Multiple sequence alignment - TraesCS2A01G544000

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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 TraesCS2A01G544000 chr2A 100.000 3772 0 0 1 3772 753612921 753616692 0.000000e+00 6966.0
1 TraesCS2A01G544000 chr2B 89.260 3231 199 52 3 3118 763837880 763841077 0.000000e+00 3908.0
2 TraesCS2A01G544000 chr2B 97.143 630 18 0 3102 3731 763841264 763841893 0.000000e+00 1064.0
3 TraesCS2A01G544000 chr2B 89.354 526 46 6 1844 2362 52188129 52187607 0.000000e+00 652.0
4 TraesCS2A01G544000 chr2B 90.465 409 32 1 1126 1527 785860452 785860860 1.990000e-147 532.0
5 TraesCS2A01G544000 chr2B 89.447 398 38 3 1146 1543 719635513 719635120 2.020000e-137 499.0
6 TraesCS2A01G544000 chr2B 84.941 425 50 7 1126 1543 737641074 737641491 5.830000e-113 418.0
7 TraesCS2A01G544000 chr2B 92.424 264 20 0 1126 1389 312364523 312364260 9.890000e-101 377.0
8 TraesCS2A01G544000 chr2D 88.345 2145 160 41 756 2834 621954300 621952180 0.000000e+00 2494.0
9 TraesCS2A01G544000 chr2D 93.452 901 37 4 2832 3731 621952085 621951206 0.000000e+00 1317.0
10 TraesCS2A01G544000 chr2D 89.821 560 37 10 987 1527 582869037 582869595 0.000000e+00 701.0
11 TraesCS2A01G544000 chr4B 89.231 585 49 9 1844 2419 378837115 378836536 0.000000e+00 719.0
12 TraesCS2A01G544000 chr3D 88.947 570 52 7 1844 2406 436318527 436319092 0.000000e+00 693.0
13 TraesCS2A01G544000 chr3D 80.218 824 96 39 956 1729 570096789 570095983 1.180000e-154 556.0
14 TraesCS2A01G544000 chr3D 84.254 362 42 8 1550 1897 277240140 277240500 4.670000e-89 339.0
15 TraesCS2A01G544000 chr3D 80.000 340 43 15 1356 1671 436318072 436318410 1.050000e-55 228.0
16 TraesCS2A01G544000 chr7B 88.396 586 53 10 1844 2419 608285942 608286522 0.000000e+00 691.0
17 TraesCS2A01G544000 chr7B 92.383 407 31 0 1126 1532 744691954 744691548 7.020000e-162 580.0
18 TraesCS2A01G544000 chr7B 85.083 362 39 10 1550 1897 234761687 234762047 4.630000e-94 355.0
19 TraesCS2A01G544000 chr7B 90.306 196 8 7 1013 1197 744692153 744691958 2.910000e-61 246.0
20 TraesCS2A01G544000 chr7B 94.872 39 1 1 3729 3767 38614404 38614441 4.070000e-05 60.2
21 TraesCS2A01G544000 chr5B 88.205 585 55 9 1844 2419 645187290 645187869 0.000000e+00 686.0
22 TraesCS2A01G544000 chr4D 86.226 363 32 13 1550 1897 166139320 166139679 9.890000e-101 377.0
23 TraesCS2A01G544000 chr4D 80.473 507 63 21 1421 1897 150648840 150648340 4.630000e-94 355.0
24 TraesCS2A01G544000 chr4D 84.916 358 39 11 1550 1893 67195425 67195069 7.750000e-92 348.0
25 TraesCS2A01G544000 chr4D 84.254 362 42 10 1550 1897 289495177 289495537 4.670000e-89 339.0
26 TraesCS2A01G544000 chr7A 86.567 335 30 8 1577 1897 305581762 305581429 4.630000e-94 355.0
27 TraesCS2A01G544000 chr7A 83.149 362 46 6 1550 1897 291106024 291105664 2.190000e-82 316.0
28 TraesCS2A01G544000 chr7A 89.655 174 16 2 1844 2017 633539545 633539374 1.760000e-53 220.0
29 TraesCS2A01G544000 chr5D 79.842 506 69 18 1421 1897 504229862 504230363 4.670000e-89 339.0
30 TraesCS2A01G544000 chr5D 84.254 362 42 6 1550 1897 511351673 511351313 4.670000e-89 339.0
31 TraesCS2A01G544000 chr5D 84.022 363 39 15 1550 1897 147619247 147619605 7.810000e-87 331.0
32 TraesCS2A01G544000 chr6B 90.230 174 15 2 1844 2017 54644999 54645170 3.790000e-55 226.0
33 TraesCS2A01G544000 chr7D 87.778 180 20 2 1552 1730 41262192 41262370 3.820000e-50 209.0
34 TraesCS2A01G544000 chr3B 87.778 180 20 2 1552 1730 345086310 345086488 3.820000e-50 209.0
35 TraesCS2A01G544000 chr6D 86.905 168 17 3 1298 1461 67036905 67036739 2.310000e-42 183.0
36 TraesCS2A01G544000 chr1B 97.674 43 0 1 3725 3767 72798815 72798774 5.230000e-09 73.1
37 TraesCS2A01G544000 chr1D 90.385 52 5 0 3721 3772 43822684 43822735 6.760000e-08 69.4


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 TraesCS2A01G544000 chr2A 753612921 753616692 3771 False 6966.0 6966 100.0000 1 3772 1 chr2A.!!$F1 3771
1 TraesCS2A01G544000 chr2B 763837880 763841893 4013 False 2486.0 3908 93.2015 3 3731 2 chr2B.!!$F3 3728
2 TraesCS2A01G544000 chr2B 52187607 52188129 522 True 652.0 652 89.3540 1844 2362 1 chr2B.!!$R1 518
3 TraesCS2A01G544000 chr2D 621951206 621954300 3094 True 1905.5 2494 90.8985 756 3731 2 chr2D.!!$R1 2975
4 TraesCS2A01G544000 chr2D 582869037 582869595 558 False 701.0 701 89.8210 987 1527 1 chr2D.!!$F1 540
5 TraesCS2A01G544000 chr4B 378836536 378837115 579 True 719.0 719 89.2310 1844 2419 1 chr4B.!!$R1 575
6 TraesCS2A01G544000 chr3D 570095983 570096789 806 True 556.0 556 80.2180 956 1729 1 chr3D.!!$R1 773
7 TraesCS2A01G544000 chr3D 436318072 436319092 1020 False 460.5 693 84.4735 1356 2406 2 chr3D.!!$F2 1050
8 TraesCS2A01G544000 chr7B 608285942 608286522 580 False 691.0 691 88.3960 1844 2419 1 chr7B.!!$F3 575
9 TraesCS2A01G544000 chr7B 744691548 744692153 605 True 413.0 580 91.3445 1013 1532 2 chr7B.!!$R1 519
10 TraesCS2A01G544000 chr5B 645187290 645187869 579 False 686.0 686 88.2050 1844 2419 1 chr5B.!!$F1 575
11 TraesCS2A01G544000 chr4D 150648340 150648840 500 True 355.0 355 80.4730 1421 1897 1 chr4D.!!$R2 476
12 TraesCS2A01G544000 chr5D 504229862 504230363 501 False 339.0 339 79.8420 1421 1897 1 chr5D.!!$F2 476

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
642 670 0.179084 TCGGAATCGCCAAGATCCAC 60.179 55.0 0.0 0.0 38.98 4.02 F
1348 1551 0.696501 TTACTCCCCACTTTGCTCCC 59.303 55.0 0.0 0.0 0.00 4.30 F
2343 2610 0.447801 CTTGCGTACCCATCACTTGC 59.552 55.0 0.0 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1965 0.037303 CCTCTGCACACTGAATGGGT 59.963 55.0 0.00 0.00 32.41 4.51 R
2728 2995 0.036732 TGGTTGCCCTGTCTTGCTAG 59.963 55.0 0.00 0.00 0.00 3.42 R
3733 4304 0.447801 CAAGCAATTCCGAACGGAGG 59.552 55.0 15.34 10.65 46.06 4.30 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
55 56 2.747989 CAAGAGTACTCTACAGTCCGCA 59.252 50.000 25.42 0.00 39.39 5.69
57 58 2.082231 GAGTACTCTACAGTCCGCACA 58.918 52.381 15.91 0.00 33.62 4.57
70 71 3.751698 AGTCCGCACAAAGGTAATTTCTC 59.248 43.478 0.00 0.00 0.00 2.87
149 150 7.594758 TGATTGCTACTCTTTGTAATTGTTTGC 59.405 33.333 0.00 0.00 0.00 3.68
154 155 5.540911 ACTCTTTGTAATTGTTTGCCCATG 58.459 37.500 0.00 0.00 0.00 3.66
158 159 5.480642 TTGTAATTGTTTGCCCATGTCAT 57.519 34.783 0.00 0.00 0.00 3.06
198 199 9.953565 ATATTTGTTTGCAGAGGTAGTACTTTA 57.046 29.630 0.00 0.00 0.00 1.85
202 203 9.953565 TTGTTTGCAGAGGTAGTACTTTATTAT 57.046 29.630 0.00 0.00 0.00 1.28
238 239 8.681486 ACAATGATAGTTTGCTGCTATTATCA 57.319 30.769 16.39 16.39 33.55 2.15
341 343 6.782494 ACAAGAATACCAAGGACCAAATTTCT 59.218 34.615 0.00 0.00 0.00 2.52
342 344 6.840780 AGAATACCAAGGACCAAATTTCTG 57.159 37.500 0.00 0.00 0.00 3.02
350 352 1.080907 CCAAATTTCTGGGCCCCCT 59.919 57.895 22.27 0.00 36.94 4.79
354 356 2.168272 AATTTCTGGGCCCCCTCACC 62.168 60.000 22.27 0.00 36.94 4.02
355 357 4.608514 TTCTGGGCCCCCTCACCA 62.609 66.667 22.27 0.00 36.94 4.17
379 381 1.451387 GTGGTCGGGGAAATGCGAT 60.451 57.895 0.00 0.00 0.00 4.58
410 412 2.125512 GGATGAAGCGTGCCTCGT 60.126 61.111 0.83 0.00 42.13 4.18
434 436 2.012414 CGGTTTCGCTCGTGACGAA 61.012 57.895 9.64 10.94 46.91 3.85
446 448 0.666577 GTGACGAACGCTTGCCTAGT 60.667 55.000 0.00 0.00 0.00 2.57
520 528 2.010497 GATCAAAGGAGAAGGCGGTTC 58.990 52.381 0.00 0.00 35.08 3.62
551 569 7.998383 ACCAACCATATGCAGATCTTACAATAA 59.002 33.333 0.00 0.00 0.00 1.40
578 596 5.943416 AGAAACATTTGTCGGTATCAATCCA 59.057 36.000 0.00 0.00 0.00 3.41
585 603 2.948979 GTCGGTATCAATCCATTTGCCA 59.051 45.455 0.00 0.00 35.16 4.92
589 607 3.003689 GGTATCAATCCATTTGCCACTCG 59.996 47.826 0.00 0.00 35.16 4.18
590 608 1.462616 TCAATCCATTTGCCACTCGG 58.537 50.000 0.00 0.00 35.16 4.63
621 649 6.313744 TCTTTTCGAGTTTCCATTTCTTCC 57.686 37.500 0.00 0.00 0.00 3.46
626 654 3.125316 CGAGTTTCCATTTCTTCCTTCGG 59.875 47.826 0.00 0.00 0.00 4.30
627 655 4.324267 GAGTTTCCATTTCTTCCTTCGGA 58.676 43.478 0.00 0.00 0.00 4.55
642 670 0.179084 TCGGAATCGCCAAGATCCAC 60.179 55.000 0.00 0.00 38.98 4.02
645 673 2.094126 GAATCGCCAAGATCCACGCG 62.094 60.000 3.53 3.53 45.76 6.01
673 701 2.125912 CGGCCCTCGAGTCAGTTG 60.126 66.667 12.31 0.00 42.43 3.16
682 710 1.067974 TCGAGTCAGTTGGAGCGAAAA 59.932 47.619 0.00 0.00 32.56 2.29
683 711 1.192534 CGAGTCAGTTGGAGCGAAAAC 59.807 52.381 0.00 0.00 0.00 2.43
693 721 1.848932 GAGCGAAAACCGTTCCCACC 61.849 60.000 0.00 0.00 41.74 4.61
702 730 1.555992 ACCGTTCCCACCGAATATCAA 59.444 47.619 0.00 0.00 31.67 2.57
759 804 3.992643 TGGGATTCAAGCAACAATGTTG 58.007 40.909 20.77 20.77 0.00 3.33
908 967 3.490759 CCTCGTGCGCATCACCAC 61.491 66.667 15.91 0.00 42.69 4.16
910 969 2.029288 CTCGTGCGCATCACCACTT 61.029 57.895 15.91 0.00 42.69 3.16
948 1025 1.207593 CAAAGCTCGACCAAAGCCG 59.792 57.895 0.00 0.00 40.75 5.52
949 1026 1.227853 AAAGCTCGACCAAAGCCGT 60.228 52.632 0.00 0.00 40.75 5.68
951 1028 2.357034 GCTCGACCAAAGCCGTGA 60.357 61.111 0.00 0.00 33.53 4.35
952 1029 2.668280 GCTCGACCAAAGCCGTGAC 61.668 63.158 0.00 0.00 33.53 3.67
953 1030 1.300620 CTCGACCAAAGCCGTGACA 60.301 57.895 0.00 0.00 0.00 3.58
954 1031 1.557443 CTCGACCAAAGCCGTGACAC 61.557 60.000 0.00 0.00 0.00 3.67
961 1038 2.113243 AAAGCCGTGACACTCCTCCC 62.113 60.000 3.68 0.00 0.00 4.30
985 1062 2.362503 GGCCCAAACCCTAGCCAC 60.363 66.667 0.00 0.00 45.07 5.01
1323 1526 2.099652 CTGCTCAACAGGTCCGTCCA 62.100 60.000 0.00 0.00 43.19 4.02
1347 1550 2.160205 GTTTACTCCCCACTTTGCTCC 58.840 52.381 0.00 0.00 0.00 4.70
1348 1551 0.696501 TTACTCCCCACTTTGCTCCC 59.303 55.000 0.00 0.00 0.00 4.30
1349 1552 1.550130 TACTCCCCACTTTGCTCCCG 61.550 60.000 0.00 0.00 0.00 5.14
1495 1708 6.494952 AGTATCGGGTACAGATTAGGATCAT 58.505 40.000 8.13 0.00 41.22 2.45
1540 1774 5.112220 CAAATGTTGCTGTATCACACTGT 57.888 39.130 0.00 0.00 0.00 3.55
1541 1775 5.149273 CAAATGTTGCTGTATCACACTGTC 58.851 41.667 0.00 0.00 0.00 3.51
1542 1776 2.766313 TGTTGCTGTATCACACTGTCC 58.234 47.619 0.00 0.00 0.00 4.02
1543 1777 2.368548 TGTTGCTGTATCACACTGTCCT 59.631 45.455 0.00 0.00 0.00 3.85
1544 1778 2.738846 GTTGCTGTATCACACTGTCCTG 59.261 50.000 0.00 0.00 0.00 3.86
1545 1779 1.276138 TGCTGTATCACACTGTCCTGG 59.724 52.381 0.00 0.00 0.00 4.45
1546 1780 1.550524 GCTGTATCACACTGTCCTGGA 59.449 52.381 0.00 0.00 0.00 3.86
1547 1781 2.169352 GCTGTATCACACTGTCCTGGAT 59.831 50.000 0.00 0.00 0.00 3.41
1558 1792 3.643792 ACTGTCCTGGATATCTTACTGCC 59.356 47.826 0.00 0.00 0.00 4.85
1565 1799 4.065088 TGGATATCTTACTGCCGAATTGC 58.935 43.478 2.05 0.00 0.00 3.56
1569 1803 2.778299 TCTTACTGCCGAATTGCTTGT 58.222 42.857 0.00 0.00 0.00 3.16
1657 1896 1.635487 TGTAGAATTTGGGCCTGAGCT 59.365 47.619 4.53 0.00 39.73 4.09
1672 1911 3.192212 CCTGAGCTCTTTGGAATTTGGTC 59.808 47.826 16.19 0.00 0.00 4.02
1673 1912 3.157087 TGAGCTCTTTGGAATTTGGTCC 58.843 45.455 16.19 0.00 38.27 4.46
1677 1916 4.289672 AGCTCTTTGGAATTTGGTCCTAGA 59.710 41.667 0.00 0.00 38.62 2.43
1695 1934 8.432805 GGTCCTAGATTGAGATTAATCTTTGGA 58.567 37.037 18.88 14.35 43.08 3.53
1718 1957 3.910627 AGATGTTAGAGTGGGTTCAAGGT 59.089 43.478 0.00 0.00 0.00 3.50
1726 1965 3.256704 AGTGGGTTCAAGGTTGGATCTA 58.743 45.455 0.00 0.00 0.00 1.98
1770 2024 5.107133 TCTTCTAATTTACCACTAGCGCAC 58.893 41.667 11.47 0.00 0.00 5.34
1938 2194 7.276658 TGATGTGTAGGTCTCTTACAAAAACA 58.723 34.615 0.00 0.00 0.00 2.83
1954 2210 6.099341 ACAAAAACAATCTGTCTGTGTTTCC 58.901 36.000 1.84 0.00 42.96 3.13
1955 2211 5.913137 AAAACAATCTGTCTGTGTTTCCA 57.087 34.783 1.84 0.00 42.96 3.53
1963 2219 8.607459 CAATCTGTCTGTGTTTCCATAGTTATC 58.393 37.037 0.00 0.00 32.13 1.75
2112 2371 6.142798 GGTGCATCTTAATTGATTATTGCGTG 59.857 38.462 0.00 0.00 31.37 5.34
2124 2389 0.867086 ATTGCGTGGCATTGTTTTGC 59.133 45.000 0.00 0.00 38.76 3.68
2212 2479 4.462483 GCCTAATCTAGAGGTCTCAGATGG 59.538 50.000 0.00 10.28 36.37 3.51
2227 2494 1.978580 AGATGGGGTCGTTGAGAAAGT 59.021 47.619 0.00 0.00 0.00 2.66
2343 2610 0.447801 CTTGCGTACCCATCACTTGC 59.552 55.000 0.00 0.00 0.00 4.01
2398 2665 5.233050 CACACAAACTTCTCTCTGTACTGTG 59.767 44.000 0.00 0.00 36.77 3.66
2413 2680 1.824852 ACTGTGCCTCATGTACGATCA 59.175 47.619 0.00 0.00 31.26 2.92
2427 2694 5.547465 TGTACGATCACCTTTTGTCTCATT 58.453 37.500 0.00 0.00 0.00 2.57
2719 2986 2.417933 GCATACTGTCAAGGCAGTTGAG 59.582 50.000 13.01 4.80 46.18 3.02
2728 2995 2.092882 GGCAGTTGAGTACCGTCGC 61.093 63.158 0.00 0.00 0.00 5.19
2996 3363 3.692257 AATCCCTGGAAGATGCTATCG 57.308 47.619 0.00 0.00 34.07 2.92
3010 3377 4.901197 TGCTATCGAAGGGCCATTATAA 57.099 40.909 0.73 0.00 0.00 0.98
3164 3735 6.122277 TCTGGGATCATAATGTTGTTTCCTC 58.878 40.000 0.00 0.00 0.00 3.71
3233 3804 7.540055 GCTCCAATCAGTCTGTTTTAGAATTTG 59.460 37.037 0.00 0.00 37.12 2.32
3319 3890 7.741027 ATCAGCATCATGATTAAGTCGAAAT 57.259 32.000 5.16 0.00 36.50 2.17
3320 3891 7.558161 TCAGCATCATGATTAAGTCGAAATT 57.442 32.000 5.16 0.00 0.00 1.82
3429 4000 8.821894 GTTTATCAACATCAATGAGTCTACCTC 58.178 37.037 0.00 0.00 35.39 3.85
3651 4222 3.777106 AATGCAAGTCAGGACAGAGAA 57.223 42.857 1.84 0.00 0.00 2.87
3741 4312 7.376435 GAGTATATAAGTACTCCCTCCGTTC 57.624 44.000 0.00 0.00 42.99 3.95
3742 4313 5.936956 AGTATATAAGTACTCCCTCCGTTCG 59.063 44.000 0.00 0.00 28.99 3.95
3743 4314 1.755179 TAAGTACTCCCTCCGTTCGG 58.245 55.000 4.74 4.74 0.00 4.30
3744 4315 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
3745 4316 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
3746 4317 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3747 4318 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
3748 4319 0.249398 ACTCCCTCCGTTCGGAATTG 59.751 55.000 14.79 6.68 33.41 2.32
3749 4320 1.078708 TCCCTCCGTTCGGAATTGC 60.079 57.895 14.79 0.00 33.41 3.56
3750 4321 1.078426 CCCTCCGTTCGGAATTGCT 60.078 57.895 14.79 0.00 33.41 3.91
3751 4322 0.676782 CCCTCCGTTCGGAATTGCTT 60.677 55.000 14.79 0.00 33.41 3.91
3752 4323 0.447801 CCTCCGTTCGGAATTGCTTG 59.552 55.000 14.79 1.97 33.41 4.01
3753 4324 1.156736 CTCCGTTCGGAATTGCTTGT 58.843 50.000 14.79 0.00 33.41 3.16
3754 4325 1.128692 CTCCGTTCGGAATTGCTTGTC 59.871 52.381 14.79 0.00 33.41 3.18
3755 4326 0.871722 CCGTTCGGAATTGCTTGTCA 59.128 50.000 5.19 0.00 0.00 3.58
3756 4327 1.399727 CCGTTCGGAATTGCTTGTCAC 60.400 52.381 5.19 0.00 0.00 3.67
3757 4328 1.262950 CGTTCGGAATTGCTTGTCACA 59.737 47.619 0.00 0.00 0.00 3.58
3758 4329 2.286713 CGTTCGGAATTGCTTGTCACAA 60.287 45.455 0.00 0.00 0.00 3.33
3759 4330 3.701241 GTTCGGAATTGCTTGTCACAAA 58.299 40.909 0.00 0.00 0.00 2.83
3760 4331 4.109050 GTTCGGAATTGCTTGTCACAAAA 58.891 39.130 0.00 0.00 0.00 2.44
3761 4332 4.377839 TCGGAATTGCTTGTCACAAAAA 57.622 36.364 0.00 0.00 0.00 1.94
3762 4333 4.942852 TCGGAATTGCTTGTCACAAAAAT 58.057 34.783 0.00 0.00 0.00 1.82
3763 4334 4.744137 TCGGAATTGCTTGTCACAAAAATG 59.256 37.500 0.00 0.00 0.00 2.32
3764 4335 4.744137 CGGAATTGCTTGTCACAAAAATGA 59.256 37.500 0.00 0.00 0.00 2.57
3765 4336 5.233902 CGGAATTGCTTGTCACAAAAATGAA 59.766 36.000 0.00 0.00 0.00 2.57
3766 4337 6.073657 CGGAATTGCTTGTCACAAAAATGAAT 60.074 34.615 0.00 0.00 0.00 2.57
3767 4338 7.073265 GGAATTGCTTGTCACAAAAATGAATG 58.927 34.615 0.00 0.00 0.00 2.67
3768 4339 7.254863 GGAATTGCTTGTCACAAAAATGAATGT 60.255 33.333 0.00 0.00 0.00 2.71
3769 4340 8.659925 AATTGCTTGTCACAAAAATGAATGTA 57.340 26.923 0.00 0.00 0.00 2.29
3770 4341 8.836268 ATTGCTTGTCACAAAAATGAATGTAT 57.164 26.923 0.00 0.00 0.00 2.29
3771 4342 7.872163 TGCTTGTCACAAAAATGAATGTATC 57.128 32.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.574428 CTAGTGTGGCGGTTGTTGC 59.426 57.895 0.00 0.00 0.00 4.17
10 11 1.457346 AATTGCTCTGCTAGTGTGGC 58.543 50.000 0.00 0.00 0.00 5.01
46 47 2.561478 ATTACCTTTGTGCGGACTGT 57.439 45.000 8.99 3.16 0.00 3.55
51 52 3.081804 AGGAGAAATTACCTTTGTGCGG 58.918 45.455 0.00 0.00 34.22 5.69
52 53 4.003648 AGAGGAGAAATTACCTTTGTGCG 58.996 43.478 0.00 0.00 34.22 5.34
55 56 7.750655 AGAAAGAGAGGAGAAATTACCTTTGT 58.249 34.615 0.00 0.00 36.57 2.83
137 138 5.011431 TCAATGACATGGGCAAACAATTACA 59.989 36.000 0.00 0.00 0.00 2.41
149 150 2.933906 GCAAAGCAATCAATGACATGGG 59.066 45.455 0.00 0.00 0.00 4.00
154 155 8.638685 ACAAATATAGCAAAGCAATCAATGAC 57.361 30.769 0.00 0.00 0.00 3.06
158 159 7.387122 TGCAAACAAATATAGCAAAGCAATCAA 59.613 29.630 0.00 0.00 31.42 2.57
204 205 7.864379 GCAGCAAACTATCATTGTAGCAATAAT 59.136 33.333 0.00 0.00 33.19 1.28
212 213 9.777297 TGATAATAGCAGCAAACTATCATTGTA 57.223 29.630 0.00 0.00 30.00 2.41
244 245 7.609760 AGCAACATCAATGAGTTAATAACGA 57.390 32.000 0.00 0.00 36.23 3.85
326 328 1.276138 GGCCCAGAAATTTGGTCCTTG 59.724 52.381 0.00 0.00 33.42 3.61
350 352 2.207229 CCGACCACTCACCTGGTGA 61.207 63.158 26.79 26.79 45.15 4.02
354 356 1.764571 TTTCCCCGACCACTCACCTG 61.765 60.000 0.00 0.00 0.00 4.00
355 357 0.840722 ATTTCCCCGACCACTCACCT 60.841 55.000 0.00 0.00 0.00 4.00
366 368 1.831389 CGTAGCATCGCATTTCCCCG 61.831 60.000 0.00 0.00 0.00 5.73
379 381 0.613572 TCATCCACCCACTCGTAGCA 60.614 55.000 0.00 0.00 0.00 3.49
417 419 3.926497 TTCGTCACGAGCGAAACC 58.074 55.556 0.00 0.00 43.98 3.27
430 432 0.666577 GTCACTAGGCAAGCGTTCGT 60.667 55.000 0.00 0.00 0.00 3.85
434 436 1.080705 GTCGTCACTAGGCAAGCGT 60.081 57.895 0.00 0.00 0.00 5.07
446 448 2.354188 CGACTTGCCACGTCGTCA 60.354 61.111 14.79 0.00 46.56 4.35
493 495 6.176183 CCGCCTTCTCCTTTGATCATATTAT 58.824 40.000 0.00 0.00 0.00 1.28
494 496 5.071788 ACCGCCTTCTCCTTTGATCATATTA 59.928 40.000 0.00 0.00 0.00 0.98
495 497 4.141390 ACCGCCTTCTCCTTTGATCATATT 60.141 41.667 0.00 0.00 0.00 1.28
508 516 2.774687 TGGTAAAAGAACCGCCTTCTC 58.225 47.619 0.00 0.00 42.91 2.87
513 521 1.320507 TGGTTGGTAAAAGAACCGCC 58.679 50.000 0.00 0.00 44.04 6.13
514 522 4.668289 CATATGGTTGGTAAAAGAACCGC 58.332 43.478 0.00 0.00 44.04 5.68
520 528 6.949352 AGATCTGCATATGGTTGGTAAAAG 57.051 37.500 4.56 0.00 0.00 2.27
551 569 7.148239 GGATTGATACCGACAAATGTTTCTTCT 60.148 37.037 0.00 0.00 0.00 2.85
594 612 9.249457 GAAGAAATGGAAACTCGAAAAGAATTT 57.751 29.630 0.00 0.00 42.41 1.82
595 613 7.867909 GGAAGAAATGGAAACTCGAAAAGAATT 59.132 33.333 0.00 0.00 0.00 2.17
596 614 7.231519 AGGAAGAAATGGAAACTCGAAAAGAAT 59.768 33.333 0.00 0.00 0.00 2.40
597 615 6.546034 AGGAAGAAATGGAAACTCGAAAAGAA 59.454 34.615 0.00 0.00 0.00 2.52
598 616 6.062095 AGGAAGAAATGGAAACTCGAAAAGA 58.938 36.000 0.00 0.00 0.00 2.52
599 617 6.319141 AGGAAGAAATGGAAACTCGAAAAG 57.681 37.500 0.00 0.00 0.00 2.27
600 618 6.512741 CGAAGGAAGAAATGGAAACTCGAAAA 60.513 38.462 0.00 0.00 0.00 2.29
621 649 1.221414 GGATCTTGGCGATTCCGAAG 58.779 55.000 0.00 0.00 38.22 3.79
626 654 1.643832 GCGTGGATCTTGGCGATTC 59.356 57.895 0.00 0.00 30.84 2.52
627 655 3.813596 GCGTGGATCTTGGCGATT 58.186 55.556 0.00 0.00 30.84 3.34
645 673 4.162690 AGGGCCGTTGGATCGAGC 62.163 66.667 0.00 0.00 0.00 5.03
682 710 1.196911 TGATATTCGGTGGGAACGGT 58.803 50.000 0.00 0.00 37.50 4.83
683 711 2.319136 TTGATATTCGGTGGGAACGG 57.681 50.000 0.00 0.00 37.50 4.44
739 775 4.255833 TCAACATTGTTGCTTGAATCCC 57.744 40.909 22.02 0.00 0.00 3.85
759 804 4.248058 CATGGTCTTTTTCCTTTGGCATC 58.752 43.478 0.00 0.00 0.00 3.91
908 967 2.497273 GGAAATGGGGATTGTGGTGAAG 59.503 50.000 0.00 0.00 0.00 3.02
910 969 1.272985 GGGAAATGGGGATTGTGGTGA 60.273 52.381 0.00 0.00 0.00 4.02
948 1025 4.083862 GGCGGGGAGGAGTGTCAC 62.084 72.222 0.00 0.00 0.00 3.67
969 1046 2.362503 GGTGGCTAGGGTTTGGGC 60.363 66.667 0.00 0.00 0.00 5.36
970 1047 2.359011 GGGTGGCTAGGGTTTGGG 59.641 66.667 0.00 0.00 0.00 4.12
985 1062 4.954970 CATTGGGATCGGCGGGGG 62.955 72.222 7.21 0.00 0.00 5.40
1323 1526 2.159382 CAAAGTGGGGAGTAAACGCAT 58.841 47.619 0.00 0.00 33.25 4.73
1368 1571 0.965866 TACTCTGGACTGGAGTGGCG 60.966 60.000 6.62 0.00 42.98 5.69
1533 1767 5.595885 CAGTAAGATATCCAGGACAGTGTG 58.404 45.833 0.00 0.00 0.00 3.82
1534 1768 4.100189 GCAGTAAGATATCCAGGACAGTGT 59.900 45.833 0.00 0.00 0.00 3.55
1535 1769 4.502259 GGCAGTAAGATATCCAGGACAGTG 60.502 50.000 0.00 0.00 0.00 3.66
1536 1770 3.643792 GGCAGTAAGATATCCAGGACAGT 59.356 47.826 0.00 0.00 0.00 3.55
1537 1771 3.305676 CGGCAGTAAGATATCCAGGACAG 60.306 52.174 0.00 0.00 0.00 3.51
1540 1774 3.238788 TCGGCAGTAAGATATCCAGGA 57.761 47.619 0.00 0.00 0.00 3.86
1541 1775 4.543590 ATTCGGCAGTAAGATATCCAGG 57.456 45.455 0.00 0.00 0.00 4.45
1542 1776 4.153117 GCAATTCGGCAGTAAGATATCCAG 59.847 45.833 0.00 0.00 0.00 3.86
1543 1777 4.065088 GCAATTCGGCAGTAAGATATCCA 58.935 43.478 0.00 0.00 0.00 3.41
1544 1778 4.319177 AGCAATTCGGCAGTAAGATATCC 58.681 43.478 0.00 0.00 35.83 2.59
1545 1779 5.237344 ACAAGCAATTCGGCAGTAAGATATC 59.763 40.000 0.00 0.00 35.83 1.63
1546 1780 5.126067 ACAAGCAATTCGGCAGTAAGATAT 58.874 37.500 0.00 0.00 35.83 1.63
1547 1781 4.513442 ACAAGCAATTCGGCAGTAAGATA 58.487 39.130 0.00 0.00 35.83 1.98
1558 1792 4.297510 TGAACAATCCAACAAGCAATTCG 58.702 39.130 0.00 0.00 0.00 3.34
1565 1799 6.332630 ACTTCAGTTTGAACAATCCAACAAG 58.667 36.000 0.00 0.00 34.49 3.16
1569 1803 4.638421 ACGACTTCAGTTTGAACAATCCAA 59.362 37.500 0.00 0.00 32.21 3.53
1657 1896 6.789268 TCAATCTAGGACCAAATTCCAAAGA 58.211 36.000 0.00 0.00 38.25 2.52
1695 1934 4.351111 ACCTTGAACCCACTCTAACATCTT 59.649 41.667 0.00 0.00 0.00 2.40
1718 1957 3.622206 GCACACTGAATGGGTAGATCCAA 60.622 47.826 0.00 0.00 40.62 3.53
1726 1965 0.037303 CCTCTGCACACTGAATGGGT 59.963 55.000 0.00 0.00 32.41 4.51
1792 2046 7.800300 AGTCTTTACTTTGTAGAGAAGGGAT 57.200 36.000 0.54 0.00 29.00 3.85
1916 2172 7.990886 AGATTGTTTTTGTAAGAGACCTACACA 59.009 33.333 0.00 0.00 0.00 3.72
1921 2177 7.227512 CAGACAGATTGTTTTTGTAAGAGACCT 59.772 37.037 0.00 0.00 0.00 3.85
1924 2180 7.552687 ACACAGACAGATTGTTTTTGTAAGAGA 59.447 33.333 0.00 0.00 0.00 3.10
1930 2186 6.099341 GGAAACACAGACAGATTGTTTTTGT 58.901 36.000 0.84 0.00 42.19 2.83
1931 2187 6.098679 TGGAAACACAGACAGATTGTTTTTG 58.901 36.000 0.84 0.00 42.19 2.44
1954 2210 9.197694 GTGGAGCACTTAATACAGATAACTATG 57.802 37.037 0.00 0.00 0.00 2.23
1955 2211 8.924303 TGTGGAGCACTTAATACAGATAACTAT 58.076 33.333 0.00 0.00 35.11 2.12
1982 2238 3.731652 TTGTCCATGTTGAAAGGCAAG 57.268 42.857 0.00 0.00 37.12 4.01
2032 2291 1.679153 GAAACCCACGTTGTGACCAAT 59.321 47.619 0.00 0.00 35.23 3.16
2087 2346 6.142798 CACGCAATAATCAATTAAGATGCACC 59.857 38.462 13.89 0.00 33.66 5.01
2112 2371 4.816786 AAATGAAGTGCAAAACAATGCC 57.183 36.364 0.00 0.00 45.83 4.40
2124 2389 9.396938 TGCGATATTGCATAAATAAATGAAGTG 57.603 29.630 13.90 0.00 40.62 3.16
2212 2479 3.064931 CCTACAACTTTCTCAACGACCC 58.935 50.000 0.00 0.00 0.00 4.46
2227 2494 1.927487 TACAAGAGCCCGACCTACAA 58.073 50.000 0.00 0.00 0.00 2.41
2398 2665 2.604046 AAGGTGATCGTACATGAGGC 57.396 50.000 0.00 0.00 0.00 4.70
2413 2680 3.817647 GAGCAGACAATGAGACAAAAGGT 59.182 43.478 0.00 0.00 0.00 3.50
2714 2981 0.169672 TGCTAGCGACGGTACTCAAC 59.830 55.000 10.77 0.00 0.00 3.18
2719 2986 0.169672 TGTCTTGCTAGCGACGGTAC 59.830 55.000 10.77 3.12 32.93 3.34
2728 2995 0.036732 TGGTTGCCCTGTCTTGCTAG 59.963 55.000 0.00 0.00 0.00 3.42
2842 3112 1.072331 AGCTTGTTTGGATCACTCGGT 59.928 47.619 0.00 0.00 0.00 4.69
2843 3113 1.813513 AGCTTGTTTGGATCACTCGG 58.186 50.000 0.00 0.00 0.00 4.63
2844 3114 5.277058 GCTATTAGCTTGTTTGGATCACTCG 60.277 44.000 8.47 0.00 38.45 4.18
2845 3115 6.054035 GCTATTAGCTTGTTTGGATCACTC 57.946 41.667 8.47 0.00 38.45 3.51
2900 3267 4.822896 ACAATGTTAACTACGCCCAGAAAA 59.177 37.500 7.22 0.00 0.00 2.29
2996 3363 5.789643 TTGAAGCATTATAATGGCCCTTC 57.210 39.130 23.57 23.64 35.46 3.46
3010 3377 7.981225 ACAACATAAAAGACACTTTTGAAGCAT 59.019 29.630 16.43 2.76 0.00 3.79
3164 3735 4.061596 GTCACAGAGTCCCTCTCAAAAAG 58.938 47.826 0.00 0.00 44.98 2.27
3233 3804 9.595823 TTTAAAGCCAACATAGACAGTACTATC 57.404 33.333 0.00 0.00 31.68 2.08
3238 3809 8.836413 GCATATTTAAAGCCAACATAGACAGTA 58.164 33.333 0.00 0.00 0.00 2.74
3359 3930 5.063180 TCTTTGCATATTGAAGCCAACAG 57.937 39.130 0.00 0.00 34.72 3.16
3651 4222 6.708054 CGATTGTTAAGGATTGAAGAGCCTAT 59.292 38.462 0.00 0.00 45.46 2.57
3731 4302 1.078708 GCAATTCCGAACGGAGGGA 60.079 57.895 15.34 2.49 46.06 4.20
3732 4303 0.676782 AAGCAATTCCGAACGGAGGG 60.677 55.000 15.34 10.34 46.06 4.30
3733 4304 0.447801 CAAGCAATTCCGAACGGAGG 59.552 55.000 15.34 10.65 46.06 4.30
3734 4305 1.128692 GACAAGCAATTCCGAACGGAG 59.871 52.381 15.34 6.36 46.06 4.63
3735 4306 1.153353 GACAAGCAATTCCGAACGGA 58.847 50.000 12.04 12.04 43.52 4.69
3736 4307 0.871722 TGACAAGCAATTCCGAACGG 59.128 50.000 6.94 6.94 0.00 4.44
3737 4308 1.262950 TGTGACAAGCAATTCCGAACG 59.737 47.619 0.00 0.00 0.00 3.95
3738 4309 3.347958 TTGTGACAAGCAATTCCGAAC 57.652 42.857 0.00 0.00 0.00 3.95
3739 4310 4.377839 TTTTGTGACAAGCAATTCCGAA 57.622 36.364 0.00 0.00 0.00 4.30
3740 4311 4.377839 TTTTTGTGACAAGCAATTCCGA 57.622 36.364 0.00 0.00 0.00 4.55
3741 4312 4.744137 TCATTTTTGTGACAAGCAATTCCG 59.256 37.500 0.00 0.00 0.00 4.30
3742 4313 6.601741 TTCATTTTTGTGACAAGCAATTCC 57.398 33.333 0.00 0.00 0.00 3.01
3743 4314 7.632721 ACATTCATTTTTGTGACAAGCAATTC 58.367 30.769 0.00 0.00 0.00 2.17
3744 4315 7.556733 ACATTCATTTTTGTGACAAGCAATT 57.443 28.000 0.00 0.00 0.00 2.32
3745 4316 8.836268 ATACATTCATTTTTGTGACAAGCAAT 57.164 26.923 0.00 0.00 0.00 3.56
3746 4317 8.296799 GATACATTCATTTTTGTGACAAGCAA 57.703 30.769 0.00 0.00 0.00 3.91
3747 4318 7.872163 GATACATTCATTTTTGTGACAAGCA 57.128 32.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.