Multiple sequence alignment - TraesCS3B01G410800

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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 TraesCS3B01G410800 chr3B 100.000 3014 0 0 1 3014 647541341 647544354 0.000000e+00 5566.0
1 TraesCS3B01G410800 chr3B 86.318 497 54 7 1846 2338 647470134 647470620 2.060000e-146 529.0
2 TraesCS3B01G410800 chr3B 75.020 1261 233 52 1005 2231 647465536 647466748 2.680000e-140 508.0
3 TraesCS3B01G410800 chr3B 76.439 556 87 29 289 830 417226614 417226089 8.290000e-66 261.0
4 TraesCS3B01G410800 chr3B 94.737 38 2 0 2977 3014 647472924 647472961 3.240000e-05 60.2
5 TraesCS3B01G410800 chr3D 92.140 1883 82 16 924 2793 484804991 484806820 0.000000e+00 2597.0
6 TraesCS3B01G410800 chr3D 84.763 2028 214 63 998 2974 484726149 484728132 0.000000e+00 1945.0
7 TraesCS3B01G410800 chr3D 90.793 782 60 2 924 1699 484734403 484735178 0.000000e+00 1035.0
8 TraesCS3B01G410800 chr3D 84.064 935 95 26 1714 2618 484735942 484736852 0.000000e+00 852.0
9 TraesCS3B01G410800 chr3D 80.910 901 144 20 16 896 484733176 484734068 0.000000e+00 686.0
10 TraesCS3B01G410800 chr3D 74.938 1217 223 51 1048 2230 484672904 484674072 1.620000e-132 483.0
11 TraesCS3B01G410800 chr3D 94.624 186 8 2 2831 3014 484806829 484807014 1.370000e-73 287.0
12 TraesCS3B01G410800 chr3D 81.481 162 28 2 1058 1218 28217892 28217732 6.780000e-27 132.0
13 TraesCS3B01G410800 chr3D 97.368 38 1 0 2977 3014 484728177 484728214 6.970000e-07 65.8
14 TraesCS3B01G410800 chr3D 97.368 38 1 0 2977 3014 484737291 484737328 6.970000e-07 65.8
15 TraesCS3B01G410800 chr3A 88.474 2117 142 52 924 2974 627785353 627787433 0.000000e+00 2464.0
16 TraesCS3B01G410800 chr3A 88.029 2105 170 35 924 3014 627817195 627819231 0.000000e+00 2416.0
17 TraesCS3B01G410800 chr3A 82.111 682 98 18 14 684 627792757 627793425 2.030000e-156 562.0
18 TraesCS3B01G410800 chr3A 85.577 416 26 12 2600 3014 627705953 627706335 3.620000e-109 405.0
19 TraesCS3B01G410800 chr3A 96.774 31 1 0 2977 3007 627787478 627787508 5.000000e-03 52.8
20 TraesCS3B01G410800 chr7D 79.753 647 120 11 128 768 259298837 259299478 2.740000e-125 459.0
21 TraesCS3B01G410800 chr2B 78.541 713 131 15 131 830 67083183 67083886 1.650000e-122 449.0
22 TraesCS3B01G410800 chr2B 76.547 614 113 16 128 737 152454263 152453677 1.050000e-79 307.0
23 TraesCS3B01G410800 chr2B 78.344 471 74 18 368 828 512634292 512633840 2.290000e-71 279.0
24 TraesCS3B01G410800 chr2B 77.622 286 47 14 555 828 34805724 34806004 1.120000e-34 158.0
25 TraesCS3B01G410800 chr5D 78.191 564 87 24 131 687 334253476 334252942 8.060000e-86 327.0
26 TraesCS3B01G410800 chr5D 75.772 615 111 31 225 827 529829871 529830459 2.960000e-70 276.0
27 TraesCS3B01G410800 chr5D 80.702 228 36 7 607 830 224867270 224867047 1.440000e-38 171.0
28 TraesCS3B01G410800 chr5A 75.312 721 130 33 128 833 661015147 661015834 4.880000e-78 302.0
29 TraesCS3B01G410800 chr5A 76.748 572 112 15 264 831 522857910 522858464 1.760000e-77 300.0
30 TraesCS3B01G410800 chr5A 75.726 585 102 31 128 702 381696282 381695728 1.070000e-64 257.0
31 TraesCS3B01G410800 chr1A 79.747 395 60 11 356 737 322793991 322793604 4.950000e-68 268.0
32 TraesCS3B01G410800 chr2A 76.680 506 87 19 336 829 553434021 553434507 4.990000e-63 252.0
33 TraesCS3B01G410800 chr4B 74.882 637 112 30 207 830 618071987 618072588 2.320000e-61 246.0
34 TraesCS3B01G410800 chrUn 77.352 287 46 16 555 828 240836831 240837111 5.200000e-33 152.0
35 TraesCS3B01G410800 chr1D 82.609 161 28 0 1058 1218 456280423 456280263 3.130000e-30 143.0


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 TraesCS3B01G410800 chr3B 647541341 647544354 3013 False 5566.000000 5566 100.000000 1 3014 1 chr3B.!!$F1 3013
1 TraesCS3B01G410800 chr3B 647465536 647472961 7425 False 365.733333 529 85.358333 1005 3014 3 chr3B.!!$F2 2009
2 TraesCS3B01G410800 chr3B 417226089 417226614 525 True 261.000000 261 76.439000 289 830 1 chr3B.!!$R1 541
3 TraesCS3B01G410800 chr3D 484804991 484807014 2023 False 1442.000000 2597 93.382000 924 3014 2 chr3D.!!$F4 2090
4 TraesCS3B01G410800 chr3D 484726149 484728214 2065 False 1005.400000 1945 91.065500 998 3014 2 chr3D.!!$F2 2016
5 TraesCS3B01G410800 chr3D 484733176 484737328 4152 False 659.700000 1035 88.283750 16 3014 4 chr3D.!!$F3 2998
6 TraesCS3B01G410800 chr3D 484672904 484674072 1168 False 483.000000 483 74.938000 1048 2230 1 chr3D.!!$F1 1182
7 TraesCS3B01G410800 chr3A 627817195 627819231 2036 False 2416.000000 2416 88.029000 924 3014 1 chr3A.!!$F3 2090
8 TraesCS3B01G410800 chr3A 627785353 627787508 2155 False 1258.400000 2464 92.624000 924 3007 2 chr3A.!!$F4 2083
9 TraesCS3B01G410800 chr3A 627792757 627793425 668 False 562.000000 562 82.111000 14 684 1 chr3A.!!$F2 670
10 TraesCS3B01G410800 chr7D 259298837 259299478 641 False 459.000000 459 79.753000 128 768 1 chr7D.!!$F1 640
11 TraesCS3B01G410800 chr2B 67083183 67083886 703 False 449.000000 449 78.541000 131 830 1 chr2B.!!$F2 699
12 TraesCS3B01G410800 chr2B 152453677 152454263 586 True 307.000000 307 76.547000 128 737 1 chr2B.!!$R1 609
13 TraesCS3B01G410800 chr5D 334252942 334253476 534 True 327.000000 327 78.191000 131 687 1 chr5D.!!$R2 556
14 TraesCS3B01G410800 chr5D 529829871 529830459 588 False 276.000000 276 75.772000 225 827 1 chr5D.!!$F1 602
15 TraesCS3B01G410800 chr5A 661015147 661015834 687 False 302.000000 302 75.312000 128 833 1 chr5A.!!$F2 705
16 TraesCS3B01G410800 chr5A 522857910 522858464 554 False 300.000000 300 76.748000 264 831 1 chr5A.!!$F1 567
17 TraesCS3B01G410800 chr5A 381695728 381696282 554 True 257.000000 257 75.726000 128 702 1 chr5A.!!$R1 574
18 TraesCS3B01G410800 chr4B 618071987 618072588 601 False 246.000000 246 74.882000 207 830 1 chr4B.!!$F1 623

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
497 523 0.106708 GCCGCCCATTCATAGAGACA 59.893 55.0 0.0 0.0 0.0 3.41 F
1644 2048 0.029834 CAACGCTTGCATCTATGGGC 59.970 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 2930 0.745845 ATCCAAGCACTGTCATCCGC 60.746 55.0 0.0 0.0 0.0 5.54 R
2680 9279 0.950836 TGATGGCAACCACGAAACTG 59.049 50.0 0.0 0.0 35.8 3.16 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
71 75 9.895138 GTAAATTAATCCTACCTACCTTCACAA 57.105 33.333 0.00 0.00 0.00 3.33
78 83 2.132686 ACCTACCTTCACAACCCTTGT 58.867 47.619 0.00 0.00 46.75 3.16
84 89 1.104577 TTCACAACCCTTGTTCCGGC 61.105 55.000 0.00 0.00 43.23 6.13
101 106 3.025619 CGCCAAGAATCCATCGCC 58.974 61.111 0.00 0.00 0.00 5.54
103 108 2.546494 GCCAAGAATCCATCGCCGG 61.546 63.158 0.00 0.00 0.00 6.13
105 110 1.819208 CAAGAATCCATCGCCGGCA 60.819 57.895 28.98 14.46 0.00 5.69
120 125 2.633657 GCAATGGCCGCGACATAG 59.366 61.111 8.23 0.00 27.35 2.23
122 127 1.436195 GCAATGGCCGCGACATAGAA 61.436 55.000 8.23 0.00 27.35 2.10
123 128 1.229428 CAATGGCCGCGACATAGAAT 58.771 50.000 8.23 0.00 27.35 2.40
171 179 3.665675 GAGGCCGTCCGCACTCAAT 62.666 63.158 0.00 0.00 40.31 2.57
269 285 2.011947 TCCTACACGACATCGACGAAT 58.988 47.619 8.54 0.00 43.02 3.34
342 361 2.283298 GACCTCACGTATACGGAGACA 58.717 52.381 29.59 12.10 44.95 3.41
354 373 0.318699 CGGAGACAGACAAGTTGCGA 60.319 55.000 1.81 0.00 0.00 5.10
361 380 2.213499 CAGACAAGTTGCGAACTCCTT 58.787 47.619 1.81 0.00 41.91 3.36
372 391 2.217429 GAACTCCTTCGAGGATGAGC 57.783 55.000 0.00 0.00 44.81 4.26
491 517 0.250124 CTTACCGCCGCCCATTCATA 60.250 55.000 0.00 0.00 0.00 2.15
497 523 0.106708 GCCGCCCATTCATAGAGACA 59.893 55.000 0.00 0.00 0.00 3.41
508 534 3.908476 TCATAGAGACAGCAGATGGAGT 58.092 45.455 0.00 0.00 0.00 3.85
590 645 2.325484 AGGTTTAGGGCAAGGTTTTGG 58.675 47.619 0.00 0.00 34.79 3.28
678 735 1.169577 AAATCCGCCGTGTTTGCATA 58.830 45.000 0.00 0.00 0.00 3.14
684 741 2.091899 CCGCCGTGTTTGCATAAATTTG 59.908 45.455 0.00 0.00 0.00 2.32
742 804 4.049640 GCGTTGGATGGCGGCAAA 62.050 61.111 18.31 2.40 0.00 3.68
743 805 2.647875 CGTTGGATGGCGGCAAAA 59.352 55.556 18.31 8.46 0.00 2.44
744 806 1.732683 CGTTGGATGGCGGCAAAAC 60.733 57.895 18.31 18.93 0.00 2.43
745 807 1.365633 GTTGGATGGCGGCAAAACA 59.634 52.632 18.31 12.71 0.00 2.83
781 853 2.683933 CTGGTACCCCTGTCCGCT 60.684 66.667 10.07 0.00 0.00 5.52
805 877 2.817839 CGGAGGTGGGAGGAAATTTGTT 60.818 50.000 0.00 0.00 0.00 2.83
862 934 6.751888 AGCAAGGTTAAAACAATGAATATCGC 59.248 34.615 0.00 0.00 0.00 4.58
871 943 8.687824 AAAACAATGAATATCGCGAAATCTTT 57.312 26.923 15.24 12.87 0.00 2.52
876 948 6.415798 TGAATATCGCGAAATCTTTGTTCA 57.584 33.333 15.24 12.92 0.00 3.18
881 953 4.245660 TCGCGAAATCTTTGTTCATCTCT 58.754 39.130 6.20 0.00 0.00 3.10
885 957 6.360681 CGCGAAATCTTTGTTCATCTCTTTTT 59.639 34.615 0.00 0.00 0.00 1.94
892 964 7.436118 TCTTTGTTCATCTCTTTTTCATTGGG 58.564 34.615 0.00 0.00 0.00 4.12
896 968 8.243961 TGTTCATCTCTTTTTCATTGGGTTAA 57.756 30.769 0.00 0.00 0.00 2.01
898 970 9.196552 GTTCATCTCTTTTTCATTGGGTTAAAG 57.803 33.333 0.00 0.00 0.00 1.85
900 972 9.142014 TCATCTCTTTTTCATTGGGTTAAAGAA 57.858 29.630 0.00 0.00 35.22 2.52
902 974 9.933723 ATCTCTTTTTCATTGGGTTAAAGAATG 57.066 29.630 0.00 0.00 35.22 2.67
986 1372 0.107361 CCCCAACCCAATCCGTAGAC 60.107 60.000 0.00 0.00 0.00 2.59
987 1373 0.461339 CCCAACCCAATCCGTAGACG 60.461 60.000 0.00 0.00 39.44 4.18
1084 1470 1.728069 GACCTACTGCGCGAGATCA 59.272 57.895 12.10 0.00 0.00 2.92
1319 1717 3.502990 TACAAGTCAACGGCCGCGT 62.503 57.895 28.58 11.36 0.00 6.01
1544 1945 0.472471 AAAGTGGTCGTGGTGGACAT 59.528 50.000 0.00 0.00 38.70 3.06
1644 2048 0.029834 CAACGCTTGCATCTATGGGC 59.970 55.000 0.00 0.00 0.00 5.36
1762 2915 2.028112 ACGCTAGCTGTGATCAAAAGGA 60.028 45.455 13.93 0.00 0.00 3.36
1904 6805 2.047061 CCGAATGTGGGATAGGAAGGA 58.953 52.381 0.00 0.00 0.00 3.36
1930 6831 1.474320 GCTATGGTGTTGCCGTATGGA 60.474 52.381 4.73 0.00 38.03 3.41
1963 6864 4.019792 TCCATTGAACTGCAGAAGCTAA 57.980 40.909 23.35 8.29 42.74 3.09
2013 6914 9.499212 AGGAACTGGTCACATATAGTGCGTTAG 62.499 44.444 0.00 0.00 43.21 2.34
2064 6965 3.370315 GGGTGCACTCATCTCTCTTCATT 60.370 47.826 17.98 0.00 0.00 2.57
2140 7044 8.380099 TGTACACCTATTATCCTTTCACAAGTT 58.620 33.333 0.00 0.00 0.00 2.66
2141 7045 9.227777 GTACACCTATTATCCTTTCACAAGTTT 57.772 33.333 0.00 0.00 0.00 2.66
2142 7046 8.110860 ACACCTATTATCCTTTCACAAGTTTG 57.889 34.615 0.00 0.00 0.00 2.93
2143 7047 7.942341 ACACCTATTATCCTTTCACAAGTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
2144 7048 8.792633 CACCTATTATCCTTTCACAAGTTTGAA 58.207 33.333 0.00 0.00 33.55 2.69
2145 7049 9.014297 ACCTATTATCCTTTCACAAGTTTGAAG 57.986 33.333 0.00 0.00 36.84 3.02
2146 7050 9.014297 CCTATTATCCTTTCACAAGTTTGAAGT 57.986 33.333 0.00 0.00 36.84 3.01
2236 7144 7.681939 ACTGTACTTCTGAAGTGTTCAAAAA 57.318 32.000 28.46 7.23 42.84 1.94
2237 7145 8.281212 ACTGTACTTCTGAAGTGTTCAAAAAT 57.719 30.769 28.46 4.49 42.84 1.82
2238 7146 8.398665 ACTGTACTTCTGAAGTGTTCAAAAATC 58.601 33.333 28.46 9.45 42.84 2.17
2239 7147 8.506168 TGTACTTCTGAAGTGTTCAAAAATCT 57.494 30.769 28.46 3.83 42.84 2.40
2240 7148 8.612619 TGTACTTCTGAAGTGTTCAAAAATCTC 58.387 33.333 28.46 1.06 42.84 2.75
2245 7153 4.340950 TGAAGTGTTCAAAAATCTCCCCAC 59.659 41.667 0.00 0.00 36.59 4.61
2250 7158 5.011023 GTGTTCAAAAATCTCCCCACTGAAT 59.989 40.000 0.00 0.00 0.00 2.57
2255 7167 8.434589 TCAAAAATCTCCCCACTGAATTTATT 57.565 30.769 0.00 0.00 0.00 1.40
2264 7176 5.128499 CCCCACTGAATTTATTGCCATGTTA 59.872 40.000 0.00 0.00 0.00 2.41
2352 7267 9.079833 GTTCTTTTATACTGCTATACACGTGAA 57.920 33.333 25.01 6.19 0.00 3.18
2374 8897 3.840666 AGAGTCAGGAAACAAGGCATCTA 59.159 43.478 0.00 0.00 0.00 1.98
2467 9017 7.538303 TTCTTTGATGCTTTGGTTTTCTTTC 57.462 32.000 0.00 0.00 0.00 2.62
2496 9046 8.458212 GTACTTGTGTACAATACTTACTGTCC 57.542 38.462 0.00 0.00 46.06 4.02
2630 9228 8.950210 ACTGTATAATTCCTTGTTTGACAGATG 58.050 33.333 5.29 0.00 36.22 2.90
2631 9229 9.166173 CTGTATAATTCCTTGTTTGACAGATGA 57.834 33.333 0.00 0.00 34.98 2.92
2632 9230 8.946085 TGTATAATTCCTTGTTTGACAGATGAC 58.054 33.333 0.00 0.00 0.00 3.06
2633 9231 8.946085 GTATAATTCCTTGTTTGACAGATGACA 58.054 33.333 0.00 0.00 0.00 3.58
2634 9232 5.954296 ATTCCTTGTTTGACAGATGACAG 57.046 39.130 0.00 0.00 0.00 3.51
2635 9233 4.687901 TCCTTGTTTGACAGATGACAGA 57.312 40.909 0.00 0.00 0.00 3.41
2636 9234 5.233083 TCCTTGTTTGACAGATGACAGAT 57.767 39.130 0.00 0.00 0.00 2.90
2666 9265 7.362662 ACACTTTGACACTAGCAATGTTATTG 58.637 34.615 0.00 0.00 33.15 1.90
2680 9279 4.314740 TGTTATTGTTTGTGTGGCCTTC 57.685 40.909 3.32 0.00 0.00 3.46
2682 9281 4.202101 TGTTATTGTTTGTGTGGCCTTCAG 60.202 41.667 3.32 0.00 0.00 3.02
2708 9307 3.440173 CGTGGTTGCCATCAGATTTAGTT 59.560 43.478 0.00 0.00 35.28 2.24
2811 9411 4.703379 TTACTTTTGTCCTCCCCGTAAA 57.297 40.909 0.00 0.00 0.00 2.01
2823 9423 5.776716 TCCTCCCCGTAAATTATTAGACGAT 59.223 40.000 12.07 0.00 37.50 3.73
2824 9424 6.947733 TCCTCCCCGTAAATTATTAGACGATA 59.052 38.462 12.07 0.23 37.50 2.92
2825 9425 7.121759 TCCTCCCCGTAAATTATTAGACGATAG 59.878 40.741 12.07 7.32 37.50 2.08
2826 9426 7.121759 CCTCCCCGTAAATTATTAGACGATAGA 59.878 40.741 12.07 6.41 37.50 1.98
2827 9427 8.585471 TCCCCGTAAATTATTAGACGATAGAT 57.415 34.615 12.07 0.00 37.50 1.98
2828 9428 9.028284 TCCCCGTAAATTATTAGACGATAGATT 57.972 33.333 12.07 0.00 37.50 2.40
2829 9429 9.298774 CCCCGTAAATTATTAGACGATAGATTC 57.701 37.037 12.07 0.00 37.50 2.52
2846 9446 8.735315 CGATAGATTCTAGATTGGTAGTGTCAT 58.265 37.037 0.00 0.00 39.76 3.06
2858 9458 7.857734 TTGGTAGTGTCATTGTGTATATTGG 57.142 36.000 0.00 0.00 0.00 3.16
2864 9464 6.038603 AGTGTCATTGTGTATATTGGCACATC 59.961 38.462 9.54 3.39 44.88 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.071479 GTCAAAGGTTAGCGATGTTGGA 58.929 45.455 0.00 0.00 0.00 3.53
1 2 3.074412 AGTCAAAGGTTAGCGATGTTGG 58.926 45.455 0.00 0.00 0.00 3.77
2 3 3.667960 GCAGTCAAAGGTTAGCGATGTTG 60.668 47.826 0.00 0.00 0.00 3.33
3 4 2.484264 GCAGTCAAAGGTTAGCGATGTT 59.516 45.455 0.00 0.00 0.00 2.71
4 5 2.076863 GCAGTCAAAGGTTAGCGATGT 58.923 47.619 0.00 0.00 0.00 3.06
5 6 1.398390 GGCAGTCAAAGGTTAGCGATG 59.602 52.381 0.00 0.00 0.00 3.84
6 7 1.679032 GGGCAGTCAAAGGTTAGCGAT 60.679 52.381 0.00 0.00 0.00 4.58
7 8 0.321298 GGGCAGTCAAAGGTTAGCGA 60.321 55.000 0.00 0.00 0.00 4.93
8 9 0.321653 AGGGCAGTCAAAGGTTAGCG 60.322 55.000 0.00 0.00 0.00 4.26
9 10 2.781681 TAGGGCAGTCAAAGGTTAGC 57.218 50.000 0.00 0.00 0.00 3.09
10 11 7.110155 TCTTTTATAGGGCAGTCAAAGGTTAG 58.890 38.462 0.00 0.00 0.00 2.34
11 12 7.023171 TCTTTTATAGGGCAGTCAAAGGTTA 57.977 36.000 0.00 0.00 0.00 2.85
12 13 5.887754 TCTTTTATAGGGCAGTCAAAGGTT 58.112 37.500 0.00 0.00 0.00 3.50
78 83 2.437716 GGATTCTTGGCGCCGGAA 60.438 61.111 28.23 28.23 0.00 4.30
84 89 2.885676 CGGCGATGGATTCTTGGCG 61.886 63.158 0.00 0.00 42.05 5.69
103 108 1.436195 TTCTATGTCGCGGCCATTGC 61.436 55.000 8.89 0.00 0.00 3.56
105 110 1.512926 GATTCTATGTCGCGGCCATT 58.487 50.000 8.89 0.00 0.00 3.16
123 128 1.144716 GCTGCTCCACGATGATGGA 59.855 57.895 0.00 0.00 46.92 3.41
171 179 2.280254 TTTTTGTCGAGCGGCGGA 60.280 55.556 9.78 0.00 41.33 5.54
269 285 1.074084 TCGAACCAACCTGCCCAATAA 59.926 47.619 0.00 0.00 0.00 1.40
332 350 2.671351 CGCAACTTGTCTGTCTCCGTAT 60.671 50.000 0.00 0.00 0.00 3.06
342 361 2.484889 GAAGGAGTTCGCAACTTGTCT 58.515 47.619 3.56 1.08 43.03 3.41
361 380 2.364186 TGCCCTGCTCATCCTCGA 60.364 61.111 0.00 0.00 0.00 4.04
405 424 3.278592 GAGACGGACCGACCCACAC 62.279 68.421 23.38 2.80 34.64 3.82
484 510 5.211174 TCCATCTGCTGTCTCTATGAATG 57.789 43.478 0.00 0.00 0.00 2.67
491 517 2.024464 ACCTACTCCATCTGCTGTCTCT 60.024 50.000 0.00 0.00 0.00 3.10
497 523 1.490574 GACCACCTACTCCATCTGCT 58.509 55.000 0.00 0.00 0.00 4.24
508 534 2.598099 TGTGTCGGCGACCACCTA 60.598 61.111 34.28 15.09 0.00 3.08
702 761 6.293900 CGCTGCCCACATACATTTCAAATATA 60.294 38.462 0.00 0.00 0.00 0.86
781 853 0.546747 ATTTCCTCCCACCTCCGTCA 60.547 55.000 0.00 0.00 0.00 4.35
788 860 2.299013 GACCAACAAATTTCCTCCCACC 59.701 50.000 0.00 0.00 0.00 4.61
790 862 2.235016 CGACCAACAAATTTCCTCCCA 58.765 47.619 0.00 0.00 0.00 4.37
805 877 2.264480 CATCTCCAACGGCGACCA 59.736 61.111 16.62 0.00 0.00 4.02
862 934 8.786937 TGAAAAAGAGATGAACAAAGATTTCG 57.213 30.769 0.00 0.00 0.00 3.46
871 943 6.729690 AACCCAATGAAAAAGAGATGAACA 57.270 33.333 0.00 0.00 0.00 3.18
876 948 9.933723 CATTCTTTAACCCAATGAAAAAGAGAT 57.066 29.630 0.00 0.00 37.45 2.75
908 980 9.549078 TGTGAAATGTGTTAGTCTTGTGTATAA 57.451 29.630 0.00 0.00 0.00 0.98
910 982 7.715249 AGTGTGAAATGTGTTAGTCTTGTGTAT 59.285 33.333 0.00 0.00 0.00 2.29
911 983 7.045416 AGTGTGAAATGTGTTAGTCTTGTGTA 58.955 34.615 0.00 0.00 0.00 2.90
912 984 5.880332 AGTGTGAAATGTGTTAGTCTTGTGT 59.120 36.000 0.00 0.00 0.00 3.72
913 985 6.363577 AGTGTGAAATGTGTTAGTCTTGTG 57.636 37.500 0.00 0.00 0.00 3.33
914 986 5.527582 GGAGTGTGAAATGTGTTAGTCTTGT 59.472 40.000 0.00 0.00 0.00 3.16
915 987 5.049405 GGGAGTGTGAAATGTGTTAGTCTTG 60.049 44.000 0.00 0.00 0.00 3.02
916 988 5.063880 GGGAGTGTGAAATGTGTTAGTCTT 58.936 41.667 0.00 0.00 0.00 3.01
917 989 4.505039 GGGGAGTGTGAAATGTGTTAGTCT 60.505 45.833 0.00 0.00 0.00 3.24
918 990 3.751698 GGGGAGTGTGAAATGTGTTAGTC 59.248 47.826 0.00 0.00 0.00 2.59
919 991 3.497942 GGGGGAGTGTGAAATGTGTTAGT 60.498 47.826 0.00 0.00 0.00 2.24
920 992 3.081804 GGGGGAGTGTGAAATGTGTTAG 58.918 50.000 0.00 0.00 0.00 2.34
921 993 2.443632 TGGGGGAGTGTGAAATGTGTTA 59.556 45.455 0.00 0.00 0.00 2.41
1084 1470 3.774336 TGGGGGTAGGCGGAGGAT 61.774 66.667 0.00 0.00 0.00 3.24
1152 1538 4.090588 TTGGGGTCGGTGGCGATC 62.091 66.667 0.00 0.00 0.00 3.69
1319 1717 2.220586 TCGACCAACCTCCATGGCA 61.221 57.895 6.96 0.00 41.89 4.92
1644 2048 2.789208 CTGCGATTACCAACAGCAATG 58.211 47.619 0.00 0.00 37.38 2.82
1777 2930 0.745845 ATCCAAGCACTGTCATCCGC 60.746 55.000 0.00 0.00 0.00 5.54
1904 6805 1.202114 CGGCAACACCATAGCAATTGT 59.798 47.619 7.40 0.00 39.03 2.71
1930 6831 5.337009 GCAGTTCAATGGATTTCCTCAACAT 60.337 40.000 0.00 0.00 36.82 2.71
1963 6864 4.757692 TCAATCTTAAACCCCAACCCAAT 58.242 39.130 0.00 0.00 0.00 3.16
2064 6965 2.551032 CTGCATTGACTCAAGCTGAACA 59.449 45.455 11.87 0.00 0.00 3.18
2140 7044 9.219603 CAGTTACCTTCATCATAGAAACTTCAA 57.780 33.333 0.00 0.00 0.00 2.69
2141 7045 8.375506 ACAGTTACCTTCATCATAGAAACTTCA 58.624 33.333 0.00 0.00 0.00 3.02
2142 7046 8.779354 ACAGTTACCTTCATCATAGAAACTTC 57.221 34.615 0.00 0.00 0.00 3.01
2143 7047 9.003658 CAACAGTTACCTTCATCATAGAAACTT 57.996 33.333 0.00 0.00 0.00 2.66
2144 7048 7.607991 CCAACAGTTACCTTCATCATAGAAACT 59.392 37.037 0.00 0.00 0.00 2.66
2145 7049 7.606456 TCCAACAGTTACCTTCATCATAGAAAC 59.394 37.037 0.00 0.00 0.00 2.78
2146 7050 7.685481 TCCAACAGTTACCTTCATCATAGAAA 58.315 34.615 0.00 0.00 0.00 2.52
2203 7107 9.694137 ACACTTCAGAAGTACAGTAAAGTTATC 57.306 33.333 15.73 0.00 40.46 1.75
2236 7144 4.218312 GGCAATAAATTCAGTGGGGAGAT 58.782 43.478 0.00 0.00 0.00 2.75
2237 7145 3.011144 TGGCAATAAATTCAGTGGGGAGA 59.989 43.478 0.00 0.00 0.00 3.71
2238 7146 3.364549 TGGCAATAAATTCAGTGGGGAG 58.635 45.455 0.00 0.00 0.00 4.30
2239 7147 3.464720 TGGCAATAAATTCAGTGGGGA 57.535 42.857 0.00 0.00 0.00 4.81
2240 7148 3.451902 ACATGGCAATAAATTCAGTGGGG 59.548 43.478 0.00 0.00 0.00 4.96
2255 7167 6.540551 TCGCTAACATAGAAAATAACATGGCA 59.459 34.615 0.00 0.00 0.00 4.92
2264 7176 5.874810 TGCTCAAGTCGCTAACATAGAAAAT 59.125 36.000 0.00 0.00 0.00 1.82
2302 7214 6.017275 ACAATAGTACACTACCATCGTAGCTC 60.017 42.308 0.00 0.00 45.11 4.09
2304 7216 6.069684 ACAATAGTACACTACCATCGTAGC 57.930 41.667 0.00 0.00 45.11 3.58
2343 7255 3.382227 TGTTTCCTGACTCTTCACGTGTA 59.618 43.478 16.51 4.82 0.00 2.90
2345 7257 2.821546 TGTTTCCTGACTCTTCACGTG 58.178 47.619 9.94 9.94 0.00 4.49
2346 7258 3.458189 CTTGTTTCCTGACTCTTCACGT 58.542 45.455 0.00 0.00 0.00 4.49
2347 7259 2.802816 CCTTGTTTCCTGACTCTTCACG 59.197 50.000 0.00 0.00 0.00 4.35
2352 7267 2.641815 AGATGCCTTGTTTCCTGACTCT 59.358 45.455 0.00 0.00 0.00 3.24
2398 8948 4.416620 CGTCCAGCTAACAACAACAAAAA 58.583 39.130 0.00 0.00 0.00 1.94
2399 8949 3.732471 GCGTCCAGCTAACAACAACAAAA 60.732 43.478 0.00 0.00 44.04 2.44
2400 8950 2.223386 GCGTCCAGCTAACAACAACAAA 60.223 45.455 0.00 0.00 44.04 2.83
2403 8953 3.748021 GCGTCCAGCTAACAACAAC 57.252 52.632 0.00 0.00 44.04 3.32
2496 9046 3.123804 CCTTGAAAGTCCGATATGACCG 58.876 50.000 0.00 0.00 35.83 4.79
2630 9228 5.403246 AGTGTCAAAGTGTATCGATCTGTC 58.597 41.667 0.00 0.00 0.00 3.51
2631 9229 5.392767 AGTGTCAAAGTGTATCGATCTGT 57.607 39.130 0.00 0.00 0.00 3.41
2632 9230 5.457148 GCTAGTGTCAAAGTGTATCGATCTG 59.543 44.000 0.00 0.00 0.00 2.90
2633 9231 5.125578 TGCTAGTGTCAAAGTGTATCGATCT 59.874 40.000 0.00 0.00 0.00 2.75
2634 9232 5.340803 TGCTAGTGTCAAAGTGTATCGATC 58.659 41.667 0.00 0.00 0.00 3.69
2635 9233 5.324784 TGCTAGTGTCAAAGTGTATCGAT 57.675 39.130 2.16 2.16 0.00 3.59
2636 9234 4.776795 TGCTAGTGTCAAAGTGTATCGA 57.223 40.909 0.00 0.00 0.00 3.59
2666 9265 2.794631 CGAAACTGAAGGCCACACAAAC 60.795 50.000 5.01 0.00 0.00 2.93
2680 9279 0.950836 TGATGGCAACCACGAAACTG 59.049 50.000 0.00 0.00 35.80 3.16
2682 9281 1.234821 TCTGATGGCAACCACGAAAC 58.765 50.000 0.00 0.00 35.80 2.78
2823 9423 9.201989 ACAATGACACTACCAATCTAGAATCTA 57.798 33.333 0.00 0.00 0.00 1.98
2824 9424 7.984050 CACAATGACACTACCAATCTAGAATCT 59.016 37.037 0.00 0.00 0.00 2.40
2825 9425 7.766278 ACACAATGACACTACCAATCTAGAATC 59.234 37.037 0.00 0.00 0.00 2.52
2826 9426 7.624549 ACACAATGACACTACCAATCTAGAAT 58.375 34.615 0.00 0.00 0.00 2.40
2827 9427 7.004555 ACACAATGACACTACCAATCTAGAA 57.995 36.000 0.00 0.00 0.00 2.10
2828 9428 6.605471 ACACAATGACACTACCAATCTAGA 57.395 37.500 0.00 0.00 0.00 2.43
2858 9458 6.072838 CCCATGTTATAAGATCAGTGATGTGC 60.073 42.308 11.20 0.00 0.00 4.57
2864 9464 4.717877 TGGCCCATGTTATAAGATCAGTG 58.282 43.478 0.00 0.00 0.00 3.66
2877 9477 2.028561 AATTTCAACCTGGCCCATGT 57.971 45.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.