Multiple sequence alignment - TraesCS7D01G433100

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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 TraesCS7D01G433100 chr7D 100.000 6385 0 0 1 6385 552960867 552967251 0.000000e+00 11791.0
1 TraesCS7D01G433100 chr7D 86.521 549 56 8 5607 6151 552987853 552988387 7.130000e-164 588.0
2 TraesCS7D01G433100 chr7D 87.766 376 23 13 5607 5982 553064269 553064621 9.900000e-113 418.0
3 TraesCS7D01G433100 chr7D 95.745 235 10 0 6150 6384 552988353 552988587 4.670000e-101 379.0
4 TraesCS7D01G433100 chr7D 93.750 144 8 1 5172 5315 553071318 553071460 1.390000e-51 215.0
5 TraesCS7D01G433100 chr7D 94.815 135 7 0 5181 5315 552987099 552987233 1.800000e-50 211.0
6 TraesCS7D01G433100 chr7D 96.203 79 1 1 5495 5571 553062751 553062829 1.870000e-25 128.0
7 TraesCS7D01G433100 chr7A 93.899 3196 113 24 2443 5606 638708021 638711166 0.000000e+00 4747.0
8 TraesCS7D01G433100 chr7A 91.969 1432 65 35 981 2394 638706626 638708025 0.000000e+00 1962.0
9 TraesCS7D01G433100 chr7A 85.423 1029 96 26 1 992 638705596 638706607 0.000000e+00 1020.0
10 TraesCS7D01G433100 chr7A 94.000 400 20 2 5755 6151 638711329 638711727 2.550000e-168 603.0
11 TraesCS7D01G433100 chr7A 97.021 235 7 0 6151 6385 638711694 638711928 4.640000e-106 396.0
12 TraesCS7D01G433100 chr7A 77.647 595 100 26 5803 6385 639292030 639291457 1.330000e-86 331.0
13 TraesCS7D01G433100 chr7A 94.215 121 5 1 5607 5727 638711210 638711328 3.930000e-42 183.0
14 TraesCS7D01G433100 chr7A 89.474 114 7 5 2106 2214 401657868 401657755 8.630000e-29 139.0
15 TraesCS7D01G433100 chr7B 92.157 2040 105 28 3586 5606 598477043 598479046 0.000000e+00 2830.0
16 TraesCS7D01G433100 chr7B 95.833 1464 46 6 4155 5606 644553999 644555459 0.000000e+00 2351.0
17 TraesCS7D01G433100 chr7B 92.973 1352 66 14 2715 4050 599413504 599414842 0.000000e+00 1943.0
18 TraesCS7D01G433100 chr7B 95.766 1181 47 1 4121 5301 599415148 599416325 0.000000e+00 1901.0
19 TraesCS7D01G433100 chr7B 86.659 1664 125 48 389 1986 644544769 644546401 0.000000e+00 1753.0
20 TraesCS7D01G433100 chr7B 86.415 1509 107 36 389 1860 598473692 598475139 0.000000e+00 1561.0
21 TraesCS7D01G433100 chr7B 85.900 1156 110 22 2181 3313 598475645 598476770 0.000000e+00 1182.0
22 TraesCS7D01G433100 chr7B 84.248 1276 114 44 1975 3198 644550031 644551271 0.000000e+00 1162.0
23 TraesCS7D01G433100 chr7B 92.484 785 41 5 5607 6385 598479232 598480004 0.000000e+00 1107.0
24 TraesCS7D01G433100 chr7B 85.443 790 66 23 5607 6385 599393098 599393849 0.000000e+00 776.0
25 TraesCS7D01G433100 chr7B 85.406 788 67 19 5607 6384 599417010 599417759 0.000000e+00 774.0
26 TraesCS7D01G433100 chr7B 96.429 392 13 1 1 391 644543830 644544221 0.000000e+00 645.0
27 TraesCS7D01G433100 chr7B 95.929 393 14 2 1 391 598472699 598473091 2.510000e-178 636.0
28 TraesCS7D01G433100 chr7B 91.176 476 27 2 5723 6192 644555790 644556256 3.250000e-177 632.0
29 TraesCS7D01G433100 chr7B 87.773 458 40 10 3553 4004 644551596 644552043 7.340000e-144 521.0
30 TraesCS7D01G433100 chr7B 82.918 562 71 10 5607 6151 599359516 599360069 3.460000e-132 483.0
31 TraesCS7D01G433100 chr7B 96.194 289 8 2 5293 5578 599416617 599416905 2.700000e-128 470.0
32 TraesCS7D01G433100 chr7B 93.455 275 15 2 2443 2717 599413140 599413411 7.710000e-109 405.0
33 TraesCS7D01G433100 chr7B 94.068 236 14 0 6150 6385 599360035 599360270 6.090000e-95 359.0
34 TraesCS7D01G433100 chr7B 95.283 212 9 1 2184 2394 599412933 599413144 1.030000e-87 335.0
35 TraesCS7D01G433100 chr7B 90.306 196 14 3 5382 5573 599392802 599392996 1.060000e-62 252.0
36 TraesCS7D01G433100 chr7B 94.771 153 5 1 5607 5759 644555645 644555794 1.070000e-57 235.0
37 TraesCS7D01G433100 chr7B 82.587 201 30 5 1859 2058 598475354 598475550 8.510000e-39 172.0
38 TraesCS7D01G433100 chr7B 91.129 124 8 2 5457 5578 599359304 599359426 1.420000e-36 165.0
39 TraesCS7D01G433100 chr7B 88.889 117 7 5 2103 2214 616929102 616929217 8.630000e-29 139.0
40 TraesCS7D01G433100 chr7B 88.889 63 7 0 3249 3311 644551282 644551344 1.910000e-10 78.7
41 TraesCS7D01G433100 chr7B 85.526 76 3 2 5539 5606 599416917 599416992 8.880000e-09 73.1
42 TraesCS7D01G433100 chr1D 79.789 950 145 23 1098 2033 366164896 366163980 0.000000e+00 647.0
43 TraesCS7D01G433100 chr1D 84.746 236 36 0 6150 6385 89230309 89230074 2.980000e-58 237.0
44 TraesCS7D01G433100 chr3A 80.910 791 109 27 1101 1875 79458285 79457521 2.560000e-163 586.0
45 TraesCS7D01G433100 chr3A 89.565 115 6 4 2106 2214 24806989 24806875 2.400000e-29 141.0
46 TraesCS7D01G433100 chr3A 89.474 114 7 5 2106 2214 247166721 247166608 8.630000e-29 139.0
47 TraesCS7D01G433100 chr4B 87.354 427 47 4 1205 1629 98452616 98452195 3.460000e-132 483.0
48 TraesCS7D01G433100 chr4B 87.225 227 15 6 1104 1330 605509139 605509351 4.940000e-61 246.0
49 TraesCS7D01G433100 chr4B 97.500 40 1 0 1564 1603 98452199 98452160 1.150000e-07 69.4
50 TraesCS7D01G433100 chr5B 78.024 678 97 30 1379 2033 11358920 11359568 4.670000e-101 379.0
51 TraesCS7D01G433100 chr5B 89.744 117 6 6 2103 2214 507342014 507342129 1.860000e-30 145.0
52 TraesCS7D01G433100 chr5A 82.857 350 58 2 1196 1545 78912262 78912609 4.810000e-81 313.0
53 TraesCS7D01G433100 chr1A 86.190 210 29 0 5753 5962 85318370 85318161 1.790000e-55 228.0
54 TraesCS7D01G433100 chr6A 83.500 200 33 0 4643 4842 104514142 104514341 3.040000e-43 187.0
55 TraesCS7D01G433100 chr6A 87.500 128 16 0 3809 3936 104513327 104513454 1.430000e-31 148.0
56 TraesCS7D01G433100 chr6A 89.744 117 6 6 2103 2214 443934699 443934814 1.860000e-30 145.0
57 TraesCS7D01G433100 chr6A 91.919 99 8 0 2559 2657 104511434 104511532 8.630000e-29 139.0
58 TraesCS7D01G433100 chr6A 88.571 105 12 0 2559 2663 104308367 104308263 1.870000e-25 128.0
59 TraesCS7D01G433100 chr6D 88.281 128 15 0 3809 3936 86732840 86732967 3.080000e-33 154.0
60 TraesCS7D01G433100 chr6D 91.919 99 8 0 2559 2657 86730937 86731035 8.630000e-29 139.0
61 TraesCS7D01G433100 chr6D 87.619 105 13 0 2559 2663 86643114 86643010 8.690000e-24 122.0
62 TraesCS7D01G433100 chr6B 87.500 128 16 0 3809 3936 164381376 164381503 1.430000e-31 148.0
63 TraesCS7D01G433100 chr6B 91.919 99 8 0 2559 2657 164378656 164378754 8.630000e-29 139.0
64 TraesCS7D01G433100 chr6B 85.938 128 18 0 3809 3936 164137201 164137074 3.100000e-28 137.0
65 TraesCS7D01G433100 chr4D 89.474 114 6 6 2106 2214 266759659 266759547 8.630000e-29 139.0
66 TraesCS7D01G433100 chr2D 89.474 114 6 6 2106 2214 205892564 205892452 8.630000e-29 139.0


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 TraesCS7D01G433100 chr7D 552960867 552967251 6384 False 11791.000000 11791 100.000000 1 6385 1 chr7D.!!$F1 6384
1 TraesCS7D01G433100 chr7D 552987099 552988587 1488 False 392.666667 588 92.360333 5181 6384 3 chr7D.!!$F3 1203
2 TraesCS7D01G433100 chr7D 553062751 553064621 1870 False 273.000000 418 91.984500 5495 5982 2 chr7D.!!$F4 487
3 TraesCS7D01G433100 chr7A 638705596 638711928 6332 False 1485.166667 4747 92.754500 1 6385 6 chr7A.!!$F1 6384
4 TraesCS7D01G433100 chr7A 639291457 639292030 573 True 331.000000 331 77.647000 5803 6385 1 chr7A.!!$R2 582
5 TraesCS7D01G433100 chr7B 598472699 598480004 7305 False 1248.000000 2830 89.245333 1 6385 6 chr7B.!!$F2 6384
6 TraesCS7D01G433100 chr7B 644543830 644556256 12426 False 922.212500 2351 90.722250 1 6192 8 chr7B.!!$F6 6191
7 TraesCS7D01G433100 chr7B 599412933 599417759 4826 False 843.014286 1943 92.086143 2184 6384 7 chr7B.!!$F5 4200
8 TraesCS7D01G433100 chr7B 599392802 599393849 1047 False 514.000000 776 87.874500 5382 6385 2 chr7B.!!$F4 1003
9 TraesCS7D01G433100 chr7B 599359304 599360270 966 False 335.666667 483 89.371667 5457 6385 3 chr7B.!!$F3 928
10 TraesCS7D01G433100 chr1D 366163980 366164896 916 True 647.000000 647 79.789000 1098 2033 1 chr1D.!!$R2 935
11 TraesCS7D01G433100 chr3A 79457521 79458285 764 True 586.000000 586 80.910000 1101 1875 1 chr3A.!!$R2 774
12 TraesCS7D01G433100 chr5B 11358920 11359568 648 False 379.000000 379 78.024000 1379 2033 1 chr5B.!!$F1 654

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
609 1215 0.391130 TGCCGCGAAACTTAGCTGAT 60.391 50.000 8.23 0.0 0.00 2.90 F
1427 2160 0.253610 TCGTGTTGTTGTTGGACCCT 59.746 50.000 0.00 0.0 0.00 4.34 F
1531 2264 1.271652 TGGGTGGATATTTGTGCGTGT 60.272 47.619 0.00 0.0 0.00 4.49 F
2710 7434 2.099756 GCTTGCTTATGCCCCTTTGTAG 59.900 50.000 0.00 0.0 38.71 2.74 F
4096 9168 0.868186 TATTCTCCCTCTCCCCTCCC 59.132 60.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 6769 0.401738 TCCCCAAGAGGAAGCAACAG 59.598 55.000 0.00 0.00 38.24 3.16 R
2724 7543 1.524621 CCGCCAGGAGCTAACATGG 60.525 63.158 1.88 1.88 43.43 3.66 R
3468 8296 5.017294 TGAATAACACATATGACAGCGGA 57.983 39.130 10.38 0.00 0.00 5.54 R
4099 9171 0.252197 GTAGGGTGTAGGGGCAAGTG 59.748 60.000 0.00 0.00 0.00 3.16 R
5975 15029 0.461339 TGATAAAGACGAAGCCGCCC 60.461 55.000 0.00 0.00 39.95 6.13 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
129 130 5.680619 TGGTTCATAGGACAATATGGTCAC 58.319 41.667 12.38 2.05 39.59 3.67
327 329 3.028850 CACATGATCCCTTTGAGGCATT 58.971 45.455 0.00 0.00 32.73 3.56
477 1083 5.390613 CGATGGCGTGTAAAAATTTCTTCT 58.609 37.500 0.00 0.00 0.00 2.85
484 1090 5.560183 CGTGTAAAAATTTCTTCTCACCGCT 60.560 40.000 0.00 0.00 0.00 5.52
537 1143 2.036604 GGAGGCCATCTAACTCTGCTAC 59.963 54.545 5.01 0.00 0.00 3.58
606 1212 0.517316 CTTTGCCGCGAAACTTAGCT 59.483 50.000 8.23 0.00 0.00 3.32
608 1214 0.601576 TTGCCGCGAAACTTAGCTGA 60.602 50.000 8.23 0.00 0.00 4.26
609 1215 0.391130 TGCCGCGAAACTTAGCTGAT 60.391 50.000 8.23 0.00 0.00 2.90
658 1278 2.224079 CCTAATCGATCAAATGCCACGG 59.776 50.000 0.00 0.00 0.00 4.94
662 1282 1.024046 CGATCAAATGCCACGGGTGA 61.024 55.000 0.00 0.00 0.00 4.02
664 1284 1.543802 GATCAAATGCCACGGGTGAAA 59.456 47.619 0.00 0.00 0.00 2.69
692 1316 7.100458 AGCTACAAAATTCAGAAACAACAGT 57.900 32.000 0.00 0.00 0.00 3.55
703 1327 7.297936 TCAGAAACAACAGTGATTCCTAGTA 57.702 36.000 0.00 0.00 37.27 1.82
704 1328 7.152645 TCAGAAACAACAGTGATTCCTAGTAC 58.847 38.462 0.00 0.00 37.27 2.73
713 1337 3.383825 GTGATTCCTAGTACCGGACACAT 59.616 47.826 9.46 0.00 31.45 3.21
714 1338 4.028131 TGATTCCTAGTACCGGACACATT 58.972 43.478 9.46 0.00 0.00 2.71
715 1339 4.468510 TGATTCCTAGTACCGGACACATTT 59.531 41.667 9.46 0.00 0.00 2.32
716 1340 3.880047 TCCTAGTACCGGACACATTTG 57.120 47.619 9.46 0.00 0.00 2.32
721 1345 1.538075 GTACCGGACACATTTGGTTGG 59.462 52.381 9.46 0.00 35.93 3.77
734 1358 1.331399 TGGTTGGCATCATGGGCATG 61.331 55.000 11.50 0.00 43.37 4.06
761 1408 9.811995 CCAAAATTTCAGTTGTGATGATGATAT 57.188 29.630 0.00 0.00 30.85 1.63
807 1454 3.634397 TCAGCAATAGTTTCTGGGAGG 57.366 47.619 0.00 0.00 0.00 4.30
812 1459 4.103311 AGCAATAGTTTCTGGGAGGATACC 59.897 45.833 0.00 0.00 37.17 2.73
861 1528 8.586570 TTCAGTTGTGTAAATATTTTTGCTGG 57.413 30.769 5.91 0.00 0.00 4.85
1361 2091 0.464735 CTCGTGAGTCCTCGATCCCT 60.465 60.000 7.73 0.00 37.61 4.20
1383 2113 0.456312 GATCTCCGTTGCGTCTCGTT 60.456 55.000 0.00 0.00 0.00 3.85
1427 2160 0.253610 TCGTGTTGTTGTTGGACCCT 59.746 50.000 0.00 0.00 0.00 4.34
1531 2264 1.271652 TGGGTGGATATTTGTGCGTGT 60.272 47.619 0.00 0.00 0.00 4.49
1558 2292 6.700520 TCTGTTTTAACGTTTGTTTGTTTGGT 59.299 30.769 5.91 0.00 39.54 3.67
1713 2488 4.172505 CTGTGACTGTATCTTCTCAGTGC 58.827 47.826 2.54 0.00 43.64 4.40
1717 2493 2.899900 ACTGTATCTTCTCAGTGCACCA 59.100 45.455 14.63 0.00 42.30 4.17
1718 2494 3.257393 CTGTATCTTCTCAGTGCACCAC 58.743 50.000 14.63 0.00 34.10 4.16
1744 2522 7.624360 TTTTGCGGTATCTTCATGTATCTTT 57.376 32.000 0.00 0.00 0.00 2.52
1745 2523 7.624360 TTTGCGGTATCTTCATGTATCTTTT 57.376 32.000 0.00 0.00 0.00 2.27
1746 2524 7.624360 TTGCGGTATCTTCATGTATCTTTTT 57.376 32.000 0.00 0.00 0.00 1.94
1747 2525 7.015226 TGCGGTATCTTCATGTATCTTTTTG 57.985 36.000 0.00 0.00 0.00 2.44
1748 2526 6.597672 TGCGGTATCTTCATGTATCTTTTTGT 59.402 34.615 0.00 0.00 0.00 2.83
1749 2527 7.120579 TGCGGTATCTTCATGTATCTTTTTGTT 59.879 33.333 0.00 0.00 0.00 2.83
1750 2528 7.968405 GCGGTATCTTCATGTATCTTTTTGTTT 59.032 33.333 0.00 0.00 0.00 2.83
1751 2529 9.840427 CGGTATCTTCATGTATCTTTTTGTTTT 57.160 29.630 0.00 0.00 0.00 2.43
1877 2887 8.706322 TGACCTGCTAGATATAGTATGTTTGA 57.294 34.615 0.00 0.00 0.00 2.69
1880 2890 9.935241 ACCTGCTAGATATAGTATGTTTGATTG 57.065 33.333 0.00 0.00 0.00 2.67
1908 2918 2.192861 CCAAGCGCAAGTTGGGTGA 61.193 57.895 19.80 0.00 41.63 4.02
1927 2937 4.514066 GGTGACTGGAGAAATAAAACGTGT 59.486 41.667 0.00 0.00 0.00 4.49
1936 2946 4.819630 AGAAATAAAACGTGTCTGGCTGAA 59.180 37.500 0.00 0.00 0.00 3.02
2078 6733 4.395959 TTTCTACCCATAGCCTAACACG 57.604 45.455 0.00 0.00 0.00 4.49
2082 6737 2.469952 ACCCATAGCCTAACACGGTAA 58.530 47.619 0.00 0.00 0.00 2.85
2114 6769 8.992835 AGCTTTCTTCATGAAACAATAATTCC 57.007 30.769 9.88 0.00 39.50 3.01
2251 6934 8.217111 TGGTTGCATCCTGATGAGTATAAATTA 58.783 33.333 14.81 0.00 41.20 1.40
2365 7049 4.577639 CAACGAATAGCTGTACGTACGTA 58.422 43.478 23.60 23.60 38.00 3.57
2445 7162 9.228949 TGATTTTTATTTCCATGTGGATTTTGG 57.771 29.630 1.98 0.00 44.98 3.28
2447 7164 8.845413 TTTTTATTTCCATGTGGATTTTGGAG 57.155 30.769 1.98 0.00 44.98 3.86
2448 7165 6.543430 TTATTTCCATGTGGATTTTGGAGG 57.457 37.500 1.98 0.00 44.98 4.30
2449 7166 3.824001 TTCCATGTGGATTTTGGAGGA 57.176 42.857 1.98 0.00 44.98 3.71
2452 7169 3.011595 TCCATGTGGATTTTGGAGGACAT 59.988 43.478 0.00 0.00 39.78 3.06
2710 7434 2.099756 GCTTGCTTATGCCCCTTTGTAG 59.900 50.000 0.00 0.00 38.71 2.74
2724 7543 6.128090 GCCCCTTTGTAGTTTGTATCTGTTAC 60.128 42.308 0.00 0.00 0.00 2.50
2913 7735 4.522789 CACCAGTATAAGGTTGGTTGCTTT 59.477 41.667 0.00 0.00 42.36 3.51
2935 7757 9.500864 GCTTTATTTCATCTTTTGATCTGTCTC 57.499 33.333 0.00 0.00 36.97 3.36
3176 8003 8.484799 GCATTTCTCATGTATGCAATATTGTTG 58.515 33.333 16.61 5.99 43.13 3.33
3258 8085 4.207165 TCAATTGCTCCCCAAGTATAAGC 58.793 43.478 0.00 0.00 36.76 3.09
3331 8158 3.243201 GCAATAAGATTGTACTGCTGGGC 60.243 47.826 0.00 0.00 0.00 5.36
3346 8173 2.506444 CTGGGCCATTGCAATGTTTTT 58.494 42.857 31.87 0.00 40.13 1.94
3468 8296 8.141909 TCATTATAGCGCTTTGAACTACAGTAT 58.858 33.333 18.68 0.00 0.00 2.12
3608 8506 7.678837 AGTGATTAAAATTCTGCCAATTTCCA 58.321 30.769 4.42 0.38 0.00 3.53
3612 8510 9.333724 GATTAAAATTCTGCCAATTTCCATGAT 57.666 29.630 0.00 0.00 0.00 2.45
3667 8565 2.274645 CCGCCACCTGCAAAATGGA 61.275 57.895 13.41 0.00 41.33 3.41
3729 8631 7.148507 TGTGCTTATGTTGTTTCTTGTTTTTGG 60.149 33.333 0.00 0.00 0.00 3.28
4021 9092 8.503196 TGTTACATAATTGTTTAGCACAGTGAG 58.497 33.333 4.15 0.00 36.48 3.51
4047 9119 7.721286 AGTTCTTCACATTAGAGTCTTTGTG 57.279 36.000 21.39 21.39 40.58 3.33
4048 9120 6.708054 AGTTCTTCACATTAGAGTCTTTGTGG 59.292 38.462 24.48 15.34 39.86 4.17
4049 9121 6.174720 TCTTCACATTAGAGTCTTTGTGGT 57.825 37.500 24.48 6.48 39.86 4.16
4050 9122 6.591935 TCTTCACATTAGAGTCTTTGTGGTT 58.408 36.000 24.48 0.00 39.86 3.67
4051 9123 7.732025 TCTTCACATTAGAGTCTTTGTGGTTA 58.268 34.615 24.48 14.91 39.86 2.85
4052 9124 8.375506 TCTTCACATTAGAGTCTTTGTGGTTAT 58.624 33.333 24.48 0.00 39.86 1.89
4053 9125 8.918202 TTCACATTAGAGTCTTTGTGGTTATT 57.082 30.769 24.48 0.00 39.86 1.40
4079 9151 7.158021 GGTCAAGTAATATTGCTCTCTGCTAT 58.842 38.462 6.52 0.00 43.37 2.97
4087 9159 2.315176 TGCTCTCTGCTATTCTCCCTC 58.685 52.381 0.00 0.00 43.37 4.30
4094 9166 1.133009 TGCTATTCTCCCTCTCCCCTC 60.133 57.143 0.00 0.00 0.00 4.30
4095 9167 1.829666 GCTATTCTCCCTCTCCCCTCC 60.830 61.905 0.00 0.00 0.00 4.30
4096 9168 0.868186 TATTCTCCCTCTCCCCTCCC 59.132 60.000 0.00 0.00 0.00 4.30
4098 9170 4.179599 CTCCCTCTCCCCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
4119 9433 1.262640 ACTTGCCCCTACACCCTACG 61.263 60.000 0.00 0.00 0.00 3.51
4133 10867 4.223477 ACACCCTACGCAGTTTATTCCTTA 59.777 41.667 0.00 0.00 37.78 2.69
4158 10892 7.651808 ACTATTTTGTTCACTTCCATTGACTG 58.348 34.615 0.00 0.00 0.00 3.51
4247 10981 6.654161 GGCTCAGATGCAGAGTTAATTATCAT 59.346 38.462 3.67 0.00 35.55 2.45
4345 11079 9.935682 GAATGTAAATCCATACATGTAAGTGTG 57.064 33.333 10.14 3.42 43.83 3.82
4351 11085 3.623060 CCATACATGTAAGTGTGGCTCAC 59.377 47.826 10.14 11.57 42.58 3.51
4919 11656 3.248266 GGACATAACGCGAAACTACAGT 58.752 45.455 15.93 0.00 0.00 3.55
5454 12810 8.918202 TTGTTCATACAATCCATCCTATAACC 57.082 34.615 0.00 0.00 39.29 2.85
5578 12939 6.859420 ATTTCCCAAAAATAGTTTGTGCAC 57.141 33.333 10.75 10.75 0.00 4.57
5584 13009 5.177327 CCAAAAATAGTTTGTGCACCATGAC 59.823 40.000 15.69 7.58 0.00 3.06
5621 14612 9.953565 ATTTTCACTTCCATGATTCATTCATTT 57.046 25.926 0.00 0.00 42.62 2.32
5652 14651 4.019174 ACCATGAAACCCAAGAATGCTAG 58.981 43.478 0.00 0.00 0.00 3.42
5653 14652 4.019174 CCATGAAACCCAAGAATGCTAGT 58.981 43.478 0.00 0.00 0.00 2.57
5657 14656 6.313519 TGAAACCCAAGAATGCTAGTATCT 57.686 37.500 0.00 0.00 0.00 1.98
5768 14816 2.588146 TTAGGCTCGACGTACAGCGC 62.588 60.000 0.00 0.00 46.11 5.92
5907 14961 2.436646 AAGCAGACGGGGCAATCG 60.437 61.111 0.00 0.00 0.00 3.34
5970 15024 2.126618 GCGTCCGTGTCATCGTCA 60.127 61.111 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.107622 ACGAACGAGGATTACCATTTACG 58.892 43.478 0.14 0.00 38.94 3.18
174 176 0.238289 AGCAAAATGTCCAAGCGTCG 59.762 50.000 0.00 0.00 0.00 5.12
414 1020 1.671850 GCGAAGAATCACCCGAAGACA 60.672 52.381 0.00 0.00 0.00 3.41
420 1026 1.521681 GGAGGCGAAGAATCACCCG 60.522 63.158 0.00 0.00 0.00 5.28
477 1083 1.587043 CTCTCTCGTTCCAGCGGTGA 61.587 60.000 17.83 0.00 0.00 4.02
484 1090 2.897436 CATGATTGCTCTCTCGTTCCA 58.103 47.619 0.00 0.00 0.00 3.53
537 1143 2.504244 GACCTCACCGACGCTTCG 60.504 66.667 5.49 5.49 45.44 3.79
544 1150 1.209504 GGATTGGATTGACCTCACCGA 59.790 52.381 0.00 0.00 39.86 4.69
606 1212 3.989817 CACTCGTGTCATTTGACTGATCA 59.010 43.478 11.67 0.00 44.99 2.92
608 1214 2.738846 GCACTCGTGTCATTTGACTGAT 59.261 45.455 11.67 0.00 44.99 2.90
609 1215 2.135139 GCACTCGTGTCATTTGACTGA 58.865 47.619 11.67 8.60 44.99 3.41
632 1251 5.177696 GTGGCATTTGATCGATTAGGAGTAC 59.822 44.000 0.00 0.00 0.00 2.73
658 1278 9.691362 TTCTGAATTTTGTAGCTATTTTTCACC 57.309 29.630 0.00 0.00 0.00 4.02
690 1314 3.022406 GTGTCCGGTACTAGGAATCACT 58.978 50.000 16.66 0.00 39.84 3.41
692 1316 3.090210 TGTGTCCGGTACTAGGAATCA 57.910 47.619 0.00 10.48 39.84 2.57
703 1327 1.460273 GCCAACCAAATGTGTCCGGT 61.460 55.000 0.00 0.00 0.00 5.28
704 1328 1.288752 GCCAACCAAATGTGTCCGG 59.711 57.895 0.00 0.00 0.00 5.14
713 1337 0.835115 TGCCCATGATGCCAACCAAA 60.835 50.000 0.00 0.00 0.00 3.28
714 1338 0.618107 ATGCCCATGATGCCAACCAA 60.618 50.000 0.00 0.00 0.00 3.67
715 1339 1.001888 ATGCCCATGATGCCAACCA 59.998 52.632 0.00 0.00 0.00 3.67
716 1340 1.444250 CATGCCCATGATGCCAACC 59.556 57.895 2.09 0.00 41.20 3.77
721 1345 0.107606 TTTTGGCATGCCCATGATGC 60.108 50.000 33.44 6.83 44.89 3.91
734 1358 5.927689 TCATCATCACAACTGAAATTTTGGC 59.072 36.000 0.00 0.00 0.00 4.52
761 1408 4.940483 TGGGTCATTTGGGTGAATTGATA 58.060 39.130 0.00 0.00 0.00 2.15
762 1409 3.788933 TGGGTCATTTGGGTGAATTGAT 58.211 40.909 0.00 0.00 0.00 2.57
763 1410 3.251016 TGGGTCATTTGGGTGAATTGA 57.749 42.857 0.00 0.00 0.00 2.57
766 1413 4.596643 TGAATTTGGGTCATTTGGGTGAAT 59.403 37.500 0.00 0.00 0.00 2.57
807 1454 5.461032 AGATGATCCGAACTCTTGGTATC 57.539 43.478 0.00 0.00 0.00 2.24
812 1459 3.118629 TGGGAAGATGATCCGAACTCTTG 60.119 47.826 0.00 0.00 40.62 3.02
947 1615 2.615262 GATCTCCCGAGTGACGTGCC 62.615 65.000 0.00 0.00 40.78 5.01
1361 2091 0.179171 GAGACGCAACGGAGATCGAA 60.179 55.000 0.00 0.00 42.43 3.71
1369 2099 3.411351 CCCAACGAGACGCAACGG 61.411 66.667 0.00 0.00 0.00 4.44
1383 2113 1.228228 GCAAGCATCAGGGATCCCA 59.772 57.895 32.69 13.87 38.92 4.37
1427 2160 1.252904 ACAGGTAGGGCGCGTTCTAA 61.253 55.000 8.43 0.00 0.00 2.10
1531 2264 8.861101 CCAAACAAACAAACGTTAAAACAGATA 58.139 29.630 0.00 0.00 0.00 1.98
1558 2292 3.357203 TGAACAGTAACACCAAGCCAAA 58.643 40.909 0.00 0.00 0.00 3.28
1717 2493 6.823689 AGATACATGAAGATACCGCAAAAAGT 59.176 34.615 0.00 0.00 0.00 2.66
1718 2494 7.251704 AGATACATGAAGATACCGCAAAAAG 57.748 36.000 0.00 0.00 0.00 2.27
1762 2540 8.864087 TGCAGTAGTATCAAGATACATGAAGAT 58.136 33.333 19.23 3.01 44.58 2.40
1763 2541 8.237811 TGCAGTAGTATCAAGATACATGAAGA 57.762 34.615 19.23 0.64 44.58 2.87
1764 2542 8.877808 TTGCAGTAGTATCAAGATACATGAAG 57.122 34.615 19.23 8.42 44.58 3.02
1765 2543 9.317936 CTTTGCAGTAGTATCAAGATACATGAA 57.682 33.333 19.23 8.98 44.58 2.57
1766 2544 7.439356 GCTTTGCAGTAGTATCAAGATACATGA 59.561 37.037 19.23 4.73 44.58 3.07
1770 2548 5.175856 CGGCTTTGCAGTAGTATCAAGATAC 59.824 44.000 11.36 11.36 42.96 2.24
1908 2918 4.755123 CCAGACACGTTTTATTTCTCCAGT 59.245 41.667 0.00 0.00 0.00 4.00
1927 2937 3.520721 TCCTCATCTCAAATTCAGCCAGA 59.479 43.478 0.00 0.00 0.00 3.86
2062 6717 2.163810 TACCGTGTTAGGCTATGGGT 57.836 50.000 0.00 3.49 33.69 4.51
2078 6733 4.893424 TGAAGAAAGCTTGTGTGTTACC 57.107 40.909 0.00 0.00 33.61 2.85
2082 6737 5.105797 TGTTTCATGAAGAAAGCTTGTGTGT 60.106 36.000 8.41 0.00 46.34 3.72
2114 6769 0.401738 TCCCCAAGAGGAAGCAACAG 59.598 55.000 0.00 0.00 38.24 3.16
2365 7049 9.874205 CAACAAATTGATAAATGTGAATAGGGT 57.126 29.630 0.00 0.00 38.15 4.34
2482 7206 7.648142 GCAAGCTGCCATTTATACTACATAAA 58.352 34.615 0.00 0.00 37.42 1.40
2724 7543 1.524621 CCGCCAGGAGCTAACATGG 60.525 63.158 1.88 1.88 43.43 3.66
2913 7735 8.045507 AGCTGAGACAGATCAAAAGATGAAATA 58.954 33.333 2.81 0.00 35.17 1.40
3055 7877 6.170506 TGTTCAAGTTAATACGCTCCAAGAT 58.829 36.000 0.00 0.00 0.00 2.40
3258 8085 6.461110 AATAATCTGAATTGGACAAGCAGG 57.539 37.500 13.96 0.00 31.59 4.85
3468 8296 5.017294 TGAATAACACATATGACAGCGGA 57.983 39.130 10.38 0.00 0.00 5.54
3729 8631 6.843069 AGGAAAAACAACATATGCAACAAC 57.157 33.333 1.58 0.00 0.00 3.32
3827 8734 2.544277 CGCTGGTGCATATTTTGGGATG 60.544 50.000 0.00 0.00 39.64 3.51
3914 8821 6.636454 AAGACTTACCCCAATCTATCAACA 57.364 37.500 0.00 0.00 0.00 3.33
3960 8867 4.785346 ATGAACAGAATAGAGCCATGGT 57.215 40.909 14.67 0.00 0.00 3.55
4021 9092 8.704234 CACAAAGACTCTAATGTGAAGAACTAC 58.296 37.037 15.25 0.00 44.52 2.73
4047 9119 8.451908 AGAGCAATATTACTTGACCAATAACC 57.548 34.615 0.00 0.00 0.00 2.85
4048 9120 9.331282 AGAGAGCAATATTACTTGACCAATAAC 57.669 33.333 0.00 0.00 0.00 1.89
4049 9121 9.330063 CAGAGAGCAATATTACTTGACCAATAA 57.670 33.333 0.00 0.00 0.00 1.40
4050 9122 7.442364 GCAGAGAGCAATATTACTTGACCAATA 59.558 37.037 0.00 0.00 44.79 1.90
4051 9123 6.261826 GCAGAGAGCAATATTACTTGACCAAT 59.738 38.462 0.00 0.00 44.79 3.16
4052 9124 5.586243 GCAGAGAGCAATATTACTTGACCAA 59.414 40.000 0.00 0.00 44.79 3.67
4053 9125 5.118990 GCAGAGAGCAATATTACTTGACCA 58.881 41.667 0.00 0.00 44.79 4.02
4079 9151 2.647949 GGGGAGGGGAGAGGGAGAA 61.648 68.421 0.00 0.00 0.00 2.87
4095 9167 2.938798 TGTAGGGGCAAGTGGGGG 60.939 66.667 0.00 0.00 0.00 5.40
4096 9168 2.355115 GTGTAGGGGCAAGTGGGG 59.645 66.667 0.00 0.00 0.00 4.96
4098 9170 0.912487 TAGGGTGTAGGGGCAAGTGG 60.912 60.000 0.00 0.00 0.00 4.00
4099 9171 0.252197 GTAGGGTGTAGGGGCAAGTG 59.748 60.000 0.00 0.00 0.00 3.16
4100 9172 1.262640 CGTAGGGTGTAGGGGCAAGT 61.263 60.000 0.00 0.00 0.00 3.16
4105 9177 1.262640 AACTGCGTAGGGTGTAGGGG 61.263 60.000 5.26 0.00 0.00 4.79
4133 10867 7.502226 TCAGTCAATGGAAGTGAACAAAATAGT 59.498 33.333 0.00 0.00 45.34 2.12
4158 10892 8.942338 TGAGTTTACATTACACTATGGTCATC 57.058 34.615 0.00 0.00 0.00 2.92
4247 10981 3.181438 TGCCAGGTAGAAACTTTAAGGCA 60.181 43.478 0.00 0.00 46.31 4.75
4345 11079 3.440228 GTTACTCTGAAGATCGTGAGCC 58.560 50.000 0.00 0.00 0.00 4.70
4351 11085 2.482142 GGGCAGGTTACTCTGAAGATCG 60.482 54.545 5.30 0.00 36.93 3.69
4919 11656 9.950680 GTAATTGTCTCAGTTTCATTTCTGAAA 57.049 29.630 5.15 5.15 46.53 2.69
4928 11665 7.252612 TCCATAGGTAATTGTCTCAGTTTCA 57.747 36.000 0.00 0.00 0.00 2.69
4999 11736 4.322198 CCTGCAAGCAACAAAGATAATGGT 60.322 41.667 0.00 0.00 0.00 3.55
5578 12939 6.757947 AGTGAAAATTGTTTGTTCAGTCATGG 59.242 34.615 0.00 0.00 30.82 3.66
5584 13009 7.492020 TCATGGAAGTGAAAATTGTTTGTTCAG 59.508 33.333 0.00 0.00 32.15 3.02
5621 14612 4.649267 TGGGTTTCATGGTCAGTTCATA 57.351 40.909 0.00 0.00 0.00 2.15
5657 14656 9.467258 CTTCAGAAATTATTTGTTCTGCTGAAA 57.533 29.630 7.68 0.00 46.79 2.69
5768 14816 4.256090 GCCCTATTTGCAGGCGCG 62.256 66.667 0.00 0.00 42.97 6.86
5970 15024 4.208686 GACGAAGCCGCCCTCGAT 62.209 66.667 16.92 4.09 39.95 3.59
5975 15029 0.461339 TGATAAAGACGAAGCCGCCC 60.461 55.000 0.00 0.00 39.95 6.13


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

AutoCloner maintained by Alex Coulton.