Multiple sequence alignment - TraesCS7D01G489600

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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 TraesCS7D01G489600 chr7D 100.000 5936 0 0 1 5936 599247233 599241298 0.000000e+00 10962.0
1 TraesCS7D01G489600 chr7D 77.102 2712 474 85 1743 4368 606107602 606110252 0.000000e+00 1432.0
2 TraesCS7D01G489600 chr7D 87.862 1104 125 3 4570 5671 598517148 598518244 0.000000e+00 1288.0
3 TraesCS7D01G489600 chr7D 77.372 2245 379 75 2195 4368 605957468 605959654 0.000000e+00 1212.0
4 TraesCS7D01G489600 chr7D 92.105 684 50 4 3894 4575 598514401 598515082 0.000000e+00 961.0
5 TraesCS7D01G489600 chr7D 80.018 1121 182 26 3180 4291 606303913 606305000 0.000000e+00 791.0
6 TraesCS7D01G489600 chr7D 76.361 1396 267 52 3188 4554 606702301 606703662 0.000000e+00 691.0
7 TraesCS7D01G489600 chr7D 90.625 256 24 0 5681 5936 598518290 598518545 2.050000e-89 340.0
8 TraesCS7D01G489600 chr7A 95.720 4603 153 12 1 4575 691469504 691464918 0.000000e+00 7369.0
9 TraesCS7D01G489600 chr7A 92.482 1104 72 5 4570 5670 691464393 691463298 0.000000e+00 1568.0
10 TraesCS7D01G489600 chr7A 76.991 2499 419 84 1920 4343 697824454 697826871 0.000000e+00 1286.0
11 TraesCS7D01G489600 chr7A 76.278 1408 275 46 3175 4554 698764774 698766150 0.000000e+00 695.0
12 TraesCS7D01G489600 chr7A 80.825 824 115 21 930 1722 697823565 697824376 1.830000e-169 606.0
13 TraesCS7D01G489600 chr7A 92.925 212 15 0 5681 5892 691463251 691463040 5.780000e-80 309.0
14 TraesCS7D01G489600 chr7A 77.688 372 72 6 3390 3760 716374232 716373871 3.600000e-52 217.0
15 TraesCS7D01G489600 chr4B 93.585 2541 134 13 2071 4587 12754840 12757375 0.000000e+00 3762.0
16 TraesCS7D01G489600 chr4B 86.445 2132 139 59 1 2078 12752545 12754580 0.000000e+00 2198.0
17 TraesCS7D01G489600 chr4B 92.784 1372 89 5 4566 5936 12757874 12759236 0.000000e+00 1977.0
18 TraesCS7D01G489600 chr4B 89.255 1033 86 9 2266 3274 12748167 12749198 0.000000e+00 1269.0
19 TraesCS7D01G489600 chr4B 88.298 282 32 1 4295 4575 12750139 12750420 2.650000e-88 337.0
20 TraesCS7D01G489600 chr7B 89.602 2866 256 22 1743 4575 677962036 677964892 0.000000e+00 3603.0
21 TraesCS7D01G489600 chr7B 89.996 2419 208 15 2192 4578 677882786 677880370 0.000000e+00 3096.0
22 TraesCS7D01G489600 chr7B 97.976 840 16 1 1 839 678661179 678660340 0.000000e+00 1456.0
23 TraesCS7D01G489600 chr7B 85.801 1317 107 33 467 1742 677960857 677962134 0.000000e+00 1323.0
24 TraesCS7D01G489600 chr7B 86.412 1126 136 10 4570 5688 677965404 677966519 0.000000e+00 1216.0
25 TraesCS7D01G489600 chr7B 86.863 1119 89 22 647 1742 677883869 677882786 0.000000e+00 1199.0
26 TraesCS7D01G489600 chr7B 89.950 796 71 6 2360 3151 677850728 677849938 0.000000e+00 1018.0
27 TraesCS7D01G489600 chr7B 88.682 645 71 2 3167 3811 678508478 678509120 0.000000e+00 785.0
28 TraesCS7D01G489600 chr7B 83.149 813 116 11 4570 5369 678510117 678510921 0.000000e+00 723.0
29 TraesCS7D01G489600 chr7B 81.730 821 104 26 936 1728 690915707 690916509 1.390000e-180 643.0
30 TraesCS7D01G489600 chr7B 80.610 820 116 21 933 1720 690094284 690095092 1.420000e-165 593.0
31 TraesCS7D01G489600 chr7B 86.722 482 64 0 5190 5671 677872725 677872244 2.430000e-148 536.0
32 TraesCS7D01G489600 chr7B 86.780 469 54 2 4923 5389 678001711 678002173 3.170000e-142 516.0
33 TraesCS7D01G489600 chr7B 89.067 375 39 2 4203 4575 677977277 677977651 1.170000e-126 464.0
34 TraesCS7D01G489600 chr7B 89.655 319 31 2 4576 4894 677879842 677879526 7.160000e-109 405.0
35 TraesCS7D01G489600 chr7B 89.068 311 34 0 4570 4880 678001401 678001711 2.590000e-103 387.0
36 TraesCS7D01G489600 chr7B 85.993 307 35 2 4884 5188 677873849 677873549 7.420000e-84 322.0
37 TraesCS7D01G489600 chr7B 80.635 315 54 7 3167 3478 691045736 691046046 2.770000e-58 237.0
38 TraesCS7D01G489600 chr7B 82.578 287 30 14 412 689 690915200 690915475 9.950000e-58 235.0
39 TraesCS7D01G489600 chr7B 83.249 197 30 3 3399 3594 691046054 691046248 1.700000e-40 178.0
40 TraesCS7D01G489600 chr7B 94.495 109 6 0 578 686 677883979 677883871 1.020000e-37 169.0
41 TraesCS7D01G489600 chr7B 90.426 94 9 0 4054 4147 678509109 678509202 2.250000e-24 124.0
42 TraesCS7D01G489600 chr7B 82.143 84 12 2 433 516 718596064 718596144 1.070000e-07 69.4
43 TraesCS7D01G489600 chrUn 85.382 773 99 4 4923 5688 343859342 343860107 0.000000e+00 789.0
44 TraesCS7D01G489600 chrUn 85.123 773 101 4 4923 5688 87277379 87278144 0.000000e+00 778.0
45 TraesCS7D01G489600 chrUn 75.938 1413 270 52 3178 4557 92706378 92705003 0.000000e+00 662.0
46 TraesCS7D01G489600 chrUn 81.598 826 107 22 936 1729 33118458 33119270 5.020000e-180 641.0
47 TraesCS7D01G489600 chrUn 89.068 311 34 0 4570 4880 87277069 87277379 2.590000e-103 387.0
48 TraesCS7D01G489600 chrUn 89.068 311 34 0 4570 4880 343859032 343859342 2.590000e-103 387.0
49 TraesCS7D01G489600 chrUn 83.083 266 32 10 534 792 33118093 33118352 4.630000e-56 230.0
50 TraesCS7D01G489600 chrUn 75.000 384 80 10 3985 4359 93195513 93195889 4.760000e-36 163.0
51 TraesCS7D01G489600 chrUn 82.143 84 12 2 433 516 329802149 329802069 1.070000e-07 69.4
52 TraesCS7D01G489600 chrUn 82.143 84 12 2 433 516 384893724 384893644 1.070000e-07 69.4
53 TraesCS7D01G489600 chr3A 81.477 826 110 21 936 1729 704695733 704694919 6.490000e-179 638.0
54 TraesCS7D01G489600 chr3A 81.455 825 111 20 936 1729 704781610 704780797 6.490000e-179 638.0
55 TraesCS7D01G489600 chr3A 81.477 826 110 20 936 1729 704841554 704840740 6.490000e-179 638.0
56 TraesCS7D01G489600 chr5D 91.935 62 3 1 578 639 459578328 459578387 1.060000e-12 86.1
57 TraesCS7D01G489600 chr5B 91.935 62 3 1 578 639 563865235 563865294 1.060000e-12 86.1
58 TraesCS7D01G489600 chr5B 90.323 62 4 1 578 639 563683918 563683977 4.930000e-11 80.5


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 TraesCS7D01G489600 chr7D 599241298 599247233 5935 True 10962.000000 10962 100.000000 1 5936 1 chr7D.!!$R1 5935
1 TraesCS7D01G489600 chr7D 606107602 606110252 2650 False 1432.000000 1432 77.102000 1743 4368 1 chr7D.!!$F2 2625
2 TraesCS7D01G489600 chr7D 605957468 605959654 2186 False 1212.000000 1212 77.372000 2195 4368 1 chr7D.!!$F1 2173
3 TraesCS7D01G489600 chr7D 598514401 598518545 4144 False 863.000000 1288 90.197333 3894 5936 3 chr7D.!!$F5 2042
4 TraesCS7D01G489600 chr7D 606303913 606305000 1087 False 791.000000 791 80.018000 3180 4291 1 chr7D.!!$F3 1111
5 TraesCS7D01G489600 chr7D 606702301 606703662 1361 False 691.000000 691 76.361000 3188 4554 1 chr7D.!!$F4 1366
6 TraesCS7D01G489600 chr7A 691463040 691469504 6464 True 3082.000000 7369 93.709000 1 5892 3 chr7A.!!$R2 5891
7 TraesCS7D01G489600 chr7A 697823565 697826871 3306 False 946.000000 1286 78.908000 930 4343 2 chr7A.!!$F2 3413
8 TraesCS7D01G489600 chr7A 698764774 698766150 1376 False 695.000000 695 76.278000 3175 4554 1 chr7A.!!$F1 1379
9 TraesCS7D01G489600 chr4B 12748167 12759236 11069 False 1908.600000 3762 90.073400 1 5936 5 chr4B.!!$F1 5935
10 TraesCS7D01G489600 chr7B 677960857 677966519 5662 False 2047.333333 3603 87.271667 467 5688 3 chr7B.!!$F4 5221
11 TraesCS7D01G489600 chr7B 678660340 678661179 839 True 1456.000000 1456 97.976000 1 839 1 chr7B.!!$R2 838
12 TraesCS7D01G489600 chr7B 677879526 677883979 4453 True 1217.250000 3096 90.252250 578 4894 4 chr7B.!!$R4 4316
13 TraesCS7D01G489600 chr7B 677849938 677850728 790 True 1018.000000 1018 89.950000 2360 3151 1 chr7B.!!$R1 791
14 TraesCS7D01G489600 chr7B 690094284 690095092 808 False 593.000000 593 80.610000 933 1720 1 chr7B.!!$F2 787
15 TraesCS7D01G489600 chr7B 678508478 678510921 2443 False 544.000000 785 87.419000 3167 5369 3 chr7B.!!$F6 2202
16 TraesCS7D01G489600 chr7B 678001401 678002173 772 False 451.500000 516 87.924000 4570 5389 2 chr7B.!!$F5 819
17 TraesCS7D01G489600 chr7B 690915200 690916509 1309 False 439.000000 643 82.154000 412 1728 2 chr7B.!!$F7 1316
18 TraesCS7D01G489600 chr7B 677872244 677873849 1605 True 429.000000 536 86.357500 4884 5671 2 chr7B.!!$R3 787
19 TraesCS7D01G489600 chr7B 691045736 691046248 512 False 207.500000 237 81.942000 3167 3594 2 chr7B.!!$F8 427
20 TraesCS7D01G489600 chrUn 92705003 92706378 1375 True 662.000000 662 75.938000 3178 4557 1 chrUn.!!$R1 1379
21 TraesCS7D01G489600 chrUn 343859032 343860107 1075 False 588.000000 789 87.225000 4570 5688 2 chrUn.!!$F4 1118
22 TraesCS7D01G489600 chrUn 87277069 87278144 1075 False 582.500000 778 87.095500 4570 5688 2 chrUn.!!$F3 1118
23 TraesCS7D01G489600 chrUn 33118093 33119270 1177 False 435.500000 641 82.340500 534 1729 2 chrUn.!!$F2 1195
24 TraesCS7D01G489600 chr3A 704694919 704695733 814 True 638.000000 638 81.477000 936 1729 1 chr3A.!!$R1 793
25 TraesCS7D01G489600 chr3A 704780797 704781610 813 True 638.000000 638 81.455000 936 1729 1 chr3A.!!$R2 793
26 TraesCS7D01G489600 chr3A 704840740 704841554 814 True 638.000000 638 81.477000 936 1729 1 chr3A.!!$R3 793

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
429 4809 1.857217 CGATGAAGGCACTCTCAATCG 59.143 52.381 0.00 0.0 38.49 3.34 F
1673 6275 0.108329 AACCGTTCATCCGCTCGATT 60.108 50.000 0.00 0.0 0.00 3.34 F
1835 6448 0.343372 ATGAGTTAGGAGGGGGAGCA 59.657 55.000 0.00 0.0 0.00 4.26 F
2829 7745 1.202268 GCTTGCCATGCTCAGAACATC 60.202 52.381 0.00 0.0 0.00 3.06 F
4473 9557 0.037326 ACGTTGACTCCATGCGTGAT 60.037 50.000 7.72 0.0 34.61 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 6291 0.105453 GATCCACCTCCCCTCTGCTA 60.105 60.000 0.00 0.0 0.00 3.49 R
3388 8356 0.103208 GCGTCCCAGGATGTACTCTG 59.897 60.000 7.71 0.0 33.91 3.35 R
3414 8382 5.805728 TCTTTGTCTTGGAGTCCTTATTCC 58.194 41.667 11.33 0.0 32.16 3.01 R
4554 9638 0.110678 TACCATTTGTGGGTGCCGAA 59.889 50.000 0.00 0.0 39.48 4.30 R
5576 13568 0.114364 TCTGCAGGTGGTAGGAGACA 59.886 55.000 15.13 0.0 0.00 3.41 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
117 4496 4.394920 TGCTAAGAGCCCTTTTTGAATACG 59.605 41.667 0.00 0.00 41.51 3.06
336 4716 4.002982 CAGAAAATCCACACCTTCGATCA 58.997 43.478 0.00 0.00 0.00 2.92
429 4809 1.857217 CGATGAAGGCACTCTCAATCG 59.143 52.381 0.00 0.00 38.49 3.34
919 5439 6.536447 AGAGGTTTTCCGGTTATGTTCTTAA 58.464 36.000 0.00 0.00 46.35 1.85
928 5455 5.398169 CGGTTATGTTCTTAAATTGCTGCA 58.602 37.500 0.00 0.00 0.00 4.41
982 5518 2.165437 TGGTGTTTTCTTTGACAGGTGC 59.835 45.455 0.00 0.00 0.00 5.01
992 5528 2.325583 TGACAGGTGCGAAGAAGTTT 57.674 45.000 0.00 0.00 0.00 2.66
1110 5647 1.300620 CGACCGTGTCTGCCTCAAA 60.301 57.895 3.15 0.00 0.00 2.69
1324 5878 2.261671 GTCCTCACCGATGTGCGT 59.738 61.111 0.00 0.00 42.46 5.24
1653 6255 1.570857 AAACCAGCGGGATCCCATCA 61.571 55.000 30.42 0.00 38.05 3.07
1673 6275 0.108329 AACCGTTCATCCGCTCGATT 60.108 50.000 0.00 0.00 0.00 3.34
1688 6290 1.456331 GATTGGATGGCCAGTGGGG 60.456 63.158 13.05 0.00 46.91 4.96
1689 6291 2.228841 GATTGGATGGCCAGTGGGGT 62.229 60.000 13.05 0.00 46.91 4.95
1690 6292 0.923729 ATTGGATGGCCAGTGGGGTA 60.924 55.000 13.05 0.00 46.91 3.69
1695 6297 3.009115 GGCCAGTGGGGTAGCAGA 61.009 66.667 12.15 0.00 39.65 4.26
1700 6302 2.040606 GTGGGGTAGCAGAGGGGA 59.959 66.667 0.00 0.00 0.00 4.81
1701 6303 2.066999 GTGGGGTAGCAGAGGGGAG 61.067 68.421 0.00 0.00 0.00 4.30
1704 6306 2.066999 GGGTAGCAGAGGGGAGGTG 61.067 68.421 0.00 0.00 0.00 4.00
1707 6309 0.399233 GTAGCAGAGGGGAGGTGGAT 60.399 60.000 0.00 0.00 0.00 3.41
1710 6312 1.075970 CAGAGGGGAGGTGGATCGA 60.076 63.158 0.00 0.00 0.00 3.59
1711 6313 1.075896 AGAGGGGAGGTGGATCGAC 60.076 63.158 0.00 0.00 0.00 4.20
1713 6315 1.677637 GAGGGGAGGTGGATCGACAC 61.678 65.000 10.22 1.93 40.60 3.67
1714 6316 1.987855 GGGGAGGTGGATCGACACA 60.988 63.158 10.22 0.00 43.08 3.72
1715 6317 1.338136 GGGGAGGTGGATCGACACAT 61.338 60.000 10.22 0.91 43.08 3.21
1719 6321 1.478510 GAGGTGGATCGACACATGAGT 59.521 52.381 10.22 0.00 43.08 3.41
1720 6322 1.902508 AGGTGGATCGACACATGAGTT 59.097 47.619 10.22 0.00 43.08 3.01
1722 6324 3.131223 AGGTGGATCGACACATGAGTTAG 59.869 47.826 10.22 0.00 43.08 2.34
1723 6325 2.860735 GTGGATCGACACATGAGTTAGC 59.139 50.000 0.00 0.00 40.99 3.09
1724 6326 2.495669 TGGATCGACACATGAGTTAGCA 59.504 45.455 0.00 0.00 0.00 3.49
1725 6327 3.119291 GGATCGACACATGAGTTAGCAG 58.881 50.000 0.00 0.00 0.00 4.24
1726 6328 2.654749 TCGACACATGAGTTAGCAGG 57.345 50.000 0.00 0.00 0.00 4.85
1728 6330 1.740380 CGACACATGAGTTAGCAGGGG 60.740 57.143 0.00 0.00 0.00 4.79
1743 6345 2.286121 GGGGGTGTGGGATCCAGA 60.286 66.667 15.23 0.00 32.34 3.86
1745 6347 1.709994 GGGGGTGTGGGATCCAGATC 61.710 65.000 15.23 0.00 32.34 2.75
1746 6348 0.695803 GGGGTGTGGGATCCAGATCT 60.696 60.000 15.23 0.00 37.92 2.75
1835 6448 0.343372 ATGAGTTAGGAGGGGGAGCA 59.657 55.000 0.00 0.00 0.00 4.26
2201 7100 8.470657 AGTCTAGAGTTCAGTATCATGCATAA 57.529 34.615 0.00 0.00 0.00 1.90
2484 7390 3.758023 TGTTTTCTATGGTGGCATGAGTG 59.242 43.478 0.00 0.00 0.00 3.51
2508 7414 7.327032 GTGATACAATTCCAAAAACAGAGAAGC 59.673 37.037 0.00 0.00 0.00 3.86
2530 7436 7.559590 AGCTGTATTGACATTATTCAAGGAC 57.440 36.000 0.00 0.00 38.87 3.85
2686 7599 7.221838 GTGCAGATTAGTTGAGCTAAACTAGAG 59.778 40.741 20.69 13.82 42.15 2.43
2813 7729 5.545658 AAACTAATATGTGTGACCGCTTG 57.454 39.130 0.00 0.00 0.00 4.01
2829 7745 1.202268 GCTTGCCATGCTCAGAACATC 60.202 52.381 0.00 0.00 0.00 3.06
2896 7820 8.946085 TGGTCAACAATAGTAATTGATCTTGTC 58.054 33.333 5.18 0.00 44.50 3.18
3380 8348 8.427902 AAGCCACATGAGTAGAGATAATGATA 57.572 34.615 0.00 0.00 0.00 2.15
3383 8351 8.090831 GCCACATGAGTAGAGATAATGATAACA 58.909 37.037 0.00 0.00 0.00 2.41
3388 8356 9.988815 ATGAGTAGAGATAATGATAACAACCAC 57.011 33.333 0.00 0.00 0.00 4.16
3432 8487 3.682999 GCCAGGAATAAGGACTCCAAGAC 60.683 52.174 0.00 0.00 33.83 3.01
3635 8691 6.873076 ACACTTGTGGTTATTTGGCATTTATG 59.127 34.615 5.72 0.00 0.00 1.90
3782 8841 7.028962 CCTCATTCTTAATTTCGATGTTTGCA 58.971 34.615 0.00 0.00 0.00 4.08
4137 9215 4.217118 GGTGATGCAAGTGAAAGACAGAAT 59.783 41.667 0.00 0.00 0.00 2.40
4455 9539 6.376018 CCTCATATAGCTCTGGTACTTCCTAC 59.624 46.154 0.00 0.00 37.07 3.18
4472 9556 0.599060 TACGTTGACTCCATGCGTGA 59.401 50.000 7.72 0.00 36.33 4.35
4473 9557 0.037326 ACGTTGACTCCATGCGTGAT 60.037 50.000 7.72 0.00 34.61 3.06
4554 9638 4.003788 CCAAGTGGTCGCGGGAGT 62.004 66.667 6.13 0.00 0.00 3.85
4567 11723 2.112297 GGAGTTCGGCACCCACAA 59.888 61.111 0.00 0.00 0.00 3.33
4606 11762 7.360946 GCACTTCAAAAACCGAGACTAATATGT 60.361 37.037 0.00 0.00 0.00 2.29
4617 11773 6.018994 CCGAGACTAATATGTTTAACAGTGGC 60.019 42.308 3.63 0.00 0.00 5.01
4619 11775 7.064134 CGAGACTAATATGTTTAACAGTGGCAA 59.936 37.037 3.63 0.00 0.00 4.52
4642 11798 8.135529 GCAAAACTATTTCTACACTTTCCAACT 58.864 33.333 0.00 0.00 0.00 3.16
4660 11816 4.580167 CCAACTTTCAGACAGATGGTTTCA 59.420 41.667 4.96 0.00 31.15 2.69
4695 11851 2.203252 CCTGATGGTGGGGATGCG 60.203 66.667 0.00 0.00 0.00 4.73
4880 12036 6.711277 TGAGCTAGACAGGTGTATTCAAATT 58.289 36.000 0.00 0.00 30.99 1.82
4924 12081 1.137675 TCATTGGAGAGGATGCTGTCG 59.862 52.381 5.28 0.00 0.00 4.35
5009 12172 6.152661 TGGACAGTTGTTGATTGATTATTCCC 59.847 38.462 0.00 0.00 0.00 3.97
5035 12198 4.019792 TCTTGCACACTGTACCATGAAT 57.980 40.909 0.00 0.00 0.00 2.57
5215 13207 2.736721 TGCATCTTTCTCCGAGAAAACG 59.263 45.455 21.22 12.66 42.95 3.60
5228 13220 2.673368 GAGAAAACGTGTAGCATCCTGG 59.327 50.000 0.00 0.00 0.00 4.45
5240 13232 0.755686 CATCCTGGGAGAGGCACTAC 59.244 60.000 0.00 0.00 41.55 2.73
5304 13296 1.600636 CACACCCGCCACAGACATT 60.601 57.895 0.00 0.00 0.00 2.71
5356 13348 5.227908 AGAACGGTAGTATCACAACACAAG 58.772 41.667 0.00 0.00 0.00 3.16
5485 13477 1.022451 CCCAACGACCACAATACGGG 61.022 60.000 0.00 0.00 0.00 5.28
5509 13501 2.677875 CCTCTGCCACCAAAGCCC 60.678 66.667 0.00 0.00 0.00 5.19
5511 13503 3.506743 TCTGCCACCAAAGCCCCA 61.507 61.111 0.00 0.00 0.00 4.96
5514 13506 2.283821 GCCACCAAAGCCCCATCA 60.284 61.111 0.00 0.00 0.00 3.07
5576 13568 1.366366 CCACGTCTTCCACCTCGTT 59.634 57.895 0.00 0.00 34.30 3.85
5831 13859 2.089201 GGGTTAGCGCATAAGTTTGGT 58.911 47.619 11.47 0.00 0.00 3.67
5884 13912 5.496133 AATGAGATTCTCGAATTGCCAAG 57.504 39.130 9.07 0.00 32.35 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 4746 3.908382 GTCCGTACGAAATATTATCGCGT 59.092 43.478 18.76 12.47 43.88 6.01
429 4809 0.978907 TACTTCCTTTGACCGGGACC 59.021 55.000 6.32 0.00 0.00 4.46
850 5362 4.634443 CCACCTCTATTAAGAAACAACGGG 59.366 45.833 0.00 0.00 0.00 5.28
905 5425 5.398169 TGCAGCAATTTAAGAACATAACCG 58.602 37.500 0.00 0.00 0.00 4.44
919 5439 0.899717 ACAACGGGGATGCAGCAATT 60.900 50.000 3.51 0.00 0.00 2.32
928 5455 4.918588 ACTGATTAAGAAACAACGGGGAT 58.081 39.130 0.00 0.00 0.00 3.85
982 5518 3.735746 GCCATGTTTTCCAAACTTCTTCG 59.264 43.478 1.33 0.00 0.00 3.79
992 5528 1.677300 ATCGCGGCCATGTTTTCCA 60.677 52.632 6.13 0.00 0.00 3.53
1110 5647 2.645802 CGCAAGAGGACCTCTAGTACT 58.354 52.381 24.56 5.59 45.03 2.73
1324 5878 2.818841 CCGTCCATGTCCGGCATA 59.181 61.111 10.44 0.00 37.43 3.14
1465 6048 5.982356 TCAGTGTATCTTGAAGATTCAGGG 58.018 41.667 13.54 9.14 38.61 4.45
1653 6255 0.108329 ATCGAGCGGATGAACGGTTT 60.108 50.000 0.00 0.00 45.44 3.27
1673 6275 2.000701 CTACCCCACTGGCCATCCA 61.001 63.158 5.51 0.00 40.85 3.41
1688 6290 0.399233 ATCCACCTCCCCTCTGCTAC 60.399 60.000 0.00 0.00 0.00 3.58
1689 6291 0.105453 GATCCACCTCCCCTCTGCTA 60.105 60.000 0.00 0.00 0.00 3.49
1690 6292 1.383803 GATCCACCTCCCCTCTGCT 60.384 63.158 0.00 0.00 0.00 4.24
1695 6297 1.686110 GTGTCGATCCACCTCCCCT 60.686 63.158 0.00 0.00 0.00 4.79
1700 6302 1.561643 ACTCATGTGTCGATCCACCT 58.438 50.000 3.94 0.00 34.35 4.00
1701 6303 2.386661 AACTCATGTGTCGATCCACC 57.613 50.000 0.03 0.00 34.35 4.61
1704 6306 3.119291 CTGCTAACTCATGTGTCGATCC 58.881 50.000 0.03 0.00 0.00 3.36
1707 6309 1.204704 CCCTGCTAACTCATGTGTCGA 59.795 52.381 0.03 0.00 0.00 4.20
1710 6312 0.620556 CCCCCTGCTAACTCATGTGT 59.379 55.000 0.00 0.00 0.00 3.72
1711 6313 3.483954 CCCCCTGCTAACTCATGTG 57.516 57.895 0.00 0.00 0.00 3.21
1726 6328 1.697754 ATCTGGATCCCACACCCCC 60.698 63.158 9.90 0.00 0.00 5.40
1728 6330 0.761802 GAGATCTGGATCCCACACCC 59.238 60.000 9.90 0.00 38.58 4.61
1730 6332 2.971330 AGATGAGATCTGGATCCCACAC 59.029 50.000 9.90 0.00 38.44 3.82
1732 6334 4.020662 GGTTAGATGAGATCTGGATCCCAC 60.021 50.000 9.90 1.57 40.51 4.61
1735 6337 3.829601 ACGGTTAGATGAGATCTGGATCC 59.170 47.826 4.20 4.20 40.51 3.36
1737 6339 4.895889 TGAACGGTTAGATGAGATCTGGAT 59.104 41.667 0.00 0.00 40.51 3.41
1738 6340 4.278310 TGAACGGTTAGATGAGATCTGGA 58.722 43.478 0.00 0.00 40.51 3.86
1739 6341 4.655762 TGAACGGTTAGATGAGATCTGG 57.344 45.455 0.00 0.00 40.51 3.86
1740 6342 5.010516 AGGATGAACGGTTAGATGAGATCTG 59.989 44.000 0.00 0.00 40.51 2.90
1741 6343 5.144100 AGGATGAACGGTTAGATGAGATCT 58.856 41.667 0.00 0.00 43.33 2.75
1742 6344 5.461032 AGGATGAACGGTTAGATGAGATC 57.539 43.478 0.00 0.00 0.00 2.75
1743 6345 5.878406 AAGGATGAACGGTTAGATGAGAT 57.122 39.130 0.00 0.00 0.00 2.75
1745 6347 5.874810 TCAAAAGGATGAACGGTTAGATGAG 59.125 40.000 0.00 0.00 0.00 2.90
1746 6348 5.800296 TCAAAAGGATGAACGGTTAGATGA 58.200 37.500 0.00 0.00 0.00 2.92
1788 6401 1.203187 TCCACCTCAGTTCTGCTACCT 60.203 52.381 0.00 0.00 0.00 3.08
1835 6448 5.419155 CGACACCACTATATATGGATCCTGT 59.581 44.000 14.23 3.84 39.87 4.00
2201 7100 9.869667 ACTAAGCTCGATTACCCATATATATCT 57.130 33.333 0.00 0.00 0.00 1.98
2259 7158 5.496556 CCATCAAACAAGTACATAGTGGGA 58.503 41.667 0.00 0.00 0.00 4.37
2444 7350 8.915871 AGAAAACATGTATGATGCAATTGTAC 57.084 30.769 7.40 1.95 0.00 2.90
2455 7361 5.504853 TGCCACCATAGAAAACATGTATGA 58.495 37.500 0.00 0.00 37.44 2.15
2461 7367 4.400251 CACTCATGCCACCATAGAAAACAT 59.600 41.667 0.00 0.00 0.00 2.71
2484 7390 7.540055 CAGCTTCTCTGTTTTTGGAATTGTATC 59.460 37.037 0.00 0.00 38.02 2.24
2508 7414 9.823647 AGTAGTCCTTGAATAATGTCAATACAG 57.176 33.333 0.00 0.00 39.49 2.74
2530 7436 9.883142 AAACTCAAGGAGATTAAAGATGAGTAG 57.117 33.333 6.01 0.00 43.64 2.57
2583 7489 8.750298 GGCACTCCTACTTTATATGCTATTCTA 58.250 37.037 0.00 0.00 0.00 2.10
2756 7670 8.870075 AAGCAGTATTATCTATGGGGATTTTC 57.130 34.615 0.00 0.00 0.00 2.29
2813 7729 1.094073 AGCGATGTTCTGAGCATGGC 61.094 55.000 25.89 25.89 44.63 4.40
2829 7745 1.157870 AACAGTTGTCGACCCAAGCG 61.158 55.000 14.12 0.00 0.00 4.68
3161 8109 9.974980 AACTTTGGAATACAAACGTTCATATTT 57.025 25.926 14.70 2.07 43.81 1.40
3165 8133 7.593644 GCTTAACTTTGGAATACAAACGTTCAT 59.406 33.333 0.00 0.00 43.81 2.57
3176 8144 5.124776 CGACCAATGGCTTAACTTTGGAATA 59.875 40.000 15.11 0.00 44.23 1.75
3230 8198 2.154462 CTTCATCACGGCCTTCTTGTT 58.846 47.619 0.00 0.00 0.00 2.83
3380 8348 3.244561 CCAGGATGTACTCTGTGGTTGTT 60.245 47.826 0.00 0.00 0.00 2.83
3383 8351 1.909302 CCCAGGATGTACTCTGTGGTT 59.091 52.381 0.00 0.00 0.00 3.67
3388 8356 0.103208 GCGTCCCAGGATGTACTCTG 59.897 60.000 7.71 0.00 33.91 3.35
3414 8382 5.805728 TCTTTGTCTTGGAGTCCTTATTCC 58.194 41.667 11.33 0.00 32.16 3.01
3432 8487 6.927381 AGAACCATCTTTTTCATTGCTCTTTG 59.073 34.615 0.00 0.00 29.15 2.77
3857 8922 2.863740 TGATCCGTGCATTACTAAAGCG 59.136 45.455 0.00 0.00 0.00 4.68
3974 9049 7.469537 TGGGAACAAAAAGAACTAAAAGTGA 57.530 32.000 0.00 0.00 37.44 3.41
4137 9215 3.781965 TCCTCTGATTGTCCATGGATGAA 59.218 43.478 19.62 14.32 0.00 2.57
4309 9393 5.934402 ACCAAATACCTCGACATTCTACT 57.066 39.130 0.00 0.00 0.00 2.57
4455 9539 1.921243 TATCACGCATGGAGTCAACG 58.079 50.000 0.00 0.00 34.19 4.10
4472 9556 6.352516 CCTTTACTTGTCTCCATCAGCTTAT 58.647 40.000 0.00 0.00 0.00 1.73
4473 9557 5.734720 CCTTTACTTGTCTCCATCAGCTTA 58.265 41.667 0.00 0.00 0.00 3.09
4554 9638 0.110678 TACCATTTGTGGGTGCCGAA 59.889 50.000 0.00 0.00 39.48 4.30
4567 11723 4.634012 TTGAAGTGCTACCAGTACCATT 57.366 40.909 0.00 0.00 30.68 3.16
4606 11762 8.904834 TGTAGAAATAGTTTTGCCACTGTTAAA 58.095 29.630 0.00 0.00 28.75 1.52
4612 11768 7.255486 GGAAAGTGTAGAAATAGTTTTGCCACT 60.255 37.037 0.00 0.00 30.74 4.00
4642 11798 3.436704 GCGATGAAACCATCTGTCTGAAA 59.563 43.478 0.00 0.00 38.57 2.69
4924 12081 1.676006 CCGGCAAAACTATCCATCCAC 59.324 52.381 0.00 0.00 0.00 4.02
5009 12172 3.402110 TGGTACAGTGTGCAAGATTGAG 58.598 45.455 13.62 0.00 0.00 3.02
5228 13220 2.383855 AGATCTGTGTAGTGCCTCTCC 58.616 52.381 0.00 0.00 0.00 3.71
5240 13232 5.647658 CACTATAGGAGGAGCTAGATCTGTG 59.352 48.000 8.10 0.00 0.00 3.66
5356 13348 6.258160 GTGGTGTTGCAGATATGTTATGAAC 58.742 40.000 0.00 0.00 0.00 3.18
5503 13495 1.586154 CGCGAAGTTGATGGGGCTTT 61.586 55.000 0.00 0.00 0.00 3.51
5504 13496 2.040544 CGCGAAGTTGATGGGGCTT 61.041 57.895 0.00 0.00 0.00 4.35
5509 13501 1.970917 GAGCCACGCGAAGTTGATGG 61.971 60.000 15.93 9.56 0.00 3.51
5511 13503 1.741770 GGAGCCACGCGAAGTTGAT 60.742 57.895 15.93 0.00 0.00 2.57
5514 13506 2.110213 TTGGAGCCACGCGAAGTT 59.890 55.556 15.93 0.00 0.00 2.66
5576 13568 0.114364 TCTGCAGGTGGTAGGAGACA 59.886 55.000 15.13 0.00 0.00 3.41
5774 13802 2.448926 TCACGTCCGACACATTTGAT 57.551 45.000 0.00 0.00 0.00 2.57
5831 13859 2.437180 CAGATCAGCTGCGCCCAA 60.437 61.111 9.47 0.00 37.90 4.12
5850 13878 4.290942 AGAATCTCATTCCGGACTAGGTT 58.709 43.478 1.83 4.12 40.13 3.50
5884 13912 9.884465 CGAAGTATGAATTTTTATCATCCCTTC 57.116 33.333 13.44 13.44 39.30 3.46


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

AutoCloner maintained by Alex Coulton.