Multiple sequence alignment - TraesCS1A01G373200

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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 TraesCS1A01G373200 chr1A 100.000 4561 0 0 1 4561 549417329 549421889 0.000000e+00 8423.0
1 TraesCS1A01G373200 chr1D 90.280 3899 223 79 722 4561 455782336 455786137 0.000000e+00 4957.0
2 TraesCS1A01G373200 chr1B 86.619 1958 133 52 665 2538 626224285 626226197 0.000000e+00 2045.0
3 TraesCS1A01G373200 chr1B 92.884 787 37 7 3794 4561 626227835 626228621 0.000000e+00 1125.0
4 TraesCS1A01G373200 chr1B 87.379 824 58 25 2953 3741 626227004 626227816 0.000000e+00 904.0
5 TraesCS1A01G373200 chr1B 91.549 142 7 2 2820 2956 626226741 626226882 1.670000e-44 191.0
6 TraesCS1A01G373200 chr6A 98.363 672 8 2 1 670 88099343 88100013 0.000000e+00 1177.0
7 TraesCS1A01G373200 chr6A 96.035 227 4 1 445 671 479407808 479408029 9.330000e-97 364.0
8 TraesCS1A01G373200 chr7D 98.358 670 10 1 1 670 28364992 28364324 0.000000e+00 1175.0
9 TraesCS1A01G373200 chr7A 98.206 669 12 0 1 669 671192924 671193592 0.000000e+00 1170.0
10 TraesCS1A01G373200 chr5B 97.329 674 10 2 1 672 522904138 522903471 0.000000e+00 1138.0
11 TraesCS1A01G373200 chr7B 92.564 780 46 3 3794 4561 399793814 399794593 0.000000e+00 1109.0
12 TraesCS1A01G373200 chr7B 88.873 701 49 13 3067 3741 399793098 399793795 0.000000e+00 835.0
13 TraesCS1A01G373200 chr7B 89.157 332 22 3 1376 1700 399792699 399793023 7.110000e-108 401.0
14 TraesCS1A01G373200 chr7B 94.958 119 6 0 492 610 49233236 49233118 2.170000e-43 187.0
15 TraesCS1A01G373200 chr3B 92.209 783 45 7 3794 4561 237975439 237976220 0.000000e+00 1094.0
16 TraesCS1A01G373200 chr3B 88.588 701 50 14 3067 3741 237974724 237975420 0.000000e+00 824.0
17 TraesCS1A01G373200 chr3B 87.651 332 27 4 1376 1700 237974326 237974650 1.550000e-99 374.0
18 TraesCS1A01G373200 chr3A 91.233 787 49 6 3788 4561 707168059 707168838 0.000000e+00 1053.0
19 TraesCS1A01G373200 chr3A 85.034 588 49 17 1122 1700 707134884 707135441 3.080000e-156 562.0
20 TraesCS1A01G373200 chr3A 92.749 331 23 1 3067 3397 707135516 707135845 1.150000e-130 477.0
21 TraesCS1A01G373200 chr3A 83.602 372 19 20 3397 3741 707167690 707168046 1.230000e-80 311.0
22 TraesCS1A01G373200 chr3D 82.212 416 50 12 13 412 500137226 500137633 2.030000e-88 337.0
23 TraesCS1A01G373200 chr3D 100.000 28 0 0 2311 2338 132983990 132983963 8.000000e-03 52.8
24 TraesCS1A01G373200 chr2D 95.122 41 2 0 632 672 627923221 627923181 1.060000e-06 65.8


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 TraesCS1A01G373200 chr1A 549417329 549421889 4560 False 8423.000000 8423 100.000000 1 4561 1 chr1A.!!$F1 4560
1 TraesCS1A01G373200 chr1D 455782336 455786137 3801 False 4957.000000 4957 90.280000 722 4561 1 chr1D.!!$F1 3839
2 TraesCS1A01G373200 chr1B 626224285 626228621 4336 False 1066.250000 2045 89.607750 665 4561 4 chr1B.!!$F1 3896
3 TraesCS1A01G373200 chr6A 88099343 88100013 670 False 1177.000000 1177 98.363000 1 670 1 chr6A.!!$F1 669
4 TraesCS1A01G373200 chr7D 28364324 28364992 668 True 1175.000000 1175 98.358000 1 670 1 chr7D.!!$R1 669
5 TraesCS1A01G373200 chr7A 671192924 671193592 668 False 1170.000000 1170 98.206000 1 669 1 chr7A.!!$F1 668
6 TraesCS1A01G373200 chr5B 522903471 522904138 667 True 1138.000000 1138 97.329000 1 672 1 chr5B.!!$R1 671
7 TraesCS1A01G373200 chr7B 399792699 399794593 1894 False 781.666667 1109 90.198000 1376 4561 3 chr7B.!!$F1 3185
8 TraesCS1A01G373200 chr3B 237974326 237976220 1894 False 764.000000 1094 89.482667 1376 4561 3 chr3B.!!$F1 3185
9 TraesCS1A01G373200 chr3A 707167690 707168838 1148 False 682.000000 1053 87.417500 3397 4561 2 chr3A.!!$F2 1164
10 TraesCS1A01G373200 chr3A 707134884 707135845 961 False 519.500000 562 88.891500 1122 3397 2 chr3A.!!$F1 2275

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
703 711 0.254178 AGCAGGTCCAATGCCTACTG 59.746 55.0 0.0 0.00 44.97 2.74 F
986 1037 0.388263 GCCAAAGAGAGCTTGCTTGC 60.388 55.0 0.0 0.82 33.79 4.01 F
1832 1926 0.396811 AGGTACACTCCAACACCTGC 59.603 55.0 0.0 0.00 39.93 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1983 0.321122 GGAAGTGCTGTGAGGTGAGG 60.321 60.0 0.0 0.0 0.0 3.86 R
1893 1990 0.321919 GCTGGATGGAAGTGCTGTGA 60.322 55.0 0.0 0.0 0.0 3.58 R
3564 4144 0.602905 ACAAACTGTGGCGTAGGAGC 60.603 55.0 0.0 0.0 0.0 4.70 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
157 158 3.328382 ACTAAAACAGACATGGCGCTA 57.672 42.857 7.64 0.00 0.00 4.26
212 213 5.700832 CAGCAAAGGAAACATGTACAGTAGA 59.299 40.000 0.00 0.00 0.00 2.59
301 304 6.495181 AGAACTAACCTCAGATTTCAGAGACA 59.505 38.462 1.89 0.00 32.00 3.41
689 692 2.806945 TCCTTATCCACCAAAGCAGG 57.193 50.000 0.00 0.00 0.00 4.85
690 693 1.992557 TCCTTATCCACCAAAGCAGGT 59.007 47.619 0.00 0.00 44.48 4.00
692 695 2.369394 CTTATCCACCAAAGCAGGTCC 58.631 52.381 0.00 0.00 40.77 4.46
693 696 1.367346 TATCCACCAAAGCAGGTCCA 58.633 50.000 0.00 0.00 40.77 4.02
695 698 0.482446 TCCACCAAAGCAGGTCCAAT 59.518 50.000 0.00 0.00 40.77 3.16
703 711 0.254178 AGCAGGTCCAATGCCTACTG 59.746 55.000 0.00 0.00 44.97 2.74
708 716 1.682087 GGTCCAATGCCTACTGTTCCC 60.682 57.143 0.00 0.00 0.00 3.97
715 723 2.054799 TGCCTACTGTTCCCTTCAAGT 58.945 47.619 0.00 0.00 0.00 3.16
717 725 2.224548 GCCTACTGTTCCCTTCAAGTGT 60.225 50.000 0.00 0.00 0.00 3.55
718 726 3.747708 GCCTACTGTTCCCTTCAAGTGTT 60.748 47.826 0.00 0.00 0.00 3.32
719 727 4.065789 CCTACTGTTCCCTTCAAGTGTTC 58.934 47.826 0.00 0.00 0.00 3.18
809 817 2.046892 CCGCCCGATCATGATCCC 60.047 66.667 26.30 15.33 34.40 3.85
817 827 1.771746 ATCATGATCCCACGGCCCT 60.772 57.895 1.18 0.00 0.00 5.19
858 870 3.489398 CGACGACCTCTTCTCCCTATTTG 60.489 52.174 0.00 0.00 0.00 2.32
861 873 4.401837 ACGACCTCTTCTCCCTATTTGTAC 59.598 45.833 0.00 0.00 0.00 2.90
862 874 4.401519 CGACCTCTTCTCCCTATTTGTACA 59.598 45.833 0.00 0.00 0.00 2.90
863 875 5.069251 CGACCTCTTCTCCCTATTTGTACAT 59.931 44.000 0.00 0.00 0.00 2.29
865 877 5.069251 ACCTCTTCTCCCTATTTGTACATCG 59.931 44.000 0.00 0.00 0.00 3.84
866 878 5.509840 CCTCTTCTCCCTATTTGTACATCGG 60.510 48.000 0.00 0.00 0.00 4.18
867 879 5.205821 TCTTCTCCCTATTTGTACATCGGA 58.794 41.667 0.00 0.00 0.00 4.55
868 880 4.931661 TCTCCCTATTTGTACATCGGAC 57.068 45.455 0.00 0.00 0.00 4.79
869 881 3.640029 TCTCCCTATTTGTACATCGGACC 59.360 47.826 0.00 0.00 0.00 4.46
870 882 2.363038 TCCCTATTTGTACATCGGACCG 59.637 50.000 7.84 7.84 0.00 4.79
872 884 2.132762 CTATTTGTACATCGGACCGGC 58.867 52.381 15.25 0.00 0.00 6.13
874 886 1.546589 TTTGTACATCGGACCGGCCT 61.547 55.000 15.25 0.00 0.00 5.19
875 887 1.952102 TTGTACATCGGACCGGCCTC 61.952 60.000 15.25 0.00 0.00 4.70
876 888 2.125961 GTACATCGGACCGGCCTCT 61.126 63.158 15.25 0.00 0.00 3.69
877 889 2.125326 TACATCGGACCGGCCTCTG 61.125 63.158 15.25 6.70 0.00 3.35
879 891 2.683933 ATCGGACCGGCCTCTGTT 60.684 61.111 15.25 0.00 0.00 3.16
901 933 0.538118 CGTCCCTCCCGAATAACCAA 59.462 55.000 0.00 0.00 0.00 3.67
902 934 1.741394 CGTCCCTCCCGAATAACCAAC 60.741 57.143 0.00 0.00 0.00 3.77
903 935 1.558294 GTCCCTCCCGAATAACCAACT 59.442 52.381 0.00 0.00 0.00 3.16
984 1035 1.239968 CGGCCAAAGAGAGCTTGCTT 61.240 55.000 2.24 0.00 33.79 3.91
986 1037 0.388263 GCCAAAGAGAGCTTGCTTGC 60.388 55.000 0.00 0.82 33.79 4.01
1086 1140 3.519930 GGCTCCTCGTCGTCCTCC 61.520 72.222 0.00 0.00 0.00 4.30
1089 1143 4.790962 TCCTCGTCGTCCTCCCCG 62.791 72.222 0.00 0.00 0.00 5.73
1254 1313 4.821589 GCGTTGGAGGAGGGCGAG 62.822 72.222 0.00 0.00 0.00 5.03
1255 1314 4.148825 CGTTGGAGGAGGGCGAGG 62.149 72.222 0.00 0.00 0.00 4.63
1323 1382 3.024356 AGGCGGAGGGAGAGGAGA 61.024 66.667 0.00 0.00 0.00 3.71
1334 1393 4.214327 GAGGAGAAGCGCGAGGGG 62.214 72.222 12.10 0.00 0.00 4.79
1533 1605 0.460459 GTACCGGCTTCTCCTTGCTC 60.460 60.000 0.00 0.00 0.00 4.26
1537 1609 1.077858 GGCTTCTCCTTGCTCCTGG 60.078 63.158 0.00 0.00 0.00 4.45
1540 1612 1.948144 GCTTCTCCTTGCTCCTGGTTC 60.948 57.143 0.00 0.00 0.00 3.62
1559 1631 6.720309 TGGTTCATTTTCAGATGTGGAGATA 58.280 36.000 0.00 0.00 0.00 1.98
1572 1644 6.607600 AGATGTGGAGATAGCTAGTTTGTGTA 59.392 38.462 0.00 0.00 0.00 2.90
1596 1690 5.973565 AGCTGAAACTTTGAACGAATTGAAG 59.026 36.000 0.00 0.00 0.00 3.02
1615 1709 4.533707 TGAAGTCCAACTGAATCTCCATCT 59.466 41.667 0.00 0.00 0.00 2.90
1623 1717 3.766591 ACTGAATCTCCATCTCGTTCTGT 59.233 43.478 0.00 0.00 0.00 3.41
1624 1718 4.142271 ACTGAATCTCCATCTCGTTCTGTC 60.142 45.833 0.00 0.00 0.00 3.51
1625 1719 3.131223 TGAATCTCCATCTCGTTCTGTCC 59.869 47.826 0.00 0.00 0.00 4.02
1629 1723 3.515502 TCTCCATCTCGTTCTGTCCAATT 59.484 43.478 0.00 0.00 0.00 2.32
1832 1926 0.396811 AGGTACACTCCAACACCTGC 59.603 55.000 0.00 0.00 39.93 4.85
1874 1971 3.182263 CCCCCACCCTGTGAACCA 61.182 66.667 0.00 0.00 35.23 3.67
1886 1983 2.182904 GTGAACCACACCGACAAAAC 57.817 50.000 0.00 0.00 43.05 2.43
1892 1989 0.661020 CACACCGACAAAACCTCACC 59.339 55.000 0.00 0.00 0.00 4.02
1893 1990 0.544697 ACACCGACAAAACCTCACCT 59.455 50.000 0.00 0.00 0.00 4.00
1896 1993 1.226746 CCGACAAAACCTCACCTCAC 58.773 55.000 0.00 0.00 0.00 3.51
1897 1994 1.474320 CCGACAAAACCTCACCTCACA 60.474 52.381 0.00 0.00 0.00 3.58
1898 1995 1.867233 CGACAAAACCTCACCTCACAG 59.133 52.381 0.00 0.00 0.00 3.66
1961 2064 1.153628 GTCGGTCCTCCACATTCCG 60.154 63.158 0.00 0.00 42.12 4.30
1992 2095 4.994907 TTCTGATTGGGCAAATCTCATG 57.005 40.909 15.40 4.19 44.42 3.07
2019 2122 3.306780 CCATCGTAGGTGGTTTCAGACTT 60.307 47.826 0.00 0.00 31.96 3.01
2063 2168 7.075851 TCTTATACTACTCTACTAGCAGCCA 57.924 40.000 0.00 0.00 0.00 4.75
2064 2169 7.691213 TCTTATACTACTCTACTAGCAGCCAT 58.309 38.462 0.00 0.00 0.00 4.40
2065 2170 7.825270 TCTTATACTACTCTACTAGCAGCCATC 59.175 40.741 0.00 0.00 0.00 3.51
2066 2171 4.171878 ACTACTCTACTAGCAGCCATCA 57.828 45.455 0.00 0.00 0.00 3.07
2067 2172 4.735369 ACTACTCTACTAGCAGCCATCAT 58.265 43.478 0.00 0.00 0.00 2.45
2068 2173 5.882040 ACTACTCTACTAGCAGCCATCATA 58.118 41.667 0.00 0.00 0.00 2.15
2069 2174 6.489603 ACTACTCTACTAGCAGCCATCATAT 58.510 40.000 0.00 0.00 0.00 1.78
2070 2175 5.657826 ACTCTACTAGCAGCCATCATATG 57.342 43.478 0.00 0.00 0.00 1.78
2071 2176 5.083122 ACTCTACTAGCAGCCATCATATGT 58.917 41.667 1.90 0.00 0.00 2.29
2169 2281 3.928727 AAACGATCCTCACACGTTCTA 57.071 42.857 0.00 0.00 46.74 2.10
2170 2282 4.451629 AAACGATCCTCACACGTTCTAT 57.548 40.909 0.00 0.00 46.74 1.98
2171 2283 4.451629 AACGATCCTCACACGTTCTATT 57.548 40.909 0.00 0.00 44.84 1.73
2214 2332 5.777802 CAGCTCTAGGATTGGTACAGTATG 58.222 45.833 0.00 0.00 42.39 2.39
2231 2349 6.446451 ACAGTATGGTAGTTTATCACCCCTA 58.554 40.000 0.00 0.00 43.62 3.53
2239 2357 4.567857 AGTTTATCACCCCTAGCTGGTAT 58.432 43.478 0.00 0.00 33.84 2.73
2240 2358 4.348168 AGTTTATCACCCCTAGCTGGTATG 59.652 45.833 0.00 0.00 33.84 2.39
2241 2359 2.496679 ATCACCCCTAGCTGGTATGT 57.503 50.000 0.00 0.00 33.84 2.29
2242 2360 3.630625 ATCACCCCTAGCTGGTATGTA 57.369 47.619 0.00 0.00 33.84 2.29
2434 2553 1.272037 TGAATCATTGTGCTGGGCTGA 60.272 47.619 0.00 0.00 0.00 4.26
2435 2554 1.820519 GAATCATTGTGCTGGGCTGAA 59.179 47.619 0.00 0.00 0.00 3.02
2489 2608 2.842188 TAGTTGCCATGCTGCTGGGG 62.842 60.000 16.33 9.52 36.75 4.96
2519 2639 5.627780 GGTTGGTTCGTTGTTTAATGTGATC 59.372 40.000 0.00 0.00 0.00 2.92
2538 2733 2.985896 TCTTTTAGAATGGGGTGAGCG 58.014 47.619 0.00 0.00 0.00 5.03
2540 2735 0.742990 TTTAGAATGGGGTGAGCGCG 60.743 55.000 0.00 0.00 0.00 6.86
2541 2736 1.609635 TTAGAATGGGGTGAGCGCGA 61.610 55.000 12.10 0.00 0.00 5.87
2546 2741 2.203070 GGGGTGAGCGCGATGAAT 60.203 61.111 12.10 0.00 0.00 2.57
2550 2745 0.510359 GGTGAGCGCGATGAATGATC 59.490 55.000 12.10 0.00 0.00 2.92
2551 2746 0.510359 GTGAGCGCGATGAATGATCC 59.490 55.000 12.10 0.00 0.00 3.36
2564 2759 0.763652 ATGATCCGAATGCCTGAGCT 59.236 50.000 0.00 0.00 40.80 4.09
2584 2779 8.128322 TGAGCTAGGATTATAAGAATCTGACC 57.872 38.462 0.00 0.00 0.00 4.02
2585 2780 7.952930 TGAGCTAGGATTATAAGAATCTGACCT 59.047 37.037 0.00 0.00 0.00 3.85
2586 2781 8.361169 AGCTAGGATTATAAGAATCTGACCTC 57.639 38.462 0.00 0.00 0.00 3.85
2587 2782 7.952930 AGCTAGGATTATAAGAATCTGACCTCA 59.047 37.037 0.00 0.00 0.00 3.86
2588 2783 8.589338 GCTAGGATTATAAGAATCTGACCTCAA 58.411 37.037 0.00 0.00 0.00 3.02
2618 2813 7.827819 TCAAGTGAACTTTAGGATATGAACG 57.172 36.000 0.00 0.00 33.11 3.95
2659 2854 1.244816 GTGGCCTTTGGTGGTAGTTC 58.755 55.000 3.32 0.00 0.00 3.01
2689 2884 3.623510 GGGTTCTGCACTTAAGATACAGC 59.376 47.826 10.09 5.69 0.00 4.40
2694 2889 7.308435 GTTCTGCACTTAAGATACAGCAAAAT 58.692 34.615 10.09 0.00 0.00 1.82
2695 2890 8.450964 GTTCTGCACTTAAGATACAGCAAAATA 58.549 33.333 10.09 0.00 0.00 1.40
2696 2891 7.974675 TCTGCACTTAAGATACAGCAAAATAC 58.025 34.615 10.09 0.00 0.00 1.89
2697 2892 7.824289 TCTGCACTTAAGATACAGCAAAATACT 59.176 33.333 10.09 0.00 0.00 2.12
2698 2893 7.974675 TGCACTTAAGATACAGCAAAATACTC 58.025 34.615 10.09 0.00 0.00 2.59
2699 2894 7.065803 TGCACTTAAGATACAGCAAAATACTCC 59.934 37.037 10.09 0.00 0.00 3.85
2802 3068 5.474578 TTAGTGCTGATCAGTTCTGAAGT 57.525 39.130 23.38 8.41 0.00 3.01
2811 3077 7.389803 TGATCAGTTCTGAAGTTGTTTTTCA 57.610 32.000 6.60 0.68 33.76 2.69
2896 3332 5.248640 CACAAGCTCTTTAGATCCCTTGAA 58.751 41.667 15.64 0.00 0.00 2.69
3068 3630 0.323725 AGGATTGGCGCCTTGATGTT 60.324 50.000 29.70 4.22 29.44 2.71
3104 3668 3.013327 GTACCCCCTTCCGCCCTT 61.013 66.667 0.00 0.00 0.00 3.95
3135 3699 3.859627 GCAGCAGATTTCAGTTTGCACAT 60.860 43.478 0.00 0.00 38.97 3.21
3136 3700 4.304110 CAGCAGATTTCAGTTTGCACATT 58.696 39.130 0.00 0.00 38.97 2.71
3145 3709 7.517614 TTTCAGTTTGCACATTACCATCTTA 57.482 32.000 0.00 0.00 0.00 2.10
3181 3745 2.096496 GTCTCTCAACCGCATCATTTGG 59.904 50.000 0.00 0.00 0.00 3.28
3196 3760 2.521958 TTTGGCAGGAGCTACTCGCC 62.522 60.000 24.64 24.64 43.28 5.54
3309 3873 3.126514 CGCAAGCATTTCTCAACAGAGAT 59.873 43.478 0.00 0.00 38.17 2.75
3331 3895 3.271014 CGGAGCTGCAGCATTTGT 58.729 55.556 38.24 19.47 45.16 2.83
3546 4125 2.192861 CCACTTTGCAAGGTCGCCA 61.193 57.895 11.81 0.00 0.00 5.69
3758 4362 1.639722 TTCTTGTCCCCATCGTCTGA 58.360 50.000 0.00 0.00 0.00 3.27
3859 4467 0.744874 TAGCTTCTTATGGCGAGCGT 59.255 50.000 0.00 0.00 39.99 5.07
3860 4468 0.108138 AGCTTCTTATGGCGAGCGTT 60.108 50.000 0.00 0.00 39.99 4.84
4336 4975 2.152297 CTGATCGAGCCCCTGATCCG 62.152 65.000 0.00 0.00 40.19 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 5.409826 GCCATCCGAAATCTAGAAAATCGAT 59.590 40.000 20.29 0.00 35.65 3.59
212 213 8.370940 TGTCTCTCAAATCTCAACTTAGTTCAT 58.629 33.333 0.00 0.00 0.00 2.57
301 304 3.746045 TTTCCTCGTACTTGCTTGACT 57.254 42.857 0.00 0.00 0.00 3.41
689 692 1.282157 AGGGAACAGTAGGCATTGGAC 59.718 52.381 0.00 0.00 0.00 4.02
690 693 1.668826 AGGGAACAGTAGGCATTGGA 58.331 50.000 0.00 0.00 0.00 3.53
692 695 3.071874 TGAAGGGAACAGTAGGCATTG 57.928 47.619 0.00 0.00 0.00 2.82
693 696 3.074538 ACTTGAAGGGAACAGTAGGCATT 59.925 43.478 0.00 0.00 0.00 3.56
695 698 2.054799 ACTTGAAGGGAACAGTAGGCA 58.945 47.619 0.00 0.00 0.00 4.75
703 711 1.617322 GGGGAACACTTGAAGGGAAC 58.383 55.000 0.00 0.00 0.00 3.62
708 716 0.955919 GAGGCGGGGAACACTTGAAG 60.956 60.000 0.00 0.00 0.00 3.02
731 739 0.250295 TCAGTGGGTCAAGGAAAGCG 60.250 55.000 0.00 0.00 0.00 4.68
835 845 0.907486 TAGGGAGAAGAGGTCGTCGA 59.093 55.000 0.00 0.00 0.00 4.20
844 854 5.068723 GTCCGATGTACAAATAGGGAGAAGA 59.931 44.000 0.00 0.00 0.00 2.87
847 859 3.640029 GGTCCGATGTACAAATAGGGAGA 59.360 47.826 0.00 0.00 0.00 3.71
858 870 2.125961 AGAGGCCGGTCCGATGTAC 61.126 63.158 14.39 0.10 40.77 2.90
861 873 2.907897 GAACAGAGGCCGGTCCGATG 62.908 65.000 14.39 11.12 40.77 3.84
862 874 2.683933 AACAGAGGCCGGTCCGAT 60.684 61.111 14.39 0.00 40.77 4.18
863 875 3.379445 GAACAGAGGCCGGTCCGA 61.379 66.667 14.39 0.00 40.77 4.55
865 877 2.579738 GAGAACAGAGGCCGGTCC 59.420 66.667 0.08 4.26 0.00 4.46
866 878 2.182030 CGAGAACAGAGGCCGGTC 59.818 66.667 0.00 0.00 0.00 4.79
867 879 2.600769 ACGAGAACAGAGGCCGGT 60.601 61.111 1.90 0.00 0.00 5.28
868 880 2.182030 GACGAGAACAGAGGCCGG 59.818 66.667 0.00 0.00 0.00 6.13
869 881 2.182030 GGACGAGAACAGAGGCCG 59.818 66.667 0.00 0.00 0.00 6.13
870 882 1.950973 GAGGGACGAGAACAGAGGCC 61.951 65.000 0.00 0.00 0.00 5.19
872 884 1.324005 GGGAGGGACGAGAACAGAGG 61.324 65.000 0.00 0.00 0.00 3.69
874 886 1.677966 CGGGAGGGACGAGAACAGA 60.678 63.158 0.00 0.00 0.00 3.41
875 887 1.248785 TTCGGGAGGGACGAGAACAG 61.249 60.000 0.00 0.00 41.81 3.16
876 888 0.613853 ATTCGGGAGGGACGAGAACA 60.614 55.000 0.00 0.00 41.81 3.18
877 889 1.396653 TATTCGGGAGGGACGAGAAC 58.603 55.000 0.00 0.00 41.81 3.01
879 891 1.396653 GTTATTCGGGAGGGACGAGA 58.603 55.000 0.00 0.00 41.81 4.04
967 1004 0.388263 GCAAGCAAGCTCTCTTTGGC 60.388 55.000 0.00 0.00 0.00 4.52
974 1011 2.273912 GGCCAAGCAAGCAAGCTCT 61.274 57.895 0.00 0.00 45.89 4.09
1251 1310 2.364317 TCCCCCTCTTGCTCCTCG 60.364 66.667 0.00 0.00 0.00 4.63
1252 1311 2.069430 CCTCCCCCTCTTGCTCCTC 61.069 68.421 0.00 0.00 0.00 3.71
1253 1312 2.041928 CCTCCCCCTCTTGCTCCT 59.958 66.667 0.00 0.00 0.00 3.69
1254 1313 2.041265 TCCTCCCCCTCTTGCTCC 59.959 66.667 0.00 0.00 0.00 4.70
1255 1314 2.069430 CCTCCTCCCCCTCTTGCTC 61.069 68.421 0.00 0.00 0.00 4.26
1258 1317 0.980231 CACTCCTCCTCCCCCTCTTG 60.980 65.000 0.00 0.00 0.00 3.02
1260 1319 2.641746 CCACTCCTCCTCCCCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
1518 1580 1.449246 CAGGAGCAAGGAGAAGCCG 60.449 63.158 0.00 0.00 43.43 5.52
1533 1605 4.081406 TCCACATCTGAAAATGAACCAGG 58.919 43.478 0.00 0.00 0.00 4.45
1537 1609 6.541641 AGCTATCTCCACATCTGAAAATGAAC 59.458 38.462 0.00 0.00 0.00 3.18
1540 1612 7.215789 ACTAGCTATCTCCACATCTGAAAATG 58.784 38.462 0.00 0.00 0.00 2.32
1559 1631 4.962155 AGTTTCAGCTACACAAACTAGCT 58.038 39.130 9.41 0.00 46.51 3.32
1572 1644 5.499139 TCAATTCGTTCAAAGTTTCAGCT 57.501 34.783 0.00 0.00 0.00 4.24
1596 1690 3.118956 ACGAGATGGAGATTCAGTTGGAC 60.119 47.826 0.00 0.00 0.00 4.02
1623 1717 3.006940 CGGAAATCGGAAGTCAATTGGA 58.993 45.455 5.42 0.00 34.75 3.53
1624 1718 2.747446 ACGGAAATCGGAAGTCAATTGG 59.253 45.455 5.42 0.00 44.45 3.16
1625 1719 4.419522 AACGGAAATCGGAAGTCAATTG 57.580 40.909 0.00 0.00 44.45 2.32
1629 1723 2.803956 GTCAAACGGAAATCGGAAGTCA 59.196 45.455 0.00 0.00 44.45 3.41
1809 1903 2.368875 AGGTGTTGGAGTGTACCTCTTG 59.631 50.000 10.11 0.00 39.23 3.02
1828 1922 2.046023 TGCGTGGAATGGAGCAGG 60.046 61.111 0.00 0.00 34.39 4.85
1832 1926 1.133025 GAAATGGTGCGTGGAATGGAG 59.867 52.381 0.00 0.00 0.00 3.86
1874 1971 0.544697 AGGTGAGGTTTTGTCGGTGT 59.455 50.000 0.00 0.00 0.00 4.16
1886 1983 0.321122 GGAAGTGCTGTGAGGTGAGG 60.321 60.000 0.00 0.00 0.00 3.86
1892 1989 1.735386 CTGGATGGAAGTGCTGTGAG 58.265 55.000 0.00 0.00 0.00 3.51
1893 1990 0.321919 GCTGGATGGAAGTGCTGTGA 60.322 55.000 0.00 0.00 0.00 3.58
1896 1993 1.404391 GAATGCTGGATGGAAGTGCTG 59.596 52.381 0.00 0.00 0.00 4.41
1897 1994 1.005097 TGAATGCTGGATGGAAGTGCT 59.995 47.619 0.00 0.00 0.00 4.40
1898 1995 1.466856 TGAATGCTGGATGGAAGTGC 58.533 50.000 0.00 0.00 0.00 4.40
1992 2095 2.203070 CCACCTACGATGGCTGCC 60.203 66.667 12.87 12.87 0.00 4.85
2019 2122 1.139498 TTGAGCATGGACCCCCTGAA 61.139 55.000 0.00 0.00 0.00 3.02
2063 2168 4.507335 GGACCATGGGCTACAACATATGAT 60.507 45.833 19.55 0.00 0.00 2.45
2064 2169 3.181445 GGACCATGGGCTACAACATATGA 60.181 47.826 19.55 0.00 0.00 2.15
2065 2170 3.149196 GGACCATGGGCTACAACATATG 58.851 50.000 19.55 0.00 0.00 1.78
2066 2171 2.782925 TGGACCATGGGCTACAACATAT 59.217 45.455 19.55 0.00 0.00 1.78
2067 2172 2.200955 TGGACCATGGGCTACAACATA 58.799 47.619 19.55 0.00 0.00 2.29
2068 2173 0.998928 TGGACCATGGGCTACAACAT 59.001 50.000 19.55 0.00 0.00 2.71
2069 2174 0.998928 ATGGACCATGGGCTACAACA 59.001 50.000 19.55 6.76 0.00 3.33
2070 2175 1.392589 CATGGACCATGGGCTACAAC 58.607 55.000 24.65 0.00 38.11 3.32
2071 2176 0.395586 GCATGGACCATGGGCTACAA 60.396 55.000 31.08 0.91 41.64 2.41
2106 2211 2.027653 TGAGTACATGGCATCCGAACAA 60.028 45.455 0.00 0.00 0.00 2.83
2108 2213 1.933853 GTGAGTACATGGCATCCGAAC 59.066 52.381 0.00 0.00 0.00 3.95
2110 2215 1.409064 GAGTGAGTACATGGCATCCGA 59.591 52.381 0.00 0.00 0.00 4.55
2111 2216 1.136891 TGAGTGAGTACATGGCATCCG 59.863 52.381 0.00 0.00 0.00 4.18
2112 2217 2.093500 TGTGAGTGAGTACATGGCATCC 60.093 50.000 0.00 0.00 0.00 3.51
2113 2218 3.251479 TGTGAGTGAGTACATGGCATC 57.749 47.619 0.00 0.00 0.00 3.91
2114 2219 3.538591 CATGTGAGTGAGTACATGGCAT 58.461 45.455 8.96 0.00 46.41 4.40
2115 2220 2.976589 CATGTGAGTGAGTACATGGCA 58.023 47.619 8.96 0.00 46.41 4.92
2119 2224 4.081642 GTGGTACCATGTGAGTGAGTACAT 60.082 45.833 19.72 0.00 37.99 2.29
2120 2225 3.257375 GTGGTACCATGTGAGTGAGTACA 59.743 47.826 19.72 0.00 35.98 2.90
2121 2226 3.368116 GGTGGTACCATGTGAGTGAGTAC 60.368 52.174 19.72 0.00 38.42 2.73
2122 2227 2.829720 GGTGGTACCATGTGAGTGAGTA 59.170 50.000 19.72 0.00 38.42 2.59
2169 2281 4.263727 TGCAACCAACCACTCCAGTATAAT 60.264 41.667 0.00 0.00 0.00 1.28
2170 2282 3.073209 TGCAACCAACCACTCCAGTATAA 59.927 43.478 0.00 0.00 0.00 0.98
2171 2283 2.640332 TGCAACCAACCACTCCAGTATA 59.360 45.455 0.00 0.00 0.00 1.47
2214 2332 3.071167 CCAGCTAGGGGTGATAAACTACC 59.929 52.174 0.00 0.00 42.91 3.18
2239 2357 7.639850 GCGTGTCGTATAAACATAACTACTACA 59.360 37.037 0.00 0.00 0.00 2.74
2240 2358 7.639850 TGCGTGTCGTATAAACATAACTACTAC 59.360 37.037 0.00 0.00 0.00 2.73
2241 2359 7.693020 TGCGTGTCGTATAAACATAACTACTA 58.307 34.615 0.00 0.00 0.00 1.82
2242 2360 6.554419 TGCGTGTCGTATAAACATAACTACT 58.446 36.000 0.00 0.00 0.00 2.57
2276 2394 3.434319 CCAATCTGCCGCGTGCTT 61.434 61.111 18.14 4.41 42.00 3.91
2348 2466 2.093235 GCATCTACACTCAAAGGGCTCT 60.093 50.000 0.00 0.00 0.00 4.09
2434 2553 3.023119 TCAGCAACATGGTTGTTCAGTT 58.977 40.909 10.44 0.00 44.24 3.16
2435 2554 2.653726 TCAGCAACATGGTTGTTCAGT 58.346 42.857 10.44 0.00 44.24 3.41
2489 2608 1.314730 ACAACGAACCAACCATCCAC 58.685 50.000 0.00 0.00 0.00 4.02
2519 2639 1.401905 GCGCTCACCCCATTCTAAAAG 59.598 52.381 0.00 0.00 0.00 2.27
2538 2733 1.135859 GGCATTCGGATCATTCATCGC 60.136 52.381 0.00 0.00 31.26 4.58
2540 2735 3.405831 TCAGGCATTCGGATCATTCATC 58.594 45.455 0.00 0.00 0.00 2.92
2541 2736 3.409570 CTCAGGCATTCGGATCATTCAT 58.590 45.455 0.00 0.00 0.00 2.57
2546 2741 1.342496 CTAGCTCAGGCATTCGGATCA 59.658 52.381 0.00 0.00 41.70 2.92
2550 2745 0.683973 ATCCTAGCTCAGGCATTCGG 59.316 55.000 0.00 0.00 45.10 4.30
2551 2746 2.540265 AATCCTAGCTCAGGCATTCG 57.460 50.000 0.00 0.00 45.10 3.34
2564 2759 9.661954 AGTTGAGGTCAGATTCTTATAATCCTA 57.338 33.333 0.00 0.00 0.00 2.94
2570 2765 7.619698 TGAAGGAGTTGAGGTCAGATTCTTATA 59.380 37.037 0.00 0.00 0.00 0.98
2578 2773 3.070159 CACTTGAAGGAGTTGAGGTCAGA 59.930 47.826 0.00 0.00 0.00 3.27
2584 2779 6.203723 CCTAAAGTTCACTTGAAGGAGTTGAG 59.796 42.308 12.93 0.00 40.04 3.02
2585 2780 6.055588 CCTAAAGTTCACTTGAAGGAGTTGA 58.944 40.000 12.93 0.00 40.04 3.18
2586 2781 6.055588 TCCTAAAGTTCACTTGAAGGAGTTG 58.944 40.000 15.45 0.00 40.83 3.16
2587 2782 6.248569 TCCTAAAGTTCACTTGAAGGAGTT 57.751 37.500 15.45 0.00 40.83 3.01
2588 2783 5.888982 TCCTAAAGTTCACTTGAAGGAGT 57.111 39.130 15.45 0.00 40.83 3.85
2618 2813 3.383761 CTTTTGACTCACAAACATGCCC 58.616 45.455 0.00 0.00 46.32 5.36
2648 2843 2.105821 CCCAAAGTCAGAACTACCACCA 59.894 50.000 0.00 0.00 33.48 4.17
2659 2854 1.972872 AGTGCAGAACCCAAAGTCAG 58.027 50.000 0.00 0.00 0.00 3.51
2689 2884 8.936864 CAAGAACAACTAGGTAGGAGTATTTTG 58.063 37.037 0.00 0.00 0.00 2.44
2694 2889 7.179966 TGATCAAGAACAACTAGGTAGGAGTA 58.820 38.462 0.00 0.00 0.00 2.59
2695 2890 6.017192 TGATCAAGAACAACTAGGTAGGAGT 58.983 40.000 0.00 0.00 0.00 3.85
2696 2891 6.378564 TCTGATCAAGAACAACTAGGTAGGAG 59.621 42.308 0.00 0.00 29.54 3.69
2697 2892 6.253758 TCTGATCAAGAACAACTAGGTAGGA 58.746 40.000 0.00 0.00 29.54 2.94
2698 2893 6.378564 TCTCTGATCAAGAACAACTAGGTAGG 59.621 42.308 0.00 0.00 33.37 3.18
2699 2894 7.397892 TCTCTGATCAAGAACAACTAGGTAG 57.602 40.000 0.00 0.00 33.37 3.18
2770 3033 1.882912 TCAGCACTAAAGTGGCACAG 58.117 50.000 21.41 11.16 45.72 3.66
2802 3068 8.958119 ACTAGTGTAGAACAGATGAAAAACAA 57.042 30.769 0.00 0.00 0.00 2.83
2811 3077 5.221641 TGCCAACAACTAGTGTAGAACAGAT 60.222 40.000 0.00 0.00 40.60 2.90
2896 3332 7.989741 GCCACATATATCCATTAGCAGAAGTAT 59.010 37.037 0.00 0.00 0.00 2.12
2920 3356 0.609662 ATGGGTTCAAAGTGCATGCC 59.390 50.000 16.68 6.65 0.00 4.40
3104 3668 1.814394 GAAATCTGCTGCACATGGTGA 59.186 47.619 0.00 0.00 35.23 4.02
3136 3700 9.817809 GACAATGTAGATTTGAGTAAGATGGTA 57.182 33.333 0.00 0.00 0.00 3.25
3145 3709 6.876257 GGTTGAGAGACAATGTAGATTTGAGT 59.124 38.462 0.00 0.00 40.76 3.41
3196 3760 2.851071 GCCGATCCTGTCCTCGAGG 61.851 68.421 26.32 26.32 37.05 4.63
3331 3895 4.820897 AGCAAGTTCATCGTCATACTTGA 58.179 39.130 19.54 0.00 46.43 3.02
3564 4144 0.602905 ACAAACTGTGGCGTAGGAGC 60.603 55.000 0.00 0.00 0.00 4.70
3704 4307 2.549633 GCATGTGTGCCTGTGTTATC 57.450 50.000 0.00 0.00 45.76 1.75
3758 4362 1.660560 GGTGCAGCTCAAATGGCGAT 61.661 55.000 9.07 0.00 34.52 4.58
3909 4538 1.424493 GCGGCGACATCAAGAAGGAG 61.424 60.000 12.98 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.