Multiple sequence alignment - TraesCS6D01G030600

Loading Multiple Alignment...

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 TraesCS6D01G030600 chr6D 100.000 6056 0 0 1 6056 12303580 12309635 0.000000e+00 11184.0
1 TraesCS6D01G030600 chr6A 95.550 3506 107 28 902 4374 13659950 13663439 0.000000e+00 5565.0
2 TraesCS6D01G030600 chr6A 96.281 1694 52 4 4369 6056 13664063 13665751 0.000000e+00 2769.0
3 TraesCS6D01G030600 chr6A 95.896 804 25 3 103 906 21231312 21232107 0.000000e+00 1295.0
4 TraesCS6D01G030600 chr6B 95.183 1806 73 12 1767 3565 22552851 22554649 0.000000e+00 2841.0
5 TraesCS6D01G030600 chr6B 94.275 1572 75 7 4488 6053 22555682 22557244 0.000000e+00 2390.0
6 TraesCS6D01G030600 chr6B 87.891 768 44 11 901 1624 22552086 22552848 0.000000e+00 857.0
7 TraesCS6D01G030600 chr6B 94.409 465 26 0 3602 4066 22554634 22555098 0.000000e+00 715.0
8 TraesCS6D01G030600 chr6B 92.230 296 17 6 4196 4490 22555311 22555601 1.210000e-111 414.0
9 TraesCS6D01G030600 chr1D 98.864 440 5 0 103 542 354727186 354727625 0.000000e+00 785.0
10 TraesCS6D01G030600 chr1D 98.646 443 6 0 463 905 354727507 354727949 0.000000e+00 785.0
11 TraesCS6D01G030600 chr4B 97.727 440 10 0 103 542 51672258 51672697 0.000000e+00 758.0
12 TraesCS6D01G030600 chr4B 96.614 443 12 2 463 905 51672579 51673018 0.000000e+00 732.0
13 TraesCS6D01G030600 chr4B 94.286 70 4 0 4684 4753 22465265 22465196 2.310000e-19 108.0
14 TraesCS6D01G030600 chr1B 96.847 444 12 1 463 906 39901878 39901437 0.000000e+00 741.0
15 TraesCS6D01G030600 chr1B 96.413 446 16 0 103 548 39902199 39901754 0.000000e+00 736.0
16 TraesCS6D01G030600 chr5B 95.937 443 16 1 463 905 257783937 257783497 0.000000e+00 717.0
17 TraesCS6D01G030600 chr5B 95.291 446 18 2 103 548 257784255 257783813 0.000000e+00 704.0
18 TraesCS6D01G030600 chr5A 94.595 444 17 3 103 542 492476527 492476967 0.000000e+00 680.0
19 TraesCS6D01G030600 chr5A 93.694 444 24 3 463 906 492476849 492477288 0.000000e+00 662.0
20 TraesCS6D01G030600 chr5A 94.264 401 23 0 103 503 509360980 509361380 1.120000e-171 614.0
21 TraesCS6D01G030600 chr2A 96.560 407 12 1 103 509 710786410 710786006 0.000000e+00 673.0
22 TraesCS6D01G030600 chr2A 96.535 404 12 1 502 905 710786091 710785690 0.000000e+00 667.0
23 TraesCS6D01G030600 chr2A 94.514 401 22 0 103 503 265592074 265592474 2.400000e-173 619.0
24 TraesCS6D01G030600 chr2A 94.307 404 19 3 502 905 265592395 265592794 3.100000e-172 616.0
25 TraesCS6D01G030600 chr2A 94.030 67 4 0 4684 4750 695776003 695776069 1.070000e-17 102.0
26 TraesCS6D01G030600 chr2A 94.030 67 4 0 4684 4750 695951719 695951785 1.070000e-17 102.0
27 TraesCS6D01G030600 chr7B 96.287 404 12 2 502 905 458597829 458597429 0.000000e+00 660.0
28 TraesCS6D01G030600 chr2B 94.286 70 4 0 4684 4753 601695495 601695564 2.310000e-19 108.0
29 TraesCS6D01G030600 chr2B 95.082 61 3 0 4693 4753 663367447 663367387 5.000000e-16 97.1
30 TraesCS6D01G030600 chr3D 92.857 70 5 0 4684 4753 482857920 482857851 1.070000e-17 102.0
31 TraesCS6D01G030600 chr2D 92.857 70 5 0 4684 4753 556200010 556200079 1.070000e-17 102.0
32 TraesCS6D01G030600 chr2D 94.030 67 4 0 4684 4750 564584240 564584306 1.070000e-17 102.0
33 TraesCS6D01G030600 chr2D 96.552 58 2 0 4696 4753 564446017 564446074 5.000000e-16 97.1


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 TraesCS6D01G030600 chr6D 12303580 12309635 6055 False 11184.0 11184 100.0000 1 6056 1 chr6D.!!$F1 6055
1 TraesCS6D01G030600 chr6A 13659950 13665751 5801 False 4167.0 5565 95.9155 902 6056 2 chr6A.!!$F2 5154
2 TraesCS6D01G030600 chr6A 21231312 21232107 795 False 1295.0 1295 95.8960 103 906 1 chr6A.!!$F1 803
3 TraesCS6D01G030600 chr6B 22552086 22557244 5158 False 1443.4 2841 92.7976 901 6053 5 chr6B.!!$F1 5152
4 TraesCS6D01G030600 chr1D 354727186 354727949 763 False 785.0 785 98.7550 103 905 2 chr1D.!!$F1 802
5 TraesCS6D01G030600 chr4B 51672258 51673018 760 False 745.0 758 97.1705 103 905 2 chr4B.!!$F1 802
6 TraesCS6D01G030600 chr1B 39901437 39902199 762 True 738.5 741 96.6300 103 906 2 chr1B.!!$R1 803
7 TraesCS6D01G030600 chr5B 257783497 257784255 758 True 710.5 717 95.6140 103 905 2 chr5B.!!$R1 802
8 TraesCS6D01G030600 chr5A 492476527 492477288 761 False 671.0 680 94.1445 103 906 2 chr5A.!!$F2 803
9 TraesCS6D01G030600 chr2A 710785690 710786410 720 True 670.0 673 96.5475 103 905 2 chr2A.!!$R1 802
10 TraesCS6D01G030600 chr2A 265592074 265592794 720 False 617.5 619 94.4105 103 905 2 chr2A.!!$F3 802

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
61 62 0.177604 GCAGGATGGGTGTCAGAGAG 59.822 60.000 0.00 0.00 35.86 3.20 F
96 97 0.189080 GGTGGGTTGGGTTTAGGGTT 59.811 55.000 0.00 0.00 0.00 4.11 F
97 98 1.413372 GGTGGGTTGGGTTTAGGGTTT 60.413 52.381 0.00 0.00 0.00 3.27 F
1618 1738 0.947244 GCAGGTGGATAAGGCATTCG 59.053 55.000 0.00 0.00 0.00 3.34 F
2195 2319 0.250166 GTTACTTCGGTGGCACAGGT 60.250 55.000 20.82 11.97 41.80 4.00 F
2204 2328 1.000843 GGTGGCACAGGTGGATTTTTC 59.999 52.381 20.82 0.00 41.80 2.29 F
3908 4046 0.322098 TTGGTATCAACTGCCACCGG 60.322 55.000 0.00 0.00 39.63 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1491 0.605589 AAAGTAAGGCGCTCACCACC 60.606 55.000 7.64 0.00 0.00 4.61 R
1618 1738 0.668706 ACATGTCTCGACTGCAGCAC 60.669 55.000 15.27 7.56 0.00 4.40 R
1944 2065 1.070914 GGGGAGAAGATTTCTAGCCGG 59.929 57.143 0.00 0.00 40.87 6.13 R
2474 2598 1.074405 TCATGACAGCCCTCAAGCTTT 59.926 47.619 0.00 0.00 42.61 3.51 R
3901 4039 1.153349 GAGAAGTCATCCCGGTGGC 60.153 63.158 0.00 0.00 0.00 5.01 R
4143 4326 3.337889 GCTTCAGCACGCGTGACA 61.338 61.111 41.19 21.19 41.59 3.58 R
5363 6305 0.395724 TCTAGCACTCCTGATCCGCA 60.396 55.000 0.00 0.00 0.00 5.69 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
17 18 3.749981 AAAGCGTGGGCAGAAGTG 58.250 55.556 0.00 0.00 43.41 3.16
18 19 1.152963 AAAGCGTGGGCAGAAGTGT 60.153 52.632 0.00 0.00 43.41 3.55
19 20 1.166531 AAAGCGTGGGCAGAAGTGTC 61.167 55.000 0.00 0.00 43.41 3.67
25 26 2.426023 GGCAGAAGTGTCCACCGT 59.574 61.111 0.00 0.00 0.00 4.83
26 27 1.961277 GGCAGAAGTGTCCACCGTG 60.961 63.158 0.00 0.00 0.00 4.94
27 28 1.069090 GCAGAAGTGTCCACCGTGA 59.931 57.895 0.00 0.00 0.00 4.35
28 29 1.222115 GCAGAAGTGTCCACCGTGAC 61.222 60.000 0.00 0.00 35.77 3.67
29 30 0.600255 CAGAAGTGTCCACCGTGACC 60.600 60.000 0.00 0.00 34.25 4.02
30 31 1.663702 GAAGTGTCCACCGTGACCG 60.664 63.158 0.00 0.00 34.25 4.79
31 32 3.802418 AAGTGTCCACCGTGACCGC 62.802 63.158 0.00 0.00 34.25 5.68
37 38 4.934942 CACCGTGACCGCGTGTGA 62.935 66.667 4.92 0.00 36.14 3.58
38 39 4.936823 ACCGTGACCGCGTGTGAC 62.937 66.667 4.92 6.30 0.00 3.67
39 40 4.934942 CCGTGACCGCGTGTGACA 62.935 66.667 14.97 0.88 29.33 3.58
40 41 3.394874 CGTGACCGCGTGTGACAG 61.395 66.667 14.97 6.50 29.33 3.51
41 42 3.702555 GTGACCGCGTGTGACAGC 61.703 66.667 4.92 0.00 30.58 4.40
48 49 2.433145 CGTGTGACAGCGCAGGAT 60.433 61.111 11.47 0.00 41.55 3.24
49 50 2.733671 CGTGTGACAGCGCAGGATG 61.734 63.158 11.47 0.29 41.55 3.51
50 51 2.046988 TGTGACAGCGCAGGATGG 60.047 61.111 11.47 0.00 35.86 3.51
58 59 2.981302 CGCAGGATGGGTGTCAGA 59.019 61.111 0.00 0.00 44.98 3.27
59 60 1.153489 CGCAGGATGGGTGTCAGAG 60.153 63.158 0.00 0.00 44.98 3.35
60 61 1.607801 CGCAGGATGGGTGTCAGAGA 61.608 60.000 0.00 0.00 44.98 3.10
61 62 0.177604 GCAGGATGGGTGTCAGAGAG 59.822 60.000 0.00 0.00 35.86 3.20
62 63 0.829333 CAGGATGGGTGTCAGAGAGG 59.171 60.000 0.00 0.00 0.00 3.69
63 64 0.712979 AGGATGGGTGTCAGAGAGGA 59.287 55.000 0.00 0.00 0.00 3.71
64 65 1.118838 GGATGGGTGTCAGAGAGGAG 58.881 60.000 0.00 0.00 0.00 3.69
65 66 1.342474 GGATGGGTGTCAGAGAGGAGA 60.342 57.143 0.00 0.00 0.00 3.71
66 67 1.754226 GATGGGTGTCAGAGAGGAGAC 59.246 57.143 0.00 0.00 35.37 3.36
68 69 1.993301 TGGGTGTCAGAGAGGAGACTA 59.007 52.381 0.00 0.00 44.43 2.59
69 70 2.291024 TGGGTGTCAGAGAGGAGACTAC 60.291 54.545 0.00 0.00 44.43 2.73
70 71 2.011222 GGTGTCAGAGAGGAGACTACG 58.989 57.143 0.00 0.00 44.43 3.51
71 72 2.011222 GTGTCAGAGAGGAGACTACGG 58.989 57.143 0.00 0.00 44.43 4.02
72 73 1.629353 TGTCAGAGAGGAGACTACGGT 59.371 52.381 0.00 0.00 44.43 4.83
73 74 2.011222 GTCAGAGAGGAGACTACGGTG 58.989 57.143 0.00 0.00 44.43 4.94
74 75 1.629353 TCAGAGAGGAGACTACGGTGT 59.371 52.381 0.00 0.00 44.43 4.16
75 76 2.011222 CAGAGAGGAGACTACGGTGTC 58.989 57.143 2.43 2.43 44.43 3.67
76 77 1.008329 GAGAGGAGACTACGGTGTCG 58.992 60.000 4.78 0.00 44.43 4.35
77 78 0.392729 AGAGGAGACTACGGTGTCGG 60.393 60.000 4.78 0.00 44.43 4.79
78 79 1.375098 GAGGAGACTACGGTGTCGGG 61.375 65.000 4.78 0.00 44.43 5.14
79 80 1.676967 GGAGACTACGGTGTCGGGT 60.677 63.158 4.78 0.00 41.47 5.28
80 81 1.505353 GAGACTACGGTGTCGGGTG 59.495 63.158 4.78 0.00 41.47 4.61
81 82 1.930908 GAGACTACGGTGTCGGGTGG 61.931 65.000 4.78 0.00 41.47 4.61
82 83 2.993264 ACTACGGTGTCGGGTGGG 60.993 66.667 0.00 0.00 41.39 4.61
83 84 2.993264 CTACGGTGTCGGGTGGGT 60.993 66.667 0.00 0.00 41.39 4.51
84 85 2.523902 TACGGTGTCGGGTGGGTT 60.524 61.111 0.00 0.00 41.39 4.11
85 86 2.775032 CTACGGTGTCGGGTGGGTTG 62.775 65.000 0.00 0.00 41.39 3.77
87 88 4.653888 GGTGTCGGGTGGGTTGGG 62.654 72.222 0.00 0.00 0.00 4.12
88 89 3.881104 GTGTCGGGTGGGTTGGGT 61.881 66.667 0.00 0.00 0.00 4.51
89 90 3.097830 TGTCGGGTGGGTTGGGTT 61.098 61.111 0.00 0.00 0.00 4.11
90 91 2.196502 GTCGGGTGGGTTGGGTTT 59.803 61.111 0.00 0.00 0.00 3.27
91 92 1.351080 TGTCGGGTGGGTTGGGTTTA 61.351 55.000 0.00 0.00 0.00 2.01
92 93 0.607217 GTCGGGTGGGTTGGGTTTAG 60.607 60.000 0.00 0.00 0.00 1.85
93 94 1.303806 CGGGTGGGTTGGGTTTAGG 60.304 63.158 0.00 0.00 0.00 2.69
94 95 1.077805 GGGTGGGTTGGGTTTAGGG 59.922 63.158 0.00 0.00 0.00 3.53
95 96 1.732355 GGGTGGGTTGGGTTTAGGGT 61.732 60.000 0.00 0.00 0.00 4.34
96 97 0.189080 GGTGGGTTGGGTTTAGGGTT 59.811 55.000 0.00 0.00 0.00 4.11
97 98 1.413372 GGTGGGTTGGGTTTAGGGTTT 60.413 52.381 0.00 0.00 0.00 3.27
98 99 2.158340 GGTGGGTTGGGTTTAGGGTTTA 60.158 50.000 0.00 0.00 0.00 2.01
99 100 3.159472 GTGGGTTGGGTTTAGGGTTTAG 58.841 50.000 0.00 0.00 0.00 1.85
100 101 2.110365 TGGGTTGGGTTTAGGGTTTAGG 59.890 50.000 0.00 0.00 0.00 2.69
101 102 2.558125 GGGTTGGGTTTAGGGTTTAGGG 60.558 54.545 0.00 0.00 0.00 3.53
313 318 4.475135 GGTCTGAGGCGGAAGGGC 62.475 72.222 0.00 0.00 42.69 5.19
494 532 2.742372 CCGGAGTTGACGGCTTGG 60.742 66.667 0.00 0.00 45.34 3.61
495 533 2.030562 CGGAGTTGACGGCTTGGT 59.969 61.111 0.00 0.00 0.00 3.67
496 534 2.317609 CGGAGTTGACGGCTTGGTG 61.318 63.158 0.00 0.00 0.00 4.17
497 535 1.966451 GGAGTTGACGGCTTGGTGG 60.966 63.158 0.00 0.00 0.00 4.61
498 536 1.966451 GAGTTGACGGCTTGGTGGG 60.966 63.158 0.00 0.00 0.00 4.61
499 537 3.670377 GTTGACGGCTTGGTGGGC 61.670 66.667 0.00 0.00 0.00 5.36
906 983 3.373110 GGGCATATTATCCAATCTCCCCC 60.373 52.174 0.00 0.00 0.00 5.40
907 984 3.269381 GGCATATTATCCAATCTCCCCCA 59.731 47.826 0.00 0.00 0.00 4.96
957 1034 2.680352 GAGTCTCCCCTGTCGCCA 60.680 66.667 0.00 0.00 0.00 5.69
1516 1630 5.103687 TCGAATACACGCAGCATTTTAGTA 58.896 37.500 0.00 0.00 0.00 1.82
1517 1631 5.005012 TCGAATACACGCAGCATTTTAGTAC 59.995 40.000 0.00 0.00 0.00 2.73
1518 1632 5.005394 CGAATACACGCAGCATTTTAGTACT 59.995 40.000 0.00 0.00 0.00 2.73
1519 1633 6.455113 CGAATACACGCAGCATTTTAGTACTT 60.455 38.462 0.00 0.00 0.00 2.24
1521 1635 3.435671 ACACGCAGCATTTTAGTACTTCC 59.564 43.478 0.00 0.00 0.00 3.46
1522 1636 3.435327 CACGCAGCATTTTAGTACTTCCA 59.565 43.478 0.00 0.00 0.00 3.53
1523 1637 4.094887 CACGCAGCATTTTAGTACTTCCAT 59.905 41.667 0.00 0.00 0.00 3.41
1618 1738 0.947244 GCAGGTGGATAAGGCATTCG 59.053 55.000 0.00 0.00 0.00 3.34
1668 1788 0.978907 ACGGATCGTTGTTTACCCCT 59.021 50.000 0.00 0.00 36.35 4.79
1669 1789 1.066645 ACGGATCGTTGTTTACCCCTC 60.067 52.381 0.00 0.00 36.35 4.30
1679 1799 7.222872 TCGTTGTTTACCCCTCTTAATTGTAA 58.777 34.615 0.00 0.00 0.00 2.41
1688 1808 8.762481 ACCCCTCTTAATTGTAATTTATCCAC 57.238 34.615 0.00 0.00 0.00 4.02
1734 1854 6.530120 TGTATATGTGAAATACGGCAAGGAT 58.470 36.000 0.00 0.00 33.37 3.24
1754 1874 8.585018 CAAGGATTGTAACTTTTAGTCCCATTT 58.415 33.333 0.00 0.00 42.34 2.32
1759 1879 8.990163 TTGTAACTTTTAGTCCCATTTTCTCT 57.010 30.769 0.00 0.00 0.00 3.10
1944 2065 4.676924 GTGATGCACAAGCTTTCAAACTAC 59.323 41.667 0.00 0.00 42.74 2.73
1965 2086 1.269831 CGGCTAGAAATCTTCTCCCCG 60.270 57.143 11.04 11.04 42.78 5.73
2032 2153 3.737559 ACATTGGGGCTTGATACTGAA 57.262 42.857 0.00 0.00 0.00 3.02
2072 2196 3.305608 GCTCTTGCTAATTTGTGGTTGCT 60.306 43.478 0.00 0.00 36.03 3.91
2181 2305 6.600882 TTGAGGATACCGAAAAGAGTTACT 57.399 37.500 0.00 0.00 37.17 2.24
2195 2319 0.250166 GTTACTTCGGTGGCACAGGT 60.250 55.000 20.82 11.97 41.80 4.00
2198 2322 3.164977 TTCGGTGGCACAGGTGGA 61.165 61.111 20.82 5.29 41.80 4.02
2204 2328 1.000843 GGTGGCACAGGTGGATTTTTC 59.999 52.381 20.82 0.00 41.80 2.29
2208 2332 2.302733 GGCACAGGTGGATTTTTCCAAT 59.697 45.455 1.10 0.00 42.10 3.16
2247 2371 4.379186 GCTCATCTGATTCCACTGTTTGTG 60.379 45.833 0.00 0.00 45.80 3.33
2341 2465 2.092538 CCTCTCATGAAGTGGGCAGATT 60.093 50.000 0.00 0.00 35.39 2.40
2350 2474 5.324409 TGAAGTGGGCAGATTAAAGAATGT 58.676 37.500 0.00 0.00 0.00 2.71
2474 2598 3.277715 TGCCAATGCATTCGAGAATACA 58.722 40.909 9.53 1.69 44.23 2.29
3276 3401 5.535333 TGTAGTAACTGTTAACTGCTCACC 58.465 41.667 11.98 0.00 30.61 4.02
3396 3522 7.047271 TCTTGTTGCTAACATCATGTAGCATA 58.953 34.615 17.39 10.42 43.89 3.14
3573 3699 8.470805 TGGAACACTGATAGTATCTTCTTCTTC 58.529 37.037 11.40 5.03 0.00 2.87
3577 3703 9.474313 ACACTGATAGTATCTTCTTCTTCTTCT 57.526 33.333 11.40 0.00 0.00 2.85
3793 3931 2.905415 TGGTGCTTGGATTGGAGAAT 57.095 45.000 0.00 0.00 0.00 2.40
3820 3958 2.494870 GACTGCTTCAAGGCCATCAATT 59.505 45.455 5.01 0.00 0.00 2.32
3908 4046 0.322098 TTGGTATCAACTGCCACCGG 60.322 55.000 0.00 0.00 39.63 5.28
4027 4165 6.705302 TCTCTGTAGCAGATGAAGACATTTT 58.295 36.000 0.00 0.00 39.92 1.82
4028 4166 6.592994 TCTCTGTAGCAGATGAAGACATTTTG 59.407 38.462 0.00 0.00 39.92 2.44
4279 4501 3.216147 GCAGTGTATGCGTGGATTTTT 57.784 42.857 0.00 0.00 46.99 1.94
4411 5263 5.991328 TTGCTCAGCTATTGTATGCTTAC 57.009 39.130 0.00 2.86 37.44 2.34
4707 5644 3.000041 GCACCGTGTCACTTGATTCATA 59.000 45.455 0.65 0.00 0.00 2.15
5056 5993 5.014966 AGGCCTATTCAAGATCCATGCTAAT 59.985 40.000 1.29 0.00 0.00 1.73
5245 6187 5.152934 ACAACTCTCCCTTGTAAGGTTCTA 58.847 41.667 9.65 0.00 44.98 2.10
5363 6305 4.922206 TGACTGCATGGTTTATTTCCTCT 58.078 39.130 0.00 0.00 0.00 3.69
5377 6319 1.039785 TCCTCTGCGGATCAGGAGTG 61.040 60.000 13.61 11.18 43.06 3.51
5392 6334 1.270678 GGAGTGCTAGACCGGTTTGTT 60.271 52.381 9.42 0.00 0.00 2.83
5402 6344 1.571215 CCGGTTTGTTCTACGGGTGC 61.571 60.000 0.00 0.00 42.48 5.01
5443 6385 0.030603 ATTGGTTTGTGGTTGGGGGT 60.031 50.000 0.00 0.00 0.00 4.95
5444 6386 0.252742 TTGGTTTGTGGTTGGGGGTT 60.253 50.000 0.00 0.00 0.00 4.11
5445 6387 0.978146 TGGTTTGTGGTTGGGGGTTG 60.978 55.000 0.00 0.00 0.00 3.77
5446 6388 0.978667 GGTTTGTGGTTGGGGGTTGT 60.979 55.000 0.00 0.00 0.00 3.32
5488 6430 3.686016 GAAGAACAAATAGACAGGGCCA 58.314 45.455 6.18 0.00 0.00 5.36
5489 6431 4.273318 GAAGAACAAATAGACAGGGCCAT 58.727 43.478 6.18 0.00 0.00 4.40
5492 6434 6.018433 AGAACAAATAGACAGGGCCATATT 57.982 37.500 6.18 1.86 0.00 1.28
5524 6468 2.284754 TGCAAGCACTTCCATTACCA 57.715 45.000 0.00 0.00 0.00 3.25
5902 6846 2.496871 AGCCTCTTGATGTCTCTGTCAG 59.503 50.000 0.00 0.00 0.00 3.51
6021 6966 2.544267 GGTCTATTGTCGCCATGCTTAC 59.456 50.000 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.152963 ACACTTCTGCCCACGCTTT 60.153 52.632 0.00 0.00 35.36 3.51
1 2 1.598130 GACACTTCTGCCCACGCTT 60.598 57.895 0.00 0.00 35.36 4.68
2 3 2.031163 GACACTTCTGCCCACGCT 59.969 61.111 0.00 0.00 35.36 5.07
3 4 3.050275 GGACACTTCTGCCCACGC 61.050 66.667 0.00 0.00 0.00 5.34
5 6 1.600916 GGTGGACACTTCTGCCCAC 60.601 63.158 0.00 0.00 46.14 4.61
6 7 2.836154 GGTGGACACTTCTGCCCA 59.164 61.111 2.13 0.00 0.00 5.36
7 8 2.358737 CGGTGGACACTTCTGCCC 60.359 66.667 2.13 0.00 0.00 5.36
8 9 1.961277 CACGGTGGACACTTCTGCC 60.961 63.158 0.00 0.00 0.00 4.85
9 10 1.069090 TCACGGTGGACACTTCTGC 59.931 57.895 8.50 0.00 0.00 4.26
10 11 0.600255 GGTCACGGTGGACACTTCTG 60.600 60.000 8.50 0.00 39.59 3.02
11 12 1.746517 GGTCACGGTGGACACTTCT 59.253 57.895 8.50 0.00 39.59 2.85
12 13 1.663702 CGGTCACGGTGGACACTTC 60.664 63.158 8.50 0.00 39.59 3.01
13 14 2.420043 CGGTCACGGTGGACACTT 59.580 61.111 8.50 0.00 39.59 3.16
14 15 4.295119 GCGGTCACGGTGGACACT 62.295 66.667 8.50 0.00 39.59 3.55
20 21 4.934942 TCACACGCGGTCACGGTG 62.935 66.667 12.47 8.88 42.78 4.94
21 22 4.936823 GTCACACGCGGTCACGGT 62.937 66.667 12.47 0.00 41.36 4.83
22 23 4.934942 TGTCACACGCGGTCACGG 62.935 66.667 12.47 0.00 41.36 4.94
23 24 3.394874 CTGTCACACGCGGTCACG 61.395 66.667 12.47 0.00 44.63 4.35
24 25 3.702555 GCTGTCACACGCGGTCAC 61.703 66.667 12.47 2.52 0.00 3.67
31 32 2.433145 ATCCTGCGCTGTCACACG 60.433 61.111 9.73 0.00 0.00 4.49
32 33 2.393768 CCATCCTGCGCTGTCACAC 61.394 63.158 9.73 0.00 0.00 3.82
33 34 2.046988 CCATCCTGCGCTGTCACA 60.047 61.111 9.73 0.00 0.00 3.58
34 35 2.821366 CCCATCCTGCGCTGTCAC 60.821 66.667 9.73 0.00 0.00 3.67
35 36 3.321648 ACCCATCCTGCGCTGTCA 61.322 61.111 9.73 0.00 0.00 3.58
36 37 2.821366 CACCCATCCTGCGCTGTC 60.821 66.667 9.73 0.00 0.00 3.51
37 38 3.612247 GACACCCATCCTGCGCTGT 62.612 63.158 9.73 0.65 0.00 4.40
38 39 2.821366 GACACCCATCCTGCGCTG 60.821 66.667 9.73 8.47 0.00 5.18
39 40 3.320879 CTGACACCCATCCTGCGCT 62.321 63.158 9.73 0.00 0.00 5.92
40 41 2.821366 CTGACACCCATCCTGCGC 60.821 66.667 0.00 0.00 0.00 6.09
41 42 1.153489 CTCTGACACCCATCCTGCG 60.153 63.158 0.00 0.00 0.00 5.18
42 43 0.177604 CTCTCTGACACCCATCCTGC 59.822 60.000 0.00 0.00 0.00 4.85
43 44 0.829333 CCTCTCTGACACCCATCCTG 59.171 60.000 0.00 0.00 0.00 3.86
44 45 0.712979 TCCTCTCTGACACCCATCCT 59.287 55.000 0.00 0.00 0.00 3.24
45 46 1.118838 CTCCTCTCTGACACCCATCC 58.881 60.000 0.00 0.00 0.00 3.51
46 47 1.754226 GTCTCCTCTCTGACACCCATC 59.246 57.143 0.00 0.00 33.75 3.51
47 48 1.360852 AGTCTCCTCTCTGACACCCAT 59.639 52.381 0.00 0.00 35.81 4.00
48 49 0.780637 AGTCTCCTCTCTGACACCCA 59.219 55.000 0.00 0.00 35.81 4.51
49 50 2.371306 GTAGTCTCCTCTCTGACACCC 58.629 57.143 0.00 0.00 35.81 4.61
50 51 2.011222 CGTAGTCTCCTCTCTGACACC 58.989 57.143 0.00 0.00 35.81 4.16
51 52 2.011222 CCGTAGTCTCCTCTCTGACAC 58.989 57.143 0.00 0.00 35.81 3.67
52 53 1.629353 ACCGTAGTCTCCTCTCTGACA 59.371 52.381 0.00 0.00 35.81 3.58
53 54 2.011222 CACCGTAGTCTCCTCTCTGAC 58.989 57.143 0.00 0.00 0.00 3.51
54 55 1.629353 ACACCGTAGTCTCCTCTCTGA 59.371 52.381 0.00 0.00 0.00 3.27
55 56 2.011222 GACACCGTAGTCTCCTCTCTG 58.989 57.143 0.00 0.00 35.65 3.35
56 57 1.405797 CGACACCGTAGTCTCCTCTCT 60.406 57.143 3.46 0.00 36.38 3.10
57 58 1.008329 CGACACCGTAGTCTCCTCTC 58.992 60.000 3.46 0.00 36.38 3.20
58 59 0.392729 CCGACACCGTAGTCTCCTCT 60.393 60.000 3.46 0.00 36.38 3.69
59 60 1.375098 CCCGACACCGTAGTCTCCTC 61.375 65.000 3.46 0.00 36.38 3.71
60 61 1.378250 CCCGACACCGTAGTCTCCT 60.378 63.158 3.46 0.00 36.38 3.69
61 62 1.676967 ACCCGACACCGTAGTCTCC 60.677 63.158 3.46 0.00 36.38 3.71
62 63 1.505353 CACCCGACACCGTAGTCTC 59.495 63.158 3.46 0.00 36.38 3.36
63 64 1.975407 CCACCCGACACCGTAGTCT 60.975 63.158 3.46 0.00 36.38 3.24
64 65 2.570181 CCACCCGACACCGTAGTC 59.430 66.667 0.00 0.00 35.19 2.59
65 66 2.993264 CCCACCCGACACCGTAGT 60.993 66.667 0.00 0.00 0.00 2.73
66 67 2.576832 AACCCACCCGACACCGTAG 61.577 63.158 0.00 0.00 0.00 3.51
67 68 2.523902 AACCCACCCGACACCGTA 60.524 61.111 0.00 0.00 0.00 4.02
68 69 4.244463 CAACCCACCCGACACCGT 62.244 66.667 0.00 0.00 0.00 4.83
70 71 4.653888 CCCAACCCACCCGACACC 62.654 72.222 0.00 0.00 0.00 4.16
71 72 2.914756 AAACCCAACCCACCCGACAC 62.915 60.000 0.00 0.00 0.00 3.67
72 73 1.351080 TAAACCCAACCCACCCGACA 61.351 55.000 0.00 0.00 0.00 4.35
73 74 0.607217 CTAAACCCAACCCACCCGAC 60.607 60.000 0.00 0.00 0.00 4.79
74 75 1.762471 CTAAACCCAACCCACCCGA 59.238 57.895 0.00 0.00 0.00 5.14
75 76 1.303806 CCTAAACCCAACCCACCCG 60.304 63.158 0.00 0.00 0.00 5.28
76 77 1.077805 CCCTAAACCCAACCCACCC 59.922 63.158 0.00 0.00 0.00 4.61
77 78 0.189080 AACCCTAAACCCAACCCACC 59.811 55.000 0.00 0.00 0.00 4.61
78 79 2.091098 AAACCCTAAACCCAACCCAC 57.909 50.000 0.00 0.00 0.00 4.61
79 80 2.110365 CCTAAACCCTAAACCCAACCCA 59.890 50.000 0.00 0.00 0.00 4.51
80 81 2.558125 CCCTAAACCCTAAACCCAACCC 60.558 54.545 0.00 0.00 0.00 4.11
81 82 2.110543 ACCCTAAACCCTAAACCCAACC 59.889 50.000 0.00 0.00 0.00 3.77
82 83 3.159472 CACCCTAAACCCTAAACCCAAC 58.841 50.000 0.00 0.00 0.00 3.77
83 84 2.790585 ACACCCTAAACCCTAAACCCAA 59.209 45.455 0.00 0.00 0.00 4.12
84 85 2.430963 ACACCCTAAACCCTAAACCCA 58.569 47.619 0.00 0.00 0.00 4.51
85 86 4.227982 TGATACACCCTAAACCCTAAACCC 59.772 45.833 0.00 0.00 0.00 4.11
86 87 5.440207 TGATACACCCTAAACCCTAAACC 57.560 43.478 0.00 0.00 0.00 3.27
87 88 6.183360 GCAATGATACACCCTAAACCCTAAAC 60.183 42.308 0.00 0.00 0.00 2.01
88 89 5.889289 GCAATGATACACCCTAAACCCTAAA 59.111 40.000 0.00 0.00 0.00 1.85
89 90 5.192923 AGCAATGATACACCCTAAACCCTAA 59.807 40.000 0.00 0.00 0.00 2.69
90 91 4.724798 AGCAATGATACACCCTAAACCCTA 59.275 41.667 0.00 0.00 0.00 3.53
91 92 3.527665 AGCAATGATACACCCTAAACCCT 59.472 43.478 0.00 0.00 0.00 4.34
92 93 3.898482 AGCAATGATACACCCTAAACCC 58.102 45.455 0.00 0.00 0.00 4.11
93 94 4.515567 GCTAGCAATGATACACCCTAAACC 59.484 45.833 10.63 0.00 0.00 3.27
94 95 5.123227 TGCTAGCAATGATACACCCTAAAC 58.877 41.667 16.84 0.00 0.00 2.01
95 96 5.366482 TGCTAGCAATGATACACCCTAAA 57.634 39.130 16.84 0.00 0.00 1.85
96 97 5.123227 GTTGCTAGCAATGATACACCCTAA 58.877 41.667 31.46 2.44 38.28 2.69
97 98 4.444306 GGTTGCTAGCAATGATACACCCTA 60.444 45.833 31.46 2.92 38.28 3.53
98 99 3.545703 GTTGCTAGCAATGATACACCCT 58.454 45.455 31.46 0.00 38.28 4.34
99 100 2.618709 GGTTGCTAGCAATGATACACCC 59.381 50.000 31.46 20.95 38.28 4.61
100 101 3.278574 TGGTTGCTAGCAATGATACACC 58.721 45.455 31.46 25.51 38.28 4.16
101 102 4.319046 CGATGGTTGCTAGCAATGATACAC 60.319 45.833 31.46 17.92 38.28 2.90
313 318 3.866883 AATTGGTAAGCATTTGGTCCG 57.133 42.857 0.00 0.00 0.00 4.79
478 516 2.030562 ACCAAGCCGTCAACTCCG 59.969 61.111 0.00 0.00 0.00 4.63
479 517 1.966451 CCACCAAGCCGTCAACTCC 60.966 63.158 0.00 0.00 0.00 3.85
480 518 1.966451 CCCACCAAGCCGTCAACTC 60.966 63.158 0.00 0.00 0.00 3.01
481 519 2.113139 CCCACCAAGCCGTCAACT 59.887 61.111 0.00 0.00 0.00 3.16
482 520 3.670377 GCCCACCAAGCCGTCAAC 61.670 66.667 0.00 0.00 0.00 3.18
1079 1169 1.617357 GTGGTAGGGTTCTGAGAACGT 59.383 52.381 18.13 10.95 0.00 3.99
1081 1171 1.067071 CGGTGGTAGGGTTCTGAGAAC 60.067 57.143 16.70 16.70 0.00 3.01
1199 1289 4.592192 CGATGGGGATGACGCGCT 62.592 66.667 5.73 0.00 34.15 5.92
1401 1491 0.605589 AAAGTAAGGCGCTCACCACC 60.606 55.000 7.64 0.00 0.00 4.61
1516 1630 5.241064 GCTGCATATTTCTGATGATGGAAGT 59.759 40.000 0.00 0.00 0.00 3.01
1517 1631 5.335740 GGCTGCATATTTCTGATGATGGAAG 60.336 44.000 0.50 0.00 0.00 3.46
1518 1632 4.521639 GGCTGCATATTTCTGATGATGGAA 59.478 41.667 0.50 0.00 0.00 3.53
1519 1633 4.077108 GGCTGCATATTTCTGATGATGGA 58.923 43.478 0.50 0.00 0.00 3.41
1521 1635 5.220381 GTTGGCTGCATATTTCTGATGATG 58.780 41.667 0.50 0.00 0.00 3.07
1522 1636 4.891168 TGTTGGCTGCATATTTCTGATGAT 59.109 37.500 0.50 0.00 0.00 2.45
1523 1637 4.096833 GTGTTGGCTGCATATTTCTGATGA 59.903 41.667 0.50 0.00 0.00 2.92
1563 1682 6.753744 GGAATCCACATGTTGAATTTAGCTTC 59.246 38.462 3.42 1.82 0.00 3.86
1570 1690 5.338544 CCATTGGGAATCCACATGTTGAATT 60.339 40.000 3.42 0.53 43.94 2.17
1618 1738 0.668706 ACATGTCTCGACTGCAGCAC 60.669 55.000 15.27 7.56 0.00 4.40
1668 1788 9.893634 TCCTTCGTGGATAAATTACAATTAAGA 57.106 29.630 0.00 0.00 40.56 2.10
1679 1799 7.736893 ACTAATAAGCTCCTTCGTGGATAAAT 58.263 34.615 0.00 0.00 45.16 1.40
1688 1808 5.869888 ACAAACAGACTAATAAGCTCCTTCG 59.130 40.000 0.00 0.00 0.00 3.79
1734 1854 8.990163 AGAGAAAATGGGACTAAAAGTTACAA 57.010 30.769 0.00 0.00 0.00 2.41
1738 1858 7.998964 TGAAGAGAGAAAATGGGACTAAAAGTT 59.001 33.333 0.00 0.00 0.00 2.66
1739 1859 7.518188 TGAAGAGAGAAAATGGGACTAAAAGT 58.482 34.615 0.00 0.00 0.00 2.66
1745 1865 6.779539 ACAAAATGAAGAGAGAAAATGGGACT 59.220 34.615 0.00 0.00 0.00 3.85
1749 1869 8.975439 CAAGAACAAAATGAAGAGAGAAAATGG 58.025 33.333 0.00 0.00 0.00 3.16
1750 1870 9.740239 TCAAGAACAAAATGAAGAGAGAAAATG 57.260 29.630 0.00 0.00 0.00 2.32
1754 1874 7.282585 TCCTCAAGAACAAAATGAAGAGAGAA 58.717 34.615 0.00 0.00 0.00 2.87
1759 1879 7.645058 AACTTCCTCAAGAACAAAATGAAGA 57.355 32.000 0.00 0.00 33.84 2.87
1944 2065 1.070914 GGGGAGAAGATTTCTAGCCGG 59.929 57.143 0.00 0.00 40.87 6.13
1965 2086 1.563577 GGAAGTCCCTCCCTGAACCC 61.564 65.000 0.00 0.00 0.00 4.11
2032 2153 7.463544 GCAAGAGCTAAACAAACAAACAAAAT 58.536 30.769 0.00 0.00 37.91 1.82
2181 2305 2.063015 AATCCACCTGTGCCACCGAA 62.063 55.000 0.00 0.00 0.00 4.30
2195 2319 3.367292 GCTTCTGCGATTGGAAAAATCCA 60.367 43.478 0.00 0.00 38.14 3.41
2198 2322 3.507233 TCAGCTTCTGCGATTGGAAAAAT 59.493 39.130 0.00 0.00 45.42 1.82
2204 2328 1.129998 CAGTTCAGCTTCTGCGATTGG 59.870 52.381 0.00 0.00 45.42 3.16
2208 2332 3.957260 GCAGTTCAGCTTCTGCGA 58.043 55.556 16.05 0.00 45.42 5.10
2247 2371 2.673368 CTGCCTCGGAAATTCTGTGTAC 59.327 50.000 1.33 0.00 0.00 2.90
2341 2465 2.513753 CTGGCCACCACACATTCTTTA 58.486 47.619 0.00 0.00 0.00 1.85
2393 2517 4.098501 GCCCAAAGGATAAAATCAGGACTG 59.901 45.833 0.00 0.00 33.47 3.51
2394 2518 4.281657 GCCCAAAGGATAAAATCAGGACT 58.718 43.478 0.00 0.00 33.47 3.85
2474 2598 1.074405 TCATGACAGCCCTCAAGCTTT 59.926 47.619 0.00 0.00 42.61 3.51
2616 2740 2.904434 CCCTAGTTCCACCTACAGTTGT 59.096 50.000 0.00 0.00 0.00 3.32
3229 3354 3.061965 GCAAGTTGCAACAAATGAACGTT 59.938 39.130 30.11 10.42 44.26 3.99
3276 3401 4.760530 TCCAGAGACTCCATGGTTTATG 57.239 45.455 12.58 4.71 35.51 1.90
3793 3931 1.174712 GCCTTGAAGCAGTCAGGCAA 61.175 55.000 17.87 0.00 44.02 4.52
3820 3958 2.097954 CAGAAGCAGCATTATCGCCAAA 59.902 45.455 0.00 0.00 0.00 3.28
3901 4039 1.153349 GAGAAGTCATCCCGGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
4027 4165 9.733556 AGTTGTAGATACACCATCAAAAATACA 57.266 29.630 0.00 0.00 35.64 2.29
4143 4326 3.337889 GCTTCAGCACGCGTGACA 61.338 61.111 41.19 21.19 41.59 3.58
4178 4361 6.007076 TGCATTGGGATAATATTTAAGGCGA 58.993 36.000 0.00 0.00 0.00 5.54
4374 4597 5.590259 AGCTGAGCAAACAGTAAAAGAAAGA 59.410 36.000 7.39 0.00 39.73 2.52
4411 5263 3.444742 TCCAATTGCAGCCAAAGTATCAG 59.555 43.478 0.00 0.00 34.05 2.90
4464 5318 8.297426 GGTATAAAAGAGTAGCTTGCAGTTTTT 58.703 33.333 0.00 0.00 36.80 1.94
4472 5326 9.606631 ATTCAAGAGGTATAAAAGAGTAGCTTG 57.393 33.333 0.00 0.00 36.80 4.01
4483 5337 6.257849 CGCACAGCTTATTCAAGAGGTATAAA 59.742 38.462 0.00 0.00 33.20 1.40
4624 5561 8.593945 ATCAATTTATTTTAACAGAGGGAGCA 57.406 30.769 0.00 0.00 0.00 4.26
4651 5588 7.814107 GCATTTGACCAAAGAGAATGAATAACA 59.186 33.333 1.57 0.00 33.32 2.41
4707 5644 7.437713 TCTTCTGACATCACCACCTAAATAT 57.562 36.000 0.00 0.00 0.00 1.28
4886 5823 6.888105 TCAGACAGGACAAAATATATGAGCA 58.112 36.000 0.00 0.00 0.00 4.26
5056 5993 5.789574 ATGAAATGGTTAAGGTACCTCCA 57.210 39.130 20.12 20.12 39.04 3.86
5161 6103 2.409948 ATGTAGAAGAGGCCAGCAAC 57.590 50.000 5.01 0.00 0.00 4.17
5218 6160 5.690997 CCTTACAAGGGAGAGTTGTTTTC 57.309 43.478 0.00 0.00 42.66 2.29
5234 6176 6.068616 ACACCTAGGACCTATAGAACCTTACA 60.069 42.308 17.98 5.12 34.42 2.41
5235 6177 6.372104 ACACCTAGGACCTATAGAACCTTAC 58.628 44.000 17.98 0.00 34.42 2.34
5245 6187 4.880164 TGCTTAGAACACCTAGGACCTAT 58.120 43.478 17.98 0.56 0.00 2.57
5363 6305 0.395724 TCTAGCACTCCTGATCCGCA 60.396 55.000 0.00 0.00 0.00 5.69
5377 6319 2.257034 CGTAGAACAAACCGGTCTAGC 58.743 52.381 8.04 0.00 0.00 3.42
5443 6385 2.830827 CGCACACCCCCACAACAA 60.831 61.111 0.00 0.00 0.00 2.83
5444 6386 4.885270 CCGCACACCCCCACAACA 62.885 66.667 0.00 0.00 0.00 3.33
5445 6387 4.572571 TCCGCACACCCCCACAAC 62.573 66.667 0.00 0.00 0.00 3.32
5446 6388 4.263572 CTCCGCACACCCCCACAA 62.264 66.667 0.00 0.00 0.00 3.33
5466 6408 2.678336 GGCCCTGTCTATTTGTTCTTCG 59.322 50.000 0.00 0.00 0.00 3.79
5488 6430 9.784531 AGTGCTTGCATAGTCATAACTAAATAT 57.215 29.630 0.00 0.00 41.25 1.28
5489 6431 9.613428 AAGTGCTTGCATAGTCATAACTAAATA 57.387 29.630 0.00 0.00 41.25 1.40
5492 6434 6.538742 GGAAGTGCTTGCATAGTCATAACTAA 59.461 38.462 0.00 0.00 41.25 2.24
5902 6846 1.459450 TTTCTTATGAACGCCAGGGC 58.541 50.000 0.00 0.00 37.85 5.19
6021 6966 9.632969 CTACTTTTATTGACGTTTATCCAATCG 57.367 33.333 2.99 0.00 33.21 3.34


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

AutoCloner maintained by Alex Coulton.