Multiple sequence alignment - TraesCS3A01G368700

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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 TraesCS3A01G368700 chr3A 100.000 4473 0 0 1 4473 618163382 618167854 0.000000e+00 8261.0
1 TraesCS3A01G368700 chr3A 95.745 47 2 0 4427 4473 66443131 66443085 4.800000e-10 76.8
2 TraesCS3A01G368700 chr3D 95.484 3078 90 15 551 3587 475442066 475445135 0.000000e+00 4868.0
3 TraesCS3A01G368700 chr3D 87.123 1460 134 26 616 2045 475587580 475589015 0.000000e+00 1605.0
4 TraesCS3A01G368700 chr3D 83.925 1549 137 56 2105 3568 475589601 475591122 0.000000e+00 1378.0
5 TraesCS3A01G368700 chr3D 95.504 734 23 3 3623 4353 475445134 475445860 0.000000e+00 1164.0
6 TraesCS3A01G368700 chr3D 82.262 1229 140 41 773 1947 475550161 475551365 0.000000e+00 990.0
7 TraesCS3A01G368700 chr3D 92.115 558 26 10 1 547 475441284 475441834 0.000000e+00 771.0
8 TraesCS3A01G368700 chr3D 87.745 612 61 8 2947 3546 475552139 475552748 0.000000e+00 702.0
9 TraesCS3A01G368700 chr3D 93.933 445 16 2 2453 2889 475551703 475552144 0.000000e+00 662.0
10 TraesCS3A01G368700 chr3D 88.554 166 14 2 595 759 475549956 475550117 3.530000e-46 196.0
11 TraesCS3A01G368700 chr3D 94.203 69 4 0 3428 3496 475552759 475552827 6.120000e-19 106.0
12 TraesCS3A01G368700 chr3D 100.000 30 0 0 2049 2078 475589041 475589070 6.250000e-04 56.5
13 TraesCS3A01G368700 chr3B 94.824 2647 92 10 551 3160 632119127 632121765 0.000000e+00 4087.0
14 TraesCS3A01G368700 chr3B 87.433 1496 134 30 616 2078 632547287 632548761 0.000000e+00 1672.0
15 TraesCS3A01G368700 chr3B 84.452 1550 140 44 2095 3555 632549321 632550858 0.000000e+00 1434.0
16 TraesCS3A01G368700 chr3B 96.567 699 18 4 3111 3806 632121758 632122453 0.000000e+00 1153.0
17 TraesCS3A01G368700 chr3B 84.029 1221 121 37 773 1948 632202895 632204086 0.000000e+00 1107.0
18 TraesCS3A01G368700 chr3B 87.848 683 65 9 2419 3084 632204416 632205097 0.000000e+00 785.0
19 TraesCS3A01G368700 chr3B 89.983 579 37 11 1 567 632118344 632118913 0.000000e+00 728.0
20 TraesCS3A01G368700 chr3B 91.362 301 18 3 3803 4095 632138768 632139068 5.390000e-109 405.0
21 TraesCS3A01G368700 chr3B 87.293 181 17 4 3375 3549 632205798 632205978 7.590000e-48 202.0
22 TraesCS3A01G368700 chr3B 87.879 165 15 2 596 759 632202690 632202850 5.910000e-44 189.0
23 TraesCS3A01G368700 chr3B 87.302 126 10 5 3428 3547 632205986 632206111 6.030000e-29 139.0
24 TraesCS3A01G368700 chr5B 86.780 295 32 3 2419 2706 619136149 619135855 5.580000e-84 322.0
25 TraesCS3A01G368700 chr5B 86.333 300 34 4 2419 2711 619069373 619069074 2.010000e-83 320.0
26 TraesCS3A01G368700 chr5B 86.333 300 34 3 2419 2711 619105302 619105003 2.010000e-83 320.0
27 TraesCS3A01G368700 chr5B 95.745 47 2 0 4427 4473 232116176 232116222 4.800000e-10 76.8
28 TraesCS3A01G368700 chr4B 97.872 47 1 0 4427 4473 512473026 512472980 1.030000e-11 82.4
29 TraesCS3A01G368700 chr4A 95.745 47 2 0 4427 4473 391746368 391746322 4.800000e-10 76.8
30 TraesCS3A01G368700 chr2B 95.745 47 2 0 4427 4473 593724217 593724171 4.800000e-10 76.8
31 TraesCS3A01G368700 chr7D 93.750 48 3 0 4426 4473 459563836 459563789 6.210000e-09 73.1
32 TraesCS3A01G368700 chr6D 93.750 48 2 1 4427 4473 107035416 107035369 2.230000e-08 71.3
33 TraesCS3A01G368700 chr6D 93.617 47 3 0 4427 4473 171022371 171022417 2.230000e-08 71.3
34 TraesCS3A01G368700 chr6D 93.617 47 3 0 4427 4473 275787825 275787779 2.230000e-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 TraesCS3A01G368700 chr3A 618163382 618167854 4472 False 8261.000000 8261 100.000000 1 4473 1 chr3A.!!$F1 4472
1 TraesCS3A01G368700 chr3D 475441284 475445860 4576 False 2267.666667 4868 94.367667 1 4353 3 chr3D.!!$F1 4352
2 TraesCS3A01G368700 chr3D 475587580 475591122 3542 False 1013.166667 1605 90.349333 616 3568 3 chr3D.!!$F3 2952
3 TraesCS3A01G368700 chr3D 475549956 475552827 2871 False 531.200000 990 89.339400 595 3546 5 chr3D.!!$F2 2951
4 TraesCS3A01G368700 chr3B 632118344 632122453 4109 False 1989.333333 4087 93.791333 1 3806 3 chr3B.!!$F2 3805
5 TraesCS3A01G368700 chr3B 632547287 632550858 3571 False 1553.000000 1672 85.942500 616 3555 2 chr3B.!!$F4 2939
6 TraesCS3A01G368700 chr3B 632202690 632206111 3421 False 484.400000 1107 86.870200 596 3549 5 chr3B.!!$F3 2953

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
661 903 0.524862 GGTTCTCAGTGGCATGCAAG 59.475 55.0 21.36 8.34 0.00 4.01 F
1330 1645 0.179189 GATTGCTCGTTTCCGGCTTG 60.179 55.0 0.00 0.00 33.31 4.01 F
1636 1962 0.034574 ATGGCGAACATAAGTGGGCA 60.035 50.0 2.04 2.04 38.26 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1862 0.886563 GCAGAACAGCTTGAATGCCT 59.113 50.0 0.0 0.0 0.0 4.75 R
2913 3979 1.089920 GCACGCTCAGGTTCATCATT 58.910 50.0 0.0 0.0 0.0 2.57 R
3570 5138 0.179073 CCCCATCCTAGCTCAACACG 60.179 60.0 0.0 0.0 0.0 4.49 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
47 48 4.769488 TGCAATAATTCCTAGCCACAAACA 59.231 37.500 0.00 0.00 0.00 2.83
88 89 4.635765 TGTAGGTTGCATTCTCATTAGCAC 59.364 41.667 0.00 0.00 36.62 4.40
90 91 2.420022 GGTTGCATTCTCATTAGCACGT 59.580 45.455 0.00 0.00 36.62 4.49
116 117 8.128582 TGAAAATGCTCATCGTACCATTTTATC 58.871 33.333 14.33 7.50 43.77 1.75
132 133 7.226720 ACCATTTTATCGCTCTTTTCGATATGT 59.773 33.333 6.03 0.00 44.95 2.29
142 143 8.368857 CGCTCTTTTCGATATGTAATGTCATAG 58.631 37.037 0.00 0.00 33.58 2.23
145 146 9.196552 TCTTTTCGATATGTAATGTCATAGCAG 57.803 33.333 0.00 0.00 36.77 4.24
147 148 8.520835 TTTCGATATGTAATGTCATAGCAGTC 57.479 34.615 0.00 0.00 36.77 3.51
148 149 7.454260 TCGATATGTAATGTCATAGCAGTCT 57.546 36.000 0.00 0.00 36.77 3.24
237 239 2.419673 GTGGATTGTGATTGCGATGTCA 59.580 45.455 0.00 0.00 0.00 3.58
289 291 5.354513 TCTGACTCGTCGTTTTCATAGATCT 59.645 40.000 0.00 0.00 0.00 2.75
302 304 5.042463 TCATAGATCTCGAGGGCCTATAG 57.958 47.826 13.56 7.22 0.00 1.31
318 320 4.745620 GCCTATAGTGATCCACTCGTTTTC 59.254 45.833 2.55 0.00 41.21 2.29
330 332 6.675026 TCCACTCGTTTTCCGATACATATAG 58.325 40.000 0.00 0.00 46.23 1.31
331 333 5.345202 CCACTCGTTTTCCGATACATATAGC 59.655 44.000 0.00 0.00 46.23 2.97
354 356 7.112122 AGCTGTATTGGTCATAGAATCAACAA 58.888 34.615 0.00 0.00 0.00 2.83
394 396 9.273016 CTTTTCACATGACTCTTTAGTAGGAAA 57.727 33.333 0.00 0.00 35.56 3.13
416 418 9.860898 GGAAATCTAAGCAAAATATCTGTTTGT 57.139 29.630 1.45 0.00 38.09 2.83
419 421 7.759489 TCTAAGCAAAATATCTGTTTGTGGT 57.241 32.000 1.45 0.00 38.09 4.16
420 422 8.856153 TCTAAGCAAAATATCTGTTTGTGGTA 57.144 30.769 1.45 0.00 38.09 3.25
421 423 9.461312 TCTAAGCAAAATATCTGTTTGTGGTAT 57.539 29.630 1.45 0.00 38.09 2.73
423 425 8.761575 AAGCAAAATATCTGTTTGTGGTATTG 57.238 30.769 1.45 0.00 38.09 1.90
424 426 8.121305 AGCAAAATATCTGTTTGTGGTATTGA 57.879 30.769 1.45 0.00 38.09 2.57
425 427 8.584157 AGCAAAATATCTGTTTGTGGTATTGAA 58.416 29.630 1.45 0.00 38.09 2.69
432 434 7.517614 TCTGTTTGTGGTATTGAATGCTTAA 57.482 32.000 0.00 0.00 0.00 1.85
512 516 9.686683 AGTACATAAGCTTGTATTTCTGGAATT 57.313 29.630 9.86 0.00 34.76 2.17
622 864 1.060553 CACACCAACGATCGAATTCCG 59.939 52.381 24.34 7.82 40.25 4.30
658 900 0.895100 TTGGGTTCTCAGTGGCATGC 60.895 55.000 9.90 9.90 0.00 4.06
659 901 1.303561 GGGTTCTCAGTGGCATGCA 60.304 57.895 21.36 2.54 0.00 3.96
661 903 0.524862 GGTTCTCAGTGGCATGCAAG 59.475 55.000 21.36 8.34 0.00 4.01
662 904 1.527034 GTTCTCAGTGGCATGCAAGA 58.473 50.000 21.36 10.55 0.00 3.02
663 905 1.467734 GTTCTCAGTGGCATGCAAGAG 59.532 52.381 21.36 18.59 0.00 2.85
664 906 0.689055 TCTCAGTGGCATGCAAGAGT 59.311 50.000 21.36 2.40 0.00 3.24
706 949 8.621286 GGACATACCTATATTTGGAAGTTTGTG 58.379 37.037 2.01 0.00 35.41 3.33
884 1159 1.006766 TGGGATCCAAGGGCCCATA 59.993 57.895 27.56 6.15 46.57 2.74
929 1214 6.367969 GTGTGTACTTGGAACGTCATATTCTT 59.632 38.462 0.00 0.00 0.00 2.52
959 1244 2.126228 GCCGTCGGATGAACGTGA 60.126 61.111 17.49 0.00 34.94 4.35
1088 1403 1.140052 TCTCTCTCTCGCTCGATTCCT 59.860 52.381 0.00 0.00 0.00 3.36
1121 1436 2.756283 CTTCGCCGACCTCCTCCT 60.756 66.667 0.00 0.00 0.00 3.69
1130 1445 1.071699 CGACCTCCTCCTTTGTTTCCA 59.928 52.381 0.00 0.00 0.00 3.53
1165 1480 4.096003 ATGGCGTCGTTGGGGGAG 62.096 66.667 0.00 0.00 0.00 4.30
1239 1554 1.674817 CGGCAGGTTCGAAAGGTACAT 60.675 52.381 0.00 0.00 0.00 2.29
1330 1645 0.179189 GATTGCTCGTTTCCGGCTTG 60.179 55.000 0.00 0.00 33.31 4.01
1439 1761 1.896660 GACAAAGACCTGCCGCCAA 60.897 57.895 0.00 0.00 0.00 4.52
1540 1862 2.865119 TTTGAGCAGCTTGATCTCCA 57.135 45.000 0.00 0.00 33.24 3.86
1636 1962 0.034574 ATGGCGAACATAAGTGGGCA 60.035 50.000 2.04 2.04 38.26 5.36
1722 2048 2.438434 CCCCGGCATCAAGGTGAC 60.438 66.667 0.00 0.00 0.00 3.67
1851 2184 2.064014 GAAGCATGCTGAACTTTTGGC 58.936 47.619 23.48 0.00 0.00 4.52
2036 2395 5.616270 TGGTCAAGCACATTAGTTCTACAA 58.384 37.500 0.00 0.00 0.00 2.41
2181 3122 2.427506 CTCAGTTTCCCTTGTAGGCAC 58.572 52.381 0.00 0.00 32.73 5.01
2215 3156 7.704047 TCATCTCTATACGCATATGAATTGCTC 59.296 37.037 6.97 0.00 37.96 4.26
2401 3390 3.309410 TGAAAAACTACCACGTTTCCGTC 59.691 43.478 0.00 0.00 46.28 4.79
2492 3485 4.514441 GTGCCAATCATCTGGAGACATTAG 59.486 45.833 0.00 0.00 41.51 1.73
2497 3490 6.320672 CCAATCATCTGGAGACATTAGCTTTT 59.679 38.462 0.00 0.00 41.51 2.27
2498 3491 6.939132 ATCATCTGGAGACATTAGCTTTTG 57.061 37.500 0.00 0.00 41.51 2.44
2499 3492 6.053632 TCATCTGGAGACATTAGCTTTTGA 57.946 37.500 0.00 0.00 41.51 2.69
2501 3494 7.114754 TCATCTGGAGACATTAGCTTTTGATT 58.885 34.615 0.00 0.00 41.51 2.57
2502 3495 6.748333 TCTGGAGACATTAGCTTTTGATTG 57.252 37.500 0.00 0.00 41.51 2.67
2545 3545 0.454600 GACTGAGGCGGACGACATAA 59.545 55.000 0.00 0.00 0.00 1.90
2553 3553 1.867233 GCGGACGACATAATGCTGATT 59.133 47.619 0.00 0.00 0.00 2.57
2821 3821 1.144057 GACGGCCAGATCGTTCCAT 59.856 57.895 2.24 0.00 41.22 3.41
2913 3979 1.446099 GTCATCGTCGCAAGCAGGA 60.446 57.895 0.00 0.00 37.18 3.86
3021 4105 2.512896 CTGCTGCCCTATGGACCC 59.487 66.667 0.00 0.00 0.00 4.46
3304 4739 8.561769 TCCAAGTACCCTATCCATTAATTTCAA 58.438 33.333 0.00 0.00 0.00 2.69
3381 4938 3.741249 TGTTGTATACTGTTGCCCGAAA 58.259 40.909 4.17 0.00 0.00 3.46
3522 5090 2.004583 TGTTTCTAGCGATTCACCCG 57.995 50.000 0.00 0.00 0.00 5.28
3570 5138 1.122849 CATCGTTGCTGTTGTGTTGC 58.877 50.000 0.00 0.00 0.00 4.17
3603 5171 1.913951 ATGGGGATCAGAGCAACGCA 61.914 55.000 0.00 0.00 0.00 5.24
3605 5173 1.817099 GGGATCAGAGCAACGCAGG 60.817 63.158 0.00 0.00 0.00 4.85
3701 5273 3.813529 CGAGAAATCTTTCGCCTTGTT 57.186 42.857 1.59 0.00 41.92 2.83
3837 5412 1.065564 GTCAGCAGCAGAGGGAAAGAT 60.066 52.381 0.00 0.00 0.00 2.40
3902 5477 3.839432 CTCCCCGCTCCGAAGTCC 61.839 72.222 0.00 0.00 0.00 3.85
3909 5484 2.507992 CTCCGAAGTCCAGCGCTG 60.508 66.667 30.52 30.52 0.00 5.18
3951 5526 1.971695 GCCTTCACCCAAACCCTCG 60.972 63.158 0.00 0.00 0.00 4.63
3958 5533 0.834687 ACCCAAACCCTCGTCTAGCA 60.835 55.000 0.00 0.00 0.00 3.49
3968 5543 1.446792 CGTCTAGCAGGCACCACTG 60.447 63.158 0.00 0.00 41.41 3.66
3978 5553 2.831770 CACCACTGCTCCACCAGT 59.168 61.111 0.00 0.00 46.47 4.00
4049 5624 0.037326 TTCAGTCGGAGCACCATGTC 60.037 55.000 0.00 0.00 35.59 3.06
4087 5662 1.137872 CTTCCATCTTCTGGTCCTCCG 59.862 57.143 0.00 0.00 46.08 4.63
4114 5689 5.475719 CACAATTCCTAGAACGTAGAACCA 58.524 41.667 0.00 0.00 0.00 3.67
4130 5705 3.901844 AGAACCACAACTCCTACAAGCTA 59.098 43.478 0.00 0.00 0.00 3.32
4151 5726 1.873591 GTGTAGCACCACAACCTTCTG 59.126 52.381 1.31 0.00 35.38 3.02
4200 5775 2.006888 GCATCCAGCTGCGTAACTTAA 58.993 47.619 8.66 0.00 41.15 1.85
4246 5821 4.568152 ACTCAAAACATGGTGTAGCAAC 57.432 40.909 0.00 0.00 0.00 4.17
4273 5848 2.028112 TGCTCAACTCCATCCAGTACAC 60.028 50.000 0.00 0.00 0.00 2.90
4290 5865 1.079543 ACACTCGAGCAGGTGCATC 60.080 57.895 13.61 0.00 45.16 3.91
4291 5866 1.217511 CACTCGAGCAGGTGCATCT 59.782 57.895 13.61 0.00 45.16 2.90
4292 5867 0.805322 CACTCGAGCAGGTGCATCTC 60.805 60.000 13.61 0.00 45.16 2.75
4293 5868 1.227205 CTCGAGCAGGTGCATCTCC 60.227 63.158 0.00 0.00 45.16 3.71
4294 5869 1.953231 CTCGAGCAGGTGCATCTCCA 61.953 60.000 0.00 0.00 45.16 3.86
4295 5870 1.521010 CGAGCAGGTGCATCTCCAG 60.521 63.158 0.00 0.00 45.16 3.86
4302 5877 0.179062 GGTGCATCTCCAGAAGCGAT 60.179 55.000 0.00 0.00 41.22 4.58
4330 5905 2.645802 AGTCTCCTCTCGACCATACAC 58.354 52.381 0.00 0.00 31.83 2.90
4353 5928 7.068839 ACACCACACAAAATATACCAACTTTGA 59.931 33.333 3.01 0.00 33.84 2.69
4354 5929 8.087750 CACCACACAAAATATACCAACTTTGAT 58.912 33.333 3.01 0.00 33.84 2.57
4355 5930 8.303876 ACCACACAAAATATACCAACTTTGATC 58.696 33.333 3.01 0.00 33.84 2.92
4356 5931 7.759433 CCACACAAAATATACCAACTTTGATCC 59.241 37.037 3.01 0.00 33.84 3.36
4357 5932 7.759433 CACACAAAATATACCAACTTTGATCCC 59.241 37.037 3.01 0.00 33.84 3.85
4358 5933 6.972328 CACAAAATATACCAACTTTGATCCCG 59.028 38.462 3.01 0.00 33.84 5.14
4359 5934 6.096282 ACAAAATATACCAACTTTGATCCCGG 59.904 38.462 0.00 0.00 33.84 5.73
4360 5935 5.640158 AATATACCAACTTTGATCCCGGA 57.360 39.130 0.73 0.00 0.00 5.14
4361 5936 5.640158 ATATACCAACTTTGATCCCGGAA 57.360 39.130 0.73 0.00 0.00 4.30
4362 5937 2.200373 ACCAACTTTGATCCCGGAAG 57.800 50.000 0.73 0.00 0.00 3.46
4363 5938 1.423921 ACCAACTTTGATCCCGGAAGT 59.576 47.619 0.73 0.15 35.27 3.01
4364 5939 2.158519 ACCAACTTTGATCCCGGAAGTT 60.159 45.455 0.73 7.82 42.55 2.66
4365 5940 2.488153 CCAACTTTGATCCCGGAAGTTC 59.512 50.000 13.65 0.00 40.54 3.01
4366 5941 3.146066 CAACTTTGATCCCGGAAGTTCA 58.854 45.455 13.65 3.85 40.54 3.18
4367 5942 2.779506 ACTTTGATCCCGGAAGTTCAC 58.220 47.619 0.73 0.00 29.81 3.18
4368 5943 2.105821 ACTTTGATCCCGGAAGTTCACA 59.894 45.455 0.73 0.00 29.81 3.58
4369 5944 2.472695 TTGATCCCGGAAGTTCACAG 57.527 50.000 0.73 0.00 0.00 3.66
4370 5945 1.639722 TGATCCCGGAAGTTCACAGA 58.360 50.000 0.73 0.00 0.00 3.41
4371 5946 1.550524 TGATCCCGGAAGTTCACAGAG 59.449 52.381 0.73 0.00 0.00 3.35
4372 5947 0.905357 ATCCCGGAAGTTCACAGAGG 59.095 55.000 0.73 0.00 0.00 3.69
4373 5948 1.376037 CCCGGAAGTTCACAGAGGC 60.376 63.158 0.73 0.00 0.00 4.70
4374 5949 1.371183 CCGGAAGTTCACAGAGGCA 59.629 57.895 0.00 0.00 0.00 4.75
4375 5950 0.671781 CCGGAAGTTCACAGAGGCAG 60.672 60.000 0.00 0.00 0.00 4.85
4376 5951 1.294659 CGGAAGTTCACAGAGGCAGC 61.295 60.000 5.01 0.00 0.00 5.25
4377 5952 0.957888 GGAAGTTCACAGAGGCAGCC 60.958 60.000 1.84 1.84 0.00 4.85
4378 5953 0.036022 GAAGTTCACAGAGGCAGCCT 59.964 55.000 16.12 16.12 36.03 4.58
4379 5954 0.250640 AAGTTCACAGAGGCAGCCTG 60.251 55.000 22.26 9.25 31.76 4.85
4380 5955 2.033141 TTCACAGAGGCAGCCTGC 59.967 61.111 22.26 8.55 44.08 4.85
4399 5974 2.956964 CGATCGCTCGGTTGCCTC 60.957 66.667 0.26 0.00 41.27 4.70
4400 5975 2.956964 GATCGCTCGGTTGCCTCG 60.957 66.667 0.00 0.00 0.00 4.63
4401 5976 4.514577 ATCGCTCGGTTGCCTCGG 62.515 66.667 0.00 0.00 0.00 4.63
4403 5978 4.514577 CGCTCGGTTGCCTCGGAT 62.515 66.667 0.00 0.00 0.00 4.18
4404 5979 2.812499 GCTCGGTTGCCTCGGATA 59.188 61.111 0.00 0.00 0.00 2.59
4405 5980 1.367840 GCTCGGTTGCCTCGGATAT 59.632 57.895 0.00 0.00 0.00 1.63
4406 5981 0.601558 GCTCGGTTGCCTCGGATATA 59.398 55.000 0.00 0.00 0.00 0.86
4407 5982 1.204941 GCTCGGTTGCCTCGGATATAT 59.795 52.381 0.00 0.00 0.00 0.86
4408 5983 2.881074 CTCGGTTGCCTCGGATATATG 58.119 52.381 0.00 0.00 0.00 1.78
4409 5984 2.231478 CTCGGTTGCCTCGGATATATGT 59.769 50.000 0.00 0.00 0.00 2.29
4410 5985 2.631062 TCGGTTGCCTCGGATATATGTT 59.369 45.455 0.00 0.00 0.00 2.71
4411 5986 3.827876 TCGGTTGCCTCGGATATATGTTA 59.172 43.478 0.00 0.00 0.00 2.41
4412 5987 3.924686 CGGTTGCCTCGGATATATGTTAC 59.075 47.826 0.00 0.00 0.00 2.50
4413 5988 4.321750 CGGTTGCCTCGGATATATGTTACT 60.322 45.833 0.00 0.00 0.00 2.24
4414 5989 5.106038 CGGTTGCCTCGGATATATGTTACTA 60.106 44.000 0.00 0.00 0.00 1.82
4415 5990 6.405508 CGGTTGCCTCGGATATATGTTACTAT 60.406 42.308 0.00 0.00 0.00 2.12
4416 5991 6.979238 GGTTGCCTCGGATATATGTTACTATC 59.021 42.308 0.00 0.00 0.00 2.08
4417 5992 6.373186 TGCCTCGGATATATGTTACTATCG 57.627 41.667 0.00 0.00 0.00 2.92
4418 5993 5.884232 TGCCTCGGATATATGTTACTATCGT 59.116 40.000 0.00 0.00 0.00 3.73
4419 5994 6.376299 TGCCTCGGATATATGTTACTATCGTT 59.624 38.462 0.00 0.00 0.00 3.85
4420 5995 7.553760 TGCCTCGGATATATGTTACTATCGTTA 59.446 37.037 0.00 0.00 0.00 3.18
4421 5996 8.566260 GCCTCGGATATATGTTACTATCGTTAT 58.434 37.037 0.00 0.00 0.00 1.89
4464 6039 9.606631 AAGTTTCTACTATCTGATCATGGAAAC 57.393 33.333 22.13 22.13 39.75 2.78
4465 6040 7.923344 AGTTTCTACTATCTGATCATGGAAACG 59.077 37.037 22.70 0.91 42.35 3.60
4466 6041 7.582667 TTCTACTATCTGATCATGGAAACGA 57.417 36.000 0.00 0.00 0.00 3.85
4467 6042 7.582667 TCTACTATCTGATCATGGAAACGAA 57.417 36.000 0.00 0.00 0.00 3.85
4468 6043 8.183104 TCTACTATCTGATCATGGAAACGAAT 57.817 34.615 0.00 0.00 0.00 3.34
4469 6044 9.297037 TCTACTATCTGATCATGGAAACGAATA 57.703 33.333 0.00 0.00 0.00 1.75
4472 6047 9.784531 ACTATCTGATCATGGAAACGAATATTT 57.215 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.954666 ACCTACAAACATTTAAGGTATGCAT 57.045 32.000 3.79 3.79 35.28 3.96
88 89 2.670905 TGGTACGATGAGCATTTTCACG 59.329 45.455 0.00 0.00 0.00 4.35
116 117 6.510746 TGACATTACATATCGAAAAGAGCG 57.489 37.500 0.00 0.00 0.00 5.03
145 146 9.104965 AGTATCTATAGACGATGCAGATAAGAC 57.895 37.037 4.10 0.00 31.78 3.01
147 148 9.103861 TGAGTATCTATAGACGATGCAGATAAG 57.896 37.037 4.10 0.00 34.92 1.73
148 149 9.449719 TTGAGTATCTATAGACGATGCAGATAA 57.550 33.333 4.10 0.00 34.92 1.75
152 153 6.903419 TGTTGAGTATCTATAGACGATGCAG 58.097 40.000 4.10 0.00 34.92 4.41
237 239 2.624636 ACTTGTTCTTTTCGTGTCGGT 58.375 42.857 0.00 0.00 0.00 4.69
289 291 1.427753 TGGATCACTATAGGCCCTCGA 59.572 52.381 0.00 0.00 0.00 4.04
318 320 6.863275 TGACCAATACAGCTATATGTATCGG 58.137 40.000 2.96 2.96 43.85 4.18
330 332 6.925610 TGTTGATTCTATGACCAATACAGC 57.074 37.500 0.00 0.00 0.00 4.40
331 333 8.722480 TCTTGTTGATTCTATGACCAATACAG 57.278 34.615 0.00 0.00 0.00 2.74
354 356 4.269183 TGTGAAAAGTGGTGTGTTGATCT 58.731 39.130 0.00 0.00 0.00 2.75
394 396 8.353423 ACCACAAACAGATATTTTGCTTAGAT 57.647 30.769 0.00 0.00 37.45 1.98
415 417 9.632807 TTTTGTATGTTAAGCATTCAATACCAC 57.367 29.630 9.26 0.00 41.98 4.16
420 422 9.289303 GTCGATTTTGTATGTTAAGCATTCAAT 57.711 29.630 0.00 0.59 41.98 2.57
421 423 7.480229 CGTCGATTTTGTATGTTAAGCATTCAA 59.520 33.333 0.00 6.21 41.15 2.69
422 424 6.958752 CGTCGATTTTGTATGTTAAGCATTCA 59.041 34.615 0.00 0.00 38.94 2.57
423 425 6.959311 ACGTCGATTTTGTATGTTAAGCATTC 59.041 34.615 0.00 0.00 38.94 2.67
424 426 6.837992 ACGTCGATTTTGTATGTTAAGCATT 58.162 32.000 0.00 0.00 38.94 3.56
425 427 6.417191 ACGTCGATTTTGTATGTTAAGCAT 57.583 33.333 0.00 0.00 41.42 3.79
432 434 6.203338 ACCTTTACAACGTCGATTTTGTATGT 59.797 34.615 17.62 13.61 37.87 2.29
644 886 1.072806 ACTCTTGCATGCCACTGAGAA 59.927 47.619 23.47 8.30 32.10 2.87
658 900 3.060272 CGTATGCGCATAAAGGACTCTTG 60.060 47.826 30.50 5.21 32.75 3.02
659 901 3.123804 CGTATGCGCATAAAGGACTCTT 58.876 45.455 30.50 4.17 34.07 2.85
661 903 1.792949 CCGTATGCGCATAAAGGACTC 59.207 52.381 32.92 19.61 36.67 3.36
662 904 1.411246 TCCGTATGCGCATAAAGGACT 59.589 47.619 33.99 14.60 36.67 3.85
663 905 1.525619 GTCCGTATGCGCATAAAGGAC 59.474 52.381 40.20 40.20 41.57 3.85
664 906 1.137282 TGTCCGTATGCGCATAAAGGA 59.863 47.619 33.99 33.99 36.67 3.36
884 1159 0.620556 ATTCCACAGACCAGGCGAAT 59.379 50.000 0.00 0.00 0.00 3.34
959 1244 2.621486 AGCCTTTAATCTCCGGGCT 58.379 52.632 0.00 0.00 46.95 5.19
1165 1480 2.094854 CAGCTCCTGGTTCAAAAGCATC 60.095 50.000 5.72 0.00 38.36 3.91
1215 1530 2.203084 TTTCGAACCTGCCGTGCA 60.203 55.556 0.00 0.00 36.92 4.57
1239 1554 3.414193 CATGGGCAGGGCTCAGGA 61.414 66.667 0.00 0.00 44.09 3.86
1330 1645 4.512914 GTGGAGGGAGGCATGCCC 62.513 72.222 33.14 23.03 46.40 5.36
1374 1696 2.902343 GCCTCAGCGCCATAACCC 60.902 66.667 2.29 0.00 0.00 4.11
1439 1761 2.264794 GTGTCGCCCCATCGTTCT 59.735 61.111 0.00 0.00 0.00 3.01
1539 1861 1.402456 GCAGAACAGCTTGAATGCCTG 60.402 52.381 0.00 0.00 0.00 4.85
1540 1862 0.886563 GCAGAACAGCTTGAATGCCT 59.113 50.000 0.00 0.00 0.00 4.75
1636 1962 1.272147 GGGAGGTGCTCTGAAATGGTT 60.272 52.381 0.00 0.00 0.00 3.67
1722 2048 3.005261 AGACTATAAGCTGCGATGGTGAG 59.995 47.826 10.39 0.00 0.00 3.51
1723 2049 2.959030 AGACTATAAGCTGCGATGGTGA 59.041 45.455 10.39 0.00 0.00 4.02
2132 3071 5.772004 ACCCCATATGGTGCTTTGTTAATA 58.228 37.500 20.46 0.00 37.20 0.98
2139 3080 3.450817 GCTAAAACCCCATATGGTGCTTT 59.549 43.478 20.46 14.75 39.05 3.51
2181 3122 8.689069 CATATGCGTATAGAGATGAATTGATCG 58.311 37.037 0.00 0.00 0.00 3.69
2215 3156 2.125912 CAGACGGCAAGGTCCTCG 60.126 66.667 0.00 0.00 37.66 4.63
2492 3485 5.047802 TCCTTCTGGAATGTCAATCAAAAGC 60.048 40.000 0.00 0.00 39.87 3.51
2497 3490 3.009363 TGCTCCTTCTGGAATGTCAATCA 59.991 43.478 0.00 0.00 42.66 2.57
2498 3491 3.376546 GTGCTCCTTCTGGAATGTCAATC 59.623 47.826 0.00 0.00 42.66 2.67
2499 3492 3.245016 TGTGCTCCTTCTGGAATGTCAAT 60.245 43.478 0.00 0.00 42.66 2.57
2501 3494 1.699083 TGTGCTCCTTCTGGAATGTCA 59.301 47.619 0.00 0.00 42.66 3.58
2502 3495 2.479566 TGTGCTCCTTCTGGAATGTC 57.520 50.000 0.00 0.00 42.66 3.06
2545 3545 1.576451 TTGTGCGCGTCAATCAGCAT 61.576 50.000 8.43 0.00 41.88 3.79
2553 3553 4.228567 TGGACCTTGTGCGCGTCA 62.229 61.111 8.43 3.08 0.00 4.35
2913 3979 1.089920 GCACGCTCAGGTTCATCATT 58.910 50.000 0.00 0.00 0.00 2.57
3304 4739 5.754543 TCGGAAAGGTAAAAACGACAAAT 57.245 34.783 0.00 0.00 0.00 2.32
3522 5090 5.567138 AATGTCGGAAACAGAAATCCATC 57.433 39.130 0.00 0.00 42.37 3.51
3570 5138 0.179073 CCCCATCCTAGCTCAACACG 60.179 60.000 0.00 0.00 0.00 4.49
3603 5171 2.584608 GTACACCTGCGCATCCCT 59.415 61.111 12.24 0.00 0.00 4.20
3605 5173 2.584608 AGGTACACCTGCGCATCC 59.415 61.111 12.24 7.14 46.55 3.51
3632 5204 0.530870 GTCCCTGCTCCATTCGTAGC 60.531 60.000 0.00 0.00 39.25 3.58
3701 5273 1.879380 CCGTGGTGAGCAAGATCAAAA 59.121 47.619 0.00 0.00 0.00 2.44
3902 5477 2.097160 GCAATGTCGACAGCGCTG 59.903 61.111 34.89 34.89 37.46 5.18
3909 5484 1.060937 GCGATGGTGCAATGTCGAC 59.939 57.895 9.11 9.11 36.25 4.20
3951 5526 4.606071 CAGTGGTGCCTGCTAGAC 57.394 61.111 0.00 0.00 0.00 2.59
4049 5624 2.414994 AGATCCAGTGCAAGTCATGG 57.585 50.000 0.00 0.00 0.00 3.66
4087 5662 5.888105 TCTACGTTCTAGGAATTGTGCTAC 58.112 41.667 0.00 0.00 0.00 3.58
4114 5689 4.082136 GCTACACTAGCTTGTAGGAGTTGT 60.082 45.833 21.55 8.56 46.27 3.32
4130 5705 1.768870 AGAAGGTTGTGGTGCTACACT 59.231 47.619 11.59 0.00 41.84 3.55
4200 5775 1.271597 GCCAGATGTTGACTCCCACTT 60.272 52.381 0.00 0.00 0.00 3.16
4246 5821 0.449388 GATGGAGTTGAGCAAAGCCG 59.551 55.000 0.00 0.00 0.00 5.52
4258 5833 1.819288 CGAGTGTGTACTGGATGGAGT 59.181 52.381 0.00 0.00 37.25 3.85
4273 5848 0.805322 GAGATGCACCTGCTCGAGTG 60.805 60.000 15.13 6.22 42.66 3.51
4290 5865 6.686630 AGACTATTATTCATCGCTTCTGGAG 58.313 40.000 0.00 0.00 0.00 3.86
4291 5866 6.294787 GGAGACTATTATTCATCGCTTCTGGA 60.295 42.308 0.00 0.00 0.00 3.86
4292 5867 5.866633 GGAGACTATTATTCATCGCTTCTGG 59.133 44.000 0.00 0.00 0.00 3.86
4293 5868 6.686630 AGGAGACTATTATTCATCGCTTCTG 58.313 40.000 0.00 0.00 40.61 3.02
4294 5869 6.719370 AGAGGAGACTATTATTCATCGCTTCT 59.281 38.462 0.00 0.00 44.43 2.85
4295 5870 6.919721 AGAGGAGACTATTATTCATCGCTTC 58.080 40.000 0.00 0.00 44.43 3.86
4302 5877 5.691896 TGGTCGAGAGGAGACTATTATTCA 58.308 41.667 0.00 0.00 44.43 2.57
4330 5905 7.759433 GGATCAAAGTTGGTATATTTTGTGTGG 59.241 37.037 0.00 0.00 33.46 4.17
4353 5928 0.905357 CCTCTGTGAACTTCCGGGAT 59.095 55.000 0.00 0.00 0.00 3.85
4354 5929 1.827399 GCCTCTGTGAACTTCCGGGA 61.827 60.000 0.00 0.00 0.00 5.14
4355 5930 1.376037 GCCTCTGTGAACTTCCGGG 60.376 63.158 0.00 0.00 0.00 5.73
4356 5931 0.671781 CTGCCTCTGTGAACTTCCGG 60.672 60.000 0.00 0.00 0.00 5.14
4357 5932 1.294659 GCTGCCTCTGTGAACTTCCG 61.295 60.000 0.00 0.00 0.00 4.30
4358 5933 0.957888 GGCTGCCTCTGTGAACTTCC 60.958 60.000 12.43 0.00 0.00 3.46
4359 5934 0.036022 AGGCTGCCTCTGTGAACTTC 59.964 55.000 17.22 0.00 0.00 3.01
4360 5935 0.250640 CAGGCTGCCTCTGTGAACTT 60.251 55.000 20.49 0.00 0.00 2.66
4361 5936 1.374190 CAGGCTGCCTCTGTGAACT 59.626 57.895 20.49 0.00 0.00 3.01
4362 5937 2.331132 GCAGGCTGCCTCTGTGAAC 61.331 63.158 28.87 0.00 37.42 3.18
4363 5938 2.033141 GCAGGCTGCCTCTGTGAA 59.967 61.111 28.87 0.00 37.42 3.18
4382 5957 2.956964 GAGGCAACCGAGCGATCG 60.957 66.667 17.57 17.57 34.64 3.69
4383 5958 2.956964 CGAGGCAACCGAGCGATC 60.957 66.667 0.00 0.00 34.64 3.69
4384 5959 4.514577 CCGAGGCAACCGAGCGAT 62.515 66.667 0.00 0.00 34.64 4.58
4386 5961 2.421877 ATATCCGAGGCAACCGAGCG 62.422 60.000 0.00 0.00 34.64 5.03
4387 5962 0.601558 TATATCCGAGGCAACCGAGC 59.398 55.000 0.00 0.00 32.87 5.03
4388 5963 2.231478 ACATATATCCGAGGCAACCGAG 59.769 50.000 0.00 0.00 32.87 4.63
4389 5964 2.244695 ACATATATCCGAGGCAACCGA 58.755 47.619 0.00 0.00 32.87 4.69
4390 5965 2.743636 ACATATATCCGAGGCAACCG 57.256 50.000 0.00 0.00 37.17 4.44
4391 5966 5.148651 AGTAACATATATCCGAGGCAACC 57.851 43.478 0.00 0.00 37.17 3.77
4392 5967 6.691818 CGATAGTAACATATATCCGAGGCAAC 59.308 42.308 0.00 0.00 0.00 4.17
4393 5968 6.792326 CGATAGTAACATATATCCGAGGCAA 58.208 40.000 0.00 0.00 0.00 4.52
4394 5969 6.373186 CGATAGTAACATATATCCGAGGCA 57.627 41.667 0.00 0.00 0.00 4.75
4438 6013 9.606631 GTTTCCATGATCAGATAGTAGAAACTT 57.393 33.333 0.09 0.00 38.21 2.66
4439 6014 7.923344 CGTTTCCATGATCAGATAGTAGAAACT 59.077 37.037 17.83 0.00 38.77 2.66
4440 6015 7.921214 TCGTTTCCATGATCAGATAGTAGAAAC 59.079 37.037 0.09 10.56 37.99 2.78
4441 6016 8.007405 TCGTTTCCATGATCAGATAGTAGAAA 57.993 34.615 0.09 0.25 0.00 2.52
4442 6017 7.582667 TCGTTTCCATGATCAGATAGTAGAA 57.417 36.000 0.09 0.00 0.00 2.10
4443 6018 7.582667 TTCGTTTCCATGATCAGATAGTAGA 57.417 36.000 0.09 0.00 0.00 2.59
4446 6021 9.784531 AAATATTCGTTTCCATGATCAGATAGT 57.215 29.630 0.09 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.