Multiple sequence alignment - TraesCS5A01G324700

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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 TraesCS5A01G324700 chr5A 100.000 2878 0 0 1 2878 535731710 535734587 0.000000e+00 5315.0
1 TraesCS5A01G324700 chr5A 90.738 1598 109 25 810 2382 658868422 658870005 0.000000e+00 2095.0
2 TraesCS5A01G324700 chr5A 93.043 805 44 7 3 797 658867256 658868058 0.000000e+00 1166.0
3 TraesCS5A01G324700 chr5A 97.024 504 15 0 2375 2878 45903587 45904090 0.000000e+00 848.0
4 TraesCS5A01G324700 chr3A 97.619 504 12 0 2375 2878 682028284 682027781 0.000000e+00 865.0
5 TraesCS5A01G324700 chr3A 84.615 78 10 2 2281 2357 575614989 575615065 3.080000e-10 76.8
6 TraesCS5A01G324700 chr7A 97.222 504 14 0 2375 2878 384346889 384346386 0.000000e+00 854.0
7 TraesCS5A01G324700 chr7A 96.667 510 17 0 2369 2878 681596293 681596802 0.000000e+00 848.0
8 TraesCS5A01G324700 chr7A 87.097 124 16 0 1743 1866 126911334 126911211 1.080000e-29 141.0
9 TraesCS5A01G324700 chr6A 97.222 504 14 0 2375 2878 602274176 602273673 0.000000e+00 854.0
10 TraesCS5A01G324700 chr6A 97.024 504 15 0 2375 2878 121687328 121686825 0.000000e+00 848.0
11 TraesCS5A01G324700 chr4A 97.222 504 14 0 2375 2878 83005113 83004610 0.000000e+00 854.0
12 TraesCS5A01G324700 chr4A 97.024 504 15 0 2375 2878 574578730 574578227 0.000000e+00 848.0
13 TraesCS5A01G324700 chr1A 97.024 504 15 0 2375 2878 338279359 338278856 0.000000e+00 848.0
14 TraesCS5A01G324700 chr1A 80.258 233 44 2 1138 1369 10175360 10175129 1.060000e-39 174.0
15 TraesCS5A01G324700 chr1A 84.810 79 9 3 2281 2358 429980666 429980742 3.080000e-10 76.8
16 TraesCS5A01G324700 chr1A 95.556 45 1 1 1797 1840 99642694 99642738 1.430000e-08 71.3
17 TraesCS5A01G324700 chr5B 81.323 257 45 3 1138 1393 429410352 429410606 3.760000e-49 206.0
18 TraesCS5A01G324700 chr2A 76.768 198 44 2 560 756 676242441 676242245 3.030000e-20 110.0
19 TraesCS5A01G324700 chr2A 85.897 78 9 2 2281 2357 550570764 550570840 6.610000e-12 82.4
20 TraesCS5A01G324700 chr2A 85.897 78 8 3 2281 2357 596359598 596359523 2.380000e-11 80.5
21 TraesCS5A01G324700 chr5D 88.462 78 7 2 2281 2357 538028051 538027975 3.050000e-15 93.5
22 TraesCS5A01G324700 chr3B 85.556 90 12 1 2178 2266 60016334 60016245 3.050000e-15 93.5
23 TraesCS5A01G324700 chr7D 78.146 151 16 10 2211 2345 155313659 155313808 2.380000e-11 80.5
24 TraesCS5A01G324700 chr7D 83.544 79 10 3 2281 2358 552070681 552070605 1.430000e-08 71.3
25 TraesCS5A01G324700 chr3D 81.818 77 11 3 2281 2356 66737491 66737565 8.610000e-06 62.1


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 TraesCS5A01G324700 chr5A 535731710 535734587 2877 False 5315.0 5315 100.0000 1 2878 1 chr5A.!!$F2 2877
1 TraesCS5A01G324700 chr5A 658867256 658870005 2749 False 1630.5 2095 91.8905 3 2382 2 chr5A.!!$F3 2379
2 TraesCS5A01G324700 chr5A 45903587 45904090 503 False 848.0 848 97.0240 2375 2878 1 chr5A.!!$F1 503
3 TraesCS5A01G324700 chr3A 682027781 682028284 503 True 865.0 865 97.6190 2375 2878 1 chr3A.!!$R1 503
4 TraesCS5A01G324700 chr7A 384346386 384346889 503 True 854.0 854 97.2220 2375 2878 1 chr7A.!!$R2 503
5 TraesCS5A01G324700 chr7A 681596293 681596802 509 False 848.0 848 96.6670 2369 2878 1 chr7A.!!$F1 509
6 TraesCS5A01G324700 chr6A 602273673 602274176 503 True 854.0 854 97.2220 2375 2878 1 chr6A.!!$R2 503
7 TraesCS5A01G324700 chr6A 121686825 121687328 503 True 848.0 848 97.0240 2375 2878 1 chr6A.!!$R1 503
8 TraesCS5A01G324700 chr4A 83004610 83005113 503 True 854.0 854 97.2220 2375 2878 1 chr4A.!!$R1 503
9 TraesCS5A01G324700 chr4A 574578227 574578730 503 True 848.0 848 97.0240 2375 2878 1 chr4A.!!$R2 503
10 TraesCS5A01G324700 chr1A 338278856 338279359 503 True 848.0 848 97.0240 2375 2878 1 chr1A.!!$R2 503

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
742 752 0.251341 GGAGGCACAACATGGAACCT 60.251 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2733 3116 0.527565 CAAAGAATGGACCCAAGGCG 59.472 55.0 0.0 0.0 0.0 5.52 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
44 52 2.444696 CCAAGGCCCATGGTTCCA 59.555 61.111 19.07 0.00 33.08 3.53
45 53 1.002017 CCAAGGCCCATGGTTCCAT 59.998 57.895 19.07 7.46 33.08 3.41
51 59 1.065491 GGCCCATGGTTCCATTTTTCC 60.065 52.381 11.73 0.00 0.00 3.13
68 77 8.611757 CCATTTTTCCTCATTTTTCTCGTTTTT 58.388 29.630 0.00 0.00 0.00 1.94
77 86 4.624336 TTTTCTCGTTTTTGCAGCTACA 57.376 36.364 0.00 0.00 0.00 2.74
88 97 0.462759 GCAGCTACATCACCTGGTCC 60.463 60.000 0.00 0.00 0.00 4.46
92 101 1.679032 GCTACATCACCTGGTCCCAAC 60.679 57.143 0.00 0.00 0.00 3.77
111 120 2.519780 GGAAACGCCCCCACAACA 60.520 61.111 0.00 0.00 0.00 3.33
248 257 3.071479 CAACACACCCGCTACTGTATTT 58.929 45.455 0.00 0.00 0.00 1.40
334 343 1.606601 GGGGAAAGGGAGTTGTGCC 60.607 63.158 0.00 0.00 0.00 5.01
342 351 2.597510 GAGTTGTGCCACACCCCC 60.598 66.667 0.00 0.00 32.73 5.40
402 411 1.396301 CGAAGCTGCCTGAACAAGATC 59.604 52.381 0.00 0.00 0.00 2.75
404 413 3.677148 CGAAGCTGCCTGAACAAGATCTA 60.677 47.826 0.00 0.00 0.00 1.98
415 424 6.351711 CCTGAACAAGATCTACAGAGGTGAAT 60.352 42.308 15.72 0.00 0.00 2.57
423 432 4.160329 TCTACAGAGGTGAATGTCTTGGT 58.840 43.478 0.00 0.00 0.00 3.67
425 434 2.439507 ACAGAGGTGAATGTCTTGGTGT 59.560 45.455 0.00 0.00 0.00 4.16
444 453 2.728817 CCTCGCCGTACATCTCCC 59.271 66.667 0.00 0.00 0.00 4.30
454 463 3.377172 CCGTACATCTCCCACCATTTTTC 59.623 47.826 0.00 0.00 0.00 2.29
459 468 7.094549 CGTACATCTCCCACCATTTTTCTTAAA 60.095 37.037 0.00 0.00 0.00 1.52
481 491 1.780860 GTTTTTGTGTCGCATGCTGTC 59.219 47.619 17.13 7.86 0.00 3.51
492 502 1.220529 CATGCTGTCACAGTGTTCGT 58.779 50.000 6.68 0.00 33.43 3.85
531 541 8.390854 GCATAAGCTGATATATCATTGTTTGC 57.609 34.615 15.71 16.61 36.02 3.68
568 578 9.950496 GGTAACATCATCAGGATCTACATTATT 57.050 33.333 0.00 0.00 32.57 1.40
577 587 4.345257 AGGATCTACATTATTCACGCCAGT 59.655 41.667 0.00 0.00 0.00 4.00
584 594 2.154567 TATTCACGCCAGTCCTAGGT 57.845 50.000 9.08 0.00 0.00 3.08
594 604 3.714391 CCAGTCCTAGGTTTATACGCAC 58.286 50.000 9.08 0.00 0.00 5.34
600 610 2.981859 AGGTTTATACGCACCTCTGG 57.018 50.000 0.00 0.00 39.37 3.86
610 620 0.464554 GCACCTCTGGGTTGGCTATC 60.465 60.000 0.00 0.00 44.73 2.08
685 695 3.699538 TCATGCGAAGGTATACACAGTCT 59.300 43.478 5.01 0.00 0.00 3.24
742 752 0.251341 GGAGGCACAACATGGAACCT 60.251 55.000 0.00 0.00 0.00 3.50
797 808 8.025243 TCGTCTGGTGTAAAATTGATTAGTTC 57.975 34.615 0.00 0.00 0.00 3.01
798 809 7.658167 TCGTCTGGTGTAAAATTGATTAGTTCA 59.342 33.333 0.00 0.00 0.00 3.18
799 810 7.957484 CGTCTGGTGTAAAATTGATTAGTTCAG 59.043 37.037 0.00 0.00 35.27 3.02
800 811 8.784043 GTCTGGTGTAAAATTGATTAGTTCAGT 58.216 33.333 0.00 0.00 35.27 3.41
801 812 8.999431 TCTGGTGTAAAATTGATTAGTTCAGTC 58.001 33.333 0.00 0.00 35.27 3.51
802 813 8.684386 TGGTGTAAAATTGATTAGTTCAGTCA 57.316 30.769 0.00 0.00 35.27 3.41
803 814 9.295825 TGGTGTAAAATTGATTAGTTCAGTCAT 57.704 29.630 0.00 0.00 35.27 3.06
804 815 9.774742 GGTGTAAAATTGATTAGTTCAGTCATC 57.225 33.333 0.00 0.00 35.27 2.92
808 819 8.868522 AAAATTGATTAGTTCAGTCATCTCCA 57.131 30.769 0.00 0.00 35.27 3.86
814 1176 4.751767 AGTTCAGTCATCTCCATTCCTC 57.248 45.455 0.00 0.00 0.00 3.71
830 1192 7.928873 TCCATTCCTCATTCCTTTTAACTAGT 58.071 34.615 0.00 0.00 0.00 2.57
832 1194 8.678199 CCATTCCTCATTCCTTTTAACTAGTTC 58.322 37.037 12.39 0.00 0.00 3.01
841 1203 6.218746 TCCTTTTAACTAGTTCTTGACGACC 58.781 40.000 12.39 0.00 0.00 4.79
935 1300 2.170397 AGCGGACCATGAATATGTGACA 59.830 45.455 0.00 0.00 32.21 3.58
972 1337 1.377725 CCAGCTCGTTGGCAAGGAT 60.378 57.895 21.45 6.65 33.50 3.24
995 1360 3.884895 TCCCGTACGACATAACTTCCTA 58.115 45.455 18.76 0.00 0.00 2.94
996 1361 4.464008 TCCCGTACGACATAACTTCCTAT 58.536 43.478 18.76 0.00 0.00 2.57
1006 1371 7.451877 ACGACATAACTTCCTATCAGATGGTAT 59.548 37.037 0.00 0.00 0.00 2.73
1007 1372 7.757173 CGACATAACTTCCTATCAGATGGTATG 59.243 40.741 9.63 9.63 42.77 2.39
1008 1373 7.390027 ACATAACTTCCTATCAGATGGTATGC 58.610 38.462 10.64 0.00 41.71 3.14
1009 1374 7.236432 ACATAACTTCCTATCAGATGGTATGCT 59.764 37.037 10.64 0.18 41.71 3.79
1011 1376 5.401750 ACTTCCTATCAGATGGTATGCTCT 58.598 41.667 0.00 0.00 0.00 4.09
1012 1377 5.843421 ACTTCCTATCAGATGGTATGCTCTT 59.157 40.000 0.00 0.00 0.00 2.85
1033 1407 1.985473 TTTTGCAGATCAGTGTGGCT 58.015 45.000 0.00 0.00 0.00 4.75
1044 1418 1.153568 GTGTGGCTCGCTGCTCATA 60.154 57.895 0.00 0.00 42.39 2.15
1049 1423 1.412343 TGGCTCGCTGCTCATATTGTA 59.588 47.619 0.00 0.00 42.39 2.41
1053 1427 4.023707 GGCTCGCTGCTCATATTGTATTTT 60.024 41.667 0.00 0.00 42.39 1.82
1054 1428 5.506317 GGCTCGCTGCTCATATTGTATTTTT 60.506 40.000 0.00 0.00 42.39 1.94
1090 1464 1.282570 CACACGCTCGCCAACAAAT 59.717 52.632 0.00 0.00 0.00 2.32
1099 1473 3.758300 CTCGCCAACAAATGAATGGTAC 58.242 45.455 10.23 0.00 36.57 3.34
1118 1492 5.116882 GGTACCAGACCTCATATGTGTTTC 58.883 45.833 7.15 0.00 45.89 2.78
1120 1494 3.054361 ACCAGACCTCATATGTGTTTCCC 60.054 47.826 1.90 0.00 0.00 3.97
1127 1501 7.027874 ACCTCATATGTGTTTCCCTCTTAAA 57.972 36.000 1.90 0.00 0.00 1.52
1231 1605 2.054021 TGTCCTTCACCCACTCATCAA 58.946 47.619 0.00 0.00 0.00 2.57
1269 1643 1.217882 ACCAACGAAAGACAAGCTCG 58.782 50.000 0.00 0.00 38.53 5.03
1272 1646 1.136502 CAACGAAAGACAAGCTCGAGC 60.137 52.381 30.01 30.01 42.49 5.03
1295 1669 1.067060 GTTGCCTGGAAACTTCACCAC 59.933 52.381 10.47 0.00 32.44 4.16
1299 1673 2.251371 GGAAACTTCACCACGCGC 59.749 61.111 5.73 0.00 0.00 6.86
1316 1690 1.359848 CGCTGTTCGACTGCCTTAAT 58.640 50.000 9.85 0.00 39.50 1.40
1337 1711 2.040278 TGAGTATTATGCTGGATGGCCC 59.960 50.000 0.00 0.00 0.00 5.80
1374 1748 1.349067 GGTGACCAAGTACCCAGTCT 58.651 55.000 0.00 0.00 0.00 3.24
1386 1760 3.686916 ACCCAGTCTTAGCTGAAGAAC 57.313 47.619 0.00 0.00 45.90 3.01
1401 1775 5.181245 GCTGAAGAACATTTTAGCAGGTACA 59.819 40.000 0.00 0.00 38.94 2.90
1410 1784 3.520290 TTAGCAGGTACATTCTCACCG 57.480 47.619 0.00 0.00 39.94 4.94
1428 1802 1.030457 CGTCTCTAATGGTACCCGCT 58.970 55.000 10.07 0.00 0.00 5.52
1431 1805 2.429610 GTCTCTAATGGTACCCGCTCAA 59.570 50.000 10.07 0.00 0.00 3.02
1456 1830 3.683365 AACTCCATGCATGTTTTTCCC 57.317 42.857 24.58 0.00 0.00 3.97
1461 1835 1.901159 CATGCATGTTTTTCCCTCCCA 59.099 47.619 18.91 0.00 0.00 4.37
1468 1842 2.433970 TGTTTTTCCCTCCCAAAGCTTG 59.566 45.455 0.00 0.00 0.00 4.01
1469 1843 2.434336 GTTTTTCCCTCCCAAAGCTTGT 59.566 45.455 0.00 0.00 0.00 3.16
1470 1844 1.703411 TTTCCCTCCCAAAGCTTGTG 58.297 50.000 0.00 0.45 0.00 3.33
1475 1849 1.479389 CCTCCCAAAGCTTGTGGACTT 60.479 52.381 21.94 0.00 38.54 3.01
1477 1851 3.562176 CCTCCCAAAGCTTGTGGACTTAT 60.562 47.826 21.94 0.00 38.54 1.73
1480 1854 4.288626 TCCCAAAGCTTGTGGACTTATACT 59.711 41.667 21.94 0.00 38.54 2.12
1528 1904 5.139727 TGAACACCAAACCAGAGATGAAAT 58.860 37.500 0.00 0.00 0.00 2.17
1530 1906 5.458041 ACACCAAACCAGAGATGAAATTG 57.542 39.130 0.00 0.00 0.00 2.32
1556 1932 0.104855 GTGTGCTCCATATCTGCCGA 59.895 55.000 0.00 0.00 0.00 5.54
1574 1950 2.473816 CGACACTATGATGGCGTCAAT 58.526 47.619 14.29 5.30 46.40 2.57
1575 1951 2.472861 CGACACTATGATGGCGTCAATC 59.527 50.000 14.29 5.96 46.40 2.67
1614 1990 4.341235 CCAAGGTCACTTATCTATCCACGA 59.659 45.833 0.00 0.00 34.49 4.35
1630 2006 2.081462 CACGACCACCTTGTTATTCCC 58.919 52.381 0.00 0.00 0.00 3.97
1656 2032 6.307155 GTTTTCTTTCAGACACACATATCCG 58.693 40.000 0.00 0.00 0.00 4.18
1657 2033 4.801330 TCTTTCAGACACACATATCCGT 57.199 40.909 0.00 0.00 0.00 4.69
1658 2034 5.147330 TCTTTCAGACACACATATCCGTT 57.853 39.130 0.00 0.00 0.00 4.44
1659 2035 5.547465 TCTTTCAGACACACATATCCGTTT 58.453 37.500 0.00 0.00 0.00 3.60
1665 2041 1.211949 CACACATATCCGTTTCCCCCT 59.788 52.381 0.00 0.00 0.00 4.79
1673 2049 1.557832 TCCGTTTCCCCCTTGTCATAG 59.442 52.381 0.00 0.00 0.00 2.23
1718 2095 8.388484 AGTTTATCTGCCTGATTGATTGATAC 57.612 34.615 0.00 0.00 36.65 2.24
1775 2152 1.742268 GGCAAAACAAAAAGGCAAGCA 59.258 42.857 0.00 0.00 0.00 3.91
1862 2239 1.552337 CTAGCACCCACTGACTCATGT 59.448 52.381 0.00 0.00 0.00 3.21
1881 2258 1.129998 GTCTTAGCGACACGTAGAGCA 59.870 52.381 10.23 0.00 42.37 4.26
1883 2260 0.169672 TTAGCGACACGTAGAGCACC 59.830 55.000 10.23 0.00 0.00 5.01
1924 2301 3.876914 GGAAATATGGTGCTGATTCGTGA 59.123 43.478 0.00 0.00 0.00 4.35
1945 2322 0.034059 CGGAAGGATCCCCATCTTCG 59.966 60.000 8.55 1.53 43.37 3.79
1961 2338 6.094048 CCCATCTTCGTTTCAAACATATCAGT 59.906 38.462 0.22 0.00 0.00 3.41
2005 2383 7.855784 ACCCCAGACATTTTTCTTTTCTATT 57.144 32.000 0.00 0.00 0.00 1.73
2029 2408 5.243426 TGTGTTTAGTTTGTTTCTCCAGC 57.757 39.130 0.00 0.00 0.00 4.85
2062 2441 3.918544 CCGACCGGCATTTGGATT 58.081 55.556 0.00 0.00 0.00 3.01
2065 2444 2.773487 CCGACCGGCATTTGGATTATA 58.227 47.619 0.00 0.00 0.00 0.98
2072 2451 5.654650 ACCGGCATTTGGATTATAAGTTTGA 59.345 36.000 0.00 0.00 0.00 2.69
2103 2482 4.288366 TGGACATCCCAAAATCTGTGTCTA 59.712 41.667 0.00 0.00 43.29 2.59
2117 2498 3.023832 TGTGTCTATTCTGAGCCGATCA 58.976 45.455 0.00 0.00 36.21 2.92
2118 2499 3.638627 TGTGTCTATTCTGAGCCGATCAT 59.361 43.478 0.00 0.00 37.28 2.45
2121 2502 2.629617 TCTATTCTGAGCCGATCATGCA 59.370 45.455 6.95 0.00 37.28 3.96
2122 2503 1.880271 ATTCTGAGCCGATCATGCAG 58.120 50.000 6.95 2.02 37.28 4.41
2132 2513 1.676916 CGATCATGCAGTGTTGACCCT 60.677 52.381 0.00 0.00 0.00 4.34
2138 2519 3.290948 TGCAGTGTTGACCCTTAGTTT 57.709 42.857 0.00 0.00 0.00 2.66
2147 2528 6.485648 GTGTTGACCCTTAGTTTCTACATGTT 59.514 38.462 2.30 0.00 29.79 2.71
2151 2532 7.458397 TGACCCTTAGTTTCTACATGTTTCAT 58.542 34.615 2.30 0.00 0.00 2.57
2155 2536 9.667107 CCCTTAGTTTCTACATGTTTCATCTAA 57.333 33.333 2.30 7.79 0.00 2.10
2170 2551 8.103305 TGTTTCATCTAAAGTAGGAAGCTGAAT 58.897 33.333 0.00 0.00 0.00 2.57
2176 2557 2.781667 AGTAGGAAGCTGAATCCCCAT 58.218 47.619 0.00 0.00 37.71 4.00
2199 2580 1.549203 GAAATATCATGCGCCCCCAT 58.451 50.000 4.18 0.00 0.00 4.00
2205 2586 2.053865 CATGCGCCCCCATTCTTGT 61.054 57.895 4.18 0.00 0.00 3.16
2206 2587 2.053865 ATGCGCCCCCATTCTTGTG 61.054 57.895 4.18 0.00 0.00 3.33
2226 2607 1.840635 GGTTCTCCCTATGCTCCAAGT 59.159 52.381 0.00 0.00 0.00 3.16
2227 2608 2.158885 GGTTCTCCCTATGCTCCAAGTC 60.159 54.545 0.00 0.00 0.00 3.01
2228 2609 2.769095 GTTCTCCCTATGCTCCAAGTCT 59.231 50.000 0.00 0.00 0.00 3.24
2229 2610 3.961408 GTTCTCCCTATGCTCCAAGTCTA 59.039 47.826 0.00 0.00 0.00 2.59
2239 2620 7.933577 CCTATGCTCCAAGTCTAAAACATCATA 59.066 37.037 0.00 0.00 0.00 2.15
2301 2684 8.700051 TCATTAAATTTCAGGTCCAAACTCAAA 58.300 29.630 0.00 0.00 0.00 2.69
2312 2695 6.777580 AGGTCCAAACTCAAAATGTACTTCAT 59.222 34.615 0.00 0.00 38.57 2.57
2313 2696 6.863126 GGTCCAAACTCAAAATGTACTTCATG 59.137 38.462 0.00 0.00 36.81 3.07
2370 2753 3.933861 ACTGTTGAACTTCTTGGGACT 57.066 42.857 0.00 0.00 0.00 3.85
2371 2754 3.809905 ACTGTTGAACTTCTTGGGACTC 58.190 45.455 0.00 0.00 0.00 3.36
2372 2755 3.456277 ACTGTTGAACTTCTTGGGACTCT 59.544 43.478 0.00 0.00 0.00 3.24
2733 3116 3.753272 TGCAATAAAAGCACTCAGTCTCC 59.247 43.478 0.00 0.00 37.02 3.71
2735 3118 2.080286 TAAAAGCACTCAGTCTCCGC 57.920 50.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 1.278537 AAATGGAACCATGGGCCTTG 58.721 50.000 18.09 12.30 36.68 3.61
44 52 8.122330 GCAAAAACGAGAAAAATGAGGAAAAAT 58.878 29.630 0.00 0.00 0.00 1.82
45 53 7.118390 TGCAAAAACGAGAAAAATGAGGAAAAA 59.882 29.630 0.00 0.00 0.00 1.94
51 59 4.741676 AGCTGCAAAAACGAGAAAAATGAG 59.258 37.500 1.02 0.00 0.00 2.90
77 86 2.602676 CCGGTTGGGACCAGGTGAT 61.603 63.158 0.00 0.00 46.91 3.06
92 101 4.958897 TTGTGGGGGCGTTTCCGG 62.959 66.667 0.00 0.00 34.94 5.14
101 110 0.392461 AATCGTCGATGTTGTGGGGG 60.392 55.000 8.83 0.00 0.00 5.40
111 120 2.196749 GACAGATGTGCAATCGTCGAT 58.803 47.619 0.75 0.75 0.00 3.59
185 194 5.264395 AGTTGAGCTATTGCCATTAGGTTT 58.736 37.500 0.00 0.00 40.80 3.27
248 257 1.047596 AGTTGGTGCAACATTGGCCA 61.048 50.000 4.62 0.00 45.66 5.36
350 359 2.526046 AAGGAGGTCCGTGGTTGGG 61.526 63.158 0.00 0.00 42.08 4.12
359 368 2.505364 AATGGGCAGCAAGGAGGTCC 62.505 60.000 0.00 0.00 0.00 4.46
402 411 4.248859 CACCAAGACATTCACCTCTGTAG 58.751 47.826 0.00 0.00 0.00 2.74
404 413 2.439507 ACACCAAGACATTCACCTCTGT 59.560 45.455 0.00 0.00 0.00 3.41
415 424 2.741092 GCGAGGGACACCAAGACA 59.259 61.111 0.00 0.00 40.13 3.41
423 432 1.379443 AGATGTACGGCGAGGGACA 60.379 57.895 16.62 12.39 0.00 4.02
425 434 1.826921 GGAGATGTACGGCGAGGGA 60.827 63.158 16.62 0.00 0.00 4.20
454 463 5.175491 AGCATGCGACACAAAAACATTTAAG 59.825 36.000 13.01 0.00 0.00 1.85
459 468 2.223782 ACAGCATGCGACACAAAAACAT 60.224 40.909 13.01 0.00 42.53 2.71
471 481 0.110509 GAACACTGTGACAGCATGCG 60.111 55.000 15.86 9.99 42.53 4.73
531 541 5.614308 TGATGATGTTACCAAGATAGGCAG 58.386 41.667 0.00 0.00 0.00 4.85
558 568 3.704566 AGGACTGGCGTGAATAATGTAGA 59.295 43.478 0.00 0.00 0.00 2.59
568 578 1.927487 TAAACCTAGGACTGGCGTGA 58.073 50.000 17.98 0.00 0.00 4.35
577 587 3.635373 CAGAGGTGCGTATAAACCTAGGA 59.365 47.826 17.98 0.00 46.97 2.94
594 604 1.139853 GACTGATAGCCAACCCAGAGG 59.860 57.143 0.00 0.00 40.04 3.69
600 610 1.065854 ACTGCTGACTGATAGCCAACC 60.066 52.381 0.00 0.00 40.42 3.77
610 620 1.532868 GTGCCAACTAACTGCTGACTG 59.467 52.381 0.00 0.00 0.00 3.51
742 752 1.717194 GGTGATTTACCGCGAAGTCA 58.283 50.000 8.23 4.45 40.26 3.41
768 778 9.672086 CTAATCAATTTTACACCAGACGAAAAA 57.328 29.630 0.00 0.00 0.00 1.94
769 779 8.842280 ACTAATCAATTTTACACCAGACGAAAA 58.158 29.630 0.00 0.00 0.00 2.29
776 787 8.783093 TGACTGAACTAATCAATTTTACACCAG 58.217 33.333 0.00 0.00 37.67 4.00
783 794 8.868522 TGGAGATGACTGAACTAATCAATTTT 57.131 30.769 0.00 0.00 37.67 1.82
786 797 7.718753 GGAATGGAGATGACTGAACTAATCAAT 59.281 37.037 0.00 0.00 37.67 2.57
790 801 6.385176 TGAGGAATGGAGATGACTGAACTAAT 59.615 38.462 0.00 0.00 0.00 1.73
797 808 4.102838 AGGAATGAGGAATGGAGATGACTG 59.897 45.833 0.00 0.00 0.00 3.51
798 809 4.305524 AGGAATGAGGAATGGAGATGACT 58.694 43.478 0.00 0.00 0.00 3.41
799 810 4.703379 AGGAATGAGGAATGGAGATGAC 57.297 45.455 0.00 0.00 0.00 3.06
800 811 5.722172 AAAGGAATGAGGAATGGAGATGA 57.278 39.130 0.00 0.00 0.00 2.92
801 812 7.559170 AGTTAAAAGGAATGAGGAATGGAGATG 59.441 37.037 0.00 0.00 0.00 2.90
802 813 7.646884 AGTTAAAAGGAATGAGGAATGGAGAT 58.353 34.615 0.00 0.00 0.00 2.75
803 814 7.032598 AGTTAAAAGGAATGAGGAATGGAGA 57.967 36.000 0.00 0.00 0.00 3.71
804 815 8.049721 ACTAGTTAAAAGGAATGAGGAATGGAG 58.950 37.037 0.00 0.00 0.00 3.86
805 816 7.928873 ACTAGTTAAAAGGAATGAGGAATGGA 58.071 34.615 0.00 0.00 0.00 3.41
806 817 8.581253 AACTAGTTAAAAGGAATGAGGAATGG 57.419 34.615 6.26 0.00 0.00 3.16
807 818 9.454859 AGAACTAGTTAAAAGGAATGAGGAATG 57.545 33.333 8.42 0.00 0.00 2.67
814 1176 8.221766 GTCGTCAAGAACTAGTTAAAAGGAATG 58.778 37.037 8.42 0.00 0.00 2.67
886 1251 2.768253 TTTCTGTCATGGCTCGACAT 57.232 45.000 9.47 0.00 42.27 3.06
888 1253 3.189287 ACAATTTTCTGTCATGGCTCGAC 59.811 43.478 0.00 0.62 0.00 4.20
889 1254 3.411446 ACAATTTTCTGTCATGGCTCGA 58.589 40.909 0.00 0.00 0.00 4.04
890 1255 3.426695 GGACAATTTTCTGTCATGGCTCG 60.427 47.826 0.00 0.00 46.31 5.03
891 1256 3.760684 AGGACAATTTTCTGTCATGGCTC 59.239 43.478 0.00 0.00 46.31 4.70
892 1257 3.771216 AGGACAATTTTCTGTCATGGCT 58.229 40.909 0.00 0.00 46.31 4.75
935 1300 4.646492 GCTGGTTCTGGATGGATATGTTTT 59.354 41.667 0.00 0.00 0.00 2.43
972 1337 4.464008 AGGAAGTTATGTCGTACGGGATA 58.536 43.478 16.52 9.05 0.00 2.59
1074 1448 0.040514 TTCATTTGTTGGCGAGCGTG 60.041 50.000 0.00 0.00 0.00 5.34
1075 1449 0.881118 ATTCATTTGTTGGCGAGCGT 59.119 45.000 0.00 0.00 0.00 5.07
1099 1473 3.200825 AGGGAAACACATATGAGGTCTGG 59.799 47.826 10.38 0.00 0.00 3.86
1118 1492 5.213891 ACTGCCAAACAAATTTAAGAGGG 57.786 39.130 0.00 0.00 0.00 4.30
1120 1494 8.882736 AGAAAAACTGCCAAACAAATTTAAGAG 58.117 29.630 0.00 0.00 0.00 2.85
1127 1501 6.410540 TGGTAAGAAAAACTGCCAAACAAAT 58.589 32.000 0.00 0.00 33.68 2.32
1211 1585 1.728323 TGATGAGTGGGTGAAGGACA 58.272 50.000 0.00 0.00 0.00 4.02
1231 1605 1.207329 GTTCGCTAGGACCATCACCTT 59.793 52.381 0.00 0.00 38.76 3.50
1269 1643 0.538287 AGTTTCCAGGCAACCAGCTC 60.538 55.000 0.00 0.00 44.79 4.09
1272 1646 1.338020 GTGAAGTTTCCAGGCAACCAG 59.662 52.381 0.00 0.00 37.17 4.00
1299 1673 3.589988 ACTCATTAAGGCAGTCGAACAG 58.410 45.455 0.00 0.00 0.00 3.16
1316 1690 2.040278 GGGCCATCCAGCATAATACTCA 59.960 50.000 4.39 0.00 35.00 3.41
1337 1711 2.693762 CCACTGGCCATCTTGCGTG 61.694 63.158 5.51 9.99 0.00 5.34
1374 1748 6.003950 ACCTGCTAAAATGTTCTTCAGCTAA 58.996 36.000 0.00 0.00 0.00 3.09
1386 1760 5.220662 CGGTGAGAATGTACCTGCTAAAATG 60.221 44.000 0.00 0.00 34.77 2.32
1401 1775 4.341520 GGTACCATTAGAGACGGTGAGAAT 59.658 45.833 7.15 0.00 34.12 2.40
1440 1814 1.207811 GGGAGGGAAAAACATGCATGG 59.792 52.381 29.41 12.50 0.00 3.66
1442 1816 2.323999 TGGGAGGGAAAAACATGCAT 57.676 45.000 0.00 0.00 0.00 3.96
1444 1818 2.871637 GCTTTGGGAGGGAAAAACATGC 60.872 50.000 0.00 0.00 0.00 4.06
1447 1821 2.433970 CAAGCTTTGGGAGGGAAAAACA 59.566 45.455 0.00 0.00 0.00 2.83
1454 1828 0.895559 GTCCACAAGCTTTGGGAGGG 60.896 60.000 20.54 8.71 35.62 4.30
1456 1830 1.986882 AAGTCCACAAGCTTTGGGAG 58.013 50.000 20.54 3.99 35.62 4.30
1461 1835 6.208797 GGGAAAAGTATAAGTCCACAAGCTTT 59.791 38.462 0.00 0.00 31.30 3.51
1468 1842 6.997239 AAATCGGGAAAAGTATAAGTCCAC 57.003 37.500 0.00 0.00 31.30 4.02
1469 1843 6.127842 GCAAAATCGGGAAAAGTATAAGTCCA 60.128 38.462 0.00 0.00 31.30 4.02
1470 1844 6.127842 TGCAAAATCGGGAAAAGTATAAGTCC 60.128 38.462 0.00 0.00 0.00 3.85
1475 1849 5.126222 TGCATGCAAAATCGGGAAAAGTATA 59.874 36.000 20.30 0.00 0.00 1.47
1477 1851 3.256879 TGCATGCAAAATCGGGAAAAGTA 59.743 39.130 20.30 0.00 0.00 2.24
1480 1854 2.827800 TGCATGCAAAATCGGGAAAA 57.172 40.000 20.30 0.00 0.00 2.29
1504 1880 4.163441 TCATCTCTGGTTTGGTGTTCAA 57.837 40.909 0.00 0.00 0.00 2.69
1556 1932 3.132824 TCAGATTGACGCCATCATAGTGT 59.867 43.478 0.00 0.00 37.11 3.55
1574 1950 3.523564 CCTTGGTAAGGGGAATCTTCAGA 59.476 47.826 0.00 0.00 45.27 3.27
1575 1951 3.891049 CCTTGGTAAGGGGAATCTTCAG 58.109 50.000 0.00 0.00 45.27 3.02
1600 1976 4.099573 ACAAGGTGGTCGTGGATAGATAAG 59.900 45.833 0.00 0.00 0.00 1.73
1614 1990 1.069775 ACCGGGAATAACAAGGTGGT 58.930 50.000 6.32 0.00 33.37 4.16
1656 2032 3.713826 TCACTATGACAAGGGGGAAAC 57.286 47.619 0.00 0.00 0.00 2.78
1657 2033 4.290985 TGAATCACTATGACAAGGGGGAAA 59.709 41.667 0.00 0.00 0.00 3.13
1658 2034 3.849574 TGAATCACTATGACAAGGGGGAA 59.150 43.478 0.00 0.00 0.00 3.97
1659 2035 3.459828 TGAATCACTATGACAAGGGGGA 58.540 45.455 0.00 0.00 0.00 4.81
1665 2041 7.555195 AGCAAAGATCATGAATCACTATGACAA 59.445 33.333 0.00 0.00 36.26 3.18
1701 2078 7.407393 TTGATTTGTATCAATCAATCAGGCA 57.593 32.000 5.01 0.00 43.93 4.75
1718 2095 4.699735 GGGTAAGGGGCAAAAATTGATTTG 59.300 41.667 0.00 0.00 42.01 2.32
1726 2103 1.062810 ACTGTGGGTAAGGGGCAAAAA 60.063 47.619 0.00 0.00 0.00 1.94
1728 2105 1.074244 GTACTGTGGGTAAGGGGCAAA 59.926 52.381 0.00 0.00 31.56 3.68
1732 2109 2.944094 GCATTGTACTGTGGGTAAGGGG 60.944 54.545 0.00 0.00 31.56 4.79
1862 2239 1.129998 GTGCTCTACGTGTCGCTAAGA 59.870 52.381 0.00 0.00 0.00 2.10
1903 2280 4.553547 GCTCACGAATCAGCACCATATTTC 60.554 45.833 0.00 0.00 35.56 2.17
1961 2338 5.825679 GGGGTACATGTTGCAAGATATTACA 59.174 40.000 20.38 8.26 0.00 2.41
1971 2348 0.767998 TGTCTGGGGTACATGTTGCA 59.232 50.000 2.30 0.00 0.00 4.08
2005 2383 6.544197 TGCTGGAGAAACAAACTAAACACATA 59.456 34.615 0.00 0.00 0.00 2.29
2010 2388 5.915196 GTCATGCTGGAGAAACAAACTAAAC 59.085 40.000 0.00 0.00 0.00 2.01
2011 2389 5.827797 AGTCATGCTGGAGAAACAAACTAAA 59.172 36.000 0.00 0.00 0.00 1.85
2029 2408 1.732259 GTCGGCAACCTTACAGTCATG 59.268 52.381 0.00 0.00 0.00 3.07
2052 2431 9.221775 CTACGTTCAAACTTATAATCCAAATGC 57.778 33.333 0.00 0.00 0.00 3.56
2062 2441 7.546667 GGATGTCCAACTACGTTCAAACTTATA 59.453 37.037 0.00 0.00 35.64 0.98
2065 2444 4.514066 GGATGTCCAACTACGTTCAAACTT 59.486 41.667 0.00 0.00 35.64 2.66
2087 2466 5.065731 GCTCAGAATAGACACAGATTTTGGG 59.934 44.000 0.00 0.00 35.82 4.12
2103 2482 1.140452 ACTGCATGATCGGCTCAGAAT 59.860 47.619 10.12 0.00 37.28 2.40
2117 2498 3.508845 AACTAAGGGTCAACACTGCAT 57.491 42.857 0.00 0.00 0.00 3.96
2118 2499 3.118038 AGAAACTAAGGGTCAACACTGCA 60.118 43.478 0.00 0.00 0.00 4.41
2121 2502 5.881923 TGTAGAAACTAAGGGTCAACACT 57.118 39.130 0.00 0.00 0.00 3.55
2122 2503 5.995897 ACATGTAGAAACTAAGGGTCAACAC 59.004 40.000 0.00 0.00 0.00 3.32
2147 2528 7.275920 GGATTCAGCTTCCTACTTTAGATGAA 58.724 38.462 0.00 0.00 45.06 2.57
2151 2532 4.409247 GGGGATTCAGCTTCCTACTTTAGA 59.591 45.833 2.99 0.00 33.53 2.10
2155 2536 2.562296 TGGGGATTCAGCTTCCTACTT 58.438 47.619 2.99 0.00 33.53 2.24
2176 2557 0.539438 GGGCGCATGATATTTCCCCA 60.539 55.000 10.83 0.00 0.00 4.96
2199 2580 2.912956 AGCATAGGGAGAACCACAAGAA 59.087 45.455 0.00 0.00 43.89 2.52
2205 2586 1.839994 CTTGGAGCATAGGGAGAACCA 59.160 52.381 0.00 0.00 43.89 3.67
2206 2587 1.840635 ACTTGGAGCATAGGGAGAACC 59.159 52.381 0.00 0.00 40.67 3.62
2350 2733 3.456277 AGAGTCCCAAGAAGTTCAACAGT 59.544 43.478 5.50 0.00 0.00 3.55
2354 2737 6.433847 TGAATAGAGTCCCAAGAAGTTCAA 57.566 37.500 5.50 0.00 0.00 2.69
2364 2747 4.774124 CTTTGAGCATGAATAGAGTCCCA 58.226 43.478 0.00 0.00 0.00 4.37
2370 2753 4.226427 ACCAGCTTTGAGCATGAATAGA 57.774 40.909 0.00 0.00 45.56 1.98
2371 2754 5.121811 AGTACCAGCTTTGAGCATGAATAG 58.878 41.667 0.00 0.00 45.56 1.73
2372 2755 5.102953 AGTACCAGCTTTGAGCATGAATA 57.897 39.130 0.00 0.00 45.56 1.75
2460 2843 3.843422 TGGTTCCAAGGTCAATGTGATT 58.157 40.909 0.00 0.00 0.00 2.57
2602 2985 8.052748 ACATGTTATTGATGTGTACCTAACCAT 58.947 33.333 0.00 0.00 32.68 3.55
2650 3033 1.595382 CGGATAAGAAGGCCGGCAG 60.595 63.158 30.85 1.61 41.29 4.85
2733 3116 0.527565 CAAAGAATGGACCCAAGGCG 59.472 55.000 0.00 0.00 0.00 5.52
2799 3182 7.298374 AGGGTAAAAAGAACTTCAAGAAGGAT 58.702 34.615 13.83 2.88 42.53 3.24


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

AutoCloner maintained by Alex Coulton.