Multiple sequence alignment - TraesCS5B01G286200

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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 TraesCS5B01G286200 chr5B 100.000 3826 0 0 1 3826 471920016 471916191 0.000000e+00 7066.0
1 TraesCS5B01G286200 chr5B 95.933 1377 54 1 1452 2828 472069413 472070787 0.000000e+00 2231.0
2 TraesCS5B01G286200 chr5B 97.867 375 8 0 995 1369 472068991 472069365 0.000000e+00 649.0
3 TraesCS5B01G286200 chr5A 89.549 3014 209 45 856 3826 494878578 494875628 0.000000e+00 3723.0
4 TraesCS5B01G286200 chr5A 94.493 1834 78 12 995 2828 494972592 494974402 0.000000e+00 2806.0
5 TraesCS5B01G286200 chr5D 96.029 1360 54 0 1469 2828 391782576 391783935 0.000000e+00 2213.0
6 TraesCS5B01G286200 chr5D 96.124 387 12 1 995 1378 391782108 391782494 2.510000e-176 628.0
7 TraesCS5B01G286200 chr5D 84.441 572 66 9 3255 3826 391759436 391758888 3.360000e-150 542.0
8 TraesCS5B01G286200 chr5D 91.703 229 19 0 2600 2828 391785078 391785306 6.170000e-83 318.0
9 TraesCS5B01G286200 chr6A 99.527 845 3 1 1 845 194809234 194810077 0.000000e+00 1537.0
10 TraesCS5B01G286200 chr6A 98.952 859 8 1 1 859 60384714 60383857 0.000000e+00 1535.0
11 TraesCS5B01G286200 chr7A 99.172 845 6 1 1 844 710681074 710680230 0.000000e+00 1520.0
12 TraesCS5B01G286200 chr7A 88.498 313 25 2 550 862 616970214 616970515 6.040000e-98 368.0
13 TraesCS5B01G286200 chr7A 88.889 252 18 9 617 862 722214001 722213754 6.210000e-78 302.0
14 TraesCS5B01G286200 chr3B 98.826 852 10 0 1 852 457028678 457027827 0.000000e+00 1519.0
15 TraesCS5B01G286200 chr3B 97.297 851 15 2 1 843 641069737 641070587 0.000000e+00 1437.0
16 TraesCS5B01G286200 chr3B 96.970 33 1 0 3088 3120 762118871 762118839 5.340000e-04 56.5
17 TraesCS5B01G286200 chr1B 98.242 853 4 1 1 842 222199361 222198509 0.000000e+00 1482.0
18 TraesCS5B01G286200 chr1B 94.406 858 33 4 1 848 16566599 16567451 0.000000e+00 1304.0
19 TraesCS5B01G286200 chr4B 99.353 773 5 0 1 773 82170284 82171056 0.000000e+00 1400.0
20 TraesCS5B01G286200 chr7B 94.635 466 20 4 1590 2055 588068990 588068530 0.000000e+00 717.0
21 TraesCS5B01G286200 chr7B 92.116 482 32 2 2056 2531 588067202 588066721 0.000000e+00 675.0
22 TraesCS5B01G286200 chr7B 79.730 148 22 5 28 174 7093273 7093413 2.430000e-17 100.0
23 TraesCS5B01G286200 chr1A 90.123 243 15 8 617 854 29878573 29878335 1.340000e-79 307.0
24 TraesCS5B01G286200 chr2B 92.308 39 3 0 3082 3120 394403823 394403861 5.340000e-04 56.5
25 TraesCS5B01G286200 chr6B 94.444 36 1 1 3086 3120 4260959 4260994 2.000000e-03 54.7


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 TraesCS5B01G286200 chr5B 471916191 471920016 3825 True 7066 7066 100.000000 1 3826 1 chr5B.!!$R1 3825
1 TraesCS5B01G286200 chr5B 472068991 472070787 1796 False 1440 2231 96.900000 995 2828 2 chr5B.!!$F1 1833
2 TraesCS5B01G286200 chr5A 494875628 494878578 2950 True 3723 3723 89.549000 856 3826 1 chr5A.!!$R1 2970
3 TraesCS5B01G286200 chr5A 494972592 494974402 1810 False 2806 2806 94.493000 995 2828 1 chr5A.!!$F1 1833
4 TraesCS5B01G286200 chr5D 391782108 391785306 3198 False 1053 2213 94.618667 995 2828 3 chr5D.!!$F1 1833
5 TraesCS5B01G286200 chr5D 391758888 391759436 548 True 542 542 84.441000 3255 3826 1 chr5D.!!$R1 571
6 TraesCS5B01G286200 chr6A 194809234 194810077 843 False 1537 1537 99.527000 1 845 1 chr6A.!!$F1 844
7 TraesCS5B01G286200 chr6A 60383857 60384714 857 True 1535 1535 98.952000 1 859 1 chr6A.!!$R1 858
8 TraesCS5B01G286200 chr7A 710680230 710681074 844 True 1520 1520 99.172000 1 844 1 chr7A.!!$R1 843
9 TraesCS5B01G286200 chr3B 457027827 457028678 851 True 1519 1519 98.826000 1 852 1 chr3B.!!$R1 851
10 TraesCS5B01G286200 chr3B 641069737 641070587 850 False 1437 1437 97.297000 1 843 1 chr3B.!!$F1 842
11 TraesCS5B01G286200 chr1B 222198509 222199361 852 True 1482 1482 98.242000 1 842 1 chr1B.!!$R1 841
12 TraesCS5B01G286200 chr1B 16566599 16567451 852 False 1304 1304 94.406000 1 848 1 chr1B.!!$F1 847
13 TraesCS5B01G286200 chr4B 82170284 82171056 772 False 1400 1400 99.353000 1 773 1 chr4B.!!$F1 772
14 TraesCS5B01G286200 chr7B 588066721 588068990 2269 True 696 717 93.375500 1590 2531 2 chr7B.!!$R1 941

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
979 1002 0.523072 CAGCGCCAGTGCAATTAACT 59.477 50.0 2.29 0.0 37.32 2.24 F
2506 3932 0.027586 AACGCGCTCAACAACAAGAC 59.972 50.0 5.73 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2777 5574 0.179037 CCATGATGGACGATGGCAGT 60.179 55.0 5.27 0.0 40.96 4.40 R
3704 6527 0.250124 AGTCGCACCAAACCGAATCA 60.250 50.0 0.00 0.0 35.00 2.57 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
327 328 6.872920 TGCCAAAATTCAGTGTAGTCTTTTT 58.127 32.000 0.00 0.00 0.00 1.94
647 658 3.058016 CGTCCATTCAAGCACATTCAACT 60.058 43.478 0.00 0.00 0.00 3.16
845 868 3.528532 GCACGGGCACTTTTACTAGTAT 58.471 45.455 3.77 0.00 40.72 2.12
923 946 1.671328 TGCTCGATCGAACTAGTCCAG 59.329 52.381 19.92 5.07 0.00 3.86
925 948 1.671328 CTCGATCGAACTAGTCCAGCA 59.329 52.381 19.92 0.00 0.00 4.41
928 951 2.792890 CGATCGAACTAGTCCAGCACAG 60.793 54.545 10.26 0.00 0.00 3.66
979 1002 0.523072 CAGCGCCAGTGCAATTAACT 59.477 50.000 2.29 0.00 37.32 2.24
981 1004 1.737793 AGCGCCAGTGCAATTAACTAC 59.262 47.619 2.29 0.00 37.32 2.73
992 1015 3.364964 GCAATTAACTACGCAGCTGTGTT 60.365 43.478 35.55 24.09 39.74 3.32
993 1016 4.783242 CAATTAACTACGCAGCTGTGTTT 58.217 39.130 35.55 26.15 39.74 2.83
1348 1391 1.017701 CGGCGAAACCTTCACCTACC 61.018 60.000 0.00 0.00 35.61 3.18
1378 1441 3.187700 GTCGACAGGGTAAGCAACATAG 58.812 50.000 11.55 0.00 0.00 2.23
1380 1443 3.130516 TCGACAGGGTAAGCAACATAGAG 59.869 47.826 0.00 0.00 0.00 2.43
1409 1494 9.240159 ACGTTTTCTTTTCTTTATTTATTGCGT 57.760 25.926 0.00 0.00 0.00 5.24
1427 1512 6.493449 TTGCGTGAAATGTCATTGATTCTA 57.507 33.333 0.00 0.00 35.80 2.10
1438 1523 8.674263 ATGTCATTGATTCTAATCTCTGAACC 57.326 34.615 4.45 0.00 36.39 3.62
1439 1524 7.050377 TGTCATTGATTCTAATCTCTGAACCC 58.950 38.462 4.45 0.00 36.39 4.11
1440 1525 6.484977 GTCATTGATTCTAATCTCTGAACCCC 59.515 42.308 4.45 0.00 36.39 4.95
1441 1526 6.388100 TCATTGATTCTAATCTCTGAACCCCT 59.612 38.462 4.45 0.00 36.39 4.79
1442 1527 6.642733 TTGATTCTAATCTCTGAACCCCTT 57.357 37.500 4.45 0.00 36.39 3.95
1443 1528 6.240549 TGATTCTAATCTCTGAACCCCTTC 57.759 41.667 4.45 0.00 36.39 3.46
1444 1529 5.966935 TGATTCTAATCTCTGAACCCCTTCT 59.033 40.000 4.45 0.00 36.39 2.85
1445 1530 5.941555 TTCTAATCTCTGAACCCCTTCTC 57.058 43.478 0.00 0.00 0.00 2.87
1446 1531 3.954904 TCTAATCTCTGAACCCCTTCTCG 59.045 47.826 0.00 0.00 0.00 4.04
1447 1532 2.239681 ATCTCTGAACCCCTTCTCGT 57.760 50.000 0.00 0.00 0.00 4.18
1448 1533 1.546961 TCTCTGAACCCCTTCTCGTC 58.453 55.000 0.00 0.00 0.00 4.20
1449 1534 1.075698 TCTCTGAACCCCTTCTCGTCT 59.924 52.381 0.00 0.00 0.00 4.18
1450 1535 1.474879 CTCTGAACCCCTTCTCGTCTC 59.525 57.143 0.00 0.00 0.00 3.36
1451 1536 1.075698 TCTGAACCCCTTCTCGTCTCT 59.924 52.381 0.00 0.00 0.00 3.10
1452 1537 2.307980 TCTGAACCCCTTCTCGTCTCTA 59.692 50.000 0.00 0.00 0.00 2.43
1453 1538 3.090037 CTGAACCCCTTCTCGTCTCTAA 58.910 50.000 0.00 0.00 0.00 2.10
1454 1539 3.503365 TGAACCCCTTCTCGTCTCTAAA 58.497 45.455 0.00 0.00 0.00 1.85
1455 1540 4.094476 TGAACCCCTTCTCGTCTCTAAAT 58.906 43.478 0.00 0.00 0.00 1.40
1456 1541 4.081642 TGAACCCCTTCTCGTCTCTAAATG 60.082 45.833 0.00 0.00 0.00 2.32
1457 1542 3.442076 ACCCCTTCTCGTCTCTAAATGT 58.558 45.455 0.00 0.00 0.00 2.71
1458 1543 3.195825 ACCCCTTCTCGTCTCTAAATGTG 59.804 47.826 0.00 0.00 0.00 3.21
1459 1544 3.195825 CCCCTTCTCGTCTCTAAATGTGT 59.804 47.826 0.00 0.00 0.00 3.72
1460 1545 4.322801 CCCCTTCTCGTCTCTAAATGTGTT 60.323 45.833 0.00 0.00 0.00 3.32
1461 1546 5.238583 CCCTTCTCGTCTCTAAATGTGTTT 58.761 41.667 0.00 0.00 0.00 2.83
1462 1547 5.701290 CCCTTCTCGTCTCTAAATGTGTTTT 59.299 40.000 0.00 0.00 0.00 2.43
1463 1548 6.347725 CCCTTCTCGTCTCTAAATGTGTTTTG 60.348 42.308 0.00 0.00 0.00 2.44
1464 1549 6.202954 CCTTCTCGTCTCTAAATGTGTTTTGT 59.797 38.462 0.00 0.00 0.00 2.83
1465 1550 6.764877 TCTCGTCTCTAAATGTGTTTTGTC 57.235 37.500 0.00 0.00 0.00 3.18
1466 1551 6.513180 TCTCGTCTCTAAATGTGTTTTGTCT 58.487 36.000 0.00 0.00 0.00 3.41
1467 1552 6.420903 TCTCGTCTCTAAATGTGTTTTGTCTG 59.579 38.462 0.00 0.00 0.00 3.51
1547 1640 0.529773 GGCTCAACGGCATGATCGTA 60.530 55.000 13.45 0.96 40.18 3.43
2393 3819 1.374125 CGACCACATGAGCCACGAA 60.374 57.895 0.00 0.00 0.00 3.85
2506 3932 0.027586 AACGCGCTCAACAACAAGAC 59.972 50.000 5.73 0.00 0.00 3.01
2531 3957 2.106683 GCACCCGTGGCATCTACAC 61.107 63.158 0.00 0.00 35.55 2.90
2633 4059 2.280628 GACCCGATCATGAAGAACACC 58.719 52.381 0.00 0.00 0.00 4.16
2763 5560 2.035155 TCTTCGAGGAGGGCGTCA 59.965 61.111 9.66 0.00 0.00 4.35
2777 5574 3.379445 GTCAAGAGGGTCGGCCGA 61.379 66.667 27.28 27.28 34.97 5.54
2846 5643 0.176219 CGGACCGGGTGCAAGTTATA 59.824 55.000 19.13 0.00 0.00 0.98
2851 5648 4.201980 GGACCGGGTGCAAGTTATAATTTC 60.202 45.833 14.36 0.00 0.00 2.17
2854 5651 5.420739 ACCGGGTGCAAGTTATAATTTCAAT 59.579 36.000 6.32 0.00 0.00 2.57
2855 5652 6.071051 ACCGGGTGCAAGTTATAATTTCAATT 60.071 34.615 6.32 0.00 0.00 2.32
2856 5653 6.816140 CCGGGTGCAAGTTATAATTTCAATTT 59.184 34.615 0.00 0.00 0.00 1.82
2858 5655 9.528018 CGGGTGCAAGTTATAATTTCAATTTAT 57.472 29.630 0.00 0.00 0.00 1.40
2925 5722 7.421087 AGGTTGATCTTACTAGGGTTAGTTC 57.579 40.000 0.00 0.00 40.55 3.01
2927 5724 7.679025 AGGTTGATCTTACTAGGGTTAGTTCTT 59.321 37.037 0.00 0.00 40.55 2.52
2928 5725 8.975295 GGTTGATCTTACTAGGGTTAGTTCTTA 58.025 37.037 0.00 0.00 40.55 2.10
2938 5735 9.892130 ACTAGGGTTAGTTCTTATTTCATTCAG 57.108 33.333 0.00 0.00 36.75 3.02
2939 5736 9.892130 CTAGGGTTAGTTCTTATTTCATTCAGT 57.108 33.333 0.00 0.00 0.00 3.41
2941 5738 9.588096 AGGGTTAGTTCTTATTTCATTCAGTTT 57.412 29.630 0.00 0.00 0.00 2.66
2942 5739 9.626045 GGGTTAGTTCTTATTTCATTCAGTTTG 57.374 33.333 0.00 0.00 0.00 2.93
2996 5794 4.157289 AGTGTACAAGGTACATACAGTCGG 59.843 45.833 11.88 0.00 28.40 4.79
2998 5796 3.863142 ACAAGGTACATACAGTCGGTC 57.137 47.619 0.00 0.00 0.00 4.79
3072 5870 8.579682 TCTTTGAGATTGTATACATGATGTCG 57.420 34.615 6.36 0.00 0.00 4.35
3073 5871 7.653311 TCTTTGAGATTGTATACATGATGTCGG 59.347 37.037 6.36 2.25 0.00 4.79
3074 5872 6.405278 TGAGATTGTATACATGATGTCGGT 57.595 37.500 6.36 0.00 0.00 4.69
3082 5895 9.687210 TTGTATACATGATGTCGGTTATAACTC 57.313 33.333 15.05 5.37 0.00 3.01
3086 5899 4.931661 TGATGTCGGTTATAACTCCTCC 57.068 45.455 15.05 0.00 0.00 4.30
3093 5906 4.081309 TCGGTTATAACTCCTCCAAACAGG 60.081 45.833 15.05 0.00 39.47 4.00
3146 5959 0.725117 GCCGAACCGATACAAAGTGG 59.275 55.000 0.00 0.00 0.00 4.00
3147 5960 1.365699 CCGAACCGATACAAAGTGGG 58.634 55.000 0.00 0.00 0.00 4.61
3148 5961 1.066716 CCGAACCGATACAAAGTGGGA 60.067 52.381 0.00 0.00 0.00 4.37
3151 5964 3.615592 CGAACCGATACAAAGTGGGAAGA 60.616 47.826 0.00 0.00 0.00 2.87
3159 5972 6.403636 CGATACAAAGTGGGAAGAAAATCTGG 60.404 42.308 0.00 0.00 0.00 3.86
3162 5975 5.660864 ACAAAGTGGGAAGAAAATCTGGAAA 59.339 36.000 0.00 0.00 0.00 3.13
3172 5985 7.014326 GGAAGAAAATCTGGAAACAAGTAGGTT 59.986 37.037 0.00 0.00 42.06 3.50
3177 5990 4.714632 TCTGGAAACAAGTAGGTTGGAAG 58.285 43.478 0.00 0.00 42.06 3.46
3178 5991 4.410883 TCTGGAAACAAGTAGGTTGGAAGA 59.589 41.667 0.00 0.00 42.06 2.87
3190 6003 9.429109 AAGTAGGTTGGAAGAAAAATAAAAGGA 57.571 29.630 0.00 0.00 0.00 3.36
3194 6007 8.713971 AGGTTGGAAGAAAAATAAAAGGACATT 58.286 29.630 0.00 0.00 0.00 2.71
3199 6012 8.251026 GGAAGAAAAATAAAAGGACATTCGGAT 58.749 33.333 0.00 0.00 0.00 4.18
3200 6013 8.986477 AAGAAAAATAAAAGGACATTCGGATG 57.014 30.769 0.88 0.88 39.25 3.51
3202 6015 8.462016 AGAAAAATAAAAGGACATTCGGATGAG 58.538 33.333 11.64 0.00 36.73 2.90
3206 6019 0.179000 AGGACATTCGGATGAGTGGC 59.821 55.000 11.64 0.00 39.06 5.01
3226 6039 3.223589 AAGTGCGGCCAACCCAAC 61.224 61.111 2.24 0.00 0.00 3.77
3228 6041 3.302344 GTGCGGCCAACCCAACAT 61.302 61.111 2.24 0.00 0.00 2.71
3229 6042 2.988684 TGCGGCCAACCCAACATC 60.989 61.111 2.24 0.00 0.00 3.06
3233 6046 2.700773 GGCCAACCCAACATCGAGC 61.701 63.158 0.00 0.00 0.00 5.03
3237 6050 1.434555 CAACCCAACATCGAGCGTAA 58.565 50.000 0.00 0.00 0.00 3.18
3240 6053 1.802365 ACCCAACATCGAGCGTAAAAC 59.198 47.619 0.00 0.00 0.00 2.43
3241 6054 1.801771 CCCAACATCGAGCGTAAAACA 59.198 47.619 0.00 0.00 0.00 2.83
3248 6067 2.669364 TCGAGCGTAAAACAAGGAGAC 58.331 47.619 0.00 0.00 0.00 3.36
3251 6070 2.479275 GAGCGTAAAACAAGGAGACACC 59.521 50.000 0.00 0.00 39.35 4.16
3270 6089 3.560068 CACCACCTCTAACAGACAACAAC 59.440 47.826 0.00 0.00 0.00 3.32
3298 6117 0.748450 TCGAACAAGGTCGGAACTGT 59.252 50.000 7.75 0.00 41.43 3.55
3301 6120 0.180406 AACAAGGTCGGAACTGTGCT 59.820 50.000 0.00 0.00 0.00 4.40
3302 6121 0.532862 ACAAGGTCGGAACTGTGCTG 60.533 55.000 0.00 0.00 0.00 4.41
3340 6159 3.009033 ACACACCATAGTACCAAGCACAT 59.991 43.478 0.00 0.00 0.00 3.21
3351 6170 1.376543 CAAGCACATCGAGCCATCTT 58.623 50.000 0.00 0.00 0.00 2.40
3354 6173 1.140452 AGCACATCGAGCCATCTTCAT 59.860 47.619 0.00 0.00 0.00 2.57
3359 6178 0.681733 TCGAGCCATCTTCATAGGGC 59.318 55.000 0.00 0.00 46.77 5.19
3363 6182 1.451504 CCATCTTCATAGGGCGCCA 59.548 57.895 30.85 9.36 0.00 5.69
3404 6223 4.003788 CGCTCCGGGTTGTGGACT 62.004 66.667 0.00 0.00 0.00 3.85
3456 6275 4.720773 AGAGATCAGAGACCATGTTGGAAT 59.279 41.667 0.00 0.00 40.96 3.01
3457 6276 5.191323 AGAGATCAGAGACCATGTTGGAATT 59.809 40.000 0.00 0.00 40.96 2.17
3501 6320 2.671070 CCACCGATGGCTCACCTT 59.329 61.111 0.00 0.00 39.82 3.50
3525 6344 2.676471 CCTTTCCGCCACCCCAAG 60.676 66.667 0.00 0.00 0.00 3.61
3547 6366 0.251742 CCCAATGGAGGTGCCTCAAA 60.252 55.000 18.75 7.77 44.40 2.69
3581 6400 2.471255 CCTTCAAGGCGACCATCAC 58.529 57.895 0.00 0.00 0.00 3.06
3585 6404 1.302431 CAAGGCGACCATCACACCA 60.302 57.895 0.00 0.00 0.00 4.17
3591 6410 1.665679 GCGACCATCACACCATTACAG 59.334 52.381 0.00 0.00 0.00 2.74
3599 6418 5.649395 CCATCACACCATTACAGAATTCACT 59.351 40.000 8.44 0.00 0.00 3.41
3620 6439 1.152694 AGCACACCACATGCAAGGT 60.153 52.632 3.26 3.26 45.92 3.50
3622 6441 1.959085 CACACCACATGCAAGGTCC 59.041 57.895 5.93 0.00 35.52 4.46
3657 6480 2.053244 TCCTACTACCTAGGAGTCCCG 58.947 57.143 17.98 6.94 45.57 5.14
3678 6501 5.294552 CCCGAATCTCCAAGAGTAACAATTC 59.705 44.000 0.00 0.00 0.00 2.17
3696 6519 5.649395 ACAATTCTGGTGATGAATGTGTAGG 59.351 40.000 0.00 0.00 34.74 3.18
3704 6527 6.126681 TGGTGATGAATGTGTAGGAGAATCAT 60.127 38.462 0.00 0.00 36.25 2.45
3719 6542 3.438360 GAATCATGATTCGGTTTGGTGC 58.562 45.455 27.90 6.67 37.97 5.01
3724 6547 1.001068 TGATTCGGTTTGGTGCGACTA 59.999 47.619 0.00 0.00 0.00 2.59
3732 6555 3.050619 GTTTGGTGCGACTATAGATCGG 58.949 50.000 19.39 7.69 39.99 4.18
3735 6558 0.516001 GTGCGACTATAGATCGGCGA 59.484 55.000 13.87 13.87 39.99 5.54
3776 6599 2.965147 AGTTCAATGGAGTTTGGTTGGG 59.035 45.455 0.00 0.00 0.00 4.12
3783 6606 4.301072 TGGAGTTTGGTTGGGAGAATAG 57.699 45.455 0.00 0.00 0.00 1.73
3796 6619 4.170845 TGGGAGAATAGAAGGGAGATGAGA 59.829 45.833 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
647 658 2.264005 AAAACGTGCACACCATCCTA 57.736 45.000 18.64 0.00 0.00 2.94
799 822 3.127589 GCAACGGGCTAACAACAAAAAT 58.872 40.909 0.00 0.00 40.25 1.82
869 892 0.782384 GTGGTCGTTGTTCTAGCACG 59.218 55.000 0.00 0.00 32.37 5.34
878 901 2.457778 GCGTGTGTGTGGTCGTTGT 61.458 57.895 0.00 0.00 0.00 3.32
928 951 2.982744 GCAAGAAGAAGCCACCCGC 61.983 63.158 0.00 0.00 37.98 6.13
974 997 2.546368 CCAAACACAGCTGCGTAGTTAA 59.454 45.455 15.27 0.00 0.00 2.01
979 1002 1.524849 TGCCAAACACAGCTGCGTA 60.525 52.632 15.27 0.00 0.00 4.42
992 1015 1.376683 GACGGTAGCATGGTGCCAA 60.377 57.895 28.04 0.00 46.52 4.52
993 1016 2.267642 GACGGTAGCATGGTGCCA 59.732 61.111 28.04 0.00 46.52 4.92
1193 1236 1.874345 GACGACGATGGTGTCACCCT 61.874 60.000 19.57 9.73 37.50 4.34
1409 1494 9.895138 TCAGAGATTAGAATCAATGACATTTCA 57.105 29.630 0.00 0.00 37.89 2.69
1427 1512 2.498078 GACGAGAAGGGGTTCAGAGATT 59.502 50.000 0.00 0.00 0.00 2.40
1437 1522 3.195825 ACACATTTAGAGACGAGAAGGGG 59.804 47.826 0.00 0.00 0.00 4.79
1438 1523 4.457834 ACACATTTAGAGACGAGAAGGG 57.542 45.455 0.00 0.00 0.00 3.95
1439 1524 6.202954 ACAAAACACATTTAGAGACGAGAAGG 59.797 38.462 0.00 0.00 0.00 3.46
1440 1525 7.169982 AGACAAAACACATTTAGAGACGAGAAG 59.830 37.037 0.00 0.00 0.00 2.85
1441 1526 6.984474 AGACAAAACACATTTAGAGACGAGAA 59.016 34.615 0.00 0.00 0.00 2.87
1442 1527 6.420903 CAGACAAAACACATTTAGAGACGAGA 59.579 38.462 0.00 0.00 0.00 4.04
1443 1528 6.201044 ACAGACAAAACACATTTAGAGACGAG 59.799 38.462 0.00 0.00 0.00 4.18
1444 1529 6.019075 CACAGACAAAACACATTTAGAGACGA 60.019 38.462 0.00 0.00 0.00 4.20
1445 1530 6.129393 CACAGACAAAACACATTTAGAGACG 58.871 40.000 0.00 0.00 0.00 4.18
1446 1531 6.907212 CACACAGACAAAACACATTTAGAGAC 59.093 38.462 0.00 0.00 0.00 3.36
1447 1532 6.597672 ACACACAGACAAAACACATTTAGAGA 59.402 34.615 0.00 0.00 0.00 3.10
1448 1533 6.785191 ACACACAGACAAAACACATTTAGAG 58.215 36.000 0.00 0.00 0.00 2.43
1449 1534 6.751514 ACACACAGACAAAACACATTTAGA 57.248 33.333 0.00 0.00 0.00 2.10
1450 1535 7.810766 AAACACACAGACAAAACACATTTAG 57.189 32.000 0.00 0.00 0.00 1.85
1451 1536 7.867909 TGAAAACACACAGACAAAACACATTTA 59.132 29.630 0.00 0.00 0.00 1.40
1452 1537 6.703607 TGAAAACACACAGACAAAACACATTT 59.296 30.769 0.00 0.00 0.00 2.32
1453 1538 6.219473 TGAAAACACACAGACAAAACACATT 58.781 32.000 0.00 0.00 0.00 2.71
1454 1539 5.777802 TGAAAACACACAGACAAAACACAT 58.222 33.333 0.00 0.00 0.00 3.21
1455 1540 5.188327 TGAAAACACACAGACAAAACACA 57.812 34.783 0.00 0.00 0.00 3.72
1456 1541 4.089923 GCTGAAAACACACAGACAAAACAC 59.910 41.667 0.00 0.00 36.38 3.32
1457 1542 4.233789 GCTGAAAACACACAGACAAAACA 58.766 39.130 0.00 0.00 36.38 2.83
1458 1543 3.612423 GGCTGAAAACACACAGACAAAAC 59.388 43.478 0.00 0.00 41.31 2.43
1459 1544 3.509575 AGGCTGAAAACACACAGACAAAA 59.490 39.130 0.00 0.00 43.78 2.44
1460 1545 3.088532 AGGCTGAAAACACACAGACAAA 58.911 40.909 0.00 0.00 43.78 2.83
1461 1546 2.423185 CAGGCTGAAAACACACAGACAA 59.577 45.455 9.42 0.00 43.78 3.18
1462 1547 2.016318 CAGGCTGAAAACACACAGACA 58.984 47.619 9.42 0.00 43.78 3.41
1463 1548 1.334869 CCAGGCTGAAAACACACAGAC 59.665 52.381 17.94 0.00 41.90 3.51
1464 1549 1.679139 CCAGGCTGAAAACACACAGA 58.321 50.000 17.94 0.00 36.38 3.41
1465 1550 0.031178 GCCAGGCTGAAAACACACAG 59.969 55.000 17.94 0.00 37.22 3.66
1466 1551 0.682532 TGCCAGGCTGAAAACACACA 60.683 50.000 17.94 0.00 0.00 3.72
1467 1552 0.249031 GTGCCAGGCTGAAAACACAC 60.249 55.000 17.94 10.06 0.00 3.82
1802 1895 1.041437 GGAGGAGGTATGTCTTCCCG 58.959 60.000 0.00 0.00 42.45 5.14
2125 3545 2.961768 CCGTGTTGTTCCATGCCC 59.038 61.111 0.00 0.00 0.00 5.36
2312 3738 2.202610 CGCTTCATCGCCACGAGA 60.203 61.111 0.00 0.00 39.91 4.04
2528 3954 2.029073 CAGAAGTCGTGCCCGTGT 59.971 61.111 0.00 0.00 35.01 4.49
2531 3957 4.003788 ACCCAGAAGTCGTGCCCG 62.004 66.667 0.00 0.00 0.00 6.13
2697 4123 3.820590 CACGTGGCAGTGGAACAA 58.179 55.556 7.95 0.00 44.16 2.83
2726 4152 1.324740 CCACACCCATGCCCATGAAG 61.325 60.000 9.73 3.76 41.20 3.02
2763 5560 3.382832 CAGTCGGCCGACCCTCTT 61.383 66.667 45.66 29.56 45.59 2.85
2777 5574 0.179037 CCATGATGGACGATGGCAGT 60.179 55.000 5.27 0.00 40.96 4.40
2976 5774 4.397417 AGACCGACTGTATGTACCTTGTAC 59.603 45.833 0.00 0.00 0.00 2.90
3060 5858 7.309867 GGAGGAGTTATAACCGACATCATGTAT 60.310 40.741 12.05 0.00 0.00 2.29
3064 5862 4.899457 TGGAGGAGTTATAACCGACATCAT 59.101 41.667 12.05 0.52 0.00 2.45
3065 5863 4.283337 TGGAGGAGTTATAACCGACATCA 58.717 43.478 12.05 2.20 0.00 3.07
3066 5864 4.931661 TGGAGGAGTTATAACCGACATC 57.068 45.455 12.05 10.55 0.00 3.06
3067 5865 5.046159 TGTTTGGAGGAGTTATAACCGACAT 60.046 40.000 12.05 2.37 0.00 3.06
3068 5866 4.283978 TGTTTGGAGGAGTTATAACCGACA 59.716 41.667 12.05 3.64 0.00 4.35
3069 5867 4.824289 TGTTTGGAGGAGTTATAACCGAC 58.176 43.478 12.05 3.16 0.00 4.79
3070 5868 4.081309 CCTGTTTGGAGGAGTTATAACCGA 60.081 45.833 12.05 0.00 38.35 4.69
3071 5869 4.189231 CCTGTTTGGAGGAGTTATAACCG 58.811 47.826 12.05 0.00 38.35 4.44
3072 5870 3.945921 GCCTGTTTGGAGGAGTTATAACC 59.054 47.826 12.05 4.03 38.35 2.85
3073 5871 4.844884 AGCCTGTTTGGAGGAGTTATAAC 58.155 43.478 7.57 7.57 38.35 1.89
3074 5872 5.514500 AAGCCTGTTTGGAGGAGTTATAA 57.486 39.130 0.00 0.00 38.35 0.98
3080 5893 1.160137 CGAAAGCCTGTTTGGAGGAG 58.840 55.000 0.00 0.00 38.35 3.69
3125 5938 0.322322 ACTTTGTATCGGTTCGGCCA 59.678 50.000 2.24 0.00 36.97 5.36
3146 5959 6.490381 ACCTACTTGTTTCCAGATTTTCTTCC 59.510 38.462 0.00 0.00 0.00 3.46
3147 5960 7.511959 ACCTACTTGTTTCCAGATTTTCTTC 57.488 36.000 0.00 0.00 0.00 2.87
3148 5961 7.201911 CCAACCTACTTGTTTCCAGATTTTCTT 60.202 37.037 0.00 0.00 0.00 2.52
3151 5964 6.133356 TCCAACCTACTTGTTTCCAGATTTT 58.867 36.000 0.00 0.00 0.00 1.82
3172 5985 7.231722 TCCGAATGTCCTTTTATTTTTCTTCCA 59.768 33.333 0.00 0.00 0.00 3.53
3177 5990 8.244113 ACTCATCCGAATGTCCTTTTATTTTTC 58.756 33.333 0.00 0.00 34.32 2.29
3178 5991 8.028938 CACTCATCCGAATGTCCTTTTATTTTT 58.971 33.333 0.00 0.00 34.32 1.94
3188 6001 0.107703 TGCCACTCATCCGAATGTCC 60.108 55.000 0.00 0.00 34.32 4.02
3190 6003 0.324614 TGTGCCACTCATCCGAATGT 59.675 50.000 0.00 0.00 34.32 2.71
3194 6007 0.320683 CACTTGTGCCACTCATCCGA 60.321 55.000 0.00 0.00 0.00 4.55
3199 6012 2.591429 CCGCACTTGTGCCACTCA 60.591 61.111 18.48 0.00 0.00 3.41
3200 6013 4.030452 GCCGCACTTGTGCCACTC 62.030 66.667 18.48 3.46 0.00 3.51
3206 6019 3.977244 GGGTTGGCCGCACTTGTG 61.977 66.667 0.00 0.00 34.97 3.33
3215 6028 2.700773 GCTCGATGTTGGGTTGGCC 61.701 63.158 0.00 0.00 0.00 5.36
3226 6039 3.060895 GTCTCCTTGTTTTACGCTCGATG 59.939 47.826 0.00 0.00 0.00 3.84
3228 6041 2.034939 TGTCTCCTTGTTTTACGCTCGA 59.965 45.455 0.00 0.00 0.00 4.04
3229 6042 2.155155 GTGTCTCCTTGTTTTACGCTCG 59.845 50.000 0.00 0.00 0.00 5.03
3233 6046 2.546789 GGTGGTGTCTCCTTGTTTTACG 59.453 50.000 0.00 0.00 37.07 3.18
3237 6050 2.127708 AGAGGTGGTGTCTCCTTGTTT 58.872 47.619 0.00 0.00 37.04 2.83
3240 6053 2.632996 TGTTAGAGGTGGTGTCTCCTTG 59.367 50.000 0.00 0.00 37.04 3.61
3241 6054 2.900546 CTGTTAGAGGTGGTGTCTCCTT 59.099 50.000 0.00 0.00 37.04 3.36
3248 6067 3.469008 TGTTGTCTGTTAGAGGTGGTG 57.531 47.619 0.00 0.00 0.00 4.17
3251 6070 2.800544 CCGTTGTTGTCTGTTAGAGGTG 59.199 50.000 0.00 0.00 0.00 4.00
3270 6089 2.539142 CGACCTTGTTCGATAGTCTCCG 60.539 54.545 0.00 0.00 41.78 4.63
3298 6117 2.195411 TGGTCTTGCAAGGCAGCA 59.805 55.556 30.67 21.92 40.61 4.41
3301 6120 1.827789 GTGGTGGTCTTGCAAGGCA 60.828 57.895 30.67 15.20 36.47 4.75
3302 6121 1.827789 TGTGGTGGTCTTGCAAGGC 60.828 57.895 25.73 24.39 0.00 4.35
3340 6159 0.681733 GCCCTATGAAGATGGCTCGA 59.318 55.000 0.00 0.00 40.77 4.04
3351 6170 2.499205 CGAGTTGGCGCCCTATGA 59.501 61.111 26.77 0.09 0.00 2.15
3404 6223 1.966148 ATCCCCTAGCAGGAGAGGCA 61.966 60.000 6.00 0.00 37.67 4.75
3430 6249 4.323333 CCAACATGGTCTCTGATCTCTGTT 60.323 45.833 0.00 0.00 31.35 3.16
3456 6275 3.343972 GCTTTGGCTCTCGCACAA 58.656 55.556 0.00 0.00 38.10 3.33
3506 6325 2.706952 CTTGGGGTGGCGGAAAGGAA 62.707 60.000 0.00 0.00 0.00 3.36
3525 6344 2.043953 GGCACCTCCATTGGGGAC 60.044 66.667 3.40 2.45 42.15 4.46
3547 6366 3.030291 TGAAGGCCAAACACAAGTGATT 58.970 40.909 5.01 0.00 0.00 2.57
3578 6397 5.003160 CCAGTGAATTCTGTAATGGTGTGA 58.997 41.667 7.05 0.00 34.02 3.58
3581 6400 4.095483 GCTCCAGTGAATTCTGTAATGGTG 59.905 45.833 7.05 7.57 34.02 4.17
3585 6404 4.697352 GTGTGCTCCAGTGAATTCTGTAAT 59.303 41.667 7.05 0.00 34.02 1.89
3591 6410 1.537202 GTGGTGTGCTCCAGTGAATTC 59.463 52.381 0.00 0.00 38.23 2.17
3599 6418 1.152798 TTGCATGTGGTGTGCTCCA 60.153 52.632 0.00 0.00 42.92 3.86
3654 6477 3.887621 TGTTACTCTTGGAGATTCGGG 57.112 47.619 1.31 0.00 33.32 5.14
3657 6480 6.881602 ACCAGAATTGTTACTCTTGGAGATTC 59.118 38.462 1.31 0.88 33.32 2.52
3678 6501 4.743057 TCTCCTACACATTCATCACCAG 57.257 45.455 0.00 0.00 0.00 4.00
3696 6519 4.731773 GCACCAAACCGAATCATGATTCTC 60.732 45.833 34.33 18.75 43.71 2.87
3704 6527 0.250124 AGTCGCACCAAACCGAATCA 60.250 50.000 0.00 0.00 35.00 2.57
3719 6542 3.741805 TGAATCGCCGATCTATAGTCG 57.258 47.619 0.00 14.15 38.75 4.18
3724 6547 5.139435 TGAAAGATGAATCGCCGATCTAT 57.861 39.130 0.00 0.00 0.00 1.98
3732 6555 7.475840 ACTTTTAGGATTGAAAGATGAATCGC 58.524 34.615 3.14 0.00 36.58 4.58
3760 6583 3.611025 TTCTCCCAACCAAACTCCATT 57.389 42.857 0.00 0.00 0.00 3.16
3761 6584 3.833559 ATTCTCCCAACCAAACTCCAT 57.166 42.857 0.00 0.00 0.00 3.41
3776 6599 9.927668 CTAAAATCTCATCTCCCTTCTATTCTC 57.072 37.037 0.00 0.00 0.00 2.87
3783 6606 6.493189 ACCTCTAAAATCTCATCTCCCTTC 57.507 41.667 0.00 0.00 0.00 3.46
3796 6619 4.837860 TCACCATTGCCAAACCTCTAAAAT 59.162 37.500 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.