Multiple sequence alignment - TraesCS4A01G421500

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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 TraesCS4A01G421500 chr4A 100.000 2527 0 0 1 2527 692078299 692080825 0.000000e+00 4667
1 TraesCS4A01G421500 chr4A 91.917 532 26 7 998 1529 692358848 692359362 0.000000e+00 728
2 TraesCS4A01G421500 chr4A 91.917 532 26 7 998 1529 693596930 693596416 0.000000e+00 728
3 TraesCS4A01G421500 chr7D 87.058 2179 155 52 32 2115 33472338 33470192 0.000000e+00 2344
4 TraesCS4A01G421500 chr7D 87.934 547 38 19 993 1529 33217068 33216540 9.930000e-174 619
5 TraesCS4A01G421500 chr7D 86.542 535 44 16 998 1529 551737769 551738278 4.720000e-157 564
6 TraesCS4A01G421500 chr7D 86.898 374 13 8 2169 2527 33469899 33469547 1.100000e-103 387
7 TraesCS4A01G421500 chr7A 88.986 1725 111 38 32 1709 34034344 34032652 0.000000e+00 2060
8 TraesCS4A01G421500 chr7A 84.430 912 90 26 1185 2064 33977761 33976870 0.000000e+00 850
9 TraesCS4A01G421500 chr7A 85.952 541 57 14 998 1529 637297952 637298482 6.100000e-156 560
10 TraesCS4A01G421500 chr7A 85.561 374 18 9 2169 2527 34031121 34030769 2.390000e-95 359
11 TraesCS4A01G421500 chr7A 86.532 297 29 8 1828 2115 34032103 34031809 1.460000e-82 316
12 TraesCS4A01G421500 chrUn 91.887 530 25 13 997 1526 81832850 81833361 0.000000e+00 725
13 TraesCS4A01G421500 chr7B 86.381 536 48 16 999 1529 596606414 596606929 1.700000e-156 562
14 TraesCS4A01G421500 chr6D 85.929 533 49 18 1001 1527 18940745 18941257 1.710000e-151 545
15 TraesCS4A01G421500 chr6B 85.150 532 55 16 1001 1527 33011592 33012104 8.010000e-145 523
16 TraesCS4A01G421500 chr3B 81.646 632 72 23 43 645 592663327 592663943 3.780000e-133 484
17 TraesCS4A01G421500 chr3D 80.818 636 75 23 43 645 450884661 450885282 2.960000e-124 455
18 TraesCS4A01G421500 chr3A 82.278 553 67 16 43 572 594031638 594032182 1.380000e-122 449


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 TraesCS4A01G421500 chr4A 692078299 692080825 2526 False 4667.000000 4667 100.000000 1 2527 1 chr4A.!!$F1 2526
1 TraesCS4A01G421500 chr4A 692358848 692359362 514 False 728.000000 728 91.917000 998 1529 1 chr4A.!!$F2 531
2 TraesCS4A01G421500 chr4A 693596416 693596930 514 True 728.000000 728 91.917000 998 1529 1 chr4A.!!$R1 531
3 TraesCS4A01G421500 chr7D 33469547 33472338 2791 True 1365.500000 2344 86.978000 32 2527 2 chr7D.!!$R2 2495
4 TraesCS4A01G421500 chr7D 33216540 33217068 528 True 619.000000 619 87.934000 993 1529 1 chr7D.!!$R1 536
5 TraesCS4A01G421500 chr7D 551737769 551738278 509 False 564.000000 564 86.542000 998 1529 1 chr7D.!!$F1 531
6 TraesCS4A01G421500 chr7A 34030769 34034344 3575 True 911.666667 2060 87.026333 32 2527 3 chr7A.!!$R2 2495
7 TraesCS4A01G421500 chr7A 33976870 33977761 891 True 850.000000 850 84.430000 1185 2064 1 chr7A.!!$R1 879
8 TraesCS4A01G421500 chr7A 637297952 637298482 530 False 560.000000 560 85.952000 998 1529 1 chr7A.!!$F1 531
9 TraesCS4A01G421500 chrUn 81832850 81833361 511 False 725.000000 725 91.887000 997 1526 1 chrUn.!!$F1 529
10 TraesCS4A01G421500 chr7B 596606414 596606929 515 False 562.000000 562 86.381000 999 1529 1 chr7B.!!$F1 530
11 TraesCS4A01G421500 chr6D 18940745 18941257 512 False 545.000000 545 85.929000 1001 1527 1 chr6D.!!$F1 526
12 TraesCS4A01G421500 chr6B 33011592 33012104 512 False 523.000000 523 85.150000 1001 1527 1 chr6B.!!$F1 526
13 TraesCS4A01G421500 chr3B 592663327 592663943 616 False 484.000000 484 81.646000 43 645 1 chr3B.!!$F1 602
14 TraesCS4A01G421500 chr3D 450884661 450885282 621 False 455.000000 455 80.818000 43 645 1 chr3D.!!$F1 602
15 TraesCS4A01G421500 chr3A 594031638 594032182 544 False 449.000000 449 82.278000 43 572 1 chr3A.!!$F1 529

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
216 234 0.107831 CACTGAACCTCCCGAAACCA 59.892 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2523 0.179032 AACCGTCCACAAGCATCACA 60.179 50.0 0.0 0.0 0.0 3.58 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
19 20 2.128771 ATGGACACGGGGAATTCTTG 57.871 50.000 5.23 0.90 0.00 3.02
20 21 0.768622 TGGACACGGGGAATTCTTGT 59.231 50.000 5.23 4.07 0.00 3.16
21 22 1.271163 TGGACACGGGGAATTCTTGTC 60.271 52.381 5.23 12.04 36.63 3.18
22 23 1.003233 GGACACGGGGAATTCTTGTCT 59.997 52.381 19.80 2.92 37.36 3.41
23 24 2.235402 GGACACGGGGAATTCTTGTCTA 59.765 50.000 19.80 0.00 37.36 2.59
24 25 3.522553 GACACGGGGAATTCTTGTCTAG 58.477 50.000 5.23 0.00 34.89 2.43
25 26 2.904434 ACACGGGGAATTCTTGTCTAGT 59.096 45.455 5.23 0.00 0.00 2.57
26 27 4.091549 ACACGGGGAATTCTTGTCTAGTA 58.908 43.478 5.23 0.00 0.00 1.82
27 28 4.529377 ACACGGGGAATTCTTGTCTAGTAA 59.471 41.667 5.23 0.00 0.00 2.24
28 29 4.868734 CACGGGGAATTCTTGTCTAGTAAC 59.131 45.833 5.23 0.00 0.00 2.50
29 30 4.081254 ACGGGGAATTCTTGTCTAGTAACC 60.081 45.833 5.23 0.00 0.00 2.85
30 31 4.081309 CGGGGAATTCTTGTCTAGTAACCA 60.081 45.833 5.23 0.00 0.00 3.67
48 49 1.270732 CCAGCATCCTAGGCTAAGCTG 60.271 57.143 25.10 25.10 46.55 4.24
75 76 6.985188 TTCAGAAATACAGTAACCAGCATC 57.015 37.500 0.00 0.00 0.00 3.91
201 208 1.021390 GGAAGGACACGCCATCACTG 61.021 60.000 0.00 0.00 36.07 3.66
216 234 0.107831 CACTGAACCTCCCGAAACCA 59.892 55.000 0.00 0.00 0.00 3.67
228 246 1.378124 CGAAACCAAACCACACCCGT 61.378 55.000 0.00 0.00 0.00 5.28
230 248 1.038681 AAACCAAACCACACCCGTCC 61.039 55.000 0.00 0.00 0.00 4.79
232 250 2.596338 CAAACCACACCCGTCCCC 60.596 66.667 0.00 0.00 0.00 4.81
250 268 3.046087 GCAGTCTGCAGAAGCGCA 61.046 61.111 20.19 0.00 44.26 6.09
302 320 4.148825 GCTCGCCGTGTCCCAGAT 62.149 66.667 0.00 0.00 0.00 2.90
349 374 0.670854 GGAGCGAAACCAGAGACCAC 60.671 60.000 0.00 0.00 0.00 4.16
415 440 2.503061 CTGATGCCGTGGGGAGAG 59.497 66.667 0.00 0.00 34.06 3.20
605 645 2.817396 GCGAGACAGGCAGAAGGC 60.817 66.667 0.00 0.00 43.74 4.35
652 704 1.304713 CTCAGCCCAAATGCCCACT 60.305 57.895 0.00 0.00 0.00 4.00
654 706 1.607178 CAGCCCAAATGCCCACTCA 60.607 57.895 0.00 0.00 0.00 3.41
833 906 2.472909 GCATCCCGAGGCCTTTTCG 61.473 63.158 6.77 6.25 37.78 3.46
882 971 1.448540 CACCTGCTCCGCCTACAAG 60.449 63.158 0.00 0.00 0.00 3.16
893 983 1.688187 CCTACAAGTACCCCCGCCT 60.688 63.158 0.00 0.00 0.00 5.52
905 995 3.782443 CCGCCTACTGTCCCCCAC 61.782 72.222 0.00 0.00 0.00 4.61
906 996 2.683933 CGCCTACTGTCCCCCACT 60.684 66.667 0.00 0.00 0.00 4.00
907 997 2.291043 CGCCTACTGTCCCCCACTT 61.291 63.158 0.00 0.00 0.00 3.16
919 1009 1.476291 CCCCCACTTTACTATTCGCCC 60.476 57.143 0.00 0.00 0.00 6.13
927 1017 1.045407 TACTATTCGCCCTTCCGCAT 58.955 50.000 0.00 0.00 0.00 4.73
931 1021 2.947938 ATTCGCCCTTCCGCATCCAG 62.948 60.000 0.00 0.00 0.00 3.86
934 1024 1.678970 GCCCTTCCGCATCCAGTTT 60.679 57.895 0.00 0.00 0.00 2.66
961 1051 1.952102 TTCCGATTCGAACCTCCCCG 61.952 60.000 7.83 0.00 0.00 5.73
990 1080 1.371183 CAGTCGACAGGAGGCCAAA 59.629 57.895 19.50 0.00 0.00 3.28
991 1081 0.671781 CAGTCGACAGGAGGCCAAAG 60.672 60.000 19.50 0.00 0.00 2.77
1136 1265 4.311606 TCATTCGTCCTTGTTGATTCGAA 58.688 39.130 0.00 0.00 40.50 3.71
1179 1311 3.001939 GGAGTTTGAATCGTCGTTGTGTT 59.998 43.478 0.00 0.00 0.00 3.32
1180 1312 4.495184 GGAGTTTGAATCGTCGTTGTGTTT 60.495 41.667 0.00 0.00 0.00 2.83
1202 1334 3.764466 CAGGCGGCGAGGAAGTCT 61.764 66.667 12.98 0.00 0.00 3.24
1365 1497 0.966920 GGACTTCAAGACGGACCTCA 59.033 55.000 0.00 0.00 0.00 3.86
1367 1499 0.969894 ACTTCAAGACGGACCTCAGG 59.030 55.000 0.00 0.00 0.00 3.86
1531 1663 2.107953 CGAGAGGGCCTAAGCTGC 59.892 66.667 5.73 0.00 39.73 5.25
1540 1672 4.554036 CTAAGCTGCCCCCTCCGC 62.554 72.222 0.00 0.00 0.00 5.54
1555 1687 4.764336 CGCCGACGCCGTTAGTGA 62.764 66.667 0.00 0.00 0.00 3.41
1556 1688 2.879462 GCCGACGCCGTTAGTGAG 60.879 66.667 0.00 0.00 0.00 3.51
1574 1712 4.221703 AGTGAGTCGGAATGAGTTGATTCT 59.778 41.667 0.00 0.00 33.52 2.40
1644 1787 7.001674 TGTGTAGAAGAAATATGGTTGTTGGT 58.998 34.615 0.00 0.00 0.00 3.67
1645 1788 8.158132 TGTGTAGAAGAAATATGGTTGTTGGTA 58.842 33.333 0.00 0.00 0.00 3.25
1646 1789 8.448615 GTGTAGAAGAAATATGGTTGTTGGTAC 58.551 37.037 0.00 0.00 0.00 3.34
1647 1790 8.158132 TGTAGAAGAAATATGGTTGTTGGTACA 58.842 33.333 0.00 0.00 0.00 2.90
1735 1885 2.292267 CCTCAGAACTGCTGTTGTTGT 58.708 47.619 14.22 0.00 45.14 3.32
1736 1886 2.684881 CCTCAGAACTGCTGTTGTTGTT 59.315 45.455 14.22 0.00 45.14 2.83
1750 1900 2.579013 GTTGTTAGCAACGACTCAGC 57.421 50.000 6.70 0.00 44.40 4.26
1751 1901 2.135933 GTTGTTAGCAACGACTCAGCT 58.864 47.619 6.70 0.00 44.40 4.24
1752 1902 2.065993 TGTTAGCAACGACTCAGCTC 57.934 50.000 0.00 0.00 39.68 4.09
1780 1930 0.541392 TCCTTGATCCCATCGTGGTG 59.459 55.000 0.00 0.00 35.17 4.17
1785 1935 1.066215 TGATCCCATCGTGGTGTTCTG 60.066 52.381 0.00 0.00 35.17 3.02
1794 1944 3.390135 TCGTGGTGTTCTGTCTTGATTC 58.610 45.455 0.00 0.00 0.00 2.52
1801 1975 2.084610 TCTGTCTTGATTCCTGCGTG 57.915 50.000 0.00 0.00 0.00 5.34
1824 1998 3.451141 TTTGATTTGGGTTGTGCTGTC 57.549 42.857 0.00 0.00 0.00 3.51
1838 2453 3.027170 CTGTCGATGGTTGCCGTGC 62.027 63.158 0.00 0.00 0.00 5.34
1846 2461 2.048503 GTTGCCGTGCGGTCTACT 60.049 61.111 12.46 0.00 37.65 2.57
1847 2462 2.092882 GTTGCCGTGCGGTCTACTC 61.093 63.158 12.46 0.00 37.65 2.59
1873 2488 4.891727 GTCGGCGGCGATGTGGAT 62.892 66.667 36.75 0.00 0.00 3.41
1886 2501 0.602638 TGTGGATGCAACCGTCTGTC 60.603 55.000 8.65 0.00 0.00 3.51
1899 2514 3.680786 CTGTCCACGGCGAGGTCA 61.681 66.667 22.43 21.04 0.00 4.02
1908 2523 1.300697 GGCGAGGTCAGACACGTTT 60.301 57.895 16.75 0.00 0.00 3.60
1951 2568 0.524862 TTTCTGCTCGACCTACCGAC 59.475 55.000 0.00 0.00 34.56 4.79
1973 2597 1.138036 CGGAATCGTGGTCGCTACA 59.862 57.895 0.00 0.00 36.96 2.74
2056 2682 0.912486 GCTGTCCCTACCATGGAGTT 59.088 55.000 21.47 0.00 30.98 3.01
2075 2701 3.003689 AGTTTGTTGAGAAGATTGTGGCG 59.996 43.478 0.00 0.00 0.00 5.69
2114 2740 2.551270 CTTCGTGCGAAGGTGTGC 59.449 61.111 22.25 0.00 45.60 4.57
2115 2741 2.202946 TTCGTGCGAAGGTGTGCA 60.203 55.556 2.65 0.00 39.13 4.57
2116 2742 1.771073 CTTCGTGCGAAGGTGTGCAA 61.771 55.000 22.25 0.00 45.60 4.08
2117 2743 1.369839 TTCGTGCGAAGGTGTGCAAA 61.370 50.000 2.65 0.00 43.75 3.68
2118 2744 1.063327 CGTGCGAAGGTGTGCAAAA 59.937 52.632 0.00 0.00 43.75 2.44
2119 2745 0.317770 CGTGCGAAGGTGTGCAAAAT 60.318 50.000 0.00 0.00 43.75 1.82
2123 3111 0.958091 CGAAGGTGTGCAAAATCCCA 59.042 50.000 0.00 0.00 0.00 4.37
2124 3112 1.545582 CGAAGGTGTGCAAAATCCCAT 59.454 47.619 0.00 0.00 0.00 4.00
2128 3116 4.806640 AGGTGTGCAAAATCCCATTAAG 57.193 40.909 0.00 0.00 0.00 1.85
2143 3131 4.998051 CCATTAAGGGGGCATGTACTTAT 58.002 43.478 0.00 0.00 0.00 1.73
2144 3132 5.010282 CCATTAAGGGGGCATGTACTTATC 58.990 45.833 0.00 0.00 0.00 1.75
2147 3135 7.458397 CATTAAGGGGGCATGTACTTATCTTA 58.542 38.462 0.00 0.00 0.00 2.10
2148 3136 4.976540 AGGGGGCATGTACTTATCTTAC 57.023 45.455 0.00 0.00 0.00 2.34
2149 3137 3.323979 AGGGGGCATGTACTTATCTTACG 59.676 47.826 0.00 0.00 0.00 3.18
2154 3142 5.462398 GGGCATGTACTTATCTTACGTCTTG 59.538 44.000 0.00 0.00 0.00 3.02
2157 3145 6.201044 GCATGTACTTATCTTACGTCTTGCAT 59.799 38.462 0.00 0.00 0.00 3.96
2158 3146 7.558991 CATGTACTTATCTTACGTCTTGCATG 58.441 38.462 0.00 0.00 0.00 4.06
2159 3147 6.627243 TGTACTTATCTTACGTCTTGCATGT 58.373 36.000 0.00 0.00 0.00 3.21
2163 3151 8.718102 ACTTATCTTACGTCTTGCATGTAATT 57.282 30.769 0.00 0.00 36.15 1.40
2164 3152 9.162764 ACTTATCTTACGTCTTGCATGTAATTT 57.837 29.630 0.00 0.00 36.15 1.82
2171 3432 9.642327 TTACGTCTTGCATGTAATTTAGAACTA 57.358 29.630 0.00 0.00 32.40 2.24
2195 3456 5.796424 ATCCAGTTCTTGACTTGCATTTT 57.204 34.783 0.00 0.00 36.10 1.82
2198 3459 5.126869 TCCAGTTCTTGACTTGCATTTTGAA 59.873 36.000 0.00 0.00 36.10 2.69
2203 3464 7.550196 AGTTCTTGACTTGCATTTTGAACATTT 59.450 29.630 15.12 0.00 33.92 2.32
2407 3671 9.950496 AACTATATGAGTTTGATTTCAGACAGT 57.050 29.630 4.32 0.00 46.79 3.55
2475 3752 4.508124 GGGTGCAAGTTGATATAGAACTCG 59.492 45.833 7.16 0.00 32.33 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.354368 ACAAGAATTCCCCGTGTCCAT 59.646 47.619 0.65 0.00 0.00 3.41
1 2 0.768622 ACAAGAATTCCCCGTGTCCA 59.231 50.000 0.65 0.00 0.00 4.02
2 3 1.003233 AGACAAGAATTCCCCGTGTCC 59.997 52.381 18.33 7.48 41.66 4.02
3 4 2.474410 AGACAAGAATTCCCCGTGTC 57.526 50.000 15.92 15.92 41.25 3.67
4 5 2.904434 ACTAGACAAGAATTCCCCGTGT 59.096 45.455 0.65 1.69 0.00 4.49
5 6 3.611766 ACTAGACAAGAATTCCCCGTG 57.388 47.619 0.65 0.00 0.00 4.94
6 7 4.081254 GGTTACTAGACAAGAATTCCCCGT 60.081 45.833 0.65 0.00 0.00 5.28
7 8 4.081309 TGGTTACTAGACAAGAATTCCCCG 60.081 45.833 0.65 0.00 0.00 5.73
8 9 5.429130 CTGGTTACTAGACAAGAATTCCCC 58.571 45.833 0.65 0.00 0.00 4.81
9 10 4.876679 GCTGGTTACTAGACAAGAATTCCC 59.123 45.833 0.65 0.00 0.00 3.97
10 11 5.488341 TGCTGGTTACTAGACAAGAATTCC 58.512 41.667 0.65 0.00 0.00 3.01
11 12 6.258947 GGATGCTGGTTACTAGACAAGAATTC 59.741 42.308 0.00 0.00 0.00 2.17
12 13 6.069963 AGGATGCTGGTTACTAGACAAGAATT 60.070 38.462 0.00 0.00 0.00 2.17
13 14 5.426833 AGGATGCTGGTTACTAGACAAGAAT 59.573 40.000 0.00 0.00 0.00 2.40
14 15 4.777896 AGGATGCTGGTTACTAGACAAGAA 59.222 41.667 0.00 0.00 0.00 2.52
15 16 4.353777 AGGATGCTGGTTACTAGACAAGA 58.646 43.478 0.00 0.00 0.00 3.02
16 17 4.744795 AGGATGCTGGTTACTAGACAAG 57.255 45.455 0.00 0.00 0.00 3.16
17 18 4.649674 CCTAGGATGCTGGTTACTAGACAA 59.350 45.833 1.05 0.00 34.50 3.18
18 19 4.215908 CCTAGGATGCTGGTTACTAGACA 58.784 47.826 1.05 0.00 34.50 3.41
19 20 3.006003 GCCTAGGATGCTGGTTACTAGAC 59.994 52.174 14.75 0.00 34.50 2.59
20 21 3.117093 AGCCTAGGATGCTGGTTACTAGA 60.117 47.826 14.75 0.00 37.76 2.43
21 22 3.235200 AGCCTAGGATGCTGGTTACTAG 58.765 50.000 14.75 0.00 37.76 2.57
22 23 3.330126 AGCCTAGGATGCTGGTTACTA 57.670 47.619 14.75 0.00 37.76 1.82
23 24 2.182516 AGCCTAGGATGCTGGTTACT 57.817 50.000 14.75 0.00 37.76 2.24
24 25 3.804063 GCTTAGCCTAGGATGCTGGTTAC 60.804 52.174 14.75 0.00 39.91 2.50
25 26 2.368875 GCTTAGCCTAGGATGCTGGTTA 59.631 50.000 14.75 0.00 39.91 2.85
26 27 1.141858 GCTTAGCCTAGGATGCTGGTT 59.858 52.381 14.75 0.00 39.91 3.67
27 28 0.761802 GCTTAGCCTAGGATGCTGGT 59.238 55.000 14.75 0.00 39.91 4.00
28 29 1.055040 AGCTTAGCCTAGGATGCTGG 58.945 55.000 14.75 0.00 39.91 4.85
29 30 1.690893 TCAGCTTAGCCTAGGATGCTG 59.309 52.381 25.82 25.82 46.21 4.41
30 31 1.969923 CTCAGCTTAGCCTAGGATGCT 59.030 52.381 14.75 9.81 42.81 3.79
48 49 6.426937 TGCTGGTTACTGTATTTCTGAAACTC 59.573 38.462 4.73 2.61 0.00 3.01
75 76 2.352805 GGGTGAAGTCTGCCAGGG 59.647 66.667 0.00 0.00 0.00 4.45
80 81 1.541588 GTGAATTGGGGTGAAGTCTGC 59.458 52.381 0.00 0.00 0.00 4.26
85 86 2.162681 GGTGAGTGAATTGGGGTGAAG 58.837 52.381 0.00 0.00 0.00 3.02
136 140 2.728435 GGGGTGTATTCCGTCGCCT 61.728 63.158 0.00 0.00 34.96 5.52
142 146 2.203015 CGGCTGGGGTGTATTCCG 60.203 66.667 0.00 0.00 0.00 4.30
176 180 1.371558 GGCGTGTCCTTCCTTCTGT 59.628 57.895 0.00 0.00 0.00 3.41
201 208 0.956633 GGTTTGGTTTCGGGAGGTTC 59.043 55.000 0.00 0.00 0.00 3.62
250 268 2.186903 CATCTGGTAAGCCCGCGT 59.813 61.111 4.92 0.00 35.15 6.01
415 440 1.621672 CCTCCTGAACCCCTCTCTGC 61.622 65.000 0.00 0.00 0.00 4.26
578 617 1.337817 CCTGTCTCGCACTTCGTTCG 61.338 60.000 0.00 0.00 39.67 3.95
579 618 1.618640 GCCTGTCTCGCACTTCGTTC 61.619 60.000 0.00 0.00 39.67 3.95
580 619 1.664965 GCCTGTCTCGCACTTCGTT 60.665 57.895 0.00 0.00 39.67 3.85
581 620 2.049063 GCCTGTCTCGCACTTCGT 60.049 61.111 0.00 0.00 39.67 3.85
605 645 0.109597 GCTGGACAGAAACGGCATTG 60.110 55.000 3.00 0.00 38.81 2.82
606 646 1.577328 CGCTGGACAGAAACGGCATT 61.577 55.000 3.00 0.00 38.90 3.56
607 647 2.034879 CGCTGGACAGAAACGGCAT 61.035 57.895 3.00 0.00 38.90 4.40
608 648 2.664851 CGCTGGACAGAAACGGCA 60.665 61.111 3.00 0.00 38.90 5.69
610 650 2.357517 AGCGCTGGACAGAAACGG 60.358 61.111 10.39 0.00 0.00 4.44
685 738 3.650950 TTCAGTGGCCTGGGCTCC 61.651 66.667 21.72 11.69 39.31 4.70
686 739 2.360475 GTTCAGTGGCCTGGGCTC 60.360 66.667 21.72 17.66 39.31 4.70
711 764 2.726691 GGATCGTTGACGTGGCGTG 61.727 63.158 0.00 0.00 41.37 5.34
712 765 2.431942 GGATCGTTGACGTGGCGT 60.432 61.111 0.00 0.00 45.10 5.68
774 847 3.121030 CGCCCCGAGAAAGCACAG 61.121 66.667 0.00 0.00 0.00 3.66
824 897 0.311477 TTACCGTTTGCGAAAAGGCC 59.689 50.000 2.89 0.00 42.80 5.19
833 906 0.535553 TGGACCCAGTTACCGTTTGC 60.536 55.000 0.00 0.00 0.00 3.68
882 971 2.429767 GGACAGTAGGCGGGGGTAC 61.430 68.421 0.00 0.00 0.00 3.34
893 983 4.403432 CGAATAGTAAAGTGGGGGACAGTA 59.597 45.833 0.00 0.00 30.86 2.74
903 993 2.864343 CGGAAGGGCGAATAGTAAAGTG 59.136 50.000 0.00 0.00 0.00 3.16
905 995 1.865340 GCGGAAGGGCGAATAGTAAAG 59.135 52.381 0.00 0.00 0.00 1.85
906 996 1.207570 TGCGGAAGGGCGAATAGTAAA 59.792 47.619 0.00 0.00 35.06 2.01
907 997 0.825410 TGCGGAAGGGCGAATAGTAA 59.175 50.000 0.00 0.00 35.06 2.24
919 1009 0.804989 GACCAAACTGGATGCGGAAG 59.195 55.000 0.00 0.00 40.96 3.46
927 1017 1.072505 GGAAGGCGACCAAACTGGA 59.927 57.895 0.00 0.00 40.96 3.86
931 1021 0.446616 GAATCGGAAGGCGACCAAAC 59.553 55.000 0.00 0.00 0.00 2.93
934 1024 1.879737 TTCGAATCGGAAGGCGACCA 61.880 55.000 1.76 0.00 31.91 4.02
961 1051 1.014044 TGTCGACTGCTGCGGATTTC 61.014 55.000 17.92 1.22 0.00 2.17
1087 1190 4.111375 TCGAAATCGAAAGAGAAGAGGG 57.889 45.455 2.51 0.00 46.30 4.30
1136 1265 3.490761 CCAAAACGTCAGCCAACAAATCT 60.491 43.478 0.00 0.00 0.00 2.40
1179 1311 2.125147 CCTCGCCGCCTGATGAAA 60.125 61.111 0.00 0.00 0.00 2.69
1180 1312 2.578163 CTTCCTCGCCGCCTGATGAA 62.578 60.000 0.00 0.00 0.00 2.57
1365 1497 4.021925 GGCGTGGCTCTGGAACCT 62.022 66.667 0.00 0.00 0.00 3.50
1367 1499 4.681978 ACGGCGTGGCTCTGGAAC 62.682 66.667 13.76 0.00 0.00 3.62
1540 1672 1.513586 GACTCACTAACGGCGTCGG 60.514 63.158 15.17 11.94 41.39 4.79
1542 1674 1.513586 CCGACTCACTAACGGCGTC 60.514 63.158 15.17 0.00 40.19 5.19
1555 1687 3.261897 ACCAGAATCAACTCATTCCGACT 59.738 43.478 0.00 0.00 33.79 4.18
1556 1688 3.600388 ACCAGAATCAACTCATTCCGAC 58.400 45.455 0.00 0.00 33.79 4.79
1574 1712 5.830991 AGCAATTAGGAACAAACTACAACCA 59.169 36.000 0.00 0.00 0.00 3.67
1663 1806 9.689976 CAAACCAAAAGTAACATCATCACATAA 57.310 29.630 0.00 0.00 0.00 1.90
1735 1885 2.035961 ACAAGAGCTGAGTCGTTGCTAA 59.964 45.455 0.00 0.00 37.16 3.09
1736 1886 1.613925 ACAAGAGCTGAGTCGTTGCTA 59.386 47.619 0.00 0.00 37.16 3.49
1743 1893 1.667467 GGACACGACAAGAGCTGAGTC 60.667 57.143 0.00 0.00 0.00 3.36
1744 1894 0.315568 GGACACGACAAGAGCTGAGT 59.684 55.000 0.00 0.00 0.00 3.41
1745 1895 0.600557 AGGACACGACAAGAGCTGAG 59.399 55.000 0.00 0.00 0.00 3.35
1746 1896 1.040646 AAGGACACGACAAGAGCTGA 58.959 50.000 0.00 0.00 0.00 4.26
1748 1898 1.040646 TCAAGGACACGACAAGAGCT 58.959 50.000 0.00 0.00 0.00 4.09
1750 1900 2.611518 GGATCAAGGACACGACAAGAG 58.388 52.381 0.00 0.00 0.00 2.85
1751 1901 1.275291 GGGATCAAGGACACGACAAGA 59.725 52.381 0.00 0.00 0.00 3.02
1752 1902 1.001974 TGGGATCAAGGACACGACAAG 59.998 52.381 0.00 0.00 0.00 3.16
1780 1930 2.158449 CACGCAGGAATCAAGACAGAAC 59.842 50.000 0.00 0.00 0.00 3.01
1785 1935 1.523758 AACCACGCAGGAATCAAGAC 58.476 50.000 0.93 0.00 41.22 3.01
1794 1944 1.605202 CCCAAATCAAAACCACGCAGG 60.605 52.381 0.00 0.00 45.67 4.85
1801 1975 2.871633 CAGCACAACCCAAATCAAAACC 59.128 45.455 0.00 0.00 0.00 3.27
1838 2453 0.795085 ACGACAGAACGAGTAGACCG 59.205 55.000 0.00 0.00 37.03 4.79
1841 2456 1.073964 CCGACGACAGAACGAGTAGA 58.926 55.000 0.00 0.00 37.03 2.59
1846 2461 4.394078 CCGCCGACGACAGAACGA 62.394 66.667 0.00 0.00 43.93 3.85
1869 2484 1.003839 GGACAGACGGTTGCATCCA 60.004 57.895 14.13 0.00 0.00 3.41
1873 2488 2.279851 CGTGGACAGACGGTTGCA 60.280 61.111 0.00 0.00 35.65 4.08
1886 2501 3.680786 TGTCTGACCTCGCCGTGG 61.681 66.667 3.22 3.22 0.00 4.94
1899 2514 2.032054 CACAAGCATCACAAACGTGTCT 59.968 45.455 0.00 0.00 35.07 3.41
1908 2523 0.179032 AACCGTCCACAAGCATCACA 60.179 50.000 0.00 0.00 0.00 3.58
1938 2555 1.714414 CGTGAGTCGGTAGGTCGAG 59.286 63.158 0.00 0.00 40.01 4.04
1973 2597 5.476945 AGCAAGGAAATATTCAAACTCCGTT 59.523 36.000 0.00 0.00 0.00 4.44
2056 2682 1.266718 GCGCCACAATCTTCTCAACAA 59.733 47.619 0.00 0.00 0.00 2.83
2123 3111 6.530601 AAGATAAGTACATGCCCCCTTAAT 57.469 37.500 0.00 0.00 0.00 1.40
2124 3112 5.987019 AAGATAAGTACATGCCCCCTTAA 57.013 39.130 0.00 0.00 0.00 1.85
2128 3116 3.070590 ACGTAAGATAAGTACATGCCCCC 59.929 47.826 0.00 0.00 43.62 5.40
2130 3118 5.197682 AGACGTAAGATAAGTACATGCCC 57.802 43.478 0.00 0.00 43.62 5.36
2131 3119 5.050972 GCAAGACGTAAGATAAGTACATGCC 60.051 44.000 0.00 0.00 43.62 4.40
2132 3120 5.518847 TGCAAGACGTAAGATAAGTACATGC 59.481 40.000 0.00 0.00 43.62 4.06
2137 3125 9.811995 AATTACATGCAAGACGTAAGATAAGTA 57.188 29.630 0.00 0.00 43.62 2.24
2143 3131 8.653338 GTTCTAAATTACATGCAAGACGTAAGA 58.347 33.333 0.00 0.00 43.62 2.10
2147 3135 8.542497 TTAGTTCTAAATTACATGCAAGACGT 57.458 30.769 0.00 0.00 0.00 4.34
2148 3136 9.988350 ATTTAGTTCTAAATTACATGCAAGACG 57.012 29.630 10.79 0.00 0.00 4.18
2171 3432 5.796424 AATGCAAGTCAAGAACTGGATTT 57.204 34.783 0.00 0.00 38.58 2.17
2306 3569 3.618351 TGAAGTTACCACCCGTGAAAAA 58.382 40.909 0.00 0.00 0.00 1.94
2307 3570 3.207778 CTGAAGTTACCACCCGTGAAAA 58.792 45.455 0.00 0.00 0.00 2.29
2308 3571 2.171027 ACTGAAGTTACCACCCGTGAAA 59.829 45.455 0.00 0.00 0.00 2.69
2309 3572 1.764134 ACTGAAGTTACCACCCGTGAA 59.236 47.619 0.00 0.00 0.00 3.18
2310 3573 1.416243 ACTGAAGTTACCACCCGTGA 58.584 50.000 0.00 0.00 0.00 4.35
2311 3574 2.249844 AACTGAAGTTACCACCCGTG 57.750 50.000 0.00 0.00 36.32 4.94
2312 3575 3.286329 AAAACTGAAGTTACCACCCGT 57.714 42.857 0.00 0.00 37.25 5.28
2395 3659 9.922305 CTTCGGATATAAAAACTGTCTGAAATC 57.078 33.333 0.00 0.00 34.74 2.17
2397 3661 8.842358 ACTTCGGATATAAAAACTGTCTGAAA 57.158 30.769 0.00 0.00 34.74 2.69
2475 3752 8.692110 TGAATGTGAATAGTTTCAAATGCATC 57.308 30.769 0.00 0.00 39.35 3.91


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

AutoCloner maintained by Alex Coulton.