Multiple sequence alignment - TraesCS7B01G162300

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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 TraesCS7B01G162300 chr7B 100.000 6544 0 0 776 7319 222694773 222701316 0.000000e+00 12085
1 TraesCS7B01G162300 chr7B 95.228 461 19 2 3340 3798 362413216 362413675 0.000000e+00 726
2 TraesCS7B01G162300 chr7B 89.504 524 44 8 3653 4176 579527256 579527768 0.000000e+00 652
3 TraesCS7B01G162300 chr7B 84.615 650 93 6 3530 4173 235124691 235124043 2.230000e-179 640
4 TraesCS7B01G162300 chr7B 100.000 339 0 0 1 339 222693998 222694336 1.730000e-175 627
5 TraesCS7B01G162300 chr7A 94.361 3192 117 25 4175 7318 263175047 263178223 0.000000e+00 4839
6 TraesCS7B01G162300 chr7A 94.659 1629 49 8 1758 3349 263173427 263175054 0.000000e+00 2492
7 TraesCS7B01G162300 chr7A 92.056 1007 64 3 776 1769 263172026 263173029 0.000000e+00 1402
8 TraesCS7B01G162300 chr7A 97.079 445 10 2 3356 3798 586278032 586277589 0.000000e+00 747
9 TraesCS7B01G162300 chr7A 96.891 193 5 1 1577 1769 263173284 263173475 9.160000e-84 322
10 TraesCS7B01G162300 chr7A 83.333 252 38 4 4 252 56656986 56656736 5.710000e-56 230
11 TraesCS7B01G162300 chr7D 97.964 1719 28 4 4175 5891 246521597 246523310 0.000000e+00 2974
12 TraesCS7B01G162300 chr7D 96.072 1273 42 6 6051 7319 246523330 246524598 0.000000e+00 2067
13 TraesCS7B01G162300 chr7D 95.204 1126 20 8 1758 2850 246519287 246520411 0.000000e+00 1749
14 TraesCS7B01G162300 chr7D 95.446 1010 29 2 776 1769 246518327 246519335 0.000000e+00 1594
15 TraesCS7B01G162300 chr7D 96.304 514 11 2 2843 3349 246521092 246521604 0.000000e+00 837
16 TraesCS7B01G162300 chr7D 95.445 461 18 2 3340 3798 375607325 375606866 0.000000e+00 732
17 TraesCS7B01G162300 chr7D 90.029 341 31 2 1 339 246517817 246518156 8.720000e-119 438
18 TraesCS7B01G162300 chr7D 86.192 239 26 7 1 237 599188549 599188782 1.220000e-62 252
19 TraesCS7B01G162300 chr7D 80.756 291 42 12 4 286 550597900 550597616 1.600000e-51 215
20 TraesCS7B01G162300 chr7D 80.070 286 41 11 4 286 603731143 603730871 1.610000e-46 198
21 TraesCS7B01G162300 chr7D 82.292 192 32 2 4 195 32213899 32213710 1.630000e-36 165
22 TraesCS7B01G162300 chr1B 91.018 668 52 3 3435 4100 100168003 100167342 0.000000e+00 894
23 TraesCS7B01G162300 chr6B 87.032 802 89 13 3380 4172 27651185 27650390 0.000000e+00 891
24 TraesCS7B01G162300 chr6B 96.602 412 9 4 3772 4182 19441415 19441822 0.000000e+00 678
25 TraesCS7B01G162300 chr6B 95.169 414 17 3 3771 4182 136907703 136907291 0.000000e+00 651
26 TraesCS7B01G162300 chr6B 84.706 255 31 8 1 252 153426180 153426429 1.580000e-61 248
27 TraesCS7B01G162300 chr6B 80.212 283 46 9 4 279 687502300 687502021 3.460000e-48 204
28 TraesCS7B01G162300 chr6B 82.051 234 32 8 4 236 204054978 204054754 2.700000e-44 191
29 TraesCS7B01G162300 chr3B 95.879 461 16 2 3340 3798 677604692 677604233 0.000000e+00 743
30 TraesCS7B01G162300 chr4D 94.839 465 19 3 3338 3798 221295424 221295887 0.000000e+00 721
31 TraesCS7B01G162300 chr4D 81.728 301 43 10 4 298 357657608 357657314 2.640000e-59 241
32 TraesCS7B01G162300 chr4B 88.870 575 54 8 3411 3980 209601049 209600480 0.000000e+00 699
33 TraesCS7B01G162300 chr4B 95.642 413 16 2 3771 4182 286229849 286229438 0.000000e+00 662
34 TraesCS7B01G162300 chr4B 92.793 444 25 4 3736 4174 508561045 508561486 2.880000e-178 636
35 TraesCS7B01G162300 chr4B 80.201 298 38 16 4 288 605946863 605946574 3.460000e-48 204
36 TraesCS7B01G162300 chr3A 80.707 736 103 22 4529 5248 685439796 685439084 3.010000e-148 536
37 TraesCS7B01G162300 chr3A 81.915 282 42 6 4 283 68125524 68125250 5.710000e-56 230
38 TraesCS7B01G162300 chr3A 82.042 284 37 8 4 282 581275695 581275421 5.710000e-56 230
39 TraesCS7B01G162300 chr5B 84.752 282 32 7 6 286 559721790 559721519 9.360000e-69 272
40 TraesCS7B01G162300 chr2D 82.857 280 39 9 4 279 108316160 108315886 7.340000e-60 243
41 TraesCS7B01G162300 chr2D 85.561 187 24 3 96 280 412849233 412849048 7.490000e-45 193
42 TraesCS7B01G162300 chr5D 82.026 306 27 18 4 286 445803020 445802720 1.230000e-57 235
43 TraesCS7B01G162300 chr5D 82.479 234 29 9 4 237 272148153 272147932 2.080000e-45 195
44 TraesCS7B01G162300 chr5D 94.000 50 2 1 1 50 457651750 457651702 2.830000e-09 75
45 TraesCS7B01G162300 chr1A 80.534 262 39 10 5 261 540410343 540410597 2.700000e-44 191
46 TraesCS7B01G162300 chr6D 78.819 288 45 11 1 287 85791986 85792258 5.830000e-41 180
47 TraesCS7B01G162300 chr6D 80.711 197 22 10 1 197 325421512 325421692 9.900000e-29 139
48 TraesCS7B01G162300 chr1D 78.049 287 47 11 4 284 302342696 302342972 4.540000e-37 167
49 TraesCS7B01G162300 chrUn 78.082 292 40 19 4 284 86301893 86302171 5.880000e-36 163


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 TraesCS7B01G162300 chr7B 222693998 222701316 7318 False 6356.000000 12085 100.000000 1 7319 2 chr7B.!!$F3 7318
1 TraesCS7B01G162300 chr7B 579527256 579527768 512 False 652.000000 652 89.504000 3653 4176 1 chr7B.!!$F2 523
2 TraesCS7B01G162300 chr7B 235124043 235124691 648 True 640.000000 640 84.615000 3530 4173 1 chr7B.!!$R1 643
3 TraesCS7B01G162300 chr7A 263172026 263178223 6197 False 2263.750000 4839 94.491750 776 7318 4 chr7A.!!$F1 6542
4 TraesCS7B01G162300 chr7D 246517817 246524598 6781 False 1609.833333 2974 95.169833 1 7319 6 chr7D.!!$F2 7318
5 TraesCS7B01G162300 chr1B 100167342 100168003 661 True 894.000000 894 91.018000 3435 4100 1 chr1B.!!$R1 665
6 TraesCS7B01G162300 chr6B 27650390 27651185 795 True 891.000000 891 87.032000 3380 4172 1 chr6B.!!$R1 792
7 TraesCS7B01G162300 chr4B 209600480 209601049 569 True 699.000000 699 88.870000 3411 3980 1 chr4B.!!$R1 569
8 TraesCS7B01G162300 chr3A 685439084 685439796 712 True 536.000000 536 80.707000 4529 5248 1 chr3A.!!$R3 719

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
71 72 0.319813 GGCTTGCGCAAAAGAACCAT 60.320 50.000 25.01 0.00 38.10 3.55 F
1408 1427 0.541392 CCCATCTCGGAATGGTGTGA 59.459 55.000 13.67 0.00 44.05 3.58 F
1940 2426 2.309528 TTATGACACCATCTCGTGCC 57.690 50.000 0.00 0.00 37.25 5.01 F
2048 2534 3.035363 TGTGACACCTGAGGTTGTCTTA 58.965 45.455 24.35 15.47 35.94 2.10 F
2235 2721 3.578282 TGCTGTGTTAGATGACCTCTCAA 59.422 43.478 0.00 0.00 35.28 3.02 F
2441 2927 4.389890 AACATGCTCATTTTGTGTGTGT 57.610 36.364 0.00 0.00 0.00 3.72 F
2608 3094 5.011943 ACCATGCTTTTAGCTTTCATTGGAA 59.988 36.000 0.00 0.00 42.97 3.53 F
3340 4534 5.414454 TGGAAAATTCGCTTGCAGTAGTAAT 59.586 36.000 0.00 0.00 0.00 1.89 F
4878 6087 4.686191 TCCTTTGGACATGTTGCAATTT 57.314 36.364 0.59 0.00 35.14 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2534 1.033746 CGACATGCCCTGATGCCTTT 61.034 55.000 0.00 0.00 0.00 3.11 R
2235 2721 0.468226 TTTGCACCGAGTTCCTCTGT 59.532 50.000 0.00 0.00 0.00 3.41 R
3045 4232 1.072489 TCATGTTGCGGAAGTGGGTAA 59.928 47.619 0.00 0.00 0.00 2.85 R
3205 4399 2.808543 AGTCTGAACGCAATGAAGGTTC 59.191 45.455 5.66 5.66 40.26 3.62 R
3951 5154 4.866921 TGTACGCGAAATAGAGTATGCAT 58.133 39.130 15.93 3.79 0.00 3.96 R
4414 5621 7.453393 AGATAGACATCAAGTTCAAACCTTCA 58.547 34.615 0.00 0.00 33.21 3.02 R
4474 5681 4.041567 TCAACTGCCTCTAATCCAAACAGA 59.958 41.667 0.00 0.00 0.00 3.41 R
4923 6133 3.081061 AGTTGCACACTCAAGAACACAA 58.919 40.909 0.00 0.00 0.00 3.33 R
6368 7610 0.804989 CGGGCAACTGGAAGATGAAC 59.195 55.000 0.00 0.00 39.37 3.18 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
41 42 3.625313 TGCAAAGTTTTAGGCAAAAAGGC 59.375 39.130 0.00 0.00 37.74 4.35
58 59 3.044235 AGGCTAAACATTTTGGCTTGC 57.956 42.857 8.65 0.00 43.74 4.01
65 66 1.598601 ACATTTTGGCTTGCGCAAAAG 59.401 42.857 25.01 14.77 40.03 2.27
68 69 1.285578 TTTGGCTTGCGCAAAAGAAC 58.714 45.000 25.01 12.49 34.19 3.01
69 70 0.529555 TTGGCTTGCGCAAAAGAACC 60.530 50.000 25.01 19.06 38.10 3.62
71 72 0.319813 GGCTTGCGCAAAAGAACCAT 60.320 50.000 25.01 0.00 38.10 3.55
73 74 1.985684 GCTTGCGCAAAAGAACCATAC 59.014 47.619 25.01 0.02 35.78 2.39
83 84 5.451242 GCAAAAGAACCATACTGAACACCAA 60.451 40.000 0.00 0.00 0.00 3.67
103 104 8.601546 ACACCAAATATTACCCAAAAATGTCAT 58.398 29.630 0.00 0.00 0.00 3.06
105 106 8.264347 ACCAAATATTACCCAAAAATGTCATCC 58.736 33.333 0.00 0.00 0.00 3.51
110 111 6.500589 TTACCCAAAAATGTCATCCCAAAA 57.499 33.333 0.00 0.00 0.00 2.44
118 119 9.235537 CAAAAATGTCATCCCAAAATTGTTTTC 57.764 29.630 0.00 0.00 0.00 2.29
122 123 6.882656 TGTCATCCCAAAATTGTTTTCTCAA 58.117 32.000 0.00 0.00 0.00 3.02
138 139 5.422666 TTCTCAACGACGAAACACTAGTA 57.577 39.130 0.00 0.00 0.00 1.82
141 142 4.776743 TCAACGACGAAACACTAGTACTC 58.223 43.478 0.00 0.00 0.00 2.59
143 144 2.158449 ACGACGAAACACTAGTACTCCG 59.842 50.000 0.00 0.13 0.00 4.63
163 164 2.591148 CGCTTCGCATGAAAATTGTCAG 59.409 45.455 4.31 0.00 32.66 3.51
183 184 1.879380 GGCATGCTTGTGACACTAACA 59.121 47.619 18.92 1.12 0.00 2.41
197 198 3.558418 ACACTAACACGAACATCCACAAC 59.442 43.478 0.00 0.00 0.00 3.32
202 203 4.647424 ACACGAACATCCACAACAAAAT 57.353 36.364 0.00 0.00 0.00 1.82
208 209 5.976534 CGAACATCCACAACAAAATTCAGAA 59.023 36.000 0.00 0.00 0.00 3.02
253 256 6.375736 TGCATTTTTAGGTATTGTTCATCCGA 59.624 34.615 0.00 0.00 0.00 4.55
286 289 4.388499 GGAGCCGAAACGCCTCCA 62.388 66.667 14.60 0.00 34.55 3.86
287 290 2.125106 GAGCCGAAACGCCTCCAT 60.125 61.111 0.00 0.00 0.00 3.41
300 303 4.776349 ACGCCTCCATGTATGAAAATACA 58.224 39.130 1.33 1.33 40.79 2.29
801 804 1.553248 CAGACACCCTTCCACCGAATA 59.447 52.381 0.00 0.00 0.00 1.75
882 885 2.611751 CGATGGTGTTTATGCGATTCCA 59.388 45.455 0.00 0.00 0.00 3.53
909 912 1.710816 CTTATCGCCTCCTCCCTCTT 58.289 55.000 0.00 0.00 0.00 2.85
938 941 2.307686 CCTAAACCCAGCAGAACCCTAA 59.692 50.000 0.00 0.00 0.00 2.69
1107 1126 2.203788 TCACTCAAGGCCTCCGGT 60.204 61.111 5.23 1.58 0.00 5.28
1403 1422 1.228063 CCAGCCCATCTCGGAATGG 60.228 63.158 9.32 9.32 44.96 3.16
1408 1427 0.541392 CCCATCTCGGAATGGTGTGA 59.459 55.000 13.67 0.00 44.05 3.58
1421 1440 8.961634 TCGGAATGGTGTGATTTATTTTTCATA 58.038 29.630 0.00 0.00 0.00 2.15
1517 1536 3.495331 TGCACTGTGGTTTATGTGGAAT 58.505 40.909 10.21 0.00 0.00 3.01
1533 1552 6.964807 TGTGGAATTTGGATATGGAATCTG 57.035 37.500 0.00 0.00 0.00 2.90
1695 2161 6.346919 GCAGTACTCGAATTACAATATGGCAG 60.347 42.308 0.00 0.00 0.00 4.85
1756 2222 9.914834 TTAGTACTAGTTGGCAAATATGGATTT 57.085 29.630 7.95 0.00 35.56 2.17
1757 2223 8.823220 AGTACTAGTTGGCAAATATGGATTTT 57.177 30.769 7.95 0.00 32.73 1.82
1758 2224 8.686334 AGTACTAGTTGGCAAATATGGATTTTG 58.314 33.333 7.95 0.00 32.73 2.44
1759 2225 7.480760 ACTAGTTGGCAAATATGGATTTTGT 57.519 32.000 7.95 0.00 36.63 2.83
1760 2226 7.547227 ACTAGTTGGCAAATATGGATTTTGTC 58.453 34.615 7.95 0.00 38.76 3.18
1761 2227 6.357579 AGTTGGCAAATATGGATTTTGTCA 57.642 33.333 0.00 0.00 44.43 3.58
1762 2228 6.400568 AGTTGGCAAATATGGATTTTGTCAG 58.599 36.000 0.00 0.00 46.01 3.51
1763 2229 4.757594 TGGCAAATATGGATTTTGTCAGC 58.242 39.130 0.00 0.00 42.10 4.26
1764 2230 4.467082 TGGCAAATATGGATTTTGTCAGCT 59.533 37.500 0.00 0.00 42.10 4.24
1765 2231 5.045872 GGCAAATATGGATTTTGTCAGCTC 58.954 41.667 0.00 0.00 38.30 4.09
1766 2232 5.394443 GGCAAATATGGATTTTGTCAGCTCA 60.394 40.000 0.00 0.00 38.30 4.26
1767 2233 6.278363 GCAAATATGGATTTTGTCAGCTCAT 58.722 36.000 0.00 0.00 36.63 2.90
1768 2234 6.759827 GCAAATATGGATTTTGTCAGCTCATT 59.240 34.615 0.00 0.00 36.63 2.57
1769 2235 7.922278 GCAAATATGGATTTTGTCAGCTCATTA 59.078 33.333 0.00 0.00 36.63 1.90
1770 2236 9.459640 CAAATATGGATTTTGTCAGCTCATTAG 57.540 33.333 0.00 0.00 32.73 1.73
1771 2237 8.757982 AATATGGATTTTGTCAGCTCATTAGT 57.242 30.769 0.00 0.00 0.00 2.24
1772 2238 9.851686 AATATGGATTTTGTCAGCTCATTAGTA 57.148 29.630 0.00 0.00 0.00 1.82
1773 2239 6.985188 TGGATTTTGTCAGCTCATTAGTAC 57.015 37.500 0.00 0.00 0.00 2.73
1774 2240 6.711277 TGGATTTTGTCAGCTCATTAGTACT 58.289 36.000 0.00 0.00 0.00 2.73
1775 2241 7.847096 TGGATTTTGTCAGCTCATTAGTACTA 58.153 34.615 0.00 0.00 0.00 1.82
1776 2242 7.981789 TGGATTTTGTCAGCTCATTAGTACTAG 59.018 37.037 2.23 0.00 0.00 2.57
1777 2243 7.982354 GGATTTTGTCAGCTCATTAGTACTAGT 59.018 37.037 0.00 0.00 0.00 2.57
1778 2244 9.372369 GATTTTGTCAGCTCATTAGTACTAGTT 57.628 33.333 0.00 0.00 0.00 2.24
1779 2245 8.534333 TTTTGTCAGCTCATTAGTACTAGTTG 57.466 34.615 0.00 5.75 0.00 3.16
1780 2246 6.208988 TGTCAGCTCATTAGTACTAGTTGG 57.791 41.667 0.00 0.00 0.00 3.77
1781 2247 5.044558 GTCAGCTCATTAGTACTAGTTGGC 58.955 45.833 0.00 6.92 0.00 4.52
1782 2248 4.709886 TCAGCTCATTAGTACTAGTTGGCA 59.290 41.667 0.00 0.00 0.00 4.92
1783 2249 5.186992 TCAGCTCATTAGTACTAGTTGGCAA 59.813 40.000 0.00 0.00 0.00 4.52
1784 2250 5.874810 CAGCTCATTAGTACTAGTTGGCAAA 59.125 40.000 0.00 0.00 0.00 3.68
1785 2251 6.540189 CAGCTCATTAGTACTAGTTGGCAAAT 59.460 38.462 5.23 5.23 0.00 2.32
1786 2252 7.710907 CAGCTCATTAGTACTAGTTGGCAAATA 59.289 37.037 0.00 3.92 0.00 1.40
1787 2253 8.432805 AGCTCATTAGTACTAGTTGGCAAATAT 58.567 33.333 7.95 1.98 0.00 1.28
1788 2254 8.499162 GCTCATTAGTACTAGTTGGCAAATATG 58.501 37.037 7.95 3.17 0.00 1.78
1789 2255 8.902540 TCATTAGTACTAGTTGGCAAATATGG 57.097 34.615 7.95 0.25 0.00 2.74
1790 2256 8.491134 TCATTAGTACTAGTTGGCAAATATGGT 58.509 33.333 7.95 6.37 0.00 3.55
1791 2257 9.120538 CATTAGTACTAGTTGGCAAATATGGTT 57.879 33.333 7.95 0.00 0.00 3.67
1792 2258 9.695155 ATTAGTACTAGTTGGCAAATATGGTTT 57.305 29.630 7.95 0.00 0.00 3.27
1873 2339 5.232463 TGTATTGGTACGGTTCTGTTTCTC 58.768 41.667 0.00 0.00 33.36 2.87
1877 2343 4.401022 TGGTACGGTTCTGTTTCTCTCTA 58.599 43.478 0.00 0.00 0.00 2.43
1940 2426 2.309528 TTATGACACCATCTCGTGCC 57.690 50.000 0.00 0.00 37.25 5.01
2048 2534 3.035363 TGTGACACCTGAGGTTGTCTTA 58.965 45.455 24.35 15.47 35.94 2.10
2144 2630 5.302568 TGCTGATCACCTGTTGAAAGATTTT 59.697 36.000 0.00 0.00 37.92 1.82
2235 2721 3.578282 TGCTGTGTTAGATGACCTCTCAA 59.422 43.478 0.00 0.00 35.28 3.02
2441 2927 4.389890 AACATGCTCATTTTGTGTGTGT 57.610 36.364 0.00 0.00 0.00 3.72
2608 3094 5.011943 ACCATGCTTTTAGCTTTCATTGGAA 59.988 36.000 0.00 0.00 42.97 3.53
2662 3159 6.128227 TGTTTGCAACGGTATTATACTTCACC 60.128 38.462 0.00 0.00 0.00 4.02
2780 3279 7.548097 TGATGATTCTGTTGACTTAGACTACC 58.452 38.462 0.00 0.00 0.00 3.18
3087 4281 9.551734 CATGATTTTGAATGAGTGATCTACCTA 57.448 33.333 0.00 0.00 0.00 3.08
3170 4364 6.392354 ACCTGCATGAACAATGTGATTTAAG 58.608 36.000 0.00 0.00 38.65 1.85
3267 4461 5.950544 TTAGACCTGCTAACATACATGGT 57.049 39.130 0.00 0.00 34.21 3.55
3340 4534 5.414454 TGGAAAATTCGCTTGCAGTAGTAAT 59.586 36.000 0.00 0.00 0.00 1.89
3341 4535 6.596106 TGGAAAATTCGCTTGCAGTAGTAATA 59.404 34.615 0.00 0.00 0.00 0.98
3342 4536 7.282224 TGGAAAATTCGCTTGCAGTAGTAATAT 59.718 33.333 0.00 0.00 0.00 1.28
3343 4537 8.770828 GGAAAATTCGCTTGCAGTAGTAATATA 58.229 33.333 0.00 0.00 0.00 0.86
3633 4831 6.752168 ACTATGGGCTCATATGCAATTTTTC 58.248 36.000 6.77 0.00 35.53 2.29
3837 5039 6.459161 GGTGTAGTTACTCCCACTTTTGTTTG 60.459 42.308 12.62 0.00 34.61 2.93
3980 5183 6.211664 ACTCTATTTCGCGTACAAATATGC 57.788 37.500 5.77 0.00 39.58 3.14
4473 5680 9.010029 TGTTGAGTTACTTGTTTTTCTTCTTCT 57.990 29.630 0.00 0.00 0.00 2.85
4474 5681 9.841880 GTTGAGTTACTTGTTTTTCTTCTTCTT 57.158 29.630 0.00 0.00 0.00 2.52
4476 5683 9.449719 TGAGTTACTTGTTTTTCTTCTTCTTCT 57.550 29.630 0.00 0.00 0.00 2.85
4517 5724 8.066595 CAGTTGAGTTAGTCACTTTTCATCTTG 58.933 37.037 0.00 0.00 35.01 3.02
4878 6087 4.686191 TCCTTTGGACATGTTGCAATTT 57.314 36.364 0.59 0.00 35.14 1.82
4890 6099 7.215789 ACATGTTGCAATTTAAATGGAAGTCA 58.784 30.769 6.77 0.64 0.00 3.41
4951 6161 5.673337 TCTTGAGTGTGCAACTAATGTTC 57.327 39.130 0.00 0.00 40.07 3.18
5057 6267 6.155475 AGTTGAGGTGAGTTATCTATCAGC 57.845 41.667 0.00 0.00 42.77 4.26
5207 6432 8.722480 TGATGACATTATTAGTCTTTGTCCTG 57.278 34.615 0.00 0.00 36.68 3.86
5271 6496 3.820557 TCCTTGCTGCTACAGAAACTTT 58.179 40.909 0.00 0.00 32.44 2.66
5478 6703 3.726557 AGGAAGCAATGGACATGAAGA 57.273 42.857 0.00 0.00 0.00 2.87
5903 7133 9.901172 AGTTTCTCGACCATTACCTTTATTAAT 57.099 29.630 0.00 0.00 0.00 1.40
5940 7182 9.636965 GAAACTTAAAAAGCATTGTTTGTCATC 57.363 29.630 0.00 0.00 0.00 2.92
5944 7186 1.909700 AGCATTGTTTGTCATCCCGT 58.090 45.000 0.00 0.00 0.00 5.28
5947 7189 2.164219 GCATTGTTTGTCATCCCGTGAT 59.836 45.455 0.00 0.00 39.48 3.06
5948 7190 3.367292 GCATTGTTTGTCATCCCGTGATT 60.367 43.478 0.00 0.00 39.48 2.57
5964 7206 7.443477 TCCCGTGATTTATATCGTGGAATTTA 58.557 34.615 5.44 0.00 32.30 1.40
5988 7230 2.704464 TGGAAGATGATGTGGCTGAG 57.296 50.000 0.00 0.00 0.00 3.35
5992 7234 3.133721 GGAAGATGATGTGGCTGAGTAGT 59.866 47.826 0.00 0.00 0.00 2.73
5996 7238 5.851720 AGATGATGTGGCTGAGTAGTTATG 58.148 41.667 0.00 0.00 0.00 1.90
6012 7254 5.086104 AGTTATGTACACTGGGACATGTC 57.914 43.478 17.91 17.91 38.20 3.06
6026 7268 4.789012 GACATGTCCAAATCACCATTGT 57.211 40.909 15.31 0.00 0.00 2.71
6032 7274 7.395772 ACATGTCCAAATCACCATTGTACATAA 59.604 33.333 0.00 0.00 0.00 1.90
6037 7279 5.811399 AATCACCATTGTACATAACACCG 57.189 39.130 0.00 0.00 38.00 4.94
6123 7365 0.806868 ACGCAAGAACGGACGAGATA 59.193 50.000 0.00 0.00 43.62 1.98
6144 7386 2.616842 AGGTGTTCCTTTTGCAGTAACG 59.383 45.455 0.00 0.00 42.12 3.18
6147 7389 3.018149 TGTTCCTTTTGCAGTAACGGTT 58.982 40.909 0.00 0.00 0.00 4.44
6294 7536 9.872684 ATTTCATTCAAGTATCCCAGTCATATT 57.127 29.630 0.00 0.00 0.00 1.28
6324 7566 1.541233 GGTGACCAGGAGTGAGTTGTG 60.541 57.143 0.00 0.00 0.00 3.33
6335 7577 2.135933 GTGAGTTGTGTGGCTACAGTC 58.864 52.381 1.83 0.00 37.52 3.51
6368 7610 1.459592 GTCCAGATCACCAAAACGTCG 59.540 52.381 0.00 0.00 0.00 5.12
6445 7703 4.170062 CATTGCTGCAGACGCCCG 62.170 66.667 20.43 0.00 37.32 6.13
6522 7780 5.815222 TGGAATTGACATCAACTACCATACG 59.185 40.000 10.29 0.00 38.86 3.06
6622 7883 4.515191 TGGACAGTCAAAGATTTTTCTCGG 59.485 41.667 2.17 0.00 0.00 4.63
6648 7909 4.398319 CCCTGTGTTGGAAGTCTTGTAAT 58.602 43.478 0.00 0.00 0.00 1.89
6715 7976 0.792031 GTTTAACACGGCCTGGTACG 59.208 55.000 0.00 10.58 0.00 3.67
6861 8122 2.049433 AAACACGCCGAGGACGAG 60.049 61.111 11.61 7.21 42.66 4.18
7035 8302 0.909610 AGCCCTTCACCATCTTCCGA 60.910 55.000 0.00 0.00 0.00 4.55
7296 8563 1.880340 GGACTTCGCCGAGATGCTG 60.880 63.158 0.00 0.00 0.00 4.41
7311 8578 3.753434 CTGCTCCTCGACGGCTGT 61.753 66.667 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.219033 GTGTTCAGTATGGTTCTTTTGCG 58.781 43.478 0.00 0.00 36.16 4.85
65 66 8.403236 GGTAATATTTGGTGTTCAGTATGGTTC 58.597 37.037 0.00 0.00 36.16 3.62
68 69 6.831353 TGGGTAATATTTGGTGTTCAGTATGG 59.169 38.462 0.00 0.00 36.16 2.74
69 70 7.873719 TGGGTAATATTTGGTGTTCAGTATG 57.126 36.000 0.00 0.00 37.54 2.39
71 72 8.707796 TTTTGGGTAATATTTGGTGTTCAGTA 57.292 30.769 0.00 0.00 0.00 2.74
73 74 8.934825 CATTTTTGGGTAATATTTGGTGTTCAG 58.065 33.333 0.00 0.00 0.00 3.02
83 84 7.986553 TGGGATGACATTTTTGGGTAATATT 57.013 32.000 0.00 0.00 0.00 1.28
103 104 5.344884 GTCGTTGAGAAAACAATTTTGGGA 58.655 37.500 0.00 0.00 31.94 4.37
105 106 5.031578 TCGTCGTTGAGAAAACAATTTTGG 58.968 37.500 0.00 0.00 31.94 3.28
110 111 5.025826 GTGTTTCGTCGTTGAGAAAACAAT 58.974 37.500 8.65 0.00 39.71 2.71
118 119 4.781071 AGTACTAGTGTTTCGTCGTTGAG 58.219 43.478 5.39 0.00 0.00 3.02
122 123 2.158449 CGGAGTACTAGTGTTTCGTCGT 59.842 50.000 5.39 0.00 0.00 4.34
163 164 1.879380 TGTTAGTGTCACAAGCATGCC 59.121 47.619 15.66 0.00 0.00 4.40
183 184 5.067153 TCTGAATTTTGTTGTGGATGTTCGT 59.933 36.000 0.00 0.00 0.00 3.85
228 229 6.375736 TCGGATGAACAATACCTAAAAATGCA 59.624 34.615 0.00 0.00 0.00 3.96
229 230 6.791303 TCGGATGAACAATACCTAAAAATGC 58.209 36.000 0.00 0.00 0.00 3.56
237 238 2.766263 TGCTCTCGGATGAACAATACCT 59.234 45.455 0.00 0.00 0.00 3.08
275 278 4.695217 TTTTCATACATGGAGGCGTTTC 57.305 40.909 0.00 0.00 0.00 2.78
300 303 9.234827 TCAATATCATTAGATTCGCCATGAAAT 57.765 29.630 0.00 0.00 40.71 2.17
788 791 4.451900 ACTTATTGCTATTCGGTGGAAGG 58.548 43.478 0.00 0.00 35.19 3.46
801 804 4.454504 CCTCGTGTTTACCAACTTATTGCT 59.545 41.667 0.00 0.00 34.17 3.91
815 818 1.441732 GCGTTTCCACCCTCGTGTTT 61.442 55.000 0.00 0.00 38.41 2.83
909 912 1.993391 CTGGGTTTAGGGGCTCGGA 60.993 63.158 0.00 0.00 0.00 4.55
1152 1171 2.964389 GCGCCAGCCTCGATCTTC 60.964 66.667 0.00 0.00 37.42 2.87
1305 1324 2.048023 CCCGTAGTCGTACAGGCCA 61.048 63.158 5.01 0.00 35.01 5.36
1421 1440 4.243270 GCAACAACGACTAGGATACAAGT 58.757 43.478 0.00 0.00 41.41 3.16
1430 1449 1.649171 CAGCTACGCAACAACGACTAG 59.351 52.381 0.00 0.00 36.70 2.57
1437 1456 2.945984 GCAGCAGCTACGCAACAA 59.054 55.556 0.00 0.00 37.91 2.83
1517 1536 9.337714 TCAGTATATCCAGATTCCATATCCAAA 57.662 33.333 0.00 0.00 0.00 3.28
1540 1559 6.049955 TGGGTAACTATCTTCCTTGTTCAG 57.950 41.667 0.00 0.00 0.00 3.02
1597 2063 2.611971 CGCCTTTAGAGGTGTGCACTTA 60.612 50.000 19.41 0.00 46.41 2.24
1756 2222 6.631016 CCAACTAGTACTAATGAGCTGACAA 58.369 40.000 14.12 0.00 0.00 3.18
1757 2223 5.394224 GCCAACTAGTACTAATGAGCTGACA 60.394 44.000 14.12 0.00 0.00 3.58
1758 2224 5.044558 GCCAACTAGTACTAATGAGCTGAC 58.955 45.833 14.12 0.00 0.00 3.51
1759 2225 4.709886 TGCCAACTAGTACTAATGAGCTGA 59.290 41.667 14.12 0.00 0.00 4.26
1760 2226 5.011090 TGCCAACTAGTACTAATGAGCTG 57.989 43.478 14.12 2.79 0.00 4.24
1761 2227 5.677319 TTGCCAACTAGTACTAATGAGCT 57.323 39.130 14.12 0.00 0.00 4.09
1762 2228 6.927294 ATTTGCCAACTAGTACTAATGAGC 57.073 37.500 14.12 14.55 0.00 4.26
1763 2229 8.993121 CCATATTTGCCAACTAGTACTAATGAG 58.007 37.037 14.12 3.41 0.00 2.90
1764 2230 8.491134 ACCATATTTGCCAACTAGTACTAATGA 58.509 33.333 14.12 0.00 0.00 2.57
1765 2231 8.677148 ACCATATTTGCCAACTAGTACTAATG 57.323 34.615 3.76 6.26 0.00 1.90
1766 2232 9.695155 AAACCATATTTGCCAACTAGTACTAAT 57.305 29.630 3.76 1.05 0.00 1.73
1767 2233 9.523168 AAAACCATATTTGCCAACTAGTACTAA 57.477 29.630 3.76 0.00 0.00 2.24
1768 2234 9.523168 AAAAACCATATTTGCCAACTAGTACTA 57.477 29.630 1.89 1.89 0.00 1.82
1769 2235 8.303876 CAAAAACCATATTTGCCAACTAGTACT 58.696 33.333 0.00 0.00 31.70 2.73
1770 2236 8.085909 ACAAAAACCATATTTGCCAACTAGTAC 58.914 33.333 0.00 0.00 40.58 2.73
1771 2237 8.184304 ACAAAAACCATATTTGCCAACTAGTA 57.816 30.769 0.00 0.00 40.58 1.82
1772 2238 7.061566 ACAAAAACCATATTTGCCAACTAGT 57.938 32.000 0.00 0.00 40.58 2.57
1773 2239 7.151308 TGACAAAAACCATATTTGCCAACTAG 58.849 34.615 0.00 0.00 40.58 2.57
1774 2240 7.055667 TGACAAAAACCATATTTGCCAACTA 57.944 32.000 0.00 0.00 40.58 2.24
1775 2241 5.923204 TGACAAAAACCATATTTGCCAACT 58.077 33.333 0.00 0.00 40.58 3.16
1776 2242 5.757808 ACTGACAAAAACCATATTTGCCAAC 59.242 36.000 0.00 0.00 40.58 3.77
1777 2243 5.923204 ACTGACAAAAACCATATTTGCCAA 58.077 33.333 0.00 0.00 40.58 4.52
1778 2244 5.543507 ACTGACAAAAACCATATTTGCCA 57.456 34.783 0.00 0.00 40.58 4.92
1779 2245 5.988561 TGAACTGACAAAAACCATATTTGCC 59.011 36.000 0.00 0.00 40.58 4.52
1780 2246 7.656707 ATGAACTGACAAAAACCATATTTGC 57.343 32.000 0.00 0.00 40.58 3.68
1786 2252 7.599998 GCATAGAAATGAACTGACAAAAACCAT 59.400 33.333 0.00 0.00 34.84 3.55
1787 2253 6.922957 GCATAGAAATGAACTGACAAAAACCA 59.077 34.615 0.00 0.00 34.84 3.67
1788 2254 6.366061 GGCATAGAAATGAACTGACAAAAACC 59.634 38.462 0.00 0.00 34.84 3.27
1789 2255 7.115378 CAGGCATAGAAATGAACTGACAAAAAC 59.885 37.037 5.20 0.00 39.81 2.43
1790 2256 7.014134 TCAGGCATAGAAATGAACTGACAAAAA 59.986 33.333 8.29 0.00 40.60 1.94
1791 2257 6.489700 TCAGGCATAGAAATGAACTGACAAAA 59.510 34.615 8.29 0.00 40.60 2.44
1792 2258 6.003326 TCAGGCATAGAAATGAACTGACAAA 58.997 36.000 8.29 0.00 40.60 2.83
1873 2339 6.072286 ACCAACATCAAGCACAGAATTTAGAG 60.072 38.462 0.00 0.00 0.00 2.43
1877 2343 4.942761 ACCAACATCAAGCACAGAATTT 57.057 36.364 0.00 0.00 0.00 1.82
1940 2426 7.910441 AATTAGCATCTTCCCAAAACAAATG 57.090 32.000 0.00 0.00 0.00 2.32
2048 2534 1.033746 CGACATGCCCTGATGCCTTT 61.034 55.000 0.00 0.00 0.00 3.11
2144 2630 2.346766 TCTCAAGCTTGTCCTTGCAA 57.653 45.000 25.19 0.00 41.47 4.08
2177 2663 3.474570 GCAGCCGTCTCAGGGGAT 61.475 66.667 0.00 0.00 0.00 3.85
2235 2721 0.468226 TTTGCACCGAGTTCCTCTGT 59.532 50.000 0.00 0.00 0.00 3.41
2441 2927 4.966168 TCTGGCCTCATATACCTGTTTGTA 59.034 41.667 3.32 0.00 0.00 2.41
2608 3094 9.480053 CAAAGAATTAACAAGTGAAATGGACAT 57.520 29.630 0.00 0.00 0.00 3.06
2756 3254 7.777095 AGGTAGTCTAAGTCAACAGAATCATC 58.223 38.462 0.00 0.00 0.00 2.92
3045 4232 1.072489 TCATGTTGCGGAAGTGGGTAA 59.928 47.619 0.00 0.00 0.00 2.85
3087 4281 9.034800 TGGAGAAGGTTGCATCTTATTTTAAAT 57.965 29.630 3.25 0.00 0.00 1.40
3106 4300 7.621428 ATGAAGTGTGATGTAAATGGAGAAG 57.379 36.000 0.00 0.00 0.00 2.85
3170 4364 8.570488 TGGAATGATGAAATAACAGCACATATC 58.430 33.333 0.00 0.00 38.95 1.63
3205 4399 2.808543 AGTCTGAACGCAATGAAGGTTC 59.191 45.455 5.66 5.66 40.26 3.62
3471 4665 6.276091 ACATACTACACGTACATACTCTCGA 58.724 40.000 0.00 0.00 0.00 4.04
3793 4992 8.181904 CTACACCCGGTAGTAGGAAAAATATA 57.818 38.462 18.15 0.00 43.73 0.86
3795 4994 6.469782 CTACACCCGGTAGTAGGAAAAATA 57.530 41.667 18.15 0.00 43.73 1.40
3951 5154 4.866921 TGTACGCGAAATAGAGTATGCAT 58.133 39.130 15.93 3.79 0.00 3.96
4414 5621 7.453393 AGATAGACATCAAGTTCAAACCTTCA 58.547 34.615 0.00 0.00 33.21 3.02
4473 5680 4.640771 ACTGCCTCTAATCCAAACAGAA 57.359 40.909 0.00 0.00 0.00 3.02
4474 5681 4.041567 TCAACTGCCTCTAATCCAAACAGA 59.958 41.667 0.00 0.00 0.00 3.41
4475 5682 4.326826 TCAACTGCCTCTAATCCAAACAG 58.673 43.478 0.00 0.00 0.00 3.16
4476 5683 4.202461 ACTCAACTGCCTCTAATCCAAACA 60.202 41.667 0.00 0.00 0.00 2.83
4814 6023 9.949174 CAAAATTATTCATCGGATGTGATGTAA 57.051 29.630 17.01 10.37 44.82 2.41
4878 6087 7.230747 TGAATGAAAGGAGTGACTTCCATTTA 58.769 34.615 4.37 0.00 39.84 1.40
4923 6133 3.081061 AGTTGCACACTCAAGAACACAA 58.919 40.909 0.00 0.00 0.00 3.33
4951 6161 3.446161 ACACCAATCAGGAAAGCATGATG 59.554 43.478 0.00 0.00 44.08 3.07
5057 6267 9.617975 GACTCCAAAAATACTGAAGAATCAAAG 57.382 33.333 0.00 0.00 34.49 2.77
5207 6432 9.502091 TGGTAGACCTAATTGATTATGCATTAC 57.498 33.333 3.54 0.00 36.82 1.89
5271 6496 4.454504 GTCTTTCTTTGAGGGCACGATAAA 59.545 41.667 0.00 0.00 0.00 1.40
5417 6642 7.012894 TGTTTGTCCAAGAATAAAGTCAACGAT 59.987 33.333 0.00 0.00 0.00 3.73
5478 6703 2.091665 CCCCCTTAGATTCCAATGCAGT 60.092 50.000 0.00 0.00 0.00 4.40
5785 7010 2.355009 CAAGCACTTTGGCGGCAC 60.355 61.111 12.92 0.00 39.27 5.01
5940 7182 6.554334 AAATTCCACGATATAAATCACGGG 57.446 37.500 0.00 0.00 31.93 5.28
5964 7206 3.889538 CAGCCACATCATCTTCCATCATT 59.110 43.478 0.00 0.00 0.00 2.57
5975 7217 5.620738 ACATAACTACTCAGCCACATCAT 57.379 39.130 0.00 0.00 0.00 2.45
5988 7230 5.974108 ACATGTCCCAGTGTACATAACTAC 58.026 41.667 0.00 0.00 34.61 2.73
5992 7234 4.481368 GGACATGTCCCAGTGTACATAA 57.519 45.455 31.37 0.00 43.94 1.90
6012 7254 6.329496 GGTGTTATGTACAATGGTGATTTGG 58.671 40.000 0.00 0.00 38.80 3.28
6026 7268 5.653769 AGTTAGTAAGCCTCGGTGTTATGTA 59.346 40.000 0.00 0.00 0.00 2.29
6032 7274 1.067071 GCAGTTAGTAAGCCTCGGTGT 60.067 52.381 0.00 0.00 0.00 4.16
6037 7279 2.352960 GCATGTGCAGTTAGTAAGCCTC 59.647 50.000 0.00 0.00 41.59 4.70
6144 7386 2.227388 CACCTCTGTTGCAGAATCAACC 59.773 50.000 4.46 0.00 44.15 3.77
6147 7389 2.771089 GTCACCTCTGTTGCAGAATCA 58.229 47.619 0.37 0.00 40.18 2.57
6324 7566 1.738099 CGGTGCAGACTGTAGCCAC 60.738 63.158 15.76 9.27 0.00 5.01
6368 7610 0.804989 CGGGCAACTGGAAGATGAAC 59.195 55.000 0.00 0.00 39.37 3.18
6426 7669 3.740397 GGCGTCTGCAGCAATGCA 61.740 61.111 18.30 2.57 45.35 3.96
6427 7670 4.487412 GGGCGTCTGCAGCAATGC 62.487 66.667 9.47 10.04 45.35 3.56
6428 7671 4.170062 CGGGCGTCTGCAGCAATG 62.170 66.667 9.47 0.00 45.35 2.82
6429 7672 4.704833 ACGGGCGTCTGCAGCAAT 62.705 61.111 9.47 0.00 45.35 3.56
6430 7673 4.927782 AACGGGCGTCTGCAGCAA 62.928 61.111 9.47 0.00 45.35 3.91
6441 7684 1.940613 GGTAAGATCATGACAACGGGC 59.059 52.381 0.00 0.00 0.00 6.13
6484 7742 6.794374 TGTCAATTCCATTGTATGTGTATGC 58.206 36.000 0.00 0.00 41.02 3.14
6512 7770 7.039504 TCCTTAAGACTCAAAACGTATGGTAGT 60.040 37.037 3.36 0.00 0.00 2.73
6522 7780 7.864882 ACTTACGTACTCCTTAAGACTCAAAAC 59.135 37.037 3.36 0.00 0.00 2.43
6720 7981 2.099652 CTCGGGAGGCAATGGCGATA 62.100 60.000 0.00 0.00 42.47 2.92
6861 8122 1.139947 CTCCTCCGCTTCTTCGTCC 59.860 63.158 0.00 0.00 0.00 4.79
6978 8245 4.821589 GGAAGAGCGTCCAGGCGG 62.822 72.222 5.58 0.00 37.65 6.13
7005 8272 2.676822 AAGGGCTCGCTCTCGTGA 60.677 61.111 0.00 0.00 36.96 4.35
7296 8563 2.048127 AAACAGCCGTCGAGGAGC 60.048 61.111 6.70 8.46 45.00 4.70


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

AutoCloner maintained by Alex Coulton.