Multiple sequence alignment - TraesCS5D01G227500

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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 TraesCS5D01G227500 chr5D 100.000 2617 0 0 1 2617 335083070 335085686 0.000000e+00 4833.0
1 TraesCS5D01G227500 chr5D 92.169 779 56 3 940 1717 335103471 335104245 0.000000e+00 1096.0
2 TraesCS5D01G227500 chr5D 81.962 1009 103 42 734 1689 335060579 335061561 0.000000e+00 782.0
3 TraesCS5D01G227500 chr5D 85.526 304 34 4 95 394 335102660 335102957 2.530000e-80 309.0
4 TraesCS5D01G227500 chr5D 80.667 450 23 19 425 865 335102958 335103352 9.160000e-75 291.0
5 TraesCS5D01G227500 chr5D 100.000 37 0 0 391 427 335083411 335083447 4.670000e-08 69.4
6 TraesCS5D01G227500 chr5D 100.000 37 0 0 342 378 335083460 335083496 4.670000e-08 69.4
7 TraesCS5D01G227500 chr5A 90.602 1362 115 8 1264 2614 436549021 436550380 0.000000e+00 1794.0
8 TraesCS5D01G227500 chr5A 90.508 1338 110 11 1291 2614 436590841 436592175 0.000000e+00 1751.0
9 TraesCS5D01G227500 chr5A 89.568 1342 108 16 1291 2614 436381890 436383217 0.000000e+00 1674.0
10 TraesCS5D01G227500 chr5A 87.573 1368 101 22 425 1755 436373920 436375255 0.000000e+00 1520.0
11 TraesCS5D01G227500 chr5A 91.228 399 26 4 775 1164 436548621 436549019 3.830000e-148 534.0
12 TraesCS5D01G227500 chr5A 85.041 488 61 7 2135 2612 436378522 436379007 1.090000e-133 486.0
13 TraesCS5D01G227500 chr5A 94.330 194 8 2 425 618 436548349 436548539 7.080000e-76 294.0
14 TraesCS5D01G227500 chr5A 93.299 194 10 2 425 618 436613759 436613949 1.530000e-72 283.0
15 TraesCS5D01G227500 chr5A 83.108 296 43 3 95 386 436546121 436546413 2.000000e-66 263.0
16 TraesCS5D01G227500 chr5A 92.308 104 4 3 652 755 436548529 436548628 7.550000e-31 145.0
17 TraesCS5D01G227500 chr5B 89.790 1283 90 19 515 1764 392048140 392049414 0.000000e+00 1605.0
18 TraesCS5D01G227500 chr5B 89.790 1283 90 19 515 1764 392106880 392108154 0.000000e+00 1605.0
19 TraesCS5D01G227500 chr5B 88.556 734 49 15 515 1216 392063125 392063855 0.000000e+00 857.0
20 TraesCS5D01G227500 chr5B 91.606 548 40 4 1218 1764 392064533 392065075 0.000000e+00 752.0
21 TraesCS5D01G227500 chr5B 91.606 548 40 4 1218 1764 392071925 392072467 0.000000e+00 752.0
22 TraesCS5D01G227500 chr5B 91.606 548 40 4 1218 1764 392112349 392112891 0.000000e+00 752.0
23 TraesCS5D01G227500 chr5B 89.861 503 39 4 677 1167 391866490 391866992 1.020000e-178 636.0
24 TraesCS5D01G227500 chr5B 86.632 576 62 7 1926 2493 392113338 392113906 7.950000e-175 623.0
25 TraesCS5D01G227500 chr5B 86.458 576 63 7 1926 2493 392065522 392066090 3.700000e-173 617.0
26 TraesCS5D01G227500 chr5B 86.458 576 63 7 1926 2493 392072914 392073482 3.700000e-173 617.0
27 TraesCS5D01G227500 chr5B 86.702 564 60 7 1926 2481 392049861 392050417 1.720000e-171 612.0
28 TraesCS5D01G227500 chr5B 86.866 434 47 5 1926 2356 392108601 392109027 6.550000e-131 477.0
29 TraesCS5D01G227500 chrUn 88.556 734 49 15 515 1216 341236154 341236884 0.000000e+00 857.0
30 TraesCS5D01G227500 chrUn 74.375 320 64 15 2061 2373 216129750 216129442 1.270000e-23 121.0
31 TraesCS5D01G227500 chr7A 82.234 985 111 33 747 1678 177344750 177343777 0.000000e+00 791.0


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 TraesCS5D01G227500 chr5D 335083070 335085686 2616 False 1657.266667 4833 100.000000 1 2617 3 chr5D.!!$F2 2616
1 TraesCS5D01G227500 chr5D 335060579 335061561 982 False 782.000000 782 81.962000 734 1689 1 chr5D.!!$F1 955
2 TraesCS5D01G227500 chr5D 335102660 335104245 1585 False 565.333333 1096 86.120667 95 1717 3 chr5D.!!$F3 1622
3 TraesCS5D01G227500 chr5A 436590841 436592175 1334 False 1751.000000 1751 90.508000 1291 2614 1 chr5A.!!$F1 1323
4 TraesCS5D01G227500 chr5A 436373920 436383217 9297 False 1226.666667 1674 87.394000 425 2614 3 chr5A.!!$F3 2189
5 TraesCS5D01G227500 chr5A 436546121 436550380 4259 False 606.000000 1794 90.315200 95 2614 5 chr5A.!!$F4 2519
6 TraesCS5D01G227500 chr5B 392048140 392050417 2277 False 1108.500000 1605 88.246000 515 2481 2 chr5B.!!$F2 1966
7 TraesCS5D01G227500 chr5B 392106880 392113906 7026 False 864.250000 1605 88.723500 515 2493 4 chr5B.!!$F5 1978
8 TraesCS5D01G227500 chr5B 392063125 392066090 2965 False 742.000000 857 88.873333 515 2493 3 chr5B.!!$F3 1978
9 TraesCS5D01G227500 chr5B 392071925 392073482 1557 False 684.500000 752 89.032000 1218 2493 2 chr5B.!!$F4 1275
10 TraesCS5D01G227500 chr5B 391866490 391866992 502 False 636.000000 636 89.861000 677 1167 1 chr5B.!!$F1 490
11 TraesCS5D01G227500 chrUn 341236154 341236884 730 False 857.000000 857 88.556000 515 1216 1 chrUn.!!$F1 701
12 TraesCS5D01G227500 chr7A 177343777 177344750 973 True 791.000000 791 82.234000 747 1678 1 chr7A.!!$R1 931

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
349 354 0.108585 ATTCGCCCCGCTTGACATAT 59.891 50.0 0.0 0.0 0.0 1.78 F
731 2676 0.248094 GCGGGTTATGAAAGAAGCGC 60.248 55.0 0.0 0.0 0.0 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 11435 0.946221 CGTTCCAGAGCTCTGCGTTT 60.946 55.0 34.09 1.08 42.47 3.60 R
2516 17471 0.250597 GGGACTTGCTTAACGGTGGT 60.251 55.0 0.00 0.00 0.00 4.16 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
22 23 4.747540 TGTGTCACTTTGTCATATGCAC 57.252 40.909 4.27 0.00 0.00 4.57
23 24 3.186205 TGTGTCACTTTGTCATATGCACG 59.814 43.478 4.27 0.00 0.00 5.34
24 25 3.431912 GTGTCACTTTGTCATATGCACGA 59.568 43.478 0.00 0.00 0.00 4.35
25 26 3.431912 TGTCACTTTGTCATATGCACGAC 59.568 43.478 0.00 5.93 0.00 4.34
26 27 2.666022 TCACTTTGTCATATGCACGACG 59.334 45.455 0.00 0.00 34.78 5.12
27 28 2.666022 CACTTTGTCATATGCACGACGA 59.334 45.455 0.00 0.00 34.78 4.20
28 29 3.306973 CACTTTGTCATATGCACGACGAT 59.693 43.478 0.00 0.00 34.78 3.73
29 30 3.551890 ACTTTGTCATATGCACGACGATC 59.448 43.478 0.00 0.00 34.78 3.69
30 31 3.436700 TTGTCATATGCACGACGATCT 57.563 42.857 0.00 0.00 34.78 2.75
31 32 3.436700 TGTCATATGCACGACGATCTT 57.563 42.857 0.00 0.00 34.78 2.40
32 33 3.372060 TGTCATATGCACGACGATCTTC 58.628 45.455 0.00 0.00 34.78 2.87
33 34 3.181491 TGTCATATGCACGACGATCTTCA 60.181 43.478 0.00 0.00 34.78 3.02
34 35 3.180584 GTCATATGCACGACGATCTTCAC 59.819 47.826 0.00 0.00 0.00 3.18
35 36 3.066760 TCATATGCACGACGATCTTCACT 59.933 43.478 0.00 0.00 0.00 3.41
36 37 4.274950 TCATATGCACGACGATCTTCACTA 59.725 41.667 0.00 0.00 0.00 2.74
37 38 3.717400 ATGCACGACGATCTTCACTAT 57.283 42.857 0.00 0.00 0.00 2.12
38 39 4.830826 ATGCACGACGATCTTCACTATA 57.169 40.909 0.00 0.00 0.00 1.31
39 40 4.625972 TGCACGACGATCTTCACTATAA 57.374 40.909 0.00 0.00 0.00 0.98
40 41 4.989044 TGCACGACGATCTTCACTATAAA 58.011 39.130 0.00 0.00 0.00 1.40
41 42 5.404096 TGCACGACGATCTTCACTATAAAA 58.596 37.500 0.00 0.00 0.00 1.52
42 43 6.040247 TGCACGACGATCTTCACTATAAAAT 58.960 36.000 0.00 0.00 0.00 1.82
43 44 6.198403 TGCACGACGATCTTCACTATAAAATC 59.802 38.462 0.00 0.00 0.00 2.17
44 45 6.611671 GCACGACGATCTTCACTATAAAATCG 60.612 42.308 0.00 0.00 41.17 3.34
46 47 6.971184 ACGACGATCTTCACTATAAAATCGTT 59.029 34.615 0.00 0.00 46.33 3.85
47 48 7.044249 ACGACGATCTTCACTATAAAATCGTTG 60.044 37.037 17.00 17.00 46.33 4.10
48 49 7.044249 CGACGATCTTCACTATAAAATCGTTGT 60.044 37.037 9.25 0.00 46.33 3.32
49 50 9.229784 GACGATCTTCACTATAAAATCGTTGTA 57.770 33.333 9.25 0.00 46.33 2.41
50 51 9.017669 ACGATCTTCACTATAAAATCGTTGTAC 57.982 33.333 2.65 0.00 44.68 2.90
51 52 9.016623 CGATCTTCACTATAAAATCGTTGTACA 57.983 33.333 0.00 0.00 33.28 2.90
53 54 8.470040 TCTTCACTATAAAATCGTTGTACACC 57.530 34.615 0.00 0.00 0.00 4.16
54 55 8.089597 TCTTCACTATAAAATCGTTGTACACCA 58.910 33.333 0.00 0.00 0.00 4.17
55 56 7.585286 TCACTATAAAATCGTTGTACACCAC 57.415 36.000 0.00 0.00 0.00 4.16
56 57 6.591062 TCACTATAAAATCGTTGTACACCACC 59.409 38.462 0.00 0.00 0.00 4.61
57 58 5.876460 ACTATAAAATCGTTGTACACCACCC 59.124 40.000 0.00 0.00 0.00 4.61
58 59 2.943036 AAATCGTTGTACACCACCCT 57.057 45.000 0.00 0.00 0.00 4.34
59 60 2.467566 AATCGTTGTACACCACCCTC 57.532 50.000 0.00 0.00 0.00 4.30
60 61 0.245539 ATCGTTGTACACCACCCTCG 59.754 55.000 0.00 0.00 0.00 4.63
61 62 2.025418 CGTTGTACACCACCCTCGC 61.025 63.158 0.00 0.00 0.00 5.03
62 63 1.670083 GTTGTACACCACCCTCGCC 60.670 63.158 0.00 0.00 0.00 5.54
63 64 2.886134 TTGTACACCACCCTCGCCC 61.886 63.158 0.00 0.00 0.00 6.13
64 65 4.091939 GTACACCACCCTCGCCCC 62.092 72.222 0.00 0.00 0.00 5.80
75 76 4.853142 TCGCCCCCGCCTACTCAT 62.853 66.667 0.00 0.00 0.00 2.90
76 77 3.861797 CGCCCCCGCCTACTCATT 61.862 66.667 0.00 0.00 0.00 2.57
77 78 2.203209 GCCCCCGCCTACTCATTG 60.203 66.667 0.00 0.00 0.00 2.82
78 79 2.510906 CCCCCGCCTACTCATTGG 59.489 66.667 0.00 0.00 0.00 3.16
79 80 2.070039 CCCCCGCCTACTCATTGGA 61.070 63.158 0.00 0.00 0.00 3.53
80 81 1.632018 CCCCCGCCTACTCATTGGAA 61.632 60.000 0.00 0.00 0.00 3.53
81 82 0.254747 CCCCGCCTACTCATTGGAAA 59.745 55.000 0.00 0.00 0.00 3.13
82 83 1.340600 CCCCGCCTACTCATTGGAAAA 60.341 52.381 0.00 0.00 0.00 2.29
83 84 1.743394 CCCGCCTACTCATTGGAAAAC 59.257 52.381 0.00 0.00 0.00 2.43
84 85 2.432444 CCGCCTACTCATTGGAAAACA 58.568 47.619 0.00 0.00 0.00 2.83
85 86 2.161609 CCGCCTACTCATTGGAAAACAC 59.838 50.000 0.00 0.00 0.00 3.32
86 87 2.811431 CGCCTACTCATTGGAAAACACA 59.189 45.455 0.00 0.00 0.00 3.72
87 88 3.440173 CGCCTACTCATTGGAAAACACAT 59.560 43.478 0.00 0.00 0.00 3.21
88 89 4.082787 CGCCTACTCATTGGAAAACACATT 60.083 41.667 0.00 0.00 0.00 2.71
89 90 5.163513 GCCTACTCATTGGAAAACACATTG 58.836 41.667 0.00 0.00 0.00 2.82
90 91 5.278957 GCCTACTCATTGGAAAACACATTGT 60.279 40.000 0.00 0.00 0.00 2.71
91 92 6.381801 CCTACTCATTGGAAAACACATTGTC 58.618 40.000 0.00 0.00 0.00 3.18
92 93 5.850557 ACTCATTGGAAAACACATTGTCA 57.149 34.783 0.00 0.00 0.00 3.58
93 94 6.219417 ACTCATTGGAAAACACATTGTCAA 57.781 33.333 0.00 0.00 0.00 3.18
96 97 5.362143 TCATTGGAAAACACATTGTCAAGGA 59.638 36.000 3.86 0.00 0.00 3.36
102 103 7.148323 TGGAAAACACATTGTCAAGGATATACG 60.148 37.037 3.86 0.00 0.00 3.06
107 108 6.312918 ACACATTGTCAAGGATATACGTTGTC 59.687 38.462 3.86 0.00 42.63 3.18
109 110 4.036567 TGTCAAGGATATACGTTGTCGG 57.963 45.455 0.00 0.00 42.63 4.79
117 118 5.180868 AGGATATACGTTGTCGGTAGATGTC 59.819 44.000 0.00 0.00 41.85 3.06
131 132 5.639506 CGGTAGATGTCTCTTGAACAACAAT 59.360 40.000 0.00 0.00 37.88 2.71
139 140 9.725019 ATGTCTCTTGAACAACAATTATCACTA 57.275 29.630 0.00 0.00 37.88 2.74
140 141 9.554395 TGTCTCTTGAACAACAATTATCACTAA 57.446 29.630 0.00 0.00 37.88 2.24
177 178 1.067516 GCACTAGTTACGGCGGGAATA 59.932 52.381 13.24 1.57 0.00 1.75
179 180 2.099592 CACTAGTTACGGCGGGAATACA 59.900 50.000 13.24 0.00 0.00 2.29
325 330 1.794701 CATGCGACTTCGGTATGGATG 59.205 52.381 0.02 0.00 40.23 3.51
342 347 2.750237 GGTGAATTCGCCCCGCTT 60.750 61.111 24.94 0.00 40.56 4.68
349 354 0.108585 ATTCGCCCCGCTTGACATAT 59.891 50.000 0.00 0.00 0.00 1.78
362 367 3.036084 CATATCGTCGGGCGTGGC 61.036 66.667 0.49 0.00 42.13 5.01
394 2326 3.036091 TGGCCCTAGTACCACTATTGAC 58.964 50.000 0.00 0.00 29.08 3.18
395 2327 3.036091 GGCCCTAGTACCACTATTGACA 58.964 50.000 0.00 0.00 29.08 3.58
396 2328 3.646637 GGCCCTAGTACCACTATTGACAT 59.353 47.826 0.00 0.00 29.08 3.06
397 2329 4.836736 GGCCCTAGTACCACTATTGACATA 59.163 45.833 0.00 0.00 29.08 2.29
398 2330 5.484290 GGCCCTAGTACCACTATTGACATAT 59.516 44.000 0.00 0.00 29.08 1.78
399 2331 6.351117 GGCCCTAGTACCACTATTGACATATC 60.351 46.154 0.00 0.00 29.08 1.63
400 2332 6.625300 GCCCTAGTACCACTATTGACATATCG 60.625 46.154 0.00 0.00 29.08 2.92
401 2333 6.433404 CCCTAGTACCACTATTGACATATCGT 59.567 42.308 0.00 0.00 29.08 3.73
402 2334 7.361885 CCCTAGTACCACTATTGACATATCGTC 60.362 44.444 0.00 0.00 36.22 4.20
403 2335 7.235080 CTAGTACCACTATTGACATATCGTCG 58.765 42.308 0.00 0.00 37.48 5.12
404 2336 7.623715 CTAGTACCACTATTGACATATCGTCGG 60.624 44.444 0.00 0.00 37.48 4.79
409 2341 3.917870 GACATATCGTCGGGCGTG 58.082 61.111 0.49 0.00 42.13 5.34
410 2342 1.660575 GACATATCGTCGGGCGTGG 60.661 63.158 0.49 0.00 42.13 4.94
411 2343 3.036084 CATATCGTCGGGCGTGGC 61.036 66.667 0.49 0.00 42.13 5.01
412 2344 4.640855 ATATCGTCGGGCGTGGCG 62.641 66.667 0.49 0.00 42.13 5.69
492 2428 6.313905 CCAAGTACCACTTACATCAGATCAAC 59.686 42.308 0.00 0.00 36.03 3.18
493 2429 6.859112 AGTACCACTTACATCAGATCAACT 57.141 37.500 0.00 0.00 32.41 3.16
505 2441 2.097056 CAGATCAACTCGTATGCATGCG 60.097 50.000 28.39 28.39 37.23 4.73
507 2443 1.010797 CAACTCGTATGCATGCGGC 60.011 57.895 32.06 9.37 45.13 6.53
552 2488 3.505464 ATTACCGTCGAGGAGAAACTG 57.495 47.619 6.70 0.00 45.00 3.16
614 2551 1.714460 CACGTACGTGTCTCTCAAAGC 59.286 52.381 34.48 0.00 40.91 3.51
632 2569 0.589979 GCGCTTTTGATTAGCTCGGC 60.590 55.000 0.00 0.00 36.49 5.54
730 2675 0.377203 GGCGGGTTATGAAAGAAGCG 59.623 55.000 0.00 0.00 0.00 4.68
731 2676 0.248094 GCGGGTTATGAAAGAAGCGC 60.248 55.000 0.00 0.00 0.00 5.92
881 2857 1.798813 CGGAGCGTGGCCTATAAATTC 59.201 52.381 3.32 0.00 0.00 2.17
957 3048 4.760530 ACAAGTAGCAATCATCTAGCCA 57.239 40.909 0.00 0.00 0.00 4.75
1006 3125 1.349627 CGCGTCTGATTCATGGCAC 59.650 57.895 0.00 0.00 0.00 5.01
1517 11432 0.820891 GAGCCGGCACCATCATGAAT 60.821 55.000 31.54 1.71 0.00 2.57
1520 11435 1.385756 CCGGCACCATCATGAATGCA 61.386 55.000 23.52 0.00 39.92 3.96
1526 11441 1.545136 ACCATCATGAATGCAAACGCA 59.455 42.857 0.00 0.00 45.23 5.24
1598 11513 2.419198 GAGATCATCACCGGCGCT 59.581 61.111 7.64 0.00 0.00 5.92
1613 11528 1.696832 GCGCTCCCTTCATCAACGTC 61.697 60.000 0.00 0.00 0.00 4.34
1631 11548 5.091910 ACGTCTAAAACTAGCTTTGTTGC 57.908 39.130 1.28 0.00 0.00 4.17
1635 11552 5.001232 TCTAAAACTAGCTTTGTTGCCGAT 58.999 37.500 1.28 0.00 0.00 4.18
1638 11555 1.067142 ACTAGCTTTGTTGCCGATCGA 60.067 47.619 18.66 0.00 0.00 3.59
1647 11564 2.670905 TGTTGCCGATCGAATAACACAG 59.329 45.455 18.66 0.00 0.00 3.66
1750 11675 5.631512 CAGTTTATACTATCGGAGCTGCTTC 59.368 44.000 2.53 0.00 31.96 3.86
1754 11679 1.202313 ACTATCGGAGCTGCTTCGTTC 60.202 52.381 27.86 3.71 33.64 3.95
1758 11683 1.807573 GGAGCTGCTTCGTTCCTCG 60.808 63.158 2.53 0.00 41.41 4.63
1804 12479 3.520290 TGGCACATAGACTAAAGACCG 57.480 47.619 0.00 0.00 0.00 4.79
1816 12491 5.655532 AGACTAAAGACCGCCAATAGACTAA 59.344 40.000 0.00 0.00 0.00 2.24
1818 12493 6.704310 ACTAAAGACCGCCAATAGACTAAAA 58.296 36.000 0.00 0.00 0.00 1.52
1824 12499 6.828785 AGACCGCCAATAGACTAAAAATCAAT 59.171 34.615 0.00 0.00 0.00 2.57
1838 12513 9.988350 ACTAAAAATCAATAAGCTTCATGTACG 57.012 29.630 0.00 0.00 0.00 3.67
1849 12536 4.513692 AGCTTCATGTACGTGCAGTTTAAA 59.486 37.500 12.93 1.30 0.00 1.52
1852 12539 6.362283 GCTTCATGTACGTGCAGTTTAAATTT 59.638 34.615 12.93 0.00 0.00 1.82
1856 12543 9.731819 TCATGTACGTGCAGTTTAAATTTAAAA 57.268 25.926 21.81 6.79 34.71 1.52
1897 12584 9.436957 GTCTGGAAATTCACTCTATGACTTAAA 57.563 33.333 0.00 0.00 36.92 1.52
2008 16956 3.008266 CACCTTCAAATTTGGCCATTCCT 59.992 43.478 17.90 0.00 35.26 3.36
2025 16973 7.148137 GGCCATTCCTTCTCGAAACTTAAATTA 60.148 37.037 0.00 0.00 0.00 1.40
2040 16988 8.650143 AACTTAAATTATTTCTCCAAGCTGGA 57.350 30.769 0.00 0.00 45.98 3.86
2331 17281 8.939201 TTTTTCATGCACTTACAATTCAAAGA 57.061 26.923 0.00 0.00 0.00 2.52
2373 17323 4.098349 TGCCTGGAAATGCACTAAATGATC 59.902 41.667 0.00 0.00 31.31 2.92
2512 17467 1.680735 GACACAAACCAATGGCTGTCA 59.319 47.619 0.00 0.00 0.00 3.58
2516 17471 1.336440 CAAACCAATGGCTGTCAACGA 59.664 47.619 0.00 0.00 0.00 3.85
2522 17477 3.041940 GGCTGTCAACGACCACCG 61.042 66.667 0.00 0.00 45.44 4.94
2534 17489 1.154197 GACCACCGTTAAGCAAGTCC 58.846 55.000 0.00 0.00 0.00 3.85
2537 17492 1.670083 ACCGTTAAGCAAGTCCCGC 60.670 57.895 0.00 0.00 0.00 6.13
2544 17499 4.858680 GCAAGTCCCGCCCCTAGC 62.859 72.222 0.00 0.00 38.52 3.42
2568 17523 3.755434 GCCATGGCCTATGTGAGC 58.245 61.111 27.24 0.00 34.87 4.26
2614 17569 3.673956 AACGCCGATCCGCCAATGA 62.674 57.895 0.00 0.00 0.00 2.57
2615 17570 3.640000 CGCCGATCCGCCAATGAC 61.640 66.667 0.23 0.00 0.00 3.06
2616 17571 2.513666 GCCGATCCGCCAATGACA 60.514 61.111 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.319405 CGTGCATATGACAAAGTGACACAA 60.319 41.667 6.97 0.00 0.00 3.33
1 2 3.186205 CGTGCATATGACAAAGTGACACA 59.814 43.478 6.97 0.00 0.00 3.72
3 4 3.431912 GTCGTGCATATGACAAAGTGACA 59.568 43.478 6.97 0.00 41.50 3.58
4 5 3.481951 CGTCGTGCATATGACAAAGTGAC 60.482 47.826 6.97 9.08 41.88 3.67
5 6 2.666022 CGTCGTGCATATGACAAAGTGA 59.334 45.455 6.97 0.00 41.88 3.41
6 7 2.666022 TCGTCGTGCATATGACAAAGTG 59.334 45.455 6.97 0.00 41.88 3.16
7 8 2.954316 TCGTCGTGCATATGACAAAGT 58.046 42.857 6.97 0.00 41.88 2.66
8 9 3.798878 AGATCGTCGTGCATATGACAAAG 59.201 43.478 6.97 2.83 41.88 2.77
9 10 3.780902 AGATCGTCGTGCATATGACAAA 58.219 40.909 6.97 4.98 41.88 2.83
10 11 3.436700 AGATCGTCGTGCATATGACAA 57.563 42.857 6.97 0.00 41.88 3.18
11 12 3.181491 TGAAGATCGTCGTGCATATGACA 60.181 43.478 6.97 1.06 41.88 3.58
12 13 3.180584 GTGAAGATCGTCGTGCATATGAC 59.819 47.826 6.97 0.00 39.06 3.06
13 14 3.066760 AGTGAAGATCGTCGTGCATATGA 59.933 43.478 6.97 0.00 0.00 2.15
14 15 3.375642 AGTGAAGATCGTCGTGCATATG 58.624 45.455 4.15 0.00 0.00 1.78
15 16 3.717400 AGTGAAGATCGTCGTGCATAT 57.283 42.857 4.15 0.00 0.00 1.78
16 17 4.830826 ATAGTGAAGATCGTCGTGCATA 57.169 40.909 4.15 0.00 0.00 3.14
17 18 3.717400 ATAGTGAAGATCGTCGTGCAT 57.283 42.857 4.15 0.00 0.00 3.96
18 19 4.625972 TTATAGTGAAGATCGTCGTGCA 57.374 40.909 4.15 0.00 0.00 4.57
19 20 5.944049 TTTTATAGTGAAGATCGTCGTGC 57.056 39.130 4.15 0.00 0.00 5.34
20 21 6.414109 ACGATTTTATAGTGAAGATCGTCGTG 59.586 38.462 8.40 0.00 44.08 4.35
21 22 6.493116 ACGATTTTATAGTGAAGATCGTCGT 58.507 36.000 8.40 0.00 44.08 4.34
22 23 6.971337 ACGATTTTATAGTGAAGATCGTCG 57.029 37.500 8.40 0.00 44.08 5.12
23 24 8.116624 ACAACGATTTTATAGTGAAGATCGTC 57.883 34.615 13.04 1.20 45.90 4.20
25 26 9.016623 TGTACAACGATTTTATAGTGAAGATCG 57.983 33.333 0.00 7.32 41.34 3.69
27 28 9.095065 GGTGTACAACGATTTTATAGTGAAGAT 57.905 33.333 0.00 0.00 0.00 2.40
28 29 8.089597 TGGTGTACAACGATTTTATAGTGAAGA 58.910 33.333 6.39 0.00 0.00 2.87
29 30 8.166706 GTGGTGTACAACGATTTTATAGTGAAG 58.833 37.037 6.39 0.00 0.00 3.02
30 31 7.118101 GGTGGTGTACAACGATTTTATAGTGAA 59.882 37.037 6.39 0.00 0.00 3.18
31 32 6.591062 GGTGGTGTACAACGATTTTATAGTGA 59.409 38.462 6.39 0.00 0.00 3.41
32 33 6.183360 GGGTGGTGTACAACGATTTTATAGTG 60.183 42.308 6.39 0.00 37.80 2.74
33 34 5.876460 GGGTGGTGTACAACGATTTTATAGT 59.124 40.000 6.39 0.00 37.80 2.12
34 35 6.110707 AGGGTGGTGTACAACGATTTTATAG 58.889 40.000 6.39 0.00 37.80 1.31
35 36 6.052405 AGGGTGGTGTACAACGATTTTATA 57.948 37.500 6.39 0.00 37.80 0.98
36 37 4.913784 AGGGTGGTGTACAACGATTTTAT 58.086 39.130 6.39 0.00 37.80 1.40
37 38 4.317488 GAGGGTGGTGTACAACGATTTTA 58.683 43.478 6.39 0.00 37.80 1.52
38 39 3.143728 GAGGGTGGTGTACAACGATTTT 58.856 45.455 6.39 0.00 37.80 1.82
39 40 2.774687 GAGGGTGGTGTACAACGATTT 58.225 47.619 6.39 0.00 37.80 2.17
40 41 1.337447 CGAGGGTGGTGTACAACGATT 60.337 52.381 6.39 0.00 37.80 3.34
41 42 0.245539 CGAGGGTGGTGTACAACGAT 59.754 55.000 6.39 0.00 37.80 3.73
42 43 1.661480 CGAGGGTGGTGTACAACGA 59.339 57.895 6.39 0.00 37.80 3.85
43 44 2.025418 GCGAGGGTGGTGTACAACG 61.025 63.158 6.39 1.76 37.80 4.10
44 45 1.670083 GGCGAGGGTGGTGTACAAC 60.670 63.158 3.20 3.20 35.48 3.32
45 46 2.745037 GGCGAGGGTGGTGTACAA 59.255 61.111 0.00 0.00 0.00 2.41
46 47 3.315949 GGGCGAGGGTGGTGTACA 61.316 66.667 0.00 0.00 0.00 2.90
47 48 4.091939 GGGGCGAGGGTGGTGTAC 62.092 72.222 0.00 0.00 0.00 2.90
58 59 4.853142 ATGAGTAGGCGGGGGCGA 62.853 66.667 0.00 0.00 0.00 5.54
59 60 3.861797 AATGAGTAGGCGGGGGCG 61.862 66.667 0.00 0.00 0.00 6.13
60 61 2.203209 CAATGAGTAGGCGGGGGC 60.203 66.667 0.00 0.00 0.00 5.80
61 62 1.632018 TTCCAATGAGTAGGCGGGGG 61.632 60.000 0.00 0.00 0.00 5.40
62 63 0.254747 TTTCCAATGAGTAGGCGGGG 59.745 55.000 0.00 0.00 0.00 5.73
63 64 1.743394 GTTTTCCAATGAGTAGGCGGG 59.257 52.381 0.00 0.00 0.00 6.13
64 65 2.161609 GTGTTTTCCAATGAGTAGGCGG 59.838 50.000 0.00 0.00 0.00 6.13
65 66 2.811431 TGTGTTTTCCAATGAGTAGGCG 59.189 45.455 0.00 0.00 0.00 5.52
66 67 5.163513 CAATGTGTTTTCCAATGAGTAGGC 58.836 41.667 0.00 0.00 0.00 3.93
67 68 6.016360 TGACAATGTGTTTTCCAATGAGTAGG 60.016 38.462 0.00 0.00 0.00 3.18
68 69 6.969366 TGACAATGTGTTTTCCAATGAGTAG 58.031 36.000 0.00 0.00 0.00 2.57
69 70 6.951062 TGACAATGTGTTTTCCAATGAGTA 57.049 33.333 0.00 0.00 0.00 2.59
70 71 5.850557 TGACAATGTGTTTTCCAATGAGT 57.149 34.783 0.00 0.00 0.00 3.41
71 72 5.693104 CCTTGACAATGTGTTTTCCAATGAG 59.307 40.000 0.00 0.00 0.00 2.90
72 73 5.362143 TCCTTGACAATGTGTTTTCCAATGA 59.638 36.000 0.00 0.00 0.00 2.57
73 74 5.599732 TCCTTGACAATGTGTTTTCCAATG 58.400 37.500 0.00 0.00 0.00 2.82
74 75 5.867903 TCCTTGACAATGTGTTTTCCAAT 57.132 34.783 0.00 0.00 0.00 3.16
75 76 5.867903 ATCCTTGACAATGTGTTTTCCAA 57.132 34.783 0.00 0.00 0.00 3.53
76 77 7.148323 CGTATATCCTTGACAATGTGTTTTCCA 60.148 37.037 0.00 0.00 0.00 3.53
77 78 7.148306 ACGTATATCCTTGACAATGTGTTTTCC 60.148 37.037 0.00 0.00 0.00 3.13
78 79 7.748847 ACGTATATCCTTGACAATGTGTTTTC 58.251 34.615 0.00 0.00 0.00 2.29
79 80 7.681939 ACGTATATCCTTGACAATGTGTTTT 57.318 32.000 0.00 0.00 0.00 2.43
80 81 7.174253 ACAACGTATATCCTTGACAATGTGTTT 59.826 33.333 0.00 0.00 0.00 2.83
81 82 6.653320 ACAACGTATATCCTTGACAATGTGTT 59.347 34.615 0.00 0.00 0.00 3.32
82 83 6.170506 ACAACGTATATCCTTGACAATGTGT 58.829 36.000 0.00 0.00 0.00 3.72
83 84 6.507929 CGACAACGTATATCCTTGACAATGTG 60.508 42.308 0.00 0.00 34.56 3.21
84 85 5.518847 CGACAACGTATATCCTTGACAATGT 59.481 40.000 0.00 0.00 34.56 2.71
85 86 5.051039 CCGACAACGTATATCCTTGACAATG 60.051 44.000 0.00 0.00 37.88 2.82
86 87 5.047847 CCGACAACGTATATCCTTGACAAT 58.952 41.667 0.00 0.00 37.88 2.71
87 88 4.082081 ACCGACAACGTATATCCTTGACAA 60.082 41.667 0.00 0.00 37.88 3.18
88 89 3.444742 ACCGACAACGTATATCCTTGACA 59.555 43.478 0.00 0.00 37.88 3.58
89 90 4.037858 ACCGACAACGTATATCCTTGAC 57.962 45.455 0.00 0.00 37.88 3.18
90 91 5.125356 TCTACCGACAACGTATATCCTTGA 58.875 41.667 0.00 0.00 37.88 3.02
91 92 5.428496 TCTACCGACAACGTATATCCTTG 57.572 43.478 0.00 0.00 37.88 3.61
92 93 5.533903 ACATCTACCGACAACGTATATCCTT 59.466 40.000 0.00 0.00 37.88 3.36
93 94 5.068636 ACATCTACCGACAACGTATATCCT 58.931 41.667 0.00 0.00 37.88 3.24
96 97 5.996513 AGAGACATCTACCGACAACGTATAT 59.003 40.000 0.00 0.00 33.88 0.86
102 103 4.436242 TCAAGAGACATCTACCGACAAC 57.564 45.455 0.00 0.00 33.45 3.32
107 108 4.556233 TGTTGTTCAAGAGACATCTACCG 58.444 43.478 0.00 0.00 33.45 4.02
150 151 4.362279 CCGCCGTAACTAGTGCTAAATAA 58.638 43.478 0.00 0.00 0.00 1.40
157 158 0.179092 ATTCCCGCCGTAACTAGTGC 60.179 55.000 0.00 0.00 0.00 4.40
160 161 3.118542 GTTGTATTCCCGCCGTAACTAG 58.881 50.000 0.00 0.00 0.00 2.57
163 164 1.009078 GGTTGTATTCCCGCCGTAAC 58.991 55.000 0.00 0.00 0.00 2.50
275 276 4.465512 GCATGGTTGTGGCGCTCG 62.466 66.667 7.64 0.00 0.00 5.03
325 330 2.750237 AAGCGGGGCGAATTCACC 60.750 61.111 3.75 3.75 0.00 4.02
406 2338 4.170062 CATCAAGCCTGCGCCACG 62.170 66.667 4.18 0.00 34.57 4.94
407 2339 3.818787 CCATCAAGCCTGCGCCAC 61.819 66.667 4.18 0.00 34.57 5.01
416 2348 4.454728 TTCTTTACAATGGCCATCAAGC 57.545 40.909 21.08 0.00 0.00 4.01
417 2349 7.910441 ATTTTTCTTTACAATGGCCATCAAG 57.090 32.000 21.08 17.71 0.00 3.02
418 2350 9.956640 ATTATTTTTCTTTACAATGGCCATCAA 57.043 25.926 21.08 10.91 0.00 2.57
482 2418 3.744942 GCATGCATACGAGTTGATCTGAT 59.255 43.478 14.21 0.00 0.00 2.90
552 2488 0.453390 GGCAGGAAAGCAGCATGTAC 59.547 55.000 0.00 0.00 39.31 2.90
614 2551 0.028110 GGCCGAGCTAATCAAAAGCG 59.972 55.000 0.00 0.00 44.87 4.68
632 2569 3.003897 TGATTCGGTTTTTGGTTTCTCGG 59.996 43.478 0.00 0.00 0.00 4.63
641 2578 4.853196 CAGCACTATGTGATTCGGTTTTTG 59.147 41.667 1.52 0.00 35.23 2.44
957 3048 3.841255 ACGAAGGAGAGAAGGGAAGAATT 59.159 43.478 0.00 0.00 0.00 2.17
1193 3332 8.368668 ACACTATGTAGAGGCTTAATTGATACC 58.631 37.037 0.00 0.00 0.00 2.73
1307 4126 2.125552 CCGTTGATGCGCTCAGGA 60.126 61.111 9.73 0.00 34.68 3.86
1520 11435 0.946221 CGTTCCAGAGCTCTGCGTTT 60.946 55.000 34.09 1.08 42.47 3.60
1526 11441 3.764466 CGGCCGTTCCAGAGCTCT 61.764 66.667 19.50 11.45 34.01 4.09
1598 11513 5.223449 AGTTTTAGACGTTGATGAAGGGA 57.777 39.130 0.00 0.00 0.00 4.20
1613 11528 4.742438 TCGGCAACAAAGCTAGTTTTAG 57.258 40.909 4.08 2.74 34.17 1.85
1631 11548 1.860950 CAGGCTGTGTTATTCGATCGG 59.139 52.381 16.41 0.00 0.00 4.18
1635 11552 2.888594 GCTACAGGCTGTGTTATTCGA 58.111 47.619 29.65 6.35 40.94 3.71
1647 11564 1.123928 ATGTCCTACCAGCTACAGGC 58.876 55.000 3.12 0.00 42.19 4.85
1657 11582 7.225538 CAGTTCTCATCATTTACATGTCCTACC 59.774 40.741 0.00 0.00 0.00 3.18
1731 11656 3.409570 ACGAAGCAGCTCCGATAGTATA 58.590 45.455 8.55 0.00 0.00 1.47
1754 11679 5.981174 TCATACAAAAAGTTTCGAACGAGG 58.019 37.500 0.00 0.00 36.23 4.63
1816 12491 6.747280 GCACGTACATGAAGCTTATTGATTTT 59.253 34.615 13.49 0.00 0.00 1.82
1818 12493 5.353956 TGCACGTACATGAAGCTTATTGATT 59.646 36.000 13.49 0.00 0.00 2.57
1824 12499 3.313012 ACTGCACGTACATGAAGCTTA 57.687 42.857 0.00 0.00 0.00 3.09
1863 12550 9.965902 ATAGAGTGAATTTCCAGACATTTAGTT 57.034 29.630 0.00 0.00 0.00 2.24
1897 12584 8.432805 ACCTTCTTCGAGGATTGTTTGATATAT 58.567 33.333 0.00 0.00 39.25 0.86
1902 12589 4.202315 TGACCTTCTTCGAGGATTGTTTGA 60.202 41.667 0.00 0.00 39.25 2.69
1910 12597 4.065088 CACAATTTGACCTTCTTCGAGGA 58.935 43.478 2.79 0.00 39.25 3.71
2040 16988 4.973168 ACATATACTGCATGGAAATCGGT 58.027 39.130 0.00 0.00 0.00 4.69
2168 17118 8.398665 ACATGGAGCTTATCGATTTTTAGTTTC 58.601 33.333 1.71 0.00 0.00 2.78
2172 17122 6.346919 CGGACATGGAGCTTATCGATTTTTAG 60.347 42.308 1.71 0.00 0.00 1.85
2331 17281 9.812347 TCCAGGCATTTAGTGAATATAATTCAT 57.188 29.630 5.68 0.00 0.00 2.57
2383 17333 6.016108 CCACAATTTGGCATTTTTCAGGATTT 60.016 34.615 0.78 0.00 39.07 2.17
2499 17454 0.889186 GGTCGTTGACAGCCATTGGT 60.889 55.000 4.26 0.00 33.68 3.67
2516 17471 0.250597 GGGACTTGCTTAACGGTGGT 60.251 55.000 0.00 0.00 0.00 4.16
2522 17477 2.044555 GGGGCGGGACTTGCTTAAC 61.045 63.158 0.00 0.00 0.00 2.01
2524 17479 1.306312 TAGGGGCGGGACTTGCTTA 60.306 57.895 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.