Multiple sequence alignment - TraesCS3B01G401500

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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 TraesCS3B01G401500 chr3B 100.000 2459 0 0 1 2459 636241538 636243996 0.000000e+00 4542.0
1 TraesCS3B01G401500 chr3B 88.305 419 41 5 954 1365 636228130 636228547 1.700000e-136 496.0
2 TraesCS3B01G401500 chr3A 90.233 1587 84 30 589 2126 620603635 620605199 0.000000e+00 2006.0
3 TraesCS3B01G401500 chr3A 86.508 504 60 7 43 540 620603132 620603633 4.620000e-152 547.0
4 TraesCS3B01G401500 chr3A 93.235 340 14 5 2128 2459 620605439 620605777 2.200000e-135 492.0
5 TraesCS3B01G401500 chr3D 94.343 990 34 8 961 1942 477009978 477010953 0.000000e+00 1498.0
6 TraesCS3B01G401500 chr3D 93.850 439 23 2 2015 2450 477010992 477011429 0.000000e+00 658.0
7 TraesCS3B01G401500 chr3D 89.021 419 38 5 954 1365 477007787 477008204 1.690000e-141 512.0
8 TraesCS3B01G401500 chr3D 82.877 292 35 10 616 897 477009450 477009736 5.250000e-62 248.0
9 TraesCS3B01G401500 chr1A 89.034 383 39 3 1059 1440 474220379 474219999 2.860000e-129 472.0
10 TraesCS3B01G401500 chr1A 83.516 91 15 0 1 91 327169412 327169502 4.360000e-13 86.1
11 TraesCS3B01G401500 chr1D 88.889 378 41 1 1063 1440 374451422 374451046 4.790000e-127 464.0
12 TraesCS3B01G401500 chr1B 84.298 484 61 13 969 1440 499219296 499218816 2.230000e-125 459.0
13 TraesCS3B01G401500 chr7B 72.546 601 123 28 74 646 372324784 372325370 9.100000e-35 158.0
14 TraesCS3B01G401500 chr5D 72.636 497 108 23 74 548 212046312 212046802 3.300000e-29 139.0
15 TraesCS3B01G401500 chr4D 81.034 174 31 2 282 454 506997467 506997639 1.190000e-28 137.0
16 TraesCS3B01G401500 chr2A 88.571 105 12 0 247 351 68834346 68834242 7.140000e-26 128.0
17 TraesCS3B01G401500 chr5A 75.720 243 51 6 268 506 703462295 703462533 5.560000e-22 115.0


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 TraesCS3B01G401500 chr3B 636241538 636243996 2458 False 4542 4542 100.00000 1 2459 1 chr3B.!!$F2 2458
1 TraesCS3B01G401500 chr3A 620603132 620605777 2645 False 1015 2006 89.99200 43 2459 3 chr3A.!!$F1 2416
2 TraesCS3B01G401500 chr3D 477007787 477011429 3642 False 729 1498 90.02275 616 2450 4 chr3D.!!$F1 1834

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
38 39 0.036732 TCGTCCATCAAAGCTGCCTT 59.963 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 3213 1.251251 CAGAAGGCAAAGGAGGGTTG 58.749 55.0 0.0 0.0 0.0 3.77 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
21 22 4.250570 CATCTGACGGACAAATTCTTCG 57.749 45.455 0.00 0.00 0.00 3.79
22 23 3.380479 TCTGACGGACAAATTCTTCGT 57.620 42.857 0.00 0.00 36.74 3.85
23 24 3.314553 TCTGACGGACAAATTCTTCGTC 58.685 45.455 9.13 9.13 46.86 4.20
24 25 2.409975 TGACGGACAAATTCTTCGTCC 58.590 47.619 12.24 9.31 46.36 4.79
28 29 7.750122 TGACGGACAAATTCTTCGTCCATCA 62.750 44.000 12.24 10.89 46.51 3.07
31 32 5.393962 GGACAAATTCTTCGTCCATCAAAG 58.606 41.667 2.98 0.00 46.98 2.77
32 33 4.798574 ACAAATTCTTCGTCCATCAAAGC 58.201 39.130 0.00 0.00 0.00 3.51
34 35 4.691860 AATTCTTCGTCCATCAAAGCTG 57.308 40.909 0.00 0.00 0.00 4.24
38 39 0.036732 TCGTCCATCAAAGCTGCCTT 59.963 50.000 0.00 0.00 0.00 4.35
40 41 0.449388 GTCCATCAAAGCTGCCTTCG 59.551 55.000 0.00 0.00 0.00 3.79
41 42 0.036732 TCCATCAAAGCTGCCTTCGT 59.963 50.000 0.00 0.00 0.00 3.85
85 89 2.359975 GGTGTTCCTCCTTGCCGG 60.360 66.667 0.00 0.00 0.00 6.13
107 111 4.360405 GCCAACCCCCGTGGATGT 62.360 66.667 0.00 0.00 38.54 3.06
110 114 2.926242 AACCCCCGTGGATGTCGT 60.926 61.111 0.00 0.00 38.00 4.34
118 122 3.716195 TGGATGTCGTGGGGCCTG 61.716 66.667 0.84 0.00 0.00 4.85
123 127 3.319198 GTCGTGGGGCCTGGAGAA 61.319 66.667 0.84 0.00 0.00 2.87
141 145 4.129737 CGAGGACGACGGTGCCAT 62.130 66.667 0.00 0.00 42.66 4.40
160 164 0.391661 TGAACCGCCTGATGAAGAGC 60.392 55.000 0.00 0.00 0.00 4.09
166 170 0.465824 GCCTGATGAAGAGCTGCCAT 60.466 55.000 0.00 0.00 0.00 4.40
170 174 0.532417 GATGAAGAGCTGCCATCGCT 60.532 55.000 0.00 0.00 41.15 4.93
173 177 0.103937 GAAGAGCTGCCATCGCTACT 59.896 55.000 0.00 0.00 37.96 2.57
208 212 3.306088 GGAGAACCAAGACTTCGACATCA 60.306 47.826 0.00 0.00 35.97 3.07
209 213 4.499183 GAGAACCAAGACTTCGACATCAT 58.501 43.478 0.00 0.00 0.00 2.45
210 214 4.499183 AGAACCAAGACTTCGACATCATC 58.501 43.478 0.00 0.00 0.00 2.92
327 332 2.266055 CCAGTCCAGTCGAAGGGC 59.734 66.667 1.65 1.65 0.00 5.19
329 334 3.382832 AGTCCAGTCGAAGGGCCG 61.383 66.667 6.17 0.00 0.00 6.13
334 339 1.301401 CAGTCGAAGGGCCGTTCAA 60.301 57.895 31.48 16.33 0.00 2.69
357 362 1.647545 GCTTCAATGCGGCACAGCTA 61.648 55.000 4.03 0.00 38.13 3.32
372 377 2.567615 ACAGCTATCGGAGTTGGTTTCT 59.432 45.455 6.95 0.00 40.55 2.52
400 405 1.226773 GGCATCCACATTGAAGCGC 60.227 57.895 0.00 0.00 29.97 5.92
406 411 2.357034 ACATTGAAGCGCCGACGT 60.357 55.556 2.29 0.00 42.83 4.34
429 434 2.017782 GAGAGGTCACGTCTATCAGCA 58.982 52.381 0.00 0.00 0.00 4.41
432 437 0.179108 GGTCACGTCTATCAGCACCC 60.179 60.000 0.00 0.00 0.00 4.61
454 459 4.735132 CACGCCCGGTCACATCGT 62.735 66.667 0.00 0.00 0.00 3.73
458 463 1.079681 GCCCGGTCACATCGTACAA 60.080 57.895 0.00 0.00 0.00 2.41
469 474 2.289382 ACATCGTACAACATCACTGCCA 60.289 45.455 0.00 0.00 0.00 4.92
491 497 0.179048 CATTGCATACTCTGGGCCGA 60.179 55.000 0.00 0.00 0.00 5.54
536 542 1.880027 ACAGACATTCGGTGGAAAAGC 59.120 47.619 0.00 0.00 35.40 3.51
543 549 3.431725 GGTGGAAAAGCGCGGGAG 61.432 66.667 8.83 0.00 0.00 4.30
544 550 3.431725 GTGGAAAAGCGCGGGAGG 61.432 66.667 8.83 0.00 0.00 4.30
559 565 3.662117 GAGGGGCAGGCGGGAATTT 62.662 63.158 0.00 0.00 0.00 1.82
560 566 2.683572 GGGGCAGGCGGGAATTTT 60.684 61.111 0.00 0.00 0.00 1.82
561 567 2.578664 GGGCAGGCGGGAATTTTG 59.421 61.111 0.00 0.00 0.00 2.44
566 572 1.609210 AGGCGGGAATTTTGGTGGG 60.609 57.895 0.00 0.00 0.00 4.61
567 573 2.264480 GCGGGAATTTTGGTGGGC 59.736 61.111 0.00 0.00 0.00 5.36
568 574 2.978000 CGGGAATTTTGGTGGGCC 59.022 61.111 0.00 0.00 0.00 5.80
569 575 1.910772 CGGGAATTTTGGTGGGCCA 60.911 57.895 0.00 0.00 44.38 5.36
572 578 1.182385 GGAATTTTGGTGGGCCACGA 61.182 55.000 29.18 24.01 46.01 4.35
573 579 0.894835 GAATTTTGGTGGGCCACGAT 59.105 50.000 29.18 17.17 46.01 3.73
574 580 0.894835 AATTTTGGTGGGCCACGATC 59.105 50.000 29.18 16.75 46.01 3.69
575 581 0.251564 ATTTTGGTGGGCCACGATCA 60.252 50.000 29.18 19.20 46.01 2.92
577 583 0.679640 TTTGGTGGGCCACGATCATC 60.680 55.000 29.18 15.29 46.01 2.92
578 584 1.846712 TTGGTGGGCCACGATCATCA 61.847 55.000 29.18 17.74 46.01 3.07
579 585 1.524621 GGTGGGCCACGATCATCAG 60.525 63.158 29.18 0.00 34.83 2.90
580 586 1.522092 GTGGGCCACGATCATCAGA 59.478 57.895 22.83 0.00 0.00 3.27
581 587 0.107456 GTGGGCCACGATCATCAGAT 59.893 55.000 22.83 0.00 37.13 2.90
582 588 0.107268 TGGGCCACGATCATCAGATG 59.893 55.000 0.00 3.71 33.72 2.90
583 589 0.107456 GGGCCACGATCATCAGATGT 59.893 55.000 4.39 0.00 33.72 3.06
585 591 1.224075 GCCACGATCATCAGATGTGG 58.776 55.000 10.34 11.17 45.76 4.17
586 592 1.202568 GCCACGATCATCAGATGTGGA 60.203 52.381 18.02 0.00 45.81 4.02
587 593 2.477825 CCACGATCATCAGATGTGGAC 58.522 52.381 10.34 0.70 45.81 4.02
596 602 3.490759 GATGTGGACGTGCAGCGG 61.491 66.667 11.09 0.00 46.52 5.52
597 603 4.314440 ATGTGGACGTGCAGCGGT 62.314 61.111 11.09 0.00 46.52 5.68
715 1765 0.881118 ACACATCCAAACATCGCACC 59.119 50.000 0.00 0.00 0.00 5.01
716 1766 0.880441 CACATCCAAACATCGCACCA 59.120 50.000 0.00 0.00 0.00 4.17
720 1770 2.258013 CCAAACATCGCACCACCGT 61.258 57.895 0.00 0.00 0.00 4.83
741 1791 2.037902 TGACGGCTGTGGATGTTTAAGA 59.962 45.455 0.80 0.00 0.00 2.10
748 1798 2.037902 TGTGGATGTTTAAGAGTCCGCA 59.962 45.455 11.84 11.84 45.92 5.69
761 1811 1.153107 TCCGCATTGGAGATGCTGG 60.153 57.895 9.07 11.00 43.74 4.85
790 1840 5.277538 CGAGAAAAAGAAAACCTGGAGACTG 60.278 44.000 0.00 0.00 0.00 3.51
814 1868 4.334203 TCTCTCTGCGATGACTCTCTTTAC 59.666 45.833 0.00 0.00 0.00 2.01
821 1875 5.107607 TGCGATGACTCTCTTTACGTTTTTC 60.108 40.000 0.00 0.00 0.00 2.29
823 1877 6.346678 GCGATGACTCTCTTTACGTTTTTCTT 60.347 38.462 0.00 0.00 0.00 2.52
828 1882 9.374838 TGACTCTCTTTACGTTTTTCTTTTAGT 57.625 29.630 0.00 0.00 0.00 2.24
934 1995 0.533308 CCGTTCCGTCAAAACCAGGA 60.533 55.000 0.00 0.00 0.00 3.86
936 1997 1.235724 GTTCCGTCAAAACCAGGAGG 58.764 55.000 0.00 0.00 42.21 4.30
995 2234 3.120086 ATCCCCAAATCCCTCCGCG 62.120 63.158 0.00 0.00 0.00 6.46
1296 2535 1.509004 GTTCGCCTTCGAGCTCTCT 59.491 57.895 12.85 0.00 46.34 3.10
1308 2547 3.217743 CTCTCTACCCCGGGCGAC 61.218 72.222 17.73 0.00 0.00 5.19
1335 2574 3.720106 CTTCGTCGCCGACTCCGAG 62.720 68.421 16.07 3.91 44.13 4.63
1545 2785 9.863845 TGTTCTACATCGTCTTTGTCATATTTA 57.136 29.630 0.00 0.00 0.00 1.40
1693 2951 7.989416 TCGATTTGTATTTGGTCCTTAAACT 57.011 32.000 0.00 0.00 0.00 2.66
1768 3029 5.013568 TCTCGGTGTTTTTGACTTCTGTA 57.986 39.130 0.00 0.00 0.00 2.74
1769 3030 4.807304 TCTCGGTGTTTTTGACTTCTGTAC 59.193 41.667 0.00 0.00 0.00 2.90
1772 3033 5.007234 TCGGTGTTTTTGACTTCTGTACATG 59.993 40.000 0.00 0.00 0.00 3.21
1775 3036 7.352739 GGTGTTTTTGACTTCTGTACATGTAG 58.647 38.462 5.62 0.00 0.00 2.74
1776 3037 7.225931 GGTGTTTTTGACTTCTGTACATGTAGA 59.774 37.037 5.62 3.84 0.00 2.59
1777 3038 8.276325 GTGTTTTTGACTTCTGTACATGTAGAG 58.724 37.037 21.11 21.11 0.00 2.43
1797 3058 8.486210 TGTAGAGTTGTCTGATAATATTTGGCT 58.514 33.333 0.00 0.00 33.84 4.75
1813 3074 6.699575 ATTTGGCTTGTTATGACTGGATAC 57.300 37.500 0.00 0.00 0.00 2.24
1844 3105 5.738783 GCCCATTAACCGTAAAATCATGCAT 60.739 40.000 0.00 0.00 0.00 3.96
1887 3153 1.295423 GGTTTGCCTACTCCAGCGA 59.705 57.895 0.00 0.00 0.00 4.93
1888 3154 0.741221 GGTTTGCCTACTCCAGCGAG 60.741 60.000 0.00 0.00 42.32 5.03
1889 3155 0.246635 GTTTGCCTACTCCAGCGAGA 59.753 55.000 0.00 0.00 38.52 4.04
1891 3157 1.195115 TTGCCTACTCCAGCGAGAAT 58.805 50.000 0.00 0.00 38.52 2.40
1892 3158 0.461548 TGCCTACTCCAGCGAGAATG 59.538 55.000 0.00 0.00 38.52 2.67
1893 3159 0.878086 GCCTACTCCAGCGAGAATGC 60.878 60.000 0.00 0.00 38.52 3.56
1895 3161 1.137872 CCTACTCCAGCGAGAATGCTT 59.862 52.381 0.00 0.00 44.46 3.91
1896 3162 2.200067 CTACTCCAGCGAGAATGCTTG 58.800 52.381 0.00 0.00 44.46 4.01
1916 3182 3.678289 TGGTTGACCATGATGAACTCAG 58.322 45.455 0.00 0.00 42.01 3.35
1924 3190 3.597255 CATGATGAACTCAGAGCAGTGT 58.403 45.455 0.00 0.00 37.28 3.55
1930 3196 2.698855 ACTCAGAGCAGTGTTTGTGT 57.301 45.000 0.00 0.00 0.00 3.72
1963 3231 0.540597 GCAACCCTCCTTTGCCTTCT 60.541 55.000 0.00 0.00 43.02 2.85
1988 3256 3.610242 CAGTATCAACAGACAGAAGCGAC 59.390 47.826 0.00 0.00 0.00 5.19
1999 3267 1.736126 CAGAAGCGACTGCATGATTGT 59.264 47.619 0.00 0.00 46.23 2.71
2008 3276 4.094739 CGACTGCATGATTGTGTTCCATTA 59.905 41.667 0.00 0.00 0.00 1.90
2009 3277 5.391843 CGACTGCATGATTGTGTTCCATTAA 60.392 40.000 0.00 0.00 0.00 1.40
2010 3278 5.713025 ACTGCATGATTGTGTTCCATTAAC 58.287 37.500 0.00 0.00 38.67 2.01
2061 3346 9.624697 CACTTAAAATAGCTTTTGTGCTAATCA 57.375 29.630 0.00 0.00 46.81 2.57
2212 3735 9.832445 TTATATTCCTTCACCTCATTACTGAAC 57.168 33.333 0.00 0.00 0.00 3.18
2216 3739 5.013079 TCCTTCACCTCATTACTGAACATGT 59.987 40.000 0.00 0.00 0.00 3.21
2294 3817 6.606796 ACATCATTCCTAACATTATTGTGCCA 59.393 34.615 0.00 0.00 35.83 4.92
2317 3841 3.444916 CACGTGGTAGATACATGTGGTC 58.555 50.000 9.11 6.78 46.75 4.02
2322 3846 5.589192 GTGGTAGATACATGTGGTCAGTAC 58.411 45.833 9.11 6.33 0.00 2.73
2429 3956 0.103208 GGCTAGCTGCGTAGATGTGT 59.897 55.000 15.72 0.00 44.05 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.679980 ACGAAGAATTTGTCCGTCAGATG 59.320 43.478 0.00 0.00 38.69 2.90
2 3 3.380479 ACGAAGAATTTGTCCGTCAGA 57.620 42.857 0.00 0.00 38.69 3.27
12 13 4.616835 GCAGCTTTGATGGACGAAGAATTT 60.617 41.667 0.00 0.00 41.25 1.82
13 14 3.119708 GCAGCTTTGATGGACGAAGAATT 60.120 43.478 0.00 0.00 41.25 2.17
14 15 2.421424 GCAGCTTTGATGGACGAAGAAT 59.579 45.455 0.00 0.00 41.25 2.40
15 16 1.806542 GCAGCTTTGATGGACGAAGAA 59.193 47.619 0.00 0.00 41.25 2.52
16 17 1.442769 GCAGCTTTGATGGACGAAGA 58.557 50.000 0.00 0.00 41.25 2.87
18 19 0.036732 AGGCAGCTTTGATGGACGAA 59.963 50.000 0.00 0.00 0.00 3.85
19 20 0.036732 AAGGCAGCTTTGATGGACGA 59.963 50.000 0.00 0.00 0.00 4.20
21 22 0.449388 CGAAGGCAGCTTTGATGGAC 59.551 55.000 0.00 0.00 0.00 4.02
22 23 0.036732 ACGAAGGCAGCTTTGATGGA 59.963 50.000 0.00 0.00 0.00 3.41
23 24 0.169672 CACGAAGGCAGCTTTGATGG 59.830 55.000 0.00 0.00 0.00 3.51
24 25 1.129998 CTCACGAAGGCAGCTTTGATG 59.870 52.381 0.00 0.00 0.00 3.07
25 26 1.446907 CTCACGAAGGCAGCTTTGAT 58.553 50.000 0.00 0.00 0.00 2.57
26 27 0.603707 CCTCACGAAGGCAGCTTTGA 60.604 55.000 0.00 0.00 38.67 2.69
28 29 0.321122 CTCCTCACGAAGGCAGCTTT 60.321 55.000 0.00 0.00 45.78 3.51
29 30 1.188219 TCTCCTCACGAAGGCAGCTT 61.188 55.000 0.00 0.00 45.78 3.74
31 32 1.446966 GTCTCCTCACGAAGGCAGC 60.447 63.158 0.00 0.00 45.78 5.25
32 33 1.153939 CGTCTCCTCACGAAGGCAG 60.154 63.158 0.00 0.00 45.78 4.85
34 35 2.182030 CCGTCTCCTCACGAAGGC 59.818 66.667 0.00 0.00 45.78 4.35
40 41 4.083862 GTGGCCCCGTCTCCTCAC 62.084 72.222 0.00 0.00 0.00 3.51
58 59 2.985847 GGAACACCACCAGCAGCC 60.986 66.667 0.00 0.00 0.00 4.85
60 61 1.302832 GGAGGAACACCACCAGCAG 60.303 63.158 0.00 0.00 39.49 4.24
85 89 4.410400 CACGGGGGTTGGCTCCTC 62.410 72.222 0.00 0.00 34.96 3.71
92 96 2.435938 CGACATCCACGGGGGTTG 60.436 66.667 2.42 4.71 41.37 3.77
93 97 2.926242 ACGACATCCACGGGGGTT 60.926 61.111 2.42 0.00 38.11 4.11
94 98 3.702048 CACGACATCCACGGGGGT 61.702 66.667 2.42 0.00 38.11 4.95
107 111 3.319198 GTTCTCCAGGCCCCACGA 61.319 66.667 0.00 0.00 0.00 4.35
110 114 3.003173 CTCGTTCTCCAGGCCCCA 61.003 66.667 0.00 0.00 0.00 4.96
118 122 2.331132 ACCGTCGTCCTCGTTCTCC 61.331 63.158 0.00 0.00 38.33 3.71
141 145 0.391661 GCTCTTCATCAGGCGGTTCA 60.392 55.000 0.00 0.00 0.00 3.18
160 164 1.886313 CAGGCAGTAGCGATGGCAG 60.886 63.158 1.50 3.46 45.14 4.85
166 170 4.457496 GCAGGCAGGCAGTAGCGA 62.457 66.667 0.00 0.00 43.41 4.93
232 237 1.308326 CCTCCTCCTCTCCGTCCTT 59.692 63.158 0.00 0.00 0.00 3.36
327 332 0.109781 CATTGAAGCGGGTTGAACGG 60.110 55.000 0.00 0.00 0.00 4.44
329 334 3.107017 GCATTGAAGCGGGTTGAAC 57.893 52.632 0.00 0.00 0.00 3.18
354 359 4.571176 CCTTAAGAAACCAACTCCGATAGC 59.429 45.833 3.36 0.00 0.00 2.97
357 362 4.576879 GTCCTTAAGAAACCAACTCCGAT 58.423 43.478 3.36 0.00 0.00 4.18
372 377 1.448893 GTGGATGCCGCGTCCTTAA 60.449 57.895 28.02 9.32 40.04 1.85
400 405 2.745100 TGACCTCTCGGACGTCGG 60.745 66.667 16.37 16.37 39.77 4.79
406 411 1.208776 TGATAGACGTGACCTCTCGGA 59.791 52.381 0.00 0.00 37.19 4.55
413 418 0.179108 GGGTGCTGATAGACGTGACC 60.179 60.000 0.00 0.00 0.00 4.02
417 422 3.630289 GGGGGTGCTGATAGACGT 58.370 61.111 0.00 0.00 0.00 4.34
454 459 0.399833 TGGCTGGCAGTGATGTTGTA 59.600 50.000 17.16 0.00 0.00 2.41
458 463 1.601419 GCAATGGCTGGCAGTGATGT 61.601 55.000 31.39 1.08 36.96 3.06
469 474 0.466922 GCCCAGAGTATGCAATGGCT 60.467 55.000 0.00 0.00 41.91 4.75
491 497 2.032550 GCTTGCTGCGTCATATTCATGT 59.967 45.455 0.00 0.00 33.57 3.21
516 522 1.880027 GCTTTTCCACCGAATGTCTGT 59.120 47.619 0.00 0.00 0.00 3.41
520 526 1.579429 GCGCTTTTCCACCGAATGT 59.421 52.632 0.00 0.00 0.00 2.71
541 547 3.662117 AAATTCCCGCCTGCCCCTC 62.662 63.158 0.00 0.00 0.00 4.30
542 548 3.238197 AAAATTCCCGCCTGCCCCT 62.238 57.895 0.00 0.00 0.00 4.79
543 549 2.683572 AAAATTCCCGCCTGCCCC 60.684 61.111 0.00 0.00 0.00 5.80
544 550 2.578664 CAAAATTCCCGCCTGCCC 59.421 61.111 0.00 0.00 0.00 5.36
547 553 1.591183 CCACCAAAATTCCCGCCTG 59.409 57.895 0.00 0.00 0.00 4.85
548 554 1.609210 CCCACCAAAATTCCCGCCT 60.609 57.895 0.00 0.00 0.00 5.52
549 555 2.978000 CCCACCAAAATTCCCGCC 59.022 61.111 0.00 0.00 0.00 6.13
550 556 2.264480 GCCCACCAAAATTCCCGC 59.736 61.111 0.00 0.00 0.00 6.13
551 557 1.910772 TGGCCCACCAAAATTCCCG 60.911 57.895 0.00 0.00 45.37 5.14
560 566 2.256072 CTGATGATCGTGGCCCACCA 62.256 60.000 8.62 0.42 46.51 4.17
561 567 1.524621 CTGATGATCGTGGCCCACC 60.525 63.158 8.62 0.00 0.00 4.61
566 572 1.202568 TCCACATCTGATGATCGTGGC 60.203 52.381 23.59 0.00 43.48 5.01
567 573 2.477825 GTCCACATCTGATGATCGTGG 58.522 52.381 23.59 18.92 44.20 4.94
568 574 2.122564 CGTCCACATCTGATGATCGTG 58.877 52.381 23.59 11.17 34.53 4.35
569 575 1.751351 ACGTCCACATCTGATGATCGT 59.249 47.619 23.59 20.66 0.00 3.73
572 578 1.207811 TGCACGTCCACATCTGATGAT 59.792 47.619 23.59 5.85 0.00 2.45
573 579 0.607620 TGCACGTCCACATCTGATGA 59.392 50.000 23.59 0.00 0.00 2.92
574 580 1.004595 CTGCACGTCCACATCTGATG 58.995 55.000 15.83 15.83 0.00 3.07
575 581 0.742281 GCTGCACGTCCACATCTGAT 60.742 55.000 0.00 0.00 0.00 2.90
577 583 2.733671 CGCTGCACGTCCACATCTG 61.734 63.158 0.00 0.00 36.87 2.90
578 584 2.433145 CGCTGCACGTCCACATCT 60.433 61.111 0.00 0.00 36.87 2.90
579 585 3.490759 CCGCTGCACGTCCACATC 61.491 66.667 0.00 0.00 41.42 3.06
580 586 4.314440 ACCGCTGCACGTCCACAT 62.314 61.111 0.00 0.00 41.42 3.21
581 587 4.961511 GACCGCTGCACGTCCACA 62.962 66.667 0.00 0.00 41.42 4.17
617 623 3.792956 CCGCAAATTCGAGATGAAAATGG 59.207 43.478 0.00 0.00 40.71 3.16
620 626 4.757799 TTCCGCAAATTCGAGATGAAAA 57.242 36.364 0.00 0.00 40.71 2.29
647 1695 2.585263 CGCTAACGGTATGAACGGG 58.415 57.895 0.00 0.00 34.97 5.28
691 1741 3.181482 TGCGATGTTTGGATGTGTTTTGT 60.181 39.130 0.00 0.00 0.00 2.83
704 1754 1.227704 TCACGGTGGTGCGATGTTT 60.228 52.632 8.50 0.00 44.03 2.83
705 1755 1.959226 GTCACGGTGGTGCGATGTT 60.959 57.895 8.50 0.00 44.03 2.71
720 1770 2.037902 TCTTAAACATCCACAGCCGTCA 59.962 45.455 0.00 0.00 0.00 4.35
741 1791 4.547859 GCATCTCCAATGCGGACT 57.452 55.556 0.00 0.00 39.64 3.85
748 1798 0.465097 CGCCTTCCAGCATCTCCAAT 60.465 55.000 0.00 0.00 0.00 3.16
761 1811 4.290969 CAGGTTTTCTTTTTCTCGCCTTC 58.709 43.478 0.00 0.00 0.00 3.46
790 1840 2.288666 AGAGAGTCATCGCAGAGAGAC 58.711 52.381 0.00 0.00 43.63 3.36
827 1881 7.112984 CGTGGATAGAAACAACTTAAAAGCAAC 59.887 37.037 0.00 0.00 0.00 4.17
828 1882 7.136119 CGTGGATAGAAACAACTTAAAAGCAA 58.864 34.615 0.00 0.00 0.00 3.91
829 1883 6.261381 ACGTGGATAGAAACAACTTAAAAGCA 59.739 34.615 0.00 0.00 0.00 3.91
934 1995 2.041251 TCGTTCGGTTGGTTTTTCCT 57.959 45.000 0.00 0.00 37.07 3.36
936 1997 3.064408 AGAGTTCGTTCGGTTGGTTTTTC 59.936 43.478 0.00 0.00 0.00 2.29
1335 2574 2.239681 TCCAGTCCTCCTTCTCCTTC 57.760 55.000 0.00 0.00 0.00 3.46
1503 2743 7.770366 TGTAGAACAGTAGAATTACAGGTGA 57.230 36.000 0.00 0.00 31.96 4.02
1693 2951 9.547753 GCTTGAGATATACACTTGGATAAGAAA 57.452 33.333 0.00 0.00 37.36 2.52
1772 3033 8.894768 AGCCAAATATTATCAGACAACTCTAC 57.105 34.615 0.00 0.00 0.00 2.59
1775 3036 7.989826 ACAAGCCAAATATTATCAGACAACTC 58.010 34.615 0.00 0.00 0.00 3.01
1776 3037 7.944729 ACAAGCCAAATATTATCAGACAACT 57.055 32.000 0.00 0.00 0.00 3.16
1797 3058 6.288294 GCCACTATGTATCCAGTCATAACAA 58.712 40.000 0.00 0.00 0.00 2.83
1813 3074 2.341846 ACGGTTAATGGGCCACTATG 57.658 50.000 9.28 0.00 0.00 2.23
1814 3075 4.506937 TTTACGGTTAATGGGCCACTAT 57.493 40.909 9.28 0.00 0.00 2.12
1821 3082 5.255710 TGCATGATTTTACGGTTAATGGG 57.744 39.130 0.00 0.00 0.00 4.00
1823 3084 7.754069 ACAATGCATGATTTTACGGTTAATG 57.246 32.000 0.00 0.00 0.00 1.90
1824 3085 9.677567 GATACAATGCATGATTTTACGGTTAAT 57.322 29.630 0.00 0.00 0.00 1.40
1825 3086 8.898761 AGATACAATGCATGATTTTACGGTTAA 58.101 29.630 0.00 0.00 0.00 2.01
1896 3162 3.937706 CTCTGAGTTCATCATGGTCAACC 59.062 47.826 0.00 0.00 37.28 3.77
1916 3182 4.875544 TTTCTGTACACAAACACTGCTC 57.124 40.909 0.00 0.00 0.00 4.26
1945 3213 1.251251 CAGAAGGCAAAGGAGGGTTG 58.749 55.000 0.00 0.00 0.00 3.77
1954 3222 4.713553 TGTTGATACTGACAGAAGGCAAA 58.286 39.130 10.08 0.00 0.00 3.68
2012 3280 9.502091 AGTGATAAGCTCATAAAAACACAAGTA 57.498 29.630 0.00 0.00 35.97 2.24
2196 3719 5.482006 CTGACATGTTCAGTAATGAGGTGA 58.518 41.667 0.00 0.00 46.12 4.02
2294 3817 3.704566 ACCACATGTATCTACCACGTGAT 59.295 43.478 19.30 0.54 36.59 3.06
2317 3841 5.720202 TGCAGGAACATAAGTACAGTACTG 58.280 41.667 21.44 21.44 39.39 2.74


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

AutoCloner maintained by Alex Coulton.