Multiple sequence alignment - TraesCS5A01G224900

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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 TraesCS5A01G224900 chr5A 100.000 3450 0 0 1 3450 439856402 439852953 0.000000e+00 6372
1 TraesCS5A01G224900 chr5A 98.222 675 12 0 2776 3450 440238374 440237700 0.000000e+00 1181
2 TraesCS5A01G224900 chr5A 96.746 676 20 2 2776 3450 331088159 331087485 0.000000e+00 1125
3 TraesCS5A01G224900 chr5A 79.110 809 130 24 1715 2498 439825852 439825058 3.950000e-144 521
4 TraesCS5A01G224900 chr5A 83.333 570 79 11 1715 2270 439773389 439772822 2.370000e-141 512
5 TraesCS5A01G224900 chr5D 94.848 1805 71 6 969 2771 339093083 339091299 0.000000e+00 2798
6 TraesCS5A01G224900 chr5D 80.197 813 120 24 1706 2498 339086504 339085713 3.860000e-159 571
7 TraesCS5A01G224900 chr5D 85.185 513 36 12 389 865 339093617 339093109 1.110000e-134 490
8 TraesCS5A01G224900 chr5D 83.091 550 79 8 1715 2251 339067460 339066912 4.000000e-134 488
9 TraesCS5A01G224900 chr5D 90.132 152 11 2 1 152 339094423 339094276 9.770000e-46 195
10 TraesCS5A01G224900 chr5D 84.211 190 27 2 160 346 339093890 339093701 7.610000e-42 182
11 TraesCS5A01G224900 chr5B 90.600 2117 107 32 389 2471 398065465 398063407 0.000000e+00 2723
12 TraesCS5A01G224900 chr5B 83.536 577 80 9 1706 2270 398059705 398059132 3.050000e-145 525
13 TraesCS5A01G224900 chr5B 82.777 569 84 5 1715 2270 397966172 397965605 2.390000e-136 496
14 TraesCS5A01G224900 chr5B 93.269 104 3 2 2655 2754 398063367 398063264 2.140000e-32 150
15 TraesCS5A01G224900 chr5B 86.408 103 12 2 2357 2458 398058950 398058849 1.010000e-20 111
16 TraesCS5A01G224900 chr2A 95.341 923 41 2 1850 2771 236918919 236917998 0.000000e+00 1465
17 TraesCS5A01G224900 chr2A 96.296 675 25 0 2776 3450 515430822 515431496 0.000000e+00 1109
18 TraesCS5A01G224900 chr6A 97.185 675 19 0 2776 3450 426198907 426199581 0.000000e+00 1142
19 TraesCS5A01G224900 chr6A 96.450 676 22 2 2776 3450 554650448 554651122 0.000000e+00 1114
20 TraesCS5A01G224900 chr1A 96.741 675 22 0 2776 3450 589885377 589886051 0.000000e+00 1125
21 TraesCS5A01G224900 chr7A 96.302 676 23 2 2776 3450 189238049 189238723 0.000000e+00 1109
22 TraesCS5A01G224900 chr6B 96.296 675 25 0 2776 3450 200368785 200368111 0.000000e+00 1109
23 TraesCS5A01G224900 chr2B 96.296 675 25 0 2776 3450 667367128 667367802 0.000000e+00 1109


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 TraesCS5A01G224900 chr5A 439852953 439856402 3449 True 6372.00 6372 100.00000 1 3450 1 chr5A.!!$R4 3449
1 TraesCS5A01G224900 chr5A 440237700 440238374 674 True 1181.00 1181 98.22200 2776 3450 1 chr5A.!!$R5 674
2 TraesCS5A01G224900 chr5A 331087485 331088159 674 True 1125.00 1125 96.74600 2776 3450 1 chr5A.!!$R1 674
3 TraesCS5A01G224900 chr5A 439825058 439825852 794 True 521.00 521 79.11000 1715 2498 1 chr5A.!!$R3 783
4 TraesCS5A01G224900 chr5A 439772822 439773389 567 True 512.00 512 83.33300 1715 2270 1 chr5A.!!$R2 555
5 TraesCS5A01G224900 chr5D 339091299 339094423 3124 True 916.25 2798 88.59400 1 2771 4 chr5D.!!$R3 2770
6 TraesCS5A01G224900 chr5D 339085713 339086504 791 True 571.00 571 80.19700 1706 2498 1 chr5D.!!$R2 792
7 TraesCS5A01G224900 chr5D 339066912 339067460 548 True 488.00 488 83.09100 1715 2251 1 chr5D.!!$R1 536
8 TraesCS5A01G224900 chr5B 398058849 398065465 6616 True 877.25 2723 88.45325 389 2754 4 chr5B.!!$R2 2365
9 TraesCS5A01G224900 chr5B 397965605 397966172 567 True 496.00 496 82.77700 1715 2270 1 chr5B.!!$R1 555
10 TraesCS5A01G224900 chr2A 236917998 236918919 921 True 1465.00 1465 95.34100 1850 2771 1 chr2A.!!$R1 921
11 TraesCS5A01G224900 chr2A 515430822 515431496 674 False 1109.00 1109 96.29600 2776 3450 1 chr2A.!!$F1 674
12 TraesCS5A01G224900 chr6A 426198907 426199581 674 False 1142.00 1142 97.18500 2776 3450 1 chr6A.!!$F1 674
13 TraesCS5A01G224900 chr6A 554650448 554651122 674 False 1114.00 1114 96.45000 2776 3450 1 chr6A.!!$F2 674
14 TraesCS5A01G224900 chr1A 589885377 589886051 674 False 1125.00 1125 96.74100 2776 3450 1 chr1A.!!$F1 674
15 TraesCS5A01G224900 chr7A 189238049 189238723 674 False 1109.00 1109 96.30200 2776 3450 1 chr7A.!!$F1 674
16 TraesCS5A01G224900 chr6B 200368111 200368785 674 True 1109.00 1109 96.29600 2776 3450 1 chr6B.!!$R1 674
17 TraesCS5A01G224900 chr2B 667367128 667367802 674 False 1109.00 1109 96.29600 2776 3450 1 chr2B.!!$F1 674

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
272 654 0.110486 AACTCACCACCACCATCACC 59.890 55.0 0.00 0.00 0.00 4.02 F
1421 1885 0.109412 GCAGTTTGCAGGCTGATGAC 60.109 55.0 20.86 12.22 44.26 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 2069 0.034476 TGATCGATGATGAGCTGCCC 59.966 55.0 0.54 0.0 0.00 5.36 R
2771 3307 0.323360 TCCCGGCAGCTTGCTTTTAT 60.323 50.0 0.00 0.0 44.28 1.40 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
36 37 2.920647 GCGTGTAGCCAAATTTCACACC 60.921 50.000 12.64 5.92 40.81 4.16
44 45 2.159707 CCAAATTTCACACCGTCTAGCG 60.160 50.000 0.00 0.33 40.95 4.26
96 97 4.768968 CCAAAATTGAGGTGTGGATCTCTT 59.231 41.667 0.00 0.00 29.65 2.85
97 98 5.105997 CCAAAATTGAGGTGTGGATCTCTTC 60.106 44.000 0.00 0.00 29.65 2.87
98 99 5.511386 AAATTGAGGTGTGGATCTCTTCT 57.489 39.130 0.00 0.00 29.65 2.85
100 101 6.627087 AATTGAGGTGTGGATCTCTTCTAA 57.373 37.500 0.00 0.00 29.65 2.10
101 102 6.627087 ATTGAGGTGTGGATCTCTTCTAAA 57.373 37.500 0.00 0.00 29.65 1.85
102 103 6.433847 TTGAGGTGTGGATCTCTTCTAAAA 57.566 37.500 0.00 0.00 29.65 1.52
104 105 6.644347 TGAGGTGTGGATCTCTTCTAAAATC 58.356 40.000 0.00 0.00 29.65 2.17
106 107 6.883744 AGGTGTGGATCTCTTCTAAAATCTC 58.116 40.000 0.00 0.00 0.00 2.75
107 108 5.751028 GGTGTGGATCTCTTCTAAAATCTCG 59.249 44.000 0.00 0.00 0.00 4.04
109 110 4.442733 GTGGATCTCTTCTAAAATCTCGCG 59.557 45.833 0.00 0.00 0.00 5.87
110 111 3.427193 GGATCTCTTCTAAAATCTCGCGC 59.573 47.826 0.00 0.00 0.00 6.86
111 112 3.503827 TCTCTTCTAAAATCTCGCGCA 57.496 42.857 8.75 0.00 0.00 6.09
126 127 0.166814 GCGCAATGTGGTCAAGTCTC 59.833 55.000 0.30 0.00 0.00 3.36
133 134 3.475566 TGTGGTCAAGTCTCTCCAAAG 57.524 47.619 0.00 0.00 0.00 2.77
142 143 5.357314 TCAAGTCTCTCCAAAGGTACTATCG 59.643 44.000 0.00 0.00 38.49 2.92
156 535 1.755380 ACTATCGTAGTGCCTCCAACC 59.245 52.381 0.00 0.00 37.69 3.77
158 537 0.537188 ATCGTAGTGCCTCCAACCTG 59.463 55.000 0.00 0.00 0.00 4.00
164 543 1.168714 GTGCCTCCAACCTGTGATTC 58.831 55.000 0.00 0.00 0.00 2.52
179 558 5.987347 CCTGTGATTCTTTTGCTTGTGATTT 59.013 36.000 0.00 0.00 0.00 2.17
222 604 3.641436 AGCATCTGTGGGTCGTATATGAA 59.359 43.478 0.00 0.00 0.00 2.57
226 608 5.453567 TCTGTGGGTCGTATATGAATGAG 57.546 43.478 0.00 0.00 0.00 2.90
228 610 2.987149 GTGGGTCGTATATGAATGAGCG 59.013 50.000 0.00 0.00 34.43 5.03
230 612 3.057526 TGGGTCGTATATGAATGAGCGAG 60.058 47.826 0.00 0.00 34.43 5.03
272 654 0.110486 AACTCACCACCACCATCACC 59.890 55.000 0.00 0.00 0.00 4.02
282 664 1.550072 CCACCATCACCAACCCAAATC 59.450 52.381 0.00 0.00 0.00 2.17
289 671 3.761897 TCACCAACCCAAATCTGTAAGG 58.238 45.455 0.00 0.00 0.00 2.69
290 672 3.139397 TCACCAACCCAAATCTGTAAGGT 59.861 43.478 0.00 0.00 0.00 3.50
297 679 6.793505 ACCCAAATCTGTAAGGTAGTAGAG 57.206 41.667 0.00 0.00 0.00 2.43
306 688 9.872721 ATCTGTAAGGTAGTAGAGTTTTAAAGC 57.127 33.333 0.00 0.00 0.00 3.51
313 695 7.040494 GGTAGTAGAGTTTTAAAGCCGAAGAT 58.960 38.462 0.00 0.00 0.00 2.40
315 697 5.805994 AGTAGAGTTTTAAAGCCGAAGATCG 59.194 40.000 0.00 0.00 40.07 3.69
336 718 0.613260 CTGGTGGGTCCTCGATGAAA 59.387 55.000 0.00 0.00 37.07 2.69
348 730 3.782889 TCGATGAAAGAGCGAGATTGA 57.217 42.857 0.00 0.00 0.00 2.57
349 731 4.110036 TCGATGAAAGAGCGAGATTGAA 57.890 40.909 0.00 0.00 0.00 2.69
351 733 4.929211 TCGATGAAAGAGCGAGATTGAAAA 59.071 37.500 0.00 0.00 0.00 2.29
358 766 2.749621 GAGCGAGATTGAAAACCACCAT 59.250 45.455 0.00 0.00 0.00 3.55
372 780 4.882842 ACCACCATCAACCCAAATTTAC 57.117 40.909 0.00 0.00 0.00 2.01
379 787 8.310382 CACCATCAACCCAAATTTACAAGATAA 58.690 33.333 0.00 0.00 0.00 1.75
422 845 3.060602 GAGGCATATTCAACGTAGGAGC 58.939 50.000 0.00 0.00 0.00 4.70
423 846 2.143925 GGCATATTCAACGTAGGAGCC 58.856 52.381 0.00 0.00 0.00 4.70
428 851 0.174845 TTCAACGTAGGAGCCCATCG 59.825 55.000 0.00 0.00 0.00 3.84
442 866 0.383590 CCATCGTGTGCACACCAAAA 59.616 50.000 37.23 23.32 43.66 2.44
492 916 1.240641 TGCATGCCCGGTTGTGTTAG 61.241 55.000 16.68 0.00 0.00 2.34
493 917 1.241315 GCATGCCCGGTTGTGTTAGT 61.241 55.000 6.36 0.00 0.00 2.24
494 918 0.802494 CATGCCCGGTTGTGTTAGTC 59.198 55.000 0.00 0.00 0.00 2.59
495 919 0.690762 ATGCCCGGTTGTGTTAGTCT 59.309 50.000 0.00 0.00 0.00 3.24
521 956 3.133691 TGCTTAGAGCGAGCATATTTGG 58.866 45.455 0.00 0.00 46.26 3.28
561 1015 9.533253 CCAATCACTTCTGTTTTCTAAAAATGT 57.467 29.630 0.00 0.00 0.00 2.71
623 1077 5.885912 ACAATACCTAATCAGCAACCGAAAT 59.114 36.000 0.00 0.00 0.00 2.17
626 1080 7.907214 ATACCTAATCAGCAACCGAAATATC 57.093 36.000 0.00 0.00 0.00 1.63
631 1085 2.675844 TCAGCAACCGAAATATCCAACG 59.324 45.455 0.00 0.00 0.00 4.10
644 1098 1.374560 TCCAACGGCAATATGGTTCG 58.625 50.000 0.00 0.00 35.66 3.95
645 1099 0.380378 CCAACGGCAATATGGTTCGG 59.620 55.000 0.00 0.00 0.00 4.30
743 1202 0.683828 AATGAATGCACGGCCCATGA 60.684 50.000 5.83 0.00 0.00 3.07
744 1203 0.468585 ATGAATGCACGGCCCATGAT 60.469 50.000 5.83 0.00 0.00 2.45
745 1204 1.361271 GAATGCACGGCCCATGATG 59.639 57.895 5.83 0.00 0.00 3.07
757 1216 3.471680 GCCCATGATGGAGTTTACTCTC 58.528 50.000 14.26 1.77 40.96 3.20
850 1314 8.695456 TGATATGAGTTACTTGATTGCTACTGA 58.305 33.333 0.00 0.00 0.00 3.41
874 1338 4.716784 TGCTCCTCAATCTGTAGTGGTAAT 59.283 41.667 0.00 0.00 0.00 1.89
889 1353 9.996554 TGTAGTGGTAATAAGAATATGGATGTG 57.003 33.333 0.00 0.00 0.00 3.21
910 1374 8.867112 ATGTGTTTTCATCTTCATTGCATATC 57.133 30.769 0.00 0.00 0.00 1.63
913 1377 7.756272 GTGTTTTCATCTTCATTGCATATCACA 59.244 33.333 0.00 0.00 0.00 3.58
914 1378 8.305317 TGTTTTCATCTTCATTGCATATCACAA 58.695 29.630 0.00 0.00 0.00 3.33
946 1410 9.558396 ACAACAATGTTGGATGTTTGATATTTT 57.442 25.926 27.15 0.48 37.66 1.82
947 1411 9.814507 CAACAATGTTGGATGTTTGATATTTTG 57.185 29.630 17.71 0.00 37.66 2.44
948 1412 8.031848 ACAATGTTGGATGTTTGATATTTTGC 57.968 30.769 0.00 0.00 0.00 3.68
949 1413 7.879160 ACAATGTTGGATGTTTGATATTTTGCT 59.121 29.630 0.00 0.00 0.00 3.91
950 1414 7.837202 ATGTTGGATGTTTGATATTTTGCTG 57.163 32.000 0.00 0.00 0.00 4.41
951 1415 6.757237 TGTTGGATGTTTGATATTTTGCTGT 58.243 32.000 0.00 0.00 0.00 4.40
952 1416 7.215789 TGTTGGATGTTTGATATTTTGCTGTT 58.784 30.769 0.00 0.00 0.00 3.16
953 1417 8.363390 TGTTGGATGTTTGATATTTTGCTGTTA 58.637 29.630 0.00 0.00 0.00 2.41
954 1418 8.863049 GTTGGATGTTTGATATTTTGCTGTTAG 58.137 33.333 0.00 0.00 0.00 2.34
955 1419 7.035004 TGGATGTTTGATATTTTGCTGTTAGC 58.965 34.615 0.00 0.00 42.82 3.09
956 1420 6.476706 GGATGTTTGATATTTTGCTGTTAGCC 59.523 38.462 0.00 0.00 41.51 3.93
957 1421 5.719173 TGTTTGATATTTTGCTGTTAGCCC 58.281 37.500 0.00 0.00 41.51 5.19
958 1422 4.630894 TTGATATTTTGCTGTTAGCCCG 57.369 40.909 0.00 0.00 41.51 6.13
959 1423 2.357637 TGATATTTTGCTGTTAGCCCGC 59.642 45.455 0.00 0.00 41.51 6.13
960 1424 2.122783 TATTTTGCTGTTAGCCCGCT 57.877 45.000 0.00 0.00 41.51 5.52
961 1425 1.256812 ATTTTGCTGTTAGCCCGCTT 58.743 45.000 0.00 0.00 41.51 4.68
962 1426 1.036707 TTTTGCTGTTAGCCCGCTTT 58.963 45.000 0.00 0.00 41.51 3.51
963 1427 1.036707 TTTGCTGTTAGCCCGCTTTT 58.963 45.000 0.00 0.00 41.51 2.27
964 1428 0.596082 TTGCTGTTAGCCCGCTTTTC 59.404 50.000 0.00 0.00 41.51 2.29
967 1431 2.081462 GCTGTTAGCCCGCTTTTCTTA 58.919 47.619 0.00 0.00 34.48 2.10
976 1440 4.462483 AGCCCGCTTTTCTTATTCATTTGA 59.538 37.500 0.00 0.00 0.00 2.69
998 1462 4.175787 ACACCAAGTCACTACGAATCTC 57.824 45.455 0.00 0.00 0.00 2.75
999 1463 3.572682 ACACCAAGTCACTACGAATCTCA 59.427 43.478 0.00 0.00 0.00 3.27
1002 1466 5.062683 CACCAAGTCACTACGAATCTCAATG 59.937 44.000 0.00 0.00 0.00 2.82
1003 1467 5.047306 ACCAAGTCACTACGAATCTCAATGA 60.047 40.000 0.00 0.00 0.00 2.57
1074 1538 0.699399 AAGAGGTCCTCCGACTCTCA 59.301 55.000 15.72 0.00 38.11 3.27
1163 1627 4.978083 AACCTGAGAATTGTGATCATGC 57.022 40.909 0.00 0.00 0.00 4.06
1273 1737 5.188327 TGTCGATCCAGAGATACATGAAC 57.812 43.478 0.00 0.00 30.90 3.18
1386 1850 2.676471 GGGCAATGTTCCGGCAGT 60.676 61.111 0.00 0.00 0.00 4.40
1421 1885 0.109412 GCAGTTTGCAGGCTGATGAC 60.109 55.000 20.86 12.22 44.26 3.06
1422 1886 1.241165 CAGTTTGCAGGCTGATGACA 58.759 50.000 20.86 3.18 34.87 3.58
1428 1892 1.832998 TGCAGGCTGATGACAGTATCA 59.167 47.619 20.86 0.00 45.04 2.15
1506 1970 1.067142 GCCAGATACACAACCGAGACA 60.067 52.381 0.00 0.00 0.00 3.41
1552 2016 6.369065 GTGTCCGATTACTTCTTGTGATTCTT 59.631 38.462 0.00 0.00 0.00 2.52
1569 2033 1.939934 TCTTTGTTGAAGCCAGACACG 59.060 47.619 0.00 0.00 35.24 4.49
1582 2046 0.667487 AGACACGCCACAAGTGATCG 60.667 55.000 0.94 7.42 41.83 3.69
1587 2051 2.472861 CACGCCACAAGTGATCGATATC 59.527 50.000 17.04 0.00 41.83 1.63
1603 2067 4.873827 TCGATATCGACGATGATGGTGATA 59.126 41.667 23.48 0.00 44.22 2.15
1605 2069 2.681152 TCGACGATGATGGTGATACG 57.319 50.000 0.00 0.00 0.00 3.06
1614 2078 1.337384 ATGGTGATACGGGCAGCTCA 61.337 55.000 0.00 0.00 34.98 4.26
1622 2086 1.005275 CGGGCAGCTCATCATCGAT 60.005 57.895 0.00 0.00 0.00 3.59
1699 2163 1.210931 CAATGTTCCAGCGGCACAG 59.789 57.895 1.45 0.00 0.00 3.66
1846 2310 2.357517 AAGAGAACGTGCTGCCCG 60.358 61.111 0.00 2.26 0.00 6.13
2271 2760 2.766313 GTGTACATTGTCTGCAGGTGA 58.234 47.619 15.13 0.00 0.00 4.02
2313 2809 1.002990 TGGATCTGCTGCACACCAG 60.003 57.895 0.00 0.00 44.67 4.00
2326 2822 4.305769 TGCACACCAGCAATTATTTTCAC 58.694 39.130 0.00 0.00 42.46 3.18
2400 2915 2.418910 GCTACCTCTGCGGCTCTGA 61.419 63.158 0.00 0.00 35.61 3.27
2473 2988 0.745486 TGAATGGTCTGCAGATGCCG 60.745 55.000 21.47 0.00 41.18 5.69
2519 3034 2.289820 TCGTCATGTCAGTACTATCGGC 59.710 50.000 0.00 0.00 0.00 5.54
2534 3050 4.935808 ACTATCGGCTTAAAAACTGGACAG 59.064 41.667 0.00 0.00 0.00 3.51
2536 3052 4.339872 TCGGCTTAAAAACTGGACAGTA 57.660 40.909 5.25 0.00 41.58 2.74
2574 3090 7.539712 TTACTACTGATTCAGTTAGCATTGC 57.460 36.000 23.53 0.00 42.59 3.56
2651 3168 8.043710 GGCAACTATATGAGCTCCATTAGTAAT 58.956 37.037 12.15 0.00 36.71 1.89
3117 4153 3.991367 GGCACGCTACCTCTACATTTAT 58.009 45.455 0.00 0.00 0.00 1.40
3124 4160 5.410746 CGCTACCTCTACATTTATCTACGGA 59.589 44.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.187967 ACCATATATCCTCCCATTTCTCGTC 59.812 44.000 0.00 0.00 0.00 4.20
77 78 6.627087 TTAGAAGAGATCCACACCTCAATT 57.373 37.500 0.00 0.00 32.07 2.32
82 83 6.406400 CGAGATTTTAGAAGAGATCCACACCT 60.406 42.308 0.00 0.00 0.00 4.00
87 88 4.611943 CGCGAGATTTTAGAAGAGATCCA 58.388 43.478 0.00 0.00 0.00 3.41
96 97 2.351418 CCACATTGCGCGAGATTTTAGA 59.649 45.455 12.10 0.00 0.00 2.10
97 98 2.095853 ACCACATTGCGCGAGATTTTAG 59.904 45.455 12.10 0.00 0.00 1.85
98 99 2.080693 ACCACATTGCGCGAGATTTTA 58.919 42.857 12.10 0.00 0.00 1.52
100 101 0.447801 GACCACATTGCGCGAGATTT 59.552 50.000 12.10 0.00 0.00 2.17
101 102 0.673333 TGACCACATTGCGCGAGATT 60.673 50.000 12.10 0.00 0.00 2.40
102 103 0.673333 TTGACCACATTGCGCGAGAT 60.673 50.000 12.10 0.00 0.00 2.75
104 105 1.133253 CTTGACCACATTGCGCGAG 59.867 57.895 12.10 0.00 0.00 5.03
106 107 1.154413 GACTTGACCACATTGCGCG 60.154 57.895 0.00 0.00 0.00 6.86
107 108 0.166814 GAGACTTGACCACATTGCGC 59.833 55.000 0.00 0.00 0.00 6.09
109 110 2.079925 GGAGAGACTTGACCACATTGC 58.920 52.381 0.00 0.00 0.00 3.56
110 111 3.407424 TGGAGAGACTTGACCACATTG 57.593 47.619 0.00 0.00 0.00 2.82
111 112 4.392940 CTTTGGAGAGACTTGACCACATT 58.607 43.478 0.00 0.00 31.87 2.71
142 143 0.685097 TCACAGGTTGGAGGCACTAC 59.315 55.000 0.00 0.00 41.55 2.73
152 153 4.505191 CACAAGCAAAAGAATCACAGGTTG 59.495 41.667 0.00 0.00 39.54 3.77
153 154 4.402155 TCACAAGCAAAAGAATCACAGGTT 59.598 37.500 0.00 0.00 0.00 3.50
156 535 7.473027 AAAATCACAAGCAAAAGAATCACAG 57.527 32.000 0.00 0.00 0.00 3.66
189 568 2.554032 CCACAGATGCTCTTCGGTTTTT 59.446 45.455 0.00 0.00 0.00 1.94
190 569 2.154462 CCACAGATGCTCTTCGGTTTT 58.846 47.619 0.00 0.00 0.00 2.43
191 570 1.611673 CCCACAGATGCTCTTCGGTTT 60.612 52.381 0.00 0.00 0.00 3.27
197 578 1.557099 TACGACCCACAGATGCTCTT 58.443 50.000 0.00 0.00 0.00 2.85
203 584 5.567623 GCTCATTCATATACGACCCACAGAT 60.568 44.000 0.00 0.00 0.00 2.90
214 596 5.724328 TCCCAATCTCGCTCATTCATATAC 58.276 41.667 0.00 0.00 0.00 1.47
217 599 4.897509 ATCCCAATCTCGCTCATTCATA 57.102 40.909 0.00 0.00 0.00 2.15
222 604 3.257873 CACTCTATCCCAATCTCGCTCAT 59.742 47.826 0.00 0.00 0.00 2.90
226 608 1.001406 CCCACTCTATCCCAATCTCGC 59.999 57.143 0.00 0.00 0.00 5.03
228 610 1.349357 GCCCCACTCTATCCCAATCTC 59.651 57.143 0.00 0.00 0.00 2.75
230 612 1.072965 CTGCCCCACTCTATCCCAATC 59.927 57.143 0.00 0.00 0.00 2.67
272 654 6.942976 TCTACTACCTTACAGATTTGGGTTG 58.057 40.000 0.00 0.00 0.00 3.77
282 664 7.275123 CGGCTTTAAAACTCTACTACCTTACAG 59.725 40.741 0.00 0.00 0.00 2.74
289 671 7.044183 CGATCTTCGGCTTTAAAACTCTACTAC 60.044 40.741 0.00 0.00 36.00 2.73
290 672 6.971184 CGATCTTCGGCTTTAAAACTCTACTA 59.029 38.462 0.00 0.00 36.00 1.82
306 688 1.141881 CCCACCAGACGATCTTCGG 59.858 63.158 1.69 8.02 45.59 4.30
313 695 2.494777 ATCGAGGACCCACCAGACGA 62.495 60.000 0.00 0.00 41.59 4.20
315 697 0.970937 TCATCGAGGACCCACCAGAC 60.971 60.000 0.00 0.00 42.04 3.51
336 718 2.224523 TGGTGGTTTTCAATCTCGCTCT 60.225 45.455 0.00 0.00 0.00 4.09
343 725 3.323403 TGGGTTGATGGTGGTTTTCAATC 59.677 43.478 0.00 0.00 32.48 2.67
346 728 2.461300 TGGGTTGATGGTGGTTTTCA 57.539 45.000 0.00 0.00 0.00 2.69
348 730 4.787135 AATTTGGGTTGATGGTGGTTTT 57.213 36.364 0.00 0.00 0.00 2.43
349 731 4.787135 AAATTTGGGTTGATGGTGGTTT 57.213 36.364 0.00 0.00 0.00 3.27
351 733 4.227197 TGTAAATTTGGGTTGATGGTGGT 58.773 39.130 0.00 0.00 0.00 4.16
379 787 8.097662 GCCTCTACACTTGATAAAGCCTATTAT 58.902 37.037 0.00 0.00 0.00 1.28
382 790 5.366768 TGCCTCTACACTTGATAAAGCCTAT 59.633 40.000 0.00 0.00 0.00 2.57
383 791 4.714802 TGCCTCTACACTTGATAAAGCCTA 59.285 41.667 0.00 0.00 0.00 3.93
384 792 3.519510 TGCCTCTACACTTGATAAAGCCT 59.480 43.478 0.00 0.00 0.00 4.58
385 793 3.873910 TGCCTCTACACTTGATAAAGCC 58.126 45.455 0.00 0.00 0.00 4.35
386 794 7.442364 TGAATATGCCTCTACACTTGATAAAGC 59.558 37.037 0.00 0.00 0.00 3.51
387 795 8.893219 TGAATATGCCTCTACACTTGATAAAG 57.107 34.615 0.00 0.00 0.00 1.85
428 851 0.248458 CGGACTTTTGGTGTGCACAC 60.248 55.000 36.56 36.56 45.72 3.82
442 866 1.341209 TCGCAAGCATATCATCGGACT 59.659 47.619 0.00 0.00 37.18 3.85
492 916 2.792116 GCTCGCTCTAAGCAATGTAGAC 59.208 50.000 0.00 0.00 42.58 2.59
493 917 2.427095 TGCTCGCTCTAAGCAATGTAGA 59.573 45.455 0.00 0.00 46.29 2.59
494 918 2.814269 TGCTCGCTCTAAGCAATGTAG 58.186 47.619 0.00 0.00 46.29 2.74
495 919 2.959507 TGCTCGCTCTAAGCAATGTA 57.040 45.000 0.00 0.00 46.29 2.29
546 999 9.535878 GGTTAACCATGACATTTTTAGAAAACA 57.464 29.630 20.12 0.00 35.64 2.83
582 1036 8.691661 AGGTATTGTTAAATGTGATGATACCC 57.308 34.615 0.00 0.00 38.87 3.69
623 1077 3.135225 CGAACCATATTGCCGTTGGATA 58.865 45.455 0.00 0.00 34.52 2.59
626 1080 0.380378 CCGAACCATATTGCCGTTGG 59.620 55.000 0.00 0.00 36.56 3.77
631 1085 2.543777 TCTAGCCGAACCATATTGCC 57.456 50.000 0.00 0.00 0.00 4.52
644 1098 6.648725 AGCTAAATCTCGATTTCAATCTAGCC 59.351 38.462 8.07 0.00 40.99 3.93
645 1099 7.650834 AGCTAAATCTCGATTTCAATCTAGC 57.349 36.000 8.07 10.22 40.99 3.42
743 1202 7.227156 ACATTCAACAAGAGAGTAAACTCCAT 58.773 34.615 6.50 0.00 43.88 3.41
744 1203 6.591935 ACATTCAACAAGAGAGTAAACTCCA 58.408 36.000 6.50 0.00 43.88 3.86
745 1204 7.442666 AGAACATTCAACAAGAGAGTAAACTCC 59.557 37.037 6.50 0.00 43.88 3.85
757 1216 6.712241 ACGTGAGATAGAACATTCAACAAG 57.288 37.500 0.00 0.00 0.00 3.16
818 1282 7.172875 GCAATCAAGTAACTCATATCATCAGCT 59.827 37.037 0.00 0.00 0.00 4.24
828 1292 6.259608 GCATCAGTAGCAATCAAGTAACTCAT 59.740 38.462 0.00 0.00 0.00 2.90
850 1314 3.110705 ACCACTACAGATTGAGGAGCAT 58.889 45.455 0.00 0.00 0.00 3.79
881 1345 6.103997 GCAATGAAGATGAAAACACATCCAT 58.896 36.000 0.00 0.00 45.20 3.41
882 1346 5.010820 TGCAATGAAGATGAAAACACATCCA 59.989 36.000 0.00 0.00 45.20 3.41
883 1347 5.472148 TGCAATGAAGATGAAAACACATCC 58.528 37.500 0.00 0.00 45.20 3.51
884 1348 8.867112 ATATGCAATGAAGATGAAAACACATC 57.133 30.769 0.00 0.00 44.65 3.06
885 1349 8.471609 TGATATGCAATGAAGATGAAAACACAT 58.528 29.630 0.00 0.00 0.00 3.21
886 1350 7.756272 GTGATATGCAATGAAGATGAAAACACA 59.244 33.333 0.00 0.00 0.00 3.72
887 1351 7.756272 TGTGATATGCAATGAAGATGAAAACAC 59.244 33.333 0.00 0.00 0.00 3.32
888 1352 7.828712 TGTGATATGCAATGAAGATGAAAACA 58.171 30.769 0.00 0.00 0.00 2.83
889 1353 8.692110 TTGTGATATGCAATGAAGATGAAAAC 57.308 30.769 0.00 0.00 0.00 2.43
900 1364 6.807720 TGTTGTTAAGCTTGTGATATGCAATG 59.192 34.615 9.86 0.00 32.18 2.82
910 1374 5.347342 TCCAACATTGTTGTTAAGCTTGTG 58.653 37.500 24.01 8.31 44.24 3.33
913 1377 6.160576 ACATCCAACATTGTTGTTAAGCTT 57.839 33.333 24.01 3.48 44.24 3.74
914 1378 5.789643 ACATCCAACATTGTTGTTAAGCT 57.210 34.783 24.01 2.24 44.24 3.74
937 1401 3.181491 GCGGGCTAACAGCAAAATATCAA 60.181 43.478 0.00 0.00 44.75 2.57
938 1402 2.357637 GCGGGCTAACAGCAAAATATCA 59.642 45.455 0.00 0.00 44.75 2.15
939 1403 2.618709 AGCGGGCTAACAGCAAAATATC 59.381 45.455 0.00 0.00 44.75 1.63
940 1404 2.654863 AGCGGGCTAACAGCAAAATAT 58.345 42.857 0.00 0.00 44.75 1.28
941 1405 2.122783 AGCGGGCTAACAGCAAAATA 57.877 45.000 0.00 0.00 44.75 1.40
942 1406 1.256812 AAGCGGGCTAACAGCAAAAT 58.743 45.000 0.00 0.00 44.75 1.82
943 1407 1.036707 AAAGCGGGCTAACAGCAAAA 58.963 45.000 0.00 0.00 44.75 2.44
944 1408 1.000717 GAAAAGCGGGCTAACAGCAAA 60.001 47.619 0.00 0.00 44.75 3.68
945 1409 0.596082 GAAAAGCGGGCTAACAGCAA 59.404 50.000 0.00 0.00 44.75 3.91
946 1410 0.250727 AGAAAAGCGGGCTAACAGCA 60.251 50.000 0.00 0.00 44.75 4.41
947 1411 0.881796 AAGAAAAGCGGGCTAACAGC 59.118 50.000 0.00 0.00 41.46 4.40
948 1412 4.394920 TGAATAAGAAAAGCGGGCTAACAG 59.605 41.667 0.00 0.00 0.00 3.16
949 1413 4.328536 TGAATAAGAAAAGCGGGCTAACA 58.671 39.130 0.00 0.00 0.00 2.41
950 1414 4.957759 TGAATAAGAAAAGCGGGCTAAC 57.042 40.909 0.00 0.00 0.00 2.34
951 1415 6.151985 TCAAATGAATAAGAAAAGCGGGCTAA 59.848 34.615 0.00 0.00 0.00 3.09
952 1416 5.650266 TCAAATGAATAAGAAAAGCGGGCTA 59.350 36.000 0.00 0.00 0.00 3.93
953 1417 4.462483 TCAAATGAATAAGAAAAGCGGGCT 59.538 37.500 0.00 0.00 0.00 5.19
954 1418 4.743493 TCAAATGAATAAGAAAAGCGGGC 58.257 39.130 0.00 0.00 0.00 6.13
955 1419 6.089417 GTGTTCAAATGAATAAGAAAAGCGGG 59.911 38.462 0.00 0.00 36.33 6.13
956 1420 6.089417 GGTGTTCAAATGAATAAGAAAAGCGG 59.911 38.462 0.00 0.00 36.33 5.52
957 1421 6.640499 TGGTGTTCAAATGAATAAGAAAAGCG 59.360 34.615 0.00 0.00 36.33 4.68
958 1422 7.945033 TGGTGTTCAAATGAATAAGAAAAGC 57.055 32.000 0.00 0.00 36.33 3.51
959 1423 9.533253 ACTTGGTGTTCAAATGAATAAGAAAAG 57.467 29.630 0.00 2.99 36.33 2.27
960 1424 9.528018 GACTTGGTGTTCAAATGAATAAGAAAA 57.472 29.630 0.00 0.00 36.33 2.29
961 1425 8.690884 TGACTTGGTGTTCAAATGAATAAGAAA 58.309 29.630 0.00 0.00 36.33 2.52
962 1426 8.134895 GTGACTTGGTGTTCAAATGAATAAGAA 58.865 33.333 0.00 0.00 36.33 2.52
963 1427 7.502226 AGTGACTTGGTGTTCAAATGAATAAGA 59.498 33.333 0.00 0.00 36.33 2.10
964 1428 7.651808 AGTGACTTGGTGTTCAAATGAATAAG 58.348 34.615 0.00 5.37 36.33 1.73
967 1431 6.293407 CGTAGTGACTTGGTGTTCAAATGAAT 60.293 38.462 0.00 0.00 36.33 2.57
976 1440 4.038763 TGAGATTCGTAGTGACTTGGTGTT 59.961 41.667 0.00 0.00 0.00 3.32
1074 1538 3.134792 ATCGTCGCGGACTGAGCT 61.135 61.111 6.13 0.00 0.00 4.09
1273 1737 4.926238 GCCATCATCGTCTACTTCCATAAG 59.074 45.833 0.00 0.00 38.77 1.73
1421 1885 2.862536 CACGATGCTTCCAGTGATACTG 59.137 50.000 2.05 2.05 45.53 2.74
1422 1886 2.159043 CCACGATGCTTCCAGTGATACT 60.159 50.000 8.56 0.00 36.79 2.12
1428 1892 1.523758 GTTTCCACGATGCTTCCAGT 58.476 50.000 0.00 0.00 0.00 4.00
1506 1970 2.124151 GGCATCTCGGTGGCCATT 60.124 61.111 9.72 0.00 46.92 3.16
1552 2016 1.444119 GGCGTGTCTGGCTTCAACAA 61.444 55.000 0.00 0.00 0.00 2.83
1569 2033 3.013276 TCGATATCGATCACTTGTGGC 57.987 47.619 23.48 0.00 44.22 5.01
1582 2046 4.964555 CGTATCACCATCATCGTCGATATC 59.035 45.833 7.56 0.00 0.00 1.63
1587 2051 1.666023 CCCGTATCACCATCATCGTCG 60.666 57.143 0.00 0.00 0.00 5.12
1603 2067 1.752358 ATCGATGATGAGCTGCCCGT 61.752 55.000 0.00 0.00 0.00 5.28
1605 2069 0.034476 TGATCGATGATGAGCTGCCC 59.966 55.000 0.54 0.00 0.00 5.36
1614 2078 7.834803 TGTCTATTATTGCTCTGATCGATGAT 58.165 34.615 0.54 0.00 0.00 2.45
1622 2086 5.744171 TGCCTTTGTCTATTATTGCTCTGA 58.256 37.500 0.00 0.00 0.00 3.27
1628 2092 5.807011 GGTTGCTTGCCTTTGTCTATTATTG 59.193 40.000 0.00 0.00 0.00 1.90
1629 2093 5.393027 CGGTTGCTTGCCTTTGTCTATTATT 60.393 40.000 0.00 0.00 0.00 1.40
1630 2094 4.096382 CGGTTGCTTGCCTTTGTCTATTAT 59.904 41.667 0.00 0.00 0.00 1.28
1631 2095 3.438781 CGGTTGCTTGCCTTTGTCTATTA 59.561 43.478 0.00 0.00 0.00 0.98
1632 2096 2.228822 CGGTTGCTTGCCTTTGTCTATT 59.771 45.455 0.00 0.00 0.00 1.73
1699 2163 2.484264 AGTAGAAGTCGTTGGCAATTGC 59.516 45.455 22.47 22.47 41.14 3.56
1791 2255 3.927548 TGCCTCACGCAGCTGACA 61.928 61.111 20.43 0.00 44.64 3.58
2213 2702 1.201812 CGACGTACATCTTGCACTTGC 60.202 52.381 0.00 0.00 42.50 4.01
2313 2809 5.932021 GTCATGGACGTGAAAATAATTGC 57.068 39.130 0.00 0.00 0.00 3.56
2400 2915 2.044946 GGTTGCCCTTCGCCATCT 60.045 61.111 0.00 0.00 36.24 2.90
2500 3015 3.992260 AGCCGATAGTACTGACATGAC 57.008 47.619 5.39 0.00 0.00 3.06
2519 3034 9.843334 CTAGTAGAGTACTGTCCAGTTTTTAAG 57.157 37.037 0.00 0.00 42.54 1.85
2771 3307 0.323360 TCCCGGCAGCTTGCTTTTAT 60.323 50.000 0.00 0.00 44.28 1.40
2772 3308 0.538516 TTCCCGGCAGCTTGCTTTTA 60.539 50.000 0.00 0.00 44.28 1.52
2773 3309 1.809567 CTTCCCGGCAGCTTGCTTTT 61.810 55.000 0.00 0.00 44.28 2.27
2774 3310 2.203480 TTCCCGGCAGCTTGCTTT 60.203 55.556 0.00 0.00 44.28 3.51
2944 3954 6.500336 ACCCAGGAGTTACTATGAGAACTAA 58.500 40.000 0.00 0.00 36.04 2.24
2945 3955 6.088541 ACCCAGGAGTTACTATGAGAACTA 57.911 41.667 0.00 0.00 36.04 2.24


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

AutoCloner maintained by Alex Coulton.