Multiple sequence alignment - TraesCS2A01G039900

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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 TraesCS2A01G039900 chr2A 100.000 2572 0 0 1 2572 16497004 16499575 0.000000e+00 4750.0
1 TraesCS2A01G039900 chr2D 92.790 1276 63 12 436 1687 14128518 14129788 0.000000e+00 1820.0
2 TraesCS2A01G039900 chr2D 88.360 756 80 6 1704 2457 14130046 14130795 0.000000e+00 902.0
3 TraesCS2A01G039900 chr2D 94.430 377 15 2 26 399 14127771 14128144 2.220000e-160 575.0
4 TraesCS2A01G039900 chr2D 78.402 338 57 10 1920 2253 549847977 549848302 3.350000e-49 206.0
5 TraesCS2A01G039900 chr2D 93.333 45 3 0 2451 2495 649674286 649674242 1.650000e-07 67.6
6 TraesCS2A01G039900 chr2D 100.000 28 0 0 1 28 14127724 14127751 5.000000e-03 52.8
7 TraesCS2A01G039900 chr2B 91.365 996 71 11 701 1687 25847816 25848805 0.000000e+00 1349.0
8 TraesCS2A01G039900 chr2B 87.312 796 89 9 1700 2490 25849046 25849834 0.000000e+00 900.0
9 TraesCS2A01G039900 chr2B 83.882 608 77 9 1704 2301 25932995 25933591 6.210000e-156 560.0
10 TraesCS2A01G039900 chr2B 90.357 280 20 4 19 292 25844012 25844290 6.770000e-96 361.0
11 TraesCS2A01G039900 chr2B 92.829 251 12 3 19 263 25794109 25794359 2.430000e-95 359.0
12 TraesCS2A01G039900 chr2B 78.005 391 77 7 1921 2309 656005717 656006100 1.190000e-58 237.0
13 TraesCS2A01G039900 chr2B 91.111 45 4 0 2451 2495 735289814 735289858 7.680000e-06 62.1
14 TraesCS2A01G039900 chr5A 79.015 467 85 8 1021 1475 643041968 643041503 8.940000e-80 307.0
15 TraesCS2A01G039900 chr5A 93.750 48 3 0 2491 2538 294244929 294244976 3.550000e-09 73.1
16 TraesCS2A01G039900 chr5D 78.587 467 87 7 1021 1475 514947919 514947454 1.940000e-76 296.0
17 TraesCS2A01G039900 chr5D 77.778 504 97 9 1021 1511 514995761 514995260 1.940000e-76 296.0
18 TraesCS2A01G039900 chr5D 77.137 503 102 7 1021 1511 515025118 515024617 1.950000e-71 279.0
19 TraesCS2A01G039900 chr7D 78.971 447 81 11 1922 2364 99960426 99960863 2.500000e-75 292.0
20 TraesCS2A01G039900 chr7D 85.542 249 28 5 19 263 503941773 503942017 1.180000e-63 254.0
21 TraesCS2A01G039900 chr7D 97.222 36 1 0 2460 2495 528799291 528799256 7.680000e-06 62.1
22 TraesCS2A01G039900 chr5B 77.645 501 96 11 1024 1511 647698140 647697643 9.000000e-75 291.0
23 TraesCS2A01G039900 chr5B 78.038 469 85 10 1024 1475 647404867 647404400 1.950000e-71 279.0
24 TraesCS2A01G039900 chr5B 77.246 501 98 10 1024 1511 647780521 647780024 1.950000e-71 279.0
25 TraesCS2A01G039900 chr5B 77.746 355 65 8 1035 1376 647656244 647655891 3.350000e-49 206.0
26 TraesCS2A01G039900 chr5B 97.222 36 1 0 2460 2495 650990182 650990147 7.680000e-06 62.1
27 TraesCS2A01G039900 chr6A 87.967 241 23 3 26 263 617803980 617803743 1.950000e-71 279.0
28 TraesCS2A01G039900 chrUn 91.457 199 17 0 19 217 108255183 108254985 9.070000e-70 274.0
29 TraesCS2A01G039900 chrUn 97.500 40 1 0 2451 2490 319649906 319649867 4.590000e-08 69.4
30 TraesCS2A01G039900 chr4B 87.391 230 23 3 19 242 665975672 665975901 2.540000e-65 259.0
31 TraesCS2A01G039900 chr4B 91.111 45 4 0 2451 2495 585803074 585803118 7.680000e-06 62.1
32 TraesCS2A01G039900 chr6D 86.307 241 27 4 26 263 471819791 471820028 9.130000e-65 257.0
33 TraesCS2A01G039900 chr6B 86.307 241 24 5 26 263 707307505 707307739 1.180000e-63 254.0
34 TraesCS2A01G039900 chr6B 93.750 48 3 0 2491 2538 281336051 281336004 3.550000e-09 73.1
35 TraesCS2A01G039900 chr6B 91.667 48 4 0 2491 2538 617173800 617173753 1.650000e-07 67.6
36 TraesCS2A01G039900 chr6B 95.122 41 1 1 2458 2498 501435880 501435919 2.140000e-06 63.9
37 TraesCS2A01G039900 chr4A 74.000 350 70 12 2010 2352 740446190 740445855 3.480000e-24 122.0
38 TraesCS2A01G039900 chr4A 100.000 28 0 0 2051 2078 427456235 427456208 5.000000e-03 52.8
39 TraesCS2A01G039900 chr3A 77.512 209 38 7 2109 2317 487442317 487442516 1.620000e-22 117.0
40 TraesCS2A01G039900 chr3A 91.111 45 4 0 2451 2495 603276077 603276121 7.680000e-06 62.1
41 TraesCS2A01G039900 chr7B 93.750 48 3 0 2491 2538 401556916 401556869 3.550000e-09 73.1
42 TraesCS2A01G039900 chr7B 93.750 48 3 0 2491 2538 570465276 570465323 3.550000e-09 73.1
43 TraesCS2A01G039900 chr7B 93.333 45 3 0 2451 2495 511462205 511462161 1.650000e-07 67.6
44 TraesCS2A01G039900 chr7B 97.222 36 1 0 2460 2495 133662796 133662761 7.680000e-06 62.1
45 TraesCS2A01G039900 chr1B 93.750 48 3 0 2491 2538 374019596 374019643 3.550000e-09 73.1
46 TraesCS2A01G039900 chr1B 92.000 50 4 0 2491 2540 249624916 249624965 1.280000e-08 71.3
47 TraesCS2A01G039900 chr1A 93.750 48 3 0 2491 2538 241076216 241076263 3.550000e-09 73.1
48 TraesCS2A01G039900 chr1D 92.000 50 4 0 2491 2540 169065384 169065335 1.280000e-08 71.3


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 TraesCS2A01G039900 chr2A 16497004 16499575 2571 False 4750.00 4750 100.000 1 2572 1 chr2A.!!$F1 2571
1 TraesCS2A01G039900 chr2D 14127724 14130795 3071 False 837.45 1820 93.895 1 2457 4 chr2D.!!$F2 2456
2 TraesCS2A01G039900 chr2B 25844012 25849834 5822 False 870.00 1349 89.678 19 2490 3 chr2B.!!$F5 2471
3 TraesCS2A01G039900 chr2B 25932995 25933591 596 False 560.00 560 83.882 1704 2301 1 chr2B.!!$F2 597
4 TraesCS2A01G039900 chr5D 514995260 514995761 501 True 296.00 296 77.778 1021 1511 1 chr5D.!!$R2 490
5 TraesCS2A01G039900 chr5D 515024617 515025118 501 True 279.00 279 77.137 1021 1511 1 chr5D.!!$R3 490

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
646 3306 0.894835 AAATCATGGTTTCCGGCCAC 59.105 50.0 2.24 0.0 39.03 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2412 5844 0.234884 CTTCGTTTGGTTGACCGAGC 59.765 55.0 0.0 0.0 39.43 5.03 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
130 153 3.672295 GAGGAGCTGGTCTTGGCCG 62.672 68.421 6.83 0.00 0.00 6.13
225 254 4.626081 AGGTTTCGCTGGCGCAGT 62.626 61.111 10.83 0.00 39.59 4.40
263 292 1.354337 TTCGCTGCTCATTGCTCGAC 61.354 55.000 0.00 0.00 42.91 4.20
288 317 1.254284 AAGTCAGCGGAGAGTCTGGG 61.254 60.000 0.00 0.00 0.00 4.45
301 330 1.343465 AGTCTGGGTCCGTAGTTGTTG 59.657 52.381 0.00 0.00 0.00 3.33
317 363 6.165659 AGTTGTTGTTCATAGTACGAATGC 57.834 37.500 6.42 0.00 0.00 3.56
329 375 0.899717 ACGAATGCACCAAGCCCATT 60.900 50.000 0.00 0.00 44.83 3.16
412 538 2.545537 GGAGCCCTATCCTAAAACCG 57.454 55.000 0.00 0.00 36.35 4.44
413 539 1.071857 GGAGCCCTATCCTAAAACCGG 59.928 57.143 0.00 0.00 36.35 5.28
415 541 2.967887 GAGCCCTATCCTAAAACCGGTA 59.032 50.000 8.00 0.00 0.00 4.02
416 542 2.970640 AGCCCTATCCTAAAACCGGTAG 59.029 50.000 8.00 0.43 0.00 3.18
417 543 2.702478 GCCCTATCCTAAAACCGGTAGT 59.298 50.000 8.00 0.16 0.00 2.73
419 545 3.323115 CCCTATCCTAAAACCGGTAGTCC 59.677 52.174 8.00 0.00 0.00 3.85
421 547 4.406649 CCTATCCTAAAACCGGTAGTCCAA 59.593 45.833 8.00 0.00 0.00 3.53
422 548 3.967332 TCCTAAAACCGGTAGTCCAAG 57.033 47.619 8.00 0.00 0.00 3.61
424 550 4.415596 TCCTAAAACCGGTAGTCCAAGTA 58.584 43.478 8.00 0.00 0.00 2.24
425 551 4.463891 TCCTAAAACCGGTAGTCCAAGTAG 59.536 45.833 8.00 0.89 0.00 2.57
426 552 4.221482 CCTAAAACCGGTAGTCCAAGTAGT 59.779 45.833 8.00 0.00 0.00 2.73
427 553 3.949842 AAACCGGTAGTCCAAGTAGTC 57.050 47.619 8.00 0.00 0.00 2.59
428 554 1.844687 ACCGGTAGTCCAAGTAGTCC 58.155 55.000 4.49 0.00 0.00 3.85
429 555 1.076024 ACCGGTAGTCCAAGTAGTCCA 59.924 52.381 4.49 0.00 0.00 4.02
431 557 2.100916 CCGGTAGTCCAAGTAGTCCATG 59.899 54.545 0.00 0.00 0.00 3.66
432 558 2.758979 CGGTAGTCCAAGTAGTCCATGT 59.241 50.000 0.00 0.00 0.00 3.21
474 3036 5.945310 ACTATGTGGCATATTTCACCATCT 58.055 37.500 0.94 0.00 35.53 2.90
476 3038 6.936900 ACTATGTGGCATATTTCACCATCTAC 59.063 38.462 0.94 0.00 35.53 2.59
483 3046 1.200519 TTTCACCATCTACGGAGGGG 58.799 55.000 0.00 0.00 46.58 4.79
487 3050 1.557832 CACCATCTACGGAGGGGAAAA 59.442 52.381 12.56 0.00 46.58 2.29
502 3065 7.883311 CGGAGGGGAAAACATATAATAATCTGT 59.117 37.037 0.00 0.00 0.00 3.41
577 3198 8.897872 ATAAAATTCTTATATGAACCCGACGT 57.102 30.769 3.35 0.00 0.00 4.34
646 3306 0.894835 AAATCATGGTTTCCGGCCAC 59.105 50.000 2.24 0.00 39.03 5.01
863 4018 9.145442 TCCATTTGCATTGATAGGATTTGATAA 57.855 29.630 0.00 0.00 0.00 1.75
989 4146 6.895898 TCATAAAATACTACTAGCCGACGAG 58.104 40.000 0.00 0.00 0.00 4.18
1008 4165 5.141182 ACGAGGCCTGTATATATGATAGGG 58.859 45.833 12.00 2.48 0.00 3.53
1012 4169 6.377912 AGGCCTGTATATATGATAGGGAGAC 58.622 44.000 3.11 0.00 0.00 3.36
1032 4189 1.523758 GTCCTTCACCGAATGCAAGT 58.476 50.000 0.00 0.00 0.00 3.16
1033 4190 2.695359 GTCCTTCACCGAATGCAAGTA 58.305 47.619 0.00 0.00 0.00 2.24
1206 4363 3.012518 CGTTCAGAGCAAGGAATGGAAT 58.987 45.455 0.00 0.00 0.00 3.01
1309 4468 7.099764 TGGTGAGAACTCTAAATCAAGTGATC 58.900 38.462 3.51 0.00 32.75 2.92
1312 4471 5.665459 AGAACTCTAAATCAAGTGATCGGG 58.335 41.667 0.00 0.00 32.75 5.14
1315 4474 6.732896 ACTCTAAATCAAGTGATCGGGTAT 57.267 37.500 0.00 0.00 32.75 2.73
1316 4475 7.125792 ACTCTAAATCAAGTGATCGGGTATT 57.874 36.000 0.00 0.00 32.75 1.89
1576 4751 4.285517 AGCCATCACTGTCCAATAGATAGG 59.714 45.833 0.00 0.00 38.01 2.57
1687 4863 2.275134 TTGATGCTTGGCTCAAGTCA 57.725 45.000 14.04 12.56 42.77 3.41
1688 4864 2.275134 TGATGCTTGGCTCAAGTCAA 57.725 45.000 14.04 0.00 42.77 3.18
1689 4865 2.799017 TGATGCTTGGCTCAAGTCAAT 58.201 42.857 14.04 7.69 42.77 2.57
1691 4867 3.575256 TGATGCTTGGCTCAAGTCAATTT 59.425 39.130 14.04 2.30 42.77 1.82
1693 4869 2.957680 TGCTTGGCTCAAGTCAATTTCA 59.042 40.909 14.04 0.00 42.77 2.69
1694 4870 3.384146 TGCTTGGCTCAAGTCAATTTCAA 59.616 39.130 14.04 0.00 42.77 2.69
1695 4871 4.141981 TGCTTGGCTCAAGTCAATTTCAAA 60.142 37.500 14.04 0.00 42.77 2.69
1696 4872 4.810491 GCTTGGCTCAAGTCAATTTCAAAA 59.190 37.500 14.04 0.00 42.77 2.44
1699 4875 7.467675 GCTTGGCTCAAGTCAATTTCAAAATTT 60.468 33.333 14.04 0.00 42.77 1.82
1700 4876 8.954950 TTGGCTCAAGTCAATTTCAAAATTTA 57.045 26.923 0.00 0.00 36.52 1.40
1701 4877 8.954950 TGGCTCAAGTCAATTTCAAAATTTAA 57.045 26.923 0.00 0.00 36.52 1.52
1702 4878 9.044150 TGGCTCAAGTCAATTTCAAAATTTAAG 57.956 29.630 0.00 0.00 36.52 1.85
1723 5141 8.547967 TTAAGTACACAGGAATTCAGATGTTC 57.452 34.615 7.93 5.88 0.00 3.18
1731 5149 8.571336 CACAGGAATTCAGATGTTCTTAAAGTT 58.429 33.333 7.93 0.00 0.00 2.66
1857 5276 6.746745 TTTCGGTTGTGGAGTAATATTTCC 57.253 37.500 0.00 0.00 0.00 3.13
1860 5279 6.419791 TCGGTTGTGGAGTAATATTTCCAAT 58.580 36.000 9.93 0.00 44.61 3.16
1938 5357 6.948309 ACCTTGTGTTAGAATAATTTGAGGCT 59.052 34.615 0.00 0.00 0.00 4.58
1948 5367 2.225068 ATTTGAGGCTACCGTCGATG 57.775 50.000 0.00 0.00 0.00 3.84
1977 5396 3.734597 GCACAAGAAATCACACAAGCACA 60.735 43.478 0.00 0.00 0.00 4.57
1980 5399 4.158394 ACAAGAAATCACACAAGCACAAGT 59.842 37.500 0.00 0.00 0.00 3.16
1984 5403 7.042797 AGAAATCACACAAGCACAAGTAATT 57.957 32.000 0.00 0.00 0.00 1.40
1986 5405 8.796475 AGAAATCACACAAGCACAAGTAATTAT 58.204 29.630 0.00 0.00 0.00 1.28
1993 5412 5.293569 ACAAGCACAAGTAATTATACCGAGC 59.706 40.000 0.00 0.00 32.08 5.03
2012 5431 3.805207 AGCTTTGTTAACGAGGTTCACT 58.195 40.909 6.81 0.00 0.00 3.41
2018 5437 7.095523 GCTTTGTTAACGAGGTTCACTAACATA 60.096 37.037 6.81 0.00 37.34 2.29
2026 5445 6.127423 ACGAGGTTCACTAACATAGCTACATT 60.127 38.462 0.00 0.00 37.34 2.71
2043 5462 0.750850 ATTCCCGGGACATGACTACG 59.249 55.000 26.87 2.73 0.00 3.51
2053 5480 1.968493 ACATGACTACGGACACACCTT 59.032 47.619 0.00 0.00 36.31 3.50
2121 5548 3.303135 AAGACAGCGCTCCGACCA 61.303 61.111 7.13 0.00 0.00 4.02
2190 5618 2.025793 TCCCTCTCGTGATCTCTGTCTT 60.026 50.000 0.00 0.00 0.00 3.01
2191 5619 3.200165 TCCCTCTCGTGATCTCTGTCTTA 59.800 47.826 0.00 0.00 0.00 2.10
2192 5620 3.563808 CCCTCTCGTGATCTCTGTCTTAG 59.436 52.174 0.00 0.00 0.00 2.18
2193 5621 3.003275 CCTCTCGTGATCTCTGTCTTAGC 59.997 52.174 0.00 0.00 0.00 3.09
2234 5662 2.835764 AGTCTATTTGGCTACCCACGAA 59.164 45.455 0.00 0.00 41.97 3.85
2238 5666 0.759959 TTTGGCTACCCACGAAGACA 59.240 50.000 0.00 0.00 41.97 3.41
2254 5685 8.528643 CCACGAAGACAATATATAATAGTCCCA 58.471 37.037 0.00 0.00 0.00 4.37
2286 5717 1.955778 TCCGACTCAAACACCTAACGA 59.044 47.619 0.00 0.00 0.00 3.85
2288 5719 2.729882 CCGACTCAAACACCTAACGAAG 59.270 50.000 0.00 0.00 0.00 3.79
2309 5740 3.936453 AGCGCGAATTACAAATCCAACTA 59.064 39.130 12.10 0.00 0.00 2.24
2312 5743 6.259167 AGCGCGAATTACAAATCCAACTATAA 59.741 34.615 12.10 0.00 0.00 0.98
2327 5758 9.998106 ATCCAACTATAACACAATCTATACACC 57.002 33.333 0.00 0.00 0.00 4.16
2336 5767 8.420374 AACACAATCTATACACCGAATACTTG 57.580 34.615 0.00 0.00 0.00 3.16
2352 5783 9.205916 CCGAATACTTGACACATTATTTTAACG 57.794 33.333 0.00 0.00 0.00 3.18
2390 5822 4.408182 ACATGCGAACTAGCTCCTTTAT 57.592 40.909 0.00 0.00 38.13 1.40
2398 5830 3.182152 ACTAGCTCCTTTATGGTGGTGT 58.818 45.455 0.00 0.00 39.91 4.16
2412 5844 4.503910 TGGTGGTGTCTATTCGAATTGAG 58.496 43.478 20.26 11.41 0.00 3.02
2458 5890 1.495574 AGCTCCCACGTACTCTATCCT 59.504 52.381 0.00 0.00 0.00 3.24
2459 5891 1.609555 GCTCCCACGTACTCTATCCTG 59.390 57.143 0.00 0.00 0.00 3.86
2466 5898 5.535406 CCCACGTACTCTATCCTGAATTACT 59.465 44.000 0.00 0.00 0.00 2.24
2470 5902 7.644551 CACGTACTCTATCCTGAATTACTTGTC 59.355 40.741 0.00 0.00 0.00 3.18
2490 5922 8.861086 ACTTGTCGTAGAAATGGATGTATCTAT 58.139 33.333 0.00 0.00 39.69 1.98
2493 5925 9.292195 TGTCGTAGAAATGGATGTATCTATACA 57.708 33.333 5.33 5.33 42.88 2.29
2504 5936 5.441709 TGTATCTATACATGTCGCGGAAA 57.558 39.130 6.13 0.00 38.28 3.13
2505 5937 6.020971 TGTATCTATACATGTCGCGGAAAT 57.979 37.500 6.13 0.00 38.28 2.17
2506 5938 5.861787 TGTATCTATACATGTCGCGGAAATG 59.138 40.000 6.13 10.55 38.28 2.32
2507 5939 3.649073 TCTATACATGTCGCGGAAATGG 58.351 45.455 6.13 0.00 31.96 3.16
2508 5940 2.613026 ATACATGTCGCGGAAATGGA 57.387 45.000 6.13 5.03 31.96 3.41
2509 5941 2.613026 TACATGTCGCGGAAATGGAT 57.387 45.000 6.13 0.00 31.96 3.41
2510 5942 1.016627 ACATGTCGCGGAAATGGATG 58.983 50.000 6.13 1.04 31.96 3.51
2511 5943 1.016627 CATGTCGCGGAAATGGATGT 58.983 50.000 6.13 0.00 0.00 3.06
2512 5944 2.209273 CATGTCGCGGAAATGGATGTA 58.791 47.619 6.13 0.00 0.00 2.29
2513 5945 2.613026 TGTCGCGGAAATGGATGTAT 57.387 45.000 6.13 0.00 0.00 2.29
2514 5946 2.479837 TGTCGCGGAAATGGATGTATC 58.520 47.619 6.13 0.00 0.00 2.24
2515 5947 2.102420 TGTCGCGGAAATGGATGTATCT 59.898 45.455 6.13 0.00 0.00 1.98
2516 5948 3.319689 TGTCGCGGAAATGGATGTATCTA 59.680 43.478 6.13 0.00 0.00 1.98
2517 5949 3.921021 GTCGCGGAAATGGATGTATCTAG 59.079 47.826 6.13 0.00 0.00 2.43
2518 5950 3.824443 TCGCGGAAATGGATGTATCTAGA 59.176 43.478 6.13 0.00 0.00 2.43
2519 5951 4.279922 TCGCGGAAATGGATGTATCTAGAA 59.720 41.667 6.13 0.00 0.00 2.10
2520 5952 4.386049 CGCGGAAATGGATGTATCTAGAAC 59.614 45.833 0.00 0.00 0.00 3.01
2521 5953 5.542779 GCGGAAATGGATGTATCTAGAACT 58.457 41.667 0.00 0.00 0.00 3.01
2522 5954 6.569801 CGCGGAAATGGATGTATCTAGAACTA 60.570 42.308 0.00 0.00 0.00 2.24
2523 5955 7.152645 GCGGAAATGGATGTATCTAGAACTAA 58.847 38.462 0.00 0.00 0.00 2.24
2524 5956 7.656137 GCGGAAATGGATGTATCTAGAACTAAA 59.344 37.037 0.00 0.00 0.00 1.85
2525 5957 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
2541 5973 7.982224 AGAACTAAAAATACGTTTAGATGCCC 58.018 34.615 10.86 0.00 41.63 5.36
2542 5974 7.827729 AGAACTAAAAATACGTTTAGATGCCCT 59.172 33.333 10.86 0.18 41.63 5.19
2543 5975 7.316544 ACTAAAAATACGTTTAGATGCCCTG 57.683 36.000 10.86 0.00 41.63 4.45
2544 5976 7.107542 ACTAAAAATACGTTTAGATGCCCTGA 58.892 34.615 10.86 0.00 41.63 3.86
2545 5977 5.813080 AAAATACGTTTAGATGCCCTGAC 57.187 39.130 0.00 0.00 0.00 3.51
2546 5978 2.973694 TACGTTTAGATGCCCTGACC 57.026 50.000 0.00 0.00 0.00 4.02
2547 5979 0.981183 ACGTTTAGATGCCCTGACCA 59.019 50.000 0.00 0.00 0.00 4.02
2548 5980 1.559682 ACGTTTAGATGCCCTGACCAT 59.440 47.619 0.00 0.00 0.00 3.55
2549 5981 2.769663 ACGTTTAGATGCCCTGACCATA 59.230 45.455 0.00 0.00 0.00 2.74
2550 5982 3.181465 ACGTTTAGATGCCCTGACCATAG 60.181 47.826 0.00 0.00 0.00 2.23
2551 5983 3.744660 GTTTAGATGCCCTGACCATAGG 58.255 50.000 0.00 0.00 37.59 2.57
2558 5990 2.221918 CCTGACCATAGGGGACACC 58.778 63.158 0.00 0.00 41.15 4.16
2559 5991 0.620410 CCTGACCATAGGGGACACCA 60.620 60.000 0.00 0.00 43.89 4.17
2560 5992 1.285280 CTGACCATAGGGGACACCAA 58.715 55.000 0.00 0.00 43.89 3.67
2561 5993 1.633432 CTGACCATAGGGGACACCAAA 59.367 52.381 0.00 0.00 43.89 3.28
2562 5994 1.353022 TGACCATAGGGGACACCAAAC 59.647 52.381 0.00 0.00 43.89 2.93
2563 5995 1.353022 GACCATAGGGGACACCAAACA 59.647 52.381 0.00 0.00 43.89 2.83
2564 5996 1.074889 ACCATAGGGGACACCAAACAC 59.925 52.381 0.00 0.00 43.89 3.32
2565 5997 1.074727 CCATAGGGGACACCAAACACA 59.925 52.381 0.00 0.00 43.89 3.72
2566 5998 2.489985 CCATAGGGGACACCAAACACAA 60.490 50.000 0.00 0.00 43.89 3.33
2567 5999 3.430453 CATAGGGGACACCAAACACAAT 58.570 45.455 0.00 0.00 43.89 2.71
2568 6000 2.470057 AGGGGACACCAAACACAATT 57.530 45.000 0.00 0.00 43.89 2.32
2569 6001 3.603965 AGGGGACACCAAACACAATTA 57.396 42.857 0.00 0.00 43.89 1.40
2570 6002 4.126520 AGGGGACACCAAACACAATTAT 57.873 40.909 0.00 0.00 43.89 1.28
2571 6003 3.831911 AGGGGACACCAAACACAATTATG 59.168 43.478 0.00 0.00 43.89 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 153 1.139058 ACCACAACCATATCCTCGCTC 59.861 52.381 0.00 0.00 0.00 5.03
263 292 0.108898 CTCTCCGCTGACTTCCACTG 60.109 60.000 0.00 0.00 0.00 3.66
288 317 5.284660 CGTACTATGAACAACAACTACGGAC 59.715 44.000 0.00 0.00 31.58 4.79
301 330 4.494199 GCTTGGTGCATTCGTACTATGAAC 60.494 45.833 8.52 7.84 42.31 3.18
317 363 4.780815 TGAAGTCTATAATGGGCTTGGTG 58.219 43.478 0.00 0.00 0.00 4.17
407 533 2.564504 GGACTACTTGGACTACCGGTTT 59.435 50.000 15.04 0.00 39.42 3.27
408 534 2.174360 GGACTACTTGGACTACCGGTT 58.826 52.381 15.04 0.00 39.42 4.44
409 535 1.076024 TGGACTACTTGGACTACCGGT 59.924 52.381 13.98 13.98 39.42 5.28
410 536 1.843368 TGGACTACTTGGACTACCGG 58.157 55.000 0.00 0.00 39.42 5.28
412 538 5.927281 TTACATGGACTACTTGGACTACC 57.073 43.478 0.00 0.00 0.00 3.18
413 539 6.812160 CAGTTTACATGGACTACTTGGACTAC 59.188 42.308 0.00 0.00 0.00 2.73
415 541 5.280011 CCAGTTTACATGGACTACTTGGACT 60.280 44.000 0.00 0.00 40.51 3.85
416 542 4.935808 CCAGTTTACATGGACTACTTGGAC 59.064 45.833 0.00 0.00 40.51 4.02
417 543 4.595781 ACCAGTTTACATGGACTACTTGGA 59.404 41.667 0.00 0.00 40.51 3.53
419 545 5.995282 TCAACCAGTTTACATGGACTACTTG 59.005 40.000 0.00 3.83 40.51 3.16
421 547 5.548406 GTCAACCAGTTTACATGGACTACT 58.452 41.667 0.00 0.00 40.51 2.57
422 548 4.387862 CGTCAACCAGTTTACATGGACTAC 59.612 45.833 0.00 0.00 40.51 2.73
424 550 3.399330 CGTCAACCAGTTTACATGGACT 58.601 45.455 0.00 0.00 40.51 3.85
425 551 2.482721 CCGTCAACCAGTTTACATGGAC 59.517 50.000 0.00 0.00 40.51 4.02
426 552 2.105134 ACCGTCAACCAGTTTACATGGA 59.895 45.455 0.00 0.00 40.51 3.41
427 553 2.500229 ACCGTCAACCAGTTTACATGG 58.500 47.619 0.00 0.00 43.87 3.66
428 554 5.676532 TTTACCGTCAACCAGTTTACATG 57.323 39.130 0.00 0.00 0.00 3.21
429 555 5.824097 AGTTTTACCGTCAACCAGTTTACAT 59.176 36.000 0.00 0.00 0.00 2.29
431 557 5.739752 AGTTTTACCGTCAACCAGTTTAC 57.260 39.130 0.00 0.00 0.00 2.01
432 558 6.991531 ACATAGTTTTACCGTCAACCAGTTTA 59.008 34.615 0.00 0.00 0.00 2.01
474 3036 9.108111 AGATTATTATATGTTTTCCCCTCCGTA 57.892 33.333 0.00 0.00 0.00 4.02
476 3038 7.883311 ACAGATTATTATATGTTTTCCCCTCCG 59.117 37.037 0.00 0.00 32.46 4.63
576 3197 9.691362 ACATTGTAAATGGAGTTTGAATAACAC 57.309 29.630 5.08 0.00 0.00 3.32
577 3198 9.906660 GACATTGTAAATGGAGTTTGAATAACA 57.093 29.630 5.08 0.00 0.00 2.41
646 3306 5.980715 ACATTTAAAACGTGCTAACAAAGGG 59.019 36.000 0.00 0.00 0.00 3.95
796 3948 6.419484 TCCTTCTTCAAGATGTAGTGAACA 57.581 37.500 0.00 0.00 43.86 3.18
797 3949 7.730364 TTTCCTTCTTCAAGATGTAGTGAAC 57.270 36.000 0.00 0.00 30.73 3.18
805 3957 7.083858 TGCGTTTTATTTCCTTCTTCAAGATG 58.916 34.615 0.00 0.00 0.00 2.90
827 3982 1.026584 TGCAAATGGATGAGGATGCG 58.973 50.000 0.00 0.00 36.62 4.73
863 4018 7.120579 TCCGAAGTGCAACATTAATTTGTAGAT 59.879 33.333 0.00 1.77 41.43 1.98
884 4039 5.726397 TCCTTTAAATGAGACGAATCCGAA 58.274 37.500 0.00 0.00 39.50 4.30
983 4140 4.902443 ATCATATATACAGGCCTCGTCG 57.098 45.455 0.00 0.00 0.00 5.12
989 4146 5.241949 CGTCTCCCTATCATATATACAGGCC 59.758 48.000 0.00 0.00 0.00 5.19
994 4151 7.774157 TGAAGGACGTCTCCCTATCATATATAC 59.226 40.741 16.46 0.00 37.25 1.47
1008 4165 1.630148 CATTCGGTGAAGGACGTCTC 58.370 55.000 16.46 6.69 0.00 3.36
1012 4169 0.443869 CTTGCATTCGGTGAAGGACG 59.556 55.000 0.00 0.00 0.00 4.79
1032 4189 7.782049 ACAGTAGTCGATTCCTCAATTGATTA 58.218 34.615 8.96 0.00 35.26 1.75
1033 4190 6.644347 ACAGTAGTCGATTCCTCAATTGATT 58.356 36.000 8.96 0.00 35.26 2.57
1188 4345 3.614092 GACATTCCATTCCTTGCTCTGA 58.386 45.455 0.00 0.00 0.00 3.27
1191 4348 1.672881 CCGACATTCCATTCCTTGCTC 59.327 52.381 0.00 0.00 0.00 4.26
1340 4511 6.094719 CACTGCATGCATTAGTTAAACACAT 58.905 36.000 22.97 0.00 0.00 3.21
1442 4617 3.593794 GAGCGGTAGGTCGGCGAT 61.594 66.667 14.79 0.00 45.16 4.58
1576 4751 7.544622 TGTACGTATCATAAGAGGGATTATGC 58.455 38.462 0.00 0.00 41.12 3.14
1695 4871 9.520515 ACATCTGAATTCCTGTGTACTTAAATT 57.479 29.630 2.27 0.00 0.00 1.82
1696 4872 9.520515 AACATCTGAATTCCTGTGTACTTAAAT 57.479 29.630 2.27 0.00 0.00 1.40
1699 4875 7.907389 AGAACATCTGAATTCCTGTGTACTTA 58.093 34.615 2.27 0.00 0.00 2.24
1700 4876 6.773638 AGAACATCTGAATTCCTGTGTACTT 58.226 36.000 2.27 0.00 0.00 2.24
1701 4877 6.365970 AGAACATCTGAATTCCTGTGTACT 57.634 37.500 2.27 3.34 0.00 2.73
1702 4878 8.547967 TTAAGAACATCTGAATTCCTGTGTAC 57.452 34.615 2.27 0.00 0.00 2.90
1755 5173 6.468956 CCGAAACATTCACCTAAAATTCGATG 59.531 38.462 6.19 0.00 0.00 3.84
1756 5174 6.551736 CCGAAACATTCACCTAAAATTCGAT 58.448 36.000 6.19 0.00 0.00 3.59
1758 5176 4.557301 GCCGAAACATTCACCTAAAATTCG 59.443 41.667 0.00 0.00 0.00 3.34
1765 5183 0.988832 AGGGCCGAAACATTCACCTA 59.011 50.000 0.00 0.00 0.00 3.08
1829 5247 1.508632 ACTCCACAACCGAAATCACG 58.491 50.000 0.00 0.00 0.00 4.35
1932 5351 2.805546 GCATCGACGGTAGCCTCA 59.194 61.111 0.00 0.00 0.00 3.86
1948 5367 0.790207 TGATTTCTTGTGCTCGACGC 59.210 50.000 0.00 0.58 39.77 5.19
1956 5375 4.031418 TGTGCTTGTGTGATTTCTTGTG 57.969 40.909 0.00 0.00 0.00 3.33
1962 5381 9.840427 GTATAATTACTTGTGCTTGTGTGATTT 57.160 29.630 0.00 0.00 0.00 2.17
1977 5396 8.598075 CGTTAACAAAGCTCGGTATAATTACTT 58.402 33.333 6.39 0.00 0.00 2.24
1980 5399 7.436080 CCTCGTTAACAAAGCTCGGTATAATTA 59.564 37.037 6.39 0.00 0.00 1.40
1984 5403 4.158394 ACCTCGTTAACAAAGCTCGGTATA 59.842 41.667 6.39 0.00 0.00 1.47
1986 5405 2.297033 ACCTCGTTAACAAAGCTCGGTA 59.703 45.455 6.39 0.00 0.00 4.02
1993 5412 6.592798 TGTTAGTGAACCTCGTTAACAAAG 57.407 37.500 6.39 2.34 32.92 2.77
2012 5431 3.322828 GTCCCGGGAATGTAGCTATGTTA 59.677 47.826 28.84 0.00 0.00 2.41
2018 5437 0.469917 CATGTCCCGGGAATGTAGCT 59.530 55.000 28.84 1.46 0.00 3.32
2026 5445 1.755395 CCGTAGTCATGTCCCGGGA 60.755 63.158 22.63 22.63 35.11 5.14
2043 5462 1.339727 GGTACATGGGAAGGTGTGTCC 60.340 57.143 0.00 0.00 0.00 4.02
2045 5464 1.440618 TGGTACATGGGAAGGTGTGT 58.559 50.000 0.00 0.00 0.00 3.72
2104 5531 3.303135 TGGTCGGAGCGCTGTCTT 61.303 61.111 18.48 0.00 0.00 3.01
2190 5618 9.669887 GACTAGACATAAGTTATAGGCTAGCTA 57.330 37.037 22.34 5.54 0.00 3.32
2191 5619 8.387813 AGACTAGACATAAGTTATAGGCTAGCT 58.612 37.037 22.34 18.90 35.25 3.32
2192 5620 8.570068 AGACTAGACATAAGTTATAGGCTAGC 57.430 38.462 22.34 6.04 35.25 3.42
2254 5685 2.244695 TGAGTCGGACATGTGTAACCT 58.755 47.619 1.15 0.00 34.36 3.50
2286 5717 3.190535 AGTTGGATTTGTAATTCGCGCTT 59.809 39.130 5.56 0.00 0.00 4.68
2288 5719 3.131240 AGTTGGATTTGTAATTCGCGC 57.869 42.857 0.00 0.00 0.00 6.86
2312 5743 7.705325 GTCAAGTATTCGGTGTATAGATTGTGT 59.295 37.037 0.00 0.00 0.00 3.72
2318 5749 6.762702 TGTGTCAAGTATTCGGTGTATAGA 57.237 37.500 0.00 0.00 0.00 1.98
2326 5757 9.205916 CGTTAAAATAATGTGTCAAGTATTCGG 57.794 33.333 0.00 0.00 0.00 4.30
2327 5758 8.721476 GCGTTAAAATAATGTGTCAAGTATTCG 58.279 33.333 0.00 0.00 0.00 3.34
2335 5766 6.561737 TCAAGGCGTTAAAATAATGTGTCA 57.438 33.333 0.00 0.00 0.00 3.58
2336 5767 6.858993 TGTTCAAGGCGTTAAAATAATGTGTC 59.141 34.615 0.00 0.00 0.00 3.67
2352 5783 4.176271 GCATGTTCCTTAATGTTCAAGGC 58.824 43.478 0.00 0.00 42.04 4.35
2390 5822 4.503910 CTCAATTCGAATAGACACCACCA 58.496 43.478 11.83 0.00 0.00 4.17
2398 5830 3.380320 TGACCGAGCTCAATTCGAATAGA 59.620 43.478 15.40 0.00 40.36 1.98
2412 5844 0.234884 CTTCGTTTGGTTGACCGAGC 59.765 55.000 0.00 0.00 39.43 5.03
2458 5890 7.822334 ACATCCATTTCTACGACAAGTAATTCA 59.178 33.333 0.00 0.00 34.45 2.57
2459 5891 8.197988 ACATCCATTTCTACGACAAGTAATTC 57.802 34.615 0.00 0.00 34.45 2.17
2490 5922 2.209273 CATCCATTTCCGCGACATGTA 58.791 47.619 8.23 0.00 0.00 2.29
2491 5923 1.016627 CATCCATTTCCGCGACATGT 58.983 50.000 8.23 0.00 0.00 3.21
2492 5924 1.016627 ACATCCATTTCCGCGACATG 58.983 50.000 8.23 6.41 0.00 3.21
2493 5925 2.613026 TACATCCATTTCCGCGACAT 57.387 45.000 8.23 0.00 0.00 3.06
2494 5926 2.102420 AGATACATCCATTTCCGCGACA 59.898 45.455 8.23 0.00 0.00 4.35
2495 5927 2.755650 AGATACATCCATTTCCGCGAC 58.244 47.619 8.23 0.00 0.00 5.19
2496 5928 3.824443 TCTAGATACATCCATTTCCGCGA 59.176 43.478 8.23 0.00 0.00 5.87
2497 5929 4.174411 TCTAGATACATCCATTTCCGCG 57.826 45.455 0.00 0.00 0.00 6.46
2498 5930 5.542779 AGTTCTAGATACATCCATTTCCGC 58.457 41.667 0.00 0.00 0.00 5.54
2499 5931 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
2515 5947 9.101655 GGGCATCTAAACGTATTTTTAGTTCTA 57.898 33.333 5.01 0.00 39.27 2.10
2516 5948 7.827729 AGGGCATCTAAACGTATTTTTAGTTCT 59.172 33.333 5.01 0.00 39.27 3.01
2517 5949 7.908601 CAGGGCATCTAAACGTATTTTTAGTTC 59.091 37.037 5.01 0.00 39.27 3.01
2518 5950 7.608761 TCAGGGCATCTAAACGTATTTTTAGTT 59.391 33.333 5.01 0.00 39.27 2.24
2519 5951 7.065443 GTCAGGGCATCTAAACGTATTTTTAGT 59.935 37.037 5.01 0.00 39.27 2.24
2520 5952 7.407337 GTCAGGGCATCTAAACGTATTTTTAG 58.593 38.462 0.00 0.00 39.50 1.85
2521 5953 6.316890 GGTCAGGGCATCTAAACGTATTTTTA 59.683 38.462 0.00 0.00 0.00 1.52
2522 5954 5.124936 GGTCAGGGCATCTAAACGTATTTTT 59.875 40.000 0.00 0.00 0.00 1.94
2523 5955 4.638865 GGTCAGGGCATCTAAACGTATTTT 59.361 41.667 0.00 0.00 0.00 1.82
2524 5956 4.196971 GGTCAGGGCATCTAAACGTATTT 58.803 43.478 0.00 0.00 0.00 1.40
2525 5957 3.199071 TGGTCAGGGCATCTAAACGTATT 59.801 43.478 0.00 0.00 0.00 1.89
2526 5958 2.769663 TGGTCAGGGCATCTAAACGTAT 59.230 45.455 0.00 0.00 0.00 3.06
2527 5959 2.181125 TGGTCAGGGCATCTAAACGTA 58.819 47.619 0.00 0.00 0.00 3.57
2528 5960 0.981183 TGGTCAGGGCATCTAAACGT 59.019 50.000 0.00 0.00 0.00 3.99
2529 5961 2.332063 ATGGTCAGGGCATCTAAACG 57.668 50.000 0.00 0.00 0.00 3.60
2530 5962 3.744660 CCTATGGTCAGGGCATCTAAAC 58.255 50.000 0.00 0.00 31.47 2.01
2540 5972 0.620410 TGGTGTCCCCTATGGTCAGG 60.620 60.000 0.00 0.00 32.55 3.86
2541 5973 1.285280 TTGGTGTCCCCTATGGTCAG 58.715 55.000 0.00 0.00 32.55 3.51
2542 5974 1.353022 GTTTGGTGTCCCCTATGGTCA 59.647 52.381 0.00 0.00 34.77 4.02
2543 5975 1.353022 TGTTTGGTGTCCCCTATGGTC 59.647 52.381 0.00 0.00 34.77 4.02
2544 5976 1.074889 GTGTTTGGTGTCCCCTATGGT 59.925 52.381 0.00 0.00 34.77 3.55
2545 5977 1.074727 TGTGTTTGGTGTCCCCTATGG 59.925 52.381 0.00 0.00 0.00 2.74
2546 5978 2.577606 TGTGTTTGGTGTCCCCTATG 57.422 50.000 0.00 0.00 0.00 2.23
2547 5979 3.825908 ATTGTGTTTGGTGTCCCCTAT 57.174 42.857 0.00 0.00 0.00 2.57
2548 5980 3.603965 AATTGTGTTTGGTGTCCCCTA 57.396 42.857 0.00 0.00 0.00 3.53
2549 5981 2.470057 AATTGTGTTTGGTGTCCCCT 57.530 45.000 0.00 0.00 0.00 4.79
2550 5982 4.186856 CATAATTGTGTTTGGTGTCCCC 57.813 45.455 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.