Multiple sequence alignment - TraesCS2A01G176800

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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 TraesCS2A01G176800 chr2A 100.000 3161 0 0 1 3161 136124834 136127994 0.000000e+00 5838.0
1 TraesCS2A01G176800 chr2A 85.192 547 54 13 1921 2458 144275328 144274800 1.290000e-148 536.0
2 TraesCS2A01G176800 chr2A 81.839 435 56 15 1471 1894 144275943 144275521 8.390000e-91 344.0
3 TraesCS2A01G176800 chr2D 90.883 1382 83 9 1807 3158 129789913 129791281 0.000000e+00 1814.0
4 TraesCS2A01G176800 chr2D 92.977 598 42 0 985 1582 129352954 129353551 0.000000e+00 872.0
5 TraesCS2A01G176800 chr2D 83.191 934 97 28 859 1764 129789006 129789907 0.000000e+00 800.0
6 TraesCS2A01G176800 chr2D 93.654 520 22 4 44 561 129351687 129352197 0.000000e+00 767.0
7 TraesCS2A01G176800 chr2D 83.256 866 88 21 1077 1901 129799144 129799993 0.000000e+00 743.0
8 TraesCS2A01G176800 chr2D 83.779 524 76 5 985 1508 136181691 136181177 3.660000e-134 488.0
9 TraesCS2A01G176800 chr2D 85.522 297 29 6 1919 2208 129800073 129800362 6.630000e-77 298.0
10 TraesCS2A01G176800 chr2D 88.446 251 21 6 728 977 136181968 136181725 2.380000e-76 296.0
11 TraesCS2A01G176800 chr2D 87.549 257 18 10 553 797 129352514 129352768 5.160000e-73 285.0
12 TraesCS2A01G176800 chr2D 80.463 389 54 12 1537 1918 136181179 136180806 8.640000e-71 278.0
13 TraesCS2A01G176800 chr2D 83.704 135 12 7 859 984 129352770 129352903 5.540000e-23 119.0
14 TraesCS2A01G176800 chr2B 90.037 1335 74 14 1819 3109 182953932 182955251 0.000000e+00 1674.0
15 TraesCS2A01G176800 chr2B 92.163 906 63 3 873 1777 182936171 182937069 0.000000e+00 1273.0
16 TraesCS2A01G176800 chr2B 91.145 926 67 6 1294 2204 182964710 182965635 0.000000e+00 1242.0
17 TraesCS2A01G176800 chr2B 82.581 1085 127 25 859 1891 183012952 183014026 0.000000e+00 900.0
18 TraesCS2A01G176800 chr2B 82.768 1091 109 38 859 1896 183198986 183200050 0.000000e+00 900.0
19 TraesCS2A01G176800 chr2B 85.480 854 105 10 859 1696 183129042 183129892 0.000000e+00 872.0
20 TraesCS2A01G176800 chr2B 89.123 570 27 8 2211 2751 182965742 182966305 0.000000e+00 676.0
21 TraesCS2A01G176800 chr2B 93.427 426 27 1 2736 3161 183007160 183007584 5.750000e-177 630.0
22 TraesCS2A01G176800 chr2B 88.158 532 50 6 859 1379 183060668 183061197 3.460000e-174 621.0
23 TraesCS2A01G176800 chr2B 91.514 436 29 5 44 475 182935045 182935476 7.550000e-166 593.0
24 TraesCS2A01G176800 chr2B 87.528 449 43 7 860 1297 182959450 182959896 1.010000e-139 507.0
25 TraesCS2A01G176800 chr2B 85.547 256 22 7 1919 2167 183014099 183014346 1.460000e-63 254.0
26 TraesCS2A01G176800 chr2B 82.550 298 30 9 1919 2208 183063135 183063418 3.150000e-60 243.0
27 TraesCS2A01G176800 chr2B 91.813 171 13 1 557 726 182959215 182959385 1.470000e-58 237.0
28 TraesCS2A01G176800 chr2B 82.879 257 26 13 553 797 183012700 183012950 6.870000e-52 215.0
29 TraesCS2A01G176800 chr2B 96.491 57 1 1 1769 1825 182952995 182953050 3.360000e-15 93.5
30 TraesCS2A01G176800 chr2B 86.517 89 2 2 473 561 182935568 182935646 4.340000e-14 89.8
31 TraesCS2A01G176800 chr2B 90.566 53 3 2 3108 3159 182955410 182955461 5.660000e-08 69.4


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 TraesCS2A01G176800 chr2A 136124834 136127994 3160 False 5838.000000 5838 100.000000 1 3161 1 chr2A.!!$F1 3160
1 TraesCS2A01G176800 chr2A 144274800 144275943 1143 True 440.000000 536 83.515500 1471 2458 2 chr2A.!!$R1 987
2 TraesCS2A01G176800 chr2D 129789006 129791281 2275 False 1307.000000 1814 87.037000 859 3158 2 chr2D.!!$F2 2299
3 TraesCS2A01G176800 chr2D 129799144 129800362 1218 False 520.500000 743 84.389000 1077 2208 2 chr2D.!!$F3 1131
4 TraesCS2A01G176800 chr2D 129351687 129353551 1864 False 510.750000 872 89.471000 44 1582 4 chr2D.!!$F1 1538
5 TraesCS2A01G176800 chr2D 136180806 136181968 1162 True 354.000000 488 84.229333 728 1918 3 chr2D.!!$R1 1190
6 TraesCS2A01G176800 chr2B 182964710 182966305 1595 False 959.000000 1242 90.134000 1294 2751 2 chr2B.!!$F6 1457
7 TraesCS2A01G176800 chr2B 183198986 183200050 1064 False 900.000000 900 82.768000 859 1896 1 chr2B.!!$F3 1037
8 TraesCS2A01G176800 chr2B 183129042 183129892 850 False 872.000000 872 85.480000 859 1696 1 chr2B.!!$F2 837
9 TraesCS2A01G176800 chr2B 182935045 182937069 2024 False 651.933333 1273 90.064667 44 1777 3 chr2B.!!$F4 1733
10 TraesCS2A01G176800 chr2B 182952995 182959896 6901 False 516.180000 1674 91.287000 557 3159 5 chr2B.!!$F5 2602
11 TraesCS2A01G176800 chr2B 183012700 183014346 1646 False 456.333333 900 83.669000 553 2167 3 chr2B.!!$F7 1614
12 TraesCS2A01G176800 chr2B 183060668 183063418 2750 False 432.000000 621 85.354000 859 2208 2 chr2B.!!$F8 1349

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
803 6483 0.165944 CAACGCCATCTTTCGTGTCC 59.834 55.0 0.0 0.0 39.06 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2741 10263 0.447801 GAGCACGGTTATGTTGCAGG 59.552 55.0 0.0 0.0 0.0 4.85 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 2.689983 CAATTCTCCCAACACCTATGGC 59.310 50.000 0.00 0.00 36.58 4.40
23 24 1.819632 CTCCCAACACCTATGGCGC 60.820 63.158 0.00 0.00 36.58 6.53
24 25 2.828549 CCCAACACCTATGGCGCC 60.829 66.667 22.73 22.73 36.58 6.53
25 26 3.202001 CCAACACCTATGGCGCCG 61.202 66.667 23.90 10.06 0.00 6.46
26 27 3.202001 CAACACCTATGGCGCCGG 61.202 66.667 23.90 19.77 0.00 6.13
31 32 4.856801 CCTATGGCGCCGGCAACT 62.857 66.667 28.98 10.21 42.43 3.16
32 33 2.108157 CTATGGCGCCGGCAACTA 59.892 61.111 28.98 16.56 42.43 2.24
34 35 2.916502 CTATGGCGCCGGCAACTACA 62.917 60.000 28.98 17.03 42.43 2.74
37 38 3.350612 GCGCCGGCAACTACAACA 61.351 61.111 28.98 0.00 39.62 3.33
38 39 2.860293 CGCCGGCAACTACAACAG 59.140 61.111 28.98 0.98 0.00 3.16
39 40 1.959226 CGCCGGCAACTACAACAGT 60.959 57.895 28.98 0.00 40.05 3.55
40 41 1.574428 GCCGGCAACTACAACAGTG 59.426 57.895 24.80 0.00 37.63 3.66
41 42 1.852067 GCCGGCAACTACAACAGTGG 61.852 60.000 24.80 0.00 37.63 4.00
42 43 0.250124 CCGGCAACTACAACAGTGGA 60.250 55.000 0.00 0.00 37.63 4.02
85 86 1.267806 ACTTTGCTGGAAATGTGAGCG 59.732 47.619 0.00 0.00 35.36 5.03
294 297 6.258230 TCTTGAGATGCAAAGGTAACAATG 57.742 37.500 0.00 0.00 35.74 2.82
304 307 5.625197 GCAAAGGTAACAATGATGAATGCCT 60.625 40.000 0.00 0.00 35.08 4.75
354 357 1.210538 AGCTTGATGATGCCTCTGGA 58.789 50.000 0.00 0.00 0.00 3.86
366 369 6.084738 TGATGCCTCTGGAGTAGGTTATTAT 58.915 40.000 0.00 0.00 36.43 1.28
367 370 6.558775 TGATGCCTCTGGAGTAGGTTATTATT 59.441 38.462 0.00 0.00 36.43 1.40
370 373 6.497259 TGCCTCTGGAGTAGGTTATTATTAGG 59.503 42.308 0.00 0.00 36.43 2.69
371 374 6.497606 GCCTCTGGAGTAGGTTATTATTAGGT 59.502 42.308 0.00 0.00 36.43 3.08
401 404 5.912360 ATTGCTTAGTTTTTCTGCTTTGC 57.088 34.783 0.00 0.00 0.00 3.68
421 424 4.852609 GCTTTTGCATGCTATTTTGAGG 57.147 40.909 20.33 0.00 46.58 3.86
450 453 2.240667 AGTTATGGTGATGCTTCTGGCT 59.759 45.455 0.88 0.00 42.39 4.75
579 6244 4.424061 TCATTGCTCAAAGTGAAATCCG 57.576 40.909 0.00 0.00 0.00 4.18
705 6372 3.623060 CCATCGGTGTACATTTTCCTCAG 59.377 47.826 0.00 0.00 0.00 3.35
726 6393 0.861837 CGGAGACACACAACTTCTGC 59.138 55.000 0.00 0.00 0.00 4.26
727 6394 1.806247 CGGAGACACACAACTTCTGCA 60.806 52.381 0.00 0.00 0.00 4.41
730 6397 0.308993 GACACACAACTTCTGCAGCC 59.691 55.000 9.47 0.00 0.00 4.85
732 6399 0.956633 CACACAACTTCTGCAGCCAT 59.043 50.000 9.47 0.00 0.00 4.40
733 6400 1.068748 CACACAACTTCTGCAGCCATC 60.069 52.381 9.47 0.00 0.00 3.51
734 6401 1.241165 CACAACTTCTGCAGCCATCA 58.759 50.000 9.47 0.00 0.00 3.07
737 6404 1.816835 CAACTTCTGCAGCCATCACAT 59.183 47.619 9.47 0.00 0.00 3.21
783 6463 1.154054 GCCACGCGCATTCATTCAA 60.154 52.632 5.73 0.00 37.47 2.69
797 6477 4.159377 TCATTCAACAACGCCATCTTTC 57.841 40.909 0.00 0.00 0.00 2.62
799 6479 1.588674 TCAACAACGCCATCTTTCGT 58.411 45.000 0.00 0.00 41.06 3.85
803 6483 0.165944 CAACGCCATCTTTCGTGTCC 59.834 55.000 0.00 0.00 39.06 4.02
823 6503 1.881973 CTCACCACCACATTTCCAGTG 59.118 52.381 0.00 0.00 36.76 3.66
844 6524 3.165071 GGAATGCCAAAGAGAAAAGGGA 58.835 45.455 0.00 0.00 0.00 4.20
845 6525 3.194329 GGAATGCCAAAGAGAAAAGGGAG 59.806 47.826 0.00 0.00 0.00 4.30
846 6526 1.620822 TGCCAAAGAGAAAAGGGAGC 58.379 50.000 0.00 0.00 0.00 4.70
847 6527 1.133513 TGCCAAAGAGAAAAGGGAGCA 60.134 47.619 0.00 0.00 0.00 4.26
848 6528 1.963515 GCCAAAGAGAAAAGGGAGCAA 59.036 47.619 0.00 0.00 0.00 3.91
894 6574 1.300233 GGAATCGAGGTAGCTGCGG 60.300 63.158 0.00 0.00 0.00 5.69
921 6608 4.416738 GCACTGGGCCTGGAGTCC 62.417 72.222 15.36 0.73 36.11 3.85
1004 6743 1.377202 GCCGGAGAAGCACAATGGA 60.377 57.895 5.05 0.00 0.00 3.41
1007 6746 1.699656 CGGAGAAGCACAATGGAGCG 61.700 60.000 0.00 0.00 35.61 5.03
1042 6781 1.445095 GTCGCCTCCTGCATGATCT 59.555 57.895 0.00 0.00 41.33 2.75
1063 6802 4.779733 TCCTCCTGCTCGTCCCCC 62.780 72.222 0.00 0.00 0.00 5.40
1239 6978 2.507102 ACGTTCCGCGAGCAGATG 60.507 61.111 8.23 0.00 44.77 2.90
1263 7002 2.971598 CGACCTGGGGCTCACCATT 61.972 63.158 0.00 0.00 42.91 3.16
1334 7073 2.807045 CACTGTCGACGAGCAGGC 60.807 66.667 22.53 4.43 37.07 4.85
1356 7095 2.722201 GCTCCTCCTGTACCACGGG 61.722 68.421 0.00 0.00 46.14 5.28
1361 7100 1.949847 CTCCTGTACCACGGGCTGAG 61.950 65.000 0.00 0.00 44.40 3.35
1385 8477 1.949847 GCTTACTCCGAGGAGCTGCA 61.950 60.000 18.37 0.00 45.54 4.41
1407 8517 1.295423 CCGGGTCTACTGGTTGTGG 59.705 63.158 0.00 0.00 41.03 4.17
1442 8558 0.835941 GATGGGGAGCAGACACTCAT 59.164 55.000 0.00 0.00 38.50 2.90
1447 8563 1.483827 GGGAGCAGACACTCATCATCA 59.516 52.381 0.00 0.00 38.50 3.07
1448 8564 2.093288 GGGAGCAGACACTCATCATCAA 60.093 50.000 0.00 0.00 38.50 2.57
1530 8646 1.244816 TCACCAAGACTGTCGTCGAT 58.755 50.000 0.00 0.00 44.93 3.59
1582 8698 0.109086 CGTGCTGATTCCGACAGAGT 60.109 55.000 0.00 0.00 37.54 3.24
1660 8791 1.739562 CTCCTGGCGCTGTGAGTTC 60.740 63.158 7.64 0.00 0.00 3.01
1687 8818 2.536365 CTGACGCTTAATTCCGCTACA 58.464 47.619 0.00 0.00 0.00 2.74
1738 8881 2.843701 CCTGTCCATAGCATCAGTTCC 58.156 52.381 0.00 0.00 0.00 3.62
1740 8883 3.464907 CTGTCCATAGCATCAGTTCCTG 58.535 50.000 0.00 0.00 0.00 3.86
1742 8885 1.839354 TCCATAGCATCAGTTCCTGCA 59.161 47.619 0.00 0.00 40.88 4.41
1845 9026 9.526286 CGTATATAGTACATTTAGTCGACAGTG 57.474 37.037 19.50 12.42 0.00 3.66
1856 9037 9.907576 CATTTAGTCGACAGTGATTTAGATTTC 57.092 33.333 19.50 0.00 0.00 2.17
1883 9068 7.691050 GGCTTTCTGTACATACGTCAATTTAAC 59.309 37.037 0.00 0.00 0.00 2.01
1947 9308 5.588958 ATTGCTCCAGCTTTTCTAAATCC 57.411 39.130 0.00 0.00 42.66 3.01
2082 9447 1.301716 TTCTCTTGTGTGCCGGCTC 60.302 57.895 29.70 25.38 0.00 4.70
2115 9480 0.896019 AGGATCGCGCTACTGCCTAT 60.896 55.000 5.56 0.00 35.36 2.57
2210 9695 1.067776 CCCTCGTATTCCCTCGTATGC 60.068 57.143 0.00 0.00 0.00 3.14
2232 9717 5.196825 GCTCTGTAGTCGTCGTATAGTTTC 58.803 45.833 0.00 0.00 0.00 2.78
2296 9782 5.048713 ACTTTTGAATCTAGGCTTCGTTTGG 60.049 40.000 0.00 0.00 0.00 3.28
2310 9796 6.407623 GCTTCGTTTGGTTTAACAAAATGTC 58.592 36.000 14.58 4.81 41.53 3.06
2312 9798 4.499758 TCGTTTGGTTTAACAAAATGTCGC 59.500 37.500 14.58 0.00 41.53 5.19
2332 9818 4.859245 TCGCTGACTATGAATTCGATATGC 59.141 41.667 0.04 0.00 0.00 3.14
2418 9911 8.823818 AGCATTTCTTTTATTGCAATATTGAGC 58.176 29.630 19.51 15.25 37.56 4.26
2478 9986 6.204301 GGGGAGTAGTTACTTTCAACAACTTC 59.796 42.308 0.00 0.00 36.50 3.01
2517 10026 4.707934 TCCTGCAAATGACATGATGTGAAT 59.292 37.500 1.23 0.00 0.00 2.57
2537 10046 0.814010 GGACGTGGCGATAAATGGCT 60.814 55.000 0.00 0.00 0.00 4.75
2628 10150 3.057969 TGCTCAGGTGTTCCATGTAAG 57.942 47.619 0.00 0.00 35.89 2.34
2655 10177 3.873361 ACTGTATTCATGATCTTGTGCGG 59.127 43.478 8.33 2.47 0.00 5.69
2697 10219 5.475564 TCGTCTAACATATATGTAGGCTGCA 59.524 40.000 18.56 7.99 40.80 4.41
2716 10238 1.404391 CAGGCTGCCAACTGATTGATC 59.596 52.381 22.65 0.00 38.15 2.92
2741 10263 2.371510 AGGAAGATGCCAGGAGCTTATC 59.628 50.000 0.00 0.00 44.23 1.75
2753 10275 4.820284 GGAGCTTATCCTGCAACATAAC 57.180 45.455 0.00 0.00 45.64 1.89
2760 10282 0.447801 CCTGCAACATAACCGTGCTC 59.552 55.000 0.00 0.00 0.00 4.26
2820 10343 1.338337 ACTAGCAGTAGCACGCATAGG 59.662 52.381 0.00 0.00 45.49 2.57
2842 10365 3.758554 GTGCCATGTTCACAGTTTATCCT 59.241 43.478 9.62 0.00 34.73 3.24
2843 10366 4.218417 GTGCCATGTTCACAGTTTATCCTT 59.782 41.667 9.62 0.00 34.73 3.36
2844 10367 4.832266 TGCCATGTTCACAGTTTATCCTTT 59.168 37.500 0.00 0.00 0.00 3.11
2877 10400 1.453155 ACCATCACACAAATCGCCTC 58.547 50.000 0.00 0.00 0.00 4.70
2896 10419 3.055385 CCTCCTTTACCTCAATTCGTCCA 60.055 47.826 0.00 0.00 0.00 4.02
2931 10454 4.056125 TGCCGACTCGCCTGACTG 62.056 66.667 0.00 0.00 0.00 3.51
2943 10466 2.800985 CGCCTGACTGATACTGATGTGG 60.801 54.545 0.00 0.00 0.00 4.17
2987 10510 1.860676 GTGTGTGCTCGGTCTGTTAA 58.139 50.000 0.00 0.00 0.00 2.01
3034 10557 2.351418 ACATATCATGTGAAACCGCGTG 59.649 45.455 4.92 0.00 43.01 5.34
3037 10560 0.249699 TCATGTGAAACCGCGTGTCT 60.250 50.000 4.92 0.00 34.36 3.41
3082 10605 6.612456 TGGATTTGAGCTATTGGATGGAAAAT 59.388 34.615 0.00 0.00 0.00 1.82
3093 10616 6.449635 TTGGATGGAAAATCAACGGATAAG 57.550 37.500 0.00 0.00 32.09 1.73
3105 10628 5.698832 TCAACGGATAAGTTTGCATGAAAG 58.301 37.500 0.00 0.00 30.96 2.62
3139 10662 0.322648 ATTTGCAAAGAGGGCCAAGC 59.677 50.000 18.19 2.23 0.00 4.01
3151 10674 1.066929 GGGCCAAGCATTTCGTCAAAT 60.067 47.619 4.39 0.00 31.91 2.32
3153 10676 3.367910 GGGCCAAGCATTTCGTCAAATTA 60.368 43.478 4.39 0.00 28.97 1.40
3158 10681 6.580476 CCAAGCATTTCGTCAAATTAAACAC 58.420 36.000 0.00 0.00 28.97 3.32
3159 10682 6.281056 CAAGCATTTCGTCAAATTAAACACG 58.719 36.000 0.00 0.00 28.97 4.49
3160 10683 4.381566 AGCATTTCGTCAAATTAAACACGC 59.618 37.500 0.00 0.00 28.97 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.251916 CGCCATAGGTGTTGGGAGAA 59.748 55.000 0.00 0.00 34.66 2.87
5 6 1.819632 GCGCCATAGGTGTTGGGAG 60.820 63.158 0.00 0.00 35.34 4.30
7 8 2.828549 GGCGCCATAGGTGTTGGG 60.829 66.667 24.80 0.00 35.34 4.12
8 9 3.202001 CGGCGCCATAGGTGTTGG 61.202 66.667 28.98 0.98 35.34 3.77
9 10 3.202001 CCGGCGCCATAGGTGTTG 61.202 66.667 28.98 6.19 35.34 3.33
16 17 2.202960 GTAGTTGCCGGCGCCATA 60.203 61.111 28.98 8.93 0.00 2.74
18 19 4.627801 TTGTAGTTGCCGGCGCCA 62.628 61.111 28.98 10.57 0.00 5.69
19 20 4.097863 GTTGTAGTTGCCGGCGCC 62.098 66.667 23.90 19.07 0.00 6.53
21 22 1.959226 ACTGTTGTAGTTGCCGGCG 60.959 57.895 23.90 5.43 35.67 6.46
23 24 0.250124 TCCACTGTTGTAGTTGCCGG 60.250 55.000 0.00 0.00 37.60 6.13
24 25 1.148310 CTCCACTGTTGTAGTTGCCG 58.852 55.000 0.00 0.00 37.60 5.69
25 26 0.875059 GCTCCACTGTTGTAGTTGCC 59.125 55.000 0.00 0.00 37.60 4.52
26 27 1.532868 CAGCTCCACTGTTGTAGTTGC 59.467 52.381 0.00 0.00 41.86 4.17
27 28 2.146342 CCAGCTCCACTGTTGTAGTTG 58.854 52.381 0.00 0.00 45.68 3.16
29 30 1.070758 CACCAGCTCCACTGTTGTAGT 59.929 52.381 0.00 0.00 45.68 2.73
31 32 0.396435 CCACCAGCTCCACTGTTGTA 59.604 55.000 0.00 0.00 45.68 2.41
32 33 1.149174 CCACCAGCTCCACTGTTGT 59.851 57.895 0.00 0.00 45.68 3.32
34 35 2.113986 GCCACCAGCTCCACTGTT 59.886 61.111 0.00 0.00 45.68 3.16
37 38 2.113986 GTTGCCACCAGCTCCACT 59.886 61.111 0.00 0.00 44.23 4.00
38 39 1.827789 TTGTTGCCACCAGCTCCAC 60.828 57.895 0.00 0.00 44.23 4.02
39 40 1.827789 GTTGTTGCCACCAGCTCCA 60.828 57.895 0.00 0.00 44.23 3.86
40 41 1.799258 CTGTTGTTGCCACCAGCTCC 61.799 60.000 0.00 0.00 44.23 4.70
41 42 1.656441 CTGTTGTTGCCACCAGCTC 59.344 57.895 0.00 0.00 44.23 4.09
42 43 2.492773 GCTGTTGTTGCCACCAGCT 61.493 57.895 10.63 0.00 45.25 4.24
85 86 0.451783 CCAGTAAAGTTGCCGATGCC 59.548 55.000 0.00 0.00 36.33 4.40
294 297 2.124151 ACCCGCCAGGCATTCATC 60.124 61.111 13.30 0.00 40.58 2.92
304 307 0.671251 CTAACAAAAAGCACCCGCCA 59.329 50.000 0.00 0.00 39.83 5.69
370 373 8.906693 GCAGAAAAACTAAGCAATTCTTCTTAC 58.093 33.333 0.00 0.00 36.25 2.34
371 374 8.850156 AGCAGAAAAACTAAGCAATTCTTCTTA 58.150 29.630 0.00 0.00 36.25 2.10
380 383 5.009854 AGCAAAGCAGAAAAACTAAGCAA 57.990 34.783 0.00 0.00 0.00 3.91
383 386 6.183360 TGCAAAAGCAAAGCAGAAAAACTAAG 60.183 34.615 0.00 0.00 33.75 2.18
390 393 2.288458 GCATGCAAAAGCAAAGCAGAAA 59.712 40.909 14.21 0.00 42.14 2.52
401 404 3.305094 CGCCTCAAAATAGCATGCAAAAG 59.695 43.478 21.98 6.84 0.00 2.27
421 424 2.030946 GCATCACCATAACTGTTCTCGC 59.969 50.000 0.00 0.00 0.00 5.03
478 575 4.158394 GCTAAACAGCCATTTTCCATCTCA 59.842 41.667 0.00 0.00 0.00 3.27
502 599 3.563808 TGAACACACAGCCTAATCAACAC 59.436 43.478 0.00 0.00 0.00 3.32
579 6244 7.421530 TGTGTTCAGAATTTAGAGTTACAGC 57.578 36.000 0.00 0.00 0.00 4.40
626 6292 1.059657 CGCTGAAATTTGACACGCCG 61.060 55.000 0.00 0.00 0.00 6.46
628 6294 0.660005 TGCGCTGAAATTTGACACGC 60.660 50.000 9.73 11.68 44.70 5.34
705 6372 2.128035 CAGAAGTTGTGTGTCTCCGAC 58.872 52.381 0.00 0.00 0.00 4.79
719 6386 2.211250 AATGTGATGGCTGCAGAAGT 57.789 45.000 20.43 0.59 0.00 3.01
783 6463 0.865769 GACACGAAAGATGGCGTTGT 59.134 50.000 0.00 0.00 38.92 3.32
797 6477 0.250295 AATGTGGTGGTGAGGACACG 60.250 55.000 0.00 0.00 46.77 4.49
799 6479 1.202879 GGAAATGTGGTGGTGAGGACA 60.203 52.381 0.00 0.00 0.00 4.02
803 6483 1.881973 CACTGGAAATGTGGTGGTGAG 59.118 52.381 0.00 0.00 0.00 3.51
823 6503 3.165071 TCCCTTTTCTCTTTGGCATTCC 58.835 45.455 0.00 0.00 0.00 3.01
844 6524 0.399454 ACACTCTCCATGTGCTTGCT 59.601 50.000 0.00 0.00 38.86 3.91
845 6525 0.801251 GACACTCTCCATGTGCTTGC 59.199 55.000 0.00 0.00 38.86 4.01
846 6526 1.271001 TGGACACTCTCCATGTGCTTG 60.271 52.381 0.00 0.00 44.99 4.01
847 6527 1.059098 TGGACACTCTCCATGTGCTT 58.941 50.000 0.00 0.00 44.99 3.91
848 6528 2.764007 TGGACACTCTCCATGTGCT 58.236 52.632 0.00 0.00 44.99 4.40
868 6548 3.070302 AGCTACCTCGATTCCAATTCTCC 59.930 47.826 0.00 0.00 0.00 3.71
894 6574 3.108288 GCCCAGTGCCCTAGCCTAC 62.108 68.421 0.00 0.00 38.69 3.18
921 6608 2.030412 GGTTTTTGGCCGGCCTTG 59.970 61.111 43.34 0.00 36.94 3.61
1042 6781 2.650116 GGACGAGCAGGAGGAGCAA 61.650 63.158 0.00 0.00 0.00 3.91
1072 6811 3.909651 GGGTGGTTGCCCCTGGAA 61.910 66.667 0.00 0.00 42.89 3.53
1263 7002 2.033602 TCGTCGTCAGGGCAGAGA 59.966 61.111 0.00 0.00 0.00 3.10
1297 7036 1.049289 AGGCTATGGAACCTCGGGAC 61.049 60.000 0.00 0.00 0.00 4.46
1334 7073 3.155167 GGTACAGGAGGAGCCCGG 61.155 72.222 0.00 0.00 37.37 5.73
1356 7095 0.249657 CGGAGTAAGCCATCCTCAGC 60.250 60.000 0.00 0.00 33.12 4.26
1361 7100 0.676736 CTCCTCGGAGTAAGCCATCC 59.323 60.000 4.02 0.00 37.47 3.51
1385 8477 1.535687 AACCAGTAGACCCGGCTGT 60.536 57.895 0.00 0.00 0.00 4.40
1396 8506 1.142060 CAACACCTCCCACAACCAGTA 59.858 52.381 0.00 0.00 0.00 2.74
1402 8512 1.525077 GCGTCAACACCTCCCACAA 60.525 57.895 0.00 0.00 0.00 3.33
1403 8513 1.978455 AAGCGTCAACACCTCCCACA 61.978 55.000 0.00 0.00 0.00 4.17
1404 8514 1.227853 AAGCGTCAACACCTCCCAC 60.228 57.895 0.00 0.00 0.00 4.61
1405 8515 1.227823 CAAGCGTCAACACCTCCCA 60.228 57.895 0.00 0.00 0.00 4.37
1406 8516 0.321653 ATCAAGCGTCAACACCTCCC 60.322 55.000 0.00 0.00 0.00 4.30
1407 8517 0.798776 CATCAAGCGTCAACACCTCC 59.201 55.000 0.00 0.00 0.00 4.30
1442 8558 3.133542 CCTGCCTCTGTAGTGATTGATGA 59.866 47.826 0.00 0.00 0.00 2.92
1447 8563 0.543749 GCCCTGCCTCTGTAGTGATT 59.456 55.000 0.00 0.00 0.00 2.57
1448 8564 1.680522 CGCCCTGCCTCTGTAGTGAT 61.681 60.000 0.00 0.00 0.00 3.06
1496 8612 1.617947 GGTGATCCTGGCCTCGTTCT 61.618 60.000 3.32 0.00 0.00 3.01
1592 8708 4.276926 CCAAAAAGTCCCAGAAGAAGTCAG 59.723 45.833 0.00 0.00 0.00 3.51
1660 8791 3.307242 CGGAATTAAGCGTCAGGAAAGAG 59.693 47.826 0.00 0.00 0.00 2.85
1738 8881 1.336148 ACACCAACAAATCGCATGCAG 60.336 47.619 19.57 10.78 0.00 4.41
1740 8883 1.062258 CACACCAACAAATCGCATGC 58.938 50.000 7.91 7.91 0.00 4.06
1742 8885 0.961019 AGCACACCAACAAATCGCAT 59.039 45.000 0.00 0.00 0.00 4.73
1826 9003 8.737175 TCTAAATCACTGTCGACTAAATGTACT 58.263 33.333 17.92 0.00 0.00 2.73
1845 9026 7.303634 TGTACAGAAAGCCGAAATCTAAATC 57.696 36.000 0.00 0.00 0.00 2.17
1856 9037 2.871133 TGACGTATGTACAGAAAGCCG 58.129 47.619 0.33 0.00 0.00 5.52
1947 9308 5.923114 AGATACAGTTAGCGTGCATAATCAG 59.077 40.000 0.00 0.00 0.00 2.90
2024 9388 1.531423 CCACAGCAAGAATCTGCAGT 58.469 50.000 14.67 0.00 45.18 4.40
2082 9447 1.938577 CGATCCTTGCACCATCTTCTG 59.061 52.381 0.00 0.00 0.00 3.02
2135 9500 1.895131 GTTCTTGTTGCCCATGTGGAT 59.105 47.619 0.00 0.00 37.39 3.41
2210 9695 6.341880 TGAAACTATACGACGACTACAGAG 57.658 41.667 0.00 0.00 0.00 3.35
2246 9732 7.545615 TGAGCAAACACTATATACACAAGTCAG 59.454 37.037 0.00 0.00 0.00 3.51
2296 9782 7.295201 TCATAGTCAGCGACATTTTGTTAAAC 58.705 34.615 10.52 0.00 34.60 2.01
2310 9796 4.622740 TGCATATCGAATTCATAGTCAGCG 59.377 41.667 6.22 0.00 0.00 5.18
2312 9798 8.026026 ACTACTGCATATCGAATTCATAGTCAG 58.974 37.037 6.22 13.47 0.00 3.51
2517 10026 1.092921 GCCATTTATCGCCACGTCCA 61.093 55.000 0.00 0.00 0.00 4.02
2628 10150 8.217115 CGCACAAGATCATGAATACAGTATAAC 58.783 37.037 4.68 0.00 0.00 1.89
2655 10177 1.532090 CGAGACCGCTGACTGTATGTC 60.532 57.143 0.00 0.00 45.54 3.06
2697 10219 1.760192 GATCAATCAGTTGGCAGCCT 58.240 50.000 14.15 0.00 35.99 4.58
2716 10238 1.808133 GCTCCTGGCATCTTCCTAACG 60.808 57.143 0.00 0.00 41.35 3.18
2741 10263 0.447801 GAGCACGGTTATGTTGCAGG 59.552 55.000 0.00 0.00 0.00 4.85
2753 10275 0.806868 ATGCACATGAAAGAGCACGG 59.193 50.000 0.00 0.00 37.90 4.94
2820 10343 3.758554 AGGATAAACTGTGAACATGGCAC 59.241 43.478 12.46 12.46 36.81 5.01
2855 10378 2.627699 AGGCGATTTGTGTGATGGTTTT 59.372 40.909 0.00 0.00 0.00 2.43
2877 10400 3.939066 AGTGGACGAATTGAGGTAAAGG 58.061 45.455 0.00 0.00 0.00 3.11
2943 10466 4.569761 ATGCTGACATGATGCTGAATTC 57.430 40.909 0.00 0.00 34.35 2.17
2987 10510 7.199766 TCTCGTTAACATTTTGCATTCTGTTT 58.800 30.769 6.39 0.00 34.02 2.83
3006 10529 5.063438 CGGTTTCACATGATATGTTCTCGTT 59.937 40.000 0.00 0.00 42.70 3.85
3008 10531 4.550831 GCGGTTTCACATGATATGTTCTCG 60.551 45.833 0.00 0.00 42.70 4.04
3082 10605 5.471797 TCTTTCATGCAAACTTATCCGTTGA 59.528 36.000 0.00 0.00 0.00 3.18
3093 10616 4.860907 CCAGCAACTATCTTTCATGCAAAC 59.139 41.667 0.00 0.00 39.42 2.93
3105 10628 2.533266 GCAAATGTGCCAGCAACTATC 58.467 47.619 0.00 0.00 45.68 2.08


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

AutoCloner maintained by Alex Coulton.