Multiple sequence alignment - TraesCS5A01G558800

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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 TraesCS5A01G558800 chr5A 100.000 2576 0 0 1 2576 709529981 709532556 0.000000e+00 4758
1 TraesCS5A01G558800 chr5A 87.955 1345 101 25 551 1881 707848898 707850195 0.000000e+00 1530
2 TraesCS5A01G558800 chr5A 86.019 1359 101 36 551 1881 707983793 707985090 0.000000e+00 1375
3 TraesCS5A01G558800 chr5A 84.412 1174 117 33 631 1776 707578379 707579514 0.000000e+00 1094
4 TraesCS5A01G558800 chr5A 89.069 247 26 1 2294 2539 707985853 707986099 3.220000e-79 305
5 TraesCS5A01G558800 chr5A 86.463 229 17 8 2071 2299 707985137 707985351 3.310000e-59 239
6 TraesCS5A01G558800 chr5A 79.635 329 29 16 8 308 707983080 707983398 4.350000e-48 202
7 TraesCS5A01G558800 chr5A 95.833 120 5 0 67 186 684312440 684312559 7.270000e-46 195
8 TraesCS5A01G558800 chr5A 80.075 266 26 10 59 309 707848262 707848515 3.410000e-39 172
9 TraesCS5A01G558800 chr5A 91.803 122 6 1 186 307 236371648 236371765 1.590000e-37 167
10 TraesCS5A01G558800 chrUn 90.383 1695 87 24 315 1955 134396295 134394623 0.000000e+00 2158
11 TraesCS5A01G558800 chrUn 87.990 1657 111 32 315 1929 30531054 30529444 0.000000e+00 1877
12 TraesCS5A01G558800 chrUn 89.972 1406 78 26 315 1691 79803660 79805031 0.000000e+00 1757
13 TraesCS5A01G558800 chrUn 88.778 1105 96 8 884 1988 29602423 29601347 0.000000e+00 1328
14 TraesCS5A01G558800 chrUn 87.444 1107 94 13 888 1988 100353103 100352036 0.000000e+00 1232
15 TraesCS5A01G558800 chrUn 87.221 986 85 11 888 1867 99741759 99740809 0.000000e+00 1085
16 TraesCS5A01G558800 chrUn 90.955 398 36 0 2133 2530 100351876 100351479 1.050000e-148 536
17 TraesCS5A01G558800 chrUn 88.235 442 16 6 1554 1988 29364175 29363763 1.780000e-136 496
18 TraesCS5A01G558800 chrUn 91.638 287 24 0 2246 2532 79805574 79805860 5.160000e-107 398
19 TraesCS5A01G558800 chrUn 92.045 264 18 2 2070 2333 29601349 29601089 4.050000e-98 368
20 TraesCS5A01G558800 chrUn 94.515 237 11 2 1753 1988 79805044 79805279 5.240000e-97 364
21 TraesCS5A01G558800 chrUn 91.803 244 19 1 2296 2539 100351404 100351162 3.180000e-89 339
22 TraesCS5A01G558800 chrUn 90.650 246 23 0 2294 2539 30529034 30528789 6.870000e-86 327
23 TraesCS5A01G558800 chrUn 88.841 233 17 4 2246 2478 134394470 134394247 7.020000e-71 278
24 TraesCS5A01G558800 chrUn 94.350 177 10 0 2400 2576 79806107 79806283 3.270000e-69 272
25 TraesCS5A01G558800 chrUn 88.655 238 4 6 631 856 28897549 28897775 4.230000e-68 268
26 TraesCS5A01G558800 chrUn 90.732 205 14 3 2336 2539 29362674 29362474 4.230000e-68 268
27 TraesCS5A01G558800 chrUn 88.655 238 4 6 631 856 29365090 29364864 4.230000e-68 268
28 TraesCS5A01G558800 chrUn 88.655 238 4 6 631 856 29602640 29602414 4.230000e-68 268
29 TraesCS5A01G558800 chrUn 90.374 187 11 3 8 187 30531573 30531387 3.310000e-59 239
30 TraesCS5A01G558800 chrUn 89.840 187 12 3 8 187 79803146 79803332 1.540000e-57 233
31 TraesCS5A01G558800 chrUn 95.536 112 1 1 197 308 79803376 79803483 2.630000e-40 176
32 TraesCS5A01G558800 chrUn 94.643 112 2 1 199 310 30531341 30531234 1.230000e-38 171
33 TraesCS5A01G558800 chrUn 89.623 106 10 1 1967 2072 122302205 122302101 1.610000e-27 134
34 TraesCS5A01G558800 chrUn 88.991 109 4 3 1884 1988 28898619 28898723 7.480000e-26 128
35 TraesCS5A01G558800 chr6D 87.036 1697 117 33 315 1980 1069738 1071362 0.000000e+00 1820
36 TraesCS5A01G558800 chr6D 91.803 305 25 0 2246 2550 1071516 1071820 2.370000e-115 425
37 TraesCS5A01G558800 chr6D 89.840 187 12 3 8 187 1069224 1069410 1.540000e-57 233
38 TraesCS5A01G558800 chr6D 95.536 112 1 1 197 308 1069454 1069561 2.630000e-40 176
39 TraesCS5A01G558800 chr4B 88.443 1445 107 25 551 1988 599464338 599462947 0.000000e+00 1688
40 TraesCS5A01G558800 chr4B 85.000 1720 146 50 315 1988 599589219 599587566 0.000000e+00 1644
41 TraesCS5A01G558800 chr4B 84.581 1362 122 35 314 1645 668363848 668365151 0.000000e+00 1271
42 TraesCS5A01G558800 chr4B 83.265 1470 121 45 314 1739 456361933 456363321 0.000000e+00 1236
43 TraesCS5A01G558800 chr4B 84.436 1330 90 44 551 1852 668513582 668514822 0.000000e+00 1201
44 TraesCS5A01G558800 chr4B 85.867 1125 97 14 863 1980 668216606 668217675 0.000000e+00 1140
45 TraesCS5A01G558800 chr4B 82.701 1370 138 32 314 1645 456381302 456379994 0.000000e+00 1125
46 TraesCS5A01G558800 chr4B 86.006 1029 87 12 959 1980 669161611 669160633 0.000000e+00 1050
47 TraesCS5A01G558800 chr4B 90.769 325 3 8 551 864 668216217 668216525 2.390000e-110 409
48 TraesCS5A01G558800 chr4B 90.351 228 21 1 2314 2540 668405601 668405828 5.390000e-77 298
49 TraesCS5A01G558800 chr4B 82.197 264 21 13 63 310 599466091 599465838 1.210000e-48 204
50 TraesCS5A01G558800 chr4B 93.388 121 2 3 197 316 668891765 668891880 9.470000e-40 174
51 TraesCS5A01G558800 chr4B 93.913 115 3 2 62 176 668363646 668363756 1.230000e-38 171
52 TraesCS5A01G558800 chr4B 92.920 113 6 1 2071 2183 668365427 668365537 2.050000e-36 163
53 TraesCS5A01G558800 chr4B 83.523 176 27 2 1 176 673413873 673413700 2.050000e-36 163
54 TraesCS5A01G558800 chr4B 92.035 113 7 1 2071 2183 668589743 668589853 9.540000e-35 158
55 TraesCS5A01G558800 chr4B 92.035 113 7 1 2071 2183 669473560 669473670 9.540000e-35 158
56 TraesCS5A01G558800 chr4B 81.013 237 9 18 315 519 599465663 599465431 3.430000e-34 156
57 TraesCS5A01G558800 chr4B 83.607 183 9 8 8 176 668445766 668445941 4.440000e-33 152
58 TraesCS5A01G558800 chr4B 90.265 113 9 1 2071 2183 669160626 669160516 2.070000e-31 147
59 TraesCS5A01G558800 chr4B 90.265 113 9 1 2071 2183 669340513 669340403 2.070000e-31 147
60 TraesCS5A01G558800 chr4B 89.565 115 6 5 2070 2183 599587568 599587459 9.610000e-30 141
61 TraesCS5A01G558800 chr4B 89.381 113 10 1 2071 2183 668974889 668974999 9.610000e-30 141
62 TraesCS5A01G558800 chr4B 100.000 54 0 0 134 187 668216148 668216201 1.630000e-17 100
63 TraesCS5A01G558800 chr5D 94.737 114 2 1 194 307 155546462 155546571 9.470000e-40 174
64 TraesCS5A01G558800 chr5D 93.805 113 3 1 194 306 187622055 187622163 1.590000e-37 167
65 TraesCS5A01G558800 chr7D 94.643 112 2 1 197 308 341864491 341864384 1.230000e-38 171
66 TraesCS5A01G558800 chr7B 90.179 112 10 1 1977 2087 29827098 29826987 7.430000e-31 145
67 TraesCS5A01G558800 chr7B 90.196 102 9 1 1972 2073 648920723 648920623 5.780000e-27 132
68 TraesCS5A01G558800 chr4A 94.565 92 5 0 1984 2075 473777173 473777264 2.670000e-30 143
69 TraesCS5A01G558800 chr3B 93.548 93 6 0 1987 2079 130628342 130628250 3.460000e-29 139
70 TraesCS5A01G558800 chr2B 91.919 99 7 1 1974 2072 77775643 77775740 1.240000e-28 137
71 TraesCS5A01G558800 chr2B 92.632 95 7 0 1980 2074 77856155 77856061 1.240000e-28 137
72 TraesCS5A01G558800 chr1B 91.089 101 5 4 1973 2072 644581756 644581853 1.610000e-27 134
73 TraesCS5A01G558800 chr5B 88.889 108 9 3 1967 2072 125481515 125481621 2.080000e-26 130


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 TraesCS5A01G558800 chr5A 709529981 709532556 2575 False 4758.000000 4758 100.000000 1 2576 1 chr5A.!!$F4 2575
1 TraesCS5A01G558800 chr5A 707578379 707579514 1135 False 1094.000000 1094 84.412000 631 1776 1 chr5A.!!$F3 1145
2 TraesCS5A01G558800 chr5A 707848262 707850195 1933 False 851.000000 1530 84.015000 59 1881 2 chr5A.!!$F5 1822
3 TraesCS5A01G558800 chr5A 707983080 707986099 3019 False 530.250000 1375 85.296500 8 2539 4 chr5A.!!$F6 2531
4 TraesCS5A01G558800 chrUn 134394247 134396295 2048 True 1218.000000 2158 89.612000 315 2478 2 chrUn.!!$R7 2163
5 TraesCS5A01G558800 chrUn 99740809 99741759 950 True 1085.000000 1085 87.221000 888 1867 1 chrUn.!!$R1 979
6 TraesCS5A01G558800 chrUn 100351162 100353103 1941 True 702.333333 1232 90.067333 888 2539 3 chrUn.!!$R6 1651
7 TraesCS5A01G558800 chrUn 29601089 29602640 1551 True 654.666667 1328 89.826000 631 2333 3 chrUn.!!$R4 1702
8 TraesCS5A01G558800 chrUn 30528789 30531573 2784 True 653.500000 1877 90.914250 8 2539 4 chrUn.!!$R5 2531
9 TraesCS5A01G558800 chrUn 79803146 79806283 3137 False 533.333333 1757 92.641833 8 2576 6 chrUn.!!$F2 2568
10 TraesCS5A01G558800 chrUn 29362474 29365090 2616 True 344.000000 496 89.207333 631 2539 3 chrUn.!!$R3 1908
11 TraesCS5A01G558800 chr6D 1069224 1071820 2596 False 663.500000 1820 91.053750 8 2550 4 chr6D.!!$F1 2542
12 TraesCS5A01G558800 chr4B 456361933 456363321 1388 False 1236.000000 1236 83.265000 314 1739 1 chr4B.!!$F1 1425
13 TraesCS5A01G558800 chr4B 668513582 668514822 1240 False 1201.000000 1201 84.436000 551 1852 1 chr4B.!!$F4 1301
14 TraesCS5A01G558800 chr4B 456379994 456381302 1308 True 1125.000000 1125 82.701000 314 1645 1 chr4B.!!$R1 1331
15 TraesCS5A01G558800 chr4B 599587459 599589219 1760 True 892.500000 1644 87.282500 315 2183 2 chr4B.!!$R5 1868
16 TraesCS5A01G558800 chr4B 599462947 599466091 3144 True 682.666667 1688 83.884333 63 1988 3 chr4B.!!$R4 1925
17 TraesCS5A01G558800 chr4B 669160516 669161611 1095 True 598.500000 1050 88.135500 959 2183 2 chr4B.!!$R6 1224
18 TraesCS5A01G558800 chr4B 668216148 668217675 1527 False 549.666667 1140 92.212000 134 1980 3 chr4B.!!$F9 1846
19 TraesCS5A01G558800 chr4B 668363646 668365537 1891 False 535.000000 1271 90.471333 62 2183 3 chr4B.!!$F10 2121

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
983 2491 0.107268 TGCTGCTGCAGTCTTCTTCA 59.893 50.0 28.5 14.49 45.31 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 4320 0.457851 CACTCACAGATCCCTCCGTC 59.542 60.0 0.0 0.0 0.0 4.79 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
52 53 9.727859 AATTAGTTAGGGTTTGTTTGTTTGTTT 57.272 25.926 0.00 0.00 0.00 2.83
53 54 8.535690 TTAGTTAGGGTTTGTTTGTTTGTTTG 57.464 30.769 0.00 0.00 0.00 2.93
54 55 6.526526 AGTTAGGGTTTGTTTGTTTGTTTGT 58.473 32.000 0.00 0.00 0.00 2.83
55 56 6.993308 AGTTAGGGTTTGTTTGTTTGTTTGTT 59.007 30.769 0.00 0.00 0.00 2.83
56 57 7.499563 AGTTAGGGTTTGTTTGTTTGTTTGTTT 59.500 29.630 0.00 0.00 0.00 2.83
57 58 6.066054 AGGGTTTGTTTGTTTGTTTGTTTG 57.934 33.333 0.00 0.00 0.00 2.93
58 59 5.590663 AGGGTTTGTTTGTTTGTTTGTTTGT 59.409 32.000 0.00 0.00 0.00 2.83
59 60 6.766467 AGGGTTTGTTTGTTTGTTTGTTTGTA 59.234 30.769 0.00 0.00 0.00 2.41
60 61 7.445707 AGGGTTTGTTTGTTTGTTTGTTTGTAT 59.554 29.630 0.00 0.00 0.00 2.29
77 89 7.211573 TGTTTGTATGGTTCGATTATCCGTAT 58.788 34.615 0.00 0.00 0.00 3.06
108 120 4.933400 TCAATCTGACGTTTTAGTTAGGGC 59.067 41.667 0.00 0.00 0.00 5.19
130 142 0.459489 GCTTGCTTGGTTGTGGTCAA 59.541 50.000 0.00 0.00 0.00 3.18
243 289 2.961526 TGCTAGATCCACTCGAAACC 57.038 50.000 0.00 0.00 0.00 3.27
244 290 2.176045 TGCTAGATCCACTCGAAACCA 58.824 47.619 0.00 0.00 0.00 3.67
245 291 2.565391 TGCTAGATCCACTCGAAACCAA 59.435 45.455 0.00 0.00 0.00 3.67
246 292 3.190874 GCTAGATCCACTCGAAACCAAG 58.809 50.000 0.00 0.00 0.00 3.61
395 651 1.523758 CACAGGCACCACTTAACCTC 58.476 55.000 0.00 0.00 0.00 3.85
431 687 2.735823 CTTTCCAGCTCTGTTGTTTGC 58.264 47.619 0.00 0.00 0.00 3.68
436 713 2.159198 CCAGCTCTGTTGTTTGCAAGTT 60.159 45.455 0.00 0.00 34.94 2.66
437 714 3.514645 CAGCTCTGTTGTTTGCAAGTTT 58.485 40.909 0.00 0.00 34.94 2.66
438 715 4.439974 CCAGCTCTGTTGTTTGCAAGTTTA 60.440 41.667 0.00 0.00 34.94 2.01
439 716 5.284079 CAGCTCTGTTGTTTGCAAGTTTAT 58.716 37.500 0.00 0.00 34.94 1.40
444 721 8.216453 GCTCTGTTGTTTGCAAGTTTATTTATG 58.784 33.333 0.00 0.00 34.94 1.90
519 800 6.816140 CCAACCAATCTCTAGTCTTCTTCTTC 59.184 42.308 0.00 0.00 0.00 2.87
520 801 7.310361 CCAACCAATCTCTAGTCTTCTTCTTCT 60.310 40.741 0.00 0.00 0.00 2.85
521 802 7.790782 ACCAATCTCTAGTCTTCTTCTTCTT 57.209 36.000 0.00 0.00 0.00 2.52
524 805 7.759433 CCAATCTCTAGTCTTCTTCTTCTTGAC 59.241 40.741 0.00 0.00 0.00 3.18
527 808 6.148150 TCTCTAGTCTTCTTCTTCTTGACGAC 59.852 42.308 0.00 0.00 33.46 4.34
541 826 4.923871 TCTTGACGACTTCTGTAAATGCTC 59.076 41.667 0.00 0.00 0.00 4.26
542 827 4.251543 TGACGACTTCTGTAAATGCTCA 57.748 40.909 0.00 0.00 0.00 4.26
543 828 3.987868 TGACGACTTCTGTAAATGCTCAC 59.012 43.478 0.00 0.00 0.00 3.51
545 830 5.048294 TGACGACTTCTGTAAATGCTCACTA 60.048 40.000 0.00 0.00 0.00 2.74
546 831 5.967088 ACGACTTCTGTAAATGCTCACTAT 58.033 37.500 0.00 0.00 0.00 2.12
548 833 5.233050 CGACTTCTGTAAATGCTCACTATGG 59.767 44.000 0.00 0.00 0.00 2.74
549 834 5.431765 ACTTCTGTAAATGCTCACTATGGG 58.568 41.667 0.00 0.00 0.00 4.00
621 1994 8.538409 AGTTTATTGTTTCCTTTGATTGATGC 57.462 30.769 0.00 0.00 0.00 3.91
662 2045 5.790593 AGATGCAATTTTCTTGCTCACAAT 58.209 33.333 10.87 0.00 45.13 2.71
663 2046 6.927416 AGATGCAATTTTCTTGCTCACAATA 58.073 32.000 10.87 0.00 45.13 1.90
664 2047 7.553334 AGATGCAATTTTCTTGCTCACAATAT 58.447 30.769 10.87 0.00 45.13 1.28
665 2048 8.689061 AGATGCAATTTTCTTGCTCACAATATA 58.311 29.630 10.87 0.00 45.13 0.86
917 2418 6.373005 TGGTCTCTTCCTGACATTAAATCA 57.627 37.500 0.00 0.00 36.26 2.57
983 2491 0.107268 TGCTGCTGCAGTCTTCTTCA 59.893 50.000 28.50 14.49 45.31 3.02
1272 2797 0.322008 CCCAGCTCAAGGTTCAGGAC 60.322 60.000 0.00 0.00 0.00 3.85
1308 2833 4.811364 GCCCTGCAAGCCCTCCTC 62.811 72.222 0.00 0.00 0.00 3.71
1317 2842 1.283029 CAAGCCCTCCTCCTCATGAAA 59.717 52.381 0.00 0.00 0.00 2.69
1318 2843 1.211456 AGCCCTCCTCCTCATGAAAG 58.789 55.000 0.00 0.00 0.00 2.62
1359 2884 6.480320 TCTTAAATCTCAGGAAGCGCTTTATC 59.520 38.462 25.84 16.47 0.00 1.75
1423 2957 0.164647 CCGAGTCAAAAAGCTGAGCG 59.835 55.000 0.00 0.00 0.00 5.03
1464 3004 6.539173 TGTTGATGGTGTACTCAAAGGTAAT 58.461 36.000 0.00 0.00 33.45 1.89
1465 3005 6.429692 TGTTGATGGTGTACTCAAAGGTAATG 59.570 38.462 0.00 0.00 33.45 1.90
1466 3006 5.496556 TGATGGTGTACTCAAAGGTAATGG 58.503 41.667 0.00 0.00 0.00 3.16
1467 3007 4.986054 TGGTGTACTCAAAGGTAATGGT 57.014 40.909 0.00 0.00 0.00 3.55
1468 3008 6.213802 TGATGGTGTACTCAAAGGTAATGGTA 59.786 38.462 0.00 0.00 0.00 3.25
1469 3009 6.436738 TGGTGTACTCAAAGGTAATGGTAA 57.563 37.500 0.00 0.00 0.00 2.85
1486 3032 4.713553 TGGTAACATTGTCTTGCTTGAGA 58.286 39.130 0.00 0.00 46.17 3.27
1521 3067 1.001974 CTGGTCAATCTGGTCACCGAA 59.998 52.381 0.00 0.00 0.00 4.30
1541 3087 1.460689 TGTTGGAGACCCCGGTTCT 60.461 57.895 0.00 0.64 37.93 3.01
1839 3469 3.557595 CACATGGAGGTATTCGCTCTTTC 59.442 47.826 0.00 0.00 0.00 2.62
1982 3700 4.751060 TGGATTCATTCATTTTGCTCTGC 58.249 39.130 0.00 0.00 0.00 4.26
1984 3702 5.105106 TGGATTCATTCATTTTGCTCTGCAT 60.105 36.000 0.00 0.00 38.76 3.96
1985 3703 5.234329 GGATTCATTCATTTTGCTCTGCATG 59.766 40.000 0.00 0.00 38.76 4.06
1986 3704 4.794278 TCATTCATTTTGCTCTGCATGT 57.206 36.364 0.00 0.00 38.76 3.21
1987 3705 5.900865 TCATTCATTTTGCTCTGCATGTA 57.099 34.783 0.00 0.00 38.76 2.29
1988 3706 5.643664 TCATTCATTTTGCTCTGCATGTAC 58.356 37.500 0.00 0.00 38.76 2.90
1989 3707 5.416639 TCATTCATTTTGCTCTGCATGTACT 59.583 36.000 0.00 0.00 38.76 2.73
1990 3708 4.952262 TCATTTTGCTCTGCATGTACTC 57.048 40.909 0.00 0.00 38.76 2.59
1991 3709 3.691118 TCATTTTGCTCTGCATGTACTCC 59.309 43.478 0.00 0.00 38.76 3.85
1992 3710 2.113860 TTTGCTCTGCATGTACTCCC 57.886 50.000 0.00 0.00 38.76 4.30
1993 3711 1.279496 TTGCTCTGCATGTACTCCCT 58.721 50.000 0.00 0.00 38.76 4.20
1994 3712 0.826715 TGCTCTGCATGTACTCCCTC 59.173 55.000 0.00 0.00 31.71 4.30
1995 3713 0.105778 GCTCTGCATGTACTCCCTCC 59.894 60.000 0.00 0.00 0.00 4.30
1996 3714 0.387202 CTCTGCATGTACTCCCTCCG 59.613 60.000 0.00 0.00 0.00 4.63
1997 3715 0.324368 TCTGCATGTACTCCCTCCGT 60.324 55.000 0.00 0.00 0.00 4.69
1998 3716 0.537188 CTGCATGTACTCCCTCCGTT 59.463 55.000 0.00 0.00 0.00 4.44
1999 3717 0.981183 TGCATGTACTCCCTCCGTTT 59.019 50.000 0.00 0.00 0.00 3.60
2000 3718 1.066430 TGCATGTACTCCCTCCGTTTC 60.066 52.381 0.00 0.00 0.00 2.78
2001 3719 1.922570 CATGTACTCCCTCCGTTTCG 58.077 55.000 0.00 0.00 0.00 3.46
2002 3720 1.203994 CATGTACTCCCTCCGTTTCGT 59.796 52.381 0.00 0.00 0.00 3.85
2003 3721 2.198827 TGTACTCCCTCCGTTTCGTA 57.801 50.000 0.00 0.00 0.00 3.43
2004 3722 2.513753 TGTACTCCCTCCGTTTCGTAA 58.486 47.619 0.00 0.00 0.00 3.18
2005 3723 3.091545 TGTACTCCCTCCGTTTCGTAAT 58.908 45.455 0.00 0.00 0.00 1.89
2006 3724 4.269183 TGTACTCCCTCCGTTTCGTAATA 58.731 43.478 0.00 0.00 0.00 0.98
2007 3725 4.336433 TGTACTCCCTCCGTTTCGTAATAG 59.664 45.833 0.00 0.00 0.00 1.73
2008 3726 3.624777 ACTCCCTCCGTTTCGTAATAGA 58.375 45.455 0.00 0.00 0.00 1.98
2009 3727 4.213513 ACTCCCTCCGTTTCGTAATAGAT 58.786 43.478 0.00 0.00 0.00 1.98
2010 3728 4.037684 ACTCCCTCCGTTTCGTAATAGATG 59.962 45.833 0.00 0.00 0.00 2.90
2011 3729 4.209538 TCCCTCCGTTTCGTAATAGATGA 58.790 43.478 0.00 0.00 0.00 2.92
2012 3730 4.037208 TCCCTCCGTTTCGTAATAGATGAC 59.963 45.833 0.00 0.00 0.00 3.06
2013 3731 4.037684 CCCTCCGTTTCGTAATAGATGACT 59.962 45.833 0.00 0.00 0.00 3.41
2014 3732 5.451520 CCCTCCGTTTCGTAATAGATGACTT 60.452 44.000 0.00 0.00 0.00 3.01
2015 3733 6.238842 CCCTCCGTTTCGTAATAGATGACTTA 60.239 42.308 0.00 0.00 0.00 2.24
2016 3734 7.198390 CCTCCGTTTCGTAATAGATGACTTAA 58.802 38.462 0.00 0.00 0.00 1.85
2017 3735 7.167136 CCTCCGTTTCGTAATAGATGACTTAAC 59.833 40.741 0.00 0.00 0.00 2.01
2018 3736 7.765307 TCCGTTTCGTAATAGATGACTTAACT 58.235 34.615 0.00 0.00 0.00 2.24
2019 3737 8.246180 TCCGTTTCGTAATAGATGACTTAACTT 58.754 33.333 0.00 0.00 0.00 2.66
2020 3738 8.866956 CCGTTTCGTAATAGATGACTTAACTTT 58.133 33.333 0.00 0.00 0.00 2.66
2062 3780 9.746711 CAAAGTTGAGTCATCTATTTTAGAACG 57.253 33.333 4.14 0.00 38.50 3.95
2063 3781 8.480643 AAGTTGAGTCATCTATTTTAGAACGG 57.519 34.615 4.14 0.00 38.50 4.44
2064 3782 7.837863 AGTTGAGTCATCTATTTTAGAACGGA 58.162 34.615 1.70 0.00 38.50 4.69
2065 3783 7.976734 AGTTGAGTCATCTATTTTAGAACGGAG 59.023 37.037 1.70 0.00 38.50 4.63
2066 3784 6.806751 TGAGTCATCTATTTTAGAACGGAGG 58.193 40.000 0.00 0.00 38.50 4.30
2067 3785 6.163135 AGTCATCTATTTTAGAACGGAGGG 57.837 41.667 0.00 0.00 38.50 4.30
2147 4368 6.769822 GGATCTGTGAGTGTCCATGATTAAAT 59.230 38.462 0.00 0.00 0.00 1.40
2160 4381 9.807649 GTCCATGATTAAATCTTTGCAAATACT 57.192 29.630 13.23 0.00 0.00 2.12
2211 4432 7.597369 TGAAGCTGAATTGAATTGAAATGTGAG 59.403 33.333 0.00 0.00 0.00 3.51
2228 4548 1.007238 TGAGTAGCCTTCCACTAGCCT 59.993 52.381 0.00 0.00 0.00 4.58
2300 5178 2.781595 ATTTCCTCTTGTCGCGCCGT 62.782 55.000 0.00 0.00 0.00 5.68
2318 5196 4.419280 GCCGTAGTCCTCAACTAAACTAC 58.581 47.826 0.00 0.00 42.11 2.73
2321 5199 3.589495 AGTCCTCAACTAAACTACGCC 57.411 47.619 0.00 0.00 36.07 5.68
2351 5229 1.763770 CTGTCACCAGCCCCTTCTT 59.236 57.895 0.00 0.00 0.00 2.52
2363 5241 1.770324 CCTTCTTTGCCCACCTCCT 59.230 57.895 0.00 0.00 0.00 3.69
2370 5248 0.772124 TTGCCCACCTCCTCCTTCTT 60.772 55.000 0.00 0.00 0.00 2.52
2393 5963 4.541973 TGACACACAGATCTAGTTGCAT 57.458 40.909 0.00 0.00 0.00 3.96
2413 6203 3.788766 GTCGCCGCGCAACAATCT 61.789 61.111 8.75 0.00 0.00 2.40
2478 6268 3.192844 CCGCAGTCCTCAACTAAACTAGA 59.807 47.826 0.00 0.00 36.07 2.43
2559 6349 2.094494 CAGATGTAGTTGAGGACTGCGT 60.094 50.000 0.00 0.00 43.16 5.24
2572 6362 2.423892 GGACTGCGTCAGATCTAGTTGA 59.576 50.000 12.77 0.00 35.18 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 6.372103 ACGGATAATCGAACCATACAAACAAA 59.628 34.615 0.00 0.00 0.00 2.83
52 53 5.421277 ACGGATAATCGAACCATACAAACA 58.579 37.500 0.00 0.00 0.00 2.83
53 54 5.978934 ACGGATAATCGAACCATACAAAC 57.021 39.130 0.00 0.00 0.00 2.93
54 55 9.761504 TTAATACGGATAATCGAACCATACAAA 57.238 29.630 0.00 0.00 0.00 2.83
55 56 9.414295 CTTAATACGGATAATCGAACCATACAA 57.586 33.333 0.00 0.00 0.00 2.41
56 57 8.030692 CCTTAATACGGATAATCGAACCATACA 58.969 37.037 0.00 0.00 0.00 2.29
57 58 8.246180 TCCTTAATACGGATAATCGAACCATAC 58.754 37.037 0.00 0.00 0.00 2.39
58 59 8.352137 TCCTTAATACGGATAATCGAACCATA 57.648 34.615 0.00 0.00 0.00 2.74
59 60 7.235935 TCCTTAATACGGATAATCGAACCAT 57.764 36.000 0.00 0.00 0.00 3.55
60 61 6.653526 TCCTTAATACGGATAATCGAACCA 57.346 37.500 0.00 0.00 0.00 3.67
77 89 8.842358 ACTAAAACGTCAGATTGATTCCTTAA 57.158 30.769 0.00 0.00 0.00 1.85
108 120 0.461135 ACCACAACCAAGCAAGCAAG 59.539 50.000 0.00 0.00 0.00 4.01
130 142 8.428063 TCATACACCATTTGAGAAACCAAAATT 58.572 29.630 0.00 0.00 39.20 1.82
243 289 3.118920 TGATCCATGGATTTGCTTGCTTG 60.119 43.478 27.93 0.00 34.60 4.01
244 290 3.101437 TGATCCATGGATTTGCTTGCTT 58.899 40.909 27.93 2.42 34.60 3.91
245 291 2.742348 TGATCCATGGATTTGCTTGCT 58.258 42.857 27.93 3.26 34.60 3.91
246 292 3.530265 TTGATCCATGGATTTGCTTGC 57.470 42.857 27.93 13.78 34.60 4.01
308 362 8.798859 AACAGAGCTAGAACATGAATTGTATT 57.201 30.769 0.00 0.00 37.68 1.89
309 363 8.671921 CAAACAGAGCTAGAACATGAATTGTAT 58.328 33.333 0.00 0.00 37.68 2.29
310 364 7.119699 CCAAACAGAGCTAGAACATGAATTGTA 59.880 37.037 0.00 0.00 37.68 2.41
311 365 6.072286 CCAAACAGAGCTAGAACATGAATTGT 60.072 38.462 0.00 0.00 41.53 2.71
312 366 6.149973 TCCAAACAGAGCTAGAACATGAATTG 59.850 38.462 0.00 0.00 0.00 2.32
384 621 5.986135 GCACATATGACTAGAGGTTAAGTGG 59.014 44.000 10.38 0.00 0.00 4.00
395 651 4.445453 TGGAAAGCAGCACATATGACTAG 58.555 43.478 10.38 3.36 0.00 2.57
519 800 4.686091 TGAGCATTTACAGAAGTCGTCAAG 59.314 41.667 0.00 0.00 0.00 3.02
520 801 4.447724 GTGAGCATTTACAGAAGTCGTCAA 59.552 41.667 0.00 0.00 0.00 3.18
521 802 3.987868 GTGAGCATTTACAGAAGTCGTCA 59.012 43.478 0.00 0.00 0.00 4.35
524 805 5.233050 CCATAGTGAGCATTTACAGAAGTCG 59.767 44.000 0.00 0.00 0.00 4.18
527 808 5.674525 TCCCATAGTGAGCATTTACAGAAG 58.325 41.667 0.00 0.00 0.00 2.85
620 1993 3.813443 TCTCCAGAATTAATGCCTCAGC 58.187 45.455 0.00 0.00 40.48 4.26
621 1994 4.215827 GCATCTCCAGAATTAATGCCTCAG 59.784 45.833 0.00 0.00 37.37 3.35
879 2375 4.290093 AGAGACCATACAGCACCAATCTA 58.710 43.478 0.00 0.00 0.00 1.98
880 2376 3.110705 AGAGACCATACAGCACCAATCT 58.889 45.455 0.00 0.00 0.00 2.40
917 2418 2.369860 TCAGACAGCACAAACAGAGGAT 59.630 45.455 0.00 0.00 0.00 3.24
983 2491 1.000843 GCATCTTTTCCTTTTGGCGGT 59.999 47.619 0.00 0.00 40.12 5.68
1123 2642 1.032657 AGGAGTGCATACGACTCGCT 61.033 55.000 0.00 0.00 40.77 4.93
1308 2833 6.726230 CATAATTGCTGAGTCTTTCATGAGG 58.274 40.000 0.00 0.00 34.68 3.86
1339 2864 3.126831 CGATAAAGCGCTTCCTGAGATT 58.873 45.455 25.24 7.59 0.00 2.40
1344 2869 1.523095 GCTACGATAAAGCGCTTCCTG 59.477 52.381 25.24 15.73 33.86 3.86
1423 2957 7.067494 ACCATCAACAGTATCCTTTAGCATTTC 59.933 37.037 0.00 0.00 0.00 2.17
1448 2982 7.916914 ATGTTACCATTACCTTTGAGTACAC 57.083 36.000 0.00 0.00 0.00 2.90
1464 3004 4.713553 TCTCAAGCAAGACAATGTTACCA 58.286 39.130 0.00 0.00 0.00 3.25
1465 3005 5.689383 TTCTCAAGCAAGACAATGTTACC 57.311 39.130 0.00 0.00 0.00 2.85
1486 3032 1.893808 CCAGCAACAGGACACGCTT 60.894 57.895 0.00 0.00 30.72 4.68
1521 3067 1.765597 GAACCGGGGTCTCCAACACT 61.766 60.000 6.32 0.00 34.36 3.55
1541 3087 7.767659 CAGAATACTCATCAGGATCACAGAAAA 59.232 37.037 0.00 0.00 0.00 2.29
1839 3469 3.761897 TCTTTTGGCATATATTCCCCCG 58.238 45.455 0.00 0.00 0.00 5.73
1982 3700 1.203994 ACGAAACGGAGGGAGTACATG 59.796 52.381 0.00 0.00 0.00 3.21
1984 3702 2.198827 TACGAAACGGAGGGAGTACA 57.801 50.000 0.00 0.00 0.00 2.90
1985 3703 3.790152 ATTACGAAACGGAGGGAGTAC 57.210 47.619 0.00 0.00 0.00 2.73
1986 3704 4.780815 TCTATTACGAAACGGAGGGAGTA 58.219 43.478 0.00 0.00 0.00 2.59
1987 3705 3.624777 TCTATTACGAAACGGAGGGAGT 58.375 45.455 0.00 0.00 0.00 3.85
1988 3706 4.277672 TCATCTATTACGAAACGGAGGGAG 59.722 45.833 0.00 0.00 0.00 4.30
1989 3707 4.037208 GTCATCTATTACGAAACGGAGGGA 59.963 45.833 0.00 0.00 0.00 4.20
1990 3708 4.037684 AGTCATCTATTACGAAACGGAGGG 59.962 45.833 0.00 0.00 0.00 4.30
1991 3709 5.184340 AGTCATCTATTACGAAACGGAGG 57.816 43.478 0.00 0.00 0.00 4.30
1992 3710 7.914346 AGTTAAGTCATCTATTACGAAACGGAG 59.086 37.037 0.00 0.00 0.00 4.63
1993 3711 7.765307 AGTTAAGTCATCTATTACGAAACGGA 58.235 34.615 0.00 0.00 0.00 4.69
1994 3712 7.982371 AGTTAAGTCATCTATTACGAAACGG 57.018 36.000 0.00 0.00 0.00 4.44
2036 3754 9.746711 CGTTCTAAAATAGATGACTCAACTTTG 57.253 33.333 0.00 0.00 34.22 2.77
2037 3755 8.936864 CCGTTCTAAAATAGATGACTCAACTTT 58.063 33.333 0.00 0.00 34.22 2.66
2038 3756 8.311836 TCCGTTCTAAAATAGATGACTCAACTT 58.688 33.333 0.00 0.00 34.22 2.66
2039 3757 7.837863 TCCGTTCTAAAATAGATGACTCAACT 58.162 34.615 0.00 0.00 34.22 3.16
2040 3758 7.222999 CCTCCGTTCTAAAATAGATGACTCAAC 59.777 40.741 0.00 0.00 34.22 3.18
2041 3759 7.265673 CCTCCGTTCTAAAATAGATGACTCAA 58.734 38.462 0.00 0.00 34.22 3.02
2042 3760 6.183360 CCCTCCGTTCTAAAATAGATGACTCA 60.183 42.308 0.00 0.00 34.22 3.41
2043 3761 6.040616 TCCCTCCGTTCTAAAATAGATGACTC 59.959 42.308 0.00 0.00 34.22 3.36
2044 3762 5.897824 TCCCTCCGTTCTAAAATAGATGACT 59.102 40.000 0.00 0.00 34.22 3.41
2045 3763 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
2046 3764 5.897824 ACTCCCTCCGTTCTAAAATAGATGA 59.102 40.000 0.00 0.00 34.22 2.92
2047 3765 6.163135 ACTCCCTCCGTTCTAAAATAGATG 57.837 41.667 0.00 0.00 34.22 2.90
2048 3766 7.068061 ACTACTCCCTCCGTTCTAAAATAGAT 58.932 38.462 0.00 0.00 34.22 1.98
2049 3767 6.430007 ACTACTCCCTCCGTTCTAAAATAGA 58.570 40.000 0.00 0.00 0.00 1.98
2050 3768 6.712179 ACTACTCCCTCCGTTCTAAAATAG 57.288 41.667 0.00 0.00 0.00 1.73
2051 3769 7.486407 AAACTACTCCCTCCGTTCTAAAATA 57.514 36.000 0.00 0.00 0.00 1.40
2052 3770 6.370186 AAACTACTCCCTCCGTTCTAAAAT 57.630 37.500 0.00 0.00 0.00 1.82
2053 3771 5.813513 AAACTACTCCCTCCGTTCTAAAA 57.186 39.130 0.00 0.00 0.00 1.52
2054 3772 5.541484 AGAAAACTACTCCCTCCGTTCTAAA 59.459 40.000 0.00 0.00 0.00 1.85
2055 3773 5.082425 AGAAAACTACTCCCTCCGTTCTAA 58.918 41.667 0.00 0.00 0.00 2.10
2056 3774 4.670765 AGAAAACTACTCCCTCCGTTCTA 58.329 43.478 0.00 0.00 0.00 2.10
2057 3775 3.508426 AGAAAACTACTCCCTCCGTTCT 58.492 45.455 0.00 0.00 0.00 3.01
2058 3776 3.957591 AGAAAACTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 0.00 3.95
2059 3777 4.414677 AGTAGAAAACTACTCCCTCCGTT 58.585 43.478 0.00 0.00 35.43 4.44
2060 3778 4.044946 AGTAGAAAACTACTCCCTCCGT 57.955 45.455 0.00 0.00 35.43 4.69
2061 3779 5.066246 CACTAGTAGAAAACTACTCCCTCCG 59.934 48.000 12.23 1.34 40.31 4.63
2062 3780 6.186234 TCACTAGTAGAAAACTACTCCCTCC 58.814 44.000 12.23 0.00 40.31 4.30
2063 3781 7.700022 TTCACTAGTAGAAAACTACTCCCTC 57.300 40.000 12.23 0.00 40.31 4.30
2064 3782 8.667592 ATTTCACTAGTAGAAAACTACTCCCT 57.332 34.615 18.18 3.41 40.31 4.20
2065 3783 8.751242 AGATTTCACTAGTAGAAAACTACTCCC 58.249 37.037 19.33 7.75 40.31 4.30
2066 3784 9.791820 GAGATTTCACTAGTAGAAAACTACTCC 57.208 37.037 20.09 11.07 37.95 3.85
2096 3964 7.656542 CCTCCGTCCCTAAATTTATAAGTCTTC 59.343 40.741 0.00 0.00 0.00 2.87
2107 4312 2.706190 CAGATCCCTCCGTCCCTAAATT 59.294 50.000 0.00 0.00 0.00 1.82
2115 4320 0.457851 CACTCACAGATCCCTCCGTC 59.542 60.000 0.00 0.00 0.00 4.79
2183 4404 8.552865 CACATTTCAATTCAATTCAGCTTCAAA 58.447 29.630 0.00 0.00 0.00 2.69
2228 4548 1.380302 GGCTCCTTTCTCCTTGGCA 59.620 57.895 0.00 0.00 0.00 4.92
2258 4579 3.371380 GGAGATATGGAGGATGGAATGGC 60.371 52.174 0.00 0.00 0.00 4.40
2300 5178 3.127548 CGGCGTAGTTTAGTTGAGGACTA 59.872 47.826 0.00 0.00 39.86 2.59
2321 5199 2.031012 TGACAGCAAGGTGGAGCG 59.969 61.111 4.16 0.00 35.48 5.03
2351 5229 0.772124 AAGAAGGAGGAGGTGGGCAA 60.772 55.000 0.00 0.00 0.00 4.52
2411 6201 1.654954 GGAGCTCGTCGTGGCTAAGA 61.655 60.000 7.83 0.00 39.05 2.10
2413 6203 1.974875 TGGAGCTCGTCGTGGCTAA 60.975 57.895 7.83 5.15 39.05 3.09
2453 6243 1.812686 TTAGTTGAGGACTGCGGCGT 61.813 55.000 9.37 0.00 39.48 5.68
2478 6268 3.537206 GACGGCAAGGTGGAGCAGT 62.537 63.158 0.00 0.00 41.72 4.40


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

AutoCloner maintained by Alex Coulton.