Multiple sequence alignment - TraesCS2A01G313900

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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 TraesCS2A01G313900 chr2A 100.000 2605 0 0 1 2605 538368640 538366036 0.000000e+00 4811.0
1 TraesCS2A01G313900 chr2D 88.345 1656 92 45 25 1636 401542720 401541122 0.000000e+00 1895.0
2 TraesCS2A01G313900 chr2D 86.207 551 29 18 1655 2175 401541066 401540533 1.050000e-153 553.0
3 TraesCS2A01G313900 chr2D 90.882 340 15 7 2192 2527 401540546 401540219 2.380000e-120 442.0
4 TraesCS2A01G313900 chr2D 100.000 30 0 0 2576 2605 401540193 401540164 3.620000e-04 56.5
5 TraesCS2A01G313900 chr2B 89.521 1002 58 16 98 1071 475611636 475610654 0.000000e+00 1225.0
6 TraesCS2A01G313900 chr2B 91.522 578 23 16 1078 1636 475610607 475610037 0.000000e+00 773.0
7 TraesCS2A01G313900 chr2B 85.938 512 26 20 1640 2128 475610001 475609513 2.990000e-139 505.0
8 TraesCS2A01G313900 chr2B 87.212 391 13 9 2192 2552 475609504 475609121 6.710000e-111 411.0
9 TraesCS2A01G313900 chr2B 92.391 92 3 3 10 101 475611995 475611908 7.570000e-26 128.0
10 TraesCS2A01G313900 chr2B 100.000 30 0 0 2576 2605 475609115 475609086 3.620000e-04 56.5
11 TraesCS2A01G313900 chr7B 91.379 58 4 1 1128 1184 612320339 612320282 7.730000e-11 78.7


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 TraesCS2A01G313900 chr2A 538366036 538368640 2604 True 4811.000000 4811 100.000000 1 2605 1 chr2A.!!$R1 2604
1 TraesCS2A01G313900 chr2D 401540164 401542720 2556 True 736.625000 1895 91.358500 25 2605 4 chr2D.!!$R1 2580
2 TraesCS2A01G313900 chr2B 475609086 475611995 2909 True 516.416667 1225 91.097333 10 2605 6 chr2B.!!$R1 2595

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
963 1275 0.037877 CAGCCCATCATCCCCTGATC 59.962 60.0 0.0 0.0 42.91 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2563 0.17907 GCCCGACTTCAATCCTCCTC 60.179 60.0 0.0 0.0 0.0 3.71 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
25 26 8.094798 CATTTACTACCTCTACAACTGCAAAA 57.905 34.615 0.00 0.00 0.00 2.44
27 28 4.056050 ACTACCTCTACAACTGCAAAACG 58.944 43.478 0.00 0.00 0.00 3.60
28 29 1.602377 ACCTCTACAACTGCAAAACGC 59.398 47.619 0.00 0.00 42.89 4.84
47 48 5.073311 ACGCTACTTAATTTCTGCAGAGA 57.927 39.130 17.43 13.58 0.00 3.10
48 49 5.105752 ACGCTACTTAATTTCTGCAGAGAG 58.894 41.667 17.43 12.76 0.00 3.20
101 102 4.829492 AGCAGCCACATTTTCTTCTTAAGT 59.171 37.500 1.63 0.00 0.00 2.24
296 573 0.814010 GTTGCCTGGACGTGTCAAGT 60.814 55.000 0.00 0.00 0.00 3.16
340 617 4.153117 GCATCTGATCGACAACTGAAAACT 59.847 41.667 0.00 0.00 0.00 2.66
359 636 7.665559 TGAAAACTAATGTACTGCTTTCTGGAT 59.334 33.333 0.00 0.00 0.00 3.41
360 637 9.162764 GAAAACTAATGTACTGCTTTCTGGATA 57.837 33.333 0.00 0.00 0.00 2.59
361 638 9.686683 AAAACTAATGTACTGCTTTCTGGATAT 57.313 29.630 0.00 0.00 0.00 1.63
407 686 2.987149 CCTGAACTGTACGCTACACAAG 59.013 50.000 0.00 0.00 34.46 3.16
449 728 8.088365 ACTTAATTTGGATAAGTGTGGCTTTTC 58.912 33.333 0.00 0.00 40.97 2.29
479 758 3.688694 ACGTTTGGCTATTCCACACTA 57.311 42.857 0.00 0.00 46.55 2.74
504 783 3.054139 TGCCATCCTCAAGCACTCTTAAT 60.054 43.478 0.00 0.00 0.00 1.40
556 835 4.881920 TGCAATTAGGAAGCCAACTTTTC 58.118 39.130 0.00 0.00 35.82 2.29
580 859 7.474445 TCTAGGAGAATATGGTTCAGCTCTAT 58.526 38.462 0.00 0.00 0.00 1.98
653 932 9.554395 TCAATATAATCGGACATGTGTGTAATT 57.446 29.630 1.15 0.00 39.09 1.40
658 937 7.441890 AATCGGACATGTGTGTAATTACAAA 57.558 32.000 19.63 12.23 39.09 2.83
791 1077 9.667107 TCTAATCGAATTGATTACCAATATCCC 57.333 33.333 0.00 0.00 45.51 3.85
794 1080 7.744087 TCGAATTGATTACCAATATCCCAAG 57.256 36.000 0.00 0.00 44.28 3.61
860 1147 7.371126 TGTTCATATTGTCATTTCAGCGTAA 57.629 32.000 0.00 0.00 0.00 3.18
875 1162 1.601663 GCGTAACAGCATTTGCCAACA 60.602 47.619 0.00 0.00 43.38 3.33
883 1170 2.038033 AGCATTTGCCAACAAGCATCTT 59.962 40.909 0.00 0.00 43.64 2.40
884 1171 3.258872 AGCATTTGCCAACAAGCATCTTA 59.741 39.130 0.00 0.00 43.64 2.10
885 1172 3.995705 GCATTTGCCAACAAGCATCTTAA 59.004 39.130 0.00 0.00 43.64 1.85
886 1173 4.632688 GCATTTGCCAACAAGCATCTTAAT 59.367 37.500 0.00 0.00 43.64 1.40
887 1174 5.811613 GCATTTGCCAACAAGCATCTTAATA 59.188 36.000 0.00 0.00 43.64 0.98
888 1175 6.480981 GCATTTGCCAACAAGCATCTTAATAT 59.519 34.615 0.00 0.00 43.64 1.28
889 1176 7.652909 GCATTTGCCAACAAGCATCTTAATATA 59.347 33.333 0.00 0.00 43.64 0.86
890 1177 9.188588 CATTTGCCAACAAGCATCTTAATATAG 57.811 33.333 0.00 0.00 43.64 1.31
891 1178 7.880160 TTGCCAACAAGCATCTTAATATAGT 57.120 32.000 0.00 0.00 43.64 2.12
892 1179 8.972458 TTGCCAACAAGCATCTTAATATAGTA 57.028 30.769 0.00 0.00 43.64 1.82
893 1180 8.378172 TGCCAACAAGCATCTTAATATAGTAC 57.622 34.615 0.00 0.00 38.00 2.73
895 1182 8.283291 GCCAACAAGCATCTTAATATAGTACAC 58.717 37.037 0.00 0.00 0.00 2.90
896 1183 9.547753 CCAACAAGCATCTTAATATAGTACACT 57.452 33.333 0.00 0.00 0.00 3.55
953 1265 2.267351 CCAAACGCACAGCCCATCA 61.267 57.895 0.00 0.00 0.00 3.07
954 1266 1.597797 CCAAACGCACAGCCCATCAT 61.598 55.000 0.00 0.00 0.00 2.45
955 1267 0.179156 CAAACGCACAGCCCATCATC 60.179 55.000 0.00 0.00 0.00 2.92
956 1268 1.315257 AAACGCACAGCCCATCATCC 61.315 55.000 0.00 0.00 0.00 3.51
957 1269 2.903855 CGCACAGCCCATCATCCC 60.904 66.667 0.00 0.00 0.00 3.85
958 1270 2.520260 GCACAGCCCATCATCCCC 60.520 66.667 0.00 0.00 0.00 4.81
959 1271 3.065787 GCACAGCCCATCATCCCCT 62.066 63.158 0.00 0.00 0.00 4.79
960 1272 1.152819 CACAGCCCATCATCCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
961 1273 1.308128 ACAGCCCATCATCCCCTGA 60.308 57.895 0.00 0.00 38.53 3.86
962 1274 0.700269 ACAGCCCATCATCCCCTGAT 60.700 55.000 0.00 0.00 45.78 2.90
963 1275 0.037877 CAGCCCATCATCCCCTGATC 59.962 60.000 0.00 0.00 42.91 2.92
964 1276 1.138863 AGCCCATCATCCCCTGATCC 61.139 60.000 0.00 0.00 42.91 3.36
965 1277 2.081955 CCCATCATCCCCTGATCCC 58.918 63.158 0.00 0.00 42.91 3.85
966 1278 1.504275 CCCATCATCCCCTGATCCCC 61.504 65.000 0.00 0.00 42.91 4.81
967 1279 0.477202 CCATCATCCCCTGATCCCCT 60.477 60.000 0.00 0.00 42.91 4.79
968 1280 0.990374 CATCATCCCCTGATCCCCTC 59.010 60.000 0.00 0.00 42.91 4.30
969 1281 0.880357 ATCATCCCCTGATCCCCTCT 59.120 55.000 0.00 0.00 40.77 3.69
970 1282 0.192064 TCATCCCCTGATCCCCTCTC 59.808 60.000 0.00 0.00 0.00 3.20
971 1283 0.839853 CATCCCCTGATCCCCTCTCC 60.840 65.000 0.00 0.00 0.00 3.71
972 1284 1.015131 ATCCCCTGATCCCCTCTCCT 61.015 60.000 0.00 0.00 0.00 3.69
979 1291 2.723464 GATCCCCTCTCCTCCTCCCG 62.723 70.000 0.00 0.00 0.00 5.14
1001 1325 3.660865 CCCTCTTTATATACCACACGCC 58.339 50.000 0.00 0.00 0.00 5.68
1012 1336 2.029073 ACACGCCAACACGAGAGG 59.971 61.111 0.00 0.00 36.70 3.69
1035 1359 1.263217 CCGAGGAAAACAGAAACCACG 59.737 52.381 0.00 0.00 36.57 4.94
1036 1360 1.263217 CGAGGAAAACAGAAACCACGG 59.737 52.381 0.00 0.00 34.12 4.94
1037 1361 2.294979 GAGGAAAACAGAAACCACGGT 58.705 47.619 0.00 0.00 0.00 4.83
1047 1371 2.436087 AAACCACGGTCGAGCTGAGG 62.436 60.000 13.48 15.32 39.69 3.86
1088 1452 2.027745 TGCACCAACCAAGAAAGCAAAA 60.028 40.909 0.00 0.00 0.00 2.44
1103 1476 2.301009 AGCAAAAGCCCAATCAAGAAGG 59.699 45.455 0.00 0.00 0.00 3.46
1104 1477 2.299867 GCAAAAGCCCAATCAAGAAGGA 59.700 45.455 0.00 0.00 0.00 3.36
1301 1677 2.125106 AAGCTCCGATGGTTCCGC 60.125 61.111 0.00 0.00 0.00 5.54
1487 1864 4.626081 ACGGTGCTGCCCTGTGAC 62.626 66.667 0.00 0.00 0.00 3.67
1488 1865 4.320456 CGGTGCTGCCCTGTGACT 62.320 66.667 0.00 0.00 0.00 3.41
1489 1866 2.670934 GGTGCTGCCCTGTGACTG 60.671 66.667 0.00 0.00 0.00 3.51
1490 1867 2.111878 GTGCTGCCCTGTGACTGT 59.888 61.111 0.00 0.00 0.00 3.55
1491 1868 2.111669 TGCTGCCCTGTGACTGTG 59.888 61.111 0.00 0.00 0.00 3.66
1492 1869 2.670934 GCTGCCCTGTGACTGTGG 60.671 66.667 0.00 0.00 0.00 4.17
1559 1944 6.656902 TGCTCAATGGAGAAGTAGATTGATT 58.343 36.000 0.00 0.00 44.26 2.57
1560 1945 7.795047 TGCTCAATGGAGAAGTAGATTGATTA 58.205 34.615 0.00 0.00 44.26 1.75
1561 1946 8.435187 TGCTCAATGGAGAAGTAGATTGATTAT 58.565 33.333 0.00 0.00 44.26 1.28
1609 1995 3.189080 TCAAGCGATTTGTTGATGTCTGG 59.811 43.478 0.00 0.00 38.01 3.86
1631 2017 5.653330 TGGAAATCTGAAGATTGCATTGCTA 59.347 36.000 10.49 2.21 43.41 3.49
1632 2018 5.975939 GGAAATCTGAAGATTGCATTGCTAC 59.024 40.000 10.49 1.57 43.41 3.58
1633 2019 6.405065 GGAAATCTGAAGATTGCATTGCTACA 60.405 38.462 10.49 0.00 43.41 2.74
1634 2020 6.710597 AATCTGAAGATTGCATTGCTACAT 57.289 33.333 10.49 0.00 42.66 2.29
1638 2024 6.151480 TCTGAAGATTGCATTGCTACATTTCA 59.849 34.615 10.49 11.39 0.00 2.69
1653 2072 8.303876 TGCTACATTTCATTCTTTTTAAGACCC 58.696 33.333 0.00 0.00 37.23 4.46
1696 2120 1.067635 GGCAAGTTTGGTGCTGTATGG 60.068 52.381 0.00 0.00 41.88 2.74
1699 2123 3.365969 GCAAGTTTGGTGCTGTATGGTAC 60.366 47.826 0.00 0.00 39.00 3.34
1700 2124 2.695359 AGTTTGGTGCTGTATGGTACG 58.305 47.619 0.00 0.00 0.00 3.67
1751 2175 4.078537 TCATGTTGGGAGTACAAACCATG 58.921 43.478 0.00 0.21 36.74 3.66
1764 2188 2.888834 AACCATGGTTTGCTTGTGAC 57.111 45.000 24.86 0.00 34.22 3.67
1782 2206 3.090037 TGACCTACTAGTGGACTTGAGC 58.910 50.000 7.98 0.00 0.00 4.26
1892 2333 2.487934 CTCACCAATAATGCCGGAGAG 58.512 52.381 5.05 0.00 32.39 3.20
1895 2336 3.069586 TCACCAATAATGCCGGAGAGTAG 59.930 47.826 5.05 0.00 0.00 2.57
1932 2373 1.873270 AAGGGTTGCCGAAATTCCGC 61.873 55.000 0.00 0.00 0.00 5.54
1934 2375 2.559330 GTTGCCGAAATTCCGCGT 59.441 55.556 4.92 0.00 0.00 6.01
1968 2409 1.135944 GCAAAGCTAGTCGGCAAAGTC 60.136 52.381 0.00 0.00 34.17 3.01
1984 2425 2.270352 AGTCGTTGCAGAAATCCCAA 57.730 45.000 0.00 0.00 0.00 4.12
2148 2611 0.689080 AGCCGAGGTGATGATGGAGT 60.689 55.000 0.00 0.00 0.00 3.85
2151 2614 0.741326 CGAGGTGATGATGGAGTCGT 59.259 55.000 0.00 0.00 0.00 4.34
2152 2615 1.947456 CGAGGTGATGATGGAGTCGTA 59.053 52.381 0.00 0.00 0.00 3.43
2154 2617 1.683917 AGGTGATGATGGAGTCGTAGC 59.316 52.381 0.00 0.00 0.00 3.58
2175 2638 1.298859 GAACGAAGCCGAGCCAACAT 61.299 55.000 0.00 0.00 39.50 2.71
2176 2639 0.889186 AACGAAGCCGAGCCAACATT 60.889 50.000 0.00 0.00 39.50 2.71
2177 2640 1.298859 ACGAAGCCGAGCCAACATTC 61.299 55.000 0.00 0.00 39.50 2.67
2178 2641 1.425428 GAAGCCGAGCCAACATTCG 59.575 57.895 0.00 0.00 36.62 3.34
2179 2642 1.298859 GAAGCCGAGCCAACATTCGT 61.299 55.000 0.00 0.00 35.14 3.85
2180 2643 0.889186 AAGCCGAGCCAACATTCGTT 60.889 50.000 0.00 0.00 35.14 3.85
2181 2644 0.889186 AGCCGAGCCAACATTCGTTT 60.889 50.000 0.00 0.00 35.14 3.60
2182 2645 0.454452 GCCGAGCCAACATTCGTTTC 60.454 55.000 0.00 0.00 35.14 2.78
2183 2646 0.871722 CCGAGCCAACATTCGTTTCA 59.128 50.000 0.00 0.00 35.14 2.69
2184 2647 1.265635 CCGAGCCAACATTCGTTTCAA 59.734 47.619 0.00 0.00 35.14 2.69
2185 2648 2.287308 CCGAGCCAACATTCGTTTCAAA 60.287 45.455 0.00 0.00 35.14 2.69
2186 2649 3.367607 CGAGCCAACATTCGTTTCAAAA 58.632 40.909 0.00 0.00 31.13 2.44
2187 2650 3.794028 CGAGCCAACATTCGTTTCAAAAA 59.206 39.130 0.00 0.00 31.13 1.94
2206 2669 2.041153 AAAAAGCCGAGCCAACAGG 58.959 52.632 0.00 0.00 0.00 4.00
2207 2670 0.467290 AAAAAGCCGAGCCAACAGGA 60.467 50.000 0.00 0.00 0.00 3.86
2208 2671 0.890996 AAAAGCCGAGCCAACAGGAG 60.891 55.000 0.00 0.00 0.00 3.69
2209 2672 1.768684 AAAGCCGAGCCAACAGGAGA 61.769 55.000 0.00 0.00 0.00 3.71
2210 2673 1.557269 AAGCCGAGCCAACAGGAGAT 61.557 55.000 0.00 0.00 0.00 2.75
2230 2693 1.316651 AGATAGACGAGTTACCGGGC 58.683 55.000 6.32 0.00 0.00 6.13
2413 2905 4.717629 TCGTCGACGCCAGCCAAG 62.718 66.667 32.19 3.93 39.60 3.61
2464 2960 3.419759 GCCCAGGTTACGTGCGTG 61.420 66.667 7.55 2.94 0.00 5.34
2475 2971 3.712881 GTGCGTGCGTGGGTTCTC 61.713 66.667 0.00 0.00 0.00 2.87
2508 3004 2.809174 CGATCCTTGTCGCGTGCA 60.809 61.111 5.77 3.73 34.56 4.57
2552 3048 0.248825 CCATCTGCTTCTCGACTCGG 60.249 60.000 0.00 0.00 0.00 4.63
2554 3050 0.453793 ATCTGCTTCTCGACTCGGTG 59.546 55.000 0.00 0.00 0.00 4.94
2555 3051 1.803519 CTGCTTCTCGACTCGGTGC 60.804 63.158 0.00 0.00 0.00 5.01
2556 3052 2.507324 GCTTCTCGACTCGGTGCC 60.507 66.667 0.00 0.00 0.00 5.01
2557 3053 2.182030 CTTCTCGACTCGGTGCCC 59.818 66.667 0.00 0.00 0.00 5.36
2568 3064 4.570663 GGTGCCCGGTCGATCGAG 62.571 72.222 21.90 7.67 0.00 4.04
2571 3067 4.933064 GCCCGGTCGATCGAGCAG 62.933 72.222 37.34 29.56 42.17 4.24
2572 3068 4.933064 CCCGGTCGATCGAGCAGC 62.933 72.222 37.34 19.20 42.17 5.25
2573 3069 4.933064 CCGGTCGATCGAGCAGCC 62.933 72.222 37.34 25.16 42.17 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.667043 TTTGCAGTTGTAGAGGTAGTAAATG 57.333 36.000 0.00 0.00 0.00 2.32
2 3 6.201425 CGTTTTGCAGTTGTAGAGGTAGTAAA 59.799 38.462 0.00 0.00 0.00 2.01
4 5 5.224888 CGTTTTGCAGTTGTAGAGGTAGTA 58.775 41.667 0.00 0.00 0.00 1.82
5 6 4.056050 CGTTTTGCAGTTGTAGAGGTAGT 58.944 43.478 0.00 0.00 0.00 2.73
6 7 3.120649 GCGTTTTGCAGTTGTAGAGGTAG 60.121 47.826 0.00 0.00 45.45 3.18
7 8 2.803956 GCGTTTTGCAGTTGTAGAGGTA 59.196 45.455 0.00 0.00 45.45 3.08
8 9 1.602377 GCGTTTTGCAGTTGTAGAGGT 59.398 47.619 0.00 0.00 45.45 3.85
23 24 5.932303 TCTCTGCAGAAATTAAGTAGCGTTT 59.068 36.000 18.85 0.00 0.00 3.60
25 26 5.073311 TCTCTGCAGAAATTAAGTAGCGT 57.927 39.130 18.85 0.00 0.00 5.07
27 28 4.272261 GCCTCTCTGCAGAAATTAAGTAGC 59.728 45.833 18.85 8.43 0.00 3.58
28 29 5.293079 GTGCCTCTCTGCAGAAATTAAGTAG 59.707 44.000 18.85 2.53 43.02 2.57
47 48 1.600916 GCTTCACCCTTTCGTGCCT 60.601 57.895 0.00 0.00 33.57 4.75
48 49 2.626780 GGCTTCACCCTTTCGTGCC 61.627 63.158 0.00 0.00 33.57 5.01
101 102 6.762187 TGTACGACCACAACTCATTTTCTTTA 59.238 34.615 0.00 0.00 0.00 1.85
109 385 3.813166 CCTTTTGTACGACCACAACTCAT 59.187 43.478 0.00 0.00 38.12 2.90
178 454 5.702622 AAAGAAAGAAACGAAAAAGCTGC 57.297 34.783 0.00 0.00 0.00 5.25
179 455 7.253783 GGAGAAAAGAAAGAAACGAAAAAGCTG 60.254 37.037 0.00 0.00 0.00 4.24
180 456 6.752351 GGAGAAAAGAAAGAAACGAAAAAGCT 59.248 34.615 0.00 0.00 0.00 3.74
181 457 6.019801 GGGAGAAAAGAAAGAAACGAAAAAGC 60.020 38.462 0.00 0.00 0.00 3.51
182 458 7.258441 AGGGAGAAAAGAAAGAAACGAAAAAG 58.742 34.615 0.00 0.00 0.00 2.27
183 459 7.165460 AGGGAGAAAAGAAAGAAACGAAAAA 57.835 32.000 0.00 0.00 0.00 1.94
275 552 0.393132 TTGACACGTCCAGGCAACAA 60.393 50.000 0.00 0.00 41.41 2.83
276 553 0.813610 CTTGACACGTCCAGGCAACA 60.814 55.000 0.00 0.00 41.41 3.33
296 573 0.320050 TCATGCTTGCTCACCGTACA 59.680 50.000 0.00 0.00 0.00 2.90
360 637 9.503427 GTAAAGCTCGAAGCAAACATTAATAAT 57.497 29.630 9.09 0.00 45.56 1.28
361 638 7.966204 GGTAAAGCTCGAAGCAAACATTAATAA 59.034 33.333 9.09 0.00 45.56 1.40
431 710 4.098914 ACTGAAAAGCCACACTTATCCA 57.901 40.909 0.00 0.00 37.75 3.41
449 728 7.531716 TGGAATAGCCAAACGTATTTAAACTG 58.468 34.615 0.00 0.00 45.87 3.16
479 758 0.330604 AGTGCTTGAGGATGGCATGT 59.669 50.000 3.81 0.00 38.27 3.21
504 783 9.162764 GTTCTAGCCTCACATGTTAGATTTTAA 57.837 33.333 8.66 0.00 0.00 1.52
518 797 4.708726 ATTGCATTTGTTCTAGCCTCAC 57.291 40.909 0.00 0.00 0.00 3.51
523 802 5.745769 GCTTCCTAATTGCATTTGTTCTAGC 59.254 40.000 4.11 3.66 0.00 3.42
556 835 7.363705 CCATAGAGCTGAACCATATTCTCCTAG 60.364 44.444 0.00 0.00 0.00 3.02
580 859 4.080356 AGCTCATAATTGTTGGTAGAGCCA 60.080 41.667 0.00 0.00 45.93 4.75
670 952 6.808321 TTATACATACCTGCCTCTCTTTGT 57.192 37.500 0.00 0.00 0.00 2.83
782 1068 2.509548 TGTGGGTCTCTTGGGATATTGG 59.490 50.000 0.00 0.00 0.00 3.16
791 1077 2.743636 ACATACGTGTGGGTCTCTTG 57.256 50.000 17.05 0.00 37.14 3.02
794 1080 3.314541 AAGAACATACGTGTGGGTCTC 57.685 47.619 17.05 7.41 38.92 3.36
860 1147 0.464870 TGCTTGTTGGCAAATGCTGT 59.535 45.000 17.05 0.00 39.43 4.40
891 1178 8.830580 GCATAGCTCTTGATGAAATAAAGTGTA 58.169 33.333 0.00 0.00 36.13 2.90
892 1179 7.337689 TGCATAGCTCTTGATGAAATAAAGTGT 59.662 33.333 0.00 0.00 36.13 3.55
893 1180 7.642978 GTGCATAGCTCTTGATGAAATAAAGTG 59.357 37.037 0.00 0.00 36.13 3.16
895 1182 7.700505 TGTGCATAGCTCTTGATGAAATAAAG 58.299 34.615 0.00 0.00 36.01 1.85
896 1183 7.628769 TGTGCATAGCTCTTGATGAAATAAA 57.371 32.000 0.00 0.00 0.00 1.40
897 1184 7.645402 CATGTGCATAGCTCTTGATGAAATAA 58.355 34.615 0.00 0.00 31.84 1.40
931 1243 2.331451 GGCTGTGCGTTTGGTGAC 59.669 61.111 0.00 0.00 0.00 3.67
953 1265 1.015131 AGGAGAGGGGATCAGGGGAT 61.015 60.000 0.00 0.00 36.13 3.85
954 1266 1.630333 AGGAGAGGGGATCAGGGGA 60.630 63.158 0.00 0.00 0.00 4.81
955 1267 1.152139 GAGGAGAGGGGATCAGGGG 60.152 68.421 0.00 0.00 0.00 4.79
956 1268 1.152139 GGAGGAGAGGGGATCAGGG 60.152 68.421 0.00 0.00 0.00 4.45
957 1269 0.178935 GAGGAGGAGAGGGGATCAGG 60.179 65.000 0.00 0.00 0.00 3.86
958 1270 0.178935 GGAGGAGGAGAGGGGATCAG 60.179 65.000 0.00 0.00 0.00 2.90
959 1271 1.669927 GGGAGGAGGAGAGGGGATCA 61.670 65.000 0.00 0.00 0.00 2.92
960 1272 1.157513 GGGAGGAGGAGAGGGGATC 59.842 68.421 0.00 0.00 0.00 3.36
961 1273 2.784654 CGGGAGGAGGAGAGGGGAT 61.785 68.421 0.00 0.00 0.00 3.85
962 1274 3.430497 CGGGAGGAGGAGAGGGGA 61.430 72.222 0.00 0.00 0.00 4.81
966 1278 4.150454 AGGGCGGGAGGAGGAGAG 62.150 72.222 0.00 0.00 0.00 3.20
967 1279 4.144727 GAGGGCGGGAGGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
968 1280 3.687828 AAGAGGGCGGGAGGAGGAG 62.688 68.421 0.00 0.00 0.00 3.69
969 1281 1.882189 TAAAGAGGGCGGGAGGAGGA 61.882 60.000 0.00 0.00 0.00 3.71
970 1282 0.764752 ATAAAGAGGGCGGGAGGAGG 60.765 60.000 0.00 0.00 0.00 4.30
971 1283 2.011122 TATAAAGAGGGCGGGAGGAG 57.989 55.000 0.00 0.00 0.00 3.69
972 1284 2.715763 ATATAAAGAGGGCGGGAGGA 57.284 50.000 0.00 0.00 0.00 3.71
979 1291 3.064931 GCGTGTGGTATATAAAGAGGGC 58.935 50.000 0.00 0.00 0.00 5.19
1001 1325 3.649277 CTCGGCCCCTCTCGTGTTG 62.649 68.421 0.00 0.00 0.00 3.33
1012 1336 0.596577 GTTTCTGTTTTCCTCGGCCC 59.403 55.000 0.00 0.00 0.00 5.80
1015 1339 1.263217 CGTGGTTTCTGTTTTCCTCGG 59.737 52.381 0.00 0.00 34.66 4.63
1016 1340 1.263217 CCGTGGTTTCTGTTTTCCTCG 59.737 52.381 0.00 0.00 36.92 4.63
1047 1371 0.179097 GGCAGAGGCAGTACAGTAGC 60.179 60.000 0.00 0.00 43.71 3.58
1088 1452 2.915604 TCTTCTCCTTCTTGATTGGGCT 59.084 45.455 0.00 0.00 0.00 5.19
1103 1476 1.147153 CGCCTCCCCCATTCTTCTC 59.853 63.158 0.00 0.00 0.00 2.87
1104 1477 3.049080 GCGCCTCCCCCATTCTTCT 62.049 63.158 0.00 0.00 0.00 2.85
1292 1668 4.802051 ATGGCGCTGCGGAACCAT 62.802 61.111 24.61 22.90 38.08 3.55
1488 1865 2.221169 GCTGTTGTCTTCATGACCACA 58.779 47.619 0.00 0.00 45.34 4.17
1489 1866 2.031682 GTGCTGTTGTCTTCATGACCAC 60.032 50.000 0.00 0.00 44.75 4.16
1490 1867 2.158769 AGTGCTGTTGTCTTCATGACCA 60.159 45.455 0.00 0.00 44.75 4.02
1491 1868 2.498167 AGTGCTGTTGTCTTCATGACC 58.502 47.619 0.00 0.00 44.75 4.02
1492 1869 5.180117 ACATTAGTGCTGTTGTCTTCATGAC 59.820 40.000 0.00 0.00 45.54 3.06
1597 1983 5.868454 TCTTCAGATTTCCAGACATCAACA 58.132 37.500 0.00 0.00 0.00 3.33
1609 1995 6.558009 TGTAGCAATGCAATCTTCAGATTTC 58.442 36.000 8.35 0.00 42.41 2.17
1722 2146 5.191727 TGTACTCCCAACATGATTGGAAT 57.808 39.130 21.54 5.64 42.06 3.01
1723 2147 4.649267 TGTACTCCCAACATGATTGGAA 57.351 40.909 21.54 7.09 42.06 3.53
1724 2148 4.649267 TTGTACTCCCAACATGATTGGA 57.351 40.909 21.54 11.07 42.06 3.53
1725 2149 4.082245 GGTTTGTACTCCCAACATGATTGG 60.082 45.833 15.95 15.95 39.25 3.16
1726 2150 4.522405 TGGTTTGTACTCCCAACATGATTG 59.478 41.667 0.00 0.09 0.00 2.67
1727 2151 4.735369 TGGTTTGTACTCCCAACATGATT 58.265 39.130 0.00 0.00 0.00 2.57
1728 2152 4.380843 TGGTTTGTACTCCCAACATGAT 57.619 40.909 0.00 0.00 0.00 2.45
1751 2175 3.746492 CACTAGTAGGTCACAAGCAAACC 59.254 47.826 1.45 0.00 0.00 3.27
1764 2188 3.093057 ACTGCTCAAGTCCACTAGTAGG 58.907 50.000 1.45 0.00 31.64 3.18
1855 2288 4.416533 GCATGGAGCAGACTCTCG 57.583 61.111 0.00 0.00 42.98 4.04
1892 2333 4.164822 TGCTTTGCTTCATTGCTTCTAC 57.835 40.909 0.00 0.00 0.00 2.59
1895 2336 2.735134 CCTTGCTTTGCTTCATTGCTTC 59.265 45.455 0.00 0.00 0.00 3.86
1934 2375 1.598430 GCTTTGCTTGCCGTTTACGAA 60.598 47.619 3.46 0.00 43.02 3.85
1943 2384 1.796796 CCGACTAGCTTTGCTTGCC 59.203 57.895 0.00 0.00 40.44 4.52
1968 2409 2.554032 AGAACTTGGGATTTCTGCAACG 59.446 45.455 0.00 0.00 30.65 4.10
1984 2425 1.206371 GGTGTGCCGTATACCAGAACT 59.794 52.381 0.00 0.00 40.11 3.01
2030 2471 1.165907 ACACACATGCACAGAACGGG 61.166 55.000 0.00 0.00 0.00 5.28
2033 2474 2.462889 CCAAACACACATGCACAGAAC 58.537 47.619 0.00 0.00 0.00 3.01
2098 2553 6.007076 ACTTCAATCCTCCTCCTTTTCTTTC 58.993 40.000 0.00 0.00 0.00 2.62
2101 2556 4.323104 CGACTTCAATCCTCCTCCTTTTCT 60.323 45.833 0.00 0.00 0.00 2.52
2102 2557 3.935828 CGACTTCAATCCTCCTCCTTTTC 59.064 47.826 0.00 0.00 0.00 2.29
2103 2558 3.307762 CCGACTTCAATCCTCCTCCTTTT 60.308 47.826 0.00 0.00 0.00 2.27
2105 2560 1.834263 CCGACTTCAATCCTCCTCCTT 59.166 52.381 0.00 0.00 0.00 3.36
2108 2563 0.179070 GCCCGACTTCAATCCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
2109 2564 1.627297 GGCCCGACTTCAATCCTCCT 61.627 60.000 0.00 0.00 0.00 3.69
2110 2565 1.153147 GGCCCGACTTCAATCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
2137 2600 2.654863 TCAGCTACGACTCCATCATCA 58.345 47.619 0.00 0.00 0.00 3.07
2151 2614 1.153823 GCTCGGCTTCGTTCAGCTA 60.154 57.895 0.00 0.00 39.97 3.32
2152 2615 2.433318 GCTCGGCTTCGTTCAGCT 60.433 61.111 4.44 0.00 39.97 4.24
2154 2617 1.667830 TTGGCTCGGCTTCGTTCAG 60.668 57.895 0.00 0.00 35.06 3.02
2188 2651 0.467290 TCCTGTTGGCTCGGCTTTTT 60.467 50.000 0.00 0.00 0.00 1.94
2189 2652 0.890996 CTCCTGTTGGCTCGGCTTTT 60.891 55.000 0.00 0.00 0.00 2.27
2190 2653 1.302832 CTCCTGTTGGCTCGGCTTT 60.303 57.895 0.00 0.00 0.00 3.51
2191 2654 1.557269 ATCTCCTGTTGGCTCGGCTT 61.557 55.000 0.00 0.00 0.00 4.35
2192 2655 0.687757 TATCTCCTGTTGGCTCGGCT 60.688 55.000 0.00 0.00 0.00 5.52
2193 2656 0.249657 CTATCTCCTGTTGGCTCGGC 60.250 60.000 0.00 0.00 0.00 5.54
2194 2657 1.403814 TCTATCTCCTGTTGGCTCGG 58.596 55.000 0.00 0.00 0.00 4.63
2195 2658 4.075682 TCTATCTATCTCCTGTTGGCTCG 58.924 47.826 0.00 0.00 0.00 5.03
2196 2659 4.083003 CGTCTATCTATCTCCTGTTGGCTC 60.083 50.000 0.00 0.00 0.00 4.70
2197 2660 3.823873 CGTCTATCTATCTCCTGTTGGCT 59.176 47.826 0.00 0.00 0.00 4.75
2198 2661 3.821600 TCGTCTATCTATCTCCTGTTGGC 59.178 47.826 0.00 0.00 0.00 4.52
2199 2662 5.067273 ACTCGTCTATCTATCTCCTGTTGG 58.933 45.833 0.00 0.00 0.00 3.77
2200 2663 6.627395 AACTCGTCTATCTATCTCCTGTTG 57.373 41.667 0.00 0.00 0.00 3.33
2201 2664 6.711645 GGTAACTCGTCTATCTATCTCCTGTT 59.288 42.308 0.00 0.00 0.00 3.16
2202 2665 6.232692 GGTAACTCGTCTATCTATCTCCTGT 58.767 44.000 0.00 0.00 0.00 4.00
2203 2666 5.349270 CGGTAACTCGTCTATCTATCTCCTG 59.651 48.000 0.00 0.00 0.00 3.86
2204 2667 5.481105 CGGTAACTCGTCTATCTATCTCCT 58.519 45.833 0.00 0.00 0.00 3.69
2205 2668 4.630940 CCGGTAACTCGTCTATCTATCTCC 59.369 50.000 0.00 0.00 0.00 3.71
2206 2669 4.630940 CCCGGTAACTCGTCTATCTATCTC 59.369 50.000 0.00 0.00 0.00 2.75
2207 2670 4.577875 CCCGGTAACTCGTCTATCTATCT 58.422 47.826 0.00 0.00 0.00 1.98
2208 2671 3.126686 GCCCGGTAACTCGTCTATCTATC 59.873 52.174 0.00 0.00 0.00 2.08
2209 2672 3.080319 GCCCGGTAACTCGTCTATCTAT 58.920 50.000 0.00 0.00 0.00 1.98
2210 2673 2.498167 GCCCGGTAACTCGTCTATCTA 58.502 52.381 0.00 0.00 0.00 1.98
2347 2836 2.320587 CCGGCCGAGCATTAGCATC 61.321 63.158 30.73 0.00 45.49 3.91
2379 2871 1.816679 GAGGACGCATCATGCAGCA 60.817 57.895 11.00 0.00 45.36 4.41
2380 2872 2.879070 CGAGGACGCATCATGCAGC 61.879 63.158 11.00 0.00 45.36 5.25
2381 2873 1.485838 GACGAGGACGCATCATGCAG 61.486 60.000 11.00 5.17 45.36 4.41
2398 2890 3.112709 GTCTTGGCTGGCGTCGAC 61.113 66.667 5.18 5.18 0.00 4.20
2413 2905 1.955080 CCGTGATGAGGGTAGTAGGTC 59.045 57.143 0.00 0.00 0.00 3.85
2464 2960 0.536460 TTCCCTTTGAGAACCCACGC 60.536 55.000 0.00 0.00 0.00 5.34
2475 2971 2.284190 GATCGGCTTCTCTTCCCTTTG 58.716 52.381 0.00 0.00 0.00 2.77
2508 3004 1.837439 TCTGATCACGGGTTAGGCAAT 59.163 47.619 0.00 0.00 0.00 3.56
2555 3051 4.933064 GCTGCTCGATCGACCGGG 62.933 72.222 15.15 0.00 0.00 5.73
2556 3052 4.933064 GGCTGCTCGATCGACCGG 62.933 72.222 15.15 14.38 0.00 5.28
2558 3054 4.194720 ACGGCTGCTCGATCGACC 62.195 66.667 15.15 12.97 0.00 4.79
2559 3055 2.652496 GACGGCTGCTCGATCGAC 60.652 66.667 15.15 11.86 0.00 4.20
2560 3056 2.824489 AGACGGCTGCTCGATCGA 60.824 61.111 18.32 18.32 0.00 3.59
2561 3057 2.653448 CAGACGGCTGCTCGATCG 60.653 66.667 4.70 9.36 34.95 3.69
2573 3069 4.707840 CTTGCACGCACGCAGACG 62.708 66.667 0.00 0.00 44.14 4.18


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

AutoCloner maintained by Alex Coulton.