38.462 8.87 0.00 33.87 4.40
3034 7454 1.953686 ACTGTTGGCGCTACACAATTT 59.046 42.857 7.64 0.00 0.00 1.82
3194 7615 5.047519 GCTCAACTTCTACACCAAGGTAGTA 60.048 44.000 0.00 0.00 41.20 1.82
3196 7617 7.549147 TCAACTTCTACACCAAGGTAGTAAT 57.451 36.000 0.00 0.00 41.20 1.89
3198 7619 9.092338 TCAACTTCTACACCAAGGTAGTAATTA 57.908 33.333 0.00 0.00 41.20 1.40
3210 7636 6.718522 AGGTAGTAATTAACTGAGAGCTCC 57.281 41.667 10.93 2.40 39.39 4.70
3214 7640 5.417225 AGTAATTAACTGAGAGCTCCCGCT 61.417 45.833 10.93 0.00 43.25 5.52
3225 7670 1.377725 CTCCCGCTCTTGCCATTGT 60.378 57.895 0.00 0.00 35.36 2.71
3227 7672 2.180017 CCGCTCTTGCCATTGTGC 59.820 61.111 0.00 0.00 35.36 4.57
3261 7707 0.107945 AGCAGCTCGAACTCCATTCC 60.108 55.000 0.00 0.00 33.26 3.01
3291 7749 3.583383 GCTGGAGCGCTGAACATT 58.417 55.556 18.48 0.00 0.00 2.71
3301 7762 2.053627 CGCTGAACATTTGCACCTTTC 58.946 47.619 0.00 0.00 0.00 2.62
3443 7904 3.183172 CCAACTATGTCGCTTGATCGATG 59.817 47.826 0.54 0.00 40.84 3.84
3602 8122 4.578601 GAAAGATCGAACTTGTAATGGCG 58.421 43.478 8.86 0.00 0.00 5.69
3608 8128 5.712217 TCGAACTTGTAATGGCGATTAAG 57.288 39.130 2.42 2.90 0.00 1.85
3625 8145 6.375377 CGATTAAGCAGAGAGTATACAGGAC 58.625 44.000 5.50 0.00 0.00 3.85
3680 8200 6.671605 TCCTCCATGGATGTTCATATTTTCA 58.328 36.000 16.63 0.00 40.56 2.69
3681 8201 7.124721 TCCTCCATGGATGTTCATATTTTCAA 58.875 34.615 16.63 0.00 40.56 2.69
3682 8202 7.286087 TCCTCCATGGATGTTCATATTTTCAAG 59.714 37.037 16.63 0.00 40.56 3.02
3683 8203 7.350744 TCCATGGATGTTCATATTTTCAAGG 57.649 36.000 11.44 0.00 0.00 3.61
3684 8204 7.124721 TCCATGGATGTTCATATTTTCAAGGA 58.875 34.615 11.44 0.00 0.00 3.36
3685 8205 7.068593 TCCATGGATGTTCATATTTTCAAGGAC 59.931 37.037 11.44 0.00 0.00 3.85
3686 8206 6.435430 TGGATGTTCATATTTTCAAGGACG 57.565 37.500 0.00 0.00 0.00 4.79
3687 8207 5.163663 TGGATGTTCATATTTTCAAGGACGC 60.164 40.000 0.00 0.00 0.00 5.19
3688 8208 4.335082 TGTTCATATTTTCAAGGACGCG 57.665 40.909 3.53 3.53 0.00 6.01
3689 8209 3.126171 TGTTCATATTTTCAAGGACGCGG 59.874 43.478 12.47 0.00 0.00 6.46
3690 8210 3.254470 TCATATTTTCAAGGACGCGGA 57.746 42.857 12.47 0.00 0.00 5.54
3691 8211 3.601435 TCATATTTTCAAGGACGCGGAA 58.399 40.909 12.47 0.00 0.00 4.30
3692 8212 4.196193 TCATATTTTCAAGGACGCGGAAT 58.804 39.130 12.47 0.00 0.00 3.01
3693 8213 5.361427 TCATATTTTCAAGGACGCGGAATA 58.639 37.500 12.47 0.00 0.00 1.75
3694 8214 5.995282 TCATATTTTCAAGGACGCGGAATAT 59.005 36.000 12.47 7.10 0.00 1.28
3695 8215 7.156000 TCATATTTTCAAGGACGCGGAATATA 58.844 34.615 12.47 9.06 0.00 0.86
3725 8245 3.126171 TGTTCATATTTTCAAGGACGCGG 59.874 43.478 12.47 0.00 0.00 6.46
3741 8261 1.935873 CGCGGAATATATCATGCTGGG 59.064 52.381 0.00 0.00 0.00 4.45
3768 8294 1.755179 CCTTGCCAATACCAGGACAG 58.245 55.000 0.00 0.00 0.00 3.51
3884 8472 5.359194 TTTACTGCCTGAATAAGAGAGGG 57.641 43.478 0.00 0.00 0.00 4.30
3890 8478 2.158696 CCTGAATAAGAGAGGGGGCAAG 60.159 54.545 0.00 0.00 0.00 4.01
3896 8484 0.988063 AGAGAGGGGGCAAGAGAAAC 59.012 55.000 0.00 0.00 0.00 2.78
4004 8596 5.424895 TGCCCAATTGCCTCATTATTTAGTT 59.575 36.000 0.00 0.00 0.00 2.24
4011 8603 4.079787 TGCCTCATTATTTAGTTGAGCCCT 60.080 41.667 0.00 0.00 36.41 5.19
4120 8713 5.647658 CCATAATACTTCAGAGCCACAACAA 59.352 40.000 0.00 0.00 0.00 2.83
4122 8715 2.717639 ACTTCAGAGCCACAACAACT 57.282 45.000 0.00 0.00 0.00 3.16
4263 9642 0.598562 ATGCCTATAGTCGAGCACCG 59.401 55.000 3.86 0.00 38.21 4.94
4285 9664 4.922103 CGTTTCTTCCTCTACTTGGTGTAC 59.078 45.833 0.00 0.00 0.00 2.90
4355 9748 0.742505 TATGTGACCCTTACTCGGCG 59.257 55.000 0.00 0.00 0.00 6.46
4415 9808 9.947433 TTCTGAATTTGCATCAAATCCTTTTAT 57.053 25.926 5.39 0.00 42.32 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.025793 TGTTGATTTAAGGATGGCGGGA 60.026 45.455 0.00 0.00 0.00 5.14
264 266 0.118346 TCTGCCACTTCTCCCCCTTA 59.882 55.000 0.00 0.00 0.00 2.69
267 269 1.920835 ACTCTGCCACTTCTCCCCC 60.921 63.158 0.00 0.00 0.00 5.40
281 283 3.578716 TCCGTCCAATTTTCTCTCACTCT 59.421 43.478 0.00 0.00 0.00 3.24
288 290 2.094700 GCCCTTTCCGTCCAATTTTCTC 60.095 50.000 0.00 0.00 0.00 2.87
301 303 1.389555 CCACTAAATCCGCCCTTTCC 58.610 55.000 0.00 0.00 0.00 3.13
359 361 1.075600 CAAAGTGGGGGTGGGTTGT 60.076 57.895 0.00 0.00 0.00 3.32
433 436 1.247567 CCGTGGAAGCCATTCAAAGT 58.752 50.000 0.00 0.00 37.15 2.66
439 442 1.674322 CCGAACCGTGGAAGCCATT 60.674 57.895 0.00 0.00 35.28 3.16
454 457 4.807631 TCTGGATCCGCGGTCCGA 62.808 66.667 29.30 25.99 38.64 4.55
495 499 9.077885 AGAAAATAAATTCTTCCTAGCAACACA 57.922 29.630 0.00 0.00 36.23 3.72
608 641 4.980434 GTCATGATTTGCTGCCATGATAAC 59.020 41.667 17.95 6.80 45.47 1.89
662 695 8.914328 AATTGAAAAGTGCTTTCCAAAAATTG 57.086 26.923 0.76 0.00 42.51 2.32
678 711 5.684626 GCAGATAGCGATCCAAATTGAAAAG 59.315 40.000 2.88 0.00 31.81 2.27
742 809 4.227134 TAGCAGGCTAGCAGCGGC 62.227 66.667 18.24 12.29 43.62 6.53
743 810 2.279784 GTAGCAGGCTAGCAGCGG 60.280 66.667 18.24 1.67 43.62 5.52
744 811 2.279784 GGTAGCAGGCTAGCAGCG 60.280 66.667 21.79 4.93 43.62 5.18
745 812 2.110006 GGGTAGCAGGCTAGCAGC 59.890 66.667 26.11 19.31 45.68 5.25
746 813 2.419198 CGGGTAGCAGGCTAGCAG 59.581 66.667 26.11 20.43 45.68 4.24
747 814 3.849951 GCGGGTAGCAGGCTAGCA 61.850 66.667 26.11 0.00 45.68 3.49
937 1022 0.994263 ATCAAGCGGCGTAACGTAAC 59.006 50.000 9.37 0.00 35.98 2.50
938 1023 1.270971 GATCAAGCGGCGTAACGTAA 58.729 50.000 9.37 0.00 35.98 3.18
939 1024 0.862701 CGATCAAGCGGCGTAACGTA 60.863 55.000 9.37 0.00 35.98 3.57
940 1025 2.156446 CGATCAAGCGGCGTAACGT 61.156 57.895 9.37 0.00 35.98 3.99
941 1026 1.870458 TCGATCAAGCGGCGTAACG 60.870 57.895 9.37 6.73 0.00 3.18
1236 1926 3.257624 AGATTAACCCAACGACGAAGAGT 59.742 43.478 0.00 0.00 0.00 3.24
1239 1929 3.991773 TCAAGATTAACCCAACGACGAAG 59.008 43.478 0.00 0.00 0.00 3.79
1240 1930 3.992643 TCAAGATTAACCCAACGACGAA 58.007 40.909 0.00 0.00 0.00 3.85
1241 1931 3.663995 TCAAGATTAACCCAACGACGA 57.336 42.857 0.00 0.00 0.00 4.20
1242 1932 4.153475 ACAATCAAGATTAACCCAACGACG 59.847 41.667 0.00 0.00 0.00 5.12
1243 1933 5.622770 ACAATCAAGATTAACCCAACGAC 57.377 39.130 0.00 0.00 0.00 4.34
1245 1935 4.390603 TCGACAATCAAGATTAACCCAACG 59.609 41.667 0.00 0.00 0.00 4.10
1288 1979 8.691797 GTCTGAAGGGGTGCAATTAATTAATAA 58.308 33.333 11.07 0.00 0.00 1.40
1399 2090 1.884235 ACTTCCAGCCTTCAGTTTCG 58.116 50.000 0.00 0.00 0.00 3.46
1414 2582 0.733150 GGCTGGCCGAAATGTACTTC 59.267 55.000 0.00 0.00 0.00 3.01
1566 5606 3.355378 TGGGACCGTCTATTCGTTAAGA 58.645 45.455 0.00 0.00 0.00 2.10
1571 5611 3.703052 ACTTATTGGGACCGTCTATTCGT 59.297 43.478 0.00 0.00 0.00 3.85
1581 5624 5.506708 ACAAGTTATGGACTTATTGGGACC 58.493 41.667 0.00 0.00 46.75 4.46
1608 5651 3.127548 GGAATGCGACAATGTTCATCTGT 59.872 43.478 3.31 0.00 0.00 3.41
1629 5702 5.066593 GCTGGATTTTAGGAGTTAGGATGG 58.933 45.833 0.00 0.00 0.00 3.51
1763 6109 1.801913 CGACGACTGCAGGTACAGC 60.802 63.158 19.93 0.00 41.60 4.40
1827 6173 2.664851 CAGCGGCTCCGTGAACAA 60.665 61.111 10.24 0.00 42.09 2.83
2078 6424 0.842030 AGAAGGTGGTGGAGATGGCA 60.842 55.000 0.00 0.00 0.00 4.92
2109 6455 0.036164 ACGTACCCAAGCAGCATCAA 59.964 50.000 0.00 0.00 0.00 2.57
2192 6538 1.078848 GAGCTTGATCGTGGGCAGT 60.079 57.895 0.00 0.00 0.00 4.40
2198 6544 2.507102 ACGGCGAGCTTGATCGTG 60.507 61.111 16.62 5.78 44.53 4.35
2311 6683 2.047274 TACTCCAAGCTGCACGCC 60.047 61.111 1.02 0.00 40.39 5.68
2356 6728 2.813226 AATTCGGTAGCAAGCCCGCA 62.813 55.000 5.09 0.00 43.87 5.69
2454 6837 2.615493 GGCCTACGGATAACATGATGGG 60.615 54.545 0.00 0.00 0.00 4.00
2489 6872 4.003648 AGAAGTCCATTCGTTCACCAATC 58.996 43.478 0.00 0.00 43.16 2.67
2491 6874 3.485463 AGAAGTCCATTCGTTCACCAA 57.515 42.857 0.00 0.00 43.16 3.67
2492 6875 4.610605 TTAGAAGTCCATTCGTTCACCA 57.389 40.909 0.00 0.00 43.16 4.17
2493 6876 5.673818 GCATTTAGAAGTCCATTCGTTCACC 60.674 44.000 0.00 0.00 43.16 4.02
2494 6877 5.106712 TGCATTTAGAAGTCCATTCGTTCAC 60.107 40.000 0.00 0.00 43.16 3.18
2538 6926 2.051879 CGTAGGTGATCATGTAGGCG 57.948 55.000 0.00 0.00 0.00 5.52
2568 6956 3.539604 AGATCGTACGTACCTTACAGCT 58.460 45.455 19.67 4.48 0.00 4.24
2616 7004 0.949105 AAGAACAGGCCGTGCTTACG 60.949 55.000 16.46 0.00 42.19 3.18
2626 7026 6.092807 ACGATGAAAGATAAGAAAGAACAGGC 59.907 38.462 0.00 0.00 0.00 4.85
2633 7033 5.225949 GCGCAAACGATGAAAGATAAGAAAG 59.774 40.000 0.30 0.00 43.93 2.62
2634 7034 5.086058 GCGCAAACGATGAAAGATAAGAAA 58.914 37.500 0.30 0.00 43.93 2.52
2635 7035 4.436852 GGCGCAAACGATGAAAGATAAGAA 60.437 41.667 10.83 0.00 43.93 2.52
2636 7036 3.063452 GGCGCAAACGATGAAAGATAAGA 59.937 43.478 10.83 0.00 43.93 2.10
2637 7037 3.063997 AGGCGCAAACGATGAAAGATAAG 59.936 43.478 10.83 0.00 43.93 1.73
2638 7038 3.006940 AGGCGCAAACGATGAAAGATAA 58.993 40.909 10.83 0.00 43.93 1.75
2639 7039 2.627945 AGGCGCAAACGATGAAAGATA 58.372 42.857 10.83 0.00 43.93 1.98
2640 7040 1.453155 AGGCGCAAACGATGAAAGAT 58.547 45.000 10.83 0.00 43.93 2.40
2641 7041 1.234821 AAGGCGCAAACGATGAAAGA 58.765 45.000 10.83 0.00 43.93 2.52
2642 7042 2.050477 AAAGGCGCAAACGATGAAAG 57.950 45.000 10.83 0.00 43.93 2.62
2656 7060 4.362476 CCGGGTGCTGCAAAAGGC 62.362 66.667 2.77 0.00 45.13 4.35
2708 7112 3.913573 CGACCGCATTCTTCGCCG 61.914 66.667 0.00 0.00 0.00 6.46
2860 7264 1.035923 AGCACGATCGAGACCATCAT 58.964 50.000 24.34 0.00 0.00 2.45
2896 7300 4.964897 TGGATCATTCTCACCTGACAGTAT 59.035 41.667 0.93 0.00 0.00 2.12
2922 7328 2.092375 AGATTGGTTTAGGTAGCCAGCC 60.092 50.000 0.00 0.00 33.41 4.85
2926 7332 5.497474 TCTTGAAGATTGGTTTAGGTAGCC 58.503 41.667 0.00 0.00 0.00 3.93
2986 7402 5.303259 TCCAATCCATGAATTCGTATCCA 57.697 39.130 0.00 0.00 0.00 3.41
3034 7454 4.244066 CCAATTCATTCGTCAATTTGCCA 58.756 39.130 0.00 0.00 0.00 4.92
3210 7636 2.180017 GCACAATGGCAAGAGCGG 59.820 61.111 0.00 0.00 43.41 5.52
3225 7670 1.105457 GCTTGCTATCCCACATTGCA 58.895 50.000 0.00 0.00 0.00 4.08
3227 7672 1.066605 GCTGCTTGCTATCCCACATTG 59.933 52.381 0.00 0.00 38.95 2.82
3261 7707 2.033407 CGCTCCAGCTCATTATGTTTCG 60.033 50.000 0.00 0.00 39.32 3.46
3282 7740 3.375782 AGAAAGGTGCAAATGTTCAGC 57.624 42.857 0.00 0.00 0.00 4.26
3290 7748 3.637769 ACCCTGTAAAGAAAGGTGCAAA 58.362 40.909 0.00 0.00 0.00 3.68
3291 7749 3.306472 ACCCTGTAAAGAAAGGTGCAA 57.694 42.857 0.00 0.00 0.00 4.08
3301 7762 3.275999 CCCGACCATAAACCCTGTAAAG 58.724 50.000 0.00 0.00 0.00 1.85
3351 7812 3.127533 GATCACCACCAGCGTGCC 61.128 66.667 0.00 0.00 38.79 5.01
3414 7875 1.009829 GCGACATAGTTGGCCTTCTG 58.990 55.000 3.32 0.00 0.00 3.02
3443 7904 3.951979 GTGCTAGCCACACACAATATC 57.048 47.619 13.29 0.00 44.06 1.63
3602 8122 7.278461 TGTCCTGTATACTCTCTGCTTAATC 57.722 40.000 4.17 0.00 0.00 1.75
3608 8128 5.073311 TGTTTGTCCTGTATACTCTCTGC 57.927 43.478 4.17 0.00 0.00 4.26
3625 8145 2.605818 CACGTCCCGGTATGTATGTTTG 59.394 50.000 0.00 0.00 0.00 2.93
3662 8182 6.460123 GCGTCCTTGAAAATATGAACATCCAT 60.460 38.462 0.00 0.00 0.00 3.41
3663 8183 5.163663 GCGTCCTTGAAAATATGAACATCCA 60.164 40.000 0.00 0.00 0.00 3.41
3664 8184 5.273944 GCGTCCTTGAAAATATGAACATCC 58.726 41.667 0.00 0.00 0.00 3.51
3665 8185 4.963953 CGCGTCCTTGAAAATATGAACATC 59.036 41.667 0.00 0.00 0.00 3.06
3666 8186 4.201910 CCGCGTCCTTGAAAATATGAACAT 60.202 41.667 4.92 0.00 0.00 2.71
3667 8187 3.126171 CCGCGTCCTTGAAAATATGAACA 59.874 43.478 4.92 0.00 0.00 3.18
3668 8188 3.372822 TCCGCGTCCTTGAAAATATGAAC 59.627 43.478 4.92 0.00 0.00 3.18
3669 8189 3.601435 TCCGCGTCCTTGAAAATATGAA 58.399 40.909 4.92 0.00 0.00 2.57
3670 8190 3.254470 TCCGCGTCCTTGAAAATATGA 57.746 42.857 4.92 0.00 0.00 2.15
3672 8192 7.822334 TGATATATTCCGCGTCCTTGAAAATAT 59.178 33.333 4.92 0.00 0.00 1.28
3673 8193 7.156000 TGATATATTCCGCGTCCTTGAAAATA 58.844 34.615 4.92 0.00 0.00 1.40
3674 8194 5.995282 TGATATATTCCGCGTCCTTGAAAAT 59.005 36.000 4.92 0.00 0.00 1.82
3675 8195 5.361427 TGATATATTCCGCGTCCTTGAAAA 58.639 37.500 4.92 0.00 0.00 2.29
3676 8196 4.951254 TGATATATTCCGCGTCCTTGAAA 58.049 39.130 4.92 0.00 0.00 2.69
3677 8197 4.594123 TGATATATTCCGCGTCCTTGAA 57.406 40.909 4.92 0.51 0.00 2.69
3678 8198 4.494484 CATGATATATTCCGCGTCCTTGA 58.506 43.478 4.92 0.00 0.00 3.02
3679 8199 3.618594 CCATGATATATTCCGCGTCCTTG 59.381 47.826 4.92 0.00 0.00 3.61
3680 8200 3.513912 TCCATGATATATTCCGCGTCCTT 59.486 43.478 4.92 0.00 0.00 3.36
3681 8201 3.096852 TCCATGATATATTCCGCGTCCT 58.903 45.455 4.92 0.00 0.00 3.85
3682 8202 3.520290 TCCATGATATATTCCGCGTCC 57.480 47.619 4.92 0.00 0.00 4.79
3683 8203 4.433615 ACATCCATGATATATTCCGCGTC 58.566 43.478 4.92 0.00 0.00 5.19
3684 8204 4.471904 ACATCCATGATATATTCCGCGT 57.528 40.909 4.92 0.00 0.00 6.01
3685 8205 4.869861 TGAACATCCATGATATATTCCGCG 59.130 41.667 0.00 0.00 0.00 6.46
3686 8206 6.932356 ATGAACATCCATGATATATTCCGC 57.068 37.500 0.00 0.00 0.00 5.54
3694 8214 9.865152 TCCTTGAAAATATGAACATCCATGATA 57.135 29.630 0.00 0.00 0.00 2.15
3695 8215 8.636213 GTCCTTGAAAATATGAACATCCATGAT 58.364 33.333 0.00 0.00 0.00 2.45
3725 8245 2.096496 GCGCACCCAGCATGATATATTC 59.904 50.000 0.30 0.00 46.13 1.75
3768 8294 2.703416 TCTCATTATCCCGCATGATGC 58.297 47.619 7.49 7.49 40.69 3.91
3867 8455 1.511613 CCCCCTCTCTTATTCAGGCA 58.488 55.000 0.00 0.00 0.00 4.75
3884 8472 3.118992 GGGAATGAATGTTTCTCTTGCCC 60.119 47.826 0.00 0.00 31.97 5.36
3890 8478 4.142093 CCACCATGGGAATGAATGTTTCTC 60.142 45.833 18.09 0.00 32.67 2.87
3896 8484 1.784358 AGCCACCATGGGAATGAATG 58.216 50.000 18.09 2.74 38.19 2.67
3925 8513 3.486383 TGCTTTGTAAGGAACCCAGAAG 58.514 45.455 0.00 0.00 0.00 2.85
3926 8514 3.486383 CTGCTTTGTAAGGAACCCAGAA 58.514 45.455 0.00 0.00 0.00 3.02
3927 8515 2.224769 CCTGCTTTGTAAGGAACCCAGA 60.225 50.000 0.00 0.00 35.40 3.86
4120 8713 3.213206 TCATGTCCTTGCTTGTTCAGT 57.787 42.857 0.00 0.00 0.00 3.41
4122 8715 3.503363 GTCATCATGTCCTTGCTTGTTCA 59.497 43.478 0.00 0.00 0.00 3.18
4263 9642 5.221581 TGGTACACCAAGTAGAGGAAGAAAC 60.222 44.000 0.00 0.00 44.35 2.78
4344 9723 0.460284 AGATTGTGCGCCGAGTAAGG 60.460 55.000 4.18 0.00 0.00 2.69
4355 9748 4.320494 CCAGAACAACCAGTAAGATTGTGC 60.320 45.833 0.00 0.00 36.69 4.57
4388 9781 8.857694 AAAAGGATTTGATGCAAATTCAGAAT 57.142 26.923 12.32 0.00 43.05 2.40


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

AutoCloner maintained by Alex Coulton.