Multiple sequence alignment - TraesCS2B01G389100

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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 TraesCS2B01G389100 chr2B 100.000 3854 0 0 1 3854 552263655 552259802 0.000000e+00 7118.0
1 TraesCS2B01G389100 chr2B 86.111 108 11 4 3105 3211 572788927 572789031 3.150000e-21 113.0
2 TraesCS2B01G389100 chr2D 90.939 1832 117 26 2050 3854 472944531 472942722 0.000000e+00 2418.0
3 TraesCS2B01G389100 chr2D 86.338 1581 115 42 2 1541 472946609 472945089 0.000000e+00 1629.0
4 TraesCS2B01G389100 chr2D 89.860 286 24 3 1551 1834 472945030 472944748 2.830000e-96 363.0
5 TraesCS2B01G389100 chr2D 97.015 201 6 0 1822 2022 472944729 472944529 4.770000e-89 339.0
6 TraesCS2B01G389100 chr2D 87.129 101 12 1 3109 3209 464519430 464519529 3.150000e-21 113.0
7 TraesCS2B01G389100 chr2D 100.000 28 0 0 378 405 475134909 475134882 7.000000e-03 52.8
8 TraesCS2B01G389100 chr2A 91.897 1592 88 13 1551 3103 614395019 614393430 0.000000e+00 2187.0
9 TraesCS2B01G389100 chr2A 86.183 1614 134 34 4 1542 614396677 614395078 0.000000e+00 1663.0
10 TraesCS2B01G389100 chr2A 80.401 648 103 12 3223 3854 614393421 614392782 4.510000e-129 472.0
11 TraesCS2B01G389100 chr2A 88.000 100 9 3 3108 3206 690920984 690920887 8.750000e-22 115.0
12 TraesCS2B01G389100 chr2A 84.956 113 12 5 3098 3208 767943918 767944027 4.070000e-20 110.0
13 TraesCS2B01G389100 chr6A 89.000 100 8 3 3108 3206 155803754 155803851 1.880000e-23 121.0
14 TraesCS2B01G389100 chr7A 88.000 100 9 3 3108 3206 26874111 26874014 8.750000e-22 115.0
15 TraesCS2B01G389100 chr5A 88.000 100 9 3 3108 3206 84159394 84159297 8.750000e-22 115.0
16 TraesCS2B01G389100 chr5D 96.774 31 1 0 375 405 17277758 17277788 7.000000e-03 52.8
17 TraesCS2B01G389100 chr3D 96.774 31 1 0 375 405 432212950 432212980 7.000000e-03 52.8


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 TraesCS2B01G389100 chr2B 552259802 552263655 3853 True 7118.000000 7118 100.000000 1 3854 1 chr2B.!!$R1 3853
1 TraesCS2B01G389100 chr2D 472942722 472946609 3887 True 1187.250000 2418 91.038000 2 3854 4 chr2D.!!$R2 3852
2 TraesCS2B01G389100 chr2A 614392782 614396677 3895 True 1440.666667 2187 86.160333 4 3854 3 chr2A.!!$R2 3850

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
585 629 0.305617 CGTCCATGGATGATGCAACG 59.694 55.000 27.27 15.32 35.03 4.10 F
587 631 0.545646 TCCATGGATGATGCAACGGA 59.454 50.000 11.44 4.68 0.00 4.69 F
1102 1198 0.691078 CTCTCCCTTCCCCCATCGAA 60.691 60.000 0.00 0.00 0.00 3.71 F
1130 1226 1.061570 GCTTGAATTCGGCTCTGCG 59.938 57.895 13.65 0.00 0.00 5.18 F
1206 1307 1.140816 GGCGCAATATTCTCGAGTCC 58.859 55.000 13.13 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1595 0.609131 ACCACAAGGGCCAGATTTCG 60.609 55.0 6.18 0.0 42.05 3.46 R
2041 2273 0.765510 AGGAACACTCTGGGTTGACC 59.234 55.0 0.00 0.0 40.81 4.02 R
2674 2938 0.533308 TGTAAGCCCACCGTTGACAC 60.533 55.0 0.00 0.0 0.00 3.67 R
2829 3093 0.783206 ATGATTGGTTCCACCCACCA 59.217 50.0 0.00 0.0 42.90 4.17 R
3188 3453 0.324460 AGTACTCCCTCGGTCCCAAG 60.324 60.0 0.00 0.0 0.00 3.61 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
121 140 7.762159 GGAACATTTGTTTTGAGGAACACTAAA 59.238 33.333 0.00 0.00 39.11 1.85
406 443 4.007659 TCTAGAAGATTCCAAAAACCGCC 58.992 43.478 0.00 0.00 0.00 6.13
438 475 0.822121 AAAACCGGTCCTGGCAGTTC 60.822 55.000 8.04 5.71 0.00 3.01
439 476 3.530910 AACCGGTCCTGGCAGTTCG 62.531 63.158 8.04 13.17 0.00 3.95
457 494 4.982916 AGTTCGCTCGCTCGATTTATAATT 59.017 37.500 0.03 0.00 38.37 1.40
461 498 3.433615 GCTCGCTCGATTTATAATTGGCT 59.566 43.478 0.00 0.00 0.00 4.75
506 546 0.941463 CGCTACGCTAGGGATTGCAG 60.941 60.000 14.59 7.17 40.83 4.41
517 557 1.499056 GATTGCAGCGGGCGATATG 59.501 57.895 6.18 0.00 46.90 1.78
522 562 1.006220 CAGCGGGCGATATGTAGCA 60.006 57.895 0.00 0.00 34.54 3.49
527 567 1.359848 GGGCGATATGTAGCATTCGG 58.640 55.000 0.00 0.00 34.54 4.30
557 598 1.118356 AAAAGCATTTGTGGCCCCGA 61.118 50.000 0.00 0.00 39.02 5.14
558 599 1.815817 AAAGCATTTGTGGCCCCGAC 61.816 55.000 0.00 0.00 36.60 4.79
559 600 4.114997 GCATTTGTGGCCCCGACG 62.115 66.667 0.00 0.00 0.00 5.12
560 601 2.671619 CATTTGTGGCCCCGACGT 60.672 61.111 0.00 0.00 0.00 4.34
585 629 0.305617 CGTCCATGGATGATGCAACG 59.694 55.000 27.27 15.32 35.03 4.10
586 630 0.664761 GTCCATGGATGATGCAACGG 59.335 55.000 19.62 0.00 0.00 4.44
587 631 0.545646 TCCATGGATGATGCAACGGA 59.454 50.000 11.44 4.68 0.00 4.69
588 632 0.949397 CCATGGATGATGCAACGGAG 59.051 55.000 5.56 0.00 0.00 4.63
874 961 4.287845 TCCTAGTCCTATACATACAGCGGA 59.712 45.833 0.00 0.00 0.00 5.54
875 962 5.008331 CCTAGTCCTATACATACAGCGGAA 58.992 45.833 0.00 0.00 0.00 4.30
1032 1128 2.433838 CTGGAGGTGCTGCTCGTG 60.434 66.667 0.00 0.00 0.00 4.35
1079 1175 4.201930 CGACTACCTCTGTAAGCTACCTTG 60.202 50.000 0.00 0.00 32.47 3.61
1102 1198 0.691078 CTCTCCCTTCCCCCATCGAA 60.691 60.000 0.00 0.00 0.00 3.71
1108 1204 1.490490 CCTTCCCCCATCGAATTCTGA 59.510 52.381 3.52 3.30 0.00 3.27
1130 1226 1.061570 GCTTGAATTCGGCTCTGCG 59.938 57.895 13.65 0.00 0.00 5.18
1133 1229 1.197721 CTTGAATTCGGCTCTGCGTTT 59.802 47.619 0.04 0.00 0.00 3.60
1142 1238 2.920912 TCTGCGTTTCCGTCCCCT 60.921 61.111 0.00 0.00 36.15 4.79
1206 1307 1.140816 GGCGCAATATTCTCGAGTCC 58.859 55.000 13.13 0.00 0.00 3.85
1210 1311 4.049186 GCGCAATATTCTCGAGTCCTTTA 58.951 43.478 13.13 0.00 0.00 1.85
1218 1319 4.801330 TCTCGAGTCCTTTATGCTTTCA 57.199 40.909 13.13 0.00 0.00 2.69
1219 1320 4.748892 TCTCGAGTCCTTTATGCTTTCAG 58.251 43.478 13.13 0.00 0.00 3.02
1356 1457 2.100879 AAAAGAGCACCGTCGCCTCT 62.101 55.000 3.41 3.41 0.00 3.69
1374 1475 4.804665 GCCTCTGGTAAATCTCTTCGTTAC 59.195 45.833 0.00 0.00 0.00 2.50
1376 1477 5.334724 TCTGGTAAATCTCTTCGTTACCC 57.665 43.478 8.86 0.00 44.11 3.69
1381 1482 6.038985 GGTAAATCTCTTCGTTACCCTACAC 58.961 44.000 0.00 0.00 40.54 2.90
1399 1500 9.793259 ACCCTACACATATTTTGTTGATATAGG 57.207 33.333 0.00 0.00 36.00 2.57
1400 1501 9.793259 CCCTACACATATTTTGTTGATATAGGT 57.207 33.333 0.00 0.00 36.00 3.08
1438 1553 7.601856 TCTTCAATTTATGGATCAACGCTTTT 58.398 30.769 0.00 0.00 0.00 2.27
1440 1555 6.918626 TCAATTTATGGATCAACGCTTTTGA 58.081 32.000 0.00 0.57 0.00 2.69
1442 1557 8.681806 TCAATTTATGGATCAACGCTTTTGATA 58.318 29.630 9.68 0.00 39.08 2.15
1505 1620 3.548793 TGGCCCTTGTGGTCATTTT 57.451 47.368 0.00 0.00 46.23 1.82
1506 1621 1.799933 TGGCCCTTGTGGTCATTTTT 58.200 45.000 0.00 0.00 46.23 1.94
1543 1658 1.888215 CACTGGTGCTGAATGAGTGT 58.112 50.000 0.00 0.00 31.33 3.55
1544 1659 1.802960 CACTGGTGCTGAATGAGTGTC 59.197 52.381 0.00 0.00 31.33 3.67
1545 1660 1.696336 ACTGGTGCTGAATGAGTGTCT 59.304 47.619 0.00 0.00 0.00 3.41
1547 1662 1.417517 TGGTGCTGAATGAGTGTCTGT 59.582 47.619 0.00 0.00 0.00 3.41
1548 1663 2.072298 GGTGCTGAATGAGTGTCTGTC 58.928 52.381 0.00 0.00 0.00 3.51
1549 1664 2.548707 GGTGCTGAATGAGTGTCTGTCA 60.549 50.000 0.00 0.00 0.00 3.58
1600 1765 6.373774 CACTTGAACAGCAGGAAAATCTAGAT 59.626 38.462 0.00 0.00 0.00 1.98
1608 1773 8.095792 ACAGCAGGAAAATCTAGATGATCATAG 58.904 37.037 8.54 3.51 33.57 2.23
1672 1841 6.946584 CGCTAAAAGCACGTTAAGTAGTTAAG 59.053 38.462 2.89 1.54 42.58 1.85
1673 1842 7.148918 CGCTAAAAGCACGTTAAGTAGTTAAGA 60.149 37.037 2.89 0.00 42.58 2.10
1675 1844 6.775939 AAAGCACGTTAAGTAGTTAAGACC 57.224 37.500 2.89 0.00 0.00 3.85
1698 1867 4.721132 TCTTATTTTCCCACCTCGTTTGT 58.279 39.130 0.00 0.00 0.00 2.83
1704 1873 3.773418 TCCCACCTCGTTTGTGATAAA 57.227 42.857 3.85 0.00 35.74 1.40
1716 1885 5.561145 CGTTTGTGATAAACCGAATCAACCA 60.561 40.000 0.00 0.00 35.23 3.67
1765 1936 7.962964 TGAAATTCATCAAGACGTAAAGAGT 57.037 32.000 0.00 0.00 0.00 3.24
1767 1938 9.483916 TGAAATTCATCAAGACGTAAAGAGTAA 57.516 29.630 0.00 0.00 0.00 2.24
1769 1940 6.922980 TTCATCAAGACGTAAAGAGTAACG 57.077 37.500 0.00 0.00 44.47 3.18
1831 2002 8.593679 TGACTTCCTTATGAGATGTAACTTGAA 58.406 33.333 0.00 0.00 0.00 2.69
1840 2042 5.869344 TGAGATGTAACTTGAATTCACTCGG 59.131 40.000 7.89 1.78 0.00 4.63
1844 2046 1.148310 ACTTGAATTCACTCGGTGCG 58.852 50.000 7.89 0.00 32.98 5.34
1911 2113 1.620819 ACCGTCTCTGAGAATGCAACT 59.379 47.619 9.31 0.00 0.00 3.16
1917 2119 3.007723 TCTCTGAGAATGCAACTGAGCTT 59.992 43.478 4.57 0.00 34.99 3.74
2022 2254 3.701040 AGCAATTTTGGTCTTGTGTCAGT 59.299 39.130 0.00 0.00 32.71 3.41
2023 2255 4.160252 AGCAATTTTGGTCTTGTGTCAGTT 59.840 37.500 0.00 0.00 32.71 3.16
2024 2256 4.869861 GCAATTTTGGTCTTGTGTCAGTTT 59.130 37.500 0.00 0.00 0.00 2.66
2025 2257 5.005682 GCAATTTTGGTCTTGTGTCAGTTTC 59.994 40.000 0.00 0.00 0.00 2.78
2026 2258 6.332630 CAATTTTGGTCTTGTGTCAGTTTCT 58.667 36.000 0.00 0.00 0.00 2.52
2027 2259 7.479980 CAATTTTGGTCTTGTGTCAGTTTCTA 58.520 34.615 0.00 0.00 0.00 2.10
2028 2260 7.823745 ATTTTGGTCTTGTGTCAGTTTCTAT 57.176 32.000 0.00 0.00 0.00 1.98
2029 2261 6.861065 TTTGGTCTTGTGTCAGTTTCTATC 57.139 37.500 0.00 0.00 0.00 2.08
2030 2262 4.894784 TGGTCTTGTGTCAGTTTCTATCC 58.105 43.478 0.00 0.00 0.00 2.59
2031 2263 3.927142 GGTCTTGTGTCAGTTTCTATCCG 59.073 47.826 0.00 0.00 0.00 4.18
2032 2264 4.557205 GTCTTGTGTCAGTTTCTATCCGT 58.443 43.478 0.00 0.00 0.00 4.69
2033 2265 4.386049 GTCTTGTGTCAGTTTCTATCCGTG 59.614 45.833 0.00 0.00 0.00 4.94
2034 2266 4.279922 TCTTGTGTCAGTTTCTATCCGTGA 59.720 41.667 0.00 0.00 0.00 4.35
2035 2267 4.594123 TGTGTCAGTTTCTATCCGTGAA 57.406 40.909 0.00 0.00 0.00 3.18
2036 2268 4.556233 TGTGTCAGTTTCTATCCGTGAAG 58.444 43.478 0.00 0.00 0.00 3.02
2037 2269 4.279922 TGTGTCAGTTTCTATCCGTGAAGA 59.720 41.667 0.00 0.00 0.00 2.87
2038 2270 5.047306 TGTGTCAGTTTCTATCCGTGAAGAT 60.047 40.000 0.00 0.00 0.00 2.40
2039 2271 5.289675 GTGTCAGTTTCTATCCGTGAAGATG 59.710 44.000 0.00 0.00 0.00 2.90
2040 2272 5.047306 TGTCAGTTTCTATCCGTGAAGATGT 60.047 40.000 0.00 0.00 0.00 3.06
2041 2273 5.289675 GTCAGTTTCTATCCGTGAAGATGTG 59.710 44.000 0.00 0.00 0.00 3.21
2042 2274 4.568359 CAGTTTCTATCCGTGAAGATGTGG 59.432 45.833 0.00 0.00 0.00 4.17
2043 2275 4.223032 AGTTTCTATCCGTGAAGATGTGGT 59.777 41.667 0.00 0.00 0.00 4.16
2044 2276 4.386867 TTCTATCCGTGAAGATGTGGTC 57.613 45.455 0.00 0.00 0.00 4.02
2045 2277 3.361786 TCTATCCGTGAAGATGTGGTCA 58.638 45.455 0.00 0.00 0.00 4.02
2046 2278 3.767131 TCTATCCGTGAAGATGTGGTCAA 59.233 43.478 0.00 0.00 0.00 3.18
2047 2279 2.163818 TCCGTGAAGATGTGGTCAAC 57.836 50.000 0.00 0.00 0.00 3.18
2048 2280 1.156736 CCGTGAAGATGTGGTCAACC 58.843 55.000 0.00 0.00 0.00 3.77
2049 2281 1.156736 CGTGAAGATGTGGTCAACCC 58.843 55.000 0.00 0.00 34.29 4.11
2050 2282 1.542328 CGTGAAGATGTGGTCAACCCA 60.542 52.381 0.00 0.00 42.51 4.51
2051 2283 2.154462 GTGAAGATGTGGTCAACCCAG 58.846 52.381 0.00 0.00 46.45 4.45
2095 2327 1.583054 GGCTGGCGGTCTTACATAAG 58.417 55.000 0.00 0.00 34.65 1.73
2137 2369 6.474102 GGCGAAATCTGTTTTTGAAACACTTA 59.526 34.615 2.34 0.00 31.22 2.24
2147 2379 7.224753 TGTTTTTGAAACACTTACAGTTTGCAA 59.775 29.630 0.00 0.00 39.15 4.08
2162 2394 4.083324 AGTTTGCAATTCGATTGATGTCGT 60.083 37.500 0.00 0.00 42.83 4.34
2222 2456 5.046529 GCATCATCCACTACAACTGAGTAG 58.953 45.833 9.37 9.37 45.44 2.57
2329 2563 6.238648 AGAGTACCGTGGAGAAATCAAAATT 58.761 36.000 0.00 0.00 0.00 1.82
2386 2620 4.993705 TTCATGTTCAGGGACTAAACCT 57.006 40.909 0.00 0.00 36.02 3.50
2424 2658 2.563179 TCCTCTGTTTCTCTGTGGCTAC 59.437 50.000 0.00 0.00 0.00 3.58
2505 2746 7.482654 AACACATATGATAAACTGATCACCG 57.517 36.000 10.38 0.00 38.64 4.94
2507 2748 5.698089 CACATATGATAAACTGATCACCGCT 59.302 40.000 10.38 0.00 38.64 5.52
2518 2759 3.086282 TGATCACCGCTACACAGTTAGA 58.914 45.455 0.00 0.00 0.00 2.10
2546 2787 7.552050 AATTCTTCTACTCCCTCCATAGATG 57.448 40.000 0.00 0.00 0.00 2.90
2549 2791 3.501349 TCTACTCCCTCCATAGATGCAC 58.499 50.000 0.00 0.00 0.00 4.57
2565 2807 1.852067 GCACCCGTTTGAGCGACAAT 61.852 55.000 0.00 0.00 38.36 2.71
2603 2845 6.552932 AGGAAGTACCATCTTTTAGCCTTTT 58.447 36.000 0.00 0.00 42.04 2.27
2652 2908 4.508662 CGGTCTTCTTTTATGCTCCTTCT 58.491 43.478 0.00 0.00 0.00 2.85
2829 3093 3.780850 AGGATCAACCCGAGGAAAACTAT 59.219 43.478 0.00 0.00 40.05 2.12
2953 3217 4.935808 AGACTGTATTTGTCGTTGATTCCC 59.064 41.667 0.00 0.00 39.24 3.97
2973 3237 6.037786 TCCCTCAATTATGGATAAGCTACG 57.962 41.667 0.00 0.00 0.00 3.51
3113 3378 5.710567 GGCCCCATTTCTTATGTAATACTCC 59.289 44.000 0.00 0.00 0.00 3.85
3118 3383 7.661847 CCCATTTCTTATGTAATACTCCACTCC 59.338 40.741 0.00 0.00 0.00 3.85
3119 3384 7.385205 CCATTTCTTATGTAATACTCCACTCCG 59.615 40.741 0.00 0.00 0.00 4.63
3145 3410 8.573035 GTCCCAAAATAAGTGTCTCAACATTAA 58.427 33.333 0.00 0.00 37.81 1.40
3182 3447 3.838244 AGTTGTACTGAAGTTGAGGCA 57.162 42.857 0.00 0.00 0.00 4.75
3188 3453 5.479306 TGTACTGAAGTTGAGGCACTTATC 58.521 41.667 0.00 0.00 41.55 1.75
3190 3455 5.234466 ACTGAAGTTGAGGCACTTATCTT 57.766 39.130 0.00 0.00 41.55 2.40
3191 3456 4.999950 ACTGAAGTTGAGGCACTTATCTTG 59.000 41.667 0.00 0.00 41.55 3.02
3193 3458 3.356529 AGTTGAGGCACTTATCTTGGG 57.643 47.619 0.00 0.00 41.55 4.12
3228 3493 5.084519 ACTAGAGAACTGGTGATGGTTGTA 58.915 41.667 0.00 0.00 36.51 2.41
3240 3505 5.394443 GGTGATGGTTGTATGCATCAATTGT 60.394 40.000 0.19 0.00 36.06 2.71
3244 3509 5.635866 TGGTTGTATGCATCAATTGTTACG 58.364 37.500 0.19 0.00 0.00 3.18
3249 3514 5.645929 TGTATGCATCAATTGTTACGAAGGT 59.354 36.000 0.19 0.00 0.00 3.50
3252 3517 4.699735 TGCATCAATTGTTACGAAGGTCAT 59.300 37.500 5.13 0.00 0.00 3.06
3279 3544 3.007074 ACTCCCTCGTCTTTCTTCCTTTC 59.993 47.826 0.00 0.00 0.00 2.62
3283 3548 3.006967 CCTCGTCTTTCTTCCTTTCTGGA 59.993 47.826 0.00 0.00 44.51 3.86
3310 3575 6.656632 AAGTGTATCTTCTGTGTTCTCTCA 57.343 37.500 0.00 0.00 0.00 3.27
3324 3589 2.382882 TCTCTCATCGATGGTGCTTCT 58.617 47.619 24.61 0.00 0.00 2.85
3351 3616 8.786826 TTTTTGTCGTAGATATTCAATCTGGT 57.213 30.769 0.00 0.00 40.67 4.00
3357 3623 6.715264 TCGTAGATATTCAATCTGGTAGCAGA 59.285 38.462 25.72 25.72 35.46 4.26
3386 3652 6.096423 GGATGAAACCCTCTTATAACAAACCC 59.904 42.308 0.00 0.00 0.00 4.11
3401 3667 0.837272 AACCCTATCGTCCATGGTGG 59.163 55.000 12.58 5.00 39.43 4.61
3478 3744 3.450507 TGGCGACACTTTCTCCGA 58.549 55.556 0.00 0.00 30.76 4.55
3481 3747 1.372997 GCGACACTTTCTCCGAGCA 60.373 57.895 0.00 0.00 0.00 4.26
3491 3757 5.409826 CACTTTCTCCGAGCAAAAGAGTTAT 59.590 40.000 13.77 0.00 34.76 1.89
3494 3760 3.260884 TCTCCGAGCAAAAGAGTTATGGT 59.739 43.478 0.00 0.00 0.00 3.55
3499 3765 4.452455 CGAGCAAAAGAGTTATGGTGACTT 59.548 41.667 0.00 0.00 0.00 3.01
3516 3782 5.922544 GGTGACTTTGACATCCTTGATTTTG 59.077 40.000 0.00 0.00 0.00 2.44
3544 3810 4.934075 TTGATCATGCTTTTCGTCTCTG 57.066 40.909 0.00 0.00 0.00 3.35
3603 3869 8.770010 AGTAGAGCTTCAATAGTGGTACTAAT 57.230 34.615 0.00 0.00 33.89 1.73
3629 3895 3.963428 AAAGCTGGTACTACTGTGAGG 57.037 47.619 0.00 0.00 0.00 3.86
3675 3945 2.209315 CCTGTTTGGGGTTGCCCTG 61.209 63.158 4.02 0.00 44.66 4.45
3688 3958 1.067916 GCCCTGGTTGTTGTGCTTG 59.932 57.895 0.00 0.00 0.00 4.01
3720 3990 1.000163 CTATCGGGTTCTCATGTCGGG 60.000 57.143 0.00 0.00 0.00 5.14
3767 4047 4.702081 GCGCTCCGTCGACACTGT 62.702 66.667 17.16 0.00 0.00 3.55
3768 4048 2.050351 CGCTCCGTCGACACTGTT 60.050 61.111 17.16 0.00 0.00 3.16
3782 4062 4.264380 CGACACTGTTAAGTTTTGGTTTGC 59.736 41.667 0.00 0.00 32.98 3.68
3786 4066 7.200455 ACACTGTTAAGTTTTGGTTTGCTATC 58.800 34.615 0.00 0.00 32.98 2.08
3790 4070 2.235016 AGTTTTGGTTTGCTATCGCCA 58.765 42.857 0.00 0.00 34.43 5.69
3796 4076 2.625790 TGGTTTGCTATCGCCAACTTTT 59.374 40.909 6.20 0.00 40.53 2.27
3803 4083 7.618502 TTGCTATCGCCAACTTTTTATTCTA 57.381 32.000 0.00 0.00 34.43 2.10
3834 4114 3.865011 TGTTGTCTGCTTGCTTTTTCA 57.135 38.095 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.301153 GTTCACAACTTTAAGAAATGTTCACAT 57.699 29.630 0.00 0.00 38.41 3.21
386 423 4.028993 AGGCGGTTTTTGGAATCTTCTA 57.971 40.909 0.00 0.00 0.00 2.10
388 425 3.128764 CCTAGGCGGTTTTTGGAATCTTC 59.871 47.826 0.00 0.00 0.00 2.87
392 429 2.823747 GTTCCTAGGCGGTTTTTGGAAT 59.176 45.455 2.96 0.00 36.23 3.01
406 443 3.999001 GACCGGTTTTACAAGGTTCCTAG 59.001 47.826 9.42 0.00 37.07 3.02
438 475 3.722082 GCCAATTATAAATCGAGCGAGCG 60.722 47.826 0.00 0.00 0.00 5.03
439 476 3.433615 AGCCAATTATAAATCGAGCGAGC 59.566 43.478 0.00 0.00 0.00 5.03
506 546 0.721718 GAATGCTACATATCGCCCGC 59.278 55.000 0.00 0.00 0.00 6.13
517 557 0.756903 TTAGAGGCCCCGAATGCTAC 59.243 55.000 0.00 0.00 0.00 3.58
558 599 3.680620 ATCCATGGACGGTGGCACG 62.681 63.158 18.99 9.61 36.66 5.34
559 600 2.114670 CATCCATGGACGGTGGCAC 61.115 63.158 18.99 9.70 36.66 5.01
560 601 1.634865 ATCATCCATGGACGGTGGCA 61.635 55.000 18.99 0.00 36.66 4.92
585 629 4.285851 GCAGGTGCAGTGTACTCC 57.714 61.111 11.32 0.00 41.59 3.85
644 688 0.255890 ATGATTGGGGAACGACAGGG 59.744 55.000 0.00 0.00 0.00 4.45
648 692 2.122783 TTGGATGATTGGGGAACGAC 57.877 50.000 0.00 0.00 0.00 4.34
652 696 1.753847 GCCGATTGGATGATTGGGGAA 60.754 52.381 1.98 0.00 37.49 3.97
681 725 3.475774 CGCGTGTCTGCCCGTAAC 61.476 66.667 0.00 0.00 0.00 2.50
710 754 4.678743 GGGGGCGGTGGCTTCTTT 62.679 66.667 0.00 0.00 39.81 2.52
785 834 1.200519 GGTGTGTGGTAGGGCATAGA 58.799 55.000 0.00 0.00 0.00 1.98
836 923 6.610830 AGGACTAGGAGTTGAAAAATGGAAA 58.389 36.000 0.00 0.00 0.00 3.13
1091 1187 2.369860 CAGATCAGAATTCGATGGGGGA 59.630 50.000 14.65 1.22 0.00 4.81
1102 1198 3.314635 GCCGAATTCAAGCAGATCAGAAT 59.685 43.478 11.55 0.00 32.45 2.40
1108 1204 2.286872 CAGAGCCGAATTCAAGCAGAT 58.713 47.619 17.14 0.00 0.00 2.90
1130 1226 2.240162 ATCGAGCAGGGGACGGAAAC 62.240 60.000 0.00 0.00 0.00 2.78
1133 1229 2.833582 GATCGAGCAGGGGACGGA 60.834 66.667 0.00 0.00 0.00 4.69
1206 1307 5.754890 ACCAGCAAAAACTGAAAGCATAAAG 59.245 36.000 0.00 0.00 40.25 1.85
1210 1311 3.385755 AGACCAGCAAAAACTGAAAGCAT 59.614 39.130 0.00 0.00 40.25 3.79
1218 1319 4.985538 TCCATTAGAGACCAGCAAAAACT 58.014 39.130 0.00 0.00 0.00 2.66
1219 1320 5.393461 CCATCCATTAGAGACCAGCAAAAAC 60.393 44.000 0.00 0.00 0.00 2.43
1338 1439 2.048127 GAGGCGACGGTGCTCTTT 60.048 61.111 0.00 0.00 34.52 2.52
1356 1457 5.716228 TGTAGGGTAACGAAGAGATTTACCA 59.284 40.000 10.97 0.00 44.54 3.25
1374 1475 9.793259 ACCTATATCAACAAAATATGTGTAGGG 57.207 33.333 0.00 0.00 42.99 3.53
1425 1540 8.827677 ACTACTAATTATCAAAAGCGTTGATCC 58.172 33.333 18.38 0.00 39.59 3.36
1466 1581 7.067494 GGGCCAGATTTCGCTATCAATAATAAT 59.933 37.037 4.39 0.00 0.00 1.28
1467 1582 6.374333 GGGCCAGATTTCGCTATCAATAATAA 59.626 38.462 4.39 0.00 0.00 1.40
1468 1583 5.880332 GGGCCAGATTTCGCTATCAATAATA 59.120 40.000 4.39 0.00 0.00 0.98
1469 1584 4.702131 GGGCCAGATTTCGCTATCAATAAT 59.298 41.667 4.39 0.00 0.00 1.28
1473 1588 1.490490 AGGGCCAGATTTCGCTATCAA 59.510 47.619 6.18 0.00 0.00 2.57
1480 1595 0.609131 ACCACAAGGGCCAGATTTCG 60.609 55.000 6.18 0.00 42.05 3.46
1542 1657 3.254166 ACTGACATGGCAAAATGACAGAC 59.746 43.478 20.35 0.00 46.53 3.51
1543 1658 3.489355 ACTGACATGGCAAAATGACAGA 58.511 40.909 20.35 0.00 46.53 3.41
1545 1660 5.243507 ACATTACTGACATGGCAAAATGACA 59.756 36.000 29.73 3.66 41.29 3.58
1547 1662 5.711506 AGACATTACTGACATGGCAAAATGA 59.288 36.000 29.73 8.26 31.22 2.57
1548 1663 5.803461 CAGACATTACTGACATGGCAAAATG 59.197 40.000 24.72 24.72 39.94 2.32
1549 1664 5.105635 CCAGACATTACTGACATGGCAAAAT 60.106 40.000 1.11 2.56 39.94 1.82
1600 1765 5.238650 TCGATCTGCGTTCTTACTATGATCA 59.761 40.000 0.00 0.00 41.80 2.92
1608 1773 4.352039 TCTGAATCGATCTGCGTTCTTAC 58.648 43.478 0.00 0.00 41.80 2.34
1672 1841 3.055312 ACGAGGTGGGAAAATAAGAGGTC 60.055 47.826 0.00 0.00 0.00 3.85
1673 1842 2.910977 ACGAGGTGGGAAAATAAGAGGT 59.089 45.455 0.00 0.00 0.00 3.85
1675 1844 4.760204 ACAAACGAGGTGGGAAAATAAGAG 59.240 41.667 0.00 0.00 0.00 2.85
1698 1867 4.849518 TCCATGGTTGATTCGGTTTATCA 58.150 39.130 12.58 0.00 0.00 2.15
1704 1873 1.846439 AGGATCCATGGTTGATTCGGT 59.154 47.619 15.82 0.00 0.00 4.69
1740 1909 8.553459 ACTCTTTACGTCTTGATGAATTTCAT 57.447 30.769 11.64 11.64 40.34 2.57
1743 1912 8.433126 CGTTACTCTTTACGTCTTGATGAATTT 58.567 33.333 0.00 0.00 33.33 1.82
1759 1930 4.820897 TGAGATGCATGACGTTACTCTTT 58.179 39.130 2.46 0.00 0.00 2.52
1762 1933 5.075670 CATTGAGATGCATGACGTTACTC 57.924 43.478 2.46 2.86 0.00 2.59
1787 1958 4.645535 AGTCAATAGCACACATGAACAGT 58.354 39.130 0.00 0.00 0.00 3.55
1792 1963 4.558226 AGGAAGTCAATAGCACACATGA 57.442 40.909 0.00 0.00 0.00 3.07
1831 2002 2.029288 CTGCACGCACCGAGTGAAT 61.029 57.895 8.04 0.00 41.83 2.57
1840 2042 1.856265 CTTCCCTTTCCTGCACGCAC 61.856 60.000 0.00 0.00 0.00 5.34
1844 2046 2.087646 GATCACTTCCCTTTCCTGCAC 58.912 52.381 0.00 0.00 0.00 4.57
1917 2119 2.899900 ACTGTCCAGTAGCTTGATGACA 59.100 45.455 0.00 0.00 40.43 3.58
1929 2131 1.376466 GCCACCATCACTGTCCAGT 59.624 57.895 0.00 0.00 43.61 4.00
2022 2254 4.221924 TGACCACATCTTCACGGATAGAAA 59.778 41.667 0.00 0.00 0.00 2.52
2023 2255 3.767131 TGACCACATCTTCACGGATAGAA 59.233 43.478 0.00 0.00 0.00 2.10
2024 2256 3.361786 TGACCACATCTTCACGGATAGA 58.638 45.455 0.00 0.00 0.00 1.98
2025 2257 3.801114 TGACCACATCTTCACGGATAG 57.199 47.619 0.00 0.00 0.00 2.08
2026 2258 3.369052 GGTTGACCACATCTTCACGGATA 60.369 47.826 0.00 0.00 35.64 2.59
2027 2259 2.615493 GGTTGACCACATCTTCACGGAT 60.615 50.000 0.00 0.00 35.64 4.18
2028 2260 1.270625 GGTTGACCACATCTTCACGGA 60.271 52.381 0.00 0.00 35.64 4.69
2029 2261 1.156736 GGTTGACCACATCTTCACGG 58.843 55.000 0.00 0.00 35.64 4.94
2030 2262 1.156736 GGGTTGACCACATCTTCACG 58.843 55.000 2.12 0.00 39.85 4.35
2031 2263 2.154462 CTGGGTTGACCACATCTTCAC 58.846 52.381 2.12 0.00 46.80 3.18
2032 2264 2.038952 CTCTGGGTTGACCACATCTTCA 59.961 50.000 2.12 0.00 46.80 3.02
2033 2265 2.039084 ACTCTGGGTTGACCACATCTTC 59.961 50.000 2.12 0.00 46.80 2.87
2034 2266 2.057922 ACTCTGGGTTGACCACATCTT 58.942 47.619 2.12 0.00 46.80 2.40
2035 2267 1.349026 CACTCTGGGTTGACCACATCT 59.651 52.381 2.12 0.00 46.80 2.90
2036 2268 1.072331 ACACTCTGGGTTGACCACATC 59.928 52.381 2.12 0.00 46.80 3.06
2037 2269 1.140312 ACACTCTGGGTTGACCACAT 58.860 50.000 2.12 0.00 46.80 3.21
2038 2270 0.916086 AACACTCTGGGTTGACCACA 59.084 50.000 2.12 0.00 46.80 4.17
2039 2271 1.594331 GAACACTCTGGGTTGACCAC 58.406 55.000 2.12 0.00 46.80 4.16
2041 2273 0.765510 AGGAACACTCTGGGTTGACC 59.234 55.000 0.00 0.00 40.81 4.02
2042 2274 2.618709 CAAAGGAACACTCTGGGTTGAC 59.381 50.000 0.00 0.00 0.00 3.18
2043 2275 2.507886 TCAAAGGAACACTCTGGGTTGA 59.492 45.455 0.00 0.00 0.00 3.18
2044 2276 2.880890 CTCAAAGGAACACTCTGGGTTG 59.119 50.000 0.00 0.00 0.00 3.77
2045 2277 2.509964 ACTCAAAGGAACACTCTGGGTT 59.490 45.455 0.00 0.00 0.00 4.11
2046 2278 2.127708 ACTCAAAGGAACACTCTGGGT 58.872 47.619 0.00 0.00 0.00 4.51
2047 2279 2.938956 ACTCAAAGGAACACTCTGGG 57.061 50.000 0.00 0.00 0.00 4.45
2048 2280 4.962155 ACTAACTCAAAGGAACACTCTGG 58.038 43.478 0.00 0.00 0.00 3.86
2049 2281 5.817816 ACAACTAACTCAAAGGAACACTCTG 59.182 40.000 0.00 0.00 0.00 3.35
2050 2282 5.817816 CACAACTAACTCAAAGGAACACTCT 59.182 40.000 0.00 0.00 0.00 3.24
2051 2283 5.007724 CCACAACTAACTCAAAGGAACACTC 59.992 44.000 0.00 0.00 0.00 3.51
2095 2327 1.666888 CGCCAAACATTTGAGCCAGTC 60.667 52.381 5.91 0.00 40.55 3.51
2137 2369 5.125100 ACATCAATCGAATTGCAAACTGT 57.875 34.783 1.71 0.00 40.05 3.55
2169 2401 4.685924 GATCATTCAATTTTGCATCCCGT 58.314 39.130 0.00 0.00 0.00 5.28
2222 2456 2.726821 TGGGATCCTGCAAGAATCAAC 58.273 47.619 12.58 0.00 34.07 3.18
2329 2563 1.658114 CGGAGTGAACGTCAGACCA 59.342 57.895 0.00 0.00 0.00 4.02
2386 2620 3.133362 AGAGGACACGGTAAAGTGAAACA 59.867 43.478 4.00 0.00 44.43 2.83
2424 2658 5.867716 ACAGTTACTAATGCAGACGTTTAGG 59.132 40.000 8.48 0.00 0.00 2.69
2505 2746 8.934507 AGAAGAATTACATCTAACTGTGTAGC 57.065 34.615 0.00 0.00 32.87 3.58
2518 2759 8.235230 TCTATGGAGGGAGTAGAAGAATTACAT 58.765 37.037 0.00 0.00 0.00 2.29
2546 2787 1.852067 ATTGTCGCTCAAACGGGTGC 61.852 55.000 0.00 0.00 39.62 5.01
2549 2791 2.224549 TGTTAATTGTCGCTCAAACGGG 59.775 45.455 0.00 0.00 39.62 5.28
2565 2807 4.100498 GGTACTTCCTCCGATCCATGTTAA 59.900 45.833 0.00 0.00 0.00 2.01
2619 2874 5.402997 AAAAGAAGACCGGGTTACTCTAG 57.597 43.478 6.32 0.00 0.00 2.43
2674 2938 0.533308 TGTAAGCCCACCGTTGACAC 60.533 55.000 0.00 0.00 0.00 3.67
2829 3093 0.783206 ATGATTGGTTCCACCCACCA 59.217 50.000 0.00 0.00 42.90 4.17
2953 3217 8.994429 AGATTCGTAGCTTATCCATAATTGAG 57.006 34.615 0.00 0.00 0.00 3.02
3118 3383 4.513692 TGTTGAGACACTTATTTTGGGACG 59.486 41.667 0.00 0.00 0.00 4.79
3119 3384 6.575162 ATGTTGAGACACTTATTTTGGGAC 57.425 37.500 0.00 0.00 38.91 4.46
3155 3420 7.603024 GCCTCAACTTCAGTACAACTTTAGTAT 59.397 37.037 0.00 0.00 0.00 2.12
3156 3421 6.927381 GCCTCAACTTCAGTACAACTTTAGTA 59.073 38.462 0.00 0.00 0.00 1.82
3157 3422 5.758784 GCCTCAACTTCAGTACAACTTTAGT 59.241 40.000 0.00 0.00 0.00 2.24
3158 3423 5.758296 TGCCTCAACTTCAGTACAACTTTAG 59.242 40.000 0.00 0.00 0.00 1.85
3159 3424 5.526111 GTGCCTCAACTTCAGTACAACTTTA 59.474 40.000 0.00 0.00 0.00 1.85
3160 3425 4.335594 GTGCCTCAACTTCAGTACAACTTT 59.664 41.667 0.00 0.00 0.00 2.66
3161 3426 3.877508 GTGCCTCAACTTCAGTACAACTT 59.122 43.478 0.00 0.00 0.00 2.66
3162 3427 3.134804 AGTGCCTCAACTTCAGTACAACT 59.865 43.478 0.00 0.00 0.00 3.16
3163 3428 3.467803 AGTGCCTCAACTTCAGTACAAC 58.532 45.455 0.00 0.00 0.00 3.32
3164 3429 3.838244 AGTGCCTCAACTTCAGTACAA 57.162 42.857 0.00 0.00 0.00 2.41
3171 3436 3.691609 CCCAAGATAAGTGCCTCAACTTC 59.308 47.826 0.00 0.00 40.77 3.01
3182 3447 1.007963 TCCCTCGGTCCCAAGATAAGT 59.992 52.381 0.00 0.00 0.00 2.24
3188 3453 0.324460 AGTACTCCCTCGGTCCCAAG 60.324 60.000 0.00 0.00 0.00 3.61
3190 3455 0.549950 CTAGTACTCCCTCGGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
3191 3456 0.842635 TCTAGTACTCCCTCGGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
3193 3458 3.118298 AGTTCTCTAGTACTCCCTCGGTC 60.118 52.174 0.00 0.00 0.00 4.79
3228 3493 4.699735 TGACCTTCGTAACAATTGATGCAT 59.300 37.500 13.59 0.00 0.00 3.96
3240 3505 0.981183 AGTGCCCATGACCTTCGTAA 59.019 50.000 0.00 0.00 0.00 3.18
3244 3509 4.645809 GGAGTGCCCATGACCTTC 57.354 61.111 0.00 0.00 34.14 3.46
3300 3565 1.929836 GCACCATCGATGAGAGAACAC 59.070 52.381 26.86 3.53 0.00 3.32
3351 3616 3.387962 AGGGTTTCATCCTCATCTGCTA 58.612 45.455 0.00 0.00 0.00 3.49
3383 3649 1.696097 GCCACCATGGACGATAGGGT 61.696 60.000 21.47 0.00 40.96 4.34
3386 3652 4.779475 GGCCACCATGGACGATAG 57.221 61.111 21.47 0.86 40.96 2.08
3409 3675 7.326063 CACTTAGGAATTCGAATGACCAAAAAC 59.674 37.037 25.84 7.73 0.00 2.43
3427 3693 8.221944 TCAATTCTTTTTAGTTCCCACTTAGGA 58.778 33.333 0.00 0.00 41.22 2.94
3428 3694 8.297426 GTCAATTCTTTTTAGTTCCCACTTAGG 58.703 37.037 0.00 0.00 34.06 2.69
3472 3738 3.260884 ACCATAACTCTTTTGCTCGGAGA 59.739 43.478 9.69 0.00 0.00 3.71
3474 3740 3.007506 TCACCATAACTCTTTTGCTCGGA 59.992 43.478 0.00 0.00 0.00 4.55
3478 3744 5.827797 TCAAAGTCACCATAACTCTTTTGCT 59.172 36.000 0.00 0.00 0.00 3.91
3481 3747 7.040409 GGATGTCAAAGTCACCATAACTCTTTT 60.040 37.037 0.00 0.00 0.00 2.27
3491 3757 3.855255 TCAAGGATGTCAAAGTCACCA 57.145 42.857 0.00 0.00 0.00 4.17
3494 3760 6.320926 TGTCAAAATCAAGGATGTCAAAGTCA 59.679 34.615 0.00 0.00 0.00 3.41
3499 3765 6.713762 ACTTGTCAAAATCAAGGATGTCAA 57.286 33.333 9.82 0.00 44.29 3.18
3516 3782 5.215160 ACGAAAAGCATGATCAAACTTGTC 58.785 37.500 16.18 16.18 0.00 3.18
3544 3810 3.072211 GCTCAGTAAAACCACTACCACC 58.928 50.000 0.00 0.00 0.00 4.61
3603 3869 5.070714 TCACAGTAGTACCAGCTTTAAACCA 59.929 40.000 0.00 0.00 0.00 3.67
3629 3895 3.760580 CCTCCCAACATAGAGGTCATC 57.239 52.381 0.00 0.00 44.01 2.92
3654 3920 3.135027 GGCAACCCCAAACAGGTTA 57.865 52.632 0.00 0.00 45.96 2.85
3675 3945 2.794631 CGACTTTCCAAGCACAACAACC 60.795 50.000 0.00 0.00 0.00 3.77
3688 3958 1.479730 ACCCGATAGTTCCGACTTTCC 59.520 52.381 0.00 0.00 37.33 3.13
3720 3990 2.668945 GCAACTAAGACGAGAAAGGCTC 59.331 50.000 0.00 0.00 40.38 4.70
3731 4011 2.924290 CGCTGGACTTAGCAACTAAGAC 59.076 50.000 18.66 13.09 44.24 3.01
3782 4062 9.482627 AGATCTAGAATAAAAAGTTGGCGATAG 57.517 33.333 0.00 0.00 0.00 2.08
3786 4066 7.711339 ACCTAGATCTAGAATAAAAAGTTGGCG 59.289 37.037 28.04 9.91 35.21 5.69
3803 4083 4.899352 AGCAGACAACAAACCTAGATCT 57.101 40.909 0.00 0.00 0.00 2.75
3809 4089 1.767759 AGCAAGCAGACAACAAACCT 58.232 45.000 0.00 0.00 0.00 3.50
3819 4099 5.120519 CACAAAAACTGAAAAAGCAAGCAGA 59.879 36.000 0.00 0.00 32.86 4.26


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

AutoCloner maintained by Alex Coulton.