Multiple sequence alignment - TraesCS2D01G459700

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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 TraesCS2D01G459700 chr2D 100.000 2773 0 0 1 2773 566303941 566301169 0.000000e+00 5121.0
1 TraesCS2D01G459700 chr2D 91.097 629 38 6 1481 2093 566656239 566655613 0.000000e+00 835.0
2 TraesCS2D01G459700 chr2D 86.261 575 69 5 1520 2094 558376217 558376781 1.550000e-172 616.0
3 TraesCS2D01G459700 chr2D 85.740 547 64 12 1562 2094 566262324 566261778 1.580000e-157 566.0
4 TraesCS2D01G459700 chr2D 88.312 462 25 12 569 1010 566263306 566262854 7.470000e-146 527.0
5 TraesCS2D01G459700 chr2D 84.949 392 43 10 2126 2503 130428042 130427653 1.710000e-102 383.0
6 TraesCS2D01G459700 chr2D 84.173 417 38 12 1007 1419 566656620 566656228 2.210000e-101 379.0
7 TraesCS2D01G459700 chr2D 83.744 406 52 8 2107 2501 606603327 606602925 3.710000e-99 372.0
8 TraesCS2D01G459700 chr2D 82.162 370 46 11 1013 1368 566262812 566262449 1.770000e-77 300.0
9 TraesCS2D01G459700 chr2D 95.238 84 2 1 467 550 566263371 566263290 6.850000e-27 132.0
10 TraesCS2D01G459700 chr2D 85.577 104 14 1 74 177 566303756 566303654 1.150000e-19 108.0
11 TraesCS2D01G459700 chr2D 85.577 104 14 1 186 288 566303868 566303765 1.150000e-19 108.0
12 TraesCS2D01G459700 chr2D 96.774 62 2 0 224 285 566263758 566263697 1.490000e-18 104.0
13 TraesCS2D01G459700 chr2D 95.312 64 2 1 1418 1481 55921413 55921351 1.930000e-17 100.0
14 TraesCS2D01G459700 chr2D 95.082 61 3 0 1421 1481 168645975 168645915 2.500000e-16 97.1
15 TraesCS2D01G459700 chr2D 100.000 32 0 0 3012 3043 566300930 566300899 3.280000e-05 60.2
16 TraesCS2D01G459700 chr2B 94.842 1299 52 9 1481 2773 679071201 679069912 0.000000e+00 2013.0
17 TraesCS2D01G459700 chr2B 90.347 1181 44 27 289 1424 679072340 679071185 0.000000e+00 1485.0
18 TraesCS2D01G459700 chr2B 91.270 630 39 5 1481 2094 679696943 679697572 0.000000e+00 845.0
19 TraesCS2D01G459700 chr2B 92.416 567 40 3 1529 2094 679743801 679744365 0.000000e+00 806.0
20 TraesCS2D01G459700 chr2B 87.199 539 64 3 1562 2095 679030813 679030275 2.590000e-170 608.0
21 TraesCS2D01G459700 chr2B 88.720 461 24 11 569 1010 679031773 679031322 3.450000e-149 538.0
22 TraesCS2D01G459700 chr2B 85.060 415 36 8 1007 1421 679696568 679696956 1.700000e-107 399.0
23 TraesCS2D01G459700 chr2B 85.122 410 35 8 1007 1416 679730097 679730480 2.200000e-106 396.0
24 TraesCS2D01G459700 chr2B 80.691 492 62 15 2 488 679032310 679031847 4.830000e-93 351.0
25 TraesCS2D01G459700 chr2B 81.044 364 44 17 1010 1368 679031283 679030940 1.800000e-67 267.0
26 TraesCS2D01G459700 chr2B 95.238 84 2 1 467 550 679031838 679031757 6.850000e-27 132.0
27 TraesCS2D01G459700 chr2A 86.934 773 41 30 673 1424 706511291 706510558 0.000000e+00 813.0
28 TraesCS2D01G459700 chr2A 90.476 630 41 8 1481 2094 706530095 706529469 0.000000e+00 813.0
29 TraesCS2D01G459700 chr2A 89.100 578 43 8 1481 2053 706510574 706510012 0.000000e+00 701.0
30 TraesCS2D01G459700 chr2A 86.239 545 62 11 1562 2094 706488844 706488301 2.030000e-161 579.0
31 TraesCS2D01G459700 chr2A 88.596 456 29 9 569 1010 706489816 706489370 1.610000e-147 532.0
32 TraesCS2D01G459700 chr2A 84.114 491 52 20 2 475 706490382 706489901 4.630000e-123 451.0
33 TraesCS2D01G459700 chr2A 84.397 423 48 11 2097 2503 136338417 136337997 1.700000e-107 399.0
34 TraesCS2D01G459700 chr2A 85.984 371 44 5 1 365 706512022 706511654 1.020000e-104 390.0
35 TraesCS2D01G459700 chr2A 80.973 452 61 22 202 635 706511733 706511289 4.860000e-88 335.0
36 TraesCS2D01G459700 chr2A 82.126 414 39 17 1007 1419 706530462 706530083 3.780000e-84 322.0
37 TraesCS2D01G459700 chr2A 82.263 327 41 12 1007 1320 706489334 706489012 1.800000e-67 267.0
38 TraesCS2D01G459700 chr2A 90.179 112 9 2 180 289 706490317 706490206 8.790000e-31 145.0
39 TraesCS2D01G459700 chr2A 92.857 84 4 1 467 550 706489881 706489800 1.480000e-23 121.0
40 TraesCS2D01G459700 chr2A 96.667 60 2 0 1422 1481 655329167 655329108 1.930000e-17 100.0
41 TraesCS2D01G459700 chr5B 85.504 407 43 10 2107 2501 573141308 573140906 7.850000e-111 411.0
42 TraesCS2D01G459700 chr5B 98.305 59 1 0 1423 1481 547552925 547552983 1.490000e-18 104.0
43 TraesCS2D01G459700 chr5B 92.308 65 5 0 1423 1487 606550102 606550038 3.230000e-15 93.5
44 TraesCS2D01G459700 chr5D 84.841 409 48 13 2102 2503 506072236 506072637 1.700000e-107 399.0
45 TraesCS2D01G459700 chr1A 85.600 375 40 12 2102 2467 296938253 296938622 6.160000e-102 381.0
46 TraesCS2D01G459700 chr1B 83.135 421 54 11 2098 2503 520376222 520376640 4.790000e-98 368.0
47 TraesCS2D01G459700 chr1B 93.939 66 3 1 1417 1481 121848564 121848499 6.940000e-17 99.0
48 TraesCS2D01G459700 chr5A 83.173 416 49 13 2097 2500 637104644 637104238 8.020000e-96 361.0
49 TraesCS2D01G459700 chrUn 95.082 61 3 0 1421 1481 55807597 55807537 2.500000e-16 97.1
50 TraesCS2D01G459700 chr6D 91.549 71 5 1 1411 1481 447057188 447057257 2.500000e-16 97.1
51 TraesCS2D01G459700 chr6B 92.424 66 4 1 1419 1484 125727364 125727428 3.230000e-15 93.5


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 TraesCS2D01G459700 chr2D 566300899 566303941 3042 True 1349.300000 5121 92.788500 1 3043 4 chr2D.!!$R6 3042
1 TraesCS2D01G459700 chr2D 558376217 558376781 564 False 616.000000 616 86.261000 1520 2094 1 chr2D.!!$F1 574
2 TraesCS2D01G459700 chr2D 566655613 566656620 1007 True 607.000000 835 87.635000 1007 2093 2 chr2D.!!$R7 1086
3 TraesCS2D01G459700 chr2D 566261778 566263758 1980 True 325.800000 566 89.645200 224 2094 5 chr2D.!!$R5 1870
4 TraesCS2D01G459700 chr2B 679069912 679072340 2428 True 1749.000000 2013 92.594500 289 2773 2 chr2B.!!$R2 2484
5 TraesCS2D01G459700 chr2B 679743801 679744365 564 False 806.000000 806 92.416000 1529 2094 1 chr2B.!!$F2 565
6 TraesCS2D01G459700 chr2B 679696568 679697572 1004 False 622.000000 845 88.165000 1007 2094 2 chr2B.!!$F3 1087
7 TraesCS2D01G459700 chr2B 679030275 679032310 2035 True 379.200000 608 86.578400 2 2095 5 chr2B.!!$R1 2093
8 TraesCS2D01G459700 chr2A 706529469 706530462 993 True 567.500000 813 86.301000 1007 2094 2 chr2A.!!$R5 1087
9 TraesCS2D01G459700 chr2A 706510012 706512022 2010 True 559.750000 813 85.747750 1 2053 4 chr2A.!!$R4 2052
10 TraesCS2D01G459700 chr2A 706488301 706490382 2081 True 349.166667 579 87.374667 2 2094 6 chr2A.!!$R3 2092

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
918 1092 0.960364 CCAAACACCCCACCGATCTG 60.96 60.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 2879 1.68611 CTACCCCTGCTCCTTCCGT 60.686 63.158 0.0 0.0 0.0 4.69 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
36 37 2.267006 CATGAGGCTCGGCAGTGT 59.733 61.111 10.42 0.00 0.00 3.55
43 44 1.290324 GCTCGGCAGTGTCTCTCAA 59.710 57.895 0.00 0.00 0.00 3.02
44 45 1.011451 GCTCGGCAGTGTCTCTCAAC 61.011 60.000 0.00 0.00 0.00 3.18
46 47 1.813178 CTCGGCAGTGTCTCTCAACTA 59.187 52.381 0.00 0.00 0.00 2.24
63 64 8.169839 TCTCAACTATTTTAAATGTCGACTCG 57.830 34.615 17.92 0.00 0.00 4.18
70 71 1.191535 AAATGTCGACTCGGGGATGA 58.808 50.000 17.92 0.00 0.00 2.92
72 73 1.414158 ATGTCGACTCGGGGATGATT 58.586 50.000 17.92 0.00 0.00 2.57
88 89 3.992943 TGATTGTATCCCCGAGTTTGT 57.007 42.857 0.00 0.00 0.00 2.83
92 93 5.536916 TGATTGTATCCCCGAGTTTGTTTTT 59.463 36.000 0.00 0.00 0.00 1.94
93 94 6.715718 TGATTGTATCCCCGAGTTTGTTTTTA 59.284 34.615 0.00 0.00 0.00 1.52
97 98 7.595604 TGTATCCCCGAGTTTGTTTTTATTTC 58.404 34.615 0.00 0.00 0.00 2.17
99 100 6.079424 TCCCCGAGTTTGTTTTTATTTCTG 57.921 37.500 0.00 0.00 0.00 3.02
100 101 4.684242 CCCCGAGTTTGTTTTTATTTCTGC 59.316 41.667 0.00 0.00 0.00 4.26
102 103 4.684242 CCGAGTTTGTTTTTATTTCTGCCC 59.316 41.667 0.00 0.00 0.00 5.36
103 104 4.684242 CGAGTTTGTTTTTATTTCTGCCCC 59.316 41.667 0.00 0.00 0.00 5.80
104 105 4.627058 AGTTTGTTTTTATTTCTGCCCCG 58.373 39.130 0.00 0.00 0.00 5.73
105 106 2.734276 TGTTTTTATTTCTGCCCCGC 57.266 45.000 0.00 0.00 0.00 6.13
106 107 1.964223 TGTTTTTATTTCTGCCCCGCA 59.036 42.857 0.00 0.00 36.92 5.69
127 132 6.873605 CCGCATCATATAGTACTCCAAAATCA 59.126 38.462 0.00 0.00 0.00 2.57
191 196 4.191804 AGTACTCCAGATGCAGTATCCT 57.808 45.455 0.00 0.00 36.40 3.24
200 205 2.672961 TGCAGTATCCTCGAGTTTGG 57.327 50.000 12.31 0.00 0.00 3.28
229 234 6.907206 TTTTGCACCACGTAATATAGTACC 57.093 37.500 4.84 0.00 0.00 3.34
323 420 5.106634 GCGTCATATAGTACTCCAGAATCGT 60.107 44.000 0.00 0.00 0.00 3.73
430 537 4.814234 ACGAATTATATCACACGGCAATGT 59.186 37.500 0.00 0.00 0.00 2.71
558 700 8.514330 AAATCCAGCATGATATTTTGCAAAAT 57.486 26.923 33.26 33.26 41.35 1.82
559 701 8.514330 AATCCAGCATGATATTTTGCAAAATT 57.486 26.923 35.18 24.27 41.35 1.82
560 702 9.616156 AATCCAGCATGATATTTTGCAAAATTA 57.384 25.926 35.18 23.83 41.35 1.40
561 703 9.616156 ATCCAGCATGATATTTTGCAAAATTAA 57.384 25.926 35.18 22.48 41.35 1.40
562 704 9.445878 TCCAGCATGATATTTTGCAAAATTAAA 57.554 25.926 35.18 21.83 41.35 1.52
648 798 5.567037 CCATTCATGTACTAATGGGAGGA 57.433 43.478 19.37 0.00 45.58 3.71
649 799 5.555017 CCATTCATGTACTAATGGGAGGAG 58.445 45.833 19.37 2.56 45.58 3.69
650 800 5.072329 CCATTCATGTACTAATGGGAGGAGT 59.928 44.000 19.37 0.00 45.58 3.85
789 940 2.595750 TCCAACCATTTCCCAACGAT 57.404 45.000 0.00 0.00 0.00 3.73
851 1015 2.755469 GGGCCCTACGTGTCGGTA 60.755 66.667 17.04 0.00 0.00 4.02
881 1047 3.949754 CGGCTTCACGGTATATATAGGGA 59.050 47.826 0.00 0.00 0.00 4.20
918 1092 0.960364 CCAAACACCCCACCGATCTG 60.960 60.000 0.00 0.00 0.00 2.90
978 1166 2.975489 AGAAAAGAGGAAGCAGAGGACA 59.025 45.455 0.00 0.00 0.00 4.02
1003 1191 3.540617 GAGAAAGGGAAGAGGAGAATGC 58.459 50.000 0.00 0.00 0.00 3.56
1005 1232 1.673767 AAGGGAAGAGGAGAATGCCA 58.326 50.000 0.00 0.00 0.00 4.92
1155 1424 1.153208 GGAGAGACGGCTCGACCTA 60.153 63.158 23.72 0.00 45.98 3.08
1211 1488 0.603569 TGCTCCTCTGTTCTTCCGAC 59.396 55.000 0.00 0.00 0.00 4.79
1340 1632 9.574516 AAATTCCGGAGAACTATATAATTTGCT 57.425 29.630 3.34 0.00 33.97 3.91
1342 1634 9.654663 ATTCCGGAGAACTATATAATTTGCTAC 57.345 33.333 3.34 0.00 33.97 3.58
1343 1635 8.418597 TCCGGAGAACTATATAATTTGCTACT 57.581 34.615 0.00 0.00 0.00 2.57
1422 1714 9.887406 GCATGATGATCAAAATTTTGTTTCTTT 57.113 25.926 25.98 16.33 39.18 2.52
1455 1747 4.297207 GGATTACCTCCGGCCTCT 57.703 61.111 0.00 0.00 33.29 3.69
1456 1748 1.749033 GGATTACCTCCGGCCTCTG 59.251 63.158 0.00 0.00 33.29 3.35
1457 1749 1.069935 GATTACCTCCGGCCTCTGC 59.930 63.158 0.00 0.00 0.00 4.26
1458 1750 1.686325 GATTACCTCCGGCCTCTGCA 61.686 60.000 0.00 0.00 40.13 4.41
1459 1751 1.056700 ATTACCTCCGGCCTCTGCAT 61.057 55.000 0.00 0.00 40.13 3.96
1460 1752 1.686325 TTACCTCCGGCCTCTGCATC 61.686 60.000 0.00 0.00 40.13 3.91
1461 1753 2.871795 TACCTCCGGCCTCTGCATCA 62.872 60.000 0.00 0.00 40.13 3.07
1462 1754 2.108566 CTCCGGCCTCTGCATCAG 59.891 66.667 0.00 0.00 40.13 2.90
1463 1755 2.685017 TCCGGCCTCTGCATCAGT 60.685 61.111 0.00 0.00 40.13 3.41
1464 1756 2.202987 CCGGCCTCTGCATCAGTC 60.203 66.667 0.00 0.00 40.13 3.51
1465 1757 2.584418 CGGCCTCTGCATCAGTCG 60.584 66.667 0.00 0.00 40.13 4.18
1466 1758 2.895680 GGCCTCTGCATCAGTCGA 59.104 61.111 0.00 0.00 40.13 4.20
1467 1759 1.445095 GGCCTCTGCATCAGTCGAT 59.555 57.895 0.00 0.00 40.13 3.59
1476 1768 0.041224 CATCAGTCGATGCATGCAGC 60.041 55.000 25.69 25.69 42.54 5.25
1477 1769 1.164662 ATCAGTCGATGCATGCAGCC 61.165 55.000 28.76 19.54 44.83 4.85
1478 1770 2.110352 CAGTCGATGCATGCAGCCA 61.110 57.895 28.76 15.42 44.83 4.75
1479 1771 1.153025 AGTCGATGCATGCAGCCAT 60.153 52.632 28.76 11.07 44.83 4.40
1480 1772 0.107268 AGTCGATGCATGCAGCCATA 59.893 50.000 28.76 12.84 44.83 2.74
1481 1773 0.946528 GTCGATGCATGCAGCCATAA 59.053 50.000 28.76 10.32 44.83 1.90
1482 1774 1.334556 GTCGATGCATGCAGCCATAAA 59.665 47.619 28.76 7.83 44.83 1.40
1483 1775 2.022934 TCGATGCATGCAGCCATAAAA 58.977 42.857 28.76 6.08 44.83 1.52
1484 1776 2.624364 TCGATGCATGCAGCCATAAAAT 59.376 40.909 28.76 7.39 44.83 1.82
1485 1777 3.068448 TCGATGCATGCAGCCATAAAATT 59.932 39.130 28.76 6.59 44.83 1.82
1486 1778 3.805422 CGATGCATGCAGCCATAAAATTT 59.195 39.130 28.76 6.01 44.83 1.82
1487 1779 4.271533 CGATGCATGCAGCCATAAAATTTT 59.728 37.500 28.76 8.75 44.83 1.82
1488 1780 4.948608 TGCATGCAGCCATAAAATTTTG 57.051 36.364 18.46 0.00 44.83 2.44
1489 1781 4.325119 TGCATGCAGCCATAAAATTTTGT 58.675 34.783 18.46 3.84 44.83 2.83
1490 1782 4.760715 TGCATGCAGCCATAAAATTTTGTT 59.239 33.333 18.46 0.00 44.83 2.83
1491 1783 5.241064 TGCATGCAGCCATAAAATTTTGTTT 59.759 32.000 18.46 0.00 44.83 2.83
1492 1784 5.796437 GCATGCAGCCATAAAATTTTGTTTC 59.204 36.000 14.21 1.38 37.23 2.78
1493 1785 6.348704 GCATGCAGCCATAAAATTTTGTTTCT 60.349 34.615 14.21 3.58 37.23 2.52
1517 1809 2.027192 TGCACTGGGATTACAGAGTTCC 60.027 50.000 0.00 0.00 40.97 3.62
1643 1952 2.266055 CGCCAGGACCTCAACCTC 59.734 66.667 0.00 0.00 35.35 3.85
1689 2007 1.878656 CGTCACCACCACCTCCTCTC 61.879 65.000 0.00 0.00 0.00 3.20
1843 2176 2.821366 CTCGCCGCCTTCAAGCAT 60.821 61.111 0.00 0.00 0.00 3.79
1874 2207 3.361977 GCGAACCCAACCATGCGT 61.362 61.111 0.00 0.00 0.00 5.24
2112 2454 2.398754 TCAGGGGAAGACTTGTGAGA 57.601 50.000 0.00 0.00 0.00 3.27
2139 2481 7.069702 TCTCACTTTAGCTGAGATCAATGAGAT 59.930 37.037 0.00 0.00 39.41 2.75
2248 2590 6.701841 TCAGCTCATAATTCGACTTCCATTAC 59.298 38.462 0.00 0.00 0.00 1.89
2408 2750 5.917462 TGTAGACATACCTCACATGAATGG 58.083 41.667 0.00 0.02 0.00 3.16
2512 2855 6.601332 TCATACAAGTCTCCCTCAAGTTTTT 58.399 36.000 0.00 0.00 0.00 1.94
2536 2879 1.957877 GTCGTCAATTGGTTGGGGAAA 59.042 47.619 5.42 0.00 35.99 3.13
2568 2911 2.302157 AGGGGTAGCTACAGAACACAAC 59.698 50.000 24.75 4.48 0.00 3.32
2585 2928 0.532115 AACGAATTTGGGCCTCATGC 59.468 50.000 4.53 0.00 40.16 4.06
2622 2965 1.237458 GGCCTGGGTCCTAGATCCT 59.763 63.158 3.28 0.00 33.22 3.24
2669 3015 4.881440 ATGCATCGCCGCCATGGT 62.881 61.111 14.67 0.00 41.21 3.55
2682 3028 2.158900 CGCCATGGTAGAGATCCAAGTT 60.159 50.000 14.67 0.00 38.52 2.66
2687 3033 2.912956 TGGTAGAGATCCAAGTTGGCTT 59.087 45.455 17.68 6.96 37.47 4.35
2706 3052 2.191641 GCCATGAGCTCCCTGTCC 59.808 66.667 12.15 0.00 38.99 4.02
2711 3057 2.125350 GAGCTCCCTGTCCTTGCG 60.125 66.667 0.87 0.00 0.00 4.85
2718 3064 1.120530 CCCTGTCCTTGCGTACCTAT 58.879 55.000 0.00 0.00 0.00 2.57
2719 3065 2.091720 TCCCTGTCCTTGCGTACCTATA 60.092 50.000 0.00 0.00 0.00 1.31
2722 3068 3.004524 CCTGTCCTTGCGTACCTATACTC 59.995 52.174 0.00 0.00 0.00 2.59
2723 3069 3.884091 CTGTCCTTGCGTACCTATACTCT 59.116 47.826 0.00 0.00 0.00 3.24
2724 3070 5.039920 TGTCCTTGCGTACCTATACTCTA 57.960 43.478 0.00 0.00 0.00 2.43
2725 3071 5.439721 TGTCCTTGCGTACCTATACTCTAA 58.560 41.667 0.00 0.00 0.00 2.10
2726 3072 6.066690 TGTCCTTGCGTACCTATACTCTAAT 58.933 40.000 0.00 0.00 0.00 1.73
2727 3073 6.016527 TGTCCTTGCGTACCTATACTCTAATG 60.017 42.308 0.00 0.00 0.00 1.90
2728 3074 6.206243 GTCCTTGCGTACCTATACTCTAATGA 59.794 42.308 0.00 0.00 0.00 2.57
2729 3075 6.774170 TCCTTGCGTACCTATACTCTAATGAA 59.226 38.462 0.00 0.00 0.00 2.57
2730 3076 7.450634 TCCTTGCGTACCTATACTCTAATGAAT 59.549 37.037 0.00 0.00 0.00 2.57
2731 3077 7.542477 CCTTGCGTACCTATACTCTAATGAATG 59.458 40.741 0.00 0.00 0.00 2.67
2745 3091 7.972277 ACTCTAATGAATGATTTGTTGCATCAC 59.028 33.333 0.00 0.00 33.42 3.06
2770 3116 1.366111 CCACCTTCATAACACCGGCG 61.366 60.000 0.00 0.00 0.00 6.46
3037 3383 4.344237 GGCTGCAAGTGCCCTATT 57.656 55.556 4.10 0.00 44.32 1.73
3038 3384 1.811860 GGCTGCAAGTGCCCTATTG 59.188 57.895 4.10 0.00 44.32 1.90
3039 3385 0.967380 GGCTGCAAGTGCCCTATTGT 60.967 55.000 4.10 0.00 44.32 2.71
3040 3386 0.890683 GCTGCAAGTGCCCTATTGTT 59.109 50.000 0.00 0.00 41.18 2.83
3041 3387 1.273327 GCTGCAAGTGCCCTATTGTTT 59.727 47.619 0.00 0.00 41.18 2.83
3042 3388 2.491693 GCTGCAAGTGCCCTATTGTTTA 59.508 45.455 0.00 0.00 41.18 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.507249 ACATTTAAAATAGTTGAGAGACACTGC 58.493 33.333 0.00 0.00 0.00 4.40
36 37 9.355215 GAGTCGACATTTAAAATAGTTGAGAGA 57.645 33.333 19.50 0.00 0.00 3.10
43 44 5.105228 TCCCCGAGTCGACATTTAAAATAGT 60.105 40.000 19.50 0.00 0.00 2.12
44 45 5.353938 TCCCCGAGTCGACATTTAAAATAG 58.646 41.667 19.50 0.00 0.00 1.73
46 47 4.210724 TCCCCGAGTCGACATTTAAAAT 57.789 40.909 19.50 0.00 0.00 1.82
70 71 7.712204 ATAAAAACAAACTCGGGGATACAAT 57.288 32.000 0.00 0.00 39.74 2.71
72 73 7.449086 AGAAATAAAAACAAACTCGGGGATACA 59.551 33.333 0.00 0.00 39.74 2.29
88 89 2.828520 TGATGCGGGGCAGAAATAAAAA 59.171 40.909 0.00 0.00 43.65 1.94
92 93 3.719268 ATATGATGCGGGGCAGAAATA 57.281 42.857 0.00 0.00 43.65 1.40
93 94 2.592102 ATATGATGCGGGGCAGAAAT 57.408 45.000 0.00 0.00 43.65 2.17
97 98 2.497675 AGTACTATATGATGCGGGGCAG 59.502 50.000 0.00 0.00 43.65 4.85
99 100 2.159085 GGAGTACTATATGATGCGGGGC 60.159 54.545 0.00 0.00 0.00 5.80
100 101 3.096852 TGGAGTACTATATGATGCGGGG 58.903 50.000 0.00 0.00 0.00 5.73
102 103 6.873605 TGATTTTGGAGTACTATATGATGCGG 59.126 38.462 0.00 0.00 0.00 5.69
103 104 7.889589 TGATTTTGGAGTACTATATGATGCG 57.110 36.000 0.00 0.00 0.00 4.73
417 524 2.861750 GCAATTGAACATTGCCGTGTGA 60.862 45.455 10.34 0.00 46.21 3.58
430 537 7.920151 CCATCCATATTTTAGTTCGCAATTGAA 59.080 33.333 10.34 0.00 0.00 2.69
438 549 5.373222 TCCACCCATCCATATTTTAGTTCG 58.627 41.667 0.00 0.00 0.00 3.95
643 792 6.532988 AAGTAGTCATTTACTCACTCCTCC 57.467 41.667 0.00 0.00 39.80 4.30
673 824 2.490115 CCGGGATTTGAATTCGTTTCCA 59.510 45.455 17.25 0.00 33.04 3.53
918 1092 1.268335 GCCGAGAGAAGACGAGATGAC 60.268 57.143 0.00 0.00 0.00 3.06
978 1166 0.252284 TCCTCTTCCCTTTCTCGGCT 60.252 55.000 0.00 0.00 0.00 5.52
1003 1191 3.480133 CCTACCCTTCCCCGCTGG 61.480 72.222 0.00 0.00 0.00 4.85
1135 1404 3.878519 GTCGAGCCGTCTCTCCCG 61.879 72.222 0.00 0.00 37.19 5.14
1340 1632 7.683578 TCTGCGGATATAGTCTAACCTAAGTA 58.316 38.462 0.00 0.00 0.00 2.24
1341 1633 6.540995 TCTGCGGATATAGTCTAACCTAAGT 58.459 40.000 0.00 0.00 0.00 2.24
1342 1634 7.337184 TGATCTGCGGATATAGTCTAACCTAAG 59.663 40.741 8.35 0.00 31.46 2.18
1343 1635 7.173032 TGATCTGCGGATATAGTCTAACCTAA 58.827 38.462 8.35 0.00 31.46 2.69
1444 1736 3.457625 CTGATGCAGAGGCCGGAGG 62.458 68.421 5.05 0.00 42.72 4.30
1445 1737 2.108566 CTGATGCAGAGGCCGGAG 59.891 66.667 5.05 0.00 40.13 4.63
1446 1738 2.685017 ACTGATGCAGAGGCCGGA 60.685 61.111 5.05 0.00 40.13 5.14
1447 1739 2.202987 GACTGATGCAGAGGCCGG 60.203 66.667 0.00 0.00 40.13 6.13
1448 1740 2.360949 ATCGACTGATGCAGAGGCCG 62.361 60.000 0.00 0.00 40.13 6.13
1449 1741 0.879400 CATCGACTGATGCAGAGGCC 60.879 60.000 0.00 0.00 45.06 5.19
1450 1742 2.602738 CATCGACTGATGCAGAGGC 58.397 57.895 0.82 0.00 45.06 4.70
1458 1750 1.164662 GGCTGCATGCATCGACTGAT 61.165 55.000 22.97 0.00 45.15 2.90
1459 1751 1.816679 GGCTGCATGCATCGACTGA 60.817 57.895 22.97 0.00 45.15 3.41
1460 1752 1.444917 ATGGCTGCATGCATCGACTG 61.445 55.000 22.97 9.56 45.15 3.51
1461 1753 0.107268 TATGGCTGCATGCATCGACT 59.893 50.000 22.97 7.54 45.15 4.18
1462 1754 0.946528 TTATGGCTGCATGCATCGAC 59.053 50.000 22.97 13.79 45.15 4.20
1463 1755 1.677942 TTTATGGCTGCATGCATCGA 58.322 45.000 22.97 15.35 45.15 3.59
1464 1756 2.495409 TTTTATGGCTGCATGCATCG 57.505 45.000 22.97 12.00 45.15 3.84
1465 1757 5.065474 ACAAAATTTTATGGCTGCATGCATC 59.935 36.000 22.97 17.75 45.15 3.91
1466 1758 4.944930 ACAAAATTTTATGGCTGCATGCAT 59.055 33.333 22.97 9.00 45.15 3.96
1467 1759 4.325119 ACAAAATTTTATGGCTGCATGCA 58.675 34.783 21.29 21.29 45.15 3.96
1468 1760 4.950434 ACAAAATTTTATGGCTGCATGC 57.050 36.364 11.82 11.82 41.94 4.06
1469 1761 7.018826 CAGAAACAAAATTTTATGGCTGCATG 58.981 34.615 2.44 0.00 0.00 4.06
1470 1762 6.711645 ACAGAAACAAAATTTTATGGCTGCAT 59.288 30.769 16.47 0.00 32.95 3.96
1471 1763 6.054295 ACAGAAACAAAATTTTATGGCTGCA 58.946 32.000 16.47 0.00 32.95 4.41
1472 1764 6.544038 ACAGAAACAAAATTTTATGGCTGC 57.456 33.333 16.47 0.00 32.95 5.25
1473 1765 6.852345 GCAACAGAAACAAAATTTTATGGCTG 59.148 34.615 2.44 11.17 32.95 4.85
1474 1766 6.541641 TGCAACAGAAACAAAATTTTATGGCT 59.458 30.769 2.44 0.00 32.95 4.75
1475 1767 6.632434 GTGCAACAGAAACAAAATTTTATGGC 59.368 34.615 2.44 0.00 32.95 4.40
1476 1768 7.851963 CAGTGCAACAGAAACAAAATTTTATGG 59.148 33.333 2.44 0.00 41.43 2.74
1477 1769 7.851963 CCAGTGCAACAGAAACAAAATTTTATG 59.148 33.333 2.44 0.00 41.43 1.90
1478 1770 7.012232 CCCAGTGCAACAGAAACAAAATTTTAT 59.988 33.333 2.44 0.00 41.43 1.40
1479 1771 6.314896 CCCAGTGCAACAGAAACAAAATTTTA 59.685 34.615 2.44 0.00 41.43 1.52
1480 1772 5.123661 CCCAGTGCAACAGAAACAAAATTTT 59.876 36.000 0.00 0.00 41.43 1.82
1481 1773 4.635324 CCCAGTGCAACAGAAACAAAATTT 59.365 37.500 0.00 0.00 41.43 1.82
1482 1774 4.081198 TCCCAGTGCAACAGAAACAAAATT 60.081 37.500 0.00 0.00 41.43 1.82
1483 1775 3.450457 TCCCAGTGCAACAGAAACAAAAT 59.550 39.130 0.00 0.00 41.43 1.82
1484 1776 2.828520 TCCCAGTGCAACAGAAACAAAA 59.171 40.909 0.00 0.00 41.43 2.44
1485 1777 2.451490 TCCCAGTGCAACAGAAACAAA 58.549 42.857 0.00 0.00 41.43 2.83
1486 1778 2.136298 TCCCAGTGCAACAGAAACAA 57.864 45.000 0.00 0.00 41.43 2.83
1487 1779 2.363306 ATCCCAGTGCAACAGAAACA 57.637 45.000 0.00 0.00 41.43 2.83
1488 1780 3.568007 TGTAATCCCAGTGCAACAGAAAC 59.432 43.478 0.00 0.00 41.43 2.78
1489 1781 3.820467 CTGTAATCCCAGTGCAACAGAAA 59.180 43.478 5.19 0.00 41.43 2.52
1490 1782 3.072330 TCTGTAATCCCAGTGCAACAGAA 59.928 43.478 10.39 0.00 40.10 3.02
1491 1783 2.637382 TCTGTAATCCCAGTGCAACAGA 59.363 45.455 9.05 9.05 41.43 3.41
1492 1784 3.005554 CTCTGTAATCCCAGTGCAACAG 58.994 50.000 4.83 4.83 41.43 3.16
1493 1785 2.371841 ACTCTGTAATCCCAGTGCAACA 59.628 45.455 0.00 0.00 41.43 3.33
1643 1952 4.489771 GTGGATGCCGTGGGAGGG 62.490 72.222 0.00 0.00 0.00 4.30
1689 2007 2.432628 GTCGAGGGTGCAGAACGG 60.433 66.667 0.00 0.00 0.00 4.44
1865 2198 4.326766 GCACACGCACGCATGGTT 62.327 61.111 0.00 0.00 38.36 3.67
2268 2610 7.671302 AGTACTTTGACACTATTCACATGAGT 58.329 34.615 0.00 0.00 0.00 3.41
2299 2641 2.224744 TGTGAATAGTGGCAGCTTTGGA 60.225 45.455 0.00 0.00 0.00 3.53
2352 2694 6.801539 AAAATCAGCTCAAAACTCGATGTA 57.198 33.333 0.00 0.00 0.00 2.29
2484 2827 6.436027 ACTTGAGGGAGACTTGTATGAGATA 58.564 40.000 0.00 0.00 0.00 1.98
2512 2855 2.226330 CCCAACCAATTGACGACTTGA 58.774 47.619 7.12 0.00 38.15 3.02
2536 2879 1.686110 CTACCCCTGCTCCTTCCGT 60.686 63.158 0.00 0.00 0.00 4.69
2599 2942 4.431524 TAGGACCCAGGCCCCCAG 62.432 72.222 0.00 0.00 0.00 4.45
2600 2943 4.431524 CTAGGACCCAGGCCCCCA 62.432 72.222 0.00 0.00 0.00 4.96
2622 2965 2.610859 GGGCTCCTTCCCAGTGGA 60.611 66.667 11.95 0.00 45.82 4.02
2640 2983 4.471908 ATGCATCGTCAGCCGGCA 62.472 61.111 31.54 7.75 37.96 5.69
2653 2999 4.168291 TACCATGGCGGCGATGCA 62.168 61.111 18.17 6.46 39.03 3.96
2654 3000 3.349006 CTACCATGGCGGCGATGC 61.349 66.667 18.17 0.00 39.03 3.91
2687 3033 2.611800 ACAGGGAGCTCATGGCCA 60.612 61.111 17.19 8.56 43.05 5.36
2718 3064 9.176460 TGATGCAACAAATCATTCATTAGAGTA 57.824 29.630 0.00 0.00 0.00 2.59
2719 3065 7.972277 GTGATGCAACAAATCATTCATTAGAGT 59.028 33.333 0.00 0.00 36.49 3.24
2722 3068 7.009815 GTGGTGATGCAACAAATCATTCATTAG 59.990 37.037 0.00 0.00 36.49 1.73
2723 3069 6.812656 GTGGTGATGCAACAAATCATTCATTA 59.187 34.615 0.00 0.00 36.49 1.90
2724 3070 5.640357 GTGGTGATGCAACAAATCATTCATT 59.360 36.000 0.00 0.00 36.49 2.57
2725 3071 5.172934 GTGGTGATGCAACAAATCATTCAT 58.827 37.500 0.00 0.00 36.49 2.57
2726 3072 4.558178 GTGGTGATGCAACAAATCATTCA 58.442 39.130 0.00 0.00 36.49 2.57
2727 3073 3.928375 GGTGGTGATGCAACAAATCATTC 59.072 43.478 0.00 0.00 36.49 2.67
2728 3074 3.579586 AGGTGGTGATGCAACAAATCATT 59.420 39.130 0.00 0.00 36.49 2.57
2729 3075 3.167485 AGGTGGTGATGCAACAAATCAT 58.833 40.909 0.00 0.00 36.49 2.45
2730 3076 2.557924 GAGGTGGTGATGCAACAAATCA 59.442 45.455 0.00 0.00 30.77 2.57
2731 3077 2.094545 GGAGGTGGTGATGCAACAAATC 60.095 50.000 0.00 0.00 30.77 2.17
2745 3091 2.618045 GGTGTTATGAAGGTGGAGGTGG 60.618 54.545 0.00 0.00 0.00 4.61
3021 3367 0.890683 AACAATAGGGCACTTGCAGC 59.109 50.000 0.00 0.00 44.36 5.25


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

AutoCloner maintained by Alex Coulton.