Multiple sequence alignment - TraesCS1D01G385100

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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 TraesCS1D01G385100 chr1D 100.000 3520 0 0 1 3520 458675119 458678638 0.000000e+00 6501.0
1 TraesCS1D01G385100 chr1B 89.543 3194 161 70 427 3520 630059834 630062954 0.000000e+00 3888.0
2 TraesCS1D01G385100 chr1B 79.896 383 33 25 1 351 630058185 630058555 1.260000e-59 241.0
3 TraesCS1D01G385100 chr1A 92.330 2086 96 28 1467 3520 551049619 551051672 0.000000e+00 2907.0
4 TraesCS1D01G385100 chr1A 88.235 969 50 28 547 1464 551048605 551049560 0.000000e+00 1099.0
5 TraesCS1D01G385100 chr7B 92.090 354 25 2 1104 1455 253370762 253371114 2.440000e-136 496.0
6 TraesCS1D01G385100 chr7B 90.099 202 13 4 1475 1676 253371179 253371373 4.510000e-64 255.0
7 TraesCS1D01G385100 chr7B 90.196 51 5 0 2886 2936 659430449 659430399 2.270000e-07 67.6
8 TraesCS1D01G385100 chr5B 91.877 357 26 2 1110 1464 668600746 668600391 2.440000e-136 496.0
9 TraesCS1D01G385100 chr5B 94.012 167 7 2 1510 1676 668600304 668600141 2.100000e-62 250.0
10 TraesCS1D01G385100 chr3B 92.241 348 24 2 1110 1455 36492396 36492742 1.140000e-134 490.0
11 TraesCS1D01G385100 chr3B 90.099 202 13 4 1475 1676 36492807 36493001 4.510000e-64 255.0
12 TraesCS1D01G385100 chr7A 90.196 51 5 0 2886 2936 64934699 64934649 2.270000e-07 67.6
13 TraesCS1D01G385100 chr7A 88.889 54 6 0 2883 2936 318403194 318403247 2.270000e-07 67.6
14 TraesCS1D01G385100 chr5A 90.196 51 5 0 2886 2936 230821214 230821164 2.270000e-07 67.6
15 TraesCS1D01G385100 chr5A 90.196 51 5 0 2886 2936 230850087 230850037 2.270000e-07 67.6
16 TraesCS1D01G385100 chr5A 88.889 54 6 0 2883 2936 593731405 593731458 2.270000e-07 67.6
17 TraesCS1D01G385100 chr4B 88.889 54 6 0 2883 2936 553913503 553913556 2.270000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G385100 chr1D 458675119 458678638 3519 False 6501.0 6501 100.0000 1 3520 1 chr1D.!!$F1 3519
1 TraesCS1D01G385100 chr1B 630058185 630062954 4769 False 2064.5 3888 84.7195 1 3520 2 chr1B.!!$F1 3519
2 TraesCS1D01G385100 chr1A 551048605 551051672 3067 False 2003.0 2907 90.2825 547 3520 2 chr1A.!!$F1 2973
3 TraesCS1D01G385100 chr7B 253370762 253371373 611 False 375.5 496 91.0945 1104 1676 2 chr7B.!!$F1 572
4 TraesCS1D01G385100 chr5B 668600141 668600746 605 True 373.0 496 92.9445 1110 1676 2 chr5B.!!$R1 566
5 TraesCS1D01G385100 chr3B 36492396 36493001 605 False 372.5 490 91.1700 1110 1676 2 chr3B.!!$F1 566

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
628 1863 0.179018 AACAGCTCCACCTGTCAACC 60.179 55.0 0.0 0.0 44.86 3.77 F
630 1865 0.321122 CAGCTCCACCTGTCAACCTC 60.321 60.0 0.0 0.0 0.00 3.85 F
1721 3105 0.462047 GAACCCCTGCGTACATCCAG 60.462 60.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 3237 0.179067 TGAAGCGGTGGAACGAAACT 60.179 50.0 0.00 0.0 38.12 2.66 R
1993 3383 0.679505 TCCATATTTCCGGAGCCTCG 59.320 55.0 3.34 0.0 0.00 4.63 R
3386 4813 0.918799 TCCCAATTGGAGCTGCCCTA 60.919 55.0 26.60 0.0 38.61 3.53 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
30 31 9.883142 CAGCTATAAATATTCTAGAGGGAAAGG 57.117 37.037 8.49 0.00 0.00 3.11
40 41 7.847711 TTCTAGAGGGAAAGGAATCATCTAG 57.152 40.000 0.00 0.00 37.96 2.43
41 42 4.972751 AGAGGGAAAGGAATCATCTAGC 57.027 45.455 0.00 0.00 0.00 3.42
42 43 4.565817 AGAGGGAAAGGAATCATCTAGCT 58.434 43.478 0.00 0.00 0.00 3.32
43 44 5.721225 AGAGGGAAAGGAATCATCTAGCTA 58.279 41.667 0.00 0.00 0.00 3.32
44 45 6.330218 AGAGGGAAAGGAATCATCTAGCTAT 58.670 40.000 0.00 0.00 0.00 2.97
45 46 7.483018 AGAGGGAAAGGAATCATCTAGCTATA 58.517 38.462 0.00 0.00 0.00 1.31
46 47 8.128346 AGAGGGAAAGGAATCATCTAGCTATAT 58.872 37.037 0.00 0.00 0.00 0.86
78 79 8.904099 ATGGAATACTAGTAAAAGGTACATGC 57.096 34.615 6.70 0.00 0.00 4.06
79 80 8.086143 TGGAATACTAGTAAAAGGTACATGCT 57.914 34.615 6.70 0.00 0.00 3.79
81 82 9.043079 GGAATACTAGTAAAAGGTACATGCTTC 57.957 37.037 6.70 1.54 0.00 3.86
83 84 9.601217 AATACTAGTAAAAGGTACATGCTTCTG 57.399 33.333 6.70 0.00 0.00 3.02
84 85 5.875359 ACTAGTAAAAGGTACATGCTTCTGC 59.125 40.000 0.00 0.00 40.20 4.26
98 99 3.130869 TGCTTCTGCATGTCAAAACACTT 59.869 39.130 0.00 0.00 45.31 3.16
99 100 3.488310 GCTTCTGCATGTCAAAACACTTG 59.512 43.478 0.00 0.00 38.48 3.16
107 108 4.596801 TGTCAAAACACTTGCATTTTGC 57.403 36.364 15.31 11.85 42.80 3.68
121 122 6.609237 TGCATTTTGCTCATATGTAGTCTC 57.391 37.500 1.90 0.00 45.31 3.36
127 128 7.615582 TTTGCTCATATGTAGTCTCCAAAAG 57.384 36.000 1.90 0.00 0.00 2.27
131 132 7.147672 TGCTCATATGTAGTCTCCAAAAGATGA 60.148 37.037 1.90 0.00 36.11 2.92
138 139 7.323420 TGTAGTCTCCAAAAGATGATGTGTAG 58.677 38.462 0.00 0.00 36.11 2.74
144 145 4.155826 CCAAAAGATGATGTGTAGCGGAAA 59.844 41.667 0.00 0.00 0.00 3.13
148 149 3.873361 AGATGATGTGTAGCGGAAACATG 59.127 43.478 2.51 0.00 34.74 3.21
152 153 4.629634 TGATGTGTAGCGGAAACATGTTAG 59.370 41.667 12.39 7.81 34.74 2.34
157 158 3.559238 AGCGGAAACATGTTAGCAAAG 57.441 42.857 25.27 11.82 0.00 2.77
173 177 2.580589 CAAAGGACCAAATAACACGCG 58.419 47.619 3.53 3.53 0.00 6.01
228 242 0.974383 ACTCCGGTTTTCATCTCCGT 59.026 50.000 0.00 0.00 42.30 4.69
249 263 4.985409 CGTTTTGGCATCCTCTAGATAGTC 59.015 45.833 0.00 0.00 32.37 2.59
255 269 4.263727 GGCATCCTCTAGATAGTCCTCTGA 60.264 50.000 0.00 0.00 32.37 3.27
263 277 8.215050 CCTCTAGATAGTCCTCTGAGTTTAGAA 58.785 40.741 3.66 0.00 0.00 2.10
269 297 6.487299 AGTCCTCTGAGTTTAGAAAGTTGT 57.513 37.500 3.66 0.00 0.00 3.32
278 306 7.919690 TGAGTTTAGAAAGTTGTGACTGAATG 58.080 34.615 0.00 0.00 35.91 2.67
284 312 4.647564 AAGTTGTGACTGAATGGAGGAT 57.352 40.909 0.00 0.00 35.91 3.24
286 314 5.091261 AGTTGTGACTGAATGGAGGATAC 57.909 43.478 0.00 0.00 33.99 2.24
287 315 4.532126 AGTTGTGACTGAATGGAGGATACA 59.468 41.667 0.00 0.00 34.44 2.29
289 317 6.384015 AGTTGTGACTGAATGGAGGATACATA 59.616 38.462 0.00 0.00 34.44 2.29
292 320 7.805163 TGTGACTGAATGGAGGATACATATTT 58.195 34.615 0.00 0.00 41.41 1.40
299 327 6.893020 ATGGAGGATACATATTTAGGGGTC 57.107 41.667 0.00 0.00 41.41 4.46
301 329 6.023603 TGGAGGATACATATTTAGGGGTCTC 58.976 44.000 0.00 0.00 41.41 3.36
302 330 6.023603 GGAGGATACATATTTAGGGGTCTCA 58.976 44.000 0.00 0.00 41.41 3.27
306 334 8.191408 AGGATACATATTTAGGGGTCTCAGACC 61.191 44.444 16.48 16.48 46.37 3.85
338 367 9.408648 GAAAATATAAGACTTTGGGAGGAATGA 57.591 33.333 0.00 0.00 0.00 2.57
342 371 4.566426 AGACTTTGGGAGGAATGAGAAG 57.434 45.455 0.00 0.00 0.00 2.85
351 380 3.261897 GGAGGAATGAGAAGTGTCAGGAA 59.738 47.826 0.00 0.00 0.00 3.36
352 381 4.249661 GAGGAATGAGAAGTGTCAGGAAC 58.750 47.826 0.00 0.00 0.00 3.62
353 382 3.648067 AGGAATGAGAAGTGTCAGGAACA 59.352 43.478 0.00 0.00 34.78 3.18
366 395 3.199880 CAGGAACACTGGGGATATGAC 57.800 52.381 0.00 0.00 43.70 3.06
367 396 1.762957 AGGAACACTGGGGATATGACG 59.237 52.381 0.00 0.00 0.00 4.35
368 397 1.485066 GGAACACTGGGGATATGACGT 59.515 52.381 0.00 0.00 0.00 4.34
369 398 2.483188 GGAACACTGGGGATATGACGTC 60.483 54.545 9.11 9.11 0.00 4.34
371 1522 1.119684 CACTGGGGATATGACGTCCA 58.880 55.000 14.12 0.92 37.49 4.02
392 1543 2.886124 GCTACGCGGAGGCTGAAC 60.886 66.667 22.20 0.00 36.88 3.18
395 1546 2.214181 CTACGCGGAGGCTGAACTGT 62.214 60.000 11.59 0.00 36.88 3.55
397 1548 1.080093 CGCGGAGGCTGAACTGTTA 60.080 57.895 0.00 0.00 36.88 2.41
400 1551 1.337823 GCGGAGGCTGAACTGTTAGAA 60.338 52.381 0.00 0.00 35.83 2.10
402 1553 2.351455 GGAGGCTGAACTGTTAGAAGC 58.649 52.381 11.74 11.74 0.00 3.86
404 1555 1.344763 AGGCTGAACTGTTAGAAGCGT 59.655 47.619 13.09 11.61 34.66 5.07
405 1556 1.727335 GGCTGAACTGTTAGAAGCGTC 59.273 52.381 13.09 0.00 34.66 5.19
406 1557 2.404215 GCTGAACTGTTAGAAGCGTCA 58.596 47.619 1.61 0.00 0.00 4.35
407 1558 2.410053 GCTGAACTGTTAGAAGCGTCAG 59.590 50.000 1.61 0.00 36.44 3.51
409 1560 2.626266 TGAACTGTTAGAAGCGTCAGGA 59.374 45.455 1.61 0.00 32.92 3.86
411 1562 3.963428 ACTGTTAGAAGCGTCAGGATT 57.037 42.857 1.61 0.00 32.92 3.01
412 1563 3.851098 ACTGTTAGAAGCGTCAGGATTC 58.149 45.455 1.61 0.00 41.36 2.52
418 1569 1.205893 GAAGCGTCAGGATTCTCCAGT 59.794 52.381 0.00 0.00 39.61 4.00
420 1571 1.086634 GCGTCAGGATTCTCCAGTGC 61.087 60.000 0.00 0.00 39.61 4.40
421 1572 0.247460 CGTCAGGATTCTCCAGTGCA 59.753 55.000 0.00 0.00 39.61 4.57
423 1574 2.559440 GTCAGGATTCTCCAGTGCATC 58.441 52.381 0.00 0.00 39.61 3.91
424 1575 1.487976 TCAGGATTCTCCAGTGCATCC 59.512 52.381 0.00 0.00 39.61 3.51
425 1576 1.211212 CAGGATTCTCCAGTGCATCCA 59.789 52.381 0.00 0.00 39.61 3.41
437 1669 1.128692 GTGCATCCAACAGCTTACGTC 59.871 52.381 0.00 0.00 0.00 4.34
439 1671 1.394917 GCATCCAACAGCTTACGTCTG 59.605 52.381 0.00 0.00 37.56 3.51
440 1672 2.930887 GCATCCAACAGCTTACGTCTGA 60.931 50.000 9.51 0.00 35.61 3.27
441 1673 3.325870 CATCCAACAGCTTACGTCTGAA 58.674 45.455 9.51 0.00 35.61 3.02
442 1674 3.678056 TCCAACAGCTTACGTCTGAAT 57.322 42.857 9.51 0.00 35.61 2.57
458 1691 2.206750 TGAATATTACAAGCGGCCGTC 58.793 47.619 28.70 19.09 0.00 4.79
483 1716 4.566759 CGCCGAGAGATTCTTCACATTAAA 59.433 41.667 0.00 0.00 0.00 1.52
484 1717 5.235186 CGCCGAGAGATTCTTCACATTAAAT 59.765 40.000 0.00 0.00 0.00 1.40
485 1718 6.563010 CGCCGAGAGATTCTTCACATTAAATC 60.563 42.308 0.00 0.00 0.00 2.17
486 1719 6.258727 GCCGAGAGATTCTTCACATTAAATCA 59.741 38.462 0.00 0.00 31.90 2.57
488 1721 8.834465 CCGAGAGATTCTTCACATTAAATCATT 58.166 33.333 0.00 0.00 31.90 2.57
520 1753 4.728608 GCAACAAGACAAAGAAACGTGTAG 59.271 41.667 0.00 0.00 0.00 2.74
545 1778 1.066587 GGCAGGAGAGATTCGGTCG 59.933 63.158 0.00 0.00 0.00 4.79
627 1862 0.947244 CAACAGCTCCACCTGTCAAC 59.053 55.000 0.00 0.00 44.86 3.18
628 1863 0.179018 AACAGCTCCACCTGTCAACC 60.179 55.000 0.00 0.00 44.86 3.77
629 1864 1.056700 ACAGCTCCACCTGTCAACCT 61.057 55.000 0.00 0.00 42.10 3.50
630 1865 0.321122 CAGCTCCACCTGTCAACCTC 60.321 60.000 0.00 0.00 0.00 3.85
631 1866 0.472734 AGCTCCACCTGTCAACCTCT 60.473 55.000 0.00 0.00 0.00 3.69
661 1903 3.820467 CACTCCAAGATTAAAGCACACCA 59.180 43.478 0.00 0.00 0.00 4.17
757 2001 9.543783 AAGATATGATATGACAATGATCGATGG 57.456 33.333 0.54 0.00 0.00 3.51
758 2002 8.921205 AGATATGATATGACAATGATCGATGGA 58.079 33.333 0.54 0.00 0.00 3.41
759 2003 9.708092 GATATGATATGACAATGATCGATGGAT 57.292 33.333 0.54 0.00 34.96 3.41
760 2004 7.787725 ATGATATGACAATGATCGATGGATG 57.212 36.000 0.54 0.64 31.51 3.51
782 2028 7.013655 GGATGCTAGCTTCCTTTTCATCATTAA 59.986 37.037 32.31 2.12 37.32 1.40
783 2029 7.325660 TGCTAGCTTCCTTTTCATCATTAAG 57.674 36.000 17.23 0.00 0.00 1.85
786 2060 8.555361 GCTAGCTTCCTTTTCATCATTAAGTAG 58.445 37.037 7.70 0.00 0.00 2.57
804 2097 8.557592 TTAAGTAGTACTTCGTCTCAGAATCA 57.442 34.615 18.77 0.00 39.51 2.57
807 2100 6.879993 AGTAGTACTTCGTCTCAGAATCAAGA 59.120 38.462 0.00 0.00 0.00 3.02
809 2102 5.708230 AGTACTTCGTCTCAGAATCAAGACT 59.292 40.000 12.02 0.00 39.80 3.24
811 2104 3.223423 TCGTCTCAGAATCAAGACTGC 57.777 47.619 12.02 0.00 39.80 4.40
812 2105 2.558359 TCGTCTCAGAATCAAGACTGCA 59.442 45.455 12.02 0.00 39.80 4.41
813 2106 3.005791 TCGTCTCAGAATCAAGACTGCAA 59.994 43.478 12.02 0.00 39.80 4.08
814 2107 3.367327 CGTCTCAGAATCAAGACTGCAAG 59.633 47.826 12.02 0.00 39.80 4.01
815 2108 4.564041 GTCTCAGAATCAAGACTGCAAGA 58.436 43.478 8.09 0.00 39.06 3.02
896 2189 4.794648 CGATCAAAGCCCCGGCCA 62.795 66.667 2.24 0.00 43.17 5.36
937 2238 1.299939 ACCTTCCATTCCCTTCCCTC 58.700 55.000 0.00 0.00 0.00 4.30
938 2239 1.203622 ACCTTCCATTCCCTTCCCTCT 60.204 52.381 0.00 0.00 0.00 3.69
1065 2371 4.431524 ATCCTTCCAGGCCGGGGA 62.432 66.667 22.79 18.37 34.61 4.81
1067 2373 2.340909 ATCCTTCCAGGCCGGGGATA 62.341 60.000 22.79 4.89 34.85 2.59
1322 2631 3.381045 GGCAGCTTGAAGGTAAAAACAC 58.619 45.455 0.00 0.00 0.00 3.32
1350 2670 6.875726 TGGCATATATACATTGCTCTTGTCTC 59.124 38.462 6.73 0.00 36.62 3.36
1383 2703 4.152045 GCTGAACTGAATCAGTGTCTCTTG 59.848 45.833 17.46 9.06 44.62 3.02
1464 2784 3.064545 GTGAGATATGCTTGCAGGTGAAC 59.935 47.826 0.87 0.00 0.00 3.18
1465 2785 2.615912 GAGATATGCTTGCAGGTGAACC 59.384 50.000 0.87 0.00 0.00 3.62
1473 2855 1.452110 TGCAGGTGAACCAATCATCG 58.548 50.000 1.62 0.00 44.36 3.84
1484 2866 6.019479 GTGAACCAATCATCGTCTCTAATCAC 60.019 42.308 0.00 0.00 40.97 3.06
1495 2877 7.543947 TCGTCTCTAATCACGTAAGAATGTA 57.456 36.000 0.00 0.00 43.62 2.29
1695 3079 5.131594 TGGATCATCTAATGCTCTTCTCG 57.868 43.478 0.00 0.00 0.00 4.04
1721 3105 0.462047 GAACCCCTGCGTACATCCAG 60.462 60.000 0.00 0.00 0.00 3.86
1802 3186 3.074412 CCCGAAAGCTGTAATCTGTTGT 58.926 45.455 0.00 0.00 0.00 3.32
1852 3237 4.464951 AGGTGAAACATACAGACATCCGTA 59.535 41.667 0.00 0.00 39.98 4.02
1862 3247 2.921754 CAGACATCCGTAGTTTCGTTCC 59.078 50.000 0.00 0.00 0.00 3.62
1865 3250 1.997606 CATCCGTAGTTTCGTTCCACC 59.002 52.381 0.00 0.00 0.00 4.61
1882 3272 5.263968 TCCACCGCTTCAAAAATTAACAA 57.736 34.783 0.00 0.00 0.00 2.83
1904 3294 3.197549 ACCTGAAACATTGTTGCAACCTT 59.802 39.130 26.14 11.13 0.00 3.50
1909 3299 3.923017 ACATTGTTGCAACCTTAGCTC 57.077 42.857 26.14 0.00 0.00 4.09
1993 3383 3.488090 GCGCTGGTCACCGTAAGC 61.488 66.667 0.00 0.00 0.00 3.09
2008 3399 1.068127 GTAAGCGAGGCTCCGGAAATA 59.932 52.381 5.23 0.00 38.25 1.40
2066 3457 2.442878 TGCATACATATGGAACCCAGCT 59.557 45.455 7.80 0.00 36.75 4.24
2078 3469 3.279434 GAACCCAGCTAATGTAACCTGG 58.721 50.000 0.00 0.00 43.47 4.45
2089 3480 2.660572 TGTAACCTGGTGTGTGCAAAT 58.339 42.857 0.00 0.00 0.00 2.32
2263 3657 5.443185 TGAAGTTTCTTGCTGAAATGGAG 57.557 39.130 8.28 0.00 45.19 3.86
2281 3675 2.159379 GGAGATGGAAATGGAACGCAAC 60.159 50.000 0.00 0.00 0.00 4.17
2415 3809 3.392616 GGGGAACAGATATGGACATCAGT 59.607 47.826 0.00 0.00 0.00 3.41
2423 3817 2.015736 ATGGACATCAGTCGTCAAGC 57.984 50.000 0.00 0.00 45.92 4.01
2424 3818 0.678950 TGGACATCAGTCGTCAAGCA 59.321 50.000 0.00 0.00 45.92 3.91
2425 3819 1.069978 TGGACATCAGTCGTCAAGCAA 59.930 47.619 0.00 0.00 45.92 3.91
2426 3820 1.728971 GGACATCAGTCGTCAAGCAAG 59.271 52.381 0.00 0.00 45.92 4.01
2427 3821 1.127582 GACATCAGTCGTCAAGCAAGC 59.872 52.381 0.00 0.00 34.60 4.01
2434 3828 1.443194 CGTCAAGCAAGCATGGCAC 60.443 57.895 2.77 0.00 37.68 5.01
2477 3871 3.444742 CAGGTGTGCCATCATGTTAACAT 59.555 43.478 15.47 15.47 37.19 2.71
2529 3931 3.855950 GTGAGTTGTGGCTGTACGTATAC 59.144 47.826 0.00 0.00 0.00 1.47
2530 3932 3.506844 TGAGTTGTGGCTGTACGTATACA 59.493 43.478 0.00 0.00 39.06 2.29
2537 3939 5.105675 TGTGGCTGTACGTATACAATCTTCA 60.106 40.000 0.00 0.00 40.84 3.02
2592 3994 1.588404 GTACATTCATGGACACTCGCG 59.412 52.381 0.00 0.00 41.36 5.87
2685 4090 7.503521 TTTAGACTTGTGCAATGTACATTCA 57.496 32.000 18.25 15.34 0.00 2.57
2756 4166 0.237235 GTTGCTCGACAATTCGCCAA 59.763 50.000 4.21 0.00 45.46 4.52
2777 4187 3.921119 TTCCAAATGCTGCTTGTGTAG 57.079 42.857 0.00 0.00 0.00 2.74
2829 4240 2.353269 TGTCGTCGACAGCACAAATTTT 59.647 40.909 23.70 0.00 37.67 1.82
2837 4248 4.616802 CGACAGCACAAATTTTGATACCAC 59.383 41.667 15.81 3.02 0.00 4.16
2850 4261 5.386958 TTGATACCACAGACAGAGTACAC 57.613 43.478 0.00 0.00 0.00 2.90
2857 4268 3.442625 CACAGACAGAGTACACCCGATAA 59.557 47.826 0.00 0.00 0.00 1.75
2864 4275 5.011329 ACAGAGTACACCCGATAAAAAGTCA 59.989 40.000 0.00 0.00 0.00 3.41
2936 4347 1.131126 GCAACAGTTCATCCATGTCCG 59.869 52.381 0.00 0.00 0.00 4.79
2983 4394 9.575783 TGGTAAAAACAGAACTACATTTTGAAC 57.424 29.630 0.00 0.00 0.00 3.18
3014 4425 5.185454 CAAGGTGCAAGTTAGGTCATCATA 58.815 41.667 0.00 0.00 0.00 2.15
3217 4643 9.959749 CAAGTAGAACCTAATCACTTCTCTATC 57.040 37.037 0.00 0.00 0.00 2.08
3386 4813 2.596631 CTGGCAGCTGCAACACCT 60.597 61.111 37.63 0.00 44.36 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.540538 CTAGATGATTCCTTTCCCTCTAGAATA 57.459 37.037 0.00 0.00 33.28 1.75
15 16 7.038373 GCTAGATGATTCCTTTCCCTCTAGAAT 60.038 40.741 7.65 0.00 33.28 2.40
20 21 4.565817 AGCTAGATGATTCCTTTCCCTCT 58.434 43.478 0.00 0.00 0.00 3.69
77 78 3.360249 AGTGTTTTGACATGCAGAAGC 57.640 42.857 0.00 0.00 42.57 3.86
78 79 3.488310 GCAAGTGTTTTGACATGCAGAAG 59.512 43.478 0.00 0.00 39.72 2.85
79 80 3.119209 TGCAAGTGTTTTGACATGCAGAA 60.119 39.130 0.00 0.00 43.57 3.02
81 82 2.811855 TGCAAGTGTTTTGACATGCAG 58.188 42.857 0.00 0.00 43.57 4.41
83 84 4.799419 AAATGCAAGTGTTTTGACATGC 57.201 36.364 0.00 0.00 40.24 4.06
84 85 4.965158 GCAAAATGCAAGTGTTTTGACATG 59.035 37.500 21.60 0.00 44.17 3.21
85 86 5.159399 GCAAAATGCAAGTGTTTTGACAT 57.841 34.783 21.60 0.00 44.17 3.06
86 87 4.596801 GCAAAATGCAAGTGTTTTGACA 57.403 36.364 21.60 0.00 44.17 3.58
99 100 5.528690 TGGAGACTACATATGAGCAAAATGC 59.471 40.000 10.38 0.00 45.46 3.56
107 108 9.205719 CATCATCTTTTGGAGACTACATATGAG 57.794 37.037 10.38 5.24 37.17 2.90
121 122 3.270027 TCCGCTACACATCATCTTTTGG 58.730 45.455 0.00 0.00 0.00 3.28
127 128 3.623060 ACATGTTTCCGCTACACATCATC 59.377 43.478 0.00 0.00 0.00 2.92
131 132 3.374058 GCTAACATGTTTCCGCTACACAT 59.626 43.478 17.78 0.00 0.00 3.21
138 139 2.227865 TCCTTTGCTAACATGTTTCCGC 59.772 45.455 17.78 16.60 0.00 5.54
144 145 6.266558 TGTTATTTGGTCCTTTGCTAACATGT 59.733 34.615 0.00 0.00 0.00 3.21
148 149 5.151389 CGTGTTATTTGGTCCTTTGCTAAC 58.849 41.667 0.00 0.00 0.00 2.34
152 153 2.324860 GCGTGTTATTTGGTCCTTTGC 58.675 47.619 0.00 0.00 0.00 3.68
157 158 0.238817 TTGCGCGTGTTATTTGGTCC 59.761 50.000 8.43 0.00 0.00 4.46
207 211 3.454371 CGGAGATGAAAACCGGAGTAT 57.546 47.619 9.46 0.00 42.48 2.12
228 242 5.219739 AGGACTATCTAGAGGATGCCAAAA 58.780 41.667 0.00 0.00 35.98 2.44
249 263 6.201806 CAGTCACAACTTTCTAAACTCAGAGG 59.798 42.308 1.53 0.00 31.71 3.69
255 269 7.054124 TCCATTCAGTCACAACTTTCTAAACT 58.946 34.615 0.00 0.00 31.71 2.66
263 277 4.647564 ATCCTCCATTCAGTCACAACTT 57.352 40.909 0.00 0.00 31.71 2.66
269 297 8.597167 CCTAAATATGTATCCTCCATTCAGTCA 58.403 37.037 0.00 0.00 0.00 3.41
278 306 6.023603 TGAGACCCCTAAATATGTATCCTCC 58.976 44.000 0.00 0.00 0.00 4.30
299 327 7.976734 AGTCTTATATTTTCTTCACGGTCTGAG 59.023 37.037 0.00 0.00 0.00 3.35
301 329 8.480643 AAGTCTTATATTTTCTTCACGGTCTG 57.519 34.615 0.00 0.00 0.00 3.51
302 330 8.936864 CAAAGTCTTATATTTTCTTCACGGTCT 58.063 33.333 0.00 0.00 0.00 3.85
306 334 8.263940 TCCCAAAGTCTTATATTTTCTTCACG 57.736 34.615 0.00 0.00 0.00 4.35
311 339 9.413734 CATTCCTCCCAAAGTCTTATATTTTCT 57.586 33.333 0.00 0.00 0.00 2.52
351 380 1.120530 GGACGTCATATCCCCAGTGT 58.879 55.000 18.91 0.00 0.00 3.55
352 381 1.069204 CTGGACGTCATATCCCCAGTG 59.931 57.143 18.91 0.00 39.50 3.66
353 382 1.414158 CTGGACGTCATATCCCCAGT 58.586 55.000 18.91 0.00 39.50 4.00
354 383 0.034059 GCTGGACGTCATATCCCCAG 59.966 60.000 18.91 14.83 45.31 4.45
356 385 1.006102 CGCTGGACGTCATATCCCC 60.006 63.158 18.91 0.00 35.12 4.81
357 386 1.006102 CCGCTGGACGTCATATCCC 60.006 63.158 18.91 0.00 41.42 3.85
358 387 1.664965 GCCGCTGGACGTCATATCC 60.665 63.158 18.91 0.00 41.42 2.59
359 388 0.596577 TAGCCGCTGGACGTCATATC 59.403 55.000 18.91 0.00 41.42 1.63
360 389 0.314302 GTAGCCGCTGGACGTCATAT 59.686 55.000 18.91 0.00 41.42 1.78
362 391 2.494918 GTAGCCGCTGGACGTCAT 59.505 61.111 18.91 0.00 41.42 3.06
377 1528 1.812686 AACAGTTCAGCCTCCGCGTA 61.813 55.000 4.92 0.00 41.18 4.42
378 1529 1.812686 TAACAGTTCAGCCTCCGCGT 61.813 55.000 4.92 0.00 41.18 6.01
381 1532 2.611518 CTTCTAACAGTTCAGCCTCCG 58.388 52.381 0.00 0.00 0.00 4.63
387 1538 2.989840 CCTGACGCTTCTAACAGTTCAG 59.010 50.000 0.00 0.00 0.00 3.02
388 1539 2.626266 TCCTGACGCTTCTAACAGTTCA 59.374 45.455 0.00 0.00 0.00 3.18
390 1541 3.963428 ATCCTGACGCTTCTAACAGTT 57.037 42.857 0.00 0.00 0.00 3.16
392 1543 4.109050 GAGAATCCTGACGCTTCTAACAG 58.891 47.826 0.00 0.00 29.64 3.16
409 1560 2.719739 CTGTTGGATGCACTGGAGAAT 58.280 47.619 0.00 0.00 0.00 2.40
411 1562 0.321919 GCTGTTGGATGCACTGGAGA 60.322 55.000 0.00 0.00 0.00 3.71
412 1563 0.322277 AGCTGTTGGATGCACTGGAG 60.322 55.000 0.00 0.00 0.00 3.86
413 1564 0.111061 AAGCTGTTGGATGCACTGGA 59.889 50.000 0.00 0.00 0.00 3.86
414 1565 1.470098 GTAAGCTGTTGGATGCACTGG 59.530 52.381 0.00 0.00 0.00 4.00
415 1566 1.129251 CGTAAGCTGTTGGATGCACTG 59.871 52.381 0.00 0.00 0.00 3.66
416 1567 1.270839 ACGTAAGCTGTTGGATGCACT 60.271 47.619 0.00 0.00 45.62 4.40
418 1569 1.001974 AGACGTAAGCTGTTGGATGCA 59.998 47.619 0.00 0.00 45.62 3.96
420 1571 2.959516 TCAGACGTAAGCTGTTGGATG 58.040 47.619 3.02 0.00 45.62 3.51
421 1572 3.678056 TTCAGACGTAAGCTGTTGGAT 57.322 42.857 3.02 0.00 45.62 3.41
423 1574 6.533723 TGTAATATTCAGACGTAAGCTGTTGG 59.466 38.462 3.02 0.00 45.62 3.77
424 1575 7.520119 TGTAATATTCAGACGTAAGCTGTTG 57.480 36.000 3.02 0.00 45.62 3.33
425 1576 7.201530 GCTTGTAATATTCAGACGTAAGCTGTT 60.202 37.037 0.00 0.00 45.62 3.16
437 1669 2.210116 ACGGCCGCTTGTAATATTCAG 58.790 47.619 28.58 0.00 0.00 3.02
439 1671 2.475487 GAGACGGCCGCTTGTAATATTC 59.525 50.000 28.58 11.30 0.00 1.75
440 1672 2.480845 GAGACGGCCGCTTGTAATATT 58.519 47.619 28.58 0.00 0.00 1.28
441 1673 1.602165 CGAGACGGCCGCTTGTAATAT 60.602 52.381 28.58 0.57 0.00 1.28
442 1674 0.248743 CGAGACGGCCGCTTGTAATA 60.249 55.000 28.58 0.00 0.00 0.98
458 1691 1.133216 TGTGAAGAATCTCTCGGCGAG 59.867 52.381 30.10 30.10 41.30 5.03
489 1722 9.180678 CGTTTCTTTGTCTTGTTGCTAATTATT 57.819 29.630 0.00 0.00 0.00 1.40
490 1723 8.349983 ACGTTTCTTTGTCTTGTTGCTAATTAT 58.650 29.630 0.00 0.00 0.00 1.28
491 1724 7.642194 CACGTTTCTTTGTCTTGTTGCTAATTA 59.358 33.333 0.00 0.00 0.00 1.40
492 1725 6.472163 CACGTTTCTTTGTCTTGTTGCTAATT 59.528 34.615 0.00 0.00 0.00 1.40
493 1726 5.971202 CACGTTTCTTTGTCTTGTTGCTAAT 59.029 36.000 0.00 0.00 0.00 1.73
494 1727 5.106475 ACACGTTTCTTTGTCTTGTTGCTAA 60.106 36.000 0.00 0.00 0.00 3.09
498 1731 5.064198 TCCTACACGTTTCTTTGTCTTGTTG 59.936 40.000 0.00 0.00 0.00 3.33
520 1753 1.416030 GAATCTCTCCTGCCTCCTTCC 59.584 57.143 0.00 0.00 0.00 3.46
545 1778 1.168714 GGCTGTTGGGAACATCTGAC 58.831 55.000 0.00 0.00 41.26 3.51
575 1808 1.169034 GGATGAGGCGGCTTTCCATC 61.169 60.000 26.90 25.08 34.48 3.51
576 1809 1.152881 GGATGAGGCGGCTTTCCAT 60.153 57.895 26.90 20.06 0.00 3.41
577 1810 2.135903 TTGGATGAGGCGGCTTTCCA 62.136 55.000 29.22 29.22 34.74 3.53
578 1811 0.965363 TTTGGATGAGGCGGCTTTCC 60.965 55.000 25.81 25.81 0.00 3.13
579 1812 0.887933 TTTTGGATGAGGCGGCTTTC 59.112 50.000 14.76 13.45 0.00 2.62
580 1813 0.603065 GTTTTGGATGAGGCGGCTTT 59.397 50.000 14.76 3.60 0.00 3.51
627 1862 0.041833 TTGGAGTGGGAGAGGAGAGG 59.958 60.000 0.00 0.00 0.00 3.69
628 1863 1.006519 TCTTGGAGTGGGAGAGGAGAG 59.993 57.143 0.00 0.00 0.00 3.20
629 1864 1.084866 TCTTGGAGTGGGAGAGGAGA 58.915 55.000 0.00 0.00 0.00 3.71
630 1865 2.173126 ATCTTGGAGTGGGAGAGGAG 57.827 55.000 0.00 0.00 0.00 3.69
631 1866 2.649742 AATCTTGGAGTGGGAGAGGA 57.350 50.000 0.00 0.00 0.00 3.71
661 1903 3.540314 TTCTTGCTTGCATTGGTTTGT 57.460 38.095 0.00 0.00 0.00 2.83
757 2001 6.388435 AATGATGAAAAGGAAGCTAGCATC 57.612 37.500 18.83 15.00 33.24 3.91
758 2002 7.559170 ACTTAATGATGAAAAGGAAGCTAGCAT 59.441 33.333 18.83 4.30 0.00 3.79
759 2003 6.886459 ACTTAATGATGAAAAGGAAGCTAGCA 59.114 34.615 18.83 0.00 0.00 3.49
760 2004 7.326968 ACTTAATGATGAAAAGGAAGCTAGC 57.673 36.000 6.62 6.62 0.00 3.42
786 2060 5.797934 CAGTCTTGATTCTGAGACGAAGTAC 59.202 44.000 12.14 0.00 45.33 2.73
811 2104 2.856032 CCGTCGCTGTTGCTCTTG 59.144 61.111 0.00 0.00 36.97 3.02
812 2105 3.044305 GCCGTCGCTGTTGCTCTT 61.044 61.111 0.00 0.00 36.97 2.85
896 2189 2.668120 GGAGCTGAGGAGGCTTGCT 61.668 63.158 0.00 0.00 40.40 3.91
937 2238 1.471684 GAGATGCCAAGCAAGGTCAAG 59.528 52.381 0.00 0.00 43.62 3.02
938 2239 1.538047 GAGATGCCAAGCAAGGTCAA 58.462 50.000 0.00 0.00 43.62 3.18
1322 2631 6.432162 ACAAGAGCAATGTATATATGCCAAGG 59.568 38.462 3.67 0.00 40.93 3.61
1350 2670 7.728358 ACTGATTCAGTTCAGCTACTGCTTTG 61.728 42.308 13.61 4.18 44.25 2.77
1366 2686 3.661944 ACTGCAAGAGACACTGATTCAG 58.338 45.455 12.17 12.17 37.43 3.02
1383 2703 1.797046 CATGTCCGATGAGCATACTGC 59.203 52.381 0.00 0.00 45.46 4.40
1464 2784 4.611943 ACGTGATTAGAGACGATGATTGG 58.388 43.478 0.00 0.00 38.94 3.16
1465 2785 7.132863 TCTTACGTGATTAGAGACGATGATTG 58.867 38.462 0.00 0.00 38.94 2.67
1484 2866 7.743400 CAGCATGCAATTATCTACATTCTTACG 59.257 37.037 21.98 0.00 0.00 3.18
1784 3168 3.186409 TGCGACAACAGATTACAGCTTTC 59.814 43.478 0.00 0.00 0.00 2.62
1829 3213 3.260884 ACGGATGTCTGTATGTTTCACCT 59.739 43.478 0.00 0.00 32.82 4.00
1852 3237 0.179067 TGAAGCGGTGGAACGAAACT 60.179 50.000 0.00 0.00 38.12 2.66
1862 3247 5.047188 AGGTTGTTAATTTTTGAAGCGGTG 58.953 37.500 0.00 0.00 0.00 4.94
1865 3250 6.820470 TTCAGGTTGTTAATTTTTGAAGCG 57.180 33.333 0.00 0.00 0.00 4.68
1882 3272 2.765699 AGGTTGCAACAATGTTTCAGGT 59.234 40.909 29.55 0.00 0.00 4.00
1909 3299 0.747283 GGAGCACCAGGAGAAGCATG 60.747 60.000 0.00 0.00 35.97 4.06
1993 3383 0.679505 TCCATATTTCCGGAGCCTCG 59.320 55.000 3.34 0.00 0.00 4.63
2008 3399 1.816863 AACGTGCGGACTGTCTCCAT 61.817 55.000 5.27 0.00 39.39 3.41
2031 3422 8.753133 CCATATGTATGCATCTAGTCTAGGAAA 58.247 37.037 0.19 0.00 36.58 3.13
2032 3423 8.116026 TCCATATGTATGCATCTAGTCTAGGAA 58.884 37.037 0.19 0.00 36.58 3.36
2033 3424 7.643123 TCCATATGTATGCATCTAGTCTAGGA 58.357 38.462 0.19 0.00 36.58 2.94
2041 3432 5.571454 GCTGGGTTCCATATGTATGCATCTA 60.571 44.000 0.19 0.00 36.58 1.98
2051 3442 5.473504 GGTTACATTAGCTGGGTTCCATATG 59.526 44.000 0.00 0.00 30.82 1.78
2066 3457 3.493767 TGCACACACCAGGTTACATTA 57.506 42.857 0.00 0.00 0.00 1.90
2078 3469 5.341727 CCACAAAACAAAAATTTGCACACAC 59.658 36.000 5.82 0.00 41.79 3.82
2089 3480 3.999663 CAGCTGGTTCCACAAAACAAAAA 59.000 39.130 5.57 0.00 33.09 1.94
2171 3562 1.992667 CTGCGTCGATAAAGCACTTCA 59.007 47.619 0.00 0.00 37.45 3.02
2263 3657 1.895051 CGTTGCGTTCCATTTCCATC 58.105 50.000 0.00 0.00 0.00 3.51
2415 3809 1.600356 TGCCATGCTTGCTTGACGA 60.600 52.632 9.60 0.00 0.00 4.20
2423 3817 1.813859 CATCCAGGTGCCATGCTTG 59.186 57.895 0.00 0.00 0.00 4.01
2424 3818 2.056223 GCATCCAGGTGCCATGCTT 61.056 57.895 3.96 0.00 39.92 3.91
2425 3819 2.441532 GCATCCAGGTGCCATGCT 60.442 61.111 3.96 0.00 39.92 3.79
2426 3820 3.896133 CGCATCCAGGTGCCATGC 61.896 66.667 0.00 4.93 42.06 4.06
2427 3821 3.214123 CCGCATCCAGGTGCCATG 61.214 66.667 0.00 0.00 42.06 3.66
2434 3828 0.962356 AGCTCAAAACCGCATCCAGG 60.962 55.000 0.00 0.00 0.00 4.45
2477 3871 8.727100 ATTATGTACACATCCTCCATCTCTTA 57.273 34.615 0.00 0.00 37.76 2.10
2529 3931 9.133627 CGATATACACAGGTATTCTGAAGATTG 57.866 37.037 0.00 0.00 46.18 2.67
2530 3932 9.078990 TCGATATACACAGGTATTCTGAAGATT 57.921 33.333 0.00 0.00 46.18 2.40
2592 3994 5.180868 ACACTTCATCTTCATTGCTTCTGAC 59.819 40.000 0.00 0.00 0.00 3.51
2756 4166 3.194116 CCTACACAAGCAGCATTTGGAAT 59.806 43.478 0.00 0.00 0.00 3.01
2777 4187 2.571653 TGCACCTATGGCTGATATACCC 59.428 50.000 0.00 0.00 0.00 3.69
2829 4240 3.762288 GGTGTACTCTGTCTGTGGTATCA 59.238 47.826 0.00 0.00 0.00 2.15
2837 4248 4.713824 TTTATCGGGTGTACTCTGTCTG 57.286 45.455 0.00 0.00 0.00 3.51
2864 4275 7.736893 ACTCAGTGTTAATCCTTAAGTCTTGT 58.263 34.615 0.97 0.00 0.00 3.16
2936 4347 6.000219 ACCATATAGTTGTGATCTGATTGCC 59.000 40.000 0.00 0.00 0.00 4.52
2982 4393 4.382386 AACTTGCACCTTGTTATAGGGT 57.618 40.909 0.00 0.00 39.80 4.34
2983 4394 4.881850 CCTAACTTGCACCTTGTTATAGGG 59.118 45.833 0.00 0.00 39.76 3.53
3217 4643 4.961551 GTGTGCGTATACGGAATTCAAATG 59.038 41.667 25.55 0.00 42.34 2.32
3386 4813 0.918799 TCCCAATTGGAGCTGCCCTA 60.919 55.000 26.60 0.00 38.61 3.53


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

AutoCloner maintained by Alex Coulton.