Multiple sequence alignment - TraesCS1B01G016400

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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 TraesCS1B01G016400 chr1B 100.000 8463 0 0 1 8463 7988141 7996603 0.000000e+00 15629.0
1 TraesCS1B01G016400 chr1B 97.010 3646 100 6 4823 8463 22704867 22708508 0.000000e+00 6120.0
2 TraesCS1B01G016400 chr1B 97.712 3103 68 2 1722 4822 22701602 22704703 0.000000e+00 5334.0
3 TraesCS1B01G016400 chr1B 92.227 952 24 16 628 1529 22700659 22701610 0.000000e+00 1303.0
4 TraesCS1B01G016400 chr1B 80.350 1715 271 38 5897 7579 144930315 144931995 0.000000e+00 1240.0
5 TraesCS1B01G016400 chr1B 84.089 1257 166 21 2736 3976 22701140 22702378 0.000000e+00 1182.0
6 TraesCS1B01G016400 chr1B 86.521 779 91 5 3209 3976 7989862 7990637 0.000000e+00 845.0
7 TraesCS1B01G016400 chr1B 86.521 779 91 5 1722 2497 7991349 7992116 0.000000e+00 845.0
8 TraesCS1B01G016400 chr1B 85.494 779 99 5 1722 2497 22703090 22703857 0.000000e+00 800.0
9 TraesCS1B01G016400 chr1B 83.666 851 117 9 5176 6007 22701771 22702618 0.000000e+00 782.0
10 TraesCS1B01G016400 chr1B 82.333 600 90 7 3377 3967 22705220 22705812 2.730000e-139 507.0
11 TraesCS1B01G016400 chr1B 81.833 600 93 7 5176 5768 7991517 7992107 2.750000e-134 490.0
12 TraesCS1B01G016400 chr1B 81.833 600 93 7 3377 3967 7993316 7993908 2.750000e-134 490.0
13 TraesCS1B01G016400 chr1B 80.833 600 99 7 5176 5768 22703258 22703848 2.780000e-124 457.0
14 TraesCS1B01G016400 chr1B 82.281 491 65 14 2736 3221 7989199 7989672 1.020000e-108 405.0
15 TraesCS1B01G016400 chr1B 82.317 492 63 16 1059 1532 7990876 7991361 1.020000e-108 405.0
16 TraesCS1B01G016400 chr1B 84.433 379 56 3 2107 2485 144929802 144930177 3.730000e-98 370.0
17 TraesCS1B01G016400 chr1B 83.827 371 50 6 1169 1532 144929799 144930166 2.260000e-90 344.0
18 TraesCS1B01G016400 chr1B 96.117 206 6 2 1524 1728 680813718 680813922 1.360000e-87 335.0
19 TraesCS1B01G016400 chr1B 95.652 207 7 2 1522 1727 7859700 7859905 1.760000e-86 331.0
20 TraesCS1B01G016400 chr1B 82.029 345 55 6 2875 3216 144926617 144926957 3.870000e-73 287.0
21 TraesCS1B01G016400 chr1B 96.753 154 5 0 471 624 22700348 22700501 3.030000e-64 257.0
22 TraesCS1B01G016400 chr1B 84.274 248 29 8 1759 1999 22705810 22706054 5.110000e-57 233.0
23 TraesCS1B01G016400 chr1D 96.444 2784 82 6 4823 7604 4824920 4827688 0.000000e+00 4577.0
24 TraesCS1B01G016400 chr1D 95.369 2224 93 4 2546 4760 4822584 4824806 0.000000e+00 3528.0
25 TraesCS1B01G016400 chr1D 97.657 811 16 2 1722 2530 4821789 4822598 0.000000e+00 1389.0
26 TraesCS1B01G016400 chr1D 97.333 750 19 1 780 1529 4821049 4821797 0.000000e+00 1273.0
27 TraesCS1B01G016400 chr1D 84.646 1257 159 21 2736 3976 4821327 4822565 0.000000e+00 1221.0
28 TraesCS1B01G016400 chr1D 96.011 727 25 3 7740 8463 4838014 4838739 0.000000e+00 1179.0
29 TraesCS1B01G016400 chr1D 80.100 1402 195 48 5417 6810 4769091 4770416 0.000000e+00 966.0
30 TraesCS1B01G016400 chr1D 93.770 626 27 6 1 624 4820084 4820699 0.000000e+00 929.0
31 TraesCS1B01G016400 chr1D 86.410 780 89 8 1722 2497 4823249 4824015 0.000000e+00 837.0
32 TraesCS1B01G016400 chr1D 80.190 1156 189 26 6434 7579 90150886 90152011 0.000000e+00 830.0
33 TraesCS1B01G016400 chr1D 82.718 839 119 14 5176 6007 4821958 4822777 0.000000e+00 723.0
34 TraesCS1B01G016400 chr1D 85.901 688 82 9 6899 7585 4774289 4774962 0.000000e+00 719.0
35 TraesCS1B01G016400 chr1D 82.500 600 89 7 3377 3967 4825274 4825866 5.860000e-141 512.0
36 TraesCS1B01G016400 chr1D 84.114 491 56 12 1059 1532 4822776 4823261 1.000000e-123 455.0
37 TraesCS1B01G016400 chr1D 86.804 341 39 1 1194 1528 4769082 4769422 8.020000e-100 375.0
38 TraesCS1B01G016400 chr1D 81.663 469 67 9 1079 1532 4825387 4825851 1.040000e-98 372.0
39 TraesCS1B01G016400 chr1D 76.327 735 147 16 6771 7479 10154339 10153606 1.340000e-97 368.0
40 TraesCS1B01G016400 chr1D 86.145 332 46 0 2138 2469 4769091 4769422 8.080000e-95 359.0
41 TraesCS1B01G016400 chr1D 83.516 364 54 6 2856 3216 4769062 4769422 1.360000e-87 335.0
42 TraesCS1B01G016400 chr1D 82.507 343 57 3 2875 3216 90148873 90149213 1.790000e-76 298.0
43 TraesCS1B01G016400 chr1D 97.419 155 3 1 628 781 4820859 4821013 6.510000e-66 263.0
44 TraesCS1B01G016400 chr1D 83.871 248 30 8 1759 1999 4825864 4826108 2.380000e-55 228.0
45 TraesCS1B01G016400 chr1D 81.319 273 47 2 7206 7474 10070163 10069891 1.430000e-52 219.0
46 TraesCS1B01G016400 chr1D 88.596 114 12 1 5901 6013 4825271 4825384 4.120000e-28 137.0
47 TraesCS1B01G016400 chr1A 95.876 2740 87 10 4871 7604 6321676 6324395 0.000000e+00 4410.0
48 TraesCS1B01G016400 chr1A 95.577 2487 99 4 1722 4197 6318357 6320843 0.000000e+00 3973.0
49 TraesCS1B01G016400 chr1A 80.641 1715 261 44 5897 7579 86238590 86240265 0.000000e+00 1262.0
50 TraesCS1B01G016400 chr1A 95.910 758 22 5 780 1529 6317609 6318365 0.000000e+00 1219.0
51 TraesCS1B01G016400 chr1A 96.332 736 27 0 7728 8463 6324392 6325127 0.000000e+00 1210.0
52 TraesCS1B01G016400 chr1A 86.410 780 91 6 1722 2497 6319847 6320615 0.000000e+00 839.0
53 TraesCS1B01G016400 chr1A 83.803 852 114 10 5176 6007 6318528 6319375 0.000000e+00 787.0
54 TraesCS1B01G016400 chr1A 94.468 470 15 3 4253 4722 6321121 6321579 0.000000e+00 713.0
55 TraesCS1B01G016400 chr1A 79.793 871 129 29 5173 6010 6319269 6320125 2.630000e-164 590.0
56 TraesCS1B01G016400 chr1A 80.728 742 106 23 5288 6010 6317914 6318637 2.080000e-150 544.0
57 TraesCS1B01G016400 chr1A 84.381 493 51 16 1059 1532 6319374 6319859 2.150000e-125 460.0
58 TraesCS1B01G016400 chr1A 81.818 473 65 10 1079 1535 6322094 6322561 2.230000e-100 377.0
59 TraesCS1B01G016400 chr1A 96.476 227 7 1 398 624 6317015 6317240 2.880000e-99 374.0
60 TraesCS1B01G016400 chr1A 81.513 476 60 15 1080 1532 86237971 86238441 4.830000e-97 366.0
61 TraesCS1B01G016400 chr1A 96.154 208 6 2 1524 1730 44329175 44328969 1.050000e-88 339.0
62 TraesCS1B01G016400 chr1A 81.924 343 59 3 2875 3216 86235732 86236072 3.870000e-73 287.0
63 TraesCS1B01G016400 chr1A 95.775 142 5 1 270 410 6301202 6301343 2.380000e-55 228.0
64 TraesCS1B01G016400 chr1A 93.137 102 6 1 628 728 6317400 6317501 1.900000e-31 148.0
65 TraesCS1B01G016400 chr1A 82.836 134 23 0 5156 5289 86238577 86238710 4.150000e-23 121.0
66 TraesCS1B01G016400 chr7B 96.602 206 7 0 1522 1727 718077363 718077158 8.130000e-90 342.0
67 TraesCS1B01G016400 chr7B 95.631 206 9 0 1522 1727 695947455 695947660 1.760000e-86 331.0
68 TraesCS1B01G016400 chr7B 95.652 207 7 2 1523 1728 732975927 732975722 1.760000e-86 331.0
69 TraesCS1B01G016400 chr7B 88.136 177 16 4 7561 7736 126549266 126549094 1.110000e-48 206.0
70 TraesCS1B01G016400 chr6B 95.215 209 10 0 1524 1732 41401973 41401765 1.760000e-86 331.0
71 TraesCS1B01G016400 chr6B 92.254 142 9 1 7594 7735 716890335 716890474 5.180000e-47 200.0
72 TraesCS1B01G016400 chr5B 94.037 218 10 3 1512 1728 38516491 38516706 2.280000e-85 327.0
73 TraesCS1B01G016400 chr5B 94.737 133 5 1 7600 7732 533628724 533628854 1.110000e-48 206.0
74 TraesCS1B01G016400 chr5B 94.074 135 6 1 7603 7737 555175729 555175597 4.000000e-48 204.0
75 TraesCS1B01G016400 chr5B 92.908 141 7 2 7603 7743 224325536 224325673 1.440000e-47 202.0
76 TraesCS1B01G016400 chr5B 75.926 162 18 12 8071 8222 369484058 369483908 7.090000e-06 63.9
77 TraesCS1B01G016400 chr3B 94.811 212 7 3 1529 1737 764366483 764366273 2.280000e-85 327.0
78 TraesCS1B01G016400 chr5A 94.074 135 6 1 7600 7734 9840826 9840958 4.000000e-48 204.0
79 TraesCS1B01G016400 chr3D 92.466 146 6 4 7588 7731 67064769 67064911 4.000000e-48 204.0
80 TraesCS1B01G016400 chr2B 95.349 129 4 1 7603 7731 349930710 349930584 4.000000e-48 204.0
81 TraesCS1B01G016400 chr6D 80.952 105 19 1 8119 8223 163934055 163934158 1.960000e-11 82.4
82 TraesCS1B01G016400 chr5D 77.124 153 24 6 8071 8222 319252939 319252797 2.530000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G016400 chr1B 7988141 7996603 8462 False 15629.000000 15629 100.00000 1 8463 1 chr1B.!!$F2 8462
1 TraesCS1B01G016400 chr1B 22700348 22708508 8160 False 1697.500000 6120 88.43910 471 8463 10 chr1B.!!$F5 7992
2 TraesCS1B01G016400 chr1B 7989199 7993908 4709 False 580.000000 845 83.55100 1059 5768 6 chr1B.!!$F4 4709
3 TraesCS1B01G016400 chr1B 144926617 144931995 5378 False 560.250000 1240 82.65975 1169 7579 4 chr1B.!!$F6 6410
4 TraesCS1B01G016400 chr1D 4838014 4838739 725 False 1179.000000 1179 96.01100 7740 8463 1 chr1D.!!$F2 723
5 TraesCS1B01G016400 chr1D 4820084 4827688 7604 False 1174.571429 4577 89.46500 1 7604 14 chr1D.!!$F4 7603
6 TraesCS1B01G016400 chr1D 4774289 4774962 673 False 719.000000 719 85.90100 6899 7585 1 chr1D.!!$F1 686
7 TraesCS1B01G016400 chr1D 90148873 90152011 3138 False 564.000000 830 81.34850 2875 7579 2 chr1D.!!$F5 4704
8 TraesCS1B01G016400 chr1D 4769062 4770416 1354 False 508.750000 966 84.14125 1194 6810 4 chr1D.!!$F3 5616
9 TraesCS1B01G016400 chr1D 10153606 10154339 733 True 368.000000 368 76.32700 6771 7479 1 chr1D.!!$R2 708
10 TraesCS1B01G016400 chr1A 6317015 6325127 8112 False 1203.384615 4410 89.59300 398 8463 13 chr1A.!!$F2 8065
11 TraesCS1B01G016400 chr1A 86235732 86240265 4533 False 509.000000 1262 81.72850 1080 7579 4 chr1A.!!$F3 6499

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
83 84 0.034574 ACACCCACACAAGAAGCACA 60.035 50.000 0.00 0.00 0.00 4.57 F
784 961 0.179171 TAGAGCAGACGCGTACAAGC 60.179 55.000 13.97 14.23 45.49 4.01 F
808 1021 1.876156 GCAGGCATATAGTTGGAGTGC 59.124 52.381 0.00 0.00 35.17 4.40 F
6381 10920 0.542702 CCAACCCTCCAGCACCATTT 60.543 55.000 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5937 10454 3.292936 ACGAAGTCGGCCGTCACT 61.293 61.111 27.15 19.76 44.95 3.41 R
6381 10920 1.881903 CTTGCAGAGAGCCTCCGACA 61.882 60.000 0.00 0.00 44.83 4.35 R
6859 11664 0.179100 CTAGGGACACACCATCTGCG 60.179 60.000 0.00 0.00 41.20 5.18 R
8419 13261 0.388649 GCACGTGAAGGATGAGACGT 60.389 55.000 22.23 0.00 45.47 4.34 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
58 59 1.010580 TGTATACGGCCATGCAAACG 58.989 50.000 2.24 0.00 0.00 3.60
59 60 1.292061 GTATACGGCCATGCAAACGA 58.708 50.000 2.24 0.00 0.00 3.85
60 61 1.666700 GTATACGGCCATGCAAACGAA 59.333 47.619 2.24 0.00 0.00 3.85
61 62 0.450184 ATACGGCCATGCAAACGAAC 59.550 50.000 2.24 0.00 0.00 3.95
62 63 0.885150 TACGGCCATGCAAACGAACA 60.885 50.000 2.24 0.00 0.00 3.18
63 64 1.729131 CGGCCATGCAAACGAACAC 60.729 57.895 2.24 0.00 0.00 3.32
68 69 1.476074 CATGCAAACGAACACACACC 58.524 50.000 0.00 0.00 0.00 4.16
83 84 0.034574 ACACCCACACAAGAAGCACA 60.035 50.000 0.00 0.00 0.00 4.57
106 107 1.289109 ACCCATGACGCTCGAAAACG 61.289 55.000 0.00 1.08 0.00 3.60
129 130 2.237751 GCTTGCACGACACGACACT 61.238 57.895 0.00 0.00 0.00 3.55
143 144 3.305094 CACGACACTAACAAGACAACGTT 59.695 43.478 0.00 0.00 0.00 3.99
144 145 3.305094 ACGACACTAACAAGACAACGTTG 59.695 43.478 26.20 26.20 0.00 4.10
146 147 3.004171 ACACTAACAAGACAACGTTGCA 58.996 40.909 27.61 4.24 0.00 4.08
147 148 3.181514 ACACTAACAAGACAACGTTGCAC 60.182 43.478 27.61 20.64 0.00 4.57
168 169 2.534349 CGAAAACGGGATGACGACATAG 59.466 50.000 0.00 0.00 36.82 2.23
171 172 1.371758 CGGGATGACGACATAGCCG 60.372 63.158 0.00 0.00 36.82 5.52
199 200 1.527433 CCTCGCTAGATCATCCGCCA 61.527 60.000 0.00 0.00 0.00 5.69
218 219 4.692475 CCCACACCCGACCCGAAC 62.692 72.222 0.00 0.00 0.00 3.95
291 292 2.501610 GATCCGACAGAGCACCCC 59.498 66.667 0.00 0.00 0.00 4.95
292 293 2.284625 ATCCGACAGAGCACCCCA 60.285 61.111 0.00 0.00 0.00 4.96
303 304 1.826487 GCACCCCAAAAGGACACGT 60.826 57.895 0.00 0.00 38.24 4.49
620 621 4.599720 TGACATTTTGATATGGTGGGGA 57.400 40.909 0.00 0.00 0.00 4.81
624 625 3.722908 TTTTGATATGGTGGGGACGAA 57.277 42.857 0.00 0.00 0.00 3.85
625 626 2.702592 TTGATATGGTGGGGACGAAC 57.297 50.000 0.00 0.00 0.00 3.95
626 627 0.462375 TGATATGGTGGGGACGAACG 59.538 55.000 0.00 0.00 0.00 3.95
627 628 0.748450 GATATGGTGGGGACGAACGA 59.252 55.000 0.14 0.00 0.00 3.85
629 630 1.196911 TATGGTGGGGACGAACGAAT 58.803 50.000 0.14 0.00 0.00 3.34
656 814 3.429547 GGCTATAGTGGCTCATACGGATG 60.430 52.174 0.00 0.00 0.00 3.51
699 857 4.705023 ACTCCCTCCAATCCGTTTTAAATG 59.295 41.667 0.00 0.00 0.00 2.32
750 927 4.081586 AGTCGGAGTGGAGTAGAATTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
781 958 1.662629 GTAGTAGAGCAGACGCGTACA 59.337 52.381 13.97 0.00 45.49 2.90
782 959 1.162698 AGTAGAGCAGACGCGTACAA 58.837 50.000 13.97 0.00 45.49 2.41
783 960 1.130749 AGTAGAGCAGACGCGTACAAG 59.869 52.381 13.97 3.20 45.49 3.16
784 961 0.179171 TAGAGCAGACGCGTACAAGC 60.179 55.000 13.97 14.23 45.49 4.01
808 1021 1.876156 GCAGGCATATAGTTGGAGTGC 59.124 52.381 0.00 0.00 35.17 4.40
935 1161 4.166144 CCCACCCACTTAAACATCTCCTAT 59.834 45.833 0.00 0.00 0.00 2.57
973 1199 3.931468 CAGACTAGCAAGAAGACCACATG 59.069 47.826 0.00 0.00 0.00 3.21
982 1208 5.334724 GCAAGAAGACCACATGAAAGAGAAG 60.335 44.000 0.00 0.00 0.00 2.85
5937 10454 3.572255 GGTAGGCAAACAAAGATGGTTCA 59.428 43.478 0.00 0.00 32.99 3.18
6351 10890 3.077907 CCAGTCGGGTGGTGGATT 58.922 61.111 0.00 0.00 32.60 3.01
6381 10920 0.542702 CCAACCCTCCAGCACCATTT 60.543 55.000 0.00 0.00 0.00 2.32
6436 10975 2.172679 TCACATGGGCAGAGTACGTAA 58.827 47.619 0.00 0.00 0.00 3.18
6859 11664 2.352960 GGAGTTGATGAATGAGCCGTTC 59.647 50.000 0.00 0.00 0.00 3.95
6879 11684 0.462759 GCAGATGGTGTGTCCCTAGC 60.463 60.000 0.00 0.00 34.77 3.42
6915 11720 1.001633 CTACCAACAGGGCTACAACGT 59.998 52.381 0.00 0.00 42.05 3.99
6954 11759 2.245159 ACGGCCTATGTGATCATGTG 57.755 50.000 0.00 0.00 35.70 3.21
7105 11910 6.147821 ACATCGATTTCGTCAACAAAGAGATT 59.852 34.615 0.00 0.00 40.80 2.40
7122 11927 0.463295 ATTGCCGGTGATCTCAGCAG 60.463 55.000 1.90 0.00 44.00 4.24
7448 12277 3.536956 TCAACAACGGATACATCTCCC 57.463 47.619 0.00 0.00 31.04 4.30
7612 12449 6.651975 ATGATTTAAGTAGTACTCCCTCCG 57.348 41.667 2.58 0.00 0.00 4.63
7616 12453 0.179936 AGTAGTACTCCCTCCGTCCG 59.820 60.000 0.00 0.00 0.00 4.79
7670 12507 8.540388 TGGGGATGTATCTAGATGTATTTTAGC 58.460 37.037 15.79 0.00 0.00 3.09
7695 12532 5.178096 TCTAGATGCATCCCTTTTTGTCA 57.822 39.130 23.06 0.00 0.00 3.58
7701 12538 6.428771 AGATGCATCCCTTTTTGTCAATTTTG 59.571 34.615 23.06 0.00 0.00 2.44
7787 12624 6.371809 TTGTTTCACGCCAATAATCTATCC 57.628 37.500 0.00 0.00 0.00 2.59
7788 12625 5.680619 TGTTTCACGCCAATAATCTATCCT 58.319 37.500 0.00 0.00 0.00 3.24
7873 12710 5.545723 ACTTTGCTCTATGGGCATATCTAGT 59.454 40.000 0.00 0.00 39.54 2.57
8267 13108 1.339631 CGCCCCTTACAATCAACTCCA 60.340 52.381 0.00 0.00 0.00 3.86
8288 13129 1.597445 GCGTAGAAATCGGAGTCCTCG 60.597 57.143 7.77 0.00 0.00 4.63
8289 13130 1.669779 CGTAGAAATCGGAGTCCTCGT 59.330 52.381 7.77 0.00 0.00 4.18
8318 13159 0.523546 CGTCGGTGAGGTCGATGAAG 60.524 60.000 0.00 0.00 43.83 3.02
8383 13225 2.035626 CGGCCCCACACCAAATCT 59.964 61.111 0.00 0.00 0.00 2.40
8419 13261 2.046023 CTTGATGTGCGGCTCCCA 60.046 61.111 0.00 0.00 0.00 4.37
8439 13281 0.388520 CGTCTCATCCTTCACGTGCA 60.389 55.000 11.67 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.267832 CGTTTGCATGGCCGTATACAC 60.268 52.381 0.00 0.00 0.00 2.90
58 59 1.745232 TCTTGTGTGGGTGTGTGTTC 58.255 50.000 0.00 0.00 0.00 3.18
59 60 2.091541 CTTCTTGTGTGGGTGTGTGTT 58.908 47.619 0.00 0.00 0.00 3.32
60 61 1.750193 CTTCTTGTGTGGGTGTGTGT 58.250 50.000 0.00 0.00 0.00 3.72
61 62 0.381801 GCTTCTTGTGTGGGTGTGTG 59.618 55.000 0.00 0.00 0.00 3.82
62 63 0.034574 TGCTTCTTGTGTGGGTGTGT 60.035 50.000 0.00 0.00 0.00 3.72
63 64 0.381801 GTGCTTCTTGTGTGGGTGTG 59.618 55.000 0.00 0.00 0.00 3.82
68 69 2.929398 GGTTTTTGTGCTTCTTGTGTGG 59.071 45.455 0.00 0.00 0.00 4.17
83 84 1.600023 TTCGAGCGTCATGGGTTTTT 58.400 45.000 0.00 0.00 0.00 1.94
106 107 2.553268 GTGTCGTGCAAGCTGCTC 59.447 61.111 1.00 0.00 45.31 4.26
118 119 2.723209 TGTCTTGTTAGTGTCGTGTCG 58.277 47.619 0.00 0.00 0.00 4.35
143 144 1.561717 CGTCATCCCGTTTTCGTGCA 61.562 55.000 0.00 0.00 42.35 4.57
144 145 1.131826 CGTCATCCCGTTTTCGTGC 59.868 57.895 0.00 0.00 42.35 5.34
146 147 0.032403 TGTCGTCATCCCGTTTTCGT 59.968 50.000 0.00 0.00 42.35 3.85
147 148 1.355971 ATGTCGTCATCCCGTTTTCG 58.644 50.000 0.00 0.00 43.67 3.46
168 169 1.806461 TAGCGAGGTGATCCATCGGC 61.806 60.000 16.23 10.45 36.04 5.54
171 172 2.822561 TGATCTAGCGAGGTGATCCATC 59.177 50.000 0.00 0.00 36.65 3.51
236 237 1.668101 ATCTCTTGTCGGGTCGGCTC 61.668 60.000 0.00 0.00 30.55 4.70
281 282 0.178992 TGTCCTTTTGGGGTGCTCTG 60.179 55.000 0.00 0.00 40.87 3.35
291 292 1.157870 AGCCGACACGTGTCCTTTTG 61.158 55.000 36.01 23.83 41.86 2.44
292 293 0.463116 AAGCCGACACGTGTCCTTTT 60.463 50.000 36.01 25.25 41.86 2.27
303 304 2.350964 GCCGATTTTTGTAAAGCCGACA 60.351 45.455 0.00 0.00 0.00 4.35
396 397 5.119588 CCGCATCGTTTTCTTCTTACAGTTA 59.880 40.000 0.00 0.00 0.00 2.24
413 414 3.490759 GACACTGTGCCCGCATCG 61.491 66.667 7.90 0.00 0.00 3.84
612 613 0.975135 TTATTCGTTCGTCCCCACCA 59.025 50.000 0.00 0.00 0.00 4.17
620 621 5.694910 CCACTATAGCCAATTATTCGTTCGT 59.305 40.000 0.00 0.00 0.00 3.85
624 625 5.221641 TGAGCCACTATAGCCAATTATTCGT 60.222 40.000 0.00 0.00 0.00 3.85
625 626 5.237815 TGAGCCACTATAGCCAATTATTCG 58.762 41.667 0.00 0.00 0.00 3.34
626 627 7.010552 CGTATGAGCCACTATAGCCAATTATTC 59.989 40.741 0.00 0.00 0.00 1.75
627 628 6.818644 CGTATGAGCCACTATAGCCAATTATT 59.181 38.462 0.00 0.00 0.00 1.40
629 630 5.337250 CCGTATGAGCCACTATAGCCAATTA 60.337 44.000 0.00 0.00 0.00 1.40
656 814 5.368256 AGTCAATCATTTCTGCAGTTGAC 57.632 39.130 26.25 26.25 43.34 3.18
750 927 1.833434 CTCTACTACTCCGCTCGCCG 61.833 65.000 0.00 0.00 0.00 6.46
784 961 1.421268 TCCAACTATATGCCTGCTGGG 59.579 52.381 12.06 1.66 38.36 4.45
935 1161 1.068055 GTCTGGTCGGTCTCGCTTAAA 60.068 52.381 0.00 0.00 36.13 1.52
5937 10454 3.292936 ACGAAGTCGGCCGTCACT 61.293 61.111 27.15 19.76 44.95 3.41
6381 10920 1.881903 CTTGCAGAGAGCCTCCGACA 61.882 60.000 0.00 0.00 44.83 4.35
6859 11664 0.179100 CTAGGGACACACCATCTGCG 60.179 60.000 0.00 0.00 41.20 5.18
6879 11684 6.640518 TGTTGGTAGTATCTTTTCAGGCTAG 58.359 40.000 0.00 0.00 0.00 3.42
6915 11720 0.685097 AGGCGAGTGCTTCCTAACAA 59.315 50.000 0.00 0.00 42.25 2.83
6979 11784 0.247736 AGGCAAAATCGACGAGCTCT 59.752 50.000 12.85 0.00 0.00 4.09
7105 11910 2.580815 CTGCTGAGATCACCGGCA 59.419 61.111 17.19 17.19 42.98 5.69
7122 11927 2.112898 CCATCTGGCCTTGTCATGC 58.887 57.895 3.32 0.00 0.00 4.06
7469 12298 6.378582 TCTTCCGTTCATAGTTGCAAATTTC 58.621 36.000 4.05 0.00 0.00 2.17
7612 12449 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
7644 12481 8.540388 GCTAAAATACATCTAGATACATCCCCA 58.460 37.037 4.54 0.00 0.00 4.96
7670 12507 4.396166 ACAAAAAGGGATGCATCTAGAACG 59.604 41.667 25.28 11.67 0.00 3.95
7695 12532 7.537306 CGTCGGAAAATACTTGTCATCAAAATT 59.463 33.333 0.00 0.00 32.87 1.82
7701 12538 4.178540 TCCGTCGGAAAATACTTGTCATC 58.821 43.478 12.68 0.00 0.00 2.92
7787 12624 5.230182 TGATAGTCAAGTACACAAGCACAG 58.770 41.667 0.00 0.00 0.00 3.66
7788 12625 5.208463 TGATAGTCAAGTACACAAGCACA 57.792 39.130 0.00 0.00 0.00 4.57
7873 12710 3.265737 TCCTCCAAATTTTGAGGGATCGA 59.734 43.478 28.88 13.32 35.63 3.59
8109 12946 9.579768 AAATACGTCTAGATGCATATGAATCTC 57.420 33.333 26.68 13.64 39.63 2.75
8202 13043 4.352595 TGAGTACTCCCTCCATTCCAAAAA 59.647 41.667 20.11 0.00 0.00 1.94
8267 13108 1.677052 GAGGACTCCGATTTCTACGCT 59.323 52.381 0.00 0.00 0.00 5.07
8288 13129 2.898343 ACCGACGGCAACCACAAC 60.898 61.111 15.39 0.00 0.00 3.32
8289 13130 2.897846 CACCGACGGCAACCACAA 60.898 61.111 15.39 0.00 0.00 3.33
8341 13182 4.176752 GTGATGGGCCCTCCGGTC 62.177 72.222 25.70 13.37 38.76 4.79
8383 13225 0.755698 GGAGGAGTGACGCTATGGGA 60.756 60.000 0.00 0.00 0.00 4.37
8419 13261 0.388649 GCACGTGAAGGATGAGACGT 60.389 55.000 22.23 0.00 45.47 4.34
8439 13281 2.888863 GCGTAGAGGAGCACTGCT 59.111 61.111 2.22 2.22 43.88 4.24


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

AutoCloner maintained by Alex Coulton.