Multiple sequence alignment - TraesCS7D01G095700

Loading Multiple Alignment...

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 TraesCS7D01G095700 chr7D 100.000 3524 0 0 1 3524 58151832 58155355 0.000000e+00 6508.0
1 TraesCS7D01G095700 chr7D 91.132 1714 106 13 931 2619 58134003 58132311 0.000000e+00 2281.0
2 TraesCS7D01G095700 chr7D 96.159 729 26 2 1 728 443159921 443160648 0.000000e+00 1190.0
3 TraesCS7D01G095700 chr7D 89.706 68 7 0 2937 3004 597284984 597284917 1.740000e-13 87.9
4 TraesCS7D01G095700 chr7D 88.000 75 7 2 2791 2865 605167409 605167337 1.740000e-13 87.9
5 TraesCS7D01G095700 chr7A 92.168 1813 90 22 931 2733 62475633 62477403 0.000000e+00 2514.0
6 TraesCS7D01G095700 chr7A 92.967 583 41 0 985 1567 62473491 62474073 0.000000e+00 850.0
7 TraesCS7D01G095700 chr7A 83.212 822 90 32 2727 3524 62477631 62478428 0.000000e+00 710.0
8 TraesCS7D01G095700 chr7A 90.404 198 13 3 735 928 62475372 62475567 4.510000e-64 255.0
9 TraesCS7D01G095700 chr7A 81.538 130 16 6 3026 3149 724171247 724171374 2.240000e-17 100.0
10 TraesCS7D01G095700 chr4A 93.025 1663 92 10 966 2619 673774529 673772882 0.000000e+00 2407.0
11 TraesCS7D01G095700 chr4A 89.436 1950 130 33 720 2619 673802486 673804409 0.000000e+00 2390.0
12 TraesCS7D01G095700 chr4A 85.822 663 42 16 2189 2825 673750481 673749845 0.000000e+00 656.0
13 TraesCS7D01G095700 chr4A 86.372 565 63 10 2960 3524 673749785 673749235 3.890000e-169 604.0
14 TraesCS7D01G095700 chr4A 86.022 186 11 8 722 894 673774819 673774636 6.010000e-43 185.0
15 TraesCS7D01G095700 chr4A 78.448 232 32 7 2788 3001 137181953 137181722 6.140000e-28 135.0
16 TraesCS7D01G095700 chr2A 88.141 1560 149 13 970 2517 3534404 3532869 0.000000e+00 1823.0
17 TraesCS7D01G095700 chr2A 86.923 1560 180 10 958 2517 3522989 3524524 0.000000e+00 1729.0
18 TraesCS7D01G095700 chr2A 84.577 992 116 12 1527 2517 505237988 505238943 0.000000e+00 950.0
19 TraesCS7D01G095700 chr2A 90.123 81 5 3 3027 3106 685747795 685747873 6.220000e-18 102.0
20 TraesCS7D01G095700 chr6B 81.688 1540 233 30 996 2517 50483033 50484541 0.000000e+00 1236.0
21 TraesCS7D01G095700 chr6D 81.161 1550 232 41 996 2517 27452139 27453656 0.000000e+00 1190.0
22 TraesCS7D01G095700 chr6D 79.917 1449 210 45 1099 2517 15257101 15255704 0.000000e+00 989.0
23 TraesCS7D01G095700 chr3B 94.061 724 30 3 1 716 39349091 39348373 0.000000e+00 1086.0
24 TraesCS7D01G095700 chr3B 93.722 446 14 4 1 432 809174320 809173875 0.000000e+00 656.0
25 TraesCS7D01G095700 chr3B 84.817 191 23 6 529 716 42338408 42338221 1.670000e-43 187.0
26 TraesCS7D01G095700 chr3B 86.243 189 5 2 455 643 809173883 809173716 6.010000e-43 185.0
27 TraesCS7D01G095700 chr3B 84.293 191 25 5 529 716 615905740 615905928 7.770000e-42 182.0
28 TraesCS7D01G095700 chr3B 86.111 72 10 0 2794 2865 158239097 158239026 1.050000e-10 78.7
29 TraesCS7D01G095700 chr7B 94.150 718 29 4 1 717 733367892 733367187 0.000000e+00 1081.0
30 TraesCS7D01G095700 chr5D 99.292 424 3 0 293 716 453341073 453341496 0.000000e+00 767.0
31 TraesCS7D01G095700 chr5D 76.667 270 33 15 2722 2973 28727273 28727016 4.780000e-24 122.0
32 TraesCS7D01G095700 chr1A 96.641 387 11 2 172 558 310870633 310870249 2.970000e-180 641.0
33 TraesCS7D01G095700 chr1A 93.785 177 11 0 1 177 310872791 310872615 2.090000e-67 267.0
34 TraesCS7D01G095700 chr1A 94.512 164 9 0 552 715 310867750 310867587 1.620000e-63 254.0
35 TraesCS7D01G095700 chr1B 91.667 312 26 0 18 329 617086206 617086517 1.940000e-117 433.0
36 TraesCS7D01G095700 chr1B 88.263 213 25 0 504 716 508035434 508035222 4.510000e-64 255.0
37 TraesCS7D01G095700 chr1B 86.239 109 10 3 2793 2899 498062934 498063039 2.880000e-21 113.0
38 TraesCS7D01G095700 chr3A 95.703 256 9 1 1 254 738748920 738749175 9.100000e-111 411.0
39 TraesCS7D01G095700 chr3A 90.741 270 11 1 310 579 738749186 738749441 7.240000e-92 348.0
40 TraesCS7D01G095700 chr3A 84.737 190 26 3 529 716 1120870 1120682 1.670000e-43 187.0
41 TraesCS7D01G095700 chr5A 84.366 339 28 15 1 339 132298353 132298666 3.420000e-80 309.0
42 TraesCS7D01G095700 chr5A 93.137 102 7 0 333 434 132298695 132298796 2.190000e-32 150.0
43 TraesCS7D01G095700 chr5A 74.134 433 69 22 2722 3118 19490548 19490123 4.740000e-29 139.0
44 TraesCS7D01G095700 chr5A 78.616 159 18 9 2962 3106 357802372 357802216 1.350000e-14 91.6
45 TraesCS7D01G095700 chr1D 93.519 108 2 1 176 283 450201771 450201873 4.710000e-34 156.0
46 TraesCS7D01G095700 chr3D 93.137 102 7 0 333 434 77388942 77388841 2.190000e-32 150.0
47 TraesCS7D01G095700 chr3D 91.304 92 8 0 248 339 77389062 77388971 3.690000e-25 126.0
48 TraesCS7D01G095700 chr2D 87.097 93 9 3 2785 2874 573900145 573900053 6.220000e-18 102.0
49 TraesCS7D01G095700 chr2B 76.000 225 38 11 2937 3149 154844156 154843936 6.220000e-18 102.0
50 TraesCS7D01G095700 chr2B 75.862 232 32 16 2766 2977 107889441 107889214 2.900000e-16 97.1
51 TraesCS7D01G095700 chr2B 81.720 93 14 3 2785 2874 689754758 689754666 1.360000e-09 75.0
52 TraesCS7D01G095700 chr5B 84.507 71 11 0 2934 3004 505475496 505475566 1.760000e-08 71.3
53 TraesCS7D01G095700 chr4B 94.286 35 2 0 2976 3010 411396078 411396044 2.000000e-03 54.7


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 TraesCS7D01G095700 chr7D 58151832 58155355 3523 False 6508.000000 6508 100.000000 1 3524 1 chr7D.!!$F1 3523
1 TraesCS7D01G095700 chr7D 58132311 58134003 1692 True 2281.000000 2281 91.132000 931 2619 1 chr7D.!!$R1 1688
2 TraesCS7D01G095700 chr7D 443159921 443160648 727 False 1190.000000 1190 96.159000 1 728 1 chr7D.!!$F2 727
3 TraesCS7D01G095700 chr7A 62473491 62478428 4937 False 1082.250000 2514 89.687750 735 3524 4 chr7A.!!$F2 2789
4 TraesCS7D01G095700 chr4A 673802486 673804409 1923 False 2390.000000 2390 89.436000 720 2619 1 chr4A.!!$F1 1899
5 TraesCS7D01G095700 chr4A 673772882 673774819 1937 True 1296.000000 2407 89.523500 722 2619 2 chr4A.!!$R3 1897
6 TraesCS7D01G095700 chr4A 673749235 673750481 1246 True 630.000000 656 86.097000 2189 3524 2 chr4A.!!$R2 1335
7 TraesCS7D01G095700 chr2A 3532869 3534404 1535 True 1823.000000 1823 88.141000 970 2517 1 chr2A.!!$R1 1547
8 TraesCS7D01G095700 chr2A 3522989 3524524 1535 False 1729.000000 1729 86.923000 958 2517 1 chr2A.!!$F1 1559
9 TraesCS7D01G095700 chr2A 505237988 505238943 955 False 950.000000 950 84.577000 1527 2517 1 chr2A.!!$F2 990
10 TraesCS7D01G095700 chr6B 50483033 50484541 1508 False 1236.000000 1236 81.688000 996 2517 1 chr6B.!!$F1 1521
11 TraesCS7D01G095700 chr6D 27452139 27453656 1517 False 1190.000000 1190 81.161000 996 2517 1 chr6D.!!$F1 1521
12 TraesCS7D01G095700 chr6D 15255704 15257101 1397 True 989.000000 989 79.917000 1099 2517 1 chr6D.!!$R1 1418
13 TraesCS7D01G095700 chr3B 39348373 39349091 718 True 1086.000000 1086 94.061000 1 716 1 chr3B.!!$R1 715
14 TraesCS7D01G095700 chr3B 809173716 809174320 604 True 420.500000 656 89.982500 1 643 2 chr3B.!!$R4 642
15 TraesCS7D01G095700 chr7B 733367187 733367892 705 True 1081.000000 1081 94.150000 1 717 1 chr7B.!!$R1 716
16 TraesCS7D01G095700 chr1A 310867587 310872791 5204 True 387.333333 641 94.979333 1 715 3 chr1A.!!$R1 714
17 TraesCS7D01G095700 chr3A 738748920 738749441 521 False 379.500000 411 93.222000 1 579 2 chr3A.!!$F1 578

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
920 5463 0.892755 AACCAGCCACGAGTTCGATA 59.107 50.0 8.72 0.0 43.02 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2783 7729 0.034896 GTTCTTCTCCGGCAAGGTCA 59.965 55.0 11.79 0.0 41.99 4.02 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
123 133 5.500645 AAACTCAAGTCCAAGTTTAGTGC 57.499 39.130 0.00 0.00 42.37 4.40
148 158 3.182967 TGGCTTTTAAACACAAACAGCG 58.817 40.909 0.00 0.00 0.00 5.18
351 2354 1.153745 CGCACAGGTCTACAGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
388 2398 1.837051 TCAGGGGCACGTCTGAGTT 60.837 57.895 0.83 0.00 35.19 3.01
395 2405 2.094182 GGGCACGTCTGAGTTTAGATGA 60.094 50.000 0.00 0.00 37.20 2.92
446 2458 4.742649 ACGGGCGCTCTCCTCTGA 62.743 66.667 5.36 0.00 0.00 3.27
716 5239 1.866063 GCCACCAAACGCATTTTTCGA 60.866 47.619 0.00 0.00 0.00 3.71
717 5240 2.050691 CCACCAAACGCATTTTTCGAG 58.949 47.619 0.00 0.00 0.00 4.04
740 5263 1.743252 GAGCCTCCTTTCTGCGTGG 60.743 63.158 0.00 0.00 0.00 4.94
819 5353 2.035421 CATGTGAATGGCCGGGATG 58.965 57.895 2.18 0.00 0.00 3.51
824 5361 1.135112 GTGAATGGCCGGGATGAAAAC 60.135 52.381 2.18 0.00 0.00 2.43
826 5363 1.134946 GAATGGCCGGGATGAAAACTG 59.865 52.381 2.18 0.00 0.00 3.16
833 5370 1.523758 GGGATGAAAACTGCACGAGT 58.476 50.000 0.00 0.00 35.94 4.18
835 5372 2.095718 GGGATGAAAACTGCACGAGTTC 60.096 50.000 0.00 0.00 44.68 3.01
870 5411 2.560105 GGCATTTTTCTGTGAAGCTCCT 59.440 45.455 0.00 0.00 0.00 3.69
898 5439 4.985044 AAAAGTTCGTCGTACCATTCTG 57.015 40.909 0.00 0.00 0.00 3.02
920 5463 0.892755 AACCAGCCACGAGTTCGATA 59.107 50.000 8.72 0.00 43.02 2.92
922 5465 1.067212 ACCAGCCACGAGTTCGATATC 59.933 52.381 8.72 0.00 43.02 1.63
928 5471 2.460918 CACGAGTTCGATATCCACACC 58.539 52.381 8.72 0.00 43.02 4.16
929 5472 2.097036 ACGAGTTCGATATCCACACCA 58.903 47.619 8.72 0.00 43.02 4.17
947 5558 6.096987 CCACACCACAATCTACATCTACTACT 59.903 42.308 0.00 0.00 0.00 2.57
1687 6337 2.682494 TCGTCCCTTTCCTCCGGG 60.682 66.667 0.00 0.00 42.05 5.73
1780 6430 0.387929 AATCGACCGTCGTATGGCAT 59.612 50.000 19.89 4.88 41.35 4.40
1781 6431 0.387929 ATCGACCGTCGTATGGCATT 59.612 50.000 19.89 0.00 41.35 3.56
1782 6432 0.526739 TCGACCGTCGTATGGCATTG 60.527 55.000 19.89 0.00 41.35 2.82
1783 6433 0.526739 CGACCGTCGTATGGCATTGA 60.527 55.000 12.91 1.08 34.72 2.57
1784 6434 0.928229 GACCGTCGTATGGCATTGAC 59.072 55.000 17.68 17.68 0.00 3.18
1785 6435 0.248012 ACCGTCGTATGGCATTGACA 59.752 50.000 23.61 0.00 0.00 3.58
1786 6436 0.930310 CCGTCGTATGGCATTGACAG 59.070 55.000 23.61 17.80 0.00 3.51
1787 6437 0.301687 CGTCGTATGGCATTGACAGC 59.698 55.000 23.61 7.06 0.00 4.40
1788 6438 1.656652 GTCGTATGGCATTGACAGCT 58.343 50.000 20.92 0.00 0.00 4.24
1791 6441 0.028505 GTATGGCATTGACAGCTGCG 59.971 55.000 15.27 0.00 39.30 5.18
1827 6486 0.467384 CGGAGGAGAAGCATGGTGAT 59.533 55.000 0.00 0.00 0.00 3.06
1996 6655 1.971167 GTCATGGCAAAGGTCCGCA 60.971 57.895 0.00 0.00 0.00 5.69
2619 7320 8.931775 TGTCTTATGTACATGTCAACATAACAC 58.068 33.333 22.05 21.63 41.37 3.32
2620 7321 8.108172 GTCTTATGTACATGTCAACATAACACG 58.892 37.037 22.05 15.84 41.37 4.49
2621 7322 4.655440 TGTACATGTCAACATAACACGC 57.345 40.909 0.00 0.00 34.26 5.34
2622 7323 3.433957 TGTACATGTCAACATAACACGCC 59.566 43.478 0.00 0.00 34.26 5.68
2623 7324 2.499197 ACATGTCAACATAACACGCCA 58.501 42.857 0.00 0.00 34.26 5.69
2624 7325 3.081061 ACATGTCAACATAACACGCCAT 58.919 40.909 0.00 0.00 34.26 4.40
2625 7326 3.126858 ACATGTCAACATAACACGCCATC 59.873 43.478 0.00 0.00 34.26 3.51
2626 7327 3.052455 TGTCAACATAACACGCCATCT 57.948 42.857 0.00 0.00 0.00 2.90
2627 7328 4.195225 TGTCAACATAACACGCCATCTA 57.805 40.909 0.00 0.00 0.00 1.98
2628 7329 3.930229 TGTCAACATAACACGCCATCTAC 59.070 43.478 0.00 0.00 0.00 2.59
2629 7330 4.181578 GTCAACATAACACGCCATCTACT 58.818 43.478 0.00 0.00 0.00 2.57
2630 7331 4.267928 GTCAACATAACACGCCATCTACTC 59.732 45.833 0.00 0.00 0.00 2.59
2631 7332 4.159693 TCAACATAACACGCCATCTACTCT 59.840 41.667 0.00 0.00 0.00 3.24
2632 7333 5.358725 TCAACATAACACGCCATCTACTCTA 59.641 40.000 0.00 0.00 0.00 2.43
2633 7334 5.847111 ACATAACACGCCATCTACTCTAA 57.153 39.130 0.00 0.00 0.00 2.10
2634 7335 6.216801 ACATAACACGCCATCTACTCTAAA 57.783 37.500 0.00 0.00 0.00 1.85
2635 7336 6.636705 ACATAACACGCCATCTACTCTAAAA 58.363 36.000 0.00 0.00 0.00 1.52
2636 7337 7.101054 ACATAACACGCCATCTACTCTAAAAA 58.899 34.615 0.00 0.00 0.00 1.94
2663 7364 7.011482 ACACGCCATCTTAATTATTCTTGTCTC 59.989 37.037 0.00 0.00 0.00 3.36
2722 7423 6.102663 GTGGGATAAGATTATCACTCGGATG 58.897 44.000 14.29 0.00 42.66 3.51
2723 7424 5.112686 GGGATAAGATTATCACTCGGATGC 58.887 45.833 13.18 0.00 39.82 3.91
2724 7425 5.105146 GGGATAAGATTATCACTCGGATGCT 60.105 44.000 13.18 0.00 39.82 3.79
2725 7426 6.096987 GGGATAAGATTATCACTCGGATGCTA 59.903 42.308 13.18 0.00 39.82 3.49
2733 7670 4.046938 TCACTCGGATGCTATTTCTCAC 57.953 45.455 0.00 0.00 0.00 3.51
2749 7686 3.067106 TCTCACGTGCCTGAAATTTCTC 58.933 45.455 18.64 8.76 0.00 2.87
2757 7694 4.451096 GTGCCTGAAATTTCTCTTCGTGTA 59.549 41.667 18.64 0.00 0.00 2.90
2767 7704 6.823678 TTTCTCTTCGTGTAAGTCACTTTC 57.176 37.500 0.00 0.00 44.16 2.62
2770 7707 6.207213 TCTCTTCGTGTAAGTCACTTTCTTC 58.793 40.000 0.00 0.00 44.16 2.87
2783 7729 6.327887 AGTCACTTTCTTCCTTCTTCCTTACT 59.672 38.462 0.00 0.00 0.00 2.24
2822 7768 4.487282 ACTAGCCCCACCATCTATCTTA 57.513 45.455 0.00 0.00 0.00 2.10
2824 7770 2.625639 AGCCCCACCATCTATCTTAGG 58.374 52.381 0.00 0.00 0.00 2.69
2825 7771 2.182312 AGCCCCACCATCTATCTTAGGA 59.818 50.000 0.00 0.00 0.00 2.94
2829 7775 5.035556 CCCCACCATCTATCTTAGGATGAT 58.964 45.833 0.00 0.00 41.05 2.45
2831 7777 5.486775 CCCACCATCTATCTTAGGATGATGT 59.513 44.000 17.65 9.31 41.05 3.06
2834 7780 7.095910 CACCATCTATCTTAGGATGATGTCAC 58.904 42.308 17.65 0.00 41.05 3.67
2837 7783 8.152898 CCATCTATCTTAGGATGATGTCACAAA 58.847 37.037 17.65 0.00 41.05 2.83
2857 7803 6.942576 CACAAACCCATTATCTATCTTAGGGG 59.057 42.308 0.00 0.00 39.15 4.79
2863 7809 2.743131 ATCTATCTTAGGGGTGGGGG 57.257 55.000 0.00 0.00 0.00 5.40
2891 7843 2.139917 TCGTGGTCGAAGGTTTTCATG 58.860 47.619 0.00 0.00 43.34 3.07
2893 7845 2.500229 GTGGTCGAAGGTTTTCATGGA 58.500 47.619 0.00 0.00 32.67 3.41
2901 7853 3.524095 AGGTTTTCATGGATGGTGTCA 57.476 42.857 0.00 0.00 0.00 3.58
2906 7858 0.543277 TCATGGATGGTGTCAGGCTC 59.457 55.000 0.00 0.00 0.00 4.70
2964 7923 4.814294 GGAGGCGGTGCACGGTAG 62.814 72.222 23.39 10.46 44.51 3.18
2965 7924 4.065281 GAGGCGGTGCACGGTAGT 62.065 66.667 23.39 10.04 44.51 2.73
3013 7972 1.458967 CGGTTAGGGAGGGGTAGGG 60.459 68.421 0.00 0.00 0.00 3.53
3014 7973 1.769295 GGTTAGGGAGGGGTAGGGC 60.769 68.421 0.00 0.00 0.00 5.19
3049 8008 7.280876 TCGGAAGAAGGAAGAATATGAACAATG 59.719 37.037 0.00 0.00 37.03 2.82
3053 8012 4.526970 AGGAAGAATATGAACAATGGCGT 58.473 39.130 0.00 0.00 0.00 5.68
3057 8016 6.204688 GGAAGAATATGAACAATGGCGTGATA 59.795 38.462 0.00 0.00 0.00 2.15
3085 8044 2.208431 GAGCGGTTGGATGAAGATCTG 58.792 52.381 0.00 0.00 0.00 2.90
3087 8046 2.437281 AGCGGTTGGATGAAGATCTGAT 59.563 45.455 0.00 0.00 0.00 2.90
3167 8126 7.448469 GTGGCTCCCATTATCATTAGTAATGTT 59.552 37.037 19.85 15.05 37.68 2.71
3233 8192 3.617263 GCGATGACGGTTCTTTTCATACT 59.383 43.478 0.00 0.00 40.15 2.12
3256 8215 5.338632 TGTAAGTCCTCCTTTGATGGTAGA 58.661 41.667 0.00 0.00 34.46 2.59
3385 8344 5.372343 AGACATACCCTTATGAATGCACA 57.628 39.130 0.00 0.00 37.86 4.57
3387 8346 3.876914 ACATACCCTTATGAATGCACACG 59.123 43.478 0.00 0.00 37.86 4.49
3464 8423 4.022068 CACCACAAAAGGCTGACAATGTAT 60.022 41.667 0.00 0.00 0.00 2.29
3470 8429 2.826428 AGGCTGACAATGTATGCTACG 58.174 47.619 9.29 0.00 0.00 3.51
3490 8449 1.391826 GCTCAGTTTGCGTCTAAGCTC 59.608 52.381 0.00 0.00 38.13 4.09
3516 8475 9.031360 CATATTTCTTTTCCTTTGATGCATGAG 57.969 33.333 2.46 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 133 5.458779 GCTGTTTGTGTTTAAAAGCCAGTAG 59.541 40.000 0.00 0.00 0.00 2.57
148 158 2.195123 AAATGCAGCACGGTTACGCC 62.195 55.000 0.00 0.00 46.04 5.68
351 2354 1.860950 GACATGTACGCACTGCTATGG 59.139 52.381 0.00 0.00 0.00 2.74
388 2398 3.073678 ACGCACATGCAAAGTCATCTAA 58.926 40.909 4.49 0.00 42.21 2.10
395 2405 2.563798 CCCCACGCACATGCAAAGT 61.564 57.895 4.49 0.00 42.21 2.66
617 5140 4.037684 GTGAGTGTATACCGCCTGTATTCT 59.962 45.833 0.00 0.00 40.64 2.40
693 5216 2.022240 AAAATGCGTTTGGTGGCCGT 62.022 50.000 4.29 0.00 0.00 5.68
716 5239 1.488393 GCAGAAAGGAGGCTCCATACT 59.512 52.381 33.86 24.16 39.61 2.12
717 5240 1.808133 CGCAGAAAGGAGGCTCCATAC 60.808 57.143 33.86 22.49 39.61 2.39
833 5370 2.998097 CCAATGGAGGCCGAGGAA 59.002 61.111 0.00 0.00 0.00 3.36
896 5437 3.740009 CGAACTCGTGGCTGGTTAACAG 61.740 54.545 8.10 0.00 41.41 3.16
897 5438 1.870580 CGAACTCGTGGCTGGTTAACA 60.871 52.381 8.10 0.00 34.11 2.41
898 5439 0.788391 CGAACTCGTGGCTGGTTAAC 59.212 55.000 0.00 0.00 34.11 2.01
920 5463 5.663106 AGTAGATGTAGATTGTGGTGTGGAT 59.337 40.000 0.00 0.00 0.00 3.41
922 5465 5.344743 AGTAGATGTAGATTGTGGTGTGG 57.655 43.478 0.00 0.00 0.00 4.17
947 5558 1.688772 GGAGCCCGTCTGTCTATGTA 58.311 55.000 0.00 0.00 0.00 2.29
1687 6337 2.747855 CCCTTGCAAGTCGAGCCC 60.748 66.667 24.35 0.00 0.00 5.19
1791 6441 3.660111 GTGGACGTGTTGGCAGCC 61.660 66.667 3.66 3.66 0.00 4.85
1996 6655 2.553086 GAGAGTGTCGTCTATCTCCGT 58.447 52.381 4.30 0.00 33.57 4.69
2633 7334 9.139174 CAAGAATAATTAAGATGGCGTGTTTTT 57.861 29.630 0.00 0.00 0.00 1.94
2634 7335 8.303876 ACAAGAATAATTAAGATGGCGTGTTTT 58.696 29.630 0.00 0.00 0.00 2.43
2635 7336 7.826690 ACAAGAATAATTAAGATGGCGTGTTT 58.173 30.769 0.00 0.00 0.00 2.83
2636 7337 7.336931 AGACAAGAATAATTAAGATGGCGTGTT 59.663 33.333 0.00 0.00 0.00 3.32
2637 7338 6.823689 AGACAAGAATAATTAAGATGGCGTGT 59.176 34.615 0.00 0.00 0.00 4.49
2638 7339 7.225538 AGAGACAAGAATAATTAAGATGGCGTG 59.774 37.037 0.00 0.00 0.00 5.34
2639 7340 7.275920 AGAGACAAGAATAATTAAGATGGCGT 58.724 34.615 0.00 0.00 0.00 5.68
2722 7423 2.010145 TCAGGCACGTGAGAAATAGC 57.990 50.000 22.23 0.00 0.00 2.97
2723 7424 5.551760 AATTTCAGGCACGTGAGAAATAG 57.448 39.130 28.27 11.28 39.14 1.73
2724 7425 5.705441 AGAAATTTCAGGCACGTGAGAAATA 59.295 36.000 28.27 14.32 39.14 1.40
2725 7426 4.520492 AGAAATTTCAGGCACGTGAGAAAT 59.480 37.500 25.26 25.26 41.11 2.17
2733 7670 2.480419 ACGAAGAGAAATTTCAGGCACG 59.520 45.455 19.99 17.96 0.00 5.34
2757 7694 5.638530 AGGAAGAAGGAAGAAAGTGACTT 57.361 39.130 0.00 0.00 0.00 3.01
2767 7704 5.241662 CAAGGTCAGTAAGGAAGAAGGAAG 58.758 45.833 0.00 0.00 0.00 3.46
2770 7707 3.339141 GCAAGGTCAGTAAGGAAGAAGG 58.661 50.000 0.00 0.00 0.00 3.46
2783 7729 0.034896 GTTCTTCTCCGGCAAGGTCA 59.965 55.000 11.79 0.00 41.99 4.02
2822 7768 3.744940 ATGGGTTTGTGACATCATCCT 57.255 42.857 0.00 0.00 0.00 3.24
2824 7770 6.949352 AGATAATGGGTTTGTGACATCATC 57.051 37.500 0.00 0.00 0.00 2.92
2825 7771 8.443176 AGATAGATAATGGGTTTGTGACATCAT 58.557 33.333 0.00 0.00 0.00 2.45
2829 7775 8.210946 CCTAAGATAGATAATGGGTTTGTGACA 58.789 37.037 0.00 0.00 0.00 3.58
2831 7777 7.202186 CCCCTAAGATAGATAATGGGTTTGTGA 60.202 40.741 0.00 0.00 0.00 3.58
2834 7780 6.942576 CACCCCTAAGATAGATAATGGGTTTG 59.057 42.308 0.00 0.00 42.25 2.93
2837 7783 5.101529 CCACCCCTAAGATAGATAATGGGT 58.898 45.833 0.00 0.00 45.73 4.51
2872 7818 1.196808 CCATGAAAACCTTCGACCACG 59.803 52.381 0.00 0.00 41.26 4.94
2873 7819 2.500229 TCCATGAAAACCTTCGACCAC 58.500 47.619 0.00 0.00 33.94 4.16
2874 7820 2.940994 TCCATGAAAACCTTCGACCA 57.059 45.000 0.00 0.00 33.94 4.02
2880 7832 3.828451 CTGACACCATCCATGAAAACCTT 59.172 43.478 0.00 0.00 0.00 3.50
2891 7843 1.222936 CCTGAGCCTGACACCATCC 59.777 63.158 0.00 0.00 0.00 3.51
2893 7845 2.673523 GCCTGAGCCTGACACCAT 59.326 61.111 0.00 0.00 0.00 3.55
2917 7876 3.345808 CCACCGTTGCTGGTCACG 61.346 66.667 0.00 0.00 41.38 4.35
2947 7906 4.814294 CTACCGTGCACCGCCTCC 62.814 72.222 12.15 0.00 34.38 4.30
3013 7972 3.540367 TTCTTCCGAACACCCCCGC 62.540 63.158 0.00 0.00 0.00 6.13
3014 7973 1.375523 CTTCTTCCGAACACCCCCG 60.376 63.158 0.00 0.00 0.00 5.73
3027 7986 6.183360 CGCCATTGTTCATATTCTTCCTTCTT 60.183 38.462 0.00 0.00 0.00 2.52
3039 7998 8.341903 CAAAATAGTATCACGCCATTGTTCATA 58.658 33.333 0.00 0.00 0.00 2.15
3049 8008 2.221055 CCGCTCAAAATAGTATCACGCC 59.779 50.000 0.00 0.00 0.00 5.68
3053 8012 5.092554 TCCAACCGCTCAAAATAGTATCA 57.907 39.130 0.00 0.00 0.00 2.15
3057 8016 3.950397 TCATCCAACCGCTCAAAATAGT 58.050 40.909 0.00 0.00 0.00 2.12
3135 8094 1.947456 GATAATGGGAGCCACGGTTTC 59.053 52.381 0.00 0.00 35.80 2.78
3137 8096 0.916086 TGATAATGGGAGCCACGGTT 59.084 50.000 0.00 0.00 35.80 4.44
3140 8099 4.008074 ACTAATGATAATGGGAGCCACG 57.992 45.455 0.00 0.00 35.80 4.94
3218 8177 6.164176 AGGACTTACAGTATGAAAAGAACCG 58.836 40.000 0.51 0.00 39.69 4.44
3233 8192 5.338632 TCTACCATCAAAGGAGGACTTACA 58.661 41.667 0.00 0.00 38.85 2.41
3349 8308 8.472007 AAGGGTATGTCTTTATTGTGTTTTGA 57.528 30.769 0.00 0.00 0.00 2.69
3359 8318 7.998383 TGTGCATTCATAAGGGTATGTCTTTAT 59.002 33.333 0.00 0.00 38.63 1.40
3367 8326 4.150897 ACGTGTGCATTCATAAGGGTAT 57.849 40.909 0.00 0.00 0.00 2.73
3385 8344 4.284178 AGGAATAGGGTGTACATGTACGT 58.716 43.478 26.59 15.54 38.85 3.57
3387 8346 7.357429 ACTTAGGAATAGGGTGTACATGTAC 57.643 40.000 25.99 25.99 36.63 2.90
3470 8429 1.391826 GAGCTTAGACGCAAACTGAGC 59.608 52.381 0.00 0.00 43.89 4.26
3490 8449 8.936070 TCATGCATCAAAGGAAAAGAAATATG 57.064 30.769 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.