Multiple sequence alignment - TraesCS7D01G394300

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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 TraesCS7D01G394300 chr7D 100.000 2648 0 0 1 2648 509574658 509572011 0.000000e+00 4891.0
1 TraesCS7D01G394300 chr7D 93.158 877 41 7 751 1624 509598840 509597980 0.000000e+00 1269.0
2 TraesCS7D01G394300 chr7D 77.585 1325 177 70 861 2120 545647062 545648331 0.000000e+00 691.0
3 TraesCS7D01G394300 chr7D 79.065 984 121 47 794 1733 545650433 545651375 4.880000e-167 597.0
4 TraesCS7D01G394300 chr7D 76.047 1265 173 70 965 2167 545622506 545621310 3.000000e-149 538.0
5 TraesCS7D01G394300 chr7D 78.604 874 121 37 792 1616 518768826 518769682 3.910000e-143 518.0
6 TraesCS7D01G394300 chr7D 93.305 239 14 2 1795 2033 509597871 509597635 4.190000e-93 351.0
7 TraesCS7D01G394300 chr7D 83.251 406 37 18 2262 2647 509554589 509554195 7.020000e-91 344.0
8 TraesCS7D01G394300 chr7D 79.192 495 60 27 1794 2267 518774796 518775268 1.190000e-78 303.0
9 TraesCS7D01G394300 chr7D 81.679 393 41 21 1796 2168 545652585 545652966 5.540000e-77 298.0
10 TraesCS7D01G394300 chr6D 98.389 745 10 1 1 745 271097116 271096374 0.000000e+00 1308.0
11 TraesCS7D01G394300 chr7B 86.190 992 73 25 795 1740 537825707 537824734 0.000000e+00 1014.0
12 TraesCS7D01G394300 chr7B 78.177 834 123 28 821 1612 589735303 589736119 6.630000e-131 477.0
13 TraesCS7D01G394300 chr7B 87.654 405 36 7 1821 2216 537746249 537745850 2.400000e-125 459.0
14 TraesCS7D01G394300 chr7B 79.552 670 83 35 970 1615 568653524 568654163 1.880000e-116 429.0
15 TraesCS7D01G394300 chr7B 84.810 395 38 16 2262 2647 537671728 537671347 6.920000e-101 377.0
16 TraesCS7D01G394300 chr7B 83.140 172 16 5 2107 2266 537824265 537824095 7.640000e-31 145.0
17 TraesCS7D01G394300 chr7B 91.781 73 3 2 2195 2267 589698199 589698130 6.030000e-17 99.0
18 TraesCS7D01G394300 chr7A 91.855 663 48 3 965 1624 580504417 580503758 0.000000e+00 920.0
19 TraesCS7D01G394300 chr7A 88.923 659 34 21 1871 2512 580482392 580481756 0.000000e+00 776.0
20 TraesCS7D01G394300 chr7A 86.882 587 30 13 1701 2267 580503754 580503195 4.840000e-172 614.0
21 TraesCS7D01G394300 chr7A 78.471 994 122 57 813 1740 626992694 626991727 1.380000e-157 566.0
22 TraesCS7D01G394300 chr7A 76.375 1236 159 75 965 2138 628492204 628491040 2.320000e-150 542.0
23 TraesCS7D01G394300 chr7A 78.129 823 111 33 965 1748 628389889 628389097 2.400000e-125 459.0
24 TraesCS7D01G394300 chr7A 79.321 677 79 31 970 1615 610441295 610441941 4.080000e-113 418.0
25 TraesCS7D01G394300 chr7A 92.609 230 12 3 2419 2647 580481753 580481528 2.540000e-85 326.0
26 TraesCS7D01G394300 chr7A 79.268 492 62 26 1794 2267 594449291 594449760 9.210000e-80 307.0
27 TraesCS7D01G394300 chr7A 81.313 396 41 16 2262 2647 580469331 580468959 9.270000e-75 291.0
28 TraesCS7D01G394300 chr7A 87.963 216 17 2 336 542 8451929 8452144 2.040000e-61 246.0
29 TraesCS7D01G394300 chr6A 76.693 1506 190 93 856 2267 158245544 158244106 0.000000e+00 688.0
30 TraesCS7D01G394300 chr6A 77.655 998 130 41 792 1742 107264350 107265301 3.020000e-144 521.0
31 TraesCS7D01G394300 chr6A 82.992 488 38 24 278 741 39064621 39064155 1.480000e-107 399.0
32 TraesCS7D01G394300 chr6A 92.174 115 9 0 1 115 39065270 39065156 2.110000e-36 163.0
33 TraesCS7D01G394300 chr6B 83.560 809 36 31 1 744 565203150 565202374 0.000000e+00 667.0
34 TraesCS7D01G394300 chr6B 85.863 481 29 14 276 745 403201261 403201713 2.390000e-130 475.0
35 TraesCS7D01G394300 chr6B 77.073 772 97 43 971 1686 216631759 216632506 3.220000e-99 372.0
36 TraesCS7D01G394300 chr6B 89.073 302 9 10 1 278 403200918 403201219 1.170000e-93 353.0
37 TraesCS7D01G394300 chr6B 80.200 500 53 23 1795 2265 216632601 216633083 1.520000e-87 333.0
38 TraesCS7D01G394300 chr1B 78.916 830 123 27 821 1612 133124159 133123344 1.410000e-142 516.0
39 TraesCS7D01G394300 chr1B 77.054 937 128 49 854 1742 426496967 426496070 2.400000e-125 459.0
40 TraesCS7D01G394300 chr5D 82.643 507 61 7 1097 1585 30056081 30056578 8.760000e-115 424.0
41 TraesCS7D01G394300 chr5D 81.458 480 43 25 1795 2267 30056612 30057052 4.190000e-93 351.0
42 TraesCS7D01G394300 chr5D 84.098 327 38 9 940 1261 42081612 42081295 1.190000e-78 303.0
43 TraesCS7D01G394300 chr5D 85.714 98 4 4 1645 1742 289726550 289726463 7.800000e-16 95.3
44 TraesCS7D01G394300 chr2B 77.226 786 105 40 861 1612 135512631 135513376 2.470000e-105 392.0
45 TraesCS7D01G394300 chr4A 90.210 286 16 3 1 278 647923103 647923384 1.940000e-96 363.0
46 TraesCS7D01G394300 chr4A 80.189 424 32 16 349 745 647923471 647923869 1.210000e-68 270.0
47 TraesCS7D01G394300 chr5A 83.333 378 30 10 277 641 28420087 28420444 4.250000e-83 318.0
48 TraesCS7D01G394300 chr5A 94.245 139 8 0 18 156 28419779 28419917 2.060000e-51 213.0
49 TraesCS7D01G394300 chr5A 88.991 109 4 4 108 212 28419893 28419997 7.690000e-26 128.0
50 TraesCS7D01G394300 chr5A 93.651 63 2 2 795 857 30651892 30651832 2.810000e-15 93.5
51 TraesCS7D01G394300 chrUn 94.203 138 8 0 19 156 46079465 46079602 7.430000e-51 211.0
52 TraesCS7D01G394300 chrUn 90.265 113 3 4 106 214 46079576 46079684 9.880000e-30 141.0
53 TraesCS7D01G394300 chrUn 90.476 84 5 2 795 878 65755206 65755286 1.000000e-19 108.0
54 TraesCS7D01G394300 chr3A 90.000 110 3 4 108 213 222447906 222447801 4.600000e-28 135.0


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 TraesCS7D01G394300 chr7D 509572011 509574658 2647 True 4891.000000 4891 100.000000 1 2648 1 chr7D.!!$R2 2647
1 TraesCS7D01G394300 chr7D 509597635 509598840 1205 True 810.000000 1269 93.231500 751 2033 2 chr7D.!!$R4 1282
2 TraesCS7D01G394300 chr7D 545621310 545622506 1196 True 538.000000 538 76.047000 965 2167 1 chr7D.!!$R3 1202
3 TraesCS7D01G394300 chr7D 545647062 545652966 5904 False 528.666667 691 79.443000 794 2168 3 chr7D.!!$F3 1374
4 TraesCS7D01G394300 chr7D 518768826 518769682 856 False 518.000000 518 78.604000 792 1616 1 chr7D.!!$F1 824
5 TraesCS7D01G394300 chr6D 271096374 271097116 742 True 1308.000000 1308 98.389000 1 745 1 chr6D.!!$R1 744
6 TraesCS7D01G394300 chr7B 537824095 537825707 1612 True 579.500000 1014 84.665000 795 2266 2 chr7B.!!$R4 1471
7 TraesCS7D01G394300 chr7B 589735303 589736119 816 False 477.000000 477 78.177000 821 1612 1 chr7B.!!$F2 791
8 TraesCS7D01G394300 chr7B 568653524 568654163 639 False 429.000000 429 79.552000 970 1615 1 chr7B.!!$F1 645
9 TraesCS7D01G394300 chr7A 580503195 580504417 1222 True 767.000000 920 89.368500 965 2267 2 chr7A.!!$R6 1302
10 TraesCS7D01G394300 chr7A 626991727 626992694 967 True 566.000000 566 78.471000 813 1740 1 chr7A.!!$R2 927
11 TraesCS7D01G394300 chr7A 580481528 580482392 864 True 551.000000 776 90.766000 1871 2647 2 chr7A.!!$R5 776
12 TraesCS7D01G394300 chr7A 628491040 628492204 1164 True 542.000000 542 76.375000 965 2138 1 chr7A.!!$R4 1173
13 TraesCS7D01G394300 chr7A 628389097 628389889 792 True 459.000000 459 78.129000 965 1748 1 chr7A.!!$R3 783
14 TraesCS7D01G394300 chr7A 610441295 610441941 646 False 418.000000 418 79.321000 970 1615 1 chr7A.!!$F3 645
15 TraesCS7D01G394300 chr6A 158244106 158245544 1438 True 688.000000 688 76.693000 856 2267 1 chr6A.!!$R1 1411
16 TraesCS7D01G394300 chr6A 107264350 107265301 951 False 521.000000 521 77.655000 792 1742 1 chr6A.!!$F1 950
17 TraesCS7D01G394300 chr6A 39064155 39065270 1115 True 281.000000 399 87.583000 1 741 2 chr6A.!!$R2 740
18 TraesCS7D01G394300 chr6B 565202374 565203150 776 True 667.000000 667 83.560000 1 744 1 chr6B.!!$R1 743
19 TraesCS7D01G394300 chr6B 403200918 403201713 795 False 414.000000 475 87.468000 1 745 2 chr6B.!!$F2 744
20 TraesCS7D01G394300 chr6B 216631759 216633083 1324 False 352.500000 372 78.636500 971 2265 2 chr6B.!!$F1 1294
21 TraesCS7D01G394300 chr1B 133123344 133124159 815 True 516.000000 516 78.916000 821 1612 1 chr1B.!!$R1 791
22 TraesCS7D01G394300 chr1B 426496070 426496967 897 True 459.000000 459 77.054000 854 1742 1 chr1B.!!$R2 888
23 TraesCS7D01G394300 chr5D 30056081 30057052 971 False 387.500000 424 82.050500 1097 2267 2 chr5D.!!$F1 1170
24 TraesCS7D01G394300 chr2B 135512631 135513376 745 False 392.000000 392 77.226000 861 1612 1 chr2B.!!$F1 751
25 TraesCS7D01G394300 chr4A 647923103 647923869 766 False 316.500000 363 85.199500 1 745 2 chr4A.!!$F1 744
26 TraesCS7D01G394300 chr5A 28419779 28420444 665 False 219.666667 318 88.856333 18 641 3 chr5A.!!$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
785 1233 0.034616 CCTCCGATCAGCCTTGGATC 59.965 60.0 0.0 0.0 38.2 3.36 F
944 1406 0.397816 CCTCCCTCGACCCATCTTCT 60.398 60.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 5732 0.096628 CACTTGAGCATCGCTTGAGC 59.903 55.0 0.0 0.0 39.88 4.26 R
1830 7140 0.096976 CGCTACTGGAAAACATGCCG 59.903 55.0 0.0 0.0 0.00 5.69 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
711 1157 1.227853 GAACGTGGGTTGCTCCTGT 60.228 57.895 0.00 0.00 36.24 4.00
726 1172 3.429547 GCTCCTGTGATCTTTTCTAGCGA 60.430 47.826 0.00 0.00 0.00 4.93
728 1176 4.017126 TCCTGTGATCTTTTCTAGCGAGA 58.983 43.478 0.00 0.00 0.00 4.04
746 1194 2.036992 GAGATCGTACGAGGGAGGTCTA 59.963 54.545 23.89 0.00 0.00 2.59
747 1195 2.037511 AGATCGTACGAGGGAGGTCTAG 59.962 54.545 23.89 0.00 0.00 2.43
748 1196 1.489481 TCGTACGAGGGAGGTCTAGA 58.511 55.000 15.28 0.00 0.00 2.43
749 1197 1.411977 TCGTACGAGGGAGGTCTAGAG 59.588 57.143 15.28 0.00 0.00 2.43
780 1228 1.053264 AGATGCCTCCGATCAGCCTT 61.053 55.000 0.00 0.00 0.00 4.35
785 1233 0.034616 CCTCCGATCAGCCTTGGATC 59.965 60.000 0.00 0.00 38.20 3.36
788 1236 0.399454 CCGATCAGCCTTGGATCCAT 59.601 55.000 17.06 0.00 38.31 3.41
809 1257 0.724549 TAGTGCGCGTTTTGGCTATG 59.275 50.000 8.43 0.00 0.00 2.23
810 1258 1.209127 GTGCGCGTTTTGGCTATGT 59.791 52.632 8.43 0.00 0.00 2.29
811 1259 0.793104 GTGCGCGTTTTGGCTATGTC 60.793 55.000 8.43 0.00 0.00 3.06
944 1406 0.397816 CCTCCCTCGACCCATCTTCT 60.398 60.000 0.00 0.00 0.00 2.85
982 1465 1.590238 GATCGGTTGATCGTTGCTCTG 59.410 52.381 0.00 0.00 41.51 3.35
986 1472 1.005037 TTGATCGTTGCTCTGCCGT 60.005 52.632 0.00 0.00 0.00 5.68
1627 5732 1.430632 GACATGCATGGAGGCGTTG 59.569 57.895 29.41 4.03 36.28 4.10
1656 5779 2.275134 TGCTCAAGTGATGGAAGCAA 57.725 45.000 0.00 0.00 36.32 3.91
1660 5783 2.490903 CTCAAGTGATGGAAGCAAAGGG 59.509 50.000 0.00 0.00 28.10 3.95
1661 5784 2.108075 TCAAGTGATGGAAGCAAAGGGA 59.892 45.455 0.00 0.00 28.10 4.20
1662 5785 2.892852 CAAGTGATGGAAGCAAAGGGAA 59.107 45.455 0.00 0.00 28.10 3.97
1663 5786 2.800250 AGTGATGGAAGCAAAGGGAAG 58.200 47.619 0.00 0.00 28.10 3.46
1676 5799 5.418209 AGCAAAGGGAAGAAGAAATCATCAG 59.582 40.000 0.00 0.00 0.00 2.90
1677 5800 5.648572 CAAAGGGAAGAAGAAATCATCAGC 58.351 41.667 0.00 0.00 0.00 4.26
1678 5801 4.581309 AGGGAAGAAGAAATCATCAGCA 57.419 40.909 0.00 0.00 0.00 4.41
1679 5802 4.525024 AGGGAAGAAGAAATCATCAGCAG 58.475 43.478 0.00 0.00 0.00 4.24
1680 5803 4.018597 AGGGAAGAAGAAATCATCAGCAGT 60.019 41.667 0.00 0.00 0.00 4.40
1748 5871 0.975040 AGAGGAAGCAGAGTCGGCAT 60.975 55.000 17.72 5.24 0.00 4.40
1760 5883 3.961408 AGAGTCGGCATTGGTACTCTTAT 59.039 43.478 0.00 0.00 44.81 1.73
1762 5885 5.597182 AGAGTCGGCATTGGTACTCTTATTA 59.403 40.000 0.00 0.00 44.81 0.98
1764 5887 6.827727 AGTCGGCATTGGTACTCTTATTAAT 58.172 36.000 0.00 0.00 0.00 1.40
1792 6394 6.072230 GCTGAGAAAAATAGAGGAAGCAAAGT 60.072 38.462 0.00 0.00 0.00 2.66
1798 7107 7.817418 AAAATAGAGGAAGCAAAGTGTGTAA 57.183 32.000 0.00 0.00 0.00 2.41
1830 7140 4.392138 GCAAGTGTGTAGGAGTATTTCACC 59.608 45.833 0.00 0.00 0.00 4.02
1848 7158 0.451783 CCGGCATGTTTTCCAGTAGC 59.548 55.000 0.00 0.00 0.00 3.58
1872 7182 4.496507 GCGAGTGAGATTCTTAATTTGGCC 60.497 45.833 0.00 0.00 0.00 5.36
1874 7184 5.447818 CGAGTGAGATTCTTAATTTGGCCAC 60.448 44.000 3.88 0.00 0.00 5.01
1947 7274 9.605275 TTTGTTTCATGTAAAAACATTGGATCA 57.395 25.926 10.86 0.00 43.85 2.92
2029 7377 8.164733 TGTTGTATGTTCCCTCCTAATAACAAA 58.835 33.333 0.00 0.00 35.63 2.83
2084 7457 6.660521 TGTGCTTGAACTATTCCTCAAATGAT 59.339 34.615 0.00 0.00 31.41 2.45
2085 7458 7.828717 TGTGCTTGAACTATTCCTCAAATGATA 59.171 33.333 0.00 0.00 31.41 2.15
2090 7463 9.547753 TTGAACTATTCCTCAAATGATAGCTAC 57.452 33.333 0.00 0.00 0.00 3.58
2108 7481 5.301555 AGCTACTTTTCAGGAGAAGAACAC 58.698 41.667 6.58 0.00 31.40 3.32
2128 7537 3.288092 ACATATGTGTGCTCGGTCTAGA 58.712 45.455 7.78 0.00 37.14 2.43
2174 7592 2.246993 TTTATTTGTCGCAGGCGCCG 62.247 55.000 23.20 17.35 39.59 6.46
2187 7605 0.943835 GGCGCCGAAAAGCATGTTTT 60.944 50.000 12.58 1.14 34.54 2.43
2250 7673 5.991606 TGCCAATAGCTCATGTGTATACTTC 59.008 40.000 4.17 0.00 44.23 3.01
2283 7706 5.836898 ACTTTGCATAATGTCCATCCATGAT 59.163 36.000 0.00 0.00 0.00 2.45
2294 7717 7.764141 TGTCCATCCATGATTTTACATATGG 57.236 36.000 7.80 0.00 41.09 2.74
2317 7740 4.566545 TGGCACACACATTGTAGAAAAG 57.433 40.909 0.00 0.00 35.67 2.27
2325 7748 6.264292 ACACACATTGTAGAAAAGGTGCAATA 59.736 34.615 1.99 0.00 43.73 1.90
2326 7749 6.803320 CACACATTGTAGAAAAGGTGCAATAG 59.197 38.462 1.99 0.00 43.73 1.73
2333 7756 8.662781 TGTAGAAAAGGTGCAATAGATATGAC 57.337 34.615 0.00 0.00 0.00 3.06
2406 7829 2.743664 TGGCGATGTTGAAGAGAACATG 59.256 45.455 3.69 0.00 44.78 3.21
2421 7844 8.535690 AAGAGAACATGTACTGTAAAGCTAAC 57.464 34.615 0.00 0.00 36.98 2.34
2422 7845 7.667557 AGAGAACATGTACTGTAAAGCTAACA 58.332 34.615 0.00 2.18 36.98 2.41
2423 7846 7.599245 AGAGAACATGTACTGTAAAGCTAACAC 59.401 37.037 0.00 0.00 36.98 3.32
2424 7847 7.442656 AGAACATGTACTGTAAAGCTAACACT 58.557 34.615 0.00 0.00 36.98 3.55
2425 7848 7.931948 AGAACATGTACTGTAAAGCTAACACTT 59.068 33.333 0.00 0.00 36.98 3.16
2426 7849 7.653767 ACATGTACTGTAAAGCTAACACTTC 57.346 36.000 0.00 0.00 35.91 3.01
2427 7850 6.365247 ACATGTACTGTAAAGCTAACACTTCG 59.635 38.462 0.00 0.00 35.91 3.79
2443 7967 5.617252 ACACTTCGAAACAGGGAGAAATAA 58.383 37.500 0.00 0.00 0.00 1.40
2452 7976 9.489084 CGAAACAGGGAGAAATAACATGATATA 57.511 33.333 0.00 0.00 0.00 0.86
2496 8020 5.044846 AGGTTAGCCCAATCTCACTGTTTAT 60.045 40.000 0.00 0.00 34.66 1.40
2540 8064 3.838244 AGCTAGTCTGGTTTCACAACA 57.162 42.857 0.00 0.00 34.15 3.33
2541 8065 4.150897 AGCTAGTCTGGTTTCACAACAA 57.849 40.909 0.00 0.00 34.15 2.83
2546 8070 5.310720 AGTCTGGTTTCACAACAACTTTC 57.689 39.130 0.00 0.00 34.15 2.62
2554 8078 5.697473 TTCACAACAACTTTCTCACACAA 57.303 34.783 0.00 0.00 0.00 3.33
2583 8107 5.499313 TCCTATCAATGCATCAAGACACAA 58.501 37.500 0.00 0.00 0.00 3.33
2637 8161 8.607713 TCCCTTGAATACCTAAATCTACAAACA 58.392 33.333 0.00 0.00 0.00 2.83
2647 8171 9.255029 ACCTAAATCTACAAACAAATTATGGCT 57.745 29.630 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 4.201812 CGCATTAACTATTGGTGGTGACTG 60.202 45.833 0.00 0.00 0.00 3.51
74 77 3.938963 CGCATTAACTATTGGTGGTGACT 59.061 43.478 0.00 0.00 0.00 3.41
711 1157 4.902443 ACGATCTCGCTAGAAAAGATCA 57.098 40.909 20.35 0.00 43.60 2.92
726 1172 0.838608 AGACCTCCCTCGTACGATCT 59.161 55.000 19.87 14.36 0.00 2.75
728 1176 2.037511 CTCTAGACCTCCCTCGTACGAT 59.962 54.545 19.87 1.81 0.00 3.73
746 1194 4.100373 AGGCATCTTTCCAACTAGTCTCT 58.900 43.478 0.00 0.00 0.00 3.10
747 1195 4.438148 GAGGCATCTTTCCAACTAGTCTC 58.562 47.826 0.00 0.00 0.00 3.36
748 1196 3.198853 GGAGGCATCTTTCCAACTAGTCT 59.801 47.826 0.00 0.00 33.55 3.24
749 1197 3.536570 GGAGGCATCTTTCCAACTAGTC 58.463 50.000 0.00 0.00 33.55 2.59
780 1228 0.107897 ACGCGCACTAAATGGATCCA 60.108 50.000 18.88 18.88 0.00 3.41
785 1233 1.335935 CCAAAACGCGCACTAAATGG 58.664 50.000 5.73 3.74 0.00 3.16
788 1236 1.227639 TAGCCAAAACGCGCACTAAA 58.772 45.000 5.73 0.00 0.00 1.85
944 1406 3.132139 CGGCGTCGGGAGAGAGAA 61.132 66.667 0.00 0.00 41.26 2.87
967 1450 1.291877 ACGGCAGAGCAACGATCAAC 61.292 55.000 0.00 0.00 0.00 3.18
986 1472 2.659063 CCCATGGTCACGGCAGAGA 61.659 63.158 11.73 0.00 0.00 3.10
1180 5138 2.125512 GGAGCAGGCACCGTGTAG 60.126 66.667 0.00 0.00 0.00 2.74
1406 5442 4.516195 GACGGCCGGCCTCTTCTC 62.516 72.222 41.01 22.91 0.00 2.87
1550 5586 1.664321 CCATGCTTCCTGCCTTGCTC 61.664 60.000 0.00 0.00 42.00 4.26
1627 5732 0.096628 CACTTGAGCATCGCTTGAGC 59.903 55.000 0.00 0.00 39.88 4.26
1656 5779 4.927049 TGCTGATGATTTCTTCTTCCCTT 58.073 39.130 0.00 0.00 0.00 3.95
1660 5783 5.876612 ACACTGCTGATGATTTCTTCTTC 57.123 39.130 0.00 0.00 0.00 2.87
1661 5784 6.370994 CACTACACTGCTGATGATTTCTTCTT 59.629 38.462 0.00 0.00 0.00 2.52
1662 5785 5.873712 CACTACACTGCTGATGATTTCTTCT 59.126 40.000 0.00 0.00 0.00 2.85
1663 5786 5.447010 GCACTACACTGCTGATGATTTCTTC 60.447 44.000 0.00 0.00 34.06 2.87
1676 5799 1.871772 CAAGCCTGCACTACACTGC 59.128 57.895 0.00 0.00 37.70 4.40
1762 5885 7.831193 TGCTTCCTCTATTTTTCTCAGCTAATT 59.169 33.333 0.00 0.00 0.00 1.40
1764 5887 6.711277 TGCTTCCTCTATTTTTCTCAGCTAA 58.289 36.000 0.00 0.00 0.00 3.09
1777 6370 6.951971 AGATTACACACTTTGCTTCCTCTAT 58.048 36.000 0.00 0.00 0.00 1.98
1792 6394 5.820423 ACACACTTGCAAACTAGATTACACA 59.180 36.000 0.00 0.00 0.00 3.72
1798 7107 5.012148 ACTCCTACACACTTGCAAACTAGAT 59.988 40.000 0.00 0.00 0.00 1.98
1830 7140 0.096976 CGCTACTGGAAAACATGCCG 59.903 55.000 0.00 0.00 0.00 5.69
1848 7158 4.783450 GCCAAATTAAGAATCTCACTCGCG 60.783 45.833 0.00 0.00 0.00 5.87
1872 7182 7.492344 TGTGATCATAATGCACAGTAACTAGTG 59.508 37.037 0.00 0.00 37.60 2.74
1874 7184 8.424274 TTGTGATCATAATGCACAGTAACTAG 57.576 34.615 0.00 0.00 42.70 2.57
1947 7274 3.502595 GCTTGCATGCATCATACTGATCT 59.497 43.478 23.37 0.00 34.28 2.75
1961 7303 1.333931 CTAGTGGCAGATGCTTGCATG 59.666 52.381 13.18 2.36 45.86 4.06
2084 7457 6.041637 TGTGTTCTTCTCCTGAAAAGTAGCTA 59.958 38.462 0.00 0.00 0.00 3.32
2085 7458 5.163301 TGTGTTCTTCTCCTGAAAAGTAGCT 60.163 40.000 0.00 0.00 0.00 3.32
2090 7463 7.524912 CACATATGTGTTCTTCTCCTGAAAAG 58.475 38.462 24.91 0.00 40.96 2.27
2108 7481 3.990318 TCTAGACCGAGCACACATATG 57.010 47.619 0.00 0.00 0.00 1.78
2121 7530 6.764560 TGTGAGGTGTAAACTTTTTCTAGACC 59.235 38.462 0.00 0.00 0.00 3.85
2128 7537 5.971763 TGCATTGTGAGGTGTAAACTTTTT 58.028 33.333 0.00 0.00 0.00 1.94
2174 7592 6.925165 TCAGGATTTCAGAAAACATGCTTTTC 59.075 34.615 18.14 18.14 38.36 2.29
2187 7605 4.080186 TGCATCAGGATTCAGGATTTCAGA 60.080 41.667 0.00 0.00 0.00 3.27
2250 7673 5.392380 GGACATTATGCAAAGTTCAGACAGG 60.392 44.000 0.00 0.00 0.00 4.00
2283 7706 5.012893 TGTGTGTGCCATCCATATGTAAAA 58.987 37.500 1.24 0.00 0.00 1.52
2291 7714 1.927487 ACAATGTGTGTGCCATCCAT 58.073 45.000 0.00 0.00 39.72 3.41
2292 7715 2.039613 TCTACAATGTGTGTGCCATCCA 59.960 45.455 0.00 0.00 41.89 3.41
2293 7716 2.710377 TCTACAATGTGTGTGCCATCC 58.290 47.619 0.00 0.00 41.89 3.51
2294 7717 4.764679 TTTCTACAATGTGTGTGCCATC 57.235 40.909 0.00 0.00 41.89 3.51
2312 7735 6.942532 TGGTCATATCTATTGCACCTTTTC 57.057 37.500 0.00 0.00 0.00 2.29
2317 7740 4.389992 CGTGATGGTCATATCTATTGCACC 59.610 45.833 0.00 0.00 0.00 5.01
2325 7748 2.630098 CTGGGTCGTGATGGTCATATCT 59.370 50.000 0.00 0.00 0.00 1.98
2326 7749 2.628178 TCTGGGTCGTGATGGTCATATC 59.372 50.000 0.00 0.00 0.00 1.63
2333 7756 2.630098 AGTCATATCTGGGTCGTGATGG 59.370 50.000 0.00 0.00 0.00 3.51
2368 7791 3.496884 TCGCCACATTCTGTTGTAAGTTC 59.503 43.478 0.00 0.00 0.00 3.01
2389 7812 8.534333 TTACAGTACATGTTCTCTTCAACATC 57.466 34.615 2.30 0.00 43.75 3.06
2406 7829 6.998258 TTCGAAGTGTTAGCTTTACAGTAC 57.002 37.500 8.82 0.00 0.00 2.73
2421 7844 5.468746 TGTTATTTCTCCCTGTTTCGAAGTG 59.531 40.000 0.00 0.00 0.00 3.16
2422 7845 5.617252 TGTTATTTCTCCCTGTTTCGAAGT 58.383 37.500 0.00 0.00 0.00 3.01
2423 7846 6.371548 TCATGTTATTTCTCCCTGTTTCGAAG 59.628 38.462 0.00 0.00 0.00 3.79
2424 7847 6.234920 TCATGTTATTTCTCCCTGTTTCGAA 58.765 36.000 0.00 0.00 0.00 3.71
2425 7848 5.800296 TCATGTTATTTCTCCCTGTTTCGA 58.200 37.500 0.00 0.00 0.00 3.71
2426 7849 6.683974 ATCATGTTATTTCTCCCTGTTTCG 57.316 37.500 0.00 0.00 0.00 3.46
2452 7976 5.751586 ACCTACGGGATGAACAATTGTAAT 58.248 37.500 12.39 8.91 36.25 1.89
2461 7985 1.202615 GGGCTAACCTACGGGATGAAC 60.203 57.143 0.00 0.00 35.85 3.18
2486 8010 5.186603 TGGCCATTGCATTAATAAACAGTGA 59.813 36.000 0.00 0.00 40.13 3.41
2540 8064 5.501156 AGGAGAAGTTTGTGTGAGAAAGTT 58.499 37.500 0.00 0.00 0.00 2.66
2541 8065 5.104259 AGGAGAAGTTTGTGTGAGAAAGT 57.896 39.130 0.00 0.00 0.00 2.66
2546 8070 6.402983 GCATTGATAGGAGAAGTTTGTGTGAG 60.403 42.308 0.00 0.00 0.00 3.51
2554 8078 6.541641 GTCTTGATGCATTGATAGGAGAAGTT 59.458 38.462 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.