Multiple sequence alignment - TraesCS2A01G530300

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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 TraesCS2A01G530300 chr2A 100.000 7475 0 0 1 7475 748203284 748210758 0.000000e+00 13804.0
1 TraesCS2A01G530300 chr2A 91.510 1814 142 11 720 2530 748285133 748286937 0.000000e+00 2486.0
2 TraesCS2A01G530300 chr2A 90.284 1904 169 13 631 2530 748503686 748501795 0.000000e+00 2477.0
3 TraesCS2A01G530300 chr2A 90.468 1836 161 11 705 2530 746620353 746622184 0.000000e+00 2409.0
4 TraesCS2A01G530300 chr2A 90.832 1778 160 3 755 2530 748437571 748439347 0.000000e+00 2377.0
5 TraesCS2A01G530300 chr2A 93.615 1018 55 5 6466 7475 746622183 746623198 0.000000e+00 1511.0
6 TraesCS2A01G530300 chr2A 92.513 561 40 2 6466 7024 748439346 748439906 0.000000e+00 802.0
7 TraesCS2A01G530300 chr2A 88.184 457 30 9 7027 7475 748452801 748452361 2.390000e-144 523.0
8 TraesCS2A01G530300 chr2A 89.901 406 33 2 7028 7425 748464677 748464272 4.000000e-142 516.0
9 TraesCS2A01G530300 chr7A 96.635 4012 48 32 2529 6467 519484865 519488862 0.000000e+00 6580.0
10 TraesCS2A01G530300 chr7A 98.252 1144 15 2 2718 3861 715130367 715131505 0.000000e+00 1997.0
11 TraesCS2A01G530300 chr7A 93.054 907 23 14 5570 6467 715133647 715134522 0.000000e+00 1290.0
12 TraesCS2A01G530300 chr7A 99.557 677 3 0 4894 5570 715131510 715132186 0.000000e+00 1234.0
13 TraesCS2A01G530300 chr7A 91.880 234 11 6 2547 2774 715130145 715130376 3.370000e-83 320.0
14 TraesCS2A01G530300 chr7A 82.946 129 13 7 2653 2774 519484953 519485079 2.850000e-19 108.0
15 TraesCS2A01G530300 chr4B 97.334 3789 53 10 2718 6467 238958479 238954700 0.000000e+00 6394.0
16 TraesCS2A01G530300 chr4B 99.126 1144 8 1 2718 3861 580779457 580780598 0.000000e+00 2056.0
17 TraesCS2A01G530300 chr4B 93.054 907 23 14 5570 6467 580782740 580783615 0.000000e+00 1290.0
18 TraesCS2A01G530300 chr4B 99.557 677 3 0 4894 5570 580780603 580781279 0.000000e+00 1234.0
19 TraesCS2A01G530300 chr4B 92.063 252 12 6 2529 2774 580779217 580779466 1.540000e-91 348.0
20 TraesCS2A01G530300 chr4B 91.667 252 13 6 2529 2774 238958719 238958470 7.180000e-90 342.0
21 TraesCS2A01G530300 chr1A 97.798 2362 7 4 4133 6449 50695679 50698040 0.000000e+00 4032.0
22 TraesCS2A01G530300 chr1A 98.793 1077 10 2 3081 4157 50694601 50695674 0.000000e+00 1914.0
23 TraesCS2A01G530300 chr2B 91.483 2043 144 24 511 2530 753931543 753929508 0.000000e+00 2782.0
24 TraesCS2A01G530300 chr2B 92.286 1776 136 1 755 2530 753792830 753794604 0.000000e+00 2519.0
25 TraesCS2A01G530300 chr2B 94.695 1018 44 4 6466 7475 753929509 753928494 0.000000e+00 1572.0
26 TraesCS2A01G530300 chr2B 91.625 1003 61 14 6466 7454 753794603 753795596 0.000000e+00 1365.0
27 TraesCS2A01G530300 chr2B 91.578 843 54 9 6466 7299 753787410 753788244 0.000000e+00 1147.0
28 TraesCS2A01G530300 chr2B 90.752 811 56 8 6673 7475 753935066 753934267 0.000000e+00 1064.0
29 TraesCS2A01G530300 chr2B 78.505 321 53 15 1 315 753808531 753808221 5.920000e-46 196.0
30 TraesCS2A01G530300 chr2B 94.444 126 1 4 222 346 753940033 753939913 9.900000e-44 189.0
31 TraesCS2A01G530300 chr2B 83.254 209 29 6 110 315 753785827 753786032 3.560000e-43 187.0
32 TraesCS2A01G530300 chr2D 91.544 1963 142 5 590 2530 617538672 617540632 0.000000e+00 2684.0
33 TraesCS2A01G530300 chr2D 90.047 1919 174 9 628 2530 617909904 617907987 0.000000e+00 2470.0
34 TraesCS2A01G530300 chr2D 97.161 1444 34 4 4133 5570 1518140 1519582 0.000000e+00 2433.0
35 TraesCS2A01G530300 chr2D 91.052 1777 157 2 755 2530 617887325 617889100 0.000000e+00 2399.0
36 TraesCS2A01G530300 chr2D 96.884 1027 27 3 4544 5570 10253648 10254669 0.000000e+00 1714.0
37 TraesCS2A01G530300 chr2D 94.597 1018 46 3 6466 7475 617635631 617636647 0.000000e+00 1567.0
38 TraesCS2A01G530300 chr2D 93.026 1018 62 4 6466 7475 617761901 617762917 0.000000e+00 1478.0
39 TraesCS2A01G530300 chr2D 93.144 598 38 3 6466 7061 617540631 617541227 0.000000e+00 874.0
40 TraesCS2A01G530300 chr2D 92.335 561 41 2 6466 7024 617548244 617548804 0.000000e+00 797.0
41 TraesCS2A01G530300 chr2D 83.721 602 56 11 9 597 617538066 617538638 1.430000e-146 531.0
42 TraesCS2A01G530300 chr2D 95.847 313 11 2 4115 4426 10253311 10253622 8.660000e-139 505.0
43 TraesCS2A01G530300 chr2D 84.736 511 42 16 5984 6467 1521523 1522024 5.250000e-131 479.0
44 TraesCS2A01G530300 chr2D 90.489 368 12 2 2628 2972 1514683 1515050 1.470000e-126 464.0
45 TraesCS2A01G530300 chr2D 87.500 288 24 5 7139 7415 617413661 617413375 9.360000e-84 322.0
46 TraesCS2A01G530300 chr2D 80.088 226 29 13 164 387 617902960 617902749 3.610000e-33 154.0
47 TraesCS2A01G530300 chr2D 97.500 40 1 0 7109 7148 617541224 617541263 1.350000e-07 69.4
48 TraesCS2A01G530300 chr6D 95.271 1438 30 11 4133 5570 426572002 426570603 0.000000e+00 2244.0
49 TraesCS2A01G530300 chr6D 96.715 1096 32 2 2718 3813 426573423 426572332 0.000000e+00 1821.0
50 TraesCS2A01G530300 chr6D 89.007 937 34 15 5570 6467 426569136 426568230 0.000000e+00 1096.0
51 TraesCS2A01G530300 chr6D 97.993 299 6 0 3816 4114 7170694 7170992 3.090000e-143 520.0
52 TraesCS2A01G530300 chr6D 91.700 253 13 8 2528 2774 426573664 426573414 2.000000e-90 344.0
53 TraesCS2A01G530300 chr3B 98.689 1144 12 1 2718 3861 672125316 672124176 0.000000e+00 2026.0
54 TraesCS2A01G530300 chr3B 98.427 1144 15 1 2718 3861 565446247 565445107 0.000000e+00 2010.0
55 TraesCS2A01G530300 chr3B 93.077 910 23 14 5570 6470 565439284 565438406 0.000000e+00 1295.0
56 TraesCS2A01G530300 chr3B 91.091 898 19 14 5570 6467 672122998 672122162 0.000000e+00 1158.0
57 TraesCS2A01G530300 chr3B 92.490 253 11 6 2528 2774 565446488 565446238 9.220000e-94 355.0
58 TraesCS2A01G530300 chr3B 92.800 250 10 6 2531 2774 672125554 672125307 9.220000e-94 355.0
59 TraesCS2A01G530300 chr5B 98.339 1144 15 2 2718 3861 437921386 437920247 0.000000e+00 2004.0
60 TraesCS2A01G530300 chr5B 92.944 907 24 14 5570 6467 437918111 437917236 0.000000e+00 1284.0
61 TraesCS2A01G530300 chr5B 92.520 254 11 6 2527 2774 437921628 437921377 2.560000e-94 357.0
62 TraesCS2A01G530300 chr5D 97.539 1016 25 0 4555 5570 59789692 59788677 0.000000e+00 1738.0
63 TraesCS2A01G530300 chr5D 98.671 301 4 0 3814 4114 319247523 319247823 1.100000e-147 534.0
64 TraesCS2A01G530300 chr5D 96.154 312 11 1 4115 4426 59790028 59789718 6.690000e-140 508.0
65 TraesCS2A01G530300 chr4A 90.462 996 72 10 4595 5570 354899301 354898309 0.000000e+00 1291.0
66 TraesCS2A01G530300 chr4A 90.996 944 62 10 4578 5500 354777062 354776121 0.000000e+00 1251.0
67 TraesCS2A01G530300 chr4A 87.359 443 34 9 4133 4558 354777489 354777052 8.720000e-134 488.0
68 TraesCS2A01G530300 chr4A 90.877 285 20 3 4143 4426 354945083 354944804 1.970000e-100 377.0
69 TraesCS2A01G530300 chr4D 98.026 304 5 1 3815 4117 482709774 482709471 1.850000e-145 527.0
70 TraesCS2A01G530300 chr1D 97.993 299 6 0 3816 4114 30903402 30903700 3.090000e-143 520.0
71 TraesCS2A01G530300 chr1D 97.342 301 8 0 3814 4114 62152140 62152440 5.170000e-141 512.0
72 TraesCS2A01G530300 chr1D 83.019 159 25 2 161 319 9877862 9878018 7.820000e-30 143.0
73 TraesCS2A01G530300 chr7D 97.368 304 8 0 3814 4117 7424429 7424126 1.110000e-142 518.0
74 TraesCS2A01G530300 chr1B 93.333 105 3 4 214 317 15558744 15558845 1.300000e-32 152.0
75 TraesCS2A01G530300 chr6B 89.256 121 9 4 211 330 566524727 566524610 1.680000e-31 148.0
76 TraesCS2A01G530300 chr3A 92.233 103 6 2 212 313 8598688 8598789 2.170000e-30 145.0
77 TraesCS2A01G530300 chr7B 85.000 120 17 1 2520 2639 601128713 601128831 3.660000e-23 121.0


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 TraesCS2A01G530300 chr2A 748203284 748210758 7474 False 13804.000000 13804 100.000000 1 7475 1 chr2A.!!$F1 7474
1 TraesCS2A01G530300 chr2A 748285133 748286937 1804 False 2486.000000 2486 91.510000 720 2530 1 chr2A.!!$F2 1810
2 TraesCS2A01G530300 chr2A 748501795 748503686 1891 True 2477.000000 2477 90.284000 631 2530 1 chr2A.!!$R3 1899
3 TraesCS2A01G530300 chr2A 746620353 746623198 2845 False 1960.000000 2409 92.041500 705 7475 2 chr2A.!!$F3 6770
4 TraesCS2A01G530300 chr2A 748437571 748439906 2335 False 1589.500000 2377 91.672500 755 7024 2 chr2A.!!$F4 6269
5 TraesCS2A01G530300 chr7A 519484865 519488862 3997 False 3344.000000 6580 89.790500 2529 6467 2 chr7A.!!$F1 3938
6 TraesCS2A01G530300 chr7A 715130145 715134522 4377 False 1210.250000 1997 95.685750 2547 6467 4 chr7A.!!$F2 3920
7 TraesCS2A01G530300 chr4B 238954700 238958719 4019 True 3368.000000 6394 94.500500 2529 6467 2 chr4B.!!$R1 3938
8 TraesCS2A01G530300 chr4B 580779217 580783615 4398 False 1232.000000 2056 95.950000 2529 6467 4 chr4B.!!$F1 3938
9 TraesCS2A01G530300 chr1A 50694601 50698040 3439 False 2973.000000 4032 98.295500 3081 6449 2 chr1A.!!$F1 3368
10 TraesCS2A01G530300 chr2B 753792830 753795596 2766 False 1942.000000 2519 91.955500 755 7454 2 chr2B.!!$F2 6699
11 TraesCS2A01G530300 chr2B 753928494 753935066 6572 True 1806.000000 2782 92.310000 511 7475 3 chr2B.!!$R3 6964
12 TraesCS2A01G530300 chr2B 753785827 753788244 2417 False 667.000000 1147 87.416000 110 7299 2 chr2B.!!$F1 7189
13 TraesCS2A01G530300 chr2D 617907987 617909904 1917 True 2470.000000 2470 90.047000 628 2530 1 chr2D.!!$R3 1902
14 TraesCS2A01G530300 chr2D 617887325 617889100 1775 False 2399.000000 2399 91.052000 755 2530 1 chr2D.!!$F4 1775
15 TraesCS2A01G530300 chr2D 617635631 617636647 1016 False 1567.000000 1567 94.597000 6466 7475 1 chr2D.!!$F2 1009
16 TraesCS2A01G530300 chr2D 617761901 617762917 1016 False 1478.000000 1478 93.026000 6466 7475 1 chr2D.!!$F3 1009
17 TraesCS2A01G530300 chr2D 1514683 1522024 7341 False 1125.333333 2433 90.795333 2628 6467 3 chr2D.!!$F5 3839
18 TraesCS2A01G530300 chr2D 10253311 10254669 1358 False 1109.500000 1714 96.365500 4115 5570 2 chr2D.!!$F6 1455
19 TraesCS2A01G530300 chr2D 617538066 617541263 3197 False 1039.600000 2684 91.477250 9 7148 4 chr2D.!!$F7 7139
20 TraesCS2A01G530300 chr2D 617548244 617548804 560 False 797.000000 797 92.335000 6466 7024 1 chr2D.!!$F1 558
21 TraesCS2A01G530300 chr6D 426568230 426573664 5434 True 1376.250000 2244 93.173250 2528 6467 4 chr6D.!!$R1 3939
22 TraesCS2A01G530300 chr3B 565438406 565439284 878 True 1295.000000 1295 93.077000 5570 6470 1 chr3B.!!$R1 900
23 TraesCS2A01G530300 chr3B 565445107 565446488 1381 True 1182.500000 2010 95.458500 2528 3861 2 chr3B.!!$R2 1333
24 TraesCS2A01G530300 chr3B 672122162 672125554 3392 True 1179.666667 2026 94.193333 2531 6467 3 chr3B.!!$R3 3936
25 TraesCS2A01G530300 chr5B 437917236 437921628 4392 True 1215.000000 2004 94.601000 2527 6467 3 chr5B.!!$R1 3940
26 TraesCS2A01G530300 chr5D 59788677 59790028 1351 True 1123.000000 1738 96.846500 4115 5570 2 chr5D.!!$R1 1455
27 TraesCS2A01G530300 chr4A 354898309 354899301 992 True 1291.000000 1291 90.462000 4595 5570 1 chr4A.!!$R1 975
28 TraesCS2A01G530300 chr4A 354776121 354777489 1368 True 869.500000 1251 89.177500 4133 5500 2 chr4A.!!$R3 1367

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
477 481 0.041833 CCTCCCTCCTGTCCTCTCAA 59.958 60.000 0.0 0.0 0.0 3.02 F
908 4005 1.287815 CGACAGTCCCAGTACGCAA 59.712 57.895 0.0 0.0 0.0 4.85 F
1559 4656 1.774110 ATGGCAAGTGTTGGTGTTCA 58.226 45.000 0.0 0.0 0.0 3.18 F
1767 4864 3.928727 TCGATGGTACGGAATGGTATC 57.071 47.619 0.0 0.0 0.0 2.24 F
3070 7886 3.548014 CGTGTCTTCTTGGTGCGAATTTT 60.548 43.478 0.0 0.0 0.0 1.82 F
5766 12530 5.194432 TGTCCTACTCCTGTACTCTTGATC 58.806 45.833 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 4733 1.243342 TTTGCGGCCATGGAGTCAAG 61.243 55.000 18.40 0.00 0.00 3.02 R
2120 5217 2.103094 ACCTTTCCTTCTTTGCAAAGGC 59.897 45.455 33.01 0.00 46.12 4.35 R
2829 5978 2.223688 CGCTCATCCTGACCTCACTAAG 60.224 54.545 0.00 0.00 0.00 2.18 R
3715 8858 4.160439 AGCAAGCACTCTAACTACTGCATA 59.840 41.667 0.00 0.00 31.71 3.14 R
5768 12532 3.386078 GGAATCAGGTGTGCTCTAGATCA 59.614 47.826 0.00 0.00 0.00 2.92 R
7202 14273 0.819259 GCCTTCCTGCGGCATGAATA 60.819 55.000 18.74 0.96 46.77 1.75 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
28 29 1.957695 GCTTGGCCTGCAACAAAGC 60.958 57.895 11.61 11.61 0.00 3.51
53 54 7.061789 GCGAGGTTTTATCTGTTTGGTAAATTG 59.938 37.037 0.00 0.00 0.00 2.32
58 59 8.495148 GTTTTATCTGTTTGGTAAATTGCAAGG 58.505 33.333 4.94 0.00 0.00 3.61
61 62 5.355596 TCTGTTTGGTAAATTGCAAGGTTG 58.644 37.500 4.94 0.00 0.00 3.77
78 79 0.459489 TTGTGTTTGGAAGCTGCCAC 59.541 50.000 15.07 3.10 37.75 5.01
90 91 4.947147 TGCCACTGTTCCACGGGC 62.947 66.667 0.00 0.00 44.82 6.13
102 103 2.159382 TCCACGGGCAAAGATTTTCTC 58.841 47.619 0.00 0.00 0.00 2.87
105 106 0.451783 CGGGCAAAGATTTTCTCGGG 59.548 55.000 0.00 0.00 0.00 5.14
172 173 3.963383 AGTAACTTTGGTTTCGCTGTG 57.037 42.857 0.00 0.00 36.92 3.66
179 180 3.347958 TTGGTTTCGCTGTGAATGAAC 57.652 42.857 4.26 0.34 36.22 3.18
182 183 3.243035 TGGTTTCGCTGTGAATGAACAAG 60.243 43.478 4.26 0.00 36.22 3.16
207 211 5.448496 CGTTGTTATAGGCTAGCATTGCAAA 60.448 40.000 18.24 0.00 0.00 3.68
208 212 6.507023 GTTGTTATAGGCTAGCATTGCAAAT 58.493 36.000 18.24 1.64 0.00 2.32
209 213 6.075762 TGTTATAGGCTAGCATTGCAAATG 57.924 37.500 18.24 3.83 0.00 2.32
302 306 5.649782 AACCTGGCTCTGATAATTTGTTG 57.350 39.130 0.00 0.00 0.00 3.33
364 368 2.360350 CAAGGCTGCATCACCGGT 60.360 61.111 0.00 0.00 0.00 5.28
380 384 3.955650 CCGGTAAGGTTTCTCTGAAGA 57.044 47.619 0.00 0.00 34.51 2.87
402 406 2.365410 AAAAACAGCTGCATCCCCC 58.635 52.632 15.27 0.00 0.00 5.40
403 407 0.178924 AAAAACAGCTGCATCCCCCT 60.179 50.000 15.27 0.00 0.00 4.79
408 412 1.304713 AGCTGCATCCCCCTGTTTG 60.305 57.895 1.02 0.00 0.00 2.93
409 413 1.304381 GCTGCATCCCCCTGTTTGA 60.304 57.895 0.00 0.00 0.00 2.69
410 414 1.318158 GCTGCATCCCCCTGTTTGAG 61.318 60.000 0.00 0.00 0.00 3.02
412 416 2.409870 GCATCCCCCTGTTTGAGCG 61.410 63.158 0.00 0.00 0.00 5.03
416 420 2.747855 CCCCTGTTTGAGCGCCTC 60.748 66.667 2.29 1.22 0.00 4.70
417 421 2.747855 CCCTGTTTGAGCGCCTCC 60.748 66.667 2.29 0.00 0.00 4.30
440 444 3.200593 GCACCAGCTGCATCGGAG 61.201 66.667 8.66 0.00 46.29 4.63
442 446 1.812922 CACCAGCTGCATCGGAGAC 60.813 63.158 8.66 0.00 42.51 3.36
472 476 2.781406 GGTCCTCCCTCCTGTCCT 59.219 66.667 0.00 0.00 0.00 3.85
473 477 1.382009 GGTCCTCCCTCCTGTCCTC 60.382 68.421 0.00 0.00 0.00 3.71
474 478 1.700985 GTCCTCCCTCCTGTCCTCT 59.299 63.158 0.00 0.00 0.00 3.69
476 480 0.851332 TCCTCCCTCCTGTCCTCTCA 60.851 60.000 0.00 0.00 0.00 3.27
477 481 0.041833 CCTCCCTCCTGTCCTCTCAA 59.958 60.000 0.00 0.00 0.00 3.02
528 3542 2.202987 CTGCCTCATCCACGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
787 3884 2.876645 CTTCACGAGAGCGCCGAC 60.877 66.667 11.49 0.03 42.48 4.79
908 4005 1.287815 CGACAGTCCCAGTACGCAA 59.712 57.895 0.00 0.00 0.00 4.85
974 4071 4.147449 CTGCAGCGATGGTCCGGA 62.147 66.667 0.00 0.00 0.00 5.14
1466 4563 7.618907 TGATCAAGGAATTGAACCCAATATCAA 59.381 33.333 0.00 0.00 41.84 2.57
1559 4656 1.774110 ATGGCAAGTGTTGGTGTTCA 58.226 45.000 0.00 0.00 0.00 3.18
1636 4733 6.176896 AGGACAAAGGAAGCTAGAGAAATTC 58.823 40.000 0.00 0.00 0.00 2.17
1767 4864 3.928727 TCGATGGTACGGAATGGTATC 57.071 47.619 0.00 0.00 0.00 2.24
1822 4919 4.273235 TCAATGCATATGCTAAACGTGGAG 59.727 41.667 27.13 6.79 42.66 3.86
1875 4972 6.485171 AGTAATGAGGCAACAAGGAGTAAAT 58.515 36.000 0.00 0.00 41.41 1.40
2066 5163 5.082425 AGCCAAGGAATTGATTTCTGAAGT 58.918 37.500 0.00 0.00 34.56 3.01
2120 5217 7.762615 TGTGTTCTTCTATCCTGTAATAAACGG 59.237 37.037 0.00 0.00 0.00 4.44
2829 5978 5.332280 GCGTTGTCTAGCCAAAATTGTTTTC 60.332 40.000 0.00 0.00 0.00 2.29
3070 7886 3.548014 CGTGTCTTCTTGGTGCGAATTTT 60.548 43.478 0.00 0.00 0.00 1.82
5766 12530 5.194432 TGTCCTACTCCTGTACTCTTGATC 58.806 45.833 0.00 0.00 0.00 2.92
5767 12531 5.044772 TGTCCTACTCCTGTACTCTTGATCT 60.045 44.000 0.00 0.00 0.00 2.75
5768 12532 5.889289 GTCCTACTCCTGTACTCTTGATCTT 59.111 44.000 0.00 0.00 0.00 2.40
5769 12533 5.888724 TCCTACTCCTGTACTCTTGATCTTG 59.111 44.000 0.00 0.00 0.00 3.02
5770 12534 5.888724 CCTACTCCTGTACTCTTGATCTTGA 59.111 44.000 0.00 0.00 0.00 3.02
5771 12535 6.549364 CCTACTCCTGTACTCTTGATCTTGAT 59.451 42.308 0.00 0.00 0.00 2.57
5772 12536 6.463995 ACTCCTGTACTCTTGATCTTGATC 57.536 41.667 3.82 3.82 0.00 2.92
5773 12537 6.194235 ACTCCTGTACTCTTGATCTTGATCT 58.806 40.000 11.31 0.00 0.00 2.75
5774 12538 7.350382 ACTCCTGTACTCTTGATCTTGATCTA 58.650 38.462 11.31 3.83 0.00 1.98
5775 12539 7.502226 ACTCCTGTACTCTTGATCTTGATCTAG 59.498 40.741 13.29 13.29 0.00 2.43
5776 12540 7.578203 TCCTGTACTCTTGATCTTGATCTAGA 58.422 38.462 18.45 18.45 32.94 2.43
5778 12542 7.270757 TGTACTCTTGATCTTGATCTAGAGC 57.729 40.000 31.86 23.46 46.87 4.09
5779 12543 6.830838 TGTACTCTTGATCTTGATCTAGAGCA 59.169 38.462 31.86 24.37 46.87 4.26
5780 12544 6.147864 ACTCTTGATCTTGATCTAGAGCAC 57.852 41.667 31.86 11.62 46.87 4.40
5781 12545 5.655974 ACTCTTGATCTTGATCTAGAGCACA 59.344 40.000 31.86 12.23 46.87 4.57
5782 12546 5.900425 TCTTGATCTTGATCTAGAGCACAC 58.100 41.667 21.90 3.36 40.01 3.82
5783 12547 4.662468 TGATCTTGATCTAGAGCACACC 57.338 45.455 19.00 1.32 35.77 4.16
5784 12548 4.285020 TGATCTTGATCTAGAGCACACCT 58.715 43.478 19.00 0.00 35.77 4.00
5785 12549 4.099113 TGATCTTGATCTAGAGCACACCTG 59.901 45.833 19.00 0.00 35.77 4.00
5786 12550 3.701664 TCTTGATCTAGAGCACACCTGA 58.298 45.455 10.89 1.85 0.00 3.86
5787 12551 4.285020 TCTTGATCTAGAGCACACCTGAT 58.715 43.478 10.89 0.00 0.00 2.90
5788 12552 4.713814 TCTTGATCTAGAGCACACCTGATT 59.286 41.667 10.89 0.00 0.00 2.57
5789 12553 4.662468 TGATCTAGAGCACACCTGATTC 57.338 45.455 6.59 0.00 0.00 2.52
5897 12733 8.853077 ATTGCTACTATGATTTATTGCTGCTA 57.147 30.769 0.00 0.00 0.00 3.49
6734 13795 6.039717 GGCAGAGGCTGATGATATGTTTTTAA 59.960 38.462 0.00 0.00 40.87 1.52
6758 13819 0.251634 GGAGAAGGCTAGCTGTGCTT 59.748 55.000 15.72 9.20 40.44 3.91
7026 14089 6.373774 TCGTACTGAAAAACAAGGTGGTAAAA 59.626 34.615 0.00 0.00 0.00 1.52
7166 14237 4.275936 AGTTTGTGGCAAAGTACTTAGCTG 59.724 41.667 8.92 4.96 0.00 4.24
7202 14273 3.297134 ACCCAATCTCCGCATTTATGT 57.703 42.857 0.00 0.00 0.00 2.29
7215 14286 3.916172 GCATTTATGTATTCATGCCGCAG 59.084 43.478 0.00 0.00 35.70 5.18
7314 14391 5.056894 GCTTTTGCTCTCTGTTGATGATT 57.943 39.130 0.00 0.00 43.35 2.57
7345 14422 7.678947 ATCATGTTCACTCTTAAAACTCCAG 57.321 36.000 0.00 0.00 0.00 3.86
7454 14531 6.991531 ACCATTGCATGTAAACTCAATTTGTT 59.008 30.769 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.061789 GCAATTTACCAAACAGATAAAACCTCG 59.938 37.037 0.00 0.00 0.00 4.63
53 54 1.136891 AGCTTCCAAACACAACCTTGC 59.863 47.619 0.00 0.00 0.00 4.01
58 59 0.459489 TGGCAGCTTCCAAACACAAC 59.541 50.000 1.25 0.00 32.18 3.32
61 62 0.031178 CAGTGGCAGCTTCCAAACAC 59.969 55.000 6.68 0.00 37.96 3.32
78 79 1.247567 AATCTTTGCCCGTGGAACAG 58.752 50.000 0.00 0.00 41.80 3.16
90 91 6.743575 AGTTATGTCCCGAGAAAATCTTTG 57.256 37.500 0.00 0.00 0.00 2.77
102 103 2.159282 ACGCTGACTTAGTTATGTCCCG 60.159 50.000 0.00 10.72 35.03 5.14
105 106 3.858238 GGACACGCTGACTTAGTTATGTC 59.142 47.826 2.12 2.12 35.60 3.06
144 145 7.010091 CAGCGAAACCAAAGTTACTTGATTTTT 59.990 33.333 0.00 0.00 34.19 1.94
154 155 4.576873 TCATTCACAGCGAAACCAAAGTTA 59.423 37.500 0.00 0.00 37.12 2.24
162 163 2.721090 GCTTGTTCATTCACAGCGAAAC 59.279 45.455 0.00 0.00 37.12 2.78
166 167 0.235665 ACGCTTGTTCATTCACAGCG 59.764 50.000 10.14 10.14 43.68 5.18
179 180 3.194861 TGCTAGCCTATAACAACGCTTG 58.805 45.455 13.29 0.00 32.76 4.01
182 183 3.607078 GCAATGCTAGCCTATAACAACGC 60.607 47.826 13.29 0.00 0.00 4.84
207 211 6.444633 CACTCTGATTTTTCTTGTTCTGCAT 58.555 36.000 0.00 0.00 0.00 3.96
208 212 5.221106 CCACTCTGATTTTTCTTGTTCTGCA 60.221 40.000 0.00 0.00 0.00 4.41
209 213 5.218139 CCACTCTGATTTTTCTTGTTCTGC 58.782 41.667 0.00 0.00 0.00 4.26
219 223 0.242017 GCTGCGCCACTCTGATTTTT 59.758 50.000 4.18 0.00 0.00 1.94
334 338 0.179009 AGCCTTGTCTTGCAGAGCAA 60.179 50.000 4.22 4.22 46.80 3.91
335 339 0.887836 CAGCCTTGTCTTGCAGAGCA 60.888 55.000 0.00 0.00 36.47 4.26
336 340 1.874562 CAGCCTTGTCTTGCAGAGC 59.125 57.895 0.00 0.00 0.00 4.09
337 341 0.887836 TGCAGCCTTGTCTTGCAGAG 60.888 55.000 0.00 0.00 0.00 3.35
338 342 0.251033 ATGCAGCCTTGTCTTGCAGA 60.251 50.000 4.65 0.00 38.95 4.26
343 347 0.957395 CGGTGATGCAGCCTTGTCTT 60.957 55.000 0.00 0.00 0.00 3.01
344 348 1.376424 CGGTGATGCAGCCTTGTCT 60.376 57.895 0.00 0.00 0.00 3.41
351 355 1.078426 ACCTTACCGGTGATGCAGC 60.078 57.895 19.93 0.00 46.80 5.25
402 406 2.328099 GGTGGAGGCGCTCAAACAG 61.328 63.158 7.64 0.00 31.08 3.16
403 407 2.281484 GGTGGAGGCGCTCAAACA 60.281 61.111 7.64 0.00 31.08 2.83
440 444 0.106894 GGACCGGGGAGATGAATGTC 59.893 60.000 6.32 0.00 0.00 3.06
442 446 0.394565 GAGGACCGGGGAGATGAATG 59.605 60.000 6.32 0.00 0.00 2.67
472 476 1.546029 CCGGATGTGAGTGACTTGAGA 59.454 52.381 0.00 0.00 0.00 3.27
473 477 1.404717 CCCGGATGTGAGTGACTTGAG 60.405 57.143 0.73 0.00 0.00 3.02
474 478 0.608130 CCCGGATGTGAGTGACTTGA 59.392 55.000 0.73 0.00 0.00 3.02
476 480 1.983224 CCCCGGATGTGAGTGACTT 59.017 57.895 0.73 0.00 0.00 3.01
477 481 2.660064 GCCCCGGATGTGAGTGACT 61.660 63.158 0.73 0.00 0.00 3.41
908 4005 1.334869 CGGCAAGAAAGTTGTTCAGCT 59.665 47.619 0.00 0.00 0.00 4.24
974 4071 2.543067 GAAGAGGGCGATGGCAAGGT 62.543 60.000 1.01 0.00 42.47 3.50
1559 4656 4.160252 AGTTCAAAGTGACAGCATTTGGTT 59.840 37.500 7.50 0.00 35.21 3.67
1636 4733 1.243342 TTTGCGGCCATGGAGTCAAG 61.243 55.000 18.40 0.00 0.00 3.02
1767 4864 6.372103 TGTTGAAAATATGGTGGTTAGGTACG 59.628 38.462 0.00 0.00 0.00 3.67
1822 4919 2.149578 GTGCATAGCCTCATCCATCAC 58.850 52.381 0.00 0.00 0.00 3.06
1875 4972 9.851686 ACAATTTGATAGCTAAATACATCTGGA 57.148 29.630 2.79 0.00 0.00 3.86
2066 5163 7.233962 TGTTAGAACACAGACCTCTATTAACCA 59.766 37.037 0.00 0.00 33.17 3.67
2120 5217 2.103094 ACCTTTCCTTCTTTGCAAAGGC 59.897 45.455 33.01 0.00 46.12 4.35
2829 5978 2.223688 CGCTCATCCTGACCTCACTAAG 60.224 54.545 0.00 0.00 0.00 2.18
3070 7886 4.870636 AGTCAATCCAGATGCCCAAAATA 58.129 39.130 0.00 0.00 0.00 1.40
3715 8858 4.160439 AGCAAGCACTCTAACTACTGCATA 59.840 41.667 0.00 0.00 31.71 3.14
5766 12530 4.669206 ATCAGGTGTGCTCTAGATCAAG 57.331 45.455 0.00 0.00 0.00 3.02
5767 12531 4.141846 GGAATCAGGTGTGCTCTAGATCAA 60.142 45.833 0.00 0.00 0.00 2.57
5768 12532 3.386078 GGAATCAGGTGTGCTCTAGATCA 59.614 47.826 0.00 0.00 0.00 2.92
5769 12533 3.640967 AGGAATCAGGTGTGCTCTAGATC 59.359 47.826 0.00 0.00 0.00 2.75
5770 12534 3.652055 AGGAATCAGGTGTGCTCTAGAT 58.348 45.455 0.00 0.00 0.00 1.98
5771 12535 3.107402 AGGAATCAGGTGTGCTCTAGA 57.893 47.619 0.00 0.00 0.00 2.43
5772 12536 3.196469 TCAAGGAATCAGGTGTGCTCTAG 59.804 47.826 0.00 0.00 0.00 2.43
5773 12537 3.173151 TCAAGGAATCAGGTGTGCTCTA 58.827 45.455 0.00 0.00 0.00 2.43
5774 12538 1.980765 TCAAGGAATCAGGTGTGCTCT 59.019 47.619 0.00 0.00 0.00 4.09
5775 12539 2.479566 TCAAGGAATCAGGTGTGCTC 57.520 50.000 0.00 0.00 0.00 4.26
5776 12540 2.575279 AGATCAAGGAATCAGGTGTGCT 59.425 45.455 0.00 0.00 0.00 4.40
5777 12541 2.681848 CAGATCAAGGAATCAGGTGTGC 59.318 50.000 0.00 0.00 0.00 4.57
5778 12542 3.054875 TCCAGATCAAGGAATCAGGTGTG 60.055 47.826 4.58 0.00 34.74 3.82
5779 12543 3.184628 TCCAGATCAAGGAATCAGGTGT 58.815 45.455 4.58 0.00 34.74 4.16
5780 12544 3.806380 CTCCAGATCAAGGAATCAGGTG 58.194 50.000 8.11 0.00 34.74 4.00
5781 12545 2.172293 GCTCCAGATCAAGGAATCAGGT 59.828 50.000 8.11 0.00 34.74 4.00
5782 12546 2.172082 TGCTCCAGATCAAGGAATCAGG 59.828 50.000 8.11 0.00 34.51 3.86
5783 12547 3.204526 GTGCTCCAGATCAAGGAATCAG 58.795 50.000 8.11 0.00 34.08 2.90
5784 12548 2.573009 TGTGCTCCAGATCAAGGAATCA 59.427 45.455 8.11 6.57 34.08 2.57
5785 12549 2.941720 GTGTGCTCCAGATCAAGGAATC 59.058 50.000 8.11 4.48 34.08 2.52
5786 12550 2.356535 GGTGTGCTCCAGATCAAGGAAT 60.357 50.000 8.11 0.00 34.08 3.01
5787 12551 1.003580 GGTGTGCTCCAGATCAAGGAA 59.996 52.381 8.11 0.00 34.08 3.36
5788 12552 0.615331 GGTGTGCTCCAGATCAAGGA 59.385 55.000 6.73 6.73 0.00 3.36
5789 12553 0.617413 AGGTGTGCTCCAGATCAAGG 59.383 55.000 0.00 0.00 0.00 3.61
5897 12733 4.469657 AGATCAAGAGGAGTAGCTTCGAT 58.530 43.478 0.00 0.00 0.00 3.59
6175 13165 2.780693 CCCTGGTCCTCCTCCTCA 59.219 66.667 0.00 0.00 34.23 3.86
6734 13795 1.912043 ACAGCTAGCCTTCTCCATTGT 59.088 47.619 12.13 2.62 0.00 2.71
6758 13819 3.582647 TGATTTAGCAGACTGGAGTTGGA 59.417 43.478 4.26 0.00 0.00 3.53
6998 14061 4.279659 CACCTTGTTTTTCAGTACGAAGC 58.720 43.478 0.00 0.00 34.32 3.86
7026 14089 4.042187 AGGAGTCAGGCTTGTTACTTCAAT 59.958 41.667 0.00 0.00 0.00 2.57
7195 14266 4.397420 TCCTGCGGCATGAATACATAAAT 58.603 39.130 1.75 0.00 35.09 1.40
7202 14273 0.819259 GCCTTCCTGCGGCATGAATA 60.819 55.000 18.74 0.96 46.77 1.75
7215 14286 2.747855 CTCCTTGGCACGCCTTCC 60.748 66.667 9.92 0.00 36.94 3.46
7345 14422 6.573664 TGAAGAGAGAGATCATAGCTTAGC 57.426 41.667 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.