Multiple sequence alignment - TraesCS3A01G514900

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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 TraesCS3A01G514900 chr3A 100.000 4858 0 0 378 5235 733463509 733468366 0.000000e+00 8972.0
1 TraesCS3A01G514900 chr3A 90.765 3346 225 38 1386 4662 733332255 733335585 0.000000e+00 4390.0
2 TraesCS3A01G514900 chr3A 88.203 2704 221 44 2102 4763 733436119 733438766 0.000000e+00 3136.0
3 TraesCS3A01G514900 chr3A 90.240 2080 137 24 2102 4154 733411324 733413364 0.000000e+00 2656.0
4 TraesCS3A01G514900 chr3A 85.570 2086 226 42 2195 4237 733039218 733041271 0.000000e+00 2115.0
5 TraesCS3A01G514900 chr3A 85.388 1663 170 36 2712 4326 733185892 733187529 0.000000e+00 1657.0
6 TraesCS3A01G514900 chr3A 82.573 1842 257 41 2163 3958 733860380 733858557 0.000000e+00 1565.0
7 TraesCS3A01G514900 chr3A 94.539 824 41 1 379 1198 733331831 733332654 0.000000e+00 1269.0
8 TraesCS3A01G514900 chr3A 79.218 1944 309 55 2176 4075 733520105 733518213 0.000000e+00 1264.0
9 TraesCS3A01G514900 chr3A 100.000 205 0 0 1 205 733463132 733463336 3.830000e-101 379.0
10 TraesCS3A01G514900 chr3A 98.049 205 4 0 1 205 733331220 733331424 1.790000e-94 357.0
11 TraesCS3A01G514900 chr3A 89.404 151 9 3 723 867 733330935 733331084 3.220000e-42 183.0
12 TraesCS3A01G514900 chr3A 97.183 71 2 0 4059 4129 733413382 733413452 2.560000e-23 121.0
13 TraesCS3A01G514900 chr3D 96.091 2942 86 12 1386 4326 603942703 603945616 0.000000e+00 4769.0
14 TraesCS3A01G514900 chr3D 90.675 1941 131 25 2102 4009 602781751 602779828 0.000000e+00 2536.0
15 TraesCS3A01G514900 chr3D 85.934 2083 232 40 2195 4240 602803981 602801923 0.000000e+00 2167.0
16 TraesCS3A01G514900 chr3D 95.661 991 36 3 379 1369 603941595 603942578 0.000000e+00 1585.0
17 TraesCS3A01G514900 chr3D 82.356 1825 265 43 2168 3953 603962606 603964412 0.000000e+00 1533.0
18 TraesCS3A01G514900 chr3D 81.385 1805 272 35 2261 4031 604237124 604235350 0.000000e+00 1413.0
19 TraesCS3A01G514900 chr3D 81.650 1733 248 33 2261 3959 604143815 604142119 0.000000e+00 1375.0
20 TraesCS3A01G514900 chr3D 80.705 1731 266 41 2261 3958 602799250 602797555 0.000000e+00 1284.0
21 TraesCS3A01G514900 chr3D 81.369 1578 233 37 2424 3958 604288262 604286703 0.000000e+00 1229.0
22 TraesCS3A01G514900 chr3D 96.232 345 12 1 4892 5235 603946256 603946600 9.840000e-157 564.0
23 TraesCS3A01G514900 chr3D 83.103 651 64 12 555 1198 603942476 603943087 7.660000e-153 551.0
24 TraesCS3A01G514900 chr3D 90.799 413 19 6 4481 4893 603945769 603946162 7.720000e-148 534.0
25 TraesCS3A01G514900 chr3D 87.557 442 36 7 4326 4763 602779628 602779202 1.310000e-135 494.0
26 TraesCS3A01G514900 chr3D 97.561 205 5 0 1 205 603941284 603941488 8.340000e-93 351.0
27 TraesCS3A01G514900 chr3D 89.404 151 9 3 723 867 603940985 603941134 3.220000e-42 183.0
28 TraesCS3A01G514900 chr3D 84.483 174 16 4 4151 4324 602779821 602779659 1.510000e-35 161.0
29 TraesCS3A01G514900 chr3D 83.673 147 24 0 410 556 603942263 603942409 7.070000e-29 139.0
30 TraesCS3A01G514900 chr3D 85.606 132 14 4 4323 4452 603945642 603945770 3.290000e-27 134.0
31 TraesCS3A01G514900 chr3B 89.212 2716 192 42 2102 4763 810970218 810972886 0.000000e+00 3299.0
32 TraesCS3A01G514900 chr3B 88.000 2750 230 53 1386 4087 810977075 810979772 0.000000e+00 3158.0
33 TraesCS3A01G514900 chr3B 95.673 1918 58 9 2410 4326 811040914 811042807 0.000000e+00 3059.0
34 TraesCS3A01G514900 chr3B 85.509 2084 237 37 2195 4240 810948009 810950065 0.000000e+00 2115.0
35 TraesCS3A01G514900 chr3B 95.941 1010 26 10 1386 2384 811039913 811040918 0.000000e+00 1624.0
36 TraesCS3A01G514900 chr3B 96.248 533 20 0 380 912 811038834 811039366 0.000000e+00 874.0
37 TraesCS3A01G514900 chr3B 82.658 790 81 21 415 1198 810976709 810977448 0.000000e+00 649.0
38 TraesCS3A01G514900 chr3B 94.145 427 23 2 943 1369 811039364 811039788 0.000000e+00 649.0
39 TraesCS3A01G514900 chr3B 83.257 651 63 12 555 1198 811039686 811040297 1.650000e-154 556.0
40 TraesCS3A01G514900 chr3B 85.787 394 37 6 378 771 810976104 810976478 2.940000e-107 399.0
41 TraesCS3A01G514900 chr3B 88.818 313 31 3 410 721 811040151 811040460 1.060000e-101 381.0
42 TraesCS3A01G514900 chr3B 90.132 304 10 7 4481 4782 811042960 811043245 1.380000e-100 377.0
43 TraesCS3A01G514900 chr3B 85.241 332 41 8 1609 1935 810976687 810977015 8.400000e-88 335.0
44 TraesCS3A01G514900 chr3B 96.907 194 6 0 1 194 811038362 811038555 5.060000e-85 326.0
45 TraesCS3A01G514900 chr3B 86.454 251 32 2 1515 1765 811039364 811039612 1.860000e-69 274.0
46 TraesCS3A01G514900 chr3B 90.099 202 12 5 723 918 810975043 810975242 6.730000e-64 255.0
47 TraesCS3A01G514900 chr3B 83.221 298 21 4 902 1198 810976579 810976848 4.050000e-61 246.0
48 TraesCS3A01G514900 chr3B 83.197 244 29 6 4095 4326 810979859 810980102 4.110000e-51 213.0
49 TraesCS3A01G514900 chr3B 88.957 163 16 2 1 161 810975837 810975999 3.200000e-47 200.0
50 TraesCS3A01G514900 chr3B 88.079 151 11 3 723 867 811038066 811038215 6.970000e-39 172.0
51 TraesCS3A01G514900 chr7D 90.164 61 4 2 2000 2059 79518086 79518027 1.560000e-10 78.7
52 TraesCS3A01G514900 chr7D 88.333 60 5 2 2000 2058 79210468 79210410 2.620000e-08 71.3
53 TraesCS3A01G514900 chr7D 88.333 60 5 2 2000 2058 79267581 79267523 2.620000e-08 71.3
54 TraesCS3A01G514900 chr7D 88.333 60 5 2 2000 2058 79301753 79301695 2.620000e-08 71.3
55 TraesCS3A01G514900 chr7B 88.889 63 5 2 1196 1256 742569432 742569494 5.620000e-10 76.8
56 TraesCS3A01G514900 chr1D 100.000 41 0 0 1196 1236 458274197 458274157 5.620000e-10 76.8
57 TraesCS3A01G514900 chr1D 86.765 68 7 2 1190 1256 463545121 463545055 2.020000e-09 75.0
58 TraesCS3A01G514900 chr5A 100.000 39 0 0 2017 2055 552234059 552234021 7.270000e-09 73.1
59 TraesCS3A01G514900 chr7A 88.333 60 5 2 2000 2058 82168563 82168505 2.620000e-08 71.3
60 TraesCS3A01G514900 chr6B 87.692 65 3 2 1196 1256 37927410 37927473 2.620000e-08 71.3
61 TraesCS3A01G514900 chr5B 93.617 47 3 0 1190 1236 221448697 221448743 2.620000e-08 71.3
62 TraesCS3A01G514900 chr1A 95.455 44 1 1 1193 1236 391251073 391251031 9.410000e-08 69.4
63 TraesCS3A01G514900 chr4A 90.385 52 4 1 1185 1236 730331046 730331096 3.380000e-07 67.6


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 TraesCS3A01G514900 chr3A 733463132 733468366 5234 False 4675.500000 8972 100.000000 1 5235 2 chr3A.!!$F6 5234
1 TraesCS3A01G514900 chr3A 733436119 733438766 2647 False 3136.000000 3136 88.203000 2102 4763 1 chr3A.!!$F3 2661
2 TraesCS3A01G514900 chr3A 733039218 733041271 2053 False 2115.000000 2115 85.570000 2195 4237 1 chr3A.!!$F1 2042
3 TraesCS3A01G514900 chr3A 733185892 733187529 1637 False 1657.000000 1657 85.388000 2712 4326 1 chr3A.!!$F2 1614
4 TraesCS3A01G514900 chr3A 733858557 733860380 1823 True 1565.000000 1565 82.573000 2163 3958 1 chr3A.!!$R2 1795
5 TraesCS3A01G514900 chr3A 733330935 733335585 4650 False 1549.750000 4390 93.189250 1 4662 4 chr3A.!!$F4 4661
6 TraesCS3A01G514900 chr3A 733411324 733413452 2128 False 1388.500000 2656 93.711500 2102 4154 2 chr3A.!!$F5 2052
7 TraesCS3A01G514900 chr3A 733518213 733520105 1892 True 1264.000000 1264 79.218000 2176 4075 1 chr3A.!!$R1 1899
8 TraesCS3A01G514900 chr3D 602797555 602803981 6426 True 1725.500000 2167 83.319500 2195 4240 2 chr3D.!!$R5 2045
9 TraesCS3A01G514900 chr3D 603962606 603964412 1806 False 1533.000000 1533 82.356000 2168 3953 1 chr3D.!!$F1 1785
10 TraesCS3A01G514900 chr3D 604235350 604237124 1774 True 1413.000000 1413 81.385000 2261 4031 1 chr3D.!!$R2 1770
11 TraesCS3A01G514900 chr3D 604142119 604143815 1696 True 1375.000000 1375 81.650000 2261 3959 1 chr3D.!!$R1 1698
12 TraesCS3A01G514900 chr3D 604286703 604288262 1559 True 1229.000000 1229 81.369000 2424 3958 1 chr3D.!!$R3 1534
13 TraesCS3A01G514900 chr3D 602779202 602781751 2549 True 1063.666667 2536 87.571667 2102 4763 3 chr3D.!!$R4 2661
14 TraesCS3A01G514900 chr3D 603940985 603946600 5615 False 978.888889 4769 90.903333 1 5235 9 chr3D.!!$F2 5234
15 TraesCS3A01G514900 chr3B 810948009 810950065 2056 False 2115.000000 2115 85.509000 2195 4240 1 chr3B.!!$F1 2045
16 TraesCS3A01G514900 chr3B 810970218 810980102 9884 False 972.666667 3299 86.263556 1 4763 9 chr3B.!!$F2 4762
17 TraesCS3A01G514900 chr3B 811038066 811043245 5179 False 829.200000 3059 91.565400 1 4782 10 chr3B.!!$F3 4781

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
781 6661 0.756294 TTCTCTTTCCAGTCGCACCA 59.244 50.000 0.00 0.0 0.00 4.17 F
1382 7304 0.110486 GGAGGCCAGTTTTGTGGAGA 59.890 55.000 5.01 0.0 40.44 3.71 F
1384 7306 0.111253 AGGCCAGTTTTGTGGAGAGG 59.889 55.000 5.01 0.0 40.44 3.69 F
1551 7583 0.610687 CCGGAGAGAGCTTCCTGTTT 59.389 55.000 0.00 0.0 0.00 2.83 F
1710 7752 2.036256 GGTCCAGGCCATGCAAGT 59.964 61.111 5.01 0.0 0.00 3.16 F
3512 9652 1.400142 TGCGATATGCTTTTTGGACCG 59.600 47.619 0.00 0.0 46.63 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 8402 1.757118 CCGAGAGATGGCAGTTTAGGA 59.243 52.381 0.00 0.0 0.00 2.94 R
2865 8960 1.134401 TGGCCCTGATTTCATCTCGAC 60.134 52.381 0.00 0.0 0.00 4.20 R
3355 9468 1.882623 CAGGAGACAAAAGAAGGCCAC 59.117 52.381 5.01 0.0 0.00 5.01 R
3459 9599 3.958860 AGGCGAGCAAACAGGGCT 61.959 61.111 0.00 0.0 46.07 5.19 R
3694 9864 1.342074 TAATCCTCGCCTGATCCTGG 58.658 55.000 0.00 0.0 0.00 4.45 R
4917 11409 0.103390 TTTCGACGGTGCTCAACTCA 59.897 50.000 0.00 0.0 0.00 3.41 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
51 5672 3.542648 GGAGTGGCCTAAACCTAATGTC 58.457 50.000 3.32 0.00 0.00 3.06
77 5699 4.919754 GGCAGCTATGAAAACTGAAAAGTG 59.080 41.667 0.00 0.00 33.10 3.16
601 6481 1.073763 TGTGCTGGTTGAGTTGGCTAT 59.926 47.619 0.00 0.00 0.00 2.97
717 6597 6.720112 TTACTGCGGGTAGATTGTACTAAT 57.280 37.500 0.00 0.00 0.00 1.73
738 6618 6.530019 AATAGTTGTTCCATTCCATTCCAC 57.470 37.500 0.00 0.00 0.00 4.02
781 6661 0.756294 TTCTCTTTCCAGTCGCACCA 59.244 50.000 0.00 0.00 0.00 4.17
1156 7078 3.939837 CTCCGTGCGTGTGATGGCT 62.940 63.158 0.00 0.00 0.00 4.75
1220 7142 3.386063 TCCCTCCGTCCCATAATGTAAA 58.614 45.455 0.00 0.00 0.00 2.01
1256 7178 6.177610 ACACAAACGTCTTACATTATGGGAT 58.822 36.000 0.00 0.00 0.00 3.85
1257 7179 6.657541 ACACAAACGTCTTACATTATGGGATT 59.342 34.615 0.00 0.00 0.00 3.01
1258 7180 7.148306 ACACAAACGTCTTACATTATGGGATTC 60.148 37.037 0.00 0.00 0.00 2.52
1260 7182 7.392113 ACAAACGTCTTACATTATGGGATTCAA 59.608 33.333 0.00 0.00 0.00 2.69
1261 7183 8.405531 CAAACGTCTTACATTATGGGATTCAAT 58.594 33.333 0.00 0.00 0.00 2.57
1262 7184 7.730364 ACGTCTTACATTATGGGATTCAATC 57.270 36.000 0.00 0.00 0.00 2.67
1264 7186 7.939039 ACGTCTTACATTATGGGATTCAATCAT 59.061 33.333 0.00 0.00 0.00 2.45
1265 7187 8.446273 CGTCTTACATTATGGGATTCAATCATC 58.554 37.037 0.00 0.00 0.00 2.92
1267 7189 9.511272 TCTTACATTATGGGATTCAATCATCAG 57.489 33.333 0.00 0.00 0.00 2.90
1311 7233 1.607467 ATGGGCTGGTTGAGTTGGC 60.607 57.895 0.00 0.00 0.00 4.52
1317 7239 1.398390 GCTGGTTGAGTTGGCTAATCG 59.602 52.381 0.00 0.00 0.00 3.34
1357 7279 1.301479 GCCAACCCGAGTTCGAGTT 60.301 57.895 2.59 0.00 40.90 3.01
1369 7291 2.852495 TTCGAGTTCATGCGGAGGCC 62.852 60.000 0.00 0.00 38.85 5.19
1370 7292 2.268920 GAGTTCATGCGGAGGCCA 59.731 61.111 5.01 0.00 38.85 5.36
1372 7294 2.045926 GTTCATGCGGAGGCCAGT 60.046 61.111 5.01 0.00 38.85 4.00
1373 7295 1.675641 GTTCATGCGGAGGCCAGTT 60.676 57.895 5.01 0.00 38.85 3.16
1374 7296 1.074775 TTCATGCGGAGGCCAGTTT 59.925 52.632 5.01 0.00 38.85 2.66
1378 7300 1.526575 ATGCGGAGGCCAGTTTTGTG 61.527 55.000 5.01 0.00 38.85 3.33
1379 7301 2.919494 GCGGAGGCCAGTTTTGTGG 61.919 63.158 5.01 0.00 41.01 4.17
1380 7302 1.228124 CGGAGGCCAGTTTTGTGGA 60.228 57.895 5.01 0.00 40.44 4.02
1381 7303 1.237285 CGGAGGCCAGTTTTGTGGAG 61.237 60.000 5.01 0.00 40.44 3.86
1382 7304 0.110486 GGAGGCCAGTTTTGTGGAGA 59.890 55.000 5.01 0.00 40.44 3.71
1383 7305 1.528129 GAGGCCAGTTTTGTGGAGAG 58.472 55.000 5.01 0.00 40.44 3.20
1384 7306 0.111253 AGGCCAGTTTTGTGGAGAGG 59.889 55.000 5.01 0.00 40.44 3.69
1431 7463 6.985188 TCCATTCCTTATTTCTCTTTCACG 57.015 37.500 0.00 0.00 0.00 4.35
1498 7530 6.213677 GCAAGAAACGTTCCTTCCTTATTTT 58.786 36.000 0.00 0.00 0.00 1.82
1499 7531 6.143919 GCAAGAAACGTTCCTTCCTTATTTTG 59.856 38.462 0.00 0.00 0.00 2.44
1504 7536 4.760204 ACGTTCCTTCCTTATTTTGTGGAG 59.240 41.667 0.00 0.00 0.00 3.86
1551 7583 0.610687 CCGGAGAGAGCTTCCTGTTT 59.389 55.000 0.00 0.00 0.00 2.83
1570 7602 4.124238 GTTTCCCACAAAACTTAAAGGCC 58.876 43.478 0.00 0.00 36.44 5.19
1710 7752 2.036256 GGTCCAGGCCATGCAAGT 59.964 61.111 5.01 0.00 0.00 3.16
1767 7809 7.658575 TGGAAACATAGTCCGGCTTAATATAAC 59.341 37.037 0.00 0.00 38.06 1.89
1768 7810 7.876582 GGAAACATAGTCCGGCTTAATATAACT 59.123 37.037 0.00 0.00 0.00 2.24
1928 7971 2.961526 ACTGCGGGTAGATTGTACTG 57.038 50.000 0.00 0.00 0.00 2.74
1982 8025 5.509163 CGACGGACCAAGAATACATATTCCT 60.509 44.000 7.82 0.00 42.29 3.36
2334 8402 8.556213 TTATAGAAACATACCGAACTTGCTTT 57.444 30.769 0.00 0.00 0.00 3.51
2689 8784 5.659463 TGCATGGACTAATATGCCAAAAAC 58.341 37.500 6.73 0.00 46.91 2.43
2848 8943 6.441604 TGGATGCTCATGCTTTCTAGGATATA 59.558 38.462 3.18 0.00 40.48 0.86
3027 9122 8.150296 TCAGACTGAACAATTTCTCATCTACAA 58.850 33.333 1.64 0.00 32.36 2.41
3038 9133 6.990341 TTCTCATCTACAAACATGGACATG 57.010 37.500 10.57 10.57 44.15 3.21
3180 9281 6.183360 CGTTGAAATTAATTTGGATGCACCTG 60.183 38.462 17.98 0.00 39.86 4.00
3217 9321 6.668541 TCTCTTAATGCATCACAAAGCTAC 57.331 37.500 0.00 0.00 0.00 3.58
3355 9468 7.301068 GCTATTATTAGCTCCAGCATTACTG 57.699 40.000 8.99 0.00 46.13 2.74
3444 9584 9.853555 TTGTAGTATTTATCAAAAGGTTGCATG 57.146 29.630 0.00 0.00 34.50 4.06
3512 9652 1.400142 TGCGATATGCTTTTTGGACCG 59.600 47.619 0.00 0.00 46.63 4.79
3566 9706 5.497474 TCAGAATGCCCCTAACTTAAAGAC 58.503 41.667 0.00 0.00 34.76 3.01
3576 9716 5.063564 CCCTAACTTAAAGACGCTTGATGTC 59.936 44.000 0.00 0.00 36.60 3.06
3694 9864 2.069273 CACTCTTCGAACACATGGGAC 58.931 52.381 0.00 0.00 0.00 4.46
3718 9941 3.070302 AGGATCAGGCGAGGATTAAAGAC 59.930 47.826 0.00 0.00 0.00 3.01
3721 9944 4.124851 TCAGGCGAGGATTAAAGACTTC 57.875 45.455 0.00 0.00 0.00 3.01
3783 10008 0.895559 CAAGGTTTCAGGGGTCTGGC 60.896 60.000 0.00 0.00 41.23 4.85
3856 10081 6.270000 TGGAAGAACTGAAGATAGAGTGGAAA 59.730 38.462 0.00 0.00 0.00 3.13
4042 10269 3.758554 TCAGCTTTCTTTATGCCAAGACC 59.241 43.478 0.00 0.00 32.28 3.85
4098 10408 0.755686 CATCAGGCAGAGGGAGTACC 59.244 60.000 0.00 0.00 40.67 3.34
4194 10509 0.524862 GTTCAGCTCGTCCCGTCTTA 59.475 55.000 0.00 0.00 0.00 2.10
4225 10541 2.036217 TCCGTGTGTCGTAAATTCCTGT 59.964 45.455 0.00 0.00 37.94 4.00
4329 10655 4.994852 GCATGAAACTGTACCTTCTGTGTA 59.005 41.667 0.00 0.00 0.00 2.90
4462 10850 5.730550 TCACTGTCGCCTTTAATATTCAGT 58.269 37.500 0.00 0.00 35.69 3.41
4478 10866 8.565896 AATATTCAGTTATTGTGTGCTTCAGA 57.434 30.769 0.00 0.00 0.00 3.27
4595 10990 7.446625 ACAGATATGGCCATTTACTTTCAGATC 59.553 37.037 26.37 15.90 0.00 2.75
4648 11043 4.131649 TGAAGGACTGAACGAGTTTCAA 57.868 40.909 0.00 0.00 43.90 2.69
4721 11118 9.681692 AAAAGTAAATACCGTATCCAAACAAAC 57.318 29.630 0.00 0.00 0.00 2.93
4739 11136 1.725803 ACCAAACCCTAGGACGAGTT 58.274 50.000 11.48 2.46 0.00 3.01
4747 11144 5.121380 ACCCTAGGACGAGTTATTACAGA 57.879 43.478 11.48 0.00 0.00 3.41
4838 11235 9.971922 AATCAAACCAGAACAATAGAAAGAAAG 57.028 29.630 0.00 0.00 0.00 2.62
4875 11272 0.896226 ACTAGCTCGGGTGGAAAGAC 59.104 55.000 0.00 0.00 0.00 3.01
4885 11282 2.807676 GGTGGAAAGACCCATGTCAAT 58.192 47.619 0.00 0.00 44.33 2.57
4903 11395 8.972349 CATGTCAATGCATATATATCGTAGACC 58.028 37.037 0.00 0.00 42.51 3.85
4917 11409 0.261991 TAGACCTGCTCCGGGATCTT 59.738 55.000 0.00 0.00 33.36 2.40
4933 11425 0.318699 TCTTGAGTTGAGCACCGTCG 60.319 55.000 0.00 0.00 0.00 5.12
5013 11506 4.675510 AGTTTGCTATGAAAATCGCATGG 58.324 39.130 0.00 0.00 31.77 3.66
5082 12071 4.972568 TCTGCCTTAATACATTGACCCCTA 59.027 41.667 0.00 0.00 0.00 3.53
5084 12073 4.475381 TGCCTTAATACATTGACCCCTACA 59.525 41.667 0.00 0.00 0.00 2.74
5094 12083 6.562228 ACATTGACCCCTACAGATATAGCTA 58.438 40.000 0.00 0.00 0.00 3.32
5176 13410 5.872617 CACAATTCAACATCGTACCTAAGGA 59.127 40.000 0.00 0.00 0.00 3.36
5181 13415 1.404391 ACATCGTACCTAAGGACGCAG 59.596 52.381 0.00 0.00 38.93 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.495878 CTCGATCAATTGCTCCCTCG 58.504 55.000 0.00 4.51 0.00 4.63
2 3 1.224965 GCTCGATCAATTGCTCCCTC 58.775 55.000 0.00 0.00 0.00 4.30
4 5 0.942962 CTGCTCGATCAATTGCTCCC 59.057 55.000 0.00 0.00 0.00 4.30
51 5672 2.076100 TCAGTTTTCATAGCTGCCACG 58.924 47.619 0.00 0.00 0.00 4.94
77 5699 2.303282 TTCCTCCCTTTACCGCCCC 61.303 63.158 0.00 0.00 0.00 5.80
428 6304 5.517299 GCCTCCCATCCAATAAAGTATCCAT 60.517 44.000 0.00 0.00 0.00 3.41
435 6311 2.001076 GGGCCTCCCATCCAATAAAG 57.999 55.000 0.84 0.00 44.65 1.85
504 6380 0.108138 GCTACCTGCGTCCTTCACAT 60.108 55.000 0.00 0.00 0.00 3.21
583 6463 1.340017 GGATAGCCAACTCAACCAGCA 60.340 52.381 0.00 0.00 0.00 4.41
601 6481 0.468226 AAGAGCACAACTTGACCGGA 59.532 50.000 9.46 0.00 0.00 5.14
738 6618 1.394917 CGGAAGGAACAGCGAGAAATG 59.605 52.381 0.00 0.00 0.00 2.32
781 6661 8.105829 ACAGAATAAATGGTGAGAGTGAATTCT 58.894 33.333 7.05 0.00 32.81 2.40
1013 6934 1.152881 GGCCCCTTGCATCGAATCT 60.153 57.895 0.00 0.00 43.89 2.40
1109 7031 4.415150 CTGGACCAGCCCACGCAT 62.415 66.667 8.99 0.00 37.52 4.73
1156 7078 7.231467 GGGCTATATTTCCATTTCTTCCTACA 58.769 38.462 0.00 0.00 0.00 2.74
1256 7178 9.545105 AAAAACAATGCTTAACTGATGATTGAA 57.455 25.926 0.00 0.00 0.00 2.69
1311 7233 1.398390 GAGCACAACTTGGCCGATTAG 59.602 52.381 0.00 0.00 0.00 1.73
1317 7239 1.269778 GGAAAAGAGCACAACTTGGCC 60.270 52.381 0.00 0.00 0.00 5.36
1325 7247 1.032014 GTTGGCAGGAAAAGAGCACA 58.968 50.000 0.00 0.00 0.00 4.57
1357 7279 1.074775 AAAACTGGCCTCCGCATGA 59.925 52.632 3.32 0.00 36.38 3.07
1369 7291 7.222611 CACAAAATAAACCTCTCCACAAAACTG 59.777 37.037 0.00 0.00 0.00 3.16
1370 7292 7.264947 CACAAAATAAACCTCTCCACAAAACT 58.735 34.615 0.00 0.00 0.00 2.66
1372 7294 6.381420 TCCACAAAATAAACCTCTCCACAAAA 59.619 34.615 0.00 0.00 0.00 2.44
1373 7295 5.894393 TCCACAAAATAAACCTCTCCACAAA 59.106 36.000 0.00 0.00 0.00 2.83
1374 7296 5.450453 TCCACAAAATAAACCTCTCCACAA 58.550 37.500 0.00 0.00 0.00 3.33
1378 7300 4.944317 CCTCTCCACAAAATAAACCTCTCC 59.056 45.833 0.00 0.00 0.00 3.71
1379 7301 4.396478 GCCTCTCCACAAAATAAACCTCTC 59.604 45.833 0.00 0.00 0.00 3.20
1380 7302 4.336280 GCCTCTCCACAAAATAAACCTCT 58.664 43.478 0.00 0.00 0.00 3.69
1381 7303 3.444034 GGCCTCTCCACAAAATAAACCTC 59.556 47.826 0.00 0.00 34.01 3.85
1382 7304 3.181423 TGGCCTCTCCACAAAATAAACCT 60.181 43.478 3.32 0.00 40.72 3.50
1383 7305 3.161866 TGGCCTCTCCACAAAATAAACC 58.838 45.455 3.32 0.00 40.72 3.27
1384 7306 3.826729 ACTGGCCTCTCCACAAAATAAAC 59.173 43.478 3.32 0.00 40.72 2.01
1431 7463 7.067372 TCTGGTGTTCAATCATCAATTATCCAC 59.933 37.037 0.00 0.00 0.00 4.02
1504 7536 1.290134 AGGGAAGGGTGAGGAATGAC 58.710 55.000 0.00 0.00 0.00 3.06
1551 7583 3.322191 AGGCCTTTAAGTTTTGTGGGA 57.678 42.857 0.00 0.00 0.00 4.37
1592 7624 1.914764 CACCTTGGCCCCTTGCATT 60.915 57.895 0.00 0.00 43.89 3.56
1645 7677 4.137543 GCCTTCCATCCGATAAATCAACT 58.862 43.478 0.00 0.00 0.00 3.16
1647 7679 3.486383 GGCCTTCCATCCGATAAATCAA 58.514 45.455 0.00 0.00 0.00 2.57
1710 7752 4.308458 CCTTCACACGCACGGGGA 62.308 66.667 0.00 0.00 0.00 4.81
1928 7971 6.930667 TTTACAGTAACACCCTTGACTTTC 57.069 37.500 0.00 0.00 0.00 2.62
2205 8261 5.967674 GTGATCTTGAATAGCAACCATTTCG 59.032 40.000 0.00 0.00 31.96 3.46
2325 8393 3.295973 TGGCAGTTTAGGAAAGCAAGTT 58.704 40.909 0.00 0.00 0.00 2.66
2334 8402 1.757118 CCGAGAGATGGCAGTTTAGGA 59.243 52.381 0.00 0.00 0.00 2.94
2369 8456 8.651588 CACTAAGTAAGTTGCTTGTTCATAGAG 58.348 37.037 15.59 5.58 35.76 2.43
2689 8784 2.480224 ATTTCCATCGCGCAGAAATG 57.520 45.000 21.82 12.25 38.47 2.32
2848 8943 8.642432 TCATCTCGACTATAATTGATCTTGGTT 58.358 33.333 0.00 0.00 0.00 3.67
2865 8960 1.134401 TGGCCCTGATTTCATCTCGAC 60.134 52.381 0.00 0.00 0.00 4.20
2871 8966 3.979501 ATAACCTGGCCCTGATTTCAT 57.020 42.857 0.00 0.00 0.00 2.57
3027 9122 4.716794 ACCAAATTTTGCATGTCCATGTT 58.283 34.783 8.91 0.00 40.80 2.71
3038 9133 2.726241 GCAGAACGAGACCAAATTTTGC 59.274 45.455 3.50 0.00 0.00 3.68
3180 9281 2.797177 AAGAGAGCCACCTCCAAATC 57.203 50.000 0.00 0.00 38.96 2.17
3355 9468 1.882623 CAGGAGACAAAAGAAGGCCAC 59.117 52.381 5.01 0.00 0.00 5.01
3459 9599 3.958860 AGGCGAGCAAACAGGGCT 61.959 61.111 0.00 0.00 46.07 5.19
3566 9706 1.990799 TACTGGAACGACATCAAGCG 58.009 50.000 0.00 0.00 0.00 4.68
3576 9716 2.766828 AGGGAGAGGATTTACTGGAACG 59.233 50.000 0.00 0.00 0.00 3.95
3694 9864 1.342074 TAATCCTCGCCTGATCCTGG 58.658 55.000 0.00 0.00 0.00 4.45
3856 10081 0.752743 TGCTGCACTCTGTTTTGCCT 60.753 50.000 0.00 0.00 38.00 4.75
4042 10269 5.997129 TGCACACATATATAACCACCATCTG 59.003 40.000 0.00 0.00 0.00 2.90
4194 10509 1.872237 CGACACACGGAACAACAGGAT 60.872 52.381 0.00 0.00 38.46 3.24
4259 10585 4.471904 TCATACAGGATGAAGGTGTCAC 57.528 45.455 0.00 0.00 41.80 3.67
4329 10655 6.935771 TGATAAATGCTTTGCTTTCCAAACAT 59.064 30.769 0.00 0.00 38.46 2.71
4462 10850 9.013229 AGTGAATAATTCTGAAGCACACAATAA 57.987 29.630 0.00 0.00 0.00 1.40
4510 10899 1.376553 AGGCTTTCCAAGAGCGAGC 60.377 57.895 0.00 0.00 41.03 5.03
4648 11043 0.325671 TTTCCCTCTGGAGCCTCGAT 60.326 55.000 0.00 0.00 43.07 3.59
4708 11105 4.948341 AGGGTTTGGTTTGTTTGGATAC 57.052 40.909 0.00 0.00 0.00 2.24
4721 11118 4.482952 AATAACTCGTCCTAGGGTTTGG 57.517 45.455 9.46 0.00 0.00 3.28
4813 11210 9.354673 TCTTTCTTTCTATTGTTCTGGTTTGAT 57.645 29.630 0.00 0.00 0.00 2.57
4852 11249 3.388841 CCACCCGAGCTAGTGGTT 58.611 61.111 17.87 0.00 46.99 3.67
4859 11256 3.069778 GGTCTTTCCACCCGAGCT 58.930 61.111 0.00 0.00 35.97 4.09
4875 11272 8.143835 TCTACGATATATATGCATTGACATGGG 58.856 37.037 3.54 0.00 0.00 4.00
4885 11282 5.299531 GGAGCAGGTCTACGATATATATGCA 59.700 44.000 0.00 0.00 33.69 3.96
4903 11395 0.539051 AACTCAAGATCCCGGAGCAG 59.461 55.000 0.73 0.00 31.88 4.24
4917 11409 0.103390 TTTCGACGGTGCTCAACTCA 59.897 50.000 0.00 0.00 0.00 3.41
4959 11451 1.532868 CTGTTTCGGCTTGTTGAGAGG 59.467 52.381 0.00 0.00 0.00 3.69
5013 11506 1.745489 GACGGGTGGTCAAGATGGC 60.745 63.158 0.00 0.00 45.36 4.40
5082 12071 7.447545 TGTTCACGAGGTTATAGCTATATCTGT 59.552 37.037 14.17 10.38 0.00 3.41
5084 12073 7.666388 AGTGTTCACGAGGTTATAGCTATATCT 59.334 37.037 14.17 13.88 0.00 1.98
5094 12083 4.827692 TGCAATAGTGTTCACGAGGTTAT 58.172 39.130 0.00 0.00 0.00 1.89
5176 13410 1.591059 GCGATGCTCATCTCTGCGT 60.591 57.895 8.09 0.00 35.72 5.24
5181 13415 2.134346 GAAGAAGGCGATGCTCATCTC 58.866 52.381 8.09 0.30 35.72 2.75


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

AutoCloner maintained by Alex Coulton.