Multiple sequence alignment - TraesCS7B01G225500

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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 TraesCS7B01G225500 chr7B 100.000 7246 0 0 1 7246 426111843 426104598 0.000000e+00 13381.0
1 TraesCS7B01G225500 chr7B 93.796 274 15 2 1351 1623 426103289 426103561 1.880000e-110 411.0
2 TraesCS7B01G225500 chr7B 83.186 226 25 10 6464 6683 426105331 426105113 2.060000e-45 195.0
3 TraesCS7B01G225500 chr7B 83.186 226 25 10 6513 6731 426105380 426105161 2.060000e-45 195.0
4 TraesCS7B01G225500 chr7B 97.778 90 1 1 2344 2433 426109421 426109333 3.500000e-33 154.0
5 TraesCS7B01G225500 chr7B 97.778 90 1 1 2423 2511 426109500 426109411 3.500000e-33 154.0
6 TraesCS7B01G225500 chr6A 97.036 4825 86 6 2423 7246 14156477 14151709 0.000000e+00 8065.0
7 TraesCS7B01G225500 chr6A 96.406 807 21 5 1629 2433 14157189 14156389 0.000000e+00 1323.0
8 TraesCS7B01G225500 chr6A 95.909 220 6 3 1351 1568 14157487 14157269 3.220000e-93 353.0
9 TraesCS7B01G225500 chr6A 95.694 209 9 0 1358 1566 14150433 14150641 3.240000e-88 337.0
10 TraesCS7B01G225500 chr6A 86.061 165 12 7 6572 6731 14152478 14152320 4.500000e-37 167.0
11 TraesCS7B01G225500 chr7A 99.493 3550 17 1 3697 7246 52223364 52219816 0.000000e+00 6455.0
12 TraesCS7B01G225500 chr7A 88.960 1250 73 32 1 1232 472570204 472569002 0.000000e+00 1483.0
13 TraesCS7B01G225500 chr7A 95.522 268 11 1 1357 1623 52218515 52218782 1.870000e-115 427.0
14 TraesCS7B01G225500 chr7A 97.638 127 3 0 1231 1357 472568946 472568820 1.220000e-52 219.0
15 TraesCS7B01G225500 chr7A 83.186 226 25 10 6513 6731 52220598 52220379 2.060000e-45 195.0
16 TraesCS7B01G225500 chr2A 87.691 4054 355 57 2421 6398 47877839 47881824 0.000000e+00 4590.0
17 TraesCS7B01G225500 chr2A 76.434 1116 190 38 1356 2426 47876836 47877923 2.970000e-148 536.0
18 TraesCS7B01G225500 chr5D 87.632 4067 346 69 2421 6405 323855514 323859505 0.000000e+00 4578.0
19 TraesCS7B01G225500 chr5D 82.692 156 18 4 7097 7246 323859825 323859977 5.900000e-26 130.0
20 TraesCS7B01G225500 chr5D 96.552 58 2 0 2161 2218 177039127 177039184 5.980000e-16 97.1
21 TraesCS7B01G225500 chr5D 94.828 58 3 0 2161 2218 466927357 466927300 2.780000e-14 91.6
22 TraesCS7B01G225500 chr6D 87.708 4019 360 55 2421 6390 2689788 2685855 0.000000e+00 4562.0
23 TraesCS7B01G225500 chr6D 83.608 1031 124 25 1435 2433 25616824 25617841 0.000000e+00 926.0
24 TraesCS7B01G225500 chr6D 94.643 392 20 1 5451 5842 25618076 25618466 2.240000e-169 606.0
25 TraesCS7B01G225500 chr6D 75.959 886 136 43 1399 2233 2690720 2689861 1.140000e-102 385.0
26 TraesCS7B01G225500 chr2D 88.795 2606 212 35 2421 4959 53697459 53700051 0.000000e+00 3121.0
27 TraesCS7B01G225500 chr4A 96.089 1790 65 4 5459 7246 676307285 676305499 0.000000e+00 2913.0
28 TraesCS7B01G225500 chr4A 95.429 350 12 2 5116 5465 676316350 676316005 8.210000e-154 555.0
29 TraesCS7B01G225500 chr4A 92.509 267 17 1 1357 1620 676261686 676261952 5.310000e-101 379.0
30 TraesCS7B01G225500 chr4A 90.741 270 24 1 1358 1626 676316676 676316407 6.910000e-95 359.0
31 TraesCS7B01G225500 chr4A 85.778 225 21 10 6513 6731 676306281 676306062 2.030000e-55 228.0
32 TraesCS7B01G225500 chr4A 85.311 177 15 7 6561 6731 676306281 676306110 9.660000e-39 172.0
33 TraesCS7B01G225500 chr6B 86.811 2593 250 47 3836 6398 679694451 679696981 0.000000e+00 2809.0
34 TraesCS7B01G225500 chr6B 88.183 1464 127 17 2421 3841 679680292 679681752 0.000000e+00 1703.0
35 TraesCS7B01G225500 chr6B 76.544 1117 184 41 1358 2426 679679290 679680376 2.300000e-149 540.0
36 TraesCS7B01G225500 chr6B 96.552 58 2 0 2161 2218 543898975 543898918 5.980000e-16 97.1
37 TraesCS7B01G225500 chr3A 90.835 2073 165 8 2629 4679 357517359 357515290 0.000000e+00 2752.0
38 TraesCS7B01G225500 chr3A 86.095 2287 220 47 4144 6398 111959550 111957330 0.000000e+00 2372.0
39 TraesCS7B01G225500 chr3A 86.524 1165 110 14 2421 3541 111960707 111959546 0.000000e+00 1238.0
40 TraesCS7B01G225500 chr3A 80.782 895 109 36 5471 6330 357515219 357514353 6.130000e-180 641.0
41 TraesCS7B01G225500 chr3A 76.344 1116 190 39 1356 2426 111961709 111960623 1.380000e-146 531.0
42 TraesCS7B01G225500 chr3A 89.474 190 20 0 1358 1547 357499901 357500090 2.610000e-59 241.0
43 TraesCS7B01G225500 chr3A 79.255 188 32 6 1358 1541 710797900 710797716 2.740000e-24 124.0
44 TraesCS7B01G225500 chr1D 80.533 3375 533 82 2609 5889 257433962 257430618 0.000000e+00 2479.0
45 TraesCS7B01G225500 chr1D 94.828 58 3 0 2161 2218 26717823 26717880 2.780000e-14 91.6
46 TraesCS7B01G225500 chr7D 80.427 3372 540 82 2609 5889 608569513 608566171 0.000000e+00 2460.0
47 TraesCS7B01G225500 chr7D 94.400 1250 45 13 1 1232 411607563 411606321 0.000000e+00 1897.0
48 TraesCS7B01G225500 chr7D 79.606 1927 314 51 4012 5889 575912307 575914203 0.000000e+00 1308.0
49 TraesCS7B01G225500 chr7D 98.425 127 2 0 1231 1357 411606265 411606139 2.630000e-54 224.0
50 TraesCS7B01G225500 chr3D 80.131 3367 539 81 2609 5880 9125759 9129090 0.000000e+00 2392.0
51 TraesCS7B01G225500 chr3D 94.828 58 3 0 2161 2218 342374272 342374329 2.780000e-14 91.6
52 TraesCS7B01G225500 chr5B 90.039 1024 87 3 2653 3661 606743555 606742532 0.000000e+00 1312.0
53 TraesCS7B01G225500 chr2B 95.035 564 26 2 1870 2433 23957580 23958141 0.000000e+00 885.0
54 TraesCS7B01G225500 chr2B 98.013 302 6 0 2423 2724 23958053 23958354 6.440000e-145 525.0
55 TraesCS7B01G225500 chrUn 88.982 717 73 4 4836 5546 87252831 87253547 0.000000e+00 881.0
56 TraesCS7B01G225500 chrUn 88.982 717 73 4 4836 5546 235068690 235069406 0.000000e+00 881.0
57 TraesCS7B01G225500 chr4D 78.488 172 33 4 1352 1521 455584329 455584498 7.690000e-20 110.0
58 TraesCS7B01G225500 chr4B 94.828 58 3 0 2161 2218 302470780 302470723 2.780000e-14 91.6


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 TraesCS7B01G225500 chr7B 426104598 426111843 7245 True 13381.000000 13381 100.000000 1 7246 1 chr7B.!!$R1 7245
1 TraesCS7B01G225500 chr6A 14151709 14156477 4768 True 8065.000000 8065 97.036000 2423 7246 1 chr6A.!!$R1 4823
2 TraesCS7B01G225500 chr6A 14152320 14157487 5167 True 614.333333 1323 92.792000 1351 6731 3 chr6A.!!$R2 5380
3 TraesCS7B01G225500 chr7A 52219816 52223364 3548 True 3325.000000 6455 91.339500 3697 7246 2 chr7A.!!$R1 3549
4 TraesCS7B01G225500 chr7A 472568820 472570204 1384 True 851.000000 1483 93.299000 1 1357 2 chr7A.!!$R2 1356
5 TraesCS7B01G225500 chr2A 47876836 47881824 4988 False 2563.000000 4590 82.062500 1356 6398 2 chr2A.!!$F1 5042
6 TraesCS7B01G225500 chr5D 323855514 323859977 4463 False 2354.000000 4578 85.162000 2421 7246 2 chr5D.!!$F2 4825
7 TraesCS7B01G225500 chr6D 2685855 2690720 4865 True 2473.500000 4562 81.833500 1399 6390 2 chr6D.!!$R1 4991
8 TraesCS7B01G225500 chr6D 25616824 25618466 1642 False 766.000000 926 89.125500 1435 5842 2 chr6D.!!$F1 4407
9 TraesCS7B01G225500 chr2D 53697459 53700051 2592 False 3121.000000 3121 88.795000 2421 4959 1 chr2D.!!$F1 2538
10 TraesCS7B01G225500 chr4A 676305499 676307285 1786 True 1104.333333 2913 89.059333 5459 7246 3 chr4A.!!$R1 1787
11 TraesCS7B01G225500 chr4A 676316005 676316676 671 True 457.000000 555 93.085000 1358 5465 2 chr4A.!!$R2 4107
12 TraesCS7B01G225500 chr6B 679694451 679696981 2530 False 2809.000000 2809 86.811000 3836 6398 1 chr6B.!!$F1 2562
13 TraesCS7B01G225500 chr6B 679679290 679681752 2462 False 1121.500000 1703 82.363500 1358 3841 2 chr6B.!!$F2 2483
14 TraesCS7B01G225500 chr3A 357514353 357517359 3006 True 1696.500000 2752 85.808500 2629 6330 2 chr3A.!!$R3 3701
15 TraesCS7B01G225500 chr3A 111957330 111961709 4379 True 1380.333333 2372 82.987667 1356 6398 3 chr3A.!!$R2 5042
16 TraesCS7B01G225500 chr1D 257430618 257433962 3344 True 2479.000000 2479 80.533000 2609 5889 1 chr1D.!!$R1 3280
17 TraesCS7B01G225500 chr7D 608566171 608569513 3342 True 2460.000000 2460 80.427000 2609 5889 1 chr7D.!!$R1 3280
18 TraesCS7B01G225500 chr7D 575912307 575914203 1896 False 1308.000000 1308 79.606000 4012 5889 1 chr7D.!!$F1 1877
19 TraesCS7B01G225500 chr7D 411606139 411607563 1424 True 1060.500000 1897 96.412500 1 1357 2 chr7D.!!$R2 1356
20 TraesCS7B01G225500 chr3D 9125759 9129090 3331 False 2392.000000 2392 80.131000 2609 5880 1 chr3D.!!$F1 3271
21 TraesCS7B01G225500 chr5B 606742532 606743555 1023 True 1312.000000 1312 90.039000 2653 3661 1 chr5B.!!$R1 1008
22 TraesCS7B01G225500 chr2B 23957580 23958354 774 False 705.000000 885 96.524000 1870 2724 2 chr2B.!!$F1 854
23 TraesCS7B01G225500 chrUn 87252831 87253547 716 False 881.000000 881 88.982000 4836 5546 1 chrUn.!!$F1 710
24 TraesCS7B01G225500 chrUn 235068690 235069406 716 False 881.000000 881 88.982000 4836 5546 1 chrUn.!!$F2 710

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
160 163 0.521735 CACTTGCCGCCCTTAAGAAC 59.478 55.000 3.36 0.00 0.00 3.01 F
1211 1235 0.387202 TGTGCAACCAAAACGATGGG 59.613 50.000 10.50 0.00 45.18 4.00 F
1586 1680 1.081442 GCCAGGGTTTTCGCGAAAG 60.081 57.895 30.60 20.27 37.84 2.62 F
2364 2535 0.764271 TTGTGACTGGACATGGCAGA 59.236 50.000 0.00 0.00 0.00 4.26 F
2365 2536 0.764271 TGTGACTGGACATGGCAGAA 59.236 50.000 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2020 1.718280 AAACAGGGGAGAGAGACGTT 58.282 50.000 0.00 0.0 0.0 3.99 R
2345 2516 0.764271 TCTGCCATGTCCAGTCACAA 59.236 50.000 9.59 0.0 0.0 3.33 R
3164 3395 2.611292 CTCATCTGTTTCTGAATCCGCC 59.389 50.000 0.00 0.0 0.0 6.13 R
3869 4100 1.693606 CCAGGGTTTGTTTGCCTCAAT 59.306 47.619 0.00 0.0 0.0 2.57 R
6818 7345 0.309302 TGACGGAAATGCAAACCACG 59.691 50.000 0.00 0.0 0.0 4.94 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
125 127 9.615295 TTTTCACTCAGTTAACTTAAACACAAC 57.385 29.630 5.07 0.00 0.00 3.32
126 128 7.908827 TCACTCAGTTAACTTAAACACAACA 57.091 32.000 5.07 0.00 0.00 3.33
127 129 8.500753 TCACTCAGTTAACTTAAACACAACAT 57.499 30.769 5.07 0.00 0.00 2.71
128 130 9.602568 TCACTCAGTTAACTTAAACACAACATA 57.397 29.630 5.07 0.00 0.00 2.29
129 131 9.646336 CACTCAGTTAACTTAAACACAACATAC 57.354 33.333 5.07 0.00 0.00 2.39
130 132 9.386010 ACTCAGTTAACTTAAACACAACATACA 57.614 29.630 5.07 0.00 0.00 2.29
160 163 0.521735 CACTTGCCGCCCTTAAGAAC 59.478 55.000 3.36 0.00 0.00 3.01
209 213 3.272574 TCCATCATCAGTCAAGGAAGC 57.727 47.619 0.00 0.00 0.00 3.86
216 220 7.333921 CCATCATCAGTCAAGGAAGCTATAATC 59.666 40.741 0.00 0.00 0.00 1.75
217 221 6.763355 TCATCAGTCAAGGAAGCTATAATCC 58.237 40.000 0.00 0.00 35.88 3.01
218 222 6.327365 TCATCAGTCAAGGAAGCTATAATCCA 59.673 38.462 5.00 0.00 38.23 3.41
219 223 5.918608 TCAGTCAAGGAAGCTATAATCCAC 58.081 41.667 5.00 0.00 38.23 4.02
220 224 5.425217 TCAGTCAAGGAAGCTATAATCCACA 59.575 40.000 5.00 0.00 38.23 4.17
221 225 5.525378 CAGTCAAGGAAGCTATAATCCACAC 59.475 44.000 5.00 0.00 38.23 3.82
233 237 1.344065 ATCCACACCCACACGACTTA 58.656 50.000 0.00 0.00 0.00 2.24
387 391 1.048601 GTCATCGGGGAGCATAGGAA 58.951 55.000 0.00 0.00 0.00 3.36
475 479 6.934645 TGATCCGTAGTTTCACTGATTTTTCT 59.065 34.615 0.00 0.00 0.00 2.52
479 483 7.444183 TCCGTAGTTTCACTGATTTTTCTGATT 59.556 33.333 0.00 0.00 0.00 2.57
654 661 3.878778 CCTCTGTGAAGTTCCCATTAGG 58.121 50.000 0.00 1.85 0.00 2.69
802 810 5.954335 AGGAAGGTTGCATTAGATTTTTCG 58.046 37.500 0.00 0.00 0.00 3.46
815 836 5.358298 AGATTTTTCGTTAGACACTTGCC 57.642 39.130 0.00 0.00 0.00 4.52
964 985 1.444119 GCGAAAAGTGACTGGTGCCA 61.444 55.000 0.00 0.00 0.00 4.92
1012 1033 3.256383 TGGTTGATTCATGGTCAGCTTTG 59.744 43.478 12.78 0.00 0.00 2.77
1134 1157 1.002544 CTGCTCCTTTTCCTCGAACCT 59.997 52.381 0.00 0.00 0.00 3.50
1138 1161 3.369576 GCTCCTTTTCCTCGAACCTATGT 60.370 47.826 0.00 0.00 0.00 2.29
1210 1234 2.215907 TTGTGCAACCAAAACGATGG 57.784 45.000 0.00 0.00 46.38 3.51
1211 1235 0.387202 TGTGCAACCAAAACGATGGG 59.613 50.000 10.50 0.00 45.18 4.00
1218 1242 1.285641 CAAAACGATGGGCGCTGTT 59.714 52.632 7.64 1.93 46.04 3.16
1311 1392 4.625311 CGCCAAAGAACAAAAAGAAGTTGT 59.375 37.500 0.00 0.00 40.92 3.32
1349 1430 2.269940 AGGGCTCATTCTAACACACCT 58.730 47.619 0.00 0.00 0.00 4.00
1396 1478 4.953579 AGGTGTCTAAACTTGGCAAGAAAA 59.046 37.500 32.50 15.45 0.00 2.29
1552 1634 2.842462 TCAGTGGCTGGACCGTGT 60.842 61.111 0.00 0.00 43.94 4.49
1582 1676 4.038080 GTGGCCAGGGTTTTCGCG 62.038 66.667 5.11 0.00 37.84 5.87
1586 1680 1.081442 GCCAGGGTTTTCGCGAAAG 60.081 57.895 30.60 20.27 37.84 2.62
1856 2020 1.339055 CCCTTGATGTTTCTCTCCGCA 60.339 52.381 0.00 0.00 0.00 5.69
1981 2146 4.332828 CGAGATGTAAGAAACCCCCTTTT 58.667 43.478 0.00 0.00 0.00 2.27
2041 2207 1.613925 GGGTTTGAAAGGGCTCTGTTC 59.386 52.381 0.00 0.00 0.00 3.18
2099 2267 2.159142 CCACCCGGTGTACTAGATTGTC 60.159 54.545 16.55 0.00 0.00 3.18
2119 2287 3.316308 GTCAGAACATGTTTGCTCCTGTT 59.684 43.478 13.36 0.00 34.68 3.16
2169 2338 9.522804 GTTTGTAATTTTCATGAAACTGTACCA 57.477 29.630 20.35 11.23 0.00 3.25
2177 2346 7.397892 TTCATGAAACTGTACCAAACTGAAA 57.602 32.000 5.45 0.00 0.00 2.69
2185 2354 9.665719 AAACTGTACCAAACTGAAATTTTTGAT 57.334 25.926 2.56 0.00 35.13 2.57
2327 2498 4.003648 AGGAAGTGTTAATTGAAGAGCCG 58.996 43.478 0.00 0.00 0.00 5.52
2340 2511 1.871080 AGAGCCGGCAATTAGATTCG 58.129 50.000 31.54 0.00 0.00 3.34
2341 2512 1.139058 AGAGCCGGCAATTAGATTCGT 59.861 47.619 31.54 1.71 0.00 3.85
2342 2513 1.527311 GAGCCGGCAATTAGATTCGTC 59.473 52.381 31.54 8.85 0.00 4.20
2343 2514 1.134521 AGCCGGCAATTAGATTCGTCA 60.135 47.619 31.54 0.00 0.00 4.35
2344 2515 1.873591 GCCGGCAATTAGATTCGTCAT 59.126 47.619 24.80 0.00 0.00 3.06
2345 2516 2.290641 GCCGGCAATTAGATTCGTCATT 59.709 45.455 24.80 0.00 0.00 2.57
2346 2517 3.243068 GCCGGCAATTAGATTCGTCATTT 60.243 43.478 24.80 0.00 0.00 2.32
2347 2518 4.282068 CCGGCAATTAGATTCGTCATTTG 58.718 43.478 0.00 0.00 0.00 2.32
2348 2519 4.201910 CCGGCAATTAGATTCGTCATTTGT 60.202 41.667 0.00 0.00 0.00 2.83
2349 2520 4.730042 CGGCAATTAGATTCGTCATTTGTG 59.270 41.667 0.00 0.00 0.00 3.33
2350 2521 5.447144 CGGCAATTAGATTCGTCATTTGTGA 60.447 40.000 0.00 0.00 0.00 3.58
2351 2522 5.739161 GGCAATTAGATTCGTCATTTGTGAC 59.261 40.000 0.00 0.00 35.59 3.67
2352 2523 6.403636 GGCAATTAGATTCGTCATTTGTGACT 60.404 38.462 6.95 0.00 36.71 3.41
2353 2524 6.467047 GCAATTAGATTCGTCATTTGTGACTG 59.533 38.462 6.95 1.73 36.71 3.51
2354 2525 6.668541 ATTAGATTCGTCATTTGTGACTGG 57.331 37.500 6.95 0.00 36.71 4.00
2355 2526 4.271696 AGATTCGTCATTTGTGACTGGA 57.728 40.909 6.95 0.00 36.71 3.86
2356 2527 3.997021 AGATTCGTCATTTGTGACTGGAC 59.003 43.478 6.95 0.00 36.71 4.02
2357 2528 2.900716 TCGTCATTTGTGACTGGACA 57.099 45.000 6.95 0.00 36.71 4.02
2358 2529 3.401033 TCGTCATTTGTGACTGGACAT 57.599 42.857 6.95 0.00 36.71 3.06
2359 2530 3.066380 TCGTCATTTGTGACTGGACATG 58.934 45.455 6.95 0.00 36.71 3.21
2360 2531 2.160219 CGTCATTTGTGACTGGACATGG 59.840 50.000 0.00 0.00 36.71 3.66
2361 2532 2.095059 GTCATTTGTGACTGGACATGGC 60.095 50.000 0.00 0.00 36.01 4.40
2362 2533 1.887854 CATTTGTGACTGGACATGGCA 59.112 47.619 0.00 0.00 0.00 4.92
2363 2534 1.608055 TTTGTGACTGGACATGGCAG 58.392 50.000 0.00 0.00 0.00 4.85
2364 2535 0.764271 TTGTGACTGGACATGGCAGA 59.236 50.000 0.00 0.00 0.00 4.26
2365 2536 0.764271 TGTGACTGGACATGGCAGAA 59.236 50.000 0.00 0.00 0.00 3.02
2366 2537 1.352017 TGTGACTGGACATGGCAGAAT 59.648 47.619 0.00 0.00 0.00 2.40
2367 2538 2.571202 TGTGACTGGACATGGCAGAATA 59.429 45.455 0.00 0.00 0.00 1.75
2368 2539 3.200605 TGTGACTGGACATGGCAGAATAT 59.799 43.478 0.00 0.00 0.00 1.28
2369 2540 4.202441 GTGACTGGACATGGCAGAATATT 58.798 43.478 0.00 0.00 0.00 1.28
2370 2541 5.104569 TGTGACTGGACATGGCAGAATATTA 60.105 40.000 0.00 0.00 0.00 0.98
2371 2542 5.822519 GTGACTGGACATGGCAGAATATTAA 59.177 40.000 0.00 0.00 0.00 1.40
2372 2543 6.488006 GTGACTGGACATGGCAGAATATTAAT 59.512 38.462 0.00 0.00 0.00 1.40
2373 2544 6.487668 TGACTGGACATGGCAGAATATTAATG 59.512 38.462 0.00 0.00 0.00 1.90
2374 2545 5.771666 ACTGGACATGGCAGAATATTAATGG 59.228 40.000 0.00 0.00 0.00 3.16
2375 2546 5.951204 TGGACATGGCAGAATATTAATGGA 58.049 37.500 0.00 0.00 0.00 3.41
2376 2547 6.372104 TGGACATGGCAGAATATTAATGGAA 58.628 36.000 0.00 0.00 0.00 3.53
2377 2548 6.838090 TGGACATGGCAGAATATTAATGGAAA 59.162 34.615 0.00 0.00 0.00 3.13
2378 2549 7.510001 TGGACATGGCAGAATATTAATGGAAAT 59.490 33.333 0.00 0.00 0.00 2.17
2379 2550 7.816031 GGACATGGCAGAATATTAATGGAAATG 59.184 37.037 0.00 0.00 0.00 2.32
2380 2551 8.253867 ACATGGCAGAATATTAATGGAAATGT 57.746 30.769 0.00 0.00 0.00 2.71
2381 2552 9.365906 ACATGGCAGAATATTAATGGAAATGTA 57.634 29.630 0.00 0.00 0.00 2.29
2382 2553 9.630098 CATGGCAGAATATTAATGGAAATGTAC 57.370 33.333 0.00 0.00 0.00 2.90
2383 2554 8.759481 TGGCAGAATATTAATGGAAATGTACA 57.241 30.769 0.00 0.00 0.00 2.90
2384 2555 9.194972 TGGCAGAATATTAATGGAAATGTACAA 57.805 29.630 0.00 0.00 0.00 2.41
2385 2556 9.463443 GGCAGAATATTAATGGAAATGTACAAC 57.537 33.333 0.00 0.00 0.00 3.32
2404 2575 9.347934 TGTACAACAGTTTTAAATGAAGTTGTG 57.652 29.630 24.08 8.64 45.13 3.33
2405 2576 7.289587 ACAACAGTTTTAAATGAAGTTGTGC 57.710 32.000 19.31 0.00 44.23 4.57
2406 2577 6.870965 ACAACAGTTTTAAATGAAGTTGTGCA 59.129 30.769 19.31 0.00 44.23 4.57
2407 2578 7.548780 ACAACAGTTTTAAATGAAGTTGTGCAT 59.451 29.630 19.31 4.52 44.23 3.96
2408 2579 8.389603 CAACAGTTTTAAATGAAGTTGTGCATT 58.610 29.630 0.00 0.00 36.35 3.56
2409 2580 7.908230 ACAGTTTTAAATGAAGTTGTGCATTG 58.092 30.769 0.00 0.00 35.11 2.82
2410 2581 7.548780 ACAGTTTTAAATGAAGTTGTGCATTGT 59.451 29.630 0.00 0.00 35.11 2.71
2411 2582 9.029243 CAGTTTTAAATGAAGTTGTGCATTGTA 57.971 29.630 0.00 0.00 35.11 2.41
2412 2583 9.593134 AGTTTTAAATGAAGTTGTGCATTGTAA 57.407 25.926 0.00 0.00 35.11 2.41
2415 2586 9.593134 TTTAAATGAAGTTGTGCATTGTAAACT 57.407 25.926 0.00 0.00 35.11 2.66
2416 2587 7.467557 AAATGAAGTTGTGCATTGTAAACTG 57.532 32.000 0.00 0.00 35.11 3.16
2417 2588 5.826601 TGAAGTTGTGCATTGTAAACTGA 57.173 34.783 0.00 0.00 33.30 3.41
2418 2589 6.201226 TGAAGTTGTGCATTGTAAACTGAA 57.799 33.333 0.00 0.00 33.30 3.02
2419 2590 6.804677 TGAAGTTGTGCATTGTAAACTGAAT 58.195 32.000 0.00 0.00 33.30 2.57
2439 2610 6.923012 TGAATTTATTTGTGACTGGACATGG 58.077 36.000 0.00 0.00 0.00 3.66
3158 3389 5.772169 AGAAATGGAGGAAGAAGGTGAAAAG 59.228 40.000 0.00 0.00 0.00 2.27
3164 3395 1.266989 GAAGAAGGTGAAAAGGGTGCG 59.733 52.381 0.00 0.00 0.00 5.34
3263 3494 3.214328 ACATGTTGACAAAGAGGTGGAC 58.786 45.455 0.00 0.00 0.00 4.02
3869 4100 6.794493 AGATGTTATGGGATTATGGAGAGGAA 59.206 38.462 0.00 0.00 0.00 3.36
6686 7213 7.598493 TGTACTGCTTTTCTTTGAATTTATGCC 59.402 33.333 0.00 0.00 0.00 4.40
6818 7345 7.866393 AGTTATCAGTCTACAGTTTGTGTGTAC 59.134 37.037 0.00 0.00 40.69 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.189736 ACTTCTGGAGAAATGTGCTATGGTA 59.810 40.000 0.00 0.00 33.07 3.25
122 124 6.306356 GCAAGTGTCAATAGCTTTGTATGTTG 59.694 38.462 0.00 2.81 0.00 3.33
123 125 6.381801 GCAAGTGTCAATAGCTTTGTATGTT 58.618 36.000 0.00 0.00 0.00 2.71
125 127 5.335127 GGCAAGTGTCAATAGCTTTGTATG 58.665 41.667 0.00 0.00 0.00 2.39
126 128 4.094887 CGGCAAGTGTCAATAGCTTTGTAT 59.905 41.667 0.00 0.00 0.00 2.29
127 129 3.435327 CGGCAAGTGTCAATAGCTTTGTA 59.565 43.478 0.00 0.00 0.00 2.41
128 130 2.226437 CGGCAAGTGTCAATAGCTTTGT 59.774 45.455 0.00 0.00 0.00 2.83
129 131 2.855180 CGGCAAGTGTCAATAGCTTTG 58.145 47.619 0.00 0.00 0.00 2.77
130 132 1.200020 GCGGCAAGTGTCAATAGCTTT 59.800 47.619 0.00 0.00 0.00 3.51
160 163 4.510038 ACAATTGCCTTTTGCTACTCTG 57.490 40.909 5.05 0.00 42.00 3.35
209 213 3.132289 AGTCGTGTGGGTGTGGATTATAG 59.868 47.826 0.00 0.00 0.00 1.31
216 220 0.320421 CCTAAGTCGTGTGGGTGTGG 60.320 60.000 0.00 0.00 0.00 4.17
217 221 0.949105 GCCTAAGTCGTGTGGGTGTG 60.949 60.000 0.00 0.00 0.00 3.82
218 222 1.119574 AGCCTAAGTCGTGTGGGTGT 61.120 55.000 0.00 0.00 0.00 4.16
219 223 0.670546 CAGCCTAAGTCGTGTGGGTG 60.671 60.000 0.00 0.00 40.83 4.61
220 224 1.671742 CAGCCTAAGTCGTGTGGGT 59.328 57.895 0.00 0.00 0.00 4.51
221 225 1.079127 CCAGCCTAAGTCGTGTGGG 60.079 63.158 0.00 0.00 0.00 4.61
284 288 5.715279 TGGTCATACTCTTACTGCTAGTGTT 59.285 40.000 0.00 0.00 0.00 3.32
387 391 4.277174 TGTCCATACAATCGTTTTGCAACT 59.723 37.500 0.00 0.00 30.91 3.16
639 646 4.715534 TCAACACCTAATGGGAACTTCA 57.284 40.909 0.00 0.00 38.76 3.02
640 647 6.590234 AAATCAACACCTAATGGGAACTTC 57.410 37.500 0.00 0.00 38.76 3.01
879 900 9.088987 TGCCATGTCACAGTTATATCTATCTTA 57.911 33.333 0.00 0.00 0.00 2.10
987 1008 3.896888 AGCTGACCATGAATCAACCAAAA 59.103 39.130 0.00 0.00 0.00 2.44
1012 1033 1.756538 CCATGTTCCATACTTTGGGGC 59.243 52.381 0.00 0.00 46.45 5.80
1134 1157 3.985127 TCCCCCGAACTTAAGAGACATA 58.015 45.455 10.09 0.00 0.00 2.29
1138 1161 3.110293 TGATCCCCCGAACTTAAGAGA 57.890 47.619 10.09 0.00 0.00 3.10
1210 1234 2.175878 ATATGATCTCCAACAGCGCC 57.824 50.000 2.29 0.00 0.00 6.53
1211 1235 2.350197 GCAATATGATCTCCAACAGCGC 60.350 50.000 0.00 0.00 0.00 5.92
1218 1242 4.859304 GCAATTGGCAATATGATCTCCA 57.141 40.909 14.05 0.00 43.97 3.86
1311 1392 3.255642 GCCCTTGTGCTTGTCATCTTTTA 59.744 43.478 0.00 0.00 0.00 1.52
1396 1478 4.685924 CAAGTTTCAGCACCAAACTGATT 58.314 39.130 8.07 0.00 42.14 2.57
1571 1665 3.351450 GGCTTTCGCGAAAACCCT 58.649 55.556 33.65 0.00 36.88 4.34
1582 1676 2.831685 AACAAATTTCGGGGGCTTTC 57.168 45.000 0.00 0.00 0.00 2.62
1586 1680 4.827692 AGAAATAAACAAATTTCGGGGGC 58.172 39.130 4.23 0.00 46.10 5.80
1856 2020 1.718280 AAACAGGGGAGAGAGACGTT 58.282 50.000 0.00 0.00 0.00 3.99
1981 2146 2.840038 AGCCACCACTACAGATGAATGA 59.160 45.455 0.00 0.00 0.00 2.57
2099 2267 3.996150 AACAGGAGCAAACATGTTCTG 57.004 42.857 12.39 15.86 39.94 3.02
2119 2287 6.608002 ACTTCTTACCCACAACCAATGTTTTA 59.392 34.615 0.00 0.00 41.46 1.52
2185 2354 8.997621 CTGTCCAAAAATACAGTTAGCTACTA 57.002 34.615 0.00 0.00 38.62 1.82
2327 2498 5.739161 GTCACAAATGACGAATCTAATTGCC 59.261 40.000 0.00 0.00 45.66 4.52
2341 2512 2.161855 GCCATGTCCAGTCACAAATGA 58.838 47.619 0.00 0.00 0.00 2.57
2342 2513 1.887854 TGCCATGTCCAGTCACAAATG 59.112 47.619 0.00 0.00 0.00 2.32
2343 2514 2.165167 CTGCCATGTCCAGTCACAAAT 58.835 47.619 0.00 0.00 0.00 2.32
2344 2515 1.142667 TCTGCCATGTCCAGTCACAAA 59.857 47.619 9.59 0.00 0.00 2.83
2345 2516 0.764271 TCTGCCATGTCCAGTCACAA 59.236 50.000 9.59 0.00 0.00 3.33
2346 2517 0.764271 TTCTGCCATGTCCAGTCACA 59.236 50.000 9.59 0.00 0.00 3.58
2347 2518 2.119801 ATTCTGCCATGTCCAGTCAC 57.880 50.000 9.59 0.00 0.00 3.67
2348 2519 4.508551 AATATTCTGCCATGTCCAGTCA 57.491 40.909 9.59 1.07 0.00 3.41
2349 2520 6.072286 CCATTAATATTCTGCCATGTCCAGTC 60.072 42.308 9.59 0.00 0.00 3.51
2350 2521 5.771666 CCATTAATATTCTGCCATGTCCAGT 59.228 40.000 9.59 0.00 0.00 4.00
2351 2522 6.005823 TCCATTAATATTCTGCCATGTCCAG 58.994 40.000 0.00 4.66 0.00 3.86
2352 2523 5.951204 TCCATTAATATTCTGCCATGTCCA 58.049 37.500 0.00 0.00 0.00 4.02
2353 2524 6.899393 TTCCATTAATATTCTGCCATGTCC 57.101 37.500 0.00 0.00 0.00 4.02
2354 2525 8.362639 ACATTTCCATTAATATTCTGCCATGTC 58.637 33.333 0.00 0.00 0.00 3.06
2355 2526 8.253867 ACATTTCCATTAATATTCTGCCATGT 57.746 30.769 0.00 0.00 0.00 3.21
2356 2527 9.630098 GTACATTTCCATTAATATTCTGCCATG 57.370 33.333 0.00 0.00 0.00 3.66
2357 2528 9.365906 TGTACATTTCCATTAATATTCTGCCAT 57.634 29.630 0.00 0.00 0.00 4.40
2358 2529 8.759481 TGTACATTTCCATTAATATTCTGCCA 57.241 30.769 0.00 0.00 0.00 4.92
2359 2530 9.463443 GTTGTACATTTCCATTAATATTCTGCC 57.537 33.333 0.00 0.00 0.00 4.85
2378 2549 9.347934 CACAACTTCATTTAAAACTGTTGTACA 57.652 29.630 20.90 0.00 42.70 2.90
2379 2550 8.318167 GCACAACTTCATTTAAAACTGTTGTAC 58.682 33.333 20.90 15.98 42.70 2.90
2380 2551 8.029522 TGCACAACTTCATTTAAAACTGTTGTA 58.970 29.630 20.90 11.52 42.70 2.41
2381 2552 6.870965 TGCACAACTTCATTTAAAACTGTTGT 59.129 30.769 18.13 18.13 44.53 3.32
2382 2553 7.288317 TGCACAACTTCATTTAAAACTGTTG 57.712 32.000 17.29 17.29 39.11 3.33
2383 2554 8.389603 CAATGCACAACTTCATTTAAAACTGTT 58.610 29.630 0.00 0.00 31.15 3.16
2384 2555 7.548780 ACAATGCACAACTTCATTTAAAACTGT 59.451 29.630 0.00 0.00 31.15 3.55
2385 2556 7.908230 ACAATGCACAACTTCATTTAAAACTG 58.092 30.769 0.00 0.00 31.15 3.16
2386 2557 9.593134 TTACAATGCACAACTTCATTTAAAACT 57.407 25.926 0.00 0.00 31.15 2.66
2389 2560 9.593134 AGTTTACAATGCACAACTTCATTTAAA 57.407 25.926 0.00 0.00 31.15 1.52
2390 2561 9.029243 CAGTTTACAATGCACAACTTCATTTAA 57.971 29.630 0.00 0.00 31.15 1.52
2391 2562 8.409371 TCAGTTTACAATGCACAACTTCATTTA 58.591 29.630 0.00 0.00 31.15 1.40
2392 2563 7.264221 TCAGTTTACAATGCACAACTTCATTT 58.736 30.769 0.00 0.00 31.15 2.32
2393 2564 6.804677 TCAGTTTACAATGCACAACTTCATT 58.195 32.000 0.00 0.00 33.56 2.57
2394 2565 6.389830 TCAGTTTACAATGCACAACTTCAT 57.610 33.333 0.00 0.00 0.00 2.57
2395 2566 5.826601 TCAGTTTACAATGCACAACTTCA 57.173 34.783 0.00 0.00 0.00 3.02
2396 2567 7.698836 AATTCAGTTTACAATGCACAACTTC 57.301 32.000 0.00 0.00 0.00 3.01
2397 2568 9.762933 ATAAATTCAGTTTACAATGCACAACTT 57.237 25.926 0.00 0.00 35.23 2.66
2398 2569 9.762933 AATAAATTCAGTTTACAATGCACAACT 57.237 25.926 0.00 0.00 35.23 3.16
2401 2572 9.539825 ACAAATAAATTCAGTTTACAATGCACA 57.460 25.926 0.00 0.00 35.23 4.57
2402 2573 9.796062 CACAAATAAATTCAGTTTACAATGCAC 57.204 29.630 0.00 0.00 35.23 4.57
2403 2574 9.755804 TCACAAATAAATTCAGTTTACAATGCA 57.244 25.926 0.00 0.00 35.23 3.96
2407 2578 9.743057 CCAGTCACAAATAAATTCAGTTTACAA 57.257 29.630 0.00 0.00 35.23 2.41
2408 2579 9.126151 TCCAGTCACAAATAAATTCAGTTTACA 57.874 29.630 0.00 0.00 35.23 2.41
2409 2580 9.394477 GTCCAGTCACAAATAAATTCAGTTTAC 57.606 33.333 0.00 0.00 35.23 2.01
2410 2581 9.126151 TGTCCAGTCACAAATAAATTCAGTTTA 57.874 29.630 0.00 0.00 36.75 2.01
2411 2582 8.006298 TGTCCAGTCACAAATAAATTCAGTTT 57.994 30.769 0.00 0.00 0.00 2.66
2412 2583 7.581213 TGTCCAGTCACAAATAAATTCAGTT 57.419 32.000 0.00 0.00 0.00 3.16
2413 2584 7.309377 CCATGTCCAGTCACAAATAAATTCAGT 60.309 37.037 0.00 0.00 0.00 3.41
2414 2585 7.031372 CCATGTCCAGTCACAAATAAATTCAG 58.969 38.462 0.00 0.00 0.00 3.02
2415 2586 6.572119 GCCATGTCCAGTCACAAATAAATTCA 60.572 38.462 0.00 0.00 0.00 2.57
2416 2587 5.807011 GCCATGTCCAGTCACAAATAAATTC 59.193 40.000 0.00 0.00 0.00 2.17
2417 2588 5.245751 TGCCATGTCCAGTCACAAATAAATT 59.754 36.000 0.00 0.00 0.00 1.82
2418 2589 4.771577 TGCCATGTCCAGTCACAAATAAAT 59.228 37.500 0.00 0.00 0.00 1.40
2419 2590 4.148079 TGCCATGTCCAGTCACAAATAAA 58.852 39.130 0.00 0.00 0.00 1.40
2468 2639 9.593134 AGTTTACAATGCACAACTTCATTTAAA 57.407 25.926 0.00 0.00 31.15 1.52
2851 3058 8.766476 TCTCTCTCATTCCTTCATTAATTGTCT 58.234 33.333 0.00 0.00 0.00 3.41
3124 3355 4.515028 TCCTCCATTTCTTCATCAGCAT 57.485 40.909 0.00 0.00 0.00 3.79
3158 3389 3.969250 TTCTGAATCCGCCGCACCC 62.969 63.158 0.00 0.00 0.00 4.61
3164 3395 2.611292 CTCATCTGTTTCTGAATCCGCC 59.389 50.000 0.00 0.00 0.00 6.13
3869 4100 1.693606 CCAGGGTTTGTTTGCCTCAAT 59.306 47.619 0.00 0.00 0.00 2.57
6818 7345 0.309302 TGACGGAAATGCAAACCACG 59.691 50.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.