Multiple sequence alignment - TraesCS1D01G007900

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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 TraesCS1D01G007900 chr1D 100.000 2549 0 0 1 2549 3967895 3970443 0.000000e+00 4708
1 TraesCS1D01G007900 chr1D 89.817 383 30 5 2039 2416 5130323 5130701 1.370000e-132 483
2 TraesCS1D01G007900 chr1A 87.589 1958 120 34 498 2416 6334854 6336727 0.000000e+00 2156
3 TraesCS1D01G007900 chr1A 89.236 1440 94 15 512 1926 4503908 4502505 0.000000e+00 1744
4 TraesCS1D01G007900 chr1A 89.236 1440 94 15 512 1926 5498669 5500072 0.000000e+00 1744
5 TraesCS1D01G007900 chr1A 91.208 944 56 8 984 1926 5500633 5501550 0.000000e+00 1258
6 TraesCS1D01G007900 chr1A 88.584 473 38 6 24 480 5498119 5498591 6.160000e-156 560
7 TraesCS1D01G007900 chr1A 89.116 441 35 4 53 480 4504426 4503986 1.040000e-148 536
8 TraesCS1D01G007900 chr1A 92.857 154 11 0 2259 2412 6293641 6293794 9.180000e-55 224
9 TraesCS1D01G007900 chr1A 98.214 56 1 0 2036 2091 4502479 4502424 5.800000e-17 99
10 TraesCS1D01G007900 chr1A 98.214 56 1 0 2036 2091 5500098 5500153 5.800000e-17 99
11 TraesCS1D01G007900 chr1A 98.214 56 1 0 2036 2091 5501576 5501631 5.800000e-17 99
12 TraesCS1D01G007900 chr1B 88.921 1724 113 31 1 1691 5761206 5759528 0.000000e+00 2054
13 TraesCS1D01G007900 chr1B 91.293 1183 72 8 531 1691 6481190 6482363 0.000000e+00 1585
14 TraesCS1D01G007900 chr1B 84.375 736 51 39 1830 2549 5759458 5758771 0.000000e+00 664
15 TraesCS1D01G007900 chr1B 83.973 730 61 34 1830 2549 6482433 6483116 0.000000e+00 649
16 TraesCS1D01G007900 chr1B 85.498 331 37 5 1379 1708 5750003 5749683 4.060000e-88 335
17 TraesCS1D01G007900 chr1B 92.982 228 13 2 1 225 6480671 6480898 1.890000e-86 329
18 TraesCS1D01G007900 chr1B 84.177 316 25 5 2259 2549 6065429 6065114 1.490000e-72 283
19 TraesCS1D01G007900 chr1B 82.609 322 25 20 2259 2549 7697699 7698020 3.250000e-64 255
20 TraesCS1D01G007900 chr1B 91.195 159 13 1 2259 2416 22666002 22666160 5.520000e-52 215
21 TraesCS1D01G007900 chr1B 88.679 159 17 1 2259 2416 6286126 6285968 2.590000e-45 193
22 TraesCS1D01G007900 chr1B 78.105 306 40 15 2259 2547 629662657 629662362 4.360000e-38 169
23 TraesCS1D01G007900 chr5B 83.781 968 95 34 865 1818 55504729 55503810 0.000000e+00 861
24 TraesCS1D01G007900 chr5B 86.813 91 10 2 2027 2116 55503676 55503587 1.610000e-17 100
25 TraesCS1D01G007900 chr5D 87.179 663 68 10 865 1519 52327723 52327070 0.000000e+00 737
26 TraesCS1D01G007900 chr5D 81.696 224 17 4 2201 2414 52326531 52326322 5.640000e-37 165


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 TraesCS1D01G007900 chr1D 3967895 3970443 2548 False 4708.000000 4708 100.000000 1 2549 1 chr1D.!!$F1 2548
1 TraesCS1D01G007900 chr1A 6334854 6336727 1873 False 2156.000000 2156 87.589000 498 2416 1 chr1A.!!$F2 1918
2 TraesCS1D01G007900 chr1A 4502424 4504426 2002 True 793.000000 1744 92.188667 53 2091 3 chr1A.!!$R1 2038
3 TraesCS1D01G007900 chr1A 5498119 5501631 3512 False 752.000000 1744 93.091200 24 2091 5 chr1A.!!$F3 2067
4 TraesCS1D01G007900 chr1B 5758771 5761206 2435 True 1359.000000 2054 86.648000 1 2549 2 chr1B.!!$R5 2548
5 TraesCS1D01G007900 chr1B 6480671 6483116 2445 False 854.333333 1585 89.416000 1 2549 3 chr1B.!!$F3 2548
6 TraesCS1D01G007900 chr5B 55503587 55504729 1142 True 480.500000 861 85.297000 865 2116 2 chr5B.!!$R1 1251
7 TraesCS1D01G007900 chr5D 52326322 52327723 1401 True 451.000000 737 84.437500 865 2414 2 chr5D.!!$R1 1549

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
117 122 1.741706 CAACTGTGGATGTCCTCATGC 59.258 52.381 4.44 0.0 41.68 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2276 0.03438 AGCAGCAGCATCAGGTGATT 60.034 50.0 3.17 0.0 45.95 2.57 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
109 114 4.292186 AGTATTCTGCAACTGTGGATGT 57.708 40.909 0.00 0.00 0.00 3.06
117 122 1.741706 CAACTGTGGATGTCCTCATGC 59.258 52.381 4.44 0.00 41.68 4.06
125 130 2.877168 GGATGTCCTCATGCTGTCAATC 59.123 50.000 0.00 0.00 38.94 2.67
198 203 3.930848 GCTTTCATGAGGCCTTCAATTTG 59.069 43.478 6.77 2.48 39.77 2.32
212 217 2.425312 TCAATTTGCGAACTGGTTGTGT 59.575 40.909 0.00 0.00 0.00 3.72
230 235 6.238897 GGTTGTGTGATTATGTTGTTGAGGAA 60.239 38.462 0.00 0.00 0.00 3.36
231 236 7.370383 GTTGTGTGATTATGTTGTTGAGGAAT 58.630 34.615 0.00 0.00 0.00 3.01
259 280 5.348986 TGAAGATATGCTAGTCCGTTTGAC 58.651 41.667 0.00 0.00 44.82 3.18
280 301 7.086685 TGACTAAAGAAAGAATGTTACCCCT 57.913 36.000 0.00 0.00 0.00 4.79
294 315 6.894735 TGTTACCCCTATAATTTGAGTGGA 57.105 37.500 0.00 0.00 0.00 4.02
345 366 4.763073 TGACTTAATCAGATGCACCTCAG 58.237 43.478 0.00 0.00 31.91 3.35
409 441 3.169908 GAGGGGTGGCCAAGAAAATTTA 58.830 45.455 7.24 0.00 0.00 1.40
443 475 4.099266 CGTCCAGATCTTTCTTCATCTCCT 59.901 45.833 0.00 0.00 0.00 3.69
495 527 4.042884 TGGAACTCCAGATCTCCATTCAT 58.957 43.478 0.00 0.00 42.01 2.57
503 581 6.086775 TCCAGATCTCCATTCATCTCCAATA 58.913 40.000 0.00 0.00 0.00 1.90
507 585 8.784994 CAGATCTCCATTCATCTCCAATAAAAG 58.215 37.037 0.00 0.00 0.00 2.27
508 586 7.943447 AGATCTCCATTCATCTCCAATAAAAGG 59.057 37.037 0.00 0.00 0.00 3.11
514 592 7.725397 CCATTCATCTCCAATAAAAGGTCCATA 59.275 37.037 0.00 0.00 0.00 2.74
559 637 7.442666 GGCTAGTATTTGCTTTCTGTTATAGCT 59.557 37.037 0.00 0.00 35.93 3.32
812 924 4.751600 GGCCTTCAATTTTTGAACTGGAAG 59.248 41.667 10.70 0.00 44.21 3.46
813 925 5.453198 GGCCTTCAATTTTTGAACTGGAAGA 60.453 40.000 10.70 0.00 44.21 2.87
814 926 6.048509 GCCTTCAATTTTTGAACTGGAAGAA 58.951 36.000 10.70 0.00 44.21 2.52
862 974 6.089476 CGATTATGTTGTTAATGCACACCAA 58.911 36.000 0.00 0.00 0.00 3.67
885 997 3.643320 TCATTCAGTATAGGTCCCAGCAG 59.357 47.826 0.00 0.00 0.00 4.24
937 1050 6.478512 TTGTTTGCTTGAATTAACCTCCTT 57.521 33.333 0.00 0.00 0.00 3.36
938 1051 7.589958 TTGTTTGCTTGAATTAACCTCCTTA 57.410 32.000 0.00 0.00 0.00 2.69
982 1098 5.522456 TGACTTTTGATTGTGATGCTGTTC 58.478 37.500 0.00 0.00 0.00 3.18
1069 1185 1.226407 CGCGATGACGAGAAGCAGA 60.226 57.895 0.00 0.00 41.48 4.26
1209 1331 2.124736 CCGCCACCCATGTACCTG 60.125 66.667 0.00 0.00 0.00 4.00
1280 1402 3.115892 CATACGCGCCGTGGTTGT 61.116 61.111 5.73 1.40 41.39 3.32
1696 1879 7.011109 CAGTTGTAGATTAATTCTGGTAACGGG 59.989 40.741 0.00 0.00 45.79 5.28
1747 1933 4.301072 TGAGTGTCCTTGAATTTAGGGG 57.699 45.455 0.00 0.00 33.41 4.79
1748 1934 3.913799 TGAGTGTCCTTGAATTTAGGGGA 59.086 43.478 0.00 0.00 33.41 4.81
1800 1989 8.883954 TTACAAAATGAGACATGAAATTTGCA 57.116 26.923 0.00 0.00 31.34 4.08
1801 1990 7.416154 ACAAAATGAGACATGAAATTTGCAG 57.584 32.000 0.00 0.00 31.34 4.41
1802 1991 6.425721 ACAAAATGAGACATGAAATTTGCAGG 59.574 34.615 0.00 0.00 31.34 4.85
1803 1992 4.730949 ATGAGACATGAAATTTGCAGGG 57.269 40.909 0.00 0.00 0.00 4.45
1804 1993 3.499338 TGAGACATGAAATTTGCAGGGT 58.501 40.909 0.00 0.00 0.00 4.34
1805 1994 3.896888 TGAGACATGAAATTTGCAGGGTT 59.103 39.130 0.00 0.00 0.00 4.11
1806 1995 4.022068 TGAGACATGAAATTTGCAGGGTTC 60.022 41.667 0.00 0.00 0.00 3.62
1807 1996 3.896888 AGACATGAAATTTGCAGGGTTCA 59.103 39.130 0.00 9.57 34.68 3.18
1808 1997 4.344679 AGACATGAAATTTGCAGGGTTCAA 59.655 37.500 0.00 0.00 33.93 2.69
1809 1998 5.033589 ACATGAAATTTGCAGGGTTCAAA 57.966 34.783 0.00 0.00 37.75 2.69
1810 1999 5.435291 ACATGAAATTTGCAGGGTTCAAAA 58.565 33.333 0.00 0.00 37.04 2.44
1811 2000 6.063404 ACATGAAATTTGCAGGGTTCAAAAT 58.937 32.000 0.00 0.00 37.04 1.82
1812 2001 6.546772 ACATGAAATTTGCAGGGTTCAAAATT 59.453 30.769 0.00 0.00 37.04 1.82
1813 2002 7.718753 ACATGAAATTTGCAGGGTTCAAAATTA 59.281 29.630 0.00 0.00 37.04 1.40
1814 2003 8.566260 CATGAAATTTGCAGGGTTCAAAATTAA 58.434 29.630 10.78 0.00 37.04 1.40
1815 2004 8.688747 TGAAATTTGCAGGGTTCAAAATTAAT 57.311 26.923 0.00 0.00 37.04 1.40
1816 2005 8.566260 TGAAATTTGCAGGGTTCAAAATTAATG 58.434 29.630 0.00 0.00 37.04 1.90
1817 2006 8.462589 AAATTTGCAGGGTTCAAAATTAATGT 57.537 26.923 0.00 0.00 37.04 2.71
1818 2007 7.671495 ATTTGCAGGGTTCAAAATTAATGTC 57.329 32.000 0.00 0.00 37.04 3.06
1819 2008 6.418057 TTGCAGGGTTCAAAATTAATGTCT 57.582 33.333 0.00 0.00 0.00 3.41
1820 2009 7.531857 TTGCAGGGTTCAAAATTAATGTCTA 57.468 32.000 0.00 0.00 0.00 2.59
1821 2010 6.919721 TGCAGGGTTCAAAATTAATGTCTAC 58.080 36.000 0.00 0.00 0.00 2.59
1822 2011 6.719370 TGCAGGGTTCAAAATTAATGTCTACT 59.281 34.615 0.00 0.00 0.00 2.57
1823 2012 7.029563 GCAGGGTTCAAAATTAATGTCTACTG 58.970 38.462 0.00 0.00 0.00 2.74
1824 2013 7.029563 CAGGGTTCAAAATTAATGTCTACTGC 58.970 38.462 0.00 0.00 0.00 4.40
1825 2014 6.719370 AGGGTTCAAAATTAATGTCTACTGCA 59.281 34.615 0.00 0.00 0.00 4.41
1826 2015 7.397192 AGGGTTCAAAATTAATGTCTACTGCAT 59.603 33.333 0.00 0.00 0.00 3.96
1827 2016 8.682710 GGGTTCAAAATTAATGTCTACTGCATA 58.317 33.333 0.00 0.00 0.00 3.14
1828 2017 9.503427 GGTTCAAAATTAATGTCTACTGCATAC 57.497 33.333 0.00 0.00 0.00 2.39
1871 2123 2.097629 GGTTCCTTGGATTTTAGCTCGC 59.902 50.000 0.00 0.00 0.00 5.03
1935 2188 2.285602 CCGTGTCGCATAAGTACATTGC 60.286 50.000 0.00 0.00 0.00 3.56
2061 2326 2.927871 GCTGCTTTGCTGGTTATTGGTG 60.928 50.000 0.00 0.00 0.00 4.17
2131 2426 5.080337 TGTTGTTAGGCATAAATGTTGGGA 58.920 37.500 0.00 0.00 0.00 4.37
2206 2516 9.890629 TTGTATTGTTCAAGCTATTCAGATACT 57.109 29.630 0.00 0.00 0.00 2.12
2215 2525 9.185680 TCAAGCTATTCAGATACTACAACACTA 57.814 33.333 0.00 0.00 0.00 2.74
2246 2561 2.173782 ACAGGAATGTTGTACACACCCA 59.826 45.455 0.00 0.00 38.61 4.51
2294 2610 2.879002 TCAAGATCAGATGGTCTCGC 57.121 50.000 0.00 0.00 0.00 5.03
2301 2617 1.152440 AGATGGTCTCGCCCTAGGG 60.152 63.158 24.89 24.89 36.04 3.53
2414 2738 6.593978 CACAGTTCAGTTGTAGAAGCAATAC 58.406 40.000 0.00 0.00 0.00 1.89
2415 2739 6.202762 CACAGTTCAGTTGTAGAAGCAATACA 59.797 38.462 0.00 0.00 0.00 2.29
2419 2743 7.715249 AGTTCAGTTGTAGAAGCAATACAAGAA 59.285 33.333 8.21 7.20 42.23 2.52
2437 2786 3.397527 AGAAAATCAGGGATCAGGCCTA 58.602 45.455 3.98 0.00 0.00 3.93
2441 2790 1.722034 TCAGGGATCAGGCCTATCAC 58.278 55.000 3.98 10.60 0.00 3.06
2442 2791 0.689623 CAGGGATCAGGCCTATCACC 59.310 60.000 3.98 6.25 0.00 4.02
2453 2802 2.959030 GGCCTATCACCCAAGAAAATCC 59.041 50.000 0.00 0.00 0.00 3.01
2478 2828 6.418819 CACAGATAAAGCCACAGTTGAAAAAG 59.581 38.462 0.00 0.00 0.00 2.27
2483 2833 9.476202 GATAAAGCCACAGTTGAAAAAGTTTAT 57.524 29.630 0.00 0.00 0.00 1.40
2491 2841 8.920665 CACAGTTGAAAAAGTTTATTGAACACA 58.079 29.630 11.91 0.00 40.84 3.72
2520 2870 3.248602 GCCAGTGTCTTGTCAGTTAACTG 59.751 47.826 26.60 26.60 45.08 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 97 1.421268 AGGACATCCACAGTTGCAGAA 59.579 47.619 0.00 0.00 38.89 3.02
109 114 5.883685 ATTCTAGATTGACAGCATGAGGA 57.116 39.130 0.00 0.00 39.69 3.71
117 122 8.816144 GCTCTAAACTGAATTCTAGATTGACAG 58.184 37.037 7.05 14.79 0.00 3.51
125 130 6.227298 TCTGGGCTCTAAACTGAATTCTAG 57.773 41.667 7.05 5.30 0.00 2.43
198 203 3.188460 ACATAATCACACAACCAGTTCGC 59.812 43.478 0.00 0.00 0.00 4.70
230 235 9.561069 AAACGGACTAGCATATCTTCATAAAAT 57.439 29.630 0.00 0.00 0.00 1.82
231 236 8.826710 CAAACGGACTAGCATATCTTCATAAAA 58.173 33.333 0.00 0.00 0.00 1.52
236 257 5.348986 GTCAAACGGACTAGCATATCTTCA 58.651 41.667 0.00 0.00 43.46 3.02
345 366 0.179119 GCCAGCCAGATCACAAATGC 60.179 55.000 0.00 0.00 0.00 3.56
409 441 8.115490 AGAAAGATCTGGACGAATTTCAAAAT 57.885 30.769 0.00 0.00 35.48 1.82
443 475 7.392766 AATAAACTGGATGGATGAGTGGATA 57.607 36.000 0.00 0.00 0.00 2.59
495 527 5.339695 GGGTGTATGGACCTTTTATTGGAGA 60.340 44.000 0.00 0.00 36.14 3.71
503 581 2.354328 TGAGGGGTGTATGGACCTTTT 58.646 47.619 0.00 0.00 36.14 2.27
507 585 3.458487 ACTTATTGAGGGGTGTATGGACC 59.542 47.826 0.00 0.00 34.96 4.46
508 586 4.772886 ACTTATTGAGGGGTGTATGGAC 57.227 45.455 0.00 0.00 0.00 4.02
514 592 2.174854 GCCCATACTTATTGAGGGGTGT 59.825 50.000 0.00 0.00 39.96 4.16
559 637 1.071987 CACAGCAGTTCTCCTGGCA 59.928 57.895 0.00 0.00 41.81 4.92
662 745 2.674357 GCATGGTCACCATTTCATTTGC 59.326 45.455 6.58 3.14 42.23 3.68
812 924 2.755836 TCTTGAACACGCAAGCTTTC 57.244 45.000 0.00 0.00 43.78 2.62
813 925 3.715628 AATCTTGAACACGCAAGCTTT 57.284 38.095 0.00 0.00 43.78 3.51
814 926 3.181487 ACAAATCTTGAACACGCAAGCTT 60.181 39.130 0.00 0.00 43.78 3.74
862 974 4.234550 TGCTGGGACCTATACTGAATGAT 58.765 43.478 0.00 0.00 0.00 2.45
885 997 7.324616 GTCTCAAGCATGTTAAACAGAATGAAC 59.675 37.037 0.00 0.00 39.69 3.18
937 1050 8.494433 AGTCAGGGATTAACAGCAAGATTTATA 58.506 33.333 0.00 0.00 0.00 0.98
938 1051 7.349598 AGTCAGGGATTAACAGCAAGATTTAT 58.650 34.615 0.00 0.00 0.00 1.40
982 1098 2.022195 CATGGCAGACAAGAATCCTGG 58.978 52.381 0.00 0.00 0.00 4.45
1069 1185 2.573915 GTTTCCTGGTCCTCCTCTTCAT 59.426 50.000 0.00 0.00 34.23 2.57
1242 1364 4.034246 TCCACCTCCTGGATCACG 57.966 61.111 0.00 0.00 44.99 4.35
1278 1400 1.967535 CACCTTCTCGCTCTCCACA 59.032 57.895 0.00 0.00 0.00 4.17
1280 1402 1.607756 AGCACCTTCTCGCTCTCCA 60.608 57.895 0.00 0.00 31.16 3.86
1525 1647 2.937689 AGCAGCTCCCATGGTGGT 60.938 61.111 11.73 4.88 40.63 4.16
1562 1702 2.888863 CTCACTCAGCCCCGACTC 59.111 66.667 0.00 0.00 0.00 3.36
1563 1703 3.386237 GCTCACTCAGCCCCGACT 61.386 66.667 0.00 0.00 43.17 4.18
1566 1706 4.504916 CTCGCTCACTCAGCCCCG 62.505 72.222 0.00 0.00 46.74 5.73
1696 1879 1.028905 TTGCCAACACCAGTAGCAAC 58.971 50.000 0.00 0.00 40.27 4.17
1747 1933 1.661341 CAAGTAGCATGGAGCCACTC 58.339 55.000 0.00 0.00 44.66 3.51
1774 1963 9.491675 TGCAAATTTCATGTCTCATTTTGTAAT 57.508 25.926 0.00 0.00 0.00 1.89
1775 1964 8.883954 TGCAAATTTCATGTCTCATTTTGTAA 57.116 26.923 0.00 0.00 0.00 2.41
1786 1975 4.255833 TGAACCCTGCAAATTTCATGTC 57.744 40.909 0.00 0.00 0.00 3.06
1793 1982 7.938490 AGACATTAATTTTGAACCCTGCAAATT 59.062 29.630 0.00 0.00 35.41 1.82
1794 1983 7.452562 AGACATTAATTTTGAACCCTGCAAAT 58.547 30.769 0.00 0.00 35.41 2.32
1795 1984 6.825610 AGACATTAATTTTGAACCCTGCAAA 58.174 32.000 0.00 0.00 33.76 3.68
1796 1985 6.418057 AGACATTAATTTTGAACCCTGCAA 57.582 33.333 0.00 0.00 0.00 4.08
1797 1986 6.719370 AGTAGACATTAATTTTGAACCCTGCA 59.281 34.615 0.00 0.00 0.00 4.41
1798 1987 7.029563 CAGTAGACATTAATTTTGAACCCTGC 58.970 38.462 0.00 0.00 0.00 4.85
1799 1988 7.029563 GCAGTAGACATTAATTTTGAACCCTG 58.970 38.462 0.00 0.00 0.00 4.45
1800 1989 6.719370 TGCAGTAGACATTAATTTTGAACCCT 59.281 34.615 0.00 0.00 0.00 4.34
1801 1990 6.919721 TGCAGTAGACATTAATTTTGAACCC 58.080 36.000 0.00 0.00 0.00 4.11
1802 1991 9.503427 GTATGCAGTAGACATTAATTTTGAACC 57.497 33.333 0.00 0.00 0.00 3.62
1809 1998 8.131100 GCACAATGTATGCAGTAGACATTAATT 58.869 33.333 10.70 0.00 46.45 1.40
1810 1999 7.500227 AGCACAATGTATGCAGTAGACATTAAT 59.500 33.333 10.70 1.15 46.45 1.40
1811 2000 6.823182 AGCACAATGTATGCAGTAGACATTAA 59.177 34.615 10.70 0.00 46.45 1.40
1812 2001 6.258507 CAGCACAATGTATGCAGTAGACATTA 59.741 38.462 10.70 0.00 46.45 1.90
1814 2003 4.573607 CAGCACAATGTATGCAGTAGACAT 59.426 41.667 0.00 0.00 45.92 3.06
1815 2004 3.934579 CAGCACAATGTATGCAGTAGACA 59.065 43.478 0.00 0.00 45.92 3.41
1816 2005 3.935203 ACAGCACAATGTATGCAGTAGAC 59.065 43.478 0.00 0.00 45.92 2.59
1817 2006 3.934579 CACAGCACAATGTATGCAGTAGA 59.065 43.478 0.00 0.00 45.92 2.59
1818 2007 3.934579 TCACAGCACAATGTATGCAGTAG 59.065 43.478 0.00 0.00 45.92 2.57
1819 2008 3.936564 TCACAGCACAATGTATGCAGTA 58.063 40.909 0.00 0.00 45.92 2.74
1820 2009 2.781923 TCACAGCACAATGTATGCAGT 58.218 42.857 0.00 0.00 45.92 4.40
1821 2010 3.835378 TTCACAGCACAATGTATGCAG 57.165 42.857 0.00 0.00 45.92 4.41
1822 2011 4.787260 ATTTCACAGCACAATGTATGCA 57.213 36.364 0.00 0.00 45.92 3.96
1823 2012 5.669357 GCAAATTTCACAGCACAATGTATGC 60.669 40.000 0.00 0.00 43.74 3.14
1824 2013 5.405873 TGCAAATTTCACAGCACAATGTATG 59.594 36.000 0.00 0.00 31.05 2.39
1825 2014 5.539979 TGCAAATTTCACAGCACAATGTAT 58.460 33.333 0.00 0.00 31.05 2.29
1826 2015 4.941657 TGCAAATTTCACAGCACAATGTA 58.058 34.783 0.00 0.00 31.05 2.29
1827 2016 3.794717 TGCAAATTTCACAGCACAATGT 58.205 36.364 0.00 0.00 31.05 2.71
1828 2017 3.185594 CCTGCAAATTTCACAGCACAATG 59.814 43.478 10.87 0.00 32.87 2.82
1838 2062 2.368221 CCAAGGAACCCTGCAAATTTCA 59.632 45.455 0.00 0.00 32.13 2.69
1839 2063 2.632512 TCCAAGGAACCCTGCAAATTTC 59.367 45.455 0.00 0.00 32.13 2.17
1871 2123 6.389906 GTTATCCAAACTCATCCCAAACAAG 58.610 40.000 0.00 0.00 0.00 3.16
1935 2188 4.489682 CGATTCATGTTTCATTTTGCAGCG 60.490 41.667 0.00 0.00 0.00 5.18
2022 2275 0.815734 GCAGCAGCATCAGGTGATTT 59.184 50.000 0.00 0.00 45.95 2.17
2023 2276 0.034380 AGCAGCAGCATCAGGTGATT 60.034 50.000 3.17 0.00 45.95 2.57
2024 2277 0.748367 CAGCAGCAGCATCAGGTGAT 60.748 55.000 3.17 0.00 45.95 3.06
2025 2278 1.376812 CAGCAGCAGCATCAGGTGA 60.377 57.895 3.17 0.00 45.95 4.02
2061 2326 4.326826 TCAACCACTCAGACATGGATTTC 58.673 43.478 0.00 0.00 39.46 2.17
2151 2449 3.325716 GTCCACCAAAAGACTGGGTAGTA 59.674 47.826 0.00 0.00 41.16 1.82
2186 2488 8.311109 TGTTGTAGTATCTGAATAGCTTGAACA 58.689 33.333 0.00 0.00 0.00 3.18
2189 2491 8.067751 AGTGTTGTAGTATCTGAATAGCTTGA 57.932 34.615 0.00 0.00 0.00 3.02
2206 2516 4.159693 CCTGTCATGTAGCCTAGTGTTGTA 59.840 45.833 0.00 0.00 0.00 2.41
2215 2525 3.009473 ACAACATTCCTGTCATGTAGCCT 59.991 43.478 0.00 0.00 33.54 4.58
2294 2610 3.107601 TCTCTGAATCAACACCCTAGGG 58.892 50.000 27.36 27.36 42.03 3.53
2301 2617 3.305629 GTCGAGCATCTCTGAATCAACAC 59.694 47.826 0.00 0.00 0.00 3.32
2359 2678 1.134580 TCTCGGTCGAGAACTATCGGT 60.135 52.381 19.09 0.00 46.89 4.69
2414 2738 2.692041 GGCCTGATCCCTGATTTTCTTG 59.308 50.000 0.00 0.00 0.00 3.02
2415 2739 2.584498 AGGCCTGATCCCTGATTTTCTT 59.416 45.455 3.11 0.00 0.00 2.52
2419 2743 3.073650 GTGATAGGCCTGATCCCTGATTT 59.926 47.826 17.99 0.00 33.88 2.17
2437 2786 4.387026 TCTGTGGATTTTCTTGGGTGAT 57.613 40.909 0.00 0.00 0.00 3.06
2441 2790 5.394553 GGCTTTATCTGTGGATTTTCTTGGG 60.395 44.000 0.00 0.00 33.71 4.12
2442 2791 5.185635 TGGCTTTATCTGTGGATTTTCTTGG 59.814 40.000 0.00 0.00 33.71 3.61
2453 2802 5.437289 TTTCAACTGTGGCTTTATCTGTG 57.563 39.130 0.00 0.00 0.00 3.66
2478 2828 7.116233 CACTGGCCTTTAATGTGTTCAATAAAC 59.884 37.037 3.32 0.00 38.43 2.01
2483 2833 3.957497 ACACTGGCCTTTAATGTGTTCAA 59.043 39.130 3.32 0.00 38.51 2.69
2491 2841 4.074970 CTGACAAGACACTGGCCTTTAAT 58.925 43.478 3.32 0.00 0.00 1.40
2520 2870 7.530010 TGTATCTATCTGTTTTTGCTTTGCTC 58.470 34.615 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.