Multiple sequence alignment - TraesCS1B01G288000

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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 TraesCS1B01G288000 chr1B 100.000 5082 0 0 1 5082 501334579 501329498 0.000000e+00 9385.0
1 TraesCS1B01G288000 chr1D 93.856 3239 115 41 1 3196 375940508 375937311 0.000000e+00 4802.0
2 TraesCS1B01G288000 chr1D 95.010 982 15 9 3376 4331 375934866 375933893 0.000000e+00 1511.0
3 TraesCS1B01G288000 chr1D 94.545 165 6 3 3218 3380 375937320 375937157 8.450000e-63 252.0
4 TraesCS1B01G288000 chr1A 94.983 2412 86 16 820 3216 474644161 474641770 0.000000e+00 3751.0
5 TraesCS1B01G288000 chr1A 93.424 1034 25 11 3211 4201 474641680 474640647 0.000000e+00 1493.0
6 TraesCS1B01G288000 chr1A 98.808 755 9 0 4322 5076 447065015 447065769 0.000000e+00 1345.0
7 TraesCS1B01G288000 chr1A 92.814 167 3 2 4168 4333 474640726 474640568 3.060000e-57 233.0
8 TraesCS1B01G288000 chr5B 99.331 747 5 0 4330 5076 48316269 48315523 0.000000e+00 1352.0
9 TraesCS1B01G288000 chr4B 99.331 747 5 0 4330 5076 5372869 5373615 0.000000e+00 1352.0
10 TraesCS1B01G288000 chr4A 99.331 747 5 0 4330 5076 212687343 212686597 0.000000e+00 1352.0
11 TraesCS1B01G288000 chr3B 99.199 749 6 0 4328 5076 547671950 547671202 0.000000e+00 1351.0
12 TraesCS1B01G288000 chr3B 99.070 753 6 1 4327 5078 556050965 556051717 0.000000e+00 1351.0
13 TraesCS1B01G288000 chr3B 99.198 748 6 0 4329 5076 481626696 481625949 0.000000e+00 1349.0
14 TraesCS1B01G288000 chr2A 99.199 749 6 0 4330 5078 438396960 438397708 0.000000e+00 1351.0
15 TraesCS1B01G288000 chr2A 82.210 742 114 15 1921 2652 717171802 717171069 1.550000e-174 623.0
16 TraesCS1B01G288000 chr2A 90.196 357 35 0 1019 1375 717173053 717172697 2.770000e-127 466.0
17 TraesCS1B01G288000 chr2A 90.260 154 15 0 1697 1850 717172505 717172352 8.630000e-48 202.0
18 TraesCS1B01G288000 chr6B 98.938 753 7 1 4324 5076 339383033 339383784 0.000000e+00 1345.0
19 TraesCS1B01G288000 chr2D 83.019 742 107 13 1921 2652 579520059 579519327 0.000000e+00 654.0
20 TraesCS1B01G288000 chr2D 86.160 513 68 3 3569 4080 579518653 579518143 7.440000e-153 551.0
21 TraesCS1B01G288000 chr2D 90.659 364 34 0 1019 1382 579521510 579521147 7.650000e-133 484.0
22 TraesCS1B01G288000 chr2D 91.163 215 19 0 2759 2973 579519180 579518966 4.980000e-75 292.0
23 TraesCS1B01G288000 chr2D 80.342 351 55 12 1508 1853 579521060 579520719 2.350000e-63 254.0
24 TraesCS1B01G288000 chr2B 81.635 746 113 17 1921 2652 697442970 697442235 9.420000e-167 597.0
25 TraesCS1B01G288000 chr2B 83.815 519 74 8 3569 4080 697144543 697144028 7.650000e-133 484.0
26 TraesCS1B01G288000 chr2B 83.789 512 82 1 3569 4080 697401331 697400821 7.650000e-133 484.0
27 TraesCS1B01G288000 chr2B 83.591 518 77 7 3569 4080 697258797 697258282 3.560000e-131 479.0
28 TraesCS1B01G288000 chr2B 83.430 519 74 10 3569 4080 697187069 697186556 5.960000e-129 472.0
29 TraesCS1B01G288000 chr2B 83.077 520 77 8 3569 4080 697362099 697361583 3.580000e-126 462.0
30 TraesCS1B01G288000 chr2B 83.077 520 77 8 3569 4080 697385219 697384703 3.580000e-126 462.0
31 TraesCS1B01G288000 chr2B 86.389 360 49 0 1019 1378 697152225 697151866 1.330000e-105 394.0
32 TraesCS1B01G288000 chr2B 86.111 360 48 1 1019 1378 697392910 697392553 2.220000e-103 387.0
33 TraesCS1B01G288000 chr2B 85.833 360 51 0 1019 1378 697332836 697332477 2.870000e-102 383.0
34 TraesCS1B01G288000 chr2B 85.556 360 52 0 1019 1378 697285395 697285036 1.340000e-100 377.0
35 TraesCS1B01G288000 chr2B 85.000 360 52 1 1019 1378 697351150 697350793 1.040000e-96 364.0
36 TraesCS1B01G288000 chr2B 89.815 216 21 1 2759 2974 697442091 697441877 5.010000e-70 276.0
37 TraesCS1B01G288000 chr2B 79.827 347 57 8 1508 1854 697444045 697443712 1.830000e-59 241.0
38 TraesCS1B01G288000 chr7A 100.000 30 0 0 622 651 483946121 483946092 7.110000e-04 56.5
39 TraesCS1B01G288000 chr6A 96.970 33 1 0 619 651 148528413 148528445 7.110000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G288000 chr1B 501329498 501334579 5081 True 9385.000000 9385 100.000000 1 5082 1 chr1B.!!$R1 5081
1 TraesCS1B01G288000 chr1D 375933893 375940508 6615 True 2188.333333 4802 94.470333 1 4331 3 chr1D.!!$R1 4330
2 TraesCS1B01G288000 chr1A 474640568 474644161 3593 True 1825.666667 3751 93.740333 820 4333 3 chr1A.!!$R1 3513
3 TraesCS1B01G288000 chr1A 447065015 447065769 754 False 1345.000000 1345 98.808000 4322 5076 1 chr1A.!!$F1 754
4 TraesCS1B01G288000 chr5B 48315523 48316269 746 True 1352.000000 1352 99.331000 4330 5076 1 chr5B.!!$R1 746
5 TraesCS1B01G288000 chr4B 5372869 5373615 746 False 1352.000000 1352 99.331000 4330 5076 1 chr4B.!!$F1 746
6 TraesCS1B01G288000 chr4A 212686597 212687343 746 True 1352.000000 1352 99.331000 4330 5076 1 chr4A.!!$R1 746
7 TraesCS1B01G288000 chr3B 547671202 547671950 748 True 1351.000000 1351 99.199000 4328 5076 1 chr3B.!!$R2 748
8 TraesCS1B01G288000 chr3B 556050965 556051717 752 False 1351.000000 1351 99.070000 4327 5078 1 chr3B.!!$F1 751
9 TraesCS1B01G288000 chr3B 481625949 481626696 747 True 1349.000000 1349 99.198000 4329 5076 1 chr3B.!!$R1 747
10 TraesCS1B01G288000 chr2A 438396960 438397708 748 False 1351.000000 1351 99.199000 4330 5078 1 chr2A.!!$F1 748
11 TraesCS1B01G288000 chr2A 717171069 717173053 1984 True 430.333333 623 87.555333 1019 2652 3 chr2A.!!$R1 1633
12 TraesCS1B01G288000 chr6B 339383033 339383784 751 False 1345.000000 1345 98.938000 4324 5076 1 chr6B.!!$F1 752
13 TraesCS1B01G288000 chr2D 579518143 579521510 3367 True 447.000000 654 86.268600 1019 4080 5 chr2D.!!$R1 3061
14 TraesCS1B01G288000 chr2B 697144028 697144543 515 True 484.000000 484 83.815000 3569 4080 1 chr2B.!!$R1 511
15 TraesCS1B01G288000 chr2B 697400821 697401331 510 True 484.000000 484 83.789000 3569 4080 1 chr2B.!!$R11 511
16 TraesCS1B01G288000 chr2B 697258282 697258797 515 True 479.000000 479 83.591000 3569 4080 1 chr2B.!!$R4 511
17 TraesCS1B01G288000 chr2B 697186556 697187069 513 True 472.000000 472 83.430000 3569 4080 1 chr2B.!!$R3 511
18 TraesCS1B01G288000 chr2B 697361583 697362099 516 True 462.000000 462 83.077000 3569 4080 1 chr2B.!!$R8 511
19 TraesCS1B01G288000 chr2B 697384703 697385219 516 True 462.000000 462 83.077000 3569 4080 1 chr2B.!!$R9 511
20 TraesCS1B01G288000 chr2B 697441877 697444045 2168 True 371.333333 597 83.759000 1508 2974 3 chr2B.!!$R12 1466

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
41 42 0.249657 GACGATGCTTCCTGCTAGGG 60.250 60.0 0.00 0.0 43.37 3.53 F
1455 1492 0.250513 CGCTCTGTTTTAGGCCTCCT 59.749 55.0 9.68 0.0 37.71 3.69 F
2016 2889 0.041535 AGGGGAATGCCATTTGCTCA 59.958 50.0 0.00 0.0 42.00 4.26 F
3459 6910 0.390209 GCCATGCATCACCGCTTTTT 60.390 50.0 0.00 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1503 0.179067 TGCGGTTCGTGAACTCCTTT 60.179 50.000 12.1 0.0 40.94 3.11 R
3252 4383 3.815809 TGACTTTCAGTACAAACCAGGG 58.184 45.455 0.0 0.0 0.00 4.45 R
3520 6971 2.689983 GGTCCAGGGTGCAGATTTTATG 59.310 50.000 0.0 0.0 0.00 1.90 R
4570 8029 1.070445 GCTCCAGTGCATAGCGGAT 59.930 57.895 0.0 0.0 0.00 4.18 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
34 35 0.892755 TTACACCGACGATGCTTCCT 59.107 50.000 0.00 0.00 0.00 3.36
41 42 0.249657 GACGATGCTTCCTGCTAGGG 60.250 60.000 0.00 0.00 43.37 3.53
64 65 2.298729 GTCTCTCCTGCTATCATGTCCC 59.701 54.545 0.00 0.00 0.00 4.46
106 107 1.003839 GTGCTTGGGTCGTGATGGA 60.004 57.895 0.00 0.00 0.00 3.41
132 133 5.657470 TTCTCGTGAATCAACTGTCTTTG 57.343 39.130 0.00 0.00 0.00 2.77
159 160 2.368875 TCTCAGAGTGACCCCTTGTTTC 59.631 50.000 0.00 0.00 0.00 2.78
161 162 0.771755 AGAGTGACCCCTTGTTTCCC 59.228 55.000 0.00 0.00 0.00 3.97
162 163 0.251209 GAGTGACCCCTTGTTTCCCC 60.251 60.000 0.00 0.00 0.00 4.81
218 219 6.400940 CGCATGTGTGTTTCTTTTGTCTTTTT 60.401 34.615 0.00 0.00 0.00 1.94
316 326 6.875972 ATATCCGCATAGGGATTTACTCTT 57.124 37.500 0.00 0.00 44.44 2.85
358 370 2.945447 TGCTTGCCATGCTTATTCAC 57.055 45.000 4.10 0.00 0.00 3.18
360 372 2.761767 TGCTTGCCATGCTTATTCACAT 59.238 40.909 4.10 0.00 0.00 3.21
365 377 6.313411 GCTTGCCATGCTTATTCACATTTTTA 59.687 34.615 0.00 0.00 0.00 1.52
388 400 2.734079 TCAAAATGGAAAAATTCGGCGC 59.266 40.909 0.00 0.00 0.00 6.53
389 401 2.736192 CAAAATGGAAAAATTCGGCGCT 59.264 40.909 7.64 0.00 0.00 5.92
407 419 2.359230 GGACTCAGGCCAGCACAC 60.359 66.667 5.01 0.00 0.00 3.82
409 421 3.170672 ACTCAGGCCAGCACACCA 61.171 61.111 5.01 0.00 0.00 4.17
431 443 6.040955 ACCACACACACGAGAGAATATCATAT 59.959 38.462 0.00 0.00 0.00 1.78
453 465 5.012328 TGGAAACAAGTTGCGGTAAAAAT 57.988 34.783 1.81 0.00 37.44 1.82
460 472 8.649973 AACAAGTTGCGGTAAAAATAAATGAA 57.350 26.923 1.81 0.00 0.00 2.57
461 473 8.649973 ACAAGTTGCGGTAAAAATAAATGAAA 57.350 26.923 1.81 0.00 0.00 2.69
462 474 9.099454 ACAAGTTGCGGTAAAAATAAATGAAAA 57.901 25.926 1.81 0.00 0.00 2.29
463 475 9.364110 CAAGTTGCGGTAAAAATAAATGAAAAC 57.636 29.630 0.00 0.00 0.00 2.43
464 476 8.880878 AGTTGCGGTAAAAATAAATGAAAACT 57.119 26.923 0.00 0.00 0.00 2.66
465 477 9.968870 AGTTGCGGTAAAAATAAATGAAAACTA 57.031 25.926 0.00 0.00 0.00 2.24
549 561 7.538303 AACACATGAAATTCCAAGTTCAAAC 57.462 32.000 6.30 0.00 44.71 2.93
551 563 7.274447 ACACATGAAATTCCAAGTTCAAACAT 58.726 30.769 6.30 0.00 44.71 2.71
569 581 8.329066 TCAAACATGTGTTAACATAACAAACG 57.671 30.769 12.26 1.90 45.50 3.60
644 656 2.289444 ACGATCTTATATTGTGGGGCGG 60.289 50.000 0.00 0.00 0.00 6.13
665 693 4.383118 CGGAGGGAGAACAGTAAATGTCAT 60.383 45.833 0.00 0.00 43.00 3.06
758 786 8.560374 GCTAATTGAATATCACCCTCTTAACAC 58.440 37.037 0.00 0.00 0.00 3.32
803 832 5.065988 ACGTGGTCTTTGTATTATCATTGCC 59.934 40.000 0.00 0.00 0.00 4.52
808 840 8.538701 TGGTCTTTGTATTATCATTGCCATTTT 58.461 29.630 0.00 0.00 0.00 1.82
867 899 1.978361 ATTCTCTCCTGGAAAGGCCT 58.022 50.000 0.00 0.00 37.63 5.19
871 903 0.768221 TCTCCTGGAAAGGCCTGTGT 60.768 55.000 5.69 0.00 37.63 3.72
884 918 2.890945 GGCCTGTGTATTTGAAACCTGT 59.109 45.455 0.00 0.00 0.00 4.00
905 939 0.458543 ATCTGTAAGTGGCGCGAGTG 60.459 55.000 12.10 0.00 33.76 3.51
906 940 1.080772 CTGTAAGTGGCGCGAGTGA 60.081 57.895 12.10 0.00 0.00 3.41
907 941 1.073216 CTGTAAGTGGCGCGAGTGAG 61.073 60.000 12.10 0.00 0.00 3.51
908 942 1.211969 GTAAGTGGCGCGAGTGAGA 59.788 57.895 12.10 0.00 0.00 3.27
909 943 0.798771 GTAAGTGGCGCGAGTGAGAG 60.799 60.000 12.10 0.00 0.00 3.20
910 944 0.958876 TAAGTGGCGCGAGTGAGAGA 60.959 55.000 12.10 0.00 0.00 3.10
911 945 2.479412 AAGTGGCGCGAGTGAGAGAC 62.479 60.000 12.10 0.00 0.00 3.36
912 946 4.103103 TGGCGCGAGTGAGAGACG 62.103 66.667 12.10 0.00 0.00 4.18
945 979 1.374252 GAGCCTCGTTTTCCTCGCA 60.374 57.895 0.00 0.00 0.00 5.10
1407 1444 4.632251 ACTCACCTCTCGCTATATATGACG 59.368 45.833 0.00 0.00 0.00 4.35
1415 1452 2.268298 GCTATATATGACGCCCGTTGG 58.732 52.381 0.00 0.00 0.00 3.77
1445 1482 4.664677 ACTCGCCGCGCTCTGTTT 62.665 61.111 8.21 0.00 0.00 2.83
1446 1483 3.414700 CTCGCCGCGCTCTGTTTT 61.415 61.111 8.21 0.00 0.00 2.43
1447 1484 2.048970 TCGCCGCGCTCTGTTTTA 60.049 55.556 8.21 0.00 0.00 1.52
1448 1485 2.014093 CTCGCCGCGCTCTGTTTTAG 62.014 60.000 8.21 0.00 0.00 1.85
1449 1486 2.785258 GCCGCGCTCTGTTTTAGG 59.215 61.111 5.56 0.00 0.00 2.69
1450 1487 2.785258 CCGCGCTCTGTTTTAGGC 59.215 61.111 5.56 0.00 0.00 3.93
1451 1488 2.750888 CCGCGCTCTGTTTTAGGCC 61.751 63.158 5.56 0.00 0.00 5.19
1452 1489 1.741770 CGCGCTCTGTTTTAGGCCT 60.742 57.895 11.78 11.78 0.00 5.19
1453 1490 1.696832 CGCGCTCTGTTTTAGGCCTC 61.697 60.000 9.68 0.00 0.00 4.70
1454 1491 1.369839 GCGCTCTGTTTTAGGCCTCC 61.370 60.000 9.68 0.00 0.00 4.30
1455 1492 0.250513 CGCTCTGTTTTAGGCCTCCT 59.749 55.000 9.68 0.00 37.71 3.69
1456 1493 1.339151 CGCTCTGTTTTAGGCCTCCTT 60.339 52.381 9.68 0.00 34.61 3.36
1457 1494 2.796557 GCTCTGTTTTAGGCCTCCTTT 58.203 47.619 9.68 0.00 34.61 3.11
1458 1495 2.489722 GCTCTGTTTTAGGCCTCCTTTG 59.510 50.000 9.68 0.00 34.61 2.77
1459 1496 3.084786 CTCTGTTTTAGGCCTCCTTTGG 58.915 50.000 9.68 0.00 34.61 3.28
1460 1497 2.714250 TCTGTTTTAGGCCTCCTTTGGA 59.286 45.455 9.68 0.00 34.61 3.53
1461 1498 3.333680 TCTGTTTTAGGCCTCCTTTGGAT 59.666 43.478 9.68 0.00 34.61 3.41
1462 1499 4.538490 TCTGTTTTAGGCCTCCTTTGGATA 59.462 41.667 9.68 0.00 34.61 2.59
1463 1500 5.014755 TCTGTTTTAGGCCTCCTTTGGATAA 59.985 40.000 9.68 0.00 34.61 1.75
1464 1501 5.646215 TGTTTTAGGCCTCCTTTGGATAAA 58.354 37.500 9.68 0.00 34.61 1.40
1465 1502 6.078664 TGTTTTAGGCCTCCTTTGGATAAAA 58.921 36.000 9.68 4.10 34.61 1.52
1466 1503 6.555360 TGTTTTAGGCCTCCTTTGGATAAAAA 59.445 34.615 9.68 3.25 34.57 1.94
1484 1521 0.942252 AAAAGGAGTTCACGAACCGC 59.058 50.000 6.30 0.00 42.06 5.68
1485 1522 0.179067 AAAGGAGTTCACGAACCGCA 60.179 50.000 6.30 0.00 42.06 5.69
1486 1523 0.878961 AAGGAGTTCACGAACCGCAC 60.879 55.000 6.30 0.00 42.06 5.34
1487 1524 2.315386 GGAGTTCACGAACCGCACC 61.315 63.158 6.30 2.64 42.06 5.01
1488 1525 2.280592 AGTTCACGAACCGCACCC 60.281 61.111 6.30 0.00 42.06 4.61
1489 1526 3.351416 GTTCACGAACCGCACCCC 61.351 66.667 0.00 0.00 35.36 4.95
1490 1527 4.973055 TTCACGAACCGCACCCCG 62.973 66.667 0.00 0.00 0.00 5.73
1494 1531 4.973055 CGAACCGCACCCCGTTGA 62.973 66.667 0.00 0.00 34.38 3.18
1495 1532 3.351416 GAACCGCACCCCGTTGAC 61.351 66.667 0.00 0.00 34.38 3.18
1496 1533 3.819877 GAACCGCACCCCGTTGACT 62.820 63.158 0.00 0.00 34.38 3.41
1497 1534 3.409605 AACCGCACCCCGTTGACTT 62.410 57.895 0.00 0.00 34.38 3.01
1498 1535 3.047877 CCGCACCCCGTTGACTTC 61.048 66.667 0.00 0.00 34.38 3.01
1499 1536 3.047877 CGCACCCCGTTGACTTCC 61.048 66.667 0.00 0.00 0.00 3.46
1500 1537 2.430367 GCACCCCGTTGACTTCCT 59.570 61.111 0.00 0.00 0.00 3.36
1501 1538 1.228154 GCACCCCGTTGACTTCCTT 60.228 57.895 0.00 0.00 0.00 3.36
1502 1539 1.235281 GCACCCCGTTGACTTCCTTC 61.235 60.000 0.00 0.00 0.00 3.46
1503 1540 0.605589 CACCCCGTTGACTTCCTTCC 60.606 60.000 0.00 0.00 0.00 3.46
1504 1541 0.767060 ACCCCGTTGACTTCCTTCCT 60.767 55.000 0.00 0.00 0.00 3.36
1505 1542 0.400594 CCCCGTTGACTTCCTTCCTT 59.599 55.000 0.00 0.00 0.00 3.36
1506 1543 1.610886 CCCCGTTGACTTCCTTCCTTC 60.611 57.143 0.00 0.00 0.00 3.46
1585 1760 2.037847 GGCATCCACTGGGCCTTT 59.962 61.111 4.53 0.00 44.32 3.11
1611 1786 0.668096 TGCGTCGCCGTGAGTAAAAT 60.668 50.000 15.88 0.00 36.15 1.82
1615 1790 2.156117 CGTCGCCGTGAGTAAAATTCAA 59.844 45.455 0.00 0.00 0.00 2.69
1618 1793 4.611366 GTCGCCGTGAGTAAAATTCAAAAG 59.389 41.667 0.00 0.00 0.00 2.27
1619 1794 4.512198 TCGCCGTGAGTAAAATTCAAAAGA 59.488 37.500 0.00 0.00 0.00 2.52
1643 1860 4.806640 AAAAGGCATCCGAATTGATTGT 57.193 36.364 0.00 0.00 0.00 2.71
1656 1873 5.748152 CGAATTGATTGTTGGTGTCTGTTTT 59.252 36.000 0.00 0.00 0.00 2.43
1829 2052 2.218454 CCACCCTCACGGTTACCCA 61.218 63.158 0.00 0.00 45.36 4.51
1888 2750 9.760077 AGATTTAGTAGTGTAATTTCCGTATGG 57.240 33.333 0.00 0.00 0.00 2.74
1914 2781 1.754226 ACAGCCCGTTTGTTGAAATGT 59.246 42.857 0.00 0.00 0.00 2.71
1915 2782 2.167487 ACAGCCCGTTTGTTGAAATGTT 59.833 40.909 0.00 0.00 0.00 2.71
1917 2784 4.142138 ACAGCCCGTTTGTTGAAATGTTTA 60.142 37.500 0.00 0.00 0.00 2.01
1989 2862 1.719063 ATGGTGGCACTGACAAGGGT 61.719 55.000 18.45 0.00 0.00 4.34
1995 2868 2.084546 GGCACTGACAAGGGTATCAAC 58.915 52.381 0.00 0.00 0.00 3.18
2016 2889 0.041535 AGGGGAATGCCATTTGCTCA 59.958 50.000 0.00 0.00 42.00 4.26
2022 2895 1.927487 ATGCCATTTGCTCACCAGAA 58.073 45.000 0.00 0.00 42.00 3.02
2133 3006 2.435938 CCGTTACATGCCAGCCGT 60.436 61.111 0.00 0.00 0.00 5.68
2236 3114 4.388378 AACCTCGGCTCTGAATAGTAAC 57.612 45.455 0.00 0.00 0.00 2.50
2791 3747 2.656646 CTGGCACGTGAGGCTGTA 59.343 61.111 22.23 0.00 34.73 2.74
3057 4041 3.748568 CCTTGGTACTGAAGAAACTGCTC 59.251 47.826 6.72 0.00 0.00 4.26
3145 4145 4.440880 TGCCATATTTTTAACTGCCATGC 58.559 39.130 0.00 0.00 0.00 4.06
3204 4333 7.944729 AAATATAAGATGTTTGCAGTGGACT 57.055 32.000 0.00 0.00 0.00 3.85
3205 4334 6.932356 ATATAAGATGTTTGCAGTGGACTG 57.068 37.500 2.19 2.19 46.40 3.51
3206 4335 2.645838 AGATGTTTGCAGTGGACTGT 57.354 45.000 8.54 0.00 45.45 3.55
3207 4336 2.936202 AGATGTTTGCAGTGGACTGTT 58.064 42.857 8.54 0.00 45.45 3.16
3208 4337 2.880890 AGATGTTTGCAGTGGACTGTTC 59.119 45.455 8.54 0.00 45.45 3.18
3209 4338 2.121291 TGTTTGCAGTGGACTGTTCA 57.879 45.000 8.54 0.00 45.45 3.18
3210 4339 2.441410 TGTTTGCAGTGGACTGTTCAA 58.559 42.857 8.54 2.78 45.45 2.69
3211 4340 2.423185 TGTTTGCAGTGGACTGTTCAAG 59.577 45.455 8.54 0.00 45.45 3.02
3212 4341 2.418368 TTGCAGTGGACTGTTCAAGT 57.582 45.000 8.54 0.00 45.45 3.16
3213 4342 3.552132 TTGCAGTGGACTGTTCAAGTA 57.448 42.857 8.54 0.00 45.45 2.24
3214 4343 3.769739 TGCAGTGGACTGTTCAAGTAT 57.230 42.857 8.54 0.00 45.45 2.12
3215 4344 4.085357 TGCAGTGGACTGTTCAAGTATT 57.915 40.909 8.54 0.00 45.45 1.89
3216 4345 5.222079 TGCAGTGGACTGTTCAAGTATTA 57.778 39.130 8.54 0.00 45.45 0.98
3368 4499 2.095567 GTGCAAGCTACCATGAACAGTG 60.096 50.000 0.00 0.00 0.00 3.66
3459 6910 0.390209 GCCATGCATCACCGCTTTTT 60.390 50.000 0.00 0.00 0.00 1.94
3520 6971 5.862924 TTAGTTTCATCAGTACAAGCAGC 57.137 39.130 0.00 0.00 0.00 5.25
3660 7116 3.758554 GTGTATGAAGAATGCCCAACAGT 59.241 43.478 0.00 0.00 0.00 3.55
4027 7486 5.012458 TGGAGATGCTAACTATGATCCCTTG 59.988 44.000 0.00 0.00 0.00 3.61
4284 7743 8.726870 AATTATGGTGTATGTAAGGTGTACAC 57.273 34.615 18.01 18.01 44.53 2.90
4570 8029 2.434185 CTCCGCACGCTTTAGCCA 60.434 61.111 0.00 0.00 37.91 4.75
5078 9382 8.879759 CACATCATGTACTCGGTTTTAGTTATT 58.120 33.333 0.00 0.00 0.00 1.40
5079 9383 9.095065 ACATCATGTACTCGGTTTTAGTTATTC 57.905 33.333 0.00 0.00 0.00 1.75
5080 9384 8.548721 CATCATGTACTCGGTTTTAGTTATTCC 58.451 37.037 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.967362 AGCATCGTCGGTGTAAATCAA 58.033 42.857 7.44 0.00 0.00 2.57
34 35 0.972983 GCAGGAGAGACACCCTAGCA 60.973 60.000 0.00 0.00 31.50 3.49
41 42 3.243704 GGACATGATAGCAGGAGAGACAC 60.244 52.174 0.00 0.00 0.00 3.67
64 65 3.442996 CCAGAAGGTAGAGCCAACG 57.557 57.895 0.00 0.00 40.61 4.10
106 107 6.867662 AGACAGTTGATTCACGAGAAAAAT 57.132 33.333 0.00 0.00 37.29 1.82
132 133 1.276705 GGGGTCACTCTGAGAACCTTC 59.723 57.143 23.37 16.17 42.63 3.46
193 194 3.694734 AGACAAAAGAAACACACATGCG 58.305 40.909 0.00 0.00 0.00 4.73
218 219 3.258372 AGAGCTCACGTGGATTACAGAAA 59.742 43.478 17.77 0.00 0.00 2.52
220 221 2.164422 CAGAGCTCACGTGGATTACAGA 59.836 50.000 17.77 0.00 0.00 3.41
224 225 1.557099 ACCAGAGCTCACGTGGATTA 58.443 50.000 23.41 0.00 35.17 1.75
304 314 7.696992 TTAATGGTCACAAAGAGTAAATCCC 57.303 36.000 0.00 0.00 0.00 3.85
332 344 1.335145 AGCATGGCAAGCAAACTCTT 58.665 45.000 17.75 0.00 0.00 2.85
360 372 9.670719 GCCGAATTTTTCCATTTTGAATAAAAA 57.329 25.926 0.00 0.00 41.88 1.94
365 377 4.142924 GCGCCGAATTTTTCCATTTTGAAT 60.143 37.500 0.00 0.00 0.00 2.57
389 401 2.848679 TGTGCTGGCCTGAGTCCA 60.849 61.111 14.77 0.00 0.00 4.02
407 419 4.110036 TGATATTCTCTCGTGTGTGTGG 57.890 45.455 0.00 0.00 0.00 4.17
409 421 6.265422 TCCATATGATATTCTCTCGTGTGTGT 59.735 38.462 3.65 0.00 0.00 3.72
431 443 4.451629 TTTTTACCGCAACTTGTTTCCA 57.548 36.364 0.00 0.00 0.00 3.53
438 450 9.320352 AGTTTTCATTTATTTTTACCGCAACTT 57.680 25.926 0.00 0.00 0.00 2.66
541 553 9.862371 TTTGTTATGTTAACACATGTTTGAACT 57.138 25.926 11.22 2.78 43.92 3.01
549 561 9.388346 ACATTACGTTTGTTATGTTAACACATG 57.612 29.630 11.22 1.23 43.70 3.21
583 595 6.910536 AAATTTGTTTTGTTATCAACCGCA 57.089 29.167 0.00 0.00 32.93 5.69
633 645 3.411517 CTCCCTCCGCCCCACAAT 61.412 66.667 0.00 0.00 0.00 2.71
644 656 8.738645 AATAATGACATTTACTGTTCTCCCTC 57.261 34.615 5.89 0.00 38.54 4.30
822 854 1.269517 GCGGAAACCAAGTTGCAATGA 60.270 47.619 0.59 0.00 0.00 2.57
867 899 9.562408 TTACAGATAACAGGTTTCAAATACACA 57.438 29.630 0.00 0.00 0.00 3.72
871 903 9.226606 CCACTTACAGATAACAGGTTTCAAATA 57.773 33.333 0.00 0.00 0.00 1.40
884 918 1.475280 ACTCGCGCCACTTACAGATAA 59.525 47.619 0.00 0.00 0.00 1.75
905 939 1.466950 CTGTCTCACTGTCCGTCTCTC 59.533 57.143 0.00 0.00 0.00 3.20
906 940 1.202830 ACTGTCTCACTGTCCGTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
907 941 1.068885 CACTGTCTCACTGTCCGTCTC 60.069 57.143 0.00 0.00 0.00 3.36
908 942 0.955178 CACTGTCTCACTGTCCGTCT 59.045 55.000 0.00 0.00 0.00 4.18
909 943 0.952280 TCACTGTCTCACTGTCCGTC 59.048 55.000 0.00 0.00 0.00 4.79
910 944 0.955178 CTCACTGTCTCACTGTCCGT 59.045 55.000 0.00 0.00 0.00 4.69
911 945 0.387878 GCTCACTGTCTCACTGTCCG 60.388 60.000 0.00 0.00 0.00 4.79
912 946 0.037790 GGCTCACTGTCTCACTGTCC 60.038 60.000 0.00 0.00 0.00 4.02
945 979 0.489567 AGGGGAGATAGATCGGGCTT 59.510 55.000 0.00 0.00 0.00 4.35
1230 1267 1.805539 CATGTCGTCGACCATGCGT 60.806 57.895 22.05 2.90 0.00 5.24
1281 1318 1.760875 GGTGCCGTAGAGGATGGGA 60.761 63.158 0.00 0.00 45.00 4.37
1341 1378 2.349755 CCGACGTTGTGGGGGAAT 59.650 61.111 1.30 0.00 0.00 3.01
1428 1465 2.758770 TAAAACAGAGCGCGGCGAGT 62.759 55.000 28.54 12.45 0.00 4.18
1429 1466 2.014093 CTAAAACAGAGCGCGGCGAG 62.014 60.000 28.54 9.37 0.00 5.03
1430 1467 2.048970 TAAAACAGAGCGCGGCGA 60.049 55.556 28.54 0.00 0.00 5.54
1431 1468 2.395690 CTAAAACAGAGCGCGGCG 59.604 61.111 19.62 19.62 0.00 6.46
1432 1469 2.785258 CCTAAAACAGAGCGCGGC 59.215 61.111 8.83 0.00 0.00 6.53
1433 1470 2.750888 GGCCTAAAACAGAGCGCGG 61.751 63.158 8.83 0.00 0.00 6.46
1434 1471 1.696832 GAGGCCTAAAACAGAGCGCG 61.697 60.000 4.42 0.00 0.00 6.86
1435 1472 1.369839 GGAGGCCTAAAACAGAGCGC 61.370 60.000 4.42 0.00 0.00 5.92
1436 1473 0.250513 AGGAGGCCTAAAACAGAGCG 59.749 55.000 4.42 0.00 28.47 5.03
1437 1474 2.489722 CAAAGGAGGCCTAAAACAGAGC 59.510 50.000 4.42 0.00 31.13 4.09
1438 1475 3.084786 CCAAAGGAGGCCTAAAACAGAG 58.915 50.000 4.42 0.00 31.13 3.35
1439 1476 2.714250 TCCAAAGGAGGCCTAAAACAGA 59.286 45.455 4.42 0.00 31.13 3.41
1440 1477 3.154827 TCCAAAGGAGGCCTAAAACAG 57.845 47.619 4.42 0.00 31.13 3.16
1441 1478 3.825908 ATCCAAAGGAGGCCTAAAACA 57.174 42.857 4.42 0.00 34.05 2.83
1442 1479 6.599356 TTTTATCCAAAGGAGGCCTAAAAC 57.401 37.500 4.42 0.00 34.05 2.43
1464 1501 1.332686 GCGGTTCGTGAACTCCTTTTT 59.667 47.619 12.10 0.00 40.94 1.94
1465 1502 0.942252 GCGGTTCGTGAACTCCTTTT 59.058 50.000 12.10 0.00 40.94 2.27
1466 1503 0.179067 TGCGGTTCGTGAACTCCTTT 60.179 50.000 12.10 0.00 40.94 3.11
1467 1504 0.878961 GTGCGGTTCGTGAACTCCTT 60.879 55.000 12.10 0.00 40.94 3.36
1468 1505 1.300697 GTGCGGTTCGTGAACTCCT 60.301 57.895 12.10 0.00 40.94 3.69
1469 1506 2.315386 GGTGCGGTTCGTGAACTCC 61.315 63.158 12.10 6.81 40.94 3.85
1470 1507 2.315386 GGGTGCGGTTCGTGAACTC 61.315 63.158 12.10 5.83 40.94 3.01
1471 1508 2.280592 GGGTGCGGTTCGTGAACT 60.281 61.111 12.10 0.00 40.94 3.01
1472 1509 3.351416 GGGGTGCGGTTCGTGAAC 61.351 66.667 4.15 4.15 40.45 3.18
1473 1510 4.973055 CGGGGTGCGGTTCGTGAA 62.973 66.667 0.00 0.00 0.00 3.18
1477 1514 4.973055 TCAACGGGGTGCGGTTCG 62.973 66.667 0.00 0.00 0.00 3.95
1478 1515 3.351416 GTCAACGGGGTGCGGTTC 61.351 66.667 0.00 0.00 0.00 3.62
1479 1516 3.409605 AAGTCAACGGGGTGCGGTT 62.410 57.895 0.00 0.00 0.00 4.44
1480 1517 3.819877 GAAGTCAACGGGGTGCGGT 62.820 63.158 0.00 0.00 0.00 5.68
1481 1518 3.047877 GAAGTCAACGGGGTGCGG 61.048 66.667 0.00 0.00 0.00 5.69
1482 1519 3.047877 GGAAGTCAACGGGGTGCG 61.048 66.667 0.00 0.00 0.00 5.34
1483 1520 1.228154 AAGGAAGTCAACGGGGTGC 60.228 57.895 0.00 0.00 0.00 5.01
1484 1521 0.605589 GGAAGGAAGTCAACGGGGTG 60.606 60.000 0.00 0.00 0.00 4.61
1485 1522 0.767060 AGGAAGGAAGTCAACGGGGT 60.767 55.000 0.00 0.00 0.00 4.95
1486 1523 0.400594 AAGGAAGGAAGTCAACGGGG 59.599 55.000 0.00 0.00 0.00 5.73
1487 1524 1.610886 GGAAGGAAGGAAGTCAACGGG 60.611 57.143 0.00 0.00 0.00 5.28
1488 1525 1.071699 TGGAAGGAAGGAAGTCAACGG 59.928 52.381 0.00 0.00 0.00 4.44
1489 1526 2.417719 CTGGAAGGAAGGAAGTCAACG 58.582 52.381 0.00 0.00 0.00 4.10
1503 1540 2.203126 GCTCCGCATCCCTGGAAG 60.203 66.667 0.00 0.00 32.89 3.46
1504 1541 2.688666 AGCTCCGCATCCCTGGAA 60.689 61.111 0.00 0.00 32.89 3.53
1505 1542 3.157252 GAGCTCCGCATCCCTGGA 61.157 66.667 0.87 0.00 0.00 3.86
1506 1543 4.598894 CGAGCTCCGCATCCCTGG 62.599 72.222 8.47 0.00 0.00 4.45
1626 1843 2.166254 ACCAACAATCAATTCGGATGCC 59.834 45.455 0.00 0.00 0.00 4.40
1637 1854 3.131933 CCCAAAACAGACACCAACAATCA 59.868 43.478 0.00 0.00 0.00 2.57
1638 1855 3.132111 ACCCAAAACAGACACCAACAATC 59.868 43.478 0.00 0.00 0.00 2.67
1640 1857 2.494073 GACCCAAAACAGACACCAACAA 59.506 45.455 0.00 0.00 0.00 2.83
1641 1858 2.096248 GACCCAAAACAGACACCAACA 58.904 47.619 0.00 0.00 0.00 3.33
1643 1860 2.650322 GAGACCCAAAACAGACACCAA 58.350 47.619 0.00 0.00 0.00 3.67
1656 1873 1.296392 CGCACATCAAGGAGACCCA 59.704 57.895 0.00 0.00 33.88 4.51
1829 2052 1.192428 ACCTAACCGAAGCGAGGAAT 58.808 50.000 2.25 0.00 33.04 3.01
1888 2750 3.977244 CAAACGGGCTGTGGGCAC 61.977 66.667 0.00 0.00 44.01 5.01
1914 2781 4.148079 TGTCCCTGCAAATCACACATAAA 58.852 39.130 0.00 0.00 0.00 1.40
1915 2782 3.760738 TGTCCCTGCAAATCACACATAA 58.239 40.909 0.00 0.00 0.00 1.90
1917 2784 2.291209 TGTCCCTGCAAATCACACAT 57.709 45.000 0.00 0.00 0.00 3.21
1989 2862 1.208706 TGGCATTCCCCTCGTTGATA 58.791 50.000 0.00 0.00 0.00 2.15
1995 2868 1.438814 GCAAATGGCATTCCCCTCG 59.561 57.895 14.04 0.00 43.97 4.63
2016 2889 3.457749 GGATCCTCTCCAAATCTTCTGGT 59.542 47.826 3.84 0.00 44.26 4.00
2133 3006 6.149973 CCTTTAGAACATCTGTGAGCAAATGA 59.850 38.462 0.00 0.00 0.00 2.57
2236 3114 7.876896 TGATGTCATGTTCACAAAATCATTG 57.123 32.000 0.00 0.00 0.00 2.82
2654 3545 5.105064 ACAGTAACAGCGGAAACATAGGTAT 60.105 40.000 0.00 0.00 0.00 2.73
2791 3747 5.272283 TCAGAAGTACCAAAGACTTTCGT 57.728 39.130 3.63 3.63 37.27 3.85
3145 4145 8.332996 AGCAATAATTTCACATCTATAGGCAG 57.667 34.615 0.00 0.00 0.00 4.85
3197 4326 9.396022 CCATAATTAATACTTGAACAGTCCACT 57.604 33.333 0.00 0.00 36.88 4.00
3198 4327 9.174166 ACCATAATTAATACTTGAACAGTCCAC 57.826 33.333 0.00 0.00 36.88 4.02
3199 4328 9.747898 AACCATAATTAATACTTGAACAGTCCA 57.252 29.630 0.00 0.00 36.88 4.02
3252 4383 3.815809 TGACTTTCAGTACAAACCAGGG 58.184 45.455 0.00 0.00 0.00 4.45
3305 4436 5.452078 TGTTTGGCTCTCAAATGGTAAAG 57.548 39.130 0.00 0.00 45.79 1.85
3368 4499 7.224949 GGTTAGTTCAGTAATGATTGGCTAGTC 59.775 40.741 0.00 0.00 0.00 2.59
3491 6942 8.224437 GCTTGTACTGATGAAACTAAAACTCTC 58.776 37.037 0.00 0.00 0.00 3.20
3520 6971 2.689983 GGTCCAGGGTGCAGATTTTATG 59.310 50.000 0.00 0.00 0.00 1.90
3660 7116 4.415881 TCTCCGCTTTCAATAATAGCCA 57.584 40.909 0.00 0.00 0.00 4.75
4151 7610 4.223477 ACCCATTATTTGCAGCAAGACATT 59.777 37.500 8.12 0.00 0.00 2.71
4201 7660 6.071952 CCAGTACCATAATTTGCAACAAGAGT 60.072 38.462 0.00 0.00 0.00 3.24
4202 7661 6.324819 CCAGTACCATAATTTGCAACAAGAG 58.675 40.000 0.00 0.00 0.00 2.85
4203 7662 5.184864 CCCAGTACCATAATTTGCAACAAGA 59.815 40.000 0.00 0.00 0.00 3.02
4204 7663 5.047377 ACCCAGTACCATAATTTGCAACAAG 60.047 40.000 0.00 0.00 0.00 3.16
4205 7664 4.835615 ACCCAGTACCATAATTTGCAACAA 59.164 37.500 0.00 0.00 0.00 2.83
4206 7665 4.411927 ACCCAGTACCATAATTTGCAACA 58.588 39.130 0.00 0.00 0.00 3.33
4207 7666 5.400066 AACCCAGTACCATAATTTGCAAC 57.600 39.130 0.00 0.00 0.00 4.17
4208 7667 6.665680 ACATAACCCAGTACCATAATTTGCAA 59.334 34.615 0.00 0.00 0.00 4.08
4570 8029 1.070445 GCTCCAGTGCATAGCGGAT 59.930 57.895 0.00 0.00 0.00 4.18
4891 8426 1.526917 GCCGGATGGATGAAGTGGG 60.527 63.158 5.05 0.00 37.49 4.61


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

AutoCloner maintained by Alex Coulton.