Multiple sequence alignment - TraesCS1A01G137300

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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 TraesCS1A01G137300 chr1A 100.000 2747 0 0 1 2747 221707758 221710504 0.000000e+00 5073.0
1 TraesCS1A01G137300 chr1D 91.106 1203 48 14 623 1780 189662070 189663258 0.000000e+00 1574.0
2 TraesCS1A01G137300 chr1D 88.425 743 40 14 2041 2747 189663644 189664376 0.000000e+00 854.0
3 TraesCS1A01G137300 chr1D 90.020 491 14 10 8 469 189661543 189662027 1.090000e-168 603.0
4 TraesCS1A01G137300 chr1D 96.569 204 4 2 1802 2004 189663245 189663446 4.380000e-88 335.0
5 TraesCS1A01G137300 chr1D 95.556 45 1 1 2005 2048 189663570 189663614 1.360000e-08 71.3
6 TraesCS1A01G137300 chr1B 86.409 1008 68 34 1802 2747 263563609 263564609 0.000000e+00 1038.0
7 TraesCS1A01G137300 chr1B 90.217 644 21 3 1167 1780 263562991 263563622 0.000000e+00 802.0
8 TraesCS1A01G137300 chr1B 93.971 481 23 2 2 482 263561321 263561795 0.000000e+00 723.0
9 TraesCS1A01G137300 chr1B 83.386 632 39 19 551 1144 263562326 263562929 2.420000e-145 525.0
10 TraesCS1A01G137300 chr5D 89.623 106 7 4 474 578 242627027 242626925 6.170000e-27 132.0
11 TraesCS1A01G137300 chr4D 88.679 106 10 2 467 572 43284003 43284106 7.980000e-26 128.0
12 TraesCS1A01G137300 chr6A 90.625 96 8 1 474 569 532902267 532902361 2.870000e-25 126.0
13 TraesCS1A01G137300 chr2B 89.109 101 9 2 474 574 716814580 716814482 1.030000e-24 124.0
14 TraesCS1A01G137300 chr2B 88.000 100 10 2 474 573 800872058 800871961 1.730000e-22 117.0
15 TraesCS1A01G137300 chr2B 84.956 113 14 3 474 586 796952352 796952243 8.040000e-21 111.0
16 TraesCS1A01G137300 chr3A 89.000 100 10 1 474 573 739275113 739275015 3.710000e-24 122.0
17 TraesCS1A01G137300 chr3A 89.691 97 7 3 474 569 77404932 77405026 1.340000e-23 121.0
18 TraesCS1A01G137300 chr3A 89.583 96 9 1 474 569 242726201 242726107 1.340000e-23 121.0


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 TraesCS1A01G137300 chr1A 221707758 221710504 2746 False 5073.00 5073 100.00000 1 2747 1 chr1A.!!$F1 2746
1 TraesCS1A01G137300 chr1D 189661543 189664376 2833 False 687.46 1574 92.33520 8 2747 5 chr1D.!!$F1 2739
2 TraesCS1A01G137300 chr1B 263561321 263564609 3288 False 772.00 1038 88.49575 2 2747 4 chr1B.!!$F1 2745

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
494 524 0.248289 CCGTCCGTCCCACAATAAGT 59.752 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2459 0.249405 ACTTGCACATGTTTTGGCGG 60.249 50.0 0.0 0.0 0.0 6.13 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
80 81 3.244215 ACGAAATCTTTCCTGTCAGAGCA 60.244 43.478 0.00 0.00 33.68 4.26
81 82 3.748048 CGAAATCTTTCCTGTCAGAGCAA 59.252 43.478 0.00 0.00 33.68 3.91
82 83 4.377841 CGAAATCTTTCCTGTCAGAGCAAC 60.378 45.833 0.00 0.00 33.68 4.17
83 84 4.363991 AATCTTTCCTGTCAGAGCAACT 57.636 40.909 0.00 0.00 0.00 3.16
86 87 3.118261 TCTTTCCTGTCAGAGCAACTGTT 60.118 43.478 0.00 0.00 45.86 3.16
87 88 2.533266 TCCTGTCAGAGCAACTGTTC 57.467 50.000 0.00 6.45 45.86 3.18
90 91 3.118261 TCCTGTCAGAGCAACTGTTCTTT 60.118 43.478 0.00 0.00 45.86 2.52
92 93 4.096984 CCTGTCAGAGCAACTGTTCTTTTT 59.903 41.667 0.00 0.00 45.86 1.94
93 94 5.296780 CCTGTCAGAGCAACTGTTCTTTTTA 59.703 40.000 0.00 0.00 45.86 1.52
94 95 6.363577 TGTCAGAGCAACTGTTCTTTTTAG 57.636 37.500 9.97 0.00 45.86 1.85
95 96 5.296780 TGTCAGAGCAACTGTTCTTTTTAGG 59.703 40.000 9.97 0.00 45.86 2.69
96 97 4.821805 TCAGAGCAACTGTTCTTTTTAGGG 59.178 41.667 9.97 0.00 45.86 3.53
97 98 4.022849 CAGAGCAACTGTTCTTTTTAGGGG 60.023 45.833 0.00 0.00 41.30 4.79
149 150 0.520847 GAAAGCTGCTGAAGAGGTGC 59.479 55.000 1.35 0.00 0.00 5.01
440 470 2.546899 TGTAGCATGAGGTTACCTGGT 58.453 47.619 9.39 4.05 31.76 4.00
476 506 6.294397 CCATGTAATTAGTACGTACTCCCTCC 60.294 46.154 30.53 17.11 37.73 4.30
482 512 1.899437 TACGTACTCCCTCCGTCCGT 61.899 60.000 0.00 0.00 36.12 4.69
483 513 2.467826 CGTACTCCCTCCGTCCGTC 61.468 68.421 0.00 0.00 0.00 4.79
484 514 2.117779 GTACTCCCTCCGTCCGTCC 61.118 68.421 0.00 0.00 0.00 4.79
485 515 3.350031 TACTCCCTCCGTCCGTCCC 62.350 68.421 0.00 0.00 0.00 4.46
486 516 4.753662 CTCCCTCCGTCCGTCCCA 62.754 72.222 0.00 0.00 0.00 4.37
489 519 3.307906 CCTCCGTCCGTCCCACAA 61.308 66.667 0.00 0.00 0.00 3.33
491 521 1.324740 CCTCCGTCCGTCCCACAATA 61.325 60.000 0.00 0.00 0.00 1.90
492 522 0.533491 CTCCGTCCGTCCCACAATAA 59.467 55.000 0.00 0.00 0.00 1.40
493 523 0.533491 TCCGTCCGTCCCACAATAAG 59.467 55.000 0.00 0.00 0.00 1.73
494 524 0.248289 CCGTCCGTCCCACAATAAGT 59.752 55.000 0.00 0.00 0.00 2.24
512 944 9.826574 ACAATAAGTGACTCAACTTTGTACTAA 57.173 29.630 0.00 0.00 40.77 2.24
518 950 9.174166 AGTGACTCAACTTTGTACTAATTTTGT 57.826 29.630 0.00 0.00 0.00 2.83
545 977 9.694137 ACTAGAACTATTACAAAGTTGAGTCAC 57.306 33.333 0.00 0.00 37.31 3.67
546 978 9.915629 CTAGAACTATTACAAAGTTGAGTCACT 57.084 33.333 0.00 0.00 37.31 3.41
573 1069 0.263765 TGGGCGGAGGGAGTACTATT 59.736 55.000 0.00 0.00 0.00 1.73
599 1096 5.754778 AGTTTTTCGTTTATTCACCCTTCG 58.245 37.500 0.00 0.00 0.00 3.79
602 1099 0.372334 CGTTTATTCACCCTTCGCGG 59.628 55.000 6.13 0.00 0.00 6.46
615 1112 2.593436 CGCGGTGGTCTGGGTTTT 60.593 61.111 0.00 0.00 0.00 2.43
617 1114 1.826487 GCGGTGGTCTGGGTTTTGT 60.826 57.895 0.00 0.00 0.00 2.83
651 1148 8.437360 TTTATACCATGCTTGAGTCTGTAATG 57.563 34.615 0.22 0.00 0.00 1.90
652 1149 4.292186 ACCATGCTTGAGTCTGTAATGT 57.708 40.909 0.22 0.00 0.00 2.71
653 1150 4.256920 ACCATGCTTGAGTCTGTAATGTC 58.743 43.478 0.22 0.00 0.00 3.06
701 1213 3.211963 GTCCCGGGACATGCATGC 61.212 66.667 42.54 17.87 44.02 4.06
708 1220 1.180029 GGGACATGCATGCTTCAGTT 58.820 50.000 26.53 4.90 0.00 3.16
772 1289 2.496291 GCAAGCCCATGGGAGATGC 61.496 63.158 36.00 31.64 37.50 3.91
773 1290 2.191513 CAAGCCCATGGGAGATGCG 61.192 63.158 36.00 11.60 37.50 4.73
774 1291 2.377810 AAGCCCATGGGAGATGCGA 61.378 57.895 36.00 0.00 37.50 5.10
775 1292 1.713005 AAGCCCATGGGAGATGCGAT 61.713 55.000 36.00 9.95 37.50 4.58
776 1293 1.970114 GCCCATGGGAGATGCGATG 60.970 63.158 36.00 3.73 37.50 3.84
838 1371 3.578716 CCACCTGACAAGTTCCTTCTCTA 59.421 47.826 0.00 0.00 0.00 2.43
846 1379 5.848406 ACAAGTTCCTTCTCTACTGTGAAG 58.152 41.667 0.00 0.00 41.10 3.02
860 1393 4.237018 ACTGTGAAGGGTAAGGGTTTCTA 58.763 43.478 0.00 0.00 0.00 2.10
861 1394 4.661709 ACTGTGAAGGGTAAGGGTTTCTAA 59.338 41.667 0.00 0.00 0.00 2.10
874 1407 0.252558 TTTCTAACTCCCCCGCCTCT 60.253 55.000 0.00 0.00 0.00 3.69
882 1415 2.042843 CCCCGCCTCTAGGACACT 60.043 66.667 0.00 0.00 37.39 3.55
883 1416 2.128507 CCCCGCCTCTAGGACACTC 61.129 68.421 0.00 0.00 37.39 3.51
891 1424 2.451490 CTCTAGGACACTCCAGCTCAA 58.549 52.381 0.00 0.00 39.61 3.02
938 1475 1.639298 CGTAGCCTCTGCAACCAAGC 61.639 60.000 0.00 0.00 41.13 4.01
972 1509 0.461961 AGCTACATTCCTCAGCGACC 59.538 55.000 0.00 0.00 40.29 4.79
978 1515 0.321653 ATTCCTCAGCGACCCAACAC 60.322 55.000 0.00 0.00 0.00 3.32
991 1528 2.882137 ACCCAACACGTTATTCAACAGG 59.118 45.455 0.00 0.00 34.05 4.00
992 1529 2.227865 CCCAACACGTTATTCAACAGGG 59.772 50.000 0.00 0.00 34.05 4.45
999 1536 4.093408 CACGTTATTCAACAGGGATCAGTG 59.907 45.833 0.00 0.00 34.05 3.66
1009 1555 2.592861 GATCAGTGATGGCCGCCC 60.593 66.667 11.20 0.00 0.00 6.13
1010 1556 4.195334 ATCAGTGATGGCCGCCCC 62.195 66.667 7.03 0.00 0.00 5.80
1407 1998 3.861797 ATGCCCGGGCTAAGGACG 61.862 66.667 43.34 5.51 42.51 4.79
1414 2005 4.176752 GGCTAAGGACGGGGCCTG 62.177 72.222 11.83 11.83 41.20 4.85
1415 2006 4.858680 GCTAAGGACGGGGCCTGC 62.859 72.222 13.63 5.17 38.58 4.85
1416 2007 4.530857 CTAAGGACGGGGCCTGCG 62.531 72.222 13.63 6.44 38.58 5.18
1526 2117 2.972505 CGTGCAGAAACAGCCGGT 60.973 61.111 1.90 0.00 0.00 5.28
1679 2297 1.151668 CGGAGAAAGCTTGTGACCAG 58.848 55.000 0.00 0.00 0.00 4.00
1765 2383 1.276421 GAGCTGAGGCAAGAGGTGTTA 59.724 52.381 0.00 0.00 41.70 2.41
1776 2394 4.156915 CAAGAGGTGTTAACTACTCGACG 58.843 47.826 18.11 10.73 35.22 5.12
1777 2395 3.406764 AGAGGTGTTAACTACTCGACGT 58.593 45.455 18.11 0.00 35.22 4.34
1778 2396 3.434984 AGAGGTGTTAACTACTCGACGTC 59.565 47.826 18.11 5.18 35.22 4.34
1779 2397 3.141398 AGGTGTTAACTACTCGACGTCA 58.859 45.455 17.16 1.87 0.00 4.35
1780 2398 3.755378 AGGTGTTAACTACTCGACGTCAT 59.245 43.478 17.16 2.63 0.00 3.06
1781 2399 4.217118 AGGTGTTAACTACTCGACGTCATT 59.783 41.667 17.16 0.81 0.00 2.57
1782 2400 4.556523 GGTGTTAACTACTCGACGTCATTC 59.443 45.833 17.16 0.00 0.00 2.67
1783 2401 5.388944 GTGTTAACTACTCGACGTCATTCT 58.611 41.667 17.16 0.00 0.00 2.40
1784 2402 5.507527 GTGTTAACTACTCGACGTCATTCTC 59.492 44.000 17.16 0.00 0.00 2.87
1785 2403 5.410746 TGTTAACTACTCGACGTCATTCTCT 59.589 40.000 17.16 0.00 0.00 3.10
1786 2404 4.603231 AACTACTCGACGTCATTCTCTC 57.397 45.455 17.16 0.00 0.00 3.20
1787 2405 3.864243 ACTACTCGACGTCATTCTCTCT 58.136 45.455 17.16 0.00 0.00 3.10
1788 2406 3.866910 ACTACTCGACGTCATTCTCTCTC 59.133 47.826 17.16 0.00 0.00 3.20
1789 2407 2.980568 ACTCGACGTCATTCTCTCTCT 58.019 47.619 17.16 0.00 0.00 3.10
1790 2408 2.933906 ACTCGACGTCATTCTCTCTCTC 59.066 50.000 17.16 0.00 0.00 3.20
1791 2409 2.933260 CTCGACGTCATTCTCTCTCTCA 59.067 50.000 17.16 0.00 0.00 3.27
1792 2410 3.335579 TCGACGTCATTCTCTCTCTCAA 58.664 45.455 17.16 0.00 0.00 3.02
1793 2411 3.751698 TCGACGTCATTCTCTCTCTCAAA 59.248 43.478 17.16 0.00 0.00 2.69
1794 2412 4.215613 TCGACGTCATTCTCTCTCTCAAAA 59.784 41.667 17.16 0.00 0.00 2.44
1795 2413 4.917998 CGACGTCATTCTCTCTCTCAAAAA 59.082 41.667 17.16 0.00 0.00 1.94
1841 2459 2.851008 GCGATGAGCCTAAACGATTTGC 60.851 50.000 0.00 0.00 40.81 3.68
1851 2469 0.103208 AACGATTTGCCGCCAAAACA 59.897 45.000 0.00 0.00 43.58 2.83
1872 2491 1.067213 TGTGCAAGTGCGATAGTGCTA 60.067 47.619 0.00 0.00 45.83 3.49
1873 2492 1.999735 GTGCAAGTGCGATAGTGCTAA 59.000 47.619 0.00 0.00 45.83 3.09
1912 2531 7.148239 GGTTGACTCAATTGTATCCTAAACCTG 60.148 40.741 5.13 0.00 31.60 4.00
2037 2782 4.583871 CCTACAACAAATCCTCTGCTCTT 58.416 43.478 0.00 0.00 0.00 2.85
2045 2790 7.617041 ACAAATCCTCTGCTCTTGTATAAAC 57.383 36.000 0.00 0.00 0.00 2.01
2077 2860 1.745653 GCATTCCTCCTTGTTGGCTAC 59.254 52.381 0.00 0.00 35.26 3.58
2091 2874 7.593644 CCTTGTTGGCTACTTACAAATTTACAC 59.406 37.037 0.01 0.00 31.98 2.90
2093 2876 6.546403 TGTTGGCTACTTACAAATTTACACCA 59.454 34.615 0.01 0.00 0.00 4.17
2094 2877 7.231722 TGTTGGCTACTTACAAATTTACACCAT 59.768 33.333 0.01 0.00 0.00 3.55
2095 2878 7.385778 TGGCTACTTACAAATTTACACCATC 57.614 36.000 0.00 0.00 0.00 3.51
2097 2880 6.183360 GGCTACTTACAAATTTACACCATCCC 60.183 42.308 0.00 0.00 0.00 3.85
2100 2883 7.604657 ACTTACAAATTTACACCATCCCAAA 57.395 32.000 0.00 0.00 0.00 3.28
2101 2884 8.201242 ACTTACAAATTTACACCATCCCAAAT 57.799 30.769 0.00 0.00 0.00 2.32
2102 2885 8.311109 ACTTACAAATTTACACCATCCCAAATC 58.689 33.333 0.00 0.00 0.00 2.17
2103 2886 6.678568 ACAAATTTACACCATCCCAAATCA 57.321 33.333 0.00 0.00 0.00 2.57
2105 2888 6.269769 ACAAATTTACACCATCCCAAATCACT 59.730 34.615 0.00 0.00 0.00 3.41
2106 2889 7.453126 ACAAATTTACACCATCCCAAATCACTA 59.547 33.333 0.00 0.00 0.00 2.74
2107 2890 8.477256 CAAATTTACACCATCCCAAATCACTAT 58.523 33.333 0.00 0.00 0.00 2.12
2134 2917 7.370383 TCATAATTCTGCTTTGAGGTTCAAAC 58.630 34.615 0.36 0.37 41.02 2.93
2135 2918 5.859205 AATTCTGCTTTGAGGTTCAAACT 57.141 34.783 0.36 0.00 41.02 2.66
2136 2919 5.859205 ATTCTGCTTTGAGGTTCAAACTT 57.141 34.783 0.36 0.00 41.02 2.66
2137 2920 4.900635 TCTGCTTTGAGGTTCAAACTTC 57.099 40.909 0.36 0.00 41.02 3.01
2138 2921 4.269183 TCTGCTTTGAGGTTCAAACTTCA 58.731 39.130 3.81 3.81 41.02 3.02
2151 2934 7.775561 AGGTTCAAACTTCAAAGTAGAGTTCAT 59.224 33.333 0.00 0.00 38.57 2.57
2318 3128 2.280457 GGTGCAGGCTATCCTCGC 60.280 66.667 0.00 1.51 41.93 5.03
2384 3200 1.791103 GAGATCTCGCGCAGGTAGCT 61.791 60.000 8.75 0.00 42.61 3.32
2411 3227 3.145551 GCCGCCCTTCGTCTCCTA 61.146 66.667 0.00 0.00 36.19 2.94
2416 3232 1.605058 GCCCTTCGTCTCCTACTGCA 61.605 60.000 0.00 0.00 0.00 4.41
2502 3333 0.970937 TTCTGAACCCGAGCCGATCT 60.971 55.000 0.00 0.00 0.00 2.75
2616 3447 3.702048 TGCCCCTTCCGGTTCTCG 61.702 66.667 0.00 0.00 38.88 4.04
2649 3480 2.741211 GGAACCACGTCGCCCTTC 60.741 66.667 0.00 0.00 0.00 3.46
2669 3500 1.003233 GCACGGCCTCCTTCTTCTT 60.003 57.895 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.476488 GGGCAAACACACAACAAGAGT 59.524 47.619 0.00 0.00 0.00 3.24
80 81 4.027437 TGTTGCCCCTAAAAAGAACAGTT 58.973 39.130 0.00 0.00 0.00 3.16
81 82 3.637769 TGTTGCCCCTAAAAAGAACAGT 58.362 40.909 0.00 0.00 0.00 3.55
82 83 4.664150 TTGTTGCCCCTAAAAAGAACAG 57.336 40.909 0.00 0.00 0.00 3.16
83 84 4.742138 GCATTGTTGCCCCTAAAAAGAACA 60.742 41.667 0.00 0.00 43.38 3.18
86 87 3.676291 GCATTGTTGCCCCTAAAAAGA 57.324 42.857 0.00 0.00 43.38 2.52
149 150 3.437049 CGCTTAAACCTCCTCCAAAGAAG 59.563 47.826 0.00 0.00 0.00 2.85
440 470 6.811253 ACTAATTACATGGAACGCTCAAAA 57.189 33.333 0.00 0.00 0.00 2.44
476 506 1.067425 TCACTTATTGTGGGACGGACG 60.067 52.381 0.00 0.00 46.20 4.79
482 512 4.974645 AGTTGAGTCACTTATTGTGGGA 57.025 40.909 0.00 0.00 46.20 4.37
483 513 5.299279 ACAAAGTTGAGTCACTTATTGTGGG 59.701 40.000 10.36 0.00 46.20 4.61
484 514 6.377327 ACAAAGTTGAGTCACTTATTGTGG 57.623 37.500 10.36 1.75 46.20 4.17
486 516 9.826574 TTAGTACAAAGTTGAGTCACTTATTGT 57.173 29.630 13.87 13.87 35.87 2.71
492 522 9.174166 ACAAAATTAGTACAAAGTTGAGTCACT 57.826 29.630 0.00 0.00 0.00 3.41
519 951 9.694137 GTGACTCAACTTTGTAATAGTTCTAGT 57.306 33.333 0.00 0.00 33.73 2.57
520 952 9.915629 AGTGACTCAACTTTGTAATAGTTCTAG 57.084 33.333 0.00 0.00 33.73 2.43
554 1046 0.263765 AATAGTACTCCCTCCGCCCA 59.736 55.000 0.00 0.00 0.00 5.36
557 1049 4.933505 ACTAAAATAGTACTCCCTCCGC 57.066 45.455 0.00 0.00 37.23 5.54
573 1069 7.856894 CGAAGGGTGAATAAACGAAAAACTAAA 59.143 33.333 0.00 0.00 0.00 1.85
599 1096 1.826487 ACAAAACCCAGACCACCGC 60.826 57.895 0.00 0.00 0.00 5.68
602 1099 1.000274 GCATCACAAAACCCAGACCAC 60.000 52.381 0.00 0.00 0.00 4.16
615 1112 3.316029 GCATGGTATAAAGCAGCATCACA 59.684 43.478 0.00 0.00 36.36 3.58
617 1114 3.824133 AGCATGGTATAAAGCAGCATCA 58.176 40.909 0.00 0.00 36.36 3.07
651 1148 2.603776 ACCCTGACCCTGACCGAC 60.604 66.667 0.00 0.00 0.00 4.79
652 1149 2.283676 GACCCTGACCCTGACCGA 60.284 66.667 0.00 0.00 0.00 4.69
653 1150 2.603473 TGACCCTGACCCTGACCG 60.603 66.667 0.00 0.00 0.00 4.79
701 1213 1.276421 ACGGACATCCCTCAACTGAAG 59.724 52.381 0.00 0.00 0.00 3.02
708 1220 0.830648 GATTGGACGGACATCCCTCA 59.169 55.000 0.00 0.00 38.06 3.86
772 1289 0.807667 CCACTTCTTCTCCGGCATCG 60.808 60.000 0.00 0.00 0.00 3.84
773 1290 0.250513 ACCACTTCTTCTCCGGCATC 59.749 55.000 0.00 0.00 0.00 3.91
774 1291 0.250513 GACCACTTCTTCTCCGGCAT 59.749 55.000 0.00 0.00 0.00 4.40
775 1292 1.671742 GACCACTTCTTCTCCGGCA 59.328 57.895 0.00 0.00 0.00 5.69
776 1293 1.079057 GGACCACTTCTTCTCCGGC 60.079 63.158 0.00 0.00 0.00 6.13
838 1371 3.053826 AGAAACCCTTACCCTTCACAGT 58.946 45.455 0.00 0.00 0.00 3.55
846 1379 2.240667 GGGGAGTTAGAAACCCTTACCC 59.759 54.545 0.00 0.00 42.86 3.69
847 1380 2.240667 GGGGGAGTTAGAAACCCTTACC 59.759 54.545 0.00 0.00 42.90 2.85
848 1381 2.093288 CGGGGGAGTTAGAAACCCTTAC 60.093 54.545 0.00 0.00 42.90 2.34
849 1382 2.190538 CGGGGGAGTTAGAAACCCTTA 58.809 52.381 0.00 0.00 42.90 2.69
850 1383 0.989602 CGGGGGAGTTAGAAACCCTT 59.010 55.000 0.00 0.00 42.90 3.95
860 1393 2.041819 CCTAGAGGCGGGGGAGTT 60.042 66.667 0.00 0.00 0.00 3.01
861 1394 3.028098 TCCTAGAGGCGGGGGAGT 61.028 66.667 0.00 0.00 34.44 3.85
874 1407 1.895798 CACTTGAGCTGGAGTGTCCTA 59.104 52.381 14.88 0.00 38.70 2.94
882 1415 0.108585 GGTTGGACACTTGAGCTGGA 59.891 55.000 0.00 0.00 0.00 3.86
883 1416 0.179020 TGGTTGGACACTTGAGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
891 1424 7.883311 GCCTATACATTTATATGGTTGGACACT 59.117 37.037 0.00 0.00 36.01 3.55
896 1429 6.653320 ACGTGCCTATACATTTATATGGTTGG 59.347 38.462 0.00 0.00 36.01 3.77
938 1475 0.103026 TAGCTGGCGAGTATGCACTG 59.897 55.000 0.00 0.00 34.21 3.66
972 1509 3.142951 TCCCTGTTGAATAACGTGTTGG 58.857 45.455 0.00 0.00 39.71 3.77
978 1515 4.503910 TCACTGATCCCTGTTGAATAACG 58.496 43.478 0.00 0.00 39.71 3.18
991 1528 2.592861 GGCGGCCATCACTGATCC 60.593 66.667 15.62 0.00 0.00 3.36
992 1529 2.592861 GGGCGGCCATCACTGATC 60.593 66.667 25.33 0.00 0.00 2.92
1467 2058 3.913573 CGAACGCCGGAAGCATCG 61.914 66.667 5.05 8.62 44.04 3.84
1604 2222 3.322466 CCGGTGCCTCCACTCCTT 61.322 66.667 0.00 0.00 41.75 3.36
1765 2383 4.255301 AGAGAGAATGACGTCGAGTAGTT 58.745 43.478 11.62 0.00 0.00 2.24
1797 2415 5.117355 TCATCTGACGTCGAGTAGTTTTT 57.883 39.130 11.62 0.00 0.00 1.94
1798 2416 4.724303 CTCATCTGACGTCGAGTAGTTTT 58.276 43.478 11.62 0.00 0.00 2.43
1799 2417 3.426426 GCTCATCTGACGTCGAGTAGTTT 60.426 47.826 11.62 0.00 0.00 2.66
1800 2418 2.096174 GCTCATCTGACGTCGAGTAGTT 59.904 50.000 11.62 0.00 0.00 2.24
1841 2459 0.249405 ACTTGCACATGTTTTGGCGG 60.249 50.000 0.00 0.00 0.00 6.13
1851 2469 0.729116 GCACTATCGCACTTGCACAT 59.271 50.000 1.48 0.00 42.21 3.21
1912 2531 6.536582 TCATGAATCTTAAGCAGCTGTAGTTC 59.463 38.462 16.64 10.49 0.00 3.01
1950 2572 4.258543 ACATGTTGGTACCAGATTAACGG 58.741 43.478 15.65 8.81 0.00 4.44
2037 2782 8.677300 GGAATGCTTCTGATTCTTGTTTATACA 58.323 33.333 0.00 0.00 31.56 2.29
2045 2790 4.525024 AGGAGGAATGCTTCTGATTCTTG 58.475 43.478 0.00 0.00 31.56 3.02
2053 2836 2.800250 CCAACAAGGAGGAATGCTTCT 58.200 47.619 0.00 0.00 41.22 2.85
2057 2840 1.745653 GTAGCCAACAAGGAGGAATGC 59.254 52.381 0.00 0.00 41.22 3.56
2062 2845 3.695830 TGTAAGTAGCCAACAAGGAGG 57.304 47.619 0.00 0.00 41.22 4.30
2077 2860 8.310382 TGATTTGGGATGGTGTAAATTTGTAAG 58.690 33.333 0.00 0.00 0.00 2.34
2094 2877 9.453572 GCAGAATTATGATATAGTGATTTGGGA 57.546 33.333 3.77 0.00 0.00 4.37
2095 2878 9.458727 AGCAGAATTATGATATAGTGATTTGGG 57.541 33.333 3.77 0.00 0.00 4.12
2101 2884 9.716531 CCTCAAAGCAGAATTATGATATAGTGA 57.283 33.333 3.77 0.00 0.00 3.41
2102 2885 9.499479 ACCTCAAAGCAGAATTATGATATAGTG 57.501 33.333 3.77 0.00 0.00 2.74
2106 2889 8.985315 TGAACCTCAAAGCAGAATTATGATAT 57.015 30.769 3.77 0.00 0.00 1.63
2107 2890 8.806429 TTGAACCTCAAAGCAGAATTATGATA 57.194 30.769 3.77 0.00 32.71 2.15
2134 2917 8.559536 TGTTTGCTTATGAACTCTACTTTGAAG 58.440 33.333 0.00 0.00 0.00 3.02
2135 2918 8.342634 GTGTTTGCTTATGAACTCTACTTTGAA 58.657 33.333 0.00 0.00 0.00 2.69
2136 2919 7.041372 GGTGTTTGCTTATGAACTCTACTTTGA 60.041 37.037 0.00 0.00 0.00 2.69
2137 2920 7.041098 AGGTGTTTGCTTATGAACTCTACTTTG 60.041 37.037 0.00 0.00 0.00 2.77
2138 2921 6.998673 AGGTGTTTGCTTATGAACTCTACTTT 59.001 34.615 0.00 0.00 0.00 2.66
2139 2922 6.428159 CAGGTGTTTGCTTATGAACTCTACTT 59.572 38.462 0.00 0.00 0.00 2.24
2140 2923 5.934625 CAGGTGTTTGCTTATGAACTCTACT 59.065 40.000 0.00 0.00 0.00 2.57
2151 2934 9.039870 CAAATAAATTGTTCAGGTGTTTGCTTA 57.960 29.630 0.00 0.00 34.16 3.09
2502 3333 2.043852 GCCTCCTCCTCTGTCGGA 60.044 66.667 0.00 0.00 0.00 4.55
2576 3407 4.309950 AGCGAAAGAACCGGCGGT 62.310 61.111 28.83 28.83 37.65 5.68
2633 3464 3.110178 CGAAGGGCGACGTGGTTC 61.110 66.667 0.00 0.00 44.57 3.62
2653 3484 1.002544 CAAGAAGAAGAAGGAGGCCGT 59.997 52.381 0.00 0.00 0.00 5.68
2660 3491 1.639298 CGGCGGCAAGAAGAAGAAGG 61.639 60.000 10.53 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.