Multiple sequence alignment - TraesCS7B01G305500

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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 TraesCS7B01G305500 chr7B 100.000 7392 0 0 1 7392 547479285 547471894 0.000000e+00 13651.0
1 TraesCS7B01G305500 chr7B 99.376 4327 22 2 2537 6861 547553410 547549087 0.000000e+00 7836.0
2 TraesCS7B01G305500 chr7B 98.283 2505 23 6 39 2541 547568722 547566236 0.000000e+00 4370.0
3 TraesCS7B01G305500 chr7B 98.980 490 5 0 6903 7392 547549086 547548597 0.000000e+00 878.0
4 TraesCS7B01G305500 chr7B 95.082 122 5 1 6518 6639 562093907 562094027 2.720000e-44 191.0
5 TraesCS7B01G305500 chr7B 94.167 120 6 1 6518 6637 484165727 484165609 1.640000e-41 182.0
6 TraesCS7B01G305500 chr7B 81.890 127 12 4 6808 6934 537824715 537824600 6.100000e-16 97.1
7 TraesCS7B01G305500 chr2B 96.990 2259 42 11 1062 3296 34647480 34649736 0.000000e+00 3771.0
8 TraesCS7B01G305500 chr2B 98.170 929 10 4 5587 6513 34649736 34650659 0.000000e+00 1615.0
9 TraesCS7B01G305500 chr2B 93.224 1033 42 14 3 1020 34646448 34647467 0.000000e+00 1495.0
10 TraesCS7B01G305500 chr2B 89.338 891 76 10 4339 5214 717347546 717348432 0.000000e+00 1101.0
11 TraesCS7B01G305500 chr2B 93.367 603 34 6 3658 4258 717346950 717347548 0.000000e+00 887.0
12 TraesCS7B01G305500 chr2B 90.547 402 9 8 6991 7392 34650905 34651277 8.560000e-139 505.0
13 TraesCS7B01G305500 chr2B 94.273 227 13 0 6580 6806 34650661 34650887 1.530000e-91 348.0
14 TraesCS7B01G305500 chr2B 96.000 125 4 1 6808 6931 25366091 25365967 1.260000e-47 202.0
15 TraesCS7B01G305500 chr2B 95.789 95 4 0 4255 4349 49649133 49649227 3.570000e-33 154.0
16 TraesCS7B01G305500 chr4D 91.595 1404 98 12 3814 5204 446106518 446105122 0.000000e+00 1921.0
17 TraesCS7B01G305500 chr4D 89.928 973 60 17 3298 4258 57885945 57884999 0.000000e+00 1219.0
18 TraesCS7B01G305500 chr4D 91.211 421 25 7 4339 4751 57885001 57884585 5.010000e-156 562.0
19 TraesCS7B01G305500 chr2A 90.071 987 61 16 3284 4258 746249601 746248640 0.000000e+00 1245.0
20 TraesCS7B01G305500 chr2A 87.879 891 87 13 4339 5214 277153595 277154479 0.000000e+00 1027.0
21 TraesCS7B01G305500 chr2A 94.570 442 20 3 3818 4258 277153159 277153597 0.000000e+00 680.0
22 TraesCS7B01G305500 chr2A 83.133 249 30 4 1715 1963 14880748 14880512 4.490000e-52 217.0
23 TraesCS7B01G305500 chr2A 95.699 93 4 0 4256 4348 712843622 712843530 4.620000e-32 150.0
24 TraesCS7B01G305500 chr2A 96.970 33 1 0 4719 4751 746248122 746248090 1.000000e-03 56.5
25 TraesCS7B01G305500 chrUn 89.897 970 63 18 3298 4258 42709549 42710492 0.000000e+00 1216.0
26 TraesCS7B01G305500 chrUn 89.804 971 62 19 3298 4258 329833653 329834596 0.000000e+00 1210.0
27 TraesCS7B01G305500 chrUn 89.506 972 66 18 3296 4258 42729344 42730288 0.000000e+00 1197.0
28 TraesCS7B01G305500 chrUn 89.506 972 66 18 3296 4258 222905387 222906331 0.000000e+00 1197.0
29 TraesCS7B01G305500 chrUn 89.506 972 63 18 3296 4258 403645074 403646015 0.000000e+00 1194.0
30 TraesCS7B01G305500 chrUn 100.000 401 0 0 6434 6834 478682214 478681814 0.000000e+00 741.0
31 TraesCS7B01G305500 chrUn 91.709 398 27 6 5174 5566 42780939 42781335 1.400000e-151 547.0
32 TraesCS7B01G305500 chrUn 91.709 398 26 4 5174 5566 419105875 419105480 5.040000e-151 545.0
33 TraesCS7B01G305500 chrUn 91.479 399 26 5 5174 5566 175783840 175783444 6.520000e-150 542.0
34 TraesCS7B01G305500 chrUn 91.479 399 26 5 5174 5566 416376616 416376220 6.520000e-150 542.0
35 TraesCS7B01G305500 chrUn 91.228 399 27 5 5174 5566 175741731 175741335 3.040000e-148 536.0
36 TraesCS7B01G305500 chrUn 91.228 399 27 5 5174 5566 231570156 231569760 3.040000e-148 536.0
37 TraesCS7B01G305500 chrUn 91.228 399 23 7 5174 5566 222906970 222907362 3.930000e-147 532.0
38 TraesCS7B01G305500 chrUn 84.615 247 26 3 1717 1963 18144614 18144848 1.240000e-57 235.0
39 TraesCS7B01G305500 chrUn 98.182 110 2 0 6518 6627 218382134 218382243 7.570000e-45 193.0
40 TraesCS7B01G305500 chrUn 98.182 110 2 0 6518 6627 218399682 218399791 7.570000e-45 193.0
41 TraesCS7B01G305500 chr5A 88.914 893 79 11 4339 5216 264610642 264611529 0.000000e+00 1083.0
42 TraesCS7B01G305500 chr5A 94.118 442 21 3 3818 4258 264610207 264610644 0.000000e+00 667.0
43 TraesCS7B01G305500 chr5A 96.667 120 3 1 6808 6927 127831754 127831872 1.630000e-46 198.0
44 TraesCS7B01G305500 chr1A 88.170 896 84 11 4339 5219 452748975 452749863 0.000000e+00 1048.0
45 TraesCS7B01G305500 chr1A 94.020 602 31 4 3658 4258 452748380 452748977 0.000000e+00 907.0
46 TraesCS7B01G305500 chr1A 96.667 120 3 1 6808 6927 134973489 134973607 1.630000e-46 198.0
47 TraesCS7B01G305500 chr1A 96.667 120 3 1 6808 6927 154418031 154418149 1.630000e-46 198.0
48 TraesCS7B01G305500 chr1A 88.288 111 12 1 6804 6914 370015694 370015803 1.670000e-26 132.0
49 TraesCS7B01G305500 chr1A 84.058 138 20 2 6808 6945 431676648 431676783 1.670000e-26 132.0
50 TraesCS7B01G305500 chr1A 86.486 111 14 1 6804 6914 370001281 370001390 3.620000e-23 121.0
51 TraesCS7B01G305500 chr5D 87.771 785 67 17 4781 5558 179135087 179135849 0.000000e+00 891.0
52 TraesCS7B01G305500 chr5D 91.969 635 38 7 3292 3917 179133839 179134469 0.000000e+00 878.0
53 TraesCS7B01G305500 chr5D 94.000 100 6 0 4241 4340 15905589 15905688 1.280000e-32 152.0
54 TraesCS7B01G305500 chr7A 93.189 602 36 4 3658 4258 471008074 471008671 0.000000e+00 880.0
55 TraesCS7B01G305500 chr7A 90.308 454 36 7 4339 4787 471008669 471009119 8.260000e-164 588.0
56 TraesCS7B01G305500 chr7A 89.239 381 36 4 4836 5214 471009119 471009496 8.680000e-129 472.0
57 TraesCS7B01G305500 chr7A 97.479 119 1 2 6808 6926 560407157 560407041 1.260000e-47 202.0
58 TraesCS7B01G305500 chr3B 92.869 603 35 7 3658 4258 98934185 98933589 0.000000e+00 869.0
59 TraesCS7B01G305500 chr3B 96.721 122 2 1 6797 6916 454671370 454671491 1.260000e-47 202.0
60 TraesCS7B01G305500 chr3D 93.527 448 23 6 3814 4258 554844281 554844725 0.000000e+00 662.0
61 TraesCS7B01G305500 chr4A 92.011 363 24 3 4339 4697 686895104 686895465 8.560000e-139 505.0
62 TraesCS7B01G305500 chr4A 86.215 428 47 7 4796 5214 686895460 686895884 3.140000e-123 453.0
63 TraesCS7B01G305500 chr4A 97.500 120 2 1 6808 6927 127407768 127407650 3.500000e-48 204.0
64 TraesCS7B01G305500 chr4A 97.500 120 2 1 6808 6927 386088235 386088117 3.500000e-48 204.0
65 TraesCS7B01G305500 chr4A 91.057 123 10 1 6808 6930 692358215 692358094 1.650000e-36 165.0
66 TraesCS7B01G305500 chr4A 93.137 102 4 3 4246 4346 621290116 621290215 5.980000e-31 147.0
67 TraesCS7B01G305500 chr2D 93.498 323 19 1 2439 2761 12547346 12547026 5.190000e-131 479.0
68 TraesCS7B01G305500 chr2D 88.235 357 41 1 5996 6352 12546961 12546606 6.850000e-115 425.0
69 TraesCS7B01G305500 chr2D 87.097 217 16 8 7184 7392 12546375 12546163 1.240000e-57 235.0
70 TraesCS7B01G305500 chr2D 96.377 138 5 0 2278 2415 12547471 12547334 2.070000e-55 228.0
71 TraesCS7B01G305500 chr2D 91.667 72 4 1 6444 6513 12429104 12429033 1.700000e-16 99.0
72 TraesCS7B01G305500 chr2D 98.113 53 1 0 2278 2330 12547466 12547518 7.900000e-15 93.5
73 TraesCS7B01G305500 chr5B 89.008 373 32 5 4841 5213 45273164 45272801 3.140000e-123 453.0
74 TraesCS7B01G305500 chr5B 99.074 108 1 0 6518 6625 78422387 78422280 2.100000e-45 195.0
75 TraesCS7B01G305500 chr5B 95.614 114 5 0 6515 6628 436561745 436561858 4.560000e-42 183.0
76 TraesCS7B01G305500 chr6B 97.500 120 3 0 6803 6922 37764449 37764568 9.720000e-49 206.0
77 TraesCS7B01G305500 chr4B 93.548 124 7 1 6516 6639 650659909 650660031 4.560000e-42 183.0
78 TraesCS7B01G305500 chr6D 89.630 135 11 2 7026 7157 263463105 263462971 1.280000e-37 169.0
79 TraesCS7B01G305500 chr1D 93.204 103 6 1 4256 4357 393171927 393172029 4.620000e-32 150.0
80 TraesCS7B01G305500 chr1B 94.000 100 4 2 4246 4343 112863566 112863665 4.620000e-32 150.0
81 TraesCS7B01G305500 chr1B 85.185 54 8 0 6878 6931 519624831 519624884 1.000000e-03 56.5
82 TraesCS7B01G305500 chr7D 87.395 119 13 2 4225 4343 146384171 146384055 1.290000e-27 135.0
83 TraesCS7B01G305500 chr7D 79.412 102 10 9 503 597 4183836 4183739 2.230000e-05 62.1
84 TraesCS7B01G305500 chr7D 97.059 34 1 0 5926 5959 121194637 121194670 2.880000e-04 58.4
85 TraesCS7B01G305500 chr6A 82.222 135 7 6 7026 7157 359041490 359041370 4.720000e-17 100.0


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 TraesCS7B01G305500 chr7B 547471894 547479285 7391 True 13651.000000 13651 100.00000 1 7392 1 chr7B.!!$R3 7391
1 TraesCS7B01G305500 chr7B 547566236 547568722 2486 True 4370.000000 4370 98.28300 39 2541 1 chr7B.!!$R4 2502
2 TraesCS7B01G305500 chr7B 547548597 547553410 4813 True 4357.000000 7836 99.17800 2537 7392 2 chr7B.!!$R5 4855
3 TraesCS7B01G305500 chr2B 34646448 34651277 4829 False 1546.800000 3771 94.64080 3 7392 5 chr2B.!!$F2 7389
4 TraesCS7B01G305500 chr2B 717346950 717348432 1482 False 994.000000 1101 91.35250 3658 5214 2 chr2B.!!$F3 1556
5 TraesCS7B01G305500 chr4D 446105122 446106518 1396 True 1921.000000 1921 91.59500 3814 5204 1 chr4D.!!$R1 1390
6 TraesCS7B01G305500 chr4D 57884585 57885945 1360 True 890.500000 1219 90.56950 3298 4751 2 chr4D.!!$R2 1453
7 TraesCS7B01G305500 chr2A 277153159 277154479 1320 False 853.500000 1027 91.22450 3818 5214 2 chr2A.!!$F1 1396
8 TraesCS7B01G305500 chr2A 746248090 746249601 1511 True 650.750000 1245 93.52050 3284 4751 2 chr2A.!!$R3 1467
9 TraesCS7B01G305500 chrUn 42709549 42710492 943 False 1216.000000 1216 89.89700 3298 4258 1 chrUn.!!$F2 960
10 TraesCS7B01G305500 chrUn 329833653 329834596 943 False 1210.000000 1210 89.80400 3298 4258 1 chrUn.!!$F7 960
11 TraesCS7B01G305500 chrUn 42729344 42730288 944 False 1197.000000 1197 89.50600 3296 4258 1 chrUn.!!$F3 962
12 TraesCS7B01G305500 chrUn 403645074 403646015 941 False 1194.000000 1194 89.50600 3296 4258 1 chrUn.!!$F8 962
13 TraesCS7B01G305500 chrUn 222905387 222907362 1975 False 864.500000 1197 90.36700 3296 5566 2 chrUn.!!$F9 2270
14 TraesCS7B01G305500 chr5A 264610207 264611529 1322 False 875.000000 1083 91.51600 3818 5216 2 chr5A.!!$F2 1398
15 TraesCS7B01G305500 chr1A 452748380 452749863 1483 False 977.500000 1048 91.09500 3658 5219 2 chr1A.!!$F6 1561
16 TraesCS7B01G305500 chr5D 179133839 179135849 2010 False 884.500000 891 89.87000 3292 5558 2 chr5D.!!$F2 2266
17 TraesCS7B01G305500 chr7A 471008074 471009496 1422 False 646.666667 880 90.91200 3658 5214 3 chr7A.!!$F1 1556
18 TraesCS7B01G305500 chr3B 98933589 98934185 596 True 869.000000 869 92.86900 3658 4258 1 chr3B.!!$R1 600
19 TraesCS7B01G305500 chr4A 686895104 686895884 780 False 479.000000 505 89.11300 4339 5214 2 chr4A.!!$F2 875
20 TraesCS7B01G305500 chr2D 12546163 12547471 1308 True 341.750000 479 91.30175 2278 7392 4 chr2D.!!$R2 5114

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
23 24 1.119684 CCCACTCCACGATGTCCATA 58.880 55.000 0.00 0.00 0.00 2.74 F
1044 1060 1.006688 CGGCCCCGGAAAACAAAAG 60.007 57.895 0.73 0.00 35.56 2.27 F
2284 2304 1.598130 GGGCTTCGATTGGATCCGG 60.598 63.158 7.39 0.00 0.00 5.14 F
2648 2668 0.111061 TGGTTCATGCTCTGCTGGTT 59.889 50.000 0.00 0.00 0.00 3.67 F
3454 3494 2.684881 GGACATATGTGCCACCTTCAAG 59.315 50.000 14.43 0.00 0.00 3.02 F
4530 4590 1.066303 GCGAGTCTGATCAGATTCCGT 59.934 52.381 31.27 15.34 39.98 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1355 0.108585 CAGCAACCACCAGTACCTGT 59.891 55.000 0.00 0.0 0.00 4.00 R
2443 2463 0.038067 TACGCCGCTTTCTAACAGCA 60.038 50.000 0.00 0.0 37.07 4.41 R
3454 3494 6.855836 TCAATTTGGCAAATGTCAGAGATAC 58.144 36.000 24.96 0.0 0.00 2.24 R
3555 3602 8.979574 GTTTGTCAAGATCGGGATTAAGTATAG 58.020 37.037 0.00 0.0 0.00 1.31 R
4783 4982 0.902516 AGTCAGCTGTGGTCTCCCTC 60.903 60.000 14.67 0.0 0.00 4.30 R
6415 6707 6.222038 TGGATCTACAACACATAGAGTTCC 57.778 41.667 0.00 0.0 32.27 3.62 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
22 23 1.626356 CCCCACTCCACGATGTCCAT 61.626 60.000 0.00 0.00 0.00 3.41
23 24 1.119684 CCCACTCCACGATGTCCATA 58.880 55.000 0.00 0.00 0.00 2.74
24 25 1.694150 CCCACTCCACGATGTCCATAT 59.306 52.381 0.00 0.00 0.00 1.78
25 26 2.897326 CCCACTCCACGATGTCCATATA 59.103 50.000 0.00 0.00 0.00 0.86
26 27 3.515502 CCCACTCCACGATGTCCATATAT 59.484 47.826 0.00 0.00 0.00 0.86
27 28 4.709886 CCCACTCCACGATGTCCATATATA 59.290 45.833 0.00 0.00 0.00 0.86
183 195 5.443185 TTTGAAAGCCTCTCAAGTCAATG 57.557 39.130 0.00 0.00 34.41 2.82
234 246 5.657470 TCGTGTGTTTTCTCTCTCATTTG 57.343 39.130 0.00 0.00 0.00 2.32
262 274 8.582433 TTGGTTTTCCTCGTTATTTTGATTTC 57.418 30.769 0.00 0.00 41.38 2.17
1038 1054 4.338710 CTGGTCGGCCCCGGAAAA 62.339 66.667 2.12 0.00 40.25 2.29
1039 1055 4.646877 TGGTCGGCCCCGGAAAAC 62.647 66.667 2.12 0.00 40.25 2.43
1040 1056 4.646877 GGTCGGCCCCGGAAAACA 62.647 66.667 0.73 0.00 40.25 2.83
1041 1057 2.595172 GTCGGCCCCGGAAAACAA 60.595 61.111 0.73 0.00 40.25 2.83
1042 1058 2.194889 GTCGGCCCCGGAAAACAAA 61.195 57.895 0.73 0.00 40.25 2.83
1043 1059 1.455217 TCGGCCCCGGAAAACAAAA 60.455 52.632 0.73 0.00 40.25 2.44
1044 1060 1.006688 CGGCCCCGGAAAACAAAAG 60.007 57.895 0.73 0.00 35.56 2.27
1713 1729 4.820897 CAGTTCTGGCAATACTGTACTCA 58.179 43.478 16.43 0.00 35.65 3.41
2133 2153 2.186826 GGGTATGCGGTGGTCATGC 61.187 63.158 0.00 0.00 0.00 4.06
2203 2223 2.436646 ATTGTCTTGCCGCTCCCG 60.437 61.111 0.00 0.00 0.00 5.14
2284 2304 1.598130 GGGCTTCGATTGGATCCGG 60.598 63.158 7.39 0.00 0.00 5.14
2648 2668 0.111061 TGGTTCATGCTCTGCTGGTT 59.889 50.000 0.00 0.00 0.00 3.67
3019 3059 4.141251 AGGGGTATCTTTGTTGTTGTGTCT 60.141 41.667 0.00 0.00 0.00 3.41
3454 3494 2.684881 GGACATATGTGCCACCTTCAAG 59.315 50.000 14.43 0.00 0.00 3.02
3555 3602 4.324267 GGTGATACCTAATACCACATGCC 58.676 47.826 0.00 0.00 34.73 4.40
4530 4590 1.066303 GCGAGTCTGATCAGATTCCGT 59.934 52.381 31.27 15.34 39.98 4.69
4783 4982 3.366883 GGCAGATATAGTGAGAGCCGAAG 60.367 52.174 0.00 0.00 0.00 3.79
5764 6056 4.102524 TGTTGCCTACCATCGGATAGATTT 59.897 41.667 0.00 0.00 37.52 2.17
6834 7183 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
6836 7185 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
6855 7204 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
6861 7210 9.698309 CAGAAATGGATGTATCTAGACGTATTT 57.302 33.333 0.00 0.00 0.00 1.40
6885 7234 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
6886 7235 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
6887 7236 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
6888 7237 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
6889 7238 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
6890 7239 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
6891 7240 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
6892 7241 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
6893 7242 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
6894 7243 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
6895 7244 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
6896 7245 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
6897 7246 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
6898 7247 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
6899 7248 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
6900 7249 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
6901 7250 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
6902 7251 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
6903 7252 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
6904 7253 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
6905 7254 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
6906 7255 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
6907 7256 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
6975 7324 9.466497 AGAAACAGGTGATCAATTATGTACATT 57.534 29.630 14.77 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.489771 CATCGTGGAGTGGGGGCC 62.490 72.222 0.00 0.00 0.00 5.80
1 2 3.682292 GACATCGTGGAGTGGGGGC 62.682 68.421 0.00 0.00 0.00 5.80
25 26 9.128715 AGGGAAGCAAACTTAGGGAATATATAT 57.871 33.333 0.00 0.00 35.82 0.86
26 27 8.520119 AGGGAAGCAAACTTAGGGAATATATA 57.480 34.615 0.00 0.00 35.82 0.86
27 28 7.408013 AGGGAAGCAAACTTAGGGAATATAT 57.592 36.000 0.00 0.00 35.82 0.86
183 195 3.058224 CACGTGAAAGATTTTGGGAGGTC 60.058 47.826 10.90 0.00 0.00 3.85
234 246 9.634163 AATCAAAATAACGAGGAAAACCAATAC 57.366 29.630 0.00 0.00 0.00 1.89
445 458 6.198687 TCTTTGCGTGTTAGAAAATGTTCAG 58.801 36.000 0.00 0.00 36.09 3.02
639 654 5.752955 AGAAACATTCACGGGTTTGAAAATG 59.247 36.000 0.00 0.00 38.95 2.32
1036 1052 5.065474 TCGACGATGTTTTCCTCTTTTGTTT 59.935 36.000 0.00 0.00 0.00 2.83
1037 1053 4.573201 TCGACGATGTTTTCCTCTTTTGTT 59.427 37.500 0.00 0.00 0.00 2.83
1038 1054 4.025145 GTCGACGATGTTTTCCTCTTTTGT 60.025 41.667 0.00 0.00 0.00 2.83
1039 1055 4.455124 GTCGACGATGTTTTCCTCTTTTG 58.545 43.478 0.00 0.00 0.00 2.44
1040 1056 3.183775 CGTCGACGATGTTTTCCTCTTTT 59.816 43.478 33.35 0.00 43.02 2.27
1041 1057 2.729882 CGTCGACGATGTTTTCCTCTTT 59.270 45.455 33.35 0.00 43.02 2.52
1042 1058 2.325761 CGTCGACGATGTTTTCCTCTT 58.674 47.619 33.35 0.00 43.02 2.85
1043 1059 1.978542 CGTCGACGATGTTTTCCTCT 58.021 50.000 33.35 0.00 43.02 3.69
1044 1060 0.365859 GCGTCGACGATGTTTTCCTC 59.634 55.000 39.74 15.14 43.02 3.71
1339 1355 0.108585 CAGCAACCACCAGTACCTGT 59.891 55.000 0.00 0.00 0.00 4.00
1521 1537 8.806146 AGTCAATTACTGCCAAGTATTTCAATT 58.194 29.630 0.00 0.00 38.69 2.32
1713 1729 9.252962 CTAGAAATTCACAAAGAAGTTGCAATT 57.747 29.630 0.59 0.00 43.86 2.32
2133 2153 0.812412 AACCGACCTGACACAAACCG 60.812 55.000 0.00 0.00 0.00 4.44
2203 2223 4.025480 CAGCAGCAAAATTTTCTCACCAAC 60.025 41.667 0.00 0.00 0.00 3.77
2284 2304 5.355350 ACAGAAGGTAGCAACAATAATCAGC 59.645 40.000 0.00 0.00 0.00 4.26
2443 2463 0.038067 TACGCCGCTTTCTAACAGCA 60.038 50.000 0.00 0.00 37.07 4.41
2648 2668 1.204704 CCAGCAGGTCGATTAGTGACA 59.795 52.381 0.00 0.00 38.10 3.58
3019 3059 0.463654 AGAAGCGACCACAAAGCACA 60.464 50.000 0.00 0.00 0.00 4.57
3454 3494 6.855836 TCAATTTGGCAAATGTCAGAGATAC 58.144 36.000 24.96 0.00 0.00 2.24
3555 3602 8.979574 GTTTGTCAAGATCGGGATTAAGTATAG 58.020 37.037 0.00 0.00 0.00 1.31
4783 4982 0.902516 AGTCAGCTGTGGTCTCCCTC 60.903 60.000 14.67 0.00 0.00 4.30
4795 5015 1.141449 GCGAGCATCAGAGTCAGCT 59.859 57.895 0.00 0.00 40.60 4.24
6415 6707 6.222038 TGGATCTACAACACATAGAGTTCC 57.778 41.667 0.00 0.00 32.27 3.62
6834 7183 5.533482 ACGTCTAGATACATCCATTTCTGC 58.467 41.667 0.00 0.00 0.00 4.26
6861 7210 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
6862 7211 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
6863 7212 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
6865 7214 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
6866 7215 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
6867 7216 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
6868 7217 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
6869 7218 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
6870 7219 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
6871 7220 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
6872 7221 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
6873 7222 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
6874 7223 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
6875 7224 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
6876 7225 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
6877 7226 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
6878 7227 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
6879 7228 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
6880 7229 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
6881 7230 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
6882 7231 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
6883 7232 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
6884 7233 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
6885 7234 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
6886 7235 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
6887 7236 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
6888 7237 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
6889 7238 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
6890 7239 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
6891 7240 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
6892 7241 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
6893 7242 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
6894 7243 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
6895 7244 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
6896 7245 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
6897 7246 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
6898 7247 0.107017 TACCTACTCCCTCCGTTCGG 60.107 60.000 4.74 4.74 0.00 4.30
6899 7248 1.403323 GTTACCTACTCCCTCCGTTCG 59.597 57.143 0.00 0.00 0.00 3.95
6900 7249 2.450476 TGTTACCTACTCCCTCCGTTC 58.550 52.381 0.00 0.00 0.00 3.95
6901 7250 2.610438 TGTTACCTACTCCCTCCGTT 57.390 50.000 0.00 0.00 0.00 4.44
6902 7251 2.610438 TTGTTACCTACTCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
6903 7252 2.167900 CCTTTGTTACCTACTCCCTCCG 59.832 54.545 0.00 0.00 0.00 4.63
6904 7253 2.504585 CCCTTTGTTACCTACTCCCTCC 59.495 54.545 0.00 0.00 0.00 4.30
6905 7254 3.447950 TCCCTTTGTTACCTACTCCCTC 58.552 50.000 0.00 0.00 0.00 4.30
6906 7255 3.572661 TCCCTTTGTTACCTACTCCCT 57.427 47.619 0.00 0.00 0.00 4.20
6907 7256 3.778629 TCATCCCTTTGTTACCTACTCCC 59.221 47.826 0.00 0.00 0.00 4.30
6975 7324 6.696441 ACCAAATGACCAGTAACGTAAAAA 57.304 33.333 0.00 0.00 0.00 1.94
6986 7335 4.616835 GCTAAGCTTCAACCAAATGACCAG 60.617 45.833 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.