Multiple sequence alignment - TraesCS7B01G028000

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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 TraesCS7B01G028000 chr7B 100.000 2465 0 0 1 2465 26690441 26692905 0.000000e+00 4553.0
1 TraesCS7B01G028000 chr7B 82.828 99 15 1 2351 2449 1487010 1486914 1.210000e-13 87.9
2 TraesCS7B01G028000 chr7D 89.342 1595 64 49 324 1885 79521622 79523143 0.000000e+00 1906.0
3 TraesCS7B01G028000 chr7D 90.631 555 39 9 1916 2462 79523141 79523690 0.000000e+00 725.0
4 TraesCS7B01G028000 chr7D 94.052 269 7 4 1 265 79521183 79521446 1.370000e-107 399.0
5 TraesCS7B01G028000 chr7A 86.097 1194 70 51 714 1882 82176179 82177301 0.000000e+00 1197.0
6 TraesCS7B01G028000 chr7A 90.157 508 42 5 1958 2462 82177499 82178001 0.000000e+00 654.0
7 TraesCS7B01G028000 chr7A 90.263 380 19 6 328 705 82175831 82176194 4.770000e-132 481.0
8 TraesCS7B01G028000 chr7A 86.290 248 22 9 1 248 82175596 82175831 2.430000e-65 259.0
9 TraesCS7B01G028000 chr7A 97.674 43 1 0 1917 1959 82177300 82177342 9.450000e-10 75.0
10 TraesCS7B01G028000 chr2B 84.058 207 26 5 2258 2462 404204165 404204366 2.500000e-45 193.0
11 TraesCS7B01G028000 chr2B 91.964 112 9 0 1973 2084 545923281 545923170 9.130000e-35 158.0
12 TraesCS7B01G028000 chr2D 81.068 206 35 2 2259 2462 398064910 398065113 7.050000e-36 161.0
13 TraesCS7B01G028000 chr1A 85.350 157 21 2 2295 2449 328822845 328823001 7.050000e-36 161.0
14 TraesCS7B01G028000 chr1A 91.071 112 10 0 1973 2084 565237070 565236959 4.250000e-33 152.0
15 TraesCS7B01G028000 chr5B 91.964 112 9 0 1973 2084 557738356 557738245 9.130000e-35 158.0
16 TraesCS7B01G028000 chr5B 91.892 111 9 0 1973 2083 272997612 272997722 3.280000e-34 156.0
17 TraesCS7B01G028000 chr3B 91.964 112 9 0 1973 2084 89816652 89816541 9.130000e-35 158.0
18 TraesCS7B01G028000 chr3B 91.964 112 9 0 1973 2084 220472503 220472614 9.130000e-35 158.0
19 TraesCS7B01G028000 chr6A 91.071 112 10 0 1973 2084 596281219 596281108 4.250000e-33 152.0
20 TraesCS7B01G028000 chr1D 84.076 157 23 2 2295 2449 256110029 256110185 1.530000e-32 150.0
21 TraesCS7B01G028000 chr5D 92.857 56 3 1 2389 2444 61837169 61837115 2.030000e-11 80.5
22 TraesCS7B01G028000 chr5D 80.000 110 18 2 2351 2460 561570368 561570473 7.310000e-11 78.7


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 TraesCS7B01G028000 chr7B 26690441 26692905 2464 False 4553.0 4553 100.000000 1 2465 1 chr7B.!!$F1 2464
1 TraesCS7B01G028000 chr7D 79521183 79523690 2507 False 1010.0 1906 91.341667 1 2462 3 chr7D.!!$F1 2461
2 TraesCS7B01G028000 chr7A 82175596 82178001 2405 False 533.2 1197 90.096200 1 2462 5 chr7A.!!$F1 2461

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
455 584 0.464735 AGTGGCACTGCGGTTTGTTA 60.465 50.0 21.37 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1703 0.179045 AATACCAAGCTAGGGCGCAG 60.179 55.0 10.83 0.0 44.37 5.18 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
67 68 3.122948 GCTTTGAAGCGAGTCGTTTGATA 59.877 43.478 19.72 5.49 42.88 2.15
209 214 1.939974 CCCACACGTCAGGATACATG 58.060 55.000 4.39 0.00 41.41 3.21
220 225 1.068281 AGGATACATGCACGCAGAGAG 59.932 52.381 0.00 0.00 41.41 3.20
248 253 4.217983 AGAGAGGCAATGAAAGCAAGAAAG 59.782 41.667 0.00 0.00 0.00 2.62
250 255 4.771054 AGAGGCAATGAAAGCAAGAAAGAT 59.229 37.500 0.00 0.00 0.00 2.40
260 265 6.150641 TGAAAGCAAGAAAGATTCATGGAGAG 59.849 38.462 0.00 0.00 0.00 3.20
265 270 6.629963 GCAAGAAAGATTCATGGAGAGAGAGA 60.630 42.308 0.00 0.00 0.00 3.10
266 271 6.720112 AGAAAGATTCATGGAGAGAGAGAG 57.280 41.667 0.00 0.00 0.00 3.20
267 272 6.434302 AGAAAGATTCATGGAGAGAGAGAGA 58.566 40.000 0.00 0.00 0.00 3.10
268 273 6.548622 AGAAAGATTCATGGAGAGAGAGAGAG 59.451 42.308 0.00 0.00 0.00 3.20
269 274 5.651612 AGATTCATGGAGAGAGAGAGAGA 57.348 43.478 0.00 0.00 0.00 3.10
270 275 5.628130 AGATTCATGGAGAGAGAGAGAGAG 58.372 45.833 0.00 0.00 0.00 3.20
272 277 4.422073 TCATGGAGAGAGAGAGAGAGAC 57.578 50.000 0.00 0.00 0.00 3.36
273 278 3.779738 TCATGGAGAGAGAGAGAGAGACA 59.220 47.826 0.00 0.00 0.00 3.41
275 280 2.909662 TGGAGAGAGAGAGAGAGACACA 59.090 50.000 0.00 0.00 0.00 3.72
276 281 3.270877 GGAGAGAGAGAGAGAGACACAC 58.729 54.545 0.00 0.00 0.00 3.82
277 282 3.307410 GGAGAGAGAGAGAGAGACACACA 60.307 52.174 0.00 0.00 0.00 3.72
280 285 3.146066 AGAGAGAGAGAGACACACACAC 58.854 50.000 0.00 0.00 0.00 3.82
282 287 2.621055 AGAGAGAGAGACACACACACAC 59.379 50.000 0.00 0.00 0.00 3.82
283 288 2.359214 GAGAGAGAGACACACACACACA 59.641 50.000 0.00 0.00 0.00 3.72
284 289 2.760650 AGAGAGAGACACACACACACAA 59.239 45.455 0.00 0.00 0.00 3.33
285 290 3.195610 AGAGAGAGACACACACACACAAA 59.804 43.478 0.00 0.00 0.00 2.83
286 291 3.262420 AGAGAGACACACACACACAAAC 58.738 45.455 0.00 0.00 0.00 2.93
287 292 3.000041 GAGAGACACACACACACAAACA 59.000 45.455 0.00 0.00 0.00 2.83
289 294 2.482336 GAGACACACACACACAAACACA 59.518 45.455 0.00 0.00 0.00 3.72
290 295 2.225491 AGACACACACACACAAACACAC 59.775 45.455 0.00 0.00 0.00 3.82
291 296 1.950216 ACACACACACACAAACACACA 59.050 42.857 0.00 0.00 0.00 3.72
292 297 2.031245 ACACACACACACAAACACACAG 60.031 45.455 0.00 0.00 0.00 3.66
293 298 2.225255 CACACACACACAAACACACAGA 59.775 45.455 0.00 0.00 0.00 3.41
295 300 2.741517 CACACACACAAACACACAGAGA 59.258 45.455 0.00 0.00 0.00 3.10
296 301 3.002791 ACACACACAAACACACAGAGAG 58.997 45.455 0.00 0.00 0.00 3.20
297 302 3.261580 CACACACAAACACACAGAGAGA 58.738 45.455 0.00 0.00 0.00 3.10
300 305 3.801050 CACACAAACACACAGAGAGAGAG 59.199 47.826 0.00 0.00 0.00 3.20
301 306 3.701542 ACACAAACACACAGAGAGAGAGA 59.298 43.478 0.00 0.00 0.00 3.10
302 307 4.202101 ACACAAACACACAGAGAGAGAGAG 60.202 45.833 0.00 0.00 0.00 3.20
304 309 4.278170 ACAAACACACAGAGAGAGAGAGAG 59.722 45.833 0.00 0.00 0.00 3.20
305 310 3.071874 ACACACAGAGAGAGAGAGAGG 57.928 52.381 0.00 0.00 0.00 3.69
306 311 2.375174 ACACACAGAGAGAGAGAGAGGT 59.625 50.000 0.00 0.00 0.00 3.85
307 312 2.749076 CACACAGAGAGAGAGAGAGGTG 59.251 54.545 0.00 0.00 0.00 4.00
308 313 2.642311 ACACAGAGAGAGAGAGAGGTGA 59.358 50.000 0.00 0.00 0.00 4.02
309 314 3.073798 ACACAGAGAGAGAGAGAGGTGAA 59.926 47.826 0.00 0.00 0.00 3.18
310 315 4.078537 CACAGAGAGAGAGAGAGGTGAAA 58.921 47.826 0.00 0.00 0.00 2.69
312 317 4.078537 CAGAGAGAGAGAGAGGTGAAACA 58.921 47.826 0.00 0.00 39.98 2.83
315 320 5.779771 AGAGAGAGAGAGAGGTGAAACAAAT 59.220 40.000 0.00 0.00 39.98 2.32
316 321 6.036577 AGAGAGAGAGAGGTGAAACAAATC 57.963 41.667 0.00 0.00 39.98 2.17
317 322 5.046663 AGAGAGAGAGAGGTGAAACAAATCC 60.047 44.000 0.00 0.00 39.98 3.01
318 323 4.019771 AGAGAGAGAGGTGAAACAAATCCC 60.020 45.833 0.00 0.00 39.98 3.85
320 325 4.352298 AGAGAGAGGTGAAACAAATCCCTT 59.648 41.667 0.00 0.00 39.98 3.95
321 326 4.401925 AGAGAGGTGAAACAAATCCCTTG 58.598 43.478 0.00 0.00 39.98 3.61
322 327 2.893489 AGAGGTGAAACAAATCCCTTGC 59.107 45.455 0.00 0.00 39.98 4.01
325 330 4.415596 AGGTGAAACAAATCCCTTGCATA 58.584 39.130 0.00 0.00 39.98 3.14
326 331 5.025453 AGGTGAAACAAATCCCTTGCATAT 58.975 37.500 0.00 0.00 39.98 1.78
353 476 3.719924 TGCAGTCAAAATTTCAAGCTGG 58.280 40.909 0.00 0.00 0.00 4.85
355 478 3.062042 CAGTCAAAATTTCAAGCTGGCC 58.938 45.455 0.00 0.00 0.00 5.36
356 479 2.967887 AGTCAAAATTTCAAGCTGGCCT 59.032 40.909 3.32 0.00 0.00 5.19
357 480 4.022068 CAGTCAAAATTTCAAGCTGGCCTA 60.022 41.667 3.32 0.00 0.00 3.93
358 481 4.774200 AGTCAAAATTTCAAGCTGGCCTAT 59.226 37.500 3.32 0.00 0.00 2.57
384 509 1.210155 GATTGCACGTGGTCAAGCC 59.790 57.895 18.88 6.52 37.90 4.35
385 510 2.513065 GATTGCACGTGGTCAAGCCG 62.513 60.000 18.88 0.00 41.21 5.52
455 584 0.464735 AGTGGCACTGCGGTTTGTTA 60.465 50.000 21.37 0.00 0.00 2.41
471 600 6.625081 CGGTTTGTTATCCAGGGAAAGATTTC 60.625 42.308 0.00 0.00 36.46 2.17
512 641 0.603975 GGAGATGGCATTACCGAGGC 60.604 60.000 0.00 0.00 43.94 4.70
522 651 0.609151 TTACCGAGGCGTCCATTTCA 59.391 50.000 0.00 0.00 0.00 2.69
595 724 3.059306 CACAAAACAGTGAAACGCAACTG 59.941 43.478 0.00 1.41 45.86 3.16
609 738 1.301401 AACTGGTACATGCGTGCGT 60.301 52.632 5.64 0.00 38.20 5.24
610 739 1.565156 AACTGGTACATGCGTGCGTG 61.565 55.000 12.31 12.31 38.20 5.34
611 740 3.367051 CTGGTACATGCGTGCGTGC 62.367 63.158 13.71 0.00 38.20 5.34
634 763 1.740380 GCGTGCATGATCTACAGTGGT 60.740 52.381 10.93 0.00 0.00 4.16
662 791 2.363795 CCCGGCCAGGACTCTGTA 60.364 66.667 14.30 0.00 45.00 2.74
688 819 1.453379 ATCTCCTGTGCATGCTGCC 60.453 57.895 20.33 7.42 44.23 4.85
702 833 1.027357 GCTGCCAGAGAGAGAGAGAG 58.973 60.000 0.00 0.00 0.00 3.20
703 834 1.408683 GCTGCCAGAGAGAGAGAGAGA 60.409 57.143 0.00 0.00 0.00 3.10
704 835 2.569059 CTGCCAGAGAGAGAGAGAGAG 58.431 57.143 0.00 0.00 0.00 3.20
705 836 2.171237 CTGCCAGAGAGAGAGAGAGAGA 59.829 54.545 0.00 0.00 0.00 3.10
706 837 2.171237 TGCCAGAGAGAGAGAGAGAGAG 59.829 54.545 0.00 0.00 0.00 3.20
707 838 2.435805 GCCAGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
817 955 6.068010 AGAGAGAGAGAGAGAGAGAGACTAG 58.932 48.000 0.00 0.00 0.00 2.57
818 956 4.586841 AGAGAGAGAGAGAGAGAGACTAGC 59.413 50.000 0.00 0.00 0.00 3.42
819 957 4.551671 AGAGAGAGAGAGAGAGACTAGCT 58.448 47.826 0.00 0.00 0.00 3.32
820 958 5.706447 AGAGAGAGAGAGAGAGACTAGCTA 58.294 45.833 0.00 0.00 0.00 3.32
887 1029 1.098050 GGCCATCAAGCTTACCTGTG 58.902 55.000 0.00 0.00 0.00 3.66
888 1030 1.614317 GGCCATCAAGCTTACCTGTGT 60.614 52.381 0.00 0.00 0.00 3.72
922 1070 1.086696 CAAATACCCAGTGCACTCCG 58.913 55.000 18.64 12.33 0.00 4.63
931 1082 4.254709 TGCACTCCGCTTGCCACT 62.255 61.111 0.00 0.00 43.06 4.00
948 1099 1.140452 CACTCATACATCCAGCCAGCT 59.860 52.381 0.00 0.00 0.00 4.24
950 1101 0.761187 TCATACATCCAGCCAGCTCC 59.239 55.000 0.00 0.00 0.00 4.70
1197 1355 2.041928 CCCCCTCCTCCTCAGCTT 59.958 66.667 0.00 0.00 0.00 3.74
1198 1356 2.373707 CCCCCTCCTCCTCAGCTTG 61.374 68.421 0.00 0.00 0.00 4.01
1199 1357 2.588989 CCCTCCTCCTCAGCTTGC 59.411 66.667 0.00 0.00 0.00 4.01
1200 1358 1.994507 CCCTCCTCCTCAGCTTGCT 60.995 63.158 0.00 0.00 0.00 3.91
1201 1359 1.221293 CCTCCTCCTCAGCTTGCTG 59.779 63.158 15.74 15.74 0.00 4.41
1202 1360 1.449956 CTCCTCCTCAGCTTGCTGC 60.450 63.158 16.91 0.00 43.29 5.25
1296 1457 2.178984 CCTCAACTATCCTCCTCCTCCT 59.821 54.545 0.00 0.00 0.00 3.69
1299 1460 2.178984 CAACTATCCTCCTCCTCCTCCT 59.821 54.545 0.00 0.00 0.00 3.69
1300 1461 2.070573 ACTATCCTCCTCCTCCTCCTC 58.929 57.143 0.00 0.00 0.00 3.71
1302 1463 0.631998 ATCCTCCTCCTCCTCCTCCA 60.632 60.000 0.00 0.00 0.00 3.86
1303 1464 1.075600 CCTCCTCCTCCTCCTCCAC 60.076 68.421 0.00 0.00 0.00 4.02
1304 1465 1.589399 CCTCCTCCTCCTCCTCCACT 61.589 65.000 0.00 0.00 0.00 4.00
1395 1556 4.432741 GAGCTGGGGTTGGAGGCC 62.433 72.222 0.00 0.00 0.00 5.19
1428 1589 1.909302 TCCACCAAGGAGGAAGATGAC 59.091 52.381 2.55 0.00 43.07 3.06
1467 1628 1.886777 GCTCGGCTGCTCTTGATCC 60.887 63.158 0.00 0.00 0.00 3.36
1479 1640 3.864583 GCTCTTGATCCATCGAGCATATC 59.135 47.826 14.10 0.00 46.06 1.63
1495 1665 3.612955 GCATATCGTTCTCCAGTCTAGCC 60.613 52.174 0.00 0.00 0.00 3.93
1502 1677 4.443621 GTTCTCCAGTCTAGCCAATTACC 58.556 47.826 0.00 0.00 0.00 2.85
1528 1703 6.658391 TCACTAGGTTGGTTCTCTAGTTAGTC 59.342 42.308 0.00 0.00 40.95 2.59
1529 1704 6.660094 CACTAGGTTGGTTCTCTAGTTAGTCT 59.340 42.308 0.00 0.00 40.95 3.24
1530 1705 5.986501 AGGTTGGTTCTCTAGTTAGTCTG 57.013 43.478 0.00 0.00 0.00 3.51
1531 1706 4.221041 AGGTTGGTTCTCTAGTTAGTCTGC 59.779 45.833 0.00 0.00 0.00 4.26
1532 1707 4.167268 GTTGGTTCTCTAGTTAGTCTGCG 58.833 47.826 0.00 0.00 0.00 5.18
1533 1708 2.163815 TGGTTCTCTAGTTAGTCTGCGC 59.836 50.000 0.00 0.00 0.00 6.09
1534 1709 2.479901 GGTTCTCTAGTTAGTCTGCGCC 60.480 54.545 4.18 0.00 0.00 6.53
1535 1710 1.390565 TCTCTAGTTAGTCTGCGCCC 58.609 55.000 4.18 0.00 0.00 6.13
1536 1711 1.064611 TCTCTAGTTAGTCTGCGCCCT 60.065 52.381 4.18 0.00 0.00 5.19
1537 1712 2.172082 TCTCTAGTTAGTCTGCGCCCTA 59.828 50.000 4.18 0.00 0.00 3.53
1538 1713 2.550606 CTCTAGTTAGTCTGCGCCCTAG 59.449 54.545 4.18 0.00 0.00 3.02
1539 1714 1.001158 CTAGTTAGTCTGCGCCCTAGC 60.001 57.143 4.18 4.77 37.71 3.42
1540 1715 0.684805 AGTTAGTCTGCGCCCTAGCT 60.685 55.000 4.18 7.16 38.13 3.32
1541 1716 0.175989 GTTAGTCTGCGCCCTAGCTT 59.824 55.000 4.18 0.00 38.13 3.74
1542 1717 0.175760 TTAGTCTGCGCCCTAGCTTG 59.824 55.000 4.18 0.00 38.13 4.01
1543 1718 1.676678 TAGTCTGCGCCCTAGCTTGG 61.677 60.000 4.18 7.29 38.13 3.61
1544 1719 3.003173 TCTGCGCCCTAGCTTGGT 61.003 61.111 13.38 0.00 38.13 3.67
1545 1720 1.684391 TCTGCGCCCTAGCTTGGTA 60.684 57.895 13.38 0.00 38.13 3.25
1546 1721 1.048724 TCTGCGCCCTAGCTTGGTAT 61.049 55.000 13.38 0.00 38.13 2.73
1547 1722 0.179045 CTGCGCCCTAGCTTGGTATT 60.179 55.000 13.38 0.00 38.13 1.89
1548 1723 1.070134 CTGCGCCCTAGCTTGGTATTA 59.930 52.381 13.38 0.00 38.13 0.98
1549 1724 1.487142 TGCGCCCTAGCTTGGTATTAA 59.513 47.619 13.38 0.00 38.13 1.40
1550 1725 2.143925 GCGCCCTAGCTTGGTATTAAG 58.856 52.381 13.38 0.00 36.60 1.85
1551 1726 2.767505 CGCCCTAGCTTGGTATTAAGG 58.232 52.381 13.38 0.50 36.60 2.69
1692 1867 7.324935 TGTATATGGTCGTGTTCACTGTTTAT 58.675 34.615 1.53 0.00 0.00 1.40
1693 1868 6.662414 ATATGGTCGTGTTCACTGTTTATG 57.338 37.500 1.53 0.00 0.00 1.90
1697 1876 4.394795 GTCGTGTTCACTGTTTATGATGC 58.605 43.478 1.53 0.00 0.00 3.91
1788 1967 8.308931 TCTCACGTGGTGTAAATACTAGAAAAT 58.691 33.333 17.00 0.00 34.79 1.82
1789 1968 9.577110 CTCACGTGGTGTAAATACTAGAAAATA 57.423 33.333 17.00 0.00 34.79 1.40
1827 2007 4.530946 TGTTTGGTTTGGACCTTTGGTTAA 59.469 37.500 0.00 0.00 46.66 2.01
1881 2061 8.701895 GGGATCGGGAAACTATATTATGACATA 58.298 37.037 0.00 0.00 0.00 2.29
1882 2062 9.530633 GGATCGGGAAACTATATTATGACATAC 57.469 37.037 0.00 0.00 0.00 2.39
2028 2366 3.622206 CGAAATGGTGAGGGAGGAAATCA 60.622 47.826 0.00 0.00 0.00 2.57
2030 2368 0.620556 TGGTGAGGGAGGAAATCAGC 59.379 55.000 0.00 0.00 40.85 4.26
2054 2392 6.282930 CCTGACAAATGTTGAAGAAAATGGT 58.717 36.000 0.00 0.00 0.00 3.55
2091 2435 2.093216 GTGCTCACCACATAGCTGC 58.907 57.895 0.00 0.00 44.06 5.25
2092 2436 0.674581 GTGCTCACCACATAGCTGCA 60.675 55.000 1.02 0.00 44.06 4.41
2096 2440 2.635714 CTCACCACATAGCTGCATTGA 58.364 47.619 1.02 0.00 0.00 2.57
2171 2516 3.211045 GGTAGAGCAAAGGTTGAACACA 58.789 45.455 0.00 0.00 0.00 3.72
2206 2551 8.044060 TCTTAGATGAATGATTTGTTGGACAC 57.956 34.615 0.00 0.00 0.00 3.67
2220 2565 3.186702 TGGACACGTCAGATTTGAACA 57.813 42.857 0.00 0.00 34.49 3.18
2225 2570 3.069586 ACACGTCAGATTTGAACAGGAGA 59.930 43.478 0.00 0.00 34.49 3.71
2240 2585 1.377536 GGAGAAGTTCCATGCTCTGC 58.622 55.000 0.00 0.00 46.01 4.26
2241 2586 1.065564 GGAGAAGTTCCATGCTCTGCT 60.066 52.381 0.00 0.00 46.01 4.24
2264 2612 8.803235 TGCTAAAGAGTGAATGTTAAGAGAGTA 58.197 33.333 0.00 0.00 0.00 2.59
2265 2613 9.078753 GCTAAAGAGTGAATGTTAAGAGAGTAC 57.921 37.037 0.00 0.00 0.00 2.73
2378 2726 0.257039 ATGCTCCACCCATCCAACTC 59.743 55.000 0.00 0.00 0.00 3.01
2381 2729 1.926426 CTCCACCCATCCAACTCCCC 61.926 65.000 0.00 0.00 0.00 4.81
2462 2810 7.042389 TCCAATTTTTGTTCCTTTTGCGTATTC 60.042 33.333 0.00 0.00 0.00 1.75
2463 2811 7.254590 CCAATTTTTGTTCCTTTTGCGTATTCA 60.255 33.333 0.00 0.00 0.00 2.57
2464 2812 7.961325 ATTTTTGTTCCTTTTGCGTATTCAT 57.039 28.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 4.263243 GCCTCATTCTCCCATGCTATACTT 60.263 45.833 0.00 0.00 0.00 2.24
191 196 1.290203 GCATGTATCCTGACGTGTGG 58.710 55.000 0.00 0.00 38.40 4.17
209 214 3.371168 CTCTCTTAATCTCTCTGCGTGC 58.629 50.000 0.00 0.00 0.00 5.34
220 225 5.824904 TGCTTTCATTGCCTCTCTTAATC 57.175 39.130 0.00 0.00 0.00 1.75
248 253 5.471456 GTCTCTCTCTCTCTCTCCATGAATC 59.529 48.000 0.00 0.00 0.00 2.52
250 255 4.227073 TGTCTCTCTCTCTCTCTCCATGAA 59.773 45.833 0.00 0.00 0.00 2.57
260 265 2.881513 TGTGTGTGTGTCTCTCTCTCTC 59.118 50.000 0.00 0.00 0.00 3.20
265 270 3.262420 GTTTGTGTGTGTGTGTCTCTCT 58.738 45.455 0.00 0.00 0.00 3.10
266 271 3.000041 TGTTTGTGTGTGTGTGTCTCTC 59.000 45.455 0.00 0.00 0.00 3.20
267 272 2.742053 GTGTTTGTGTGTGTGTGTCTCT 59.258 45.455 0.00 0.00 0.00 3.10
268 273 2.482336 TGTGTTTGTGTGTGTGTGTCTC 59.518 45.455 0.00 0.00 0.00 3.36
269 274 2.225491 GTGTGTTTGTGTGTGTGTGTCT 59.775 45.455 0.00 0.00 0.00 3.41
270 275 2.031595 TGTGTGTTTGTGTGTGTGTGTC 60.032 45.455 0.00 0.00 0.00 3.67
272 277 2.225255 TCTGTGTGTTTGTGTGTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
273 278 2.483877 CTCTGTGTGTTTGTGTGTGTGT 59.516 45.455 0.00 0.00 0.00 3.72
275 280 3.002791 CTCTCTGTGTGTTTGTGTGTGT 58.997 45.455 0.00 0.00 0.00 3.72
276 281 3.261580 TCTCTCTGTGTGTTTGTGTGTG 58.738 45.455 0.00 0.00 0.00 3.82
277 282 3.195610 TCTCTCTCTGTGTGTTTGTGTGT 59.804 43.478 0.00 0.00 0.00 3.72
280 285 4.037327 TCTCTCTCTCTCTGTGTGTTTGTG 59.963 45.833 0.00 0.00 0.00 3.33
282 287 4.321156 CCTCTCTCTCTCTCTGTGTGTTTG 60.321 50.000 0.00 0.00 0.00 2.93
283 288 3.826157 CCTCTCTCTCTCTCTGTGTGTTT 59.174 47.826 0.00 0.00 0.00 2.83
284 289 3.181434 ACCTCTCTCTCTCTCTGTGTGTT 60.181 47.826 0.00 0.00 0.00 3.32
285 290 2.375174 ACCTCTCTCTCTCTCTGTGTGT 59.625 50.000 0.00 0.00 0.00 3.72
286 291 2.749076 CACCTCTCTCTCTCTCTGTGTG 59.251 54.545 0.00 0.00 0.00 3.82
287 292 2.642311 TCACCTCTCTCTCTCTCTGTGT 59.358 50.000 0.00 0.00 0.00 3.72
289 294 4.079253 GTTTCACCTCTCTCTCTCTCTGT 58.921 47.826 0.00 0.00 0.00 3.41
290 295 4.078537 TGTTTCACCTCTCTCTCTCTCTG 58.921 47.826 0.00 0.00 0.00 3.35
291 296 4.380843 TGTTTCACCTCTCTCTCTCTCT 57.619 45.455 0.00 0.00 0.00 3.10
292 297 5.461032 TTTGTTTCACCTCTCTCTCTCTC 57.539 43.478 0.00 0.00 0.00 3.20
293 298 5.046663 GGATTTGTTTCACCTCTCTCTCTCT 60.047 44.000 0.00 0.00 0.00 3.10
295 300 4.019771 GGGATTTGTTTCACCTCTCTCTCT 60.020 45.833 0.00 0.00 0.00 3.10
296 301 4.019771 AGGGATTTGTTTCACCTCTCTCTC 60.020 45.833 0.00 0.00 0.00 3.20
297 302 3.913163 AGGGATTTGTTTCACCTCTCTCT 59.087 43.478 0.00 0.00 0.00 3.10
300 305 3.057245 GCAAGGGATTTGTTTCACCTCTC 60.057 47.826 0.00 0.00 39.08 3.20
301 306 2.893489 GCAAGGGATTTGTTTCACCTCT 59.107 45.455 0.00 0.00 39.08 3.69
302 307 2.627699 TGCAAGGGATTTGTTTCACCTC 59.372 45.455 0.00 0.00 39.08 3.85
304 309 3.683365 ATGCAAGGGATTTGTTTCACC 57.317 42.857 0.00 0.00 39.08 4.02
326 331 9.955208 CAGCTTGAAATTTTGACTGCATATATA 57.045 29.630 0.00 0.00 0.00 0.86
342 465 2.091994 AGCTCATAGGCCAGCTTGAAAT 60.092 45.455 9.45 0.00 43.80 2.17
345 468 2.612760 AGCTCATAGGCCAGCTTGA 58.387 52.632 9.45 3.45 43.80 3.02
349 472 0.110104 ATCCAAGCTCATAGGCCAGC 59.890 55.000 5.01 4.79 35.73 4.85
350 473 2.228059 CAATCCAAGCTCATAGGCCAG 58.772 52.381 5.01 0.00 0.00 4.85
351 474 1.751733 GCAATCCAAGCTCATAGGCCA 60.752 52.381 5.01 0.00 0.00 5.36
353 476 1.336125 GTGCAATCCAAGCTCATAGGC 59.664 52.381 0.00 0.00 0.00 3.93
355 478 2.031314 CACGTGCAATCCAAGCTCATAG 59.969 50.000 0.82 0.00 0.00 2.23
356 479 2.009051 CACGTGCAATCCAAGCTCATA 58.991 47.619 0.82 0.00 0.00 2.15
357 480 0.806868 CACGTGCAATCCAAGCTCAT 59.193 50.000 0.82 0.00 0.00 2.90
358 481 1.236616 CCACGTGCAATCCAAGCTCA 61.237 55.000 10.91 0.00 0.00 4.26
385 510 0.107800 TCTCTCTCCAAGCATGCAGC 60.108 55.000 21.98 0.00 46.19 5.25
386 511 1.654317 GTCTCTCTCCAAGCATGCAG 58.346 55.000 21.98 11.91 0.00 4.41
455 584 2.648059 CAGCGAAATCTTTCCCTGGAT 58.352 47.619 8.73 0.00 38.68 3.41
479 608 1.200020 CATCTCCCCTTTGTCAAACGC 59.800 52.381 0.00 0.00 0.00 4.84
512 641 0.321298 AACCGACCCTGAAATGGACG 60.321 55.000 0.00 0.00 0.00 4.79
522 651 2.355115 GGCCATTCAACCGACCCT 59.645 61.111 0.00 0.00 0.00 4.34
595 724 3.418913 TGCACGCACGCATGTACC 61.419 61.111 0.00 0.00 36.86 3.34
612 741 2.207590 CACTGTAGATCATGCACGCAT 58.792 47.619 0.00 0.00 37.08 4.73
662 791 1.201424 TGCACAGGAGATGATGAGCT 58.799 50.000 0.00 0.00 0.00 4.09
688 819 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
702 833 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
703 834 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
704 835 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
705 836 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
706 837 6.041409 TCAATCTCTCTCTCTCTCTCTCTCTC 59.959 46.154 0.00 0.00 0.00 3.20
707 838 5.901853 TCAATCTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
817 955 1.406069 CCCAGTCCATCACACACTAGC 60.406 57.143 0.00 0.00 0.00 3.42
818 956 2.093973 GTCCCAGTCCATCACACACTAG 60.094 54.545 0.00 0.00 0.00 2.57
819 957 1.899814 GTCCCAGTCCATCACACACTA 59.100 52.381 0.00 0.00 0.00 2.74
820 958 0.687354 GTCCCAGTCCATCACACACT 59.313 55.000 0.00 0.00 0.00 3.55
887 1029 1.860676 TTTGTACTGGCGACACAGAC 58.139 50.000 8.84 0.00 40.97 3.51
888 1030 2.831685 ATTTGTACTGGCGACACAGA 57.168 45.000 8.84 0.00 40.97 3.41
922 1070 1.945394 CTGGATGTATGAGTGGCAAGC 59.055 52.381 0.00 0.00 0.00 4.01
931 1082 0.761187 GGAGCTGGCTGGATGTATGA 59.239 55.000 0.00 0.00 0.00 2.15
977 1132 1.671328 TGTCGATCGAGCCTTACAGAG 59.329 52.381 20.09 0.00 0.00 3.35
1068 1223 1.002430 CAGAAGCTGCAGGTGTAGGAA 59.998 52.381 20.97 0.00 0.00 3.36
1180 1338 2.041928 AAGCTGAGGAGGAGGGGG 59.958 66.667 0.00 0.00 0.00 5.40
1181 1339 3.041469 GCAAGCTGAGGAGGAGGGG 62.041 68.421 0.00 0.00 0.00 4.79
1182 1340 1.994507 AGCAAGCTGAGGAGGAGGG 60.995 63.158 0.00 0.00 0.00 4.30
1208 1366 2.671963 TTCCAGCAGCAGCAGCAG 60.672 61.111 12.92 3.65 45.49 4.24
1299 1460 4.783621 GATGGCTGCGGCAGTGGA 62.784 66.667 28.88 14.70 42.43 4.02
1399 1560 3.052082 CTTGGTGGAGCACTGCGG 61.052 66.667 0.00 0.00 34.40 5.69
1400 1561 3.052082 CCTTGGTGGAGCACTGCG 61.052 66.667 0.00 0.00 38.35 5.18
1409 1570 1.406069 CGTCATCTTCCTCCTTGGTGG 60.406 57.143 1.55 1.55 37.07 4.61
1428 1589 2.223923 CCTAAGCTCAAGATCCAGACCG 60.224 54.545 0.00 0.00 0.00 4.79
1479 1640 2.969628 ATTGGCTAGACTGGAGAACG 57.030 50.000 0.00 0.00 0.00 3.95
1480 1641 4.162509 AGGTAATTGGCTAGACTGGAGAAC 59.837 45.833 0.00 0.00 0.00 3.01
1486 1656 4.744795 AGTGAGGTAATTGGCTAGACTG 57.255 45.455 0.00 0.00 0.00 3.51
1502 1677 5.986501 AACTAGAGAACCAACCTAGTGAG 57.013 43.478 0.00 0.00 41.38 3.51
1528 1703 0.179045 AATACCAAGCTAGGGCGCAG 60.179 55.000 10.83 0.00 44.37 5.18
1529 1704 1.124780 TAATACCAAGCTAGGGCGCA 58.875 50.000 10.83 0.00 44.37 6.09
1530 1705 2.143925 CTTAATACCAAGCTAGGGCGC 58.856 52.381 0.00 0.00 44.37 6.53
1531 1706 2.104281 ACCTTAATACCAAGCTAGGGCG 59.896 50.000 4.31 0.00 44.37 6.13
1532 1707 3.391626 AGACCTTAATACCAAGCTAGGGC 59.608 47.826 4.31 0.00 39.06 5.19
1533 1708 5.279556 GCTAGACCTTAATACCAAGCTAGGG 60.280 48.000 0.00 2.88 0.00 3.53
1534 1709 5.304614 TGCTAGACCTTAATACCAAGCTAGG 59.695 44.000 0.00 0.00 0.00 3.02
1535 1710 6.041069 ACTGCTAGACCTTAATACCAAGCTAG 59.959 42.308 0.00 0.00 0.00 3.42
1536 1711 5.897824 ACTGCTAGACCTTAATACCAAGCTA 59.102 40.000 0.00 0.00 0.00 3.32
1537 1712 4.717280 ACTGCTAGACCTTAATACCAAGCT 59.283 41.667 0.00 0.00 0.00 3.74
1538 1713 5.024785 ACTGCTAGACCTTAATACCAAGC 57.975 43.478 0.00 0.00 0.00 4.01
1539 1714 6.217294 GCTACTGCTAGACCTTAATACCAAG 58.783 44.000 0.00 0.00 36.03 3.61
1540 1715 6.158023 GCTACTGCTAGACCTTAATACCAA 57.842 41.667 0.00 0.00 36.03 3.67
1541 1716 5.786264 GCTACTGCTAGACCTTAATACCA 57.214 43.478 0.00 0.00 36.03 3.25
1569 1744 4.035324 CAGCCATTCTCATAGCTTGAACTG 59.965 45.833 0.00 0.00 32.78 3.16
1672 1847 4.637276 TCATAAACAGTGAACACGACCAT 58.363 39.130 0.00 0.00 36.20 3.55
1673 1848 4.061357 TCATAAACAGTGAACACGACCA 57.939 40.909 0.00 0.00 36.20 4.02
1692 1867 1.616327 ACCCTGGGCAGTAGCATCA 60.616 57.895 14.08 0.00 44.61 3.07
1693 1868 1.153086 CACCCTGGGCAGTAGCATC 60.153 63.158 14.08 0.00 44.61 3.91
1697 1876 2.670148 GGGTCACCCTGGGCAGTAG 61.670 68.421 14.08 0.00 41.34 2.57
1757 1936 4.866508 ATTTACACCACGTGAGAGAGAA 57.133 40.909 19.30 4.96 36.96 2.87
1827 2007 1.468520 GCAATGTATGTCTGCGTTGGT 59.531 47.619 0.00 0.00 35.31 3.67
1911 2091 8.528643 GGGCTTGATTTTACCAAATTTAGTAGT 58.471 33.333 0.00 0.00 32.35 2.73
1912 2092 7.979537 GGGGCTTGATTTTACCAAATTTAGTAG 59.020 37.037 0.00 0.00 32.35 2.57
1913 2093 7.455008 TGGGGCTTGATTTTACCAAATTTAGTA 59.545 33.333 0.00 0.00 32.35 1.82
1914 2094 6.271159 TGGGGCTTGATTTTACCAAATTTAGT 59.729 34.615 0.00 0.00 32.35 2.24
1920 2100 3.711704 TGTTGGGGCTTGATTTTACCAAA 59.288 39.130 0.00 0.00 39.43 3.28
2006 2344 2.489938 TTTCCTCCCTCACCATTTCG 57.510 50.000 0.00 0.00 0.00 3.46
2014 2352 0.914644 CAGGCTGATTTCCTCCCTCA 59.085 55.000 9.42 0.00 0.00 3.86
2028 2366 5.596836 TTTTCTTCAACATTTGTCAGGCT 57.403 34.783 0.00 0.00 0.00 4.58
2030 2368 6.201425 CACCATTTTCTTCAACATTTGTCAGG 59.799 38.462 0.00 0.00 0.00 3.86
2054 2392 3.925913 GCACAAAGCAAACTGTTCTTTCA 59.074 39.130 4.73 0.00 44.79 2.69
2206 2551 4.310769 ACTTCTCCTGTTCAAATCTGACG 58.689 43.478 0.00 0.00 0.00 4.35
2220 2565 1.065564 GCAGAGCATGGAACTTCTCCT 60.066 52.381 0.00 0.00 45.64 3.69
2225 2570 4.260170 CTCTTTAGCAGAGCATGGAACTT 58.740 43.478 0.00 0.00 42.96 2.66
2236 2581 7.896811 TCTCTTAACATTCACTCTTTAGCAGA 58.103 34.615 0.00 0.00 0.00 4.26
2237 2582 7.816995 ACTCTCTTAACATTCACTCTTTAGCAG 59.183 37.037 0.00 0.00 0.00 4.24
2238 2583 7.671302 ACTCTCTTAACATTCACTCTTTAGCA 58.329 34.615 0.00 0.00 0.00 3.49
2239 2584 9.078753 GTACTCTCTTAACATTCACTCTTTAGC 57.921 37.037 0.00 0.00 0.00 3.09
2251 2599 7.042335 CGGGAGAAAATGTACTCTCTTAACAT 58.958 38.462 9.09 0.00 38.52 2.71
2264 2612 2.244000 CGTGCACGGGAGAAAATGT 58.756 52.632 31.15 0.00 35.37 2.71
2283 2631 2.187946 CATGCACGGACCTCCTCC 59.812 66.667 0.00 0.00 35.33 4.30
2284 2632 1.690219 ATCCATGCACGGACCTCCTC 61.690 60.000 2.23 0.00 38.07 3.71
2285 2633 1.274703 AATCCATGCACGGACCTCCT 61.275 55.000 2.23 0.00 38.07 3.69
2378 2726 9.500785 TTTGAAAGCTAAAATAAAAATCAGGGG 57.499 29.630 0.00 0.00 0.00 4.79
2414 2762 7.703328 TGGACTTTCAGTTCAAAAGATACAAC 58.297 34.615 2.84 0.00 37.22 3.32


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

AutoCloner maintained by Alex Coulton.